title: Pt9, BMMC, D090postTCR-Tinfusion

city: Seattle

first: Scott

middle: N

last: Furlan

address: 1100 Fairview Ave N

institute: CRD

description:
spmat.mtx
meta.csv
genes.csv
Pt9_D090

library_source: transcriptomic single cell

data_processing:
demultiplexed using cellranger mkfastq
cellranger count
Assembly: GRCh38 + HA-1 TCR transgene
Supplementary files format and content: mtx file, a sparse matrix of expression counts for filtered annotated data used in the manuscript
Supplementary files format and content: csv file, metadata for samples used in manuscript
Supplementary files format and content: csv file, gene IDs

source_name: marrow

extract_protocol:
Cells were captured using 10x Genomics Chromium Next GEM 5' v2 technology, in which single cells are captured, lysed, and undergo reverse-transcription in gel beads in emulsion .
Single-cell gene expression libraries were constructed using  10x Genomics Chromium Next GEM 5' v2 technology according to manufacturer's specifications.

treatment_protocol: Patients were treated for post-hematopoietic cell transplantation relapse of acute myeloid leukemia or myelodysplastic syndromes on a clinical trial (clinicaltrials.gov NCT03326921)

value: marrow

tag: cells

value: BMMC

tag: cell selection

value: unselected

tag: disease


title: Pt6, PBMC, D018postTCR-Tinfusion

status: Public on Jan 01 2024

type: SRA

country: USA

description:
spmat.mtx
meta.csv
genes.csv
P6_D018

molecule: total RNA

organism: Homo sapiens

source_name: blood

tag: tissue

value: blood

value: PBMC

tag: treatment


title: genomic DNA from polyp patient 8

type: genomic

city: Harbin

first: Xishan

last: Wang

address: Xue Fu Road 246

country: China

institute: The Second Affiliated Hospital of Harbin Medical University

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

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

data_processing: BeadStudio

label: Cy5 and Cy3

molecule: genomic DNA

source_name: polyp 8

label_protocol: Standar Illumina protocol

extract_protocol: genomic DNA was extracted and purified from tissue samples using QIAamp DNA Blood and Tissue Kit according to standard instructions

treatment_protocol: Standard Illumina Protocol

tag: gender

value: Male

tag: age

tag: disease state

value: polyp

value: colorectal polyp sample


title: Pt5, BMMC, D177postTCR-Tinfusion_2, replicate1

description:
spmat.mtx
meta.csv
genes.csv
Pt5_D177_2_a


title: Pt5, BMMC, D177postTCR-Tinfusion_2, replicate2

description:
spmat.mtx
meta.csv
genes.csv
Pt5_D177_2_b


title: Pt6, BMMC, D002preTCR-T, prelymphodepletion

description:
spmat.mtx
meta.csv
genes.csv
Pt6_preinf


title: HumanMethylation 450 Epic Array OVCAR5 DMSO_1

city: Chicago

first: Daniela

last: Matei

address: 420 E. Superior St.

institute: Northwestern University Feinberg School of Medicine

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: Cy3 and Cy5

label_protocol: standard Illumina protocol

growth_protocol: OVCAR5 were maintained in RPMI-1640 with L-glutamine (Corning, Cat# 10-040-CV) plus 10% FBS, 1% GlutaMAX, and 1% penicillin-streptomycin.

extract_protocol: For HumanMethylation 450 Epic Array, genomic DNA were extracted using QIAmp DNA Mini Kit.

treatment_protocol: OVCAR5 cells were treated with DMSO, NTX301 (10nM, 100nM) for 3 days.

tag: cell line

value: DMSO


title: genomic DNA from polyp patient 1

source_name: polyp 1


title: genomic DNA from polyp patient 6

source_name: polyp 6


title: right hippocampus, exercise, biological replicate 3 KO

city: Melbourne

first: Maria

last: Kuznetsova

state: Victoria

address: 30 Royal parade

department: Florey Institute

country: Australia

institute: University of Melbourne

library_source: transcriptomic

data_processing:
Primers were trimmed from the reads using Cutadapt v2.3.
mirnaQC was used to check the quality of the reads. Reads between 18 and 40 nucleotides were retained for the subsequent analysis.
All reads were aligned to the GRCm38/mm10 mouse genome using Burrows–Wheeler Alignment (BWA) tool.
https//github.com/mariku01/miRNA_data_analysis_script_2023/tree/5c76f898779855dcb0e229d4d86fe46e30353e34.
The reads were then mapped to the miRNA database to perform feature counting using subread featureCounts[26]. miRNAs were only considered for the subsequent analysis if they had a minimum abundance of 20 CPM and were present in at least half of the samples.
Normalization and differential gene expression analysis on the miRNA count data was performed using limma-voom software package v. 3.54.1. The significance threshold for FDR-adjusted p value was set at < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimites text file includes raw counts for each sample

organism: Mus musculus

source_name: right hippocampus

extract_protocol:
Frozen samples of hippocampus were homogenised in QIAzol lysis buffer (QIAGEN, Clayton, VIC, Australia). Total RNA was isolated according to the manufacturer’s instructions and eluted in RNase-free water (QIAGEN). The concentration and quality of small RNA and total RNA were determined using the small RNA and RNA6000 assay and run on the Agilent Bioanalyser (Agilent Technologies, Santa Clara, CA, USA).
Total RNA of 3 ug per sample was enriched for small RNA and ligated to sequencing adapters to construct small RNA libraries using the Ion Total RNA-Seq Kit V2 (Life Technologies, Australia) according to the manufacturers’ protocol and as previously published (14). Libraries also contained a unique index barcode (Ion Xpress™ RNA-Seq Barcode 1-16 Kit, Life Technologies, Australia). The yield and size distribution of the small RNA libraries were assessed using the Agilent 2100 Bioanalyzer™ instrument with the High sensitivity DNA chip (Agilent Technologies). Equally pooled libraries were prepared for deep sequencing using the Ion Chef system (Life Technologies) and sequenced on the Ion Torrent S5™ using Ion™ 540 chips (Life Technologies) and 200bp chemistry (Life Technologies).

value: right hippocampus

tag: genotype

value: 5-HTT KO

tag: strain

value: C57Bl/6 J

value: exercise

tag: biological replicate

value: biological replicate 3


title: right hippocampus, water, biological replicate 5 WT

value: wildtype

value: water

value: biological replicate 5


title: genomic DNA from polyp patient 4

source_name: polyp 4


title: genomic DNA from CRC patient 7

source_name: CRC 7

tag: Stage

value: I/II

value: cancer


title: genomic DNA from CRC patient 4

source_name: CRC 4

value: colorectal cancer sample


title: Pt5, BMMC, unselected, D056postTCR-Tinfusion_2

description:
spmat.mtx
meta.csv
genes.csv
Pt5_D056_2_W

value: marrow

value: BMMC

value: unselected


title: right hippocampus, exercise, biological replicate 2 KO

value: biological replicate 2


title: genomic DNA from polyp patient 5

source_name: polyp 5

value: Male

value: polyp

value: colorectal polyp sample


title: genomic DNA from polyp patient 3

source_name: polyp 3


title: genomic DNA from CRC patient 1

source_name: CRC 1


title: right hippocampus, corticosterone, biological replicate 5 WT

value: right hippocampus

value: corticosterone


title: right hippocampus, corticosterone, biological replicate 4 WT

value: C57Bl/6 J

value: biological replicate 4


title: right hippocampus, corticosterone, biological replicate 3 WT

value: wildtype

value: biological replicate 3


title: Pt5, BMMC, unselected, D056postTCR-Tinfusion_1

description:
spmat.mtx
meta.csv
genes.csv
Pt5_D056_1_W


title: Pt5, BMMC, CD3neg, D056postTCR-Tinfusion_2

description:
spmat.mtx
meta.csv
genes.csv
Pt5_D056_2_L


title: right hippocampus, exercise, biological replicate 1 KO

value: 5-HTT KO

value: exercise

value: biological replicate 1


title: Pt5, BMMC, CD3pos, D056postTCR-Tinfusion_2

description:
spmat.mtx
meta.csv
genes.csv
Pt5_D056_2_T


title: Pt5, BMMC, CD3pos, D056postTCR-Tinfusion_1

description:
spmat.mtx
meta.csv
genes.csv
Pt5_D056_1_T


title: Sir2-FLAG-HUR20-Input-rep2

city: Charlestown

first: Richard

last: Joh

state: MA

department: Center for Cancer Research

institute: Mass General Hospital

library_source: genomic

data_processing:
Mapping by BWA
BW generated by DeepTools
Assembly: S pombe
Supplementary files format and content: BW

