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Sample GSM4971804 Query DataSets for GSM4971804
Status Public on Apr 13, 2021
Title BRN2_HOM_TUM_2
Sample type RNA
 
Source name Primary tumor
Organism Mus musculus
Characteristics genotype: Tyr::CreErT2::BrafV600E F/+ Pten F/+ BRN2 F/F
Sex: female
rin: 8.7
category: Braf-Pten-Brn2-hom
mouseid: 19A-21-22-28 1442
Growth protocol Newborn mice were treated dorsally with 0.4 μg/day/mouse tamoxifen from P1 to P3. Developing skin excrescences > 3 mm diameter were considered to be melanomas, and validated after growth. Mice were sacrificed and autopsied four weeks after tumor appearance or once the tumors reached 2 cm3. Only melanoma having a volume of 1cm^3 were used for the transcriptomic analysis. For mice harbouring multiple melanome, only the biggest melanomas on each mouse was harvested. Tumors were then excised, rinsed in cold PBS and snap-frozen in liquid nitrogen.
Extracted molecule total RNA
Extraction protocol total RNA was extracted using the miRneasy, Qiagen extraction kit according to the manufacturer's instructions.
Label biotin
Label protocol The IVT reaction was carried out in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix for cRNA amplification and biotin labelling.
 
Hybridization protocol Complementary RNA (cRNA) was synthesized using the GeneChip 3′IVT Plus reagent Kit, according to the manufacturer’s protocol. Then 11μg cRNA were hybridized to mouse MOE430 gene expression Affymetrix microarrays
Scan protocol After washing and staining, using the Affymetrix fluidics station 450, the probe arrays were scanned using an Affymetrix GeneChip Scanner 3000.
Data processing Data processing was done using R/Bioconductor. CEL files were read using the oligo package and normalized using the RMA - Robust Multichip Average algorithm. The highest-IQR probe for each gene was retained.
 
Submission date Dec 12, 2020
Last update date Apr 13, 2021
Contact name Lionel Larue
Phone +33 1 69 86 71 07
Organization name Institut Curie
Department UMR3347 CNRS - U1021 INSERM, Institut Curie
Lab Normal and Pathological Development of Melanocytes
Street address Bat 110, Centre universitaire
City Orsay
ZIP/Postal code 91405
Country France
 
Platform ID GPL1261
Series (2)
GSE126524 Gene expression data from Tyr::CreErT2::BrafV600E Pten F/+ mouse tumors according to defloxing status of Brn2 [tumors]
GSE163086 Gene expression data from Tyr::CreErT2::BrafV600E Pten F/+ mouse tumors according to defloxing status of Brn2

Data table header descriptions
ID_REF
VALUE RMA signal intensity (log2)

Data table
ID_REF VALUE
1415671_at 10.442
1415672_at 11.041
1415673_at 8.546
1415675_at 8.276
1415676_a_at 10.446
1415677_at 10.537
1415679_at 10.681
1415681_at 9.333
1415685_at 8.520
1415697_at 8.720
1415698_at 8.725
1415699_a_at 9.625
1415700_a_at 11.454
1415702_a_at 10.687
1415707_at 9.291
1415710_at 7.681
1415714_a_at 9.822
1415718_at 8.908
1415720_s_at 7.816
1415721_a_at 8.995

Total number of rows: 20394

Table truncated, full table size 344 Kbytes.




Supplementary file Size Download File type/resource
GSM4971804_MM52-ARN0030_s1h1_Moe430p2.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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