title: hepatocyte-like cell - Day 20_TNF_7.5_TP-8_REP-A [Bas449]

description:
Bas449
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha


title: adult_HSC_mll3ko_h3k4me1.3

status: Public on Feb 18 2021

type: SRA

city: St Louis

first: Jeffery

last: Magee

state: Missouri

address: 660 S Euclid Ave.

department: Internal Medicine - Cardiovascular Division

country: USA

institute: Washington University School of Medicine

description:
Kmt2c f/f; Vav-Cre HSCs
adult_HSC_mll3ko_h3k4me1.fc.signal.bigwig
adult_HSC_mll3ko_h3k4me1.filt.narrowPeak.gz

library_source: genomic

data_processing:
Sequencing reads were demultiplexed and aligned to mouse genome (mm10) by novoalign (versoin 3.04.06)
Signal strength relative to the control samples were generated using MACS2.
Optimal set of peaks were generated using the Kundaje lab AQUAS TF and histone ChIP-seq pipeline (https://github.com/kundajelab/chipseq_pipeline version 0.33)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwig, narrowPeak

molecule: genomic DNA

organism: Mus musculus

source_name: Kmt2c f/f; Vav-Cre HSCs

extract_protocol:
HSCs and HPCs were soted and then fixed for chromatin isolation per Schmidl et l., Nature Methods 10:963.
Chipmentation - Chromatin isolation with the indicated antibody followed by tagmentation with Tn5 as per Schmidl et l., Nature Methods 10:963.

tag: cell type

value: HSCs

tag: chip target

tag: chip antibody

tag: genotype

value: Kmt2c f/f; Vav-Cre HSCs

tag: age

value: 8 weeks old

tag: treatment


title: MLC33398

city: Hangzhou

first: Yang

last: Xia

state: Zhejiang

address: 88 Jiefang Road

department: Department of Respiratory and Critical Care Medicine

country: China

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

molecule: total RNA

organism: Bronchus

source_name: Bronchial epithelial cell

extract_protocol:
Bronchial epithelial cells were obtained via bronchial brushings. RNA was extracted using a protocol of the RNeasy Kit (Qiagen, Hilden, Germany).
RNA libraries were prepared according to the manufacturer’s instructions for the NEB Next® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).

tag: diagnosis

value: Non-cancer

tag: smoking status

value: Current smoker

tag: Sex

value: Male

tag: tissue

value: Bronchial epithelial cell


title: MLC33473

institute: Second Affiliated Hospital of Zhejiang University School

value: Cancer


title: hepatocyte-like cell - Day 20_TNF_5_TP-8_REP-C [Bas443]

city: Leiden

first: Bob

last: van de Water

address: Einsteinweg 55

department: Division of Drug Discovery and Safety

country: Netherlands

institute: Leiden Academic Centre for Drug Research (LACDR), Leiden University

description:
Bas443
Cell lysate
count.txt
count_log2LibSizenorm.txt

data_processing:
Library strategy: TempO-seq
Alignment of reads was done using the TempO-seqR package done by BioSpyder Technologies.
Samples were excluded for further analysis if library size was lower than 100.000 counts.
Raw counts were normalized using the DESeq2 R package (Love et al. 2014).
Normalized counts were log2 transformed.
Genome_build: BioSpyder manifest "Human Tox Panel TempO-Seq Probe Manifest 041416".
Supplementary_files_format_and_content: count.txt: Matrix table with raw counts for every probe and every sample.
Supplementary_files_format_and_content: count_log2LibSizenorm.txt: Matrix table with log2 normalized counts for every probe and every sample.

organism: Homo sapiens

source_name: hepatocyte-like cell - Day 20

extract_protocol:
Cells were washed with PBS and lysed with 1x BNN lysis buffer (provided by BioSpyder) followed by incubation of 15 min at RT. Thereafter plate with cell lysates was sealed and stored at -80 degrees until shipment. Cell lysates were send to BioSpyder for TempO-seq targeted transcriptome analysis.
mRNA in the lysates was hybridized with detector oligo mix, and amplified using barcoded primer pairs to add a unique tag for each of the samples. The detector oligo mix targets a set of genes which were selected based on the S1500+ gene list of NIEHS (Mav et al. 2018). This list contains 2736 genes that provide maximal toxicogenomic information on chemical perturbations that reflect general cellular responses. We supplemented this list with another 245 genes that are involved in hiPSC to hepatocyte differentiation, cellular stress pathways activated in PHH and were missing in the S1500 list. Sample amplicons were pooled and purified. The libraries were sequenced using a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA).

value: Hepatocyte-like cells

tag: compound

tag: concentration

value: 5 ng/mL

tag: time point

value: 8 hr

tag: replicate


title: adult_HSC_mll3ko_h3k4me1.1


title: ip_293_22

city: Uppsala

first: Peter

last: Seiron

address: Rudbecklaboratoriet

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description:
normalized_counts
raw_counts

data_processing:
The raw counts were generated at a separate facility using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit, the Ion 550™ Kit, and the S5 XL (IonS5XL, Thermo Fisher®) instrument with a 550 chip. The primer pool hg19_AmpliSeq_Transcriptome_21K_v1, containing primers for 20,813 amplicons, was used.  The produced reads were aligned to hg19 AmpliSeq Transcriptome ERCC v1. All further analysis was done using the raw counts estimated after mapping. Raw sequence data is not available.
Normalization of the raw count data was performed using the edgeR workflow(calcNormFactors and cpm(, method="TMM", log=FALSE) after filtering out lowly expressed genes with the filterByExpr command using default settings.
Raw counts from 5 samples (#31-35) were used from a previously uploaded project collected in a similar fashion. All samples were normalized together and corrected for batch effect.
ip_293_25 was excluded due to not passing QC analysis after sequencing. Ip_293_24 was excluded as an outlier after visual inspection of a principal component analysis.
Genome_build: hg19 AmpliSeq Transcriptome ERCC v1
Supplementary_files_format_and_content: Raw_counts.xlsx, normalized_counts.xlsx

source_name: human pancreatic islet tissue

extract_protocol:
Pancreases from heart-beating organ donors were used. Biopsies were immediately snap-frozen in liquid nitrogen and subsequently stored at -80 °C. The frozen biopsies  were sectione, thawed and dehydrated. Laser Capture Microdissection (LCM) was used to extract islets, >20 islet sections per sample. Samples were subsequently incubated in 20 µl of RLT Plus buffer with 1% beta-Mercaptoethanol in a heating block, lysing the tissue. total RNA was extracted with the RNeasy Plus Micro kit.
Libraries were constructed using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit. total RNA seq was then done using the Ion 550™ Kit, and the S5 XL (IonS5XL, Thermo Fisher®) instrument with a 550 chip. The primer pool hg19_AmpliSeq_Transcriptome_21K_v1, containing primers for 20,813 amplicons, was used.

value: Islet tissue

tag: gender

value: M


title: hepatocyte-like cell - Day 20_TNF_5_TP-8_REP-B [Bas442]

description:
Bas442
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: adult_HSC_mll3ko_h3k4me1.2


title: ip_293_21

description:
normalized_counts
raw_counts


title: MLC33373

value: Former smoker


title: adult_HSC_mll3het_h3k4me1.3

description:
Kmt2c f/+; Vav-Cre HSCs
adult_HSC_mll3het_h3k4me1.fc.signal.bigwig
adult_HSC_mll3het_h3k4me1.filt.narrowPeak.gz

source_name: Kmt2c f/+; Vav-Cre HSCs

value: Kmt2c f/+; Vav-Cre HSCs


title: MLC33298

value: Non-smoker

value: Female


title: ip_293_20

description:
normalized_counts
raw_counts


title: hepatocyte-like cell - Day 20_TNF_5_TP-8_REP-A [Bas441]

description:
Bas441
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha


title: hepatocyte-like cell - Day 20_TNF_7.5_TP-8_REP-C [Bas451]

description:
Bas451
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 7.5 ng/mL


title: adult_HSC_mll3het_h3k4me1.2

value: HSCs

value: 8 weeks old


title: MLC33273

value: Non-cancer


title: ip_293_19

description:
normalized_counts
raw_counts

value: F


title: hepatocyte-like cell - Day 20_TNF_2.5_TP-8_REP-C [Bas435]

description:
Bas435
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 2.5 ng/mL


title: adult_HSC_mll3het_h3k4me1.1


title: MLC33198

value: Cancer

value: Male

value: Bronchial epithelial cell


title: ip_293_17

description:
normalized_counts
raw_counts


title: hepatocyte-like cell - Day 20_TNF_2.5_TP-8_REP-B [Bas434]

description:
Bas434
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatocyte-like cells

value: 8 hr


title: adult_HPC_wt_h3k4me1.3

description:
wild type HPCs
adult_HPC_wt_h3k4me1.fc.signal.bigwig
adult_HPC_wt_h3k4me1.filt.narrowPeak.gz

source_name: wild type HPCs

value: HPCs

value: wild type HPCs


title: ip_293_16

description:
normalized_counts
raw_counts

value: Islet tissue


title: hepatocyte-like cell - Day 20_TNF_2.5_TP-8_REP-A [Bas433]

description:
Bas433
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: adult_HPC_wt_h3k4me1.2


title: adult_HPC_wt_h3k4me1.1


title: ip_293_15

description:
normalized_counts
raw_counts

value: M


title: hepatocyte-like cell - Day 20_TNF_1_TP-8_REP-B [Bas426]

description:
Bas426
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 ng/mL


title: hepatocyte-like cell - Day 20_TNF_1_TP-8_REP-C [Bas427]

description:
Bas427
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha


title: ip_293_14

description:
normalized_counts
raw_counts


title: MLC33073

value: Non-smoker

value: Female


title: adult_HPC_mll3ko_h3k4me1.3

description:
Kmt2c f/f; Vav-Cre HPCs
adult_HPC_mll3ko_h3k4me1.fc.signal.bigwig
adult_HPC_mll3ko_h3k4me1.filt.narrowPeak.gz

source_name: Kmt2c f/f; Vav-Cre HPCs

value: Kmt2c f/f; Vav-Cre HPCs

value: 8 weeks old


title: MLC30774

value: Non-cancer


title: MLC33098

value: Former smoker


title: hepatocyte-like cell - Day 20_TNF_1_TP-8_REP-A [Bas425]

description:
Bas425
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC30746

value: Cancer


title: adult_HPC_mll3ko_h3k4me1.2


title: hepatocyte-like cell - Day 20_MEDIUM_0_TP-8_REP-C [Bas462]

description:
Bas462
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: MEDIUM


title: ip_293_13

description:
normalized_counts
raw_counts


title: ip_293_18

description:
normalized_counts
raw_counts


title: ip_293_12

description:
normalized_counts
raw_counts

value: F


title: adult_HPC_mll3ko_h3k4me1.1


title: ip_293_11

description:
normalized_counts
raw_counts


title: hepatocyte-like cell - Day 20_MEDIUM_0_TP-8_REP-C [Bas416]

description:
Bas416
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatocyte-like cells


title: MLC30674

value: Current smoker

value: Male

value: Bronchial epithelial cell


title: adult_HPC_mll3het_h3k4me1.3

description:
Kmt2c f/+; Vav-Cre HPCs
adult_HPC_mll3het_h3k4me1.fc.signal.bigwig
adult_HPC_mll3het_h3k4me1.filt.narrowPeak.gz

source_name: Kmt2c f/+; Vav-Cre HPCs

value: HPCs

value: Kmt2c f/+; Vav-Cre HPCs


title: MLC33173

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.


title: hepatocyte-like cell - Day 20_MEDIUM_0_TP-8_REP-B [Bas455]

description:
Bas455
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: adult_HPC_mll3het_h3k4me1.2


title: ip_293_9

description:
normalized_counts
raw_counts

value: Islet tissue

value: M


title: hepatocyte-like cell - Day 20_MEDIUM_0_TP-8_REP-B [Bas408]

description:
Bas408
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC30646


title: MLC30546

value: Non-smoker

value: Female


title: adult_HPC_mll3het_h3k4me1.1

value: 8 weeks old


title: ip_293_10

description:
normalized_counts
raw_counts


title: hepatocyte-like cell - Day 20_MEDIUM_0_TP-8_REP-A [Bas448]

description:
Bas448
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ip_293_8

description:
normalized_counts
raw_counts


title: MLC30374


title: hepatocyte-like cell - Day 20_MEDIUM_0_TP-8_REP-A [Bas400]

description:
Bas400
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: ip_293_7

description:
normalized_counts
raw_counts


title: MLC30474


title: MLC30346

value: Non-cancer


title: adult_HSC_wt.1

description:
adult_HSC_wt.fc.signal.bigwig
adult_HSC_wt.filt.narrowPeak.gz

data_processing:
Sequencing reads were demultiplexed and aligned to mouse genome (mm10) by bowtie2 (versoin 2.2.6)
Signal strength relative to the control samples were generated using MACS2.
Optimal set of peaks were generated using the Kundaje lab ATAC-seq and DNase-seq processing pipeline (https://github.com/kundajelab/atac_dnase_pipelines, version 0.33)
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: bigwig, narrowPeak

source_name: wild type HSCs

extract_protocol:
per Corces et al., Nature Methods 14:959
tagmentation with Tn5 transposase

value: HSCs

tag: treament

value: wild type HSCs


title: hepatocyte-like cell - Day 20_DMSO_0_TP-8_REP-C [Bas440]

description:
Bas440
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: DMSO


title: adult_HSC_mll3ko.2

description:
adult_HSC_mll3ko.fc.signal.bigwig
adult_HSC_mll3ko.filt.narrowPeak.gz

value: Kmt2c -/- HSCs


title: ip_293_6

description:
normalized_counts
raw_counts

value: F


title: ip_293_5

description:
normalized_counts
raw_counts


title: hepatocyte-like cell - Day 20_DMSO_0_TP-8_REP-C [Bas392]

description:
Bas392
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatocyte-like cells


title: adult_HSC_mll3ko.1


title: ip_293_4

description:
normalized_counts
raw_counts


title: hepatocyte-like cell - Day 20_DMSO_0_TP-8_REP-B [Bas432]

description:
Bas432
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: adult_HPC_wt.4

description:
adult_HPC_wt.fc.signal.bigwig
adult_HPC_wt.filt.narrowPeak.gz

value: wild type HPCs


title: hepatocyte-like cell - Day 20_DMSO_0_TP-8_REP-B [Bas384]

description:
Bas384
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC30074

value: Male

value: Bronchial epithelial cell


title: MLC30146

value: Current smoker


title: adult_HPC_wt.3

value: HPCs


title: hepatocyte-like cell - Day 20_DMSO_0_TP-8_REP-A [Bas424]

description:
Bas424
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: adult_HPC_wt.2


title: adult_HSC_wt.2


title: MLC29830


title: ip_293_1

description:
normalized_counts
raw_counts

value: Islet tissue

value: M


title: hepatocyte-like cell - Day 20_DMSO_0_TP-8_REP-A [Bas376]

description:
Bas376
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: adult_HPC_wt.1


title: hepatocyte-like cell - Day 20_DEM_3300_TP-8_REP-B [Bas414]

description:
Bas414
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: MLC30174

value: Non-smoker

value: Female


title: Trophozoites exposed to H202 replicate 2

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

description:
T2-OS
total RNA

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.1.  Only sequences at least 25 nt in length were considered for further analysis
Bowtie version 1.2.2, with default parameters, was used for alignment on the reference genome
Genes were counted using featureCounts version 1.4.6-p3 from the Subreads package (parameters: -t gene -g ID -s 1).
Count data were then analysed using R version 3.5.3 and the Bioconductor package DESeq2 version 1.22.2. Normalization and dispersion estimation were performed with DESeq2 (using the default parameters)and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model including (i) the effect of stress (+OS vs -OS), (ii) the presence of queuine (Qvs. T) and (iii) the interaction term was set up in order to test for inter-condition differences in expression and to test the interaction between stress and queuine. For each pairwise comparison,raw p-values were adjusted for multiple testing using the Benjamini and Hochberg procedure. Genes with an adjusted p-value below 0.05 were considered to be differentially expressed.
Genome_build: Entamoeba histolytica, from amoebaDB1,2
Supplementary_files_format_and_content: Normalized counts from DESeq2

organism: Entamoeba histolytica

source_name: Ankri-lab

growth_protocol: E.histolytica trophozoites HM-1:IMSS strain were grown under axenic condition at 37°C in Trypticase YeastExtract Iron Serum(TYI-S-33) medium prepared according to a previously reported protocol. The trophozoites were harvested during the logarithmic phase of growth by chilling the culture tubes at 4°Cand pelleted by centrifugation at 500 g for five minutes. The pellet was washed twice with ice-cold phosphate-buffered saline.Trophozoites were grown with 0.1 μM queuine for 3 days at 37°C.

extract_protocol:
Total RNA was extracted from control trophozoites, trophozoites pre-incubated with LB or KB and then exposed (or not) to H2O2(in three biological replicates) using the TRI reagent kit, according to the manufacturer’s instructions (Sigma-Aldrich). Libraries were built using a Truseq mRNA-Seq Library Preparation Kit (Illumina), according to the manufacturer’s recommendations. Quality control was performed on an Agilent Bioanalyzer. Sequencing was performed on a HiSeq 2500 system (Illumina) and produced 65-base single-end reads
Libraries were constructed using Truseq mRNA-Seq Library Preparation Kit (Illumina) following manufacturer’s recommendations and were quality controlled using Agilent Bioanalyzer.  Sequencing was performed on a HiSeq 2500 (Illumina) to obtain 65 base single-end reads.

tag: culture

value: grown in standard TYI-S-33 medium for 3 days

tag: oxydative stress

value: exposed to 2.5mM H202 for 30 minutes at 37°C


title: MLC29730

value: Cancer


title: MLC29630

value: Non-cancer


title: adult_HPC_mll3ko.2

description:
adult_HPC_mll3ko.fc.signal.bigwig
adult_HPC_mll3ko.filt.narrowPeak.gz

tag: cell type

value: 8 weeks old

value: Kmt2c -/- HPCs


title: Trophozoites exposed to H202 replicate 1

description:
T1-OS
total RNA


title: hepatocyte-like cell - Day 20_DEM_3300_TP-8_REP-A [Bas413]

description:
Bas413
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatocyte-like cells


title: adult_HPC_mll3ko.1


title: Trophozoites grown in standard TYI-S-33 medium replicate 3

description:
T3
total RNA

value: no


title: ip_293_3

description:
normalized_counts
raw_counts

value: F


title: MLC29430

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

value: Current smoker

value: Male

value: Bronchial epithelial cell


title: hepatocyte-like cell - Day 20_DEM_1000_TP-8_REP-C [Bas407]

description:
Bas407
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: MLC29530


title: Trophozoites grown in standard TYI-S-33 medium replicate 2

description:
T2
total RNA


title: Ins2td-Irx3/5dHet pooled

city: Toronto

first: Chi-chung

last: Hui

state: ON

address: 686 Bay street

country: Canada

institute: The Hospital for Sick Children

data_processing:
Illumina HiSeq 2500 used for base calling.
CellRanger mkfastq was used to convert files from bcl to fastq format.
CelRanger count was used to align reads to the mm10 mouse reference genome and generate feature-barcode matrices for downstream analysis. Default parameters were used and the expected number of recovered cells was set to 8000 and 7980 for Ins2td-Ctrl and Ins2td-Irx3/5dHet samples, respectively.
Genome_build: mm10
Supplementary_files_format_and_content: Feature-barcode matrices generated by the CellRanger analysis pipeline. Each element in the matrix is the number of UMIs associated with a feature and barcode.
Supplementary_files_format_and_content: Features (genes) are row indices. For each feature, gene ID and name are stored in the first and second column of the feature.tsv.gz file.
Supplementary_files_format_and_content: Barcode sequences are column indices. Contains only detected barcodes.

source_name: Arcuate nucleus-median eminence of the hypothalamus

extract_protocol:
Ins2-Cre;Ai14 tdTomato mice were dissected at P10 for tdTomato+ cell sorting. Hypothalami were rapidly extracted. Pooled hypothalamus samples from 5-6 mice were digested by papain solution (Worthington Biochemical) with DNase in Hybernate A media for 30 minutes at 37 °C with gentle agitation. Digestion was stopped by dilution with Hybernate A containing B27 (Thermo), Glutamax (Thermo) and 0.5% Trehalose (Sigma-Aldrich), then gently triturated using a series of three Pasteur pipettes with tips fire-polished to incrementally smaller openings. Cell suspension was centrifuged at 300g for 5 min, resuspended in Hank’s balanced salt solution (HBSS) with 0.5% BSA and 0.5% Trehalose. Sytox blue (Thermo, 1:1000) was added to the cell suspension, and cells were filtered a second time through a 70-mm cell strainer. Viable (Sytox blue-negative) tdTomato+ cells were subsequently sorted using a MoFlo Astrios (Beckman Coulter) cell sorter. Following cell sorting, cells were adjusted to a final concentration of 140,000 cells/mL. scRNA-Seq was then carried out at the The Centre for Applied Genomics (Toronto, ON) using 10x Genomics Chromium platform according to the manufacturer’s protocol.
For each genotype, approximately 5,000 cells were loaded onto the Chromiun Controller and partioned into GEMs (gel beads in emulsion) on Chromium Chip B. Full length cDNA synthesis, amplification and subsequent library construction were performed using the Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3 (part 1000075). cDNAs and their corresponding 10X libraries were evaluated using the Agilent 2100 Bioanalyzer system and quantified using the the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). The 10X libraries were sequenced on the Illumina HiSeq 2500 in High Output run mode using HiSeq SBS v4 chemistry with paired-end sequencing, single indexing and 29+8+101 cycles.

tag: strain

value: tdTomato+ FACS sorted cells of arcuate nucleus-median eminence

value: Postnatal day 10

tag: number of aminals pooled


title: MLC29930


title: ip_293_2

description:
normalized_counts
raw_counts

value: Islet tissue

tag: age

value: M


title: Ins2td-Ctrl pooled

tag: genotype


title: Trophozoites grown in standard TYI-S-33 medium replicate 1

description:
T1
total RNA

value: grown in standard TYI-S-33 medium for 3 days


title: hepatocyte-like cell - Day 20_DEM_1000_TP-8_REP-B [Bas406]

description:
Bas406
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: Pg OCP-2

city: Birmingham

first: Ping

last: Zhang

state: Alabama

address: 1919 7th Ave S

department: Pediatric Dentistry

institute: University of Alabama at Birmingham

data_processing:
Genewiz took the sequenced reads and trimmed to remove possible adapter sequences and nucleotides with poor quality bases (MQ<30) at the ends.
Then the trimmed sequence reads were mapped to the Mus musculsus genome(GRCm38/mm10) with CLC Genomics Server program.
Gene hit counts were measured and RPKM values were calculated.
Differential gene expression analyses were performed using DESeq2 to identify genes differentially expressed between Ctrl and Pg SPL OCP .
Gene Set Enrichment Analysis (GSEA) was performed according to the instructions from the Broad Institute.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts of each genes for each samples

source_name: SPL CD11b+c-fms+Ly6Chi OCP

extract_protocol:
Total RNA was extracted using a miRNeasy Mini kit (QIAGEN)
RNA was sent to Genewiz for their standard library construction

treatment_protocol: SPL CD11b+c-fms+Ly6Chi OCP were flow sorted

value: wild type

tag: agent

value: Porphyromonas gingivalis

value: SPL CD11b+c-fms+Ly6Chi OCP


title: hepatocyte-like cell - Day 20_DEM_1000_TP-8_REP-A [Bas405]

