JUNB emerged as a prominently affected transcription factor and has previously been shown to control neutrophil activation36and to be highly expressed upon neutrophil activation43. On the other hand, CEBPB has previously been shown to be a key transcription factor mediating emergency granulopoiesis...
13a), decreased the expression of Pre-INS transcript levels49 was observed. Neither the β-cell transcription factor NKX6.1 nor the endocrine marker NEUROD1 were significantly altered. In contrast, SST was increased in MAFB knockdown cells and there were increases in PDX1 and the δ-cell ...
This approach, however, can miss some true integration sites that do not produce a chimeric transcript. It will also miss sites where one read of a pair maps completely to the virus and the other completely to the host. Future studies using long-read whole-genome sequencing or targeted ...
In this study we combine RNA-seq data from different primary tissues, cell lines and cellular compartments to characterise the human protein coding transcriptome from a functional perspective. We show that in a given condition most protein coding genes not only express one major transcript, as recen...
Thus, we could avoid counting each transcript several times. Down-sampling Analysis To check whether the sequencing depth is enough for the subsequent analyses, we selected an embryo (male, 20 week, 88 single cells sequenced) to down-sample the raw data to 10%, 20%, 30%, 40%, 50%, ...
We next explored possible regulatory mechanisms responsible for the observed increase in mTEChitranscript initiation stochasticity. We first searched for known transcription factor binding motifs within 200 base pairs of each TSR and calculated the mTEChi:mTECloOR for each of these known motifs (Fig....
The SRA files of the 1,019 cell lines from the CCLE 2019 data6were downloaded from the GEO using SRA Toolkit (v2.11.3) and were subsequently converted into raw fastq files. The RNA-seq data processing followed the same pipeline as the HPA project. Transcript expression levels were quantified...
(Additional file2). As expected, since PTRs are defined as protein divided by transcript abundance, we observed an inverted codon signature related to mRNAs (Additional file1: Fig. S5A, Additional file3). Conversely, proteomics data alone led to a similar but less pronounced codon pattern as ...
The effect of the mutation on the transcript, p value, factor loading coefficient, and number of times the mutation was found are provided for each mutation tested for association with TMB for which the corrected p value was <0.05. (XLSX 81 kb) Additional file 8: Table S4. Summary of ...
As described in a previous study, normalized data were sorted for significance and then filtered according to the Transcript Support Level (TSL) used by the Ensembl gene annotation system [27]. This annotation system is a method to highlight the well supported and poorly supported transcript ...