title: NONO△ER replicate 3, scRNAseq

city: Nanjing

first: Yan

last: Yitong

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

institute: Nanjing Medical University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Testis

growth_protocol: collect adult NONO and NONO△ER mice testis,

extract_protocol:
NONO and NONO△ER mice testis were collected and separated into single cell mixture by enzyme digestion and analyzed using scRNAseq.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

treatment_protocol:
None
None

value: Testicular Cells

value: Testis

tag: strain

value: Adult

value: NONO deltaER


title: NONO△ER replicate 2, scRNAseq

status: Public on Aug 08 2024

type: SRA

country: China

description: 10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: tissue

tag: age

tag: genotype


title: NONO△ER replicate 1, scRNAseq

description: 10x Genomics


title: ICS [S18110500013]

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

country: United Kingdom

institute: University of  Oxford

library_source: transcriptomic

data_processing:
Sequences in fastq files (in single and pair ends) were aligned using STAR aligner (version 2.7.1a)
; R package (17)Rsubread was employed for quantification of reads assigned to genes
Assembly: GRCh38
Supplementary files format and content: Raw_counts_B_BR_Pl.txt
Supplementary files format and content: Normalized_counts_B_BR_Pl.txt

organism: Homo sapiens

source_name: BRUSHING

extract_protocol:
Total RNA was extracted from subjects biopsies and brushing using RNeasy mini kits (Qiagen).
TruSeq library preparation kits were used for RNA samples. Starting with total RNA, the messenger RNA was first purified using polyA.

treatment_protocol: Randomised open-label bronchoscopy study of high dose ICS therapy in 30 healthy adult volunteers randomised 2:1 to i) fluticasone propionate 500 mcg bd or ii) no treatment, for 4 weeks. Laboratory staff were blinded to allocation. Biopsies and brushings were analysed by bulk RNA sequencing.

value: BRUSHING

tag: treatment


title: LAP2alpha knockout myoblasts, proliferating, Input 1

city: Vienna

first: Roland

last: Foisner

address: Dr.-Bohr-Gasse 9

department: Center for Medical Biochemistry

country: Austria

institute: Max Perutz Labs, Medical University of Vienna

library_source: genomic

data_processing:
Raw sequencing reads in bam format were converted into fastq using bamtofastq from bedtools
Qualities of the reads were evaluated using FastQC
Reads were mapped to the reference genome using NextGenMap with default settings
EDD was used to generate the log2ratio files for Lamin AC and LAP2alpha samples
bamCoverage from deepTools was used to generate the histone mark coverage files with the RPKM normalization method
Assembly: Mus musculusgenome assembly GRCm38 (mm10)
Supplementary files format and content: Lamin AC (LAC_3A6 and LAC_E1) and LAP2alpha (LAP2a) processed files contain log2ratios calculated by normalizing CHIP signals to INPUT signals
Supplementary files format and content: Processed files of all input (Input1,2,3) and histone mark samples (H3K27ac and H3K4me3) contain RPKM normalized coverage signals

molecule: genomic DNA

source_name: immortalized myoblasts

growth_protocol: Ham's F10 nutrient mix with 20% fetal calf serum, 100 U/ml penicillin and 100 μg/ml streptomycin; cells were cultured at 37°C and 5%CO2

extract_protocol:
Cells were fixed in 1% formaldehyde, followed by formaldehyde quenching, washing and cell lysis. Lysed cells were sonicated using the Bioruptor PICO sonicator (Diagenode).
Libraries were prepared by the Next Generation Sequencing facility at the Vienna Biocenter Core Facilities, Vienna, Austria, using the NEBNext® UltraTM II DNA Library Prep Kit for Illumina and unique NEB adaptors. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: To induce differentiation, cells were grown to confluence and switched to 5% fetal calf serum for 48 hours (day 2 of differentiation)

value: immortalized myoblasts

value: LAP2alpha knockout; p53 knockout

value: proliferating

tag: chip antibody

value: no antibody - Input


title: wildtype myoblasts, differentiating (D2), Input 1

value: LAP2alpha wildtype; p53 knockout

value: Day 2 of differentiation


title: Sarcoidosis (Progressive) 20 [miRNA-seq]

city: Aurora

first: Ivana

last: Yang

state: CO

country: USA

institute: University of Colorado - Anschutz Medical Campus

data_processing:
forward read of FASTQ files were aligned to sequences from miRBase v22.1 using miR-MaGiC
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

source_name: bronchoalveolar lavage cells

growth_protocol: Cells were stored in RLT buffer at –80°C

extract_protocol:
DNA and RNA were extracted using the Qiagen AllPrep DNA/RNA extraction mini kit.
miRNA libraries were constructed using Lexogen Small RNA-Seq library preparation kits

value: bronchoalveolar lavage cells

tag: diagnosis

value: sarcoidosis (progressive)

tag: Sex

value: male

tag: race

value: white

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

value: never

tag: scadding stage

tag: acute disease

value: n

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

value: y

tag: pc1 (mirna)

tag: pc2 (mirna)

tag: pc3 (mirna)

tag: pc4 (mirna)

tag: pc5 (mirna)


title: Sarcoidosis (Progressive) 21 [miRNA-seq]

tag: tissue

tag: diagnosis

tag: age

value: female


title: Sarcoidosis (Progressive) 3 [miRNA-seq]

tag: Sex

tag: race

value: black

tag: ethnicity

value: former


title: Sarcoidosis (Progressive) 2 [miRNA-seq]

tag: smoking status

tag: scadding stage

tag: acute disease


title: ICS [S18110500012]

value: BRUSHING

tag: treatment


title: NONO replicate 3, scRNAseq

description: 10x Genomics

tag: cell type

value: Testicular Cells

value: Testis

tag: strain

value: Adult

tag: genotype

value: NONO


title: ICS [S18110500011]


title: wildtype myoblasts, proliferating, Input 1

value: immortalized myoblasts

value: LAP2alpha wildtype; p53 knockout

value: proliferating

tag: chip antibody

value: no antibody - Input


title: LAP2alpha knockout myoblasts, differentiating (D2), lamin AC 3A6 ChIP, rep 1

description: linked to Input 1

value: LAP2alpha knockout; p53 knockout

value: Day 2 of differentiation

value: lamin A/C antibody 3A6 (PMID:26798136)


title: Sarcoidosis (Progressive) 18 [miRNA-seq]

value: bronchoalveolar lavage cells

value: sarcoidosis (progressive)

value: white

value: not Hispanic or Latino

value: never

value: n

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)

tag: pc2 (mirna)

tag: pc3 (mirna)


title: eTreg floxed control 5

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

data_processing:
Quality of sequencing data was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were trimmed for adapters and low quality base calls using Trim Galore, with default parameters (v0.6.5; https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Reads were then mapped to the GRCm38 mouse reference genome using Hisat2 (v2.1.0; Kim et al., 2019).
BAM files were imported into Seqmonk (v1.47.0; http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), excluding those with mapping quality < 30, and reads were quantified over merged mRNA isoforms from the GRCm38 Ensembl release 90 annotation, using the RNA-seq quantitation pipeline.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files containing gene names and IDs, together with raw read counts over each gene, generated in Seqmonk using merged mRNA isoforms

source_name: Spleen + lymph node

growth_protocol: Single cell suspensions were prepared from pooled spleen and pLN, from an individual mouse of the indicated genotype. For Foxp3-YFP-Cre control and knockout mice, CD4+ cells were enriched by negative depletion using biotinylated anti-B220, anti-CD8 and anti-CD11b followed by Streptavidin Dynabeads (Dynal). For Zfp36l1fl/fl Zfp36l2fl/fl control mice, negative depletion was performed using the CD4+ T Cell Isolation Kit for mouse (Miltenyi 130-104-454). Naïve or effector Treg were sorted based on the indicated markers; all samples were sorted to >95% purity.

extract_protocol:
RNA was prepared from sorted Treg cells using the RNeasy Micro kit (Qiagen), and quality was assessed using the Bioanalyzer RNA chip
cDNA was generated using the SMARTseq v4 ultra low input RNA kit for sequencing, and libraries prepared from the cDNA using the Nextera XT DNA library preparation kit.

tag: tissue

value: Spleen + lymph node

value: effector Treg

value: Zfp36l1fl/fl Zfp36l2fl/fl

tag: Sex

value: Male

tag: age

value: 9.3 weeks

tag: flow markers


title: NONO replicate 2, scRNAseq

description: 10x Genomics

value: Testicular Cells

value: Testis

value: Adult

value: NONO


title: ICS [S18110500017]

value: BRUSHING

tag: treatment


title: ICS [S18110500008]


title: Sarcoidosis (Progressive) 17 [miRNA-seq]

tag: diagnosis

value: male

tag: race

value: black

tag: ethnicity

tag: smoking status

value: former

tag: scadding stage

tag: acute disease

value: y

tag: pc4 (mirna)

tag: pc5 (mirna)


title: ICS [S18110500007]


title: NONO replicate 1, scRNAseq

description: 10x Genomics

tag: cell type

tag: strain

tag: genotype


title: ICS [S18110500006]


title: eTreg floxed control 3

value: 9.1 weeks


title: Sarcoidosis (Progressive) 15 [miRNA-seq]

value: bronchoalveolar lavage cells

value: sarcoidosis (progressive)

value: white

value: not Hispanic or Latino

value: never

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)

tag: pc2 (mirna)

tag: pc3 (mirna)


title: eTreg floxed control 4

tag: tissue

value: Spleen + lymph node

value: effector Treg

value: Zfp36l1fl/fl Zfp36l2fl/fl

tag: Sex

value: Male

tag: age

tag: flow markers


title: Sarcoidosis (Progressive) 16 [miRNA-seq]

tag: diagnosis

value: female

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease

value: n

tag: pc4 (mirna)


title: 1mm bone defect, scRNA-seq

city: St Louis

first: Jie

last: Shen

state: MO

address: 425 S. Euclid Ave

institute: Washington University in St Louis

description: 10x Genomics

data_processing:
CellRanger pipeline (v7.1.0, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/what-is-cell-ranger) was utilized to align reads, extract cell barcodes and unique molecular identifier (UMI) counts, and generate feature-barcode matrices. The reads were mapped to the mouse (mm10) reference genome following the standard workflow of 10× Genomics.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: regenerative tissue

extract_protocol:
The regenerative tissues from the defect gap were harvested at 3 weeks post-surgery and dissociated in 2 mg/mL Collagenase P and 2 mg/mL pronase at room temperature for 1 hour. The erythrocytes were removed using anti-GYPA and Streptavidin Microbubbles. Subsequently, the cell suspension was filtered through a 30 μm strainer to yield a single-cell suspension.
Two sets of single-cell libraries were prepared: one from cells derived from a 1 mm bone defect (control, n=3) and the other from cells obtained from a 3 mm bone defect (nonunion, n=3). For each sample, ten thousand cells were loaded for processed to generate single-cell mRNA libraries using the Chromium Single Cell 3′ kit (v3.1 Chemistry, 10× Genomics Inc).

