|
Status |
Public on May 03, 2021 |
Title |
C2C12_ATAC_rep1 |
Sample type |
SRA |
|
|
Source name |
C2C12_ATAC
|
Organism |
Mus musculus |
Characteristics |
strain background: C3H cell line: C2C12 cell type: skeletal muscle cell line genotype: WT
|
Treatment protocol |
none
|
Growth protocol |
C2C12 control and C2C12 Hira KO cell lines were collected when grown in high serum medium at low density (proliferating conditions)
|
Extracted molecule |
genomic DNA |
Extraction protocol |
C2C12 cells were harvested and cell pellets were resuspended in lysis buffer, pelleted and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina) Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems)
|
|
|
Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
alignment: BWA algorithm (mem mode; default settings) Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file and with the –nomodel option Genome_build: mm10 Supplementary_files_format_and_content: Signal maps and peak locations were used as input data to Active Motif’s proprietary analysis program
|
|
|
Submission date |
Nov 08, 2020 |
Last update date |
May 03, 2021 |
Contact name |
Joana Esteves de Lima |
E-mail(s) |
joanaesteveslima@gmail.com
|
Organization name |
INSERM
|
Department |
IMRB INSERM U955
|
Lab |
Team RELAIX
|
Street address |
8 rue du general sarrail
|
City |
Creteil |
ZIP/Postal code |
94000 |
Country |
France |
|
|
Platform ID |
GPL19057 |
Series (2) |
GSE161053 |
Genome-wide changes in chromatin accessibility in myoblasts lacking Hira [ATAC-seq] |
GSE161056 |
ATAC-seq, ChIP-seq and RNA-seq studies in myoblasts lacking Hira |
|
Relations |
BioSample |
SAMN16706613 |
SRA |
SRX9460289 |