Noi/NOTES/2014-7-7
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Summary of RRBS sequencing libraries and their corresponding index[edit]
1) HiSeq Rapid run at IGM (140709_SN1001)[edit]
Original Library ID | Library ID (for sequencing) | Sample ID | TruSeq Index | Sequencing platform/at | Lane # | Inout DNA amount (ng) | Note |
NP-RRBS-6T_set1_100ng-Jun28 | NP_RRBS_6T_100ng_20140708 | 6-T-1_1 | 1 | Rapid run/IGM | 1 | 100 | Solid tumor tissue from UCSD-006 project |
NP-RRBS-6T_set1_100ng-Jun28 | NP_RRBS_6T_100ng_20140708 | 6-T-2_2 | 4 | Rapid run/IGM | 1 | 100 | Solid tumor tissue from UCSD-006 project |
NP-RRBS-6T_set1_100ng-Jun28 | NP_RRBS_6T_100ng_20140708 | 6-T-3_1 | 5 | Rapid run/IGM | 1 | 100 | Solid tumor tissue from UCSD-006 project |
NP-RRBS-6T_set1_100ng-Jun28 | NP_RRBS_6T_100ng_20140708 | 6-T-4_1 | 7 | Rapid run/IGM | 1 | 100 | Solid tumor tissue from UCSD-006 project |
NP-RRBS-6T_set1_100ng-Jun28 | NP_RRBS_6T_100ng_20140708 | 6-T-5_1 | 25 | Rapid run/IGM | 1 | 100 | Solid tumor tissue from UCSD-006 project |
NP-RRBS-6T-set2_100ng-Jun28 | NP_RRBS_6T_100ng_20140708 | 6-T-1_2 | 2 | Rapid run/IGM | 1 | 100 | Solid tumor tissue from UCSD-006 project |
NP-RRBS-6T-set2_100ng-Jun28 | NP_RRBS_6T_100ng_20140708 | 6-T-2_1 | 23 | Rapid run/IGM | 1 | 100 | Solid tumor tissue from UCSD-006 project |
NP-RRBS-6T-set2_100ng-Jun28 | NP_RRBS_6T_100ng_20140708 | 6-T-3_2 | 6 | Rapid run/IGM | 1 | 100 | Solid tumor tissue from UCSD-006 project |
NP-RRBS-6T-set2_100ng-Jun28 | NP_RRBS_6T_100ng_20140708 | 6-T-5_2 | 10 | Rapid run/IGM | 1 | 100 | Solid tumor tissue from UCSD-006 project |
NP-RRBS-6T-4_2-set2_100ng-Jun28 | NP_RRBS_6T_100ng_20140708 | 6-T-4_2 | 8 | Rapid run/IGM | 1 | 100 | Solid tumor tissue from UCSD-006 project |
NP-RRBS-7T_set1_100ng-Jun28 | NP_RRBS_7T_100ng_20140708 | 7-T-1_1 | 13 | Rapid run/IGM | 2 | 100 | Solid tumor tissue from UCSD-007 project |
NP-RRBS-7T_set1_100ng-Jun28 | NP_RRBS_7T_100ng_20140708 | 7-T-2_1 | 15 | Rapid run/IGM | 2 | 100 | Solid tumor tissue from UCSD-007 project |
NP-RRBS-7T_set1_100ng-Jun28 | NP_RRBS_7T_100ng_20140708 | 7-T-3_1 | 27 | Rapid run/IGM | 2 | 100 | Solid tumor tissue from UCSD-007 project |
NP-RRBS-7T_set1_100ng-Jun28 | NP_RRBS_7T_100ng_20140708 | 7-T-4_1 | 19 | Rapid run/IGM | 2 | 100 | Solid tumor tissue from UCSD-007 project |
NP-RRBS-7T_set1_100ng-Jun28 | NP_RRBS_7T_100ng_20140708 | 7-T-5_1 | 21 | Rapid run/IGM | 2 | 100 | Solid tumor tissue from UCSD-007 project |
NP-RRBS-7T_set2_100ng-Jun28 | NP_RRBS_7T_100ng_20140708 | 7-T-1_2 | 14 | Rapid run/IGM | 2 | 100 | Solid tumor tissue from UCSD-007 project |
NP-RRBS-7T_set2_100ng-Jun28 | NP_RRBS_7T_100ng_20140708 | 7-T-2_2 | 16 | Rapid run/IGM | 2 | 100 | Solid tumor tissue from UCSD-007 project |
NP-RRBS-7T_set2_100ng-Jun28 | NP_RRBS_7T_100ng_20140708 | 7-T-3_2 | 18 | Rapid run/IGM | 2 | 100 | Solid tumor tissue from UCSD-007 project |
NP-RRBS-7T_set2_100ng-Jun28 | NP_RRBS_7T_100ng_20140708 | 7-T-4_2 | 20 | Rapid run/IGM | 2 | 100 | Solid tumor tissue from UCSD-007 project |
NP-RRBS-7T_set2_100ng-Jun28 | NP_RRBS_7T_100ng_20140708 | 7-T-5_2 | 22 | Rapid run/IGM | 2 | 100 | Solid tumor tissue from UCSD-007 project |
2) HiSeq Rapid run at Illumina (140712)[edit]
- PE 100+7
- Sample Info
- DNA Extraction
- Library prep
- Library pooling
- Need to double check with Dr. Zhang if he wants to sequence more plasma sequencing library from project UCSD-004-P (PC-P) and normal control (NC-P).
