Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

64 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Determining open chromatin profiles of a specific population of cells isolated from zebrafish embryos at 10 hours post fertilization using the ATAC-seq method

ABSTRACT: Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer (10.7554/eLife.03848). Specifically, the 2.7 kb Mouse Smarcd3-F6 sequence (chr5: 24113559 -24116342 from mm9 assembly) was sub-cloned from a gateway entry vector into the Zebrafish Enhancer Detection (ZED). Tol2-mediated transgenesis was performed and stable lines were created. The Smarcd3-F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3-F6:EGFPhsc70 embryos were dissociated at 10 hours post fertilization for fluorescent activated cell sorting (FACS). 30,000-50,000 GFP positive and negative cells were collected from FACS for ATAC-seq. ATAC-seq libraries were created with Tn5 transposase and single-end sequenced on the Illumina HiSeq 2500 platform

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Danio rerio

SUBMITTER: Michael Wilson

PROVIDER: E-MTAB-6078 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Determining single-cell mRNA expression profiles of a specific population isolated from zebrafish embryos at 10 hours post fertilization

Project description:Stable zebrafish cell lines were created that expressed GFP under the control of a previously characterized mouse Smarcd3 enhancer (10.7554/eLife.03848). Specifically, the 2.7 kb Mouse Smarcd3-F6 sequence (chr5: 24113559 -24116342 from mm9 assembly) was sub-cloned from a gateway entry vector into the Zebrafish Enhancer Detection (ZED). Tol2-mediated transgenesis was performed and stable lines were created. The Smarcd3-F6:EGFPhsc70 allele was used for all genomics experiments. Smarcd3-F6:EGFPhsc70 embryos were dissociated at 10 hours post fertilization for fluorescent activated cell sorting (FACS) to collect GFP+ cells. Single-cell cDNA libraries were prepared using Fluidgim C1 system ((Fluidgim, PN 100-7168 Rev. B1)). 96 single-cell libraries were collected from three batches of experiments and sequenced on the Illumina HiSeq 2500 platform. Data from 92 cells (number of genes detected > 2000) were kept for clustering analysis. For the tube control experiments we performed mRNA-seq on ~4000 cells from the same embryo batches as the scRNA-seq experiments. GFP negative cells were also included to enable a GFP+ versus GFP- comparison. Libraries were made following the Fluidgim C1 mRNA-seq tube control protocol (Fluidgim, PN 100-7168 Rev. B1). Polyadenylated mRNA was captured by Oligo-dT primers and PCR amplified after reverse transcription. Final sequencing libraries were made using Nextera XT DNA Sample Preparation Kit and pair-end sequenced on the Illumina HiSeq 2500 platform.

2018-08-20 | E-MTAB-6077 | biostudies-arrayexpress

ATAC-seq in neuroblastoma IMR-32 cell line

Project description:ATAC-seq to define open chromatin in the neuroblastoma IMR-32 cell line.

2018-08-16 | E-MTAB-6562 | biostudies-arrayexpress

ATAC-seq of gata5GFP+/- cells in WT and Gata5/6 deficient zebrafish embryos during gastrulation

Project description:Gata5/6 are essential regulators in zebrafish heart development. To understand how Gata5/6 affects the chromatin accessibility and regulates cardiac gene expression, we FACS-isolated GFP+ and GFP- cells from Tg(gata5:GFP) transgenic embryos in both control and Gata5/6 deficient embryos (injected with Gata5/6 morpholinos) and conducted ATAC-seq. We performed the experiments at 8 hours post fertilization, intending to dissect the role of Gata5/6 in the earliest step in cardiac lineage specification. We did 2-3 biological replicates for each sample. ATAC-seq libraries were made using previously published protocol (Buenrostro et al., Nat. Methods, 2013. DOI: 10.1038/nmeth.2688) and sequenced on Illumina Hiseq2500.

2021-12-31 | E-MTAB-10427 | biostudies-arrayexpress

scGET-seq profile of NIH-3T3 cells with Kdm5c knockdown

Project description:scGET-seq profiling of NIH3T3 cells in which Kdm5c was silenced with antisense shRNA or with a control scramble shRNA.

2021-08-17 | E-MTAB-9651 | biostudies-arrayexpress

scGET-seq profile of patient derived organoids

Project description:Two patient-derived organoids from liver metastasis of CRC samples were profiled by scGET-seq to analyze their genomic composition

2021-08-17 | E-MTAB-10219 | biostudies-arrayexpress

scGET-seq profile of patient derived organoids from colorectal cancer samples

Project description:One patient-derived organoids from liver metastasis of CRC samples were profiled by scGET-seq to analyze their genomic composition

2024-06-03 | E-MTAB-13126 | biostudies-arrayexpress

Epigenetic profile of iPSC differentiation process by scGET-seq

Project description:Induced pluripotent stem cells (iPSC) derived from fibroblasts of two healthy individuals were differentiated into NPC. Cells were profiled by scGET-seq.

2021-08-17 | E-MTAB-10218 | biostudies-arrayexpress

Epigenetic profile of iPSC differentiation process by scGET-seq

Project description:Induced pluripotent stem cells (iPSC) derived from fibroblasts of two healthy individuals were differentiated into NPC. Cells were profiled by scGET-seq.

2021-08-17 | E-MTAB-9649 | biostudies-arrayexpress

Gene expression is a circular process

Project description:This study involves the role of yeast mRNA decay factors in transcription. The experiment included here are the ChIP-exo results of three decay factors: Xrn1, Dcp2 & Lsm1. Four experiments were made: Xrn1, Dcp2, Lsm1 and control (no-TAP tag), in two replicates.

2013-05-23 | E-GEOD-44312 | biostudies-arrayexpress

Transcriptional dysregulation associated with chromatin accessibility of iPSC and hepatocytes derived from a Cornelia de Lange syndrome patient (ATAC-Seq - iPSCs [N])

Project description:Cornelia de Lange syndrome (CdLS) is a rare genetic disease associated with cohesinopathy. A novel iPSC line was generated from the CdLS patient carrying a heterozygous missense point-mutation of the NIPBL gene. iPSC lines prepared from the healthy parents and the mutation-corrected isogenic cell lines are used as the respective controls. Upon differentiation into hepatocytes, the patient-derived iPSC demonstrate the capacity to express hepatocyte-specific marker transcripts and the respective proteins, however, the efficiency of differentiation is significantly inferior to those of the respective controls, demonstrated by single-cell RNA sequencing and immune-fluorescent analyses. Global change of transcriptome in the patient-derived iPSC relative to the control cells is associated with altered chromatin accessibility, assessed by RNAseq combined with ATACseq analysis. Differentially down-regulated genes in the patient-derived iPSC, in particular, are those coding for proteins related to neural differentiation and transcription factors, while up-regulated genes contain some of antisense RNA coding genes, pseudo genes and long non-coding RNAs. Some of the differentially regulated genes are consistent with the altered chromatin accessibility and this observation is consistent during hepatocyte differentiation. Thus, the mutation in the NIPBL gene of the CdLS patient could be responsible for defects of differentiation primarily due to alteration of chromatin accessibility.

2023-11-01 | E-MTAB-13240 | biostudies-arrayexpress

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