title: 7dpf_tinaja_Rep3

data_processing:
Raw reads were mapped using STAR aligner v2.7.3a against the UCSC genome astMex_2.0 genome, using Ensembl 102 gene models for annotations.
Transcript abundance was quantified using RSEM v1.3.0.
Assembly: UCSC genome astMex_2.0
Supplementary files format and content: comma separated file with raw counts

organism: Astyanax mexicanus

source_name: Liver

growth_protocol: Surface, Tinaja and Pachón morphs of Astyanax mexicanus were raised in polycarbonate recirculating aquaculture racks (Pentair Aquatic Eco-Systems, Apopka, FL), with a 14:10 h light:dark photoperiod. Each rack system is equipped with mechanical, chemical, and biological filtration and UV disinfection. Water quality parameters are monitored daily as described in previous studies (Xiong et., al 2022). Fish were housed at a density of ~2 fish per liter. Fish embryos spawned at the same time from different parent tanks were mixed in order to reduce effects from specific backgrounds. Only embryos screened as healthy were raised and randomly selected for experiment. Embryos up to 5 days after fertilization were maintained at 24.5 °C in E2 embryo media. Animal husbandry followed protocol 2021-122 approved by the Institutional Animal Care and Use Committee (IACUC) of the Stowers Institute for Medical Research. Housing conditions meet federal regulations and are accredited by AAALAC International.

extract_protocol:
Livers from 40 larvae / replicate were dissected and collected in the lysis buffer from ReliaPrepTM RNA Miniprep Systems (Promega, Z6110). RNA was isolated from the lysed tissue by following the manufacture’s instruction.
cDNA synthesis, library preparation and Illumina sequencing was performed according to the manufacturer’s instructions using the TruSeq Stranded mRNA Preparation Kit for Illumina (Ilumina #20020594). Purified libraries were quantified using a Quibit fluorometer (Life Technologies) and the quality assessed on the Agilent Bioanalyzer (Agilent Technologies).

treatment_protocol: Livers were collected from 5 dpf larvae or larvae that were fasted until 7 dpf.

value: Liver

tag: genotype

value: Tinaja


title: Tumor sample from Patient 12, post-immunotherapy treatment

status: Public on Jan 11 2024

type: RNA

city: Cambridge

first: Danish

last: Memon

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description: RMA expression value derived from Affymetrix Expression Console software

hyb_protocol: Hybridization was performed using the following protocol: "GeneChip WT Pico Reagent Kit Manual Target Preparation for GeneChip Whole-Transcript Expression Arrays".

scan_protocol: The Affymetrix GCS3000 scanner was used along with Affymetrix GeneChip Command Console software for imaging processing.

data_processing: The RNA samples quantification on Affymetrix Arrays was performed in two separate batches. Samples from each batch were processed independently using Affymetrix Expression Console Software version 1.4.1.46. Initially the samples were normalized using the SST-RMA algorithm and outlier samples were excluded. Samples from the two batches were then combined into a single dataset and subject to batch normalization using ComBat. Finally all the samples were further normalized together using LOESS normalization. For genes with multiple measurements, we selected the measurement with the highest coefficient of variation. Here we provide the CHP files with the SST-RMA normalization alone, but we can provide the SST-RMA+loess normalize gene expression values upon request.   affymetrix-algorithm-name = sst-rma-gene-full  affymetrix-algorithm-version = 1.0  affymetrix-array-type = Clariom_D_Human  program-name = Expression Console  program-version = 1.4.1.46

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: NSCLC patient

label_protocol: Labeling was performed using the following protocol: "GeneChip WT Pico Reagent Kit Manual Target Preparation for GeneChip Whole-Trascript Expression Arrays".

extract_protocol: RNA was extracted from FFPE samples using the RecoverAll Total Nucleic Acid Isolation from Thermo Fisher Scientific (Catalog Number: AM1975).

tag: gender

value: Male

tag: tumor site

value: Adrenal

tag: tumor type

value: Non-Small Cell Lung Cancer (NSCLC)

tag: timepoint

value: Post-treatment

tag: sample type

value: FFPE


title: Subject 100458, P+3H

type: SRA

city: CRETEIL

first: Cecile

last: LEFEBVRE

address: 51 Avenue du Maréchal de Lattre de Tassigny, Bât R+1 Eq16 U955

country: France

institute: INSERM

description: Column name in processed data file: 158

library_source: transcriptomic

data_processing:
raw counts were normalized as Log2 counts per million
Assembly: hg18
Supplementary files format and content: normalized_counts_050523.csv, corresponding to 59 subjects

source_name: Blood

extract_protocol:
Total RNA was purified from whole blood with the Tempus™ Spin RNA Isolation Kit (Invitrogen) and globine mRNA depletion carried out with GLOBINclear™ Kit
mRNA libraries were prepared with the NEBNext single cell/low input RNA library prep kit for Illumina. Single read of 101 bp sequencing was performed on the Illumina HiSeq 2500 at Vaccine Research Institute genomic Platform

tag: subject

tag: tissue

value: Blood

tag: treatment

tag: group

value: Prime


title: 7dpf_tinaja_Rep2

city: Greater Noida

first: Sumeet

middle: Pal

last: Singh

state: Uttar Pradesh

address: NH91, Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar Institution of Eminence

molecule: polyA RNA


title: Subject 100420, P+3H

description: Column name in processed data file: 157


title: Subject 100420, B+7D

description: Column name in processed data file: 159

value: MVA-BN-Filo

value: Boost


title: 7dpf_tinaja_Rep1


title: 7dpf_surface_Rep3

value: Surface


title: Subject 100420, B+1D

description: Column name in processed data file: 155


title: Tumor sample from Patient 12, pre-immunotherapy treatment

value: Pre-treatment


title: Tumor sample from Patient 09, pre-immunotherapy treatment


title: Tumor sample from Patient 11, post-immunotherapy treatment

value: Lymph node


title: Tumor sample from Patient 10, post-immunotherapy treatment

value: Female

value: Lung


title: 7dpf_surface_Rep1


title: Tumor sample from Patient 08, post-immunotherapy treatment


title: 7dpf_surface_Rep2


title: Tumor sample from Patient 06, post-immunotherapy treatment


title: Tumor sample from Patient 08, pre-immunotherapy treatment


title: Tumor sample from Patient 05, post-immunotherapy treatment


title: Tumor sample from Patient 07, post-immunotherapy treatment


title: TLR2-activated WT BMDMs sample 1

city: New Haven

first: Rihao

last: Qu

state: CT

address: 300 George Street

country: USA

institute: Yale University

description: Activated WT-1

data_processing:
Adapter sequences were removed from the raw sequencing reads using the tool Cutadapt (https://journal.embnet.org/index.php/embnetjournal/article/view/200).
STAR v2.5.3 was then used to align the trimmed sequencing reads to the mouse genome (mm10) with default parameters.
After sorting the generated SAM files (as the output of alignment) with Picard Toolkit (Picard Toolkit.” 2019. Broad Institute, GitHub Repository. https://broadinstitute.github.io/picard/; Broad Institute), we counted the number of reads mapped to each gene using HTSeq v0.6.1.
Subsequently, we employed DESeq2 v1.26.0 R package to identify significantly differential genes between naïve and TLR2-activated (24h) WT and IL-10 KO BMDMs.
Assembly: mm10
Supplementary files format and content: Read count table

organism: Mus musculus

source_name: Bone marrow derived macrophage

growth_protocol: bone marrow cells were cultured for 8 days in DMEM +10% FBS+1% pen/step+ glutamine + NaPyr +0.05ng/mL M-CSF

extract_protocol:
cells were lysed in trizol, extracted with chloroform. Aqueous phase was mixed 1:1 with 70% ethanol and put onto Qiagen RNAeasy column following the rest of the manufactorer's protocol
Poly-A

treatment_protocol: on Day 8 post differentiation, BMDMs were left naïve or activted with 50ng/mL Pam3CSK4 (TLR2 Ligand) for 24h

value: Bone marrow derived macrophage


title: Naïve WT BMDMs sample 2

description: Naive WT-2


title: IL-10R/CerS2 DKO CD45.2

library_source: transcriptomic single cell

data_processing:
Cellranger v6.0.1 was used to align scRNA-seq samples to the mouse genome (mm10).
Data analysis was performed using Seurat v4.3.0 R package, including cell-type identification and comparative analyses between conditions.
In the step of quality control, poor-quality cells with the number of expressed genes < 300 or > 5000 were filtered out. We also excluded cells if their mitochondrial gene percentages were over 10%. After combining cells from all samples, we first normalized the raw count matrix and then defined 2000 top variable genes. We then applied principal component analysis (PCA) for dimensionality reduction and retained 30 leading principal components for cell clustering.
After identifying cluster-specific genes, we annotated cell types based on canonical marker genes (Lyz2 for macrophage) and focused on macrophage populations in the downstream analyses.
To test the differential expression of inflammatory genes between IL-10R KO and Cers2/IL-10R DKOs, we first applied ALRA to impute the gene expression profiles and then used the non-parametric Wilcoxon rank sum test to get their p-values.
Assembly: mm10
Supplementary files format and content: "barcodes.tsv.gz" contains cell barcodes, "features.tsv.gz" contains metadata for genes, "matrix.mtx.gz" contains digital expression matrix

source_name: colon

extract_protocol:
single cells were isolated with collagenase D from colons of chimeric mice engrafted with either IL-10R KO or IL-10R/CerS2 DKO Cd45.2 donors. Single cells were sorted with a BD Aria FACS sorter for CD11b/C11c/CD64+ cells. Sorted cells were processed with 10x Chromium Controller
scRNAseq libraries were generated using the Chromium Next GEM Single Cell 3’ v3.1 Library & Gel Bead Kit (10X Genomics) according to the manufacturer’s protocol. Briefly, emulsions were generated using the 10X Chromium Controller (10X Genomics) for a targeted recover 10,000 cells. Barcoded cDNAs were isolated from the emulsion and amplified by PCR (11 cycles). The cDNAs underwent fragmentation, end repair, and A-tailing before addition of sample indexes by PCR (16 cycles).

value: colon

tag: cell type

value: colon macrophage

value: IL-10R/CerS2 DKO donor into CD45.1 recipient


title: TLR2-activated WT BMDMs sample 2

description: Activated WT-2


title: Tumor sample from Patient 06, pre-immunotherapy treatment

value: Male

value: Bone


title: IL-10R KO CD45.2

value: IL-10R KO donor into CD45.1 recipient


title: Tumor sample from Patient 01, post-immunotherapy treatment

value: Non-Small Cell Lung Cancer (NSCLC)

value: Post-treatment

value: FFPE


title: Subject 100458, P+7D

description: Column name in processed data file: 152

value: Blood

value: Prime


title: Subject 100420, D0

description: Column name in processed data file: 153

value: Control


title: Tumor sample from Patient 04, post-immunotherapy treatment

value: Brain


title: Naïve WT BMDMs sample 1

description: Naïve WT-1


title: 5dpf_tinaja_Rep3

value: Liver

value: Tinaja


title: Tumor sample from Patient 03, post-immunotherapy treatment

value: Lymph node


title: Subject 100458, B+7D

description: Column name in processed data file: 156

value: MVA-BN-Filo

value: Boost


title: Subject 100420, P+1D

description: Column name in processed data file: 151


title: TLR2-activated IL-10 KO BMDMs sample 2

description: Activated KO-2

value: Bone marrow derived macrophage


title: Tumor sample from Patient 09, post-immunotherapy treatment


title: 5dpf_tinaja_Rep2


title: Subject 100315, B+7D

description: Column name in processed data file: 150


title: TLR2-activated IL-10 KO BMDMs sample 1

description: Activated KO-1


title: 5dpf_tinaja_Rep1


title: Naïve IL-10 KO BMDMs sample 1

description: Naïve KO-1


title: 5dpf_surface_Rep3

value: Surface


title: Naïve IL-10 KO BMDMs sample 2

description: Naive KO-2


title: Knockout High Cholesterol_5

city: Cleveland

first: Mark

last: Brown

state: OH

department: Cancer Bio

institute: Cleveland Clinic

data_processing:
reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Assembly: reference genome available on ENSEMBL using the STAR aligner v.2.5.2b,GRCm38
Supplementary files format and content: counts.txt

