title: LDB1_AID_auxin_TT-seq_rep3

city: Philadelphia

first: Siqing

state: PENNSYLVANIA

address: 3401 Civic Center Blvd

department: Department of Pediatrics, Division of Hematology

institute: Children’s Hospital of Philadelphia

description:
Nascent RNA
4_LDB1

library_source: other

data_processing:
Fastq files were generated with Bclfastq2 v2.15.04
The paired-end TT-seq reads were trimmed using Trim Galore v0.6.10 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) were aligned to the mouse mm9 and Drosophila dm6 assemblies and sorted using STAR v2.7.10b4.
Index and skip alignments with MAPQ smaller than 7 in the resulting genome alignment BAM files using SAMtools v1.145.
The TT-seq signal and bigwig files normalized by spike-in reads was generated by deepTools v3.5.26.
Assembly: mm9
Supplementary files format and content: bw: strand-specific bigwig tracks of TT-seq signals (fwd: forward strand. rev: reverse strand).
Library strategy: TT-seq

molecule: other

source_name: cell line

extract_protocol:
Exponentially growing cells in T-150 flasks were labeled with 500 μM 4-thiouridine (4SU) (MedChemExpress), for 5 minutes. The cells were processed with 2 mL TRIzol Reagent (Invitrogen) for every 10 million G1E-ER4 cells and total RNAs was extracted following the user manual. 500 ng of 4SU-labeled Drosophila Schneider 2 (S2) cells total RNA as spike in was mixed with 100 μg of collected 4SU-labeled G1E-ER4 total RNA. Mixed RNA was fragmentated using a final concentration of 0.2 M NaOH for 18 minutes and neutralized with a final concentration of 0.5 M Tris-HCl (pH 6.8). RNA was purified by isopropanol precipitation. Labelled RNA was biotinylated in 300 μL of biotinylation mix (fragmented total RNA, 10 mM HEPES pH 7.5, 1 mM EDTA, 0.167 mg/mL MTSEA-biotin (Biotium)) for 1 hour at room temperature and purified with phenol/chloroform/isoamyl alcohol (25:24:1 (vol/vol/vol)) extraction. Denature the biotinylated RNA from at 65 °C for 10 minutes, followed by rapid cooling on ice for 5 minutes. The denatured biotinylated RNA was bound with Dynabeads MyOne Streptavidin C1 (Invitrogen) at room temperature for 30 minutes, eluted with 100 mM DTT and subsequently purified by isopropanol precipitation. Quality of total RNA extraction, RNA fragmentation (we aimed for an RNA size distribution between 25 and 500 nt), and purified 4SU-labeled RNA were determined using Agilent TapeStation RNA ScreenTape (Agilent).
Strand-specific sequencing libraries were generated with the Illumina Stranded Total RNA Prep (Illumina) and IDT for Illumina RNA UD Indexes Set A, Ligation (Illumina). Library size was determined using Agilent TapeStation High Sensitivity DNA ScreenTape (Agilent).

value: cell line

value: Erythroblast

value: LDB1-AID subline

value: 4 hour auxin


title: EMT6-Base-3

status: Public on Jan 22 2025

type: SRA

city: Tsukuba

first: Megumi

last: Kuronishi

state: Ibaraki

address: Tokodai 5-1-3

country: Japan

institute: Eisai Co., Ltd.

library_source: transcriptomic

data_processing:
Illumina bcl2fastq was used to de-multiplex and convert reads to FASTQ.
Sequencing data were processed by using Trimmomatic (version 0.36) to remove all Illumina adaptor sequences and bases with low quality scores.
Filtered reads were mapped to the mouse genome (Mm10 and Ensembl 88) by using STAR software (version 2.5.2b) .
Gene expression levels, in transcripts per million, were estimated for all samples by using RSEM software (version 1.2.31).
Assembly: GRCm38
Supplementary files format and content: TSV file containing TPM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: tumor tissue

extract_protocol:
RNA was purified using Maxwell RSC simplyRNA Tissue Kit (Promega) following manufacturer’s instructions.
RNA libraries were prepared for sequencing with rRNA depletion and sequenced at GeneWiz.

treatment_protocol: Tumors were collected Day8 after treatment with lenvatinib at 10 mg/kg.

tag: tissue

value: tumor tissue

tag: cell line

tag: strain

value: BALB/cAnNCrlCrlj

tag: treatment

value: NT

tag: time

value: Baseline


title: LDB1_AID_auxin_TT-seq_rep2

last: Wang

country: USA

description:
Nascent RNA
4_LDB1

tag: cell type

tag: genotype


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 2522

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

description:
cell-free DNA 5hmC
PLCO-439

library_source: genomic

data_processing:
Adapter sequences were removed from raw sequencing reads using Trimmomatic
Low quality bases at the 5’ and 3’ were trimmed based on phred score to a minimum length of 30 bp
The sequencing reads were then aligned to the human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode
Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length
Alignments with Mapping Quality Score ≥ 10 were counted based on the GENCODE gene body annotations using featureCounts without strand information
The raw read counts were then normalized using DESeq2, which performs an internal normalization that corrects for library size.
Assembly: hg19
Supplementary files format and content: Text file with normalized reads counts for all samples.
Library strategy: 5hmC-Seal sequencing

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral plasma

growth_protocol: Not applicable

extract_protocol:
Cell-free DNA was extracted using the QIAmp Circulating cfDNA Extraction Kit (Qiagen)
3-8 ng cfDNA was used in the 5hmC-Seal assay (see Li W, Zhang X, Lu X, You L, Song Y, Luo Z, et al. 5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers. Cell Res 2017;27:1243-57). Libraries were constructed on-bead using the KAPA HyperPlus kit (Roche).

treatment_protocol: Not applicable

value: peripheral plasma

tag: dna source

value: cell-free DNA


title: LDB1_AID_auxin_TT-seq_rep1

description:
Nascent RNA
4_LDB1


title: hepatopancreas, Crane-top red goldfish, Repeat 3

city: YangZhou

first: Jianqiao

address: 48 Wenhui East Road

country: China

institute: Yangzhou University

data_processing:
Index of the reference genome was built using STAR and paired-endclean reads were aligned to the reference genome using STAR (v 2.5.1b)
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.
Differential expression analysis of twoconditions/groups (two biological replicates per condition) was performed using theDESeq2 R package (1.10.1).
Geneswith an adjusted P-value <0.05 found by DESeq2 were assigned as differentiallyexpressed.
Assembly: GCF_003368295.1
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Carassius auratus

source_name: hepatopancreas

extract_protocol:
Total RNA was extracted from the hepatopancreas of goldfish using TRIzol reagent. 3 μg of total RNA was used for construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’srecommendations.

value: hepatopancreas

tag: breed

value: Crane-top red goldfish (HDH)


title: LDB1_AID_untreated_TT-seq_rep3

description:
Nascent RNA
3_LDB1

value: Untreated


title: EMT6-Base-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 9750

description:
cell-free DNA 5hmC
PLCO-438


title: LDB1_AID_untreated_TT-seq_rep1

description:
Nascent RNA
3_LDB1


title: EMT6-Base-1


title: CT26-Base-3


title: LDB1_AID_untreated_TT-seq_rep2

description:
Nascent RNA
3_LDB1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UQ 6067

description:
cell-free DNA 5hmC
PLCO-437


title: s22_MIN3

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Illumina and Nextera adapter contaminations were removed from reads using Cutadapt.
Processed reads were mapped against MM10 whole genome using bowtie2.
Alignments were filtered with samtools to retain only properly mapped, non duplicate reads, with mapping quality above 0, not aligning to unlocalized or unassembled contigs, the mitochondrial genome, or chromosome Y.
Peaks were called with MACS3, using parameters "--nomodel --shift -100 --extsize 200", and "-q 0.05" as the false discovery rate cut-off.
Assembly: mm10
Supplementary files format and content: ENCODE narrow peak files (extended bed format) including coordinates, score and qvalue for ATAC-seq peaks, using MACS3.

source_name: Bone marrow

growth_protocol: 6-8-week-old male wild-type or Clec4e-/- mice were treated (DSS) or not (CTR) in drinking water with dextran sulfate sodium (DSS) 36–55 KDa 3% w/v for 5 days, after a 5-day rest the mice were sacrificed. Morevover isolated E.faecalis from bone marrow was heak killed (80ºC-15min) and 200 FCU were used to injected C57BL/6 mice.

extract_protocol:
Flow sorted mouse GMPs were collected in ice-cold Flow cytometry buffer and 30.000-50.000 cells were obtained pooling two biological replicates for every condition. Samples were immediately processed following previously published protocol (Buenrostro et al, 2013). The transposition reaction was started by adding Nextera’s Tn5 Transposase in reaction buffer and maintained by incubation for 30minutes at 37°C. DNA was purified using a Quiagen MinElute PCR purification kit.
ATAC-seq libraries were purified using a PCR purification MinElute kit (Quiagen) and quantified using a 2100 Bioanalyzer instrument (Agilent). Finally, libraries were sequenced 2x50 in a paired end flowcell (PE) run on Illuminaa NextSeq 2000 System.

treatment_protocol: Bone marrow cells were incubated in cold flow cytometry buffer with a panel of antibodies against lineage committed cells (CD3, CD45R, CD11b, Ter-119, Gr-1) all biotinylated and from BD Pharmigen. After washing, cells were incubated with streptavidin magnetic beads (Miltenyi) and passed through LS columns (Miltenyi) . Thus, collected cells were stained with Sca-1, c-kit (CD117), CD48, CD150 antibodies and with the viability marker Hoechst 33258 prior to be sorted by FACS Aria II. GMP were indenfied Lin-c-kit+ sca-11- CD48+ CD150- cells

value: Bone marrow

value: Progenitors cells

value: GMP

value: Control


title: Renca-Base-3

value: Renca


title: s21_MIN2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 0636

description:
cell-free DNA 5hmC
PLCO-436


title: s20_MIN1


title: CT26-Base-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID KF 5214

description:
cell-free DNA 5hmC
PLCO-435


title: s18_MO2

value: DSS 3%


title: CT26-Base-1


title: s17_MO1


title: S.pombe, RNA-IP of Nrl1-MTP_Prp43-6xFlag, replicate2

city: Melbourne

first: Attila

last: Horvath

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: RNA-IP Nrl1-MTP_Prp43-6xFlag Rep2
total RNA isolated from the RNA-IP

data_processing:
sequence reads were filtered for low quality reads with PRINSEQ++ 1.2 (-min-len 36, -trim_qual_left 15, trim_qual_right 15) and trimmed with Trimmomatic-0.39 for adapter sequences
Paired-end RNA-seq reads were aligned to the S. pombe reference genome (ASM294v2) using HISAT2.2.1 allowing a maximum intron length of 2,000 bps
Alignment files were sorted and indexed using SAMtools1.21101. Un-normalized bigwig files were generated with bamCoverage from deepTools3.5.5102 with 1 bp resolution.
To avoid any bias from rRNAs transcribed on chromosome III, raw signals were normalized by the coverage of chromosome I (CovNChrI4E8 bw files) with in-house scripts
For Extended Fig 7j we normlised bigwigfiles for the geometric mean of median exon coverage of all annotated ORFs in S. pombe with in-house scripts (MedGmean50 bw files)
Assembly: Schizosaccharomyces pombe (fission yeast) genome assembly ASM294v2
Supplementary files format and content: xxx.CovNChrI4e8.f.bw and xxx.CovNChrI4e8.r.bw files are Chromosome I coverage normlaised bigwig files with forward(f) or reverse(r) signal
Supplementary files format and content: xxx.MedGmean50.f.bw and xxx.MedGmean50.r.bw files are bigwig files normliased for the geometric mean of median exon coverage of all annotated ORFs in S. pombe with forward (f) or reverse (r) signal

organism: Schizosaccharomyces pombe

source_name: yeast cells

growth_protocol: cultured at 30C in YAE medium

extract_protocol:
RNP complex was harvested from ~10-12 L YEA cultures of the yeast strain grown to OD600 of 1.8-2.2. Cell pellets were snap-frozen in liquid nitrogen and subsequently mechanically lysed by a cryogenic cell mill (Retsch MM400). The cell lysate was resuspended in lysis buffer containing 20 mM HEPES pH 7.5, 100 mM NaCl, 1.5 mM MgCl2 supplemented with 0.05 % NP-40 (Sigma-Aldrich), 1 mM DTT, 1 mM phenylmethylsulfonyl fluoride, protease inhibitor cocktail (EDTA-free, Roche) and RiboLock RNase inhibitor (Thermo Fischer Scientific). The cell lysate was cleared by centrifugation and the supernatant was loaded onto IgG Sepharose 6 Fast Flow beads (Cytiva) for overnight (ON) incubation at 4 °C. Non-specifically bound proteins were removed by washing with lysis buffer supplemented with 0.01 % NP-40, followed by TEV cleavage for 5 h at 4 °C. For the second affinity purification, the eluate from IgG beads was loaded onto Flag beads (Anti-Flag M2 Affinity Gel, Sigma-Aldrich) for ON incubation at 4 °C. The beads were washed and eluted with buffer containing 3X Flag peptide at a final concentration of 0.4 mg/mL. RNA was isolated from the Flag-eluate, using RNA Clean and Concentrator Kit (Zymo Research), treated with 20 U Turbo DNase (Thermo Fischer) at 37C for 30 minutes. RNA Clean and Concentration Kit was used once again to remove DNase and full amount of RNA was used to prepare sequencing libraries. For total RNA sequencing, RNA was isolated by TRI reagent (ThermoFIscher AM9738) following the manufacturer's instructions), treated with 20 U Turbo DNase (Thermo Fischer) at 37C for 30 minutes and RNA Clean and Concentration Kit was used  again to remove DNase. 100ng total RNA was used to library preparation.
RNA sequencing libraries were prepared using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® (NEB) Section 4: Protocol for use with Purified mRNA or rRNA Depleted RNA, following the manufacturer’s instructions.

treatment_protocol: no treatment

value: yeast cells

value: h+ HIS leu1-32 ade6-216 ura4-D18 Nrl1-13*Myc-Tev-ProA::NatNt2 prp43-6flag::kanMX6


title: s19_MO3


title: 4T1-Base-3

value: tumor tissue


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 4003

description:
cell-free DNA 5hmC
PLCO-440


title: s16_DSS3

value: WT


title: s14_DSS1


title: 4T1-Base-2

value: BALB/cAnNCrlCrlj

value: NT


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 0494

description:
cell-free DNA 5hmC
PLCO-433

value: peripheral plasma


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IP 7731

description:
cell-free DNA 5hmC
PLCO-432

value: cell-free DNA


title: s13_CT6


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 5263

description:
cell-free DNA 5hmC
PLCO-431


title: s12_CT5


title: s11_CT4


title: s6_iv3

value: HK-EF iv


title: s5_iv2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID KD 7668

description:
cell-free DNA 5hmC
PLCO-430


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 5081

description:
cell-free DNA 5hmC
PLCO-429


title: s3_CT3

value: PBS iv


title: s2_CT2


title: s15_DSS2


title: RAG-Base-2

value: RAG

value: Baseline


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 7776

description:
cell-free DNA 5hmC
PLCO-428


title: p300_iHAT_NT_rep3_NT_A486_3

city: Munich

first: Eva

last: Hoermanseder

state: Bavaria

address: Feodor-Lynen-Str. 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Center Munich

description:
Library name: p300_iHAT_NT_rep3_NT_A486_3
2x50 bp reads

data_processing:
Paired sequencing reads were processed using Kallisto (v0.48) for pseudoalignment and quantification of transcript abundance.
Transcript and annotation files were downloaded from Xenbase (v10.1) for Xenopus laevis (transcripts and annotation).
After quantification, transcript-level abundances were imported using 'tximport' and converted to a 'SummarizedExperiment' object in R (v4.3.1).
Datasets of two independent batches were merged and subjected to differential expression analysis performed with DESeq2 (v1.40.2).
Assembly: Xenopus laevis 10.1
Supplementary files format and content: Kallisto output containing transcript abundance as transcript per million.

organism: Xenopus laevis

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, 74104) according to the manufacturer’s instructions. To lyse the embryonic tissue, samples were vortexed on high speed for 10 min at 4°C. DNase digestion was performed according to the manufacturer’s instructions, using RNase-free DNase (QIAGEN, 79254).
Per sample, 400 ng total RNA of animal cap (ectoderm) tissue and 300 ng of endoderm donor tissue were used to isolate mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).  Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760), following the manufacturer’s instructions, using 12-13 PCR amplification cycles. Libraries were multiplexed and sequenced on a NextSeq 6000 platform.

treatment_protocol: IVF-derived gastrulae (NF stage 12) were treated with 40 µM SGC-CBP30 (Sigma, SML1133), 30 µM A-485 (Tcris, #6387) or DMSO in 0.1x MMR at 23°C until they reached neurula stage (NF stage 18)59. The embryos were collected at synchronized stages to eliminate influences from different cell numbers or developmental stages. The embryos were either used as donors for nuclear transfer as described above, or frozen for RNA-extraction.Endoderm was dissected from neurula-stage embryos (NF stage 18) and allowed to dissociate into single cells in calcium- and magnesium-free 1x modified Barth saline (MBS, 88 mM NaCl, 1mM KCl, 10mM HEPES, 2.5 mM NaHCO3, pH 7.4) with 1 mM EDTA and 0.1% BSA in a Petri dish coated with 0.1% agarose in H2O. Donor cells were immediately used for NT.

value: ectoderm


title: s1_CT1

value: Bone marrow

value: Progenitors cells

value: GMP


title: RAG-Base-1


title: p300_iHAT_NT_rep3_NT_A486_1

description:
Library name: p300_iHAT_NT_rep3_NT_A486_1
2x50 bp reads


title: BNL-Base-2

value: BNL 1ME A.7R.1


title: p300_iHAT_NT_rep3_NT_A486_2

description:
Library name: p300_iHAT_NT_rep3_NT_A486_2
2x50 bp reads


title: BNL-Base-3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 7358

description:
cell-free DNA 5hmC
PLCO-426


title: p300_iHAT_NT_rep3_NT_A485_3

description:
Library name: p300_iHAT_NT_rep3_NT_A485_3
2x50 bp reads


title: p300_iHAT_NT_rep3_NT_A485_2

description:
Library name: p300_iHAT_NT_rep3_NT_A485_2
2x50 bp reads


title: 4T1-Base-1


title: p300_iHAT_NT_rep3_NT_A485_1

description:
Library name: p300_iHAT_NT_rep3_NT_A485_1
2x50 bp reads

value: endoderm


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 5249

description:
cell-free DNA 5hmC
PLCO-425


title: RAG-Base-3


title: p300_iHAT_NT_rep3_Donor_A486_2

description:
Library name: p300_iHAT_NT_rep3_Donor_A486_2
2x50 bp reads


title: p300_iHAT_NT_rep3_Donor_A486_1

description:
Library name: p300_iHAT_NT_rep3_Donor_A486_1
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 3365

description:
cell-free DNA 5hmC
PLCO-424


title: COLON-7DPI-31

city: Shanghai

first: ZIYU

last: SUN

address: HAIKE RD 100

institute: IRCBC

description: Sample 81

data_processing:
About ~50 million reads for each sample were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
Then about ~48 million clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. The processed data flles we uploaded were FPKM data.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: colon

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer. RNA integrity was assessed using the Agilent 2100 Bioanalyzer.
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer's instructions

value: colon

value: DHO

value: 7 DPI


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UY 3062

description:
cell-free DNA 5hmC
PLCO-427


title: s4_iv1

value: WT


title: p300_iHAT_NT_rep3_Donor_A485_2

description:
Library name: p300_iHAT_NT_rep3_Donor_A485_2
2x50 bp reads


title: COLON-7DPI-30

description: Sample 80


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UY 3586

description:
cell-free DNA 5hmC
PLCO-434


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID II 0456

description:
cell-free DNA 5hmC
PLCO-423


title: p300_iHAT_NT_rep3_Donor_A485_1

description:
Library name: p300_iHAT_NT_rep3_Donor_A485_1
2x50 bp reads


title: p300_iHAT_NT_rep3_IVF_4

description:
Library name: p300_iHAT_NT_rep3_IVF_4
2x50 bp reads


title: p300_iHAT_NT_rep3_IVF_3

description:
Library name: p300_iHAT_NT_rep3_IVF_3
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 3681

description:
cell-free DNA 5hmC
PLCO-422


title: COLON-7DPI-29

description: Sample 79


title: p300_iHAT_NT_rep3_IVF_1

description:
Library name: p300_iHAT_NT_rep3_IVF_1
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID II 0218

description:
cell-free DNA 5hmC
PLCO-421


title: BNL-Base-1

value: tumor tissue

value: BALB/cAnNCrlCrlj

value: NT


title: COLON-7DPI-28

description: Sample 78


title: p300_iHAT_NT_rep3_IVF_2

description:
Library name: p300_iHAT_NT_rep3_IVF_2
2x50 bp reads


title: COLON-7DPI-27

description: Sample 77


title: p300_iHAT_NT_rep2_NT_A486_4

description:
Library name: p300_iHAT_NT_rep2_NT_A486_4
2x50 bp reads


title: p300_iHAT_NT_rep2_NT_A486_3

description:
Library name: p300_iHAT_NT_rep2_NT_A486_3
2x50 bp reads


title: p300_iHAT_NT_rep2_NT_A486_5

description:
Library name: p300_iHAT_NT_rep2_NT_A486_5
2x50 bp reads


title: COLON-7DPI-26

description: Sample 76


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IH 4853

description:
cell-free DNA 5hmC
PLCO-420

value: peripheral plasma

value: cell-free DNA


title: p300_iHAT_NT_rep2_NT_A486_2

description:
Library name: p300_iHAT_NT_rep2_NT_A486_2
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 1228

description:
cell-free DNA 5hmC
PLCO-419


title: COLON-7DPI-25

description: Sample 75


title: p300_iHAT_NT_rep2_NT_A485_5

description:
Library name: p300_iHAT_NT_rep2_NT_A485_5
2x50 bp reads


title: p300_iHAT_NT_rep2_NT_A485_4

description:
Library name: p300_iHAT_NT_rep2_NT_A485_4
2x50 bp reads


title: COLON-7DPI-24

description: Sample 74


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 8021

description:
cell-free DNA 5hmC
PLCO-418


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IL 4919

description:
cell-free DNA 5hmC
PLCO-417


title: p300_iHAT_NT_rep2_NT_A485_2

description:
Library name: p300_iHAT_NT_rep2_NT_A485_2
2x50 bp reads


title: COLON-7DPI-23

description: Sample 73


title: p300_iHAT_NT_rep2_NT_A485_3

description:
Library name: p300_iHAT_NT_rep2_NT_A485_3
2x50 bp reads


title: p300_iHAT_NT_rep2_NT_A485_1

description:
Library name: p300_iHAT_NT_rep2_NT_A485_1
2x50 bp reads


title: p300_iHAT_NT_rep2_Donor_A486_2

description:
Library name: p300_iHAT_NT_rep2_Donor_A486_2
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IY 7321

