Dataset Information

RNA-seq of patient-derived melanoma cells depleted for GLI1 and SOX2

ABSTRACT: We report the RNA-seq of melanoma cells depleted for SOX2 and GLI1. Three pairs of total RNAs from each condition were generated for library preparations and subsequent RNA-seq. All samples had over 50 million reads with over 93% of the reads mapping to the human genome (obtained from the UCSC Genome Browser assembly ID:hg19). Using differential expression analysis (fold change (FC)>1.5, false discovery rate (FDR)<0.1 as standard cut-offs), we identified 1104 entities commonly altered in both SOX2- and GLI1-knocked down cells. We grouped genes into enrichment clusters revealed by DAVID functional annotation tool (https://david.ncifcrf.gov/).

ORGANISM(S): Homo sapiens

PROVIDER: GSE159049 | GEO | 2020/10/06

REPOSITORIES: GEO

ACCESS DATA

Similar Datasets

Project description:Chromatin accessibility captures the binding status of protein factors to chromosomes in vivo, and has been considered a highly informative proxy for functional protein-DNA interactions. Existing DNase I and Tn5 transposase based assays generally require tens of thousands to millions of fresh cells. Applying Tn5 tagmentation to single cells yields very sparse maps. Here we present a transposome hypersensitive sites sequencing assay (THS-seq) for highly sensitive characterizations of chromatin accessibility. Validation of THS-seq method, and comparison of DNase-seq, ATAC-seq and THS-seq methods for quantitation of chromatin accessibility. GSE47753, GSM1155957 GM12878_ATACseq_50k_Rep1, data downsampled to 8,351,125 reads for analysis: pub_SRR891268_ATAC-seq_50k_cells_Rep1_downsampled_dfilter_peaks.bed.gz GSE47753, GSM1155958 GM12878_ATACseq_50k_Rep2, data downsampled to 8,351,125 reads for analysis: pub_SRR891269_ATAC-seq_50k_cells_Rep2_downsampled_dfilter_peaks.bed.gz GSE47753, GSM1155959 GM12878_ATACseq_50k_Rep3, data downsampled to 8,351,125 reads for analysis: pub_SRR891270_ATAC-seq_50k_cells_Rep3_downsampled_dfilter_peaks.bed.gz GSE47753, GSM1155960 GM12878_ATACseq_50k_Rep4, data downsampled to 8,351,125 reads for analysis: pub_SRR891271_ATAC-seq_50k_cells_Rep4_downsampled_dfilter_peaks.bed.gz GSE47753, GSM1155961 GM12878_ATACseq_500_Rep1, data downsampled to 8,351,125 reads for analysis: pub_SRR891272_ATAC-seq_500_cells_Rep1_downsampled_dfilter_peaks.bed.gz GSE47753, GSM1155962 GM12878_ATACseq_500_Rep2, data downsampled to 8,351,125 reads for analysis: pub_SRR891273_ATAC-seq_500_cells_Rep2_downsampled_dfilter_peaks.bed.gz raw data files were merged, alignment with bowtie 1.3 using parameters, bowtie -n1 -k1 --best --chunkmbs 10240 --strata -l32 -m1 -p4 --nomaqround --sam, followed by clonal read removal for the final data file for further analysis. GSM816665, raw data obtained from UCSC genome browser, https://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeOpenChromDnase: wgEncodeOpenChromDnaseGm12878RawData_merged_unique_dfilter_peaks.bed.gz raw data files were merged, alignment with bowtie 1.3 using parameters, bowtie -n1 -k1 --best --chunkmbs 10240 --strata -l32 -m1 -p4 --nomaqround --sam, followed by clonal read removal for the final data file for further analysis. GSM864360, raw data obtained from UCSC genome browser, https://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeOpenChromFaire: wgEncodeOpenChromFaireGm12878RawData_merged_unique_dfilter_peaks.bed.gz raw data files were merged, alignment with bowtie 1.3 using parameters, bowtie -n1 -k1 --best --chunkmbs 10240 --strata -l32 -m1 -p4 --nomaqround --sam, followed by clonal read removal for the final data file for further analysis. GSM736496, GSM736620, raw data obtained from UCSC genome browser, https://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeUwDnase: wgEncodeUwDnaseGm12878RawData_merged_unique_dfilter_peaks.bed.gz

Dataset Information

RNA-seq of patient-derived melanoma cells depleted for GLI1 and SOX2

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure