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[[http://genome-tech.ucsd.edu/LabNotes/index.php/Nongluk_(Noi)_Plongthongkum Back]]
= MONOD's Project (March, 2014) =
=== Sample record ===
[[Nongluk_(Noi)_Plongthongkum| Back]]
==== [[Noi:Samples from Moores Cancer Center  | Samples from Moores Cancer Center ]] ====
=== <span style="color:mediumblue">Sample record</span> ===
* <u>'''2014-03-04:'''</u> Received 4 aliquots of plasma, serum, and buffy coat from 3 cases from Cancer Center.  
==== [[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: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2014-5-31#DNA_extraction_of_10_serum_samples_from_Cancer_Center]]
** 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/2014-6-9]]
** 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/2014-6-16]]
** 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: Match pair - gDNA - human primary tissue: colon. Conc.: 0.076ug/ul or 76ng/ul, amount: 2ug --> expected volumed ~26.31ul
*** 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]

Back

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.
    • The samples were used for DNA isolation comparison using four different kits
      • Experimental design & results: [[1]], [[2]], [[3]]
  • 2014-05-27: Received 10 pancreatic adenocarcinoma specimens (2 serum aliquots/case) from Cancer Center (Sharmeela Kaushal).
  • 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).
  • 2014-06-26: Received 10 colon cancer specimens (3 plasma aliquots/case) from Cancer Center (Sharmeela Kaushal).
  • 2014-06-26: Received 10 Lung cancer specimens (3 plasma aliquots/case) from Cancer Center (Sharmeela Kaushal).
  • 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).
  • 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).


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 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
    • RRBS library preparation of 5ng input DNA: [[10]]
    • RRBS library preparation of 100ng input DNA: [[11]]


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.