Supplementary Table 1. Source data used for this study (provided as a separate excel file).

Transcription

1 Supplementary ables Supplementary able 1. Source data used for this study (provided as a separate excel file). Supplementary able 2. Data sets used for this study. Data sets H 1 to 3 contain the indel frequencies at integrated target sequences and were obtained from three independent high-throughput experiments conducted in. he data set from high-throughput experiment A was divided into data sets H 1-1 and H 1-2 by random sampling. Indel frequencies at endogenous human coding and non-coding regions were included in data sets -lenti, -plasmid, and HC-plasmid. In the case of the experiment for data set -lenti, indel frequencies were evaluated at both the integrated target sequences and the corresponding endogenous target sites. Different delivery methods and cell lines were used for the generation of data sets lenti, -plasmid, and HC-plasmid and are described in the table. Data set Method/ Experimen t Cell line Data size arget information Usage Development of H 1-1 Highthroughput experiment A 15,000 Integrated target sequences (sequences derived from human coding regions) Seq-deepCpf1 and conventional machine learning-based models Validation of H 1-2 Highthroughput experiment A 1,292 Integrated target sequences (sequences derived from human coding regions) Seq-deepCpf1 and conventional machine learning-based

2 models (Fig. 1c, Supplementary Fig 6) Validation of Seq-deepCpf1 and H 2 Highthroughput experiment B 2,963 Integrated target sequences (sequences derived from human coding regions) conventional machine learning-based models (Fig. 1c, Supplementary Fig 6) Validation of Seq-deepCpf1 and H 3 Highthroughput experiment C 1,251 Integrated target sequences (sequences derived from mouse and human coding regions) conventional machine learning-based models (Fig. 1c, Supplementary Fig 6) lenti Lentiviral transductio n 148 Integrated target sequences and their corresponding endogenous target sites (human coding and noncoding regions) Fine-tuning, model validation (Fig. 2a-d Supplementary Fig. 7a, 10, 11, 12 and 14) plasmi d Plasmid transfection 55 Endogenous target sites (human coding and noncoding regions) Fine-tuning, model validation (Fig. 2a, 2b, 2d, Supplementary

3 Fig. 7b, 9a, 10a, 11a, 12 and 14) Fine-tuning, HCplasmi d Plasmid transfection HC Endogenous target sites (human coding and noncoding regions) model validation (Fig. 2a, 2c, 2d, Supplementary Fig. 7c, 9b, 10b, 11b, 12 and 14) Kleinsti ver 2016 Plasmid transfection U2O S 22 Endogenous target sites (human coding and noncoding regions) Model validation (Fig. 2d) Chari 2017 Plasmid transfection 18 Endogenous target sites (human coding regions) Model validation (Fig. 2d) Kim 2016 Plasmid transfection 10 Endogenous target sites (human coding and noncoding regions) Model validation (Fig. 2d)

4 Supplementary able 3. Model selection results of Seq-deepCpf1 (provided as a separate excel file). We explored a total of 180 convolutional neural network architectures with different hyperparameter configurations (i.e., we varied each of the following hyperparameters to generate these combinations of architectures: the number of filters, filter lengths, the number of fully connected layers, and the number of units in each fully connected layer). he other hyperparameters used are as follows (these were fixed for all 180 models): a rectified linear unit (ReLU) activation function, a dropout rate of 0.3, the Adam optimizer, and the mean squared objective loss function. Of the 180 models that were explored, model 157 delivered the minimum average value of the validation loss, and the hyperparameters of model 157, highlighted in red, were selected to define the final model for Seq-deepCpf1.

