title: Day 42 LPL H2-Ab1^Villin biol rep 2

city: Birmingham

first: Casey

middle: T

last: Weaver

state: AL

address: 1900 University Blvd, THT Building

institute: University of Alabama at Birmingham

description:
Library name: D42LV2
10x Genomics

data_processing:
The demultiplexing, barcode processing, and gene counts were made using Cell Ranger v8.0.1(https://www.10xgenomics.com/support/software/cell-ranger/8.0)
Assembly: GRCm39
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Mid-distal colon

extract_protocol:
Three cellular compartments were isolated separately to capture spatial organization of immune responses. Intestinal epithelial cells (IECs) were isolated from 4 cm mid-distal colon tissue that was flushed with 1X PBS, opened longitudinally, and cut into 1 cm strips. Tissue pieces were incubated for 20 min at 37°C with 1 mM DTT, followed by 2 mM EDTA in H5H media (1X HBSS, 5% FBS, 20 mM HEPES, and 2.5 mM 2-β-ME). Tissue pieces were vortexed briefly after each 20 min incubation, followed by washing with H5H prior to centrifugation at 1750 rpm for 10 min at 4°C. IECs were then purified on a 40%/75% Percoll gradient by centrifugation for 20 min at 25°C and 2000 rpm with no brake. Intraepithelial lymphocytes (IELs) were obtained from the epithelial fraction during IEC isolation. Lamina propria lymphocytes (LPLs) were isolated from colonic tissue that was flushed with 1X PBS, opened longitudinally, cut into small pieces, and minced for 2-3 min before being transferred into complete R10 media (1X RPMI 1640, 10% FBS, 1X Pen/Strep, 1X NEAA, 1mM Sodium pyruvate, 2 mM L-glutamine, and 2.5 mM 2-β-ME) with collagenase IV (100 U/mL) and DNase I (20 μg/mL). Tissue was digested at 37°C for 40 min with stirring, filtered through a 70 μm filter, washed with complete R10 media, centrifuged at 1750 rpm at 4°C for 10 min, and then purified on a 40%/75% Percoll gradient. Following isolation, single-cell suspensions were stained and FACS-sorted to obtain live EpCAM⁺ IECs, live CD45⁺ IELs, and live CD45⁺ LPLs. B cells were depleted using anti-CD19 antibody during FACS to enrich for rare T cell populations. Post-sort viability was confirmed to be ≥90% by trypan blue exclusion, and sorted cells were collected directly into 5 μL PBS supplemented with 5% FBS and 0.1 mM EDTA.
Single-cell RNA sequencing libraries were prepared using the Chromium Single Cell 3' Gene Expression Kit (10x Genomics) at the FCSC Core Facility (UAB) according to the manufacturer's protocol. For each sample, 10,000 live sorted cells were loaded onto the 10x Chromium Controller. All 52 libraries were pooled and sequenced on two Illumina NovaSeq 6000 S4 flow cells using 2×100 bp paired-end reads.

value: Mid-distal colon

value: cKO


title: V5_ph_deltaSAM_1-3hr_exp3_chrom1

status: Public on Aug 11 2026

type: SRA

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz

country: Germany

institute: Max Planck Institute of Biochemistry

description: Library name: sample 32

library_source: genomic

data_processing:
Reads from fastq files were aligned to the dm6 genome (and to the D. pseudoobscura dp3 genome for subsequent normalization) using STAR (Dobin et al., 2013). Only sequences that mapped uniquely to the genome with a maximum of two mismatches were considered for further analyses.
Bam files were used as inputs to run Bioconductor packages.
The proportion of D. pseudoobscura reads as compared to D. melanogaster reads in input and in samples was used to normalize the ChIP-seq datasets for histone marks in embryos. Reference samples for normalization with D. pseudoobscura chromatin are indicated. Other samples were normalized based on total read number per million reads. Normalization factor for each sample is indicated.
Assembly: dm6
Supplementary files format and content: Normalized bigwig files (bin size = 1) were generated with deepTools (Ramirez et al., 2016).

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: 1-3hr old embryos

growth_protocol: Drosophila embryos were grown on standard medium at 25˚C

extract_protocol:
Lysates were clarified from sonicated fixed nuclei. Histone/Protein-DNA complexes were isolated with antibody. D. pseudoobscura chromatin was spiked in before the addition of the antibody.
Libraries were prepared according to manufacturer's instructions.
ChIP-Seq

tag: tissue

value: 1-3hr old embryos

tag: genotype

tag: antibodies

value: V5 (Cell Signalling (#D3H8Q))

tag: normalization factor


title: PFBS_HTR_N3_5um

status: Public on Aug 10 2026

city: San Diego

first: Elana

middle: R

last: Elkin

state: CA

address: 5500 Campanile Drive

department: School of Public Health

country: USA

institute: San Diego State University

description: Library name: PFBS_HTR_N3_5um

library_source: transcriptomic

data_processing:
Reads were aligned to the human genome using STAR.
Aligned reads were assigned to GRCh38 genes using featureCounts.
Genes with mean read counts-per-million less than 100 across all samples were filtered out and excluded from the analysis.
Data were normalized using the trimmed mean of M values (TMM) method
Differential gene expression testing was performed using the DeSeq2 package (version 4.1) for R statistical computing.
Assembly: hg38
Supplementary files format and content: tabular files

molecule: total RNA

organism: Homo sapiens

source_name: placenta

growth_protocol: HTR-8/SVneo cells: Cells were cultured between passages 25-75 and maintained in RPMI 1640 medium supplemented with 10% FBS and 1% P/S at 37 °C in a 5% CO2 humidified incubator. Cells were split and passaged at 70-90% confluence prior to use for experiments. Villous Explants: Term trimester placental tissues (N = 7, 4 male, 3 female) were obtained from full-term, non-laboring elective cesarean sections performed at UC San Diego Medical Center under Institutional Review Board approval with written informed consent. Tissues were collected in collaboration with UC San Diego Center for Perinatal Discovery. Following collection, tissues were transported back to the lab in ice-cold media. Tissues were repeatedly washed in PBS and blood clots removed. Chorionic villous tissue was carefully dissected out to form explants. Explants were further dissected into approximately 5 mg (wet) pieces. Four to six explants were placed in each experimental well, yielding a total of approximately 25 mg per well. Explants were cultured in RPMI 1640 medium supplemented with 10% FBS and 1% P/S and placed in experimental conditions immediately after dissections.

extract_protocol:
RNeasy Mini Kit (cells) miRNeasy Mini Kit (tissues)
TruSeq mRNA Library Prep Kit with poly(A) enrichment (Illumina, San Diego, CA, USA)

treatment_protocol: Explant Tissues: Immediately prior to each experiment 1M PFBS stock was quickly thawed in a 37°C water bath and diluted in complete RPMI 1640 medium (supplemented with 10% FBS and 1% P/S) to prepare a 1 mM intermediate working solution. The working solution was further diluted in RPMI 1640 medium to final concentrations of 100 nM-100 µM, depending on experiments. Final concentrations for RNA transcriptomic experiments were 0 and 5µM in cells, and 0, 5, and 20 µM PFBS in tissue explants.

value: placenta

tag: cell line

tag: cell type

value: Extravillous trophoblast

tag: exposure time

value: 24 hours

tag: treatment

value: 5 µM PFBS

tag: sequencing batch

value: batch 2025


title: PFBS_HTR_N3_Control

description: Library name: PFBS_HTR_N3_Control


title: Day 42 IEC H2-Ab1^Villin biol rep 2

description:
Library name: D42IVneg2
10x Genomics

library_source: transcriptomic single cell

organism: Mus musculus

value: EpCAM+ CD45-


title: PFBS_HTR_N2_Control

description: Library name: PFBS_HTR_N2_Control


title: PFBS_HTR_N2_5um

description: Library name: PFBS_HTR_N2_5um


title: Day 42 LPL H2-Ab1^Villin biol rep 1

description:
Library name: D42LV1
10x Genomics


title: PFBS_HTR_N1_5um

description: Library name: PFBS_HTR_N1_5um


title: PFBS_HTR_N1_Control

description: Library name: PFBS_HTR_N1_Control


title: Day 42 IEL H2-Ab1^Villin biol rep 1

description:
Library name: D42IVPos1
10x Genomics

value: EpCAM- CD45+


title: Day 42 IEC H2-Ab1^Villin biol rep 1

description:
Library name: D42IVNeg1
10x Genomics


title: input_ph_wt_1-3hr_exp3_chrom1

description: Library name: sample 22


title: PFBS_placenta7_5um_female

description: Library name: PFBS_placenta7_5um_female

tag: Sex

value: female

value: Explants-various cells

tag: placental donor

value: batch 2026


title: Day 42 LPL H2-Ab1^fl/fl biol rep 2

description:
Library name: D42LC2
10x Genomics

value: Wild-type


title: PFBS_placenta7_Control_female

description: Library name: PFBS_placenta7_Control_female


title: Day 42 LPL H2-Ab1^fl/fl biol rep 1

description:
Library name: D42LC1
10x Genomics


title: PFBS_placenta6_5um_male

description: Library name: PFBS_placenta6_5um_male


title: PFBS_placenta6_20um_male

description: Library name: PFBS_placenta6_20um_male


title: Day 42 IEL H2-Ab1^fl/fl biol rep 1

description:
Library name: D42ICPos1
10x Genomics


title: Day 42 IEC H2-Ab1^fl/fl biol rep 1

description:
Library name: D42ICNeg1
10x Genomics


title: PFBS_placenta5_20um_female

description: Library name: PFBS_placenta5_20um_female


title: Day 14 LPL H2-Ab1^Villin biol rep 2

description:
Library name: D14LVCD45_2
10x Genomics


title: Day 14 IEL H2-Ab1^Villin biol rep 2

description:
Library name: D14IVpos_2
10x Genomics


title: PFBS_placenta5_5um_female

description: Library name: PFBS_placenta5_5um_female


title: PFBS_placenta5_Control_female

description: Library name: PFBS_placenta5_Control_female


title: PFBS_placenta4_20um_female

description: Library name: PFBS_placenta4_20um_female

value: male


title: Day 14 IEC H2-Ab1^Villin biol rep 2

description:
Library name: D14IVneg_2
10x Genomics


title: Day 14 LPL H2-Ab1^Villin biol rep 1

description:
Library name: D14LVCD45_1
10x Genomics


title: HeLa cells, Coxiella infected, acetate-treated

city: Glendale

first: Dhritiman

last: Samanta

state: Arizona

institute: Midwestern University

description:
Library name: HeLa-Coxiella-infected-Acetate
ZCXBY5_4_4_WT_50mM

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id.
Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.  Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation. Differential expression was done with edgeR v4.0.16 using standard practice including filtering for low-expressed genes with edgeR::filterByExprwith default values. Functional enrichment, when available, is performed using gene set enrichment analysis with gseapy v0.12 using the MSigDB Hallmark gene set.
Assembly: GRCh38_114
Supplementary files format and content: comma separated values, raw counts for all samples
Supplementary files format and content: tab-separated values, gene expression matrix

source_name: HeLa

growth_protocol: HeLa cells were plated in a 6-well plate (5x10^4 per well) and either mock-infected or infected with WT C. burnetii for 2 h. After washing extensively with PBS, cells were incubated in 10% RPMI.

extract_protocol:
Cells were then centrifuged at 400xg for 5 min, and the pellet was washed once with PBS and centrifuged again. Pellets were then resuspended in 50 µL Zymo DNA/RNA shieldTM (Zymo Research, Irvine, CA, USA) and vortexed thoroughly to lyse the cells and shear the chromosomal DNA. A total of four samples, named Mock-PBS, Mock-acetate, WT-PBS, and WT-acetate, were then sent for RNAseq and analysis to Plasmidsaurus (South San Francisco, CA, USA). The authors did not perform the extraction in-house. Therefore we quote the following from Plasidsaurus website - " We extract total RNA using a bead-based extraction approach from cells preserved in Zymo DNA/RNA Shield". Also from Plasmidsaurus website - "We assess post-extraction (or received purified RNA) concentration using a fluorescence based plate reader assay and normalize sample concentrations before proceeding. Please note we do not assess an RNA Integrity Number (RIN) before proceeding, nor do we hold samples if the extracted RNA concentration is low. Making sure you send an adequate number of intact cells is key to getting optimal results."
From Plasmidsaurus website - "we convert mRNA into complementary DNA (cDNA) via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification."

treatment_protocol: At 2 dpi, cells were treated with either PBS or 50 mM acetate and incubated in the treatment conditions for 24 h. At 3 dpi, cells were harvested, counted, and diluted to 2x10^5 cells/mL.

value: HeLa

value: Cervical epithelial

value: WT

value: Coxiella infection + 50 mM sodium acetate


title: HeLa cell, uninfected, 50mM acetate-treated

description:
Library name: HeLa-Uninfected-Acetate
ZCXBY5_2_2_Control_50mM

value: 50 mM sodium acetate


title: Day 14 IEL H2-Ab1^Villin biol rep 1

description:
Library name: D14IVpos_1
10x Genomics

value: Mid-distal colon

value: cKO


title: PFBS_placenta4_Control_female

description: Library name: PFBS_placenta4_Control_female

value: placenta

value: 24 hours


title: Day 14 IEC H2-Ab1^Villin biol rep 1

description:
Library name: D14IVneg_1
10x Genomics


title: Day 14 LPL H2-Ab1^fl/fl biol rep 2

description:
Library name: D14LCCD45_2
10x Genomics


title: PFBS_Placenta3_5um_male

description: Library name: PFBS_Placenta3_5um_male

value: batch 2025


title: PFBS_Placenta3_Control_male

description: Library name: PFBS_Placenta3_Control_male


title: Day 14 IEC H2-Ab1^fl/fl biol rep 2

description:
Library name: D14ICneg_2
10x Genomics

value: EpCAM+ CD45-


title: PFBS_Placenta2_20um_male

description: Library name: PFBS_Placenta2_20um_male


title: Day 14 IEL H2-Ab1^fl/fl biol rep 2

description:
Library name: D14ICpos_2
10x Genomics

value: EpCAM- CD45+


title: Day 14 LPL H2-Ab1^fl/fl biol rep 1

description:
Library name: D14LCCD45_1
10x Genomics


title: Day 14 IEC H2-Ab1^fl/fl biol rep 1

description:
Library name: D14ICneg_1
10x Genomics


title: PFBS_Placenta1_20um_male

description: Library name: PFBS_Placenta1_20um_male


title: Day 9 IEL H2-Ab1^Villin biol rep 3

description:
Library name: D9IVPos3
10x Genomics


title: PFBS_Placenta1_5um_male

description: Library name: PFBS_Placenta1_5um_male


title: Day 9 IEC H2-Ab1^Villin biol rep 3

description:
Library name: D9IVNeg3
10x Genomics


title: PFBS_Placenta1_Control_male

description: Library name: PFBS_Placenta1_Control_male


title: imidazole propionate 100uM, experiment 3, replicate 2

city: Oslo

first: Peder

middle: Rustøen

last: Braadland

address: Sognsvannsveien 20

country: Norway

institute: Oslo University Hospital

description: Library name: E6

data_processing:
Raw Illumina sequencing reads were filtered to remove adapter sequences and low-quality reads. Clean reads were aligned to the reference genome. Gene-level fragment counts were generated by assigning mapped fragments to annotated genes. Gene expression was also quantified as FPKM (Fragments Per Kilobase of transcript per Million mapped fragments) using StringTie.
Assembly: GRCh38 (Ensembl release 95)
Supplementary files format and content: Tab-delimited .txt file containing gene-level raw fragment counts. Variables include 'ens' (Ensembl gene IDs), 'gene_symbol' (gene symbols), and individual samples mapping to 'library names'. Values represent the number of mapped sequencing fragments assigned to each gene in each sample.

growth_protocol: H69 cells were treated as described in Carpino, G. et al. Neoplastic Transformation of the Peribiliary Stem Cell Niche in Cholangiocarcinoma Arisen in Primary Sclerosing Cholangitis. Hepatology 69, 622–638 (2019).

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen 74106) and measured RNA concentration and quality using Nanodrop.
Qualified RNA were processed for library construction. The procedures are described as follows: (1) mRNA was isolated by Oligo(dT)-attached magnetic beads. (2) mRNA was then randomly fragmented in fragmentation buffer. (3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads. (4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp. (5) cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.

treatment_protocol: The cells were grown in FBS-free culture media overnight and were then amino acid-deprived by replacing the medium with EBSS for 1h. Next, the cells were cultured for another four hours with ImP or urocanate at concentrations of 10 or 100uM. The experiment was run in biological triplicates with technical duplicates (n=6 samples per condition).

value: wild-type


title: Day 9 IEL H2-Ab1^Villin biol rep 2

description:
Library name: D9IVPos2
10x Genomics


title: imidazole propionate 100uM, experiment 3, replicate 1

description: Library name: E5


title: Day 9 IEC H2-Ab1^Villin biol rep 2

description:
Library name: D9IVNeg2
10x Genomics


title: Day 9 LPL H2-Ab1^Villin biol rep 1

description:
Library name: D9LVCD45_1
10x Genomics


title: PFBS_Placenta2_5um_male

description: Library name: PFBS_Placenta2_5um_male

value: Explants-various cells


title: Day 14 IEL H2-Ab1^fl/fl biol rep 1

description:
Library name: D14ICpos_1
10x Genomics


title: PFBS_Placenta2_Control_male

description: Library name: PFBS_Placenta2_Control_male


title: imidazole propionate 100uM, experiment 2, replicate 1

description: Library name: E3


title: PFOA 700 ng/L from 3.5 hpf, 24 hpf, biological replicate 2

city: Durham

first: Zainab

last: Afzal

state: NC

address: 700 George Street, BBRI/Kumar Lab

institute: North Carolina Central University

description: Library name: Z10

data_processing:
Raw sequencing reads underwent quality-control assessment.
Reads were aligned to the Danio rerio reference genome assembly GRCz11.
Gene-level read counts were generated from aligned reads.
Differential expression analysis was performed using the edgeR algorithm in the Novomagic analysis platform.
Assembly: GRCz11
Supplementary files format and content: csv file contains raw counts for each sample
Supplementary files format and content: csv file contains FPKM values for each sample

organism: Danio rerio

source_name: whole embryo

growth_protocol: Wild-type Danio rerio adults were maintained under standard zebrafish husbandry conditions. Embryos were generated from independent spawning events, staged by hours post-fertilization, and maintained in embryo medium until collection at 24 hpf.

extract_protocol:
Total RNA was extracted from pooled whole embryos using the Direct-zol RNA Miniprep Kit (Zymo Research, catalog R2073-A), including on-column DNase treatment to remove genomic DNA.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep protocol. Libraries were sequenced on an Illumina NovaSeq platform to generate 150-bp paired-end reads.

treatment_protocol: Embryos were left untreated or exposed to 700 ng/L PFOA at different developmental timepoints begining at the 1-cell, 3.5 hpf, 5 hpf, or 8 hpf stage. All treatment groups were collected at 24 hpf for RNA extraction.

value: whole embryo

value: Embryos were exposed to 700 ng/L perfluorooctanoic acid (PFOA) beginning at 3.5 hpf and collected at 24 hpf.

tag: group

value: PFOA treated

tag: batch

value: total RNA


title: imidazole propionate 100uM, experiment 1, replicate 2

description: Library name: E2


title: Day 9 IEC H2-Ab1^Villin biol rep 1

description:
Library name: D9IVneg_1
10x Genomics


title: Day 9 IEL H2-Ab1^Villin biol rep 1

description:
Library name: D9IVpos_1
10x Genomics


title: PFOA 700 ng/L from 1-cell, 24 hpf, biological replicate 2

description: Library name: Z6

value: Embryos were exposed to 700 ng/L perfluorooctanoic acid (PFOA) beginning at 1-cell and collected at 24 hpf.


title: TET2KO lung endothelial cells, AngII, rep 2

city: London

first: Hashum

last: Sum

address: 125 Coldharbour Lane

country: United Kingdom

institute: King's College London

description:
Library name: EC5
BAM: EC5.bam

data_processing:
Sequence reads were trimmed to remove adapter sequences and low-quality bases using Trimmomatic v.0.36.
Trimmed reads were mapped to the Mus musculus GRCm38 reference genome using the STAR aligner v.2.5.2b.
Unique gene hit counts were quantified using featureCounts from the Subread package v.1.5.2.
Differential gene expression analysis between wild-type and TET2KO groups was performed using DESeq2.
Assembly: Mus_musculus/GRCm38
Supplementary files format and content: raw_counts.csv: Comma-separated text file containing raw gene hit counts for all samples.
Supplementary files format and content: TPM_values.csv: Comma-separated text file containing Transcripts Per Million (TPM) normalized expression values.

molecule: polyA RNA

source_name: lung

growth_protocol: Mice were subjected to 28 days of chronic Angiotensin II infusion, after which lung endothelial cells were isolated.

extract_protocol:
Total RNA was extracted using standard procedures, followed by poly(A)-selected mRNA library preparation.
Libraries were prepared using poly(A) selection and sequenced as paired-end (2x150 bp) on the Illumina NovaSeq platform.

treatment_protocol: Chronic infusion of Angiotensin II for 28 days in wild-type and endothelial-specific TET2 knockout mice.

value: lung

value: lung endothelial cells

value: Angiotensin II


title: WT heart, AngII, rep 3

description:
Library name: H3
BAM: H3.bam

data_processing:
Raw sequence reads were trimmed to remove adapter sequences and low-quality bases using Trimmomatic v.0.36. Paired-end reads were aligned to the Mus musculus GRCm38 (mm10) reference genome using the STAR aligner v.2.5.2b, yielding alignment files (sample.bam).
Gene-level hit counts were extracted using featureCounts from the Subread package v.1.5.2 (hit-counts/raw_counts.csv).
Gene expression levels were quantified and normalized as TPM values (hit-counts/TPM_values.csv).
Differential gene expression analysis was performed using DESeq2, and Gene Ontology (GO) enrichment analyses were conducted using GeneSCF (Significant-DEGs.csv, Differential_expression_analysis_table.csv, GO_analysis).
Assembly: mm10
Supplementary files format and content: Comma-delimited CSV file containing raw gene read counts (hit-counts/raw_counts.csv).
Supplementary files format and content: Comma-delimited CSV file containing TPM expression values (hit-counts/TPM_values.csv).

