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| Status |
Public on Oct 23, 2015 |
| Title |
F3 |
| Sample type |
SRA |
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| Source name |
medial prefrontal cortex
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
tissue: medial prefrontal cortex
gender: Female
estrous cycle: Proestrus
chip antibody: Egr1 (Santa Cruz, catalog# sc-110-X, lot# H1611)
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| Treatment protocol |
Following five days of habituation and handling under pair-housing, the estrous cycle of female rats was monitored by daily vaginal smearing and subsequent cytological analysis for a minimum of two cycles.
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| Growth protocol |
N/A
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Brains were dissected out, flash frozen, and stored at -80C until sectioning on a cryostat at -20C for tissue-punching of the medial prefrontal cortex. Chromatin was then crosslinked and sheared to fragments of 200-500 bp using a Bioruptor sonicator (Diagenode, Denville, NJ, USA). Next, pre-cleared chromatin was immunoprecipitated overnight at 4℃ with an antibody directed against Egr1 (sc-110-X, 4 μg, Santa Cruz Biotechnology, Dallas, TX, USA). After washes, elution from beads, and reversal of the cross-link, immunoprecipitated DNA was purified.
ChIP-Seq libraries were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina and barcoded primers (New England Biolabs) following the manufacturer’s protocol (#E7370). For each biological sample, two libraries were prepared (IP and Input), resulting in a total of 22 barcoded libraries.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
PvM_annotated_regions.csv
PvD_annotated_regions.csv
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| Data processing |
Illumina Casava1.9 software used for basecalling.
Trimmomatic v0.32 was used to remove adapter sequences, and quality filtering using the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. Reads shorter than 36 bp after trimming were thus removed from the study.
Filtered reads were then aligned to the reference genome using Bowtie2 (v2.1.0) with the --very-sensitive-local preset. Aligned reads were thus filtered using samtools (v0.1.19) and Picard Tools (v1.84) to retain only reads mapping uniquely, with a mapping quality score above 30, and deduplicated.
Differential ChIP-seq signal was then analyzed using the DiffReps tool (v1.55.4) for each pair-wise comparison, Proestrus vs. Males, Diestrus vs. Males, and Proestrus vs. Diestrus with --nsd 2 --window 500 --step 50, and annotated with the R package ChIPpeakAnno (v2.14.1)
Genome_build: Rnor_5.0 Ensembl Release 76 (August 2014)
Supplementary_files_format_and_content: PvM_annotated_regions.csv: comma-separated file of annotated genomic regions displaying a differential Egr1 binding between Proestrus and Males, as detected by DiffReps
Supplementary_files_format_and_content: DvM_annotated_regions.csv: comma-separated file of annotated genomic regions displaying a differential Egr1 binding between Diestrus and Males, as detected by DiffReps
Supplementary_files_format_and_content: PvD_annotated_regions.csv: comma-separated file of annotated genomic regions displaying a differential Egr1 binding between Proestrus and Diestrus, as detected by DiffReps
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| Submission date |
Jun 11, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mohamed Kabbaj |
| E-mail(s) |
[email protected]
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| Phone |
850-644-4930
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| Organization name |
Florida State University
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| Department |
Biomedical Sciences
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| Street address |
1115 W Call St
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| City |
Tallahassee |
| State/province |
Florida |
| ZIP/Postal code |
32306 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (2) |
| GSE69772 |
The influence of the estrous cycle on sex differences in the rat adult medial prefrontal cortex transcriptome [ChIP-Seq] |
| GSE69773 |
The influence of the estrous cycle on sex differences in the rat adult medial prefrontal cortex transcriptome |
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| Relations |
| BioSample |
SAMN03769793 |
| SRA |
SRX1056323 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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