 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 15, 2022 |
| Title |
Aged satellite cell ATAC-Seq 2 |
| Sample type |
SRA |
| |
|
| Source name |
satellite cells
|
| Organism |
Mus musculus |
| Characteristics |
age: 26 months
strain: Tg(Pax7-EGFP)#Tajb
tissue: skeletal muscle
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
5000 satellite cells were isolated by Fluorescence-Activated Cell Sorting (FACS), selected for the GFP+/DAPI-, from 2 young and 2 aged Pax7-eGFP male mice, and sorted directly into ATAC-Seq Lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin). Following the lysis, cells were washed with wash buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) and spun down at 800g. Tagmentation was performed for 20 minutes at 37 °C in transposition mixture (5 μl of Tagment DNA (TD) buffer, 3.2 μl PBS, 0.89 μl Tn5, 0.1% Tween-20, 0.01% Digitonin and 0.75 μl water). After tagmentation, DNA was purified using column purification and PCR amplification with Illumina Nextera XT adapters was performed. The amplified DNA was then size selected and purified for sequencing. Each sample was processed using a modified version of the OMNI ATAC-Seq protocol (Corces, M. R. et al. Nature Methods, 2017).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
8-Old900-T0-rep2_S3
|
| Data processing |
Illumina BaseSpace software was used for basecalling.
Data was analyzed using ENCODE pipeline https://github.com/ENCODE-DCC/atac-seq-pipeline
Peaks were called using MACS2(v2.1.0)
Optimal peaks per condition were determined using the IDR pipeline https://github.com/nboley/idr
Project’s Website (reproducible notebooks): https://csglab.github.io/transcriptional_reprogramming_muscle_cells/
Genome_build: mm10
|
| |
|
| Submission date |
Apr 05, 2021 |
| Last update date |
Jan 13, 2023 |
| Contact name |
Vahab Soleimani |
| E-mail(s) |
vahab.soleimani@mcgill.ca
|
| Organization name |
McGill University
|
| Department |
Human Genetics
|
| Street address |
3640 rue University
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H3A 0C7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE171534 |
ATAC-Seq of young and aged satellite cells |
| GSE171998 |
Transcriptional reprogramming of skeletal muscle stem cells by the niche environment |
|
| Relations |
| BioSample |
SAMN18623017 |
| SRA |
SRX10516737 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5226659_8-Old900-T0-rep2_S3_L001_R1_001.trim.merged.nodup.no_chrM_MT.tn5.fc.signal.bigwig |
453.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM5226659_8-Old900-T0-rep2_S3_L001_R1_001.trim.merged.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.gz |
4.6 Mb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
