title: RWPE1 - Control Vector - Paraquat (CAD7)

value: Control Vector

value: paraquat


title: OPSCC194

status: Public on Apr 13 2021

type: SRA

city: Chicago

first: Xiaowei

last: Wang

state: IL

address: 909 S Wolcott Ave, Rm 5137

country: USA

institute: University of Illinois at Chicago

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to the NCBI reference sequence database to identify human coding genes with Bowtie v1.2.2.
Transcripts Per Million (TPM) were calculated. The read counts of  one gene were normalized by the average length of all isoforms and by the size of the all mapped mRNA reads.
Genome_build: NCBI reference sequence database
Supplementary_files_format_and_content: Tab-delimited text file includes TPM-normalized gene counts for all samples

molecule: total RNA

organism: Homo sapiens

source_name: Oropharyngeal squamous cell carcinoma

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) tumor tissues were collected for pathologic analysis from biopsy or primary surgical resection.
Ribosomal RNA (rRNA) was removed with the RiboMinus kit (Life Technologies) and custom DNA oligonucleotide probes. The RNA was used to construct RNA-seq libraries with the NEBNext Ultra mRNA Library Prep kit (New England BioLabs). The resulting cDNA libraries were PCR amplified and subject to sequencing with Illumina HiSeq 3000 at Washington University Genome Technology Access Center.

tag: hpv status

value: HPV+

tag: tissue

value: FFPE

tag: cohort

value: WashU cohort


title: p53_long-term_Rep16

city: Zurich

first: Tanja

last: Rothgangl

address: Winterthurerstrasse, 190

department: Pharmacology and Toxicology

country: Switzerland

institute: UZH Zurich

library_source: genomic

data_processing:
Library strategy: targeted amplicon sequencing
CIRCLE-seq pipeline (https://github.com/tsailabSJ/circleseq)
CHANGE-seq pipeline (https://github.com/tsailabSJ/changeseq)
iGUIDE pipeline (https://github.com/cnobles/iGUIDE)
For all targeted amplicon sequencing files, we used CRISPRESSO2 for the analysis: https://crispresso.pinellolab.partners.org/submission . This platform directly reads in a fastq.gz file and provides a summary about editing rates and allele frequency.
Genome_build: Hg38, mm10
Supplementary_files_format_and_content: for CIRCLE, CHANGE-seq and iGUIDE: text files containing identified off-target sites; html report file containing identified off-target sites; fastq-index output file generated by Miseq

molecule: genomic DNA

organism: Mus musculus

source_name: whole liver lysate

growth_protocol: DMEM growth medium supplemented with 10% FBS and 1% P/S for HEK293T and Hepa1-6 cells; EMEM with same supplements for HepG2 cells

extract_protocol:
Detachment with TryplE, wash with PBS, lysis and DNA isolation for cell lines and whole tissue or primary hepatocyte isolation for in vivo samples.
targeted amplicon sequencing; CIRCLE-seq, CHANGE-seq or iGUIDE library preparation

treatment_protocol: per 48 well plate: 1 ug total DNA with 1.5 ul Lipofectamine2000, cells were treated with the respective base-editor targeting the indicated locus. For HepG2 cells, the base editor and sgRNA was inroduced by NEON electroporation. In vivo treatment was delivery by AAV or LNP mediated delivery via tail vein injection.

value: on-target, AAV delivery

value: tail vein

value: targeted amplicon sequencing

tag: genotype

value: base-edited PCSK9


title: p53_long-term_Rep17


title: p53_long-term_Rep12


title: OPSCC193


title: CIRCLE-seq  mus musculus control

source_name: mus musculus gDNA

value: in situ gDNA digest

value: Cas9 digest without sgRNA

value: CIRCLE-seq

value: Untreated


title: p53_long-term_Rep11


title: p53_long-term_Rep15


title: p53_long-term_Rep10


title: p53_long-term_Rep9


title: DBaiP_4_16PAH_Rep4

city: Richland

first: Ryan

last: McClure

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

institute: Pacific Northwest National Laboratory

description: lane2-s018-indexRPI18-GTCCGC-F3_S18_L002

data_processing:
Raw fastq files were trimmed if necessary to remove adaptor sequences or basepairs with a phred score below 25
Each fastq file was aligned to the Genome Reference Consortium Zebrafish Build 11 (GRCz11) (https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.6/) using the Star Aligner (Dobin et al. 2013) with default settings
Resulting SAM files were then used to count reads aligning to genes using HTSeq (https://htseq.readthedocs.io/en/release_0.11.1/) along with the gff file for the Z11 genome (GCF_000002035.6_GRCz11_genomic.gff)
This led to a file of 39,701 genes with raw counts assigned to them.  From this file any gene that had a count of ‘0’ in at least 43/170 (more than 25% of the datasets had a ‘0’ for that gene), was removed from further analysis.  This led to a dataset of 21,854 genes across 170 datasets.
Raw counts were normalized with DESEQ2.  This program was also used to identify fold changes and associated adjusted p-values for those fold changes
Genome_build: GRCz11
Supplementary_files_format_and_content: .csv, Normalized gene expression levels

organism: Danio rerio

growth_protocol: To collect zebrafish embryos spawning funnels were placed in the tanks at night and the following morning embryos were collected and age staged (Kimmel et al. 1995; Westerfield 2007). Embryos were maintained in embryo medium (EM) in an incubator at 28°C until further processing. EM consisted of 15 mM NaCl, 0.5 mM KCl, 1 mMMgSO4, 0.15 mMKH2PO4, 0.05 mM Na2HPO4, and 0.7 mMNaHCO3.

extract_protocol:
Following exposure, 48-hpf whole embryos were homogenized using RNAzol (Molecular Research Center, Inc).  RNA was purified using the Direct-zol MiniPrep kit (Zymo Research)
100 bp sequencing was conducted using an Illumina HiSeq 3000 sequencer
mRNAs were enriched by polyA selection. Libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow (Wafergen Biosystems)

treatment_protocol: Embryos were exposed to chemicals above and RNA was harvested at 48 hpf

value: 48 hour post fertilization embryo

tag: chemical

value: Dibenzo[a,i]pyrene

tag: concentration

value: 5 uM


title: OPSCC186


title: p53_long-term_Rep7


title: Carbazole_1_16PAH_Rep1

description: lane6-s066-indexRPI18-GTCCGC-F11_S66_L006

value: Carbazole

value: 50 uM


title: p53_long-term_Rep6


title: DBaiP_1_16PAH_Rep1


title: p53_long-term_Rep5


title: OPSCC182


title: p53_long-term_Rep13


title: TBPH_2_FRC_Rep2

description: lane2-s019-indexRPI10-TAGCTT-22_S19_L002

extract_protocol:
Following exposure, 48-hpf whole embryos were homogenized using RNAzol (Molecular Research Center, Inc).  RNA was purified using the Direct-zol MiniPrep kit (Zymo Research) and included the optional in-column DNase 1 digestion treatment for 15 minutes
100 bp sequencing was conducted using an Illumina HiSeq 3000 sequencer
mRNAs were enriched by polyA selection. Libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow (Wafergen Biosystems)

