title: NN-0-3_combined_R

city: Dalian

middle: Xin

last: Lin

address: Dalian

institute: Dalian Minzu University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited EXCEL files include RPKM values for each Sample

organism: Xanthoceras sorbifolium

source_name: Feather compound leaf

growth_protocol: Yellowhorn seeds were soaked in water at 50 °C for 3 days. Then, seeds were wrapped with cotton cloth soaked in water to keep them moist until they germinated. Sprouted seeds were transplanted into flowerpots filled with sand and cultivated for two months.Irrigation of nutrient solution containing 2 mmol/l nitrogen source once every 3 days.

extract_protocol:
The top tender leaves of yellowhorn were selected, frozen in liquid N, and stored at -80 °C. According to the manufacturer's instructions, total RNA was extracted using a total RNA extractor (Trizol) kit (B511311, Chinese laborers) and treated with DNase I without RNase to remove genomic DNA contamination.
In short, mRNA was extracted from total RNA using oligo d(T)18, and then random fragments of purified mRNA were reverse transcribed into cDNA. After being linked with adapters at both ends, DNA fragments were selectively amplified and enriched. Subsequently, the purified PCR product was quantified using the Agilent Bioanalyzer 2100 system. After cluster generation, the final cDNA library was sequenced on Illumina HiSeq platform.

treatment_protocol: The experiment was carried out as follows: yellowhorn of the same growth and similar size were equally divided into three groups and treated with nutrient solutions of three different concentrations. The nutrient solution was 945 mg/l calcium sulfate, 506 mg/l potassium sulfate, 80 mg/l ammonium nitrate, 136 mg/l dipotassium hydrogen phosphate, 493 mg/l magnesium sulfate, 5.56 g/l ferrous sulfate heptahydrate, 7.46 g/l EDTA, 0.83 mg/l potassium iodide, 6.2 mg/l boric acid, 22.3 mg/l manganese sulfate, 8.6 mg/l zinc sulfate, 0.25 mg/l sodium molybdate, 0.025 mg/l copper sulfate, and 0.025 mg/l cobalt chloride. Ammonium nitrate was used as the sole N source, at 0, 0.2, and 2 mmol/l (NN, LN, and CK, respectively)(The general standard of cultivated soil is that the nitrogen concentration is 150-200mg/Kg.). During 15 days, plants were watered with 400 ml of nutrient solution per basin once every three days.

value: Feather compound leaf

value: Nitrogen-free stress


title: FVB/N: Hippocampus 3

status: Public on Jan 21 2023

type: SRA

city: Jerusalem

first: Hermona

last: Soreq

state: Israel

address: The Edmond J. Safra Campus, Givat Ram

department: Biological Chemistry

country: Israel

institute: The Hebrew University of Jerusalem

library_source: transcriptomic

data_processing:
Base calling, QC and fastq file generation by the illumina Basespace platform
Quality control was performed using FastQC
Short RNA was aligned to the miRBase version 21 using miRExpress 2.0 with default parameters.
Normalization and Differencial expression using Deseq2
Genome_build: mirBase v.21
Supplementary_files_format_and_content: .fq.txt File per sample with alligned miR counts

molecule: total RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from murine brain tissues using the miRNeasy Mini Kit (Qiagen, 217004). Four TgR and three FVB/N mice were used for the prefrontal cortex (PFC), and three TgR and three FVB/N mice were used for the hippocampus. RNA quality and quantity were measured using a Nanodrop 2000 (PeqLab/Thermo Scientific). RNA integrity was tested using the 2100 Bioanalyzer (Agilent Technologies) RNA 6000 Nano LabChip Kits (Agilent Technologies) which revealed RIN values range of 8.6-9.3.
300ng of RNA were subjected to small-RNA sequencing. Libraries were generated using an RNA Library prep kit (NEBNext Multiplex Small RNA Library Prep Set for Illumina, E7300) following manufacturer’s instructions.

tag: strain

value: FVB/N

tag: genotype

value: WT

tag: tissue

value: Hippocampus


title: FVB/N: Hippocampus 2


title: Colorectal carcinoma tissue C18

city: 上海市

first: Shiyi

last: Yang

state: 上海

address: 中国上海市徐汇区华山路1954号

country: China

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp ).
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

organism: Homo sapiens

source_name: Colorectum

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colorectum

tag: tissue pair

value: tissue pair:colorectal carcinoma tissue C18


title: HCT116 cells, Cystine deprovation, 48hours-2

address: 中国上海市徐汇区华山路1954号

description:
Cys_dep48_2
rsem_tpm.xls

growth_protocol: HCT116 human colorectal caricinoma cells were maintained in full DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 1.The following day, cystine deprivation cells were washed and fed with warm DMEM supplemented with 10% fetal bovine serun (FBS), antibiotics and 0 mM cystine for 24 or 48 hours.   2.Control cells were still maintained in full DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics for 24 or 48 hours.

tag: cell line

tag: cell type

value: Human Colorectal Carcinoma Cells

tag: treatment

value: Amino acid deprivation

tag: time


title: NN-0-1_combined_R

first: Li


title: NN-0-2_combined_R


title: LN-0-3_combined_R

value: Low nitrogen stress


title: Colorectal carcinoma tissue C15

address: 中国上海市徐汇区华山路1954号

value: tissue pair:colorectal carcinoma tissue C15


title: TgR: PFC animal 4

source_name: Prefrontal cortex

value: hACHE-R overexpression

value: Prefrontal cortex


title: LN-0-2_combined_R


title: Colorectal carcinoma tissue C14

address: 中国上海市徐汇区华山路1954号

value: tissue pair:colorectal carcinoma tissue C14


title: Colorectal carcinoma tissue C20

address: 中国上海市徐汇区华山路1954号

value: tissue pair:colorectal carcinoma tissue C20


title: CK-0-3_combined_R

value: Standard nitrogen content


title: HCT116 cells, Control, 48hours-3

address: 中国上海市徐汇区华山路1954号

description:
Cys48_3
rsem_tpm.xls

value: control


title: HCT116 cells, Control, 48hours-2

address: 中国上海市徐汇区华山路1954号

description:
Cys48_2
rsem_tpm.xls


title: LN-0-1_combined_R

value: Feather compound leaf


title: CK-0-1_combined_R


title: Colorectal carcinoma tissue C12

address: 中国上海市徐汇区华山路1954号

value: tissue pair:colorectal carcinoma tissue C12


title: Colorectal carcinoma tissue C13

address: 中国上海市徐汇区华山路1954号

value: tissue pair:colorectal carcinoma tissue C13


title: TgR: PFC animal 3

value: FVB/N


title: TgR: PFC animal 2


title: CK-0-2_combined_R


title: HCT116 cells, Cystine deprivation, 24hours-1

address: 中国上海市徐汇区华山路1954号

description:
Cys_dep24_1
rsem_tpm.xls

value: WT


title: FVB/N: PFC  animal 1


title: Colorectal carcinoma tissue C1

address: 中国上海市徐汇区华山路1954号

value: Colorectum

value: tissue pair:colorectal carcinoma tissue C1


title: HCT116 cells, Control, 24hours-2

address: 中国上海市徐汇区华山路1954号

description:
Cys24_2
rsem_tpm.xls

value: Human Colorectal Carcinoma Cells


title: HCT116 cells, Cystine deprivation, 24hours-2

address: 中国上海市徐汇区华山路1954号

description:
Cys_dep24_2
rsem_tpm.xls

value: Amino acid deprivation


title: HCT116 cells, Control, 24hours-1

address: 中国上海市徐汇区华山路1954号

description:
Cys24_1
rsem_tpm.xls


title: S.tuberosum cultivar CG, Rs infection 2

status: Public on Jan 20 2023

city: Gödöllő

first: Zsófia

last: Bánfalvi

address: Szent-Györgyi Albert u. 4.

department: Genetics and Biotechnology Institute

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

data_processing:
It was carried out by  Novogene (UK) Company Ltd. (Cambridge, UK), using standard protocol
Assembly: Solanum tuberosum group Phureja DM1-3 v.6.1
Supplementary files format and content: tab delimited txt file, raw read counts, one sample per column

organism: Solanum tuberosum

source_name: root

growth_protocol: The plants were maintained and propagated in vitro from single node stem segments in test tubes in RM medium (MS medium without vitamins; Murashige and Skoog, 1962) supplemented with 20 g l-1 sucrose and 8 g l-1 agar at a constant 24 °C with a 16 h photoperiod at a light intensity of 75 μmol m-2 s-1. Apical fragments with two-three leaves of 4-week-old plants were cut and placed in RM medium in a Phytatray vessel (Sigma-Aldrich, St. Luis, MI, USA, product no.: P5929). After 7-10 days, five plantlets with roots were transferred into rectangular Petri dishes (Greiner, Kremsmünster, Austria, product no.: 688102) containing the RM medium only in the lower half of the dishes, which was covered with a folded sterile filter paper to separate the roots from the medium. The Petri dishes with four-six plants were placed in a vertical position and incubated at a constant 24 °C with a 16 h photoperiod for an additional 10-12 days before the inoculation. In general, 20 plantlets were tested for Rs inoculation per accession.

extract_protocol:
Total RNA was extracted according to Stiekema et al.  (doi:10.1007/BF00027383)
Libraries were prepared by Novogene (UK) Company Ltd. (Cambridge, UK), RNA-seq, paired-end, poly-A selected

treatment_protocol: The Rs strain UW551 (wild-type geranium isolate; Swanson et al., 2005) transformed with the pDSK-GFPuv plasmid (Wang et al., 2007) containing the GFP reporter gene under the control of the constitutive psbA promoter was grown on CPG medium (casamino acid 1 g l-1, peptone 10 g l-1, glucose 5 g l-1, agar 17 g l-1, pH 6.5) supplemented with 30 mg l−1 kanamycin and incubated at 28 °C for 48 h, then re-grown for another 48 h. Finally, bacteria were suspended at a concentration of 5-7 × 108 CFU ml-1 (O.D.600 = 0.8) in sterile deionized water. For inoculations, the plant roots were wounded by sterile scalpels approximately 1 cm above their tip and pipetted with 350 μl of bacterial suspension/plant.

value: root

tag: cultivar

value: cultivar Calalo Gaspar

value: Rs infected


title: HCT116 cells, Control, 24hours-3

address: 中国上海市徐汇区华山路1954号

description:
Cys24_3
rsem_tpm.xls


title: S.tuberosum cultivar CG, Rs infection 3


title: S.tuberosum cultivar Desirée, Control 1

value: cultivar Desiree


title: S.tuberosum cultivar Desirée, Control 2


title: S.tuberosum cultivar CR, Rs infection 2

value: cultivar Cruza 148


title: FVB/N: PFC animal 2

value: Prefrontal cortex


title: FVB/N: PFC animal 3


title: HCT116 cells, Control, 48hours-1

address: 中国上海市徐汇区华山路1954号

description:
Cys48_1
rsem_tpm.xls


title: TgR: PFC animal 1

value: hACHE-R overexpression


title: S.tuberosum cultivar CG, Control 2

value: control


title: S.tuberosum cultivar CR, Rs infection 1


title: Colorectal carcinoma tissue C11

address: 中国上海市徐汇区华山路1954号

value: tissue pair:colorectal carcinoma tissue C11


title: Colorectal carcinoma tissue C10

address: 中国上海市徐汇区华山路1954号

value: tissue pair:colorectal carcinoma tissue C10


title: S.tuberosum cultivar Desirée, Control 3


title: Differentiated Mc

city: New York

first: Qi

last: Sun

state: NY

address: 550 1st Avenue, Smilow 410

department: Dermatology

country: USA

institute: New York University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v.6.0.1
Supplementary files format and content: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: skin

extract_protocol:
For Activated McSC sample, melanocyte stem cells were isolated from the back skin of Dct-rtTA; tetO-H2B-GFP mice at 4 days after depilation. For Differentiated_Mc sample, the hair bulb area of Anagen VI hair follicles from the back skin of 5 weeks old Dct-rtTA; tetO-H2B-GFP mice wre dissected out add dissociated into single cells. FACS for GFP+ cells were utilized to enrich for melanocytes.
Single-cell RNA-Seq library for the Differentiated_Mc sample was prepared using the following Chromium Single Cell 3' v2 Reagent Kits: Chromium™ Single Cell 3′ Library & Gel Bead Kit v2 PN-120237; Single Cell 3′ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262 (10x Genomics) following the Single Cell 3′ Reagent Kits v2 User Guide (Manual Part # CG00052 Rev A). Single-cell RNA-Seq library for the Activated_McSC sample was prepared using the following Chromium Single Cell 3' v3 Reagent Kits: Chromium™ Single Cell 3′ Library & Gel Bead Kit v3 PN-1000075; Single Cell 3ʹ Feature Barcode Library Kit PN-1000079; Single Cell B Chip Kit PN-1000073 and i7 Multiplex Kit PN-120262 (10x Genomics) following the Single Cell 3′ Reagent Kits v3 User Guide (Manual Part # CG000201 RevA).

