|
| Status |
Public on Sep 01, 2016 |
| Title |
Control_BA9_10 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Homo sapiens |
| Characteristics |
disease stage: Control
brain region: Brodmann's Area 9
tissue: brain
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
the tissue samples were homogenized in TRIzol solvent (Invitrogen, Carlsbad, CA, USA), and the total RNA was isolated with RNeasy Lipid Tissue Mini Kit (Qiagen # 74804) and QIAzol Lysis Reagent (Qiagen # 79306). Beads with oligo(dT) were used to isolate poly(A) mRNA after total RNA was collected from all samples.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq reads were mapped to the human reference genome (version hg19) using Tophat (version 2.0.13) with default parameters. Only uniquely mapped reads with no more than two mismatches were retained.
Read counts for each lincRNA and protein-coding gene (PCG) were computed using HTSeq.
Fragments per kilobase of transcript per million fragments mapped (FPKM) value was calculated for each lincRNA and PCG. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw count and FPKM values for each Sample ...
|
| |
|
| Submission date |
Mar 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jing Hu |
| E-mail(s) |
[email protected]
|
| Organization name |
Harbin medical university
|
| Department |
College of Bioinformatics Science and Technology
|
| Street address |
157 Baojian Road
|
| City |
Harbin |
| State/province |
Heilongjiang |
| ZIP/Postal code |
150086 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE78936 |
Systematically characterizing dysfunctional long intergenic non-coding RNAs in multiple brain regions of major psychosis |
|
| Relations |
| BioSample |
SAMN04535239 |
| SRA |
SRX1615714 |
