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Research: Long-read DNA and cDNA sequencing identify cancer-predisposing deep intronic variation in tumor-suppressor genes
- Suleyman Gulsuner,
- Amal AbuRayyan,
- Jessica B. Mandell,
- Ming K. Lee,
- Greta V. Bernier,
- Barbara M. Norquist,
- Sarah B. Pierce,
- Mary-Claire King,
- and Tom Walsh
Genome Res. November 2024 34: 1825-1831; Published in Advance September 13, 2024, doi:10.1101/gr.279158.124
..., long-read cDNA sequencing coverage was &gt;100× at the critical gene for each of the samples. All seven variants with scores ≥0.10 yielded transcripts including pseudoexons ( Table 1 ), with all results confirmed by RT-PCR and Sanger sequencing ( Supplemental Fig. S1 ). No pseudoexons were detected...
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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
...a comparison and includes equivalent data for the current mouse reference assembly GRCm39 (NCBI Mus musculus annotation release 109). Although the mouse assembly annotation arises from a different data set of mouse RefSeq sequences, which includes a larger accumulation of cDNA and other sequencing data...
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Method: CRISPR-based modular assembly of a UAS-cDNA/ORF plasmid library for more than 5500 Drosophila genes conserved in humans
- Ping Wei,
- Wen Xue,
- Yun Zhao,
- Guang Ning,
- and Jiwu Wang
Genome Res. January 2020 30: 95-106; Published in Advance November 13, 2019, doi:10.1101/gr.250811.119
...of every single gene including primer design and synthesis, PCR, gel purification, and sequencing. Particularly, construction of UAS-cDNA/ORF plasmids for long cDNAs or ORFs by the recombinational (Gateway) cloning technique is truly problematic. Therefore, the technical difficulties of construction...
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Resource: Genome-scale targeted mutagenesis in Brassica napus using a pooled CRISPR library
- Jianjie He,
- Kai Zhang,
- Shuxiang Yan,
- Mi Tang,
- Weixian Zhou,
- Yongtai Yin,
- Kang Chen,
- Chunyu Zhang,
- and Maoteng Li
Genome Res. May 2023 33: 798-809; Published in Advance June 8, 2023, doi:10.1101/gr.277650.123
...and HiScript III enzyme mix (Vazyme) for RT. Quantitative PCR (qPCR) was performed on a QuantStudio 3 real-time PCR system (Applied Biosystems) with a mixed 20-μL solution of 1-μL cDNA, 0.8-μL primers (10 μM), 8.2-μL ddH2O, and 10-μL SYBR Green master mix (Yeasen). Each experiment was conducted...
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Resource: Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse (Acomys) ear
- Henriëtte van Beijnum,
- Tim Koopmans,
- Antonio Tomasso,
- Vanessa Disela,
- Severin te Lindert,
- Jeroen Bakkers,
- Anna Alemany,
- Eugene Berezikov,
- and Kerstin Bartscherer
Genome Res. August 2023 33: 1424-1437; Published in Advance September 19, 2023, doi:10.1101/gr.277538.122
...for every fifth section, followed by reverse transcription and barcoding. The barcoded cDNA was pooled and linear-amplified, and the resulting sequencing libraries were sequenced using the Illumina NextSeq 500 (Fig. 3A). We assessed the reproducibility of the three biological replicates with the Pearson...
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Method: Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing
- Charles Cole,
- Ashley Byrne,
- Matthew Adams,
- Roger Volden,
- and Christopher Vollmers
Genome Res. April 2020 30: 589-601; Published in Advance April 20, 2020, doi:10.1101/gr.257188.119
...was purified and size selected to >300 nt using Select-a-size DNA Clean and Concentrator kits (Zymo). In a 20-cycle PCR reaction, the cDNA is then amplified with primer completing Nextera sequences as well as Illumina i5 and i7 indexes to enable multiplexing of the libraries. Libraries were then sequenced...
ARTICLE: Construction of subtractive cDNA library using magnetic beads and PCR.
- A Lönneborg,
- P Sharma,
- and P Stougaard
Genome Res. February 1995 4: S168-S176
.... Nucleic Acids Res. 19 : 4010 . 9.. Houge, G. Houge, G. 1993 . Simplified construction of a subtracted cDNA library using asymmetric PCR. PCR Methods Appl. 2 : 204 – 209 . 10.. Jepson, I., , Bray, J. , Jenkins, G. , Schuch, W. , Edwards. K. Jepson, I., Bray, J. Jenkins, G. Schuch, W. and Edwards. K. 1991...
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Method: Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT
- Andrea Cracco and
- Alexandru I. Tomescu
Genome Res. July 2023 33: 1198-1207; Published in Advance May 30, 2023, doi:10.1101/gr.277615.122
...Bruijn graphs are one of the most fundamental data structures in computational genomics. Colored compacted de Bruijn graphs are a variant built on a collection of sequences and associate to each k-mer the sequences in which it appears. We present GGCAT, a tool for constructing both types of graphs, based...
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Research: The subgenomes show asymmetric expression of alleles in hybrid lineages of Megalobrama amblycephala × Culter alburnus
- Li Ren,
- Wuhui Li,
- Qinbo Qin,
- He Dai,
- Fengming Han,
- Jun Xiao,
- Xin Gao,
- Jialin Cui,
- Chang Wu,
- Xiaojing Yan,
- Guoliang Wang,
- Guiming Liu,
- Jia Liu,
- Jiaming Li,
- Zhong Wan,
- Conghui Yang,
- Chun Zhang,
- Min Tao,
- Jing Wang,
- Kaikun Luo,
- Shi Wang,
- Fangzhou Hu,
- Rurong Zhao,
- Xuming Li,
- Min Liu,
- Hongkun Zheng,
- Rong Zhou,
- Yuqin Shu,
- Yude Wang,
- Qinfeng Liu,
- Chenchen Tang,
- Wei Duan,
- and Shaojun Liu
Genome Res. November 2019 29: 1805-1815; Published in Advance October 24, 2019, doi:10.1101/gr.249805.119
...identification and AR sequence detection by Illumina sequencing, PCR validation of AR genes, library construction and PacBio sequencing, and AR gene detection by -wide long-read alignments could be found in the Supplemental Methods.Global expression patternsIn-house Perl scripts were used to calculate the number...
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RESOURCE: A Subtracted cDNA Library from the Zebrafish (Danio rerio) Embryonic Inner Ear
- Roney S. Coimbra,
- Dominique Weil,
- Phillipe Brottier,
- Stéphane Blanchard,
- Michael Levi,
- Jean-Pierre Hardelin,
- Jean Weissenbach,
- and Christine Petit
Genome Res. June 1, 2002 12: 1007-1011; doi:10.1101/gr.227502
...otocysts and from the liver of adult zebrafish. Ear and liver cDNA were produced with the CLONTECH SMART PCR cDNA synthesis kit (CLONTECH). Liver cDNA was subtracted from the ear cDNA using the CLONTECH PCR-Select cDNA subtraction kit. Manufacturer's instructions were followed, except that two rounds...

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