title: TDP2seq_Ecoli_DNA_SPO11_YF_rep2

description: For mapping in vitro SPO11 cleavage sites, Escherichia coli genomic DNA digested by SPO11 in vitro was embedded in plugs together with wild type C57BL/6J mouse testis cells (0.5–1 million cells per plug), whose DNA acted as carrier during library preparation

data_processing:
Reads were trimmed and filtered by Trim Galore version 0.6.10 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>
Reads were mapped against the pUC19 plasmid sequence, Escherichia coli (ASM584v2), Saccharomyces cerevisiae (sacCer3) or mouse (mm10) reference sequence by bowtie2 version 2.3.5 (ref. 1) with the arguments -N 1 -X 1000. (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools version 1.19.2 with the arguments -u -f 2 -q 20 <http://www.htslib.org/>.
Reads were counted at which a nucleotide next to biotinylated adaptor DNA was mapped. Maps were analyzed using R versions 4.2.3 and 4.3.2 <http://www.r-project.org>.
Top- and bottom-strand peaks were separately called as nucleotide positions with >3,000, >10 and >15 RPM of strand-specific read counts using averaged pUC19, E. coli, and S. cerevisiae TDP2-seq data, respectively. Positions with less read counts than those located at –1 and +1 positions on top and bottom strands, respectively, were not defined as peaks because those reads could be false-positively enriched due to incomplete fill-in of 5-prime overhangs at DNA ends before adaptor ligation.
Assembly: mm10, pUC19, ASM584v2, SacCer3
Supplementary files format and content: bigWig files contain read counts at positions of DNA double-strand break ends. Reads were not normalized to RPM (reads per million mapped). Letter "F" or "R" in sample names indicates that reads were mapped on forward or reverse strand, respectively.
Supplementary files format and content: bed files contain peak locations. If only one file per experiment is submitted, peaks were determined based on average profiles of the two replicates.
Library strategy: TDP2-seq

organism: Escherichia coli

source_name: Mus musculus, Escherichia coli DNA

extract_protocol:
Testis cells from adult mice were obtained as described previously (ref. 1,2). Cells were embedded in plugs of low-melting point agarose to protect DNA from shearing. For in vitro SPO11 treated plasmid or genomic DNA samples, the treated DNA was mixed with wild type B6 (C57BL/6J) mouse testis cells right before plug formation to provide carrier DNA during library preparation. Plugs were treated with SDS, Proteinase K and RNAse as described previously (ref. 1,2). In-plug removal of covalently bound SPO11 using human TDP2 was performed as described with minor modifications (ref. 3). In brief, plugs were equilibrated in TDP2 buffer (0.05 M Tris-HCl pH 8, 0.15 M NaCl, 10 mM Mg2Cl, 0.5 mM Dithriothreitol, 30 μg/ml BSA, 2 mM ATP) and incubated with purified human TDP2 protein (490 pmol per plug, TopoGEN) at 37°C for 30 min according to the TopoGEN protocol. DNA ends were filled-in with T4 DNA polymerase (New England Biolabs) and ligated to biotinylated adaptors as described previously (ref. 1,2,4,5). To minimize the loss of small plasmid fragments through diffusion out of the plugs, the washing step after ligation of the first adaptor was reduced from overnight to 1h for samples containing plasmid DNA. After ligation to biotinylated adaptors, DNA was purified from the agarose, sheared by sonication, purified with streptavidin, ligated to second-end adaptors, amplified, and sequenced as described previously with minor modifications (ref. 1,2,4,5). For end repair after DNA shearing, NEBNext End repair Kit (New England Biolabs) was used. (ref. 1) Yamada et al., Molecular structures and mechanisms of DNA break processing in mouse meiosis. Genes Dev 34, 806-818 (2020). (ref. 2) Kim et al., Optimized methods for mapping DNA double-strand-break ends and resection tracts and application to meiotic recombination in mouse spermatocytes. bioRxiv 2024.08.10.606181; https://doi.org/10.1101/2024.08.10.606181, (2024).(ref. 3) Gittens et al., A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome. Nat Commun 10, 4846 (2019). (ref. 4) Mimitou et al., S. A global view of meiotic double-strand break end resection. Science 355, 40-45 (2017). (ref. 5) Mimitou et al., S1-seq Assay for Mapping Processed DNA Ends. Methods Enzymol 601, 309-330 (2018).
After quality control by Agilent BioAnalyzer, libraries were pooled equimolar and run on an Illumina NextSeq 1000 sequencer. A spike-in of PhiX was added to the run to increase diversity when necessary and for quality control purposes.
Reads were trimmed and filtered by Trim Galore version 0.6.10 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>.
Sequencing reads were mapped against the pUC19 plasmid sequence, Escherichia coli (ASM584v2), Saccharomyces cerevisiae (sacCer3) or mouse (mm10) reference sequence by bowtie2 version 2.3.5 (ref. 1) with the arguments -N 1 -X 1000. (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools version 1.19.2 with the arguments -u -f 2 -q 20 <http://www.htslib.org/>.
Reads were counted at which a nucleotide next to biotinylated adaptor DNA was mapped. Maps were analyzed using R versions 4.2.3 and 4.3.2 <http://www.r-project.org>.


title: WT Pancreas_Ptf1a line_repl 3

status: Public on Aug 20 2024

type: SRA

city: London

first: Christopher

middle: L

last: Pin

state: Ontario

address: 1151 Richmond St

country: Canada

institute: University of Western Ontario

description: Batch 2

library_source: transcriptomic

data_processing:
Quality check was performed using Fastqc
Reads were aligned to mouse genome mm10 and sorted by coordinate using STAR 2.7.9a
Gene counts were generated using the featureCounts function of the Subread aligner v2.0.3
Subsequent differential expression analysis was performed using the DESeq2 v1.38.3
Assembly: mm10
Supplementary files format and content: tab delimited format (txt) includes raw counts for each sample in each line (Ptf1a line and Mist1 line)
Supplementary files format and content: tab delimited format (txt) includes differentially expressed genes (DESeq2) for the KRAS samples from each line (Ptf1a line and Mist1 line) compared to their corresponding WT

molecule: total RNA

organism: Mus musculus

source_name: Pancreas

extract_protocol:
RNA was isolated from pancreatic tissue 22 days after initial TX gavage using Trizol (ThermoFisher Scientific, 15596018) and the PureLink RNA mini kit (ThermoFisher Scientific, 12183018A)
Illumina NextSeq High Output 150 cycle sequencing kit was used for library making following rRNA reduction.

tag: tissue

value: Pancreas

tag: genotype

value: WT

tag: treatment

value: Tamoxifen oral gavage


title: DMSO1

city: Shanghai

first: Minfeng

last: Shu

state: State...

address: No.131 Dongan Road II Xuhui district

country: China

institute: Fudan University

description: DMSO treatment

data_processing:
Cutadapt software was used to remove the reads that contained adaptor contamination. And After removed the low quality bases and undetermined bases ,we used HISAT2 software to map reads to the genome
The mapped reads of each sample were assembled using StringTie with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software.
After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM.
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR or DESeq2.
Then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Genome_build: Rnor_6.0.
Supplementary_files_format_and_content: Excel files include FPKM values and raw gene counts for every gene and every sample

organism: Rattus norvegicus

growth_protocol: C6 Cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Yeasen),100 units/ml penicillin, and 100 μg/ml streptomycin in a humidified atmosphere of 5% CO2 at 37°C。

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C6 Cells were treated with DMSO or FSK for 24 hours

tag: cell line

tag: cell type

value: rat glioma cells

value: treated with DMSO for 24 hours


title: WT Pancreas_Ptf1a line_repl 2

description: Batch 1


title: TDP2seq_Ecoli_DNA_SPO11_YF_rep1

city: New York

first: Meret

last: Arter

address: 430 E 67th Street

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

molecule: genomic DNA

value: Escherichia coli genomic DNA digested by SPO11 in vitro


title: WT Pancreas_Ptf1a line_repl 1

description: Batch 1


title: RNA-seq_neonatal_CM_PTBP1-OE.1

city: Beijing

first: Wang

last: Li

address: 167 Beilishi Rd

department: State Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences

data_processing:
After sequencing, adapters in the RNA-seq reads were trimmed by the Cutadapt program (v1.8.1). Clean reads were then collected and aligned to the mouse reference genome (mm10 version).
Differentially expressed isoforms and genes were identified by the RSEM package (v1.3.1) or DEseq2 package (v1.38.3) according to the alignments. Alternative splicing events were identified and quantified by the rMATS software (v4.1.2).
Assembly: mm10
Supplementary files format and content: alignments in bigWig format

molecule: polyA RNA

source_name: heart

extract_protocol:
Total RNA was extracted from mouse ventricular cardiomyocytes using the GeneJet RNA Purification Kit (Thermo Scientific, K0732).
RNAs from different samples performed quality control using 2100 Bioanalyzer, and RNAs passed quality control constructed libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB #E7760L) for sequencing.

tag: strain

tag: developmental stage

value: neonatal

value: heart

value: CM

value: wild type

value: Ptbp1 OE


title: KRAS Pancreas_Ptf1a line_repl 3

description: Batch 2


title: TDP2seq_Ecoli_DNA_SPO11_WT_rep2


title: 10x_7_CSP

city: Heidelberg

first: Anna

last: Obraztsova

address: Im Neuenheimer Feld 280

department: B Cell Immunology

country: Germany

institute: German Cencer Research Center (DKFZ)

description:
Cell surface protein (CSP)
CSP library: read1 file contains cell barcode and UMI; read2 file contains hashtag or antigen DNA barcode

library_source: other

data_processing:
10x Genomics Cell Ranger v6.1.2 multi was used to map the reads to human genome and assemble full length VDJ transcripts
Assembly: GRCh38-2020-A
Supplementary files format and content: Comma-separated value files and matrix files; matrix files are available on GEX samples.
Library strategy: CITE-seq

molecule: protein

organism: Homo sapiens

source_name: Plasmablasts and S+ and CD71+ B cells, CSP

extract_protocol:
S-reacitve B cells (S+), activated B cells (CD71+) and plasmablasts (CD27+CD38+) were isolated from PBMC samples by fluorescence-activated cell sorting (FACS). Sorted single cells were captured using Chromium controller (10x Genomics) according to the Chromium Single Cell 5’ Reagent Kit (CG000330 Rev C) protocols.
Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) with Feature Barcode technology for Cell Surface Protein & Immune Receptor Mapping

value: PBMC

value: B cell

value: 2 doses of BNT162b2

tag: library type

value: CSP


title: 10x_6_GEX

description:
polyA RNA
GEX (5' mRNA) library: read1 contains cell barcode and UMI; read2 file contains transcript

library_source: transcriptomic single cell

data_processing:
10x Genomics Cell Ranger v6.1.2 multi was used to map the reads to human genome and assemble full length VDJ transcripts
Assembly: GRCh38-2020-A
Supplementary files format and content: Comma-separated value files and matrix files; matrix files are available on GEX samples.

