Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

E-MTAB-8036

ABSTRACT: RNA-seq of whole mouse placentas at E10.5 comparing C57Bl/6 male conceptuses that had undergone blastocyst transfer to non-transferred C57Bl/6 male conceptuses

PROVIDER: E-MTAB-8036 | ExpressionAtlas | 2019-09-09

REPOSITORIES: ExpressionAtlas

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	E-MTAB-8036-analysis-methods.tsv	Tabular
	E-MTAB-8036-analytics.tsv	Tabular
	E-MTAB-8036-atlasExperimentSummary.Rdata	Rdata
	E-MTAB-8036-configuration.xml	Xml
	E-MTAB-8036-g1_g2-mvaPlot.png	Other

Items per page:

1 - 5 of 21

Similar Datasets

RNA-seq of whole mouse placentas at E10.5 comparing C57Bl/6 male conceptuses that had undergone blastocyst transfer to non-transferred C57Bl/6 male conceptuses

Project description:RNA-seq of whole mouse placentas at E10.5 comparing C57Bl/6 male conceptuses that had undergone blastocyst transfer to non-transferred C57Bl/6 male conceptuses

| PRJEB32962 | ENA

RNA-seq of whole mouse placentas at E10.5 comparing C57Bl/6 male conceptuses that had undergone blastocyst transfer to non-transferred C57Bl/6 male conceptuses

Project description:The RNA-seq experiment was designed to determine the effects of blastocyst transfer on the transcriptome of whole placentas at embryonic day (E) 10.5. C57Bl/6 blastocysts that were from natural matings without superovulation were transferred into the uteri of pseudopregnant B6D2F1 females (at gestational day 2.5 equivalent). RNA libraries were prepared from whole male placentas at E10.5 (N = 4 placentas) from the transfer group alongside RNA libraries from control placentas from C57Bl/6 conceptuses derived from natural matings and did not undergo the transfer process (N = 4 placentas). Libraries were muliplexed and pooled for sequencing on the Illumina NextSeq500 platform with 75-base-pair single-end reads. Sequencing was performed in duplicate to provide at least 18 million reads per sample, and 1% PhiX Control (Illumina) spike-in was used. Quality control of Fastq files was performed using FastQC and fastq_screen. Sequences were trimmed with Trim Galore!, and alinged to GRCm38 mouse genome using STAR aligner.Alignments were processed using custom ClusterFlow (v0.5dev) pipelines and assessed using MultiQC (0.9.dev0). Gene quantification was determined with HTSeq-Counts (v0.6.1p1). Additional quality control was performed with rRNA and mtRNA counts script, feature counts (v 1.5.0-p2) and qualimap (v2.2). Differential gene expression was performed with DESeq2 package (v1.16.1, R v3.4.0). Read counts were normalised on the estimated size factors.

2019-12-31 | E-MTAB-8036 | biostudies-arrayexpress

(1) Murine CD4 T cells: naïve vs peptide treated and naïve vs peptide+LPS treated. (2) Murine CD8 T cells naïve vs HY-specific cells from tolerant mice and naïve vs cells from rejecting mice

Project description:(1) Transcriptional profiling of mouse CD4 T cells comparing naïve HY-specific TCR transgenic T cells with the same cells recovered after adoptive transfer into WT female C57BL/6 mice on day 5 following treatment with HY peptide (100microgrammes intranasally days 1,2 and 3) and comparing naïve HY-specific TCR transgenic T cells with the same cells recovered after adoptive transfer into WT female C57BL/6 mice on day 5 following treatment with HY peptide plus LPS (100microgrammes peptide and 20microgrammes LPS intranasally day 1) (2)Transcriptional profiling of mouse CD8 T cells comparing naïve CD8 T cells with HY-tetramer positive cells recovered from tolerant peptide treated (see above) WT female C57BL/6 mice on day 22 after male skin graft or 10-15 days after treatment with male spleen cells and comparing naïve CD8 T cells with HY-tetramer positive cells recovered from untreated (rejecting) WT female C57BL/6 mice on day 22 after male skin graft or 10-15 days after treatment with male spleen cells.

