title: 83-shCD97-3

city: Kaifeng

first: Xiong

last: Jin

state: Henan

address: Jin Ming Avenue

department: School of Life Sciences & School of Pharmacy

institute: Henan University

data_processing:
Clean data (clean reads) were obtained from raw data (raw reads) of fastq format by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
Paired-end clean reads were aligned to the reference genome (GRCh37 assembly) by using Hisat2 software (v2.1.0).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
For quantification purposes, the relative abundance of the transcript/gene was measured by a normalized method, Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM).
Differential expression analysis of two groups was performed using the DESeq2 R package (v1.16.1).
Assembly: GRCh37
Supplementary files format and content: txt/raw_count and FPKM

source_name: GBM stem cells

growth_protocol: Patient-derived GSCs (528, 83, and CSC2) were maintained in DMEM/F-12 supplemented with B27 (Invitrogen), EGF (10 ng/ml, R&D Systems), and bFGF (5 ng/ml, R&D Systems).

extract_protocol:
RNA was extracted from tissues by using TRIzol reagent kit (Ambion, Invitrogen, USA) according to the reagent protocols.
Sequencing libraries were generated using TruSeq Stranded mRNA LT Sample Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Briefly, 3-4×106 293T cells were plated on 100-mm culture dishes, incubated for 24 h, and then cotransfected with 4.5 μg of lentiviral constructs (pLKO-shCtrl and pLKO-shCD97-3), 3 μg of psPAX2 (Addgene), and 1.5 μg of pMD2.G (Addgene) using 27 μL of Lipofectamine 2000 (Invitrogen). The medium was changed 6 h after transfection, and 48 h after transfection, the medium containing lentivirus was harvested. The viral particles were concentrated and purified using a Lenti-X concentrator (Clontech). The cells were infected with lentivirus in the presence of 6 μg/ml polybrene.

value: Patient-derived GBM stem cells


title: EBNALP_KO_ATAC_Rep1

status: Public on Dec 03 2024

type: SRA

city: Minneapolis

first: Chong

last: Wang

state: MINNESOTA

country: USA

institute: University of Minnesota

library_source: genomic

data_processing:
ATAC-seq and Cut&Run reads were aligned to humen genome (hg19) using Bowtie v2.4.1. ATAC-seq and Cut&Run peaks were called on each replicate samples using MACS v2.2.7.1
RNA-seq reads were aligned to human (hg19) genome using STAR v2.7.3a. featureCounts v1.6.1 was used to calculate gene expression reads counts based on GENCODE v34 annotation.
HiChIP paired-end reads were mapped to human (hg19) genome using HiC-Pro v2.11.4 (default settings with LIGATION_SITE set as GATCGATC for MboI) All valid interaction read pairs were then analyzed with hichipper v0.7.7 for detection of significant long-range interactions.
Assembly: hg19
Supplementary files format and content: ATAC_seq and Cut&Run peaks
Supplementary files format and content: HiChIP long range interactions
Supplementary files format and content: Gene expression files

molecule: genomic DNA

organism: Homo sapiens

source_name: Human naive B cell

growth_protocol: Wild-type or EBNALP mutant EBV virus infectd naïve B cells were rountinly cultured in RPMI1640 supplemented with 10% FCS.

extract_protocol: ATAC-seq library was constructed using kit NEBNext® Ultra™II DNA Library Prep Kit for Illumina Beads

treatment_protocol: Naïve B cells extracted from blood were infected with either wild-type or EBNALP mutant EBV virus

tag: tissue

value: Human naive B cell

tag: cell type

value: B cell

tag: treatment

value: EBNALP mutant EBV virus infection of naïve B cells ATAC-seq replication 1


title: s42001.na.37.0.YPD, rep3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

library_source: transcriptomic

data_processing:
Illumina NovaSeq 6000 using NovaSeq Control Software v1.7.0, RTA v3.4.4. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNASeq analysis was conducted using the nf-core/rnaseq pipeline (version 3.11.1), with STAR for genome alignment and Salmon for transcript quantification. The bioconductor package tximport (version 1.28.0) was used to prepare gene-level summaries.
Assembly: S288c R64-1-1 version 109
Supplementary files format and content: charliew_julietb_081724_IntCt.txt.gz is a tab-delimited text file of integer count data
Supplementary files format and content: charliew_julietb_081724_l2tpm.txt.gz  is a tab-delimited text file of log 2 TPM values with a +1 offset.

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in yeast extract and peptone supplemented with adenine (0.055 mg/mL) and either 2% dextrose (YPD), 2% dextrose and 1M sorbitol (YPD + sorbitol), or 2% dextrose and 0.5M NaCl (YPD + NaCl). All time-course experiments were initiated with cells growing in log phase (0.2 < OD600 < 0.8) in their respective media and diluted to OD600 of 0.2 in equivalent, sterile media. All cultures of cells were maintained in log-phase growth throughout the duration of time-course experiments by diluting the culture with sterile medium. This sterile medium contained 15 ug/mL nocodazole when added to mad1∆ bub2∆ cells. Cell culture was conducted at 30C for mad1∆ bub2∆ cells, 24C for exponentially-growing, haploid cdc24-1 swe1∆ cells. To induce genome duplication in cdc24-1 swe1∆ cells, cells were cultured at 37C, in a shaking water bath.

extract_protocol:
Cells were collected for RNA extraction by centrifugation, resuspension in diethyl pyrocarbonate-treated water, and immediately flash-freezing in liquid nitrogen. Total RNA was extracted from cells using an RNEasy Mini kit (QIAGEN) and the manufacturer’s protocol for RNA extraction from yeast with the following specifications. Cells were mechanically lysed by bead milling, using a FastPrep-24 5G instrument (MP Biomedicals). Samples contained between 0.5 X 106 and 2 X 107 cells, 600 uL of acid-washed glass beads (Sigma-Aldrich) and 600 uL lysis buffer (with -mercaptoethanol), in 2 mL tubes, and were agitated for 2-8 rounds of 60 seconds at 6.5 m/s, with chilling on ice for 5 minutes intervening rounds, until cells were completely lysed. Complete lysis was confirmed by microscopy. The concentration and integrity of the extracted total RNA was determined using a 2100 BioAnalyzer (Agilent).
mRNA was isolated and fragmented using an NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs) and cDNA was synthesized, ligated to adaptors, and PCR- amplified for sequencing using an NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs). Sequencing was conducted on NovaSeq6000 using an S4 flow cell (Illumina).

treatment_protocol: To induce genome duplication in mad1∆ bub2∆ cells, the cells were treated with 15 ug/mL nocodazole (Millipore Sigma) at the initiation of each experiment. Nocodazole was dissolved to a concentration of 10 mg/mL in DMSO (Millipore Sigma). To prevent the effects of cells’ adaptation to the presence of nocodazole, an additional 7.5 ug/mL of nocodazole was added to cultures every 4 hrs. Volume-equivalents of DMSO were added to all exponentially-growing mad1∆ bub2∆ control cultures. To induce genome duplication in cdc24-1 swe1∆ cells, the cells were added to flasks pre-warmed to 37°C in a shaking water bath at the initiation of each experiment, and grown at 37°C for the durations of the experiments. Exponentially-growing cdc24-1 swe1∆ control cultures were maintained at 24°C, in a shaker with air-cooling.

tag: strain

tag: temperature (degrees_c)

tag: time (hours)

tag: genotype

value: CCS

tag: mean dna_content_(arbitrary_units)


title: 528-shCD97-3

country: China


title: CSC2-shCD97-3


title: s42001.na.37.12.YPD, rep1


title: s41994.nocodazole.30.8.YPD, rep1

value: MB

value: nocodazole


title: s41994.nocodazole.30.8.YPD, rep3


title: 83-con


title: s42001.na.37.16.YPD, rep2


title: 528-con


title: s41994.nocodazole.30.8.YPD, rep2


title: SNU-475 Cells vector (Replicate_3)

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: SNU-475 Cells

growth_protocol: SNU-387 and SNU-475 cells were grown in RPMI medium with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition, Huh7 cells were grown in DMEM medium with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Huh7, SNU-387, and SNU-475 Cells used for preparing the total RNA and to perfrom gene expression array.

tag: genotype/variation

value: Vector Expressing cells

tag: sample type

value: Cell line


title: CSC2-con


title: SNU-475 Cells vector (Replicate_1)


title: s41994.nocodazole.30.4.YPD, rep3


title: s41994.nocodazole.30.4.YPD, rep1


title: SNU-475 Cells vector (Replicate_2)


title: s41994.nocodazole.30.4.YPD, rep2


title: s41994.nocodazole.30.16.YPD, rep3


title: SNU-475 Cells b-catenin (Replicate_2)

value: b-catenin Expressing cells


title: s41994.nocodazole.30.16.YPD, rep2


title: SNU-475 Cells b-catenin (Replicate_1)


title: s41994.nocodazole.30.16.YPD, rep1


title: s42001.na.37.0.YPD, rep2


title: SNU-387 Cells vector (Replicate_3)

source_name: SNU-387 Cells


title: SNU-387 Cells vector (Replicate_2)


title: s41994.nocodazole.30.12.YPD, rep3


title: s41994.nocodazole.30.12.YPD, rep2


title: SNU-387 Cells vector (Replicate_1)


title: s41994.nocodazole.30.0.YPD, rep3


title: SNU-387 Cells b-catenin (Replicate_2)


title: SNU-387 Cells b-catenin (Replicate_3)


title: s41994.nocodazole.30.0.YPD, rep2


title: SNU-387 Cells b-catenin (Replicate_1)


title: SNU-475 Cells b-catenin (Replicate_3)


title: s41994.nocodazole.30.0.YPD, rep1


title: Huh7 Cells vector (Replicate_3)

source_name: Huh7 Cells


title: s41994.dmso.30.16.YPD, rep2

value: dmso


title: s41994.dmso.30.16.YPD, rep3


title: Huh7 Cells vector (Replicate_1)


title: Huh7 Cells vector (Replicate_2)


title: s41994.dmso.30.0.YPD, rep2


title: Huh7 Cells b-catenin (Replicate_1)


title: s41994.dmso.30.0.YPD, rep3


title: s41994.dmso.30.0.YPD, rep1


title: Huh7 Cells b-catenin (Replicate_3)


title: Huh7 Cells b-catenin (Replicate_2)


title: s41742.na.37.8.YPD, rep3

value: CS


title: ex vivo Treg, STAT5B

city: Bethesda

first: Peng

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: Library name: Sample19

data_processing:
Sequenced reads were obtained with the Illumina CASAVA pipeline and mapped to the mouse genome mm10 (GRCm38, Dec. 2011) using Bowtie 2.2.6. Only uniquely mapped reads were retained. The mapped outputs were converted to browser-extensible data files using IGVTools 2.4.13 for viewing on the IGV browser. HiChIP data was mapped and processed using HiC-pro and FitHiChIP pipeline.
Assembly: mm10/GRCm38
Supplementary files format and content: Wiggle Track Files (.wig) and browser extensible data paired-end (.bedpe)

organism: Mus musculus

source_name: spleen

growth_protocol: CD4+, CD8+ and Tregs were isolated using StemCell Technologies kits. NK cells were purified from spleens using a Miltenyi kit and expanded in IL-15 (10 ng/ml) for 10 days for use in ChIP-Seq experiments.

