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Status |
Public on May 12, 2015 |
Title |
CIT578 |
Sample type |
RNA |
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Source name |
Frozen tissue of non tumoral colorectal mucosa
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Organism |
Homo sapiens |
Characteristics |
organism: Homo sapiens dataset: Non Tumoral Sex: Female age.at.diagnosis (year): 71 tnm.stage: 2 tnm.t: T3 tnm.n: N0 tnm.m: M0 tumor.location: distal chemotherapy.adjuvant: Y chemotherapy.adjuvant.type: FUFOL rfs.event: 0 rfs.delay: 85 os.event: 0 os.delay (months): 85 mmr.status: pMMR 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: N/A kras.mutation.dna: N/A kras.mutation.exon.number: N/A kras.mutation.protein: N/A braf.mutation: N/A braf.mutation.dna: N/A braf.mutation.exon.number: N/A braf.mutation.protein: N/A cit.molecularsubtype: N/A dependancy sample: CIT370 rna.extraction.method: E3
|
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 |
E3: total RNA was extracted using Manual-Rneasy Micro (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).
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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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Data processing |
RMA normalisation (Bioconductor R affy package) + ComBat (R sva package )
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Submission date |
May 12, 2015 |
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 |
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