title: +IAA, Tachyzoite, biol rep 3

city: wuhan

first: xue

last: lilan

state: 请选择...

address: shizishan

institute: huazhong agriculture university

description:
AIP1-mAID +IAA _3
Transcription of AIP1-mAID strains under addition and subtraction of IAA
AIP1_RNAseq.xlsx

data_processing:
Clean reads were mapped to the T. gondii ME49 genome (ToxoDB) using Hisat2 software
Transcript levels were calculated using the transcript per million (TPM) method, and differentially expressed genes were identified using DESeq2 v1.24.0 with a p-value < 0.01 and a minimum fold change of 2.
Assembly: T. gondii reference genome (TGME49)
Supplementary files format and content: xls file includes raw counts for each sample

organism: Toxoplasma gondii

source_name: Tachyzoite

growth_protocol: To obtain tachyzoite samples,parasites  were cultured in human foreskin fibroblasts (HFF), in Dulbecco’s Modified Eagle Medium (DMEM) (Sigma-Aldrich, USA), supplemented with 2% heat-inactivated fetal bovine serum (FBS) (Gibco, USA), 1% penicillin-streptomycin, and 5 mM L-glutamine. In order to obtain samples of bradyzoites, parasites were cultured in RPMI 1640 medium (pH = 8.2) containing 1% fetal bovine serum, along with ambient CO2.

extract_protocol:
Intracellular parasites were harvested, released by needle passage, and purified by filtration through membranes with 3 μm pore size to remove host cell debris. Total RNA was extracted from purified parasites using transZol Up reagent (TransGen Biotech, China) following the manufacturer’s instructions. The RNA quality was assessed using an Agilent 2100 Bioanalyzer (Agilent, USA).
Libraries for RNA sequencing were prepared using the TruSeq RNA Sample Prep Kit (Illumina, USA) and sequenced on a DNBSEQ-T7 sequencer (MGI Tech Co., Ltd, China) with the PE150 model.

treatment_protocol: To obtain tachyzoite samples, ME49 and ME49ΔXII-5 were grown under normal culture conditions, and in addition, AIP was required to be treated with plus or minus IAA drug. To obtain tachyzoite samples, ME49 and ME49ΔXII-5 were  grown under induced bradyzoite culture conditions.

value: Tachyzoite

value: +IAA


title: SAMPLE_02_000010_W0_TL

status: Public on Dec 19 2024

type: SRA

city: Kiel

first: Rashmi

last: Tandon

address: Rosalind-Franklin-Strasse 9

country: Germany

institute: UKSH

library_source: transcriptomic

data_processing:
Illumina standard primers were trimmed using trim_galore (version 0.6.6)
Reads were mapped to the human reference genome (GRCh38, Ensembl release 103) using hisat2 (version 2.2.1)
Mapped reads were cleaned and sorted using samtools (version 1.11)
Number of reads for each gene was counted using rsubread (version 2.2.6)
Assembly: GRCh38, Ensembl release 103
Supplementary files format and content: Comma-separated text file including raw counts of sequencing reads for each gene and sample

molecule: polyA RNA

organism: Homo sapiens

source_name: skin

extract_protocol:
Total RNA was isolated using the mirVanaTM miRNA Isolation Kit (Lifetechnologies, Carlsbad,CA)
RNA samples were prepared for sequencing using the Illumina stranded mRNA protocol and sequenced on the NovaSeq6000 with 2x100bp

tag: tissue

value: skin

tag: cohort number

tag: subject number

tag: timepoint

tag: sample type

value: TL


title: +IAA, Tachyzoite, biol rep 2

country: China

description:
AIP1-mAID +IAA _2
Transcription of AIP1-mAID strains under addition and subtraction of IAA
AIP1_RNAseq.xlsx

molecule: total RNA

tag: cell type

tag: genotype

tag: treatment


title: SAMPLE_02_000009_W0_TL


title: SAMPLE_02_000008_W0_TL


title: Ercc1d/- DR/sAct Kidney #3

city: Utrecht

first: Wilbert

last: Vermeij

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center

description:
IG48
Kidney_counts_file.txt

data_processing:
Trimmomatic: version 0.39 using default settings
STAR: version 2.7.0f using default settings
featurecounts: (SubRead version 1.6.4) default settings with multimapping
EdgeR: version 3.40.2  using default settings
Assembly: GRCm38.p6.genome.fa, gencode.vM20.annotation.gtf
Supplementary files format and content: Tab-delimited count files produced by featureCounts
Supplementary files format and content: Kidney_counts_file.txt, Muscle_counts_file.txt

organism: Mus musculus

source_name: Kidney

extract_protocol:
Total RNA was isolated from tissue specimens using the Qiagen miRNeasy kit. Concentration and quality of RNA was measured by Nanodrop One (Thermo Fisher Scientific, USA) and BioAnalyser 2100 (Agilent, USA).
RNA library was prepared by Novogene from ≥ 200 ng RNA.

value: Kidney

tag: strain

value: F1 Hybrid C57BL6J/FVBN

tag: Sex

value: male

value: DR/sActRIIB


title: Pt25_TIL-RNA

city: Tampa

first: Dongliang

last: Du

address: 111 Magnolia

country: USA

institute: Moffitt

library_source: transcriptomic single cell

data_processing:
For single-cell RNA-seq data, Cell Ranger (v3.0, 10X Genomics) was used for sequencing reads mapping against GRCh38 human transcriptome, UMI counting, and barcodes filtering. Only barcodes with UMI counts passing threshold for cell detection were imported to Seurat v4.070 for analysis. Then cells with less than 200 genes detected or greater than 10% mitochondrial UMIs were filtered out; genes detected in less than three cells were also excluded. Doublets were detected using Scrublet71, doubletCells implemented in scran72, DoubletFinder73, and scDblFinder74, assuming 0.08% doublet rate for every 1000 cells sequenced in 10X experiments. Cells identified as doublets by >=2 methods were removed from further analysis. Raw UMI counts were log normalized and top 500 variable genes were detected in each sample independently. T cell receptor and immunoglobulin genes were removed from the variable gene list to prevent clustering based on V(D)J transcripts. S and G2/M cell cycle phase scores were assigned to cells using CellCycleScoring() function. To remove batch effects between samples, individual patient samples were further integrated using FindIntegrationAnchors() and IntegrateData() functions75 with parameter anchor.features =8000. Scaled z-scores for each gene were calculated using ScaleData() function by regressing against % of mitochondrial UMIs, cell cycle phases score, and total reads count. Principal component analysis was performed on the integrated data. A shared nearest neighbor (SNN) graph was constructed based on the first 30 principle components. A total of 23 clusters were identified using the FindClusters() function by Louvain clustering76 at resolution=0.9. Uniform manifold approximation and projection (UMAP) was used to visualize clustering and gene expression.
Assembly: GRCh38
Supplementary files format and content: tsv and matrix files

source_name: Tumor

growth_protocol: TIL was cultured at Moffitt Cell Therapy Facility, following a previously described protocol (https://doi.org/10.1038/s41591-021-01462-y).

extract_protocol:
1. For isolated TIL: Tumor was minced and carefully mixed in digestion medium with collagenase (type II and type IV), hyaluronidase and DNAase (Thermo Fisher Scientific). Then undigested tumor was filtered from the cell suspension to generate a single-cell suspension. Intact cells were enriched with a Ficoll-Hypaque (GE Healthcare Bio-Sciences) gradient and viable tumor cells were enumerated by trypan blue exclusion. The tumor digested was stained with anti-human CD3 and Zombie NIR. Isolated TIL was sorted as the CD3+ Zombie NIR- population and sent for single cell sequencing.  2. For cultured TIL: Samples were stained with anti-human CD3 and Zombie NIR, and flow sorting was conducted to sort CD3+Zombie NIR- TIL for single cell sequencing.
The cell suspension was loaded onto the 10X Genomics Chromium Single Cell Controller (10X Genomics, Inc., Pleasanton, CA) at a concentration of about one thousand cells per microliter and the single cells, reagents, and 10x Genomics gel beads were encapsulated into individual nanoliter-sized Gelbeads in Emulsion (GEMs).  Revers transcription of poly-adenylated mRNA was performed inside each droplet, and cDNA generated from cells encapsulated with a 10X Genomics Chromium NextGEM Single Cell V(D)J Reagent Kit was enriched using VDJ primers provided in the kit.  A portion of the DNA library generated from antibody-labeled cells was amplified using primers provided by 10X Genomics to prepare a cell surface protein library, and the cDNA, feature barcoding and VDJ-enriched libraries were completed in bulk reactions using the 10X Genomics Chromium NextGEM Single Cell 3’ or 5’ V(D)J Reagent Kits.

value: Tumor

tag: cell line

value: TIL

value: T cells

value: cultured


title: Smartseq2_205

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
SmartSeq2 Analysis: Fastq files from SmartSeq2 libraries were aligned to the mouse genome (mm39) with Gencode M29 annotations using STAR (v2.7.10a). Genome-mapped BAM files were quantified with RSEM (v1.3.1), and the resulting gene/UMI count matrix was processed in Seurat (v4.1.2). Data were normalized using the LogNormalize method, with mitochondrial gene expression and library size bias regressed out via the ScaleData function. Cells with >5% mitochondrial reads were excluded. Clustering, differential expression, and gene signature scoring were performed in Seurat. Differentially expressed genes were identified using the Wilcoxon Rank Sum test, with Bonferroni-adjusted P-values < 0.05 and log2 fold changes > 0.5 considered significant.
Bulk RNA-Seq raw Fastq files were aligned to the mouse genome (mm39) with Gencode M29 annotations using STAR (v2.7.10a). The count matrix was processed in R with the DESeq2 package (v1.34). Genes with fewer than ten reads were filtered out, and sample normalization was applied using a negative binomial distribution model. Differential gene expression between conditions was assessed with the Wald test. Genes with adjusted P-values (FDR) < 0.1 were retained, and log2 fold changes were shrunk using the apeglm algorithm.
10x Genomics Analysis: Fastq files from cDNA and hashtag libraries generated on the Chromium platform (10x Genomics) were processed using Cell Ranger (v7.0.1). The resulting quantification matrix was processed in Seurat (v5.0) with normalization using the SCTransform function. Non-myeloid cell contaminants were removed based on the PanglaoDB_Augmented_2021 database and EnrichR package for R. Cells were classified by biological condition using the HTODemux function. Differentially expressed genes were identified with the Wilcoxon rank test, with Bonferroni-adjusted P-values < 0.05 and log2 fold changes > 0.3 considered significant. Signature scores were calculated using Seurat’s AddModuleScore function.
Assembly: mm10
Supplementary files format and content: Tab files from bulk RNA-Seq tab files containing the STAR gene quantification.
Supplementary files format and content: gene.results from RSEM quantification of Smartseq2 data
Supplementary files format and content: mtx, cellranger output from 10x genomics libraries.
Supplementary files format and content: rds, images of Seurat objects used in the analysis

source_name: D-LN

extract_protocol:
Lymph nodes and gut tissue were dissected, finely chopped, and digested in RPMI medium with Collagenase D to obtain single-cell suspensions. For gut-associated lymph nodes, duodenal lymph nodes were identified using anatomical markers. Dendritic cells were isolated from the duodenal lamina propria by separating intestines, removing mucus with PBS and DTT, and stripping epithelium with EDTA. The tissue was further digested with DNaseI and collagenase, followed by Percoll gradient centrifugation to isolate DCs. Single-cell sorting of DCs was conducted into 96-well plates with TCL buffer and stored at –80°C.
Library Preparation for Single-cell RNA-seq (SmartSeq2). Single cells were sorted onto plates, covering all conditions in each replicate. RNA was extracted using RNAClean XP SPRI beads, then reverse-transcribed into cDNA with RT and TSO primers. The cDNA was amplified, cleaned with SPRI beads, and tagmented using the Nextera XT DNA Library Preparation Kit (Illumina). Barcoded libraries were pooled and sequenced on the Illumina Nextseq 550 platform. Library Preparation for Single-cell RNA-Seq (10x Genomics). Cells were labeled with hashtag oligonucleotide (HTO)-tagged antibodies, sorted, and counted for viability. scRNA-seq libraries were generated using the 10x Genomics Chromium system, following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq SP flowcell at a minimum depth of 30,000 reads per cell. Library Preparation for Bulk RNA-seq. RNA was isolated using RNAClean XP beads. Reverse transcription was performed with specific primers, followed by cDNA amplification with KAPA HiFi HS Ready Mix. The amplified product was cleaned with RNAClean XP beads and tagmented using the Nextera XT DNA Library Preparation Kit (Illumina). Libraries were pooled and sequenced as 75-base single-end reads on an Illumina NextSeq platform.

