|
| Status |
Public on Jul 08, 2016 |
| Title |
Poly(A)-selected 0 |
| Sample type |
SRA |
| |
|
| Source name |
Poly(A)-selected 0
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Akata cells
|
| Treatment protocol |
One day prior to induction, near-saturation cell cultures were diluted with equal volumes of fresh RPMI 1640 (with 10% FBS and 0.5% pen/strep). The next day, cells were spun down and resuspended at a concentration of 1×106 cells/ml in fresh RPMI 1640 (with 10% FBS and 0.5% pen/strep) plus either 10 μg/ml anti-IgG or no anti-IgG (uninduced). For GapmeR treatment, 3 × 106 cells in RPMI (with 10% FBS) were nucleofected (Lonza) with 600 pmol of either negative control GapmeR A or targeted GapmeR. On the following day an equal volume of RPMI (with 10% FBS) was added with either 20 μg/ml anti-IgG or no anti-IgG (uninduced).
|
| Growth protocol |
Cells were grown at 37°C and 5% CO2 in a humidified incubator and were cultured in RPMI 1640 plus 10% fetal bovine serum and 0.5% Penicillin-Streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
TRIzol reagent (Ambion) followed byb DNase (Ambion) treatment
Illumina TruSeq Stranded protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina 1.9 basecalling
Alignment to the Akata EBV genome (NCBI accession number KC207813.1) using STAR version 2.3.0.1 with default parameters
Generation of signalmap files using IGVTools
Genome_build: KC207813.1
Supplementary_files_format_and_content: Signalmap coverage files for the Akata genome
|
| |
|
| Submission date |
Mar 16, 2016 |
| Last update date |
Jan 31, 2022 |
| Contact name |
Erik K Flemington |
| E-mail(s) |
eflemin@tulane.edu
|
| Phone |
504 988-1167
|
| Organization name |
Tulane Health Sciences Center
|
| Department |
Pathology
|
| Street address |
1430 Tulane Ave., SL79
|
| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70112 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE79304 |
Global transcript structure resolution of high gene density genomes through multi-platform data integration: Illumina RNA-Seq |
| GSE79337 |
Global transcript structure resolution of high gene density genomes through multi-platform data integration |
|
| Relations |
| BioSample |
SAMN04563764 |
| SRA |
SRX1639560 |
