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=2014 sample tracking= ==March 18, 2014 (BSC samples from Illumina) == == BSC samples from Illumina == - Received 12 BSC sample derived from amplified and un-amplified circulating tumor DNA from patients from Illumina {| {{table}} class = wikitable | align="center" style="background:#f0f0f0;"|'''Sample_ID''' | align="center" style="background:#f0f0f0;"|'''Sample_wel''' | align="center" style="background:#f0f0f0;"|'''BSC input (ng)''' | align="center" style="background:#f0f0f0;"|'''Preamp?''' | align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul)''' | align="center" style="background:#f0f0f0;"|'''Volume (ul)''' |- | BSC_10ng_restored_1-1||A1||10||Yes||569.3||10 |- | BSC_10ng_restored_1-2||A2||10||Yes||577.6||10 |- | BSC_1ng_restored_1-1||A3||1||Yes||427.9||10 |- | BSC_1ng_restored_1-2||A4||1||Yes||437.0||10 |- | BSC_10ng_restored_2-1||A5||10||Yes||546.8||10 |- | BSC_10ng_restored_2-2||A6||10||Yes||494.3||10 |- | BSC_1ng_restored_2-1||A7||1||Yes||338.8||10 |- | BSC_1ng_restored_2-2||A8||1||Yes||358.0||10 |- | BSC_80ng_restored||A9||80||Yes||566.7||10 |- | BSC_30ng_restored||A10||30||Yes||615.3||10 |- | BSC_80ng||B1||80||No||8.0||10 |- | BSC_30ng_1||B2||30||No||3.0||10 |- | BSC_30ng_2||B3||30||No||3.0||10 |} * The concentration of these samples were changed because I added more TE buffer and re-quantified concentration by Qubit quantification == April 14, 2014 (8 additional amplified DNA samples from Illumina) == * Received 8 additional amplified DNA samples from Xuyu Cai * No information of sample was provide only 5ul for each one and concentration ~200ng/ul * I added more H2O to bring volume to 12ul, transfered samples to 8-tube strip with individual cap, and re-quantified concentration with Qubit ssDNA HS assay ==== Qubit dsDNA assay HS results ==== {| {{table}} class = wikitable | align="center" style="background:#f0f0f0;"|'''Sample''' | align="center" style="background:#f0f0f0;"|'''Conc. in the Qubit''' | align="center" style="background:#f0f0f0;"|'''Unit''' | align="center" style="background:#f0f0f0;"|'''uL used''' | align="center" style="background:#f0f0f0;"|'''Dilution''' | align="center" style="background:#f0f0f0;"|'''Sample conc. (ng/ul)''' | align="center" style="background:#f0f0f0;"|'''Total volume''' | align="center" style="background:#f0f0f0;"|'''Total amount (ng)''' |- | #1||173||ng/mL||1||200||34.6||12||415.2 |- | #2||152||ng/mL||1||200||30.4||12||364.8 |- | #3||199||ng/mL||1||200||39.9||12||478.8 |- | #4||207||ng/mL||1||200||41.4||12||496.8 |- | #5||108||ng/mL||1||200||21.6||12||259.2 |- | #6||154||ng/mL||1||200||30.9||12||370.8 |- | #7||181||ng/mL||1||200||36.1||12||433.2 |- | #8||172||ng/mL||1||200||34.4||12||412.8 |} '''5-06-2014''' * Received ~30ul of polymerase with property similar to Amplitaq Stoffel fragment. Conc. 3U/ul. She is not allowed to provide any further info. of this enzyme. == May 22, 2014 (Plasma samples from normal samples with no cancer history == * Received 30 plasma samples 1mL each from Kang Zhang's lab * All samples were collected in 2014 {| {{table}} class = wikitable | align="center" style="background:#f0f0f0;"|'''Zhang Id''' | align="center" style="background:#f0f0f0;"|'''phenotype_category''' | align="center" style="background:#f0f0f0;"|'''sex''' | align="center" style="background:#f0f0f0;"|'''date_of_birth''' | align="center" style="background:#f0f0f0;"|'''Age''' | align="center" style="background:#f0f0f0;"|'''ethnicity''' |- | 15849001||Normal - Other||M||2/13/1946||68||Caucasian - European |- | 15898001||Normal Control||F||1/21/1983||31||Caucasian - European |- | 16188001||Normal Control||M||2/21/1954||60||Caucasian - European |- | 16191001||Normal Control||M||9/25/1964||50||Caucasian - European |- | 16296003||Normal Control||F||8/8/1976||38||Caucasian - European |- | 16345002||Normal Control||F||3/31/1986||28||Caucasian - European |- | 16405003||Normal Control||F||8/9/1960||54||Caucasian - European |- | 16408001||Normal Control||M||3/12/1944||70||Caucasian - European |- | 16409002||Normal Control||F||10/30/1943||71||Caucasian - European |- | 16409003||Normal Control||M||8/10/1971||43||Caucasian - European |- | 16416001||Normal Control||F||11/4/1949||65||Caucasian - European |- | 16461001||Normal Control||F||1/31/1936||78||Caucasian - European |- | 16508001||Normal Control||M||8/13/1973||41||Caucasian - European |- | 16509001||Normal Control||F||3/8/1964||50||Caucasian - European |- | 16510002||Normal Control||M||8/26/1957||57||Caucasian - European |- | 16512001||Normal Control||M||6/1/1982||32||Caucasian - European |- | 16517001||Normal Control||M||4/3/1949||65||Caucasian - European |- | 16518001||Normal Control||M||1/18/1955||59||Caucasian - European |- | 16519001||Normal Control||F||6/13/1976||38||Caucasian - European |- | 16520001||Normal Control||M||12/30/1954||60||Caucasian - European |- | 16523001||Normal Control||M||7/8/1955||59||Caucasian - European |- | 16524001||Normal Control||F||1/11/1953||61||Caucasian - European |- | 16534001||Normal Control||F||3/4/1992||22||Caucasian - European |- | 16553001||Normal Control||F||3/11/1938||76||Caucasian - European |- | 16557001||Normal Control||M||6/8/1948||66||Caucasian - European |- | 16561001||Normal Control||F||8/28/1972||42||Caucasian - European |- | 16562001||Normal Control||M||3/8/1983||31||Caucasian - European |- | 16563001||Normal Control||M||1/31/1954||60||Caucasian - European |- | 16564001||Normal Control||F||2/23/1986||28||Caucasian - European |- | 16565001||Normal Control||F||10/22/1968||46||Caucasian - European |} ---- =November5, 2010 (Mouse gDNA from La Spada's lab, UCSD)= * received 8 gDNA samples from Paula Ladd<br> {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Samples''' | align="center" style="background:#f0f0f0;"|'''Sample ID''' | align="center" style="background:#f0f0f0;"|'''concentration (ng/ul)''' | align="center" style="background:#f0f0f0;"|'''volume (ul)''' |- | 1. wild-type cortex||WT-CTX||2000.0||3.8 |- | 2. wild-type cerebellum||WT-CBL||100.0||8.2 |- | 3. wild-type brain stem||WT-BS||600.0||8.5 |- | 4. wild-type retina||WT-RET||1800.0||4.0 |- | 5. transgenic cortex||TG-CTX||250.0||17.0 |- | 6. transgenic cerebellum||TG-CBL||400.0||14.0 |- | 7. transgenic brain stem||TG-BS||1000.0||6.5 |- | 8. transgenic retina||TG-RET||2000.0||8.0 |} Note: WT: wild-type, TG: transgenic Samples were diluted to 200ng/ul based on original concentration from Paula and confirmed by Nanodrop {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Samples''' | align="center" style="background:#f0f0f0;"|'''Sample ID''' | align="center" style="background:#f0f0f0;"|'''total volume (ul) after diluted''' | align="center" style="background:#f0f0f0;"|'''concentration(ng/ul)''' |- | 1. wild-type cortex||WT-CTX||25.0||223.2 |- | 2. wild-type cerebellum||WT-CBL||25.0||663.5 |- | 3. wild-type brain stem||WT-BS||25.0||86.0 |- | 4. wild-type retina||WT-RET||25.0||163.7 |- | 5. transgenic cortex||TG-CTX||20.0||219.2 |- | 6. transgenic cerebellum||TG-CBL||25.0||109.4 |- | 7. transgenic brain stem||TG-BS||25.0||103.0 |- | 8. transgenic retina||TG-RET||25.0||126.6 |}<br> labnote: 2010_11_08 =December 7, 2010 (Sarah's African gDNA, UPenn )= * received 48 methylome samples from Tishkoff's lab delivered by UPS<br> William R Beggs, Jr.<br>Tishkoff Lab - Dept of Genetics, University of Pennsylvania<br>430 Clinical Research Building<br>415 Curie Blvd<br>Philadelphia, PA 19104-6145 {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''LabID''' | align="center" style="background:#f0f0f0;"|'''1M sample #''' | align="center" style="background:#f0f0f0;"|'''Well''' | align="center" style="background:#f0f0f0;"|'''Volume ul''' | align="center" style="background:#f0f0f0;"|'''Conc ng/ul approx''' |- | CAPB016||||A01||50||100 |- | CAPB046||||B01||50||100 |- | CAPB056a||||C01||50||100 |- | CAPL056||||D01||50||100 |- | CAPM007||||E01||50||100 |- | TZHZ018A||||F01||50||100 |- | TZHZ033B||||G01||50||100 |- | TZHZ075A||||H01||50||100 |- | TZHZ214||||A02||50||100 |- | TZHZ221B||||B02||50||100 |- | TZSW067||||C02||50||100 |- | TZSW128B||||D02||50||100 |- | TZSW131A||||E02||50||100 |- | TZSW132B||||F02||50||100 |- | TZSW135B||||G02||50||100 |- | CAMF013A||||H02||50||100 |- | CAFU043||||A03||50||100 |- | CAFU042||||B03||50||100 |- | CAFU028||||C03||50||100 |- | CAMF022A||||D03||50||100 |- | CAPB043||||E03||50||100 |- | CAPL049||||F03||50||100 |- | CAPM001A||||G03||50||100 |- | CAPL036||||H03||50||100 |- | KEBR007A||||A04||50||100 |- | KEBR028A||||B04||50||100 |- | KEBR042B||||C04||50||100 |- | KEBR040A||||D04||50||100 |- | KEBR061A||||E04||50||100 |- | KEPK003A||||F04||50||100 |- | KEPK006A||||G04||50||100 |- | KEPK007A||||H04||50||100 |- | KEPK010A||||A05||50||100 |- | KEPK016A||||B05||50||100 |- | CAPM047||son||C05||50||100 |- | CAPM003A||parent||D05||50||100 |- | CAPM004A||parent||E05||50||100 |- | CAPM056A||daughter||F05||50||100 |- | ETAM042||||G05||50||100 |- | ETAM071||||H05||50||100 |- | ETAM077||||A06||50||100 |- | ETAM058||||B06||50||100 |- | ETAM065||||C06||50||100 |- | ETSB008||||D06||50||100 |- | ETSB027||||E06||50||100 |- | ETSB031||||F06||50||100 |- | ETSB035||||G06||50||100 |- | ETSB036||||H06||50||100 |} * aliquot 21ul out of 50ul samples into another 96-well plate * Related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2010-12-16]]<br> ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2010-12-18]]<br> ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-1-20]]<br> * Data analysis: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-4-16]]<br> ** More sample info: [[Media:48SamplelistUPenn.xlsx]]<br> =December 10, 2010 (normal/tumor gDNA from JHU)= * received 48 normal/tumor gDNA samples from JHU delivered by FedEx<br> Eirikur Briem<br> John Hopkins University<br> 855N. Wolfe Street<br> Rangos 580.14<br> Baltimore, MD 21205 {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Sample_ID''' | align="center" style="background:#f0f0f0;"|'''Kun_Well''' | align="center" style="background:#f0f0f0;"|'''Final Volume (uL)''' | align="center" style="background:#f0f0f0;"|'''Final_Conc (ng/uL)''' |- | 395||G3||50||30 |- | 970||H4||50||30 |- | 12||A1||50||30 |- | 258||F2||50||30 |- | 299||A3||50||30 |- | 335||C3||50||30 |- | 440||A5||50||30 |- | 503||E5||50||30 |- | 736||G6||50||30 |- | 895||F4||50||30 |- | 84||E1||50||30 |- | 198||H1||50||30 |- | 203||B2||50||30 |- | 368||E3||50||30 |- | 388||F3||50||30 |- | 436||H3||50||30 |- | 524||F5||50||30 |- | 686||F6||50||30 |- | 48||C1||50||30 |- | 85||F1||50||30 |- | 107||G1||50||30 |- | 253||D2||50||30 |- | 467||D5||50||30 |- | 569||H5||50||30 |- | 850||B4||50||30 |- | 894||E4||50||30 |- | 893||D4||30||50 |- | 659||E6||30||50 |- | 538||G5||30||50 |- | 967||G4||30||50 |- | 304||B3||30||50 |- | 256||E2||30||50 |- | 42||B1||30||50 |- | 77||D1||30||50 |- | 201||A2||30||50 |- | 222||C2||30||50 |- | 280||G2||30||50 |- | 282||H2||30||50 |- | 362||D3||30||50 |- | 445||B5||30||50 |- | 455||C5||30||50 |- | 572||A6||30||50 |- | 607||B6||30||50 |- | 619||C6||30||50 |- | 621||D6||30||50 |- | 743||H6||30||50 |- | 791||A4||30||50 |- | 881||C4||30||50 |} * sort out sample ID into plate layout {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Plate layout''' | align="center" style="background:#f0f0f0;"|'''1''' | align="center" style="background:#f0f0f0;"|'''2''' | align="center" style="background:#f0f0f0;"|'''3''' | align="center" style="background:#f0f0f0;"|'''4''' | align="center" style="background:#f0f0f0;"|'''5''' | align="center" style="background:#f0f0f0;"|'''6''' |- | A||12||201||299||791||440||572 |- | B||42||203||304||850||445||607 |- | C||48||222||335||881||455||619 |- | D||77||253||362||893||467||621 |- | E||84||256||368||894||503||659 |- | F||85||258||388||895||524||686 |- | G||107||280||395||967||538||736 |- | H||198||282||436||970||569||743 |} = December 16, 2010 (Bisulfite converted mouse gDNA from JHU) = * Received 4 bisulfite converted mouse gDNA from Yuan Gao<br> Yuan Gao<br>Forrest City Baltimore<br> 855 N. Wolfe St. STE 102<br> Baltimore, MD 21205<br> {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Sample ID''' | align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul) confirmed by Qubit''' | align="center" style="background:#f0f0f0;"|'''Volume (ul)''' | align="center" style="background:#f0f0f0;"|'''Total amount (ng)''' |- | WT||2.40||7.00||16.80 |- | WT ECT||5.54||6.00||33.24 |- | G45B KO||3.04||7.00||21.28 |- | G45B ECT KO||4.14||6.00||24.84 |}<br> = February 2, 2011 (Brain gDNA of Parkinson's patients from Burnham Institute, human frozen cerebral cortex) = * Received 18 human brain samples from Parkinson's patients. This includes control and Parkinson's patient samples. {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Pair''' | align="center" style="background:#f0f0f0;"|'''Control Sample ID''' | align="center" style="background:#f0f0f0;"|'''Sample code''' | align="center" style="background:#f0f0f0;"|'''Sex''' | align="center" style="background:#f0f0f0;"|'''age (year.day)''' | align="center" style="background:#f0f0f0;"|'''Postmortem time''' | align="center" style="background:#f0f0f0;"|'''Conc. (ug/ul)/ volume (ul)''' | align="center" style="background:#f0f0f0;"|'''PD Sample ID''' | align="center" style="background:#f0f0f0;"|'''Sample code''' | align="center" style="background:#f0f0f0;"|'''Sex''' | align="center" style="background:#f0f0f0;"|'''age (year.day)''' | align="center" style="background:#f0f0f0;"|'''Postmortem time''' | align="center" style="background:#f0f0f0;"|'''Conc. (ug/ul)/ volume (ul)''' |- | 1||5028||P1C||M||67.293||P18||0.5ug/ul/ 4ul||1947||P1P||M||70.251||P17||0.5ug/ul/ 4ul |- | 2||4789||P2C||F||72.053||P19||0.5ug/ul/ 4ul||4977||P2P||F||76.081||P14||0.5ug/ul/ 4ul |- | 3||5171||P3C||M||79.088||P05||0.5ug/ul/ 4ul||4879||P3P||M||75.351||P15||0.5ug/ul/ 4ul |- | 4||1818||P4C||M||76.294||P03||0.5ug/ul/ 4ul||4526||P4P||M||78.182||P01||0.5ug/ul/ 4ul |- | 5||5089||P5C||M||89.018||P14||0.5ug/ul/ 4ul||5203||P5P||M||89.06||P10||0.5ug/ul/ 4ul |- | 6||5237||P6C||M||52.291||P13||0.5ug/ul/ 4ul||1910||P6P||M||51.243||P10||0.5ug/ul/ 4ul |- | 7||1569||P7C1||F||77.089||P08||0.5ug/ul/ 4ul||1401||P7P||F||80.215||P04||0.5ug/ul/ 4ul |- | 7||5219||P7C2||F||76.348||P03||0.5ug/ul/ 4ul|||||||||||| |- | 8||4735||P8C||M||73.184||P21||0.5ug/ul/ 4ul||1741||P8P1||M||71.348||P20||0.5ug/ul/ 4ul |- | 8||||||||||||||5306||P8P2||M||76.311||P21||0.5ug/ul/ 4ul |}<br> * related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-2-15]] * Data analysis: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-3-17]] = March 10, 2011, Cell pellet samples from Belmonte's lab, Salk Institute = * Received 5 cell pellet samples from Belmonte's lab * Extracted gDNA using DNeasy Blood and Tissue kit (Qiagen) <br> {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Samples''' | align="center" style="background:#f0f0f0;"|'''No. of cell''' | align="center" style="background:#f0f0f0;"|'''gDNA conc. (ng/ul)''' | align="center" style="background:#f0f0f0;"|'''Elution volume (ul)''' | align="center" style="background:#f0f0f0;"|'''Yields (ug)''' |- | 1. HGPS||1.0E6||75.7||300||22.71 |- | 2. cHGPS1||1.0E6||57.1||300||17.13 |- | 3. cHGPS40||1.0E6||100.2||300||30.06 |- | 4. AWS||1.0E6||42.2||300||12.66 |- | 5. cAWS1||1.0E6||130.1||300||39.03 |} * related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-3-10]] ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-3-18]] * Data analysis: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-3-29]]<br> = April 21, 2011, PGP1 iPS gDNA from Harvard = * Received one sample of PGP1 CD1 iPS P16 from Harvard Medical School<br> Jihyuk Lee<br> Harvard Medical School<br> 77 Avenue Louis Pasteur<br> Boston, MA 02115<br> {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Sample name''' | align="center" style="background:#f0f0f0;"|'''Sample ID''' | align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul)''' | align="center" style="background:#f0f0f0;"|'''Total amount (ug)''' |- | PGP1 CD1 iPS P16||PGP1 iPS||129||39 |}<br> * Related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-5-3]] * Mapping data: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-5-26]] = April 27, 2011, gDNA of TET study from Harvard Medical School = * Received 24 gDNA sample from Yeguang (from Yujiang Geno Shi's lab) {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Tube Number''' | align="center" style="background:#f0f0f0;"|'''Sample description''' | align="center" style="background:#f0f0f0;"|'''concentration (ng/ul)''' | align="center" style="background:#f0f0f0;"|'''9 sample choice''' | align="center" style="background:#f0f0f0;"|'''12 sample choice''' |- | #1||Scr-1||117.1||X||X |- | #2||Sh3513-1||116.5||X||X |- | #3||Sh1-1||80.3||||X |- | #4||Scr-2||235||||X |- | #5||Sh3513-2||313||||X |- | #6||Sh1-2||142||||X |- | #7||Mock||117||X||X |- | #8||TET2-35#||113||X||X |- | #9||TET2-75#||138||X||X |- | #10||HMEC-Scr||215||X||X |- | #11||HMEC-Sh3513||246||X||X |- | #12||HMEC-Sh1||51.3||||X |- | #13||Scr-3||161||X|| |- | #14||Sh3513-3||159||X|| |- | #15||T2-SCr-1||186|||| |- | #16||T2m-Scr-1||187 |- | #17||T2-Scr-2||298 |- | #18||T2m-Scr-2||291 |- | #19||NB4-Scr||93.9 |- | #20||NB4-Sh3513||53.8 |- | #21||NB4-Sh2513||74.6 |- | #22||NB4-Sh5372||77.8 |- | #23||NB4-T2||89.5 |- | #24||NB4-T2m||138.4 |}<br> * Related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-5-3]]<br> * Mapping data: **[[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-5-26]] = May 19, 2011, gDNA from the blood samples of HIV patients, UCSD Medical School = * Received 39 samples from Josué Pérez-Santiago (from Christopher Woelk's lab, UCSD medical School) * Each sample volume 21ul, conc. 100ng/ul {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Sample ID''' | align="center" style="background:#f0f0f0;"|'''PID''' | align="center" style="background:#f0f0f0;"|'''Place in 96plate''' | align="center" style="background:#f0f0f0;"|'''Volume (ul)''' | align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul)''' | align="center" style="background:#f0f0f0;"|'''Total amount (ug)''' |- | 3||26406 102||A1||21||100||2.1 |- | 4||26406 108||A2||21||100||2.1 |- | 5||26604 054||A3||21||100||2.1 |- | 6||26604 066||A4||21||100||2.1 |- | 11||NW578 000||A5||21||100||2.1 |- | 12||NW578 012||A6||21||100||2.1 |- | 13||58346 006||A7||21||100||2.1 |- | 14||58346 012||A8||21||100||2.1 |- | 15||CA198 006||A9||21||100||2.1 |- | 16||CA198 C12||A10||21||100||2.1 |- | 17||CA219 000||A11||21||100||2.1 |- | 18||CA219 006||A12||21||100||2.1 |- | 19||CA275 000||B1||21||100||2.1 |- | 20||CA275 006||B2||21||100||2.1 |- | 21||CB252 000||B3||21||100||2.1 |- | 22||CB252 006||B4||21||100||2.1 |- | 24||CC182 012||B5||21||100||2.1 |- | 25||24371 000||B6||21||100||2.1 |- | 26||24371 012||B7||21||100||2.1 |- | 27||NW470 012||B8||21||100||2.1 |- | 28||NW470 024||B9||21||100||2.1 |- | 30||27054 012||B10||21||100||2.1 |- | 31||CA239 000||B11||21||100||2.1 |- | 33||CE214 000||B12||21||100||2.1 |- | 34||CE214 006||C1||21||100||2.1 |- | 35||CB255 000||C2||21||100||2.1 |- | 36||CB255 006||C3||21||100||2.1 |- | 37||21003 000||C4||21||100||2.1 |- | 38||21003 012||C5||21||100||2.1 |- | 39||CG139 006||C6||21||100||2.1 |- | 40||CG139 018||C7||21||100||2.1 |- | 41||NM633 012||C8||21||100||2.1 |- | 42||NM633 024||C9||21||100||2.1 |- | 43||NM805 012||C10||21||100||2.1 |- | 44||NM805 024||C11||21||100||2.1 |- | 45||CB199 000||C12||21||100||2.1 |- | 46||26592 060||D1||21||100||2.1 |- | 47||24054 030||D2||21||100||2.1 |- | 48||24054 036||D3||21||100||2.1 |}<br> * Spreadsheet: [[Media:gDNA from TropherLab_2011_05_19.xlsx]]<br> * Related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-5-28]] ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-6-6]] * Mapping data: = May 25, 2011, gDNA of 10 different tissues from Billi Li, Standforf Univ = * Received gDNA samples for all the tissues of individual N37 from Jin Billi Li, Standford Univ.<br> Jin Billy Li<br> Standford University Genetics Dept.