|
| Status |
Public on Jul 26, 2021 |
| Title |
OVCAR3_siNMNAT-2_GFP Polysome-rep2.fastq.gz |
| Sample type |
SRA |
| |
|
| Source name |
OVCAR3 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: OVCAR3
genotype/variation: OVCAR3 transfected with siNMNAT-2 and GFP
rna isolated from: polysome fractions
molecule subtype: cDNA from reverse transcribed RNA
|
| Treatment protocol |
OVCAR3 cells were transfected with lentiviral particles encoding for GFP or NMNAT-2 and positive clones were selected using 500 µg/mL G418 The cells were maintained in 250 µg/mL G418 after selection. FT194 cells were transfected with lentiviral particles encoding for vector or NMNAT-2 and positive clones were selected and maintained in 250 µg/mL G418.
|
| Growth protocol |
OVCAR3 cells were cultured in RPMI media containing 10% FBS, 1% Pencillin-streptavidin, 1% Glutamax and 250 µg/mL G418 . FT194 cells were cutured in DMEM-F12 media containing 10% FBS and 150 µg/mL G418
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Input RNA and polysome associated RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer’s instructions from 2 individual 15 cm plates per replicate per treatment.
The total RNA was then enriched for polyA+ RNA using Dynabeads Oligo(dT)25 (Invitrogen). The polyA+ RNA was then used to generate RNA-seq libraries. The RNA-seq libraries were subjected to QC analyses (i.e., number of PCR cycles required to amplify each library, the final library yield, and the size distribution of final library DNA fragments) and sequenced using an Illumina Nextseq 500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Replicates merged
|
| Data processing |
The RNA-seq reads were aligned to the hg38 human reference genome using the Bowtie software package (Langmead et al, 2009) .
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and bigwig files were generated to for presentation as browser tracks using custom R scripts.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig
|
| |
|
| Submission date |
May 14, 2021 |
| Last update date |
Jul 26, 2021 |
| Contact name |
W. Lee Kraus |
| E-mail(s) |
lee.kraus@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-8511 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE146458 |
Cytoplasmic NAD+ Synthesis and Ribosomal Protein Mono(ADP-Ribosyl)ation Maintain Proteostasis in Ovarian Cancer |
|
| Relations |
| BioSample |
SAMN19193717 |
| SRA |
SRX10889500 |