organism: Schizosaccharomyces pombe

source_name: cells

extract_protocol:
H3K9me2 ChIP
NEB Ultra II Library Prep Kit for Illumina

value: cells

tag: cell type


title: right hippocampus, water, biological replicate 3 WT

value: water


title: Pt9, PBMC, D180postTCR-Tinfusion

description:
spmat.mtx
meta.csv
genes.csv
Pt9_D180

value: blood

value: PBMC


title: right hippocampus, water, biological replicate 2 WT

value: biological replicate 2


title: Pt5, BMMC, CD3neg, D056postTCR-Tinfusion1

description:
spmat.mtx
meta.csv
genes.csv
Pt5_D056_1_L

value: marrow

value: BMMC


title: genomic DNA from CRC patient 6

source_name: CRC 6

value: Male

value: III/IV

value: cancer

value: colorectal cancer sample


title: right hippocampus, water, biological replicate 3 KO

value: right hippocampus

value: C57Bl/6 J


title: genomic DNA from CRC patient 2

source_name: CRC 2


title: Pt2, PBMC, D118postTCR-Tinfusion

description:
spmat.mtx
meta.csv
genes.csv
Pt2_D118

value: unselected


title: genomic DNA from polyp patient 7

source_name: polyp 7

value: polyp

value: colorectal polyp sample


title: genomic DNA from CRC patient 3

source_name: CRC 3

value: I/II


title: Pt4, BMMC, D011preTCR-Tinfusion, prelymphodepletion

description:
spmat.mtx
meta.csv
genes.csv
Pt4_preinf

source_name: marrow


title: Pt4, PBMC, D029postTCR-Tinfusion

description:
spmat.mtx
meta.csv
genes.csv
Pt4_D029

source_name: blood


title: right hippocampus, water, biological replicate 1 WT

value: wildtype

value: biological replicate 1


title: right hippocampus, water, biological replicate 4 WT

value: water

value: biological replicate 4


title: Pt9, BMMC, D030preTCR-T, prelymphodepletion

description:
spmat.mtx
meta.csv
genes.csv
Pt9_preinf


title: Pt2, PBMC, D145postTCR-Tinfusion

description:
spmat.mtx
meta.csv
genes.csv
Pt2_D145

value: blood

value: PBMC


title: Pt2, PBMC, D090postTCR-Tinfusion

description:
spmat.mtx
meta.csv
genes.csv
Pt2_D090


title: siNC_2

city: tianjin

first: kan

last: li

address: Tianjin Medical University, 22 Qixiangtai Road, Tianjin, China

institute: Tianjin Medical University

data_processing:
SOAPnuke (v1.5.2) HISAT (v2.1.0) Bowtie2 (v2.2.5)
clean reads require the use of filtering software SOAPnuke (v1.5.2) to remove reads of low quality, contaminated joints and high levels of unknown base N.
After obtaining the clean reads, we used HISAT (v2.1.0) to align the clean reads to GRCh38 genome sequence.
The RESM(v1.2.8)  software package was  used to calculate the gene expression levels of each sample.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file inclued FPKM values and TPM values for each sample

source_name: HASMCs

growth_protocol: HASMCs were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and were cultured in Dulbecco’s modified Eagle medium (DMEM) F12 medium with 10% fetal bovine serum (FBS) in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
RNA was harvested with Trizol, 1μg of total RNA was used for the construction of sequencing libraries.
Libraries were sequenced with 150 paired-end using MGISEQ-2000 sequencing platform for an average of 45 million reads per sample.

treatment_protocol: HASMCs treated with siNC or siST3GAL5.

value: HASMCs

value: WT'


title: siNC_1


title: Pt2, PBMC, D070postTCR-Tinfusion

description:
spmat.mtx
meta.csv
genes.csv
Pt2_D070


title: genomic DNA from CRC patient 5

source_name: CRC 5

value: Male

value: III/IV


title: Wing, rep 3

city: Nijmegen

first: Jieqiong

last: Qu

address: Geert Grooteplein Zuid 28

department: Department of Medical Microbiology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences, Radboud University Medical Center

data_processing:
initial quality control by FastQC
raw sequence reads were aligned to the reference genome, Ae. aegypti LVP (Vectorbase, release 56) using STAR
Quantification of gene expression (FPKM) was performed with Cuffdiff
R package DESeq2 was used for differential gene expression analysis (with adjusted p value < 0.05)
pyGenomeTracks from the deepTools package was used to visualize gene expression pattern
Assembly: Ae. aegypti LVP (Vectorbase, release 56)
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

molecule: polyA RNA

organism: Aedes aegypti

source_name: Wing

growth_protocol: Ae. aegypti mosquitoes (Black Eye Liverpool strain, obtained from BEI resources) were reared at 28 °C, with 70% humidity and an automated room lighting set of a 12:12 hours light/dark cycle. Larvae were fed with Tetramin Baby fish food (Tetra). Adult mosquitoes were fed with a 10% sucrose solution. 3-5 day-old female mosquitoes were used for experiment unless stated otherwise.

extract_protocol:
Afterwards, mosquitoes were dissected into tissue samples, including crop, fat body, leg, Malpighian tubules, midgut, ovary, salivary glands, and wings. Tissues from about 20 mosquitoes were pooled, homogenized in 1 mL RNA-Solv reagent (Omega Bio-Tek) for RNA isolation, using a Precellys 24 homogenizer (Bertin technologies).
TruSeq Stranded mRNA kit (Illumina) was used for library preparation from total RNA according to the manufacturer’s protocol.

treatment_protocol: 3-5 day-old female mosquitoes were first anesthetized on CO2 pad, washed in 70% ethanol and then 1× PBS buffer for three times, to get rid of any bacteria or fungi contamination.

value: Wing

value: female

value: 3-5 day-old female mosquitoes


title: Wing, rep 2


title: siST3_2

value: ST3GAL5 knockdown


title: intestine, 30°C, 6h 2

city: Qingdao

first: Dongxue

last: Xu

address: Changcheng road No.700

institute: Qingdao Agricultural University

data_processing:
Sequence reads were trimmed for adaptor sequence and low-quality sequence in order to acquire the clean reads.
Clean reads were mapped to genome of Apostichopus japonicus.
Gene expression profiling was based on the number of reads.
FPKM (fragments per kb of exon model per million mapped reads) values were used to estimate the expressed values and transcript levels.
Assembly: GCA_002754855.1
Supplementary files format and content: tab-delimited text file includes FPKM values for all samples

organism: Apostichopus japonicus

source_name: intestine

growth_protocol: sea cucumber (around 100g)

extract_protocol:
Total RNA of each individua was extracted using Trizol RNA isolation reagent (Invitrogen) following the manufacturer’s instructions.
The mRNA was purified from the total RNA and cut into fragments using the TruSeq RNA Sample Prep Kit (Illumina). Qualified RNA samples were prepared to build cDNA libraries. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. After purification with AMPureXP beads, the ligated products with about 250-300 bp were amplified to generate high quality cDNA libraries, which were then sequenced by an Illumina Hiseq platform at Novogene Bioinformatics Technology (Beijing, China).

treatment_protocol: heat stress at 26°C or 30°C

value: intestine

value: heat stress 30°C for 6h


title: intestine, 30°C, 6h 1


title: siST3_1


title: Wing, rep 1


title: Salivary glands, rep 3

source_name: Salivary glands

value: Salivary glands


title: Salivary glands, rep 2


title: intestine, 26°C, 48h 2

value: heat stress 26°C for 48h


title: Salivary glands, rep 1


title: intestine, 26°C, 48h 1


title: intestine, 26°C, 48h 3


title: intestine, 26°C, 6h 3

value: heat stress 26°C for 6h


title: intestine, 26°C, 6h 2


title: intestine, Control 3

value: normal growth temperature


title: Ovary, rep 3

source_name: Ovary

value: Ovary


title: Mid gut, rep 3

source_name: Mid gut

value: Mid gut


title: intestine, 30°C, 6h 3


title: Pt2, BMMC, D032postTCR-Tinfusion

description:
spmat.mtx
meta.csv
genes.csv
Pt2_D032

value: marrow

value: BMMC

value: unselected


title: Mid gut, rep 2


title: intestine, 26°C, 6h 1


title: intestine, Control 2


title: genomic DNA from CRC patient 8

source_name: CRC 8

value: Female

value: cancer

value: colorectal polyp sample


title: intestine, Control 1


title: Malpighian Tubules, rep 3

source_name: Malpighian Tubules

value: Malpighian Tubules

value: female


title: Mid gut, rep 1

value: 3-5 day-old female mosquitoes


title: Streptomyces rosesporus MT19, ΔdhyR

city: Chengdu

first: Fuqiang

last: He

state: Sichuan

address: No.17, 3rd Section of People's South Road.

institute: Sichuan University

data_processing:
Trimmomatic software was first used for quality control and linker removal, and thenlow-quality bases and N-bases or low-quality reads were filtered out.
Using Rockhopper2 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Streptomyces filamentosus

source_name: Streptomyces rosesporus cells

growth_protocol: S. roseosporus MT19 and ΔdhyR were cultured in fermentation mediumfor fermenting at 220 rpm and at 30℃.

extract_protocol:
RNA was harvested using RNAprep Pure bacterial total RNA extraction kit (TIANGEN). The rRNA from total RNA of each sample was eliminated using Ribo-Zero Magnetic Kit  according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: Streptomyces rosesporus cells

value: deletion of dhyR gene


title: Malpighian Tubules, rep 2


title: Streptomyces rosesporus MT19, WT

value: WT


title: Malpighian Tubules, rep 1


title: Ovary, rep 2


title: unT-185-03, methylseq

city: University Park

first: KELLY

middle: Johanna

last: GOMEZ-CAMPO

state: Pennsylvania

address: 212 Mueller Laboratory

department: Biology

institute: PSU

description: Sample 31

data_processing:
Methylation analysis was performed using Bismark 020.0 (Krueger and Andrews, 2011). Briefly, FASTQ files were quality-filtered, and adapter sequences trimmed using Trim Galore 0.5.0 (Krueger, 2018). A bisulfite-converted reference genome file was generated using Bismark-Bowtie2 algorithm, and the epigenome library sequenced data was aligned to the Acropora palmata genome
Methylation information was then extracted from the output SAM files and resulting genome tracks were used for the visualization and reporting of downstream differential methylation calculations. Methylated and unmethylated read counts for all cytosines across the genome in the CG, CHG, and CHH context were obtained from census files.
Assembly: Acropora palmata genome, assembled and annotated by Sheila Kitchen 2023, in prep. Associated fasta is uploaded as well as the associated annotation file
Supplementary files format and content: tab-delimited text files include bismark report

organism: Acropora palmata

source_name: Polyp-Tissue

extract_protocol:
Genomic DNA (gDNA) was extracted from 32 A. palmata fragments (n= 8 per group condition; 16 fragments per genet). We used the DNeasy Blood and Tissue Kit (Qiagen, Switzerland), as per the manufacturer’s protocol. gDNA concentration was quantified at 0.5-1.5 μg (Qubit® dsDNA BR Assay Kit on a Qubit® 2.0. Fluorometer) and sent for Whole Genome Bisulfite Sequencing (WGBS) at Admera Health (New Jersey, USA).
Sequencing libraries were prepared with an average sequencing library insert size of 450 bp and according to TruSeq® DNA Methylation Kit protocol, Sample Preparation Guide (Illumina Inc., USA). Briefly, standard reaction mix consisting of 130 µl of the CT Conversion Reagent and 20 µl of each DNA sample were used for bisulfite conversion (EZ DNA Methylation-Gold™ Kit) in a thermal cycler (Eppendorf® Mastercycler® Pro S). After the incubation period, bisulfite converted DNA was purified following the protocol of EZ DNA Methylation-Gold™ Kit. The bisulfite converted sequencing library was enriched following the TruSeq® DNA Methylation Kit protocol. Libraries were validated and quantified with qPCR. Sequencing was performed in Illumina Hi-Seq platform with pair-end reads of 2x150 and a mean depth coverage of 30x (Illumina Inc., USA). The estimated number of passed filter reads per sample was 110-120 million paired-end reads (55-60M reads in each direction).