<br> Standford Univ ALWAY BLDG M-341<br> 259 CAMPUS DR ALWAY BLDG Standford, CA 94035<br> {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Number''' | align="center" style="background:#f0f0f0;"|'''Sample''' | align="center" style="background:#f0f0f0;"|'''Concentration (ug/ul)''' | align="center" style="background:#f0f0f0;"|'''Volume (ul)''' | align="center" style="background:#f0f0f0;"|'''Total amount (ug)''' | align="center" style="background:#f0f0f0;"|'''NewID''' |- | 1.00||Cerebellum||1.38||1.45||2.00||N37-1 |- | 2.00||Colon||1.44||1.39||2.00||N37-2 |- | 3.00||Frontal lobe||0.91||2.20||2.00||N37-3 |- | 4.00||Heart||0.73||2.74||2.00||N37-4 |- | 5.00||Small intestine||1.09||1.83||1.99||N37-5 |- | 6.00||Liver||0.93||2.15||2.00||N37-6 |- | 7.00||Lung||0.50||4.00||2.00||N37-7 |- | 8.00||Skeletal muscle||0.57||3.51||2.00||N37-8 |- | 9.00||Pancrease||1.48||1.35||2.00||N37-9 |- | 10.00||Stomach||1.17||1.71||2.00||N37-10 |}<br> * Related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-5-28]] ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-6-6]]<br> * Mapping data: = July 8, 2011, gDNA from the blood samples of control and GA patients from Kang Zhang's lab, UCSD = * Received 48 control and 48 GA gDNA blood samples (GA methylation plate1) from Zhao Ling (Dr. Kang Zhang's post doc)<br> * The concentration of every samples was adjusted to 100ng/ul, total amount 2ug. <br><br> {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Sample number''' | align="center" style="background:#f0f0f0;"|'''Well''' | align="center" style="background:#f0f0f0;"|'''Phenotype''' | align="center" style="background:#f0f0f0;"|'''ID''' |- | GA-methylation plate1-1||A1||GA||565003 |- | GA-methylation plate1-2||B1||GA||773002 |- | GA-methylation plate1-3||C1||GA||786015 |- | GA-methylation plate1-4||D1||GA||788001 |- | GA-methylation plate1-5||E1||GA||819002 |- | GA-methylation plate1-6||F1||GA||875012 |- | GA-methylation plate1-7||G1||GA||881006 |- | GA-methylation plate1-8||H1||GA||1069001 |- | GA-methylation plate1-9||A2||GA||1100001 |- | GA-methylation plate1-10||B2||GA||1104001 |- | GA-methylation plate1-11||C2||GA||1150004 |- | GA-methylation plate1-12||D2||GA||1191002 |- | GA-methylation plate1-13||E2||GA||1271001 |- | GA-methylation plate1-14||F2||GA||1315001 |- | GA-methylation plate1-15||G2||GA||1378001 |- | GA-methylation plate1-16||H2||GA||1447001 |- | GA-methylation plate1-17||A3||GA||1592002 |- | GA-methylation plate1-18||B3||GA||1603001 |- | GA-methylation plate1-19||C3||GA||1977001 |- | GA-methylation plate1-20||D3||GA||2030010 |- | GA-methylation plate1-21||E3||GA||2200001 |- | GA-methylation plate1-22||F3||GA||2274002 |- | GA-methylation plate1-23||G3||GA||2456001 |- | GA-methylation plate1-24||H3||GA||2939001 |- | GA-methylation plate1-25||A4||GA||2996001 |- | GA-methylation plate1-26||B4||GA||4705001 |- | GA-methylation plate1-27||C4||GA||5462001 |- | GA-methylation plate1-28||D4||GA||6001001 |- | GA-methylation plate1-29||E4||GA||6035002 |- | GA-methylation plate1-30||F4||GA||6328001 |- | GA-methylation plate1-31||G4||GA||10004001 |- | GA-methylation plate1-32||H4||GA||11402001 |- | GA-methylation plate1-33||A5||GA||11596001 |- | GA-methylation plate1-34||B5||GA||11597001 |- | GA-methylation plate1-35||C5||GA||11599001 |- | GA-methylation plate1-36||D5||GA||11622001 |- | GA-methylation plate1-37||E5||GA||11923001 |- | GA-methylation plate1-38||F5||GA||12113001 |- | GA-methylation plate1-39||G5||GA||12556001 |- | GA-methylation plate1-40||H5||GA||12622001 |- | GA-methylation plate1-41||A6||GA||12625001 |- | GA-methylation plate1-42||B6||GA||12687001 |- | GA-methylation plate1-43||C6||GA||12967001 |- | GA-methylation plate1-44||D6||GA||13174001 |- | GA-methylation plate1-45||E6||GA||13447001 |- | GA-methylation plate1-46||F6||GA||13976001 |- | GA-methylation plate1-47||G6||GA||14033001 |- | GA-methylation plate1-48||H6||GA||14137001 |- | GA-methylation plate1-49||A7||Control||825002 |- | GA-methylation plate1-50||B7||Control||880003 |- | GA-methylation plate1-51||C7||Control||888003 |- | GA-methylation plate1-52||D7||Control||1373001 |- | GA-methylation plate1-53||E7||Control||6925001 |- | GA-methylation plate1-54||F7||Control||6988001 |- | GA-methylation plate1-55||G7||Control||7161001 |- | GA-methylation plate1-56||H7||Control||7419001 |- | GA-methylation plate1-57||A8||Control||7528001 |- | GA-methylation plate1-58||B8||Control||7529001 |- | GA-methylation plate1-59||C8||Control||7729002 |- | GA-methylation plate1-60||D8||Control||7781002 |- | GA-methylation plate1-61||E8||Control||10174001 |- | GA-methylation plate1-62||F8||Control||10182001 |- | GA-methylation plate1-63||G8||Control||10214001 |- | GA-methylation plate1-64||H8||Control||10223001 |- | GA-methylation plate1-65||A9||Control||10272001 |- | GA-methylation plate1-66||B9||Control||10555001 |- | GA-methylation plate1-67||C9||Control||10703001 |- | GA-methylation plate1-68||D9||Control||10741001 |- | GA-methylation plate1-69||E9||Control||10914001 |- | GA-methylation plate1-70||F9||Control||10958001 |- | GA-methylation plate1-71||G9||Control||11029001 |- | GA-methylation plate1-72||H9||Control||11066001 |- | GA-methylation plate1-73||A10||Control||11167001 |- | GA-methylation plate1-74||B10||Control||11198001 |- | GA-methylation plate1-75||C10||Control||11200001 |- | GA-methylation plate1-76||D10||Control||11201001 |- | GA-methylation plate1-77||E10||Control||11202001 |- | GA-methylation plate1-78||F10||Control||11210001 |- | GA-methylation plate1-79||G10||Control||11285001 |- | GA-methylation plate1-80||H10||Control||11324001 |- | GA-methylation plate1-81||A11||Control||11340001 |- | GA-methylation plate1-82||B11||Control||11379001 |- | GA-methylation plate1-83||C11||Control||11394002 |- | GA-methylation plate1-84||D11||Control||11424001 |- | GA-methylation plate1-85||E11||Control||11434001 |- | GA-methylation plate1-86||F11||Control||11585001 |- | GA-methylation plate1-87||G11||Control||11594001 |- | GA-methylation plate1-88||H11||Control||11595001 |- | GA-methylation plate1-89||A12||Control||11720001 |- | GA-methylation plate1-90||B12||Control||11748001 |- | GA-methylation plate1-91||C12||Control||11756001 |- | GA-methylation plate1-92||D12||Control||11779001 |- | GA-methylation plate1-93||E12||Control||11783001 |- | GA-methylation plate1-94||F12||Control||11790001 |- | GA-methylation plate1-95||G12||Control||11792001 |- | GA-methylation plate1-96||H12||Control||11793001 |}<br> * GA-methylation plate1: [[Media:GA_methylation_sample_plate1.xlsx]]<br> * Note: Since the capture of the GA plate1 failed, and I needed to repeated the experiment, Ling brought the new plate (called GA plate1-2) with the same samples to me and all concentration were measured again by Nanodrop. * Related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-7-28]] (the experiment which the capture failed) ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-8-9]]<br> = July 29, 2011, gDNA of 3 human iPS lines with single nonsynonymous mutations, UCSD = * Received 3 gDNA sample from Alice that are iPS lines with single nonsynonymous mutation)<br> ** 1) 2HFF 8d_10, conc. by Nanodrop: 214.60 ng/ul ** 2) 218HHF211, conc. by Nanodrop: 411.10 ng/ul ** 3) 218HHF411, conc. by Nanodrop: 359.60 ng/ul<br> * Related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-8-4]]<br> = August 1, 2011, gDNA of the blood samples of schizophrenia disorder patients from Dr. Roel Ophoff, UCLA = * Received 96 gDNA samples (in 96-well plate) of the blood samples of schizophrenia disorder patients from Dr. Roel Ophoff, UCLA '''Eric Strengman'''<br> '''UCLA 695 Charles E. Young Dr. S'''<br>'''Gonda 4335'''<br>'''Los Angeles, CA 90095'''<br> * Each sample was remeasured the DNA conc. by Nanodrop * Related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-8-14]]<br> * Note: Since I thought that they all are brain tissue samples, some labeling of library name or images used brain instead of blood. To prevent confusing, every labeling should be changed. = August25, 2011, gDNA from fibroblast cells that are the somatic line of the three single nonsynonymous mutation iPS on the record of July29, 2011 = * Received 2 gDNA samples from fibroblast cells that are the somatic lines of the three single nonsynonymous mutation iPS from Alice. Both of them were from the first elution in DNA purification {| {{table}} | align="center" style="background:#f0f0f0;"|'''Sample ID''' | align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul) by Sergio''' | align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul)confirmed by Nanodrop''' | align="center" style="background:#f0f0f0;"|'''260/280''' | align="center" style="background:#f0f0f0;"|'''260/230''' |- | 1. 2HFF p6||283.50||280.10||2.02||1.87 |- | 2. 218 HFF p7||586.30||446.10||2.05||2.00 |} * Related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-16]] ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-18]] = September16, 2011, gDNA from Sergio, Salk Institute = {| {{table}} | align="center" style="background:#f0f0f0;"|'''Sample ID''' | align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul) by Sergio''' | align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul)confirmed by Nanodrop''' | align="center" style="background:#f0f0f0;"|'''260/280''' | align="center" style="background:#f0f0f0;"|'''260/230''' |- | 1. H9 P43 mTeSR||62.00||62.80||1.89||0.99 |- | 2. H9 p43+Activin 100ng/mL 5days||90.80||90.80||1.85||0.70 |- | 3. H9 p43+BMP4 50ng/mL 5days||91.10||93.70||1.85||1.15 |- | 4. HUViPS4F1 p19||95.20||98.00||1.84||1.22 |- | 5. HUViPS4F1 p19+Activin 100ng/mL 5days||83.80||84.80||1.79||0.78 |- | 6. HUViPS4F1 p19+BMP4 50ng/mL 5days||80.00||78.60||1.84||0.96 |- | 7. HUViPS4F3||96.80||96.90||1.87||1.12 |- | 8. HUViPS4F3+Activin 100ng/mL 5days||90.20||91.90||1.78||0.80 |- | 9. HUViPS4F3+BMP4 50ng/mL 5days||80.20||80.60||1.86||0.96 |} * Related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-16]] ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-18]] ** 330k BSPP capture of all of these samples were repeated again for PNAS revision (May2012): *** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-20]] *** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-21]] *** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-25]] = September16, 2011, received 3 more gDNA from UPenn to repeat the capture of the samples with low QC values = {| {{table}} | align="center" style="background:#f0f0f0;"|'''Sample