title: E3 CAF

data_processing:
The quality of the data in the fastq files from the human samples was evaluated using FastqQC.
STAR (v2.5.2b) was used trim the reads on the fly using the clip3pAdapterSequence option.
STAR (v2.5.2b) was used to align the reads to the reference human genome with two pass mapping multi-sample setting.
STAR (v2.5.2b) was used to obtain read counts for the genes annotated in GENCODE (v24) using the quantmode GeneCounts option.
Genome_build: GRCh38
Supplementary_files_format_and_content: text file in tab-separated value format with read counts from STAR

source_name: DLBCL lymph node FRCs

growth_protocol: LN FRCs were cultured up to passage 3. DLBCL LN biopsies were enzimatically digested and FRCs expanded until they reached 100% confluency (p1)

treatment_protocol: Healthy LN FRCs were left alone or co-cultured with DLBCL lymphoma cells (primary or cell lines) for 48h using transwell (pore size 0.4µm)

tag: treatmnent

value: enzimatic digestion and culture until stroma reached 100% confluency

value: passage 1  lymph node FRCs


title: 8 Cre HFD

status: Public on Jun 16 2023

type: SRA

city: Philadelphia

first: Nathaniel

last: Snyder

state: Pennsylvania

address: 3500 N Broad St, 455 Merb

country: USA

institute: Temple University

library_source: transcriptomic

data_processing:
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Reads were trimmed using cutadapt1. Quality scores were assessed using FastQC2. Reads were aligned to the Mus musculus genome build GRCm38 using STAR3. Individual sample reads were quantified using HTseq4and normalized via Relative Log Expression (RLE) using DESeq2 R library5.
1. Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads.EMBnet.journal17, 10–12 (2011).
2. Andrews, S. FastQC: a quality control tool for high throughput sequence data. (2010).
3. Dobin, A.et al. STAR: ultrafast universal RNA-seq aligner.Bioinformatics29, 15–21 (2013).
4. Anders, S., Pyl, P. T. & Huber, W. HTSeq--a Python framework to work with high-throughput sequencing data.Bioinformatics31, 166–169 (2015).
5. Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.Genome Biol.15, 550 (2014).
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Mus musculus

source_name: Quadriceps (white)

growth_protocol: Mice, male, aged 11-14 wks

extract_protocol:
Norgen Biotek (cat 25700): RNA extraction from animal tissue
NEB Next Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: mice fed 7 days of 60% high fat diet

tag: tissue

value: Quadriceps (white)

tag: Sex

value: Male

tag: age

tag: genotype

value: CKM Cre (Acot2 ko in muscle)

tag: treatment

value: high fat diet


title: 5 Cre HFD


title: 6 Cre HFD


title: 4 Loxp HFD

value: Loxp/Loxp


title: 3 Loxp HFD


title: ATAC-seq_D8_F_FABV_3

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

library_source: genomic

data_processing:
Transcripts were aligned to the indexed reference for mm10 with default settings using TopHat2 v2.1.1 (Kim et al. 2013).
Reads were filtered using bamtools using the following settings: -isDuplicate false -mapQuality “>10” (Barnett et al. 2011).
Transcript reads were counted post-alignment using StringTie (Pertea et al. 2015).
Differential expression testing was performed using edgeR v3.16.5 (Robinson and Smyth 2007; Robinson and Smyth 2008; Robinson et al. 2010; McCarthy et al. 2012; Zhou et al. 2014) and limma v3.30.13 (Ritchie et al. 2015) packages in R v3.3.2.
Low level genes were removed within each condition using median log2-transformed counts per gene per million mapped reads (cpm) of 1 and a union generated from those lists.
Differential expression testing was performed using a general linear model (GLM) framework. For comparing FAB and FAB+V, a covariate for replicate was included to correct for batch effect.
Sequencing reads were aligned to the mm10 genome using Bowtie2 v2.3.0 (Langmead and Salzberg 2012) and SAMtools v0.1.19 (Li et al. 2009; Li 2011).
Peak calling was performed using MACS2 callpeak (Zhang et al. 2008; Feng et al. 2012) using the settings --nomodel --shift -100 --extsize 200 -q 0.1 after pooling biological replicates.
A fold-enrichment track was generated using MACS2 using the bdgcmp function (-m FE) for visualization on the genome browser.
Following removal of ENCODE blacklist sites (Amemiya et al. 2019; ENCODE Project Consortium 2012), a union set of sites was generated by identifying summits that overlapped within 200bp and arbitrarily selecting the summit of highest positional value. Summits were then extended by 200bp in both directions to create the set of union sites.
Fold-enrichment scores were assigned to each site using the multiBigwigSummary function from deepTools (Ramírez et al. 2016).
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq_Compilation.txt contains all outputs related to the RNA-seq datasets, including TPM values for every biological replicate and differential expression testing. TSS_TAD.bed contains the TSS and TAD assignments. UnifiedATAC_Dataset.txt contains a list of the union sites, positional information, and fold-enrichment scores. edgeR_Results_FABVoverFAB.txt is the differential accessibility testing comparing the FAB+V and FAB conditions. All files "_summits_noBlacklist.bed" contain the summit calls from MACS2 following removal of ENCODE blacklist sites. All "_FE.bw" are bigWig files containing the MACS2 fold-enrichment scores.

molecule: genomic DNA

source_name: mouse embryonic stem cells

growth_protocol: Bry-GFP and ZX1 ES cell lines were maintained in a serum- and feeder-free culture system (Ying et al. 2003; Gadue et al. 2006; Ying et al. 2008; Kattman et al. 2011). Neurobasal medium and DMEM/F12 (50%/50%; Thermo Fisher Scientific) were supplemented with N2 (Thermo Fisher Scientific), B27 (Thermo Fisher Scientific), 0.05% BSA (MilliporeSigma), 150mM mono-thioglycerol (MilliporeSigma), 1000unit Mouse LIF (MilliporeSigma), 1μM PD0325901 (Stemgent), 3μM CHIR99021 (Stemgent), L-glutamine (Life Technologies), penicillin-streptomycin (Thermo Fisher Scientific). PD0325901 and CHIR99021 were not added at 2 days prior to start differentiation. For differentiation start, ES cells were dissociated with trypLE express (Thermo Fisher Scientific) and cultured, at 1.0x105 cells/ml for 48hrs (Gadue et al. 2006; Kattman et al. 2011). In brief, IMDM and Ham’s F12 medium (75%/25%) were supplemented with N2, B27, BSA, L-glutamine, 0.5mM ascorbic acid (MilliporeSigma), 450mM mono-thioglycerol (MilliporeSigma), penicillin-streptomycin. The cells were differentiated in 10 cm petri-dishes (Becton Dickenson). The 48hr-old embryoid bodies (EBs) were dissociated with trypLE express and the cells were re-aggregated in StemPro-34 SFM medium (Thermo Fisher Scientific) in the present of L-glutamine, 200μg/ml human transferrin, 500μM ascorbic acid, 450μM mono-thioglycerol, 6ng/ml bFGF, 8ng/ml Activin A and 1ng/ml BMP4 for Bry+, PDGFRα+ and Flk1+ mesoderm induction. 5ng/ml VEGF was treated at D2 for bipotential mesoderm induction. Human Activin A, human BMP4, mouse VEGF, human bFGF were purchased from R&D systems. For hematopoietic lineage and cardiac lineage induction, sorted cells were cultured in StemPro-34 SF medium, supplemented with 2 mM L-glutamine, 1 mM ascorbic acid (MilliporeSigma), and 10 ng/ml bFGF (Kattman et al. 2006; Kattman et al. 2011). 2×105/ml sorted cells were seeded into individual wells of a 48-well flat bottom plate (Becton Dickenson) coated with gelatin after sorting.

extract_protocol:
Total RNA was extracted using NucleoSpin RNAII kit (Clonetech). ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) was performed as previously described (Buenrostro et al. 2015).
For RNA-seq, library preparation was performed by the University of Chicago Genomics Facility using the Illumina TruSeq RNA Sample prep kit v2 (Part #RS-122-2001). Library fragments were approximately 275bps in length and were quantitated using the Agilent Bio-analyzer 2100 and pooled in equimolar amounts. Single-ended, 51bp sequencing was performed on the Illumina HiSeq2500 in Rapid Run Mode by the University of Chicago Facility. For ATAC-seq, libraries were amplified and normalized with the Illumina Nextera DNA Library prep kit (FC-121–1031) according to the manufacturer's protocols. Libraries were quantitated using the Agilent Bioanalyzer, pooled in equimolar amounts, and sequenced with 50-bp single-end reads on the Illumina HiSeq following the manufacturer's protocols through the Genomics Core Facility at the University of Chicago.

value: mouse embryonic stem cells

tag: day

value: Day 8

value: FAB+V

tag: sort

value: P-F+


title: T-cell Receptor Li124T-T

city: New York

first: Darwin

last: D'Souza

state: NY

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

description:
T-cell Receptor
TCR RNA
paired-end
Illumina NovaSeq 6000
TCR library: read1 file contains cell barcode and UMI; read2 file contains recepter sequence
Tumor, Normal, Lymph Node and PBMC

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the hg19 1.2.0 genome build and Ensembl 82 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: hg19 1.2.0
Supplementary files format and content: Processed counts from CellRanger in an R object, data_SingleCellExperiment_object.Rda; Additional metadata in “sample_annots.csv” and “full_HCC_cluster_annotation.csv”

organism: Homo sapiens

source_name: Liver

extract_protocol:
Human tumor lesions and non-involved adjacent tissues were digested as described in the material and method. Briefly, samples received mechanical and enzymatic digestion, filtration and the cell suspension was enriched in immune cells using a Percoll gradient, followed by a RBC lysis. Lymph nodes were digested mechanically and enzymatically followed by RBC lysis. Blood samples were processed by Ficoll followed by RBC lysis.
Library was prepared using Chromium Single Cell 3ʹ v2 protocol/3ʹ  protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell associated protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell associated protocol (10x Genomics). For antibody-derived tagged library, we used the KAPA HiFI HotStart Library Amplification Kit (Roche) with the following primers and amplification program:
-CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C f¬¬or 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 primer as i7 primer (Illumina).
-HASH-seq library: amplification was performed at 95°C for 3’ followed by ten cycles 95°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGC-3’ TruSeq D701_s primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for both CITE- and HASH- seq library amplification.
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.
OTHER: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

value: Liver

tag: cell type

value: Tumor, Normal, Lymph Node and PBMC

tag: library type

value: TCR

tag: antibodies/tags


title: ATAC-seq_D8_F_FABV_2


title: 7 Cre HFD


title: OCI-Ly18

city: London

first: Alan

last: Ramsay

state: -- Select One --

address: Great Maze Pond

country: United Kingdom

institute: King's College London

source_name: Lymph node FRCs

extract_protocol:
FRCs were lysed using trizol and RNA extracted using  RNeasy Micro Kit from Qiagen
TruSeq stranded mRNA kit (Illumina)

value: 48h conditioning with DLBCL cell line using transwell (pore size 0.4µm)

value: passage 3  lymph node FRCs


title: 2 Loxp HFD


title: 1 Loxp HFD


title: TMD8


title: T-cell Receptor Li121T-T


title: T-cell Receptor Li124N-T


title: 8 Cre Fasted 3251

extract_protocol:
Norgen Biotek (cat 25700): RNA extraction from animal tissue
TruSeq Stranded RNA Library Prep Kit Set A/B

treatment_protocol: Overnight fasted mice

value: Overnight fasted


title: ATAC-seq_D8_PF_FABV_3

value: P+F+


title: ATAC-seq_D8_F_FABV_1


title: ADT-derived cDNA and HTO-derived cDNA R1001_1-AH

description:
ADT-derived cDNA and HTO-derived cDNA
protein
paired-end
Illumina NovaSeq 6000
ADT and HTO
Tumor, Normal, Lymph Node and PBMC

value: ADT and HTO

value: see meta_features.csv located in supplementary files for Antibody name and barcode and meta_sample.csv in supplmentary files for Hashtag to sample mappings


