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| Status |
Public on Sep 12, 2023 |
| Title |
RNA-Seq_Saline_rep1 |
| Sample type |
SRA |
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| Source name |
Cortical neuron
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| Organism |
Macaca mulatta |
| Characteristics |
cell type: Adult cortical neuron purified from the cortex regio
treatment: treated with saline as a control
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| 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.
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
RNA-Seq_M004_rep1
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| 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
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| Submission date |
Feb 06, 2022 |
| Last update date |
Sep 12, 2023 |
| Contact name |
Liang Wang |
| E-mail(s) |
whmichelle@yeah.net
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| Organization name |
University of Helsinki
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| Street address |
Viikinkaari 5
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| City |
Helsinki |
| ZIP/Postal code |
00014 |
| Country |
Finland |
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| 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 |
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| Relations |
| BioSample |
SAMN25690264 |
| SRA |
SRX14059573 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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