title: islets of Langerhans-44% fat+fiber-CAST/EiJ-F (ORSAM8081)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8081

tag: strain


title: islets of Langerhans-44% fat+fiber-CAST/EiJ-F (ORSAM8082)

status: Public on Dec 31 2023

type: SRA

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

country: USA

institute: The Jackson Laboratory

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8082

library_source: transcriptomic

data_processing:
raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script and gathering_GBRS_total_counts_batch2.R.
counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation).
Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/Processing_normalization.R and Processing_normalization_batch2.R scripts.
gene annotation file ENSEMBL version 84
Assembly: GRCm38
Supplementary files format and content: counts_matrix.csv
Supplementary files format and content: mrna_annots.csv
Supplementary files format and content: vst_matrix.csv
Supplementary files format and content: Three Bears Islet Numbers.csv

molecule: polyA RNA

organism: Mus musculus

source_name: islets of Langerhans

extract_protocol:
KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA was isolated from pancreatic islets using the RNeasy Micro kit (Qiagen), according to manufacturers’ protocols, including the optional DNase digest step. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico or RNA ScreenTape assay (Agilent Technologies).
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction.  Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. Libraries were sequenced on an Illumina NovaSeq 6000 using the S4 Reagent Kit.  Pancreatic islet libraries were sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs.

treatment_protocol: Three inbred mouse strains, NZO/HlLTJ, CAST/EiJ, and C57BL/6J, were placed on control or high fat, high sugar diet starting at six weeks of age. Tissue was collected at fifteen weeks of age.

tag: tissue

value: islets of Langerhans

tag: diet

value: 44% fat + fiber

value: CAST/EiJ

tag: Sex

value: Female

tag: genotype

value: WT

tag: treatment


title: 202163530054_R03C01:BDB1P02067

type: genomic

city: Lebanon

first: Ji-Qing

last: Chen

state: New Hampshire

address: 1 Medical Center Drive, Williamson level 6

department: Epidemiology

institute: Dartmouth College

description:
IlluminaHumanMethylationEPIC
White blood cell

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
R studio
minfi Processed Average Beta

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

value: Blood

tag: gender

value: male

tag: age

tag: muscle-invasive

value: no


title: 203751390082_R08C01:A00000FBN

value: female


title: 202172220041_R07C01:BDB1P01023


title: 576_966708-35

city: Seattle

first: Naresh

last: Doni Jayavelu

state: WA

address: 1201 9th AVE

department: Systems Immunology/Bioinformatics

institute: Benaroya Research Institute at Virginia Mason

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2) was used to remove any remaining adapter sequence.
Reads were aligned by STAR v2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2), and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: raw_counts_ITN_GRASS_PBMC_samples.csv is a csv file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

molecule: total RNA

source_name: PBMC

extract_protocol:
RNA was extracted from TRIzol following the manufacturer’s protocol (Invitrogen)
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.

value: PBMC

value: Male

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id

tag: visit number

value: SCIT

tag: sts timepoint

value: PostChallenge


title: islets of Langerhans-44% fat+fiber-C57BL/6J-M (ORSAM8079)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8079


title: 575_970797-35


title: 203751380110_R07C01:A00000EBG


title: 573_966725-31

value: Placebo

value: PreChallenge


title: 574_966725-35


title: HT1080_EGFP_3D_1

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

data_processing:
Alignment was performed using STAR version 2.6 using the ENSEMBL GRCh38 assembly reference genome
Gene expression was quantified using HTseq python framework version 0.9.1
MLS_2645-94_2D_3.1 and MLS_2645-94_2D_3.2 were sequenced from the same sample and were collapsed as technical replicates after read count, before downstream analysis. The collapsed sample is referred to as MLS_2645-94_2D_3_collapsed in the read count file.
Assembly: ENSEMBL GRCh38
Supplementary files format and content: Excel file containing matrix of unnormalized reads mapped to each transcript as a result from HTseq analysis.

source_name: Fibrosarcoma cell line

growth_protocol:
For monolayer culture, RPMI Glutamax cell culture media was supplemented with 5% or 10% fetal bovine serum, 100U/ml penicillin and 100 mg/ml streptomycin. Stable expression of EGFP constructs were maintained by addition of 500µg/ml Geneticin.
For scaffold culture, tumor pieces retrieved from a myxoid liposarcoma patient-derived xenograft model were decellularized using detergent wash. The scaffolds were cut into small pieces and added to 48-well culture plates. 3x105 cells were added onto the scaffold in 0.5ml complete media and cultured for 21 days before harvesting for downstream analysis. Scaffold pieces were transferred to new wells with fresh media if cells were growing outside the scaffold area.

extract_protocol:
Scaffold samples were lysed in RLT lysis buffer and homogenized in a Qiagen TissueLyzer II using stainless steel beads. 2D samples were lysed in RLT lysis buffer or QIAzol lysis buffer. RNA was extracted from all samples using Qiagen RNeasy micro kit or miRNeasy micro kit, including DNase treatment.
The library was generated using the Smart-seq2 protocol (Picelli, Faridani et al. 2014) with some modifications.

tag: cell line

tag: transfected gene

value: EGFP

tag: culture method

value: Scaffold culture


title: 203752100047_R04C01:5668DS

tag: tissue


title: islets of Langerhans-10% fat+fiber-C57BL/6J-M (ORSAM8080)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8080

value: islets of Langerhans

tag: diet

value: 10% fat + fiber

tag: strain

tag: Sex


title: 203751390065_R04C01:A00000EDI

tag: gender

value: yes


title: 202172220123_R05C01:BDB1P01077

tag: age


title: HT1080_WT_3D_1


title: MLS_1765-92_2D_4

source_name: Myxoid liposarcoma cell line

value: Adherent 2D culture


title: HT1080_WT_3D_3


title: islets of Langerhans-10% fat+fiber-C57BL/6J-F (ORSAM8078)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8078

value: Female

tag: genotype

value: WT

tag: treatment


title: 572_963064-31

tag: fastq total_reads

tag: percent aligned


title: 203751390082_R01C01:A00000ECO

value: Blood

tag: muscle-invasive


title: MLS_1765-92_2D_3


title: HT1080_WT_3D_2


title: islets of Langerhans-44% fat+fiber-C57BL/6J-F (ORSAM8076)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8076

value: 44% fat + fiber


title: islets of Langerhans-44% fat+fiber-C57BL/6J-F (ORSAM8075)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8075


title: MLS_1765-92_2D_2


title: 570_970806-35

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id


title: islets of Langerhans-44% fat+fiber-NZO/HlLtJ-M (ORSAM7668)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7668

value: NZO/HlLtJ


title: MLS_1765-92_2D_1

tag: cell line


title: 202172220064_R07C01:BDB1P01039

value: male

value: no


title: 568_958691-35

value: PBMC

value: Male

tag: visit number

tag: sts timepoint


title: islets of Langerhans-10% fat+fiber-NZO/HlLtJ-M (ORSAM7666)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7666

tag: tissue


title: MLS_2645-94_2D_4

tag: transfected gene

tag: culture method


title: islets of Langerhans-10% fat+fiber-C57BL/6J-F (ORSAM8077)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM8077

tag: diet

tag: strain

tag: Sex


title: 203751390067_R01C01:A00000EEI

tag: gender

tag: age


title: 566_970846-35

tag: fastq total_reads

tag: treatment

value: Placebo

value: PostChallenge


title: islets of Langerhans-44% fat+fiber-NZO/HlLtJ-F (ORSAM7664)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7664

tag: genotype


title: 203751380009_R08C01:A00000EDU

tag: muscle-invasive


title: MLS_2645-94_2D_3.2

description: Technical replicate together with MLS_2645-94_2D_3.1. The samples were collapsed as technical replicates after read count before downstream analysis, referred to as MLS_2645-94_2D_3_collapsed.


title: islets of Langerhans-44% fat+fiber-NZO/HlLtJ-F (ORSAM7663)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7663


title: 565_970846-31

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

value: PreChallenge


title: MLS_2645-94_2D_3.1

description: Technical replicate together with MLS_2645-94_2D_3.2. The samples were collapsed as technical replicates after read count before downstream analysis, referred to as MLS_2645-94_2D_3_collapsed.

tag: cell line


title: 571_963064-35

tag: participant id

tag: visit number

tag: sts timepoint


title: 564_963101-35

tag: tissue


title: islets of Langerhans-10% fat+fiber-NZO/HlLtJ-F (ORSAM7662)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7662

tag: diet


title: 203755070020_R03C01:A00000ECD


title: MLS_2645-94_2D_2

tag: transfected gene

tag: culture method


title: 562_966726-35

tag: Sex


title: MLS_2645-94_2D_1


title: islets of Langerhans-10% fat+fiber-NZO/HlLtJ-F (ORSAM7661)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7661

tag: strain


title: 203755070052_R03C01:A00000EF6

tag: gender

value: female

tag: age


title: 563_958676-31

tag: fastq total_reads

tag: treatment


title: 202172220016_R07C01:BDB1P02007

tag: muscle-invasive


title: MCF10A ⍺-/-;βin, replicate 3

city: La Jolla

first: Brooke

middle: M.

last: Emerling

state: CA

address: 10901 North Torrey Pines Road

department: Cell and Molecular Biology of Cancer Program

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Data processing was performed using Illumina Basespace workflow version “3.19.5.13-master” using human genome version UCSC hg19. Differential expression was performed using DESeq2 Basespace pipeline version “3.18.20.11+master”.
Assembly: hg19
Supplementary files format and content: Tab-delimited file containing TPM (transcripts per millions) for each sample

extract_protocol:
RNA was extracted from cell pellets washed with PBS using Directzol RNA MiniPrep (Zymo Research Corporation; 50-444-628). RNA yield and purity was tested using the Qubit 4 Fluorometer prior to analysis.
Sequencing libraries were prepared using 250ng RNA using standard Illumina Tru-seq single indexing protocols and sequenced using the Illumina NextSeq 500 instrument.

tag: cell type

value: breast epithelial cell

tag: genotype

value: MCF10A {alpha}-/-;{beta}in

value: 3-day doxycycline


title: 203723180011_R02C01:A00000ECV

value: yes


title: 561_966726-31

value: Female

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage


title: islets of Langerhans-44% fat+fiber-CAST/EiJ-M (ORSAM7660)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7660

value: islets of Langerhans

value: CAST/EiJ

value: WT


title: islets of Langerhans-10% fat+fiber-CAST/EiJ-M (ORSAM7659)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7659

value: 10% fat + fiber


title: MCF10A ⍺-/-;βin, replicate 2

tag: cell line


title: islets of Langerhans-44% fat+fiber-CAST/EiJ-F (ORSAM7658)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7658

tag: tissue

value: 44% fat + fiber


title: 203734300103_R06C01:A00000EEA

description:
IlluminaHumanMethylationEPIC
White blood cell

value: Blood

value: male

value: no


title: 203734290015_R01C01:A00000EB1


title: MCF10A ⍺-/-;βin, replicate 1


title: 560_958676-35

value: PBMC

tag: participant id

tag: visit number

value: Placebo

tag: sts timepoint


title: 203734300093_R03C01:A00000EBR


title: islets of Langerhans-10% fat+fiber-CAST/EiJ-F (ORSAM7657)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7657

tag: diet

tag: Sex


title: 202163530102_R07C01:BDB1P04063

tag: gender


title: 559_963101-31

tag: age

value: PreChallenge


title: SCRin control, replicate 3

value: wild-type


title: 558_966679-35

value: Male

tag: fastq total_reads

value: PostChallenge


title: 203751380037_R01C01:A00000FBF


title: SCRin control, replicate 1

value: breast epithelial cell

tag: treatment

value: 3-day doxycycline


title: islets of Langerhans-10% fat+fiber-C57BL/6J-M (ORSAM7655)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7655

tag: strain


title: SCRin control, replicate 2

tag: cell type


title: 203752100058_R04C01:5482DS

tag: muscle-invasive


title: 556_970789-35

tag: percent aligned


title: islets of Langerhans-10% fat+fiber-C57BL/6J-F (ORSAM7653)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7653

value: Female

tag: genotype


title: Differentiated organoids ZZ, biol rep 2

city: Madrid

first: Beatriz

last: Martinez-Delgado

address: Carretera Majadahonda-Pozuelo Km 2

department: Molecular Genetic Unit

country: Spain

institute: ISCIII/IIER

data_processing:
RNASeq pipeline written in Nextflow
Fastq files were analyze for quality control using FastQC, v0.11.8
Raw reads were trimmed using Trimmomatic v.0.38 (4-base wide sliding window; removed reads with less than 50 nucleotides)
Read aligment was done with STAR v2.6.1d and quality control performed using RseQC v3.0.0
Gene quatification was calculated using Subread´s featurecounts package v1.6.4
Assembly: Ensembl GRCh38
Supplementary files format and content: tab-delimited text files include "normalized count" values for all Sample
Supplementary files format and content: 1 file with all samples

source_name: Liver

extract_protocol:
RNA was isolated using TriReagent (Sigma) followed by DNAseI digestion. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-Seq were prepared using TruSeq Stranded mRNA Kit (Illumina) following manufacturer's protocols.

