title: FB87_patB17_tumor_pre_NR

value: SR


title: FB82_patB25_tumor_pre_LR

status: Public on Jan 21 2026

type: RNA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Agilent miRNA hybridization protocol

scan_protocol: Standard Agilent scanning protocol

data_processing: The data were processed and normalised using the Bioconductor limma implementation in R

molecule: total RNA

organism: Homo sapiens

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Agilent MicroRNA Expression Profiling Assay Guide).

extract_protocol: RNA was extracted with FFPE miRNeasy kit in accordance with manufacture's protocol (QIAGEN).

tag: sample type

value: tumor

tag: sample class

value: PRE

tag: patient class

value: LR

tag: sample body site

value: C/SC

tag: drug

value: BRAFi


title: FB83_patB31_tumor_pre_LR


title: B1_HLA-A2_CAR_unstim

type: SRA

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

country: Germany

institute: Leibniz Institute for Immunotherapy

description:
p138_counts.tsv
HLA2_CAR_RPKM.xlsx
HLA2_CAR_dds.rds

library_source: transcriptomic

data_processing:
Demultiplexing was performed with bcl2fastq v2.20.0.422 (NextSeq550), Dragon bclconvert version 3.8.4 (NextSeq200)
Quality control and read mapping to the mouse reference genome (GRCm38, gencode,release23) was performed using an adapted version of the SnakePipes version 2.5.1
Inside the snakePipes Pipeline mapping was performed using STAR  with default values and gene counts were created by featrureCounts.
Quality control of the count matrix and DE-Gene calling was performed with DESeq2. Gene counts were imported and prefiltered with edgeR:filterByExpr and the fdr was set to 0.05. GO-Analysis was performed with genes UP-regulated with a log2FC>1 and fdr<0.05 using goseq. GESA analysis was performed using fgsea. Plots were created with ggplot2 and EnhancedVolcano
Assembly: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/GRCh38.primary_assembly.genome.fa.gz
Assembly: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.primary_assembly.annotation.gtf.gz
Supplementary files format and content: rds files: R version 4.1.1,DESeq2_1.34.0, contains the respective DESeq2DataSet object.

organism: Mus musculus

source_name: isolated spleen, then expanded and transduced

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Micro Kit and RNA was eluted in 14 µL RNAse-free water. RNA quality was assessed using the Tapestation system 4200 and High-Sensitivity RNA screentape (Agilent).
7 µl of the RNA was used for generating RNA-seq libraries using the SMART-seq Stranded Kit from Takara.
Indexed libraries were pooled in an equimolar ratio and sequenced on an Illumina NextSeq 550 machine with NextSeq 500/550 High Output Kit v2.5 (75 cycles) or NextSeq2000

tag: tissue

tag: cell line

value: primary cell

tag: cell type

value: regulatory T-cell

tag: sorting

value: sorted on CD4+CD25+CD90.1+


title: KT-47 resistance2_1

type: genomic

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hospital

description: genomic DNA from KT-47R2 chemotherapy resistant Wilms tumor patient-derived xenograft

hyb_protocol: Genomic DNA from each KT-47 WTPDX phenotype/timepoint were bisulfite converted using the EZ DNA Methylation kit (Zymo Research). Converted samples were processed and hybridized to the Infinium Methylation EPIC Bead-Chip (v1) system

scan_protocol: Unprocessed IDAT files containing summarized information from the beadchip array were processed using the subset-quantile within array normalization (SWAN) function as previously described.

data_processing: The methylation score of each CpG site in the array is represented as a beta (β) value (methylated signal/methylated +unmethylated signals) and was computed using the R package minifi.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: kidney tumor

label_protocol: Standard Illumina protocol

growth_protocol: KT-47 was heterotopically engrafted into the flanks of C.B-17 scid (C.B-Igh-1b/IcrTac-Prkdcscid) mice (6–8 weeks old; Taconic Farms, Hudson, NY, USA) without cell culture intermediates.

extract_protocol: Genomic DNA extraction from snap frozen samples of WTPDX tumors at each of the chemotherapy resistance phenotypes / timepoints (Pre-treatment, Pre-resistance, Resistance 1, Resistance 2) was performed using the Qiagen DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) and confirmed using the Thermo Scientific NanoDrop™ One Microvolume UV-Vis Spectrophotometer (Thermo Fisher Scientific, Waltham, Massachusetts).

treatment_protocol: Tumor-bearing mice were treated with actinomycin-D (0.30 mg/kg intraperitoneal q21 days x 3; Baxter Oncology, Lebanon, NJ), vincristine (1 mg/kg intraperitoneal q7 days x 8; Hospira, Lake Forest, IL), and doxorubicin (4 mg/kg IV q7 days x 8; Pfizer, New York, NY, USA). Three timepoints were selected as experimental groups during this treatment schema for further inquiry: pre-treatment (no VAD chemotherapy exposure in WTPDX model), pre-resistance (VAD chemotherapy exposure without evidence of complete chemoresistance), and resistance (VAD chemotherapy exposure with complete chemotherapy resistance documented). The resistance timepoint was separated into resistance clone 1 and resistance clone 2 (KT-47R1, KT-47R2) which were originally derived from two different mice.

value: kidney tumor

value: Wilms tumor patient-derived xenograft

tag: treatment

value: VAD


title: EY99_patB31_tumor_pre_LR

value: LN


title: Knockdown-KO-Young-F2_S61_L004

city: New York

first: Guilherme Henrique

last: Souza Bomfim

state: NY

address: 1 Washington Square Village 2R

department: Department of Molecular Pathobiology

institute: New York University (NYU)

description:
Library name: Sample 12
Collumn name in raw_counts_all_samples: Knockdown-KO-Young-F2_S61_L004
02_GHS002 DEG KO Young vs WT Aged.xlsx

data_processing:
Raw paired-end FASTQ files were transferred to the NYU Greene High Performance Computing (HPC) cluster. Adapter sequences and low-quality bases were removed using Fastp (v0.24.0). The cleaned reads were aligned to the mouse reference genome (GRCm39, Ensembl release v113) using STAR (v2.7.11b) to generate BAM files. Gene-level read counts were obtained using featureCounts from the Subread package (v2.0.8). Quality control reports from all steps were aggregated with MultiQC (v1.25.1). Raw counts from all samples were merged into a count matrix. Ensembl gene identifiers were mapped to Entrez Gene IDs, and only genes with valid Entrez IDs were retained. A DESeq2 dataset (DESeq2 v1.42.1) was then constructed from these counts. Genes were further filtered to retain those with at least 10 counts in at least 90% of samples.
Assembly: The cleaned reads were aligned to the mouse reference genome (GRCm39, Ensembl release v113) using STAR (v2.7.11b)
Supplementary files format and content: Tab-delimited text file (csv/xlsx) include normalized values were scaled to convert to z-scores at p< 0.05 with log2FC ˃1. significance at adjusted P < 0.05

source_name: Aorta

extract_protocol:
RNA from cleaned aortic tissues was isolated using RNeasy Mini Kit (Qiagen cat #217004), as indicated by the manufacturer. RNA quality and RNA sequencing (RNA-seq) were conducted at NYU Langone's Genome Technology Center (RRID: SCR_017929). Aortic tissue from 2 different mice (~20mg) were combined, totalizing 5 samples (n=5).
All samples were processed in the same time period, following the same protocol in order to limit the batch effects. Next, the RNASeq enrichment libraries were prepared using the low-input RNA sequencing, TruSeq Stranded RNA Library Prep Gold.

value: Aorta

tag: genotype

value: Knockdown-KO

tag: developmental stage

value: Young

tag: Sex

value: Female


title: PTR cells, shKdm4a-#4, replicate 2

city: Houston

first: Guocan

last: Wang

state: TX

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

data_processing:
RNA fastqs were aligned to the mus musculus (version mm10 from Genome Reference Consortium GRCm38) using STAR (2.6.0b) (Dobin et al., 2013), raw counts are obtained using HTSeq (Anders et. al. 2014) (python/3.6/anaconda3/bin/htseq-count, with options -m union -a 10 -s no) ( rsem-calculate-expression (1.2.3) with options --bowtie2 (2.2.3) against reference mm10.refgenes were run separated for to obtain TPM ((transcripts per million reads)) ).
Assembly: mm10
Supplementary files format and content: HTSeq Rawcounts

source_name: PTR

growth_protocol: PTR cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared according to Roche KAPA Stranded RNA-Seq Library Prep Kit (Illumina). Briefly, polyA+ mRNAs were enriched by oligo (dT) magnetic beads from the total RNA samples; RNA-seq library preparation using KAPA Stranded RNA-Seq Library Prep Kit (Illumina), which incorporates dUTP into the second cDNA strand and renders the RNA-seq library strand-specific; The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute quantification qPCR method; The barcoded libraries were mixed, denatured to single strands in NaOH, captured on Illumina flow cell, amplified in situ, and sequenced for 150 cycles for paired-ends on an Illumina llumina NextSeq550 system.

value: PTR

value: prostate cancer cells

value: Pb-Cre+,Pten f/f, Trp53 f/f, Rb1 f/f_shKdm4a-#4


title: A3_CD40_AIR_unstim

description:
p138_counts.tsv
CD40L_CAR_RPKM.xlsx
CD40L_CAR_dds.rds

value: isolated spleen, then expanded and transduced


title: Wild-type-Aged-A2-F3_S57_L004

description:
Library name: Sample 8
Collumn name in raw_counts_all_samples: Wild-type-Aged-A2-F3_S57_L004
01_GHS002 DEG WT Young vs WT Aged.xlsx

value: Wild-type

value: Aged


title: dleo1-2

city: Chuncheon-si

first: Shinae

last: Park

address: Kangwondaehak-gil

country: South Korea

institute: Kangwon National University

description: Library name: 4_RNA-seq leo1Δ_rep2

data_processing:
The Illumina Hiseq generates raw images utilizing HCS(HiSeq Control Software v2.2) for system control
Base calling through an integrated primary analysis software called RTA(Real Time Analysis. v1.18)
The BCL(base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq(v1.8.4)
Adapters are not trimmed away from the reads.
bedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: Saccharomyces cerevisiae S288C genome assembly R64 (sacCer3)
Supplementary files format and content: bigwig

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: total cells

growth_protocol: Yeast cells are cultured at 10ml YPD(1% Yeast extract, 2% Peptone, 2% Glucose) in 100ml flask (30℃, 230rpm) and harvested at OD600=1.0

extract_protocol:
RNA was harvested according to the MN RNA-isolation kit(MN;#7409555.50) standard protocols. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina(NEB #E7420S) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: total cells

tag: strain

value: yeast cell

value: LEO1 knockout


title: KT-47 resistance1_3

description: genomic DNA from KT-47R1 chemotherapy resistant Wilms tumor patient-derived xenograft

value: kidney tumor


title: Wild-type-Aged-A2-F5_S59_L004

description:
Library name: Sample 10
Collumn name in raw_counts_all_samples: Wild-type-Aged-A2-F5_S59_L004
01_GHS002 DEG WT Young vs WT Aged.xlsx


title: PTR cells, shKdm4a-#4, replicate 3


title: Wild-type-Aged-A2-F4_S58_L004

description:
Library name: Sample 9
Collumn name in raw_counts_all_samples: Wild-type-Aged-A2-F4_S58_L004
01_GHS002 DEG WT Young vs WT Aged.xlsx


title: KT-47 resistance1_1

value: Wilms tumor patient-derived xenograft


title: Wild-type-Aged-A2-F2_S56_L004

description:
Library name: Sample 7
Collumn name in raw_counts_all_samples: Wild-type-Aged-A2-F2_S56_L004
01_GHS002 DEG WT Young vs WT Aged.xlsx


title: KT-47 resistance1_4

value: VAD


title: KT-47 preresistance_2

description: genomic DNA from KT-47 pre-resistance  Wilms tumor patient-derived xenograft


title: EY98_patB02_tumor_pre_LR

value: tumor

value: PRE

value: LR

value: LN

value: BRAFi


title: Wild-type-Aged-A2-F1_S55_L004

description:
Library name: Sample 6
Collumn name in raw_counts_all_samples: Wild-type-Aged-A2-F1_S55_L004
01_GHS002 DEG WT Young vs WT Aged.xlsx