source_name: gonadal Adipose Tissue

growth_protocol: GRAMD1C wild type and knockout mice genotype on C57Bl6/N Background

extract_protocol:
Mice were euthanized, and perfused with saline. The liver tissue was removed and  flash frozen in liquid nitrogen. Total RNA was extracted by Azenta Bioscience using Qiagen Rneasy Plus Universal Mini kit
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina and sequenced using an Illumina NovaSeq 6000 by Azenta Bioscience

treatment_protocol: High and low cholesterol diet feeding for 4 weeks

value: gonadal Adipose Tissue

value: Knockout (Gramd1c -/-)

value: High Cholesterol


title: Subject 100420, P+7D

description: Column name in processed data file: 149


title: Subject 100315, P+29D

description: Column name in processed data file: 148


title: Knockout High Cholesterol_2


title: Knockout High Cholesterol_1


title: Wild Type High Cholesterol_5

value: Wild Type (Gramd1c +/+)


title: Knockout High Cholesterol_4


title: Knockout High Cholesterol_3


title: 5dpf_surface_Rep1


title: Wild Type High Cholesterol_4


title: Subject 100420, P+57D

description: Column name in processed data file: 147


title: Subject 100315, B+3H

description: Column name in processed data file: 146


title: Wild Type High Cholesterol_3


title: MJ008_TCR Pt4 iITx POD1606 ileum explant IEL (Recipient T)

city: New York

first: Jianing

last: Fu

state: NY

institute: Columbia University Medical Center

data_processing:
The Seurat analysis pipeline (Butler et al., 2018; Hao et al., 2021; Stuart et al., 2019) was used to perform the downstream analysis of scRNA-seq data, such as QC, normalization, down sampling, clustering and differential gene expression analysis.
Assembly: GRCh38
Supplementary files format and content: Seurat object (rds) with gene by cell matrix used for cell type annotation and TCR clonotypes to define alloreactive clones used for downstream analyses

source_name: ileum

extract_protocol:
scRNA-seq was performed using the 10x Genomics (Pleasanton, CA) platform for simultaneous measurement of mRNA expression and paired V(D)J TCR α and β sequences at the single cell level.
For scRNA-seq analysis, intestinal T cells isolated from IEL and LPL were thawed, washed and sorted separately or combined for viable recipient HLA+CD45+CD3+ T cells using the BD Influx cell sorter. Cells were then mixed with 10x Chromium 5’ RT reagents and loaded into a Chromium microfluidics chip and controller for droplet formation, with each productive droplet containing one single cell and one single 10x barcoded primer bead. Full-length first strand cDNAs were synthesized in individual droplets from polyadenylated mRNAs and labeled with a unique 10x cell-bead barcode. For 5’ gene expression sequencing (5’GEX-seq), cDNAs were amplified and Illumina-compatible sequencing libraries were prepared and sequenced on an Illumina NovaSeq 6000 Sequencer.

value: ileum

value: ileum explant IEL (Recipient T)

value: FACS-sorted recipient HLA+ CD45+ CD3+ T cells


title: MJ009_TCR Pt4 iITx POD1606 ileum explant LPL (Recipient T)

value: ileum explant LPL (Recipient T)


title: Subject 100420, B+3H

description: Column name in processed data file: 145

value: Blood


title: Wild Type High Cholesterol_2


title: Subject 100315, D0

description: Column name in processed data file: 144

value: Control


title: Wild Type High Cholesterol_1

value: Liver


title: Knockout Low Cholesterol_4

value: Low Cholesterol


title: Tumor sample from Patient 02, post-immunotherapy treatment

value: Male

value: Lymph node

value: Non-Small Cell Lung Cancer (NSCLC)

value: Post-treatment

value: FFPE


title: Tumor sample from Patient 01, pre-immunotherapy treatment

value: Lung

value: Pre-treatment


title: MJ005_TCR Pt14 iITx POD1764 ileum explant IEL + LPL (Recipient T)

value: ileum explant IEL + LPL (Recipient T)


title: MJ019_TCR Pt21 MVTx POD1145 ileum explant LPL (Recipient T)


title: Knockout Low Cholesterol_3

value: gonadal Adipose Tissue

value: Knockout (Gramd1c -/-)


title: 5dpf_surface_Rep2

value: Surface


title: Subject 100370, B+1D

description: Column name in processed data file: 143

value: MVA-BN-Filo

value: Boost


title: Subject 100458, P+1D

description: Column name in processed data file: 154

value: Blood

value: Prime


title: Knockout Low Cholesterol_2

value: Liver


title: Knockout Low Cholesterol_1

value: Low Cholesterol


title: MJ018_TCR Pt21 MVTx POD1145 ileum explant IEL (Recipient T)

value: ileum

value: ileum explant IEL (Recipient T)

value: FACS-sorted recipient HLA+ CD45+ CD3+ T cells


title: MJ006_TCR Pt21 MVTx POD626 ileum stoma IEL + LPL (Recipient T)

value: ileum stoma IEL + LPL (Recipient T)


title: Wild Type Low Cholesterol_5

value: Wild Type (Gramd1c +/+)


title: Wild Type Low Cholesterol_3


title: Subject 100370, D0

description: Column name in processed data file: 141

value: Control


title: MJ017_TCR Pt16'' MVTx POD1004 ileum stoma LPL (Recipient T)

value: ileum stoma LPL (Recipient T)


title: Wild Type Low Cholesterol_2


title: MJ016_TCR Pt16'' MVTx POD1004 ileum stoma IEL (Recipient T)

value: ileum stoma IEL (Recipient T)


title: 2cell_early_Klf17matKO_KLF17_rep2

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

country: China

institute: Beijing Institute of Radiation Medicine

data_processing:
RNA-seq reads were mapped to the mm9 genome by STAR v2.5.0a
stacc-seq reads were mapped to mm10 whole genome using bowtie v1.3.0 with parameters --end-to-end --very-sensitive --no-mixed --no-discordant --phred33   --no-unal  -I 10 -X 700
replicates of same stage were pooled together and RPKM in wiggle files were counted by the number of reads falling into 100bp bin in the genome
FPKM_count.py is used to calculate the reads FPKM of each exon
Assembly: mm10
Supplementary files format and content: plain txt file, each contains two column. First column means the gene ID, the second column means sample's FPKM

source_name: early 2 cells

growth_protocol: Mice were housed under SPF environmental conditions with free access to water and food, 20–22°C ,50–70% humidity, and a 12/12-hour light and dark cycle in the Animal Core Facility of Nanjing Medical University. Animal care and experimental procedures were conducted according to the guidelines of the Animal Research Committee of Nanjing Medical University.

extract_protocol:
For RNA-seq, the collected embryos were washed twice with 1xPBS and then immediately placed in lysis buffer( Combine 0.2% (vol/vol) Triton X-100 and 2 U µl–1 RNase inhibitor);For Stacc-seq, embryos were  collected and transferred into a 200-μl low-binding tube (total volume with buffer less than 1 μl). Six microlitres of DB-1  (10 mM Tris-HCl pH = 7.4, 150 mM NaCl, 0.5 mM spermidine, 1 × EDTA-free Roche complete protease inhibitor, 0.005% digitonin (Sigma, D141)) buffer was added.
For RNA-seq, samples were taken out from -80℃ freezer, and thawed on ice, 1μl of 10μM oligo-dT primer, 1μl of 10 mM dNTP mix were added to the lysis buffer. cDNA synthesis and amplification were performed following the Smart-seq2 ; Stacc-seq was performed following the previously reported protocol designed by Bofeng Liu etc. pG–Tn5 (Vazyme,TD901) and RNA pol ll antibody (Active motif,39097,lot102660) was used. The precipitated DNA was processed into sequencing libraries using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme,TD904 )following the manufacturer's instructions.

treatment_protocol: Embryos in this study were derived from IVF( In Vitro Fertilization). Female mice were superovulated by 5 IU PMSG injection, followed by 5 IU hCG injection 48 h later. COCs were isolated. Embryos at different stages were collected after adding the sperm of wild type male mice at different time periods.

tag: strain

tag: developmental stage

value: embryo


title: Subject 100370, B+3H

description: Column name in processed data file: 139


title: 2cell_early_Klf17matKO_KLF17_rep1


title: 2cell_early_Ctrl_KLF17_rep2

value: wild type


title: Subject 100315, P+3H

description: Column name in processed data file: 140


title: MJ003_TCR Pt13 iITx POD1032 ileum stoma LPL (Recipient T)


title: Subject 100315, P+1D

description: Column name in processed data file: 138


title: 2cell_early_Ctrl_KLF17_rep1


title: 4th round ICB resistant CT26 cells, IFNγ untreated [C4th4-N]

data_processing:
Sequences were trimmed using Trimmomatic v.0.36 and mapped to Mus Musculus GRCm38 reference genome using STAR aligner v.2.5.2b.
Unique gene hits were calculated by using featureCounts from the Subread package v.1.5.2.
Only unique reads that fell in exonic regions were counted.
Assembly: Mus Musculus GRCm38
Supplementary files format and content: Tab delimited file that includes raw counts for each sample

growth_protocol: BALB/C mice were acquired from The Jackson Laboratory, after several days of acclimation, mice were inoculated with 500k CT26 on the rear flank. When the average tumor volume reached 80-100 mm3 (indicating day 0), mice were given a series of intraperitoneal injections of anti-PD-1 (clone RMP1-14; BioXcell), consisting of 100 μg each on days 0, 3, and 6. Tumors were excised from mice that did not respond to anti-PD-1 therapy, approximately 10-14 days following the initial treatment. Tumors were dissociated using collagenase (Stemcell Technologies), washed in 1X PBS, and plated in IMDM culture media supplemented in 10% fetal bovine serum, 1% GLUTiMAX, and 1% Antibiotic-Antimycotic (all GIBCO). Cells were passaged at least 5 times and then inoculated into new recipient mice according to the same protocol as above. Again, when tumors reached 80-100 mm3, another treatment course of anti-PD-1 began. This process was repeated for a total of four rounds, at which point none of the treated mice responded to anti-PD-1 therapy. The cell lines generated after two rounds of anti-PD1 selection are referred to throughout this manuscript as ‘2nd round’, ‘2nd generation’ or ‘F2 generation’, and the cell line generated after four rounds of anti-PD1 selection are referred to as ‘4th round’, ‘4th generation’, or ‘F4 generation’.

extract_protocol:
The following day, RNA was isolated from cells using Qaigen RNAeasy reagents according to manufacturer’s instructions, including QiaShredder homogenization and on-column DNaseI digestion.
Isolated RNA was sent to Genewiz (www.genewiz.com) for library generation, RNA-sequencing, and data processing. Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. Sequencing libraries were generated and sequenced on an Illumina HiSeq (2x150 paired end reads), targeting >20x106 reads per sample.

treatment_protocol: Three distinct vials of parental CT26 cells (ATCC; ‘experimental replicates’), two independently isolated tumors from ‘2nd round’ mice, and four independently isolated tumors from ‘4th round’ mice (both ‘biological replicates’), were cultured +/- 20 ng/ml of mouse IFNγ (Biolegend) for 24 hours at 37oC/5%CO2.