source_name: Plasmablasts and S+ and CD71+ B cells, GEX

value: GEX


title: TDP2seq_Ecoli_DNA_SPO11_WT_rep1


title: CAD RGG rescue +dox neurite rep 3

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

data_processing:
Adapters were trimmed using Cutadapt
Transcript abundances were calculated using salmon
Gene-level abundances were calculated using tximport
Assembly: mm10
Supplementary files format and content: Salmon-calculated transcript abundances

source_name: CAD

growth_protocol: CAD cells were grown in DMEM/F12. N2A cells were grown in DMEM. Both were supplemented with 10% FBS. To differentiate cells, FBS was removed.

extract_protocol:
RNA was extracted with Zymo Quick RNA microprep kits
Libraries were constructed using Lexogen 3' end RNAseq kit

treatment_protocol: To induce rescue expression, 2 ug / mL doxycycline was added for 48 hrs

value: CAD

value: RGG mutant HNRNPA2 rescue

value: plus dox


title: 10x_6_VDJ

description:
VDJ-enriched RNA
VDJ (5' mRNA) library: read1 contains cell barcode and UMI; read2 file contains BCR transcript

data_processing:
10x Genomics Cell Ranger v6.1.2 multi was used to map the reads to human genome and assemble full length VDJ transcripts
Assembly: GRCh38-2020-A
Supplementary files format and content: Comma-separated value files and matrix files; matrix files are available on GEX samples.
Library strategy: VDJ-seq

source_name: Plasmablasts and S+ and CD71+ B cells, VDJ

value: VDJ


title: 10x_6_CSP


title: KRAS Pancreas_Ptf1a line_repl 2

description: Batch 2

value: Pancreas

value: Tamoxifen oral gavage


title: 10x_5_VDJ


title: RNA-seq_neonatal_CM_NCBP2-OE.1

value: Ncbp2 OE


title: KRAS Pancreas_Ptf1a line_repl 1

description: Batch 1


title: RNA-seq_neonatal_CM_GFP.2

value: neonatal

value: GFP OE


title: RNA-seq_neonatal_CM_NCBP2-OE.2

value: heart

value: CM


title: Sample F8, Spared nerve injury, Knockout, Spinal cord

city: GRANADA

first: Enrique

middle: José

last: Cobos del Moral

state: Granada

address: Departamento de Farmacología, Facultad de Medicina, Torre B, Planta 11, Despacho. B11-04.

department: Pharmacology

country: Spain

institute: University of Granada

data_processing:
Quality control was carried out using FastQC (version 0.11.5).
Alignment of RNA was performed using Hisat2 aligner and RSEM software with default parameters and using the GRCm38.primary_assembly as reference genome.
Assembly: GRCm38.primary_assembly
Supplementary files format and content: Raw_expression.tsv file: Tab-delimited text files with processed data that cointain the raw expression counts of each biological replicate. Raw expression is considered as the Expected count  obtained with RSEM pipeline which was used in the subsequent analyses.
Supplementary files format and content: TMM_Normalised_expression.tsv file: Tab-delimited text files with processed data that cointain the TMM normalisation of the raw expression counts.

source_name: Spinal Cord

extract_protocol:
RNA was extracted using the RNeasy Plus Universal Min Kit (QIAcube / QIAGEN) according to the manufacturer’s instructions. Concentration and quality of extracted RNA were measured using the Qubit 4 Fluorometer (Thermo Fisher Scientific, MA, USA) and the 2100 Bioanalyzer Instrument (Agilent Technologies, CA, USA)
Libraries from mRNA were prepared using 1 μg of RNA starting material and the TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA) according to the manufacturer’s protocol

treatment_protocol: Naive vs spared nerve injury

value: Spinal Cord

value: Knockout

value: SNI


title: CAD RGG rescue +dox neurite rep 1


title: RNA-seq_neonatal_CM_PTBP1-OE.2

value: wild type

value: Ptbp1 OE


title: Sample F7, Spared nerve injury, Wild type, Spinal cord

value: Wild Type


title: 10x_5_CSP

value: PBMC

value: B cell

value: 2 doses of BNT162b2

value: CSP


title: RNA-seq_neonatal_CM_G3BP1-OE.1

value: G3bp1 OE


title: CAD RGG rescue -dox neurite rep 3

value: CAD

value: RGG mutant HNRNPA2 rescue

value: minus dox


title: CAD RGG rescue +dox neurite rep 2

value: plus dox


title: RNA-seq_neonatal_CM_G3BP1-OE.2

value: neonatal

value: heart


title: 10x_4_VDJ

value: VDJ


title: Sample F6, Spared nerve injury, Knockout, Spinal cord

value: Spinal Cord

value: Knockout


title: Sample F5, Spared nerve injury, Wild type, Spinal cord

value: SNI


title: CAD RGG rescue -dox neurite rep 1


title: CAD RGG rescue -dox neurite rep 2


title: 10x_4_GEX

value: GEX


title: 10x_4_CSP


title: RNA-seq_neonatal_CM_GFP.1

value: CM

value: wild type

value: GFP OE


title: RNA-seq_adult_CM_NCBP2-OE.2

value: adult

value: Ncbp2 OE


title: 10x_5_GEX

value: PBMC

value: B cell

value: 2 doses of BNT162b2


title: CAD RGG rescue +dox soma rep 3

value: CAD

value: RGG mutant HNRNPA2 rescue


title: 10x_3_VDJ


title: Sample F3, Spared nerve injury, Wild type, Dorsal root ganglion

source_name: DRG (Dorsal root ganglion)

value: DRG (Dorsal root ganglion)

value: Wild Type


title: CAD RGG rescue +dox soma rep 2

value: plus dox


title: RNA-seq_adult_CM_NCBP2-OE.1

value: heart


title: RNA-seq_adult_CM_GFP.4


title: 10x_3_GEX


title: CAD RGG rescue +dox soma rep 1


title: Sample F1, Spared nerve injury, Wild type, Dorsal root ganglion


title: Sample F2, Spared nerve injury, Knockout, Dorsal root ganglion

value: Knockout


title: 10x_3_CSP

value: CSP


title: Sample E8, Spared nerve injury, Knockout, Spinal cord

value: Spinal Cord

value: SNI


title: CAD RGG rescue -dox soma rep 3

value: minus dox


title: RNA-seq_adult_CM_GFP.3

value: CM

value: wild type

value: GFP OE


title: RNA-seq_adult_CM_NCBP2-OE.4

value: adult

value: Ncbp2 OE


title: 10x_2_VDJ

value: PBMC

value: B cell

value: 2 doses of BNT162b2

value: VDJ


title: RNA-seq_adult_CM_GFP.2


title: Sample E7, Spared nerve injury, Wild type, Spinal cord

value: Wild Type


title: Sample F4, Spared nerve injury, Knockout, Dorsal root ganglion

value: DRG (Dorsal root ganglion)


title: CAD RGG rescue -dox soma rep 1

value: CAD

value: RGG mutant HNRNPA2 rescue


title: RNA-seq_adult_CM_NCBP2-OE.3

value: heart


title: Sample E6, Spared nerve injury, Knockout, Spinal cord

value: Spinal Cord

value: Knockout


title: 10x_2_CSP

value: CSP


title: RNA-seq_adult_CM_GFP.1

value: CM


title: CAD WT rescue +dox neurite rep 3

value: WT HNRNPA2 rescue

value: plus dox


title: CLIP-seq.FB_PTBP1_rep2

data_processing:
*library strategy: CLIP-seq
The Cutadapt program (v1.8.1) was used to remove adapters in CLIP-seq reads. Clean reads longer than 33 nt were then mapped against the mouse genome (mm10 version) by the BWA-MEM algorithm (v0.7.17) with default parameters. RBP binding sites were identified by the CLIPper program (https://github.com/YeoLab/clipper) based on the alignment of CLIP-seq reads
Assembly: mm10
Supplementary files format and content: text files that list RNAs bound by the RBP

extract_protocol:
Neonatal CMs, ECs, or FBs (2.0×107) cells were UV-cross-linked at a dose of 300 mJ/cm2 at 254 nm, and harvested with a cell scraper. Cells were lysed in two volumes of radio immunoprecipitation assay lysis buffer (RIPA) containing 150 mM NaCl, 50 mM Tris-HCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, and 1 × protease inhibitor cocktail (Roche, 05892970001) for 30 minutes in a rotation wheel at 4°C. Lysate was cleared by centrifugation at 14,000 rpm for 15 min at 4°C. A volume of 20 μl lysate was saved as input. Ten micrograms of antibodies were washed with 1 ml ice-cold wash buffer for four times, and added to lysates followed by incubation for 14 hours on a rotation wheel at 4°C. Then, beads were added to the lysates, and incubation was continued for 4 hours on a rotation wheel at 4°C. Supernatant was removed and saved as flow-through, and beads were washed six times with 1 ml of ice-cold wash buffer. RNAs not bound by the protein was degraded using MNase (Thermo Fisher Scientific, N0181) for 10 min at 37°C. Afterwards, the products were washed, the 3’ phosphate group was removed for 30 min at 37°C using FastAP (Life Technologies, EF0652), and RNA was ligated in a 3’App-DNA linker ligation assay for 60 min at 65°C using T4 RNA ligase 2 (NEB, M0351). The volume of 250 μl of elution solution was added to each sample and was rotated to elute. Then, the eluent, 50 μl of input protein, and 50 μl of flow-through protein were separated by SDS-PAGE (Thermo Fisher Scientific, NP0321BOX) and then transferred to a nitrocellulose membrane (Bio-Rad, 162-0115). The membrane was incubated in one volume of proteinase K solution including 100 mM Tris-Cl (pH 7.4), 50 mM NaCl, 20 mM EDTA and 5% NP-40 for 45 min at 55°C to release RNA. Then, the released RNA was extracted using an extraction buffer (Solarbio, SL2041-100mL), and 5’linker ligation was performed. Finally, modified RNA was reverse transcribed using SuperScript III Reverse Transcriptase (Invitrogen, 18080093) and amplified using the Phusion High-Fidelity DNA polymerase (Thermo Fisher Scientific, F530S) for sequencing.
The reverse transcribed cDNA was amplified using the Phusion High-Fidelity DNA polymerase (Thermo Fisher Scientific, F530S) and P5 and P7 primers including different indices combination for libraries construction.

value: neonatal

value: FB

value: wild type

tag: clip antibody


title: Sample E5, Spared nerve injury, Wild type, Spinal cord

value: SNI


title: 10x_1_VDJ

value: PBMC

value: B cell

value: 2 doses of BNT162b2


title: 10x_2_GEX

value: GEX


title: Sample E4, Spared nerve injury, Knockout, Dorsal root ganglion

value: DRG (Dorsal root ganglion)


title: CLIP-seq.FB_PTBP1_rep1


title: 10x_1_GEX


title: CAD WT rescue +dox neurite rep 2

value: CAD


title: CLIP-seq.FB_NCBP2_rep2

value: heart


title: Sample E3, Spared nerve injury, Wild type, Dorsal root ganglion

value: Wild Type


title: CAD RGG rescue -dox soma rep 2

value: RGG mutant HNRNPA2 rescue

value: minus dox


title: CAD WT rescue -dox neurite rep 3


title: CAD WT rescue +dox neurite rep 1


title: CLIP-seq.FB_NCBP2_rep1


title: 10x_1_CSP

value: CSP


title: CLIP-seq.FB_G3BP1_rep2


title: Sample E2, Spared nerve injury, Knockout, Dorsal root ganglion

value: Knockout


title: transplanted PD3

city: Leeds

first: Marine

last: Krzisch

state: West Yorkshire

address: Woodhouse Lane

department: School of Biomedical Sciences

country: United Kingdom

institute: University of Leeds

data_processing:
The Illumina pair-end reads were mapped to with STAR (version 2.7.1a), which index files were created with the gene annotation including Ensembl human hg38 version 108 and mouse mm10 version 102 with --sjdbOverhang 50 option.
The genes counts were obtained using featureCounts function from Subread package with unstranded option. Only reads assigned to human genes are included.
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw counts for each sample

source_name: Embryonic stem cell line BGO1 with inserted heterozygous A53T mutation in SNCA gene

growth_protocol: transplantation into the mouse brain or differentiation into microglia using a previously published protocol (McQuade  et al. Molecular Neurodegeneration 2018)

extract_protocol:
The RNA was extracted from cells using the RNeasy Plus Micro Kit (Qiagen). Transplanted microglia were extracted from the mouse brain using a previously published protocol of cold extraction (Svoboda et al. PNAS 2018).
Libraries were generated using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® kit (NEB).

treatment_protocol: No treatment

value: A53T in SNCA

value: transplanted into mouse brain


title: CAD WT rescue -dox neurite rep 2

value: WT HNRNPA2 rescue


title: Sample E1, Spared nerve injury, Wild type, Dorsal root ganglion


title: transplanted PD2

source_name: Embryonic stem cell line WIBR3 with inserted heterozygous A53T mutation in SNCA gene


title: CLIP-seq.FB_G3BP1_rep1

value: neonatal

value: FB

value: wild type


title: Sample C6, No treated, Knockout, Spinal cord

value: Spinal Cord


title: transplanted PD1

source_name: Familial Parkinson patient-derived induced pluripotent stem cell line with heterozygous A53T mutation in SNCA gene


title: CAD WT rescue +dox soma rep 3

value: plus dox


title: CLIP-seq.EC_PTBP1_rep2

value: EC


title: CAD WT rescue +dox soma rep 2


title: Sample C5, No treated, Wild type, Spinal cord


title: CLIP-seq.EC_PTBP1_rep1


title: CAD WT rescue +dox soma rep 1


title: transplanted Control2

source_name: Human embryonic stem cell line WIBR3

value: Human embryonic stem cell line WIBR3

value: control


title: Sample C2, No treated, Knockout, Dorsal root ganglion

value: DRG (Dorsal root ganglion)


title: CLIP-seq.EC_NCBP2_rep2

value: heart


title: Sample C1, No treated, Wild type, Dorsal root ganglion

value: Wild Type


title: transplanted Control1

source_name: Induced pluripotent stem cell line with corrected A53T mutation in SNCA gene


title: CAD WT rescue -dox soma rep 3

value: CAD

value: minus dox


title: Sample B8, No treated, Knockout, Spinal cord

value: Knockout


title: CLIP-seq.EC_G3BP1_rep2


title: CAD WT rescue -dox soma rep 2


title: in vitro PD3

value: Embryonic stem cell line BGO1 with inserted heterozygous A53T mutation in SNCA gene

value: A53T in SNCA

value: in vitro


title: CLIP-seq.EC_NCBP2_rep1

value: neonatal


title: Sample B6, No treated, Knockout, Spinal cord


title: CAD WT rescue -dox soma rep 1

value: WT HNRNPA2 rescue


title: CLIP-seq.EC_G3BP1_rep1

value: wild type


title: CAD WT rescue -dox neurite rep 1


title: transplanted Control3

source_name: Human embryonic stem cell line BGO1

value: Human embryonic stem cell line BGO1

value: transplanted into mouse brain


title: Sample B5, No treated, Wild type, Spinal cord

value: Spinal Cord


title: CAD HNRNPB1 rescue +dox neurite rep 2

value: HNRNPB1 rescue

value: plus dox


title: CLIP-seq.CM_PTBP1_rep1

value: CM


title: CLIP-seq.CM_PTBP1_rep2

value: heart


title: Sample B4, No treated, Knockout, Dorsal root ganglion

value: DRG (Dorsal root ganglion)


title: in vitro Control3

value: control


title: in vitro Control2

value: Human embryonic stem cell line WIBR3


title: CAD HNRNPB1 rescue +dox neurite rep 3

value: CAD


title: CAD HNRNPB1 rescue +dox neurite rep 1


title: Sample B3, No treated, Wild type, Dorsal root ganglion

value: Wild Type


title: CAD HNRNPB1 rescue -dox neurite rep 3

value: minus dox


title: CLIP-seq.CM_NCBP2_rep2


title: in vitro Control1

value: Induced pluripotent stem cell line with corrected A53T mutation in SNCA gene

value: in vitro


title: in vitro PD2

value: Embryonic stem cell line WIBR3 with inserted heterozygous A53T mutation in SNCA gene

value: A53T in SNCA


title: Sample B2, No treated, Knockout, Dorsal root ganglion

value: Knockout


title: Sample B7, No treated, Wild type, Spinal cord


title: CAD HNRNPB1 rescue -dox neurite rep 2


title: in vitro PD1

value: Familial Parkinson patient-derived induced pluripotent stem cell line with heterozygous A53T mutation in SNCA gene


title: Sample B1, No treated, Wild type, Dorsal root ganglion


title: CLIP-seq.CM_NCBP2_rep1

value: neonatal

value: wild type


title: Sample A8, No treated, Knockout, Spinal cord

value: Spinal Cord


title: CAD HNRNPB1 rescue -dox neurite rep 1

value: HNRNPB1 rescue


title: UCLA1 naïve hESC, inducible ZIC3, DOX, rep2 (ATAC-seq)

city: Montreal

first: William

middle: A.

last: Pastor

state: Quebec

address: 3655 Promenade Sir-William-Osler

department: Biochemistry

institute: McGill University

description: P26+14+2 (5iLAF d15)

data_processing:
Raw reads were trimmed to 50bp using TrimGalore!
Reads were aligned against the GRCh38 reference genome using bwa mem.
Reads were filtered for unique alignments, marked for duplicates and sorted using samtools
Mitochondrial reads were removed prior to making coverage files and differential analysis.
Effciency biases were calculated using csaw and scale factor was calculated to make coverage tracks, where necessary. Otherwise reads per 1x genome coverage (RPGC) was used for generating coverage files.
Differentially accessible regions were calculated using csaw.
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: Naïve human embryonic stem cells

growth_protocol: Primed hESCs were cultured on hESC-qualified matrigel coated plates in TESR-E8 medium. Primed hESCs were cultured in media supplemented with 10 µM Y27632 24h prior to eletroporation experiments and upon plating of electroporated cells. hESCs collected during reversion from primed to naive pluripotency were plated on a feeder layer of mouse embryonic fibroblasts and cultured in 5iLAF  or 4iLAF+0.25µM IM-12 (t5iLAF) medium for the specified period of time. Both during reversion to and upon full acquisition of naive pluripotency, hESCs were cultured in 5 % O2 and 5 % CO2. Reverting and naive hESCs were depleted of MEFs prior to collection for experiments.

extract_protocol:
Cells were lysis in 50 ul ATAC resuspension buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl and 3 mM MgCl2) supplemented with 0.1% Tween-20, 0.1% NP-40 and 0.01% digitonin, and incubated on ice for three minutes. Lysis  buffer was then diluted with 1 ml ATAC resuspension buffer supplemented with 0.1% Tween-20 and tubes were inverted three times. Nuclei were pelleted by centrifugation at 500g for 10 minutes at  4°C. Transposition reaction was carried out in 50 ul volume for each sample by resuspending nuclei in 25 ul 2x TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2 and 20 DMF), 2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20 and 5 ul H2O. Reactions were incubated at 37°C  for 30 minutes in a thermomixer with 1000 RPM mixing. Reactions were quenched with 5x volume of buffer PB and DNA was purified using the MinElute PCR purification kit (Qiagen). Libraries were next amplified using Illumina-compatible primers.
Libraries were constructed as described in Corces et al (2017) Nature Methods.

treatment_protocol: Cells were treated with 100 ng/ml doxycycline hyclate or DMSO of equivalent v/v concentration, where specified.