description:
cell-free DNA 5hmC
PLCO-416


title: p300_iHAT_NT_rep2_Donor_A486_1

description:
Library name: p300_iHAT_NT_rep2_Donor_A486_1
2x50 bp reads


title: COLON-7DPI-22

description: Sample 72


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IL 4874

description:
cell-free DNA 5hmC
PLCO-415


title: COLON-7DPI-21

description: Sample 71

value: HO


title: p300_iHAT_NT_rep2_Donor_A485_1

description:
Library name: p300_iHAT_NT_rep2_Donor_A485_1
2x50 bp reads


title: p300_iHAT_NT_rep2_Donor_A485_2

description:
Library name: p300_iHAT_NT_rep2_Donor_A485_2
2x50 bp reads


title: p300_iHAT_NT_rep2_IVF_4

description:
Library name: p300_iHAT_NT_rep2_IVF_4
2x50 bp reads


title: COLON-7DPI-20

description: Sample 70


title: p300_iHAT_NT_rep2_IVF_3

description:
Library name: p300_iHAT_NT_rep2_IVF_3
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 5700

description:
cell-free DNA 5hmC
PLCO-414


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 5447

description:
cell-free DNA 5hmC
PLCO-413


title: p300_iHAT_NT_rep2_IVF_2

description:
Library name: p300_iHAT_NT_rep2_IVF_2
2x50 bp reads


title: COLON-7DPI-19

description: Sample 69


title: p300_iHAT_NT_rep2_IVF_1

description:
Library name: p300_iHAT_NT_rep2_IVF_1
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UJ 8022

description:
cell-free DNA 5hmC
PLCO-412


title: p300_iHAT_NT_rep2_NT_A486_1

description:
Library name: p300_iHAT_NT_rep2_NT_A486_1
2x50 bp reads


title: COLON-7DPI-18

description: Sample 68


title: p300_iHAT_NT_rep1_NT_A486_4

description:
Library name: p300_iHAT_NT_rep1_NT_A486_4
2x50 bp reads


title: p300_iHAT_NT_rep1_NT_A486_5

description:
Library name: p300_iHAT_NT_rep1_NT_A486_5
2x50 bp reads


title: p300_iHAT_NT_rep1_NT_A486_3

description:
Library name: p300_iHAT_NT_rep1_NT_A486_3
2x50 bp reads


title: COLON-7DPI-17

description: Sample 67


title: p300_iHAT_NT_rep1_NT_A486_1

description:
Library name: p300_iHAT_NT_rep1_NT_A486_1
2x50 bp reads


title: p300_iHAT_NT_rep1_NT_A486_2

description:
Library name: p300_iHAT_NT_rep1_NT_A486_2
2x50 bp reads


title: COLON-7DPI-16

description: Sample 66


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UU 7540

description:
cell-free DNA 5hmC
PLCO-410


title: p300_iHAT_NT_rep1_NT_A485_3

description:
Library name: p300_iHAT_NT_rep1_NT_A485_3
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 2086

description:
cell-free DNA 5hmC
PLCO-409


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 5213

description:
cell-free DNA 5hmC
PLCO-411


title: COLON-7DPI-15

description: Sample 65


title: p300_iHAT_NT_rep1_Donor_A486_2

description:
Library name: p300_iHAT_NT_rep1_Donor_A486_2
2x50 bp reads


title: p300_iHAT_NT_rep1_NT_A485_1

description:
Library name: p300_iHAT_NT_rep1_NT_A485_1
2x50 bp reads


title: COLON-7DPI-14

description: Sample 64


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 4321

description:
cell-free DNA 5hmC
PLCO-408


title: p300_iHAT_NT_rep1_Donor_A486_1

description:
Library name: p300_iHAT_NT_rep1_Donor_A486_1
2x50 bp reads


title: COLON-7DPI-13

description: Sample 63


title: p300_iHAT_NT_rep1_Donor_A485_2

description:
Library name: p300_iHAT_NT_rep1_Donor_A485_2
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 5399

description:
cell-free DNA 5hmC
PLCO-407


title: p300_iHAT_NT_rep1_Donor_A485_1

description:
Library name: p300_iHAT_NT_rep1_Donor_A485_1
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 2803

description:
cell-free DNA 5hmC
PLCO-406


title: COLON-7DPI-12

description: Sample 62


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 9915

description:
cell-free DNA 5hmC
PLCO-405


title: p300_iHAT_NT_rep1_IVF_2

description:
Library name: p300_iHAT_NT_rep1_IVF_2
2x50 bp reads


title: COLON-7DPI-11

description: Sample 61


title: p300_iHAT_NT_rep1_IVF_4

description:
Library name: p300_iHAT_NT_rep1_IVF_4
2x50 bp reads


title: p300_iHAT_NT_rep1_IVF_3

description:
Library name: p300_iHAT_NT_rep1_IVF_3
2x50 bp reads


title: p300_iHAT_NT_rep1_IVF_1

description:
Library name: p300_iHAT_NT_rep1_IVF_1
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 2226

description:
cell-free DNA 5hmC
PLCO-404


title: p300_iBD_NT_rep3_Donor_CBP30_1

description:
Library name: p300_iBD_NT_rep3_Donor_CBP30_1
2x50 bp reads


title: COLON-7DPI-10

description: Sample 60


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 3061

description:
cell-free DNA 5hmC
PLCO-403


title: p300_iBD_NT_rep3_Donor_DMSO_1

description:
Library name: p300_iBD_NT_rep3_Donor_DMSO_1
2x50 bp reads


title: p300_iBD_NT_rep3_Donor_DMSO_2

description:
Library name: p300_iBD_NT_rep3_Donor_DMSO_2
2x50 bp reads


title: COLON-7DPI-9

description: Sample 59


title: p300_iBD_NT_rep2_Donor_CBP30_2

description:
Library name: p300_iBD_NT_rep2_Donor_CBP30_2
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 4464

description:
cell-free DNA 5hmC
PLCO-401


title: p300_iBD_NT_rep2_Donor_CBP30_1

description:
Library name: p300_iBD_NT_rep2_Donor_CBP30_1
2x50 bp reads


title: COLON-7DPI-8

description: Sample 58


title: p300_iHAT_NT_rep1_NT_A485_2

description:
Library name: p300_iHAT_NT_rep1_NT_A485_2
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LO 0633

description:
cell-free DNA 5hmC
PLCO-400


title: COLON-7DPI-7

description: Sample 57


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 2534

description:
cell-free DNA 5hmC
PLCO-398


title: p300_iBD_NT_rep2_Donor_DMSO_2

description:
Library name: p300_iBD_NT_rep2_Donor_DMSO_2
2x50 bp reads


title: p300_iBD_NT_rep2_Donor_DMSO_1

description:
Library name: p300_iBD_NT_rep2_Donor_DMSO_1
2x50 bp reads


title: p300_iBD_NT_rep1_Donor_CBP30_2

description:
Library name: p300_iBD_NT_rep1_Donor_CBP30_2
2x50 bp reads


title: p300_iBD_NT_rep1_Donor_CBP30_1

description:
Library name: p300_iBD_NT_rep1_Donor_CBP30_1
2x50 bp reads


title: COLON-7DPI-6

description: Sample 56


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 3323

description:
cell-free DNA 5hmC
PLCO-397


title: COLON-7DPI-5

description: Sample 55


title: p300_iBD_NT_rep1_Donor_DMSO_2

description:
Library name: p300_iBD_NT_rep1_Donor_DMSO_2
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 3217

description:
cell-free DNA 5hmC
PLCO-396


title: p300_iBD_NT_rep1_Donor_DMSO_1

description:
Library name: p300_iBD_NT_rep1_Donor_DMSO_1
2x50 bp reads


title: p300_iBD_NT_rep3_NT_CBP30_2

description:
Library name: p300_iBD_NT_rep3_NT_CBP30_2
2x50 bp reads


title: COLON-7DPI-4

description: Sample 54


title: p300_iBD_NT_rep3_NT_CBP30_1

description:
Library name: p300_iBD_NT_rep3_NT_CBP30_1
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 3142

description:
cell-free DNA 5hmC
PLCO-395


title: COLON-7DPI-3

description: Sample 53


title: p300_iBD_NT_rep3_NT_DMSO_4

description:
Library name: p300_iBD_NT_rep3_NT_DMSO_4
2x50 bp reads


title: p300_iBD_NT_rep3_NT_DMSO_5

description:
Library name: p300_iBD_NT_rep3_NT_DMSO_5
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 6676

description:
cell-free DNA 5hmC
PLCO-394


title: p300_iBD_NT_rep3_NT_DMSO_2

description:
Library name: p300_iBD_NT_rep3_NT_DMSO_2
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 9012

description:
cell-free DNA 5hmC
PLCO-393


title: p300_iBD_NT_rep3_NT_DMSO_1

description:
Library name: p300_iBD_NT_rep3_NT_DMSO_1
2x50 bp reads


title: COLON-7DPI-2

description: Sample 52


title: COLON-7DPI-1

description: Sample 51


title: p300_iBD_NT_rep3_IVF_4

description:
Library name: p300_iBD_NT_rep3_IVF_4
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 9094

description:
cell-free DNA 5hmC
PLCO-391


title: p300_iBD_NT_rep3_IVF_3

description:
Library name: p300_iBD_NT_rep3_IVF_3
2x50 bp reads


title: COLON-3DPI-35

description: Sample 50

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer. RNA integrity was assessed using the Agilent 2100 Bioanalyzer.
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer's instruction

treatment_protocol: The mice with indicated genotypes were injucted with 3 daily intraperitoneal administrations of 80 mg/kg tamoxifen dissolved in corn oil/ethanol to induce TAK1 deletion, and collected the sample at indicated day(3dpi or 7dpi).

value: 3 DPI


title: p300_iBD_NT_rep3_IVF_2

description:
Library name: p300_iBD_NT_rep3_IVF_2
2x50 bp reads

value: ectoderm


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 4976

description:
cell-free DNA 5hmC
PLCO-389


title: p300_iBD_NT_rep3_IVF_1

description:
Library name: p300_iBD_NT_rep3_IVF_1
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UK 0472

description:
cell-free DNA 5hmC
PLCO-390


title: COLON-3DPI-34

description: Sample 49


title: p300_iBD_NT_rep3_NT_CBP30_3

description:
Library name: p300_iBD_NT_rep3_NT_CBP30_3
2x50 bp reads


title: p300_iBD_NT_rep2_NT_CBP30_5

description:
Library name: p300_iBD_NT_rep2_NT_CBP30_5
2x50 bp reads


title: COLON-3DPI-33

description: Sample 48


title: p300_iBD_NT_rep2_NT_CBP30_2

description:
Library name: p300_iBD_NT_rep2_NT_CBP30_2
2x50 bp reads


title: p300_iBD_NT_rep2_NT_CBP30_4

description:
Library name: p300_iBD_NT_rep2_NT_CBP30_4
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 7010

description:
cell-free DNA 5hmC
PLCO-387


title: p300_iBD_NT_rep2_NT_CBP30_1

description:
Library name: p300_iBD_NT_rep2_NT_CBP30_1
2x50 bp reads


title: p300_iBD_NT_rep2_NT_DMSO_3

description:
Library name: p300_iBD_NT_rep2_NT_DMSO_3
2x50 bp reads


title: COLON-3DPI-32

description: Sample 47


title: p300_iBD_NT_rep2_NT_CBP30_3

description:
Library name: p300_iBD_NT_rep2_NT_CBP30_3
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 0733

description:
cell-free DNA 5hmC
PLCO-388


title: COLON-3DPI-31

description: Sample 46


title: p300_iBD_NT_rep2_NT_DMSO_2

description:
Library name: p300_iBD_NT_rep2_NT_DMSO_2
2x50 bp reads


title: p300_iBD_NT_rep3_NT_DMSO_3

description:
Library name: p300_iBD_NT_rep3_NT_DMSO_3
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 2155