value: regenerative tissue

tag: cell type

value: primary cells

tag: genotype

value: C57BL/6J wild-type

tag: sample type

value: 1mm defect


title: Sarcoidosis (Progressive) 14 [miRNA-seq]

value: male

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

value: y

tag: pc1 (mirna)

tag: pc5 (mirna)


title: UHE-HL-g004

city: Heidelberg

first: Thomas

last: Korff

address: INF 326

department: Institute of Physiology and Pathophysiology

country: Germany

institute: Heidelberg University

description: 10 X Genomics

data_processing:
Single-cell mRNA sequencing was performed at Single Cell Discoveries, a single-cell sequencing service provider in the Netherlands, according to standard 10x Genomics [5’ v2 Single Cell Immune Profiling, or 3’ V3.1 Single Cell Gene Expression] dual index chemistry guidelines
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Lungs were digested in DMEM/F12 containing 4 U/ml Dispase and 10 µg/ml DNaseI at 37°C for 45 min. Digested tissues were filtered through a 100 µm cell strainer. Erythrocytes were lysed using ACK buffer. An anti-mouse CD16/32 dimer antibody was employed to inhibit non-specific binding of antibodies to FcγII and FcγIII. The cell suspension was incubated with anti-CD31 MicroBeads to pre-select PECAM-1high cells using MACS LS columns and a magnetic separator. Samples were cryopreserved and thawed according to 10x Genomics guidelines. Cells were washed, filtered, counted, and loaded at a concentration of 700–1200 cells/µl on a 10x Genomics chip. The chip was then run on a Chromium controller to initiate GEM formation.
Library preparation was performed, following standard 10x Genomics guidelines

tag: tissue

value: Lung

value: FAC-sorted lung endothelial cells

value: NFAT5 (EC)-/-

tag: treatment

value: Normobaric hypoxia (10% oxygen, 7 days)


title: eTreg floxed control 1

tag: strain

tag: Sex

tag: age

value: 10 weeks

tag: flow markers


title: 3mm bone defect, scRNA-seq

description: 10x Genomics

value: 3mm defect


title: Sarcoidosis (Progressive) 13 [miRNA-seq]

value: bronchoalveolar lavage cells

tag: diagnosis

value: sarcoidosis (progressive)

tag: race

value: white

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

value: never

tag: scadding stage

tag: acute disease

tag: pc2 (mirna)

tag: pc3 (mirna)

tag: pc4 (mirna)


title: Placebo [620260389413]

source_name: BIOPSY

value: BIOPSY


title: eTreg floxed control 2

value: Spleen + lymph node

tag: cell type

value: effector Treg

tag: genotype

value: Zfp36l1fl/fl Zfp36l2fl/fl

value: Male

value: 10.4 weeks


title: Placebo [620260389612]

tag: tissue


title: nTreg floxed control 6

value: naive Treg

value: 11.3 weeks


title: nTreg floxed control 5


title: UHE-HL-g002

description: 10X Genomics

value: Lung

value: FAC-sorted lung endothelial cells

value: NFAT5 (EC)-/-

tag: treatment

value: Normoxia


title: Placebo [620260389313]


title: Sarcoidosis (Progressive) 12 [miRNA-seq]

value: bronchoalveolar lavage cells

value: female

value: former

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

value: y

tag: pc1 (mirna)

tag: pc5 (mirna)


title: Placebo [620091230301]


title: UHE-HL-g003

description: 10 X Genomics

value: NFAT5 flox/flox (control)

value: Normobaric hypoxia (10% oxygen, 7 days)


title: Sarcoidosis (Progressive) 10 [miRNA-seq]

tag: diagnosis

value: sarcoidosis (progressive)

tag: age

tag: Sex

value: male

tag: race

value: white

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

value: never


title: nTreg floxed control 4

tag: strain

value: Spleen + lymph node

tag: cell type

value: naive Treg

value: Zfp36l1fl/fl Zfp36l2fl/fl

value: Male

value: 10 weeks

tag: flow markers


title: UHE-HL-g001

description: 10 X Genomics

tag: tissue

value: Lung

value: FAC-sorted lung endothelial cells

tag: genotype

tag: treatment

value: Normoxia


title: nTreg floxed control 3

value: 9.5 weeks


title: ICS [S18110500005]

value: BRUSHING


title: Sarcoidosis (Progressive) 1 [miRNA-seq]

value: bronchoalveolar lavage cells

tag: scadding stage

tag: acute disease

value: n

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

value: y

tag: pc2 (mirna)

tag: pc3 (mirna)

tag: pc4 (mirna)


title: Placebo [620091230101]

value: BIOPSY


title: SampleH_TCR

city: Qingdao

first: XIAOTIAN

last: CHANG

state: Shandong

address: 1677 Wutaishan road

institute: The Affiliated Hospital of Qingdao University

description: 10× Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell
Library strategy: TCR-seq

source_name: aortic tissue of ApoE-/- mice that were fed with high-fat food and simultaneously treated with methoxazolamide,TCR

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific).
For 5 'single-cell transcriptome ： Adjust the cell concentration of freshly prepared single-cell suspension to 700-1200 cell/μl. Water-in-oil preparation and cDNA library amplification were performed according to the operating instructions of 10×Genomics Chromium Next GEM Single Cell 5ʹ Reagent Kits v2.0(1000165).The DNA library was constructed using Chromium™ single cell 3'/5' library construction kit (1000020). For 5 'single-cell TCR: T Cell V(D)J enrichment was performed according to the 10×Genomics Chromium™ single-cell V(D)J enrichment kit and mouse T cell operating instructions(1000071).The library was amplified using Chromium single-cell mouse TCR amplification kit (1000254), and the experiments were performed according to the product instructions. For 5 'single-cell BCR: B Cell V(D)J enrichment was performed according to the 10×Genomics Chromium™ single-cell V(D)J enrichment kit and mouse B cell operating instructions(1000072). The library was amplified using Chromium single-cell mouse BCR amplification kit (1000255). The experimental procedures were performed according to the product instructions.

value: aortic tissues

value: ApoE-/-


title: Sarcoidosis (Non-Progressive) 9 [miRNA-seq]

tag: diagnosis

value: sarcoidosis (non-progressive)

tag: age

tag: Sex

value: female

tag: race

value: white

value: not Hispanic or Latino

value: never

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)

tag: pc5 (mirna)


title: nTreg floxed control 2

tag: strain

tag: tissue

value: Spleen + lymph node

tag: cell type

value: naive Treg

tag: genotype

value: Zfp36l1fl/fl Zfp36l2fl/fl

value: Male

tag: flow markers


title: Placebo [620091229903]

tag: treatment


title: SampleH_BCR

description: 10× Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell
Library strategy: BCR-seq

source_name: aortic tissue of ApoE-/- mice that were fed with high-fat food and simultaneously treated with methoxazolamide,BCR


title: nTreg floxed control 1

value: 9.5 weeks


title: Placebo [S18110500168]


title: Placebo [S18110500186]


title: SampleH_GEX

description: 10× Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: aortic tissue of ApoE-/- mice that were fed with high-fat food and simultaneously treated with methoxazolamide,GEX


title: Sarcoidosis (Non-Progressive) 7 [miRNA-seq]

value: male

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: pc2 (mirna)


title: nTreg FYC dKO 5

tag: Sex

value: Female

tag: age

value: 7.3 weeks


title: Sarcoidosis (Non-Progressive) 6 [miRNA-seq]

value: bronchoalveolar lavage cells

tag: diagnosis

tag: race

value: n

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

value: y

tag: pc1 (mirna)

tag: pc3 (mirna)

tag: pc4 (mirna)

tag: pc5 (mirna)


title: SampleG_BCR

description: 10× Genomics

source_name: aortic tissue of ApoE-/- mice that were fed with high-fat food and treated with methoxazolamide after atherosclerosis was established,BCR

tag: tissue

value: aortic tissues

tag: genotype

value: ApoE-/-

tag: treatment


title: Sarcoidosis (Non-Progressive) 5 [miRNA-seq]

value: sarcoidosis (non-progressive)

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease

tag: multiorgan involvement


title: nTreg FYC dKO 4

tag: strain

tag: cell type

tag: Sex

tag: age

value: 11 weeks

tag: flow markers


title: SampleG_TCR

description: 10× Genomics

source_name: aortic tissue of ApoE-/- mice that were fed with high-fat food and treated with methoxazolamide after atherosclerosis was established,TCR


title: Sarcoidosis (Non-Progressive) 4 [miRNA-seq]

tag: diagnosis

value: female

tag: race

value: white

value: not Hispanic or Latino

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)

tag: pc2 (mirna)


title: nTreg FYC dKO 3

tag: tissue

value: Spleen + lymph node

value: naive Treg

tag: genotype

value: 11.1 weeks


title: SampleF_TCR

description: 10× Genomics

source_name: aortic tissue of ApoE-/- mice that were fed with high-fat food,TCR

tag: treatment

value: high-fat food


title: SampleG_GEX

description: 10× Genomics

source_name: aortic tissue of ApoE-/- mice that were fed with high-fat food and treated with methoxazolamide after atherosclerosis was established,GEX


title: Placebo [S18110500165]

value: BIOPSY


title: Placebo [S18110500166]


title: SampleF_BCR

description: 10× Genomics

source_name: aortic tissue of ApoE-/- mice that were fed with high-fat food,BCR


title: Sarcoidosis (Non-Progressive) 38 [miRNA-seq]

tag: ethnicity

tag: smoking status

value: never

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: pc3 (mirna)

tag: pc4 (mirna)

tag: pc5 (mirna)


title: nTreg FYC dKO 2

tag: strain

tag: cell type

tag: Sex

value: Female

tag: age

tag: flow markers


title: Placebo [S18110500146]


title: Sarcoidosis (Non-Progressive) 8 [miRNA-seq]

value: bronchoalveolar lavage cells

tag: diagnosis

tag: race

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)

tag: pc2 (mirna)


title: Sarcoidosis (Non-Progressive) 37 [miRNA-seq]

tag: tissue

tag: ethnicity

tag: smoking status

value: former

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

value: n


title: SampleF_GEX

description: 10× Genomics

source_name: aortic tissue of ApoE-/- mice that were fed with high-fat food ,GEX

value: aortic tissues

tag: genotype

tag: treatment


title: SampleE_TCR

description: 10× Genomics

source_name: aortic tissue of ApoE-/- mice without treatment,TCR

value: ApoE-/-


title: nTreg FYC dKO 1

tag: strain

tag: cell type

tag: Sex

tag: age

value: 13.9 weeks

tag: flow markers


title: Placebo [S18110500145]


title: Sarcoidosis (Non-Progressive) 36 [miRNA-seq]

tag: diagnosis

value: sarcoidosis (non-progressive)

tag: race

value: black

value: y

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc3 (mirna)

tag: pc4 (mirna)

tag: pc5 (mirna)


title: Placebo [S18110500142]

tag: tissue


title: nTreg FYC dKO 6

value: 7.8 weeks


title: nTreg FYC control 7

value: Spleen + lymph node


title: nTreg FYC control 6

value: naive Treg

value: 7.3 weeks


title: Placebo [S18110500141]


title: Sarcoidosis (Non-Progressive) 35 [miRNA-seq]

value: female

value: white

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)

tag: pc2 (mirna)


title: Placebo [S18110500167]

value: BIOPSY

tag: treatment


title: Sarcoidosis (Non-Progressive) 33 [miRNA-seq]

value: bronchoalveolar lavage cells

tag: diagnosis

tag: age

tag: Sex

tag: race

value: never


title: Sarcoidosis (Non-Progressive) 34 [miRNA-seq]

value: n

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc3 (mirna)


title: Placebo [S18110500138]

tag: tissue


title: nTreg FYC control 4

tag: strain

tag: cell type

tag: genotype

value: Female

value: 11 weeks

tag: flow markers


title: nTreg FYC control 5


title: Placebo [S18110500137]


title: striatum, METH-F2-4

city: Shinagawa-ku

first: Sakiko

last: Munetomo-Aoki

state: Tokyo

address: 1-5-8, Hatanodai

department: School of Pharmacy

country: Japan

institute: Showa University Graduate School

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Transcripts Per Million(TPM) were calculated by using StringTie version 2.1.3b, with parameter --rf -l -o -G -A -e
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: striatum

growth_protocol: Mice were housed in plastic cages in a temperature-controlled room (22±1 ℃) and maintained at a 12-h light-dark cycle, with free access to food and water.