value: Naïve human embryonic stem cells

value: UCLA1 naive hESCs

value: Human embryonic stem cells

value: Stable integration of 3x-Flag ZIC3 and M2rtTA ORFs; clone 4

value: Cultured in medium supplemented with 100 ng/ml doxycycline for 72 hours


title: HeLa, ZBTB17, ChIP

first: hongqin

last: liu

address: 230 Haike Road, Zhangjiang Hi-Tech Park

department: SLST

data_processing:
ChIP-seq reads were aligned to the hg38 reference genome using Bowtie2(2.3.4.3)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.1.2) was used to call peaks with the sonicated input as a control and an initial threshold p-value of 0.001 as cutoff
Assembly: GRCh38
Supplementary files format and content: bigwig files were generated using Deeptools(3.1.3)
Supplementary files format and content: NarrowPeak files were generated using MACS2(2.1.2) (excpet for input sample)

source_name: Uterus; cervix

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium  supplemented with 10% fetal bovine serum , 1% penicillin-streptomycin and 5% CO2 in 37 °C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with ZBTB17(Santa Cruz,#sc-136985X )
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). DNA were used for library construction using the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) with 15 cycles of PCR. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Uterus; cervix

value: HeLa

tag: chip antibody

value: ZBTB17(Santa Cruz,#sc-136985X )


title: CAD HNRNPB1 rescue +dox soma rep 3

value: CAD

value: plus dox


title: CLIP-seq.CM_G3BP1_rep1

value: heart

value: CM


title: Sample A7, No treated, Wild type, Spinal cord

value: Wild Type


title: UCLA1 naïve hESC, inducible ZIC3, DOX, rep1 (ATAC-seq)

description: P26+14+2 (5iLAF d15)


title: Sample A6, No treated, Knockout, Spinal cord

value: Knockout


title: UCLA1 naïve hESC, inducible ZIC3, DMSO, rep2 (ATAC-seq)

description: P26+14+2 (5iLAF d15)

value: Cultured in medium supplemented with DMSO for 72 hours


title: CAD HNRNPB1 rescue +dox soma rep 2


title: L138_72_TCDD

city: East Lansing

first: Timothy

last: Zacharewski

state: MI

address: 603 Wilson Rd., BCH Building RM#212

department: Biochemistry and Molecular Biology

institute: Michigan State University

data_processing:
CellRanger 4.0.0 was used to align reads to a custom reference genome which included introns and exons to consider pre-mRNA and mature mRNA present in the nuclei.
Raw counts were further analysed using Scanpy v1.9.3. Each sample was filtered for (i) genes expressed in at least 3 nuclei, (ii) nuclei which express at least 100 genes, and (iii) ≤1% mitochondrial genes
Scrublet v0.2.3 was used to remove putative doublets.
All libraries were integrated using using scVI v0.20.3, while accounting for dose and time as categorical covariates and using a latent variable of 40.
Assembly: mm10
Supplementary files format and content: Processed data files for individual sample are CellRanger filtered_feature_bc_matrix.H5 Hierarchical Data Format version 5 (HDF5) files.
Supplementary files format and content: The HDF5 Annotated Data (.h5ad) file represents the full scVI processed anndata object.

molecule: nuclear RNA

source_name: Liver

extract_protocol:
Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle.
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) - CG000315 Rev A
snRNAseq (Single-Nuclei RNA-Sequencing)

treatment_protocol:
Mice were gavaged once with sesame oil vehicle or 30 ug/kg TCDD and livers collected at 2, 4, 8, 12, 24, or 72 hours following gavage.
Mice given a single bolus dose by oral gavage

tag: org ontology

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: toxic substance

value: Harlan Teklad

tag: toxic substance_ontology

tag: toxic substance_vendor

value: Accustandard

tag: toxic substance_catalog__number

tag: vehicle substance

value: sesame oil

tag: vehicle substance_ontology

tag: administration route

value: oral gavage

tag: administration route_ontology

value: TCDD

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit_ontology

tag: library kit

value: 10X Genomics Chromium Single Cell 3’ v3 kit

tag: biological replicate


title: L137_72_TCDD

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue

value: Liver

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: start age

tag: end age

tag: age unit

tag: age unit_ontology

tag: duration

tag: duration unit

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

tag: humidity unit_ontology

tag: light cycle

tag: cage type

tag: treatment


title: Sample A5, No treated, Wild type, Spinal cord

tag: tissue

value: Spinal Cord

tag: genotype

value: Wild Type


title: CAD HNRNPB1 rescue +dox soma rep 1

tag: cell line

value: CAD

value: HNRNPB1 rescue

value: plus dox


title: HeLa, input

value: Uterus; cervix

value: HeLa

tag: chip antibody

value: none (input)


title: CAD HNRNPB1 rescue -dox soma rep 3

value: minus dox


title: UCLA1 naïve hESC, inducible ZIC2, DOX, rep2 (ATAC-seq)

description: P26+50+2 (5iLAF d15)

value: Naïve human embryonic stem cells

value: UCLA1 naive hESCs

tag: cell type

value: Human embryonic stem cells

value: Stable integration of 3x-Flag ZIC2 and M2rtTA ORFs; clone 7

value: Cultured in medium supplemented with 100 ng/ml doxycycline for 72 hours


title: CLIP-seq.CM_G3BP1_rep3

tag: strain

tag: developmental stage

value: neonatal

value: heart

value: CM

value: wild type

tag: clip antibody


title: Sample A4, No treated, Wild type, Dorsal root ganglion

value: DRG (Dorsal root ganglion)

value: Knockout


title: CAD HNRNPB1 rescue -dox soma rep 2

value: CAD

value: HNRNPB1 rescue


title: L123_72_vehicle

tag: org ontology

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

value: degree Celcius

value: percent

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: toxic substance

value: Harlan Teklad

tag: toxic substance_ontology

tag: toxic substance_vendor

value: Accustandard

tag: toxic substance_catalog__number

tag: vehicle substance

value: sesame oil

tag: vehicle substance_ontology

tag: administration route

value: oral gavage

tag: administration route_ontology

value: vehicle

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit_ontology

tag: library kit

value: 10X Genomics Chromium Single Cell 3’ v3 kit

tag: biological replicate


title: Sample A3, No treated, Wild type, Dorsal root ganglion

tag: tissue

value: DRG (Dorsal root ganglion)

tag: genotype

value: Wild Type

tag: treatment


title: CAD HNRNPB1 rescue -dox soma rep 1

tag: cell line

value: CAD

value: HNRNPB1 rescue

value: minus dox


title: UCLA1 naïve hESC, inducible ZIC3, DMSO, rep1 (ATAC-seq)

description: P26+14+2 (5iLAF d15)

value: Naïve human embryonic stem cells

value: UCLA1 naive hESCs

tag: cell type

value: Human embryonic stem cells

value: Stable integration of 3x-Flag ZIC3 and M2rtTA ORFs; clone 4

value: Cultured in medium supplemented with DMSO for 72 hours


title: UCLA1 naïve hESC, inducible ZIC2, DOX, rep1 (ATAC-seq)

description: P26+50+2 (5iLAF d15)

value: Stable integration of 3x-Flag ZIC2 and M2rtTA ORFs; clone 7

value: Cultured in medium supplemented with 100 ng/ml doxycycline for 72 hours


title: Sample A2, No treated, Wild type, Dorsal root ganglion

value: Knockout


title: CAD HNRNPA2 rescue +dox neurite rep 3

value: HNRNPA2 rescue

value: plus dox


title: UCLA1 naïve hESC, inducible ZIC2, DMSO, rep2 (ATAC-seq)

description: P26+50+2 (5iLAF d15)


title: L122_72_vehicle

tag: org ontology

tag: strain

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: toxic substance

value: Harlan Teklad

tag: toxic substance_ontology

value: Accustandard

value: sesame oil

value: oral gavage

value: vehicle

value: microgram per kilogram


title: UCLA1 naïve hESC, inducible ZIC2, DMSO, rep1 (ATAC-seq)

description: P26+50+2 (5iLAF d15)

tag: tissue

value: Naïve human embryonic stem cells

tag: cell line

value: UCLA1 naive hESCs

tag: cell type

value: Human embryonic stem cells

tag: genotype

value: Stable integration of 3x-Flag ZIC2 and M2rtTA ORFs; clone 7

tag: treatment

value: Cultured in medium supplemented with DMSO for 72 hours


title: Sample A1, No treated, Wild type, Dorsal root ganglion

value: DRG (Dorsal root ganglion)

value: Wild Type


title: CLIP-seq.CM_G3BP1_rep2

tag: strain

tag: developmental stage

value: neonatal

value: heart

value: CM

value: wild type

tag: clip antibody


title: L118_24_TCDD

tag: org ontology

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

tag: toxic substance_vendor

tag: toxic substance_catalog__number

tag: vehicle substance

tag: vehicle substance_ontology

tag: administration route

tag: administration route_ontology

value: TCDD

tag: dose

tag: dose unit

tag: dose unit_ontology

tag: library kit

value: 10X Genomics Chromium Single Cell 3’ v3 kit

tag: biological replicate


title: CAD HNRNPA2 rescue +dox neurite rep 2

tag: cell line

value: CAD

tag: genotype

value: HNRNPA2 rescue

tag: treatment

value: plus dox


title: P28

description: Takara iCell8

data_processing:
Raw binary base call (BCL) files were exported to FASTQ files using bcl2fastq (2.18.0.12). Paired reads were filtered by cutadapt (v1.8.1) with parameters: -m 20 --trim-n --max-n 0.7 –q 20. Clean reads were then mapped to the mm10 reference genome with STAR (v2.5.2b) and alignments were assigned to GENCODE annotation vM15 by featureCounts.
We employed BRIE2 to accurately identify splicing phenotypes in scRNA-seq data, and quantify isoform proportions and their uncertainty (Huang and Sanguinetti, 2021). First, we used briekit-event and briekit-event-filter to extract the reference alternative splicing (AS) annotations from mouse genome mm10 and gene annotation vM15 from ENCODE. The distribution of AS types in the mouse genome was counted from briekit-event-filter output. Then, we used brie-count to process single-cell alignments (BAM files) with the splicing annotations to identify the reads containing splicing junctions. Next, we utilized brie-quant to quantify the splicing proportion PSI (percent spliced in), and detect variable splicing events/genes along with cell-level features. To be able to perform dimension reductions such as PCA and UMAP on splicing PSI matrix, we added an aggregated imputation step with argument --interceptMode gene.
Assembly: mm10
Supplementary files format and content: csv, raw counts
Supplementary files format and content: csv, raw PSI values
Supplementary files format and content: tab-delimited text, cell meta and proceesed information

source_name: Heart

extract_protocol:
For isolation of cells from neonatal mice, mice were sacrificed, and hearts were transferred to PBS containing heparin sodium (1000 units in 50 ml PBS) for washing. Ventricles were chopped into small pieces, and digested with the Pierce™ Primary Cardiomyocyte Isolation Kit (Thermo, 88281) according to the manufacturer’s instructions with minor modifications. To obtain relatively pure cardiomyocytes and non-cardiomyocytes, we used the differential velocity adherence method to culture isolated cells for 1 hour, and non-adherent cells were collected as cardiomyocytes. For isolation of cells from adult mouse hearts, mice were injected with 100 μl heparin sodium (1000 units in 50 ml PBS) 20 minutes before sacrifice, and hearts were transferred to Tyrode's solution for washing, after which they underwent digestion using the Langendorff perfusion technique. In brief, hearts were perfused with Tyrode's solution for 5 min using the Langendorff apparatus, followed by digestion with the heart dissociation enzyme stock solution (0.7 mg/ml Collagenase type II and 0.7 mg/ml Bovine Serum Albumin Tyrode's Solution) for 30 minutes. Tissues from ventricles were collected, chopped into pieces, and gently dissociated into single cells. Digestion was stopped by Tyrode's solution containing 10% FBS. Finally, cell suspension was centrifuged (100 × g, 2 min at room temperature) three times to separate cardiomyocytes from non-cardiomyocytes.
scRNA-seq libraries were generated using the ICELL8 single-cell system (Takara Bio). Briefly, isolated cells were stained with a mixture of Hoechst 33342 and Propidium Iodide (PI) (Thermo, R37610) per manufacturer’s instructions. The cells were counted on the MoxiTM Z Automated Cell Counter after PBS wash. A cell suspension of 20,000 cells/ml was transferred to the SmartChipTM MultiSample NanoDispenser (MSND, Takara Bio) for single cell preparation. Dispensed cells were then imaged on the imaging station, and live single cells were selected based on Hoechst+PI- staining. The reverse transcription and first-step amplification were performed on a Chip Cycler (Bio-Rad), followed by cDNA purification and size-selection with Agencourt AMPure XP beads (A63880, Beckman Coulter). One nanogram of purified cDNA was used to generate a sequencing library with the Nextera XT DNA Library Prep Kit (Illumina, FC-131-1024), and then sequenced on the NextSeq 500 sequencer (Illumina) using the 26nt and 50nt paired-end sequencing protocol.

