|
| Status |
Public on Nov 02, 2023 |
| Title |
Input_Aged_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Neural stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Neural stem cells
tissue type: Brain SVZ
age: 18 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 |
NSCs were fixed with 1% formaldehyde for 10 min and quenched with glycine solution for 20 min at room temperature. The fixed NSCs were lysed in ChIP lysis buffer on ice. Chromatin was released during cell lysis and sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-Seq libraries were prepared based on the protocol of KAPA HyperPrep Kit (Roche) complemented with the NEXTflex DNA Barcodes (Bioo Scientific).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
ChIP-Seq reads were aligned to the mm10 genome using Bowtie software with default settings. Only uniquely mapping reads with at most two mismatches were retained. The reads of repeated samples were merged in the BAM file for peak calling analysis. Peaks were called using MACS2 with default settings. Bedgraph (Bdg) files were generated using MACS2.
Assembly: mm10
Supplementary files format and content: Bedgraph files with peaks (except for input samples)
|
| |
|
| 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 |
GPL19057 |
| Series (2) |
| GSE212725 |
Transcriptional and epigenetic dysregulation impairs generation of proliferative neural stem and progenitor cells during brain aging |
| GSE214978 |
Transcriptional dysregulation impairs efficacy of neural stem cell activation during aging [ChIP-seq] |
|
| Relations |
| BioSample |
SAMN31190260 |
| SRA |
SRX17823961 |