value: Bis(2-ethylhexyl) tetrabromophthalate

value: 72 uM


title: DBahP_2_16PAH_Rep2

description: lane3-s033-indexRPI33-CAGGCG-C6_S33_L003

value: Dibenzo[a,h]pyrene

value: 10 uM


title: p53_long-term_Rep3

value: on-target, AAV delivery


title: OPSCC190

value: HPV+

value: FFPE

value: WashU cohort


title: OPSCC180


title: p53_long-term_Rep2

value: tail vein

value: targeted amplicon sequencing

value: base-edited PCSK9


title: BkF_4_16PAH_Rep4

description: lane2-s014-indexRPI14-AGTTCC-B3_S14_L002

value: Benzo[k]fluoranthene


title: OPSCC189


title: LNP_testis_Rep3

source_name: whole tissue lysate

value: off-target; LNP delivery


title: LNP_spleen_Rep3


title: LNP_skeletal_muscle_Rep3


title: BjF_4_16PAH_Rep4

description: lane2-s024-indexRPI24-GGTAGC-F4_S24_L002

value: 48 hour post fertilization embryo

value: Benzo[j]fluoranthene


title: DBahP_1_16PAH_Rep1

description: lane1-s011-indexRPI11-GGCTAC-E2_S11_L001


title: OPSCC188


title: OPSCC187

value: HPV-


title: Carbazole_4_16PAH_Rep4

description: lane6-s064-indexRPI16-CCGTCC-D11_S64_L006

value: Carbazole

value: 50 uM


title: OPSCC175


title: Carbazole_3_16PAH_Rep3

description: lane4-s041-indexRPI41-GACGAC-E7_S41_L004


title: p53_long-term_Rep8


title: Carbazole_2_16PAH_Rep2

description: lane3-s035-indexRPI35-CATTTT-E6_S35_L003


title: OPSCC185


title: TBPH_4_FRC_Rep4

description: lane3-s034-indexRPI12-CTTGTA-24_S34_L003

value: Bis(2-ethylhexyl) tetrabromophthalate

value: 72 uM


title: LNP_heart_Rep3


title: OPSCC172


title: BbF_3_16PAH_Rep3

description: lane4-s048-indexRPI48-TCGGCA-F8_S48_L004

value: Benzo[b]fluoranthene


title: OPSCC183


title: LNP_Diaphragm_Rep3


title: TBPH_3_FRC_Rep3

description: lane3-s033-indexRPI11-GGCTAC-23_S33_L003


title: LNP_testis_Rep2


title: BjF_3_16PAH_Rep3

description: lane5-s055-indexRPI7-CAGATC-A10_S55_L005


title: p53_long-term_Rep4

value: on-target, AAV delivery


title: OPSCC173

value: HPV+


title: OPSCC181

value: FFPE


title: OPSCC170

value: WashU cohort


title: TBPH_1_FRC_Rep1


title: LNP_spleen_Rep2

value: tail vein


title: OPSCC184


title: OPSCC179


title: BbF_1_16PAH_Rep1

description: lane2-s017-indexRPI17-GTAGAG-E3_S17_L002


title: p53_long-term_Rep1

value: targeted amplicon sequencing


title: LNP_skeletal_muscle_Rep2

value: base-edited PCSK9


title: Anthrac_3_16PAH_Rep3

description: lane4-s047-indexRPI47-TCGAAG-E8_S47_L004

value: Anthracene


title: OPSCC167


title: OPSCC178


title: BbF_2_16PAH_Rep2

description: lane6-s062-indexRPI14-AGTTCC-B11_S62_L006


title: BkF_2_16PAH_Rep2

description: lane3-s034-indexRPI34-CATGGC-D6_S34_L003

value: Benzo[k]fluoranthene


title: OPSCC177


title: LNP_kidney_Rep2

value: off-target; LNP delivery


title: BkF_1_16PAH_Rep1

description: lane6-s061-indexRPI13-AGTCAA-A11_S61_L006

value: 48 hour post fertilization embryo


title: OPSCC176


title: LNP_heart_Rep2


title: BkF_3_16PAH_Rep3

description: lane4-s046-indexRPI46-TCCCGA-D8_S46_L004


title: OPSCC174

value: HPV-


title: LNP_Lung_Rep3


title: OPSCC165


title: LNP_kidney_Rep3


title: LNP_Diaphragm_Rep2


title: OPSCC164


title: OPSCC169


title: Acenaph_4_16PAH_Rep4

description: lane2-s020-indexRPI20-GTGGCC-B4_S20_L002

value: Acenapthene


title: LNP_testis_Rep1


title: BjF_1_16PAH_Rep1

description: lane6-s070-indexRPI2-CGATGT-D12_S70_L006

value: Benzo[j]fluoranthene


title: BjF_2_16PAH_Rep2

description: lane5-s060-indexRPI12-CTTGTA-F10_S60_L005


title: OPSCC171


title: Acenaph_3_16PAH_Rep3

value: 50 uM


title: Anthrac_4_16PAH_Rep4

description: lane2-s019-indexRPI19-GTGAAA-A4_S19_L002


title: OPSCC162


title: LNP_spleen_Rep1


title: OPSCC168


title: Acenaph_1_16PAH_Rep1

description: lane4-s037-indexRPI37-CGGAAT-A7_S37_L004


title: Anthrac_2_16PAH_Rep2

description: lane4-s044-indexRPI44-TATAAT-B8_S44_L004


title: LNP_Lung_Rep1


title: OPSCC166


title: OPSCC160


title: Anthrac_1_16PAH_Rep1


title: OPSCC163


title: LNP_heart_Rep1


title: LNP_Lung_Rep2


title: OPSCC157


title: long-term_LNP_Rep2

value: on,target; LNP delivery


title: X4H.CPdefP_4_16PAH_Rep4

description: lane2-s016-indexRPI16-CCGTCC-D3_S16_L002


title: Acenaph_2_16PAH_Rep2

description: lane3-s027-indexRPI27-ATTCCT-C5_S27_L003


title: LNP_skeletal_muscle_Rep1


title: OPSCC161


title: X9.MA_4_16PAH_Rep4

description: lane2-s023-indexRPI23-GAGTGG-E4_S23_L002


title: LNP_kidney_Rep1


title: OPSCC159


title: OPSCC158


title: X9.MA_2_16PAH_Rep2


title: X9.MA_1_16PAH_Rep1

description: lane3-s030-indexRPI30-CACCGG-F5_S30_L003


title: OPSCC156


title: OPSCC152


title: X4H.CPdefP_3_16PAH_Rep3

description: lane3-s032-indexRPI32-CACTCA-B6_S32_L003


title: OPSCC155


title: LNP_Diaphragm_Rep1


title: P1_3mg/kg_Liver_Rep3

value: on,target; LNP delivery, P1


title: 24h_Liver_Rep3


title: long-term_LNP_Rep1


title: X4H.CPdefP_2_16PAH_Rep2


title: OPSCC154


title: OPSCC149


title: X3.NF_1_16PAH_Rep1

description: lane6-s067-indexRPI19-GTGAAA-A12-rd_S67_L006


title: P1_3mg/kg_PrimHep_Rep3

source_name: primary hepatocytes


title: X9.MA_3_16PAH_Rep3

description: lane6-s069-indexRPI1-ATCACG-C12_S69_L006


title: X4H.CPdefP_1_16PAH_Rep1

description: lane3-s026-indexRPI26-ATGAGC-B5_S26_L003


title: OPSCC148


title: 24h_Liver_Rep2


title: 24h_Liver_Rep1


title: X3.NF_4_16PAH_Rep4

description: lane2-s022-indexRPI22-CGTACG-D4_S22_L002


title: P1_3mg/kg_PrimHep_Rep2


title: P1_3mg/kg_redose_Liver_Rep3


title: OPSCC153


title: P1_3mg/kg_Liver_Rep2


title: OPSCC145


title: OPSCC151


title: P1_3mg/kg_redose_PrimHep_Rep3


title: TBBPA_4_FRC_Rep4

value: 3,3',5,5'-tetrabromobisphenol A

value: 4 uM


title: OPSCC146

value: HPV+

value: FFPE


title: X3.NF_2_16PAH_Rep2


title: TBBPA_2_FRC_Rep2


title: X2.MN_3_16PAH_Rep3

description: lane6-s068-indexRPI20-GTGGCC-B12_S68_L006


title: P1_1mg/kg_PrimHep_Rep3

value: tail vein


title: X3.NF_3_16PAH_Rep3


title: P1_3mg/kg_PrimHep_Rep1

value: targeted amplicon sequencing


title: TBBPA_1_FRC_Rep1


title: TBBPA_3_FRC_Rep3


title: OPSCC150

value: WashU cohort


title: OPSCC143

value: Vanderbilt cohort


title: X2.MN_2_16PAH_Rep2

description: lane3-s025-indexRPI25-ACTGAT-A5_S25_L003


title: OPSCC142


title: P1_1mg/kg_Liver_Rep2

value: base-edited PCSK9


title: P1_3mg/kg_Liver_Rep1


title: OPSCC147


title: X2.MN_4_16PAH_Rep4


title: OPSCC144


title: BDE.47_4_FRC_Rep4

description: lane2-s022-indexRPI20-GTGGCC-44_S22_L002

value: 2,2,4,4-tetra-bromodiphenyl ether

value: 85 uM


title: P1_1mg/kg_Liver_Rep3


title: OPSCC141


title: P1_1mg/kg_PrimHep_Rep2


title: X2.MN_1_16PAH_Rep1

description: lane1-s010-indexRPI10-TAGCTT-D2_S10_L001

value: 48 hour post fertilization embryo


title: P1_1mg/kg_PrimHep_Rep1


title: OPSCC140


title: BDE.47_2_FRC_Rep2

description: lane2-s021-indexRPI18-GTCCGC-42_S21_L002


title: P1_1mg/kg_Liver_Rep1


title: BDE.47_1_FRC_Rep1


title: P1_3mg/kg_redose_PrimHep_Rep2


title: BDE.47_3_FRC_Rep3

description: lane3-s036-indexRPI19-GTGAAA-43_S36_L003


title: P1_3mg/kg_redose_Liver_Rep2


title: X1.5.DMN_4_16PAH_Rep4


title: P1_3mg/kg_redose_PrimHep_Rep1


title: OPSCC139

value: HPV-


title: OPSCC138


title: OPSCC137


title: OPSCC136


title: X1.5.DMN_3_16PAH_Rep3

description: lane4-s042-indexRPI42-TAATCG-F7_S42_L004


title: eCLIP_HeLa_rep2

city: Cambridge

first: Alexis

middle: A

last: Jourdain

state: MA

address: 415 Main Street

institute: Broad Institute of MIT & Harvard

description: immunoprecipitated RNA

data_processing:
Raw reads were mapped using STAR (Dobin et al., 2013) to the hg19 genome following standard ENCODE guidelines.
Read length was relaxed to accommodate the slightly shorter average eCLIP read length (  outFilterMatchNminOverLread 0.33). Duplicate PCR reads were removed from the mapped reads to generate final reads. Mapped reads were then processed into peaks using CLIPper (Lovci et al., 2013) with standard specifications.
Genome_build: hg19
Supplementary_files_format_and_content: Peak text file with coordinates, P values and apex.

source_name: HeLa cells

growth_protocol: Wild-type HeLa and K562 cells were were maintained in DMEM containing 1mM sodium pyruvate (ThermoFisher Scientific) with 25 mM glucose, 10% fetal bovine serum (FBS, ThermoFisher Scientific), 50 μg/mL uridine (Sigma), and 100 U/mL penicillin/streptomycin (ThermoFisher Scientific) under 5% CO2 at 37°C.

extract_protocol:
K562 and Hela cells (2e7 for each replicate) were UV crosslinked (254 nm, 400 mJ/cm2), then lysed and sonicated (Bioruptor) in eCLIP lysis buffer (50 mM Tris–HCl pH 7.4, 100 mM NaCl, 1% NP-40 (Igepal CA630), 0.1% SDS, 0.5% sodium deoxycholate, 1:200 Protease Inhibitor Cocktail I, in RNase/DNase-free H2O). RNA fragments were created by incubating lysates with RNase I (Ambion) and LUC7L2:RNA complexes were immunoprecipitated for 2h at 4C using Dynabeads bound to 4ug of LUC7L2-specific affinity-purified antibody (HPA051631). In parallel, libraries were generated from size-matched input (SMInput) samples containing RNAs present in the whole cell lysates, i.e. sans RBP-specific IP. For the IPs, a series of stringent washes (High salt wash buffer: 50 mM Tris–HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate (protect from light), in RNase/DNase-free H2O. ; Wash buffer: 20 mM Tris–HCl pH 7.4, 10 mM MgCl2, 0.2% Tween-20, in RNase/DNase-free H2O.) was followed by RNA dephosphorylation with FastAP (ThermoFisher Scientific) and T4 PNK (NEB) then ligation of an adaptor to the 3 ends of the RNAs with T4 RNA ligase 1 (NEB). Protein:RNA complexes were separated on 4-12%  polyacrylamide gels, transferred to a nitrocellulose membranes, and RNA was extracted from the membranes using Proteinase K (NEB).
SMInput RNA were dephosphorylated and 3′-ligated and all samples were reverse transcribed with Superscript III (Invitrogen). Free primers were removed with ExoSap-IT (Affymetrix) and a DNA adaptor was ligated to the 3′ ends of the cDNA with T4 RNA ligase 1. cDNA was quantified by qPCR and PCR amplified using Q5 Master Mix (NEB) and resulting libraries were purified prior to Illumina sequencing.

tag: cell type

value: HeLa cells

value: Wild-type

tag: culture condition

value: DMEM with 25mM glucose


title: eCLIP_K562_rep1

description: immunoprecipitated RNA

source_name: K562 cells

value: K562 cells


title: input_K562_rep1


title: input_K562_rep2


title: eCLIP_HeLa_rep1

description: immunoprecipitated RNA


title: input_HeLa_rep2


title: input_HeLa_rep1


title: P1_3mg/kg_redose_Liver_Rep1

value: on,target; LNP delivery, P1


title: X1.5.DMN_2_16PAH_Rep2

description: lane4-s039-indexRPI39-CTATAC-C7_S39_L004

value: 50 uM


title: AAV_long_term_Rep3

value: on,target; AAV delivery


title: eCLIP_K562_rep2

description: immunoprecipitated RNA


title: OPSCC134

value: HPV+

value: FFPE


title: OPSCC132


title: TE7 PD resistant replicate 3

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

description:
TE7 PD resistant replicate 3
Diehl-Yoshida-TE7-redux_Counts.txt
Diehl-Yoshida-TE7-redux_Counts_PDR.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

source_name: human esophageal cells

growth_protocol: Palbociclib (PD) resistant cells (PDR) were generated from 1205Lu and TE7 cells via sustained treatment with 1uM PD and kept in PD-containing medium. Parental cells (1205Lu and TE7) were cultured in parallel in standard growth media.

extract_protocol: Total RNA was extracted with a RNeasy Mini Kit by Qiagen

treatment_protocol: Cells were seeded (without drugs) in standard culture media and treated with 1uM PD for 24hours or 8 days

value: Cancer cell line

tag: developmental stage

value: a primary esophageal squamous cell carcinoma

value: 1uM PD


title: OPSCC135

value: Vanderbilt cohort


title: AAV_long_term_Rep2

value: tail vein

value: targeted amplicon sequencing

value: base-edited PCSK9


title: OPSCC131


title: X1.5.DMN_1_16PAH_Rep1

value: 48 hour post fertilization embryo


title: invitro_mus musculus_control_mP01_Rep2

source_name: direct cell lysis Hepa1-6

value: on-target, Lipofection

value: Untreated


title: Ct_untagged_rpmi-1

city: Irapuato

first: Eugenio

last: Mancera

state: Guanajuato

address: Km. 9.6 Libramiento Norte Carretera Irapuato-Leon

department: Ingenieria Genetica

country: Mexico

institute: Cinvestav

data_processing:
Quality analysis performed with FastQC
ChIP-seq reads were mapped to their corresponding genome using Bowtie 2 with default parameters
SAMtools package was used to convert, sort and index the sequenced reads to BAM format
Peak calling was performed using MACS2 with a q-value cutoff of 0.01; the shiftsize parameter was determined using the SPP package in R
Genome_build: http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly21/archive/C_albicans_SC5314_version_A21-s02-m09-r02_chromosomes.fasta.gz; http://www.candidagenome.org/download/sequence/C_dubliniensis_CD36/archive/C_dubliniensis_CD36_version_s01-m02-r08_chromosomes.fasta.gz; http://www.candidagenome.org/download/sequence/C_tropicalis_MYA-3404/current/C_tropicalis_MYA-3404_chromosomes.fasta.gz
Supplementary_files_format_and_content: enrich.txt files have the maximum fold enrichment between tagged and untagged control experiment for each upstream intergenic region in the genome.

organism: Candida tropicalis

source_name: a/alpha cell

growth_protocol: Experiments were performed under biofilm growth conditions in 6-well polystyrene plates as previously described (Nobile et al., Cell, 2012). After 48 hours of biofilm growth in Spider and Spider 1% glucose for C. albicans and C. dubliniensis, and in RPMI 1% glucose and Spider 1% for C. tropicalis, samples were harvested.  Biofilm growth was done at 37°C and 200 rpm.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. Cell disruption and immunoprecipitation were performed as previously described (Hernday et al., Methods Enzymol 470: 737-758, 2010) using a c-Myc tag monoclonal antibody (RRID: AB_2536303).
Performed using an NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina sequencing

tag: dna-binding gene

tag: epitope

value: untagged

tag: growth

value: biofilm

tag: media

value: RPMI 1% glucose

tag: chip antibody

value: c-Myc tag monoclonal antibody (RRID:AB_2536303)


title: Ct_untagged_spglu-1

value: Spider 1% glucose


title: AAV_long_term_Rep1

value: on,target; AAV delivery


title: Ct_untagged_rpmi-2


title: OPSCC128

value: HPV+

value: FFPE


title: OPSCC129


title: TE7 PD resistant replicate 2

description:
TE7 PD resistant replicate 2
Diehl-Yoshida-TE7-redux_Counts.txt
Diehl-Yoshida-TE7-redux_Counts_PDR.txt

value: Cancer cell line

value: a primary esophageal squamous cell carcinoma


title: OPSCC130

value: Vanderbilt cohort


title: TE7 PD resistant replicate 1

description:
TE7 PD resistant replicate 1
Diehl-Yoshida-TE7-redux_Counts.txt
Diehl-Yoshida-TE7-redux_Counts_PDR.txt

value: 1uM PD


title: Ct_Ndt80_spglu-2

description:
ChIPspglu_II_CEM266
samples for processed file: ChIPspglu_II_CEM266 - ChIPspglu_II_CEM229
ctrop_bothmedia.enrich.txt

value: c-myc


title: OPSCC133


description:
TE7 parental PD treated for 8 days replicate 3
Diehl-Yoshida-TE7-redux_Counts.txt
Diehl-Yoshida-TE7-redux_Counts_PD8d.txt


title: invitro_mus musculus_control_mP01_Rep1

value: targeted amplicon sequencing


title: invitro_mus musculus_ABEmax_sgRNA_mP01_Rep4

value: ABEmax, sgRNA-mP01

value: base-edited PCSK9


title: Ct_untagged_spglu-2


title: OPSCC127


title: Ct_Ndt80_spglu-1

description:
ChIPspglu_I_CEM266
samples for processed file: ChIPspglu_I_CEM266 - ChIPspglu_I_CEM229
ctrop_bothmedia.enrich.txt


title: invitro_mus musculus_ABEmax_sgRNA_mP01_Rep3

value: on-target, Lipofection


title: invitro_mus musculus_control_mP01_Rep3

value: Untreated


description:
TE7 parental PD treated for 8 days replicate 2
Diehl-Yoshida-TE7-redux_Counts.txt
Diehl-Yoshida-TE7-redux_Counts_PD8d.txt


