|
| Status |
Public on Jul 01, 2024 |
| Title |
Panx2peaks_treatment_repeat_2 |
| Sample type |
SRA |
| |
|
| Source name |
Hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Hippocampus
cell line: primary cells
cell type: Neural progenitor cells
strain: C57BL/6
Sex: Male
|
| Growth protocol |
DMEM, 8mM HEPES, B27 supplement, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Plus sonication (Diagenode).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina. 10 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 12 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using AMPure XP beads from Beckman Coulter. Libraries were validated using the Qubit High Sensitivity DNA Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls were performed using fastq for Illumina output.
ChIP-seq reads were trimmed with a cut-off quality score > 30, using the Trim galore software
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 2.3.5.
Peaks were called uing MACS v3.0.0a5 with the significance cut-off q-value <=0.01
Assembly: Bedgraph files were generated using bdgpeakcall of MACS3. narrowPeak and broadPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: mm10
Supplementary files format and content: Bedgraph files, narrowPeak /broadPeak (except for Input sample)
|
| |
|
| Submission date |
May 10, 2022 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Diji Kuriakose |
| E-mail(s) |
diji.kuriakose@monash.edu
|
| Organization name |
Monash University
|
| Lab |
ADB
|
| Street address |
Wellington road
|
| City |
Melbourne |
| State/province |
Victoria |
| ZIP/Postal code |
3800 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE202645 |
Identifying the binding sites for miRSome on miR-9 genomic locus with ChIP-seq |
|
| Relations |
| BioSample |
SAMN28177562 |
| SRA |
SRX15224916 |
