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Sample GSM2038696 Query DataSets for GSM2038696
Status Public on Feb 22, 2016
Title In-vitro iHep mHSC, rep 2
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 2
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 1.240687
A_51_P100034 10.825695
A_51_P100174 7.006640
A_51_P100208 5.382987
A_51_P100289 10.649382
A_51_P100298 5.564788
A_51_P100309 2.588874
A_51_P100327 8.798812
A_51_P100347 0.963380
A_51_P100519 1.059435
A_51_P100537 1.741207
A_51_P100573 8.881817
A_51_P100624 0.854029
A_51_P100625 4.118918
A_51_P100768 0.796087
A_51_P100776 3.982398
A_51_P100787 12.000510
A_51_P100828 13.105628
A_51_P100852 5.610424
A_51_P100991 5.868149

Total number of rows: 39430

Table truncated, full table size 878 Kbytes.

Supplementary file Size Download File type/resource
GSM2038696_iHep_mHSC-rep2.txt.gz 9.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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