title: C34A-flotillin-1, MDA-MB-234

city: Austin

first: Bryan

last: McClellan

state: TX

address: 1601B Trinity St, Hdb 6.302

institute: University of Texas at Austin

data_processing:
Genewix performed basic computational analysis for quality controls and constructed the gene matrices.
Gene matrices were normalized using DESeq2 size factors and filtering for a minimum of 4 read per condition.
Gene matrices were normalized using reads per million counts
Assembly: GRCh38
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: .csv file contains combined raw counts for all samples

growth_protocol: GFP-flotillin-1 WT and dTomato flotillin-1-C34A MDA-MB-231 cells   were implanted at 100,000 per mouse in the #4 mammary fat pad of NOD/SCID female mice. Xenografted tumors grew for 8-weeks before being harvested.

extract_protocol:
PureLink RNA mini Kit
cDNA

treatment_protocol: Tumors were minced with scalpel and digested in collagenase IV _+ DNAse at 37 degress for 3 hours. Digested tumors were then passed through a 70 µM nylon strainer. Single cells were resupended in PBS and flow sorted based on GFP (WT) or dTomato (C34A) expression. Sorted cells were normalized to 100,000 cells per condition and then resuspended in RNA lysis buffer and isolated using a commercial kit. Extracted RNA was then sent to GENEWIZ for library prep and bulk mRNA sequencing.

value: Breast Cancer Cell


title: embryo, 58h, rep3

status: Public on Mar 15 2024

type: SRA

city: Knoxville

first: Jianbin

last: Wang

state: TN

address: 1311 Cumberland Avenue

department: Biochemistry & Cellular and Molecular Biology

country: USA

institute: University of Tennessee Knoxville

library_source: genomic

data_processing:
Only read 1 (R1) files were processed. Reads containing two sequential telomeric repeats (TTAGGCTTAGGC or GCCTAAGCCTAA) were filtered from the data using an in-house Perl script
Reads were mapped to the appropriate genome with Bowtie2 (local alignment) and processed with SAMtools
For samples treated with restriction enzyme BEDTools intersect was used to remove reads mapped to restriction sites
The 5’-end position of each read was mapped, separated by strand, and normalized to ten million genome-mapped reads using BEDtools genomecov
The mapping results were converted to bigWig format using bedGraphToBigWig
To analyze new telomere addition during PDE developmental stages, END-seq reads containing two consecutive telomere repeats (filtered in step 1) were converted to the G-rich strand (TTAGGC).
Reads were mapped to the genome with Bowtie2 end-to-end alignment
Mapped reads were false-positive telomeric reads. Unmapped reads were trimmed with fastx_clipper “-v -n -l 25 -a TTAGGCTTAGGC” parameters.
Trimmed reads were mapped to the genome with bowtie2 (local alignment) and processed as described above except except the 3’-positions (the sites where new telomeres are added) rather than 5’-positions were obtained with BEDTools genomecov
Assembly: Ascaris suum ASM1343314v1, Parascaris univalens (Pu_v2)
Supplementary files format and content: bigWig file containing the 5' end of reads on the forward strand
Supplementary files format and content: bigWig file containing the 5' end of reads on the reverse strand
Supplementary files format and content: bigWig file with the 3' end of reads on the forward strand which contained two telomeric repeats (TTAGGCTTAGGC)
Supplementary files format and content: bigWig file with the 3' end of reads on the reverse strand which contained two telomeric repeats (TTAGGCTTAGGC)
Library strategy: END-seq

molecule: genomic DNA

organism: Ascaris suum

source_name: Embryo

extract_protocol:
Ascaris females were collected, and the fertilized embryos (0hr, 1-cell before prenuclear fusion) were harvested and processed as previously described (Wang et al. 2011, Wang et al. 2014). Ascaris 0hr samples were incubated at 30°C with constant shaking for the desired time (from 50hr to 98hr). For all molecular experiments, the eggshells were first de-coated with bleach treatment (0.4 M KOH, 2% sodium hypochlorite) for 1.5 hours at 30°C. Parascaris samples were collected as described (Simmons et al. 2023, Wang et al. 2017). Parascaris eggs were prepared similarly to Ascaris, except the incubation was carried out at 37°C and the embryonation time was shorter (10-14hr).
An adapted END-seq protocol was used (Canela et al. 2016, Wong et al. 2021). Embryos were embedded in agarose plugs. Some plugs were treated with the restriction enzymes as internal controls. Plugs were treated with exonuclease VII and exonuclease T. Blunt ends were A-tailed and capped with END-seq adaptor 1 (Canela et al. 2016). Plugs were melted and DNA was sheared to 200-300 bp with a Covaris M220 focused ultrasonicator. DNA fragments containing END-seq adaptor 1 were isolated with Dynabeads MyOne Streptavidin C1. END-seq adaptor 2 was ligated to the sheared ends of the A-tailed DNA fragments. The hairpins within the adaptors were digested with USER, and the DNA was amplified with Illumina TruSeq primers and barcodes. The following modifications were made to the END-seq protocol to capture break ends with different features. For the direct capture method, we excluded the exonuclease VII and exonuclease T treatments. For the all-END protocol, the plugs were treated with T4 polymerase (with dNTPs).

tag: tissue

value: Embryo

tag: developmental stage


title: PBS-1. Input

city: Shanghai

first: Jing

state: Select...

address: huangpu Distinc, Ruijin Hospital

country: China

institute: 瑞金医院

description:
Differentially_methylated_sites.mRNA.xlsx
mRNA Expression Profiling.xlsx

library_source: transcriptomic

data_processing:
cutadapt software, CLC Genomics Workbench v11.0.1
Differential m6A site information, Fold change, and P-value information identified by diffReps software.
Assembly: mm10
Supplementary files format and content: Differentially_methylated_sites.mRNA.xlsx

molecule: total RNA

organism: Mus musculus

source_name: lung

extract_protocol:
Mouse AECs were isolated by fluorescence-activated cell sorting (FACS) using CD326-FITC (Thermo Fisher scientific), CD45-APC (BD Biosciences). Total mRNA was extracted from mouse AECs
m6A-Seq:TruSeq Stranded mRNA Sample Pre Kit (Illumina) was used to construct the library from immunoprecipitated mRNA and input mRNA following to a published protocol. mRNA-Seq:RNA libraries for RNA-Seq were preapred using SMARTER-Seq Library Prep Kit following manufatures's protocols.
m6a-seq, mRNA-seq

value: lung

tag: cell type

value: primary airway epithelial cells

tag: genotype

value: WT

tag: treatment

value: PBS

tag: fraction

value: Input


title: WT_CMP_rep 2

city: Tianjin

first: ZhaoFeng

last: Zheng

address: 288 Nanjing Road, Heping District, Tianjin, China

institute: Institute of Hematology & Blood Diseases Hospital,

data_processing:
Raw data  of fastq format were  processed via in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Bone marrow cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Fisher).
The RNA sequencing libraries were prepared following standard Illumina protocols.

treatment_protocol: LT-HSC, MEP and CMP cells were isolated from Mx1cre; Atf4fl/fl mice (cKO) and  Atf4fl/fl mice (WT).

value: Bone marrow cells

tag: strain

value: CMP cells

value: wild type

tag: cell subtype

value: FACS-sorted CMP cells  (Lin-cKit+Sca1-CD34+CD16/32low)


title: HDM-1

data_processing:
cutadapt software, CLC Genomics Workbench v11.0.1
Assembly: mm10
Supplementary files format and content: mRNA Expression Profiling.xlsx

extract_protocol:
Mouse AECs were isolated by fluorescence-activated cell sorting (FACS) using CD326-FITC (Thermo Fisher scientific), CD45-APC (BD Biosciences). Total mRNA was extracted from mouse AECs
mRNA-Seq:RNA libraries for RNA-Seq were preapred using SMARTER-Seq Library Prep Kit following manufatures's protocols.

tag: cell line

value: primary cells

value: epithelial cell

value: HDM


title: WT_CMP_rep 1


title: WT_LT-HSC_rep 1

value: LT-HSC cells

value: FACS-sorted CMP cells  (Lin-cKit+Sca1-CD34-CD135-)


title: C34A-flotillin-1, MDA-MB-233

organism: Homo sapiens


title: WT-flotillin-1, MDA-MB-232


title: HDM-2. IP

description: Differentially_methylated_sites.mRNA.xlsx

value: IP


title: embryo, 54h, rep3


title: HDM-2. Input


title: embryo, 50h, rep3


title: s48_FA

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description: zebrafish embryo treated with folic acid

data_processing:
STAR2 v2.5.4 with default settings for mapping step
HTSeq v0.11.0 for counting step
transcrits with at least 10 reads were kept for normalization and downstream analysis
Data were first linearized using voom function from Limma R package then we applied a quantile normalize and log2 transformation.
Assembly: Danio_rerio.GRCz11.dna.primary_assembly.fa
Supplementary files format and content: tabular texte file

molecule: polyA RNA

organism: Danio rerio

source_name: whole embryo

extract_protocol:
quiazol
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: the embryo were maintain and treated in dutch standard water(demineralized water supplemented with 100 mg/l NaHCO3, 20 mg/l KHCO3, 200 mg/l CaCl2 2H2O, and 180 mg/l MgSO4·7H2O and then aerated for 24hrs at 27°C) plus 0.01% DSMO

value: whole embryo

value: Folic acid


title: embryo, 68h, all-END

value: Embryo

value: AsiSI+PmeI+AscI


title: WT-flotillin-1, MDA-MB-231

value: Breast Cancer Cell

value: WT


title: s47_FA


title: HDM-1. IP

value: lung

value: primary airway epithelial cells


title: s40_RA

description: zebrafish embryo treated with all-trans retinoic acid

value: All-trans retinoic acid


title: s41_VPA

description: zebrafish embryo treated with valproic acid

value: Valproic acid


title: Hoxa11CreER Hif1a, replicate 3

city: Dallas

first: Sneha

last: Korlakunta

address: 6000 Harry Hines Blvd

department: Surgery

institute: UT Southwestern Medical Center

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
cellranger-5.0.1
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tendon injury

extract_protocol:
Burn and tenotomy was performed as previously described (PMID 26274052) in Hoxa11CreER;ROSA-LSL-TdTomato;Hif1a fl/fl. Tenotomy injury site was harvested from Day 7 post-tenotomy mice. Tissue samples were digested for 45 minutes in 750U/ml Type 1 Collagenase and 7U/ml Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37°C under constant agitation of 160rpm. Digestions were subsequently quenched with 2% FBS in PBS and filtered through 40?m sterile strainers. Cells were then washed in 2% FBS in PBS, counted and resuspended at a concentration of 1000-1200 cells/ul. Cell viability was assessed with Trypan blue exclusion on a Countess II (Thermo Fisher Scientific) automated counter and only samples with >85% viability were used for scRNA sequencing.
Single Cell 3' v3

treatment_protocol: Mice were induced with tamoxifen (75 mg/kg) daily intraperitoneal injection for 5 days. Mice were allowed a nine-day washout period prior to the procedure. Mice received pre-operative treatment with 0.05 mg/kg buprenorphine SR subcutaneously and were anesthetized with 2% isofluorane inhalation. The left limb was shaved using clippers and cleaned with three rounds of alternating alcohol and betadine. A small incision was made over the Achilles tendon. The tendon was then isolated by blunt dissection and transected at its midpoint. The skin was closed with 5-0 vicyl suture. The mouse recovered in a warmed chamber by heating pad.

value: tendon injury

value: unsorted

value: Burn/tenotomy


title: s39_RA


title: MX1_CMP-1

first: chao

last: tang

state: Tianjin

address: 288 Nanjing Road

institute: Institute of Hematology and Blood Diseases Hospital

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: gzip file contains barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. The scRNA-seq data of sorted bone marrow CMP cells from atf4 fl/fl mice in homeostasis.
Supplementary files format and content: gzip file contains barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. The scRNA-seq data of sorted bone marrow CMP cells from atf4 KO mice in homeostasis.

source_name: Bone marrow

extract_protocol:
Freshly sorted Lin-cKit+ and CMP cells from the BM of WT or KO mice.
For 10x Genomics scRNA-seq, samples with cell viability >80%, a cell concentration ranging from 700 cells/ml to 1,200 cells/ml (based on trypan blue staining), and cell diameters ranging from 5 mm to 40 mm were collected and analyzed. A Chromium Single cell 30 Library and Gel Bead Kit V2 (10x Genomics) were used to generate single-cell gel beads in emulsion for reverse transcription and library preparation. Sequencing was performed on an Illumina HiSeq PE150 platform with 50,000 to 100,000 reads per cell and a 70–80% saturation level, as recommended by the manufacturer (10x Genomics).

value: Bone marrow

value: CMP

value: atf4 KO


title: s38_DSW

description: zebrafish embryo control

value: NT


title: PDAC Immune cells library 1

city: St. Louis

first: David

last: DeNardo

email: johnbaer@wustl.edu, ddenardo@wustl.edu

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine

institute: Washington University in St. Louis

data_processing:
Libraries were sequenced on a NovaSeq 6000 sequencing system (Illumina) with a minimum target of 50,000 mean reads per cell. The cellranger mkfastq pipeline (10X Genomics) was used to demultiplex IIllumina base call files to FASTQ files. Files from the KPPC tumors were demultiplexed with > 95% valid barcodes, and > 95% q30 reads. Mouse FASTQ files from each sample were processed with Cellranger count v6 (10X Genomics) and aligned to the mm10 reference genome (mouse reference mm10-2020-A from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz) to generate a feature barcode matrix. Analysis was run with introns included to improve transcriptome coverage.
Assembly: mouse reference mm10-2020-A from https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz
Supplementary files format and content: Cell barcodes: TSV, features: TSV, expression matrix: MTX

source_name: Pancreas

extract_protocol:
Mice were anesthetized with isofluorane and euthanized by trans-cardiac PBS/heparin perfusion. Tissues were harvested and minced into a slurry with a scalpel. The tissue was digested in HBSS supplemented with 10% FBS (Gibco), 2 mg/mL collagenase A (Roche), and 50μg/ml DNase-I (Roche), for 30 min at 37°C with constant agitation. Tissue digests were filtered through 100μm cell strainers, then cells were counted with a Countessa II automated cell counter (Life technologies). Cells were counted, washed, and stained with fluorescently conjugated antibodies. Samples were washed and resuspended in flow cytometry buffer containing annexin V viability dye, then sorted for viable immune cells (CD45+) using an Aria-II cell sorter (BD Biosciences). To maximize viability, cell sorting was done through a 100m nozzle into ice-cold HBSS supplemented with 20% FBS. For each library, equal numbers of sorted cells from 2-3 replicate mice were pooled, washed, and resuspended in PBS with 0.04%BSA. Cell count and post-sort viability were assessed with a BD Rhapsody single cell system (BD Biosciences). After a second confirmation of >85% viability, cells were resuspended at 1000cells/uL in PBS with 0.04%BSA and processed with the 10X GEM-bead cell capture kit with a target of 10000 cells.
Single-cell RNA-sequencing library preparation was then conducted by the Genome Technology Access Center at Washington University. Samples were encapsulated into droplets and libraries were prepared using the Chromium Single Cell 3’v3 Reagent kit (10x Genomics).

treatment_protocol: LSL-KRASG12D;p53flox;p48-CRE;INK-ATTAC (KPPC-IA) KPPC-IA  mice were bred to a C57Bl/6J background and verified by congenic markers. For senescent cell depletion in KPPC-IA mice, 10mg/kg of AP20187 (ApexBioT) was administered intraperitoneally 3 times per week for 3 weeks, starting at 1 month of age. Mice were sacrificed before experiment endpoints in cases of >15% body weight loss, tumor burden >1.8 cm in diameter, moribund appearance, or severe cachexia. In all studies, care was taken to include littermates and sex- and age-matched vehicle treated controls in the experimental setup. All animal studies were approved by the Washington University School of Medicine IACUC review board.

value: Pancreas

value: IP injection of AP20187


title: PDAC Immune cells library 2


title: HDM-1. Input

value: HDM

value: Input


title: s37_DSW

description: zebrafish embryo control

value: whole embryo


title: A_CMP-1

value: atf4 fl/fl


title: s36_FA

value: Folic acid


title: EO771_Isotype_lane2, TCR

city: Holon

first: Roy

last: Granit

address: 26 Harokmim St. Bldg D

country: Israel

institute: Compugen LTD

description: 10x Genomics

data_processing:
The CellRanger single-cell software suite (V7.0) pipeline from 10x Genomics was utilized to identify cell hashing & VDJ features, and map reads to the reference transcriptome. Modified gene reference (based on GENCODE) was employed to align the reads, resulting in the generation of unique molecular identifier (UMI) count matrices.  The data underwent downstream analyses using the scanpy package (V1.9.3)
Assembly: GRCm38
Supplementary files format and content: anti-IL18BP_scdata.h5ad
Library strategy: scTCR-Seq

source_name: syngeneic tumor model

extract_protocol:
Mouse tumors were enzymatically dissociated to generate singe cell suspensions and enriched for immune cell populations using CD45 MicroBeads (Miltenyi). Individual samples from each mouse were hashed using Total-seq-c antibodies (Biolegend). For each treatment, 6 mice were pooled together, and 40,000 cells were loaded into each channel of Chromium single-cell 5’ Chip to create a single cell GEM using the Chromium X machine. cDNA and the subsequent libraries were prepared according to the manufacturer’s recommendations. Libraries from two 10x channels were pooled and sequenced together using Illumina NovaSeq S1.
Library was constructed according to 10x genomics manufacturer instructions for 5' chromium kit

treatment_protocol: Mice were treated either with anti-IL-18BP Ab or isotype control (15mg/kg) twice a week for total of 3 treatments

value: syngeneic tumor model

value: Immune cells

value: Isotype


title: s35_FA


title: s42_VPA

value: Valproic acid


title: EO771_aIL18BP,lane2, TCR

description: 10x Genomics


title: EO771_Isotype_lane1, TCR

description: 10x Genomics


title: s30_VPA


title: EO771_aIL18BP,lane1, TCR

description: 10x Genomics


title: s29_VPA


title: Hoxa11CreER Hif1a, replicates 1 & 2

description: 10X Genomics

value: tendon injury

value: unsorted


title: s27_RA

value: All-trans retinoic acid


title: s28_RA


title: EO771_aIL18BP,lane2, HTO

description: 10x Genomics

library_source: other

data_processing:
The CellRanger single-cell software suite (V7.0) pipeline from 10x Genomics was utilized to identify cell hashing & VDJ features, and map reads to the reference transcriptome. Modified gene reference (based on GENCODE) was employed to align the reads, resulting in the generation of unique molecular identifier (UMI) count matrices.  The data underwent downstream analyses using the scanpy package (V1.9.3)
Assembly: GRCm38
Supplementary files format and content: anti-IL18BP_scdata.h5ad

molecule: protein


title: s26_DSW

description: zebrafish embryo control


title: s25_DSW

description: zebrafish embryo control


title: EO771_aIL18BP,lane1, HTO

description: 10x Genomics


title: EO771_Isotype_lane2, GEX

description: 10x Genomics


title: s24_FA


title: EO771_Isotype_lane1, GEX

description: 10x Genomics


title: s23_FA


title: EO771_Isotype_lane2, HTO

description: 10x Genomics


title: EO771_Isotype_lane1, HTO

description: 10x Genomics


title: EO771_aIL18BP,lane2, GEX

description: 10x Genomics


title: s18_VPA


title: EO771_aIL18BP,lane1, GEX

description: 10x Genomics


title: s17_VPA


title: cKO_t-1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: gzip file contains barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. The scRNA-seq data of sorted bone marrow Lin-cKit+ cells from Atf4 fl/fl mice in homeostasis.
Supplementary files format and content: gzip file contains barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. The scRNA-seq data of sorted bone marrow Lin-cKit+ cells from Atf4 fl/fl mice after secon transplantation.
Supplementary files format and content: gzip file contains barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. The scRNA-seq data of sorted bone marrow Lin-cKit+ cells from Atf4 KO mice in homeostasis.
Supplementary files format and content: gzip file contains barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. The scRNA-seq data of sorted bone marrow Lin-cKit+ cells from Atf4 KO mice after secon transplantation.

value: Bone marrow

value: Lin-cKit+

value: Atf4 KO

value: 2nd transplantation


title: s16_RA


title: 20230310_Unstimulated PBMCs, ATAC-derived cDNA

city: New York

first: Sophie

middle: L

last: Gray-Gaillard

state: New York

address: 429 E. 29th Street, room 314

institute: NYU School of Medicine

description: 10x Genomics

data_processing:
RNA and ATAC libraries were aligned using cellranger-arc software v1.2.0 (10x Genomics) against the human genome (GRCh38 ensemble). Primary data analysis and statistical analysis were then performed using the R environment. BarCounter, Seurat v4.3.0, and Signac v1.9.0 were used to process single cell libraries and integrate all the TEA-seq modalities. Open chromatin regions were normalized across batches using integration functions in Seurat, and peak calling was performed using MACS2.
Assembly: GRCh38 ensemble
Supplementary files format and content: barcodes.tsv.gz, matrix.mtx.gz, features.tsv.gz, atac_fragments.tsv.gz.tbi, HTO_Tag_Counts.csv, HTO_taglist.csv

source_name: Peripheral blood mononuclear cells

extract_protocol:
Cells were processed for transcriptomic, epitope, and accessibility measurement (TEA-seq) using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (10X Genomics). Cells were pooled and loaded onto Chromium J Chips and ran on a Chromium controller (10X Genomics).
Gene expression and ATAC libraries were made using the Chromium Next GEM Single Cell Multiome ATAC Kit A, Chromium Next GEM Single Cell Multiome Reagent Kit A, Library Construction Kit (10X Genomics) following the protocols recommended by the manufacturer. Surface protein expression libraries were made as detailed in the TEA-seq protocol.
TEA-seq

treatment_protocol: Following written informed consent, peripheral blood was drawn by standard phlebotomy longitudinally from 24 adults (12 vaccine-primed and 12 infection-primed) in observational studies in accordance with NYU Institutional Review Board protocols (s18-02035 and s18-02037). Blood draws occurred around six months after second vaccination (“PostSecondDose”) or SARS-CoV-2 infection (“PostInfection). Peripheral blood mononuclear cells (PBMC) were isolated from CPT vacutainers (BD Biosciences) within four hours of the blood draw and cryopreserved in liquid nitrogen. Briefly, cryopreserved PBMCs were thawed and rested overnight at 37°C. The next day, cells were stimulated with 15-mer peptide pools encompassing the SARS-CoV-2 Spike protein (S1, S, and S+ PepTivators, Miltenyi). Sterile water was used for the unstimulated controls. After stimulation for 20 hours at 37°C , CD4+ T cells were isolated using the EasySep Human CD4+ T Cell Isolation Kit (STEMCELL Technologies). Next, isolated CD4+ T cells were stained with antibodies against CD69 and CD137 conjugated to PE-Dazzle 594 and PE, respectively (Biolegend) and hashtag oligos, to allow multiplexing and doublet detection (Biolegend), for 30 minutes at room temperature in the dark, followed by magnetic bead enrichment using the EasySep Human PE Positive Selection Kit (STEMCELL Technologies).