extract_protocol:
Cells were harvested and total RNA was extracted using Direct-zol RNA MiniPrep kit (#R2052, Zymo Research) according to the kit’s protocol.
ChIP-Seq and HiChIP: Libraries were prepared using the KAPA HyperPrep kit (Roche) and indexed with Illumina primers. PCR products were bar-coded (indexed) and sequenced using a HiSeq 2500 or NovaSeq6000 (both Illumina)

treatment_protocol: For short-term analysis of NK cells, purified NK cells were incubated with IL-15 (10 ng/ml) without or with IL-12 (10 ng/ml) for 2–4 days. CD8+ T cells were cultured in RPMI-1640 medium containing 10% FBS and stimulated with IL-2 (100 or 1000 U/ml) or anti-CD3/anti-CD28 for 2 days, rested 4 hours, and IL-2 was added for the indicated times. For iTreg cultures, naïve CD4+ T cells were isolated from spleens and cultured with anti-CD3/anti-CD28, TGFβ (2 ng/ml), IL-2 (1000 U/ml), anti-IFNγ (10 μg/ml), and anti-IL-4 (10 μg/ml) for 4 days. DN thymocytes were enriched by depleting total thymus with anti-CD4 and anti-CD8 antibodies (Miltenyi). Enriched DN3 cells were isolated from Rag2 KO mice

value: spleen

value: Treg cells

value: wild-type

value: ex vivo Treg


title: ex vivo DN3, STAT5B

description: Library name: Sample18

source_name: thymus

value: thymus

value: DN3 cells

value: ex vivo DN3


title: s41742.na.37.8.YPD, rep2


title: s41994.nocodazole.30.12.YPD, rep1


title: s41742.na.37.8.YPD, rep1


title: CD8T, pre-activated, IL-2, Med1

description: Library name: Sample17

value: CD8+ T cells

value: pre-activated CD8T, treated with IL-2


title: s41742.na.37.4.YPD, rep2


title: s41742.na.37.4.YPD, rep3


title: s41994.dmso.30.16.YPD, rep1


title: CD8T, pre-activated, Cont, Med1

description: Library name: Sample16

value: pre-activated CD8T, not treated


title: s41742.na.37.16.YPD, rep3


title: s41742.na.37.4.YPD, rep1


title: CD8T, Intron Deletion, CD3+IL2, 24h, H3K27ac

description: Library name: Sample14

value: mutants

value: CD8T, treated with CD3+IL2


title: CD8T, Upstream Deletion, CD3+IL2, 24h, H3K27ac

description: Library name: Sample15


title: s41742.na.37.16.YPD, rep1


title: DN2, IL7, 2h, STAT5B

description: Library name: Sample11

value: DN2 cells

value: DN2, treated with IL-7


title: s41742.na.37.12.YPD, rep3


title: DN2, Cont, H3K27ac

description: Library name: Sample10

value: DN2, not treated


title: DN2, IL7, 2h, H3K27ac

description: Library name: Sample12


title: CD8T, WT, CD3+IL2, 24h, H3K27ac

description: Library name: Sample13


title: s41742.na.37.16.YPD, rep2


title: s41742.na.37.12.YPD, rep2


title: DN2, Cont, STAT5B

description: Library name: Sample9


title: NK, IL15, STAT5B

description: Library name: Sample8

value: NK cells

value: NK cells, treated with IL-2


title: s41742.na.37.12.YPD, rep1

value: CS


title: Mast cells, IgE, STAT5B

description: Library name: Sample6

value: spleen

value: Mast cells

value: Mast cells, treated with IgE


title: s41742.na.37.0.YPD, rep3


title: s41742.na.37.0.YPD, rep2


title: Mast cells, IgE, IgG

description: Library name: Sample5

value: wild-type

value: Mast cells, IgG control


title: s41742.na.37.0.YPD, rep1


title: iTreg, IL2, STAT5B

description: Library name: Sample4

value: iTreg cells

value: iTreg, treated with IL-2


title: s41742.na.25.16.YPD, rep3


title: CD8T, pre-activated, IL-2, STAT5B

description: Library name: Sample2

value: CD8+ T cells

value: pre-activated CD8T, treated with IL-2


title: s41742.na.25.16.YPD, rep1


title: s41742.na.25.0.YPD, rep3


title: s2587.nocodazole.30.8.YPD, rep3

value: WT

value: nocodazole


title: s41742.na.25.0.YPD, rep1


title: s2587.nocodazole.30.8.YPD, rep1


title: NK, Cont, STAT5B

description: Library name: Sample7

value: NK cells, not treated


title: s2587.nocodazole.30.4.YPD, rep1


title: CD8T, pre-activated, Cont, STAT5B

description: Library name: Sample1

value: pre-activated CD8T, not treated


title: s2587.nocodazole.30.16.YPD, rep3


title: s2587.nocodazole.30.4.YPD, rep2


title: LY49CI_pos_NKG2A_neg_KO_8

city: Seattle

first: Delphine

middle: M

last: Depierreux

state: WA

address: 1000 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
Library name: 37
CI_pos_A_neg_KO_8

data_processing:
The quality control of the reads was done using FastQC v0.11.4
Reads were trimmed using TrimGalore v0.5.0.
Reads were mapped using STAR v2.7.1. to the Ensembl Mus_musculus GRCm38 (release 103) reference genome
Differential gene expression analysis was done using the counted reads and the R package edgeR version 3.26.5 (R version 3.6.1).
Correction for GC content and gene length bias was applied using CQN bioconductor package (version 1.30.0).
Assembly: Reads were mapped using STAR [3] v2.7.1. Ensembl Mus_musculus GRCm38 (release 103) reference genome was used to do the mapping of reads, using the annotated transcripts from the ensembl Mus_musculus.GRCm38.103.gtf file.
Supplementary files format and content: tab-delimited text file includes raw count for each sample
Supplementary files format and content: tab-delimited text file includes RPKM for each sample

source_name: Pregnant uterus

growth_protocol: At gestation day 9.5-10.5, mice were culled by cervical dislocation and pregnant uterus were collected in sterile conditions

extract_protocol:
Total RNA was extracted with RNeasy Micro Kit (#74004, Qiagen) according to manufacturer’s protocol.
The SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, USA) was used to generate cDNAs. The Nextera XT DNA Library Prep Kit (Illumina) was used to generate libraries from 125 pg of input cDNA.

treatment_protocol: Organs were enzymatically and mechanically processed into a single suspension, in sterile and RNAse free conditions, as previously described (PMID: 34723937). Three cell populations were collected (Ly49C/I neg_NKG2A neg ; LY49C/I neg_NKG2A pos ; LY49C/I pos_NKG2A neg). Double positive were not collected due to limited sample size.

value: Pregnant uterus

tag: cell line

value: Primary cells

value: uterine Natural Killer

value: NKG2A KO C57BL6


title: LY49CI_pos_NKG2A_neg_KO_7

description:
Library name: 36
CI_pos_A_neg_KO_7


title: s2587.nocodazole.30.8.YPD, rep2


title: LY49CI_pos_NKG2A_neg_KO_4

description:
Library name: 33
CI_pos_A_neg_KO_4


title: s2587.nocodazole.30.4.YPD, rep3


title: s2587.nocodazole.30.12.YPD, rep2


title: s2587.nocodazole.30.12.YPD, rep1


title: LY49CI_pos_NKG2A_neg_B6_6

description:
Library name: 32
CI_pos_A_neg_B6_8


title: s2587.nocodazole.30.16.YPD, rep2


title: MPRA FIRE SM BV2 cDNA Rep1

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

data_processing:
Enhancer - barcode assignment files are processed with a custom script. Enhancers and barcodes are separated with cutadapt.
Raw cDNA and gDNA reads are first processed with a custom script to extract and count each barcode before associating them to the corresponding enhancer based on the enhancer - bc assignment list.
Enhancer activity from MPRA assay is estimated via a custom R script. Enhancers are first filtered based on the number of BCs identified in the sequencing reads. Thresholds of 4 BCs per enhancer are selected based on the complexity of the library and the sequencing saturation of the enhancer - BC assignment samples. For the remaining enhancers, BC counts are aggregated per enhancer and then a count per million (CPM) normalisation is applied. gDNA (input) and cDNA (output) samples are merged by keeping only enhancers remaining in both samples after filtering. Input normalisation is done by dividing CPM normalised cDNA counts by CPM normalised plasmid counts resulting in a FC value.
Assembly: mm10
Supplementary files format and content: FIRE saturation mutagenesis table has 2 columns: Region; LogFC

growth_protocol: BV2 cells were cultured with DMEM + 10% FBS + 0.5% penicillin/streptomycin in an incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from the cell with the innuPREP RNA Mini Kit 2.0 (Analytik Jena) , followed by mRNA isolation using the Dynabeads mRNA purification kit (Ambion). cDNA synthesis was performed with the GoScript RT kit and oligo dT primer (Promega). Genomic DNA was extracted with Blood and Tissue kit from Qiagen.
Plasmid libraries, extracted genomic DNA and cDNA were prepared for sequencing with two rounds of PCR. The first PCR targets the random barcode present within the transcript. The second PCR adds sequencing indexes to the PCR product.
DNA sequencing; targeted RNA-seq


title: s2587.nocodazole.30.16.YPD, rep1


title: LY49CI_pos_NKG2A_neg_B6_5

description:
Library name: 31
CI_pos_A_neg_B6_7


title: iTreg, Cont, STAT5B

description: Library name: Sample3

value: spleen

value: iTreg, not treated


title: s2587.nocodazole.30.0.YPD, rep3


title: s41742.na.25.16.YPD, rep2

value: CS


title: s41742.na.25.0.YPD, rep2


title: s2587.nocodazole.30.0.YPD, rep2


title: LY49CI_pos_NKG2A_neg_B6_4

description:
Library name: 30
CI_pos_A_neg_B6_5


title: LY49CI_pos_NKG2A_neg_B6_3

description:
Library name: 29
CI_pos_A_neg_B6_4


title: s2587.nocodazole.30.0.YPD, rep1


title: LY49CI_pos_NKG2A_neg_B6_2

description:
Library name: 28
CI_pos_A_neg_B6_2


title: LY49CI_pos_NKG2A_neg_KO_5

description:
Library name: 34
CI_pos_A_neg_KO_5


title: Ly49CI_neg_NKG2A_pos_B6_9

description:
Library name: 26
CI_neg_A_pos_B6_9


title: LY49CI_pos_NKG2A_neg_B6_1

description:
Library name: 27
CI_pos_A_neg_B6_1


title: s2587.nocodazole.30.12.YPD, rep3


title: Embryo_Salt_rep2

city: Anderson

first: Renfang

middle: Song

last: Taylor

state: IN

address: 1100 5th Street

department: Biology

institute: Anderson University

data_processing:
Reference genome and gene model annotation files were downloaded from genome website2directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end cleanreads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as themapping tool for that Hisat2 can generate a database of splice junctions based on the genemodel annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.etal. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as wellas an optional de novo assembly step to assemble and quantitate fulllength transcriptsrepresenting multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And thenFPKM of each gene was calculated based on the length of the gene and reads count mappedto this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence perMillions base pairs sequenced, considers the effect of sequencing depth and gene length forthe reads count at the same time, and is currently the most commonly used method forestimating gene expression levels.
(For DESeq2 with biological replicates) Differential expression analysis of two
conditions/groups (two biological replicates per condition) was performed using the DESeq2R package (1.20.0). DESeq2 provide statistical routines for determining differential expressionin digital gene expression data using a model based on the negative binomial distribution. Theresulting P-values were adjusted using the Benjamini and Hochberg’s approach for controllingthe false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 wereassigned as differentially expressed.(For edgeR without biological replicates) Prior to differential gene expression analysis, foreach sequenced library, the read counts were adjusted by edgeR program package through onescaling normalized factor. Differential expression analysis of two conditions was performedusing the edgeR R package (3.22.5). The P values were adjusted using the Benjamini &Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the3threshold for significantly differential expression.
Assembly: GRCz11
Supplementary files format and content: gene_count.txt includes all samples

organism: Danio rerio

source_name: Embryos

growth_protocol: Zebrafish embryos are grown according to the standard protocol

extract_protocol:
RNA was extracted  with ZYMO-RNA kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
Standard Illumina hybridization protocol The data were normalized using quantile normalization with IlluminaGUI in R

treatment_protocol: The samples are treated with Glucose and Salt

value: Embryos

value: High Salt


title: Embryo_Salt_rep1


title: LY49CI_pos_NKG2A_neg_KO_6

description:
Library name: 35
CI_pos_A_neg_KO_6


title: Embryo_Glu_rep3

value: High Glucose


title: Ly49CI_neg_NKG2A_pos_B6_7

description:
Library name: 24
CI_neg_A_pos_B6_7


title: Embryo_Glu_rep1


title: Embryo_Glu_rep2


title: Ly49CI_neg_NKG2A_pos_B6_6

description:
Library name: 23
CI_neg_A_pos_B6_6


title: Ly49CI_neg_NKG2A_pos_B6_5

description:
Library name: 22
CI_neg_A_pos_B6_5


title: Ly49CI_neg_NKG2A_pos_B6_8

description:
Library name: 25
CI_neg_A_pos_B6_8


title: Ly49CI_neg_NKG2A_pos_B6_4

description:
Library name: 21
CI_neg_A_pos_B6_4


title: Embryo_contro_rep3

value: Control


title: Embryo_contro_rep1


title: Ly49CI_neg_NKG2A_pos_B6_3

description:
Library name: 20
CI_neg_A_pos_B6_3


title: Embryo_contro_rep2


title: Ly49CI_neg_NKG2A_pos_B6_2

description:
Library name: 19
CI_neg_A_pos_B6_2


title: Ly49CI_neg_NKG2A_pos_B6_1

description:
Library name: 18
CI_neg_A_pos_B6_1


title: G2M-enriched

city: New York

first: Kenneth

last: Birnbaum

state: NY

address: 12 Waverly Place

department: Biology Department

institute: New York Univerisity

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
For scRNA-seq the mkfastq function in Cell Ranger 5.0.1 was used to generate fastq files from the raw sequencing output.
Count matrices for scRNA-seq experiments were then generated with the count function and the TAIR 10.38 release of the Arabidopsis genome.
After generating count matrices using Cell Ranger, Seurat was used to filter cells based on the number of features detected (more than 2000 and less than 10000), percent mitochondrial reads (less than 5), and total RNA molecules detected (less than 100000).
Libraries were integrated using the sctransform workflow in Seurat.
Assembly: TAIR 10.38
Supplementary files format and content: An R object containing a Seurat object with cells that passed quality control and including all cell annotations.
Supplementary files format and content: Barcode and feature matrix output from cell ranger (barcode.tsv, feature.tsv. And matrix.mtx files).