source_name: heart

growth_protocol: Mice were maintained under standard housing conditions with ad libitum access to food and water.

extract_protocol:
Total RNA was extracted from mid-ventricular heart tissue samples using standard RNA isolation protocols.
Sequencing libraries were prepared from mouse total RNA using poly(A) selection for mRNA enrichment, followed by Illumina-compatible library preparation kits for paired-end sequencing (PE 2x150) on the Illumina NovaSeq 6000 platform.

treatment_protocol: Adult wild-type and endothelial-specific TET2 knockout mice were subjected to chronic infusion of Angiotensin II (1.0 mg/kg/day) via subcutaneous osmotic minipumps for 28 days to induce cardiac hypertrophy and hypertensive remodeling.

value: heart

value: cardiac muscle tissue

value: WT


title: imidazole propionate 100uM, experiment 1, replicate 1

description: Library name: E1


title: imidazole propionate 10uM, experiment 3, replicate 1

description: Library name: D5


title: Day 9 IEC H2-Ab1^fl/fl biol rep 3

description:
Library name: D9ICNeg3
10x Genomics

value: Mid-distal colon

value: Wild-type


title: Day 9 IEL H2-Ab1^fl/fl biol rep 3

description:
Library name: D9ICPos3
10x Genomics


title: imidazole propionate 10uM, experiment 3, replicate 2

description: Library name: D6


title: Day 9 LPL H2-Ab1^Villin biol rep 2

description:
Library name: D9LV2
10x Genomics

value: cKO


title: 154_PEMCs_PBMCs_mRNA_VDJ_Sample_Tag

city: Sydney

first: Jennifer

last: Simpson

address: 176 Hawkesbury Rd

country: Australia

institute: WIMR

description:
Library name: 206_154_23MWK3LT4_GCTACGCT-TATAGCCT_mRNA_VDJ_SampleTag
127 and 154 Sample Tag sequences.xlsx

data_processing:
Seven Bridges Pipeline, Seurat
Assembly: GRCH 38
Supplementary files format and content: barcodes.tsv (barcodes for RNAseq), features.tsv (gene names for RNAseq), matrix.mtx (data for RNAseq), files ending in "_VDJ_Dominant_Contigs_AIRR" is TCR data, and files ending in "Sample_Tag_Calls" shows Sample tag details

source_name: PEMCs/PBMCs

extract_protocol: BD Rhapsody protocol

value: PEMCs/PBMCs


title: imidazole propionate 10uM, experiment 2, replicate 2

description: Library name: D4

value: wild-type


title: Day 9 LPL H2-Ab1^fl/fl biol rep 2

description:
Library name: D9LC2
10x Genomics


title: Day 9 IEL H2-Ab1^fl/fl biol rep 2

description:
Library name: D9ICPos2
10x Genomics

value: EpCAM- CD45+


title: Mouse lung tissue, room temperature control, biological replicate 3

city: Shanghai

first: Junkun

last: Jiang

address: 500 Zhennan Road, Putuo District

country: China

institute: Tongji University

description: Library name: Control_3

data_processing:
RNA-seq data were processed using CLC Genomics Workbench.
Sequencing reads were quality assessed and adapter sequences were removed.
Clean reads were aligned to the mouse reference genome (mm10) using CLC Genomics Workbench.
Gene-level read counts were extracted using CLC Genomics Workbench to generate the raw count matrix.
Assembly: mm10
Supplementary files format and content: Excel file containing gene-level raw read count matrix for all samples.

source_name: Lung

growth_protocol: Male C57BL/6J mice were maintained under standard laboratory conditions with free access to food and water.

extract_protocol:
Total RNA was extracted from mouse lung tissues using standard RNA extraction methods.
RNA-seq libraries were constructed using the NEBNext Ultra II RNA Library Prep Kit following the manufacturer's instructions.

treatment_protocol: Mice were exposed to cold temperature (4 °C) for 6 h or maintained at room temperature as control. Lung tissues were collected after treatment.

value: Lung

value: wild type

value: room temperature control


title: HeLa cell, uninfected, PBS-treated

description:
Library name: HeLa-Uninfected-PBS
ZCXBY5_1_1_Control_DPBS

value: HeLa

value: Cervical epithelial

value: PBS (control)


title: imidazole propionate 10uM, experiment 2, replicate 1

description: Library name: D3


title: imidazole propionate 10uM, experiment 1, replicate 1

description: Library name: D1


title: Day 9 IEC H2-Ab1^fl/fl biol rep 2

description:
Library name: D9ICNeg2
10x Genomics

value: EpCAM+ CD45-


title: Day 9 LPL H2-Ab1^fl/fl biol rep 1

description:
Library name: D9LCCD45_1
10x Genomics


title: Day 9 IEL H2-Ab1^fl/fl biol rep 1

description:
Library name: D9ICpos_1
10x Genomics


title: imidazole propionate 10uM, experiment 1, replicate 2

description: Library name: D2


title: urocanate 100uM, experiment 3, replicate 2

description: Library name: C6


title: WT, 3 months #13

city: Calgary

first: Paul

last: Gordon

state: AB

address: 3330 Hospital Drive NW

country: Canada

institute: University of Calgary

description: Library name: WT-3-13-F

data_processing:
Kallisto 0.48.0 pseudo-mapping with k-mer=31, against Danio rerio Ensembl transcriptome
Assembly: GRCz11
Supplementary files format and content: tab-delimited file containing the raw counts for each transcript (Ensembl identifiers)

source_name: ovary

extract_protocol:
RNA was extracted using Qiagen RNAeasy kit.
NEB UltraExpress RNA Library Prep Kit (pol;y dT capture)

value: ovary

value: WT- Female

value: 3 months post fertilisation


title: rABS+shCtrl-1

city: Miami

first: Wael

last: El-Rifai

state: FL

address: Griffin Cancer Research Building,1425 NW 10th Ave

department: Department of Surgery and Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

description: Library name: Ctrl-1

data_processing:
Raw paired-end reads were trimmed to remove adapter sequences and low-quality nucleotides using Trimmomatic v0.36. The trimmed reads were aligned to the Homo sapiens GRCh38 reference genome available from Ensembl using STAR v2.5.2b. Unique gene-level read counts were generated using featureCounts from the Subread package v1.5.2. Counts were summarized using the gene_id feature in the annotation file, and only uniquely mapped reads falling within annotated exon regions were counted.
Assembly: GRCh38
Supplementary files format and content: The processed data file, rABS_RNAseq_Genewiz_2025_12samples_count_matrix.tsv.gz, is a gzip-compressed, tab-delimited gene-level raw-count matrix. Rows represent genes identified by Ensembl gene_id identifiers, columns represent the 12 biological samples, and values are unnormalized integer read counts.

source_name: esophageal adenocarcinoma (EAC)

growth_protocol: OE33 cells were cultured RPMI1640 supplemented with 10% FBS,  and 1% Pen-Step with 5% CO2 at 37C.

extract_protocol:
RNA was extracted from cells using RLT buffer (RNeasy Kit Qiagen)
Standard RNA-sequencing (mRNA-Seq) in eukaryotic samples: Polyadenylated mRNA is selectively enriched from total RNA using oligo(dT) magnetic beads. High-temperature thermal treatment in divalent cation buffer fragments the mRNA to ~250–300 bp.

treatment_protocol: human EAC cells (OE33) were exposed to an acidified bile salt cocktail (200 µM, pH 5.5) for 20 minutes daily over 15 days (rABS), while untreated parental cells served as baseline controls. Following the 15-day selection protocol, the surviving rABS-adapted OE33 cells were stably transduced with either a non-targeting control shRNA (shCtrl) or an APE1-targeted shRNA (shAPE1).

value: esophageal adenocarcinoma (EAC)

value: Epithelial

value: repeated ABS with shCtrl


title: urocanate 100uM, experiment 3, replicate 1

description: Library name: C5


title: Day 9 IEC H2-Ab1^fl/fl biol rep 1

description:
Library name: D9ICneg_1
10x Genomics

value: Mid-distal colon

value: Wild-type


title: Day 0 LPL H2-Ab1^Villin biol rep 2

description:
Library name: D0LV2
10x Genomics

value: cKO


title: urocanate 100uM, experiment 2, replicate 2

description: Library name: C4

value: wild-type


title: Day 0 IEL H2-Ab1^Villin biol rep 2

description:
Library name: D0IVpos2
10x Genomics

value: EpCAM- CD45+


title: Day 42 IEL H2-Ab1^Villin biol rep 2

description:
Library name: D42IVpos2
10x Genomics


title: urocanate 100uM, experiment 2, replicate 1

description: Library name: C3


title: Day 0 IEC H2-Ab1^Villin biol rep 2

description:
Library name: D0IVneg2
10x Genomics


title: urocanate 100uM, experiment 1, replicate 1

description: Library name: C1


title: urocanate 100uM, experiment 1, replicate 2

description: Library name: C2


title: Day 0 IEL H2-Ab1^Villin biol rep 1

description:
Library name: D0IVpos1
10x Genomics


title: urocanate 10uM, experiment 3, replicate 2

description: Library name: B6


title: Day 0 LPL H2-Ab1^Villin biol rep 1

description:
Library name: D0LV1
10x Genomics


title: imidazole propionate 100uM, experiment 2, replicate 2

description: Library name: E4


title: Day 0 IEC H2-Ab1^Villin biol rep 1

description:
Library name: D0IVneg1
10x Genomics


title: urocanate 10uM, experiment 3, replicate 1

description: Library name: B5


title: Day 0 LPL H2-Ab1^fl/fl biol rep 2

description:
Library name: D0LC2
10x Genomics


title: urocanate 10uM, experiment 2, replicate 2

description: Library name: B4


title: Day 0 IEL H2-Ab1^fl/fl biol rep 2

description:
Library name: D0ICpos2
10x Genomics


title: Day 0 IEC H2-Ab1^fl/fl biol rep 2

description:
Library name: D0ICneg2
10x Genomics


title: Day 0 LPL H2-Ab1^fl/fl biol rep 1

description:
Library name: D0LC1
10x Genomics


title: urocanate 10uM, experiment 1, replicate 1

description: Library name: B1


title: Day 0 IEL H2-Ab1^fl/fl biol rep 1

description:
Library name: D0ICpos1
10x Genomics


title: urocanate 10uM, experiment 2, replicate 1

description: Library name: B3


title: vehicle, experiment 3, replicate 2

description: Library name: A6


title: vehicle, experiment 3, replicate 1

description: Library name: A5


title: QC04-21-H2Az-Y2-IP_rep2

city: Beijing

first: Mingzhao

last: Zhu

address: 15 Da Tun Rd, Chaoyang District

department: Key Laboratory of Infection and Immunity

institute: Institute of Biophysics, Chinese Academy of Sciences

description: Library name: QC04-21-H2Az-Y2-IP

data_processing:
Raw sequencing data were trimmed and filtered by using Trim Galore v0.6.7.
Bowtie2 v2.5.1 was used to align reads to the mouse genome with default parameters and then sorted using the Samtools v1.15.
MACS2 v2.2.7.1 was used to call peaks.
bamCoverage v3.5.1 was used to generate bigwig files from bam files.
Assembly: mm10
Supplementary files format and content: bigWig files

source_name: spleen

extract_protocol:
Immature single postive CD8+ T cell, mature single postive CD8+ T cell and naive CD8+ T cells were sorted from thymus and spleen of WT mice. Naïve CD8+ T (CD62L+CD44lo) cells were purified from spleens of  WT and IL-7R-cKO, BCL2+ WT and BCL2+ IL-7R-cKO, and young and aged mice. DNA for CUT&Tag-seq was cleavaged Under Target & Tagmentation by H2A.Z antibody (abcam, #ab4174) in Tcells and Genomic DNA was extracted using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, #TD904). The ChIP experiment was conducted using the ULI-NChIP protocol to detect the enrichment of H3K27ac (abcam, #ab4729).
CUT&Tag libraries was performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, #TD904), following the manufacturer’s instructions. ChIP libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, #E7645L), following the manufacturer's instructions.

