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Sample GSM4097942 Query DataSets for GSM4097942
Status Public on Sep 26, 2022
Title Hepatocyte_6h _rep1
Sample type RNA
Source name Rat primary hepatocyte, 6h, replicate1
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 replicate1 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
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
VALUE Normalized signal intensity

Data table
GE_BrightCorner 15.352009
DarkCorner 2.507365
A_44_P550748 1.5136504
CUST_R2_06928 5.945941
CUST_R2_17773 1.6837751
A_64_P114354 9.042818
A_44_P307151 2.911084
CUST_R2_03844 9.667976
A_43_P15023 1.6203278
A_44_P1004737 1.4424648
A_44_P1088551 1.4322292
CUST_R2_09504 4.2201734
CUST_R2_06980 2.3868809
CUST_R2_19172 2.7694638
A_64_P119472 1.5303288
CUST_R2_14403 9.358476
CUST_R2_10562 3.1782274
A_44_P1096839 5.145094
A_44_P1102733 1.5002153
A_44_P187830 8.10045

Total number of rows: 51323

Table truncated, full table size 1161 Kbytes.

Supplementary file Size Download File type/resource
GSM4097942_liver1-6h.txt.gz 8.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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