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Series GSE158149 Query DataSets for GSE158149
Status Public on Jan 12, 2021
Title Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density [Osteoclast_48H_samples]
Sample organism Mus musculus
Experiment type Expression profiling by array
Third-party reanalysis
Summary The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored the International Mouse Phenotyping Consortium (IMPC) for the analysis of skeletal data from 3,974 mutant strains for bone mineral density (BMD), a measure that is frequently altered in a range of bone pathologies including osteoporosis. A total of 200 genes were found to significantly affect BMD. This gene pool comprised 141 genes that were previously not known to have a function in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 BMD genes also caused skeletal abnormalities. Further, evidence suggested a direct role for several of the identified BMD genes in osteoclasts and osteoblasts, and candidate genes for further investigation were prioritized. Overall, the results add novel pathophysiological and molecular insight into bone health and disease
 
Overall design We downloaded and re-analysed the gene expression profile of the datasets published by Wang et al., (2013) PMID: 23593435 with GEO accession number GSE43811. We re-analysed only the Osteoclastogenic cell line after 48h hours of induction compared to not inducted, to identify osteoclast specific genes and their expression levels after 48h of induction to apply GeneNet Schaefer and Strimmer algorythm for learning large-scale gene association networks (http://www.strimmerlab.org/software/genenet/). This method allows to statistically assess the reliability of a given network (nodes and edges) using gene expression data to compute q-values and posterior probabilities for each potential edge connecting in a pairwise manner the nodes of the network we built in silico using REACTOME ans STRING databases . Data pre-processing and annotation: The raw intensity measurements of the arrays downloaded from the GEO platform in .txt where normalized using limma Quantile based normalization algorithm producing the summaries at the probe/transcript level. The probes were gene and transcript annotated using the specific annotaton file MoGene-1_0-st-v1.na36.mm10.transcript.csv downloaded from https://www.thermofisher.com/es/es/home/life-science/microarray-analysis/microarray-data-analysis/genechip-array-annotation-files.html. Differential expression analysis (DEA): We carried on the differential expression analysis in R environment using limma. We provide the limma normalized expression data matrix to be used for GeneNet.
Web link https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009190
 
Contributor(s) Muñiz Moreno MM, Herault Y, Mayer-Kuckuk P, Hrabe de Angelis M
Citation(s) 33370286
Submission date Sep 17, 2020
Last update date Jan 12, 2021
Contact name maria del mar muñiz moreno
E-mail(s) munizmom@igbmc.fr
Organization name IGBMC
Department Translational medicine and neurogenetics
Lab Physiopathology of aneuploidy, gene dosage effect and Down syndrome - Yann Herault team
Street address 1 Rue Laurent Fries
City Strasbourg
State/province Alsace
ZIP/Postal code 67400
Country France
 
This SubSeries is part of SuperSeries:
GSE158151 Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density
Relations
Reanalysis of GSM1071626
Reanalysis of GSM1071627
Reanalysis of GSM1071628
Reanalysis of GSM1071629
Reanalysis of GSM1071630
Reanalysis of GSM1071631

subSeries_GSE43811_Osteoclast_48H_samples header descriptions
GEO_GSE_ID
GEO_GSM_ID
Sample_name
title
Raw data file
source_name
organism
cell_type
cell_culture_induction
biosample
GEO_platform_id
chip_name

Data table
GEO_GSE_ID GEO_GSM_ID Sample_name title Raw data file source_name organism cell_type cell_culture_induction biosample GEO_platform_id chip_name
GSE43811 GSM1071626 OsteoclastPrecursors_2days_1 H10_stimulated_RANKL_2 days_rep1 GSM1071626_MoGene1_070611W_MG01_H10_1_.CEL H10 (Osteoclastogenic cell line) stimulated with RANKL for 2 days, rep1 Mus musculus H10 cell line 2 days Osteoclastogenic cell line_stimulated RANKL_2 days_rep1 GPL6246 [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]
GSE43811 GSM1071627 OsteoclastPrecursors_2days_2 H10_stimulated_RANKL_2 days_rep2 GSM1071627_MoGene1_070611W_MG02_H10_2_.CEL H10 (Osteoclastogenic cell line) stimulated with RANKL for 2 days, rep2 Mus musculus H10 cell line 2 days Osteoclastogenic cell line_stimulated RANKL_2 days_rep2 GPL6246 [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]
GSE43811 GSM1071628 OsteoclastPrecursors_2days_3 H10_stimulated_RANKL_2 days_rep3 GSM1071628_MoGene1_070611W_MG03_H10_3_.CEL H10 (Osteoclastogenic cell line) stimulated with RANKL for 2 days, rep3 Mus musculus H10 cell line 2 days Osteoclastogenic cell line_stimulated RANKL_2 days_rep3 GPL6246 [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]
GSE43811 GSM1071629 Control_2days_1 C8_stimulated_RANKL_2 days_rep1 GSM1071629_MoGene1_070611W_MG04_C8_1_.CEL C8 (non Osteoclastogenic cell line) stimulated with RANKL for 2 days, rep1 Mus musculus C8 cell line 2 days Non Osteoclastogenic cell line_stimulated RANKL_2 days_rep1 GPL6246 [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]
GSE43811 GSM1071630 Control_2days_2 C8_stimulated_RANKL_2 days_rep2 GSM1071630_MoGene1_070611W_MG05_C8_2_.CEL C8 (non Osteoclastogenic cell line) stimulated with RANKL for 2 days, rep2 Mus musculus C8 cell line 2 days Non Osteoclastogenic cell line_stimulated RANKL_2 days_rep2 GPL6246 [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]
GSE43811 GSM1071631 Control_2days_3 C8_stimulated_RANKL_2 days_rep3 GSM1071631_MoGene1_070611W_MG06_C8_3_.CEL C8 (non Osteoclastogenic cell line) stimulated with RANKL for 2 days, rep3 Mus musculus C8 cell line 2 days Non Osteoclastogenic cell line_stimulated RANKL_2 days_rep3 GPL6246 [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]

Total number of rows: 6


Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE158149_GSE43811_Osteoclast_48H_samples.xlsx 3.1 Mb (ftp)(http) XLSX
Processed data are available on Series record

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