description:
Bas405
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Queuine-treated trophozoites exposed H202 replicate 3

description:
Q-OS3
total RNA

value: grown with 0.1µM queuine for 3 days

value: exposed to 2.5mM H202 for 30 minutes at 37°C


title: hepatocyte-like cell - Day 20_DEM_3300_TP-8_REP-C [Bas415]

description:
Bas415
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatocyte-like cells


title: MLC29230

tag: diagnosis

value: Cancer

tag: smoking status

value: Non-smoker

value: Female


title: MLC29030

value: Current smoker

tag: Sex

value: Male

tag: tissue

value: Bronchial epithelial cell


title: Pg OCP-1


title: hepatocyte-like cell - Day 20_DEM_333_TP-8_REP-C [Bas399]

description:
Bas399
Cell lysate
count.txt
count_log2LibSizenorm.txt

tag: compound

tag: concentration

value: 8 hr


title: Ctrl OCP-2

value: Ctrl


title: MLC28977


title: Queuine-treated trophozoites exposed H202 replicate 1

description:
Q-OS1
total RNA


title: MLC28975

value: Non-cancer


title: Queuine-treated trophozoites exposed H202 replicate 2

description:
Q-OS2
total RNA


title: Hypo3_scRNA

city: Cincinnati

first: Yin Yeng

last: Lee

state: Ohio

address: 3333 Burnet Avenue

department: Department of Pediatrics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Raw bcl output were demultiplexed and aligned to genome reference using cellRanger v2.1.1. Technical replicates (e.g. Ctrl_1_1 and Ctrl 1_2) are merged during cellranger count to generate single gene count matrix.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: barcode.tsv, genes.tsv, matrix.mtx for each samples

source_name: whole lung

extract_protocol:
Lung cells are dissociated and loaded to the 10X chromium platform
Library were constructed using Single Cell 3' Reagent Kit (v2 Chemistry). For each experiment, library from control and hypoxia are pooled and loaded into two seperate Rapid v2 flow cell and sequenced twice (technical replicates).

value: 8-10 weeks

value: whole lung


title: Trophozoites grown with queuine replicate 3

description:
Q3
total RNA

value: no


title: Hypo2_scRNA


title: Trophozoites grown with queuine replicate 2

description:
Q2
total RNA


title: MLC29330


title: hepatocyte-like cell - Day 20_DEM_333_TP-8_REP-A [Bas397]

description:
Bas397
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)

tag: time point

tag: replicate


title: MLC28809


title: MLC28877

value: Former smoker


title: hepatocyte-like cell - Day 20_DEM_100_TP-8_REP-B [Bas390]

description:
Bas390
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Hypo1_scRNA


title: hepatocyte-like cell - Day 20_DEM_100_TP-8_REP-A [Bas389]

description:
Bas389
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC28875


title: Trophozoites grown with queuine replicate 1

description:
Q1
total RNA

value: grown with 0.1µM queuine for 3 days


title: Ctrl3_scRNA


title: hepatocyte-like cell - Day 20_DEM_10_TP-8_REP-C [Bas383]

description:
Bas383
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: MLC28777


title: Ctrl2_scRNA


title: hepatocyte-like cell - Day 20_DEM_333_TP-8_REP-B [Bas398]

description:
Bas398
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatocyte-like cells


title: MLC28709

value: Cancer


title: Ctrl OCP-1

value: wild type

value: SPL CD11b+c-fms+Ly6Chi OCP


title: Ctrl1_scRNA


title: hepatocyte-like cell - Day 20_DEM_10_TP-8_REP-A [Bas381]

description:
Bas381
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: hepatocyte-like cell - Day 20_DEM_100_TP-8_REP-C [Bas391]

description:
Bas391
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC28675

value: Current smoker


title: AngII 24h-antiEZH2

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

data_processing:
Illumina NextSeq 500 for RIP-seq
The reads were mapped to mouse genome (mm10) using TopHat2, and visualized on the UCSC browser (http://genome.ucsc.edu).
LncRNAs were picked out according to NONCODE database
Screening criteria was set as reads >1.0; ratio of anti-EZH2 group relative to normal IgG group >2 in at least one tissue.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: Left ventricle

growth_protocol: Male mice aged 10 weeks were housed in specific-pathogenfree (SPF) conditions with controlled temperature, humidity, and light and free access to food and water. Animal experiments were performed conforming to the 8th Edition of the Guide for the Care and Use of Laboratory Animals (Guide NRC, 2011) published by the US National Institutes of Health.

extract_protocol:
Left ventricles were the quickly separated, washed in PBS and frozen in liquid nitrogen until use. Saline was infused instead of AngII for Sham groups. RNA immune-precipitation (RIP) was performed essentially as previously described. Left ventricles weighting ∼100 mg from each group were homogenized in 500 µl of polysome lysis buffe. The suspension was centrifuged at 14,000 g at 4◦C for 10 min to remove debris. Lysates were incubated with 500 ng normal IgG or anti-EZH2 at 4◦C overnight on an inverse rotator. Protein A-sepharose beads were first blocked in NT2 buffer supplemented with 5% BSA, 0.02% sodium azide and 0.02 mg/mL heparin at 4◦C for 1 h, and then added into the lysates followed by a 3-h incubation at 4◦C on an inverse rotator. The beads were subsequently washed five times in NT2 buffer. RNAs were released by incubating in proteinase K buffer for 30 min at 65◦C, pelleted by adding an equal volume of isopropanol and centrifuged at 12,000 g at 4◦C for 10 min. RNAs were washed once with 75% ethanol and stored at −80◦C until use.
Two independent RIP products from each group were mixed before reverse transcription into cDNA sequencing library using KAPA Stranded RNA-Seq Library Preparation Kit. The libraries were subjected to quality validation using the Agilent Bioanalyzer 2100, and sequenced using Illumina NextSeq 500 in DNA Link USA Inc.

treatment_protocol: Mice were randomly assigned to Sham, Angiotensin II (AngII) 4 h and AngII 24 h groups with two mice for each group. An osmotic minipump (Alzet, Cupertino, CA, USA) was implanted subcutaneously to deliver AngII (Sigma, St. Louis, MO) at a rate of 1 mg/kg/min as previously described (30). After infusion for 4 or 24 h, mice were sacrificed by dislocation of infra-cervical spine.

value: 10 weeks

tag: treatment

value: AngII 24h

tag: rip antibody


title: AngII 4h-antiEZH2

value: AngII 4h


title: hepatocyte-like cell - Day 20_DEM_1_TP-8_REP-C [Bas375]

description:
Bas375
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 uM

value: 8 hr


title: MLC28609

value: Non-cancer

value: Non-smoker

value: Female

value: Bronchial epithelial cell


title: Sham-antiEZH2

value: Untreated


title: MLC28509

value: Male


title: MLC28575


title: hepatocyte-like cell - Day 20_DEM_1_TP-8_REP-B [Bas374]

description:
Bas374
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: hepatocyte-like cell - Day 20_DEM_1_TP-8_REP-A [Bas373]

description:
Bas373
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatocyte-like cells


title: Rhesus Cortex snRNA-Seq

first: Nathan

last: Salomonis

state: OH

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
Single-nuclei RNA-Seq
Rh_Fetal_Cortex-snRNA-Seq-scaled-corrected-counts.zip

data_processing:
The raw scRNA-Seq and snRNA-Seq data (10x Genomics 3' version 3) were aligned to the Ensembl version 91 reference transcriptome using the Cell Ranger version 3.1.0 workflow. For the snRNA-Seq, a combined intron-exon reference was produced as described using the vendor-provided “Generating a Cell Ranger compatible “pre-mRNA” Reference Package” guidelines (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references), prior to analysis. From the output for Cell Ranger for the snRNA-Seq, we corrected for ambient background RNA using the R package SoupX, selecting a correction factor of 0.5. In SoupX, we used the inferNonExpressedGenes() function to determine which genes had the highest probability of being ambient mRNA, and the strainCells() function in order to transform count matrices. The unique molecular index (UMI) counts produced from these analyses were scaled per cell (counts per ten-thousand) and log2 adjusted in the software AltAnalyze version 2.1.4 (EnsMart 91, Macaca mulatta database) using the “--dataFormat counts” option. Counts from all biological replicates of the cortex scRNA-Seq (Cell Ranger filtered matrix barcodes) were combined prior to further analysis (--accessoryAnalysis MergeFiles option). To identify cell populations in both the scRNA-Seq and snRNA-Seq, the software ICGS2 (Iterative Clustering and Guide-gene selection version 2), was run using the default options (cosine clustering) in addition to stringent exclusion of cell-cycle effects(--excludeCellCycle). Associated UMAP and marker genes (MarkerFinder algorithm) were directly obtained from the ICGS2 results.
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: Rh_Fetal_Cortex-scRNA-Seq-scaled-counts.zip
Supplementary_files_format_and_content: Rh_Fetal_Cortex-snRNA-Seq-scaled-corrected-counts.zip

organism: Macaca mulatta

source_name: 3rd trimester renal cortex (129-131 GA)

extract_protocol:
Dissociated single-cells were obtained prior to a cold-active protease digestion protocol (PMC5665481).
Single-cell nuclear RNA-Seq was further processed using a previously described protocol (PMC6317600).
The 10x Genomics 3' version 3 library chemistry and 10x Chromium controller were used to prepare and process singel-cell or single-nuclei, prior to high throughput sequencing on an Illumina NovaSeq.

value: renal cortex


title: hepatocyte-like cell - Day 20_DEM_10_TP-8_REP-B [Bas382]

description:
Bas382
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: Rhesus Cortex scRNA-Seq-B

description:
Single-cell RNA-Seq
Rh_Fetal_Cortex-scRNA-Seq-scaled-counts.zip
Cortex-B


title: hepatocyte-like cell - Day 20_CPT_100_TP-8_REP-C [Bas461]

description:
Bas461
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)


title: AngII 4h-IgG

value: IgG


title: MLC28677

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

value: Cancer


title: hepatocyte-like cell - Day 20_CPT_100_TP-8_REP-B [Bas460]

description:
Bas460
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Rhesus Cortex scRNA-Seq-A

description:
Single-cell RNA-Seq
Rh_Fetal_Cortex-scRNA-Seq-scaled-counts.zip
Cortex-A


title: Sham-IgG

value: 10 weeks


title: MLC28475

value: Former smoker


title: hepatocyte-like cell - Day 20_CPT_100_TP-8_REP-A [Bas459]

description:
Bas459
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Rhesus Cortex scRNA-Seq-2

description:
Single-cell RNA-Seq
Rh_Fetal_Cortex-scRNA-Seq-scaled-counts.zip
Kidney-Cortex-20190718


title: Poor response to NACRT rep3

type: RNA

city: Jinan

first: Ying

middle: ying

state: Shandong

address: Jingshi 16766

institute: The first Affiliated Hospital of Shandong first Medical University

description:
Poor response to NACRT rep3
circRNA

hyb_protocol: 0.6μg of cy3-labelled cRNA (specific activity >10.0 pmol cy3/μg cRNA) was fragmented at 60℃ for 30min in a reaction volume of 22.5μl containing 1× Agilent fragmention buffer and 2×Agilent blocking agent following the manufacture's instruction. On completion of the fragmentation reaction, 22.5μl of 2× Agilent hybrization buffer was added to yhe fragmentation mixture and hybridized to Agilent Human circRNA Expression microarray for 17 hours at 65℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1min at room temperature with GE wash buffer 1 (Agilent) and 1min with 37℃ GE wash buffer 2, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray scanner (G2505C) using one color scan setting.

data_processing: The scanned images were analyzed with feature extration software (Agilent) using default parameters to obtain background substracted and spatially detrended processed signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring software. Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: rectal cancer tumor tissue rep6

label_protocol: Cy3 labeled cRNA was prepared from 0.2μg RNA using the one-color low RNA input linear amplification plus kit (Agilent) according to the manufacture's instructions, followed by RNAeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop-1000 spectrophometer.

