|
| Status |
Public on May 13, 2020 |
| Title |
E SOR Rep 2 [SOR_E_71_9_5_I2] |
| Sample type |
SRA |
| |
|
| Source name |
primary cardiomyocytes_Sorafenib
|
| Organism |
Homo sapiens |
| Characteristics |
source organ: Heart
cell type: cardiac myocytes
treatment condition: Sorafenib
concentration: 1uM
treatment time (hrs): 48
vendor: PromoCell
cat #: C-12810
lot #: 2120301.2
well: I2
investigative unit: 71
sample id: 9
rna amount (ng): 200
nanodrop 260/280: 1.65
rna conc (ng/ul): 24.8
rna volume (ul): 8.1
h2o volume (ul): 11.9
|
| Treatment protocol |
Fully confluent and differentiated cells were treated with drugs or vehicle (DMSO) for 48 hours (see DToxS SOP CE – 4.0: Drug Treatment and Cell Lysis)
|
| Growth protocol |
Cultured under growth conditions with antibiotic free growth media and differentiated for four weeks with antibiotic free differentiation media (see DToxS SOP CE – 1.0: PromoCell Cardiomyocyte Subculture, DToxS SOP CE – 2.0: PromoCell Cardiomyocyte Plating for Drug Test)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol (see DToxS SOP A – 1.0: Total RNA Isolation)
Using the sample name scheme [Treatment Condition]_[Cell Line]_[Investigative Unit]_[Sample ID]_[Plate Number]_[Well Number], library was prepared using 150ng (for the samples with the plate number 1 and 2) and 200ng (for the samples with the plate number 4 and 5) of total RNA enriched for mRNA using polyA beads and the TruSeq RNA Library Prep Kit (Illumina, Cat: RS-122-2001) per manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RNAseq_20161108.I2
Sample SOR_E_71_9_5_I2
|
| Data processing |
Data preparation and analysis workflow for 3'-DGE mRNA-seq dataset: https://github.com/DToxS/DGE-GEO-Depot
Aligning 3'-DGE mRNA sequence reads: https://github.com/DToxS/Sequence-Alignment
Mapping aligned 3'-DGE sequence reads to reference genes: https://github.com/DToxS/Feature-Counts
Identifying differentially expressed genes for 3'-DGE mRNA-seq dataset: https://github.com/DToxS/Differential-Comparison
Genome_build: Reference-Library.tar.gz: a compressed file containing the UCSC human genome referece library (version hg38)
Supplementary_files_format_and_content:
DGE-RNAseq-Experiment-Design-20150409.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20150409 dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20150409.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20150409 dataset
Differential-Comparison-Configs-20150409.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20150409 dataset
Differential-Comparison-Params-20150409.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20150409 dataset
DEG-Calc-FDR-0.1-20150409.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the 20150409 dataset
DGE-RNAseq-Experiment-Design-20150503.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20150503 dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20150503.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20150503 dataset
Differential-Comparison-Configs-20150503.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20150503 dataset
Differential-Comparison-Params-20150503.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20150503 dataset
DGE-RNAseq-Experiment-Design-20151120.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20151120 dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20151120.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20151120 dataset
Differential-Comparison-Configs-20151120.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20151120 dataset
Differential-Comparison-Params-20151120.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20151120 dataset
DEG-Calc-FDR-0.1-20151120.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the 20151120 dataset
DGE-RNAseq-Experiment-Design-20161108-Cor.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20161108-Cor dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20161108-Cor.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20161108-Cor dataset
Differential-Comparison-Configs-20161108-Cor.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20161108-Cor dataset
Differential-Comparison-Params-20161108-Cor.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20161108-Cor dataset
DEG-Calc-FDR-0.1-20161108-Cor.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the 20161108-Cor dataset
DGE-RNAseq-Experiment-Design-20161108-Spec-Fixed.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20161108-Spec-Fixed dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20161108-Spec-Fixed.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20161108-Spec-Fixed dataset
Differential-Comparison-Configs-20161108-Spec-Fixed.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20161108-Spec-Fixed dataset
Differential-Comparison-Params-20161108-Spec-Fixed.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20161108-Spec-Fixed dataset
DEG-Calc-FDR-0.1-20161108-Spec-Fixed.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the 20161108-Spec-Fixed dataset
DGE-RNAseq-Experiment-Design-20161108-Spec-Var-1.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20161108-Spec-Var-1 dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20161108-Spec-Var-1.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20161108-Spec-Var-1 dataset
Differential-Comparison-Configs-20161108-Spec-Var-1.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20161108-Spec-Var-1 dataset
Differential-Comparison-Params-20161108-Spec-Var-1.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20161108-Spec-Var-1 dataset
DEG-Calc-FDR-0.1-20161108-Spec-Var-1.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the 20161108-Spec-Var-1 dataset
DGE-RNAseq-Experiment-Design-20161108-Spec-Var-2.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20161108-Spec-Var-2 dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20161108-Spec-Var-2.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20161108-Spec-Var-2 dataset
Differential-Comparison-Configs-20161108-Spec-Var-2.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20161108-Spec-Var-2 dataset
Differential-Comparison-Params-20161108-Spec-Var-2.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20161108-Spec-Var-2 dataset
DEG-Calc-FDR-0.1-20161108-Spec-Var-2.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the 20161108-Spec-Var-2 dataset
DGE-RNAseq-Experiment-Design-20161108-Spec-Var-3.tsv.gz: a compressed file containing the experiment design table of all the samples from the 20161108-Spec-Var-3 dataset to be used by the DEG-comparison pipeline
DGE-RNAseq-Read-Counts-20161108-Spec-Var-3.tsv.gz: a compressed file containing the read counts table of the uniquely aligned sequence fragments for the 20161108-Spec-Var-3 dataset
Differential-Comparison-Configs-20161108-Spec-Var-3.tar.gz: a compressed file containing the configuration of the DEG-comparison pipeline file for the 20161108-Spec-Var-3 dataset
Differential-Comparison-Params-20161108-Spec-Var-3.tar.gz: a compressed file containing the input parameter files of the DEG-comparison pipeline file for the 20161108-Spec-Var-3 dataset
DEG-Calc-FDR-0.1-20161108-Spec-Var-3.tar.gz: a compressed file containing a set of statistical comparison results of differentially expressed genes at each drug-treated condition with the file names in a form of Human-[Cell Line]-Hour-48-Plate-[Plate Number]-Calc.CTRL-[Drug Name].tsv for the 20161108-Spec-Var-3 dataset
Program-Source-Codes.tar.gz: a compressed file containing the source codes for sequence alignment, feature counts, and differential comparison.
|
| |
|
| Submission date |
Feb 28, 2020 |
| Last update date |
May 13, 2020 |
| Contact name |
Ravi Iyengar |
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Pharmacological Sciences
|
| Street address |
1425 Madison Avenue, Room 12-70C
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE146096 |
Transcriptomic profiling of human cardiac cells predicts protein kinase inhibitor-associated cardiotoxicity [DGE] |
| GSE146097 |
Transcriptomic profiling of human cardiac cells predicts protein kinase inhibitor-associated cardiotoxicity |
|
| Relations |
| BioSample |
SAMN14245976 |
| SRA |
SRX7817225 |