value: skin

value: primary cell

value: mature melanocyte

tag: cell state

value: Differentiated

value: Dct-rtTA; tetO-H2B-GFP


title: S.tuberosum cultivar CG, Rs infection 1


title: GM12878_FC6

city: Guangzhou

first: Jiayong

last: Zhong

address: Jinsui Road No.7

department: State Key Laboratory of Ophthalmology, Clinical Research Center for Ocular Disease

institute: Zhongshan Ophthalmic Centre, Sun Yat-sen University

library_source: genomic

data_processing:
Basecalls were performed using Guppy v4.5.3 with high-accuracy basecalling model “dna_r9.4.1_450bps_hac_prom.cfg”, and reads with quality score less than 7 were filtered.
HiPore-C reads were aligned and annotated with our in-house  developed MapPore-C pipeline.
The 5mC methylation were called using Megalodon v2.0.3 with model “res_dna_r941_prom_modbases_5mC_v001.cfg” in GPU servers.
Genome pairwise-contacts were generated by in-house python scripts, and cool/mool, hic files were generated using cooler v0.8.6.post0  and  juice tools v1.22.1, respectively.
Assembly: hg38
Supplementary files format and content: alignment_csv, cool, mcool, bigWig, CpG_context
Library strategy: in situ HiPore-C Seq

molecule: genomic DNA

source_name: blood

growth_protocol: Human B lymphocytes GM12878 cells(Coriell Institue) and K562 cells were incubated in 1 × RPMI1640 media supplemented with 15%(GM12878) or 10%(K562) fetal bovine serum at 37 °C with 5% CO2.

extract_protocol:
15 million GM12878 or K562 cells were spun down and resuspended in 10 ml fresh medium. Cells were fixed with 1% formaldehyde and incubating for 10 minutes at room temperature (RT). After quenching, cell were lysed and cell nuclei were collected, then chromatin was digested with DpnII restriction enzyme and ligated with T4 DNA ligase, and recrosslinking reversal was performed with Proteinase K or Pronase.  Finally DNA was purified using Phenol-Chloroform Isoamyl alcohol method.
A total amount of 3-4ug purified DNA per sample was used as input material for the ONT library preparations. After the sample was qualified, size select of ligation DNA > 3kb were performed using the PippinHT system(Sage Science, USA). Next, the ends of DNA were repaired, and A-ligation reaction were conducted with NEBNext Ultra II End Repair/dA-tailing Kit(Cat# E7546). The adapter in the SQK-LSK109(Oxford Nanopore Technologies, UK) was used for further ligation reaction and DNA library was measured by Qubit 4.0 Fluorometer(Invitrogen, USA).

value: blood

value: B-Lymphocyte

value: WT

tag: Sex

value: female


title: Activated McSC

description: 10x Genomics

value: melanocyte stem cell

value: Activated


title: K562_FC1

source_name: bone marrow

value: bone marrow

value: Lymphoblast


title: GM12878_FC5


title: F4

city: Spring House

first: Vinod

last: Krishna

state: Pennsylvania

address: 1400 McKean Road

institute: Janssen R&D LLC

data_processing:
The raw fastq files were examined for sequencing quality and adapter contamination using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), after which alignment to the human transcriptome was performed using STAR (36) with GRCh38 as the reference.
Quantification of the reads at the transcript level were performed using RSEM, and gene level quantification was obtained by the summarizeToGene function in the tximport R package
Supplementary files format and content: counts in gzipped text file format

source_name: Pulmonary Arterial Smooth Muscle

growth_protocol: RNA sequencing analysis was carried out on total RNA extracted from PAH-PASMCs exposed or not to BIX01294at 10mM for 48 hours. Qualitative and quantitative analysis of RNA was performed using NanoDrop2000 spectrophotometer (Thermo Scientific, USA).

extract_protocol: Library preparation and paired end RNAseq were performed by Cofactor genomics (St. Louis, MO) using Illumina HiSeq, on the PASMC samples at a read length of 150 bp and an average read depth of 50 million read pairs. Adapters were removed by the sequencing provider

value: Pulmonary Arterial Smooth Muscle

value: PAH-PASMC

value: Vehicle


title: F5


title: S.tuberosum cultivar Desirée, Rs infection 1

value: root

value: cultivar Desiree

value: Rs infected


title: GM12878_FC1

description: The read alignment result file contains genome annotation information for HiPore-C reads and ligated fragments.

data_processing:
Basecalls were performed using Guppy v4.5.3 with high-accuracy basecalling model “dna_r9.4.1_450bps_hac_prom.cfg”, and reads with quality score less than 7 were filtered.
HiPore-C reads were aligned and annotated with our in-house  developed MapPore-C pipeline.
The 5mC methylation were called using Megalodon v2.0.3 with model “res_dna_r941_prom_modbases_5mC_v001.cfg” in GPU servers.
Genome pairwise-contacts were generated by in-house python scripts, and cool/mool, hic files were generated using cooler v0.8.6.post0  and  juice tools v1.22.1, respectively.
Assembly: hg38
Supplementary files format and content: alignment_csv
Library strategy: in situ HiPore-C Seq


title: K562_FC4


title: F3


title: S.tuberosum cultivar CG, Control 1

value: cultivar Calalo Gaspar

value: control


title: GM12878_FC9


title: F1


title: WT BAL

city: Chicago

first: Gye Young

last: Park

state: IL

address: 909 S. Wolcott Avenue CMRB 3080

department: Medicine

institute: University of Illinois at Chicago

data_processing:
Raw reads were demultiplexed and single-cell gene expression quantified using CellRanger (10X Genomics).
Single-cell transcriptomes were analyzed further using Seurat. We removed cells with >=15% mitochondrial expression; and cells UMI counts <=1000 and number of genes <=500. We performed feature selection to retain the 6000 genes with the most variable expression, controlling for mean expression level, as these are likely to be most informative in differentiating cell sub-populations.
Normalized gene expression was computed in units of CPM (counts per million) and log-scaled. Dimensionality reduction was performed using PCA (principle component analysis), retaining the top 24 principle components based on statistical significance (JackStraw).
Genome_build: not provided
Supplementary_files_format_and_content: m5BA_stats_res.0.5.xlsx

source_name: bronchoalveolar lavage

extract_protocol:
Single cell capture with barcoded oligo-dT-containing gel bead was carried out using the 10x Genomics Chromium controller according to the manufacturer’s instructions.
Library preparation was performed using the 10X Chromium v3 kit, according to the manufacturer’s protocol (#CG000183).
Library was multiplexed in one S4 lane in Novaseq 6000 and sequenced with 2x150nt cycles.

treatment_protocol: Airway cells were collected by bronchoalveolar lavage with PBS in the wild type mouse.

value: Wild type

tag: age

value: 12 weeks

value: Bronchoalveolar lavage cells


title: H2

value: WT

value: BIX


title: S.tuberosum cultivar CR, Control 2

value: cultivar Cruza 148


title: GM12878_FC3

value: blood

value: B-Lymphocyte

value: female


title: H1

value: Pulmonary Arterial Smooth Muscle


title: K562_FC2

value: bone marrow

value: Lymphoblast


title: hiPSC_dervied_ETV2positive_nonEC_day4 [D5_D4_SP]

city: Leiden

first: Valeria

last: Orlova

address: Einthovenweg 20

country: Netherlands

institute: Leiden University Medical Center

data_processing:
LUMC BIOPET Gentrap pipeline was used to process raw data (https://github.com/biopet/biopet). Trimming of low-quality read ends was done with Sickle (v1.2). Cutadapt (v1.1) was used for adapters clipping. Using GSNAP (gmap-2014-12-23) reads were aligned to the human reference genome GRCh38. Gene read quantification was done with with htseq-count (v0.6.1p1) against the Ensembl v87 annotation. The R package cqn (v1.24.0) was used to normalize gene length and GC content bias.
Genome_build: GRch38
Supplementary_files_format_and_content: RPKM_normalized_ETV2_bulk.csv: RPKM normalized based on gene length and GC content.

growth_protocol: CMEC differentiation was performed as follow: Briefly, 25 × 10^3 cells per cm2 were seeded on plates coated with 75 µg/ml matrigel growth factor reduced (Corning) the day before differentiation (day -1). At day 0, cardiac mesoderm was induced by changing E8 to BPEL medium (Bovine Serum Albumin [BSA] Polyvinyl alcohol Essential Lipids; 5, supplemented with a mixture of cytokines (20 ng/ml BMP4, R&D Systems; 20 ng/ml ACTIVIN A, Miltenyi Biotec; 1.5 μM GSK3 inhibitor CHIR99021, Axon Medchem). After 3 days, cytokines were removed and a Wnt inhibitor (5 μM XAV939, Tocris) and VEGF (50 ng/ml, R&D Systems) was added for 3 days. BPEL medium was refreshed every 3 days supplemented with VEGF (50 ng/ml).

extract_protocol:
Total RNA for bulk samples was purified using the NucleoSpin RNA Kit  (Bioke’) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: VEC+ cells with and withot ETV2+ expression were sorted on day 4, 5, 6, 8 of CMEC differentiation. Total RNA were extracted from all samples and sent for bulk RNAseq.

tag: source cell line

value: ETV2 reporter hiPSC line

tag: timepoint


title: S.tuberosum cultivar Desirée, Rs infection 3

value: root

value: cultivar Desiree


title: S.tuberosum cultivar CG, Control 3

value: cultivar Calalo Gaspar


title: hiPSC_dervied_ETV2positive_nonEC_day5 [D4_D5_SP]


title: hiPSC_dervied_ETV2positive_nonEC_day4 [D4_D4_SP]


title: hiPSC_dervied_ETV2positive_EC_day6 [D3_D6_DP]


title: hiPSC_dervied_ETV2positive_nonEC_day6 [D3_D6_SP]


title: hiPSC_dervied_ETV2positive_nonEC_day8 [D4_D8_SP]


title: S.tuberosum cultivar Desirée, Rs infection 2

value: Rs infected


title: GM12878_FC4


title: hiPSC_dervied_ETV2positive_EC_day8 [D2_D8_DP]


title: F2

value: PAH-PASMC

value: Vehicle


title: S.tuberosum cultivar CR, Control 1

value: control


title: hiPSC_dervied_ETV2positive_nonEC_day5 [D2_D5_SP]


title: hiPSC_dervied_ETV2positive_EC_day6 [D2_D6_DP]


title: hiPSC_dervied_ETV2positive_EC_day8 [D3_D8_DP]


title: hiPSC_dervied_ETV2positive_EC_day5 [D4_D5_DP]


title: hiPSC_dervied_ETV2positive_EC_day4 [D2_D4_DP]


title: hiPSC_dervied_ETV2positive_nonEC_day6 [D4_D6_SP]


title: hiPSC_dervied_ETV2positive_EC_day8 [D1_D8_DP]


title: hiPSC_dervied_ETV2positive_EC_day5 [D1_D5_DP]


title: hiPSC_dervied_ETV2positive_EC_day6 [D1_D6_DP]


title: K562_FC3

value: WT


title: GM12878_FC2


title: HIPSC_CMEC_BATCH2

data_processing:
For scRNA-seq: Single-cell expression was quantified using unique molecular identifiers (UMIs) by 10x Genomics’ “Cell Ranger” software.
For bulk RNA seq: LUMC BIOPET Gentrap pipeline was used to process raw data (https://github.com/biopet/biopet). Trimming of low-quality read ends was done with Sickle (v1.2). Cutadapt (v1.1) was used for adapters clipping. Using GSNAP (gmap-2014-12-23) reads were aligned to the human reference genome GRCh38. Gene read quantification was done with with htseq-count (v0.6.1p1) against the Ensembl v87 annotation. The R package cqn (v1.24.0) was used to normalize gene length and GC content bias.
Genome_build: GRch38
Supplementary_files_format_and_content: Cell Ranger-generated files for scRNA-seq samples:  barcodes.tsv, genes.tsv, matrix.mtx.  RPKM_normalized_CMEC_PMEC_bulk.csv for bulkRNA-seq samples: RPKM normalized based on gene length and GC content.

