|
| Status |
Public on Dec 25, 2019 |
| Title |
PRDM15_E6.5 (ChIP-seq) |
| Sample type |
SRA |
| |
|
| Source name |
6.5 d.p.c embryos
|
| Organism |
Mus musculus |
| Characteristics |
tissue: embryo
strain: C57BL/6
chip antibody: PRDM15 Antibody (Guccione lab)
|
| Treatment protocol |
Embryos were fixed using 1% formaldehyde, collected in SDS lysis buffer and frozen for ChIP. Detailed experimental procedures can be found in the supplemental method section of the paper.
|
| Growth protocol |
N/A
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated cells and histone-DNA complexes were enriched using PRDM15 antibody. Antibody is an in-house produced rabbit polyclonal antibody against PRDM15.
Directional RNA library was prepared according to Illumina's standard protocol. Detailed experimental procedures and bioinformatics analysis can be found in the supplemental method section of the paper.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 2
Peak calling was done using MACS 2.1.1 with the following configurations: -q 1e-5 --llocal=10000 --bw 300 -m 5,30 --slocal=1000 -B --keep-dup=1
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were produced using bamCoverage in the deeptools package
|
| |
|
| Submission date |
Jan 28, 2019 |
| Last update date |
Dec 26, 2019 |
| Contact name |
Diana HP Low |
| E-mail(s) |
dlow@imcb.a-star.edu.sg
|
| Organization name |
Institute of Molecular and Cell Biology
|
| Lab |
Chromatin, Epigenetics & Differentiation
|
| Street address |
#03-06, 61 Biopolis Drive, Proteos
|
| City |
Singapore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE125750 |
Identification of PRDM15 cistrome in the mouse embryo (6.5 d.p.c) |
| GSE125752 |
PRDM15 loss-of-function causes brain malformations through defective embryonic anterior-posterior patterning |
|
| Relations |
| BioSample |
SAMN10832722 |
| SRA |
SRX5299924 |
