Single cell analysis of the transcriptomes during neuronal differentiation
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Mus musculus
SUBMITTER:
PROVIDER: E-ERAD-201 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This study aims at performing a genome wide comparative epigenomic and transcriptomic analysis of normal ex-vivo primary populations of lymphocytes of the adaptive immune system. Stocks of adult C57BL/6J mice are used for the isolation of pure and synchronous populations of resting B and nave CD4+ T-lymphocytes to avoid confounding cell cycle effects in our analysis. Integrative analysis of single-nucleotide 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) maps, histone marks and total stranded RNA-seq profiles have been performed to identify cell-type specific epigenetic signatures. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2016-05-20 | E-ERAD-494 | biostudies-arrayexpress
Project description:This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ Schistosomiasis is a severe debilitating illness that represents one of the most important parasitic diseases in tropical areas. It affects over 200 million people across 74 countries. The complete genome sequence of Schistosoma mansoni was published in 2009, but immune response against this parasite is not well characterized. This study is to investigate the overall immune response, antibody and TCR repertoire of immunologically nave mice, mice infected with S.mansoni and mice challenged with a secondary schistosome infection.RNA-seq data will be used to characterise the systemic immune response of mouse to Schistosoma infection, including both whole-transcriptome sequencing for a global picture of the immune response, and sequencing the lymphocyte antigen receptor genes to get a detailed picture of the adaptive immune response.
2013-01-07 | E-ERAD-59 | biostudies-arrayexpress
Project description:Study was designed to compare the transcriptome of Th2 cells in presence or absence of 4m8c. Murine splenic naive T helper cells were activated in presence of anti-CD3e, anti-CD28 antibodies and IL4 and IL2 cytokines for 3 days. Cells were then transferred from activation plate to resting for 3 days. Cells were reactivated by anti-CD3e antibidy. Similar culture were maintained in presence of 15uM 4m8c.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2015-04-21 | E-ERAD-367 | biostudies-arrayexpress
Project description:RNA sequencing of peripheral immune cells from patients +/- an IBD risk variant. Peripheral immune cells +/- in vitro test compound treatment.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2016-07-11 | E-ERAD-443 | biostudies-arrayexpress
Project description:Effect of low-doses of ionizing radiation on the behaviour of epithelial cells. The aim of the study is to check whether a single exposure of 50 mGy of ioninzing radiation promotes changes in RNA transcription levels and/or mutations.
2016-02-23 | E-ERAD-429 | biostudies-arrayexpress
Project description:The Arabidopsis Branching Enzyme 1 (BE1) gene encodes a putative glycoside hydrolase involved in carbohydrate metabolism. A partial loss-of-function mutation of the BE1 gene (be1-3 mutant) severely impaired adventitious shoot formation and somatic embryogenesis but not root formation in tissue culture. To gain a better understanding of the molecular mechanism underlying the in vitro plant regeneration defects caused by the BE1 gene mutation, we performed RNA sequencing analysis (RNA-seq) to examine the differential gene expression between WS and be1-3 mutant at dedifferentiation and redifferentiation stages.
2014-02-12 | E-MTAB-4394 | biostudies-arrayexpress
Project description:The concurrent epigenetic changes during this period of remarkable improvement in maize grain yield remain unknown. Here, we performed MethylC-seq and RNA-seq on 4 related inbred lines with known pedigree information. Analysis of epigenetic changes over the course of historical maize breeding is a valuable new avenue in the exploration for crop improvement. These data lead us to suggest that novel epihaplotypes, in addition to DNA variation, are a substrate of selection during breeding, and that epigenetic variation between parents may also contribute to heterosis in hybrids. Xie, S; et al. 2013. Maize Genetics Conference Abstracts. 54:P326
2015-06-01 | E-MTAB-4238 | biostudies-arrayexpress
Project description:Maize exhibits levels of structural variation (SV) of non-repeat sequences that are unprecedented among higher eukaryotes. This SV includes hundreds of copy number variants (CNVs) and thousands of presence/absence variants (PAVs). Many of the PAVs contain intact, expressed, single-copy genes that are present in one haplotype but absent from another. The goal of this project is to test the hypothesis that differences in gene copy number (both gains and losses) contribute to the extraordinary phenotypic diversity and plasticity of maize. Maize is a good model for these studies because it exhibits a rapid decay of linkage disequilibrium (LD) and because a draft genome sequence of the B73 inbred and mapping populations are available. As a first step, the Zeanome, a near-complete set of genes present in B73, other maize lines and the wild ancestor of maize (teosinte), is being defined using transcriptomic data. Note: All samples in SRA were assigned the same sample accession (SRS302561). This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
2012-03-29 | E-MTAB-4386 | biostudies-arrayexpress
Project description:Over expression study of FLOWERING LOCUS T, a transcriptome study
2015-07-12 | E-MTAB-4236 | biostudies-arrayexpress
Project description:For this project, we have sequenced, assembled and annotated a transcriptome of a diploid wheat Triticum urartu accession PI 428198. The sequencing libraries were prepared from shoot and root tissues harvested from 2-3 week old seedlings. All sequencing was carried out on the Illumina HiSeq platform using the 100 bp pair-end protocol (248.5 million reads). The assembly was constructed using a multiple k-mer approach with a de novo assembly algorithm implemented in CLC Genomics Workbench 5.5 and additional redundancy reduction with CD-HIT and blast2cap3 programs. Open reading frames and proteins were predicted using BLASTX searches and a findorf algorithm.
2013-06-11 | E-MTAB-5037 | biostudies-arrayexpress