extract_protocol: RNA isolation was performed using TRIzol reagent according to the manufacturer’s protocol.

treatment_protocol: All patients were acquired NACRT treatment, and divided into good response and poor response groups.

value: rectal tissue

tag: tumor stage

value: IIIc


title: MLC28409


title: AngII 24h-IgG

value: AngII 24h


title: hepatocyte-like cell - Day 20_CPT_33_TP-8_REP-C [Bas454]

description:
Bas454
Cell lysate
count.txt
count_log2LibSizenorm.txt

tag: cell type

value: 33 uM

value: 8 hr


title: Poor response to NACRT rep1

description:
Poor response to NACRT rep1
circRNA

source_name: rectal cancer tumor tissue rep4


title: Rhesus Cortex scRNA-Seq-1

description:
Single-cell RNA-Seq
Rh_Fetal_Cortex-scRNA-Seq-scaled-counts.zip
Cortex


title: 4w-4

city: kumamoto-city

first: Michihiro

last: Hashimoto

state: kumamoto

address: 2-2-1 honjyo, 3-10-15 kuhonji chuo-ku

department: IRCMS

country: Japan

institute: kumamoto university

data_processing:
mRNA profile generated by deep sequencing using Illumina Next-Seq 500
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using CLC genomic workbench v.11.0.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by CLC genomic workbench v.12.0.4
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM, RPKM, and Read number for each Sample.

source_name: hematopoietic stem cells

extract_protocol:
After 100 cells were sorted, first strand cDNA were synthesized followed by generating 2nd strand by minorly modified method that was previously reported (Hiyashi et al. Nature Communication, 2018: 9) .
Using Nextera XT DNA sample Prep Kit (Illumina Inc., San Diego, CA), libraries were prepared by minorly modified method that was previously reported (Hiyashi et al. Nature Communication, 2018: 9) .

tag: strain

value: Bone marrow

value: 4 weeks


title: 4w-3


title: hepatocyte-like cell - Day 20_CPT_33_TP-8_REP-B [Bas453]

description:
Bas453
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC28477

source_name: Bronchial epithelial cell

value: Non-cancer

value: Current smoker

value: Male

value: Bronchial epithelial cell


title: MLC28377

value: Non-smoker


title: MLC28375

value: Female


title: Poor response to NACRT rep2

description:
Poor response to NACRT rep2
circRNA

source_name: rectal cancer tumor tissue rep5


title: hepatocyte-like cell - Day 20_CPT_10_TP-8_REP-C [Bas447]

description:
Bas447
Cell lysate
count.txt
count_log2LibSizenorm.txt

source_name: hepatocyte-like cell - Day 20

value: Hepatocyte-like cells

value: Cisplatin (CPT)

value: 10 uM


title: hepatocyte-like cell - Day 20_CPT_33_TP-8_REP-A [Bas452]

description:
Bas452
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: 4w-1


title: 4w-2


title: MLC28277

value: Former smoker


title: p5-4


title: MassTitr_rep3_.049uM_EVH1_gateC

city: Cambridge

first: Theresa

last: Hwang

address: 77 Massachusetts Ave

institute: MIT

data_processing:
Library strategy: Amplicon-SEQ
Illumina software used for basecalling
bcl files converted to FASTQ with bcl2fastq
Custom analysis and C pipelines from the MIT BioMicro Center to generate combined paired-end .unused files, one for each unique combination of barcode and index DNA
Reads were paired and aligned by custom scripts provided in an uploaded GitHub repo:  https://github.com/KeatingLab/highThroughputScripts
Total reads for each bin and concentration were converted to an expected fluorescence value on a FACS plot at each of eight concentrations (custom scripts in GitHub repo)
fitting of average positions by concentration for each clone to get concentration-dependent binding (custom script)
Supplementary_files_format_and_content: comma separated values files. Each file is one replicate with a list of sequences and their corresponding read counts at a given gate and concentration of ENAH. XLSX file is supplementary table describing samples in further detail.  Column headers are provided in a supplementary file.

organism: Escherichia coli

source_name: Bacterial Plasmid DNA

growth_protocol: Cells were grown overnight prior to day of experiment, and then to OD 0.5-0.6 before induction of display construct

extract_protocol:
E coli collected from FACS gates were mini-prepped for DNA contents, and cloned into amplicons containing two variable barcodes as identifiers
DNA libraries were prepared using Illumina protocols and barcode sequences.

treatment_protocol: Induced cells were labeled by anti-FLAG-APC and SA-PE for FACS sorting to detect construct expression and biotinylated receptor binding, respectively

tag: sequenced molecule

value: amplicon DNA


title: MLC28275

value: Cancer


title: MassTitr_rep3_.049uM_EVH1_gateD


title: Preenriched_input_library


title: MassTitr_rep3_.049uM_EVH1_gateB


title: hepatocyte-like cell - Day 20_CPT_10_TP-8_REP-B [Bas446]

description:
Bas446
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC28177


title: hepatocyte-like cell - Day 20_CPT_10_TP-8_REP-A [Bas445]

description:
Bas445
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: p5-2

tag: age


title: MassTitr_rep3_.049uM_EVH1_gateA


title: Good response to NACRT rep2

description:
Good response to NACRT rep2
circRNA

source_name: rectal cancer tumor tissue rep2

value: rectal tissue

value: IIIc


title: MLC28175


title: Good response to NACRT rep1

description:
Good response to NACRT rep1
circRNA

source_name: rectal cancer tumor tissue rep1


title: hepatocyte-like cell - Day 20_CPT_3.3_TP-8_REP-C [Bas439]

description:
Bas439
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: MLC28109


title: hepatocyte-like cell - Day 20_CPT_3.3_TP-8_REP-B [Bas438]

description:
Bas438
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC28077


title: p5-1

value: Bone marrow


title: MassTitr_rep3_.12uM_EVH1_gateC


title: MassTitr_rep3_.12uM_EVH1_gateA


title: MassTitr_rep3_.12uM_EVH1_gateB


title: hepatocyte-like cell - Day 20_CPT_3.3_TP-8_REP-A [Bas437]

description:
Bas437
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC28009


title: MassTitr_rep3_.30uM_EVH1_gateD


title: hepatocyte-like cell - Day 20_CPT_1_TP-8_REP-B [Bas430]

description:
Bas430
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 uM


title: p5-3


title: MLC28075


title: Lungs.Treg.WT#3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description:
Sorted Mouse Tregs as DAPI–TCRβ+CD4+GFP+CD25+, from ∆Foxp3.ires.GFP and Foxp3.ires.Gfp from 3-week-old male mice.
Lungs.Treg.WT#3

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts (subread 2.0.0) with GENCODE annotation (vM25)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: CD4 TReg Cell

extract_protocol:
Lungs and spleen were collected from 21-day-old FOXP3.ires.GFP and C57BL/6 ∆Foxp3.ires.GFP mice. A single cell suspension was obtained from murine splenocytes after mechanical dissociation through a 40 μm strainer. After careful perfusion with 5 mL of sterile PBS, the right lung was harvested, minced, and enzymatically dissociated in RPMI containing 0.5 mg/mL DNASE I (Sigma), 1.5 mg/mL collagenase IV (Sigma), 10% FBS and 2 mM EDTA with constantly stirring at 37°C for 35 min. Red blood cell lysis was performed using 1 mL of ACK (Lonza) for 1 min on ice. Single cell suspensions were then filtered through a 70-μm strainer and washed twice with 10% FBS + 2mM EDTA RPMI buffer. Lung CD4+ T cells were enriched before staining and sorting, using negative magnetic selection (Stem Cell).
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

value: Lungs

tag: genotype

value: 21 days

value: male


title: Lungs.Treg.[delta]Foxp3#3

description:
Sorted Mouse Tregs as DAPI–TCRβ+CD4+GFP+CD25+, from ∆Foxp3.ires.GFP and Foxp3.ires.Gfp from 3-week-old male mice.
Lungs.Treg.∆Foxp3#3


title: Lungs.Treg.[delta]Foxp3#2

description:
Sorted Mouse Tregs as DAPI–TCRβ+CD4+GFP+CD25+, from ∆Foxp3.ires.GFP and Foxp3.ires.Gfp from 3-week-old male mice.
Lungs.Treg.∆Foxp3#2


title: hepatocyte-like cell - Day 20_CPT_1_TP-8_REP-C [Bas431]

description:
Bas431
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Good response to NACRT rep3

description:
Good response to NACRT rep3
circRNA

source_name: rectal cancer tumor tissue rep3


title: Lungs.Treg.[delta]Foxp3#1

description:
Sorted Mouse Tregs as DAPI–TCRβ+CD4+GFP+CD25+, from ∆Foxp3.ires.GFP and Foxp3.ires.Gfp from 3-week-old male mice.
Lungs.Treg.∆Foxp3#1


title: hepatocyte-like cell - Day 20_CPT_1_TP-8_REP-A [Bas429]

description:
Bas429
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC27951

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

value: Bronchial epithelial cell


title: MassTitr_rep3_.12uM_EVH1_gateD


title: Lungs.Treg.WT#2

description:
Sorted Mouse Tregs as DAPI–TCRβ+CD4+GFP+CD25+, from ∆Foxp3.ires.GFP and Foxp3.ires.Gfp from 3-week-old male mice.
Lungs.Treg.WT#2


title: MLC27851

value: Non-cancer

value: Non-smoker


title: MassTitr_rep3_.30uM_EVH1_gateC


title: hepatocyte-like cell - Day 20_CPT_0.01_TP-8_REP-C [Bas423]

description:
Bas423
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatocyte-like cells


title: MLC27651

value: Male


title: Lungs.Treg.WT#1

description:
Sorted Mouse Tregs as DAPI–TCRβ+CD4+GFP+CD25+, from ∆Foxp3.ires.GFP and Foxp3.ires.Gfp from 3-week-old male mice.
Lungs.Treg.WT#1


title: MassTitr_rep3_.30uM_EVH1_gateB


title: hepatocyte-like cell - Day 20_CPT_0.01_TP-8_REP-B [Bas422]

description:
Bas422
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)


title: MLC27451


title: Spleen.Treg.[delta]Foxp3#3

description:
Sorted Mouse Tregs as DAPI–TCRβ+CD4+GFP+CD25+, from ∆Foxp3.EGFP.iCre X R26.YFP and Foxp3.ires.Gfp from 3-week-old male mice.
Spleen.Treg.∆Foxp3#3

value: C57BL/6 [delta]Foxp3.EGFP.iCre X R26.YFP

value: Spleen

value: deltaFoxp3.EGFP.iCre X R26.YFP


title: MassTitr_rep3_.30uM_EVH1_gateA

value: amplicon DNA


title: Spleen.Treg.[delta]Foxp3#2

description:
Sorted Mouse Tregs as DAPI–TCRβ+CD4+GFP+CD25+, from ∆Foxp3.EGFP.iCre X R26.YFP and Foxp3.ires.Gfp from 3-week-old male mice.
Spleen.Treg.∆Foxp3#2


title: MLC27351

value: Female


title: Hepatoblast - Day 8_TUN_100_TP-8_REP-C [Bas233]

description:
Bas233
Cell lysate
count.txt
count_log2LibSizenorm.txt

source_name: Hepatoblast - Day 8

value: Hepatoblasts

value: Tunicamycin (TUN)

value: 8 hr


title: MassTitr_rep3_.77uM_EVH1_gateD


title: MassTitr_rep3_.77uM_EVH1_gateC


title: Spleen.Treg.[delta]Foxp3#1

description:
Sorted Mouse Tregs as DAPI–TCRβ+CD4+GFP+CD25+, from ∆Foxp3.EGFP.iCre X R26.YFP and Foxp3.ires.Gfp from 3-week-old male mice.
Spleen.Treg.∆Foxp3#1

