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Sample GSM1084903 Query DataSets for GSM1084903
Status Public on Dec 31, 2017
Title viral fibroblast iPSC line IMR90-1
Sample type RNA
 
Source name viral fibroblast iPSC clone iPS(IMR90)-1
Organism Homo sapiens
Characteristics cell type: viral fibroblast iPSC clone iPS(IMR90)-1
passage: p63
sample type: Obtained from WiCell (Madison, WI). Originally derived in Yu et al. Science 318:1917-1920. 1997.
Extracted molecule total RNA
Extraction protocol Total RNA was prepared as described in the miRNeasy Mini Kit (Qiagen) with on-column DNase I digestion.
Label Cy3
Label protocol 150 ng total RNA from each sample was labeled using the miRNA Labeling Reagent & Hybridization Kit (Agilent Technologies, Santa Clara, CA) as described in the instruction manual.
 
Hybridization protocol All arrays were hybridized at 55ºC for 20 hours followed by wash procedure according to the miRNA Microarray System Protocol, Version 1.5, December 2007 (Agilent Technologies).
Scan protocol Fluorescent signals were obtained by scanning with an Agilent scanner controlled by Agilent Scan Control 7.0 software.
Description Individual sample
Data processing Data were acquired with Agilent Feature Extraction 9.5.3.1 software for miRNA microarray. MicroRNA Expression data were extracted from Agilent miRNA Kits by Agilent Feature Extraction software and then Partek and Spotfire were employed for their normalization and analysis. The fluorescent signal data were imported into Partek where duplicate probe information was merged and were then normalized to the 75th percentile. The 75th percentile normalization process is similar to median normalization, above, except that each gene’s 75th percentile value is subtracted rather than its median. (Agilent recommends the 75th percentile based on the observation that about half the microRNAs are not expressed, so the 75th percentile is near the median for those that are).
 
Submission date Feb 20, 2013
Last update date Dec 31, 2017
Contact name Elias Thomas Zambidis
Organization name Johns Hopkins School of Medicine
Department Oncology
Street address 733 N. Broadway
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platform ID GPL10850
Series (2)
GSE44423 Microarray global microRNA expression of donor cells, fibroblast-derived iPSC, and stromal-primed cord-blood iPSC
GSE82233 Quality of reprogramming to induced pluripotency as a function of reprogramming method

Data table header descriptions
ID_REF
VALUE 75th percentile normalized signal values

Data table
ID_REF VALUE
hsa-miR-720 134.061
hsa-miR-587 0.928889
hsa-miR-1236 0.994815
hsa-miR-607 0.920741
hsa-miR-1253 0.92
hsa-miR-369-3p 0.922222
hsa-miR-657 0.931852
hsa-miR-526b 1.1363
hsa-miR-515-3p 1.18667
hsa-miR-586 0.942222
hsa-miR-485-5p 0.917778
hsa-miR-507 0.908148
hsa-miR-551b* 0.917037
hsa-miR-326 0.907407
hsa-miR-146b-3p 0.954074
hsa-miR-1283 0.894074
hsa-miR-622 1.03926
hsa-miR-556-5p 0.907407
hsa-miR-708* 0.897037
hsa-miR-555 0.922963

Total number of rows: 851

Table truncated, full table size 17 Kbytes.




Supplementary file Size Download File type/resource
GSM1084903_jhu_252182712308_S01_miRNA_107_Sep09_1_4_IMR1.txt.gz 1.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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