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Sample GSM5091121 Query DataSets for GSM5091121
Status Public on Jun 30, 2021
Title CCL4_16d_rep1
Sample type RNA
 
Source name liver
Organism Mus musculus
Characteristics strain: C57BL/6N
tissue: liver
Sex: male
treatment: CCL4
time post treatment: 16d
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 7.331384950
1415671_at 8.958180696
1415672_at 9.882354226
1415673_at 6.098392716
1415674_a_at 8.142956003
1415675_at 7.332016272
1415676_a_at 10.048243330
1415677_at 9.372805736
1415678_at 9.651739143
1415679_at 10.109907030
1415680_at 7.617465623
1415681_at 8.743173815
1415682_at 6.867279169
1415683_at 9.386694343
1415684_at 8.010346923
1415685_at 8.190220945
1415686_at 8.906341078
1415687_a_at 9.778068618
1415688_at 9.318017622
1415689_s_at 7.920901215

Total number of rows: 45101

Table truncated, full table size 1032 Kbytes.




Supplementary file Size Download File type/resource
GSM5091121_Patricio_D16M1_51_Mouse430_2_.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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