organism: Arabidopsis thaliana

source_name: Arabidopis Root Protoplasts

growth_protocol: Seedlings were germinated on sterile mesh on MS media and grown vertically for 7 days.

extract_protocol:
Root tips were then protoplasted and single cells were used as input for library preparation with 10X genomics V3.
10X libraries were prepared from protoplasts to generate scRNA-seq libraries using the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10X Genomics) following manufacturer’s instructions.

treatment_protocol: Seedlings were transferred to MS media supplemented with 10 micromolar hydroxyurea for 6 (S phase), 17 (G2M phase), or 22 (G1 phase) hours to enrich for cells in the indicated phase. Phse enrichment was verified by monitoring expression of the cell cycle reporter, PlaCCI.

value: Arabidopis Root Protoplasts

value: 17 hour hydroxyurea synchronization


title: G1-enriched

description: 10x Genomics

value: 22 hour hydroxyurea synchronization


title: Ly49CI_neg_NKG2A_neg_KO_8

description:
Library name: 17
CI_neg_A_neg_KO_8


title: Ly49CI_neg_NKG2A_neg_KO_7

description:
Library name: 16
CI_neg_A_neg_KO_7


title: G2M-1

data_processing:
Reads were trimmed using Trimmomatic version 0.39.
Trimmed reads were mapped to the Arabidopsis TAIR10 genome using HISAT2 version 2.2.1.
Reads mapping to genes were counted with Rsubread (version 1.22.1) featureCounts in single end mode with a minimum overlap of 5 and counting only primary alignments and ignoring duplicates.
Assembly: TAIR 10.38
Supplementary files format and content: Raw counts are provided as a tsv.
Supplementary files format and content: TPM normalized counts are provided as a tsv.

growth_protocol: Seedlings were germinated on MS media and grown vertically for 7 days.

extract_protocol:
Cells were sorted into qiagen buffer RLT supplemented with betamercapto ethanol and then extracted using the qiagen RNeasy micro kit.
cDNA was synthesized using the SMART-Seq v4 full-length transcriptome analysis kit from Takara (product # 634888). The resulting cDNA was used to generate sequencing libraries with the Ovation Ultralow Library System V2 from Tecan (product # 0344).

treatment_protocol: Root tips were protoplasted and then cells were sorted based on ploidy using FACS as a proxy for phase.

value: FACS sorted 4n ploidy


title: S-2

value: FACS sorted between 2n and 4n ploidy


title: Ly49CI_neg_NKG2A_neg_KO_6

description:
Library name: 15
CI_neg_A_neg_KO_6


title: Ly49CI_neg_NKG2A_neg_KO_5

description:
Library name: 14
CI_neg_A_neg_KO_5


title: G1-2

value: FACS sorted 2n ploidy


title: G2M-2


title: S-1


title: Ly49CI_neg_NKG2A_neg_KO_3

description:
Library name: 12
CI_neg_A_neg_KO_3

value: Pregnant uterus


title: Ly49CI_neg_NKG2A_neg_KO_4

description:
Library name: 13
CI_neg_A_neg_KO_4

value: Primary cells


title: 180m ZT rep3

city: Harbin

first: Lu

last: Bai

address: Changjiang Road 600

institute: Northeast Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
Genomic localization analysis of sequence using Bowtie 2.2.3
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were estimation of gene expression level (Trapnell, Cole, et al., 2010)
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: whole seedling

extract_protocol:
Each sample was blotted dry and flash-frozen in liquid nitrogen. Total RNA was extracted with the UNIQ-10 Column Trizol Total RNA Isolation Kit (Sangon, B511321, China). RNA quality was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocals

value: whole seedling

value: 180m ZT rep3

tag: time point


title: Ly49CI_neg_NKG2A_neg_KO_1

description:
Library name: 10
CI_neg_A_neg_KO_1

value: uterine Natural Killer

value: NKG2A KO C57BL6


title: LY49CI_neg_NKG2A_neg_B6_9

description:
Library name: 9
CI_neg_A_neg_B6_9

value: WT


title: Ly49CI_neg_NKG2A_neg_KO_2

description:
Library name: 11
CI_neg_A_neg_KO_2


title: LY49CI_neg_NKG2A_neg_B6_8

description:
Library name: 8
CI_neg_A_neg_B6_8


title: 8M10T-BLOOD

city: Houston

first: Amrit

last: Koirala

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Paired-end reads were trimmed using TrimGalore
Trimmed fastq files were mapped using HISAT2
Features were quantified using featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample

source_name: Blood

extract_protocol:
RNA was isolated using RNeasy (Qiagen) and treated with DNase (Qiagen) as per the manufacturer’s instructions.
Library preparation was conducted using the Illumina TruSeq Stranded Total RNA Protocol

treatment_protocol: C57Bl/6 mice were exposed via maternal consumption of tributyltin (TBT) in drinking water at 0.5 mg/kg body weight per day [3.07 μM] until weaning

value: Blood

tag: Sex

value: male

tag: age

value: 10 months

tag: exposure

value: Tributyltin (TBT)


title: 180m eBL rep3

value: 180m eBL rep3


title: S-enriched

description: 10x Genomics

value: Arabidopis Root Protoplasts

value: 6 hour hydroxyurea synchronization


title: 7M10V-BLOOD

value: Vehicle


title: 180m eBL rep2

value: 180m eBL rep2


title: 7M10T-BLOOD


title: 180m ZT rep1

value: 180m ZT rep1


title: 6M10T-BLOOD


title: LY49CI_neg_NKG2A_neg_B6_6

description:
Library name: 6
CI_neg_A_neg_B6_6

value: Pregnant uterus


title: 5M10V-BLOOD


title: 6M10V-BLOOD


title: 180m eBL rep1

value: 180m eBL rep1


title: 5M10T-BLOOD


title: LY49CI_neg_NKG2A_neg_B6_5

description:
Library name: 5
CI_neg_A_neg_B6_4

value: Primary cells


title: 4M10V-BLOOD


title: 180m GA3 rep3

value: whole seedling

value: 180m GA3 rep3


title: G1-1

value: FACS sorted 2n ploidy


title: 4M10T-BLOOD


title: LY49CI_neg_NKG2A_neg_B6_4

description:
Library name: 4
CI_neg_A_neg_B6_4

value: uterine Natural Killer

value: WT


title: 180m ZT rep2

value: 180m ZT rep2


title: 3M10V-BLOOD

value: Blood

value: male

value: 10 months

tag: liver tumor

value: yes


title: 180m GA3 rep2

value: 180m GA3 rep2


title: LY49CI_neg_NKG2A_neg_B6_3

description:
Library name: 3
CI_neg_A_neg_B6_3


title: LY49CI_neg_NKG2A_neg_B6_7

description:
Library name: 7
CI_neg_A_neg_B6_7


title: 2M10V-BLOOD

value: Vehicle


title: 180m GA3 rep1

value: 180m GA3 rep1


title: 1M10V-BLOOD


title: 2M10T-BLOOD

value: Tributyltin (TBT)


title: LY49CI_neg_NKG2A_neg_B6_2

description:
Library name: 2
CI_neg_A_neg_B6_2

value: Pregnant uterus


title: 1M10T-BLOOD


title: 180m IAA rep3

value: 180m IAA rep3


title: LY49CI_neg_NKG2A_neg_B6_1

description:
Library name: 1
CI_neg_A_neg_B6_1

value: Primary cells


title: Liver_8M3T

source_name: Liver

value: Liver

value: Male

value: 3 weeks

tag: risk group

tag: sequencing batch


title: 180m IAA rep1

tag: tissue

value: whole seedling

value: 180m IAA rep1


title: Liver_6M3T


title: Liver_7M3T


title: 180m IAA rep2

tag: treatment

value: 180m IAA rep2


title: CAR-T

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University of Freiburg Medical Center

description: Library name: T

data_processing:
For image aquisition, intensity extraction and basecalling Illumina NextSeq 550 control software with bcl2fastq
fastq files were aligned useing the cellranger multi workflow within cellranger-7.1.0
Counts tables were processed within Seurat v5 and monocle3
Assembly: mm10-2020-A
Supplementary files format and content: h5 10x, Seurat v5 processed, monocle3 files

molecule: polyA RNA

source_name: Syngeneic brain tumors

growth_protocol: SPF breeding facility

extract_protocol:
Tumor tissues were excised and mechanically dissociated in ice-cold HBSS supplemented with glucose (10 mM) and HEPES (10 mM) and using glass shearing with a 10-ml Potter-Elvehjem pestle and glass-tube homogenizer (Merck). The resulting suspension was passed through a 70-µm cell strainer (BD Biosciences). The cells were incubated with FC blocking (BD Biosciences). Simultaneously, 20 µl of Cell Multiplexing Oligo (CMO) lipid solution (3' CellPlex Kit, 10X Genomics) was added for multiplexing for 20 minutes. Afterwards, cells were washed with flow cytometry buffer and incubated for additional 20 minutes with anti-CD45 or anti-CD45.2 antibodies (Biolegend). Cell sorting was performed on a MoFlo Astrios (Beckman Coulter). A total of 50,000 cells were sorted per sample and analyzed using 10X Genomics 3’ single-cell mRNA sequencing (v3.1 chemistry), resulting in a final yield of approximately 10,000 sequenced cells per reaction.
Library preparation were performed according to the user guide for the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (CG000204 or CG000390) with 3’ Feature Barcoding kit (10X Genomics, USA) for library preparation of multiplexed samples.

treatment_protocol: Female C57BL/6CD45.2 (#SC-C57N-F) mice of 6 to 12 weeks of age were purchased from Janvier Labs. C57BL/6CD45.1 mice were bred in pathogen-free facilities at the University of Zurich (Zurich, Switzerland). For intracranial tumor implantation, GL-261 (2 x 104), GL-261 iRFP720 (4 x 104) or SB-28 (4 x 104) cells were stereotaxically implanted into the right striatum. Mice were observed daily for the development of symptoms. If not indicated otherwise, adoptive cell transfer of mock, CAR or multifunctional CAR immune effector cells was performed as following: 5 Mio cells were intravenously injected via the tail vein on day 5 and 10 after tumor cell implantation; 2 Mio cells were locally injected into the tumor on day 5 and 10 after tumor cell implantation. Blood was collected 12 days after tumor cell implantation and clinical parameters analyzed by the Veterinary Laboratory at University of Zurich using a Roche Cobas c501 analyzer.

value: Syngeneic brain tumors

value: Primary

tag: cell type

value: Sorted CD45+ cells from syngeneic brain tumors

value: wild type

value: CAR-T


title: Liver_4M3T

tag: strain


title: Liver_5M3T


title: 180m GV rep3

value: 180m GV rep3


title: Liver_3M3T


title: CAR-NK

description: Library name: NK

value: CAR-NK


title: 3M10T-BLOOD

value: Blood

value: male

value: 10 months

value: Tributyltin (TBT)


title: Liver_2M3T

value: Liver


title: Liver_1M3T

value: Male


title: 180m GV rep2

value: 180m GV rep2


title: Liver_7M3V

value: 3 weeks

value: Vehicle


title: Liver_6M3V


title: CAR-Macrophage

description: Library name: MF

value: CAR-Macrophage


title: Liver_5M3V


title: LDHA WT3 Untreated BMDMs

first: Gunars

last: Osis

state: Alabama

address: 1720 2nd Avenue South

department: Medicine

data_processing:
Data was processed through the STAR (v2.5) pipeline for alignment using the GRCm38 mouse reference genome.
Individual gene read number counting was conducted by HTseq (v. 0.6) software, generating FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
DESeq2/edgeR was utilized for differential expression calculation and statistical analysis.
Assembly: GRCm38
Supplementary files format and content: csv containing normalized values for read counts for all samples

source_name: Bone Marrow

growth_protocol: Briefly, mouse femurs were flushed and passed through a 40 µm cell strainer (BD Falcon), and red blood cells were lysed in Ammonium-Chloride-Potassium (ACK) buffer. Cells were then centrifuged, plated, and incubated for 7 days in DMEM medium (Corning Cellgro) containing 15% FBS (Atlanta Biologicals), 1x Antibiotic-Antimycotic Solution (Corning), 1x Non-essential amino acids (Corning) and 30 ng/mL MCSF (Miltenyi Biotec).

extract_protocol:
RNA was extracted with a guanidinium-phenol (Trizol) reagent (Invitrogen, Carlsbad, CA, United States). RNA quality was checked using Eukaryote Total RNA Nano assay.
NEB Next Ultra II Directional RNA kit with poly A selection was used.

treatment_protocol: Polarization of cells was performed using recombinant mouse interferon-gamma (IFN-γ) (R&D Systems, Minneapolis, MN) towards M1 state and interleukin 4 (IL-4) (R&D Systems, Minneapolis, MN) towards M2 for 24 hours.

value: Bone Marrow

value: Bone Marrow Derived Macrophages

value: LDHA WT

value: Untreated


title: Liver_3M3V_S16


title: LDHA WT1 Untreated BMDMs

value: Primary


title: Liver_3M3V_S1


title: 180m Control rep2

value: whole seedling

value: 180m Control rep2


title: 180m Control rep1

value: 180m Control rep1


title: Liver_1M3V


title: LDHA KO3 Untreated BMDMs

value: LDHA KO


title: Liver_15M5T

value: 5 months

value: high risk TBT


title: Liver_9M5T

value: Liver

value: Tributyltin (TBT)


title: 30m ZT rep3

value: 30m ZT rep3


title: Liver_2M3V

value: Male

value: 3 weeks


title: LDHA KO2 Untreated BMDMs


title: Liver_4M5T


title: PBS

description: Library name: PBS

value: Syngeneic brain tumors

value: Sorted CD45+ cells from syngeneic brain tumors

value: wild type

value: PBS


title: Liver_16M5T

value: low risk TBT


title: 180m GV rep1

value: 180m GV rep1


title: LDHA KO1 Unreated BMDMs

value: Bone Marrow

value: Primary

value: Bone Marrow Derived Macrophages

value: Untreated


title: 30m ZT rep1

value: whole seedling

value: 30m ZT rep1


title: Liver_7M5T

value: Liver

value: 5 months


title: LDHA WT3 IL4 Treated BMDMs

value: LDHA WT


title: 30m eBL rep3

value: 30m eBL rep3


title: Liver_5M5T

value: Male

value: Tributyltin (TBT)


title: 180m Control rep3

value: 180m Control rep3


title: Liver_6M5T


title: Liver_4M3V

value: 3 weeks

value: Vehicle


title: Liver_3M5T

value: low risk TBT


title: LDHA WT2 IL4 Treated BMDMs


title: Liver_2M5T


title: 30m eBL rep2

value: 30m eBL rep2


title: Liver_9M5V


title: LDHA WT2 Untreated BMDMs

value: Bone Marrow


title: LDHA WT1 IL4 Treated BMDMs

value: Primary


title: Liver_5M5V


title: Liver_6M5V_S61


title: 30m ZT rep2

value: 30m ZT rep2


title: LDHA KO3 IL4 Treated BMDMs

value: Bone Marrow Derived Macrophages

value: LDHA KO


title: LDHA KO2 IL4 Treated BMDMs


title: Liver_3M5V


title: 30m GA3 rep3

value: whole seedling

value: 30m GA3 rep3


title: 30m GA3 rep2

value: 30m GA3 rep2


title: LDHA KO1 IL4 Treated BMDMs


title: Liver_1M5V

value: Liver

value: 5 months


title: Liver_2M5V

value: Male


title: Liver_Tumor_12M10T

value: 10 months

value: Tributyltin (TBT)

value: Tumor


title: Liver_Tumor_11M10T


title: Liver_Tumor_7M10T


title: 30m GA3 rep1

value: 30m GA3 rep1


title: LDHA WT3 IFN Treated BMDMs

value: LDHA WT

value: IFN


title: Liver_Tumor_6M10T


title: 30m IAA rep3

value: 30m IAA rep3


title: Liver_Tumor_5M10T


title: 30m IAA rep2

value: 30m IAA rep2


title: LDHA WT1 IFN Treated BMDMs

value: Bone Marrow

value: Primary


title: LDHA WT2 IFN Treated BMDMs

value: Bone Marrow Derived Macrophages


title: Liver_Tumor_1M10T


title: Liver_Tumor_3M10T


title: 30m IAA rep1

value: whole seedling

value: 30m IAA rep1


title: 30m eBL rep1

value: 30m eBL rep1


title: Liver_4M5V

value: Liver

value: Vehicle


title: Liver_UL_7M10T

value: Male

value: high risk TBT (uninvolved liver)


title: Liver_UL_12M10T

value: 10 months

value: Tributyltin (TBT)


title: 30m GV rep3

value: 30m GV rep3


title: Liver_UL_6M10T


title: Liver_UL_5M10T


title: LDHA KO2 IFN Treated BMDMs

value: LDHA KO


title: LDHA KO3 IFN Treated BMDMs

value: IFN


title: Liver_UL_3M10T


title: 30m GV rep2

value: 30m GV rep2


title: Liver_UL_1M10T


title: LDHA KO1 IFN Treated BMDMs


title: Liver_LR_10M10T

value: low risk TBT


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Control High AAV 02

city: Glasgow

first: Thomas

middle: G

last: Bird

address: Switchback Road, Bearsden

department: CRUK Scotland Institute

country: United Kingdom

institute: Beatson Institute

description: Ctnnb1tm1Mmt (HET), Gt(ROSA)26Sortm1(MYC)Djmy (HOM) + AAV8.TBG.PI.Cre.rBG (2*10^11 GC/mouse)

data_processing:
RNA-Seq paired-end reads were aligned using TopHat2.
Read counts were created using HTSeq
Assembly: GRCm38.75 version of the Mus musculus genome
Supplementary files format and content: comma-delimited text file of raw counts per sample

extract_protocol:
RNA was isolated using a Trizol (Invitrogen) extraction protocol.
Illumina TruSeq stranded mRNA Kit

value: Control high dose


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Control High AAV 03

value: Ctnnb1tm1Mmt (HET), Gt(ROSA)26Sortm1(MYC)Djmy (HOM) + AAV8.TBG.PI.Cre.rBG (2*10^11 GC/mouse)


title: Liver_LR_8M10T


title: Liver_LR_4M10T


title: Liver_LR_9M10T


title: 30m Control rep2

value: 30m Control rep2


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Control High AAV 01


title: 30m Control rep1

value: whole seedling

value: 30m Control rep1


title: Liver_6M10V


title: Liver_5M10V


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Control 03

description: Ctnnb1tm1Mmt (HET), Gt(ROSA)26Sortm1(MYC)Djmy (HOM) + AAV8.TBG.PI.Cre.rBG (6.4*10^8 GC/mouse)

value: Control non-tumour


title: 5m ZT rep3

value: 5m ZT rep3


title: Liver_7M10V

value: Liver

value: Vehicle


title: Liver_4M10V

value: Male


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Control 02

value: Ctnnb1tm1Mmt (HET), Gt(ROSA)26Sortm1(MYC)Djmy (HOM) + AAV8.TBG.PI.Cre.rBG (6.4*10^8 GC/mouse)


title: Liver_LR_2M10T

value: 10 months

value: Tributyltin (TBT)


title: Liver_2M10V


title: Liver_3M10V

value: Vehicle (tumor)


title: Liver_1M10V


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Control 01


title: 74_ST

type: genomic

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Epidemiology

institute: University of Michigan

description: we provide matched samples (within subject) of whole villous tissue or cell types enriched from that tissue; letters correspond to quandrant-based subsampling within the same placenta for a subset of 4 subjects

hyb_protocol: Samples were sent to the University of Michigan Advanced Genomics Core for hybridization to the Infinium MethylationEPIC BeadChip v1.0 array (Illumina, #WG-317-1003), washing, and scanning according to the manufacturer’s instructions.

scan_protocol: According to manufacturer’s instructions for Illumina DNA methylation arrays with the Illumina iScan+.

data_processing:
Data were processed in R statistical software (version 4.2.2). Raw DNA methylation data were preprocessed and managed via the minfi package v1.38.0 and the ewastools package v1.7. We preprocessed raw DNA methylation data with Noob background correction and dye-bias normalization. No samples were flagged for low-intensity values below 10.5 relative fluorescence units or for genotype or sex mismatches. We excluded 1 probe with an average bead count less than 5, 19,760 probes with >5% failure rate for detection p-value >0.01, 23,448 cross-reactive probes (Pidsley et al.), and 17,767 sex-specific probes. Finally, to correct for type I vs. type II probe bias, we also performed Beta MIxture Quantile dilation normalization via the ChAMP package v2.22.0. All downstream DNA methylation analyses used the methylation rate for a given site, also known as beta values.
All downstream DNA methylation analyses used the methylation rate for a given site, also known as beta values based on the methods described in data processing.

label: Cy5 and Cy3

source_name: placenta

label_protocol: DNA was submitted to the University of Michigan Epigenomics Core for quality assessment and bisulfite conversion. DNA quantity was measured with the Qubit High Sensitivity dsDNA assay (ThermoFisher Scientific, #Q32854). DNA quality was assessed with the TapeStation genomic DNA kit (Agilent, #5067-5365). Samples too diluted to be compatible with the kit were first concentrated using AMPure Beads (Beckman Coulter, #A63880) and re-quantified. An aliquot of 250 ng DNA from each sample was bisulfite converted using the EZ DNA Methylation kit (Zymo Research, #D5001) according to manufacturer’s instructions for Illumina DNA methylation arrays.

extract_protocol: To collect whole tissue DNA samples, approximately 15mg of snap-frozen villous tissue was added to 180 μL Buffer ATL (Qiagen, #939011) and 20 μL proteinase K (Qiagen, #19131) to Lysing Matrix D vials (MP Biomedicals, #116913050-CF). Samples were homogenized on the MP-24 FastPrep homogenizer (MP Biomedicals, #116004500) at 6m/s, setting MP24x2 for 35 seconds. The cryogenically stored cell type fractions were quickly thawed at 37 °C for less than five minutes. DNA was extracted from each fraction using the DNeasy Blood and Tissue Kit (Qiagen, #69504, lot #157020715, 1630203096, 563011175) according to manufacturer’s instruction for each magnetically separated sample, the syncytiotrophoblast-enriched sample, and the bulk whole villous tissue sample after homogenization.

value: placenta

value: syncytiotrophoblast

tag: subject

value: M

tag: gestational age

tag: mode of delivery

value: C-section, low transverse

tag: complications


title: 30m GV rep1

value: 30m GV rep1


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Tumour 13

source_name: Liver tumor

value: Liver tumor

tag: genotype

value: Tumour


title: 72_CT

value: cytotrophoblast

value: F


title: 5m ZT rep1

value: whole seedling

value: 5m ZT rep1


title: 5m eBL rep3

value: 5m eBL rep3


title: 30m Control rep3

value: 30m Control rep3


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Tumour 12

value: Ctnnb1tm1Mmt (HET), Gt(ROSA)26Sortm1(MYC)Djmy (HOM) + AAV8.TBG.PI.Cre.rBG (6.4*10^8 GC/mouse)

value: Male


title: 76_VT

value: villous tissue


title: 79_A_ST


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Tumour 11


title: 5m eBL rep2

value: 5m eBL rep2


title: 5m eBL rep1

value: 5m eBL rep1


title: 84_C_CT

value: placenta


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Tumour 10


title: 69_FB

value: fibroblast

value: M


title: 78_C_FB

value: C-section, low transverse


title: 77_C_ST

value: syncytiotrophoblast


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Tumour 09

value: Liver tumor

value: Tumour


title: 5m GA3 rep3

value: 5m GA3 rep3


title: 5m GA3 rep2

value: whole seedling

value: 5m GA3 rep2


title: 79_B_VT


title: 5m ZT rep2

value: 5m ZT rep2


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Tumour 08


title: 72_HB

value: hofbauer

value: F


title: 84_B_CT

value: cytotrophoblast


title: 77_B_VT

value: villous tissue


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Tumour 07

value: Ctnnb1tm1Mmt (HET), Gt(ROSA)26Sortm1(MYC)Djmy (HOM) + AAV8.TBG.PI.Cre.rBG (6.4*10^8 GC/mouse)

value: Male


title: 5m IAA rep3

value: 5m IAA rep3


title: 69_CT

value: placenta


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Tumour 06


title: 76_HB


title: 84_A_VT


title: 5m IAA rep2

value: 5m IAA rep2


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Tumour 05


title: 68_CT

value: C-section, low transverse


title: 5m IAA rep1

value: 5m IAA rep1


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Tumour 04

value: Liver tumor


title: 70_CT


title: 84_A_ST

value: syncytiotrophoblast


title: 77_D_VT


title: 66_VT

value: M


title: 5m GV rep3

value: whole seedling

value: 5m GV rep3


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Tumour 03

value: Tumour


title: 5m GV rep2

value: 5m GV rep2


title: 79_B_FB

value: fibroblast


title: 78_A_VT


title: 78_A_ST


title: 68_VT

value: F


title: 5m GV rep1

value: 5m GV rep1


title: 5m GA3 rep1

value: 5m GA3 rep1


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Tumour 01

value: Ctnnb1tm1Mmt (HET), Gt(ROSA)26Sortm1(MYC)Djmy (HOM) + AAV8.TBG.PI.Cre.rBG (6.4*10^8 GC/mouse)

value: Male


title: Mouse Liver Ctnnb1-tmtMmt, MYC, Tumour 02


title: 5m Control rep3

value: 5m Control rep3


title: 5m Control rep2

value: 5m Control rep2


title: 72_ST

value: placenta

value: C-section, low transverse


title: Liver_22M5T

value: Liver

value: 5 months

value: Tributyltin (TBT)

value: high risk TBT


title: 77_B_FB


title: 65_VT

value: villous tissue


title: 5m Control rep1

value: whole seedling

value: 5m Control rep1


title: Liver_17M5T


title: 74_VT

value: M


title: 73_CT

value: cytotrophoblast

value: F


title: Liver_13M5T


title: 64_HB

value: hofbauer


title: 78_D_ST

value: syncytiotrophoblast


title: Liver_25M5T

value: Male


title: KEPi36_VAL+S.2

city: Bron

first: Yannicke

last: Pijoff

state: Rh^ne-Alpes

address: 18 Avenue du Doyen Lépine

country: France

institute: INSERM

data_processing:
Illumina RTA software used for basecalling.
Demultiplexing was performed using bcl2fastq2 (version 2.18.12) and adapters were trimmed with Cutadapt (version 1.15 and 3.2) so that only reads longer than 10 bp were kept.
Reads were mapped to the rabbit genome (OryCun2_ensembl92) using tophat2.
Count tables were generated using FeatureCounts (version 1.5.0-p2). Each samples was analysed in triplicates (.1 ; .2 ; .3). Three samples were sequenced twice (.1a -and- .1b) and then mapping files were fused.
Assembly: OryCun2_ensembl92
Supplementary files format and content: tab-delimited text files with raw gene counts for every feature and every sample

organism: Oryctolagus cuniculus

source_name: rabbit iPS cells

extract_protocol:
Total RNA was isolated using trizol/chloroform protocol followed by RNeasy mini kit (Qiagen #74106) with a DNase I (Qiagen #79254) treatment. Three nanograms of total RNA were used for amplification using the SMART-Seq V4 Ultra Low Input RNA kit (Clontech) according to the manufacturer’s recommendations (10 PCR cycles were performed). cDNA quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit.
Libraries were prepared from 0.15 ng cDNA using the Nextera XT Illumina library preparation kit. Libraries were pooled in equimolar proportions and sequenced (Paired-end 50–34 bp) on an Illumina NextSeq500 instrument, using a NextSeq 500 High Output 75 cycles kit.

