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Sample GSM6303868

Query DataSets for GSM6303868

Status

Public on Aug 31, 2022

Title

CC_0_P

Sample type

SRA

Source name

Primary rat co-cultures containing cortical neurons, astrocytes, and oligodendrocyte-lineage cell

Organism

Rattus

Characteristics

strain: Sprague Dawley
agent: Untreated

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.

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).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

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 .

Submission date

Jul 06, 2022

Last update date

Aug 31, 2022

Contact name

Stephen Patrick Wilson

E-mail(s)

wilson265@llnl.gov

Organization name

LLNL

Department

BBTD