|
| Status |
Public on Jul 12, 2018 |
| Title |
IMR90 WGBS |
| Sample type |
SRA |
| |
|
| Source name |
IMR90
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
cell line: IMR90
cell type: Fetal lung fibroblast
|
| Growth protocol |
IMR90 cells were grown in ATCCÂformulated Eagle's Minimum Essential Medium with 10%FBS and Penicillin-Sterptomycin. The cells were placed in 37 degree humidified incubator containing 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
NA12878 genomic DNA was purchased from ATCC. IMR90 high molecular weight genomic DNA was extract from cultured cells using SDS+proteinase K lysis/phenol-chloroform treatment. Extracted DNA was treated DNase-free RNase A.
100 ng of genomic DNA was treated with Tn5 transposase for tagmentation, then tagged DNA was filled with methylated dCTP, dATP, dGTP, dTTP mixture. The filled DNA was bisulphite treated using EZ DNA methylation Gold kit (Zymo research). The bisulphite treated samples were amplified with custom and Illumina index adapters. The amplified products were size selected using AMPureXP beads.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
FASTQ reads were adapter asked using cutadapt v1.9.1 for bisulfite converted adapter sequences
Masked reads were aligned to hg19 using bwa-meth v0.10 with default parameters
Aligned reads were marked for duplicates using Picard v2.4.1
A custom perl script was used to filter "fill-in" artifact be qc-fail flagging reads with 3 or more methylated CHH's outside the first 11 cycles
Methylation ratios were determined, by CpG, CHG, CHH context, using MethylDackel v0.1.13 with min baseQ >= 20, min mapQ >=20 and excluding the first 11bases of R1 and R2 alignments
Genome_build: hg19
Supplementary_files_format_and_content: Compressed methylKit files were generated which capture CpG CHG, CHH methylation and coverage (https://github.com/al2na/methylKit)
|
| |
|
| Submission date |
Sep 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew Johnston |
| E-mail(s) |
Andrew.Johnston@med.einstein.yu.edu
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Genetics
|
| Lab |
Price 314
|
| Street address |
1301 Morris Park Avenue
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE103503 |
Whole genome bisulphite sequencing using the Illumina X system [Bisulfite-Seq] |
| GSE103505 |
Whole genome bisulphite sequencing using the Illumina X system |
|
| Relations |
| BioSample |
SAMN07605798 |
| SRA |
SRX3161708 |