source_name: hiPSCs

growth_protocol: CMEC differentiation was performed as follow: Briefly, 25 × 10e3 cells per cm2 were seeded on plates coated with 75 µg/ml matrigel growth factor reduced (Corning) the day before differentiation (day -1). At day 0, cardiac mesoderm was induced by changing E8 to BPEL medium (Bovine Serum Albumin [BSA] Polyvinyl alcohol Essential Lipids; 5, supplemented with a mixture of cytokines (20 ng/ml BMP4, R&D Systems; 20 ng/ml ACTIVIN A, Miltenyi Biotec; 1.5 μM GSK3 inhibitor CHIR99021, Axon Medchem). After 3 days, cytokines were removed and a Wnt inhibitor (5 μM XAV939, Tocris) and VEGF (50 ng/ml, R&D Systems) was added for 3 days. BPEL medium was refreshed every 3 days. PMEC differentiation was performed as follow: hiPSCs were split with a 1:12 ratio and seeded on 6-well plates coated with 75 µg/mL (growth factor reduced) Matrigel (Corning) on day -1. At day 0, paraxial mesoderm was induced by changing TeSR-E8 to BPEL medium, supplemented with 8 µM CHIR99021 (Axon Medchem). At day 2, cells were refreshed with BPEL supplemented 5 µM XAV939 (Tocris Bioscience). At day 3, cells were refreshed with BPEL supplemented 8 µM CHIR99021. From day 5 onwards, cells were refreshed every 3 days with BPEL medium supplemented with 50 ng/ml VEGF.

extract_protocol:
MTs were incubated in 290 U/mg of pre-warmed collagenase type II (Worthington) in HBSS solution (Sigma Aldrich). Single cells were used for single-cell RNAseq. Total RNA for bulk samples was purified using the NucleoSpin RNA Kit  (Bioke’) according to the manufacturer’s protocol.
10X library: Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kit, Version 2 Chemistry (10x Genomics) according to the manufacturer's protocol. For bulk RNA-seq: RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Prior to microtissue (MT) formation, hiPSC-ECs and hiPSC-CFs were prepared as follow: briefly, 2-3 days before MT formation, a vial of cryopreserved hiPSC-ECs and a vial of cryopreserved hiPSC-CFs were thawed and cultured either in BPEL medium supplemented with VEGF on plates coated with fibronectin (hiPSC-ECs), or in FGM3 medium on uncoated plates (hiPSC-CFs). The day of MT formation (day 0), hiPSC-ECs, hiPSC-CFs, SFs, ACFs, Cx43-sh-RNA CFs, SFs Empty LV and SFs CX43 LV were detached using TrypLE 1X for 5 min at 37 oC, 5% CO2, centrifuged for 3 min at 1100 rpm, resuspended in BPEL medium and counted. hiPSC-CMs at day 14-21 that showed > 80% purity, measured as the percentage of troponin positive cells by FACS analysis, were dissociated using the Multi Tissue Dissociation Kit 3 (Miltenyi Biotec) following the manufacturer’s instructions, resuspended in BPEL medium and counted. For MT, cell suspensions were combined together to 5000 cells (70% cardiomyocytes, 15% endothelial cells and 15% cardiac fibroblasts) per 50μl BPEL medium supplemented with VEGF (50 ng/ml) and FGF2 (5 ng/ml).  For all microtissues, cell suspensions were seeded on V-bottom 96 well microplates (Greiner bio-one) and centrifuged for 10 min at 1100 rpm. MTs were incubated at 37 oC, 5% CO2 for 21 days with media refreshed every 3-4 days. Dibutyryl cAMP (dbcAMP) treatment was performed on CMECFs in BPEL medium supplemented with 0.5 mM dbcAMP for 7 days (from day 14 to day 21). scRNAseq analysis of all MTs was performed after 21 days.

value: hiPSC-derived CMEC

tag: batch


title: hiPSC_dervied_ETV2positive_nonEC_day4 [D2_D4_SP]


title: hiPSC_dervied_ETV2positive_nonEC_day8 [D3_D8_SP]


title: hiPSC_dervied_ETV2positive_EC_day5 [D3_D5_DP]


title: hiPSC_dervied_ETV2positive_nonEC_day8 [D1_D8_SP]


title: hiPSC_dervied_ETV2positive_EC_day8 [D4_D8_DP]


title: H4

value: BIX


title: BSPCR-rep2-MSI1_ZF

city: Los Angeles

first: Zhenhui

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: BSPCR data replicate2 of MSI1_ZF

data_processing:
All libraries were sequenced at a length of 50 bps with HiSeq 2500 or NovaSeq 6000 platforms following manufacturer’s instructions (Illumina). Raw reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie2 (v2.1.0)43, allowing only uniquely mapped reads with perfect matches. Duplicated reads were removed with Samtools (v1.9)44. Peaks were called using MACS2 (v2.1.1)45.
BS-sPCR reads were mapped to TAIR10 reference genome by bsmap (v2.90) with allowing 2 mismatches and 1 best hit (-v 2 -w 1)46. Reads with three or more consecutively methylated CHH sites were considered as non-converted reads and removed from the analyses. DNA methylation levels were calculated by #C/ (#C + #T). Differential Methylated Regions (DMRs) were called by methdiff function with every 100bp bin for where the difference in CG, CHG, and CHH methylation are at least 0.4, 0.2, and 0.1, respectively.
Assembly: tair10
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf tissue

growth_protocol: Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown under green house condition (16 h light/8 h dark, 22C). Leaf tissues were collected from 4-5 week plants

extract_protocol: ChIP seq: Libraries were prepared with Ovation Ultra Low System V2 kits following the manufacturer’s instructions. BS seeq: 300 ng of DNA was sheared to 200bp with a Covaris S2 (Covaris). Libraries were prepared with the Epitect Bisulfite Conversion kit (QIAGEN) and the Ovation Ultralow Methyl-seq kit (NuGEN) following the manufacturer’s instructions. RNA seq: 1 ug of total RNA was used for library preparation with TruSeq Stranded mRNA kit (Illumina). Libraries were sequenced on HiSeq 2500 or NovaSeq 6000 (Illumina).

value: leaf tissue

tag: developmental stage

value: 4-5 weeks


title: BSPCR-rep2-ZF-SUVH2

description: BSPCR data replicate2 of ZF-SUVH2


title: BSPCR-rep2-YPET-ZF

description: BSPCR data replicate2 of YPET-ZF


title: hiPSC_dervied_ETV2positive_nonEC_day6 [D1_D6_SP]


title: hiPSC_dervied_ETV2positive_nonEC_day6 [D2_D6_SP]


title: BSPCR-rep2-HD2A_ZF

description: BSPCR data replicate2 of HD2A_ZF


title: BSPCR-rep2-HD2C_ZF

description: BSPCR data replicate2 of HD2C_ZF


title: hiPSC_dervied_ETV2positive_EC_day4 [D3_D4_DP]


title: BSPCR-rep2-LHP1_ZF

description: BSPCR data replicate2 of LHP1_ZF


title: BSPCR-rep2-HD2B_ZF

description: BSPCR data replicate2 of HD2B_ZF


title: BSPCR-rep2-Col-0

description: BSPCR data replicate2 of Col-0


title: hiPSC_dervied_ETV2positive_nonEC_day4 [D3_D4_SP]


title: hiPSC_dervied_ETV2positive_EC_day6 [D4_D6_DP]


title: hiPSC_dervied_ETV2positive_EC_day4 [D4_D4_DP]


title: hiPSC_dervied_ETV2positive_EC_day5 [D2_D5_DP]


title: BSPCR-rep2-JMJ18_ZF

description: BSPCR data replicate2 of JMJ18_ZF


title: hiPSC_dervied_ETV2positive_nonEC_day5 [D3_D5_SP]


title: He_1000_3

city: Wuhan

first: Satheeswaran

last: Thanagraj

state: Hubei

address: Lumo Road

department: Marine Science

institute: China University of Geosciences

data_processing:
We eliminated the low-quality reads and those with a high percentage (0.05%) of unknown bases (N) using PrintSeq (v0.20.4) and Trimmomatic (v0.38)
The resulting Q20 clean reads were then matched to reference gene sequences using Bowtie2 (v2.2.5).
The Trinity de novo assembler (v2.8.4) was used to perform de novo sequence assembly based on high-quality reads.
The raw assembly data were filtered using TransDecoder (v5.5.0) on the basis of a 300-nucleotide transcript length and identifiable CDSs
Using BUSCO (v3)78, alternative CDS splice isoforms or transcripts were selected as unigenes.
Supplementary files format and content: We calculated the FDR for each p-value, and terms with an FDR less than 0.01 were considered to be significantly enriched.

organism: Heterosigma akashiwo

source_name: Whole cell

growth_protocol: The raphidophyte (H. akashiwo) was isolated from the Qinhuangdao coastal waters, Bohai Sea. Once isolated the stock culture was maintained in an artificial seawater medium. Cells were maintained with light intensity of 100–120 µmol photons m-2 s-1 by white light in a 12:12 light: dark cycle at a temperature of 21 °C.

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, USA) following the manufacturer’s instructions. For each sample, approximately 5 µg of RNA was used to construct a cDNA library. The RNA quality was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
First-strand cDNA was then generated to create the final cDNA library on an Illumina platform (San Diego, USA) with 90 nucleotide pair reads.
The cDNA library was sequenced using paired-end reads of 90 nucleotides on an Illumina HiSeq 2000 (San Diego, USA).

treatment_protocol: Cells were transferred into three 1000 mL tissue culture flasks containing ASM medium subjected to the present, 21°C:400 ppm (Low Temperature-LT; Low Carbon-dioxide-LC) and future ocean conditions, 25°C and 1000 ppm (High Temperature-HT; High Carbon-dioxide-HC).

value: Whole cell

value: whole cell

value: Eukaryote


title: He_400_3


title: BSPCR-rep1-HDA6-ZF

description: BSPCR data replicate1 of HDA6-ZF


title: BSPCR-rep1-ZF-SUVH2

description: BSPCR data replicate1 of ZF-SUVH2


title: HIPSC_CMEC_BATCH1


title: BSPCR-rep1-HD2A-ZF

description: BSPCR data replicate1 of HD2A-ZF


title: BSPCR-rep2-HDA6_ZF

description: BSPCR data replicate2 of HDA6_ZF


title: He_1000_2


title: BSPCR-rep1-YPET-ZF

description: BSPCR data replicate1 of YPET-ZF


title: BSPCR-rep1-JMJ14

description: BSPCR data replicate1 of JMJ14


title: hiPSC_dervied_ETV2positive_nonEC_day5 [D1_D5_SP]


title: BSPCR-rep2-JMJ14_ZF

description: BSPCR data replicate2 of JMJ14_ZF


title: He_400_1


title: BSPCR-rep1-MSI1-ZF

description: BSPCR data replicate1 of MSI1-ZF


title: BSPCR-rep1-HD2C-ZF

description: BSPCR data replicate1 of HD2C-ZF


title: BSPCR-rep1-LHP1-ZF

description: BSPCR data replicate1 of LHP1-ZF


title: BSPCR-rep1-JMJ18

description: BSPCR data replicate1 of JMJ18


title: hiPSC_dervied_ETV2positive_nonEC_day8 [D2_D8_SP]


title: ChIPseq-SET9-PolII-ELF7-ZF-rep2

description: ChIP-seq data set9 of Pol II-ELF7-ZF repliate2

tag: antibody

value: anti-Pol II (Abcam)

tag: target protein

value: Pol II


title: ChIPseq-SET9-PolII-fwa-rep2

description: ChIP-seq data set9 of Pol II-fwa repliate2

tag: strain


title: ChIPseq-SET9-H3-ELF7-ZF-rep2

description: ChIP-seq data set9 of H3-ELF7-ZF repliate2

tag: tissue

value: anti-H3 (Abcam)


title: BSPCR-rep2-fwa

description: BSPCR data replicate2 of fwa


title: BSPCR-rep2-ELF7_ZF

description: BSPCR data replicate2 of ELF7_ZF


title: ChIPseq-SET8-PolII-HD2A-ZF-rep1

description: ChIP-seq data set8 of Pol II-HD2A-ZF repliate1


title: ChIPseq-SET8-PolII-ELF7-ZF-rep1

description: ChIP-seq data set8 of Pol II-ELF7-ZF repliate1


title: He_1000_1


title: BSPCR-rep2-CPL2

description: BSPCR data replicate2 of CPL2


title: ChIPseq-SET8-PolII-fwa-rep1

description: ChIP-seq data set8 of Pol II-fwa repliate1


title: BSPCR-rep1-Col-0

description: BSPCR data replicate1 of Col-0


title: ChIPseq-SET8-H3-fwa-rep1

description: ChIP-seq data set8 of H3-fwa repliate1


title: CIR_2

city: Wuxi

first: Jin

last: Zhao

address: 299 Qingyang Road

institute: Wuxi People’s Hospital Affiliated to Nanjing Medical University

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Excel files include fpkm, tpm, and read count values for each Sample

source_name: left lung

extract_protocol:
RNA was extracted with the TRIzol method using standard TRIzol RNA extraction protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The donor lungs were recovered after being flushed with 10ml LPD solution and inflated with 50% oxygen. Cold ischemia was induced by storing donor lungs in 20ml LPD at 4°C for 24 hours. Then, the left donor lung was cuffed and implanted into recipients within 45 minutes. After the 4-hour reperfusion, the recipient mice were sacrificed and the transplanted lungs were collected

