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Sample GSM4399913 Query DataSets for GSM4399913
Status Public on Jan 25, 2021
Title P56_4_mPFC
Sample type SRA
Source name P56_mPFC
Organism Mus musculus
Characteristics strain: C57BL/6
age: post natal day 56
tissue: medial prefrontal cortex (mPFC)
replicate: 4
Treatment protocol N/A
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol Total RNA including miRNA fractions were isolated using Qiagen miRNeasy mini kit according to the manufacturer’s protocol. RNA integrity was assessed with an Agilent 2100 Bioanalyzer using an Agilent Bioanalyzer 6000 Nano kit.
Input of 400ng of total RNA was used as starting material for each sample and libraries were prepared using 99 TruSeq Stranded Total RNA LT with Ribo-Zero Gold Depletion Kit from Illumina. Quantification was performed using KAPA Library Quantification Kit and the average size of 300 bp was determined by using a High Sensitivity DNA Kit. The libraries were pooled and diluted to 13 pM to load on an Illumina HiSeq 2500 Instrument.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
Description P56_4_mPFC
Data processing Basecalling and sample de-multiplexing was performed with CASAVA-1.8.4 and default parameters
Reads were quality check with fastqc v0.11.5 default parameters
Reads for each sample/replicate were mapped against the mouse genome assembly and counted using STAR read aligner v2.7.3a
Antisense contigs were assembled using the Trinity platform v2.8.4
Genome_build: Ensembl GRCm38 with assembled antisense contigs
Supplementary_files_format_and_content: Read counts per gene/contig
Submission date Mar 09, 2020
Last update date Jan 28, 2021
Contact name Roland Schmucki
Organization name F. Hoffmann - La Roche AG
Street address Grenzacherstrase
City Basel
ZIP/Postal code 4058
Country Switzerland
Platform ID GPL17021
Series (1)
GSE146628 Identification of Natural Antisense Transcripts in Mouse Brain and Their Association with Autism Spectrum Disorder Risk Genes
BioSample SAMN14336209
SRA SRX7875161

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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