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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Comparison of Ly6D- common lymphoid progenitors (CLPs) from OcnCre;iDTR control and mutant mice.

ABSTRACT: We performed gene expression microarray comparing Ly6D- CLPs isolated from OcnCre;iDTR control and mutant mice by flow cytometry. Ly6D- CLPs were isolated from the bone marrow of OcnCre;iDTR control or mutant mice by flow cytometry and subjected to Affymetrix microarray comparison of gene expression. Markers used to define Ly6D- CLP by flow cytometry was: LineageLo, cKit+, Sca+, CD127+, Thy1.2-, Ly6D-

ORGANISM(S): Mus musculus

SUBMITTER: Vionnie Yu

PROVIDER: E-GEOD-66102 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Comparison of Ly6D- common lymphoid progenitors (CLPs) from OcnCre;iDTR control and mutant mice.

Project description:We performed gene expression microarray comparing Ly6D- CLPs isolated from OcnCre;iDTR control and mutant mice by flow cytometry.

2015-04-10 | GSE66102 | GEO

Comparison of gene expression profiles of ex vivo sorted Common Lymphoid Progenitors (CLPs) and in vitro cultured cCLPs.

Project description:A common lymphoid progenitor cell culture system was established, maintaining a multipotent, proliferating state of CLPs. Cells can be cultured and expanded in vitro for several months, maintaining their in vitro and in vivo lymphoid differentiation potential. We were interested, whether cCLP are changing, with regards to their gene expression program, compared to in vivo CLPs, during their expansion in culture. Therefore we compared the gene expression profile of cultured cCLPs and their counterparts in vivo, by NextGenSeq. CLPs were sorted from bone marrow of 6-10 weeks old C57BL/6 mice (n=4). Cells were sorted for Lin-, IL7R+, Flk2+, CD27+, Ly6d- marker expressing CLPs by Flow Cytometry for gene expression analysis. In parallel the same cell population was sorted and cultured under cCLP culture conditions. After two months culture the cells sorted again for Lin-, CD27+, Ly6d- cells by Flow Cytometry for gene expression analysis (n=4). The analysis shows that cCLPs maintain a very similar transcription profile to ex vivo sorted common lymphoid progenitors.

2018-04-01 | GSE109805 | GEO

Comparison of Osx+ cells and Ocn+ cells in the bone marrow.

Project description:We performed gene expression microarray comparing Osx-mCherry cells and Ocn-Topaz cells isolated from the OsxCre-mCherry;OcnCre-Topaz double transgenic mice by flow cytometry. In the OsxCre-mCherry;OcnCre-Topaz mouse model, Osx+ cells were labeled red, Ocn+ cells were green, and Osx+Ocn+ cells were yellow within the same animal. This system allows isolation of osteolineage subsets within the same animal by flow cytometry.

2015-04-10 | E-GEOD-66042 | biostudies-arrayexpress

Expression data from CpG treated Common Lymphoid Progenitors

Project description:Common Lymphoid Progenitors (CLPs) have two subsets, Ly-6d- which are mutli-potent, and Ly-6d, which derive from Ly-6d- and are committeed to the B-cell fate. Treatment of a mouse with CpG DNA causes an inflammatory response that alters both subsets. We used expression data to understand the changes in transcription in the transition of Ly-6d- CLPs to Ly-6d+ CLPs ion the presence and absence of CpG induced inflammation. C57BL/6 mice were treated over 10 days with either PBS or 50 ug of CpG1826. On day 10, bone marrow was harvested and CLPs populations were sorted by flow cytometry directly into RNAeasy buffer (Qiagen).

2015-03-01 | E-GEOD-59762 | biostudies-arrayexpress

Expression profiling of early lymphoid progenitors deficient for Ebf1 and Foxo1

Project description:Foxo1 and Ebf1 deficiency leads to a similar disruption of normal B-cell development at the level of the common lymphoid progenitor (CLP). Both mouse strains display the existance of LY6D+ CLPs but a marked/complete lack of proB cells. To investigate similarities of the developmental defects observed we generated gene expression profiles from both genotypes (with corresponding WT controls). This illustrated a shared gene expression signature in Ebf1/Foxo1 deficient CLPs. Gene expression profiling was done using highly purified (FACS sorted) progenitor cells. Cells were purified from bone marrow of wild-type, Foxo1 deficient and Ebf1 deficient mice. Ebf1 deficient bone marrow was aquired by transplantation of Ebf1 deficient progenitors into irradiated hosts. Populations analysed were CLP LY6D-, CLP LY6D+ and proB cells.

