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| Status |
Public on Aug 31, 2022 |
| Title |
CC_10_C |
| Sample type |
SRA |
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| Source name |
Primary rat co-cultures containing cortical neurons, astrocytes, and oligodendrocyte-lineage cell
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| Organism |
Rattus |
| Characteristics |
strain: Sprague Dawley
agent: 10 microM fentanyl
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| Treatment protocol |
Complex primary rat cultures containing cortical neurons (Lonza, Walkersville, MD), astrocytes (Lonza), and oligodendrocyte precursor cells (ScienCell, Carlsbad, CA) were treated without or with a high or low dose of fentanyl (Henry Schein, Melville, NY) for 4 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Primary cultures treated and untreated with fentanyl for 4 days were lysed with RLT buffer containing beta-mercaptoethanol, and the supernatant collected. Total RNA was extracted and purified from the collected supernatant using the RNAeasy mini spin columns (Qiagen).
Poly(A)+-enriched cDNA libraries were generated using the Illumina TruSeq RNA Library Prep kit v2 (Illumina Inc., Hayward, CA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Sequence reads were aligned against rat reference genome (rn6) using STAR. After read alignment, the number of read counts per gene locus was summarized with ‘featureCounts’ from Rsubread package. Read counts were subsequently normalized using TMM normalization from edgeR. RUVseq was then used to identify factors of unwanted variation. Differential expression analysis was performed using edgeR.
Assembly: rn6
Supplementary files format and content: CSV file with CPM values for each Sample .
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| Submission date |
Jul 06, 2022 |
| Last update date |
Aug 31, 2022 |
| Contact name |
Stephen Patrick Wilson |
| E-mail(s) |
wilson265@llnl.gov
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| Organization name |
LLNL
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| Department |
BBTD
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| Street address |
7000 East Ave
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| City |
Livermore |
| State/province |
CA |
| ZIP/Postal code |
94550 |
| Country |
USA |
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| Platform ID |
GPL32431 |
| Series (1) |
| GSE207606 |
Dose-dependent consequences of sub-chronic fentanyl exposure on neuron and glial co-cultures |
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| Relations |
| BioSample |
SAMN29543372 |
| SRA |
SRX16046783 |
| 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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