value: Liver

value: organoid

value: ZZ

value: hepatocyte differentiation


title: 203723180011_R01C01:A00000EGI


title: 203752100046_R05C01:A00000ED3

value: yes


title: islets of Langerhans-44% fat+fiber-C57BL/6J-F (ORSAM7654)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7654

value: islets of Langerhans

value: 44% fat + fiber

value: WT


title: 555_970789-31

value: PBMC

tag: aligned counts_in_millions

tag: median cv_coverage


title: 202172220173_R06C01:BDB1P02046

tag: tissue

value: Blood

value: male

value: no


title: 553_963051-35

value: Male

tag: participant id

value: Placebo


title: 554_963051-31

tag: visit number

value: PreChallenge


title: Differentiated organoids ZZ, biol rep 3

description: ZZDiFNEG


title: Differentiated organoids MM, biol rep 4

value: MM


title: islets of Langerhans-44% fat+fiber-C57BL/6J-M (ORSAM7656)

description:
Islets sequenced 150 bp paired-end to a targeted read depth of 100 million read pairs
ORSAM7656


title: 552_958499-35

tag: sts timepoint

value: PostChallenge


title: Differentiated organoids MM, biol rep 3

value: Liver


title: 557_966679-31


title: Differentiated organoids MM, biol rep 2

description: MMDiFNEG

value: organoid


title: heart-10% fat+fiber-NZO/HlLtJ-M (ORSAM8923)

data_processing:
raw counts quantified by EMASE and processed by /RNAseq/Raw/GBRS/QTLViewer_setup/gathering_GBRS_total_counts.R script and gathering_GBRS_total_counts_batch2.R.
counts normalized by DESeq2 vst() function (quick version of variance stabilizing transformation).
Matrix generated by /RNAseq/Raw/GBRS/QTLViewer_setup/Processing_normalization.R and Processing_normalization_batch2.R scripts.
gene annotation file ENSEMBL version 84
Assembly: GRCm38
Supplementary files format and content: counts_matrix.csv
Supplementary files format and content: mrna_annots.csv
Supplementary files format and content: vst_matrix.csv

source_name: heart

extract_protocol:
RNA was isolated from tissue using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher) and the KingFisher Flex purification system (ThermoFisher). Frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in TRIzol (ThermoFisher Scientific) using a gentleMACS dissociator (Miltenyi Biotec Inc). After the addition of chloroform to the TRIzol homogenate, the RNA-containing aqueous layer was removed for RNA isolation, according to the manufacturer’s protocol, beginning with the RNA bead binding step. RNA concentration and quality were assessed using the Nanodrop 8000 spectrophotometer (Thermo Scientific) and the RNA 6000 Pico or RNA ScreenTape assay (Agilent Technologies).
2 ul of diluted (1:1000) ERCC Spike-in Control Mix 1 (Ambion by Life Technologies) was added to 100ng of each RNA sample prior to library construction.  Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche Sequencing and Life Science), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. ibraries were sequenced on an Illumina NovaSeq 6000 using the S4 Reagent Kit. Libraries were sequenced 100 bp paired-end to a targeted read depth of 30 million read pairs.

value: heart

tag: diet

value: 10% fat + fiber

value: NZO/HlLtJ


title: heart-10% fat+fiber-NZO/HlLtJ-M (ORSAM8924)

tag: Sex


title: Differentiated organoids MM, biol rep 1

value: hepatocyte differentiation


title: 549_966733-31

value: Female


title: RH4_DMSO_4hr_1_ATAC

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

library_source: genomic

data_processing:
RNA-seq was mapped using STAR with hg19 as reference.
RNA-seq read abundance for each gene counted (TPM) using RSEM
RNA-seq raw reads normalized using DESeq2
ChIP-seq was mapped using BWA with hg19 as reference.
ChIP-seq peaks were called using MACS2. https://github.com/CBIIT/ChIP_seq.
ATAC-seq was mapped using BWA with hg19 as reference.
ATAC-seq peaks were called using MACS2. https://github.com/CBIIT/ChIP_seq.
scRNA-seq demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
Hi-C was mapped to hg19 using omni-c_qc.sh from Dovetail Github (https://github.com/dovetail-genomics)
Hi-C Technical repliaces were merged using Pairtools' merge.
Assembly: hg19/GRCh37
Supplementary files format and content: ChIP-seq peak files are tab delimited bed text files for each sample.
Supplementary files format and content: RNA-seq processed files are quantification matrices of TPM (transcripts per million) at the gene level.
Supplementary files format and content: ATAC-seq peak files are tab delimited bed text files for each sample.
Supplementary files format and content: scRNA-seq files are Tab delimited values files and matrix files
Supplementary files format and content: Hi-C files are merged processed .hic files

source_name: muscle

growth_protocol: Cells were maintained in DMEM with 10% FBS and Penn/Strep at 37 °C incubation.

extract_protocol:
Bulk RNA is extracted using QIAGEN Rneasy Plus Mini Kit. ChIP samples were fixed with 1% formaldehyde for 15 mins, sonicated, immunoprecipitated using antibody and Dynabeads, washed, eluted, and reverse crosslinked.  ATAC samples were tagmented, PCR amplified, and purified. scRNA-seq samples were processed using the 10x Genomics Chromium Next GEM single cell 3' kit.  Hi-C samples were processed using the Dovetail Micro-C kit.
Illumina TruSeq Stranded mRNA and Total RNA library prep, Illumina TruSeq ChIP Library Prep, scRNA-seq using Chromium Next GEM single Cell 3' Reagent kits v3.1, ATAC library from tagmentation and PCR amplification, Hi-C library contructed using Dovetail Micro-C kit

treatment_protocol: Cells were treated with either DMSO or compound of interest for the specified amount of time.

value: muscle

tag: cell line

value: Rhabdomyosarcoma

value: wt

tag: time

value: 4 hr

value: DMSO


title: 548_970840-31

value: PBMC

tag: age

tag: fastq total_reads


title: RH4_UPCM_10uM_4hr_1_ATAC

tag: treatment


title: Differentiated organoids ZZ, biol rep 1

tag: cell type

value: ZZ


title: 547_970840-35

value: Placebo


title: RH4_PFI90_Pol2_ser2

tag: antibody

value: RNA pol2 ser2 (Cell Signaling, 13499)

value: 24 hr


title: 203734290102_R05C01:A00000ED0

value: Blood

tag: gender

value: male

tag: muscle-invasive

value: yes


title: 202172220158_R02C01:BDB1P04034

value: no


title: 203734290015_R05C01:5542DS


title: 203755070060_R05C01:A00000EEC


title: 202172220016_R05C01:BDB1P02005


title: 551_958499-31

value: Male

tag: percent aligned

tag: aligned counts_in_millions

value: PreChallenge


title: heart-44% fat+fiber-NZO/HlLtJ-F (ORSAM8922)

tag: tissue

value: heart

value: 44% fat + fiber

tag: strain

value: NZO/HlLtJ

value: Female

tag: genotype

value: WT


title: heart-44% fat+fiber-NZO/HlLtJ-F (ORSAM8921)


title: 546_963123-31

tag: median cv_coverage

tag: participant id

tag: visit number

tag: sts timepoint


title: 203751380061_R08C01:A00000EBC


title: heart-10% fat+fiber-C57BL/6J-F (ORSAM8910)

tag: diet

value: 10% fat + fiber

tag: Sex


title: heart-44% fat+fiber-NZO/HlLtJ-M (ORSAM8074)


title: heart-44% fat+fiber-C57BL/6J-F (ORSAM8911)


title: heart-44% fat+fiber-CAST/EiJ-F (ORSAM8918)

value: CAST/EiJ


title: 550_966733-35

value: PBMC

tag: age

tag: fastq total_reads

value: PostChallenge


title: heart-44% fat+fiber-CAST/EiJ-M (ORSAM8920)

tag: treatment


title: RH4_DMSO_Pol2_ser2

value: muscle

tag: cell line

tag: cell type

value: Rhabdomyosarcoma

value: wt

tag: antibody

value: RNA pol2 ser2 (Cell Signaling, 13499)

tag: time

value: DMSO


title: 545_963123-35

tag: percent aligned

tag: aligned counts_in_millions

value: Placebo


title: heart-44% fat+fiber-NZO/HlLtJ-M (ORSAM8073)

tag: tissue

tag: strain

value: Male


title: 203751380062_R03C01:A00000EFY

value: Blood

tag: gender

value: female

tag: muscle-invasive

value: no


title: RH4_PFI90_Pol2_ser5

tag: genotype

value: RNA pol2 ser5 (Cell Signaling, 13523)

value: 24 hr


title: 203755070019_R04C01:A00000EAP

value: male


title: 203734300103_R04C01:5472DS


title: RH4_DMSO_Pol2_ser5


title: 203723190028_R04C01:A00000EB0


title: 543_958461-35

value: Female

tag: median cv_coverage

tag: participant id

tag: visit number

tag: sts timepoint


title: 203755070020_R04C01:A00000EEJ

tag: age


title: 542_970791-35

tag: Sex

tag: fastq total_reads

tag: treatment

value: SLIT


title: 203751380062_R05C01:A00000EBD


title: 540_966663-31

value: PBMC

value: PreChallenge


title: RH4_PFI90_1_24h_H3K9me2

value: muscle

tag: cell line

tag: cell type

tag: antibody

value: H3K9me2 (Abcam, ab1220)


title: heart-10% fat+fiber-NZO/HlLtJ-F (ORSAM8071)

value: heart

tag: diet

value: 10% fat + fiber

value: NZO/HlLtJ

value: WT


title: heart-10% fat+fiber-CAST/EiJ-F (ORSAM8067)

tag: tissue

value: CAST/EiJ


title: heart-10% fat+fiber-NZO/HlLtJ-F (ORSAM8072)

tag: strain


title: 203723180011_R07C01:5693DS

value: Blood

tag: gender

value: yes


title: 202172220064_R08C01:BDB1P01040

value: female

tag: muscle-invasive

value: no


title: heart-44% fat+fiber-CAST/EiJ-M (ORSAM7644)

value: 44% fat + fiber

value: Male

tag: genotype


title: heart-44% fat+fiber-C57BL/6J-M (ORSAM8063)


title: 539_966663-35

value: Female

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

value: PostChallenge


title: RH4_PFI90_1_24h_H3K27me3

value: Rhabdomyosarcoma

value: wt

value: H3K27me3 (Active Motif, 39155)

tag: time

value: 24 hr


title: RH4_DMSO_24h_H3K27me3

value: muscle

value: DMSO


title: 203752100058_R06C01:A00000FCA

value: male

tag: age


title: 544_958461-31

value: PBMC

tag: Sex

tag: participant id

tag: visit number

value: Placebo

tag: sts timepoint

value: PreChallenge


title: RH4_DMSO_24h_H3K9me2

tag: cell line

tag: cell type

value: H3K9me2 (Abcam, ab1220)

tag: treatment


title: 541_963058-35

tag: tissue

tag: fastq total_reads

value: SLIT


title: heart-10% fat+fiber-CAST/EiJ-M (ORSAM8070)

value: heart

tag: diet

value: 10% fat + fiber

tag: strain

value: CAST/EiJ

value: WT


title: 537_963058-31

value: Female


title: RH4_DMSO_Pol2_201212

value: Rhabdomyosarcoma

tag: genotype

tag: antibody

value: RNA pol2 total (Millipore, 05-623)


title: RH4_PFI90_1_24h_H3K4me3

value: wt

value: H3K4me3 (Active Motif, 39159)


title: 203751390065_R06C01:A00000FBV

value: Blood

tag: gender

tag: muscle-invasive

value: no


title: heart-10% fat+fiber-C57BL/6J-M (ORSAM8064)

