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= List of reagent in -20C, -80C, and 4C (December 2014) = [[Nongluk_(Noi)_Plongthongkum| Back]] == Nimblegen SeqCap (UMRv1) == * SeqCap Epi probe pool (Design name: 140923_HG19_UMR_v1_Epi_H) was aliquot 4.5ul in each 0.2mL PCR tube as described in [[Noi/NOTES/2014-10-29#Things_to_do_upon_receive_the_probe_pool|'''2014-10-29''']] '''Label PCR tube:''' Hg19 UMR v1 141029 '''Original note from 2014-10-29''' '''Location:''' -20C, in original box within Noi Library prep kit box. I got total '''16 tubes of 4.5ul aliquot'''. The instruction said it's normal to get extra volume of the probe. I have used 5 tubes for the 1st and 2nd SeqCap hybridization capture experiments * There are total 11 tubes left in a small original plastic box that put the cupboard box in -20C freezer labeled '''''Library Prep Kit Noi Zhanglab''''' as shown in picture below. [[File:NP_photo 2.JPG|450px]] ==== Additional reagent of Nimblegen SeqCap kit are listed below ==== ** SeqCap Epi Accessory Kit (-20C freezer in sequencing room, image below) ** SeqCap Hybridization and Wash Kits ** SeqCap EZ HE-Oligo Kit A and SeqCap EZ HE-Oligo Kit B. These oligos were resuspend as recommended by instruction from the kit. (-20C freezer in sequencing room (image below) ** SeqCap Adaptor oligo kit A. This kit should be equivalent to Illumina TruSeq adaptor set A. I have not used this kit as I generated WGBS libraries using TruSeq adaptor from Illumina. This kit is new and has not been resuspended yet (-20C freezer in sequencing room, image below) [[File:NP_photo 4-1.JPG|450px]] **SeqCap Pure Capture Bead Kit (4C, new fridge by the door, image below) [[File:NP_photo 10.JPG|450px]] == WGBS libraries of normal and cancer patients == * Please note that there are two batches of WGBS libraries of ctDNA from cancer patients. The first batch I generated using the protocol similar to RRBS but skipped DNA digestion and used 1ng of ctDNA as starting materials as described in XXXX. This batch of WGBS libraries was used for the first Nimblegen SeqCap hybridization capture experiment on XXXX, I have them all (24 libraries in PCR rack that contain in ''Noi Losen Stuffs 2'' at -20C as shown I'n picture above. * '''The second batch of WGBS from ctDNA of cancer patients''' were generated using '''KAPA Hyper Prep Kit''' with more input of starting material (in the range of 1.5-20ng). They were generated on XXXX and should be located in the PCR rack with cover (on the left of image below). [[File:NP_photo 8-e.JPG|450px]] * I also have WGBS of cfDNA from normal control generated on XXXX in the same box of the first batch of WGBS libraries of cancer patients (Noi Losen Stuffs 2 box). However, I have performed re-amplification of these normal samples and stored in different location that will be described below. I may not suggest to use all WGBS libraries in Noi Losen Stuffs 2 box. * There are 24 WGBS of normal control re-amplified on XXXX, However, these WGBS are generated by the method similar to RRBS without DNA digestion or any fragmentation. I did not generate more WGBS libraries of normal control using KAPA Hyper Prep Kit as they showed good result either in BSPP capture and SeqCap hybridization capture. Dr. Zhang suggested to generate more WGBS libraries only for those cancer samples which have poor results. ==== Final conc. of WGBS libraries ==== ==== WGBS libraries of ctDNA from cancer patients ==== (The tube should be labeled ~2014-12-13) :{| {{table}} border = 1 | align="center" style="width:100px;background:#f0f0f0;"|'''Sample''' | align="center" style="width:80px;background:#f0f0f0;"|'''Conc. (ng/ul)''' | align="center" style="width:80px;background:#f0f0f0;"|'''TruSeq Indx''' |- | PCP-9||26.13||8 |- | PCP-4||21.73||3 |- | PCP-8||19.07||7 |- | PCP-6||20.13||5 |- | PCP-7||22.80||6 |- | PCP-2||22.13||1 |- | PCP-3||21.47||2 |- | PCP-5||21.47||4 |- | 6P-1||26.00||9 |- | 6P-8||24.80||14 |- | 6P-10||22.27||16 |- | 6P-9||20.27||15 |- | 6P-5||24.67||13 |- | 6P-2||19.60||10 |- | 6P-3||19.87||11 |- | 6P-4||19.20||12 |- | 7P-8||22.80||25 |- | 7P-3||19.07||20 |- | 7P-10||25.33||27 |- | 7P-7||29.60||23 |- | 7P-6||26.93||22 |- | 7P-1||14.67||18 |- | 7P-2||19.73||19 |- | 7P-5||18.00||21 |} ==== WGBS libraries of cfDNA from normal controls ==== (The tube should be labeled ~2014-12-16) :{| {{table}} border = 1 | align="center" style="width:100px;background:#f0f0f0;"|'''Sample''' | align="center" style="width:80px;background:#f0f0f0;"|'''Conc. (ng/ul)''' | align="center" style="width:80px;background:#f0f0f0;"|'''TruSeq Indx''' |- | NC-1||13.73||1 |- | NC-2||16.00||2 |- | NC-3||16.93||4 |- | NC-5||13.07||5 |- | NC-6||15.33||6 |- | NC-7||13.73||7 |- | NC-8||15.87||8 |- | NC-9||16.53||10 |- | NC-12||14.80||13 |- | NC-13||13.19||14 |- | NC-14||14.93||15 |- | NC-15||13.60||16 |- | NC-16||13.87||27 |- | NC-17||13.47||18 |- | NC-18||14.67||19 |- | NC-19||13.47||20 |- | NC-20||12.79||11 |- | NC-21||12.31||12 |- | NC-22||16.00||21 |- | NC-23||13.60||22 |- | NC-24||11.97||3 |- | NC-27||14.67||9 |- | NC-29||12.96||23 |- | NC-30||15.47||25 |}
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