description:
TE7 parental PD treated for 8 days replicate 1
Diehl-Yoshida-TE7-redux_Counts.txt
Diehl-Yoshida-TE7-redux_Counts_PD8d.txt


title: Ct_Ndt80_rpmi-2

description:
ChIP_II_CEM266
samples for processed file: ChIP_II_CEM266 - ChIP_II_CEM229
ctrop_bothmedia.enrich.txt

value: biofilm


description:
TE7 parental PD treated for 24 hours replicate 3
Diehl-Yoshida-TE7-redux_Counts.txt
Diehl-Yoshida-TE7-redux_Counts_PD1d.txt


title: OPSCC125


title: OPSCC126


title: invitro_mus musculus_ABEmax_sgRNA_mP01_Rep2


title: invitro_mus musculus_ABEmax_sgRNA_mP01_Rep1


title: OPSCC124


title: Ct_Ndt80_rpmi-1

description:
ChIP_I_CEM266
samples for processed file: ChIP_I_CEM266 - ChIP_I_CEM229
ctrop_bothmedia.enrich.txt

value: RPMI 1% glucose


description:
TE7 parental PD treated for 24 hours replicate 2
Diehl-Yoshida-TE7-redux_Counts.txt
Diehl-Yoshida-TE7-redux_Counts_PD1d.txt


title: Treated_invitro_CIRCLE-off-target-site10_Rep3

source_name: gDNA

value: Lipofection/tailvein


title: Ct_untagged_hom-1

data_processing:
Quality analysis performed with FastQC
ChIP-seq reads were mapped to their corresponding genome using Bowtie 2 with default parameters
SAMtools package was used to convert, sort and index the sequenced reads to BAM format
Adjusted the number of reads in the different treatment-control dataset pairs using SAMtools view -s function prior to peak calling
Peak calling was performed using MACS2 with a q-value cutoff of 0.01; the shiftsize parameter was determined using the SPP package in R
Genome_build: http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly21/archive/C_albicans_SC5314_version_A21-s02-m09-r02_chromosomes.fasta.gz; http://www.candidagenome.org/download/sequence/C_dubliniensis_CD36/archive/C_dubliniensis_CD36_version_s01-m02-r08_chromosomes.fasta.gz; http://www.candidagenome.org/download/sequence/C_tropicalis_MYA-3404/current/C_tropicalis_MYA-3404_chromosomes.fasta.gz; www.candidagenome.org/download/sequence/C_parapsilosis_CDC317/archive/C_parapsilosis_CDC317_version_s01-m03-r13_chromosomes.fasta.gz
Supplementary_files_format_and_content: peaks.txt files were generated for each experiment with tagged proteins using untagged strains as a control in MACS2.

growth_protocol: Experiments were performed under biofilm growth conditions in 6-well polystyrene plates as previously described (Nobile et al., Cell, 2012). After 48 hours of biofilm growth in Spider 1% glucose at 37°C and 200 rpm

value: untagged

value: Spider 1% glucose

value: c-Myc tag monoclonal antibody (RRID:AB_2536303)


title: Ct_untagged_hom-2


description:
TE7 parental PD treated for 24 hours replicate 1
Diehl-Yoshida-TE7-redux_Counts.txt
Diehl-Yoshida-TE7-redux_Counts_PD1d.txt


title: OPSCC123

value: HPV+

value: FFPE


title: OPSCC122


title: TE7 parental Control replicate 3

description:
TE7 parental Control replicate 3
Diehl-Yoshida-TE7-redux_Counts.txt
Diehl-Yoshida-TE7-redux_Counts_PD1d.txt
Diehl-Yoshida-TE7-redux_Counts_PD8d.txt
Diehl-Yoshida-TE7-redux_Counts_PDR.txt

value: Cancer cell line

value: a primary esophageal squamous cell carcinoma

value: vehicle control


title: Treated_invitro_CIRCLE-off-target-site10_Rep1


title: Ct_Tec1_hom-1

description:
ChIPspglu-I-CEM360
samples for processed file: ChIPspglu-I-CEM360 - ChIPspglu_I_CEM300

value: c-myc


title: Ct_Tec1_hom-2

description:
ChIIPspglu-II-CEM360
samples for processed file: ChIIPspglu-II-CEM360 - ChIPspglu_II_CEM300


title: Treated_invitro_CIRCLE-off-target-site10_Rep2

value: targeted amplicon sequencing


title: TE7 parental Control replicate 2

description:
TE7 parental Control replicate 2
Diehl-Yoshida-TE7-redux_Counts.txt
Diehl-Yoshida-TE7-redux_Counts_PD1d.txt
Diehl-Yoshida-TE7-redux_Counts_PD8d.txt
Diehl-Yoshida-TE7-redux_Counts_PDR.txt


title: OPSCC121

value: Vanderbilt cohort


title: Ct_Rob1_hom-2

description:
ChIIPspglu-II-CEM359
samples for processed file: ChIIPspglu-II-CEM359 - ChIPspglu_II_CEM300


title: TE7 parental Control replicate 1

description:
TE7 parental Control replicate 1
Diehl-Yoshida-TE7-redux_Counts.txt
Diehl-Yoshida-TE7-redux_Counts_PD1d.txt
Diehl-Yoshida-TE7-redux_Counts_PD8d.txt
Diehl-Yoshida-TE7-redux_Counts_PDR.txt


title: OPSCC120


title: Treated_invitro_CIRCLE-off-target-site1_Rep2

value: base-edited PCSK9


title: Ct_Rob1_hom-1

description:
ChIPspglu-I-CEM359
samples for processed file: ChIPspglu-I-CEM359 - ChIPspglu_I_CEM300


title: OPSCC119


title: Treated_invitro_CIRCLE-off-target-site1_Rep1


title: OPSCC118


title: Ct_Ndt80_hom-2

description:
ChIIPspglu-II-CEM358
samples for processed file: ChIIPspglu-II-CEM358 - ChIPspglu_II_CEM300


title: LNP_invivo_CIRCLE-off-target-site1_Rep2


title: Ct_Efg1_hom-2

description:
ChIIPspglu-II-CEM357
samples for processed file: ChIIPspglu-II-CEM357 - ChIPspglu_II_CEM300


title: OPSCC117


title: LNP_invivo_CIRCLE-off-target-site1_Rep3


title: Ct_Ndt80_hom-1

description:
ChIPspglu-I-CEM358
samples for processed file: ChIPspglu-I-CEM358 - ChIPspglu_I_CEM300


title: 1205Lu PD resistant clone 7 replicate 1

description:
PDResCln7_vs_Control.txt
PDResCln7: 1445__PDResCln7-A
PDResCln7_vs_PD192.txt
PDResCln7: 1445__PDResCln7-A

source_name: human melanoma cells

value: Cancer cell

value: Xenograft MET to WM793

value: 1uM PD


title: 1205Lu PD resistant clone 7 replicate 2

description:
PDResCln7_vs_Control.txt
PDResCln7: 1446__PDResCln7-B
PDResCln7_vs_PD192.txt
PDResCln7: 1446__PDResCln7-B


title: 1205Lu PD resistant clone 6 replicate 3

description:
PDResCln6_vs_Control.txt
PDResCln6: 1444__PDResCln6-C
PDResCln6_vs_PD192.txt
PDResCln6: 1444__PDResCln6-C


title: 1205Lu PD resistant clone 6 replicate 2

description:
PDResCln6_vs_Control.txt
PDResCln6: 1443__PDResCln6-B
PDResCln6_vs_PD192.txt
PDResCln6: 1443__PDResCln6-B


title: LNP_invivo_CIRCLE-off-target-site1_Rep1


title: OPSCC114


title: OPSCC115

value: HPV-


title: Ct_Brg1_hom-2

description:
ChIIPspglu-II-CEM356
samples for processed file: ChIIPspglu-II-CEM356 - ChIPspglu_II_CEM300

value: biofilm


title: Untreated_invivo_CIRCLE-off-target-site1_Rep2

value: Lipofection/tailvein

value: Untreated


title: 1205Lu PD resistant clone 2 replicate 3

description:
PDResCln2_vs_Control.txt
PDResCln2: 1441__PDResCln2-C
PDResCln2_vs_PD192.txt
PDResCln2: 1441__PDResCln2-C


title: 1205Lu PD resistant clone 7 replicate 3

description:
PDResCln7_vs_Control.txt
PDResCln7: 1447__PDResCln7-C
PDResCln7_vs_PD192.txt
PDResCln7: 1447__PDResCln7-C


title: OPSCC116


title: 1205Lu PD resistant clone 6 replicate 1

description:
PDResCln6_vs_Control.txt
PDResCln6: 1442__PDResCln6-A
PDResCln6_vs_PD192.txt
PDResCln6: 1442__PDResCln6-A


title: Ct_Brg1_hom-1

description:
ChIPspglu-I-CEM356
samples for processed file: ChIPspglu-I-CEM356 - ChIPspglu_I_CEM300

value: Spider 1% glucose

value: c-Myc tag monoclonal antibody (RRID:AB_2536303)


title: Ct_Bcr1_hom-2

description:
ChIIPspglu-II-CEM355
samples for processed file: ChIIPspglu-II-CEM355 - ChIPspglu_II_CEM300


title: OPSCC112

value: FFPE


title: 1205Lu PD resistant clone 2 replicate 2

description:
PDResCln2_vs_Control.txt
PDResCln2: 1440__PDResCln2-B
PDResCln2_vs_PD192.txt
PDResCln2: 1440__PDResCln2-B


title: AAV_invivo_CIRCLE-off-target-site1_Rep3


title: Treated_invitro_CIRCLE-off-target-site1_Rep3


title: 1205Lu PD resistant clone 2 replicate 1

description:
PDResCln2_vs_Control.txt
PDResCln2: 1439__PDResCln2-A
PDResCln2_vs_PD192.txt
PDResCln2: 1439__PDResCln2-A


title: OPSCC111

value: HPV+


title: Ct_Bcr1_hom-1

description:
ChIPspglu-I-CEM355
samples for processed file: ChIPspglu-I-CEM355 - ChIPspglu_I_CEM300


title: 1205Lu PD resistant clone 1 replicate 3

description:
PDResCln1_vs_Control.txt
PDResCln1: 1438__PDResCln1-C
PDResCln1_vs_PD192.txt
PDResCln1: 1438__PDResCln1-C


title: YA_2

city: hangzhou

first: xiao

middle: chen

last: wen

address: desheng_road NO.298

country: China

institute: Zhejiang Academy of Agricultural Sciences

description:
Drug treatment for 120 hours
genes_fpkm_expression.txt

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (NCBI Trichophyton_mentagrophytes GCA_003118255.1),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Genome_build: NCBI GCA_003118255.1(https://www.ncbi.nlm.nih.gov/genome/9043?genome_assembly_id=374468)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Trichophyton mentagrophytes

source_name: Fungi cell

growth_protocol: T. mentagrophytes strain in eumycetes, which was grown in Tryptic Soy Broth (TSB) at 28°C for 7days.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an IlluminaHiseq4000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Briefly, the fungi were cultured at 30000 cells/mL, in presence of different chemical drugs with 120 hours, respectively.

tag: treatment

value: Adriamycin hydrochloride (YA)


title: 1205Lu PD resistant clone 1 replicate 2

description:
PDResCln1_vs_Control.txt
PDResCln1: 1437__PDResCln1-B
PDResCln1_vs_PD192.txt
PDResCln1: 1437__PDResCln1-B


title: YA_3


title: AAV_invivo_CIRCLE-off-target-site1_Rep1


title: OPSCC110


title: Untreated_invivo_CIRCLE-off-target-site1_Rep3


title: Ct_Efg1_hom-1

description:
ChIPspglu-I-CEM357
samples for processed file: ChIPspglu-I-CEM357 - ChIPspglu_I_CEM300


title: Untreated_invivo_CIRCLE-off-target-site1_Rep1


title: 1205Lu parental PD treated for 8 days replicate 3

description:
PD192_vs_Control.txt
PD192: 1435__PD192-C
PD192_vs_PD24.txt
PD192: 1435__PD192-C
PDResCln1_vs_PD192.txt
PDResCln2_vs_PD192.txt
PDResCln6_vs_PD192.txt
PDResCln7_vs_PD192.txt
PD192: 1435__PD192-C


title: 1205Lu PD resistant clone 1 replicate 1

description:
PDResCln1_vs_Control.txt
PDResCln1: 1436__PDResCln1-A
PDResCln1_vs_PD192.txt
PDResCln1: 1436__PDResCln1-A


title: Treated_invitro_CIRCLE-off-target-site9_Rep3


title: Treated_invitro_CIRCLE-off-target-site9_Rep2


title: OPSCC109


title: 1205Lu parental PD treated for 8 days replicate 2

description:
PD192_vs_Control.txt
PD192: 1434__PD192-B
PD192_vs_PD24.txt
PD192: 1434__PD192-B
PDResCln1_vs_PD192.txt
PDResCln2_vs_PD192.txt
PDResCln6_vs_PD192.txt
PDResCln7_vs_PD192.txt
PD192: 1434__PD192-B


title: EB_2

value: Ethidium bromide (EB)


title: EB_3


title: Treated_invitro_CIRCLE-off-target-site8_Rep3


title: OPSCC108


title: OPSCC106


title: 1205Lu parental PD treated for 8 days replicate 1

description:
PD192_vs_Control.txt
PD192: 1433__PD192-A
PD192_vs_PD24.txt
PD192: 1433__PD192-A
PDResCln1_vs_PD192.txt
PDResCln2_vs_PD192.txt
PDResCln6_vs_PD192.txt
PDResCln7_vs_PD192.txt
PD192: 1433__PD192-A


