Main folder name: RawData-Perochon et al. 2021 - NCB. “Dynamic adult tracheal plasticity drives stem cell adaptation to changes in intestinal homeostasis.”

Folder organisation:
-	1 folder per figure named FigureX or Extended data FigureX 
-	1 subfolder per panel named FigureXpanelY (XY) or Extended data FigureXpanelZ (Extended data XZ)
-	1 README file describing organisation and content of raw data.

Details of content (Folders are in bold):
Figure1:
-	1a: 1 file .lsm raw picture named by genotype.
-	1b: 1 file .tif 
-	1c: 1 file .tif
-	1d: 2 files .lsm raw picture named by genotype.
-	1e: 1 file .pzfx; 1 folder “Pictures for quantification” containing 4 subfolders (each named by condition: 1-X, 2-Y…) where each of them contains raw pictures .lsm of gut associated trachea (named by genotype) and 1 folder named “squeletonize” containing processed pictures .tif (named by genotype).
-	1f: 2 files .lsm raw picture named by genotype.
-	1g: 1 file .pzfx; 1 file .xls = raw data for single cell clone (SCC); 1 folder named “pictures” containing 2 subfolders (each named by condition) which contain raw pictures .lsm.
-	1h: 2 files .lsm raw picture named by genotype; 1 file .pzfx; 1 file .xls and 1 folder named “Pictures for quantification” containing raw pictures .lsm.
-	1i: 1 file .lsm raw picture and 1 file .tif processed picture.
-	1j: 1 file .pzfx; 1 file .xls = raw data and 1 folder named “pictures for quantification” containing 2 subfolders (each named by condition) where each of them contains raw pictures .lsm and 1 folder named “tif” containing processed picture .tif (named by genotype).
-	1k: 1 file .pzfx; 1 file .xls and 1 folder named “ pictures for quantification” containing 2 subfolders (each named by condition) where each of them contains raw pictures .lsm and 1 folder named “tif” containing processed picture .tif (named by genotype).
-	1l: 1 file .pzfx and 1 folder named “pictures for quantification” containing 9 subfolders (each named by condition) where each of them contains raw pictures .lsm and 1 folder named “squeletonize” containing processed picture .tif (named by genotype).
-	1m: 1 file .pzfx
-	1n: 2 files .czi raw picture named by genotype.
Figure2:
-	2a: 2 files .lsm raw picture named by genotype.
-	2b: 1 file .pzfx and 1 folder named “pictures for quantification” containing 2 subfolders (each named by condition) where each of them contains raw pictures .lsm and 1 folder named “squeletonize” containing processed picture .tif (named by genotype).
-	2c: 1 file .pzfx
-	2d: 1 file .pzfx
-	2e: 4 files .czi raw picture named by genotype.
-	2f: 1 file .pzfx
-	2g: 1 file .pzfx and 1 folder named “pictures for quantification” containing 4 subfolders (each named by condition and genotype) where each of them contains raw pictures .czi.
-	2h: 4 files .lsm raw picture named by genotype.
-	2i: 1 file .pzfx and 1 folder named “pictures for quantification” containing 4 subfolders (each named by condition and genotype) where each of them contains raw pictures .lsm and 1 folder named “squeletonize” containing processed picture .tif (named by genotype).
-	2j: 1 file .pzfx
-	2k-l: 4 files .lsm raw picture named by genotype.
-	2m: 1 file .pzfx; 1 file .xls and 1 folder named “ pictures for quantification” containing  4 subfolders (each named by condition) where each of them contains raw pictures .lsm (named by genotype).
Figure3:
-	3a: 4 files .lsm raw picture named by genotype.
-	3b: 1 file .pzfx and 1 folder named “pictures for quantification” containing 4 subfolders (each named by condition and genotype) where each of them contains raw pictures .lsm and 1 folder named “squeletonize” containing processed picture .tif (named by genotype).
-	3c: 1 file .pzfx
-	3d: 4 files .lsm raw picture named by genotype.
-	3e: 1 file .pzfx and 1 folder named “pictures for quantification” containing 6 subfolders (each named by condition and genotype) where each of them contains raw pictures .lsm and 1 folder named “squeletonize” containing processed picture .tif (named by genotype).
-	3f: 1 file .pzfx
-	3g: 2 files .lsm raw picture named by genotype.
-	3h: 2 files .lsm raw picture named by genotype.
-	3i: 1 file .pzfx; 1 file .xls and 1 folder named “pictures for quantification” containing 4 subfolders (each named by condition) where each of them contains raw pictures .lsm.
-	3j: 4 files .lsm raw picture named by genotype.
-	3k: 1 file .pzfx and 1 folder named “pictures for quantification” containing 6 subfolders (each named by condition and genotype) where each of them contains raw pictures .lsm and 1 folder named “squeletonize” containing processed picture .tif (named by genotype).
-	3l: 1 file .pzfx

