|
| Status |
Public on Oct 01, 2013 |
| Title |
PolII ChIP-seq for GM19204 |
| Sample type |
SRA |
| |
|
| Source name |
lymphoblastoid cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: GM19204
cell type: lymphoblastoid cell line
population: YRI
ethnicity: Yoruba
country of origin: Nigeria
chip antibody: PolII (Santa Cruz sc-9001)
chip antibody manufacturer: Santa Cruz
chip antibody catalog #: sc-9001
|
| Biomaterial provider |
Coriell; http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=GM19204
|
| Growth protocol |
Ten lymphoblastoid cell lines from unrelated Yoruba individuals were obtained from the Coriell Institute. Cells were grown in RPMI media with 15% FBS, supplemented with 2mM L-glutamate, 100 I.U./mL penicillin, and 100 ug/mL streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was extracted using protocol described in Cain et al. 2011, except that for some samples chromatin was sheared with a Covaris S2 (settings: 40 min duty cycle 20%, intensity 8, 200 cycles/burst, 500 uL at a time in 12 x 24 mm tubes).
Prepared Illumina sequencing libraries as described by the ENCODE Project Consortium (2011), starting with 20 uL of ChIP output or 4 ng of pooled input sample.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls by Illumina CASAVA 1.7.0
Mapped reads to hg18 using BWA 0.6.1, allowing up to 2 mismatches per read (-n 2), and excluding gapped alignments (-o 0)
Discarded reads that did not uniquely map, taking into account SNPs in YRI 1000 genomes samples as described in Degner 2012.
Discarded reads overlapping multiple SNPs and reads overlapping indels
Discarded duplicate reads mapping to same location and strand randomly (rather than retaining highest scoring)
Extracted reads in 2kb surrounding each segregating SNP and counted reads that could be assigned to each haplotype
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited files containing all information used for tests of genetic association. Each row represents 2kb region flanking a test-SNP and gives total number of reads for one individual as well as number of allele-specific reads that can be assigned to each haplotype.
|
| |
|
| Submission date |
Jun 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Graham McVicker |
| E-mail(s) |
gmcvicker@salk.edu
|
| Organization name |
Salk Institute
|
| Lab |
McVicker
|
| Street address |
10010 N Torrey Pines Rd
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE47991 |
Identification of genetic variants that affect histone modifications in human cells |
|
| Relations |
| SRA |
SRX306580 |
| BioSample |
SAMN02204426 |