description:
cell-free DNA 5hmC
PLCO-386


title: COLON-3DPI-30

description: Sample 45


title: COLON-3DPI-29

description: Sample 44


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 0825

description:
cell-free DNA 5hmC
PLCO-385


title: p300_iBD_NT_rep2_IVF_1

description:
Library name: p300_iBD_NT_rep2_IVF_1
2x50 bp reads


title: p300_iBD_NT_rep2_IVF_3

description:
Library name: p300_iBD_NT_rep2_IVF_3
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UU 9461

description:
cell-free DNA 5hmC
PLCO-384


title: p300_iBD_NT_rep1_NT_CBP30_3

description:
Library name: p300_iBD_NT_rep1_NT_CBP30_3
2x50 bp reads


title: COLON-3DPI-28

description: Sample 43


title: p300_iBD_NT_rep1_NT_CBP30_1

description:
Library name: p300_iBD_NT_rep1_NT_CBP30_1
2x50 bp reads


title: p300_iBD_NT_rep1_NT_CBP30_2

description:
Library name: p300_iBD_NT_rep1_NT_CBP30_2
2x50 bp reads


title: COLON-3DPI-27

description: Sample 42


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 9676

description:
cell-free DNA 5hmC
PLCO-382


title: p300_iBD_NT_rep1_NT_DMSO_3

description:
Library name: p300_iBD_NT_rep1_NT_DMSO_3
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IB 8092

description:
cell-free DNA 5hmC
PLCO-381


title: p300_iBD_NT_rep1_NT_DMSO_1

description:
Library name: p300_iBD_NT_rep1_NT_DMSO_1
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 1417

description:
cell-free DNA 5hmC
PLCO-380


title: p300_iBD_NT_rep2_NT_DMSO_1

description:
Library name: p300_iBD_NT_rep2_NT_DMSO_1
2x50 bp reads


title: p300_iBD_NT_rep1_IVF_4

description:
Library name: p300_iBD_NT_rep1_IVF_4
2x50 bp reads


title: p300_iBD_NT_rep1_IVF_3

description:
Library name: p300_iBD_NT_rep1_IVF_3
2x50 bp reads


title: p300_iBD_NT_rep1_IVF_2

description:
Library name: p300_iBD_NT_rep1_IVF_2
2x50 bp reads


title: p300_iBD_NT_rep2_IVF_2

description:
Library name: p300_iBD_NT_rep2_IVF_2
2x50 bp reads


title: COLON-3DPI-23

description: Sample 38


title: p300_iBD_NT_rep1_IVF_1

description:
Library name: p300_iBD_NT_rep1_IVF_1
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 7853

description:
cell-free DNA 5hmC
PLCO-378


title: p300_iBD_NT_rep1_NT_DMSO_2

description:
Library name: p300_iBD_NT_rep1_NT_DMSO_2
2x50 bp reads


title: HA-PRCC-TFE3_2_ChIP-seq

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

institute: Kumamoto University

data_processing:
Strand NGS software (Strand Life Sciences)
Peak detection was performed using the MACS algorithm.  The significant enrichment of each signal over input-DNA peaks was determined at a P cut-off value of 10-5.
Assembly: hg19
Supplementary files format and content: BED files with peak coordinates and scores

source_name: Kidney

growth_protocol: HA-PRCC-TFE3-inducible HK-2 cell lines which express HA-PRCC-TFE3 in a doxycycline-dependent manner were cultured with advanced DMEM/F-12 supplemented with 1.5% FCS, 100 U/ml penicillin, 100 microg/ml streptomycin.

extract_protocol:
SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) (#9005, Cell Signaling) was utilized for ChIP. Cell cross-linking, chromatin preparation and chromatin immunoprecipitation by anti HA Affinity Matrix (#11815016001, Roche) was performed according to the manufacturer's instructions.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: HA-PRCC-TFE3-inducible HK-2 cells were cultured with 0.2 microg/ml of doxycycline for 24hr.

value: Kidney

value: HA-PRCC-TFE3-inducible cell

value: Doxycycline +


title: COLON-3DPI-22

description: Sample 37


title: COLON-3DPI-25

description: Sample 40


title: HA-PRCC-TFE3_1_ChIP-seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UQ 4452

description:
cell-free DNA 5hmC
PLCO-377


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IB 8674

description:
cell-free DNA 5hmC
PLCO-383


title: p300_iBD_NT_rep1_NT_DMSO_4

description:
Library name: p300_iBD_NT_rep1_NT_DMSO_4
2x50 bp reads


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 2884

description:
cell-free DNA 5hmC
PLCO-376


title: N159V02_Rd5_GPEX

city: Groton

first: Mark

last: Sheehan

state: CT

address: 274 Eastern Point Rd

department: Drug Safety R&D

institute: Pfizer

description: Library name: N159V02_Rd5_GPEX_S7

library_source: transcriptomic single cell

data_processing:
For single-cell RNAseq and V(D)J sequencing analysis, sequence reads were demultiplexed using CellRanger multi (10x Genomics) and normalized, QC filtered and merged using the R package Seurat. Cell clusters were annotated using the human PBMC reference (HuBMAP Consortium).
Assembly: Human GRCh38 (GENCODE v32/Ensembl98) CellRanger 2020-A reference package; Human V(D)J reference GRCh38 CR7.1
Supplementary files format and content: RDS containing Seurat object with raw and normalized counts, cell and subject level metadata. Generated with Seurat version 5.1.0.

source_name: PBMC

extract_protocol:
Single Cell RNAseq was performed by the 10x Genomics single-cell 5′ Gene Expression and V(D)J library platform. Dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec).
Single-cell libraries were generated with Chromium Single Cell 5’ Gene Expression and V(D)J Reagent Kit (10x Genomics) per manufacturer’s instruction. Purified libraries were sequenced on the Illumina NextSeq 2000 with 200 cycle kits.

value: PBMC

tag: subject

tag: group

value: Control

value: AC

tag: Sex

value: Female

tag: age

value: Ipilimumab + Nivolumab

tag: steroid

tag: batch


title: COLON-3DPI-26

description: Sample 41

value: colon

value: DHO


title: COLON-3DPI-20

description: Sample 35


title: COLON-3DPI-24

description: Sample 39


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LO 0804

description:
cell-free DNA 5hmC
PLCO-373


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UQ 2259

description:
cell-free DNA 5hmC
PLCO-379


title: N158V02_Rd5_TCR

description: Library name: N158V02_Rd5_TCR_S13

value: Male


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 4011

description:
cell-free DNA 5hmC
PLCO-375


title: N158V02_Rd5_GPEX

description: Library name: N158V02_Rd5_GPEX_S5


title: N158V01_Rd5_TCR

description: Library name: N158V01_Rd5_TCR_S12

value: BC


title: COLON-3DPI-19

description: Sample 34


title: COLON-3DPI-18

description: Sample 33


title: input DNA


title: N150V02_Rd5_TCR

description: Library name: N150V02_Rd5_TCR_S11


title: COLON-3DPI-17

description: Sample 32


title: N158V01_Rd5_GPEX

description: Library name: N158V01_Rd5_GPEX_S4


title: N150V02_Rd5_GPEX

description: Library name: N150V02_Rd5_GPEX_S3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UQ 6085

description:
cell-free DNA 5hmC
PLCO-372

value: peripheral plasma


title: COLON-3DPI-16

description: Sample 31


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 0583

description:
cell-free DNA 5hmC
PLCO-371

value: cell-free DNA


title: N150V01_Rd5_GPEX

description: Library name: N150V01_Rd5_GPEX_S2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 1703

description:
cell-free DNA 5hmC
PLCO-370


title: N159V02_Rd5_TCR

description: Library name: N159V02_Rd5_TCR_S15


title: N147V01_Rd5_TCR

description: Library name: N147V01_Rd5_TCR_S9

value: ChILI

value: TOL


title: N159V01_Rd5_TCR

description: Library name: N159V01_Rd5_TCR_S14


title: COLON-3DPI-21

description: Sample 36

value: HO

value: 3 DPI


title: N159V01_Rd5_GPEX

description: Library name: N159V01_Rd5_GPEX_S6


title: COLON-3DPI-15

description: Sample 30


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UQ 5714

description:
cell-free DNA 5hmC
PLCO-369


title: N131V01_Rd5_TCR

description: Library name: N131V01_Rd5_TCR_S16

value: n


title: COLON-3DPI-14

description: Sample 29


title: N131V01_Rd5_GPEX

description: Library name: N131V01_Rd5_GPEX_S8


title: COLON-3DPI-13

description: Sample 28


title: N138V02_Rd4b_GPEX

description: Library name: N138V02_Rd4b_GPEX_S4

value: y


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UQ 5507

description:
cell-free DNA 5hmC
PLCO-368


title: N138V01_Rd4b_TCR

description: Library name: N138V01_Rd4b_TCR_S11

value: PBMC


title: COLON-3DPI-12

description: Sample 27

value: WT


title: N138V02_Rd4b_TCR

description: Library name: N138V02_Rd4b_TCR_S12


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 1411

description:
cell-free DNA 5hmC
PLCO-367


title: N150V01_Rd5_TCR

description: Library name: N150V01_Rd5_TCR_S10

value: Control


title: N138V01_Rd4b_GPEX

description: Library name: N138V01_Rd4b_GPEX_S3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 1388

description:
cell-free DNA 5hmC
PLCO-366


title: N136V02_Rd4b_GPEX

description: Library name: N136V02_Rd4b_GPEX_S2

value: Female


title: N136V01_Rd4b_TCR

description: Library name: N136V01_Rd4b_TCR_S9

value: Ipilimumab + Nivolumab


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IM 4810

description:
cell-free DNA 5hmC
PLCO-365


title: COLON-3DPI-11

description: Sample 26

value: colon


title: N136V01_Rd4b_GPEX

description: Library name: N136V01_Rd4b_GPEX_S1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 8382

description:
cell-free DNA 5hmC
PLCO-364


title: COLON-3DPI-9

description: Sample 24


title: N147V01_Rd5_GPEX

description: Library name: N147V01_Rd5_GPEX_S1


title: N106V02_Rd4b_TCR

description: Library name: N106V02_Rd4b_TCR_S14

value: AC


title: N087V02_Rd4b_TCR

description: Library name: N087V02_Rd4b_TCR_S16

value: Male


title: N106V02_Rd4b_GPEX

description: Library name: N106V02_Rd4b_GPEX_S6


title: N087V02_Rd4b_GPEX

description: Library name: N087V02_Rd4b_GPEX_S8


title: N063V02_Rd4b_TCR

description: Library name: N063V02_Rd4b_TCR_S13


title: N136V02_Rd4b_TCR

description: Library name: N136V02_Rd4b_TCR_S10


title: COLON-3DPI-8

description: Sample 23


title: N063V02_Rd4b_GPEX

description: Library name: N063V02_Rd4b_GPEX_S5


title: COLON-3DPI-7

description: Sample 22


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 5168

description:
cell-free DNA 5hmC
PLCO-361


title: N055V02_Rd4b_GPEX

description: Library name: N055V02_Rd4b_GPEX_S7


title: N055V02_Rd4b_TCR

description: Library name: N055V02_Rd4b_TCR_S15


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IM 4621

description:
cell-free DNA 5hmC
PLCO-360


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 2627

description:
cell-free DNA 5hmC
PLCO-363


title: N129V02_Rd4a_TCR

description: Library name: N129V02_Rd4a_TCR_S16


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IY 7248

description:
cell-free DNA 5hmC
PLCO-362


title: N129V02_Rd4a_GPEX

description: Library name: N129V02_Rd4a_GPEX_S8


title: COLON-3DPI-5

description: Sample 20


title: COLON-3DPI-4

description: Sample 19


title: COLON-3DPI-10

description: Sample 25


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IM 9649

description:
cell-free DNA 5hmC
PLCO-359


title: N129V01_Rd4a_TCR

description: Library name: N129V01_Rd4a_TCR_S15

value: BC


title: N129V01_Rd4a_GPEX

description: Library name: N129V01_Rd4a_GPEX_S7


title: N128V01_Rd4a_TCR

description: Library name: N128V01_Rd4a_TCR_S13


title: N128V02_Rd4a_TCR

description: Library name: N128V02_Rd4a_TCR_S14


title: N128V01_Rd4a_GPEX

description: Library name: N128V01_Rd4a_GPEX_S5


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 3956

description:
cell-free DNA 5hmC
PLCO-358

value: peripheral plasma


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 7945

description:
cell-free DNA 5hmC
PLCO-357

value: cell-free DNA


title: N128V02_Rd4a_GPEX

description: Library name: N128V02_Rd4a_GPEX_S6


title: COLON-3DPI-2

description: Sample 17


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 0847

description:
cell-free DNA 5hmC
PLCO-356


title: N127V00_Rd4a_GPEX

description: Library name: N127V00_Rd4a_GPEX_S3

value: ChILI


title: COLON-3DPI-6

description: Sample 21


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UU 5866

description:
cell-free DNA 5hmC
PLCO-355


title: ILEUM-3DPI-15

description: Sample 15

source_name: ileum

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer. RNA integrity was assessed using the Agilent 2100 Bioanalyzer.
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer's instructions