tag: cell line

value: CT26 cells

value: murine colorectal carcinoma cell line


title: Subject 100370, P+3H

description: Column name in processed data file: 137


title: 4th round ICB resistant CT26 cells, IFNγ treated [C4th3-Y]


title: Subject 100315, P+7D

description: Column name in processed data file: 136


title: 4th round ICB resistant CT26 cells, IFNγ treated [C4th2-Y]


title: 4th round ICB resistant CT26 cells, IFNγ untreated [C4th3-N]


title: Wild Type Low Cholesterol_4

value: gonadal Adipose Tissue


title: Subject 100315, B+1D

description: Column name in processed data file: 142

value: Blood

value: MVA-BN-Filo

value: Boost


title: 4th round ICB resistant CT26 cells, IFNγ untreated [C4th2-N]


title: 4th round ICB resistant CT26 cells, IFNγ treated [C4th1-Y]


title: Wild Type Low Cholesterol_1

value: Liver

value: Low Cholesterol


title: Subject 100336, D0

description: Column name in processed data file: 134


title: 2nd round ICB resistant CT26 cells, IFNγ treated [C2nd2-Y]


title: BO-SARS-3

city: Kyoto

first: Kazuo

last: Takayama

state: Kyoto

address: Shogoin Kawaharacho 53, Sakyo-ku

department: Center for iPS Cell Research and Application

country: Japan

institute: Kyoto University

data_processing:
Sequencing was performed on an Illumina NextSeq550 platform in a 76-base single-end mode.
Illumina RTA version 2.11.3 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
Adapter sequences and low-quality bases were trimmed from the raw reads by Cutadapt v1.14. The trimmed reads were mapped to the human reference genome sequences (hg38) using STAR v2.5.3a with the GENCODE (release 36, GRCh38.p13) gtf file.
The raw counts were calculated using htseq-count v0.12.4 with the GENCODE gtf file. Gene expression levels were determined as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: infected BO

extract_protocol:
RNA-seq in BO: Total RNA was isolated from the BO using an RNeasy Protect Mini Kit (Qiagen).
RNA-seq in BO: Library preparation was performed using TruSeq Stranded mRNA Library Prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: human bronchial organoids

value: SARS-CoV-4 infected


title: BO-SARS-2

value: SARS-CoV-3 infected


title: Subject 100370, P+1D

description: Column name in processed data file: 135

value: Prime


title: 4th round ICB resistant CT26 cells, IFNγ untreated [C4th1-N]


title: MJ001_TCR Pt15 MVTx POD1194 ileum Bx IEL + LPL (Recipient T)

value: ileum

value: ileum Bx IEL + LPL (Recipient T)

value: FACS-sorted recipient HLA+ CD45+ CD3+ T cells


title: MJ007_TCR D251 ileum IEL + LPL

value: ileum IEL + LPL


title: MJ002_TCR Pt13 iITx POD1032 ileum stoma IEL (Recipient T)

value: ileum stoma IEL (Recipient T)


title: Subject 100370, P+7D

description: Column name in processed data file: 133


title: 2nd round ICB resistant CT26 cells, IFNγ treated [C2nd1-Y]

value: CT26 cells


title: 4th round ICB resistant CT26 cells, IFNγ treated [C4th4-Y]

value: murine colorectal carcinoma cell line


title: BO-SARS-1

value: SARS-CoV-2 infected


title: BO_CNT-3

source_name: uninfected BO

value: no virus


title: parental CT26 cells, IFNγ treated [CPar3-Y]

source_name: parental CT26 cells, IFNγ treated

value: parental CT26 cells, IFNγ treated


title: 2nd round ICB resistant CT26 cells, IFNγ untreated [C2nd1-N]


title: Subject 100336, B+7D

description: Column name in processed data file: 132

value: Blood

value: MVA-BN-Filo

value: Boost


title: Subject 100370, P+57D

description: Column name in processed data file: 131


title: parental CT26 cells, IFNγ untreated [CPar3-N]

source_name: parental CT26 cells, IFNγ untreated

value: parental CT26 cells, IFNγ untreated


title: BO_CNT-2

value: human bronchial organoids


title: parental CT26 cells, IFNγ untreated [CPar2-N]


title: parental CT26 cells, IFNγ treated [CPar2-Y]


title: BO_CNT-1


title: Subject 100336, B+3H

description: Column name in processed data file: 130


title: parental CT26 cells, IFNγ treated [CPar1-Y]


title: Subject 100370, B+7D

description: Column name in processed data file: 129


title: TEC_control_Rep4

city: Rehovot

first: Jakub

last: Abramson

address: 234 Herzl st.

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

description:
AREG_IT_TEC_P10_6
Bulk Mars-Seq (3' end-RNA-seq)

data_processing:
Data was processed using UTAP transcriptome analysis pipeline (Kohen et al., 2019). Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq). R1 Fastq data submitted.
Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.5.2b (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of RefSeq annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting proceeded using HTSeq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package.
Differential expression analysis was performed using DESeq2 with betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts, normalized abundance measurements and DESeq2 analysis.

source_name: Thymus

extract_protocol:
Thymi were removed and enzymatically dissociated with Liberase TH and DNase. Thymic epithelial cells (TEC) were sorted into lysis binding buffer and RNA was extracted using Dynabeads. MARSseq protocol was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using the MARSseq protocol (Jaitin et al. 2014).

treatment_protocol: Mice were injected with rAREG (1ug) or vehicle (PBS) 10 days before sacrificed.

value: Thymus

value: Thymic epithelial cells

value: WT

tag: Sex

value: Male

value: Vehicle


title: TEC_control_Rep3

description:
AREG_IT_TEC_P10_3
Bulk Mars-Seq (3' end-RNA-seq)


title: Subject 100336, B+1D

description: Column name in processed data file: 128


title: parental CT26 cells, IFNγ untreated [CPar1-N]


title: TEC_control_Rep2

description:
AREG_IT_TEC_P10_2
Bulk Mars-Seq (3' end-RNA-seq)


title: Subject 100336, P+3H

description: Column name in processed data file: 126

value: Prime


title: TEC_control_Rep1

description:
AREG_IT_TEC_P10_1
Bulk Mars-Seq (3' end-RNA-seq)


title: Subject 100373, B+3H

description: Column name in processed data file: 125


title: 2nd round ICB resistant CT26 cells, IFNγ untreated [C2nd2-N]


title: TEC_rAREG_Rep5

description:
AREG_IT_TEC_A10_6
Bulk Mars-Seq (3' end-RNA-seq)

value: rAREG


title: Subject 100336, P+1D

description: Column name in processed data file: 124


title: TEC_rAREG_Rep4

description:
AREG_IT_TEC_A10_4
Bulk Mars-Seq (3' end-RNA-seq)


title: Subject 100373, D0

description: Column name in processed data file: 123

value: Control


title: TEC_rAREG_Rep3

description:
AREG_IT_TEC_A10_3
Bulk Mars-Seq (3' end-RNA-seq)


title: Subject 100336, P+7D

description: Column name in processed data file: 122


title: Subject 100373, B+1D

description: Column name in processed data file: 127


title: TEC_rAREG_Rep2

description:
AREG_IT_TEC_A10_2
Bulk Mars-Seq (3' end-RNA-seq)


title: Subject 100373, P+3H

description: Column name in processed data file: 121


title: Subject 100347, B+7D

description: Column name in processed data file: 120


title: Subject 100373, P+7D

description: Column name in processed data file: 119


title: Male_NT_2

city: Beer Sheva

first: Adrian

last: Israelson

address: Ben Gurion Blv. 1

institute: Ben Gurion University of the Negev

data_processing:
The sequences were quality trimmed and filtered using Trim Galore (v0.4.5) and cutadapt (v1.15).
Alignment of the reads to the mouse genome (GRCm38) was done using STAR (v2.5.2a)
The number of reads per gene per sample was counted using RSEM (v1.2.28)
Assembly: mm10
Supplementary files format and content: Normalized Counts

source_name: Spinal cord

extract_protocol:
RNA was extracted using RNeasy plus mini kit (Qiagen)
The library was prepared using MARS seq in which the 3'UTR of the transcripts are captured and 8 bp Unique Molecular Identifiers (UMIs) are added to the DNA fragments to reduce errors and quantitative bias caused by the amplification.

treatment_protocol: Treated group was injected with AAV-PHP.eB-MIF-HA after the disease onset

value: Spinal cord

value: Non transgenic

value: Not treated


title: Male_SOD_1


title: Male_SOD_MIF_2


title: Male_NT_6


title: Male_SOD_2


title: Male_SOD_MIF_3


title: Male_NT_3


title: Male_SOD_3


title: Female_SOD_3

value: Female


title: Male_NT_1


title: Male_SOD_MIF_4


title: Male_NT_4


title: Male_SOD_5


title: Male_SOD_7


title: Female_SOD_1


title: Male_NT_7


title: Female_NT_3


title: Subject 100347, B+1D

description: Column name in processed data file: 118

value: Blood


title: Female_NT_2


title: Il25WT ILC2_Rep3

description:
il25ko_ss_wt3
Bulk Mars-Seq (3' end-RNA-seq)

extract_protocol:
Thymi were removed and enzymatically dissociated with Liberase TM and DNase. ILC2 were sorted into lysis binding buffer and RNA was extracted using Dynabeads. MARSseq protocol was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using the MARSseq protocol (Jaitin et al. 2014).

value: Il25 WT


title: Il25WT ILC2_Rep2

description:
il25ko_ss_wt2
Bulk Mars-Seq (3' end-RNA-seq)


title: Il25WT ILC2_Rep4

description:
il25ko_ss_wt4
Bulk Mars-Seq (3' end-RNA-seq)


title: TEC_rAREG_Rep1

description:
AREG_IT_TEC_A10_1
Bulk Mars-Seq (3' end-RNA-seq)


title: Male_NT_5


title: Female_NT_1


title: Subject 100373, P+57D

description: Column name in processed data file: 117


title: Subject 100373, P+1D

description: Column name in processed data file: 115


title: XV0008C1_Orthotopic PDAC tumor Biological Replicate (ROI3)

city: Singapore

first: Melissa

last: Ng

address: 8A Biomedical Grove, #03-06 Immunos Building, Singapore

country: Singapore

institute: Singapore Immunology Network

description: Fresh Frozen Spatial Transcriptome Sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm 10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected tissue image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors _json.json.gz: scalefactors in json format
Supplementary files format and content: tissue hires image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue lowres image.png.gz: low-res image of tissue
Supplementary files format and content: tissue positions list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: PDAC tumor

growth_protocol: The luciferase-stable pancreatic ductal adenocarcinoma FC1242L cell line was generated as described in Leong et al., and was derived from the FC1242 cell line (kind gift from Dr Dannielle Engle, Tuveson lab, Cold Spring Harbour Laboratory) derived from Pdx1Cre; KrasG12D/+; Trp53R172H/+ (KPC) mice. FC1242L was culturecultured in complete media (cDMEM) comprising Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 10% fetal calf serum (FCS), 1% Penicillin-Streptomycin (Gibco) and seeded at a density of 2 X 10^5 cells/mL in T75 cell culture flask. Cells were grown at 37°C in 5% CO2 incubator until they reached 80% confluency. Upon reaching confluency, cells were trypsinized with pre-warmed 0.25% Trypsin with Ethylenediaminetetraacetic acid (EDTA), phenol red (Gibco) for 5 minutes at 37°C in 5% CO2 incubator, washed with pre-warmed cDMEM and counted, before seeding at a density of 2 X 10^5 cells/mL for the next passage.

extract_protocol:
At 6 weeks post injection, tumors were excised from tumor-bearing mice and weighed before mincing into smaller pieces using surgical scissors. Frech frozen tissue were OCT embedded, and 10um frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

treatment_protocol: Mice were administered intrapancreatic injections of FC1242L tumor cells. The mice were anaesthetized, the pancreas was exposed by surgical excision, and 10,000 FC1242L cels were re-suspended in 1X phosphate buffered saline (PBS) and mixed with Matrigel (BD) in a 1:1 ratio, and were injected as a volume of 50 µL into the body of the pancreas to form a visible bolus.

value: PDAC tumor

tag: tumor stage

value: 6wk post surgery

tag: model

value: Orthotopic KPC


title: Il25KO ILC2_Rep2

description:
il25ko_ss_ko304
Bulk Mars-Seq (3' end-RNA-seq)

value: Thymus

tag: genotype

value: Il25 KO


title: Subject 100373, B+7D

description: Column name in processed data file: 113

value: MVA-BN-Filo

value: Boost


title: Il25KO ILC2_Rep4

description:
il25ko_ss_ko306
Bulk Mars-Seq (3' end-RNA-seq)

value: Male


title: Il25WT ILC2_Rep1

description:
il25ko_ss_wt1
Bulk Mars-Seq (3' end-RNA-seq)


title: Thymic hematopoietic non-T cells, untreated1+18h dex2, Ab

description:
Hashtag-derived oligonucleotide (HTO), Antibody-derived oligonucleotide (ADT)
Ab library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
A_filtered_feature_bc_matrix.h5

library_source: other

data_processing:
Sequencing data from the 10x Genomics libraries was demultiplexed, aligned to the mm10 genome and UMI-collapsed using the count function of the Cellranger toolkit (version 5.0.0) provided by 10X Genomics, with the transcriptome refdata-gex-mm10-2020-A.
Further demultiplexing of the hashtag oligos was performed using the Seurat R package (version 3.9.9.9024) (DOI:https://doi.org/10.1016/j.cell.2021.04.048) according to the instructions in the vignette: https://satijalab.org/seurat/articles/hashing_vignette.html. Doublets (cells with two antibody tags) and negatives (no antibody tag) were removed and the singlets were assigned to the relevant samples. Cells with more than 5% mitochondrial UMI counts, cells with less than 500 UMI counts (function subset) and cells in the top or bottom 1% of genes or UMI counts (function which) were removed from the analysis.
single cell analyses were performed using the Seurat R package (version 3.9.9.9024). The data was normalized using the function SCTransform (https://doi.org/10.1186/s13059-019-1874-11). Dimensionality reduction was performed using PCA (RunPCA). The functions RunTSNE and FindNeighbors were applied using 20 PCs. The clustering was performed with a resolution of 1.2 (FindClusters), and 35 clusters were detected. Differential gene expression was calculated using the functions FindAllMarkers (logfc.threshold = 0.7, only.pos = TRUE) or FindMarkers with the default statistical test Wilcoxon rank-sum test. Plots were made using Seurat functions RidgePlot, DotPlot, DimPlot and FeaturePlot. Sub-clustering of cluster 29 was done using Seurat function FindSubCluster with resolution 0.8.
Assembly: mm10
Supplementary files format and content: Cell ranger output files: A_filtered_feature_bc_matrix.h5
Supplementary files format and content: Cell ranger output files: B_filtered_feature_bc_matrix.h5
Supplementary files format and content: Cell ranger output files: C_filtered_feature_bc_matrix.h5
Supplementary files format and content: Seurat output file: mySeurat.rds
Supplementary files format and content: Gene expression average per cluster file: general_filt_clust_20_pcs_1_2_res_SCT_average_expression.xlsx
Library strategy: CITE-Seq

molecule: protein

extract_protocol:
Mice were sacrificed and perfused, thymi were surgically removed, trimmed of fat and connective tissues, and placed in PBS on ice. Thymi were disintegrated by enzymatic digestion for 30 min in a 37°C water bath, using 0.016 mg/ml Liberase TM (Roche, 5401127001) and 10 ng/ml DNase I (Sigma-Aldrich, DN25) in RPMI, then filtered through a 50-μm mesh filter. Cells were washed with 5–10 ml MACS buffer. 5 million cells per sample were first stained with 5 μl anti-mouse CD16/CD32 monoclonal antibody (Biolegend, 101302) in 50 μl labeling buffer (PBS + 1% BSA) for 10 min at 4 °C, then an antibody mix containing both TotalSeq-B and flow cytometry antibodies in labeling buffer was added to complete to ~100 μl total volume, and cells were incubated for 30 min at 4 °C. TotalSeq-B antibody mix was prepared in advance per sample in labeling buffer (PBS + 1% bovine serum albumin, BSA) at a total volume of 50 μl and centrifuged at 14,000 x g for 10 min at room temperature, prior to its combination with the flow cytometry antibody mix and incubation with the cells. Cells were then washed 3 times with 5 ml labeling buffer. 10 minutes before each sample was sorted, it was incubated with a viability dye for 5 min at room temperature, then washed and resuspended in PBS + 2% BSA. Cells were sorted into PBS supplemented with 50% FBS and then washed and resuspended in PBS + 0.04% BSA, counted on a hemocytometer, and volume was adjusted to a concentration of 1,000,000 cells/ml. Each two non-replicate samples were combined evenly into one pool.
scRNA-Seq and CITE-Seq libraries were prepared using the Chromium 10x Genomics platform and Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index). Loading and library preparation were done according to the manufacturer’s instructions (10X genomics).

treatment_protocol: Mice were injected I.P. with dexamethasone (200ug/10gr body weight) 4d or 18h before sacrificed, or untreated.

value: Thymic hematopoietic non-T cells

value: WT

value: Combined samples (Untreated 1+ 18h Dex 2)

tag: library type

value: Ab

tag: hto

value: TotalSeq-B0303 anti-mouse Hashtag 3, TotalSeq-B0306 anti-mouse Hashtag 6

tag: adt

value: TotalSeq-B0015 anti-mouse Ly-6G, TotalSeq-B0115 anti-mouse FcεRIα, TotalSeq-B0093 anti-mouse CD19, TotalSeq-B0118 anti-mouse NK-1.1, TotalSeq-B0106 anti-mouse CD11c, TotalSeq-B0431 anti-mouse CD170 (Siglec-F), TotalSeq-B0014 anti-mouse/human CD11b, TotalSeq-B0114 anti-mouse F4/80, TotalSeq-B0211 anti-mouse TCR Vγ2, TotalSeq-B0117 anti-mouse I-A/I-E


title: Thymic hematopoietic non-T cells, untreated2+4d dex1, Ab

description:
Hashtag-derived oligonucleotide (HTO), Antibody-derived oligonucleotide (ADT)
Ab library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
B_filtered_feature_bc_matrix.h5

value: Combined samples (Untreated 2+ 4d Dex 1)

value: TotalSeq-B0304 anti-mouse Hashtag 4, TotalSeq-B0307 anti-mouse Hashtag 7


title: control airway epithelium

city: La Jolla

first: Xin

last: Sun

state: CA

address: Cellular and Molecular Medicine East 1087, 9500 Gilman Drive

institute: University of California San Diego

description:
control_snRNAseq
single nucleus RNA seq
snRNA-airwayIntegrated.rds

data_processing:
Cell Ranger version 3.0.2 was used to align reads on the mouse reference genome (mm10) and generate the feature-barcode matrix.
R package Seurat was used to perform data quality control, normalization, scaling, principal component analysis (PCA) and canonical correlation analysis (CCA) based data integration.
Assembly: mouse mm10
Supplementary files format and content: h5 files from Cell Ranger

extract_protocol:
Lung tissue was resuspended in nuclei permeabilization buffer 0.1% Triton-X-100, 1X protease inhibitor, 1 mM DTT, and 0.2 U/µL RNase inhibitor, 2% BSA in PBS). Sample was incubated on a rotator for 5 min at 4°C and then centrifuged at 500 rcf for 5 min (4°C, run speed 3/3). Supernatant was removed and pellet was resuspended in 400 µL of sort buffer (1 mM EDTA 0.2 U/µL RNase inhibitor, 2% BSA in PBS) and stained with DRAQ7. 75,000 nuclei were sorted using a SH800 sorter (Sony) into 50 µL of collection buffer consisting of 1 U/µL RNase inhibitor in 5% BSA. FACS gating strategy based on particle size, DRAQ7 and GFP fluorescence was used to sort nuclei.
12,000 nuclei were loaded onto a Chromium Controller (10x Genomics). Libraries were generated using the Chromium Single-Cell 3′ Library Construction Kit v3 (10x Genomics

value: Lung tissue

value: Airway

value: Sox2-creER; SUN1-GFP

value: Tamoxifen injections


title: Il25KO ILC2_Rep1

description:
il25ko_ss_ko303
Bulk Mars-Seq (3' end-RNA-seq)

value: Thymus


title: Il25KO ILC2_Rep3

description:
il25ko_ss_ko305
Bulk Mars-Seq (3' end-RNA-seq)

value: Il25 KO


title: Subject 100347, B+3H

description: Column name in processed data file: 114

tag: timepoint

value: Blood

value: MVA-BN-Filo


title: Thymic hematopoietic non-T cells, 18h Dex1+4d dex2, Ab

description:
Hashtag-derived oligonucleotide (HTO), Antibody-derived oligonucleotide (ADT)
Ab library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
C_filtered_feature_bc_matrix.h5

value: Male

value: Combined samples (18h Dex 1+ 4d Dex 2)

value: TotalSeq-B0305 anti-mouse Hashtag 5, TotalSeq-B0308 anti-mouse Hashtag 8


title: 25 dpi airway epithelium

description:
flu_snRNAseq
single nucleus RNA seq
snRNA-airwayIntegrated.rds

value: Tamoxifen injections, Influnza PR8


title: Subject 100347, P+29D

description: Column name in processed data file: 116

value: Prime


title: Thymic hematopoietic non-T cells, untreated1+18h dex2, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
A_filtered_feature_bc_matrix.h5

value: Thymic hematopoietic non-T cells

value: WT

value: Combined samples (Untreated 1+ 18h Dex 2)

value: mRNA


title: Thymic hematopoietic non-T cells, 18h Dex1+4d dex2, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
C_filtered_feature_bc_matrix.h5


title: Subject 100347, D0

description: Column name in processed data file: 112

value: Control


title: Male_SOD_6

value: Spinal cord

value: Not treated


title: Male_SOD_MIF_1


title: Male_SOD_4


title: Female_SOD_2

value: Female


title: Subject 100356, B+3H

description: Column name in processed data file: 111

value: Boost


title: 2cell_early_WT_NC_rep2

library_source: genomic

data_processing:
RNA-seq reads were mapped to the mm9 genome by STAR v2.5.0a
stacc-seq reads were mapped to mm10 whole genome using bowtie v1.3.0 with parameters --end-to-end --very-sensitive --no-mixed --no-discordant --phred33   --no-unal  -I 10 -X 700
replicates of same stage were pooled together and RPKM in wiggle files were counted by the number of reads falling into 100bp bin in the genome
FPKM_count.py is used to calculate the reads FPKM of each exon
Assembly: mm10
Supplementary files format and content: plain txt file, each contains two column. First column means the gene ID, the second column means sample's FPKM
Library strategy: CUT&Tag

molecule: genomic DNA

value: embryo

value: wild type

tag: antibody

value: No antibody


title: Ex vivo tuft_control_Rep3

description:
Tuft_UT3
Bulk Mars-Seq (3' end-RNA-seq)

growth_protocol: Thymi were removed and enzymatically dissociated with Liberase TH and DNase. Tuft cells were sorted into supplemented DMEM medium, cultured in V-shaped 96 wells and centrifuged at 230g for 5 minutes to form an aggregate. The cells were grown ex vivo for 12h, then medium was replaced and cells were grown for another 24h before treatments.

extract_protocol:
24h after treatment, medium was removed and cells were collected from the wells using lysis binding buffer. RNA was extracted using Dynabeads. MARSseq protocol was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using the MARSseq protocol (Jaitin et al. 2014).

treatment_protocol: Ex vivo grown cells were treated with 20ng/mL rIL-13 or vehicle only (PBS) for 24h.

