|
| Status |
Public on Nov 10, 2020 |
| Title |
RNA_WT_R6 |
| Sample type |
SRA |
| |
|
| Source name |
Mice hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
strain: CBA x C57BL/6 (50% CBA & 50% C57BL6)
genotype/variation: WT
tissue: hippocampal tissue
age: 30-week-old mice
chip antibody: NA
|
| Treatment protocol |
Frozen hippocampal tissue from WT and R6/1 mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq: RNA was isolated from 9 independent biological replicates for each genotype using the Qiagen RNeasy Plus Kit according to the manufacturer’s instructions. Quality assessment was performed using Bioanalyser eukaryiotic total RNA nano series II chip and all samples achieved a RNA integration number (RIN) between 9-10. Libraries were prepared from 9 biological replicates of each condition using the Truseq Stranded mRNA Library Prep Kit following manufacturer’s instructions and sequenced using the HiSeq-2500 sequencing platform.
Libraries were prepared according to Illumina instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
RNA-seq experiment
|
| Data processing |
Sequence reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. Analysis of differential expression performed by DESeq2 (PubMed ID 25516281)
Genome_build: mm9
Supplementary_files_format_and_content: Files .txt (RNAseq expression values)
|
| |
|
| Submission date |
Nov 04, 2019 |
| Last update date |
Nov 10, 2020 |
| Contact name |
Enrique Blanco |
| E-mail(s) |
enrique.blanco@crg.eu
|
| Phone |
+34 93 316 01 00
|
| Organization name |
Center for Genomic Regulation (CRG)
|
| Department |
Gene Regulation, Stem Cells and Cancer
|
| Lab |
Epigenetic Events in Cancer (L. Di Croce's lab)
|
| Street address |
Dr. Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE139884 |
Huntington’s disease as a lamin B1 nuclear envelopathy |
|
| Relations |
| BioSample |
SAMN13191134 |
| SRA |
SRX7098824 |
