title: HC10 [S58]


title: In-vitro Z.tritici strain Zt74, replicate 3

status: Public on Jan 13 2023

type: SRA

city: Harpenden

first: Daniel

last: Smith

state: Hertfordshire

address: West Common

department: IDE

country: United Kingdom

institute: Rothamsted Research

library_source: transcriptomic

data_processing:
Reads mapped using HiSat2 (v2.0.5)
Mapped reads counted using Subread FeatureCounts (v1.6.2)
Assembly: pangenome assembly: Pangenome_Zt_17I_IPO323_v3.fasta ; annotation: annotation_pangenomveV3_2.gtf (bespoke for this paper, data archived and included here)
Supplementary files format and content: FeatureCount gene counts: ztriticiPangenomePlantaCounts.txt

molecule: total RNA

organism: Zymoseptoria tritici

source_name: in-vitro fungal culture

growth_protocol: in-vitro broth culture or in-planta wheat infections as described above

extract_protocol:
TRIzol (Invitrogen)
Illumina 100bp  paired-end reads

treatment_protocol: Sampling at log phase in vitro or at stated days post infection in-planta

tag: strain

tag: in-vitro growth phase

value: log phase growth

tag: in-vitro medium

value: Culture medium:YPD broth


title: RBM7,Rep,1,negative

city: Aarhus

first: Ross

middle: Andrew Alex

last: Cordiner

address: Universitetsbyen 81

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

data_processing:
Demultiplexing and quality control: Reads were demultiplexed using rtCLIP barcodes initially to identify RBP and biological rep using pyBarcodeFilter.py using options -m 1 -k (version 3.0). Next, umi_tools (version 0.5.5) was used to append UMI to header using the extract function with following options --bc-pattern=NNNXXXXNN --bc-pattern2=XXXXXXXXN --log extract.log . Another round of demultiplexing applying the BCBarcodes to identify timepoints from specific RBP biological replicates using pyBarcodeFilter.py with the following options -b$BCBarcodes.txt -m 1 -k –search reverse . Finally, trim_galore was used for QC using the following options --stringency 4 --phred33 --fastqc --illumina -a2 AGATCGGAAGAGC --clip_R1 4 --clip_R2 8 --three_prime_clip_R1 9 --three_prime_clip_R2 9 --trim1 (version 0.5.0)
Mapping and QC: Reads were mapped using hisat2 (version 2.1.0)  with the following options -t --rna-strandness FR --fr --phred33 -p 10 --new-summary --no-softclip --known-splicesite-infile . samtools (version 1.9) was used to sort, index and remove secondary reads.  umi_tools was used to remove PCR duplicates from the mapped reads using the dedup function with the following options --paired (version 0.5.5)
Making read1 and read2, and derivative cross-link and 3CLIP bigwig files: samtools (version 1.9) and bedtools (version v2.28.0) was used to extract read 1 and 2, and custom awk scripts were used to flip read2 strand identity. Custom awk scripts were also used to extract the cross-link site and 3CLIP from read1 and read2 bed files. Bedtools and bedGraphToBigWig (version 4) from UCSC tools were used to generate bigwig files. Bigwig files were scaled to the number of reads mapped to 30 rRNA genes.
Assembly: hg38

organism: Homo sapiens

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM (10 %FCS) supplemented with penicillin streptomycin, and incubated at 37°C with 5% CO2.

extract_protocol:
Cells were lysed via sonication and RNA was extracted via immunoprecipitation of the relevant cross-linked RNA binding protein.
Standard iCLIP library construction was used with a few alterations from the original protocol (Konig et al. 2011) . iCLIP libraries were constructed from each UV cross-linked sample. As the adapters used in the first ligation reaction contained an inline barcode, all timepoints and controls for a given biological replicate were pooled after gel-extraction. Reverse transcription was performed on the pooled RNA using standard RtClip oligos that contained a 2nd in-line barcode which was used to identify the RBP and the biological replicate.

treatment_protocol: HeLa cells at 70% confluency were incubated with 100uM DRB, or the equivalent volume of organic solvent (DMSO) for 3 hours to pause RNAPII transcription. After 3 hours, the DRB block was released by aspirating the drug-containing media and replacing with fresh media. At the appropriate timepoint cells were UV cross-linked for 30 seconds and cells were scraped, pelleted and frozen at -80°C until required. Timepoint 0 (t00) samples were UV cross-linked immediately after 3 hours DRB incubation.

tag: cell line

value: HeLa

tag: cell type

value: Human papillomavirus-related endocervical adenocarcinoma

tag: genotype

value: WT

tag: treatment

value: DMSO

tag: time


title: S011080

type: RNA

city: Edinburgh

first: Max

last: Bylesjo

state: Scotland

address: BioCube 1, Edinburgh BioQuarter, 13 Little France Road

institute: Fios Genomics Ltd

hyb_protocol: The samples were hybridized to Clariom S Human Array Plates according to standard Affymetrix GeneTitan protocol

scan_protocol: Array plates were scanned using the Affymetrix GeneTitan Scanner with AGCC and exported as CEL files

data_processing: CEL files were imported into R and the input data was normalised using RMA, resulting in normalised expression levels in log base 2

label: biotin

source_name: PBMC

label_protocol: Samples were labeled with biotin using the GeneChip WT Plus Reagent Kit according to the manufacturer's instructions.

extract_protocol: RNA was extracted from whole blood collected with PAXgene RNA tubes according to the manufacturer's recommendations

tag: individual (patient id)

value: Baseline

tag: center

value: AUH

tag: patient group

value: FT Long-term (> 3 yrs) rejection-free survival

tag: gender

value: F

tag: tissue

value: blood

value: PBMC


title: In-vitro Z.tritici strain Zt74, replicate 2


title: HC9 [S9]

city: Paris

first: Gaspard

last: Kerner

address: 25-28 rue du docteur roux

country: France

institute: Institut Pasteur

data_processing:
BAM files were converted to a raw count’s expression matrix using ‘featurecount’. Raw count data was normalized using DEseq2. The Ensembl IDs targeting multiple genes were collapsed (average), and a final data matrix gene was generated for downstream analysis. Gene set enrichment analysis (GSEA) was conducted based on the fold-change (pairwise analysis of stimulated vs non-stimulated sample) ranking against the Hallmark (HM) gene sets (http://www.gsea-msigdb.org/gsea/msigdb/genesets.jsp?collection=H).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: T-cell blast

growth_protocol: T-blasts were induced from 2 million peripheral blood mononuclear cells (PBMCs; fresh or cryopreserved) in 2 ml ImmunoCult™-XF T Cell Expansion Medium (StemCell Technologies, 10981) supplemented with 10 ng/ml IL-2 (Gibco, PHC0023) and 1:40 diluted ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (StemCell Technologies, 10970). T-blasts were then cultured in ImmunoCult Medium with IL-2 for 2-3 weeks, before they were re-stimulated in the same manner.

extract_protocol:
Total RNA was isolated from cells using the Quick-RNA MicroPrep spin column kit (Zymogen, R1050), following manufacturer’s protocol. RNA was then submitted for RNA sequencing library preparation and deep-sequencing to Rockefeller University Genomics Core Facility.
RNA-sequencing was performed on the Illumina NovaSeq platform, with a read length of 100bp and read depth of 30-40 million reads. All FASTQ files passed QC and were aligned to reference genome GRCh38 using STAR (2.6.1d).

treatment_protocol: T-cell blasts were starved off IL-2 over-night. Then, they were stimulated with 50 ng/ml IL-12 (R&D Systems, CAT: 219-IL-005) or 100 ng/ml IL-23 (R&D Systems, Cat: 1290-IL) for 6 hours or with 2.5 ng/ml IL1ß (R&D Systems, CAT: 201-LB-005)- for 24 hours. Double stimulated cells were stimulated with IL-1ß for 18 hours and then with IL-23 and IL-1ß for 6 hours.

value: T-cell blast

value: WT/WT

value: Unstimulated


title: CBP80,Rep,3,t40

value: DRB

value: 40 min


title: CBP80,Rep,3,t60

value: 60 min


title: HC9 [S33]


title: HC9 [S21]


title: S001481

value: FT Stable < 3 yrs post-transplant

value: M


title: S000807

value: PL Stable < 3 yrs post-transplant


title: In-vitro Z.tritici strain Zt74, replicate 1

value: log phase growth

value: Culture medium:YPD broth


title: In-vitro Z.tritici strain Zt48, replicate 3


title: CBP80,Rep,3,t20

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: 20 min


title: In-vitro Z.tritici strain Zt48, replicate 2


title: S010755

value: Baseline

value: CUB

value: Healthy adult volunteer


title: RBM7,Rep,1,DMSO

value: DMSO


title: CBP80,Rep,3,t15

value: 15 min


title: S004126

value: FT Long-term (> 3 yrs) rejection-free survival

value: blood

value: PBMC


title: HC9 [S57]

value: T-cell blast

value: WT/WT


title: S013952

value: RCSI

value: Non-transplanted corneal disease

value: M


title: In-vitro Z.tritici strain Zt48, replicate 1

value: log phase growth

value: Culture medium:YPD broth


title: HC8 [S8]

value: Unstimulated


title: S003970


title: CBP80,Rep,3,t05

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB

value: 05 min


title: S004577

value: Baseline

value: AUH

value: FT Stable < 3 yrs post-transplant


title: CBP80,Rep,3,t00

value: 00 min


title: S012932

value: PL Acute rejection < 3 yrs post-transplant

value: F

value: blood

value: PBMC


title: In-vitro Z.tritici strain Zt36, replicate 3


title: HC8 [S32]

value: T-cell blast

value: WT/WT


title: S014263

value: RCSI

value: M


title: HC8 [S20]


title: HC9 [S45]


title: In-vitro Z.tritici strain Zt36, replicate 1

value: log phase growth

value: Culture medium:YPD broth


title: HC8 [S44]


title: CBP80,Rep,3,t10

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: 10 min


title: HC8 [S56]


title: CBP80,Rep,2,t60

value: DRB

value: 60 min


title: S002906

value: Baseline

value: CUB

value: Healthy adult volunteer


title: S004129

value: FT Stable < 3 yrs post-transplant

value: F


title: In-vitro Z.tritici strain Zt118, replicate 2


title: HC6 [S6]

value: Unstimulated


title: In-vitro Z.tritici strain Zt118, replicate 1


title: In-vitro Z.tritici strain Zt36, replicate 2


title: S010330

value: AUH

value: FT Long-term (> 3 yrs) rejection-free survival

value: blood

value: PBMC


title: CBP80,Rep,3,negative

value: WT

value: DMSO


title: S002223


title: CBP80,Rep,3,DMSO

value: HeLa


title: In-vitro Z.tritici strain Zt118, replicate 3

value: log phase growth

value: Culture medium:YPD broth


title: CBP80,Rep,2,t15

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB

value: 15 min


title: CBP80,Rep,2,t10

value: 10 min


title: HC6 [S42]

value: T-cell blast

value: WT/WT


title: S007991

value: Baseline

value: F


title: In-vitro Z.tritici strain Zt117, replicate 1


title: CBP80,Rep,2,t05

value: 05 min


title: In-vitro Z.tritici strain Zt116, replicate 3


title: HC6 [S54]


title: S001208

value: CUB

value: FT Long-term (> 3 yrs) rejection-free survival


title: HC5 [S5]

value: Unstimulated


title: HC6 [S30]


title: CBP80,Rep,2,t20

value: 20 min


title: In-vitro Z.tritici strain Zt117, replicate 3


title: S002701

value: AUH

value: PL Long-term (> 3 yrs) rejection-free survival

value: M

value: blood

value: PBMC


title: HC6 [S18]


title: In-vitro Z.tritici strain Zt116, replicate 2

value: log phase growth

value: Culture medium:YPD broth


title: S010094

value: RCSI

value: FT Acute rejection < 3 yrs post-transplant


title: In-vitro Z.tritici strain Zt117, replicate 2


title: HC5 [S29]

value: T-cell blast

value: WT/WT


title: CBP80,Rep,2,t00-1

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB

value: 00 min


title: In-vitro Z.tritici strain Zt116, replicate 1


title: S010530

value: Baseline

value: PL Stable < 3 yrs post-transplant


title: HC5 [S17]


title: CBP80,Rep,2,negative

value: WT

value: DMSO


title: In-vitro Z.tritici strain Zt114, replicate 3


title: S006309

value: Non-transplanted corneal disease

value: F


title: HC5 [S41]


title: S013885

value: UBR

value: Healthy adult volunteer

value: blood

value: PBMC


title: In-vitro Z.tritici strain Zt114, replicate 1

value: log phase growth

value: Culture medium:YPD broth


title: CBP80,Rep,1,t60

value: 60 min


title: CBP80,Rep,1,t40

value: HeLa

value: 40 min


title: ZF_Ko_H5_EW20

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

country: USA

institute: Baylor College of Medicine

description: PAC-seq strategy as described in Jensen et al, 2021.

