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Sample GSM5121288 Query DataSets for GSM5121288
Status Public on Jul 06, 2021
Title RB9 (expression)
Sample type RNA
Source name retinoblastoma sample RB9
Organism Homo sapiens
Characteristics geo dataset serie: SAMPLE 7
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 10ยตg 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
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
VALUE RMA normalized, Brainarray annotated expression values, logscale

Data table
100009676_at 3.22541013827481
10000_at 5.43753564859176
10001_at 7.57499552249964
10002_at 4.90749666739271
100038246_at 3.25425458129293
10003_at 4.70230533745993
100048912_at 2.73062460452995
100049716_at 3.76106917720978
10004_at 4.08955109435288
10005_at 6.12348333160668
10006_at 7.50568357694461
10007_at 7.23983442063437
10008_at 3.81307821497302
100093630_at 8.45577850498835
100093698_at 2.47899829148518
10009_at 6.27954050525031
1000_at 8.81947412943378
100101467_at 5.87392821942411
100101938_at 3.30025272823943
10010_at 6.36501552749625

Total number of rows: 20408

Table truncated, full table size 521 Kbytes.

Supplementary file Size Download File type/resource
GSM5121288_RB01_ARN0014_s1h1s1_U133p2.CEL.gz 4.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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