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Sample GSM3271446 Query DataSets for GSM3271446
Status Public on Feb 27, 2019
Title MM at diagnosis, sample 5
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 http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/21.0.0/version.html). Annotations were referred to miRBase Release 21 definition.
 
Submission date Jul 13, 2018
Last update date Feb 27, 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 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
Relations
Reanalysis of GSM2341442

Data table header descriptions
ID_REF
VALUE RMA-normalized log2 signal

Data table
ID_REF VALUE
HAIRPIN_hsa-let-7a-1_at 10.90779495
HAIRPIN_hsa-let-7a-2_at 11.09081155
HAIRPIN_hsa-let-7a-3_at 10.94826098
HAIRPIN_hsa-let-7b_at 10.20422322
HAIRPIN_hsa-let-7c_at 9.348524289
HAIRPIN_hsa-let-7d_at 10.4358555
HAIRPIN_hsa-let-7e_at 4.858112955
HAIRPIN_hsa-let-7f-1_at 7.63584939
HAIRPIN_hsa-let-7f-2_at 7.634229248
HAIRPIN_hsa-let-7g_at 8.676155552
HAIRPIN_hsa-let-7i_at 9.255769149
HAIRPIN_hsa-mir-1-1_at 1.556752194
HAIRPIN_hsa-mir-1-2_at 1.555082823
HAIRPIN_hsa-mir-100_at 2.049801398
HAIRPIN_hsa-mir-101-1_at 2.029609829
HAIRPIN_hsa-mir-101-2_at 2.262928965
HAIRPIN_hsa-mir-103a-1_at 11.39067129
HAIRPIN_hsa-mir-103a-2_at 11.3926406
HAIRPIN_hsa-mir-103b-1_at 11.40234599
HAIRPIN_hsa-mir-103b-2_at 11.3974515

Total number of rows: 3204

Table truncated, full table size 113 Kbytes.




Supplementary file Size Download File type/resource
GSM3271446_GSM2341442_mirMM.040.CEL.gz 826.5 Kb (ftp)(http) CEL
Processed data included within Sample table

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