|
| Status |
Public on Jul 23, 2015 |
| Title |
PM_ATAC-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: No antibody
|
| Treatment protocol |
Cell were treated with transposase (Illumina #FC-121-1030)
|
| 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 |
Libraries were prepared according to previous protocol (Buenrostro et al., 2013) using KAPA HiFi PCR kit (KAPA biosystems, # KK2601)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ATAC-seq of WT PM
|
| Data processing |
Library strategy: ATAC (assay for transposase-accessible chromatin)
Basecalls were obtained using CASAVA version 1.8.4.
Illumina adaptors were removed using a custom python script, reads were treamed to 50 bp.
Reads were aligned to the mm9 genome assembly using Bowtie2 with default options, mitochondrial reads were removed from the analysis .
Replicated reads were removed using Picard tools, MarkDuplicates.
Reads with insert size smaller than 140 bases were selected for peak detectection, that was performed using the MACS2 callpeak function for broad peaks.
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) |
kfirum@weizmann.ac.il
|
| 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 |
| GSE63573 |
Transcription factor Runx1 cooperates with MyoD and c-Jun to regulate the balance of myoblast proliferation/differentiation [ATAC-Seq] |
|
| Relations |
| BioSample |
SAMN03217766 |
| SRA |
SRX766230 |
