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Sample GSM2038695 Query DataSets for GSM2038695
Status Public on Feb 22, 2016
Title In-vitro iHep mHSC, rep 1
Sample type RNA
Source name In-vitro iHep mHSC
Organism Mus musculus
Characteristics strain/background: Balb/c AnNCrl
cell type: in-vitro myofibroblasts-derived induced hepatocytes
reprogrammed: yes
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the cells.
Label Alexa Fluor 555
Label protocol 100 ng of total DNA-free RNA was used as input to prepare the aminoallyl-UTP-modified (aaUTP) cRNAs (Amino Allyl MessageAmp II Kit, #AM1753, Life Technologies) as directed by the company. The aaUTP-cRNAs were labelled with Alexa Fluor 555 Reactive Dye (#A32756, LifeTechnologies). Prior to the reverse transcription reaction, 1μl of a 1:5000 dilution of Agilent's One-Color spike-in Kit stock solution (#5188-5282, Agilent Technologies) was added to 100ng of total RNA of each analyzed sample.
Hybridization protocol The cRNA fragmentation, hybridization, and washing steps were carried out according to Agilent's One-Color Microarray-Based Gene Expression Analysis Protocol V5.7 except that 500ng of each labelled cRNA sample were used for hybridization.
Scan protocol Slides were scanned on the Agilent Micro Array Scanner G2565 CA (pixel resolution 5 micrometers, bit depth 20). Data extraction was performed with the Feature Extraction Software V10.7.3.1.
Description Replicate 1
Data processing Variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the quantile method implemented in the lumi package of R-Bioconductor. Data post-processing and graphics were performed with in-house developed functions in MATLAB. Hierarchical clusters of genes and samples were performed with the one minus the sample correlation metric and the Unweighted Pair-Group Method using Average (UPGMA) linkage method.
Submission date Jan 13, 2016
Last update date Jan 15, 2022
Contact name Marcos J. Araúzo-Bravo
Phone +34 943 00 6108
Organization name Max Planck Institute for Molecular Biomedicine
Department Cell and Developmental Biology
Lab Computational Biology and Bionformatics
Street address Rogentstrasse
City Muenster
ZIP/Postal code 48149
Country Germany
Platform ID GPL11202
Series (1)
GSE76843 Direct reprogramming of hepatic myofibroblasts into hepatocytes in vivo attenuates liver fibrosis

Data table header descriptions
VALUE Quantile-normalized log2 value

Data table
(-)3xSLv1 1.007858
A_51_P100034 11.666333
A_51_P100174 6.069346
A_51_P100208 4.386827
A_51_P100289 10.441360
A_51_P100298 6.184216
A_51_P100309 1.973766
A_51_P100327 8.910256
A_51_P100347 1.367625
A_51_P100519 0.964834
A_51_P100537 2.149017
A_51_P100573 9.399907
A_51_P100624 0.900022
A_51_P100625 2.698180
A_51_P100768 0.785653
A_51_P100776 3.571269
A_51_P100787 11.781539
A_51_P100828 13.300719
A_51_P100852 5.215697
A_51_P100991 6.182103

Total number of rows: 39430

Table truncated, full table size 878 Kbytes.

Supplementary file Size Download File type/resource
GSM2038695_iHep_mHSC-rep1.txt.gz 9.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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