tag: tissue

value: Heart

tag: strain

tag: cell type

value: cardiomyoctyes and non-cardiomyocytes

tag: developmental stage


title: P14

description: Takara iCell8


title: UCLA1 naïve hESC, inducible ZIC2, DOX, ACBI1-treated (ATAC-seq)

description: P26+39+3 (5iLAF d17)

value: Naïve human embryonic stem cells

value: UCLA1 naive hESCs

value: Human embryonic stem cells

value: Stable integration of 3x-Flag ZIC2 and M2rtTA ORFs; clone 7

value: Cultured in medium supplemented with 100 ng/ml doxyclycline and 300 nM ACBI1 for 72 hours


title: CAD HNRNPA2 rescue +dox neurite rep 1


title: L136_72_TCDD

tag: org ontology

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

tag: water

tag: feed

tag: toxic substance

tag: toxic substance_ontology

tag: toxic substance_vendor

value: Accustandard

tag: toxic substance_catalog__number

value: sesame oil

value: oral gavage

value: microgram per kilogram


title: UCLA1 naïve hESC, inducible ZIC2, DOX, untreated (ATAC-seq)

description: P26+39+3 (5iLAF d17)

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: Cultured in medium supplemented with 100 ng/ml doxycycline for 72 hours


title: CAD HNRNPA2 rescue -dox neurite rep 3

value: CAD

value: HNRNPA2 rescue

value: minus dox


title: L116_24_TCDD

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: start age

tag: end age

tag: age unit

tag: age unit_ontology

tag: duration

tag: duration unit

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

tag: temperature unit_ontology

tag: housing humidity

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

tag: vehicle substance

tag: vehicle substance_ontology

tag: administration route

tag: administration route_ontology

value: TCDD

tag: dose

tag: dose unit

tag: dose unit_ontology

tag: library kit

value: 10X Genomics Chromium Single Cell 3’ v3 kit

tag: biological replicate


title: P10

description: Takara iCell8

tag: tissue

value: Heart

tag: strain

tag: cell type

value: cardiomyoctyes and non-cardiomyocytes

tag: developmental stage


title: UCLA1 naïve hESC, inducible ZIC2, DMSO, ACBI1-treated (ATAC-seq)

description: P26+39+3 (5iLAF d17)

value: Naïve human embryonic stem cells

tag: cell line

value: UCLA1 naive hESCs

value: Human embryonic stem cells

tag: genotype

value: Stable integration of 3x-Flag ZIC2 and M2rtTA ORFs; clone 7

tag: treatment

value: Cultured in medium supplemented with DMSO and 300 nM ACBI1 for 72 hours


title: CAD HNRNPA2 rescue -dox neurite rep 2


title: L103_24_vehicle

tag: org ontology

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

tag: water

tag: feed

tag: toxic substance

tag: toxic substance_ontology

tag: toxic substance_vendor

value: Accustandard

tag: toxic substance_catalog__number

value: sesame oil

value: oral gavage

value: vehicle

value: microgram per kilogram


title: P7

description: Takara iCell8

tag: tissue

value: Heart

tag: strain

tag: cell type

value: cardiomyoctyes and non-cardiomyocytes

tag: developmental stage


title: UCLA1 naïve hESC, inducible ZIC2, DMSO, untreated (ATAC-seq)

description: P26+39+3 (5iLAF d17)

value: Naïve human embryonic stem cells

tag: cell line

value: UCLA1 naive hESCs

value: Human embryonic stem cells

tag: genotype

tag: treatment

value: Cultured in medium supplemented with DMSO for 72 hours


title: L121_72_vehicle

tag: org ontology

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

tag: age unit_ontology

tag: duration

tag: duration unit

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

tag: humidity unit_ontology

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

tag: vehicle substance

tag: vehicle substance_ontology

tag: administration route

tag: administration route_ontology

tag: dose

tag: dose unit

tag: dose unit_ontology

tag: library kit

value: 10X Genomics Chromium Single Cell 3’ v3 kit

tag: biological replicate


title: L102_24_vehicle

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

value: degree Celcius

value: percent

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

tag: water

tag: feed

tag: toxic substance

tag: toxic substance_ontology

tag: toxic substance_vendor

value: Accustandard

tag: toxic substance_catalog__number

value: sesame oil

tag: treatment


title: UCLA1 naïve hESC, inducible ZIC2, DOX 8h, BRG1 CUT&Tag

data_processing:
Raw reads were trimmed to 50bp using TrimGalore!
Reads were aligned against the GRCh38 reference genome using bwa mem.
Reads were filtered for unique alignments, marked for duplicates and sorted using samtools
Mitochondrial reads were removed prior to making coverage files.
Effciency biases were calculated using csaw and scale factor was calculated to make coverage tracks.
Assembly: GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Naive human embryonic stem cells

growth_protocol: Primed hESCs were cultured on hESC-qualified matrigel coated plates in mTESR-plus medium. Primed hESCs were cultured in media supplemented with 10 µM Y27632 24h prior to eletroporation experiments and upon plating of electroporated cells. hESCs collected during reversion from primed to naive pluripotency were plated on a feeder layer of mouse embryonic fibroblasts and cultured in 4iLAF+0.25µM IM-12 (t5iLAF) medium for the specified period of time. Both during reversion to and upon full acquisition of naive pluripotency, hESCs were cultured in 5 % O2 and 5 % CO2. Naive hESCs were depleted of MEFs prior to collection for experiments.

extract_protocol:
Cells were fixed in 0.1% paraformaldehyde for 10 minutes at room temperature and the reaction was quenched with 0.14 M glycine. Cell pellets were resuspended in 200 μl cold nuclear extraction (NE) buffer (20 mM HEPES pH 7.9, 10 mM KCl, 20% glycerol, 0.1% Triton X-100, 0.5 mM spermidine, 0.15 mM spermine and protease inhibitors) and incubated for 5 minutes on ice. Nuclei were resuspended in 50 μl NE buffer and incubated with activated Concanavalin A-coated magnetic beads for 10 minutes at room temperature. Supernatant was removed using a magnetic stand and nuclei resuspended in 25 µL antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.15 mM spermine, 20% glycerol and 2 mM EDTA) containing 0.5 μg primary antibody. Samples were then incubated overnight at 4 °C on a nutator. To remove unbound antibody, bead-nuclei complexes were washed twice with 150 buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.15 mM spermine, 20% glycerol) using a magnetic stand and resuspended in 25 µL 150 buffer containing 0.5 μg anti-mouse or rabbit secondary antibody for CUTANATM CUT&Tag workflows (EpiCypher). Samples were then incubated for 30 minutes at room temperature. After two washes with 150 buffer, bead/nuclei complexes were resuspended in 12 µl 1x pA/G-Tn5 pre-loaded adapter complex (EpiCypher, USA) made in 150 buffer and incubated for 1 hour at room temperature on a nutator. Bead/nuclei complexes were washed twice in 150 buffer, resuspended in 50 μl cold CUTAC-hex buffer (10 mM TAPS, 5 mM MgCl2, 10% 1,6-hexanediol, 20% glycerol and protease inhibitors) and incubated for 2 minutes at 4 °C followed by 20 minutes at 37 °C. To release pAG-Tn5 from tagmented DNA, bead/nuclei complexes were then resuspended in 5 μl 0.1% SDS and incubated for 1 hour at 58 °C. To generate libraries, 15 μl of 0.67% Triton X-100 neutralization solution was added to each sample followed by 2 μl 10 μM universal or barcoded i5 primers, 2 μl 10 μM uniquely barcoded i7 primers and 25 μl NEBNext High-Fidelity buffer (non-hot-start NEBNext formulation; NEB, USA). Samples were then placed in a thermocycler under the following cycling conditions: 5 min at 58 °C, 5 minutes at 72 °C, 45 seconds at 98 °C, 15 seconds at 98 °C (melting) and 10 seconds at 60 °C (annealing and extension). The last 2 steps were repeated for a total of 14-21 cycles followed by a 1-minute final extension at 72 °C. To purify libraries, 25 μl AMPure XP beads (Beckman Coulter, Canada) were added to the reactions and samples were incubated for 10 minutes at room temperature on a nutator. DNA was washed twice with 70% ethanol using a magnetic stand and once with 100% ethanol. DNA was eluted in 15 μl in pre-warmed 10 mM Tris pH 8 buffer using a magnetic stand.
Libraries were constructed by tagmentation such that chromatin upon treatment with Tn5 was simultaneously fragmented and tagged with Illumina-compatible sequencing adapters.

