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Sample GSM3271444 Query DataSets for GSM3271444
Status Public on Feb 27, 2019
Title MM at diagnosis, sample 3
Sample type RNA
Source name Highly purified PCs from MM patient
Organism Homo sapiens
Characteristics tissue: Bone marrow plasma cells
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 500 ng of total RNA were converted to biotin-labeled RNA using the FlashTag Biotin HSR Labeling kit, according to Affimetrix protocol
Hybridization protocol Byotin-labeled RNA samples were hybridized for 16 hours at 48°C on GeneChip miRNA 3.0 array, according to the standard manifacturer's 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.
Description hyperdiploid karyotype
Data processing Raw data were extracted from CEL files and then normalized using robust multi-array average (RMA) procedure in the affy package for Bioconductor and the miRbase Release 21 annotations included in the corresponding cdf definition files available at the University of Michigan Brainarray portal at Annotations were referred to miRBase Release 21 definition.
Submission date Jul 13, 2018
Last update date Feb 27, 2019
Contact name Luca Agnelli
Phone +390223903581
Organization name IRCCS Istituto Nazionale dei Tumori
Department Department of Advanced Diagnostics
Street address Venezian 1
ZIP/Postal code 20133
Country Italy
Platform ID GPL25329
Series (2)
GSE117113 New and subgroup-specific miRNAs and miRNA-offset RNA unraveled by RNA-sequencing in multiple myeloma [array]
GSE117366 New and subgroup-specific miRNAs and miRNA-offset RNA unraveled by RNA-sequencing in multiple myeloma
Reanalysis of GSM2341437

Data table header descriptions
VALUE RMA-normalized log2 signal

Data table
HAIRPIN_hsa-let-7a-1_at 10.61086076
HAIRPIN_hsa-let-7a-2_at 10.8110059
HAIRPIN_hsa-let-7a-3_at 10.6522133
HAIRPIN_hsa-let-7b_at 12.08284349
HAIRPIN_hsa-let-7c_at 9.909337666
HAIRPIN_hsa-let-7d_at 11.11566311
HAIRPIN_hsa-let-7e_at 5.60008914
HAIRPIN_hsa-let-7f-1_at 7.064754729
HAIRPIN_hsa-let-7f-2_at 7.282629927
HAIRPIN_hsa-let-7g_at 9.104911526
HAIRPIN_hsa-let-7i_at 10.2413874
HAIRPIN_hsa-mir-1-1_at 1.564878752
HAIRPIN_hsa-mir-1-2_at 1.564135767
HAIRPIN_hsa-mir-100_at 2.41567266
HAIRPIN_hsa-mir-101-1_at 2.179725666
HAIRPIN_hsa-mir-101-2_at 2.508540139
HAIRPIN_hsa-mir-103a-1_at 11.27064888
HAIRPIN_hsa-mir-103a-2_at 11.27026953
HAIRPIN_hsa-mir-103b-1_at 11.27979119
HAIRPIN_hsa-mir-103b-2_at 11.27342173

Total number of rows: 3204

Table truncated, full table size 113 Kbytes.

Supplementary file Size Download File type/resource
GSM3271444_GSM2341437_mirMM.030.CEL.gz 805.5 Kb (ftp)(http) CEL
Processed data included within Sample table

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