|
| Status |
Public on Jul 17, 2015 |
| Title |
AGS2 LCL RRBS |
| Sample type |
SRA |
| |
|
| Source name |
Lymphoblastoid cell line
|
| Organism |
Homo sapiens |
| Characteristics |
mutation: RNASEH2B
sample type: Lymphoblastoid cell line
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using phenol chloroform.
Myers lab RRBS protocol
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
DRIP-seq, MethylC-seq, RNA-seq: All fastq files were trimmed with FastqMcf and custom Perl script before mapping.
DRIP-seq: Trimmed fastq reads were mapped to hg19 using BWA 0.6.1. Peak calling was first performed by MACS 1.4.2 using input library as control. DRIP peaks were further assigned onto restriction fragments using custom Perl script. DRIP peaks from 2 AGS2 and 2 AGS4 cells were merged into one sample, respectively.
RNA-seq: Trimmed fastq reads were mapped to hg19 using TopHat 2.0.5. Count table was generated using HTSeq using the "intersection-nonempty" option.
MethylC-seq: Trimmed fastq reads were mapped to hg19 using Bismark 0.7.7. Wig files containing percent methylation were generated using custom Perl script.
RRBS: Fastq files were trimmed with Trim Galore before mapping to hg19 using Bismark 0.7.7. Wig files containing percent methylation were generated using custom Perl script.
Genome_build: hg19
|
| |
|
| Submission date |
May 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yoong Wearn Lim |
| E-mail(s) |
ywlim@ucdavis.edu
|
| Organization name |
University of California, Davis
|
| Department |
Molecular and Cellular Biology
|
| Lab |
Chedin
|
| Street address |
One Shields Avenue
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE57353 |
Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi-Goutières syndrome |
|
| Relations |
| BioSample |
SAMN02749581 |
| SRA |
SRX534122 |
