title: cetuximab resistant CAL27 cytoplasmic RNA

city: Shanghai City

first: Peisong

address: Zhizaoju Rd. No.639

institute: Shanghai Jiao Tong universisy medical school affiliated Shanghai ninth people's hospital

data_processing:
The basic reads were converted into sequence data (also called raw data/reads) by base calling. Low-quality reads were filtered, and the reads with 5’ primer contaminants and poly (A) were removed. The reads without 3’adapter and insert tag, the reads shorter than 15 nt and longer than 41nt from the raw data were filtered, and the clean reads were obtained.For primary analysis, the length distribution of the clean sequences in the reference genome was determined. Non-coding RNAs were annotated as rRNAs, tRNAs, small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs).
These RNAs were aligned and then subjected to the BLAST search against Rfam v.10.1 and GenBank databases.
The known miRNAs were identified by aligning against miRBase v.21 database, and the known miRNA expression patterns in different samples were analyzed.
Unannotated small RNAs were analyzed by mirdeep2 to predict novel miRNAs.
Based on the hairpin structure of a pre-miRNA and the miRBase database, the corresponding miRNA star sequence was also identified.
Assembly: mm10
Supplementary files format and content: Excel spreadsheet with counts for each sample.
Supplementary files format and content: Excel spreadsheet with transcript per million (TPM) for each sample.

molecule: cytoplasmic RNA

growth_protocol: The human tongue cancer cell line CAL27 and its cetuximab resistant counterpart cell line were cultured in high-glucose Dulbecco’s modified Eagle’s medium containing 10% foetal bovine serum and supplemented with 100 U/mL penicillin and 100 µg/mL streptomycin in a humidified 37°C incubator with a 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted using a mirVana miRNA Isolation Kit (Ambion, USA) according to the manufacturer’s protocol. A total of 5 μg of total RNA per sample was used for small RNA library construction.
Small RNA library construction using TruSeq Small RNA Sample Prep Kits (Illumina, USA.). Briefly, total RNA was ligated to adapters at each end. Then, the adapter-ligated RNA was reverse transcribed to cDNA, and PCR amplification was performed. PCR products ranging from 140–160 bp were isolated and purified as small RNA libraries. Library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High-Sensitivity Chips.

treatment_protocol: The cetuximab resistant CAL27 was cultured in 300 μg/mL cetuximab.

tag: cell line

value: Tongue carconoma cells

tag: genotype

value: WT

value: cetuximab 300 microg/mL


title: cetuximab resistant CAL27 nuclear RNA

status: Public on Jan 01 2024

type: SRA

last: Zhai

country: China

library_source: transcriptomic

molecule: nuclear RNA

organism: Homo sapiens

tag: cell type

tag: treatment


title: spleenTreg_6-2_noGvHD_Tcrb_R1

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
mTRB_222_Tx198-10-4183_S_ra_A.RunAB.clonotypes.TRB.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

molecule: total RNA

organism: Mus musculus

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

tag: tissue

value: spleen

tag: treg donor

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: Beta

tag: techn. replicate


title: cetuximab resistant CAL27 total RNA


title: spleenTreg_6-1_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_219_Tx198-10-4181_S_ra_A.RunAB.clonotypes.TRB.txt


title: CAL27 nuclear RNA


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

city: Salt Lake City

first: W. Zac

last: Stephens

state: UT

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

department: Pathology

country: USA

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: SPF

tag: developmental stage

tag: Sex

value: M


title: h42B_P

city: West Hollywood

first: Simon

last: Knott

state: California

address: 8687 Melrose Ave

department: BFG

institute: Cedars Sinai

library_source: transcriptomic single cell

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

molecule: polyA RNA

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

value: female

value: Pembrolizumab

tag: disease state

value: Triple-receptor negative breast cancer


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


title: CAL27 total RNA

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: liverTreg_7-6_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_252_Tx198-12-4216_L_rp_AB.RunAB.clonotypes.TRB.txt

tag: strain

tag: sampleID

tag: mouse (pool/culture no.)

tag: type

value: poly

tag: model

value: liver


title: h42A_TCR

tag: tissue

value: Baseline


title: h42A_N


title: CAL27 cytoplasmic RNA

value: Tongue carconoma cells

value: WT


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

value: F


title: h42A_P


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


title: Combination_3

city: Shanghai

first: Xinrui

last: Wang

address: 197 Ruijin Rd II

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat2.
Read counts for each gene were carried out using HT-Seq using the hg38 refSeq refFlat GTF file.
Genes with adjusted P-value < 0.01 and |foldChange| > 2 were defined as differentially expressed genes (DEGs).
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
The total RNA of cells in each group was isolated using RNAiso Plus (TakaRa, 9108) and stored at -80℃. The concentration and purity of RNA were determined using a NanoPhotometer (ThermoFisher Scientific Intertek, Cat. 3100668).
RNA purification, cDNA synthesis and RNA-Seq of each group (n = 3) were performed by Oebiotech company (Shanghai, China). RNA integrity was analyzed through the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara). The RNA integrity number ≥ 7 was subjected to the following analysis. The cDNA libraries were constructed through TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA).Shanghai

value: breast cancer

value: CAR 10umol/L+JQ-1 25umol/L


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


title: liverTreg_6-6_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_235_Tx198-10-4196_L_rp_AB.RunAB.clonotypes.TRB.txt

value: C57BL/6 Foxp3GFP+

value: BMT control

tag: treg donor

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: Beta


title: liverTreg_7-5_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_249_Tx198-12-4214_L_rp_AB.RunAB.clonotypes.TRB.txt

tag: techn. replicate


title: liverTreg_6-5_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_232_Tx198-10-4193_L_rp_AB.RunAB.clonotypes.TRB.txt


title: h39C_N

tag: age

tag: Sex

value: Pembrolizumab + Radiation

tag: disease state


title: h39C_TCR

value: Breast


title: Combination_2

tag: cell line

tag: cell type

tag: genotype


title: liverTreg_7-4_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_255_Tx198-12-4205_L_rp_AB.RunAB.clonotypes.TRB.txt

tag: strain

tag: sampleID


title: JQ1_2

tag: treatment

value: JQ-1 25umol/L


title: JQ1_3


title: h39C_P

value: adult

value: female


title: liverTreg_6-4_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_229_Tx198-10-4192_L_rp_AB.RunAB.clonotypes.TRB.txt

tag: mouse (pool/culture no.)

tag: type

tag: model


title: Combination_1


title: liverTreg_7-2_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_240_Tx198-12-4208_L_ra_AB.RunAB.clonotypes.TRB.txt

value: allo

tag: tissue

tag: treg donor

tag: recipient


title: h39B_P

value: Pembrolizumab

value: Triple-receptor negative breast cancer


title: h39B_TCR


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

value: Pancreatic Islet

tag: microbiota

value: SPF

tag: developmental stage


title: h39A_TCR

tag: age

value: Baseline


title: liverTreg_7-3_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_243_Tx198-12-4209_L_ra_AB.RunAB.clonotypes.TRB.txt

value: liver

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

tag: techn. replicate


title: h39B_N

tag: Sex

tag: disease state


title: JQ1_1

tag: cell line

tag: cell type

value: breast cancer

tag: genotype

value: WT


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

value: M


title: CAR_3

tag: treatment

value: CAR 10umol/L


title: h39A_N


title: Pancreatic islets, SPF, P15 [scRNA-seq]

data_processing:
Reads were demultiplexed and count matrices created with cellranger (version 7.0.1)
Assembly: mm10
Supplementary files format and content: 3 files are provided for each sample, in one archive. The cell barcodes, the gene identifiers and the matrix of counts.

extract_protocol:
Purification from acinar tissue was achieved by several rounds of hand picking. Islets from 20 animals in each group were pooled and digested using Gibco Enzyme Free Cell Dissociation Buffer at 37 C for 15 minutes. Samples were vortexed every 5 minutes throughout the incubation. Washed and resuspended cells from the islet dissociation were run through a CD45 positive selection column (Miltenyi Biotec, CD45 MicroBeads mouse) followed by a dead cell removal kit (Miltenyi Biotec) to isolate live cells.
Next GEM Single Cell 3’ Gene Expression Library Prep version 3.1 with UDI (10X Genomics).


title: CAR_2


title: liverTreg_6-2_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_223_Tx198-10-4183_L_ra_AB.RunAB.clonotypes.TRB.txt

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

tag: type

tag: model

value: BMT control

value: Beta


title: h39A_P

tag: tissue

value: Breast


title: Con

city: Guangzhou

first: Fangfang

last: Chen

state: Guangdong

address: No.132 Waihuandong Road, University Town

department: School of Pharmaceutical Sciences

institute: Sun Yat-sen University

description: Con

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling
clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Hisat2 can generate a database of splice junctions based on the gene model annotation file
The mapped reads of each sample were assembled using StringTie with default parameters. Then, all transcripts from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software.
RSEM was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: exceL spreadsheet file includes gene name and read counts for each samples

source_name: mouse leukocytes

growth_protocol: Cells were isolated from mouse peripheral blood leukocytes.

