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Sample GSM5121297 Query DataSets for GSM5121297
Status Public on Jul 06, 2021
Title RB25 (expression)
Sample type RNA
 
Source name retinoblastoma sample RB25
Organism Homo sapiens
Characteristics geo dataset serie: SAMPLE 18
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 3.46208694753046
10000_at 5.78059777019431
10001_at 8.18488434065236
10002_at 4.77170323616937
100038246_at 3.44681199449164
10003_at 5.51949946705052
100048912_at 2.81737685528705
100049716_at 3.65009569893771
10004_at 3.6839901652959
10005_at 6.96044440704571
10006_at 7.60741596684172
10007_at 7.21023237374556
10008_at 3.66721933473713
100093630_at 8.84134257561843
100093698_at 2.54407794671904
10009_at 6.78479323174233
1000_at 8.45961642518642
100101467_at 5.88255027386239
100101938_at 2.82909195867144
10010_at 6.98439934996061

Total number of rows: 20408

Table truncated, full table size 521 Kbytes.




Supplementary file Size Download File type/resource
GSM5121297_RB01_ARN0008_s1h1s1_U133p2.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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