value: Aorta

value: Female


title: KT-47 preresistance_4


title: KT-47 preresistance_1


title: PTR cells, shControl, replicate 1

value: PTR

value: prostate cancer cells

value: Pb-Cre+,Pten f/f, Trp53 f/f, Rb1 f/f_sh202


title: KT-47 resistance1_2


title: Wild-type-Young-F5_S54_L004

description:
Library name: Sample 5
Collumn name in raw_counts_all_samples: Wild-type-Young-F5_S54_L004
01_GHS002 DEG WT Young vs WT Aged.xlsx

value: Wild-type

value: Young


title: PTR cells, shControl, replicate 3


title: EY97_patB06_tumor_pre_LR

value: C/SC


title: EY92_patB16_tumor_post_LR

value: POST

value: V


title: KT-47 preresistance_3

value: kidney tumor

value: Wilms tumor patient-derived xenograft


title: PTR cells, shKdm4a-#4, replicate 1

value: Pb-Cre+,Pten f/f, Trp53 f/f, Rb1 f/f_shKdm4a-#4


title: PTR cells, shControl, replicate 2


title: KT-47 pretreatment_4

description: genomic DNA from KT-47PT chemotherapy sensitive Wilms tumor patient-derived xenograft


title: Wild-type-Young-F1_S50_L004

description:
Library name: Sample 1
Collumn name in raw_counts_all_samples: Wild-type-Young-F1_S50_L004
01_GHS002 DEG WT Young vs WT Aged.xlsx


title: Wild-type-Young-F4_S53_L004

description:
Library name: Sample 4
Collumn name in raw_counts_all_samples: Wild-type-Young-F4_S53_L004
01_GHS002 DEG WT Young vs WT Aged.xlsx


title: cDC1s from  B16-OVA at day 21 #3

first: Hongbo

last: Chi

department: Immunology

description: Library name: cDC1_d21_S3

library_source: genomic

data_processing:
Adapter sequences were removed using cutadapt v.1.9
and aligned them to the mouse genome mm10 (GRCm38_68 from Sanger; ftp://ftp-mouse.sanger.ac.uk/ref/GRCm38_68.fa) using the Burrows–Wheeler algorithm32 (version 0.5.9-r26-dev, default parameter)
duplicated reads were then marked with Picard (version 1.65 (1160)) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2 (version 2.1.0.20150603, default parameters with ‘–extsize 200 –nomodel’, merged by bedtools if within 100 bp) for individual samples
Assembly: mm10
Supplementary files format and content: Consensus peaks and fragment counts for all samples

source_name: Tumor

growth_protocol: Intratumoral cDC1s  were sort purified from B16-OVA tumors

extract_protocol:
Cells were lysed in 50 μl ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10 min. Resulting nuclei were pelleted at 500g for 10 min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50 μl transposase reaction mix (25 μl 2 × TD buffer, 22.5 μl nuclease-free water, 2.5 μl transposase) and incubated for 30 min at 37 °C. After the reaction, the DNA was cleaned up using the Qiagen MinElute kit
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles

value: Tumor

value: Intratumoral cDC1s purified from the B16-OVA tumors at 21 days after tumor inoculation

value: Intratumoral cDC1s

value: Wild type


title: cDC1s from  B16-OVA at day 21 #4

description: Library name: cDC1_d21_S4


title: EY90_patB16_tumor_pre_LR

value: tumor

value: PRE

value: LR

value: BRAFi


title: YFP+ oviductal stromal cells sorted from Pdgfra-Cre;Esr1(fl/fl);R26Y experimental female mouse 3

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

description: Library name: Pdgfra_Esr1_R26Y_3

data_processing:
Visualization Pipeline for RNAseq (Viper) analysis tool developed by Center for Functional Cancer Epigenetics (CFCE) at Dana-Farber Cancer Institute was used to generate standard outputs.
Assembly: mm10
Supplementary files format and content: Tab-delimited csv file include normalized TPM matrices for each sample

source_name: Fallopian tube

extract_protocol:
YFP+ fallopian tube stromal cells were sorted from young adult female mice with the corresponding genotypes, and total RNA was prepared from the sorted cells using Zymo RNA extraction kit.
RNA libraries were prepared for sequencing using Low Input mRNA Library (Takara SMARTer) v4 kit

value: Fallopian tube

value: Sorted YFP+ fallopian tube stromal cells


title: EY95_patB16_tumor_pre_LR


title: KT-47 pretreatment_3


title: Wild-type-Young-F2_S51_L004

description:
Library name: Sample 2
Collumn name in raw_counts_all_samples: Wild-type-Young-F2_S51_L004
01_GHS002 DEG WT Young vs WT Aged.xlsx

value: Aorta

value: Wild-type

value: Young

value: Female


title: EY91_patB31_normal_pre_LR

value: normal

value: LN


title: cDC1s from  B16-OVA at day 21 #1

description: Library name: cDC1_d21_S1


title: EY94_patB31_tumor_pre_LR


title: KT-47 pretreatment_2

value: kidney tumor

value: Wilms tumor patient-derived xenograft


title: EY87_patB25_normal_pre_LR


title: Wild-type-Young-F3_S52_L004

description:
Library name: Sample 3
Collumn name in raw_counts_all_samples: Wild-type-Young-F3_S52_L004
01_GHS002 DEG WT Young vs WT Aged.xlsx


title: YFP+ oviductal stromal cells sorted from Pdgfra-Cre;Esr1(fl/fl);R26Y experimental female mouse 1

description: Library name: Pdgfra_Esr1_R26Y_1


title: KT-47 pretreatment_1


title: YFP+ oviductal stromal cells sorted from Pdgfra-Cre;Esr1(fl/fl);R26Y experimental female mouse 2

description: Library name: Pdgfra_Esr1_R26Y_2


title: sputum_visit 2 [C1P98AC-v2]

city: Montpellier

first: Albertina

last: DE SARIO

address: 641, av du doyen Gaston Giraud

department: PhyMedExp

country: France

institute: INSERM 1046-CNRS 9214-Univ Montpellier

description: genomic DNA from sputum

hyb_protocol: One microgram of genomic DNA was bisulfite converted with the EpiTect® Fast 96 DNA Bisulfite Kit (Qiagen) according to the manufacturer’s instructions. Genome-wide DNA methylation was analysed on 850000 CpGs with the Infinium Human MethylationEPIC Kit (Illumina) according to the manufacturer’s instructions.

scan_protocol: The arrays were scanned on an Illumina iScan platform

data_processing:
Bioconductor champ 2.14 R package
Normalized (BMIQ) Average Beta

label: Cy5 and Cy3

source_name: sputum

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from sputum samples using the QIAamp DNA Mini kit (#51304, Qiagen) and a protocol we detailed in Pineau et al. 2021 (PMID: 33808877).

value: sputum

tag: disease

value: cystic fibrosis

tag: visit


title: cDC1s from  B16-OVA at day 21 #2

description: Library name: cDC1_d21_S2

value: Tumor

value: Intratumoral cDC1s purified from the B16-OVA tumors at 21 days after tumor inoculation

value: Intratumoral cDC1s

value: Wild type


title: EY84_patB19_tumor_pre_NR

value: tumor

value: PRE

value: SR

value: BRAFi


title: sputum_visit 1 [C1P98AC-v1]

description: genomic DNA from sputum


title: sputum_visit 2 [C1P99CT-v2]

description: genomic DNA from sputum


title: cDC1s from  B16-OVA at day 7 #3

description: Library name: cDC1_d7_S3

value: Intratumoral cDC1s purified from the B16-OVA tumors at 7 days after tumor inoculation


title: YFP+ oviductal stromal cells sorted from Pdgfra-Cre;R26Y control female mouse 3

description: Library name: Pdgfra_R26Y_3

value: Fallopian tube

value: Sorted YFP+ fallopian tube stromal cells

value: Pdgfra-Cre;R26Y wild-type


title: YFP+ oviductal stromal cells sorted from Pdgfra-Cre;R26Y control female mouse 2

description: Library name: Pdgfra_R26Y_2


title: cDC1s from  B16-OVA at day 7 #4

description: Library name: cDC1_d7_S4


title: EY88_patB27_normal_pre_LR

value: normal

value: LR

value: C/SC


title: EY79_patB16_tumor_pre_LR


title: cDC1s from  B16-OVA at day 7 #2

description: Library name: cDC1_d7_S2


title: EY78_patB16_tumor_pre_LR


title: cDC1s from  B16-OVA at day 7 #1

description: Library name: cDC1_d7_S1


title: EY82_patB06_tumor_pre_LR

value: LN


title: sputum_visit 2 [C1P96DE-v2]

description: genomic DNA from sputum

value: sputum

value: Female

value: cystic fibrosis


title: sputum_visit 2 [C1P95GC-v2]

description: genomic DNA from sputum


title: sputum_visit 1 [C1P97MG-v1]

description: genomic DNA from sputum

value: Male


title: sputum_visit 1 [C1P95GC-v1]

description: genomic DNA from sputum


title: sublib2

city: Iowa City

first: Stanley

last: Perlman

state: Iowa

address: 51 Newton Road

department: Dept of Microbiology and Immunology

institute: University of Iowa

description:
Library name: sublib2
mixed samples

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0.
Assembly: Mouse mm10
Assembly: GISAID EPI_ISL_1666328
Supplementary files format and content: Seurat object containing the output from Cell Ranger along with cell metadata, including four experimental groups (mock, 6 dpi, 30 dpi, and 100 dpi).

source_name: brain

extract_protocol:
Animals were deeply anesthetized with ketamine–xylazine and perfused transcardially with 10 mL PBS. Brains were collected, and brain single-cell suspensions were prepared using the Adult Mouse Brain Dissociation Kit (Miltenyi) according to the manufacturer’s instructions. CD45+ cells were then enriched by staining with CD45 magnetic microbeads and applying them to an LS column (Miltenyi) following the manufacturer’s protocol. Isolated cells were pelleted and fixed overnight in 10x Genomics Fixation Buffer (10x Genomics).
Samples from 4–5 mice per experimental time point were pooled before submission to the University of Illinois Urbana-Champaign Genomics Core for processing with the 10x Genomics Chromium Fixed RNA Profiling (Flex) Gene Expression assay (10x Genomics). All libraries were prepared and sequenced together on the Illumina NovaSeq X Plus System, generating 28 × 90 nt reads. Notably, probes targeting the SARS-CoV-2 ORF1ab and nucleocapsid (N) genes were custom-designed and spiked into the Chromium Mouse Transcriptome Probe Set (v1.0.1), following the manufacturer’s instructions. Probe sequences were as follows: ORF1ab: TACTAGTGCCTGTGCCGCACGGTGTAAGACGGGCTGCACTTACACCGCAA; ATAGATTACCAGAAGCAGCGTGCATAGCAGGGTCAGCAGCATACACAAGT; GAGCAAGAACAAGTGAGGCCATAATTCTAAGCATGTTAGGCATGGCTCTA. N: CCATTCTGGTTACTGCCAGTTGAATCTGAGGGTCCACCAAACGTAATGCG; AGTTGTAGCACGATTGCAGCATTGTTAGCAGGATTGCGGGTGCCAATGTG; TGGAACGCCTTGTCCTCGAGGGAATTTAAGGTCTTCCTTGCCATGTTGAG.

treatment_protocol: SARS-CoV-2 N501YMA30 infection

value: brain

value: SARS-CoV-2 N501YMA30 infection or mock


title: sublib1

description:
Library name: sublib1
mixed samples


title: OPA1KO_cDC1_3

description: Library name: 2580911

source_name: Spleen

growth_protocol: cDC1 were sort purified from WT or CD11c-Cre;OPA1 flox mice

value: Spleen

value: Primary conventional type 1 dendritic cell (cDC1)

value: Splenic cDC1

value: Splenic cDC1 purified from the CD11c-Cre;OPA1 flox mice


title: sputum_visit 2 [C1P94DG-v2]

description: genomic DNA from sputum


title: EY75_patB19_normal_pre_NR

value: PRE

value: SR

value: BRAFi


title: OPA1KO_cDC1_2

description: Library name: 2580910


title: PBP-null FTE cells sorted from FTE+SC organoid culture treated with E2, replicate 2

description: Library name: PBPT_FTE+SC_E2-2

data_processing:
Visualization Pipeline for RNAseq (Viper) analysis tool developed by Center for Functional Cancer Epigenetics (CFCE) at Dana-Farber Cancer Institute was used to generate standard outputs.
Assembly: mm10
Supplementary files format and content: Tab-delimited csv file include normalized TPM matrices for each sample.