value: Polyp-Tissue


title: Leg, rep 3

source_name: Leg

value: Leg


title: unT-185-04, methylseq

description: Sample 32


title: unT-185-02, methylseq

description: Sample 30


title: unT-185-01, methylseq

description: Sample 29


title: Leg, rep 1


title: Ovary, rep 1


title: Fat body, rep 1

source_name: Fat body

value: Fat body


title: upC-185-04, methylseq

description: Sample 28


title: upC-185-02, methylseq

description: Sample 26


title: Fat body, rep 3


title: upC-185-03, methylseq

description: Sample 27


title: Crop, rep 2

source_name: Crop

value: Crop


title: Fat body, rep 2


title: Crop, rep 3


title: upC-185-01, methylseq

description: Sample 25


title: shControl_pooled_input

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

country: Germany

institute: University of Freiburg

data_processing:
Sequencing data was processed in usegalaxy.eu platform.
Fastq Quality Control using FastQC  (v0.11.9).
 high quality and uniquely mapping reads were retained (mapq > 5).
Adapter trimming and quality filtering was done using Trimmomatic (v 0.38)with the following configurations: ILLUMINACLIP:$TRIMMOMATIC_ADAPTERS_PATH/TruSeq3-SE.fa:2:30:10 MINLEN:20 -trimlog trimlog 2>&1 | tee trimmomatic.log && if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi && mv fastq_out.'fastqsanger.gz'
Trimmed and quality filtered reads were aligned to mm10 genome assembly using Bowtie 2(v 2.3.4.1) using the following command: set -o | grep -q pipefail && set -o pipefail;   ln -s '/data/dnb05/galaxy_db/files/0/2/f/dataset_02fe6c06-864b-43e2-8311-2fc1e1a81253.dat' input_f.fastq.gz &&   bowtie2  -p ${GALAXY_SLOTS:-4}  -x '/data/db/reference_genomes/mm10/bowtie2_index/mm10'   -U 'input_f.fastq.gz'               --sensitive         2> '/data/jwd/main/033/625/33625182/outputs/galaxy_dataset_fb42ac29-feb2-48ce-bc4d-15a12528fe2a.dat'  | samtools sort -@${GALAXY_SLOTS:-2} -O bam -o '/data/jwd/main/033/625/33625182/outputs/galaxy_dataset_0fc27fd7-4cc2-4fde-996a-c523cb87f985.dat'
Peaks were called using MACS2 ( v. 2.2.6) using default parameters from filtered BAM files. ChIPSeeker (Galaxy Version 1.28.3+galaxy0) was used to annotate peak coordiantes to genes.
Assembly: Input-normalised bigwig files (bamcompare) from treated and control samples were compared and normalised to log2ratio using bigwigCompare. deeptools Galaxy Version 3.3.2.0.0.
Supplementary files format and content: mm10

source_name: Neuro2a (N2A) cells

growth_protocol: Mouse neuroblastoma cell line, Neuro-2a (N2a) was cultured and maintained at 37°C, 95% relative humidity and 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM, ThermoScientific, Schwerte, Germany) supplemented with 10% fetal bovine serum (FBS, ThermoScientific), 1% non-essential amino acids (NEAA, ThermoScientific), 1% L-glutamine, and 1% penicillin, streptomycin, and neomycin (PSN, ThermoScientific).

extract_protocol:
N2a cells were fixed with freshly prepared room temperature 1% PFA (pH 8.0, Life technologies) for 5min at room temperature. Fixation was stopped with 125mM Glycine, and fixed cells were washed twice with ice-cold PBS. Cells were collected in ice-cold PBS and centrifuged (5min, 600g ). Lysis buffer (1% SDS, 10mM EDTA, 50mM Tris HCl (pH 8.0), 1% Protease Inhibitor cocktail) was added on the pellet and incubated on ice for 5min. Shearing was done using Bioruptor with the settings: 3x10min 30s pulse, 30s pause and chromatin was centrifuged for 5min at 13.000 rpm and the chromatin samples were saved. Chromatin samples were precleared with protein G dynabeads (Invitrogen). Genomic DNA regions of interest were isolated using 4μg of H3K79me2 antibody (ab3594, abcam). Complexes were washed, eluted from the beads with SDS buffer (1% SDS, 0.1M NaHCO3), and subjected to RNase and Proteinase  K treatment. Crosslink was reversed by incubation overnight at 65oC, and ChIP DNA was purified by Qiagen MinElute kit according to the manufacturer’s instructions. Quantification was performed by using PicoDrop and the PicoGreen quantification kit .
Libraries were prepared using the NEBNext Ultra II DNA library preparation Kit for Illumina (Biolabs).
The ChIP-seq library was sequenced using HiSeq 3000 (Illumina)  (paired-end, 51bp reads).

treatment_protocol: N2a cells were transfected with shNPM1 (NPM1 KD) or shControl plasmid (CTR) and were grown on 6 wells plates (~6 Mio cells) for 72h. Two independent biological replicates per conditions were used. The following plasmid were used for transfection: pLKO.1-shCTR (Sigma, Non Target #3), pLKO.1-shNpm1 (Sigma, TRCN0000115430). For NPM1 Knockd Down (NPM1 KD) experiments, N2a cells were selected with 9.3 µg/ml Puromycin starting 24hs after transfection and for the remaining time until fixation or collection.

value: Neuro2a (N2A) cells

value: shControl plasmid (CTR)

tag: div (days_in_vitro)

tag: antibody

value: none (input)


title: Crop, rep 1


title: unT-183-04, methylseq

description: Sample 24


title: unT-183-02, methylseq

description: Sample 22


title: shNpm1_pooled_input

value: shNPM1 (NPM1 KD)


title: unT-183-03, methylseq

description: Sample 23


title: right hippocampus, exercise, biological replicate 3 WT

source_name: right hippocampus

value: right hippocampus

value: wildtype

value: C57Bl/6 J

value: exercise

value: biological replicate 3


title: unT-183-01, methylseq

description: Sample 21


title: upC-183-04, methylseq

description: Sample 20


title: Leg, rep 2

value: female

value: 3-5 day-old female mosquitoes


title: H3K79me2_shControl_n1

value: H3K79me2 antibody (ab3594, abcam)


title: H3K79me2_shNpm1_n1


title: H3K79me2_shNpm1_n2


title: unC-183-04, methylseq

description: Sample 16


title: upC-183-02, methylseq

description: Sample 18


title: upC-183-01, methylseq

description: Sample 17


title: UpC-185-03, rnaseq

data_processing:
Gene count normalization and differential expression analysis was performed using DESeq2 3.12.0. Significant Differentially Expressed Genes (DEGs) were determined via pairwise comparison among control and treatment groups (UnCLL vs UnTLL-HL and UpCHL vs UpTHL-LL) and genet, with a false discovery rate-adjusted P value (FDR) of < 0.05.
Assembly: Acropora palmata genome, assembled and annotated by Sheila Kitchen 2023, in prep. Associated fasta is uploaded as well as the associated annotation file that corresponds with gene headers
Supplementary files format and content: tab-delimited text file with genecount for all samples. Each sample and raw gene counts are concatenated into one file, where each column represents a sample, and each row is a gene aligned against, with raw counts in each cell.

extract_protocol:
Total RNA was extracted from the same 32 A. palmata fragments used in WGBS as previously noted. The tissue from each fragment was homogenized in TRIzol reagent (Ambion, Life Technology) before centrifugation with chloroform for 15 minutes at 12,000 x g at 4 ºC. The aqueous phase was then isolated and cleaned using Qiagen RNeasy Mini kit (Qiagen), as per the manufacturer’s protocol with an additional on-column DNase treatment using RNase-Free DNase Set (Qiagen). Total RNA was sent to Admera Health (New Jersey, USA) where concentration and purity was re-analyzed (Qubit® dsDNA BR Assay Kit on a Qubit® 2.0. Fluorometer).  5 of these samples failed sequencing and were not included in the final transcriptomic analysis
RNA libraries for 2x150bp paired-end sequencing were prepared using the NEBNext Ultra II Nondirectional Library Prep Kit with polyA selection (New England Biolabs, Inc.). Samples were run on one plate of the Illumina NovaSeq platform. Illumina universal adapters and reads below PHRED of 22 were trimmed using Cutadapt62. Filtered reads were aligned to the Acropora palmata genome assembled by Sheila Kitchen 2023; unpublished using the program STAR, and read counts compiled into a .tab file


title: UpC-185-04, rnaseq


title: unC-183-03, methylseq

description: Sample 15


title: UpC-185-01.1, rnaseq


title: upT-185-04, methylseq

description: Sample 14


title: upT-185-03, methylseq

description: Sample 13


title: unC-183-01, methylseq

description: Sample 11


title: UnT-185-04.1, rnaseq


title: UnT-183-04, rnaseq


title: UnT-183-01, rnaseq


title: UnT-183-02, rnaseq


title: UpC-185-01, rnaseq


title: unC-183-02, methylseq

description: Sample 12


title: unC-185-04, methylseq

description: Sample 10


title: unC-185-03, methylseq

description: Sample 9


title: H3K79me2_shControl_n2


title: UpC-183-03, rnaseq


title: upT-183-03, methylseq

description: Sample 7


title: UpC-183-04, rnaseq


title: upC-183-03, methylseq

description: Sample 19


title: upT-185-02, methylseq

description: Sample 6


title: upT-185-01, methylseq

description: Sample 5


title: UpC-185-03.1, rnaseq


title: upT-183-02, methylseq

description: Sample 4


title: UnC-183-04, rnaseq


title: UpC-183-01, rnaseq


title: UpC-183-02, rnaseq


title: upT-183-01, methylseq

description: Sample 3


title: UnC-183-03.1, rnaseq


title: unC-185-01, methylseq

description:
Sample 1
No reports for Samples 1 and 2.  Only raw data uploaded as downstream processessing failed, thus analyses were not continued using Samples 1 or 2.


