|
Status |
Public on Feb 01, 2016 |
Title |
DMSO_A |
Sample type |
SRA |
|
|
Source name |
hESCs
|
Organism |
Homo sapiens |
Characteristics |
cell type: embryonic stem cells cell line: H9 hESCs expressing pJAZ NLS-GFP-OsJAZ33 agent: DMSO
|
Treatment protocol |
H9 human embryonic stem cells (hESCs) expressing pJAZ NLS-GFP-OsJAZ33 were treated cultured in mTeSR-1 media supplemented with 50 micromolar coronatine (Cor) or 0.1% DMSO for two days on Matrigel-coated plates. Cells were collected by trypsinization and RNA was prepared using TRIZOL (Ambion). Experiment was repeated twice (Replicate A and B)
|
Growth protocol |
H9 hESCs were cultured in mTeSR-1 media on Matrigel-coated plates
|
Extracted molecule |
total RNA |
Extraction protocol |
For mRNA-Seq sample preparation, the total RNA was isolated using Trizol reagent following the manufacturer’s instructions. Quality and quantity of total RNA was assayed using Nanodrop and Agilent Bioanalyzer. For mRNA-seq, libraries were prepared using the TrueSeq protocol from Illumina. The concentration of the libraries was assayed using Agilent Bioanalyzer and sequenced using 1*75bp on an NextSeq 500 platform
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
wildtype hESCs
|
Data processing |
RNASeq: Fastq files were mapped to the genome using Tophat: tophat -o -p 4 RNASeq: Output ".bam" files were process to get counts: cuffquant -o -p 4 RNASeq: Output ".cxb" files were processed to get differential gene expression values: cuffdiff -o -L Genome_build: hg19 Supplementary_files_format_and_content: genes_fpkm.xlsx
|
|
|
Submission date |
Oct 28, 2015 |
Last update date |
May 15, 2019 |
Contact name |
avinash waghray |
E-mail(s) |
avinash.waghray@gmail.com
|
Organization name |
Massachussets General Hospital
|
Department |
Center for Regenerative Medicine
|
Lab |
Rajagopal
|
Street address |
185 Cambridge Street, CPZN Room 4254A
|
City |
Boston |
State/province |
MA |
ZIP/Postal code |
02114 |
Country |
USA |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE74457 |
A Dual Molecular Analog Tuner for Dissecting Mammalian Protein Function |
|
Relations |
BioSample |
SAMN04221477 |
SRA |
SRX1395017 |