value: Male


title: 536_958500-31

value: PBMC

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage


title: RH4_PFI90_Pol2_201212

value: muscle

tag: time

value: 24 hr


title: 538_970791-31

tag: age

tag: Sex

tag: participant id

tag: visit number

value: PreChallenge


title: 203755070050_R04C01:A00000EDV

value: male


title: RH4_DMSO_24h_H3K4me3

tag: cell line

tag: cell type

tag: treatment

value: DMSO


title: 203751390046_R08C01:A00000FBY

tag: tissue

value: female

value: yes


title: heart-44% fat+fiber-CAST/EiJ-F (ORSAM7642)

value: heart

tag: diet

value: 44% fat + fiber

tag: strain

value: CAST/EiJ

value: WT


title: 534_966738-31

tag: fastq total_reads

value: Placebo

tag: sts timepoint


title: 203789410029_R06C01:A00000EFA

tag: gender

tag: muscle-invasive


title: 203752110028_R04C01:A00000FBO


title: 203734290015_R06C01:A00000FBS


title: 532_970836-31

tag: percent aligned

tag: aligned counts_in_millions


title: heart-10% fat+fiber-C57BL/6J-M (ORSAM7639)

value: 10% fat + fiber

tag: genotype


title: 203751390067_R03C01:A00000ECL

value: Blood

tag: age


title: RH4_PFI90_1_24h_PAX3FOXO1

value: Rhabdomyosarcoma

value: wt

tag: antibody

value: PAX3-FOXO1 (in house)

tag: time


title: RH4_PFI90_1uM_24h_H3K27ac

value: muscle

value: H3K27ac (Active Motif, 39133)


title: RH4_DMSO_24h_H3K27ac

value: 24 hr


title: heart-10% fat+fiber-CAST/EiJ-M (ORSAM7643)

tag: Sex

value: Male


title: Dorsal Vagal Complex-10% fat+fiber-CAST/EiJ-F (ORSAM9508)

source_name: solitary tract nucleus and dorsal motor nucleus of vagus nerve

value: Female


title: 531_970836-35

value: PBMC

tag: median cv_coverage

tag: participant id

tag: visit number

value: PostChallenge


title: heart-44% fat+fiber-C57BL/6J-M (ORSAM7640)

tag: tissue

value: heart

tag: treatment


title: 203789410029_R03C01:A00000EH7

value: female

value: no


title: heart-10% fat+fiber-CAST/EiJ-F (ORSAM7641)

tag: diet

tag: strain

value: CAST/EiJ

value: WT


title: RH4_Tumor_PFI90_5D_Mice924

tag: cell line

tag: cell type

value: 5 days


title: heart-44% fat+fiber-C57BL/6J-F (ORSAM7638)

value: 44% fat + fiber


title: 533_966738-35

tag: fastq total_reads

value: Placebo

tag: sts timepoint


title: RH4_Tumor_PFI90_5D_Mice920

value: Rhabdomyosarcoma

value: wt


title: heart-10% fat+fiber-C57BL/6J-F (ORSAM7637)

value: 10% fat + fiber


title: 529_963083-31

tag: percent aligned

tag: aligned counts_in_millions

value: PreChallenge


title: RH4_Tumor_DMSO_5D_Mice923

value: muscle

tag: genotype

value: DMSO


title: Dorsal Vagal Complex-10% fat+fiber-CAST/EiJ-F (ORSAM9507)

value: solitary tract nucleus and dorsal motor nucleus of vagus nerve

value: Female


title: 528_958686-35

value: PBMC

tag: age

value: Male

value: PostChallenge


title: 203723190040_R08C01:A00000FBK

value: Blood

tag: gender

value: male

tag: muscle-invasive

value: no


title: RH4_DMSO_24h_PAX3FOXO1

tag: antibody

value: PAX3-FOXO1 (in house)

tag: time

value: 24 hr


title: 203752100070_R04C01:A00000FC3

value: female


title: Dorsal Vagal Complex-44% fat+fiber-CAST/EiJ-F (ORSAM9506)

value: 44% fat + fiber

value: CAST/EiJ

tag: Sex

value: WT


title: 530_963083-35

tag: tissue

tag: median cv_coverage

tag: participant id

tag: visit number

value: Placebo


title: 206752720148_R05C01:BDB1P01044

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor


title: Dorsal Vagal Complex-44% fat+fiber-C57BL/6J-M (ORSAM9505)

tag: diet

tag: strain

tag: treatment


title: RH4_NegCtrl_A_CRISPRi_7D

value: muscle

tag: cell line

tag: cell type

value: Rhabdomyosarcoma

value: Control knockdown

value: 7 days

value: Neg Control CRISPRi


title: 525_966716-31

value: PBMC

value: Male

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

value: SCIT

tag: sts timepoint

value: PreChallenge


title: 526_966716-35

tag: age

value: PostChallenge


title: 206752720148_R04C01:BDB1P03058

description:
IlluminaHumanMethylationEPIC
Tumor

tag: gender

value: male

tag: muscle-invasive

value: no


title: Dorsal Vagal Complex-44% fat+fiber-CAST/EiJ-M (ORSAM9504)

value: solitary tract nucleus and dorsal motor nucleus of vagus nerve

value: 44% fat + fiber

tag: Sex

tag: genotype


title: RH4_KDM5A_A_CRISPRi_7D

tag: tissue

value: KDM5A knockdown

tag: time

value: KDM5A CRISPRi


title: 206752720148_R03C01:BDB1P02094

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor


title: 523_970858-35

tag: median cv_coverage

tag: participant id

tag: visit number


title: 206752720142_R07C01:A00000EGL

description:
IlluminaHumanMethylationEPIC
Tumor


title: 521_958673-35

tag: treatment


title: Dorsal Vagal Complex-44% fat+fiber-CAST/EiJ-F (ORSAM9500)

tag: diet

tag: strain

value: CAST/EiJ

value: Female

value: WT


title: Dorsal Vagal Complex-44% fat+fiber-CAST/EiJ-M (ORSAM9502)


title: RH4_KDM3B_KDM5A_CRISPRi_7D

value: muscle

tag: cell line

tag: cell type

value: Rhabdomyosarcoma

value: KDM3B KDM5A knockdown

value: 7 days

value: KDM3B KDM5A CRISPRi


title: 522_963089-35

value: PBMC

value: Male

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

value: SCIT


title: 206752720148_R02C01:BDB1P04022

description:
IlluminaHumanMethylationEPIC
Tumor

tag: gender

value: male

tag: age

value: no


title: RH4_KDM3B_KDM4B_CRISPRi_7D

value: KDM3B KDM4B knockdown

value: KDM3B KDM4B CRISPRi


title: Dorsal Vagal Complex-44% fat+fiber-CAST/EiJ-F (ORSAM9501)

value: solitary tract nucleus and dorsal motor nucleus of vagus nerve

value: 44% fat + fiber

tag: Sex


title: RH4_KDM3B_B_CRISPRi_7D

tag: genotype

value: KDM3B knockdown

value: KDM3B CRISPRi


title: 527_958686-31

tag: tissue

value: Placebo

tag: sts timepoint

value: PreChallenge


title: 206752720142_R06C01:BDB1P02031

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor

tag: muscle-invasive


title: 520_963089-31

tag: median cv_coverage

tag: participant id


title: RH4_Tumor_DMSO_5D_Mice913

value: muscle

value: Rhabdomyosarcoma

value: wt

tag: time

value: 5 days

tag: treatment

value: DMSO


title: RH4_KDM1A_KDM5A_CRISPRi_7D

value: KDM1A KDM5A knockdown

value: 7 days

value: KDM1A KDM5A CRISPRi


title: Dorsal Vagal Complex-44% fat+fiber-CAST/EiJ-M (ORSAM9503)

tag: diet

tag: strain

value: CAST/EiJ

value: Male

value: WT


title: 519_958673-31

value: PBMC

tag: visit number

value: SCIT


title: 206752720148_R01C01:BDB1P03023

description:
IlluminaHumanMethylationEPIC
Tumor

value: male

value: no


title: 524_970858-31

tag: fastq total_reads

value: PreChallenge


title: 206752720142_R04C01:BDB1P04015

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor


title: RH4_KDM1A_KDM3B_CRISPRi_7D

value: muscle

tag: cell line

tag: cell type

value: KDM1A KDM3B knockdown

value: KDM1A KDM3B CRISPRi


title: 206752720142_R03C01:BDB1P03010

description:
IlluminaHumanMethylationEPIC
Tumor

tag: gender


title: Dorsal Vagal Complex-44% fat+fiber-NZO/HlLtJ-M (ORSAM9497)

value: solitary tract nucleus and dorsal motor nucleus of vagus nerve

value: 44% fat + fiber

value: NZO/HlLtJ


title: Dorsal Vagal Complex-44% fat+fiber-NZO/HlLtJ-M (ORSAM9499)


title: 206752720142_R02C01:BDB1P04008

description:
IlluminaHumanMethylationEPIC
Tumor

tag: age


title: 206752720142_R01C01:BDB1P03083

description:
IlluminaHumanMethylationEPIC
Tumor


title: Dorsal Vagal Complex-44% fat+fiber-C57BL/6J-F (ORSAM9496)

tag: Sex

value: Female


title: 517_966705-31

tag: percent aligned

tag: aligned counts_in_millions


title: RH4_KDM1A_A_CRISPRi_7D

tag: tissue

value: Rhabdomyosarcoma

tag: genotype

value: KDM1A knockdown

value: 7 days

value: KDM1A CRISPRi


title: 516_970827-31

value: PBMC

value: Male

tag: median cv_coverage

tag: sts timepoint


title: Dorsal Vagal Complex-44% fat+fiber-C57BL/6J-M (ORSAM9495)

value: WT


title: 206752720136_R07C01:BDB1P01075

description:
IlluminaHumanMethylationEPIC
Tumor

value: female

tag: muscle-invasive

value: no


title: 206752720136_R06C01:BDB1P02029

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor

value: male


title: RH4_PFI90_lo_24h

value: muscle

value: wt

tag: time

value: 24 hr

tag: treatment

value: PFI-90 24 hr


title: Dorsal Vagal Complex-44% fat+fiber-C57BL/6J-M (ORSAM9494)

value: solitary tract nucleus and dorsal motor nucleus of vagus nerve

tag: diet

value: 44% fat + fiber

tag: strain


title: RH4_PFI90_lo_6h

value: Rhabdomyosarcoma

value: 6 hr

value: PFI-90 6 hr


title: Dorsal Vagal Complex-10% fat+fiber-C57BL/6J-M (ORSAM9493)

value: 10% fat + fiber


title: 206752720136_R05C01:BDB1P03034

description:
IlluminaHumanMethylationEPIC
Tumor


title: Dorsal Vagal Complex-44% fat+fiber-NZO/HlLtJ-M (ORSAM9498)

value: NZO/HlLtJ


title: 518_966705-35

value: PBMC

value: Male

tag: fastq total_reads

tag: participant id

tag: visit number

value: SCIT

value: PostChallenge


title: 513_963108-31

value: PreChallenge


title: Dorsal Vagal Complex-10% fat+fiber-CAST/EiJ-F (ORSAM9492)

value: CAST/EiJ

value: Female

value: WT


title: RH4_DMSO_1_24h

value: muscle

tag: cell line

tag: cell type

value: wt

value: 24 hr

value: DMSO 24 hr


title: 206752720136_R03C01:BDB1P03069

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor

tag: gender

value: male

tag: age

value: yes


title: 515_970827-35

tag: Sex

tag: percent aligned

tag: aligned counts_in_millions


title: RH4_shP3F_48

tag: tissue

value: Rhabdomyosarcoma

tag: genotype

value: 48 hr

value: PAX3-FOXO1 shRNA


title: RH4_scr_48

value: scrambled


title: 206752720136_R01C01:BDB1P04036

description:
IlluminaHumanMethylationEPIC
Tumor

tag: muscle-invasive

value: no


title: Dorsal Vagal Complex-44% fat+fiber-C57BL/6J-F (ORSAM9491)

value: solitary tract nucleus and dorsal motor nucleus of vagus nerve

value: 44% fat + fiber


title: 510_966715-35

value: PBMC

tag: median cv_coverage

value: SLIT

tag: sts timepoint

value: PostChallenge


title: 511_958498-35

value: Male

tag: treatment

value: SCIT


title: 512_958498-31

value: PreChallenge


title: 205045240164_R07C01:A00000FBG

description:
IlluminaHumanMethylationEPIC
Tumor

value: female


title: Dorsal Vagal Complex-10% fat+fiber-C57BL/6J-M (ORSAM9489)