value: Peripheral blood mononuclear cells

tag: library type

value: ATAC

tag: antibodies/tags


title: s15_RA


title: 20230310_Unstimulated PBMCs, mRNA-derived cDNA

description: 10x Genomics

value: mRNA


title: WT_t-1

value: Atf4 fl/fl


title: 20230310_Unstimulated PBMCs, HTO-derived cDNA

description: 10x Genomics

value: HTO

value: TotalSeq-A0251 anti-human Hashtag 1 Antibody, TotalSeq-A0252 anti-human Hashtag 2 Antibody, TotalSeq-A0253 anti-human Hashtag 3 Antibody, TotalSeq-A0254 anti-human Hashtag 4 Antibody, TotalSeq-A0256 anti-human Hashtag 6 Antibody, TotalSeq-A0257 anti-human Hashtag 7 Antibody,TotalSeq-A0258 anti-human Hashtag 8 Antibody, TotalSeq-A0259 anti-human Hashtag 9 Antibody


title: s14_DSW

description: zebrafish embryo control

value: whole embryo

value: NT


title: WT_BM-1

value: homeostasis


title: 20230310_Stimulated PBMCs, lane 3,  ATAC-derived cDNA

description: 10x Genomics


title: 20230310_Stimulated PBMCs, lane 3,  HTO-derived cDNA

description: 10x Genomics


title: s12_FA

value: Folic acid


title: s13_DSW

description: zebrafish embryo control


title: ECG_LVI(-)_6

type: genomic

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

description: LVI(-) EGC FFPE sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5, Cy3

source_name: ECG,LVI(-)

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from FFPE samples using the QIAamp DNA FFPE Tissue Kit according to standard instructions

tag: gender

value: Male

tag: sample type

value: FFPE

tag: disease state

value: ECG,LVI(-)


title: s11_FA


title: 20230310_Stimulated PBMCs, lane 2,  ATAC-derived cDNA

description: 10x Genomics


title: ECG_LVI(-)_10

description: LVI(-) EGC FFPE sample


title: ECG_LVI(-)_3

description: LVI(-) EGC FFPE sample


title: s5_VPA

value: Valproic acid


title: ECG_LVI(-)_5

description: LVI(-) EGC FFPE sample


title: P14 T cells sorted from B16-OVA tumor treated with rVSV-LCMVG, Replicate 3

city: Xiamen

first: Jinhang

last: He

state: Fujian

address: No.4221, South Xiang'an Road

institute: Xiamen University

description:
Singleron Matrix GEXSCOPE
VSVgp_P14_3

data_processing:
The demultiplexing, barcoded processing, alignment, gene counting and aggregation were made using the Singleron Celescope software version 1.10.0 (https://github.com/singleron-RD/CeleScope)
The doublet were removed by using Doubletfinder R package and personal checking for conserved markers.
The R package Seurat version 4.1.1 was used for normalization, clustering and reduction. Cell type was annotated based on conserved markers.
Differential gene expression analysis and enrichment analysis were performed by using MAST and clusterProfiler R package.
Assembly: GRCm38
Supplementary files format and content: Compressed .tar.gz file containing genes, barcodes and matrix for each sample

extract_protocol:
Single-cell suspensions with 1×105 cells/mL in concentration in PBS were prepared. Single-cell suspensions were loaded into microfluidic devices and scRNA-seq libraries were constructed following the Singleron GEXSCOPER protocol by GEXSCOPER Single-Cell RNA Library Kit (Singleron Biotechnologies).
Indivaidual libraries of each sample were then dilyted to 4nM, pooled and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.


title: ECG_LVI(-)_4

description: LVI(-) EGC FFPE sample


title: ECG_LVI(-)_9

description: LVI(-) EGC FFPE sample


title: ECG_LVI(-)_7

description: LVI(-) EGC FFPE sample


title: ECG_LVI(-)_8

description: LVI(-) EGC FFPE sample


title: s4_RA

value: All-trans retinoic acid


title: KO_BM-1

value: Bone marrow

value: Lin-cKit+

value: Atf4 KO


title: OT1 T cells sorted from B16-OVA tumor treated with rVSV-LCMVG, Replicate 1

description:
Singleron Matrix GEXSCOPE
VSVgp_OT1_1


title: P14 T cells sorted from B16-OVA tumor treated with rVSV-LCMVG, Replicate 2

description:
Singleron Matrix GEXSCOPE
VSVgp_P14_2


title: 20230310_Stimulated PBMCs, lane 3, mRNA-derived cDNA

description: 10x Genomics

value: Peripheral blood mononuclear cells


title: ECG_LVI(-)_1

description: LVI(-) EGC FFPE sample


title: s6_VPA


title: ECG_LVI(+)_10

description: LVI(+) EGC FFPE sample

source_name: ECG,LVI(+)

value: ECG,LVI(+)


title: OT1 T cells sorted from B16-OVA tumor treated with rVSV-LCMVG, Replicate 2

description:
Singleron Matrix GEXSCOPE
VSVgp_OT1_2


title: 20230310_Stimulated PBMCs, lane 2, mRNA-derived cDNA

description: 10x Genomics

value: mRNA


title: P14 T cells sorted from B16-OVA tumor treated with rVSV-LCMVG, Replicate 1

description:
Singleron Matrix GEXSCOPE
VSVgp_P14_1


title: ECG_LVI(+)_9

description: LVI(+) EGC FFPE sample


title: 20230310_Stimulated PBMCs, lane 1,  HTO-derived cDNA

description: 10x Genomics

value: HTO


title: s2_DSW

description: zebrafish embryo control


title: P14 T cells sorted from B16-OVA tumor treated with PBS, Replicate 3

description:
Singleron Matrix GEXSCOPE
PBS_P14_3


title: ECG_LVI(+)_8

description: LVI(+) EGC FFPE sample


title: 20230310_Stimulated PBMCs, lane 2,  HTO-derived cDNA

description: 10x Genomics

value: TotalSeq-A0251 anti-human Hashtag 1 Antibody, TotalSeq-A0252 anti-human Hashtag 2 Antibody, TotalSeq-A0253 anti-human Hashtag 3 Antibody, TotalSeq-A0254 anti-human Hashtag 4 Antibody, TotalSeq-A0256 anti-human Hashtag 6 Antibody, TotalSeq-A0257 anti-human Hashtag 7 Antibody,TotalSeq-A0258 anti-human Hashtag 8 Antibody, TotalSeq-A0259 anti-human Hashtag 9 Antibody


title: 20230310_Stimulated PBMCs, lane 1,  ATAC-derived cDNA

description: 10x Genomics

value: ATAC


title: ECG_LVI(+)_6

description: LVI(+) EGC FFPE sample


title: ECG_LVI(+)_4

description: LVI(+) EGC FFPE sample


title: P14 T cells sorted from B16-OVA tumor treated with PBS, Replicate 1

description:
Singleron Matrix GEXSCOPE
PBS_P14_1


title: P14 T cells sorted from B16-OVA tumor treated with PBS, Replicate 2

description:
Singleron Matrix GEXSCOPE
PBS_P14_2


title: s3_RA

value: whole embryo


title: ECG_LVI(+)_1

description: LVI(+) EGC FFPE sample


title: ECG_LVI(+)_7

description: LVI(+) EGC FFPE sample

value: Female


title: LEV - Animal 14

city: Washington

first: Patrick

middle: Alexander

last: Forcelli

state: DC

address: 3970 Reservoir Road NW NRB W209B

department: Pharmacology & Physiology

institute: Georgetown University

data_processing:
Reads were aligned using STAR aligner 2.7.3a in PartekFlow; aligned reads were subjected to QC and a single sample (Control 11) was excluded due to low average base quality, and low coverage.
Reads were quantified to the rn6 annotation model using the Quantify to annotation model (Partek E/M) procedure in PartekFlow
Aligned reads were batch corrected using a general linear model approach with main effects of batch and drug by batch interactions removed
Differential expression analysis was performed using DESeq2 (PB vs VEH, LEV vs VEH) with a FDR step-up correction and median ratio normalization
Assembly: rn6
Supplementary files format and content: raw_counts.txt; output after quantitation to annotation model
Supplementary files format and content: DESeq2_results.txt; output of DESeq2 analysis

organism: Rattus norvegicus

source_name: Hippocampus

growth_protocol: Timed pregnant female Sprague Dawley (E15) rats were purchased from Envigo/Charles River, at postnatal day 7 (P7) male pups were weighed and randomly assigned to treatment group. Animals were purchased over two orders and one animal per litter was taken per treatment group. After drug administration animals were returned to dam.

extract_protocol:
Total RNA was extracted using Trizol, separated with chloroform and isopropanol. 1mg of RNA was used for library preparation
1 mg of RNA per samples was used to generate libraries using NEBNext Ultra RNA Library Prep Kit for Illumina® (NEB, USA)

treatment_protocol: On P7 pups were given, intraperitoneally, either saline, phenobarbital (75 mg/kg) or levetiracetam (200 mg/kg)

value: Hippocampus

value: Sprague Dawley

value: LEVETIRACETAM (200 mg/kg)


title: 20230310_Stimulated PBMCs, lane 1, mRNA-derived cDNA

description: 10x Genomics


title: ECG_LVI(+)_5

description: LVI(+) EGC FFPE sample

value: Male

value: FFPE


title: ECG_LVI(+)_3

description: LVI(+) EGC FFPE sample


title: LEV - Animal 13


title: ECG_LVI(+)_2

description: LVI(+) EGC FFPE sample


title: OT1 T cells sorted from B16-OVA tumor treated with PBS, Replicate 2

description:
Singleron Matrix GEXSCOPE
PBS_OT1_2


title: OT1 T cells sorted from B16-OVA tumor treated with PBS, Replicate 3

description:
Singleron Matrix GEXSCOPE
PBS_OT1_3


title: 20220819_Unstimulated PBMCs, mRNA-derived cDNA

description: 10x Genomics


title: 20220819_Unstimulated PBMCs, HTO-derived cDNA

description: 10x Genomics

value: TotalSeq-A0251 anti-human Hashtag 1 Antibody, TotalSeq-A0252 anti-human Hashtag 2 Antibody, TotalSeq-A0253 anti-human Hashtag 3 Antibody, TotalSeq-A0254 anti-human Hashtag 4 Antibody


title: ECG_LVI(-)_2

description: LVI(-) EGC FFPE sample

value: ECG,LVI(-)


title: s1_DSW

description: zebrafish embryo control

value: NT


title: OT1 T cells sorted from B16-OVA tumor treated with PBS, Replicate 1

description:
Singleron Matrix GEXSCOPE
PBS_OT1_1


title: LEV - Animal 11


title: 20220819_Stimulated PBMCs, lane 3,  ATAC-derived cDNA

description: 10x Genomics


title: CS054

first: Cathy

last: Mendelsohn

state: NY

address: 1130 St. Nicholas Ave

department: Urology

institute: Columbia University Medical Center

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming
Pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Mouse:GRCm38.p6) using kallisto (0.44.0)
Assembly: mm10
Supplementary files format and content: excel file with DESeq2 output

source_name: 72h Rosiglitazone+Tramtinib treated BBN963 cells

extract_protocol:
RNA was extracted with Qiagen miRNeasy micro kit
Poly-A pull-down was used to enrich mRNAs from total RNA samples before library construction using Illumina TruSeq chemistry.

value: cell line

value: basal bladder cancer urothelial cells

value: C57bl/6 WT

value: Rosiglitazone+Trametinib

tag: time


title: 20220819_Stimulated PBMCs, lane 3,  HTO-derived cDNA

description: 10x Genomics

value: Peripheral blood mononuclear cells

value: HTO


title: LEV - Animal 10


title: 20220819_Stimulated PBMCs, lane 3, mRNA-derived cDNA

description: 10x Genomics

value: mRNA


title: LEV- Animal 9


title: CS053


title: 20220819_Stimulated PBMCs, lane 2,  ATAC-derived cDNA

description: 10x Genomics

value: ATAC


title: LEV- Animal 8


title: 20220819_Stimulated PBMCs, lane 2,  HTO-derived cDNA

description: 10x Genomics


title: CS051


title: LEV - Animal 7


title: 20220819_Stimulated PBMCs, lane 2, mRNA-derived cDNA

description: 10x Genomics


title: CS050


title: 20220819_Unstimulated PBMCs, ATAC-derived cDNA

description: 10x Genomics


title: LEV - Animal 12


title: CS049

source_name: 72h Trametinib treated BBN963 cells

value: Trametinib


title: LEV - Animal 6

value: Hippocampus


title: 20220819_Stimulated PBMCs, lane 1,  ATAC-derived cDNA

description: 10x Genomics


title: 20220819_Stimulated PBMCs, lane 1,  HTO-derived cDNA

description: 10x Genomics


title: LEV - Animal 4

value: Sprague Dawley


title: CS047


title: 20220819_Stimulated PBMCs, lane 1, mRNA-derived cDNA

description: 10x Genomics


title: LEV - Animal 3

value: LEVETIRACETAM (200 mg/kg)


title: Amplicon sequencing of COL17A1 on-target in untreated + ssODN control

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

data_processing:
Reads were analyzed using the CRISPResso2 package using the base editor output and the following settings: window of 40 around the cleavage site, quality 30, ignoring substitutions.
Assembly: hg38
Supplementary files format and content: Include the CRISPResso2 output files 'alleles frequency table' and 'nucleotide frequency table'
Library strategy: Amplicon sequencing

source_name: Keratinocytes

growth_protocol: Primary RDEB and JEB keratinocytes were cultivated in CNT-PRIME medium supplemented with 50 mg/mL primocin (invivoGen) and maintained at 37°C and 5% carbon dioxide in a humidified incubator.

extract_protocol:
Genomic DNA was extracted using the ReliaPrep™ Blood gDNA Miniprep System kit (Promega) according to the manufacturer’s protocol
80 ng of genomic DNA was used as a template for amplification via a 30-cycle PCR using Q5® Hot Start High-Fidelity DNA Polymerase (New England Biolabs, NEB). PCR fragments were purified using the QIAquick PCR Purification Kit (QIAGEN), subjected to Sanger sequencing (Eurofins Genomics) and analyzed using DECODR.57 Alternatively, purified PCR products were pooled and prepared for NGS using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB), and sequenced on Illumina HiSeq or NovaSeq platforms with 2× 150 bp read length (GENEWIZ, Azenta Life Sciences).
Sequencing was outsourced to service NGS provider Genewiz (part of Azenta Life Sciences) where it was performed on a Illumina NovaSeq6000 device collecting 2x150 bp paired-end reads.

treatment_protocol: Electroporation of RNPs into keratinocytes was performed using the Neon transfection system (Thermo Fisher Scientific) under the following conditions: 1,400 Volt, 20 ms, 2 pulses. 250,000 cells were treated with Alt-R™ SpCas9 Nuclease V3 or Alt-R™ SpCas9 D10A Nickase V3 (IDT) together with the gRNA (IDT) at a ratio of 4:1 (3µg + 750ng). 250 ng of ssODN were added to the electroporation reaction

value: Keratinocytes

value: Patient-derived keratinocytes

value: PCR-derived amplicons from gDNA

value: COL17A1, homozygous c.3899_3900delCT

value: non-treated+ssODN


title: Amplicon sequencing of COL17A1 on-target in Cas9n-g3+4+ssODN treated sample


title: CS052

value: cell line


title: LEV - Animal 1


title: CS045

value: basal bladder cancer urothelial cells


title: PB - Animal 14

value: PHENOBARBITAL (75 mg/kg)


title: Amplicon sequencing of COL7A1 on-target in untreated+ssODN control

value: RDEB223, homozygous c.425A>G


title: CS044

source_name: 72h Rosiglitazone treated BBN963 cells

value: C57bl/6 WT

value: Rosiglitazone


title: CS043


title: PB - Animal 13


title: CS042


title: Amplicon sequencing of COL7A1 on-target in Cas9n-g1+2+ssODN treated sample


title: LEV - Animal 5


title: CS048


title: Amplicon sequencing of COL7A1 on-target in Cas9-g2+ssODN treated sample


title: PB - Animal 12


title: CS041


title: Amplicon sequencing of COL7A1 on-target in Cas9-g1+ssODN treated sample


title: CS040


title: PB - Animal 11


title: CS046


title: LEV - Animal 2


title: PB - Animal 10


title: CS039

source_name: 72h DMSO control BBN963 cells

value: DMSO


title: PB- Animal 9


title: HSC, shZNF469_3

city: Pathumwan

first: Archittapon

last: Nokkeaw

state: Bangkok

address: Padtayapatana Building, 1873, Henri Dunant Road

department: Biochemistry

country: Thailand

institute: Chulalongkorn university, faculty of medicine

data_processing:
The acquisition of clean data was achieved by filtering and removing raw data that had adapters, low-quality data, and readings with a Q-score below 30. Subsequently, the transcriptome was assembled using StringTie (V2.2.1), and the clean reads were mapped to the human-specific genome GRCH38 using HISAT2 software (V2.0.4). The DESeq2 R software (V1.38.3) was utilized to conduct differential expression analysis between two groups. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were utilized to identify gene biological function and investigate signaling networks.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

source_name: Primary hepatic stellate cell

growth_protocol: Human HSCs (lot #27742) were obtained from ScienCellTM Research Laboratories (San Diego, CA, United States) and grown in culture medium (SteCM; catalog #5301) supplemented with growth factors provided by the manufacturer.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepare using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

value: Primary hepatic stellate cell

value: Stromal cells

value: ZNF469 knockdown


title: CS038


title: HSC, shZNF469_1


title: CS037


title: PB- Animal 8

value: Hippocampus

value: Sprague Dawley


title: HSC, shControl_3

value: WT


title: HSC, shControl_2


title: PB - Animal 6


title: PB - Animal 5


title: CX053

source_name: 5 days Rosiglitazone+Trametinibtreated bladder tumor tissue

value: tissue

value: Rosiglitazone+Trametinib

value: 5 days


title: 22Rv1-AUR-3

city: Ann Arbor

first: Arul

last: Chinnaiyan

state: MI

address: 1500 East Medical Center Dr

department: MCTP

institute: University of Michigan

data_processing:
The FASTQ sequence data from whole exome libraries were initially aligned to the GRCh38 reference genome using Novoalign, followed by transformation into BAM files with the aid of SAMtools.
The primary somatic call-set was generated using Strelka based on specific selection criteria: allele frequency exceeding 0.05 in the “22RV1 AUR treated samples”, allele frequency less than 0.01 in the normalized data, a minimum of five variant reads, normal depth surpassing 50, and Somatic Evidence Score (EVS) over the 90th percentile of the overall EVS distribution.
These detected signals were further enhanced by mutations confidently identified by VarDict in genes that are repeatedly mutated in prostate cell lines 22RV1
Visual representation of mutation calls was facilitated using cBioPortal.
Assembly: hg38
Supplementary files format and content: csv file with the filtered somatic mutation calls
Library strategy: whole exome seq

source_name: prostate

growth_protocol: Cells were cultured in ATCC-formulated RPMI with 10% FBS and penicillin.streptomycin

extract_protocol: 1–3 μg of genomic DNA was sheared using a Covaris S2 to a peak target size of 250 base pairs (bp). Fragmented DNA was concentrated using AMPure beads, followed by end-repair, A-base addition, ligation of the Illumina indexed adapters, and size selection on 3% Nusieve agarose gels (Lonza). Fragments between 300 to 350 bp were recovered, amplified using Illumina index primers, and purified by AMPure beads. One microgram of the library was hybridized to the Agilent SureSelect Human All Exon v.4. The targeted exon fragments were captured and enriched following the manufacturer’s protocol (Agilent). Paired-end whole-exome libraries were analysed by an Agilent 2100 Bioanalyzer and DNA 1000 reagents and sequenced using an Illumina Nova 6000 (Illumina).

treatment_protocol: Cell were treated with AU-15330 dissolved in DMSO at 1uM and accquired resistance to AU-15330.

value: prostate


title: HSC, shControl_1


title: PB - Animal 4


title: 22Rv1 WT


title: CX050


title: CX052


title: 22Rv1-AUR-1


title: HSC, shZNF469_2


title: 22Rv1-AUR-2


title: CX049


title: 22Rv1_AUR3_rep2

data_processing:
Files were first processed using FastQC for quality check then run through kallisto quant.
Individual samples were combined into one TPM table using tidyverse in R and the hg38 transcript to gene key. R package edgeR was then used to generate the cpm table.
Additional downstream analysis was performed in R using packages limma, edgeR, gsea.
Assembly: hg38
Supplementary files format and content: A single combined CPM table in csv format has been generated for all samples.

extract_protocol: Riboerase was selected for WT and AUR2 samples. WT exp2, AUR3 samples were selected PolyA +RNA isolation, cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA protocol (Illumina). Libraries were size selected for 250–300 bp cDNA fragments on a 3% Nusieve 3:1 (Lonza) gel, recovered using QIAEX II reagents (QIAGEN), and PCR amplified using Phusion DNA polymerase (New England Biolabs). Library quality was measured on an Agilent 2100 Bioanalyzer for product size and concentration. Paired-end libraries were sequenced with the Illumina X, (2×100 nucleotide read length) with sequence coverage to 15-20M paired reads.


title: PB - Animal 1


title: Vehicle treated - Animal 14

value: VEHICLE


title: CX059

source_name: 5 days vehicle treated bladder tumor tissue

value: basal bladder cancer urothelial cells

value: 0.5% hydroxypropyl methylcellulose and 0.2% Tween 80 in distilled water and 0.7% DMSO


title: CX057


title: Vehicle treated - Animal 13


title: PB - Animal 7

value: PHENOBARBITAL (75 mg/kg)


title: 22Rv1_AUR3_rep1


title: CS036

value: cell line

value: C57bl/6 WT


title: CS035

value: DMSO


title: 22Rv1_WT_exp2_rep2


title: CX056


title: CX025

source_name: No BBN WT


title: Vehicle treated - Animal 12


title: 22Rv1_WT_exp2_rep1


title: Vehicle treated - Animal 11


title: PB - Animal 3


title: CX023


title: Vehicle treated - Animal 10


title: Vehicle treated - Animal 9


title: 22Rv1_AUR2_rep1


title: 22Rv1_AUR2_rep2


title: CX016

source_name: 1 month Rosiglitazone+Trametinibtreated bladder tumor tissue

value: 1 month


title: PB - Animal 2


title: Vehicle treated - Animal 7 - EXCLUDED


title: CX010


title: CX012


title: Vehicle treated - Animal 8


title: Vehicle treated - Animal 6


title: L642A/W161A/T159A PADI2_1

city: Rochester

first: Dominik

last: Saul

state: Minnesota

address: 200 First Street SW Rochester

institute: Mayo Clinic

data_processing:
Sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing software (version 3) and SCS data collection software (version 1.4.8)
Base calling was performed using Illumina RTA (version 1.12.4.2)
Paired-end reads from the raw RNAseq data were aligned using TopHat (version 2.0.6)
Quality control assessments were made using RSeQC software
Gene counts were generated using HTSeq software and gene annotation files were obtained from Illumina
Assembly: Genome_build: GRCm38
Supplementary files format and content: tab-delimited text files include count values for each Sample.

