cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.17955906
title: Data, scripts, and files for Allospecific splenic Tr1 cells drive effector T cell exhaustion through upregulated Areg-EGFR signaling to promote transplant tolerance

description: Article abstract

Inducing stable tolerance to transplants remains a challenge in immunology. Previously, we induced tolerance to allogeneic islets in nonhuman primates by preemptive alloantigen delivery to antigen-presenting cells in situ. Here, mass cytometry phenotyping with incorporated donor-derived MHC-I peptide-loaded MHC-II tetramers revealed accumulation of allospecific CD4+ T cell clusters in the spleen of tolerant recipients. Areg+Tr1 regulatory and terminally exhausted EGFRhi T (Tex) cells represented the predominant allospecific subsets. Trajectory analysis showed that antigen-experienced effector memory T cells differentiated into suppressive Areg+Tr1 and EGFR+TOX+Nur77+TCF-1- Tex subsets. Cell-cell communication mapping showed that exhausted and effector memory T cells engaged with allospecific Tr1 cells via the Areg-EGFR axis. Gene silencing studies confirmed that Tr1 cells utilize Areg-EGFR signaling to drive the metabolic suppression and epigenetic reprogramming of CD4⁺ T cells through a Nur77-dependent pathway. These findings point to the splenic Areg⁺Tr1 cell-EGFR⁺Teff cell axis as a critical immunoregulatory pathway in peripheral transplant tolerance.

 

Brief explanation

Here we provide the raw and processed CyTOF (mass cytometry by time of flight) data and R analysis scripts used to arrive at these conclusions for each cell type mentioned above. CyTOF data is provided as FCS-format files representing counts for thousands of cells and up to 36 mass-tagged protein markers.
description: In the attached dataset, there are four separate directories representing four main cell groupings presented in the paper. Each directory comprises raw and transformed FCS files for the CyTOF data, a sample metadata file, R scripts for transformation of fcs files and conversion to Seurat R objects, and the R object itself.

Directories



Total_cells

MHCI+_CD4_T_cells

MHCI+_PD-1hi

MHCI+_Tr1


Directory contents

raw



directory containing untransformed FCS files


transformed



directory containing arcsinh transformed FCS files


process_raw_[cell_type].txt



R script that reads in raw files, transforms and performs centroid correction and write transformed files


make_seurat_[cell_type].txt



R script that reads in transformed FCS files and metadata (see file below) creating a combined Seurat object for each individual and tissue


sample_ref_[cell_type].txt



tab-sepated file containing sample metadata. 

explanation of columns



file - name of the .fcs CyTOF file

tissue - tissue of origin (spleen (spl) or peripheral blood (pbl))

cohort - experimental group of animal

animal - individual animal ID

batch - batch that CyTOF data was collected in




all_data_[cell_type].rds



Seurat objects containing transformed marker counts and metadata for each tissue in each individual


Software Information



R version 4+

Seurat version 4.3+

Necessary R packages are shown in the R script files
DOI: 10.5281/zenodo.17955907
title: Data, scripts, and files for Allospecific splenic Tr1 cells drive effector T cell exhaustion through upregulated Areg-EGFR signaling to promote transplant tolerance

description: Article abstract

Inducing stable tolerance to transplants remains a challenge in immunology. Previously, we induced tolerance to allogeneic islets in nonhuman primates by preemptive alloantigen delivery to antigen-presenting cells in situ. Here, mass cytometry phenotyping with incorporated donor-derived MHC-I peptide-loaded MHC-II tetramers revealed accumulation of allospecific CD4+ T cell clusters in the spleen of tolerant recipients. Areg+Tr1 regulatory and terminally exhausted EGFRhi T (Tex) cells represented the predominant allospecific subsets. Trajectory analysis showed that antigen-experienced effector memory T cells differentiated into suppressive Areg+Tr1 and EGFR+TOX+Nur77+TCF-1- Tex subsets. Cell-cell communication mapping showed that exhausted and effector memory T cells engaged with allospecific Tr1 cells via the Areg-EGFR axis. Gene silencing studies confirmed that Tr1 cells utilize Areg-EGFR signaling to drive the metabolic suppression and epigenetic reprogramming of CD4⁺ T cells through a Nur77-dependent pathway. These findings point to the splenic Areg⁺Tr1 cell-EGFR⁺Teff cell axis as a critical immunoregulatory pathway in peripheral transplant tolerance.