Figure4:
-	4a: 4 files .lsm raw picture named by genotype.
-	4b-c: 2 files .pzfx named by cell type analysed (ECs or ISCs/EBs) ; 1 file .xls and 1 folder named “pictures for quantification” containing 4 subfolders (each named by condition) where each of them contains raw pictures .lsm.
-	4d: 4 files .lsm raw picture named by genotype.
-	4e: 1 file .pzfx; 1 file .xls and 1 folder named “pictures for quantification” containing 4 subfolders (each named by condition) where each of them contains raw pictures .lsm.
-	4f: 4 files .lsm raw picture named by genotype.
-	4g: 1 file .pzfx and 1 folder named “pictures for quantification” containing 6 subfolders (each named by condition) where each of them contains raw pictures .lsm and 1 folder named “squeletonize” containing processed picture .tif (named by genotype).
-	4h: 1 file .pzfx.
-	4i: 4 files .lsm raw picture named by genotype; 2 files .jpg processed pictures named by genotype and 2 files .tif processed pictures named by genotype.
-	4j: 1 file .pzfx and 1 folder named “pictures for quantification” containing 4 subfolders (each named by condition and genotype) where each of them contains raw pictures .lsm.
-	4k: 1 file .pzfx.

Figure5:
-	5a: 1 file .ppt slide DamID method and 2 files .lsm raw picture named by genotype.
-	5b: 1 file .ppt slide containing GO term analysis in homeostasis.
-	5c: 1 file .ppt slide containing list of genes associated to neuronal processes showing significant RNA Pol II binding in TTCs following damage.
-	5d: 1 file .ppt slide containing chromatin binding profile for Imp.
-	5e: 1 file .pzfx and 1 file .xls = raw data qPCR for Imp and act5c.
-	5f: 2 files .lsm raw picture named by genotype.
-	5g: 2 files .lsm raw picture named by genotype.
-	5h: 1 file .pzfx; 1 file .xls and 1 folder named “pictures for quantification” containing 4 subfolders (each named by condition) where each of them contains raw pictures .lsm.
-	5i: 4 files .lsm raw picture named by genotype.
-	5j: 1 file .pzfx and 1 folder named “pictures for quantification” containing 4 subfolders in total (3 named by genotype) where each of them contains raw pictures .lsm and 1 subfolder named “squeletonize” organised in 3 subfolders itself containing processed picture .tif (named by genotype).
-	5k: 2 files .tif processed picture named by genotype.
-	5l: 1 file .pzfx
-	5m:  1 file .pzfx
-	5n: 2 files .tif processed picture named by genotype.
-	5o:  1 file .pzfx
-	5p:  1 file .pzfx

Figure6:
-	6a: 4 files .lsm raw picture named by genotype.
-	6b: 1 file .pzfx; 1 file .xls and 1 folder named “pictures for quantification” containing 4 subfolders (each named by condition and genotype) where each of them contains raw pictures .lsm.
-	6c: 4 files .lsm raw picture named by genotype.
-	6d: 1 file .pzfx and 1 folder named “pictures for quantification” containing 5 subfolders in total (4 named by genotype) where each of them contains raw pictures .lsm and 1 subfolder named “squeletonize” organised in 4 subfolders itself containing processed picture .tif (named by genotype).
-	6e: 1 file .pzfx.