data_processing:
Raw reads were trimed using fastp
Trimed reads were aligned to the reference genome using bowtie2
PCR duplicates were removed using umi tools
Samtools were used to sort, convert and index alignment files
Deeptools were used to generate bigwig files
Assembly: GRCz11
Supplementary files format and content: bigwig files
Library strategy: PAC-seq

organism: Danio rerio

source_name: cpsf6-/- 6dpf head

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries.
We reverse transcribed 1 ug of total RNA with the partial P7 adapter (Illumina_4N_21T) and dNTPs with the addition of spiked-in azido-nucleotides (AzVTPs) at 5:1. We click-ligated the p5 adapter (IDT) to the 5′ end of the cDNA with CuAAC. The p5 adaptor contained a UMI. We then amplified the cDNA for 17 cycles with 5' and 3′ indexing primer and purified it on a 2% agarose gel by extracting amplicon from 200-300 base pairs. We pooled the libraries and sequenced single-end, 100 base-pair reads on a NovaSeq (Illumina).

value: head


title: HC4 [S28]

value: T-cell blast

value: WT/WT


title: S013529

value: Baseline

value: CUB

value: M


title: HC4 [S4]

value: Unstimulated


title: ZF_Ko_H4_EW19


title: CBP80,Rep,1,t20

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB

value: 20 min


title: HC4 [S16]


title: ZF_Ko_H3_EW18


title: S008492

value: RCSI

value: FT Long-term (> 3 yrs) rejection-free survival

value: blood


title: S001300

value: PL Stable < 3 yrs post-transplant

value: F

value: PBMC


title: CBP80,Rep,1,t15

value: HeLa

value: 15 min


title: HC4 [S40]

value: T-cell blast


title: CBP80,Rep,1,t10

value: 10 min


title: In-vitro Z.tritici strain Zt114, replicate 2

value: log phase growth

value: Culture medium:YPD broth


title: HC5 [S53]

value: WT/WT


title: S004463

value: Baseline


title: ZF_Ko_H2_EW17

value: head


title: CBP80,Rep,2,DMSO

value: Human papillomavirus-related endocervical adenocarcinoma

value: DMSO


title: HC4 [S52]


title: S002298

value: AUH


title: ZF_Ko_H1_EW16


title: CBP80,Rep,1,t05

value: DRB

value: 05 min


title: HC3 [S3]

value: Unstimulated


title: S007341

value: RCSI

value: FT Stable < 3 yrs post-transplant

value: M

value: blood


title: Zf_Wt_H5_EW15

source_name: wild-type 6dpf head

value: wild-type


title: S002030

value: PL Stable < 3 yrs post-transplant

value: F

value: PBMC


title: CBP80,Rep,1,t00-2

value: HeLa

value: 00 min


title: S008715

value: Baseline

value: CUB

value: PL Chronic graft injury (> 3 yrs post-transplant)


title: HC3 [S27]

value: T-cell blast

value: WT/WT


title: CBP80,Rep,1,t00-1

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB


title: HC3 [S15]


title: Zf_Wt_H3_EW13

value: head


title: Zf_Wt_H4_EW14


title: HC3 [S39]


title: Zf_Wt_H2_EW12


title: CBP80,Rep,1,DMSO

value: DMSO


title: CBP80,Rep,1,negative

value: WT


title: HC3 [S51]


title: S007558

value: AUH

value: blood


title: S006934

value: PL Long-term (> 3 yrs) rejection-free survival


title: CBP20,Rep,3,t60

value: 60 min


title: S014451

value: PL Stable < 3 yrs post-transplant

value: M

value: PBMC


title: S006084

value: Baseline

value: RCSI

value: FT Stable < 3 yrs post-transplant


title: S013702

value: NANT

value: FT Long-term (> 3 yrs) rejection-free survival

value: F


title: Zf_Ko_5_EW10

source_name: cpsf6-/- 6dpf whole-larva

value: whole-larva


title: HC2 [S26]

value: T-cell blast

value: WT/WT


title: Zf_Ko_4_EW9


title: S003941

value: CUB

value: FT Chronic graft injury (> 3 yrs post-transplant)


title: HC2 [S14]


title: Zf_Ko_3_EW8


title: CBP20,Rep,3,t10

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB

value: 10 min


title: CBP20,Rep,3,t20

value: 20 min


title: Zf_Wt_H1_EW11

value: head

value: wild-type


title: HC2 [S38]


title: CBP20,Rep,3,t05

value: 05 min


title: Zf_Ko_2_EW7


title: S004730

value: Baseline

value: AUH

value: FT Stable < 3 yrs post-transplant

value: blood

value: PBMC


title: HC1 [S1]

value: T-cell blast

value: Unstimulated


title: HC2 [S50]

value: WT/WT


title: HC2 [S2]


title: CBP20,Rep,3,t15

value: 15 min


title: CBP20,Rep,3,t00

value: HeLa

value: 00 min


title: Zf_Ko_1_EW6

value: whole-larva


title: S004428

value: PL Stable < 3 yrs post-transplant

value: M


title: S005117

value: RCSI


title: CBP20,Rep,3,negative

value: Human papillomavirus-related endocervical adenocarcinoma

value: WT

value: DMSO


title: Zf_Wt_5_EW5

source_name: wild-type 6dpf whole-larva

value: wild-type


title: Zf_Wt_4_EW4


title: HC1 [S25]


title: HC1 [S13]


title: Zf_Wt_3_EW3


title: S011228

value: Baseline

value: AUH

value: FT Long-term (> 3 yrs) rejection-free survival

value: F


title: HC1 [S37]

value: T-cell blast


title: CBP20,Rep,2,t60

value: DRB

value: 60 min


title: CBP20,Rep,3,DMSO

value: HeLa


title: Zf_Wt_2_EW2


title: HC1 [S49]

value: WT/WT


title: S003176

value: blood

value: PBMC


title: CBP20,Rep,2,t40

value: 40 min


title: S007401


title: S002152

value: RCSI


title: TLR3 Poly

data_processing:
RNA-sequencing was performed on the Illumina NovaSeq platform, with a read length of 100bp and read depth of 30-40 million reads. All FASTQ files passed QC and were aligned to reference genome GRCh38 using STAR (2.6.1d).
Differential gene expression analyses were conducted by contrasting the extracellular Poly(I:C)-stimulated samples or the intracellular Poly(I:C)-stimulated samples, with the non-stimulated samples. Genes displaying significant differences in expression were selected according to the following criteria: FDR ≤ 0.05 and |log2(FoldChange)| ≥ 1. Differential gene expression was plotted as a heatmap with ‘ComplexHeatmap’, and genes and samples were clustered based on complete linkage and the Euclidean distances of gene expression z score values.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Primary fibroblast

growth_protocol: Primary human fibroblasts were established from skin biopsy specimens from individuals that carry the homozygous TLR3 ancestral or derived L412F variation, or from a previously published patient with complete TLR3 deficiency. Fibroblasts were cultured in DMEM medium (GIBCO) with 10% fetal bovine serum (FBS) (GIBCO). 450.000 cells/well were seeded in 6-well plates and incubated for 16h.

extract_protocol: Total RNA was isolated from cells using the Quick-RNA MicroPrep spin column kit (Zymogen, R1050), following manufacturer’s protocol. RNA was then submitted for RNA sequencing library preparation and deep-sequencing to Rockefeller University Genomics Core Facility.

treatment_protocol: For intracellular poly(I:C) stimulation, cells were treated with Lipofectamine 2000: Poly(I:C) ratio of 1:5, for 8h with 10ug/mL of poly(I:C). For Poly(I:C) extracellular stimulation, cells were treated for 6 hours with 10ug/mL of Poly(I:C). Non-stimulated cells were left untreated and harvested at the same time as intracellular or extracellular Poly(I:C) stimulated cells.

value: Primary fibroblast

value: Poly


title: CBP20,Rep,2,t20

value: Human papillomavirus-related endocervical adenocarcinoma

value: 20 min


title: C2C12 cell line, olanzapine and calcitriol

city: Kyoto

first: Kazuki

last: Nagayasu

address: 46-29 Yoshidashimoadachicho, Sakyo

department: Graduate School of Pharmaceutical Sciences

country: Japan

institute: Kyoto University

data_processing:
The reads were cleaned using SOAPnuke v1.5.2
The clean reads were mapped to the genome and gene sequences using HISAT and Bowtie2, respectively.
Gene expression was calculated using RSEM.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: .xls files include fpkm, tpm, and read counts for each sample

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
After treatment, cultured cell samples were collected in ISOGEN reagent. Total RNA was isolated using ISOGEN reagent.
RNA libraries were prepared for sequencing using standard BGISEQ protocols

value: Myocyte

value: Calcitriol for 24 hours and olanzapine + calcitriol for 12 hours


title: S011715

value: Baseline

value: AUH

value: PL Acute rejection < 3 yrs post-transplant

value: M


title: S013857

value: UBR

value: FT Acute rejection < 3 yrs post-transplant

value: F


title: TLR3 NS

value: NS


title: C2C12 cell line, olanzapine and calcifediol

value: Calcifediol for 24 hours and olanzapine + calcifediol for 12 hours


title: S002482

value: PL Stable < 3 yrs post-transplant

value: blood

value: PBMC


title: HOM4 Poly

value: Primary fibroblast

value: Poly


title: C2C12 cell line, olanzapine

value: vehicle for 24 hours and olanzapine for 12 hours


title: S000438

value: Non-transplanted corneal disease


title: CBP20,Rep,2,t10

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB

value: 10 min


title: HOM4 NS


title: S007070

value: Baseline

value: CUB

value: PL Long-term (> 3 yrs) rejection-free survival

value: M


title: C2C12 cell line, vehicle

value: Myocyte

value: vehicle for 36 hours


title: HOM4 Lipo

value: Lipo


title: Zf_Wt_1_EW1

value: whole-larva

value: wild-type


title: CBP20,Rep,2,t05

value: 05 min


title: CBP20,Rep,2,t15

value: 15 min


title: CBP20,Rep,2,t00-1

value: 00 min


title: Adipocyte, olanzapine and calcitriol

source_name: Adipocyte

value: Adipocyte

value: Calcitriol for 24 hours and olanzapine + calcitriol for 12 hours


title: CBP20,Rep,2,t00-2

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma


title: HOM3 Poly

value: Primary fibroblast

value: Poly


title: CBP20,Rep,2,negative

value: WT

value: DMSO


title: Adipocyte, olanzapine and calcifediol

value: Calcifediol for 24 hours and olanzapine + calcifediol for 12 hours


title: HOM3 NS

value: NS


title: Adipocyte, olanzapine

value: vehicle for 24 hours and olanzapine for 12 hours


title: S004521

value: Baseline

value: RCSI

value: PL Stable < 3 yrs post-transplant

value: M

value: blood

value: PBMC


title: HOM3 Lipo

value: Lipo


title: S007097

value: CUB

value: FT Acute rejection < 3 yrs post-transplant


title: CBP80,Rep,2,t40

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB

value: 40 min


title: CBP20,Rep,2,DMSO

value: DMSO


title: Adipocyte, vehicle

value: Adipocyte

value: vehicle for 36 hours


title: S010527

value: Non-transplanted corneal disease


title: S002516

value: Baseline


title: S005022

value: AUH

value: FT Stable < 3 yrs post-transplant


title: S002839

value: FT Chronic graft injury (> 3 yrs post-transplant)

