Chromatin context shapes SPT5 regulation of promoter-proximal Pol II, fine-tuning gene expression changes during Drosophila embryogenesis

spike-in CUT&Tag bigwig tracks (SPT5 TimeCourse):

• SPT5 CUT&Tag – 10-12h – merged
• SPT5 CUT&Tag – 14-16h – merged
• SPT5 CUT&Tag – 18-20h – merged
• SPT5 CUT&Tag – 2-4h – merged
• SPT5 CUT&Tag – 6-8h – merged
• SPT5 CUT&Tag – 10-12h – rep1
• SPT5 CUT&Tag – 10-12h – rep2
• SPT5 CUT&Tag – 14-16h – rep1
• SPT5 CUT&Tag – 14-16h – rep2
• SPT5 CUT&Tag – 18-20h – rep1
• SPT5 CUT&Tag – 18-20h – rep2
• SPT5 CUT&Tag – 2-4h – rep1
• SPT5 CUT&Tag – 2-4h – rep2
• SPT5 CUT&Tag – 6-8h – rep1
• SPT5 CUT&Tag – 6-8h – rep2

DFF-seq bigwig tracks:

• DFF-seq – 20h – merged
• DFF-seq – 3h – merged
• DFF-seq – 4h – merged

Depletion spike-in CUT&Tag bigwig tracks – merged, Dark vs Blue Light:

• SPT5-LEXY – 10-12h – 2h depletion – Blue Light – NELF – merged
• SPT5-LEXY – 10-12h – 2h depletion – Blue Light – Pol2ser2 – merged
• SPT5-LEXY – 10-12h – 2h depletion – Blue Light – Pol2ser5 – merged
• SPT5-LEXY – 10-12h – 2h depletion – Blue Light – SPT5 – merged
• SPT5-LEXY – 10-12h – 2h depletion – Dark – NELF – merged
• SPT5-LEXY – 10-12h – 2h depletion – Dark – Pol2ser2 – merged
• SPT5-LEXY – 10-12h – 2h depletion – Dark – Pol2ser5 – merged
• SPT5-LEXY – 10-12h – 2h depletion – Dark – SPT5 – merged
• SPT5-LEXY – 18-20h – 2h depletion – Blue Light – NELF – merged
• SPT5-LEXY – 18-20h – 2h depletion – Blue Light – Pol2ser2 – merged
• SPT5-LEXY – 18-20h – 2h depletion – Blue Light – Pol2ser5 – merged
• SPT5-LEXY – 18-20h – 2h depletion – Blue Light – SPT5 – merged
• SPT5-LEXY – 18-20h – 2h depletion – Dark – NELF – merged
• SPT5-LEXY – 18-20h – 2h depletion – Dark – Pol2ser2 – merged
• SPT5-LEXY – 18-20h – 2h depletion – Dark – Pol2ser5 – merged
• SPT5-LEXY – 18-20h – 2h depletion – Dark – SPT5 – merged
• SPT5-LEXY – 3-4h – 1h depletion – Blue Light – NELF – merged
• SPT5-LEXY – 3-4h – 1h depletion – Blue Light – Pol2ser2 – merged
• SPT5-LEXY – 3-4h – 1h depletion – Blue Light – Pol2ser5 – merged
• SPT5-LEXY – 3-4h – 1h depletion – Blue Light – SPT5 – merged
• SPT5-LEXY – 3-4h – 1h depletion – Dark – NELF – merged
• SPT5-LEXY – 3-4h – 1h depletion – Dark – Pol2ser2 – merged
• SPT5-LEXY – 3-4h – 1h depletion – Dark – Pol2ser5 – merged
• SPT5-LEXY – 3-4h – 1h depletion – Dark – SPT5 – merged
• SPT5-LEXY – 3-4h – 3h depletion – Blue Light – NELF – merged
• SPT5-LEXY – 3-4h – 3h depletion – Blue Light – Pol2ser2 – merged
• SPT5-LEXY – 3-4h – 3h depletion – Blue Light – Pol2ser5 – merged
• SPT5-LEXY – 3-4h – 3h depletion – Blue Light – SPT5 – merged
• SPT5-LEXY – 3-4h – 3h depletion – Dark – NELF – merged
• SPT5-LEXY – 3-4h – 3h depletion – Dark – Pol2ser2 – merged
• SPT5-LEXY – 3-4h – 3h depletion – Dark – Pol2ser5 – merged
• SPT5-LEXY – 3-4h – 3h depletion – Dark – SPT5 – merged

