Journal: Frontiers in Pharmacology

Article Title: Phosphodiesterase 7: a potential novel therapeutic target in ovarian cancer

doi: 10.3389/fphar.2025.1566330

Figure Lengend Snippet: Validation of gene expression by RT-qPCR. (A-I) The relative expression of genes in seven fallopian tube samples and seven samples from HGSC patients, as determined by RNA sequencing data, was validated using RT-qPCR.

Article Snippet: Amongst the first twenty genes from the high-throughput RNA sequencing data (data gently provided by Dr. Shih from Johns Hopkins University), we designed primers for nine of them.

Techniques: Biomarker Discovery, Gene Expression, Quantitative RT-PCR, Expressing, RNA Sequencing

Journal: International Journal of Molecular Sciences

Article Title: Identification of Tomato microRNAs in Late Response to Trichoderma atroviride

doi: 10.3390/ijms25031617

Figure Lengend Snippet: General analysis in Trichoderma atroviride T11-treated (T11) Solanum lycopersicum or untreated (C) plants libraries. ( A ) Length distribution and abundance of the miRNAs that showed at least 10 read counts against their miRNA* sequence in S. lycopersicum plants treated (T11) or not (C). The percentage is calculated over the total number of reads that aligned to the miRNA candidates identified in plants from both conditions (including those with less than 10 read counts against their miRNA* sequence and/or those that were solely transcribed in one sample per condition). The length of the miRNAs identified ranged from 20–24 nt; ( B ) Venn diagram showing the number of miRNAs (that displayed at least 10 read counts against their miRNA* sequence) identified in both conditions, solely in T11 (green) or in untreated control plants (blue).

Article Snippet: Quality control of the sequencing data and the identification of known and novel miRNA candidates were performed by Sequentia Biotech S.L. (Barcelona, Spain) as follows.

Techniques: Sequencing, Control

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: Human-specific tandem repeat expansion and differential gene expression during primate evolution

doi: 10.1073/pnas.1912175116

Figure Lengend Snippet: STR/VNTR sequence composition plots. The 4 loci represent STRs/VNTRs with ≥40 tandem repeat copies. The sequences from each human and NHP haplotype were colored according to their k-mer abundance (Materials and Methods). For the CHM13 sample, sequences from both CLR and HiFi assemblies have been included labeled as “CHM13” and “CHM13_HiFi,” respectively, which provide a replicate measure of sequence accuracy. (A) An STR located upstream of RNF219 is composed of 7 to 62 uninterrupted tandem copies of an AAAG expansion in humans. Three human haplotypes contain clustered AAGG interruptions, while 1 chimpanzee haplotype contains a clustered interruption of AG repeats. (B) A human-specific STR expansion is located in the intron of PHLDB2 and is composed of 18 to 70 uninterrupted repeats of AAG. Periodic interruptions of AGG exist in 3 human haplotypes and GRCh38. (C) An STR located in the intron of ADGRE2 contains 3 to 42 uninterrupted tandem repeat copies of TTTC. A cluster of a continuous tract of pure TC repeats interrupts the tetranucleotide repeat in 1 of the Puerto Rican haplotypes. (D) A human-specific VNTR expansion is located in the intron of CLCN5 and is composed of 21 to 80 tandem repeat copies of a 26-bp motif. A single interruption by a 30-bp motif that contains 3 additional adenines in position 23 occurs in the Puerto Rican and Yoruban haplotypes (gray bars).

Article Snippet: 3) Validation with orthogonal long-read sequence datasets: we carried out an additional orthogonal validation for STRs and VNTRs from the CHM13 continuous long-read (CLR) assembly using orthogonal high-fidelity (HiFi) circular consensus sequencing data and ultralong Oxford Nanopore Technologies (UL-ONT) sequence reads generated from the same source cell line (CHM13) ( 29 ).

Techniques: Sequencing, Labeling