Figure7:
-	7a: 1 file .ppt slide containing chromatin binding profile for trh.
-	7b: 1 file .pzfx and 1 file .xls = raw data qPCR for trh and act5c.
-	7c: 2 files .lsm raw picture named by genotype.
-	7d: 1 file .pzfx; 1 file .xls and 1 folder named “pictures for quantification” containing 2 subfolders (each named by condition) where each of them contains raw pictures .lsm.
-	7e: 4 files .lsm raw picture named by genotype.
-	7f: 1 file .pzfx; 1 file .xls and 1 folder named “pictures for quantification” containing 4 subfolders (each named by condition) where each of them contains raw pictures .lsm.
-	7g: 6 files .lsm raw picture named by genotype.
-	7h: 1 file .pzfx and 1 folder named “pictures for quantification” containing 4 subfolders in total (3 named by condition) where each of them contains raw pictures .lsm and 1 subfolder named “squeletonize” organised in 3 subfolders itself containing processed picture .tif (named by genotype).
-	7i: 1 file .pzfx.
-	7j: 1 file .ppt slide working model.

Extended data Figure 1:
-	Extended data 1a: 1 file .lsm raw picture and 3 files .tif processed pictures illustrating the different steps for quantifying tracheal coverage.
-	Extended data 1b: 3 files .lsm raw picture named by genotype.
-	Extended data 1c: 2 files .lsm raw picture named by genotype.
-	Extended data 1d, e: 1 file .pzfx; 1 file .xls and 1 folder named “pictures for quantification” containing 2 subfolders (each named by condition) where each of them contains raw pictures .lsm and 1 folder named “squeletonize” containing processed picture .tif (named by genotype).
-	Extended data 1f: 2 files .lsm raw picture and 2 files .tif processed pictures.
-	Extended data 1g: 1 file .pzfx and 1 folder named “pictures for quantification” containing 2 subfolders (each named by condition) containing raw pictures .lsm (named by genotype).
-	Extended data 1h: 9 files .lsm raw picture and 9 files .tif processed pictures, each named by genotype.
-	Extended data 1i: 1 file .pzfx.

Extended data Figure 2:
-	Extended data 2a: 2 files .lsm raw picture named by genotype.
-	Extended data 2b: 1 file .pzfx; 1 file .xls and 1 folder named “pictures for quantification” containing 2 subfolders (each named by condition) where each of them contains raw pictures .lsm (named by genotype).
-	Extended data 2c: 1 file .pzfx and 1 folder named “pictures for quantification” containing 2 subfolders (each named by condition) containing raw pictures .lsm (named by genotype) and 1 folder named “squeletonize” containing processed picture .tif (named by genotype).
-	Extended data 2d: 2 files .lsm raw picture named by genotype.
-	Extended data 2e: 4 files .lsm raw picture named by genotype.
-	Extended data 2f: 1 file .pzfx; 1 file .xls and 1 folder named “pictures for quantification” containing 2 subfolders (each named by condition) where each of them contains raw pictures .lsm (named by genotype).
-	Extended data 2g: 1 file .pzfx; 1 file .xls and 1 folder named “pictures for quantification” containing 4 subfolders (each named by condition) where each of them contains raw pictures .lsm (named by genotype).
-	Extended data 2h: 4 files .lsm raw picture named by genotype.
-	Extended data 2i: 1 file .pzfx; 1 file .xls and 1 folder named “pictures for quantification” containing 4 subfolders (each named by condition) where each of them contains raw pictures .lsm (named by genotype).

Extended data Figure 3:
-	Extended data 3a: 4 files .czi raw picture named by strength of scoring.
-	Extended data 3b: 1 file .pzfx; 2 files .tif processed picture named by genotype and 1 folder named “confocal” containing 3 subfolders in total (2 named by condition) where each of them contains raw pictures .lsm and 1 subfolder named “squeletonize” organised in 2 subfolders itself containing processed picture .tif (named by genotype).
-	Extended data 3c: 1 file .pzfx; 2 files .tif processed picture named by genotype and 1 folder named “LM” containing 2 subfolders (each named by condition) containing raw pictures .czi (named by genotype).
-	Extended data 3d: 4 files .czi raw picture named by genotype.
-	Extended data 3e: 1 file .pzfx and 1 folder named “pictures for quantification” containing 4 subfolders (each named by condition) where each of them contains raw pictures .czi (named by genotype).
-	Extended data 3f: 1 file .pzfx.
-	Extended data 3g: 2 files .tif processed picture named by genotype.
-	Extended data 3h: : 1 file .pzfx and 1 folder named “pictures for scoring” containing 2 subfolders (each named by genotype) containing each raw picture .czi (named by genotype) and processed pictures .tif (named by genotype).
-	Extended data 3i: 1 file .pzfx.