Depletion spike-in CUT&Tag bigwig tracks – merged, log2FC (Dark/Blue Light):

• SPT5-LEXY – 10-12h – 2h depletion – log2FC (Dark/Blue Light) – NELF
• SPT5-LEXY – 10-12h – 2h depletion – log2FC (Dark/Blue Light) – Pol2ser2
• SPT5-LEXY – 10-12h – 2h depletion – log2FC (Dark/Blue Light) – Pol2ser5
• SPT5-LEXY – 10-12h – 2h depletion – log2FC (Dark/Blue Light) – SPT5
• SPT5-LEXY – 18-20h – 2h depletion – log2FC (Dark/Blue Light) – NELF
• SPT5-LEXY – 18-20h – 2h depletion – log2FC (Dark/Blue Light) – Pol2ser2
• SPT5-LEXY – 18-20h – 2h depletion – log2FC (Dark/Blue Light) – Pol2ser5
• SPT5-LEXY – 18-20h – 2h depletion – log2FC (Dark/Blue Light) – SPT5
• SPT5-LEXY – 3-4h – 1h depletion – log2FC (Dark/Blue Light) – NELF
• SPT5-LEXY – 3-4h – 1h depletion – log2FC (Dark/Blue Light) – Pol2ser2
• SPT5-LEXY – 3-4h – 1h depletion – log2FC (Dark/Blue Light) – Pol2ser5
• SPT5-LEXY – 3-4h – 1h depletion – log2FC (Dark/Blue Light) – SPT5
• SPT5-LEXY – 3-4h – 3h depletion – log2FC (Dark/Blue Light) – NELF
• SPT5-LEXY – 3-4h – 3h depletion – log2FC (Dark/Blue Light) – Pol2ser2
• SPT5-LEXY – 3-4h – 3h depletion – log2FC (Dark/Blue Light) – Pol2ser5
• SPT5-LEXY – 3-4h – 3h depletion – log2FC (Dark/Blue Light) – SPT5

Depletion spike-in CUT&Tag bigwig tracks – replicates, Dark vs Blue Light:

