|
| Status |
Public on Aug 11, 2017 |
| Title |
THAP1_sample1 |
| Sample type |
SRA |
| |
|
| Source name |
wild type mouse ES cells derived from C57Bl/6 blastocysts
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
tissue: Embryonic stem cells derived from blastocysts
|
| Growth protocol |
ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Data were filtered using the following specifications fastq_quality_filter -Q 64 -q 20 -p 80
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2
peaks were called using macs2 with the specifications: -f SAM -g mm -n GGACTC-s_2_2 -B -q 0.01
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph files
|
| |
|
| Submission date |
Sep 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Chengguo Wei |
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Medicine
|
| Street address |
1428 Madison Ave1468 Madison Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL9185 |
| Series (1) |
| GSE86911 |
ChIP-Seq based analysis of THAP1 binding in mouse ES cells |
|
| Relations |
| BioSample |
SAMN05771140 |
| SRA |
SRX2163116 |