tag: cell line

value: KEPi rabbit iPS cells

value: VALGoX+Shield


title: 78_C_HB

value: placenta


title: 77_B_ST

value: C-section, low transverse


title: 77_B_CT


title: KEPi36_VAL+S.3


title: 84_B_HB


title: Liver_12M5T

value: Liver


title: 78_D_VT


title: 67_VT


title: 76_FB

value: fibroblast


title: Liver_10M5T

value: 5 months

value: Tributyltin (TBT)


title: KEPi36_VAL+S-S.3


title: KEPi36_VAL+S.1


title: 69_VT

value: villous tissue


title: KEPi36_VAL+S-S.2


title: 79_C_CT


title: 84_C_ST


title: Liver_26M5T

value: low risk TBT


title: 64_FB


title: 78_B_VT


title: KEPi36_VAL+S-S.1


title: Liver_24M5T


title: 73_HB


title: 79_B_ST


title: KEPi28_VAL+S.3


title: Liver_21M5T


title: 62_VT


title: 79_C_FB


title: KEPi28_VAL+S.2


title: 79_A_VT


title: Liver_23M5T


title: 77_A_CT


title: KEPi28_VAL+S.1


title: KEPi28_VAL+S-S.3


title: 77_A_ST


title: Liver_1M5T

value: high risk TBT


title: 74_CT

value: M


title: 77_C_VT


title: 72_VT


title: KEPi28_VAL+S-S.2


title: Liver_19M5T


title: Liver_20M5T


title: KEPi28_VAL+S-S.1


title: 78_C_ST


title: 68_HB


title: 79_C_HB


title: KEPi18_VAL+S.3


title: Liver_14M5T


title: KEPi18_VAL+S.2


title: Liver_11M5T


title: 64_VT


title: Liver_8M5T


title: 84_D_ST


title: KEPi18_VAL+S.1


title: 84_A_FB


title: KEPi18_VAL+S-S.3


title: Liver_8M5V

value: Vehicle


title: 76_CT

value: cytotrophoblast

value: F


title: 78_B_HB

value: hofbauer


title: Liver_18M5T

value: Male


title: 78_B_CT


title: KEPi18_VAL+S-S.2

value: KEPi rabbit iPS cells


title: 79_C_VT


title: KEPi18_VAL+S-S.1b


title: 73_ST

value: syncytiotrophoblast


title: 84_A_CT

value: placenta


title: KEPi18_VAL+S-S.1a


title: Liver_Tumor_10mo_repressive_2022_input_2022

data_processing:
Data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore
ChIP-Seq reads were mapped to the mouse genome build UCSC mm10 using bowtie2 and duplicate reads were removed
Peaks were called using MACS2
bigWig files were generated using deeptools v3.5.2
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Chromatin was cross-linked with formaldehyde, the reaction stopped with glycine, and sonicated with a bioruptor to obtain fragment sizes of 100–300 bp for ChIP-seq. ChIP-validated antibodies used were directed against H3K4me3 (Active Motif #39915), H3K4me1 (Abcam ab8895), H3K27ac (Abcam ab4729), H3K27me3 (Active Motif #61017), and H3K9me3 (Active Motif #61013). Immunoprecipitated DNA was recovered and purified using the QIAquick PCR Purification kit (Qiagen)
QIAseq FX DNA library kit or the QIAseq Ultralow Input Library Kit

value: 10 months

value: TBT

tag: ID

tag: batch

tag: chip antibody


title: Liver_UL_10mo_repressive_2022_input_2022

value: Liver

tag: Sex

tag: age

tag: exposure


title: 63_VT

value: C-section, low transverse


title: Liver_Veh_10mo_repressive_2022_input_2022

tag: risk group


title: Liver_LR_10mo_repressive_2022_input_2022

tag: tissue


title: 78_C_VT


title: 73_VT


title: KEPi18_KF.3

value: KF


title: Liver_Tumor_7M10T_27me3_2022

value: Tumor


title: 73_FB

value: fibroblast


title: KEPi18_KF.2


title: 79_B_CT


title: 84_D_VT

value: villous tissue


title: KEPi18_KF.1


title: 70_ST


title: 78_B_FB

value: M


title: Liver_Tumor_5M10T_27me3_2022


title: 84_A_HB


title: 62_CT


title: KEPi13_VAL+S.3

value: VALGoX+Shield


title: 72_FB


title: 78_C_CT

value: cytotrophoblast


title: 70_VT

value: F


title: KEPi13_VAL+S.2


title: Liver_Tumor_3M10T_27me3_2022


title: Liver_Tumor_1M10T_27me3_2022


title: 62_FB


title: 77_A_VT


title: 79_D_VT


title: 64_CT


title: 79_C_ST


title: KEPi13_VAL+S-S.3b


title: Liver_UL_7M10T_27me3_2022

value: high risk TBT (uninvolved liver)


title: 79_B_HB

value: hofbauer


title: KEPi13_VAL+S-S.3a

value: KEPi rabbit iPS cells


title: Liver_UL_6M10T_27me3_2022

value: Male


title: KEPi13_VAL+S.1


title: 61_CT

value: placenta


title: 79_D_ST

value: syncytiotrophoblast


title: Liver_Tumor_6M10T_27me3_2022

value: 10 months

value: TBT


title: 68_FB

value: C-section, low transverse


title: 69_HB


title: KEPi13_VAL+S-S.1b


title: Liver_UL_1M10T_27me3_2022

value: Liver


title: 84_C_VT


title: KEPi13_VAL+S-S.1a


title: 77_D_ST


title: Liver_LR_9M10T_27me3_2022

value: low risk TBT


title: 77_C_CT


title: KEPi13_KF.3

value: KF


title: 84_B_VT

value: villous tissue


title: Liver_LR_8M10T_27me3_2022


title: KEPi13_KF.2


title: Liver_LR_2M10T_27me3_2022


title: KEPi13_KF.1


title: Liver_LR_4M10T_27me3_2022


title: Liver_LR_10M10T_27me3_2022


title: KEPi13_VAL+S-S.2


title: Liver_UL_5M10T_27me3_2022


title: Liver_UL_3M10T_27me3_2022


title: 79_A_CT

value: M


title: B19_VAL_48h.3

value: B19 rabbit iPS cells


title: B19_VAL_48h.2


title: KO3

city: Bunkyo-ku

first: Yu

last: Yamashita

state: Tokyo

address: Yushima 1-5-45

department: Cell Signaling

country: Japan

institute: Institute of Science Tokyo

data_processing:
Data were acquired on an Ion Proton (Thermo Fisher)
The software used for the analysis was CLC Genomics Workbench ver. 9 (CLC).
The reads acquired were aligned to the Mm10 genome assembly.
Filtering parameters were as follows; Mismatch cost, 2; Insertion cost, 3; Deletion cost, 3; Length fraction, 0.8 and Similarity fraction, 0.8.
RPKM value was calculated and regarded as gene expression.
Assembly: Mm10

source_name: osteoblast

extract_protocol: Total RNA was isolated using Sepasol-RNA I Super G (Nacalai Tesque). cDNA was synthesized and amplified using a SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories).

value: osteoblast

value: Fam102a KO

tag: time

value: Day 7


title: B19_VAL_48h.1


title: KO2

tag: cell type


title: B19_VAL_14d.3


title: Liver_Veh_2M10V_27me3_2022

tag: strain

value: Vehicle


title: KO1


title: WT3

value: Wild-type


title: Liver_Veh_1M10V_27me3_2022

value: Male


title: WT2


title: B19_VAL_14d.2


title: B19_VAL_14d.1


title: H3K9me3_WI38_Input

city: Grand Rapids

first: Scott

last: Rothbart

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

description: Library name: WI38_ChIP_H3K9me3_9

data_processing:
ChIP sequencing reads were 3’ trimmed and filtered for quality and adapter content using TrimGalore (v0.6.0) with “trim_galore --quality 25 –fastqc --paried” and the quality was assessed by FastQC (v0.11.8). Reads were aligned to human assembly hg38 with bowtie2 (v2.3.5) using “bowtie2 -I 0 -X 1000 --end-to-end --sensitive” and were deduplicated using removeDups from samblaster (v.0.1.24). SAM files were converted to BAM files, sorted, and indexed using samtools (v1.9). MACS2 and siQ-ChIP were used independently for peak calling and signal normalization. MACS2 peaks were called using “macs2 callpeak -f BAMPE --broad -B” for H3K9me3  ChIP-seq, with Input as the control. For siQ-ChIP normalization, aligned SAM files were then processed for pair-end reads with high mapping quality (MAQ > 20), correct pair orientation (Sam Flags = 99, 163), and fragment length as described for siQ-ChIP (https://github.com/BradleyDickson/siQ-ChIP) using “awk -v MAQ=20 '$5>=MAQ && $2==99 || $5>=MAQ && $2==163 {print $3"\t"$4"\t"$4+$9-1}' sample.sam | awk '$2<=$3 {print $1"\t"$2"\t"$3"\t"$3-$2}' | sort -k1,1 -k2,2n > sample.bed”. Param.in files were prepared for each sample with all required parameters and measurements required for siQ-ChIP normalization. IP tracks (bigwig files) (with H3K9me3 efficiency values) were generated with the execution of “./getsiq.sh > errorfile” with the EXPlayout file (NOTE: params.in and EXPlayout files are provided with the GEO accession).
Assembly: hg38
Supplementary files format and content: bigwig
Supplementary files format and content: broadPeak
Supplementary files format and content: siQ-ChIP EXPlayout
Supplementary files format and content: siQ-ChIP parameters

growth_protocol: WI-38 cells were cultured in Eagle's Minimum Essential Medium(ATCC) supplemented with 10% Fetal Bovine Serum (Millipore Sigma) at 5% CO2 and 37°C. Cells were passaged every 6 days by removal of medium, wash in PBS, dissociation by 1X trypsin, resuspension in medium, and pelleting by centrifugation, followed by resuspension, and plating at a density of approximately 1 million cells/10 cm dish.

extract_protocol:
Chromatin preparation: After the indicated treatments, WI-38 cells were crosslinked with 1% formaldehyde. The chromatin preparation was performed using sonication-based chromatin shearing as follows: About 10 million cells were resuspended in cell lysis buffer and nuclei were isolated and chromatin was fragmented with a Covaris E220 Evolution Focused-Ultrasonicator for 12 min with default settings. IP: 5 ul H3K9me3 antibody (Active Motif,Cat#39161) and 1 ug of soluble chromatin were incubated at 4°C for 18 hours. Samples were immunoprecipitated with 30 ul Dynabeads Protein A magnetic beads (Thermo Fisher Scientific) at 4°C for 2 hours followed by washes. IP chromatin was eluted and the eluted chromatin was subject to reverse crosslink and DNA purification before sequencing.
Libraries for Input and IP samples were prepared by the Van Andel Genomics Core from at least 1 ng of input material and all available IP material using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, end repaired and A-tailed DNA fragments were ligated to uniquely barcoded dual indexes (IDT, Coralville, IA USA). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). 50 bp, paired-end sequencing was performed on an Element AVITI sequencer to a minimum read depth of 50M read pairs per IP library and 100M read pairs per Input library. Base calling was done by Illumina RTA3 and the output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq (v1.9.0).

treatment_protocol: WI-38 cells were introduced with doxycycline (Dox)-inducible shRNA targeting UHRF1 (tet-on shUHRF1). UHRF1 knockdown (KD) was performed by 6-day treatment with 20ng/mL Dox before cell collection. DNMT1 inhibition was performed by 3-day treatment with 1uM GSK862 before cell collection. Equivalent amount of DMSO was added to un-treated cell as DMSO control.

