Curated gene expression dataset of differentiating 3T3-L1 adipocytes under pharmacological and genetic perturbations

Figures & data

Figure 1. Diagram of the data curation and processing. Metadata were obtained from gene expression omnibus (GEO) and the original articles. Studies were examined and filtered for the details of complete experimental design. Sample information was curated using a unified language across studies. Probe intensities were obtained from GEO, mapped and collapsed to genes. Expression data were log₂-transformed and normalized, and batch effects were removed. The curated metadata and the expression matrix were packaged in a R/Bioconductor experiment data package (curatedAdipoArray)

Figure 2. The experimental design of the curated datasets. A schematic description of the experimental design of the MDI-induced 3T3-L1 adipocytes under A) genetic or B) pharmacological perturbations. Each dataset is described by the target of the modification (right), the time point of intervention in hours (top) and the type of modification (▼, knockdown; ▲, overexpression; ● drug treatment). The time course was divided into four stages (0 and before, None; after 0 to 48, Early; after 48 to 144, Intermediate; after 144 hours, Late). Each dataset was represented by a separate colour (box) around the data points

Table 1. Datasets of genetically modified adipocyte differentiation course. GEO, gene expression omnibus; Ref., reference

GEO ID	Time (hr)	Treatment	Target	Ref.
GSE102403	6	knockdown	Cd24a	[27]
GSE58193	240	knockdown	Ebf1	[28]
GSE64154	48	overexpression	Fbxl10	[29]
GSE69313	0/6/24/72	knockdown	Fto	[30]
GSE40565	48/0	overexpression	Isl1	[31]
GSE28587	240	knockdown	Kat5/Usp7	[32]
GSE25423	0	knockdown	Kdm1a	[33]
GSE18598	24	knockdown	Kdm1a/Rfk	[34]
GSE97241	0/168	knockdown	Paral1	[35]
GSE18599	24	knockdown	Phf21a	[34]
GSE12929	−48/0/24/48/72/96/120/144	knockdown	Pparg	[18]
GSE14004	336	knockdown	Pparg	[17]
GSE73231	0/36/48	knockdown	Setdb1/Mbd1/Mcaf1	[17]
GSE122054	48/96/0/-48	knockdown	slincRAD	[36]
GSE93637	0/168	knockdown	Trp53inp2	[37]

Table 2. Datasets of pharmacologically modified adipocyte differentiation course. GEO, gene expression omnibus; Ref., reference

GEO ID	Time (hr)	Target	Treatment	Ref.
GSE42330	240	adipocytokine	asbestose	[38]
GSE14888	144	AMPK	linoleic acide/CLA/metformin/CLA,metformin	[39]
GSE17404	168	AMPK	linoleic acide/CLA/phenoformin	[40]
GSE8681	288	AMPK	linoleic acide/CLA	[41]
GSE8683	0	AMPK	linoleic acide/CLA	[41]
GSE8684	288	AMPK	CLA/linoleic acide	[41]
GSE94539	0/144	AMPK	adenine/AICAR	[42]
GSE56440	240	BECN1	berberine	[43]
GSE1458	288	insulin response	pioglitazone/rosiglitazone/troglitazone	[44]
GSE14810	168	insulin response	rosiglitazone	[45]
GSE24105	168	insulin response	dexamethasone	[46]
GSE4683	192	insulin response	insulin, glucose/rosiglitazone,insulin,glucose/glucose/insulin/rosiglitazone	[47]
GSE56688	168	insulin response	rosiglitazone	[48]
GSE62635	336	insulin response	dexamethasone/TNF	[49]
GSE18598	24	Kdm1a/Rfk/LSD1	siRNA/LSD1 inhibitor	[34]
GSE21157	48	lipogenesis	bilberry/anthocyanidins	[50]
GSE42220	192	lipogenesis	SFA	[51]
GSE53004	0	lipogenesis/non-lipogenic	rosiglitazone/butylparaben/ethylene brassylate/bis (2-ethylhexyl) phthalate/bisphenol A/butylbenzyl phthalate/propylparaben/tributyltin	[52]
GSE26207	312	PPARD/PPARG	PPARD agonist/PPARG agonist	[53]
GSE64075	168	PPARG/insulin response	diclofenac/indomethacin/rosiglitazone/ibuprofen/GQ16	[54]
GSE70854	240	protease	ritonavir/tenofovir/ritonavir,dmso/ritonavir,CLA	[55]
GSE51905	168	SCD1	SCD inhibitor	[56]
GSE8682	288	stress response	tunicamycin	[41]
GSE15018	0	ZFP68	prieurianin	[57]

Figure 3. Principal component analysis of differentiating Pparg-knockdown 3T3-L1 pre-adipocytes. Principal component analysis was applied before and after removing batch effects. A) The amount of variance explained and B) the correlation of (study) and (stage) of differentiation with the first three components are shown before and after applying the procedure. C) The first and second principal components are shown. Samples are coloured by the study of origin (red, GSE12929; blue, GSE14004). D) The second and third principal components are shown. Samples are coloured by the stage of differentiation (red, none; green, early; blue, intermediate; magenta, late stage)

Figure 4. Differential expression and gene set enrichment analysis of differentiating Pparg-knockdown 3T3-L1 pre-adipocytes. Differential expression analysis was applied to the process data to identify regulated genes between Pparg-knockdown and control conditions. A) Fold-change (log₂) and p-values (-log₁₀) of previously identified PPARG target genes are shown. B) Differentially expressed genes were ranked by fold-change and used to calculate the enrichment score and p-values of relevant gene ontology terms. Brown fat cell differentiation (GO:0050873); positive regulation of fat cell differentiation (GO:0045600); response to lipid (GO:0033993); fatty acid oxidation (GO:0019395); nuclear receptor transcription coactivator activity (GO:0030374)

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