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Sample GSM1644866 Query DataSets for GSM1644866
Status Public on Sep 29, 2016
Title Human Induced Pluripotent Stem Cells (iPSCs) [NHDF-iPS(S)-rep 1]
Sample type RNA
 
Channel 1
Source name HiPSC-NHDF(S)
Organism Homo sapiens
Characteristics cell line: NHDF-iPS(S)
gender: Male
Treatment protocol The cells were cultured in normal condition and were collected for microarray untill they were 70% confluency.
Growth protocol Human ESCs and iPSCs were maintained on Matrigel (growth-factor-reduced; BD Biosciences)-coated plates with mTeSR1 (Stemcell Technologies) according to Wicell protocols. Cells were passaged every 4-5 days at ~80% confluence by using 0.02% EDTA (Versene). The NSCs were maintained on Poly-L-ornithine/ Laminin (Sigma) coated flasks with the N2B27 medium containing: DMEM/F12, N2 supplement (1:100), B27 supplement (1:50, Invitrogen), 100 mM nonessential amino acids (Invitrogen) plus 10 ng/mL FGF2 (R&D Systems), 10 ng/mL EGF (R&D Systems). The cells were passaged every 4-6 days at ~90% confluence by using Accutase. All NSCs used in this study were between passage 6-10.
Extracted molecule total RNA
Extraction protocol Total RNA isolated was done using the ReliaPrep™ RNA Cell Minprep System (Promega);
Label Cy3
Label protocol The total RNA were labled with Cy3 (Samples) or Cy5 (References) by following the protocol of Two-Color Microarray-Based Gene Expression Analysis from Agilent.
 
Channel 2
Source name Pooled Agilent's Universal Human Reference RNA
Organism Homo sapiens
Characteristics cell lines: mixture of 10 human cell lines
reference: Pooled Agilent's Universal Human Reference RNA, catalog#740000
Treatment protocol The cells were cultured in normal condition and were collected for microarray untill they were 70% confluency.
Growth protocol Human ESCs and iPSCs were maintained on Matrigel (growth-factor-reduced; BD Biosciences)-coated plates with mTeSR1 (Stemcell Technologies) according to Wicell protocols. Cells were passaged every 4-5 days at ~80% confluence by using 0.02% EDTA (Versene). The NSCs were maintained on Poly-L-ornithine/ Laminin (Sigma) coated flasks with the N2B27 medium containing: DMEM/F12, N2 supplement (1:100), B27 supplement (1:50, Invitrogen), 100 mM nonessential amino acids (Invitrogen) plus 10 ng/mL FGF2 (R&D Systems), 10 ng/mL EGF (R&D Systems). The cells were passaged every 4-6 days at ~90% confluence by using Accutase. All NSCs used in this study were between passage 6-10.
Extracted molecule total RNA
Extraction protocol Total RNA isolated was done using the ReliaPrep™ RNA Cell Minprep System (Promega);
Label Cy5
Label protocol The total RNA were labled with Cy3 (Samples) or Cy5 (References) by following the protocol of Two-Color Microarray-Based Gene Expression Analysis from Agilent.
 
 
Hybridization protocol Oligoarray control targets and hybridization buffer (Agilent Gene Expression Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent Microarray Hybridization Chambers. After hybridization, slides were washed sequential
Scan protocol Scanned on a Agilent C Scanner
Description Biological replicate 1 of 2. Human iPSCs-NHDF(S).
Data processing Agilent Feature Extraction (FE) software was used for background subtraction and LOWESS normalization.
 
Submission date Mar 26, 2015
Last update date Apr 23, 2018
Contact name LILI ZHU
E-mail(s) lili.zhu@ncl.ac.uk
Phone +441912418817
Organization name Newcastle University
Street address Central Parkway
City Newcastle upon Tyne
State/province ----
ZIP/Postal code NE1 3 BZ
Country United Kingdom
 
Platform ID GPL17077
Series (1)
GSE67325 Human ESCs vs Human iPSCs & Human NSCs-ES vs Human NSCs-iPS
Relations
Reanalyzed by GSE113533

Data table header descriptions
ID_REF
VALUE normalized log10 ratio (Cy3/Cy5) representing test/reference

Data table
ID_REF VALUE
A_23_P117082 0.70650285
A_33_P3246448 5.6756167
A_33_P3318220 -0.2593567
A_33_P3236322 -1.2723081
A_33_P3319925 -1.0097628
A_21_P0000509 2.5609074
A_21_P0000744 1.9603491
A_24_P215804 1.2160379
A_23_P110167 2.3934917
A_33_P3211513 0.7670065
A_23_P103349 0.21544991
A_32_P61480 -0.24104986
A_33_P3788124 -4.63861
A_33_P3414202 3.4311028
A_33_P3316686 -0.41216847
A_33_P3300975 6.477524
A_33_P3263061 0.28142068
A_33_P3261373 -0.22824427
A_24_P278460 -0.8856821
A_21_P0013109 -0.22375053

Total number of rows: 50737

Table truncated, full table size 1220 Kbytes.




Supplementary file Size Download File type/resource
GSM1644866_NHDF-iPSC_S_-Rep1.txt.gz 21.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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