5 Supplementary able 4. Information about 125 cell lines used for the DeepCpf1 web tool. he information is from ref. 11. Cell line issue Cell type / origin lineage Full description (from ENCODE) AoAF Blood Normal human aortic adventitial Fibroblast vessel fibroblast CMK Blood Megakaryocyte, Human acute megakaryocytic leukemia GM06990 Blood B-Lymphocyte, B-lymphocytes GM12864 Blood B-Lymphocyte, B-lymphocytes GM12865 Blood B-Lymphocyte, B-lymphocytes GM12878 Blood B-Lymphocyte, Lymphoblastoid B-Lymphocyte, Lympho-blastoid, GM12891 Blood Epstein-Barr Virus transformed B-Lymphocyte, International hapmap Project, CEPH/Utah pedigree 1463, reatment: GM12892 Blood B-Lymphocyte, Lympho-blastoid, Epstein-Barr Virus transformed B-Lymphocyte, International hapmap Project, CEPH/Utah pedigree 1463, reatment: GM18507 Blood Lympho-blastoid, International hapmap transformed B-Lymphocyte, Project, Yoruba in Ibadan, Nigera, reatment: Epstein-Barr Virus GM19238 Blood B-Lymphocytes, Lympho-blastoid, Barr Virus transformed B-Lymphocyte, International hapmap Project, Yoruba in Ibadan, Nigera, reatment: Epstein- GM19239 Blood B-Lymphocyte, B-Lymphocytes, Lympho-blastoid,

6 International hapmap project, Yoruba in Ibadan, Nigera, preatment: Epstein- Barr virus transformed GM19240 Blood B-Lymphocytes, Lympho-blastoid, Virus transformed B-Lymphocyte, International hapmap project, Yoruba in Ibadan, Nigera, treatment: Epstein-Barr HL-60 Blood Promyelocyte, Human promyelocytic leukemia Jurkat Blood -lymphocyte, lympho-blastoid cell line derived from an acute cell leukemia K562 Blood Myeloid cell, blood cell Leukemia Monocytes-CD14+ are CD14-positive Monocyte Monocyte, blood Blood from human leukapheresis s-cd14+ cell product NB4 Blood Promyelocyte, Acute promyelocytic leukemia cell line h0 Blood -lymphocyte, Unstimulated h0 isolated from adults' blood h1 Blood -lymphocyte, Primary human h1 h2 Blood -lymphocyte, Primary human h2 CD34 Blood Hematopoietic Mobilized primary CD34-positive progenitor cell, from human leukapheresis product CLL Blood -lymphocyte, Chronic lymphocytic leukemia, - cell lymphocytes CD20 Blood B-Lymphocyte, Human B Osteobl Bone Osteoblast Normal human osteoblasts (nhost) BE2_C Brain Neuronal progenitor cell Human neuroblastoma

7 Gliobla Brain Glial cell Glioblastoma, these (aka H54 and D54) come from a surgical resection from a patient with glioblastoma multiforme (WHO Grade IV). D54 is a commonly studied glioblastoma cell line that has been thoroughly described HAc Brain Astrocyte Human astrocytes-cerebellar HAh Brain Astrocyte Human astrocytes-hippocampal HBMEC Brain Endothelial cell Human brain microvascular endothelial HCPEpiC Brain Epithelial cell Human choroid plexus epithelial Medullo-blastoma (aka D721), surgical Medullo Brain Bigner (1997) Neuronal resection from a patient with medulloblastoma as described by Darrell progenitor cell Neuro-epithelioma cell line derived SK_N_M Brain Epithelial cell from a metastatic supra-orbital human C brain tumor SK-N- Neuronal Neuroblastoma cell line differentiated Brain SH_RA progenitor cell w/ retinoic acid NH-A Brain Astrocyte Normal human astrocytes HMEC Breast Epithelial cell Human mammary epithelial HMF Breast Fibroblast Human mammary fibroblasts MCF-7 Breast Epithelial cell Mammary gland, adeno-carcinoma MCF- MCF7 treated with hypoxia and 7/Hypoxia Breast Epithelial cell lactose _LacAcid -47D Breast Epithelial cell A human epithelial cell line derived from a mammary ductal carcinoma HeLa-S3 Cervix Epithelial cell Cervical carcinoma HeLa- Cervical carcinoma treated with S3/IFNa4 Cervix Epithelial cell IFN-alpha for 4h h