value: F


title: S018434

value: UBR

value: M

value: blood

value: PBMC


title: Hepatocyte, olanzapine and calcitriol

source_name: Hepatocyte

value: Hepatocyte

value: Calcitriol for 24 hours and olanzapine + calcitriol for 12 hours


title: HOM2 NS

value: Primary fibroblast

value: NS


title: Hepatocyte, olanzapine and calcifediol

value: Calcifediol for 24 hours and olanzapine + calcifediol for 12 hours


title: Hepatocyte, olanzapine

value: vehicle for 24 hours and olanzapine for 12 hours


title: CBP20,Rep,1,t40

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB

value: 40 min


title: CBP20,Rep,1,t20

value: 20 min


title: HOM2 Lipo

value: Lipo


title: CBP20,Rep,1,t15

value: 15 min


title: HOM1 Poly

value: Poly


title: Hepatocyte, vehicle

value: vehicle for 36 hours


title: CBP20,Rep,1,t60

value: 60 min


title: S002354

value: Baseline

value: CUB

value: FT Chronic graft injury (> 3 yrs post-transplant)

value: F

value: blood

value: PBMC


title: S006099

value: RCSI

value: FT Stable < 3 yrs post-transplant

value: M


title: HOM2 Poly

value: Primary fibroblast


title: HOM1 Lipo


title: S001519

value: Healthy adult volunteer


title: CBP20,Rep,1,t10

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB

value: 10 min


title: CBP20,Rep,1,t00-2

value: 00 min


title: HC2 Poly

value: WT/WT

value: Poly


title: S012659

value: Baseline

value: UBR

value: PL Stable < 3 yrs post-transplant


title: HC2 NS

value: NS


title: HC2 Lipo

value: Lipo


title: S001677

value: CUB

value: FT Chronic graft injury (> 3 yrs post-transplant)

value: F

value: blood

value: PBMC


title: CBP20,Rep,1,t00-1

value: HeLa


title: CBP20,Rep,3,t40

value: Human papillomavirus-related endocervical adenocarcinoma

value: 40 min


title: HOM1 NS

value: Primary fibroblast


title: CBP20,Rep,1,t05

value: DRB

value: 05 min


title: S002706

value: RCSI

value: PL Chronic graft injury (> 3 yrs post-transplant)


title: HC1 Poly

value: WT/WT

value: Poly


title: S013139

value: Baseline

value: AUH

value: PL Acute rejection < 3 yrs post-transplant

value: M


title: CBP20,Rep,1,DMSO

value: DMSO


title: HC1 NS

value: NS


title: S006715

value: PL Stable < 3 yrs post-transplant

value: blood

value: PBMC


title: ALYREF,Rep,2,t60

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: ALYREF-GFP

value: 60 min


title: S000271

value: Non-transplanted corneal disease

value: F


title: ALYREF,Rep,2,t40

value: DRB

value: 40 min


title: HC1 Lipo

value: Primary fibroblast

value: WT/WT

value: Lipo


title: CBP20,Rep,1,negative

value: WT


title: ALYREF,Rep,2,t20

value: 20 min


title: ALYREF,Rep,2,t15

value: 15 min


title: n_sp1_H, replicate 1, scRNAseq

city: Guangzhou

first: Lipeng

last: Mao

state: Guangdong

address: No.601, West Huangpu Avenue

department: Department of Microbiology and Immunology

country: China

institute: Jinan University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The 10x Genomics Cell Ranger software (v6.1.0) was used to process the fastq files with Human reference GRCh38-2020-A for the scRNA-Seq and hashtag antibodies sequencing, with default parameter settings.
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files(with gz) ,which stored in covid19singlecell.tar.gz

source_name: Blood

extract_protocol:
Blood from unexposed donors was collected from healthy individuals registered at the Guangzhou Blood Center until 2019. The donors had no known history of any significant systemic diseases, including, but not limited to, hepatitis B or C, HIV, diabetes, kidney or liver diseases, malignant tumors, or autoimmune diseases. The samples were confirmed by negative reports of SARS-CoV-2 RNA real-time reverse transcription polymerase chain reaction (RT-PCR) assays. PBMCs were isolated from HLA-A2+ healthy donors using EasySep Human negative selection (Stemcell, Cat#17953, Canada) according to the manufacture instruction. Each type of epitope specific CD8 T cells was generated with the method described above. Each epitope-specific CD8 T cells were labeled with PE conjugated corresponding epitope based tetramers and APC conjugated anti-CD8 antibody, and sorted by flow cytometer FACS Aria (BD). Hashtags were used to label different epitope specific CD8 T cells (Table S2). Cell number and viability were checked after surface protein hashtag staining (cell viability > 80%).
Then droplet-encapsulation single-cell sequencing experiments were performed, and 10,000 living single cells were loaded onto each of the Chromium Controller (10x Genomics). After droplet-encapsulation, single-cell cDNA synthesis, amplification and sequencing libraries were generated using Chromium Single Cell 5' Feature Barcode Library Kit (10x Genomics), Chromium Single Cell 5' Library & Gel Bead Kit (10x Genomics), and Chromium Single Cell V(D)J Enrichment Kit (Human T Cell, 10x Genomics) according to the manufacturer’s instructions. The libraries from each loaded channel (up to eight channels) were multiplexed together and sequenced on an Illumina Novaseq 6000.

value: CD8 cell

value: Blood


title: I757_H, replicate 1, scRNAseq

description: 10x Genomics


title: Epcam+ RNA seq SCC10 [Lgr5 mixte SCC10 Epcam+]

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Adaptors sequences were removed with TrimmomaticPE using options “ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 HEADCROP:8”
Reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR software
Duplicate reads were removed by Picard tools, MarkDuplicates module.
After transcripts assembling, gene level counts were obtained using Htseq with annotations Grcm38.87 and normalized to 20 millions of aligned reads.
Assembly: mm10/Grcm38
Supplementary files format and content: Normalized gene expression of Rhoj shRNA treated and control samples
Supplementary files format and content: Normalized gene expression of mixed SCC on Lgr5 mouse model, difference between expression of Epcam

source_name: squamous cell carcinoma

extract_protocol:
RNA extraction from FACS isolated cells was performed using the RNeasy micro kit (QIAGEN) according to the manufacturer’s recommendations with DNAse treatment
Indexed cDNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’s recommendations.

value: squamous cell carcinoma

value: wild type Epcam+ cells

value: Lgr5CreER/KRasG12D/p53cKO/ Rosa-YFP


title: Epcam- RNA seq SCC10 [Lgr5 mixte SCC10 Epcam-]

value: wild type Epcam- cells


title: E357_H, replicate 1, scRNAseq

description: 10x Genomics


title: n_sp1, replicate 1, scRNAseq

description: 10x Genomics


title: S013756

value: Baseline

value: UBR

value: PL Acute rejection < 3 yrs post-transplant

value: blood

value: PBMC


title: CBP80,Rep,2,t00-2

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB

value: 00 min


title: S000027

value: AUH

value: Healthy adult volunteer

value: F


title: Epcam- RNA seq SCC12 [Lgr5 mixte SCC12 Epcam -]


title: S009186

value: CUB

value: Non-transplanted corneal disease

value: M


title: S000405

value: FT Long-term (> 3 yrs) rejection-free survival


title: S000034


title: ALYREF,Rep,2,t10

value: ALYREF-GFP

value: 10 min


title: ALYREF,Rep,2,t05

value: 05 min


title: ALYREF,Rep,2,t00-2


title: S013707

value: Baseline

value: RCSI


title: Epcam+ RNA seq SCC12 [Lgr5 mixte SCC12 Epcam+]

value: squamous cell carcinoma

value: wild type Epcam+ cells

value: Lgr5CreER/KRasG12D/p53cKO/ Rosa-YFP


title: RhoJ sh-RNA Epcam- cell A3 [Rhojsh_A3_MD28]

value: RhoJ sh-RNA knock-down Epcam- cell


title: S004179

value: PL Stable < 3 yrs post-transplant

value: blood

value: PBMC


title: ALYREF,Rep,2,negative

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: WT

value: DMSO


title: Control sh-RNA Epcam- cell A3 [Ctl_A3_ MD26]

value: sh-RNA control Epcam- cell


title: S008354

value: CUB

value: Non-transplanted corneal disease

value: M


title: F10-Input, rep1

city: Umeå

first: Yuri

last: Schwartz

address: Building 6K, 6L  University Hospital Area

department: Molecular Biology

country: Sweden

institute: Umeå University

library_source: genomic

data_processing:
For all fastq.gz files that do not start with "TB-2458" base calling and quality score assignment were done with HiSeq Control Software 2.2.58/RTA 1.18.64. The Bcl to FastQ conversion was performed using bcl2fastq_v2.19.1.403 from the CASAVA software suite.
For all fastq.gz files started with "TB-2458" base calling and quality score assignment were done with NovaSeq Control Software 1.6.0/RTA v3.4.4. The Bcl to FastQ conversion was performed using bcl2fastq_2.20.0.422 from the CASAVA software suite.
The sequencing reads were aligned to human GRCh38/hg38 reference genome using bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) set to --phred33 -p 8
Reads with MAPQ scores less than 10 were removed using samtools (v1.3.1) (Li et al., 2009) view command and the following parameters: -h -b -@ 8 -q 10
Significantly enriched regions were identified from the filtered bowtie2 alignments with MACS2 (v2.1.2) (Zhang et al., 2008) callpeak command using the following parameters: -f BAM -g hs --broad --min-length 1000 -B --nomodel --extsize 180 --SPMR
Assembly: hg38
Supplementary files format and content: Read count profiles in BedGraph format, broadPeak

molecule: genomic DNA

source_name: cultured cells

growth_protocol: NTERA-2 (NT2-D1 ATCC® CRL-1973™), TIG-3 (see (Cameron et al., 2018) for more details), 293T (ATCC® CRL-3216™) and Hela (ATCC® CCL-2™) were cultured in high-glucose DMEM (Gibco) supplemented with 10% fetal bovine serum (Sigma), 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate (Gibco), and 1.5 g/liter sodium bicarbonate (Sigma) at 37 °C in an atmosphere of 5% CO2. F10 cells (clone of KBM7-1-55-S2-24 cell line) were cultured in Iscove’s Modified Dulbecco’s Medium (1X) (Gibco) supplemented with 15% of heat inactivated serum (Sigma), 100U/ml of Penicillin G, 100ug/ml of Streptomycin sulfate (Gibco), and 3.024 g/liter sodium bicarbonate at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
Live cells were crosslinked with 1% formaldehyde for 10 min at 37C. Soluble chromatin was prepared and immunoprecipitation performed as described in Kahn et al. Nucleic Acids Res. 2016. 44:10132-10149
Libraries were prepared with NEBNext Ultra II FS DNA Library Prep Kit for Illumina (E7805) and NEBNext Multiplex Oligos for Illumina Index Primers Set 1 (E7335) according to manufacturer’s instructions. Briefly, 2 ng of ChIP DNAs were fragmented for 20 minutes to the average length of 180bp, followed by adaptor ligation and 8 cycles of PCR amplification.
HiSeq2500, 1x51 setup, 'HiSeq Rapid SBS Kit v2' chemistry
NovaSeq SP,100bp read length, v1 sequencing chemistry

treatment_protocol: no treatment

tag: chip antibody


title: E357, replicate 1, scRNAseq

description: 10x Genomics

value: CD8 cell

value: Blood


title: ALYREF,Rep,2,DMSO

value: ALYREF-GFP


title: S000675

value: Baseline

value: FT Stable < 3 yrs post-transplant

value: F


title: RhoJ sh-RNA Epcam – cell  T2 [Rhojsh_T2_ MD25]

value: squamous cell carcinoma

value: RhoJ sh-RNA knock-down Epcam- cell

value: Lgr5CreER/KRasG12D/p53cKO/ Rosa-YFP


title: F10-H3K27me3, rep2

value: Abcam, #ab6002


title: S002062

value: AUH

value: blood

value: PBMC


title: S000554

value: FT Chronic graft injury (> 3 yrs post-transplant)


title: F10-Input, rep2


title: Control sh-RNA Epcam- cell T2 [Ctl_ T2_MD23]

value: sh-RNA control Epcam- cell


title: 9259684122_R01C01

type: genomic

city: Bologna

first: Maria Giulia

last: Bacalini

address: Via Altura 3

department: Brain Aging Laboratory

country: Italy

institute: IRCCS Istituto delle Scienze Neurologiche di Bologna

description: genomic DNA from DU-145 cells treated with 2.5*10-4 M SAM

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Infinium BeadChip using standard Illumina protocol

scan_protocol: HiScan scanner (Illumina)

data_processing: Signal intensities files were extracted using the minfi Bioconductor package. The preprocessFunnorm function implemented in minfi was applied to normalize raw data.

label: Cy3 and Cy5

label_protocol: Standard Illumina Protocol

growth_protocol: DU-145 were provided by ATCC. DU-145 cells were grown at 37°C in RPMI containing 10% fetal bovine serum, 2 mM glutamine and 105 U/l penicillin–streptomycin and maintained in a humidified atmosphere of 5% CO2. The cells were grown in 75 cm2 flasks and passed once every 4–7 days on a 1:2 split.

extract_protocol: Total DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, Germany). Bisulfite treatment of 1 µg of genomic DNA was performed using the EZ DNA Methylation-Gold Kit (Zymo Research).

treatment_protocol: DU-145 cells were plated in 6-well plates and treated with 10-5 M 5-aza-2’-deoxycytidine (AZA) or 2.5*10-4 M S-adenosylmethionine (SAM). After 3 days, total DNA was extracted.


title: ALYREF,Rep,1,t60

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB

value: 60 min


title: 9259684122_R03C01

description: genomic DNA from DU-145 cells treated with 10-5 M AZA

source_name: DU-145 cells treated with 10-5 M AZA

value: 10-5 M AZA


title: F10-H3K27me3, rep1


title: S000469

value: Baseline

value: PL Acute rejection < 3 yrs post-transplant


title: F10-SUZ12, rep2

value: Cell signaling, #3737P


title: ALYREF,Rep,1,t20

value: ALYREF-GFP

value: 20 min


title: sorted non-classical monocytes HLA-DR+ CD11c+ CD14lo CD16+ healthy control 3

city: Utrecht

first: Arjan

last: Boltjes

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center

description:
HC3ncMo
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.

data_processing:
Sequencing reads were mapped against the reference human genome (hg19, NCBI37) using Burrows-Wheeler Aligner (BWA) (-c –l 25 –k 2 –n 10)
Cisgenome v2.0 software package was used to calculate raw gene counts and reads per 1000 base pairs of transcript per million reads sequenced (RPKM) values for all RefSeq annotated genes
Assembly: hg19/NCBI37
Supplementary files format and content: AB_raw_QN_rna_GEO.txt: raw counts
Supplementary files format and content: AB_RPKM_QN_rna_GEO.txt: RPKM counts

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted using TRIzol reagent. mRNA was selected using poly(A) purist MAG kit (Life Technologies) and additionally purified with a mRNA-ONLY Eukaryotic mRNA Isolation Kit (Epicentre)
Transcriptome libraries were constructed using SOLiD total RNA-seq kit (Applied Biosystems)

treatment_protocol: Synovial fluid (SF) was first treated with hyaluronidase for 30min (37°C, 5% CO2) to reduce the viscosity. Then SF mononuclear cells were isolated making use of Ficoll-Paque density gradient centrifugation. Cell types were stained (see title of samples) and FACSsorted to obtain the three cell types of interest. Sorted cells were dissolved in TRIzol and frozen at -80 degrees Celcius until further use

value: Peripheral blood

value: Non-classical monocyte

tag: disease state

value: Healthy control

value: None, directly ex vivo


title: ALYREF,Rep,1,t40

value: 40 min


title: sorted intermediate monocytes HLA-DR+ CD11c+ CD14+ CD16+ healthy control 4

description:
HC4iMo
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.

value: Intermediate monocyte


title: F10-SUZ12, rep1


title: S013782

value: NANT

value: FT Long-term (> 3 yrs) rejection-free survival

value: M

value: blood

value: PBMC


title: S000127

value: AUH

value: Healthy adult volunteer


title: ALYREF,Rep,1,t10

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: DRB

value: 10 min


title: 9259684035_R04C02

value: 10-5 M AZA


title: F10-RING, rep2


title: 9259684035_R02C02

source_name: DU-145 cells treated with 2.5*10-4 M SAM


title: F10-RING, rep1


title: sorted intermediate monocytes HLA-DR+ CD11c+ CD14+ CD16+ healthy control 2

description:
HC2iMo
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.

value: Peripheral blood


title: 9259684035_R05C01


title: ALYREF,Rep,1,t05

value: ALYREF-GFP

value: 05 min


title: ALYREF,Rep,1,t15

value: 15 min


title: sorted intermediate monocytes HLA-DR+ CD11c+ CD14+ CD16+ healthy control 3

description:
HC3iMo
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.

value: Intermediate monocyte

value: Healthy control

value: None, directly ex vivo


title: 9259684035_R03C01


title: sorted intermediate monocytes HLA-DR+ CD11c+ CD14+ CD16+ healthy control 1

description:
HC1iMo
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.


title: F10-BMI1, rep2

value: SHDS, 8/6/15, clone 1H1


title: 9259684035_R06C01

description: genomic DNA from DU-145 cells

source_name: DU-145 cells

value: untreated


title: S006849

value: Baseline

value: F

value: blood

value: PBMC


title: 9259684035_R05C02

description: genomic DNA from DU-145 cells


title: ALYREF,Rep,1,t00-1

source_name: HeLa

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: 00 min


title: F10-BMI1, rep1


title: ALYREF,Rep,1,t00-2

value: DRB


title: sorted classical monocytes HLA-DR+ CD11c+ CD14hi CD16- healthy control 4

description:
HC4cMo
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.

value: Peripheral blood

value: Classical monocyte


title: TIG3-Input, rep3


title: ALYREF,Rep,1,negative

value: WT

value: DMSO


title: sorted classical monocytes HLA-DR+ CD11c+ CD14hi CD16- healthy control 3

description:
HC3cMo
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.


title: 9259684035_R01C01

description: genomic DNA from DU-145 cells


title: ALYREF,Rep,2,t00-1

value: ALYREF-GFP


title: TIG3-H3K27me3, rep2

value: Abcam, #ab6002


title: sorted classical monocytes HLA-DR+ CD11c+ CD14hi CD16- healthy control 2

description:
HC2cMo
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.

value: Healthy control

value: None, directly ex vivo


title: TIG3-H3K27me3, rep1


title: sorted classical monocytes HLA-DR+ CD11c+ CD14hi CD16- healthy control 1

description:
HC1cMo
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.


title: Sorted cDC2 HLA-DR+ CD11c+ CD14- CD16- CD141-/dim CD1c hi healthy control 3

description:
HC3mDC1
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.

value: cDC1 dendritic cell


title: TIG3-RING, rep2


title: S001018

source_name: PBMC

value: Baseline

value: AUH

value: PL Acute rejection < 3 yrs post-transplant

value: M


title: Sorted cDC2 HLA-DR+ CD11c+ CD14- CD16- CD141-/dim CD1c hi healthy control 2

description:
HC2mDC1
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.


title: TIG3-RING, rep1


title: S012387

value: CUB

value: FT Long-term (> 3 yrs) rejection-free survival

value: blood

value: PBMC


title: NT2-Input, rep3


title: LNVg4RNA

city: Hannover

first: Tao

last: Yang

address: Carl-Neuberg-Straße 1

country: Germany

institute: Hannover Medical School

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger 3.1 (scRNA-seq) or Cell Ranger ATAC 1.2 (scATAC-seq) (10x Genomics)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: γdelta T cells

extract_protocol:
After blocking and staining, sorting was performed by using the FACSAria Fusion (BD)
Thymic and pLNs Vg4 cells were directly subjected to scRNA-seq or scATAC-seq library construction using the Kits from 10xGenomics

value: γdelta T cells

value: peripheral lymph nodes

value: 7-12 weeks old


title: LNVg4ATAC

description: 10x Genomics


title: ThyVg4RNA

description: 10x Genomics

value: thymus


title: ThyVg4ATAC

description: 10x Genomics


title: Sorted cDC2 HLA-DR+ CD11c+ CD14- CD16- CD141-/dim CD1c hi healthy control 1

description:
HC1mDC1
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.

value: Peripheral blood


title: S001921

value: Healthy adult volunteer

value: F


title: InduThyVg4ATAC

description: 10x Genomics


title: NT2-H3K27me3, rep2

value: Abcam, #ab6002


title: sorted monocytes HLA-DR+ CD11c+ CD14+ CD16+ patient 4

description:
JIA4iMo
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.

source_name: Synovial fluid

value: Synovial fluid

value: Monocyte

value: Juvenile idiopathic arthritis

value: None, directly ex vivo


title: S003689

value: Baseline

value: FT Stable < 3 yrs post-transplant


title: S010888

value: AUH

value: PL Long-term (> 3 yrs) rejection-free survival


title: S001344

value: blood

value: PBMC


title: NT2-H3K27me3, rep1


title: sorted monocytes HLA-DR+ CD11c+ CD14+ CD16+ patient 3

description:
JIA3iMo
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.


title: NT2-RING, rep2


title: ALYREF,Bio Rep,1,DMSO

value: HeLa

value: Human papillomavirus-related endocervical adenocarcinoma

value: ALYREF-GFP

value: DMSO


title: S000978

value: CUB

value: PL Stable < 3 yrs post-transplant


title: sorted monocytes HLA-DR+ CD11c+ CD14+ CD16+ patient 2

description:
JIA2iMo
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.


title: S002140

value: FT Long-term (> 3 yrs) rejection-free survival

value: M


title: NT2-RING, rep1


title: PreDC_Patient_D046T9

first: Philippe

last: Benaroch

address: 12, rue Lhomond

department: INSERM U932 Immunity and Cancer

institute: Institut Curie

data_processing:
Sample demultiplexing, alignment, UMI counting, and cell calling is performed using CellRanger v2.1.0 with default parameters
Assembly: GRCh38
Supplementary files format and content: tsv and mtx files containing the gene/cell expression matrices (UMI counts)

extract_protocol:
Chromium Single Cell 3' Reagent Kits v2 (10X Genomics)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ex vivo primary dendritic cells


title: sorted monocytes HLA-DR+ CD11c+ CD14+ CD16+ patient 1

description:
JIA1iMo
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.

value: Synovial fluid

value: Monocyte

value: Juvenile idiopathic arthritis


title: Sorted cDC2 HLA-DR+ CD11c+ CD14- CD16- CD141-/dim CD1c hi patient 4

description:
JIA4mDC1
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.