title: OPSCC107


title: YA_1


title: OPSCC105


title: EB_1


title: Treated_invitro_CIRCLE-off-target-site8_Rep2


title: OPSCC113


title: AAV_invivo_CIRCLE-off-target-site1_Rep2


title: TB-3

value: Terbinaphthol (TB)


title: 1205Lu parental PD treated for 24 hours replicate 3

description:
PD192_vs_PD24.txt
PD24: 1432__PD24-C
PD24_vs_Control.txt
PD24: 1432__PD24-C


title: TB-2


title: OPSCC104


title: Treated_invitro_CIRCLE-off-target-site8_Rep1

value: targeted amplicon sequencing


title: OPSCC102

value: Vanderbilt cohort


title: TB-1


title: OPSCC101


title: 1205Lu parental Control replicate 3

description:
PD192_vs_Control.txt
Control: 1429__Control-C
PD24_vs_Control.txt
Control: 1429__Control-C
PDResCln1_vs_Control.txt
PDResCln2_vs_Control.txt
PDResCln6_vs_Control.txt
PDResCln7_vs_Control.txt
Control: 1429__Control-C

value: vehicle control


title: CIRCLE-off-target-site8_ReSeq

value: base-edited PCSK9


title: Treated_invitro_CIRCLE-off-target-site9_Rep1


title: 1205Lu parental Control replicate 2

description:
PD192_vs_Control.txt
Control: 1428__Control-B
PD24_vs_Control.txt
Control: 1428__Control-B
PDResCln1_vs_Control.txt
PDResCln2_vs_Control.txt
PDResCln6_vs_Control.txt
PDResCln7_vs_Control.txt
Control: 1428__Control-B

value: Cancer cell

value: Xenograft MET to WM793


title: CIRCLE-off-target-site7_ReSeq


title: CIRCLE-off-target-site6_ReSeq


title: CIRCLE-off-target-site10_ReSeq


title: Fe_1

value: Fenarimol (FE)


title: OPSCC100


title: 1205Lu parental Control replicate 1

description:
PD192_vs_Control.txt
Control: 1427__Control-A
PD24_vs_Control.txt
Control: 1427__Control-A
PDResCln1_vs_Control.txt
PDResCln2_vs_Control.txt
PDResCln6_vs_Control.txt
PDResCln7_vs_Control.txt
Control: 1427__Control-A


title: MK_3

value: Miconazole nitrate salt (MK)


title: 1205Lu parental PD treated for 24 hours replicate 1

description:
PD192_vs_PD24.txt
PD24: 1430__PD24-A
PD24_vs_Control.txt
PD24: 1430__PD24-A

value: 1uM PD


title: OPSCC98


title: CIRCLE-off-target-site5_ReSeq

value: Lipofection/tailvein


title: 1205Lu parental PD treated for 24 hours replicate 2

description:
PD192_vs_PD24.txt
PD24: 1431__PD24-B
PD24_vs_Control.txt
PD24: 1431__PD24-B


title: CIRCLE-off-target-site9_ReSeq


title: CIRCLE-off-target-site4_ReSeq


title: C. albicans CEM175 Biofilm Growth in Spider Glucose Replicate 2

type: RNA

hyb_protocol: Equal amounts of the Cy3 and Cy5 labeled cDNA hybridized to the array overnight, as described in the Agilent protocol. Following hybridization, the arrays were washed as specified by Agilent.

scan_protocol: Arrays were scanned at 5 μm, averaging 2 lines, with an Axon GenePix 4000A scanner.

data_processing: Arrays were gridded using GenePix Pro version 5.1. Global Lowess normalization analysis was performed for each array using a Goulphar script (The R Foundation for Statistical Computing). Normalized data was collapsed first by averaging the result for all duplicate probes and finally by taking the median of the probes for each ORF. Data was transformed as described for each experiment. Note that comparisons between arrays can only be made if they share a pooled reference (Ch2)

organism: Candida albicans

source_name: CEM175 spider glucose biofilm

label_protocol: cDNA was dried and resuspended in 5 μL 0.1 M sodium bicarbonate. An equivalent volume of Cy3 (pool) or Cy5 (individual) dye (Amersham) was added (dyes were resuspended in 60 μL of DMSO) and the reaction incubated at 65° for 20 minutes in the dark. Labeled cDNAs were purified using a Clean and Concentrator -5 kit (Zymo Research).

growth_protocol: Cultures for the extraction of total RNA under biofilm growth conditions were performed on biofilms grown on the bottom of 6-well polystyrene plates for 48 hours at 37°C and 200 rpm as previously described (Nobile et al. 2012). The media used was Spider 1% glucose and Spider. Planktonic cultures for total RNA were grown in the same media by inoculating with cells from an overnight 30°C YPD culture to an OD600 of 0.05. Cultures were then grown in flasks at 37°C with shaking at 225 rpm until they reached an OD600 of 1.0.

extract_protocol: RNA was isolated and reverse transcribed as previously described (Nobile et al. 2012). Additionally, reverse transcription reactions were performed on either individual samples or on RNA in which an equivalent amount of each RNA sample was pooled.

treatment_protocol: Nobile et al. Cell 2012

value: Spider glucose

value: biofilm

source_name: pooled reference

tag: sample type

value: pooled reference


title: C. albicans CEM175 Biofilm Growth in Spider Replicate 2

source_name: CEM175 spider biofilm

value: Spider


title: OPSCC103

value: HPV-

value: FFPE


title: MK_2


title: OPSCC97


title: MK_1


title: Fe_2


title: CIRCLE-off-target-site3_ReSeq


title: OPSCC99

value: HPV+


title: OPSCC95


title: CIRCLE-off-target-site2_ReSeq

value: targeted amplicon sequencing


title: BB_3

value: Berberine hydrochloride (BB)


title: OPSCC96

value: Vanderbilt cohort


title: BB_2


title: OPSCC94


title: Treated_invitro_CIRCLE-off-target-site7_Rep3

value: base-edited PCSK9


title: Treated_invitro_CIRCLE-off-target-site7_Rep2


title: BB_1


title: KM_3

value: Clotrimazole (KM)


title: OPSCC92


title: C. albicans CEM175 Planktonic Growth in Spider Glucose Replicate 2

source_name: CEM175 spider glucose planktonic

value: planktonic


title: Treated_invitro_CIRCLE-off-target-site7_Rep1


title: KM_2


title: C. albicans CEM175 Planktonic Growth in Spider Replicate 2

source_name: CEM175 spider planktonic


title: C. albicans CEM175 Biofilm Growth in Spider Replicate 1


title: C. albicans CEM175 Biofilm Growth in Spider Glucose Replicate 1


title: C. albicans CEM175 Planktonic Growth in Spider Glucose Replicate 1


title: OPSCC90

source_name: Oropharyngeal squamous cell carcinoma


title: KM_1


title: LNP_invivo_CIRCLE-off-target-site7_Rep2


title: C. albicans CEM175 Planktonic Growth in Spider Replicate 1


title: DM_3

value: DMSO(DM)


title: P12707_217

city: Solna

first: Staffan

last: Holmin

state: Non US/Canada

address: Visionsgatan 4, J5:20

country: Sweden

institute: Karolinska Institutet

data_processing:
STAR for mapping reads to genome
featureCounts for counting genes
DESeq2 for count normalization and transformation
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: count matrix of reads mapped to genes

organism: Sus scrofa

source_name: Whole blood

extract_protocol:
RNAdvance Tissue kit with modifications: Reduce reagent volumes by dividing with 13. Use vortexing + centrifugation to homogenize samples.
SMARTer Pico

value: Whole blood

tag: sample location

value: blood

tag: swine id

tag: timepoint

value: baseline


title: Untreated_invivo_CIRCLE-off-target-site7_Rep3

value: Lipofection/tailvein

value: Untreated


title: P12707_216

source_name: Left heart ventricle

tag: tissue

value: Left heart ventricle

value: lateral

value: Day 14


title: LNP_invivo_CIRCLE-off-target-site7_Rep1

tag: genotype


title: OPSCC93

tag: hpv status

value: FFPE

tag: cohort


title: DM_2


title: P12707_215


title: OPSCC89

value: HPV+


title: OPSCC88


title: OPSCC91


title: P12707_213


title: Untreated_invivo_CIRCLE-off-target-site7_Rep2

value: targeted amplicon sequencing


title: OPSCC87

value: HPV-


title: SD_3

value: Sabouraud Dextrose Agar (SDA)


title: P12707_212

value: Day 2


title: OPSCC86

value: Vanderbilt cohort


title: LNP_invivo_CIRCLE-off-target-site7_Rep3

value: base-edited PCSK9


title: Untreated_invivo_CIRCLE-off-target-site7_Rep1


title: P12707_211

value: apical


title: OPSCC85


title: SD_1


title: AAV_invivo_CIRCLE-off-target-site7_Rep3


title: OPSCC84


title: AAV_invivo_CIRCLE-off-target-site7_Rep2


title: P12707_208

value: Whole blood


title: OPSCC83


title: AAV_invivo_CIRCLE-off-target-site7_Rep1


title: GR_2

value: Congo Red (GR)


title: OPSCC82


title: Treated_invitro_CIRCLE-off-target-site6_Rep3


title: OPSCC81


title: GR_1


title: P12707_206


title: OPSCC80


title: P12707_205

value: blood


title: Ge_3

value: Genistein (Ge)


title: OPSCC79


title: Treated_invitro_CIRCLE-off-target-site6_Rep1

value: Lipofection/tailvein


title: P12707_209

value: Left heart ventricle


title: P12707_204


title: P12707_203


title: LNP_invivo_CIRCLE-off-target-site6_Rep3


title: Ge_1


title: OPSCC78


title: LNP_invivo_CIRCLE-off-target-site6_Rep2


title: GR_3


title: SD_2


title: Fe_3

value: Fenarimol (FE)


title: Treated_invitro_CIRCLE-off-target-site6_Rep2


title: P12707_202

value: lateral


title: P12707_207

value: Day 14


title: OPSCC77

value: FFPE


title: LNP_invivo_CIRCLE-off-target-site6_Rep1

value: targeted amplicon sequencing


title: OPSCC76

value: HPV+


title: P12707_187


title: Untreated_invivo_CIRCLE-off-target-site6_Rep3

value: Untreated


title: P12707_201


title: OPSCC75


title: Ge_2


title: Untreated_invivo_CIRCLE-off-target-site6_Rep2


title: OPSCC74


title: Untreated_invivo_CIRCLE-off-target-site6_Rep1


title: P12707_186


title: P12707_185

value: Day 2


title: AAV_invivo_CIRCLE-off-target-site6_Rep3


title: AAV_invivo_CIRCLE-off-target-site6_Rep2


title: OPSCC72

value: Vanderbilt cohort


title: OPSCC71

value: HPV-


title: P12707_182

value: apical


title: OPSCC70


title: P12707_181


title: OPSCC69


title: P12707_179


title: Treated_invitro_CIRCLE-off-target-site5_Rep2

value: base-edited PCSK9


title: Treated_invitro_CIRCLE-off-target-site5_Rep3


title: OPSCC73


title: P12707_178


title: DM_1

value: DMSO(DM)


title: OPSCC68


title: Treated_invitro_CIRCLE-off-target-site5_Rep1


title: P12707_183


title: P12707_177

value: baseline


title: OPSCC67


title: AAV_invivo_CIRCLE-off-target-site6_Rep1


title: LNP_invivo_CIRCLE-off-target-site5_Rep3


title: P12707_176


title: OPSCC66


title: LNP_invivo_CIRCLE-off-target-site5_Rep2


title: P12707_175


title: OPSCC65


title: LNP_invivo_CIRCLE-off-target-site5_Rep1


title: Untreated_invivo_CIRCLE-off-target-site5_Rep3


title: P12707_172

value: Whole blood

value: blood


title: P12707_173

value: Left heart ventricle


title: OPSCC63


title: Untreated_invivo_CIRCLE-off-target-site5_Rep2

value: Lipofection/tailvein


title: P12707_171


title: OPSCC62


title: Untreated_invivo_CIRCLE-off-target-site5_Rep1


title: OPSCC61


title: AAV_invivo_CIRCLE-off-target-site5_Rep3


title: OPSCC64


title: OPSCC60


title: P12707_170


title: OPSCC59


title: AAV_invivo_CIRCLE-off-target-site5_Rep2


title: P12707_168


title: FlatCoatedRetriever2 - PBMCs input

city: Bethesda

first: Alexander

middle: Christian

last: Harris

state: Maryland

address: 50 South Drive

department: National Human Genome Research Institute

institute: National Institutes of Health

data_processing:
Basecalling was performed with RTA 2.4.11
Reads were aligned with BWA-MEM and converted to BAM files using samtools 1.10
Peaks were called with MACS2 2.2.1
Genome_build: CanFam 3.1
Supplementary_files_format_and_content: peak text files

organism: Canis lupus familiaris

source_name: peripheral blood mononuclear cells

growth_protocol: Fresh whole blood samples were collected in ACD tubes

extract_protocol:
PBMCs were isolated with FICOLL-paque plus. SimpleChIP® Plus Enzymatic Chromatin IP kit, digested chromatin was sonicated, and Abcam #ab8895 and #ab8580 antibodies were used.
ChIPseq libraries were constructed using Ovation UltralowSystem V2 1-96 with 15 cycles of PCR amplification. Final libraries were twice purified with Ampure XP PCR Purification Beads (Agencourt). Pooled libraries were run with MiSeq Nano kit version 2.

