Integrated genome browser

Manufactured by Thermo Fisher Scientific

The Integrated Genome Browser (IGB) is a software tool that allows users to visualize and analyze genomic data. It provides a comprehensive view of various genomic features, including genes, transcripts, and regulatory elements, within a genomic context. The IGB software is designed to facilitate the exploration and interpretation of large-scale genomic datasets.

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Lab products found in correlation

Ion torrent proton, by Thermo Fisher Scientific (1 mentions) Ion xpress plus fragment library kit, by Thermo Fisher Scientific (1 mentions) Fungal bacterial dna microprep kit, by Zymo Research (1 mentions) Tiling analysis software, by Thermo Fisher Scientific (1 mentions)

4 protocols using integrated genome browser

Genome-Wide Upf1 and Pol II Binding Analysis

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We used the Model-based Analysis of Tiling Arrays (MAT) software to analyse the Affymetrix hybridization data (28 (link)). ChIP input DNA sample was used as the control and was compared against Upf1 (asynchronous and S-phase) and Pol II samples. A P-value cut off of 10^–4 or 10^–3 was used, whereas the remaining MAT parameters remained as default. Results produced by the MAT software were visualised in Affymetrix's Integrated Genome Browser (IGB) (29 (link)). When 50% or more of a genomic region was significantly bound by Upf1 and Pol II, we called it an enriched gene/genomic region. Enrichment scores were assigned to genomic features using the S. pombe genome coordinates (ftp://ftp.sanger.ac.uk/pub/yeast/pombe/GFF). The average enrichment was calculated between the start and end coordinates of enriched genomic regions, thereby giving each enriched region a score based on fold enrichment. Identification of significantly bound genomic features and enrichment score calculation was done using the statistical computing language R (http://www.R-project.org/). Functional annotation of the enriched regions was done using DAVID (30 (link)).

De S., Edwards D.M., Dwivedi V., Wang J., Varsally W., Dixon H.L., Singh A.K., Owuamalam P.O., Wright M.T., Summers R.P., Hossain M.N., Price E.M., Wojewodzic M.W., Falciani F., Hodges N.J., Saponaro M., Tanaka K., Azzalin C.M., Baumann P., Hebenstreit D, & Brogna S. (2021). Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe. Nucleic Acids Research, 50(1), 350-367.

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Sequencing and Alignment of Nipped-B Mutant DNA

Cited 1 time

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Genomic DNA was purified from ~100 homozygous Nipped-B⁴⁰⁷ mutant 2^nd instar larvae using the Zymo Research Fungal/Bacterial DNA MicroPrep kit according the manufacturer’s instructions and 50 nanograms of purified DNA was used to prepare a sequencing library with the Ion Xpress Plus Fragment Library Kit (Life Technologies) following the supplier’s methods with the exception that final library size selection was performed using Beckman Agencourt AMPure beads. The library was sequenced with an Ion Torrent Proton (Life Technologies) with a mean read length of 175 bp and aligned genome coverage of ~25-fold. Alignment to the Drosophila release 5 genome sequence (April 2006, modified by removal of chrU and Uextra sequences) was performed using the TMAP aligner map4 algorithm [69 ] with no soft-clipping and a minimum seed length of 20. The resulting bam files were sorted and indexed using SAMtools [70 (link)]. The sequence of the Nipped-B gene and surrounding region was inspected for indels and nucleotide changes in the aligned sequence files with the Affymetrix Integrated Genome Browser (IGB) [71 (link)].

Wu Y., Gause M., Xu D., Misulovin Z., Schaaf C.A., Mosarla R.C., Mannino E., Shannon M., Jones E., Shi M., Chen W.F., Katz O.L., Sehgal A., Jongens T.A., Krantz I.D, & Dorsett D. (2015). Drosophila Nipped-B Mutants Model Cornelia de Lange Syndrome in Growth and Behavior. PLoS Genetics, 11(11), e1005655.

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Genome-wide Transcription Factor Binding Analysis in Fission Yeast

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Raw microarray data files (.cel format) were normalized using either R or Affymetrix Tiling Analysis Software (TAS). TAS was used to generate log2 ratios of Fft2‐myc or Fft3‐myc to a control no‐epitope myc‐ChIP (Hu303) using two‐sample analysis quantile normalization together and a bandwidth of 100. Probe signals were assigned to S. pombe genome coordinates (Sanger 2007). TAS was also used to generate log2 ratios of mutant to WT expression arrays using the same normalization. Data analysis was performed in R (http://www.r-project.org) using the Bioconductor (http://www.bioconductor.org) packages “affy”, “affxparser”, and “preprocessCore” with standard parameters. CEL‐files were imported and quantile normalized as described in 73.
Data was visualized using Podbat 33, R, and the Integrated Genome Browser (IGB, Affymetrix). R was used to generate average gene occupancy graphs. Box‐and‐whisker plots were created in R using the “boxplot” function with standard parameters. Significance tests between data subsets were performed using the Wilcoxon–Mann–Whitney test function “wilcox.test” with standard parameters.

Persson J., Steglich B., Smialowska A., Boyd M., Bornholdt J., Andersson R., Schurra C., Arcangioli B., Sandelin A., Nielsen O, & Ekwall K. (2016). Regulating retrotransposon activity through the use of alternative transcription start sites. EMBO Reports, 17(5), 753-768.

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Genome-wide Analysis of Upf1 and Pol II Binding

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We used the Model-based Analysis of Tiling Arrays (MAT) software to analyse the Affymetrix hybridization data (Johnson et al., 2006) . ChIP input DNA sample was used as control and was compared against the Upf1 (asynchronous and S-phase) and Pol II samples.
A p-value cut off of 10 -4 or 10 -3 was used, whereas the remaining MAT parameters remained as default. Results of MAT were visualised in Affymetrix's Integrated Genome Browser (IGB) (Nicol et al., 2009) . When 50% or more of a genomic region was significantly bound by Upf1 and Pol II, we called it an enriched gene/genomic region. Enrichment scores were assigned to genomic features using the S. pombe genome coordinates (ftp://ftp.sanger.ac.uk/pub/yeast/pombe/GFF). The average enrichment was calculated between the start and end coordinates of enriched genomic regions, thereby giving each enriched region a score based on fold enrichment. Identification of significantly bound genomic features and enrichment score calculation was done using the statistical computing language R (http://www.R-project.org/). Functional annotation of the enriched regions was done using DAVID (Dennis et al., 2003) .

De S., Dwivedi V., Wang J., Edwards D.M., Varsally W., Singh A.K., Dixon H.L., Wojewodzic M.W., Falciani F., Hodges N.J., Saponaro M., Tanaka K., Azzalin C.M., Baumann P., Hebenstreit D., & Brogna S. (2021). Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe.

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