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Sample GSM5121299 Query DataSets for GSM5121299
Status Public on Jul 06, 2021
Title RB28 (expression)
Sample type RNA
Source name retinoblastoma sample RB28
Organism Homo sapiens
Characteristics geo dataset serie: SAMPLE 20
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
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 3.53512479625176
10000_at 6.12743784394561
10001_at 7.67319809214063
10002_at 4.38948161659215
100038246_at 3.87443630141421
10003_at 5.68100149375553
100048912_at 3.09251131498201
100049716_at 4.05721459645606
10004_at 3.56239246955441
10005_at 6.40772261746548
10006_at 7.43025075374057
10007_at 7.04070538523594
10008_at 3.69268761460069
100093630_at 8.55286938280969
100093698_at 2.67953894271065
10009_at 6.57929826165213
1000_at 8.69280111129203
100101467_at 6.35779261745171
100101938_at 3.30813617023795
10010_at 6.58912902596018

Total number of rows: 20408

Table truncated, full table size 521 Kbytes.

Supplementary file Size Download File type/resource
GSM5121299_RB01_ARN0011_s1h1s1_U133p2.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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