tag: diet

value: 10% fat + fiber

tag: strain

value: WT


title: 205045240164_R08C01:BDB1P01050

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor


title: 509_966715-31

value: Female

tag: fastq total_reads

tag: participant id


title: 205045240164_R06C01:BDB1P03024

description:
IlluminaHumanMethylationEPIC
Tumor

value: male


title: 514_963108-35

tag: visit number


title: 508_970829-35


title: RH4_NP005584

value: muscle

tag: cell line

tag: cell type

value: Rhabdomyosarcoma

value: wt

tag: time

value: 24 hr


title: RH4_UPCMLD0ENAT5834780


title: RH4_KUC102648N


title: Dorsal Vagal Complex-10% fat+fiber-NZO/HlLtJ-F (ORSAM9488)

value: solitary tract nucleus and dorsal motor nucleus of vagus nerve

value: NZO/HlLtJ

tag: Sex


title: RH4_KUC100517N


title: 205045240164_R05C01:A00000EC4

description:
IlluminaHumanMethylationEPIC
Tumor

tag: gender

tag: age

value: no


title: 507_970829-31

tag: tissue

value: PBMC

tag: percent aligned

tag: aligned counts_in_millions

value: SLIT


title: Dorsal Vagal Complex-10% fat+fiber-NZO/HlLtJ-M (ORSAM9487)

value: Male

tag: genotype


title: 205045240164_R04C01:A00000EFX

description:
IlluminaHumanMethylationEPIC
Tumor

tag: muscle-invasive


title: Dorsal Vagal Complex-10% fat+fiber-C57BL/6J-M (ORSAM9486)

tag: treatment


title: RH4_IMMLG5770


title: Dorsal Vagal Complex-10% fat+fiber-C57BL/6J-F (ORSAM9485)

tag: diet


title: 205045240164_R03C01:A00000FBW

description:
IlluminaHumanMethylationEPIC
Tumor


title: 506_963034-31

tag: median cv_coverage

tag: sts timepoint

value: PreChallenge


title: RH4_78902794023


title: 205045240164_R02C01:A00000EFD

description:
IlluminaHumanMethylationEPIC
Tumor


title: RH4_DMSO

value: DMSO


title: 504_958682-31

tag: fastq total_reads

tag: participant id


title: RH4_78800610218

tag: cell line


title: 205045240164_R01C01:5286DS

description:
IlluminaHumanMethylationEPIC
Tumor

value: female


title: 502_966719-31

tag: visit number

value: Placebo


title: Dorsal Vagal Complex-10% fat+fiber-C57BL/6J-F (ORSAM9483)

value: 10% fat + fiber

tag: strain

value: WT


title: Dorsal Vagal Complex-10% fat+fiber-C57BL/6J-F (ORSAM9484)

tag: Sex

value: Female


title: Dorsal Vagal Complex-10% fat+fiber-CAST/EiJ-M (ORSAM9482)

value: CAST/EiJ


title: 73_S15

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

institute: Hospital del Mar Research Institute

data_processing:
Qiagen adapters were removed (allowing 1 mismatch) and UMI sequences were retained with UMI tools version 0.5.4 (extract module). Reads shorter than 15bp were removed with Cutadapt version 2.1.
Reads in the fastq files were mapped with STAR version 2.6.0 (A.Dobin et al. 2013) against miRBase v22.1. The table of counts was obtained with FeatureCounts function in the package subread, version 1.6.4 (Y.Liao, GK.Smyth, and W.Shi 2014) and posterior counting of unique UMIs with UMI tools version 0.5.4 (count, default method “directional”).
For the differential gene expression analysis (DEG) genes having less than 3 counts in at least 2 samples were excluded from the analysis. Read counts were converted to log2-counts-per-million (logCPM) and the mean-variance relationship was modelled with precision weights using voom approach in limma package using a linear model design adjusting for the sum of risk factors.
Assembly: miRBase v22.1
Supplementary files format and content: tab delimited file containing the table of raw counts

source_name: serum

extract_protocol:
miRNeasy Serum/Plasma kit (QIAGEN)
NGS smallRNA libraries were prepared according to the manual QIAseq miRNA Library Kit Handbook for Illumina (QIAGEN) (Version 1.0, 12/18)

value: serum

tag: condition

value: non-HIV

tag: extraction batch

tag: run


title: 205045240122_R08C01:BDB1P01062

description:
IlluminaHumanMethylationEPIC
Tumor

tag: tissue

value: Tumor

tag: gender

value: male

tag: age


title: 501_970842-35

tag: percent aligned

tag: aligned counts_in_millions

value: PostChallenge


title: RH4_DMSO_1_6h

value: muscle

tag: cell type

value: Rhabdomyosarcoma

tag: genotype

value: wt

tag: time

value: 6 hr

tag: treatment

value: DMSO 6 hr


title: 205045240122_R07C01:BDB1P02041

description:
IlluminaHumanMethylationEPIC
Tumor

tag: muscle-invasive

value: no


title: 205045240122_R06C01:A00000EDA

description:
IlluminaHumanMethylationEPIC
Tumor


title: 505_963034-35

value: PBMC

tag: fastq total_reads

tag: median cv_coverage

tag: participant id

value: SLIT

tag: sts timepoint


title: Dorsal Vagal Complex-44% fat+fiber-NZO/HlLtJ-F (ORSAM9479)

value: solitary tract nucleus and dorsal motor nucleus of vagus nerve

tag: diet

value: 44% fat + fiber

tag: strain

value: NZO/HlLtJ

tag: Sex


title: Dorsal Vagal Complex-44% fat+fiber-C57BL/6J-F (ORSAM9490)

tag: tissue

value: Female

value: WT


title: 72_S11

value: serum

tag: condition

value: non-HIV

value: female

tag: extraction batch

tag: run


title: 69_S13

value: HIV+ 48-w

value: male


title: 205045240122_R05C01:A00000FBP

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor

tag: gender

tag: age


title: 499_966719-35

value: Male

tag: percent aligned

tag: aligned counts_in_millions

tag: visit number

value: Placebo

value: PostChallenge


title: 205045240122_R04C01:BDB1P01018

description:
IlluminaHumanMethylationEPIC
Tumor

tag: muscle-invasive

value: no


title: 503_958682-35

value: PBMC

tag: fastq total_reads

tag: treatment


title: 500_970842-31

tag: median cv_coverage

tag: participant id

value: PreChallenge


title: Dorsal Vagal Complex-10% fat+fiber-CAST/EiJ-M (ORSAM9481)

value: solitary tract nucleus and dorsal motor nucleus of vagus nerve

tag: diet

value: 10% fat + fiber

value: CAST/EiJ

tag: genotype


title: Dorsal Vagal Complex-44% fat+fiber-NZO/HlLtJ-F (ORSAM9478)

value: 44% fat + fiber

tag: strain

value: NZO/HlLtJ

tag: Sex

value: Female


title: 205045240122_R02C01:BDB1P02001

description:
IlluminaHumanMethylationEPIC
Tumor

tag: tissue


title: 67_S5

value: serum

tag: condition

tag: extraction batch


title: 497_958493-35

tag: sts timepoint


title: Dorsal Vagal Complex-10% fat+fiber-NZO/HlLtJ-M (ORSAM9476)

value: WT


title: 66_S3

value: HIV+ 48-w

value: female

tag: run


title: Dorsal Vagal Complex-44% fat+fiber-NZO/HlLtJ-F (ORSAM9477)


title: Dorsal Vagal Complex-10% fat+fiber-NZO/HlLtJ-M (ORSAM9475)


title: 205045240122_R03C01:A00000EBV

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor

tag: gender

value: male

tag: age


title: 495_963103-31

value: Male

tag: percent aligned

tag: aligned counts_in_millions

tag: visit number

value: Placebo


title: 71_S6

value: non-HIV


title: 65_S9


title: 496_958493-31

value: PBMC

tag: fastq total_reads

tag: treatment


title: Dorsal Vagal Complex-10% fat+fiber-NZO/HlLtJ-F (ORSAM9474)


title: 64_S12


title: 493_970822-31

tag: median cv_coverage

tag: participant id

value: PreChallenge


title: 205045240119_R08C01:BDB1P04052

description:
IlluminaHumanMethylationEPIC
Tumor

tag: muscle-invasive

value: no


title: Dorsal Vagal Complex-10% fat+fiber-NZO/HlLtJ-F (ORSAM9473)

value: solitary tract nucleus and dorsal motor nucleus of vagus nerve

tag: diet

value: 10% fat + fiber

tag: strain

tag: genotype


title: 205045240119_R07C01:A00000EH3

description:
IlluminaHumanMethylationEPIC
Tumor

tag: tissue


title: adipose-10% fat+fiber-NZO/HlLtJ-M (ORSAM8894)

source_name: gonadal fat pad

value: gonadal fat pad

tag: Sex


title: 492_966682-31

tag: sts timepoint


title: 205045240119_R06C01:A00000FBE

description:
IlluminaHumanMethylationEPIC
Tumor

value: yes


title: 62_S3

tag: condition

tag: extraction batch

tag: run


title: 490_966682-35

tag: age

tag: percent aligned

value: PostChallenge


title: adipose-10% fat+fiber-NZO/HlLtJ-M (ORSAM8893)

value: NZO/HlLtJ


title: 61_S18

value: serum


title: 205045240119_R05C01:BDB1P04013

description:
IlluminaHumanMethylationEPIC
Tumor

tag: gender


title: 205045240119_R04C01:5385DS

description:
IlluminaHumanMethylationEPIC
Tumor


title: 491_958679-35

tag: fastq total_reads

tag: aligned counts_in_millions

tag: visit number


title: 205045240119_R03C01:BDB1P04035

description:
IlluminaHumanMethylationEPIC
Tumor


title: adipose-44% fat+fiber-NZO/HlLtJ-F (ORSAM8892)

value: 44% fat + fiber

value: Female

value: WT

tag: treatment


title: 489_963109-31

tag: median cv_coverage

tag: participant id


title: 59_S6

value: Naive-HIV

value: male


title: adipose-44% fat+fiber-NZO/HlLtJ-F (ORSAM8891)

tag: diet

tag: strain


title: 60_S14

tag: tissue


title: 488_963109-35

tag: Sex

value: Male

value: Placebo


title: 58_S4


title: adipose-44% fat+fiber-CAST/EiJ-M (ORSAM8890)

value: CAST/EiJ

tag: genotype


title: 205045240119_R02C01:A00000FC6

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor

tag: muscle-invasive


title: 63_S8

tag: condition

value: HIV+ 48-w

value: female

tag: extraction batch


title: 487_958679-31

value: PBMC

tag: age

tag: sts timepoint

value: PreChallenge


title: 205045240122_R01C01:BDB1P01016

description:
IlluminaHumanMethylationEPIC
Tumor

tag: gender

value: no


title: RH4_KDM4B_A_CRISPRi_7D

value: muscle

tag: cell line

tag: cell type

value: Rhabdomyosarcoma

value: KDM4B knockdown

tag: time

value: 7 days

value: KDM4B CRISPRi


title: adipose-10% fat+fiber-CAST/EiJ-M (ORSAM8889)

value: gonadal fat pad

value: 10% fat + fiber

value: WT

tag: treatment


title: 68_S1

value: serum

value: male

tag: run


title: 57_S8

value: Naive-HIV


title: 205045240119_R01C01:5668DS

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor


title: Dorsal Vagal Complex-10% fat+fiber-CAST/EiJ-M (ORSAM9480)

value: solitary tract nucleus and dorsal motor nucleus of vagus nerve

value: CAST/EiJ

value: Male


title: adipose-44% fat+fiber-CAST/EiJ-F (ORSAM8888)

value: 44% fat + fiber

value: Female


title: 485_970838-31

value: PBMC

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

tag: participant id

tag: visit number

value: SLIT

value: PreChallenge


title: 205045240113_R07C01:BDB1P01023

description:
IlluminaHumanMethylationEPIC
Tumor

tag: tissue

tag: muscle-invasive

value: no


title: adipose-10% fat+fiber-CAST/EiJ-F (ORSAM8887)

tag: diet

tag: strain

tag: Sex

tag: genotype


title: 205045240113_R08C01:BDB1P02067

description:
IlluminaHumanMethylationEPIC
Tumor

tag: gender

tag: age


title: 55_S7

tag: condition

value: female

tag: extraction batch


title: 480_959050-35

tag: treatment

tag: sts timepoint

value: PostChallenge


title: 54_S11

tag: run


title: 53_S2


title: 479_959050-31

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions


title: adipose-44% fat+fiber-C57BL/6J-M (ORSAM8885)

value: gonadal fat pad


title: adipose-10% fat+fiber-CAST/EiJ-F (ORSAM8886)