treatment_protocol: Mice were treated with dietary ovalbumin (OVA) to induce tolerance. For infection conditions, mice were infected with Heligmosomoides polygyrus (H.p.) or Strongyloides venezuelensis (S.v.) to model chronic and acute type 2 immune responses, respectively.

value: D-LN

tag: number of_cells_sorted

value: SV


title: SAMPLE_02_000007_W0_TL


title: Smartseq2_204


title: CD-1 distal ileum, control pup 2

city: Oklahoma City

first: Kathryn

last: Burge

state: OK

address: 800 Research Parkway

department: Pediatrics

institute: University of Oklahoma Health Sciences Center

description: Fresh frozen bulk transcriptome sequencing

data_processing:
Sequences were analyzed through a custom computational pipeline on the OSCER HPC (high performance computing) consisting of the open-source gSNAP, Cufflinks, and R for sequence alignment and evaluation of differential gene expression.
Reads generated were mapped to the mouse genome (mm10) by gSMAP, expression (fragments per kilobase of transcript per million mapped reads, FPKM) derived by Cufflinks, and differential expression analyzed using R.
Assembly: mm10
Supplementary files format and content: Comma separated values file including FPKM values for all genes for each sample
Supplementary files format and content: Comma separated values file including FPKM values for differentially expressed genes (p<0.05) for each sample

source_name: distal ileum

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen), and quality and quantity evaluated by a NanoDrop Lite spectrophotometer. Sequencing libraries were constructed using 200-500 ng of high-quality RNA.
RNA libraries for RNA-seq were prepared using the CORALL Total RNA-Seq Library Prep Kit v2 (Lexogen), following manufacturer's protocols.

treatment_protocol: CD-1 pups were treated once daily with 30 mg/kg body weight HA35 dissolved in sterile water (HA35) or an equal volume of sterile water (control) from P7-P14.

value: distal ileum

tag: age

value: F

value: wild-type

value: Control


title: Smartseq2_206


title: -IAA, Tachyzoite, biol rep 2

description:
AIP1-mAID -IAA _2
Transcription of AIP1-mAID strains under addition and subtraction of IAA
AIP1_RNAseq.xlsx

value: Tachyzoite

value: -IAA


title: -IAA, Tachyzoite, biol rep 3

description:
AIP1-mAID -IAA _3
Transcription of AIP1-mAID strains under addition and subtraction of IAA
AIP1_RNAseq.xlsx


title: Ercc1d/- DR/sAct Kidney #2

description:
IG47
Kidney_counts_file.txt


title: Ercc1d/- DR/sAct Kidney #1

description:
IG46
Kidney_counts_file.txt


title: SAMPLE_02_000005_W0_TL

value: skin

value: TL


title: -IAA, Tachyzoite, biol rep 1

description:
AIP1-mAID -IAA _1
Transcription of AIP1-mAID strains under addition and subtraction of IAA
AIP1_RNAseq.xlsx


title: SAMPLE_02_000006_W0_TL


title: Ercc1d/- AL/sAct Kidney #3

description:
IG45
Kidney_counts_file.txt

value: Kidney

value: F1 Hybrid C57BL6J/FVBN

value: AL/sActRIIB


title: Smartseq2_202

value: Filtered


title: SAMPLE_02_000004_W0_TL


title: Smartseq2_209


title: Ercc1d/- AL/sAct Kidney #1

description:
IG43
Kidney_counts_file.txt

value: male


title: Smartseq2_201


title: SAMPLE_02_000003_W0_TL


title: Smartseq2_200


title: Ercc1d/- AL/sAct Kidney #2

description:
IG44
Kidney_counts_file.txt


title: +IAA, Tachyzoite, biol rep 1

description:
AIP1-mAID +IAA _1
Transcription of AIP1-mAID strains under addition and subtraction of IAA
AIP1_RNAseq.xlsx

value: +IAA


title: KOAP2XII5, Bradyzoite, biol rep 1

description:
KO125BZ1
Transcription of ME49 and ΔXII-5 strains induced to form bradyzoites in vitro
AP2XII5_BZ_RNAseq.xls

source_name: Bradyzoite

value: Bradyzoite

value: ME49 delta_XII-5

value: Induce bradyzoite in vitro


title: Smartseq2_199

value: D-LN

value: SV


title: SAMPLE_02_000002_W0_TL


title: Smartseq2_203


title: SAMPLE_02_000001_W0_TL


title: Ercc1d/- DR/Mock Kidney #2

description:
IG41
Kidney_counts_file.txt

value: DR/Mock


title: ME49, Bradyzoite, biol rep 2

description:
WT_BZ_2
Transcription of ME49 and ΔXII-5 strains induced to form bradyzoites in vitro
AP2XII5_BZ_RNAseq.xls


title: Ercc1d/- DR/Mock Kidney #3

description:
IG42
Kidney_counts_file.txt


title: ME49, Bradyzoite, biol rep 3

description:
WT_BZ_3
Transcription of ME49 and ΔXII-5 strains induced to form bradyzoites in vitro
AP2XII5_BZ_RNAseq.xls


title: SAMPLE_02_000027_W0_NL

value: NL


title: Smartseq2_198


title: ME49, Bradyzoite, biol rep 1

description:
WT_BZ_1
Transcription of ME49 and ΔXII-5 strains induced to form bradyzoites in vitro
AP2XII5_BZ_RNAseq.xls


title: SAMPLE_02_000026_W0_NL


title: Ercc1d/- AL/Mock Kidney #3

description:
IG39
Kidney_counts_file.txt

value: AL/Mock


title: Ercc1d/- DR/Mock Kidney #1

description:
IG40
Kidney_counts_file.txt


title: Smartseq2_196


title: Smartseq2_197


title: KOAP2XII5, Bradyzoite, biol rep 3

description:
KO125BZ3
Transcription of ME49 and ΔXII-5 strains induced to form bradyzoites in vitro
AP2XII5_BZ_RNAseq.xls


title: KOAP2XII5, Tachyzoite, biol rep 3

description:
KO125TZ3
Transcription of ME49 and ΔXII-5 strains which cultured in tachyzoites condition
AP2XII5_TZ_RNAseq.xls

value: Tachyzoite

value: Tachyzoite culture


title: Smartseq2_195


title: SAMPLE_02_000024_W0_NL

value: skin


title: Ercc1d/- AL/Mock Kidney #2

description:
IG38
Kidney_counts_file.txt

value: Kidney


title: KOAP2XII5, Tachyzoite, biol rep 2

description:
KO125TZ2
Transcription of ME49 and ΔXII-5 strains which cultured in tachyzoites condition
AP2XII5_TZ_RNAseq.xls


title: KOAP2XII5, Bradyzoite, biol rep 2

description:
KO125BZ2
Transcription of ME49 and ΔXII-5 strains induced to form bradyzoites in vitro
AP2XII5_BZ_RNAseq.xls


title: SAMPLE_02_000023_W0_NL


title: KOAP2XII5, Tachyzoite, biol rep 1

description:
KO125TZ1
Transcription of ME49 and ΔXII-5 strains which cultured in tachyzoites condition
AP2XII5_TZ_RNAseq.xls


title: Ercc1+/+ AL/Mock Kidney #3

description:
IG27
Kidney_counts_file.txt

value: F1 Hybrid C57BL6J/FVBN

value: Ercc1+/+ (wildtype)


title: Smartseq2_193


title: Ercc1+/+ AL/Mock Kidney #2

description:
IG26
Kidney_counts_file.txt


title: SAMPLE_02_000022_W0_NL


title: Ercc1+/+ AL/Mock Kidney #1

description:
IG25
Kidney_counts_file.txt


title: ME49, Tachyzoite, biol rep 3

description:
WT_TZ_3
Transcription of ME49 and ΔXII-5 strains which cultured in tachyzoites condition
AP2XII5_TZ_RNAseq.xls


title: SAMPLE_02_000025_W0_NL


title: Smartseq2_192

value: OV


title: SAMPLE_02_000021_W0_NL


title: Smartseq2_191


title: SAMPLE_02_000020_W0_NL


title: Ercc1d/- DR/sAct Muscle #3

description:
IG24
Muscle_counts_file.txt

source_name: Quadriceps Muscle

value: Quadriceps Muscle

value: male

value: DR/sActRIIB


title: Smartseq2_190


title: SAMPLE_02_000019_W0_NL


title: Ercc1d/- DR/sAct Muscle #2

description:
IG23
Muscle_counts_file.txt


title: Ercc1d/- DR/sAct Muscle #1

description:
IG22
Muscle_counts_file.txt


title: SAMPLE_02_000018_W0_NL


title: 1c- B cells, control, rep2

city: Guangzhou

first: yueming

last: sun

state: Guangdong

address: Zhongshan secand street 74

department: basic medicine

institute: Sun Yat-sen University

description:
smartseq2
1cn2

data_processing:
raw fastq files were aligned and quantified against the GRCh38 reference genome using default parameters in STAR 46 (v2.7.11b) and RSEM 47 (v1.3.3).
Assembly: GRCh38
Supplementary files format and content: deg of total B.xlsx

source_name: peripheral blood

extract_protocol:
RNA was harvested using Trizol method, Invitrogen TRIZOL Reagent (Cat.No. 15596-018).
RNA libraries for RNAseq was prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® following manufactor's protocls.

value: peripheral blood

value: 1c-B cell

value: control


title: 1c- B cells, control, rep1

description:
smartseq2
1cn


title: Smartseq2_189

value: D-LN


title: Smartseq2_188


title: Ercc1d/- AL/Mock Kidney #1

description:
IG37
Kidney_counts_file.txt


title: Smartseq2_194

value: SV


title: SAMPLE_02_000017_W0_NL

value: NL


title: Ercc1d/- AL/sAct Muscle #3

description:
IG21
Muscle_counts_file.txt

value: AL/sActRIIB


title: SAMPLE_02_000016_W0_NL


title: 1c+ B cells, control, rep1

description:
smartseq2
1cp

value: 1c+B cell


title: 1c+ B cells, control, rep2

description:
smartseq2
1cp2


title: Smartseq2_187


title: ME49, Tachyzoite, biol rep 2

description:
WT_TZ_2
Transcription of ME49 and ΔXII-5 strains which cultured in tachyzoites condition
AP2XII5_TZ_RNAseq.xls

value: Tachyzoite

value: Tachyzoite culture


title: ME49, Tachyzoite, biol rep 1

description:
WT_TZ_1
Transcription of ME49 and ΔXII-5 strains which cultured in tachyzoites condition
AP2XII5_TZ_RNAseq.xls


title: Ercc1d/- AL/sAct Muscle #2

description:
IG20
Muscle_counts_file.txt


title: Smartseq2_186


title: Ercc1d/- AL/sAct Muscle #1

description:
IG19
Muscle_counts_file.txt


title: 1c- B cells,culture with MSC, rep2

description:
smartseq2
1cnM2

value: co-culture with MSC


title: SAMPLE_02_000015_W0_NL

value: skin


title: 1c- B cells,culture with MSC, rep1

description:
smartseq2
1cnM


title: Ercc1d/- DR/Mock Muscle #3

description:
IG18
Muscle_counts_file.txt

value: F1 Hybrid C57BL6J/FVBN

value: DR/Mock


title: Smartseq2_185

value: OV


title: SAMPLE_02_000014_W0_NL


title: SAMPLE_02_000012_W0_NL


title: Ercc1d/- DR/Mock Muscle #2

description:
IG17
Muscle_counts_file.txt

value: Quadriceps Muscle

value: male


title: 1c+ B cells,culture with MSC, rep1

description:
smartseq2
1cpM

value: peripheral blood


title: Ercc1d/- DR/Mock Muscle #1

description:
IG16
Muscle_counts_file.txt


title: SAMPLE_02_000011_W0_NL


title: SAMPLE_02_000013_W0_NL


title: Smartseq2_184


title: Smartseq2_182

value: Filtered


title: Smartseq2_181


title: SAMPLE_02_000010_W0_NL


title: Ercc1d/- AL/Mock Muscle #3

description:
IG15
Muscle_counts_file.txt

value: AL/Mock


title: Ercc1d/- AL/Mock Muscle #2

description:
IG14
Muscle_counts_file.txt


title: total B cells, control, rep3

description:
smartseq2
B3

value: B cell

value: control


title: SAMPLE_02_000009_W0_NL

value: NL


title: total B cells, control, rep2

description:
smartseq2
B2


title: total B cells, control, rep1

description:
smartseq2
B1


title: Smartseq2_180

value: D-LN


title: Ercc1d/- AL/Mock Muscle #1

description:
IG13
Muscle_counts_file.txt


title: Ercc1+/+ AL/Mock Muscle #3

description:
IG3
Muscle_counts_file.txt

value: Ercc1+/+ (wildtype)


