NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3271450 Query DataSets for GSM3271450
Status Public on Feb 27, 2019
Title MM at diagnosis, sample 9
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 no information about hyperdiploid status, no major IgH (14q32) chromosomal translocations
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 GSM2341449

Data table header descriptions
ID_REF
VALUE RMA-normalized log2 signal

Data table
ID_REF VALUE
HAIRPIN_hsa-let-7a-1_at 11.33603899
HAIRPIN_hsa-let-7a-2_at 11.63317801
HAIRPIN_hsa-let-7a-3_at 11.43097184
HAIRPIN_hsa-let-7b_at 11.97530304
HAIRPIN_hsa-let-7c_at 11.01182428
HAIRPIN_hsa-let-7d_at 11.35765428
HAIRPIN_hsa-let-7e_at 6.159208878
HAIRPIN_hsa-let-7f-1_at 8.791347272
HAIRPIN_hsa-let-7f-2_at 8.727186741
HAIRPIN_hsa-let-7g_at 9.775922481
HAIRPIN_hsa-let-7i_at 10.87805333
HAIRPIN_hsa-mir-1-1_at 1.585089793
HAIRPIN_hsa-mir-1-2_at 1.598302947
HAIRPIN_hsa-mir-100_at 7.482611046
HAIRPIN_hsa-mir-101-1_at 2.223881226
HAIRPIN_hsa-mir-101-2_at 2.580483285
HAIRPIN_hsa-mir-103a-1_at 10.78015384
HAIRPIN_hsa-mir-103a-2_at 10.79131288
HAIRPIN_hsa-mir-103b-1_at 10.79663519
HAIRPIN_hsa-mir-103b-2_at 10.79625655

Total number of rows: 3204

Table truncated, full table size 113 Kbytes.




Supplementary file Size Download File type/resource
GSM3271450_GSM2341449_mirMM.056.CEL.gz 813.6 Kb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap