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| Status |
Public on Apr 20, 2022 |
| Title |
P4_BNST_Female_E2_1 |
| Sample type |
SRA |
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| Source name |
Bed nucleus of the stria terminalis
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| Organism |
Mus musculus |
| Characteristics |
genotype: Esr1Cre/+; ROSA26CAG-Sun1-sfGFP-Myc/+
tissue: BNST
Sex: Female
treatment: Estradiol
age: Postnatal day 4
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| Treatment protocol |
Animals were injected subcutaneously with 5 ug estradiol benzoate or vehicle control (corn oil) on the day of birth (P0)
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| Growth protocol |
Esr1Cre/+; ROSA26CAG-Sun1-sfGFP-Myc/+ female mice
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Four days after injection, animals were rapidly decapitated, and 400-μm sections were collected in ice-cold homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 120 mM tricine-KOH, pH 7.8) on a microtome. The BNST was microdissected (4 animals pooled per condition) and collected in 1 ml of cold homogenization buffer containing 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, and 1X EDTA-free PIC, and 0.4 U/ml RNAseOUT. The tissue was dounce-homogenized 15x in a 1 ml glass tissue grinder (Wheaton) with a loose pestle. 0.3% IGEPAL CA-630 was added, and the suspension was homogenized 5x with a tight pestle. The homogenate was filtered through a 40-μm strainer then centrifuged at 500 x g for 15 min at 4oC. The pellet was resuspended in 0.5 ml homogenization buffer containing 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X EDTA-free PIC, and 0.2 U/ml RNAseOUT. 12,000 GFP+ nuclei were collected into cold Buffer RLT Plus supplemented 1:100 with β-mercaptoethanol using the Sony SH800S Cell Sorter (purity mode) with a 100-μm sorting chip. Samples were stored at -80degC until RNA extraction. RNA extraction was performed with Qiagen RNeasy Plus Micro Kit.
Libraries were prepared using the Tecan Genomics Ovation SoLo RNA-seq kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
For adult dataset, reads were adapter trimmed and quality filtered (q>30) using the Fast-X toolkit (http://hannonlab.cshl.edu/fastx_toolkit). For neonatal dataset, reads were adapter trimmed and quality filtered (q>30) using cutadapt.
Filtered reads were mapped to the mm10 reference genome using STAR.
The number of reads mapped to each gene (exons only) was calculated using featureCounts. For the neonatal dataset, technical duplicate reads were removed using the manufacturer's nudup.py script (https://github.com/tecangenomics/nudup). The number of reads mapping to each gene (including introns) was calculated using featureCounts.
Differential expression analysis was performed with DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content:
RNASeq_BNST: xls file with differential expression results and read counts for all samples.
Neonatal_BNST: xlsx file with differential expression results and read counts for all samples.
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| Submission date |
Oct 01, 2020 |
| 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) |
| GSE144717 |
Gene regulation by gonadal hormone receptors defines brain sex differences-[RNA-Seq] |
| GSE144718 |
Gene regulation by gonadal hormone receptors defines brain sex differences |
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| Relations |
| BioSample |
SAMN16338446 |
| SRA |
SRX9233806 |
| 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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