growth_protocol: HeLa cells (ATCC CCL-2) were grown in DMEM with 10% FBS and 100U/ml penicillin-streptomycin according to the ATCC’s recommendations

extract_protocol:
GFP-positive singlet cells and live cells were suspended in 1ml of PBS+BSA 0.05%. Cells were centrifuged at 400 rcf during 5 min at 4° in order to bring the cell concentration to 300-1000 cells/µl. Cell concentration and viability were determined by manual counting using a Neubauer chamber and staining the cells with Trypan blue. Cells were partitioned into Gel Bead-In-Emulsions (GEMs) by using the Chromium Controller system (10X Genomics), with a target recovery of 5000 total cells per sample.
NovaSeq 6000 using the following sequencing conditions: 28 bp (Read 1) + 10 bp (i7 index) + 10 bp (i5 index) + 90 bp (Read 2), to obtain approximately 20-30.000 reads per cell.

value: HeLa


title: 22Rv1_WT_rep1


title: Vehicle treated - Animal 5


title: PADI2 WT2

value: wild type


title: CX021

source_name: 1 month vehicle treated bladder tumor tissue


title: Vehicle treated - Animal 4

value: Hippocampus


title: CX009


title: Vehicle treated - Animal 3

value: Sprague Dawley


title: OT1 T cells sorted from B16-OVA tumor treated with rVSV-LCMVG, Replicate 3

description:
Singleron Matrix GEXSCOPE
VSVgp_OT1_3


title: CX024

value: WT


title: CX020

value: tissue


title: PADI2 WT1


title: Vehicle treated - Animal 2


title: Dasatinib+Ibruinib3 treated CNS-infiltrating cells

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1E

department: School of Medicine, Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
salmon.merged.gene_counts_scaled.tsv
DASAIBR3

data_processing:
Sequencing data was processed using nf-core/rna-seq pipeline (version 3.8) (45). Briefly, read quality was assessed by FastQC and MultiQC. Reads were first trimmed to remove adapter sequences and poor-quality reads were removed with TrimGalore.
Filtered reads were then aligned to the Mouse genome (mm10) using STAR and read counts per gene were quantified using Salmon and post-processed with SAMtools and picard MarkDuplicates.
The differential gene expression analysis was performed with the limma + voom pipeline (v. 3.16). Genes were filtered by using edgeR package filterByExpr function removing low count genes across all the libraries and keeping as many genes as possible with significant counts. Filtered counts were transformed to log2-counts per million (log-CPM) with voom function in limma package. Differential gene expression analysis was performed by using limma package for linear model fitting (lmFit), making comparisons of interest (contrast.fit), and computing standard errors and t-statistics (eBayes) (46). The significance threshold was set to adjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: bigWig RNA-seq signal files, separately for plus and minus strand
Supplementary files format and content: tab-delimited text file includes scaled and bias corrected count matrix for each sample

source_name: 159 mouse cell subline

growth_protocol: RPM1 1640 Medium supplemented with 10% fetal bovine serum und 1 % Penicilin/Streptomicin/Glutamine

extract_protocol:
RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s instructions
Truseq stranded mRNA kit (Illumina), Ligation with Ribo-Zero Plus kit.

treatment_protocol: Vehicle vs Dasatinib, Ibrutinib, Dasatinib+Ibrutinib

value: 159 mouse cell subline

value: CNS-infiltrating E2A-PBX1+/preBCR+ ALL cells

value: dasatinb+ibrutinib

tag: replicate

value: replicate 3


title: 22Rv1_WT_rep2


title: Dasatinib+Ibruinib2 treated CNS-infiltrating cells

description:
salmon.merged.gene_counts_scaled.tsv
DASAIBR2

value: replicate 2


title: Vehicle treated - Animal 1

value: VEHICLE


title: Ibruinib3 treated CNS-infiltrating cells

description:
salmon.merged.gene_counts_scaled.tsv
IBR3

value: ibrutinib


title: Dasatinib+Ibruinib1 treated CNS-infiltrating cells

description:
salmon.merged.gene_counts_scaled.tsv
DASAIBR1

value: replicate 1


title: Seedlings, 3d at 4°C, replicate 3

city: Berlin

first: Lea

middle: Andree Charlotte

last: Faivre

state: Berlin

address: Königin Luise Str. 12-16

department: Biologie, Chemistry, Pharmacy

institute: Freie Universitaet Berlin

data_processing:
The reads were mapped to the reference genome of Arabidopsis thaliana (TAIR10) using STAR (Dobin et al., 2013), using a minimum and maximum intron size of 60 and 6000 bases respectively.
The counting was performed using featureCounts (Liao, Smyth and Shi, 2014), using only reads with an alignment score superior to 10
Assembly: TAIR10
Supplementary files format and content: text file containing the raw counts for each protein-coding gene from FeatureCount

organism: Arabidopsis thaliana

source_name: Whole seedlings

growth_protocol: Arabidopsis thaliana plants were grown for 21 days in short days (8h light, 16h dark) at 20°C, on 1/2MS plates with 1.5% agar.

extract_protocol:
RNA was extracted from 100mg of seedlings using the innuPREP plant RNA kit (Analytik Jena)
mRNA library was prepared using polyA enrichment and the NEBnext Ultra RNA Library Prep Kit producing unstranded data.

treatment_protocol: Plants were cold treated at 4°C in short day conditions for 3h or 3d.

value: Whole seedlings

value: Wild type

tag: condition

value: 4degree C


title: Ibruinib2 treated CNS-infiltrating cells

description:
salmon.merged.gene_counts_scaled.tsv
IBR2


title: L642A/W161A/T159A PADI2_2

value: HeLa


title: Seedlings, Naive, replicate 3

tag: tissue

value: Control


title: Seedlings, 3d at 4°C, replicate 2


title: Seedlings, 3h at 4°C, replicate 2


title: Ibruinib1 treated CNS-infiltrating cells

description:
salmon.merged.gene_counts_scaled.tsv
IBR1


title: Dasatinib3 treated CNS-infiltrating cells

description:
salmon.merged.gene_counts_scaled.tsv
DASA3

value: dasatinib


title: Seedlings, Naive, replicate 2


title: Seedlings, 3d at 4°C, replicate 1


title: Dasatinib2 treated CNS-infiltrating cells

description:
salmon.merged.gene_counts_scaled.tsv
DASA2


title: Seedlings, 3h at 4°C, replicate 1


title: Dasatinib1 treated CNS-infiltrating cells

description:
salmon.merged.gene_counts_scaled.tsv
DASA1


title: Vehicle2 treated CNS-infiltrating cells

description:
salmon.merged.gene_counts_scaled.tsv
CNT2

value: vehicle


title: Vehicle3 treated CNS-infiltrating cells

description:
salmon.merged.gene_counts_scaled.tsv
CNT3


title: Seedlings, Naive, replicate 1


title: BCR-ABLT315I-bio repl 3

city: Beirut

first: Margret

last: Shirinian

address: Bliss street

country: Lebanon

institute: American University of Beirut

description: RNA-seq

data_processing:
Quality check for raw sequencing reads was performed using FastQC v0.11.8
RNA-seq reads were aligned to dm6 genome assembly using hisat2 v2.1.0 with parameters --rna-strandness RF --dta --max-intronlen 300000
RNA-seq featurecounts matrix was generated using featureCounts v2.0.1 from SubRead package
Assembly: dm6
Supplementary files format and content: processed data files include featureCounts file

organism: Drosophila melanogaster

source_name: Hemocytes

growth_protocol: Flies were maintained on standard cornmeal-agar medium at room temperature at 18˚C for maintenance and 25°C for experiments.

extract_protocol:
For RNA-seq samples, 300 larvae were bled in 240-300 µl PBS then put in 700-760 µl of Trizol (TRI reagent, Sigma Aldrich). RNA was extracted using the TRI Reagent (Sigma-Aldrich). Three different biological replicates (N=3) with 300 third-instar larvae for each replicate were used for RNA-seq (900 larvae total) in the following conditions: W1118 (control), BCR-ABLp210 and BCR-ABLT315I. Samples were sent to Macrogen (Seoul, South Korea) for RNA-Seq analysis.
Illumina TruSeq stranded total RNA with ribo-zero

value: Hemocytes

tag: developmental stage

value: Third instar larvae


title: BCR-ABLT315I-bio repl 2

description: RNA-seq

tag: cell type


title: Vehicle1 treated CNS-infiltrating cells

description:
salmon.merged.gene_counts_scaled.tsv
CNT1

value: 159 mouse cell subline

tag: genotype


title: Seedlings, 3h at 4°C, replicate 3


title: BCR-ABLp210-bio repl 3

description: RNA-seq


title: e9d_1401_2

city: Cambridge

first: Thulasi

last: Warrier

state: MA

address: 415 Main Street

department: IDMP

institute: Broad Institute

data_processing:
BWA to align reads to reference and read counts generated using custom scripts.
DESeq2 (1.28.1) package in R was used to obtain fold changes in gene expression across multiple conditions
Assembly: NC_0088463.1 (UCBPP-PA14)
Supplementary files format and content: comma separated file with counts for each sample for each gene

organism: Pseudomonas aeruginosa UCBPP-PA14

source_name: bacterial cell

growth_protocol: Bacterial cultures were inoculated from glycerol stocks, grown overnight with appropriate selection antibiotics at 37ºC with shaking and sub-cultured at 37ºC with shaking until log-phase growth. Cultures were diluted to an OD600nm of 0.2-0.4.

extract_protocol:
At the end of the incubation period, samples were mixed with 30uL of 3X RNAgem Blue Buffer (Zygem, Charlottesville VA), and chemically lysed by incubation in a thermocycler at 75°C for 10 minutes. Total RNA was then extracted using the Direct-zol kit (Zymo Research, Irvin CA), and RNA quality and quantity were analyzed using the RNA ScreenTape with the 2200 TapeStation (Agilent, Santa Clara CA).
RNA-Seq libraries were prepared using the RNA TagSeq protocol previously described (Shishkin, A. et al. Nature methods. 2015. https://doi.org/10.1038/nmeth.3313)

treatment_protocol: LB medium with appropriate drugs such as BRD1401 or inducers such as arabinose was prepared at 2X final concentration and dispensed into 384 well plates. Diluted bacterial suspensions were added on top to achieve a final bacterial density of 0.1-0.2 OD600nm and incubated at 37ºC for 120 minutes. Three biological replicates were included.