extract_protocol:
striatum collected from 7-week-old F1 mice and F2 mice were flash-frozen in liquid nitrogen and stored at -80℃ until total RNA was extracted. Total RNA was isolated from the tissue using RNeasy Mini Kit (QIAGEN Inc., CA USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Six-week-old male ICR mice (F0) were administered METH(5 mg/kg) or saline (10 mL/kg) subcutaneously for 21 consecutive days and mated with drug-untreated female mice during their estrous cycle.

value: striatum

value: ICR

value: neuronal cell

value: wild type

value: male

tag: time


title: SampleE_GEX

description: 10× Genomics

source_name: aortic tissue of ApoE-/- mice without treatment,GEX

value: aortic tissues

value: ApoE-/-


title: Sarcoidosis (Non-Progressive) 32 [miRNA-seq]

source_name: bronchoalveolar lavage cells

value: sarcoidosis (non-progressive)

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: ever treated_for_sarcoidosis

value: y

tag: pc1 (mirna)

tag: pc4 (mirna)

tag: pc5 (mirna)


title: Placebo [S18110500132]

tag: treatment


title: nTreg FYC control 3

source_name: Spleen + lymph node

value: Spleen + lymph node

value: naive Treg

tag: Sex

tag: age


title: striatum, METH-F2-2

tag: tissue

tag: strain


title: nTreg FYC control 2

tag: cell type

tag: genotype


title: Placebo [S18110500131]

value: BIOPSY


title: Sarcoidosis (Non-Progressive) 31 [miRNA-seq]

value: bronchoalveolar lavage cells

tag: diagnosis

value: female

tag: race

value: black

value: not Hispanic or Latino

value: former

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc2 (mirna)

tag: pc3 (mirna)


title: Sarcoidosis (Non-Progressive) 30 [miRNA-seq]

value: white

tag: ethnicity

tag: smoking status

value: never

tag: scadding stage

tag: acute disease

value: n

tag: multiorgan involvement

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)


title: Placebo [S18110500126]

tag: tissue

tag: treatment


title: nTreg FYC control 1

tag: strain

tag: cell type

tag: genotype

tag: Sex

value: Female

tag: age

value: 14.3 weeks

tag: flow markers


title: Sarcoidosis (Non-Progressive) 3 [miRNA-seq]

tag: diagnosis

tag: race

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc2 (mirna)

tag: pc4 (mirna)

tag: pc5 (mirna)


title: SampleE_BCR

description: 10× Genomics

source_name: aortic tissue of ApoE-/- mice without treatment,BCR

value: aortic tissues


title: Placebo [S18110500125]


title: striatum, control-F2-3

value: striatum

value: ICR

value: neuronal cell

value: wild type

value: saline (10 ml/kg)

value: male

tag: time


title: ICS [620356899802]

tag: tissue

value: BIOPSY


title: striatum, control-F2-2

tag: treatment


title: ICS [620356901414]


title: Sarcoidosis (Non-Progressive) 29 [miRNA-seq]

value: bronchoalveolar lavage cells

value: sarcoidosis (non-progressive)

value: female

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: ever treated_for_sarcoidosis

value: y

tag: pc1 (mirna)

tag: pc3 (mirna)


title: ICS [620260389513]


title: Sarcoidosis (Non-Progressive) 27 [miRNA-seq]

tag: diagnosis

tag: age

tag: Sex

tag: race

value: black

value: not Hispanic or Latino

tag: fvc (%_predicted)


title: striatum, control-F2-1

tag: strain

tag: cell type

tag: genotype


title: striatum, METH-F1-3

tag: tissue

tag: treatment

tag: time


title: Sarcoidosis (Non-Progressive) 25 [miRNA-seq]

value: white

tag: ethnicity

tag: smoking status

value: never

tag: scadding stage

value: n

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc2 (mirna)

tag: pc4 (mirna)

tag: pc5 (mirna)


title: ICS [620260389014]


title: Sarcoidosis (Non-Progressive) 26 [miRNA-seq]

tag: diagnosis

tag: age

tag: Sex

tag: acute disease

tag: multiorgan involvement

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)

tag: pc3 (mirna)


title: striatum, METH-F1-2

tag: tissue

tag: strain

tag: cell type

tag: genotype

tag: treatment

tag: time


title: striatum, METH-F1-1


title: striatum, METH-F2-3


title: Sarcoidosis (Non-Progressive) 23 [miRNA-seq]

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc2 (mirna)


title: ICS [620091230603]


title: ICS [620091230701]


title: striatum, METH-F2-1

tag: Sex


title: striatum, control-F1-4


title: striatum, control-F1-3


title: Sarcoidosis (Non-Progressive) 22 [miRNA-seq]

tag: diagnosis

tag: age

value: former

tag: acute disease

tag: multiorgan involvement

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)

tag: pc4 (mirna)

tag: pc5 (mirna)


title: striatum, control-F2-4

tag: tissue

value: striatum

tag: strain

tag: cell type

tag: genotype

tag: treatment

tag: time


title: Sarcoidosis (Non-Progressive) 28 [miRNA-seq]

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc3 (mirna)


title: ICS [620091230001]


title: Sarcoidosis (Non-Progressive) 21 [miRNA-seq]

tag: diagnosis

tag: age

tag: Sex

tag: acute disease

tag: multiorgan involvement

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)

tag: pc2 (mirna)


title: striatum, control-F1-2

tag: tissue

tag: strain

value: ICR

tag: cell type

tag: genotype

tag: treatment

tag: time


title: ICS [S18110500191]


title: Sarcoidosis (Non-Progressive) 20 [miRNA-seq]

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: pc4 (mirna)

tag: pc5 (mirna)


title: ICS [S18110500170]


title: striatum, control-F1-1

value: neuronal cell

tag: Sex


title: ICS [620260389112]


title: LAP2alpha knockout myoblasts, proliferating, H3K4me3 ChIP

description: linked to Input 2

source_name: immortalized myoblasts

value: immortalized myoblasts

value: LAP2alpha knockout; p53 knockout

value: proliferating

tag: chip antibody

value: H3K4me3 antibody (Merck/Millipore, #07-473)


title: Sarcoidosis (Non-Progressive) 24 [miRNA-seq]

value: bronchoalveolar lavage cells

tag: diagnosis

tag: age

tag: acute disease

tag: multiorgan involvement

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)

tag: pc2 (mirna)

tag: pc3 (mirna)


title: Sarcoidosis (Non-Progressive) 19 [miRNA-seq]

tag: tissue

value: sarcoidosis (non-progressive)

value: male

tag: race

tag: ethnicity

tag: smoking status


title: wildtype myoblasts, differentiating (D2), H3K4me3 ChIP

description: linked to Input 2

tag: cell type

tag: genotype

value: LAP2alpha wildtype; p53 knockout

tag: treatment

value: Day 2 of differentiation


title: ICS [S18110500169]

source_name: BIOPSY

value: BIOPSY


title: LAP2alpha knockout myoblasts, differentiating (D2) , H3K4me3 ChIP

description: linked to Input 2

tag: chip antibody


title: wildtype myoblasts, proliferating, H3K4me3 ChIP

description: linked to Input 2


title: Sarcoidosis (Non-Progressive) 17 [miRNA-seq]

tag: diagnosis

tag: Sex

value: female

value: white

value: not Hispanic or Latino

tag: scadding stage

value: y

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: pc4 (mirna)

tag: pc5 (mirna)


title: ICS [S18110500162]


title: Sarcoidosis (Non-Progressive) 16 [miRNA-seq]

tag: age

value: Hispanic or Latino

value: never

tag: acute disease

value: n

tag: multiorgan involvement

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)

tag: pc2 (mirna)


title: LAP2alpha knockout myoblasts, differentiating (D2), H3K27ac ChIP, rep 2

description: linked to Input 2

tag: cell type

value: immortalized myoblasts

tag: genotype

value: H3K27ac antibody (Merck/Millipore, #07-360)


title: Sarcoidosis (Non-Progressive) 14 [miRNA-seq]

tag: tissue

tag: race

tag: ethnicity

tag: smoking status

tag: pc3 (mirna)


title: ICS [S18110500160]

tag: treatment


title: Sarcoidosis (Non-Progressive) 13 [miRNA-seq]

tag: diagnosis

tag: Sex

value: former

tag: scadding stage

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: pc4 (mirna)


title: LAP2alpha knockout myoblasts, differentiating (D2), H3K27ac ChIP, rep 1

description: linked to Input 3

value: LAP2alpha knockout; p53 knockout

tag: chip antibody


title: LAP2alpha knockout myoblasts, proliferating, H3K27ac ChIP, rep 2

description: linked to Input 2

value: proliferating


title: ICS [S18110500161]


title: Sarcoidosis (Non-Progressive) 11 [miRNA-seq]

value: bronchoalveolar lavage cells

value: sarcoidosis (non-progressive)

tag: age

value: asian

tag: acute disease

tag: multiorgan involvement

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)

tag: pc5 (mirna)


title: ICS [S18110500158]

tag: tissue


title: ICS [S18110500159]


title: wildtype myoblasts, differentiating (D2), H3K27ac ChIP, rep 2

description: linked to Input 2

tag: cell type

tag: genotype

value: LAP2alpha wildtype; p53 knockout

value: Day 2 of differentiation


title: Sarcoidosis (Non-Progressive) 1 [miRNA-seq]

tag: diagnosis

value: female

tag: race

tag: ethnicity

tag: smoking status

tag: pc2 (mirna)

tag: pc3 (mirna)


title: Sarcoidosis (Non-Progressive) 10 [miRNA-seq]

tag: Sex

value: black

tag: scadding stage

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: pc4 (mirna)


title: wildtype myoblasts, differentiating (D2), H3K27ac ChIP, rep 1

description: linked to Input 3

tag: treatment

tag: chip antibody


title: Sarcoidosis (Non-Progressive) 2 [miRNA-seq]

tag: age

value: not Hispanic or Latino

tag: acute disease

tag: multiorgan involvement

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc1 (mirna)

tag: pc5 (mirna)


title: ICS [S18110500163]

tag: tissue

value: BIOPSY


title: Sarcoidosis (Non-Progressive) 18 [miRNA-seq]

tag: diagnosis

tag: race

value: white

tag: ethnicity

value: Hispanic or Latino

tag: smoking status

value: y

tag: pc2 (mirna)


title: ICS [S18110500164]


title: ICS [S18110500155]


title: wildtype myoblasts, proliferating, H3K27ac ChIP, rep 2

description: linked to Input 2

tag: cell type

value: immortalized myoblasts

tag: genotype


title: ICS [S18110500154]

tag: treatment


title: Healthy Control 8 [miRNA-seq]

value: control

tag: Sex

value: male

value: never

tag: scadding stage

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: pc3 (mirna)

tag: pc4 (mirna)


title: Healthy Control 7 [miRNA-seq]

tag: age

tag: acute disease

tag: multiorgan involvement

tag: dlco (%_predicted)

tag: pc1 (mirna)


title: LAP2alpha knockout myoblasts, differentiating (D2), lamin AC 3A6 ChIP, rep 2

description: linked to Input 2

value: LAP2alpha knockout; p53 knockout

tag: chip antibody

value: lamin A/C antibody 3A6 (PMID:26798136)


title: wildtype myoblasts, proliferating, H3K27ac ChIP, rep 1

description: linked to Input 3

value: proliferating

value: H3K27ac antibody (Merck/Millipore, #07-360)


title: LAP2alpha knockout myoblasts, proliferating, lamin AC 3A6 ChIP, rep 2

description: linked to Input 2


title: Healthy Control 4 [miRNA-seq]

