Noi/NOTES/2014-7-7: Difference between revisions

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** All NC-P libraries
** 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.
** 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.
'''Useful note from Dr. Zhang'''<br>
"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."
{| {{table}} class = wikitable
{| {{table}} class = wikitable
| align="center" style="width:200px;background:#f0f0f0;"|'''Original Library ID'''
| align="center" style="width:200px;background:#f0f0f0;"|'''Original Library ID'''

Revision as of 23:58, 8 July 2014

Summary of RRBS sequencing libraries and their corresponding index

Calendar

HiSeq Rapid run at IGM ( XXXXXX)

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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 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_20140628 7-T-5_2 22 Rapid run/IGM 2 100 Solid tumor tissue from UCSD-007 project

HiSeq Rapid run at Illumina ( XXXXXX)

  • PE 100+7
  • Library prep
  • 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.

Useful 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