 

Brief explanation

Here we provide the raw and processed CyTOF (mass cytometry by time of flight) data and R analysis scripts used to arrive at these conclusions for each cell type mentioned above. CyTOF data is provided as FCS-format files representing counts for thousands of cells and up to 36 mass-tagged protein markers.
description: In the attached dataset, there are four separate directories representing four main cell groupings presented in the paper. Each directory comprises raw and transformed FCS files for the CyTOF data, a sample metadata file, R scripts for transformation of fcs files and conversion to Seurat R objects, and the R object itself.

Directories



Total_cells

MHCI+_CD4_T_cells

MHCI+_PD-1hi

MHCI+_Tr1


Directory contents

raw



directory containing untransformed FCS files


transformed



directory containing arcsinh transformed FCS files


process_raw_[cell_type].txt



R script that reads in raw files, transforms and performs centroid correction and write transformed files


make_seurat_[cell_type].txt



R script that reads in transformed FCS files and metadata (see file below) creating a combined Seurat object for each individual and tissue


sample_ref_[cell_type].txt



tab-sepated file containing sample metadata. 

explanation of columns



file - name of the .fcs CyTOF file

tissue - tissue of origin (spleen (spl) or peripheral blood (pbl))

cohort - experimental group of animal

animal - individual animal ID

batch - batch that CyTOF data was collected in




all_data_[cell_type].rds



Seurat objects containing transformed marker counts and metadata for each tissue in each individual


Software Information



R version 4+

Seurat version 4.3+

Necessary R packages are shown in the R script files
DOI: 10.60586/snt257.zzxw.745
title: 10x Multiome data from the liver of a 71-year-old white male
DOI: 10.25574/12994
title: Chandra X-ray Observatory ObsId 12994

description: REMNANTS, BINARIES, AND DIFFUSE EMISSION IN THE NEARBY GRAND DESIGN SPIRAL M83
DOI: 10.60586/snt373.xvcv.862
title: 10x Multiome data from the liver of a 22-year-old black or african american female
DOI: 10.60586/snt764.ggmc.945
title: 10x Multiome data from the liver of a 33-year-old white female
DOI: 10.25574/12995
title: Chandra X-ray Observatory ObsId 12995

description: REMNANTS, BINARIES, AND DIFFUSE EMISSION IN THE NEARBY GRAND DESIGN SPIRAL M83
DOI: 10.60586/snt433.qjhx.634
title: Histology data from the lung (right) of a 43-year-old white male
DOI: 10.25574/12996
title: Chandra X-ray Observatory ObsId 12996

description: REMNANTS, BINARIES, AND DIFFUSE EMISSION IN THE NEARBY GRAND DESIGN SPIRAL M83
DOI: 10.60586/snt249.grcl.874
title: Histology data from the lung (right) of a 43-year-old white male
DOI: 10.60586/snt946.zgvf.236
title: Histology data from the lung (right) of a 43-year-old white male
DOI: 10.25574/12997
title: Chandra X-ray Observatory ObsId 12997

description: The brightest ultraluminous X-ray sources across the sky
DOI: 10.60586/snt456.cphg.654
title: Histology data from the heart of a 43-year-old white male
DOI: 10.60586/snt879.kndg.637
title: Histology data from the heart of a 43-year-old white male
DOI: 10.60586/snt436.grtv.897
title: Histology data from the heart of a 43-year-old white male
DOI: 10.25574/12998
title: Chandra X-ray Observatory ObsId 12998

description: The brightest ultraluminous X-ray sources across the sky
DOI: 10.60586/snt996.qcdl.442
title: Histology data from the heart of a 43-year-old white male
DOI: 10.25574/12999
title: Chandra X-ray Observatory ObsId 12999

