|
| Status |
Public on Sep 18, 2015 |
| Title |
TW18_D8 KO Th1_2 |
| Sample type |
RNA |
| |
|
| Source name |
Tcf7 deficient Th1 cells
|
| Organism |
Mus musculus |
| Characteristics |
infection: LCMV
cell type: SMARTA CD4 Tcells
cell type (separated by facs): Th1 cells
genotype/variation: Tcf7 deficient
|
| Treatment protocol |
Mice were infected with LCMV
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Human HuGene-1_0-st-v1 GeneChips (Affymetrix, Inc). DNase treatment was included as part of isolation to remove possible contaminating DNA. Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. 300 ng of total RNA was used for labeling with theAmbion WT Expression Kit (cat#4411974) and Affymetrix kit (Cat # 900652).After hybridization, the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).
|
| |
|
| Hybridization protocol |
The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Mouse MoGene-2_0-st microarrays. The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.
|
| Scan protocol |
Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.
|
| Data processing |
Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.
|
| |
|
| Submission date |
Feb 05, 2015 |
| Last update date |
Sep 18, 2015 |
| Contact name |
abdel G Elkahloun |
| E-mail(s) |
[email protected]
|
| Phone |
301 402 3170
|
| Organization name |
NHGRI-NIH
|
| Lab |
MICROARRAY CORE
|
| Street address |
50, SOUTH DRIVE
|
| City |
BETHESDA |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE65660 |
TCF1 is required for the differentiation of T follicular helper (TFH) cells during viral infections |
|