• SPT5-LEXY – 10-12h – 2h depletion – Blue Light – NELF – rep1
• SPT5-LEXY – 10-12h – 2h depletion – Blue Light – NELF – rep2
• SPT5-LEXY – 10-12h – 2h depletion – Dark – NELF – rep1
• SPT5-LEXY – 10-12h – 2h depletion – Dark – NELF – rep2
• SPT5-LEXY – 18-20h – 2h depletion – Blue Light – NELF – rep1
• SPT5-LEXY – 18-20h – 2h depletion – Blue Light – NELF – rep2
• SPT5-LEXY – 18-20h – 2h depletion – Dark – NELF – rep1
• SPT5-LEXY – 18-20h – 2h depletion – Dark – NELF – rep2
• SPT5-LEXY – 3-4h – 1h depletion – Blue Light – NELF – rep1
• SPT5-LEXY – 3-4h – 1h depletion – Blue Light – NELF – rep2
• SPT5-LEXY – 3-4h – 1h depletion – Dark – NELF – rep1
• SPT5-LEXY – 3-4h – 1h depletion – Dark – NELF – rep2
• SPT5-LEXY – 3-4h – 3h depletion – Blue Light – NELF – rep1
• SPT5-LEXY – 3-4h – 3h depletion – Blue Light – NELF – rep2
• SPT5-LEXY – 3-4h – 3h depletion – Dark – NELF – rep1
• SPT5-LEXY – 3-4h – 3h depletion – Dark – NELF – rep2
• SPT5-LEXY – 10-12h – 2h depletion – Blue Light – Pol2ser2 – rep1
• SPT5-LEXY – 10-12h – 2h depletion – Blue Light – Pol2ser2 – rep2
• SPT5-LEXY – 10-12h – 2h depletion – Dark – Pol2ser2 – rep1
• SPT5-LEXY – 10-12h – 2h depletion – Dark – Pol2ser2 – rep2
• SPT5-LEXY – 18-20h – 2h depletion – Blue Light – Pol2ser2 – rep1
• SPT5-LEXY – 18-20h – 2h depletion – Blue Light – Pol2ser2 – rep2
• SPT5-LEXY – 18-20h – 2h depletion – Dark – Pol2ser2 – rep1
• SPT5-LEXY – 18-20h – 2h depletion – Dark – Pol2ser2 – rep2
• SPT5-LEXY – 3-4h – 1h depletion – Blue Light – Pol2ser2 – rep1
• SPT5-LEXY – 3-4h – 1h depletion – Blue Light – Pol2ser2 – rep2
• SPT5-LEXY – 3-4h – 1h depletion – Dark – Pol2ser2 – rep1
• SPT5-LEXY – 3-4h – 1h depletion – Dark – Pol2ser2 – rep2
• SPT5-LEXY – 3-4h – 3h depletion – Blue Light – Pol2ser2 – rep1
• SPT5-LEXY – 3-4h – 3h depletion – Blue Light – Pol2ser2 – rep2
• SPT5-LEXY – 3-4h – 3h depletion – Dark – Pol2ser2 – rep1
• SPT5-LEXY – 3-4h – 3h depletion – Dark – Pol2ser2 – rep2
• SPT5-LEXY – 10-12h – 2h depletion – Blue Light – Pol2ser5 – rep1
• SPT5-LEXY – 10-12h – 2h depletion – Blue Light – Pol2ser5 – rep2
• SPT5-LEXY – 10-12h – 2h depletion – Dark – Pol2ser5 – rep1
• SPT5-LEXY – 10-12h – 2h depletion – Dark – Pol2ser5 – rep2
• SPT5-LEXY – 18-20h – 2h depletion – Blue Light – Pol2ser5 – rep1
• SPT5-LEXY – 18-20h – 2h depletion – Blue Light – Pol2ser5 – rep2
• SPT5-LEXY – 18-20h – 2h depletion – Dark – Pol2ser5 – rep1
• SPT5-LEXY – 18-20h – 2h depletion – Dark – Pol2ser5 – rep2
• SPT5-LEXY – 3-4h – 1h depletion – Blue Light – Pol2ser5 – rep1
• SPT5-LEXY – 3-4h – 1h depletion – Blue Light – Pol2ser5 – rep2
• SPT5-LEXY – 3-4h – 1h depletion – Dark – Pol2ser5 – rep1
• SPT5-LEXY – 3-4h – 1h depletion – Dark – Pol2ser5 – rep2
• SPT5-LEXY – 3-4h – 3h depletion – Blue Light – Pol2ser5 – rep1
• SPT5-LEXY – 3-4h – 3h depletion – Blue Light – Pol2ser5 – rep2
• SPT5-LEXY – 3-4h – 3h depletion – Dark – Pol2ser5 – rep1
• SPT5-LEXY – 3-4h – 3h depletion – Dark – Pol2ser5 – rep2
• SPT5-LEXY – 10-12h – 2h depletion – Blue Light – SPT5 – rep1
• SPT5-LEXY – 10-12h – 2h depletion – Blue Light – SPT5 – rep2
• SPT5-LEXY – 10-12h – 2h depletion – Dark – SPT5 – rep1
• SPT5-LEXY – 10-12h – 2h depletion – Dark – SPT5 – rep2
• SPT5-LEXY – 18-20h – 2h depletion – Blue Light – SPT5 – rep1
• SPT5-LEXY – 18-20h – 2h depletion – Blue Light – SPT5 – rep2
• SPT5-LEXY – 18-20h – 2h depletion – Dark – SPT5 – rep1
• SPT5-LEXY – 18-20h – 2h depletion – Dark – SPT5 – rep2
• SPT5-LEXY – 3-4h – 1h depletion – Blue Light – SPT5 – rep1
• SPT5-LEXY – 3-4h – 1h depletion – Blue Light – SPT5 – rep2
• SPT5-LEXY – 3-4h – 1h depletion – Dark – SPT5 – rep1
• SPT5-LEXY – 3-4h – 1h depletion – Dark – SPT5 – rep2
• SPT5-LEXY – 3-4h – 3h depletion – Blue Light – SPT5 – rep1
• SPT5-LEXY – 3-4h – 3h depletion – Blue Light – SPT5 – rep2
• SPT5-LEXY – 3-4h – 3h depletion – Dark – SPT5 – rep1
• SPT5-LEXY – 3-4h – 3h depletion – Dark – SPT5 – rep2