title: OCI-Ly10


title: 7 Cre Fasted 3205

value: Quadriceps (white)

value: Male


title: 6 Cre Fasted 3206

value: CKM Cre (Acot2 ko in muscle)


title: ATAC-seq_D8_PF_FABV_1


title: DHL10


title: LN16 CAF

value: enzimatic digestion and culture until stroma reached 100% confluency

value: passage 1  lymph node FRCs


title: ATAC-seq_D6_F_FABV_3

value: mouse embryonic stem cells

value: Day 6


title: 5 Cre Fasted 3210


title: DHL16


title: T-cell Receptor Li121N-T


title: ATAC-seq_D6_F_FABV_2

value: FAB+V

value: P-F+


title: 4 Loxp Fasted 3208

value: Loxp/Loxp


title: RL


title: 3 Loxp Fasted 3250


title: ATAC-seq_D6_F_FABV_1


title: DHL4


title: ATAC-seq_D8_PF_FABV_2

value: Day 8


title: 5546

value: 48h conditioning with primary DLBCL cells using transwell (pore size 0.4µm)


title: T-cell Receptor Li121LN-T

value: Liver

value: Tumor, Normal, Lymph Node and PBMC

value: TCR


title: 2 Loxp Fasted 3204

value: Overnight fasted


title: ATAC-seq_D6_PF_FABV_2

value: P+F+


title: NHL

value: 48h conditioning with DLBCL cell line using transwell (pore size 0.4µm)

value: passage 3  lymph node FRCs


title: ATAC-seq_D6_PF_FABV_3


title: T-cell Receptor Li104T-T


title: 1 Loxp Fasted 3209

value: Quadriceps (white)

value: Male


title: ATAC-seq_D6_PF_FABV_1


title: ATAC-seq_D4_F_FABV_3

value: Day 4


title: LN16 FRC


title: E3 FRC


title: 8 Cre Chow Fed 3097

treatment_protocol: Chow-fed mice (Purina diet 5001)

value: CKM Cre (Acot2 ko in muscle)

value: Chow-fed


title: 7 Cre Chow Fed 3119


title: 8421


title: T-cell Receptor Li104Ppost-T


title: 6 Cre Chow Fed 3152


title: FRC 6

value: untreated


title: ATAC-seq_D4_F_FABV_1

value: mouse embryonic stem cells

value: FAB+V

value: P-F+


title: 5 Cre Chow Fed 3103


title: ATAC-seq_D4_F_FABV_2


title: 4 Loxp Chow Fed 3102

value: Loxp/Loxp


title: ATAC-seq_D4_PF_FABV_1


title: 2 Loxp Chow Fed 3098


title: FRC 2


title: LGK974_FZD5_Agonist, rep3

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. Supplementary files use ENSEMBL gene IDs, counts and RPKM statistics.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw count and RPKM values for each Sample

source_name: Lung

extract_protocol:
RNA is isolated using RNAeasy kit and quantified using 260/280 absorbance
0.1 μg of total RNA was used for library preparation with a TruSeq Stranded Total RNA Library Prep Kit (Illumina)

treatment_protocol:
Cells were treated with following Wnt modulators for 8-12 hrs:
LGK974+CHIR99201 (control)
LGK974+Wnt
LGK974 24h (24 hrs CHIR99201 withdrawal)
LGK974 48h (48 hrs CHIR99201 withdrawal)
LGK974+Fzd6 agonist (Fzd6 agonist)
LGK974+Fzd5 agonist (Fzd5 agonist)

value: Lung

value: Alveolar type 2

value: Fzd5 agonist


title: ATAC-seq_D4_PF_FABV_2


title: ATAC-seq_D4_PF_FABV_3


title: FRC 1


title: 1 Loxp Chow Fed 3153


title: T-cell Receptor Li104N-T

value: Liver

value: Tumor, Normal, Lymph Node and PBMC

value: TCR


title: LGK974_FZD5_Agonist, rep2


title: 3 Loxp Chow Fed 3120


title: LGK974_FZD6_Agonist, rep3

value: Fzd6 agonist


title: ATAC-seq_D4_P_FABV_2

value: P+F-


title: ATAC-seq_D4_P_FABV_1


title: K27ac_D4PF_AB_Input

data_processing:
Paired-end ChIP-seq reads were aligned to the mouse reference genome mm10 using Bowtie2 with the “--no-mixed --no-discordant -X 1000” parameter set, and then aligned reads with MAPQ >20 were retained.
H3K27ac-enriched peaks were identified using MACS with two biological replicates of ChIP and one biological replicate of the input data, with the default narrow-peak option.
For data visualization, input-normalized per-base fold-enrichment scores were computed using MACS2 with two biological replicates of ChIP and one biological replicate of the input data.
We then computed the sum of the signal coverage of the fold-enrichment data within 50-bp windows across the genome, and the 50-bpwindow data were quantile-normalized across all experimental conditions (Day4 PF–VEGF, Day4 PF, and Day 5 F) using normalize.quantiles function in the preprocessCore package (v1.36.0) in software R.
Assembly: mm10
Supplementary files format and content: Files ending in .bw are bigwig files for data visualization. The per library bigwig files are genome normalized, while the other tracks are the MACS2 input normalized tracks shown in the manuscript.
Supplementary files format and content: Files ending in .narrowPeak are peak calls from MACS2.

growth_protocol: Bry-GFP and ZX1 ES cell lines were maintained in a serum- and feeder-free culture system (Ying et al. 2003; Gadue et al. 2006; Ying et al. 2008; Kattman et al. 2011). Neurobasal medium and DMEM/F12 (50%/50%; Thermo Fisher Scientific) were supplemented with N2 (Thermo Fisher Scientific), B27 (Thermo Fisher Scientific), 0.05% BSA (MilliporeSigma), 150mM mono-thioglycerol (MilliporeSigma), 1000unit Mouse LIF (MilliporeSigma), 1μM PD0325901 (Stemgent), 3μM CHIR99021 (Stemgent), L-glutamine (Life Technologies), penicillin-streptomycin (Thermo Fisher Scientific). PD0325901 and CHIR99021 were not added at 2 days prior to start differentiation. For differentiation start, ES cellswere dissociated with trypLE express (Thermo Fisher Scientific) and cultured, at 1.0x105 cells/ml for 48hrs (Gadue et al. 2006; Kattman et al. 2011). In brief, IMDM and Ham’s F12 medium (75%/25%) were supplemented with N2, B27, BSA, L-glutamine, 0.5mM ascorbic acid (MilliporeSigma), 450mM mono-thioglycerol (MilliporeSigma), penicillin-streptomycin. The cells were differentiated in 10cm petri-dishes (Becton Dickenson). The 48hr-old embryoid bodies (EBs) were dissociated with trypLE express and the cells were re-aggregated in StemPro-34 SFM medium (Thermo Fisher Scientific) in the present of L-glutamine, 200μg/ml human transferrin, 500μM ascorbic acid, 450μM mono-thioglycerol, 6ng/ml bFGF, 8ng/ml Activin A and 1ng/ml BMP4 for Bry+, PDGFRα+ and Flk1+ mesoderm induction. 5ng/ml VEGF was treated at D2 for bipotential mesoderm induction. Human Activin A, human BMP4, mouse VEGF, human bFGF were purchased from R&D systems. For hematopoietic lineage and cardiac lineage induction, sorted cells were cultured in StemPro-34 SF medium, supplemented with 2mM L-glutamine, 1mM ascorbic acid (MilliporeSigma), and 10ng/ml bFGF (Kattman et al. 2006; Kattman et al. 2011). 2×105/ml sorted cells were seeded into individual wells of a 48-well flat bottom plate (Becton Dickenson) coated with gelatin after sorting.

extract_protocol:
Cells sorted at Day 4 or Day 5 of differentiation and frozen with liquid nitrogen were crosslinked in 0.5% formaldehyde for 5 min at room temperature, and then the reaction was quenched with 125 mM glycine. Cross-linked cells were rinsed with PBST (PBS with 0.1% Tween 20) and then resuspended in LB3-Triton (1 mM EDTA, 0.5 mM EGTA, 10 mM Tris-HCl pH 8, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroyl sarcosine, 1% Triton) supplemented with a protease inhibitor cocktail (Calbiochem 539131). Chromatin was extracted by sonication using Bioruptor (Diagenode). Cell extract was cleared by centrifugation and an aliquot was saved for input DNA sequencing.
Cell extract from 0.5 million cells was incubated with mouse monoclonal anti-H3K27ac antibody (Wako MABI0309, Lot 14007; 2 μL per IP) in a 200 μL reaction for 12 hours or longer at 4oC. Immunocomplex was captured by Protein G-conjugated magnetic dynabeads (ThermoFisher) and washed. Immunoprecipitated DNA was reverse-crosslinked and used to construct high-throughput sequencing libraries using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs). DNA libraries were processed on an Illumina HiSeq machine for paired-end sequencing.

value: FAB

value: P+F+

tag: chip antibody

value: Input


title: K27ac_D5F_ABV_Input

value: Day 5


title: ATAC-seq_D4_P_FABV_3

value: Day 4


title: ATAC-seq_D2_unsort_FABV_3

value: mouse embryonic stem cells

value: Day 2

value: Pretreatment

value: Unsorted


title: LGK974_FZD5_Agonist, rep1

value: Lung


title: K27ac_D4PF_ABV_Input

value: FAB+V


title: LGK974_FZD6_Agonist, rep2

value: Alveolar type 2


title: K27ac_D5F_ABV_rep2

value: P-F+


title: LGK_CHIR99201, rep3


title: LGK974_FZD6_Agonist, rep1


title: ATAC-seq_D2_unsort_FABV_2


title: ATAC-seq_D2_unsort_FABV_1


title: K27ac_D5F_ABV_rep1


title: LGK_CHIR99201, rep2


title: ATAC-seq_D0_unsort_FABV_3

value: Day 0


title: K27ac_D4PF_AB_rep2


title: ATAC-seq_D0_unsort_FABV_2


title: K27ac_D4PF_AB_rep1


title: 24hourwithdrawal, rep3


title: LGK_CHIR99201, rep1


title: ATAC-seq_D0_unsort_FABV_1


title: K27ac_D4PF_ABV_rep2


title: RNA-seq_Day8_PmFp_3

molecule: polyA RNA

value: Day 8


title: 24hourwithdrawal, rep2


title: 24hourwithdrawal, rep1


title: H3K27ac


title: 48hourwithdrawal, rep3


title: RNA-seq_Day8_PmFp_1


title: HTO-derived cDNA Li57_2-H

description:
HTO-derived cDNA
protein
paired-end
Illumina NovaSeq 6000
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Tumor, Normal, Lymph Node and PBMC

value: Liver

value: Tumor, Normal, Lymph Node and PBMC

value: HTO

value: see meta_features.csv located in supplementary files for Antibody name and barcode and meta_sample.csv in supplmentary files for Hashtag to sample mappings


title: B12, snRNAseq

city: Göttingen

first: Hannelore

last: Ehrenreich

address: Hermann-Rein-Str 3

department: Clinical Neuroscience

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1
Background removal was done through CellBender version 0.2.1
Output files from CellBender were filtered using Seurat to remove low quality nuclei
Counts and metadata files were extracted and are made available here
Assembly: mm10
Supplementary files format and content: Comma-separated values files

source_name: Hippocampus

extract_protocol:
On P49, 24 h after the last EPO/PL injection, 23 mice (N=11 EPO, N=12 PL) were sacrificed by cervical dislocation. The brain was immediately removed, the right hippocampus dissected on an ice-cold plate, quickly immersed in liquid nitrogen and kept at -80°C. Two right hippocampi of the same treatment group were collected in one tube for sequencing (one tube in the EPO group with only one right hippocampus).
Nuclei were isolated according as previously described by Corces et al., 2017 (https://doi.org/10.1038/nmeth.4396). Briefly, frozen tissue was transferred into 2ml of pre-chilled homogenization buffer (320mM sucrose, 0.1% NP40, 0.1mM EDTA, 5mM CaCl2, 3mM Mg(Ac)2, 10mM pH 7.8 Tris, 167uM β-mercaptoethanol and 1x protease inhibitor (Roche)). Tissue was carefully homogenised and filtered through an 80μm strainer, and further centrifuged for 1min under 100 rcf. For each sample, 400 ul supernatant was collected into a pre-chilled 2ml low-binding Eppendorf tube, followed by adding 400ul 50% iodixanol solution (in 1x homogenization buffer containing 480mM sucrose) to reach a 25% iodixanol concentration. By layering 600ul of 29% iodixanol underneath the 25% iodixanol mixture, then 600ul of 35% iodixanol underneath the 29% iodixanol, two clear interfaces between different concentrations of buffers were created, and the tube was centrifuged for 20 min under 3000 rcf. After centrifugation, nuclei were collected from the band between the 29% and the 35% iodixanol layers and transferred to a fresh pre-chilled tube. Isolated nuclei were washed and resuspended in cold resuspension buffer (1xPBA, 1% BSA, 0.1U/ul RNase inhibitor) and further subjected to single-nuclei transcriptome libraries using the chromium single cell 3’ reagent kit according to the manufacturer's instruction (10x Genomics). The constructed libraries were sequenced using NovaSeq 6000 (Illumina).

