Project description:We report the immediate effects of estrogen signaling on the transcriptome of breast cancer cells using Global Run-On and sequencing (GRO-seq). We found that estrogen signaling directly regulates a strikingly large fraction of the transcriptome in a rapid, robust, and unexpectedly transient manner. In addition to protein-coding genes, estrogen regulates the distribution and activity of all three RNA polymerases, and virtually every class of non-coding RNA that has been described to date. This data submission covers >95% of mapped reads comprising nearly all transcript classes described. Reads mapping to intergenic and enhancer transcripts were removed from this data submission and will be reported separately (manuscripts in preparation). Bed files are tab-separated text files in which columns represent: chrom, chromStart (5' End of the read), chromEnd (chromStart+1), name (unused always 'n'), score (the number of mismatches), and strand. Note that because of the inclusion of reads mapping to the rRNA chromosome, bed files cannot be uploaded to the UCSC genome browser directly. Instead, use the wiggle files (coming soon!) for this purpose.
Project description:Sequencing files, and processed data correspond to Figure 3 of Regenerating Human Skeletal Muscle Forms an Emerging Niche In Vivo to Support PAX7 cells. Data contains single nucleus RNA seq from Pax7 ablated mdx-NSG mice, control mdx-NSG mice, with or without an injury. These mice offer superior engraftment by human skeletal muscle stem and progenitor cells. Pax7 ablation model enables evaluation of human stem cell niche formation in the absence of mouse Pax7 cell competition. Included in this dataset is everything required to run independent analysis. We have included raw Fastq files and processed files that are ready to be uploaded into Loupe Browser or R-Studio/Seurat V3. To summarize Cloupe Files can be uploaded to Loupe Browers and the BC_Matrix.H5 files can be uploaded directly to R. Furthermore, the RDS files are processed R-program files that can be immediately uploaded into R for analysis. We have included an example R script for users to follow and a few PDFs of excepted UMAPs using all combined files at PCA 35.
Project description:We report the immediate effects of estrogen signaling on the transcriptome of breast cancer cells using Global Run-On and sequencing (GRO-seq). We found that estrogen signaling directly regulates a strikingly large fraction of the transcriptome in a rapid, robust, and unexpectedly transient manner. In addition to protein-coding genes, estrogen regulates the distribution and activity of all three RNA polymerases, and virtually every class of non-coding RNA that has been described to date. This data submission covers >95% of mapped reads comprising nearly all transcript classes described. Reads mapping to intergenic and enhancer transcripts were removed from this data submission and will be reported separately (manuscripts in preparation). Bed files are tab-separated text files in which columns represent: chrom, chromStart (5' End of the read), chromEnd (chromStart+1), name (unused always 'n'), score (the number of mismatches), and strand. Note that because of the inclusion of reads mapping to the rRNA chromosome, bed files cannot be uploaded to the UCSC genome browser directly. Instead, use the wiggle files (coming soon!) for this purpose. Using GRO-seq over a time course (0, 10, 40, 160 min) of estrogen signaling in ER-alpha positive MCF-7 human breast cancer cells.
Project description:These are the ribosomal subunit fractions from the polysome gradients. investigating effect of heat shock on procyclic-form trypanosomes.
Project description:Overview: RNA-seq was used to profile the whole-transcriptome gene expression of highly replicated schizont-stage cultures of W2mef and Dd2 grown under static and suspended conditions. Methods: Transcript profiles of schizont stages of static and suspended W2mef and Dd2 were generated by RNA sequencing. Two to eight replicates were sequenced per sample. Illumina stranded TruSeq libraries were sequenced using an Illumina MiSeq. Hisat2 was used to align paired-end fastQ files and indexed bam files generated with samtools. Bam files were filtered to exclude reads with MAPQ scores below 60, reads counted using the SummarizeOverlaps feature of the GenomicAlignments package in R and differential expression analysis conducted using DESeq2 in R. Results: We show that in addition to invasion-related genes, parasites that have been induced to switch invasion phenotype upon culturing in suspension increase the expression of a number of genes most of which belong to gene families that code for exported proteins. Conclusions: Our data suggest that in addition to invasion phenotype switch, suspension cultures may select for other parasite properties that may be essential for parasite survival in vivo.
Project description:Targeted metabolomics platforms included amino acids and metabolites related to glucose-mediated energy production. The targeted metabolome changed with chemotheraphy-induced cachexia, and the changes were reversed with potential treatment of the cachexia. .rdb files were included as raw data files where detailed information regarding MRM transitions and internal standards can be found. Several amino acids (Gly, Pro, Gln, Taurine) were analyzed after dilution because their peak intensities were too high. Thus their analysis was performed separately from other amino acids, and their rdb files were saved in separate rdb files.