value: {delta}oprL-MW cB

value: bacterial cell

tag: treatment


title: e9d_1401_3

value: replicate 3


title: BCR-ABLp210-bio repl 2

description: RNA-seq


title: BCR-ABLp210-bio repl 1

description: RNA-seq


title: e9d_1401_1


title: e10b_1401_1

value: {delta}oprL-MW cD


title: e10b_1401_2

value: replicate 2


title: e10b_1401_3


title: Control -bio repl 2

description: RNA-seq

value: W1118 Control


title: Control -bio repl 1

description: RNA-seq


title: Control -bio repl 3

description: RNA-seq


title: pa14_1401_1

value: replicate 1


title: pa14_1401_3


title: pa14_1401_2


title: d50630_1401_2


title: HH > UQCR-C1, 120 h AEL + infection, rep 2

city: Tampere

first: Laura

last: Vesala

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

institute: Tampere University

data_processing:
Sequence alignment was done STAR aligner, version "STAR-2.7.10a"
Gene annotations were obtained from Ensembl database and annotated data files were created using R library Rsubread
R libraries edgeR and limma were used to obtain counts per million base pairs (CPMs) for each gene, make comparisons between sample groups and create differentially expressed gene lists
Genes that were lowly expressed (less than 10 reads in total per sample group) were discarded
Assembly: dm6
Supplementary files format and content: Text file containing normalized read counts for genes in all samples (CPMs)

source_name: hemocytes

growth_protocol: Drosophila larvae were grown from egg to 3rd instar larvae at 29°C

extract_protocol:
RNA was extracted using  Norgen single Cell RNA purification kit (Norgen Biotek Corp, Ontario, Canada) including a DNase treatment (RNase free Dnase I kit, Norgen).
Illumina Stranded mRNA Library Preparation, Illumina (1000000124518)

treatment_protocol: Hemolymph was released by dissecting larvae open in drops of ice-cold 1xPBS. Samples were kept on ice, centrifuged 7 min at 2500g at +4°C to spin the hemocytes down. After centrifuging, excess plasma was pipetted off and hemocytes frozen at -80°C

value: hemocytes

value: KD_48 hours after Leptopilina boulardi strain G486 infection


title: d50630_1401_3


title: HH > UQCR-C1, 120 h AEL + infection, rep 1


title: HH > UQCR-C1, 120 h AEL + infection, rep 3


title: d50630_1401_1


title: HH x w1118, 120 h AEL + infection, rep 3

value: WT_48 hours after Leptopilina boulardi strain G486 infection


title: HH x w1118, 120 h AEL + infection, rep 2


title: BCR-ABLT315I-bio repl 1

description: RNA-seq


title: bep.hypo_1401_3

value: oprL-hypomorph


title: HH x w1118, 120 h AEL + infection, rep 1


title: HH > UQCR-C1, 120 h AEL, rep 2


title: bep.hypo_1401_2


title: HH > UQCR-C1, 120 h AEL, rep 3


title: bep.hypo_1401_1


title: e9d_dmso_3


title: HH > UQCR-C1, 120 h AEL, rep 1


title: HH x w1118, 120 h AEL, rep 3


title: e9d_dmso_2


title: HH > UQCR-C1, 90 h AEL, rep 3


title: e9d_dmso_1


title: HH x w1118, 120 h AEL, rep 2


title: e10b_dmso_2


title: pa14_dmso_3


title: HH > UQCR-C1, 90 h AEL, rep 1


title: pa14_dmso_2


title: HH x w1118, 90 h AEL, rep 3


title: pa14_dmso_1


title: HH x w1118, 90 h AEL, rep 2


title: HH x w1118, 90 h AEL, rep 1


title: d50630_dmso_3


title: vaccinated+SVCV, scRNAseq Kidney leukocyte

city: Hangzhou

first: Chongbin

last: Hu

state: Zhejiang Province

address: 866 Yuhangtang Rd

department: College of Life Sciences

institute: Zhejiang University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney

extract_protocol:
Leukocytes were collected from the kidney samples through Ficoll-Hypaque (1.080 g/mL) density-gradient centrifugation. Briefly, zebrafish were anesthetized by MS222 after 7 days of SVCV challenge. The kidney was carefully excised and transferred through a 40 μm stainless nylon mesh (Greiner Bio-OneGmbH, Germany). The cell suspension was suspended in Leibovitz's L-15 Medium (L-15, Gibco) supplemented with penicillin (100 U/ml, Sigma-Aldrich), streptomycin (100 μg/ml, Sigma-Aldrich) and heparin sodium (10 U/ml, Sigma-Aldrich). The cell suspension was slowly added into a Ficoll-Hypaque (1.080 g/mL) density-gradient centrifugation, centrifuged at 1,200 g for 25 min, and the cell layer of the interface was carefully aspirated and then washed with ice-cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue (Sigma, St. Louis, MO, USA), which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: leukocyte

value: Kidney

value: AB

tag: age

value: 5-7 weeks old

tag: agent

value: vaccinated+SVCV


title: SVCV, scRNAseq Kidney leukocyte

description: 10x Genomics

tag: strain

value: SVCV


title: d50630_dmso_1


title: PBS, scRNAseq Kidney leukocyte

description: 10x Genomics

value: PBS


title: d50630_dmso_2

value: bacterial cell


title: HH x w1118, 120 h AEL, rep 1


title: bep.hypo_dmso_3

value: replicate 3


title: e10b_dmso_3

value: {delta}oprL-MW cD


title: HH > UQCR-C1, 90 h AEL, rep 2


title: brd1401r.e10b.c1.3

description: replicate 3

source_name: Pseudomonas aeruginosa UCBPP-PA14

treatment_protocol: LB medium with appropriate drugs such as BRD1401 or inducers such as arabinose was prepared at 2X final concentration and dispensed into 384 well plates. Diluted bacterial suspensions were added on top to achieve a final bacterial density of 0.1-0.2 OD600nm and incubated at 37ºC for 90 minutes. Three biological replicates were included.

value: oprL-MW cD 1401R1

value: Pseudomonas aeruginosa UCBPP-PA14

value: 0.5percent NaCl + 0.5percent DMSO


title: bep.hypo_dmso_1

value: replicate 1


title: hPASMCs, shSMN_1st

city: Wuhan

first: muqing

last: yu

address: 1095 Jiefang Avenue

department: Department of Respiratory and Critical Care Medicine, Tongji Hospital

institute: Huazhong University of Science and Technology

data_processing:
FASTX-Toolkit (Version 0.0.13)
Raw reads were filtered to discarded which contained more than 2-N bases, adaptors and low-quality bases
clean reads were aligned to the GRch38 genome using tophat2 allowing 4 mismatches
Uniquely mapped reads were used for gene reads number counting and FPKM calculation
Assembly: hg18
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Human pulmonary artery

growth_protocol: The hPASMCs were cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum, 100 µg/mL streptomycin, and 100 U/mL penicillin at 37℃.

extract_protocol:
The transfected cells were collected after 48h for subsequent experiments.
Total RNA of HPASMCs was extracted with Trizol (Ambion, USA).
RNA libraries for RNA-seq were prepared using a cDNA synthesis kit (Abcolnal, China).

treatment_protocol: The shRNA contained the control sequence or SMN knock-down sequence were transfected to hPASMCs.

value: Human pulmonary artery

value: Human primary pulmonary artery smooth muscle cells

value: SMN knockdown


title: brd1401r.e10b.c1.1

description: replicate 1


title: hPASMCs, shCtrl_3rd

value: WT


title: hPASMCs, shSMN_2nd


title: hPASMCs, shCtrl_2nd


title: hPASMCs, shCtrl_1st


title: hPASMCs, shSMN_3rd


title: brd1401r.e10b.c1.2

description: replicate 2


title: e10b_dmso_1


title: x7a2.5c.0.063parab.125umbrd1401.3

description: replicate 3

value: oprL-knockdown

value: 0.5percent NaCl + 125 microM BRD1401 + 0.0625percent arabinose


title: x7a2.5c.0.063parab.125umbrd1401.2

description: replicate 2


title: x7a2.5c.0.063parab.125umbrd1401.1

description: replicate 1


title: SNF2KO_mESC_TrAEL-seq_2

first: Sarah

last: Inglesfield

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

data_processing:
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated taking UMIs as well as mapping position into account, using UmiBam (v0.2.0; https://github.com/FelixKrueger/Umi-Grinder).
Samples were imported into Seqmonk v1.47, truncated to a single base and polarity calculated in 100kb windows in 25kb steps as (%reverse reads/total reads)-50. Polarity indicates replication fork direction
Assembly: GRCm38
Supplementary files format and content: Tab delimited text file. Contains the %tage read polarity in each 100kb window
Library strategy: TrAEL-seq

growth_protocol: Dulbeco’s modified eagle medium (invitrogen) supplemented with 15% FCS (Invitrogen), L-Glutamine (Gibco), NEAs (Gibco), B-mercaptoethanol (Sigma) and LIF and cultured on plates coated with 0.2% gelatinous (Sigma).

extract_protocol:
1x106 cells were washed once in 5 ml L buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl) and resuspended in 60 µl L buffer in a 2 ml tube. Samples were heated to 50°C for 2-3 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl digestion buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl, 1% sodium N-lauroyl sarcosine, 0.1 mg/ml Proteinase K) and incubated overnight at 50°. Plugs were rinsed with 1 ml TE, then washed three times with 1 ml TE for 1-2 hours at room temperature with rocking, 10 mM PMSF was added to the second and third washes from 100 mM stock (Merck 93482). Plugs were then digested 1 h at 37°C with 1 µl 1000 U/ml RNase T1 (Thermo EN0541) in 200 µl TE.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined.An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA chip (Agilent 5067-4626). Ideal cycle number should bring final library to final concentration of 1-3 nM, noting that the final library will be 3 cycles more concentrated than the test anyway. 21 µl of library was then amplified with 2 µl each of NEBNext Universal and chosen Index primer and 25 µl NEBNext Ultra II Q5 PCR master mix using same conditions as above for calculated cycle number. Amplified library was cleaned with 40 µl AMPure XP beads (Beckman A63881) and eluted with 26 µl 0.1x TE, then 25 µl of this was again purified with 20µl AMPure XP beads and eluted with 11µl 0.1x TE.

tag: cell line

value: embryonic stem cell


title: SNF2KO_mESC_TrAEL-seq_1


title: brd1401r.bephypo.c11.3

description: replicate 3

value: oprL-hypomorph 1401R11


title: mESC_TrAEL-seq_2

value: wildtype


title: brd1401r.bephypo.c11.2

description: replicate 2


title: bep.hypo_dmso_2

value: oprL-hypomorph

value: replicate 2


title: mESC_TrAEL-seq_1


title: Amplicon sequencing of untreated control [Amp-LAMA3-UT]

description:
PCR-derived amplicons from gDNA
non-treated control, ON and OT1

data_processing:
Reads were analyzed using the CRISPResso2 package with the following settings: window of 20 around the cleavage site, quality 30, ignoring substitutions. For double nickase-edited samples, a window of 40 was set around the middle of the two cleavage sites. In one case (Figure 3D, OT1*), insertions were ignored due to a minor amplification of an unspecific fragment. Significance was determined using CRISPResso Compare.
Assembly: hg38
Supplementary files format and content: tab-delimited text file output from Crispresso.
Library strategy: Amplicon-Seq

source_name: Patient-derived keratinocytes

treatment_protocol: Electroporation of RNPs into keratinocytes was performed using the Neon transfection system (Thermo Fisher Scientific) under the following conditions: 1,400 Volt, 20 ms, 2 pulses. 250,000 cells were treated with Alt-R™ SpCas9 Nuclease V3 or Alt-R™ SpCas9 D10A Nickase V3 (IDT) together with the gRNA (IDT) at a ratio of 4:1 (3µg + 750ng).

