|
| Status |
Public on Apr 23, 2021 |
| Title |
00078A1837_LHB |
| Sample type |
SRA |
| |
|
| Source name |
Brain region: Lateral habenula
|
| Organism |
Rattus norvegicus |
| Characteristics |
population: Heterogeneous Stock
Sex: F
rat batch: Batch03
brain region: Lateral habenula
|
| Treatment protocol |
All rats were naïve to behavioral or pharmacology treatment.
|
| Growth protocol |
All rats were group housed under standard laboratory conditions.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
1) Brain region dissection: Brains were taken out of a minus 80 degree freezer and cryosectioned into 60um sections, which were mounted onto RNase-free glass slides. Slides were stored in minus 80 degree until dissection. During dissection, slides were placed on a minus 20 degree cold plate. One drop (approximately 50 ul) of RNAlater was placed on the brain region of interest. Each brain region then was dissected out under a dissecting video camera by using a pair of fine tipped forceps with the assistance of an 18 gauge needle with a bent tip. Bilateral tissue of the same brain region from each rat was immediately transferred into 350 ul Buffer RLT (containing beta-mercaptoethanol) and placed on dry ice. Tissue was stored in minus 80 degree before RNA extraction. 2) RNA extraction: Tissue was thawed on ice and homogenized by using a clean stainless steel bead using Qiagen TissueLyser (40Hz, 3 min). AllPrep DNA/RNA mini kit (Qiagen) was used to extract RNA. Samples were processed by using the QIAcube robot following standard protocols. The optional DNase digestion step was included for RNA samples.
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 |
| |
|
| Data processing |
Reads were first trimmed for adapter and poor-quality base calls using cutadapt
Reads were then aligned to the Ensembl Rat Transcriptome using RSEM
Upper quantile adjusted was applied to estimated gene read counts using DESeq2
Samples were filtered based on low reads counts, mismatched genotypes, and expression PCA outliers
Genes were eliminated if less than 25% of libraries had more than one read or if the total number of reads among all libraries for the gene was less than 100
Read counts were log base 2 transformed after the addition of 1 to each read count (to avoid taking the log of zero)
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Tab-separated table with row names (Ensembl gene IDs) and column names (sample IDs) containing log2(read count + 1) values
|
| |
|
| Submission date |
Apr 22, 2021 |
| Last update date |
Apr 23, 2021 |
| Contact name |
Daniel Munro |
| E-mail(s) |
dmunro@scripps.edu
|
| Organization name |
UC San Diego
|
| Department |
Psychiatry
|
| Lab |
Palmer Lab
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL22396 |
| Series (2) |
| GSE173138 |
Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research [Lateral habenula] |
| GSE173141 |
Mapping genotype-expression associations in Heterogeneous Stock rat brains to advance behavioral genetics research |
|
| Relations |
| BioSample |
SAMN18836194 |
| SRA |
SRX10660168 |
