|
| Status |
Public on Apr 01, 2021 |
| Title |
WT Cortex 10 months male mRNA rep1 [10_19_24_mo] |
| Sample type |
SRA |
| |
|
| Source name |
Cortex
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: Cerebral Cortex
genotype: Wild type
age: 10 months
Sex: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen mRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
mRNA
Q1300131_01_Cortex
processed data file: HDGSE260_Genes.Count.txt
processed data file: HDGSE260_Genes.FPKM.txt
|
| Data processing |
Libraries for RNA-seq were sequenced using an Illumina NovaSeq6000.
Sequenced reads were trimmed for adaptor sequence using Omitsoft aligner and then mapped to rat genome Rat.B6.0.
a) Trimmed low-quality bases from the reads, aligned reads to the rat reference genome (Ensembl R89) with OmicSoft Aligner and quantitated the reads per gene with OmicSoft Quantitate. b) Fragments Per Kilobase of exon model per million reads mapped were calculated with OmicSoft. c) Generated the QC plots (PCA, Volcano, Bar charts of QC metrics).
Genome_build: Rat.B6.0
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM and Count values for each Sample.
|
| |
|
| Submission date |
Mar 22, 2021 |
| Last update date |
Apr 01, 2021 |
| Contact name |
Jeff Aaronson |
| E-mail(s) |
jeff.aaronson@chdifoundation.org
|
| Phone |
(609) 945-9616
|
| Organization name |
CHDI
|
| Department |
Discovery & Systems Biology
|
| Street address |
155 Village Boulevard, Suite 200
|
| City |
Princeton |
| State/province |
New Jersey |
| ZIP/Postal code |
08540 |
| Country |
USA |
| |
|
| Platform ID |
GPL25947 |
| Series (2) |
| GSE169386 |
Transcriptional profiling of brain tissues from a Q130 Long Evans Knock-in rat model of Huntington’s disease at 10-, 19- and 24-months of age |
| GSE169388 |
Transcriptional profiling of brain tissues from a Q130 Long Evans Knock-in rat model of Huntington’s disease at 2-, 6-, 10-, 12-, 19- and 24-months of age |
|
| Relations |
| BioSample |
SAMN18434818 |
| SRA |
SRX10414595 |
