|
| Status |
Public on Apr 22, 2013 |
| Title |
T22_H2AZ_ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
T22, 2nd pair, 2nd individual
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: CD14 cells
individual identifier: T22
monozygotic twin relationship: MZ twin of T21
chip antibody: anti-H2A.Z (Active Motif, Cat no: 39113)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The chromatin immunoprecipitation (ChIP) assay was performed on 5 x 105 CD14+ cells according to previously published protocols. Chromatin was sonicated to get fragments of 100-500 bp and immunoprecipitated with 10 ul of anti-H2A.Z antibody (Active Motif, Cat no: 39113). ChIP-seq libraries were prepared following the Illumina protocol and ligated to standard PE adaptors and sequenced on an Illumina GAIIx instrument.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
PE76
|
| Data processing |
ChIP-seq reads were aligned to the reference sequence using bwa-0.6.6 then sorted and indexed using samtools
Read pairs with quality scores >=10 were extracted and the number of read pairs overlapping each probe on the Illumina HumanMethylation450K array were counted.
RNA-seq was aligned with TopHat 1.3.1 and FPKM values were generated using CuffLinks 1.0.3
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Fragment coverage across Illumina HumanMethylation450K probes (GEO Platform GPL13534) for ChIP data.
Supplementary_files_format_and_content: Transcript FPKM numbers for nearest TSS for RNA-seq data.
|
| |
|
| Submission date |
Apr 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas A Down |
| E-mail(s) |
thomas.down@gurdon.cam.ac.uk
|
| Organization name |
University of Cambridge
|
| Department |
WT/CRUK Gurdon Institute
|
| Street address |
Tennis Court Road
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 1QN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE46217 |
Inactive or moderately active human promoters are enriched for inter-individual epialleles [Seq] |
| GSE46220 |
Inactive or moderately active human promoters are enriched for inter-individual epialleles |
|
| Relations |
| BioSample |
SAMN02053615 |
| SRA |
SRX268693 |
