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=== Sample record === | = MONOD's Project (March, 2014) = | ||
==== [[Noi:Samples from Moores Cancer Center | Samples from Moores Cancer Center ]] ==== | [[Nongluk_(Noi)_Plongthongkum| Back]] | ||
* <u>'''2014-03-04:'''</u> Received 4 aliquots of plasma, serum, and buffy coat from 3 cases from Cancer Center. | === <span style="color:mediumblue">Sample record</span> === | ||
==== [[Noi:Samples from Moores Cancer Center | Samples from Moores Cancer Center]] ==== | |||
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-03-04|2014-03-04:]]'''</u> Received 4 aliquots of plasma, serum, and buffy coat from 3 cases from Cancer Center. | |||
** The samples were used for DNA isolation comparison using four different kits | ** The samples were used for DNA isolation comparison using four different kits | ||
*** Experimental design & results: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-2-28]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-3-11]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-4-4]] | *** Experimental design & results: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-2-28]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-3-11]], [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-4-4]] | ||
* <u>'''2014-05-27:'''</u> Received 10 pancreatic adenocarcinoma specimens (2 serum aliquots/case) from Cancer Center (Sharmeela Kaushal). | * <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-05-27|2014-05-27:]]'''</u> Received 10 pancreatic adenocarcinoma specimens (2 serum aliquots/case) from Cancer Center (Sharmeela Kaushal). | ||
** DNA extraction result: [[ | ** DNA extraction result: [[Noi/NOTES/2014-5-31#DNA_extraction_of_10_serum_samples_from_Cancer_Center|Noi/NOTES/2014-5-31 ]] | ||
* <u>'''2014-06-05:'''</u> Received 10 pancreatic adenocarcinoma specimens (3 plasma aliquots/case) and 5 tumor tissues from the same patient from cancer center (Sharmeela Kaushal). | * <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-06-05|2014-06-05:]]'''</u> Received 10 pancreatic adenocarcinoma specimens (3 plasma aliquots/case) and 5 tumor tissues from the same patient from cancer center (Sharmeela Kaushal). | ||
** These samples were derived from the same patients in 2014-05-27 | ** These samples were derived from the same patients in 2014-05-27 | ||
** DNA extraction result: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6- | ** DNA extraction result: [[Noi/NOTES/2014-6-9]] | ||
** RRBS library preparation of 100ng input DNA from tumor tissue: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6- | ** RRBS library preparation of 100ng input DNA from tumor tissue: [[Noi/NOTES/2014-6-16]] | ||
** RRBS library preparation of 1ng input DNA from plasma samples: [[Noi/NOTES/2014-6-20]] | |||
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-06-26| 2014-06-26]]:'''</u> Received 10 colon cancer specimens (3 plasma aliquots/case) from Cancer Center (Sharmeela Kaushal). | |||
** Project ID: UCSD-006-P | |||
** [[Noi/NOTES/2014-6-27#Part_2:_DNA_extraction_from_plasma_samples|DNA extraction result]] | |||
** RRBS library preparation of 1ng input DNA from plasma sample: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-29]] | |||
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-06-26| 2014-06-26]]:'''</u> Received 10 Lung cancer specimens (3 plasma aliquots/case) from Cancer Center (Sharmeela Kaushal). | |||
** Project ID: UCSD-007-P | |||
** [[Noi/NOTES/2014-6-27#Part_2:_DNA_extraction_from_plasma_samples|DNA extraction result]] | |||
** RRBS library preparation of 1ng input DNA from plasma sample: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-29]] | |||
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-06-27|2014-06-27:]]'''</u> Received 5 colon solid tumor tissue samples (20mg/case) from Cancer Center. Matched pairs samples with plasma samples of colon project (Sharmeela Kaushal). | |||
