|
| Status |
Public on Sep 29, 2014 |
| Title |
hESC_ZNF486_192 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells, ZNF486 ChIP
|
| Organism |
Homo sapiens |
| Characteristics |
transchromosomic: no
plasmid: none
chip_or_input: ZNF486 ChIP
chip antibody: ZNF486 (abcam ab104878, lot#GR52278-1)
nickname: KZNF (hESC) r2
|
| Growth protocol |
MEF feeders + W8 (fj044,FJ083, FJ084, fj148-150, FJ191-192), feeder-free GMEM+Lif (fj212-215).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
O'Geen H, Echipare L, Farnham PJ. Using ChIP-seq technology to generatehigh-resolution profiles of histone modifications. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20. PubMed PMID: 21913086.
TrueSeq DNA library prep, low input protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
fj192
DNA from Chromatin IP
|
| Data processing |
Paired-end samples that were sequenced to 100x100bp were trimmed from the 3' end to 80x80bp. Samples that were sequenced to 50x50bp were not trimmed.
The (possibly trimmed) paired-end reads were mapped with bowtie to the hg19 assembly (human samples) or mm9+hg19chr11 (mouse samples).
For multiply mapped reads, only the best scoring mapping per bowtie2 were kept. Only mappings with both of the paired-end reads mapped were kept.
Potential PCR duplicates were removed with samtools rmdup.
Based on the paired-end mappings, the median length of the fragments was determined for each sample. For input to MACS 1.4 only the read1 mappings were used and the median fragment length was used to determine the "-shiftsize" parameter.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Excel workbook with MACS results.
|
| |
|
| Submission date |
Aug 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Sofie Salama |
| E-mail(s) |
[email protected]
|
| Phone |
8314592814
|
| Organization name |
Univerity of California, Santa Cruz
|
| Department |
Center for Biomolecular Science and Engineering
|
| Lab |
Haussler
|
| Street address |
MS: CBSE, 1156 High St
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95060 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE60210 |
Human stem cell and mouse transchromosomic (hsa11) embryonic stem cell (with and without ectopic ZNF91 expression) ChIP-seq |
| GSE60211 |
An evolutionary arms race between KRAB zinc finger genes 91/93 and SVA/L1 retrotransposons |
|
| Relations |
| BioSample |
SAMN02954659 |
| SRA |
SRX671997 |