value: ileum

value: DHO


title: N127V00_Rd4a_TCR

description: Library name: N127V00_Rd4a_TCR_S11


title: N131V01_Rd4a_TCR

description: Library name: N131V01_Rd4a_TCR_S12

value: TOL


title: COLON-3DPI-1

description: Sample 16

value: 3 DPI


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 6639

description:
cell-free DNA 5hmC
PLCO-352


title: ILEUM-3DPI-14

description: Sample 14


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 7260

description:
cell-free DNA 5hmC
PLCO-353


title: N032V01_Rd4a_GPEX

description: Library name: N032V01_Rd4a_GPEX_S2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 4595

description:
cell-free DNA 5hmC
PLCO-351


title: ILEUM-3DPI-13

description: Sample 13


title: N005V02_Rd4a_GPEX

description: Library name: N005V02_Rd4a_GPEX_S1


title: COLON-3DPI-3

description: Sample 18


title: N064V02_Rd3_TCR

description: Library name: N064V02_Rd3_TCR_S16

value: y


title: ILEUM-3DPI-12

description: Sample 12


title: N064V02_Rd3_GPEX

description: Library name: N064V02_Rd3_GPEX_S8

value: PBMC


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 9690

description:
cell-free DNA 5hmC
PLCO-350


title: N064V01_Rd3_TCR

description: Library name: N064V01_Rd3_TCR_S15


title: N064V01_Rd3_GPEX

description: Library name: N064V01_Rd3_GPEX_S7


title: ILEUM-3DPI-11

description: Sample 11


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 9635

description:
cell-free DNA 5hmC
PLCO-349


title: N012V02_Rd3_TCR

description: Library name: N012V02_Rd3_TCR_S14


title: N012V02_Rd3_GPEX

description: Library name: N012V02_Rd3_GPEX_S6


title: ILEUM-3DPI-10

description: Sample 10

value: HO


title: N012V01_Rd3_TCR

description: Library name: N012V01_Rd3_TCR_S13


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UV 7208

description:
cell-free DNA 5hmC
PLCO-347


title: N032V01_Rd4a_TCR

description: Library name: N032V01_Rd4a_TCR_S10

value: Control


title: N012V01_Rd3_GPEX

description: Library name: N012V01_Rd3_GPEX_S5


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 3480

description:
cell-free DNA 5hmC
PLCO-348


title: N131V01_Rd4a_GPEX

description: Library name: N131V01_Rd4a_GPEX_S4

value: Female

value: n


title: N005V02_Rd4a_TCR

description: Library name: N005V02_Rd4a_TCR_S9

value: Ipilimumab + Nivolumab


title: N002V02_Rd3_TCR

description: Library name: N002V02_Rd3_TCR_S12


title: ILEUM-3DPI-9

description: Sample 9


title: ILEUM-3DPI-8

description: Sample 8


title: N002V02_Rd3_GPEX

description: Library name: N002V02_Rd3_GPEX_S4


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LT 3143

description:
cell-free DNA 5hmC
PLCO-346


title: N002V01_Rd3_TCR

description: Library name: N002V01_Rd3_TCR_S11


title: ILEUM-3DPI-6

description: Sample 6


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 9099

description:
cell-free DNA 5hmC
PLCO-344


title: N002V01_Rd3_GPEX

description: Library name: N002V01_Rd3_GPEX_S3


title: N001V02_Rd3_GPEX

description: Library name: N001V02_Rd3_GPEX_S2


title: N001V02_Rd3_TCR

description: Library name: N001V02_Rd3_TCR_S10


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 3937

description:
cell-free DNA 5hmC
PLCO-342


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 2716

description:
cell-free DNA 5hmC
PLCO-341


title: ILEUM-3DPI-5

description: Sample 5

value: WT


title: N038V02_Rd2_GPEX

description: Library name: N038V02_Rd2_GPEX_S8

value: AC

value: Male


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 9796

description:
cell-free DNA 5hmC
PLCO-340

value: peripheral plasma


title: N038V01_Rd2_TCR

description: Library name: N038V01_Rd2_TCR_S15

value: BC


title: N038V02_Rd2_TCR

description: Library name: N038V02_Rd2_TCR_S16


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IQ 6220

description:
cell-free DNA 5hmC
PLCO-339

value: cell-free DNA


title: ILEUM-3DPI-7

description: Sample 7

value: ileum


title: N038V01_Rd2_GPEX

description: Library name: N038V01_Rd2_GPEX_S7


title: N018V02_Rd2_TCR

description: Library name: N018V02_Rd2_TCR_S12


title: N018V02_Rd2_GPEX

description: Library name: N018V02_Rd2_GPEX_S4


title: N032V02_Rd2_TCR

description: Library name: N032V02_Rd2_TCR_S14


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 7885

description:
cell-free DNA 5hmC
PLCO-338


title: ILEUM-3DPI-2

description: Sample 2


title: N032V02_Rd2_GPEX

description: Library name: N032V02_Rd2_GPEX_S6


title: ILEUM-3DPI-1

description: Sample 1


title: N001V01_Rd3_GPEX

description: Library name: N001V01_Rd3_GPEX_S1

value: ChILI


title: N001V01_Rd3_TCR

description: Library name: N001V01_Rd3_TCR_S9

value: TOL


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 0649

description:
cell-free DNA 5hmC
PLCO-336


title: N005V01_Rd2_GPEX

description: Library name: N005V01_Rd2_GPEX_S1


title: N018V01_Rd2_TCR

description: Library name: N018V01_Rd2_TCR_S11


title: N018V01_Rd2_GPEX

description: Library name: N018V01_Rd2_GPEX_S3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IB 7608

description:
cell-free DNA 5hmC
PLCO-337


title: N043V02_Rd1_TCR

description: Library name: N043V02_Rd1_TCR_S14


title: SFB.4.CD44neg.4

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the GENCODE v27 reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: tab delimited text file of RPKM normalized read counts for each gene

molecule: polyA RNA

source_name: Small intestine

extract_protocol:
1e6 cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

value: Small intestine

value: Epithelial cells

tag: diet

value: Standard chow

tag: sorting markers

value: live CD45-CD31-EpCAM+CD44-

value: colonized with SFB


title: N005V01_Rd2_TCR

description: Library name: N005V01_Rd2_TCR_S9

value: PBMC

value: Control


title: N043V02_Rd1_GPEX

description: Library name: N043V02_Rd1_GPEX_S6

value: Ipilimumab + Nivolumab

value: y


title: ILEUM-3DPI-3

description: Sample 3

tag: tissue

value: WT


title: SFB.2.CD44neg.2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UU 8754

description:
cell-free DNA 5hmC
PLCO-335


title: N043V01_Rd1_TCR

description: Library name: N043V01_Rd1_TCR_S13

value: Male


title: SFB.3.CD44neg.3


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 3129

description:
cell-free DNA 5hmC
PLCO-333

value: peripheral plasma


title: NFF.4.CD44neg.4

value: Low fermentable fiber


title: N043V01_Rd1_GPEX

description: Library name: N043V01_Rd1_GPEX_S5


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IQ 6454

description:
cell-free DNA 5hmC
PLCO-332

value: cell-free DNA


title: N037V01_Rd1_GPEX

description: Library name: N037V01_Rd1_GPEX_S4

value: BC


title: N037V01_Rd1_TCR

description: Library name: N037V01_Rd1_TCR_S12

value: ChILI


title: SFB.1.CD44neg.1


title: N035V01_Rd1_TCR

description: Library name: N035V01_Rd1_TCR_S16

value: TOL

value: Female

value: n


title: N022V02_Rd1_TCR

description: Library name: N022V02_Rd1_TCR_S11


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UJ 7747

description:
cell-free DNA 5hmC
PLCO-331


title: ILEUM-3DPI-4

description: Sample 4

value: ileum


title: NFF.2.CD44neg.2

value: Small intestine

value: Epithelial cells

value: live CD45-CD31-EpCAM+CD44-


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 2858

description:
cell-free DNA 5hmC
PLCO-330


title: N035V01_Rd1_GPEX

description: Library name: N035V01_Rd1_GPEX_S8

value: PBMC


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UY 3560

description:
cell-free DNA 5hmC
PLCO-334


title: NFF.3.CD44neg.3


title: N022V01_Rd1_TCR

description: Library name: N022V01_Rd1_TCR_S10

value: Ipilimumab + Nivolumab


title: N022V02_Rd1_GPEX

description: Library name: N022V02_Rd1_GPEX_S3

value: y


title: NFF.1.CD44neg.1

value: WT


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IQ 8192

description:
cell-free DNA 5hmC
PLCO-328


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 4236

description:
cell-free DNA 5hmC
PLCO-329


title: N016V01_Rd1_TCR

description: Library name: N016V01_Rd1_TCR_S15


title: N016V01_Rd1_GPEX

description: Library name: N016V01_Rd1_GPEX_S7


title: Control.5.CD44neg.5

value: Standard chow


title: N014V01_Rd1_TCR

description: Library name: N014V01_Rd1_TCR_S9

value: Male


title: Control.4.CD44neg.4


title: N014V01_Rd1_GPEX

description: Library name: N014V01_Rd1_GPEX_S1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 0631

description:
cell-free DNA 5hmC
PLCO-326

value: peripheral plasma


title: N043_chili_FU1

description: Library name: itox009636

data_processing:
For bulk RNAseq data analysis, reads were pseudo-aligned to the Homo sapiens reference genome GRCh38.p14 and quantified using Salmon version 1.10.0. Normalization factors were determined using the edgeR package (version 3.40.2) for expression data normalization and processing. Pairwise comparisons were run for differential expression, defined by timepoint (before and after checkpoint inhibitor) and outcome (ChILI and non-ChILI control). Benjamini-Hochberg multiple testing correction was performed on p-values. Heatmaps were generated using the internally-developed, publicly available application “MegaOmics” (https://github.com/pfizer-opensource/Open-Hotgenes).
Assembly: GRCh38.p14 from Ensembl v. 110
Supplementary files format and content: Ensembl gene ID by sample matrix of raw counts

source_name: Blood

extract_protocol:
RNA was isolated from blood preserved in PAXgene tubes (Qiagen) using the PAXgene Blood RNA Kit (Qiagen) according to manufacturer’s protocol. Full methods are detailed in the Data Supplement.
100ng RNA was used as input for the Lexogen QuantSeq 3’mRNA-Seq Library Preparation kit for Illumina (FWD) (Lexogen, #015.96) and libraries were prepared according to the manufacturer’s protocol.  After elution, libraries were quantified using the Qubit 4 Fluorometer (ThermoFisher Scientific, #Q33238) using the Qubit 1X dsDNA HS Assay Kit (ThermoFisher Scientific, #Q33231).

