Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ScRNA-seq of sea lamprey (Petromyzon marinus) brain regions

ABSTRACT: scRNA-seq was used in order to produce a cell type atlas of the larval and adult sea lamprey (Petromyzon marinus) brain. This resource enabled us to reveal the cell type composition and molecular organization of a representative of a lineage (i.e., the cyclostomes) that diverged from the rest of vertebrates around 500 million years ago, and lays the foundations for a better comprehension of vertebrate brain evolution

INSTRUMENT(S): NextSeq 550

ORGANISM(S): Petromyzon marinus

SUBMITTER: Francesco Lamanna

PROVIDER: E-MTAB-11087 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Maternal to paternal epigenome reprogramming during early sea lamprey (Petromyzon marinus) development (BioCAP)

Project description:Maternal to paternal epigenome reprogramming during early sea lamprey (Petromyzon marinus) development

2023-05-26 | GSE220551 | GEO

Transcriptional dysregulation associated with chromatin accessibility of iPSC and hepatocytes derived from a Cornelia de Lange syndrome patient (scRNA-Seq) [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.

2024-08-18 | E-MTAB-14245 | biostudies-arrayexpress

Maternal to paternal epigenome reprogramming during early sea lamprey (Petromyzon marinus) development (Bisulfite-Seq)

Project description:Maternal to paternal epigenome reprogramming during early sea lamprey (Petromyzon marinus) development

2023-05-26 | GSE220552 | GEO

Lineage recording in human cerebral organoids (Visium)

Project description:Induced pluripotent stem cell (iPSC) derived organoid systems provide models to study human organ development. Single-cell transcriptome sequencing enables highly-resolved descriptions of cell state heterogeneity within these systems and computational methods can reconstruct developmental trajectories. However, new approaches are needed to directly measure lineage relationships in these systems. Here we establish an inducible dual channel lineage recorder, iTracer, that couples reporter barcodes, inducible CRISPR/Cas9 scarring, and single-cell transcriptomics to analyze state and lineage relationships in iPSC-derived systems. This data set include the spatial iTracer data of three slices of one cerebral organoid measured by 10x Visium.

2021-11-03 | E-MTAB-10972 | biostudies-arrayexpress

Petromyzon marinus

Project description:Nanopore sequencing of the sea lamprey (Petromyzon marinus) genome

| PRJNA783432 | ENA

Petromyzon marinus

Project description:Gene expression analysis of developing Sea Lamprey (Petromyzon marinus)

| PRJNA306044 | ENA

RNAseq of mutant TP53 HCT116 cell line clones generated via CRISPR editing

Project description:To compare the impact of several TP53 mutant variants in an isogenic setting, different TP53 mutations were introduced in HCT116 colorectal carcinoma cells. This parental cell line is wild-type for TP53 and shows a prototypical p53 response. To ensure unambigous genotype-phenotype correlations, the cell were haploidized prior to CRISPR-editing by introducing inactivating deletions of intronic splicing into one of the two TP53 alleles, leaving only one functional copy of TP53. The remaining TP53 allele was altered by inserting a LoxP-flanked transcriptional stop cassette (Lox-Stop-Lox, LSL) into intron 4, which allowed reversible silencing of TP53 expression. The LSL cassette was then specifically targeted with CRISPR/Cas9 to introduce a variety of different mutant p53 alleles. The competency of the mutated p53 allele to induce a p53 response upon activation using Nutlin-3a was then assessed in an RNAseq experiment.

2024-10-16 | E-MTAB-12734 | biostudies-arrayexpress

Petromyzon marinus

Project description:Genome-scale methylome analysis of the sea lamprey, Petromyzon marinus

| PRJNA284426 | ENA

Petromyzon marinus isolate:kPetMar1

Project description:Petromyzon marinus (Sea Lamprey) genome, kPetMar1, alternate haplotype

| PRJNA562012 | ENA

Petromyzon marinus isolate:kPetMar1

Project description:Petromyzon marinus (Sea Lamprey) genome, kPetMar1, primary haplotype

| PRJNA562011 | ENA