ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/052/SRR13091952/SRR13091952_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/044/SRR13091944/SRR13091944_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/048/SRR13091948/SRR13091948_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/045/SRR13091945/SRR13091945_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/049/SRR13091949/SRR13091949_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/046/SRR13091946/SRR13091946_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/058/SRR13091958/SRR13091958_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/057/SRR13091957/SRR13091957_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/057/SRR13091957/SRR13091957_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/053/SRR13091953/SRR13091953_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/047/SRR13091947/SRR13091947_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/045/SRR13091945/SRR13091945_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/051/SRR13091951/SRR13091951_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/054/SRR13091954/SRR13091954_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/056/SRR13091956/SRR13091956_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/050/SRR13091950/SRR13091950_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/046/SRR13091946/SRR13091946_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/048/SRR13091948/SRR13091948_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/056/SRR13091956/SRR13091956_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/058/SRR13091958/SRR13091958_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/055/SRR13091955/SRR13091955_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/054/SRR13091954/SRR13091954_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/052/SRR13091952/SRR13091952_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/051/SRR13091951/SRR13091951_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/055/SRR13091955/SRR13091955_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/053/SRR13091953/SRR13091953_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/050/SRR13091950/SRR13091950_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/044/SRR13091944/SRR13091944_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/047/SRR13091947/SRR13091947_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR130/049/SRR13091949/SRR13091949_1.fastq.gzprimaryOK200GenomicsFazzio lab, Molecular, Cell and Cancer Biology, University of Massachusetts medical schoolhttps://www.ebi.ac.uk/ena/browser/view/PRJNA679790Mus musculusxref:PubMed:34478875We performed mRNA-seq on mouse embryonic stem cells, with four DEAD-box family proteins, DDX10, DDX24, DDX27, DDX54 being partially depleted using RNA interference. Knockdown of EGFP was carried out as a control. By comparing all four knockdowns, we observed misregulation of a highly-overlapping set of genes, indicating that they regulate mRNA levels through a shared pathway. Overall design: mRNA profiles of knockdowns of 4 Ddx genes, with EGFP knockdown as control, all performed with three biological replicatesENAEmbryonic, Modification, Gene., RNA, Post Transcriptional RNA Processing, Gene Expressions, Posttranscriptional, Embryonic Stem Cell, RNA Processing, Processing, Proteins, Stem Cells, Modifications, Post-Transcriptional RNA Modification, Gene, Post Transcriptional RNA Modification, Expressions, Cell, Protein Gene Products, Gene Proteins, Post-Transcriptional RNA Modifications, Posttranscriptional RNA, Post-Transcriptional, Stem Cell, RNA Modifications, Protein, Cells, Gene Products, Post Transcriptional, Post-Transcriptional RNA, Expression, RNA Modification, Post-Transcriptional RNA Processing, Embryonic Stem, Posttranscriptional RNA ProcessingEmbryonic, Modification, Gene., RNA, Post Transcriptional RNA Processing, Gene Expressions, Posttranscriptional, Embryonic Stem Cell, RNA Processing, Processing, Proteins, Stem Cells, Modifications, Post-Transcriptional RNA Modification, Gene, Post Transcriptional RNA Modification, Expressions, Cell, Protein Gene Products, Gene Proteins, Post-Transcriptional RNA Modifications, Posttranscriptional RNA, Post-Transcriptional, Stem Cell, RNA Modifications, Protein, Cells, Gene Products, Post Transcriptional, Post-Transcriptional RNA, Expression, RNA Modification, Post-Transcriptional RNA Processing, Embryonic Stem, Posttranscriptional RNA ProcessingfalseCharacterization of R-loop-interacting proteins in embryonic stem cells reveals roles in ribosomal RNA processing and gene expressionCharacterization of R-loop-interacting proteins in embryonic stem cells reveals roles in ribosomal RNA processing and gene expression2025-09-242021-08-29PRJNA679790GSE1618901009034478875