This 2020-BBAGRM-Bapst_readme.txt file was generated on 2020-06-09 by Andreas M. Bapst GENERAL INFORMATION 1. Title of Dataset: Cre-mediated, loxP independent sequential recombination of a tripartite transcriptional stop cassette allows for partial read-through transcription. DOI: 10.5061/dryad.bk3j9kd7t 2. Author Information A. Principal Investigator Contact Information Name: Roland H. Wenger Institution: Institute of Physiology, University of Zurich Address: Winterthurerstrasse 190, 8057 Zurich, Switzerland Email: roland.wenger@access.uzh.ch B. Associate or Co-investigator Contact Information Name: Andreas M. Bapst Institution: Institute of Physiology, University of Zurich Address: Winterthurerstrasse 190, 8057 Zurich, Switzerland Email: andreas.bapst@uzh.ch 3. Date of data collection (single date, range, approximate date): Between 2019-05-07 and 2020-04-20 4. Geographic location of data collection: Zurich, Switzerland 5. Information about funding sources that supported the collection of the data: Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung, Award: 310030_184813 National Centre of Competence in Research, Award: “Kidney.CH” SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: This work is licensed under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication license. This releases your work to the public domain for any use. 2. Links to publications that cite or use the data: This dataset is supplement to http://dx.doi.org/10.1016/j.bbagrm.2020.194568 3. Links to other publicly accessible locations of the data: - 4. Links/relationships to ancillary data sets: - 5. Was data derived from another source? yes/no No. 6. Recommended citation for this dataset: Bapst, Andreas M; Dahl, Sophie L; Knöpfel, Thomas; Wenger, Roland H (2020). Cre-mediated, loxP independent sequential recombination of a tripartite transcriptional stop cassette allows for partial read-through transcription. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms, 1863(8):194568. DOI: 10.1016/j.bbagrm.2020.194568 DATA & FILE OVERVIEW 1. File List: 190507_AMB_AB2-22fwd.ab1 308.68 kB application/octet-stream ## sequence file Suppl. Fig. 1 190507_AMB_AB2-22fwd.fasta 513 B application/octet-stream ## sequence file Suppl. Fig. 1 190507_AMB_AB2-22rev.ab1 308.96 kB application/octet-stream ## sequence file Suppl. Fig. 1 190507_AMB_AB2-22rev.fasta 518 B application/octet-stream ## sequence file Suppl. Fig. 1 190507_AMB_F1-10fwd.ab1 308.86 kB application/octet-stream ## sequence file Suppl. Fig. 1 190507_AMB_F1-10fwd.fasta 513 B application/octet-stream ## sequence file Suppl. Fig. 1 190507_AMB_F1-10rev.ab1 321.30 kB application/octet-stream ## sequence file Suppl. Fig. 1 190507_AMB_F1-10rev.fasta 1.02 kB application/octet-stream ## sequence file Suppl. Fig. 1 190507_AMB_TK4fwd.ab1 319.79 kB application/octet-stream ## sequence file Suppl. Fig. 1 190507_AMB_TK4fwd.fasta 1.03 kB application/octet-stream ## sequence file Suppl. Fig. 1 190507_AMB_TK4rev.ab1 307.99 kB application/octet-stream ## sequence file Suppl. Fig. 1 190507_AMB_TK4rev.fasta 152 B application/octet-stream ## sequence file Suppl. Fig. 1 190807_AMB__1D-Ai14recombGel.Tif 3.84 MB image/tiff ## agarose gel Fig. 1D 190807_AMB__1D-Ai14recombGel.png 1.02 MB image/png ## agarose gel Fig. 1D 191018_AMB_1C-CHO_TurboLUT.tif 1.44 MB image/tiff ## microscopy image Fig. 3C (fluoresence with LUT) 191018_AMB_1C-CHOmerge.tif 11.80 MB image/tiff ## microscopy image Fig. 3C (fluorescence + brightfield merge) 191018_AMB_1C-CHOmerge_crop.png 1.62 MB image/png ## cropped microscopy image Fig. 3C (fluor. + brightfield merge) 191111_AMB_1C-F1-10FACS.fcs 9.55 MB application/octet-stream ## FACS file Fig. 1C (F1-10 only) 191111_AMB_1C-F1-10_iCreFACS.fcs 9.20 MB application/octet-stream ## FACS file Fig. 1C (F1-10-iCre) 191111_AMB_1C-mixedFACS.fcs 9.20 MB application/octet-stream ## FACS file Fig. 1C (F1-10 + F1-10-iCre) 191113_AMB_1B-F1-...reERT2-0.1uM.tif 2.88 MB image/tiff ## Microscopy picutre Fig. 2B 191113_AMB_1B-F1-...2CreERT2-0uM.tif 2.88 MB image/tiff ## Microscopy picutre Fig. 2B 191113_AMB_1B-F1-...2CreERT2-1uM.tif 2.88 MB image/tiff ## Microscopy picutre Fig. 2B 191113_AMB_1B-F1-10-iCreHigh.tif 2.88 MB image/tiff ## Microscopy picutre Fig. 2B 191113_AMB_1B-F1-10-iCreLow.tif 2.88 MB image/tiff ## Microscopy picutre Fig. 2B 191113_AMB_1B-F1-...0-iCreMedium.tif 