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| Status |
Public on Jul 27, 2019 |
| Title |
PFC-COC3-RNAseq |
| Sample type |
SRA |
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| Source name |
Cocaine-treated
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| Organism |
Rattus norvegicus |
| Characteristics |
tissue: PFC
strain: Sprague-Dawley
Sex: male
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using Trizol reagent. KAPA Stranded RNA-Seq Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
ATAC-seq: Nuclei from flash frozen PFC tissue were extracted and 100,000 nuclei were tagmented. DNA were prepared using Nextera library prep kit.
RNA and DNA 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 HiSeq 2000 |
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| Description |
Cocaine-treated
PFC_FPKM.xls
sample name in processed data file:
Coc_3
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| Data processing |
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, and only reads mapping as matched pairs and being uniquely mapped (mapping quality >= 1) were used for further analysis. The 42 base pair (bp) length of the reads were used for peak-calling and the generic term “interval” was used to describe genomic regions with local enrichments in tag numbers. Intervals were defined by the chromosome number, and a start and end coordinate.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff p-value of 1e-7 and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.
HISAT2 was used to map filtered sequenced reads to the reference rat genome, HTSeq was used to analyze gene expression levels (in union mode)
DESeq was used for differential gene expression analysis
rMATS (replicate multivariate analysis of transcript splicing) was used for detection of differential alternative splicing (AS)
Genome_build: RN6(Nacc-RNAseq and ATACseq), RN5(PFC-RNAseq)
Supplementary_files_format_and_content: xlsx files including FPKM value for each sample
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| Submission date |
Jul 26, 2019 |
| Last update date |
Jul 27, 2019 |
| Contact name |
Philippe Melas |
| Organization name |
Columbia University
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| Lab |
Kandel's lab
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| Street address |
1051 Riverside Drive
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| City |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL14844 |
| Series (1) |
| GSE134935 |
Cannabinoid exposure in rat adolescence reprograms the initial behavioral, molecular, and epigenetic response to cocaine |
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| Relations |
| BioSample |
SAMN12370772 |
| SRA |
SRX6597837 |
| 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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