Noi:MONOD's project: Difference between revisions
Jump to navigation
Jump to search
>Noi |
>Noi mNo edit summary |
||
(One intermediate revision by the same user not shown) | |||
Line 35: | Line 35: | ||
** 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> | <br> | ||
==== FFPE and Frozen Matched Pair Genomic DNA:Human Tumor Tissue: Colon ==== | ==== FFPE and Frozen Matched Pair Genomic DNA:Human Tumor Tissue: Colon ==== | ||
Line 57: | Line 58: | ||
::- '''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> | ||
<br> | |||
==== [[Noi:Samples from Illumina | Samples from Illumina]] ==== | |||
=== <span style="color:mediumblue">BSPP capture</span> === | === <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]] | ||
Line 65: | Line 67: | ||
* 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]]<br> | * 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> === | === <span style="color:mediumblue">Sequencing record</span> === | ||
* HiSeq Rapid run at IGM, UCSD: <u>2014-06-27</u> | * HiSeq Rapid run at IGM, UCSD: <u>2014-06-27</u> |
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.