2.88 MB image/tiff ## Microscopy picutre Fig. 2B 191119_AMB_1B-TK4...sAB2-22_tube.png 767.66 kB image/png ## Photograph tubes TK4 + AB2-22 Fig. 1B 191123_AMB_CHO-Se...ncing-Subcl.docx 18.70 kB application/octet-stream ## Collection of CHO sequencing results (Supp. Fig. 3) 191123_AMB_F1-10C...2_Tmx-Subcl.docx 23.04 kB application/octet-stream ## Collection of FAIK1-10 sequencing results (Supp. Fig. 2) 191123_AMB_FirstS...ing-noSubcl.docx 13.43 kB application/octet-stream ## Collection of direct sequencing results (Supp. Fig. 1) 191127_AMB_1C-tdTqPCR.xlsx 14.09 kB application/octet-stream ## qPCR results AB2-22 vs. TK4, Fig. 1C 191129_AMB_1D-F1-10_Ai14Gel.tif 3.84 MB image/tiff ## Agarose gel FAIK1-10 + iCre, Fig. 3D 200226_AMB_1C-inV...focal_zStack.tif 217.17 MB image/tiff ## Kidney fluorescence image z-Stack, Figure 4C 200226_AMB_1D-inV...cal_MaxZProj.tif 601.35 kB image/tiff ## Kidney fluorescence maximum z projection image, Figure 4C 200228_AMB_1E-Pri...yCellsStrong.tif 17.69 MB image/tiff ## primary cells fluorescence image (strong), Fig. 4E 200228_AMB_1E-Pri...Strong_Turbo.tif 1.44 MB image/tiff ## primary cells fluorescence image (strong), Fig. 4E 200228_AMB_1E-Pri...aryCellsWeak.tif 17.69 MB image/tiff ## primary cells fluorescence image (weak), Fig. 4E 200228_AMB_1E-Pri...lsWeak_Turbo.tif 1.44 MB image/tiff ## primary cells fluorescence image (weak), Fig. 4E 200313_AMB_1D-CHO_Ai14Gel.tif 1.92 MB image/tiff ## CHO + ERT2-Cre-ERT2 agarose gel, Fig. 3D 200318_AMB_1E-AB2-22-iCre.tif 5.90 MB image/tiff ## AB2-22 + iCre fluorescence microscopy image, Fig. 2E 200318_AMB_1E-AB2-22.tif 5.90 MB image/tiff ## AB2-22 untransfected microscopy image, Fig. 2E 200318_AMB_1G-tdTqPCR.xlsx 11.18 kB application/octet-stream ## AB2-22(+iCre) qPCR data, Fig. 2G 200319_AMB_1F-AB2...i14RecombGel.tif 3.84 MB image/tiff ## AB2-22(+iCre) agarose gel, Fig. 2F 200420_AMB_1D-F1-10_Ai14Gel.tif 772.42 kB image/tiff ## F1-10 + iCre agarose gel, Fig. 2D 201003_AMB_1A-FullKidney.tif 829.85 MB image/tiff ## Full kidney slide scan, Fig. 4A A4_500_3_M13.ab1 343.22 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) A4_500_3_M13.fasta 1.22 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) A4_500_4_M13_M13.ab1 340.76 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) A4_500_4_M13_M13.fasta 1.23 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) A4_500_5_M13_M13.ab1 339.62 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) A4_500_5_M13_M13.fasta 1.15 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) A4_500_6_M13_M13.ab1 343 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) A4_500_6_M13_M13.fasta 1.23 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) A4_500_7_M13_M13.ab1 343.90 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) A4_500_7_M13_M13.fasta 1.26 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) A4_800_1_M13.ab1 341.77 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 2) A4_800_1_M13.fasta 1.22 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 2) A4_800_2_M13_M13.ab1 342.88 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 2) A4_800_2_M13_M13.fasta 1.28 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 2) A4_800_3_M13_M13.ab1 343.95 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 2) A4_800_3_M13_M13.fasta 1.17 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 2) A4_800_4_M13_M13.ab1 340.77 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 2) A4_800_4_M13_M13.fasta 1.23 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 2) A4_800_5_M13_M13.ab1 336.44 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 2) A4_800_5_M13_M13.fasta 1.12 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 2) A4_800_6_M13_M13.ab1 336.97 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 2) A4_800_6_M13_M13.fasta 1.13 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 2) A4_800_7_M13_M13.ab1 343.31 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 2) A4_800_7_M13_M13.fasta 1.18 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 2) D2_200_1_M13.ab1 342.33 kB application/octet-stream ## Sequencing data 0 x pA (Supp. Fig. 2) D2_200_1_M13.fasta 1.18 kB application/octet-stream ## Sequencing data 0 x pA (Supp. Fig. 2) D2_200_2_M13_M13.ab1 346.82 kB application/octet-stream ## Sequencing data 0 x pA (Supp. Fig. 