Noi:Sample tracking: Difference between revisions
>Noi |
>Noi |
||
(3 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
=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)= | =November5, 2010 (Mouse gDNA from La Spada's lab, UCSD)= | ||
* received 8 gDNA samples from Paula Ladd<br> | * received 8 gDNA samples from Paula Ladd<br> | ||
Line 48: | Line 195: | ||
| 8. transgenic retina||TG-RET||25.0||126.6 | | 8. transgenic retina||TG-RET||25.0||126.6 | ||
|}<br> labnote: 2010_11_08 | |}<br> labnote: 2010_11_08 | ||
=December 7, 2010 (Sarah's African gDNA, UPenn )= | =December 7, 2010 (Sarah's African gDNA, UPenn )= | ||
Line 1,170: | Line 1,316: | ||
= June 12, 2013, received 32 gDNA samples (DNA methylation assay for Blueprint project) = | = 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. | * 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]] |
Latest revision as of 01:23, 27 May 2014
2014 sample tracking[edit]
March 18, 2014 (BSC samples from Illumina)[edit]
BSC samples from Illumina[edit]
- Received 12 BSC sample derived from amplified and un-amplified circulating tumor DNA from patients from Illumina
Sample_ID | Sample_wel | BSC input (ng) | Preamp? | Conc. (ng/ul) | 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)[edit]
- 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[edit]
Sample | Conc. in the Qubit | Unit | uL used | Dilution | Sample conc. (ng/ul) | Total volume | 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[edit]
- Received 30 plasma samples 1mL each from Kang Zhang's lab
- All samples were collected in 2014
Zhang Id | phenotype_category | sex | date_of_birth | Age | 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)[edit]
- received 8 gDNA samples from Paula Ladd
Samples | Sample ID | concentration (ng/ul) | 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
Samples | Sample ID | total volume (ul) after diluted | 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 |
labnote: 2010_11_08
December 7, 2010 (Sarah's African gDNA, UPenn )[edit]
- received 48 methylome samples from Tishkoff's lab delivered by UPS
William R Beggs, Jr.
Tishkoff Lab - Dept of Genetics, University of Pennsylvania
430 Clinical Research Building
415 Curie Blvd
Philadelphia, PA 19104-6145
LabID | 1M sample # | Well | Volume ul | 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:
- Data analysis:
- [[4]]
- More sample info: Media:48SamplelistUPenn.xlsx
- [[4]]
December 10, 2010 (normal/tumor gDNA from JHU)[edit]
- received 48 normal/tumor gDNA samples from JHU delivered by FedEx
Eirikur Briem
John Hopkins University
855N. Wolfe Street
Rangos 580.14
Baltimore, MD 21205
Sample_ID | Kun_Well | Final Volume (uL) | 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
Plate layout | 1 | 2 | 3 | 4 | 5 | 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)[edit]
- Received 4 bisulfite converted mouse gDNA from Yuan Gao
Yuan Gao
Forrest City Baltimore
855 N. Wolfe St. STE 102
Baltimore, MD 21205
Sample ID | Conc. (ng/ul) confirmed by Qubit | Volume (ul) | 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 |
February 2, 2011 (Brain gDNA of Parkinson's patients from Burnham Institute, human frozen cerebral cortex)[edit]
- Received 18 human brain samples from Parkinson's patients. This includes control and Parkinson's patient samples.
Pair | Control Sample ID | Sample code | Sex | age (year.day) | Postmortem time | Conc. (ug/ul)/ volume (ul) | PD Sample ID | Sample code | Sex | age (year.day) | Postmortem time | 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 |
March 10, 2011, Cell pellet samples from Belmonte's lab, Salk Institute[edit]
- Received 5 cell pellet samples from Belmonte's lab
- Extracted gDNA using DNeasy Blood and Tissue kit (Qiagen)
Samples | No. of cell | gDNA conc. (ng/ul) | Elution volume (ul) | 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 |
April 21, 2011, PGP1 iPS gDNA from Harvard[edit]
- Received one sample of PGP1 CD1 iPS P16 from Harvard Medical School
Jihyuk Lee
Harvard Medical School
77 Avenue Louis Pasteur
Boston, MA 02115
Sample name | Sample ID | Conc. (ng/ul) | Total amount (ug) |
PGP1 CD1 iPS P16 | PGP1 iPS | 129 | 39 |
April 27, 2011, gDNA of TET study from Harvard Medical School[edit]
- Received 24 gDNA sample from Yeguang (from Yujiang Geno Shi's lab)
Tube Number | Sample description | concentration (ng/ul) | 9 sample choice | 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 |
May 19, 2011, gDNA from the blood samples of HIV patients, UCSD Medical School[edit]
- Received 39 samples from Josué Pérez-Santiago (from Christopher Woelk's lab, UCSD medical School)
- Each sample volume 21ul, conc. 100ng/ul
Sample ID | PID | Place in 96plate | Volume (ul) | Conc. (ng/ul) | 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 |
- Spreadsheet: Media:gDNA from TropherLab_2011_05_19.xlsx
- Related lab note:
- Mapping data:
May 25, 2011, gDNA of 10 different tissues from Billi Li, Standforf Univ[edit]
- Received gDNA samples for all the tissues of individual N37 from Jin Billi Li, Standford Univ.
