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| Status |
Public on Jan 04, 2023 |
| Title |
hdc_wt_dorsal_striatum_1b_CGTCGCT |
| Sample type |
SRA |
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| Source name |
dorsal_striatum
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| Organism |
Mus musculus |
| Characteristics |
genotype: Hdc wt
age: 2-3 months
tissue: dorsal_striatum
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse brains rapidly dissected on ice. Dissected tissues were ventral and dorsal striatum, hypothalamus, and motor cortex. Tissue was rapidly frozen and stored at -80° until processing using the RNeasy MinElute columns (Qiagen, Valencia, CA).
RNA quality and quantity were confirmed with a Bioanalyzer (Agilent Technologies, Santa Clara, CA). We generated double-stranded complementary DNA using the Ovation RNA-Seq system V2 (NuGEN Technologies, Inc., San Carlos, CA), starting from 5 ng of RNA. Standard sequencing libraries (Illumina, Inc., San Diego, CA) were generated from 1-2 µg of cDNA, sheared to ~200 bp. Sequencing was performed at the Genome Technology Access Center (GTAC) at Washington University in St. Louis.
Fastq files containing demultiplexed, single-end 50 base-pair reads were used as the basis for exploratory analysis.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
5’ and 3’ adapter sequences were trimmed from each read using Trimmomatic (v0.32), and all reads shorter than 20 bases after adapter clipping were discarded
rRNA reads were identified by mapping to a mouse rRNA reference sequence using Bowtie2 (v2.2.3) and were discarded
The remaining reads were aligned to the mouse genome (Ensembl GRCm38 annotation 75) using STAR (v2.3.1z8)
SAMtools (v0.1.19) was used to convert SAM format to BAM format, then to create sorted and indexed BAM files for visualization
Default union mode in HTSeq-count (v0.6.1p1) was used to compute read counts for reads uniquely mapping to exons in the mouse genome
Genome_build: Ensembl 75 (mouse) genome
Supplementary_files_format_and_content: txt files with counts of certain gene for each sample
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| Submission date |
Nov 11, 2020 |
| Last update date |
Jan 04, 2023 |
| Contact name |
Joseph D Dougherty |
| Organization name |
Washington University
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| Department |
Genetics and Psychiatry
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| Street address |
4566 Scott Ave, box 8232
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| City |
St Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE161252 |
White matter abnormalities in the Hdc knockout mouse, a model of tic and OCD pathophysiology |
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| Relations |
| BioSample |
SAMN16770246 |
| SRA |
SRX9474256 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4903993_CGTCGCT_72.count2.txt.gz |
108.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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