extract_protocol:
Total RNA was extrated from each cell sample using a RNeasy Mini Kit (Qiagen, USA). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (CatalogE7530L, NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Cells were treated with 0.01 μg/ml Fn1792(Fn-MliC) protein or PBS for 12 h

value: mouse leukocytes

value: PBS


title: Pancreatic islets, GF, P15 [scRNA-seq]

tag: microbiota

value: GF

tag: developmental stage


title: h30C_TCR

tag: age

value: adult

value: female

value: Pembrolizumab + Radiation


title: FN1792

value: 0.01 μg/ml Fn1792(Fn-MliC) protein for 12 h


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

value: Pancreatic Islet

value: SPF

value: F


title: liverTreg_6-3_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_226_Tx198-10-4190_L_ra_AB.RunAB.clonotypes.TRB.txt

value: allo

value: liver

tag: treg donor

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain


title: colonTreg_7-6_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_253_Tx198-12-4216_C_rp_A.RunAB.clonotypes.TRB.txt

value: poly

value: colon

tag: techn. replicate


title: CAR_1

tag: cell line

tag: cell type

value: breast cancer

tag: genotype

value: WT

value: CAR 10umol/L


title: CON_3

tag: treatment

value: DMSO


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

tag: Sex


title: liverTreg_6-1_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_220_Tx198-10-4181_L_ra_AB.RunAB.clonotypes.TRB.txt

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

tag: type

value: BMT control

value: Beta


title: Diabetic, replicate 1, scRNAseq

city: TianJin

first: Kaiwen

last: Bao

institute: Tianjin Medical University

description: 10X Genomics

data_processing:
We used the Cell Ranger software suite (version 7.0.0) to perform single-cell barcode processing, read alignment, and feature barcode matrix generation. Specifically, we used the Mus musculus genome mm10 as the reference genome and applied STAR (v.2.7.10b) software (15) for FASTQs alignment. The cell barcodes were automatically determined based on the distribution of the UMI counts.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Retina

extract_protocol:
Single live CD31+ cells from the retina were enriched using CD31 microbeads. The cell suspensions were mixed with filtered trypan blue to evaluate cell viability and concentration.
we performed the following steps on a 10x Genomics chromium single-cell platform, and libraries were constructed according to the manufacturer’s instructions of 10x Chromium Single Cell 3′ Regent Kit v3 protocol (10X Genomics, 1000121).

tag: disease state

value: Diabetic

tag: tissue

value: Retina

value: CD31+ cell


title: liverTreg_7-1_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_246_Tx198-12-400_L_ra_AB.RunAB.clonotypes.TRB.txt

tag: model

tag: treg donor


title: CON_2


title: colonTreg_7-4_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_256_Tx198-12-4205_C_rp_A.RunAB.clonotypes.TRB.txt

tag: recipient

tag: pcr1 cy. no.


title: Diabetic, replicate 2, scRNAseq

description: 10X Genomics


title: h30C_P

value: Breast

tag: age

value: adult

value: female

value: Pembrolizumab + Radiation

value: Triple-receptor negative breast cancer


title: h30B_TCR

value: Pembrolizumab


title: CON_1


title: colonTreg_7-5_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_250_Tx198-12-4214_C_rp_A.RunAB.clonotypes.TRB.txt

value: poly

value: colon

tag: pcr2 cy. no.

tag: chain

tag: techn. replicate


title: HCT116 cells, shNUDT21_1

city: SHANGHAI

first: zhenyu

last: huang

state: SHANGHAI

address: No.1665 kongjiang RD. Yangpu District

institute: xinhua hospital affiliated to shanghai jiaotong university school of medcine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg18 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GR38p7
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

tag: cell type

value: Epithelial tumor cells

tag: genotype

value: NUDT21 knockdown

tag: time


title: h30A_TCR

tag: Sex

tag: treatment

value: Baseline


title: HCT116 cells, shPLKO2

value: WT


title: HCT116 cells, shNUDT21_5


title: WT+CDAHFD

first: Jiangtao

last: Fu

address: Guohe Road 325

institute: Naval medical university

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 10%;   Cell Gene Number < Median Gene Number * 2;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: Single cell matrix files

source_name: Liver

extract_protocol:
Pulmonary artery tissues were placed in DMEM/F12(Gibco), and cut into small fragments and digested them with collagenase II (Invitrogen) for 2h at 37℃. After digestion, the obtained cells were filtered through a 70μm filter and collect it into a collection tube.
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: Liver

value: CDAHFD


title: colonTreg_6-5_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_233_Tx198-10-4193_C_rp_A.RunAB.clonotypes.TRB.txt

tag: strain

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

tag: type

value: BMT control

value: Beta


title: Ctrl, replicate 2, scRNAseq

description: 10X Genomics

tag: disease state

value: Ctrl

tag: tissue

value: Retina

value: CD31+ cell


title: h30B_P

value: Breast

value: adult

value: female


title: colonTreg_6-6_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_236_Tx198-10-4196_C_rp_A.RunAB.clonotypes.TRB.txt

value: poly

tag: model

tag: treg donor

tag: recipient

tag: pcr1 cy. no.


title: Ctrl, replicate 1, scRNAseq

description: 10X Genomics


title: h26C_TCR

tag: age

value: Pembrolizumab + Radiation

value: Triple-receptor negative breast cancer


title: DENSpm + Cytokines biol rep 3

city: Chicago

first: Sarah

middle: A

last: Tersey

state: IL

department: Medicine

institute: University of Chicago

data_processing:
Data was analyzed using Rosalind.
Reads were trimmed using catadapt. Quality scores were assessed using FastQC.
Individual sample reads were quantified using Htseq and normalized via Relative Log Expression using DESeq2 R library.
Assembly: mm10
Supplementary files format and content: excel files with raw counts
Supplementary files format and content: excel files with normalized counts

source_name: MIN6 cells

growth_protocol: MIN6 cells were maintained at 37 °C in DMEM-High Glucose medium containing 15% FBS, 1% P/S, 1% Glutamine (2mM).

extract_protocol:
RNA was extracted using Qiagen RNAeasy Mini Kit.
RNA quality and quantity was assessed using the Agilent bio-analyzer. Strand-specfiic RNA-seq libraries were prepared using an TruSEQ mRNA-SEQ library protocol (Illumina provided).
Library quality and quantity was assessed using the Agilent bio-analyzer and libraries were seqenced using an Illumina NovaSEQ6000.

treatment_protocol: MIN6 β cells were treated with vehicle, 5 mM DFMO, or 10 μM DENSpm with or without a proinflammatory cytokine mix (100 ng/lg IFN-γ, 50 mg/ml TNF-α, and 25 ng/ml IL-1β) for 24 h prior to RNA isolation.

tag: cell line

value: MIN6 cells

value: mouse beta cell line

value: DENSpm + Cytokines


title: DENSpm + Cytokines biol rep 2

tag: cell type


title: h30A_P

value: Baseline


title: h26C_P


title: HCT116 cells, shPLKO1

value: Epithelial tumor cells

tag: genotype

value: WT


title: DENSpm + Cytokines biol rep 1


title: NCI-H460 cells, shAPE1 [sh3]

city: Nanjing

first: Fan

last: Yang

state: China

address: Wenyuan road 1

institute: Nanjing Normal University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: RPKM values for each Sample

value: Non-small cell lung cancer cells

value: APE1 knockdown


title: colonTreg_7-2_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_241_Tx198-12-4208_C_ra_A.RunAB.clonotypes.TRB.txt

value: C57BL/6 Foxp3GFP+

value: allo

value: BMT control

value: colon

tag: pcr2 cy. no.

tag: chain

value: Beta

tag: techn. replicate


title: NCI-H460 cells, shAPE1 [sh2]


title: colonTreg_7-3_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_244_Tx198-12-4209_C_ra_A.RunAB.clonotypes.TRB.txt

tag: strain


title: h26B_P

value: Breast

value: adult

tag: Sex

value: female

tag: treatment

value: Pembrolizumab


title: DENSpm Alone biol rep 3

value: MIN6 cells

value: DENSpm Alone


title: NCI-H460 cells, shAPE1 [sh1]


title: h26B_TCR

value: Triple-receptor negative breast cancer


title: NCI-H460 cells, shControl [NC3]


title: DENSpm Alone biol rep 1

value: mouse beta cell line


title: DENSpm Alone biol rep 2


title: h26A_TCR

value: Baseline


title: NCI-H460 cells, shControl [NC2]

value: WT


title: DFMO + Cytokines biol rep 3

value: DFMO + Cytokines


title: NCI-H460 cells, shControl [NC1]

value: Non-small cell lung cancer cells


title: colonTreg_6-4_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_230_Tx198-10-4192_C_rp_A.RunAB.clonotypes.TRB.txt

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: mouse (pool/culture no.)

tag: type

value: poly


title: colonTreg_6-2_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_224_Tx198-10-4183_C_ra_AB.RunAB.clonotypes.TRB.txt

value: allo

tag: model

value: BMT control

tag: tissue


title: colonTreg_6-1_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_221_Tx198-10-4181_C_ra_A.RunAB.clonotypes.TRB.txt

value: colon

tag: treg donor

tag: recipient

value: Beta


title: K562_THRA_ChIP

first: Shanhe

last: Yu

address: 197# Rui Jin Road II

institute: Shanghai Institute of Hematology，Rui Jin Hospital

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg38 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control and an initial threshold q-value of 0.01 as cutoff
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using Deeptools(3.5.0)

molecule: genomic DNA

growth_protocol: K562 were grown in RPMI 1640 supplemented with 10% FBS, at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: human erythroleukemic cells

tag: chip antibody

value: THRA (ORIGENE, TA805187)


title: DFMO + Cytokines biol rep 2

tag: cell line


title: K562_THRA_input

tag: cell type


title: colonTreg_7-1_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_247_Tx198-12-400_C_ra_A.RunAB.clonotypes.TRB.txt

tag: pcr1 cy. no.


