|
Status |
Public on Jan 19, 2018 |
Title |
KO1 ThyDP69+ Rep1 |
Sample type |
RNA |
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|
Source name |
KO_E18.5 DP69+ Thymocytes
|
Organism |
Mus musculus |
Characteristics |
genotype/variation: Gli3 -/- developmental stage: E18.5 tissue: fetal thymus cell type: thymocytes cell subtype: DP69+ (CD4+CD8+CD69+) 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.
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|
|
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.
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Scan protocol |
Arrays were scanned with an Affymetrix Gene ChIP Scanner 3000 7G
|
Description |
KO1 ThyDP69+
|
Data processing |
Data was normalised using rma function from the oligo package in R
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|
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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 |
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