ROSE是一个python包,代码放在Github上(https://github.com/stjude/ROSE),直接下载压缩包就可以了。 wget https://github.com/stjude/ROSE/archive/refs/heads/master.zip unzip master.zip 解压之后文件夹中包含以下内容: image.png 用到的脚本都放在bin目录下。可以通过指定bin目录的位置调用命令: ...
The raw fastq file (GSE36354) from the European Nucleotide Archive was download by using Aspera, and reads are then mapped to the reference using Bowtie2, and Samtools was used for sorting and indexing. BigWig files were created from bam files for each sample using genomeCoverageBed and bedG...
and may also occur in meningiomas23. However, the molecular mechanisms that lead to increasedIHHexpression in neoplasia have not been established. Unraveling these processes may elucidate important routes to oncogenesis in tumors that lack established genomic drivers, particularly those that exhibit Hh p...
Other datasets used in this analysis were downloaded from the European Genome–Phenome Archive (EGAD00001004142, EGAD00001006087 and EGAD00001003783)10,34; dbGaP (phs000235.v14.p2 and phs000527.v3.p1); the NCBI (SRP020237); the GEO (GSE89688 (H3K27Ac data of normal GC B cells) and GSE6...
The publicly available histone modification ChIP-seq data used in this study are available in the GEO database under accession code GSE14593822 and in the European Nucleotide Archive (ENA) database under accession code PRJEB256059. The publicly available RNA-seq data from the Blueprint Consortium...
H3K27ac ChIP seq data for ER + patients was obtained from European Nucleotide Archive under project no. PRJEB22757 and for TNBC patient samples and TNBC cell lines under project no. PRJEB33558. Acquired/lost super-enhancer identification Acquired super-enhancer regions were classified at ...
Under an Elsevier user license Open archiveHighlights Summary Super-enhancers are an emerging subclass of regulatory regions controlling cell identity and disease genes. However, their biological function and impact on miRNA networks are unclear. Here, we report that super-enhancers drive the biogenesis...
Under an Elsevier user license open archiveHighlights Summary Although enhancers play critical roles in cancer, quantifying enhancer activities in clinical samples remains challenging, especially for super-enhancers. Enhancer activities can be inferred from enhancer RNA (eRNA) signals, which requires enhancer...
The RNA-seq, ChIP-seq, ATAC-seq and eCLIP data reported in this paper have been deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database, under accession codes PRJNA678286 and GSE234078. The mass spectrometry proteomics data are deposited in ...
data have been deposited in the GEO under accession no.GSE211589and the Genome Sequence Archive in BIG Data Center under accession no. HRA000095 (https://ngdc.cncb.ac.cn/gsa-human/browse/HRA000095). The following datasets were used to generate the data: PAAD clinical features and batch...