title: ago1d_lt_rep3

city: Shenzhen

first: Chuanlin

last: Shi

address: Dapeng

institute: Chinese Academy of Agricultural Sciences

description:
Degradome sequencing
Target genes prediction and validation under low temperature conditions.xlsx

data_processing:
library strategy: Degradome sequencing
The degradome sequencing raw data were processed through in-house perl scripts by removing the 5’ adapter, reads with more than 10% N and reads with more than 50% nucleotides with Qphred <= 5.
The clean reads were mapped to the Oryza sativa v.7.0 genome sequences (MSU Rice Genome Annotation Project) using Bowtie.
Targets prediction and validation of the degradome sequencing was conducted by CleaveLand4 and GSTAr.
Assembly: The clean reads were mapped to Oryza sativa v.7.0 genome sequences (MSU Rice Genome Annotation Project)
Supplementary files format and content: tab-delimited text files include target genes of small sRNAs identified by CleaveLand4 and GSTAr

organism: Oryza sativa

source_name: anthers

growth_protocol: The ago1d mutant rice developed by CRISPR/Cas9 genome editing was from our previous work (Shi et al. 2022). Both ago1d mutant and the rice cultivar Nipponbare (Oryza sativa L.) used as wildtype in this study were grown in paddy fields in Shanghai, China during summer. When the anther development was initiated during the reproductive growth stages, the wildtype and ago1d mutant plants were transferred to growth chambers at an average temperature of 22°C for the lower temperature treatment and 28°C for the normal control temperature treatment, at 75% relative humidity under a 12 h/12 h, light/dark photoperiod until anthesis.

extract_protocol:
All samples were harvested and frozen immediately in liquid nitrogen and total RNA was extracted with TRIzol reagent (Invitrogen)
Total RNA was isolated from each sample and purified with oligo(dT) beads. The purified poly(A) RNAs containing a 5′ monophosphate of the 3′ cleavage product of the mRNA were ligated to 5’-adaptor. First-strand cDNA was reversely transcribed using 3′-adapter random primers, and size selection was performed with AMPureXP beads. Then the cDNAs were amplified with PCR by the following conditions: initial denaturation at 95 °C for 3 min; 15 cycles of denaturation at 98 °C for 15 sec, annealing at 60 °C for 15 sec, and extension at 72 °C for 30 sec; and then final extension at 72 °C. The final products were sequenced (single-end 50-bp) on an Illumina Hiseq2500 platform

value: anthers

tag: cultivar

value: Nipponbare (Oryza sativa L.)

tag: genotype

value: ago1d knockout

value: 22 °C treatment


title: DFMO + Cytokines biol rep 1

value: MIN6 cells

value: mouse beta cell line


title: colonTreg_6-3_noGvHD_Tcrb_R1

description:
re-isolated
mTRB_227_Tx198-10-4190_C_ra_AB.RunAB.clonotypes.TRB.txt

tag: pcr2 cy. no.

tag: chain

tag: techn. replicate


title: polyTreg_6_donor_Tcrb_R1

description:
expanded
mTRB_218_Tx198-10-241_d12_rp_A.RunAB.clonotypes.TRB.txt

tag: strain

value: in vitro

value: donor


title: polyTreg_4_donor_Tcrb_R1

description:
expanded
mTRB_103_Tx198-4-208_d11_rp_A.RunAB.clonotypes.TRB.txt

tag: sampleID


title: h23B_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: h23B_TCR

tag: tissue


title: DFMO Alone biol rep 3

value: DFMO Alone


title: h23C_TCR

value: Pembrolizumab + Radiation


title: DFMO Alone biol rep 2


title: polyTreg_3_donor_Tcrb_R1

description:
expanded
mTRB_Tx198-2-d12-rp_AB.RunAB.clonotypes.TRB.txt

value: C57BL/6 Foxp3GFP+

tag: mouse (pool/culture no.)

tag: type

value: poly

tag: model

tag: treg donor

tag: recipient

value: Beta


title: h26A_P

value: Baseline


title: ago1d_lt_rep1

treatment_protocol: Both ago1d mutant and the rice cultivar Nipponbare (Oryza sativa L.) used as wildtype in this study were grown in paddy fields in Shanghai, China during summer. When the anther development was initiated during the reproductive growth stages, the wildtype and ago1d mutant plants were transferred to growth chambers at an average temperature of 22°C for the lower temperature treatment and 28°C for the normal control temperature treatment, at 75% relative humidity under a 12 h/12 h, light/dark photoperiod until anthesis.

value: anthers

tag: cultivar

value: Nipponbare (Oryza sativa L.)

value: ago1d knockout


title: h23A_TCR


title: wt_lt_rep2

tag: genotype

value: wild-type

value: 22 °C treatment


title: ago1d_lt_rep2


title: wt_lt_rep3


title: h23A_P


title: polyTreg_2_donor_Tcrb_R1

description:
expanded
mTRB_Tx198-1-d13-rp_AB.RunAB.clonotypes.TRB.txt

value: in vitro

value: donor

tag: pcr1 cy. no.

tag: pcr2 cy. no.


title: DFMO Alone biol rep 1

tag: cell line

value: MIN6 cells

tag: cell type

value: mouse beta cell line


title: h23C_P

value: Breast

value: adult

value: female


title: polyTreg_7_donor_Tcrb_R1

description:
expanded
mTRB_238_Tx198-12-245_d12_rp_A.RunAB.clonotypes.TRB.txt

tag: strain

tag: sampleID

tag: chain

tag: techn. replicate


title: Vehicle + Cytokines biol rep 3

tag: treatment

value: Vehicle + Cytokines


title: h20C_TCR

tag: tissue

tag: age

tag: Sex

value: Pembrolizumab + Radiation

tag: disease state

value: Triple-receptor negative breast cancer


title: polyTreg_1_donor_Tcrb_R1

description:
expanded
mTRB_176_Treg_d14_poly_A.RunAB.clonotypes.TRB.txt

value: C57BL/6 WT

tag: mouse (pool/culture no.)

tag: type

value: poly

tag: model

tag: treg donor

value: Beta


title: Vehicle + Cytokines biol rep 1


title: Vehicle + Cytokines biol rep 2


title: alloTreg_7_donor_Tcrb_R1

description:
expanded
mTRB_237_Tx198-12-245_d12_ra_A.RunAB.clonotypes.TRB.txt

value: C57BL/6 Foxp3GFP+

value: allo

tag: recipient

tag: pcr1 cy. no.


title: ago1d_nt_rep3

description:
Degradome sequencing
Target genes prediction and validation under normal temperature conditions.xlsx

value: anthers

tag: cultivar

value: Nipponbare (Oryza sativa L.)

tag: genotype

value: ago1d knockout

value: 28 °C treatment


title: h20B_TCR

value: Pembrolizumab


title: ago1d_nt_rep2


title: wt_lt_rep1

value: wild-type

value: 22 °C treatment


title: Vehicle biol rep 2

tag: cell line

value: MIN6 cells

tag: cell type

value: mouse beta cell line

value: Vehicle


title: h20B_P

value: Breast

value: adult

value: female


title: alloTreg_3_donor_Tcrb_R1

description:
expanded
mTRB_Tx198-2-d12-ra_AB.RunAB.clonotypes.TRB.txt

tag: strain

tag: sampleID

value: in vitro

value: donor

tag: pcr2 cy. no.

tag: chain


title: h20C_P

tag: tissue

tag: age

tag: treatment

value: Pembrolizumab + Radiation

value: Triple-receptor negative breast cancer


title: Vehicle biol rep 3


title: ago1d_nt_rep1

value: anthers


title: alloTreg_4_donor_Tcrb_R1

description:
expanded
mTRB_102_Tx198-4-208_d11_ra_A.RunAB.clonotypes.TRB.txt

value: C57BL/6 Foxp3GFP+

tag: mouse (pool/culture no.)

value: allo

value: Beta

tag: techn. replicate


title: alloTreg_1_donor_Tcrb_R1

description:
expanded
mTRB_196_Treg_d14_allo_A.RunAB.clonotypes.TRB.txt

value: C57BL/6 WT

tag: type

tag: model


title: h19C_TCR

tag: Sex

tag: disease state


title: alloTreg_2_donor_Tcrb_R1

description:
expanded
mTRB_Tx198-1-d13-ra_AB.RunAB.clonotypes.TRB.txt

tag: treg donor

tag: recipient

tag: pcr1 cy. no.


title: wt_nt_rep2

tag: cultivar

value: Nipponbare (Oryza sativa L.)

tag: genotype

value: wild-type

value: 28 °C treatment


title: WYKNIU2

city: Chapel Hill

first: William

last: Kim

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software v6.1.1
Assembly: mm10
Supplementary files format and content: H5 format files of cell ranger output for each scRNAseq samples

source_name: scraped urothelium

extract_protocol:
Single cell suspensions were generated using the Miltenyi Biotec Tumor Dissociation Kit and the gentleMACS Dissociator. Red blood cells were lysed using Miltenyi Biotec Red Blood Cell Lysis Solution and dead cells were removed using the Miltenyi Biotec Dead Cell Removal Kit. Single cell suspensions were subsequently loaded onto the 10X Genomics Chromium Controller to generate single-cell gel beads in emulsions (GEMs)
scRNAseq libraries were prepared using Chromium Single Cell 3' Reagent Kits (v3.1 Chemistry) according to the manufacter's instructions

value: scraped urothelium

tag: strain


title: Vehicle biol rep 1

tag: cell line

value: MIN6 cells

tag: cell type

value: mouse beta cell line

value: Vehicle


title: h20A_P

tag: tissue

value: Breast

value: adult

value: female

value: Baseline


title: alloTreg_6_donor_Tcrb_R1

description:
expanded
mTRB_217_Tx198-10-241_d12_ra_A.RunAB.clonotypes.TRB.txt

tag: sampleID

value: in vitro

value: donor

tag: pcr2 cy. no.

tag: chain


title: Setd2-CD_yolk sac_HO_rep2

first: Shubei

address: No.1954 Huashan Rd

institute: School of Life Sciences & Biotechnology, Shanghai Jiao Tong University

description:
Setd2-CD_yolk sac_HO-2_Raw
Setd2_E9.5_yolk sac.txt

data_processing:
Raw reads were filtered by fastp(0.22.0) with default set, clean sequenced reads were alignmented to mm10 by hisat2(2.2.1), suppress unpaired alignments for paired reads,suppress discordant alignments for paired reads.
Aligned reads were extracted by featureCounts(2.0.1) with default parameters and normalized by DEseq2(1.32.0).
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Mortazavi et al., Nature Methods, 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: *.txt: Tab-delimited text files include gene counts and FPKM values for each Sample.

source_name: Yolk sac

extract_protocol:
Whole embryos or yolk sacs was harvested for RNA extraction with TRIzol Reagent (Invitrogen).
Libraries were generated using the KAPA mRNA HyperPrep kit (v4.17) (Kapa Biosystems) and sequenced with Illumina NovaSeq6000.

tag: developmental stage

value: Embryonic day 9.5

value: Yolk sac

value: Homozygous


title: spleenCD62LposTreg_6_resident_Tcra_R1

description:
isolated
mTRA_196_Treg_d0_allo_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 WT

tag: mouse (pool/culture no.)

tag: type

value: homeostatic control

value: spleen

value: alpha

tag: techn. replicate


title: wt_nt_rep1

value: anthers

value: Nipponbare (Oryza sativa L.)

value: wild-type

tag: treatment

value: 28 °C treatment


title: h19C_P

value: Breast

tag: age

tag: Sex

value: Pembrolizumab + Radiation

tag: disease state

value: Triple-receptor negative breast cancer


title: h19B_TCR

value: adult

value: female

value: Pembrolizumab


title: C.elegans, THz treated 3

city: Xi'an

first: Sen

last: Shang

address: West Xianning Road

institute: Xi'an Jiaotong University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this  step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing  poly-N and low quality reads from raw data.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw  sequences were transformed into clean reads after data processing. These clean reads were then  mapped to the reference genome sequence by STAR. Only reads with a perfect match or one  mismatch were further analyzed and annotated based on the reference genome.
HTSeq v 0.5.4 p3 was used to count the reads numbers mapped to each gene. Gene expression levels  were estimated by fragments per kilobase of transcript per million fragments mapped (FPKM).
Differential expression analysis of two conditions/groups was performed using the DESeq R  package (1.10.1). DESeq provide statistical routines for determining differential expression in  digital gene expression data using a model based on the negative binomial distribution. The resulting  P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false  discovery rate. Genes with an adjusted P-value < 0.05 found by DESeq were assigned as  differentially expressed
Assembly: WBcel235
Supplementary files format and content: FPKMs for all samples

organism: Caenorhabditis elegans

source_name: Whole  body

extract_protocol:
The RNA of C.elegans was extracted by TRIzol (Invitrogen, CA, USA)
RNA libraries were contructed by TruSeq RNA Library Preparation kit v2 (Illumina)

value: Whole  body

value: THz


title: h20A_TCR

value: Baseline


title: C.elegans, THz treated 2


title: spleenCD62LposTreg_5_resident_Tcra_R1

description:
isolated
mTRA_176_Treg_d0_poly_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 WT

tag: model

tag: treg donor

tag: recipient

tag: pcr1 cy. no.


title: Setd2-CD_yolk sac_HO_rep1

description:
Setd2-CD_yolk sac_HO-1_Raw
Setd2_E9.5_yolk sac.txt

tag: strain

value: Embryonic day 9.5

value: Yolk sac

tag: genotype

value: Homozygous


title: Setd2-CD_yolk sac_HE_rep2

description:
Setd2-CD_yolk sac_HE-2_Raw
Setd2_E9.5_yolk sac.txt

tag: tissue

value: Heterozygous


title: Setd2-CD_yolk sac_HE_rep1

description:
Setd2-CD_yolk sac_HE-1_Raw
Setd2_E9.5_yolk sac.txt


title: h19A_TCR


title: wt_nt_rep3

value: anthers

tag: cultivar

value: Nipponbare (Oryza sativa L.)


title: h19B_P


title: h19A_P


title: h18C_TCR


title: spleenCD62LposTreg_3_resident_Tcra_R1

description:
isolated
mTRA_205_d0_S_Cd62lpos_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: sampleID

value: homeostatic control

value: spleen

tag: pcr2 cy. no.

tag: chain

value: alpha


title: C.elegans, THz treated 1


title: spleenCD62LposTreg_4_resident_Tcra_R1

description:
isolated
mTRA_257-010-S-rn-pos_A.RunAB.clonotypes.TRA.txt

tag: mouse (pool/culture no.)

tag: type


title: C.elegans, Control2

tag: treatment

value: Control


title: spleenCD62LnegTreg_4_resident_Tcra_R1

description:
isolated
mTRA_258-010-S-rn-neg_A.RunAB.clonotypes.TRA.txt

tag: techn. replicate


title: Setd2-CD_yolk sac_WT_rep2

description:
Setd2-CD_yolk sac_WT-2_Raw
Setd2_E9.5_yolk sac.txt

tag: developmental stage

value: Wild type


title: spleenCD62LposTreg_2_resident_Tcra_R1

description:
isolated
mTRA_203_d0_S_Cd62lpos_A.RunAB.clonotypes.TRA.txt


title: spleenCD62LnegTreg_3_resident_Tcra_R1

description:
isolated
mTRA_206-004-S-rn-neg_A.RunAB.clonotypes.TRA.txt


title: C.elegans, Control3


title: h18C_P

value: Breast

tag: age

value: adult

tag: Sex

value: female

value: Pembrolizumab + Radiation

tag: disease state

value: Triple-receptor negative breast cancer


title: Setd2-null_yolk sac_HO_rep2

description:
Setd2-null_yolk sac_HO-2_Raw
Setd2_E9.5_yolk sac.txt

value: Embryonic day 9.5


title: spleenCD62LposTreg_1_resident_Tcra_R1

description:
isolated
mTRA_201_d0_S_Cd62lpos_A.RunAB.clonotypes.TRA.txt

tag: model

tag: treg donor

tag: recipient


title: C.elegans, Control1

value: Whole  body


title: HCC-ES

first: YuLi

middle: yang

last: Li

address: Dongan Road

department: 2Department of Immunology

institute: Fudan University

description: Tumor

data_processing:
GEMs (Gel Bead in Emulsion) were constructed for single cell separation according to the number of cells to be harvested. After GEMs were normally formed, GEMs were collected for reverse transcription in a PCR machine for labeling
The GEMs were oil-treated, and the amplified cDNA was purified by magnetic beads, and then subjected to cDNA amplification and quality inspection
Each single-cell RNA-seq library was sequenced twice in two lanes of HiSeq 4000 (Illumina) to obtain single-end, 91 bp, approximately 300 million reads per library.
The 3' Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation,adaptor ligation, sample index PCR, etc.,the library is finally quantitatively examined.
The final library pool was sequenced on the Illumina xx instrument using 150-base-pair paired-end reads.
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: HCC Tumor

extract_protocol:
Digested tissues were filtered through a 100-µm nylon mesh before centrifuging at 1500 rpm for 5 min. The single-cell suspensions were re-suspended with treated with 1ml of RBC lysis buffer (Biolegend, Cat#: 420301) on ice and added PBS with 1% BSA after 3 minutes, followed by centrifuging at 1500 rpm for 5 min. For the quality check and counting of single cell suspension, the cell survival rate is generally above 80%. The cells that have passed the test are washed and resuspended to prepare a suitable cell concentration of 700~1200 cells/ul for 10x Genomics ChromiumTM. The system is operated on the machine.
RNA libraries were prepared for sequencing with Single Cell 3′ library and Gel Bead Kit v.3 according to the manufacturer's protocol

value: HCC Tumor

value: dissection of tumor tissue at week 4


title: spleenCD62LnegTreg_1_resident_Tcra_R1

description:
isolated
mTRA_202-002-S-rn-neg_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

tag: strain

tag: pcr1 cy. no.


title: Setd2-null_yolk sac_WT_rep2

description:
Setd2-null_yolk sac_WT-2_Raw
Setd2_E9.5_yolk sac.txt

tag: tissue

value: Yolk sac

tag: genotype


title: liverCD62LposTreg_5_resident_Tcra_R1

description:
isolated
mTRA_259-010-L-rn-pos_A.RunAB.clonotypes.TRA.txt

tag: sampleID

value: liver

tag: pcr2 cy. no.


title: h18B_TCR

value: Pembrolizumab


title: HCC-NL

description: Normal

source_name: Normal Liver

value: Normal Liver

value: dissection of normal liver tissue at week 0


title: Setd2-null_yolk sac_HO_rep1

description:
Setd2-null_yolk sac_HO-1_Raw
Setd2_E9.5_yolk sac.txt

value: Homozygous


title: Setd2-null_yolk sac_WT_rep1

description:
Setd2-null_yolk sac_WT-1_Raw
Setd2_E9.5_yolk sac.txt


title: h18A_P

value: Baseline


title: liverCD62LposTreg_4_resident_Tcra_R1

description:
isolated
mTRA_213-004-L-rn-pos_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: mouse (pool/culture no.)

value: homeostatic control

tag: chain

value: alpha


title: HCC-LS

description: Tumor

tag: treatment

value: dissection of tumor tissue at week 10


title: h17C_TCR

value: Breast

value: adult

value: female

value: Pembrolizumab + Radiation


title: spleenCD62LnegTreg_2_resident_Tcra_R1

description:
isolated
mTRA_204-003-S-rn-neg_A.RunAB.clonotypes.TRA.txt

tag: type

value: spleen

tag: techn. replicate


title: Setd2-null_yolk sac_HE_rep2

description:
Setd2-null_yolk sac_HE-2_Raw
Setd2_E9.5_yolk sac.txt

tag: developmental stage

value: Embryonic day 9.5

value: Heterozygous


title: HCC-MS

description: Tumor

value: HCC Tumor

value: dissection of tumor tissue at week 8


title: h18B_N

tag: age

tag: Sex

value: Pembrolizumab

value: Triple-receptor negative breast cancer


title: Setd2-null_yolk sac_HE_rep1

description:
Setd2-null_yolk sac_HE-1_Raw
Setd2_E9.5_yolk sac.txt

value: Yolk sac


title: h18B_P

tag: disease state


title: Setd2-CD_yolk sac_WT_rep1

description:
Setd2-CD_yolk sac_WT-1_Raw
Setd2_E9.5_yolk sac.txt

value: Wild type


title: h17C_P


title: h17B_TCR


title: h18A_TCR

value: Baseline


title: h17B_P


title: liverCD62LposTreg_2_resident_Tcra_R1

description:
isolated
mTRA_209-002-L-rn-pos_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: model

value: homeostatic control

value: liver

tag: treg donor


title: Abcd1-/-Abcd2-/- + LPS 3

city: Dijon

first: Stéphane

last: Savary

address: 6 Bd Gabriel

country: France

institute: University of Bourgogne

data_processing:
Reads were preprocessed using cutadapt version 1.10 in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20), reads shorter than 40 bases were discarded for further analysis.
Reads mapping to rRNA were discarded (this mapping was performed using bowtie version 2.2.8).
Reads were mapped onto the mm10 assembly of human genome using STAR version 2.5.3a.
Gene expression was quantified using htseq-count version 0.6.1p1 and gene annotations from Ensembl release 91.
Assembly: mm10
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

growth_protocol: WT and mutant BV-2 cells were grown in DMEM supplemented with 10% heat-inactivated FBS (Corning), 100 U/ml penicillin and 100 µg/ml streptomycin (Gibco). Cultures were maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted from 3 independent batches of BV-2 cells for each genotype (WT, Abcd1-/-Abcd2-/- and Acox1-/-) using RNeasy kit (Qiagen).
RNA-Seq libraries were generated from 1000 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA). Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: WT and mutant BV-2 cells were seeded in 6-well plates at a density of 2105 cells/well. The day after, cells were treated for 24 h with 1 µg/ml LPS from Escherichia coli O55:B5 (Sigma-Aldrich). A vehicle containing 0.01% ethanol and 0.5 mM α-cyclodextrin was applied in each condition

tag: cell line

tag: cell type

value: microglia

value: 24 h with 1 ug/ml LPS from Escherichia coli O55:B5 (Sigma-Aldrich)


title: Setd2-CD_embryo_WT_rep2

description:
Setd2-CD_embryo_WT-2_S40
Setd2_E9.5_embryos.txt

source_name: Embryo

tag: strain

tag: tissue

value: Embryo


title: Setd2-CD_embryo_HO_rep1

description:
Setd2-CD_embryo_HO-1_S43
Setd2_E9.5_embryos.txt

tag: genotype

value: Homozygous


title: Acox1-/- + LPS 3


title: Acox1-/- + LPS 2


title: Setd2-CD_embryo_HO_rep2

description:
Setd2-CD_embryo_HO-2_S44
Setd2_E9.5_embryos.txt


title: liverCD62LposTreg_1_resident_Tcra_R1

first: Michael

institute: University Hospital Regensburg

description:
isolated
mTRA_207-001-L-rn-pos_A.RunAB.clonotypes.TRA.txt

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

tag: sampleID

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.

value: alpha


title: Acox1-/- + LPS 1

tag: treatment


title: liverCD62LnegTreg_1_resident_Tcra_R1

description:
isolated
mTRA_208-001-L-rn-neg_A.RunAB.clonotypes.TRA.txt

tag: mouse (pool/culture no.)

tag: type

tag: chain

tag: techn. replicate


title: h17A_P

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

value: Breast

tag: age

value: adult

tag: Sex

value: female

tag: disease state


title: Setd2-CD_embryo_HE_rep2

description:
Setd2-CD_embryo_HE-2_S42
Setd2_E9.5_embryos.txt

tag: developmental stage

value: Embryonic day 9.5

value: Heterozygous


title: WT + LPS 3

tag: cell line

tag: cell type

value: WT


title: colonTreg_5_resident_Tcra_R1

description:
isolated
mTRA_264-010-C-rn-neg_A.RunAB.clonotypes.TRA.txt

tag: strain

tag: model

tag: tissue

value: colon

tag: treg donor


title: Setd2-null_embryo_HO_rep1

description:
Setd2-null_embryo_HO-1_S38
Setd2_E9.5_embryos.txt

tag: genotype


title: liverCD62LnegTreg_4_resident_Tcra_R1

description:
isolated
mTRA_260-010-L-rn-neg_A.RunAB.clonotypes.TRA.txt

tag: sampleID

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.


title: h16C_N

tag: treatment

value: Pembrolizumab + Radiation

value: Triple-receptor negative breast cancer


title: liverCD62LnegTreg_3_resident_Tcra_R1

description:
isolated
mTRA_214-004-L-rn-neg_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: mouse (pool/culture no.)

tag: type

tag: chain

tag: techn. replicate


title: h17A_TCR

tag: age

tag: Sex

value: Baseline

tag: disease state


title: liverCD62LnegTreg_2_resident_Tcra_R1

description:
isolated
mTRA_210-002-L-rn-neg_A.RunAB.clonotypes.TRA.txt

tag: strain

value: homeostatic control

value: liver


title: Abcd1-/-Abcd2-/- + LPS 1

tag: cell line

tag: cell type

value: microglia

value: 24 h with 1 ug/ml LPS from Escherichia coli O55:B5 (Sigma-Aldrich)


title: WT + LPS 1


title: Setd2-null_embryo_HE_rep1

description:
Setd2-null_embryo_HE-1_S35
Setd2_E9.5_embryos.txt

tag: developmental stage

tag: tissue

value: Embryo


title: colonTreg_2_resident_Tcra_R1

description:
isolated
mTRA_261-007-C-rn-neg_A.RunAB.clonotypes.TRA.txt

tag: sampleID

tag: model

tag: treg donor

value: alpha


title: spleenTreg_3-6_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-349-S-rp_A.RunAB.clonotypes.TRA.txt

value: poly

value: GvHD

value: spleen

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.


title: Setd2-CD_embryo_WT_rep1

description:
Setd2-CD_embryo_WT-1_S39
Setd2_E9.5_embryos.txt

value: Embryonic day 9.5

tag: genotype

value: Wild type


title: h16C_TCR

value: Breast

value: adult

value: female

tag: treatment


title: WT + LPS 2

value: WT


title: Setd2-null_embryo_HO_rep2

description:
Setd2-null_embryo_HO-2_S32
Setd2_E9.5_embryos.txt

value: Homozygous


title: colonTreg_4_resident_Tcra_R1

description:
isolated
mTRA_263-009-C-rn-neg_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: mouse (pool/culture no.)

tag: type

value: colon

tag: chain

tag: techn. replicate


title: spleenTreg_3-5_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-347-S-rp_A.RunAB.clonotypes.TRA.txt

tag: strain


title: Abcd1-/-Abcd2-/- + LPS 2

tag: cell line


title: Abcd1-/-Abcd2-/- 3

tag: cell type


title: Setd2-CD_embryo_HE_rep1

description:
Setd2-CD_embryo_HE-1_S41
Setd2_E9.5_embryos.txt

tag: developmental stage

value: Heterozygous


title: Abcd1-/-Abcd2-/- 1

value: microglia


title: Setd2-null_embryo_HE_rep2

description:
Setd2-null_embryo_HE-2_S36
Setd2_E9.5_embryos.txt

tag: tissue


title: colonTreg_3_resident_Tcra_R1

description:
isolated
mTRA_262-008-C-rn-neg_A.RunAB.clonotypes.TRA.txt

tag: sampleID

value: homeostatic control


title: h16C_P

tag: age

tag: Sex

value: Pembrolizumab + Radiation

tag: disease state

value: Triple-receptor negative breast cancer


title: h16A_P

value: Baseline


title: Control SCFA treated Replicate 3

city: New York

first: Sergei

last: Koralov

state: NY

address: 550 1st Avenue

institute: NYU School of Medicine

data_processing:
Samples were sequenced using an sp100 Illumina Novaseq 6000 flow cell.
Reads were cleaned, trimmed, and then aligned using the STAR program.
featureCounts was used to generate count data for mapped reads.
Assembly: mm10
Supplementary files format and content: tab-delimited csv file

source_name: Bone Marrow

growth_protocol: At 8 weeks bone marrow was collected from mice and cultured for ~ 24 hours in alpha-MEM media. Following, non-adherent bone marrow progenitor cells were collected for RNA extraction.

extract_protocol:
Qiagen RNeasy Plus Micro Kit
RNA libraries were prepared using the Cloentech Low Input PolyA protocol

treatment_protocol: Mice received either no treatment or SCFA treatment in drinking water until about 8 weeks of age.

value: Bone Marrow

value: Progenitors

value: control

value: SCFA treated


title: WT 2


title: Acox1-/- 3


title: h16A_N

first: Simon

institute: Cedars Sinai

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


title: Setd2-null_embryo_WT_rep2

description:
Setd2-null_embryo_WT-2_S34
Setd2_E9.5_embryos.txt

value: Embryonic day 9.5

value: Embryo

value: Wild type


title: Acox1-/- 2


title: h16B_N

value: adult

value: female

value: Pembrolizumab


title: WT 1

value: WT


title: Setd2-null_embryo_WT_rep1

description:
Setd2-null_embryo_WT-1_S33
Setd2_E9.5_embryos.txt


title: spleenTreg_2-5_GvHD_Tcra_R1

last: Rehli

description:
re-isolated
mTRA_Tx198-1-298-S-rp_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

value: poly

tag: model

value: GvHD

value: spleen

tag: treg donor

tag: recipient

tag: pcr1 cy. no.

value: alpha


title: h15B_TCR

tag: treatment

value: Triple-receptor negative breast cancer


title: h16B_P


title: Homozygous SCFA treated Replicate 3

value: Bone Marrow

value: Progenitors

tag: genotype

value: STAT3Cstopfl/fl CD4Cre


title: spleenTreg_3-4_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-343-S-rp_A.RunAB.clonotypes.TRA.txt

tag: mouse (pool/culture no.)

tag: type

tag: pcr2 cy. no.

tag: chain


title: spleenTreg_3-1_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-341-S-ra_A.RunAB.clonotypes.TRA.txt

tag: strain

value: allo

tag: techn. replicate


title: h16A_TCR

tag: tissue

value: Breast

value: Baseline


title: Abcd1-/-Abcd2-/- 2

tag: cell line

tag: cell type

value: microglia


title: Gene expression library

city: Pittsburgh

first: Alok

last: Joglekar

state: PA

address: Assembly 3045, 5051 Center Ave

department: Immunology

institute: University of Pittsburgh

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Melanoma tumors

extract_protocol:
Single-cell suspensions from tumors (n = 4 per condition) were prepared as described above except as follows. Cells were purified via an enrichment for CD90.2+ cells using EasySep™ Mouse CD90.2 Positive Selection Kit II (STEMCELL, 18951). Samples were stained using anti-TCRβ (Alexa Fluor® 700, BD Biosciences, 560705), anti-CD4 (BUV395, BD Biosciences, 563790), anti-CD8a (BUV737, BD Biosciences, 612759), and each sample was stained with TotalSeq™-C03NN anti-mouse Hashtag 1 Antibodies with unique hashtag oligonucleotides (HTOs) in staining buffer for 30 min on ice (Biolegend Cat # 155861, 155863, 155865, 155867, 155871, 155873, 155875, 155877). For dead cell exclusion, cells were stained with LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit (Invitrogen, L34957) for 10 min on ice. Doublets and dead cells were excluded. From each animal, 8,000 CD8+ live cells were sorted using a 5-laser Aria-10 cytometer, and samples from the same condition were pooled in PBS + 0.04% BSA.
GEM formation and library preparation was performed using Chromium Next GEM Single Cell 5' v2 workflow from 10x Genomics (Chromium Next GEM Single Cell 5' Kit v2, 16 rxns PN-1000263, Library Construction Kit, 16 rxns PN-1000190, 5' Feature Barcode Kit, 16 rxns PN-1000256, Chromium Next GEM Chip K Single Cell Kit, 48 rxns PN-1000286, Dual Index Kit TT Set A, 96 rxns PN-1000215, Dual Index Kit TN Set A, 96 rxns PN-1000250).
Hashtagged cells from 8 mice (4 PBS treated and 4 L. reuteri treated) were pooled onto a single lane of the 10x chip to allow sample multiplexing. Prepared libraries were quality-checked on Agilent TapeStation and sequenced on HiSeq4000 (Novogene Inc).

value: Melanoma tumors

value: CD3+ T cells isolated from the tumors

value: L-reuteri or none


title: spleenTreg_2-6_GvHD_Tcra_R1

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

description:
re-isolated
mTRA_Tx198-1-299-S-rp_A.RunAB.clonotypes.TRA.txt

tag: sampleID


title: Homozygous SCFA treated Replicate 2

value: SCFA treated


title: Control SCFA treated Replicate 1

value: control


title: Homozygous Untreated Replicate 2

value: Untreated


title: Homozygous SCFA treated Replicate 1


title: h15A_P

last: Knott

tag: age

value: adult

tag: Sex

value: female

tag: disease state


title: Cited2 overexpression, rep 4

city: London

first: Franziska

last: Müller

address: Du Cane Road

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

data_processing:
Sequences were demulitplexed and adapters trimmed with bcl2fastq.
Quality control, read alignment, signal track generation, and peak called were done using the Kundaje lab's ATAC-seq processing pipeline
ATAC-seq reads were aligned to GrCM38/mm10 using Bowtie 2-v1.10
Peaks were called using MACS with significant cut-off q-value <=0.05
For promoter analysis, genomic bins +/- 1000 bp of TSS were generated. HTSeq-v0.6.1 was used to obtain gene counts per genomic bin from mapped reads. For enhancer analysis, read counts per peak were obtained using mapped reads with HTSeq-v0.6.1
Differential accesssibility analysis was carried out with EdgeR-v3.8.6
Assembly: GrCM38/mm10
Supplementary files format and content: narrowPeak for pooled GFP control
Supplementary files format and content: narrowPeak for pooled Cited2

source_name: L4-6 DRG

extract_protocol:
DRGs were dissociated using 1 mg/ml Dispase II, 2.5 mg/ml Collagenase Type II, and Papain. Released cells were placed into 15% BSA in DMEM gradient to obtain a neuronal enriched cell population
Neurons were lysed to obtain nuclei, transposition reagents (Illumina) were added, DNA was purified using QIAGEN MinElute kit. Library was amplified (NEBNext HF 2x PCR Master Mix) with barcoded primers (Illumina). Library was purified using AMPure XP beads, followed by DNA elution.

treatment_protocol: AAV-GFP or AAV-Cited2 overexpressed mice underwent DCA injury and sacrificed after 24 hours.

value: L4-6 DRG

value: male

value: 8-10 weeks


title: h16B_TCR

address: 8687 Melrose Ave

value: Pembrolizumab

value: Triple-receptor negative breast cancer


title: WT 3

value: WT


title: spleenTreg_2-4_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-1-297-S-rp_A.RunAB.clonotypes.TRA.txt

source_name: CD4+CD25+ regulatory T cells

value: C57BL/6 Foxp3GFP+

value: poly

tag: model

value: GvHD

value: spleen

tag: treg donor

tag: recipient

value: alpha


title: h12C_TCR

value: Breast

tag: treatment

value: Pembrolizumab + Radiation


title: h15C_TCR


title: Cited2 overexpression, rep 3


title: Control SCFA treated Replicate 2

value: Bone Marrow

value: Progenitors

tag: genotype

value: control

value: SCFA treated


title: Control Untreated Replicate 3

value: Untreated


title: spleenTreg_3-3_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-348-S-ra_A.RunAB.clonotypes.TRA.txt

tag: mouse (pool/culture no.)

tag: type

value: allo

tag: pcr1 cy. no.


title: h15C_P

value: adult

value: female


title: spleenTreg_3-2_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-346-S-ra_A.RunAB.clonotypes.TRA.txt

tag: strain

tag: pcr2 cy. no.

