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Sample GSM6341138 Query DataSets for GSM6341138
Status Public on Jul 19, 2022
Title Ventral polyA-enriched 6
Sample type SRA
 
Source name Ventral Hippocampus
Organism Rattus norvegicus
Characteristics rna fraction: polyA-enriched
tissue: Ventral Hippocampus
strain: Wistar
animal id: 6
Sex: male
Treatment protocol Control handled rats not subjected to any treatments
Extracted molecule polyA 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 311vHC
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 SAMN29782346
SRA SRX16306598

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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