value: left lung

tag: genotype

value: wild type

value: Adult

value: Male

value: cold Ischemia 24 hours, reperfusion 4 hours


title: ChIPseq-SET8-H3-HD2A-ZF-rep1

description: ChIP-seq data set8 of H3-HD2A-ZF repliate1


title: Control_3

value: native


title: Control_2


title: He_400_2

tag: cell line


title: ChIPseq-SET8-H3-ELF7-ZF-rep1

description: ChIP-seq data set8 of H3-ELF7-ZF repliate1


title: BSPCR-rep1-ELF7-ZF

description: BSPCR data replicate1 of ELF7-ZF


title: ChIPseq-SET7-H3K9ac-MSI1-ZF-rep1

description: ChIP-seq data set7 of H3K9ac-MSI1-ZF repliate1

value: anti-H3K9ac (Abcam)


title: ChIPseq-SET7-H3K9ac-MSI1-ZF-rep2

description: ChIP-seq data set7 of H3K9ac-MSI1-ZF repliate2


title: CIR_4


title: ChIPseq-SET7-H3K9ac-HDA6-ZF-rep2

description: ChIP-seq data set7 of H3K9ac-HDA6-ZF repliate2


title: CIR_3


title: BSPCR-rep1-CPL2-ZF

description: BSPCR data replicate1 of CPL2-ZF


title: ND_5

city: Beijing

first: Boyuan

last: Ma

address: Qinghuayuan 1

institute: Tsinghua University

data_processing:
For each sample, a total of >20 M reads (single-end, 50 nt) were produced. Adapters were then deleted, and the reads were quality filtered utilizing Trimmomatic ver. 0.33, with the average base quality score cutoff threshold set at 20 over a three-base window. Reads with a post-trimming length of less than 20 bases were excluded.
Assembly: STAR version STAR 2.5.2b was used to map the cleaned reads to the Mus musculus genome reference (GRCm38). The featureCounts function of the subread package version 1.6.0 was used to calculate the number of reads aligned to the exon regions of each of the identified genes. Multiple mapped reads and reads overlapping with multiple features were excluded.
Supplementary files format and content: FPKM, TPM, and read counts

source_name: Liver tissue

growth_protocol: 1. Wildtype (WT) and albumin-knockout (AKO) were fed with normal diet. We harvested the liver tissues from WT and AKO mice at 3-week, 8-week, and 10-month of age. 2. Wildtype (WT) and albumin-knockout (AKO) mice were fed with Normal diet (ND) or Western diet (WD) for 8 weeks from the age of 8 weeks. We harvested the liver tissues from WT-ND, WT-WD, AKO-ND, AKO-WD mice . 3. Wildtype (WT) mice fed with HFD from the age of 8 weeks were injected by 17-AAG at the 3rd, 4th, 5th, 6.5th, and 8th weeks of the HFD feeding process. The control group was injected by the solvent. Another group of mice at the same age was fed with normal diet (ND). We harvested the liver tissues ND, Ctrl, and 17-AAG mice.

extract_protocol:
The mirVana RNA Isolation Kit (Life Technologies) was used to isolate total hepatic or cellular mRNAs.  Agilent 2200 TapeStation Nucleic Acid System was used to determine the RNA integrity number (RIN) and concentration of all RNA samples (Agilent, CA). For the construction of the cDNA library, RNA samples having a RIN greater than 8.5 were employed. rRNA was depleted using hybridization capture to facilitate the identification of protein-coding RNAs.
DNase I degrade double-stranded and single-stranded DNA contaminant in RNA samples. mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. mRNA were fragmented into small pieces using fragmentation reagent. First-strand cDNA was generated using random hexamer-primed reverse transcription, then was followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were  ligated to the ends of these 3’ adenylated cDNA fragments. This process is to amplify the cDNA fragments with adaptors from previous step. PCR products are purified with the SPRI beads, and dissolved in EB solution. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. Library was validating on the Agilent Technologies 2100 bioanalyzer.

value: Liver tissue

value: Wildtype (WT)

value: Normal diet (ND)


title: BSPCR-rep1-HD2B-ZF

description: BSPCR data replicate1 of HD2B-ZF

value: leaf tissue

value: 4-5 weeks


title: ChIPseq-SET7-H3K9ac-HDA6-ZF-rep1

description: ChIP-seq data set7 of H3K9ac-HDA6-ZF repliate1


title: ND_2


title: ND_1


title: ChIPseq-SET7-H3K9ac-fwa-rep1

description: ChIP-seq data set7 of H3K9ac-fwa repliate1


title: Ctrl_5

value: HFD, solvent injection


title: ChIPseq-SET7-H3K14ac-MSI1-ZF-rep1

description: ChIP-seq data set7 of H3K14ac-MSI1-ZF repliate1

value: anti-H3K14ac (Abcam)


title: Ctrl_4


title: ChIPseq-SET7-H3K14ac-fwa-rep2

description: ChIP-seq data set7 of H3K14ac-fwa repliate2


title: ChIPseq-SET7-H3K14ac-fwa-rep1

description: ChIP-seq data set7 of H3K14ac-fwa repliate1


title: ChIPseq-SET7-H3-MSI1-ZF-rep2

description: ChIP-seq data set7 of H3-MSI1-ZF repliate2


title: AAG_4

value: HFD, injected by 17-AAG


title: BSPCR-rep1-fwa

description: BSPCR data replicate1 of fwa


title: ChIPseq-SET9-H3-HD2A-ZF-rep2

description: ChIP-seq data set9 of H3-HD2A-ZF repliate2


title: CIR_1


title: ChIPseq-SET9-PolII-HD2A-ZF-rep2

description: ChIP-seq data set9 of Pol II-HD2A-ZF repliate2

value: anti-Pol II (Abcam)

value: Pol II


title: ChIPseq-SET7-H3-HDA6-ZF-rep1

description: ChIP-seq data set7 of H3-HDA6-ZF repliate1

value: anti-H3 (Abcam)


title: ChIPseq-SET7-H3-fwa-rep2

description: ChIP-seq data set7 of H3-fwa repliate2


title: WT_WD_6

value: Western diet (WD) for 8 weeks


title: ChIPseq-SET9-H3-fwa-rep2

description: ChIP-seq data set9 of H3-fwa repliate2


title: WT_WD_5


title: WT_WD_3


title: ND_4


title: ChIPseq-SET6-H3K9ac-HD2A-ZF-rep2

description: ChIP-seq data set6 of H3K9ac-HD2A-ZF repliate2


title: ChIPseq-SET6-H3-HD2A-ZF-rep2

description: ChIP-seq data set6 of H3-HD2A-ZF repliate2


title: ChIPseq-SET6-H3K9ac-fwa-rep2

description: ChIP-seq data set6 of H3K9ac-fwa repliate2


title: ChIPseq-SET7-H3K14ac-MSI1-ZF-rep2

description: ChIP-seq data set7 of H3K14ac-MSI1-ZF repliate2


title: ChIPseq-SET7-H3K9ac-fwa-rep2

description: ChIP-seq data set7 of H3K9ac-fwa repliate2


title: ChIPseq-SET7-H3-MSI1-ZF-rep1

description: ChIP-seq data set7 of H3-MSI1-ZF repliate1


title: Ctrl_2


title: WT_ND_8

value: Normal diet (ND) for 8 weeks


title: ChIPseq-SET5-H4K16ac-HD2C-ZF-rep2

description: ChIP-seq data set5 of H4K16ac-HD2C-ZF repliate2

value: anti-H4K16ac (Abcam)


title: ChIPseq-SET5-H4K16ac-HD2B-ZF-rep2

description: ChIP-seq data set5 of H4K16ac-HD2B-ZF repliate2


title: ChIPseq-SET5-H4K16ac-fwa-rep2

description: ChIP-seq data set5 of H4K16ac-fwa repliate2


title: Control_1

value: left lung

value: wild type

value: Adult

value: Male


title: ChIPseq-SET5-H3-HD2C-ZF-rep2

description: ChIP-seq data set5 of H3-HD2C-ZF repliate2


title: AAG_2

value: Liver tissue

value: Wildtype (WT)


title: ChIPseq-SET5-H3-HD2B-ZF-rep2

description: ChIP-seq data set5 of H3-HD2B-ZF repliate2

value: leaf tissue


title: Ctrl_1


title: ChIPseq-SET7-H3K14ac-HDA6-ZF-rep1

description: ChIP-seq data set7 of H3K14ac-HDA6-ZF repliate1

value: 4-5 weeks


title: ChIPseq-SET7-H3K14ac-HDA6-ZF-rep2

description: ChIP-seq data set7 of H3K14ac-HDA6-ZF repliate2


title: ChIPseq-SET5-H3-HD2A-ZF-rep2

description: ChIP-seq data set5 of H3-HD2A-ZF repliate2


title: WT_WD_10


title: WT_WD_1


title: WT_WD_8


title: AKO_WD_5

value: albumin-knockout (AKO)


title: AAG_3


title: ND_3

value: Normal diet (ND)


title: AKO_WD_3


title: AAG_1

value: HFD, injected by 17-AAG


title: WT_ND_10


title: ChIPseq-SET4-H3K27ac-HD2C-ZF-rep2

description: ChIP-seq data set4 of H3K27ac-HD2C-ZF repliate2-L2

value: anti-H3K27ac (Abcam)


title: AKO_WD_2


title: ChIPseq-SET4-H3K27ac-HD2B-ZF-rep2

description: ChIP-seq data set4 of H3K27ac-HD2B-ZF repliate2-L2


title: AKO_WD_1


title: AKO_ND_6


title: ChIPseq-SET5-H3-fwa-rep2

description: ChIP-seq data set5 of H3-fwa repliate2


title: Ctrl_3

value: HFD, solvent injection


title: AKO_ND_5


title: ChIPseq-SET4-H3K27ac-fwa2-rep2

description: ChIP-seq data set4 of H3K27ac-fwa2 repliate2-L2


title: ChIPseq-SET5-H4K16ac-HD2A-ZF-rep2

description: ChIP-seq data set5 of H4K16ac-HD2A-ZF repliate2


title: ChIPseq-SET7-H3-HDA6-ZF-rep2

description: ChIP-seq data set7 of H3-HDA6-ZF repliate2

value: anti-H3 (Abcam)


title: WT_ND_6


title: ChIPseq-SET4-H3-HD2B-ZF-rep2

description: ChIP-seq data set4 of H3-HD2B-ZF repliate2-L2


title: AKO_ND_4


title: ChIPseq-SET4-H3-fwa2-rep2

description: ChIP-seq data set4 of H3-fwa2 repliate2-L2


title: AKO_ND_1


title: ChIPseq-SET4-H3-fwa1-rep2

description: ChIP-seq data set4 of H3-fwa1 repliate2-L2


title: ChIPseq-SET6-H3-fwa-rep2

description: ChIP-seq data set6 of H3-fwa repliate2


title: ChIPseq-SET7-H3-fwa-rep1

description: ChIP-seq data set7 of H3-fwa repliate1


title: ChIPseq-SET3-H4K16ac-HD2C-ZF-rep1

description: ChIP-seq data set3 of H4K16ac-HD2C_ZF repliate1


title: WT_10M_2

value: 10 months


title: WT_10M_1


title: AKO_ND_2

value: Normal diet (ND) for 8 weeks


title: WT_8W_2

value: 8 weeks


title: WT_8W_1


title: ChIPseq-SET3-H4K16ac-fwa2-rep1

description: ChIP-seq data set3 of H4K16ac-fwa2 repliate1

value: anti-H4K16ac (Abcam)


title: WT_ND_5


title: ChIPseq-SET4-H3K27ac-HD2A-ZF-rep2

description: ChIP-seq data set4 of H3K27ac-HD2A-ZF repliate2-L2


title: WT_ND_3


title: AKO_WD_7

value: Western diet (WD) for 8 weeks


title: ChIPseq-SET3-H4K16ac-fwa1-rep1

description: ChIP-seq data set3 of H4K16ac-fwa1 repliate1


title: WT_ND_1


title: ChIPseq-SET4-H3-HD2C-ZF-rep2

description: ChIP-seq data set4 of H3-HD2C-ZF repliate2-L2


title: WT_3W_1

value: 3 weeks


title: AKO_WD_6


title: AKO_10M_2


title: WT_10M_3


title: WT_8W_3


title: AKO_8W_3


title: ChIPseq-SET4-H3K27ac-fwa1-rep2

description: ChIP-seq data set4 of H3K27ac-fwa1 repliate2-L2


title: WT_3W_3


title: AKO_8W_2


title: AKO_ND_3


title: ChIPseq-SET3-H4K16ac-HD2B-ZF-rep1

description: ChIP-seq data set3 of H4K16ac-HD2B_ZF repliate1


title: ChIPseq-SET3-H4K16ac-HD2A-ZF-rep1

description: ChIP-seq data set3 of H4K16ac-HD2A_ZF repliate1


title: ChIPseq-SET3-H3K9ac-HD2C-ZF-rep1

description: ChIP-seq data set3 of H3K9ac-HD2C_ZF repliate1

value: anti-H3K9ac (Abcam)


