|
| Status |
Public on Oct 09, 2019 |
| Title |
Coc_Rep2 [Coc2] |
| Sample type |
SRA |
| |
|
| Source name |
neuro cells Cocaine
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: primary cortical culture
treatment: treated with 25um Cocaine
strain: sprague dawley
|
| Treatment protocol |
Rat primary cortical cultures were treated with 60ng/ml TAT for 48 hours and then treated with 25um Cocaine for another 24 hours. RK33 was added at the same time with TAT.
|
| Growth protocol |
Rat primary cortical cultures were maintain in Neurobasal mediim supplemented with B-27 and 1% penicillin-strptomycin and 2mM L-glutamine.The cells were plated in 6-well plate.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Quick-RNA MicroPrep Kit(ZYMO) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit(NEB#E7490/NEB#E7760)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
20190214_RatNeuro_cpm_AVG(glmFit)
Coc2
|
| Data processing |
Indexed sequences were checked by FastQC | version: 0.11.5
Trimed adapter by TrimGalore-0.4.5
Reads were mapped to the Rattus_6.0_r93 reference genome using STAR | version 2.5 with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes Rattus_norvegicus.Rnor_6.0.93.gtf were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -T 10
Genome_build: Rattus_6.0_r93
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample
|
| |
|
| Submission date |
Sep 25, 2019 |
| Last update date |
Oct 09, 2019 |
| Contact name |
HAO JI |
| E-mail(s) |
ji5@email.sc.edu
|
| Phone |
8037774689
|
| Organization name |
University of South Carolina
|
| Department |
College of Pharmacy
|
| Street address |
715 SUMTER ST CLS RM 109
|
| City |
COLUMBIA |
| State/province |
SC |
| ZIP/Postal code |
29208 |
| Country |
USA |
| |
|
| Platform ID |
GPL22396 |
| Series (1) |
| GSE137988 |
Inhibition of the Dead Box RNA Helicase 3 prevents HIV-1 Tat and cocaine-induced neurotoxicity by targeting microglia activation |
|
| Relations |
| BioSample |
SAMN12840116 |
| SRA |
SRX6902894 |