value: Blood

value: chili

value: male


title: N035_chili_TOL

description: Library name: itox009632

value: TOL

value: female


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 4843

description:
cell-free DNA 5hmC
PLCO-325

value: cell-free DNA


title: BMDMs, S100A89-4

city: Tianjin

first: Mei

last: Sun

state: Tianjin

address: 251 Fukang Road, Xiqing District, Tianjin, China

institute: Tianjin Medical University Eye Hospital

data_processing:
The data generated from Illumina/BGI platform were used for bioinformatics analysis.
Raw data of fastq format were firstly processed through in-house perl scripts. In this step, remove the adapter sequence and filter out low quality and N ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
The clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
FeatureCounts (http://subread.sourceforge.net/) 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.
For RNA seq analysis, DEseq2 (v1.34.0) was applied to calculate the differential expression of TPM (Transcripts Per Kilobase of exon model per Million mapped reads) values. KEGG enrichment analysis was performed using DAVID (https://david.ncifcrf.gov/).
Assembly: UCSC mm10
Supplementary files format and content: processed data_all.txt

source_name: bone marrow

extract_protocol:
Total RNAs of Vehicle- or S100A8/A9-treated BMDCs were extracted using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen).
Total RNA was treated with RNase-free DNase I for 30 min according to the manufacturer’s protocols. The poly(A)-containing mRNA was purified using Oligo(dT) beads from the total RNA and then fragmented into 100- 200 nt using divalent cations at elevated temperature. The fragmented mRNA was reverse transcribed with SuperScript II and further extended into double-stranded cDNA using RNaseH and DNA Pol I by random priming. The cDNA was subsequently adapter-ligated with unique indices and amplified following PCR. The libraries were analyzed by Agilent Bioanalyzer 4200 and quantified by qPCR before being sequenced on the Illumina sequencing platform.

value: bone marrow

value: bone marrow-derived dendritic cell

value: treat with recombinant S100A8/A9


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 3178

description:
cell-free DNA 5hmC
PLCO-324


title: N043_chili_TOL

description: Library name: itox009635

value: n


title: BMDMs, S100A89-2


title: N022V01_Rd1_GPEX

description: Library name: N022V01_Rd1_GPEX_S2

value: PBMC

value: ChILI


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 8400

description:
cell-free DNA 5hmC
PLCO-322


title: BMDMs, S100A89-3


title: N028_control_AC

description: Library name: itox009629

value: control

value: AC

value: Nivolumab


title: N029_control_AC

description: Library name: itox009631

value: Avelumab


title: N029_control_BC

description: Library name: itox009630

value: BC


title: N035_chili_FU1

description: Library name: itox009633

value: Blood

value: Ipilimumab + Nivolumab


title: Control.2.CD44neg.2

value: Small intestine

value: Epithelial cells

value: Standard chow

value: WT

value: live CD45-CD31-EpCAM+CD44-


title: N043_chili_BC

description: Library name: itox009634

value: chili

value: male


title: N027_control_AC

description: Library name: itox009627

value: Pembrolizumab


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 9158

description:
cell-free DNA 5hmC
PLCO-321

value: peripheral plasma

value: cell-free DNA


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 3853

description:
cell-free DNA 5hmC
PLCO-320


title: N026_control_BC

description: Library name: itox009624

value: control


title: BMDMs, Control-4

value: bone marrow

value: bone marrow-derived dendritic cell

value: treat with PBS


title: N028_control_BC

description: Library name: itox009628

value: BC

value: Nivolumab


title: N025_control_BC

description: Library name: itox009622

value: Blood


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IQ 6764

description:
cell-free DNA 5hmC
PLCO-317


title: N026_control_AC

description: Library name: itox009625

value: AC


title: N027_control_BC

description: Library name: itox009626


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IQ 7106

description:
cell-free DNA 5hmC
PLCO-318


title: BMDMs, Control-3


title: N025_control_AC

description: Library name: itox009623


title: BMDMs, Control-2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 1080

description:
cell-free DNA 5hmC
PLCO-316


title: N023_control_AC

description: Library name: itox009621


title: WD_WD_3

city: tianjin

first: kan

last: li

address: Tianjin Medical University, 22 Qixiangtai Road, Tianjin, China

institute: Tianjin Medical University

data_processing:
Samples were quality controlled using FastQC (version 0.12.1) to remove low-quality reads. The adapters of raw reads were removed using Trim Galore (version 0.6.10). Paired end reads of 150 bp were aligned to the GENCODE Mus musculus reference genome (build GRCm38/mm10) using HISAT2 (version 2.2.1). The SAM files were converted into BAM files by Samtools (version 1.13). Table of raw read counts was then generated with featureCounts (version 2.0.1).
Assembly: GRCm38/mm10
Supplementary files format and content: table-delimited text file inclued DESeq2 normalized gene expression for each sample

source_name: MAECs

extract_protocol:
RNA was harvested with Trizol, 1μg of total RNA was used for the construction of sequencing libraries.
The RNA libraries were sequenced on the illumina Novaseq™ 6000 platform.

value: MAECs


title: N023_control_BC

description: Library name: itox009620


title: WD_WD_2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 8152

description:
cell-free DNA 5hmC
PLCO-314


title: N018_control_AC

description: Library name: itox009615

value: female

value: Ipilimumab + Nivolumab


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 4839

description:
cell-free DNA 5hmC
PLCO-315


title: N019_control_AC

description: Library name: itox009617


title: N022_chili_FU1

description: Library name: itox009619

value: y


title: N022_chili_TOL

description: Library name: itox009618

value: chili

value: TOL


title: WD_WD_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UT 1370

description:
cell-free DNA 5hmC
PLCO-312


title: BMDMs, S100A89-1

value: treat with recombinant S100A8/A9


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LR 1295

description:
cell-free DNA 5hmC
PLCO-311

value: peripheral plasma


title: N015_control_BC

description: Library name: itox009611

value: male

value: Pembrolizumab


title: CD_WD_3


title: N019_control_BC

description: Library name: itox009616

value: control


title: N018_control_BC

description: Library name: itox009614


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UV 5419

description:
cell-free DNA 5hmC
PLCO-313

value: cell-free DNA


title: N022_chili_BC

description: Library name: itox009610


title: N035_chili_BC

description: Library name: itox009613


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 9721

description:
cell-free DNA 5hmC
PLCO-310


title: N015_control_AC

description: Library name: itox009612


title: CD_WD_1


title: N013_control_AC

description: Library name: itox009609


title: CD_WD_2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 3202

description:
cell-free DNA 5hmC
PLCO-309


title: N013_control_BC

description: Library name: itox009608


title: N012_chili_TOL

description: Library name: itox009606


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UL 2057

description:
cell-free DNA 5hmC
PLCO-308


title: N010_control_BC

description: Library name: itox009604


title: BMDMs, Control-1

value: bone marrow

value: bone marrow-derived dendritic cell

value: treat with PBS


title: N012_chili_FU1

description: Library name: itox009607

value: Blood


title: N010_control_AC

description: Library name: itox009605

value: AC


title: WD_CD_3

value: MAECs


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UJ 0002

description:
cell-free DNA 5hmC
PLCO-307


title: WD_CD_2


title: N003_control_AC

description: Library name: itox009599


title: N003_control_BC

description: Library name: itox009598

value: BC


title: N007_control_BC

description: Library name: itox009602


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 8229

description:
cell-free DNA 5hmC
PLCO-306


title: N005_control_BC

description: Library name: itox009600

value: Ipilimumab + Nivolumab


title: N007_control_AC

description: Library name: itox009603


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UU 7215

description:
cell-free DNA 5hmC
PLCO-305


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 7579

description:
cell-free DNA 5hmC
PLCO-304


title: CD_CD_2


title: WD_CD_1


title: N002_chili_TOL

description: Library name: itox009596

value: n


title: N005_control_AC

description: Library name: itox009601


title: CD_CD_3


title: CD_CD_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 5051

description:
cell-free DNA 5hmC
PLCO-303


title: N001_chili_FU1

description: Library name: itox009595

value: chili

value: female

value: y


title: N001_chili_TOL

description: Library name: itox009594

value: TOL


title: N159_control_AC

description: Library name: itox014994


title: TM3, nomal, RNA-seq, Rep2

city: Guangzhou

first: Zixin

last: Chen

state: 广东

address: Dongchuan Road

institute: Guangdong General Hospital

data_processing:
After obtaining raw data, paired-end reads were harvested and trimmed by fastp (version 0.20.1) to remove adaptor sequences and low-quality nucleotides.
High-quality reads were then aligned to ENSEMBL GRCh38 or GRCm39 reference genome using HISAT2 (version 2.2.1) with default parameters
For RNA-seq, featureCounts (version 2.0.1) software was used to count reads mapped to RefSeq genes, and differential gene expression analysis was conducted using DESeq2 R package (version 1.38.3).
m6A peaks on RefSeq transcripts and differentially m6A peaks were analyzed using exomePeak2 R package (version 1.10.0).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes diffpeaks of BPA exposure vs nomal cells

extract_protocol:
The RNA was extracted using the Dynabeads® mRNA DIRECT kit (Thermo Fisher, 61011) to efficiently remove ribosomal RNA and prevent any potential DNA contamination. The purified product was divided into two equal portions, one designated for RNA-seq analysis and the other allocated for MeRIP-seq experimentation.
The RNA was initially fragmented to approximately 100-nt using a fragmentation kit (NEB, E6150S). A portion of fragmented mRNA was subjected to m6A immunoprecipitation (IP) using the EpiMark® N6-Methyladenosine Enrichment Kit (NEB, E1610S) following the manufacturer's protocol. The RNA libraries were prepared for both input RNA and m6A-enriched mRNA following IP, utilizing the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, NR605-01) according to the manufacturer's instructions and sequencing using the illumina NovaSeq PE150.
RNA-seq, MeRIP-seq

value: cell line

tag: cell line

value: Mouse leydig cell


title: N159_control_BC

description: Library name: itox014993

value: control


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID KD 7816

description:
cell-free DNA 5hmC
PLCO-302

value: peripheral plasma

value: cell-free DNA


title: N158_control_BC

description: Library name: itox014991

value: male


title: TM3, nomal, RNA-seq, Rep1


title: N002_chili_FU1

description: Library name: itox009597


title: N150_control_BC

description: Library name: itox014989


title: N158_control_AC

description: Library name: itox014992


title: TM3, nomal, MeRIP, Rep2


title: N150_control_AC

description: Library name: itox014990


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 5137

description:
cell-free DNA 5hmC
PLCO-301


title: N149_control_BC

description: Library name: itox014987


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UX 2292

description:
cell-free DNA 5hmC
PLCO-298


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 7745

description:
cell-free DNA 5hmC
PLCO-300


title: TM3, nomal, MeRIP, Rep1


title: TM3, BPA exposure, RNA-seq, Rep2


title: N149_control_AC

description: Library name: itox014988


title: TM3, BPA exposure, MeRIP, Rep2


title: N143_control_AC

description: Library name: itox014984


title: TM3, BPA exposure, RNA-seq, Rep1


title: N143_control_BC

description: Library name: itox014983


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 1286

description:
cell-free DNA 5hmC
PLCO-296


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 6775

description:
cell-free DNA 5hmC
PLCO-297


title: N146_control_BC

description: Library name: itox014985


title: N141_control_BC

description: Library name: itox014981


title: N137_control_AC

description: Library name: itox014980


title: N137_control_BC

description: Library name: itox014979


title: TM3, BPA exposure, MeRIP, Rep1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 4789

description:
cell-free DNA 5hmC
PLCO-295


title: N133_control_AC

description: Library name: itox014978


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IM 5942

description:
cell-free DNA 5hmC
PLCO-294


title: db4, heart, RNA-seq

city: Wuhan

first: Li

last: Zhou

address: Tongji Hospital Research Building, Wuxian Road, Caidian District, Wuhan, Hubei Province, People's Republic of China

department: Division of Cardiology, Departments of Internal Medicine

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Illumina Novaseq 6000 software used for basecalling.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Heart

extract_protocol:
RNA was harvested from the hearts of 24-week-old male mice. High-quality total RNA (3 μg/sample) was used as input material for the construction of sequencing libraries.
The sequencing library was conducted by NEBNext UltraTM RNA Library Prep Kit for Illumina(NEB,USA), and purified by AMPure XP system, according to the standard Illumina protocols.