title: Smartseq2_179


title: total B cells ,culture with MSC, rep3

description:
smartseq2
B3M


title: SAMPLE_02_000007_W0_NL


title: Smartseq2_178


title: SAMPLE_02_000008_W0_NL


title: 1c+ B cells,culture with MSC, rep2

description:
smartseq2
1cpM2

value: 1c+B cell


title: Smartseq2_177


title: SAMPLE_02_000006_W0_NL


title: Ercc1+/+ AL/Mock Muscle #2

description:
IG2
Muscle_counts_file.txt


title: total B cells ,culture with MSC, rep1

description:
smartseq2
B1M


title: SAMPLE_02_000005_W0_NL


title: Ercc1+/+ AL/Mock Muscle #1

description:
IG1
Muscle_counts_file.txt


title: Smartseq2_176


title: Smartseq2_183


title: pancreatic islet, H-ins2-O, rep4

city: Shanghai

first: Fangzhen

last: Xia

address: Zhizaoju Road NO.639

institute: Department of endocrinology, Shanghai Ninth People's Hospital

description:
H-ins2-O4
FPKM_anno over expression.txt

data_processing:
Data were processed by Oebiotech
Assembly: mm10
Supplementary files format and content: txt file include FPKM value for each sample

source_name: pancreatic islet

extract_protocol:
RNA was harvested by total RNA Extraction Kit 2.0 Plus
The RNA libraries were sequenced on the illumina NovaseqTM 6000 platform by OE Biotech, Inc., Shanghai, China.

value: pancreatic islet


title: Smartseq2_175


title: pancreatic islet, H-ins2-O, rep3

description:
H-ins2-O3
FPKM_anno over expression.txt


title: pancreatic islet, H-ins2-O, rep2

description:
H-ins2-O2
FPKM_anno over expression.txt


title: SAMPLE_02_000004_W0_NL


title: SAMPLE_02_000003_W0_NL


title: HCEC shFOXO3 rep2

city: Stockholm

first: Jiawei

last: Zhong

address: Blickagången 16, Flemingsberg

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

data_processing:
Illumina Casava1.7 software used for basecalling.
Adapter was trimmed and  low-quality reads were removed by Trim Galore (version 0.4.4)
Remaining reads were aligned to human genome (hg38) with STAR (version 2.7.3a) in the pair-end mode with default parameters. Genome annotation reference was based on gencode release_30.
Uniquely mapped reads were kept and counted by HTSeq (version 0.11.2) to generate a gene-sample matrix.
DEGs between shFOXO3 group and shCtrl group were identified by DESeq2 (version 1.26.0) with the criteria of absolute fold change > 1.3 and false discovery rate (FDR) adjusted P value < 0.05.
Genome_build: Hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Cornea

growth_protocol: Human immortalized corneal epithelial cells (HCECs) were cultured in DMEM-F12 media supplemented with 5 μg/mL human insulin (MCE), 10 ng/ml recombinant human EGF (Sigma) and 1% streptomycin at 37 °C and 5% CO2 atmosphere and passaged with 0.05% Trypsin-EDTA.

extract_protocol:
FOXO3 knowndown HCEC and scrambled control were harvested. Total RNA was obtained using TRIzol Reagent (Thermo Fisher Scientific) and RNA quality was confirmed by the Bioanalyzer 2100 system (Agilent Technologies).
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit (NEB) and sequenced on Illumina HiSeq X Ten. We set 2 biological replicates for each group to eliminate technical variance.

treatment_protocol: Generation of shRNA lentiviral vector against human FOXO3, generation of FOXO3 over-expression lentiviral vector and lentivirus packing were conducted by VectorBuilder (Guangzhou, China). To increase or decrease the expression of FOXO3, HCEC cells were seeded before the day of lentiviral infection. After the overnight cultured, the lentivirus at a multiplicity of infection (MOI) of 10 in the presence of 10 µg/ml polybrene was added into the culture medium. After an 11-hour infection, the medium containing lentivirus was removed and maintained by fresh culture medium. The incubation and recovery times depended on the selection efficiency and the following experiments.

value: corneal epithelial cells

value: FOXO3 knockdown


title: HCEC shCtrl rep1

value: scramble control


title: Smartseq2_174


title: Smartseq2_173


title: SAMPLE_02_000002_W0_NL

value: skin


title: HCEC shFOXO3 rep1


title: HCEC shCtrl rep2


title: pancreatic islet, H-ins2-O, rep1

description:
H-ins2-O1
FPKM_anno over expression.txt


title: total B cells ,culture with MSC, rep2

description:
smartseq2
B2M

value: co-culture with MSC


title: SAMPLE_02_000001_W0_NL


title: Smartseq2_172

value: OV


title: ipsilateral_muralcells_sample12

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

country: United Kingdom

institute: King's College London

description: Library name: IPSI_12_P

data_processing:
Reads were aligned to mouse (Mus_musculus.GRCm38) using kallisto version 0.50.1 (Bray et al., 2016). Differential expression analysis was performed using DESeq2 (Love et al., 2014).
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: Excel, TPM values and DESEQ outputs

source_name: sciatic nerve

extract_protocol:
Nerve cells were dissociated from Pdgfrb-CreERT2-tdtomato mice using the methods described in the associated paper. Pdgfrb+ and Pdgfrb+/CD146+ populations were sorted using FACS into 4µl SMART-seq2 lysis buffer. We sorted a maximum of 100 cells per tube, so as to not overload the solution.
Sequencing libraries were then prepared in batch controlled fashion using the Smart-seq2 protocol described by Picelli and colleagues (Picelli et al., 2014). Sequencing was performed on these by Novogene Europe.

value: sciatic nerve

value: ipsilateral nerve 5 days post PSNL


title: pancreatic islet, H-ins2-C, rep4

description:
H-ins2-C5
FPKM_anno over expression.txt


title: Smartseq2_171


title: ipsilateral_muralcells_sample11

description: Library name: IPSI_11_P


title: SAMPLE_01_000015_W16_TL

value: TL


title: Smartseq2_170

value: Filtered


title: pancreatic islet, H-ins2-C, rep3

description:
H-ins2-C3
FPKM_anno over expression.txt


title: SAMPLE_01_000014_W16_TL


title: pancreatic islet, H-ins2-C, rep2

description:
H-ins2-C2
FPKM_anno over expression.txt


title: Smartseq2_169


title: ipsilateral_muralcells_sample9

description: Library name: IPSI_9_P


title: ipsilateral_muralcells_sample10

description: Library name: IPSI_10_P


title: pancreatic islet, H-ins2-C, rep1

description:
H-ins2-C1
FPKM_anno over expression.txt


title: SAMPLE_01_000013_W16_TL


title: SAMPLE_01_000012_W16_TL


title: Smartseq2_168


title: ipsilateral_muralcells_sample8

description: Library name: IPSI_8_P


title: ipsilateral_muralcells_sample7

description: Library name: IPSI_7_P


title: pancreatic isle, Flox, rep4

description:
flox21
FPKM_anno cKO.txt


title: Smartseq2_167


title: pancreatic isle, Flox, rep3

description:
flox20
FPKM_anno cKO.txt


title: SAMPLE_01_000011_W16_TL


title: ipsilateral_muralcells_sample6

description: Library name: IPSI_6_P


title: Smartseq2_165


title: SAMPLE_01_000010_W16_TL


title: pancreatic isle, Flox, rep2

description:
flox17
FPKM_anno cKO.txt


title: ipsilateral_muralcells_sample5

description: Library name: IPSI_5_P


title: pancreatic isle, Flox, rep1

description:
flox16
FPKM_anno cKO.txt


title: SAMPLE_01_000009_W16_TL


title: SAMPLE_01_000008_W16_TL


title: ipsilateral_muralcells_sample4

description: Library name: IPSI_4_P


title: Smartseq2_164


title: SAMPLE_01_000007_W16_TL


title: Smartseq2_163


title: pancreatic isle, cKO, rep4

description:
CKO38
FPKM_anno cKO.txt


title: pancreatic isle, cKO, rep3

description:
CKO12
FPKM_anno cKO.txt


title: ipsilateral_muralcells_sample3

description: Library name: IPSI_3_P


title: SAMPLE_01_000006_W16_TL


title: Smartseq2_162


title: pancreatic isle, cKO, rep2

description:
CKO9
FPKM_anno cKO.txt


title: SAMPLE_01_000005_W16_TL


title: ipsilateral_muralcells_sample2

description: Library name: IPSI_2_P


title: pancreatic isle, cKO, rep1

description:
CKO8
FPKM_anno cKO.txt


title: Smartseq2_166


title: Smartseq2_160


title: contralateral_muralcells_sample13

description: Library name: CONTRA_13_P

value: contralateral uninjured nerve


title: SAMPLE_01_000004_W16_TL


title: Smartseq2_159


title: SjD Susceptible mice male rep2

city: Gainesville

first: Cuong

last: Nguyen

state: Florida

address: 2015 SW 16th Ave

institute: University of Florida

data_processing:
The raw data from each sample were demultiplexed and aligned to the GRCm38 reference genome, and the UMI counts were quantified using the 10x Genomics Cell Ranger pipeline (v 7.0.1).
Assembly: GRCm38
Supplementary files format and content: tab-separated values (TSV) files and matrix files

source_name: salivary gland

extract_protocol:
Salivary glands of C57BL/6.NOD-Aec1/2 (51 weeks old, n=2 female, 2 male) and B6 (64 weeks old, n=2 female, 2 male) mice were explanted and digested in a buffer containing 1 mg/ml DNase (Sigma-Aldrich, St. Louis, MO) and 1 mg/ml Collagenase Type 4 (Worthington, Lakewood, NJ, USA) in RPMI (Lonza, Allendale, NJ) complete media (10% FBS, 2 mM L-glutamine, 0.05 mM β-mercaptoethanol).  Tissues were placed in a MACS C tube (Miltenyi Biotec, San Diego, CA) for desiccation on GentleMACS V1.02 for a pulse of 38 seconds. After a 10-minute incubation at 37°C, the digest buffer was removed and placed into 4°C RPMI complete media.  The process was repeated twice. Single-cell suspensions were centrifuged (2500 rpm, 10 min, 4°C) and resuspended in PBS for filtration through a 70-μm sterile cell strainer (Fisher, Pittsburgh, PA). After a wash with PBS, cells were resuspended again in PBS for lymphocyte isolation with Lympholyte-M cell separation media (Cedar Lane, Burlington, Canada) per the manufacturer's instructions. Single-cell suspensions were stained for DAPI, and live cells were sorted with a sorter (SH800S, Sony, San Jose, CA) into RPMI containing 10% FBS on ice for single-cell sequencing library preparation.
Samples were prepared using the Chromium Next GEM Single Cell V(D)J Kit v1.1, Mouse (10x Genomics, Pleasanton, CA) following the manufacturer's instructions. In brief, sorted single cells of the salivary glands for each sample were resuspended in RPMI containing 10% FBS to a final concentration of 700-1200 cells/µl. A total of 8 samples were loaded onto a Chromium Next GEM Chip G, analyzed by the Chromium Controller (10x Genomics, Pleasanton, CA) for Gel Beads-in-emulsion (GEMs) generation and reverse transcription. The generated cDNA was purified with SPRIselect (Beckman Coulter Inc, Indianapolis, IN) and used for 5′ gene expression library construction. The cDNAs and libraries were examined for quality control using D5000 ScreenTape (Agilent Technologies, Waldbronn, Germany), and Qubit (Thermo Fisher Scientific, Waltham, MA) was used for quantification. To achieve 20,000 reads per cell for 5ʹ gene expression libraries, the libraries were sequenced using Illumina NovaSeq6000 system (Illumina, San Diego, CA).

