|
| Status |
Public on Jan 21, 2011 |
| Title |
Naive CD4+ T-cell, sample 3 |
| Sample type |
RNA |
| |
|
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Naive CD4+ T-cell
batch: HTA3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from TriZol. The concentration of RNA was quantified using the RiboGreen© RNA Quantitation Kit (Invitrogen, San Diego, CA)
|
| Label |
biotin
|
| Label protocol |
Ten nanograms of total RNA were amplified using the Ovation Biotin RNA Amplification and Labeling System (NuGEN, San Carlos, CA).
|
| |
|
| Hybridization protocol |
The cDNA was fragmented, labeled and hybridized to Affymetrix HG_U133AAofAv2 microarrays (Affymetrix, Santa Clara, CA)
|
| Scan protocol |
standard Affymetrix protocol
|
| Data processing |
Transcript levels were processed from data image files using RMA method, implemented by Bioconductor R package. To reduce batch effects, transcript levels were further corrected with the ComBat method (Johnson, 2007), which applies empirical Bayes framework for adjusting data for batch effects. Final dataset which was used in the paper and contains 8968 genes is included in the supplementary file GSE24759_data.sort.txt.
|
| |
|
| Submission date |
Oct 18, 2010 |
| Last update date |
Mar 22, 2017 |
| Contact name |
Noa Novershtern |
| E-mail(s) |
noa.novershtern@weizmann.ac.il
|
| Organization name |
Weizmann Institute of Science
|
| Department |
Molecular Genetics
|
| Street address |
Weizmann Institute
|
| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL4685 |
| Series (1) |
| GSE24759 |
Densely interconnected transcriptional circuits control cell states in human hematopoiesis |
|