value: Heart

tag: strain

value: 24-week old

value: db/db


title: N133_control_BC

description: Library name: itox014977

value: Blood

tag: treatment


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UJ 8746

description:
cell-free DNA 5hmC
PLCO-299


title: N146_control_AC

description: Library name: itox014986

tag: time

value: AC


title: db3, heart, RNA-seq


title: N162_chili_TOL

description: Library name: itox014976

value: Ipilimumab + Nivolumab


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 5082

description:
cell-free DNA 5hmC
PLCO-293


title: N162_chili_BC

description: Library name: itox014975

value: BC


title: db2, heart, RNA-seq


title: N141_control_AC

description: Library name: itox014982


title: db1, heart, RNA-seq


title: N129_control_AC

description: Library name: itox012846


title: Tr4, heart, RNA-seq

value: db/m


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IX 0850

description:
cell-free DNA 5hmC
PLCO-290


title: N128_control_BC

description: Library name: itox012843


title: N128_control_AC

description: Library name: itox012844


title: N122_control_AC

description: Library name: itox012842


title: Tr3, heart, RNA-seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UQ 3665

description:
cell-free DNA 5hmC
PLCO-288


title: N121_control_BC

description: Library name: itox012839


title: N120_control_AC

description: Library name: itox012838


title: Tr2, heart, RNA-seq


title: Tr1, heart, RNA-seq


title: N120_control_BC

description: Library name: itox012837


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 7769

description:
cell-free DNA 5hmC
PLCO-287


title: db4, heart, ATAC-seq

data_processing:
Illumina Novaseq 6000 software used for basecalling.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
50,000 counted nuclei were then subjected to a Tn5 transposition reaction which was incubated at 37 ℃ for 30 min. The transposed DNA were purified with the MinElute PCR Purification Kit (Qiagen) and were amplified with the NEBNext High-Fidelity 1X PCR Master Mix (New England Biolabs, MA).
The assays for transposase-accessible chromatin with high throughput sequencing (ATAC) assays were performed in Jiayin Biotechnology Ltd using standard Illumina protocols.


title: N112_control_AC

description: Library name: itox012836


title: db3, heart, ATAC-seq


title: N147_chili_TOL

description: Library name: itox014973

value: chili


title: N154_chili_TOL

description: Library name: itox014974

value: Pembrolizumab


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UN 5400

description:
cell-free DNA 5hmC
PLCO-291

extract_protocol:
Cell-free DNA was extracted using the QIAmp Circulating cfDNA Extraction Kit (Qiagen)
3-8 ng cfDNA was used in the 5hmC-Seal assay (see Li W, Zhang X, Lu X, You L, Song Y, Luo Z, et al. 5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers. Cell Res 2017;27:1243-57). Libraries were constructed on-bead using the KAPA HyperPlus kit (Roche).


title: N138_chili_FU1

description: Library name: itox012834

value: y


title: N129_control_BC

description: Library name: itox012845


title: N112_control_BC

description: Library name: itox012835


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IB 8308

description:
cell-free DNA 5hmC
PLCO-285


title: N138_chili_TOL

description: Library name: itox012833

value: TOL


title: db2, heart, ATAC-seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 5307

description:
cell-free DNA 5hmC
PLCO-292


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 7091

description:
cell-free DNA 5hmC
PLCO-284


title: N136_chili_FU1

description: Library name: itox012832

value: female


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 1520

description:
cell-free DNA 5hmC
PLCO-289


title: db1, heart, ATAC-seq


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IF 1675

description:
cell-free DNA 5hmC
PLCO-283


title: N122_control_BC

description: Library name: itox012841

value: control


title: N121_control_AC

description: Library name: itox012840


title: N132_chili_TOL

description: Library name: itox012829


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID US 1229

description:
cell-free DNA 5hmC
PLCO-286

value: peripheral plasma


title: N132_chili_BC

description: Library name: itox012827


title: N131_chili_BC

description: Library name: itox012828


title: N119_chili_FU2

description: Library name: itox012826


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UO 4549

description:
cell-free DNA 5hmC
PLCO-282

value: cell-free DNA


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UY 4732

description:
cell-free DNA 5hmC
PLCO-281


title: Tr3, heart, ATAC-seq


title: N119_chili_FU1

description: Library name: itox012825

value: n


title: N119_chili_TOL

description: Library name: itox012824


title: N117_chili_FU1

description: Library name: itox012822

value: male


title: Tr1, heart, ATAC-seq

value: Heart

value: 24-week old


title: Tr2, heart, ATAC-seq


title: N117_chili_TOL

description: Library name: itox012821

value: Blood


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UY 5341

description:
cell-free DNA 5hmC
PLCO-280


title: N117_chili_FU2

description: Library name: itox012823


title: N132_chili_FU1

description: Library name: itox012830


title: LNP-M/pR282W-mAb2, scRNA-seq-TCR (Tumor)

city: Houston

first: Dafei

last: Chai

state: Texas

address: Alkek Building One Baylor Plaza

institute: Baylor College of Medicine

description: 10× Genomics

data_processing:
The CellRanger Count v7.1.0 pipeline (https://cloud.10xgenomics.com) was used to process the raw sequence data in FASTQ format. The data were aligned to the mouse reference genome, using default barcode assignment and Unique Molecular Identifier (UMI) counting, with a 2020-A version of the mouse (mm10) genome reference. line used the default parameters with the mouse GRCm38/mm10 reference genome.
Assembly: mm10
Supplementary files format and content: gz

source_name: Tumor

growth_protocol: For preventive spike vaccine immunization, BALB/c mice were grown to 6-8 weeks old, immunization was administered.. For a syngeneic mouse colon cancer model, C57BL/6 mice were inoculated with MC38-p53KO/R282W cells (5 × 105 cells/mouse) subcutaneously. When the tumors were palpable (~100 mm3), treatment was administered.

extract_protocol:
The single-cell suspension of spleens from mice immunized 3 times vaccine was prepared, and CD45+ cells were purified using the EasySep™ Mouse TIL (CD45) Positive Selection Kit following the manufacturer’s instructions. Tumors were harvested 14 days following LNP-pR282W-mAb or LNP-Ctrl treatment, single cell suspensions were prepared. The cells of spleen or tumor samples were resuspended in RPMI1640 with 5% FBS. To create the scRNA-seq libraries, equivalent numbers of single cells from three mice per group were combined at a density of 1 × 103 cells/μl in a 10% FBS RPMI1640 medium. Each group used about 10,000 cells, which were converted to barcoded scRNA-seq libraries using the ChromiumTM Next GEM Single Cell 5′ Kit v2 (10× Genomics, Pleasanton, CA, USA; 1000263) according to the manufacturer’s protocol. To prepare full-length T-cell Receptor (TCR) and B-cell Receptor (BCR)V(D)J libraries, Chromium Single Cell Mouse TCR Amplification Kit (10× Genomics, 1000254) and Chromium Single Cell Mouse BCR Amplification Kit (10× Genomics, 1000255) was used to enrich amplified cDNA from the 5′ libraries.
Approximately 10,000 cells were allocated for the 10× Genomics 5′ v2 single-cell assay. TCR/BCR libraries were prepared using the Chromium™ single cell V(D)J enrichment kit (10× Genomics). Reverse transcription, cDNA amplification and library preparation were executed following the manufacturer’s protocol.

treatment_protocol: For preventive spike vaccine immunization, mice were intramuscularly immunized with LNP-M/Ctrl, LNP-M/Spike-mRNA, EP/pSpike, and LNP-M/pSpike. Each group was immunized three times biweekly with a dose of 40 μg/mouse for DNA or 5 μg/mouse for mRNA. For a syngeneic mouse colon cancer model, a single-dose treatment of LNP-M/Ctrl or LNP-M/pR282W-mAb (40 μg/mouse) was administered intratumorally on day 14 post-tumor inoculation.

value: 6–8 weeks old

value: Tumor

value: The MC38-p53KO/R282W subcutaneous tumor model was established by inoculating MC38-p53KO/E285K cells (5 × 105 cells/mouse) subcutaneously. On day 14 post-tumor inoculation, when the tumors were palpable (~100 mm3), a single-dose treatment of LNP-M/pR282W-mAb (40 μg/mouse) was administered intratumorally.

tag: cell type

value: Immune and non-immune cells


title: N136_chili_TOL

description: Library name: itox012831

value: chili

value: Ipilimumab + Nivolumab


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 0012

description:
cell-free DNA 5hmC
PLCO-279


title: N111_chili_BC

description: Library name: itox012820

value: BC


title: N101_chili_BC

description: Library name: itox012819


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IM 5503

description:
cell-free DNA 5hmC
PLCO-278


title: N086_chili_BC

description: Library name: itox011669

value: Avelumab + Axitinib


title: N96_control_AC

description: Library name: itox011670

value: AC


title: LNP-M/pR282W-mAb1, scRNA-seq-TCR (Tumor)

description: 10× Genomics


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 1879

description:
cell-free DNA 5hmC
PLCO-277


title: LNP-M/Ctrl2, scRNA-seq-TCR (Tumor)

description: 10× Genomics

value: The MC38-p53KO/R282W subcutaneous tumor model was established by inoculating MC38-p53KO/E285K cells (5 × 105 cells/mouse) subcutaneously. On day 14 post-tumor inoculation, when the tumors were palpable (~100 mm3), a single-dose treatment of LNP-M/Ctrl (40 μg/mouse) was administered intratumorally.


title: N87_control_BC

description: Library name: itox011668

value: control


title: Tr4, heart, ATAC-seq

tag: genotype

value: db/m


title: LNP-M/Ctrl1, scRNA-seq-TCR (Tumor)

description: 10× Genomics


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LQ 9420

description:
cell-free DNA 5hmC
PLCO-275

value: peripheral plasma

tag: dna source

value: cell-free DNA


title: LNP-M/pR282W-mAb2, scRNA-seq (Tumor)

description: 10× Genomics


title: N106_control_BC

description: Library name: itox011664

value: female


title: N87_control_AC

description: Library name: itox011667

value: male


title: N96_control_BC

description: Library name: itox011666

value: Blood


title: N113_chili_TOL

description: Library name: itox011665

value: TOL

value: Pembrolizumab

value: y


title: N111_chili_TOL

description: Library name: itox011663

value: n


title: N106_control_AC

description: Library name: itox011662


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 4643

description:
cell-free DNA 5hmC
PLCO-273


title: N100_chili_TOL

description: Library name: itox011661

value: chili


title: N101_chili_TOL

description: Library name: itox011660

value: Ipilimumab + Nivolumab


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 5760

description:
cell-free DNA 5hmC
PLCO-271


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IT 4707

description:
cell-free DNA 5hmC
PLCO-272


title: LNP-M/pR282W-mAb1, scRNA-seq (Tumor)

description: 10× Genomics

value: 6–8 weeks old

value: Tumor

value: The MC38-p53KO/R282W subcutaneous tumor model was established by inoculating MC38-p53KO/E285K cells (5 × 105 cells/mouse) subcutaneously. On day 14 post-tumor inoculation, when the tumors were palpable (~100 mm3), a single-dose treatment of LNP-M/pR282W-mAb (40 μg/mouse) was administered intratumorally.

