PhD Thesis Appendix
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
Appendix files associated with the PhD thesis "Chromatin organization and gene regulation in granulocytic cells" by Elsie Carlota Jacobson
Supplementary table 1.
Significantly differentially expressed genes. All genes with significantly
differential gene expression (false discovery rate (FDR) <0.05) between either 5µm pores compared to
control, 14µm pores compared to control, or 5µm pores compared to 14µm pores.
Sets refer to those described in Chapter 2. HUGO gene names,
Ensembl gene names and IDs are provided as identifiers. Columns suffixed with
‘_5’ represent results from 5µm pore compared to control. Columns suffixed with
‘_14’ represent results from 14µm pore compared to control. Columns suffixed
with ‘_5v14’ represent results from 5µm pore compared to 14µm pore. The ‘padj’
shows the FDR adjusted p-value.
Supplementary table 2. PC1 values and correlation between the interaction patterns of 100kb
bins. Each 100kb bin has both a PC1 value indicating
compartment status, and an interaction pattern with every other bin in the
chromosome. When bins have a low correlation (R<0.6) and an opposite PC1
value, this is considered a disruption to the compartment status of this
region. Calculated using the runHiCpca.pl and getHiCcorrDiff.pl scripts in
HOMER. Regions with missing values, and chromosomes with PC1 values indicating
chromosome arm, are excluded from this table.
table 3. Significantly
differentially expressed genes in promyelocytes treated with TNF-a, differentiated into granulocytes
and macrophages, and granulocytes treated with TNF-a. All genes with significantly
differential gene expression (false discovery rate (FDR) <0.05) in promyelocytes treated with TNF-a, differentiated into granulocytes and macrophages, and granulocytes treated with TNF-a. Categories refer to those described in Chapter 3. Ensembl gene names and IDs are provided as identifiers. Columns suffixed with
‘_proTNF’ represent results from undifferentiated promyelocytic cells treated with TNF-a. Columns suffixed with '_granTNF' represent results from all-trans retinoic acid (ATRA) differentiated granulocytic cells treated with TNF-a. Columns suffixed with
‘_ATRA’ represent results from cells differentiated into granulocytes with ATRA. Columns suffixed
with ‘_TPA’ represent results from cells differentiated into macrophages with 12-O-tetradecanoylphorbol-13-acetate (TPA). The ‘padj’
shows the FDR adjusted p-value.
Supplementary table 4. Hic-breakfinder filtered results for all samples. This table shows all breakpoints over 10Mb apart. The log-odds score indicates the strength of the call. The bias value predicts which coordinate is closest to the breakpoint. A “+” bias indicates the “end” coordinate is closest to the breakpoint, while a “-” bias indicates the “start” coordinate is closest to the breakpoint. The resolution indicates the maximum resolution the breakpoint was identified at, as hic_breakfinder identifies breakpoints at multiple resolutions. The sample column indicates which dataset the breakpoint was identified in.
Supplementary table 5. STAR-Fusion filtered results for all samples. This table has the gene fusion predictions for all samples of the 17 fusions identified in all replicates of at least one condition. Each row provides the STAR-Fusion results for a single RNA-seq library, thus each gene fusion may fill up to 29 rows. The first three columns indicate the dataset, condition, and replicate of the library. The remaining columns include detailed information about the predicted fusion as outputted by STAR-Fusion, including specific breakpoint locations and the number of junction and spanning reads.
Supplementary table 6. HiCUP QC results for HL-60/S4-HindIII.