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Temporal gene expression across osteoblastogenesis.

ABSTRACT: Purpose: Osteoblast cells mature from a mesenchymal stem cell pool to become cells capable of forming bone matrix and mineralizing this matrix. The goal of this study was to characterize temporal changes in the transcriptome across osteoblast maturation, starting with committed mesenchymal stem cell/ early pre-osteoblast stage through to mature osteoblasts capable of matrix mineralization. Methods: Enriched populations of pre-osteoblast like cells were obtained from neonatal calvaria from C57BL/6J mice expressing CFP under the control of the Col3.6 promoter. These cells were placed into culture for 4 days, removed from culture and subjected FACS sorting based on the presence/absence of CFP expression. Cells expressing CFP were returned to culture, subjected to an osteoblast differentiation cocktail and RNA was collected at 2, 4, 6, 8, 10, 12, 14, 16 and 18 days post differentiation. Methods II: mRNA profiles for each time point were generated by next generation RNA sequencing, using an Illumina HiSeq 2000. Three technical replicates per samples were sequenced. The alignments for abundance estimation of transcripts was conducted using Bowtie version 0.12.9, using the NCBIm37 reference genome. Expression level per gene was calculated using RSEM version 1.2.0 with the parameters of --fragment-length-mean 280 and --fragment-length-sd 50, and the expression level for each sample was normalized relative to the per sample upper quartile.

ORGANISM(S): Mus musculus

PROVIDER: GSE54461 | GEO | 2014/06/23

SECONDARY ACCESSION(S): PRJNA236568

REPOSITORIES: GEO

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Temporal gene expression across osteoblastogenesis.

Project description:Purpose: Osteoblast cells mature from a mesenchymal stem cell pool to become cells capable of forming bone matrix and mineralizing this matrix. The goal of this study was to characterize temporal changes in the transcriptome across osteoblast maturation, starting with committed mesenchymal stem cell/ early pre-osteoblast stage through to mature osteoblasts capable of matrix mineralization. Methods: Enriched populations of pre-osteoblast like cells were obtained from neonatal calvaria from C57BL/6J mice expressing CFP under the control of the Col3.6 promoter. These cells were placed into culture for 4 days, removed from culture and subjected FACS sorting based on the presence/absence of CFP expression. Cells expressing CFP were returned to culture, subjected to an osteoblast differentiation cocktail and RNA was collected at 2, 4, 6, 8, 10, 12, 14, 16 and 18 days post differentiation. Methods II: mRNA profiles for each time point were generated by next generation RNA sequencing, using an Illumina HiSeq 2000. Three technical replicates per samples were sequenced. The alignments for abundance estimation of transcripts was conducted using Bowtie version 0.12.9, using the NCBIm37 reference genome. Expression level per gene was calculated using RSEM version 1.2.0 with the parameters of --fragment-length-mean 280 and --fragment-length-sd 50, and the expression level for each sample was normalized relative to the per sample upper quartile. Gene expression in calvarial osteoblasts from neonatal C57BL/6J-Col3.6 CFP mice at 9 time points post differentiation

2014-06-23 | E-GEOD-54461 | biostudies-arrayexpress

Expression data from Arabidopsis rosette leaves

Project description:The focus of this study was to identify changes in host gene expression induced by the transcription-dependent function of the viral AC2 protein, and induced by the interaction of AC2/C2 with SnRK1.2 (AtAKIN11). We used microarrays to identify changes in host gene expression induced by the transcription-dependent function of the geminivirus-encoded AC2 protein, and induced by the interaction of AC2 with a host serine-threonine kinase, SnRK1. Distinct classes of genes were up- and down regulated during this process. For experiment 1, Arabidopsis rosette leaves were infused with Agrobacterium capable of expressing full-length Cabbage leaf curl virus (CaLCuV) AC2 protein, a truncated version of AC2 lacking the C-terminal 29 amino acids (AC2del), or an empty vector control (530). In experiment 2, Arabidopsis rosette leaves were infused with Agrobacterium capable of expressing full-length Spinach curly top virus C2 protein, a truncated version of C2 lacking the C-terminal 29 amino acids (C2del), antisense (as) SnRK1.2 (AsAKIN11), or an empty vector control (530). Infused Arabidopsis rosette leaves were selected at 1, 2 or 3 days post-infusion for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of plants at each time point in order to increase the temporal resolution of expression profiles. To that end, we isolated total RNA from four individual plants, for three independent sets of plants infused with the different constructs. This resulted in three independent samples per treatment per time point.

2014-10-09 | E-GEOD-62180 | biostudies-arrayexpress

RNAi of TbNMD3 in procyclic form Trypanosoma brucei lines

Project description:A procyclic form Trypansome brucei RNAi line (PTT parental line, transfected with pALC14 incorporating a TbNMD3 gene fragment) capable of inducing depletion of TbNMD3 was analysed for mRNA expression by RNAseq Cells were grown for 72 hours in culture; RNAi was induced in cells by the addition of 1 microgram/ml of tetracycline

2015-04-28 | E-GEOD-67246 | biostudies-arrayexpress

Rattus norvegicus

Project description:Fragment Length of Circulating Tumor DNA

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Expression data from Arabidopsis rosette leaves

2014-10-09 | GSE62180 | GEO

Subclonal cooperation drives metastasis through modulating local and systemic immune microenvironments