value: 10% fat + fiber

value: WT


title: 205045240113_R06C01:A00000FBN

description:
IlluminaHumanMethylationEPIC
Tumor


title: 205045240113_R05C01:A00000EBG

description:
IlluminaHumanMethylationEPIC
Tumor

value: male


title: 477_966647-35

tag: median cv_coverage

tag: participant id

tag: visit number

value: Placebo


title: adipose-44% fat+fiber-C57BL/6J-M (ORSAM8884)

tag: tissue

tag: diet


title: adipose-10% fat+fiber-C57BL/6J-M (ORSAM8883)

tag: strain

tag: Sex


title: 52_S19

value: serum

value: Naive-HIV


title: 205045240113_R04C01:A00000EDI

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor

tag: gender

tag: muscle-invasive

value: yes


title: 51_S9

tag: condition


title: 205045240113_R03C01:BDB1P01077

description:
IlluminaHumanMethylationEPIC
Tumor

tag: age


title: 474_958451-35

value: Male

tag: treatment


title: 50_S8

tag: extraction batch


title: 56_S11

tag: run


title: 472_970798-31

tag: fastq total_reads

tag: sts timepoint


title: 484_963094-31

value: Female

tag: percent aligned

tag: aligned counts_in_millions


title: 205045240113_R02C01:A00000ECO

description:
IlluminaHumanMethylationEPIC
Tumor


title: adipose-44% fat+fiber-C57BL/6J-F (ORSAM8881)

value: 44% fat + fiber

tag: genotype


title: adipose-10% fat+fiber-C57BL/6J-M (ORSAM8882)


title: adipose-10% fat+fiber-C57BL/6J-F (ORSAM8880)


title: 476_966647-31

value: PBMC

tag: median cv_coverage

tag: participant id

tag: visit number


title: 471_963111-35

tag: tissue


title: adipose-44% fat+fiber-NZO/HlLtJ-M (ORSAM8185)

tag: diet

tag: strain

value: NZO/HlLtJ

tag: Sex


title: 469_970843-35

value: SCIT


title: 205045240105_R06C01:A00000EDU

description:
IlluminaHumanMethylationEPIC
Tumor

tag: gender

tag: muscle-invasive

value: no


title: 46_S7

tag: condition

value: non-HIV


title: 468_966712-35

tag: age

tag: treatment

value: PostChallenge


title: 467_966712-31

tag: fastq total_reads

value: PreChallenge


title: 49_S4

value: female

tag: extraction batch

tag: run


title: 466_963116-35

tag: percent aligned

tag: aligned counts_in_millions

tag: sts timepoint


title: 44_S8

value: male


title: adipose-10% fat+fiber-NZO/HlLtJ-F (ORSAM8184)

value: gonadal fat pad

value: 10% fat + fiber

tag: genotype

value: WT


title: 205045240113_R01C01:BDB1P02007

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor


title: adipose-10% fat+fiber-NZO/HlLtJ-F (ORSAM8183)


title: 48_S9

value: serum

value: HIV+ 48-w


title: 43_S2


title: 205045240105_R04C01:A00000ECD

description:
IlluminaHumanMethylationEPIC
Tumor


title: 465_958508-35

value: Female

tag: median cv_coverage

tag: participant id

tag: visit number


title: 498_963103-35

tag: tissue

value: Male

value: Placebo


title: 205045240105_R08C01:BDB1P01039

description:
IlluminaHumanMethylationEPIC
Tumor


title: 205045240105_R03C01:A00000EF6

description:
IlluminaHumanMethylationEPIC
Tumor


title: adipose-10% fat+fiber-CAST/EiJ-M (ORSAM8182)

tag: diet

tag: strain

value: CAST/EiJ

tag: Sex


title: 47_S13

tag: condition


title: 42_S10


title: adipose-44% fat+fiber-CAST/EiJ-M (ORSAM8181)

value: 44% fat + fiber


title: 41_S7


title: adipose-44% fat+fiber-NZO/HlLtJ-M (ORSAM8186)

value: NZO/HlLtJ


title: 461_966689-35

value: PBMC

tag: age


title: 205045240105_R01C01:A00000EEA

description:
IlluminaHumanMethylationEPIC
Tumor

tag: gender

tag: muscle-invasive

value: no


title: adipose-44% fat+fiber-CAST/EiJ-M (ORSAM8180)

tag: treatment


title: 205045240105_R02C01:A00000ECV

description:
IlluminaHumanMethylationEPIC
Tumor

value: yes


title: adipose-10% fat+fiber-CAST/EiJ-F (ORSAM8179)


title: 40_S12

tag: extraction batch

tag: run


title: 458_958452-35

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

value: PostChallenge


title: 205045240103_R08C01:A00000EB1

description:
IlluminaHumanMethylationEPIC
Tumor

value: female


title: 205045240103_R07C01:BDB1P04063

description:
IlluminaHumanMethylationEPIC
Tumor


title: 38_S9

value: non-HIV

value: male


title: 205045240105_R07C01:A00000EEI

description:
IlluminaHumanMethylationEPIC
Tumor


title: 37_S5


title: 39_S10

value: Naive-HIV


title: 457_958452-31

tag: median cv_coverage

tag: sts timepoint

value: PreChallenge


title: 456_963044-31

tag: participant id

tag: visit number


title: 205045240103_R06C01:A00000FBF

description:
IlluminaHumanMethylationEPIC
Tumor

tag: tissue

value: Tumor


title: adipose-44% fat+fiber-CAST/EiJ-F (ORSAM8178)

value: gonadal fat pad

tag: diet

tag: strain

tag: genotype

value: WT


title: 462_966689-31

tag: age

tag: Sex

value: Female


title: 35_S15

value: serum

tag: condition


title: adipose-44% fat+fiber-C57BL/6J-M (ORSAM8175)

value: Male

tag: treatment


title: adipose-10% fat+fiber-C57BL/6J-M (ORSAM8176)

value: 10% fat + fiber


title: 34_S16

value: HIV+ 48-w

tag: extraction batch


title: 205045240103_R04C01:A00000ED3

description:
IlluminaHumanMethylationEPIC
Tumor

tag: gender

tag: muscle-invasive


title: 459_970861-35

value: PBMC

tag: fastq total_reads

tag: percent aligned

value: Placebo


title: 454_970862-35

tag: aligned counts_in_millions

tag: median cv_coverage

value: SLIT


title: 205045240103_R03C01:A00000EGI

description:
IlluminaHumanMethylationEPIC
Tumor

value: no


title: 33_S17

tag: run


title: adipose-10% fat+fiber-C57BL/6J-F (ORSAM8174)


title: 31_S1


title: 205045240103_R02C01:BDB1P02046

description:
IlluminaHumanMethylationEPIC
Tumor


title: 30_S7


title: adipose-44% fat+fiber-CAST/EiJ-F (ORSAM8177)

value: 44% fat + fiber

value: CAST/EiJ


title: adipose-44% fat+fiber-C57BL/6J-F (ORSAM8172)


title: 451_966723-35

tag: participant id

tag: visit number

tag: sts timepoint

value: PostChallenge


title: 205045240103_R01C01:BDB1P02005

description:
IlluminaHumanMethylationEPIC
Tumor

tag: tissue

value: male


title: 450_963098-35


title: 205045240055_R08C01:BDB1P04034

description:
IlluminaHumanMethylationEPIC
Tumor


title: adipose-44% fat+fiber-C57BL/6J-F (ORSAM8171)

tag: diet

tag: strain

tag: genotype


title: 205045240103_R05C01:5482DS

description:
IlluminaHumanMethylationEPIC
Tumor

tag: age


title: 27_S19

tag: condition

tag: Sex


title: 455_963044-35

tag: treatment


title: 449_963098-31

value: PreChallenge


title: 448_958490-35


title: 205045240055_R07C01:A00000EEC

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor

tag: gender

tag: muscle-invasive


title: adipose-44% fat+fiber-NZO/HlLtJ-M (ORSAM7763)

value: gonadal fat pad

value: NZO/HlLtJ


title: 26_S6

tag: extraction batch


title: 205045240055_R06C01:A00000ED0

description:
IlluminaHumanMethylationEPIC
Tumor

value: yes


title: adipose-10% fat+fiber-C57BL/6J-F (ORSAM8173)

value: Female

value: WT


title: 446_963107-31

value: Male

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

value: SCIT


title: 24_S2

value: serum

value: Naive-HIV

tag: run


title: adipose-10% fat+fiber-NZO/HlLtJ-M (ORSAM7761)

value: 10% fat + fiber


title: 452_966723-31

value: PBMC

tag: median cv_coverage

tag: participant id

tag: visit number

value: SLIT


title: adipose-10% fat+fiber-NZO/HlLtJ-M (ORSAM7762)

tag: tissue

tag: diet


title: adipose-44% fat+fiber-NZO/HlLtJ-F (ORSAM7760)

value: 44% fat + fiber

tag: strain

tag: genotype


title: 205045240055_R03C01:A00000EB0

description:
IlluminaHumanMethylationEPIC
Tumor

tag: age

value: no


title: 23_S4

tag: condition

value: HIV+ 48-w

tag: Sex

value: female


title: 205045240055_R04C01:A00000EAP

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor

tag: gender

value: male


title: 444_966704-31

tag: treatment

tag: sts timepoint

value: PreChallenge


title: 442_970863-35

tag: fastq total_reads

value: PostChallenge


title: 22_S14

tag: extraction batch


title: 29_S14

value: non-HIV


title: 447_958490-31

tag: percent aligned

tag: aligned counts_in_millions


title: 441_970863-31

tag: median cv_coverage


title: 25_S20

tag: run


title: 205045240055_R05C01:5542DS

description:
IlluminaHumanMethylationEPIC
Tumor

tag: muscle-invasive


title: 205045240055_R01C01:A00000EFY

description:
IlluminaHumanMethylationEPIC
Tumor

tag: tissue


title: adipose-44% fat+fiber-NZO/HlLtJ-M (ORSAM7764)

value: gonadal fat pad

tag: diet

value: NZO/HlLtJ

value: WT


title: adipose-10% fat+fiber-NZO/HlLtJ-F (ORSAM7758)

tag: strain

value: Female


title: adipose-10% fat+fiber-NZO/HlLtJ-F (ORSAM7757)

tag: genotype


title: 20_S2

value: serum


title: adipose-44% fat+fiber-NZO/HlLtJ-F (ORSAM7759)


title: 21_S5


title: 440_958462-31

tag: age

value: Male

tag: participant id

tag: visit number

value: SCIT


title: 439_963107-35

value: PBMC

tag: Sex


title: 205045240041_R08C01:5472DS

description:
IlluminaHumanMethylationEPIC
Tumor

tag: gender


title: adipose-44% fat+fiber-CAST/EiJ-M (ORSAM7756)

value: 44% fat + fiber

value: CAST/EiJ

tag: treatment


title: 19_S18

tag: condition

value: Naive-HIV


title: 205045240041_R06C01:A00000EBD

description:
IlluminaHumanMethylationEPIC
Tumor

value: no


title: 205045240055_R02C01:A00000EBC

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor


title: adipose-10% fat+fiber-CAST/EiJ-M (ORSAM7755)

value: 10% fat + fiber


title: 17_S3

value: female

tag: extraction batch


title: 437_958509-31

tag: fastq total_reads

tag: percent aligned

value: Placebo

tag: sts timepoint

value: PreChallenge


title: 18_S5

value: male

tag: run


title: 205045240041_R07C01:A00000EEJ

description:
IlluminaHumanMethylationEPIC
Tumor

tag: muscle-invasive


title: 438_970854-35

tag: tissue

tag: aligned counts_in_millions

tag: median cv_coverage

value: PostChallenge


title: adipose-44% fat+fiber-CAST/EiJ-F (ORSAM7754)

value: gonadal fat pad

tag: diet

tag: strain

tag: genotype

value: WT


title: 205045240041_R05C01:BDB1P01040

description:
IlluminaHumanMethylationEPIC
Tumor

tag: age


title: 16_S17

value: serum

tag: Sex


title: 435_970854-31

value: Male

tag: participant id

tag: visit number


title: 205045240041_R04C01:A00000EDV

description:
IlluminaHumanMethylationEPIC
Tumor

tag: gender


title: adipose-44% fat+fiber-C57BL/6J-M (ORSAM7752)

tag: treatment


title: 15_S15

tag: condition

tag: extraction batch


title: 205045240041_R03C01:5693DS

description:
IlluminaHumanMethylationEPIC
Tumor

value: yes


title: 434_963062-31

value: PBMC

tag: fastq total_reads

tag: percent aligned

tag: sts timepoint


title: 14_S1

tag: tissue

tag: run


title: adipose-44% fat+fiber-C57BL/6J-F (ORSAM7750)

value: 44% fat + fiber

value: Female


title: 433_966677-31

tag: aligned counts_in_millions

tag: median cv_coverage


title: adipose-10% fat+fiber-CAST/EiJ-F (ORSAM7753)

tag: diet

tag: strain

value: CAST/EiJ


title: 13_S4

value: Naive-HIV


title: 205045240041_R02C01:A00000FCA

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor

tag: age

tag: muscle-invasive

value: no


title: 205045240041_R01C01:A00000FBV

description:
IlluminaHumanMethylationEPIC
Tumor


title: adipose-10% fat+fiber-C57BL/6J-M (ORSAM7751)

value: 10% fat + fiber

tag: Sex

tag: genotype


title: 205038940165_R08C01:A00000FBY

description:
IlluminaHumanMethylationEPIC
Tumor

tag: gender

value: female


title: adipose-10% fat+fiber-C57BL/6J-F (ORSAM7749)

tag: treatment


title: 436_966677-35

tag: participant id

tag: visit number

value: Placebo


title: 205038940165_R07C01:A00000FBO

description:
IlluminaHumanMethylationEPIC
Tumor

value: male


title: YRG_SETDB1-sg2 tumor, control, aIFNAR-treated, HTO-derived cDNA

city: New Haven

first: Meaghan

last: McGeary

state: CT

address: 300 Cedar St.

