Introduction Cellular senescence (CS) plays a critical role in cancer development, including clear cell renal carcinoma (ccRCC). Traditional RNA sequencing cannot detect precise molecular composition changes within tumors. This study aimed to analyze cellular senescence’s biochemical characteristics ccRCC using single (ScRNA-seq) and traditional (Bulk RNA-seq). Methods Researchers analyzed the ...

background: the opening and closing of the implantation window is important for successful pregnancy in eutherians. the recent study demonstrated that the window of uterine receptivity was prepared by the sole action of progesterone in mice, but the mechanism to close the window remained to be elucidated. methods: the pregnant mice were ovariectomized on the evening on the third day of pregnanc...

this study was done to gain insights into transcriptional regulation of negative energy balance (neb) assoctiated genes. overexpressed genes in neb were identified using microarray and rna-seq data and promoter analysis of these overexpressed genes was applied to identify novel transcription factors. moreever, string database was used to construct a regulatory network of identified transcriptio...

Bulked segregant analysis (BSA) is an efficient method to rapidly and efficiently map genes responsible for mutant phenotypes. BSA requires access to quantitative genetic markers that are polymorphic in the mapping population. We have developed a modification of BSA (BSR-Seq) that makes use of RNA-Seq reads to efficiently map genes even in populations for which no polymorphic markers have been ...

7 Genomic read coverage along transripts or CDSs 9 7.1 Binned CDS coverage to compare many transcripts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 7.2 Coverage upstream and downstream of start and stop codons . . . . . . . . . . . . . . . . . . . . . . . . 9 7.3 Combined coverage for both binned CDS and start/stop codons . . . . . . . . . . . . . . . . . . . . . . 10 7.4 Nucleot...

We present a period-luminosity-amplitude analysis of 5899 red giant and binary stars in the Large Magellanic Cloud, using publicly available observations of the MACHO project. For each star, we determined new periods, which were double-checked in order to exclude aliases and false periods. The period-luminosity relations confirm the existence of a short-period, small-amplitude P–L sequence at p...

High-occupancy target (HOT) regions are the segments of the genome with unusually high number of transcription factor binding sites. These regions are observed in multiple species and thought to have biological importance due to high transcription factor occupancy. Furthermore, they coincide with house-keeping gene promoters and the associated genes are stably expressed across multiple cell typ...

MOTIVATION The innovation of restriction-site associated DNA sequencing (RAD-seq) method takes full advantage of next-generation sequencing technology. By clustering paired-end short reads into groups with their own unique tags, RAD-seq assembly problem is divided into subproblems. Fast and accurately clustering and assembling millions of RAD-seq reads with sequencing errors, different levels o...

High-density genetic maps are essential for high resolution mapping of quantitative traits. Here, we present a new genetic map for an Arabidopsis Bayreuth × Shahdara recombinant inbred line (RIL) population, built on RNA-seq data. RNA-seq analysis on 160 RILs of this population identified 30,049 single-nucleotide polymorphisms (SNPs) covering the whole genome. Based on a 100-kbp window SNP binn...

Global transcriptomic analysis via RNA-seq is often hampered by the high abundance of ribosomal (r)RNA in bacterial cells. To remove rRNA and enrich coding sequences, subtractive hybridization procedures have become the approach of choice prior to RNA-seq, with their efficiency varying in a manner dependent on sample type and composition. Yet, despite an increasing number of RNA-seq studies, co...