value: salivary gland

value: male

value: Lympholyte-M and FASC sorting live


title: contralateral_muralcells_sample12

description: Library name: CONTRA_12_P


title: SAMPLE_01_000003_W16_TL


title: SAMPLE_01_000002_W16_TL


title: SjD Susceptible mice male rep1


title: contralateral_muralcells_sample11

description: Library name: CONTRA_11_P


title: Smartseq2_158

value: D-LN


title: contralateral_muralcells_sample10

description: Library name: CONTRA_10_P


title: SAMPLE_01_000001_W16_TL


title: SjD Susceptible mice female rep2

value: female


title: contralateral_muralcells_sample9

description: Library name: CONTRA_9_P


title: SAMPLE_01_000016_W2_TL


title: SjD Susceptible mice female rep1


title: Smartseq2_157


title: Smartseq2_156


title: Smartseq2_155


title: SAMPLE_01_000015_W2_TL


title: contralateral_muralcells_sample8

description: Library name: CONTRA_8_P


title: B6 mice male rep2


title: contralateral_muralcells_sample7

description: Library name: CONTRA_7_P


title: Smartseq2_161


title: SAMPLE_01_000014_W2_TL


title: contralateral_muralcells_sample6

description: Library name: CONTRA_6_P


title: Smartseq2_154


title: B6 mice female rep2


title: Smartseq2_153


title: B6 mice female rep1


title: Smartseq2_152


title: contralateral_muralcells_sample4

description: Library name: CONTRA_4_P


title: contralateral_muralcells_sample5

description: Library name: CONTRA_5_P


title: SAMPLE_01_000011_W2_TL


title: Sample22_wells.R848+Rho.OVA.3

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

data_processing:
Bulk RNAseq analysis: On average we received 22 million paired ends for each of the replicates. RNAseq libraries were checked for their quality using the fastqc program http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. The results from fastqc were aggregated using multiqc software1. Reads were mapped with the “splice aware” aligner ‘STAR’,2 to the transcriptome and genome of mm10 genome build. The HTseq3 software will be used to count aligned reads that map onto each gene. The count table was imported to R to perform differential gene expression analysis using the DESeq2 package4. Low expressed genes (genes expressed only in a few replicates and had low counts) was excluded from the analysis before identifying differentially expressed genes. Data normalization, dispersion estimates, and model fitting (negative binomial) was carried out with the DESeq function. The log-transformed, normalized gene expression of 500 most variable genes will be used to perform an unsupervised principal component analysis. The differentially expressed genes was ranked based on the log2fold change and FDR corrected p-values. The ranked file was used to perform pathway analysis using GSEA software5.  The enriched pathways were selected based on enrichment scores as well as normalized enrichment scores. The Enrichment Analysis for Gene Ontology was performed by topGO. The heatmaps were generated using pheatmap function in R.
Assembly: Mus musculus GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: murine lymph node

growth_protocol: Lymph node slices for on-chip and well plate conditons were cultured in "complete RPMI" media consisting of RPMI, %10 fetal bovine serum (FBS),1x L-glutamine, 50 U/mL Pen/Strep, beta-mercaptoethanol, 1 mM sodium pyruvate, 20 mM HEPES, and 1x non-essential amino acids in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested from each sample using a RNeasy Plus Mini kit (Qiagen) following manufacturer's protocols. Prior to extraction, all samples were placed in RLT buffer and homogenized using a Model 150 VT Ultrasonic Homogenizer at 30% power for 7 pulses over 2 min, then vortexed at maximum speed for 1 min.
RNA samples were sent to NovoGene Co for sequencing, where a non-directional low-input eukaryotic mRNA library was prepared.

treatment_protocol: For in vivo vaccinations, male and female C57Bl/6 mice were vaccinated subcutaneously with four 50 µL injections per animal at the shoulders and hips. The vaccine consisted of 100 μg/mL R848 (InvivoGen) and 500 μg/mL rhodamine-labeled ovalbumin (Rho-OVA) in sterile 1x PBS, or PBS as a vehicle control. The skin-draining lymph nodes (axillary, brachial, and inguinal) were harvested 6 hrs later. For well plate and on-chip vaccination, LN slices were collected from naive animals and were either incubated with 0.2 μg/mL R848 and 2 μg/mL Rho-OVA or PBS loaded in 3% agarose for 6 hours, at which time the LN slices were collected.

value: murine lymph node

value: R848 and Rho-OVA was loaded in mock skin and placed in a well plate LN slice on-chip for 6 hrs (replicate 3)


title: Smartseq2_151


title: Sample21_wells.PBS.3

value: PBS was loaded in mock skin and placed in a well plate LN slice on-chip for 6 hrs (replicate 3)


title: SAMPLE_01_000010_W2_TL


title: contralateral_muralcells_sample2

description: Library name: CONTRA_2_P


title: Sample20_onChip.R848+Rho.OVA.3

value: R848 and Rho-OVA was loaded in mock skin and co-cultured with downstream LN slice on-chip for 6 hrs (replicate 3)


title: Smartseq2_149


title: B6 mice male rep1


title: SAMPLE_01_000009_W2_TL

value: skin


title: contralateral_muralcells_sample1

description: Library name: CONTRA_1_P


title: Sample19_onChip.PBS.3

value: PBS was loaded in mock skin and co-cultured with downstream LN slice on-chip for 6 hrs (replicate 3)


title: SAMPLE_01_000008_W2_TL


title: Smartseq2_147

value: OV


title: SAMPLE_01_000013_W2_TL


title: SAMPLE_01_000007_W2_TL


title: ipsilateral_Pdgfrb_fibroblasts_sample10

description: Library name: IPSI_10_F

value: sciatic nerve


title: SAMPLE_01_000012_W2_TL


title: Sample17_inVivo.PBS.3

value: PBS was injected subcut. in a mouse and LNs were collected after 6 hr (replicate 3)


title: Smartseq2_146


title: ipsilateral_Pdgfrb_fibroblasts_sample8

description: Library name: IPSI_8_F

value: ipsilateral nerve 5 days post PSNL


title: contralateral_muralcells_sample3

description: Library name: CONTRA_3_P


title: SAMPLE_01_000005_W2_TL

value: TL


title: Smartseq2_145

value: Filtered


title: Smartseq2_144


title: Sample15_wells.PBS.2

value: PBS was loaded in mock skin and placed in a well plate LN slice on-chip for 6 hrs (replicate 2)


title: Smartseq2_150


title: ipsilateral_Pdgfrb_fibroblasts_sample7

description: Library name: IPSI_7_F


title: SAMPLE_01_000004_W2_TL


title: Smartseq2_148


title: SAMPLE_01_000003_W2_TL


title: Sample13_onChip.PBS.2

value: PBS was loaded in mock skin and co-cultured with downstream LN slice on-chip for 6 hrs (replicate 2)


title: ipsilateral_Pdgfrb_fibroblasts_sample5

description: Library name: IPSI_5_F


title: ipsilateral_Pdgfrb_fibroblasts_sample11

description: Library name: IPSI_11_F


title: Sample14_onChip.R848+Rho.OVA.2

value: R848 and Rho-OVA was loaded in mock skin and co-cultured with downstream LN slice on-chip for 6 hrs (replicate 2)


title: Smartseq2_142

value: D-LN


title: Sample18_inVivo.R848+Rho.OVA.3

value: R848 and Rho-OVA was injected subcut. in a mouse and LNs were collected after 6 hr (replicate 3)


title: SAMPLE_01_000002_W2_TL


title: ipsilateral_Pdgfrb_fibroblasts_sample4

description: Library name: IPSI_4_F


title: Smartseq2_141


title: SAMPLE_01_000006_W2_TL


title: Sample16_wells.R848+Rho.OVA.2

value: murine lymph node

value: R848 and Rho-OVA was loaded in mock skin and placed in a well plate LN slice on-chip for 6 hrs (replicate 2)


title: Sample11_inVivo.PBS.2

value: PBS was injected subcut. in a mouse and LNs were collected after 6 hr (replicate 2)


title: Sample12_inVivo.R848+Rho.OVA.2

value: R848 and Rho-OVA was injected subcut. in a mouse and LNs were collected after 6 hr (replicate 2)


title: Smartseq2_140


title: SAMPLE_01_000001_W2_TL

value: skin


title: ipsilateral_Pdgfrb_fibroblasts_sample2

description: Library name: IPSI_2_F


title: SAMPLE_01_000016_W0_TL


title: Sample6_inVivo.R848+Rho.OVA.1

value: R848 and Rho-OVA was injected subcut. in a mouse and LNs were collected after 6 hr (replicate 1)


title: SAMPLE_01_000015_W0_TL


title: Smartseq2_139

value: OV


title: ipsilateral_Pdgfrb_fibroblasts_sample6

description: Library name: IPSI_6_F

value: sciatic nerve


title: ipsilateral_Pdgfrb_fibroblasts_sample1

description: Library name: IPSI_1_F


title: SAMPLE_01_000014_W0_TL


title: Smartseq2_143


title: Smartseq2_138


title: contralateral_Pdgfrb_fibroblasts_sample14

description: Library name: CONTRA_14_F

value: contralateral uninjured nerve


title: Sample4_wells.R848+Rho.OVA.1

value: R848 and Rho-OVA was loaded in mock skin and placed in a well plate LN slice on-chip for 6 hrs (replicate 1)


title: Smartseq2_137


title: SAMPLE_01_000013_W0_TL

value: TL


title: ipsilateral_Pdgfrb_fibroblasts_sample3

description: Library name: IPSI_3_F

value: ipsilateral nerve 5 days post PSNL


title: contralateral_Pdgfrb_fibroblasts_sample13

description: Library name: CONTRA_13_F


title: contralateral_Pdgfrb_fibroblasts_sample12

description: Library name: CONTRA_12_F


title: SAMPLE_01_000012_W0_TL


title: Sample2_onChip.R848+Rho.OVA.1

value: R848 and Rho-OVA was loaded in mock skin and co-cultured with downstream LN slice on-chip for 6 hrs (replicate 1)


title: Sample3_wells.PBS.1

value: PBS was loaded in mock skin and placed in a well plate LN slice on-chip for 6 hrs (replicate 1)


title: Smartseq2_135


title: contralateral_Pdgfrb_fibroblasts_sample11

description: Library name: CONTRA_11_F


title: SAMPLE_01_000011_W0_TL


title: Sample1_onChip.PBS.1

value: PBS was loaded in mock skin and co-cultured with downstream LN slice on-chip for 6 hrs (replicate 1)


title: SAMPLE_01_000010_W0_TL


title: MGJ2

city: Shijiazhuang

first: Siming

last: Jia

address: 河北省石家庄市河北医科大学第三医院

institute: 河北医科大学

description: 10x Genomics

data_processing:
Cellranger standard processing
**Cell filter** Seurat allows to easily explore QC metrics and filter cells, we can visualize gene and molecule counts, plot their relationship, and exclude cells with a clear outlier number of genes detected as potential multiplets. Followed criteria were used to filter cells: 1.gene counts 500-Inf per cell. 2.UMI counts 3. the percentage of mitochondrial genes < 25% %(customized). 4.DoubletFinder for detecting doublets.
**Cell clustering** Cell clustering contains the following steps: 1)Normalizing the data After removing unwanted cells from the dataset, the next step is to normalize the data. By default, we employ a global-scaling normalization method “LogNormalize” that normalizes the gene expression measurements for each cell by the total expression.
PCA(Principal component analysis): To overcome the extensive technical noise in any single gene for scRNA-seq data, Seurat clusters cells based on their PCA scores, with each PC essentially representing a ‘metagene’ that combines information across a correlated gene set.
t-SNE (t-distributed Stochastic Neighbor Embedding) visualization: Seurat continues to use t-SNE as a powerful tool to visualize and explore these datasets. The tSNE aims to place cells with similar local neighborhoods in high-dimensional space together in low-dimensional space.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Callus tissue

extract_protocol:
The callus was isolated from each mouse and dissociated into a single-cell suspension by enzyme digestion, single cells were suspended in calcium- and magnesium -free PBS containing 0.04% weight/volume BSA
Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp)

value: Callus tissue

value: wt mice

value: Femoral fracture model


title: Sample5_inVivo.PBS.1

value: murine lymph node

value: PBS was injected subcut. in a mouse and LNs were collected after 6 hr (replicate 1)


title: SAMPLE_01_000009_W0_TL


title: Smartseq2_134

value: D-LN


title: contralateral_Pdgfrb_fibroblasts_sample10

description: Library name: CONTRA_10_F


title: contralateral_Pdgfrb_fibroblasts_sample9

description: Library name: CONTRA_9_F


title: Smartseq2_133

value: Filtered


title: MGJ

address: 河北省石家庄市河北医科大学第三医院

description: 10x Genomics


title: SAMPLE_01_000008_W0_TL

value: skin


title: contralateral_Pdgfrb_fibroblasts_sample8

description: Library name: CONTRA_8_F


title: xenograft mouse, sgGATA6, rep5

city: Chicago

first: Feng

last: Yue

state: IL

address: 303 E Superior St

department: Biochemistry and Molecular Genetics

institute: Northwestern university

data_processing:
Illunuma BaseSpace CLItools v.1.0.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore v.0.6.10
Trimmed sequence reads were mapped to hg38 using STAR.
The TPM value of gene expression was caculated using RSEM.
Assembly: Hg38
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 TPM values for each Sample

source_name: xenograft mouse

growth_protocol: DLD-1 cells(ATCC ) was gifted by Dr. Ali Shilatifard Lab.DLD-1 cells were cultured in RPMI1640 Medium (Gibco, 11875093) supplemented with 10% fetal bovine serum (ThermoFisher, 12440053) and 1% penicillin–streptomycin.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II directional with Poly-A Selection Kit.