department: Immunobiology

institute: Yale School of Medicine

description:
protein
5'- HTO library: Read 1 contains 10x barcode, UMI; Read 2 contains HTO barcode; I read contains Sample Index

library_source: transcriptomic single cell

data_processing:
Samples were preliminarily processed using the Cellranger software suite commands cellranger mkfastq to generate fastq files, and cellranger multi to both align gene expression reads to the mm10 reference genome, assemble V (D)J contigs, generate a filtered gene expression matrix and make clonotypes calls. Cellranger aggr was then used to generate a single dataset from all samples sequenced with no normalization.
Aggregated counts table was analyzed using the Seurat package for R (v. 4.3.0). Briefly, counts were read in as a Seurat object, and cells with less than 25 transcripts were filtered from the dataset. Expression values were log-normalized, variable genes detected, and values were scaled to number of UMIs. Principle component analysis was performed, and top 100 PCs were used to find nearest neighbors, perform clustering, and run dimensional reduction using the UMAP algorithm according to standard Seurat workflow.
Assembly: mm10
Supplementary files format and content: 10X Genomics output files: barcodes.tsv.gz; features.tsv.gz; matrix.mtx.gz
Supplementary files format and content: 10X VDJ Library output: filtered_contig_annotations.csv

source_name: subcutaneous tumor

growth_protocol: 2 x 106 cells were injected subcutaneously into the right hindlimb of 9 to 12-week-old male C57BL/6J mice (Jackson Laboratories). Tumors were harvested at day 10 post-injection.

extract_protocol:
dissociated on ice in digest buffer (RPMI + 2% FBS, 100U/ml collagenase (Sigma) + 1X DNAse I (Sigma)). Samples were filtered through a 70uM strainers, pelleted, and treated with ACK Buffer to lyse red blood cells. Single-cell suspensions were spun, pelleted, and stained with TotalSeqC Hashtag antibodies (BioLegend) by tumor ID then pooled by sample. Samples were stained with antibodies to CD45, CD3e, CD8, Fixable Live/Dead Aqua (Life Tech), and sorted using BD FACS Aria system by the Yale Flow Cytometry Core. Cells were pooled in the following groups/ratios using cell counts from the cytometer: CD45- (25%); CD45+ CD3- (25%); CD8+ (50%). 5000 cells per sample were loaded onto the 10X Chromium Library.
5000 cells per sample were loaded onto the 10X Chromium Library. Preparation was performed using 10x Genomics reagents according to the manufacturer’s instructions by the Yale Center for Genome Analysis (YCGA) and passed quality control. Libraries were sequenced using an Illumina NovaSeq at the YCGA.
scRNAseq: 5' GEX library was prepared by YCGA per manufacturer instructions using the 10X Genomics v2 Dual Index Chemistry for 5' Gene Expression, 5' VDJ sequencing and HTO sequencing.

treatment_protocol: For blockade experiments, mice were treated twice weekly with intraperitoneal injection of 200ug aIFNAR (MAR1-5A43; BioXcell) beginning at tumor engraftment and continuing twice weekly thorughout the experiment.

value: subcutaneous tumor

tag: cell line

tag: cell type

value: tumor cells

tag: host mouse_strain

value: aIFNAR

tag: antibodies/tags

value: 1:HTO TotalSeqC #5; 2:HTO TotalSeqC #6; 3:HTO TotalSeqC #8


title: 11_S19

tag: tissue

value: serum

tag: condition

value: non-HIV

tag: extraction batch

tag: run


title: 205038940165_R06C01:A00000EFA

description:
IlluminaHumanMethylationEPIC
Tumor


title: 8_S13


title: YRG_SETDB1-sg2 tumor, control, aIFNAR-treated, scTCR cDNA

description:
TCR RNA
5' VDJ library: Read 1 contains 10X Barcode, UMI; Read 2 contains Insert; Read 3 contains i5 sample index; I Read contains I7 sample index


title: 205038940165_R05C01:A00000ECL

description:
IlluminaHumanMethylationEPIC
Tumor


title: 432_963062-35

value: PBMC

value: Male

tag: fastq total_reads

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

tag: sts timepoint

value: PostChallenge


title: YRG_SETDB1-sg2 tumor, control, aIFNAR-treated, mRNA cDNA

description:
polyA RNA
5' mRNA library: Read 1 contains 10X Barcode, UMI; Read 2 contains Insert; Read 3 contains i5 sample index; I Read contains I7 sample index


title: YRG_SETDB1-sg1 tumor, control, aIFNAR-treated, HTO-derived cDNA


title: 205038940165_R04C01:A00000FBS

description:
IlluminaHumanMethylationEPIC
Tumor

tag: gender

tag: age

tag: muscle-invasive

value: yes


title: 428_970835-31

tag: Sex

tag: participant id

tag: visit number

tag: treatment

value: SLIT

value: PreChallenge


title: 426_963078-31


title: YRG_SETDB1-sg1 tumor, control, aIFNARtreated, mRNA cDNA

tag: cell line

tag: cell type

tag: host mouse_strain

tag: antibodies/tags


title: 427_970835-35

tag: tissue


title: 205038940165_R03C01:A00000EH7

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor

value: no


title: 424_963078-35

tag: fastq total_reads


title: 3_S10

tag: condition

value: female

tag: extraction batch

tag: run


title: 425_966740-35

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

tag: sts timepoint


title: 430_959048-35

tag: age

tag: Sex


title: 205038940165_R02C01:A00000FC3

description:
IlluminaHumanMethylationEPIC
Tumor

tag: gender

tag: muscle-invasive


title: 1_S18

value: Naive-HIV


title: 12_S20


title: 5_S12

value: HIV+ 48-w

value: male


title: YRG_SETDB1-sg1 tumor, control, a-IFNAR-treated, scTCR cDNA

value: subcutaneous tumor

tag: cell line

value: tumor cells

tag: treatment


title: 205038940165_R01C01:A00000FBK

description:
IlluminaHumanMethylationEPIC
Tumor


title: hypothalamus organoid

city: Seoul

first: Yanuar

middle: Alan

last: Sulistio

address: Wangsimni-ro 222

department: Biomedical Science

country: South Korea

institute: Hanyang University

data_processing:
Raw sequence was checked using FastQC v0.11.7
Demultiplexes raw base call (BCL) files generated by Illumina sequencers  into FASTQ files using bcl2fastq v2.20
Cellranger v5.0.0 used to performs alignment,  filtering, barcode counting, and UMI counting.
Assembly: GRCh38-2020-A
Supplementary files format and content: CellRanger output file of count matrix

source_name: h9 hESC

extract_protocol:
hypothalamus organoid dissociated using papain
Chromium Next GEM Single Cell 3p RNA library v3.1

value: h9 hESC

tag: cell type

value: hypothalamus organoid

value: Differentiation 70 days


title: 422_970852-31

value: PBMC

tag: participant id

tag: visit number


title: Mesangial-IM CHIP [CHIP4-MES-IM]

city: Waltham

first: Seyedramin

last: Pajoumshariati

state: MA

address: 35 Gatehouse Dr

institute: AstraZeneca

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hsa_GRCH38.94
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: ACBRI 127

growth_protocol: all cells after podocyte differentiation were maintained in the complete CSC medium with Rocket fuel-R supplemented with 0.5% fetal bovine serum (FBS) and antibiotics in  TGC and BGC chips in Zoe where flow applied on them in an incubator (humidified atmosphere with 5% CO2 at 37C)

extract_protocol:
Extraction protocol:TRIzol™ reagent; For RNA preparation from monocultures each cell type was lysed separately in lysis reagent (TRI Reagent, Sigma). For chip experiments GECs were extracted using TrypLE (TrypLE™, Gibco) and then lysed with TRI reagent. GMCs remained behind after this procedure and were isolated by injecting lysis reagent into the bottom channel and aspirating. For podocyte extraction, lysis reagent was injected into the top channel and aspirated. RNA extraction and RNA-seq analysis was performed by Lexogen (Lexogen, Vienna, Austria).B87
QuantSeq FWD 3’ library preparation kit following manufacturer's protocols.

treatment_protocol: three main groups are plate cultures (monocultures), TGCs (tri-culture), and BGCs (co-culture)

value: ACBRI 127

value: Primary human glomerular mesangial cells

tag: genotype

value: WT

value: cultured in IM chips

tag: time

value: Day 1


title: 423_959048-31

tag: tissue

value: Male

tag: fastq total_reads

value: SLIT

value: PreChallenge


title: YRG_SETDB1-sg2 tumor, control, untreated, HTO-derived cDNA

tag: host mouse_strain

tag: antibodies/tags

value: 1:HTO TotalSeqC #5; 2:HTO TotalSeqC #6; 3:HTO TotalSeqC #8


title: 2_S21

value: serum

tag: condition

value: HIV+ 48-w

tag: extraction batch

tag: run


title: 421_966730-35

tag: age

tag: Sex

tag: percent aligned

tag: aligned counts_in_millions

tag: median cv_coverage

tag: sts timepoint

value: PostChallenge


title: Mesangial-IM CHIP [CHIP3-MES-IM]

tag: cell line

tag: cell type

tag: treatment


title: 420_966730-31

tag: participant id

tag: visit number


title: YRG_SETDB1-sg2 tumor, control, untreated, mRNA cDNA

tag: tissue

value: subcutaneous tumor

value: tumor cells


title: YRG_SETDB1-sg1 tumor, control, untreated, HTO-derived cDNA

tag: host mouse_strain


title: 419_970852-35

tag: fastq total_reads


title: YRG_SETDB1-sg1 tumor, control, untreated, scTCR cDNA


title: Mesangial-IM CHIP [CHIP2-MES-IM]

tag: genotype

tag: time


title: 418_963091-35


title: Mesangial-IM CHIP [CHIP1-MES-IM]


title: YRG_SETDB1-sg2 tumor, control, untreated, scTCR cDNA


title: YRG_SETDB1-sg1 tumor, control, untreated, mRNA cDNA

tag: antibodies/tags


title: Mesangial-Plate [MESANGIAL 4-plate]

value: cultured on plates

value: Day 0


title: 416_963091-31

value: PBMC

tag: age


title: Mesangial-Plate [MESANGIAL 3-plate]

value: ACBRI 127


title: YRG tumor, control, untreated, HTO-derived cDNA


title: Mesangial-Plate [MESANGIAL 2-plate]

value: Primary human glomerular mesangial cells


title: YRG tumor, control, untreated, scTCR cDNA


title: 413_966692-31

tag: Sex

value: SCIT


title: YRG tumor, control, untreated, mRNA cDNA


title: Mesangial-Plate [MESANGIAL 1-plate]

value: WT


title: Mesangial-Triculture-nonStretched [12M-Triculture-non-stretched]

value: cultured in TGC

value: Day 12


title: 412_966692-35

value: Male

tag: percent aligned


title: Day 5 infection Tfh-2 [ATAC-seq]

