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Sample GSM4618394 Query DataSets for GSM4618394
Status Public on Jun 06, 2023
Title Control-0h-Rep1
Sample type RNA
 
Source name Control-0h_E17.5 Rag1-/- Thymocytes
Organism Mus musculus
Characteristics genotype: Rag1-/-
tissue: E17.5 Fetal Thymus
cell type: Thy1.2+ cells
Treatment protocol Fetal Thymi were dissected from E17.5 Rag1-/- embryos. Thy1.2+ cells were magnetically purified from fresh E17.5 thymi (Control-0h) and 40h stimulated with anti-CD3 + DMSO (Control-DMSO-40h) or anti-CD3 + 50uM 79-6 (79-6-40h). 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
Data processing Data was normalised using rma function from the oligo package in R
 
Submission date Jun 16, 2020
Last update date Jun 06, 2023
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 GPL6246
Series (1)
GSE152577 The transcription factor Bcl6 represses active Notch signalling in fetal thymocytes

Data table header descriptions
ID_REF
VALUE GC-RMA signal intensity

Data table
ID_REF VALUE
10338001 6193.831818
10338003 1574.289481
10338004 700.2787666
10338017 10838.20645
10338025 582.4989396
10338026 13020.07516
10338029 1418.828808
10338035 706.1962962
10338036 993.1757215
10338037 20.12162101
10338041 3491.257742
10338042 1359.295236
10338044 6755.130571
10338047 27.87864781
10338056 20.21683334
10338059 13270.47568
10338060 18.19034406
10338063 19.5562346
10338064 17.718555
10338065 20.67299854

Total number of rows: 34760

Table truncated, full table size 709 Kbytes.




Supplementary file Size Download File type/resource
GSM4618394_G29_0A.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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