tag: cell type

value: peripheral blood mononuclear cells

tag: breed

value: Flat Coated Retriever

tag: antibody


title: P12707_166

value: lateral


title: Treated_invitro_CIRCLE-off-target-site4_Rep3

value: targeted amplicon sequencing


title: P12707_167


title: OPSCC58

value: HPV+

value: FFPE


title: OPSCC57


title: Treated_invitro_CIRCLE-off-target-site4_Rep2


title: FlatCoatedRetriever2 - PBMCs H3K4me1

data_processing:
Basecalling was performed with RTA 2.4.11
Reads were aligned with BWA-MEM and converted to BAM files using samtools 1.10
Peaks were called with MACS2 2.2.1
Genome_build: CanFam 3.1
Supplementary_files_format_and_content: peak text files
For file FCR2_H3K4me1_peaks.narrowPeak, the file itself represents a failure for that sample and originally a 0 byte file


title: AAV_invivo_CIRCLE-off-target-site5_Rep1


title: FlatCoatedRetriever1 - PBMCs input


title: P12707_164

value: Day 2


title: FlatCoatedRetriever1 - PBMCs H3K4me3


title: FlatCoatedRetriever2 - PBMCs H3K4me3


title: OPSCC55

value: Vanderbilt cohort


title: OPSCC56

value: HPV-


title: LNP_invivo_CIRCLE-off-target-site4_Rep3


title: FlatCoatedRetriever1 - PBMCs H3K4me1


title: P12707_162

value: apical

value: Day 14


title: P12707_165


title: OPSCC54


title: LNP_invivo_CIRCLE-off-target-site4_Rep2

value: base-edited PCSK9


title: P12707_160


title: BerneseMountainDog6 - PBMCs input

value: Bernese Mountain Dog


title: OPSCC53


title: Treated_invitro_CIRCLE-off-target-site4_Rep1


title: BerneseMountainDog6 - PBMCs H3K4me3


title: OPSCC52


title: LNP_invivo_CIRCLE-off-target-site4_Rep1


title: Untreated_invivo_CIRCLE-off-target-site4_Rep3

value: Untreated


title: P12707_158


title: BerneseMountainDog6 - PBMCs H3K4me1


title: P12707_157


title: OPSCC51


title: Untreated_invivo_CIRCLE-off-target-site4_Rep2


title: BerneseMountainDog5 - PBMCs input


title: P12707_161

value: Whole blood

value: blood


title: Control_ThirdRepeat_after_10days

type: genomic

city: Szczecin

first: Tomasz

middle: K

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

description: DNA extracted from non-treated cells after 10 days incubation, 3rd repeat

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Data were processed in R, normalized using BMIQ normalization.

label: Cy5 and Cy3

source_name: cell line SH-SY5Y

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from SH-SY5Y samples NucleoSpin® TriPrep (Macherey Nagel, Düren, Germany) following the manufacturer's instructions

tag: time point

value: non-treated

tag: repeat

tag: cell line

value: SH-SY5Y neuroblastoma cell line


title: Control_SecondRepeat_after_10days

description: DNA extracted from non-treated cells after 10 days incubation, 2nd repeat


title: Control_SecondRepeat_after_24h

description: DNA extracted from non-treated cells after 24 hours incubation, 2nd repeat


title: BerneseMountainDog5 - PBMCs H3K4me3

value: peripheral blood mononuclear cells


title: OPSCC49


title: Untreated_invivo_CIRCLE-off-target-site4_Rep1

value: Lipofection/tailvein


title: AAV_invivo_CIRCLE-off-target-site4_Rep3

value: targeted amplicon sequencing


title: Control_FirstRepeat_after_10days

description: DNA extracted from non-treated cells after 10 days incubation, 1st repeat


title: BerneseMountainDog5 - PBMCs H3K4me1


title: OPSCC48

value: HPV+


title: P12707_154

value: Left heart ventricle

value: baseline


title: Lenalidomide_FirstRepeat_after_24h

description: DNA extracted from cells immediately after 24 hours of lenalidomide treatment, 1st repeat

value: lenalidomide


title: Lenalidomide_ThirdRepeat_after_10days

description: DNA extracted from cells 10 days after 24 hours of lenalidomide treatment, 3rd repeat


title: Lenalidomide_SecondRepeat_after_10days

description: DNA extracted from cells 10 days after 24 hours of lenalidomide treatment, 2nd repeat


title: Control_ThirdRepeat_after_24h

description: DNA extracted from non-treated cells after 24 hours incubation, 3rd repeat


title: BTZ_SecondRepeat_after_24h

description: DNA extracted from cells immediately after 24 hours of BTZ treatment, 2nd repeat

value: bortezomib


title: BerneseMountainDog4 - PBMCs input


title: Lenalidomide_ThirdRepeat_after_24h

description: DNA extracted from cells immediately after 24 hours of lenalidomide treatment, 3rd repeat


title: OPSCC47

value: FFPE

value: Vanderbilt cohort


title: P12707_153

value: Day 2


title: AAV_invivo_CIRCLE-off-target-site4_Rep1

value: base-edited PCSK9


title: AAV_invivo_CIRCLE-off-target-site4_Rep2


title: P12707_152

value: apical


title: BerneseMountainDog4 - PBMCs H3K4me3

value: Bernese Mountain Dog


title: OPSCC46


title: Lenalidomide_SecondRepeat_after_24h

description: DNA extracted from cells immediately after 24 hours of lenalidomide treatment, 2nd repeat


title: BTZ_ThirdRepeat_after_10days

description: DNA extracted from cells 10 days after 24 hours of BTZ treatment, 3rd repeat


title: BTZ_SecondRepeat_after_10days

description: DNA extracted from cells 10 days after 24 hours of BTZ treatment, 2nd repeat


title: BerneseMountainDog4 - PBMCs H3K4me1


title: OPSCC45

value: HPV-


title: Treated_invitro_CIRCLE-off-target-site3_Rep2


title: OPSCC50


title: Control_FirstRepeat_after_24h

description: DNA extracted from non-treated cells after 24 hours incubation, 1st repeat

value: non-treated


title: P12707_151

value: lateral


title: BTZ_FirstRepeat_after_24h

description: DNA extracted from cells immediately after 24 hours of BTZ treatment, 1st repeat

value: SH-SY5Y neuroblastoma cell line


title: P12707_156


title: Lenalidomide_FirstRepeat_after_10days

description: DNA extracted from cells 10 days after 24 hours of lenalidomide treatment, 1st repeat


title: BerneseMountainDog3 - PBMCs input

value: peripheral blood mononuclear cells


title: Treated_invitro_CIRCLE-off-target-site3_Rep3

value: Lipofection/tailvein

value: targeted amplicon sequencing


title: P12707_150

value: Left heart ventricle


title: Treated_invitro_CIRCLE-off-target-site3_Rep1


title: P12707_149


title: OPSCC44


title: BTZ_ThirdRepeat_after_24h

description: DNA extracted from cells immediately after 24 hours of BTZ treatment, 3rd repeat


title: LNP_invivo_CIRCLE-off-target-site3_Rep3


title: BerneseMountainDog3 - PBMCs H3K4me1


title: BerneseMountainDog3 - PBMCs H3K4me3


title: P12707_148

value: Day 14


title: OPSCC43

value: HPV+


title: OPSCC42


title: BerneseMountainDog2 - PBMCs input


title: P12707_147


title: LNP_invivo_CIRCLE-off-target-site3_Rep2


title: OPSCC41


title: LNP_invivo_CIRCLE-off-target-site3_Rep1


title: P12707_155


title: BTZ_FirstRepeat_after_10days

description: DNA extracted from cells 10 days after 24 hours of BTZ treatment, 1st repeat

value: bortezomib


title: P12707_146

value: Whole blood

value: blood

value: baseline


title: BerneseMountainDog2 - PBMCs H3K4me3


title: OPSCC40

value: FFPE

value: Vanderbilt cohort


title: BerneseMountainDog2 - PBMCs H3K4me1

value: Bernese Mountain Dog


title: Untreated_invivo_CIRCLE-off-target-site3_Rep3

value: base-edited PCSK9


title: OPSCC39


title: P12707_145


title: BerneseMountainDog1 - PBMCs input


title: P12707_144

value: apical


title: Untreated_invivo_CIRCLE-off-target-site3_Rep2


title: OPSCC38


title: Untreated_invivo_CIRCLE-off-target-site3_Rep1

value: Untreated


title: BerneseMountainDog1 - PBMCs H3K4me3


title: AAV_invivo_CIRCLE-off-target-site3_Rep3


title: P12707_143


title: BerneseMountainDog1 - PBMCs H3K4me1


title: P12707_140


title: AAV_invivo_CIRCLE-off-target-site3_Rep2


title: hypertrophic cardiomyocytes 3 induced by isoproterenol

city: Shenyang

first: Ai

address: Nanjing Bei Street

institute: the first hospital of China Medical University

description:
neonatal rat ventricular  cardiomyocytes Cells 3 of  intervention group , treated with 10 μM isoproterenol, harvested after several passages.
total RNA(lncRNA Mattrix1,mRNA Matrix2)

hyb_protocol: Hybridization was performed in Agilent's SureHyb Hybridization Chambers

scan_protocol: After washing,slides were scanned with the Agilent DNA Microarray Scanner

data_processing:
Data was extracted using Agilent Feature Extration software.Normalization was performed using the Agilent GeneSpring GX v12.1
lowess normalized log2 ratio

organism: Rattus norvegicus

source_name: newborn Sprague-Dawley rats

label_protocol: Arraystar Flash RNA Labeling Kit was used for sample labeling

growth_protocol: 1-3days old normal growth newborn Sprague-Dawley rats

extract_protocol: total RNA extrcted  using  Trizol following manufacturer's instructions

treatment_protocol: Cold Hank’s equilibrium salt solution with no Ca2+ or Mg2+was used to store the ventricle tissues. These tissues were then transferred into trypsin-0.125% EDTA and stored overnight (16-20 h) at 4˚C. Collagenase II was added to a shaking water bath for 30 min at 37˚C. Isolated cells were prepared in an uncoated flask at 37˚C to remove cardiac fibroblasts, and cells were harvested from the supernatants after 1.5 h. Neonatal rat ventricular myocytes （NRVMs）were seeded in a plating medium containing 45% Dulbecco’s modified Eagle’s medium (DMEM) , 45% M199 medium, 10% fetal bovine serum and 100 U/ml penicillin and 100 μg/ml streptomycin for 24 h at 37˚C. The next day, the plating medium was substituted with a maintenance medium containing 50% DMEM, 50% M199 without serum, 100 U/ml penicillin and 100 μg/ml streptomycin, after which the medium cultured for an additional 24 h at 37˚C prior to experiment. Then NRVMs continued to incubate with or without 10 μM isoproterenol for 24 h. All cells were cultured in 6-well plates, with 1×106 to 1×107 cells seeded per well.

tag: age

value: one to three days

value: ventricular myocytes


title: hypertrophic cardiomyocytes 2 induced by isoproterenol

description:
neonatal rat ventricular  cardiomyocytes Cells 2 of intervention group , treated with 10 μM isoproterenol , harvested after several passages.
total RNA(lncRNA Mattrix1,mRNA Matrix2)


title: OPSCC36


title: OPSCC37


title: AAV_invivo_CIRCLE-off-target-site3_Rep1

value: Lipofection/tailvein


title: OPSCC35


title: P12707_139

value: Day 2


title: P12707_137

value: Left heart ventricle

value: lateral


title: Treated_invitro_CIRCLE-off-target-site2_Rep3

value: targeted amplicon sequencing


title: OPSCC33

value: HPV+


title: Treated_invitro_CIRCLE-off-target-site2_Rep2


title: Control  cardiomyocytes 3

description:
neonatal rat ventricular  cardiomyocytes Cells 3 of control group , untreated, harvested after several passages.
total RNA(lncRNA Mattrix1,mRNA Matrix2)


title: Treated_invitro_CIRCLE-off-target-site2_Rep1


title: OPSCC31


title: P12707_135


title: LNP_invivo_CIRCLE-off-target-site2_Rep3


title: P12707_134

value: Day 14


title: Control cardiomyocytes 2

description:
neonatal rat ventricular  cardiomyocytes Cells 2 of  control group , untreated, harvested after several passages.
total RNA(lncRNA Mattrix1,mRNA Matrix2)


title: P12707_133


title: OPSCC30


title: LNP_invivo_CIRCLE-off-target-site2_Rep2


title: P12707_131


title: LNP_invivo_CIRCLE-off-target-site2_Rep1


title: P12707_129

value: Whole blood

value: blood


title: OPSCC28

value: HPV-

value: FFPE

value: WashU cohort


title: OPSCC34

value: Vanderbilt cohort


title: WK2_R2_MSA

city: Oxford

first: Devika

last: Agarwal

address: JR hospital, Headley way

department: The MRC Weatherall Institute of molecular medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Pairend end files (150 bp) were geenerated for each sample
Kallisto (v0.46.2)  was used to estimate transcript abundance for Ensembl (release 102) protein-coding genes from RNAseq reads
Count data was imported into R using tximport and genes with less than 10 reads across the six samples used in the comparison were filtered out
Differential gene expression was performed in DESeq2 using the Wald test with an FDR threshold of 0.05 and a log2 fold change threshold on 0.25
Genome_build: GRCh38 (Ensemble release 102)
Supplementary_files_format_and_content: Kallisto quantification files  (tsv files and HDF5 binary files ) for each sample with run info, transcript abundance estimates, TPM,bootstrap estimates, and transcript length information length

molecule: polyA RNA

source_name: iPSC-derived dopaminergic neurons

growth_protocol: iPSCs were seeded onto Geltrex coated 6-well plates, expanded until >80% confluency and mTeSR1 media was changed to day in vitro (DIV) 0 media (2 uM A83-01, 100 nM LDN in neural induction base medium). DIV1-4 media contained 2 uM A83-01, 100 nM LDN, 300 ng/ml SHH C25II, 2 uM purmorphamine and 200ng/ml FGF8a in neural induction base medium. 3 uM CHIR-99021 was added from day 3 until day 12. DIV5-6 media contained 100 nM LDN, 300 ng/ml SHH C25II, 2 uM purmorphamine, 3 uM CHIR-99021 and 200 ng/ml FGF8a in neural induction base medium. DIV7-10 media contained 100 nM LDN and 3 uM CHIR-99021 in neural induction base medium. DIV11-19 medium contained 20 ng/ml BDNF, 20 ng/ml GDNF, 1 ng/ml TGFb3, 10 uM DAPT, 200 uM Ascorbic acid, 500 uM db-cAMP in neural differentiation media and 1 ug/ml of laminin was added from 17 to 25 days of differentiation.