value: spleen

value: naive CD8+ T cell

value: WT

value: unstimulated


title: vehicle, experiment 2, replicate 1

description: Library name: A3


title: QC04-21-H2Az-Y1-IP_rep1

description: Library name: QC04-21-H2Az-Y1-IP


title: vehicle, experiment 1, replicate 2

description: Library name: A2


title: L2C Control

city: Barcelona

first: Manel

last: Esteller

state: Barcelona

address: Carrer de Sant Quintí, 77, Horta-Guinardó, 08041 Barcelona

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: IR Sant Pau

description: FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space ranger pipeline to generate FASTQ files and sequences were aligned to GRCh38 genome using 10x Genomics default human reference genome and probe set files.
Assembly: GRCh38
Supplementary files format and content: filtered_barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: filtered_features.tsv.gz: list of gene Ids
Supplementary files format and content: filtered_matrix.mt.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots

extract_protocol:
RNA was extracted using a protocol from Qiagen (Rneasy FFPE Kit 73504), following extraction, the product was analyzed by TapeStation.  Samples with DV200 ≥ 22% were selected for experiments.
Spatial transcriptome sequencing libraries were preapred with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer´s construction.
Spatial Transcriptomics

value: Lung

tag: disease state

value: Control


title: QC04-21-H2Az-Y2-input_rep2

description: Library name: QC04-21-H2Az-Y2-input


title: QC04-21-H2Az-Y1-input_rep1

description: Library name: QC04-21-H2Az-Y1-input


title: L14C Control

description: FFPE Spatial transcriptome sequencing


title: vehicle, experiment 1, replicate 1

description: Library name: A1


title: QC04-21-H2Az-A2-IP_rep2

description: Library name: QC04-21-H2Az-A2-IP


title: L3C Control

description: FFPE Spatial transcriptome sequencing


title: multi_seq_3

city: Pittsburgh

first: guang

last: li

state: PA

address: 530 45th St. 8116 Rangos Research Center

institute: university of pittsburgh

description: Library name: multival3

data_processing:
Single cell samples were mapped to human genome using CellRanger and further demultiplxed using deMULTIPlex. The data in each sample was further analyzed with Seurat.
Assembly: hg38
Supplementary files format and content: Seurat object for each scRNA-seq dataset

source_name: organoids

extract_protocol:
For the single cell RNA-seq experiments, cells were dissociated with accutase, stained with MULTI-seq barcode, and pooled and loaded to 10X Genomics V3.1 kit for RNA revers transcription.
The single cell mRNA-seq libraries were constructed with 10X Genomics V3.1 kit, and the MULTI-seq libraries were made with Kapa HiFi HotStart PCR Kit.

value: organoids

value: valve cells

value: endothelial cell, valve interstitial cell


title: HRC4 AcuteDAD

description: FFPE Spatial transcriptome sequencing

value: Acute DAD


title: QC04-21-H2Az-A2-input_rep2

description: Library name: QC04-21-H2Az-A2-input


title: multi_seq_2

description: Library name: multival2


title: HRC18 AcuteDAD

description: FFPE Spatial transcriptome sequencing


title: HRC2 AcuteDAD

description: FFPE Spatial transcriptome sequencing


title: QC04-21-H2Az-A1-IP_rep1

description: Library name: QC04-21-H2Az-A1-IP


title: L12P AcuteDAD

description: FFPE Spatial transcriptome sequencing


title: L24P AcuteDAD

description: FFPE Spatial transcriptome sequencing


title: multi_seq_1

description: Library name: multival1


title: L14P AcuteDAD

description: FFPE Spatial transcriptome sequencing


title: QC04-21-H2Az-A1-input_rep1

description: Library name: QC04-21-H2Az-A1-input


title: geneexpression_3

description: Library name: geneval3


title: L5P AcuteDAD

description: FFPE Spatial transcriptome sequencing


title: HRC17 ProliferativeDAD

description: FFPE Spatial transcriptome sequencing

value: Proliferative DAD


title: N_WT-H2AZ-CUTandTag_rep2

description: Library name: N_WT-H2AZ-CUTandTag_N2

data_processing:
Raw sequencing data were trimmed and filtered by using Trim Galore v0.6.7.
Bowtie2 v2.5.1 was used to align reads to the mouse genome with default parameters and then sorted using the Samtools v1.15.
MACS2 v2.2.7.1 was used to call peaks.
bamCoverage v3.5.1 was used to generate bigwig files from bam files.
Assembly: mm10
Supplementary files format and content: bigWig files
Library strategy: CUT&Tag


title: HRC13 ProliferativeDAD

description: FFPE Spatial transcriptome sequencing


title: N_WT-H2AZ-CUTandTag_rep1

description: Library name: N_WT-H2AZ-CUTandTag_N1


title: geneexpression_1

description: Library name: geneval1


title: HRC12 ProliferativeDAD

description: FFPE Spatial transcriptome sequencing


title: geneexpression_2

description: Library name: geneval2


title: 127_PEMCs_PBMCs_mRNA_VDJ_Sample_Tag

description:
Library name: 127_Rhapsody_Gabriel_22W3W3LT3_GCTACGCT-TATAGCCT_mRNA_VDJ_Sample_Tag
127 and 154 Sample Tag sequences.xlsx

value: PEMCs/PBMCs


title: HRC10 ProliferativeDAD

description: FFPE Spatial transcriptome sequencing


title: HRC8 ProliferativeDAD

description: FFPE Spatial transcriptome sequencing


title: HRC6 ProliferativeDAD

description: FFPE Spatial transcriptome sequencing


title: iPSC-RGC_rep3

city: Aoba-ku, Sendai

first: Seiya

last: Kanno

state: Miyagi

address: 1-1 Seiryo-cho

department: Department of Ophthalmology

country: Japan

institute: Tohoku University Graduate School of Medicine

description:
Library name: Sample3
WT_WT.3

data_processing:
The RNA-seq libraries were sequenced using 150 bp paired-end reads on a DNBSEQ-G400 instrument (MGI Tech), aiming for a sequencing depth of 30 million paired-end reads per sample. The obtained reads were mapped to the human reference genome (GRCh38/hg38) using STAR software (version 2.7.11b). Reads corresponding to annotated genes were counted using featureCounts software (version 2.0.6).
Assembly: GRCh38/hg38
Supplementary files format and content: The .txt file contains Counts Per Million (CPM) mapped reads for each sample.

growth_protocol: A human iPSC line, 201B7 (HPS0063, Riken Cell Bank; Japan), was routinely cultured in StemFit medium (AK03N, Ajinomoto Healthy Supply; Japan) on culture plates coated with 0.5 μg/cm^2 of iMatrix-511 (892012, Matrixome; Japan). The cells were incubated at 37°C in a humidified chamber containing 5% CO2.

extract_protocol:
RGCs were isolated and purified via MACS using magnetic beads conjugated with an anti-Thy1.2 antibody, yielding 1 × 10^5 cells per sample. Total RNA was extracted from the purified RGCs using the miRNeasy Mini Kit (217004, Qiagen) following the manufacturer’s protocol.
Double-strand cDNA libraries were prepared using the QIAseq UPX 3' Transcriptome Library Kit (333088, Qiagen) and the MGIEasy Universal Library Conversion Kit (App-A) (1000004155, MGI Tech; China).

treatment_protocol: Human iPSCs were dissociated into single cells and seeded onto iMatrix511-coated plates in StemFit medium supplemented with 10 µM Y-27632 (day -1). From day 1 to 30, all small molecules were added to N2B27 medium and supplied to the cells as indicated in the previous study (Sluch en al., 2017). The N2B27 medium was fully exchanged every two days, except for the time points when the additive composition was changed. From day 30 until MACS purification, the cells were cultured in N2B27 medium supplemented with 25 µM forskolin, with daily full medium changes.

value: induced pluripotent stem cells

value: POU4F2-P2A-EGFP-P2A-Thy1.2 knock-in

value: Retinal ganglion cell differentiation


title: HRC5 ProliferativeDAD

description: FFPE Spatial transcriptome sequencing


title: N_IgG_Ctr

description: Library name: N_IgG


title: iPSC-RGC_rep2

description:
Library name: Sample2
WT_WT.2


title: Dev_naiveCD8_H2AZ-CUTandTag_rep2

description: Library name: Dev_naiveCD8_H2AZ-CUTandTag_2


title: iPSC-RGC_rep1

description:
Library name: Sample1
WT_WT.1


title: L2P ProliferativeDAD

description: FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space ranger pipeline to generate FASTQ files and sequences were aligned to GRCh38 genome using 10x Genomics default human reference genome and probe set files.
Assembly: GRCh38
Supplementary files format and content: filtered_barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: filtered_features.tsv.gz: list of gene Ids
Supplementary files format and content: filtered_matrix.mt.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

extract_protocol:
RNA was extracted using a protocol from Qiagen (Rneasy FFPE Kit 73504), following extraction, the product was analyzed by TapeStation.  Samples with DV200 ≥ 22% were selected for experiments.
Spatial transcriptome sequencing libraries were preapred with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer´s construction.


