Project description:Four Kcng4-cre;stop-YFP mouse retinas from two mice were dissected, dissociated and FACS sorted, and single cell RNA-seq libraries were generated for 384 single cells using Smart-seq2. Aligned bam files are generated for 383 samples as one failed to align.
Project description:Stroma extracts were isolated from 2-week-old WT plants and incubated with either BSF-specific antibodies or with the pre-immune serum. IgGs were captured with SiMAG-Protein G beads (Chemicell) and recovered RNA was used for generation of libraries with the ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre). Primary reads were aligned to the Arabidopsis chloroplast genome (accession number NC_000932.1) using CLC Genomics Workbench. BAM files were extracted and sorted in Galaxy . Sorted BAM files were converted into RPKM-normalized bigwig files and displayed in IGB. The differential enrichment of BSF/control of the two replicates was displayed across the entire chloroplast genome to identify the RNA targets of BSF.
Project description:Investigation of whole genome gene expression level changes in human osteosarcoma cell line MNNG/HOS treated by TGF-beta1 for three days (mesophase) and five days (sarcospheres iOSCs), compared to non-treatment cells (residual adherent cells). A three chip study using total RNA cover from three cultures of non-treatment human osteosarcoma cell line MNNG/HOS (residual adherent cells), TGF-beta1 treated three days osteosarcoma cell line MNNG/HOS (mesophase) and TGF-beta1 treated five days osteosarcoma cell line MNNG/HOS ( only collected the suspending sarcospheres iOSCs). Each chip measures the expression level of 45033 genes from osteosarcoma cell line MNNG/HOS.
Project description:Purpose: RNase Y is a major enzyme responsible for mRNA degradation in Streptococcus pyogenes. The goals of this study are to understand whether RNase Y plays a role in operon transcription of S. pyogenes NZ131 by using RNA-seq analysis. Methods: S. pyogenes mRNA profiles of wild type (WT) and RNase Y mutant (∆rny) were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000. The sequence reads were aligned to the S. pyogenes genome using Bowtie2. The aligned files were sorted to BAM format and indexed using Samtools. The read depth of each base was derived from BAM files using BEDtools. Operon organization of S. pyogenes WT and ∆rny strains were predicted based on base reads. Results: A total of 11 to 12 billion reads were obtained from each sample. More than 99% of these reads were mapped to the S. pyogenes genome. Predictions of operon organization using WT and ∆rny samples showed little difference between the two strains. Conclusions: Our result shows that the mutation of RNase Y does not affect the operon organization of S. pyogenes NZ131.
Project description:Invastigation of whole genome gene expression level changes in human osteosarcoma cell line MNNG/HOS sarcospheres,hypoxia-induced sarcospheres and TGF-beta1 induced sarcospheres. A three chip study using total RNA cover from three cultures of human osteosarcoma cell line MNNG/HOS sarcospheres, hypoxia-induced sarcospheres and TGF-beta1-induced sarcospheres. Each chip measures the expression level of 45033 genes from osteosarcoma cell line MNNG/HOS.
Project description:Purpose: A method for mapping chromatin accessibility genome-wide, to reveal chromatin accessibility in Intestinal stem cells. Methods: Intestinal stem cells(Lgr5-high cells) were sorted by flow cytometry from wild type mice. The samples were prepared in duplicate. HISAT2 was used to align the sequences to the mouse genome and generate bam files. bamCoverage was used to generate bigwig files from bam files. MACS2 (v2.2.5) was used for peak calling and to generate bed files from aligned reads. Conclusions: ATAC-seq analysis confirmed that Fosb binding sites in Chip-seq assay were correlated with the chromatin accessibility .
Project description:The study was done to identify the differentially expressed genes in response to Doxorubicin drug resistance in the 143B human osteosarcoma cell line, using the Microarray technology. Keywords: drug resistance; dual channel; cell line based; doxorubicin resistance; Human osteosarcoma cell line