|
| Status |
Public on Jul 19, 2022 |
| Title |
Dorsal ribosome-depleted 3 |
| Sample type |
SRA |
| |
|
| Source name |
Dorsal Hippocampus
|
| Organism |
Rattus norvegicus |
| Characteristics |
rna fraction: ribosome-depleted
tissue: Dorsal Hippocampus
strain: Wistar
animal id: 10
Sex: male
|
| Treatment protocol |
Control handled rats not subjected to any treatments
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Poly-A enriched data: total RNA was extracted using Qiazol reagent according to manufacturer’s protocol. Ribosomal RNA depleted data: total RNA was extracted using ExtractRNA reagent (Evrogen, Russia) following manufacturer’s protocol. Depletion of ribosomal RNA was performed using MGIEasy rRNA Depletion kit.
1) mRNA isolation from total RNA with oligo(dT)-coated magnetic beads; 2) RNA fragmentation; 3) cDNA generation by reverse transcription using random primers followed by double-stranded cDNA synthesis; 4) reparation of ends, 3'-adenylation, ligation of adapters; 5) polymerase chain reaction using adapters. PCR products were purified with Ampure XP Beads and dissolved in EB solution; 6) the library has been validated with an Agilent Technologies 2100 bioanalyzer; 7) the double-stranded PCR product was denatured and cyclic molecules were synthesized from it using the splint oligo sequence. The result was a library of single-stranded cyclic molecules; 8) the library was amplified with phi29 DNA polymerase to form nanodroplets containing more than 300 copies of a single DNA molecule
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
341
|
| Data processing |
Sequenced reads were mapped to the Rnor6.0 version of rat genome using STAR (v. 2.7.9a) with default parameters.
For each dataset, raw read counts were obtained using FeatureCounts (v 2.0.1) with GTF file for Rnor 6.0, taken from ENSEMBL ftp. Used parameters: -T 8 -p -a Rattus_norvegicus.Rnor_6.0.101.gtf -s 0 (for polyA dataset, unstranded) -s 2 (for ribosome-depleted dataset, reverse-stranded).
Counts from both datasets were combined in single matrix and normalized by “median-of-ratios” method from DESeq2 (v 1.29) R-package.
Assembly: Rnor6.0
Supplementary files format and content: tab-delimited text file, that includes normalized expression values for each sample (column).
|
| |
|
| Submission date |
Jul 16, 2022 |
| Last update date |
Jul 19, 2022 |
| Contact name |
Alexander Beletsky |
| E-mail(s) |
apbeletskiy@gmail.com
|
| Organization name |
IHNA
|
| Street address |
Butlerova street, building 5a
|
| City |
Moscow |
| ZIP/Postal code |
117290 |
| Country |
Russia |
| |
|
| Platform ID |
GPL30103 |
| Series (1) |
| GSE208330 |
Detailed analysis of dorsal-ventral gradients of gene expression in the rat hippocampus |
|
| Relations |
| BioSample |
SAMN29782339 |
| SRA |
SRX16306605 |