tag: tissue

value: bronchoalveolar lavage cells

tag: diagnosis

tag: race

tag: ethnicity

tag: smoking status

tag: pc5 (mirna)


title: Healthy Control 6 [miRNA-seq]

tag: Sex

tag: scadding stage

tag: pc2 (mirna)


title: wildtype myoblasts, differentiating (D2), lamin AC 3A6 ChIP, rep 2

description: linked to Input 2

tag: cell type

tag: genotype

value: LAP2alpha wildtype; p53 knockout

tag: treatment

value: Day 2 of differentiation


title: wildtype myoblasts, proliferating, lamin AC 3A6 ChIP, rep 2

description: linked to Input 2


title: Healthy Control 3 [miRNA-seq]

tag: age

value: female

value: asian

tag: acute disease

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: pc3 (mirna)

tag: pc4 (mirna)


title: ICS [S18110500150]

tag: tissue

value: BIOPSY


title: LAP2alpha knockout myoblasts, proliferating, H3K27ac ChIP, rep 1

description: linked to Input 3

tag: chip antibody


title: wildtype myoblasts, differentiating (D2), LAP2alpha ChIP, rep 2

description: linked to Input 2

value: LAP2alpha antibody 1H11 (PMID:26798136)


title: ICS [S18110500157]


title: Healthy Control 2 [miRNA-seq]

tag: diagnosis

tag: race

value: white

tag: ethnicity

value: not Hispanic or Latino

tag: multiorgan involvement

tag: dlco (%_predicted)

tag: pc1 (mirna)


title: ICS [S18110500149]


title: ICS [S18110500156]


title: Healthy Control 16 [miRNA-seq]

tag: Sex

tag: smoking status

tag: scadding stage

tag: pc2 (mirna)

tag: pc5 (mirna)


title: wildtype myoblasts, proliferating, LAP2alpha ChIP, rep 2

description: linked to Input 2

tag: cell type

value: immortalized myoblasts

tag: genotype

tag: treatment


title: ICS [S18110500152]


title: Healthy Control 9 [miRNA-seq]

value: control

tag: age

tag: acute disease

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: pc3 (mirna)

tag: pc4 (mirna)


title: LAP2alpha knockout myoblasts, differentiating (D2), Input 3

tag: chip antibody

value: no antibody - Input


title: Healthy Control 15 [miRNA-seq]

tag: tissue

tag: diagnosis

value: male

tag: race

tag: ethnicity

value: never

tag: multiorgan involvement

tag: dlco (%_predicted)


title: ICS [S18110500151]


title: Healthy Control 14 [miRNA-seq]

tag: Sex

tag: smoking status

tag: scadding stage

tag: pc1 (mirna)

tag: pc2 (mirna)

tag: pc5 (mirna)


title: wildtype myoblasts, differentiating (D2), Input 3

tag: cell type

tag: genotype

tag: treatment


title: ICS [S18110500147]


title: ICS [S18110500153]


title: ICS [S18110500144]


title: wildtype myoblasts, proliferating, Input 3


title: ICS [S18110500143]


title: Healthy Control 12 [miRNA-seq]

tag: age

tag: acute disease

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: pc3 (mirna)

tag: pc4 (mirna)


title: ICS [S18110500140]

tag: tissue


title: ICS [S18110500139]


title: LAP2alpha knockout myoblasts, proliferating, Input 2

value: LAP2alpha knockout; p53 knockout

tag: chip antibody


title: Healthy Control 11 [miRNA-seq]

tag: diagnosis

tag: Sex

tag: race

tag: ethnicity

tag: multiorgan involvement

tag: dlco (%_predicted)


title: Healthy Control 1 [miRNA-seq]

tag: smoking status

tag: scadding stage

tag: pc1 (mirna)

tag: pc2 (mirna)

tag: pc5 (mirna)


title: wildtype myoblasts, proliferating, Input 2

tag: cell type

tag: genotype

tag: treatment

value: proliferating


title: ICS [S18110500136]


title: wildtype myoblasts, differentiating (D2), Input 2


title: Sarcoidosis (Progressive) 4

data_processing:
RNA paired-end reads were aligned at the gene level to Ensembl GrCh38 using STAR
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

extract_protocol:
DNA and RNA were extracted using the Qiagen AllPrep DNA/RNA extraction mini kit.
mRNA libraries were prepared from 500 ng total RNA with TruSeq stranded mRNA library preparation kits (Illumina)

value: sarcoidosis (progressive)

tag: age

value: former

tag: acute disease

value: n

value: y

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc1 (mrna)

tag: pc2 (mrna)

tag: pc3 (mrna)

tag: pc4 (mrna)

tag: pc5 (mrna)


title: ICS [S18110500135]

tag: tissue


title: ICS [S18110500134]


title: Sarcoidosis (Progressive) 7

value: bronchoalveolar lavage cells

tag: diagnosis

tag: Sex

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: multiorgan involvement

tag: dlco (%_predicted)


title: Sarcoidosis (Progressive) 3

tag: age

value: black

tag: acute disease

tag: fvc (%_predicted)


title: LTα_LTBR_5

city: Tarrytown

first: Wei-Yi

last: Cheng

state: NY

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals, Inc.

description:
LTα expression_LTBR agonist mAb
an_geo_2023.h5ad

data_processing:
Cell Ranger Single Cell Software Suite (10X Genomics, 6.1.1) was used to perform sample de-multiplexing, alignment, filtering, and UMI counting.
Assembly: GRCm38
Supplementary files format and content: In the processed h5a files, the scaled log-CP10K values were stored in the `X` layer. The `obs` field contains basic statistics in each cell, and the cluster assignment

source_name: colon

growth_protocol: For tumor studies with LTBR agonist treatment, 1x106 cells of MC38-OVA or transgenic variants, 5x105 cells of B16-F10 or 5x105 cells of F1242 with 50% Matrigel (Corning) were subcutaneously implanted into the right flanks of female C57BL/6 mice, 1x106 cells of Colon26 or transgenic variants were subcutaneously implanted into the right flanks of female BALB/c mice and 5x105 cells of 4T1 cells were injected into the mammary fat pad of female BALB/c mice.

extract_protocol:
Tumors were excised, mechanically minced, dissociated to single cell suspensions using the mouse Tumor Dissociation Kit according to the manufacturer’s protocol (Miltenyi)
The cell suspensions were loaded on a Chromium Connect Single Cell Liquid Handler (10X Genomics) and RNA-seq libraries were prepared using Chromium Next GEM Automated Single Cell 5’ Kit, v2 (10X Genomics)

treatment_protocol: When tumors reached 50-100 mm3, animals were randomized into treatment groups and injected intraperitoneally

value: colon

tag: cell line

tag: treatment

value: Combo


title: LAP2alpha knockout myoblasts, proliferating, Input 3

tag: cell type

tag: genotype

tag: chip antibody


title: Healthy Control 13 [miRNA-seq]

tag: tissue

value: female

value: white

tag: fev1 (%_predicted)

tag: pc1 (mirna)

tag: pc2 (mirna)

tag: pc3 (mirna)

tag: pc4 (mirna)

tag: pc5 (mirna)


title: TRAMP prostate

city: New Orleans

first: Michael

last: Lan

state: LA

address: 533 Bolivar Street, CSRB Room 623E

department: School of Medicine

institute: LSUHSC

data_processing:
Illumina NovaSeq 6000 (NovaSeq Control Software v1.8; RTA v3)
cellranger-6.1.2 for C4-2B; Alevin-Fry for TRAMP
Seurat V5
Assembly: GRCh38/ mm10
Supplementary files format and content: mtx files of counts

source_name: Mouse prostate tissue

extract_protocol:
C4-2B xenograft and TRAMP tumor tissues were harvested and dissociated using “Tumor Dissociation Kit, human, #130-095-929” and “Tumor Dissociation Kit, mouse, #130-096-730” from Miltenyi Biotec.
Samples were assessed and processed for single cell 3’ sequencing. GEMs (Gel Bead-in Emulsions) were generated in a Chromium Controller (10x Genomics). RNA contained in the GEMs was reverse transcribed, barcoded, and cDNA was recovered. cDNA was assessed with the Agilent TapeStation D5000 High Sensitivity Kit (Agilent Technologies). All samples underwent manual library processing with the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1: cDNA was fragmented, processed, and size selected. Adaptors were ligated and samples were cleaned up. Dual indexes were attached via PCR. The completed libraries were cleaned up and assessed for quality with the Agilent TapeStation D5000 High Sensitivity Kit. Libraries were quantitated with qPCR (NEBNext Library Quant Kit for Illumina, Bio-rad CFX96 Touch Real-Time PCR). Libraries were normalized to 1.5 pM and pooled. The library pool was denatured and diluted to approximately 300 pM. A library of 1.5 pM PhiX was spiked in as an internal control

value: Mouse prostate tissue

value: transgenic adenocarcinoma of the mouse prostate (TRAMP)

value: CX


title: ICS [S18110500133]

value: BIOPSY


title: Sarcoidosis (Progressive) 25

tag: diagnosis

tag: Sex

value: male

tag: race

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

tag: scadding stage

tag: multiorgan involvement

tag: ever treated_for_sarcoidosis

tag: pc1 (mrna)

tag: pc2 (mrna)

tag: pc3 (mrna)

tag: pc4 (mrna)

tag: pc5 (mrna)


title: ICS [S18110500129]

tag: tissue

tag: treatment


title: ICS [S18110500124]


title: ICS [S18110500130]


title: LTα_ISO_5

description:
LTα expression_Isotype control
an_geo_2023.h5ad

tag: cell line

value: LTalpha


title: ICS [S18110500148]


title: LTα_ISO_4


title: Healthy Control 10 [miRNA-seq]

value: control

tag: age

value: never

tag: acute disease

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc1 (mirna)

tag: pc2 (mirna)

tag: pc3 (mirna)

tag: pc4 (mirna)

tag: pc5 (mirna)


title: LTα_LTBR_4


title: Sarcoidosis (Progressive) 18

tag: diagnosis

value: sarcoidosis (progressive)

tag: Sex

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

value: n

tag: multiorgan involvement

tag: ever treated_for_sarcoidosis

tag: pc1 (mrna)

tag: pc2 (mrna)


title: ICS [S18110500123]

tag: tissue

tag: treatment


title: EV_LTBR_5

description:
EV_LTBR agonist mAb
an_geo_2023.h5ad

tag: cell line

value: LTBR


title: HL60_shCTRL_Polysomes_3

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

institute: University of Veterinary Medicine, Vienna

description:
RNA extracted from polysomes fractions
POLYSOME_HL60_shDDX6.tsv

data_processing:
Genome wide screen:
Nextflow pipeline available at: https://github.com/ZuberLab/crispr-process-nf
Trimming with: fastx_trimmer from the fastx-toolkit, demultiplexing with fastx_barcode_splitter, alignment with Bowtie2 and quantification with featureCounts
Nextlow pipeline: https://github.com/ZuberLab/crispr-mageck-nf applying MAGeCK
Normalization with inhouse R script (see methods)
RNA-seq:
Quality check with FastQC, alignment against the human reference genome (GRCh38) with STAR. Alignments were post-processed with SAMtools and counts per gene were obtained with featureCounts.
Normalization of counts and the differential gene expression analysis (input shRenilla versus input shDDX6) where  done with DESeq2
Polysome-seq:
Quality check with FastQC and alignement against the human reference genome (GRCh38) with STAR. We processed the alignments with SAMtools and obtained counts per gene with featureCounts. Differential translation analysis with Xtail with parameters bins=10000 and minMeanCount=20
Assembly: hg38
Supplementary files format and content: POLYSOME tsv from polysome-seq: xtail results
Supplementary files format and content: GWS tsv from genome wide screen: logfold-change and normalized lfc
Supplementary files format and content: RIP and RNA tsv´s from RIP- and RNA-seq: DESeq2 results
Library strategy: polysome-Seq

