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Status |
Public on May 22, 2013 |
Title |
CIT102 |
Sample type |
RNA |
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Source name |
Frozen tissue of primary colorectal Adenocarcinoma (discovery)
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Organism |
Homo sapiens |
Characteristics |
organism: Homo sapiens dataset: discovery Sex: Female age.at.diagnosis (year): 75 tnm.stage: 2 tnm.t: T3 tnm.n: N0 tnm.m: M0 tumor.location: proximal chemotherapy.adjuvant: N chemotherapy.adjuvant.type: N/A rfs.event: 0 rfs.delay: 60 os.event: 0 os.delay (months): 60 mmr.status: N/A cimp.status: + cin.status: - tp53.mutation: N/A tp53.mutation.dna: N/A tp53.mutation.exon.number: N/A tp53.mutation.protein: N/A kras.mutation: WT kras.mutation.dna: N/A kras.mutation.exon.number: N/A kras.mutation.protein: N/A braf.mutation: M braf.mutation.dna: N/A braf.mutation.exon.number: N/A braf.mutation.protein: N/A cit.molecularsubtype: C2 dependancy sample: N/A rna.extraction.method: Manual-Rneasy Mini (Qiagen)
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Treatment protocol |
Total RNA was performed according to the manufacturer's instructions.
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Growth protocol |
Samples stored at -80 C
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Extracted molecule |
total RNA |
Extraction protocol |
E1: total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), E2: total RNA was extracted using Manual-Cesium Chloride, E3: total RNA was extracted using Manual-Rneasy Micro (Qiagen), E4: total RNA was extracted using Manual-Rneasy Mini (Qiagen), E5: total RNA was extracted using RNA NOW, E6: total RNA was extracted using TriReagent & Manual-Rneasy Mini (Qiagen)
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Label |
biotin
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Label protocol |
Biotinylated cRNA targets were prepared from 3.0 mg of total RNA, according to the GeneChip Expression Analysis Technical Manual : One-Cycle Target Labeling Assay (P/N 701021 Rev.5, Affymetrix, Santa Clara, USA).
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Hybridization protocol |
Following fragmentation, 10 μg of cRNAs were hybridized for 16 hours at 45°C, 60 rpm on Human GeneChip HG-U133 Plus 2.0 arrays (Affymetrix). The chips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix) using the EukGE-WS2v5_450.
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Scan protocol |
Scanner GeneChip 3000 7G ; Wavelenght : 570 nm, size pixel: 1.56 µm ; each chip is scanned once; Http://www.affymetrix.com/support/technical/manual/expression_manual.affx
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Description |
################ Mutation Details ################
ND: not determined NA: Not applicable
When gene.mutation=M (mutated), than we have details in exon, protein and DNA.
gene.mutation=WT (wild type), the exon, protein and DNA columns are NA (not applicable).
BRAF.mutation.DNA means the CDS Mutation (http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=521) And BRAF.mutation.Protein means the AA Mutation (http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=521)
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Data processing |
RMA normalisation (Bioconductor R affy package) + ComBat (R sva package )
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Submission date |
Jul 23, 2012 |
Last update date |
Jun 18, 2021 |
Contact name |
Nabila Elarouci |
E-mail(s) |
[email protected]
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Organization name |
Ligue Nationale contre le Cancer
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Department |
Recherche
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Lab |
Carte d'identité des tumeurs
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Street address |
14 rue Corvisart
|
City |
Paris |
ZIP/Postal code |
75 013 |
Country |
France |
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Platform ID |
GPL570 |
Series (2) |
GSE39582 |
Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [Expression] |
GSE40967 |
Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics |
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