|
| Status |
Public on Mar 06, 2024 |
| Title |
142A |
| Sample type |
SRA |
| |
|
| Source name |
ventral white matter (BA 47)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: ventral white matter (BA 47)
diagnosis: Normal
suicide: N
age: 71
Sex: F
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from ~30-50 mg white matter tissue using RNeasy Lipid Tissue Mini Kit (Qiagen, #74804) according to the manufacturer’s instructions
Globin mRNA was removed from total RNA using GLOBINclear (Invitrogen/Ambion). Next, RNA samples were subject to Ribo-zero depletion, and libraries prepared using the Illumina Truseq library preparation kit and sequenced on the Illumina HiSeq 2500 (2 x 50), generating a mean of 48 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA-seq reads were aligned to hg19 using STAR aligner
Reads were annotated to transcripts using Gencode v18 annotation
Assembly: Gencode v18
Supplementary files format and content: CSV file includes raw counts for each samples
|
| |
|
| Submission date |
Nov 20, 2023 |
| Last update date |
Mar 06, 2024 |
| Contact name |
Fatemeh Haghighi |
| E-mail(s) |
fatemeh.haghighi@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Neuroscience
|
| Lab |
Haghighi Lab
|
| Street address |
1425 Madison Ave, 9-20D
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE248260 |
Brain and Blood Transcriptome Profiles Delineate Common Genetic Pathways across Suicidal Ideation and Suicide II |
|
| Relations |
| BioSample |
SAMN38338069 |
| SRA |
SRX22589007 |
