|
| Status |
Public on Jul 23, 2015 |
| Title |
H3K27ac-2_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Primary proliferating myoblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell type: primary
days in culture: 3
strain: C57BL/6
chip antibody: anti H3K27ac
|
| Treatment protocol |
Cell were fixed with formaldehyde and nuclear lysate were made
|
| Growth protocol |
We isolatedf SC from gastrocnemius muscles of 2-3 weeks old C57bl/6 WT or Runx1f/f mice. Cells were grown at 37°C, 5% CO2 on GHR MatrigelTM (BD Biosciences, USA) in proliferation medium (BIOAMF-2, Biological Industries, Israel), which was replaced daily.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei (sonicated to yield DNA fragments of ~300bp) and histone-DNA complexes were isolated with relevant antibody, washed and DNA was purified using Qiagen Minelute kit.
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 |
| |
|
| Description |
second IP experiement of H3K27ac (abcam, ab4729)
|
| Data processing |
For all samples, basecalls were performed using CASAVA version 1.8.4.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie with the following options: -a -m 1 --best --strata -v 1.
Peaks of enriched binding regions were detected by merging for each biological replicate of Ipusing the same IgG as control. Peaks were called using MACS2.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files containing peaks detected by MACS2.
|
| |
|
| Submission date |
Nov 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
kfir baruch Umansky |
| E-mail(s) |
[email protected]
|
| Phone |
97289342318
|
| Organization name |
Weizmann Institute
|
| Street address |
POB 25
|
| City |
Rehovot |
| State/province |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE56131 |
Transcription factor Runx1 cooperates with MyoD and c-Jun to regulate the balance of myoblast proliferation/differentiation |
| GSE63572 |
Transcription factor Runx1 cooperates with MyoD and c-Jun to regulate the balance of myoblast proliferation/differentiation [ChIP-Seq Histone] |
|
| Relations |
| BioSample |
SAMN03217769 |
| SRA |
SRX766229 |