value: Whole hippocampus (Multiple cell types)

value: Hippocampus

tag: strain

value: Placebo


title: 48hourwithdrawal, rep2


title: 48hourwithdrawal, rep1


title: RNA-seq_Day8_PpFp_3

value: mouse embryonic stem cells

value: P+F+


title: B10, snRNAseq

description: 10x Genomics


title: RNA-seq_Day8_PpFp_2


title: B9, snRNAseq

description: 10x Genomics


title: RNA-seq_Day8_PpFp_1


title: HTO-derived cDNA Li57_1-H


title: LGK974_WNT, rep3

value: Wnt


title: LGK974_WNT, rep2


title: B8, snRNAseq

description: 10x Genomics


title: ADT-derived cDNA Li57_1-A

description:
ADT-derived cDNA
protein
paired-end
Illumina NovaSeq 6000
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Tumor, Normal, Lymph Node and PBMC

value: ADT

value: see meta_features.csv located in supplementary files for Antibody name and barcode


title: HTO-derived cDNA Li15_2-H


title: RNA-seq_Day8_PmFp_2

value: FAB+V


title: SPCs-3

city: Hachioji

first: Junji

last: Yamauchi

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: The University of Pharmacy and Life Science

data_processing:
Samples are aligned to the genome using the STAR RNA-seq alignera (STAR 2.5.2b), using default parameters. Alignment information for each read is stored in the BAM format.
Fragment Assignment: The number of fragments overlapping predefined genomic features of interest (e.g. genes) are counted.
Only read pairs that have both ends aligned are counted. Read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands are discarded.
The gene annotations we use were obtained from Subread package. These annotations were originally from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Rattus norvegicus

source_name: Dorsal root ganglion

growth_protocol: cultured in DMEM-based modified Sato medium

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen).
500 ng of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit (Cat# 20020594)

treatment_protocol: Untreated

value: Dorsal root ganglion

tag: cell line

value: Schwann cell precursor cell

value: primary peripheral glial cells

value: Wild type

value: no treatment


title: A6, snRNAseq

description: 10x Genomics

value: EPO


title: LGK974_WNT, rep1

value: Lung

value: Alveolar type 2


title: A5, snRNAseq

description: 10x Genomics

value: Whole hippocampus (Multiple cell types)


title: ADT-derived cDNA Li57_2-A

value: Liver

value: Tumor, Normal, Lymph Node and PBMC


title: B11, snRNAseq

description: 10x Genomics

value: Hippocampus

value: Placebo


title: A4, snRNAseq

description: 10x Genomics


title: SPCs-1


title: SPCs-2


title: ADT-derived cDNA Li15_1-A


title: HTO-derived cDNA Li15_1-H

value: HTO

value: see meta_features.csv located in supplementary files for Antibody name and barcode and meta_sample.csv in supplmentary files for Hashtag to sample mappings


title: A2, snRNAseq

description: 10x Genomics


title: A3, snRNAseq

description: 10x Genomics


title: A1, snRNAseq

description: 10x Genomics


title: 5Gy x4, replicate 2

city: Chengdu

first: Bin

last: Shi

address: Yulin Street

country: China

institute: Sichuan University

data_processing:
library strategy: Circle-seq
Fastp software were used to get high quality clean reads according to stringent filtering standards: Removing reads containing adapters or more than 10% of unknown nucleotides; Removing reads that are all A bases; Removing reads containing more than 50% of low quality.
The software bwa(Burrows-Wheeler Aligner)was used to align the clean reads to the reference genome, picard was used to sort the results and mark the repeated sequences, and bedtools is used to make genome coverage statistics.
We use 100kb as the standard to distinguish eccDNA from ecDNA. For eccDNA detection, we used the circular DNA analysis software Circle-Map for circular DNA detection. We used eccDNA screened based on the following criteria for subsequent  analysis. 1) the length is not more than 100kb; 2) The detected split reads in at least one sample is greater than or equal to 1.
In the same way as eccDNA identification, for ecDNA detection, we used the circular DNA analysis software Circle-Map[5] for circular DNA detection. The length of DNA between 100kb and 10M was identified as ecDNA.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Skin

growth_protocol: WT SD rats were housed in SPF environments.

extract_protocol:
We use Plasmid Mini AX kit to enrich circular DNA, then use exonuclease to remove linear DNA, and finally purify circular DNA by AMPureXp beads. 50 ng of circular DNA was used for the construction of sequencing libraries.
Circular DNA libraries for Circle-seq were prepared using TruePrep DNA Library Prep Kit V2 following manufacturer's protocols.

treatment_protocol: The back skin of the rats were irradiated with 5Gy every week, and the skin samples were taken on the 7th day after 2 and 4 times of fractionated irradiation, respectively.

value: SD

value: Skin

value: WT

value: 5Gy x4

tag: molecule type

value: Circular DNA


title: 5Gy x4, replicate 1


title: 5Gy x2, replicate 4

value: 5Gy x2


title: 5Gy x4, replicate 4


title: parental - rep1 - batch2

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

data_processing:
Raw reads were trimmed using Trimmomatic v0.32. First, adaptors and other Illumina-specific sequences from each read were removed using palindrome mode. Then, a four-nucleotide sliding window removes the bases once the average quality within the window falls below 30. Next, the first four bases at the start of each read were removed. Finally, reads shorter than 30 base pairs were dropped.
Cleaned reads were aligned to the human reference genome build hg19 using STAR v2.3.0e with default settings. Reads mapping to more than 10 locations in the genome (MAPQ < 1) were discarded.
Gene expression levels were estimated by quantifying mapped reads to exonic regions (the maximal genomic locus of each gene and its known isoforms) using featureCounts v1.4.4 and the hg19 ensGene annotation set from Ensembl.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Ensembl.ensGene.exon.raw_counts.tsv: Raw read counts (exonic part of the genes) for all the samples in a tab-separated text file.

source_name: triple negative breast cancer cell line

extract_protocol:
We extracted RNA from cultured cells using the QIAGEN RNeasy micro kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell population

value: parental


title: parental - rep3 - batch2


title: RNA-seq_Day8_VEGF_2

value: mouse embryonic stem cells

value: Day 8

value: FAB+V

value: P+F+


title: B7, snRNAseq

description: 10x Genomics

value: Whole hippocampus (Multiple cell types)


title: ADT-derived cDNA Li15_2-A

value: Liver

value: Tumor, Normal, Lymph Node and PBMC

value: ADT

value: see meta_features.csv located in supplementary files for Antibody name and barcode


title: RNA-seq_Day8_VEGF_1


title: 5Gy x2, replicate 3


title: parental - rep2 - batch2


title: RNA-seq_Day8_PDGFAA_2

value: FAB+P


title: parental - rep2 - batch1


title: RNA-seq_Day8_PDGFAA_1


title: parental - rep3 - batch1


title: parental - rep1 - batch1


title: 5Gy x2, replicate 1

value: SD


title: RNA-seq_Day8_AABMP4_3

value: FAB


title: Con, replicate 4

value: Skin

value: WT

value: untreated


title: 5Gy x4, replicate 3

value: 5Gy x4

value: Circular DNA


title: RNA-seq_Day8_AABMP4_2

value: mouse embryonic stem cells


title: 5Gy x2, replicate 2

value: 5Gy x2


title: Con, replicate 3


title: fast - rep2 - batch2

value: captured based on their trajectory

value: fast


title: RNA-seq_Day8_AABMP4_1

value: Day 8

value: P+F+


title: Con, replicate 2


title: fast - rep1 - batch2


title: Con, replicate 1


title: RNA-seq_Day6_VEGF_1

value: Day 6

value: FAB+V


title: fast - rep3 - batch1


title: fast - rep2 - batch1


title: RNA-seq_Day6_PDGFAA_2


title: JJN3_iPRMT1_3

city: Cluj-Napoca

first: Oana

last: Tudoran

address: Str. Republicii 34-36

department: Department of Genetics

country: Romania

institute: The Oncology Institute “Prof. Dr. Ion Chiricuță” in Cluj-Napoca

data_processing:
Fastqc was used for analyzing read quality while trimmomatic was utilized for removing identified low-quality reads and adapters.
Passing reads were further aligned to Hg38 genome and Gencode V35 (hg38) genomic annotation by STAR
Transcriptome was quantified by Salmon (Quasi-mapping mode) using Hg38 reference Gentrome (a combined reference of Hg38 reference genome and Gencode V35 transcriptome)
Quantified read counts were further normalized to transcript-per-million (TPM) on transcript-level and gene-level.
Log2(TPM+1) transformation was conducted to rescale expression levels.
Assembly: Hg38
Supplementary files format and content: tab-delimited file
Supplementary files format and content: Log2(TPM+1) transformed whole transcriptome profile

extract_protocol:
Wildtype JJN3, PRMT1-KO JJN3, and MS023 treated JJN3 cells were harvested for RNA isolation. Total RNAs were sent out for sequencing.
Samples were purified with Zymo kit. 3ug total RNAs were sent out for sequencing. >60 million read-pairs were sequenced per sample.

value: multiple myeloma


title: fast - rep1 - batch1


title: RNA-seq_Day6_PDGFAA_1

value: FAB+P


title: RNA-seq_Day6_AABMP4_3


title: JJN3_iPRMT1_1


title: JJN3_iPRMT1_2


title: Multi-genotype zebrafish skin snRNAseq

city: Seattle

first: Lauren

last: Saunders

state: WA

address: 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: single nucleus RNA sequencing library with 3'-end transcriptome measurments for each cell

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were performed using the processing pipeline from Cao et al., 2017 (doi: 10.1126/science.aam8940).
Count matrix was loaded into Monocle3 for further analysis
Assembly: GRCz11
Supplementary files format and content: Count Matrix (RDS file), Cell Metadata (comma separated values- .csv), Gene Metadata (comma separated values- .csv)
Supplementary files format and content: zskin_wildtype_cds.RDS: monocle3 cell_data_set object
Supplementary files format and content: zskin_wildtype_raw_counts.RDS: dgCMatrix with raw counts
Supplementary files format and content: zskin_wildtype_cell_metadata.csv: cell metadata table (comma separated)
Supplementary files format and content: zskin_wildtype_gene_metadata.csv: gene metadata table (comma separated)
Supplementary files format and content: zskin_all_genotypes_cds.RDS: monocle3 cell_data_set object
Supplementary files format and content: zskin_all_genotypes_raw_counts.RDS: dgCMatrix with raw counts
Supplementary files format and content: zskin_all_genotypes_cell_metadata.csv: cell metadata table (comma separated)
Supplementary files format and content: zskin_all_genotypes_gene_metadata.csv: gene metadata table (comma separated)

organism: Danio rerio

source_name: Whole skin tissue

growth_protocol: Zebrafish were raised at 28.5℃ and selected for dissection based on staging landmarks (Parichy et al., 2009).

