|
| Status |
Public on Jan 19, 2018 |
| Title |
KO1 ThySP4 Rep1 |
| Sample type |
RNA |
| |
|
| Source name |
KO_E18.5 SP4 Thymocytes
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Gli3 -/-
developmental stage: E18.5
tissue: fetal thymus
cell type: thymocytes
cell subtype: SP4 (CD4+CD8-) cells
|
| Treatment protocol |
Fetal Thymi were dissected from E18.5 embryos for each genotype and stained for surface markers CD4, CD8 and CD69. DP69- (CD4+CD8+CD69-), DP69+ (CD4+CD8+CD69+) and SP4 (CD4+CD8-) thymocytes were sorted and RNA was extracted from these cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the PicoPure RNA Isolation Kit (ThermoFisher, Cat. KIT0202) performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Up to 5.5g of total RNA was fragmented and labelled using the Affymetrix GeneChip Whole Transcript Sense Target Labelling Assay as outlined in the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
Hybridisation to Affymetrix Mouse Gene 2.0 ST arrays was performed for 16 hours at 45C with constant rotation. Samples were hybridised according to the Affymetrix specifications: hybridisation cocktails were heated at 99C for 5 minutes and then at 45C for another 5 minutes. Samples were centrifuged at max speed for 1 minute and 200ul was transferred to each array. Hybridisation was carried out for 16 hours at 45C and 60 rpm. Fluidics washing was FS450_0001.
|
| Scan protocol |
Arrays were scanned with an Affymetrix Gene ChIP Scanner 3000 7G
|
| Description |
KO1 ThySP4
|
| Data processing |
Data was normalised using rma function from the oligo package in R
|
| |
|
| Submission date |
Sep 29, 2016 |
| Last update date |
Jan 20, 2018 |
| Contact name |
Tessa Crompton |
| Organization name |
UCL
|
| Department |
Immunobiology
|
| Street address |
30 Guilford Street
|
| City |
London |
| ZIP/Postal code |
WC1N 1EH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL16570 |
| Series (1) |
| GSE87499 |
The transcription factor Gli3 promotes differentiation from double positive to CD4 single positive thymocyte by repression of Shh |
|
