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Sample GSM1133426 Query DataSets for GSM1133426
Status Public on Jul 01, 2013
Title E9.5_mouse_liver
Sample type RNA
Source name Liver cells from E9.5 mice
Organism Mus musculus
Characteristics tissue: CD45- Ter119- liver cells
gender: pooled
age: E9.5
Extracted molecule total RNA
Extraction protocol RNA was prepared using the RNeasy Mini Purification kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent High-Resolution Microarray Scanner using one color scan setting for 4x44k v2 array slides.
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
The raw signal intensities of samples were log2-transformed and normalised by the quantile algorithm.
(A total of 16,523 orthologs across the human 4x44K v.2 Agilent oligonucleotide array, and the mouse 4x44K v.2 Agilent oligonucleotide array.)
Submission date May 03, 2013
Last update date Jul 01, 2013
Contact name Yasuharu Ueno
Phone +81-45-787-8963
Fax +81-45-787-8963
Organization name Yokohama City University
Department Graduate School of Medicine
Lab Department of Regenerative Medicine
Street address 3-9 Fuku-ura, Kanazawa-ku
City Yokohama City
State/province Kanagawa
ZIP/Postal code 236-0004
Country Japan
Platform ID GPL11202
Series (1)
GSE46631 Vascularised and functional human liver from an iPSC-derived organ bud transplant

Supplementary file Size Download File type/resource
GSM1133426_mE9.5_raw.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data are available on Series record

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