extract_protocol:
Fish were staged and selected for dissection, euthanized with MS-222 and processed immediately. Following removal of the head and fins, skins were removed with forceps and immediately flash frozen in liquid nitrogen then stored at -80°C prior to isolation of nuclei.
3' end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis, tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.

treatment_protocol: Hypothyroid zebrafish, Tg(tg:nVenus-v2a-nfnB)wprt8Tg, underwent a metronidazole treatment to ablate the thyroid gland at 5 dpf.

value: Whole skin tissue

tag: developmental stage

value: 9.6 SSL (SP, squamation onset posterior)

value: wild-type, eda mutant homozygous, bnc2 mutant homozygous, hypothryoid


title: MP_ FOS3

city: Tianshui

first: Fang

last: Ma

state: Qinzhou District

address: South Xihe Road

department: College of Bioengineering and Technology

institute: Tianshui normal university

data_processing:
Raw reads were further filtered using fastp(version 0.18.0). After removal of reads containing adapters, containing more than 10% of unknown nucleotides (N) and low quality reads containing more than 50% of low quality (Q-value≤20) bases. The rRNA mapped reads were removed by using Short reads alignment tool Bowtie2
The remaining clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1in a reference-based approach.
The expression abundance and variations of each gene was estimated using abundance and variations by calculated FPKM （fragment per kilobase of transcript per million mapped reads）value. RNAs differential expression analysis was performed by DESeq2 between two different groups
The transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed transcripts.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Gallus gallus

source_name: ileum of Taiping chicken

extract_protocol:
Total RNA of the six libraries  was extracted using the standard TRIzol™. Agarose gel electrophoresis, Nano Photometer® Spectrophotometer and Bioanalyzer 2100 System  were  employed to evaluate the quantity and quality of the total RNAs.
About 3 μg total RNA from each sample was used  to construct RNA library. Six sequencing libraries were generated using the NEBNext® Multiplex small RNA Library Prep Kit for Illumina®

tag: breed

value: Taiping

tag: diet

value: MP_ FOS

value: ileum

value: two months

tag: gender

value: male


title: MP_ FOS2

tag: tissue

tag: age


title: fast - rep3 - batch2

tag: treatment


title: RNA-seq_Day6_AABMP4_2

value: mouse embryonic stem cells

tag: day

value: FAB


title: JJN3_isgCtrl_2

tag: genotype

value: isgCtrl


title: MP_ FOS1


title: RNA-seq_Day6_AABMP4_1

tag: sort


title: CT_3

value: CT


title: CT_2


title: RNA-seq_Day4_VEGF_2

value: Day 4

value: P+F+


title: RNA-seq_Day4_VEGF_3

value: FAB+V


title: RNA-seq_Day6_VEGF_2

value: Day 6


title: JJN3_MS023_3

tag: cell type

value: multiple myeloma


title: RNA-seq_Day4_VEGF_1


title: CT_1


title: JJN3_MS023_2


title: JJN3_MS023_1


title: RNA-seq_Day4_PDGFAA_3

value: FAB+P


title: RNA-seq_Day4_PDGFAA_2


title: JJN3_DMSO_3

value: DMSO


title: JJN3_DMSO_2


title: RNA-seq_Day4_PDGFAA_1


title: WT-OD2.0+3h-Rep1

city: Shanghai

last: Liu

address: Life Science Research Building 320 Yueyang Road, Xuhui District

institute: Institut Pasteur of Shanghai, Chinese Academy of Sciences

data_processing:
The raw sequencing reads in fastq files were processed by cutadapt to trim the adaptor sequence and remove low-quality ends.
The first 25 nucleotides of high-quality paired-end reads were taken and mapped to the genome of Salmonella strain SL1344 (NC_016810.1) using the BWA software with default parameters.
If two mates of a sequenced fragment were mapped to different genomic locations and the distance is greater than 1000 nt, the fragment was declared as chimera. Otherwise, the fragment was defined as singleton when the mates mapped to the same transcript or within a distance of 1,000 nt.
Significant chimeras (S-chimera) were analyzed by comparing the detected pairwise interactions to the counts of random ligations using a Fisher’s exact test, as previously reported (Melamed et al., 2018, 2016). Each Chimera was assigned a p-value and an Odds Ratio value by multiple hypotheses testing.
Chimeras with a p-value ≤ 0.05 and an Odds Ratio ≥ 1 were defined as S-chimeras. Only Schimeras with ≥ 10 sequenced fragments were presented and further investigated.
Assembly: NC_016810.1
Supplementary files format and content: Tab-delimited text include counts of statistically significant chimeras

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: Bacterial cells

growth_protocol: Salmonella enterica serovar Typhimurium SL1344 wild type strain carrying the plasmid pYC582 were grown in LB medium at 37 °C with 220 rpm shaking.

extract_protocol:
50 OD of bacterial cells per sample were collected by centrifugation at 12,000 g for 5 min at 4 °C. The pellets were washed twice with 10 ml precooled PBS and resuspended in 600 µl ice-cold lysis buffer (20 mM Tris pH 8.0, 150 mM KCl, 1 mM of MgCl2, 1 mM DTT, 0.05% Tween-20), and lysed for 10 min with 500 µl glass beads using Cryolys Evolution at 4 °C. Cell lysates were collected by centrifugation for 30 min at 13,000 rpm at 4 °C, and transferred to new tubes. The lysates were incubated with anti-FLAG antibody (Thermo Fisher) conjugated protein G magnetic beads (Sigma Aldrich) for 1 hour at 4 °C with rotation. The beads were washed five times with 500 µl ice-cold lysis buffer and resuspended in 100 µl lysis buffer. The Hfq-bound RNA was purified using RNA clean & concentrator columns (Sangon, Shanghai). The RNA pellets were dissolved  in nuclease-free water.
LiRIP-seq libraries were constructed using the RNAtag-Seq protocol with a few modifications (Melamed et al., 2018). Briefly, RNA was subjected to fragmentation and DNase I treatment, and purified with 2.5x Agencourt AMPure XP beads and 1.5x isopropanol. RNA was ligated to the 3’ barcoded adaptor and purified with 2.5x AMPure XP beads and 1.5x isopropanol. Ribosomal RNA was removed using Ribo-off rRNA depletion Kit (#N407-01, Vazyme). The rRNA depleted sample was purified with 2.5x AMPure XP beads and 1.5x isopropanol. First strand cDNA was synthesized using HiScript II 1st Strand cDNA Synthesis Kit (#R211-01, Vazyme). RNA was degraded by 1 M NaOH. cDNA was purified with 2.5x AMPure XP beads and 1.5x isopropanol. The cDNA 3’ end was attached to a second adaptor and cleaned up twice with 2.5x AMPure XP beads and 1.5x isopropanol. Libraries were PCR amplified with Illumina P5 and P7 primers using Q5 High-Fidelity DNA Polymerase (#M0491L, NEB), and purified with 1.5x AMPure XP beads. The libraries were then sequenced by 150 bp paired-end sequencing with an Illumina NovaSeq 6000 instrument.

treatment_protocol: When bacterial cultures grown reached OD600 of 2.0+2.5h, T4 RNA ligase was induced for 30 min by addition of L-arabinose (final concentration 0.2%).

value: Bacterial cells

value: wild-type

value: T4 RNA ligase induced overexpressed plasmid pYC582


title: JJN3_isgCtrl_3


title: WT-OD2.0-Rep2

treatment_protocol: When bacterial cultures grown reached OD600 of 1.5, T4 RNA ligase was induced for 30 min by addition of L-arabinose (final concentration 0.2%).


title: WT-OD2.0-Rep1


title: RNA-seq_Day4_AABMP4_3


title: WT-OD2.0+3h-Rep2


title: WT-OD0.5-Rep2

treatment_protocol: When bacterial cultures grown reached OD600 of 0.3, T4 RNA ligase was induced for 30 min by addition of L-arabinose (final concentration 0.2%).


title: JJN3_DMSO_1


title: JJN3_isgCtrl_1


title: RNA-seq_Day4_AABMP4_2


title: RNA-seq_Day4_AABMP4_1


title: E_T_8_L

city: Kaifeng City, Henan Province

first: Hua

last: Yang

state: Henan Province

address: Jinming Campus of Henan University

institute: Henan University

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format. SOAPnuke(Version v1.5.2)  Official Websitehttps://github.com/BGI-flexlab/SOAPnuke
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads. HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these

source_name: mouse ear

growth_protocol: mouse ear skin was extracted on the 13th day and the effects of GSK1562590 on the expression of pruritis and inflammatory factors were detected by RNA-seq.

extract_protocol:
Mouse ear skins were separated on a sterile workbench for liquid nitrogen quick freezing, and the tissues were ground in a mortar by liquid nitrogen grinding method. Add 1ml Trnzol reagent per 50mg to fully grind the tissue. Tissue homogenates were collected and transferred to a new EP tube, 0.2 mL chloroform was added, violently shaken for 15 s, left at room temperature for 5 min, and then centrifuged at 4 ° C at 12,000rpm for 15 min. After centrifugation, the upper water phase, which retained RNA, was transferred to a new tube of isopropyl alcohol supernatant in the same volume and centrifuged at 4℃ for 10 min at 12000 rpm. After the supernatant was thrown away, the RNA pellets were washed twice with 1 mL 75% ethanol, then centrifuged at 13000rpm at 4℃ for 5 min, the ethanol was discarded, and then air-dried in a biosafety cabinet for 3 min. Finally, 30 μL ~100 μL Nase-free ddH20 was added. Total RNA was then identified and quantified using Nano Drop and Agilent 2100 Bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSeq platform (BGI-Shenzhen, China)

value: mouse ear


title: E_T_10_L


title: Hfq-OD2.0+3h-Rep2

growth_protocol: Salmonella enterica serovar Typhimurium SL1344 hfq::3xFLAG tagged strain carrying the plasmid pYC582 were grown in LB medium at 37 °C with 225 rpm shaking.


title: WT-OD0.5-Rep1


title: E_T_7_L


title: Hfq-OD2.0+3h-Rep1

growth_protocol: Salmonella enterica serovar Typhimurium SL1344 hfq::3xFLAG tagged strain carrying the plasmid pYC582 were grown in LB medium at 37 °C with 224 rpm shaking.


title: E_T_4_L


title: Hfq-OD2.0-Rep2

growth_protocol: Salmonella enterica serovar Typhimurium SL1344 hfq::3xFLAG tagged strain carrying the plasmid pYC582 were grown in LB medium at 37 °C with 223 rpm shaking.


title: E_T_6_L


title: E_C_12_L


title: E_C_10_L


title: E_C_11_L


title: WT-EV-Rep2

growth_protocol: Salmonella enterica serovar Typhimurium SL1344 wild type strain carrying the empty plasmid pBAD-control were grown in LB medium at 37 °C with 220 rpm shaking.