source_name: Fallopian tube (Oviduct)

growth_protocol: Established P14 WT or PBP-null FTE organoids were co-cultured with fresh MACS sorted CD24- fallopian tube stromal cells for 7 days in BET culture medium.

extract_protocol:
Epcam+ fallopian tube epithelial cells were sorted from co-culture system with the corresponding genotypes, and total RNA was prepared from the sorted cells using Zymo RNA extraction kit.
RNA libraries were prepared for sequencing using Low Input Stranded Total RNAseq with Takara SMARTer Stranded Total RNAseq v3 Pico Mammalian Kit using random priming and Post-cDNA synthesis rRNA removal using ZapR technology

treatment_protocol: 1nM 17β-estradiol was added to culture medium and incubated for 7 days before harvesting the cells.

value: Fallopian tube (Oviduct)

value: Sorted Epcam+ fallopian tube epithelial cells

value: 7 days culture in BET medium with E2


title: sublib3

description:
Library name: sublib3
mixed samples


title: EY71_patB12_tumor_pre_NR

value: tumor

value: C/SC


title: EY76_patB16_normal_pre_LR

value: normal

value: LR


title: OPA1KO_cDC1_1

description: Library name: 2580909


title: PBP-null FTE cells sorted from FTE+SC organoid culture treated with E2, replicate 1

description: Library name: PBPT_FTE+SC_E2-1


title: OPA1KO_cDC1_4

description: Library name: 2580912


title: sputum_visit 1 [C1P93CS-v1]

description: genomic DNA from sputum

value: sputum

value: Female

value: cystic fibrosis


title: PBP-null FTE cells sorted from FTE+SC organoid culture, replicate 1

description: Library name: PBPT_FTE+SC1

value: 7 days culture in BET medium


title: WT_cDC1_4

description: Library name: 2580908

value: Spleen

value: Primary conventional type 1 dendritic cell (cDC1)

value: WT

value: Splenic cDC1 purified from the WT mice


title: EY68_patB04_tumor_post_LR

value: POST


title: WT_cDC1_3

description: Library name: 2580907

value: Splenic cDC1


title: PBP-null FTE cells sorted from FTE+SC organoid culture, replicate 2

description: Library name: PBPT_FTE+SC2

value: Fallopian tube (Oviduct)


title: sputum_visit 1 [C1P92DV-v1]

description: genomic DNA from sputum

value: Male


title: EY67_patB13_tumor_pre_LR

value: PRE

value: BRAFi


title: sputum_visit 1 [C1P91RA-v1]

description: genomic DNA from sputum


title: PBP-null FTE cells sorted from FTE only organoid culture treated with E2, replicate 2

description: Library name: PBPT_FTE_E2-2

value: Sorted Epcam+ fallopian tube epithelial cells

value: 7 days culture in BET medium with E2


title: PBP-null FTE cells sorted from FTE only organoid culture treated with E2, replicate 1

description: Library name: PBPT_FTE_E2-1


title: sputum_visit 1 [C1P90PT-v1]

description: genomic DNA from sputum


title: EY66_patB04_tumor_pre_LR

value: tumor

value: LR

value: C/SC


title: WT_cDC1_1

description: Library name: 2580905


title: Liver derived from liver specific NgBR (Nus1) KO mice, HFD, 16 weeks,Biol Rep 1

city: New Haven

first: Abhishek

middle: K

last: Singh

state: CT

address: 10 Amistad Street

department: Pharmacology and VBT

institute: Yale University

description:
Barcoded cDNA 10X single cell RNA seq
Sample_3KO_MMT_S3_L003

data_processing:
Data processing- The mouse genome mm9 was used for alignment of reads through the CellRanger software (10x Genomics). Clustering of cells was performed by utilizing the Seurat R package, with filtered genes by barcode expression matrices being used as inputs.
Assembly: mm9
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Liver plus tumor

extract_protocol:
Liver cells were isolated from both wild-type (WT) and N-LKO mice fed WD obtained from the Yale Liver Facility Center using a multi-step mechanism. The mice were anesthetized with Isoflurane and attached to a Styrofoam tray, and a ligature was placed around the mid-portal vein and IVC, after which the abdomen was wet with 70% ethanol. The portal vein was cannulated with a 22 G catheter, and perfused with Hanks A followed by Hanks B with collagenase. The liver was removed, and the hepatocytes were released by shaking. The resulting cell suspension was filtered through a 40 μm mesh, and the cells were pelleted by centrifugation. The cell pellet was then resuspended in L-15 media.
Samples were prepared according to the instruction of 10x Genomics Single Cell 3, Reagent Kits v3. Single cell suspensions in RT Master Mix were loaded onto the 10x Genomics Single Cell A Chip to convert poly-adenylated mRNA into barcoded cDNA. Barcoded cDNA was amplified by PCR to generate a sufficient mass for library construction.

value: Liver plus tumor

value: NgBR KO

value: WD for 16 weeks


title: EY64_patB03_normal_pre_NR

value: normal

value: SR

value: LN


title: PBP-null FTE cells sorted from FTE only organoid culture, replicate 1

description: Library name: PBPT_FTE1

value: 7 days culture in BET medium


title: PBP-null FTE cells sorted from FTE only organoid culture, replicate 2

description: Library name: PBPT_FTE2


title: EY60_patB04_normal_pre_LR


title: WT FTE cells sorted from FTE+SC organoid culture treated with E2, replicate 2

description: Library name: WT_FTE+SC_E2-2

value: wild-type


title: EY59_patB02_normal_pre_LR


title: sputum_visit 2 [C1P89PM-v2]

description: genomic DNA from sputum

value: sputum

value: cystic fibrosis


title: sputum_visit 2 [C1P93CS-v2]

description: genomic DNA from sputum

value: Female


title: sputum_visit 1 [C1P88BA-v1]

description: genomic DNA from sputum


title: sputum_visit 1 [C1P87DE-v1]

description: genomic DNA from sputum


title: EY69_patB03_tumor_pre_NR

value: PRE

value: BRAFi


title: Liver derived from WT mice, HFD, 16 weeks,Biol Rep 1

description:
Barcoded cDNA 10X single cell RNA seq
Sample_1WT_MMT_S1_L003

source_name: Liver

value: Liver

value: CTRL


title: WT_cDC1_2

description: Library name: 2580906

value: Spleen

value: Primary conventional type 1 dendritic cell (cDC1)

value: Splenic cDC1

value: WT

value: Splenic cDC1 purified from the WT mice


title: WT FTE cells sorted from FTE+SC organoid culture treated with E2, replicate 1

description: Library name: WT_FTE+SC_E2-1

value: Fallopian tube (Oviduct)

value: Sorted Epcam+ fallopian tube epithelial cells

value: 7 days culture in BET medium with E2


title: sputum_visit 1 [C1P86VC-v1]

description: genomic DNA from sputum


title: CF2166, 72h, mRNA, rep3

city: Fort Collins

first: Taiowa

middle: A

last: Montgomery

state: CO

address: 1878 Campus Delivery

department: Department of Biology

institute: Colorado State University

description:
Library name: mRNA283
tcer-1_mRNA_norm_counts.csv

data_processing:
Small RNA data processing was done using the default configuration in the tinyRNA pipeline (https://github.com/MontgomeryLab/tinyRNA).
mRNA data prcocessing was done using a custom pipeline including fastp, RSEM, STAR, and DESeq2.
Assembly: WS279
Supplementary files format and content: tcer-1_sRNA_norm_counts.csv: CSV formatted file containing reads per million total mapped reads for each feature in each of the conditions indicated.
Supplementary files format and content: tcer-1_mRNA_norm_counts.csv: CSV formatted file containing geometric mean-normalized reads for each feature in each of the conditions indicated.

organism: Caenorhabditis elegans

source_name: gravid hermaphroditic adult whole animals

growth_protocol: Worms were grown for 72 hours (gravid adult stage) from synchronized L1 larvae at 20˚C on media containing E. coli (OP50).

extract_protocol:
Worms were washed from plates and rinsed with M9 3 times and flash frozed in liquid nitrogen. Total RNA from cell lysates was isolated using trizol/chloroform and isopropanol precipitation.
For small RNA libraries, small RNAs (~16-30-nt) were purified from total RNA by size selection using 17% polyacrylamide gels and treated with polyphosphatase to facilitate capture of 22G-RNAs. Libraries were then prepared according to the NEBNext Multiplex Small RNA kit protocol. PCR products (~134-148 bp) were size selected using 10% polyacrylamide gels.  For mRNA libraries, total RNA was DNase treated and rRNA was depleted using the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat, Illumina). rRNA-depleted RNA was size selected (>200 nucleotides) to remove 5S rRNA and tRNA using the Clean & Concentrator-5 Kit (Zymo Research). RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).

tag: molecule type

value: DNase-treated, rRNA-depleted total RNA >200 nt  from cell lysate


title: CF2166, 72h, mRNA, rep2

description:
Library name: mRNA282
tcer-1_mRNA_norm_counts.csv

value: gravid hermaphroditic adult whole animals


title: WT FTE cells sorted from FTE+SC organoid culture, replicate 2

description: Library name: WT_FTE+SC2

value: wild-type

value: 7 days culture in BET medium


title: AGP278, 72h, mRNA, rep3

description:
Library name: mRNA280
tcer-1_mRNA_norm_counts.csv


title: WT FTE cells sorted from FTE+SC organoid culture, replicate 1

description: Library name: WT_FTE+SC1


title: CF2166, 72h, mRNA, rep1

description:
Library name: mRNA281
tcer-1_mRNA_norm_counts.csv


title: EY48_patB38_normal_pre_LR

tag: sample type

value: normal

value: LR

value: C/SC


title: sputum_visit 2 [C1P85MA-v2]

description: genomic DNA from sputum

value: sputum

value: Male

value: cystic fibrosis


title: sputum_visit 1 [C1P84AL-v1]

description: genomic DNA from sputum

value: Female


title: EY56_patB04_tumor_pre_LR

value: tumor

tag: sample class

value: PRE

value: BRAFi


title: EY58_patB04_tumor_pre_LR

tag: patient class

value: LN


title: sputum_visit 2 [C1P87DE-v2]

description: genomic DNA from sputum


title: AGP278, 72h, mRNA, rep1

description:
Library name: mRNA278
tcer-1_mRNA_norm_counts.csv


title: WT FTE cells sorted from FTE only organoid culture, replicate 2

description: Library name: WT_FTE2

value: Fallopian tube (Oviduct)

value: Sorted Epcam+ fallopian tube epithelial cells


title: EY49_patB33_normal_pre_LR

tag: sample body site


title: sputum_visit 2 [C1P84AL-v2]

description: genomic DNA from sputum


title: sputum_visit 1 [C1P83BM-v1]

description: genomic DNA from sputum


title: EY46_patB26_tumor_post_NR

value: POST

value: SR

tag: drug


title: EY44_patB09_tumor_pre_LR


title: sputum_visit 2 [C1P82RG-v2]

description: genomic DNA from sputum

tag: tissue


title: WT FTE cells sorted from FTE only organoid culture, replicate 1

description: Library name: WT_FTE1

value: wild-type


title: WT FTE cells sorted from FTE only organoid culture treated with E2, replicate 1

description: Library name: WT_FTE_E2-1

value: 7 days culture in BET medium with E2


title: N2, 72h, mRNA, rep3

description:
Library name: mRNA277
tcer-1_mRNA_norm_counts.csv

value: gravid hermaphroditic adult whole animals

value: wild-type (N2)

value: DNase-treated, rRNA-depleted total RNA >200 nt  from cell lysate


title: N2, 72h, mRNA, rep1

description:
Library name: mRNA275
tcer-1_mRNA_norm_counts.csv


title: N2, 72h, mRNA, rep2

description:
Library name: mRNA276
tcer-1_mRNA_norm_counts.csv


title: WTY-Liver_M_VEH-2

city: GRONINGEN

first: Marco

last: Demaria

state: Groningen

address: Antonius Deusinglaan, 1

country: Netherlands

institute: umcg

description: Library name: WTY-Liver_M_VEH-2

data_processing:
Raw sequencing reads were quality checked using FastQC (v0.11.9) (Wingett & Andrews, 2018)  and trimmed for adapters using TrimGalore (v0.6.10) with default parameters. Clean reads were pseudoaligned to a pre-built mouse decoy transcriptome index (via refgenie) using Salmon (v1.10.3) (Patro et al., 2017) with the flags --gcBias, --seqBias, and --validateMappings. Transcript-level quantification was aggregated into gene-level counts using tximport (v1.24.0) (Soneson et al., 2015). Genes with <3 reads were excluded.
Assembly: mm10
Supplementary files format and content: Comma-Separated file includes raw counts for each sample

source_name: liver

growth_protocol: All animal procedures were conducted at the Central Animal Facility (CDP) of the University Medical Center Groningen (UMCG) under standard housing conditions.Both male and female mice were allowed to age naturally.

