|
| Status |
Public on May 20, 2022 |
| Title |
mouse EPN cells, ChIP-Sox9 |
| Sample type |
SRA |
| |
|
| Source name |
derived from Rela fusion EPN
|
| Organism |
Mus musculus |
| Characteristics |
tissue: derived from Rela fusion EPN
cell line: derived from Rela fusion EPN
cell type: control
genotype: EPN control
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue was dissociated, crosslinked with 1.1% formaldehyde for 10 min, quenched and frozen. After thawing, cells were lysed to release nuclei, followed by nuclear lysis. Lysates were sonicated using a Diagenode Bioruptor.
ChIP-Seq libraries were prepared using the TruSeq ChIP Library Preparation Kit (Ilumina, IP-202-1012). 10 ng of DNA was used as starting material for Input and IP samples. Libraries ranging from 250-350 bp were extracted from agarose gel incisions and PCR amplified for 18 cycles. Libraries were purified using AMPure XP beads and library quality was validated using a Standard Sensitivity NGS Fragment Analysis Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Quality control was performed using fastQC (v0.11.17) and MultiQC (v0.9).
Reads were mapped to the mouse genome mm10 or human genome hg38 assembly using bowtie2
Using the HOMER software suite, bedgraph files and tag directories were made
findPeaks command in histone (for H3K27ac) or factor (for Sox9) mode was used to filter ChIP peaks enriched over Input control
Annotation of enriched peaks was performed using annotatePeaks with mm10 or hg38 assembly
Assembly: Integrated Genome Browser compatible files were made using samtools, sort and index, deepTools bamCompare
Supplementary files format and content: mm10; hg38
Supplementary files format and content: bw, narrowPeak
|
| |
|
| Submission date |
May 13, 2022 |
| Last update date |
May 20, 2022 |
| Contact name |
Debosmita Sardar |
| E-mail(s) |
sardar@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE202960 |
Sox9 directs divergent epigenomic states in brain tumor subtypes (ChIP-Seq) |
| GSE202961 |
Sox9 directs divergent epigenomic states in brain tumor subtypes |
|
| Relations |
| BioSample |
SAMN28233636 |
| SRA |
SRX15259357 |