tag: tissue

value: Naive human embryonic stem cells

tag: cell line

value: UCLA1 naive hESCs

tag: cell type

tag: genotype

value: Stable integration of 3x-Flag ZIC2 and M2rtTA ORFs

value: Cultured in medium supplemented with DMSO for 64 hours followed by 100ng/ml doxycycline for 8 hours


title: L101_24_vehicle

tag: org ontology

tag: strain

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

tag: age unit_ontology

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

tag: humidity unit_ontology

tag: vehicle substance

tag: vehicle substance_ontology

tag: administration route

value: oral gavage

tag: administration route_ontology

value: vehicle

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit_ontology

tag: library kit

tag: biological replicate


title: P6

description: Takara iCell8

tag: tissue

value: Heart

tag: strain

tag: cell type

value: cardiomyoctyes and non-cardiomyocytes

tag: developmental stage


title: CAD HNRNPA2 rescue +dox soma rep 3

tag: cell line

value: CAD

tag: genotype

value: HNRNPA2 rescue

tag: treatment

value: plus dox


title: P5

description: Takara iCell8


title: UCLA1 naïve hESC, inducible ZIC2, DOX 72h, BRG1 CUT&Tag

value: Human embryonic stem cells

value: Cultured in medium supplemented with 100ng/ml doxycycline for 72 hours


title: CAD HNRNPA2 rescue +dox soma rep 2


title: L098_18_TCDD

tag: org ontology

tag: strain ontology

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: toxic substance

value: Harlan Teklad

tag: toxic substance_ontology

tag: toxic substance_vendor

value: Accustandard

tag: toxic substance_catalog__number

value: sesame oil

value: TCDD

value: 10X Genomics Chromium Single Cell 3’ v3 kit


title: P4

description: Takara iCell8

tag: tissue

value: Heart

tag: strain

tag: cell type

value: cardiomyoctyes and non-cardiomyocytes

tag: developmental stage


title: L117_24_TCDD

tag: org ontology

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

tag: age unit_ontology

tag: duration

tag: duration unit

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

tag: temperature unit_ontology

tag: vehicle substance

tag: vehicle substance_ontology

tag: administration route

value: oral gavage

tag: administration route_ontology

tag: treatment

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit_ontology

tag: library kit

tag: biological replicate


title: CAD HNRNPA2 rescue +dox soma rep 1

tag: cell line

value: CAD

tag: genotype

value: HNRNPA2 rescue

value: plus dox


title: P3

description: Takara iCell8

tag: tissue

tag: strain

tag: cell type

tag: developmental stage


title: L097_18_TCDD

tag: org ontology

tag: strain ontology

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

tag: feed

tag: toxic substance

tag: toxic substance_ontology

tag: toxic substance_vendor

tag: toxic substance_catalog__number


title: UCLA1 naïve hESC, inducible ZIC2, DOX 24h, BRG1 CUT&Tag

tag: tissue

value: Naive human embryonic stem cells

tag: cell line

value: UCLA1 naive hESCs

tag: cell type

value: Human embryonic stem cells

tag: genotype

value: Stable integration of 3x-Flag ZIC2 and M2rtTA ORFs

tag: treatment

value: Cultured in medium supplemented with DMSO for 48 hours followed by 100ng/ml doxycycline for 24 hours


title: UCLA1 naïve hESC, inducible ZIC2, DOX 0h, BRG1 CUT&Tag

value: Cultured in medium supplemented with DMSO for 72 hours


title: CAD HNRNPA2 rescue -dox soma rep 3

value: minus dox


title: CAD HNRNPA2 rescue -dox soma rep 2


title: P2

description: Takara iCell8

value: Heart

tag: strain

value: cardiomyoctyes and non-cardiomyocytes

tag: developmental stage


title: CAD HNRNPA2 rescue -dox neurite rep 1

value: CAD

value: HNRNPA2 rescue


title: UCLA1 primed hESC, Inducible ZIC3 DOX 16h, Input

data_processing:
Reads were aligned against the GRCh38 reference genome using bwa mem.
Reads were filtered for unique alignments, marked for duplicates and sorted using samtools
Effciency biases were calculated using csaw and scale factor was calculated to make coverage tracks, where necessary. Otherwise reads per 1x genome coverage (RPGC) was used for generating coverage files.
Differentially accessible regions were calculated using csaw.
Deeptools was used to generate coverage tracks.
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: Primed human embryonic stem cells

growth_protocol: Primed hESCs were cultured on hESC-qualified matrigel coated plates in TESR-E8 or mTESR-plus medium. Primed hESCs were cultured in media supplemented with 10 µM Y27632 24h prior to eletroporation experiments and upon plating of electroporated cells. hESCs collected during reversion from primed to naive pluripotency were plated on a feeder layer of mouse embryonic fibroblasts and cultured in 5iLAF  or 4iLAF+0.25µM IM-12 (t5iLAF) medium for the specified period of time. Both during reversion to and upon full acquisition of naive pluripotency, hESCs were cultured in 5 % O2 and 5 % CO2. Reverting and naive hESCs were depleted of MEFs by plating of dissociated single cell suspension on 0.1% gelatin for 30 minutes prior to collection for experiments.

extract_protocol:
Cells were fixed with 1% paraformaldehyde for 10 min, and quenched with 0.14 M glycine for 10 min. Cells were then resuspended with 1 ml lysis buffer 1 (10 mM TrisHCl pH 8.0, 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 1x Protease inhibitors (Roche), 1 mM NaF, 1 mM Na2VO3 and 1 mM PMSF), then rotated 15 minutes. Nuclei were pelleted by centrifugation at 1200g for 5 minutes at 4 °C. Nuclei were then resuspended with 1 ml lysis buffer 2 (10 mM TrisHCl pH 8.0, 200 mM NaCl, 10 mM EDTA, 0.5 mM EGTA, 1x Protease inhibitor, 1mM NaF, 1mM Na2VO3 and 1mM PMSF) and rotated 10 minutes at 4 °C. Nuclei were then pelleted and resuspended in 900 μl lysis buffer 3 (10 mM Tris-HCL pH 8, 10 mM EDTA, 0.5 mM EGTA, 0.1% SDS, 1 mM NaF, 1 mM Na2VO3 and 1 mM PMSF), and chromatin was fragmented using the Covaris M220 sonicator. Chromatin was pre-cleared with ProtA/G beads for 2 hours at  4 °C. Antibodies were then added to pre-cleared lysates and incubated overnight with end-over-end shaking at 4 °C. Immunocomplexes were then immobiilzed on prot A/G beads, which were then washed 2×4 minutes with 500 μl Wash Buffer A (50 mM HEPES pH 7.9, 1% TritonX-100, 0.1% Deoxycholate, 1mM EDTA, 140 mM NaCl), 500 μl Wash Buffer B (50 mM HEPES pH 7.9, 0.1% SDS, 1% Triton X100, 0.1% Deoxycholate, 1 mM EDTA, 500 mM NaCl), and 500 μl TE buffer (10 mM TrisHCl pH 8.0, 1 mM EDTA). DNA was eluted in 100 μl elution buffer (50 mM TrisHCl pH 8.0, 1 mM EDTA, 1% SDS) after incubation at 65 °C for 10 minutes at 1400 rpm. The elute was collected, and the beads were subjected to a second round of elution with 150 μl elution buffer. The ChIP eluants were pooled, and the input sample was diluted to 250 μl with elution buffer. These samples were incubated 65 °C overnight to promote decrosslinking. The samples were then allowed to cool to room temperature, 15 μg of RNAse A (Purelink, ThermoFisher) was added, and the samples were incubated 30 minutes at 37 °C to degrade RNA. 100 μg Proteinase K was then added and the samples were incubated 56 °C for two hours. DNA was purified using a MinElute PCR Purification kit (Qiagen).
Purified DNA was fragmented to 200 bp by sonication. Following this, libraires were prepared using the Swift DNA library kit or NEBNext Ultra II DNA Library Prep Kit, according to manufacturers' instructions.

treatment_protocol: Cells were treated with 100 ng/ml doxycycline hyclate, 1 uM flavopiridol, 500 nM triptolide, 25 uM STM2457 or DMSO of equivalent v/v concentration, where specified for the appropriate period of time.

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: Stable integration of 3x-Flag ZIC3 and M2rtTA ORFs; clone 4

value: Cultured in medium supplemented with 100 ng/ml doxycycline for 16 hours

tag: antibody

tag: passage description

value: passage 26+16


title: UCLA1 primed hESC, Inducible ZIC3 DOX 16h, Flag ChIP-seq

value: anti-Flag M2 (Sigma F3165)


title: L083_18_vehicle

tag: org ontology

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Accustandard

tag: vehicle substance

value: sesame oil

tag: vehicle substance_ontology

tag: administration route

value: oral gavage

tag: administration route_ontology

value: vehicle

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit_ontology

tag: library kit

value: 10X Genomics Chromium Single Cell 3’ v3 kit

tag: biological replicate


title: CAD HNRNPA2 rescue -dox soma rep 1

tag: cell line

value: CAD

tag: genotype

value: HNRNPA2 rescue

tag: treatment

value: minus dox


title: P1

description: Takara iCell8

tag: tissue

value: Heart

tag: strain

tag: cell type

value: cardiomyoctyes and non-cardiomyocytes

tag: developmental stage


title: E18.5

description: Takara iCell8


title: UCLA1 primed hESC, ZIC2-/-ZIC5-/- +sgZIC3, Input

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: Human embryonic stem cells

value: ZIC2-/-ZIC3-/-ZIC5-/- (done on ZIC2-/-ZIC5-/- clone 10)

value: ZIC2- and ZIC5-deficient primed hESCs electroporated with Cas9 and sgRNAs targeting ZIC3

tag: antibody

value: anti-ZIC3 (Abcam ab222124)

tag: passage description


title: L081_18_vehicle

tag: org ontology

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: toxic substance

value: Harlan Teklad

tag: toxic substance_ontology

tag: toxic substance_vendor

value: Accustandard

tag: toxic substance_catalog__number

tag: vehicle substance

tag: vehicle substance_ontology


title: UCLA1 primed hESC, ZIC2-/- +sgZIC3, EZH2 CUT&Tag

tag: tissue

value: Primed human embryonic stem cells

tag: cell line

value: UCLA1 primed hESCs

tag: cell type

tag: genotype

tag: treatment

value: ZIC2-deficient primed  hESCs electroporated with Cas9 and sgRNAs targeting ZIC3


title: L082_18_vehicle

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: start age

tag: end age

tag: age unit

tag: age unit_ontology

tag: duration

tag: duration unit

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

tag: humidity unit_ontology

value: sesame oil

tag: administration route

value: oral gavage

tag: administration route_ontology

value: vehicle

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit_ontology

tag: library kit

value: 10X Genomics Chromium Single Cell 3’ v3 kit

tag: biological replicate


title: L079_12_TCDD

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

value: hours

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed

tag: toxic substance

tag: toxic substance_ontology

tag: toxic substance_vendor

tag: toxic substance_catalog__number

tag: vehicle substance

tag: vehicle substance_ontology

tag: treatment

value: TCDD


title: UCLA1 primed hESC, ZIC2-/-ZIC5-/- +sgNT, ZIC3 ChIP-seq, rep1

tag: tissue

tag: cell line

tag: cell type

value: Human embryonic stem cells

tag: genotype

value: ZIC2-/-ZIC5-/- clone 4

value: ZIC2- and ZIC5-deficient primed hESCs electroporated with Cas9 and non-target sgRNA

tag: antibody

value: anti-ZIC3 (Abcam ab222124)

tag: passage description

value: paasage 27+14+9


title: UCLA1 primed hESC, WT +sgNT, EZH2 CUT&Tag

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs

value: WT

value: WT primed hESCs electroporated with Cas9 and non-target sgRNA


title: L077_12_TCDD

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: start age

tag: end age

tag: age unit

tag: age unit_ontology

tag: duration

tag: duration unit

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Accustandard

value: sesame oil

tag: administration route

value: oral gavage

tag: administration route_ontology

tag: dose

tag: dose unit

tag: dose unit_ontology

tag: library kit

tag: biological replicate


title: Callus, mutant, rep3

city: Berkeley

first: Yangnan

last: Gu

state: California

address: 371A Koshland Hall

department: Plant & Microbial Biology

institute: UC Berkeley

data_processing:
Clean mRNA-seq reads were aligned to the Arabidopsis thaliana reference genome (TARI10) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated with HTseq (v0.6.1p1) with the union mode.
Assembly: TAIR 10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Callus

growth_protocol: 5-7 mm of hypocotyls from etiolated seedlings were grown on callus induction media (CIM) for 4 days and then moved to shoot induction media (SIM) for 10 days before RNA extraction.