title: ARPE19-2

city: Shanghai

first: Haibin

last: Tian

address: 1239 Siping Road

institute: Tongji University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome
Genome_build: hg38
Supplementary_files_format_and_content: TPM.txt

source_name: cell line

extract_protocol:
Total RNA was isolated from the samples and RNA integrity was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: RPE cells


title: UpT-185-04, rnaseq

value: Polyp-Tissue


title: UpT-185-03, rnaseq


title: ARPE19-1


title: iRPE cells-2

source_name: human UCMSCs

value: iRPE from hUCMSC cells


title: UnC-185-03, rnaseq


title: upT-183-04, methylseq

description: Sample 8


title: iRPE cells-1


title: UpT-183-04, rnaseq


title: UnC-183-02, rnaseq


title: hUCMSC-2

description: human UCMSC-2

source_name: human umbilical cord

value: hUCMSC cells


title: UnC-183-01, rnaseq


title: iPSC-RPE cells-2

source_name: Human iPSCs

value: iPSC-RPE cells


title: UpT-183-03, rnaseq


title: iPSC-RPE cells-1


title: UpT-185-02, rnaseq


title: unC-185-02, methylseq

description: Sample 2


title: UnC-183-03, rnaseq


title: shC-C

city: New Brunswick

first: Daniel

last: Herranz

state: New Jersey

address: 195 Little Albany Street

institute: Rutgers Cancer Institute of New Jersey

description: Doxycicline induce shControl expression

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Gene abundance estimates were obtained for each sample using kallisto 0.44.0, with the UCSC hg38 transcriptome as the reference
The abundance levels were normalized using the DESeq between-sample normalization approach
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated values file includes the DESeq normalized counts for all samples

growth_protocol: DND41 cells were plated in triplicates in RPMI supplemented with 10% FBS.

extract_protocol:
RNA was extracted using QIAGEN QIAshredder (#79656) and Rneasy Mini (#74106) kits.
Strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DND41 cells were treated with doxycylcine to induce the expression of the shRNA-Control or shRNA-SIRT1 in RPMI supplemented with 10% FBS for 72h.

value: T-ALL cell line

value: Control


title: UpT-185-04.1, rnaseq


title: UpT-185-01, rnaseq


title: UpT-183-01, rnaseq


title: sh3-C

description: Doxycicline induce shControl expression

value: Sirt1 Inhibited


title: UpT-183-02, rnaseq


title: sh3-B

description: Doxycicline induce shSIRT1 expression


title: UnC-185-02, rnaseq


title: hUCMSC-1

description: human UCMSC-1


title: shC-A

description: Doxycicline induce shControl expression


title: UnC-185-01, rnaseq


title: sh3-A

description: Doxycicline induce shSIRT1 expression


title: sh1-C

description: Doxycicline induce shSIRT1 expression


title: Lung, Rat3789

first: Kevin

middle: J

last: Cheung

state: WA

department: Public Health Sciences

institute: Fred Hutchinson Cancer Center

description: RNA-seq of 4T1 xenograft tumor in rats: lung met

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

organism:
Mus musculus
Rattus norvegicus

source_name: lung

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: lung

value: breast cancer

value: no treatment


title: Tumor non-necrotic rim, Rat3867

description: RNA-seq of 4T1 xenograft tumor in rats: tumor rim

source_name: mammary tumor

value: mammary tumor

value: wildtype


title: sh1-A

description: Doxycicline induce shSIRT1 expression


title: sh1-B

description: Doxycicline induce shSIRT1 expression


title: csa mutant-12h-3

first: Linlin

last: Sun

address: Dong chuan Rd. 800 Ming hang

institute: SJTU

description: csa mutant-12h-3

data_processing:
Reads were mapped to the O. sativa genome (RGAP v. 7.0)
Gene expression levels were calculated, and were normalized to reads per kilobase per million reads (RPKM)(Wang et al., 2010; Kawahara et al. 2013; Sun et al., 2021).
DEseq2 was used to identify DEGs, using false discovery rate (FDR) ≤ 0.05 and |log2(fold change)| ≥ 1(Audic, 1997). Heatmaps were plotted with Rpackage “pheatmap” (Kolde, 2019; Sun et al., 2021).
Plant promotor motif analysis were sourced from software TBtools (Chen et al., 2020), and predicted on the website PlantCare (Lescot et al., 2002)
Expression profile during seed germination for DEGs of interest were sourced from the Rice Expression Profile Database (RiceXPro) (Sato et al., 2013).
Genome_build: O. sativa genome (RGAP v. 7.0)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Oryza sativa

source_name: rice seed

growth_protocol: Dried and dehulled seeds were surface-sterilized with 70 % ethanol for 1 min, then sterilized with 2 % (v/v) sodium hypochlorite solution for 15 min and washed with sterile double-distilled water 7 times for 30 s. Seeds (80–100) were placed in a translucent germinating box and incubated at 28 °C, 16 h light/8 h dark in ½×MS solution

extract_protocol:
Total RNA was extracted from 5 seeds in triplicate at 3, 6, and 12 h post-imbibition using RNAiso Plus (Takara), according to the manual. For each sample, 10 μg of total RNA was used for library construction and RNA-seq by BGI Genomics (Wuhan, China), using an Illumina HiSeq 3000 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: csa mutant

tag: tissue source

value: germinating rice seed

value: embryo

value: after imbibition 12 hours


title: Lung, Rat3869


title: csa mutant-12h-1

description: csa mutant-12h-1


title: csa mutant-12h-2

description: csa mutant-12h-2


title: csa mutant-6h-3

description: csa mutant-6h-3

value: after imbibition 6 hours


title: Tumor necrotic core, Rat3867

description: RNA-seq of 4T1 xenograft tumor in rats: tumor necrotic core


title: Tumor necrotic core, Rat3875


title: Tumor non-necrotic rim, Rat3869


title: csa mutant-6h-2

description: csa mutant-6h-2


title: Lung, Rat3875


title: csa mutant-3h-3

description: csa mutant-3h-3

value: after imbibition 3 hours


title: Tumor necrotic core, Rat3876


title: csa mutant-3h-1

description: csa mutant-3h-1


title: csa mutant-6h-1

description: csa mutant-6h-1


title: Lung, Rat3876


title: Tumor non-necrotic rim, Rat3875


title: csa mutant-3h-2

description: csa mutant-3h-2


title: Tumor necrotic core, Rat3877


title: Lung, Rat3877


title: 9522-12h-3

description: wild type-12h-3


title: Tumor non-necrotic rim, Rat3876


title: 9522-12h-2

description: wild type-12h-2

value: wild type


title: 9522-12h-1

description: wild type-12h-1


title: 7ML3

city: Tulln

first: Miriam

last: Schalamun

address: Konrad Lorenz Strasse 24

country: Austria

institute: Austrian Institute of Technology

data_processing:
quality filtering and trimming bbduk version 38.18
Mapping using HISAT2 version 2.2.1
Read count extraction by feautreCounts version 2.0.1
Supplementary files format and content: tab-delimited text files include raw counts

organism: Trichoderma reesei QM6a

growth_protocol: Trichoderma reesei WT (QM6a) and deletion mutant QM6aΔ72004 were grown in minimal medium with celluloseas carbon source at 28°C at for 96h

extract_protocol:
RNA was extracted using Rneasy plant mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using RNA stranded kit, NEB, rRNA depletion  by the Next Generation Sequencing Facility (Vienna Biocenter Core Facilities)

treatment_protocol: cultivation under at constant light or constant darkness and supplemented with or without 5mM L-methionine

value: mycelium

value: 72004 deletion

value: cellulose in light + 5mM L-methionine

tag: time


title: 7ML2


title: Tumor necrotic core, Rat3869


title: 9522-6h-2

description: wild type-6h-2


title: Tumor non-necrotic rim, Rat3877


title: 9522-6h-1

description: wild type-6h-1


title: 9522-3h-2

description: wild type-3h-2


title: 9522-3h-3

description: wild type-3h-3


title: 7ML1


title: 7L3

value: cellulose in light


title: QML3

value: WT


title: 7L2


title: spleenCD62LposTreg_5_resident_Tcrb_R2

city: Regensburg

first: Michael

last: Rehli

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

department: Internal Med III

institute: University Hospital Regensburg

description:
isolated
mTRB_176_Treg_d0_poly_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

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.

value: C57BL/6 WT

tag: sampleID

tag: mouse (pool/culture no.)

tag: type

tag: model

value: homeostatic control

value: spleen

tag: treg donor

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.