description: The brightest ultraluminous X-ray sources across the sky
DOI: 10.60586/snt396.hlvz.722
title: Histology data from the lung (right) of a 43-year-old white male
DOI: 10.60586/snt497.xvbh.665
title: Histology data from the lung (right) of a 43-year-old white male
DOI: 10.25574/13000
title: Chandra X-ray Observatory ObsId 13000

description: The brightest ultraluminous X-ray sources across the sky
DOI: 10.60586/snt669.nhft.999
title: Histology data from the lung (right) of a 43-year-old white male
DOI: 10.60586/snt594.rrpt.577
title: Histology data from the heart of a 43-year-old white male
DOI: 10.60586/snt665.bcww.993
title: Histology data from the heart of a 43-year-old white male
DOI: 10.25574/13001
title: Chandra X-ray Observatory ObsId 13001

description: The brightest ultraluminous X-ray sources across the sky
DOI: 10.60586/snt357.xfct.686
title: Histology data from the heart of a 43-year-old white male
DOI: 10.60586/snt957.dfhr.839
title: Histology data from the heart of a 43-year-old white male
DOI: 10.25574/13002
title: Chandra X-ray Observatory ObsId 13002

description: The brightest ultraluminous X-ray sources across the sky
DOI: 10.60586/snt936.qbzj.656
title: Histology data from the lung (right) of a 43-year-old white male
DOI: 10.60586/snt982.mkzr.896
title: Histology data from the lung (right) of a 43-year-old white male
DOI: 10.25574/13003
title: Chandra X-ray Observatory ObsId 13003

description: The brightest ultraluminous X-ray sources across the sky
DOI: 10.60586/snt864.hfsw.749
title: Histology data from the lung (right) of a 43-year-old white male
DOI: 10.60586/snt669.grkb.946
title: Histology data from the heart of a 43-year-old white male
DOI: 10.25574/13004
title: Chandra X-ray Observatory ObsId 13004

description: The brightest ultraluminous X-ray sources across the sky
DOI: 10.60586/snt626.bwkg.954
title: Histology data from the heart of a 43-year-old white male
DOI: 10.60586/snt232.mnfk.526
title: Histology data from the heart of a 43-year-old white male
DOI: 10.25574/13005
title: Chandra X-ray Observatory ObsId 13005

description: The brightest ultraluminous X-ray sources across the sky
DOI: 10.60586/snt875.prxh.662
title: Histology data from the heart of a 43-year-old white male
DOI: 10.60586/snt896.xvpj.574
title: Histology data from the lung (right) of a 43-year-old white male
DOI: 10.25574/13006
title: Chandra X-ray Observatory ObsId 13006

description: The brightest ultraluminous X-ray sources across the sky
DOI: 10.60586/snt666.tbrq.722
title: Histology data from the lung (right) of a 43-year-old white male
DOI: 10.60586/snt529.tcnl.495
title: Histology data from the lung (right) of a 43-year-old white male
DOI: 10.15468/dl.htvhk5
title: Occurrence Download

description: A dataset containing 6108 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Opsanus beta",
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 },
 {
 "or" : [
 "CoordinateUncertaintyInMeters is less than 10000",
 "CoordinateUncertaintyInMeters is null"
 ]
 }
 ]
}

 The dataset includes 6108 records from 63 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0055361-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.cwg9x3
title: Occurrence Download

description: A dataset containing 1184 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Oclemena reticulata (Pursh) G.L.Nesom"
 ]
}

 The dataset includes 1184 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050039-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yeb98c
title: Occurrence Download

description: A dataset containing 856 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Dinopium everetti (Tweeddale, 1878)"
 ]
}

 The dataset includes 856 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0173893-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-221471
title: The Magazine of the Romanian Pentecostal Church, 1976, vol. 24, no. 9-10 = Buletinul Cultului Penticostal din Romania, 1976, anul XXIV, nr 9-10

description: [description english/roman)] The Magazine of the Pentecostal Church is the periodical, oficial publication of the Romanian Penticostal Church during communist times. It has been published between 1953-1989.
DOI: 10.15468/dl.gbluiq
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Aralia atropurpurea Franch.",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 33 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006663-181108115102211/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.rup8j7
title: Occurrence Download

description: A dataset containing 51 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Argentina",
 "TaxonKey is Cyperus unioloides R.Br."
 ]
}

 The dataset includes 51 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0029224-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-228747
title: The Word of Truth, 2008, vol. 19, no. 3 = Cuvantul Adevarului, 2008, anul XIX, nr 3

description: [description english/roman)] The Word of Truth is the periodical, official publication of the Romanian Pentecostal Church beginning from 1990 to present.
DOI: 10.15468/dl.pu3bjz
title: Occurrence Download

description: A dataset listing the 3 species recorded in GBIF matching the query:
{
 "TaxonKey" : [
 "is Campomanesia velutina (Cambess.) O.Berg"
 ]
}

 The dataset's 3 records were derived from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0144211-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tf4w6b
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Athyrium nudifrons Ching"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0048688-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-228739
title: The Word of Truth, 2008, vol. 19, no. 3 = Cuvantul Adevarului, 2008, anul XIX, nr 3

description: [description english/roman)] The Word of Truth is the periodical, official publication of the Romanian Pentecostal Church beginning from 1990 to present.
DOI: 10.15468/dl.e37kg4
title: Occurrence Download

description: A dataset containing 6838 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Spain",
 "Geometry POLYGON((-9.5 36,0.3 36,0.3 38.8,-9.5 38.8,-9.5 36))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Calandrella brachydactyla (Leisler, 1814)",
 "Year 1985-2023"
 ]
}

 The dataset includes 6838 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0088399-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.m378k7
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Erucaria hispanica var. tanacetifolia Oppenh."
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054159-220831081235567/datasets/export for details.
DOI: 10.15468/dl.gs23nt
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Zinnia guanajuatensis (Calderón & Rzed.) B.L.Turner"
 ]
}

 The dataset includes 40 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004813-240425142415019/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-228800
title: The Word of Truth, 2008, vol. 19, no. 5 = Cuvantul Adevarului, 2008, anul XIX, nr 5

description: [description english/roman)] The Word of Truth is the periodical, official publication of the Romanian Pentecostal Church beginning from 1990 to present.
DOI: 10.15468/dl.umvxax
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sisymbrium hararense Engl."
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054169-220831081235567/datasets/export for details.
DOI: 10.15468/dl.ht7squ
title: Occurrence Download

description: A dataset containing 242 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eumops underwoodi Goodwin, 1940"
 ]
}

 The dataset includes 242 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058714-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.sf28ae
title: Occurrence Download

description: A dataset containing 287 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pachyloma huberioides (Naudin) Triana"
 ]
}

 The dataset includes 287 records from 32 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057908-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-220845
title: The Magazine of the Romanian Pentecostal Church, 1971, vol. 19, no. 11-12 = Buletinul Cultului Penticostal din Romania, 1971, anul XIX, nr 11-12

description: [description english/roman)] The Magazine of the Pentecostal Church is the periodical, official publication of the Romanian Pentecostal Church during communist times. It has been published between 1953 and 1989.
DOI: 10.15468/dl.5sqx38
title: Occurrence Download

description: A dataset containing 192 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Taeniamia biguttata (Lachner, 1951)"
 ]
}

 The dataset includes 192 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054153-220831081235567/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nwzses
title: Occurrence Download

description: A dataset containing 769 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-19.21930 36.81228,64.21930 36.81228,64.21930 70.18772,-19.21930 70.18772,-19.21930 36.81228))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Cucujus cinnaberinus (Scopoli, 1763)",
 "Year 1930-2020"
 ]
}

 The dataset includes 769 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0064787-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wmm4bd
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pachyloma setosum Wurdack"
 ]
}

 The dataset includes 54 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0057910-230530130749713/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.25549/pcra-c14-220816
title: The Magazine of the Romanian Pentecostal Church, 1971, vol. 19, no. 9-10 = Buletinul Cultului Penticostal din Romania, 1971, anul XIX, nr 9-10

description: [description english/roman)] The Magazine of the Pentecostal Church is the periodical, official publication of the Romanian Pentecostal Church during communist times. It has been published between 1953 and 1989.
DOI: 10.15468/dl.9ggr5j
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Fabrisinapis fruticosus C.C.Towns."
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0054187-220831081235567/datasets/export for details.