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Sequencing adapters are removed with cutadpt with -m 35 -a  CTGTCTCTTATA -A CTGTCTCTTATACACATCTGACGCTGCCGACGA
Trimmed reads are mapped to mouse reference genome mm10 with bwa
Peaks are called with macs2
Assembly: mm10
Supplementary files format and content: narrowPeak file generated by macs2

source_name: Day 5 infection Tfh

growth_protocol: Sample groups: Group 1, infection-elicited non-Tfh cells, Group 2, infection-elicited Tfh cells, Group 3, immunization-elicited non-Tfh cells, Group 4, immunization-elicited Tfh cells

extract_protocol:
Briefly, the sorted cell pellets were washed and treated in lysis buffer for 3 min on ice.
The extracted nuclei were resuspended in transposition mix containing 2.5 μl Transposase (Illumina) and incubated at 37oC for 30 min. The products are purified with MinElute Reaction Cleanup Kit (Qiagen), and then amplified by PCR for 13 cycles with barcoded Nextera primers (Illumina)
DNA fragments in the range of 150-1,000 bp are recovered from 2% E-Gel EX Agarose Gels (Invitrogen/ThermoFisher Scientific)

treatment_protocol: The Tfh and non-Tfh cells are used for extracting genomic DNA to perform ATAC-seq, five to ten thousand cells for each replicate are used to prepare ATAC-seq libraries as previously described.

value: Primary

value: Tfh

value: Infection


title: 411_970810-31

tag: aligned counts_in_millions

value: PreChallenge


title: Day 5 infection Tfh-1 [ATAC-seq]


title: 410_970810-35

tag: median cv_coverage

value: PostChallenge


title: Mesangial-Triculture-nonStretched [11M-Triculture-non-stretched]


title: Day 5 immunization Tfh-2 [ATAC-seq]

source_name: Day 5 immunization Tfh

value: Immunization


title: 414_963075-31

tag: sts timepoint


title: 409_958504-35


title: Mesangial-Triculture-nonStretched [9M-Triculture-non-stretched]

tag: cell line


title: Mesangial-Triculture-nonStretched [10M-Triculture-non-stretched]

tag: cell type


title: Day 5 immunization Tfh-1 [ATAC-seq]

tag: treatment


title: 408_963075-35

tag: participant id


title: Day 5 infection non-Tfh-2 (Th1-2) [ATAC-seq]

source_name: Day 5 infection non-Tfh


title: IM-IM-chip [CHIP 4 IM-IM]

source_name: hiPSC (PGP1 (the Personal Genome Project)-derived intermediate mesoderm cells

value: hiPSC-derived intermediate mesoderm cells

value: cultured in IM chips

value: Day 1


title: 407_958504-31

value: PBMC

tag: visit number


title: Day 5 infection non-Tfh-1 (Th1-1) [ATAC-seq]


title: IM-IM-chip [CHIP 3 IM-IM]

value: hiPSC (PGP1 (the Personal Genome Project)-derived intermediate mesoderm cells


title: Day 5 immunization non-Tfh-2 (Th1-2) [ATAC-seq]

source_name: Day 5 immunization non-Tfh


title: Day 5 immunization non-Tfh-1 (Th1-1) [ATAC-seq]


title: 404_970812-35

source_name: PBMC

tag: tissue


title: 406_966702-35


title: 205045240105_R05C01:A00000EBR

description:
IlluminaHumanMethylationEPIC
Tumor

value: Tumor

tag: gender

value: male

tag: muscle-invasive

value: no


title: IM-IM-chip [CHIP 2 IM-IM]

tag: genotype

value: WT


title: 402_963106-31

tag: fastq total_reads

value: SCIT


title: 401_958468-31

value: Male


title: Mm_Cortex_RNA_A164_KD_rep3

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA

data_processing:
Reads are aligned and counted at gene level by STAR
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count at gene level for each Sample

source_name: Brain Cortex

growth_protocol: The mice were housed in HEPA-filtered rooms with controlled temperature (22-24°C) and humidity (40-60%).  The mice were maintained on 12 hour light and dark cycle and allowed free choice consumption of water throughout the study.  Following weaning, the mice were group housed (up to 4 mice per cage) and provided ad libitum access to a chow diet (TestDiet 5001; TestDiet, St. Louis, MO).  At six months of age, the mice were randomly assigned to diet groups (control or ketogenic diets) and singly housed for the duration of the study to allow accurate control of food intake.  The ketogenic diet contained (%kcal) <0.5% carbohydrates, 10% protein, and 90% fat and the control diet contained 74% carbohydrates, 10% protein, and 16% fat.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen), following manufacture's instructions.  300 ng of purified RNA was used for the generation of sequencing libraries.
Libraries were prepared using TruSeq Stranded Total RNA Library Prep Gold kit (Illumina, San Diego, CA, USA)

treatment_protocol: mice were euthanized by exsanguination under isoflurane anesthesia and tissues were collected for gene expression measurements. Tissues were snap frozen in liquid nitrogen.

value: Brain Cortex

tag: diet

value: KD


title: IM-Plate [IM4-plate]

value: cultured on plates

tag: time

value: Day 0


title: IM-Plate [IM3-plate]


title: Mm_Cortex_RNA_A76_KD_rep2


title: Mm_Cortex_RNA_A196_KD_rep1


title: IM-Plate [IM2-plate]


title: 394_958681-31

tag: age

tag: Sex

value: SLIT

value: PreChallenge


title: Mm_Cortex_RNA_A96_SD_rep4

value: SD


title: 397_966742-35

tag: percent aligned

tag: aligned counts_in_millions

value: PostChallenge


title: Podocyte-Plate [PODO4-plate]

source_name: hiPSC (PGP1 (the Personal Genome Project)-derived podocytes

value: hiPSC-derived podocytes


title: Mm_Cortex_RNA_A212_SD_rep2


title: 392_963053-35

value: PBMC

tag: median cv_coverage

tag: sts timepoint


title: IM-IM-chip [CHIP 1 IM-IM]

tag: cell line

value: hiPSC (PGP1 (the Personal Genome Project)-derived intermediate mesoderm cells

tag: cell type

value: hiPSC-derived intermediate mesoderm cells

value: cultured in IM chips

value: Day 1


title: Podocyte-Plate [PODO3-plate]

value: hiPSC (PGP1 (the Personal Genome Project)-derived podocytes

value: WT

tag: treatment


title: 393_963053-31

value: Male

tag: participant id

tag: visit number


title: Mm_Cortex_RNA_A70_SD_rep3

tag: tissue

value: Brain Cortex


title: IM-Plate [IM1-plate]


title: 391_958681-35


title: bisulfite treated genomic DNA from MDA-MB-231 cells treated twice with paclitaxel [MDA_PAC2_Rep2]

first: Min Kyung

last: Lee

state: NH

address: 1 Medical Center Dr

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

data_processing: SeSAMe bioconductor R package

label: Cy3, Cy5

source_name: MDA-MB-231 cells

label_protocol: standard Illumina Protocol

extract_protocol: genomic DNA was extracted using QIAamp DNA Kits, Cat #51304, according to standard instructions

treatment_protocol: Stock solutions for eribulin (10 mM) were prepared using double distilled water,  and paclitaxel was prepared using DMSO, further diluted in the base diluent to the  appropriate concentrations. The half-maximal inhibitory concentration (IC50) was  determined at different concentrations from 0.5nM to 100nM using a 2-fold dilution series for MDA-MB-231 cells.

value: epithelial, human breast cancer cell line

value: paclitaxel treated cells


title: Mm_Cortex_RNA_A207_SD_rep1


title: E. faecalis infected wound from dorsal skin replicate 2

city: Singapore

first: Guillaume

last: Thibault

address: 60 Nanyang Dr

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were conducted using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)  with cellranger count command
Assembly: mm10-2020-A (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/6.1)
Supplementary files format and content: Tab-separated values for features and barcodes and mtx files for count matrices

source_name: Dorsal skin

growth_protocol: 5-6 week old, male C57BL/6 mice purchased from InVivos (Singapore) and fed on standard diet throughout the experiment.

extract_protocol:
6-mm biopsy punch was used to isolate the wounds that were washed with 0.5% BSA/HBSS on ice. Any underlying fat tissue were removed and the tissues were cut into smaller pieces using scissors and blades. The minced tissue were incubated in Dispase/Liberase/Collagenase I cocktail at 37°C for two hours, followed by smashing with a piston. Partly digested tissue was sifted through a 70µm cell strainer, and rinsed three times with 0.5% BSA/HBSS. The flow-through was kept on ice. Undigested remaining tissue in the cell strainer was incubated in 0.05% trypsin/EDTA/HBSS for 15 minutes at 37°C. The trypsin-digested tissue was smashed once more, and sifted through a 70µm cell strainer. The flow-throughs from both incubations were pooled per sample and filtered through a 40µm cell strainer. Cell suspensions were centrifuged 300 xg for 10 min at 4°C twice, where the supernatant from each run were carefully discarded and the pellets were resuspended in 500µL of 0.04% BSA/PBS. Cell viability was determined by mixing 10µL of cell suspension with 10µL of trypan blue, and at least four separate counts were averaged for one sample. Cell concentrations were adjusted to 1200 cells/µl with 0.04% BSA/PBS. A more detailed protocol can be found at dx.doi.org/10.17504/protocols.io.yxmvmn8m9g3p/v1.
Library was performed according to the manufacture’s instructions (10X Genomics, Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 Protocol [CG000315]). Briefly, cells isolated from the infected and uninfected skin wounds were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was transcribed to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: For the infection condition, 2 x 10^9 bacteria/µl grown statically at 37°C for 16h were inoculated on the wounds of the mice.

value: mixed

value: Dorsal skin

tag: tissue subtype

value: E. faecalis infected wound

tag: strain

value: 5-6 weeks old


title: Podocyte-Plate [PODO2-plate]

tag: genotype

value: cultured on plates

value: Day 0


title: 390_966699-35

value: PBMC

tag: fastq total_reads

value: SLIT

value: PostChallenge


title: Podocyte-Plate [PODO1-plate]

value: hiPSC-derived podocytes

tag: time


title: bisulfite treated genomic DNA from MDA-MB-231 cells treated twice with eribulin [MDA_ERI2_Rep1]

value: eribulin treated cells


title: 389_966699-31

tag: age

value: PreChallenge


title: E. faecalis infected wound from dorsal skin replicate 1

description: 10x Genomics


title: bisulfite treated genomic DNA from MDA-MB-231 cells treated once with paclitaxel [MDA_PAC1_Rep1]


title: 387_970834-35

tag: Sex


title: Podocyte-Biculture-nonStretched [24P-Biculture-non-stretched]

value: hiPSC (PGP1 (the Personal Genome Project)-derived podocytes

value: WT

value: cultured in BGC

value: Day 12


title: Podocyte-Biculture-nonStretched [23P-Biculture-non-stretched]


title: bisulfite treated genomic DNA from MDA-MB-231 cells untreated [MDA_P_Rep1]

value: epithelial, human breast cancer cell line

value: untreated cells


title: 386_963102-35

value: Male

tag: percent aligned


title: bisulfite treated genomic DNA from MDA-MB-231 cells treated twice with eribulin [MDA_ERI2_Rep2]


title: bisulfite treated genomic DNA from MDA-MB-231 cells untreated [MDA_P_Rep3]


title: Podocyte-Biculture-nonStretched [22P-Biculture-non-stretched]


title: bisulfite treated genomic DNA from MDA-MB-231 cells treated twice with paclitaxel [MDA_PAC2_Rep1]

value: paclitaxel treated cells


title: Uninfected wound from dorsal skin replicate 1

description: 10x Genomics

value: mixed

value: Dorsal skin

value: Uninfected wound

value: 5-6 weeks old


title: bisulfite treated genomic DNA from MDA-MB-231 cells treated once with eribulin [MDA_ERI1_Rep1]


title: Genomic DNA from VCaP-CR

first: Brian

last: Hanratty

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

hyb_protocol: Illumina Infinium MethylationEPIC standard protocol

data_processing: Methylation data were analyzed from the Illumina Human MethylationEPIC microarray platform using the minfi package in R. Samples were normalized using the subset-quantile within array normalization (SWAN) method. Probes with a detection p value of >0.01 in 50% or more of samples and probes that contained a SNP at the CpG interrogation site or at the single nucleotide extension were removed. Probes were annotated using the lluminaHumanMethylationEPICanno.ilm10b2.hg19 package.

