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Sample GSM4618397 Query DataSets for GSM4618397
Status Public on Jun 06, 2023
Title Control-DMSO-40h-Rep2
Sample type RNA
 
Source name Control-DMSO-40h_E17.5 Rag1-/- Thymocytes
Organism Mus musculus
Characteristics genotype: Rag1-/-
treatment: DMSO
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 6698.310115
10338003 1715.962311
10338004 895.9179221
10338017 11749.66169
10338025 724.5843814
10338026 14149.21428
10338029 1657.807094
10338035 822.8742829
10338036 1306.612026
10338037 20.7284559
10338041 4295.140819
10338042 1593.829395
10338044 8069.227515
10338047 27.82192189
10338056 20.95740366
10338059 13599.96196
10338060 18.41827498
10338063 20.25603341
10338064 18.37247174
10338065 21.43450273

Total number of rows: 34760

Table truncated, full table size 709 Kbytes.




Supplementary file Size Download File type/resource
GSM4618397_G29_CB.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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