treatment_protocol:
GATA6 protein degradation was induced by treating positive GATA6-IAA7 clones with DLD-1 complete medium supplemented with 500uM IAA (sigma, I5148) for various timepoints.
For IAA washout, we removed IAA 12 hours after IAA treatment. Cells were first washed with 1x DPBS three times and then maintained in DLD-1 complete medium for 24 or 48 hours.
For mouse xenograft, ten 5-6 weeks old athymic nude mice were used for each condition. 1M DLD-1 control or GATA6-KO cells were injected into the right flank of nude mice. Daily measurement of tumor size started 4 days after inoculation. All procedures were performed in accordance with the Institutional Animal Care and Use Committee (IACUC) at Northwestern university

value: xenograft mouse

value: colorectal adenocarcinoma

value: GATA6 CRISPR KO


title: Smartseq2_132

value: OV


title: SAMPLE_01_000007_W0_TL

value: TL


title: Smartseq2_131


title: Smartseq2_130


title: Smartseq2_136


title: xenograft mouse, sgGATA6, rep4


title: contralateral_Pdgfrb_fibroblasts_sample7

description: Library name: CONTRA_7_F

value: sciatic nerve

value: contralateral uninjured nerve


title: SAMPLE_01_000006_W0_TL


title: contralateral_Pdgfrb_fibroblasts_sample6

description: Library name: CONTRA_6_F


title: Smartseq2_129


title: contralateral_Pdgfrb_fibroblasts_sample5

description: Library name: CONTRA_5_F


title: xenograft mouse, sgGATA6, rep2


title: Smartseq2_128


title: SAMPLE_01_000004_W0_TL


title: SAMPLE_01_000003_W0_TL


title: contralateral_Pdgfrb_fibroblasts_sample3

description: Library name: CONTRA_3_F


title: contralateral_Pdgfrb_fibroblasts_sample4

description: Library name: CONTRA_4_F


title: Smartseq2_127


title: xenograft mouse, sgGATA6, rep3


title: xenograft mouse, ctrl, rep5

value: WT


title: Smartseq2_126


title: xenograft mouse, sgGATA6, rep1


title: SAMPLE_01_000002_W0_TL


title: xenograft mouse, ctrl, rep4


title: SAMPLE_01_000001_W0_TL


title: SAMPLE_01_000015_W0_NL

value: NL


title: Smartseq2_124


title: contralateral_Pdgfrb_fibroblasts_sample2

description: Library name: CONTRA_2_F


title: Mouse mesenchyme, 2 months post nerve injury, batch 2

description:
Library name: SNL_chronic_2
10X Genomics

data_processing:
The resulting fastq files were aligned to mouse (Mus_musculus.GRCm38) in Google Colabs using kb-bustools (Melsted et al., 2021), with kallisto version 0.46.2 and bustools version 0.40.0. Count matrices were then imported into R and further analysed in Seurat (version 4.3). The R script used to generate the figures in this manuscript is available as a Supplementary File provided with the original publication.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: kb bustools unfiltered counts & Seurat object

source_name: Sciatic Nerve

extract_protocol:
At acute (4-6 days after partial sciatic nerve ligation, PSNL) and chronic (2 months after PSNL) timepoints, C57BL/6J wild-type mice were transcardially perfused with phosphate buffered saline, after which ipsilateral sciatic nerves were dissected and trimmed in F12 solution (Gibco, New York, NY, Cat# 21765-029) to either a 0.5 cm piece (for scRNA-seq and flow data in Figure 5A) or a 1 cm piece around the lesion site (all other experiments). In either case, the distal and proximal pieces were kept at the same length (0.25 or 0.5 cm each). The suture was removed at this point, if still present. A single cell solution was generated as described previously (Liang et al., 2020), after which cells were stained with the nuclear marker DRAQ5, the live-dead stain DAPI, PercCP-Cy5-5-conjugated myelin beads, BUV737-CD45 to stain immune cells and BV786-Ter119 to stain erythrocyte precursors. DRAQ5+DAPI-,Myelin-,CD45-,Ter119- singlets were sorted into 1.5ml tubes, pre-coated with FBS, containing 3 µl of 3% BSA in PBS buffer.
Library preparation (Chromium 10X  single cell 3’ version 3)  proceeded following manufacturer's instructions and was carried out by specialists in the NIHR Maudsley Biomedical Research Centre (BRC) Genomics & Biomarker Core Facility at King’s College London. Sequencing was performed on an Illumina NextSeq system.

treatment_protocol: Experiments were conducted in 2 batches. In the first batch, we processed n = 4 injured and n = 4 sham nerves (50% male/female), collected them two months after surgery and pooled them into two 10X wells (injury vs. sham) in the same FACS, library preparation and sequencing run. In the second batch, we processed n = 4 sham and n = 4 injured nerves each, at two different timepoints: 5 days and 2 months after surgery. 50% of samples were male, 50% female; they were run on the same day and the same 10X chip, pooled by group across 4 wells (sham-day5, PSNL-day5, sham-month2, PSNL-month2). Library preparation and sequencing proceeded at the same time.

value: Sciatic Nerve

value: PSNL surgery

tag: batch


title: contralateral_Pdgfrb_fibroblasts_sample1

description: Library name: CONTRA_1_F


title: SAMPLE_01_000005_W0_TL


title: Mouse mesenchyme, 2 months post sham surgery, batch 2

description:
Library name: SHAM_chronic_2
10X Genomics

value: sham surgery


title: Smartseq2_123


title: SAMPLE_01_000014_W0_NL


title: xenograft mouse, ctrl, rep1


title: SAMPLE_01_000013_W0_NL


title: Smartseq2_122


title: Mouse mesenchyme, 5 days post SNL surgery, batch 2

description:
Library name: SNL_acute
10X Genomics


title: WAT, KO, rep3

city: Suita

first: Yosuke

last: Okuno

address: 2-2, Yamadaoka

country: Japan

institute: Osaka University Graduate School of Medicine

data_processing:
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat ver. 2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19. The number of FPKMs was calculated using Cuffnorm ver. 2.2.1.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts and FPKM values for each sample

source_name: adipose tissue

extract_protocol:
Total RNA was extracted from tissues using TRI Reagent and RNeasy kit
Library preparation was performed using a TruSeq stranded mRNA sample prep kit.

value: adipose tissue

value: adipocyte-specific Armc5 KO


title: Smartseq2_121

value: D-LN


title: SAMPLE_01_000012_W0_NL

source_name: skin


title: Smartseq2_125


title: WAT, flox, rep3

value: control


title: xenograft mouse, ctrl, rep3


title: Mouse mesenchyme, 2 months post nerve injury, batch 1

description:
Library name: SNL_chronic_1
10X Genomics


title: WAT, flox, rep2


title: SAMPLE_01_000010_W0_NL

value: skin


title: Smartseq2_119


title: Smartseq2_118


title: WAT, KO, rep2


title: SAMPLE_01_000009_W0_NL


title: xenograft mouse, ctrl, rep2

value: xenograft mouse


title: WAT, KO, rep1


title: SAMPLE_01_000011_W0_NL


title: Smartseq2_120


title: Smartseq2_117

value: Filtered


title: WAT, flox, rep1


title: mRNA of RES WT mouse TE cells, replicate 5

city: Rehovot

first: Amir

last: Szitenberg

address: 234 Herzl St

department: INCPM

country: Israel

institute: Weizmann Institute

data_processing:
Quality and adaptor trimming with cutadapt
Read mapping with STAR
Read counting and UMI counting with HTSeq
Assembly: GRCm39
Supplementary files format and content: TSV matrix raw counts
Supplementary files format and content: TSV matrix umi corrected counts

source_name: T-cells

extract_protocol:
Qiagen RNAeasy minikit according to the manufacturer's protocol
INCPM Bulk-MARSSeq: RNA-seq libraries were prepared at the Crown Genomics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science. A bulk adaptation of the MARS-Seq protocol (Jaitin et al., Science, 2014; Keren-Shaul et al., Nature Protocols, 2019) was used to generate RNA-Seq libraries for expression profiling of XXX. Briefly, (30 ng of input) RNA from each sample was barcoded during reverse transcription and pooled. Following Agencourct Ampure XP beads cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.  Libraries were quantified by Qubit and TapeStation as well as by qPCR  as previously described (Jaitin et al., Science, 2014; Keren-Shaul et al., Nature Protocols, 2019).
Poly-A and 3' UTR targeting

value: T-cells

value: TE

value: Immune cells

value: RES


title: SAMPLE_01_000007_W0_NL


title: Mouse mesenchyme, 5 days post sham surgery, batch 2

description:
Library name: SHAM_acute
10X Genomics


title: mRNA of RES WT mouse TE cells, replicate 4


title: SAMPLE_01_000008_W0_NL


title: Smartseq2_116

value: OV


title: mRNA of RES WT mouse TE cells, replicate 6

value: WT


title: Highfatdiet_STZ_XMUMP1_3

first: Bin

last: LI

address: 58th Zhongshan Road II

department: Department of Nephrology, The First Affiliated Hospital

description: High-fat diet, streptozotocin and XMU-MP-1

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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: Renal cortex

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).
The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. 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. At last, 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.

value: Renal cortex


title: mRNA of RES WT mouse TE cells, replicate 3


title: Smartseq2_115

source_name: D-LN


title: Smartseq2_114


title: Highfatdiet_STZ_XMUMP1_2

value: High-fat diet, streptozotocin and XMU-MP-1


title: SAMPLE_01_000005_W0_NL

data_processing:
Illumina standard primers were trimmed using trim_galore (version 0.6.6)
Reads were mapped to the human reference genome (GRCh38, Ensembl release 103) using hisat2 (version 2.2.1)
Mapped reads were cleaned and sorted using samtools (version 1.11)
Number of reads for each gene was counted using rsubread (version 2.2.6)
Assembly: GRCh38, Ensembl release 103
Supplementary files format and content: Comma-separated text file including raw counts of sequencing reads for each gene and sample

extract_protocol:
Total RNA was isolated using the mirVanaTM miRNA Isolation Kit (Lifetechnologies, Carlsbad,CA)
RNA samples were prepared for sequencing using the Illumina stranded mRNA protocol and sequenced on the NovaSeq6000 with 2x100bp

value: NL


title: mRNA of RES WT mouse TE cells, replicate 2


title: mRNA of RES WT mouse TE cells, replicate 1


title: Highfatdiet_STZ_XMUMP1_1


title: Mouse mesenchyme, 2 months post sham surgery, batch 1

description:
Library name: SHAM_chronic_1
10X Genomics

value: Sciatic Nerve

value: sham surgery


title: Highfatdiet_STZ_Vehicle_3

description: High-fat diet and streptozotocin

value: High-fat diet and streptozotocin


title: Smartseq2_113

value: D-LN


title: Highfatdiet_STZ_Vehicle_2

description: High-fat diet and streptozotocin


title: Smartseq2_112


title: mRNA of ACT WT mouse TE cells, replicate 5

value: ACT


title: Smartseq2_111


title: Highfatdiet_STZ_Vehicle_1

description: High-fat diet and streptozotocin


title: mRNA of ACT WT mouse TE cells, replicate 6


title: SAMPLE_01_000002_W0_NL

value: skin


title: mRNA of ACT WT mouse TE cells, replicate 4


title: SAMPLE_01_000001_W0_NL


title: mRNA of ACT WT mouse TE cells, replicate 3


title: Smartseq2_109


title: Normaldiet_Citratebuffer_XMUMP1_3

description: Normal diet and XMU-MP-1

value: Normal diet and XMU-MP-1


title: Smartseq2_108


title: SAMPLE_01_000003_W0_NL


title: SAMPLE_01_000006_W0_NL


title: T_02

first: Hexia

state: --- Select One ---

address: No.419 Fangxie Rd. Shanghai

institute: Obstetrics and Gynecology Hospital of Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: ovarian teratoma with NMDAR-E