ID''' | align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul) by Sergio''' | align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul)confirmed by Nanodrop''' | align="center" style="background:#f0f0f0;"|'''260/280''' | align="center" style="background:#f0f0f0;"|'''260/230''' |- | 1. KEBR028A||50.00||23.80||1.83||0.51 |- | 2. TZHZ031A||50.00||55.10||1.88||1.78 |- | 3. TZHZ041A||50.00||54.60||1.88||1.35 |} * Related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-16]] ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-18]] = September 17, 2011, received 3 cell pellet samples from Alice (sample from Yang Xu's lab) = * I extracted gDNA and elutee 150ul in elute1 and elute2. The concentration was was measure by Nanodrop. {| {{table}} | align="center" style="background:#f0f0f0;"|'''Sample ID''' | align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul)confirmed by Nanodrop''' | align="center" style="background:#f0f0f0;"|'''Volume (ul)''' | align="center" style="background:#f0f0f0;"|'''Yields (ug)''' | align="center" style="background:#f0f0f0;"|'''260/280''' | align="center" style="background:#f0f0f0;"|'''260/230''' |- | 1. Hues1 (elute1)||341.90||150.00||51.29||2.06||2.02 |- | Hues1 (elute2)||64.00||150.00||9.60||2.04||2.07 |- | 2. Hues3 (elute1)||696.90||150.00||104.54||2.35||3.16 |- | Hues3 (elute2)||183.90||150.00||27.59||2.10||2.08 |- | 3. Hues8 (elute1)||410.60||150.00||61.59||2.05||2.01 |- | Hues8 (elute2)||125.00||150.00||18.75||2.07||2.04 |} * Related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-16]] ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-9-18]] = December 13, 2011, received one sequencing library from Baylor, RC-1 = * RC-1 --> labeled conc. 70 ng/ul, volume ~ 8ul. I added 8ul of H2O to ncrease the volume, so the final conc. ~35ng/ul * This library was constructed using the same protocol as I did on the LC sciences's BSPP library. I performed qPCR with the barcode primers * Related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-12-13]] ** Re-amplified with library-free protocol: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-23]] *** Summary of mapping data: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-7#Mapping_to_hg19_.28on_Triton_cluster.29]] = March 1, 2012, received 6 gDNA samples (PGP1F hiPS) from Alice = {| {{table}} | align="center" style="background:#f0f0f0;"|'''Cap labeling''' | align="center" style="background:#f0f0f0;"|'''Sample ID''' | align="center" style="background:#f0f0f0;"|'''Lab ID''' | align="center" style="background:#f0f0f0;"|'''Conc. (ng/ul)''' | align="center" style="background:#f0f0f0;"|'''Passage''' |- | 19||12.5-2x#1||2x#1||55.7||P5 |- | 20||12.5-1x#2||1x#2||68.1||P6 |- | 21||12.5-1x#3||1x#3||149.9||P5 |- | 22||12.5-2x#5||2x#5||34.5||P5 |- | 23||12.5-2x#6||2x#6||96.7||P5 |- | 24||12.5-1x#1||1x#1||114.6||P5 |} * Related lab note: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-3-7]] = April 15, 2012, Cell pellet samples from Sergio to Dinh = {| {{table}} | align="center" style="background:#f0f0f0;"|'''No.''' | align="center" style="background:#f0f0f0;"|'''Sample ID''' | align="center" style="background:#f0f0f0;"|'''Lab ID''' |- | ||hESC lines|| |- | 1||HUES2 p41||Ap15-1 |- | ||hiPSC lines:|| |- | 2||ASThiPS4F1 p12||Ap15-2 |- | 3||ASThiPS4F2 p12||Ap15-3 |- | ||Differentiate experiments:|| |- | 4||HUES6 p39 Control TeSR||Ap15-4 |- | 5||HUES6 p39 ACTIVIN||Ap15-5 |- | 6||HUES6 p39 BMP4||Ap15-6 |- | 7||HUES9 p39 Control TeSR||Ap15-7 |- | 8||HUES9 p39 ACTIVIN||Ap15-8 |- | 9||HUES9 p39 BMP4||Ap15-9 |- | 10||HUES3 p36 Control TeSR||Ap15-10 |- | 11||HUES3 p36 ACTIVIN||Ap15-11 |- | 12||HUES3 p36 BMP4||Ap15-12 |- | 13||H1 p54 Control TeSR||Ap15-13 |- | 14||H1 p54 ACTIVIN||Ap15-14 |- | 15||ASThiPS4F5 p16 Control TeSR||Ap15-15 |- | 16||ASThiPS4F5 p16 ACTIVIN||Ap15-16 |- | 17||ASThiPS4F4 p36 Control TeSR||Ap15-17 |- | 18||ASThiPS4F4 p36 ACTIVIN||Ap15-18 |- | 19||ASThiPS4F4 p36 BMP4||Ap15-19 |} * Related labnote: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-17#May_15.2C_2012.2C_Cell_pellet_samples_from_Sergio_to_Dinh]] ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-20]] ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-21]] ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-25]] (included the sample on May15, 2012), ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-31]] = May 15, 2012, Cell pellet samples from Sergio to Dinh = {| {{table}} | align="center" style="background:#f0f0f0;"|'''No.''' | align="center" style="background:#f0f0f0;"|'''Sample ID''' | align="center" style="background:#f0f0f0;"|'''Lab ID''' |- | ||hESC lines:|| |- | 1||H1 p48||Ma15-2 |- | 2||H9 p42 ||Ma15-3 |- | 3||HUES3 p33||Ma15-4 |- | 4||HUES6 p26||Ma15-5 |- | 5||HUES8 p35||Ma15-6 |- | 6||HUES9 p36||Ma15-7 |- | ||iPSC lines:|| |- | 7||ASThiPS4F3 p24 (derived from Astrocytes)||Ma15-8 |- | 8||ASThiPS4F4 p16 (derived from Astrocytes)||Ma15-9 |- | 9||FiPS4F2 p32 (derived from IMR90 fibroblasts)||Ma15-10 |- | 10||FiPS4F5 p29 (derived from IMR90 fibroblasts)||Ma15-11 |- | 