source_name: Cell line

growth_protocol: PDX lines were grown as described in PMID: 28156002. Cell lines were grown under standard growth media conditions

extract_protocol: Qiagen Dneasy, Bisulfite conversion with DNA Methylation Kit (Zymo Research)

treatment_protocol: No specific treatment

value: Cell line


title: bisulfite treated genomic DNA from MDA-MB-231 cells treated once with paclitaxel [MDA_PAC1_Rep2]


title: Genomic DNA from RWPE

scan_protocol: Illumina Infinium MethylationEPIC standard protocol


title: Podocyte-Biculture-nonStretched [21P-Biculture-non-stretched]


title: bisulfite treated genomic DNA from MDA-MB-231 cells untreated [MDA_P_Rep2]


title: Podocyte-Triculture-nonStretched [12P-Triculture-non-stretched]

value: cultured in TGC


title: Genomic DNA from VCaP

label_protocol: Illumina Infinium MethylationEPIC standard protocol


title: 384_963102-31

value: PBMC

tag: aligned counts_in_millions

value: SLIT


title: KD, replicate 1, snRNAseq

city: Portland

first: Xiao-Tong

last: Su

state: OR

address: 3181 SW Sam Jackson Park Road, LBRB 540, L334

institute: Oregon Health and Science University

description:
10x Genomics
ALL_DCT.rds

data_processing:
Fastq files were prepared using bcl2fastq (Illumina) and then aligned to a reference genome using Cellranger v. 6.1.2 (10x Genomics). Reads were mapped to both exonic and intronic regions to include the pre-mRNA transcriptome.
Ambient RNA contamination was estimated and removed using SoupX v. 1.6.1
Cells with cleaned-up reads were then subjected to doublet removal using DoubletFinder v. 2.0
Mitochondrial features were manually removed by excluding all features starting with mt-
The normalized count matrix integration, batch effect correctiong, and cell clustering were performed using Seurat v. 4.2.0
Assembly: mm10
Supplementary files format and content: Raw and filtered feature-barcode matrices from each replicate
Supplementary files format and content: Integrated seurat objects containing multiple replicates

source_name: Kidney

extract_protocol:
Kidney cortex was dissected out after PBS washout via aortic perfusion and snap-frozen in liquid nitrogen immediately after dissection. Frozen tissue was stored at -80 °C until subsequent tissue processing. Prepare the nuclei isolation buffer (NIB, includes 146 mM NaCl, 10 mM Tris-HCl, 1 mM CaCl2, 21 mM MgCl2, 0.03% Tween-20, 0.01% BSA, pH 7.5), and add 1 tablet of cOmplete ULTRA per 10 ml NIB. The samples were ground for 30 times in 2ml NIB1 (4mL NIB + 20µl RNasin Plus + 20µl SUPERaseIN) with a 2ml Dounce grinder and a loose pestle, then homogenate was passed through a 200 µm strainer. The homogenate was ground for 15 times with a tight pestle, then 2 ml NIB1 was added and the homogenate was incubated for 5 min on ice. The homogenate was passed through a 40 µm strainer, then centrifuged at 500g for 5 min at 4°C. The pellet was resuspended in 4 ml NIB2 (4mL NIB + 4µl RNasin Plus + 4µl SUPERaseIN) and the suspension was incubated on ice for 5 min, then centrifuged at 500g for 5 min at 4°C. The pellet was resuspended in 1.5 ml of nuclei resuspension buffer (NSB, 10mL DPBS + 10µl RNasin Plus), then centrifuged at 500g for 5 min at 4°C. Repeat this step, then the suspension was passed through a 5 µm strainer. The suspension was centrifuged at 500g for 5 min at 4°C, and the pellet was resuspended in 10 ml NSB. The nuclei suspension was mixed with 5µl Vybrant Ruby stain and incubated on ice for 15 min. The nuclei were sorted in 500 µl final resuspension buffer (FSB, 1ml DPBS with 1% BSA + 5 µl Protector RNase inhibitor) with a low flow rate and pressure to ensure high viability. Two main gates were used. A 561+683 emission for the ruby stain and a 488 530/40 emission for GFP. Low trigger pulse width was used as singlet discriminator. One hundred thousand nuclei were collected and centrifuged at 500g for 5 min at 4°C. The top supernatant was carefully removed, and 50 µl volume was left to resuspend the nuclei pellet.
Single nucleus RNA-seq was performed using a Chromium Next GEM Single Cell 3′ Reagent Kit v3.1 (10x Genomics). Single nuclei were partitioned in droplets with single Gel Beads, which contained primers with cell-tagging indexes. Single nucleus suspensions with concentration of at least 300/µl were loaded targeting 10,000 nuclei per sample. The resulting cDNA was profiled on a Bioanalyzer NanoChip (Agilent), then used as a template for library preparation according to the reagent kit protocol. ( https://www.10xgenomics.com/support/single-cell-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry )

value: Female

value: NCC-Cre-INTACT

value: Kidney

value: Distal convoluted tubule nuclei

value: Control potassium diet

value: 23 wks


title: Podocyte-Triculture-nonStretched [11P-Triculture-non-stretched]

value: hiPSC (PGP1 (the Personal Genome Project)-derived podocytes

value: hiPSC-derived podocytes

value: WT

value: Day 12


title: bisulfite treated genomic DNA from MDA-MB-231 cells treated once with eribulin [MDA_ERI1_Rep2]

value: epithelial, human breast cancer cell line

value: eribulin treated cells


title: 383_958675-31

value: Male

tag: median cv_coverage

value: PreChallenge


title: 385_958675-35

tag: sts timepoint

value: PostChallenge


title: 382_966687-31

value: PBMC


title: Genomic DNA from SkCaP-1

source_name: Patient-derived xenograft

value: Patient-derived xenograft


title: NK, replicate 3, snRNAseq

description:
10x Genomics
CONTROL_DCT.rds
CONTROL_DCT1.rds
CONTROL_DCT2.rds
ALL_DCT.rds

value: Female

value: 12 wks


title: Genomic DNA from PC-82


title: Uninfected wound from dorsal skin replicate 2

description: 10x Genomics

value: mixed

value: Dorsal skin

value: Uninfected wound

value: 5-6 weeks old


title: KD, replicate 2, snRNAseq

description:
10x Genomics
ALL_DCT.rds

value: NCC-Cre-INTACT

value: Kidney

value: Distal convoluted tubule nuclei

value: Control potassium diet

value: 14 wks


title: Podocyte-Triculture-nonStretched [9P-Triculture-non-stretched]

tag: cell line

value: hiPSC (PGP1 (the Personal Genome Project)-derived podocytes

value: hiPSC-derived podocytes

value: WT

value: cultured in TGC

value: Day 12


title: NK, replicate 2, snRNAseq

tag: cell type


title: Genomic DNA from PLNCaP-1

value: Patient-derived xenograft


title: Genomic DNA from PREC

value: Cell line


title: Genomic DNA from PC3


title: Genomic DNA from LvCaP-1


title: C57 mouse lung tissue miRNA, Experimental group 3

city: jiangxi

first: wei

last: deng

state: China

address: 17 Yongwai Zhengjie, Donghu District, Nanchang City, Jiangxi Province, China

country: China

institute: Department of Critical Care Medicine, First Affiliated Hospital of Nanchang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The miRNA's expressions were normalized corrected according to  UMI counts and normalized to transcript per millioncounts per million (TPM)
Assembly: ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
Exosomes from three sham group and three CLP groups were used to perform RNA sequencing. MiRNeasy Serum/Plasma Advanced Kit (Qiagen, cat. No. 217204) was used for the extraction and purification of total RNA from lung tissue exosomes according to the instructions of the kit.
For the small RNA libraries, the total RNA amount of each sample is 3ng, which is used as the input material for RNA sample preparation. According to the manufacturer's recommendations, the QIAseq miRNA library kit (Qiagen, Frederick, MD) was used to generate the sequencing library, and add the index codes to the attribute sequences of each sample. Reverse transcription (RT) primers with unique molecular index (UMI) were introduced to analyze the quantification of miRNA expression during cDNA synthesis and PCR amplification


title: Genomic DNA from LvCaP-2


title: Endothelial-IM CHIP [CHIP 4 ENDO-IM]

source_name: ACBRI 128

value: ACBRI 128

value: Primary human glomerular microvascular endothelial cells

tag: treatment

value: cultured in IM chips

value: Day 1


title: Endothelial-IM CHIP [CHIP 2 ENDO-IM]


title: Genomic DNA from LvCaP-3


title: 376_970868-35

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina).
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3’ end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0)
FastqMcf (v1.1.2) was used to remove any remaining adapter sequence.
Reads were aligned by STAR v2.4.2a to GRCh38
Gene counts were generated using HTSeq-count (v0.4.1). Quality metrics were compiled from PICARD (v1.134, http://broadinstitute.github.io/picard/), FASTQC (v0.11.3, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), Samtools (v1.2), and HTSeq-count (v0.4.1).
Assembly: GRCh38
Supplementary files format and content: raw_counts_ITN_GRASS_PBMC_samples.csv is a csv file. The first column contains Ensembl gene IDs The remaining columns include raw read counts assigned for each library.

extract_protocol:
RNA was extracted from TRIzol following the manufacturer’s protocol (Invitrogen)
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.

value: PBMC

value: Male

tag: participant id

value: SCIT

value: PostChallenge


title: Endothelial-IM CHIP [CHIP 1 ENDO-IM]


title: C57 mouse lung tissue miRNA, Experimental group 2


title: Genomic DNA from LNCaP95


title: C57 mouse lung tissue miRNA, Experimental group 1


title: Endothelial-IM CHIP [CHIP 3 ENDO-IM]


title: 377_963038-31

tag: visit number

value: SLIT

value: PreChallenge


title: 375_970868-31

tag: tissue


title: 381_966687-35


title: C57 mouse lung tissue miRNA, Control 3


title: KD, replicate 3, snRNAseq

description:
10x Genomics
ALL_DCT.rds

value: Female

value: NCC-Cre-INTACT

value: Kidney

value: Distal convoluted tubule nuclei

value: Control potassium diet

value: 13 wks


title: NK, replicate 1, snRNAseq

value: 23 wks


title: Podocyte-Triculture-nonStretched [10P-Triculture-non-stretched]

value: hiPSC (PGP1 (the Personal Genome Project)-derived podocytes

value: hiPSC-derived podocytes

value: WT

value: cultured in TGC

value: Day 12


title: Endothelial-Plate [GLOM ENDO 4-plate]

value: ACBRI 128

value: Primary human glomerular microvascular endothelial cells

value: cultured on plates

value: Day 0


title: C57 mouse lung tissue miRNA, Control 2


title: Genomic DNA from LNCaP-abl

value: Cell line


title: Endothelial-Plate [GLOM ENDO 3-plate]


title: C57 mouse lung tissue miRNA, Control 1


title: 374_958466-35

value: PBMC

value: Male

value: SCIT

value: PostChallenge


title: 373_966670-35


title: Endothelial-Plate [GLOM ENDO 2-plate]


title: Genomic DNA from LvCaP-2R


title: Genomic DNA from LgCaP-1


title: C57 mouse lung tissue, Experimental group 2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The expression of  mRNA and lncRNA were normalized to FPKM
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Lung tissue

extract_protocol:
Exosomes from three sham group and three CLP groups were used to perform RNA sequencing. MiRNeasy Serum/Plasma Advanced Kit (Qiagen, cat. No. 217204) was used for the extraction and purification of total RNA from lung tissue exosomes according to the instructions of the kit.
According to the manufacturer's recommendations, SMARTer Stranded total RNA-Seq Kit V2 (Takara Bio USA, Inc.) was used for the construction of sequencing library with 4.5 ng RNA of each sample as the input material, and the index codes was then add to the attribute sequences of each sample.

value: Lung tissue


title: C57 mouse lung tissue, Experimental group 3


title: 371_966670-31

value: PreChallenge


title: 370_963049-35


title: C57 mouse lung tissue, Experimental group 1


title: 369_958466-31


title: Endothelial-Plate [GLOM ENDO 1-plate]


title: Endothelial-Biculture-non-stretched [24E-Biculture-non-stretched]

value: cultured in BGC


title: Genomic DNA from LAPC4-CR


title: Genomic DNA from DU145


title: Endothelial-Biculture-non-stretched [22E-Biculture-non-stretched]


title: 367_966720-31

value: Female


title: C57 mouse lung tissue, Control 2


title: Genomic DNA from LAPC4


title: C57 mouse lung tissue, Control 1


title: Endothelial-Triculture-Non stretched [12E-Triculture-non-stretched]


title: Genomic DNA from H660


title: Genomic DNA from C42B


title: 380_957431-31

value: SLIT


title: 365_970873-35


title: Endothelial-Triculture-Non stretched [11E-Triculture-non-stretched]

value: WT