2) D2_200_2_M13_M13.fasta 1.30 kB application/octet-stream ## Sequencing data 0 x pA (Supp. Fig. 2) D2_200_3_M13_M13.ab1 337.03 kB application/octet-stream ## Sequencing data 0 x pA (Supp. Fig. 2) D2_200_3_M13_M13.fasta 1.42 kB application/octet-stream ## Sequencing data 0 x pA (Supp. Fig. 2) D2_200_4_M13_M13.ab1 342.33 kB application/octet-stream ## Sequencing data 0 x pA (Supp. Fig. 2) D2_200_4_M13_M13.fasta 1.25 kB application/octet-stream ## Sequencing data 0 x pA (Supp. Fig. 2) D2_500_1_M13.ab1 331.30 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) D2_500_1_M13.fasta 946 B application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) D2_500_2_M13_M13.ab1 346.26 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) D2_500_2_M13_M13.fasta 1.21 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) D2_500_3_M13_M13.ab1 336.73 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) D2_500_3_M13_M13.fasta 1.11 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) D2_500_4_M13_M13.ab1 340.51 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) D2_500_4_M13_M13.fasta 1.23 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) D2_500_5_M13_M13.ab1 342.14 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) D2_500_5_M13_M13.fasta 1.14 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 2) pB_CHO1000_1_M13.ab1 316.16 kB application/octet-stream ## Sequencing data 3 x pA (Supp. Fig. 3) pB_CHO1000_1_M13.fasta 1.22 kB application/octet-stream ## Sequencing data 3 x pA (Supp. Fig. 3) pB_CHO200_1_M13.ab1 318.13 kB application/octet-stream ## Sequencing data 0 x pA (Supp. Fig. 3) pB_CHO200_1_M13.fasta 1.19 kB application/octet-stream ## Sequencing data 0 x pA (Supp. Fig. 3) pB_CHO500_2_M13.fasta 1.17 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 3) pB_CHO500_2_M13_(1).ab1 310.63 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 3) pB_CHO500_3_M13.ab1 311.56 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 3) pB_CHO500_3_M13.fasta 1.23 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 3) pB_CHO500_4_M13.ab1 315.04 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 3) pB_CHO500_4_M13.fasta 1.23 kB application/octet-stream ## Sequencing data 1 x pA (Supp. Fig. 3) pB_CHO800_1_M13.ab1 310.56 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 3) pB_CHO800_1_M13.fasta 1.18 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 3) pB_CHO800_2_M13.ab1 316.65 kB application/octet-stream ## Sequencing data 2 x pA (Supp. Fig. 3) 2. Relationship between files, if important: -- 3. Additional related data collected that was not included in the current data package: -- 4. Are there multiple versions of the dataset? yes/no no METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: Cell line generation described in: Imeri, F. et al. Generation of renal Epo-producing cell lines by conditional gene tagging reveals rapid HIF-2 driven Epo kinetics, cell autonomous feedback regulation, and a telocyte phenotype. Kidney International 95, 375–387 (2019). DOI: 10.1016/j.kint.2018.08.043 Remaining methods described in: A.M. Bapst, S.L. Dahl, T. Knopfel, R.H. Wenger, Cre-mediated, loxP independent sequential recombination of a tripartite transcriptional stop cassette allows for partial read-through transcription, Biochimica et biophysica acta. Gene regulatory mechanisms, (2020) 194568. https://doi.org/10.1016/j.bbagrm.2020.194568 2. Methods for processing the data: Image data were processed and analyzed using the FIJI distribution of ImageJ. Remaining data were processed using Microscoft Excel and Graphpad Prism. 3. Instrument- or software-specific information needed to interpret the data: qPCR data was acquired using Agilent Mx3000P qPCR systems and evaluated using the software provided with the system. FACS data were acquired using a FACS Aria II and analyzed using FloJo software. 4. Standards and calibration information, if appropriate: All qPCR data were normalized to plasmid standard titrations. 5. Environmental/experimental conditions: Described in the methods section of the publication. 6. Describe any quality-assurance procedures performed on the data: qPCR: replicates for each sample, no-RT controls, water controls. 7. People involved with sample collection, processing, analysis and/or submission: Prof. Roland H. Wenger Andreas M. Bapst Sophie L. Dahl Dr. Thomas Knöpfel