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Sample GSM2804282 Query DataSets for GSM2804282
Status Public on Apr 04, 2018
Title Hepa1c1c7_Empty
Sample type RNA
 
Source name Hepa1c1c7_Empty
Organism Mus musculus
Characteristics tissue: liver
Treatment protocol Hepa1c1c7 cells were transfected Mst1r or Slpi vector. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol RNA was prepared using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations. The protocol include an on-column DNase digestion. 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 100 ng RNA using the One-Color Low RNA Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
 
Hybridization protocol 600 ng 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 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE Ver 2.0 Microarrays (G4858A) for 17 hours at 65℃ 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℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um high sensitivity, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression of Hepa1c1c7 transfected empty vector
Data processing The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Oct 05, 2017
Last update date Apr 04, 2018
Contact name Keiko Nohara
E-mail(s) keikon@nies.go.jp
Phone 81-29-850-2500
Organization name National Institute for Environmental Studies
Department Center for Health and Environmental Risk Research
Street address 16-2 Onogawa
City Tsukuba
ZIP/Postal code 305-8506
Country Japan
 
Platform ID GPL21163
Series (1)
GSE104626 Gene expression profiling in Hepa1c1c7 transfected Mst1r or Slpi

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 9993.63
ETG10_236652 4.14
ETG10_234183 5.61
ETG10_195139 4.11
ETG10_13482 4.10
ETG09_48764 4.14
ETG09_35454 12.41
ETG09_205211 4.12
ETG08_142674 4.21
ETG07_105829 4.86
ETG05_66023 36.41
ETG05_36762 4.41
ETG04_27747 4.69
ETG02_36680 4.23
ERCC-00171_229 4.18
ERCC-00170_100 28.19
ERCC-00168_248 4.24
ERCC-00165_60 4.20
ERCC-00164_60 5.31
ERCC-00163_81 4.22

Total number of rows: 56745

Table truncated, full table size 1089 Kbytes.




Supplementary file Size Download File type/resource
GSM2804282_Hepa1c1c7_001.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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