Schema for NELF RNAi vs. Mock MNase - NELF RNAi vs. Mock MNase-Seq for Drosophila S2 Cells

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Schema for NELF RNAi vs. Mock MNase - NELF RNAi vs. Mock MNase-Seq for Drosophila S2 Cells

Database: dm6 Primary Table: GSE22119_NELF_vs_Mock_smoothed Row Count: 1 Data last updated: 2022-10-20

field	example	SQL type	info
`fileName`	/gbdb/dm6/bbi/MACC/GSE22119...	`varchar(255)`	values

Sample Rows

fileName
/gbdb/dm6/bbi/MACC/GSE22119_NELF_vs_Mock_smoothed.bw

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

NELF RNAi vs. Mock MNase (GSE22119_diff_MNase) Track Description


	Description These tracks show changes in nucleosome positions based on the analysis of Micrococcal Nuclease sequencing (MNase-seq) of mock treated and NELF-RNAi treated Drosophila S2 cells. The datasets were retrieved from the Gene Expression Omnibus database at NCBI under the accession number GSE22119. The MNase-seq reads were mapped against the D. melanogaster genome using bowtie with the following parameters: `-m 1 -v 2 --fr`. The differential nucleosome positions and the smoothed coverage track were created using DANPOS2 with default parameters and `--paired 1`. Credits Gilchrist DA, Dos Santos G, Fargo DC, Xie B, Gao Y, Li L, Adelman K. Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation. Cell. 2010 Nov 12;143(4):540-51. Chen K, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S, He X, Li W. DANPOS: dynamic analysis of nucleosome position and occupancy by sequencing. Genome Res. 2013 Feb;23(2):341-51.