value: cDC2 dendritic cell

value: None, directly ex vivo


title: iBMDM_Mab_Hi_Rep3

city: East Lansing

first: Andrew

last: Olive

state: MI

address: 567 Wilson Rd

department: Microbiology and Molecular Genetics

institute: Michigan State University

data_processing:
Illumina software was used for Basecalls
FastQC (v0.11.5) was used to assess the quality of raw data.
Cutadapt (v2.9) was used to removeadapter sequences
Assembly: sgRNA counts were determined using MAGeCK "count" function with trimmed FASTq files as input
significant changes in gene representation were quantified using MAGeCK "test" using the robust rank algorithm
Supplementary files format and content: Normalized Count table was generated using MAGeCK

source_name: immortalized bone marrow-derived Macrophages

growth_protocol: Macrophages were grown in DMEM with 10% FBS  for the duration of the experiment

extract_protocol:
Cells were lysed and total genomic DNA was isolated using aluminum acetate purification
Libraries were constructed using Truseq primers and indexes

treatment_protocol: Transduced library was infected with mEmerald M. abscessus for four hours then cells were sorted into infected and uninfected populations

value: Bone marrow

tag: derivation

value: J2 immortalized and Cas9 Transduced


title: iBMDM_Mab_Lo_Rep2


title: iBMDM_Mab_Lo_Rep1


title: iBMDM_Mab_Hi_Rep2


title: iBMDM_Mab_Lo_Rep3


title: S006577

value: Baseline

value: AUH

value: Non-transplanted corneal disease

value: blood

value: PBMC


title: preDC_AD8_plus_Vpx_24h

data_processing:
A concatenated reference sequence for human and HIV is built with Cellranger mkref
Sample demultiplexing, alignment, UMI counting, and cell calling is performed using CellRanger v2.1.0 with default parameters
Gene-cell expression matrices for all samples are imported and merged with Seurat v2.3.4. Cells with <200 detected genes (UMI>0) and genes detected in <3 cells across the samples are filtered out
Expression values are normalized and log-transformed (log((xij+1)/nj) where x is the UMI count of gene j in cell i and nj is the total UMI count for cell j); normalized gene expression values are centered and scaled (z-score)
Assembly: GRCh38
Assembly: NC_001802
Supplementary files format and content: tsv and mtx files containing the gene/cell expression matrices (UMI counts)

growth_protocol: Isolated cells were cultured in Xvivo medium (Lonza)

treatment_protocol: Cells were cultured with HIV-1 NL-AD8 complemented or not with Vpx (plasmid VPX-any-VPR) for 24 hours

value: preDC

tag: time point (hour)

value: HIV-1 NL-AD8 complemented with Vpx


title: Sorted cDC2 HLA-DR+ CD11c+ CD14- CD16- CD141-/dim CD1c hi patient 3

description:
JIA3mDC1
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.


title: iBMDM_Mab_Hi_Rep1

tag: strain


title: Sorted cDC2 HLA-DR+ CD11c+ CD14- CD16- CD141-/dim CD1c hi patient 2

description:
JIA2mDC1
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.


title: S004491

value: FT Stable < 3 yrs post-transplant

value: F


title: S012446

value: CUB


title: S000803

value: FT Long-term (> 3 yrs) rejection-free survival

value: M


title: preDC_AD8_24h

value: HIV-1 NL-AD8


title: S012164

value: PL Long-term (> 3 yrs) rejection-free survival


title: ARKOTalKO-6956

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

data_processing:
BaseSpace
Sequence reads were trimmed for adaptor sequence
Trimmed reads were mapped to mm10 of the mouse genome in Cufflinks (with Bowtie)
Raw gene counts used for data analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes matrix of raw gene counts for all samples

source_name: liver

extract_protocol:
RNA was extracted from livers using the Qiagen RNeasy kit (Qiagen). Sequencing libraries were quantified using the KAPA Library Quantification Complete Kit Universal (KAPA Biosystems). The pooled library (1.4pM) was loaded onto the NextSeq 500 instrument, using the NextSeq 500/550 High Output v2 Kit for 75 cycles (Illumina). Cufflinks software was used to quantify gene expression and to detect transcript isoforms. Normalized data appear as Reads per Kilobase per Million reads (RPKM).
Sequencing library preparation was done with the Illumina TruSeq Stranded Total RNA with RiboZero Gold kit following manufacturer's instructions.

value: liver

tag: age

value: 14-16 weeks old

value: TalKO/ArKO

tag: Sex

value: female


title: Sorted cDC2 HLA-DR+ CD11c+ CD14- CD16- CD141-/dim CD1c hi patient 1

description:
JIA1mDC1
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.

value: Synovial fluid

value: cDC2 dendritic cell

value: Juvenile idiopathic arthritis

value: None, directly ex vivo


title: cDC2_AD8_plus_Vpx_24h


title: ARKOTalKO-6959


title: Sorted cDC1 HLA-DR+ CD11c+ CD14- CD16- CD1c- CD141hi patient 4

description:
JIA4mDC2
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.

value: cDC1 dendritic cell


title: cDC2_AD8_24h


title: sorted non-classical monocytes HLA-DR+ CD11c+ CD14lo CD16+ healthy control 4

description:
HC4ncMo
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.

value: Peripheral blood

value: Non-classical monocyte

value: Healthy control


title: Sorted cDC1 HLA-DR+ CD11c+ CD14- CD16- CD1c- CD141hi patient 3

description:
JIA3mDC2
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.


title: MOCK_24h

value: mock medium


title: ARKOTalKO-7188


title: preDC_D0

value: preDC


title: Sorted cDC1 HLA-DR+ CD11c+ CD14- CD16- CD1c- CD141hi patient 2

description:
JIA2mDC2
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.


title: S002382

value: Baseline

value: CUB

value: FT Chronic graft injury (> 3 yrs post-transplant)

value: M

value: blood

value: PBMC


title: ARKOTalKO-7341

value: liver

value: 14-16 weeks old

value: TalKO/ArKO

value: female


title: S001095

value: AUH

value: FT Acute rejection < 3 yrs post-transplant

value: F


title: S011296

value: UBR

value: Healthy adult volunteer


title: S013585

value: Non-transplanted corneal disease


title: S013101


title: S010699


title: Sorted cDC1 HLA-DR+ CD11c+ CD14- CD16- CD1c- CD141hi patient 1

description:
JIA1mDC2
The raw RNA-seq data from the cohort are not publicly available due to research participant privacy/consent.

value: Synovial fluid

value: cDC1 dendritic cell

value: Juvenile idiopathic arthritis

value: None, directly ex vivo


title: cDC_D0


title: S014234

value: Baseline

value: CUB

value: FT Stable < 3 yrs post-transplant


title: heart_E10.5_WT

city: Nanjing

first: Jimiao

last: Gao

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10X Genomics spaceranger-1.3.1  (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/using/count)
Assembly: mm10
Supplementary files format and content: *.tar.gz: Each processed spatial data file includes the outputs of SpaceRanger - cloupe, molecule_info.h5, filtered_feature_matrix.h5, metrics_summary.csv, raw_feature_bc_matrix.h5, and all spatial images (jpg and png) with scale factors and tissue positions

source_name: heart

extract_protocol:
The tissues obtained from emryonic day 10.5 heart were treated with cleanroom wipers. After removing blood stains on the tissue surface, resh tissue was embedded with OCT then snap frozen at -80℃. Cryosections were cut at 10-µm thickness, mounted onto the ST arrays .Next, the tissue was dehydrated with isopropanol for 1 min followed by staining with H&E. Slides were mounted in 80% glycerol and brightfield images were taken on a Leica DN6B at 20× resolution
Library preparation slides used were purchased from the Spatial Transcriptomics team (https://www.10xgenomics.com/), Each of the spots printed onto the array is 55µm in diameter and 100µm from center to center, covering an area of 6.5×6.5 mm2.Each slide Includes 4 Capture Areas, each with ~5,000 unique gene expression spots.After brightfield imaging, the ST slide was prewarmed to 42 °C and attached to a microarray slide module (Grace Biolabs). i. Add 70 μl Permeabilization Enzyme to B1 along the side of the well (30 min) and tap cassette.ii. Apply Slide Seal to the Slide Cassette and place on the Thermocycler Adaptor at 37°C. Close lid. iii.After 6 min, remove the Slide Cassette from Thermocycler Adaptor and remove seal. iv.Add 70 µl Permeabilization Enzyme along the side of the well to the C1 and incubate on the Thermocycler Adaptor at 37°C with the lid closed. v. Repeat process, working backwards to the shortest incubation time (3 min). Remove Slide Cassette from the Thermocycler Adaptor after time course completion.Using a pipette, remove Permeabilization Enzyme from each well without touching the tissue sections.Add 100 µl 0.1X SSC to all wells except the positive control. Using a pipette, remove 0.1X SSC from each well. Add 50 µl Fluorescent RT Master Mix to each well, ensuring that the well surface is uniformly covered with the Master Mix.Apply Slide Seal on the Slide Cassette firmly and place on the Thermocycler Adaptor on the pre-heated thermal cycler. Close thermal cycler lid(53°C 45min) then Skip Pre-equilibrate to initiate cDNA Synthesis.
Libraries were prepared after the above operations. Libraries were diluted to 4 nM and paired-end sequencing was performed on an Illumina NovaSeq 6000 sequencer, with 31 cycles for read 1 and 55 cycles for read 2. Between 100 million and 200 million raw read-pairs were generated for each sequenced library.

value: heart

value: wild type

value: embryonic day 10.5


title: ArKOTalWT-6966

value: liver

value: 14-16 weeks old

value: TalWT/ArKO

value: female


title: heart, Input, WT

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
CHIP reads were trimmed using trim_galore (v0.6.4) with default settings (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Sequencing reads were mapped to the mm10 reference genome using Burrow-Wheeler Aligner Maximal Exact Matches (BWA-MEM v0.7.17)
PCR duplicates were removed using Piccard
Peaks were identified using MACS2 (v2.2.6)(parameters —shift 0 —extsize 200 -f BAMPE —nomodel -g mm -q 0.05 keep-dup all)
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
400 snap-frozen E10.5 heart samples were cross-linked for 10 min in 1% ChIP-seq–grade formaldehyde and washed in 1X PBS and then dispersed into a single cell suspension using a Dounce homogenizer (Fisher scientific # 06–435A). The product was sonicated, and the DNA sheared to fragments of 300 to 500 base pairs.
DNA libraries (Vazyme, Cat #ND607-02) were prepared from the CHIP and input DNA using the standard consecutive enzymatic steps to end polishing, dA addition and adaptor ligation using Active Motif’s custom liquid handling robotics pipeline. After the final 15-cycle PCR amplification step, the resulting DNA libraries were quantified (concentration > 10 nM) and sequenced with PE150 sequencing on the Illumina Novaseq sequencer (Illumina)


title: ARKOTalKO-7052

value: TalKO/ArKO


title: ArKOTalWT-6967


title: SEM sh2

city: New York

first: Sonali

last: Narang

address: 435 east 30th street

institute: NYU Langone

library_source: genomic single cell

data_processing:
Aigned to reference genome (hg19) using Bowtie2
Reads filtered for accepted intra-chromosomal read-pairs by the GenomicTools tools-hic filter command in the hic-bench platform
Interaction matrices for each chromosome separately were created by the hic-bench platform at 40kb resolution
Filtered read counts were normalized by iterative correction and eigenvector decomposition
To account for variances in read counts of more distant loci, distance normalization for each chromosome matrix was performed.
Assembly: hg19
Supplementary files format and content: .hic files consist of hic signal for each cell line

source_name: B-ALL cell line

growth_protocol: The B-lineage leukemia cell lines RS4;11, Reh (ATCC, Manassas, VA), 697, RCH-ACV (DSMZ, Braunschweig, Germany), and SEM (kindly gifted by Jun Yang, St. Jude Children’s Hospital) were grown in RPMI1640 medium. All media were supplemented with 10% FBS, 1% penicillin/streptomycin under 5% CO2 at 37°C. No cell lines were used beyond passage 20.

extract_protocol:
Five million cells from actively growing NSD2 High and Low cell lines were crosslinked with 2% PFA and quenched with glycine. Following crosslinking, cells were lysed, DNA digested and proximally ligated following Arima Genomics’ Hi-C kit User Guide for Mammalian Cell Lines by the NYU Langone Genome Technology Center.
Hi-C libraries were generated using Arima HiC Kit along with Swift 2S Plus Kit and Swift Indexing Kit following Arima-HiC Kit Library Preparation using Swift Biosciences(R) Accel-NGS(R) 2S Plus DNA Library Kit User Guide.

