|
| Status |
Public on Dec 17, 2018 |
| Title |
5456_NAcc_pos (RNA-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
NeuN positive nuclei sorted from nucleus accumbens (NAcc)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: NeuN pos
tissue: nucleus accumbens (NAcc)
individual id: 5456
|
| Treatment protocol |
RNA was extracted from neuronal and non-neuronal nuclei isolated from nucleus accumbens or prefrontal cortex (BA9) tissues (for samples with "_pos" or "_neg" at end of sample ID) and sorted via FACS based on NeuN staining as in Montano et al. 2013.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy Mini kit (cat#: 74104 )
SMARTer Stranded Total RNA-Seq Kit – Pico Input Mammalian
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
We trimmed the first 3 bp of read1, which were derived from template switching oligos and not the cDNA of interest, using seqtk (https://github.com/lh3/seqtk; v1.2-r94) with the following parameters: seqtk trimfq -b 3 ${READ1}. We then quasi-mapped these trimmed reads to a FASTA file of protein-coding and lncRNA genes from GENCODE v19 (http://www.gencodegenes.org/releases/19.html) and performed transcript-level quantification using Salmon (v0.7.2).
We used tximport (v1.2.0) to compute normalized gene-level counts from the transcript-level abundance estimates (scaling these using the average transcript length over samples and the library size). Only autosomal genes with at least 1 cpm in at least 4 libraries (the size of the smallest group of samples) were retained for downstream analysis.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: Matrix of gene-level read counts for each gene from all samples.
|
| |
|
| Submission date |
Mar 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew P. Feinberg |
| Organization name |
Johns Hopkins University School of Medicine
|
| Street address |
855 N. Wolfe St
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE96613 |
Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability [RNA-Seq] |
| GSE96615 |
Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability |
|
| Relations |
| BioSample |
SAMN06603216 |
| SRA |
SRX2640560 |