2012-11-01 | E-GEOD-41931 | biostudies-arrayexpress

Common lymphoid progenitor-independent pathways of innate and T lymphocyte development

Project description:All lymphocytes are thought to develop from common lymphoid progenitors (CLPs). However, lymphoid-primed multi-potent progenitors (LMPPs) are more efficient than CLPs in differentiating into T cells and group 2 innate lymphoid cells (ILC2s). Here, we have divided LMPPs into CD127− (LMPP-s) and CD127+ (LMPP+s) subsets and compared them with Ly6D− and Ly6D+ CLPs. Adult LMPP+s differentiated into T cells and ILCs more rapidly and efficiently than other progenitors in transplantation assays. The development of T cells and ILC2s is highly active in the neonatal period. Neonatal CLPs are rare and, unlike prominent neonatal LMPP+s, do not efficiently differentiate into T cells and ILC2s. ILC2s generated in the neonatal period are long-lived and persist in adult tissues. These results suggest that some ILCs and T cells may develop from LMPP+s via CLP-independent pathways.

2016-02-17 | GSE67034 | GEO

Expression profiling of early lymphoid progenitors deficient for Ebf1 and Foxo1

2012-11-01 | GSE41931 | GEO

High-throughput phenotyping of lung cancer somatic mutations [main experiment]

Project description:Recent genome sequencing efforts have identified millions of somatic mutations in cancer. However, the functional impact of most variants is poorly understood. Here we characterize 194 somatic mutations identified in primary lung adenocarcinomas using L1000 high-throughput gene-expression assays followed by expression-based variant impact phenotyping (eVIP), a method that uses gene expression changes to distinguish impactful from netural somatic mutations. This series represents the main experiment of the study where 8 replicates of wild-type and mutant ORFs are introduced into A549 cell lines. An ORF library containing wild-type and mutated versions of genes found to be mutated in lung cancer are introduced in A549 cell lines and measurements are made using the L1000 high-throughput gene-expression assay. These are done with 8 replicate experiemnts. The data are processed through a computational system, that converts raw fluorescence intensities into differential gene expression signatures. The data at each stage of the pre-processing are available: (LXB) - raw, unprocessed flow cytometry data from Luminex scanners. One LXB file is generated for each well of a 384-well plate, and each file contains a fluorescence intensity value for every observed analyte in the well. (Q2NORM) - gene expression profiles of directly measured landmark transcripts. Normalized using invariant set scaling followed by quantile normalization. (Z-SCORES) - signatures with differentially expressed genes computed by robust z-scores for each profile relative to control (relative to plate population as control)

2016-06-28 | E-GEOD-83744 | biostudies-arrayexpress

Paramecium tetraurelia strain:51

Project description:Paramecium flow cytometry-based nucleus purification

| PRJNA327166 | ENA

Robust enumeration of cell subsets from tissue expression profiles (BeadChip)

Project description:We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles. When applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen, and fixed tissues, including solid tumors, CIBERSORT outperformed other methods with respect to noise, unknown mixture content, and closely related cell types. CIBERSORT should enable large-scale analysis of RNA specimens for cellular biomarkers and therapeutic targets (http://cibersort.stanford.edu). To evaluate the performance of CIBERSORT against flow cytometry, gene expression profiling was performed on a set of 20 PBMC samples comprised of adults of varying ages receiving influenza immunization (NCT01827462). These samples were analyzed by flow cytometry to enumerate several leukocyte subsets. Normalized gene expression data and accompanying flow cytometry data are available at the CIBERSORT website (http://cibersort.stanford.edu/download.php).

2015-03-29 | E-GEOD-65133 | biostudies-arrayexpress

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