value: Patient-derived keratinocytes

value: LAMA3, homozygous c.466_467delCA

value: non-treated


title: brd1401r.bephypo.c11.1

description: replicate 1

value: Pseudomonas aeruginosa UCBPP-PA14


title: Amplicon sequencing of on- and off-targets on sample treated with Cas9 double nickase [Amp-LAMA3-Cas9n-g6]

description:
PCR-derived amplicons from gDNA
pooled amplicons ON


title: Amplicon sequencing of on- and off-targets on sample treated with Cas9 double nickase [Amp-LAMA3-Cas9n-g5]

description:
PCR-derived amplicons from gDNA
pooled amplicons ON and OT1


title: x7a2.5c.0.063parab.3

description: replicate 3

value: 0.5percent NaCl + 0.5percent DMSO + 0.0625percent arabinose


title: Heart, Rest_2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides.
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.10a  Aligned reads were filtered to remove  ribosomal reads.
Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes . The raw count matrix was normalized with DESeq2 version 1.30.1.
Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data (Activities at the Universal Protein Resource (UniProt)).
Assembly: mm10
Supplementary files format and content: library-size normalized counts

source_name: heart

extract_protocol:
Mitochondria and remaining tissue fraction were isolated as previosly described (10.1007/978-1-4939-2257-4_11). RNA was isolated using the TRIzol in combination with RNeasy Mini Kit (Qiagen # 217004) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen #79254) according to manufacturer’s instruction.
10ng of total RNA was used as input for Pico Input Mammalian (Takara Bio)

value: heart

value: tissue minus mitochondria


title: Heart, Rest_1


title: x7a2.5c.0.063parab.2

description: replicate 2


title: Amplicon sequencing of on- and off-targets on sample treated with Cas9 double nickase [Amp-LAMA3-Cas9n-g5+6]


title: Amplicon sequencing of on- and off-targets on sample treated with Cas9 nuclease [Amp-LAMA3-Cas9-g6]

description:
PCR-derived amplicons from gDNA
pooled amplicons ON; non-treated control for Amp-COL17A1


title: x7a2.5c.0.063parab.1

description: replicate 1


title: K27 p300 KD-1

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
The raw sequences are aligned to the GRCm38 reference genome, then duplicates are removed using Picard. After removing duplicates, the reads that are mapped to the blacklist region from UCSC are filtered. Then bedGraph was generated using the deepTools.
Assembly: GRCm38
Supplementary files format and content: gzipped bedGraph file from deepTools

source_name: Flow cytometry sorted astrocytes

extract_protocol:
Each CNS was isolated per mouse. A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, and washed in PBS. Cells were sorted by flow cytometry based on a negative selection strategy for astrocytes.
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).

tag: Sex

value: Female

tag: disease

value: induced EAE

value: astrocytes


title: brd1401r.bephypo.c10.3

description: replicate 3

value: oprL-hypomorph 1401R10

value: 0.5percent NaCl + 0.5percent DMSO


title: brd1401r.bephypo.c10.2

description: replicate 2


title: Amplicon sequencing of untreated control [Amp-COL17A1-UT]

description:
PCR-derived amplicons from gDNA
non-treated control, ON and OT1-4, OT1

value: COL17A1, homozygous c.3899_3900delCT


title: Amplicon sequencing of on- and off-targets on sample treated with Cas9 single nickase [Amp-COL17A1-Cas9n-g4]

description:
PCR-derived amplicons from gDNA
pooled amplicons ON and OT 1


title: Amplicon sequencing of on- and off-targets on sample treated with Cas9 nuclease [Amp-LAMA3-Cas9-g5]


title: TX31

city: New York

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming
Pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Mouse:GRCm38.p6) using kallisto (0.44.0)
Assembly: mm10
Supplementary files format and content: excel file with DESeq2 output

source_name: 72h Rosiglitazone+Tramtinib treated BBN963 cells

value: cell line

value: basal bladder cancer urothelial cells

value: C57bl/6 WT

value: Rosiglitazone+Trametinib


title: TX32


title: Amplicon sequencing of on- and off-targets on sample treated with Cas9 single nickase [Amp-COL17A1-Cas9n-g3]

description:
PCR-derived amplicons from gDNA
pooled amplicons ON and OT 1-4

value: Patient-derived keratinocytes


title: TX30


title: brd1401r.bephypo.c10.1

description: replicate 1


title: x7a2.5c.0.5parab.125umbrd1401.3

description: replicate 3

value: oprL-knockdown

value: 0.5percent NaCl + 125 microM BRD1401 + 0.5percent arabinose


title: x7a2.5c.0.5parab.125umbrd1401.2

description: replicate 2

value: Pseudomonas aeruginosa UCBPP-PA14


title: TX29


title: Amplicon sequencing of on- and off-targets on sample treated with Cas9 nuclease [Amp-COL17A1-Cas9-g4]


title: Amplicon sequencing of on- and off-targets on sample treated with Cas9 double nickase [Amp-COL17A1-Cas9n-g3+4]

description:
PCR-derived amplicons from gDNA
pooled amplicons ON and OT1-4, OT1


title: TX16

source_name: 24h Rosiglitazone+Tramtinib treated BBN963 cells


title: x7a2.5c.0.5parab.125umbrd1401.1

description: replicate 1


title: Heart, Mito_2

value: WT

value: isolated mitochondria


title: Heart, Mito_1

value: heart


title: TX14


title: brd1401r.bephypo.c9.3

description: replicate 3

value: oprL-hypomorph 1401R9


title: Amplicon sequencing of on- and off-targets on sample treated with Cas9 nuclease [Amp-COL17A1-Cas9-g3]


title: Seedling, 3d at 4°C, H3K27me3, replicate 2

data_processing:
The reads were mapped to the TAIR10 reference genome of Arabidopsis thaliana using Bowtie2
PCR duplicates and reads with an aligment quality MAPQ < 10 were removed using samtools rmdup and samtools view
peak calling was performed using MACS2, using the broad option and a p-value threshold of 0.01
Bigwig tracks were generated by pooling the two replicates and normalizing as RPKM using DeepTools bamCoverage, using a bin size of 10bp
Assembly: TAIR10
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak (except for input samples)

extract_protocol:
For each replicate, 1g of seedlings was crosslinked with PFA and chromatin was extracted as described in Vyse et al. (2020). The chromatin was immunoprecipitated using 1 μg of α-H3K27me3 (C15410195 Diagenode) or α-H3K4me3 (C15410003, Diagenode).
DNA was purified and concentrated using the ChIP DNA Clean and Concentrator lit (Zymo Research). The libraries were prepared using the ThruPLEX DNA-seq kit (Takara Bio) and indexes from the SMARTer DNA HT Dual Index kit (Takara Bio). DNA fragments were then selected based on size using AMPure beds (Beckman Coulter). The concentration of the samples was measured using the Qubit dsDNA High Sensitivity kit and the Qubit Fluorometer (ThermoFisher Scientific) and the library quality was assessed using the High Sensitivity DNA ScreenTape and the TapeStation (Agilent).

value: Whole seedlings

value: Wild type

value: 4degree C

tag: antibody

value: H3K27me3 (C15410195 Diagenode)


title: Seedling, 3d at 4°C, H3K4me3, replicate 2

value: H3K4me3 (C15410003, Diagenode)


title: TX13

extract_protocol:
RNA was extracted with Qiagen miRNeasy micro kit
Poly-A pull-down was used to enrich mRNAs from total RNA samples before library construction using Illumina TruSeq chemistry.

value: cell line


title: Amplicon sequencing of on- and off-targets on sample treated with Cas9 single nickase [Amp-COL7A1-Cas9n-g2]

extract_protocol:
Genomic DNA was extracted using the ReliaPrep™ Blood gDNA Miniprep System kit (Promega) according to the manufacturer’s protocol
80 ng of genomic DNA was used as a template for amplification via a 30-cycle PCR using Q5® Hot Start High-Fidelity DNA Polymerase (New England Biolabs, NEB). PCR fragments were purified using the QIAquick PCR Purification Kit (QIAGEN), subjected to Sanger sequencing (Eurofins Genomics) and analyzed using DECODR.57 Alternatively, purified PCR products were pooled and prepared for NGS using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB), and sequenced on Illumina HiSeq or NovaSeq platforms with 2× 150 bp read length (GENEWIZ, Azenta Life Sciences).
Sequencing was outsourced to service NGS provider Genewiz (part of Azenta Life Sciences) where it was performed on a Illumina NovaSeq6000 device collecting 2x150 bp paired-end reads.

value: RDEB223, homozygous c.425A>G


title: Seedling, 3d at 4°C, input, replicate 2


title: brd1401r.bephypo.c9.1

description: replicate 1

value: 0.5percent NaCl + 0.5percent DMSO


title: TX23

source_name: 72h ATRA treated BBN963 cells

value: basal bladder cancer urothelial cells

value: C57bl/6 WT

value: all-trans RA


title: brd1401r.bephypo.c9.2

description: replicate 2


title: Seedling, 3h at 4°C, H3K27me3, replicate 2


title: Amplicon sequencing of on- and off-targets on sample treated with Cas9 single nickase [Amp-COL7A1-Cas9n-g1]

description:
PCR-derived amplicons from gDNA
pooled amplicons ON and OT 1-18

value: Patient-derived keratinocytes


title: TX22


title: Seedling, 3h at 4°C, H3K4me3, replicate 2


title: Amplicon sequencing of on- and off-targets on sample treated with Cas9 double nickase [Amp-COL7A1-Cas9n-g1+2]


title: TX15

value: Rosiglitazone+Trametinib


title: x7a2.5c.0.5parab.3

description: replicate 3

value: oprL-knockdown

value: Pseudomonas aeruginosa UCBPP-PA14

value: 0.5percent NaCl + 0.5percent DMSO + 0.5percent arabinose


title: x7a2.5c.0.5parab.2

description: replicate 2


title: x7a2.5c.0.5parab.1

description: replicate 1


title: TX21


title: Seedling, 3h at 4°C, input, replicate 2


title: Amplicon sequencing of on- and off-targets on sample treated with Cas9 nuclease [Amp-COL7A1-Cas9-g1]


title: TX20


title: CX019

value: tissue

value: WT

value: 0.5% hydroxypropyl methylcellulose and 0.2% Tween 80 in distilled water and 0.7% DMSO

value: 1 month


title: pa14.0pnacl.3

description: replicate 3

value: 0percent NaCl + 0.5percent DMSO


title: Amplicon sequencing of on- and off-targets on sample treated with Cas9 nuclease [Amp-COL7A1-Cas9-g2]


title: TX12


title: Amplicon sequencing of untreated control [Amp-COL7A1-UT]

description:
PCR-derived amplicons from gDNA
non-treated control, ON and OT1-18

value: non-treated


title: Lama3-UT2

description:
CAST-seq derived amplicons from gDNA
used as non-treated control for Cas9-g6, D10ACas9n-g5+6

data_processing:
Mate paired reads were merged using BBmerge from BBmap (v38.76) software. BBmap  was also used for filtering and trimming as follow: merged reads containing the designer nuclease target site were filtered-in, whereas PCR mispriming products reads were filtered-out. Linker sequences, Illumina adapter sequences, targeted elongation sequence and bad quality reads were trimmed.
Selected reads were aligned to the human genome GRCh38 (hg38) using Bowtie2 (v2.3.4.2) and the very-sensitive preset parameters. Aligned reads with good mapping quality (MAPQ >15) were selected. The aligned BAM file was converted into bed file using bedtools (v2.27.1).
Translocated sites were identified using the D-CAST pipeline with default parameters, as described on https://github.com/AG-Boerries/CAST-Seq
Assembly: hg38
Supplementary files format and content: matrix table of translocation sites detected with D-CAST pipeline. It includes the genomic coordinates of translocated sites, read coverage, alignment score against gRNA, translocation event classification and nearest genes annotation.