extract_protocol:
Total RNA was extracted from mouse liver tissue using the ISOLATE II RNA Mini Kit (Bioline, cat# BIO-52073) following the manufacturer’s protocol. RNA concentration was measured using a NanoDrop spectrophotometer (Thermo Fisher Scientific) and RNA integrity was assessed using the Agilent TapeStation system.
RNA-seq libraries were generated at the ERIBA Research Sequencing Facility (UMCG, Groningen, The Netherlands) using the Smart-3SEQ protocol (Foley et al., 2019) with 15 ng of input total RNA per sample. Libraries were pooled and sequenced on the Illumina NovaSeq X Plus PE150 platform (Novogene, Munich, Germany).

treatment_protocol: Starting at 16–18 months of age, p16-3MR transgenic mice received monthly treatments with either vehicle (VEH; pH11 water) or ganciclovir (GCV; 150 mg kg–1 in pH11 water) administered intraperitoneally for five consecutive days. As an additional control, a cohort of age-matched wild-type (WT) male and female mice began receiving monthly VEH or GCV treatment from 6 months of age. After 3 months, livers were collected for RNA sequencing analysis (N = 3 per group).

value: liver

value: wild type

value: VEH

tag: batch

value: batch 2


title: CIr-24h-3

city: Guilin

first: Houmin

last: Lin

state: Guangxi

address: 15 Lequn Road, Guilin, 541001, Guangxi, China

country: China

institute: The First Affiliated Hospital of Guilin Medical University

description: Library name: Sample6

data_processing:
Raw sequencing reads were generated in FASTQ format. No additional processing was applied.
Assembly: Homo_sapiens.GRCh38.109
Supplementary files format and content: annotated gene expression values (FPKM, count) for each sample

source_name: breast

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions. RNA concentration and purity were assessed using a NanoDrop spectrophotometer (Thermo Scientific, USA). For each sample, 1.0 μg of total RNA was used for RNA-seq library construction.
RNA-seq libraries were constructed from 1.0 μg of total RNA using a standard poly(A) mRNA enrichment protocol following the manufacturer’s instructions.

value: breast

tag: cell line

tag: cell type

value: TNBC cells


title: EY50_patB33_tumor_post_LR

value: tumor

value: LR

value: V

value: BRAFi


title: WT FTE cells sorted from FTE only organoid culture treated with E2, replicate 2

description: Library name: WT_FTE_E2-2

value: Fallopian tube (Oviduct)

value: Sorted Epcam+ fallopian tube epithelial cells

tag: treatment


title: WTY-Liver_M_VEH-3

description: Library name: WTY-Liver_M_VEH-3

tag: genotype


title: EY42_patB30_tumor_post_LR

value: POST

value: C/SC


title: EY39_patB23_normal_pre_LR

value: normal

value: PRE


title: sputum_visit 1 [C1P82RG-v1]

description: genomic DNA from sputum

value: sputum

value: Male

value: cystic fibrosis


title: EY47_patB35_normal_pre_NR

value: SR


title: EY37_patB07_tumor_pre_NR

value: LN


title: EY38_patB35_normal_pre_NR


title: EY43_patB09_tumor_pre_LR


title: sputum_visit 2 [C1P79PJ-v2]

description: genomic DNA from sputum


title: CIr-24h-1

description: Library name: Sample4

value: breast


title: AGP278, 72h, mRNA, rep2

description:
Library name: mRNA279
tcer-1_mRNA_norm_counts.csv

value: gravid hermaphroditic adult whole animals

value: DNase-treated, rRNA-depleted total RNA >200 nt  from cell lysate


title: WTY-Liver_M_GCV-1

description: Library name: WTY-Liver_M_GCV-1

value: liver

value: wild type

value: GCV

value: batch 2


title: WTY-Liver_M_GCV-3

description: Library name: WTY-Liver_M_GCV-3


title: WTY-Liver_M_VEH-1

description: Library name: WTY-Liver_M_VEH-1

value: VEH


title: sputum_visit 2 [C1P81MS-v2]

description: genomic DNA from sputum


title: sputum_visit 1 [C1P80LM-v1]

description: genomic DNA from sputum

value: Female


title: EY35_patB17_normal_pre_NR

value: C/SC

value: BRAFi


title: sputum_visit 1 [C1P77PA-v1]

description: genomic DNA from sputum


title: WTY-Liver_M_GCV-2

description: Library name: WTY-Liver_M_GCV-2


title: sputum_visit 1 [C1P81MS-v1]

description: genomic DNA from sputum


title: WTY-Liver_F_VEH-4

description: Library name: WTY-Liver_F_VEH-4


title: CK-3

description: Library name: Sample3

value: TNBC cells


title: sputum_visit 1 [C1P78SC-v1]

description: genomic DNA from sputum

value: sputum


title: CIr-24h-2

description: Library name: Sample5


title: sputum_visit 2 [C1P77PA-v2]

description: genomic DNA from sputum


title: VCaP cells, control, replicate2

city: Chicago

first: Rendong

last: Yang

state: IL

address: 420 E Superior St

department: Urology

institute: Northwestern University

data_processing:
RNA-seq reads were aligned to the UCSC hg38 genome using HISAT2 version 2.1.0.
Read quantification using featureCounts version 1.5.2, NCBI RefSeq annotation v109 uses as reference transcriptome.
Assembly: hg38
Supplementary files format and content: featureCounts output files gzipped (raw counts of reads)

source_name: VCaP

extract_protocol:
RNA was extracted from VCaP cells using Qiagen RNeasy Plus Mini Kit (Z6011). 1 ug of total RNA was used for mRNA enrichment and construction of sequencing libraries.
RNA libraries for RNA-seq were prepared through PolyA selection + NEB Ultra II Directional RNA Library Prep Kit.

treatment_protocol: For SMARCA1/SMARCA4 knockdown, two different siRNAs were designed targeting on SMARCA1 or SMARCA4, respectively, and purchased from OriGene Technologies. VCaP cells in 6 well plate were transfected with 30 pmol siRNAs using Lipofectamine® RNAiMAX (Invitrogen) according to the manufacture instruction, and cells were harvested for RNA extraction 72 h after transfection.

value: VCaP

value: epithelial cell

value: WT


title: EY33_patB21_tumor_post_LR

value: tumor

value: POST

value: LR

value: LN


title: WTY-Liver_F_VEH-5

description: Library name: WTY-Liver_F_VEH-5

value: liver


title: WTY-Liver_F_VEH-6

description: Library name: WTY-Liver_F_VEH-6

value: wild type


title: EY28_patB17_normal_pre_NR

value: normal

value: PRE

value: SR

value: BREAST


title: VCaP cells, control, replicate1


title: sputum_visit 1 [C1P76PF-v1]

description: genomic DNA from sputum

value: Male

value: cystic fibrosis


title: CK-2

description: Library name: Sample2

value: breast

value: TNBC cells


title: CK-1

description: Library name: Sample1


title: VCaP cells, siSMARCA4, SiB, replicate2

value: VCaP

value: SMARCA4 knockdown


title: EY26_patB07_tumor_pre_NR

value: BRAFi


title: sputum_visit 1 [C1P72DT-v1]

description: genomic DNA from sputum

value: sputum


title: EY24_patB14_tumor_pre_NR

value: tumor


title: VCaP cells, siSMARCA4, SiA, replicate1

value: epithelial cell


title: EY30_patB08_tumor_pre_LR

value: LR

value: C/SC


title: sputum_visit 1 [C1P75LA-v1]

description: genomic DNA from sputum

value: Female


title: VCaP cells, siSMARCA4, SiB, replicate1


title: WTY-Liver_F_GCV-6

description: Library name: WTY-Liver_F_GCV-6

value: liver

value: wild type

value: GCV

value: batch 2


title: WTY-Liver_F_GCV-5

description: Library name: WTY-Liver_F_GCV-5


title: WTY-Liver_F_GCV-4

description: Library name: WTY-Liver_F_GCV-4


title: VCaP cells, siSMARCA4, SiA, replicate2


title: EY22_patB35_tumor_pre_NR

value: PRE

value: SR


title: sputum_visit 1 [C1P74SD-v1]

description: genomic DNA from sputum

value: Male

value: cystic fibrosis


title: sputum_visit 2 [C1P72DT-v2]

description: genomic DNA from sputum


title: EY29_patB08_tumor_pre_LR

value: LN


title: EY32_patB30_tumor_pre_LR


title: 3MR_Liver_M_VEH_S26

description: Library name: 3MR_Liver_M_VEH_S26

value: VEH

value: batch 1


title: 3MR_Liver_M_VEH_S24

description: Library name: 3MR_Liver_M_VEH_S24


title: 3MR_Liver_M_VEH_S25

description: Library name: 3MR_Liver_M_VEH_S25


title: VCaP cells, siSMARCA1, SiC, replicate2

value: VCaP

value: SMARCA1 knockdown


title: sputum_visit 2 [C1P71CM-v2]

description: genomic DNA from sputum

value: sputum


title: 3MR_Liver_M_GCV_S34

description: Library name: 3MR_Liver_M_GCV_S34


title: sputum_visit 1 [C1P71CM-v1]

description: genomic DNA from sputum


title: sputum_visit 1 [C1P70BF-v1]

description: genomic DNA from sputum


title: VCaP cells, siSMARCA1, SiC, replicate1

value: epithelial cell


title: EY20_patB23_tumor_post_LR

value: tumor

value: POST

value: LR

value: C/SC

value: BRAFi


title: VCaP cells, siSMARCA1, SiA, replicate2


title: EY18_patB38_tumor_pre_LR


title: 3MR_Liver_M_GCV_S32

description: Library name: 3MR_Liver_M_GCV_S32

value: liver

value: GCV


title: VCaP cells, siSMARCA1, SiA, replicate1


title: 3MR_Liver_M_GCV_S30

description: Library name: 3MR_Liver_M_GCV_S30


title: VCaP, control, replicate3

extract_protocol:
RNA was extracted from VCaP cells using Promega ReliaPrep RNA Cell system(Z6011). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Kit following manufacturer's protocols.

treatment_protocol: For IGF1R-AS1 knockdown, two siRNAs were designed targeting on exon1 of IGF1R-AS and purchased from Horizon Discovery. VCaP cells were reverse transfected  with 100pmol siRNAs using RNAiMAX(Invitrogen)  according to the manufacture instruction, cells were  harvested for analysis 72 h after transfection.

value: WT


title: EY17_patB33_tumor_pre_LR

extract_protocol: RNA was extracted with FFPE miRNeasy kit in accordance with manufacture's protocol (QIAGEN).

