|
| Status |
Public on Dec 01, 2017 |
| Title |
AS HR site 2 iPSCs |
| Sample type |
SRA |
| |
|
| Source name |
AS HR site 2 iPSCs
|
| Organism |
Homo sapiens |
| Characteristics |
source cell type: B-lymphocyte
cell type: iPSC line derived from Angelman syndrome patient
genotype/variation: CpG free neo cassette is integrated in SNURF/SNRPN locus at site2
genotype/variation: DNA methylation-corrected AS iPSCs
|
| Biomaterial provider |
Coriell Cell repositories; http://ccr.coriell.org/
http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM20409
|
| Growth protocol |
ESCs and iPSCs were cultured with TeSR medium on a Matrigel coated plate.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified from iPSCs using DNeasy Blood & Tissue Kit (Qiagen).
Target enrichment-genome methyl sequence was performed by using SureSelectXT Methyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing (Agilent Technologies) with customized capture library following manufacturer's protocol. The biotinylated RNA capture probe library to capture specific genomic loci was designed to include three loci, chr3: 36600000-37410000, chr6: 144000000-144800000, and chr15: 24900000-25700000.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
library strategy: Target enrichment-genome bisulfite sequencing
Base calling was carried out using bcl2fastq v1.8.4 (Illumina Inc.) using the arguments "--fastq-cluster-count 0 --force --mismatches 1"
Read quality was confirmed using fastqc with default options
Reads were mapped to the hg19 genome with Bismark (v0.7.12). Bismark uses a C to T converted version of the genome and Bowtie (v1.0.1) alignment to identified base-specific methylation percentages.
A custom script was run to generate methylated and unmethylated bedGraph files describing the percentage of methylated to unmethylated cytosines across the genome.
Methylation at enriched loci was checked manually using the Integrated Genome Viewer (IGV) v2.3.38
To confirm phasing of reads aligning to the MLH1 and SNRPN loci, bisulfite reads were mapped to custom sequences representing insertion of exogenous CpG free neo sequence into the MLH1 and SNRPN loci (MLH1andSNRPN.fa) as compared to the annotated endogenous MLH1 and SNRPN loci.
genome build: GRCh37/hg19
processed data files format and content: bedGraph files containg continuous-valued data in track format. This display type is useful for probability scores and transcriptome data. This track type is similar to the wiggle (WIG) format, but unlike the wiggle format, data exported in the bedGraph format are preserved in their original state. Two files are provided for each processed sample representing the methylated and unmethylated tracks. Methylated tracks have a mCpG.bedGraph or _m.bedGraph suffix, while unmethylated tracks have a unmCpG.bedGraph or _u.bedGraph suffix. The fasta file, MLH1andSNRPN.fa has sequences describing the exogenous CpG free and neo ex sequences that were used for read phasing.
|
| |
|
| Submission date |
Dec 13, 2016 |
| Last update date |
Mar 28, 2022 |
| Contact name |
April Elizabeth Williams |
| E-mail(s) |
apriljack06@gmail.com, awilliams@salk.edu
|
| Phone |
7345461645
|
| Organization name |
Salk Institute for Biological Studies
|
| Department |
IGC
|
| Street address |
10010 N Torrey Pines Rd
|
| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE63938 |
Targeted CpG island methylation in human pluripotent stem cells |
|
| Relations |
| BioSample |
SAMN06140260 |
| SRA |
SRX2420168 |