title: Mouse 1 tumor CD8 T cells treated with anti-PD1, anti-CTLA4, CD40 agonist, and CD4 depletion

city: Groningen

first: Marco

last: de Bruyn

address: Hanzeplein 1

department: Obstetrics&Gynecology

country: Netherlands

institute: University Medical Center Groningen

description: Library name: Pool2_MR260626_024_S1_R1_001

data_processing:
Data was demultiplexed into individual FASTQ files followed by alignment to the mouse reference genome using STAR (version 2.5.2).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files with raw readcounts per sample

source_name: Tumor

growth_protocol: Tissue harvested from wild-type Balb/c OlaHsd Mus Musculus organs

extract_protocol:
At the end of the experiment, mice were euthanized and spleen, tumor-draining lymph node (tdLN), and tumor were collected and placed in RPMI media supplemented with 10% FCS. Spleens were mashed through a 70-μm filter and centrifuged at 1200 rpm for 5 min at 4°C. Supernatant was discarded and pellet was resuspended in 1 mL of RBC lysis buffer and incubated for 5 min on ice. Next, cells were washed with 20 mL of 1× PBS, centrifuged at 1200 rpm for 5 min at 4°C, supernatant was discarded, and cells were frozen in FCS supplemented with 10% DMSO. Lymph nodes were mashed through a 70-μm filter, the filter was rinsed a few times with PBS and suspension was collected. Next, samples were centrifuged at 1200 rpm for 5 min at 4°C and resuspended in FCS supplemented with 10% DMSO prior to freezing. Tumors were excised with the skin and weighed before cutting them. A piece of the tumor was separated from the skin and chopped with a scalpel into ~1–2-mm pieces. These were then transferred to a 25 mL flask with 5 mL of digestion media (RPMI 1640 containing collagenase IV (Sigma Aldrich, 1 mg/mL) and Pulmozyme (Roche, 12.6 U/mL)) and incubated for 1–1.5 hours at 37°C. Following incubation, the digested tumor was poured onto a 70-μm strainer placed in a 50 mL tube. The 25 mL flask was rinsed with 5 mL of 1× PBS and added to the digested sample. The tumor was mashed with a plunger through the 70-μm strainer, which was then rinsed a few times with 1× PBS. Suspensions were then centrifuged at 1200 rpm for 5 min at 4°C and single-cell suspensions of tumor were frozen in FCS supplemented with 10% DMSO. Samples were kept at –80°C until ready to use.
Frozen single-cell suspensions were thawed in FCS. Next, cells were washed 2 times with 1× PBS at 1200 rpm for 5 min. Cells were then stained for live/dead using Zombie Aqua (BioLegend) for 15–20 min at room temperature (RT) according to manufacturer’s instructions. Cells were washed with 2 mL of 1× PBS/5% FBS and resuspended in 100 µL with the appropriate surface antibodies (Table S7) for 45 min at 4°C. After the incubation period, cells were washed with 1× PBS/2% FCS, resuspended in 500–800 µL of 1× PBS/2% FCS and cells were sorted in a 96-well plate containing lysis buffer, dNTPs (10 mM) and 10 µM oligo(dT) primer. The sorting strategy for tumor-infiltrating lymphocytes was as follows: single cells, live cells, CD45+ NKp46− γδ-TCR− CD3+ CD4− CD8+. The sorting strategy for T cells from the lymph nodes was: single cells, live cells, CD45+ NKp46− γδ-TCR− CD3+ CD4− CD8+ PD1+. After the last sample was sorted, plates were incubated at 72°C for 3 min, spun down and reverse transcription mix was added to all corresponding wells. Subsequent steps were performed as previously described (72). Quality controls of the libraries were performed after each step using Qubit (Thermo Fisher) and TapeStation (Agilent). Finally, samples were prepared in 2 superpools by equimolar pooling. 700 pM of each superpool was sequenced independently on a NextSeq 500 (Illumina Inc., San Diego, CA, USA) using a NextSeq high-output reagent kit (400M, single read).

treatment_protocol: Treated with anti-PD1+anti-CTLA4 antagonistic therapeutic antibodies with or without anti-CD40 agonist antibody and/or anti-CD4 depleting antibodies

value: Tumor

value: CD8 T cell

value: Balb/c OlaHsd wild-type


title: Dev_naiveCD8_H2AZ-CUTandTag_rep1

description: Library name: Dev_naiveCD8_H2AZ-CUTandTag_1

value: spleen

value: naive CD8+ T cell


title: Input_R1

city: IOWA CITY

first: Thomas

last: rutkowski

state: Iowa

address: 51 newton Rd

department: Anatomy and Cell Biology

institute: uiowa

description: Library name: Input_R1

data_processing:
Reads were aligned to the mouse reference genome mm10 by Bowtie with at most 2 mismatches. Reads that appeared more than twice at the same position on the same strand were discarded to remove PCR duplication. After filtering bam files by Samtools v1.9 and Sambamba v0.7.1, we used MACS2 v2.1.2 to call peaks with default parameters. The R package ChIPseeker was applied to annotate peaks.
Assembly: mouse reference genome mm10
Supplementary files format and content: bigWig, narrowPeak (except for input)

source_name: Liver

extract_protocol:
ChIP-seq was performed by Zymo Research using pooled samples from 3 mice treated with 1 mg/kg b.w. TM for 8h. IP was with CHOP antibody B-3 (sc7351, Santa Cruz), previously validated for specificity (Chikka et al. 2013 ), and validated prior to ChIP-seq against control Ig (12-371, Millipore Sigma) for the known CHOP-binding region in the Gadd34 promoter (Marciniak et al. 2004 ). Approximately 100-250 μg of chromatin was used. ChIP-seq libraries were prepared using a proprietary library preparation protocol from Zymo Research. ChIP-Seq libraries were diluted to 2 nM before being multiplexed and run on the Next-Gen Sequencing platform –HiSeq using single-end reads. For sequencing data analysis, FastQC was applied to conduct quality control for ChIP-seq data. Reads were aligned to the mouse reference genome mm10 by Bowtie with at most 2 mismatches. Reads that appeared more than twice at the same position on the same strand were discarded to remove PCR duplication. After filtering bam files by Samtools v1.9 and Sambamba v0.7.1, we used MACS2 v2.1.2 to call peaks with default parameters. The R package ChIPseeker was applied to annotate peaks. ChIP-seq motif analysis was performed with HOMER, searching against IMAGE known motifs. Pathway analysis for RNA-seq and ChIP-seq was performed using DAVID (Dennis et al. 2003 ), and enriched transcription factor binding sites were analyzed using ChEA3 (Keenan et al. 2019 ) and the ReMap database.
Approximately 100-250 μg of chromatin was used. ChIP-seq libraries were prepared using a proprietary library preparation protocol from Zymo Research

treatment_protocol: Tunicamycin 1 mg/kg.b.w. for 8h I.P.

value: Liver

value: WT

value: Tunicamycin


title: Mouse 2 lymph node CD8 T cells treated with anti-PD1, anti-CTLA4, CD40 agonist, and CD4 depletion

description: Library name: Pool2_MR260626_023_S2_R1_001

source_name: lymph node

value: lymph node


title: Dev_mSP8_H2AZ-CUTandTag_rep2

description: Library name: Dev_mSP8_H2AZ-CUTandTag_2

source_name: thymus

value: thymus

value: mature single postive CD8+ T cell

value: unstimulated


title: Mouse 2 lymph node CD8 T cells treated with anti-PD1, anti-CTLA4, and CD4 depletion

description: Library name: Pool2_MR260626_022_S3_R1_001


title: CHOP_698_699_709_R1

description: Library name: CHOP_698_699_709_R1


title: Mouse 1 lymph node CD8 T cells treated with anti-PD1, anti-CTLA4, and CD4 depletion

description: Library name: Pool2_MR260626_021_S4_R1_001


title: Mouse 2 lymph node CD8 T cells isotype control

description: Library name: Pool2_MR260626_020_S5_R1_001

value: isotype


title: Mouse 2 lymph node CD4 T cells isotype control

description: Library name: Pool2_MR260626_019_S6_R1_001

value: CD4 T cell


title: Mouse 2 tumor CD8 T cells treated with anti-PD1, anti-CTLA4, CD40 agonist, and CD4 depletion

description: Library name: Pool2_MR260626_018_S7_R1_001


title: Mouse 2 tumor CD8 T cells treated with anti-PD1, anti-CTLA4, and CD4 depletion

description: Library name: Pool2_MR260626_017_S8_R1_001


title: Dev_imSP8_H2AZ-CUTandTag_rep1

description: Library name: Dev_imSP8_H2AZ-CUTandTag_1

value: immature single postive CD8+ T cell


title: Mouse 1 tumor CD8 T cells treated with anti-PD1, anti-CTLA4, and CD4 depletion

description: Library name: Pool2_MR260626_016_S9_R1_001


title: HeLa, +DOX, day1, rep2

city: Lanzhou

first: Wenyuan

state: Gansu

address: South Tianshui Road

institute: Lanzhou University

description: Library name: HeLa_+DOX_day1_rep2

data_processing:
Upon receipt of the sequencing data, bioinformatics analysis was performed. Raw reads were processed using Trim Galore (v0.6.10) (https://github.com/FelixKrueger/TrimGalore) to remove adapter sequences and low-quality bases.
Cleaned reads were aligned to both the human reference genome (hg38) and the Arabidopsis thaliana reference genome (TAIR10) using STAR (v2.5.2b) under default parameters.
Gene-level read counts were quantified using featureCounts from the Subread package (v1.5.3)82 to generate raw count matrices.
Size factors for normalization were estimated based on the spike-in RNA counts using the estimateSizeFactors function in the R package DESeq2 (v1.42.1)83, and these factors were subsequently applied to normalize the human gene expression matrix prior to differential expression analysis. Differentially expressed genes were identified using thresholds of |log₂(fold change)| > 1 and an adjusted p-value < 0.05.
Assembly: hg38
Supplementary files format and content: xlsx file include spike-in normalized counts for each sample

source_name: Cervix

growth_protocol: HeLa cells was cultured in Dulbecco’s Modified Eagle’s Media (G4511, Servicebio, Wuhan, China) supplemented with 10% fetal calf serum (G8003, Servicebio, Wuhan, Chin) and pen/strep. cells were maintained at 37°C, 90% humidity, and 5% CO2.

extract_protocol:
Cells were harvested following trypsin digestion and counted after induction with Dox for various time points. To each sample containing 5×105 cells, 1 μg of total RNA isolated from Arabidopsis thaliana (provided by Dr. Bo Li’s laboratory at Lanzhou University) was added as a spike-in control. The cell samples supplemented with Arabidopsis RNA were then submitted to Biomarker Technologies Co., Ltd. (Beijing, China) for mRNA extracting.
The library construction was accomplished by biomker Technologies Co., Ltd. (Beijing, China).

treatment_protocol: The control group was not induced by Dox, and the experimental group was induced by Dox(1 μg/mL) for 1 day and 4 days. Dox could induce nGDOWN1.

value: Cervix

value: HeLa

value: Epithelial cell

value: inducible nGDOWN1

value: doxycycline induced, day1


title: Mouse 2 tumor CD8 T cells isotype control

description: Library name: Pool2_MR260626_015_S10_R1_001

value: Tumor

value: CD8 T cell

value: Balb/c OlaHsd wild-type


title: Bcl2_WT_H2AZ-CUTandTag_rep2

description: Library name: Bcl2_WT_H2AZ-CUTandTag_2

value: spleen

value: naive CD8+ T cell

value: BCL2+ WT


title: HeLa, +DOX, day1, rep1

description: Library name: HeLa_+DOX_day1_rep1


title: Mouse 2 tumor CD4 T cells isotype control

description: Library name: Pool2_MR260626_013_S12_R1_001


title: Bcl2_WT_H2AZ-CUTandTag_rep1

description: Library name: Bcl2_WT_H2AZ-CUTandTag_1


title: Mouse 2 lymph node CD8 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: Pool2_MR260626_012_S13_R1_001

value: lymph node


title: urocanate 10uM, experiment 1, replicate 2

description: Library name: B2

data_processing:
Raw Illumina sequencing reads were filtered to remove adapter sequences and low-quality reads. Clean reads were aligned to the reference genome. Gene-level fragment counts were generated by assigning mapped fragments to annotated genes. Gene expression was also quantified as FPKM (Fragments Per Kilobase of transcript per Million mapped fragments) using StringTie.
Assembly: GRCh38 (Ensembl release 95)
Supplementary files format and content: Tab-delimited .txt file containing gene-level raw fragment counts. Variables include 'ens' (Ensembl gene IDs), 'gene_symbol' (gene symbols), and individual samples mapping to 'library names'. Values represent the number of mapped sequencing fragments assigned to each gene in each sample.