source_name: Peripheral blood

growth_protocol: Cells were maintained in RPMI supplemented 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
For genome wide screen, genomic DNA was extracted using phenol/chloroform
For RNA- and polysome-seq, total and polysomes RNAs were extracted using TRIzol
DNA library for Genome wide screen was performed as previously described by Michlits et al, 2020 Nature Methods (DOI:  10.1038/s41592-020-0850-8)
RNA libraries for RIP-seq were constructed using NEBNext Ultra II Directional RNA library prep and Unique Dual Index Primer Pairs
RNA libraries for total and polysomes RNA-seq were constructed at Beijing Genomics Institute (BGI Group)

value: Peripheral blood

tag: genotype

value: Acute myeloid leukemia


title: Sarcoidosis (Progressive) 16

value: bronchoalveolar lavage cells

tag: age

value: former

tag: acute disease

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc3 (mrna)

tag: pc4 (mrna)

tag: pc5 (mrna)


title: EV_LTBR_4

description:
EV_LTBR agonist mAb
an_geo_2023.h5ad

value: colon


title: LAP2alpha knockout myoblasts, differentiating (D2), Input 2

tag: cell type

value: immortalized myoblasts

value: LAP2alpha knockout; p53 knockout

value: Day 2 of differentiation

tag: chip antibody

value: no antibody - Input


title: EV_ISO_5

description:
EV_Isotype control
an_geo_2023.h5ad

value: ctrl


title: Sarcoidosis (Progressive) 17

tag: diagnosis

tag: Sex

value: male

tag: race

value: black

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

tag: scadding stage

tag: multiorgan involvement

tag: ever treated_for_sarcoidosis

value: y


title: HL60_shCTRL_Polysomes_2

tag: tissue

tag: cell line

tag: genotype


title: Sarcoidosis (Progressive) 14

value: sarcoidosis (progressive)

tag: age

value: white

value: never

tag: acute disease

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc1 (mrna)

tag: pc2 (mrna)


title: EV_ISO_4

description:
EV_Isotype control
an_geo_2023.h5ad

tag: treatment


title: HL60_shCTRL_Polysomes_1

value: Peripheral blood


title: Sarcoidosis (Progressive) 23

tag: diagnosis

tag: Sex

tag: race

value: n

tag: pc3 (mrna)

tag: pc4 (mrna)

tag: pc5 (mrna)


title: LTα_LTBR_3

tag: tissue

value: Combo


title: LTα_LTBR_2

tag: cell line


title: HL60_shCTRL_Input_3

description:
total RNA
POLYSOME_HL60_shDDX6.tsv
RNA_HL60_shDDX6_vs_shRenilla.tsv

tag: genotype

value: Acute myeloid leukemia


title: Sarcoidosis (Progressive) 10

value: bronchoalveolar lavage cells

tag: age

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: multiorgan involvement

tag: ever treated_for_sarcoidosis


title: HL60_shCTRL_Input_1


title: Sarcoidosis (Progressive) 12

value: female

value: former

tag: acute disease

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc1 (mrna)

tag: pc2 (mrna)


title: LTα_LTBR_1

value: colon

tag: treatment


title: LTα_ISO_3

value: LTalpha


title: HL60_shDDX6_Polysomes_3


title: Sarcoidosis (Non-Progressive) 4

tag: diagnosis

value: sarcoidosis (non-progressive)

tag: Sex

tag: race

tag: pc3 (mrna)

tag: pc4 (mrna)

tag: pc5 (mrna)


title: HL60_shDDX6_Polysomes_2

tag: tissue

tag: cell line

tag: genotype


title: LTα_ISO_2


title: LTα_ISO_1


title: HL60_shDDX6_Polysomes_1


title: Sarcoidosis (Non-Progressive) 38

tag: age

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: multiorgan involvement

tag: ever treated_for_sarcoidosis


title: Sarcoidosis (Progressive) 15

value: male

tag: acute disease

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc1 (mrna)

tag: pc2 (mrna)


title: Sarcoidosis (Non-Progressive) 37

tag: diagnosis

tag: Sex

tag: race

tag: pc3 (mrna)

tag: pc4 (mrna)


title: HL60_shDDX6_Input_3

tag: tissue

tag: cell line

tag: genotype


title: EV_LTBR_3

description:
EV_LTBR agonist mAb
an_geo_2023.h5ad

tag: treatment

value: LTBR


title: HL60_shCTRL_Input_2


title: Sarcoidosis (Non-Progressive) 33

tag: age

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

tag: scadding stage

tag: multiorgan involvement

tag: pc5 (mrna)


title: HL60_shDDX6_Input_2


title: EV_LTBR_2

description:
EV_LTBR agonist mAb
an_geo_2023.h5ad


title: Sarcoidosis (Non-Progressive) 30

tag: acute disease

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

value: y

tag: pc1 (mrna)


title: NF1

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned against mouse mm10 genome using HISAT2 (v2.0.5)
Each gene-level raw counts were calculated using featureCounts (v1.5.2)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited  raw count file

source_name: NF1-4 month repeat

extract_protocol:
Sciatic nerves were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: sciatic nerve

value: 4 months

value: Nf1fl/fl; Dhh Cre


title: HL60_shDDX6_Input_1

tag: tissue

value: Peripheral blood


title: EV_LTBR_1

description:
EV_LTBR agonist mAb
an_geo_2023.h5ad

tag: cell line


title: Sarcoidosis (Non-Progressive) 7

tag: diagnosis

tag: Sex

tag: race

value: white

value: never

value: n

tag: pc2 (mrna)

tag: pc3 (mrna)

tag: pc4 (mrna)


title: Sarcoidosis (Non-Progressive) 28

value: bronchoalveolar lavage cells

tag: age

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: multiorgan involvement


title: PKO-NF1

tag: genotype

value: P2RY14-/- Nf1fl/f Dhh Cre


title: PKO

source_name: PKO only


title: Sarcoidosis (Non-Progressive) 27

value: female

value: black

tag: acute disease

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc5 (mrna)


title: EV_ISO_3

description:
EV_Isotype control
an_geo_2023.h5ad

tag: tissue

value: colon

tag: cell line

tag: treatment

value: ctrl


title: EV_ISO_2

description:
EV_Isotype control
an_geo_2023.h5ad


title: EV_ISO_1

description:
EV_Isotype control
an_geo_2023.h5ad


title: WT

source_name: WT

tag: strain


title: Trm2KO 50ug/mL hygB #2

city: Ann Arbor

first: Rachel

middle: Orion

last: Niederer

state: MI

address: 1150 W. Medical Center Dr

department: Biological Chemistry

institute: University of Michigan

data_processing:
This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq). BCL Convert Conversion Software v3.9.3 (Illumina) was used to generate de-multiplexed Fastq files
We use Snakemake(Köster and Rahmann, 2012)to manage the bioinformatics workflow in a reproducible manner
The reads were trimmed using Cutadapt v2.3(Martin, 2011)
The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data
Reads were mapped to the reference genome Saccharomyces_cerevisia (ENSEMBL ), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011)
Assembly: Saccharomyces_cerevisia (ENSEMBL )
Supplementary files format and content: .txt files, read counts

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: trm2KO Saccharomyces cerevisiaewere grown in the presence of 200 μg/mL Geneticin. Briefly, 10 mL of YPD medium was inoculated with a single colony selected from a plate and allowed to grow overnight at 30℃ and 250 RPM. The cells were diluted to an OD600of 0.1 with 200 mL of YPD medium and were grown to an OD600between 0.6 and 0.8 at 30℃ and 250 RPM.

extract_protocol:
The 200 mL cell pellet was resuspended in 8 mL of lysis buffer (60 mM sodium acetate pH 5.5, 8.4 mM EDTA) and 800 μL of 10% SDS. One volume (8.8 mL) of phenol was added and vigorously vortexed. The mixture was incubated at 65℃ for five minutes and was again vigorously vortexed. The incubation at 65℃ and vortexing was repeated once. Then, the mixture was rapidly chilled in an ethanol/dry ice bath and centrifuged for 15 minutes at 15,000 x g. The total RNA was extracted from the upper aqueous phase using a standard acid phenol-chloroform extraction. The extracted total RNA was treated with 140 U RNase-free DNase I (Roche, 10 U/μL) at 37℃ for 30 min. The DNase I was removed through an acid phenol-chloroform extraction.
First, small RNA (tRNA and small rRNA) was diminished using the MEGAclear Transcription Clean-Up Kit (Invitrogen) to purify RNA >200nt. Then, two consecutive Dynabeads oligo-dT magnetic bead selections (Invitrogen, USA) were used to purify poly(A) RNAs from 140 μg of small RNA depleted RNA. The resulting RNA was ethanol precipitated and resuspended in 14 μL. Subsequently, we used the commercial riboPOOL rRNA depletion kit (siTOOLs Biotech, Germany) to remove residual 5S, 5.8S, 18S, and 28S rRNA.

treatment_protocol: Translational stressS. cerevisiaewere grown with 50 μg/mL hygromycin B or 100 ng/mL cycloheximide. Hygromycin BS. cerevisiaewere grown to an OD600of 0.4 to ensure cells were in mid-log phase growth. This cell culture was pelleted at 15,000 x g at 4℃ and used for the RNA extraction.

tag: cell type

value: yeast

value: 50ug/mL Hygromycin B


title: Trm2KO no hygB #2


title: Sarcoidosis (Non-Progressive) 26

tag: diagnosis

value: sarcoidosis (non-progressive)

tag: age

tag: Sex

tag: race

value: not Hispanic or Latino

tag: pc1 (mrna)

tag: pc2 (mrna)

tag: pc3 (mrna)

tag: pc4 (mrna)


title: Trm2KO no hygB #1

tag: genotype


title: Py8119_Ribotag_Tumor_63A6_5_HA

city: Chicago

first: Jan

middle: K

last: Kitajewski

state: IL

address: 909 S. Wolcott Ave. MC 901

department: Dept. of Physiology and Biophysics

institute: University of Illinois at Chicago

data_processing:
Raw reads (fastq) were aligned with the mouse genome (mm10) using STAR (version 2.7.4a).
The same files were processed to obtain raw counts by FeatureCounts (version 2.0.1)
Differential gene expression analysis was performed using a design formula in DESeq2 (design = ~condition) and changes in gene expression were assessed by Log-fold changes (LFC).
Assembly: Human Genome (ENSEMBL/GRCh38); Mouse Genome (UCSC/mm10)
Supplementary files format and content: Raw count files (.txt) were generated using FeatureCounts (v1.5.2) ; Normalized count files (.csv) were generated by DESeq2.

