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Sample GSM2038688 Query DataSets for GSM2038688
Status Public on Feb 22, 2016
Title Pr-mHSC, rep 3
Sample type RNA
 
Source name Pr-mHSC
Organism Mus musculus
Characteristics strain/background: Balb/c AnNCrl
cell type: primary myofibroblasts derived from hepatic stellate cells
reprogrammed: no
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 3
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
E-mail(s) mararabra@yahoo.co.uk
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
ID_REF
VALUE Quantile-normalized log2 value

Data table
ID_REF VALUE
(-)3xSLv1 1.109317
A_51_P100034 9.755650
A_51_P100174 7.106482
A_51_P100208 4.537335
A_51_P100289 11.599946
A_51_P100298 6.138112
A_51_P100309 2.287593
A_51_P100327 8.088575
A_51_P100347 1.547453
A_51_P100519 0.984024
A_51_P100537 2.227273
A_51_P100573 9.416107
A_51_P100624 0.879752
A_51_P100625 2.405706
A_51_P100768 0.796744
A_51_P100776 3.925703
A_51_P100787 11.675959
A_51_P100828 12.938611
A_51_P100852 4.582707
A_51_P100991 5.293948

Total number of rows: 39430

Table truncated, full table size 879 Kbytes.




Supplementary file Size Download File type/resource
GSM2038688_Pr-mHSC-rep3.txt.gz 9.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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