value: wild-type


title: Day 0 IEC H2-Ab1^fl/fl biol rep 1

city: Birmingham

first: Casey

last: Weaver

address: 1900 University Blvd, THT Building

institute: University of Alabama at Birmingham

description:
Library name: D0ICneg1
10x Genomics

data_processing:
The demultiplexing, barcode processing, and gene counts were made using Cell Ranger v8.0.1(https://www.10xgenomics.com/support/software/cell-ranger/8.0)
Assembly: GRCm39
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Mid-distal colon

extract_protocol:
Three cellular compartments were isolated separately to capture spatial organization of immune responses. Intestinal epithelial cells (IECs) were isolated from 4 cm mid-distal colon tissue that was flushed with 1X PBS, opened longitudinally, and cut into 1 cm strips. Tissue pieces were incubated for 20 min at 37°C with 1 mM DTT, followed by 2 mM EDTA in H5H media (1X HBSS, 5% FBS, 20 mM HEPES, and 2.5 mM 2-β-ME). Tissue pieces were vortexed briefly after each 20 min incubation, followed by washing with H5H prior to centrifugation at 1750 rpm for 10 min at 4°C. IECs were then purified on a 40%/75% Percoll gradient by centrifugation for 20 min at 25°C and 2000 rpm with no brake. Intraepithelial lymphocytes (IELs) were obtained from the epithelial fraction during IEC isolation. Lamina propria lymphocytes (LPLs) were isolated from colonic tissue that was flushed with 1X PBS, opened longitudinally, cut into small pieces, and minced for 2-3 min before being transferred into complete R10 media (1X RPMI 1640, 10% FBS, 1X Pen/Strep, 1X NEAA, 1mM Sodium pyruvate, 2 mM L-glutamine, and 2.5 mM 2-β-ME) with collagenase IV (100 U/mL) and DNase I (20 μg/mL). Tissue was digested at 37°C for 40 min with stirring, filtered through a 70 μm filter, washed with complete R10 media, centrifuged at 1750 rpm at 4°C for 10 min, and then purified on a 40%/75% Percoll gradient. Following isolation, single-cell suspensions were stained and FACS-sorted to obtain live EpCAM⁺ IECs, live CD45⁺ IELs, and live CD45⁺ LPLs. B cells were depleted using anti-CD19 antibody during FACS to enrich for rare T cell populations. Post-sort viability was confirmed to be ≥90% by trypan blue exclusion, and sorted cells were collected directly into 5 μL PBS supplemented with 5% FBS and 0.1 mM EDTA.
Single-cell RNA sequencing libraries were prepared using the Chromium Single Cell 3' Gene Expression Kit (10x Genomics) at the FCSC Core Facility (UAB) according to the manufacturer's protocol. For each sample, 10,000 live sorted cells were loaded onto the 10x Chromium Controller. All 52 libraries were pooled and sequenced on two Illumina NovaSeq 6000 S4 flow cells using 2×100 bp paired-end reads.

value: Mid-distal colon

value: EpCAM+ CD45-

value: Wild-type


title: vehicle, experiment 2, replicate 2

description: Library name: A4

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen 74106) and measured RNA concentration and quality using Nanodrop.
Qualified RNA were processed for library construction. The procedures are described as follows: (1) mRNA was isolated by Oligo(dT)-attached magnetic beads. (2) mRNA was then randomly fragmented in fragmentation buffer. (3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads. (4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp. (5) cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.


title: HeLa, control, rep2

description: Library name: HeLa_control_rep2

value: uninduced


title: Mouse 2 lymph node CD4 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: Pool2_MR260626_011_S14_R1_001

value: CD4 T cell


title: Mouse 1 lymph node CD4 T cells treated with anti-PD1, anti-CTLA4, and CD40 agonist

description: Library name: Pool2_MR260626_014_S11_R1_001

value: anti-PD1+anti-CTLA4+CD40 agonist


title: Bcl2_IL-7R-cKO_H2AZ-CUTandTag_rep2

description: Library name: Bcl2_IL-7R-cKO_H2AZ-CUTandTag_2

value: BCL2+ IL-7R-cKO

value: unstimulated


title: Mouse 2 tumor CD8 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: Pool2_MR260626_010_S15_R1_001


title: HeLa, control, rep1

description: Library name: HeLa_control_rep1

value: Cervix

value: HeLa

value: Epithelial cell

value: inducible nGDOWN1


title: Mouse 2 tumor CD4 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: Pool2_MR260626_009_S16_R1_001

value: Tumor

value: Balb/c OlaHsd wild-type


title: Bcl2_IL-7R-cKO_H2AZ-CUTandTag_rep1

description: Library name: Bcl2_IL-7R-cKO_H2AZ-CUTandTag_1

value: spleen

value: naive CD7+ T cell


title: Mouse 1 lymph node CD8 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: Pool2_MR260626_008_S17_R1_001

value: lymph node

value: CD8 T cell


title: Human keratinocyte bulk RNA-seq, IFNg (10 ng/mL) + IL-17A (10 ng/mL), donor 4, rep 2

city: San Francisco

first: Charlotte

last: Hurabielle

address: 513 Parnassus Avenue

institute: University of California, San Francisco

description:
Library name: KC_RNAseq_IFNg_IL17a_donor4_rep2
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IFNg (10 ng/mL) + IL-17A (10 ng/mL), applied daily from day 7 to day 14. Donor 4, technical replicate 2.

data_processing:
Raw FASTQ files were trimmed with fastp (v1.0.1) and quality-checked with FastQC and MultiQC (v1.32).
Transcript abundance was quantified by pseudoalignment to GRCh38 using Kallisto (v0.46.2). Gene-level abundance was estimated from transcript abundance using tximport (v1.34.0).
Differential gene expression was identified using DESeq2 (v1.46.0), modeling batch (donor) and cytokine treatment effects. Volcano plots were generated using adjusted DESeq2 outputs with ashr (v2.2-63).
Pre-ranked gene set enrichment analysis (GSEA) was performed using t-statistics from DESeq2 outputs with fgsea (v1.32.4) on GO ontology gene sets from MSigDB and custom gene sets.
Module scores were calculated using the AddModuleScore() function from Seurat (v5.3.1).
Assembly: GRCh38
Supplementary files format and content: Gene-level count matrix (tab-delimited .txt): rows are genes (Ensembl ID + gene symbol), columns are samples; values are estimated counts from tximport.
Supplementary files format and content: DESeq2 differential expression results tables (.csv): log2 fold change, Wald statistic, p-value, and adjusted p-value for each pairwise comparison.

source_name: primary human keratinocyte

growth_protocol: Primary human keratinocytes were isolated from neonatal foreskins and expanded in T175 flasks to ~70% confluence. 500,000 cells were seeded into 12-well Millicell hanging inserts (0.4 um PET membrane; Millipore) pre-coated with CellStart (Invitrogen) diluted 1:10 in DPBS, using Epilife supplemented with Human Keratinocyte Growth Supplement (Gibco) as initial medium. At 72 hours (day 3), medium was switched to CNT-Prime Epithelial 3D Airlift Medium (CELLnTEC) in both apical and basal compartments. After 24 hours submerged, cultures were air-lifted by aspirating apical medium and reducing basal medium to 1.5 mL. From day 4, cultures were fed daily with 1 mL differentiation medium.

extract_protocol:
Total RNA was extracted from air-lifted 3D keratinocyte cultures at day 14.
Poly-A selected RNA libraries were prepared and sequenced as paired-end reads.

treatment_protocol: Beginning on day 7, cultures received one of the following daily supplements: IL-17A (10 ng/mL; BioLegend 570504), IFNg (10 ng/mL; BioLegend 713906), both (IL-17A 10 ng/mL + IFNg 10 ng/mL), or control medium alone. On day 12, cultures were transferred to a dry incubator to complete terminal differentiation. Cultures were harvested on day 14.

value: primary human keratinocyte

value: IFNg (10 ng/mL) + IL-17A (10 ng/mL)


title: HRC16 ProliferativeDAD

description: FFPE Spatial transcriptome sequencing

value: Lung

value: Proliferative DAD


title: Mouse 1 lymph node CD4 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: Pool2_MR260626_007_S18_R1_001

value: CD4 T cell


title: RAW264.7 cells, LPS+Extract-3

city: Guangzhou

first: Zhaokun

last: Yin

state: Guangdong

address: 132#, Waihuan Dong Road

institute: Sun Yat-Sen University

description:
Library name: ET_3
FPKM.M_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: RAW264.7 cells

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: RAW264.7 cells

value: Macrophage


title: HRC11 ProliferativeDAD

description: FFPE Spatial transcriptome sequencing


title: Mouse 1 lymph node CD8 T cells isotype control

description: Library name: Pool2_MR260626_006_S19_R1_001

value: isotype


title: Human keratinocyte bulk RNA-seq, IFNg (10 ng/mL) + IL-17A (10 ng/mL), donor 4, rep 1

description:
Library name: KC_RNAseq_IFNg_IL17a_donor4_rep1
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IFNg (10 ng/mL) + IL-17A (10 ng/mL), applied daily from day 7 to day 14. Donor 4, technical replicate 1.


title: N_IL7R-cKO-H2AZ-CUTandTag_rep1

description: Library name: N_IL7R-cKO-H2AZ-CUTandTag_N1

value: naive CD8+ T cell

value: unstimulated


title: Mouse 1 lymph node CD4 T cells isotype control

description: Library name: Pool2_MR260626_005_S20_R1_001


title: RAW264.7 cells, LPS+Extract-2

description:
Library name: ET_2
FPKM.M_2


title: N_IL7R-cKO-H2AZ-CUTandTag_rep2

description: Library name: N_IL7R-cKO-H2AZ-CUTandTag_N2


title: Mouse 1 tumor CD8 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: Pool2_MR260626_004_S21_R1_001


title: Human keratinocyte bulk RNA-seq, IFNg (10 ng/mL) + IL-17A (10 ng/mL), donor 3, rep 2

description:
Library name: KC_RNAseq_IFNg_IL17a_donor3_rep2
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IFNg (10 ng/mL) + IL-17A (10 ng/mL), applied daily from day 7 to day 14. Donor 3, technical replicate 2.