tag: chain

value: Beta

tag: techn. replicate


title: spleenCD62LposTreg_6_resident_Tcrb_R2

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

tag: strain

tag: tissue


title: QML2

tag: cell type

tag: genotype

tag: treatment


title: spleenCD62LposTreg_4_resident_Tcrb_R2

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

value: C57BL/6 Foxp3GFP+


title: QL3


title: QL2


title: QL1


title: 7MD3

value: cellulose in darkness + 5mM L-methionine


title: WGZC8

city: Kunming

first: Peng

last: Ji

address: Fengyuan raod 452

institute: Yunnan Agricultural University

data_processing:
Raw data in FASTQ format (raw reading) were first processed using a Perl script. Clean data were obtained by removing readings containing adapters, poly-N, and low-quality readings from the original data. Simultaneously, the Q20, Q30, GC content and sequence repetition levels of the clean data were calculated. All downstream analyses were based on clean high-quality data.
Connectors and low-quality sequence reads were removed from the dataset. After data processing, the original sequences were converted to a clean read. These reads were plotted against the reference genome sequence. Hisat2 software was used to compare the reference genomes. and StringTie comparisons were performed to assemble the reads.
Gene functions were annotated based on the following databases: Nr (NCBI non-redundant protein sequences), Nt (NCBI non-redundant nucleotide sequences), Pfam (protein family), KOG/COG (Clusters of Orthologous Groups of proteins), Swiss-Prot (a manually annotated and reviewed protein sequence database), KO (KEGG Ortholog database), and GO (Gene Ontology).
Assembly: Sscrofa11.1_ncbi
Supplementary files format and content: xls files include RPKM values for each Sample

organism: Sus scrofa

source_name: liver

extract_protocol:
RNA was harvested using RNAsimple Total RNA Kit (Tiangen Biotech Co., Ltd., Beijing, China).  1.3 ug of total RNA was used for the construction of sequencing libraries. The total of 1 μg RNA in each sample was used as the input material for RNA sample preparation.
According to the manufacturer's suggestion, a NEBNext Ultra RNA Library Prep Kit (Illumina, Nebraska, USA) was used to generate a sequencing library.

value: liver

tag: breed

value: Wujin

value: NOT PROVIDED; REQUESTED


title: spleenCD62LposTreg_1_resident_Tcrb_R2

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


title: spleenCD62LposTreg_2_resident_Tcrb_R2

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


title: spleenCD62LnegTreg_4_resident_Tcrb_R2

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


title: 9522-6h-3

description: wild type-6h-3

tag: genotype/variation

tag: tissue source

value: germinating rice seed

value: embryo

value: after imbibition 6 hours


title: spleenCD62LposTreg_3_resident_Tcrb_R2

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

tag: sampleID

tag: mouse (pool/culture no.)


title: 7MD2

value: mycelium

tag: time


title: 7L1

value: 72004 deletion


title: 7MD1


title: 9522-3h-1

description: wild type-3h-1

value: wild type

value: after imbibition 3 hours


title: 7D2

value: cellulose in darkness


title: WGZC2


title: 7D3


title: WGZA7


title: spleenCD62LnegTreg_3_resident_Tcrb_R2

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

tag: type

tag: model

tag: treg donor


title: 7D1


title: spleenCD62LnegTreg_2_resident_Tcrb_R2

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

tag: recipient

tag: pcr1 cy. no.

tag: pcr2 cy. no.


title: QMD3

value: WT


title: QMD2


title: QML1

value: cellulose in light + 5mM L-methionine


title: liverCD62LposTreg_5_resident_Tcrb_R2

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

tag: strain

value: homeostatic control

tag: chain

tag: techn. replicate


title: WGZB4

tag: tissue


title: QMD1

tag: cell type

tag: genotype

tag: treatment


title: QD2


title: QD3


title: WGZB5

tag: breed


title: WGZC7


title: liverCD62LposTreg_4_resident_Tcrb_R2

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

tag: sampleID

value: Beta


title: WGZB6


title: liverCD62LposTreg_2_resident_Tcrb_R2

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

value: C57BL/6 Foxp3GFP+

tag: mouse (pool/culture no.)


title: QD1

tag: time


title: HEK293T cells, Vec-IFN_b_3

city: Tianjin

first: Fengqi

last: Li

state: Tianjin

address: No. 92, Weijin Road, Xuefu Street, Nankai District

department: School of Pharmaceutical Science and Technology

institute: Tianjin university

data_processing:
Fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp.
We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).
After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
Assembly: hg18
Supplementary files format and content: genes_fpkm_expression.txt

growth_protocol: HEK293, HEK293T cells and HeLa cells were cultured in Dulbecco’s modified Eagle medium (DMEM) (Gibco, 10569-010) supplemented with 10% fetal bovine serum (FBS) (Gibco, 10099141), and 1% penicillin/streptomycin (Solarbio, P1400) at 37℃ in a 5% CO2 humidified atmosphere.

extract_protocol:
The total RNA was isolated from cells by using  total RNA purification kit (Tiangen, Cat# DP419)
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.
We performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: HEK293 cells in 10-cm dish were transfected with plasmids expressing MDA5 for 24 h or treated with IFNβ at 1,000 IU for 6 h. Total RNA was extracted (Vazyme, R401-1) and subject to poly(A) selection-RNA sequencing by LC-Biotechnology (Hangzhou, China).

tag: cell line

value: human embryonic kidney (HEK) 293 cell line

value: transfection IFN β


title: HEK293T cells, Vec-IFN_b_2


title: WGZA3

value: liver

value: Wujin


title: liverCD62LposTreg_1_resident_Tcrb_R2

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

tag: type

tag: model


title: WGZA2

value: NOT PROVIDED; REQUESTED


title: HEK293T cells, Vec-IFN_b_1


title: HEK293T cells, Vec_1

value: transfection Empty Vector


title: liverCD62LnegTreg_4_resident_Tcrb_R2

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

tag: treg donor

tag: recipient


title: spleenCD62LnegTreg_1_resident_Tcrb_R2

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

value: spleen

tag: pcr1 cy. no.

tag: pcr2 cy. no.


title: HEK293T cells, Vec_2


title: HEK293T cells, MDA5_3

value: transfection WT MDA5


title: LW_Tes_3.RNAseq

city: Yunnan Kunming

first: Huo

last: Jinlong

address: Jinhei Road 95

data_processing:
The SRs were aligned to the susScr11 reference genome using STAR (version 2.7.10a, parameters --alignEndsType EndToEnd --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All -- outSAMtype BAM).
Illumina paired-end short reads were quantified using Salmon (v1.9.0), and TPM values were summaized in the processed data table.
Illumina single-end small RNA reads were predicted potential miRNA using miRDeep2 (v0.1.3). Small RNA reads were mapped to mature miRNA and precursor miRNA from the prediction and miRbase (Release 22.1) using bowtie (v1.3.1).
Assembly: susScr11
Supplementary files format and content: tab-delimited text files include TPM values and RPM values for each Sample

source_name: testis

growth_protocol: All samples were acquired from 12-month adult male pigs. Pigs were housed in a temperature (64-79°F) and humidity (30-70%) controlled room.

extract_protocol:
Total RNAs were extracted using Trizol followed by acid phenol extraction. rRNA depletion was done for Illumina RNAseq.
Illumina paired-end sequencing uses standard RNAseq library construction protocol. Illumina single-end sequencing library was constructed using TruSeq small RNA sample prep Kits (Illumina, SanDiego, USA)

value: testis

value: Large white


title: liverCD62LnegTreg_3_resident_Tcrb_R2

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

tag: strain

tag: chain


title: LW_Tes_2.RNAseq

tag: tissue


title: HEK293T cells, MDA5_1

tag: cell type


title: HEK293T cells, MDA5-GOF_3

value: transfection GOF MDA5


title: liverCD62LnegTreg_2_resident_Tcrb_R2

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

tag: techn. replicate


title: HEK293T cells, MDA5-GOF_2

tag: treatment


title: liverCD62LnegTreg_1_resident_Tcrb_R2

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


title: HeLa, Rho-7 10 μM [T006]

city: Worcester

first: Patipark

last: Kueanjinda

address: 368 Plantation St

institute: University of Massachusetts Medical School

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp module in galaxy (default parameters).
Trimmed sequence reads were mapped to GRCh38.p14 using RNA STAR module in galaxy (default parameters).
BAM files were converted to fastq formats using SamToFastq module prior to quantification using Kallisto in galaxy (default parameters).
Read count extraction and normalization were performed using R.
Assembly: GRCh38.p14
Supplementary files format and content: comma-separated values file includes read count in TPM values for each sample.

source_name: Uterus; cervix

growth_protocol: Cells were maintained in Dulbecco’s modified eagle medium (DMEM) or RPMI 1640 medium, medium supplemented with 10% fetal bovine serum, 100 U/mL penicillin and, 100 µg/mL streptomycin and under incubation condition of 5% CO2 at 37 oC.

extract_protocol:
Total RNA was extracted from the cells using  GenUP total RNA kit (biotechrabbit).
Approximately 500 ng of the total RNAs from each sample was used to create individually indexed strand-specific RNA-Seq libraries by using QIAseq Stranded mRNA Library kits (QIAGEN). The reactions were subjected to fragmentation and cDNA synthesis. QIAseq Beads (QIAGEN) were used to separate the cDNAs from the reaction mix. Indexing adapters were ligated to the cDNAs, and subsequently all cDNA libraries were inspected for quality by using Agilent 2100 Bioanalyzer (Agilent) and quantified with DeNovix fluorometer (DeNovix). The indexed sequencing libraries were pooled in equimolar quantity and subjected to cluster generation and paired end 150 nucleotide read sequencing on Illumina NovaSeq sequencer.

treatment_protocol: Cells were incubated with DMSO as a control or 10 μM of Rho-7 compound for 24 h.

