|
| Status |
Public on Dec 05, 2012 |
| Title |
CordBlood_CD4+_PIM123_siRNA_Act+IL4_6h__rep3 |
| Sample type |
RNA |
| |
|
| Source name |
human cord blood CD4+ cells, PIM123 siRNA treated, Act+IL4
|
| Organism |
Homo sapiens |
| Characteristics |
genotype/variation: PIM kinase (PIM1+PIM2+PIM3) knockdown
tissue: cord blood
cell type: CD4+ T cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with RNeasy mini kit (Qiagen) according to manufacturers instructions. In-column DNase (RNase-Free Dnase Set, Qiagen) treatment was performed for 15 minutes. RNA was eluted in dH2O.
|
| Label |
Biotin
|
| Label protocol |
Amplification was started from 250 ng of total RNA using the Affymetrix GeneChip 3_IVT Express Kit (P/N 901229), and cDNA/cRNA synthesis reactions and sample cleanup steps were performed according to manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Samples were hybridized to GeneChip Human Genome U219 array plate wit specific protocold for using the GeneTitan Hybridization, Wash and Stain Kit for 3_IVT Array Plates (P/N 901530).
|
| Scan protocol |
GeneTitan Instrument was used to scan the arrays. Affymetrix GeneChip Command Console (AGCC) 3.1 was used to control the GeneTitan hybridization process and in summarizing probe cell intensity data.
|
| Description |
CD4+ cell culture from cord blood of human neonates
|
| Data processing |
Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.
|
| |
|
| Submission date |
Nov 13, 2012 |
| Last update date |
Dec 05, 2012 |
| Contact name |
Kartiek Kanduri |
| Phone |
+358-2-333-8001
|
| Organization name |
Turku Centre for Biotechnology
|
| Lab |
Molecular Systems Immunology / Lahesmaa
|
| Street address |
Tykistokatu 6
|
| City |
Turku |
| ZIP/Postal code |
20520 |
| Country |
Finland |
| |
|
| Platform ID |
GPL13667 |
| Series (1) |
| GSE40542 |
Proviral integration site for Moloney murine leukemia virus (PIM) kinases promote human T helper 1 cell differentiation |
|
