|
| Status |
Public on May 03, 2019 |
| Title |
20 |
| Sample type |
SRA |
| |
|
| Source name |
frontal cortex of the human brain
|
| Organism |
Homo sapiens |
| Characteristics |
project.sampleid: 20
tissuebank.id: 4680
age: 46
Sex: Male
race: White
dist.dx: Schizophrenia
tissuebank: Sepulveda
pmi: 11.6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
none provided by the submitter
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Ribo-depleted RNA
|
| Data processing |
Base calling was done by Illumina NextSeq Control Software (NCS) v2.0 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
Trimgalore (v0.11.5) was used for adapter removal prior to genome alignment. STAR33 (v2.3.5a) index was generated using Ensemble GRCh38 p10 primary assembly genome and the Gencode v26 primary assembly annotation. Read alignment was performed using a STAR two-pass mode.
Gene counts matrix was imported into R (3.4.1) and low expressed genes (counts per million (CPM) < 1 in all samples) were removed prior to differential expression in EdgeR. Gene counts were normalized using the trimmed mean of M-values, fitted in a generalized linear model and differentially tested using a likelihood ratio test. The generalized linear model contained covariates age, sex, post mortem interval and neuronal cell composition.
Genome_build: hg38
Supplementary_files_format_and_content: SCZ_RNAseq_STAR_counts.csv - raw gene-level transcript counts per sample. CSV format
|
| |
|
| Submission date |
Mar 30, 2018 |
| Last update date |
May 03, 2019 |
| Contact name |
Shraddha Pai |
| E-mail(s) |
shraddha.pai@utoronto.ca
|
| Organization name |
University of Toronto
|
| Street address |
160 College Street, Room 602
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5S 3E1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE112523 |
DNA methylation in neurons from post-mortem brains in schizophrenia and bipolar disorder (RNA-Seq) |
| GSE112525 |
DNA methylation in neurons from post-mortem brains in schizophrenia and bipolar disorder |
|
| Relations |
| BioSample |
SAMN08822051 |
| SRA |
SRX3866123 |