- Dr. Zhang suggested to sequence more plasma libraries from previous batch
- All NC-P libraries
- PC-P-(2,3,4,8,10). However, I have used up sample PC-P-10 since it's conc. is very low. I need to include the whole pool including PC-P-10 sample for sequencing. Sample PC-P-8 is in anther pool. This mean that I need to sequence more 10 libraries of PC-P libraries instead of 5 libraries.
Helpful note from Dr. Zhang
"The reason to do more sequencing on these plasma libraries is that a decent fraction of plasma DNA are small fragments, even before Msp I digestion. Therefore with the RRBS protocol, we are actually getting whole genome libraries for those small fragments, and reduced representation libraries for those large fragments. This is clearly the case as there are many regions covered by single reads in the plasma RRBS libraries, but not in the tumor RRBS libraries."
Original Library ID | Library ID (for sequencing) | Sample ID | TruSeq Index | Sequencing platform/at | Lane | Inout DNA amount (ng) | Note |
NP-RRBS-6P_1ng-Jun29 | NP_RRBS_PCP-6P_1ng_20140709 | 6-P-1 | 13 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-006 project |
NP-RRBS-6P_1ng-Jun29 | NP_RRBS_PCP-6P_1ng_20140709 | 6-P-2 | 14 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-006 project |
NP-RRBS-6P_1ng-Jun29 | NP_RRBS_PCP-6P_1ng_20140709 | 6-P-3 | 15 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-006 project |
NP-RRBS-6P_1ng-Jun29 | NP_RRBS_PCP-6P_1ng_20140709 | 6-P-4 | 16 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-006 project |
NP-RRBS-6P_1ng-Jun29 | NP_RRBS_PCP-6P_1ng_20140709 | 6-P-5 | 27 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-006 project |
NP-RRBS-6P_1ng-Jun29 | NP_RRBS_PCP-6P_1ng_20140709 | 6-P-6 | 18 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-006 project |
NP-RRBS-6P_1ng-Jun29 | NP_RRBS_PCP-6P_1ng_20140709 | 6-P-7 | 19 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-006 project |
NP-RRBS-6P_1ng-Jun29 | NP_RRBS_PCP-6P_1ng_20140709 | 6-P-8 | 20 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-006 project |
NP-RRBS-6P_1ng-Jun29 | NP_RRBS_PCP-6P_1ng_20140709 | 6-P-9 | 21 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-006 project |
NP-RRBS-6P_1ng-Jun29 | NP_RRBS_PCP-6P_1ng_20140709 | 6-P-10 | 22 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-006 project |
NP-RRBS-PC-P-1ng-p1-Jun20 | NP_RRBS_PCP-6P_1ng_20140709 | PC-P-1 | 1 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-004 project |
NP-RRBS-PC-P-1ng-p1-Jun20 | NP_RRBS_PCP-6P_1ng_20140709 | PC-P-2 | 2 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-004 project |
NP-RRBS-PC-P-1ng-p1-Jun20 | NP_RRBS_PCP-6P_1ng_20140709 | PC-P-3 | 4 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-004 project |
NP-RRBS-PC-P-1ng-p1-Jun20 | NP_RRBS_PCP-6P_1ng_20140709 | PC-P-4 | 5 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-004 project |
NP-RRBS-PC-P-1ng-p1-Jun20 | NP_RRBS_PCP-6P_1ng_20140709 | PC-P-5 | 6 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-004 project |