Project description:Bulk RNA-Seq: Gene expression analysis of stromal and tumor fractions of primary and metastatic lesions of polyclonal and monoclonal origin. Primary tumor control samples consist of monoclonal Thy1.1 (no replicates), monoclonal parental (no replicates), monoclonal IL11 (duplicate), monoclonal FIGF (duplicate), and monoclonal CFP (duplicate). Primary polyclonal tumor samples consist of separated Thy 1.1 (duplicate), CFP (no replicates), IL11 (triplicate), and FIGF (triplicate). Metastatic tumor samples consist of monoclonal CFP (duplicate), monoclonal IL11 (quadruplicate), monoclonal FIGF (quadruplicate), monoclonal Thy1.1 (duplicate), and polyclonal samples (duplicate). Metastatic stromal fractions consist of monoclonal CFP (duplicate), monoclonal FIGF (quadruplicate), monoclonal IL11 (quadruplicate), monoclonal parental (duplicate), monoclonal Thy1.1 (duplicate), and polyclonal samples (triplicate). Primary stromal samples consist of monoclonal CFP (duplicate), monoclonal FIGF (duplicate), monoclonal IL11 (duplicate), monoclonal parental (no replicates), monoclonal Thy1.1 (duplicate), and polyclonal samples (triplicate). Further stromal controls consisted of a single fatpad sample and lung sample. Single cell RNA-Seq: Blood, tumors and lungs were isolated from test groups (DOX+ and DOX-) and tumor-naÃ¯ve animals. Samples were pooled across 3 animals per group, and CD45+populations were FACS-sorted. Two thousand single cells were targeted for each sample.

2019-09-24 | GSE109281 | GEO

Brain vascular transcriptomes of mouse hyperglycemia mutants and controls

Project description:Purpose:To take a comprehensive effort in characterizing the brain vasculature gene expression upon hyperglycemia. Methods: We extracted mRNA from brain microvasculature fragments isolated from a genetic mouse model of hyperglycemia (Ins2-AKITA) and WT mice and analyzed their transcriptome with RNA sequencing The samples were sequenced on an Illumina HiSeq 2500 sequencer at the SNP&SEQ sequencing facility (Science for Life laboratory (SciLifeLab), Uppsala sequencing node). The reads were aligned to the Ensembl mouse gene assembly (NCBIM37) using Tophat2 software (version 2.0.4). The duplicated reads were removed using the picard tool (version 1.92). To identify the genes significantly enriched in the pericyte samples as compared with microvascular samples, statistical tests were performed using the Cufflinks tool (version 2.2.1) Results: Twenty-three genes were significantly regulated in mutant when compared to WT (False Discovery Rate < 0.05)

2018-12-11 | GSE113919 | GEO

Next-generation sequencing to characterize the molecular basis for the differentiation of ES cells into testicular somatic cell-like cells and germ cell-like cells

Project description:Taking advantage of the tesco-cfp transgenic mouse line in which CFP is exclusively expressed in Sertoli cells under the control of a testis-specific enhancer (tesco), we established an embryonic stem cell from the mouse line (i.e. tcESC). We also created tcESC constitutively expressing mouse Sf1 transgene (tc;Sf1ESC). When we induced the differentiation of the two ESC lines into testicular somatic cell-like cells (TesLCs), tc;Sf1ESCs efficiently developed seminiferous tubule-like structures with the appearance of CFP-positive Setoli cell-like cells (SCLCs) in the tubules. On the other hand, epiblast-like cells (EpiLCs) were generated from ESCs having a germ cell-specific Prdm1-gfp transgene. Co-culture of tc;Sf1TesLCs with Prdm1-gfp EpiLCs resulted in self-organised aggregates, or testicular organoids. In the organoid, the EpiLCs differentiated into GFP-positive PGCLCs or gonocyte-like cells that were enclosed within a seminiferous tubule-like structure composed of CFP-positive SCLCs.

2021-06-18 | GSE149932 | GEO

MSE vs IM-MSE comparison - The experiment was conducted to compare the MSE and IM-MSE acquisiton modes

Project description:The experiment was conducted to compare the MSE and IM-MSE acquisiton modes as well as to find the optimal on column loading. This was done using 1DLC and cytosolic e coli digest.Raw data were processed and searched using Proteinlynx Global Server version 3.0. The following parameters were used to generate peak lists: minimum intensity for precursors was set to 140, minimum intensity for fragment ions 30 and total bin-count was set to minimum of 400. Processed data was searched against the UniprotKB, Escherichia coli K12 strain, concatenated with 125 common laboratory contaminates. Fixed modification was set to carbamidomethylation of C and variable modification was set to oxidation of M. Searches were conducted against a froward and reverse sequence database. Minimum identification criteria included 3 fragment ions per peptide, 5 fragment ions per protein, minimum peptide identification score of 5.9 and minimum of 2 peptides per protein. Search results and spectra were imported into Scaffold and the global false discovery rate was less than 1%.

2013-02-18 | PXD000150 | Pride

expression profile of prostate basal epithelial cells relative to luminal epithelial cells

Project description:We present the results of a microarray analysis in which we compare gene expression in CFP+ basal and CFP- luminal epithelia cell populations derived from whole prostates of CK5/CFP adult mice. Several genes that have previously been identified as potential stem cell markers in stem cells from various organs are over-expressed in CFP+ cells relative to CFP- cells.

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