title: CONTROL2 Control

description: FFPE Spatial transcriptome sequencing

value: Control


title: Mouse 1 tumor CD8 T cells isotype control

description: Library name: Pool2_MR260626_002_S23_R1_001

value: Tumor


title: RAW264.7 cells, LPS+Extract-1

description:
Library name: ET_1
FPKM.M_1


title: PFBS_placenta7_20um_female

city: San Diego

first: Elana

last: Elkin

address: 5500 Campanile Drive

institute: San Diego State University

description: Library name: PFBS_placenta7_20um_female

data_processing:
Reads were aligned to the human genome using STAR.
Aligned reads were assigned to GRCh38 genes using featureCounts.
Genes with mean read counts-per-million less than 100 across all samples were filtered out and excluded from the analysis.
Data were normalized using the trimmed mean of M values (TMM) method
Differential gene expression testing was performed using the DeSeq2 package (version 4.1) for R statistical computing.
Assembly: hg38
Supplementary files format and content: tabular files

source_name: placenta

extract_protocol:
RNeasy Mini Kit (cells) miRNeasy Mini Kit (tissues)
TruSeq mRNA Library Prep Kit with poly(A) enrichment (Illumina, San Diego, CA, USA)

value: placenta

value: female

value: Explants-various cells

value: 24 hours

value: batch 2026


title: Mouse 1 tumor CD4 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: Pool2_MR260626_003_S22_R1_001

value: Balb/c OlaHsd wild-type


title: L11P ProliferativeDAD

description: FFPE Spatial transcriptome sequencing


title: Human keratinocyte bulk RNA-seq, IFNg (10 ng/mL) + IL-17A (10 ng/mL), donor 3, rep 1

description:
Library name: KC_RNAseq_IFNg_IL17a_donor3_rep1
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IFNg (10 ng/mL) + IL-17A (10 ng/mL), applied daily from day 7 to day 14. Donor 3, technical replicate 1.

value: primary human keratinocyte

value: IFNg (10 ng/mL) + IL-17A (10 ng/mL)


title: RAW264.7 cells, LPS-3

description:
Library name: M_3
FPKM.ET_3


title: Mouse M234 tumor CD8 T cells treated with anti-PD1, anti-CTLA4, CD40 agonist, and CD4 depletion

description: Library name: M234_Tumor_CD8_ICB_aCD40_aCD4_S7_R1_001

value: CD8 T cell


title: Mouse 1 tumor CD4 T cells isotype control

description: Library name: Pool2_MR260626_001_S24_R1_001

value: CD4 T cell


title: L19P ProliferativeDAD

description: FFPE Spatial transcriptome sequencing

value: Lung

value: Proliferative DAD


title: Human keratinocyte bulk RNA-seq, IFNg (10 ng/mL) + IL-17A (10 ng/mL), donor 2, rep 2

description:
Library name: KC_RNAseq_IFNg_IL17a_donor2_rep2
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IFNg (10 ng/mL) + IL-17A (10 ng/mL), applied daily from day 7 to day 14. Donor 2, technical replicate 2.


title: Mouse M234 lymph node CD8 T cells treated with anti-PD1, anti-CTLA4, CD40 agonist, and CD4 depletion

description: Library name: M234_LN_CD8_ICB_aCD40_aCD4_S1_R1_001

value: lymph node


title: RAW264.7 cells, LPS-2

description:
Library name: M_2
FPKM.ET_2

value: RAW264.7 cells

value: Macrophage


title: Mouse M232 tumor CD8 T cells treated with anti-PD1, anti-CTLA4, CD40 agonist, and CD4 depletion

description: Library name: M232_Tumor_CD8_ICB_aCD40_aCD4_S8_R1_001


title: Human keratinocyte bulk RNA-seq, IFNg (10 ng/mL) + IL-17A (10 ng/mL), donor 2, rep 1

description:
Library name: KC_RNAseq_IFNg_IL17a_donor2_rep1
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IFNg (10 ng/mL) + IL-17A (10 ng/mL), applied daily from day 7 to day 14. Donor 2, technical replicate 1.


title: Mouse M232 lymph node CD8 T cells treated with anti-PD1, anti-CTLA4, CD40 agonist, and CD4 depletion

description: Library name: M232_LN_CD8_ICB_aCD40_aCD4_S2_R1_001


title: RAW264.7 cells, LPS-1

description:
Library name: M_1
FPKM.ET_1


title: Mouse M225 tumor CD8 T cells treated with anti-PD1, anti-CTLA4, and CD4 depletion

description: Library name: M225_Tumor_CD8_ICB_aCD4_S9_R1_001


title: Human keratinocyte bulk RNA-seq, IL-17A (10 ng/mL), donor 4, rep 2

description:
Library name: KC_RNAseq_IL17a_donor4_rep2
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IL-17A (10 ng/mL), applied daily from day 7 to day 14. Donor 4, technical replicate 2.


title: RAW264.7 cells, Normal-3

description:
Library name: C_3
FPKM.C_3


title: Mouse M224 tumor CD8 T cells treated with anti-PD1, anti-CTLA4, and CD4 depletion

description: Library name: M224_tumor_CD8_ICB_aCD4_S10_R1_001


title: Mouse M225 lymph node CD8 T cells treated with anti-PD1, anti-CTLA4, and CD4 depletion

description: Library name: M225_LN_CD8_ICB_aCD4_S3_R1_001


title: Human keratinocyte bulk RNA-seq, IL-17A (10 ng/mL), donor 4, rep 1

description:
Library name: KC_RNAseq_IL17a_donor4_rep1
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IL-17A (10 ng/mL), applied daily from day 7 to day 14. Donor 4, technical replicate 1.


title: Mouse M224 lymph node CD8 T cells treated with anti-PD1, anti-CTLA4, and CD4 depletion

description: Library name: M224_LN_CD8_ICB_aCD4_S4_R1_001


title: Dev_mSP8_H2AZ-CUTandTag_rep1

description: Library name: Dev_mSP8_H2AZ-CUTandTag_1

value: thymus

value: mature single postive CD8+ T cell

value: WT

value: unstimulated


title: Mouse M218 tumor CD8 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: M218_Tumor_CD8_ICB_S11_R1_001

value: Tumor


title: RAW264.7 cells, Normal-2

description:
Library name: C_2
FPKM.C_2


title: Human keratinocyte bulk RNA-seq, IL-17A (10 ng/mL), donor 3, rep 1

description:
Library name: KC_RNAseq_IL17a_donor3_rep1
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IL-17A (10 ng/mL), applied daily from day 7 to day 14. Donor 3, technical replicate 1.


title: RAW264.7 cells, Normal-1

description:
Library name: C_1
FPKM.C_1


title: Mouse M218 lymph node CD8 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: M218_LN_CD8_ICB_S5_R1_001


title: Mouse M218 tumor CD4 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: M218_Tumor_CD4_ICB_S12_R1_001


title: Human keratinocyte bulk RNA-seq, IL-17A (10 ng/mL), donor 2, rep 2

description:
Library name: KC_RNAseq_IL17a_donor2_rep2
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IL-17A (10 ng/mL), applied daily from day 7 to day 14. Donor 2, technical replicate 2.


title: HeLa, +DOX, day4, rep2

description: Library name: HeLa_+DOX_day4_rep2

value: Cervix

value: HeLa

value: Epithelial cell

value: inducible nGDOWN1

value: doxycycline induced, day4


title: JR5558 mouse retina-3, 8 weeks

city: Eveleigh

first: Ting

last: Zhang

state: NSW

address: C81 Biomedical Building, 1 Central Ave

institute: The University of Sydney

description: Library name: Sample 12

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: Excel .xls file includes both raw read counts and FPKM-normalized gene expression values for each sample

source_name: retina

extract_protocol:
Total RNA from the retinas of 4-week and 8-week-old JR5558 mice and age-matched C57BL/6 mice (n = 3) was extracted using a GenElute™ Single Cell RNA Purification Kit (RNB30, Sigma-Aldrich).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

value: retina


title: Mouse M217 tumor CD8 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: M217_Tumor_CD8_ICB_S15_R1_001

value: CD8 T cell

value: Balb/c OlaHsd wild-type


title: Mouse M218 lymph node CD4 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: M218_LN_CD4_ICB_S6_R1_001

value: CD4 T cell


title: Human keratinocyte bulk RNA-seq, IL-17A (10 ng/mL), donor 2, rep 1

description:
Library name: KC_RNAseq_IL17a_donor2_rep1
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IL-17A (10 ng/mL), applied daily from day 7 to day 14. Donor 2, technical replicate 1.

value: primary human keratinocyte


title: Mouse M217 tumor CD4 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: M217_Tumor_CD4_ICB_S16_R1_001


title: JR5558 mouse retina-2, 8 weeks

description: Library name: Sample 11


title: Mouse M217 lymph node CD8 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: M217_LN_CD8_ICB_S13_R1_001

value: lymph node


title: Dev_imSP8_H2AZ-CUTandTag_rep2

description: Library name: Dev_imSP8_H2AZ-CUTandTag_2

value: immature single postive CD8+ T cell


title: Mouse M217 lymph node CD4 T cells treated with anti-PD1 and anti-CTLA4

description: Library name: M217_LN_CD4_ICB_S14_R1_001


title: Human keratinocyte bulk RNA-seq, IL-17A (10 ng/mL), donor 1, rep 2

description:
Library name: KC_RNAseq_IL17a_donor1_rep2
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IL-17A (10 ng/mL), applied daily from day 7 to day 14. Donor 1, technical replicate 2.


title: JR5558 mouse retina-1, 8 weeks

description: Library name: Sample 10


title: HeLa, +DOX, day4, rep1

description: Library name: HeLa_+DOX_day4_rep1


title: Mouse M123 tumor CD4 T cells isotype control

description: Library name: M123_Tumor_CD4_iso_S22_R1_001

value: isotype


title: Human keratinocyte bulk RNA-seq, IL-17A (10 ng/mL), donor 1, rep 1

description:
Library name: KC_RNAseq_IL17a_donor1_rep1
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IL-17A (10 ng/mL), applied daily from day 7 to day 14. Donor 1, technical replicate 1.


title: Mouse M123 lymph node CD8 T cells isotype control

description: Library name: M123_LN_CD8_iso_S17_R1_001


title: Mouse M123 tumor CD8 T cells isotype control

description: Library name: M123_Tumor_CD8_iso_S21_R1_001


title: Human keratinocyte bulk RNA-seq, IFNg (10 ng/mL), donor 4, rep 2

description:
Library name: KC_RNAseq_IFNg_donor4_rep2
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IFNg (10 ng/mL), applied daily from day 7 to day 14. Donor 4, technical replicate 2.

value: IFNg (10 ng/mL)


title: Mouse M123 lymph node CD4 T cells isotype control

description: Library name: M123_LN_CD4_iso_S18_R1_001


title: Mouse M122 tumor CD8 T cells isotype control

description: Library name: M122_Tumor_CD8_iso_S23_R1_001


title: JR5558 mouse retina-3, 4 weeks

description: Library name: Sample 9


title: Mouse M122 lymph node CD8 T cells isotype control

description: Library name: M122_LN_CD8_iso_S19_R1_001


title: Mouse M122 tumor CD4 T cells isotype control

description: Library name: M122_Tumor_CD4_iso_S24_R1_001


title: Human keratinocyte bulk RNA-seq, IFNg (10 ng/mL), donor 3, rep 1

description:
Library name: KC_RNAseq_IFNg_donor3_rep1
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IFNg (10 ng/mL), applied daily from day 7 to day 14. Donor 3, technical replicate 1.


