|
| Status |
Public on Dec 01, 2023 |
| Title |
Neonatal oligodendrocyte progenitor cell input biol rep 3 (P5) |
| Sample type |
SRA |
| |
|
| Source name |
Forebrain
|
| Organism |
Mus musculus |
| Characteristics |
age: postnatal day 5
tissue: Forebrain
cell line: Primary
cell type: nOPCs
genotype: Pdgfr{alpha}H2BEGFP
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Neonatal and adult OPCs were sorted from PdgfrαH2BEGFP mice at P5 and P60 respectively. Chromatin was crosslinked with 1 % paraformaldehyde and quenched with 125 mM glycine during nuclei purification
Libraries were prepared using 2 ng of ChIP DNA and 10 ng of Input DNA (KAPA Hyper Prep Kit, KK8502)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
C-nOPC-Input
|
| Data processing |
The adapter sequences were removed from the FASTQ files using Trim Galore
Trimmed reads were aligned to the Mus musculus reference genome GRCm38 using Bowtie2 (v.2.4.5) program
SAMTools was used to remove PCR duplicates and reads mapped to blacked list regions and alignments with low mapping quality (q < 20).
The deepTools bamCompare function (Ramírez et al., 2016) was used to normalize the ChIP samples to their respective input samples
MACS2 algorithm was used for peak calling
DiffBind was used for differential binding of H4K8ac in aOPCs compared to nOPCs.
Annotation of the H4K8ac peaks was performed with ChIPseeker in R package
Functional enrichment of annotation performed with GREAT tool
Assembly: GRCm38
Supplementary files format and content: bigWig, narrowPeak (except for input samples)
|
| |
|
| Submission date |
Aug 10, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Patrizia Casaccia |
| E-mail(s) |
pcasaccia@gc.cuny.edu
|
| Organization name |
ASRC-CUNY
|
| Department |
Neuroscience
|
| Street address |
85 St Nicholas Terrace
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10031 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE240522 |
The epigenetic landscape of oligodendrocyte progenitors changes with time |
|
| Relations |
| BioSample |
SAMN36923058 |
| SRA |
SRX21324536 |
