|
| Status |
Public on Nov 04, 2019 |
| Title |
NB-CTRL, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
male Sprague Dawley Non-behavioral
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: amygdala
age: postnatal day 38
Sex: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from amygdala using a Qiagen miRNA easy micro kit (Germantown, MD) which is specialized for isolation of RNA from lipid rich tissue (n=3). Each RNA sample containing 1 µg of RNA was used for poly A selected RNA-seq library preparation using the NEB Ultra-Directional RNA Library Prep Kit for Illumina, Cat# E7420.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Non-behavioral
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to Ensembl transcript (release 84) then rn6 whole genome using STAR aligner 2.5.4b with parameters --chimSegmentMin 2 --outFilterMismatchNmax 3 --alignEndsType EndToEnd --out SAMstrandField intronMotif
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cuffdiff v2.2.1 with uniquely and properly mapped pairs.
Genome_build: rn6
Supplementary_files_format_and_content: an excel file includes FPKM values for each Sample.
|
| |
|
| Submission date |
Feb 01, 2019 |
| Last update date |
Nov 04, 2019 |
| Contact name |
Juw Won Park |
| E-mail(s) |
juw.park@louisville.edu
|
| Organization name |
University of Louisville
|
| Department |
CECS
|
| Lab |
Bioinformatics
|
| Street address |
213 Duthie Center
|
| City |
Louisv |
| State/province |
KY |
| ZIP/Postal code |
40292 |
| Country |
USA |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE126023 |
Proteomic and transcriptional profiling of rat amygdala following social play |
|
| Relations |
| BioSample |
SAMN10862958 |
| SRA |
SRX5325802 |