title: ChIPseq-SET3-H3K27ac-HD2A-ZF-rep1

description: ChIP-seq data set3 of H3K27ac-HD2A-ZF repliate1


title: ChIPseq-SET3-H3K27ac-fwa2-rep1

description: ChIP-seq data set3 of H3K27ac-fwa2 repliate1


title: AKO_10M_1

value: Liver tissue


title: WT_3W_2

value: Wildtype (WT)


title: ChIPseq-SET4-H3-HD2A-ZF-rep2

description: ChIP-seq data set4 of H3-HD2A-ZF repliate2-L2

value: leaf tissue


title: ChIPseq-SET3-H3K9ac-HD2B-ZF-rep1

description: ChIP-seq data set3 of H3K9ac-HD2B_ZF repliate1

value: 4-5 weeks


title: AKO_3W_1

value: albumin-knockout (AKO)


title: ChIPseq-SET3-H3-HD2A-ZF-rep1

description: ChIP-seq data set3 of H3-HD2A-ZF repliate1


title: ChIPseq-SET3-H3-HD2B-ZF-rep1

description: ChIP-seq data set3 of H3-HD2B-ZF repliate1


title: ChIPseq-SET3-H3K9ac-HD2A-ZF-rep1

description: ChIP-seq data set3 of H3K9ac-HD2A_ZF repliate1


title: AKO_3W_2


title: ChIPseq-SET3-H3K27ac-HD2B-ZF-rep1

description: ChIP-seq data set3 of H3K27ac-HD2B-ZF repliate1


title: AKO_10M_3


title: ChIPseq-SET3-H3K9ac-fwa2-rep1

description: ChIP-seq data set3 of H3K9ac-fwa2 repliate1


title: ChIPseq-SET3-H3K9ac-fwa1-rep1

description: ChIP-seq data set3 of H3K9ac-fwa1 repliate1


title: ChIPseq-SET3-H3K27ac-HD2C-ZF-rep1

description: ChIP-seq data set3 of H3K27ac-HD2C_ZF repliate1


title: ChIPseq-SET20-H3K36me3-fwa-rep2

description: ChIP-seq data set20 of H3K36me3-fwa repliate2_R1.fastq.gz

value: anti-H3K36me3 (Abcam)


title: AKO_3W_3


title: CAM15F_102

city: Nouzilly

first: Sophie

last: REHAULT-GODBERT

address: INRAE Centre Val de Loire, UMR BOA

country: France

institute: INRAE

data_processing:
Platform HiSeqPE-150
Clustering and sequencing The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Quality control Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Data filtering Raw reads are filtered to remove reads with adapter contamination or reads with low quality (Discard reads with adaptor contamination;Discard reads when uncertain nucleotides constitute more than 10% of either read (N > 10%);  Discard reads when low quality nucleotides (base quality less than 20) constitute more than 50% of the read)
Mapping to reference genome Reference genome (GRCg6a (GCA_000002315.5)) and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads.
Quantification HTSeq was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: (GRCg6a (GCA_000002315.5))
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Gallus gallus

source_name: Chorioallantoic membrane

growth_protocol: Fertilized eggs (ROSS 308) were stored 3 days (16°C, 80% relative humidity) prior to incubation during 11 or 15 days (55% Relative humidity, 37,8°C). After 11 or 15 days of incubation, eggs were opened and embryos were decapited following IACUC guidelines. A piece of embryo neck was removed to perform molecular sexing. Chorioallantoic membranes were removed from eggs, quickly rinsed in sterile physiologic solution and frozen in liquid nitrogen. Samples were all stored at -80°C prior to RNA extraction.

extract_protocol:
RNA extraction was achieved using Macherey Nagel Nucleospin RNA kit. RNA concentration was determined using Nanodrop and RNA quality control was checked using Agilent. A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: breed

value: Ross 308 broiler

value: Chorioallantoic membrane

value: Prehatch :15 days of incubation

tag: gender

value: Female


title: ChIPseq-SET3-H3-fwa2-rep1

description: ChIP-seq data set3 of H3-fwa2 repliate1

value: anti-H3 (Abcam)


title: ChIPseq-SET20-H3K36me2-fwa-rep2

description: ChIP-seq data set20 of H3K36me2-fwa repliate2_R1.fastq.gz

value: anti-H3K36me2 (Abcam)


title: ChIPseq-SET3-H3K27ac-fwa1-rep1

description: ChIP-seq data set3 of H3K27ac-fwa1 repliate1

value: anti-H3K27ac (Abcam)


title: ChIPseq-SET3-H3-fwa1-rep1

description: ChIP-seq data set3 of H3-fwa1 repliate1


title: AKO_8W_1

value: 8 weeks


title: CAM15M_98

value: Male


title: ChIPseq-SET20-H3K36me2-ELF7-ZF-rep2

description: ChIP-seq data set20 of H3K36me2-ELF7-ZF repliate2_R1.fastq.gz


title: Sheep_4

city: Maastricht

first: Vanessa

last: LaPointe

address: Universiteitssingel 40

institute: MERLN Institute

data_processing:
BCL files resulting from sequencing were transformed to FASTQ and read 1 was used to identify the Illumina library index and CEL-seq sample barcode.
Read 2 was aligned to the specific RefSeq reference genome of each species using STAR genome aligner (Dobin et al. 2013)
The data from all samples were loaded in R (version 4.1.2) (R Core Team 2013) to perform analysis.
Assembly: Human: Hg38
Assembly: Sheep: ARS-UI_Ramb_v2.0
Assembly: Rabbit: OryCun2.0
Supplementary files format and content: _total.ReadCounts.tsv final datasets containing the read counts for all genes across each species

organism: Ovis aries

source_name: Cornea

growth_protocol: All human corneas were stored up to 22 days in organ culture media at 31 °C and had a minimum endothelial cell density of 2300 cells/mm2. Organ culture media comprised the following: minimum essential medium (MEM) supplemented with 20 mM HEPES, 26 mM sodium bicarbonate, 2% (v/v) newborn calf serum (Thermo Fisher Scientific), 10 IU/mL penicillin, 0.1 mg/mL streptomycin and 0.25 μg/mL amphotericin.

extract_protocol:
Corneal endothelium samples were extracted from the tissue and sequenced as follows:  Isolation of human corneal endothelium  Of the five human corneal endothelial samples, four were discarded peripheral endothelial rims (1.5 mm wide) resulting from tissue preparation for Descemet’s membrane endothelial Keratoplasty (DMEK) according to clinical practice (Català et al. 2020) and one (Human 5) was a whole endothelium stripped from a cornea deemed unsuitable for transplant (Table 1).     The four endothelial rims were lysed in 300 μL trizol within 48 h after tissue preparation. From the whole cornea, the complete endothelium was manually stripped following lysis in 300 μL trizol. Briefly, the cornea was vacuum-fixed in a punch base (e.janach) endothelial-cell side up and trephined with a 10 mm Ø corneal punch at a fixed depth of 100 μm (e.janach). To delimit the endothelial trephined line, the cornea was stained with a trypan blue solution (0.4%) for 30 s, and washed with balanced salt solution (BSS) ophthalmic irrigation solution. The corneal endothelium was then gently lifted using a DMEK cleavage hook (e.janach), fully stripped using angled McPherson tying forceps, and immediately transferred to trizol. All sample lysates were stored at -80 °C until further use.    Isolation of sheep corneal endothelium  All samples (n=5) were obtained from Texel sheep used for a dorsal titanium implant study from the animal facility at Maastricht University (Table 1). Five eyes were enucleated from 1 to 2-year-old female Texel sheep within 4 h of sacrifice, and corneoscleral disks were excised from whole ocular gloves. Corneal endothelial cells were enzymatically treated and scrapped from the corneoslceral disks because stripping of the endothelium proved not successful due to the tissue characteristics. For this purpose, corneoscleral disks were rinsed with Dulbecco's phosphate buffered saline (DPBS), vaccum-fixed in a punch base (e.janach) endothelial-side up and treated with approximately 150 μL of StemPro Accutase (Thermo Fisher Scientific) for 20 min at ambient temperature. Corneal endothelial cells were then gently scraped using a DMEK cleavage hook (e.janach) and rinsed off the corneoscleral disk with approximately 2 mL of MEM (Thermo Fisher Scientific). The cell suspension was then transferred to a 15 mL tube, centrifuged at 800 × g for 5 min and lysed in 300 μL trizol. All sample lysates were stored at -80 °C until further use.    Isolation of rabbit corneal endothelium  Eyes were obtained from New Zealand White rabbits used for other experimental purposes from the Utrecht University animal facility (n=3) and MSD Animal testing facility (n=2) in Boxmeer, the Netherlands (Table 1). Eyes were enucleated 30 min to 4 h after sacrifice, corneoscleral disks were excised from whole ocular globes, and corneal endothelium stripped. In brief, corneoscleral disks were rinsed with PBS, vacuum-fixed in a punch base endothelial-side up and trephined with a 10 mm Ø corneal punch at a fixed depth of 100 μm. To delimit the endothelial trephined line, the cornea was stained with a trypan blue solution (0.4%) for 30 s, and washed with BSS ophthalmic irrigation solution. The corneal endothelium was then gently lifted using a DMEK cleavage hook, fully stripped using angled McPherson tying forceps, and immediately transferred to 300 μL trizol. All sample lysates were stored at -80 °C until further use.
RNA isolation and bulk RNA sequencing  RNA isolation was performed following trizol isolation procedure, and RNA integrity was assessed with a 2100 Bioanalyzer (Agilent). RNA sequencing was performed at Single Cell Discoveries (Utrecht, the Netherlands). Libraries were prepared following CEL-seq2 protocol (Hashimshony et al. 2016) to enable sample multiplexing. Paired-end sequencing was performed on Illumina Nextseq500, high output 2 × 75 bp run mode, at a sequencing depth of 20 million reads/sample.     Data analysis and pre-processing  BCL files resulting from sequencing were transformed to FASTQ and read 1 was used to identify the Illumina library index and CEL-seq sample barcode. Read 2 was aligned to the specific RefSeq reference genome of each species, namely: hg19 for human, OryCun2.0 for rabbit, and ARS-UI_Ramb_v2.0 for sheep using STAR genome aligner (Dobin et al. 2013).   The data from all samples were loaded in R (version 4.1.2) (R Core Team 2013) to perform analysis. Gene homology mapping from rabbit and sheep to human was performed using the orthogene R-package (version 1.1.0) with the g:profiler method (Raudvere et al. 2019). The three datasets were combined and only genes with homologs in all three species were included in the downstream analyses. Once the data was combined quantile normalization was performed using the limma package (version 3.52.2) (Ritchie et al. 2015).

