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| Status |
Public on Apr 13, 2018 |
| Title |
I16R031a17 |
| Sample type |
SRA |
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| Source name |
striatum
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: striatum
genotype: WT
environment: EE
age: 2 months
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| Extracted molecule |
total RNA |
| Extraction protocol |
Striatum was removed, flash-frozen on dry ice, and RNA was harvested using the AllPrep DNA/RNA Mini Kit (Qiagen). TruSeq RNA Sample Prep Kit (Illumina) was used with 500 ng of total RNA to construct sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Poly(A) selected sequencing libraries (68 bp paired-end reads) were generated according to the manufacturer’s instructions. All libraries were sequenced on an Illumina HiSeq 2500 platform at a depth of 12–25 million reads each.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Read quality of RNA-seq data in fastq files was assessed using FastQC (v0.11.4) to identify sequencing cycles with low average quality, adaptor contamination, or repetitive sequences from PCR amplification.
Reads were aligned using STAR (v2.5.2b) allowing gapped alignments to account for splicing against the Ensembl Rattus norvegicus genome v87
Raw counts describing gene-level abundances were derived from DESeq2 (v1.16.1)
Genome_build: Ensembl Rattus norvegicus v87
Supplementary_files_format_and_content: comma seperated text file with raw read counts per gene identified by Ensembl gene ID
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| Submission date |
Nov 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Julia Maria Schulze-Hentrich |
| E-mail(s) |
juliamschulze@gmail.com
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| Organization name |
Saarland University
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| Department |
Genetics and Epigenetics
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| Street address |
Campus, Building A2.4
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| City |
Saarbrücken |
| ZIP/Postal code |
66123 |
| Country |
Germany |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE107259 |
Environment-dependent striatal gene expression in the BACHD rat model for Huntington disease |
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| Relations |
| BioSample |
SAMN08057328 |
| SRA |
SRX3415597 |
| 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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