NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4097944 Query DataSets for GSM4097944
Status Public on Sep 26, 2022
Title Hepatocyte_6h_rep3
Sample type RNA
 
Source name Rat primary hepatocyte, 6h, replicate3
Organism Rattus norvegicus
Characteristics cell: primary hepatocyte
gender: male
weight: 320g
Treatment protocol The treatment in our study in the different length of in vitro culture.
Growth protocol Primary hepatocytes isolated from rat liver were resuspended in William's E medium supplemented with 10% FBS (GBICO), 1% ITS, dexamethasone, 1 X L-glutamine/ penicillin /streptomycin and plated onto collagen-I-coated plate at the density of 6× 105 cells/ml. After 3 hours, non-attached cells were washed away and the medium was replaced with William's E free of FBS.
Extracted molecule total RNA
Extraction protocol RNA was prepared using the RNasey Mini Kit (Qiagen p/n 74104) following the manufacturer's recommendations.
Label cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-2305) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104). Dye incorporation and cRNA yield were checked with theNanoDrop ND-2000 Spectrophotometer.
 
Hybridization protocol 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x GEx Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent Rat lncRNA Microarray V3 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 Agilent Microarray Scanner (Agilent p/n G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression at 6h in replicate3 of primary hepatocytes
Data processing The scanned images were analyzed with Agilent Feature Extraction software using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Sep 26, 2019
Last update date Sep 26, 2022
Contact name jiang zhengyi
E-mail(s) zhengyijiang@zju.edu.cn
Phone 15858111920
Organization name Zhejiang University
Street address Qingchun 79 Road
City Hang Zhou
State/province State...
ZIP/Postal code 310000
Country China
 
Platform ID GPL27537
Series (1)
GSE138071 Integrative proteomics of primary hepatocytes during dedifferentiation

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 16.094822
DarkCorner 2.0179517
A_44_P550748 1.3831489
CUST_R2_06928 5.515633
CUST_R2_17773 1.3831489
A_64_P114354 8.894881
A_44_P307151 3.7132566
CUST_R2_03844 11.044889
A_43_P15023 1.3831489
A_44_P1004737 1.9042242
A_44_P1088551 1.5408131
CUST_R2_09504 2.6292622
CUST_R2_06980 2.0893261
CUST_R2_19172 5.3534765
A_64_P119472 3.0772605
CUST_R2_14403 7.468563
CUST_R2_10562 4.1122174
A_44_P1096839 5.7750726
A_44_P1102733 1.3831489
A_44_P187830 7.181471

Total number of rows: 51323

Table truncated, full table size 1162 Kbytes.




Supplementary file Size Download File type/resource
GSM4097944_liver3-6h.txt.gz 8.2 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap