title: Control, E11.5, Sorted CNCCs

city: Iowa City

first: Eric

last: Van Otterloo

state: Iowa

address: 801 Newton Rd

institute: University of Iowa

description: 10x Genomics

data_processing:
Quality control, integration, and UMAP visualization: Sequencing results were demultiplexed and converted to a FASTQ format using the Illumina bcl2fastq software. Reads were processed and aligned to the mm10 reference genome assembly with the Cell Ranger Count function. Seurat v4.3.0 was used for quality control, filtering out cells with >10% mitochondrial counts, less than 200 features, and more than 7,500 features. We then integrated Tfap2HET and Tfap2NCKO conditions (Hao et al., 2021), where RNA counts were normalized and FindVariableFeatures was run with the following parameters: selection.method = “vst”, nfeatures = 2,000. Cell clustering by Uniform Manifold Approximation and Projection (UMAP) plots was deployed by RunPCA and then RunUMAP (dims 1:30). The UMAP visualizing all CNCCs was generated with FindClusters using a resolution of 0.40. Major CNCC derivatives were annotated based on published immunofluorescence and scRNA-seq profiling (Soldatov et al., 2019). Gene expression was plotted on UMAP plots by FeaturePlot. Gene expression mapping of CNCC lineage markers was done using the FeaturePlot function. Gene expression-based cell cycle analysis: The CellCycleScoring function was performed as previously described, with minor modifications (Hao et al., 2021). The UMAP resolution was changed to 0.05 to segregate the major CNCC lineages as individual clusters (i.e., mesenchyme, neuron, glia). Bioconductor BiomaRt v2.46.3 (Durinck et al., 2005) was used to convert a published list of cell cycle genes (Kowalczyk et al., 2015) from human to mouse gene nomenclature. Cell cycle scores were then mapped directly onto the UMAP, while GraphPad Prism was used to graph the scores as a percentage relative to each cluster. Cellular distribution analysis: To examine genotype cellular distributions in each cluster, each condition was expressed as a percentage per cluster. These analyses were visualized in GraphPad Prism. For the initial UMAP containing all sorted cells, a resolution of 0.05 was used. For the MAGIC-clustered UMAP, a resolution of 0.10 was used (see “Annotation of mesenchyme positional identities”). Annotation of mesenchyme positional identities: To better define the facial prominence subpopulations, we subset and re-clustered the “Mesenchyme” clusters using MAGIC v2.0.3 (van Dijk et al., 2018) with RunUMAP dims 1:20. Major mesenchyme populations were then annotated based on known gene markers, which were plotted on the MAGIC-clustered UMAP with DefaultAssay = “MAGIC_RNA”. A cluster resolution of 0.10 was chosen to best visualize each prominence population and the second pharyngeal arch as individual clusters based on published in situ data, ChIP-seq, ATAC-seq, and transcriptomic datasets (Gu et al., 2022; Hooper et al., 2020; Minoux et al., 2017). To visualize co-expression of two genes on the UMAP, we used FeaturePlot (flag blend = “TRUE”). Gene-set and gene expression analyses: The UMAP resolution was set to 0.05 to distinguish the major cell groupings, to which we then subset the “pseudobulked” mesenchyme group. We then used the FindMarkers function with ident.1 = Tfap2HET and ident.2 = Tfap2NCKO on CNCCs, to generate a list of differentially expressed genes (adjusted p-value < 0.05 and a log fold-change threshold of 0.10) (Table S2, Tab 9). For gene-set enrichment, ontology, and pathway analysis, lists of either up- or downregulated genes, generated from the mesenchyme “pseudobulk” approach, in the Tfap2NCKO condition were inputted in the Enrichr pipeline. Control-versus-mutant expression analysis of select genes was visualized as a violin plot using the VlnPlot function on the MAGIC-clustered UMAP, with DefaultAssay = “RNA”. Differential gene expression was validated for a select set of genes-of-interest by targeted approaches (see real-time PCR).
Assembly: mm10

source_name: Wnt1-CRE recombined cells (i.e., eGFP+) cell sorted from dissocated E11.5 heads (rostral to the otic placode)

extract_protocol: Single-cell dissociation, cell sorting, and sequencing: To isolate CNCCs, E11.5 embryonic heads were cut just below pharyngeal arch 2 and the otic vesicle by microdissection. Using Wnt1:CRE-mediated recombination of the mTmG reporter allele (Muzumdar et al., 2007), CRE-positive embryos were selected for further processing. Tissue samples were then subject to a cold protease single-cell dissociation protocol (Adam et al., 2017), with modifications. Embryo heads were incubated in a protease cocktail comprised of Bacillus licheniformis Subtilisin A (Creative Enzymes), Accumax, and Accutase (Fisher Scientific) suspended in DEPC-PBS as previously described (Sekiguchi and Hauser, 2019). The tissue was then carefully disrupted using a disposable Eppendorf pellet pestle and placed on a rotator at 4°C for 30 min. During this step, samples were gently triturated every 10 min using a wide bore 1 mL pipette tip. The enzymatic reaction was quenched using an equal volume of 10% heat-inactivated FBS (Fisher Scientific) in 1X phenol red-free DMEM (ThermoFisher). Dissociated cells were washed thrice in DEPC-PBS by centrifugation at 600 x g at 4°C for 5 min and then transferred, through Bel Art SP Scienceware Flowmi 40-μm strainers (ThermoFisher), into chilled flow tubes precoated with DEPC-PBS. After GFP-positive sorting on the University of Iowa Flow Cytometry Facility’s ARIA II system (Becton Dickinson), CNCCs were re-suspended in DEPC-PBS containing 0.04% non-acetylated BSA (New England Biolabs). Cell viability was determined to be >95% by Trypan Blue staining. During cell sorting, genotypes were confirmed by rapid genotyping, allowing isolation of GFP-positive cells from two Tfap2HET control and two sibling-matched Tfap2NCKO mutant embryos. Cells from each “biological replicate” were combined to generate a single control and mutant sample. ~6,000 GFP-positive CNCCs from each condition were subject to library preparation by the University of Iowa Genomics Division on the 3’ expression scRNA-seq 10X Chromium v3.1 pipeline. Libraries were sequenced on an Illumina NovaSeq 6000 platform as 100-bp paired-end reads. Over 20,000 reads per cell were acquired, resulting in ~1.5 x 108 reads per condition.

tag: genotype

value: control (Tfap2a wt/flox; Tfap2b wt/flox; r26 mTmG/mTmG; Wnt1CRE+)


title: K2_495

status: Public on Jan 01 2024

type: SRA

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

library_source: transcriptomic

data_processing:
reads were quality filterred by rcorrector and Trimmomatic
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Oryza sativa cDNA dataset (version 7.0, source: http://rice.uga.edu/)
Supplementary files format and content: sf files generated by Salmon software, include TPM values

molecule: total RNA

organism: Oryza sativa

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. Sampling of 17-days-old plants was done 2 h after dawn.

extract_protocol:
protocol from Spectrum Plant Total RNA Kit (Sigma-Aldrich)
performed by sequencing service company (Eurofins Genomics)

tag: tissue

value: roots

tag: biological replicates

tag: cell type

value: 17-day-old seedlings

value: ssp. japonica var. Kitaake

tag: treatment

value: control (time after recovery - related to C2)


title: Chronic IFNG LLC1, rep3

city: Philadelphia

first: Jingya

last: Qiu

state: PA

address: 421 Curie Blvd, 532

department: Radiation Oncology

country: USA

institute: University of Pennsylvania

data_processing:
Adapter sequences trimmed using cutadapt v2.9 (parameters -m 30 -e 0.2 -q 10 -O 3)
Reads were pseudo-aligned and genes were quantified using salmon v1.8.0 (parameters --validateMappings --rangeFactorizationBins 4 --numBootstraps 3 --seqBias --gcBias)
Salmon counts were imported into R with tximport v1.22.0 and a count matrix summarized at the gene-level was generated.
Counts were vst normalized using DESeq2 v1.34.0
Assembly: GRCm38/mm10
Supplementary files format and content: vst-normalized RNA count matrix (.csv)

organism: Mus musculus

source_name: CD45- cancer cells

growth_protocol: We utilized two syngeneic mouse lung cancer models: the Kraslox-stop-lox(lsl)-G12D/+; p53flox/flox (KP) genetically engineered mouse model and the Lewis lung carcinoma (LLC1). Mice were injected with tumor cells. On day 15, CD45- tumor cells were harvested and sorted.

extract_protocol:
On day 15 tumors were harvested, red blood cell lysis was performed, and a single cell suspension was created. Tumor cells were stained with Live/Dead Aqua and CD45. Samples were sorted on an Aria (BD) by gating on live, CD45 negative cells. Total RNA was isolated and purified from the cells using Isol-RNA Lysis Reagent (Fisher) and treated with DNase I (Fisher).
RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina), samples were pooled and sequenced on Illumina Novaseq 6000 with 100 cycles (50 bp paired-end reads)

value: CD45- cancer cells

tag: cell line

tag: group

value: Chronic IFNG LLC1


title: spleenTreg_7-1_noGvHD_Tcra_R2

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

description:
re-isolated
mTRA_245_Tx198-12-400_S_ra_A.RunAB.clonotypes.TRA.txt

data_processing:
base calling: Base-calling and demultiplexing based on Illumina barcodes was carried out using the bcl2fastq Conversion Software (v1.8.4) provided by Illumina (Illumina INc., San Diego, California, USA).
paired-end read alignment: UMI-barcoded and paired TCR-sequencing reads were joined using PEAR (v0.9.11).
UMI-based generation of MIGs: Demultiplexing on the basis of UMI-barcodes and adaptor trimming was done using MIGEC (v1.2.9) resulting in consensus sequences of molecular identifier groups (MIGs).
MIG mapping: MIGs were mapped using MIXCR (v3.0.13).
Assembly: RepSeq.IO library v1.6
Supplementary files format and content: Mapping output of MIXCR
Library strategy: TCR-seq

source_name: CD4+CD25+ regulatory T cells

growth_protocol: Splenocytes were stained with anti-CD25-PE and anti-PE UltraPure MicroBeads and enriched for CD25+ cells by MACS® (Miltenyi Biotec). The CD25+ fraction was further stained for CD8, CD4 and CD62L and Treg were sorted on a FACSAria IIuTM or a FACSAriaTM Fusion (BD Biosciences) as CD4+CD25highCD62L+ cells; purity of sorted cells was >98%. Polyclonal in vitro expansion of Treg was performed as recently described {Riegel, 2020 #61}. In brief, sorted Treg were cultured in DMEM (high glucose, Gibco/Invitrogen) with 10% FCS, 2mM L-glutamine, 10mM HEPES, 1% NEAA (PAN Biotech), 50U/ml penicillin, 50µg/ml streptomycin and 5x10-5 M 2-mercaptoethanol  (Gibco/Invitrogen) (cDMEM) in 96-U-well plates (1x104/well) and stimulated with CD3/CD28-beads (Treg-Expansion Kit, Miltenyi Biotec, 4 beads/cell) and rhIL-2 (2000 U/ml; Proleukin®, Chiron). Cultures received 100 µl/well fresh medium on d4, were restimulated on d7 with 1 bead/cell after transfer into 24-well-plates (1x106 cells/ml/well), fed and split on d10 as needed and harvested on d12. For allospecific in vitro expansion sorted Treg were seeded at 5x104/well in cDMEM together with 2,5x104/well (d0) or 1x104/well (restimulation on d7) anti-CD11c MicroBead-enriched (Miltenyi Biotec) and irradiated (30 Gy) CD11c+ DC  from BALB/c mice. Cells received fresh medium on d4 and d10 and were harvested on d12.

extract_protocol:
Total cellular RNA was isolated from Treg (freshly isolated, in vitro expanded, or re-isolated after BMT) using the RNeasy Mini Kit or the RNeasy Micro Kit (Qiagen). Following the manufacturer’s recommendations, samples originating from 500 to 500k cells were processed with the Micro Kit whereas the Mini Kit was applied to all samples exceeding 500k cells. RNA concentration and quality were simultaneously assessed using RNA Screentape Analysis or High Sensitivity RNA Screentape Analysis (Agilent), depending on the expected yield.
Total cellular RNA was obtained as described in section “RNA-seq library preparation”. TCR repertoire sequencing libraries for Illumina sequencing were prepared on the basis of {Mamedov, 2013 #7} and the protocol was adapted, as follows. For the generation of 5’RACE-ready cDNA total RNA ranging from 10 - 200 ng (low input) or 200 - 1000 ng (high input) in a total of 10 µl RNAse-free water was combined with 1 µL of 12 µM or 25 µM 5’-CDS Primer A in a total volume of 11 µL, respectively. Reactions were incubated at 72°C for 3 min followed by 42°C for 2 min for poly-dT primer annealing. Next, 1 µL of 10 µM (low input) or 50 µM (high input) TCR_UMI_Smarter template-switching oligo (TSO) was added at room temperature. RT Buffer Mix (5x First-Strand-Buffer Mix, 20mM dNTP, 100 mM DTT) was freshly prepared on ice before it was supplemented with RNaseOUT™ Recombinant Ribonuclease Inhibitor (40 U/µL) (Thermo Fisher Scientific) and SMARTScribe Reverse Transcriptase (100 U/µL) (Takara) at room temperature. A volume of 8 µL of the resulting reverse transcription master mix was added to each reaction. After homogenization, the 20 µL reactions were incubated at 42°C for 90 min followed by 70°C for 10 min and put on hold at 10°C in a hot-lid thermal cycler. Following reverse transcription, excess TSO was digested using Uracil-DNA Glycosylase (UDG) (New England Biolabs) by adding 4 µL of UDG master mix adjusted for TSO input amount and successive incubation at 37°C for 60 min. The master mix for PCR1 was prepared on ice using the Advantage 2 PCR Kit (Takara) along with primers specific for the constant regions of the Trac and Trbc loci as well as a universal forward primer specific for a binding sequence introduced via the TSO. 24 µL of RACE-ready cDNA were combined with 26 µL of PCR1 master mix and subjected to a two-step PCR program (95°C, 1min; 95°C, 30 s & 68°C, 70 s (x times); 68°C, 7 min; 8°C, hold). Depending on the RNA input amount, PCR cycle numbers ranged from 16 to 28. The 50 µL PCR product was purified with 27.5 µL of AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions. After elution in 23.5 µL of Monarch® DNA Elution Buffer (New England Biolabs), reactions were split into 10 µL technical replicates for successive extension PCR (PCR2). PCR2 master mix was assembled using the Advantage 2 PCR Kit (Takara) and gene-specific nested primers (Trac, Trbc loci) introducing Illumina Nextera XT i5 indices (S501, S502, S503, S508, S517, S520, S507), distinguishing Tcra from Tcrb libraries within each reaction. After addition of 36 µl PCR2 master mix, 4 µL of Nextera XT Index Kit v2 (Illumina) adapters were used for indexing libraries individually. Libraries were amplified using the same program as in PCR1 with 18 PCR cycles. Library purification was carried out using  AMPure XP beads (Beckman Coulter) at a volume ratio of 0.8 according to the manufacturer’s instructions. After final elution in 17 µL of Monarch® DNA Elution Buffer (New England Biolabs), concentration was measured with the Qubit™ dsDNA HS Assay Kit (Thermo Fisher Scientific) and fragment size profile was assessed using the High Sensitivity D1000 or D5000 ScreenTape Assay (Agilent). Libraries were stored at -20°C until sequencing (paired-end 300bp) on the Illumina MiSeq system. Oligonucleotide sequences are summarized in Supplemental Table 3, Libraries are summarized in Supplemental Tables 4-7.
poly-dT-primed, gene-specifically enriched TRA/TRB library preparation

treatment_protocol: Single cell suspensions from BM (femora and tibiae of both hind legs) and spleen were prepared. T cells were depleted from BM (T cell depleted bone marrow; TCDBM) by using anti-CD90.2 MicroBeads with the MidiMACS® system (Miltenyi Biotec). CD4+CD25- conventional T cells (Tconv) were isolated from splenocytes by depletion of CD25+ cells using anti-CD25-PE (all antibodies used in this study are listed in Supplemental Table 2)  and anti-PE UltraPure MicroBeads (Miltenyi Biotec), followed by enrichment of CD4+ cells from the CD25- fraction through labeling with anti-CD4 MicroBeads (Miltenyi Biotec) using the MidiMACS® system. For short-term (d7) FACS and RNA-seq experiments BALB/c recipients were lethally irradiated (8 Gy) on the day of BMT and transplanted i.v. with 2.5 x106 TCDBM cells and 1x106 Tconv from B6-CD45.1 mice with or without in vitro expanded allo or polyTreg from Foxp3gfp mice at a 1:1 ratio. Recipients of the ‘no GvHD’ group received TCDBM and Treg only. In long-term survival experiments lethally irradiated BALB/c recipients were transplanted with 2.5 x106 TCDBM on d0 and 0.25 x106 Tconv were administered on d2 for GvHD induction. Mice of the GvHD prophylaxis groups (allo or poly) received additional 0.25x106 in vitro expanded Treg from B6 WT mice on d0. Recipients were monitored daily, body weight and GvHD symptoms assessed twice weekly by non-blinded investigators applying a standardized scoring system (Cooke et al., 1996). Single cell suspensions from BM, spleen and mesenteric lymph nodes were prepared. Erythrocytes were lysed in splenic and BM cell suspensions. For leukocyte isolation from the liver, the organ was flushed with PBS through the portal vein and the gallbladder was removed before it was excised, transferred to a petri dish and dissected into small pieces using a scalpel. Fragments were suspended in RPMI (Lonza/Biozym)/5% FCS, strained and washed in RPMI w/o FCS before Percoll centrifugation (40%/80%; 800 x g/20 min/20°C, w/o break). Leukocytes were resuspended in RPMI/5% FCS, erythrocytes were lysed, cells were washed in RPMI/10% FCS and kept on ice until further use. For intestinal leukocyte isolation, large intestine was excised, cut into 0.5 cm pieces, incubated twice for 20 min at 37 °C in HBSS/5mM EDTA/1mM DTT (Sigma-Aldrich) followed by vigorous shaking to isolate intraepithelial leukocytes (IEL). For lamina propria leukocytes (LPL), the fragments were transferred to HBSS without phenol red containing calcium and magnesium with 5% FCS together with enzymes of the Lamina propria dissociation kit (Miltenyi Biotec) and incubated for 30 min at 37°C. The fragments were further mechanically dissociated using the GentleMACS system (protocol: m_intestine_01; Miltenyi Biotec), strained, washed and pooled together with IEL before Percoll (Sigma-Aldrich)  centrifugation (30%; 512 xg/15 min/20°C). For baseline (no BMT) colon Treg sorts IEL were not included (no Tregs in untreated animals) and colonic LPL were further enriched using anti-CD45 MicroBeads (Miltenyi Biotec) and the AutoMACS® system (Miltenyi Biotec). Splenocytes were enriched for CD25+ cells by MACS® using anti-CD25-PE and anti-PE UltraPure MicroBeads before sorting. Cells were further stained for CD8, CD4 and CD62L (also CD45 for colon-derived cells) and Treg were sorted on a FACSAriaTM IIu or a FACSAriaTM Fusion (Becton Dickinson). From spleen and liver, CD62L+ and CD62L– subpopulations were isolated, from colon, only CD62L–- cells were obtained (sorting strategy is shown in detail in Supplemental Fig.2a). For re-isolation of donor Treg on day 7 after transplantation, single cell suspensions from spleen, liver and colon were prepared as described, stained for H-2Kb, CD45.1, CD45.2, TCRβ and CD4 and sorted on a FACSAria IIuTM or a FACSAriaTM Fusion (for detailed sorting strategy see Supplemental Fig.2b). Staining was performed in PBS/2%FCS with anti-CD16/CD32 antibodies to block FcR-binding and DAPI (Sigma-Aldrich) or Fixable Viability Dye (Thermo Fisher) to exclude dead cells. Detailed information on all antibodies used in this study is listed in Supplemental Table 2. For staining of intracellular markers, the Foxp3/Transcription Factor Staining Buffer Set® (eBioscience) was used.  Multicolour FACS staining for surface markers was performed using Brilliant Stain Buffer (BD Biosciences) where applicable. Data was acquired on a FACSymphony® A5 SORP (Becton Dickinson) and analyzed using FlowJo® software (v10.7.1 or v10.8.0; Treestar Inc). For clustering and embedding of multiparameter flow cytometry data (as presented in Supplemental Fig.2a) FlowJo® plugins DownSample_v3.3 and UMAP_v3.1 were used. The UMAP plot in Supplemental Fig. 2a was created on the basis of 27 samples from spleen, liver and colon (all n=3) from 3 experimental groups: alloTreg prophylaxis, polyTreg prophylaxis and GvHD control and 3 independent experiments, with every sample representing a cell pool of 2-3 mice. Cells were stained for CD45.1, CD45.2, H-2kb, TER119, TCRβ, CD8α, CD4, CD19, Nkp46, CD11b, Ly6C, Gr-1 and CD25. Dead cells were excluded with DAPI. Samples were gated on live single CD45.1+TER119- and CD45.2+TER119- cells, downsampled to 15.000 cells each and assembled into one file.

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

tag: type

value: allo

tag: model

value: BMT control

value: spleen

tag: treg donor

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: alpha

tag: techn. replicate


title: sample28

city: Los Angeles

first: Gloria Cecilia

last: Galvan

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

data_processing:
Sequenced reads were mapped with BBMap to human (GENCODE human genome: Release 38(GRCh38.p13)) and mouse (MOUSE Genome: Release M22(GRCm38.p6)) genome. Reads unique to mouse alone were removed.
An established STAR-RSEM mapping and quantification pipeline was used for read alignment to the human genome and transcript quantification.
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each sample

extract_protocol:
Total RNA was isolated with Direct-Zol RNA isolation kit. RNA quantity and quality were assessed using QuBit Fluorometer (ThermoFisher Scientific) and 2100 Bioanalyzer (Agilent Technologies)
Up to one µg of total RNA per sample was used for library construction using the Illumina TruSeq Stranded mRNA library preparation kit (Illumina).  Library concentration was measured with a Qubit fluorometer and library size on an Agilent 4200 TapeStation (Agilent Technologies). Libraries were multiplexed and sequenced on a NovaSeq 6000 (Illumina) using 75bp single-end sequencing. On average, approximately 30 million reads were generated from each sample.

treatment_protocol: Mice were injected with LAPC-4 cells into the lower right flank. When tumor volumes reached 200mm3 on average, mice were single-housed and randomized to a high or low glycemic index Western diet provided ad libitum.

tag: tissue

value: tumor

value: lgw


title: K2_436

tag: biological replicates

tag: genotype


title: Mutant, E11.5, Sorted CNCCs

description: 10x Genomics

library_source: transcriptomic single cell

molecule: polyA RNA

value: Wnt1-CRE recombined cells (i.e., eGFP+) cell sorted from dissocated E11.5 heads (rostral to the otic placode)

value: Tfap2a/Tfap2b neural crest mutant (Tfap2a flox/flox; Tfap2b flox/flox; r26 mTmG/mTmG; Wnt1CRE+)


title: sample27

tag: treatment


title: h66B_N

city: West Hollywood

first: Simon

last: Knott

state: California

address: 8687 Melrose Ave

department: BFG

institute: Cedars Sinai

data_processing:
All immune cells following the single cell pipeline outlined in Methods
All non-immune cells following the single cell pipeline outlined in Methods
All TCR data
Assembly: hg38
Supplementary files format and content: H5AD file containing celltype, subtype, patient, batch, pCR and other metadata columns for each immune cell
Supplementary files format and content: H5AD file containing celltype, subtype, patient, batch, pCR and other metadata columns for each non-immune cell
Supplementary files format and content: CSV file containing TCR data

organism: Homo sapiens

source_name: Breast

extract_protocol:
Human TNBC core needle biopsies were dissociated using the Miltenyi BiotecHuman Tumor Dissociation Kit, then CD45-positive cells were enriched using the Miltenyi Biotec anti-human CD45 microbeads and CD45-negative cells were obtained from the non-enriched portion
Single-cell gene expression and paired TCR (CD45-positive only) librarieswere prepared according to the 10X Genomics Single Cell 5’ v1 protocol.

value: Breast

tag: age

value: adult

tag: Sex

value: female

value: Pembrolizumab

tag: disease state

value: Triple-receptor negative breast cancer


title: spleenTreg_7-3_noGvHD_Tcra_R2

description:
re-isolated
mTRA_242_Tx198-12-4209_S_ra_AB.RunAB.clonotypes.TRA.txt

tag: strain

tag: sampleID


title: Chronic IFNG LLC1, rep1

tag: cell line

tag: group


title: sample26

value: hgw


title: K1_470

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. Sampling of 14-days-old plants was done 2 h after dawn.

value: roots

tag: cell type

value: 14-day-old seedlings

value: ssp. japonica var. Kitaake

value: control (time after stress - related to C1)


title: spleenTreg_6-2_noGvHD_Tcra_R2

description:
re-isolated
mTRA_222_Tx198-10-4183_S_ra_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: mouse (pool/culture no.)

tag: type

value: allo

tag: model

value: BMT control

tag: treg donor

tag: recipient


title: h66B_P

tag: tissue


title: Parental LLC1, rep1

value: CD45- cancer cells

value: Parental LLC1


title: h66A_N

value: Baseline


title: spleenTreg_6-3_noGvHD_Tcra_R2

description:
re-isolated
mTRA_225_Tx198-10-4190_S_ra_A.RunAB.clonotypes.TRA.txt

value: spleen

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: alpha

tag: techn. replicate


title: h66A_TCR

value: Breast

tag: age

value: adult

tag: Sex

tag: treatment


title: h66A_P

value: female

tag: disease state


title: h66C_P

value: Pembrolizumab + Radiation

value: Triple-receptor negative breast cancer


title: sample20

value: tumor

value: hgw


title: K0_517

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. Sampling of 13-days-old plants was done 2 h after dawn.

value: roots

tag: biological replicates

value: 12-day-old seedlings

tag: genotype

value: ssp. japonica var. Kitaake

value: control (time before stress - related to acclimation A0)


title: sample19

value: lgw


title: h64C_TCR


title: K2_435

tag: cell type

value: 17-day-old seedlings

value: control (time after recovery - related to C2)


title: K0_454


title: h64C_N


title: liverTreg_7-5_noGvHD_Tcra_R2

description:
re-isolated
mTRA_249_Tx198-12-4214_L_rp_AB.RunAB.clonotypes.TRA.txt

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

value: poly

value: BMT control

value: liver


title: h64C_P

value: Breast

value: adult


title: C-R2_608

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 13 days 2 h after dawn, plants were transfered to special thermoregulatory vessels (keeping 5°C of new medium) into chamber (20°C of air) for 24 h. Two hours after dawn (14-days-old plants), plants were transfered to control conditions (medium was changed) and left under control conditions for 3 days (recovery). Sampling was done after recovery 2 h after dawn.

value: cold stress targeted on roots (leaves at 20°C, roots at 5°C, 24 h) -> recovery under control conditions (3 days)

tag: treatment time


title: C-R2_607


title: liverTreg_7-4_noGvHD_Tcra_R2

description:
re-isolated
mTRA_255_Tx198-12-4205_L_rp_AB.RunAB.clonotypes.TRA.txt

tag: type

tag: model

tag: treg donor

tag: recipient

value: alpha


title: h64B_TCR

tag: tissue

value: female

value: Pembrolizumab

value: Triple-receptor negative breast cancer


title: B159

city: Seoul

first: Kyung-Ok

middle: for Aging and Metabolic

last: Cho

state: --- Select One ---

address: 222 Banpo-daero, Seocho-gu

department: Department of Pharmacology

country: South Korea

institute: The Catholic University of Korea

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
Read count 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 file including read counts, FPKM/RPKM values, and TPM values for each sample.

source_name: Hippocampus

extract_protocol:
Mice were anesthetized and briefly perfused transcardially with cold saline. Total RNA from the hippocampi was isolated using TRIzol reagent according to the manufacturer’s instructions. In brief, tissues were frozen in liquid nitrogen, pulverized, homogenized in 1 mL of TRIzol reagent, and incubated for 5 min at room temperature. Then, 200 mL of chloroform was added, vigorously mixed, and incubated for 3 min at room temperature. Samples were centrifuged (14,000 rpm for 20 min), and the aqueous phases were transferred to fresh tubes with equal volumes of isopropanol and incubated on ice for 30 min. After centrifugation at 14,000 rpm for 15 min, the RNA pellets were washed in 75% ethanol and dissolved in RNase-free water. RNA qualities and concentrations were assessed by Nanodrop (Thermo Scientific).
After RNA extraction, libraries were generated using TruSeq stranded total RNA LT sample prep kits (Illumina).

treatment_protocol: saline-treated sham vs. pilocarpine-induced status epilepticus, LIN28A WT vs. cKO

value: Hippocampus

value: pilocarpine 260mg/kg(male), 280mg/kg (female)

tag: time

value: day 3

tag: biological replicate

value: Biol rep 2


title: cKOSE154aac

value: Biol rep 3


title: liverTreg_6-6_noGvHD_Tcra_R2

description:
re-isolated
mTRA_235_Tx198-10-4196_L_rp_AB.RunAB.clonotypes.TRA.txt

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

tag: techn. replicate


title: liverTreg_6-5_noGvHD_Tcra_R2

description:
re-isolated
mTRA_232_Tx198-10-4193_L_rp_AB.RunAB.clonotypes.TRA.txt


title: K0_518

value: roots

tag: biological replicates

value: 12-day-old seedlings

tag: genotype

value: ssp. japonica var. Kitaake

tag: treatment

value: control (time before stress - related to acclimation A0)


title: B132

value: Biol rep 1


title: C-R2_565

tag: cell type

value: 17-day-old seedlings


title: h64B_N

value: Breast

tag: age

value: adult

tag: Sex

tag: disease state


title: CR1_594

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 13 days 2 h after dawn, plants were transfered to special thermoregulatory vessels (keeping 5°C of new medium) into chamber (20°C of air) for 24 h. Sampling was done 2 h after dawn (14-days-old plants).

value: 14-day-old seedlings

value: cold stress targeted on roots (leaves at 20°C, roots at 5°C, 24 h)

tag: treatment time


title: C-R1_593


title: liverTreg_7-3_noGvHD_Tcra_R2

description:
re-isolated
mTRA_243_Tx198-12-4209_L_ra_AB.RunAB.clonotypes.TRA.txt

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

tag: type

value: allo

tag: model

value: BMT control

value: liver

tag: treg donor

value: alpha


title: B153

tag: tissue

value: Hippocampus

value: pilocarpine 260mg/kg(male), 280mg/kg (female)

tag: time

value: day 3

tag: biological replicate

value: Biol rep 2


title: WTSE131C

value: Biol rep 3


title: C-R1_587

value: roots

tag: biological replicates

value: ssp. japonica var. Kitaake


title: sample16

value: tumor

value: hgw


title: spleenTreg_6-1_noGvHD_Tcra_R2

description:
re-isolated
mTRA_219_Tx198-10-4181_S_ra_A.RunAB.clonotypes.TRA.txt

value: spleen

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

tag: techn. replicate


title: liverTreg_6-4_noGvHD_Tcra_R2

description:
re-isolated
mTRA_229_Tx198-10-4192_L_rp_AB.RunAB.clonotypes.TRA.txt

value: poly


title: h64B_P

value: Breast

tag: age

value: adult

tag: Sex

value: female

tag: treatment

value: Pembrolizumab

tag: disease state

value: Triple-receptor negative breast cancer


title: liverTreg_7-6_noGvHD_Tcra_R2

description:
re-isolated
mTRA_252_Tx198-12-4216_L_rp_AB.RunAB.clonotypes.TRA.txt

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

value: BMT control

value: liver

value: alpha


title: B150

value: Hippocampus

tag: genotype

value: pilocarpine 260mg/kg(male), 280mg/kg (female)

value: day 3

value: Biol rep 1


title: liverTreg_7-2_noGvHD_Tcra_R2

description:
re-isolated
mTRA_240_Tx198-12-4208_L_ra_AB.RunAB.clonotypes.TRA.txt

tag: type

value: allo

tag: model

tag: tissue

tag: treg donor


title: h64A_N

value: Baseline


title: CL2_720

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 13 days 2 h after dawn, plants were transfered to special thermoregulatory vessels (keeping 20°C of new medium) into pre-cooled chamber (5°C of air) for 24 h. Two hours after dawn (14-days-old plants), plants were transfered to control conditions (medium was changed) and left under control conditions for 3 days (recovery). Sampling was done after recovery 2 h after dawn.

value: roots

tag: biological replicates

tag: cell type

value: 17-day-old seedlings

value: ssp. japonica var. Kitaake

value: cold stress targeted on leaves (leaves at 5°C, roots at 20°C, 24 h) -> recovery under control conditions (3 days)

tag: treatment time


title: h64A_P

value: Breast

value: adult

value: female


title: B448

value: saline-treated sham

tag: time

tag: biological replicate

value: Biol rep 3


title: C-L2_673


title: B447

value: Biol rep 2


title: h63C_N

tag: age

value: Pembrolizumab + Radiation

value: Triple-receptor negative breast cancer


title: h63C_TCR

tag: Sex


title: B446

value: Hippocampus

tag: treatment


title: liverTreg_6-2_noGvHD_Tcra_R2

description:
re-isolated
mTRA_223_Tx198-10-4183_L_ra_AB.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

value: BMT control

value: liver

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: alpha

tag: techn. replicate


title: liverTreg_6-3_noGvHD_Tcra_R2

description:
re-isolated
mTRA_226_Tx198-10-4190_L_ra_AB.RunAB.clonotypes.TRA.txt

tag: strain

tag: sampleID

tag: mouse (pool/culture no.)

tag: type

value: allo


title: h64A_TCR

tag: tissue

value: Baseline

tag: disease state


title: h63B_TCR

value: Pembrolizumab


title: h63C_P


title: colonTreg_7-6_noGvHD_Tcra_R2

description:
re-isolated
mTRA_253_Tx198-12-4216_C_rp_A.RunAB.clonotypes.TRA.txt

value: poly

tag: model

value: colon

tag: treg donor


title: C-L1_652

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 13 days 2 h after dawn, plants were transfered to special thermoregulatory vessels (keeping 20°C of new medium) into pre-cooled chamber (5°C of air) for 24 h. Sampling was done 2 h after dawn (14-days-old plants).

value: roots

tag: biological replicates

tag: cell type

value: 14-day-old seedlings

tag: genotype

value: ssp. japonica var. Kitaake

value: cold stress targeted on leaves (leaves at 5°C, roots at 20°C, 24 h)

tag: treatment time


title: C2_503

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 13 days 2 h after dawn, plants were transfered to cold stress (5°C; the medium and the climate chamber was pre-cooled) for 24 h. Two hours after dawn (14-days-old plants), plants were transfered to control conditions (medium was changed) and left under control conditions for 3 days (recovery). Sampling was done after recovery 2 h after dawn.

value: 17-day-old seedlings

tag: treatment

value: cold stress on the whole plant (5°C, 24 h) -> recovery under control conditions (3 days)


title: B442

value: saline-treated sham

tag: time

value: day 3

tag: biological replicate

value: Biol rep 3


title: colonTreg_7-5_noGvHD_Tcra_R2

description:
re-isolated
mTRA_250_Tx198-12-4214_C_rp_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

value: BMT control

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain


title: B437

value: Hippocampus

value: Biol rep 1


title: C-L1_651


title: B441

value: Biol rep 2


title: h63B_N

value: Breast

tag: age

value: adult

tag: Sex

value: female

value: Pembrolizumab

value: Triple-receptor negative breast cancer


title: colonTreg_7-4_noGvHD_Tcra_R2

description:
re-isolated
mTRA_256_Tx198-12-4205_C_rp_A.RunAB.clonotypes.TRA.txt

tag: strain

tag: sampleID

tag: mouse (pool/culture no.)

tag: type

value: poly

tag: tissue

value: colon

value: alpha

tag: techn. replicate


title: liverTreg_7-1_noGvHD_Tcra_R2

description:
re-isolated
mTRA_246_Tx198-12-400_L_ra_AB.RunAB.clonotypes.TRA.txt

value: allo

tag: model

value: liver

tag: treg donor


title: colonTreg_6-6_noGvHD_Tcra_R2

description:
re-isolated
mTRA_236_Tx198-10-4196_C_rp_A.RunAB.clonotypes.TRA.txt


title: h63B_P

tag: treatment

tag: disease state


title: CL1_657

value: roots

tag: biological replicates

tag: cell type

value: 14-day-old seedlings

tag: genotype

value: ssp. japonica var. Kitaake

value: cold stress targeted on leaves (leaves at 5°C, roots at 20°C, 24 h)

tag: treatment time


title: C2_441

value: 17-day-old seedlings

value: cold stress on the whole plant (5°C, 24 h) -> recovery under control conditions (3 days)


title: colonTreg_6-5_noGvHD_Tcra_R2

description:
re-isolated
mTRA_233_Tx198-10-4193_C_rp_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

value: BMT control

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain


title: B449

value: Hippocampus

value: saline-treated sham

tag: time

value: day 3

tag: biological replicate

value: Biol rep 4


title: h63A_N

value: Breast

tag: age

value: adult

tag: Sex

value: female

value: Baseline

value: Triple-receptor negative breast cancer


title: Intestine, Ddit4-/-, fasted and refed, doxorubicin, 24H [J41]

city: Houston

first: Jason

middle: C

last: Mills

state: TX

address: 1 Baylor Plaza

department: Gastroenterology

institute: Baylor College of Medicine

description: Sample J41

data_processing:
The raw fastq files were first trimmed using TrimGalore, and those that passed the quality check were retained.
The trimmed fastq files were then mapped to mouse reference genome mm10 by STAR mapping. Raw counts of protein coding genes were obtained from the STAR aligner.
Transcript isoforms were collapsed by sum and genes with a total read count of <10 across all samples were excluded, resulting in a total of 16,259 genes.
Raw counts were normalized for library depth and composition using the DESeq2 median of ratios approach.
Normalized counts were also log transformed using the DESeq2 rlog function, accounting for genes with high dispersion across samples.
Assembly: mm10
Supplementary files format and content: .txt file, tab delimited, processed normalized data counts

source_name: proximal small intestine

extract_protocol:
RNA was extracted from whole tissue proximal intestine samples using the AllPrep DNA/RNA/Protein Mini Kit (80004, Qiagen) according to the manufacture’s protocol. RNA pellet was resuspended in water, and concentrations were measured using a NanoDrop.
Samples were submitted to Novogene and underwent sample quality control, library preparation, sequencing, and data quality control. For sample quality control, RNA was quantified, and purity was determined using NanoDrop. Sample integrity was determined using bioanalyzer by Agilent. All samples passed Novogene quality control. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. Next, the sample was assessed by Qubit and real-time PCR (RT-PCR) for quantification and bioanalyzer for size distribution detection. The clustering of index-coded samples was performed according to the manufacturer’s instructions. After clustering generation, the library preparations were sequenced on Illumina platform, NovaSeq PE150 sequencing at 20 million reads per sample, and paired-end reads were generated.

treatment_protocol: Wild type and DDIT4 knockout male mice were ad libitum fed or fasted for 24 hours then treated with 20 mg/kg of doxorubicin by intraperitoneal injection.

value: Male

tag: tissue

value: proximal small intestine

tag: fed state

value: 24 hour fast and 24H Refed

tag: drug treatment

value: Doxorubicin

tag: time with_respect_to_drug_treatment


title: C1_535

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 13 days 2 h after dawn, plants were transfered to cold stress (5°C; the medium and the climate chamber was pre-cooled) for 24 h. Sampling was done 2 h after dawn (14-days-old plants).

value: roots

value: 14-day-old seedlings

value: ssp. japonica var. Kitaake

tag: treatment

value: cold stress on the whole plant (5°C, 24 h)


title: C2_502

tag: biological replicates

value: 17-day-old seedlings

value: cold stress on the whole plant (5°C, 24 h) -> recovery under control conditions (3 days)


title: h63A_TCR

tag: disease state


title: Intestine, Ddit4-/-, fasted and refed, doxorubicin, 12H [J39]

description: Sample J39

tag: genotype

value: 24 hour fast and 12H Refed


title: liverTreg_6-1_noGvHD_Tcra_R2

description:
re-isolated
mTRA_220_Tx198-10-4181_L_ra_AB.RunAB.clonotypes.TRA.txt

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

tag: type

value: allo

tag: model

value: BMT control

value: liver

tag: treg donor

value: alpha

tag: techn. replicate


title: h63A_P

value: Breast

tag: age

value: adult

value: female

value: Baseline

value: Triple-receptor negative breast cancer


title: colonTreg_6-4_noGvHD_Tcra_R2

description:
re-isolated
mTRA_230_Tx198-10-4192_C_rp_A.RunAB.clonotypes.TRA.txt

value: poly

value: colon

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain


title: C1_479

tag: tissue

value: roots

tag: cell type

value: 14-day-old seedlings

value: ssp. japonica var. Kitaake

tag: treatment time


title: Intestine, Ddit4-/-, ad libitum, doxorubicin, 12H [J38]

description: Sample J38

tag: Sex

value: Male

value: proximal small intestine

tag: fed state

value: ad libitum

tag: drug treatment

value: Doxorubicin

tag: time with_respect_to_drug_treatment


title: colonTreg_7-3_noGvHD_Tcra_R2

description:
re-isolated
mTRA_244_Tx198-12-4209_C_ra_A.RunAB.clonotypes.TRA.txt

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

value: allo

value: BMT control


title: h57C_TCR

value: Breast

tag: treatment

value: Pembrolizumab + Radiation

tag: disease state


title: Intestine, Ddit4-/-, fasted and refed, doxorubicin, 6H [J37]

description: Sample J37

tag: genotype

value: 24 hour fast and 6H Refed


title: colonTreg_7-2_noGvHD_Tcra_R2

description:
re-isolated
mTRA_241_Tx198-12-4208_C_ra_A.RunAB.clonotypes.TRA.txt

tag: type

tag: model

tag: treg donor

tag: recipient

value: alpha

tag: techn. replicate


title: C1_424

tag: tissue

tag: biological replicates

tag: cell type

value: cold stress on the whole plant (5°C, 24 h)


title: h57C_N

tag: age

value: adult

tag: Sex

value: female

value: Triple-receptor negative breast cancer


title: Intestine, Ddit4-/-, ad libitum, doxorubicin, 6H [J36]

description: Sample J36

tag: fed state

tag: drug treatment

tag: time with_respect_to_drug_treatment


title: colonTreg_7-1_noGvHD_Tcra_R2

description:
re-isolated
mTRA_247_Tx198-12-400_C_ra_A.RunAB.clonotypes.TRA.txt

tag: strain

tag: sampleID

tag: mouse (pool/culture no.)

value: colon

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain


title: ACR2_627

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Two hours after dawn, plants were transfered to special thermoregulatory vessels (keeping 5°C of new medium) into chamber (20°C of air) for 24 h. Two hours after dawn (14-days-old plants), plants were transfered to control conditions (medium was changed) and left under control conditions for 3 days (recovery). Sampling was done after recovery 2 h after dawn.

value: roots

value: 17-day-old seedlings

tag: genotype

value: ssp. japonica var. Kitaake

tag: treatment

value: acclimation (15°C, 12 h) -> cold stress targeted on roots (leaves at 20°C, roots at 5°C, 24 h) -> recovery under control conditions (3 days)

tag: treatment time


title: h57C_P

tag: tissue

tag: disease state


title: Intestine, Ddit4-/-, fasted and refed, doxorubicin, 2H [J35]

description: Sample J35

value: Male

value: proximal small intestine

value: 24 hour fast and 2H Refed

value: Doxorubicin


title: ACR2_626

tag: biological replicates

tag: cell type


title: h57B_TCR

value: Breast

tag: age

tag: Sex

value: Pembrolizumab


title: colonTreg_6-3_noGvHD_Tcra_R2

description:
re-isolated
mTRA_227_Tx198-10-4190_C_ra_AB.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: type

value: allo

tag: model

value: BMT control

tag: treg donor

tag: recipient

tag: techn. replicate


title: Intestine, Ddit4-/-, ad libitum, doxorubicin, 24H [J40]

description: Sample J40

tag: fed state

value: ad libitum

tag: drug treatment

tag: time with_respect_to_drug_treatment


title: AC-R2_619

tag: genotype


title: h57B_N

value: adult

value: female

tag: treatment


title: colonTreg_6-2_noGvHD_Tcra_R2

description:
re-isolated
mTRA_224_Tx198-10-4183_C_ra_AB.RunAB.clonotypes.TRA.txt

tag: strain

tag: sampleID

tag: mouse (pool/culture no.)

value: colon

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: alpha


title: Intestine, WT, fasted and refed, untreated, 24H [J26]

description: Sample J26

tag: Sex

tag: tissue

value: wild type

value: 24 hour fast and 24H Refed


title: AC-R1_580

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Two hours after dawn, plants were transfered to special thermoregulatory vessels (keeping 5°C of new medium) into chamber (20°C of air) for 24 h. Sampling was done 2 h after dawn (14-days-old plants).

value: roots

tag: biological replicates

tag: cell type

value: 14-day-old seedlings

value: ssp. japonica var. Kitaake

value: acclimation (15°C, 12 h) -> cold stress targeted on roots (leaves at 20°C, roots at 5°C, 24 h)

tag: treatment time


title: CL2_719

value: 17-day-old seedlings

value: cold stress targeted on leaves (leaves at 5°C, roots at 20°C, 24 h) -> recovery under control conditions (3 days)


title: colonTreg_6-1_noGvHD_Tcra_R2

description:
re-isolated
mTRA_221_Tx198-10-4181_C_ra_A.RunAB.clonotypes.TRA.txt

tag: type

tag: model

tag: treg donor

tag: recipient

tag: techn. replicate


title: polyTreg_7_donor_Tcra_R2

description:
expanded
mTRA_238_Tx198-12-245_d12_rp_A.RunAB.clonotypes.TRA.txt

value: poly

value: in vitro

value: donor


title: h57B_P

value: Breast

tag: age

tag: treatment

value: Pembrolizumab

tag: disease state

value: Triple-receptor negative breast cancer


title: h57A_N

value: adult

value: female

value: Baseline


title: AC-R1_579

tag: genotype


title: Intestine, WT, fasted and refed, untreated, 12H [J24]

description: Sample J24

value: Male

value: proximal small intestine

value: wild type

tag: fed state

value: 24 hour fast and 12H Refed

tag: drug treatment

value: Doxorubicin

tag: time with_respect_to_drug_treatment


title: polyTreg_6_donor_Tcra_R2

description:
expanded
mTRA_218_Tx198-10-241_d12_rp_A.RunAB.clonotypes.TRA.txt

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: alpha


title: ACL2_714

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Two hours after dawn, plants were transfered to special thermoregulatory vessels (keeping 20°C of new medium) into pre-cooled chamber (5°C of air) for 24 h. Two hours after dawn (14-days-old plants), plants were transfered to control conditions (medium was changed) and left under control conditions for 3 days (recovery). Sampling was done after recovery 2 h after dawn.

tag: tissue

value: roots

tag: biological replicates

tag: cell type

value: 17-day-old seedlings

value: ssp. japonica var. Kitaake

value: acclimation (15°C, 12 h) -> cold stress targeted on leaves (leaves at 5°C, roots at 20°C, 24 h) -> recovery under control conditions (3 days)

tag: treatment time


title: ACR1_573

value: 14-day-old seedlings

value: acclimation (15°C, 12 h) -> cold stress targeted on roots (leaves at 20°C, roots at 5°C, 24 h)


title: Intestine, WT, ad libitum, doxorubicin, 12H [J23]

description: Sample J23

tag: Sex

value: ad libitum


title: polyTreg_4_donor_Tcra_R2

description:
expanded
mTRA_103_Tx198-4-208_d11_rp_A.RunAB.clonotypes.TRA.txt

tag: type

value: poly

tag: model

value: in vitro

value: donor

tag: treg donor

tag: recipient

tag: techn. replicate


title: Intestine, WT, fasted and refed, untreated, 6H [J22]

description: Sample J22

value: Male

tag: genotype

tag: fed state

value: 24 hour fast and 6H Refed

tag: drug treatment

tag: time with_respect_to_drug_treatment


title: ACL2_713

tag: treatment


title: h56C_TCR

value: Breast

tag: age

value: adult

value: female

value: Pembrolizumab + Radiation

tag: disease state

value: Triple-receptor negative breast cancer


title: h56C_N

tag: tissue


title: Intestine, WT, fasted and refed, untreated, 2H [J20]

description: Sample J20

value: proximal small intestine

value: wild type

value: 24 hour fast and 2H Refed

value: Doxorubicin


title: ACL1_702

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Two hours after dawn, plants were transfered to special thermoregulatory vessels (keeping 20°C of new medium) into pre-cooled chamber (5°C of air) for 24 h. Sampling was done 2 h after dawn (14-days-old plants).

value: roots

tag: biological replicates

value: 14-day-old seedlings

value: ssp. japonica var. Kitaake

value: acclimation (15°C, 12 h) -> cold stress targeted on leaves (leaves at 5°C, roots at 20°C, 24 h)


title: polyTreg_2_donor_Tcra_R2

description:
expanded
mTRA_Tx198-1-d13-rp_AB.RunAB.clonotypes.TRA.txt

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

value: poly

value: in vitro

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: alpha


title: h56C_P

value: Breast

tag: Sex


title: AC-L2_645

tag: cell type

value: 17-day-old seedlings

value: acclimation (15°C, 12 h) -> cold stress targeted on leaves (leaves at 5°C, roots at 20°C, 24 h) -> recovery under control conditions (3 days)

tag: treatment time


title: alloTreg_7_donor_Tcra_R2

description:
expanded
mTRA_237_Tx198-12-245_d12_ra_A.RunAB.clonotypes.TRA.txt

tag: type

value: allo

tag: model

value: donor

tag: treg donor

tag: recipient

tag: techn. replicate


title: Intestine, WT, ad libitum, doxorubicin, 2H [J19]

description: Sample J19

value: Male

value: proximal small intestine

tag: genotype

tag: fed state

value: ad libitum

tag: drug treatment

tag: time with_respect_to_drug_treatment


title: polyTreg_1_donor_Tcra_R2

description:
expanded
mTRA_176_Treg_d14_poly_A.RunAB.clonotypes.TRA.txt

tag: strain

value: C57BL/6 WT

tag: sampleID

tag: tissue


title: h56B_TCR

tag: age

value: adult

value: female

tag: treatment

value: Pembrolizumab

tag: disease state

value: Triple-receptor negative breast cancer


title: h57A_P

tag: Sex

value: Baseline


title: ACL1_701

value: roots

tag: biological replicates

tag: cell type

value: 14-day-old seedlings

value: ssp. japonica var. Kitaake

value: acclimation (15°C, 12 h) -> cold stress targeted on leaves (leaves at 5°C, roots at 20°C, 24 h)

tag: treatment time


title: Intestine, WT, ad libitum, doxorubicin, 24H [J25]

description: Sample J25

value: wild type

value: Doxorubicin


title: ACL1_668


title: Intestine, Ddit4-/-, fasted and refed, untreated, 6H [J17]

description: Sample J17

value: 24 hour fast and 6H Refed

value: Untreated


title: Intestine, Ddit4-/-, fasted and refed, untreated, 2H [J15]

description: Sample J15

value: Male

value: 24 hour fast and 2H Refed


title: h56B_N

value: Breast


title: polyTreg_3_donor_Tcra_R2

description:
expanded
mTRA_Tx198-2-d12-rp_AB.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: mouse (pool/culture no.)

tag: type

value: poly

tag: model

value: in vitro

value: donor

tag: treg donor

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: alpha


title: Intestine, WT, ad libitum, doxorubicin, 6H [J21]

description: Sample J21

value: proximal small intestine

tag: genotype

tag: fed state

value: ad libitum

tag: drug treatment

tag: time with_respect_to_drug_treatment


title: Intestine, Ddit4-/-, fasted, untreated, 0H [J14]

description: Sample J14

tag: tissue

value: 24 hour fast


title: h56B_P

tag: age

value: adult

value: female

tag: treatment

value: Pembrolizumab

tag: disease state

value: Triple-receptor negative breast cancer


title: alloTreg_6_donor_Tcra_R2

description:
expanded
mTRA_217_Tx198-10-241_d12_ra_A.RunAB.clonotypes.TRA.txt

tag: strain

tag: sampleID

value: allo

tag: recipient

tag: techn. replicate


title: h56A_TCR

tag: Sex

value: Baseline


title: alloTreg_4_donor_Tcra_R2

description:
expanded
mTRA_102_Tx198-4-208_d11_ra_A.RunAB.clonotypes.TRA.txt

tag: mouse (pool/culture no.)

tag: type

tag: model

tag: treg donor


title: AC2_509

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Two hours after dawn, plants were transfered to cold stress (5°C; the medium and the climate chamber was pre-cooled) for 24 h. Two hours after dawn (14-days-old plants), plants were transfered to control conditions (medium was changed) and left under control conditions for 3 days (recovery). Sampling was done after recovery 2 h after dawn.

value: roots

tag: biological replicates

tag: cell type

value: 17-day-old seedlings

tag: genotype

value: ssp. japonica var. Kitaake

value: acclimation (15°C, 12 h) -> cold stress on the whole plant (5°C, 24 h) -> recovery under control conditions (3 days)

tag: treatment time


title: Intestine, Ddit4-/-, ad libitum, untreated, 0H [J13]

description: Sample J13

value: Male

tag: tissue

tag: fed state

tag: drug treatment

value: Untreated

tag: time with_respect_to_drug_treatment


title: h56A_N

value: Breast

tag: age

tag: treatment

tag: disease state


title: AC2_448


title: Intestine, WT, fasted and refed, untreated, 6H [J5]

description: Sample J5

value: wild type

value: 24 hour fast and 6H Refed


title: alloTreg_3_donor_Tcra_R2

description:
expanded
mTRA_Tx198-2-d12-ra_AB.RunAB.clonotypes.TRA.txt

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

value: in vitro

value: donor

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: alpha

tag: techn. replicate


title: AC2_447

tag: biological replicates

tag: cell type


title: AC1_486

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Two hours after dawn, plants were transfered to cold stress (5°C; the medium and the climate chamber was pre-cooled) for 24 h. Sampling was done 2 h after dawn (14-days-old plants).

value: 14-day-old seedlings

tag: genotype

value: acclimation (15°C, 12 h) -> cold stress on the whole plant (5°C, 24 h)

tag: treatment time


title: AC1_487

tag: tissue


title: Intestine, WT, fasted and refed, untreated, 2H [J3]

description: Sample J3

tag: Sex

value: proximal small intestine

tag: fed state

value: 24 hour fast and 2H Refed

tag: drug treatment


title: h53C_TCR

tag: age

value: adult

value: female

tag: treatment

value: Pembrolizumab + Radiation

value: Triple-receptor negative breast cancer


title: h53C_N

tag: disease state


title: AC1_429

value: roots

value: ssp. japonica var. Kitaake


title: Intestine, WT, ad libitum, untreated, 0H [J1]

description: Sample J1

value: Male

value: ad libitum

value: Untreated

tag: time with_respect_to_drug_treatment


title: h56A_P

value: Breast

value: Baseline


title: spleenCD62LposTreg_6_resident_Tcrb_R1

description:
isolated
mTRB_196_Treg_d0_allo_A.RunAB.clonotypes.TRB.txt

tag: strain

value: C57BL/6 WT

tag: sampleID

tag: mouse (pool/culture no.)

tag: type

tag: model

value: homeostatic control

value: spleen

tag: treg donor

tag: recipient

value: Beta


title: h53C_P


title: Intestine, WT, fasted, untreated, 0H [J2]

description: Sample J2

value: proximal small intestine

tag: genotype

value: wild type

value: 24 hour fast


title: spleenCD62LposTreg_5_resident_Tcrb_R1

description:
isolated
mTRB_176_Treg_d0_poly_A.RunAB.clonotypes.TRB.txt

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

tag: techn. replicate


title: spleenCD62LposTreg_4_resident_Tcrb_R1

description:
isolated
mTRB_257-010-S-rn-pos_A.RunAB.clonotypes.TRB.txt

value: C57BL/6 Foxp3GFP+

tag: tissue


title: spleenCD62LposTreg_3_resident_Tcrb_R1

description:
isolated
mTRB_205_d0_S_Cd62lpos_A.RunAB.clonotypes.TRB.txt


title: OMCD of mice under High Salt Diet 4

city: PARIS

first: Caroline

last: Prot-Bertoye

address: 15 rue Ecole de Médecine

country: France

institute: CNRS EMR8228, INSERM UMRS 1138

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads
Dragen v3.7.5 has been used with rna-enable option
Quantification has been done with Dragen v3.7.5 with rna-enable option
Assembly: mm10
Supplementary files format and content: tab-delimited text files including expecting counts and TPM

source_name: kidney

extract_protocol:
OMCD were microdissected from liberase-treated kidneys as previously described. All media were prepared and used in RNA-free environment. After dissection pools of 100-120 strutures from a single mouse were thoroughly rinsed and stored at -80°C on Lysis Buffer (Quiagen, RNeasy micro kit). RNAs were extracted according to the manufactured protocol.
Libraries were prepared from the extracted RNA using the KAPA Stranded mRNA-Seq Kit from ROCHE

treatment_protocol: Mice were under normal salt (0,3 %) or high salt (3 %) diet for 3 days before tubules dissection.

value: kidney

value: high salt (3percent) diet


title: A0_524

growth_protocol: Plants were grown in Sanyo chambers in Araponics hydroponics (Yoshida), 120 μmol/m2/s, 14/10 h 27/23°C light/dark, 70% RH. After 12 days, plants were placed to 15°C for 12 h at the beginning of the night (acclimation; A). Sampling was done 2 h after dawn.

value: roots

tag: biological replicates

tag: cell type

value: 12-day-old seedlings

value: acclimation (15°C, 12 h)

tag: treatment time


title: h53B_TCR

tag: age

value: adult

tag: Sex

value: female

tag: treatment

value: Pembrolizumab

tag: disease state

value: Triple-receptor negative breast cancer


title: alloTreg_1_donor_Tcra_R2

description:
expanded
mTRA_196_Treg_d14_allo_A.RunAB.clonotypes.TRA.txt

tag: strain

value: C57BL/6 WT

tag: sampleID

tag: mouse (pool/culture no.)

tag: type

value: allo

value: in vitro

value: donor

value: alpha


title: alloTreg_2_donor_Tcra_R2

description:
expanded
mTRA_Tx198-1-d13-ra_AB.RunAB.clonotypes.TRA.txt

tag: model

tag: treg donor

tag: recipient


title: grp_dm_heat_treatment_repeat3

city: 杭州市

first: 闯

last: 杨

state: 浙江省

address: 浙江省杭州市西湖区余杭塘路866号浙大紫金港校区生科院511

country: China

institute: 浙江大学

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.

source_name: whole plant

growth_protocol: Germinated seeds were placed into 96-well plates and grown in Kimura B nutrient solution under 20 000 lux white fluorescent light (13 h light/ 11 h dark) at 29 ℃ and with 65% relative humidity.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: 8-day-old seedlings were used for heat stress treatments：45℃,42h.

value: whole plant

tag: genotype

value: GRP3 and GRP164 knock out


title: h53B_P

value: Breast


title: OMCD of mice under High Salt Diet 1

value: kidney


title: A0_523

value: ssp. japonica var. Kitaake


title: A0_463

value: roots


title: OMCD of mice under High Salt Diet 2

value: high salt (3percent) diet


title: grp_dm_heat_treatment_repeat2

address: 浙江省杭州市西湖区余杭塘路866号浙大紫金港校区生科院511

value: GRP3 and GRP163 knock out


title: spleenCD62LposTreg_1_resident_Tcrb_R1

description:
isolated
mTRB_201_d0_S_Cd62lpos_A.RunAB.clonotypes.TRB.txt

growth_protocol: Splenocytes were stained with anti-CD25-PE and anti-PE UltraPure MicroBeads and enriched for CD25+ cells by MACS® (Miltenyi Biotec). The CD25+ fraction was further stained for CD8, CD4 and CD62L and Treg were sorted on a FACSAria IIuTM or a FACSAriaTM Fusion (BD Biosciences) as CD4+CD25highCD62L+ cells; purity of sorted cells was >98%. Polyclonal in vitro expansion of Treg was performed as recently described {Riegel, 2020 #61}. In brief, sorted Treg were cultured in DMEM (high glucose, Gibco/Invitrogen) with 10% FCS, 2mM L-glutamine, 10mM HEPES, 1% NEAA (PAN Biotech), 50U/ml penicillin, 50µg/ml streptomycin and 5x10-5 M 2-mercaptoethanol  (Gibco/Invitrogen) (cDMEM) in 96-U-well plates (1x104/well) and stimulated with CD3/CD28-beads (Treg-Expansion Kit, Miltenyi Biotec, 4 beads/cell) and rhIL-2 (2000 U/ml; Proleukin®, Chiron). Cultures received 100 µl/well fresh medium on d4, were restimulated on d7 with 1 bead/cell after transfer into 24-well-plates (1x106 cells/ml/well), fed and split on d10 as needed and harvested on d12. For allospecific in vitro expansion sorted Treg were seeded at 5x104/well in cDMEM together with 2,5x104/well (d0) or 1x104/well (restimulation on d7) anti-CD11c MicroBead-enriched (Miltenyi Biotec) and irradiated (30 Gy) CD11c+ DC  from BALB/c mice. Cells received fresh medium on d4 and d10 and were harvested on d12.

value: C57BL/6 Foxp3GFP+

value: homeostatic control

value: spleen

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: Beta

tag: techn. replicate


title: h53A_TCR

tag: tissue

value: adult

value: female

value: Baseline

value: Triple-receptor negative breast cancer


title: OMCD of mice under Control Diet 4

value: normal salt (0.3 percent) diet


title: grp_dm_heat_treatment_repeat1

address: 浙江省杭州市西湖区余杭塘路866号浙大紫金港校区生科院511

value: whole plant

value: GRP3 and GRP162 knock out


title: h53A_P

value: Breast

tag: age


title: spleenCD62LnegTreg_4_resident_Tcrb_R1

description:
isolated
mTRB_258-010-S-rn-neg_A.RunAB.clonotypes.TRB.txt


title: h53A_N

tag: Sex


title: OMCD of mice under Control Diet 1

value: kidney

tag: treatment


title: spleenCD62LnegTreg_3_resident_Tcrb_R1

description:
isolated
mTRB_206-004-S-rn-neg_A.RunAB.clonotypes.TRB.txt


title: h53B_N

value: Pembrolizumab

tag: disease state


title: ZH11_heat_treatment_repeat3

address: 浙江省杭州市西湖区余杭塘路866号浙大紫金港校区生科院511

value: WT


title: OMCD of mice under Control Diet 3

tag: strain


title: h52C_TCR

value: Pembrolizumab + Radiation


title: OMCD of mice under Control Diet 2


title: OMCD of mice under High Salt Diet 3

value: high salt (3percent) diet


title: spleenCD62LnegTreg_2_resident_Tcrb_R1

description:
isolated
mTRB_204-003-S-rn-neg_A.RunAB.clonotypes.TRB.txt

value: C57BL/6 Foxp3GFP+

tag: sampleID


title: spleenCD62LposTreg_2_resident_Tcrb_R1

description:
isolated
mTRB_203_d0_S_Cd62lpos_A.RunAB.clonotypes.TRB.txt

tag: mouse (pool/culture no.)

value: homeostatic control


title: h52C_N


title: h52C_P


title: ZH11_heat_treatment_repeat1

address: 浙江省杭州市西湖区余杭塘路866号浙大紫金港校区生科院511


title: liverCD62LposTreg_5_resident_Tcrb_R1

description:
isolated
mTRB_259-010-L-rn-pos_A.RunAB.clonotypes.TRB.txt

tag: type

value: liver


title: liverCD62LposTreg_4_resident_Tcrb_R1

description:
isolated
mTRB_213-004-L-rn-pos_A.RunAB.clonotypes.TRB.txt

tag: model

value: Beta


title: grp_dm_no_treatment_repeat3

address: 浙江省杭州市西湖区余杭塘路866号浙大紫金港校区生科院511

value: GRP3 and GRP164 knock out


title: liverCD62LposTreg_2_resident_Tcrb_R1

description:
isolated
mTRB_209-002-L-rn-pos_A.RunAB.clonotypes.TRB.txt

tag: treg donor


title: ZH11_no_treatment_repeat3

address: 浙江省杭州市西湖区余杭塘路866号浙大紫金港校区生科院511


title: grp_dm_no_treatment_repeat2

address: 浙江省杭州市西湖区余杭塘路866号浙大紫金港校区生科院511

value: GRP3 and GRP163 knock out


title: liverCD62LnegTreg_4_resident_Tcrb_R1

description:
isolated
mTRB_260-010-L-rn-neg_A.RunAB.clonotypes.TRB.txt

tag: recipient


title: grp_dm_no_treatment_repeat1

address: 浙江省杭州市西湖区余杭塘路866号浙大紫金港校区生科院511

tag: genotype


title: ZH11_no_treatment_repeat2

address: 浙江省杭州市西湖区余杭塘路866号浙大紫金港校区生科院511


title: spleenCD62LnegTreg_1_resident_Tcrb_R1

description:
isolated
mTRB_202-002-S-rn-neg_A.RunAB.clonotypes.TRB.txt

value: spleen

tag: pcr1 cy. no.


title: ZH11_heat_treatment_repeat2

address: 浙江省杭州市西湖区余杭塘路866号浙大紫金港校区生科院511


title: hf_80

city: Saint Louis

first: Fan

last: He

state: MO

address: Room 8834, 320 S. Euclid Ave, CSRB building

institute: Washington University School of Medicine in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values of raw counts.

source_name: bone marrow

extract_protocol:
Total RNA from bone marrow cells was extracted with RNeasy Mini Kit (Qiagen, Hilden, Germany) with DNAse treatment following the manufacturer's protocol.
Ribosomal RNA was removed by an RNase-H method using RiboErase kits. Samples were then indexed, pooled, and sequenced by Illumina NovaSeq 6000 following standard Illumina protocol.

value: bone marrow

tag: cell type

value: BMMC

value: regular water


title: hf_87

value: α-KG


title: hf_88


title: hf_91


title: liverCD62LnegTreg_2_resident_Tcrb_R1

description:
isolated
mTRB_210-002-L-rn-neg_A.RunAB.clonotypes.TRB.txt

tag: pcr2 cy. no.

tag: chain


title: h52B_P

tag: tissue

value: Breast

value: adult

value: female

value: Triple-receptor negative breast cancer


title: h52A_N

tag: age

value: Baseline


title: hf_90


title: hf_78


title: h48C_TCR

tag: Sex

value: Pembrolizumab + Radiation


title: h52A_P

tag: treatment


title: hf_86


title: h52B_N

value: Pembrolizumab

tag: disease state


title: liverCD62LposTreg_1_resident_Tcrb_R1

description:
isolated
mTRB_207-001-L-rn-pos_A.RunAB.clonotypes.TRB.txt

tag: strain

value: C57BL/6 Foxp3GFP+

value: homeostatic control

tag: techn. replicate


title: h48C_N


title: hf_76


title: liverCD62LnegTreg_3_resident_Tcrb_R1

description:
isolated
mTRB_214-004-L-rn-neg_A.RunAB.clonotypes.TRB.txt

tag: sampleID

tag: mouse (pool/culture no.)

value: liver

value: Beta


title: h52B_TCR


title: h52A_TCR


title: hf_79


title: OsTOPBP1C-overexpressor_0h_3

city: Beijing

first: Wenxue

last: Zhai

state: Beijing

address: NO.1 Beichen West Road, Chaoyang District, Beijing 100101, China

department: Molecular Agrobiology

institute: Institute of Genetics and Developmental Biology

data_processing:
The sequencing quality were assessed with FastQC (v0.11.5) and then low quality data were filtered using Fastp software.
The clean reads were then aligned to the reference rice genome Oryza_sativa.IRGSP-1.0 using using HISAT2 (v2.1.0) with default parameters.The processed reads from each sample were aligned using HISAT2 against the reference genome
The gene expression analyses were performed with featureCounts and StringTie.
DESeq(v1.28.0) was used to analyze the DEGs between samples. Parameters for classifying significantly DEGs are ≥2-fold differences (|log2FC|≥1, FC: the   fold change of expressions) in the transcript abundance and p ≤ 0.05.
Genome_build: Oryza_sativa.IRGSP-1.0
Supplementary_files_format_and_content: abundance measurements

organism: Oryza sativa Japonica Group

growth_protocol: The Japanica rice (Oryza sativa L.) cultivars Nipponbare (NIP), and transgenic palnts ostopbp1c mutant and OsTOPBP1C-overexpressor, were cultivated in the experimental fields in Beijing

extract_protocol:
Every sample was pooled with infected leaves collected from 15 plants in one plot to diminish the individual environment differences.Total RNA from the mentioned samples were extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s recommendation.
NEB Next Poly(A) mRNA Magnetic Isolation Module (NEB) kit was used to enrich the poly(A) tailed mRNA molecules from 1 μg total RNA. The mRNA was fragmented into ~200 base pair pieces. The first-strand cDNA was synthesized from the mRNA fragments reverse transcriptase and random hexamer primers, and then the second-strand cDNA was synthesized using DNA  polymerase I and RNaseH. The end of the cDNA fragment was subjected to an end repair process that included the addition of a single “A” base, followed by ligation of the adapters. Products were purified and enriched by polymerase chain reaction (PCR) to amplify the library DNA. The final libraries were quantified using KAPA Library Quantification kit (KAPA Biosystems, South Africa) and an Agilent 2100 Bioanalyzer. After quantitative reverse transcription-polymerase chain reaction (RT-qPCR) validation, libraries were subjected to paired-end sequencing with pair  end 150-base pair reading length on an Illumina NovaSeq sequencer (Illumina)

treatment_protocol: Leaves were inoculated with Xoo pathotype GIV at the tillering stage by the leaf-clipping method. And leaf  samples were collected at 0 and 24 hpi from Nipponbare (NIP), ostopbp1c mutant and OsTOPBP1C-overexpressor, respectively.

tag: genotype/variation

tag: treatment/time point

value: at 0 hour under Xoo pathotype GIV treatment

tag: developmental stage

value: at the tillering stage

value: Leaf


title: Pancreatic islet, GF, P10, Female, biol rep 7

city: Salt Lake City

first: W. Zac

last: Stephens

state: UT

address: 15 N. Medical Drive, EEJMRB 4208, EEJMRB 4208

department: Pathology

institute: University of Utah

data_processing:
Raw reads were adapter trimmed and quality filtered with trim galore (0.6.6) using minimum quality of 20 and minimum length of 20 after trimming.
Adapter/quality-trimmed reads were processed with Salmon (1.3.0) using the quant command against the mm10 reference transcriptome with  fragment GC bias correction enabled.
Assembly: mm10
Supplementary files format and content: Directory of Salmon quant output files including quant.sf reporting transcript counts and auxilliary files.

source_name: Pancreatic Islet

extract_protocol:
Purification from acinar tissue was achieved by several rounds of hand picking and islets were immersed in TRIzol before RNA extraction with Direct-zol RNA miniprept kit (Zymo Research).
Total RNA was first hybridized with the NEBNext rRNA Depletion kit v2 (NEB, cat# E7400) to diminish rRNA from the samples. Stranded RNA sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, cat# E7760L).

value: Pancreatic Islet

tag: microbiota

value: GF

value: F


title: h48B_N

value: Breast


title: OsTOPBP1C-overexpressor_6h_3

value: at 6 hours under Xoo pathotype GIV treatment


title: OsTOPBP1C-overexpressor_0h_2


title: colonTreg_4_resident_Tcrb_R1

description:
isolated
mTRB_263-009-C-rn-neg_A.RunAB.clonotypes.TRB.txt

tag: type

tag: model

value: colon

tag: treg donor

tag: recipient

tag: pcr1 cy. no.


title: colonTreg_5_resident_Tcrb_R1

description:
isolated
mTRB_264-010-C-rn-neg_A.RunAB.clonotypes.TRB.txt

tag: tissue

tag: pcr2 cy. no.

tag: chain


title: liverCD62LnegTreg_1_resident_Tcrb_R1

description:
isolated
mTRB_208-001-L-rn-neg_A.RunAB.clonotypes.TRB.txt


title: ZH11_no_treatment_repeat1

address: 浙江省杭州市西湖区余杭塘路866号浙大紫金港校区生科院511

value: whole plant

tag: genotype

value: WT

tag: treatment


title: colonTreg_2_resident_Tcrb_R1

description:
isolated
mTRB_261-007-C-rn-neg_A.RunAB.clonotypes.TRB.txt

tag: strain

tag: techn. replicate


title: OsTOPBP1C-overexpressor_6h_2


title: Pancreatic islet, GF, P10, Female, biol rep 5

tag: Sex


title: ostopbp1c_6h_3

tag: genotype/variation


title: OsTOPBP1C-overexpressor_6h_1

tag: treatment/time point


title: spleenTreg_3-6_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-349-S-rp_A.RunAB.clonotypes.TRB.txt

tag: sampleID

tag: mouse (pool/culture no.)

value: poly

value: GvHD

value: spleen


title: spleenTreg_3-5_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-347-S-rp_A.RunAB.clonotypes.TRB.txt

value: C57BL/6 Foxp3GFP+

tag: type


title: h48A_TCR

tag: age

value: adult

value: female

value: Baseline

tag: disease state

value: Triple-receptor negative breast cancer


title: colonTreg_3_resident_Tcrb_R1

description:
isolated
mTRB_262-008-C-rn-neg_A.RunAB.clonotypes.TRB.txt

tag: model

value: homeostatic control

tag: treg donor

tag: recipient

value: Beta


title: h48C_P

tag: tissue

value: Pembrolizumab + Radiation


title: Pancreatic islet, GF, P10, Female, biol rep 6

value: Pancreatic Islet

tag: microbiota

value: GF

tag: developmental stage

value: F


title: hf_77

value: bone marrow

tag: cell type

value: BMMC

tag: treatment

value: regular water


title: OsTOPBP1C-overexpressor_0h_1

value: at 0 hour under Xoo pathotype GIV treatment

value: at the tillering stage

value: Leaf


title: Pancreatic islet, GF, P10, Female, biol rep 4


title: h48A_P

value: Breast


title: ostopbp1c_0h_2


title: h48B_P

value: adult

value: Pembrolizumab


title: h48B_TCR

value: female


title: ostopbp1c_6h_2

value: at 6 hours under Xoo pathotype GIV treatment


title: Pancreatic islet, GF, P10, Female, biol rep 3


title: h47C_P

value: Triple-receptor negative breast cancer


title: ostopbp1c_0h_1


title: h48A_N

value: Baseline


title: ostopbp1c_6h_1


title: spleenTreg_3-4_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-343-S-rp_A.RunAB.clonotypes.TRB.txt

tag: strain

value: C57BL/6 Foxp3GFP+

value: poly

value: GvHD

value: spleen

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: Beta

tag: techn. replicate


title: Pancreatic islet, GF, P10, Male, biol rep 6

value: Pancreatic Islet

value: GF

tag: Sex

value: M


title: NIP_6h_3

tag: genotype/variation

value: NIP

tag: treatment/time point

value: at the tillering stage


title: spleenTreg_2-6_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-299-S-rp_A.RunAB.clonotypes.TRB.txt

tag: sampleID

tag: mouse (pool/culture no.)

tag: type


title: NIP_6h_2

value: Leaf


title: Pancreatic islet, GF, P10, Female, biol rep 2

value: F


title: ostopbp1c_0h_3

value: at 0 hour under Xoo pathotype GIV treatment


title: Pancreatic islet, GF, P10, Male, biol rep 5


title: spleenTreg_2-5_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-298-S-rp_A.RunAB.clonotypes.TRB.txt

tag: model

tag: treg donor

tag: recipient


title: h47C_N

tag: tissue

value: Breast

tag: age

value: adult

value: female

value: Pembrolizumab + Radiation

tag: disease state


title: spleenTreg_3-1_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-341-S-ra_A.RunAB.clonotypes.TRB.txt

tag: strain

value: C57BL/6 Foxp3GFP+

value: allo


title: Pancreatic islet, GF, P10, Female, biol rep 1

tag: microbiota

tag: developmental stage


title: spleenTreg_2-3_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-296-S-ra_A.RunAB.clonotypes.TRB.txt

value: GvHD

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain


title: h47B_P

tag: Sex

tag: treatment

value: Pembrolizumab

value: Triple-receptor negative breast cancer


title: spleenTreg_2-4_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-297-S-rp_A.RunAB.clonotypes.TRB.txt

tag: sampleID

value: poly

value: spleen

value: Beta

tag: techn. replicate


title: h47C_TCR


title: Pancreatic islet, GF, P10, Male, biol rep 3

value: Pancreatic Islet

value: GF

value: M


title: Pancreatic islet, GF, P10, Male, biol rep 1


title: h47A_TCR

value: Baseline


title: NIP_0h_2

tag: genotype/variation

value: NIP

tag: treatment/time point

value: at 0 hour under Xoo pathotype GIV treatment

value: at the tillering stage

value: Leaf


title: Pancreatic islet, GF, P10, Male, biol rep 2


title: h47B_TCR

value: Breast

value: adult

value: female


title: spleenTreg_3-2_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-346-S-ra_A.RunAB.clonotypes.TRB.txt

value: C57BL/6 Foxp3GFP+

tag: mouse (pool/culture no.)

tag: type

value: allo

tag: model

value: GvHD

tag: treg donor


title: Pancreatic islet, GF, P10, Male, biol rep 4

tag: tissue


title: h47B_N

tag: age

value: Pembrolizumab

tag: disease state

value: Triple-receptor negative breast cancer


title: NIP_0h_1

tag: developmental stage


title: NIP_0h_3


title: H1993 cells, spheroid culture

city: Taipei

first: Jiun-Han

last: Lin

address: No. 155, Sec. 2, Linong St. Beitou Dist., Taipei City

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
CLC Genomics Workbench 11.0.1
Assembly: Homo sapiens (hg38) sequence
Supplementary files format and content: Text files include TPM and RPKM for each sample.

extract_protocol:
Total RNA was prepared by Illustra RNAspin mini RNA isolation kit.
Sample Prep. Kit : Illumina TruSeq Stranded mRNA Sample Prep Kit + limited cycles of PCR by KAPA HiFi Polymerase.

tag: cell line

tag: cell type

value: lung epithelial cell

tag: culture type

value: spheroid


title: Pancreatic islet, GF, P20, Female, biol rep 8

value: Pancreatic Islet

tag: microbiota

value: GF

tag: Sex

value: F


title: NIP_6h_1

value: NIP

value: at 6 hours under Xoo pathotype GIV treatment


title: spleenTreg_2-1_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-293-S-ra_A.RunAB.clonotypes.TRB.txt

tag: strain

tag: sampleID

value: spleen

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: Beta


title: Pancreatic islet, GF, P20, Female, biol rep 6


title: spleenTreg_3-3_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-348-S-ra_A.RunAB.clonotypes.TRB.txt

tag: mouse (pool/culture no.)

tag: type

tag: model

tag: techn. replicate


title: h46C_N

tag: tissue

value: Breast

tag: age

tag: treatment

value: Pembrolizumab + Radiation

tag: disease state


title: h47A_N

value: adult

value: female

value: Baseline


title: h46C_TCR


title: liverTreg_3-6_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-349-L-rp_A.RunAB.clonotypes.TRB.txt

value: C57BL/6 Foxp3GFP+

value: poly

value: GvHD

value: liver

tag: treg donor


title: A549 cells, spheroid culture

tag: cell line

tag: cell type

value: lung epithelial cell

tag: culture type

value: spheroid


title: spleenTreg_2-2_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-294-S-ra_A.RunAB.clonotypes.TRB.txt

tag: strain

tag: sampleID

value: allo


title: h47A_P

tag: Sex

value: Triple-receptor negative breast cancer


title: h46C_P


title: Pancreatic islet, GF, P20, Female, biol rep 9

value: Pancreatic Islet

tag: microbiota

value: GF

tag: developmental stage

value: F


title: A549 cells, adherent culture

value: adherent


title: Pancreatic islet, GF, P20, Female, biol rep 7


title: Pancreatic islet, GF, P20, Male, biol rep 5

value: M


title: H1993 cells, adherent culture


title: liverTreg_2-5_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-298-L-rp_A.RunAB.clonotypes.TRB.txt

tag: mouse (pool/culture no.)

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: Beta


title: Pancreatic islet, GF, P20, Female, biol rep 4

tag: tissue


title: liverTreg_3-4_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-343-L-rp_AB.RunAB.clonotypes.TRB.txt

tag: type

tag: model

tag: techn. replicate


title: Pancreatic islet, GF, P20, Female, biol rep 3


title: liverTreg_2-4_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-297-L-rp_A.RunAB.clonotypes.TRB.txt

tag: treg donor


title: h46B_N

value: Breast

tag: age

value: adult

tag: treatment

value: Pembrolizumab

tag: disease state


title: A375 0 Gy

city: GuangZhou

first: shuo

last: Han

address: Shatai South Road

institute: Southern medical university

data_processing:
The raw data (raw reads) obtained from Illumina HiSeqTM 2500 sequencing were first filtered by removing the adapters at both ends of the reads, discarding reads with insert fragments <17nt and low-quality reads, etc., to obtain high-quality data (clean reads). The clean reads were then aligned to the reference genome to obtain a whole-genome read distribution map, and ncRNA classification annotation was performed on the clean reads. The identified miRNAs were subjected to expression level calculation, miRNA expression clustering, and differential miRNA expression analysis between samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: skin

extract_protocol:
Total RNAs from cells were extracted using TransZol reagent (TransGen Biotech Co., Ltd.) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using SNARTER mRNA-Seq Library Prep Kit following manufacturer‘s protocol.

value: skin

tag: cell line

tag: cell type

value: melanoma cells

tag: genotype

value: WT

value: control


title: A375 8 Gy

value: IR


title: h46B_TCR

tag: Sex

value: female


title: h46B_P


title: 51187_88-5

city: Duarte

first: Zhenlong

last: Li

address: 1500 East Duarte Road

institute: City of hope

data_processing:
Real-time analysis (RTA) 2.2.38 software was used to process the image analysis and base calling.
Sequencing was performed using the single-read mode of 51 cycles of read1 and 7 cycles of index read with V4 reagents on a Hiseq 2500 system (Illumina).

source_name: Expanded ILC2s + U937 + anti-DNAM-1

growth_protocol: ILC2s were cultured with the ILC2 medium. The medium was supplemented with 10% human AB serum (Sigma-Aldrich), IL-2 (500 IU/ml), IL-7 (20 ng/ml), and/or IL-15 (20 ng/ml). Medium and cytokines were refreshed every two days by replacing half of the media containing 1× concentration of cytokines. Every four days, ILC2s were re-cultured onto new plates with fresh OP9.

extract_protocol:
ILC2s were sorted using BD FACSAriaTM Fusion. Total RNA was isolated from ILC2s using a miRNeasy mini kit (QIAGEN).
SMART-Seq® Ultra Low Input RNA Kit for Sequencing–v4 (Takara Bio) was used for getting double-strand cDNA from each sample with 2 ng of input total RNA. The resulting cDNA was sheared using a Covaris LE220 sonicator. The sheared DNA was used for to prepare a sequencing library, using a KAPA HyperPrep Kit. The final libraries were quantified using the Qubit Assay Kit (Thermo Fisher Scientific) and Bioanalyzer (Agilent). Sequencing was performed using the single-read mode of 51 cycles of read1 and 7 cycles of index read with V4 reagents on a Hiseq 2500 system (Illumina). Real-time analysis (RTA) 2.2.38 software was used to process the image analysis and base calling.

treatment_protocol: ILC2s were co-cultured with or without 20 ng/ml IL-15

value: Expanded human ILC2s


title: Pancreatic islet, GF, P20, Female, biol rep 1

tag: microbiota

tag: developmental stage


title: liverTreg_3-2_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-346-L-ra_ABC.RunAB.clonotypes.TRB.txt

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

value: allo

value: GvHD

value: liver

tag: recipient

tag: pcr1 cy. no.


title: Pancreatic islet, GF, P20, Male, biol rep 4

tag: tissue

value: Pancreatic Islet

value: GF


title: Pancreatic islet, GF, P20, Male, biol rep 3

value: M


title: liverTreg_2-3_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-296-L-ra_A.RunAB.clonotypes.TRB.txt

tag: type

tag: model

tag: pcr2 cy. no.

tag: chain

value: Beta

tag: techn. replicate


title: 51186_88-4

source_name: Expanded ILC2s + U937


title: liverTreg_2-6_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-299-L-rp_A.RunAB.clonotypes.TRB.txt

value: poly

tag: treg donor


title: 51184_88-2

source_name: Expanded ILC2s + MOLM13

tag: cell type


title: liverTreg_3-1_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-341-L-ra_A.RunAB.clonotypes.TRB.txt


title: 51185_88-3

source_name: Expanded ILC2s + MOLM13+ anti-DNAM-1


title: liverTreg_3-3_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-348-L-ra_A.RunAB.clonotypes.TRB.txt


title: h46A_TCR

value: Breast

tag: age

value: adult

tag: treatment

value: Baseline

tag: disease state

value: Triple-receptor negative breast cancer


title: h46A_P

tag: Sex


title: 51182_87-5


title: colonTreg_3-6_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-349-C-rp_A.RunAB.clonotypes.TRB.txt

tag: strain

value: colon


title: Pancreatic islet, GF, P20, Male, biol rep 2

tag: microbiota

tag: developmental stage


title: h45C_TCR

value: Pembrolizumab + Radiation


title: colonTreg_3-5_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-347-C-rp_A.RunAB.clonotypes.TRB.txt

tag: sampleID

tag: mouse (pool/culture no.)

tag: recipient


title: 51183_88-1

source_name: Expanded ILC2s


title: h45B_TCR

tag: tissue

value: female

value: Pembrolizumab


title: Pancreatic islet, SPF, P20, Clodronate-treated, Female, biol rep 5

value: clodronate

value: SPF

value: F


title: 51180_87-3

value: Expanded human ILC2s


title: liverTreg_2-1_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-293-L-ra_A.RunAB.clonotypes.TRB.txt

value: C57BL/6 Foxp3GFP+

tag: type

value: allo

tag: model

value: GvHD

value: liver

tag: pcr1 cy. no.


title: liverTreg_2-2_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-294-L-ra_A.RunAB.clonotypes.TRB.txt

tag: pcr2 cy. no.

tag: chain

value: Beta

tag: techn. replicate


title: Pancreatic islet, GF, P20, Female, biol rep 2

value: Pancreatic Islet

value: GF


title: Pancreatic islet, GF, P20, Male, biol rep 1

value: M


title: 51179_87-2

tag: cell type


title: h45B_P

value: Breast

tag: age

value: adult

tag: treatment

value: Triple-receptor negative breast cancer


title: colonTreg_2-6_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-299-C-rp_AB.RunAB.clonotypes.TRB.txt

value: poly

value: colon

tag: treg donor


title: Pancreatic islet, SPF, P20, Clodronate-treated, Female, biol rep 2

value: clodronate

tag: Sex


title: colonTreg_2-5_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-298-C-rp_AB.RunAB.clonotypes.TRB.txt

tag: strain


title: h45C_N

value: female

value: Pembrolizumab + Radiation

tag: disease state


title: Pancreatic islet, SPF, P20, Clodronate-treated, Female, biol rep 6

tag: microbiota

value: SPF

tag: developmental stage

value: F


title: 51181_87-4

value: Expanded human ILC2s


title: h45C_P


title: 51176_86-4


title: h45A_N

value: Baseline


title: h46A_N


title: Pancreatic islet, SPF, P20, Clodronate-treated, Female, biol rep 3


title: 51178_87-1


title: liverTreg_3-5_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-347-L-rp_A.RunAB.clonotypes.TRB.txt

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

value: GvHD

value: liver

tag: recipient


title: 51174_86-2


title: h43C_TCR

tag: tissue


title: h45A_TCR


title: Pancreatic islet, SPF, P20, Clodronate-treated, Male, biol rep 4

value: Pancreatic Islet


title: h43C_N


title: h45A_P


title: Pancreatic islet, SPF, P20, Clodronate-treated, Male, biol rep 5

value: M


title: Pancreatic islet, SPF, P20, Clodronate-treated, Male, biol rep 1


title: S12

source_name: Expanded ILC2s cultured with IL-15


title: colonTreg_2-4_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-297-C-rp_A.RunAB.clonotypes.TRB.txt

tag: type

tag: model

tag: pcr1 cy. no.

value: Beta


title: colonTreg_3-4_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-343-C-rp_A.RunAB.clonotypes.TRB.txt

tag: pcr2 cy. no.

tag: chain

tag: techn. replicate


title: Pancreatic islet, SPF, P10, Female, biol rep 4


title: h43C_P

value: Breast

tag: age

value: adult

tag: treatment


title: colonTreg_3-3_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-348-C-ra_A.RunAB.clonotypes.TRB.txt

value: allo

tag: treg donor


title: 51175_86-3

tag: cell type


title: S11


title: Pancreatic islet, SPF, P20, Clodronate-treated, Female, biol rep 4

tag: Sex


title: Pancreatic islet, SPF, P20, Clodronate-treated, Male, biol rep 3

tag: microbiota


title: h45B_N

value: Pembrolizumab

tag: disease state

value: Triple-receptor negative breast cancer


title: colonTreg_3-2_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-346-C-ra_ABC.RunAB.clonotypes.TRB.txt

tag: strain

tag: sampleID

value: colon


title: Pancreatic islet, SPF, P20, Clodronate-treated, Male, biol rep 2

value: clodronate

tag: developmental stage


title: h43B_N

tag: tissue

value: female


title: colonTreg_3-1_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-2-341-C-ra_A.RunAB.clonotypes.TRB.txt

tag: mouse (pool/culture no.)

tag: type

tag: recipient


title: spleenTreg_7-6_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_251_Tx198-12-4216_S_rp_A.RunAB.clonotypes.TRB.txt

value: poly

tag: model

value: BMT control

value: spleen

tag: pcr1 cy. no.

tag: pcr2 cy. no.


title: 51173_86-1

value: Expanded human ILC2s


title: 51177_86-5


title: spleenTreg_7-5_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_248_Tx198-12-4214_S_rp_A.RunAB.clonotypes.TRB.txt

value: C57BL/6 Foxp3GFP+

tag: chain

tag: techn. replicate


title: colonTreg_2-3_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-296-C-ra_AB.RunAB.clonotypes.TRB.txt

value: GvHD

tag: treg donor


title: h43B_TCR

tag: age

tag: treatment


title: Pancreatic islet, SPF, P10, Male, biol rep 3

value: Pancreatic Islet

tag: microbiota

value: SPF

tag: Sex


title: colonTreg_2-1_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-293-C-ra_AB.RunAB.clonotypes.TRB.txt

tag: strain

value: Beta


title: spleenTreg_7-4_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_254_Tx198-12-4205_S_rp_A.RunAB.clonotypes.TRB.txt

tag: sampleID


title: N11

source_name: Expanded ILC2s cultured without IL-15

tag: cell type


title: colonTreg_2-2_GvHD_Tcrb_R1

description:
re-isolated
mTRB_Tx198-1-294-C-ra_AB.RunAB.clonotypes.TRB.txt

tag: tissue


title: h43A_TCR

value: Breast

value: Baseline

tag: disease state


title: Pancreatic islet, SPF, P10, Female, biol rep 2

tag: developmental stage

value: F


title: spleenTreg_6-6_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_234_Tx198-10-4196_S_rp_A.RunAB.clonotypes.TRB.txt

tag: mouse (pool/culture no.)

tag: type

tag: recipient


title: h43A_P

value: adult


title: S10


title: Pancreatic islet, SPF, P10, Male, biol rep 2

value: M


title: Pancreatic islet, SPF, P10, Female, biol rep 1


title: Pancreatic islet, SPF, P10, Male, biol rep 1


title: h43A_N

value: Triple-receptor negative breast cancer


title: Pancreatic islet, SPF, P10, Female, biol rep 3


title: spleenTreg_6-5_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_231_Tx198-10-4193_S_rp_A.RunAB.clonotypes.TRB.txt

tag: model

tag: pcr1 cy. no.

tag: pcr2 cy. no.


title: M2-ATAC

city: Jinan

first: zhang

last: shi

address: handong First Medical University

institute: handong First Medical University

data_processing:
We focused on ATAC-seq peaks that were located near the transcription initiation sites (TSSs) of ZBP1. These peaks were extracted and visualized in a plot showing their distribution in the reads. Additionally, motif analysis of the peak regions was conducted using the HOMER tool and the findMotifsGenome.pl function.
peaks.txt file generated by MACS version 1.4.3
Assembly: hg19
Supplementary files format and content: peaks file

source_name: cd14+ cell

extract_protocol: We performed ATAC-seq experiments with some modifications based on the protocol described by Daniel [16, 17]. M0, M1, and M2 macrophages were isolated and the number of cells was adjusted to 50 cells/ml in phosphate buffer saline (PBS). The nuclei of these macrophages were then isolated using ATAC-LB. Following DNA fragmentation and purification, the DNA was amplified through 14 cycles. To assess the fragment distribution of the libraries, an Agilent Bioanalyzer was used, and the libraries were subsequently sequenced on a HiSeq 2500 platform.

value: M2 macrophage


title: h43B_P

value: female

value: Pembrolizumab


title: N12


title: M1-ATAC

value: M1 macrophage


title: h42C_TCR

value: Pembrolizumab + Radiation


title: spleenTreg_6-4_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_228_Tx198-10-4192_S_rp_AB.RunAB.clonotypes.TRB.txt

source_name: CD4+CD25+ regulatory T cells

value: poly

value: BMT control

value: spleen

tag: treg donor

tag: chain

tag: techn. replicate


title: Pancreatic islet, SPF, P20, Female, biol rep 8

value: Pancreatic Islet

tag: microbiota


title: h42C_N

source_name: Breast

tag: age

tag: Sex

tag: treatment


title: M0-ATAC

tag: cell type

value: M0 macrophage


title: h42C_P

tag: tissue


title: spleenTreg_7-3_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_242_Tx198-12-4209_S_ra_AB.RunAB.clonotypes.TRB.txt

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

value: allo

value: Beta


title: N10

value: Expanded human ILC2s


title: Pancreatic islet, SPF, P20, Female, biol rep 9

value: SPF

tag: developmental stage

value: F


title: Pancreatic islet, SPF, P20, Female, biol rep 7


title: spleenTreg_7-2_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_239_Tx198-12-4208_S_ra_A.RunAB.clonotypes.TRB.txt

tag: mouse (pool/culture no.)

tag: type


title: h42B_TCR

value: Breast

value: adult

tag: disease state

value: Triple-receptor negative breast cancer


title: Pancreatic islet, SPF, P20, Male, biol rep 5

value: M


title: spleenTreg_7-1_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_245_Tx198-12-400_S_ra_A.RunAB.clonotypes.TRB.txt

tag: model

tag: recipient

tag: pcr1 cy. no.


title: h42B_N

value: female

value: Pembrolizumab


title: Pancreatic islet, SPF, P20, Male, biol rep 4