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Sample GSM1405074 Query DataSets for GSM1405074
Status Public on Jul 30, 2014
Title CD19-enriched CLL patient sample, patient #9005
Sample type RNA
 
Source name CLL clinical sample, CD19-enriched
Organism Homo sapiens
Characteristics subject status: relapsed chronic lymphocytic leukemia (CLL) patient
patient id: patient #9005
binet stage: B
tissue: CD19-enriched CLL patient sample
Treatment protocol not applicable
Growth protocol Pretreatment specimens from relapsed chronic lymphocytic leukemia patients
Extracted molecule total RNA
Extraction protocol CLL samples were positively enriched by magnetic cell sorting using CD19 microbeads and MACS columns (Miltenyi Biotec Ltd, Surrey, UK). Total RNA was isolated using Trizol (Invitrogen) and RNeasy kit (QIAGEN).
Label biotin
Label protocol Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)
 
Hybridization protocol Samples were hybridized using Affymetrix hybridization kit materials per manufacturers recommendation. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 (fluidics protocol FS450_0001).
Scan protocol Arrays were scanned using the Affymetrix GCS 3000 7G and Gene-Chip Operating Software v.1.3.0 to produce .CEL intensity files.
Description CD19-enriched CLL clinical sample
A0020412
Data processing .CEL files were background adjusted, quantile normalized and summarized at the transcript level using only core probesets that mapped to RefSeq transcripts, by apt (Affymetrix Power Tool version 1.12.0) software that used the RMA algorithm.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na29.hg18.probeset.csv
 
Submission date Jun 05, 2014
Last update date Jul 30, 2014
Contact name Ru-Fang Yeh
E-mail(s) yeh.rufang@gene.com
Organization name Genentech
Street address 1 DNA Way
City South San Francisco
State/province CA
ZIP/Postal code 94040
Country USA
 
Platform ID GPL18761
Series (1)
GSE58211 Expression data of chronic lymphocytic leukemia patient samples from the REACH study

Data table header descriptions
ID_REF
VALUE Gene-level RMA value of core probesets representing RefSeq transcripts

Data table
ID_REF VALUE
2315251 2.76837
2315554 7.05302
2315633 6.6889
2315674 6.65613
2315739 6.95736
2315894 7.90431
2315918 5.30811
2315951 7.88954
2316069 7.09022
2316218 5.68529
2316245 7.85465
2316379 8.85204
2316558 6.79425
2316605 6.63365
2316746 6.89039
2316905 5.90941
2316953 6.70957
2317246 5.7412
2317317 7.14963
2317434 7.32941

Total number of rows: 17782

Table truncated, full table size 276 Kbytes.




Supplementary file Size Download File type/resource
GSM1405074_A0020412.CEL.gz 21.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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