value: Uterus; cervix

value: HeLa

value: epithelial cell

value: Rho-7 compound


title: HEK293T cells, MDA5-GOF_1


title: DU_Tes_3.RNAseq

tag: breed

value: Western Duroc


title: HeLa, Rho-7 10 μM [T005]


title: DU_Tes_2.RNAseq


title: HeLa, Rho-7 10 μM [T004]


title: colonTreg_5_resident_Tcrb_R2

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

value: C57BL/6 Foxp3GFP+

tag: sampleID

value: homeostatic control

value: colon

value: Beta


title: DU_Tes_1.RNAseq


title: colonTreg_3_resident_Tcrb_R2

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

tag: mouse (pool/culture no.)


title: HEK293T cells, MDA5_2

value: human embryonic kidney (HEK) 293 cell line


title: HEK293T cells, Vec_3


title: HeLa, control [T002]

value: vehicle control, DMSO


title: HeLa, control [T003]


title: colonTreg_4_resident_Tcrb_R2

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


title: scRNA_seq_dI0 jejunum

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes
map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Genome_build: susScr11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: jejunum cell

extract_protocol: Single-cell RNA-seq libraries were prepared using Single Cell 3’ Library Gel Bead Kit V3 (10x Genomics Inc., Pleasanton, CA, USA) following the manufacture’s introduction.

tag: age

value: 0 day

value: jejunum

tag: Sex

value: male


title: colonTreg_2_resident_Tcrb_R2

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

tag: type


title: HeLa, control [T001]

tag: cell line


title: LW_Tes_1.RNAseq

value: testis


title: scRNAseq_16_PulpMildCariesBorn1996

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software version 7.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: grch38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: dental pulp

extract_protocol:
Teeth were collected immediately after extraction and placed in sterile 0.9% NaCl, on ice. Dental pulp was obtained from carious teeth following the protocol we previously applied for the isolation of healthy human pulp tissues.66 Briefly, each tooth was cracked with a press, and carefully opened with forceps. Isolated dental pulp was placed in a Petri dish filled with cold HBSS and minced into smaller pieces (<2 mm diameter) for easier dissociation. The dental pulp pieces were transferred to falcon tubes and dissociated using 5 U/mL Collagenase P (11 213 873 001, Sigma-Aldrich, Buchs, Switzerland) in PBS for 40 min at 37 °C. After incubation in the enzymatic solution, tissue pieces were further mechanically disaggregated by pipetting and centrifuged at 300 × g at 4 °C for 10 min. Cell pellet was resuspended in HBSS containing 0.002% Bovine Serum Albumin (BSA; 0163.2, Roth AG, Arlesheim, Switzerland) and filtered through a 70 μm cell strainer.
Cells were loaded into the 10X Chromium Next GEM Chip G, aiming the recovery of ~10000 cells per sample. scRNAseq libraries were generated according to 10X Chromium Next Gem Single Cell 3’ Reagent Kits v3.1 (CG000204 Rev D) and sequenced on the Illumina Novaseq 6000 system

value: dental pulp


title: C92_scRNAseq_12_Lower_Carious_Pulp


title: scRNAseq_17_Carious_1989


title: spleenTreg_3-5_GvHD_Tcrb_R2

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

value: poly

tag: model

value: GvHD

value: spleen

tag: treg donor


title: C92_scRNAseq_11_Upper_Carious_Pulp


title: spleenTreg_3-6_GvHD_Tcrb_R2

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

tag: recipient

tag: pcr1 cy. no.


title: NRSF/REST_ChIPseq_Eq_R2

city: IRVINE

first: Shan

last: Jiang

address: 2300E Biological Sciences III

institute: UNIVERSITY OF CALIFORNIA, IRVINE

description: NRSF/REST.peaks.Eq.txt

data_processing:
ChIP and input sequencing reads were aligned using Bowtie v.0.12.8
After alignment, peaks were detected using MACS v.1.4.2, retaining all statistically enriched regions ( p<10-4.5). Binding regions were considered reproducible when they were identified in both replicates. Consensus binding regions were then merged and called subpeaks using PeakSplitter_Cpp v.1.0. Subpeaks in 50bp were merged. Peaks having (1) higher signal in control than ChIP replicates in each species or (2) signal in control is higher than 1.4 RPM in each species or (3) in Blacklist (ENCODE Project Consortium. 2012) in human and mouse were filtered out as artificially high signal peaks.
Genome_build: GRCh37/hg19,GRCm38/mm10, CanFam3.1, EquCab2.0
Supplementary_files_format_and_content: peak calling results for each species in .txt format. (chromosome, start, end)

organism: Equus caballus

source_name: Skin fibroblasts

growth_protocol: Mouse macrophage cells (RAW264.7, ATCC, Manassas, VA) were grown in DMEM medium (30-2002, ATCC, Manassas, VA) supplemented with 10% FBS (VWR, Radnor, PA) and penicillin/streptomycin (Life Technologies). Dog myelomonocytic leukemia cells (ML2, ATCC, Manassas, VA) were grown in RPMI-1640 medium (Life Technologies, Carlsbad, CA) supplemented with 1000 mM Hepes, 10mM MEM NEAA, 100mM Sodium pyruvate, 55mM β- mercaptoethanol, 10% FBS and penicillin/streptomycin. Horse skin fibroblast (E.Derm, ATCC, Manassas, VA) were grown in EMEM(30-2003, ATCC, Manassas, VA) supplemented with 10% FBS and penicillin/streptomycin. Trypan Blue (VWR) staining was performed before harvesting the cells for each assay to make sure that at least 90% of the cells were viable.

extract_protocol:
We cross-linked about 20 million cells with 1% formaldehyde for each replicate. Cross-linked chromatin was sonicated into 200-300bp fragments. DNA fragments were incubated with Dynabeads protein G (Thermo Fisher Scientific) bound by NRSF monoclonal antibody (Caltech Protein Expression Center, Pasadena, CA, USA, 12C11-1B11) overnight to perform immunoprecipitation. Then chromatin was reverse cross-linked to extract NRSF-bound DNA.
DNA fragments recovered from ChIPs were end-repaired, ligated to adapters, size selected (200 to 300bp) and PCR-amplified to make the libraries for sequencing. The libraries were made based on Myers Lab protocol v042211 (http://myers.hudsonalpha.org/documents/Myers%20Lab%20ChIP-seq%20Protocol%20v042211.pdf).

value: Skin fibroblasts

tag: passages

tag: strain

value: E.Derm (NBL-6)-quarterhorse

tag: chip antibody


title: NRSF/REST_ChIPseq_Eq_Input

tag: cell type


title: NRSF/REST_ChIPseq_Eq_R1

description: NRSF/REST.peaks.Eq.txt

value: NRSF monoclonal antibody (Caltech Protein Expression Center, Pasadena, CA, USA, 12C11-1B11)


title: GES-1 cells, incubated by PBS, 2

city: Guangzhou

first: hongfa

last: wei

state: Guangdong Province

address: No. 74 Zhongshan Second Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen University

description: PBS incubated GES-1 cells

data_processing:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).
The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).
And polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: stomach

growth_protocol: Cells cultured in RMPI-1640 medium supplemented with 10% fetal bovine serum (Gibco, Australia) and a 1% penicillin/streptomycin mixture.

extract_protocol:
Total RNA was harvested, and cDNA was generated by a reverse transcription reagent kit (AG11706, Accurate Biology, China).
RNA libraries for RNA-seq were prepared using mRNA-Seq Library Prep Kit foliowing manufacturer's protocols.

treatment_protocol: The control group of the PBS and the experimental group of MNNG ( 200μmol/L, 48 hours) were dissolved in 0.3% DMSO, in order to avoid the cell toxicity.

tag: tissue

value: stomach

value: GES-1 cells

value: Normal gastric tissue

tag: genotype

value: WT

value: PBS incubated cells


title: PLGC cells, induced by MNNG, 2

description: MNNG incubated GES-1 cells

value: induced by MNNG

tag: treatment

value: MNNG incubated cells


title: Tbxt_insASAY_homo_mouse_female

city: Cambridge

first: Bo

last: Xia

address: 415 Main Street

institute: Broad institute

data_processing:
Sequencing results were demultiplexed with Illumina bcl2fastq v2.20 requiring a perfect match to indexing BC sequences. Low quality reads/bases and Illumina adapters were trimmed with Trimmomatic v0.39. Reads were then mapped to the mouse genome (mm10) using bwa 0.7.17. The coverage and mutations in and around Tbxt locus were checked through visualization in a mirror version of UCSC genome browser.
Assembly: mm10
Supplementary files format and content: Processed data are generated to bigwig files mapped to reference genome (mm10).
Library strategy: Capture-seq

source_name: ear clip

extract_protocol:
Genomic DNA was purified from mESCs or ear punches of mice of interest using Zymo Quick-DNA Miniprep Plus Kit (Cat. No. D4068) according to the manufacturer’s protocol.
DNA sequencing libraries compatible for Illumina sequencers were prepared following the standard protocol. Briefly, 1µg of gDNA was sheared to 500-900 base pairs in a 96-well microplate using the Covaris LE220 (450 W, 10% Duty Factor, 200 cycles per burst, and 90-s treatment time), followed by purification with a DNA Clean and Concentrate-5 Kit (Zymo Research, Cat. No. D4013). Sheared and purified DNA were then treated with end repair enzyme mix (T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase, NEB, Cat. No. M0203, M0210 and M0201, respectively), and A-tailed using Klenow 3'-5'exo- enzyme (NEB, Cat. No. M0212). Illumina sequencing library adapters were subsequently ligated to DNA ends, followed by PCR amplification with KAPA 2X Hi-Fi Hotstart Readymix (Roche, Cat. No. KR0370). Following library preparation, custom biotinylated probes were prepared as bait through nick translation, using BAC DNA and/or plasmids as the template. The probes were prepared to comprehensively cover the whole locus. We used BAC lines RP24-88H3 and RP23-159G7, purchased from BACPAC Genomics, to generate bait probes covering mouse Tbxt locus and ~200kb flanking sequences in both upstream and downstream regions. The pooled whole-genome sequencing libraries were hybridized with the biotinylated baits in solution and purified through streptavidin-coated magnetic beads. Following pull-down, DNA sequencing libraries were quantified with Qubit 3.0 Fluorometer (Invitrogen, Cat. No. Q33216) using a dsDNA HS Assay Kit (Invitrogen, Cat. No. Q32851). The sequencing libraries were subsequently sequenced on an Illumina NextSeq 500 sequencer in paired-end mode.