extract_protocol:
RNeasy Plus Mini Kit, Qiagen (Cat No./ID: 74134)
Library was prepared using standard illumina protocols
Unstranded library, poly-A enriched RNA-Seq

treatment_protocol: Matured neurons (DIV45) were treated with exogenous fibrils at 1 uM (either de novo generated fibrils or brain-amplified fibrils from PD and MSA brains) and assayed at 1 week post fibril addition (DIV52) and 2 weeks post fibril addition (DIV59).

value: iPSC-derived dopaminergic neurons

tag: clone

value: SNCA triplication Clone 3

tag: replicate

value: MSA


title: WK2_R3_MSA

tag: treatment


title: Untreated_invivo_CIRCLE-off-target-site2_Rep3

value: Untreated


title: OPSCC29


title: WK2_R1_MSA


title: hypertrophic cardiomyocytes 1 induced by isoproterenol

description:
neonatal rat ventricular  cardiomyocytes Cells 1 of intervention group , treated with 10 μM isoproterenol, harvested after several passages.
total RNA(lncRNA Mattrix1,mRNA Matrix2)

value: one to three days

value: ventricular myocytes


title: P12707_136

tag: sample location

value: Day 2


title: WK2_R3_PD

value: PD


title: P12707_127

value: Left heart ventricle

value: apical

tag: swine id

value: baseline


title: Untreated_invivo_CIRCLE-off-target-site2_Rep2

value: Lipofection/tailvein

value: targeted amplicon sequencing


title: P12707_124

tag: timepoint


title: OPSCC26

value: HPV+

tag: tissue


title: OPSCC32

value: FFPE


title: Untreated_invivo_CIRCLE-off-target-site2_Rep1

tag: genotype


title: Control cardiomyocytes 1

description:
neonatal rat ventricular  cardiomyocytes Cells 1 of  control group , untreated, harvested after several passages.
total RNA(lncRNA Mattrix1,mRNA Matrix2)


title: WK2_R2_PD


title: P12707_123

value: Whole blood

value: blood

value: Day 14


title: AAV_invivo_CIRCLE-off-target-site2_Rep3

value: base-edited PCSK9


title: OPSCC25

tag: hpv status

value: HPV-

value: WashU cohort


title: P12707_122


title: WK2_R1_PD

value: iPSC-derived dopaminergic neurons

value: SNCA triplication Clone 3


title: OPSCC24

tag: cohort


title: AAV_invivo_CIRCLE-off-target-site2_Rep2


title: WK2_R3_FIB

tag: cell type

value: Fibrils


title: OPSCC27


title: OPSCC22


title: OPSCC21


title: Untreated_invivo_CIRCLE-off-target-site10_Rep3

value: Untreated


title: AAV_invivo_CIRCLE-off-target-site2_Rep1


title: P12707_120

value: Left heart ventricle

value: lateral


title: WK2_R1_FIB


title: P12707_121

value: baseline


title: Untreated_invivo_CIRCLE-off-target-site9_Rep3

value: Lipofection/tailvein


title: WK2_R2_FIB


title: OPSCC23


title: Untreated_invivo_CIRCLE-off-target-site8_Rep3

value: targeted amplicon sequencing


title: P12707_119

value: apical


title: Untreated_invivo_CIRCLE-off-target-site10_Rep2


title: WK2_R3_NSC

value: NSC


title: OPSCC19

value: HPV+

value: FFPE


title: WK2_R1_NSC


title: P12707_117


title: OPSCC18


title: OPSCC17


title: WK1_R3_MSA

value: MSA


title: P12707_115

value: Whole blood

value: blood

value: Day 2


title: Untreated_invivo_CIRCLE-off-target-site8_Rep2


title: P12707_118


title: WK1_R2_MSA

value: iPSC-derived dopaminergic neurons


title: Untreated_invivo_CIRCLE-off-target-site9_Rep2


title: OPSCC16

value: HPV-

value: WashU cohort


title: Untreated_invivo_CIRCLE-off-target-site10_Rep1

value: Untreated


title: OPSCC20


title: OPSCC15


title: Untreated_invivo_CIRCLE-off-target-site9_Rep1


title: P12707_113

value: Left heart ventricle

value: Day 14


title: OPSCC14


title: WK1_R1_MSA

value: SNCA triplication Clone 3


title: P12707_111


title: P12707_112


title: P12707_116


title: OPSCC13


title: Untreated_invivo_CIRCLE-off-target-site8_Rep1

value: Lipofection/tailvein


title: WK2_R2_NSC


title: AAV_invivo_CIRCLE-off-target-site10_Rep3

value: targeted amplicon sequencing

value: base-edited PCSK9


title: WK1_R1_PD

value: PD


title: OPSCC12


title: WK1_R3_FIB

value: Fibrils


title: AAV_invivo_CIRCLE-off-target-site9_Rep3


title: P12707_109

value: lateral


title: AAV_invivo_CIRCLE-off-target-site8_Rep3


title: P12707_110

value: apical


title: OPSCC10

value: HPV+

value: FFPE


title: P12707_114

value: Day 2


title: WK1_R2_FIB

value: iPSC-derived dopaminergic neurons


title: P12707_108

value: Whole blood

value: blood

value: baseline


title: WK1_R3_PD


title: WK1_R1_FIB


title: P12707_106

value: Left heart ventricle


title: WK1_R2_PD


title: AAV_invivo_CIRCLE-off-target-site9_Rep2


title: OPSCC9

value: WashU cohort


title: OPSCC8

value: HPV-


title: P12707_104

value: Day 14


title: WK1_R3_NSC

value: SNCA triplication Clone 3

value: NSC


title: WK1_R2_NSC


title: OPSCC7


title: AAV_invivo_CIRCLE-off-target-site8_Rep2

value: Lipofection/tailvein

value: targeted amplicon sequencing

value: base-edited PCSK9


title: AAV_invivo_CIRCLE-off-target-site10_Rep1


title: P12707_101

value: apical


title: P12707_103


title: OPSCC11

value: HPV+


title: Heart-10wks-LV

city: Los Angeles

first: Reza

last: Ardehali

state: CA

address: 675 Charles E Young dr

department: Cardiology

institute: UCLA

data_processing:
RNA-seq data was mapped with OLego (v.1.1.5) and normalized by using TPM (transcripts per millions) analysis
Total number of reads mapped to a known transcript annotation was estimated using featureCounts version v1.5.0-p2
Expression levels for each transcript were determined by normalizing the counts returned by featureCounts using a custom Perl script
Genome_build: GRCH38/hg38
Supplementary_files_format_and_content: Raw feature counts for each sample

source_name: Human  Fetal Heart

extract_protocol:
as described in paper
as described in paper
single cell RNA-seq

value: Human Fetal Heart


title: AAV_invivo_CIRCLE-off-target-site9_Rep1


title: WK1_R1_NSC


title: OPSCC5

value: FFPE


title: AAV_invivo_CIRCLE-off-target-site8_Rep1


title: Heart-10wks-RV


title: BRCA1D11_S12_CRISPR_screen_T14_Parpi

city: Shanghai

first: Wei

last: Wu

state: Shanghai

address: 320 yueyang road

department: Center for Excellence in Molecular Cell Science

data_processing:
Library strategy: CRISPR-Cas9 screen
Genes enriched or depleted in the PARPi-treated samples were determined with the MAGeCK software package version 0.5.9.2.
Genome_build: mm10
Supplementary_files_format_and_content: Count table files were made by MAGeCK software package version 0.5.9.2.

source_name: Mouse embryonic fibroblasts

growth_protocol: The Brca1D11 and Brca1D11Trp53bp1S25A mouse embryonic fibroblasts (MEFs) were generated from E13.5 embryos and grown in Dulbecco’s Modified Eagle’s Medium (DMEM, GIBCO) supplemented with 15% heat-inactivated fetal bovine serum (FBS, Gemini Bio-Products) and 1% penicillin plus streptomycin (GIBCO). To establish immortalized MEF cell lines, primary MEFs between passages 2-4 were transiently transfected with a vector encoding SV40 T-antigen (pCMV-SV40T). SV40-immortalized MEFs were routinely cultured in DMEM supplemented with 10 or 15% FBS.

extract_protocol: Surviving clones from each condition were collected, and genomic DNA (gDNA) was isolated (Blood & Cell Culture DNA Midi Kit, Qiagen) and subjected to PCR with Illumina-compatible primers, followed by Illumina sequencing.

treatment_protocol: CRISPR–Cas9 screen was performed using genome-scale mouse Brie CRISPR knockout pooled library (Addgene #73633). Cas9+Brca1D11 and Cas9+Brca1D11Trp53bp1S25A MEFs were transduced at a multiplicity of infection (MOI) of 0.3 and 400-fold coverage of the library. Cells were then selected with puromycin for 3 days before treatment with the clinically-approved inhibitor Olaparib (PARPi, 100nM) for a further 14 days.  This dose corresponds with to the IC95 for the BRCA1-deficient cells.

value: Mouse embryonic fibroblasts

value: BRCA1D11 Cas9

tag: strain

tag: treament

value: PARPi


title: 200724_WT_MEF_THAP1

institute: Center for Excellence in Molecular Cell Science

data_processing:
mouse reads were aligned to the GRCm38p2/mm10 .Alignment is done using bowtie version 1.1.2, with the parameters: -l 50 -n 2 -m 1.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were made by Bedtools genomecov function followed by UCSC toolkit function bedGraphToBigWig

growth_protocol: The wild-type mouse embryonic fibroblasts (MEFs) was generated from E13.5 embryos and grown in Dulbecco’s Modified Eagle’s Medium (DMEM, GIBCO) supplemented with 15% heat-inactivated fetal bovine serum (FBS, Gemini Bio-Products) and 1% penicillin plus streptomycin (GIBCO). To establish immortalized MEF cell lines, primary MEFs between passages 2-4 were transiently transfected with a vector encoding SV40 T-antigen (pCMV-SV40T). SV40-immortalized MEFs were routinely cultured in DMEM supplemented with 10 or 15% FBS.

extract_protocol:
Twenty million MEFs were fixed in fresh media by adding 37% formaldehyde (F1635, Sigma) to attain a final concentration of 1% and incubated at 37°C for 10 min. Fixation was quenched by addition of 1 M glycine (Sigma) in PBS at a final concentration of 125 mM. Cells were washed twice with cold PBS and pellets were snap frozen in dry ice and stored at -80°C.
Fixed cell pellets were thawed on ice and resuspended in 2 ml of cold RIPA buffer (10 mM TrisHCl pH 7.5, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, supplemented with proteinase inhibitor (Complete Mini EDTA free, Roche)). Sonication was performed using the Covaris S220 sonicator at duty cycle 20%, peak incident power 175, cycle/burst 200 for 30 cycles of 60 s sonication and 30 s of pause at 4°C. Chromatin was clarified by centrifugation at 21,000 g at 4°C for 10 min and precleared with 80 μl prewashed Dynabeads protein A (ThermoFisher) for 30 min at 4°C. 40 μl of prewashed Dynabeads protein A were incubated with 10 μg of antibody in 100 μl of PBS for 30 min at room temperature under continuous mixing, washed twice in PBS for 5 min and added to 1 ml of chromatin followed by overnight incubation at 4°C on a rotator. Beads were then collected in a magnetic separator (DynaMag-2 Invitrogen), washed twice with cold RIPA buffer, twice with RIPA buffer containing 0.3 M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (10 mM Tris pH 8.0, 1mM EDTA) plus 0.2% Triton X-100, and once with TE. Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/ml of Proteinase K (Ambion). DNA was purified using Zymo ChIP DNA clean and concentrator kit (Zymo Research) and eluted in 20 μl. The entire ChIP DNA was used to prepare Illumina sequencing libraries. End-repair was performed in 75 μl of T4 ligase reaction buffer, 0.4 mM of dNTPs, 4 U of T4 DNA polymerase (NEB), 13.5 U of T4 Polynucleotide Kinase (NEB) and 1.5 U of Klenow fragment (NEB) at 24°C for 30 min in a ThermoMixer C at 400 rpm. End-repair reaction was cleaned using 2X Agencourt AMPure XP beads and eluted in 16.5 μl of EB that was used for A-tailing reaction in 20 μl of NEBNext dA-Tailing reaction buffer (NEB) with 7.5 U of Klenow fragment exo- (NEB) at 37°C for 30 min. The 20 μl of the A-tailing reaction was mixed with Quick Ligase buffer 2X (NEB), 3,000 U of Quick ligase and 5 nM of annealed adaptor (Illumina truncated adaptor) in a volume of 50 μl and incubated at 25°C for 20 min. Ligation was stopped by adding 50 mM of EDTA and cleaned with 1.8X Agencourt AM- Pure XP beads and eluted in 15 μl of EB that was used for PCR amplification in a 50 μl reaction with 1 μM primers TruSeq barcoded primer p5, TruSeq barcoded primer p7, and 2X Kapa HiFi HotStart Ready mix (Kapa Biosciences). The temperature settings during the PCR amplification were 45 s at 98°C followed by 14 cycles of 15 s at 98°C, 30 s at 63°C, 30 s at 72°C and a final 5 min extension at 72°C . PCR reactions were cleaned with Agencourt AMPure XP beads (Beckman Coulter), run on a 2% agarose gel and a smear of 200-500bp was cut and gel purified using QIAquick Gel Extraction Kit (QIAGEN). Library concentration was determined with KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems). Sequencing was performed on the Illumina Nextseq500 (75bp single-end reads).