source_name: Non-treated control CAST-seq sample for treated samples

extract_protocol:
Genomic DNA was extracted using the ReliaPrep™ Blood gDNA Miniprep System kit (Promega) according to the manufacturer’s protocol
Library construction was essentially performed as described by Turchiano et. al (Cell Stem Cell, 2021). Briefly, gDNA was fragmented by enzymatic digestion using the NEBNext® Ultra™ II FS DNA Library Prep (NEB) to obtain average fragment lengths of 350 bp. The DNA was end repaired and a protruding 3’-A nucleotide was added according to the manufacturer’s instructions  in order to enable the ligation of a linker sequence with a protruding 3’-T. After linker ligation, fragments were purified using the QIAquick PCR Purification Kit (NEB). The region of interest (on-target site) was amplified in two rounds of PCR using Q5® Hot Start High-Fidelity DNA Polymerase (NEB). PCR conditions were: 20 cycles at 95°C for 15 s, 63°C (first reaction) or 68°C (second reaction) for 20 s, 72°C for 20 s. The first reaction was performed with primers complementary to the linker sequence and to a sequence in close proximity to the on-target site (bait primer). Two decoy primers were introduced to reduce full-length amplification of the fragments which contain the on-target sequence without a chromosomal aberration event. The second PCR utilized nested primers to reduce the amount of mis-amplified fragments and to introduce a binding platform for barcoding primers. DNA fragments from the second PCR were purified using the QIAquick® PCR purification kit (Qiagen) and barcoded.
Third PCR introduced the barcoded Illumina adapter for sequencing (NEBNext® Multiplex Oligos for Illumina; Index Primers Sets 1-4). Sequencing was outsourced to service NGS provider Genewiz (part of Azenta Life Sciences) where it was performed on a Illumina NovaSeq6000 device collecting 2x150 bp paired-end reads.

value: LAMA3, homozygous c.466_467delCA


title: Seedling, Naive, H3K4me3, replicate 2

value: Whole seedlings

value: Wild type

value: Control

value: H3K4me3 (C15410003, Diagenode)


title: pa14.0pnacl.2

description: replicate 2


title: TX9

source_name: 24h ATRA treated BBN963 cells

value: cell line

value: basal bladder cancer urothelial cells

value: C57bl/6 WT

value: all-trans RA


title: pa14.0pnacl.1

description: replicate 1

value: Pseudomonas aeruginosa UCBPP-PA14


title: Lama3-UT1

description:
CAST-seq derived amplicons from gDNA
used as non-treated control for Cas9-g5

value: Patient-derived keratinocytes


title: Seedling, Naive, input, replicate 2


title: D10ACas9n-g5+6

description:
CAST-seq derived amplicons from gDNA
2 replicates

source_name: CAST-seq on sample treated with Cas9 double nickase


title: TX8


title: Seedling, 3d at 4°C, H3K27me3, replicate 1

value: 4degree C

value: H3K27me3 (C15410195 Diagenode)


title: pao1.0pnacl.3

description: replicate 3


title: Cas9-g6

source_name: CAST-seq on sample treated with Cas9 nuclease


title: TX7


title: Seedling, 3d at 4°C, H3K4me3, replicate 1

source_name: Whole seedlings


title: pao1.0pnacl.2

description: replicate 2


title: Seedling, Naive, H3K27me3, replicate 2


title: Cas9-g5


title: bep_hypo.0pnacl.3

description: replicate 3

value: oprL-hypomorph


title: TX4


title: Seedling, 3d at 4°C, input, replicate 1


title: TX5


title: D10ACas9n-g3

source_name: CAST-seq on sample treated with Cas9 single nickase

value: COL17A1, homozygous c.3899_3900delCT


title: TX19

source_name: 72h DMSO control BBN963 cells

value: DMSO


title: bep_hypo.0pnacl.1

description: replicate 1

value: 0percent NaCl + 0.5percent DMSO


title: Seedling, 3h at 4°C, H3K4me3, replicate 1


title: Seedling, 3h at 4°C, input, replicate 1


title: D10ACas9n-g3+4


title: bep_hypo.0pnacl.2

description: replicate 2


title: D10ACas9n-g4


title: COL17A1_UT1

description:
CAST-seq derived amplicons from gDNA
used as non-treated control for Cas9-g3, Cas9-g4, D10ACas9n-g3+4, D10ACas9n-g3, D10ACas9n-g4, COL17A1_UT1

value: non-treated


title: pao1.0pnacl.1

description: replicate 1


title: Cas9-g4


title: Seedling, Naive, H3K4me3, replicate 1

value: Whole seedlings


title: pa14.0.5pnacl.2

description: replicate 2

value: 0.5percent NaCl + 0.5percent DMSO


title: Cas9-g3


title: TX6


title: COL7A1_UT2

description:
CAST-seq derived amplicons from gDNA
used as non-treated control for Cas9-g2, D10ACas9n-g2

value: RDEB223, homozygous c.425A>G


title: COL7A1_UT1

description:
CAST-seq derived amplicons from gDNA
used as non-treated control for Cas9-g1, D10ACas9n-g1+2, D10ACas9n-g1


title: TX1

source_name: 24h DMSO control BBN963 cells


title: RosiTram17

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie version 1.1.2.
To create ATAC-seq coverage plots, the locations of the mapped ATAC-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: basal bladder cancer urothelial cells

extract_protocol:
Cells (3.0× 105) were lysed in RSB containing NP40, Digitonin, and Tween-20.
DNA was incubated with transposition reaction mix containing PBS, 1%Digitonin, Tween-20, andTransposase(llumina). ATAC-seq libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 100-600bp in length using HighPrep™ PCR Clean-up beads from MagBio. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: 5 days Rosiglitazone+Trametinibtreated bladder tumor tissue

value: tissue


title: D10ACas9n-g2


title: RosiTram90

value: basal bladder cancer urothelial cells


title: TX18

value: cell line

value: C57bl/6 WT


title: TX17


title: bep_hypo.0.5pnacl.2

description: replicate 2

source_name: Pseudomonas aeruginosa UCBPP-PA14

value: Pseudomonas aeruginosa UCBPP-PA14


title: bep_hypo.0.5pnacl.1

description: replicate 1


title: D10ACas9n-g1+2

value: Patient-derived keratinocytes


title: RosiTram56


title: embryo, 70h, xRay

city: Knoxville

first: Jianbin

last: Wang

address: 1311 Cumberland Avenue

institute: University of Tennessee Knoxville

data_processing:
Only read 1 (R1) files were processed. Reads containing two sequential telomeric repeats (TTAGGCTTAGGC or GCCTAAGCCTAA) were filtered from the data using an in-house Perl script
Reads were mapped to the appropriate genome with Bowtie2 (local alignment) and processed with SAMtools
For samples treated with restriction enzyme BEDTools intersect was used to remove reads mapped to restriction sites
The 5’-end position of each read was mapped, separated by strand, and normalized to ten million genome-mapped reads using BEDtools genomecov
The mapping results were converted to bigWig format using bedGraphToBigWig
To analyze new telomere addition during PDE developmental stages, END-seq reads containing two consecutive telomere repeats (filtered in step 1) were converted to the G-rich strand (TTAGGC).
Reads were mapped to the genome with Bowtie2 end-to-end alignment
Mapped reads were false-positive telomeric reads. Unmapped reads were trimmed with fastx_clipper “-v -n -l 25 -a TTAGGCTTAGGC” parameters.
Trimmed reads were mapped to the genome with bowtie2 (local alignment) and processed as described above except except the 3’-positions (the sites where new telomeres are added) rather than 5’-positions were obtained with BEDTools genomecov
Assembly: Ascaris suum ASM1343314v1, Parascaris univalens (Pu_v2)
Supplementary files format and content: bigWig file containing the 5' end of reads on the forward strand
Supplementary files format and content: bigWig file containing the 5' end of reads on the reverse strand
Supplementary files format and content: bigWig file with the 3' end of reads on the forward strand which contained two telomeric repeats (TTAGGCTTAGGC)
Supplementary files format and content: bigWig file with the 3' end of reads on the reverse strand which contained two telomeric repeats (TTAGGCTTAGGC)
Library strategy: END-seq

source_name: Embryo

extract_protocol:
Ascaris females were collected, and the fertilized embryos (0hr, 1-cell before prenuclear fusion) were harvested and processed as previously described (Wang et al. 2011, Wang et al. 2014). Ascaris 0hr samples were incubated at 30°C with constant shaking for the desired time (from 50hr to 98hr). For all molecular experiments, the eggshells were first de-coated with bleach treatment (0.4 M KOH, 2% sodium hypochlorite) for 1.5 hours at 30°C. Parascaris samples were collected as described (Simmons et al. 2023, Wang et al. 2017). Parascaris eggs were prepared similarly to Ascaris, except the incubation was carried out at 37°C and the embryonation time was shorter (10-14hr).
An adapted END-seq protocol was used (Canela et al. 2016, Wong et al. 2021). Embryos were embedded in agarose plugs. Some plugs were treated with the restriction enzymes as internal controls. Plugs were treated with exonuclease VII and exonuclease T. Blunt ends were A-tailed and capped with END-seq adaptor 1 (Canela et al. 2016). Plugs were melted and DNA was sheared to 200-300 bp with a Covaris M220 focused ultrasonicator. DNA fragments containing END-seq adaptor 1 were isolated with Dynabeads MyOne Streptavidin C1. END-seq adaptor 2 was ligated to the sheared ends of the A-tailed DNA fragments. The hairpins within the adaptors were digested with USER, and the DNA was amplified with Illumina TruSeq primers and barcodes. The following modifications were made to the END-seq protocol to capture break ends with different features. For the direct capture method, we excluded the exonuclease VII and exonuclease T treatments. For the all-END protocol, the plugs were treated with T4 polymerase (with dNTPs).

value: Embryo

value: 200Gy X-ray


title: TX3


title: Seedling, Naive, H3K27me3, replicate 1

value: Wild type

value: Control

value: H3K27me3 (C15410195 Diagenode)


title: Seedling, Naive, input, replicate 1


title: pa14.0.5pnacl.3

description: replicate 3


title: TX2

value: DMSO


title: pa14.0.5pnacl.1

description: replicate 1


title: pao1.0.5pnacl.3

description: replicate 3


title: pao1.0.5pnacl.2

description: replicate 2


title: Seedling, 3h at 4°C, H3K27me3, replicate 1

value: 4degree C


title: Veh68

value: 5 days vehicle treated bladder tumor tissue


title: bep_hypo.0.5pnacl.3

description: replicate 3

value: oprL-hypomorph

value: 0.5percent NaCl + 0.5percent DMSO


title: embryo, 70h, xRay_control

value: X-ray control


title: pao1.0.5pnacl.1

description: replicate 1


title: D10ACas9n-g1

value: RDEB223, homozygous c.425A>G


title: Cas9-g1


title: pa14.2pnacl.250umbrd1401.3

description: replicate 3

value: 2percent NaCl + 250 microM BRD1401


title: RosiTram61

value: 5 days Rosiglitazone+Trametinibtreated bladder tumor tissue

value: tissue

value: basal bladder cancer urothelial cells


title: pa14.2pnacl.250umbrd1401.2

description: replicate 2

value: Pseudomonas aeruginosa UCBPP-PA14


title: embryo, 98h, rep2

value: Embryo