8 Caco-2 Colon Epithelial cell Colorectal adeno-carcinoma HC-116 Colon Epithelial cell Colorectal carcinoma HAEpiC Embryo Epithelial cell Human amniotic epithelial HR8svn Embryo rophoblast rophoblast (HR-8/svneo) cell line. A thin layer of ectoderm that forms the wall of many mammalian blastulas and functions in the nutrition and implantation of the embryo Chorion Embryo rophoblast Chorion (outermost of two fetal membranes), fetal membranes were collected from women who underwent planned cesarean delivery at term, before labor and without rupture of membranes. HEEpiC Esophagus Epithelial cell Human esophageal epithelial HConF Eye Fibroblast Human conjunctival fibroblasts HIPEpiC Eye Epithelial cell Human iris pigment epithelial HNPC- Human non-pigment ciliary epithelial Eye Epithelial Cell EpiC HRPEpiC Eye Epithelial cell Human retinal pigment epithelial WERI-Rb- 1 Eye Retinoblastoma Retinoblastoma AG09319 Gingiva Fibroblast Adult human gum tissue fibroblasts HGF Gingiva Fibroblast Human gingival fibroblasts HCF Heart Fibroblast Human cardiac fibroblasts HCFaa Heart Fibroblast Human cardiac fibroblasts-adult atrial HCM Heart Myocyte Human cardiac myocytes HRCEpiC Kidney Epithelial cell Human renal cortical epithelial (normal) HRE Kidney Epithelial cell Human renal epithelial (normal) HRGEC Kidney Endothelial cell Human renal glomerular endothelial RPEC Kidney Epithelial cell Renal proximal tubule epithelial

9 Kidney Epithelial cell Human embryonic kidney cell Primary human hepatocytes; liver was Hepatocyt Liver Hepatocyte perfused with enzymes to generate es single cell suspension HepG2 Liver Hepatocyte Liver carcinoma Huh-7 Liver Hepatocyte Hepatocellular carcinoma Huh-7.5 Liver Hepatocyte Hepatocellular carcinoma, hepatocytes selected for high levels of hepatitis C replication Stellate Liver Stellate cell Human hepatic stellate ; liver was perfused with collagenase and hepatic stellate were selected by density gradient A549 Lung Epithelial cell Epithelial cell line derived from a lung carcinoma tissue AG04450 Lung Fibroblast Fetal lung fibroblasts HMVEC- Normal human blood microvascular Lung Endothelial cell LBl endothelial, lung-derived HMVEC- Normal human lymphatic microvascular Lung Endothelial cell LLy endothelial, lung-derived HPAEC Lung Endothelial cell Human pulmonary artery endothelial HPAF Lung Fibroblast Human pulmonary artery fibroblasts HPF Lung Fibroblast Human pulmonary fibroblasts NHLF Lung Fibroblast Normal human lungfibroblasts SAEC Lung Epithelial cell Small airway epithelial WI-38 Lung Fibroblast Embryonic lung fibroblast, htert immortalized, includes Raf1 construct WI- Embryonic lung fibroblasts immortilized Lung Fibroblast 38_AM htert -amoxifen treated Human pancreas adeno-carcinoma 8988 Pancreas Epithelial cell (PA-U-8988), "established in 1985 from the liver metastasis of a primary pancreatic adeno-carcinoma from a 64-

10 year-old woman" -DSMZ HPDE6- Pancreatic duct Normal human pancreatic duct Pancreas E6E7 cell immortalized with E6E7 gene of HPV PANC-1 Pancreas Epithelial cell Pancreatic carcinoma PanIsletD Pancreas Dedifferentiated human pancreatic islet Pancreatic islet from one of the sources for cell PanIslets PanIslets Pancreas Pancreatic islet cell Human pancreatic islet HPdLF Periodontiu Normal human periodontal ligament Fibroblast m fibroblast HVMF Placenta Fibroblast Human villous mesenchymal fibroblast LNCaP Prostate Epithelial cell Prostate adeno-carcinoma Prostate adeno-carcinoma treated with androgen, "lncap clone FGC was isolated in 1977 by J.S. Horoszewicz, et al., from a needle aspiration biopsy LNCaP/a Prostate Epithelial cell of the left supraclavicular lymph node ndrogen of a 50-year-old caucasian male (blood type B+) with confirmed diagnosis of metastatic prostate carcinoma." ACC. PrEC Prostate Epithelial cell Human prostate epithelial cell line (prec/nhpre) RWPE1 Prostate Epithelial cell Prostate epithelial HSMM_e Skeletal mb Muscle Myoblast Embryonic myoblasts HSMM Skeletal Normal human skeletal muscle Myoblast Muscle myoblasts HSMM Skeletal Normal human skeletal muscle Myoblast tube Muscle myoblasts SKMC Skeletal Skeletal muscle Muscle cell Human skeletal muscle