value: Thymus

value: Tuft cells

value: Male

value: Vehicle

tag: time


title: Ex vivo tuft_control_Rep2

description:
Tuft_UT2
Bulk Mars-Seq (3' end-RNA-seq)

tag: tissue


title: Thymic hematopoietic non-T cells, untreated2+4d dex1, GEX

description:
polyA RNA
GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
B_filtered_feature_bc_matrix.h5

tag: treatment

value: Combined samples (Untreated 2+ 4d Dex 1)


title: XV0008D1 -Orthotopic PDAC tumor Biological Replicate (ROI4)

value: PDAC tumor

value: 6wk post surgery

value: Orthotopic KPC


title: Replicate 1 HTO

first: Li

last: Zeng

address: 11 Jln Tan Tock Seng

institute: National Neuroscience Institute

description: 10X Genomics

data_processing:
The quality of sequencing reads was evaluated using FastQC and MultiQC. Cell Ranger (version 2.2.0) was used to align the sequencing reads (fastq) to the mm10 mouse transcriptome and quantify the expression of transcripts in each cell. This pipeline resulted in a gene expression matrix for each sample, which records the number of UMIs for each gene associated with each cell barcode.
The gene expression matrix was subsequently analyzed in R using the Seurat package (4.0.5). Hashtags were demultiplexed using CITE-seq-Count. Doublets and multiplets were filtered out, as well as UMIs which had 2 or more hashtags associated with it, which resulted in 11, 682 remaining single cell transcriptomes. Additional QC included removing UMIs with excess mitochondrial reads (>5%), number of features less than 200 (low read counts) and more than 4200 (outliers).
After QC, the standard Seurat pipeline running NormalizeData(), FindVariableFeatures(selection.method =”vst”, nfeatures =2000), and ScaleData(). ScoreJackStraw() and JackstrawPlot was used to determine the number of dimensions before running RunPCA(), FindNeighbours(dims = 1:35), and FindClusters(resolution =0.8). RunUMAP(dim=1:35, n.neighbours =30) was used to visualize the data.
Assembly: mm10
Supplementary files format and content: Tab-separated barcodes and features file, and matrix files
Supplementary files format and content: Comma-separated metadata

source_name: Neutrophils

extract_protocol:
Tumor: At 6 weeks post injection, tumors were excised from tumor-bearing mice and weighed before mincing into smaller pieces using surgical scissors. Digestion mix (RPMI, 10% FCS, 500U/mL DNase I, 385U/mL collagenase D) was added to the minced tumor and incubated at 37°C for 30 minutes. Digestion enzymes were quenched with FACS buffer, and minced tumors were transferred into the gentleMACS™ C tubes (Miltenyi Biotec) for mechanical homogenization by the Xiril Dispomix using 2 rounds of Program 5 (20 seconds). Homogenized cells were filtered through 70-µm nylon mesh filter and washed with 20mL FACS buffer. Samples were then spun down at 400g for 5 minutes before RBC lysis with 1 X RBC lysis buffer for 3 minutes. Cells were washed filtered through a 70-µm nylon mesh filter. Blood: Murine blood was collected via cardiac puncture or incision in the submandibular region using a 5mm single-use lancet. 200 µL was transferred into an Eppendorf tube containing 20 µL of 0.5M EDTA. Blood samples were then lysed in 1 X red blood cell (RBC) lysis buffer (eBioscience) for 4 min. Samples were quenched with fluorescence-activated cell sorting (FACS) Buffer (1 X PBS, 4mM EDTA, 3% FCS) and spun down at 400g for 5 minutes. RBC lysis was repeated for a second time for another 2 minutes. Spleen: Spleens were excised from mice and single-cell suspensions were obtained by homogenizing spleen samples through a 70-µm nylon mesh filter with FACS buffer. Samples were then spun down at 400g for 5 minutes and lysed with 1 X RBC lysis buffer for 3 minutes. Cells were quenched with FACS buffer and filtered through a 70-µm nylon mesh filter. Bone marrow: A 23-gauge needle through the marrow cavity of the femur and the bone marrow was flushed out with 2 ml of FACS buffer using a 1ml syringe. For sorting purposes that required large cell numbers, both femur and tibia bones were used. Cells were then filtered and washed with FACS buffer, cells were spun down at 400g for 5 minutes. Sorting and hashtag labelling: Total neutrophils were sorted from the bone marrow, spleen, blood, and tumors from pancreatic tumor mice and identified as Lin-CD45+CD115-Ly6ClowSiglec-F-Gr1+CD11b+Ly6G+. Neutrophils were spun down and incubated with Totalseq-A anti-mouse Hashtag antibodies 1-8 at a concentration of 0.5ug per 100,000 cells for 30 minutes at 4°C. Cells were washed with FACS buffer, spun down, and resuspended in PBS with 1% bovine serum albumin.
Hashtagged neutrophils were counted and pooled, before used for input for the 10x Genomics 3' (v3) workflow following the manufacturer's instructions

tag: hashtag

value: Neutrophils


title: Replicate 1 RNA

description: 10X Genomics

tag: cell type


title: 2cell_early_WT_NC_rep1

tag: strain


title: Subject 100356, B+1D

description: Column name in processed data file: 109

tag: subject

value: Blood

value: MVA-BN-Filo

tag: group


title: 2cell_early_Klf17Zp3cKO_Pol2_rep2

tag: developmental stage

value: RNA pol ll antibody (Active motif,39097,lot102660)


title: 2cell_early_Klf17Zp3cKO_Pol2_rep1


title: 2cell_early_Klf17Zp3cKO+Klf17mRNA_Pol2_rep1


title: 2cell_early_WT_KLF17_rep1


title: 2cell_early_WT_Pol2_rep2


title: Ex vivo tuft_rIL-13_Rep2

description:
Tuft_T2
Bulk Mars-Seq (3' end-RNA-seq)

value: WT

tag: Sex


title: Subject 100347, P+1D

description: Column name in processed data file: 108

value: Prime


title: Ex vivo ST2+ ILC2_control_Rep3

description:
ilcb_ut3
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_ILC2_exvivo_IL33.xlsx

data_processing:
Data was processed using UTAP transcriptome analysis pipeline (Kohen et al., 2019). Bcl files were converted into fastq by bcl2fastq. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq). R1 Fastq data submitted.
Reads were trimmed using Cutadapt (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25) and mapped to the Mus_musculus genome using STAR v2.5.2b (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of RefSeq annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream). Counting proceeded using HTSeq-count (union mode). Genes having minimum 5 UMI-corrected reads in at least one sample, were considered. Normalization of the counts and differential expression analysis was performed using DESeq2 package.
Differential expression analysis was performed using DESeq2 with betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Differentially expressed genes were defined as genes that had a significant adjusted p value of less than 0.05 and at least 2-fold change.
Assembly: mm10
Supplementary files format and content: Excel files include raw counts, normalized abundance measurements and DESeq2 analysis.

growth_protocol: Thymi were removed and enzymatically dissociated with Liberase TM and DNase. IL-25Rhi or ST2+ ILC2 were sorted into supplemented DMEM medium containing 10ng/mL IL-7 and grown ex-vivo in flat-bottom 96 wells. Sorted cells were grown ex vivo for 12h, then medium was replaced and cells were grown for another 24h before treatments.

treatment_protocol: Ex vivo grown cells were treated with 10ng/mL rIL-25, 10ng/mL rIL-33, both, or vehicle only (PBS) for 24h.

value: ST2+ ILC2


title: 2cell_late_Klf17Zp3cKO+Klf17mRNA_rep2

source_name: late 2 cells

value: embryo


title: Subject 100356, D0

description: Column name in processed data file: 107

value: Control


title: Ex vivo tuft_rIL-13_Rep3

description:
Tuft_T3
Bulk Mars-Seq (3' end-RNA-seq)

value: Thymus


title: Ex vivo tuft_rIL-13_Rep1

description:
Tuft_T1
Bulk Mars-Seq (3' end-RNA-seq)

value: Tuft cells


title: 2cell_early_Klf17Zp3cKO+Klf17mRNA_Pol2_rep2


title: Subject 100347, P+7D

description: Column name in processed data file: 106


title: 2cell_late_Klf17Zp3cKO+Klf17mRNA_rep3


title: Ex vivo ST2+ ILC2_control_Rep4

description:
ilcb_ut4
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_ILC2_exvivo_IL33.xlsx

value: Male


title: 2cell_early_WT_Pol2_rep1

value: wild type


title: Subject 100356, P+3H

description: Column name in processed data file: 105


title: Subject 100412, B+3H

description: Column name in processed data file: 104

value: Boost


title: Ex vivo ST2+ ILC2_control_Rep2

description:
ilcb_ut2
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_ILC2_exvivo_IL33.xlsx

value: Vehicle


title: Subject 100347, P+3H

description: Column name in processed data file: 110


title: 2cell_early_WT_KLF17_rep2


title: Ex vivo tuft_control_Rep1

description:
Tuft_UT1
Bulk Mars-Seq (3' end-RNA-seq)


title: Ex vivo ST2+ ILC2_control_Rep1

description:
ilcb_ut1
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_ILC2_exvivo_IL33.xlsx


title: Subject 100412, B+7D

description: Column name in processed data file: 102


title: Ex vivo ST2+ ILC2_rIL33_Rep4

description:
ilcb_t4
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_ILC2_exvivo_IL33.xlsx


title: Subject 100356, P+7D

description: Column name in processed data file: 101


title: Ex vivo ST2+ ILC2_rIL33_Rep3

description:
ilcb_t3
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_ILC2_exvivo_IL33.xlsx


title: Ex vivo ST2+ ILC2_rIL33_Rep2

description:
ilcb_t2
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_ILC2_exvivo_IL33.xlsx


title: 2cell_late_WT_rep1


title: 2cell_late_Klf17Zp3cKO_Pol2_rep2


title: 2cell_late_Klf17Zp3cKO+Klf17mRNA_rep1


title: 2cell_late_Klf17Zp3cKO_Pol2_rep3


title: 2cell_late_Klf17Zp3cKO_Pol2_rep1


title: Subject 100412, B+1D

description: Column name in processed data file: 100


title: 2cell_late_WT_rep3


title: Zygotes_Klf17Zp3cKO+Klf17mRNA_rep2

source_name: zygotes


title: ChIP_H3K4me3

city: Niigata

first: Tomoyuki

last: Yamanaka

address: 1-757 Asahimachidori, Chuo-ku

department: Brain Research Institute

institute: Niigata University

data_processing:
ChIP-seq reads were quality checked using fastqc and confirmed to be containing no error.
ChIP-seq reads were mapped to NCBI GRCm38 using Bowtie 2 v2.2.8. Only uniquely mapped reads were retained.
Peaks were called using MACS2 v2.1.2 with the significant cut off p<0.001 (NF-YC ChIP) or q<0.05 (H3K4me3 ChIP).
ChIP-seq genes were annotated using ChIPpeakAnno.
Assembly: GRCm38
Supplementary files format and content: narrowPeaks except of input sample
Supplementary files format and content: bedGraph

source_name: Embryonic brain cortex

extract_protocol:
Isolated E13.5 cortices were minced with blades in 1% Pierce formalin / PBS and further incubated ar room temperature for 10 min, followed by blocking with 1M glycine/PBS and washing with PBS twice. After adding SDS lysis buffer, the tissues were sonicated by Bioruptor.
ChIP-seq libraries were prepared using the Takara ThruPLEX DNA-seq Kit. The libraries were size selected using AMPure XP beads, and validated using a Agilent TapeStation.

value: Embryonic brain cortex

tag: chip antibody

tag: Stage


title: Zygotes_Klf17Zp3cKO_Pol2_rep2

tag: genotype


title: Zygotes_Klf17Zp3cKO_Pol2_rep3


title: 2cell_late_WT_rep2


title: Zygotes_Klf17Zp3cKO+Klf17mRNA_rep3


title: Subject 100356, P+1D

description: Column name in processed data file: 103

data_processing:
raw counts were normalized as Log2 counts per million
Assembly: hg18
Supplementary files format and content: normalized_counts_050523.csv, corresponding to 59 subjects

source_name: Blood

extract_protocol:
Total RNA was purified from whole blood with the Tempus™ Spin RNA Isolation Kit (Invitrogen) and globine mRNA depletion carried out with GLOBINclear™ Kit
mRNA libraries were prepared with the NEBNext single cell/low input RNA library prep kit for Illumina. Single read of 101 bp sequencing was performed on the Illumina HiSeq 2500 at Vaccine Research Institute genomic Platform


title: Ex vivo ST2+ ILC2_rIL33_Rep1

description:
ilcb_t1
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_ILC2_exvivo_IL33.xlsx


title: ChIP_NFYC

value: NF-YC


title: Subject 100412, P+29D

description: Column name in processed data file: 98


title: Ex vivo IL25R+ ILC2_rIL33_Rep3

description:
10_ex_vivo_ILC2_il33_3
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_exvivo_IL25.xlsx

value: IL25R+ ILC2


title: Subject 100356, B+7D

description: Column name in processed data file: 97

value: Blood


title: CD4_Tumour_3

first: Rahul

last: Roychoudhuri

address: Tennis Court Road

department: Department of Pathology

description: Cells were isolated by fluorescence-activated cell sorting and stored in 40 µl RNAlater™ Stabilization Solution at -80 °C Samples were processed using the QIAshredder Kit (Qiagen) according to the manufacturer’s protocol RNA was extracted from samples using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA Libraries were prepared using the SmartSeq2 protocol on an automated Hamilton NGS-STAR library preparation system and sequenced using a HiSeq instrument