value: Immune and non-immune cells


title: LNP-M/Ctrl2, scRNA-seq (Tumor)

description: 10× Genomics

value: The MC38-p53KO/R282W subcutaneous tumor model was established by inoculating MC38-p53KO/E285K cells (5 × 105 cells/mouse) subcutaneously. On day 14 post-tumor inoculation, when the tumors were palpable (~100 mm3), a single-dose treatment of LNP-M/Ctrl (40 μg/mouse) was administered intratumorally.


title: N063_control_AC

description: Library name: itox010117

value: control

value: AC


title: LNP-M/Ctrl1, scRNA-seq (Tumor)

description: 10× Genomics


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 3109

description:
cell-free DNA 5hmC
PLCO-270

value: peripheral plasma

value: cell-free DNA


title: N055_control_AC

description: Library name: itox010115

value: male


title: N063_control_BC

description: Library name: itox010116

value: Blood

value: BC


title: N055_control_BC

description: Library name: itox010114


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 7201

description:
cell-free DNA 5hmC
PLCO-269


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LN 9101

description:
cell-free DNA 5hmC
PLCO-276


title: LNP-M/pSpike, scRNA-seq-BCR (Spleen)

description: 10× Genomics

source_name: Spleen

value: BALB/c

value: Spleen

value: Mice were intramuscularly immunized with LNP-M/pSpike. Each group was immunized three times biweekly with a dose of DNA 40 μg/mouse.

value: CD45+ cells


title: N050_control_AC

description: Library name: itox010113

value: Ipilimumab + Nivolumab


title: N050_control_BC

description: Library name: itox010112


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 2575

description:
cell-free DNA 5hmC
PLCO-268


title: N038_control_AC

description: Library name: itox010111


title: N038_control_BC

description: Library name: itox010110


title: LNP-M/mRNA-Spike, scRNA-seq-BCR (Spleen)

description: 10× Genomics

value: 6–8 weeks old

value: Mice were intramuscularly immunized with LNP-M/Spike-mRNA. Each group was immunized three times biweekly with a dose of mRNA 5 μg/mouse.


title: N032_control_AC

description: Library name: itox010109

value: female


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UZ 7224

description:
cell-free DNA 5hmC
PLCO-267


title: LNP-M/Ctrl, scRNA-seq-BCR (Spleen)

description: 10× Genomics

value: Mice were intramuscularly immunized with LNP-M/Ctrl. LNP-M/Ctrl group was immunized three times biweekly with a dose of DNA 40 μg/mouse.


title: N032_control_BC

description: Library name: itox010108


title: N043_chili_FU2

description: Library name: itox010107

value: chili

value: y


title: LNP-M/pSpike, scRNA-seq-TCR (Spleen)

description: 10× Genomics


title: EP/pSpike, scRNA-seq-TCR (Spleen)

description: 10× Genomics

value: Mice were intramuscularly immunized with EP/pSpike using ICHOR medical systems. Each group was immunized three times biweekly with a dose of DNA 40 μg/mouse.


title: N078_chili_FU1

description: Library name: itox010103


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LT 2728

description:
cell-free DNA 5hmC
PLCO-264

value: peripheral plasma


title: N002_chili_FU2

description: Library name: itox010104

value: n


title: N012_chili_FU2

description: Library name: itox010105

value: male


title: EP/pSpike, scRNA-seq-BCR (Spleen)

description: 10× Genomics


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID KF 9214

description:
cell-free DNA 5hmC
PLCO-262

value: cell-free DNA


title: N073_chili_FU1

description: Library name: itox010101

value: Blood


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IU 0771

description:
cell-free DNA 5hmC
PLCO-265


title: N022_chili_FU2

description: Library name: itox010106


title: N072_chili_TOL

description: Library name: itox010099

value: TOL


title: N078_chili_TOL

description: Library name: itox010102


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UW 5400

description:
cell-free DNA 5hmC
PLCO-261


title: N064_chili_FU2

description: Library name: itox010097


title: N073_chili_TOL

description: Library name: itox010100


title: EP/pSpike, scRNA-seq (Spleen)

description: 10× Genomics

value: BALB/c

value: Spleen

value: Mice were intramuscularly immunized with electroporation (EP) with pSpike (EP/pSpike) using ICHOR medical systems. Each group was immunized three times biweekly with a dose of DNA 40 μg/mouse.


title: LNP-M/pSpike, scRNA-seq (Spleen)

description: 10× Genomics

value: Mice were intramuscularly immunized with LNP-M/pSpike. Each group was immunized three times biweekly with a dose of DNA 40 μg/mouse.

value: CD45+ cells


title: N064_chili_TOL

description: Library name: itox010095

value: Ipilimumab + Nivolumab


title: LNP-M/mRNA-Spike, scRNA-seq (Spleen)

description: 10× Genomics

value: 6–8 weeks old

value: Mice were intramuscularly immunized with LNP-M/Spike-mRNA. Each group was immunized three times biweekly with a dose of mRNA 5 μg/mouse.


title: N064_chili_FU1

description: Library name: itox010096

value: chili


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IC 1817

description:
cell-free DNA 5hmC
PLCO-259


title: N064_chili_BC

description: Library name: itox010094

value: BC


title: N072_chili_BC

description: Library name: itox010098


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID UP 6083

description:
cell-free DNA 5hmC
PLCO-266


title: LNP-M/Ctrl, scRNA-seq (Spleen)

description: 10× Genomics

value: Mice were intramuscularly immunized with LNP-M/Ctrl. LNP-M/Ctrl group was immunized three times biweekly with a dose of DNA 40 μg/mouse.


title: LNP-M/Ctrl, scRNA-seq-TCR (Spleen)

description: 10× Genomics


title: Endoderm_H3K79me3_ChIP_Xencode_Group3_2

description: Library name: Endoderm_H3K79me3_ChIP_Xencode_Group3_2

data_processing:
Raw ChIP-seq data were aligned to the Xenopus laevis genome (v10.1) using BWA (v0.7.17-foss-2018b).
Low-quality mapped reads (MAPQ < 10) were discarded using samtools (v1.16.1), and PCR duplicates were removed with sambamba (v0.8.2). Coverage track files (.bigwig) were generated using deepTools (v3.5.1), with normalization to Counts Per Million (CPM).
Assembly: Xenopus laevis 10.1
Supplementary files format and content: bigwig coverage tracks, merged replicates with input subtracted

source_name: endoderm

extract_protocol:
As described in Hörmanseder et al 2017.
ChIP-seq library preparation with the TruSeq DNA kit (Illumina, FC-121-2001).

treatment_protocol: No treatment

value: endoderm

value: WT


title: LNP-M/mRNA-Spike, scRNA-seq-TCR (Spleen)

description: 10× Genomics


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID KF 9352

description:
cell-free DNA 5hmC
PLCO-263

data_processing:
Adapter sequences were removed from raw sequencing reads using Trimmomatic
Low quality bases at the 5’ and 3’ were trimmed based on phred score to a minimum length of 30 bp
The sequencing reads were then aligned to the human genome reference (hg19) using Bowtie2 with the end-to-end alignment mode
Read pairs were concordantly aligned with fragment length ≤ 500 bp and with average ≤ 1 ambiguous base and up to four mismatched bases per 100 bp length
Alignments with Mapping Quality Score ≥ 10 were counted based on the GENCODE gene body annotations using featureCounts without strand information
The raw read counts were then normalized using DESeq2, which performs an internal normalization that corrects for library size.
Assembly: hg19
Supplementary files format and content: Text file with normalized reads counts for all samples.
Library strategy: 5hmC-Seal sequencing

value: peripheral plasma


title: Endoderm_H3K27me3_ChIP_Xencode_Group3_2

description: Library name: Endoderm_H3K27me3_ChIP_Xencode_Group3_2


title: Endoderm_H3K36me3_ChIP_Xencode_Group3_2

description: Library name: Endoderm_H3K36me3_ChIP_Xencode_Group3_2


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID IB 6921

description:
cell-free DNA 5hmC
PLCO-258

value: cell-free DNA


title: Endoderm_H3K36me3_ChIP_Xencode_Group3_1

description: Library name: Endoderm_H3K36me3_ChIP_Xencode_Group3_1


title: ms_liver_hfhc_25weeks_rep4_TCR

city: Aurora

first: Matthew

middle: Alan

last: Burchill

state: Colorado

department: Department of Medicine

institute: University of Colorado - Anschutz Medical Campus

description:
T cell receptor sequencing (TCR)
mouse_metadata.tsv.gz

data_processing:
Cellranger 6.0.1 for demultiplexing, barcode processing, and gene counting.
Ambient RNA was removed using DecontX(1.14.2). Cells containing >50% ambient RNA were also removed.
Multiplets were identified and removed with DoubletFinder(2.0.3)
Cells were filtered and retained if they had 500-20,000 UMIs and <5% UMIs from genes encoded by mitocondrial genes
Cells were noramlized, corrected for batch, and projected into latent space using Suerat(4.3.0)
Assembly: mm10
Supplementary files format and content: mouse_metadata.tsv.gz; sample assignments and related metadata, including TCR clonotype, for all filtered cell barcodes
Supplementary files format and content: mouse_cell_barcodes.tsv.gz, mouse_normalized_rna_matrix.mtx, mouse_normalized_rna_features.tsv.gz; Normalized RNA counts matrix and column/row labels
Library strategy: TCR-seq

source_name: liver

extract_protocol:
Livers were perfused, extracted, digested, then put into a single cell suspension and enriched for T cells and live cells using cell isolation kits.
Library construction was preformed per manufacturers instructions with the Chromium Next GEM Single Cell 5' Kit V2 (GEX) or the Chromium Single Cell Mouse TCR Amplification Kit (TCR).  cDNA libraries were sequenced on a NovaSeq6000 at a depth of 50,000 reads / cell for RNA and 4,000 reads / cell for TCRs.

value: liver

value: HFHC diet


title: Endoderm_Input_Xencode_Group3_2

description: Library name: Endoderm_Input_Xencode_Group3_2


title: Endoderm_H3K79me3_ChIP_Xencode_Group3_1

description: Library name: Endoderm_H3K79me3_ChIP_Xencode_Group3_1


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID ID 3683

description:
cell-free DNA 5hmC
PLCO-257

source_name: peripheral plasma


title: Endoderm_H3K27me3_ChIP_Xencode_Group3_1

description: Library name: Endoderm_H3K27me3_ChIP_Xencode_Group3_1


title: ms_liver_hfhc_25weeks_rep2_TCR


title: PLCO Study Subject Plasma, extracted cell-free DNA, NCI-provided PLCO_ID LP 5042

description:
cell-free DNA 5hmC
PLCO-260


title: Endoderm_H3K27ac_ChIP_Xencode_Group3_1

description: Library name: Endoderm_H3K27ac_ChIP_Xencode_Group3_1


title: Endoderm_H3K4me3_ChIP_Xencode_Group3_1

description: Library name: Endoderm_H3K4me3_ChIP_Xencode_Group3_1