treatment_protocol: Not applicable to this study

tag: sample number

tag: gender - age

value: Female - 1-2 years

tag: dissection

value: Endothelium


title: ChIPseq-SET3-H3-HD2C-ZF-rep1

description: ChIP-seq data set3 of H3-HD2C-ZF repliate1


title: CAM15M_100


title: Sheep_2


title: Sheep_1


title: Sheep_5


title: ChIPseq-SET20-H3-fwa-rep2

description: ChIP-seq data set20 of H3-fwa repliate2_R1.fastq.gz


title: ChIPseq-SET20-H3K36me3-ELF7-ZF-rep2

description: ChIP-seq data set20 of H3K36me3-ELF7-ZF repliate2_R1.fastq.gz


title: CAM15F_95


title: ChIPseq-SET20-H3-ELF7-ZF-rep2

description: ChIP-seq data set20 of H3-ELF7-ZF repliate2_R1.fastq.gz


title: CAM15M_93


title: Sheep_3


title: CAM15F_83


title: ChIPseq-SET2-H3K4me3-fwa-rep2

description: ChIP-seq data set2 of H3K4me3-fwa repliate2

value: anti-H3K4me3 (Millipore Sigma)


title: CAM15F_88


title: ChIPseq-SET2-H3K4me3-JMJ14-ZF-rep2

description: ChIP-seq data set2 of H3K4me3-JMJ14-ZF repliate2


title: CAM15M_81


title: ChIPseq-SET2-H3K4me3-ELF7-ZF-rep2

description: ChIP-seq data set2 of H3K4me3-ELF7-ZF repliate2


title: CAM15M_86


title: ChIPseq-SET2-H3K27me3-MSI1-ZF-rep2

description: ChIP-seq data set2 of H3K27me3-MSI1-ZF repliate2

value: anti-H3K27me3 (Millipore Sigma)


title: CAM15F_79


title: ChIPseq-SET2-H3K27me3-LHP1-ZF-rep2

description: ChIP-seq data set2 of H3K27me3-LHP1-ZF repliate2

value: leaf tissue


title: ChIPseq-SET2-H3K27me3-fwa-rep2

description: ChIP-seq data set2 of H3K27me3-fwa repliate2

value: 4-5 weeks


title: CAM15M_76


title: CAM15F_74


title: CAM15F_64


title: CAM15M_72


title: CAM15F_59


title: ChIPseq-SET2-H3-MSI1-ZF-rep2

description: ChIP-seq data set2 of H3-MSI1-ZF repliate2


title: CAM15M_67


title: CAM15F_70


title: ChIPseq-SET2-H3K27me3-ELF7-ZF-rep2

description: ChIP-seq data set2 of H3K27me3-ELF7-ZF repliate2


title: CAM15M_57


title: CAM15F_54


title: ChIPseq-SET2-H3-JMJ14-ZF-rep2

description: ChIP-seq data set2 of H3-JMJ14-ZF repliate2


title: ChIPseq-SET2-H3K27me3-JMJ14-ZF-rep2

description: ChIP-seq data set2 of H3K27me3-JMJ14-ZF repliate2


title: CAM11F_46

value: Prehatch :11 days of incubation


title: ChIPseq-SET2-H3-fwa-rep2

description: ChIP-seq data set2 of H3-fwa repliate2


title: CAM11M_44


title: UVDDB_UV_r2

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Commercially synthesized, high-density, single-stranded DNA microarrays from Agilent were first double-stranded via primer extension as done in previous assays (Berger et al, Nature Biotechnology 2006; Shen et al, Cell Systems 2018). The arrays were partially irradiated with UVC such that only some chambers were exposed to UVC while others were not. In order to irradiate only certain parts of the array, and protect the rest from UV irradiation, a cover/gasket slide was cut to the desired size are used to partially cover the DNA array. Next, the gasket slide was fully covered using Cryo-Babies® labels, and the array-gasket slide sandwich was placed in an open container with 1x PBS. To irradiate the DNA on the array, we used a Stratalinker® UV Crosslinker 1800 instrument and conducted a series of irradiations with UVC. Using the energy mode, the container was irradiated with 100 J/m2, randomly repositioned inside the crosslinker 15 times to achieve 1,500 J/m2. Midway through the series, the PBS was replaced in order to keep the solution at room temperature. This procedure resulted in a DNA array with some chambers of the array irradiated by UV and others not irradiated. Samples with the “UV” condition used irradiated chambers while those with a “Non-UV” condition used non-irradiated chambers. The arrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk for 1 hour as done in prior assays (Shen et al, Cell Systems 2018). Proteins were incubated at the indicated concentration using the buffers referred to in the manuscript for 1 hour. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min (Shen et al, Cell Systems 2018). Then the arrays were incubated with either Penta-His Alexa488-conjugated antibody and Penta-His Alexa647-conjugated antibody (1:20 and 1:40 ratio respectively) in a buffer with 2% (wt/vol) milk and 0.05% Tween for 1 hour (buffer details described in the manuscript). After incubation, the arrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min as done in prior work (Shen et al, Cell Systems 2018).

scan_protocol: Protein bound microarrays were scanned at 488nm using a GenePix 4400A at multiple laser power and gain settings to best capture the signal and avoid saturation of spots. The resulting TIF images were processed using GenePix Pro 7.3.

data_processing: The raw data collected using the GenePix® 4400A microarray scanner was processed using the Seed and Wobble suite (Berger et al, Nature Biotechnology 2006), with modifications to adapt the k-mer data to our UV-Bind universal design, as described in the manuscript. For each unique sequence tested, median values over the spots containing that sequence were used unless otherwise noted (i.e. for the universal design sequences and for the competition tests). The number of replicate spots for each sequence varied between 3 and 20, depending on the DNA library. Processing of k-mers and PWMs using Seed-and-Wobble was done using the adjusted signal (i.e. Alexa488Adjusted or Alexa635Adjusted column) in the alldata.txt file as done by default (Berger et al, Nature Biotechnology 2006).

label: Alexa 488

molecule: protein

source_name: Human UVDDB

label_protocol: Label protocol is detailed in the manuscript for all tested transcription factors and antibodies.

growth_protocol: Cell growth protocol is detailed in the manuscript for all tested transcription factors and antibodies.

extract_protocol: Extract protocol is detailed in the manuscript for all tested transcription factors and antibodies.

tag: protein

value: UVDDB

tag: protein concentration

tag: array condition

value: UV


title: UVDDB_UV_r1


title: CAM15M_52

value: Ross 308 broiler

value: Chorioallantoic membrane

tag: age


title: UVDDB_NonUV_r1

value: Non-UV


title: 64PP_NonUV

type: other

description: Antibody

hyb_protocol: Commercially synthesized, high-density, single-stranded DNA microarrays from Agilent were first double-stranded via primer extension as done in previous assays (Berger et al, Nature Biotechnology 2006; Shen et al, Cell Systems 2018). The arrays were partially irradiated with UVC such that only some chambers were exposed to UVC while others were not. In order to irradiate only certain parts of the array, and protect the rest from UV irradiation, a cover/gasket slide was cut to the desired size are used to partially cover the DNA array. Next, the gasket slide was fully covered using Cryo-Babies® labels, and the array-gasket slide sandwich was placed in an open container with 1x PBS. To irradiate the DNA on the array, we used a Stratalinker® UV Crosslinker 1800 instrument and conducted a series of irradiations with UVC. Using the energy mode, the container was irradiated with 100 J/m2 , randomly repositioned inside the crosslinker 15 times to achieve 1,500 J/m2 . Midway through the series, the PBS was replaced in order to keep the solution at room temperature. This procedure resulted in a DNA array with some chambers of the array irradiated by UV and others not irradiated. Samples with the “UV” condition used irradiated chambers while those with a “Non-UV” condition used non-irradiated chambers. The arrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk for 1 hour as done in prior assays (Shen et al, Cell Systems 2018). Antibodies for CPD and 6-4PP were incubated in a 1:400 and 1:80 ratio respectively in a 1x PBS buffer of 2% (wt/vol) milk and 0.05% Tween for 1 hour. After incubation, the arrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min as done in prior work (Shen et al, Cell Systems 2018). Then the arrays were incubated with a secondary antibody of conjugated anti-mouse 488 at 1.3% volume in a PBS buffer with 2% (wt/vol) milk and 0.05% Tween for 1 hour. The arrays were then washed as previously described.

scan_protocol: Anti-CPD and anti-6-4PP bound microarrays were scanned at 488nm using a GenePix 4400A at multiple laser power and gain settings to best capture the signal and avoid saturation of spots. The resulting TIF images were processed using GenePix Pro 7.3.

molecule: other

source_name: Mouse Anti-6-4PP

label_protocol: Label protocol is detailed in the manuscript for all tested proteins and antibodies.

growth_protocol: Cell growth protocol is detailed in the manuscript for all tested proteins and antibodies.

extract_protocol: Extract protocol is detailed in the manuscript for all tested proteins and antibodies.

value: Anti-6-4 Photoproduct

tag: antibody ratio


title: 64PP_UV

description: Antibody


title: CAM11M_48


title: UVDDB_NonUV_r2


title: CAM11F_41

value: Female


title: ChIPseq-SET18-FLAG-Col-0-rep1

description: ChIP-seq data set18 of FLAG-Col-0 repliate1

source_name: Arabidopsis floral tissue

value: floral tissue

tag: developmental stage

value: anti-FLAG M2 (Sigma)

value: FLAG


title: CAM11M_27

value: Male


title: CPD_NonUV

description: Antibody

source_name: Mouse Anti-CPD

tag: antibody

value: Anti-Cyclobutane Pyrimidine Dimer


title: CAM11M_38


title: CAM11F_26


title: ChIPseq-SET2-H3-ELF7-ZF-rep2

description: ChIP-seq data set2 of H3-ELF7-ZF repliate2

value: anti-H3 (Abcam)

tag: target protein


title: CPD_UV

description: Antibody


title: ChIPseq-SET2-H3-LHP1-ZF-rep2

description: ChIP-seq data set2 of H3-LHP1-ZF repliate2

tag: strain


title: ChIPseq-SET17-FLAG-ELF7-rep2

description: ChIP-seq data set17 of FLAG-ELF7 repliate2

tag: tissue


title: ChIPseq-SET17-FLAG-Col-0-rep2

description: ChIP-seq data set17 of FLAG-Col-0 repliate2


title: CAM11F_22


title: CAM11F_39


title: CAM11F_29


title: CAM11M_24


title: CAM11M_16


title: ChIPseq-SET18-FLAG-HD2A-rep1

description: ChIP-seq data set18 of FLAG-HD2A repliate1


title: CAM11F_20


title: CAM11M_9


title: ChIPseq-SET16-FLAG-fwa

description: ChIP-seq data set16 of FLAG-fwa


title: ChIPseq-SET16-FLAG-TRB1-ZF

description: ChIP-seq data set16 of FLAG-TRB1-ZF


title: CAM11F_11


title: CAM11F_6


title: MITF_NonUV

source_name: Human MITF

value: MITF


title: CAM11M_7


title: MITF_UV


title: EGR1_UV

source_name: Human EGR1


title: ChIPseq-SET16-FLAG-ELF7-rep1

description: ChIP-seq data set16 of FLAG-ELF7 repliate1


title: Bcl11b KO CD4 T cells, stimulated, biol rep 4

city: Nashville

first: Andrew

middle: R.

last: Patterson

state: TN

address: 1161 21st Avenue South

department: Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center

institute: Vanderbilt University Medical Center

data_processing:
Sequence reads were aligned to GRCm39/mm39 using Hisat2
Aligned reads were quantified using Featurecounts  with Gencode vM30 as a reference for annotations
Assembly: GRCm39
Supplementary files format and content: CSV file of raw counts for each sample

source_name: CD4+ T cells

growth_protocol: CD4+ T cells were maintained in IMDM supplemented with 10% heat inactivated fetal bovine serum (FBS),

extract_protocol:
RNA extraction was conducted with DNAse treatment according to the RNeasy Plus Mini kit (Qiagen)
RNA librariesfor RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were cultured with recombinant mouse IL-7 or stimulated with platebound 3 µg/ml anti-CD3 + 2 µg/ml anti-CD28 for 3 days.

tag: Sex

tag: cell type

value: CD4+ T cells

tag: genotype

value: Bcl11b KO

tag: treatment

tag: time

value: Day 3


title: CAM11M_14

tag: breed

value: Prehatch :11 days of incubation

tag: gender


title: Bcl11b KO CD4 T cells, stimulated, biol rep 5


title: CAM11M_2


title: Bcl11b KO CD4 T cells, stimulated, biol rep 3


title: Bcl11b KO CD4 T cells, stimulated, biol rep 2


title: ChIPseq-SET16-FLAG-Col-0-rep1

description: ChIP-seq data set16 of FLAG-Col-0 repliate1

value: 4-5 weeks


title: ChIPseq-SET15-H4K16ac-fwa-rep1

description: ChIP-seq data set15 of H4K16ac-fwa repliate1

value: leaf tissue

value: anti-H4K16ac (Abcam)


title: NeuT 980

type: RNA

city: Milano

first: Milena

last: Perrone

address: Via Amadeo 42

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

description: Gene expression data from MSCs isolated from the bone of NeuT mice (ID 980) at 24 weeks

hyb_protocol: Hybridization was performed according to manufacturer's standard protocols

scan_protocol: Gene microarrays were scanned with the Gene Chip System 3000 Scanner

data_processing: Raw data were pre-processed using the sst-RMA algorithm implemented in the Transcriptome Analysis Console software (Thermo Fisher Scientific).

label: biotin

source_name: BM-MSC isolated from tumor-bearing NeuT mice at 24 weeks

label_protocol: RNA was labeled according to manufacturer's recommended protocols

extract_protocol: Total RNA was extracted using the Mirneasy mini kit (QIAGEN).

