Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

10x Genomics Chromium WGS of Tursiops Aduncus

ABSTRACT: 10x Genomics Chromium WGS of Tursiops Aduncus

PROVIDER: PRJEB29244 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2849716_1.fastq.gz	Fastqsanger.gz
	ERR2849716_2.fastq.gz	Fastqsanger.gz
	ERR2849717_1.fastq.gz	Fastqsanger.gz
	ERR2849717_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

10x Genomics Chromium WGS of Tursiops Aduncus

Project description:This data and additional PacBio Sequel data were collected from the same individual for a de-novo genome assembly

2022-01-01 | E-MTAB-7310 | biostudies-arrayexpress

Tursiops aduncus

Project description:Tursiops aduncus overview

| PRJNA1150682 | ENA

Tursiops aduncus

Project description:Tursiops aduncus Raw sequence reads

| PRJNA1150531 | ENA

PacBio Sequel WGS of Tursiops Aduncus

Project description:This data and additional 10x Genomics Chromium data were collected from the same individual for a de-novo genome assembly

2022-01-01 | E-MTAB-7308 | biostudies-arrayexpress

PacBio Sequel WGS of Tursiops Aduncus

Project description:PacBio Sequel WGS of Tursiops Aduncus

| PRJEB29382 | ENA

Tursiops aduncus

Project description:Fecal microbiota of wild and captive Indo-Pacific bottlenose dolphins (Tursiops aduncus)

| PRJDB35601 | ENA

Single cell RNA-sequencing of Spike-ins and Control RNA using 10x Genomics Chromium system

Project description:In this study, we assess technical differences between commonly used single-cell RNA-Sequencing (scRNA-Seq) methods. In this dataset, we assess the RNA detection rates using high-throughput 10x Genomics Chromium system. We mix equal volume of Control Brain RNA (3ul; FirstChoice Total Brain RNA; #AM7962) and ERCC spikes (3ul 1:4 dilution; #4456653) to make a '2x Control RNA+ERCC' master mix. The '2x Control RNA+ERCC' master mix is diluted with equal volume nuclease-free water to make '1x Control RNA+ERCC' master mix. 3ul of '1x Control RNA+ERCC' master mix is added to Chromium single cell suspension and processed as per Chromium guidelines. The sample-data relationship format (SDRF) file for this submission contains only a high-level representation of the sample, library and run information per flow cell, and not per cell. For meta-data at the level of individual cells, please refer to the supplementary file called single_cells_list.txt, which is included as part of this ArrayExpress submission.

2017-03-08 | E-MTAB-5480 | biostudies-arrayexpress

Direct Comparative Analyses of 10X Genomics Chromium and Smart-seq2.

Project description:Single-cell RNA sequencing (scRNA-seq) is generally used for profiling transcriptome of individual cells. The droplet-based 10X Genomics Chromium (10X) approach and the plate-based Smart-seq2 full-length method are two frequently used scRNA-seq platforms, yet there are only a few thorough and systematic comparisons of their advantages and limitations. Here, by directly comparing the scRNA-seq data generated by these two platforms from the same samples of CD45- cells, we systematically evaluated their features using a wide spectrum of analyses. Smart-seq2 detected more genes in a cell, especially low abundance transcripts as well as alternatively spliced transcripts, but captured higher proportion of mitochondrial genes. The composite of Smart-seq2 data also resembled bulk RNA-seq data more. For 10X-based data, we observed higher noise for mRNAs with low expression levels. Approximately 10%-30% of all detected transcripts by both platforms were from non-coding genes, with long non-coding RNAs (lncRNAs) accounting for a higher proportion in 10X. 10X-based data displayed more severe dropout problem, especially for genes with lower expression levels. However, 10X-data can detect rare cell types given its ability to cover a large number of cells. In addition, each platform detected distinct groups of differentially expressed genes between cell clusters, indicating the different characteristics of these technologies. Our study promotes better understanding of these two platforms and offers the basis for an informed choice of these widely used technologies.

| S-EPMC8602399 | biostudies-literature

Single cell Chromatin Accessibility profiling of forelimb bud at stage E11.5 in WT and Hox13 mutant (10x Chromium)

Project description:Single cell Chromatin Accessibility profiling of forelimb bud at stage E11.5 in WT and Hox13 mutant (10x Chromium)

2020-03-26 | GSE145657 | GEO

Single-cell RNAseq analysis (10X Genomics Chromium) of refilled lung interstium macrophages on day 4 after depletion

Project description:Lung interstitium macrophages (IMs) are non-alveolar resident tissue macrophages which contribute to the lung homeostasis. These cells were reported to be heterogeneous by our group and other teams, which contains two main distinct subpopulations: CD206+ IMs and CD206- IMs. However, the exact origin of IMs and the transcriptional programs that regulate IM differentiation remains unclear. In recent report, we analyzed the refilled IMs in the course of time after induced IM depletion with single-cell RNA sequencing (10X Genomics Chromium) and bulk RNA sequencing. The IMs in Day 4 post-depletion were compared to the those without depletion. Results showed that refilled IMs had a lower ratio of CD206+ IM vs CD206- subpopulation comparing to IMs without depletion, but they shared high similarity to each other, indicating that the de novo IM population had been established before Day 4 post-depletion.

2023-02-07 | GSE193894 | 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