extract_protocol:
Total RNA was extracted from about 50 mg samples using Direct-zol RNA Miniprep kit (Genesee Scientific, Catalog #11-330).
mRNA-Seq¬†(Strand-Specific)¬† libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Callus

tag: ecotype

tag: time

value: 4 day CIM, 10 day SIM

tag: genotype

value: pnet1 knockout

tag: treatment


title: Callus, overexpression line, rep3

value: PNET1 overexpression


title: UCLA1 primed hESC, ZIC2-/- +sgZIC3, BRG1 CUT&Tag, rep1

value: Primed human embryonic stem cells

tag: cell line

value: UCLA1 primed hESCs

tag: cell type

value: Human embryonic stem cells

value: ZIC2-deficient primed  hESCs electroporated with Cas9 and sgRNAs targeting ZIC3


title: Callus, overexpression line, rep2


title: UCLA1 primed hESC, ZIC2-/-ZIC5-/- +sgNT, Input, rep1

value: ZIC2-/-ZIC5-/- clone 4

value: ZIC2- and ZIC5-deficient primed hESCs electroporated with Cas9 and non-target sgRNA

tag: antibody

tag: passage description

value: paasage 27+14+9


title: Callus, mutant, rep2


title: UCLA1 primed hESC, ZIC2-/- +sgZIC3, BRG1 CUT&Tag, rep2


title: L078_12_TCDD

tag: org ontology

tag: strain

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed

tag: toxic substance

tag: toxic substance_ontology

tag: toxic substance_vendor

tag: toxic substance_catalog__number

tag: vehicle substance

tag: vehicle substance_ontology

value: TCDD

value: microgram per kilogram

value: 10X Genomics Chromium Single Cell 3’ v3 kit


title: L064_12_vehicle

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: start age

tag: end age

tag: age unit

tag: age unit_ontology

tag: duration

tag: duration unit

tag: duration unit_ontology

tag: house temperature

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Accustandard

value: sesame oil

tag: administration route

value: oral gavage

tag: administration route_ontology

tag: treatment

value: vehicle

tag: dose

tag: dose unit

tag: dose unit_ontology

tag: library kit

tag: biological replicate


title: L096_18_TCDD

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: temperature unit

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

tag: humidity unit_ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed

tag: toxic substance

tag: toxic substance_ontology

tag: toxic substance_vendor

tag: toxic substance_catalog__number

tag: vehicle substance

tag: vehicle substance_ontology


title: UCLA1 primed hESC, ZIC2-/-ZIC5-/- +sgNT, ZIC3 ChIP-seq, rep2

tag: tissue

value: Primed human embryonic stem cells

tag: cell line

value: UCLA1 primed hESCs

tag: cell type

value: Human embryonic stem cells

tag: genotype

value: ZIC2-/-ZIC5-/- clone 10

tag: treatment

value: ZIC2- and ZIC5-deficient primed hESCs electroporated with Cas9 and non-target sgRNA

tag: antibody

value: anti-ZIC3 (Abcam ab222124)

tag: passage description

value: paasage 27+14+9


title: Callus, mutant, rep1

value: Callus

tag: ecotype

tag: time

value: 4 day CIM, 10 day SIM

value: pnet1 knockout


title: UCLA1 primed hESC, Inducible ZIC2 DOX 16h, Input

value: Stable integration of 3x-Flag ZIC2 and M2rtTA ORFs

value: Cultured in medium supplemented with 100 ng/ml doxycycline for 16 hours

value: passage 26+52


title: UCLA1 primed hESC, ZIC2-/-ZIC5-/- +sgNT, Input, rep2


title: L062_12_vehicle

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Accustandard

value: sesame oil

tag: administration route

value: oral gavage

tag: administration route_ontology

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit_ontology

tag: library kit

value: 10X Genomics Chromium Single Cell 3’ v3 kit

tag: biological replicate


title: UCLA1 primed hESC, ZIC2-/-ZIC5-/- +sgZIC3, ZIC3 ChIP-seq

tag: tissue

value: Primed human embryonic stem cells

tag: cell line

value: UCLA1 primed hESCs

tag: cell type

value: Human embryonic stem cells

tag: genotype

value: ZIC2-/-ZIC3-/-ZIC5-/- (done on ZIC2-/-ZIC5-/- clone 10)

tag: treatment

value: ZIC2- and ZIC5-deficient primed hESCs electroporated with Cas9 and sgRNAs targeting ZIC3

tag: antibody

tag: passage description


title: UCLA1 primed hESC, WT +sgNT, H3K4me3 CUT&Tag

value: WT

value: WT primed hESCs electroporated with Cas9 and non-target sgRNA


title: UCLA1 primed hESC, ZIC2-/- +sgZIC3, H3K4me3 CUT&Tag

value: ZIC2-deficient primed  hESCs electroporated with Cas9 and sgRNAs targeting ZIC3


title: L063_12_vehicle

tag: org ontology

tag: strain

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

tag: feed

tag: toxic substance

tag: toxic substance_ontology

tag: toxic substance_vendor

tag: toxic substance_catalog__number

tag: vehicle substance

tag: vehicle substance_ontology

value: vehicle


title: Callus, control, rep3

tag: tissue

value: Callus

tag: ecotype

tag: time

value: 4 day CIM, 10 day SIM

tag: genotype

value: wild type

tag: treatment


title: Callus, overexpression line, rep1

value: PNET1 overexpression


title: UCLA1 primed hESC, Inducible ZIC2 DOX 16h, Flag ChIP-seq

value: Primed human embryonic stem cells

tag: cell line

value: UCLA1 primed hESCs

tag: cell type

value: Human embryonic stem cells

value: Stable integration of 3x-Flag ZIC2 and M2rtTA ORFs

value: Cultured in medium supplemented with 100 ng/ml doxycycline for 16 hours

tag: antibody

value: anti-Flag M2 (Sigma F3165)

tag: passage description

value: passage 26+52


title: UCLA1 primed hESC, Input, rep5

value: WT

value: Cultured in medium supplemented with DMSO

value: anti-ZIC2 (Abcam ab150404)

value: passage 44


title: Callus, control, rep2


title: UCLA1 primed hESC, WT +sgNT, H3K27ac CUT&Tag

value: WT primed hESCs electroporated with Cas9 and non-target sgRNA


title: L057_8_TCDD

tag: org ontology

tag: strain

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

value: Accustandard

value: sesame oil

tag: administration route

value: oral gavage

tag: administration route_ontology

value: TCDD

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit_ontology

tag: library kit

value: 10X Genomics Chromium Single Cell 3’ v3 kit

tag: biological replicate


title: 1974_D28_DB_pos

first: Jean-Sebastien

last: Delisle

address: 5415 Boulevard de l'Assomption

institute: Centre de recherche de l'Hôpital Maisonneuve-Rosemont

data_processing:
Ion Reporter software (version 5.12) was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and mapped to hg19 whole genome using the Ion Reporter software (version 5.12).
Counting data of referenced clones were generated by the Ion Reporter software (version 5.12).
Genome_build: hg19
Supplementary_files_format_and_content: Coma-separated value files include VDJ genes associated with CDR3 amino acid and nuclotide sequences, read counts, and read proportions for each sample.

source_name: T lymphocytes

growth_protocol: Cells were stimulated weekly with LMP2-pulsed dendritic cells and cultured in complete media.

extract_protocol:
FACS-sorted LMP2 multimer-positive and multimer-negative T cells were harvested. RNA was isolated using Trizol reagent in combination with the PureLink RNA mini and microcolumn system.
Oncomine™ TCR Beta-SR Assay for RNA was used for the construction of sequencing libraries. Sequencing was completed on the Ion S5 semiconductor platform using an Ion 540 chip.

treatment_protocol: Cells were treated or not with anti-PD-L1 and anti-TIM3 antibodies.