value: [delta]Foxp3.EGFP.iCre X R26.YFP


title: Spleen.Treg.WT#3

description:
Sorted Mouse Tregs as DAPI–TCRβ+CD4+GFP+CD25+, from ∆Foxp3.EGFP.iCre X R26.YFP and Foxp3.ires.Gfp from 3-week-old male mice.
Spleen.Treg.WT#3

value: 21 days


title: MLC27251


title: Hepatoblast - Day 8_TUN_100_TP-8_REP-B [Bas232]

description:
Bas232
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MassTitr_rep3_.77uM_EVH1_gateA


title: Hepatoblast - Day 8_TUN_100_TP-8_REP-A [Bas231]

description:
Bas231
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Hepatoblast - Day 8_TUN_10_TP-8_REP-C [Bas225]

description:
Bas225
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: Spleen.Treg.WT#2

description:
Sorted Mouse Tregs as DAPI–TCRβ+CD4+GFP+CD25+, from ∆Foxp3.EGFP.iCre X R26.YFP and Foxp3.ires.Gfp from 3-week-old male mice.
Spleen.Treg.WT#2

value: male


title: MLC27151

value: Non-cancer

value: Former smoker

value: Bronchial epithelial cell


title: MassTitr_rep3_1.9uM_EVH1_gateD


title: Spleen.Treg.WT#1

description:
Sorted Mouse Tregs as DAPI–TCRβ+CD4+GFP+CD25+, from ∆Foxp3.EGFP.iCre X R26.YFP and Foxp3.ires.Gfp from 3-week-old male mice.
Spleen.Treg.WT#1


title: MLC25922

value: Cancer

value: Current smoker

value: Male


title: MLC25822


title: Hepatoblast - Day 8_TUN_10_TP-8_REP-B [Bas224]

description:
Bas224
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MassTitr_rep3_1.9uM_EVH1_gateC


title: MLC25722

value: Non-smoker


title: s4902_wt_HSC_5FU_H3K4me1.3

description:
5-fluorouracil 150 mg/kg every 3 weeks x3
wild type 5-FU treated HSCs
wt_HSC_5FU_H3K4me1_combined.fc.signal.bigwig
wt_HSC_5FU_H3K4me1_combined.filt.narrowPeak.gz

extract_protocol:
HSCs and HPCs were soted and then fixed for chromatin isolation per Schmidl et l., Nature Methods 10:963.
Chipmentation - Chromatin isolation with the indicated antibody followed by tagmentation with Tn5 as per Schmidl et l., Nature Methods 10:963.
ChIPmentation, Illumina

value: wild type 5-FU treated HSCs

value: 16 weeks old


title: hepatocyte-like cell - Day 20_CPT_0.01_TP-8_REP-A [Bas421]

description:
Bas421
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatocyte-like cells

value: Cisplatin (CPT)


title: s4902_wt_HSC_5FU_H3K4me1.2


title: MLC25622

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.


title: Hepatoblast - Day 8_TUN_1_TP-8_REP-C [Bas217]

description:
Bas217
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatoblasts

value: Tunicamycin (TUN)

value: 1 uM


title: MassTitr_rep3_1.9uM_EVH1_gateA

value: amplicon DNA


title: MassTitr_rep3_4.8uM_EVH1_gateD


title: s4902_wt_HSC_5FU_H3K4me1.1


title: MassTitr_rep3_.77uM_EVH1_gateB


title: Hepatoblast - Day 8_TUN_1_TP-8_REP-B [Bas216]

description:
Bas216
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: MLC25522

value: Female


title: s4902.input.1


title: MLC25422


title: Hepatoblast - Day 8_TUN_1_TP-8_REP-A [Bas215]

description:
Bas215
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC25322


title: s5060_wt_HSC_PBS_H3K4me1.4

description:
vehicle (PBS) every 3 weeks x3
wild type PBS treated HSCs
wt_HSC_PBS_H3K4me1_s5060.fc.signal.bigwig
wt_HSC_PBS_H3K4me1_s5060.filt.narrowPeak.gz

value: wild type PBS treated HSCs


title: Hepatoblast - Day 8_TUN_0.1_TP-8_REP-B [Bas208]

description:
Bas208
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Hepatoblast - Day 8_TUN_0.1_TP-8_REP-C [Bas209]

description:
Bas209
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: s5060.input.1


title: MLC25222


title: MassTitr_rep3_4.8uM_EVH1_gateB


title: s5060_wt_HSC_PBS_H3K4me1.3


title: Hepatoblast - Day 8_TUN_10_TP-8_REP-A [Bas223]

description:
Bas223
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: MassTitr_rep3_1.9uM_EVH1_gateB


title: MLC25122

value: Non-cancer

value: Former smoker

value: Bronchial epithelial cell


title: MassTitr_rep3_4.8uM_EVH1_gateA


title: s5060_wt_HSC_PBS_H3K4me1.2


title: Hepatoblast - Day 8_TUN_0.1_TP-8_REP-A [Bas207]

description:
Bas207
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Hepatoblast - Day 8_TUN_0.01_TP-8_REP-C [Bas201]

description:
Bas201
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MassTitr_rep3_12uM_EVH1_gateD


title: s5060_wt_HSC_PBS_H3K4me1.1


title: MassTitr_rep3_12uM_EVH1_gateC


title: MLC23973


title: MassTitr_rep3_12uM_EVH1_gateB


title: MassTitr_rep3_12uM_EVH1_gateA


title: Hepatoblast - Day 8_TUN_0.01_TP-8_REP-A [Bas199]

description:
Bas199
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC23898

value: Cancer

value: Current smoker

value: Male


title: Hepatoblast - Day 8_TUN_0.01_TP-8_REP-B [Bas200]

description:
Bas200
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MassTitr_rep3_4.8uM_EVH1_gateC


title: s5060_wt_HSC_5FU_H3K4me1.2

value: wild type 5-FU treated HSCs

value: 16 weeks old


title: MassTitr_rep3_30uM_EVH1_gateD


title: s5060_wt_HSC_5FU_H3K4me1.1


title: MLC23798


title: MassTitr_rep3_30uM_EVH1_gateC


title: MLC23773

value: Non-smoker


title: s5060_mll3ko_HSC_PBS_H3K4me1.3

description:
vehicle (PBS) every 3 weeks x3
Kmt2c f/f; Vav-Cre PBS treated HSCs
mll3ko_HSC_PBS_H3K4me1_s5060.fc.signal.bigwig
mll3ko_HSC_PBS_H3K4me1_s5060.filt.narrowPeak.gz

value: Kmt2c f/f; Vav-Cre PBS treated HSCs


title: MLC23873


title: Hepatoblast - Day 8_TUN_0.001_TP-8_REP-A [Bas191]

description:
Bas191
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatoblasts

value: Tunicamycin (TUN)


title: s5060_mll3ko_HSC_PBS_H3K4me1.2


title: MLC23998


title: MLC23698


title: Hepatoblast - Day 8_TNF_50_TP-8_REP-C [Bas279]

description:
Bas279
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 50 ng/mL


title: s5060_mll3ko_HSC_PBS_H3K4me1.1


title: MLC23573

value: Female


title: Hepatoblast - Day 8_TNF_50_TP-8_REP-B [Bas278]

description:
Bas278
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: MassTitr_rep2_.049uM_EVH1_gateD

value: amplicon DNA


title: MassTitr_rep3_30uM_EVH1_gateA


title: MassTitr_rep2_.049uM_EVH1_gateC


title: Hepatoblast - Day 8_TUN_0.001_TP-8_REP-C [Bas193]

description:
Bas193
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: s5060_mll3ko_HSC_5FU_H3K4me1.3

description:
5-fluorouracil 150 mg/kg every 3 weeks x3
Kmt2c f/f; Vav-Cre 5-FU treated HSCs
mll3ko_HSC_5FU_H3K4me1_s5060.fc.signal.bigwig
mll3ko_HSC_5FU_H3K4me1_s5060.filt.narrowPeak.gz

value: Kmt2c f/f; Vav-Cre 5-FU treated HSCs


title: Hepatoblast - Day 8_TNF_10_TP-8_REP-C [Bas272]

description:
Bas272
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 ng/mL


title: MLC23498

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

value: Bronchial epithelial cell


title: Hepatoblast - Day 8_TNF_50_TP-8_REP-A [Bas277]

description:
Bas277
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC23473

value: Cancer

value: Former smoker


title: s5060_mll3ko_HSC_5FU_H3K4me1.2


title: MLC23373

value: Non-cancer

value: Male


title: s5060_mll3ko_HSC_5FU_H3K4me1.1

value: 16 weeks old


title: MassTitr_rep2_.049uM_EVH1_gateA


title: Hepatoblast - Day 8_TUN_0.001_TP-8_REP-B [Bas192]

description:
Bas192
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC23398


title: Hepatoblast - Day 8_TNF_10_TP-8_REP-B [Bas271]

description:
Bas271
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Hepatoblast - Day 8_TNF_10_TP-8_REP-A [Bas270]

description:
Bas270
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: s5060_wt_HSC_5FU_H3K4me1.3

description:
5-fluorouracil 150 mg/kg every 3 weeks x3
wild type 5-FU treated HSCs
wt_HSC_5FU_H3K4me1_combined.fc.signal.bigwig
wt_HSC_5FU_H3K4me1_combined.filt.narrowPeak.gz

value: wild type 5-FU treated HSCs


title: neuron#3

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Enteric neurons

extract_protocol:
1,000 Cells were double-sorted (Tconv: GFP-; Treg: GFP+; enteric neurons: CD45-) by Moflo into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma). Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

treatment_protocol: Naïve T cells from spleens in Foxp3-GFP mice were co-cultured with or without enteric neurons for 3 days in iTreg culture conditions, and Tconvs, Treg or enteric neurons were sorted and processed for RNAseq

value: colon

value: Enteric neurons

value: wild type

tag: protocol

value: cultured enteric neurons


title: Hepatoblast - Day 8_TNF_7.5_TP-8_REP-C [Bas265]

description:
Bas265
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatoblasts

value: TNF-alpha

value: 7.5 ng/mL


title: neuron#2


title: MassTitr_rep2_.12uM_EVH1_gateC

value: amplicon DNA


title: MassTitr_rep2_.049uM_EVH1_gateB


title: MassTitr_rep2_.12uM_EVH1_gateD


title: MLC23273

tag: diagnosis


title: MLC23298

tag: smoking status

value: Non-smoker


title: Hepatoblast - Day 8_TNF_7.5_TP-8_REP-B [Bas264]

description:
Bas264
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: s5060_mll3ko_HSC_5FU_H3K4me1.4

value: Kmt2c f/f; Vav-Cre 5-FU treated HSCs


title: neuron#1


title: MLC23198

tag: Sex

value: Female

value: Bronchial epithelial cell


title: MassTitr_rep2_.12uM_EVH1_gateB


title: Hepatoblast - Day 8_TNF_7.5_TP-8_REP-A [Bas263]

description:
Bas263
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MassTitr_rep2_.12uM_EVH1_gateA


title: MLC23173

value: Non-cancer

value: Current smoker

tag: tissue


title: Treg#3

source_name: Treg

value: spleen

value: Treg


title: Hepatoblast - Day 8_TNF_5_TP-8_REP-C [Bas257]

description:
Bas257
Cell lysate
count.txt
count_log2LibSizenorm.txt

tag: compound

value: 5 ng/mL


title: Treg#2


title: MassTitr_rep2_.30uM_EVH1_gateD


title: MLC23098

value: Cancer

value: Former smoker

value: Male


title: Hepatoblast - Day 8_TNF_5_TP-8_REP-B [Bas256]

description:
Bas256
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatoblasts

tag: concentration


title: MLC23073


title: MLC20974


title: MassTitr_rep2_.30uM_EVH1_gateB


title: MassTitr_rep2_.30uM_EVH1_gateC


title: MassTitr_rep2_.30uM_EVH1_gateA


title: Treg#1

value: wild type


title: Treg+neuron#3

value: Treg in T cell/neuron co-cultures


title: Hepatoblast - Day 8_TNF_2.5_TP-8_REP-C [Bas249]