value: NeuT

tag: disease state

value: late stage of breast cancer tumorigenesis

value: bone marrow

value: bone marrow-mesenchymal cells (BM-MSCs)

value: 24 weeks


title: EGR1_NonUV

tag: protein

tag: protein concentration

value: Non-UV


title: CREB1_NonUV

source_name: Human CREB1

tag: array condition


title: ChIPseq-SET15-H4K16ac-fwa-rep2

description: ChIP-seq data set15 of H4K16ac-fwa repliate2


title: ChIPseq-SET15-H4K16ac-EYFP-ZF-rep2

description: ChIP-seq data set15 of H4K16ac-EYFP-ZF repliate2


title: Bcl11b KO CD4 T cells, stimulated, biol rep 1

value: Male


title: Wildtype CD4 T cells, stimulated, biol rep 4

value: Female

value: WT


title: Wildtype CD4 T cells, stimulated, biol rep 5


title: Wildtype CD4 T cells, stimulated, biol rep 3


title: CAM11F_3

value: Ross 308 broiler

value: Chorioallantoic membrane

tag: age


title: Wildtype CD4 T cells, stimulated, biol rep 2

value: CD4+ T cells


title: ChIPseq-SET15-H3K9ac-fwa-rep2

description: ChIP-seq data set15 of H3K9ac-fwa repliate2

tag: developmental stage

value: anti-H3K9ac (Abcam)


title: Bcl11b KO CD4 T cells, Resting, biol rep 3

value: Bcl11b KO

value: IL-7 (Resting)

value: Day 3


title: NeuT 971

description: Gene expression data from MSCs isolated from the bone of NeuT mice (ID 971) at 24 weeks


title: Bcl11b KO CD4 T cells, Resting, biol rep 2


title: Bcl11b KO CD4 T cells, Resting, biol rep 1


title: NeuT 973

description: Gene expression data from MSCs isolated from the bone of NeuT mice (ID 973) at 24 weeks


title: BALB/c 964

description: Gene expression data from MSCs isolated from the bone of BALB/c mice (ID 964) at 24 weeks

source_name: BM-MSC isolated from control BALB/c at 24 weeks

value: BALB/c

value: control


title: Wildtype CD4 T cells, Resting, biol rep 3


title: CREB1_UV

value: UV


title: BALB/c 982

description: Gene expression data from MSCs isolated from the bone of BALB/c mice (ID 982) at 24 weeks

value: bone marrow


title: Wildtype CD4 T cells, Resting, biol rep 2


title: NeuT 965

description: Gene expression data from MSCs isolated from the bone of NeuT mice (ID 965) at 24 weeks

value: NeuT

value: late stage of breast cancer tumorigenesis

value: bone marrow-mesenchymal cells (BM-MSCs)


title: BALB/c 974

description: Gene expression data from MSCs isolated from the bone of BALB/c mice (ID 974) at 24 weeks

value: 24 weeks


title: ChIPseq-SET15-H3K9ac-EYFP-ZF-rep2

description: ChIP-seq data set15 of H3K9ac-EYFP-ZF repliate2

value: leaf tissue

value: 4-5 weeks

tag: antibody


title: ChIPseq-SET15-H4K16ac-EYFP-ZF-rep1

description: ChIP-seq data set15 of H4K16ac-EYFP-ZF repliate1

value: anti-H4K16ac (Abcam)

tag: target protein


title: Wildtype CD4 T cells, stimulated, biol rep 1

value: Male

value: WT


title: Wildtype CD4 T cells, Resting, biol rep 1

value: CD4+ T cells


title: ChIPseq-SET15-H3K27ac-fwa-rep2

description: ChIP-seq data set15 of H3K27ac-fwa repliate2

tag: strain

value: anti-H3K27ac (Abcam)


title: ChIPseq-SET15-H3K9ac-EYFP-ZF-rep1

description: ChIP-seq data set15 of H3K9ac-EYFP-ZF repliate1

tag: tissue

value: anti-H3K9ac (Abcam)


title: RAW264.7 cells- TIP- biol rep 2 m6A-IP

city: nanjing

first: Zhang

last: Jun

state: jiangsu

address: longmiandadao

institute: China Pharmaceutical University

data_processing:
fastp software was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
HISAT2 was used to map reads to the reference genome mus musculus (Version: v107).
Peak calling and diff peak analysis were performed by R package exomePeak, and peaks were annotated by intersection with gene architecture using R package ANNOVAR.
MEME and HOMER were used for de novo and known motif finding followed by localization of the motif with respect to peak summit.
Assembly: the reference genome mus musculus (Version: v107)
Supplementary files format and content: bigWig

growth_protocol: Mouse macrophage RAW264.7 cells were cultured in Dulbecco’s modified Eagle medium (DMEM) containing 10% fetal bovine serum (FBS), 1% 100×penicillin and streptomycin. Serial subculture dilution was performed when the cell confluence reached 70-80%.

extract_protocol:
Total RNA was extracted using TRIzol Reagent and MeRIP-seq samples were immunoprecipitated by m6A-specific antibody.
The IP RNA was reverse-transcribed to cDNA, which was next used to synthesize U-labeled second-stranded DNAs. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR.

treatment_protocol: Samples were treated with 100 μM TCP, 100 μM TBP or 100 μM TIP for 24 h, respectively.

tag: cell line

value: macrophage

value: wild type

value: TIP

value: m6A-specific antibody


title: NeuT 763

description: Gene expression data from MSCs isolated from the bone of NeuT mice (ID 763) at 12 weeks

source_name: BM-MSC isolated from tumor-bearing NeuT mice at 12 weeks

value: early stage of breast cancer tumorigenesis

value: bone marrow

tag: cell type

value: 12 weeks


title: RAW264.7 cells- TIP- biol rep 1 m6A-IP

tag: genotype


title: BALB/c 972

description: Gene expression data from MSCs isolated from the bone of BALB/c mice (ID 972) at 24 weeks

value: BALB/c

value: control

value: bone marrow-mesenchymal cells (BM-MSCs)


title: ChIPseq-SET15-H3K27ac-fwa-rep1

description: ChIP-seq data set15 of H3K27ac-fwa repliate1

source_name: Arabidopsis leaf tissue

value: leaf tissue

value: 4-5 weeks


title: RAW264.7 cells- TBP- biol rep 1 m6A-IP

tag: treatment

value: TBP


title: RAW264.7 cells- TCP- biol rep 2 m6A-IP

value: TCP


title: RAW264.7 cells- Control- biol rep 2 m6A-IP

value: Control


title: RAW264.7 cells- TCP- biol rep 1 m6A-IP


title: ChIPseq-SET15-H3K27ac-EYFP-ZF-rep2

description: ChIP-seq data set15 of H3K27ac-EYFP-ZF repliate2

value: anti-H3K27ac (Abcam)


title: RAW264.7 cells- TBP- biol rep 2 m6A-IP


title: RAW264.7 cells- Control- biol rep 1 m6A-IP


title: NeuT 759

description: Gene expression data from MSCs isolated from the bone of NeuT mice (ID 769) at 12 weeks

value: NeuT


title: NeuT 756

description: Gene expression data from MSCs isolated from the bone of NeuT mice (ID 756) at 12 weeks


title: RAW264.7 cells- TIP- biol rep 2 input

value: macrophage


title: NeuT 752

description: Gene expression data from MSCs isolated from the bone of NeuT mice (ID 752) at 12 weeks


title: ChIPseq-SET15-H3K14ac-fwa-rep1

description: ChIP-seq data set15 of H3K14ac-fwa repliate1

value: anti-H3K14ac (Abcam)


title: RAW264.7 cells- TBP- biol rep 2 input

value: wild type


title: RAW264.7 cells- TCP- biol rep 1 input


title: NeuT 757

description: Gene expression data from MSCs isolated from the bone of NeuT mice (ID 757) at 12 weeks


title: RAW264.7 cells- TBP- biol rep 1 input


title: RAW264.7 cells- Control- biol rep 2 input


title: RAW264.7 cells- TIP- biol rep 1 input

value: TIP


title: ChIPseq-SET15-H3K14ac-EYFP-ZF-rep2

description: ChIP-seq data set15 of H3K14ac-EYFP-ZF repliate2


title: RAW264.7 cells- TCP- biol rep 2 input


title: BALB/c 762

description: Gene expression data from MSCs isolated from the bone of BALB/c mice (ID 762) at 12 weeks

source_name: BM-MSC isolated from control BALB/c at 12 weeks


title: ChIPseq-SET15-H3K27ac-EYFP-ZF-rep1

description: ChIP-seq data set15 of H3K27ac-EYFP-ZF repliate1


title: ChIPseq-SET15-H3-fwa-rep2

description: ChIP-seq data set15 of H3-fwa repliate2

value: anti-H3 (Abcam)


title: RAW264.7 cells- Control- biol rep 1 input


title: BBN021-P5

city: Buffalo

first: Mark

middle: D

last: Long

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
Reads were aligned to the mouse genome GRCM38 M16 (gencode) using STAR v2.6.0a
Aligned reads were quantified using RSEM v1.3.1.
Assembly: GRCm38
Supplementary files format and content: The first column represents gene symbol. The other columns are  RSEM estimated raw counts for all the samples.

growth_protocol: Mice were housed in the Laboratory Animal Shared Resource (LASR) at Roswell Park in a limited access barrier facility. LASR is an AAALAC International Accredited Animal Program.  Male and female C57BL/6NTac mice at 8 weeks of age received 0.1% of BBN (TCI Chemicals, Cat # B0938) in their drinking water ad libitum for up to 36 weeks. Weekly abdominal palpitations monitored bladder tumor formation. The high-grade disease was determined by detection of tumor on abdominal palpation and/or by detection of blood in the urine, at which time the mice were euthanized as per Roswell Park Institutional Animal Care and Use Committee (IACUC) guidelines. Bladders were removed and processed for passage subcutaneously into sex-matched C57BL/6NTac host mice. Mice treated with BBN that developed primary bladder tumors were denoted as donor mice. The tumors that grew from the first subcutaneous passage from donor mice were referred to as P0 passage, and the subsequent passages as P1, P2, etc. The allograft models were considered stable BURP tumor lines after no histological drift was observed between passages, usually after P2.

extract_protocol:
Total and small RNA was isolated and purified using the miRNeasy mini kit (Qiagen, Cat # 217084) according to the manufacturer’s directions.
The sequencing libraries were prepared with the RNA HyperPrep Kit with RiboErase (HMR) (Roche Sequencing Solutions) using 500 ng of total RNA.

value: bladder allograft

value: BBN-induced Urothelium Roswell Park (BURP) tumor line


title: BBN024-P2


title: BALB/c 758

description: Gene expression data from MSCs isolated from the bone of BALB/c mice (ID 758) at 12 weeks

value: BALB/c

value: bone marrow

value: 12 weeks


title: ChIPseq-SET15-H3K14ac-fwa-rep2

description: ChIP-seq data set15 of H3K14ac-fwa repliate2

value: leaf tissue


title: C6: Culture nociceptors IL-13 3

city: Montréal

first: Theo

last: Crosson

state: Quebec

address: 2900 Boulevard Edouard Montpetit

country: Canada

institute: Université de Montréal

data_processing:
Demultiplexing
trimming for sequencing adapters and low quality 3' bases
Alignement to GRCm38 with STAR version 2.7.1
FPKM calculation
Assembly: GRCm38
Supplementary files format and content: STAR readcount
Supplementary files format and content: FPKM

source_name: Jugular-nodose complex (JNC)

extract_protocol:
RNA was separated from protein and DNA by mixing 500μL sample in Trizol with 100μL chloroform before ultracentrifugation (15min, 16000g, 4°). The upperphase was mixed with a half volume of 100° isopropanol, transferred to a purification column, and the RNA purified using the kit PureLink™ RNA Micro Scale (Thermofisher #12183016) following manufacturer’s instructions.
KAPA mRNA HyperPrep Kit (KapaBiosystems #KR1352)
Capture mRNA with oligo-dT bead, RT with random priming, second strand synthesis with dUTP, adapter ligation and strand specific library amplification

value: Jugular-nodose complex (JNC)

value: Nociceptors (Nav1.8+)


title: BBN016-P5


title: BALB/c 753

description: Gene expression data from MSCs isolated from the bone of BALB/c mice (ID 753) at 12 weeks

value: control

value: bone marrow-mesenchymal cells (BM-MSCs)


title: BALB/c 760

description: Gene expression data from MSCs isolated from the bone of BALB/c mice (ID 760) at 12 weeks


title: BBN021-P4.2


title: BBN021-P4


title: C5: Culture nociceptors vehicle 3

value: Vehicle


title: BBN018-P4


title: ChIPseq-SET15-H3-fwa-rep1

description: ChIP-seq data set15 of H3-fwa repliate1

value: 4-5 weeks


title: ChIPseq-SET14-PolII-fwa-rep1

description: ChIP-seq data set14 of Pol II-fwa repliate1

value: anti-Pol II (Abcam)

value: Pol II


title: BBN016-C74-MNT


title: BBN017-P4


title: BALB/c 751

description: Gene expression data from MSCs isolated from the bone of BALB/c mice (ID 751) at 12 weeks


title: 6C: Glial cells AAI 3

value: Glial cells (Nav1.8-)

value: AAI


title: ChIPseq-SET14-PolII-EYFP-ZF-rep2

description: ChIP-seq data set14 of Pol II-EYFP-ZF repliate2


title: ChIPseq-SET15-H3K14ac-EYFP-ZF-rep1

description: ChIP-seq data set15 of H3K14ac-EYFP-ZF repliate1

value: anti-H3K14ac (Abcam)