tag: chain


title: liverTreg_3-5_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-347-L-rp_A.RunAB.clonotypes.TRA.txt

tag: tissue

value: liver

tag: techn. replicate


title: Cell hashing library

description: 10x Genomics

value: Melanoma tumors

tag: cell type

value: CD3+ T cells isolated from the tumors

value: L-reuteri or none


title: Homozygous Untreated Replicate 3

tag: cell line

value: STAT3Cstopfl/fl CD4Cre


title: h12B_P

tag: age

tag: Sex

value: Pembrolizumab

value: Triple-receptor negative breast cancer


title: GFP Control, rep 4

value: L4-6 DRG

value: male

value: 8-10 weeks

value: AAV-GFP


title: AML, Sample 3

city: Philadelphia

first: Peter

last: Kurre

address: 3615 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

data_processing:
Cell Ranger 7.0.1. was used to map the sequencing data. Cell Ranger consists of a set of analysis pipelines developed by 10x Genomics to process the single-cell RNA-sequencing output. The raw sequencing data (FASTQ files) was mapped to the mouse reference genome 2020-A (GRCm38, GENCODE vM23/Ensembl 98), provided by 10x Genomics, using the cellranger count pipeline. For the downstream analysis, the filtered count matrices were used.
Preprocessing:  The data from all samples were loaded in R (version 4.2.2) and processed using the Seurat package (version 4.3.0 – Hao et al. Cell 2021). Cells with low UMI counts were filtered out. The filtering thresholds were determined independently for each library to exclude outliers (A1: 1800 UMIs/cell; A2: 3000 UMIs/cell; A3: 1800 UMIs/cell; B1: 2000 UMIs/cell; B3: 2000 UMIs/cell). Cells with more than 10% mitochondrial genes were also removed. Cells from library B2 were excluded due to the low quality of the library.  The dataset was normalized for sequencing depth per cell and log-transformed using a scaling factor of 10,000. Principal component analysis (PCA) was performed on the 2,000 most variable features. The first 29 PCs were used to generate the UMAP. Cell cycle was scored using the CellCycleScoring function of Seurat. Inspection of the UMAP revealed differential distribution assigned to cell cycle. Cell cycle effects were then regressed out using the vars.to.regress parameter in Seurat’s ScaleData function. After regression, principal component analysis (PCA) was performed again on the 2,000 most variable features, and the first 27 PCs were used for dimensionality reduction and clustering. Batch effects between libraries were removed using the Harmony package (version 0.1.1).
Pseudobulk analysis: Differentially expressed genes between conditions (AML vs PBS) were calculated using the Wilcoxon rank sum test as implemented in the FindAllMarkers function in Seurat with parameters logfc.threshold = 0.1, return.thresh = 0.01 and min.pct = 0.1. We then performed an over-representation analysis of the significantly differentially expressed genes using the enricher function in the clusterProfiler package (version 4.6.2) with the collections “MH: hallmark gene sets”, “M2: curated gene sets”, “M5: ontology gene sets” and “M8: cell type signature gene sets” from the Mouse Molecular Signatures Database.
Cell type annotation and differential expression analysis:  We annotated cells using gene signatures for HSPCs identified in Pietras et al, 2015. The gene signature for each population was defined by the top 100 genes ranked by the Significance Analysis of Microarrays (SAM) scores. We calculated a module score for each cell based on the average expression levels of every gene signature, subtracted by the aggregated expression of randomly selected control genes using Seurat’s AddModuleScore function. Each cell was assigned to the population with the highest positive score. Cells with only negative scores were annotated as “Unclassified”. Differentially expressed genes between conditions (AML vs PBS) per cell type were calculated using the Wilcoxon rank sum test as implemented in the FindAllMarkers function in Seurat with parameters logfc.threshold = 0.25, return.thresh = 0.01 and min.pct = 0.1. Over-representation analysis of the resulting gene lists was performed using the collections “MH: hallmark gene sets”, “M2: curated gene sets” and “M5: ontology gene sets”.
Assembly: mm10-2020-A
Supplementary files format and content: tab separated values and matrix files

source_name: Bone marrow

growth_protocol: C1498 cells were cultured in vitro using DMEM media supplemented with 10% FBS and 1% P/S.

extract_protocol:
At sacrifice, hind legs were dissected and bone marrow (BM) cells were harvested by flushing both femur and tibia. Whole BM cells were subjected to RBC lysis and were lineage-depleted using a magnetic-activated cell sorting (MACS)-based method with EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit (StemCell Technologies). Lineage-depleted BM cells were stained and HSPCs were fluorescence-activated cell sorting (FACS)-sorted using the FACSAria Fusion sorter (BD). RNA were extracted from HSPCs using RNeasy Micro Plus Kit (Qiagen) according to manufactuer's protocol.
Library were constructed using Chromium GEM V3 chemistry (10X Genomics) according to manufacturer's protocol

value: Bone marrow

value: N/A - in vivo

value: HSPC (Lin- cKit+ Sca1+)

value: C1498 AML


title: spleenTreg_2-2_GvHD_Tcra_R1

city: Regensburg

description:
re-isolated
mTRA_Tx198-1-294-S-ra_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: sampleID

value: allo

tag: model

value: GvHD

value: spleen

value: alpha


title: AML, Sample 2


title: h12C_P

source_name: Breast

value: Breast

value: adult

value: female

value: Pembrolizumab + Radiation

tag: disease state


title: h12A_P

tag: treatment

value: Baseline

value: Triple-receptor negative breast cancer


title: GFP Control, rep 2

value: L4-6 DRG

value: male

value: 8-10 weeks


title: Cited2 overexpression, rep 2


title: Control Untreated Replicate 2

value: Bone Marrow

value: Progenitors

tag: genotype

value: control

value: Untreated


title: liverTreg_3-4_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-343-L-rp_AB.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: mouse (pool/culture no.)

value: poly

value: liver

tag: treg donor

tag: recipient


title: liverTreg_3-6_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-349-L-rp_A.RunAB.clonotypes.TRA.txt

tag: strain

tag: type

value: GvHD

tag: pcr1 cy. no.

value: alpha


title: spleenTreg_2-3_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-1-296-S-ra_A.RunAB.clonotypes.TRA.txt

value: allo

tag: tissue

value: spleen

tag: pcr2 cy. no.

tag: chain


title: h15B_P

value: Breast

value: adult

value: female

value: Pembrolizumab


title: h11C_TCR

value: Pembrolizumab + Radiation

value: Triple-receptor negative breast cancer


title: Acox1-/- 1

tag: cell line

tag: cell type

value: microglia


title: Cited2 overexpression, rep 1

value: L4-6 DRG

tag: Sex

value: male

tag: age

value: 8-10 weeks


title: Control Untreated Replicate 1

value: Bone Marrow

value: Progenitors

value: control

value: Untreated


title: GFP Control, rep 1

value: AAV-GFP


title: PBS, Sample 3

value: Bone marrow

value: N/A - in vivo

value: HSPC (Lin- cKit+ Sca1+)

value: PBS


title: h12A_TCR

value: Breast

value: adult

value: female

value: Baseline


title: GFP Control, rep 3


title: liverTreg_2-4_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-1-297-L-rp_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: sampleID

value: poly

tag: model

value: GvHD

value: liver

value: alpha

tag: techn. replicate


title: h11C_P

tag: treatment

value: Pembrolizumab + Radiation

tag: disease state

value: Triple-receptor negative breast cancer


title: liverTreg_2-6_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-1-299-L-rp_A.RunAB.clonotypes.TRA.txt

tag: mouse (pool/culture no.)

tag: treg donor


title: liverTreg_3-3_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-348-L-ra_A.RunAB.clonotypes.TRA.txt

tag: strain

value: allo

tag: recipient


title: spleenTreg_2-1_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-1-293-S-ra_A.RunAB.clonotypes.TRA.txt

tag: type

value: spleen

tag: pcr1 cy. no.


title: Purkinje cells, nm3888-/-, rep1

city: La Jolla

first: Susan

last: Ackerman

state: CA

address: 9500 Gilman Drive

department: CMM

institute: UCSD

data_processing:
Fastp was used to trim adapter off of sequences
Bowtie2 was used to align files to the mm10 genome
Samtools FeatureCounts was used to count number of reads mapped at the gene level
DESeq2 was used for differential expression analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: cerebellum

extract_protocol:
Each cerebellum was homogenized using a dounce homogenizer in 1.5mL lysis buffer (1% NP-40, 100mM KCl, 50mM Tris pH 7.4, 12mM MgCl2, 0.1mg/mL cycloheximide, protease inhibitor cocktail (Sigma, 11836170001), 1mg/mL heparin, 5µL/mL RNAseOUT (ThermoFisher 10777019)). Ribosomes were then isolated as previously described (Sanz 2009) Briefly, lysates containing tagged ribosomes were incubated for 4 hours at 4˚C with 5µg rat anti-HA antibody (Roche, 11867423001) after which 400µL protein G-coupled dynabeads (Thermo Scientific, 10004D) were added to the lysate and incubated at 4˚C overnight. The following day ribosome-bound beads were washed three times with high salt buffer (0.3M KCl, 1% NP-40, 50mM Tris pH 7.4, 12mM MgCl2, 0.1mg/mL cycloheximide, 0.5mM DTT), and mRNA was isolated using buffer RLT and spin columns (Qiagen RNEasy Mini Kit). RNA was eluted in 30µL H2O
Libraries were constructed using the Kapa Stranded mRNA-Seq Kit (#KR0960) in accordance with manufacteur’s instructions.

tag: tissue

value: cerebellum

value: Purkinje cells

tag: genotype

value: 3 weeks

value: Female

tag: antibody for_ip


title: h12B_TCR

city: West Hollywood

value: Breast

value: Pembrolizumab


title: PBS, Sample 2

value: Bone marrow

tag: cell line

value: N/A - in vivo

tag: cell type

value: HSPC (Lin- cKit+ Sca1+)

value: PBS


title: PBS, Sample 1


title: liverTreg_2-5_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-1-298-L-rp_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

value: poly

value: GvHD

tag: pcr2 cy. no.

