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Sample GSM3227636 Query DataSets for GSM3227636
Status Public on Jun 18, 2019
Title MM.263: MM at diagnosis, sample 29
Sample type RNA
 
Source name Highly purified PCs from MM patient
Organism Homo sapiens
Characteristics tissue: Bone marrow plasma cells
diagnosis: Multiple myeloma (MM)
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
Relations
Alternative to GSM2932352

Data table header descriptions
ID_REF
VALUE RMA-normalized log2 signal

Data table
ID_REF VALUE
ENSG00000000003.14 9.417295822
ENSG00000000005.5 3.550667407
ENSG00000000419.12 10.91430749
ENSG00000000457.13 8.912065302
ENSG00000000460.16 6.763204925
ENSG00000000938.12 6.314933383
ENSG00000000971.15 7.0247972
ENSG00000001036.13 8.642642115
ENSG00000001084.10 7.560830499
ENSG00000001167.14 9.786461255
ENSG00000001460.17 6.874579669
ENSG00000001461.16 7.770741774
ENSG00000001497.16 8.38855067
ENSG00000001561.6 8.526198362
ENSG00000001617.11 6.693419548
ENSG00000001626.14 2.998224627
ENSG00000001629.9 10.16340696
ENSG00000001630.15 6.086607987
ENSG00000001631.15 9.999026885
ENSG00000002016.17 7.798240448

Total number of rows: 35458

Table truncated, full table size 1046 Kbytes.




Supplementary file Size Download File type/resource
GSM3227636_MM.263.CEL.gz 8.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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