|
| Status |
Public on Sep 01, 2023 |
| Title |
Female_placentae_pooled |
| Sample type |
SRA |
| |
|
| Source name |
Placenta
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Placenta
gender: Female
strain: C57BL/6
antibody: REST antibody
|
| Treatment protocol |
none
|
| Growth protocol |
Gestation day 15 of wildtype mice. The vaginal plug was observed was considered day 0.5 of gestation to detemine gestational age.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Freshly collected day 15 placentae from three biological replicates were pooled that was used to preapre ChIP DNA using Zymo-Spin ChIP Kit (Catalog# D5210).
The REST antibody from Millipore-sigma (Catalog# 17-641) was validated and used to prepare the ChIP DNA.
ChIP-seq approach was adopted for library prepartion, and Illumina Hiseq was used to sequence the libraries.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The raw sequence files were first chekced for quality by FASTQC.
The quality control was performed using cutadpat
Bowtie2 was used for read aligment to processd genome sequences
MACS2 was used to call peaks.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: bed file for narrowpeaks
|
| |
|
| Submission date |
Sep 06, 2020 |
| Last update date |
Sep 01, 2023 |
| Contact name |
Susanta K. Behura |
| E-mail(s) |
behuras@missouri.edu
|
| Organization name |
Univeristy of Missouri
|
| Department |
Division of Animal Sciences
|
| Street address |
920 East Campus Drive
|
| City |
Columbia |
| State/province |
Missouri |
| ZIP/Postal code |
65211 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE157552 |
Insights into the regulation of the brain-placental axis (ChIP-seq) |
| GSE157556 |
Insights into the regulation of the brain-placental axis |
|
| Relations |
| BioSample |
SAMN16070427 |
| SRA |
SRX9084750 |