** Project ID: UCSD-006-T | |||
** [[Noi/NOTES/2014-6-27#Part_1:_DNA_extraction_from_solid_tumor_tissue_samples|DNA extraction result]] | |||
** RRBS library preparation of 100ng input DNA from tumor tissue: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-28]] | |||
* <u>'''[[noi:Samples_from_Moores_Cancer_Center#2014-06-27|2014-06-27:]]'''</u> Received 5 lung solid tumor tissue samples (20mg/case) from Cancer Center. Matched pairs samples with plasma samples of lung project (Sharmeela Kaushal). | |||
** Project ID: UCSD-007-T | |||
** [[Noi/NOTES/2014-6-27#Part_1:_DNA_extraction_from_solid_tumor_tissue_samples|DNA extraction result]] | |||
** RRBS library preparation of 100ng input DNA from tumor tissue: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-28]] | |||
<br> | |||
==== Samples from Kang Zhang's lab ==== | ==== Samples from Kang Zhang's lab ==== | ||
* <u>'''2014-05-22:'''</u> Received 30 plasma samples from Kang Zhang's lab | * <u>'''2014-05-22:'''</u> Received 30 plasma samples from Kang Zhang's lab | ||
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** They are all from normal samples with no cancer history | ** They are all from normal samples with no cancer history | ||
** DNA extraction results: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-30]] | ** DNA extraction results: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-30]] | ||
** RRBS library preparation of 1ng input DNA from plasma samples: [[Noi/NOTES/2014-6-20]] | |||
<br> | |||
==== FFPE and Frozen Matched Pair Genomic DNA:Human Tumor Tissue: Colon ==== | ==== FFPE and Frozen Matched Pair Genomic DNA:Human Tumor Tissue: Colon ==== | ||
*<u>'''2014-05-23:'''</u> Received two tubes of FFPE and frozen matched pair gDNA from Biochain | *<u>'''2014-05-23:'''</u> Received two tubes of FFPE and frozen matched pair gDNA from Biochain | ||
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*** Catalog number: D8235090-FP, lot. B609045 | *** Catalog number: D8235090-FP, lot. B609045 | ||
*** Tube1: Matched pair - gDNA - human primary tissue: colon. Conc.: 0.58ug/ul or 580ng/ul, amount: 2ug --> expected volume ~3.44ul | *** Tube1: Matched pair - gDNA - human primary tissue: colon. Conc.: 0.58ug/ul or 580ng/ul, amount: 2ug --> expected volume ~3.44ul | ||
*** Tube2: | *** Tube2: Matched pair - gDNA - human primary tissue: colon. Conc.: 0.076ug/ul or 76ng/ul, amount: 2ug --> expected volumed ~26.31ul | ||
**** (2014-06-01) I added TE buffer to make conc. to 50ng/ul (total volume 40ul) based on original conc. and re-measured conc. with Qubit dsDNA HS assay again (1ul). | **** (2014-06-01) I added TE buffer to make conc. to 50ng/ul (total volume 40ul) based on original conc. and re-measured conc. with Qubit dsDNA HS assay again (1ul). | ||
::{| {{table}} class = wikitable | ::{| {{table}} class = wikitable | ||
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::- '''CTT = colon tumor tissue''' | ::- '''CTT = colon tumor tissue''' | ||
** RRBS library preparation of 5ng input DNA: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-3]] | ** RRBS library preparation of 5ng input DNA: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-3]] | ||
** RRBS library preparation of 100ng input DNA: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-13]] | ** RRBS library preparation of 100ng input DNA: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-6-13]]<br> | ||
=== BSPP capture === | <br> | ||
==== [[Noi:Samples from Illumina | Samples from Illumina]] ==== | |||
=== <span style="color:mediumblue">BSPP capture</span> === | |||
