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Sample GSM3271469 Query DataSets for GSM3271469
Status Public on Feb 27, 2019
Title MM at diagnosis, sample 28
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 GSM2341502

Data table header descriptions
VALUE RMA-normalized log2 signal

Data table
HAIRPIN_hsa-let-7a-1_at 10.92827385
HAIRPIN_hsa-let-7a-2_at 11.15794367
HAIRPIN_hsa-let-7a-3_at 10.98343081
HAIRPIN_hsa-let-7b_at 12.63118795
HAIRPIN_hsa-let-7c_at 11.23799889
HAIRPIN_hsa-let-7d_at 11.47620187
HAIRPIN_hsa-let-7e_at 5.695485871
HAIRPIN_hsa-let-7f-1_at 7.320353856
HAIRPIN_hsa-let-7f-2_at 7.45980949
HAIRPIN_hsa-let-7g_at 8.871440258
HAIRPIN_hsa-let-7i_at 9.406927681
HAIRPIN_hsa-mir-1-1_at 1.567077769
HAIRPIN_hsa-mir-1-2_at 1.576957294
HAIRPIN_hsa-mir-100_at 7.589578181
HAIRPIN_hsa-mir-101-1_at 2.068371854
HAIRPIN_hsa-mir-101-2_at 2.34070335
HAIRPIN_hsa-mir-103a-1_at 11.06479719
HAIRPIN_hsa-mir-103a-2_at 11.05496305
HAIRPIN_hsa-mir-103b-1_at 11.07112012
HAIRPIN_hsa-mir-103b-2_at 11.05922257

Total number of rows: 3204

Table truncated, full table size 113 Kbytes.

Supplementary file Size Download File type/resource
GSM3271469_GSM2341502_mirMM.392.CEL.gz 824.1 Kb (ftp)(http) CEL
Processed data included within Sample table

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