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Sample GSM4971826 Query DataSets for GSM4971826
Status Public on Apr 13, 2021
Title Cell_line_Braf-Pten-Brn2-hom_2
Sample type RNA
 
Source name cell line derived from mouse melanoma tumor
Organism Mus musculus
Characteristics tissue: cell line derived from mouse melanoma tumor
genotype: Tyr::CreERT2::BrafV600E F/+ Pten F/+ BRN2 F/F
Sex: female
rin: 9.8
designation: BRN2_HOM_CELL_2
mouseid: 19A-21-22-28 1831
Growth protocol Murine Braf-Pten-Brn2-wt, Braf-Pten-Brn2-het & Braf-Pten-Brn2-hom melanoma cell line were established respectively from melanoma arising from Braf-Pten-Brn2-wt, Braf-Pten-Brn2-het & Braf-Pten-Brn2-hom mice. Small pieces (≈10 mm3) of primary tumors were cleaned, washed in PBS, and subcutaneously implanted into the neck pad of C57BL/6 mice. Once the implanted tumor reached a volume of ≈1 cm3, it was removed from the mouse, tumors were dissociated as single cells prior to establishing them in culture as previously described (Gallagher et al., 2011).
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 not provided
 
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.
Description cell_line_M76
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)
GSE163085 Gene expression data from Tyr::CreErT2::BrafV600E Pten F/+ mouse tumors according to defloxing status of Brn2 [cell lines]
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 11.249
1415672_at 11.195
1415673_at 10.308
1415675_at 9.315
1415676_a_at 11.174
1415677_at 10.918
1415679_at 12.121
1415681_at 10.872
1415685_at 7.111
1415697_at 8.661
1415698_at 9.117
1415699_a_at 10.809
1415700_a_at 11.129
1415702_a_at 11.442
1415707_at 10.373
1415710_at 8.799
1415712_at 7.444
1415714_a_at 11.332
1415718_at 9.287
1415720_s_at 9.262

Total number of rows: 20394

Table truncated, full table size 344 Kbytes.




Supplementary file Size Download File type/resource
GSM4971826_MM52-ARN0027_s1h1_Moe430p2.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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