data_processing:
FastQ files underwent quality control with FastQC, adaptor trimming with Cutadapt and alignment to the NCBIM37 Mus musculus genome annotation. Count tables containing genic read counts were normalised using intergenic read density as background for subtraction
Differential gene expression analysis was performed using DESeq2 and differentially expressed genes were futher analysed using R
Assembly: Genome_build: mm9
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text files include FPM values

source_name: Tumour-infiltrating T cells

growth_protocol: Syngeneic B16-F10 melanoma cells were subcutaneously implanted into Foxp3EGFP-DTR mice and ablated  Treg cells through administration of DTx. T cells were isolated by FACS and subjected to RNA-Seq analysis

extract_protocol:
Single-cell suspensions were purified by total CD4+ T cell enrichment followed by FACS-sorting stored in 40 µl RNAlater™ Stabilization Solution at -80 °C Samples were processed using the QIAshredder Kit (Qiagen) according to the manufacturer’s protocol RNA was extracted from samples using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol RNA Libraries were prepared using the SmartSeq2 protocol on an automated Hamilton NGS-STAR library preparation system and sequenced using a Illumina sequencing instrument
SmartSeq2, Samples were individually barcoded

treatment_protocol: Animals were administered PBS or DTx as indicated

value: Tumour-infiltrating T cells

value: CD4+ Tconv cell

value: PBS


title: Input


title: Ex vivo IL25R+ ILC2_rIL33_Rep2

description:
10_ex_vivo_ILC2_il33_2
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_exvivo_IL25.xlsx

value: WT


title: Zygotes_Klf17Zp3cKO+Klf17mRNA_rep1


title: Subject 100356, P+57D

description: Column name in processed data file: 99

value: Prime


title: Ex vivo IL25R+ ILC2_rIL25_Rep2

description:
10_ex_vivo_ILC2_il25_2
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_exvivo_IL25.xlsx


title: Ex vivo IL25R+ ILC2_rIL25_Rep3

description:
10_ex_vivo_ILC2_il25_3
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_exvivo_IL25.xlsx


title: CD8_Tumour_DTx_3

value: CD8+ Tconv cell

value: DTx


title: Treg_Tumour_3

value: Treg cell


title: Zygotes_WT_rep3

value: embryo


title: Subject 100412, P+3H

description: Column name in processed data file: 94


title: Subject 100254, D0

description: Column name in processed data file: 93

value: Control


title: Zygotes_Klf17Zp3cKO_Pol2_rep1


title: MII_Klf17Zp3cKO_Pol2_rep1

source_name: MII oocytes

value: oocyte


title: CD4_Tumor_DTx_3


title: MII_Klf17Zp3cKO_Pol2_rep3


title: Ex vivo IL25R+ ILC2_rIL25_Rep1

description:
10_ex_vivo_ILC2_il25_1
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_exvivo_IL25.xlsx

value: Thymus

value: Male


title: Subject 100254, P+3H

description: Column name in processed data file: 91


title: Ex vivo IL25R+ ILC2_control_Rep3

description:
10_ex_vivo_ILC2_cont_3
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_exvivo_IL25.xlsx

value: Vehicle


title: Subject 100412, P+7D

description: Column name in processed data file: 92


title: CD4_Tumour_2


title: Subject 100254, B+3H

description: Column name in processed data file: 95

value: MVA-BN-Filo

value: Boost


title: MII_Klf17Zp3cKO_Pol2_rep2


title: Ex vivo IL25R+ ILC2_control_Rep2

description:
10_ex_vivo_ILC2_cont_2
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_exvivo_IL25.xlsx

value: IL25R+ ILC2


title: Subject 100412, D0

description: Column name in processed data file: 96

value: Blood


title: CD8_Tumour_3

value: Tumour-infiltrating T cells


title: Ex vivo IL25R+ ILC2_rIL33_Rep1

description:
10_ex_vivo_ILC2_il33_1
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_exvivo_IL25.xlsx


title: Ex vivo IL25R+ ILC2_control_Rep1

description:
10_ex_vivo_ILC2_cont_1
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_exvivo_IL25.xlsx


title: MII_WT_rep3

value: wild type


title: Zygotes_WT_rep2


title: MII_WT_rep2


title: Zygotes_WT_rep1


title: CD8_Tumour_2

value: PBS


title: Treg_Tumour_2


title: CD8_Tumour_DTx_2


title: MII_WT_rep1


title: CD4_Tumor_DTx_2

value: CD4+ Tconv cell


title: Treg_Tumour_1


title: CD4_Tumor_DTx_1


title: Subject 100308, B+7D

description: Column name in processed data file: 90


title: NKT_vehicle_Rep5

description:
Shir_NKT_Et5
Bulk Mars-Seq (3' end-RNA-seq)

extract_protocol:
Thymi were removed and mechanically dissociated through a strainer. NKT cells were sorted into lysis binding buffer and RNA was extracted using Dynabeads. MARSseq protocol was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using the MARSseq protocol (Jaitin et al. 2014).

treatment_protocol: Mice were injected I.P. with dexamethasone (200ug/10gr body weight) or vehicle (8% EtOH) at various time points before sacrificed.

value: NKT

value: WT


title: Ex vivo IL25R+ ILC2_rIL25 rIL33_Rep2

description:
10_ex_vivo_ILC2_both_2
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_exvivo_IL25.xlsx

value: rIL-25 and rIL-33


title: Postnatal day 2 WT mouse heart, 3 day post-Sham, replicate 2

city: Houston

first: Jong

middle: H

last: Kim

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description:
10X single-nucleus RNA-seq  RNA-seq on heart section
metadata.csv.gz
norm_umi.csv.gz
raw_umi.csv.gz

data_processing:
After sequencing, preprocessing steps were performed by using CellRanger 7.1.0 with default settings. Matrices were postprocessed with CellBender v0.1.
Single nuclei were quality controled and based on criteria detailed in the associated publication. The UMI count matrices were normalized using the Seurat (v4).
Assembly: mm10
Supplementary files format and content: comma-separated metadata files and matrix files

source_name: Heart

extract_protocol:
10X Nuclei Isolation Kit
10X Library Construction Kit

treatment_protocol: P2 animals were subject to sham or myocardial infarction surgery (permanent LAD ligation), hearts were collected at P5

value: Heart

value: Cardiac cells

tag: age

value: Postnatal day 5 at collection

tag: stain

value: Female

value: Sham


title: Ex vivo IL25R+ ILC2_rIL25 rIL33_Rep1

description:
10_ex_vivo_ILC2_both_1
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_exvivo_IL25.xlsx

value: Thymus

value: Male


title: NKT_vehicle_Rep4

description:
Shir_NKT_Et4
Bulk Mars-Seq (3' end-RNA-seq)

value: Vehicle


title: Postnatal day 2 WT mouse heart, 3 day post-MI, replicate 1

value: MI


title: Postnatal day 2 WT mouse heart, 3 day post-MI, replicate 2


title: NKT_vehicle_Rep3

description:
Shir_NKT_Et3
Bulk Mars-Seq (3' end-RNA-seq)


title: Postnatal day 2 C3-/- mouse heart, 3 day post-Sham, replicate 2


title: NKT_vehicle_Rep2

description:
Shir_NKT_Et2
Bulk Mars-Seq (3' end-RNA-seq)


title: Ex vivo IL25R+ ILC2_rIL25 rIL33_Rep3

description:
10_ex_vivo_ILC2_both_3
Bulk Mars-Seq (3' end-RNA-seq)
Deseq_all_results_ILC2_exvivo_IL25.xlsx

value: IL25R+ ILC2


title: Postnatal day 2 WT mouse heart, 3 day post-Sham, replicate 1


title: Postnatal day 2 C3-/- mouse heart, 3 day post-Sham, replicate 1


title: NKT_vehicle_Rep1

description:
Shir_NKT_Et1
Bulk Mars-Seq (3' end-RNA-seq)


title: Postnatal day 2 C3-/- mouse heart, 3 day post-MI, replicate 2


title: CD8_Tumour_DTx_1

description: Cells were isolated by fluorescence-activated cell sorting and stored in 40 µl RNAlater™ Stabilization Solution at -80 °C Samples were processed using the QIAshredder Kit (Qiagen) according to the manufacturer’s protocol RNA was extracted from samples using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA Libraries were prepared using the SmartSeq2 protocol on an automated Hamilton NGS-STAR library preparation system and sequenced using a HiSeq instrument

value: Tumour-infiltrating T cells

value: CD8+ Tconv cell

value: DTx


title: MCT3

city: Nanjing

first: Feng

last: Chen

state: Jiangsu Province

address: 101 Longmian Ave

department: Department of forensic medicine

institute: Nanjing Medical University

data_processing:
Filtering of Clean Reads  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 will be further filtered according to the following rules:  1) removing reads containing adapters;  2) removing reads containing more than 10% of unknown nucleotides (N);  3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads will be removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2  (version 2.0.3.12), respectively. The alignment parameters were as follows:  1) Maximum read mismatch is 2  2) The distance between mate-pair reads is 50bp  3) The error of distance between mate-pair reads is ±80bp
Assembly: Rattus norvegicus Rnor_6.0
Supplementary files format and content: Comma-delimited text file includes raw counts for each Sample
Supplementary files format and content: Comma-delimited text file includes FPKM for each Sample

organism: Rattus norvegicus

source_name: lung

growth_protocol: Male Sprague-Dawley rats (200-250g) were kept in the specific pathogen-free (SPF) facility with suitable humidity and temperature, while food and drinking water were in sufficient supply

extract_protocol:
RNA was harvested using RNAiso Plus kit(TaKaRa),1.3ug of total RNA was used for the construction sequencing libraries
The enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters.

treatment_protocol: MCT models, rats were established by a single intraperitoneal injection of 60 mg/kg monocrotaline . Rats in the control group were given an equal volume of saline subcutaneously.

value: lung

value: Rats  received a single subcutaneous injection of 60 mg/kg monocrotaline


title: NKT_3d Dex_Rep4

description:
Shir_NKT_Dex3d5
Bulk Mars-Seq (3' end-RNA-seq)

value: NKT

value: WT

value: Dexamethasone


title: Postnatal day 2 C3-/- mouse heart, 3 day post-MI, replicate 1

value: Heart

value: Cardiac cells


title: NKT_3d Dex_Rep3

description:
Shir_NKT_Dex3d4
Bulk Mars-Seq (3' end-RNA-seq)


title: Subject 100254, P+1D

description: Column name in processed data file: 85

tag: timepoint

value: Blood

value: Prime


title: Subject 100254, B+1D

description: Column name in processed data file: 89

value: MVA-BN-Filo

value: Boost


title: Subject 100254, P+57D

description: Column name in processed data file: 83


title: Subject 100308, P+3H

description: Column name in processed data file: 82


title: Subject 100254, B+7D

description: Column name in processed data file: 81


title: Subject 100308, D0

description: Column name in processed data file: 84

value: Control


title: Subject 100308, B+3H

description: Column name in processed data file: 88


title: control3

value: Rats  were given an equal volume of saline subcutaneously


title: control2


title: MCT2


title: control1


title: Subject 100271, P+7D

description: Column name in processed data file: 79


title: Subject 100305, P+1D

description: Column name in processed data file: 80


title: Subject 100308, P+29D

description: Column name in processed data file: 86


title: MCT1


title: Subject 100254, P+7D

description: Column name in processed data file: 87


title: scRNA-Seq_TCRb+_Tcells_DTx2

description: Cells were isolated by fluorescence-activated cell sorting and subjected to sc-RNA-Seq using the Chromium 10x scRNA-Seq platform, barcoded and sequenced

data_processing:
Chromium 10x libraries were demultiplexed and subjected to Chromium cellranger analysis as per manufacturer instructions
Cellranger gene expression profiles were analysed using Seurat
Assembly: mm9
Supplementary files format and content: tab-delimited text files include normalised gene expression values

