|
| Status |
Public on Feb 01, 2016 |
| Title |
DMSO_B |
| 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 |
SAMN04221479 |
| SRA |
SRX1395019 |