value: Empty plasmid pBAD-Control


title: E_C_3_L


title: Collinsella aerofaciens, no uric acid, replicate 3

city: Stanford

first: Dylan

last: Dodd

address: 269 Campus Drive

department: Pathology

institute: Stanford University

data_processing:
CLC Genomics Workbench v 21.0.4
Reads were trimmed using a quality score limit of 0.05 and ambiguous nucleotides (n = 2), and automatic read-through adapter trimming was performed.
Genomes were downloaded from NCBI in GenBank file format (.gbff) for each of the three bacteria (NCBI assembly accession numbers: GCF_010509075.1, Collinsella aerofaciens ATCC 25986; GCF_000144625.1, Lacrimispora saccharolyticum WM1; GCF_000155085.1, Clostridium sporogenes ATCC 15579).
Genomes were uploaded into CLC Genomics Workbench and converted to tracks.
RNAseq was performed using the genome track as the reference sequence and genes for the gene track. Mapping settings included: Mismatch cost, 2; Insertion cost, 3; Deletion cost, 3; Length fraction, 0.8; Similarity fraction, 0.8; maximum number of hits for a read, 10. Expression settings included: Strand setting, both; Library type setting, bulk; Expression value, TPM.
Statistical comparisons were made between organisms cultured with or without uric acid using multi-factorial statistics based on a negative binomial GLM as implemented in CLC Genomics Workbench (v.21.0.4).
The expression and CDS tracks were then exported as Excel files and expression and annotation tracks were merged in Excel using the VLOOKUP function based on the chromosome coordinates.
Assembly: NCBI assembly accession numbers: GCF_010509075.1, Collinsella aerofaciens ATCC 25986; GCF_000144625.1, Lacrimispora saccharolyticum WM1; GCF_000155085.1, Clostridium sporogenes ATCC 15579
Supplementary files format and content: tab-delimited text files include Chromosome, Region, Annotation, Locus Tag, Protein ID, Gene Name, reads, TPM, for each Sample

organism: Collinsella aerofaciens ATCC 25986

growth_protocol: All growth experiments were performed anaerobically at 37 degrees Celsius. Three individual colonies were selected for each bacterium and were inoculated into separate overnight cultures in Mega medium. The following day, each culture was precultured in Mega medium, and after three hours diluted to an OD of 0.1 into two experimental cultures, one containing standard Mega medium and one with Mega medium containing 5 mM uric acid. Bacteria were allowed to grow until reaching an OD that was commensurate with approximately 50% uric acid degradation as determined by previous experiments.

extract_protocol:
Cells were then subjected to lysozyme digestion, Proteinase K digestion and mechanical disruption with a mixer mill (RETSCH MM400) at 4 °C, 25/s, for 30 min. RNA was then purified using RNeasy kit (Qiagen), followed by DNase digestion and second RNA purification step using the RNeasy kit (Qiagen).
Ribosomal RNA was removed with the Ribo-Zero Bacteria kit (Illumina). The RNA-seq libraries were prepared using a TruSeq Stranded mRNAseq Sample Prep kit with each sample individually ligated with unique adapters (Illumina). The libraries were quantitated by qPCR, pooled, and sequenced on one lane for 101 cycles from one end of the fragments on a NovaSeq 6000 using a NovaSeq SP reagent kit. Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina) and adaptors were removed from the 3’ end of the reads. Read 1 aligns to the antisense strand and read 2 aligns to the sense strand.

treatment_protocol:
Cells were cultured in rich medium with or without supplemental uric acid (5 mM final concentration).
Cell cultures were combined with two volumes of RNAprotect (Qiagen) in an anaerobic chamber, mixed thoroughly and then allowed to sit for five minutes. Cells were then centrifuged (5,000 x g, 4 °C, 10 min) and the supernatant was decanted.

value: no uric acid


title: Hfq-OD0.5-Rep1

growth_protocol: Salmonella enterica serovar Typhimurium SL1344 hfq::3xFLAG tagged strain carrying the plasmid pYC582 were grown in LB medium at 37 °C with 220 rpm shaking.


title: WT-EV-Rep1


title: E_C_9_L


title: WT-T4-Rep2


title: Collinsella aerofaciens, no uric acid, replicate 2


title: Collinsella aerofaciens, no uric acid, replicate 1


title: Hfq-EV-Rep1

growth_protocol: Salmonella enterica serovar Typhimurium SL1344 hfq::3xFLAG tagged strain carrying the empty plasmid pBAD-control were grown in LB medium at 37 °C with 220 rpm shaking.


title: Hfq-EV-Rep2


title: Hfq-OD2.0-Rep1

growth_protocol: Salmonella enterica serovar Typhimurium SL1344 hfq::3xFLAG tagged strain carrying the plasmid pYC582 were grown in LB medium at 37 °C with 222 rpm shaking.


title: S2_SC

city: Guangzhou

first: Xueting

address: Changgangdong 250

institute: The Second Affiliated Hospital of Guangzhou Medical University

description: SADBE-induced group, biological rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end cleanreads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, 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.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: ACD_Spinal cord

extract_protocol:
Cervical spinal cords were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Once a day for three consecutive days, 20 μl of 1% SADBE (dissolved in acetone) was applied to the shaved abdomen skin of mice. Five days later, the SADBE treatment group was challenged with 20 μl of 1% SADBE topically applied to the shaved nape skin once daily for three consecutive days, whereas acetone alone was used as a vehicle control.

tag: strain background

tag: group

value: SADBE-induced ACD (Allergic contact dermatitis) model

value: Cervical spinal cord


title: Hfq-OD0.5-Rep2

growth_protocol: Salmonella enterica serovar Typhimurium SL1344 hfq::3xFLAG tagged strain carrying the plasmid pYC582 were grown in LB medium at 37 °C with 221 rpm shaking.


title: C7_SC

description: control group, biological rep3

source_name: control_Spinal cord

value: Control


title: S3_SC

description: SADBE-induced group, biological rep3


title: S1_SC

description: SADBE-induced group, biological rep1


title: C6_SC

description: control group, biological rep2


title: Hfq-T4-Rep1


title: 7011 LN

data_processing:
CellRanfer mkfastq to prepare fastqfiles (v6.1.1)
CellRanger count to prepare gene count (v6.1.1)
Sample filtering and reclustering using Seurat (v4.0.4)
Further analysis using Loupe browser (v 5.1.0)

source_name: lymph nodes

growth_protocol: not applicable

extract_protocol:
After lymph nodes enzymatic digestion, stromal cells were collected and flow sorted using the following markers: CD45 neg, PDPN pos, CD31 pos.
10x RNAseq protocol

treatment_protocol: not applicable

tag: mouse strain and genotype

value: C57/B6 Iu-BCL6

tag: mouse age

value: age >16 months

value: flow sorted stromal cells


title: Collinsella aerofaciens, uric acid, replicate 2

tag: strain

value: uric acid


title: 5992 LN


title: Inoculation_5day_replication3

status: Public on Jun 15 2023

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

institute: RIKEN

data_processing:
base-calling:RTA and bcl2fastq
adapter trim: trimmomatic
alignment: HISAT2
aligned reads count: featureCounts
normalize: DESeq2
Assembly: Manihot esculenta v8.1
Supplementary files format and content: tab-delimited text

organism: Manihot esculenta

source_name: Leaf

extract_protocol:
The total RNA from inoculated leaves was purified by use of the Plant RNA reagent (Thermofisher) following RNeasy Plant Mini Kit (QIAGEN). A 0.5 mL of Plant RNA reagent was added to about 0.1 g of fresh weight of finely powdered leaf tissue that was crushed by a Multi-Beads Shocker (2,000 rpm, 15 s) and its mixture was mixed gently. After incubating for 5 minutes at room temperature, the supernatant was collected by centrifuging at 12,000 × g for 2 minutes at room temperature. The supernatant was transferred to a clean RNase-free tube. A 0.1 mL of 5 M NaCl was added to supernatant and tube was mixed by tapping. A 0.3 mL of chloroform was added to the supernatant and mixed thoroughly by inverting. The supernatant was collected by centrifugation at 12,000 x g for 10 minutes at 4°C to separate the phases. The upper aqueous phase was transferred to a clean RNase-free tube. After an equal volume of isopropyl alcohol was added to the collected aqueous phase, the mixture was incubated at room temperature for 10 minutes. After centrifuging the mixture at 12,000 x g for 10 minutes at 4°C, the precipitation was washed by 1.0 mL of 75% ethanol. After the solubilization of the precipitates in 40 μL of RNase-free water, the solution was treated with DNase I (10 U)(Takara) and RNase inhibitor (40 U) (Nippongene) in 50 μL of reaction at 37°C for 20 min. The 50 μL of solution was added to the 350 uL of RLT buffer in RNeasy Plant Mini Kit (QIAGEN) and the RNA preparation was performed as described by manual procedure. The total RNA quality was evaluated by electrophoresis with the bioanalyzer system (Agilent, USA). The total RNA was stored at -80°C until further use.
We used 500 ng of the total RNA of each sample for library preparation. The library was prepared by following the Lasy-Seq (Kamitani et al. 2019) version 1.1 protocol (https://sites.google.com/view/lasy-seq/).

value: Leaf

value: HuayBong 60

value: 5 day after Mealybug inoculation


title: WT-T4-Rep1


title: Inoculation_10day_replication2

value: 10 day after Mealybug inoculation


title: Inoculation_3day_replication1

value: 3 day after Mealybug inoculation


title: Inoculation_5day_replication2


title: Inoculation_1day_replication4

value: 1 day after Mealybug inoculation


title: Inoculation_1day_replication3


title: LN-2

value: C57/B6 WT


title: Inoculation_1day_replication1


title: Inoculation_1day_replication2


title: Hfq-T4-Rep2

value: Bacterial cells

value: T4 RNA ligase induced overexpressed plasmid pYC582


title: Collinsella aerofaciens, uric acid, replicate 3


title: C5_SC

description: control group, biological rep1


title: non-treatment_replication1

value: non-treatment


title: Collinsella aerofaciens, uric acid, replicate 1


title: Nrf2 KO 786-O 4-OI UI (3)

city: Aarhus c

first: Per

last: Qvist

state: Danmark

address: Høegh-Guldbergs Gade 10

department: Biomedicine

country: Denmark

institute: Aarhus University

description:
Sample 18
4-OI 75uM

data_processing:
Reads were aligned to, respectively, the human genome (GRCh38 - Ensembl release 108) and the VSV genome (GenBank assembly accession: GCA_000850045.1) using HISAT2 aligner (v2.1.1).
Transcript quantification was performed using StringTie (v2.2.1) 2 and the read counts were normalized for effective gene length, and sequencing depth to yield Transcripts Per Kilobase Million (TPM).
Differentially expressed genes were determined from count tables using EdgeR (v3.36.0).
Assembly: GRCh38 - Ensembl release 108 / VSV genome (GenBank assembly accession: GCA_000850045.1).
Supplementary files format and content: Naziia_NormalizedExpressionMatrix_TPM.txt: Tab-delimited text file includes TPM values for each Sample.

extract_protocol:
High pure RNA isolation kit (Roche, 11828665001).
DNBSEQ Eukaryotic Strand-specific mRNA library.

tag: cell line

value: Kidney adenocarcinoma

value: Nrf2 Knock out

tag: infection

value: Uninfected


title: Inoculation_10day_replication3


title: Nrf2 KO 786-O UT VSVd51 (2)

description:
Sample 20
VSVd51M (0.01 MOI)

value: Untreated


title: Nrf2 KO 786-O 4-OI UI (2)

description:
Sample 17
4-OI 75uM


title: Nrf2 KO 786-O 4-OI VSVd51 (2)

description:
Sample 23
4-OI + VSVd51M


title: Nrf2 KO 786-O 4-OI UI (1)

description:
Sample 16
4-OI 75uM


title: Nrf2 KO 786-O UT VSVd51 (1)

description:
Sample 19
VSVd51M (0.01 MOI)


title: Nrf2 KO 786-O UT VSVd51 (3)

description:
Sample 21
VSVd51M (0.01 MOI)


title: Inoculation_10day_replication1


title: Inoculation_3day_replication2


title: Inoculation_5day_replication1


title: Nrf2 KO 786-O UT UI (2)

description:
Sample 14
DMSO 0.1%


title: non-treatment_replication2


title: Nrf2 KO 786-O UT UI (1)

description:
Sample 13
DMSO 0.1%


title: NKO 786-O 4-OI VSVd51 (2)

description:
Sample 11
4-OI + VSVd51M

value: pLenti control


title: NKO 786-O 4-OI VSVd51 (1)

description:
Sample 10
4-OI + VSVd51M


title: NKO 786-O UT VSVd51 (2)

description:
Sample 8
VSVd51M (0.01 MOI)


title: Nrf2 KO 786-O 4-OI VSVd51 (1)

description:
Sample 22
4-OI + VSVd51M


title: NKO 786-O UT VSVd51 (3)

description:
Sample 9
VSVd51M (0.01 MOI)


title: NKO 786-O 4-OI UI (3)

description:
Sample 6
4-OI 75uM


title: Nrf2 KO 786-O 4-OI VSVd51 (3)

description:
Sample 24
4-OI + VSVd51M


title: NKO 786-O UT VSVd51 (1)

description:
Sample 7
VSVd51M (0.01 MOI)


title: NKO 786-O 4-OI UI (2)

description:
Sample 5
4-OI 75uM


title: NKO 786-O UT UI (3)

description:
Sample 3
DMSO 0.1%


title: NKO 786-O 4-OI UI (1)

description:
Sample 4
4-OI 75uM


title: NKO 786-O UT UI (1)

description:
Sample 1
DMSO 0.1%


title: NKO 786-O UT UI (2)

description:
Sample 2
DMSO 0.1%


title: Nrf2 KO 786-O UT UI (3)

description:
Sample 15
DMSO 0.1%


title: DF12 26c3 p60

city: Chicago

first: Davi

middle: Marco

last: Lyra Leite

state: Illinois

address: 320 E Superior St 8-450

institute: Northwestern University

data_processing:
Using SOAPnuke, sequence files were trimmed for adaptors, low-quality reads, and N reads.
Clean sequencing reads were mapped to the GRCh38 reference genome using STAR and counted using RSEM.
Assembly: GRCh38
Supplementary files format and content: Organized .xlsx file includes TPM values for each sample.

