Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic analysis of femoral diaphysis and primary osteoprogenitor cells cultures from mouse strains with SHIP1 deficiency and controls

ABSTRACT: Investigation of the SHIP1 (Inpp5d)-dependent and Rag2/Il2rg-dependent transcriptional changes in bone and osteoprogenitor cells cultures from murine strains with SHIP1 deficiency (Inpp5dm1Btlr/ m1Btlr, http://www.informatics.jax.org/allele/key/65037) and controls. Specifically, transcriptomic analysis was performed from femoral diaphysis from SHIPstyx/styx, SHIP1+/styx, wild-type (C57BL6/J), Rag2-/-/Il2rg-/-/SHIP1styx/styx, Rag2-/-/Il2rg-/-/SHIP1+/styx, and Rag2-/-/Il2rg-/-/SHIP1+/+ mice (n=3 for each genotype). Alternatively, osteoprogenitor cells isolated from bone marrow from the same genotypes as above were differentiated in vitro into primary osteoclasts in the presence or absence of RANKL. After 5 days, RNA was extracted from these cultures for transcriptomic analysis (n=3 for each genotype). Experimental Designs: Transcripts were analyzed in femoral diaphysis of SHIPstyx/styx, SHIP1+/styx, wild-type (C57BL6/J), Rag2-/-/Il2rg-/-/SHIP1styx/styx, Rag2-/-/Il2rg-/-/SHIP1+styx, and Rag2-/-/Il2rg-/-/SHIP1+/+ mice (n=3 for each genotype). Alternatively, transcripts were analyzed in primary osteoclast cultures from bone marrow cells isolated from SHIPstyx/styx, SHIP1+/styx, wild-type (C57BL6/J), Rag2-/-/Il2rg-/-/SHIP1styx/styx, Rag2-/-/Il2rg-/-/SHIP1+styx, and Rag2-/-/Il2rg-/-/SHIP1+/+ mice (n=3 for each genotype), which were supplemented or not with RANKL.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Fatemeh Safari

PROVIDER: E-MTAB-13164 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Expression data from long-term Ebf1-deficient, CD19+, Bcl2tg cells

Project description:An assessment of a role of Ebf1 in committed B lineage cells. In this study, we adopted the strategy of deleting Ebf1 after reconstitution of Rag2-/-Il2rg-/- mice and found that committed pre-B cells could be converted into T cells and ILCs upon deletion of Ebf1. We used µ-arrays to gain insight into changes in gene expression of CD19+ Ebf1-deficient cells. The dataset was compared with microarray data available for different hematopoietic developmental stages (GSE15907). The complete dataset is linked below as a supplementary file.

2013-06-01 | E-GEOD-46349 | biostudies-arrayexpress

Comparison of gene expression profile in RAG2+ B lineage cells from the small intestinal lamina propria and RAG2+ B lineage cells from the bone marrow

Project description:We used a RAG2-GFP reporter mouse to show that RAG+ B lineage cells can be found in the small intestinal lamina proria in normally-housed mice at weaning age. We used microarry expression analysis to compare the RAG2+ population in the gut to the RAG2+ B lineage population in the bone marrow. Microarray was used to compare RAG2+ lamina propria B cells to RAG2+ bone marrow B cells. For each experiment, RAG2-GFP+ cells from 8-12 post-natal day 17-25 RAG2-GFP reporter mice were sorted from small intestinal lamina propria lymphocyte preparations and bone marrow. RNA extracted from trizol was used for the analysis. 3 independent replicates were performed.

2013-07-12 | E-GEOD-48805 | biostudies-arrayexpress

Circadian control of hepatitis B virus replication

Project description:Fah-/-, Rag2-/-, IL2Rg-/-, non-obese diabetic (FRG-NOD) mice transplanted with primary human hepatocytes were infected with 10^9 HBV genome equivalents purified from concentrated supernatant of the HepG2.2.15 cell line (HBV genotype D subtype ayw). Eight weeks later mice were treated twice a day by intraperitoneal injection of either vehicle or 100 mg/kg SR9009 for 2 weeks. At the end of experiment, mouse livers were collected for RNA-seq analysis. The sequence reads were mapped to the human or mouse genome.

2020-12-16 | GSE163285 | GEO

Identification and characterization of regenerative innate lymphoid cells from pluripotent stem cells [WT_ILC/R9_iILC_SmartSeq2]

Project description:We identified that synergistic and inducible expression of Runx1 and Hoxa9 in pluripotent stem cells gave rise to engraftable iHPC capable of developing into mature ILCs in the Rag2-/-Il2rg-/- recipients. We performed single-cell RNA-seq on the entire regenerative CD45.2+GFP+Lin-CD127+ R9-ILC population from the intestine of Rag2-/-Il2rg-/- recipient mice and the CD45.2+Lin-CD127+ WT-ILC population from the intestine of wild type mice (C57BL/6, CD45.2). Single-cell transcriptome illustrated the transcriptome landscape of the R9-ILCs and wild type ILCs including ILC1, ILC2 and ILC3.

