|
Status |
Public on Jul 01, 2013 |
Title |
Normal Brain 2 |
Sample type |
SRA |
|
|
Source name |
Dorsolateral prefrontal cortex
|
Organism |
Homo sapiens |
Characteristics |
tissue: brain Sex: female pathology: normal
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was harvested from frozen brain tissue using Trizol reagent. Illumina small RNA Sample Prep kit (#FC-102-1009) was used to construct libraries from 30ug total RNA. Instead of initial size fractionation, rRNAs were depleted by one round of Ribominus (Invitrogen).
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
rRNA-depleted RNA
|
Data processing |
Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adapter sequence using cutadapt v0.9 with options "-e 0.06 -O 6 -m 14 -n 2" Reads were mapped to the genome (hg19) using bowtie with options "--best --strata -v 2 -k 100" and non-unique mappers were removed. Reads with a mismatch rate > 6% were discarded. Reads mapping to known ribosomal RNA sequences via Bowtie were discarded. Genome_build: hg19 Supplementary_files_format_and_content: tab-delimited text files containing read counts for each trimmed, rRNA-masked sequence
|
|
|
Submission date |
Apr 30, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Paul Ryvkin |
Organization name |
University of Pennsylvania
|
Department |
Pathology
|
Lab |
Li-San Wang's Lab
|
Street address |
423 Guardian Dr, 1404 Blockley Hall
|
City |
Philadelphia |
State/province |
PA |
ZIP/Postal code |
19104 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE46523 |
Whole transcriptome RNA-seq of undiseased human prefrontal cortex |
|
Relations |
BioSample |
SAMN02087661 |
SRA |
SRX272964 |