growth_protocol: hiPSC cell lines were cultured in 12 well plates either in DMEM/F12 or BMEM, in humidified atmosphere with 5% CO2, 5% O2, at 37C.

extract_protocol:
RNA was extracted using 150 µL/well of TRIzol Reagent. RNA was then purified using the Direct-zol RNA MicroPrep kit, including on-column DNase digestion to remove genomic DNA.
RNA libraries for RNA-seq were prepared using DNBSEQ Eukaryotic strand-specific mRNA library protocol.

value: hiPSC

value: WT

tag: medium


title: BMEM 26c3 p59

value: BMEM


title: BMEM 23c1 p61


title: DF12 26c3 p61


title: DF12 23c1 p51


title: BMEM 26c3 p60


title: BMEM 26c3 p61


title: DF12 23c1 p61


title: BMEM 23c1 p51


title: DF12 23c1 p50


title: BMEM 23c1 p50


title: NKO 786-O 4-OI VSVd51 (3)

description:
Sample 12
4-OI + VSVd51M


title: DF12 22c10 p62


title: BMEM 22c10 p62


title: BMEM 22c10 p61


title: DF12 22c10 p61


title: DF12 22c10 p60


title: BMEM 22c10 p60


title: DF12 21c10 p44


title: DF12 21c10 p43


title: BMEM 21c10 p43


title: DF12 21c10 p42


title: BMEM 21c10 p42


title: BMEM 19c3 p64


title: DF12 19c3 p64


title: DF12 19c3 p50


title: DF12 19c3 p49


title: BMEM 19c3 p50


title: BMEM 19c3 p49


title: Normal control

city: Tianjin

first: Xiuxue

last: Mo

address: Weijin Road 94, Nankai District

institute: Nankai University

description:
Chromium, 1000006
10x Genomics

data_processing:
Single-cell RNA-seq data were quantified using the 10x software package CellRanger 2.2.0 to map the data to the Rat (Rnor6) reference genome.
Assembly: Rnor6
Supplementary files format and content: Seurat object for the gene expressions

source_name: myocardium

extract_protocol:
The cells were suspended in 500 μl of staining buffer containing anti-CD45-BB515 (BD Biosciences) at a dilution of 1:200 per 1e6 cells, incubated on ice for 20 min and then washed twice with PBS. Stained cells were then stained with a 1:20 dilution of 7-AAD (BD Biosciences, 559925) and subjected to FACS.
The scRΝΑ-seq libraries were prepared using a single-cell 5’ solution v2 reagent kit (Chromium, 1000006) according to the protocol provided with the 10x Genomics Chromium Single-Cell Immune Profiling Solution

value: myocardium

value: control

tag: time

value: 0 days


title: Giant Cell Myocarditis

description:
Chromium, 1000006
10x Genomics

value: Treated with myosin heavy-chain-α peptides

value: 21 days


title: wox13-2_20191101_4

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: TRIP Headquarters Advanced General Intelligence for Science Program

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
FACS_WT04
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]

data_processing:
BCL files generated by Illumina NextSeq500 were converted to fastq files by bcl2fastq2 (v2.17.1.14) with demultiplexing pool barcodes.
We trimmed read2 length to 62 nucleotides by using FASTX-Toolkit (version 0.0.14).
Data for Quartz-Seq2 was processed by Drop-seq tools (version 1.11) and correct_bacode program (https://github.com/rikenbit/correct_barcode) to convert fastq files to digital expression matrix.
Transcript reads were mapped to BenjaminColearabidopsis.fa, Shulse et al (2019, Cell Reports) using STAR2.7.0e
read1 = cell barcode (1-15), UMI (15-23), read2 = transcrip
Assembly: BenjaminColearabidopsis.gtf, Shulse et al (2019, Cell Reports)
Supplementary files format and content: tab-delimited text files include UMI counts for each gene for each cell

organism: Arabidopsis thaliana

source_name: wox13-2 mutant

extract_protocol:
For single-cell RNA-seq analysis, we performed Quartz-Seq2 as reported previously [Sasagawa et al., Genome Biology 19:29(2018), https://doi.org/10.1186/s13059-018-1407-3].
Sequence library DNA for single-cell RNA-seq was prepared according to previous paper [Sasagawa et al., Genome Biology 19:29(2018), https://doi.org/10.1186/s13059-018-1407-3]. Reverse transcription primers (v3.2a) were used for cell-barcoding. Sequence library DNA was analyzed with NextSeq500 HOP 75 cycles kit v2.5.

treatment_protocol: Single-cells were isolated from Arabidopsis callus (WT and wox13-2 mutant) that was generated by two-step tissue culture. For both datasets, cell suspensions from >170 hypocotyl explants (SIM d 7) were prepared for each genotype and designated as biological replicate1 and biological replicate2, respectively. We used CellenOne for replicate1 and BD FACS Aria II SORP for replicate2 for single cell collection. Cell suspensions were stained with PI to remove dead cells. Isolated single-cells were analyzed by single-cell RNA-seq method.

value: callus

value: multiple cell-types

tag: platform for single-cell collection

value: BD FACS Aria II

tag: id for biological replicate

tag: id for technical replicate


title: wox13-2_20191101_3

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
FACS_WT03
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]

tag: tissue


title: wild-type_20191101_2

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
FACS_mt02
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]

source_name: Colombia

value: wild-type


title: wild-type_20191101_4

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
FACS_mt04
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]


title: wild-type_20191101_1

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
FACS_mt01
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]


title: wild-type_20191101_3

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
FACS_mt03
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]


title: wild-type_20191001_3

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
Cellen_WT03
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]

value: CellenOne


title: wild-type_20191001_4

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
Cellen_WT04
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]


title: wox13-2_20191101_1

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
FACS_WT01
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]


title: wox13-2_20191101_2

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
FACS_WT02
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]


title: wild-type_20191001_2

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
Cellen_WT02
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]


title: BMEM 21c10 p44


title: wox13-2_20191001_4

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
Cellen_mt04
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]


title: wox13-2_20191001_3

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
Cellen_mt03
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]


title: wox13-2_20191001_2

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
Cellen_mt02
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]


title: wox13-2_20191001_1

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
Cellen_mt01
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]


title: D4 hEEs, Sox17 positive fraction, Replicate 1

city: New Haven

first: Berna

last: Sozen

state: CT

address: 333 Cedar St

institute: Yale School of Medicine

description: WGBS

data_processing:
Bisulfite-converted reads were quality filtered and adapter trimmed using cutadapt (v2.4), followed by alignment to the hg19 reference genome with bsmap using the following parameter: -v 0.01 -s 16 -w 100 -S 1 -R -u -q 20.
Duplicate reads were removed using GATK MarkDuplicates (v4.1.0.0).
Methylation rates were called using mcall using default parameter and subsequently filtered for coverage (min 10 reads, max 150) as well as autosomes.
Assembly: hg19
Supplementary files format and content: Bigwig file of 10X filtered methylation rates

source_name: Cell line

growth_protocol: hEPSCs were cultured in human expanded potential-complete media (hEP-LCDM media) as described in Yang et al., 2017 with addition of 1 µM WNT inhibitor IWR and 2 µM ROCK inhibitor (Y27632) (hEP-LCDMYI).

extract_protocol:
DNA purification using a DNA lysis buffer comprised of 10 mM Tris, 10 mM NaCl, 10 mM EDTA and 0.5 % SDS and 300 mg/mL molecular biology grade Proteinase K (Roche), ~6 hours of incubation at 55ºC, phenol:chloroform purification and ethanol based purification.'
Genomic DNA was sheared using a Covaris S220 Ultrasonicator to ~400 bp.  Re-concentrated DNA was then Bisulfite converted using the EZ-DNA methylation Gold Kit (Zymo Research) and synthesized into libraries using the xGen™ methylation sequencing DNA methylation kit using unique dual index adapters (IDT).  Final libraries were amplified with 10 PCR cycles.

treatment_protocol: hEEs are generated by plating single cells onto AggreWell plates in Spontaneous Differentiation Media (SDM) supplemented with 5µM of ROCK inhibitor (Y27632) for the first 24h of aggregation.  At D3, media is exchanged with mIVC2 media (described in Xiang et al. 2020).  Cells were then trypsinized to single cell, FACS purified using a Sony SH800S Cell Sorter to a minimum of 10,000 cells for each fraction, and snap frozen.

value: Cell line

value: Human Embryonic Stem Cell Line

value: RUES2 cell line (NIHhESC-09-0013) containing Sox2 and Sox17 reporters (see PMID:29795348)

tag: treatment

value: 4 day differentiation into hEEs


title: D4 hEEs, Sox17 positive fraction, Replicate 2

description: WGBS

tag: genotype


title: D4 hEEs, Sox2 positive fraction, Replicate 1

description: WGBS


title: D4 hEEs, double negative fraction, Replicate 1

description: WGBS


title: Undifferentiated hPSCS Replicate 2

description: WGBS

value: Undifferentiated


title: Undifferentiated hPSCS Replicate 1

description: WGBS


title: DF12 26c3 p59

value: hiPSC

value: WT


title: wild-type_20191001_1

description:
Type of cell-barcodes:
384 indexes, Quartz-Seq2 v3.2a
Cellen_WT01
We analyzed single-cells, which were isolated to 384-wells in total. [read1 = cell barcode (1-14), UMI (15-22), read2 = transcript.]


title: CES1KD_THP-1 cells M2_3

city: Starkville

first: Oluwabori

last: Adekanye

state: MS

address: 240 Wise Center drive

institute: Mississippi State University

data_processing:
Original images are tranformed to sequence read (Raw data) by CASAVA base recognition. Raw Data was stored as Fastq file
Alignment to reference was performed by HISAT2 according to Novogene workflow
Gene Expression Quantification was estimated by Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced according to Novogen Inc workflow
Differential gene expression was performed by Novogene using DESeq software. It included raw readcount normalization, statistical modeling to determine the hypothesis test's probablity, and multiple hypothesis testing corrections.

source_name: cell line

growth_protocol: THP-1 monocytes were maintained in RPMI medium supplemented with 10% fetal bovine serum, 50 uM 2 mercaptoethanol, and gentamycin antibiotic (complete medium).

