NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7994892 Query DataSets for GSM7994892
Status Public on May 21, 2024
Title MOCK2
Sample type RNA
 
Source name primary hepatocyte, BSA, 24hr, replicate 2
Organism Homo sapiens
Characteristics cell type: primary hepatocyte
donor sex: male
donor age: 54y
donor race: caucasian
Treatment protocol The hepatocytes of 10E6 each well were incubated with 1μg BSA (MOCK), 1μg CD100 or 200ng TNF-a (as positive control) for stimulation.
Growth protocol The primay hepatocytes were cultured in hepatocyte plating/mantenance medium (Zenbio, Research Triangle, Raleigh-Durham, NC, US.)
Extracted molecule total RNA
Extraction protocol the total RNA were extracted by TRIzol reagent (CWbio, China), using the standard protocol for trizol extract. 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 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy 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 DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression after 24hr with BSA incubation
Data processing The scanned images were analyzed with Feature Extraction Software v11.0.0.1 (Agilent) using Agilent GeneSpring GX v12.1 for dada standardization and to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Dec 27, 2023
Last update date May 21, 2024
Contact name Chao Fan
E-mail(s) superfancity@hotmail.com
Organization name The Fourth Military Medical University
Street address #169, Changle Road, Xincheng District
City Xi'an
ZIP/Postal code 710032
Country China
 
Platform ID GPL13497
Series (1)
GSE252134 CD100 stimulation on primary hepatocyte

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner 16.35739
DarkCorner 2.3651206
A_23_P146146 2.722957
A_23_P42935 8.931804
A_23_P117082 12.348722
A_23_P2683 8.9226675
A_24_P358131 12.300489
A_33_P3367647 7.387032
A_23_P157316 9.02102
A_32_P14850 13.503824
A_23_P158596 6.9114466
A_23_P350107 7.7177496
A_23_P388190 6.8223157
A_23_P106544 11.221869
A_33_P3219745 2.3254054
A_32_P85539 5.978277
A_23_P94998 8.820262
A_33_P3235677 2.3254054
A_23_P417014 2.3254054
A_23_P103905 8.655353

Total number of rows: 34183

Table truncated, full table size 759 Kbytes.




Supplementary file Size Download File type/resource
GSM7994892_C2.txt.gz 2.1 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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