source_name: T cells from tumors

extract_protocol:
Single-cell suspensions were purified by FACS-sorting of total TCR-b+ T cells from tumors of PBS- or DTx-treated Foxp3-EGFP-DTR animals. Cell suspensions were subjected to scRNA-Seq using the Chromium 10x scRNA-Seq platform
Chromium 10x scRNA-Seq 5’ library preparation with TCR enrichment was performed according to manufacturer's instructions
Samples were individually barcoded according to Chromium 10x 5' kit instructions

value: T cells from tumors

value: TCR-b+ T cells


title: scRNA-Seq_TCRb+_Tcells_DTx3


title: NKT_3d Dex_Rep2

description:
Shir_NKT_Dex3d3
Bulk Mars-Seq (3' end-RNA-seq)

value: Thymus

value: Male


title: Subject 100305, B+7D

description: Column name in processed data file: 78


title: MJ009_GEX Pt4 iITx POD1606 ileum explant LPL (Recipient T)

data_processing:
The Seurat analysis pipeline (Butler et al., 2018; Hao et al., 2021; Stuart et al., 2019) was used to perform the downstream analysis of scRNA-seq data, such as QC, normalization, down sampling, clustering and differential gene expression analysis.
Assembly: GRCh38
Supplementary files format and content: Seurat object (rds) with gene by cell matrix used for cell type annotation and TCR clonotypes to define alloreactive clones used for downstream analyses

source_name: ileum

extract_protocol:
scRNA-seq was performed using the 10x Genomics (Pleasanton, CA) platform for simultaneous measurement of mRNA expression and paired V(D)J TCR α and β sequences at the single cell level.
For scRNA-seq analysis, intestinal T cells isolated from IEL and LPL were thawed, washed and sorted separately or combined for viable recipient HLA+CD45+CD3+ T cells using the BD Influx cell sorter. Cells were then mixed with 10x Chromium 5’ RT reagents and loaded into a Chromium microfluidics chip and controller for droplet formation, with each productive droplet containing one single cell and one single 10x barcoded primer bead. Full-length first strand cDNAs were synthesized in individual droplets from polyadenylated mRNAs and labeled with a unique 10x cell-bead barcode. For 5’ gene expression sequencing (5’GEX-seq), cDNAs were amplified and Illumina-compatible sequencing libraries were prepared and sequenced on an Illumina NovaSeq 6000 Sequencer.

value: ileum

value: ileum explant LPL (Recipient T)

value: FACS-sorted recipient HLA+ CD45+ CD3+ T cells


title: Subject 100271, P+3H

description: Column name in processed data file: 77


title: MJ008_GEX Pt4 iITx POD1606 ileum explant IEL (Recipient T)

value: ileum explant IEL (Recipient T)


title: Subject 100305, B+1D

description: Column name in processed data file: 76


title: NKT_18h Dex_Rep5

description:
Shir_NKT_Dex18h5
Bulk Mars-Seq (3' end-RNA-seq)

value: NKT

value: WT

value: Dexamethasone


title: NKT_3d Dex_Rep1

description:
Shir_NKT_Dex3d1
Bulk Mars-Seq (3' end-RNA-seq)


title: NKT_18h Dex_Rep3

description:
Shir_NKT_Dex18h3
Bulk Mars-Seq (3' end-RNA-seq)


title: Subject 100271, P+1D

description: Column name in processed data file: 75

value: Blood


title: scRNA-Seq_TCRb+_Tcells_PBS3

value: PBS


title: scRNA-Seq_TCRb+_Tcells_DTx1

value: DTx


title: CCR8pos_DTX_2

description: Tconv cells from Foxp3-EGFP-DTR tumor bearing animals treated with DTx

data_processing:
FastQ files underwent quality control with FastQC, adaptor trimming with Cutadapt and alignment to the NCBIM37 Mus musculus genome annotation. Count tables containing genic read counts were generated using HTSeq
Differential gene expression analysis was performed using DESeq2 and differentially expressed genes were futher analysed using R
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPM values

extract_protocol:
Single-cell suspensions were purified by total CD4+ T cell enrichment followed by FACS-sorting stored in 40 µl RNAlater™ Stabilization Solution at -80 °C Samples were processed using the QIAshredder Kit (Qiagen) according to the manufacturer’s protocol RNA was extracted from samples using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol
RNA Libraries were prepared using the Clontech Smarter low-input RNA-Seq library preparation kit according to manufacturer's instructions
Samples were individually barcoded following library preparation according to Clontech Smarter manufacturer instructions

value: Tumour-infiltrating T cells

value: Foxp3EGFP-ve Tconv cells


title: Subject 100305, B+3H

description: Column name in processed data file: 74

value: MVA-BN-Filo

value: Boost


title: MJ019_GEX Pt21 MVTx POD1145 ileum explant LPL (Recipient T)


title: CCR8pos_DTX_1


title: NKT_18h Dex_Rep1

description:
Shir_NKT_Dex18h1
Bulk Mars-Seq (3' end-RNA-seq)


title: NKT_18h Dex_Rep2

description:
Shir_NKT_Dex18h2
Bulk Mars-Seq (3' end-RNA-seq)


title: Tuft_Untreated_Rep5

description:
TEC_tuft_ut5
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_TEC_dex_tuft_umi_counts_20210505_175126.xlsx

extract_protocol:
Thymi were removed and enzymatically dissociated with Liberase TH and DNase. Tuft cells were sorted into lysis binding buffer and RNA was extracted using Dynabeads. MARSseq protocol was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using the MARSseq protocol (Jaitin et al. 2014).

treatment_protocol: Mice were injected I.P. with dexamethasone (200ug/10gr body weight) at various time points before sacrificed, or left untreated.

value: Tuft cells

value: Untreated


title: scRNA-Seq_TCRb+_Tcells_PBS1

value: T cells from tumors

value: TCR-b+ T cells


title: Tuft_Untreated_Rep4

description:
TEC_tuft_ut4
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_TEC_dex_tuft_umi_counts_20210505_175126.xlsx

value: Thymus

value: Male


title: NKT_18h Dex_Rep4

description:
Shir_NKT_Dex18h4
Bulk Mars-Seq (3' end-RNA-seq)


title: MJ017_GEX Pt16'' MVTx POD1004 ileum stoma LPL (Recipient T)

value: ileum

value: ileum stoma LPL (Recipient T)

value: FACS-sorted recipient HLA+ CD45+ CD3+ T cells


title: MJ018_GEX Pt21 MVTx POD1145 ileum explant IEL (Recipient T)

value: ileum explant IEL (Recipient T)


title: MJ016_GEX Pt16'' MVTx POD1004 ileum stoma IEL (Recipient T)

value: ileum stoma IEL (Recipient T)


title: MJ006_GEX Pt21 MVTx POD626 ileum stoma IEL + LPL (Recipient T)

value: ileum stoma IEL + LPL (Recipient T)


title: MJ005_GEX Pt14 iITx POD1764 ileum explant IEL + LPL (Recipient T)

value: ileum explant IEL + LPL (Recipient T)


title: CCR8neg_DTX_2

value: Tumour-infiltrating T cells

value: DTx


title: CCR8neg_DTX_1

value: Foxp3EGFP-ve Tconv cells


title: MJ003_GEX Pt13 iITx POD1032 ileum stoma LPL (Recipient T)


title: scRNA-Seq_TCRb+_Tcells_PBS2

value: PBS


title: Tuft_Untreated_Rep3

description:
TEC_tuft_ut3
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_TEC_dex_tuft_umi_counts_20210505_175126.xlsx

value: Tuft cells

value: WT


title: CCR8pos_DTX_4


title: Tuft_Untreated_Rep2

description:
TEC_tuft_ut2
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_TEC_dex_tuft_umi_counts_20210505_175126.xlsx

value: Untreated


title: Tuft_Untreated_Rep1

description:
TEC_tuft_ut1
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_TEC_dex_tuft_umi_counts_20210505_175126.xlsx


title: MJ001_GEX Pt15 MVTx POD1194 ileum Bx IEL + LPL (Recipient T)

value: ileum Bx IEL + LPL (Recipient T)


title: CCR8neg_DTX_4


title: CCR8pos_DTX_3


title: Tuft_3d Dex_Rep5

description:
TEC_tuft_3d5
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_TEC_dex_tuft_umi_counts_20210505_175126.xlsx

value: Thymus

value: Dexamethasone


title: CCR8neg_DTX_3


title: MJ007_GEX D251 ileum IEL + LPL

value: ileum

value: ileum IEL + LPL


title: Tuft_3d Dex_Rep4

description:
TEC_tuft_3d4
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_TEC_dex_tuft_umi_counts_20210505_175126.xlsx

value: Male


title: Tuft_3d Dex_Rep3

description:
TEC_tuft_3d3
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_TEC_dex_tuft_umi_counts_20210505_175126.xlsx


title: Sox2cKO YFP+ cells

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the STARSolo 2.7.9a and downstream analysis performed using Seurat v4
Assembly: mm39
Supplementary files format and content: h5 file

source_name: Lung

extract_protocol:
Target cells were FACS sorted and were loaded onto the 10x Chromium (10X Genomics) aiming for 10,000 cells per sample.
Libraries were prepared according to the manufacturer’s protocol using Chromium Single Cell 3’ v2 chemistry.

value: Epithelial cells

value: Sox2CreERT2/Flox; R26REYFP

value: Lung

value: mixed CD1 and C57BL/6

value: 8 week-old


title: Control YFP+ cells

description: 10x Genomics

value: Sox2CreERT2/WT; R26REYFP


title: siYTHDF1+Sorafenib3

city: Guangzhou

first: Xinyue

last: Zhang

state: guangdong

address: zhongshan road 2

institute: Sun Yat-sen University First Affiliated Hospital

description: tumor tissue-RNA-seq

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp(version 0.18.0).
Assembly: GRCh38
Supplementary files format and content: Supplementary_files_format_and content_processed_data.xls

source_name: Liver cancer

growth_protocol: MHCC97H cells were matained in 10%FBS DMEM

extract_protocol:
Total RNAs were isolated using Trizol RNA extraction reagent (Ambion).
The enriched mRNAs and ncRNAs were fragmented into short fragments by using fragmentation buffer and reverse transcribed into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP (dUTP instead of dTTP) and buffer. Next, the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters.

treatment_protocol: the orthotopic xenograft implantation HCC model was developed through MHCC97H cells. Three weeks after inoculation, Mice were treated by combined LNP-siYTHDF1 (every 3 days for 4 times) with sorafenib (12.5 mg/kg)

value: Liver cancer

tag: cell line

value: Human liver cancer cells


title: siYTHDF1+Sorafenib2

description: tumor tissue-RNA-seq


title: siYTHDF1+Sorafenib1

description: tumor tissue-RNA-seq


title: BKV_890

city: Cologne

first: Giuliano

last: Crispatzu

address: Joseph-Stelzmann-Straße 26

department: CECAD

country: Germany

institute: University of Cologne (UoC), Germany

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics), trimmed with cutadapt and read statistics were obtained with Samtools.
Reads were mapped to the murine reference assembly (mm10) using kallisto.
Read count means, fold-change (FC) and p-values were calculated with sleuth.
Gene expression for the individual samples was calculated as TPMs.
Assembly: GRCm38

source_name: dTomato FAC-sorted podocytes from C57BL/6 (MyD88flox x ) PodCre mice.

growth_protocol: MyD88flox mice were a kind gift by Manolis Pasparakis (Vlantis, Gut, 2016). They were mated with our recently published Podocin.2a.iCre.2a.mT (PodCre) mouse 14, which combines podocyte-specific Cre-Expression with expression of the fluorophore mTomato, which facilitates the identification and sorting of podocytes for expression studies. All mice were kept on a C57BL/6 background and housed under specific pathogen-free conditions. Animal experiments were performed according to national and institutional animal care and ethical guidelines, and they were approved by the LANUV NRW.

extract_protocol:
Organs were harvested at the indicated time points after cardial perfusion with PBS. For fluorescent activated cell sorting (FACS), MyD88pko mice and PodCre/wt x MyD88wt/wt controls were used.
Due to low amount of input material, pre-amplification using the Ovation RNASeq System V2 was performed. Total RNA was used for first strand cDNA synthesis, using both poly(T) and random primers, followed by second strand synthesis and isothermal strand-displacement amplification. For library preparation, the Illumina Nextera XT DNA sample preparation protocol was used, with 1 ng cDNA input. After validation (Agilent 2200 TapeStation) and quantification (Invitrogen Qubit System) all six transcriptome libraries were pooled. The pool was quantified using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT system.

