 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 01, 2021 |
| Title |
ERa_veh_CR_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Limbic system
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
Sex: Male
developmental stage: Adult
|
| Treatment protocol |
10-12 week-old C57/BL6 males were gonadectomized to clear circulating hormones. 3 weeks post-gonadectomy, males were treated for 4 hr prior to nuclei isolation.
|
| Growth protocol |
Animals were injected subcutaneously with 5 ug estradiol benzoate or vehicle (corn oil).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue was homogenized 15x with a loose pestle in a glass homogenizer containing Homogenization Medium (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X Roche EDTA-free protease inhibitor cocktail, pH 7.8). 0.3% IGEPAL CA-630 was added, and the tissue was further dounced 5x with a tight pestle. After douncing, the homogenate was filtered through a 40 µm strainer and mixed 1:1 with 50% OptiPrep solution (Millipore Sigma) prepared in Dilution Buffer (150 mM KCl, 30 mM MgCl2, 120 mM Tricine-KOH, pH 7.8). The homogenate was underlaid with 5 ml of 30% and 40% OptiPrep solution, respectively, and centrifuged at 10,000xg for 18 min at 4°C in an ultracentrifuge. ~2 ml of nuclei solution were removed from the 30 - 40% OptiPrep. interface by direct tube puncture. Following nuclei isolation, 0.4% IGEPAL CA-630 was added to improve binding to concanavalin A magnetic beads. Takara SMARTer ThruPlex DNA-seq Kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Paired-end reads were trimmed to remove low-quality basecalls and adapters (cutadapt -q 30). Trimmed reads were aligned to mm10 using Bowtie2 with the following flags: --dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 --minins 10 --maxins 700. After alignment, duplicate reads were removed using Picard MarkDuplicates. Read pairs with MAPQ < 40 (samtools view) and fragment length > 120 bp were removed (deeptools alignmentSieve). Read pairs aligning to the mitochondrial DNA or incomplete assemblies were also removed (samtools view). Peaks were called using MACS2 callpeak (q < 0.01). Filtered BAM files were normalized by coverage (bamCoverage -bs 1 --normalizeUsing CPM) to generate bigwig tracks.
Genome_build: mm10
|
| |
|
| Submission date |
Sep 25, 2020 |
| Last update date |
Mar 01, 2021 |
| Contact name |
Bruno Gegenhuber |
| E-mail(s) |
bruno_gegenhuber@hms.harvard.edu
|
| Organization name |
Harvard Medical School
|
| Department |
Neurobiology
|
| Street address |
220 Longwood Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE141434 |
Estrogen Drives Melanocortin Neurons To Reduce Sedentary Behavior |
|
| Relations |
| BioSample |
SAMN16264365 |
| SRA |
SRX9192496 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4803359_ERa_veh_CR_rep3.bed.gz |
435.1 Kb |
(ftp)(http) |
BED |
| GSM4803359_ERa_veh_CR_rep3.bw |
57.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
