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| Status |
Public on Dec 30, 2016 |
| Title |
Control rep10 |
| Sample type |
SRA |
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| Source name |
DLPFC
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Post-mortem brain (DLPFC) tissue
condition: Control
batch: 2
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue from dorsal lateral prefrontal cortex (DLPFC) was pulverized over dry ice. Approximately 300 mg was weighed while frozen and stored at 80°C until extraction. Total RNA was extracted with TRIzol Reagent (Invitrogen Life Science, Cat. No. 15596-018, Mount Waverley, Victoria), using a polytron. Total RNA pellets were re-suspended in DEPC treated water. The yield of total RNA was then analysed using a spectrophotometer (Nanodrop ND-1000, Thermo Scientific). Total RNA was not further purified through a column. The quality of extracted total RNA was determined by high resolution capillary electrophoresis using the Agilent Bioanalyzer 2100.
Twelve micrograms of RNA from each of the samples was used in creation of the library for sequencing. RNA was DNase treated using TURBO DNA-free (Ambion, Austin TX, USA) before the depletion of ribosomal RNA using the Ribominus kit (Invitrogen, Carlsbad, CA, USA). The resulting RNA was fragmented and the SOLiD library prepared using the Total RNA-Seq kit (Invitrogen). Quality control of the library was assessed by size (480% and within 200--300 bp) using a bioanalyser.
Samples were run with four individuals per slide on the SOLiDv4 (Life Technologies, Carlsbad, CA, USA). Reads were unpaired and 50nt in length. Average reads per individual were 135 355 990 (±32 081 820) and did not differ between diagnostic groups.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD 4 System |
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| Description |
processed data column: T30
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| Data processing |
RNA libraries sequenced on theSOLiDv4 platform (Life Technologies, Carlsbad, CA, USA)
Sequenced reads werer mapped to the human genome (hg19) using TopHat2 (v 2.0.4) calling the Bowtie aligner (v 0.12.8) using the default parameters.
HTSeq-count (Python package HTSeq, python v 2.7.3) was used to generate counts of reads uniquely mapped to annotated genes using the Ensembl annotation file GRCh37.66_chr.gtf
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with read count for each sample.
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| Submission date |
Sep 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Susan Corley |
| E-mail(s) |
s.corley@unsw.edu.au
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| Phone |
+61 02 9385 8853
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| Organization name |
UNSW
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| Department |
Biotechnology & Biomolecular Sciences
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| Lab |
Systems Biology Initiative
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| Street address |
D26, Kensignton Campus
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| City |
Sydney |
| State/province |
NSW |
| ZIP/Postal code |
2052 |
| Country |
Australia |
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| Platform ID |
GPL13393 |
| Series (1) |
| GSE87194 |
Schizophrenia: postmortem dorsal lateral prefrontal cortex (DLPFC) |
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| Relations |
| BioSample |
SAMN05804556 |
| SRA |
SRX2184637 |
| 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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