description:
Bas249
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 2.5 ng/mL

tag: time point


title: Treg+neuron#1


title: Treg+neuron#2


title: Hepatoblast - Day 8_TNF_2.5_TP-8_REP-A [Bas247]

description:
Bas247
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr

tag: replicate


title: MassTitr_rep3_30uM_EVH1_gateB

value: amplicon DNA


title: MLC20774

value: Non-smoker

value: Female


title: MassTitr_rep2_.77uM_EVH1_gateC


title: MassTitr_rep2_.77uM_EVH1_gateD


title: Tconv#3

source_name: Tconvs

value: Tconvs

value: Tconv


title: Hepatoblast - Day 8_TNF_2.5_TP-8_REP-B [Bas248]

description:
Bas248
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC20746

value: Non-cancer

value: Bronchial epithelial cell


title: Hepatoblast - Day 8_TNF_1_TP-8_REP-C [Bas241]

description:
Bas241
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 ng/mL


title: MLC20674

value: Cancer


title: MassTitr_rep2_.77uM_EVH1_gateA


title: Tconv#2

value: spleen


title: Tconv#1


title: MLC20646

value: Current smoker

value: Male


title: Hepatoblast - Day 8_TNF_5_TP-8_REP-A [Bas255]

description:
Bas255
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatoblasts

value: 5 ng/mL


title: Hepatoblast - Day 8_TNF_1_TP-8_REP-B [Bas240]

description:
Bas240
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha


title: MassTitr_rep2_1.9uM_EVH1_gateD


title: Tconv+neuron#3

value: wild type

value: Tconv in T cell/neuron co-cultures


title: Hepatoblast - Day 8_TNF_1_TP-8_REP-A [Bas239]

description:
Bas239
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: Hepatoblast - Day 8_MEDIUM_0_TP-8_REP-C [Bas276]

description:
Bas276
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: MEDIUM


title: MassTitr_rep2_1.9uM_EVH1_gateC

value: amplicon DNA


title: MLC20574

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.


title: MLC20946

value: Non-smoker


title: Tconv+neuron#2

value: Tconvs


title: Hepatoblast - Day 8_MEDIUM_0_TP-8_REP-C [Bas230]

description:
Bas230
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MassTitr_rep2_1.9uM_EVH1_gateB


title: Tconv+neuron#1


title: MLC20474


title: Hepatoblast - Day 8_MEDIUM_0_TP-8_REP-B [Bas269]

description:
Bas269
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MassTitr_rep2_1.9uM_EVH1_gateA


title: EP.1d.Pm#1

source_name: MMP

extract_protocol:
The whole tissue were peeled off from the colons, cut into 2cm segments, lyzed and homogenized in 400ul TCL buffer (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

treatment_protocol: Germ-free mice were gavaged with vehcle, P.magnus or C.ramosum for 24 hours, and the whole MMP tissues were prepared and further processed for RNAseq

value: colon

value: MMP

value: GF mice gavage with P.magnus for 24hours


title: MLC20446

extract_protocol:
Bronchial epithelial cells were obtained via bronchial brushings. RNA was extracted using a protocol of the RNeasy Kit (Qiagen, Hilden, Germany).
RNA libraries were prepared according to the manufacturer’s instructions for the NEB Next® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).

value: Cancer

value: Bronchial epithelial cell


title: EP.1d.Pm#2


title: Hepatoblast - Day 8_MEDIUM_0_TP-8_REP-B [Bas222]

description:
Bas222
Cell lysate
count.txt
count_log2LibSizenorm.txt

extract_protocol:
Cells were washed with PBS and lysed with 1x BNN lysis buffer (provided by BioSpyder) followed by incubation of 15 min at RT. Thereafter plate with cell lysates was sealed and stored at -80 degrees until shipment. Cell lysates were send to BioSpyder for TempO-seq targeted transcriptome analysis.
mRNA in the lysates was hybridized with detector oligo mix, and amplified using barcoded primer pairs to add a unique tag for each of the samples. The detector oligo mix targets a set of genes which were selected based on the S1500+ gene list of NIEHS (Mav et al. 2018). This list contains 2736 genes that provide maximal toxicogenomic information on chemical perturbations that reflect general cellular responses. We supplemented this list with another 245 genes that are involved in hiPSC to hepatocyte differentiation, cellular stress pathways activated in PHH and were missing in the S1500 list. Sample amplicons were pooled and purified. The libraries were sequenced using a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA).


title: MassTitr_rep2_.77uM_EVH1_gateB


title: MLC20174


title: EP.1d.Ctr#1

value: GF mice gavage with vehicles


title: Hepatoblast - Day 8_MEDIUM_0_TP-8_REP-A [Bas262]

description:
Bas262
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Hepatoblast - Day 8_MEDIUM_0_TP-8_REP-A [Bas214]

description:
Bas214
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MassTitr_rep2_4.8uM_EVH1_gateC


title: MLC20146

value: Non-cancer

value: Female


title: MassTitr_rep2_4.8uM_EVH1_gateB


title: MLC20546

value: Current smoker

value: Male


title: Hepatoblast - Day 8_DMSO_0_TP-8_REP-C [Bas254]

description:
Bas254
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatoblasts

value: DMSO


title: Hepatoblast - Day 8_DMSO_0_TP-8_REP-C [Bas206]

description:
Bas206
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: EP.1d.Cr#2

value: wild type

value: GF mice gavage with C.ramosum for 24hours


title: MassTitr_rep2_12uM_EVH1_gateD

value: amplicon DNA


title: MLC20074

value: Former smoker


title: MassTitr_rep2_4.8uM_EVH1_gateA


title: EP.1d.Cr#1

value: colon


title: MLC20046

value: Non-smoker


title: MassTitr_rep2_12uM_EVH1_gateC


title: Hepatoblast - Day 8_DMSO_0_TP-8_REP-B [Bas198]

description:
Bas198
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MassTitr_rep2_4.8uM_EVH1_gateD


title: MassTitr_rep2_12uM_EVH1_gateB


title: MLC19930


title: MLC19830


title: Neu.CR.d7.MP#4

extract_protocol:
1,000 Cells were sorted as CD45-Sca1-CD9hi by Moflo into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

treatment_protocol: Germ-free mice were gavaged with vehcle, P.magnus or C.ramosum for the indicated time, and the enteric neurons were sorted, and further processed for RNAseq

value: Enteric neurons

value: GF mice gavage with C.ramosum for 7 days


title: Hepatoblast - Day 8_DMSO_0_TP-8_REP-A [Bas238]

description:
Bas238
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC20274

value: Cancer

value: Bronchial epithelial cell


title: MassTitr_rep2_12uM_EVH1_gateA


title: Neu.CR.d7.MP#3


title: EP.1d.Ctr#2

value: MMP

value: GF mice gavage with vehicles


title: Neu.CR.d7.MP#2


title: MassTitr_rep2_30uM_EVH1_gateD


title: MLC19730

value: Non-cancer


title: Hepatoblast - Day 8_DMSO_0_TP-8_REP-A [Bas190]

description:
Bas190
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Hepatoblast - Day 8_DEM_3300_TP-8_REP-C [Bas229]

description:
Bas229
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: Hepatoblast - Day 8_DMSO_0_TP-8_REP-B [Bas246]

description:
Bas246
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatoblasts


title: MassTitr_rep2_30uM_EVH1_gateC


title: Neu.CR.d2.MP#3

value: GF mice gavage with C.ramosum for 2 days


title: MassTitr_rep2_30uM_EVH1_gateB


title: Hepatoblast - Day 8_DEM_3300_TP-8_REP-B [Bas228]

description:
Bas228
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: MLC19430

value: Female


title: Neu.CR.d2.MP#2

value: wild type


title: Hepatoblast - Day 8_DEM_3300_TP-8_REP-A [Bas227]

description:
Bas227
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Neu.CR.d7.MP#1


title: MassTitr_rep2_30uM_EVH1_gateA

value: amplicon DNA


title: Hepatoblast - Day 8_DEM_1000_TP-8_REP-C [Bas221]

description:
Bas221
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Neu.CR.d1.MP#3

value: GF mice gavage with C.ramosum for 1 day


title: Hepatoblast - Day 8_DEM_1000_TP-8_REP-B [Bas220]

description:
Bas220
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MassTitr_rep1_.049uM_EVH1_gateC


title: Neu.CR.d1.MP#2

value: colon


title: MLC19130

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

value: Non-smoker


title: MassTitr_rep1_.049uM_EVH1_gateD


title: Hepatoblast - Day 8_DEM_1000_TP-8_REP-A [Bas219]

description:
Bas219
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Neu.CR.d1.MP#1

value: Enteric neurons


title: MLC19630

value: Current smoker

value: Male


title: MLC19030

value: Cancer

value: Bronchial epithelial cell


title: MLC18977


title: Neu.PM.d7.MP#4

value: GF mice gavage with P.magnus for 7 days


title: MLC19530

value: Non-cancer


title: MassTitr_rep1_.049uM_EVH1_gateB


title: Neu.PM.d7.MP#3


title: MassTitr_rep1_.049uM_EVH1_gateA


title: Hepatoblast - Day 8_DEM_333_TP-8_REP-B [Bas212]

description:
Bas212
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: MLC19330

value: Former smoker


title: MassTitr_rep1_.12uM_EVH1_gateD


title: Hepatoblast - Day 8_DEM_333_TP-8_REP-A [Bas211]

description:
Bas211
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatoblasts


title: MassTitr_rep1_.12uM_EVH1_gateC


title: Neu.PM.d7.MP#2


title: MLC18877


title: Hepatoblast - Day 8_DEM_100_TP-8_REP-C [Bas205]

description:
Bas205
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: Neu.PM.d7.MP#1


title: MassTitr_rep1_.12uM_EVH1_gateB


title: Hepatoblast - Day 8_DEM_100_TP-8_REP-B [Bas204]

description:
Bas204
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Neu.PM.d2.MP#3

value: GF mice gavage with P.magnus for 2 days


title: Neu.PM.d2.MP#2

value: wild type


title: MLC18809

value: Female


title: MLC18777


title: Neu.PM.d2.MP#1

value: GF mice gavage with P.magnus for 2 day


title: Hepatoblast - Day 8_DEM_100_TP-8_REP-A [Bas203]

description:
Bas203
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC18775


title: Hepatoblast - Day 8_DEM_333_TP-8_REP-C [Bas213]

description:
Bas213
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Hepatoblast - Day 8_DEM_10_TP-8_REP-B [Bas196]

description:
Bas196
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: Neu.PM.d1.MP#3

value: colon

value: GF mice gavage with P.magnus for 1 day


title: MLC18975

value: Current smoker


title: Hepatoblast - Day 8_DEM_10_TP-8_REP-C [Bas197]

description:
Bas197
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC18909

value: Male


title: MassTitr_rep1_.30uM_EVH1_gateC

value: amplicon DNA


title: MLC18709

value: Cancer

value: Non-smoker

value: Bronchial epithelial cell


title: Neu.PM.d1.MP#2

value: Enteric neurons


title: Hepatoblast - Day 8_DEM_10_TP-8_REP-A [Bas195]

description:
Bas195
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Diethyl-maleate (DEM)


title: MassTitr_rep1_.30uM_EVH1_gateB


title: MLC18677


title: MLC18675

value: Non-cancer


title: Neu.PM.d1.MP#1


title: Hepatoblast - Day 8_DEM_1_TP-8_REP-C [Bas189]

description:
Bas189
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatoblasts

value: 1 uM

value: 8 hr


title: MassTitr_rep1_.77uM_EVH1_gateD


title: Neu.GF.M.MP#6

value: wild type

value: GF mice


title: MassTitr_rep1_.12uM_EVH1_gateA


title: MLC18609

value: Former smoker


title: MassTitr_rep1_.30uM_EVH1_gateD


title: MLC18577

value: Female


title: Neu.GF.M.MP#5

value: colon


title: Hepatoblast - Day 8_DEM_1_TP-8_REP-A [Bas187]

