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Sample GSM5121296 Query DataSets for GSM5121296
Status Public on Jul 06, 2021
Title RB24 (expression)
Sample type RNA
 
Source name retinoblastoma sample RB24
Organism Homo sapiens
Characteristics geo dataset serie: SAMPLE 17
batch: RB01
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 3.4150266441127
10000_at 5.63186112283938
10001_at 7.47006393520837
10002_at 4.73033626093204
100038246_at 3.38046636926644
10003_at 5.14778927812067
100048912_at 2.96170309282127
100049716_at 3.77801045321245
10004_at 3.95695780394097
10005_at 6.15191229968528
10006_at 7.24549724862264
10007_at 7.03737320188099
10008_at 3.83680624354013
100093630_at 8.5964314608847
100093698_at 2.40828255396639
10009_at 6.39072116892984
1000_at 8.6378640400987
100101467_at 6.26857748774922
100101938_at 3.37259124633565
10010_at 6.40819329097082

Total number of rows: 20408

Table truncated, full table size 521 Kbytes.




Supplementary file Size Download File type/resource
GSM5121296_RB01_ARN0007_s1h1s1_U133p2.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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