 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 17, 2015 |
| Title |
C2_input |
| Sample type |
SRA |
| |
|
| Source name |
induced pluripotent stem cell line
|
| Organism |
Pan troglodytes |
| Characteristics |
tissue: induced pluripotent stem cell line
passage: 15+8
Sex: Male
antibody: input
|
| Treatment protocol |
n/a
|
| Growth protocol |
Standard iPSC and precursor cell line conditions as described in text
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed and chromatin sheared with a Covaris S2 (settings: 4 minutes, duty cycle 10%, 5 intensity, 200 cycles per burst in 4 6x16mm tubes per individual). H3K27ac- and H3K27me3-enriched regions were isolated using 5 ug of either H3K27ac antibody (ab4729, Abcam, Cambridge, MA, USA) or H3K27me3 antibody (07-449, Millipore, Billerica, MA, USA).
ChIP and input DNA from each individual were end-repaired, A-tailed and ligated to Illumina Truseq sequencing adapters before 18 cycles of PCR amplification. 200-300 bp DNA fragments were selected for sequencing.
Single end 50 bp; Input libraries were multiplexed and sequenced on one lane of an Illumina HiSeq2500 using the rapid run mode, ChIP libraries were multiplexed and sequenced on three lanes of an Illumina HiSeq2500 using the rapid run mode.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChIP-seq input
|
| Data processing |
Mapping with BWA 0.7.9
Removal of reads that did not map uniquely to the genome, had poor mapping quality or originated from PCR duplicates.
Peak calling with MACS or RSEG
Genome_build: hg19/PanTro3
Supplementary_files_format_and_content: MACS peaks and RSEG peaks bed files, summary table
|
| |
|
| Submission date |
Jun 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Irene Gallego Romero |
| E-mail(s) |
ireneg@uchicago.edu
|
| Phone |
773 834 1984
|
| Organization name |
University of Chicago
|
| Department |
Human Genetics
|
| Lab |
Gilad
|
| Street address |
920 E 58th St, CLSC 317
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL19148 |
| Series (2) |
| GSE61343 |
Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics |
| GSE69919 |
Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics [ChIP-Seq] |
|
| Relations |
| BioSample |
SAMN03776727 |
| SRA |
SRX1059778 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
| Processed data not applicable for this record |
|
|
|
|
 |