* GP1V4 or MONOD V1 and GP1V6 capture on 5 cancer samples and 3 blood samples (UCLA, SZ 96 sample set): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-12-24]] | * GP1V4 or MONOD V1 and GP1V6 capture on 5 cancer samples and 3 blood samples (UCLA, SZ 96 sample set): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2013-12-24]] | ||
* MONOD V2 BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-3-2]] | * MONOD V2 BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-3-2]] | ||
* MONOD V3 BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-3-30#DNA_methylation_assay_-_MONOD_Project.2C_MONOD_V3_12k_probe_set_.28BSPP_capture.29]] | * MONOD V3 BSPP capture: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-3-30#DNA_methylation_assay_-_MONOD_Project.2C_MONOD_V3_12k_probe_set_.28BSPP_capture.29]] | ||
* Amplified DNA from Illumina captured with GP1V4 using Stoffel Fragment and Illumina's polymerase (no positive control, PC): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-13]] | * Amplified DNA from Illumina captured with GP1V4 using Stoffel Fragment and Illumina's polymerase (no positive control, PC): [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-13]] | ||
* Comparison of cancer DNA samples and amplified DNA from Illumina GP1V4 capture using three different DNA polymerases, Stoffel Fragment, Hemo KlenTaq and Illumina's polymerase: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-23]] | * Comparison of cancer DNA samples and amplified DNA from Illumina GP1V4 capture using three different DNA polymerases, Stoffel Fragment, Hemo KlenTaq and Illumina's polymerase: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-23]]<br> | ||
<br> | |||
=== <span style="color:mediumblue">Sequencing record</span> === | |||
* HiSeq Rapid run at IGM, UCSD: <u>2014-06-27</u> | |||
** [[Noi/NOTES/2014-7-2|Sample summary]] | |||
** PE 100+7 | |||
** Raw data on genome-miner: /media/SeqStore2/140627_SN1001_0363/2nd_attemp/ | |||
** Dinh did mapping | |||
* MiSeq run at Palsson's lab: <u>2014-06-30</u> | |||
** [[Noi/NOTES/2014-7-2|Sample summary]] | |||
** PE 150+7 | |||
** Raw data on genome-miner: ?? | |||
** Dinh did mapping | |||
* HiSeq Rapid run at IGM, UCSD: <u>2014-07-08</u> | |||
** [[Noi/NOTES/2014-7-7#HiSeq_Rapid_run_at_Illumina_.28_XXXXXX.29| Sample summary]] | |||
** PE 100+7 | |||
** Sequencing libraries of solid tumor tissue from UCSD-006-T and UCSD-007-T project | |||
* HiSeq Rapid run at Illumina: <u>2014-07-09</u> | |||
** [[Noi/NOTES/2014-7-7#HiSeq_Rapid_run_at_Illumina_.28_XXXXXX.29| Sample summary]] | |||
** PE 100+7 | |||
** Sequencing libraries of plasma DNA from UCSD-006-P and UCSD-007-P project and plasma sequencing libraries from UCSD-004-P (PC-P) and NC-P from previous batch. |
Latest revision as of 19:30, 13 September 2014
MONOD's Project (March, 2014)[edit]
Sample record[edit]
Samples from Moores Cancer Center[edit]
- 2014-03-04: Received 4 aliquots of plasma, serum, and buffy coat from 3 cases from Cancer Center.
- 2014-05-27: Received 10 pancreatic adenocarcinoma specimens (2 serum aliquots/case) from Cancer Center (Sharmeela Kaushal).
- DNA extraction result: Noi/NOTES/2014-5-31
- 2014-06-05: Received 10 pancreatic adenocarcinoma specimens (3 plasma aliquots/case) and 5 tumor tissues from the same patient from cancer center (Sharmeela Kaushal).
- These samples were derived from the same patients in 2014-05-27
- DNA extraction result: Noi/NOTES/2014-6-9
- RRBS library preparation of 100ng input DNA from tumor tissue: Noi/NOTES/2014-6-16
- RRBS library preparation of 1ng input DNA from plasma samples: Noi/NOTES/2014-6-20
- 2014-06-26: Received 10 colon cancer specimens (3 plasma aliquots/case) from Cancer Center (Sharmeela Kaushal).
- Project ID: UCSD-006-P
- DNA extraction result
- RRBS library preparation of 1ng input DNA from plasma sample: [[4]]
- 2014-06-26: Received 10 Lung cancer specimens (3 plasma aliquots/case) from Cancer Center (Sharmeela Kaushal).