value: bone marrow

tag: cell line

value: SEM

value: NSD2 sh2


title: S010838

data_processing: CEL files were imported into R and the input data was normalised using RMA, resulting in normalised expression levels in log base 2

extract_protocol: RNA was extracted from whole blood collected with PAXgene RNA tubes according to the manufacturer's recommendations

value: Healthy adult volunteer

value: F

value: blood

tag: cell type

value: PBMC


title: heart, H3K4me3, activemotif, WT, rep2

value: H3K4me3 (Active Motif,39159)


title: ArKOTalWT-7185

tag: genotype


title: RS411 sh2

tag: treatment


title: ArKOTalWT-6993


title: SEM NT

value: NSD2 NT


title: S010672

tag: time

value: Baseline

value: CUB

value: M


title: heart, H3K27ac, activemotif, WT, rep2

value: heart

value: H3K27ac (Active Motif,39133)


title: In-planta Z.tritici strain Zt99 infection, 9 days post infection, replicate 4

first: Daniel

last: Smith

address: West Common

institute: Rothamsted Research

data_processing:
Reads mapped using HiSat2 (v2.0.5)
Mapped reads counted using Subread FeatureCounts (v1.6.2)
Assembly: pangenome assembly: Pangenome_Zt_17I_IPO323_v3.fasta ; annotation: annotation_pangenomveV3_2.gtf (bespoke for this paper, data archived and included here)
Supplementary files format and content: FeatureCount gene counts: ztriticiPangenomePlantaCounts.txt

organism: Triticum aestivum

source_name: wheat leaves

extract_protocol:
TRIzol (Invitrogen)
Illumina 100bp  paired-end reads

tag: cultivar

value: Panorama

tag: infection

value: Zymoseptoria tritici strain Zt99


title: RCH sh2

value: RCH-ACV


title: heart, H3K4me3, activemotif, WT, rep1


title: In-planta Z.tritici strain Zt99 infection, 9 days post infection, replicate 3


title: RS411 NT

value: bone marrow


title: ArKOTalWT-7337

value: liver

value: 14-16 weeks old

value: TalWT/ArKO

value: female


title: In-planta Z.tritici strain Zt99 infection, 9 days post infection, replicate 1


title: S010782

tag: individual (patient id)

tag: center

tag: patient group

value: Healthy adult volunteer

value: blood


title: heart, H3K27ac, activemotif, WT, rep1

tag: tissue

tag: chip antibody


title: TalKO-7122

value: TalKO/ArWT


title: I757, replicate 1, scRNAseq

description: 10x Genomics

value: CD8 cell

value: Blood


title: RCH NT

value: NSD2 NT


title: S009620

value: Baseline

value: AUH

value: Non-transplanted corneal disease

tag: gender

value: F

value: PBMC


title: S009757

value: RCSI

value: FT Stable < 3 yrs post-transplant


title: nsp1

data_processing:
Library strategy: TCR-seq
cellranger
Seurat performs cell clustering and TCR analysis
Genome_build: Homo_sapiens_Ensemble_94
Supplementary_files_format_and_content: Matrix table  for TCR with raw counts

extract_protocol: 10X single cell TCR  libraries were prepared for sequencing using standard Illumina protocols

value: young


title: In-planta Z.tritici strain Zt99 infection, 6 days post infection, replicate 4

value: Panorama

value: Zymoseptoria tritici strain Zt99


title: heart, RNA pol II, activemotif, WT, rep2

value: heart

value: RNA pol II (Active Motif,39097)


title: TalKO-6945

value: liver

value: 14-16 weeks old

value: female


title: In-planta Z.tritici strain Zt99 infection, 6 days post infection, replicate 3


title: I757

value: CD8 cell


title: heart, RNA pol II, activemotif, WT, rep1


title: TalKO-7028

value: TalKO/ArWT


title: TalKO-6866


title: E357


title: S005936

value: Baseline

value: PL Long-term (> 3 yrs) rejection-free survival

value: blood


title: heart, H3K4me1, activemotif, WT, rep2

value: H3K4me1 (Active Motif,61781)


title: TalKO-7347


title: TalWT-6867

value: TalWT/ArWT


title: heart, H3K4me1, activemotif, WT, rep1


title: TalWT-6944


title: In-planta Z.tritici strain Zt93 infection, 9 days post infection, replicate 3

value: Zymoseptoria tritici strain Zt93


title: BY_CD8_2

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 Homo sapiens whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Genome_build: Homo_sapiens_Ensemble_94
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CD8 cell

extract_protocol:
Total RNA was isolated from CD8+ T, CD4+ T and B cells of 3 young and older people using TRIzol Reagent (Invitrogen)  (7-days post second vaccination dose) . RNA purity was checked by the NanoPhotomerer spectrophotometer (IMPLEN), and integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies). Then cDNA libraries were constructed using 0.1 µg RNA per sample with the NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: vaccine

value: before vaccine

value: Young


title: BY_CD8_3


title: TalWT-7029

tag: strain


title: In-planta Z.tritici strain Zt93 infection, 9 days post infection, replicate 4

value: Panorama


title: BY_CD4_3

source_name: CD4 cell

value: CD4 cell

tag: age


title: BY_CD8_1


title: heart_8W_rep2

data_processing:
fastp(Version 0.18.0)
Raw data were filtered and processed by fastqp and aligned to the mouse reference genome GRCm38/mm10 with STAR software (v2.5.3a)
Assembly and quantification of the transcripts were accomplished with RESM software (Version1.3.3) guided by the Ensembl gtf gene annotation file (http://www.ensembl.rog/)
Assembly: mm10
Supplementary files format and content: tab-delimited matrix included raw counts for each Sample

extract_protocol:
Total RNA was extracted with TrizolTM X-100 (Thermo) treatment and a total amount of 2 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using VAHTS mRNA-seq v2 Library Prep Kit (Illumina). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and cut into small fragments for cDNA synthesis. After adenylation of 3’ ends of DNA fragments, adaptor with hairpin loop structure were ligated, and then PCR was performed. High-throughput RNA sequencing were carried out using Illumina NovaSeq platform

value: heart

value: WT

value: untreated

value: postnatal week 8


title: In-planta Z.tritici strain Zt93 infection, 9 days post infection, replicate 2


title: heart_8W_rep3


title: TalWT-7112

value: liver

value: 14-16 weeks old

tag: Sex

value: female


title: In-planta Z.tritici strain Zt93 infection, 6 days post infection, replicate 4


title: heart_8W_rep1


title: heart_4W_rep3

value: postnatal week 4


title: TalWT-7346


title: BY_CD4_1


title: BY_CD4_2


title: heart_4W_rep2


title: In-planta Z.tritici strain Zt99 infection, 6 days post infection, replicate 2

value: Zymoseptoria tritici strain Zt99


title: BY_B_cell_3

source_name: B cell

value: B cell


title: heart_4W_rep1


title: P27-P29 scRNA-seq, iCON (Control) cochlea

city: Boston

first: Brikha

middle: Raj

last: Shrestha

state: MA

address: 243 Charles Street

department: Otolaryngology

institute: Harvard Medical School

description: 10x Genomics

data_processing:
Cell Ranger (10x Genomics) was used for de-multiplexing and initial processing; subsequent analysis using raw count matrix was performed in Seurat. After a preliminary clustering analysis that identified SGN-specific clusters, cells with less than 5000 genes detected were discarded and genes expressed in fewer than 3 cells were discarded before further analysis.
Assembly: mm10
Supplementary files format and content: csv format; log-normalized and scaled count matrix for SGNs that passed quality filters; processed in Seurat (R package)

source_name: Cochlea

extract_protocol:
10x Genomics 3' assay v3
Dual-indexed single cell transcriptomic libraries were created using the 10X Genomics Chromium Single Cell 3' GEM Library and Gel Bead Kit v3. Libraries were sequenced using the NextSeq 500/550 High Output Kit v2.5 (75 Cycles, Illumina).

value: Cochlea

value: Spiral Ganglion Neurons

value: iCON (Runx1-CreER/+; Ai14/+)

value: Tamoxifen treatment at P1


title: BY_B_cell_2

value: before vaccine

value: Young


title: P27-P29 scRNA-seq, Runx1-iCKO cochlea

description: 10x Genomics

value: iCKO (Runx1-CreER/Runx1F; Ai14/+


title: P30-P33 scRNA-seq, Runx1-CKO cochlea cko6

description:
P30-P33 scRNA-seq, Runx1-CKO cochlea
10x Genomics

data_processing:
Cell Ranger (10x Genomics) was used for de-multiplexing and initial processing; subsequent analysis using raw count matrix was performed in Seurat. After a preliminary clustering analysis that identified SGN-specific clusters, cells with less than 4000 genes detected were discarded and genes expressed in fewer than 5 cells were discarded before further analysis.
Assembly: mm10
Supplementary files format and content: csv format; log-normalized and scaled count matrix for SGNs that passed quality filters; processed in Seurat (R package)

value: CKO (bhlhb5-Cre/+; Ai14/+; Runx1F/F)

value: Genetic ablation of Runx1 expression


title: BY_B_cell_1


title: In-planta Z.tritici strain Zt92 infection, 9 days post infection, replicate 2

city: Harpenden

value: Panorama

value: Zymoseptoria tritici strain Zt92


title: heart_2W_rep2

value: heart

value: WT

value: untreated

value: postnatal week 2


title: In-planta Z.tritici strain Zt92 infection, 9 days post infection, replicate 1


title: heart_2W_rep3


title: P30-P33 scRNA-seq, Runx1-CKO cochlea cko5


title: In-planta Z.tritici strain Zt93 infection, 6 days post infection, replicate 3

value: Zymoseptoria tritici strain Zt93


title: BO_CD8_3

value: CD8 cell

value: Old


title: P30-P33 scRNA-seq, Runx1-CKO cochlea cko4

value: Cochlea

value: Spiral Ganglion Neurons


title: In-planta Z.tritici strain Zt92 infection, 6 days post infection, replicate 2


title: In-planta Z.tritici strain Zt92 infection, 6 days post infection, replicate 3


title: BO_CD8_2


title: In-planta Z.tritici strain Zt93 infection, 6 days post infection, replicate 2


title: heart_2W_rep1


title: heart_1W_rep3

value: postnatal week 1


title: BO_CD8_1

value: before vaccine


title: P30-P33 scRNA-seq, Control cochlea con4

description:
P30-P33 scRNA-seq, Control cochlea
10x Genomics

value: Control (bhlhb5-Cre/+; Ai14/+)


title: P30-P33 scRNA-seq, Control cochlea con5


title: BO_CD4_3

value: CD4 cell


title: heart_1W_rep2


title: In-planta Z.tritici strain Zt88 infection, 9 days post infection, replicate 4

value: Zymoseptoria tritici strain Zt88


title: In-planta Z.tritici strain Zt92 infection, 9 days post infection, replicate 4


title: heart_1W_rep1


title: BO_CD4_2


title: PBMC, CTRL_10

city: Changchun

first: Xiaosong

last: Wang

state: Jilin

address: No.519 Dongminmin Street Changchun 130021, China

institute: Department of Translational Medicine, the First Hospital of Jilin University

data_processing:
Firstly, ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA) and rRNA-free residues were cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit (NEB, USA) following the manufacturer’s recommendations. Sequencing library quality was assessed on Agilent Bioanalyzer 2100 system. Finally, sequencing was performed with Illumina HiSeq X Ten (paired-end 150-bp reads).
StringTie (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding transcripts in each sample. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
edgeR is a Bioconductor software package for examining differential expression of replicated count data. Gene Ontology (GO) enrichment analysis of differentially expressed genes or lncRNA target genes were implemented by the GOseq R package. We used KOBAS software to test the statistical enrichment of differential expression genes or lncRNA target genes in KEGG pathways.
Assembly: hg38
Supplementary files format and content: Transcript_FPKM.txt: Tab-delimited text file includes FPKM values.