source_name: IP_Endothelial Cells

growth_protocol: Py8119 tumor cells were implanted into the left fifth mammary fat pad of female C57BL/6J mice

extract_protocol:
After the mice were euthanized, tumors were rapidly resected and snap frozen in liquid nitrogen. Samples were stored at -80oC until polysome immunoprecipitation. To isolate actively translating mRNA from endothelial cell polysomes, the tumor tissue was pulverized with a mortar and pestle in liquid nitrogen and suspended in RNA tissue lysis buffer [50mM Tris pH 7.5 (Invitrogen), 100mM KCl (Invitrogen), 15mM MgCl2 (Invitrogen), 100μg of  cycloheximide (Sigma Aldrich), 1% Triton X-100 (Fisher Sci), 1mM DTT (Sigma Aldrich), 7.5μL/mL Protector RNA (Roche), 12μL/mL Turbo DNAse (Thermofisher), 10μL/mL Halt Protease Inhbitor (Thermofisher), RNAse-Free H2O (Fisher Sci)]. The mixture was transferred to a glass Dounce homogenizer on ice and then lysed with 10 strokes of pestle A followed by an additional 10 strokes with pestle B. The lysed mixture was transferred to an ice-cold microcentrifuge tube and spun at 16000x G for 10mins at 4oC. The supernatant was aspirated and 100μL was set aside for input analysis. The remainder of the supernatant was added to Dynabeads (Thermofisher) conjugated to anti-HA antibodies (Abcam) and rocked on ice for 2hrs. The beads were separated by magnetic separation, washed twice with wash buffer, and then eluted using TRIzol (Thermofisher). The mRNA was isolated using a TRIzol Microprep Kit (Zymo Research) and eluted into 13μL of RNAse free H2O. Prior to submitting the samples for sequencing, RNA quality and concentration was assessed using an Agilent TapeStation 4200. Sequencing was performed on the NovaSeq 6000 (SP flow cell, 100bp single reads)
RNA quality and concentration was assessed using an Agilent TapeStation 4200. Sequencing was performed on the NovaSeq 6000 (SP flow cell, 100bp single reads)

treatment_protocol: Once tumors reached ~30mm3, mice were randomized and then injected intravenously through the retro-orbital sinus with either 25mg/kg of 6-3-A6 antibody or control mouse IgG (Jackson ImmunoResearch) twice weekly for 10 days.

tag: ribotag mice

value: Rpl22HA/HA x Cdh5CreERT2

tag: tumor type

value: Py8119 mammary tumors

tag: developmenta stage

value: 3 weeks old

value: IP_Endothelial Cells

tag: treatment harvest_time

value: 10 days after treatment


title: WT 50ug/mL hygB #2

value: WT


title: control-12-CVB4-1

city: New York

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v6.1.1).
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference (GRCh38-2020-A) plus SARS-CoV-2 viral genome (NC_045512.2) and CVB4 viral genome (AF311939.1) and to extract gene expression UMI counts matrix.
Assembly: GRCh38
Supplementary files format and content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

source_name: islets

extract_protocol:
Total RNA was extracted in TRIzol (Invitrogen) and DNase I treated using Directzol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions.
scRNAseq libraries were prepared using the Chromium Next GEM Single Cell 3' v3.1 (Dual index) according to the manufacturer’s instructions.

value: islets


title: control-12-CVB4-2


title: Py8119_Ribotag_Tumor_63A6_4_HA


title: Sarcoidosis (Non-Progressive) 24

tag: tissue

value: bronchoalveolar lavage cells

value: white

tag: ethnicity

tag: smoking status

value: never

tag: scadding stage

tag: acute disease

value: n

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc5 (mrna)


title: control-12-mock

tag: cell type

tag: treatment

value: mock


title: WT 50ug/mL hygB #1

tag: strain

tag: genotype


title: Py8119_Ribotag_Tumor_63A6_3_HA

tag: ribotag mice

tag: tumor type

tag: developmenta stage


title: Trm2KO 50ug/mL hygB #1


title: WT no hygB #2


title: control-11-SARS-CoV-2


title: Sarcoidosis (Non-Progressive) 22

tag: tissue

tag: diagnosis

tag: age

tag: Sex

value: male

tag: race

tag: ethnicity

value: former

value: y

tag: pc1 (mrna)

tag: pc2 (mrna)

tag: pc3 (mrna)

tag: pc4 (mrna)


title: WT no hygB #1

tag: cell type

value: yeast


title: Sarcoidosis (Non-Progressive) 21

value: sarcoidosis (non-progressive)

value: female

value: not Hispanic or Latino

tag: smoking status

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc5 (mrna)


title: control-10-CVB4

tag: treatment


title: ATACseq_gastruloids_dTAG@96H_120H_rep2

city: Amsterdam

first: Mikhail

last: Magnitov

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

description: ATAC-seq samples were used to perform deconvolution, but not downstream analyses. Therefore, these samples do not have any processed data files.

data_processing:
ATAC-seq: ATAC-seq reads were mapped to the mm10 mouse reference genome assembly bwa mem. Uniquely mapped reads that were not mapped to mitochondrial DNA and had MAPQ > 10 were selected using SAMtools. Duplicate reads were filtered out using the Picard “MarkDuplicates” function. RNA-seq: RNA-seq reads were mapped to the mm10 mouse reference genome assembly using STAR with GENCODE vM25 gene annotation. Read counts per gene were obtained using the "quantMode" parameter in STAR.
Assembly: mm10
Supplementary files format and content: RNA-seq: read counts per gene in TXT format.

source_name: Whole gastruloid

growth_protocol: Mouse Embryonic Stem Cells E14Tg2A (129/Ola) cell lines were cultured on 0.1% gelatin-coated plates in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%, Gibco), 10 × 4 U of Leukaemia Inhibitory Factor (LIF) (Millipore), MEK inhibitor PD0325901 (1 μM, Selleckchem), GSK3-β inhibitor CHIR99021 (3 μM, Cayman Chemical) and 1-Thioglycerol (1.5 × 10−4 M, Sigma-Aldrich). The cell lines were passaged every 2 days in daily culture.

extract_protocol:
ATAC-seq: Cells were washed in cold PBS and subjected to lysis using a 2x lysis buffer. Subsequently, the cells were centrifuged, and the resulting pellet was treated with 2xTD buffer and 2 uL of transposon mix. RNA-seq: RNA was first isolated using standard RNA isolation procedure from Qiagen RNeasy Mini Kit (Qiagen), including a DNaseI treatment.
ATAC-seq: PCR amplification was conducted using KAPA HiFi HotStart ReadyMix (Roche). Fragments ranging from 200 to 700 bp were purified utilising AMPure XP beads (Beckman Coulter). RNA-seq: Libraries were prepared following the TruSeq Stranded mRNA kit (Illumina) with TruSeq RNA Single Indexes set A (Illumina).

treatment_protocol: For the knock-in of the FKBP sequence at the genes of interest, cells were transfected with the plasmids containing the gRNA sequence and the donor plasmid designed to include the FKBP-2xHA-P2A-GFP in between two homology arms for the gene of interest. To induce ZFP143 degradation, the cells were treated with 500 nM dTAG-V1 or DMSO as a control.

tag: tissue

value: Whole gastruloid

tag: cell line

tag: genotype

tag: collection time


title: Py8119_Ribotag_Tumor_63A6_5_Input

source_name: Homogenate

tag: strain

tag: ribotag mice

value: Rpl22HA/HA x Cdh5CreERT2

tag: tumor type

value: Py8119 mammary tumors

tag: developmenta stage

value: 3 weeks old

value: Homogenate

tag: treatment harvest_time


title: Sarcoidosis (Non-Progressive) 20

value: bronchoalveolar lavage cells

tag: diagnosis

tag: age

tag: Sex

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease

tag: pc1 (mrna)

tag: pc2 (mrna)

tag: pc3 (mrna)

tag: pc4 (mrna)


title: Sarcoidosis (Non-Progressive) 29

tag: tissue

value: white

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

tag: pc5 (mrna)


title: Sarcoidosis (Non-Progressive) 25

tag: diagnosis

tag: age

tag: Sex

value: never


title: Py8119_Ribotag_Tumor_63A6_2_HA

tag: strain

tag: ribotag mice

tag: tumor type

tag: developmenta stage

tag: cell type

value: IP_Endothelial Cells

tag: treatment

tag: treatment harvest_time

value: 10 days after treatment


title: control-10-SARS-CoV-2

value: islets


title: Sarcoidosis (Non-Progressive) 2

tag: tissue

tag: race

value: black

tag: ethnicity

tag: smoking status

value: former

tag: scadding stage

tag: acute disease

value: n

tag: pc1 (mrna)

tag: pc2 (mrna)

tag: pc3 (mrna)

tag: pc4 (mrna)


title: ATACseq_gastruloids_dTAG@72H_120H_rep2

tag: cell line

tag: genotype

tag: collection time


title: Py8119_Ribotag_Tumor_63A6_4_Input

tag: strain

tag: ribotag mice

tag: tumor type

tag: developmenta stage


title: control-10-mock

tag: cell type

tag: treatment

value: mock


title: Sarcoidosis (Non-Progressive) 16

tag: tissue

tag: diagnosis

value: sarcoidosis (non-progressive)

tag: age

tag: Sex

value: male

tag: race

tag: ethnicity

value: Hispanic or Latino

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: ever treated_for_sarcoidosis

value: y

tag: pc5 (mrna)


title: control-11-mock


title: ATACseq_gastruloids_dTAG@72H_96H_rep2

value: Whole gastruloid

tag: cell line

tag: genotype

tag: collection time


title: Py8119_Ribotag_Tumor_63A6_3_Input

tag: strain

tag: ribotag mice

value: Rpl22HA/HA x Cdh5CreERT2

tag: tumor type

value: Py8119 mammary tumors

tag: developmenta stage

value: 3 weeks old

tag: cell type

tag: treatment harvest_time


title: control-9-SARS-CoV-2

tag: treatment


title: ATACseq_gastruloids_dTAG@48H_120H_rep2

tag: tissue


title: Sarcoidosis (Non-Progressive) 11

value: bronchoalveolar lavage cells

tag: diagnosis

tag: age

tag: Sex

tag: race

value: asian

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: pc1 (mrna)

tag: pc2 (mrna)

tag: pc3 (mrna)

tag: pc4 (mrna)


title: ATACseq_gastruloids_dTAG@48H_96H_rep2

tag: cell line

tag: genotype

tag: collection time


title: Py8119_Ribotag_Tumor_63A6_2_Input

tag: strain

tag: ribotag mice

tag: tumor type

tag: developmenta stage

tag: cell type

value: Homogenate

tag: treatment

tag: treatment harvest_time

value: 10 days after treatment


title: control-9-mock

value: islets


title: Healthy Control 9

tag: tissue

tag: diagnosis

value: control

tag: age

tag: Sex

tag: race

value: white

tag: ethnicity

tag: smoking status

value: never

tag: scadding stage

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc5 (mrna)


title: Py8119_Ribotag_Tumor_63A6_1_HA

tag: strain

tag: ribotag mice

tag: tumor type

value: IP_Endothelial Cells


title: Py8119_Ribotag_Tumor_63A6_1_Input

tag: developmenta stage

tag: cell type

tag: treatment


title: ATACseq_gastruloids_dTAG@48H_72H_rep2

tag: tissue

tag: cell line

tag: genotype

tag: collection time


title: Day 10 HyA-FMB organoid, donor 1, scRNAseq

city: Bethesda

first: Pamela

middle: Gehron

last: Robey

state: MD

address: 30 Convent Dr

department: NIDCR

institute: NIH

description: 10x Genomics

data_processing:
Reads were mapped using GRCh38-2020-A reference transcriptome
Libraries were processed using Cell Ranger version 7.0.
Secondary analysis was performed using Seurat's R package
Assembly: Reads were mapped using GRCh38-2020-A reference transcriptome
Supplementary files format and content: Cellranger filtered feature barcode matrix in HDF5 format
Supplementary files format and content: Cellranger raw feature barcode matrix in HDF5 format

source_name: Bone marrow (right hip)

extract_protocol:
Control and HyA-FMB organoids from days 1-10 and ectopic HyA-FMB transplant were digested in high-glucose DMEM containing 0.2% collagenase II, 0.1% hyaluronidase, and 0.1% dispase with gentle pipetting every 20-30 minutes.  Enzymatic digestion was observed in 6 well-plates, and digestion was terminated when aggregates were completely dissolved, for up to 2 hours.  Enzyme was inhibited with 20% FBS, and cells were filtered through 70 µm strainers and re-suspended in PBS supplemented with 0.04% high-quality bovine serum albumin at 1000 cells/µL for single-cell capture.  Naïve hBMSC/SSC controls (from donor 3) required a 10-minute incubation with collagenase II on monolayer cultures prior to cell detachment and cell capture.
Single-cell RNA sequencing was performed using 10X Genomics Chromium instruments.