Extended data Figure 4:
-	Extended data 4a: 1 file .pzfx and 1 file .xls = raw data qPCR for bs/dSRF and gapdh1.
-	Extended data 4b: 2 files .lsm raw picture named by genotype.
-	Extended data 4c: 1 file .pzfx; 1 file .xls and 1 folder named “pictures for quantification” containing 2 subfolders (each named by condition) where each of them contains raw pictures .lsm (named by genotype).
-	Extended data 4d: 2 files .lsm raw picture named by genotype.
-	Extended data 4e: 1 file .pzfx; 1 file .xls and 1 folder named “pictures for quantification” containing 2 subfolders (each named by condition) where each of them contains raw pictures .lsm (named by genotype).
-	Extended data 4f: 4 files .lsm raw picture named by genotype.
-	Extended data 4g: 1 file .pzfx and 1 folder named “pictures for quantification” containing 3 subfolders in total ( 2 named by genotype) containing raw picture .lsm (named by genotype) and 1 folder named “squeletonize” containing 2 subfolders itself (named by genotype) containing processed pictures .tif (named by genotype).
-	Extended data 4h: 1 file .pzfx.

Extended data Figure 5:
-	Extended data 5a: 2 files .lsm raw picture named by genotype.
-	Extended data 5b: 1 file .pzfx; 1 file .xls and 1 folder named “pictures for quantification” containing 2 subfolders (each named by condition) where each of them contains raw pictures .lsm (named by genotype).
-	Extended data 5c: : 1 file .pzfx and 1 folder named “pictures for quantification” containing 2 subfolders (each named by genotype) containing raw picture .lsm (named by genotype).
-	Extended data 5d: 1 file .pzfx.
-	Extended data 5e: 4 files .czi raw picture named by genotype.
-	Extended data 5f: 1 file .pzfx and 1 folder named “pictures for quantification” containing 4 subfolders (each named by genotype) containing raw picture .czi (named by genotype).
-	Extended data 5g: 1 file .pzfx.
-	Extended data 5h: 4 files .czi raw picture named by genotype.
-	Extended data 5i: 1 file .pzfx and 1 folder named “pictures for quantification” containing 4 subfolders (each named by genotype) containing raw picture .czi (named by genotype).
-	Extended data 5j: 1 file .pzfx.
-	Extended data 5k: 4 files .czi raw picture named by genotype.
-	Extended data 5l: 1 file .pzfx.
-	Extended data 5m: 1 file .pzfx.
-	Extended data 5n: 4 files .czi raw picture named by genotype.
-	Extended data 5o: 1 file .pzfx.
-	Extended data 5p: 1 file .pzfx.

Extended data Figure 6:
-	Extended data 6a: 4 files .czi raw picture and 4 files .jpg processed pictures named by genotype.
-	Extended data 6b: 1 file .pzfx and 1 folder named “pictures for quantification” containing 2 subfolders (each named by genotype) containing raw picture .czi (named by genotype).
-	Extended data 6c: 1 file .pzfx.
-	Extended data 6d: 4 files .lsm raw picture named by genotype.
-	Extended data 6e: 1 file .pzfx; 1 file .xls and 1 folder named “pictures for quantification” containing 2 subfolders (each named by condition) where each of them contains raw pictures .lsm (named by genotype).

Extended data Figure 7:
-	Extended data 7a: 1 file .ppt slide scatterplots indicating correlation between TaDa replicates for each of the conditions used in this study.
-	Extended data 7b: 1 file .ppt slide containing chromatin binding profile for bnl.