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were treated with TRIzol reagent (Invitrogen, Carlsbad, California, USA) and stored at –80°C (5 × 10^6 cells/mL).
RNA purity was tested using NanoPhotometer® (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit on a Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). RNA integrity was assessed using RNA Nano 6000 Assay Kit on a Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: Peripheral blood mononuclear cells

tag: diagnosis

value: Healthy


title: In-planta Z.tritici strain Zt88 infection, 9 days post infection, replicate 3

value: Panorama


title: heart_P1_rep3

value: heart

value: postnatal day 1


title: BO_B_cell_3

value: B cell


title: In-planta Z.tritici strain Zt88 infection, 6 days post infection, replicate 4


title: BO_CD4_1


title: PBMC, CTRL_8

tag: cell type


title: heart_P1_rep2

tag: genotype

value: WT

value: untreated


title: PBMC, CTRL_9


title: In-planta Z.tritici strain Zt88 infection, 9 days post infection, replicate 2


title: PBMC, CTRL_7


title: heart_E18.5_rep3

tag: treatment

value: embryonic day 18.5


title: heart_P1_rep1

tag: time


title: PBMC, CTRL_5


title: In-planta Z.tritici strain Zt92 infection, 6 days post infection, replicate 1

tag: cultivar

value: Zymoseptoria tritici strain Zt92


title: heart_E18.5_rep2


title: BO_B_cell_1

value: Old


title: PBMC, CTRL_6


title: In-planta Z.tritici strain Zt88 infection, 6 days post infection, replicate 1

tag: infection


title: heart_E18.5_rep1


title: PBMC, CTRL_4


title: A2Y_CD8_2

value: vaccine 2 dose

value: CD8 cell

value: Young


title: A2Y_CD8_3


title: In-planta Z.tritici strain Zt80 infection, 9 days post infection, replicate 3

value: Zymoseptoria tritici strain Zt80


title: heart_E16.5_rep3

value: embryonic day 16.5


title: In-planta Z.tritici strain Zt80 infection, 9 days post infection, replicate 4


title: A2Y_CD8_1


title: heart_E16.5_rep2


title: In-planta Z.tritici strain Zt80 infection, 9 days post infection, replicate 2


title: PBMC, CTRL_3


title: PBMC, CTRL_2


title: In-planta Z.tritici strain Zt80 infection, 6 days post infection, replicate 4


title: heart_E16.5_rep1


title: PBMC, CTRL_1


title: In-planta Z.tritici strain Zt88 infection, 6 days post infection, replicate 2

value: Zymoseptoria tritici strain Zt88


title: A2Y_CD4_3

value: CD4 cell


title: A2Y_CD4_2


title: BO_B_cell_2

value: before vaccine


title: PBMC, LN_10

value: Peripheral blood mononuclear cells

value: SLE with LN


title: A2Y_CD4_1


title: In-planta Z.tritici strain Zt80 infection, 6 days post infection, replicate 1

value: Panorama


title: A2Y_B_cell_3

value: B cell


title: heart_E14.5_rep3

value: heart

value: WT

value: embryonic day 14.5


title: PBMC, LN_9


title: heart_E14.5_rep1

value: untreated


title: heart_E14.5_rep2


title: In-planta Z.tritici strain Zt74 infection, 9 days post infection, replicate 4

value: Zymoseptoria tritici strain Zt74


title: A2Y_B_cell_1

value: vaccine 2 dose


title: In-planta Z.tritici strain Zt74 infection, 9 days post infection, replicate 1


title: PBMC, LN_8


title: A2Y_B_cell_2


title: heart_E12.5_rep2

value: embryonic day 12.5


title: PBMC, LN_6


title: PBMC, LN_7


title: PBMC, LN_5


title: heart_E12.5_rep1


title: A2O_CD8_3

value: CD8 cell

value: Old


title: In-planta Z.tritici strain Zt80 infection, 6 days post infection, replicate 3

value: Zymoseptoria tritici strain Zt80


title: heart_E12.5_rep3


title: In-planta Z.tritici strain Zt74 infection, 6 days post infection, replicate 2


title: heart_E10.5_rep3

value: embryonic day 10.5


title: A2O_CD8_2


title: In-planta Z.tritici strain Zt74 infection, 6 days post infection, replicate 1


title: PBMC, LN_4


title: PBMC, LN_3


title: In-planta Z.tritici strain Zt74 infection, 9 days post infection, replicate 3


title: In-planta Z.tritici strain Zt48 infection, 9 days post infection, replicate 2

value: Zymoseptoria tritici strain Zt48


title: PBMC, LN_2


title: heart_E10.5_rep1


title: PBMC, LN_1


title: A2O_CD4_2

value: CD4 cell


title: A2O_CD4_1


title: In-planta Z.tritici strain Zt48 infection, 9 days post infection, replicate 1


title: PBMC, SLE without LN_10

value: Peripheral blood mononuclear cells

value: SLE without LN


title: Mouse RNA-seq - PE 1day rep4

city: Beijing

first: Di

last: Zhang

address: No.5 YiHeYuan Road, Haidian District

institute: Peking University

data_processing:
Data manipulation included removing reads containing adapter, reads containing poly-N, and low-quality reads from raw data.
Then the clean reads were mapped to the mouse reference genome GRCm38.p6 from the National Center for Biotechnology Information (NCBI) database using Hissat2 v2.0.5.
Genes with zero count in all samples were filtered out, leaving 24,188 genes under ISO treatment and 23,526 genes under PE treatment. The mRNA levels were normalized to gene length and total counts as transcripts per million (TPM).
Assembly: GRCm38.p6
Supplementary files format and content: Raw gene counts FPKM, and TPM values for every gene and every sample.

source_name: Heart

extract_protocol:
After 1 hour, 1 day, or 3 days, mice were euthanatized following anesthetization with an overdose of pentobarbital. The heart tissue was collected for further determination. A total amount of 1 μg RNA was used as input material for the RNA sample preparations. mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X).
First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using dNTP with DNA Polymerase I system. After adenylation of 3’ ends of DNA fragments, the adaptor with hairpin loop structure was ligated for hybridization. To select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). After PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. To ensure the quality of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

treatment_protocol: All animal experiments were approved by Peking University Institutional Review Board Animal Welfare Committee (LA2021013) and conformed to the guidelines for animal experiments of Peking University Health Science center. The 12-week-old male C57BL/6N mice were bought from Vital River Laboratory Animal Technology Company (Beijing, China) and housed in a specific pathogen-free environment in the Animal Department of Peking University Health Science Center. Mice were randomly allocated into different groups and subcutaneously injected with a single dose of isoprenaline (ISO, 5 mg/kg) or phenylephrine (PE, 10 mg/kg). The dosage was chosen according to our previous studies.

value: male

value: Heart

value: PE treatment

tag: sampling time

value: 1 day


title: Mouse RNA-seq - PE 1day rep5


title: A2O_CD8_1


title: A2O_B_cell_2

value: B cell


title: In-planta Z.tritici strain Zt48 infection, 6 days post infection, replicate 3

value: Panorama


title: Mouse RNA-seq - PE 1day rep2


title: PBMC, SLE without LN_8


title: A2O_B_cell_1


title: In-planta Z.tritici strain Zt48 infection, 6 days post infection, replicate 1


title: Mouse RNA-seq - PE 1day rep1


title: PBMC, SLE without LN_7


title: In-planta Z.tritici strain Zt48 infection, 9 days post infection, replicate 4


title: A2O_CD4_3


title: Mouse RNA-seq - PE 1hour rep5

value: 1 hour


title: In-planta Z.tritici strain Zt36 infection, 9 days post infection, replicate 4

value: Zymoseptoria tritici strain Zt36


title: preDC_CD11cneg_MOCK_D730

city: Paris

data_processing:
Raw fastq reads were trimmed to remove remaining Illumina adaptors using TrimGalore v.0.6.2
A reference sequence for human (hg38) is built with STAR 2.7.3a
A reference sequence for the HIV genome is built with STAR 2.7.3a
Reads were first mapped on the human genome
Unmapped reads on the human genome were mapped on the HIV genome
Counting tables were obtained using featureCounts from Subread 1.5.1
Genome_build: GRCh38
Genome_build: NC_001802
Supplementary_files_format_and_content: tsv files containing human ENSEMBL IDs raw expression values
Supplementary_files_format_and_content: tsv file containing TPM normalized (Transcripts Per Million) expression matrix for human ENSEMBL IDs

growth_protocol: Isolated DC populations were cultured in Xvivo medium (Lonza)

extract_protocol:
SMART-Seq® v4 Ultra® Low Input RNA kit from Takara Bio
RNA libraries were prepared with KAPA HyperPlus kit from Roche

treatment_protocol: Cells were cultured with HIV-1 NL-AD8 complemented or not with Vpx (plasmid VPX-any-VPR),with or without azidothymidine (Azt, 25µM) and neverapin (Nvp, 5µM), for 24 hours

tag: time point (hour)

value: mock medium


title: preDC_CD11cneg_AD8vpx_D730

value: HIV-1 NL-AD8 + Vpx +AZT NVP


title: PBMC, SLE without LN_5


title: In-planta Z.tritici strain Zt36 infection, 9 days post infection, replicate 3


title: A2O_B_cell_3

value: vaccine 2 dose

value: Old


title: In-planta Z.tritici strain Zt36 infection, 9 days post infection, replicate 1


title: Mouse RNA-seq - PE 1hour rep4


title: PBMC, SLE without LN_9


title: Mouse RNA-seq - PE 1hour rep3


title: PBMC, SLE without LN_4


title: preDC_CD11cpos_MOCK_D730


title: In-planta Z.tritici strain Zt36 infection, 6 days post infection, replicate 4


title: Mouse RNA-seq - PE 1hour rep2


title: PBMC, SLE without LN_3


title: In-planta Z.tritici strain Zt48 infection, 6 days post infection, replicate 2


title: preDC_CD11cneg_AD8vpx_D724

value: HIV-1 NL-AD8 + Vpx


title: In-planta Z.tritici strain Zt36 infection, 6 days post infection, replicate 3


title: Mouse RNA-seq - PE 1hour rep1


title: PBMC, SLE without LN_2


title: In-planta Z.tritici strain Zt74 infection, 6 days post infection, replicate 3

value: Zymoseptoria tritici strain Zt74


title: PBMC, SLE without LN_6


title: In-planta Z.tritici strain Zt36 infection, 6 days post infection, replicate 2


title: Mouse RNA-seq - PE Control rep4

value: Control


title: In-planta Z.tritici strain Zt118 infection, 9 days post infection, replicate 3

value: Zymoseptoria tritici strain Zt118


title: preDC_CD11cpos_AD8vpx_D724


title: preDC_CD11cpos_MOCK_D724


title: preDC_CD11cpos_AD8vpx_D730


title: Mouse RNA-seq - PE Control rep2


title: PBMC, SLE without LN_1

value: Peripheral blood mononuclear cells

value: SLE without LN


title: preDC_CD11cneg_AD8vpx_D723


title: Mutant-2

city: 泰安

first: 孙

last: 静

address: 山东农业大学岱宗校区

institute: 山东农业大学

data_processing:
CLC Genomics Workbench
Sequence reads were trimmed for adaptor sequence using CLC genomic benchwork.
Read count extraction and normalization were performed using CLC genomic benchwork.