tag: antibody

value: Active Motif,Cat#39161

tag: treatment

value: DMSO


title: Liver_Tumor_7M10T_9me3_2022

value: 10 months

value: Tumor


title: Liver_Veh_5M10V_27me3_2022


title: H3K9me3_WI38_UHRF1 KD+DNMT1i_rep2

description: Library name: WI38_ChIP_H3K9me3_8

value: DNMT1 inhibitor_GSK3484862 + shUHRF1


title: H3K9me3_WI38_UHRF1 KD+DNMT1i_rep1

description: Library name: WI38_ChIP_H3K9me3_7


title: KEPc44_VAL.3

data_processing:
Illumina RTA software used for basecalling.
Demultiplexing was performed using bcl2fastq2 (version 2.18.12) and adapters were trimmed with Cutadapt (version 1.15 and 3.2) so that only reads longer than 10 bp were kept.
Reads were mapped to the rabbit genome (OryCun2_ensembl92) using tophat2.
Count tables were generated using FeatureCounts (version 1.5.0-p2). Each samples was analysed in triplicates (.1 ; .2 ; .3).
Assembly: OryCun2_ensembl92
Supplementary files format and content: tab-delimited text files with raw gene counts for every feature and every sample

value: KEPc rabbit iPS cells

value: VALGoX


title: WT1


title: H3K9me3_WI38_UHRF1 KD_rep2

description: Library name: WI38_ChIP_H3K9me3_6


title: Liver_Tumor_6M10T_9me3_2022

value: Liver

value: TBT


title: Liver_Tumor_5M10T_9me3_2022


title: H3K9me3_WI38_UHRF1 KD_rep1

description: Library name: WI38_ChIP_H3K9me3_5


title: H3K9me3_WI38_DNMT1i_rep2

description: Library name: WI38_ChIP_H3K9me3_4

value: DNMT1 inhibitor_GSK3484862


title: Liver_Tumor_3M10T_9me3_2022


title: H3K9me3_WI38_DNMT1i_rep1

description: Library name: WI38_ChIP_H3K9me3_3


title: KEPc44_KF.3

value: KF


title: Liver_Tumor_1M10T_9me3_2022


title: H3K9me3_WI38_DMSO control_rep1

description: Library name: WI38_ChIP_H3K9me3_1


title: HeLa, MMS-treated, dRNH-IP, YTHDC1 KD, rep2

city: Saint Louis

first: Ning

last: Tsao

state: MO

address: 660 S Euclid Ave

institute: Washington University in St Louis

description: Library name: MapR_dRNH_YTHDC1_KD_MMS_Rep2

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a (for CLIP); Bowtie2 (version 2.4.1) for m1A-DIP and MapR.
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting (for CLIP). Peaks calling of m1A-DIP and MapR data were determined by MACS2 (version 2.1.1) callpeak module with the --keep-dup all option
Assembly: Ensembl GRCh38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format (for CLIP)
Supplementary files format and content: Peak call data of m1A-DIP and MapR shown as .xlsx files

source_name: HeLa

extract_protocol:
For YTHDC1-CLIP, cells were crosslinked by UV and processed with cell lysis and RNase T1 digestion. After immunoprecipitation, the immunocomplexes were digested with protease K and the bound RNAs were purified by using RNA Clean & Concentrator-5 kit (Zymo Research). For m1A-DIP, cells were processed with nuclear extraction and then genomic DNA purification by using DNeasy Blood & Tissue Kit (Qiagen). For MapR, the genomic DNAs were recovered from cell lysates by using MiniElute® PCR purification kit (Qiagene #28004) after digesting with the MNase-conjugated proteins.
NEBNext Ultra DNA library kit (for m1A-DIP)

value: HeLa

value: MMS


title: H3K9me3_WI38_DMSO control_rep2

description: Library name: WI38_ChIP_H3K9me3_2


title: HeLa, MMS-treated, Mnase-IP, YTHDC1 KD, rep2

description: Library name: MapR_Mnase_YTHDC1_KD_MMS_Rep2


title: HeLa, MMS-treated, Mnase-IP, control, rep2

description: Library name: MapR_Mnase_Control_MMS_Rep2


title: KEPc44_VAL.2


title: KEPc44_KF.1


title: HeLa, MMS-treated, dRNH-IP, control, rep2

description: Library name: MapR_dRNH_Control_MMS_Rep2


title: KEPc42_VAL.3


title: KEPc44_VAL.1


title: Liver_UL_5M10T_9me3_2022

value: high risk TBT (uninvolved liver)


title: HeLa, non-treated, dRNH-IP, YTHDC1 KD, rep2

description: Library name: MapR_dRNH_YTHDC1_KD_Rep2


title: Liver_UL_1M10T_9me3_2022


title: HeLa, MMS-treated, dRNH-IP, control, rep1

description: Library name: MapR_dRNH_Control_MMS_Rep1


title: HeLa, MMS-treated, Mnase-IP, YTHDC1 KD, rep1

description: Library name: MapR_Mnase_YTHDC1_KD_MMS_Rep1


title: HeLa, MMS-treated, Mnase-IP, control, rep1

description: Library name: MapR_Mnase_Control_MMS_Rep1


title: HeLa, MMS-treated, dRNH-IP, YTHDC1 KD, rep1

description: Library name: MapR_dRNH_YTHDC1_KD_MMS_Rep1


title: Liver_UL_3M10T_9me3_2022


title: KEPc42_VAL.2


title: KEPc42_VAL.1


title: KEPc44_KF.2


title: Liver_UL_7M10T_9me3_2022


title: HeLa, non-treated, Mnase-IP, YTHDC1 KD, rep2

description: Library name: MapR_Mnase_YTHDC1_KD_Rep2


title: Liver_LR_9M10T_9me3_2022

value: low risk TBT


title: KEPc42_KF.3


title: HeLa, non-treated, dRNH-IP, YTHDC1 KD, rep1

description: Library name: MapR_dRNH_YTHDC1_KD_Rep1


title: HeLa, non-treated, dRNH-IP, control, rep1

description: Library name: MapR_dRNH_Control_Rep1


title: HeLa, non-treated, dRNH-IP, control, rep2

description: Library name: MapR_dRNH_Control_Rep2


title: Liver_LR_4M10T_9me3_2022


title: HeLa, non-treated, Mnase-IP, control, rep1

description: Library name: MapR_Mnase_Control_Rep1


title: Liver_LR_8M10T_9me3_2022


title: HeLa, non-treated, Mnase-IP, control, rep2

description: Library name: MapR_Mnase_Control_Rep2


title: HeLa, MMS-treated, IP, YTHDC1 KD, rep2

description: Library name: m1A_IP_YTHDC1_KD_Rep2


title: HeLa, MMS-treated, IP, control, rep2

description: Library name: m1A_IP_Control_Rep2


title: Liver_LR_2M10T_9me3_2022


title: KEPc42_KF.1


title: KEPc39_VAL.3


title: HeLa, MMS-treated, Input, YTHDC1 KD, rep2

description: Library name: m1A_Input_YTHDC1_KD_Rep2


title: HeLa, non-treated, Mnase-IP, YTHDC1 KD, rep1

description: Library name: MapR_Mnase_YTHDC1_KD_Rep1


title: KEPc42_KF.2


title: Liver_LR_10M10T_9me3_2022


title: KEPc39_VAL.2


title: HeLa, MMS-treated, Input, control, rep2

description: Library name: m1A_Input_Control_Rep2


title: HeLa, MMS-treated, IP, control, rep1

description: Library name: m1A_IP_Control_Rep1


title: KEPc39_VAL.1


title: Ewing sarcoma (ES) tumor of sample B5

city: Santiago de Compostela

first: Angel

last: Diaz-Lagares

state: A Coruña

address: C/ Choupana s/n

department: ONCOMET

country: Spain

institute: Health Research Institute of Santiago (IDIS)

description:
B5-T
Primary tumor originated in athymic mice after injection of A673 ES established cell line in the gastronemious muscle.

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to human Infinium MethylationEPIC BeadChip (Illumina) using standard Infinium HD Methylation Protocol (Illumina).

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner settings

data_processing: RnBeads package in R environment (v4.1.1)

source_name: ES tumor of sample B5

label_protocol: Standard Infinium HD Methylation Protocol from Illumina

extract_protocol: Genomic DNA was extracted using the QIAamp DNA Mini Kit (Qiagen) following the manufacturer’s instructions.

value: tumor (from mice model; injected A673 human cells)

tag: disease state

value: Primary Tumor


title: HeLa, MMS-treated, Input, control, rep1

description: Library name: m1A_Input_Control_Rep1


title: HeLa, MMS-treated, Input, YTHDC1 KD, rep1

description: Library name: m1A_Input_YTHDC1_KD_Rep1


title: Liver_Veh_1M10V_9me3_2022

value: Male

value: Vehicle


title: KEPc39_KF.3


title: Liver_Veh_2M10V_9me3_2022

value: 10 months


title: Ewing sarcoma (ES) metastasis 2 of sample B5

description:
B5-M2
Lung metastasis spontaneously originated in athymic mice after resection of the primary tumor once grown. This primary tumor was generated via injection of A673 ES established cell line in the gastronemious muscle.

source_name: ES metastasis 2 of sample B5

value: metastasis (from mice model; spontaneously originated from A673 tumor in mice)

value: Metastasis


title: Ewing sarcoma (ES) metastasis 3 of sample B5

description:
B5-M3
Lung metastasis spontaneously originated in athymic mice after resection of the primary tumor once grown. This primary tumor was generated via injection of A673 ES established cell line in the gastronemious muscle.

source_name: ES metastasis 3 of sample B5


title: HeLa, MMS-treated, YTHDC1 CLIP, rep1

description: Library name: CLIP_YTHDC1_IP_MMS_Rep1


title: KEPc39_KF.2

value: KEPc rabbit iPS cells


title: HeLa, non-treated, YTHDC1 CLIP, rep2

description: Library name: CLIP_YTHDC1_IP_Control_Rep2


title: Liver_TBT_10mo_4me3_2021_input_2021


title: KEPc39_KF.1


title: Ewing sarcoma (ES) tumor of sample B3

description:
B3-T
Primary tumor originated in athymic mice after injection of A673 ES established cell line in the gastronemious muscle.

source_name: ES tumor of sample B3


title: Liver_Veh_5M10V_9me3_2022


title: Liver_Tumor_6M10T_4me3_2021

value: Tumor


title: Ewing sarcoma (ES) tumor of sample 6

description:
6-T
Primary tumor originated in athymic mice after injection of A673 ES established cell line in the gastronemious muscle.

source_name: ES tumor of sample 6


title: Ewing sarcoma (ES) metastasis 2 of sample B3

description:
B3-M2
Lung metastasis spontaneously originated in athymic mice after resection of the primary tumor once grown. This primary tumor was generated via injection of A673 ES established cell line in the gastronemious muscle.

source_name: ES metastasis 2 of sample B3


title: HeLa, non-treated, YTHDC1 CLIP, rep1

description: Library name: CLIP_YTHDC1_IP_Control_Rep1


title: Ewing sarcoma (ES) metastasis 1 of sample B5

description:
B5-M1
Lung metastasis spontaneously originated in athymic mice after resection of the primary tumor once grown. This primary tumor was generated via injection of A673 ES established cell line in the gastronemious muscle.

source_name: ES metastasis 1 of sample B5


title: HeLa, MMS-treated, Input

description: Library name: CLIP_Input_MMS


title: Ewing sarcoma (ES) metastasis 1 of sample B3

description:
B3-M
Lung metastasis spontaneously originated in athymic mice after resection of the primary tumor once grown. This primary tumor was generated via injection of A673 ES established cell line in the gastronemious muscle.

source_name: ES metastasis 1 of sample B3


title: KEPc37_VAL.3

value: VALGoX


title: KEPc37_VAL.2


title: HeLa, TKO, rep2

city: philadelphia

first: Suresh

last: Joseph

state: PA

address: 1020 Locust street

institute: Thomas Jefferson University

description: Library name: Sample 11

data_processing:
All library construction and data processing was carried out by LC Sciences, Houston, TX
Sequence reads were trimmed for adapter sequences and low quality sequences using Cutadapt.
HISAT2 was used to map reads to the human genome (ftp://ftp.ensemble.org/pub/release-96/fasta/homo-sapiens/dna/)
Mapped reads were assembled using StringTie
Supplementary files format and content: tab-limited text files includes gene counts and FPKM for each sample

growth_protocol: HEK293 and HeLa cells were maintained in 5% FBS and antibiotics in 5% CO2 humidified atmosphere at 37oC

extract_protocol:
RNA was isolated using Direct-zol RNA miniprep kit (Zymo Research, cat R2052)
RNA sequencing library was prepared following Illumina’s Tru-Seq-standard-mRNA sample preparation protocol. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature.

