Searching journal content for articles similar to Keller et al. 3 (1): 32.

Displaying results 1-10 of 5805

For checked items

view abstracts
download to citation manager

Select this article
Research: Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion
- Joshua Lee,
- Elizabeth A. Snell,
- Joanne Brown,
- Charlotte E. Booth,
- Rosamonde E. Banks,
- Daniel J. Turner,
- Naveen S. Vasudev,
- and Dimitris Lagos
Genome Res. November 2024 34: 1849-1864; Published in Advance September 16, 2024, doi:10.1101/gr.278801.123
...DRS and PCS to study clear cell renal cell carcinoma (ccRCC), focusing on new transcript and gene discovery. Twelve primary ccRCC archival tumors, six from patients who went on to relapse, were analyzed. Results were validated in an independent cohort of 20 patients by qRT-PCR and compared to DRS...
OPEN ACCESS ARTICLE
Select this article
Research: Chimeric mitochondrial RNA transcripts predict mitochondrial genome deletion mutations in mitochondrial genetic diseases and aging
- Amy R. Vandiver,
- Allen Herbst,
- Paul Stothard,
- and Jonathan Wanagat
Genome Res. January 2025 35: 55-65; Published in Advance November 27, 2024, doi:10.1101/gr.279072.124
...measured by PCR-based approaches. These relationships strongly suggest that the chimeric mtRNAs are transcriptional products of the mtDNA deletion events.Many aspects of the chimeric mtRNAs strengthen what is known about mtDNA deletion mutations from DNA-based assays such as Southern blot (Corral...
Select this article
Research: Physiological intron retaining transcripts in the cytoplasm abound during human motor neurogenesis
- Marija Petrić Howe,
- Hamish Crerar,
- Jacob Neeves,
- Jasmine Harley,
- Giulia E. Tyzack,
- Pierre Klein,
- Andres Ramos,
- Rickie Patani,
- and Raphaëlle Luisier
Genome Res. October 2022 32: 1808-1825; Published in Advance September 30, 2022, doi:10.1101/gr.276898.122
...showing qPCR analysis of candidate C5 IR levels in cytoplasmic (left) and whole-cell (right) MN (DIV = 21) samples upon DROSHA knockdown. IR ratio values are calculated as levels of IRT over total transcript expression for each candidate. Data are presented as mean ± SEM. Data are derived from three...
OPEN ACCESS ARTICLE
Select this article
Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
...@iisermohali.ac.inAbstractIsoform diversity is known to enhance a gene's functional repertoire by producing protein variants with distinct functional implications. Despite numerous studies on transcriptome diversifying processes (alternative splicing/transcription), understanding their extent and correlated impact on proteome diversity...
Select this article
Method: Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
- Ju Heon Maeng,
- H. Josh Jang,
- Alan Y. Du,
- Shin-Cheng Tzeng,
- and Ting Wang
Genome Res. December 2023 33: 2143-2155; Published in Advance December 8, 2023, doi:10.1101/gr.277061.122
...or alternate promoters, which can generate transcripts that encode tumor-specific unannotated proteins. Thus, TE-derived transcripts (TE transcripts) have the potential to produce tumor-specific, but recurrent, antigens shared among many tumors. Identification of TE-derived tumor antigens holds the promise...
OPEN ACCESS ARTICLE
Select this article
Method: PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments
- Peng Liu,
- Alexandra A. Soukup,
- Emery H. Bresnick,
- Colin N. Dewey,
- and Sündüz Keleş
Genome Res. November 2020 30: 1655-1666; Published in Advance September 21, 2020, doi:10.1101/gr.252445.119
...approach outperforms the conventional 2-Step approach in data-driven computational experiments. In our application of PRAM to mouse and human s, we discovered unannotated transcripts in hematopoietic cell systems, which were supported by multiple lines of genomic data evidence and validated by semi-qRT-PCR...
OPEN ACCESS ARTICLE
Select this article
Research: TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells
- Kasper D. Rasmussen,
- Ivan Berest,
- Sandra Keβler,
- Koutarou Nishimura,
- Lucía Simón-Carrasco,
- George S. Vassiliou,
- Marianne T. Pedersen,
- Jesper Christensen,
- Judith B. Zaugg,
- and Kristian Helin
Genome Res. April 2019 29: 564-575; Published in Advance February 22, 2019, doi:10.1101/gr.239277.118
...endogenously tagged TET2. The number of peaks enriched in parental cells are also shown (inverse peak calling). (C) ChIP-qPCR for TET2 binding in ES cells using antibodies raised against endogenous TET2. Two positive regions (an intronic DNase I hypersensitivity site in Tet3 and an enhancer region in the Manba...
Select this article
Method: A long-read RNA-seq approach to identify novel transcripts of very large genes
- Prech Uapinyoying,
- Jeremy Goecks,
- Susan M. Knoblach,
- Karuna Panchapakesan,
- Carsten G. Bonnemann,
- Terence A. Partridge,
- Jyoti K. Jaiswal,
- and Eric P. Hoffman
Genome Res. June 2020 30: 885-897; Published in Advance July 6, 2020, doi:10.1101/gr.259903.119
...annotations, we also identified and quantified previously unannotated transcripts. Results were confirmed by endpoint PCR and Sanger sequencing, which revealed muscle-type-specific differential expression of these novel transcripts. The improved transcript identification and quantification shown by our...
OPEN ACCESS ARTICLE
Select this article
Research: SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission
- Nicolae Sapoval,
- Medhat Mahmoud,
- Michael D. Jochum,
- Yunxi Liu,
- R.A. Leo Elworth,
- Qi Wang,
- Dreycey Albin,
- Huw A. Ogilvie,
- Michael D. Lee,
- Sonia Villapol,
- Kyle M. Hernandez,
- Irina Maljkovic Berry,
- Jonathan Foox,
- Afshin Beheshti,
- Krista Ternus,
- Kjersti M. Aagaard,
- David Posada,
- Christopher E. Mason,
- Fritz J. Sedlazeck,
- and Todd J. Treangen
Genome Res. April 2021 31: 635-644; Published in Advance February 18, 2021, doi:10.1101/gr.268961.120
...: Annotation of SARS-CoV-2 (gray), PCR primer designs (dark red), transcription-regulating sequences (TRS) (orange), intra-host variant density including iSNVs (blue), deletions start sites (red), duplication start sites (yellow), and inversion start sites (green) along the entire . For SNPs + iSNVs + SVs, we...
OPEN ACCESS ARTICLE
Select this article
Method: Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR
- Marta Puig,
- Jon Lerga-Jaso,
- Carla Giner-Delgado,
- Sarai Pacheco,
- David Izquierdo,
- Alejandra Delprat,
- Magdalena Gayà-Vidal,
- Jack F. Regan,
- George Karlin-Neumann,
- and Mario Cáceres
Genome Res. May 2020 30: 724-735; Published in Advance May 18, 2020, doi:10.1101/gr.255273.119
...-Soler et al. 2018), among other applications. Recently, ddPCR-based linkage calculations have also been used to phase variants separated by up to 200 kb (Regan et al. 2015), including deletions (Boettger et al. 2016), or for fusion transcript detection (Hoff et al. 2016). Here, we have developed new ddPCR...
OPEN ACCESS ARTICLE

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Keller et al. 3 (1): 32.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: