ArticleMeta gene2016
IsoSeq analysis and functional annotation of the infratentorial ependymoma tumor tissue on PacBio RSII platform.
Article in Meta gene, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
8 citing papers in PubMed, 17 citations in OpenAlex.
- Accurate Long-Read RNA Sequencing Analysis Reveals the Key Pathways and Candidate Genes under Drought Stress in the Seed Germination Stage in Faba Bean.International journal of molecular sciences · 2024Article
- Genome sequencing reveals chromosome fusion and extensive expansion of genes related to secondary metabolism in Artemisia argyi.Plant biotechnology journal · 2022Article
- Nanopore long-read RNA-seq and absolute quantification delineate transcription dynamics in early embryo development of an insect pest.Scientific reports · 2021Article
- Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins.High-throughput · 2019Article
- ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq.International journal of genomics · 2018Article
- Long Non-coding RNAs in Endothelial Biology.Frontiers in physiology · 2018Review
- Alternative Polyadenylation: Methods, Findings, and Impacts.Genomics, proteomics & bioinformatics · 2017Review
- Analyses of alternative polyadenylation: from old school biochemistry to high-throughput technologies.BMB reports · 2017Review
Corrections and comments
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Authors and funding
10 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here, we sequenced and functionally annotated the long reads (1-2 kb) cDNAs library of an infratentorial ependymoma tumor tissue on PacBio RSII by Iso-Seq protocol using SMRT technology. 577 MB, data was generated from the brain tissues of ependymoma tumor patient, producing 1,19,313 high-quality reads assembled into 19,878 contigs using Celera assembler followed by Quiver pipelines, which produced 2952 unique protein accessions in the nr protein database and 307 KEGG pathways. Additionally, when we compared GO terms of second and third level with alternative splicing data obtained through HTA Array2.0. We identified four and twelve transcript cluster IDs in Level-2 and Level-3 scores respectively with alternative splicing index predicting mainly the major pathways of hallmarks of cancer. Out of these transcript cluster IDs only transcript cluster IDs of gene PNMT, SNN and LAMB1 showed Reads Per Kilobase of exon model per Million mapped reads (RPKM) values at gene-level expression (GE) and transcript-level (TE) track. Most importantly, brain-specific genes--PNMT, SNN and LAMB1 show their involvement in Ependymoma.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.