Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Full-length, single cell RNA-sequencing of human bone marrow subpopulations reveals hidden complexity

ABSTRACT: Full-length, single cell RNA-sequencing of human bone marrow subpopulations reveals hidden complexity

PROVIDER: PRJNA750817 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR15346702_subreads.fastq.gz	Fastqsanger.gz
	SRR15346703_subreads.fastq.gz	Fastqsanger.gz
	SRR15304567_1.fastq.gz	Fastqsanger.gz
	SRR15304567_2.fastq.gz	Fastqsanger.gz
	SRR15304568_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Full-length, single cell RNA-sequencing of human bone marrow subpopulations reveals hidden complexity

Project description:Here, we investigate the extent to which individual cells within the total bone marrow (tot-BM) and the lineage negative (Lin-neg) populations exhibit this isoform diversity and whether distinct subpopulations in tot-BM and Lin-neg cells intersect based on transcript isoform usage. We extracted healthy donor human bone marrow tissues from discarded harvesting filters. From this total bone marrow cell preparation (tot-BM) we enriched for lineage-negative progenitor cells (Lin-neg) by magnetic selection as described earlier (Deslattes Mays et al. 2019). We then analyzed total and Lin-neg cell populations by droplet-based single cell RNA sequencing (10xGenomics). In order to increase the number of mRNA molecules detectable per cell we reduced the cell input to approximately 500 cells for each experiment. After single-cell selection, the barcoded cDNA libraries were equally divided and each pool was analyzed in parallel by short-read sequencing (Illumina) and by single-molecule real-time (SMRT) full-length RNA sequencing (Pacific Biosciences).

2023-04-06 | GSE181160 | GEO

Direct full-length RNA sequencing reveals unexpected transcriptome complexity during C. elegans development

Project description:High throughput RNA sequencing (RNA-seq) using cDNA has played a key role in delineating transcriptome complexity, including alternative transcription initiation, splicing, polyadenylation and base modification. However, the reads derived from current RNA-seq technologies are usually short and deprived of information on modification during reverse transcription, compromising their potential in defining transcriptome complexity. Here we applied a direct RNA sequencing method with ultra-long reads from Oxford Nanopore Technologies (ONT) to study the transcriptome complexity in C. elegans. We sequenced native poly-A tailed mRNAs by generating approximately six million reads from embryos, L1 larvae and young adult animals, with average read lengths ranging from 900 to 1,100 bps across stages. Around half of the reads represent full-length transcripts, judged by the presence of a splicing-leader or their full coverage of an existing transcript. To take advantage of the full-length transcripts in defining transcriptome complexity, we devised a novel algorithm to predict novel isoforms or group them with exiting isoforms using their mapping tracks rather than the existing intron/exon structures, which allowed us to identify roughly 57,000 novel isoforms and recover at least 26,000 out of the 33,500 existing isoforms. Intriguingly, stage-specific expression at the level of gene and isoform demonstrates little correlation. Finally, we observed an elevated level of modification in all bases in the coding region relative to the UTR. Taken together, the ONT long reads are expected to deliver new insights into RNA processing and modification and their underlying biology.

2019-09-10 | GSE130044 | GEO

Direct full-length RNA sequencing reveals unexpected transcriptome complexity during C. elegans development

Project description:Direct full-length RNA sequencing reveals unexpected transcriptome complexity during C. elegans development

| PRJNA533634 | ENA

Portunus trituberculatus Transcriptome (full-length)

Project description:Portunus trituberculatus Transcriptome (full-length)

| PRJEB40076 | ENA

Scylla Paramamosain Transcriptome (full-length)

Project description:Scylla Paramamosain Transcriptome (full-length)

| PRJEB40077 | ENA

Phascolosoma esculenta Transcriptome (full-length)

Project description:Phascolosoma esculenta Transcriptome (full-length)

| PRJEB38426 | ENA

Full-length HLA class II sequences

Project description:Full-length HLA class II sequences

| PRJEB42469 | ENA

Quantifying full-length circular RNAs in cancer

Project description:Quantifying full-length circular RNAs in cancer

| PRJNA693503 | ENA

Assembly of full-length macaque gene models

Project description:Assembly of full-length macaque gene models

| PRJNA547993 | ENA

Assembly of full-length macaque gene models

Project description:We reported an atlas of de novo-defined, full-length macaque gene models on the basis of single molecule long-read transcriptome sequencing (Iso-seq).

2021-06-01 | GSE132413 | 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