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Sample GSM4618395 Query DataSets for GSM4618395
Status Public on Jun 06, 2023
Title Control-0h-Rep2
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 6185.491853
10338003 1545.868015
10338004 720.8774422
10338017 9755.210343
10338025 621.4814465
10338026 12429.57516
10338029 1387.060181
10338035 710.1980358
10338036 1037.803768
10338037 20.19860257
10338041 3357.451289
10338042 1278.416739
10338044 6726.510791
10338047 27.12456
10338056 19.94232831
10338059 13128.63146
10338060 18.18777909
10338063 19.37873594
10338064 17.46976916
10338065 20.77932435

Total number of rows: 34760

Table truncated, full table size 709 Kbytes.




Supplementary file Size Download File type/resource
GSM4618395_G29_0B.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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