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Sample GSM3227660 Query DataSets for GSM3227660
Status Public on Jun 18, 2019
Title PCL.013: PCL at diagnosis, sample 3
Sample type RNA
 
Source name Highly purified PCs from PCL patient
Organism Homo sapiens
Characteristics tissue: Bone marrow plasma cells
diagnosis: Plasma cell leukemia (PCL)
genotype/variation: t(4;14)
Treatment protocol Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was > 90% in all cases.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL).
Label biotin
Label protocol Biotinylated single stranded cDNA samples were prepared starting from 100-250 nanograms of total RNA, according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).
 
Hybridization protocol The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip Gene 2.0 ST array, according to the standard Affymetrix protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol Scanning of the arrays was performed using the GeneChip Scanner 7G.
Data processing Normalized expression values were obtained using Robust Multi Array Average (RMA) procedure. A custom annotation pipeline was applied that combined GENCODE v25 (Ensembl v87) annotations with the CDF (Chip Definition File) version 21 for Human GeneChip Gene 2.0 ST transcript annotations freely available at http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/ genecodet.asp, in order to withdraw probes that map to regions where ambiguous detection due to transcript overlap might occur. Only genes identified by probesets with 4 or more specifc probes within were retained. The gained CDF results a umich GENCODEG-like annotation that retains only unambiguous signals for lncRNA and coding genes that partially overlap in thier genomic position.
 
Submission date Jun 26, 2018
Last update date Jun 18, 2019
Contact name Luca Agnelli
E-mail(s) luca.agnelli@istitutotumori.mi.it, luca.agnelli@gmail.com
Phone +390223903581
Organization name IRCCS Istituto Nazionale dei Tumori
Department Department of Advanced Diagnostics
Street address Venezian 1
City MILAN
ZIP/Postal code 20133
Country Italy
 
Platform ID GPL25249
Series (1)
GSE116294 Deregulated high expression of NEAT1 lncRNA in multiple myeloma is unrelated to molecular features and clinical outcome

Data table header descriptions
ID_REF
VALUE RMA-normalized log2 signal

Data table
ID_REF VALUE
ENSG00000000003.14 4.371536128
ENSG00000000005.5 3.707609188
ENSG00000000419.12 11.86687884
ENSG00000000457.13 8.053384213
ENSG00000000460.16 6.855947334
ENSG00000000938.12 6.514561024
ENSG00000000971.15 6.509276218
ENSG00000001036.13 9.23789347
ENSG00000001084.10 9.100917094
ENSG00000001167.14 8.906117363
ENSG00000001460.17 6.979323361
ENSG00000001461.16 7.529192709
ENSG00000001497.16 9.026886671
ENSG00000001561.6 8.377814627
ENSG00000001617.11 5.974181817
ENSG00000001626.14 3.32556388
ENSG00000001629.9 11.26081133
ENSG00000001630.15 7.500104743
ENSG00000001631.15 9.618795501
ENSG00000002016.17 7.360959685

Total number of rows: 35458

Table truncated, full table size 1047 Kbytes.




Supplementary file Size Download File type/resource
GSM3227660_PCL.013.CEL.gz 8.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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