|
| Status |
Public on May 12, 2016 |
| Title |
VHIP_Susceptible_28d_3 |
| Sample type |
SRA |
| |
|
| Source name |
adult ventral hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
brain region: adult ventral hippocampus
timepoint: 28d post CSDS
phenotype: susceptible
strain: C57BL/6J
|
| Treatment protocol |
Please see "Experimental Procedures" from Bagot et al. "Circuit-wide transcriptional profiling reveals region specific gene co-expression networks regulating depression susceptibility " for detailed descriptions of sequencing experiments
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TriZol reagent (Invitrogen) and purified with RNAeasy micro kits from Qiagen. All RNA samples were determined to have 260/280 and 260/230 values ≥1.8.
RNA integrity was assessed using either an Agilent 2100 Bioanalyzer with the RNA 6000 Nano assay or an Agilent 2200 TapeStation with the R6K ScreenTape (Agilent, Santa Clara, CA). Average RIN values were above 9. Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 protocol (Illumina, San Diego, CA). Briefly, the cDNA was synthesized from poly-A-selected and then fragmented total RNA using random hexamers, followed by end-repair and ligation with sequencing adaptors. The libraries were then size selected and purified using AMPure XP beads (Beckman Coulter, Brea, CA). Barcode bases (6 bp) were introduced at one end of the adaptors during PCR amplification steps. Library size and concentration were measured by Bioanalyzer or Tape Station (Life Technologies, Grand Island, NY) before sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file = VHIP_control_vs_susceptible_28day.diff_list.xlsx
|
| Data processing |
Bowtie2, version 2.1.0, parameters: default
TopHat2, version 2.0.9, parameters: --no-novel-juncs --b2-very-sensitive
Cuffdiff, version 2.1.1, parameters: -b path_to/mm9.fa --multi-read-correct
Genome_build: NCBIM37
Supplementary_files_format_and_content: text and excel format with cuffdiff output. Supplementary files are available in a tar archive on the series record.
|
| |
|
| Submission date |
Aug 25, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Immanuel Purushothaman |
| E-mail(s) |
immanuel.purushothaman@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Neuroscience
|
| Street address |
1425 Madison Avenue
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE72343 |
Circuit-wide transcriptional profiling reveals region specific gene co-expression networks regulating depression susceptibility |
|
| Relations |
| BioSample |
SAMN04010340 |
| SRA |
SRX1163752 |