title: JR5558 mouse retina-1, 4 weeks

description: Library name: Sample 7


title: Mouse M122 lymph node CD4 T cells isotype control

description: Library name: M122_LN_CD4_iso_S20_R1_001


title: C57BL/6J mouse retina-3, 8 weeks

description: Library name: Sample 6


title: 30S 6 min KMnO4 + NaHCO3

city: El Paso

first: Eda

last: Kocui

state: TX

address: 500 W. University Avenue

department: Chemistry and Biochemistry

institute: University of Texas at El Paso

description:
Library name: Sample 11
16S rRNA from 30S

library_source: other

data_processing:
Base calls were performed uising Illumina RTA version 1.18. 54 or 3.4.4
The next generation sequencing reads were aligned to the rrlB and rrsB  genes of Bl21 (DE3)  E Coli and the mutations were counted using Shape-Mapper 1.2
Assembly: Escherichia coli BL21(DE3): B21_04498 (rrlB) ; Escherichia coli BL21(DE3): B21_04496 (rrsB)
Supplementary files format and content: *.csv files contain counted mutations per nucleotide position of RNA sequence of interest as output from Shape-Mapper 1.2

molecule: other

organism: Escherichia coli

source_name: BLR(DE3) Delta dbpA:  Kan, expressing wild-type DbpA pET-3a

growth_protocol: The cells were grown at 37ºC in 200 mL of media containing 10g/L tryptone, 1g/L yeast extract, 100μg/mL carbenicillin, and 34μg/mL chloramphenicol. When the cell reached an optical density at 600 nm of about 0.3, the cell growth was arrested by adding 200 ml of ice.

extract_protocol:
The ribosomal particles were isoalate using a  20-40% gradients were made in a buffer consisting of 20mM HEPES KOH pH 7.5, 150mM NH4Cl, 1mM MgCl2 and 4mM BME.
The NGS sequencing library was performed following the randomer workflow of the Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) protocol(Smola et al. 2015)

treatment_protocol: Some of the RNA samples were treated with KMnO4 for either 3 or 6 minutes followed by treatment with NaHCO3

value: Bacteria

value: BLR(DE3) Delta dbpA: Kan

value: 6 min KMno4 followed by NaHCO3


title: Human keratinocyte bulk RNA-seq, IFNg (10 ng/mL), donor 2, rep 2

description:
Library name: KC_RNAseq_IFNg_donor2_rep2
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: IFNg (10 ng/mL), applied daily from day 7 to day 14. Donor 2, technical replicate 2.


title: 30S 3 min KMnO4 + NaHCO3

description:
Library name: Sample 10
16S rRNA from 30S

value: BLR(DE3) Delta dbpA: Kan, expressing wild-type DbpA pET-3a

value: 3 min KMno4 followed by NaHCO3


title: 50S 6 min KMnO4 + NaHCO3

description:
Library name: Sample 9
23S rRNA from 50S


title: C57BL/6J mouse retina-2, 8 weeks

description: Library name: Sample 5


title: 50S 3 min KMnO4 + NaHCO3

description:
Library name: Sample 8
23S rRNA from 50S


title: 27S Untreated Replicate 2

description:
Library name: Sample 7
23S rRNA from 27S

source_name: BLR(DE3) Delta dbpA:  Kan, expressing R331A DbpA pET-3a


title: 35S Untreated Replicate 2

description:
Library name: Sample 5
23S rRNA from 35S and 16S rRNA from 30S

value: BLR(DE3) Delta dbpA: Kan, expressing R331A DbpA pET-3a


title: 35S Untreated Replicate 1

description:
Library name: Sample 4
23S rRNA from 35S (.fastq file has been previously uploaded on GEO:GSE196821 but was aligned to 16S rRNA instead of 23S)


title: C57BL/6J mouse retina-3, 4 weeks

description: Library name: Sample 3


title: 45S Untreated Replicate 2

description:
Library name: Sample 3
23S rRNA from 45S


title: Human keratinocyte bulk RNA-seq, untreated control, donor 4, rep 2

description:
Library name: KC_RNAseq_Untreated_donor4_rep2
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: untreated control, applied daily from day 7 to day 14. Donor 4, technical replicate 2.

value: untreated control


title: HCCO1_RNAseq

first: Zhaozhao

last: Zhao

address: Songhu Road 2005

institute: FUDAN UNIVERSITY

description: Library name: Sample5

data_processing:
Raw scRNA-seq data were processed using Cell Ranger (v8.0.1) from 10x Genomics (with Count functionality) for read alignment to the prebuilt GRCh38 genome reference. The resulting gene-by-cell unique molecular identifier (UMI) count matrix was analyzed using R package Seurat.  Code used for the assignment of cells to reference expression profiles is available at https://github.com/broadinstitute/single_cell_classification. Aligned BAM files were used as input for transcript-level peak calling with the SCAPTURE pipeline. The high-confidence PASs were used to construct a PAS-based GTF annotation, which was subsequently quantified using UMI-tools (v1.1.6) protocol. The final PAS-by-cell count matrix represented the expression of transcripts with distinct PASs at single-cell resolution. To assess the impact of JTE-607 treatment on transcriptomic heterogeneity, we calculated the diversity score for each treatment condition based on the PAS-based transcript expression profiles. We performed PCA to project the expression profiles of all cells, enabling the extraction of key features while minimizing noise. The top 30 PCs were selected. We performed 1,000 down-sampling analyses by randomly sampling 1,000 cells without replacement, and defined diversity as the average distance of the sampled cells to the centroid. To mitigate the influence of outliers on diversity score calculation, we excluded the cells with all the first three PCs exceeding 3 standard deviations from the mean.
Assembly: GRCh38
Supplementary files format and content: mtx file with raw UMI counts for every gene and cell. Does not have row or column names, these are found in the additional txt files
Supplementary files format and content: txt file with gene names;  txt file with cell barcodes and sample names. The sample name is separated from the barcode by an underscore

source_name: Lung cancer organoid

extract_protocol:
Samples were processed using the Chromium Single Cell 3′ (v2 Chemistry), platform with the target of ∼10,000 cells (10x Genomics) following manufacturer's instructions. Briefly, cells were added onto a chip to form Gel Bead-in-Emulsion (GEMs) in the Chromium instrument followed by cell lysis, barcoding, fragmentation, adaptor ligation and addition of sample index to the libraries before sequencing.
cDNA from GEMs was recovered and amplified by PCR. Subsequently, cDNA fragment length was optimized by enzymatic digestion and fragment screening. Finally, library construction was completed by end repair and addition of traditional second-generation sequencing junctions, and a standard sequencing DNA library was obtained by PCR amplification. High-throughput sequencing was performed on the constructed library using the double-end sequencing mode of Illumina sequencing platform.

value: Lung cancer organoid

value: liver

value: No treatment


title: 50S Untreated Replicate 1

description:
Library name: Sample 1
23S rRNA from 50S


title: LACO2_RNAseq

description: Library name: Sample4

value: lung


city: Bloomington

first: Cristina

last: Landeta

state: Indiana

address: 1001 E 3rd St

department: Biology

institute: Indiana University

description:
Library name: DE-12268-FadoliTnegC
Vermamoeba vermiformis mock infected control for Fadolivirus samples  replica C
FadoliTnegC_S54

data_processing:
The Illumina integrate system was used to separate the bar-coded sequences and demultiplex paired end reads into FASTQ files.
The pre-trimmed RNA-seq data was validated with FastQC (v0.11.5) and MultiQC (v1.33). The data was re-trimmed using fastp (v0.21.0).
The paired-end reads were them mapped using HISAT2 to the combined fasta files consisting of the Yasminevirus GU-2018, Fadolivirus algeromassiliense and the Vermamoeba vermiformis CDC-19.
The subread algorithm featureCounts was used to generate gene-level quantification.
The data was then processed through the R (v4.5.1) package deseq2 to identify differentially expressed genes.
Assembly: combined fasta files consisting of the Yasminevirus GU-2018 (NCBI), Fadolivirus algeromassiliense (NCBI), and the Vermamoeba vermiformis CDC-19
Supplementary files format and content: Tab deliminted text files containing counts of reads overlapping with coding regions of the genes.

organism: Vermamoeba vermiformis

growth_protocol: A suspension of V. vermiformis was prepared by successive cycles of centrifugation (3,000 × g for 10 min) and resuspension in starvation medium.

extract_protocol:
RNA extraction was performed as per manufacturer’s instructions with DNase treatement (Ozyme, Quick-RNA MiniPrep kit). mRNA was then captured with poly(A) tail using oligo(dT) coated magnetic beads following standard kit recommendations (NEBNext Poly(A) mRNA Magnetic Isolation Module, New England Biolabs).
After poly(A)+ RNA enrichment, a cDNA library was prepared using SuperScript IV Reverse Transcriptase (ThermoFisher), then a second brin synthesis was done using DNA Klenow I polymerase (New England Biolabs). cDNA libraries were done using COVIDSeq tests and sequenced using paired-end strategy (2*150 bp) using Illumina Novaseq Sequencer (Illumina Inc.).

treatment_protocol: Triplicates 30 mL cultures of amoebae at 106 cells/mL, quantified using an inverted microscope (Kovaslide), were inoculated with Yasminevirus or Fadolivirus at a multiplicity of infection (MOI) of 10 (TCID50 to quantify viral stocks were performed before infection cycles) in a 75-cm2 culture flask. After 30 min of incubation at 30°C for viral entry, the supernatant was carefully aspirated to remove extracellular Yasminevirus or Fadolivirus particles and maintain amoeba’ monolayers. The cells were resuspended in 10 mL of fresh medium for a second incubation at 30°C for 16 h. This time point was considered hour zero (H0). At H2, H4, H6, H8, H10, H12, and H16 of each triplicate amoebae were collected and after centrifugation of 0.5 mL aliquot the sample was used for RNA extraction.

value: Whole cells

value: WT

value: mock infected

tag: time

value: mock infected control


title: Oragnoid_pool_scRNAseq_JTE607

city: Shanghai

description: Library name: Sample2

source_name: Lung cancer and liver cancer

value: Lung cancer and liver cancer

value: lung and liver


title: Human keratinocyte bulk RNA-seq, untreated control, donor 3, rep 1

description:
Library name: KC_RNAseq_Untreated_donor3_rep1
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: untreated control, applied daily from day 7 to day 14. Donor 3, technical replicate 1.

value: primary human keratinocyte


description:
Library name: DE-12267-Fadoli-CH16
Vermamoeba vermiformis infected with Fadolivirus algeromassiliense FV1/VV64 at 16 h post-infection  replica C
Fadoli-CH16_S53

value: Fadolivirus infected

value: 16 h post-infection


title: Organoid_pool_scRNAseq_DMSO

description: Library name: Sample1

value: DMSO


title: 45S Untreated Replicate 1

description:
Library name: Sample 2
23S rRNA from 45S

value: Bacteria

value: BLR(DE3) Delta dbpA: Kan


title: Human keratinocyte bulk RNA-seq, untreated control, donor 2, rep 2

description:
Library name: KC_RNAseq_Untreated_donor2_rep2
Bulk RNA-seq of primary human neonatal foreskin keratinocytes grown as air-lifted 3D epidermal equivalents (Millicell hanging inserts, 0.4 um PET). Treatment: untreated control, applied daily from day 7 to day 14. Donor 2, technical replicate 2.

value: untreated control