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Sample GSM5091148 Query DataSets for GSM5091148
Status Public on Jun 30, 2021
Title CCL4_8d_rep2
Sample type RNA
 
Source name liver
Organism Mus musculus
Characteristics strain: C57BL/6N
tissue: liver
Sex: male
treatment: CCL4
time post treatment: 8d
Extracted molecule total RNA
Extraction protocol RNA was isolated using the TRIzol method. Briefly, 1 ml TRIzol was added to 5 x 106 cells followed by vortexing, a 5-min incubation at room temperature, and the addition of 200 μl chloroform. After mixing, further incubation at room temperature for 2–3 min and centrifugation (12,000 g) at 4 °C for 5 min, the clear supernatant was mixed with 500 μl isopropanol and incubated at room temperature for 10 min. After centrifugation (12,000 g) at 4 °C for 10 min, the supernatant was discarded and the pellet washed with 1 ml cold 75% ethanol followed by vortexing and centrifugation (7,500 g, 4 °C, 5 min). The pellet was dried and dissolved in RNase-free water.
Label biotin
Label protocol Affymetrix gene array analysis was performed using the Affymetrix GenChip® Mouse Genome 430 2.0 arrays (Santa Clara, CA, USA). Briefly, five µg RNA were transcribed into cDNA by oligo dT primers, and reverse transcribed to biotinylated cRNA with the Gene Chip IVTÒ Labeling kit (Affymetrix, High Wycombe, UK). Cleanup of the IVT product was done using CHROMA SPIN-100 columns (Clontech, USA). Spectrophotometric analysis was used for the quantification of cRNA with an acceptable A260/A280 ratio of 1.9 to 2.1. Afterward, the cRNA was fragmented using the standard protocol of Affymetrix.
 
Hybridization protocol Labeled and fragmented cRNA was hybridized to Mouse Genome 430 2.0 Affymetrix GeneChips for 16 h at 45 °C according to the manufacturer’s instructions. Microarrays were washed using an Affymetrix fluidics station 450 and stained initially with streptavidin-phycoerythrin. For each sample the signal was further enhanced by incubation with biotinylated goat anti-streptavidin followed by a second incubation with streptavidin-phycoerythrin and a second round of intensities were measured.
Scan protocol Microarrays were scanned with an Affymetrix scanner controlled by Affymetrix Microarray Suite software (Campos et al., 2014; DOI: 10.1007/s00204-014-1240-8).
Data processing A probe-level model was fitted to the raw data to control the array quality based on the relative log expression values (RLE) and the normalized unscaled standard errors (NUSE) using the R/Bioconductor package oligo (version 1.52.0). Arrays that deviated more than 0.1 from 0 for RLE and from 1 for NUSE were discarded due to expected poor quality. Subsequently, the raw data was normalized with the RMA algorithm, also implemented within the oligo package.
 
Submission date Feb 18, 2021
Last update date Jun 30, 2021
Contact name Christian H. Holland
E-mail(s) cholland2408@gmail.com
Organization name Heidelberg University
Department Institute for Computational Biomedicine
Street address Im Neuenheimer Feld 267
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL1261
Series (2)
GSE166868 Mouse models of acute and chronic liver damage
GSE167033 Expression data of the livers of male C57Bl6/N mice after i.p. injection of CCl4

Data table header descriptions
ID_REF
VALUE RMA normalized log2 intensities

Data table
ID_REF VALUE
1415670_at 7.357474507
1415671_at 9.085713065
1415672_at 9.994345327
1415673_at 6.116230802
1415674_a_at 8.294714065
1415675_at 7.355222729
1415676_a_at 9.879890773
1415677_at 9.119270992
1415678_at 9.547622065
1415679_at 10.053304700
1415680_at 7.428854800
1415681_at 8.724305687
1415682_at 6.820203111
1415683_at 9.103355672
1415684_at 8.306300263
1415685_at 8.302289175
1415686_at 9.012423596
1415687_a_at 9.950832237
1415688_at 9.245862374
1415689_s_at 7.826643954

Total number of rows: 45101

Table truncated, full table size 1032 Kbytes.




Supplementary file Size Download File type/resource
GSM5091148_Patricio_D8M2_47_Mouse430_2_.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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