NP-RRBS-PC-P-1ng-p1-Jun20 | NP_RRBS_PCP-6P_1ng_20140709 | PC-P-6 | 7 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-004 project |
NP-RRBS-PC-P-1ng-p1-Jun20 | NP_RRBS_PCP-6P_1ng_20140709 | PC-P-7 | 8 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-004 project |
NP-RRBS-PC-P-1ng-p1-Jun20 | NP_RRBS_PCP-6P_1ng_20140709 | PC-P-10 | 12 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-004 project |
NP-RRBS-PC-P-1ng-p2-Jun20 | NP_RRBS_PCP-6P_1ng_20140709 | PC-P-8 | 10 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-004 project |
NP-RRBS-PC-P-1ng-p2-Jun20 | NP_RRBS_PCP-6P_1ng_20140709 | PC-P-9 | 11 | Rapid run/ILMN | 1 | 1 | Plasma from UCSD-004 project |
NP-RRBS-7P_1ng-Jun29 | NP_RRBS_NCP-7P_1ng_20140709 | 7-P-1 | 1 | Rapid run/ILMN | 2 | 1 | Plasma from UCSD-007 project |
NP-RRBS-7P_1ng-Jun29 | NP_RRBS_NCP-7P_1ng_20140709 | 7-P-2 | 2 | Rapid run/ILMN | 2 | 1 | Plasma from UCSD-007 project |
NP-RRBS-7P_1ng-Jun29 | NP_RRBS_NCP-7P_1ng_20140709 | 7-P-3 | 4 | Rapid run/ILMN | 2 | 1 | Plasma from UCSD-007 project |
NP-RRBS-7P_1ng-Jun29 | NP_RRBS_NCP-7P_1ng_20140709 | 7-P-4 | 5 | Rapid run/ILMN | 2 | 1 | Plasma from UCSD-007 project |
NP-RRBS-7P_1ng-Jun29 | NP_RRBS_NCP-7P_1ng_20140709 | 7-P-5 | 6 | Rapid run/ILMN | 2 | 1 | Plasma from UCSD-007 project |
NP-RRBS-7P_1ng-Jun29 | NP_RRBS_NCP-7P_1ng_20140709 | 7-P-6 | 7 | Rapid run/ILMN | 2 | 1 | Plasma from UCSD-007 project |
NP-RRBS-7P_1ng-Jun29 | NP_RRBS_NCP-7P_1ng_20140709 | 7-P-7 | 8 | Rapid run/ILMN | 2 | 1 | Plasma from UCSD-007 project |
NP-RRBS-7P_1ng-Jun29 | NP_RRBS_NCP-7P_1ng_20140709 | 7-P-8 | 10 | Rapid run/ILMN | 2 | 1 | Plasma from UCSD-007 project |
NP-RRBS-7P_1ng-Jun29 | NP_RRBS_NCP-7P_1ng_20140709 | 7-P-9 | 11 | Rapid run/ILMN | 2 | 1 | Plasma from UCSD-007 project |
NP-RRBS-7P_1ng-Jun29 | NP_RRBS_NCP-7P_1ng_20140709 | 7-P-10 | 12 | Rapid run/ILMN | 2 | 1 | Plasma from UCSD-007 project |
NP-RRBS-NC-P-1ng-p1-Jun20 | NP_RRBS_NCP-7P_1ng_20140709 | NC-P-2 | 14 | Rapid run/ILMN | 2 | 1 | Normal control plasma from Kang Zhang's lab |
NP-RRBS-NC-P-1ng-p1-Jun20 | NP_RRBS_NCP-7P_1ng_20140709 | NC-P-3 | 15 | Rapid run/ILMN | 2 | 1 | Normal control plasma from Kang Zhang's lab |
NP-RRBS-NC-P-1ng-p1-Jun20 | NP_RRBS_NCP-7P_1ng_20140709 | NC-P-5 | 16 | Rapid run/ILMN | 2 | 1 | Normal control plasma from Kang Zhang's lab |
NP-RRBS-NC-P-1ng-p1-Jun20 | NP_RRBS_NCP-7P_1ng_20140709 | NC-P-6 | 27 | Rapid run/ILMN | 2 | 1 | Normal control plasma from Kang Zhang's lab |
NP-RRBS-NC-P-1ng-p2-Jun20 | NP_RRBS_NCP-7P_1ng_20140709 | NC-P-1 | 13 | Rapid run/ILMN | 2 | 1 | Normal control plasma from Kang Zhang's lab |
NP-RRBS-NC-P-1ng-p2-Jun20 | NP_RRBS_NCP-7P_1ng_20140709 | NC-P-7 | 18 | Rapid run/ILMN | 2 | 1 | Normal control plasma from Kang Zhang's lab |
NP-RRBS-NC-P-1ng-p2-Jun20 | NP_RRBS_NCP-7P_1ng_20140709 | NC-P-8 | 19 | Rapid run/ILMN | 2 | 1 | Normal control plasma from Kang Zhang's lab |
NP-RRBS-NC-P-1ng-p2-Jun20 | NP_RRBS_NCP-7P_1ng_20140709 | NC-P-9 | 20 | Rapid run/ILMN | 2 | 1 | Normal control plasma from Kang Zhang's lab |