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Sample GSM2332754 Query DataSets for GSM2332754
Status Public on Jan 19, 2018
Title WT2 ThyDP69+ Rep2
Sample type RNA
 
Source name WT_E18.5 DP69+ Thymocytes
Organism Mus musculus
Characteristics genotype/variation: Wildtype
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 WT2 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 117.3770962
17200003 93.19269444
17200005 11.37232602
17200007 53.6730467
17200009 83.43327633
17200011 54.43770159
17200013 70.60844123
17200015 73.77025439
17200017 8.629562874
17200019 20.276577
17200021 22.58463266
17200023 68.68495173
17200025 43.23377517
17200027 132.1008944
17200029 17.66346146
17200031 37.75708431
17200033 93.33237573
17200035 83.28153084
17200037 93.29202139
17200039 24.74923617

Total number of rows: 41345

Table truncated, full table size 843 Kbytes.




Supplementary file Size Download File type/resource
GSM2332754_29_WTDP690110.CEL.gz 9.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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