|
| Status |
Public on Jul 01, 2013 |
| Title |
Normal Brain 3 |
| 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 |
SAMN02087662 |
| SRA |
SRX272965 |