Jin Billy Li
Standford University Genetics Dept.
Standford Univ ALWAY BLDG M-341
259 CAMPUS DR ALWAY BLDG
Standford, CA 94035
Number | Sample | Concentration (ug/ul) | Volume (ul) | Total amount (ug) | 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 |
July 8, 2011, gDNA from the blood samples of control and GA patients from Kang Zhang's lab, UCSD[edit]
- Received 48 control and 48 GA gDNA blood samples (GA methylation plate1) from Zhao Ling (Dr. Kang Zhang's post doc)
- The concentration of every samples was adjusted to 100ng/ul, total amount 2ug.
Sample number | Well | Phenotype | 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 |
- GA-methylation plate1: Media:GA_methylation_sample_plate1.xlsx
- 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:
July 29, 2011, gDNA of 3 human iPS lines with single nonsynonymous mutations, UCSD[edit]
- Received 3 gDNA sample from Alice that are iPS lines with single nonsynonymous mutation)
- 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
- Related lab note:
- [[20]]
- [[20]]
August 1, 2011, gDNA of the blood samples of schizophrenia disorder patients from Dr. Roel Ophoff, UCLA[edit]
- Received 96 gDNA samples (in 96-well plate) of the blood samples of schizophrenia disorder patients from Dr. Roel Ophoff, UCLA
Eric Strengman
UCLA 695 Charles E. Young Dr. S
Gonda 4335
Los Angeles, CA 90095
- Each sample was remeasured the DNA conc. by Nanodrop
- Related lab note:
- [[21]]
- [[21]]
- 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[edit]
- 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
Sample ID | Conc. (ng/ul) by Sergio | Conc. (ng/ul)confirmed by Nanodrop | 260/280 | 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 |
September16, 2011, gDNA from Sergio, Salk Institute[edit]
Sample ID | Conc. (ng/ul) by Sergio | Conc. (ng/ul)confirmed by Nanodrop | 260/280 | 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:
September16, 2011, received 3 more gDNA from UPenn to repeat the capture of the samples with low QC values[edit]
Sample ID | Conc. (ng/ul) by Sergio | Conc. (ng/ul)confirmed by Nanodrop | 260/280 | 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 |
September 17, 2011, received 3 cell pellet samples from Alice (sample from Yang Xu's lab)[edit]
- I extracted gDNA and elutee 150ul in elute1 and elute2. The concentration was was measure by Nanodrop.
Sample ID | Conc. (ng/ul)confirmed by Nanodrop | Volume (ul) | Yields (ug) | 260/280 | 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 |
December 13, 2011, received one sequencing library from Baylor, RC-1[edit]
- 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:
March 1, 2012, received 6 gDNA samples (PGP1F hiPS) from Alice[edit]
Cap labeling | Sample ID | Lab ID | Conc. (ng/ul) | 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:
- [[36]]
April 15, 2012, Cell pellet samples from Sergio to Dinh[edit]
No. | Sample ID | 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 |
May 15, 2012, Cell pellet samples from Sergio to Dinh[edit]
No. | Sample ID | 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)[edit]
- 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
Sample IDs | Conc. (ng.ul) by Nanodrop (from Harvard) |
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 |
August 22, 2012, got 2 gDNA and 3 cell pellet samples for 330k BSPP capture fromAlice (samples from Dr. Yang Xu)[edit]
No. | SampleID | LabIDs | Nanodrop (ng/ul) | A260 | 260/280 | 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)[edit]
No. | Sample description | Mark on the tube | Lab ID | Nanodrop (ng/ul) | A260 | 260/280 | 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)[edit]
- 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