Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Pacbio long read Iso-sequencing is performed to acquire a high-precision transcription landscape after STAMBPL1 knockingdown in Huh7 cells（Long-read）

ABSTRACT: Pacbio long read Iso-sequencing is performed to acquire a high-precision transcription landscape after STAMBPL1 knockingdown in Huh7 cells（Long-read）

PROVIDER: PRJNA1157740 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Pacbio long read Iso-sequencing is performed to acquire a high-precision transcription landscape after STAMBPL1 knockingdown in Huh7 cells（Long-read）

Project description:STAMBPL1 plays a previously unappreciated role in post-transcriptional regulation, especially in RNA splicing pathways. Thus, PacBio long-read iso-sequencing was performed to acquire a high-precision transcription landscape after STAMBPL1 knockingdown in Huh7 cells

2024-09-11 | GSE276508 | GEO

Reference Long-Read Transcriptomes of Human Peripheral Blood Lymphocytes (PacBio Iso-Seq, Matched to Illumina RNA-Seq Data)

Project description:Long-read sequencing technologies such as Iso-Seq (PacBio Inc.) generate highly accurate sequences of full-length mRNA transcript isoforms. Long-read transcriptomics may be especially useful in the context of lymphocyte functional plasticity as it relates to human health and disease. However, no long-read isoform-aware reference transcriptomes of human circulating lymphocytes seem to be publicly available despite being valuable as benchmarks in a variety of transcriptomic studies. To begin to fill this gap, we purified four lymphocyte subsets (CD4 T, CD8 T, NK, and Pan B cells) from the peripheral blood of a healthy male donor and obtained high-quality RNA (RIN>8) for PacBio Iso-Seq analysis and parallel RNA-Seq analysis.

2022-09-16 | GSE202327 | GEO

Reference Short-Read Transcriptomes of Human Peripheral Blood Lymphocytes (Illumina RNA-Seq, Matched to PacBio Iso-Seq Data)

2022-09-16 | GSE202328 | GEO

nf-core/isoseq: simple gene and isoform annotation with PacBio Iso-Seq long-read sequencing.

Project description:MotivationIso-Seq RNA long-read sequencing enables the identification of full-length transcripts and isoforms, removing the need for complex analysis such as transcriptome assembly. However, the raw sequencing data need to be processed in a series of steps before annotation is complete. Here, we present nf-core/isoseq, a pipeline for automatic read processing and genome annotation. Following nf-core guidelines, the pipeline has few dependencies and can be run on any of platforms.Availability and implementationThe pipeline is freely available online on the nf-core website (https://nf-co.re/isoseq) and on GitHub (https://github.com/nf-core/isoseq) under MIT License (DOI: 10.5281/zenodo.7116979).

| S-EPMC10199315 | biostudies-literature

PacBio long read sequencing of silver fir (Abies alba)

Project description:PacBio long read sequencing of silver fir (Abies alba)

| PRJEB52007 | ENA

LocusMasterTE: long-read assisted short-read RNA-seq TE quantification [long]

Project description:LocusMasterTE: long-read assisted short-read RNA-seq TE quantification [long]

| PRJNA935368 | ENA

Pk long read sequencing

Project description:Plasmodium knowlesi long read sequencing

| PRJEB19298 | ENA

A bioinformatic pipeline for analysis of M.EcoGII methylation footprint PacBio long-read sequence data

Project description:Recent studies have combined DNA methyltransferase footprinting of genomic DNA in nuclei with long-read sequencing, resulting in detailed chromatin maps for multi-kilobase stretches of genomic DNA from one cell. Nucleosome footprints and nucleosome-depleted regions can be identified, yielding unprecedented information concerning their degree of correlation within the same cell. The enzyme of choice is M.EcoGII, which methylates adenines in any sequence context, potentially resulting in very high resolution. However, in practice, the methylation efficiency (defined as the fraction of each genomic adenine that is methylated), is quite low, resulting in false footprints predicted by random unmethylated gaps between methylated adenines. We report PacBio long-read sequence data for budding yeast nuclei treated with M.EcoGII. We present a bioinformatic pipeline which accounts for methylation efficiency, as well as an observed bias against methylation as a function of increasing AT content. It also accounts for our observation that some methylation occurs within nucleosomes, breaking up their footprints. Comparison of long reads for each gene indicates the extent of chromatin heterogeneity within the cell population. Although the population average is consistent with that derived using other techniques, we observe a wide range of heterogeneity in nucleosome positions at the single-molecule level.

2024-03-15 | GSE243114 | GEO

Long-read Proteogenomics Internal Standard triggered PRM (LRP-IS-PRM)

Project description:Long-read proteogenomic data was used to create sample-matched protein database for WTC11 sample. This includes many potential alternative protein isoforms (major and minor isoforms) per gene. The IS-PRM method called Tomahto was tested versus DDA to demonstrate improved coverage of isoform-specific peptides. We called this overall method of long-read RNA informed Tomahto targeting LRP-IS-PRM and used it for protein-level evidence of multiple isoforms derived from alternative splicing.

2024-07-17 | PXD050909 | Pride

Long-read Proteogenomics Internal Standard triggered PRM (LRP-IS-PRM)

2024-07-17 | PXD050904 | Pride