value: PRE


title: sputum_visit 1 [C1P66TV-v1]

description: genomic DNA from sputum

value: Male

value: cystic fibrosis


title: VCaP, control, replicate2


title: sputum_visit 1 [C1P67IF-v1]

description: genomic DNA from sputum


title: EY16_patB38_tumor_pre_LR


title: 3MR_Liver_F_VEH_S29

description: Library name: 3MR_Liver_F_VEH_S29

value: VEH


title: 3MR_Liver_F_VEH_S28

description: Library name: 3MR_Liver_F_VEH_S28

value: batch 1


title: VCaP, control, replicate1

value: VCaP


title: EY15_patB35_tumor_pre_NR

value: SR


title: EY13_patB30_tumor_pre_LR


title: 3MR_Liver_F_VEH_S27

description: Library name: 3MR_Liver_F_VEH_S27


title: VCaP, si033, replicate3

value: IGF1R-AS1 knockdown


title: sputum_visit 1 [C1P68FM-v1]

description: genomic DNA from sputum

value: sputum

value: Female


title: sputum_visit 1 [C1P69KM-v1]

description: genomic DNA from sputum


title: EY12_patB23_tumor_pre_LR

value: tumor


title: VCaP, si033, replicate2

value: epithelial cell


title: sputum_visit 1 [C1P65TT-v1]

description: genomic DNA from sputum


title: sputum_visit 1 [C1P64NN-v1]

description: genomic DNA from sputum


title: EY11_patB35_tumor_post_NR

value: POST

value: C/SC


title: 3MR_Liver_F_GCV_S33

description: Library name: 3MR_Liver_F_GCV_S33

value: liver


title: 3MR_Liver_F_GCV_S35

description: Library name: 3MR_Liver_F_GCV_S35

value: GCV


title: VCaP, si033, replicate1


title: sputum_visit 2 [C1P63FF-v2]

description: genomic DNA from sputum


title: sputum_visit 1 [C1P62DT-v1]

description: genomic DNA from sputum


title: VCaP, si025, replicate3


title: 3MR_Liver_F_GCV_S31

description: Library name: 3MR_Liver_F_GCV_S31


title: EY10_patB29_tumor_pre_NR

value: BRAFi


title: EY07_patB22_tumor_pre_NR

value: PRE

value: LN


title: sputum_visit 1 [C1P61KA-v1]

description: genomic DNA from sputum

value: Male

value: cystic fibrosis


title: VCaP, si025, replicate2


title: Colon

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: 237 Tower Road

department: Biomedical Engineering

institute: Cornell University

description: Library name: CO

data_processing:
Metatranscriptomic sequencing data were processed using a custom computational workflow. Adapter trimming and quality filtering were performed using BBDuk (v38.90). Filtered reads were aligned to the mouse genome (GRCm39) with STAR (v2.7.10a) using GENCODE M32 annotations. Gene-level quantification was carried out with featureCounts (v2.0.0). Duplicate reads were identified and marked using Picard MarkDuplicates (v2.19.2). Reads that did not align to the host genome were extracted and taxonomically classified using Kraken2 (v2.0.9). Relative abundances are calculated at the genus level excluding possible contaminant taxa based on sterile (non-intestinal) controls.
Assembly: GRCm39
Supplementary files format and content: RNA-seq gene counts
Supplementary files format and content: Microbial relative abundance (genus level)

organism: mouse gut metagenome

source_name: intestinal tissue

extract_protocol:
For each intestinal region, adjacent cryosections corresponding to Visium and Visium+PAP samples were processed for bulk metatranscriptomic analysis. Total RNA was extracted using the NucleoSpin RNA Stool Kit (Takara Bio, 740130.50). To remove contaminating genomic DNA, DNase treatment was performed using a two-step protocol: an initial treatment with Baseline-ZERO DNase (1 μL; LGC Biosciences, DB0715K) followed by a second treatment with TURBO DNase (3 μL; Thermo Fisher Scientific, AM2238) in 10 μL of the supplied buffer. A 1 μL aliquot of RNA was diluted in 99 μL of nuclease-free water, incubated at 37 °C for 30 minutes, and then placed on ice. RNA cleanup was performed using the RNA Clean & Concentrator kit (Zymo Research, R1013), with elution in 10 μL of nuclease-free water.
Stranded total RNA-seq libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v3 -Pico Input Mammalian (Takara Bio, 634485), following the manufacturer’s protocol. The four libraries were pooled and sequenced with MiniSeq sequencer (Miniseq High Output Reagent Cartridge, 150 Cycles, Ilumina).

tag: host tissue

value: Colon

tag: host genotype

tag: host sex

value: M

tag: host age

value: 13 weeks


title: sputum_visit 2 [C1P59SA-v2]

description: genomic DNA from sputum

tag: Sex

tag: disease

tag: visit


title: sputum_visit 1 [C1P60BT-v1]

description: genomic DNA from sputum


title: EY05_patB01_tumor_post_NR

data_processing: The data were processed and normalised using the Bioconductor limma implementation in R

tag: sample type

tag: sample class

value: SR


title: EY06_patB36_tumor_pre_NR

tag: patient class

tag: sample body site

value: V


title: fibroblasts, spironolactone sample 2, biol rep 2

city: Columbus

first: Jill

last: Rafael-Fortney

state: OH

address: 460 W. 12th Ave

department: Physiology & Cell Biology

institute: The Ohio State University

description:
Library name: S2_2
VEHvsSPR_deg.txt
ALDOvsSPR_deg.txt

data_processing:
The index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5
Reads mapped to genes were counted using featureCounts v1.5.0-p3. Differential expression analysis was performed using the DESeq2RPackage (1.20.0). P-values were adjusted using the Benjamini-Hochberg method. P ≤ 0.05 and |log2 fold change| ≥ 1 were used to determine significance.
Assembly: mm39
Supplementary files format and content: comparisons between each 2 treatments; counts and pvaluse for all detected genes included

source_name: skeletal muscle

growth_protocol: Fibroblasts were isolated from hindlimb skeletal muscle of C57/BL10 wild-type 3-day postnatal mice (n = 2). Fibroblasts were grown in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin in a humidified atmosphere with 5% CO2 at 37 degrees C. 24 hours prior to treatment, fibroblast growth media was switched to DMEM supplemented with 10% charcoal-stripped FBS and 1% penicillin-streptomycin to remove endogenous steroids.

extract_protocol:
Fibroblasts were lysed directly in the plates using 100 uL of TRIzol reagent (Invitrogen) and detached from the plates using a cell scraper. RNA was isolated using the Direct-zol RNA microprep kit (Zymo Research). 12 uL of total RNA from each sample at 50 ng/uL were sent to Novogene Co., Ltd. (Davis, CA) for sequencing.  RNA integrity was assessed using a Bioanalyzer 2100 system (Agilent  Technologies).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The nondirectional library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Fibroblasts were pooled for each mouse and re-plated for treatment (Two replicate plates/mouse/treatment). Fibroblasts were treated for 48 hours with 1 uM aldosterone (Sigma-Aldrich), 1 uM spironolactone (Sigma-Aldrich), or vehicle control (DMSO) (Sigma-Aldrich).

tag: tissue

value: skeletal muscle

value: primary neonatal hindlimb skeletal muscle fibroblast

value: spironolactone


title: fibroblasts, spironolactone sample 1, biol rep 2

description:
Library name: S1_2
VEHvsSPR_deg.txt
ALDOvsSPR_deg.txt


title: fibroblasts, aldosterone sample 2, biol rep 2

description:
Library name: A2_2
ALDOvsVEH_deg.txt
ALDOvsSPR_deg.txt

value: aldosterone


title: fibroblasts, spironolactone sample 1, biol rep 1

description:
Library name: S1_1
VEHvsSPR_deg.txt
ALDOvsSPR_deg.txt


title: sputum_visit 2 [C1P58BA-v2]

description: genomic DNA from sputum

value: sputum


title: Cecum

description: Library name: CE

value: Cecum


title: EY03_patB17_tumor_pre_NR

first: Loris

last: De Cecco

value: tumor

value: BREAST

tag: drug


title: fibroblasts, spironolactone sample 2, biol rep 1

description:
Library name: S2_1
VEHvsSPR_deg.txt
ALDOvsSPR_deg.txt


title: VCaP, si025, replicate1

tag: cell line

value: VCaP

value: epithelial cell

value: IGF1R-AS1 knockdown


title: EY02_patB20_tumor_pre_NR

value: PRE

value: C/SC

value: BRAFi


title: Ileum

description: Library name: IL

value: Ileum

value: M

value: 13 weeks


title: fibroblasts, aldosterone sample 2, biol rep 1

description:
Library name: A2_1
ALDOvsVEH_deg.txt
ALDOvsSPR_deg.txt

value: skeletal muscle

tag: cell type


title: sputum_visit 2 [C1P57JT-v2]

description: genomic DNA from sputum

value: Male

value: cystic fibrosis


title: Proximal Small Intestine

description: Library name: PS

value: Proximal Small Intestine


title: B6 2 scTCR-seq

city: Chiba

first: Ryo

last: Nasu

state: Chiba

address: 1-8-1 Inohana, Chuo-ku

country: Japan

institute: Chiba University

description: Library name: B6 2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation for scTCR-seq were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0 (10X Genomics)
Supplementary files format and content: csv files include contig annotations and cell barcode information
Library strategy: TCR-seq

source_name: thymus

extract_protocol:
A FACSAria III cell sorter (BD) was used for live cell sorting.
Libraries were prepared using Chromium Next GEM Single Cell 5' Kit v2 and Chromium Single Cell Mouse TCR Amplification Kit according to manufacturer’s protocol (10X Genomics).

value: thymus

value: iNKT cells


title: EY00_patB37_tumor_pre_NR

city: Milan

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

value: tumor

value: SR


title: EY01_patB07_tumor_pre_NR

value: LN


title: B6 1 scTCR-seq

description: Library name: B6 1


title: 06:00, Day 12, Colony 2, Replicate 2

city: Bangalore

first: Axel

last: Brockmann

state: Karnataka

address: Bellary Road

department: Neurobiology

country: India

institute: National Centre for Biological Sciences, Tata Institute of Fundamental Research (NCBS-TIFR)

data_processing:
Raw RNA-seq reads were trimmed to remove adaptors using Trimmomatic. FastQC was done for each sample pre- and post-trimming.
Reads were mapped to Apis mellifera genome (NCBI Assembly Amel_HAv3.1) using STAR RNA-seq aligner.
The number of reads aligning to each gene was counted using featureCounts.
The DESeq2 package within R was used for differential expression analyses.
The MetaCycle package within R was used to evaluate circadian oscillation.
Assembly: NCBI Assembly Amel_HAv3.1
Supplementary files format and content: Comma delimited file contains raw counts for each sample.

organism: Apis mellifera

source_name: sKC-enriched cell population

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus Micro Kit components (Catalogue no. 74034).
mRNA was isolated from extracted whole RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module (Catalogue no. E7490L). Stranded mRNA libraries were prepared with NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalogue no. E7765L).

tag: colony

value: Colony 2

value: sKC-enriched cell population

tag: time


title: fibroblasts, aldosterone sample 1, biol rep 1

description:
Library name: A1_1
ALDOvsVEH_deg.txt
ALDOvsSPR_deg.txt

value: primary neonatal hindlimb skeletal muscle fibroblast

tag: genotype

tag: treatment

value: aldosterone


title: EX99_patB05_tumor_pre_NR

value: PRE

value: BRAFi


title: sputum_visit 1 [C1P56AA-v1]

description: genomic DNA from sputum

value: sputum

value: Female


title: sputum_visit 1 [C1P58BA-v1]

description: genomic DNA from sputum


title: fibroblasts, aldosterone sample 1, biol rep 2

description:
Library name: A1_2
ALDOvsVEH_deg.txt
ALDOvsSPR_deg.txt

value: skeletal muscle


title: fibroblasts, vehicle sample 2, biol rep 2

description:
Library name: V2_2
ALDOvsVEH_deg.txt
VEHvsSPR_deg.txt

value: vehicle


title: BALB/c 2 scTCR-seq

description: Library name: BALB/c 2

value: BALB/c


title: 06:00, Day 12, Colony 2, Replicate 1


title: sputum_visit 2 [C1P55GM-v2]

description: genomic DNA from sputum

value: cystic fibrosis


title: 06:00, Day 12, Colony 1, Replicate 2

value: Colony 1


title: sputum_visit 1 [C1P55GM-v1]

description: genomic DNA from sputum


title: 06:00, Day 12, Colony 1, Replicate 1


title: sputum_visit 2 [C1P54DM-v2]

description: genomic DNA from sputum


title: fibroblasts, vehicle sample 2, biol rep 1

description:
Library name: V2_1
ALDOvsVEH_deg.txt
VEHvsSPR_deg.txt


title: B6 2 scRNA-seq

description: Library name: B6 2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation for scRNA-seq were made using the Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: refdata-gex-mm10-2020-A (10X Genomics)
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

extract_protocol:
A FACSAria III cell sorter (BD) was used for live cell sorting.
Libraries were prepared using Chromium Next GEM Single Cell 5' Kit v2 according to manufacturer’s protocol (10X Genomics).

