|
Status |
Public on Jul 08, 2016 |
Title |
Akata_induced_rep1_DNase |
Sample type |
SRA |
|
|
Source name |
Akata_induced_rep1_DNase
|
Organism |
Homo sapiens |
Characteristics |
cell type: Akata cells treatmemt: DNAse
|
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).
|
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 |
total RNA |
Extraction protocol |
TRIzol (Ambion). A portion of each replicate was treated with DNAse (Ambion) and a portion left untreated for a total of 4 samples. nAnT-iCAGE
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
CAGE |
Instrument model |
Illumina HiSeq 2500 |
|
|
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 with IGVTools, using reads with primary alignments 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 |
GPL16791 |
Series (2) |
GSE79293 |
Global transcript structure resolution of high gene density genomes through multi-platform data integration: deepCAGE |
GSE79337 |
Global transcript structure resolution of high gene density genomes through multi-platform data integration |
|
Relations |
BioSample |
SAMN04564259 |
SRA |
SRX1639579 |