|
| Status |
Public on Jul 05, 2023 |
| Title |
Input Control rep2 |
| Sample type |
SRA |
| |
|
| Source name |
P7 Ventricles
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Arid1a f/f Control
tissue: Ventricles
age: P7
chip antibody: none
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Formaldehyde crosslinked nuclei were sonicated and histone-DNA complexes were isolated using anti-H3K27Ac (Active Motif, cat# 39133).
NEXTFLEX® Rapid DNA-Seq Library Prep Kit for Illumina® Platforms
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
mapping to reference genome with BWA 0.7.17-r1188
peak caliing with Homer v4.11 findPeaks -style histone
differential peak occupancy analysis with Diffbind 2.12.0 with option -minOverlap 2 and DESeq2_1.24.0
generate bedGraph files with Homer v4.11 makeUCSCfile normalized to 1e7 reads
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files
|
| |
|
| Submission date |
Jul 24, 2020 |
| Last update date |
Jul 05, 2023 |
| Contact name |
Cornelis J. Boogerd |
| E-mail(s) |
k.boogerd@hubrecht.eu
|
| Organization name |
Hubrecht Institute
|
| Department |
Developmental Biology and Stem Cell Research
|
| Street address |
Uppsalalaan 8
|
| City |
Utrecht |
| ZIP/Postal code |
3584CT |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE155100 |
Arid1a is essential in cardiomyocytes for neonatal heart maturation [ChIP-seq] |
| GSE155102 |
Arid1a is essential in cardiomyocytes for neonatal heart maturation |
|
| Relations |
| BioSample |
SAMN15641137 |
| SRA |
SRX8820340 |
