|
| Status |
Public on Nov 02, 2023 |
| Title |
ATAC-Seq_Young_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Neural stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Neural stem cells
tissue type: Brain SVZ
age: 2 months
|
| Growth protocol |
Primary NSCs were isolated from the brain SVZs of young (2 months) and aged (18 months) mice, respectively (Nat Protoc. 2012 Nov; 7(11):2005-2012). Briefly, microdissection of the brain SVZ was performed on ice. The tissue pieces of SVZ from 6 mice were pooled and dissociated into single cells using Neural Tissue Dissociation kit. The NSCs were maintained in the initial proliferation medium at 37°C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Primary NSCs were dissociated into single cells and examined for cell viability using trypan blue staining. About 2×104 NSCs with cell viability > 90% were added in cell lysis on ice (lysis buffer: 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630). Cell nuclei were collected in a tube by centrifugation at 500 g at 4 °C and used for the tagmentation reaction in ATAC-Seq assay.
ATAC-Seq libraries were prepared based on the protocol of TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme #TD501).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
ATAC-Seq_Young_peaks.bdg
|
| Data processing |
ATAC-Seq reads were aligned to the mm10 genome using Burrows-Wheeler Aligner (BWA) with default settings. Only uniquely mapping reads with at most two mismatches were retained. The reads of repeated samples were merged for peak calling. All the reads were shifted +4 bp at the + strand and -5 bp at the - strand in the BAM file before peak calling. Peaks were called using MACS2 with --nomodel and --extsize 200 options. Bedgraph (Bdg) files were generated using MACS2.
Assembly: mm10
Supplementary files format and content: Bedgraph files with peaks
|
| |
|
| Submission date |
Oct 06, 2022 |
| Last update date |
Nov 02, 2023 |
| Contact name |
Chengyang Peter Huang |
| E-mail(s) |
chengyhuang@hotmail.com
|
| Organization name |
Shantou University Medical College
|
| Street address |
22 Xinling Street
|
| City |
Shantou |
| ZIP/Postal code |
515041 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE212725 |
Transcriptional and epigenetic dysregulation impairs generation of proliferative neural stem and progenitor cells during brain aging |
| GSE214971 |
Transcriptional dysregulation impairs efficacy of neural stem cell activation during aging [ATAC-seq] |
|
| Relations |
| BioSample |
SAMN31185658 |
| SRA |
SRX17821541 |