value: cervical cancer

value: TKO

value: untreated


title: HeLa, TKO, rep3

description: Library name: Sample 12

value: HeLa


title: HeLa, wild-type, rep3

description: Library name: Sample 9

value: WT


title: Liver_Tumor_3M10T_4me3_2021

value: Liver

value: TBT


title: HeLa, non-treated, Input

description: Library name: CLIP_Input_Control


title: HeLa, wild-type, rep2

description: Library name: Sample 8


title: KEPc37_VAL.1


title: HeLa, TKO, rep1

description: Library name: Sample 10


title: Liver_Tumor_5M10T_4me3_2021


title: HeLa, wild-type, rep1

description: Library name: Sample 7


title: Liver_Tumor_1M10T_4me3_2021


title: HEK293, TKO, rep3

description: Library name: Sample 6

value: human embryonic kidney


title: KEPc37_KF.3

value: KF


title: Liver_UL_6M10T_4me3_2021

value: Male

value: high risk TBT (uninvolved liver)


title: HEK293, TKO, rep2

description: Library name: Sample 5


title: HEK293, wild-type, rep3

description: Library name: Sample 3


title: HEK293, wild-type, rep2

description: Library name: Sample 2


title: Liver_UL_5M10T_4me3_2021

value: 10 months


title: HEK293, TKO, rep1

description: Library name: Sample 4


title: KEPc37_KF.2


title: KEPc37_KF.1


title: Liver_UL_3M10T_4me3_2021


title: HEK293, wild-type, rep1

description: Library name: Sample 1


title: Liver_UL_1M10T_4me3_2021


title: B19_VAL.3

value: B19 rabbit iPS cells


title: B19_VAL.2


title: Liver_LR_9M10T_4me3_2021

value: low risk TBT


title: B19_VAL.1


title: B19_KF.2


title: B19_KF.3


title: Liver_LR_4M10T_4me3_2021


title: Liver_LR_2M10T_4me3_2021


title: T1R-affected, antigen-stimulated libray 10

city: Montreal

first: Wilian

last: Macedo

state: Quebec

address: 1001 Decarie Blvd

country: Canada

institute: McGill-MUHC

data_processing:
Raw fastq files were quality-checked with FastQC v0.11.8 [13], RSeQC v2.6.1 [14] and processed with cutadapt v2.6 [15] to remove leftover adaptors and low-quality bases (≤ 20 Phred score) allowing for a minimum read size of 50bp.
Sequences were aligned to the human reference genome with STAR v2.7.3a, mapped reads projected to transcriptome coordinate. STAR was used with the parameters: “sjdbOverhang = 74”, “twopassMode = Basic”, “quantTranscriptomeBan = IndelSoftclipSingleend”, “outFilterScoreMinOverLread = 0.80” and “outFilterMatchNminOverLread = 0.80”.
BAM files were input to Salmon v1.4.0 to obtain transcript expression estimates. Salmon parameters were “libType = ISR”, “seqBias”, “gcBias” and “discardOrphans”.
Assembly: GRCh38.p13, ENSEMBL release 102
Supplementary files format and content: Tab-delimited text files with raw estimated counts.
Supplementary files format and content: Tab-delimited text files with estimated counts transformed with tximport’s lengthScaledTPM.
Supplementary files format and content: Tab-delimited text files with estimated counts transformed with tximport’s dtuScaledTPM.

source_name: whole-blood

growth_protocol: Blood samples were obtained and immediately processed for treatment with antigen..

extract_protocol:
Total RNA was extracted using LeukoLOCK leukocytes filters (Ambion) and RNeasy kit (Qiagen), quantified and quality assessed with Agilent 2100 Bioanalyzer (Agilent).
KAPA Stranded mRNA-Seq Kit (Roche, KK8421) and sequenced as 75-bp paired-end reads on Illumina HiSeq 4000 with an expected throughput of 50 million reads per library.

treatment_protocol: Whole blood was divided in two aliquots with one part being stimulated with M. leprae sonicate (20 µg/ml) for approximately 32 hrs or incubated with medium only

value: whole-blood

value: RPMI/HEPES + M. lepraesonicate 20 ug/ml

tag: age at_diag

tag: leprosy class

value: BB/BL

tag: multibacilary

tag: lesion (n)


title: Liver_LR_10M10T_4me3_2021

source_name: Liver

tag: ID

tag: batch


title: Normal Fibroblasts 4 Paricalcitol

city: Crawley

first: Andrew

middle: William

last: Stevenson

state: Western Australia

address: Room 112b, Curnow Building, Hackett Drive Carpark Entrance 2, UWA

department: School of Biomedical Sciences

country: Australia

institute: University of Western Australia

description:
Library name: ST8
ST8

data_processing:
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.7.5 and Real Time Analysis (RTA) v3.4.4, running on the instrument computer. The Illumina DRAGEN BCL Convert 07.021.609.3.9.3 pipeline was used to generate the sequence data. The data generated here meet the AGRF quality standards. 2.20.0.422 pipeline was used to generate the sequence data.
QC of raw reads was performed using FastQC (Version 0.11.3) and reads of poor quality trimmed using fastp software
Raw RNA sequences were aligned to the Human GRCh38.p102 reference genome13 using STAR read aligner (Version 2.7)
BAM files representing the aligned sequences were generated using SAMtools (Version 1.9)
Principal Component Analysis (PCA) and hierarchical clustering methods were performed to explore sample similarity using the rlog transformed raw read counts. Differential gene expression analysis was performed using DESeq2 (Version 1.24.0) on R (Version 3.6.1).
Assembly: Human GRCh38.p102
Supplementary files format and content: csv files with raw abundance counts

source_name: skin

growth_protocol: 3mm punch biopsies were taken from the forearm scar site the attendant physician. Tissue was transported to the lab where it was placed in a petri dish and sliced into three equal sized potions. Pieces of the biopsy were then placed dermis side down in a T-25 (25 cm2) (Greiner Bio-One, Germany) culture flask without any media, and incubated for 1 hours at 37 degrees. They were then cultured in DMEM with 10% FBS and 5% pen/strep until ready for treatment.

extract_protocol:
RNA was prepared using the RNeasy mini kit (Cat. No. 74104, QIAGEN, Netherlands), as per manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Treated samples were cultured in DMEM F12 media +10%FBS and 1% Pen/strep with 3.125 ng/mL paricalcitol added for 48 hours. Untreated were cultured the same way minus the paracalcitol.

value: skin

tag: cell line

value: primary skin cells

value: skin fibroblasts

tag: genotype

value: Paricalcitol


title: Liver_Veh_10mo_4me3_2021_input_2021

tag: Sex

tag: age

tag: exposure

value: Vehicle

tag: chip antibody


title: Normal Fibroblasts 4 Untreated

description:
Library name: ST7
ST7

tag: tissue

tag: cell type

value: WT

value: Untreated


title: HeLa, MMS-treated, IP, YTHDC1 KD, rep1

description: Library name: m1A_IP_YTHDC1_KD_Rep1

value: HeLa

value: MMS


title: T1R-affected, antigen-stimulated libray 9

value: Male

value: BL


title: Normal Fibroblasts 3 Paricalcitol

description:
Library name: ST6
ST6


title: Liver_Veh_5M10V_4me3_2021

value: Liver

tag: strain

value: 10 months

tag: risk group


title: Normal Fibroblasts 3 Untreated

description:
Library name: ST5
ST5

tag: treatment


title: T1R-affected, antigen-stimulated libray 8

tag: age at_diag


title: Normal Fibroblasts 2 Untreated

description:
Library name: ST3
ST3


title: Liver_Veh_2M10V_4me3_2021


title: Normal Fibroblasts 2 Paricalcitol

description:
Library name: ST4
ST4


title: T1R-affected, antigen-stimulated libray 7

tag: leprosy class

value: BB


title: Normal Fibroblasts 1 Paricalcitol

description:
Library name: ST2
ST2


title: Liver_Veh_1M10V_4me3_2021


title: T1R-affected, antigen-stimulated libray 6

value: whole-blood

value: BT

tag: multibacilary


title: B19_KF.1

value: B19 rabbit iPS cells

value: KF


title: Pt 3 Keloid Fibroblasts Paricalcitol

description:
Library name: K6
K6

value: skin

value: primary skin cells


title: Liver_TBT_10mo_4me1_2021_input_2021

value: TBT


title: Liver_Tumor_6M10T_4me1_2021

value: Tumor


title: Normal Fibroblasts 1 Untreated

description:
Library name: ST1
ST1

value: skin fibroblasts

value: WT


title: T1R-affected, antigen-stimulated libray 5

value: RPMI/HEPES + M. lepraesonicate 20 ug/ml

tag: lesion (n)


title: Liver_LR_8M10T_4me3_2021

tag: ID

value: low risk TBT


title: Stroma, replicate 3

city: Chicago

first: Aubrey

last: Converse

state: IL

address: 303 E superior

institute: Northwestern University Feinberg School of Medicine

description: Library name: Str_3_S11

data_processing:
The read quality, in FASTQ format, was evaluated using FastQC
Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt
Trimmed reads were aligned to the Mus musculus genome (mm10) using STAR
Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for mm10 obtained from Ensembl
Assembly: mm10
Supplementary files format and content: Csv file contains unnormalized counts for each sample

source_name: Ovary

extract_protocol:
RNA was isolated using RNeasy Micro Kit (Qiagen). Cell content was used as direct input for cDNA generation and 200ug of cDNA was used as input for library generation.
RNA libraries were prepared with a Illumina Nextera XT DNA library preparation kit following the manufacturer's protocol.

value: Ovary

value: Stroma


title: T1R-affected, antigen-stimulated libray 4

value: Male


title: Stroma, replicate 2

description: Library name: Str_2_S10


title: Pt 3 Keloid Fibroblasts Untreated

description:
Library name: K5
K5

value: Untreated


title: Stroma, replicate 1

description: Library name: Str_1_S9


title: Pt 2 Keloid Fibroblasts Paricalcitol

description:
Library name: K4
K4

value: Paricalcitol


title: Liver_Tumor_3M10T_4me1_2021

value: Liver

value: 10 months

tag: batch


title: Liver_Tumor_5M10T_4me1_2021


title: T1R-affected, antigen-stimulated libray 3

value: whole-blood

value: BB


title: MNGC, replicate 4

description: Library name: MNGC_4_S4

value: Multinucleated giant cell


title: T1R-affected, antigen-stimulated libray 2


title: Pt 2 Keloid Fibroblasts Untreated

description:
Library name: K3
K3

value: skin

tag: cell line

value: primary skin cells


title: Liver_Tumor_1M10T_4me1_2021

value: TBT

value: Tumor


title: Stroma, replicate 4

description: Library name: Str_4_S12

tag: genotype

value: WT


title: T1R-affected, antigen-stimulated libray 1

value: RPMI/HEPES + M. lepraesonicate 20 ug/ml

tag: Sex

value: BT/BB


title: Pt 1 Keloid Fibroblasts Paricalcitol

description:
Library name: K2
K2

value: skin fibroblasts


title: MNGC, replicate 2

description: Library name: MNGC_1_S1

value: Ovary


title: T1R-free, antigen-stimulated libray 22

value: Male


title: Liver_UL_6M10T_4me1_2021

tag: age

value: high risk TBT (uninvolved liver)


title: MNGC, replicate 3

description: Library name: MNGC_3_S3


title: Pt 1 Keloid Fibroblasts Untreated

description:
Library name: K1
K1

value: Untreated


title: Liver_UL_5M10T_4me1_2021

value: Liver

tag: exposure


title: MNGC, replicate 1

description: Library name: MNCG_2_S2


title: HeLa, MMS-treated, YTHDC1 CLIP, rep2

description: Library name: CLIP_YTHDC1_IP_MMS_Rep2

value: HeLa

value: MMS


title: Liver_UL_3M10T_4me1_2021

value: 10 months

tag: chip antibody


title: T1R-free, antigen-stimulated libray 20

value: whole-blood

value: BT


title: T1R-free, antigen-stimulated libray 21


title: Macrophage, replicate 3

description: Library name: Mac_3_S19

tag: tissue

value: priamary macrophage


title: Liver_UL_1M10T_4me1_2021

value: TBT


title: 4006-46S

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

institute: Burnet Institute

data_processing:
Fastq files underwent quality trimming with Skewer v0.2.2 to remove bases from the 3’ ends with Phred quality less than 20.
Reads were the mapped to the human transcriptome (Gencode V37) using Kallisto v0.46.2.
Transcript-level counts were read into R v4.2.1 and were aggregated to the gene level for downstream analysis.
Assembly: Transcriptome Gencode V37
Supplementary files format and content: Gene counts only
Supplementary files format and content: Gene counts in tab separated values format (TSV).