extract_protocol:
RNA was extracted using the QIAshredder RNA kits (QIAGEN). Concentration >400ng and RNA integrity number > 4.0 was sent to Novogene for library construction.
RNA was sent to Novogene Inc for library preparation

treatment_protocol:
THP-1 monocytes were differentiated into macrophage with 20 nM phorbol 12-myristate 13-acetate in complete medium for 72 hours.
M1 cells were treated with 1ug/ml LPS and 100ng/ml interferon Gamma in RPMI medium, while M2 cells were treated with 100ng/ml IL-4 in RPMI medium

value: cell line

value: Macrophages

value: CES1 Knock down


title: CES1KD_THP-1 cells M1_4

value: LPS + Interferon Gamma


title: CES1KD_THP-1 cells M2_1


title: CES1KD_THP-1 cells M2_2


title: CES1KD_THP-1 cells M1_3


title: CES1KD_THP-1 cells M2_4


title: WT_THP-1 cells M2_1


title: WT_THP-1 cells M1_4


title: CES1KD_THP-1 cells M1_2


title: CES1KD_THP-1 cells M0_2

value: Resting


title: WT_THP-1 cells M2_3


title: CES1KD_THP-1 cells M0_3


title: CES1KD_THP-1 cells M0_4


title: CES1KD_THP-1 cells M0_1


title: WT_THP-1 cells M2_4


title: WT_THP-1 cells M2_2


title: WT_THP-1 cells M0_1


title: WT_THP-1 cells M0_3


title: Intermittent hypoxia IL1b pool 3

city: TROMSOE

first: Casper

middle: Jan Elis

last: Wahlund

address: Hansine Hansens veg 18

department: Clinical Medicine

country: Norway

institute: UiT - The Arctic university of Norway

description:
MonIHIL1B3
salmon-merged.transcript_counts.csv
cpm.csv

data_processing:
Reads were pseudomapped to the human transcriptome (GRCh38.p13) using Salmon v1.5.1. Counts were combined and imported into R data downstream data analysis.
Transcripts were summed to gene level and filtered if 5 or less counts were detected in 3 samples, or less. Patient-level batch effects were corrected using ComBat implemented in the sva package
Differential gene expression was carried out in EdgeR using interaction between hypoxic condition and stimulant, where genes with fold change above 1.5 and p-value below 0.001 were considered significant
Selected genes were grouped into gene modules of similar expression by hierarchical clustering on correlation distance and "ward.D2” linkage, which were further used for gene set analysis using enrichR
Assembly: GRCh38
Supplementary files format and content: Metadata for each sample is supplied in an xlsx file
Supplementary files format and content: CPMs and merged transcripts are supplied in separate .csv files

source_name: Peripheral venous blood

growth_protocol: PBMCs were isolated from perihperal venous blood using Fiqoll, then primary monocytes were isolated using negative selection based on magentic isolation and kept in RPMI + 5% FBS without antibiotics

extract_protocol:
Total RNA was  isolated using a miRNeasy kit according to manufacturer’s protocol
Libraries of cDNA were prepared by TruSeq RNA library kit (Illumina)

treatment_protocol: After 20 minutes of settling in gas-permeable cell culturing plates, the monocytes were stimulated 4.5 hours in normoxia (17% O2), sustained hypoxia (1% O2) or intermittent hypoxia (1-17% O2)

value: Peripheral venous blood

value: Monocytes

value: Intermittent hypoxia IL1b


title: Intermittent hypoxia IL1b pool 2

description:
MonIHIL1B2
salmon-merged.transcript_counts.csv
cpm.csv


title: WT_THP-1 cells M1_2


title: D4 hEEs, Sox2 positive fraction, Replicate 2

description: WGBS


title: WT_THP-1 cells M1_3


title: WT_THP-1 cells M0_4


title: Intermittent hypoxia IL1b pool 1

description:
MonIHIL1B1
salmon-merged.transcript_counts.csv
cpm.csv


title: WT_THP-1 cells M0_2


title: CES1KD_THP-1 cells M1_1


title: Sustained hypoxia CTRL pool 3

description:
MonHypCTR3
salmon-merged.transcript_counts.csv
cpm.csv

value: Sustained hypoxia CTRL


title: Intermittent hypoxia CTRL pool 2

description:
MonIHCTR2
salmon-merged.transcript_counts.csv
cpm.csv

value: Intermittent hypoxia CTRL


title: Sustained hypoxia IL1b pool 3

description:
MonHypIL1B3
salmon-merged.transcript_counts.csv
cpm.csv

value: Sustained hypoxia IL1b


title: Intermittent hypoxia CTRL pool 1

description:
MonIHCTR1
salmon-merged.transcript_counts.csv
cpm.csv


title: Sustained hypoxia CTRL pool 1

description:
MonHypCTR1
salmon-merged.transcript_counts.csv
cpm.csv


title: Intermittent hypoxia CTRL pool 3

description:
MonIHCTR3
salmon-merged.transcript_counts.csv
cpm.csv


title: WT_THP-1 cells M1_1


title: Sustained hypoxia IL1b pool 1

description:
MonHypIL1B1
salmon-merged.transcript_counts.csv
cpm.csv


title: Sustained hypoxia IL1b pool 2

description:
MonHypIL1B2
salmon-merged.transcript_counts.csv
cpm.csv


title: Sustained hypoxia CTRL pool 2

description:
MonHypCTR2
salmon-merged.transcript_counts.csv
cpm.csv


title: Normoxia CTRL pool 1

description:
MonNormCTR1
salmon-merged.transcript_counts.csv
cpm.csv

value: Normoxia CTRL


title: Normoxia IL1b pool 2

description:
MonNormIL1B2
salmon-merged.transcript_counts.csv
cpm.csv

value: Normoxia IL1b


title: Normoxia CTRL pool 2

description:
MonNormCTR2
salmon-merged.transcript_counts.csv
cpm.csv


title: Normoxia CTRL pool 3

description:
MonNormCTR3
salmon-merged.transcript_counts.csv
cpm.csv


title: Normoxia IL1b pool 1

description:
MonNormIL1B1
salmon-merged.transcript_counts.csv
cpm.csv


title: Normoxia IL1b pool 3

description:
MonNormIL1B3
salmon-merged.transcript_counts.csv
cpm.csv


title: RRBS data from noncancer WBC [WBC-RRBS-519]

city: Los Angeles

first: Shuo

last: Li

address: 630 Charles E Young Dr S

institute: UCLA

data_processing:
We removed the UMI sequence and trimmed the raw sequencing reads. Our custom adapters contain an 8 bp random UMI and a 5 bp fixed sequence at the beginnings of both forward and reverse reads. These sequences are removed before adapter trimming (and written into the read name). Then Trimgalore [4] was used to trim the default Illumina adapters from the sequencing reads (using the options --three_prime_clip_R1 15 --three_prime_clip_R2 13 --clip_R2 2 --length 15 --phred33). Then, we performed sequence alignment, deduplication, and methylation calling. We first used Bismark [5] to align the trimmed reads to the reference genome hg19 [6] (GRCh37 (GCA 000001405.1)). Then Umi-Grinder [7] was used to remove PCR duplicates based on the UMI labels (now in the read names), allowing 4 mismatches in the total 16 bp UMI. Bismark methylation extractor was then used to call methylation in the mapped, deduplicated reads. The methylation levels were then reformated in the bed format (.bed.gz files). We utilized wgbstools to extract fragment-level methylation information from the deduplicated reads. The fragment-level methylation information was stored in pat format (.pat.gz and .pat.gz.csi files).
Assembly: hg19
Supplementary files format and content: The .bed.gz files contained the methylation levels of all CpGs covered in the RRBS data.
Supplementary files format and content: The .pat.gz and .pat.gz.csi files contained the fragment-level methylation information of all fragments in the RRBS data.

source_name: WBC

extract_protocol:
DNA was isolated from tissue using the Qiagen Gentra Puregene method  (QIAGEN) following the manufacturers specifications.
The RRBS libraries of the genomic DNA from the 521 tissue samples were constructed following the standard RRBS protocol. 100-200 ng of intact genomic DNA in the volume of 21.5 ul was used as input material. Restriction digestion was done with 2.5 ul 10xCutSmart buffer and 1 ul MspI (NEB) for 18 h at 37 oC and 20 min at 65 oC. 0.5 ul 10xCutSmart buffer, 0.3 ul dACGTP mixture (100 mM dATP, 10 mM dCTP, 10 mM dGTP), 1 ul Klenow (exo-, 5U/ul, NEB) and 2.6 ul RT-PCR water, 0.6 ul 50 mM DTT (ThermoFisher) was added to the mixture for end repair and A-overhang addition with the program 30 oC for 20 min, 37 oC for 1 h and 75 oC for 20 min. Adapter ligation was then performed with 1 ul 10xThermoFisher HC T4 ligase buffer, 0.4 ul 100 mM ATP (ThermoFisher), 0.2 ul 50 mM DTT, 1 ul ThermoFisher HC T4 DNA ligase (30 Weiss Unit/ul), 30 ng home-made duplex UMI adapter with all the cytosines methylated (protocol adopted from Kennedy et al.) at 16 oC for 20 h and 65 oC for 20 min. Bisulfite conversion of the adapter-ligated product was carried out with QIAGEN EpiTect plus DNA bisulfite kit following their protocol for two rounds of conversion. The converted product was purified with Qiagen MinElute spin column and eluted with 20 ul RT-PCR water. PCR amplification was done using the NEBNext Multiplex Oligos for Illumina (2.5 ul of universal and index primer each) and 25 ul KAPA HiFi HotStart Uracil+ ReadyMix (Roche) with the following cycling conditions: 98 oC for 45 s, 9 cycles of 98 oC for 15 s, 60 oC for 30 s and 72 oC for 30 s, followed by a final extension at 72 oC for 5 min. The PCR product was purified with 1x AmpureXP beads and eluted with 30 ul EB buffer. DNA concentration was measured by Qubit 1xdsDNA HS assay. 5% TBE-UREA PAGE and bioanalyzer assay was performed as quality control on each library before sequencing.

value: WBC


title: RRBS data from noncancer WBC [WBC-RRBS-518]


title: RRBS data from noncancer WBC [WBC-RRBS-521]


title: RRBS data from noncancer WBC [WBC-RRBS-517]


title: RRBS data from noncancer WBC [WBC-RRBS-513]


title: RRBS data from noncancer WBC [WBC-RRBS-511]


title: RRBS data from noncancer WBC [WBC-RRBS-514]


title: RRBS data from noncancer WBC [WBC-RRBS-512]


title: RRBS data from noncancer WBC [WBC-RRBS-510]


title: RRBS data from noncancer WBC [WBC-RRBS-520]


title: RRBS data from noncancer WBC [WBC-RRBS-508]


title: RRBS data from noncancer WBC [WBC-RRBS-515]


title: RRBS data from noncancer WBC [WBC-RRBS-516]


title: RRBS data from noncancer WBC [WBC-RRBS-509]


title: RRBS data from noncancer WBC [WBC-RRBS-507]


title: RRBS data from noncancer WBC [WBC-RRBS-500]


title: RRBS data from noncancer WBC [WBC-RRBS-501]


title: RRBS data from noncancer WBC [WBC-RRBS-497]


title: RRBS data from noncancer WBC [WBC-RRBS-503]


title: RNA_558_rescue_exp_r2_tech1

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

institute: Novo Nordisk Foundation Center for Protein Research

data_processing:
Sequences were trimmed for adapters and adapting filtering for low quality reads was performed with trimmomatic (version 0.39) with default parameters. Mapping (mm10) was performed with STAR (version 2.7.1a) using GENCODE (version M23) annotations with parameters --twopassMode Basic --twopass1readsN -1 --alignSJDBoverhangMin 10 and multimapping parameters -winAnchorMultimapNmax 200 --outFilterMultimapNmax 100 for further repeats quantification
Gene level and repeat quantification at the subfamily level was obtained from processed bam files using the TEcount (version 2.1.3) program from the TEtoolkit suite, using the provided curated repeat annotations for mm10 (http://labshare.cshl.edu/shares/mhammelllab/www-data/TEtranscripts/TE_GTF/).
Assembly: mm10
Supplementary files format and content: RNAseq_MCM2_rescue_gene_and_repeat_counts.txt.gz is a tab separated text file with raw counts for genes (ENSEMBL ids) and repeats (Tecounts mm10 repeat ids)

growth_protocol: ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 degrees with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA.

