|
| Status |
Public on Sep 27, 2017 |
| Title |
H1 at D3, chip HG-U133B, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
H1 human embryonic stem cells, day 3 of retinoic acid differentiation
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human embryonic stem cells
cell line: H1
agent: retinoic acid
time: day 3
status: differentiating in retinoic acid for 3 days
|
| Growth protocol |
All hESC lines were maintained in mTeSR media on Matrigel-coated plates and passaged every 5-6 days. H1 hESCs were differentiated in the presence of 5μM retinoic acid.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol, treated with DNAseI to eliminate genomic DNA, and subjected to 1:1 phenol:chloriform extraction, with precipitation and dilution of RNA in water.
|
| Label |
biotin
|
| Label protocol |
1 μg of total RNA was converted into biotinylated cRNA using the Illumina TotalPrep RNA Amplification Kit (Ambion) following the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 μg of cRNA were hybridized for 16 hours at 45°C on the Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 7G with AutoLoader Carousel.
|
| Description |
H1_d3_B-1
Gene expression data from H1 hESCs differentiating in retinoic acid (day 3)
|
| Data processing |
Expression data were extracted using the MAS5.0 software package (Affymetrix). Data analyses were performed in MatLab R2010b (The MathWorks Inc.). Data were normalized using cubic spline normalization algorithm with H1 d0 array used as a reference sample.
|
| |
|
| Submission date |
Sep 23, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Natalia Ivanova |
| Organization name |
Yale University
|
| Department |
Genetics
|
| Lab |
Ivanova Lab
|
| Street address |
10 Amistad Street, Room 220
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06519 |
| Country |
USA |
| |
|
| Platform ID |
GPL97 |
| Series (1) |
| GSE104173 |
Expression data from retinoic acid-induced differentiation of human embryonic stem cells (hESCs) |
|