value: thymus

value: iNKT cells


title: sputum_visit 1 [C1P57JT-v1]

description: genomic DNA from sputum

value: Male


title: BALB/c 1 scTCR-seq

description: Library name: BALB/c 1


title: 02:00, Day 12, Colony 2, Replicate 2


title: sputum_visit 1 [C1P53DA-v1]

description: genomic DNA from sputum


title: fibroblasts, vehicle sample 1, biol rep 2

description:
Library name: V1_2
ALDOvsVEH_deg.txt
VEHvsSPR_deg.txt


title: 02:00, Day 12, Colony 2, Replicate 1


title: fibroblasts, vehicle sample 1, biol rep 1

description:
Library name: V1_1
ALDOvsVEH_deg.txt
VEHvsSPR_deg.txt


title: 02:00, Day 12, Colony 1, Replicate 2


title: B6 1 scRNA-seq

description: Library name: B6 1


title: sputum_visit 2 [C1P53DA-v2]

description: genomic DNA from sputum


title: Mouse intestinal "spheroids", Sox9-mEGFP, Replicate 3

city: Berkeley

first: Robert

last: Tjian

state: CA

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

description:
Library name: Sample 15
RTCC77O_trimmed_htseqCounts_noCommentLines.txt

data_processing:
Reads were trimmed with cutadapt (version 4.5 with Python 3.10.13).
Reads were aligned with STAR RNA-Seq aligner (version 2.7.10b) with the following options: --outSJfilterReads Unique --outFilterMultimapNmax 1 --outFilterIntronMotifs RemoveNoncanonical --outSAMstrandField intronMotif
STAR output .sam files were converted to .bam files with samtools2 (version 1.15.1).
.bam files were sorted by name (-n) with samtools2 (version 1.15.1).
Reads overlapping annotated genes (Ensembl GRCm39 annotations) were counted with HTSeq (version 2.0.2) with the following options: htseq-count --stranded=no –order=name -f bam --additional-attr=gene_name -m union.
HTSeq output raw counts were used to find differentially expressed genes with DESeq2, run with default parameters within the Galaxy platform5 (DESeq2 Galaxy Version 2.11.40.8+galaxy0).
bigWig coverage files were generated with deepTools bamCoverage (version 3.5.1) with the following options: --binSize 50 --normalizeUsing BPM --samFlagInclude 64
Assembly: mm39
Supplementary files format and content: *htseqCounts.txt: raw transcripts counts for each condition and replicate; HTSeq output.
Supplementary files format and content: Normalized_counts_file.tabular: single table containing the DESeq2 output of normalized transcripts counts for each replicate of each condition
Supplementary files format and content: All_vs_all_Halo_V5_vs_Sox9_Halo_organoids.tabular: table containing the result of DESeq2 differential gene expression analysis comparing the two conditions specified in the file name; columns are as follows: EnsembleGeneVersion, mean_counts, log2FC, StErr_log2FC, WaldStat, pValue, pValueAdj
Supplementary files format and content: All_vs_all_Halo_V5_vs_Sox9_mEGFP_organoids.tabular: table containing the result of DESeq2 differential gene expression analysis comparing the two conditions specified in the file name; columns are as follows: EnsembleGeneVersion, mean_counts, log2FC, StErr_log2FC, WaldStat, pValue, pValueAdj
Supplementary files format and content: All_vs_all_Sox9_Halo_organoids_vs_Sox9_mEGFP_organoids.tabular: table containing the result of DESeq2 differential gene expression analysis comparing the two conditions specified in the file name; columns are as follows: EnsembleGeneVersion, mean_counts, log2FC, StErr_log2FC, WaldStat, pValue, pValueAdj
Supplementary files format and content: All_vs_all_Halo_V5_vs_Sox9_Halo_spheroids.tabular: table containing the result of DESeq2 differential gene expression analysis comparing the two conditions specified in the file name; columns are as follows: EnsembleGeneVersion, mean_counts, log2FC, StErr_log2FC, WaldStat, pValue, pValueAdj
Supplementary files format and content: All_vs_all_Halo_V5_vs_Sox9_mEGFP_spheroids.tabular: table containing the result of DESeq2 differential gene expression analysis comparing the two conditions specified in the file name; columns are as follows: EnsembleGeneVersion, mean_counts, log2FC, StErr_log2FC, WaldStat, pValue, pValueAdj
Supplementary files format and content: All_vs_all_Sox9_Halo_organoids_vs_Sox9_Halo_spheroids.tabular: table containing the result of DESeq2 differential gene expression analysis comparing the two conditions specified in the file name; columns are as follows: EnsembleGeneVersion, mean_counts, log2FC, StErr_log2FC, WaldStat, pValue, pValueAdj
Supplementary files format and content: All_vs_all_Sox9_mEGFP_organoids_vs_Sox9_mEGFP_spheroids.tabular: table containing the result of DESeq2 differential gene expression analysis comparing the two conditions specified in the file name; columns are as follows: EnsembleGeneVersion, mean_counts, log2FC, StErr_log2FC, WaldStat, pValue, pValueAdj

source_name: Small intestine

growth_protocol: Mouse small intestinal organoids were generated and cultured as described in Walther et al., Cell Reports, 2024 (https://www.cell.com/cell-reports/fulltext/S2211-1247(24)01265-8).

extract_protocol:
Organoids/"spheroids" were added of 1 mL TRIzol reagent and stored at -20 °C until extracted. After thawing, samples were spun in a microfuge at 4 °C, at max. speed for 5 minutes and total RNA extraction was performed according to TRIzol manufacturer's instructions.
Poly-A purification and library preparation were performed with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490S) followed by the NEBNext Ultra II RNA Library Prep Kit for Illumina (E7770S) with the NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1).

treatment_protocol: Stable mouse small intestinal organoids were generated via lentiviral transduction and antibiotic selection as described in Walther et al., Cell Reports, 2024 (https://www.cell.com/cell-reports/fulltext/S2211-1247(24)01265-8).

value: Small intestine

value: Primary cultures

value: Organoids

value: Transduction with lentiviral plasmids


title: BALB/c 2 scRNA-seq

description: Library name: BALB/c 2


title: BALB/c 1 scRNA-seq

description: Library name: BALB/c 1


title: 02:00, Day 12, Colony 1, Replicate 1

value: sKC-enriched cell population


title: Mouse intestinal "spheroids", Sox9-mEGFP, Replicate 1

description:
Library name: Sample 13
RTCC77E_trimmed_htseqCounts_noCommentLines.txt


title: sputum_visit 1 [C1P52DR-v1]

description: genomic DNA from sputum


title: Mouse intestinal "spheroids", Sox9-mEGFP, Replicate 2

description:
Library name: Sample 14
RTCC77J_trimmed_htseqCounts_noCommentLines.txt


title: 22:00, Day 11, Colony 2, Replicate 2

value: Colony 2


title: sputum_visit 2 [C1P51MA-v2]

description: genomic DNA from sputum


title: B6CF2 8 ATAC-seq

description: Library name: B6CF2 8

data_processing:
Peaks were called using MACS2 software with the broad option.
Reproducible ATAC peaks were annotated to the closest gene or transcriptional start site with proximity-based annotation using HOMER annotatePeaks.pl (mm10 genome build).
Cumulative normalized tag counts of these ATAC peaks were used to detect the genes showing variation in accessibility.
BigWig files were generated from the aligned SAM file formats by deeptool v3.1 and normalized to 1 million reads.
The Integrative Genomics Viewer software program (https://software.broadinstitute.org/software/igv/) was used for the visualization of BigWig files.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig

extract_protocol:
A FACSAria III cell sorter (BD) was used for live cell sorting.
50,000 cells were used to extract the nuclei. The nuclei were treated with Tn5 transposase (Illumina) to tag and fragmentize the accessible chromatin. The fragmentized DNA was purified using a QIAGEN MinElute kit (QIAGEN) and amplified by 10−12 PCR cycles, based on the amplification curve. The libraries were sequenced for 100 cycles.

value: DP thymocytes


title: Mouse intestinal "spheroids", Sox9-Halo, Replicate 3

description:
Library name: Sample 12
RTCC77N_trimmed_htseqCounts_noCommentLines.txt


title: B6CF2 7 ATAC-seq

description: Library name: B6CF2 7


title: sputum_visit 1 [C1P51MA-v1]

description: genomic DNA from sputum

extract_protocol: Genomic DNA was extracted from sputum samples using the QIAamp DNA Mini kit (#51304, Qiagen) and a protocol we detailed in Pineau et al. 2021 (PMID: 33808877).

value: sputum


title: B6CF2 6 ATAC-seq

description: Library name: B6CF2 6


title: 22:00, Day 11, Colony 2, Replicate 1


title: B6CF2 5 ATAC-seq

description: Library name: B6CF2 5


title: 22:00, Day 11, Colony 1, Replicate 2


title: Mouse intestinal organoids, Sox9-mEGFP, Replicate 3

description:
Library name: Sample 9
RTCC77M_trimmed_htseqCounts_noCommentLines.txt


title: CF2166, 72h, sRNA, rep3

description:
Library name: Lib416
tcer-1_sRNA_norm_counts.csv

value: gravid hermaphroditic adult whole animals

tag: molecule type

value: polyphosphatase -treated, 16-30 nt purified RNAs from cell lysate


title: 22:00, Day 11, Colony 1, Replicate 1


title: BALB/c 4 ATAC-seq

description: Library name: BALB/c 4


title: BALB/c 3 ATAC-seq

description: Library name: BALB/c 3


title: Mouse intestinal organoids, Sox9-mEGFP, Replicate 2

description:
Library name: Sample 8
RTCC77H_trimmed_htseqCounts_noCommentLines.txt


title: 18:00, Day 11, Colony 1, Replicate 2


title: CF2166, 72h, sRNA, rep1

description:
Library name: Lib414
tcer-1_sRNA_norm_counts.csv


title: CF2166, 72h, sRNA, rep2

description:
Library name: Lib415
tcer-1_sRNA_norm_counts.csv


title: 18:00, Day 11, Colony 2, Replicate 2


title: AGP278, 72h, sRNA, rep3

description:
Library name: Lib413
tcer-1_sRNA_norm_counts.csv


title: 18:00, Day 11, Colony 1, Replicate 1


title: 18:00, Day 11, Colony 2, Replicate 1


title: Mouse intestinal organoids, Sox9-mEGFP, Replicate 1

description:
Library name: Sample 7
RTCC77C_trimmed_htseqCounts_noCommentLines.txt


title: B6 4 ATAC-seq

description: Library name: B6 4


title: AGP278, 72h, sRNA, rep2

description:
Library name: Lib412
tcer-1_sRNA_norm_counts.csv


title: Mouse intestinal organoids, Sox9-Halo, Replicate 2

description:
Library name: Sample 5
RTCC77G_trimmed_htseqCounts_noCommentLines.txt


title: B6 3 ATAC-seq

description: Library name: B6 3


title: Mouse intestinal "spheroids", Sox9-Halo, Replicate 1

description:
Library name: Sample 10
RTCC77D_trimmed_htseqCounts_noCommentLines.txt


title: B6CF2 4 ATAC-seq

description: Library name: B6CF2 4


title: Mouse intestinal "spheroids", Sox9-Halo, Replicate 2

description:
Library name: Sample 11
RTCC77I_trimmed_htseqCounts_noCommentLines.txt


title: Mouse intestinal organoids, Sox9-Halo, Replicate 3

description:
Library name: Sample 6
RTCC77L_trimmed_htseqCounts_noCommentLines.txt


title: N2, 72h, sRNA, rep3

description:
Library name: Lib410
tcer-1_sRNA_norm_counts.csv

value: wild-type (N2)


title: 14:00, Day 11, Colony 2, Replicate 2


title: B6CF2 3 ATAC-seq

description: Library name: B6CF2 3


title: Mouse intestinal organoids, Sox9-Halo, Replicate 1

description:
Library name: Sample 4
RTCC77B_trimmed_htseqCounts_noCommentLines.txt


title: sputum_visit 1 [C1P100DM-v1]

description: genomic DNA from sputum

value: Female


title: 14:00, Day 11, Colony 2, Replicate 1


title: Mouse intestinal organoids, Halo-NLS, Replicate 3

description:
Library name: Sample 3
RTCC77K_trimmed_htseqCounts_noCommentLines.txt


title: B6CF2 2 ATAC-seq

description: Library name: B6CF2 2


title: B6CF2 1 ATAC-seq

description: Library name: B6CF2 1


title: N2, 72h, sRNA, rep1

description:
Library name: Lib408
tcer-1_sRNA_norm_counts.csv


title: 14:00, Day 11, Colony 1, Replicate 2


title: N2, 72h, sRNA, rep2

description:
Library name: Lib409
tcer-1_sRNA_norm_counts.csv


title: Mouse intestinal organoids, Halo-NLS, Replicate 2

description:
Library name: Sample 2
RTCC77F_trimmed_htseqCounts_noCommentLines.txt


title: AGP278, 72h, sRNA, rep1

description:
Library name: Lib411
tcer-1_sRNA_norm_counts.csv


title: BALB_thy_2 RNA-Seq

description: Library name: BALB_thy_2

data_processing:
Sequencing of the library fragments was performed using a HiSeq 1500 System (Illumina, USA).
Read sequences (50 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz; December 2011) using Hisat2 v2.2.0 (PMID: 25751142).
The gene expression was summarized using HTSeq-counts v2.0.5 (PMID: 25260700).
The DESeq2 package v1.42.1 (PMID: 25516281) was used to normalize the raw counts and identify differentially expressed genes (|log2-fold change| ≥ 0.5 and adjusted p-value < 0.05).
Assembly: mm10
Supplementary files format and content: Tab delimeted text files

extract_protocol:
A FACSAria III cell sorter (BD) was used for live cell sorting.
For cDNA library construction, we used the TruSeq RNA Sample Prep Kit v2 (Illumina), according to the manufacturer’s protocol.

