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Sample GSM2152412 Query DataSets for GSM2152412
Status Public on Feb 10, 2017
Title Embryonic cTEC Rep2
Sample type RNA
 
Source name Embryonic day 14.5 Fetal Thymus cTEC + 7days in Culture
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: E14.5 Fetal Thymus+ 7days in Culture
genotype: Wildtype
age: Embryonic day 14.5 + 7days in Culture
Treatment protocol 10-15 fetal thymi were dissected from E14.5 wildtype embryos and cultured for 7 days in AIM-V. For isolation of embryonic TEC, thymic lobes were dissected and washed once in PBS followed by an incubation of 15 min in PBS containing 0.25% trypsin and 0.02% EDTA and gentle mechanical dissociation to obtain cell suspensions. For isolation of adult TEC, thymic lobes were dissected and cut into small pieces (~10 mm × 10 mm), excess thymocytes removed by sequential washes in HBSS containing FCS 10% (v/v) and incubated for 30 min at 37 °C in HBSS containing FCS, 3.3 mg/ml Liberase and 0.5 mg/ml DNaseI (Roche Diagnostics UK). After incubation, cells suspensions were prepared by gentle mechanical dissociation.
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 Gene expression data from E14.5 Fetal Thymus cTEC 7 days in culture
Data processing Data was normalised using rma function from the oligo package in R
 
Submission date May 13, 2016
Last update date Feb 10, 2017
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)
GSE81433 Gene Expression Data from Adult and Embryo Thymic Epithelial Cells (TEC)

Data table header descriptions
ID_REF
VALUE GC-RMA signal intensity

Data table
ID_REF VALUE
17200001 48.21348837
17200003 46.51776429
17200005 13.05245919
17200007 43.25987973
17200009 47.14320181
17200011 48.93440161
17200013 56.65187268
17200015 57.79948372
17200017 17.05958489
17200019 12.25526758
17200021 25.97027641
17200023 94.573155
17200025 65.55034108
17200027 155.5993042
17200029 25.56243081
17200031 31.20649058
17200033 28.02980279
17200035 16.66784735
17200037 74.64647237
17200039 30.49632759

Total number of rows: 41345

Table truncated, full table size 843 Kbytes.




Supplementary file Size Download File type/resource
GSM2152412_5_UnStimcTEC2.CEL.gz 9.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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