value: Bone marrow (right hip)

tag: age

value: 14 year old

tag: Sex

value: female

value: hBMSC/SSC

value: HyA-FMB scaffold


title: Day 10 control organoid, donor 1, scRNAseq

description: 10x Genomics

value: control (no scaffold)


title: Healthy Control 8

source_name: bronchoalveolar lavage cells

tag: diagnosis

value: male

tag: race

tag: ethnicity

value: Hispanic or Latino

tag: smoking status

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: pc1 (mrna)

tag: pc2 (mrna)

tag: pc3 (mrna)

tag: pc4 (mrna)


title: Py8119_Ribotag_Tumor_Ctl_5_HA

tag: strain

tag: ribotag mice

value: Rpl22HA/HA x Cdh5CreERT2

tag: tumor type

value: Py8119 mammary tumors

tag: developmenta stage

value: 3 weeks old

tag: cell type

tag: treatment

value: Control IgG

tag: treatment harvest_time


title: ATACseq_gastruloids_DMSO@120H_rep2

tag: tissue

value: Whole gastruloid

tag: cell line

tag: genotype

tag: collection time


title: Healthy Control 7

value: bronchoalveolar lavage cells

tag: diagnosis

value: control

tag: age

tag: Sex

tag: race

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

tag: scadding stage

tag: acute disease

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc5 (mrna)


title: Py8119_Ribotag_Tumor_Ctl_3_HA

tag: strain

tag: ribotag mice

tag: tumor type

tag: developmenta stage

tag: cell type

value: IP_Endothelial Cells

tag: treatment

tag: treatment harvest_time

value: 10 days after treatment


title: Py8119_Ribotag_Tumor_Ctl_4_HA


title: Healthy Control 4

tag: tissue

tag: diagnosis

tag: age

tag: Sex

value: white

value: never

tag: multiorgan involvement

tag: pc1 (mrna)

tag: pc2 (mrna)

tag: pc3 (mrna)

tag: pc4 (mrna)


title: Day 5 HyA-FMB organoid, donor 1, scRNAseq

description: 10x Genomics

value: Bone marrow (right hip)

value: 14 year old

value: female

value: hBMSC/SSC


title: Healthy Control 6

value: male

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc5 (mrna)


title: Sarcoidosis (Non-Progressive) 14

tag: tissue

tag: diagnosis

value: sarcoidosis (non-progressive)

value: n

tag: ever treated_for_sarcoidosis


title: ATACseq_gastruloids_DMSO@72H_rep2

tag: cell line

tag: genotype

tag: treatment

tag: collection time


title: Day 5 control organoid, donor 1, scRNAseq

description: 10x Genomics

tag: age

tag: Sex

tag: cell type

value: control (no scaffold)


title: ATACseq_gastruloids_DMSO@96H_rep2


title: Day 3 HyA-FMB organoid, donor 1, scRNAseq

description: 10x Genomics

value: HyA-FMB scaffold


title: ATACseq_gastruloids_dTAG@96H_120H_rep1

value: Whole gastruloid


title: Py8119_Ribotag_Tumor_Ctl_1_HA

tag: strain

tag: ribotag mice

value: Rpl22HA/HA x Cdh5CreERT2

tag: tumor type

value: Py8119 mammary tumors

tag: developmenta stage

value: 3 weeks old

value: Control IgG

tag: treatment harvest_time


title: Healthy Control 3

value: bronchoalveolar lavage cells

value: control

tag: race

value: asian

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc1 (mrna)

tag: pc2 (mrna)

tag: pc3 (mrna)

tag: pc4 (mrna)


title: ATACseq_gastruloids_dTAG@72H_120H_rep1

tag: tissue

tag: cell line

tag: genotype

tag: treatment

tag: collection time


title: Py8119_Ribotag_Tumor_Ctl_5_Input

tag: strain

tag: ribotag mice

tag: tumor type

tag: developmenta stage

tag: cell type

value: Homogenate

tag: treatment harvest_time

value: 10 days after treatment


title: Healthy Control 2

tag: diagnosis

tag: age

tag: Sex

tag: race

value: white

tag: ethnicity

tag: smoking status

value: never

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: pc5 (mrna)


title: Day 1 HyA-FMB organoid, donor 1, scRNAseq

description: 10x Genomics

tag: tissue

value: Bone marrow (right hip)

value: 14 year old

value: female

value: hBMSC/SSC

tag: treatment


title: Healthy Control 16

value: male

tag: dlco (%_predicted)

tag: pc1 (mrna)

tag: pc2 (mrna)

tag: pc3 (mrna)

tag: pc4 (mrna)


title: ATACseq_gastruloids_dTAG@48H_120H_rep1

value: Whole gastruloid

tag: cell line

tag: genotype

tag: collection time


title: Py8119_Ribotag_Tumor_Ctl_4_Input

tag: strain

tag: ribotag mice

value: Rpl22HA/HA x Cdh5CreERT2

tag: tumor type

value: Py8119 mammary tumors

tag: developmenta stage

tag: cell type

tag: treatment harvest_time


title: Day 1 control organoid, donor 1, scRNAseq

description: 10x Genomics

tag: age

tag: Sex

value: control (no scaffold)


title: ATACseq_gastruloids_DMSO@120H_rep1

tag: tissue

tag: treatment


title: Healthy Control 15

value: bronchoalveolar lavage cells

tag: diagnosis

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc1 (mrna)

tag: pc5 (mrna)


title: Healthy Control 14

value: control

tag: pc2 (mrna)

tag: pc3 (mrna)

tag: pc4 (mrna)


title: RNAseq_dTAG_72H_rep2

description: rnaseq_ZFP143_depletion_time_course.gene_counts.txt

tag: cell line

tag: cell type

value: Embryonic Stem Cell

tag: genotype

tag: time


title: Py8119_Ribotag_Tumor_Ctl_2_HA

tag: strain

tag: ribotag mice

tag: tumor type

tag: developmenta stage

value: 3 weeks old

value: IP_Endothelial Cells

tag: treatment

value: Control IgG

tag: treatment harvest_time


title: Py8119_Ribotag_Tumor_Ctl_2_Input

value: Homogenate

value: 10 days after treatment


title: Py8119_Ribotag_Tumor_Ctl_3_Input


title: Healthy Control 12

tag: tissue

tag: diagnosis

tag: age

tag: Sex

tag: race

value: white

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

value: never

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: fvc (%_predicted)

tag: fev1 (%_predicted)


title: Treg scRNA multiplex oligos

description:
CM
features.tsv.gz
barcodes.tsv.gz
matrix.mtx.gz
filtered_feature_bc_matrix.h5

library_source: other

data_processing:
Since the feature barcoding libraries contained both multiplexing and CD127 (IL7-Ra) tags, the fastq files were first split based on whether an exact match to one of the hashtag oligos for multiplexing was found starting in position 11 in the “R2” feature barcoding fastq file (with read length 90). These split files are those provided within this accession.
The separated multiplexing and antibody-derived tag fastq files, together with the gene expression fastq files, were then processed using Cell Ranger v6.1.2, first with cellranger multi, using the GRCm38 mouse genome reference, and specifying the antibody tag/multiplexing oligo sequences as beginning at position 11.
The data from cells assigned as control or knockout were then merged from the per sample outputs, using cellranger aggr; control and knockout cells were indicated by the suffix "-1" and "-2", respectively, appended to the cell barcodes.
Downstream analysis was performed using the Seurat package (https://doi.org/10.1016/j.cell.2019.05.031)
Assembly: GRCm38
Supplementary files format and content: Tab-delimited files containng the features, cell barcodes and count matrix output from cellranger aggr. Note that the suffix "-1" on the cell barcodes indicates a control cell, whilst "-2" indicated a Zfp36l1/Zfp36l2 knockout cell.
Supplementary files format and content: h5 file output from cellranger aggr. As above, the suffix "-1" on the cell barcodes indicates a control cell, whilst "-2" indicated a Zfp36l1/Zfp36l2 knockout cell.
Library strategy: Multiplexing Capture

molecule: protein

source_name: Lymph node

extract_protocol:
Single cell suspensions were prepared from pooled LN from one control (Foxp3-YFP-Cre) and one conditional knockout (Foxp3-YFP-Cre Zfp36l1-fl/fl Zfp36l2-fl/fl) mouse at 14 weeks of age. CD4+ cells were enriched by negative depletion using biotinylated anti-B220, anti-CD8 and anti-F4/80 followed by Streptavidin Dynabeads (Dynal). Treg were sorted to >95% purity as CD4+FR4+YFP+ cells. Cells were labelled using Totalseq oligo-conjugated antibodies (BioLegend) to enable multiplexing of control (hashtag 1: ACCCACCAGTAAGAC) and conditional knockout (hashtag 2: GGTCGAGAGCATTCA) samples, and feature barcoding of CD127 (IL7-Ra; GTGTGAGGCACTCTT).
The sorted and labelled single cell suspensions were mixed and loaded onto a Chromium single cell device (10x Genomics) for encapsulation with barcoded gel beads according to the manufacturer’s Single Cell 3' v3.1 (Dual Index) protocol. 3’GEX and 3’ Feature barcoding libraries were prepared according to the standard manufacturer’s protocol. The resulting libraries were sequenced on an Illumina NovaSeq 6000 S1 flowcell

tag: strain

value: Lymph node

tag: cell type

value: Treg

tag: genotype

value: Mix of Foxp3YFP-Cre and Foxp3YFP-Cre Zfp36l1fl/fl Zfp36l2fl/fl

value: Male

value: 14 weeks


title: RNAseq_dTAG_72H_rep1

tag: cell line

tag: treatment

tag: time


title: RNAseq_dTAG_48H_rep2


title: Treg scRNA IL7-Ra antibody tag

description:
FB
features.tsv.gz
barcodes.tsv.gz
matrix.mtx.gz
filtered_feature_bc_matrix.h5

data_processing:
Since the feature barcoding libraries contained both multiplexing and CD127 (IL7-Ra) tags, the fastq files were first split based on whether an exact match to one of the hashtag oligos for multiplexing was found starting in position 11 in the “R2” feature barcoding fastq file (with read length 90). These split files are those provided within this accession.
The separated multiplexing and antibody-derived tag fastq files, together with the gene expression fastq files, were then processed using Cell Ranger v6.1.2, first with cellranger multi, using the GRCm38 mouse genome reference, and specifying the antibody tag/multiplexing oligo sequences as beginning at position 11.
The data from cells assigned as control or knockout were then merged from the per sample outputs, using cellranger aggr; control and knockout cells were indicated by the suffix "-1" and "-2", respectively, appended to the cell barcodes.
Downstream analysis was performed using the Seurat package (https://doi.org/10.1016/j.cell.2019.05.031)
Assembly: GRCm38
Supplementary files format and content: Tab-delimited files containng the features, cell barcodes and count matrix output from cellranger aggr. Note that the suffix "-1" on the cell barcodes indicates a control cell, whilst "-2" indicated a Zfp36l1/Zfp36l2 knockout cell.
Supplementary files format and content: h5 file output from cellranger aggr. As above, the suffix "-1" on the cell barcodes indicates a control cell, whilst "-2" indicated a Zfp36l1/Zfp36l2 knockout cell.
Library strategy: Antibody Capture

tag: tissue


title: Healthy Control 11

tag: diagnosis

tag: age

value: male

tag: dlco (%_predicted)

tag: pc1 (mrna)

tag: pc2 (mrna)

tag: pc3 (mrna)

