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| Status |
Public on May 01, 2020 |
| Title |
Input_WT_3 |
| Sample type |
SRA |
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| Source name |
E6.5 decidua
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| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl6/J
tissue: whole decidua minus myometrium
developmental stage: E6.5
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| Treatment protocol |
WT and homozygous EGFP-Blimp1 females were mated with C57BL6/J studs. For staging purposes, E0.5 was defined as midday on the day of vaginal plug. Whole decidua minus the overlying myometrium were harvested at E6.5.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Multiple pools of freshly dissected decidua (E6.5) from mice expressing an endogenous N-terminal EGFP tagged Blimp1 protein (Mitani et al., 2017) and WT mice were minced using a razor blade in a drop of culture media (RPMI-1640, 10% FCS, 0.0004% β-mercaptoethanol, 1x Pen/Strep, 2mM glutamine) and cross-linked in 1% formaldehyde in culture media for 20 min at ambient temperature. After quenching in 0.125 M glycine for 5 min, cells were washed in PBS and processed for ChIP using 6 micrograms of rabbit anti-GFP antibody (Ab290, Abcam). Triplicate test (GFP ChIP of Prdm1NEG/NEG) and duplicate control (GFP ChIP of WT) decidual samples, and their respective input samples were analysed.
DNA was multiplexed and paired end sequencing was performed over two lanes of Illumina HiSeq4000 platform.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Paired-end sequence reads were mapped to the mm10 genome using bwa-MEM (0.7.15-r1140)
PCR duplicates were removed using Samtools 1.9 (Li et al., 2009).
Peaks were called against input DNA using MACS 2.1.2 (Zhang et al., 2008) with default parameters.
Bigwig files were generated using Deeptools2 (Ramirez et al., 2016)
Genome_build: mm10
Supplementary_files_format_and_content: [.bw] bigWig represent genome coverage generated using Deeptools2.
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| Submission date |
Dec 06, 2019 |
| Last update date |
May 02, 2020 |
| Contact name |
Arne Wyndham Mould |
| E-mail(s) |
[email protected]
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| Organization name |
Oxford University
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| Department |
Psychiatry
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| Lab |
Neural Correlates of Gene Function
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| Street address |
Warneford Hospital
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| City |
Oxford |
| State/province |
Oxfordshire |
| ZIP/Postal code |
OX3 7JX |
| Country |
United Kingdom |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE141611 |
The transcriptional repressor Blimp-1/Prdm1 controls the maternal decidual response during pregnancy [ChIP-seq] |
| GSE141613 |
The transcriptional repressor Blimp-1/Prdm1 controls the maternal decidual response during pregnancy |
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| Relations |
| BioSample |
SAMN13501929 |
| SRA |
SRX7283310 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4209535_Input_WT_3.bw |
204.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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