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| Status |
Public on Aug 10, 2016 |
| Title |
control-39 |
| Sample type |
SRA |
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| Source name |
dorsal striatum, control
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| Organism |
Homo sapiens |
| Characteristics |
age (years): 66
Sex: female
postmortem interval (hours): 25
rin: 2.5
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| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen postmortem dorsal striatum samples were transferred to RNAlater-ICE (Ambion) and stored at -20C upon receipt. Total RNA was extracted from dissected caudate-putamen tissue by Trizol (Life Technologies), column-purified by the RNeasy Lipid Tissue Kit (Qiagen) and treated with the Turbo DNA-free Kit (Life Technologies). RNA samples were assayed on the BioAnalyzer (Agilent, Santa Clara, CA) to obtain RNA integrity number (RIN) values.
Ribosomal RNA (rRNA) was depleted from samples using the RiboMinus Eukaryote Kit v2 (Life Technologies). Strand-specific cDNA libraries were made using the Next Ultra Directional RNA Library Prep Kit (NEB) and sequenced on the Illumina HiSeq2000.
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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 |
Raw reads were processed by trimming out adapter sequences and low-quality base calls (PHRED < 30).
Reads were first aligned against a custom ribosomal DNA reference using BowTie2,23 and reads mapping to rRNA genes were purged.
The splice-aware aligner TopHat24 (v2.0.12) was used to map remaining reads against the reference human genome (GRCh38 from Ensemble 76). The HTSeq-count script in HTSeq25 (v0.6.0) was run in “union” mode to count all reads that mapped uniquely to annotated exons of each gene. TopHat and HTSeq parameters included a reverse setting for library strandedness; other parameters were set as default.
Genes located on alternative/unplaced scaffolds and the Y chromosome were removed, as well as certain categories of noncoding genes.
Duplicate gene symbols: for different Ensembl IDs sharing the same gene symbol, rows were collapsed by summing read counts if entries were on the same chromosome and strand; only the most recent Ensembl ID was retained otherwise.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file contains read counts/gene
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| Submission date |
Apr 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ronald L Davis |
| E-mail(s) |
rdavis@scripps.edu
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| Organization name |
The Scripps Research Institute - Scripps Florida
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| Department |
Neuroscience
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| Street address |
130 Scripps Way
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| City |
Jupiter |
| State/province |
Florida |
| ZIP/Postal code |
33458 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE80336 |
Transcriptome profiling of the human dorsal striatum in bipolar disorder |
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| Relations |
| BioSample |
SAMN04859287 |
| SRA |
SRX1708324 |
| 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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