2011-03-28 | GSE26908 | GEO

Mus musculus

Project description:RNA-seq in whole mouse embryos at stage E10.5

| PRJNA203332 | ENA

The mouse aging proteomic atlas

Project description:This database provides TMT-labeled proteomic data of aorta (thoracic aorta), brain, heart, kidney, liver, lung, muscle (gastrocnemius muscle), and skin (abdominal skin) of 6, 15, 24, and 30 months old male C57BL/6 mice. In addition to the whole-tissue lysate, low-soluble protein-enriched fraction was also analyzed for heart, kidney, lung, muscle, and skin. Bulk RNA-Seq data are available for brain, heart, kidney, liver, lung, muscle, and skin. The tissues used for transcriptomic analysis and proteomic analysis of whole-tissue lysate and low-soluble protein-enriched fraction were collected from the same mice. All analyses were conducted with 4 biological replicates.

2024-09-17 | PXD040722 | Pride

RNA-seq in whole mouse embryos at stage E10.5

Project description:An increasing number of studies, including mutant expression profiling and comparative transcriptomic analyses, require reference RNA-seq data collections in mice. Particularly, to complement previous profiling data sets based on arrays, a full RNA-seq developmental series will be required for whole embryos. E10.5 is a key reference stage as it represents the early organogenesis stage. Here, we have performed high-throughput sequencing of total RNA form whole mice embryos at embryonic stage E10.5. Sequencing of the total RNA of whole embryos of mouse at embryonic stage E10.5.

2014-03-25 | E-GEOD-47033 | biostudies-arrayexpress

Transcriptome profile of wildtype and Ret homozygote null male mouse guts at E10.5

Project description:Total mRNA seq was perfomed on widtype and Ret null male mouse embryonic gut at E10.5

2018-04-01 | GSE99232 | GEO

Expression data from mouse colon tissue response to T cell transfer at week 0, 2, 4 and 6

Project description:Temporal geneome profiling of T cell transfer colitis model T cells critically regulate clinical inflammatory bowel diseases and T cell dependent experimental colitis models have gained prominent favor as useful models to identify potential pathogenic mechanisms. The naïve CD4+CD45Rbhigh cell transfer model into recombinase activating gene-1 deficient (RAG-/-) mice induces both colitis and small bowel inflammation reflecting Crohn's disease with unclear pathogenic mechanisms. Given the pathological similarities between the T cell transfer model of colitis and clinical disease, we sought to identify changes in whole genome expression profiles over time during the delelopment of colitis. Male RAG-1-/- C57BL/6 mice were injected with a half million CD4+CD45RBhigh T cells from healthy wild type C57BL/6 male mice. The colon tissue from individual cohorts were collected at weeks 0, 2, 4 and 6. Total RNA were extracted from the colon tissue and detected by Affymetrix GeneChip Mouse Genome 430 2.0 Array.

2013-01-11 | E-GEOD-27302 | biostudies-arrayexpress

Gene Expression data from synovium in mouse serum transfer arthritis model (STA) model

Project description:To find regulated genes during peak inflammation of rheumatoid arthritis (RA), we have collected synovium from mouse Serum Transfer Arthtitis (STA) model at day 0 (Non Arthritic) and day 10 (Peak Inflammation). Serum transfer arthritis was induced in 12-week-old male C57BL/6J mice (The Jackson Laboratory) by intraperitoneal injection of 150 μl of arthritogenic serum on days 0, 2, and 7. Nonarthritic mice received 150 μl of sterile phosphate buffered saline at each time point.

2016-09-28 | GSE71599 | GEO

Constitutive Piezo 1 knock out in mouse brain development

Project description:E10.5 whole brain were isolated from WT and Piezo1-KO mice (C57BL/6J strain backgound) described in Ranade et al 2014. https://doi.org/10.1073/pnas.1409233111

2022-08-20 | GSE193099 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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