Searching journal content for articles similar to Jiang et al. 21 (9): 1543.

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Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
- Qiang Su,
- Yi Long,
- Deming Gou,
- Junmin Quan,
- Xiaoming Zhou,
- and Qizhou Lian
Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
...features from primary to tertiary levels associated with sequencing biases. (A) Spike-in synthetic RNAs were processed using the hexamer-based standard VAHTS Universal V8 RNA-seq library preparation protocol. Sequencing counts for each spike-in were obtained and subsequently used for downstream grouping...
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Research: Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data
- Aaron T.L. Lun,
- Fernando J. Calero-Nieto,
- Liora Haim-Vilmovsky,
- Berthold Göttgens,
- and John C. Marioni
Genome Res. November 2017 27: 1795-1806; Published in Advance October 13, 2017, doi:10.1101/gr.222877.117
...yields s2vol = var(ui) − var(u∗i ) It should be stressed that this variance estimate is relevant to all experiments using the same protocol for spike-in addition, even if the identity or concentration of the spike-in set is different. Generally, scaling normalization of RNA-seq data is performed...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...provided by synthetic spike-in RNA variants (SIRVs) or Sequins spike-in controls (Hardwick et al. 2016), to those in a real sample. For example, we used the SQANTI3 framework to analyze the reads associated with Lexogen's E0 mix SIRV transcripts spiked into the aforementioned mouse brain samples, sequenced...
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Research: Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay
- Marcus J. Viscardi,
- Enisha Sehgal,
- and Joshua A. Arribere
Genome Res. June 2025 35: 1337-1348; Published in Advance May 9, 2025, doi:10.1101/gr.280046.124
...reads’ tail lengths, and the right (in dark gray) shows unadapted reads. The three violins to the right show the tail length distributions for three spike-in RNA standards. Long dashed lines indicate the means, and short dashed lines indicate first and fourth quartile boundaries. (B) Poly(A) tail length...
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Method: Long-read reconstruction of many diverse haplotypes with devider
- Jim Shaw,
- Christina Boucher,
- Yun William Yu,
- Noelle Noyes,
- and Heng Li
Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
...with spike-in metaWe extended the previous AMR haplotyping experiment to a metagenomics setting. In metagenomics, the input is a mixture of microbial genomic reads and reads from AMR genes. Thus, we mixed the previously simulated AMR reads into a simulated long-read mouse gut meta from CAMI2 (labeled...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...isoform reads derived from simulated data and from real data as derived from our application of high-throughput PacBio long-read RNA-seq, MAS-ISO-seq, to the Seraseq Fusion RNA Mix v4 control sample containing 16 spiked-in oncogenic fusion transcripts and to nine cancer cell lines. CTAT...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...: In this window In a new window Table 2. Transcription factor binding site motifs enriched in active enhancersTo further validate that the enriched TFBS motifs correlate with TFs that are highly expressed in phNPCs, we analyzed their expression using single-cell RNA-seq (scRNA-seq) data generated in the ph...
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Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
- Junling Shi,
- Jiaqi Xu,
- Jun Ma,
- and Feng He
Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
...RNA reads) or E. coli tRNALysUUU as a spike-in control (RPKE, reads per kilo E. coli tRNA reads). Error bars represent SEM (standard error of the mean) computed from two or three biological replicates. Asterisks indicate significant differences (Student's t-test P < 0.01 denoted as **). (D) Linear models...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...are the gold standard for high-throughput transcriptome profiling (Wang et al. 2009). RNA-sequencing (RNA-seq) has been used to investigate gene expression (The ENCODE Project Consortium 2012), canonical and alternative mRNA splicing (Wright et al. 2022a), noncoding RNAs, and post-transcriptional modifications...
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Research: Global loss of cellular m⁶A RNA methylation following infection with different SARS-CoV-2 variants
- Roshan Vaid,
- Akram Mendez,
- Ketan Thombare,
- Rebeca Burgos-Panadero,
- Rémy Robinot,
- Barbara F. Fonseca,
- Nikhil R. Gandasi,
- Johan Ringlander,
- Mohammad Hassan Baig,
- Jae-June Dong,
- Jae Yong Cho,
- Björn Reinius,
- Lisa A. Chakrabarti,
- Kristina Nystrom,
- and Tanmoy Mondal
Genome Res. March 2023 33: 299-313; Published in Advance March 1, 2023, doi:10.1101/gr.276407.121
...%–95% of infected cells for all the variants (Supplemental Fig. S1A). We isolated total RNA 48 h postinfection and evaluated gene expression changes using RNA sequencing (RNA-seq). We first checked viral RNA levels postinfection and observed that RNA-seq reads mapping to the viral were comparable for the three SARS...
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