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Sample GSM3609501 Query DataSets for GSM3609501
Status Public on Jun 30, 2021
Title CLLCCAID2810
Sample type RNA
 
Source name peripheral blood mononuclear cells
Organism Homo sapiens
Characteristics disease state: chronic lymphocytic leukaemia
prognostic association with gep signature: indolent GEP signature
antibody pretreatment: Rituximab-naive
sensitivity to chemotherapy: Fludarabine untreated/sensitive
ecog: ECOG≤1
clinical course: intermediate/late progression
Treatment protocol Ficoll density gradient centrifugation for isolation of mononuclear cells with or without subsequent immunomagnetic tumor cell enrichment via CD19.
Growth protocol Peripheral blood mononuclear cells were collected from CLL patients before initiation of treatment on randomized trial with fludarabine and cyclophosphomide +/- rituximab.
Extracted molecule total RNA
Extraction protocol Total RNA for mRNA profiling was extracted from whole cell lysates of CLL patient samples according to the Allprep DNA/RNA mini kit (Qiagen). Quality control was assessed using the Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip (Agilent Technologies). RNA for gene expression profiling had a RIN of at least 7.
Label Biotin
Label protocol Samples from CLL patients were analyzed for mRNA expression using the Affymetrix GeneChip® Human Exon 1.0 ST Array (Affymetrix, Santa Clara, CA, USA). The experiment was conducted according to the manufacturer’s protocol. In brief, 250 ng RNA per sample were amplified, transcribed to cDNA, fragmented and subsequently labeled with Biotin.
 
Hybridization protocol Array hybridization was performed at 45°C for 16-18h in the Affymetrix GeneChip® Hybridization Oven 640, arrays were subsequently washed in the Fluidics Station 450.
Scan protocol Arrays were scanned on the GeneChip scanner 3000 7G.
Description Gene expression data from CLL sample
Data processing Raw Affymetrix Human Exon array (HuEx-1_0-st-v2) data files have been normalized using the RMA algorithm using aroma.affymetrix
 
Submission date Feb 14, 2019
Last update date Feb 13, 2023
Contact name Johannes Bloehdorn
E-mail(s) johannes.bloehdorn@gmail.com
Organization name University of Ulm
Street address Albert-Einstein-Allee 23
City Ulm
ZIP/Postal code 89081
Country Germany
 
Platform ID GPL5175
Series (1)
GSE126595 Expression data from CLL patient samples investigated to define biologic heterogeneity.

Data table header descriptions
ID_REF
VALUE log2, RMA normalized

Data table
ID_REF VALUE
2315554 6.437073
2315633 6.579123
2315674 6.606695
2315739 6.426653
2315894 8.885337
2315918 5.677989
2315951 8.607189
2316218 5.697323
2316245 6.885023
2316379 8.664142
2316558 7.859574
2316605 6.415094
2316746 6.893296
2316905 6.411932
2316953 6.429954
2317246 6.143197
2317317 6.259344
2317434 7.596094
2317472 5.817818
2317512 5.619019

Total number of rows: 22011

Table truncated, full table size 363 Kbytes.




Supplementary file Size Download File type/resource
GSM3609501_CLLCCAID2810S14711000000900512017.CEL.gz 21.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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