extract_protocol:
RNA was extracted from 5*10^6 cells using RNeasy Plus Mini Kit (Qiagen) and DNA was eliminated by treatment with the RNase-Free DNase Set (Qiagen). RNA was treated with the NEBNext rRNA Depletion kit (NEB #E7405L) and strand-specific RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep with Beads (NEB #E7765S)
NEBNext Ultra II Directional RNA Library Prep with Beads (NEB #E7765S) following the manufacturers protocol.

value: Embryonic stem cells

value: wildtype


title: RRBS data from noncancer WBC [WBC-RRBS-505]


title: RRBS data from noncancer WBC [WBC-RRBS-499]


title: RRBS data from noncancer WBC [WBC-RRBS-504]


title: RRBS data from noncancer WBC [WBC-RRBS-498]


title: RRBS data from noncancer WBC [WBC-RRBS-502]


title: RRBS data from noncancer WBC [WBC-RRBS-506]


title: RNA_558_rescue_exp_r4_tech1

description: RNAseq_MCM2_rescue_gene_and_repeat_counts.txt.gz


title: RNA_558_rescue_exp_r3_tech1


title: RRBS data from noncancer WBC [WBC-RRBS-496]


title: RRBS data from noncancer WBC [WBC-RRBS-495]


title: RNA_558_rescue_exp_r1_tech1


title: RNA_442_rescue_exp_r4_tech2


title: RRBS data from noncancer WBC [WBC-RRBS-494]


title: RNA_442_rescue_exp_r4_tech1


title: RNA_442_rescue_exp_r3_tech2


title: RRBS data from noncancer WBC [WBC-RRBS-493]


title: RRBS data from noncancer WBC [WBC-RRBS-492]


title: RRBS data from noncancer WBC [WBC-RRBS-491]


title: RNA_410_rescue_exp_r4_tech2


title: RNA_442_rescue_exp_r2_tech1


title: RNA_442_rescue_exp_r1_tech1


title: RRBS data from noncancer WBC [WBC-RRBS-490]


title: RNA_410_rescue_exp_r3_tech2


title: RRBS data from noncancer WBC [WBC-RRBS-489]


title: RRBS data from noncancer WBC [WBC-RRBS-487]


title: RRBS data from noncancer WBC [WBC-RRBS-488]


title: RRBS data from noncancer WBC [WBC-RRBS-484]


title: RNA_410_rescue_exp_r2_tech1


title: RRBS data from noncancer WBC [WBC-RRBS-482]


title: RRBS data from noncancer WBC [WBC-RRBS-486]


title: ChIP_442_K4me3_input_rescue_exp_r3

data_processing:
Files were processed using the ENCODE ChIP-seq pipeline version 1.3.6: adapters and low quality reads were filtered with cutadapt version 2.5 and mapped to the genome with bwa version 0.7.15
duplicate reads were removed with picard (version 2.20.7) and bam files converted to tagAlign files
Narrow (H3K4me3, H3K27ac and SUZ12) peaks were called with MACS (version 2.1.0) with parameters –nomodel -p 0.05 and either the "optimal overlap" (H3K4me3, H3K27ac) set or the "IDR optimal" (SUZ12) from the encode pipleine was used. Broad peaks (H3K27me3 and H3K9me3) were called using danpos2 regions with default parameters, to obtain a reproducible set of peaks for each clone, peaks were called on pooled replicates and only peaks overlapped by at least 50% bps of peaks in at least 2 out of 3 replicates were kept.
Assembly: mm10
Supplementary files format and content: Bed files of ChIP-seq reproducible peak sets called with macs2 for narrow peaks (H3K4me3, H3K27ac, SUZ12) or danpos2 regions for broad peaks (H3K27me3, H3K9me3)

growth_protocol: ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 °C with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA or TrypLE.

extract_protocol:
Native ChIP: Cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase. Native Drosophila chromatin was spiked in and mononucleosomal fragments were immunoprecipitated, followed by library preparation and sequencing. Crosslinked ChIP: Cells were crosslinked with formaldehyde for 10 min and collected by scraping. Nuclei were isolated and chromatin was solubilized using a Covaris sonicator. Crosslinked Drosophila chromatin was spiked in.
Libraries were prepared using standard Illumina protocols (KAPA Hyper Prep kit).

treatment_protocol: Samples were untreated.

tag: antibody


title: RNA_410_rescue_exp_r1_tech1

tag: cell type


title: RRBS data from noncancer WBC [WBC-RRBS-485]


title: RRBS data from noncancer WBC [WBC-RRBS-481]


title: ChIP_588_K4me3_input_rescue_exp_r2


title: ChIP_410_K4me3_input_rescue_exp_r2


title: ChIP_442_K4me3_input_rescue_exp_r2


title: RRBS data from noncancer WBC [WBC-RRBS-483]


title: ChIP_588_K4me3_input_rescue_exp_r1


title: ChIP_410_K4me3_input_rescue_exp_r3


title: ChIP_442_K4me3_input_rescue_exp_r1


title: RRBS data from noncancer WBC [WBC-RRBS-478]


title: RRBS data from noncancer WBC [WBC-RRBS-480]


title: RRBS data from noncancer WBC [WBC-RRBS-477]


title: ChIP_410_K4me3_input_rescue_exp_r1


title: ChIP_588_H3K4me3_rescue_exp_r3


title: ChIP_442_H3K4me3_rescue_exp_r3


title: ChIP_410_H3K4me3_rescue_exp_r3

description: 410_H3K4me3_ChIP_pr_R1.rescue.reproducible_peaks.narrowPeak.bed.gz


title: RRBS data from noncancer WBC [WBC-RRBS-475]


title: RNA_410_rescue_exp_r3_tech1


title: RRBS data from noncancer WBC [WBC-RRBS-474]


title: ChIP_588_K4me3_input_rescue_exp_r3


title: RRBS data from noncancer WBC [WBC-RRBS-473]


title: ChIP_588_H3K4me3_rescue_exp_r2


title: RRBS data from noncancer WBC [WBC-RRBS-472]


title: RRBS data from noncancer WBC [WBC-RRBS-470]


title: RRBS data from noncancer WBC [WBC-RRBS-471]


title: ChIP_588_H3K4me3_rescue_exp_r1


title: RRBS data from noncancer WBC [WBC-RRBS-469]


title: ChIP_442_H3K4me3_rescue_exp_r1


title: RRBS data from noncancer WBC [WBC-RRBS-468]


title: ChIP_410_H3K4me3_rescue_exp_r1


title: ChIP_442_H3K4me3_rescue_exp_r2


title: RRBS data from noncancer WBC [WBC-RRBS-467]


title: RRBS data from noncancer WBC [WBC-RRBS-476]


title: RRBS data from noncancer WBC [WBC-RRBS-466]


title: ChIP_442_K9me3_input_rescue_exp_r3


title: ChIP_588_K9me3_input_rescue_exp_r3


title: ChIP_410_H3K4me3_rescue_exp_r2


title: RRBS data from noncancer WBC [WBC-RRBS-465]


title: ChIP_410_K9me3_input_rescue_exp_r3


title: RRBS data from noncancer WBC [WBC-RRBS-479]


title: ChIP_588_K9me3_input_rescue_exp_r2


title: RRBS data from noncancer esophagus tissue [GTEX-ZYT6-1226-SM-L36SN]

source_name: esophagus

value: esophagus


title: ChIP_442_K9me3_input_rescue_exp_r2


title: ChIP_410_K9me3_input_rescue_exp_r2


title: RRBS data from noncancer vagina tissue [GTEX-ZXES-0626-SM-L36RK]

source_name: vagina

value: vagina


title: ChIP_588_K9me3_input_rescue_exp_r1


title: RRBS data from noncancer testis tissue [GTEX-ZVTK-0126-SM-L36S1]

source_name: testis

value: testis


title: RRBS data from noncancer thyroid tissue [GTEX-ZYT6-0426-SM-L36QZ]

source_name: thyroid

value: thyroid


title: ChIP_442_K9me3_input_rescue_exp_r1


title: RRBS data from noncancer prostate tissue [GTEX-ZUA1-2826-SM-L36RW]

source_name: prostate

value: prostate


title: ChIP_410_K9me3_input_rescue_exp_r1


title: RRBS data from noncancer ovary tissue [GTEX-YFC4-2726-SM-L36R3]

source_name: ovary

value: ovary


title: ChIP_588_H3K9me3_rescue_exp_r3


title: RRBS data from noncancer esophagus tissue [GTEX-YFC4-1226-SM-L36TZ]


title: RRBS data from noncancer thyroid tissue [GTEX-Y111-1926-SM-L36SA]


title: ChIP_410_H3K9me3_rescue_exp_r3

description: 410_H3K9me3_ChIP_pr_R1.rescue.reproducible_peaks.broadPeak.bed.gz


title: RRBS data from noncancer esophagus tissue [GTEX-Y111-1626-SM-L36S2]


title: RRBS data from noncancer testis tissue [GTEX-XQ3S-2726-SM-L36S5]


title: ChIP_588_H3K9me3_rescue_exp_r2


title: RRBS data from noncancer esophagus tissue [GTEX-XQ3S-1026-SM-L36TN]


title: ChIP_442_H3K9me3_rescue_exp_r2


title: ChIP_442_H3K9me3_rescue_exp_r1


title: RRBS data from noncancer esophagus tissue [GTEX-WHSE-1426-SM-L36SQ]


title: RRBS data from noncancer pancreas tissue [GTEX-U8XE-2026-SM-L36R2]

source_name: pancreas

value: pancreas


title: ChIP_410_H3K9me3_rescue_exp_r1


title: RRBS data from noncancer skin tissue [GTEX-U8XE-0226-SM-L36SO]

source_name: skin

value: skin


title: ChIP_588_K27me3_input_rescue_exp_r3


title: RRBS data from noncancer blood vessel tissue [GTEX-XPT6-0426-SM-L36SV]

source_name: blood vessel

value: blood vessel


title: ChIP_442_K27me3_input_rescue_exp_r3


title: ChIP_588_K27me3_input_rescue_exp_r2


title: ChIP_410_K27me3_input_rescue_exp_r3


title: ChIP_410_H3K9me3_rescue_exp_r2


title: RRBS data from noncancer cervix uteri tissue [GTEX-U3ZN-1626-SM-L36TV]

source_name: cervix uteri

value: cervix uteri


title: RRBS data from noncancer cervix uteri tissue [GTEX-TSE9-2826-SM-L36SR]


title: RRBS data from noncancer uterus tissue [GTEX-TMMY-2226-SM-L36RG]

source_name: uterus

value: uterus


title: RRBS data from noncancer cervix uteri tissue [GTEX-T6MO-1426-SM-L36SD]


title: RRBS data from noncancer fallopian tube tissue [GTEX-T5JW-0326-SM-L36RS]

source_name: fallopian tube

value: fallopian tube


title: ChIP_442_K27me3_input_rescue_exp_r2


title: ChIP_442_H3K9me3_rescue_exp_r3


title: RRBS data from noncancer pancreas tissue [GTEX-S33H-1226-SM-L36S8]


title: ChIP_410_K27me3_input_rescue_exp_r2


title: ChIP_588_H3K9me3_rescue_exp_r1


title: ChIP_588_K27me3_input_rescue_exp_r1


title: RRBS data from noncancer prostate tissue [GTEX-RWSA-2026-SM-L36ST]


title: ChIP_442_K27me3_input_rescue_exp_r1


title: RRBS data from noncancer bladder tissue [GTEX-S32W-1126-SM-L36TD]

source_name: bladder

value: bladder


title: ChIP_410_K27me3_input_rescue_exp_r1


title: RRBS data from noncancer salivary gland tissue [GTEX-1AMEY-1126-SM-L36RJ]

source_name: salivary gland

value: salivary gland


title: RRBS data from noncancer adipose tissue [GTEX-183FY-0326-SM-L36T7]

source_name: adipose tissue

value: adipose tissue


title: RRBS data from noncancer spleen tissue [GTEX-17F96-1426-SM-L36RY]

source_name: spleen

value: spleen