value: whole thymocytes

value: wild type


title: BALB/c 2 ATAC-seq

description: Library name: BALB/c 2

value: thymus

value: BALB/c


title: Liver derived from WT mice, CD, 8 weeks,Biol Rep 4

description:
Library name: WT3
WT3_168_025_S4_L003

data_processing:
Reads aligned to mm9 genome with STAR
Quantified to mm9 RefSeq annotation model through Partek E/M
Genes were normalized as counts per million
Assembly: mm9
Supplementary files format and content: tab-delimited text file include cpm values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were generated from control cells using TrueSeq Small RNA Library preparation (Illumina)

value: Liver

value: WT

value: CD for 16 weeks


title: Mouse intestinal organoids, Halo-NLS, Replicate 1

description:
Library name: Sample 1
RTCC77A_trimmed_htseqCounts_noCommentLines.txt

value: Small intestine

value: Primary cultures

value: Organoids


title: B6 2 ATAC-seq

description: Library name: B6 2


title: Liver derived from liver specific NgBR (Nus1) KO mice, CD, 8 weeks,Biol Rep 4

description:
Library name: NLKO2
NLKO2_132_061_S7_L003

value: NgBR KO


title: 10:00, Day 11, Colony 1, Replicate 2

value: Colony 1

value: sKC-enriched cell population


title: 10:00, Day 11, Colony 2, Replicate 1

value: Colony 2


title: BALB/c 1 ATAC-seq

description: Library name: BALB/c 1

value: DP thymocytes


title: BALB_DP_2 RNA-Seq

description: Library name: BALB_DP_2


title: Liver derived from liver specific NgBR (Nus1) KO mice, CD,  8 weeks,Biol Rep 3

description:
Library name: NLKO4
NLKO4_108_085_S9_L003


title: B6 1 ATAC-seq

description: Library name: B6 1


title: 10:00, Day 11, Colony 1, Replicate 1


title: BALB_DP_1 RNA-Seq

description: Library name: BALB_DP_1


title: B6_thy_2 RNA-Seq

description: Library name: B6_thy_2


title: 06:00, Day 11, Colony 2, Replicate 2


title: Liver derived from WT mice, CD, 8 weeks,Biol Rep 3

description:
Library name: WT1
WT1_192_001_S2_L003


title: Liver derived from liver specific NgBR (Nus1) KO mice, CD, 8 weeks,Biol Rep 2

description:
Library name: NLKO3
NLKO3_120_073_S8_L003


title: 10:00, Day 11, Colony 2, Replicate 2


title: 06:00, Day 11, Colony 1, Replicate 2


title: 14:00, Day 11, Colony 1, Replicate 1


title: B6_thy_1 RNA-Seq

description: Library name: B6_thy_1


title: Liver derived from liver specific NgBR (Nus1) KO mice, CD, 8 weeks,Biol Rep 1

description:
Library name: NLKO1
NLKO1_144_049_S6_L003


title: 06:00, Day 11, Colony 1, Replicate 1


title: Liver derived from WT mice, CD, 8 weeks,Biol Rep 2

description:
Library name: WT2
WT2_180_013_S3_L003


title: BALB_thy_1 RNA-Seq

description: Library name: BALB_thy_1


title: GD1783, Stomach, H felis infected, female, mouse 3

city: Morgantown

first: Lei

last: Wang

state: West Virginia

address: 64 Medical Center Drive

department: Department of Microbiology, Immunology and Cell Biology

institute: west virginia university

description: Library name: sample 6

data_processing:
Reads were aligned to mouse genome (mm10) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by rpkm (PMID: 18516045) with an in-house script.
Assembly: mm10
Supplementary files format and content: Txt file, from left to right represent entrz ID, gene symbol, and gene expression values in log2(RPKM+1)+0.0001 for each samples.

source_name: Stomach

extract_protocol:
Gastric tissue RNA biopsies were collected from the greater curvature using a 2-mm biopsy punch. RNA was extracted in TRIzol (Thermo Fisher Scientific) and precipitated from the aqueous phase using 1 volume of 100% ethanol. The mixture was transferred to an RNA isolation column (Omega Bio-Tek) and the remaining steps were followed according to the manufacturer’s recommendations. RNA was treated with RNase-free DNase I (Omega Bio-Tek) as part of the isolation procedure.
RNA libraries were prepared using a NEB Ultra II Directional RNA Library Prep Kit with poly-A selection (Admera Health). Sequencing was performed on a paired-end platform, generating 150 bp reads with a depth of 40 million reads per sample.

value: Stomach

tag: strain

value: female

value: Helicobacter felis infected


title: C1q_2

city: Los Angeles

first: Thomas

last: Rando

state: California

address: 615 Charles E Young Drive

institute: University of California, Los Angeles

description: Library name: Sample 5

data_processing:
Reads were adapter- and quality-trimmed with trimmomatic (quality cutoff 20).
Trimmed reads were mapped to mm10 mouse genome with HISAT2
Exonic reads uniquely mapped were summarized over genes with the featureCounts module
Raw counts were analyzed with DESeq2
Assembly: mm10
Supplementary files format and content: Processed data FAP control C1q

source_name: hind limb muscles

growth_protocol: FAPs were FACS-purified from hindlimb muscle of mice at 4-5 months of age.

extract_protocol:
Total RNA was extracted from FACS-purified MuSCs with Qiagen Rneasy Plus Micro Kit
Reverse transcription was performed with 10ng of total RNA with Clontech SMART-SEQ v4 Ultra Low Input RNA Kit for Sequencing. Sequencing libraries were generated with Nugen Ovation Ultralow System v2.

treatment_protocol: FAPs were either treated with vehicle control or C1q (100 ug/ml).

value: hind limb muscles

value: Fibroadipogenic progenitors

value: wild type


title: ExVivoCell_24hr_nc_rep1

city: Shanghai

first: Lingjie

last: Kong

address: 83 Fen Yang Road

institute: Fudan University

description: gene expression in HUVECs while they were stimulated by H2O2 for 24 h, and then left untreated for another 24 h, rep1

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2534-60012) for 17 hours at 65 ℃ in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 ℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using Profile AgilentG3_GX_1Color for 4x180K  microarrays.

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Next, the raw data was normalized with the quantile algorithm.

source_name: Human umbilical vein endothelial cells, 24hr, nc, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the LowInput Quick-Amp Labeling Kit，one-color (24×) (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini kit (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: RNA was prepared using the mirVanaTM RNA Isolation Kit (AM1561) following the manufacturer's recommendations. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: cell

value: Human umbilical vein endothelial cells

tag: gender

value: male


title: C1q_3

description: Library name: Sample 6


title: B6_DP_2 RNA-Seq

description: Library name: B6_DP_2

value: thymus


title: ExVivoCell_24hr_nc_rep3

description: gene expression in HUVECs while they were stimulated by H2O2 for 24 h, and then left untreated for another 24 h, rep3

source_name: Human umbilical vein endothelial cells, 24hr, nc, replicate 3


title: ExVivoCell_24hr_exo_rep3

description: gene expression in HUVECs while they were stimulated by H2O2 for 24 h, and then cocultured with MSC-exos for another 24 h, rep3

source_name: Human umbilical vein endothelial cells, 24hr, exo, replicate 3


title: ExVivoCell_24hr_nc_rep2

description: gene expression in HUVECs while they were stimulated by H2O2 for 24 h, and then left untreated for another 24 h, rep2

source_name: Human umbilical vein endothelial cells, 24hr, nc, replicate 2


title: B6_DP_1 RNA-Seq

description: Library name: B6_DP_1


title: Ileum with tumor, replicate 2

description: Library name: A612

data_processing:
Raw sequencing reads were first trimmed using Cutadapt,  and aligned to the mouse genome using the STAR Solo pipeline (STAR version 2.7.10b), which generates a feature-by-spot barcode expression matrix. The GRCm39 reference genome with GENCODE M28 annotations was used, or alternatively, the same reference was appended with the Reovirus Type 1-Lang sequence and annotations. Unmapped reads were taxonomically classified using Kraken2(kraken2.09) to generate a taxon-by-spot barcode matrix.
Assembly: GRCm39
Supplementary files format and content: HDF5 files contain the raw gene expression count matrix (UMI counts) per spot barcode, along with complementary information, including spot barcode assignments to cells based on segmentation and the raw microbial NCBI taxid presence count matrix (UMI counts) per spot barcode
Library strategy: Spatial Transcriptomics

source_name: Ileum

extract_protocol:
Cryosections were obtained from the ileum of  two 13 weeks old mice (male and female). For spatial total RNA sequencing, tissue sections (10 µm thick) were processed with a modified Stereoseq (STOmics) protocol. The sections were mounted onto STOmics mini chip and fixed in freshly prepared methacarn (60% methanol, 30% glacial acetic acid, 10% chloroform) for 15 minutes at room temperature. Staining and imaging was performed according to the Stereoseq/STOmics protocol. In situ polyadenylation was performed using yeast Poly(A) Polymerase (yPAP; Thermo Scientific). Capture areas were equilibrated with 1X wash buffer, followed by the addition of yPAP enzyme mix and incubation at 37°C . After enzyme removal, a 12-minute enzymatic permeabilization step was conducted before continuing with the standard STOmics library preparation to generate cDNA and sequencing libraries.
The cDNA ibraries were prepared following the stereoseq/STOmics protocol instructions. sequencing was carried out on a Complete Genomics DNBSEQ-T7 Sequencer using the DNBSEQ-T7 High-throughput Sequencing Set (FCL PE100) and the associated STEROmics primer set. The sequencing run consisted of a 50 bp read 1 (with dark cycles from bases 26 to 40), a 100 bp read 2, and a 10 bp index read.