description:
Bas187
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Hepatoblast - Day 8_DEM_1_TP-8_REP-B [Bas188]

description:
Bas188
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MassTitr_rep1_.77uM_EVH1_gateC


title: Neu.GF.MP#4


title: MLC18575


title: MassTitr_rep1_.77uM_EVH1_gateB


title: MassTitr_rep1_.77uM_EVH1_gateA


title: MassTitr_rep1_.30uM_EVH1_gateA


title: MLC18509

value: Current smoker


title: Hepatoblast - Day 8_CPT_100_TP-8_REP-C [Bas275]

description:
Bas275
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)


title: Hepatoblast - Day 8_CPT_100_TP-8_REP-B [Bas274]

description:
Bas274
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Neu.GF.MP#3


title: Neu.GF.MP#2


title: MassTitr_rep1_1.9uM_EVH1_gateD

value: amplicon DNA


title: MLC18477

value: Cancer


title: MassTitr_rep1_1.9uM_EVH1_gateC


title: Hepatoblast - Day 8_CPT_100_TP-8_REP-A [Bas273]

description:
Bas273
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC18475

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

value: Male


title: Hepatoblast - Day 8_CPT_33_TP-8_REP-C [Bas268]

description:
Bas268
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 33 uM


title: MLC18409

value: Bronchial epithelial cell


title: Hepatoblast - Day 8_CPT_33_TP-8_REP-B [Bas267]

description:
Bas267
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Neu.GF.MP#1

value: Enteric neurons


title: MassTitr_rep1_1.9uM_EVH1_gateA


title: wt_HSC_PBS_H3K27ac.2

description:
wild type PBS treated HSCs
wt_HSC_PBS_H3K27ac.fc.signal.bigwig
wt_HSC_PBS_H3K27ac.filt.narrowPeak.gz

source_name: wild type PBS treated HSCs

extract_protocol:
HSCs and HPCs were soted and then fixed for chromatin isolation per Schmidl et l., Nature Methods 10:963.
Chipmentation - Chromatin isolation with the indicated antibody followed by tagmentation with Tn5 as per Schmidl et l., Nature Methods 10:963.

value: HSCs

tag: chip target

tag: chip antibody

tag: treatment

value: wild type PBS treated HSCs

value: 16 weeks old

value: vehicle (PBS) every 3 weeks x3


title: wt_HSC_PBS_H3K27ac.1

tag: cell type


title: MLC18375


title: Hepatoblast - Day 8_CPT_33_TP-8_REP-A [Bas266]

description:
Bas266
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatoblasts

value: 8 hr


title: MassTitr_rep1_4.8uM_EVH1_gateD

tag: strain


title: Hepatoblast - Day 8_CPT_10_TP-8_REP-C [Bas261]

description:
Bas261
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: MLC18309

value: Non-cancer

value: Non-smoker

value: Female


title: MassTitr_rep1_4.8uM_EVH1_gateC

tag: sequenced molecule


title: wt_HSC_5FU_H3K27ac.3

description:
wild type 5-FU treated HSCs
wt_HSC_5FU_H3K27ac.fc.signal.bigwig
wt_HSC_5FU_H3K27ac.filt.narrowPeak.gz

source_name: wild type 5-FU treated HSCs

value: wild type 5-FU treated HSCs

value: 5-fluorouracil 150 mg/kg every 3 weeks x3


title: MLC18275

value: Cancer

value: Current smoker


title: MLC18209


title: MassTitr_rep1_4.8uM_EVH1_gateB

value: amplicon DNA


title: Hepatoblast - Day 8_CPT_10_TP-8_REP-A [Bas259]

description:
Bas259
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Cisplatin (CPT)


title: wt_HSC_5FU_H3K27ac.2


title: wt_HSC_5FU_H3K27ac.1


title: MLC18177

value: Male

value: Bronchial epithelial cell


title: MassTitr_rep1_4.8uM_EVH1_gateA


title: Hepatoblast - Day 8_CPT_3.3_TP-8_REP-C [Bas253]

description:
Bas253
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: wt_HSC_PBS_H3K27ac.3

value: HSCs

value: wild type PBS treated HSCs


title: MassTitr_rep1_1.9uM_EVH1_gateB


title: mll3ko_HSC_PBS_H3K27ac.3

description:
Kmt2c f/f; Vav-Cre PBS treated HSCs
mll3ko_HSC_PBS_H3K27ac.fc.signal.bigwig
mll3ko_HSC_PBS_H3K27ac.filt.narrowPeak.gz

source_name: Kmt2c f/f; Vav-Cre PBS treated HSCs

value: Kmt2c f/f; Vav-Cre PBS treated HSCs

value: 16 weeks old

value: vehicle (PBS) every 3 weeks x3


title: MassTitr_rep1_12uM_EVH1_gateD


title: MLC18175


title: MassTitr_rep1_12uM_EVH1_gateC


title: Hepatoblast - Day 8_CPT_3.3_TP-8_REP-B [Bas252]

description:
Bas252
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatoblasts

value: 8 hr


title: MLC18109


title: Hepatoblast - Day 8_CPT_3.3_TP-8_REP-A [Bas251]

description:
Bas251
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: mll3ko_HSC_PBS_H3K27ac.2


title: MassTitr_rep1_12uM_EVH1_gateB


title: MLC18009


title: MassTitr_rep1_12uM_EVH1_gateA


title: mll3ko_HSC_5FU_H3K27ac.3

description:
Kmt2c f/f; Vav-Cre 5-FU treated HSCs
mll3ko_HSC_5FU_H3K27ac.fc.signal.bigwig
mll3ko_HSC_5FU_H3K27ac.filt.narrowPeak.gz

source_name: Kmt2c f/f; Vav-Cre 5-FU treated HSCs

value: Kmt2c f/f; Vav-Cre 5-FU treated HSCs


title: mll3ko_HSC_PBS_H3K27ac.1


title: Hepatoblast - Day 8_CPT_1_TP-8_REP-C [Bas245]

description:
Bas245
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 1 uM


title: MassTitr_rep1_30uM_EVH1_gateD


title: Hepatoblast - Day 8_CPT_10_TP-8_REP-B [Bas260]

description:
Bas260
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 uM


title: Hepatoblast - Day 8_CPT_1_TP-8_REP-B [Bas244]

description:
Bas244
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: mll3ko_HSC_5FU_H3K27ac.2

value: 5-fluorouracil 150 mg/kg every 3 weeks x3


title: MassTitr_rep1_30uM_EVH1_gateC


title: MLC17951

source_name: Bronchial epithelial cell

value: Non-cancer


title: Hepatoblast - Day 8_CPT_1_TP-8_REP-A [Bas243]

description:
Bas243
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: Hepatoblast - Day 8_CPT_0.01_TP-8_REP-C [Bas237]

description:
Bas237
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: mll3ko_HSC_5FU_H3K27ac.1


title: MLC17851

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.

value: Cancer

value: Non-smoker


title: MLC17751

value: Former smoker


title: MassTitr_rep1_30uM_EVH1_gateB

value: amplicon DNA


title: MLC17651

value: Female

value: Bronchial epithelial cell


title: PBS_control.4

description:
PBS_control.fc.signal.bigwig
PBS_control.filt.narrowPeak.gz

extract_protocol:
per Corces et al., Nature Methods 14:959
tagmentation with Tn5 transposase

value: HSCs

tag: age

tag: treament

value: PBS treated wild type HSCs


title: MassTitr_rep1_30uM_EVH1_gateA


title: s4911.input.1

description: input chromatin

source_name: input chromatin

value: none (input)

tag: genotype

value: 8 weeks old


title: Hepatoblast - Day 8_CPT_0.01_TP-8_REP-B [Bas236]

description:
Bas236
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Hepatoblasts

value: Cisplatin (CPT)


title: Hepatoblast - Day 8_CPT_0.01_TP-8_REP-A [Bas235]

description:
Bas235
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: GFP-KI WO III - ST

city: New York

first: Shruti

last: Naik

state: NY

address: 435 East 30th Street

department: Pathology

institute: NYU Langone Health

data_processing:
Sequencing output and the histology images were processed using space ranger software (10X Genomics).  The space ranger mkfastq function was used for sample demultiplexing and to converting spatial barcodes and reads into FASTQ format.
The space ranger count function was used to align reads from FATSQ files to mouse genome (mm10/GRCm38) and then align microscopic slide image and transcriptome to generate barcode/UMI counts, feature spot matrices, cluster data, and perform gene expression analysis.
Genome_build: (mm10/GRCm38)
Supplementary_files_format_and_content: Filtered feature-barcode matrices (filtered_feature_bc_matrix) containing only spot barcodes in MEX format for each sample. Spatial folder output from space ranger count function containing QC images for aligned fiducials and detetected tissue in jpg format, scalefactors_json.json, high and low resolution versions of the input image in png format, and tissue_positions_list.csv

molecule: polyA RNA

source_name: Skin wound

growth_protocol: Spatial transcriptomics from unwounded and wounded skin

extract_protocol: Tissues were embedded in OCT and frozen in liquid nitrogen-chilled isopentane within 15 minutes of harvesting. 10-µm cryosections were mounted onto the ST arrays (10X Visium)  where reverse transcription of cellular transcripts took place in situ after tissue permeabilisation.

treatment_protocol: Mice were wounded 3 days before collecting tissue

value: Post-wounded skin day 3

tag: batch

value: Batch 2

value: GFP-KI


title: MLC18075

tag: diagnosis

tag: smoking status


title: GFP-KI WO II - ST

tag: tissue


title: Definitive Endoderm - Day 4_TUN_10_TP-8_REP-C [Bas132]

description:
Bas132
Cell lysate
count.txt
count_log2LibSizenorm.txt

source_name: Definitive Endoderm - Day 4

value: Definitive Endoderm

tag: compound

value: Tunicamycin (TUN)

value: 10 uM


title: PBS_control.3

value: 16 weeks old

value: vehicle (PBS) every 3 weeks x3


title: MLC17351

value: Cancer

value: Current smoker

tag: Sex

value: Male


title: Definitive Endoderm - Day 4_TUN_10_TP-8_REP-A [Bas130]

description:
Bas130
Cell lysate
count.txt
count_log2LibSizenorm.txt

tag: concentration

tag: time point


title: MLC17051

value: Non-smoker

value: Female

value: Bronchial epithelial cell


title: PBS_control.1

value: HSCs

value: PBS treated wild type HSCs


title: Definitive Endoderm - Day 4_TUN_10_TP-8_REP-B [Bas131]

description:
Bas131
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr

tag: replicate


title: WT WO II - ST

value: Post-wounded skin day 3

value: WT


title: 5FU_3cycles.4

description:
5FU_3cycles.fc.signal.bigwig
5FU_3cycles.filt.narrowPeak.gz

value: 5-fluorouracil 150 mg/kg every 3 weeks x3

value: 5-FU treated wild type HSCs


title: GFP-KI WO I- ST

value: Batch 1

value: GFP-KI


title: MLC15922


title: 5FU_3cycles.3

value: 16 weeks old


title: WT WO I - ST


title: MLC15722

value: Former smoker


title: Definitive Endoderm - Day 4_TUN_1_TP-8_REP-C [Bas124]

description:
Bas124
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Definitive Endoderm

value: Tunicamycin (TUN)

value: 1 uM


title: Definitive Endoderm - Day 4_TUN_1_TP-8_REP-B [Bas123]

description:
Bas123
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: WT UNWO I - ST

source_name: Normal skin

value: Normal / Healthy skin

value: Batch 2


title: 5FU_3cycles.2


title: MLC15522

value: Non-cancer

value: Male

value: Bronchial epithelial cell


title: Definitive Endoderm - Day 4_TUN_1_TP-8_REP-A [Bas122]

description:
Bas122
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: MLC15622

value: Cancer


title: 5FU_3cycles.1

value: HSCs


title: WT-A5-NEG-3 - BulkRNA

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software
The fastq files were trimmed for adaptor sequences using trimmomatic version 0.36 in paried end mode with parameters - minimal read length option set to 35 base pairs, trailing set to 5 and sliding window set to 4:15.
After trimming, the data was aligned to the mouse genome (mm10/GRCm38) using STAR.
The featureCounts program was used to generate raw counts for each gene.
Genome_build: (mm10/GRCm38)
Supplementary_files_format_and_content: The raw counts are stored in .csv format.

growth_protocol: Isolate epithlial cells from mouse skin tissue directly

extract_protocol:
A ring with width 0.25 mm of skin adjacent to the wound edge of control and Rorgt deficient animals (2 or 3 mice pooled per group per sequencing run) was excised and digested with Librase TL(Roche) . Wound edge epithelium was FACS purified from live Epcam+ cells based on integrin a6 and integrin a5 expression, while excluding CD45+ immune cells, CD31+ endothelial cells and CD117+ melanocytes. Total RNA was extracted from FACS purified integrin a6+ integrin a5+ (migrating tongue) and integrin a6+ integrin a5- (wound edge) samples using RNeasy Plus Micro Kit (Life Technologies)
Libraries were generated with SMART-Seq® v4 Ultra™ Low Input RNA Kit for Sequencing and SMARTer® ThruPLEX® DNA-Seq Kit (Takara Bio) flollowing te manufacturer's protocol.

treatment_protocol: mice were wounded 3 days before cell harvesting

value: Post-wounded skin

tag: time

value: day 3

value: WT

tag: a5 status


title: WT-A5-POS-3 - BulkRNA


title: Definitive Endoderm - Day 4_TUN_0.1_TP-8_REP-C [Bas116]

description:
Bas116
Cell lysate
count.txt
count_log2LibSizenorm.txt

tag: cell type


title: Definitive Endoderm - Day 4_TUN_0.1_TP-8_REP-B [Bas115]

description:
Bas115
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC15122

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample

value: Current smoker


title: PBS_control.2

value: 16 weeks old

value: vehicle (PBS) every 3 weeks x3

value: PBS treated wild type HSCs


title: YoungTreg_naive_5_RNAseq

city: Chicago

first: Benjamin

middle: D.

last: Singer

state: Illinois

address: 303 E. Superior St., Simpson Querrey 5th floor

institute: Northwestern University Feinberg School of Medicine

data_processing:
Basecalls performed using Illumina RTA2 software.
BCL2FASTQ v2.17.1.14 was used to convert bcl files to fastq files (default parameters).
Fastq files were aligned to the mm10 reference genome using Tophat v.2.1.0, and SeqMonk v1.45.4 was used to generate gene and transcript expression levels for protein-coding genes.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text file including raw counts values for each sample generated for uniquely mapped reads over exons was obtained using SeqMonk v1.45.4.

source_name: Lung Treg cells (CD3e+CD4+CD25hiFR4+)

extract_protocol:
RNA was extracted from sorted cells using the Qiagen AllPrep DNA/RNA Micro Kit.
NEB Next RNA Ultra, with polyA enrichment (Total, ribodRNA) and dual indexes

value: 2-months old

tag: exposure

value: naïve

value: Lung Treg cells (CD3e+CD4+CD25hiFR4+)


title: YoungTreg_naive_4_RNAseq


title: GFP-KI-A5-POS-3- BulkRNA

value: RORgt deficient


title: MLC15422

value: Non-smoker

value: Female


title: Definitive Endoderm - Day 4_TUN_0.01_TP-8_REP-C [Bas108]

description:
Bas108
Cell lysate
count.txt
count_log2LibSizenorm.txt

data_processing:
Library strategy: TempO-seq
Alignment of reads was done using the TempO-seqR package done by BioSpyder Technologies.
Samples were excluded for further analysis if library size was lower than 100.000 counts.
Raw counts were normalized using the DESeq2 R package (Love et al. 2014).
Normalized counts were log2 transformed.
Genome_build: BioSpyder manifest "Human Tox Panel TempO-Seq Probe Manifest 041416".
Supplementary_files_format_and_content: count.txt: Matrix table with raw counts for every probe and every sample.
Supplementary_files_format_and_content: count_log2LibSizenorm.txt: Matrix table with log2 normalized counts for every probe and every sample.

value: Definitive Endoderm

value: Tunicamycin (TUN)


title: MLC15822

value: Cancer

value: Bronchial epithelial cell


title: MLC13973

value: Former smoker

value: Male


title: GFP-KI-A5-NEG-3- BulkRNA

value: Post-wounded skin

value: day 3


title: MLC13798

value: Current smoker


title: YoungTreg_naive_2_RNAseq


title: YoungTreg_naive_3_RNAseq


title: Definitive Endoderm - Day 4_TUN_0.1_TP-8_REP-A [Bas114]

description:
Bas114
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 8 hr


title: MLC13773

value: Non-cancer


title: GFP-KI-A5-NEG-2 - BulkRNA


title: Definitive Endoderm - Day 4_TUN_0.01_TP-8_REP-B [Bas107]

description:
Bas107
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: AgedTreg_naive_5_RNAseq

value: 18-months old


title: Definitive Endoderm - Day 4_TUN_0.01_TP-8_REP-A [Bas106]

description:
Bas106
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: WT-A5-POS-2 - BulkRNA

value: WT


title: MLC13698

description: The upload of raw data was not approved by the Institutional Review Boards of Second Affiliated Hospital of Zhejiang University School of Medicine for the sake of security. However, raw data is available upon the special request by the editor temporarily.


title: GFP-KI-A5-POS-2 - BulkRNA


title: Definitive Endoderm - Day 4_TUN_0.001_TP-8_REP-C [Bas100]

description:
Bas100
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: AgedTreg_naive_4_RNAseq

value: naïve

value: Lung Treg cells (CD3e+CD4+CD25hiFR4+)


title: Definitive Endoderm - Day 4_TUN_0.001_TP-8_REP-B [Bas099]

description:
Bas099
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: WT-A5-NEG-2 - BulkRNA


title: AgedTreg_naive_3_RNAseq


title: AgedTreg_naive_2_RNAseq


title: WT-A5-POS-1 - BulkRNA


title: MLC13573


title: Definitive Endoderm - Day 4_TNF_50_TP-8_REP-B [Bas185]

description:
Bas185
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 50 ng/mL


title: WT-A5-NEG-1 - BulkRNA


title: AgedTreg_naive_1_RNAseq


title: Definitive Endoderm - Day 4_TUN_0.001_TP-8_REP-A [Bas098]

description:
Bas098
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Definitive Endoderm


title: MLC13473


title: GFP-KI-A5-NEG-1 - BulkRNA

value: RORgt deficient


title: YoungTreg_naive_1_RNAseq

value: 2-months old


title: MLC13498

value: Non-smoker

value: Female

value: Bronchial epithelial cell


title: Definitive Endoderm - Day 4_TNF_50_TP-8_REP-A [Bas184]

description:
Bas184
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: YoungTreg_flu_4_RNAseq

value: flu


title: Definitive Endoderm - Day 4_TNF_10_TP-8_REP-A [Bas177]

description:
Bas177
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 10 ng/mL


title: YoungTreg_flu_3_RNAseq


title: MLC13373

value: Cancer

value: Former smoker

value: Male


title: MLC13398


title: YoungTreg_flu_2_RNAseq


title: Definitive Endoderm - Day 4_TNF_7.5_TP-8_REP-B [Bas171]

description:
Bas171
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 7.5 ng/mL

value: 8 hr


title: MLC13673


title: Definitive Endoderm - Day 4_TNF_5_TP-8_REP-C [Bas164]

description:
Bas164
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 5 ng/mL


title: MLC13173


title: SE13_PMAiono

city: Tampere

first: Ilkka

last: Junttila

state: Tampere

address: Arvo Ylpön katu 34

department: Institute of Medical and Life Science

country: Finland

institute: University of Tampere

data_processing:
Constructed libraries were sequenced using Novogene RNA-seq, Illumina Platform PE150 (NovoSeq 6000)
Basecalling was performed by Novogen company
Sequenced reads were mapped to the reference genome (GRCm38.p6.genome.fa) using STAR software (version 2.7.). Annotation file used: gencode.vM23.annotation.gtf
Raw counts were obtained using –quantMode GeneCounts option in STAR. The raw count matrix was imported into R and used as input for DESeq2 for normalization and differential gene expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: raw_counts.csv – collected read counts from STAR-generated output files
Supplementary_files_format_and_content: DESeq2_normalized_counts.csv – read counts following DESeq2 normalization. Rows (corresponding transcripts, marked with ENSEMBL ID) with zero values in all columns (corresponding EL-4 clones with or without stimulation) are filtered.

source_name: EL-4 cell line

growth_protocol: Wild type (“empty”, e) and super-enhancer deleted (SE) EL-4 clones were maintained in growth medium: RPMI-1640, 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, 100 U/ml streptomycin, 1 mM sodium pyruvate, 4.5 g/l glucose, 0.05 mM 2-mercaptoethanol.

extract_protocol:
Total RNA was isolated using RNeasy kit (Qiagen) according to the manufacturer’s protocol.
rRNA removed using the Ribo-Zero kit. Libraries were prepared according to Illumina's instructions. Briefly, the RNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using RNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Then, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.
RNA-Seq (lncRNA library)

treatment_protocol: Prior activation, cells were first starved in 1% FBS containing culture medium for 1 h then left unstimulated or stimulated with 10 ng/ml PMA  and 100 ng/ml ionomycin for 6 h.

value: Lymphoblast

value: SE-deleted

tag: treatment

value: PMA (10 ng/ml) + ionomycin (100 ng/ml)


title: SE4_PMAiono


title: MLC13598

value: Non-cancer


title: YoungTreg_flu_1_RNAseq

tag: age

value: Lung Treg cells (CD3e+CD4+CD25hiFR4+)


title: MLC13098


title: GFP-KI-A5-POS-1 - BulkRNA

value: Post-wounded skin

value: day 3

value: RORgt deficient


title: Definitive Endoderm - Day 4_TNF_5_TP-8_REP-B [Bas163]

description:
Bas163
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Definitive Endoderm

value: TNF-alpha


title: AgedTreg_flu_5_RNAseq

value: 18-months old

value: flu


title: YoungTreg_flu_5_RNAseq

value: 2-months old


title: MLC10946

value: Former smoker

value: Male

value: Bronchial epithelial cell


title: MLC10846

value: Cancer

value: Current smoker


title: SE2_PMAiono

value: Lymphoblast

value: SE-deleted


title: Definitive Endoderm - Day 4_TNF_2.5_TP-8_REP-C [Bas156]

description:
Bas156
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 2.5 ng/mL

value: 8 hr


title: Definitive Endoderm - Day 4_TNF_5_TP-8_REP-A [Bas162]

description:
Bas162
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: 5 ng/mL


title: SE13_unstim

value: unstimulated


title: AgedTreg_flu_3_RNAseq

value: Lung Treg cells (CD3e+CD4+CD25hiFR4+)


title: AgedTreg_flu_2_RNAseq


title: Definitive Endoderm - Day 4_TNF_10_TP-8_REP-B [Bas178]

description:
Bas178
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: Definitive Endoderm

value: 10 ng/mL


title: AgedTreg_flu_4_RNAseq

value: 18-months old


title: Definitive Endoderm - Day 4_TNF_1_TP-8_REP-C [Bas148]

description:
Bas148
Cell lysate
count.txt
count_log2LibSizenorm.txt

value: TNF-alpha

value: 1 ng/mL


title: MLC10746

value: Non-cancer


title: Definitive Endoderm - Day 4_TNF_1_TP-8_REP-B [Bas147]

description:
Bas147
Cell lysate
count.txt
count_log2LibSizenorm.txt


title: MLC10674

value: Male


title: SE2_unstim