PRO-seq bigwig tracks:

• PRO-seq – 18-20h – BL2h – merged
• PRO-seq – 18-20h – dark – merged
• PRO-seq – 3-4h – BL1h – merged
• PRO-seq – 3-4h – BL3h – merged
• PRO-seq – 3-4h – dark – merged
• PRO-seq – 18-20h – BL2h – rep1
• PRO-seq – 18-20h – BL2h – rep2
• PRO-seq – 18-20h – dark – rep1
• PRO-seq – 18-20h – dark – rep2
• PRO-seq – 3-4h – BL1h – rep1
• PRO-seq – 3-4h – BL1h – rep2
• PRO-seq – 3-4h – BL3h – rep1
• PRO-seq – 3-4h – BL3h – rep2
• PRO-seq – 3-4h – dark – rep1
• PRO-seq – 3-4h – dark – rep2

RNA-seq bigwig tracks (SPT5-LEXY) – merged:

• RNA-seq – 12-16h – BlueLight12-16h – merged
• RNA-seq – 12-16h – BlueLight8-12hDark12-16h – merged
• RNA-seq – 12-16h – Dark12-16h – merged
• RNA-seq – 16-20h – BlueLight12-16hDark16-20h – merged
• RNA-seq – 16-20h – BlueLight16-20h – merged
• RNA-seq – 16-20h – BlueLight8-12hDark12-20h – merged
• RNA-seq – 16-20h – BlueLight8-20h – merged
• RNA-seq – 16-20h – Dark16-20h – merged
• RNA-seq – 3-4h – BlueLight1h – merged
• RNA-seq – 3-4h – BlueLight3h – merged
• RNA-seq – 3-4h – Dark – merged
• RNA-seq – 8-12h – BlueLight8-12h – merged
• RNA-seq – 8-12h – Dark8-12h – merged

RNA-seq bigwig tracks (SPT5-LEXY) – replicates:

• RNA-seq – 12-16h – BlueLight12-16h – rep1
• RNA-seq – 12-16h – BlueLight12-16h – rep2
• RNA-seq – 12-16h – BlueLight8-12hDark12-16h – rep1
• RNA-seq – 12-16h – BlueLight8-12hDark12-16h – rep2
• RNA-seq – 12-16h – Dark – rep1
• RNA-seq – 12-16h – Dark – rep2
• RNA-seq – 16-20h – BlueLight12-16hDark16-20h – rep1
• RNA-seq – 16-20h – BlueLight12-16hDark16-20h – rep2
• RNA-seq – 16-20h – BlueLight16-20h – rep1
• RNA-seq – 16-20h – BlueLight16-20h – rep2
• RNA-seq – 16-20h – BlueLight8-12hDark12-20h – rep1
• RNA-seq – 16-20h – BlueLight8-12hDark12-20h – rep2
• RNA-seq – 16-20h – BlueLight8-20h – rep1
• RNA-seq – 16-20h – BlueLight8-20h – rep2
• RNA-seq – 16-20h – Dark – rep1
• RNA-seq – 16-20h – Dark – rep2
• RNA-seq – 3-4h – BlueLight1h – rep1
• RNA-seq – 3-4h – BlueLight1h – rep2
• RNA-seq – 3-4h – BlueLight3h – rep1
• RNA-seq – 3-4h – BlueLight3h – rep2
• RNA-seq – 3-4h – Dark – rep1
• RNA-seq – 3-4h – Dark – rep2
• RNA-seq – 8-12h – BlueLight8-12h – rep1
• RNA-seq – 8-12h – BlueLight8-12h – rep2
• RNA-seq – 8-12h – Dark – rep1
• RNA-seq – 8-12h – Dark – rep2

RNA-seq bigwig tracks (whole embryo, Sue Celniker normalization, 25bp bins, merged):

• RNA-seq (whole embryo) – 10-12h – merged, 25bp bins
• RNA-seq (whole embryo) – 14-16h – merged, 25bp bins
• RNA-seq (whole embryo) – 18-20h – merged, 25bp bins
• RNA-seq (whole embryo) – 2-4h – merged, 25bp bins
• RNA-seq (whole embryo) – 6-8h – merged, 25bp bins