value: WT


title: OPSCC4

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to the NCBI reference sequence database to identify human coding genes with Bowtie v1.2.2.
Transcripts Per Million (TPM) were calculated. The read counts of  one gene were normalized by the average length of all isoforms and by the size of the all mapped mRNA reads.
Genome_build: NCBI reference sequence database
Supplementary_files_format_and_content: Tab-delimited text file includes TPM-normalized gene counts for all samples

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) tumor tissues were collected for pathologic analysis from biopsy or primary surgical resection.
Ribosomal RNA (rRNA) was removed with the RiboMinus kit (Life Technologies) and custom DNA oligonucleotide probes. The RNA was used to construct RNA-seq libraries with the NEBNext Ultra mRNA Library Prep kit (New England BioLabs). The resulting cDNA libraries were PCR amplified and subject to sequencing with Illumina HiSeq 3000 at Washington University Genome Technology Access Center.


title: AAV_invivo_CIRCLE-off-target-site10_Rep2

data_processing:
Library strategy: targeted amplicon sequencing
CIRCLE-seq pipeline (https://github.com/tsailabSJ/circleseq)
CHANGE-seq pipeline (https://github.com/tsailabSJ/changeseq)
iGUIDE pipeline (https://github.com/cnobles/iGUIDE)
For all targeted amplicon sequencing files, we used CRISPRESSO2 for the analysis: https://crispresso.pinellolab.partners.org/submission . This platform directly reads in a fastq.gz file and provides a summary about editing rates and allele frequency.
Genome_build: Hg38, mm10
Supplementary_files_format_and_content: for CIRCLE, CHANGE-seq and iGUIDE: text files containing identified off-target sites; html report file containing identified off-target sites; fastq-index output file generated by Miseq

source_name: gDNA

extract_protocol:
Detachment with TryplE, wash with PBS, lysis and DNA isolation for cell lines and whole tissue or primary hepatocyte isolation for in vivo samples.
targeted amplicon sequencing; CIRCLE-seq, CHANGE-seq or iGUIDE library preparation


title: LNP_invivo_CIRCLE-off-target-site10_Rep3


title: OPSCC3


title: BRCA1D11_S12_CRISPR_screen_T0


title: OPSCC2


title: BRCA1D11_14223_CRISPR_screen_T14_Parpi


title: LNP_invivo_CIRCLE-off-target-site9_Rep3


title: LNP_invivo_CIRCLE-off-target-site8_Rep3


title: OPSCC6


title: OPSCC1


title: LNP_invivo_CIRCLE-off-target-site9_Rep2


title: FTC133_siSREBF1

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

description:
FTC-133 cells transfected with SREBF1 siRNA
none

data_processing:
FastQC
Trimmomatic v0.38 (parameter: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:20, MINLEN:36)
HISHAT2 v2.1.0
featureCounts v2.0.0
Genome_build: GRCh38
Supplementary_files_format_and_content: a tab-delimited text file contains TPM values for each sample

source_name: Thyroid cancer cells

extract_protocol:
Cells were harvested, and RNA was extracted using Trizol reagent. RNA QC: total >= 2 ug, concentration >= 50 ng/ul, RIN >= 6.8, RQN >= 7.6, OD260/OD230 >= 2.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: transfection

value: SREBF1-specific siRNA


title: BRCA1D11_14223_CRISPR_screen_T14_Untreat


title: 8505C_SREBF1

description:
8505C cells transfected with SREBF1-overexpressing vector
none

value: SREBF1-overexpressing vector


title: BRCA1D11_14223_CRISPR_screen_T0


title: K1_Empty

description:
K1 cells transfected with empty vector
none

value: empty vector


title: LNP_invivo_CIRCLE-off-target-site10_Rep2


title: Cp_Tec1_untagged-1

organism: Candida parapsilosis

source_name: a/alpha cell

tag: dna-binding gene

tag: epitope

value: untagged

tag: growth

value: biofilm

tag: media

value: Spider 1% glucose

tag: chip antibody

value: c-Myc tag monoclonal antibody (RRID:AB_2536303)


title: FTC133_siControl

description:
FTC-133 cells transfected with control siRNA
none

value: control siRNA


title: 8505C_Empty

description:
8505C cells transfected with empty vector
none


title: Cp_Tec1_untagged-2


title: Cp_Ndt80_untagged-4


title: BRCA1D11_S12_CRISPR_screen_T14_Untreat


title: BRCA1D11_Trp53BP1S25A_CRISPR_screen_T14_Untreat

value: BRCA1D11 Trp53BP1S25A Cas9


title: LNP_invivo_CIRCLE-off-target-site8_Rep2

value: Lipofection/tailvein

value: targeted amplicon sequencing

value: base-edited PCSK9


title: BHT101_siSREBF1

description:
BHT-101 cells transfected with SREBF1 siRNA
none


title: BHT101_siControl

description:
BHT-101 cells transfected with control siRNA
none


title: LNP_invivo_CIRCLE-off-target-site9_Rep1


title: K1_SREBF1

description:
K1 cells transfected with SREBF1-overexpressing vector
none


title: BRCA1D11_Trp53BP1S25A_CRISPR_screen_T0


title: Cp_Efg1_untagged-4


title: LNP_invivo_CIRCLE-off-target-site8_Rep1


title: A D2: shATGL +Doxycycline 2

city: El Paso

first: Anna

middle: M

last: Eiring

state: TX

address: 5001 El Paso Drive, MSB1 Room 2112, MSC 32002

department: Molecular and Translational Medicine

institute: Texas Tech University Health Sciences Center at El Paso

description: shATLG vector (Cellecta Inc.)

data_processing:
Raw data QC base recognition by CASAVA: error date distribution, GC-content distribution, and data filtering.
Mapping to reference genome and gene expression quantification, which included: correlation analysis and GSEA enrichment.
Differential expression analysis.
Funtional analysis: enrichment analysis, oncogene analysis and protein-protein interaction analysis.
Enrichment analysis: GO enrichment, KEGG enrichment, Reactome enrichment, DO enrichment, and DisGeNET enrichment.
Genome_build: hg19

source_name: Bone marrow

growth_protocol: K562 cell lines were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 1% L-glutamine.

extract_protocol:
Total RNA was extracted using the PureLink RNA Mini Kit by Invitrogen.
Sample quality was assayed by the Agilent RNA Screentape electrophoresis.

treatment_protocol: Cell lines were lentivirally transduced (shNT, shG0S2, pLVX G0S2, shATGL) and selected in the presence of puromycin (2 ug/ml). Resulting cells were treated with doxycycline (0.1 ug/ml, 72 h) to induce vector expression.

tag: cell line

value: Bone marrow

tag: disease

value: chronic myeloid leukemia (CML)

tag: treatment

value: Downregulated ATGL + DOX


title: ABEmax_3mg/kg_Primary_Hepatocytes_Rep6

source_name: primary hepatocytes

value: LNP-mediated delivery

value: tail vein


title: Cp_Efg1_untagged-1


title: A D1: shATGL +Doxycycline 1

description: shATLG vector (Cellecta Inc.)


title: 200716_WT_MEF_THAP1

source_name: THAP-1 ChIP-Seq

value: Mouse embryonic fibroblasts

value: WT


title: THAP1KO_BRCA1D11_nsRNA_seq_rep5

growth_protocol: The wild-type and Brca1D11 mouse embryonic fibroblasts (MEFs) were generated from E13.5 embryos and grown in Dulbecco’s Modified Eagle’s Medium (DMEM, GIBCO) supplemented with 15% heat-inactivated fetal bovine serum (FBS, Gemini Bio-Products) and 1% penicillin plus streptomycin (GIBCO). To establish immortalized MEF cell lines, primary MEFs between passages 2-4 were transiently transfected with a vector encoding SV40 T-antigen (pCMV-SV40T). SV40-immortalized MEFs were routinely cultured in DMEM supplemented with 10 or 15% FBS.

extract_protocol:
Four million MEFs were labeled with 0.5 mM 5-ethynyl uridine (EU) for 30 min. Total RNA was extracted using TRIzol (Ambion). The NEBNext rRNA Depletion kit (human/mouse/rat) (New England Biosciences) was used to deplete rRNA from 1 μg of total RNA prior to sample biotinylation through Click-it reactions (Click-iT Nascent RNA Capture Kit, ThermoFisher C10365) as per the manufacturer's specification.
First-strand cDNA synthesis of the captured nascent RNA was done using the SuperScript VILO cDNA synthesis kit (Invitrogen), followed by AMPure XP purification (1.8X) and elution in (20 μl), Thereafter, second-strand cDNA synthesis was carried out in a total reaction volume of 30 μl that contained 0.6 mM dNTP, 1.2 mM of dUTP, 2 units of RNase H (Invitrogen) and 20 units of E. coli DNA polymerase I (Invitrogen), for 2.5 hr at 16°C. Double stranded cDNA was cleaned using 1.8X Agencourt AMPure XP beads and eluted in 20 μl of EB that was used for end-repair. End-repair was performed in 50 μl of T4 ligase reaction buffer containing 0.4 mM of dNTPs, 3 units of T4 DNA polymerase (NEB), 9 units of T4 Polynucleotide Kinase (NEB) and 1 unit of Klenow fragment (NEB) at 24°C for 30 min in a ThermoMixer C at 400 rpm. End-repair reaction was cleaned using 1.8X Agencourt AMPure XP beads and eluted in 15 μl of EB that was used for A-tailing reaction in 30 μl of NEBNext dA-Tailing reaction buffer (NEB) with 7.5 units of Klenow fragment exo- (NEB) at 37°C for 30 min. The 30 μl of the A-tailing reaction were mixed with Quick Ligase buffer 2X (NEB), 3,000 units of Quick ligase and 5 nM of annealed adaptor (Illumina truncated adaptor) in a volume of 50 μl and incubated at 25°C for 20 min. The adaptor was prepared by annealing the following HPLC-grade oligos: 5′-Phos/GATCGGAAGAGCACACGTCT-3′and 5′-ACACTCTTTCCCTACACGACGCTCTTCCGATC∗T-3′ (∗phosphorothioate bond). The ligation reaction was terminated by adding 50 mM of EDTA and cleaned with 1.8X Agencourt AMPure XP beads and eluted in 15 μl of EB. Thereafter, samples were treated with 0.5 units of Uracil-DNA glycosylase (Thermofisher) for 15 min at 37°C and used for PCR amplification in a 50 μl reaction volume containing 1 μM of TruSeq barcoded primer p5, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATC*T, TruSeq barcoded primer p7, CAAGCAGAAGACGGCATACGAGANNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T, (NNNNNNNN represents barcode and * a phosphothiorate bond), and 2X Kapa HiFi HotStart Ready mix (Kapa Biosciences). The temperature settings during the PCR amplification were 45 s at 98°C followed by 15 cycles of 15 s at 98°C, 30 s at 63°C, 30 s at 72°C and a final 5 min extension at 72°C. PCR reactions were cleaned with Agencourt AMPure XP beads (Beckman Coulter), run on a 2% agarose gel and a smear of 200-500bp was cut and gel purified using QIAquick Gel Extraction Kit (QIAGEN). Library concentration was determined with KAPA Library Quantification Kit for Illumina Platforms (Kapa Biosystems). Sequencing was performed on the Illumina Nextseq500 (75 bp single end reads).
Nascent RNA-seq


title: BRCA1D11_Trp53BP1S25A_CRISPR_screen_T14_Parpi

value: PARPi


title: P D2: pLVX G0S2 +Doxycycline 2

description: pLVX G0S2 vector (Clontech)

value: Upregulated G0S2 + DOX


title: Cp_Brg1_untagged-1

value: untagged

value: biofilm


title: ABEmax_3mg/kg_Primary_Hepatocytes_Rep5


title: LNP_invivo_CIRCLE-off-target-site10_Rep1


title: THAP1KO_BRCA1D11_nsRNA_seq_rep4


title: P D1: pLVX G0S2 +Doxycycline 1

description: pLVX G0S2 vector (Clontech)


title: Cp_Tec1_2_2

description:
ChIPspglu_II-2_CEM407
samples for processed file: ChIPspglu_II-2_CEM407 - ChIPspglu_II-2_CEM403

value: c-myc

value: Spider 1% glucose

value: c-Myc tag monoclonal antibody (RRID:AB_2536303)


title: THAP1KO_BRCA1D11_nsRNA_seq_rep3


title: ABEmax_3mg/kg_Liver_Rep6

source_name: whole liver lysate


title: ABEmax_3mg/kg_Liver_Rep5


title: Cp_Tec1_1_2

description:
ChIPspglu_I-2_CEM407
samples for processed file: ChIPspglu_I-2_CEM407 - ChIPspglu_I-2_CEM403


title: Cp_Ndt80_untagged-3


title: THAP1KO_BRCA1D11_nsRNA_seq_rep2


title: G D1: shG0S2 +Doxycycline 1

description: shG0S2 vector (Cellecta Inc.)

