Brachyury dataset

The non-book component contains supplementary data to support Chapters 3, 4, and 5.<br><br>In addition, the thesis abstract is attached.<b>Abstract.docx</b><br><br><br>Files containing the code used to run the analyses:<b>atac_seq.txt</b> (annotating NarrowPeak files in Homer)<br><b>ChIP_ATAC_RNA_seq.txt </b>(ChIP-seq and ATAC-seq data manipulation)<br><b>fastqc.sh </b>(shell script for running FASTQC - reads quality check)<br><b>trimmomatic.sh </b>(shell script for running Trimmomatic - trimming the low quality reads)<br><b>salmon.sh</b> (shell script for running Salmon - transcriptome mapping and quantification)<br><b>deseq2.R</b> (R script for running differential gene expression)<br><br><br>Data discussed in <b>Chapter 3 ‘EXPLORING THE BRACHYURY PROTEIN STRUCTURE:’</b><br>1. Pairwise alignment of P. lividus and S. purpuratus Brachyury proteinsequence<br><b>S_purpuratus_P_lividus_pairwise_alignment.txt</b><br><br>2. Full alignment of the echinoderm Brachyury protein sequences coming from <i>S. purpuratus</i>, <i>H. pulcherrimus</i>, <i>P. lividus</i>, <i>L. variegatus</i>, <i>S. mirabilis</i>, <i>A. manni</i>, C<b>. </b><i>japonicus</i>, <i>P. japonica</i>, <i>P. pectinifera</i>, <i>P. miniata</i> with marked important amino acid residues in <i>S. purpuratus</i> and <i>H. pulcherrimus</i> sequences<b>Figure 3.6.1.png</b><br><br><br>Data discussed in <b>Chapter 4 'DIFFERENTIAL GENE EXPRESSION ANALYSIS AFTER BRACHYURY KNOCKDOWN IN <i>STRONGYLOCENTROTUS PURPURATUS</i>:'</b><br>1. Differential RNA-seq unfiltered result tables<b>IHWsp27wt_bra_results.csv</b> (wild type condition vs. Bra knock-down embryos at 27hpf)<br><b>IHWsp48wt_bra_results.csv</b> (wild type condition vs. Bra knock-down embryos at 48hpf)<br><b>IHWsp48ctrlmo_results.csv</b> (wild type condition vs. control-MASO injected embryos at 48hpf)<br><br>2. Differential RNA-seq p-adjusted value filtered result tables<b>sp27bra_annotated.xlsx</b> (wild type condition vs. Bra knock-down embryos at 27hpf p-adjusted value 0.05)<br><b>sp48bra_annotated.xlsx</b> (wild type condition vs. Bra knock-down embryos at 48 hpf p-adjusted value 0.05)<br><b>IHW_sp48ctrlmo_filtered_padj005.csv </b>(wild type condition vs. control-MASO injected embryos at 48hpf p-adjusted value 0.05)<br><br>3. Tables containing <i>S. purpuratus </i>ChIP-seq – ATAC-seq intersected peaksfiltered by the differential RNA-seq results and presence of Brachyury motifs. Annotated by gene name<br><b>chip_atac_seq_intersect_bra_motifs_annotated_peaks_24_27wt.xlsx </b>(24hpf Brachyury ChIP-seq intersected with the 27hpf wild type ATAC-seq dataset)<br><b>chip_atac_seq_intersect_bra_motifs_annotated_peaks_48wt.xlsx</b> (48hpf Brachyury ChIP-seq intersected with the wild type 48hpf ATAC-seq dataset)<br><br>4. HTML report of <i>de novo </i>discovered motifs from 24hpf Brachyury ChIP-seqhigh stringency dataset<br><b>dreme.txt </b>(analysis results)<br><b>dreme.xml</b> (a file necessary for visual representation in a web browser)<br><b>m01nc_CYCYTTT.png</b> (motif 1 image file)<br><b>m01nc_CYCYTTT.eps</b> (file necessary for visual representation in a web browser)<br><b>m02nc_GTGYGA.png</b> (motif 2 image file)<br><b>m02nc_GTGYGA.eps</b> (file necessary for visual representation in a web browser)<br><b>m03nc_WCAATAG.png </b>(motif 3 image file)<br><b>m03nc_WCAATAG.eps</b> (file necessary for visual representation in a web browser)<br><b>dreme.html</b> (to be open in a web browser for visual representation)<br><br><br>Data discussed in <b>Chapter 5 'DIFFERENTIAL GENE EXPRESSION ANALYSIS AFTER BRACHYURY KNOCKDOWN IN <i>P. LIVIDUS</i>:'</b><br>1. Differential RNA-seq unfiltered result tables<b>ihw_pl18wt_bramo_results.csv</b> (wild type condition vs. Bra knock-down embryos at 18hpf)<br><b>ihw_pl24wt_bramo_results.csv</b> (wild type condition vs. Bra knock-down embryos at 24 hpf)<br><b>IHW_pl24wt_ctrlmo_results.csv</b> (wild type condition vs. control-MASO injected embryos at 24hpf)<br>2. Differential RNA-seq p-adjusted value filtered result tables<b>pl18_annotated.xlsx</b> (wild type condition vs. Bra knock-down embryos at 18hpf p-adjusted value 0.05)<br><b>pl24_annotated.xlsx</b> wild type condition vs. Bra knock-down embryos at 24hpf p-adjusted value 0.05)<br><b>IHW_pl24wt_vs_ctrlmomo_results_filtered_padj005.csv</b> (wild type condition vs. control-MASO injected embryos at 24hpf p-adjusted value 0.05)<br>