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Sample GSM2332757 Query DataSets for GSM2332757
Status Public on Jan 19, 2018
Title KO1 ThyDP69+ Rep1
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 KO1 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 78.5710224
17200003 62.56538962
17200005 13.06555054
17200007 42.31328802
17200009 70.85228006
17200011 58.31275209
17200013 35.69620986
17200015 74.34004464
17200017 8.795964371
17200019 11.05068555
17200021 13.26034117
17200023 115.4516184
17200025 52.85375504
17200027 113.0509163
17200029 32.97634239
17200031 27.67390815
17200033 64.60428987
17200035 8.9161324
17200037 94.46105969
17200039 30.82574119

Total number of rows: 41345

Table truncated, full table size 843 Kbytes.




Supplementary file Size Download File type/resource
GSM2332757_22_KODP692907.CEL.gz 9.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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