value: ear clip

value: Tbxt-insASAY/insASAY


title: Tbxt_insASAY_homo_mouse_male


title: spleenTreg_3-4_GvHD_Tcrb_R2

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

value: C57BL/6 Foxp3GFP+

tag: sampleID

tag: pcr2 cy. no.

tag: chain

value: Beta

tag: techn. replicate


title: PLGC cells, induced by MNNG, 1

description: MNNG incubated GES-1 cells


title: Beta_Donor2_RFX6KD

city: Stanford

first: Vy

last: Coykendall

state: California

address: 279 Campus Drive W

department: Developmental Biology

institute: Stanford University

description:
RNAseq_Donor2_Beta_RFX6KD
V10

data_processing:
Barcodes were trimmed using Trimgalore_0.5.0.
Reads were aligned to the human genome (GRCh38, Ensembl release 104) using STAR v2.6.1d (Dobin et al. 2013)
Estimated counts and transcripts per million (TPM) were quantified using RSEM v1.3.1 (Li and Dewey 2011)
Differentially expressed genes with fold change were detected using the DESeq2 R package (Love et al. 2014)
Assembly: hg38 (GRCh38) transcriptome
Supplementary files format and content: csv file containing raw estimated counts
Supplementary files format and content: csv file containing transcripts per million (TPM)

source_name: cadaveric pancreatic tissue

growth_protocol: Primary islets were dispersed and transduced with lentiviruses and cultured for 5 days

extract_protocol:
SMART-seq v4 Ultra Low input RNA kit (Clontech)
Nextera XT DNA Library Preparation Kit (Illumina)
RNA-seq; paired-end 150bp reads on the Illumina NovaSeq 6000 platform

treatment_protocol: Lentiviral shRNAs against RFX6 vs. non-targeting shRNA control

value: cadaveric pancreatic tissue

value: primary islet cells

value: beta cells

value: RFX6 shRNA


title: Beta_Donor4_RFX6KD

description:
RNAseq_Donor4_Beta_RFX6KD
M7


title: scRNAseq_6_Carious_Pulp

value: dental pulp


title: Beta_Donor3_RFX6KD

description:
RNAseq_Donor3_Beta_RFX6KD
M3


title: spleenTreg_2-5_GvHD_Tcrb_R2

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

tag: mouse (pool/culture no.)

tag: type

value: poly

value: GvHD

value: spleen


title: Tbxt_insRCS2_homo_mouse_female


title: Beta_Donor3_Control

description:
RNAseq_Donor3_Beta_Control
M1

tag: cell line

value: control

value: non-targeting shRNA control


title: Beta_Donor4_Control

description:
RNAseq_Donor4_Beta_Control
M5


title: Tbxt_delE6_het_mouse_founder_3


title: Tbxt_insRCS2_homo_mouse_male


title: GES-1 cells, incubated by PBS, 3

description: PBS incubated GES-1 cells

value: stomach

value: GES-1 cells

value: Normal gastric tissue

value: WT

value: PBS incubated cells


title: Alpha_Donor4_Control

description:
RNAseq_Donor4_Alpha_Control
M6

value: alpha cells


title: Alpha_Donor4_RFX6KD

description:
RNAseq_Donor4_Alpha_RFX6KD
M8


title: Alpha_Donor3_RFX6KD

description:
RNAseq_Donor3_Alpha_RFX6KD
M4


title: spleenTreg_3-3_GvHD_Tcrb_R2

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

value: C57BL/6 Foxp3GFP+

value: allo

tag: model

tag: treg donor

value: Beta


title: Beta_Donor1_Control

description:
RNAseq_Donor1_Beta_Control
V1

value: cadaveric pancreatic tissue

value: primary islet cells

value: beta cells


title: Tbxt_delE6_het_mouse_founder_2

value: ear clip


title: Tbxt_delE6_het_mouse_founder_1


title: spleenTreg_2-3_GvHD_Tcrb_R2

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

value: GvHD

tag: recipient

tag: pcr1 cy. no.


title: spleenTreg_3-2_GvHD_Tcrb_R2

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

tag: strain

value: spleen


title: Beta_Donor1_RFX6KD

description:
RNAseq_Donor1_Beta_RFX6KD
V4

value: RFX6 shRNA


title: Tbxt_mouse_WT

value: wild type


title: Alpha_Donor2_Control

description:
RNAseq_Donor2_Alpha_Control
V8

value: control

value: non-targeting shRNA control


title: Alpha_Donor2_RFX6KD

description:
RNAseq_Donor2_Alpha_RFX6KD
V11


title: spleenTreg_2-2_GvHD_Tcrb_R2

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


title: Beta_Donor2_Control

description:
RNAseq_Donor2_Beta_Control
V7


title: Alpha_Donor1_Control

description:
RNAseq_Donor1_Alpha_Control
V2


title: spleenTreg_2-6_GvHD_Tcrb_R2

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

value: poly


title: Alpha_Donor1_RFX6KD

description:
RNAseq_Donor1_Alpha_RFX6KD
V5


title: Tbxt_mESC_delE6homo

description: Cultured cells

source_name: mESC MK6

value: mESC MK6

value: embryonic stem cells


title: spleenTreg_2-4_GvHD_Tcrb_R2

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


title: spleenTreg_3-1_GvHD_Tcrb_R2

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


title: CandR_Donor7_FLAG

data_processing:
Trimmomatic (Bolger et al. 2014) was used for trimming
Bowtie2 (Langmead and Salzberg 2012) was used for alignment
HOMER (Heinz et al. 2010) was used for peak calling
GREAT (McLean et al. 2010) was used for gene annotation
Assembly: hg19 (GRCh37) transcriptome
Supplementary files format and content: txt file containing peaks data
Library strategy: CUT&RUN

growth_protocol: Primary human islets were dispersed and transduced with lentiviruses and cultured for 5 days

extract_protocol:
CUTANA ChIC/CUT&RUN protocol v3.1 (Epicypher 14-1048)
CUTANA CUT&RUN Library Prep Kit (Epicypher 14-1001)

treatment_protocol: Lentiviruses expressing RFX6-FLAG

value: whole pseudoislets

value: RFX6-FLAG overexpression

value: Lentiviruses expressing RFX6-FLAG

tag: antibody

value: anti-Flag


title: CandR_Donor7_IgG

value: cadaveric pancreatic tissue

tag: cell type

value: anti-IgG


title: Tbxt_mESC_halfWT_half_delE6homo

description: Cultured cells


title: CandR_Donor6_FLAG

tag: tissue

value: primary islet cells


title: CandR_Donor6_IgG

tag: genotype


title: liverTreg_3-6_GvHD_Tcrb_R2

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

value: C57BL/6 Foxp3GFP+

value: liver

value: Beta


title: spleenTreg_2-1_GvHD_Tcrb_R2

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

value: allo

value: GvHD

value: spleen


title: liverTreg_3-5_GvHD_Tcrb_R2

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


title: Alpha_Donor3_Control

description:
RNAseq_Donor3_Alpha_Control
M2

value: alpha cells

value: control

tag: treatment

value: non-targeting shRNA control


title: Tbxt_mESC_WT

description: Cultured cells

value: mESC MK6

value: embryonic stem cells

value: wild type


title: 63_S12

city: Aachen

first: Kai Markus

last: Schneider

address: Pauwelsstraße 30

department: Medicine III

institute: University Hospital RWTH Aachen

data_processing:
Pseudo-alignment of the sequencing reads to the reference transcriptome was conducted using Salmon v1.10.1.
Transcript-level quantification data was imported and organized using Tximeta v1.16.1
DESeq2 v1.38.3 was employed for differential gene expression analysis.
functional enrichment analysis was carried out using clusterProfiler v4.6.0.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: Salmon format flies include TPM values for each sample

source_name: liver, 24 weeks, CTRL

extract_protocol:
RNA was harvested using PureLink RNA Mini Kit (Invitrogen).  500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: Sex

value: male

value: CTRL


title: CandR_Donor5_IgG

value: cadaveric pancreatic tissue

value: whole pseudoislets

value: RFX6-FLAG overexpression

value: Lentiviruses expressing RFX6-FLAG


title: CandR_Donor5_FLAG

value: primary islet cells

value: anti-Flag


title: liverTreg_3-4_GvHD_Tcrb_R2

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

value: C57BL/6 Foxp3GFP+

tag: sampleID

value: poly

value: liver

tag: pcr2 cy. no.

value: Beta


title: Mus musulus 770351

city: Durham

first: Vincent

middle: Michael

last: Perez

state: NC

address: 25 Alexandria Wy

department: Translational reasearch

institute: Tempus AI

data_processing:
All FASTQ files were processed using a combination of STAR v2.7.10a and Salmon v1.2.0 with the mouse build GRCh38 - mm10 as a reference). FASTQ files from the same sample, but different lanes, were merged with STAR’s fastq_channel_merged_paired function. Reads were mapped using STAR’s fastq_channel_merged_paired_star function. Picard and QC, count matrix assembly, and bam files were generated for each sample using both Picard v2.27.4, STAR v2.7.10a, and Salmon v1.2.0. TRUST4 v1.0.12 (Tcr Repertoire Utilities for Solid Tissue) were used to reconstruct TCR and BCR sequences from BAM files generated from the STAR/Salmon outputs. All parameters for TRUST4 were set to default. The final output from TRUST4 was summary matrices for each sample that included hypervariable complementarity-determining region 3 (CDR3) nucleotide and amino acid sequences, counts, frequencies, and V, D, and J chain names.
Assembly: GRCm38
Supplementary files format and content: Complete gene count matrix (expression_raw_annotated.csv), gene count matrix normalized with Deseq2 and converted to log2 scale (expression_normalized_log2.csv), output from TRUST4 algorithm (processed_trust4.zip).

