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Sample GSM1094235 Query DataSets for GSM1094235
Status Public on Dec 31, 2017
Title TSA-treated nonviral 7F stromal primed cord blood iPSC clone 19.11 p25
Sample type RNA
 
Channel 1
Source name TSA-treated sp-CB_iPSC-19.11-7FE p25
Organism Homo sapiens
Characteristics cell type: sp-CB_iPSC-19.11-7FE p25
passage: p25
sample type: non-integrated stromal primed cord blood iPSC generated in the Zambidis laboratory
treatment: 300 nanomolar TSA for 18 hour
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 sp-CB_iPSC-19.11-7FE p25
Organism Homo sapiens
Characteristics cell type: sp-CB_iPSC-19.11-7FE p25
passage: p25
sample type: non-integrated stromal primed cord blood 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 0.634228511
2 0.10372655
3 -0.01115859
4 0.147527549
5 0.110849062
6 0.147527549
7 0.072817638
8 0.11638165
9 0.102032192
10 -0.100252245
11 0.151837012
12 0.247886932
13 0.244837346
14 0.180071434
15 -0.186107392
16 0.575728537
17 -0.080623962
18 -0.132687854
19 0.186895827
20 -0.087427232

Total number of rows: 45220

Table truncated, full table size 799 Kbytes.




Supplementary file Size Download File type/resource
GSM1094235_jhu_251485058514_S01_GE2_107_Sep09_1_2_19.11-P25_TSA-Cy5_19.11-P25_untreated-Cy3.txt.gz 15.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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