tag: chain


title: Purkinje cells, nm3888-/-, rep2

tag: age

tag: Sex


title: h11B_TCR

value: adult

value: female

tag: treatment


title: liverTreg_3-2_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-346-L-ra_ABC.RunAB.clonotypes.TRA.txt

tag: sampleID

value: allo

tag: model

value: liver

value: alpha

tag: techn. replicate


title: MC38T_2,scRNAseq

first: Tuxiong

last: Huang

address: 1066 Xueyuan Avenue

institute: Shenzhen University

description: 10x Genomics

data_processing:
Qualitycontrol: We use FastQC to perform basic statistics on the quality of the raw reads.
Generation and Analysis of Single-Cell Transcriptomes: Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline using default parameters. Downstream single-cell analyses were performed using Cell Ranger and Seurat. A gene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes.
Assembly: The raw sequencing reads were aligned to the murine genome (GRCm38/mm10, ENSEMBL)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: MC38 tumor

extract_protocol:
Control or Atp6v0a1 knockdown MC38 tumors were dissected from C57BL/6J mice. The dissections were done in ice-cold Ca2+-free HBSS solution and the tumor tissues were dissociated to single cells using the mouse tumor dissociation kit (Miltenyi Biotec) as the user manual. Following the lysis of red blood cells with easysep RBC lysis beffer (STEMCELL), the cells were washed and resuspended in HBSS buffer. After cell counting and  cell-viability measurement, the GEM Generation & Barcoding were performed using Chromium Next GEM Single Cell 3' Reagent Kits v3.1.
Libraries were prepared according to Chromium Next GEM Single Cell 3' Reagent Kits v3.1. Briefly, silane magnetic beads were used to purify the first-strand cDNA from the post GEM-RT reaction mixture. The full-length cDNA were amplified via PCR to generate sufficient mass for library construction. After end repair, A-tailing,adaptor ligation and PCR amplification, the final libraries were ready for sequencing.

value: MC38 tumor

value: MC38 cells

value: Epithelial cells

value: Atp6v0a1 knockdown

tag: strain


title: h11A_P

value: Breast

value: Baseline

tag: disease state

value: Triple-receptor negative breast cancer


title: Purkinje cells, wild type, rep1

value: cerebellum

value: Purkinje cells

value: Wild type

value: 3 weeks

value: Female


title: h11B_P

value: adult

value: Pembrolizumab


title: h11A_TCR

value: female


title: liverTreg_3-1_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-341-L-ra_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: mouse (pool/culture no.)

tag: type

value: allo

value: GvHD

value: liver

tag: treg donor

tag: recipient


title: Purkinje cells, wild type, rep2

tag: tissue

tag: genotype

tag: antibody for_ip


title: ITGB1AWT_B

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

data_processing:
Illumina bcl2fastq software (v.2.20.0) used for basecalling.
Sequenced reads were mapped to UCSC mm10 whole genome using STAR v2.7.4a with default parameters
Raw counts are produced by htseq-count (HTSeq v.0.9.1)
Normalization and differential expression analysis were performed with edgeR v.3.38.4
Assembly: UCSC mm10
Supplementary files format and content: rawcounts.txt = tab-delimited text files include rawcount values for each Sample

source_name: Embryonic endothelial cells eEnd2

growth_protocol: Transfected mouse embryonic endothelial eEnd2 cells were cultured in DMEM supplemented with 10% fetal calf serum and 2% antibiotics in humidified atmospher with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted by using the RNA and protein extraction kit (Macherey-Nagel) according to the manufacturer instruction.
Illumina Ribo-Zero plus

treatment_protocol: No treatment

tag: transfection

tag: cell line

value: Embryonic endothelial cells eEnd2


title: MC38T_1,scRNAseq

description: 10x Genomics

value: MC38 tumor

value: MC38 cells

tag: cell type

value: Epithelial cells

value: WT


title: liverTreg_2-3_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-1-296-L-ra_A.RunAB.clonotypes.TRA.txt

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: alpha


title: 4T1 cell pellet

city: Seattle

first: Kevin

middle: J

last: Cheung

state: WA

address: 1100 Fairview Ave N

department: Public Health Sciences

institute: Fred Hutchinson Cancer Center

description: RNA-seq of 4T1 cell pellet

data_processing:
Reads trimmed with TrimGalore
Trimmed reads aligned to catenated mouse-rat genome using STAR.
Aligned reads mapped to genomic features using FeatureCounts
TMM library normalization and differential expression analysis performed with limma/voom pipeline
Assembly: GRCm38, Rnor_6.0
Supplementary files format and content: Processed data files “cpm_voom_tidy_mm.csv” and “cpm_voom_tidy_rn.csv”  are files with a matrix of normalized gene-wise abundance values (CPM) for expression of rat(rn) or mouse (mm) genes. Tumor region column: in, out, lung corresponds to necrotic region (in), non-necrotic rim (out), or lung (lung).
Supplementary files format and content: Processed files ‘crossmap_gene_counts_mm.csv’ and “crossmap_gene_counts_rn.csv’ are unnormalized read counts mapped to the mouse (mm) or rat (rn) genomes using the disambiguation procedure. Columns correspond to samples

source_name: mammary tumor

growth_protocol: 4T1 cells transplanted into SRG host mammary fat pads and tissue collected after 27 days.

extract_protocol:
The primary tumors were cut in half to expose the cross-section, and the tumors were dissected to isolate the necrotic core region and the non-necrotic rim region. Samples were snap frozen and sent to Genewiz-Azenta for RNA extraction, library prep, and next-gen sequencing.
Library was constructed by Genewiz-Azenta using PolyA selection.

value: mammary tumor

value: breast cancer

value: wildtype

tag: treatment

value: no treatment


title: ITGB1AWT_C


title: liverTreg_2-2_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-1-294-L-ra_A.RunAB.clonotypes.TRA.txt

tag: sampleID

tag: model

tag: techn. replicate


title: ITGB1AKQ_B


title: h10C_TCR

value: Breast

tag: age

value: adult

tag: Sex

value: Pembrolizumab + Radiation

tag: disease state

value: Triple-receptor negative breast cancer


title: Cited2 overexpression, rep3

data_processing:
Sequence reads and trimmed reads quality control was carried out using FastQC-v0.11.9
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore!-v0.6.6 (parameter - Phred33 quality limit: 20)
Trimmed sequence reads were mapped to M25 Gencode reference genome (GrCM38/mm10) and read counts per transcript obtained using Salmon-v1.6.0 in mapping-based mode (parameters- gcBias, seqBias)
Salmon output files were imported and converted for DESeq2 using Tximeta-v1.12.4
Differential gene expression analysis was carried out using DESeq2-v1.34.0 in R-v4.1.2
Normalised counts were generated using the median of ratios method in DESeq2.
Assembly: M25
Supplementary files format and content: tab-delimited txt file represents the raw expression data as TPM, produced by Salmon
Supplementary files format and content: tab-delimited txt file represents the normalised expression data, produced by DESeq2

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol:
AAV-GFP or AAV-Cited2 overexpressed mice underwent DCA injury and sacrificed after 24 hours.
DRGs were dissociated using 1 mg/ml Dispase II, 2.5 mg/ml Collagenase Type II, and Papain. Released cells were placed into 15% BSA in DMEM gradient to obtain a neuronal enriched cell population

value: L4-6 DRG

tag: strain

value: Male

value: 8-10 weeks


title: liverTreg_2-1_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-1-293-L-ra_A.RunAB.clonotypes.TRA.txt

value: C57BL/6 Foxp3GFP+

tag: mouse (pool/culture no.)

tag: type

value: allo

value: GvHD

tag: tissue

value: liver

tag: treg donor

tag: recipient


title: GFP Control, rep2

value: AAV-GFP


title: Cited2 overexpression, rep2


title: h10C_P

value: female


title: colonTreg_3-6_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-349-C-rp_A.RunAB.clonotypes.TRA.txt

value: poly

value: colon

value: alpha


title: h10A_P

value: Baseline


title: colonTreg_3-5_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-347-C-rp_A.RunAB.clonotypes.TRA.txt


title: ITGB1AWT_A

tag: transfection

tag: cell line

value: Embryonic endothelial cells eEnd2


title: ITGB1AKQ_A


title: Cited2 overexpression, rep1


title: colonTreg_2-5_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-1-298-C-rp_AB.RunAB.clonotypes.TRA.txt

tag: pcr1 cy. no.

tag: pcr2 cy. no.


title: colonTreg_2-6_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-1-299-C-rp_AB.RunAB.clonotypes.TRA.txt

tag: chain


title: h09C_TCR

value: Breast

value: adult

tag: treatment


title: colonTreg_3-4_GvHD_Tcra_R1

description:
re-isolated
mTRA_Tx198-2-343-C-rp_A.RunAB.clonotypes.TRA.txt

tag: sampleID

tag: model


title: h10B_TCR

tag: age

value: Pembrolizumab

value: Triple-receptor negative breast cancer


title: GFP Control, rep1

value: L4-6 DRG

tag: Sex

value: Male


title: h10A_TCR

tag: disease state


title: GFP Control, rep3

tag: strain

value: 8-10 weeks