source_name: p53/MCA sarcoma

extract_protocol:
Tumors were dissected from mice, minced, and digested using the Miltenyi Biotec tumor dissociation kit. Tumor specimens and matched muscle control were harvested and stored in RNALater (Ambion) at −80°C until all samples were collected. RNA extractions from each sample were performed using RNeasy Fibrous Tissue Mini Kit (Qiagen). Extracted total RNA quality and concentration were assessed on a NanoDrop Spectrophomoter (Thermo Fisher Scientific).
RNA-seq libraries were prepared using TruSeq Small RNA Library Preparation Kits (Illumina) following the manufacturer’s protocol. RNA sequencing was performed on an Illumina Novoseq in 151 base pair, paired-end configuration. Greater than 50,000 reads per cell were collected per the manufacturer's recommendation.

value: p53/MCA sarcoma

value: 129/SVJ WT

value: Muscle control


title: NdKO-4

city: Seoul

first: AHee

last: Yun

address: 52, Ewhayeodae-gil, Seodaemun-gu, Seoul 03760

country: South Korea

institute: Ewha Womans University

data_processing:
Raw sequence reads were trimmed for adaptor sequence using Cutadapt.
Trimmed sequence reads were mapped to GRCh38 using STAR Aligner.
Read count extraction and normalization were performed using RSEM.
Assembly: GRCh38
Supplementary files format and content: A tab-delimited text file includes TPM (transcripts per million) counts for all samples

extract_protocol:
Total RNA was extracted using the microRNeasy Mini Kit (Qiagen, Hilden, Germany). RNA quality was evaluated by RNA integrity number by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Poly-A RNA isolation from total RNA was carried out using the Illumina Stranded mRNA Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
cDNA libraries were prepared using the Illumina Stranded mRNA Prep Kit (Illumina) according to the manufacturer’s instructions.

value: Osteosarcoma


title: Mus musulus 770350

description: TruSeq Small RNA Library Preparation Kits


title: 60_S9


title: 61_S10


title: Mus musulus 770214

value: Grp 8-RT+Iso for OX40+CpG+Iso for PD-1


title: liverTreg_2-5_GvHD_Tcrb_R2

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

value: GvHD

tag: chain

tag: techn. replicate


title: liverTreg_2-6_GvHD_Tcrb_R2

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

tag: mouse (pool/culture no.)

tag: type


title: NdKO-2

tag: cell line


title: 59_S8

value: male

value: CTRL


title: liverTreg_2-4_GvHD_Tcrb_R2

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

tag: model

tag: treg donor


title: Mus musulus 770309


title: NdKO-1


title: liverTreg_3-3_GvHD_Tcrb_R2

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

value: allo

tag: recipient

tag: pcr1 cy. no.


title: Mus musulus 770303


title: liverTreg_3-2_GvHD_Tcrb_R2

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

tag: strain


title: 74_S16

source_name: liver, 24 weeks, WSD

value: WSD


title: N2KO-4

tag: cell type


title: 62_S11

tag: tissue


title: Mus musulus 770335

tag: genotype


title: 58_S7

tag: treatment


title: liverTreg_2-3_GvHD_Tcrb_R2

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


title: 55_S6

tag: Sex


title: Mus musulus 770260


title: 78_S17


title: N2KO-3


title: liverTreg_2-2_GvHD_Tcrb_R2

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

tag: sampleID


title: 52_S2


title: N2KO-1


title: Mus musulus 770324

value: Grp 10-NO RT+Iso for OX40+CpG+Iso PD-1


title: liverTreg_2-1_GvHD_Tcrb_R2

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

tag: pcr2 cy. no.


title: N1KO-4


title: N1KO-3


title: 66_S15

source_name: liver, 24 weeks, CTRL+beta-Glucan

value: CTRL+beta-Glucan


title: N1KO-2


title: liverTreg_3-1_GvHD_Tcrb_R2

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

tag: chain


title: Mus musulus 770287


title: 64_S13


title: Mus musulus 770293


title: colonTreg_3-5_GvHD_Tcrb_R2

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

value: colon

tag: techn. replicate


title: colonTreg_2-6_GvHD_Tcrb_R2

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

value: C57BL/6 Foxp3GFP+

tag: mouse (pool/culture no.)


title: Mus musulus 770295


title: colonTreg_3-4_GvHD_Tcrb_R2

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

tag: type

value: poly


title: N2KO-2

tag: cell line


title: Mus musulus 770326

value: Grp 2-RT+Iso OX40+Ctl CpG+Iso for PD-1


title: 40_S1

value: liver


title: N1KO-1


title: 65_S14


title: WT-4


title: 39_S3


title: colonTreg_2-5_GvHD_Tcrb_R2

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

tag: model

value: Beta


title: colonTreg_3-6_GvHD_Tcrb_R2

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

tag: treg donor


title: WT-3


title: WT-2


title: Mus musulus 770281

value: p53/MCA sarcoma

value: 129/SVJ WT


title: colonTreg_2-4_GvHD_Tcrb_R2

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

tag: recipient


title: colonTreg_3-3_GvHD_Tcrb_R2

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

tag: pcr1 cy. no.


title: Mus musulus 770313

description: TruSeq Small RNA Library Preparation Kits


title: 84_S20

source_name: liver, 24 weeks, WSD+beta-Glucan

value: WSD+beta-Glucan


title: Mus musulus 770265


title: Mus musulus 770334


title: colonTreg_3-2_GvHD_Tcrb_R2

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

tag: strain


title: Mus musulus 770331


title: 83_S19


title: WT-1

tag: cell type

value: Osteosarcoma


title: HK-2_KO_3

first: Yutong

last: Hou

address: 227 South Chongqing Road

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp.
Trimmed sequence reads were mapped to GRCm38.102/hg38 or GRCh38.102/mm10 using Hisat2.
Read count extraction and normalization were performed using Stringtie.
Assembly: hg38; mm10
Supplementary files format and content: Tab-delimited text files include raw counts and FPKM values for each Sample.

extract_protocol:
RNA was harvested using TRNzol Universal Reagent (TIANGEN). 2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using mRNA-seq Lib Prep Kit for Illumina (ABclonal, China) following Sample Preparation Guide.

value: PCMT1 KO


title: HK-2_KO_2


title: Mus musulus 770277

tag: tissue

value: Grp 4-NO RT+Iso for OX40+Ctl CpG+Iso PD-1


title: Mus musulus 770294

tag: genotype


title: scTCR-seq_Spleen recipient 3

data_processing:
ScRNA:Sequencing reads were demultiplexed using cellranger mkfastq (version 4.0.0),scTCR:Fastq files were processed using cellranger (version 5.0.0)
ScRNA:The reads were subsequently mapped to the mouse genome using cellranger count (version 4.0.0).
ScRNA: Quality control and analysis was performed with the Seurat package (v4.0.0) in R.
scTCR:Fastq files were processed using cellranger (version 5.0.0)
ScTCR:The reads were subsequently mapped to the mouse genome using cellranger count (version 5.0.0).
ScTCR: Quality control and analysis was performed with the Seurat package (v5.0.0) in R
Assembly: ScRNA: Mouse reference, mm10 (GENCODE vM23/Ensembl98),scTCR: mm10 reference genome (refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0
Supplementary files format and content: cellranger output, rds (R.4.1.1), loom (python 3.8.13), H5ad (python 3.8.13)
Library strategy: scTCR-seq

source_name: Donor allo reisolated from Recipient 3

growth_protocol: Donor Treg Expansion: Splenocytes from transgenic FoxP3EGFP mice (B6; CD45.2; H-2b) 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 CD4, CD8 and CD62L and Treg were sorted on a FACSAriaTM IIu or FACSAriaTM Fusion (Becton Dickinson) as CD4+CD25highCD62L+ cells; purity of sorted cells was >98%. 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:
For re-isolation of donor Treg on day 7 after transplantation, single cell suspensions from spleen, liver and colon were prepared, stained for H-2Kb, CD45.1, CD45.2, TCRβ and CD4 and sorted on a FACSAria IIuTM or a FACSAriaTM Fusion.
ScRNA-seq libraries were constructed using 13-16 cycles of PCR. Products were purified using Ampure XP beads and quality was controlled using Agilent Tapestation.  ScTCR-seq libraries were generated from the same cDNAs using the Single Cell V(D)J Enrichment Kit, Mouse T Cell (10x Genomics).
ScRNA-libraries were sequenced using single-read sequencing (S1 flow cell, 100 bp) on the Illumina NovaSeq™. scTCR-libraries were sequenced on the Illumina NextSeq 550 with 150 cycles single-read sequencing.

treatment_protocol: Prophylactic treatment of GvHD: 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 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 alloTreg from Foxp3gfp mice at a 1:1 ratio.

tag: phenotype

value: female

value: Donor Treg allo reisolated from Spleen recipient 3

tag: cell markers


title: 82_S18

tag: Sex

value: male

tag: treatment


title: 37_S2


title: scTCR-seq_Liver recipient 3

value: transgenic FoxP3EGFP mice (B6; CD45.2; H-2b)

value: Donor Treg allo reisolated from Liver recipient 3


title: NdKO-3


title: Mus musulus 770299


title: Mus musulus 770246


title: HK-2_CTL_2

value: WT


title: Mus musulus 770250