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Sample GSM2332758 Query DataSets for GSM2332758
Status Public on Jan 19, 2018
Title KO2 ThyDP69+ Rep2
Sample type RNA
 
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.
 
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 KO2 ThyDP69+
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

Data table header descriptions
ID_REF
VALUE GC-RMA signal intensity

Data table
ID_REF VALUE
17200001 98.88696728
17200003 110.644627
17200005 19.26955054
17200007 38.54649929
17200009 52.95931925
17200011 77.67787992
17200013 100.4653836
17200015 64.29710926
17200017 12.96581385
17200019 12.29262984
17200021 25.6719793
17200023 113.1566721
17200025 52.92502162
17200027 186.4707597
17200029 37.14091638
17200031 34.77458241
17200033 27.06307942
17200035 18.73019436
17200037 81.33710177
17200039 18.47093221

Total number of rows: 41345

Table truncated, full table size 843 Kbytes.




Supplementary file Size Download File type/resource
GSM2332758_31_KODP690110.CEL.gz 9.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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