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Sample GSM4042357 Query DataSets for GSM4042357
Status Public on Aug 23, 2019
Title CP-44_miRNA
Sample type RNA
 
Source name Colorectal tissue
Organism Homo sapiens
Characteristics tissue: colorectal carcinomas
age: 75
Sex: male
tumor type: Conventional Carcinoma
Treatment protocol The clinico-pathological features of the patients have been previously reported. Updated follow-up information was obtained from cancer registry files and approval for the study was granted by the Local Ethical Board. SACs were diagnosed on the basis of criteria proposed by Mäkinen et al., and hmMSI-Hs according to prior established criteria (mucinous, signet-ring cell, and medullary carcinoma, tumor infiltrating and peritumoral lymphocytes, “Crohn-like” inflammatory response, poor differentiation, tumor heterogeneity, and “pushing” tumor border) and later cofirm using MSI-H testing (MSI Analysis System, version 1.2 provided by Promega (Madison, USA)).
Extracted molecule total RNA
Extraction protocol A volume of approximately 10mm3 was extracted from each frozen tissue using the disposable sterile biopsy punch Acupunch 2mm (Acuderm Inc, Lauderdale, FL, USA). RNA was extracted following the manufacturer´s instructions (Qiagen, Hilden, Germany). Briefly, tissue was disrupted and homogenized in 700µl of Qiazol (Qiagen ref:1023537) using a Tissueruptor by Qiagen for 20 seconds. The homogenate was incubated at room temperature for 5 minutes. After adding 140µl of chloroform and centrifuging at 12,000xg for 15 minutes at 4ºC, 350µl of the aqueous phase was subjected to automatic total RNA extraction using the Qiacube equipment and the miRNeasy Mini Kit (ref:217004), both provided by Qiagen.
Label biotin
Label protocol Total RNA was quantified by spectrometry (NanoDrop ND1000, NanoDrop Technologies, Wilminton, Delaware USA) and quality confirmed by RNA 6000 Nano Bioanalyzer (Agilent Technologies, Palo Alto, California USA) assay. Using NanoDrop measurements, an approximately 50 ng/ul dilution was prepared from each total RNA sample. All steps of the procedure were performed according to the Affymetrix standardized protocol for miRNA 3.0 arrays.
 
Hybridization protocol All steps of the procedure were performed according to the Affymetrix standardized protocol for miRNA 3.0 arrays.
Scan protocol All steps of the procedure were performed according to the Affymetrix standardized protocol for miRNA 3.0 arrays.
Description miRNA
Data processing The Affymetrix raw data were normalized using the robust multichip average algorithm from ‘oligo’ Bioconductor package in R version 3.0.1. Normalized miRNA expression data were evaluated using Bioconductor LIMMA differential expression analysis.
 
Submission date Aug 22, 2019
Last update date Aug 23, 2019
Contact name Angel Esteban-Gil
E-mail(s) angel.esteban@ffis.es
Phone +34868885229
Organization name Institute for Biomedical Research of Murcia (IMIB)
Department Biomedical Informatics and Bioinformatics Platform
Street address Campus de Ciencias de la Salud Carretera Buenavista s/n
City Murcia
State/province Murcia
ZIP/Postal code 30120
Country Spain
 
Platform ID GPL16384
Series (1)
GSE136194 miRNA profiling from different histological subtypes of colorectal carcinoma

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
14q0_st 1.09040337283286
14qI-1_st 0.694939439367302
14qI-1_x_st 0.245714155554265
14qI-2_st 0.385087255928166
14qI-3_x_st 1.05891098747845
14qI-4_st 1.86501267556139
14qI-4_x_st 1.05472467315228
14qI-5_st 0.791079192919506
14qI-6_st 1.049446115903
14qI-6_x_st 0.331231101093888
14qI-7_st 2.91506568010477
14qI-8_st 1.68571026396516
14qI-8_x_st 1.15335370479621
14qI-9_x_st 0.486377927890405
14qII-1_st 7.32818041838272
14qII-1_x_st 6.70353423284939
14qII-10_st 0.85572422995393
14qII-10_x_st 0.381996682010987
14qII-11_st 0.486377927890405
14qII-11_x_st 0.519093437644262

Total number of rows: 25119

Table truncated, full table size 850 Kbytes.




Supplementary file Size Download File type/resource
GSM4042357_08B4635T_CT_miRNA-3_0_.CEL.gz 748.9 Kb (ftp)(http) CEL
Processed data included within Sample table

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