|
| Status |
Public on Mar 24, 2013 |
| Title |
Wild Type Homecage - Replicate 2402 |
| Sample type |
SRA |
| |
|
| Source name |
WildType_Homecage_dosal hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6J
genotype/variation: wild type
sample group: homecage; sacrificed directly from the animal's cage
tissue: dorsal hippocampus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from bilateral, dorsal hippocampus using the using RNeasy minikit (Qiagen, 74104).
cDNA libraries for each group were prepared as described in the TruSeq RNA Sample Preparation v2 Guide (Illumina).
Samples were multiplexed so that each behavioral group was represented in each flow cell of the sequencer. 10nM of each library was pooled together in four multiplex libraries and sequenced on an IlluminaHiSeq 2000 instrument during a single-end 50 cycles sequencing run by the Genomics High-Throughput Facility (GHTF) at the University of California, Irvine.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
WTHC_2402
Tissue harvested directly from home cage
|
| Data processing |
Basecalling performed using RTA version 1.13.48
Demultiplexing performed using CASAVA version 1.8.2
Alignments to reference assembly mm9 performed using ELAND v2e and bowtie version 0.12.8
Filtering and selection performed using in-house tools
Expression analysis performed using CASAVA version 1.8.2
Differential analysis performed using CyberT: http://cybert.ics.uci.edu
Genome_build: mm9
Supplementary_files_format_and_content: RPKM values for each replicate have been combined in a single text file (RPKM_Values.txt), the differential analysis results from CyberT have been summarized and annotated in a single excel file (Differential_Analysis.xls)
|
| |
|
| Submission date |
Feb 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Annie Vogel Ciernia |
| E-mail(s) |
annie.ciernia@ubc.ca
|
| Phone |
6048270752
|
| Organization name |
University of British Columbia
|
| Street address |
2215 Wesbrook Mall room 4550, Centre for Brain Health
|
| City |
Vancouver |
| State/province |
British Columbia |
| ZIP/Postal code |
V6T 2A1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE44229 |
The Neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory. |
|
| Relations |
| SRA |
SRX234850 |
| BioSample |
SAMN01919537 |