11 AG04449 Skin Fibroblast Fetal buttock/thigh fibroblasts AG09309 Skin Fibroblast Adult human toe fibroblasts AG10803 Skin Fibroblast Adult human abdominal skin fibroblasts BJ Skin Fibroblast Skin fibroblasts Fibrobl Skin Fibroblast Normal child fibroblasts HFF Skin Fibroblast Human foreskin fibroblasts HFF_Myc Skin Fibroblast Human foreskin fibroblasts HMVECdAd endothelial Adult human dermal microvascular Skin Endotherial cell Normal adult human blood HMVECdBl-Ad Skin Endothelial cell microvascular endothelial, dermalderived Normal neonatal human blood HMVECdBl-Neo Skin Endothelial cell microvascular endothelial, dermalderived Normal adult human blood HMVECdLy-Ad Skin Endothelial cell microvascular endothelial, dermalderived Normal neonatal human lymphatic HMVECdLy-Neo Skin Endothelial cell microvascular endothelial, dermalderived Normal neonatal human microvascular HMVECdNeo Skin Endothelial cell endothelial (single donor), dermalderived Melano Skin Melanocyte Epidermal melanocytes NHDF-Ad Skin Fibroblast Adult normal human dermal fibroblasts NHDFneo Skin Fibroblast Neonatal human dermal fibroblasts N Skin Keratinocyte Normal human epidermal keratinocytes ProgFib Skin Fibroblast Fibroblasts, Hutchinson-Gilford progeria syndrome (cell line HGPS, HGADFN167, Progeria Research Foundation) HA-sp Spinal Cord Astrocyte Human astrocytes from? spinal cord

12 H7-hESC Embryo Stem cell Un-differentiated human embryonic stem H9ES Embryo Stem cell Human embryonic stem cell (hesc) H9 HESC Embryo Stem cell H1 human embryonic stem ips Skin Stem cell Induced pluripotent stem derived from skin fibroblast N2-D1 estis Germ Cell Human malignant pluripotent embryonal cancer cell line innduced by RA to neuronal phenotype? phe rachea Epithelial cell Primary human tracheal epithelial HUVEC Umbilical Vein Endothelial cell Human umbilical vein endothelial FibroP Unspecified Fibroblast Normal fibroblasts taken from individuals with Parkinson's disease; AG20443, AG08395, and AG08396 were pooled for this sample Urothelia Ureter Urothelial cell A primary culture of urothelial derived from a 12 year-old girl and immortalized by transfection with a temperature-sensitive SV-40 large antigen gene, normal human ureter Urothelia/ U189 Ureter Urothelial cell Urotsa infected by U189 Ishikawa/ Endometrial adeno-carcinoma 4OHAM Uterus Epithelial cell treated with 100 nm 4-OH amoxifen _100nM_ for 30 min 30m Ishikawa/ Endometrial adeno-carcinoma Estradiol_ Uterus Epithelial cell treated with 10 nm 17-bestradiol for 30 10nM_30 min m Myometr Uterus Smooth muscle cell Myometrial

13 AoSMC/s erum_free _media Blood vessel Smooth muscle cell Aortic smooth muscle treated in serum-free media for 36 h

14 Supplementary able 5. Oligonucleotides used in this study (provided as a separate excel file). Supplementary able 6. Filtering conditions for data set generation from highthroughput experiments. o increase the accuracy of analysis, different filtering conditions were used for each high-throughput experiment, depending on the required sizes of the data sets, required accuracy of each component of the data sets, the total number of reads, and the background indel frequency in the library. Highthroughput experiment (Data set) Number of designed pairs Conditions for filtering (Negative control) Conditions for filtering (Cpf1 delivered) Number of filtered pairs A (H H 1-2) 55,003 Read counts above 200, background indel frequency below 8% Read counts above ,292 B (H 2) 12,298 Read counts above 100, background indel frequency below 8% Read counts above 100 2,963 C (H 3, from ref. 8) 2,381 Read counts above 100, background indel frequency below 8% Read counts above 100 1,251 Supplementary able 7. Confidence intervals for the result values. Supplementary Code. he source codes of Seq-deepCpf1 and DeepCpf1 (provided as a separate zip file).