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| Status |
Public on Jul 09, 2021 |
| Title |
ChIP-MR_replicate-A |
| Sample type |
SRA |
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| Source name |
Early morning baseline_MR_ChIPSeq
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
Sex: Male
conditions: Early morning baseline conditions
tissue: whole hippocampus
chip antibody: MR (MR H-300, sc11412x, Santa Cruz)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole hippocampus were dissected, snap frozen in liquid N2 and stored at -80C until processing. Hippocampi from 2 rats were cross-linked in 1% formaldehyde containing inhibitors and sonicated to extract chromatin. Chromatin was immunoprecipitated using antibodies against MR (MR H-300, sc11412x, Santa Cruz) or GR (GR H-300, sc8992x, Santa Cruz) and inputs were prepared from original chromatin sample in the absence of antibody.
Libraries were prepared according to Illumina’s instructions accompanying the DNA Sample Kit (WaferGen PrepX Complete ILMN 32i) using an Apollo system for end-repair, A-tailing, and ligation. The adapter-ligated samples were then single-indexed and PCR amplified.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
A-MR
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| Data processing |
Sequencing adapters and primers still present in unmapped reads were trimmed using Skewer (version 0.1.125).
Reads were mapped to the reference genome using BWA (version 0.7.15).
Bamtools (version 2.3.0) was used to filter out reads with poor quality, not properly paired and with too long insert size.
Since samples were sequenced across 5 lanes, their mapped / filtered reads were merged and deduplicated using Picard (version 1.111).
Mapped reads were analysed for standard ChIP-Seq quality metrics; in particular, for each sample, the Normalized Strand Cross-correlation and the Relative Strand Cross-correlation was calculated.
Peaks were called using the software MACS2 (version 2.1.1.20160309) with default parameters for narrow regions. Input samples (named “*-I”) were used as controls for the corresponding IP samples (named “*-GR” or “*-MR”) from the same animal and experimental condition.
Genome_build: Rnor_6.0 (Ensembl)
Supplementary_files_format_and_content: narrowPeak files (BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue)
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| Submission date |
Feb 13, 2019 |
| Last update date |
Jul 09, 2021 |
| Contact name |
Johannes Reul |
| Organization name |
University of Bristol
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| Department |
Bristol Medical School
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| Lab |
Neuro-Epigenetics Research Group
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| Street address |
Dorothy Hodgkin Building, Whitson Street
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| City |
Bristol |
| ZIP/Postal code |
BS1 3NY |
| Country |
United Kingdom |
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| Platform ID |
GPL22396 |
| Series (2) |
| GSE126510 |
Glucocorticoid action in the hippocampus revealed by integrated genome-wide ChIP and RNA analysis [ChIP-seq] |
| GSE126706 |
Glucocorticoid action in the hippocampus revealed by integrated genome-wide ChIP and RNA analysis |
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| Relations |
| BioSample |
SAMN10924939 |
| SRA |
SRX5371945 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3602752_A_MR_baselineAM_peaks.narrowPeak.gz |
5.4 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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