value: Downregulated G0S2 + DOX


title: ABEmax_3mg/kg_Primary_Hepatocytes_Rep4

value: targeted amplicon sequencing


title: ABEmax_3mg/kg_Liver_Rep4

value: base-edited PCSK9


title: THAP1KO_BRCA1D11_nsRNA_seq_rep1


title: Cp_Ndt80_4

description:
ChIPspglu_IV_CEM401
samples for processed file: ChIPspglu_IV_CEM401 - ChIPspglu_IV_CEM397


title: NT D2: shNT +Doxycycline 2

description: shNT vector (Cellecta Inc.)

value: Bone marrow

value: Non-targeting + DOX


title: BRCA1D11_nsRNA_seq_rep3


title: Cp_Ndt80_3

description:
ChIPspglu_III_CEM401
samples for processed file: ChIPspglu_III_CEM401 - ChIPspglu_III_CEM397


title: ABEmax_3mg/kg_Primary_Hepatocytes_Rep3


title: NT D1: shNT +Doxycycline 1

description: shNT vector (Cellecta Inc.)

value: chronic myeloid leukemia (CML)


title: BRCA1D11_nsRNA_seq_rep2


title: Cp_Efg1_4

description:
ChIPspglu_IV_CEM391
samples for processed file: ChIPspglu_IV_CEM391 - ChIPspglu_IV_CEM387


title: Cp_Brg1_untagged-2


title: ABEmax_3mg/kg_Liver_Rep3

value: LNP-mediated delivery


title: NT: shNT No Doxycycline

description: shNT vector (Cellecta Inc.)

value: Non-targeting


title: G D2: shG0S2 +Doxycycline 2

description: shG0S2 vector (Cellecta Inc.)


title: BRCA1D11_nsRNA_seq_rep1

value: Mouse embryonic fibroblasts


title: Cpar_Efg1-1

description:
ChIPspglu_I_CEM391
samples for processed file: ChIPspglu_I_CEM391 - ChIPspglu_I_CEM387


title: NSC

city: Seoul

first: Kyung-Tae

last: Lee

address: Yonsei-ro 50

department: Biotechnology

country: South Korea

institute: Yonsei University

description: Presented as NSC in processed data file

data_processing:
NovaSeq 6000 Sequencing System (Illumina) following User Guide Document #1000000019358 v02
Sequenced reads were trimmed to remove the adaptor sequence and masked for low-complexity or low-quality sequence using Trimmomatic 0.38.
Reads were aligned to the genome data of Homo sapiens using HISAT2 version 2.1.0 with Bowtie2 2.3.4.1.
Transcript assembly and abundance estimation were performed by Stringtie v1.3.4d using -e option.
Genome_build: hg19
Supplementary_files_format_and_content: Microsoft excel sheets containing read count, FPKM, and TPM

source_name: NSCs in BHEM hydrogel

growth_protocol: The NSCs in BHEM hydrogel on top of Transwell insert were co-cultured with ECs on the bottom of the Transwell.

extract_protocol:
Total RNA was isolated from NSCs using the RNeasy Mini kit (Qiagen).
cDNA was constructed with a TruSeq Stranded mRNA kit (Illumina, San Diego, CA, USA) following the TruSeq Stranded mRNA Sample Preparation Guide (Part #15031047 Rev. E).

treatment_protocol: Two different culture conditions (NSC−EC versus NSC alone)

tag: passage

tag: culture condition

value: on the Transwell, NSC alone


title: Cpar_Brg1-2

description:
ChIPspglu_II_CEM385
samples for processed file: ChIPspglu_II_CEM385 - ChIPspglu_II_CEM381

data_processing:
Quality analysis performed with FastQC
ChIP-seq reads were mapped to their corresponding genome using Bowtie 2 with default parameters
SAMtools package was used to convert, sort and index the sequenced reads to BAM format
Adjusted the number of reads in the different treatment-control dataset pairs using SAMtools view -s function prior to peak calling
Peak calling was performed using MACS2 with a q-value cutoff of 0.01; the shiftsize parameter was determined using the SPP package in R
Genome_build: http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly21/archive/C_albicans_SC5314_version_A21-s02-m09-r02_chromosomes.fasta.gz; http://www.candidagenome.org/download/sequence/C_dubliniensis_CD36/archive/C_dubliniensis_CD36_version_s01-m02-r08_chromosomes.fasta.gz; http://www.candidagenome.org/download/sequence/C_tropicalis_MYA-3404/current/C_tropicalis_MYA-3404_chromosomes.fasta.gz; www.candidagenome.org/download/sequence/C_parapsilosis_CDC317/archive/C_parapsilosis_CDC317_version_s01-m03-r13_chromosomes.fasta.gz
Supplementary_files_format_and_content: peaks.txt files were generated for each experiment with tagged proteins using untagged strains as a control in MACS2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. Cell disruption and immunoprecipitation were performed as previously described (Hernday et al., Methods Enzymol 470: 737-758, 2010) using a c-Myc tag monoclonal antibody (RRID: AB_2536303).
Performed using an NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina sequencing


title: ABEmax_1mg/kg_Primary_Hepatocytes_Rep2

value: tail vein

tag: genotype


title: ABEmax_1mg/kg_Liver_Rep3


title: ABEmax_invitro_Rep3

data_processing:
Raw reads were trimmed and filtered using fastp version version 0.20.0
Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
variants were called using HaplotypeCaller (GATK version 4.1.2.0)
Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
Supplementary_files_format_and_content: Variant call format (VCF)

source_name: HEK cells

growth_protocol: for in vitro:DMEM growth medium supplemented with 10% FBS and 1% P/S; in vivo samples were isolated from C58BL/6J animals

extract_protocol:
in vitro: Detachment with TryplE, wash with PBS, lysis in RLT buffer and RNA isolation following RNAeasy protocol; in vivo: primary hepatocyte isolation
total RNA

treatment_protocol: in vitro: per 48 well plate: 1 ug total DNA with 1.5 ul Lipofectamine2000; in vivo: LNP- or AAV-mediated delivery

value: Lipofection

value: HEK cells


title: ABEmax_1mg/kg_Liver_Rep2

growth_protocol: DMEM growth medium supplemented with 10% FBS and 1% P/S for HEK293T and Hepa1-6 cells; EMEM with same supplements for HepG2 cells


title: THAP1KO_nsRNA_seq_rep3


title: THAP1KO_nsRNA_seq_rep1


title: ABEmax_1mg/kg_Primary_Hepatocytes_Rep1


title: Mouse epiblast stem cells - Blastocyst-like Hemisphere Reprogramming Day 7 population

city: Kobe

first: Cody

last: Kime

state: Hyogo

address: Minatojima Minamimachi, 2-2-3

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

data_processing:
BAM files were produced with Cell Ranger (Version 3.1)
Counts were split to intron and exon counts with dropEst
Basic cell quality filtering was performed in Seurat
SkewC was performed after Seurat to remove skewed and retain typical cells, producing a final total high quality filtering of cell samples to the filteredcellbarcodes list.
Final exon, intron, and sum (exon+intron) count tables from DropEst are generated from filtered barcodes set for downstream use as R Data files (*modifiedCCM.rds).
Genome_build: Mus musculus mm10 reference genome with EGFP and mCherry transgenes in custom GTF, included as genes.gtf.
Supplementary_files_format_and_content: List of post-filtered cell barcodes used in the study, prepared as a tsv file.
Supplementary_files_format_and_content: *modifiedCCM.rds with processed count tables and barcodes for each sample.

source_name: XGFP and MERVL::mCherry reporter mouse epiblast stem cells undergoing reprogramming

extract_protocol:
Cells were digested to single cell with accutase for 10-15 minutes, screened, and resuspended in low FBS Phosphate Buffered Saline solution, counted 16 times for cell concentration, viability, and doublet rate, and then diluted to approprate loading concentrations for the 10X Genomics Chromium Controller.
scRNA-seq libraries were prepared with 10x Genomics Chromium system using 3' (V3.0 chemistry) GEM beads and i7 Index kit following standard protocol. Libraries were diluted and submitted to Macrogen for sequencing under the library strategy.
Libraries were sequenced using paired-end sequencing (150bp Read 1 and 150bp Read 2) with a single sample per lane on the Illumina HiSeq X

tag: strain/genotype

value: Tg(CAG-EGFP)D4Nagy; 129X1/SvJ x 129S1/Sv)F1-Kitl; Piggybac MERVL::mCherry

tag: culture protocol

tag: culture plate

value: Fibronectin coated plate


title: ABEmax_invitro_Rep2

city: Zurich

first: Tanja

address: Winterthurerstrasse, 190

institute: UZH Zurich

tag: cell type


title: WT_nsRNA_seq_rep3

value: WT

tag: strain


title: Mouse embryonic stem cells and stabilized MERVL(2C)+ sub-population duality coculture

source_name: BL6 mouse ES cells with MERVL::mCherry reporter and unique MERVL+ population

value: iMatrix511 coated plate


title: ABEmax_invitro_Rep1


title: WT_nsRNA_seq_rep2


title: Mouse epiblast stem cells - stock starting population

source_name: XGFP and MERVL::mCherry reporter mouse epiblast stem cells

value: NDiff227 + 12ng/mL bFGF + 20ng/mL Activin A, + Pen/Strep


title: Control_invitro_Rep3

value: control


title: ABEmax_3mg/kg_Primary_Hepatocytes_Rep2

value: targeted amplicon sequencing

value: base-edited PCSK9


title: WT_nsRNA_seq_rep1


title: ABEmax_1mg/kg_Primary_Hepatocytes_Rep3


title: THAP1KO_nsRNA_seq_rep2


title: Cpar_Brg1-1

description:
ChIPspglu_I_CEM385
samples for processed file: ChIPspglu_I_CEM385 - ChIPspglu_I_CEM381

value: c-myc

value: biofilm

value: Spider 1% glucose

value: c-Myc tag monoclonal antibody (RRID:AB_2536303)


title: CO

description: presented as CO in processed data file

source_name: NSCs in BHEM hydrogel co-cultured with Ecs

value: on the Transwell, Top (NSC) and bottom (EC)


title: Paracoccus denitrificans ATCC19367-florfenicol-treated-3

city: Guangzhou

first: Mei

last: Wang

state: Guangdong

address: 483 Wushan Road

department: College of Veterinary Medicine

institute: South China Agricultural University

data_processing:
Bcl2fastq v2.17.1.14 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Paracoccus denitrificans ASM406373v1 whole genome using bowtie2 (v2.2.6).
Fragments Per Kilo bases per Million reads (FPKM) were calculated using a protocol from Mortazavi and Williams, Nature methods, 2008.
Genome_build: Paracoccus denitrificans ASM406373v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Paracoccus denitrificans

extract_protocol:
Paracoccus denitrificans was collected by centrifugation, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard IIIuminia protocols

tag: agent

value: florfenicol


title: BG-H3K9me3-ChIP-MT-2

city: Xiamen

first: shaoxuan

last: chen

state: Fujian Province

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District

institute: xiamen university

data_processing:
The image analysis and base calling were performed by using Illumina’s Genome Analysis pipeline.
clean reads were aligned to the mouse genome (GRCm38/mm10) using Bowtie2 (version 2.2.8).
Enriched peaks of H3K9me3 were identified by HOMER v4.10.1 with histone style (http://homer.ucsd.edu/homer).
Genome_build: mm10

source_name: cerebellum

extract_protocol:
Approximately 5 x 10^6 Bergmann glial cells isolated as above was fixed in 1% formaldehyde for 10 min at room temperature (RT), followed by quenching in 125 nM glycine for 5 min. Cell nuclei were collected and lysed in lysing buffer (50 mM HEPES/KOH pH 7.6, 1 mM EDTA, 140 nM NaCl, 10 % v/v Glycerol, 0.5 % NP-40, 0.25 % v/v Triton X-100) supplemented with protease inhibitor. Nuclei were subjected to sonication to acquire DNA fragments of 200-350 bp. The sonicated chromatin was applied to immunoprecipitation by incubation with 1.5μg H3K9me3 antibody (rabbit, Abcam, #ab232324) overnight at 4 °C, followed with collection using 30 μL protein A/G plus agarose beads (Millipore).
The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 7962347001)

tag: tissue

value: Bergmann glia

tag: antibody

tag: age

value: post natal day 10


title: ABEmax_3mg/kg_Liver_Rep2

last: Rothgangl

value: LNP-mediated delivery

value: tail vein


title: Paracoccus denitrificans ATCC19367-florfenicol-treated-2


title: Control_invitro_Rep1

value: Lipofection

value: HEK cells


title: Control_invitro_Rep2


title: BG-H3K9me3-ChIP-MT-1


title: BG-H3K9me3-ChIP-WT-2