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Sample GSM5862796 Query DataSets for GSM5862796
Status Public on Sep 12, 2023
Title RNA-Seq_Saline_rep1
Sample type SRA
 
Source name Cortical neuron
Organism Macaca mulatta
Characteristics cell type: Adult cortical neuron purified from the cortex regio
treatment: treated with saline as a control
Treatment protocol Four male rhesus monkeys (Macaca mulatta; 3-4-year old; weighing from 3.0 to 5.0 kg), were randomly divided into saline group (n=2) and morphine group (n=2). Morphine was subcutaneously (s.c.) injected into the back legs of monkey three times daily (at 9:00, 14:00, and 21:00 o’clock) for 90 days continuously to produce dependence. The doses of morphine were gradually elevated as following paradigm: day 1-7:3 mg/kg, day 8-14:6 mg/kg, day 15-21:9 mg/kg, day 22-28:12 mg/kg, day 29-90:15 mg/kg. Monkeys in saline group was injected subcutaneously three times daily with same volume of 0.9% saline (0.5 mL/kg) as a control.
Extracted molecule polyA RNA
Extraction protocol Total RNA of each sample was extracted using AxyPrep Multisource RNA Miniprep Kit(Axygen). Polyadenylated mRNA was purified using NEBNext Poly(A) mRNA Magnetic Isolation Module
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description RNA-Seq_M004_rep1
Data processing Clean reads were aligned to a Bowtie2 2.1.0 indexed human genome (hg19 sourced from UCSC).
The mapped reads of each sample were assembled using StringTie with default settings.
StringTie and DESeq2 1.18.1 were used to estimate the expression levels of all transcripts.
StringTie was used to perform expression level for mRNAs by calculating FPKM.Differential gene expression was called using DESeq2 1.18.1
Genome_build: hg19
Supplementary_files_format_and_content: bigWig,tsv
 
Submission date Feb 06, 2022
Last update date Sep 12, 2023
Contact name Liang Wang
E-mail(s) whmichelle@yeah.net
Organization name University of Helsinki
Street address Viikinkaari 5
City Helsinki
ZIP/Postal code 00014
Country Finland
 
Platform ID GPL27943
Series (2)
GSE196210 Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neuron [RNA-seq]
GSE196212 Morphine Re-arranges Chromatin Spatial Architecture of Primate Cortical Neuron
Relations
BioSample SAMN25690264
SRA SRX14059573

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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