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer. RNA integrity was assessed using the Agilent 2100 Bioanalyzer.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: ovarian teratoma with NMDAR-E

value: female


title: Normaldiet_Citratebuffer_XMUMP1_1

description: Normal diet and XMU-MP-1


title: Smartseq2_107


title: SAMPLE_01_000004_W0_NL

first: Rashmi


title: T_01


title: mRNA of ACT WT mouse TE cells, replicate 2

value: T-cells

value: TE


title: Smartseq2_106


title: mRNA of ACT WT mouse TE cells, replicate 1

value: Immune cells


title: Smartseq2_110

value: OV


title: mRNA of RES NZB mouse TE cells, replicate 6

value: NZB

value: RES


title: C_04

source_name: ovarian teratoma without NMDAR-E

value: ovarian teratoma without NMDAR-E

value: operation


title: Normaldiet_Citratebuffer_Vehicle_2

description: Normal diet

value: Renal cortex

value: WT

value: Normal diet


title: T_03

value: hormone therapy+operation


title: Normaldiet_Citratebuffer_Vehicle_3

description: Normal diet


title: mRNA of RES NZB mouse TE cells, replicate 5


title: Normaldiet_Citratebuffer_XMUMP1_2

description: Normal diet and XMU-MP-1


title: C_02


title: mRNA of RES NZB mouse TE cells, replicate 4


title: Smartseq2_105

value: D-LN


title: Smartseq2_104


title: C_03


title: Normaldiet_Citratebuffer_Vehicle_1

description: Normal diet


title: Z8-3

first: Hanling

last: Wang

address: Shanghai

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Science

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19

source_name: prostate

extract_protocol:
LNCaP partially ZMYND8-OE were cutured with CSS for indicated times
The scRNA-seq libraries were generated using the 10´ Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits (10X Genomics, Pleasanton, CA) according to the manufacturer’s recommendations. The experiments were performed by NovelBio Bio-Pharm Technology Co., Ltd.

value: prostate cells

value: prostate

value: WT & ZMYND8-OE

tag: time point


title: Smartseq2_103

data_processing:
SmartSeq2 Analysis: Fastq files from SmartSeq2 libraries were aligned to the mouse genome (mm39) with Gencode M29 annotations using STAR (v2.7.10a). Genome-mapped BAM files were quantified with RSEM (v1.3.1), and the resulting gene/UMI count matrix was processed in Seurat (v4.1.2). Data were normalized using the LogNormalize method, with mitochondrial gene expression and library size bias regressed out via the ScaleData function. Cells with >5% mitochondrial reads were excluded. Clustering, differential expression, and gene signature scoring were performed in Seurat. Differentially expressed genes were identified using the Wilcoxon Rank Sum test, with Bonferroni-adjusted P-values < 0.05 and log2 fold changes > 0.5 considered significant.
Bulk RNA-Seq raw Fastq files were aligned to the mouse genome (mm39) with Gencode M29 annotations using STAR (v2.7.10a). The count matrix was processed in R with the DESeq2 package (v1.34). Genes with fewer than ten reads were filtered out, and sample normalization was applied using a negative binomial distribution model. Differential gene expression between conditions was assessed with the Wald test. Genes with adjusted P-values (FDR) < 0.1 were retained, and log2 fold changes were shrunk using the apeglm algorithm.
10x Genomics Analysis: Fastq files from cDNA and hashtag libraries generated on the Chromium platform (10x Genomics) were processed using Cell Ranger (v7.0.1). The resulting quantification matrix was processed in Seurat (v5.0) with normalization using the SCTransform function. Non-myeloid cell contaminants were removed based on the PanglaoDB_Augmented_2021 database and EnrichR package for R. Cells were classified by biological condition using the HTODemux function. Differentially expressed genes were identified with the Wilcoxon rank test, with Bonferroni-adjusted P-values < 0.05 and log2 fold changes > 0.3 considered significant. Signature scores were calculated using Seurat’s AddModuleScore function.
Assembly: mm10
Supplementary files format and content: Tab files from bulk RNA-Seq tab files containing the STAR gene quantification.
Supplementary files format and content: gene.results from RSEM quantification of Smartseq2 data
Supplementary files format and content: mtx, cellranger output from 10x genomics libraries.
Supplementary files format and content: rds, images of Seurat objects used in the analysis

extract_protocol:
Lymph nodes and gut tissue were dissected, finely chopped, and digested in RPMI medium with Collagenase D to obtain single-cell suspensions. For gut-associated lymph nodes, duodenal lymph nodes were identified using anatomical markers. Dendritic cells were isolated from the duodenal lamina propria by separating intestines, removing mucus with PBS and DTT, and stripping epithelium with EDTA. The tissue was further digested with DNaseI and collagenase, followed by Percoll gradient centrifugation to isolate DCs. Single-cell sorting of DCs was conducted into 96-well plates with TCL buffer and stored at –80°C.
Library Preparation for Single-cell RNA-seq (SmartSeq2). Single cells were sorted onto plates, covering all conditions in each replicate. RNA was extracted using RNAClean XP SPRI beads, then reverse-transcribed into cDNA with RT and TSO primers. The cDNA was amplified, cleaned with SPRI beads, and tagmented using the Nextera XT DNA Library Preparation Kit (Illumina). Barcoded libraries were pooled and sequenced on the Illumina Nextseq 550 platform. Library Preparation for Single-cell RNA-Seq (10x Genomics). Cells were labeled with hashtag oligonucleotide (HTO)-tagged antibodies, sorted, and counted for viability. scRNA-seq libraries were generated using the 10x Genomics Chromium system, following the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq SP flowcell at a minimum depth of 30,000 reads per cell. Library Preparation for Bulk RNA-seq. RNA was isolated using RNAClean XP beads. Reverse transcription was performed with specific primers, followed by cDNA amplification with KAPA HiFi HS Ready Mix. The amplified product was cleaned with RNAClean XP beads and tagmented using the Nextera XT DNA Library Preparation Kit (Illumina). Libraries were pooled and sequenced as 75-base single-end reads on an Illumina NextSeq platform.


title: C_01

value: female


title: mRNA of RES NZB mouse TE cells, replicate 2

value: T-cells


title: mRNA of RES NZB mouse TE cells, replicate 3

value: TE


title: Z8-2

description: 10x Genomics


title: Smartseq2_102


title: AR

library_source: genomic

data_processing:
Paired-end fastq files were trimmed and uniquely aligned to the hg19 human genome assembly using BWA.
After alignment, reads mapped to the same genomic positions were filtered by PICARD-MarkDuplicates (Galaxy Version 2.18.2.2)
Bam coverage was used to transform the BAM alignment files to their representative BigWig files.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
Assembly: hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: LNCap cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Purified DNA was prepared for sequencing as per the manufacturer’s instructions (Illumina). Libraries were quantified and sequenced on the Illumina NovaSeq 6000 Sequencer.

value: LNCap cell line

value: epithelial

value: EV

tag: chip antibody


title: CKO3

address: 河北省石家庄市河北医科大学第三医院

description: 10x Genomics

value: Callus tissue

value: Col2CreERT; Piezo3-/-

value: Femoral fracture model


title: Smartseq2_101

value: Filtered


title: Z8-1

description: 10x Genomics


title: mRNA of RES NZB mouse TE cells, replicate 1

value: Immune cells

value: NZB

value: RES


title: Smartseq2_100

value: D-LN

value: OV


title: mRNA of ACT NZB mouse TE cells, replicate 6

value: ACT


title: mRNA of ACT NZB mouse TE cells, replicate 5


title: Human PBMCs from AILD AIH patients, TCR Sample  4

city: Nantes

first: Christine

last: Chauveau

address: 30 Boulevard Jean Monnet

country: France

institute: CR2TI UMR 1064

description:
V(d)J RNA sequence TCR
Sample 4 : TCR library: read1 file contains cell barcode and UMI; read2 file contains V(d)J reads
AmR053_harmony_azimuth_V4regRB.rds

library_source: other

data_processing:
CellRanger v7.0.1 multi function to process RNA across sequencing lanes into a single set of  barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz as well as identify the V(d)J sequences from the TCR library.
The two data sets from cellranger, RNA and TCR have been processed with a custom script using Seurat 4.1, harmony 1.1.0 and azimut 0.4.5 as main packges, full script at : https://gitlab.univ-nantes.fr/braud-m-3/amr053-scrnaseq-tcr.git
Assembly: GrCH38
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv
Supplementary files format and content: Seurat Analysis output : AmR053_harmony_azimuth_V4regRB.rds
Library strategy: CITE-seq VdJ Immunoprofiling

molecule: other

source_name: blood

extract_protocol:
Cells were counted, centrifuged (500g, 5 min, 4°c) then resuspended at the recommended dilution for a 20000 cell loading per sample onto a Next GEM Chip K (PN-1000286) and run on a Chromium Single Cell Controller using the Chromium Single Cell 5′ V2 Next GEM single cell kit (PN-1000263) according to the manufacturer's instructions. Gex and VDJ-TCR libraries were then prepared (PN-1000190, PN-1000252, PN-1000215 also from 10X genomics)
The cell hashing protocol described by Stoeckius et al  (Stoeckius et al.,2017)  was used to generate a hashtag oligo (HTO) library, adapted with a 5’v2 immune profiling protocol with TCR. https://citeseq.files.wordpress.com/2019/02/cite-seq_and_hashing_protocol_190213.pdf

treatment_protocol: After PBMCs extraction and staining, PD-1+CD45RA-CXCR5- CD4 T cells were sorted on BD FACSAriaII.

value: blood

value: pbmc

value: no treatment

tag: library type

value: TCR


title: Human PBMCs from AILD AIH patients, GEX Sample 4

description:
polyA RNA
Sample 4 : GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
AmR053_harmony_azimuth_V4regRB.rds

tag: tissue

value: mRNA


title: CKO1

address: 河北省石家庄市河北医科大学第三医院

description: 10x Genomics


title: Smartseq2_99

first: Tiago


title: CKO2

address: 河北省石家庄市河北医科大学第三医院

description: 10x Genomics


title: mRNA of ACT NZB mouse TE cells, replicate 4

value: T-cells

value: TE


title: Human PBMCs from AILD AIH patients, TCR Sample 3

description:
V(d)J RNA sequence TCR
Sample 3 : TCR library: read1 file contains cell barcode and UMI; read2 file contains V(d)J reads
AmR053_harmony_azimuth_V4regRB.rds


title: Smartseq2_98


title: CON 3

address: 河北省石家庄市河北医科大学第三医院

description: 10x Genomics

value: Callus tissue

value: wt


title: Smartseq2_97


title: Human PBMCs from AILD AIH patients, TCR Sample 2

description:
V(d)J RNA sequence TCR
Sample 2 : TCR library: read1 file contains cell barcode and UMI; read2 file contains V(d)J reads
AmR053_harmony_azimuth_V4regRB.rds


title: Human PBMCs from AILD AIH patients, GEX Sample 3

description:
polyA RNA
Sample 3 : GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
AmR053_harmony_azimuth_V4regRB.rds


title: mRNA of ACT NZB mouse TE cells, replicate 3


title: P63+ Lung progenitors_P0

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

data_processing:
The resulting sequencing libraries were loaded onto an Illumina NovaSeq with 2 × 150 paired-end kits at Novogene China. The raw sequencing reads were processed using the Cell Ranger v.3.1.0 pipeline from 10× Genomics. This involved demultiplexing the reads, aligning them to the human GRCh38 genome, and quantifying UMI counts per gene per cell to generate a gene-barcode matrix. The data from different samples were aggregated and normalized to the same sequencing depth, resulting in a combined gene-barcode matrix.
Assembly: GRCh38-1.2.0
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz

source_name: Lung

extract_protocol:
The cell suspension was loaded into Chromium microfluidic chips with 3’ v3 chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed.
Sequencing libraries were constructed with reagents from a Chromium Single Cell 3’ v3 reagent kit (10X Genomics) according to the manufacturer’s instructions.

value: Lung

value: P63+ lung progenitor cells

value: lung progenitor cells

tag: patient diagnosis

value: IPF


title: Smartseq2_96

value: Filtered


title: mRNA of ACT NZB mouse TE cells, replicate 2

value: Immune cells

value: NZB


title: CON 2

address: 河北省石家庄市河北医科大学第三医院

description: 10x Genomics

value: Femoral fracture model


title: Smartseq2_95

value: D-LN

value: OV


title: KO mus hepatocytes, AAV control, rep2

city: Nan jing

first: jing

last: ye

address: Jiangsu Province Nanjing,Qixia District, Xianlin Road No.163

institute: Nanjing University

description:
KO3
AAV_KO_FPKM.txt

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation
System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s
instructions. After cluster generation, the library preparations were sequenced on an Illumina
Novaseq platform and 150 bp paired-end reads were generated.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts and FPKMs for each sample

source_name: liver

extract_protocol:
Cells were calculated and RNA samples were extracted from 1 × 10^6 HepaRG cells and mus hepatocytes using trizol. cDNA libraries were prepared using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
cDNA libraries were prepared using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions

value: liver

value: hepatocyte

value: KO

value: AAV control


title: Human PBMCs from AILD AIH patients, TCR Sample 1

description:
V(d)J RNA sequence TCR
Sample 1 : TCR library: read1 file contains cell barcode and UMI; read2 file contains V(d)J reads
AmR053_harmony_azimuth_V4regRB.rds

value: blood

value: pbmc

value: no treatment

value: TCR


title: CON 1

address: 河北省石家庄市河北医科大学第三医院

description: 10x Genomics

value: Callus tissue

value: wt


title: Human PBMCs from AILD AIH patients, GEX Sample 1

description:
polyA RNA
Sample 1 : GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
AmR053_harmony_azimuth_V4regRB.rds

value: mRNA


title: KO mus hepatocytes, AAV control, rep3

description:
KO4
AAV_KO_FPKM.txt


title: Smartseq2_94

last: Castro

address: 1230 York Avenue

institute: The Rockefeller University


title: Smartseq2_92


title: CD4+ Foxp3 eGFP+ mTO-iTreg cell, rep1

first: Sonia

last: Aristin Revilla

state: Utrecht

address: Heidelberglaan 100

department: CMM

institute: UMC Utrecht

data_processing:
The mapping process and the generation of count tables were executed using the MapAndGo script available at https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo. Counts were normalized for sequencing depth and RNA composition, using DESeq2's median of ratios method
RNA sequencing data were further analyzed using DESeq2 within the R2: Genomics Analysis and Visualization Platform (http://r2.amc.nl).
Assembly: Sequencing reads were aligned to the mm10 mouse transcriptome (RefSeq: NM_016701.3) employing the Burrows-Wheeler Alignment (BWA) tool (Li et al 2010).
Supplementary files format and content: All samples are normalized together in a text file (.txt): "DESeqNormData - Total - GEO.txt"

source_name: T cells

growth_protocol: Murine CRC tumor-organoids are cultured in BME dropplets overlaid with medium and incubate at 37oC with 5% CO2. The medium consisted of DMEM/F12 medium supplemented with 10 mM N’-2-Hydroxyethylpiperazine-N’-2 ethanesulphonic acid (HEPES, Lonza), 2 mM Glutamax (Gibco), 50 U/ml penicillin-streptomycin (Gibco), 100 ng/ml Noggin conditioned medium (produced by lentiviral transfection), 1 mM N-acetylcysteine (Sigma), 2% B27 serum free supplement (Gibco) and 10 nM murine recombinant fibroblast growing factor (PeproTech)

extract_protocol:
Cells were lysed in 100 µl TRIzol (Invitrogen) and stored at -80°C before shipping them on dry ice to Single Cell Discoveries B.V. (Utrecht, The Netherlands). RNA extraction was performed using the standard protocol.
Bulk-cell RNA sequencing was conducted using a modified CELSeq protocol (Hashimshony et al 2012;Simmini et al 2014).

treatment_protocol: When co-cultures were established, the media was supplemented with soluble IL-2 (20 U/ml, PeproTech) and functional grade anti-CD3 (aCD3, 1 µg/mL) and anti-CD28 (aCD28, 1 µg/mL) murine monoclonal antibodies (Invitrogen). For the control of TGFβ-iTreg cells, the media was supplemented with 10 ng/ml recombinant TGFβ (R&B systems), soluble IL-2 (300 U/ml, PeproTech) and functional grade anti-CD3 (aCD3, 1 µg/mL) and anti-CD28 (aCD28, 1 µg/mL) murine monoclonal antibodies (Invitrogen).

value: B6.Cg-Foxp3tm2(EGFP)Tch/J, The Jackson Laboratory, stock no. 006772

value: T cells

value: Hemizygous for Foxp3<tm2Tch>

value: day 5

value: Co-cultured with CRC tumor-organoids, aCD3/aCD28, IL-2


title: CD4+ Foxp3 eGFP+ mTO-iTreg cell, rep3


title: KO mus hepatocytes, AAV human HSD17B13, rep3

description:
AAV3
AAV_KO_FPKM.txt

value: AAV human HSD17B13


title: KO mus hepatocytes, AAV control, rep1

description:
KO2
AAV_KO_FPKM.txt

value: liver


title: CD4+ Foxp3 eGFP+ mTO-iTreg cell, rep2


title: Smartseq2_91

value: D-LN

value: Filtered


title: Human PBMCs from AILD AIH patients, GEX Sample 2

description:
polyA RNA
Sample 2 : GEX (3' mRNA) library: read1 file contains cell barcode and UMI; read2 file contains transcript
AmR053_harmony_azimuth_V4regRB.rds


title: HCT116, SY5609, Input

city: Boulder

first: Olivia

last: Luyties

state: CO

address: 3415 Colorado Ave, JSC Biotech Building

department: Biochemistry

institute: University of Colorado Boulder

data_processing:
All samples were sequenced on a NovaSeq 6000 by the Gates Institute Genomics Core at CU Anschutz. Sequencing was done in two runs to achieve greater depth, and resulting fastq files from each run were concatenated and repaired with the bbmap repair function.
Initial sample processing and quality control was performed using the Dowell Lab ChIP-Flow pipeline (https://github.com/Dowell-Lab/ChIP-Flow).
Adapters were trimmed and reads were mapped to the GRCh38 reference genome (UCSC Assembly, December 2013) using hisat2 and bbmap.
Duplicate, multimapping, and non-mapping reads were removed via sambamba. Indices for bams containing only uniquely mapped reads were generated using samtools 1.18.0. Data was then normalized to 1x read coverage via the DeepTools bamCoverage package.
Assembly: hg38
Supplementary files format and content: bigWigs

growth_protocol: HCT116 cells (ATCC# CCL-247) were grown to 70-90% confluency in McCoy’s 5A medium and supplemented with 10% Fetal Bovine Serum and 1% Penicillin/Streptomycin antibiotic at 37°C and 5% CO2.

extract_protocol:
Cells were crosslinked with a final concentration of 1% methanol-free formaldehyde for ten minutes while shaking at 145 RPM on an orbital shaker. Cells were quenched with 2.5 M Glycine to a final concentration of 125 mM for 8-10 minutes. Cells were harvested, washed with ice cold PBS (no calcium, no magnesium), and incubated in NRO buffer at a concentration of 80 μL/1 million cells for five minutes twice. Nuclei were pelleted, frozen in liquid nitrogen, and stored at -76°C for future use. Nuclei were thawed on ice for 1.5-3 hours. Once pellets thawed, nuclei were resuspended in 1 mL Covaris Lysis Buffer B + 1x Protease Inhibitors and incubated for 10 minutes at 4°C with nutation. Nuclei were then washed with 1 mL Covaris Wash Buffer C + 1x Protease Inhibitors and incubated for 10 minutes at 4°C with nutation. Nuclei were washed with 500 μL Shearing Buffer D3 + 1x Protease Inhibitors and resuspended in 1 mL of the same solution per ~20 million cells. Nuclei were then aliquoted into AFA millitubes (1 mL/tube) and sheared on the Covaris M220 Focused Ultrasonicator for 12 minutes at 6°C, duty factor 10%, peak power 75, 200 cycles/burst. Sheared chromatin was divided into 750-780 μL aliquots (~15 million cells/aliquot) into pre-chilled Eppendorf tubes, frozen in liquid nitrogen, and stored at -76°C for future use if not immediately proceeding to the IP step. If needed, sheared chromatin was thawed on ice for 2-3 hours.
Libraries were prepared using the KAPA Hyperprep Kit. 1 ng of total DNA from each sample was diluted in 50 μL 0.1x TE buffer and subjected to end repair and A-tailing. Following ligation, a 0.8x bead cleanup was performed, and the libraries were amplified 14 cycles.

treatment_protocol: Cells treated with SY-5609 received a final concentration of 50 nM. Working concentrations of all inhibitors were created to ensure an equal volume of drug was applied to all conditions except those treated with both inhibitors. Control cells received an equivalent volume of DMSO. Cells were incubated with either inhibitor or DMSO for 30 minutes at 37°C and 5% CO2, at which point IFNγ was added to the same media to a final concentration of 10 ng/mL. Cells were incubated with interferon for 45 minutes at 37°C and 5% CO2.

value: human colorectal cancer

value: 10ng/mL IFN, 50nM SY-5609


title: HCT116, SY5609, RNAPII, ChIP


title: Smartseq2_93

value: OV


title: KO mus hepatocytes, AAV human HSD17B13, rep2

description:
AAV2
AAV_KO_FPKM.txt

value: hepatocyte

value: KO


title: CD4+ Foxp3 eGFP+ TGFβ-iTreg cells, rep3

city: Utrecht

value: TGFbeta,aCD3/aCD28, IL-2


title: CD4+ Foxp3 eGFP+ TGFβ-iTreg cells, rep2


title: Smartseq2_90


title: mRNA of ACT NZB mouse TE cells, replicate 1

value: T-cells

value: TE

value: Immune cells

value: NZB

value: ACT


title: KO mus hepatocytes, AAV human HSD17B13, rep1

description:
AAV1
AAV_KO_FPKM.txt


title: HCT116, IFN, Input

value: 10ng/mL IFN


title: Smartseq2_89


title: CD4+ Foxp3 eGFP+ TGFβ-iTreg cells, rep1

value: B6.Cg-Foxp3tm2(EGFP)Tch/J, The Jackson Laboratory, stock no. 006772

value: T cells

value: Hemizygous for Foxp3<tm2Tch>

value: day 5


title: HCT116, IFN, RNAPII NTD, ChIP


title: HCT116, SY5609, pSer7, ChIP

value: Millipore-Sigma (#04-1570-I)


title: Smartseq2_88

value: D-LN


title: P12 neonatal Tra2b-cPEko, rep D

city: Newcastle upon Tyne

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

data_processing:
reads were mapped to mm39 using HISAT2 version 2.2.1
SAM output was converted to BAM with samtools version 1.7.1
sample level counts (*tsv) were made with htseq-count from HTSeq version 2.0.2  with annotation GCF_000001635.27_GRCm39_genomic.gtf from NCBI
bigwig (*bw) files were made with bamCoverage from DeepTools version 3.5.1
Assembly: mm39
Supplementary files format and content: tsv (tab-delimited text) containing sample level counts
Supplementary files format and content: bw: Bigwig format containing coverage tracks for visualisation in UCSC Genome Browser

source_name: testis

extract_protocol:
Total RNA was extracted from isolated testes using ReliaPrep RNA Tissue Miniprep System (Promega Z6111).
Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: testis

