|
| Status |
Public on May 22, 2013 |
| Title |
CIT488 |
| Sample type |
RNA |
| |
|
| Source name |
Frozen tissue of primary colorectal Adenocarcinoma (validation)
|
| Organism |
Homo sapiens |
| Characteristics |
organism: Homo sapiens
dataset: validation
Sex: Male
age.at.diagnosis (year): 73
tnm.stage: 3
tnm.t: T4
tnm.n: N2
tnm.m: MX
tumor.location: proximal
chemotherapy.adjuvant: Y
chemotherapy.adjuvant.type: 5FU
rfs.event: 1
rfs.delay: 5
os.event: 1
os.delay (months): 14
mmr.status: dMMR
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: M
kras.mutation.dna: c.38G>A
kras.mutation.exon.number: c.38G>A
kras.mutation.protein: p.G13D
braf.mutation: WT
braf.mutation.dna: N/A
braf.mutation.exon.number: N/A
braf.mutation.protein: N/A
cit.molecularsubtype: C4
dependancy sample: N/A
rna.extraction.method: Manual-Trizol
|
| Treatment protocol |
Total RNA was performed according to the manufacturer's instructions.
|
| Growth protocol |
Samples stored at -80 C
|
| 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)
|
| Label |
biotin
|
| 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).
|
| |
|
| 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.
|
| 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
|
| 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)
|
| Data processing |
RMA normalisation (Bioconductor R affy package) + ComBat (R sva package )
|
| |
|
| Submission date |
Jul 23, 2012 |
| Last update date |
Jun 18, 2021 |
| Contact name |
Nabila Elarouci |
| E-mail(s) |
Nabila.Elarouci@ligue-cancer.net
|
| Organization name |
Ligue Nationale contre le Cancer
|
| Department |
Recherche
|
| Lab |
Carte d'identité des tumeurs
|
| Street address |
14 rue Corvisart
|
| City |
Paris |
| ZIP/Postal code |
75 013 |
| Country |
France |
| |
|
| 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 |
|