value: Ileum

tag: Sex

value: M

tag: age

value: 13 weeks

tag: tile id


title: ExVivoCell_24hr_exo_rep2

description: gene expression in HUVECs while they were stimulated by H2O2 for 24 h, and then cocultured with MSC-exos for another 24 h, rep2

source_name: Human umbilical vein endothelial cells, 24hr, exo, replicate 2


title: GD1769, Stomach, H felis infected, male, mouse 3

description: Library name: sample 3


title: Liver derived from WT mice, CD, 8 weeks,Biol Rep 1

description:
Library name: WT4
WT4_156_037_S5_L003

source_name: Liver

value: Liver

value: WT

value: CD for 16 weeks


title: GD1781, Stomach, H felis infected, female, mouse 1

description: Library name: sample 4


title: Control 2

description: Library name: Sample 2

value: vehicle control


title: Control 3

description: Library name: Sample 3


title: C1q_1

description: Library name: Sample 4


title: MAF-1_rep3

city: Saitama

first: Kyosuke

last: Mukae

state: Kitaadachi-gun

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

institute: Saitama Cancer Center

description: tumor

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851C) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the SureScan Agilent DNA Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Cranial neural crest cells from 414C2 hiPSC, tumor generated by injection subcutaneously  immune-deficient mice.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions (Protocol version 6.9), followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The human iPSCs were maintained on feeder layers of mitomycin C-treated embryonic mouse fibroblasts in primate embryonic stem cell medium (REPROCELL, Tokyo, Japan) supplemented with 4 ng/mL recombinant human fibroblast growth factor 2 (FUJIFILM, Tokyo, Japan). Differentiation of iPSC into cranial NCC (cNCC) was induced using a previously described protocol (PMID: 25464501). Cranial NCCs were cultured in Iscove’s modified Dulbecco’s medium (Thermo Fisher Scientific)/Ham’s F-12 (Thermo Fisher Scientific) 1:1 supplemented with 1x chemically defined lipid concentrate (GIBCO), 15 mg/ml apo-transferrin (Sigma), 450 mM monothioglycerol (Sigma), 5 mg/ml purified BSA (Sigma), 7 mg/ml Insulin (FUJIFILM) and 50 μg/mL penicillin/streptomycin (Sigma). 20 ng/ml EGF (R&D) and 20 ng/ml FGF2 (FUJIFILM) were used to maintain cNCCs. Cultures were maintained at 37ºC under 5% CO2 in air.

extract_protocol: Total cellular RNA for preparing RT–PCR templates was extracted using ISOGEN II (Nippon Gene KK). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was guaranteed by an RNA Integrity Number (RIN) > 8.

treatment_protocol: In the preparation of the overexpression/lentivirus, the packaging cell line HEK 293T (4 × 10^6) was plated on a 10-cm dish and co-transfected the next day with 1.5 μg of each of the plasmids (pCDH-CMV-MYCN-EF1a-puro, pCDH-SFFV-ALK(WT)-EF1a-bsd or pCDH-SFFV-ALK(F1174L)-EF1a-bsd) and 2.0 μg of the packaging vectors (Sigma-Aldrich) using the Fugene HD transfection reagent (Promega) according to the manufacturer’s protocol. Medium was changed the next day and cells were cultured for another 24 h. Conditioned medium was collected and cleared of debris by filtering through a filter with 0.45-μm pores.  Thereafter, 1 × 10^5 cNCCs were seeded on each well of a 6-well plate, and infected by lentiviral-conditioned media with 4 μg/mL polybrene. The infected cNCCs were cultured in medium containing 1 μg/ml puromycin for 3 d or 4 µg/mL blasticidin for 4 d, and were mixed with 0.3% agar dissolved in growth medium (CDMi + SB431542 + EGF + FGF2) and plated on top of a bottom layer of 0.5% agar dissolved in growth medium in a 35 mm dish. The transformed clones were isolated and injected subcutaneously immune-deficient mice.

value: human,  cell line


title: Ileum with tumor, replicate 1, section b

description: Library name: E611

value: F


title: GD1768, Stomach, H felis infected, male, mouse 2

description: Library name: sample 2

value: Stomach


title: MAF-2_rep3

description: tumor

value: female


title: Stereoseq heart and testis, with in situ polyadenylation

description: Library name: STO2

data_processing:
Raw sequencing reads were first trimmed using Cutadapt,  and aligned to the mouse genome using the STAR Solo pipeline (STAR version 2.7.10b), which generates a feature-by-spot barcode expression matrix. The GRCm39 reference genome with GENCODE M28 annotations was used, or alternatively, the same reference was appended with the Reovirus Type 1-Lang sequence and annotations.
Assembly: GRCm39
Supplementary files format and content: Feature Barcode Market Exchange Matrices
Library strategy: Spatial Transcriptomics

source_name: heart, testis

extract_protocol:
Frozen testis from DBA/2J mice and frozen reovirus-induced myocarditic hearts collected at 7 days post infection (dpi) following oral gavage with Reovirus type 1 Lang (T1L) were processed for Spatial Total RNA Sequencing using a modified Stereoseq (STOmics) workflow. Tissues were cryosectioned at 10 µm thickness and mounted onto a 1 cm × 1 cm STOmics Stereoseq chip. Sections were fixed in ice-cold methanol for 30 min at −20°C, followed by staining and imaging according to the manufacturer’s Stereoseq/STOmics protocol. In situ polyadenylation was then performed using yeast poly(A) polymerase (yPAP; Thermo Scientific): capture areas were equilibrated with 1× wash buffer, incubated with yPAP enzyme mix at 37°C, and the enzyme was removed by washing. A 15-min enzymatic permeabilization step was subsequently performed prior to continuing with the standard STOmics library preparation workflow to generate cDNA and sequencing libraries.
The cDNA ibraries were prepared following the stereoseq/STOmics protocol instructions. sequencing was carried out on a Complete Genomics DNBSEQ-T7 Sequencer using the DNBSEQ-T7 High-throughput Sequencing Set (FCL PE100) and the associated STEROmics primer set. The sequencing run consisted of a 50 bp read 1 (with dark cycles from bases 26 to 40), a 100 bp read 2, and a 10 bp index read.

value: heart, testis


title: Control 1

description: Library name: Sample 1

value: hind limb muscles

value: Fibroadipogenic progenitors


title: Mus CD8+ T cell, WT, active 12h,biol rep 2

city: Beijing

first: Yushan

last: YI

address: No.38 Xueyuan Road, Haidian District, Beijing

department: Department of Immunology

institute: Peking University

description: Library name: W2

data_processing:
ATAC-seq data were analyzed using the ENCODE ATAC-seq pipeline v2.2.2. Raw reads were subjected to quality control, trimmed, and aligned to the GRCm38 reference genome to generate BAM files. Peaks were called using Genrich tool in ATAC-seq mode. Differential chromatin accessibility was assessed using DiffBind (v3.12.0) in R. Genomic location features of differential peaks were annotated via ChIPseeker (v1.38.0).
Assembly: GRCm39
Supplementary files format and content: Peaks and annotation

source_name: lymph node

extract_protocol:
For ATAC-seq,nuclei were pelleted at 500 g for 10 min, then resuspended in transposase reaction mix (Illumina) and incubated at 37℃ for 30 min. DNA was purified using a MinElute kit (QIAGEN).
For ATAC-seq, the DNA fragments were amplified in a 12-cycle PCR to add unique indices for sequencing and purified using a MinElutekit.

value: lymph node

value: CD8+ T cells

value: active 12h


title: MAF-2_rep1

description: tumor


title: MAF-2_rep2

description: tumor


title: ExVivoCell_24hr_exo_rep1

description: gene expression in HUVECs while they were stimulated by H2O2 for 24 h, and then cocultured with MSC-exos for another 24 h, rep1

source_name: Human umbilical vein endothelial cells, 24hr, exo, replicate 1

value: Human umbilical vein endothelial cells

value: male


title: GD1782, Stomach, H felis infected, female, mouse 2

description: Library name: sample 5

value: wild type

value: Helicobacter felis infected


title: Proximal Small Intestine, with in situ polyadenylation

description: Library name: E312

source_name: Proximal Small Intestine

extract_protocol:
Cryosections were obtained from four cites of the intestine of  a 13 weeks old male mouse (proximal small intestine, ileum, cecum, distal colon) and from the proximal colon of a female 13 week old mouse. The tissue sections (10 µm thick) were processed with a modified Stereoseq (STOmics) protocol. The sections were mounted onto STOmics mini chip and fixed in freshly prepared methacarn (60% methanol, 30% glacial acetic acid, 10% chloroform) for 15 minutes at room temperature. Staining and imaging was performed according to the Stereoseq/STOmics protocol. In situ polyadenylation was performed using yeast Poly(A) Polymerase (yPAP; Thermo Scientific). Capture areas were equilibrated with 1X wash buffer, followed by the addition of yPAP enzyme mix and incubation at 37°C . After enzyme removal, a 12-minute enzymatic permeabilization step was conducted before continuing with the standard STOmics library preparation to generate cDNA and sequencing libraries.
The cDNA ibraries were prepared following the stereoseq/STOmics protocol instructions. sequencing was carried out on a Complete Genomics DNBSEQ-T7 Sequencer using the DNBSEQ-T7 High-throughput Sequencing Set (FCL PE100) and the associated STEROmics primer set. The sequencing run consisted of a 50 bp read 1 (with dark cycles from bases 26 to 40), a 100 bp read 2, and a 10 bp index read.

value: Proximal Small Intestine

value: M

value: 13 weeks


title: MAF-1_rep1

description: tumor

value: human,  cell line


title: B. Females - Scan 3 | 016 | IBA1 _ TMEM119

city: Camden

first: Khalid

last: Hanafy

state: NJ

address: 401 Broadway,

department: Biomedical Sciences

institute: Cooper Medical School of Rowan Univ

description: Library name: DSP-1001660019265-C-B03_S32

library_source: other

data_processing:
FASTQ fileswere processed using the NanoString GeoMx NGS Pipeline v2.0 or v2.2. Briefly, reads were trimmed to remove low quality bases and adapter sequences. Paired end reads were stitched and aligned, and the barcode and UMI sequences were extracted. Barcodes were matched to known probe barcodes with maximum one mismatch allowed. Reads matching the same barcode were deduplicated by UMI. The number of raw reads was highly linearly correlated with the number of unique UMIs at all AOI sizes, suggesting largely uniform library amplification. However, to correct for any PCR amplification bias, all analyses in this study use UMI deduplicated counts. Data were exported to Excel for further analysis.
Supplementary files format and content: xlsx
Library strategy: Spatial Transcriptomics

molecule: other

source_name: Brain

extract_protocol:
Frozen sections of 4%PFA perfused prefixed mouse brains were sent to the University of Minnesota Genomics Center for probe hybridization, immunofluorescence staining, and selection of ROIs for analysis. 1x Tris-EDTA (pH9.0) solution and steaming the solution to 95⁰C method were used for antigen retrieval followed by Proteinase K digestion at 37⁰C for 5 minutes (1 µg/mL) to expose RNA targets.
Library preparation was performed according to the NanoString GeoMx-NGS Readout Library Prep manual. The DSP aspirate was dried and resuspended in 10 μL DEPC-treated water, and 4 μL was used in a PCR reaction. NanoString SeqCode primers were used to amplify the tags and add Illumina adaptor sequences and sample demultiplexing barcodes. PCR products were pooled either in equal volumes or in proportion relative to AOI size, depending on the experiment, and purified with two rounds of AMPure XP beads (Beckman Coulter).Libraries were sequenced on an Illumina NextSeq 2000, according to the manufacturer’s instructions, with at least 27 × 27 paired end reads.

tag: animal group

value: BMM-cKO-females

value: Brain

value: Macrophage

value: BMM-cKO


title: B. Females - Scan 3 | 015 | IBA1 _ TMEM119

description: Library name: DSP-1001660019265-C-B02_S31

value: female


title: Mus CD8+ T cell, KO, active 12h,biol rep 2

description: Library name: K2

value: KO


title: Ileum with tumor, replicate 1, section a

description: Library name: E514

value: Ileum

value: F


title: Ileum, with in situ polyadenylation

description: Library name: G511


title: Mus CD8+ T cell, KO, active 12h,biol rep 1

description: Library name: K1

value: lymph node

value: CD8+ T cells

value: active 12h


title: Distal Colon, with in situ polyadenylation

description: Library name: D112

source_name: Distal Colon

value: Distal Colon


title: B. Females - Scan 3 | 013 | IBA1 _ TMEM119

description: Library name: DSP-1001660019265-C-A12_S29


title: MAF-1_rep2

description: tumor


title: GD1766, Stomach, H felis infected, male, mouse 1

description: Library name: sample 1

value: Stomach

value: male

value: wild type

value: Helicobacter felis infected


title: Mus CD8+ T cell, WT, active 12h,biol rep 1

description: Library name: W1

value: WT


title: B. Females - Scan 3 | 012 | IBA1 _ TMEM119

description: Library name: DSP-1001660019265-C-A11_S28

value: MG-cKO-females

value: MG-cKO


title: Proximal Colon, with in situ polyadenylation

description: Library name: F312

source_name: Proximal Colon

value: Proximal Colon

value: 13 weeks


title: MAW-2_rep3

description: tumor

value: human,  cell line

value: female


title: B. Females - Scan 3 | 011 | IBA1 _ TMEM119

description: Library name: DSP-1001660019265-C-A10_S27

value: Brain

value: Macrophage