|
| Status |
Public on Feb 14, 2014 |
| Title |
Acute Coc Rep3 |
| Sample type |
SRA |
| |
|
| Source name |
NAc dissection from 3-5 animals
|
| Organism |
Mus musculus |
| Characteristics |
passages: 8-10 weeks
strain: C57BL/6
treatment: Repeated saline I.P. injection for 6 days followed by cocaine I.P. injection for 1 day at 20mg/kg
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
following trizol RNA isolation protocol
Illumina RNA seq library prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using CASAVA
Adapter (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) sequences were removed from 3' end by fastx.
RNA-seq reads were aligned to the mm9 genome assembly using Tophat with options --frag-bias-correct and --multi-read-correct. Novel transcript assembly was not attempted.
Differential analysis was performed by Cuffdiff. An FDR<10% was used as cutoff.
Genome_build: Ensembl NCBIM37.62
Supplementary_files_format_and_content: acute_gene.diff file produced by Cuffdiff is a tab-delimited text file that contains the differential analysis information for each item tested.
|
| |
|
| Submission date |
Dec 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Li Shen |
| E-mail(s) |
li.shen@mssm.edu
|
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Neuroscience
|
| Lab |
Shen
|
| Street address |
1425 Madison Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE42805 |
Chronic cocaine-regulated epigenome in mouse [RNA-Seq] |
| GSE42811 |
Chronic cocaine-regulated epigenome in mouse |
|
| Relations |
| BioSample |
SAMN02429240 |
| SRA |
SRX386040 |