11||KiPS4FA p54 (derived from keratinocytes)||Ma15-12 |- | 12||Huv-iPS4F6 p23 (derived from HUVECs)||Ma15-13 |- | ||Somatic lines|| |- | 13||IMR90 p6||Ma15-14 |- | 14||Keratinocytes p3||Ma15-15 |- | ||Differentiation experiments:|| |- | 15||H1 p47 Control||Ma15-16 |- | 16||H1 p47 BMP-4||Ma15-17 |- | 17||ASThiPS4F5 p12 Control||Ma15-18 |- | 18||ASThiPS4F5 p12 BMP-4||Ma15-19 |- | 19||Huv-iPS4F6 p23 Control||Ma15-20 |- | 20||Huv-iPS4F6 p23 BMP-4||Ma15-21 |- | 21||Huv-iPS4F6 p23 ACTIVIN||Ma15-1 |- | ||Three samples below will not be captured with this batch|| |- | ||HUES2 p38|| |- | ||ASThiPS4F1 p8 (derived from Astrocytes) |- | ||ASThiPS4F2 p8 (derived from Astrocytes) |} = May 24, 2012, got more 8 gDNA for 330k BSPP capture from Anwesha (ASM and ASCM in human cells project, Harvard's group) = * Note: All of gDNA, cDNA and ChIPed samples for this projected were stored by Alan. * For gDNA samples in the first batch, all of 8 samples have conc. of 38ng/ul and volume ~20ul * for the second batch, Anwesha sent total volume 40ul for each sample {| {{table}} | align="center" style="background:#f0f0f0;"|'''Sample IDs''' | align="center" style="background:#f0f0f0;"|'''Conc. (ng.ul) by Nanodrop<br> (from Harvard)''' | align="center" style="background:#f0f0f0;"|'''Amount (ug) in 40ul''' |- | GM gDNA 4-5-12||64.52||2.58 |- | P10E3 gDNA 4-5-12||37.86||1.51 |- | DF2 gDNA 4-5-12||70.00||2.80 |- | H0 gDNA 4-5-12||84.52||3.38 |- | H7 gDNA 4-5-12||184.33||7.37 |- | H14 gDNA 4-5-12||167.18||6.69 |- | H16 gDNA 4-5-12||120.60||4.82 |} * Related labnote: ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-24]] ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-5-31]] * Mapping data: (not finished yet ** [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-6-27]] = August 22, 2012, got 2 gDNA and 3 cell pellet samples for 330k BSPP capture fromAlice (samples from Dr. Yang Xu) = {| {{table}} border = 1 | width="30pt" align="center" style="background:#f0f0f0;"|'''No.''' | align="center" style="background:#f0f0f0;"|'''SampleID''' | width="50pt" align="center" style="background:#f0f0f0;"|'''LabIDs''' | align="center" style="background:#f0f0f0;"|'''Nanodrop (ng/ul)''' | width="50pt" align="center" style="background:#f0f0f0;"|'''A260''' | width="50pt" align="center" style="background:#f0f0f0;"|'''260/280''' | width="50pt" align="center" style="background:#f0f0f0;"|'''Yields (ug)''' |- | 1||2-1C-8||AL-1||226.6||NA||NA||NA |- | 2||3-5C-3||AL-2||375.5||NA||NA||NA |- | 3||34HHP||AL-3||256.8||5.136||2.08||51.4 |- | 4||34HHF_Y-53-A6||AL-4||142.1||2.842||2.04||28.4 |- | 5||34HHF_Y-53-B3||AL-5||140.1||2.802||2||28 |} * Note: I got gDNA of sample ID AL-1 and AL-2 from Alice. Sample AL-3-5 as cell pellets. = August 22, 2012, Received 16 cell pellet (1x10^6 cells/tube) samples for 330k BSPP capture from Guanghui (Dr. Belmonte's lab) = {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''No.''' | align="center" style="background:#f0f0f0;"|'''Sample description''' | align="center" style="background:#f0f0f0;"|'''Mark on the tube''' | width="50pt" align="center" style="background:#f0f0f0;"|'''Lab ID''' | align="center" style="background:#f0f0f0;"|'''Nanodrop (ng/ul)''' | width="50pt" align="center" style="background:#f0f0f0;"|'''A260''' | align="center" style="background:#f0f0f0;"|'''260/280''' | align="center" style="background:#f0f0f0;"|'''Yields (ug)''' |- | 1||WT-ESC||H9-WT-ES||GL-1||295.8||5.916||2.04||16.3 |- | 2||LRRK2-GS-ESC||H9-LRRK-ES||GL-2||220.6||4.412||2.07||12.1 |- | 3||WT-NSCs||H9-WT-NSC-P9||GL-3||149.7||2.994||2.01||8.2 |- | 4||LRRK2-GS-NSCs||H9-LRRK-NSC-P9||GL-4||172.3||3.445||2.06||9.5 |- | 5||2nd-iPSCs-WT#5 (early passage)||H9-WT-NSC-iPSC#5 P18||GL-5||285.2||5.704||2.05||15.7 |- | 6||2nd-iPSCs-WT#3 (early passage)||H9-WT-NSC-iPSC#3 P18||GL-6||296.6||5.932||2.03||16.3 |- | 7||2nd-iPSCs-LK2-GS#2 (early passage)||H9-LRRK-NSC-iPSC#2 P18||GL-7||320.0||6.400||2.03||17.6 |- | 8||2nd-iPSCs-LK2-GS#6 (early passage)||H9-LRRK-NSC-iPSC#6 P18||GL-8||339.3||6.786||2.04||18.7 |- | 9||2nd-iPSCs-WT#5 (late passage)||W5-ips P34||GL-9||467.5||9.349||2.02||25.7 |- | 10||2nd-iPSCs-WT#3 (late passage)||W2-ips P34||GL-10||431.7||8.633||2.01||23.7 |- | 11||2nd-iPSCs-LK2-G2#2 (late passage)||L2-ips P34||GL-11||349.1||6.981||2.03||19.2 |- | 12||2nd-iPSCs-LK2-GS#6 (late passage)||L6-ips P34||GL-12||234.5||4.691||2.04||12.9 |- | 13||Cardiomyocyes||combine two tube to get 1M cells||GL-13||72.2||1.445||1.89||4.0 |- | 14||WT-NSCs||FA52-#6-NSC||GL-14||137.3||2.747||2.01||7.6 |- | 15||FA-NSCs||FA123#2-NSC||GL-15||207.5||4.150||2.03||11.4 |- | 16||Corrected FA-NSCs||FA-GC-16-NEO-NSC||GL-16||135.5||2.710||2.00||7.5 |} * Sample code GL1-GL13 for Project 1 * Sample code GL14-GL16 for Project 2 = June 12, 2013, received 32 gDNA samples (DNA methylation assay for Blueprint project) = * The concentration of each sample was not provided. They only said 1ug of each sample, and volume is varied. * [[Media:epigenetic_biomarker_benchmarking-sample_annotation_table_for_participants_edit.xlsx]]
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