2022-09-30 | GSE186777 | GEO

Opposing roles of E2A and Id3 that orchestrate and enforce the naive T cell fate

Project description:It is established that E2A and its antagonist, Id3, modulate developmental progression at the pre-TCR and TCR checkpoints. Here we show at a global scale how E2A promotes commitment to the T cell lineage and how pre-TCR mediated signalling affects E2A genome-wide occupancy. We find aberrant development of CD4 memory-like and TFH-like cells, T-B cell conjugates and, remarkably, B cell follicles in Id3-/-thymi. We also find that Id3-/-CD4 splenocytes exhibit increased numbers of TFH-like cells. We propose a model in which Id3 modulates the naive versus effector/memory cell fate. Collectively, these data show how E2A acts globally to orchestrate T-lineage development and that Id3 antagonizes E2A activity beyond the pre-TCR checkpoint to enforce the naive T cell fate. ChIP-Seq was performed in thymocytes isolated from either untreated Rag2-/-mice (DN3 cells) or Rag2-/- mice injected with anti-CD3e antibody (DN4 cells). ChIP used antibodies against either E2A or H3K4me1.

2011-07-31 | E-GEOD-30518 | biostudies-arrayexpress

Identification and characterization of regenerative innate lymphoid cells from pluripotent stem cells [WT-CHILP/iR9-CHILP_SmartSeq2]

Project description:We identified that synergistic and inducible expression of Runx1 and Hoxa9 in pluripotent stem cells (PSCs) gave rise to engraftable iHPC capable of developing into common helper innate lymphoid progenitors (CHILPs) in the Rag2-/-Il2rg-/- recipients. To assess the gene-expression pattern of the PSC-derived R9-iCHILPs, we performed single-cell RNA-seq on the regenerative CD45.2+GFP+Lin-CD127+CD135-α4β7+Sca1mid/-CD25- R9-iCHILPs from the bone marrow of Rag2-/-Il2rg-/- recipient mice and the CD45.2+Lin-CD127+CD135-α4β7+Sca1mid/-CD25- WT-CHILPs from the bone marrow of wild type mice (C57BL/6, CD45.2).

2022-09-30 | GSE210861 | GEO

High throughput sequencing of immunoglobulin (Ig) heavy (IgH) and light (IgL) chain repertoires

Project description:We used 454 sequencing to assess the repertoire of B cell subsets from bone marrow, spleen, and small intestinal lamina propria from two mouse strains. We used a RAG2-GFP reporter mouse strain (129Sve background) to isolate CD19+ RAG2+ B lineage cells from bone marrow and small intestinal lamina propria and total splenic B cells. We used 5' RACE to amplify cDNA libraries using primers specific for the mu constant region of IgH and the Ig kappa constant region. We also used this technique to analyze total B cell libraries from Swiss Webster germ-free mice to compare to littermate controls that were cohoused with regular specific pathogen free (SPF) mice for 7 days. Examination of the Ig kappa repertoire and IgH repertoire in RAG2+ bone marrow B lineage cells compared to RAG2+ small intestinal lamina propria B lineage cells or total splenic B cells. There are 8 (Ig kappa) or 4 (IgH) independent experiments comparing repertoires in RAG2-GFP mice. Each experiment in RAG2-GFP+ mice consisted of a pool of 8-12 mice. There are 3 experiments comparing germ-free to colonized mouse total B cell repertoires, each consisting of one mouse per condition.

2013-07-16 | E-GEOD-48870 | biostudies-arrayexpress

Transcriptional landscape of Rag2 -/- thymocytes [Mnase-Seq]

Project description:We performed ChIP-Seq for hallmark TFs (Ets1, Runx1), histone modification marks (H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3), total RNA Pol II, short RNA-Seq as well as nucleosome mapping mainly in murine Rag2 -/- thymocytes. We also performed ChIP-Seq for E47 as well as nucleosome mapping, gene expression microarray analysis in CD4+ CD8+ DP thymocytes. Overall, we find a key role for the transcription factor Ets1, contributing towards alpha beta T cell lineage commitment via differential transactivation of stage-specific genes orchestrated by dynamic, co-association -mediated chromatin remodeling, as well as transcription dependent generation of a specialized chromatin structure at the TCR beta locus. Genome-wide analysis via ChIP-Seq for Ets1, Runx1, total RNA Pol II binding, H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3, short RNA-Seq, Mnase-Seq in murine Rag2 -/- thymocytes, ChIP-Seq for E47, Mnase-Seq and gene expression microarray analysis in DP thymocytes This Series represents Mnase-Seq data.

2014-04-01 | E-GEOD-56360 | biostudies-arrayexpress

Expression data from long-term Ebf1-deficient, CD19+, Bcl2tg cells

2013-06-01 | GSE46349 | GEO

In vivo gene expression data from wild type and CTLA-4 KO 5C.C7 T cells

Project description:CTLA-4 is thought to inhibit effector T cells both intrinsically, by competing with CD28 for B7 ligands, and extrinsically, through the action of regulatory T cells. We studied in vivo responses of normal and CTLA-4-deficient antigen-specific murine effector CD4+ T cells. In order to do these studies in a physiological model of immunity to foreign antigen, we transferred small numbers of congenically marked RAG2-deficient 5C.C7 T cells with either a normal or knockout allele of CTLA-4 into normal syngeneic B10.A recipient mice. The T cells were then activated by immunization with MCC peptide and LPS. To look for transcriptional signatures of negative regulation of T cell responses by CTLA-4, we used microarray analysis to compare transcripts in wild type and CTLA-4 KO 5C.C7 T cells four days after immunization. This is the first instance in which differences are observed in extent of accumulation of wild type and CTLA-4 KO 5C.C7 T cells. To compare the gene expression profile between wild type and CTLA-4 KO adoptively transferred T cells 4 days after immunization.

2012-09-05 | E-GEOD-37563 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data