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Sample GSM4950066 Query DataSets for GSM4950066
Status Public on Sep 22, 2022
Title mPFC-SI-rep3
Sample type SRA
 
Source name medial prefrontal cortex
Organism Mus musculus
Characteristics tissue: medial prefrontal cortex
strain: C57BL/6
treatment: Post-weaning social isolation for 3 weeks
age: 6 weeks
Extracted molecule total RNA
Extraction protocol Total RNA from the mPFC was extracted with RNAiso Plus (Takara, #9109) according to the manufacturer’s instructions. The RNA quality and quantity were measured using NanoDrop 2000 (Thermo Scientific)
RNA library was constructed using the BGISEQ-500 platform according to the manufacturer's instruction; after that, adapters were ligated to each end of the RNAs and subsequently reverse transcribed to create single-stranded cDNA and sequenced on the BGISEQ-500 platform with a read length of 50 bps
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model BGISEQ-500
 
Data processing The sequencing reads which containing low-quality, adaptor-polluted and high content of unknown base (N) reads, should be processed to be removed before downstream analyses.
After reads filtering, we map clean reads to reference genome using HISAT
We map clean reads to reference transcripts using Bowtie2, then calculate gene expression level for each sample with RSEM .
Genome_build: mm10
 
Submission date Nov 30, 2020
Last update date Sep 22, 2022
Contact name ** **
Organization name ***
Street address ***
City ***
ZIP/Postal code ***
Country China
 
Platform ID GPL23479
Series (1)
GSE162343 RNA-sequencing in medial prefrontal cortex of early socially isolated mice
Relations
BioSample SAMN16956280
SRA SRX9605800

Supplementary file Size Download File type/resource
GSM4950066_SIMA3.gene.fpkm.txt.gz 1.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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