tag: lmp2 specificity

value: positive

tag: days in culture

tag: treatment

value: PD-L1/TIM3 double blockade


title: UCLA1 primed hESC, WT +sgNT, BRG1 CUT&Tag, rep2

tag: tissue

value: Primed human embryonic stem cells

tag: cell line

value: UCLA1 primed hESCs

tag: cell type

value: Human embryonic stem cells

tag: genotype

value: WT

value: WT primed hESCs electroporated with Cas9 and non-target sgRNA


title: UCLA1 primed hESC, WT +sgNT, BRG1 CUT&Tag, rep1


title: UCLA1 primed hESC, STM2457 24h, ZIC2 ChIP-seq, rep2

value: Cultured in medium supplemented with 25uM STM2457 for 4 hours

tag: antibody

value: anti-ZIC2 (Abcam ab150404)

tag: passage description

value: passage 83


title: L042_8_vehicle

tag: org ontology

tag: strain

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: toxic substance

value: Harlan Teklad

tag: toxic substance_ontology

tag: toxic substance_vendor

tag: toxic substance_catalog__number

tag: vehicle substance

tag: vehicle substance_ontology

value: vehicle


title: L043_8_vehicle

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: start age

tag: end age

tag: age unit

tag: age unit_ontology

tag: duration

tag: duration unit

tag: duration unit_ontology

tag: house temperature

value: Accustandard

value: sesame oil

tag: administration route

value: oral gavage

tag: administration route_ontology

tag: treatment

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit_ontology

tag: library kit

value: 10X Genomics Chromium Single Cell 3’ v3 kit

tag: biological replicate


title: L056_8_TCDD

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue

value: Liver

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: temperature unit

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

tag: humidity unit_ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed

tag: toxic substance

tag: toxic substance_ontology

tag: toxic substance_vendor

tag: toxic substance_catalog__number

tag: vehicle substance

tag: vehicle substance_ontology

value: TCDD


title: UCLA1 primed hESC, FLV 4h, ZIC2 ChIP-seq, rep2

tag: tissue

value: Primed human embryonic stem cells

tag: cell line

value: UCLA1 primed hESCs

tag: cell type

value: Human embryonic stem cells

tag: genotype

value: WT

tag: treatment

value: Cultured in medium supplemented DMSO for 20 hours followed by 1uM flavopiridol for 4 hours

tag: antibody

value: anti-ZIC2 (Abcam ab150404)

tag: passage description

value: passage 83


title: 1974_D28_DB_neg

tag: lmp2 specificity

value: negative

tag: days in culture

value: PD-L1/TIM3 double blockade


title: L041_8_vehicle

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

value: Harlan Teklad 22/5 Rodent Diet 8940

value: Harlan Teklad

tag: administration route

tag: administration route_ontology

value: vehicle

tag: dose

tag: dose unit

tag: dose unit_ontology

tag: library kit

tag: biological replicate


title: UCLA1 primed hESC, FLV 4h, Input, rep2

tag: tissue

value: Primed human embryonic stem cells

tag: cell line

value: UCLA1 primed hESCs

tag: cell type

value: Human embryonic stem cells

tag: genotype

value: WT

tag: treatment

tag: antibody

tag: passage description


title: 1932_D28_DB_pos

tag: lmp2 specificity

value: positive

tag: days in culture


title: L039_4_TCDD

tag: org ontology

tag: strain

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: start age

tag: end age

tag: age unit

tag: age unit_ontology

tag: duration

tag: duration unit

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

tag: humidity unit_ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed

tag: toxic substance

tag: toxic substance_ontology

tag: toxic substance_vendor

value: Accustandard

tag: toxic substance_catalog__number

tag: vehicle substance

value: sesame oil

tag: vehicle substance_ontology

value: oral gavage

value: TCDD

value: microgram per kilogram

value: 10X Genomics Chromium Single Cell 3’ v3 kit


title: UCLA1 primed hESC, ZIC2 ChIP-seq, rep5

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: Cultured in medium supplemented with DMSO

tag: antibody

tag: passage description

value: passage 44


title: UCLA1 primed hESC, STM2457 24h, Input, rep2

value: Cultured in medium supplemented with 25uM STM2457 for 4 hours

value: passage 83


title: UCLA1 primed hESC, DMSO, ZIC2 ChIP-seq, rep2

value: Cultured in medium supplemented with DMSO for 24 hours

value: anti-ZIC2 (Abcam ab150404)


title: UCLA1 primed hESC, DMSO, Input, rep2

value: Primed human embryonic stem cells

value: UCLA1 primed hESCs


title: 1932_D28_Ctrl_pos

tag: lmp2 specificity

tag: days in culture

value: Untreated


title: 1932_D28_Ctrl_neg

value: negative


title: Callus, control, rep1

value: Callus

tag: ecotype

tag: time

value: 4 day CIM, 10 day SIM

value: wild type


title: L036_4_TCDD

tag: org ontology

tag: strain

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: toxic substance

value: Harlan Teklad

value: Accustandard

value: sesame oil

tag: administration route

value: oral gavage

tag: administration route_ontology

tag: dose

tag: dose unit

tag: dose unit_ontology

tag: library kit

tag: biological replicate


title: L058_8_TCDD

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: start age

tag: end age

tag: age unit

tag: age unit_ontology

tag: duration

tag: duration unit

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

tag: temperature unit_ontology

tag: toxic substance_ontology

tag: toxic substance_vendor

tag: toxic substance_catalog__number

tag: vehicle substance

tag: vehicle substance_ontology

tag: treatment

value: TCDD

value: microgram per kilogram

value: 10X Genomics Chromium Single Cell 3’ v3 kit


title: L023_4_vehicle

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue

value: Liver

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: housing humidity

tag: humidity unit

tag: humidity unit_ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: feed

tag: toxic substance

tag: administration route

tag: administration route_ontology

value: vehicle

tag: dose

tag: dose unit

tag: dose unit_ontology

tag: library kit

tag: biological replicate


title: 1867_D28_DB_pos

tag: lmp2 specificity

value: positive

tag: days in culture

tag: treatment

value: PD-L1/TIM3 double blockade


title: UCLA1 primed hESC, STM2457 24h, Input, rep1

tag: tissue

value: Primed human embryonic stem cells

tag: cell line

value: UCLA1 primed hESCs

tag: cell type

value: Human embryonic stem cells

tag: genotype

value: WT

value: Cultured in medium supplemented with 25uM STM2457 for 4 hours

tag: antibody

tag: passage description

value: passage 72


title: 1974_D28_Ctrl_neg

value: negative

value: Untreated


title: 1867_D28_Ctrl_pos


title: UCLA1 primed hESC, FLV 4h, ZIC2 ChIP-seq, rep1

value: Cultured in medium supplemented DMSO for 20 hours followed by 1uM flavopiridol for 4 hours

value: anti-ZIC2 (Abcam ab150404)


title: 1867_D28_DB_neg


title: L021_4_vehicle

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: toxic substance

value: Harlan Teklad

tag: toxic substance_ontology

tag: toxic substance_vendor

value: Accustandard

tag: toxic substance_catalog__number

tag: vehicle substance

value: sesame oil

tag: vehicle substance_ontology

value: oral gavage


title: UCLA1 primed hESC, FLV 4h, Input, rep1

tag: tissue

value: Primed human embryonic stem cells

tag: cell line

value: UCLA1 primed hESCs

tag: cell type

value: Human embryonic stem cells

tag: genotype

value: WT

tag: treatment

tag: antibody

tag: passage description

value: passage 72


title: 1867_D28_Ctrl_neg

tag: lmp2 specificity

value: negative

tag: days in culture

value: Untreated


title: L038_4_TCDD

tag: org ontology

tag: strain

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

tag: humidity unit_ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: administration route

tag: administration route_ontology

value: TCDD

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit_ontology

tag: library kit

value: 10X Genomics Chromium Single Cell 3’ v3 kit

tag: biological replicate


title: 1832_D28_DB_pos

tag: lmp2 specificity

value: positive

tag: days in culture

tag: treatment

value: PD-L1/TIM3 double blockade


title: L018_2_TCDD

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: start age

tag: end age

tag: age unit

tag: age unit_ontology

tag: duration

tag: duration unit

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

tag: temperature unit_ontology

tag: housing humidity

value: percent

value: Innovive cage

value: ALHPA-dri (Shepherd Specialty Papers)

value: Aquavive water (Innovive)

tag: feed

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: toxic substance

value: Harlan Teklad

tag: toxic substance_ontology

tag: toxic substance_vendor

value: Accustandard

tag: toxic substance_catalog__number

tag: vehicle substance

value: sesame oil

tag: vehicle substance_ontology

value: oral gavage


title: UCLA1 primed hESC, DMSO, ZIC2 ChIP-seq, rep1

tag: tissue

value: Primed human embryonic stem cells

tag: cell line

value: UCLA1 primed hESCs

tag: cell type

value: Human embryonic stem cells

tag: genotype

value: WT

tag: treatment

value: Cultured in medium supplemented with DMSO for 24 hours

tag: antibody

value: anti-ZIC2 (Abcam ab150404)

tag: passage description

value: passage 72


title: L019_2_TCDD

tag: org ontology

tag: strain

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

value: degree Celcius

tag: humidity unit

tag: humidity unit_ontology

tag: light cycle

tag: cage type

tag: bedding

tag: water

tag: administration route

tag: administration route_ontology

value: TCDD

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit_ontology

tag: library kit

value: 10X Genomics Chromium Single Cell 3’ v3 kit

tag: biological replicate


title: UCLA1 primed hESC, DMSO, Input, rep1

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment

tag: antibody

tag: passage description


title: 1832_D28_DB_neg

tag: lmp2 specificity

value: negative

tag: days in culture

value: PD-L1/TIM3 double blockade


title: UCLA1 primed hESC, TRP 1h, ZIC2 ChIP-seq

value: Primed human embryonic stem cells

value: Cultured in medium supplemented with 500 nM triptolide for 1 hour

value: passage 46


title: UCLA1 primed hESC, TRP 1h, Input

value: UCLA1 primed hESCs

value: Human embryonic stem cells

value: WT


title: UCLA1 primed hESC, STM2457 24h, ZIC2 ChIP-seq, rep1

value: Cultured in medium supplemented with 25uM STM2457 for 4 hours

value: anti-ZIC2 (Abcam ab150404)

value: passage 72


title: L016_2_TCDD

tag: org ontology

tag: strain

tag: strain ontology

value: Liver

tag: tissue ontology

tag: Sex

value: male

tag: sex ontology

tag: start age

tag: end age

tag: age unit

value: days

tag: age unit_ontology

tag: duration

tag: duration unit

tag: duration unit_ontology

tag: house temperature

tag: temperature unit

tag: temperature unit_ontology

tag: housing humidity

tag: humidity unit

value: percent

tag: humidity unit_ontology

tag: light cycle

tag: cage type

value: Innovive cage

tag: bedding

value: ALHPA-dri (Shepherd Specialty Papers)

tag: water

value: Aquavive water (Innovive)

tag: feed

value: Harlan Teklad 22/5 Rodent Diet 8940

tag: toxic substance

value: Harlan Teklad

tag: toxic substance_ontology

tag: toxic substance_vendor

value: Accustandard

tag: toxic substance_catalog__number

tag: vehicle substance

value: sesame oil

tag: vehicle substance_ontology

value: oral gavage


title: L003_2_vehicle

tag: org ontology

tag: strain

tag: strain ontology

tag: tissue

tag: tissue ontology

tag: Sex

tag: sex ontology

tag: start age

tag: end age

tag: age unit

tag: age unit_ontology

tag: duration

tag: duration unit

value: hours

tag: duration unit_ontology

tag: house temperature

value: degree Celcius

tag: administration route

tag: administration route_ontology

tag: treatment

value: vehicle

tag: dose

tag: dose unit

value: microgram per kilogram

tag: dose unit_ontology

tag: library kit

value: 10X Genomics Chromium Single Cell 3’ v3 kit

tag: biological replicate