- Project ID: UCSD-007-P
- DNA extraction result
- RRBS library preparation of 1ng input DNA from plasma sample: [[5]]
- 2014-06-27: Received 5 colon solid tumor tissue samples (20mg/case) from Cancer Center. Matched pairs samples with plasma samples of colon project (Sharmeela Kaushal).
- Project ID: UCSD-006-T
- DNA extraction result
- RRBS library preparation of 100ng input DNA from tumor tissue: [[6]]
- 2014-06-27: Received 5 lung solid tumor tissue samples (20mg/case) from Cancer Center. Matched pairs samples with plasma samples of lung project (Sharmeela Kaushal).
- Project ID: UCSD-007-T
- DNA extraction result
- RRBS library preparation of 100ng input DNA from tumor tissue: [[7]]
Samples from Kang Zhang's lab[edit]
- 2014-05-22: Received 30 plasma samples from Kang Zhang's lab
- Sample info.: [[8]].
- They are all from normal samples with no cancer history
- DNA extraction results: [[9]]
- RRBS library preparation of 1ng input DNA from plasma samples: Noi/NOTES/2014-6-20
FFPE and Frozen Matched Pair Genomic DNA:Human Tumor Tissue: Colon[edit]
- 2014-05-23: Received two tubes of FFPE and frozen matched pair gDNA from Biochain
- Sample info.
- Catalog number: D8235090-FP, lot. B609045
- Tube1: Matched pair - gDNA - human primary tissue: colon. Conc.: 0.58ug/ul or 580ng/ul, amount: 2ug --> expected volume ~3.44ul
- Tube2: Matched pair - gDNA - human primary tissue: colon. Conc.: 0.076ug/ul or 76ng/ul, amount: 2ug --> expected volumed ~26.31ul
- (2014-06-01) I added TE buffer to make conc. to 50ng/ul (total volume 40ul) based on original conc. and re-measured conc. with Qubit dsDNA HS assay again (1ul).
- Sample info.
Sample Original conc. (ng/ul) Estimate volume (ul) Dilute to 50ng/ul (total volume) Add TE buffer (ul) Qubit conc. (ng/ul) CTT-Frozen 580.00 3.45 40.00 36.55 52.3 CTT-FFPE 76.00 26.32 40.00 13.68 64.8
- - CTT = colon tumor tissue
Samples from Illumina[edit]
BSPP capture[edit]
- GP1V4 or MONOD V1 and GP1V6 capture on 5 cancer samples and 3 blood samples (UCLA, SZ 96 sample set): [[12]]
- MONOD V2 BSPP capture: [[13]]
- MONOD V3 BSPP capture: [[14]]
- Amplified DNA from Illumina captured with GP1V4 using Stoffel Fragment and Illumina's polymerase (no positive control, PC): [[15]]
- Comparison of cancer DNA samples and amplified DNA from Illumina GP1V4 capture using three different DNA polymerases, Stoffel Fragment, Hemo KlenTaq and Illumina's polymerase: [[16]]
Sequencing record[edit]
- HiSeq Rapid run at IGM, UCSD: 2014-06-27
- Sample summary
- PE 100+7
- Raw data on genome-miner: /media/SeqStore2/140627_SN1001_0363/2nd_attemp/
- Dinh did mapping
- MiSeq run at Palsson's lab: 2014-06-30
- Sample summary
- PE 150+7
- Raw data on genome-miner: ??
- Dinh did mapping
- HiSeq Rapid run at IGM, UCSD: 2014-07-08
- Sample summary
- PE 100+7
- Sequencing libraries of solid tumor tissue from UCSD-006-T and UCSD-007-T project
- HiSeq Rapid run at Illumina: 2014-07-09
- Sample summary
- PE 100+7
- Sequencing libraries of plasma DNA from UCSD-006-P and UCSD-007-P project and plasma sequencing libraries from UCSD-004-P (PC-P) and NC-P from previous batch.