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Sample GSM1094226 Query DataSets for GSM1094226
Status Public on Dec 31, 2017
Title DAC-treated nonviral 7F Adult fibroblast iPSC clone 6.6 p17
Sample type RNA
 
Channel 1
Source name DAC-treated fF_iPSC-6.6-7FE p17
Organism Homo sapiens
Characteristics cell type: fF_iPSC-6.6-7FE p17
passage: p17
sample type: non-integrated fetal Fibroblast iPSC generated in the Zambidis laboratory
treatment: 5 micromolar 5-AZA (DAC) for 96 hours
Extracted molecule total RNA
Extraction protocol Trizol extraction based on the manufacturer's instructions, followed by RNeasy cleanup as per the manufacturer's instructions.
Label Cy5
Label protocol Agilent low RNA input linear amplification kit.
 
Channel 2
Source name Control-treated fF_iPSC-6.6-7FE p17
Organism Homo sapiens
Characteristics cell type: fF_iPSC-6.6-7FE p17
passage: p17
sample type: non-integrated fetal Fibroblast iPSC generated in the Zambidis laboratory
treatment: 1x PBS for 96 hours
Extracted molecule total RNA
Extraction protocol Trizol extraction based on the manufacturer's instructions, followed by RNeasy cleanup as per the manufacturer's instructions.
Label Cy3
Label protocol Agilent low RNA input linear amplification kit.
 
 
Hybridization protocol Agilent Gene Expression Hybridization Kit using the manufacturer's protocol.
Scan protocol Microarrays are scanned with the Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays.
Description Individual sample
Data processing Loess normalization as implemented in the Limma package from Bioconductor.
 
Submission date Mar 07, 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 GPL4133
Series (2)
GSE44941 Cancer-related epigenome changes among induced pluripotent stem cell lines
GSE82233 Quality of reprogramming to induced pluripotency as a function of reprogramming method

Data table header descriptions
ID_REF
VALUE Log2 ratio of Cy5/Cy3

Data table
ID_REF VALUE
1 0.080607247
2 0.228000258
3 -0.139791689
4 0.131690308
5 0.059729979
6 0.154438373
7 0.149548897
8 0.123419499
9 0.077215324
10 -0.044399842
11 -0.193157702
12 1.190355361
13 0.104078218
14 0.303564626
15 -0.179536123
16 -0.131432617
17 -0.214712652
18 -1.071256509
19 -0.167595407
20 0.424771318

Total number of rows: 45220

Table truncated, full table size 799 Kbytes.




Supplementary file Size Download File type/resource
GSM1094226_jhu_251485061919_S01_GE2_107_Sep09_1_3_6.6_iPS-P12+5_DAC-Cy5_6.6_iPS-P12+5_untreated-Cy3.txt.gz 15.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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