treatment_protocol: Groups of PodCre/wt x MyD88flox/flox mice (referred to as MyD88pko) and Podwt/wt x MyD88flox/flox littermate controls (referred to as WT) were analyzed between the ages of 8-52 weeks. NTN was induced in 8 to 16 week old male MyD88pko and WT controls by tail vein injection of 9µl per gram body weight of nephrotoxic sheep serum (Probetex) on two consecutive days.

value: podocytes

tag: disease state

value: nephrotoxic nephritis


title: MJ002_GEX Pt13 iITx POD1032 ileum stoma IEL (Recipient T)

tag: tissue

value: ileum stoma IEL (Recipient T)

value: FACS-sorted recipient HLA+ CD45+ CD3+ T cells


title: Subject 100244, B+7D

city: CRETEIL

first: Cecile

last: LEFEBVRE

address: 51 Avenue du Maréchal de Lattre de Tassigny, Bât R+1 Eq16 U955

institute: INSERM

description: Column name in processed data file: 67

value: Blood

tag: treatment

value: MVA-BN-Filo

value: Boost


title: Subject 100244, P+1D

description: Column name in processed data file: 63

value: Prime


title: Subject 100244, P+7D

description: Column name in processed data file: 65


title: Subject 100271, P+57D

description: Column name in processed data file: 71


title: Sorafenib3

description: tumor tissue-RNA-seq

treatment_protocol: the orthotopic xenograft implantation HCC model was developed through MHCC97H cells. Three weeks after inoculation, Mice were treated by sorafenib (12.5 mg/kg/everyday for 12 days)

value: Sorafenib


title: Subject 100305, P+29D

description: Column name in processed data file: 72


title: Subject 100305, D0

description: Column name in processed data file: 68

value: Control


title: Subject 100271, B+3H

description: Column name in processed data file: 73


title: Subject 100262, B+1D

description: Column name in processed data file: 64


title: Subject 100305, P+3H

description: Column name in processed data file: 66


title: Subject 100271, B+1D

description: Column name in processed data file: 69


title: Subject 100305, P+7D

description: Column name in processed data file: 70


title: Tuft_3d Dex_Rep2

description:
TEC_tuft_3d2
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_TEC_dex_tuft_umi_counts_20210505_175126.xlsx

source_name: Thymus

value: Thymus

value: Tuft cells

value: WT

value: Male

value: Dexamethasone

tag: time


title: Tuft_3d Dex_Rep1

description:
TEC_tuft_3d1
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_TEC_dex_tuft_umi_counts_20210505_175126.xlsx

tag: cell type


title: Sorafenib2

description: tumor tissue-RNA-seq

value: Liver cancer


title: Subject 100262, B+7D

description: Column name in processed data file: 62


title: Subject 100244, D0

description: Column name in processed data file: 61


title: BKV_884

tag: strain


title: Sorafenib1

description: tumor tissue-RNA-seq

value: Human liver cancer cells


title: BKV_889

value: podocytes


title: Tuft_18h Dex_Rep3

description:
TEC_tuft_18h4
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_TEC_dex_tuft_umi_counts_20210505_175126.xlsx


title: Tuft_18h Dex_Rep2

description:
TEC_tuft_18h2
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_TEC_dex_tuft_umi_counts_20210505_175126.xlsx


title: AOL_1265

value: nephrotoxic nephritis


title: siYTHDF1+Lenvatinib3

description: tumor tissue-RNA-seq

treatment_protocol: the orthotopic xenograft implantation HCC model was developed through MHCC97H cells. Three weeks after inoculation, Mice were treated by combined LNP-siYTHDF1 (every 3 days for 4 times) with lenvatinib (10 mg/kg/ everyday for 12 days)


title: Tuft_18h Dex_Rep1

description:
TEC_tuft_18h1
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_TEC_dex_tuft_umi_counts_20210505_175126.xlsx


title: AOL_1231


title: Subject 100244, P+3H

description: Column name in processed data file: 59

tag: subject


title: Il13ra1WT_tuft cells_6d Dex_Rep4

description:
il13_tuft_6d_wt4
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL13ra1_tuft6d_umi_counts_20230303_014125.xlsx

value: Il13ra1 WT


title: siYTHDF1+Lenvatinib2

description: tumor tissue-RNA-seq


title: Il13ra1WT_tuft cells_6d Dex_Rep3

description:
il13_tuft_6d_wt3
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL13ra1_tuft6d_umi_counts_20230303_014125.xlsx


title: Il13ra1WT_tuft cells_6d Dex_Rep2

description:
il13_tuft_6d_wt25
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL13ra1_tuft6d_umi_counts_20230303_014125.xlsx


title: Lenvatinib3

description: tumor tissue-RNA-seq

treatment_protocol: the orthotopic xenograft implantation HCC model was developed through MHCC97H cells. Three weeks after inoculation, Mice were treated by lenvatinib (10 mg/kg/ everyday for 14 days)

value: Lenvatinib


title: Subject 100262, B+3H

description: Column name in processed data file: 58

value: Blood

tag: group


title: Il13ra1KO_tuft cells_6d Dex_Rep4

description:
il13_tuft_6d_ko4
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL13ra1_tuft6d_umi_counts_20230303_014125.xlsx

value: Il13ra1 KO


title: siYTHDF1+Lenvatinib1

description: tumor tissue-RNA-seq


title: Il13ra1WT_tuft cells_6d Dex_Rep1

description:
il13_tuft_6d_wt1
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL13ra1_tuft6d_umi_counts_20230303_014125.xlsx


title: BKV_733

value: healthy


title: Lenvatinib2

description: tumor tissue-RNA-seq

treatment_protocol: the orthotopic xenograft implantation HCC model was developed through MHCC97H cells. Three weeks after inoculation, Mice were treated by lenvatinib (10 mg/kg/ everyday for 13 days)


title: Il13ra1KO_tuft cells_6d Dex_Rep3

description:
il13_tuft_6d_ko3
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL13ra1_tuft6d_umi_counts_20230303_014125.xlsx


title: Lenvatinib1

description: tumor tissue-RNA-seq

treatment_protocol: the orthotopic xenograft implantation HCC model was developed through MHCC97H cells. Three weeks after inoculation, Mice were treated by lenvatinib (10 mg/kg/ everyday for 12 days)


title: Subject 100244, B+3H

description: Column name in processed data file: 55

value: MVA-BN-Filo

value: Boost


title: AOL_1086


title: AOL_1225


title: AOL_1082


title: Subject 100262, P+3H

description: Column name in processed data file: 60

value: Prime


title: ribo-YTHDF1-sh2

description: Ribo-seq TE


title: AOL_1081


title: ribo-shNC

description: Ribo-seq TE

value: shNC


title: Il13ra1KO_tuft cells_6d Dex_Rep2

description:
il13_tuft_6d_ko2
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL13ra1_tuft6d_umi_counts_20230303_014125.xlsx

value: Thymus

value: Tuft cells


title: Subject 100339, B+3H

description: Column name in processed data file: 52


title: YTHDF1-sh2-2

description: RNA-seq


title: YAP5SA-AAV mouse heart CD45-enriched scRNA-seq

description:
10X 3' scRNA-seq profiling immune cells in YAP5SA AAV injected heart
scRNA_integrated.meta_data.csv.gz
scRNA_integrated.normalized_count.csv.gz
scRNA_integrated.raw_count.csv.gz

data_processing:
Visium Spatial RNA-seq: H&E images were manually aligned to spots selected by Loupe Browser 4.0.0 (10X Genomics). The Space Ranger 1.0.0 pipeline (10X Genomics) was then used to generate feature-spot matrices from the sequencing data aligned to the mm10 mouse reference genome.
Visium Spatial RNA-seq: Sequencing data and images were aligned by using the Space Ranger 1.0.0 pipeline to derive a feature spot-barcode expression matrix (10X Genomics). Seurat toolkit version v.4.0 in R v.3.8 was used to perform downstream analyses. Spots were filtered for UMI counts (5000 < UMI counts < 30,000), genes (no genes > 500) and mitochondrial genes (mitochondrial % < 40%). The UMI count matrices of cells that passed previous filtering were normalized by using the Seurat function SCTransform.
Visium Spatial RNA-seq: Atrial spots were identified based on the H&E images and were manulally removed from the expression matrices before subsequent analyses
Assembly: mm10
Supplementary files format and content: Visium Spatial RNA-seq: H&E image, comma-separated metadata files and matrix files
scRNA-seq: After sequencing, preprocessing steps were performed by using CellRanger 3.0.1, without including intronic reads. Matrices were postprocessed with CellBender v0.1.
scRNA-seq: Single nuclei were filtered for unique molecular identifier (UMI) counts (500 < UMI Counts < 25,000), genes (no genes > 500), mitochondrial genes (mitochondrial % < 5%), and scrublet score (doublet score < 0.25). Seurat Toolkit version v.4.0 4 in R v.3.8 was used to perform downstream analyses. The UMI count matrices of cells that passed previous filtering were normalized by using the Seurat function SCTransform.
Supplementary files format and content: scRNA-seq: comma-separated metadata files and matrix files

extract_protocol:
Visium Spatial RNA-seq: Frozen tissue sections from control (MCM) and Yap5SA (MCM Yap5SA) hearts were mounted on 10X Visium slide capture areas, each with 5000 barcoded RNA capture spots. Hematoxylin and eosin (H&E)-stained images of whole tissue sections were obtained by using the BioTek Cytation 5 with image stitching. Optimal permeabilization time for the release of mRNA from 10-μm thick tissue sections for both genotypes was 12 minutes, determined by using the Visium Tissue Optimization Kit.
Visium Spatial RNA-seq: Spatially barcoded cDNA libraries were generated from mRNA released from each tissue section by using the Visium Spatial Gene Expression Reagent Kit, before being sequenced on an Illumina NovaSeq 6000 with 150 cycle paired-end setting (read 1 = 28 cycles, read 2 = 90 cycles, index 1 = 10 cycles, index 2 = 10 cycles).
scRNA-seq: Control (n=3) and YAP5SA (n=3) mouse hearts were explanted and perfused with cold PBS (20 mM KCl). The hearts were then minced with a razor blade and digested using 30 ml of HBSS with type II collagenase (100 U/ul, Worthington LS004177) at 37 degrees C for 30 minutes. The samples were then filtered through 40 um strainers and centrifuged at 500g for 10 minutes. Red blood cells in the pellet were lysed by ACK lysing buffer (Thermo Fisher, A1049201). The samples were suspended in 1% BSA/PBS, with dead cells removed by using a dead cell removal kit (Miltenyi Biotec, 130-052-301).
scRNA-seq: Samples were diluted to obtain 15,000 – 18,000 live cells for single cell library construction according to the 10x single cell gene expression workflow (10x Genomics, Chromium Next GEM Single Cell 3’ Kit v3.1, 1000269). The libraries were sequenced on an Illumina NovaSeq 6000 instrument.

treatment_protocol: Visium Spatial RNA-seq: TAM injection 40 ug/g weight daily for 4 days

value: Heart

value: Cardiac immune cells

value: 8-10 weeks old adult

tag: strain background

value: WT


title: BKV_729

value: podocytes


title: Subject 100244, P+57D

description: Column name in processed data file: 57


title: Il13ra1KO_tuft cells_6d Dex_Rep1

description:
il13_tuft_6d_ko15
Bulk Mars-Seq (3' end-RNA-seq)
DESeq2_IL13ra1_tuft6d_umi_counts_20230303_014125.xlsx

tag: Sex

value: Male

value: Dexamethasone


title: Subject 100262, P+7D

description: Column name in processed data file: 56


title: Subject 100262, P+1D

description: Column name in processed data file: 53


title: Subject 100339, B+7D

description: Column name in processed data file: 54


title: Subject 100339, B+1D

description: Column name in processed data file: 50


title: Subject 100257, P+29D

description: Column name in processed data file: 51