source_name: Synovium

extract_protocol:
Tissues were homogenised using a handheld homogeniser, ~20mg of tissue was homogenised in trizol and total RNA was isolated using RNeasy columns (Qiagen, Hilden, Germany), according to manufacturer’s instructions.
Sequencing libraries were generated from 0.5 µg of total RNA using TruSeq Stranded Total RNA preparation kit (Illumina, San Diego, USA) as per manufacturer’s instructions.
Illumina Stranded Total RNA Prep with Ribo-Zero

value: Synovium

value: F

tag: quickdash


title: 4006-46M

source_name: Muscle

value: Muscle


title: Liver_LR_8M10T_4me1_2021

tag: strain

value: low risk TBT


title: Macrophage, replicate 2

description: Library name: Mac_2_S18

tag: cell type

value: WT


title: 4006-46C

source_name: Capsule

value: Capsule


title: 4006-46F

source_name: Fat

value: Fat


title: Macrophage, replicate 1

description: Library name: Mac_1_S17

value: Ovary


title: T1R-free, antigen-stimulated libray 18

tag: treatment

value: RPMI/HEPES + M. lepraesonicate 20 ug/ml

value: Male

value: BL


title: Liver_LR_2M10T_4me1_2021

value: Liver

tag: risk group


title: T1R-free, antigen-stimulated libray 17

tag: age at_diag

tag: leprosy class

value: BB


title: RKO_DMSO_rep2

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to The Infinium MethylationEPIC v2.0 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged on an Illumina iScan system following the manufacturer’s standard protocol

data_processing: Raw IDAT files for each sample were processed using the Bioconductor package SeSAMe (v1.18.4) for extraction of probe signal intensity values, normalization of probe signal intensity values, and calculation of β-values from the normalized probe signal intensity values.

source_name: RKO cell

label_protocol: Standard Illumina Protocol

growth_protocol: RKO cells were cultured on gelatin-coated dishes in RPMI 1640 medium with L-glutamine (Gibco), supplied with 1X penicillin/streptomycin (Invitrogen), 0.1 mM non-essential amino acids (GIBCO), 1 mM Sodium Pyruvate (GIBCO), and 10% Fetal Bovine Serum (Millipore Sigma) at 5% CO2 and 37°C. Cells were passaged every 2−3 days by removal of medium, wash in PBS, dissociation by 1X trypsin, resuspension in medium, and pelleting by centrifugation, followed by resuspension, and plating at a density of approximately 1 million cells/10 cm dish.

extract_protocol: Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen 69504) following the standard protocol. Samples were then treated with 1 mg/ml RNase A at 37°C for 30 minutes. DNA was re-precipitated with 1/10 volume 3 M sodium acetate pH 4.8 and 2.5 volumes 100% ethanol and stored overnight at -20°C. Precipitated DNA was pelleted by centrifugation at 17,090 x g for 30 minutes at 4°C. The pelleted DNA was washed twice with 70% ethanol, allowed to dry for 15 minutes, and resuspended in nuclease-free water.

treatment_protocol: RKO cells were introduced with doxycycline (Dox)-inducible shRNA targeting UHRF1 (tet-on shUHRF1). UHRF1 knockdown (KD) was performed by 4-day treatment with 20ng/mL Dox before cell collection. DNMT1 inhibition was performed by 2-day treatment with 1uM GSK862 before cell collection. Equivalent amount of DMSO was added to un-treated cell as DMSO control.

value: DMSO control


title: RKO_DMSO_rep1


title: 4006-46B

source_name: Bone

value: Bone


title: T1R-free, antigen-stimulated libray 16

value: whole-blood

tag: multibacilary

tag: lesion (n)


title: 4005-45S


title: Liver_LR_10M10T_4me1_2021

value: 10 months

value: TBT

tag: ID

tag: batch


title: T1R-free, antigen-stimulated libray 15

value: BT


title: Liver_Veh_10mo_4me1_2021_input_2021

value: Vehicle


title: Macrophage, replicate 4

description: Library name: Mac_4_S20

value: priamary macrophage

tag: genotype


title: 4005-45M

value: Muscle

tag: Sex

value: F


title: 4005-45F

value: Fat

tag: age


title: T1R-free, antigen-stimulated libray 19


title: T1R-free, antigen-stimulated libray 14


title: WI-38_DNMT1i_rep1

source_name: WI-38 cell

treatment_protocol: DNMT1 inhibition was performed by 3-day treatment with 1uM GSK862 before cell collection. Equivalent amount of DMSO was added to un-treated cell as DMSO control.

value: 1uM DNMT1 inhibitor GSK3484862


title: WI-38_DNMT1i_rep2


title: WI-38_DMSO_rep2


title: Liver_Veh_5M10V_4me1_2021

tag: exposure


title: Liver_Veh_4M10T_4me1_2021

tag: chip antibody


title: Liver_LR_4M10T_4me1_2021

tag: tissue

value: low risk TBT


title: T1R-free, antigen-stimulated libray 13

value: RPMI/HEPES + M. lepraesonicate 20 ug/ml

value: Male


title: 4005-45C

value: Capsule

tag: quickdash


title: T1R-free, antigen-stimulated libray 12


title: WI-38_DMSO_rep1


title: Liver_Veh_1M10V_4me1_2021

value: Liver

tag: strain


title: T1R-free, antigen-stimulated libray 11

tag: cell type

value: BB


title: Liver_TBT_10mo_27ac_2021_input_2021


title: 4004-44M


title: T1R-free, antigen-stimulated libray 10

tag: treatment

value: BT/BB


title: 4005-45B

value: Bone


title: RKO_UHRF1_KD+DNMT1i_rep2

value: DNMT1 inhibitor + UHRF1 KD


title: RKO_UHRF1_KD+DNMT1i_rep1


title: 4004-44F


title: T1R-free, antigen-stimulated libray 9

value: whole-blood


title: T1R-free, antigen-stimulated libray 8


title: RKO_DNMT1i_rep2


title: 4004-44C


title: RKO_DNMT1i_rep1


title: T1R-free, antigen-stimulated libray 7


title: RKO_UHRF1_KD_rep2

value: Doxycycline UHRF1 KD


title: Liver_UL_6M10T_9me3_2022

value: 10 months

value: TBT

tag: risk group

value: high risk TBT (uninvolved liver)


title: Liver_Tumor_3M10T_27ac_2021

value: Tumor


title: Liver_UL_6M10T_27ac_2021


title: T1R-free, antigen-stimulated libray 6

tag: age at_diag


title: Liver_Tumor_1M10T_27ac_2021


title: 4003-43S

value: Synovium

value: F


title: 4003-43M

value: Muscle


title: T1R-free, antigen-stimulated libray 5

value: RPMI/HEPES + M. lepraesonicate 20 ug/ml

tag: leprosy class


title: Liver_UL_5M10T_27ac_2021

value: Male


title: Liver_Tumor_6M10T_27ac_2021


title: 4004-44S


title: 4003-43C

value: Capsule


title: T1R-free, antigen-stimulated libray 3

tag: multibacilary


title: Liver_Tumor_5M10T_27ac_2021

value: Liver


title: 4003-43F

value: Fat


title: HiChIP H3K27ac, CD8T, WT, Cont

city: Bethesda

first: Peng

last: Li

address: 9000 Rockville Pike

institute: NIH

description: Library name: Sample24

data_processing:
*library strategy: HiChIP-seq
Sequenced reads were obtained with the Illumina CASAVA pipeline and mapped to the mouse genome mm10 (GRCm38, Dec. 2011) using Bowtie 2.2.6. Only uniquely mapped reads were retained. The mapped outputs were converted to browser-extensible data files using IGVTools 2.4.13 for viewing on the IGV browser. HiChIP data was mapped and processed using HiC-pro and FitHiChIP pipeline.
Assembly: mm10/GRCm38
Supplementary files format and content: Wiggle Track Files (.wig) and browser extensible data paired-end (.bedpe)

source_name: spleen

extract_protocol:
Cells were harvested and total RNA was extracted using Direct-zol RNA MiniPrep kit (#R2052, Zymo Research) according to the kit’s protocol.
ChIP-Seq and HiChIP: Libraries were prepared using the KAPA HyperPrep kit (Roche) and indexed with Illumina primers. PCR products were bar-coded (indexed) and sequenced using a HiSeq 2500 or NovaSeq6000 (both Illumina)

value: spleen

value: CD8+ T cells

value: wild-type

value: pre-activated CD8T, not treated


title: HiChIP H3K27ac, CD8T, WT, IL2

description: Library name: Sample25

value: pre-activated CD8T, treated with IL-2


title: T1R-free, antigen-stimulated libray 2

value: whole-blood

value: BB

tag: lesion (n)


title: 4003-43B

value: Bone


title: Liver_UL_1M10T_27ac_2021

value: 10 months

value: TBT

tag: ID

value: high risk TBT (uninvolved liver)


title: 4004-44B

value: F


title: Liver_LR_9M10T_27ac_2021

value: low risk TBT

tag: batch


title: HiChIP H3K27ac, CD8T, Upstream, Cont

description: Library name: Sample22

tag: genotype

value: mutants


title: RKO_UHRF1_KD_rep1

value: Doxycycline UHRF1 KD


title: 4002-42S

value: Synovium

tag: Sex

value: M


title: HiChIP H3K27ac, CD8T, Intron, IL2

description: Library name: Sample21

value: spleen


title: T1R-affected, non-stimulated libray 10

value: RPMI/HEPES

value: Male

value: BB/BL


title: T1R-free, antigen-stimulated libray 1

value: RPMI/HEPES + M. lepraesonicate 20 ug/ml


title: T1R-free, antigen-stimulated libray 4

value: whole-blood

value: BT/BB


title: 4002-42M

value: Muscle

tag: age


title: Liver_LR_4M10T_27ac_2021

value: Liver

value: 10 months

tag: exposure


title: Liver_UL_3M10T_27ac_2021

value: TBT

value: high risk TBT (uninvolved liver)

tag: chip antibody


title: 4002-42F

tag: tissue

value: Fat


title: Liver_LR_2M10T_27ac_2021

value: low risk TBT


title: T1R-affected, non-stimulated libray 8

value: BL


title: 4002-42C

value: Capsule

tag: quickdash


title: Ankrd WT

city: Hangzhou

first: Tianhui

last: Pan

state: Zhejiang

address: jiefang Road 88

institute: Zhejiang University

description: Library name: M_WT

data_processing:
Raw sequencing data were converted to the FASTQ format using Bcl2fastq software
The output CellRanger expression profile matrix was loaded into Seurat (version 4.1.0) for filtering low-quality cells. Cells were projected onto 2D space using tSNE
Hypergeometric testing was used to perform GO and KEGG enrichment analysis on the differential genes
Monocle 2 software was used to model single-cell trajectories and identify branching points, simulating cellular developmental evolution based on gene expression.
Assembly: mm9
Supplementary files format and content: csv files include barcoses  for each Sample
Supplementary files format and content: csv files include  features for each Sample
Supplementary files format and content: mtx files include matrixs for each Sample

source_name: peritoneal F4/80+ cells

extract_protocol:
Single  Cell 3’ v3 Reagent Kit(10× Genomics)
Single  Cell 3’ v3 Reagent Kit(10× Genomics)

treatment_protocol: F4/80+ cells were sorted from the peritoneal lavage fluids of Ankrd22+/+ and Ankrd22-/- mice using FACS for scRNA-Seq.

value: peritoneal F4/80+ cells


title: T1R-affected, non-stimulated libray 7

value: BB


title: KO-CTCF [CUT&Tag]

city: Beijing

first: Ruifeng

address: haidian

institute: Tsinghua University

data_processing:
1) The  CUT&Tag reads were mapped to reference genome by using bowtie2 with the “-p 5 -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant” options, followed by removing low mapped quality reads, mitochondrial reads, duplications. PCR duplicates were removed using picard MarkDuplicates. Macs2 was used for peak calling with the setting of “-f BAM -B --nomodel --keep-dup all”. 2)  CUT&Tag Differential Peak Analysis. The differential peak was analyzed by R package DiffBind73  with the FDR ≤ 0.01 and FC ≥ 1.5. ChIP seeker was used for peak annotation.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: spleens and lymph nodes

extract_protocol:
The CUT&Tag experiments were performed as previously described(Vazyme TD903 kit) to generate DNA libraries derived from cells
The CUT&Tag experiments were performed as previously described(Vazyme TD903 kit) to generate DNA libraries derived from cells.

value: spleens and lymph nodes

value: cd8+ T cell

value: CTCF knockout


title: Liver_LR_10M10T_27ac_2021

city: Houston

first: Amrit

last: Koirala

address: 1 Baylor Plaza

institute: Baylor College of Medicine

tag: strain

value: Male


title: HiChIP H3K27ac, CD8T, Upstream, IL2

state: MD

description: Library name: Sample23

value: spleen

tag: cell type

value: CD8+ T cells

value: mutants

value: pre-activated CD8T, treated with IL-2


title: 4002-42B

value: Bone

value: M


title: Liver_Veh_10mo_27ac_2021_input_2021

value: Liver

value: 10 months

value: Vehicle


title: T1R-affected, non-stimulated libray 6

value: whole-blood

tag: treatment

value: RPMI/HEPES

value: BT


title: 4001-41S

value: Synovium

value: F


title: 4001-41M

value: Muscle


title: Liver_Veh_5M10V_27ac_2021

tag: risk group


title: KO_Igg [CUT&Tag]

value: spleens and lymph nodes

value: cd8+ T cell

value: CTCF knockout