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Sample GSM3496055 Query DataSets for GSM3496055
Status Public on Jan 21, 2019
Title OCI-P5X miR-181a low-n2
Sample type RNA
 
Source name OCI-P5X miR-181a low
Organism Homo sapiens
Characteristics cell line: high-grade serous ovarian carcinoma (HGSOC) cell line
cell line: OCI-P5X miR-181a low
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cell lysates of OCI-P5X miR-181a high and OCI-P5X miR-181a low cells in triplicate and submitted for Microarray using Affymetrix Human Clariom S array and the WT Plus chemistry.
Label biotin
Label protocol In brief, for the WT Plus assay, 150ng of total RNA was labeled using a reverse transcription priming method to prime the entire length of each RNA transcript, including both polyA and non-polyA mRNA to provide complete and un­biased trans­criptome coverage. This protocol efficiently generated amplified and biotiny­lated sense-stranded DNA targets, avoiding loss of specificity due to antisense strand interference. Data was check for quality before being assessed on the Affymetrix Clariom S Human MicroArray. Changes in mRNA expression were then identified us­ing the Clariom S Human MicroArray. On this array expression for each gene was assessed by approximately 11 probes, which were tiled throughout the transcript. The array provides basic gene level coverage of known genes.
 
Hybridization protocol Labeled samples were hybridized to the arrays overnight in a rotating Hybridization Oven.
Scan protocol Arrays were stained and washed in Affymetrix FS45U Fluidics Stations according to Affymetrix automated procedures.
Description dif-a18005.dif-a1-10.rma-gene-full-Signal
Data processing Data is collected using the GC3000 scanner with autoloader. The Clariom S Assays for the microarray data were downloaded. The data was pre-processed with RMA (Robust multichip average algorithm) using the R/Bioconductor package Oligo (42) where background subtraction, quantile normalization, and summarization (via median-polish) was accomplished.
 
Submission date Nov 29, 2018
Last update date Jan 21, 2019
Contact name Analisa DiFeo
E-mail(s) adifeo@med.umich.edu
Organization name The University of Michigan
Department Pathology
Street address 1600 Huron Parkway
City Ann Arbor
State/province MI
ZIP/Postal code 48105
Country USA
 
Platform ID GPL23159
Series (1)
GSE123121 A miRNA-mediated approach to dissect the complexity of tumor-initiating cell function and identify miRNA-targeting drugs

Data table header descriptions
ID_REF
VALUE normalized

Data table
ID_REF VALUE
TC0100006437.hg.1 15.35641
TC0100006476.hg.1 110.2848
TC0100006479.hg.1 136.0045
TC0100006480.hg.1 88.77991
TC0100006483.hg.1 93.66927
TC0100006486.hg.1 199.7075
TC0100006490.hg.1 34.80578
TC0100006492.hg.1 68.00227
TC0100006494.hg.1 274.6038
TC0100006497.hg.1 55.25474
TC0100006499.hg.1 181.3887
TC0100006501.hg.1 209.9495
TC0100006502.hg.1 20.16249
TC0100006514.hg.1 46.313
TC0100006516.hg.1 107.0565
TC0100006517.hg.1 14.78291
TC0100006524.hg.1 106.6507
TC0100006540.hg.1 25.38568
TC0100006548.hg.1 22.83358
TC0100006550.hg.1 34.86395

Total number of rows: 24351

Table truncated, full table size 659 Kbytes.




Supplementary file Size Download File type/resource
GSM3496055_dif-a18005.CEL.gz 1.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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