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Sample GSM5121337 Query DataSets for GSM5121337
Status Public on Jul 06, 2021
Title RB221 (expression)
Sample type RNA
 
Source name retinoblastoma sample RB221
Organism Homo sapiens
Characteristics geo dataset serie: SAMPLE 78
batch: RT09
tissue: retinoblastoma
Growth protocol Immediately following enucleation, a needle was inserted through the anterior chamber of the eye to extract a tumor sample by aspiration. The tumor specimen was placed in RPMI medium on ice, cells were re-suspended, counted and separated into two tubes (for DNA and RNA preparation). The tubes were then centrifuged to remove all media and snap frozen for later extraction.
Extracted molecule total RNA
Extraction protocol Tumor RNA was extracted using Qiazol (Qiagen, Courtaboeuf, France) according to the manufacturer instructions and purified using miRNeasy Mini kit (Qiagen).
Label biotin
Label protocol 100ng of total RNA were amplified to produced biotinylated complementary RNAs, as recommended by Affymetrix.
 
Hybridization protocol Affymetrix microarrays were hybridized with 10µg of biotinylated cRNA according the supplier recommendations. Microarrays were washed and stained using FS450 fluidics upon a protocol provided by Affymetrix, corresponding to the U133plus 2.0 arrays
Scan protocol Microarrays were scanned using a 7G, Affymetrix GCS3000 scanner, raw data were acquired with Affymetrix Genechip Command Console.
Description Gene expression data from retinoblastoma samples
Data processing Signal reconstruction was performed with the RMA algorithm as implemented in Bioconductor affy package on R statistical software using the Dai custom CDF package: HGU133Plus2_Hs_ENTREZG, Brainarray Custom CDF EntrezG version 23, Batch effects were corrected with the help of the bioconductor package SVA,
 
Submission date Mar 01, 2021
Last update date Jul 06, 2021
Contact name Elodie chapeaublanc
E-mail(s) elodie.chapeaublanc@pasteur.fr
Organization name Institut Curie
Department UMR 144
Lab Equipe Radvanyi
Street address 26 rue d'ulm
City paris
ZIP/Postal code 75248
Country France
 
Platform ID GPL28718
Series (2)
GSE58780 Retinoblastoma gene expression data
GSE58785 Pan-genomic study of primary human retinoblastoma samples

Data table header descriptions
ID_REF
VALUE RMA normalized, Brainarray annotated expression values, logscale

Data table
ID_REF VALUE
100009676_at 3.54315052515918
10000_at 5.43070554761158
10001_at 7.46069140811211
10002_at 4.61416277863174
100038246_at 3.50722491755578
10003_at 3.31145341761915
100048912_at 2.95295010580284
100049716_at 4.00577185619098
10004_at 3.66032877517587
10005_at 7.35078426643311
10006_at 7.33505884673512
10007_at 7.53231649160112
10008_at 4.53833341905385
100093630_at 8.99261408101419
100093698_at 2.59047700891191
10009_at 6.09347779147088
1000_at 8.33847996001599
100101467_at 6.30441769299023
100101938_at 3.08297638599161
10010_at 6.85256960736166

Total number of rows: 20408

Table truncated, full table size 521 Kbytes.




Supplementary file Size Download File type/resource
GSM5121337_RT09_ARN0010_s2h1_U133p2.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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