title: C4: Culture nociceptors IL-13 2


title: C3: Culture nociceptors vehicle 2


title: C1: Culture nociceptors vehicle 1


title: BBN025-C102-M30

value: bladder allograft


title: ChIPseq-SET14-PolII-EYFP-ZF-rep1

description: ChIP-seq data set14 of Pol II-EYFP-ZF repliate1


title: BBN017-C165-M30

value: BBN-induced Urothelium Roswell Park (BURP) tumor line


title: 4C: Glial cells AAI 2


title: BBN024-C81-M30


title: ChIPseq-SET14-PolII-fwa-rep2

description: ChIP-seq data set14 of Pol II-fwa repliate2


title: ChIPseq-SET15-H3-EYFP-ZF-rep1

description: ChIP-seq data set15 of H3-EYFP-ZF repliate1

value: anti-H3 (Abcam)


title: ChIPseq-SET15-H3-EYFP-ZF-rep2

description: ChIP-seq data set15 of H3-EYFP-ZF repliate2


title: BBN017-C152-M1


title: BBN024-C81-M1


title: 3C: Glial cells naive 2

value: Naive


title: BBN025-C102-M1


title: 2C: Glial cells AAI 1


title: C2: Culture nociceptors IL-13 1


title: BBN012-C47-M3


title: BBN025-C102-M3


title: 5C: Glial cells naive 3


title: ChIPseq-SET14-H3K4me3-fwa-rep2

description: ChIP-seq data set14 of H3K4me3-fwa repliate2

value: anti-H3K4me3 (Millipore Sigma)


title: YUMMER1.7 tumor

city: New York

first: Amanda

last: Lund

state: New York

address: 522 First Ave

institute: NYU Langone Health

description: 10x Genomics Chromium; Fluidigm C1 Auto Prep System

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Quality control and subsetting to Cd8+ Cells was carried out in Seurat v4
Assembly: mm10 (GRC38)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: murine YUMMMER1.7 intradermal melanoma

extract_protocol:
Cell suspensions from YUMMER1.7 tumors (n=3) were created by mincing tumors followed by enzymatic digestion with 10 mg/ml collagenase D and 80 U/ml DNase for 20 minutes at 37C with shaking. Suspensions were then passed through a 70um cell strainer and washed with PBS. Cell suspensions were  immunostained with CD45-APC antibodies and then CD45+ cells enriched for Miltenyi APC microbeads and the QuadroMACs Magnetic Seperator and LS Columns. Enriched CD45+ cell suspensions were stained with DAPI and then sorted on SY3200 HAPS sorter to improve purity of live CD45+ cells. 2.5e5 cells were sorted from each tumor and then pooled.
Library prep was performed according to 10x Genomics single cell 3’ kit (v3.1) protocol. Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: 5x10^5 YUMMER1.7 murine melanoma cells were intradermally implanted (50 ul/injection) into 3 C57Bl/6 mice. Tumors were harvested at day 21 and digested into single cell susepension. All three mice were pooled for analysis.

value: murine YUMMMER1.7 intradermal melanoma

value: CD45+ cells

value: intradermally implanted tumor


title: BBN018-C149-M3


title: ChIPseq-SET14-H3K36me3-ELF7-ZF-rep1

description: ChIP-seq data set14 of H3K36me3-ELF7-ZF repliate1

value: leaf tissue

value: anti-H3K36me3 (Abcam)


title: BBN016-C73-M10


title: BBN012-C47-M30


title: BBN018-C148-M3


title: BBN019-C80-M1


title: ChIPseq-SET14-H3K4me3-fwa-rep1

description: ChIP-seq data set14 of H3K4me3-fwa repliate1


title: ChIPseq-SET14-H3K4me3-EYFP-ZF-rep1

description: ChIP-seq data set14 of H3K4me3-EYFP-ZF repliate1


title: ChIPseq-SET14-H3K36me2-fwa-rep1

description: ChIP-seq data set14 of H3K36me2-fwa repliate1

value: anti-H3K36me2 (Abcam)


title: priB_TriC_B18AIDKO_IgG3capture_LPS_d0_rep3

city: Vienna

first: Maximilian

middle: Christian

last: von der Linde

state: Vienna

address: Campus-vienna-biocenter 1, IMP, Pavri GRP

country: Austria

institute: Institute of Molecular Pathology

description: Tri-C

data_processing:
Tri-C
Demulitplexed reads were submitted to the CCseqBasicS5 pipeline with following options: bowtie2 alignment to NCBI mm9 , --tric, --flashbases 10
matrices were generated using the modified TriC_matrix_simple_MO.py script
Reads with alt least three interactions were extracted with TriCgetreads.py
Visualisation with pyplot in TriCplot.py
Find more information and scripts at https://github.com/PavriLab/tric
Assembly: mm9
Supplementary files format and content: Tab separated matrix showing normalized interaction counts
Library strategy: Tri-C

source_name: primary B-cells

growth_protocol: Complete RPMI medium with LPS and IL4 for activation

extract_protocol:
TriC was performed as described (Downes et al 2022 with modifications desribed in Costea, Schoeberl et al 2022). In short, 10x10^6 or 15x10^6 (0h) cells were crosslinked with 2% HCHO for 8 min at room temperature. After quenching with 0,133M glycine, cells were lysed and nuclei isolated. Next, nuclei were lysed followed by NlaIII digestion (overnight), T4-DNA-ligation (overnight), Proteinase K digestion (overnight) and genomic DNA extraction. DNA was sonicated on Covaris S2 sonicator.
TriC library was prepared of 3x2µg sonicated DNA using NEBUltraII and barcoding PCRs were performed using Nextflex unique dual index barcode sequences. For capture using reagents of the Roche HyperCap target enrichment kit and mouse Cot-1, 1-2µg of libraries were 2x (72h, 24h) hybridized to 2.9nM of individual biotinylated capture probes, followed by streptavidin pull down and PCR amplification using P5 and P7 (Illumina) primer sequences. Samples were multiplexed for sequencing on NextSeq or NovaSeq (Illumina) platforms

tag: capture probe

value: IgG3 pool capture

value: WT

tag: clone

value: clone 1

tag: replicate

value: replicate 3


title: BBN019-C80-M3


title: BBN019-C80-M30


title: 5B: Visceral nociceptors naive 3

value: Jugular-nodose complex (JNC)

value: Visceral Nociceptors (Nav1.8+DID-)


title: 1C: Glial cells naive 1

value: Glial cells (Nav1.8-)


title: ChIPseq-SET14-H3K36me3-fwa-rep1

last: Zhong

description: ChIP-seq data set14 of H3K36me3-fwa repliate1

value: 4-5 weeks


title: ChIPseq-SET14-H3K4me3-EYFP-ZF-rep2

description: ChIP-seq data set14 of H3K4me3-EYFP-ZF repliate2


title: Ductal_KC

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

institute: Genomics Consulting

description: 10xGenomics 3’scRNAseq protocol

data_processing:
Illumina bcl files were basecalled, demultiplexed and aligned to the mouse mm10 genome using the cellranger software (version 3.1.0, 10xGenomics)
Raw counts were imported into R and single cell data was analyzed with the 'Seurat' package v.3.2.2
After filtering for library size and mitochondrial gene expression, pre-processing was performed using Seurat functions for counts normalization (SCT), dimension reduction with principal component analysis (PCA) (RunPCA with default parameters), construction of a Shared Nearest Neighbor (SNN) graph and clustering.
Assembly: mm10
Supplementary files format and content: csv files containing normalized expression matrices. Suggested cell identities have been added to the first row (rowname = “Identity”)
Supplementary files format and content: demultiplexed data files: filtered feature matrices (output of cellranger count)

source_name: KC cells

extract_protocol:
FACS purified KC ductal cells acquired on a BD FACS ARIA (BD Biosciences) and sorted cells collected in Dulbecco’s Modified Eagle Medium (DMEM) containing 20% FCS.
Cell encapsulation, barcoding, and library preparation followed the standard scRNAseq protocol comprising reverse transcription, amplification, and indexing (10xGenomics).
Sequencing was performed using a NovaSeq Illumina device (Illumina).

treatment_protocol: previously established LSL-KrasG12D/+;Ptf1a-Cre mice (termed KC mice) [ref: PMID: 14706336]

tag: strain/genotype

value: pool of five KC or 4KC mice (LSL-KrasG12D/+;Ptf1a-Cre mice)

value: FACS purified ductal tumor cells


title: ChIPseq-SET14-H3K27me3-fwa-rep1

description: ChIP-seq data set14 of H3K27me3-fwa repliate1

value: anti-H3K27me3 (Millipore Sigma)


title: priB_TriC_B18AIDKO_Emucapture_+1hTPL_rep3

description: Tri-C

value: Emu capture

value: 72h activated, 1h TPL treated


title: priB_TriC_B18AIDKO_IgG3capture_LPS_d3_rep3

description: Tri-C

value: 72h activated


title: BBN012-C41-M3

value: bladder allograft

value: BBN-induced Urothelium Roswell Park (BURP) tumor line


title: ChIPseq-SET14-H3K27me3-fwa-rep2

description: ChIP-seq data set14 of H3K27me3-fwa repliate2

value: leaf tissue


title: priB_TriC_B18AIDKO_Emucapture_+3hTPL_rep2

description: Tri-C

value: 72h activated, 3h TPL treated

value: replicate 2


title: priB_TriC_B18AIDKO_IgG3capture_LPS_d3_rep2

description: Tri-C

value: IgG3 pool capture

value: clone 1


title: ChIPseq-SET14-H3-fwa-rep2

description: ChIP-seq data set14 of H3-fwa repliate2

value: anti-H3 (Abcam)


title: priB_TriC_B18AIDKO_Emucapture_-TPL_rep3_2

description: Tri-C

value: 72h activated, no TPL treatment

value: replicate 3


title: 4A: Airway nociceptors AAI 2

value: Jugular-nodose complex (JNC)

value: Airway Nociceptors (Nav1.8+DID+)

value: AAI


title: priB_TriC_B18AIDKO_IgG3capture_LPS_d3_rep1

description: Tri-C

value: replicate 1


title: priB_TriC_B18AIDKO_IgG3capture_LPS_d0_rep2

description: Tri-C

value: WT


title: priB_TriC_B18AIDKO_IgG3capture_LPS_d0_rep1

description: Tri-C


title: ChIPseq-SET14-H3K36me2-ELF7-ZF-rep1

description: ChIP-seq data set14 of H3K36me2-ELF7-ZF repliate1

value: 4-5 weeks

value: anti-H3K36me2 (Abcam)


title: 6B: Visceral nociceptors AAI 3

value: Visceral Nociceptors (Nav1.8+DID-)


title: 4B: Visceral nociceptors AAI 2


title: 1B: Visceral nociceptors naive 1

value: Naive


title: priB_TriC_B18AIDKO_Emucapture_-TPL_rep2_2

description: Tri-C

value: Emu capture


title: priB_TriC_B18AIDKO_Emucapture_-TPL_rep1_2

description: Tri-C


title: iWAT pAd PSAP 2

city: Boston

first: Melanie

middle: J

last: Mittenbühler

address: 360 Longwood Ave

institute: Dana-Farber Cancer Institute

data_processing:
Raw reads were mapped or aligned to the reference organism using STAR software
Differential gene expression testing was performed by DESeq and resulting fold change values were used as a pre-ranked gene list for gene set enrichment analysis.
For DESeq analysis data are expressed as (PSAP pAd/GFP pAd).
Assembly: mm10
Supplementary files format and content: STAR Gene counts TPM and a list of differentially-expressed genes deseq

source_name: primary iWAT cells

growth_protocol: Inguinal white adipose stromal-vascular fraction (SVF) was isolated and cultured as described previously (Seale et al., 2011). For experiments, cells were grown until confluency. Afterwards, differentiation of pre-adipocytes was induced by treatment with an adipogenic cocktail (1 μM rosiglitazone (Cayman Chemical, 71740), 0.5 mM 3-Isobutyl-1-methylxanthine (IBMX) (Sigma Aldrich, I5879), 1 μM dexamethasone (Sigma Aldrich, D4902), 870 nM insulin (Sigma Aldrich, I5500)) in complete adipocyte culture medium for 2 days. Subsequently, medium was changed to complete adipocyte maintenance medium containing 1 μM rosiglitazone and 870 nM insulin.

extract_protocol:
cells were harvested and flash frozen on liquid nitrogen, and total RNA was harvested using Trizol reagent and RNeasy column (QIAGEN).
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7

treatment_protocol: Adenoviral transduction was performed at day 3-4 post differentiation initiation at an multiplicity of infection (MOI) of 100 per cell. Medium was changed 24 h afterwards and cells were harvested 72 h post transduction.

value: primary iWAT cells

value: pAd PSAP

tag: time

value: 3 days


title: iWAT pAd PSAP 1