source_name: axillary bud

extract_protocol:
RNA was harvested using Rneasy mini plus kit.
RNA libraries for RNA-seq were prepared using SMAR TER mRNA-Seq Library Prep Kit following manufacturer's protocols/

value: axillary bud


title: preDC_CD11cneg_MOCK_D724


title: heart_E10.5_rep2

value: heart

value: WT

value: untreated

value: embryonic day 10.5


title: In-planta Z.tritici strain Zt118 infection, 9 days post infection, replicate 1

value: Panorama


title: Mutant-3


title: Mouse RNA-seq - PE Control rep1

value: male

value: Heart


title: Mutant-1


title: preDC_CD11cneg_MOCK_D723

value: mock medium


title: In-planta Z.tritici strain Zt118 infection, 9 days post infection, replicate 2


title: In-planta Z.tritici strain Zt118 infection, 6 days post infection, replicate 4


title: Mouse RNA-seq - ISO 1day rep5

value: ISO treatment

value: 1 day


title: Fielder-3

value: Fielder


title: preDC_CD11cpos_AD8vpx_D723

value: HIV-1 NL-AD8 + Vpx


title: In-planta Z.tritici strain Zt118 infection, 6 days post infection, replicate 2


title: Mouse RNA-seq - ISO 1day rep4


title: preDC_CD11cpos_MOCK_D723


title: Fielder-2


title: Mouse RNA-seq - PE Control rep3

value: Control


title: In-planta Z.tritici strain Zt118 infection, 6 days post infection, replicate 1

value: Zymoseptoria tritici strain Zt118


title: Fielder-1


title: Mouse RNA-seq - ISO 1day rep3


title: cDC2_AD8vpx_AZTNVP_D602

value: HIV-1 NL-AD8 + Vpx + AZT NVP


title: Mouse RNA-seq - ISO 1day rep2


title: In-planta Z.tritici strain Zt117 infection, 9 days post infection, replicate 4

value: Zymoseptoria tritici strain Zt117


title: cDC2_AD8vpx_D602


title: In-planta Z.tritici strain Zt117 infection, 9 days post infection, replicate 2


title: cDC2_AD8_D602

value: HIV-1 NL-AD8


title: Mouse RNA-seq - ISO 1hour rep5

value: 1 hour


title: FMT with PD patient-1

first: Xiaoyun

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description:
The whole Drosophila were collected after FMT experiments
FMT with PD patient.txt

data_processing:
All raw sequencing data were quality controlled by fastqc. Adapters, reads with more than 10% unknown nucleotide (N) content,  and reads with more than half low quality (Q-value <20) bases were removed.
For RNA-seq data, The clean reads were mapped to the dm6 Drosophila reference genome using HISAT2.
For RNA-seq data, The mapped reads of each sample were assembled and quantified by StringTie (version 1.3.1) in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated.
For RNA-seq data, RNA differential expression analyses among groups were performed by DESeq2 (version 1.36.0). The genes/transcripts with the a false discovery rate (FDR) < 0.05 and absolute fold change >2 were considered as differentially expressed genes/transcripts and used for downstream analyses.
Assembly: dm6
Supplementary files format and content: Tab-delimited text file (.txt) include raw read counts for the RNA-seq data of sterile samples

organism: Drosophila melanogaster

source_name: Whole adult

growth_protocol: Drosophila melanogaster w1118 was reared at 25℃ under 12 h light/12 h dark cycles on yeast-glucose medium (1 L water, 100 g yeast, 100 g glucose, 1.2% agar, 0.1% potassium sorbate)

extract_protocol:
Total RNA of RNA-seq samples were homogenized in 1 ml TRIzol (Accurate Biotechnology) and precipitaed by isopropyl alcohol.
After total RNAs of each samples were extracted, the mRNAs enriched by Oligo(dT) beads were fragmented using fragmenta-tion buffer and reverse transcripted into cDNAs with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP, and buffer. The cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen), and were end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina NovaSeq 6000 by Berry Genomics.

treatment_protocol: adult Drosophila were cultured in a yeast-glucose based medium containing 250 μM rotenone (C23H22O6, dissolved in DMSO)

value: Whole adult

tag: growth protocol

value: Feeding with yeast-glucose medium

value: Conventional Drosophila FMT with fecal samples from PD patients

tag: replicate


title: FMT with PD patient-2

tag: tissue


title: FMT with PD patient-3


title: In-planta Z.tritici strain Zt117 infection, 6 days post infection, replicate 4

value: Panorama


title: preDC_AD8vpx_AZTNVP_D602

value: Axl+DC


title: In-planta Z.tritici strain Zt117 infection, 6 days post infection, replicate 3


title: Mouse RNA-seq - ISO 1hour rep3

value: male

value: Heart


title: FMT with Normal control-2

description:
The whole Drosophila were collected after FMT experiments
FMT with Normal control.txt

value: Conventional Drosophila FMT with fecal samples from healthy controls


title: Mouse RNA-seq - ISO 1hour rep2

value: ISO treatment


title: preDC_AD8vpx_D602


title: In-planta Z.tritici strain Zt117 infection, 6 days post infection, replicate 2


title: preDC_AD8_D602


title: PWOFC-3

description:
The whole Drosophila were collected after FMT experiments
dmel-count.txt

value: Parkinson's Drosophila without FMT from control Drosophila


title: In-planta Z.tritici strain Zt116 infection, 9 days post infection, replicate 2

value: Zymoseptoria tritici strain Zt116


title: In-planta Z.tritici strain Zt116 infection, 9 days post infection, replicate 4


title: FMT with Normal control-1


title: preDC_MOCK_D602

value: mock medium


title: Mouse RNA-seq - ISO 1hour rep1


title: Mouse RNA-seq - ISO Control rep5

value: Control


title: FMT with Normal control-3


title: In-planta Z.tritici strain Zt116 infection, 9 days post infection, replicate 1


title: cDC2_AD8vpx_AZTNVP_D601

value: HIV-1 NL-AD8 + Vpx + AZT NVP


title: Mouse RNA-seq - ISO Control rep4


title: PWOFC-1


title: In-planta Z.tritici strain Zt116 infection, 6 days post infection, replicate 3


title: cDC2_AD8vpx_D601

value: HIV-1 NL-AD8 + Vpx


title: In-planta Z.tritici strain Zt116 infection, 6 days post infection, replicate 2


title: In-planta Z.tritici strain Zt117 infection, 9 days post infection, replicate 1

value: Zymoseptoria tritici strain Zt117


title: PWFC-3

value: Parkinson's Drosophila with FMT from control Drosophila


title: Mouse RNA-seq - ISO Control rep3


title: Mouse RNA-seq - ISO Control rep2


title: PWFC-2

value: Whole adult


title: Mouse RNA-seq - ISO Control rep1


title: PWFC-1

value: Feeding with yeast-glucose medium


title: cDC2_MOCK_D601


title: preDC_AD8vpx_AZTNVP_D601


title: In-planta Z.tritici strain Zt114 infection, 9 days post infection, replicate 3

value: Zymoseptoria tritici strain Zt114


title: Dlx3WT_AdGFP_Rep2

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
Demultiplex and convert to FastQ using bcl2fastq v2.20.0.422
Map to mm10 using Tophat 2.1.1
Calculate RPKM (Partek GS 7.0)
ANOVA comparison (Partek GS)
Genome_build: mm10
Supplementary_files_format_and_content: RPKM and ANOVA results in Excel format

source_name: Primary cultured cells

extract_protocol:
Skin epidermis was dissected using a protocol derived from Li et al., 2017, from the transgenic mice and the cells were plated. After 24 hours, cells were transduced with adeno-virus (either Ad-GFP or SAd-Dlx3).
RNA libraries were prepared according to standard Illumina protocol (NEBNext Ultra II RNA Library Prep kit for Illumina; Cat# E7775)

tag: transduction

value: AdGFP

value: Primary cultured cells


title: preDC_AD8vpx_D601

source_name: PBMC

value: Axl+DC


title: In-planta Z.tritici strain Zt114 infection, 9 days post infection, replicate 2

value: Panorama


title: In-planta Z.tritici strain Zt114 infection, 9 days post infection, replicate 1


title: CWOFP-2

city: Guangzhou

value: control Drosophila without FMT from Parkinson's Drosophila


title: preDC_AD8_D601

value: HIV-1 NL-AD8


title: cDC2_AD8_D601


title: Dlx3WT_AdDlx3_Rep2


title: CWFP-3

value: control Drosophila with FMT from Parkinson's Drosophila


title: CWOFP-1


title: Dlx3WT_AdGFP_Rep1


title: In-planta Z.tritici strain Zt114 infection, 6 days post infection, replicate 3


title: cDC2_MOCK_D584


title: In-planta Z.tritici strain Zt114 infection, 6 days post infection, replicate 2


title: Dlx3WT_AdDlx3_Rep1


title: preDC_MOCK_D601


title: In-planta Z.tritici strain Zt116 infection, 6 days post infection, replicate 1

value: Zymoseptoria tritici strain Zt116


title: Dlx3KO_AdGFP_Rep2


title: Mouse RNA-seq - PE 1day rep3

value: male

value: Heart

value: PE treatment

value: 1 day


title: CWOFP-3


title: CWFP-2


title: cDC2_AD8_D584


title: In-planta mock infection, 9 days post infection, replicate 3


title: cDC2_AD8vpx_D584

value: HIV-1 NL-AD8 + Vpx


title: PD-3

description:
The whole Drosophila were collected after rotenone treatment
dmel-count.txt

value: Parkinson's Drosophila reared in based medium with rotenone


title: Mouse RNA-seq - ISO 1day rep1

value: ISO treatment


title: cDC2_AD8vpx_AZTNVP_D584

value: HIV-1 NL-AD8 + Vpx + AZT NVP


title: Dlx3KO_AdDlx3_Rep2


title: Dlx3KO_AdDlx3_Rep1


title: In-planta mock infection, 9 days post infection, replicate 2


title: PD-1

value: Whole adult

value: Feeding with yeast-glucose medium


title: preDC_AD8vpx_AZTNVP_D584


title: preDC_AD8vpx_D584


title: PD-2


title: In-planta mock infection, 9 days post infection, replicate 1


title: CTRL-3

description:
The whole Drosophila were collected were used as controls
dmel-count.txt

value: control Drosophila reared in based medium with DMSO


title: Rhox6 shRNA 2

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

data_processing:
Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from MajorBio company. 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 of MajorBio.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

source_name: 46C mouse embryonic stem cells

extract_protocol:
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. Illumina X ten was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryo

tag: lentiviruses

value: Rhox6 shRNA


title: Rhox6 shRNA 1


title: In-planta mock infection, 6 days post infection, replicate 2

value: Panorama


title: CWFP-1


title: Scramble 2

value: scramble control


title: In-planta Z.tritici strain Zt114 infection, 6 days post infection, replicate 1

value: Zymoseptoria tritici strain Zt114


title: preDC_MOCK_D584

value: Axl+DC

value: mock medium


title: Dlx3KO_AdGFP_Rep1

value: AdGFP

value: Primary cultured cells


title: CTRL-2


title: CTRL-1


title: Scramble 1


title: CS, replicate 1, scRNAseq

status: Public on Jan 12 2023

first: Zhen

middle: Zhen

last: Du

state: Beijing

address: No. 2, Yuanmingyuan West Road, Malianwa Street, Haidian DistrictNo. 2, Yuanmingyuan West Road, Malianwa Street, Haidian District

institute: Institute of Plant Protection,Chinese Academy of Agricultural Sciences

data_processing:
The Cell Ranger software pipeline (Version 5.0.0) was used to demultiplex cellular barcodes, map reads to the reference genome and transcriptome using the STAR aligner, which produced a matrix of gene counts versus cells finally. The genome and GTF annotation information of Chinese Spring was downloaded from URGI (https://wheat-urgi.versailles.inra.fr/Seq-Repository). The unique molecular identifier (UMI) count matrix was processed by the R package Seurat  (V 3.1.1).The unique molecular identifier (UMI) count matrix was processed by the R package Seurat  (V 3.1.1). To remove low quality cells and likely multiplet captures, cells with UMI/gene numbers out of the limit of mean value +/- 2 fold of standard deviations were filtered out. Additionally, low-quality cells where >10% of the counts belonged to mitochondrial genes were discarded. We also applied DoubletFinder package (Version 2.0.2) to identify potential doublet.
Assembly: IWGSC RefSeq v2.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: root tip cells

extract_protocol:
Root tips about 1 cm of 40 wheat (CS) seedlings were collected. The wheat (CS) root tips were collected and placed in RNase-free enzyme solution (20mM MES (pH=5.7), 20mM KCl, 8% D-mannitol, 2% Cellulase R-10, 1%Pectinase, 0.4% Macerozyme R-10,0.02M CaCl2, 0.1% BSA), then the mixture was incubated for 4 h in a shaker (room temperature; 90 rpm/min). The protoplasts were filtered twice through a 40um cell strainers, and washed three times with washing solution (20 mM MES (pH=5.7), 20 mM KCl, 0.1% BSA, 0.4 M D-mannitol). After centrifugation, the supernatant was removed, then the adjusted to a concentration of 1000 cells/μl with 8% mannitol solution.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: root tip cells

tag: cell line

value: about 1 cm of root tips

value: most of the major cell types in wheat (CS) root, including cortex, epidermis, endormeris, root hair, non-hair, stele, meristem, stem cell niche, fiber cells of xylem, tracheary elements of xylem, pholem.

value: Hexaploid bread wheat

value: Chinese Spring

value: healthy wheat plants cultured on filter paper socked with water


title: preDC_AD8_D584

value: HIV-1 NL-AD8


title: In-planta mock infection, 6 days post infection, replicate 4


title: In-planta mock infection, 6 days post infection, replicate 1