value: mixed

value: conditional knockout of Tra2b poison exon

value: whole testis RNAseq


title: HCT116, IFN, pSer7, ChIP

value: human colorectal cancer


title: Foxp3 eGFP- CD4+ T cells, rep3

value: day 0


title: Foxp3 eGFP- CD4+ T cells, rep2


title: P12 neonatal Tra2b-cPEko, rep B


title: P12 neonatal Tra2b-cPEko, rep C


title: Smartseq2_87

city: New York

value: OV


title: Smartseq2_86


title: HCT116, SY5609, pSer5, ChIP

value: Millipore-Sigma (#04-1572-I)

value: 10ng/mL IFN, 50nM SY-5609


title: Foxp3 eGFP- CD4+ T cells, rep1


title: P12 neonatal Tra2b-cPEko, rep A


title: Smartseq2_85


title: Adult_CTX_MECP2_N-terminus_0.5_CNT

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

data_processing:
Raw reads were trimmed using cutadapt (v2.5) and aligned to mouse reference genome mm10 using bowtie2 (v2.4.2). The duplicate reads were removed using samtools (v1.6) 55. The CUT&RUN final bigwig file was generated using makeUCSC program of HOMER and CUT&TAG bigwig files (CPM and RPKM) files were genearted using bamCoverage tool of deeptools (v.3.5.0)
SICER was used  to identify H3K9me3-enriched regions compared to H3 using parameters of W=500; G=1,500; FDR<0.001.
Assembly: mm10
Supplementary files format and content: bigWig (normalized coverage)
Supplementary files format and content: BED (peaks)

source_name: Brain Cortex

extract_protocol:
For CUT&TAG, cortices were collected from 10-week-old wild type mice, and dounced 15 times in HB buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH pH7.8, 1mM DTT, 0.15 mM spermine, 0.5 mM spermidine, Roche protease inhibitor tablets, 10mM Sodium Butyrate).  IGEPAL CA-630 (Sigma) was added to a final concentration of 0.3% and the lysates were dounced 5 more times.  The lysates were filtered through 40µm cell strainers and spun down at 500g for 5 minutes at 4C.  The pellet was resuspended in cold wash buffer 1 (WB1) (20mM HEPES pH 7.5, 150mM NaCl, 0.2% Tween-20, 0.5 mM spermidine, EDTA-free complete protease inhibitor tablet (Roche), 1mg/mL BSA).  20µl of concanavalin A beads pre-washed with binding buffer (20mM HEPES-KOH pH 7.9, 10mM KCl, 1mM CaCl2, 1mM MnCl2) were added to each sample and incubated for 10 minutes at room temperature to bind nuclei to beads.  The supernatant was discarded and 50µl antibody buffer (WB1 with 2mM EDTA, 0.1% Triton) (along with respective antibodies) was added to the beads and incubated overnight at 4C.  Next, the supernatant was discarded, and beads were incubated for 1 hour at room temperature with secondary antibodies diluted 100X in antibody buffer (either pig anti-rabbit antibodies (Novus Biologicals NBP172763) or rabbit anti-mouse antibodies (Abcam ab46540)). After the incubation, beads were washed 3 times with WB1.  The beads were then incubated for 1 hour at room temperature with 0.025µM pA-Tn5 adapter complex diluted in 100 µl wash buffer 2 (WB2) (20mM HEPES pH 7.5, 300mM NaCl, 0.2% Tween-20, 0.5 mM spermidine, EDTA-free complete protease inhibitor tablet (Roche), 1mg/mL BSA). The beads were next washed three times with WB2 and then were incubated for 1 hour at 37C with 300µl tagmentation buffer (WB2 with 10mM MgCl2).  After the incubation, 10ul of 0.5M EDTA, 3µl of 10% SDS, and 2.5µl of 20mg/mL proteinase K were added and incubated for 1 hour at 50°C followed by 70°C for 10 minutes.  The DNA was extracted by phenol-chloroform extractions.  The samples were PCR amplified with KAPA HiFi polymerase along with 1X KAPA HiFi Buffer, 0.3 mM dNTPs, 10µM universal primer (AATGATACGGCGACCACCGAGATCTACACTCGTCGGCAGCGTCAGATGTG) and 10µM index primer (CAAGCAGAAGACGGCATACGAGAT[index]GTCTCGTGGGCTCGGAGATGT) with the following cycles: (1) 72C for 5 minutes (2) 98C for 30 seconds (3) 98C for 10 seconds (4) 63°C for 30 seconds (5) 72°C for 1 minute (6) 72°C for 5 minutes, (7) go to step 3 thirteen times (8) 12°C hold.  After the PCR, 25µl of Ampure XP beads (0.5x volume) were added and incubated for 10 minutes at room temperature. The supernatant was transferred to a new tube, and an additional 65µl of AMPure beads were added and incubated for 10 minutes at room temperature. The beads were washed twice with 80% ethanol and libraries were eluted with Qiagen EB buffer.
ChIP Libraries were constructed by using the Ovation Ultralow Library System (Nugen).  All libraries were sequenced using an Illumina NextSeq 500
CUT&RUN and CUT&TAG

treatment_protocol: CUT&RUN experiments were performed exactly as previously described by Stroud et. al, 2020 using freshly harvested cortices from adult mice (7-10 weeks). The exceptions were for control experiments. where we altered the experiments in the following ways: (1) Increased anti-MECP2 antibodies by 20-fold. (2) Increased the pA-MNase incubation time after adding CaCl2 from 30 minutes to 2 hours, (3) instead of collecting fragmented chromatin by passive diffusion out from the nuclei, we performed total DNA extraction as previously described by Skene et. al 2017). ChIP-seq experiments were performed exactly as previously described by Stroud et. al 2017

value: Brain Cortex

value: Wild type

tag: antibody

value: anti-MECP2 (N-terminus) (Sigma M7443)


title: P12 neonatal wild type testis, rep D


title: Smartseq2_84


title: HCT116, IFN, pSer5, ChIP

value: 10ng/mL IFN


title: P12 neonatal wild type testis, rep C


title: Adult_CTX_H3_0.5_Native_CNR

value: Increased anti-MECP2 antibodies by 20-fold.

value: anti-H3 (Abcam ab1791)


title: Adult_CTX_MECP2_C-terminus_0.5_CNT

value: anti-MECP2 (C-terminus) (Chen et al., 2003)


title: P12 neonatal wild type testis, rep B


title: HCT116, IFN, pSer2, ChIP

value: Millipore-Sigma (#04-1571-I)


title: Smartseq2_82

value: D-LN


title: P12 neonatal wild type testis, rep A

value: testis

value: mixed


title: Adult_CTX_MECP2_10_Native_CNR

value: anti-MECP2 (C-terminus) (Chen et al., 2003),


title: DLD-1 cells, sgGATA6, rep3

data_processing:
Illunuma BaseSpace CLItools v.1.0.0
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore v.0.6.10
Trimmed sequence reads were mapped to hg38 using STAR.
The TPM value of gene expression was caculated using RSEM.
Assembly: Hg38
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 TPM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II directional with Poly-A Selection Kit.

value: colorectal adenocarcinoma

value: GATA6 CRISPR KO


title: Adult_CTX_IgG_0.5_Nativelyse_CNR

value: Rabbit IgG (Cell Signaling 2729S)


title: Smartseq2_83

value: OV


title: Smartseq2_80

value: Filtered


title: Adult_CTX_MECP2_0.5_Nativelyse_CNR

value: Brain Cortex


title: Smartseq2_81


title: DLD-1 cells, WT, rep3

value: WT


title: Adult_CTX_IgG_0.5_Native2hr_CNR

value: Wild type

value: Increased the pA-MNase incubation time after adding CaCl2 from 30 minutes to 2 hours


title: TIL_Prdm1-/-_UT_rep2

first: Maria

last: Vila de Mucha

address: 72 Huntley Street

institute: UCL Cancer Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v 3.0.2 or v7.0.0) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumour-infiltrating

extract_protocol:
Following dissection, tumors were mechanically disrupted using scissors, followed by digestion with 0.33 mg/ml Liberase TL (Roche) and 0.2 mg/ml DNase (Roche) in serum-free RPMI at 37°C for 30 min. Tumors were dispersed through a 70 μm filter using PBS + 2 mM EDTA and cells resuspended in cRPMI. Lymphocytes were enriched from tumor samples by centrifugation using a Histopaque 1119 density gradient.  (Sigma-Aldrich). Cells were stained using directly conjugated antibodies against extracellular antigens and Live, CD3+ cells sorted.
Single cell RNA sequencing was carried out using the using the Chromium Single Cell 5’ V(D)J Reagent kit, v1 and v2 (10X Genomics). Purified single cell suspensions were loaded onto the 10X Chromium Controller and libraries prepared as per the manufacturer’s instructions, using AMPure beads for size selection and purification and the Bioanalyzer High sensitivity DNA assay (Agilent) to assess cDNA concentration and size of final libraries. Library concentrations were quantified by qPCR using the Illumina Library Quantification kit (KAPA). Libraries were pooled for sequencing at a final concentration of 10 nM. Pooled libraries were sequenced using a NextSeq High output run or on the NovaSeq platform using 26 x 91 paired end reads.

treatment_protocol: C57BL/6J wild-type or transgenic mice were injected subcutaneously with 0.5x10^6 MCA205 cells. Mice received 100 μg αCTLA-4 (clone 4F10-IgG2a, Evitria) on days 6 and 9, and were sacrificed on day 10.

value: Tumour-infiltrating

value: Tumor-infiltrating CD3+ T cells

value: Cd4Cre Prdm1fl/fl

value: Untreated


title: TIL_Bcl6-/-_aCTLA-4_rep1

description: 10x Genomics

value: Cd4Cre Bcl6fl/fl


title: Smartseq2_79

value: D-LN


title: DLD-1 cells, sgGATA6, rep2


title: Smartseq2_78


title: DLD-1 cells, sgGATA6, rep1


title: DLD-1 cells, WT, rep2


title: Smartseq2_77


title: DLD-1 cells, WT, rep1


title: TIL_Bcl6-/-_UT_rep1

description: 10x Genomics


title: Adult_CTX_IgG_0.5_Native_CNR


title: Smartseq2_76


title: Adult_CTX_MECP2_0.5_Native_CNR


title: DLD-1 cells, AID, +Auxin, 72h, rep3

value: +Auxin

tag: time


title: Smartseq2_75


title: TIL_CD4Cre_aCTLA-4_rep1

description: 10x Genomics


title: TIL_CD4Cre_UT_rep2

description: 10x Genomics


title: KPS2.SIY replicate 3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

data_processing:
Illumina NextSeq 500 using v3 chemistry. NextSeq Software: Control v4.0.0.19, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Sequence reads were processed using nf-core/rnaseq workflow revision 3.14.0 and tximport version 1.28.0
Assembly: mm10 with ensembl version 110 annotation
Supplementary files format and content: 210602GerA_intCt.txt.gz is a tab delimited text of integer count data
Supplementary files format and content: 210602GerA_l2tpm.txt.gz is a tab delimited text of log2 TPM data with a +1 offset

source_name: KPS2.SIY cell line (KrasG12D, Trp53-/-, Sox2) expressing SIY-GFP and overexpressing SOX2

growth_protocol: KPCt.SIY and KPS2.SIY cells were seeded in 15 cm dishes and cultured in DMEM supplemented with 10%FBS, 1X HEPES, and 1% Penicillin/streptomycin and collected after 72 hours, when cells were 90% confluent.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen, Cat#15596026) following the manufacturer’s instruction. The aqueous phase containing the RNA was then purified using the RNeasy MinElute Cleanup Kit (Qiagen, Cat# 74204) according to the manufacturer’s instruction.
NEB polyA prep using 250 ng input and 1 to 5 adaptor dilution with 14 cycles of amplification

value: Lung adenocarcinoma cell line

value: KrasG12D and Trp53-/-; expressing SIY-GFP and with overexpression of Sox2


title: Smartseq2_74


title: DLD-1 cells, AID, +Auxin, 72h, rep2

first: Feng

value: colorectal adenocarcinoma


title: KPS2.SIY replicate 2

value: KPS2.SIY cell line (KrasG12D, Trp53-/-, Sox2) expressing SIY-GFP and overexpressing SOX2