|
| Status |
Public on Jul 27, 2021 |
| Title |
KO_Y_3_K27Ac |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
age: 8 weeks old
strain: C57BL/6
chip antibody: H3K27ac(abcam ab4729)
genotype: CTCF fl/fl Albcre+
|
| 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 HiSeq 2500 |
| |
|
| Data processing |
sequnced using Illumina Hiseq2500 platform
Raw ChIP-seq reads were trimmed for adaptor sequence, and aligned to the mm10 genome assembly using bwa mem v0.7.12 with default parameters
aligned files were filtered for MAPQ > 5 and sorting, deduplication were processed using PICARD v1.77
peaks were called using macs2 v2.1.2 with the following setting: -g mm --extsize ($predicted d) --shift {($predicted d)/2} -q 0.001 (--broad-cutoff 0.1 --broad for H3K27ac,H3K27me3 ChIP-seq peak calling)
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.1.3
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak, broadPeak, CPM normalized bigwig
|
| |
|
| Submission date |
May 30, 2020 |
| Last update date |
Jul 27, 2021 |
| Contact name |
Hyoung-Pyo Kim |
| E-mail(s) |
kimhp@yuhs.ac
|
| Organization name |
Yonsei University College of Medicine
|
| Department |
Department of Tropical Medicine
|
| Street address |
Yonsei-ro 50-1
|
| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE151502 |
Genome-wide maps of chromatin state in liver. |
| GSE151503 |
RNA-Seq, ChIP-Seq and HiC of Wild Type and CTCF cKO Liver |
|
| Relations |
| BioSample |
SAMN15063589 |
| SRA |
SRX8430737 |