tag: pc4 (mrna)

tag: pc5 (mrna)


title: Healthy Control 10

value: bronchoalveolar lavage cells

tag: Sex

tag: race

tag: ethnicity

tag: smoking status

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: fvc (%_predicted)


title: Day 3 control organoid, donor 1, scRNAseq

description: 10x Genomics

tag: tissue

value: Bone marrow (right hip)

value: 14 year old

value: female

tag: cell type

value: hBMSC/SSC

tag: treatment

value: control (no scaffold)


title: RNAseq_dTAG_24H_rep2

tag: cell line

value: Embryonic Stem Cell

tag: genotype

tag: time


title: Healthy Control 13

tag: diagnosis

value: control

tag: age

tag: fev1 (%_predicted)

tag: dlco (%_predicted)

tag: pc1 (mrna)

tag: pc2 (mrna)

tag: pc3 (mrna)


title: Treg scRNA 3' gene expression

description:
GEX
features.tsv.gz
barcodes.tsv.gz
matrix.mtx.gz
filtered_feature_bc_matrix.h5

data_processing:
Since the feature barcoding libraries contained both multiplexing and CD127 (IL7-Ra) tags, the fastq files were first split based on whether an exact match to one of the hashtag oligos for multiplexing was found starting in position 11 in the “R2” feature barcoding fastq file (with read length 90). These split files are those provided within this accession.
The separated multiplexing and antibody-derived tag fastq files, together with the gene expression fastq files, were then processed using Cell Ranger v6.1.2, first with cellranger multi, using the GRCm38 mouse genome reference, and specifying the antibody tag/multiplexing oligo sequences as beginning at position 11.
The data from cells assigned as control or knockout were then merged from the per sample outputs, using cellranger aggr; control and knockout cells were indicated by the suffix "-1" and "-2", respectively, appended to the cell barcodes.
Downstream analysis was performed using the Seurat package (https://doi.org/10.1016/j.cell.2019.05.031)
Assembly: GRCm38
Supplementary files format and content: Tab-delimited files containng the features, cell barcodes and count matrix output from cellranger aggr. Note that the suffix "-1" on the cell barcodes indicates a control cell, whilst "-2" indicated a Zfp36l1/Zfp36l2 knockout cell.
Supplementary files format and content: h5 file output from cellranger aggr. As above, the suffix "-1" on the cell barcodes indicates a control cell, whilst "-2" indicated a Zfp36l1/Zfp36l2 knockout cell.

tag: strain

tag: Sex


title: RNAseq_dTAG_48H_rep1


title: RNAseq_dTAG_24H_rep1


title: Omental adipose tissue fibroblasts, mRNA-derived cDNA

city: Boston

first: Heather

last: Faust

state: MA

address: 60 Fenwood Road

institute: Brigham and Women's Hopsital

description:
contains Subject_IDs P11, P10, P49, P08, and P50 pooled
Meta_data_healthy_adipose_tissue_fibroblasts.csv
Normalized_count_matrix_healthy_adipose_tissue_fibroblasts.csv
BRI458

data_processing:
Reads were processed with Cell Ranger v3.1, which demultiplexed cells from different samples and quantified transcript counts per putative cell. Quantification was performed using the STAR aligner against the GRCh38-3.0.0 transcriptome.
Further processing was done with Seurat v 4.0.1 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: GRCh38-3.0.0
Supplementary files format and content: csv file includes normalized counts for each cell

source_name: Omental adipose tissue

extract_protocol:
Samples were thawed in a 37ºC water bath and strained over 100µm gauze with PBS to wash out remaining CellSTOR™. Thereafter, adipose explants were extensively mechanically minced and placed into 6 mL pre-warmed (37ºC) adipose tissue media (referred to as adipose buffer hereon in) at pH 7.4 containing 5.5mM D-glucose (Sigma-Aldrich), 140mM sodium chloride, 4.7mM potassium chloride, 1.25mM magnesium sulfoxide heptahydrate, 2.5mM calcium chloride dihydrate, 10mM HEPES, 2.5mM sodium phosphate monobasic dihydrate, and 2 % bovine serum albumin (BSA) fraction V, spiked with type-1 collagenase (250U/mL) (Worthington Biochemical). Samples were agitated at 180–200 rpm on a orbital shaker () at 37ºC for 45–60 minutes. Digestions were terminated with 2 volumes of PBS containing 10 % FBS with 2mM ethylenediaminetetraacetic acid (EDTA). Following digestion, samples were passed through a 400 μm gauze and centrifuged at 100 x g for 1 minute at RT, whereupon the adipocyte fraction was aspirated and discarded. The remaining post-digestion solution was centrifuged at 300 x g for 7 minutes at RT, and was thereafter incubated with 9 volumes erythrocyte lysis buffer for 10 minutes at RT. Post-lysis, samples were topped up with adipose buffer, centrifuged once more at 300 x g for 7 minutes at RT and the supernatant discarded before topping up with adipose buffer for filtering through 100 μm gauze, and centrifuged once more at 300 x g for 7 minutes at RT before being resuspended in PBS containing 2mM EDTA and 2 % FBS (referred to hereon in as FACS buffer). Following stromal cell isolation cell sorting was undertaken on a BD™FACSAria III cell sorter (BD Biosciences) to separate CD45+/- events.
Library generation was performed according to the manufacturer’s protocol (Chromium Single Cell 3ʹ kit (10x Genomics).

value: Omental adipose tissue

value: fibroblasts

value: mRNA


title: Healthy Control 1

tag: race

value: white

tag: ethnicity

value: not Hispanic or Latino

tag: smoking status

value: never

tag: scadding stage

tag: acute disease

tag: multiorgan involvement

tag: pc4 (mrna)

tag: pc5 (mrna)


title: RNAseq_DMSO_rep2

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: DMSO


title: Piezo2_KO_IR_1

city: Shanghai

first: Wenwen

last: Li

address: Room 1004, West #5 Building, 280 South Chongqing Road, Shanghai 200025, China

institute: Shanghai Institute of Immunology; Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine

data_processing:
Using HISAT2 RNA-sequencing alignment software, the raw reads were aligned to the mouse reference genome
The mapping rate was 96%, on average, across all the samples in the dataset. The alignment files (bam files) were processed to generate read counts for every gene using HISAT and HTSeq.
The read counts were normalized using the R package DESeq2 and then were centered and scaled for each gene, generating z-scores. P values obtained from multiple tests were adjusted using the Benjamini-Hochberg correction.
Assembly: mm10
Supplementary files format and content: csv file includes read counts for each sample

extract_protocol:
total RNA from samples was extracted using Trizol Reagent following standard protocols and 1 ug of total RNA was used for the construnction of sequencing libraries.
RNA libraries for RNA-seq were preparing using bulk RNA-seq following manufacturer's protocols.

treatment_protocol: WT-MC38 (CRISPR-Ctrl) or Piezo2-KO MC38 (Piezo2-gRNA1) tumor cells were subjected to single fraction of X-ray (30 Gy).

value: Epithelial cell line

value: Piezo2 KO

value: IR


title: Subcutaneous adipose tissue fibroblasts, mRNA-derived cDNA

description:
contains Subject_IDs P11, P10, P49, P08, and P50 pooled
Meta_data_healthy_adipose_tissue_fibroblasts.csv
Normalized_count_matrix_healthy_adipose_tissue_fibroblasts.csv
BRI456

source_name: Subcutaneous adipose tissue

tag: tissue

value: Subcutaneous adipose tissue


title: RNAseq_DMSO_rep1


title: S41

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
For 10X analyses, alignment and UMI counting were performed by using the Cellranger program with default parameters and human hg38 reference genome plus S41 sequence (AF316321). Feature-barcode count matrix obtained from Cellranger was used for the downstream analyses using Seurat in R.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hESC-derived spinal neuronal cultures

growth_protocol: H7 ESCs were differentiated toward motor neurons using a well-established protocol as previously published (Hor et al., 2021; Hor et al., 2018; Ng et al., 2015).

extract_protocol:
EV71-infected (MOI 5) and mock-infected cells were harvested at 6 hpi for scRNA-Seq. Cells were detached by accutase treatment for 10 minutes at 37°C and single-cell suspensions were resuspended in PBS+0.02% BSA.
Single-cell RNA sequencing libraries were prepared using 10x genomics Chromium Single cell 3 prime workflow and sequenced in Novogene 6000.

value: hESC-derived spinal neuronal cultures


title: Piezo2_KO_nonIR_2

value: Non-IR


title: wt 14h IAA BR4

city: Freiburg

first: Elham

last: Bavafaye Haghighi

address: Breisacherstr. 153

department: Institut für Medizinische Bioinformatik und Systemmedizin

institute: University Hospital of Freiburg

description: File name 2 has barcodes and UMIs, please see protocols and preprocessing

data_processing:
Dropseq tool v1.12 (Macosko et al., 2015) was used for mapping raw sequencing data to the reference genome with default parameters
Create bam file without alignment
java -jar PATHTOPICARD/picard.jar FastqToSam F1=FORWARDREAD F2=REVERSEREAD O=RUNNAME.bam SM=RUNNAME
Sort bam file according to read ID
java -jar PATHTOPICARD/picard.jar SortSam I=RUNNAME.bam O=RUNNAME_sorted.bam SORT_ORDER=queryname
Start Dropseq tool
PATHTODROPSEQTOOLS/Drop-seq_alignment.sh -g PATHTOSTARINDEX -r PATHTOGENOMEREFERENCE -d PATHTODROPSEQTOOLS -s PATHTOSTARALIGNER -o OUTPUTFOLDER RUNNAME_sorted.bam
Get UMI filtered matix
PATHTODROPSEQTOOLS/DigitalExpression' -m 30g -t I=star_gene_exon_tagged.bam O=DGE_Matrix.txt CELL_BARCODE_TAG=XC MOLECULAR_BARCODE_TAG=XM CELL_BC_FILE=BARCODESUSED
Assembly: Gencode gene annotations v28 and the human reference genome GRCh38 were derived from the Gencode homepage (EMBL-EBI).
Supplementary files format and content: Tab-delimited text file includes raw count values for each sample.

source_name: HaCaT

growth_protocol: Cells were cultured in DMEM (gibco, art N° 41965062), supplemented with 10% FCS (anprotec, art N° AC-SM-0190) and 1% penicillin/streptomycin (gibco, art N° 15140130).

extract_protocol:
Direct-zol™ RNA MicroPrep with TRI Reagent® from Zymo Research, art N° R2061
Total RNA was isolated from purified Treg cells and Tconv cells with RNAeasy Plus micro kit (QIAGEN). Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies). RNaseq analysis: library preparation for bulk 30-sequencing of poly(A)-RNA was done as described previously (Parekh et al., 2016). Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adaptor. 50 ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. NEB UltraII FS kit was used to fragment cDNA. After end repair and A-tailing a TruSeq adapter was ligated and 3’-end-fragments were finally amplified using primers with Illumina P5 and P7 overhangs. In comparison to Parekh et al. (2016), the P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 75 cycles for the cDNA in read1 and 16 cycles for the barcodes and UMIs in read2.

treatment_protocol: Auxin (IAA, indole-3-acetic acid) was dissolved in 50mM stock in DMSO. 250K cells were seeded and treated the next day: Media was changed and cells were treated with fresh media supplemented with auxin (20µM) or DMSO as solvent control.

value: HaCaT

value: immortalized human keratinocytes

value: CrisprLV2_iCADE4ko_puro - pFUG147EV16_Tir1_PGK_Hygro_W -  pEF1a_GW_iCADMutE4_mAID_GFP_puro

value: Auxin (3-indolacetic acid, IAA) 20µM, 14h

tag: time

value: 14 hours


title: Mock


title: wt 14h IAA BR3