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| Status |
Public on Apr 20, 2022 |
| Title |
Neonatal_ATAC-seq_NV_male_1 |
| Sample type |
SRA |
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| Source name |
Bed nucleus of the stria terminalis
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| Organism |
Mus musculus |
| Characteristics |
tissue: BNST
Sex: Male
treatment: Vehicle
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| Treatment protocol |
Animals were injected subcutaneously with 5 ug estradiol benzoate or vehicle control (corn oil) 4 days prior to brain dissection.
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| Growth protocol |
Esr1Cre/+; Sun1-GFP/+ male mice were treated on P0 and harvested on P4.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tissue (4-5 animals pooled per replicate) 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.The nuclei were diluted 2:1 with cold, supplemented homogenization buffer and immediately used for sorting. 30,000 GFP+ nuclei were collected into cold ATAC-RSB (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2) using the Sony SH800S Cell Sorter (purity mode) with a 100-μm sorting chip. After sorting, 0.1% Tween-20 was added, and the nuclei were centrifuged at 500 x g for 5 min at 4degC. The nuclei pellet was directly resuspended in transposition reaction mix.
library input: 30,000 nuclei
Nextera DNA Library Prep Kit
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Fastq files were processed using the ENCODE ATAC-seq pipeline with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files represent normalized genomic coverage. narrowPeak files represent regions of enriched signal.
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| Submission date |
Jan 13, 2022 |
| Last update date |
Apr 20, 2022 |
| Contact name |
Melody Wu |
| E-mail(s) |
mwu@cshl.edu
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| Organization name |
Cold Spring Harbor Laboratory
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| Street address |
1 Bungtown Rd
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| City |
Cold Spring Harbor |
| ZIP/Postal code |
11724 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (2) |
| GSE144706 |
Gene regulation by gonadal hormone receptors defines brain sex differences-[ATAC-Seq] |
| GSE144718 |
Gene regulation by gonadal hormone receptors defines brain sex differences |
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| Relations |
| BioSample |
SAMN24960419 |
| SRA |
SRX13776353 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5815291_P4_ATAC_male_1_S1_R1_001.trim.srt.nodup.no_chrM_MT.tn5.pval0.01.300K.bfilt.narrowPeak.gz |
3.6 Mb |
(ftp)(http) |
NARROWPEAK |
| GSM5815291_P4_ATAC_male_1_S1_R1_001.trim.srt.nodup.no_chrM_MT.tn5.sort.bw |
366.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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