title: Porcine brain RNA-Seq sample 22122XR-01-17, infected treated 120h, blue capsule, parenchymal

city: Lima

first: Carla

middle: Angelica

last: Apaza-Quiroz

address: Honorio Delgado 430 San Martin de Porres

country: Peru

institute: Universidad Peruana Cayetano Heredia

description:
Library name: 22122XR-01-17
Column name in Counts_AllSamples.txt: 22122XR-01-17

data_processing:
Read quality was assessed using FastQC and summarized with MultiQC before and after trimming.
Adapter trimming and quality filtering were performed using BBDuk from the BBTools suite. Residual adapter sequences were removed, low-quality bases were trimmed using a Q20 threshold, reads shorter than 35 bp after trimming were discarded, and low-complexity sequences were filtered.
Transcript-level quantification was performed using Salmon in quasi-mapping mode against the Sus scrofa Sscrofa11.1 reference transcriptome.
Assembly: Sus scrofa Sscrofa11.1
Supplementary files format and content: Counts_AllSamples.txt: tab-delimited matrix containing gene-level counts for all samples.

organism: Sus scrofa domesticus

source_name: brain tissue

extract_protocol:
Samples were thawed on ice and tissue fragments were removed from the preservation buffer using sterile forceps. Tissue was cut to an appropriate size for extraction, and the remaining tissue was returned to the preservation buffer. Samples were homogenized in 1 mL of QIAzol using Macherey-Nagel Type G bead tubes in a TissueLyser for 2 min at 25 Hz per side. Total RNA was isolated using the RNeasy Lipid Tissue Mini Kit according to the manufacturer's instructions (Qiagen, Hilden, Germany). RNA quality was assessed using RNA ScreenTape on a TapeStation system (Agilent Technologies, CA, USA), and RNA concentration was measured using the Qubit 2.0 RNA HS Assay (Thermo Fisher Scientific, MA, USA). Samples with DV200 ≥ 60% were retained for downstream analysis.
Ribosomal RNA depletion was performed using the Ribo-Zero Plus rRNA Depletion Kit (Illumina, CA, USA). RNA-seq libraries were prepared using the NEBNext Ultra II Non-Directional RNA Library Prep Kit for Illumina (New England BioLabs, MA, USA). Final library quantity was assessed using Qubit 2.0, and library quality was assessed using TapeStation HSD1000 ScreenTape. Final library size was approximately 420 bp, with an insert size of approximately 300 bp. Illumina 8-nt dual indices were used. Libraries were pooled equimolarly based on QC values and sequenced on an Illumina NovaSeq platform using 150 bp paired-end sequencing, targeting approximately 40 million paired-end reads per sample.

treatment_protocol: Pigs were experimentally infected by intracarotid injection of activated Taenia solium oncospheres. Infection with viable brain cysticerci was confirmed five months post-infection by magnetic resonance imaging. Infected pigs were either left untreated or treated with albendazole plus praziquantel. Brain tissue specimens were collected from uninfected controls, infected untreated pigs with viable clear-capsule cyst-associated tissue, and infected treated pigs with disrupted blue-capsule cyst-associated tissue.

value: brain tissue

value: Albendazole plus praziquantel

value: 120 h post-treatment


title: DMSO 2, Dual ZF, 2

status: Public on Jun 08 2026

type: SRA

city: Lausanne

first: Nicolas

last: Thomä

address: Rte Cantonale

country: Switzerland

institute: EPFL

description:
Library name: DMSO 2 Dual ZF 2
ALV2_processed.txt

library_source: other

data_processing:
Data was processed and matched to its expected sequence with Mutscan. Then the logFC was calculated with edgeR and Limma (Singe/Dual) or Loess (DMS). Additional details in the corresponding manuscript.
Assembly: Reference sequences were used forr alignment
Supplementary files format and content: Tab delimmited text files. Contains count, logFC, Pvalues and dna sequence for alignment.

molecule: other

organism: Saccharomyces cerevisiae

extract_protocol:
For all Single ZF and Dual ZF libraries, DNA was extracted using a custom yeast Miniprep protocol. For the DMS library, DNA was extracted using a custom yeast Midiprep protocol.
Sequencing libraries wer constructed by PCR with primers containing the illumina adapters

tag: cell line

tag: treatment

value: DMSO 2, Dual ZF


title: Porcine brain RNA-Seq sample 22122XR-01-15, infected treated 120h, blue capsule, corticomeningeal

description:
Library name: 22122XR-01-15
Column name in Counts_AllSamples.txt: 22122XR-01-15

library_source: transcriptomic

molecule: total RNA

tag: cell type

tag: time


title: RNAPII 16h total ATRi ChIP-Seq

city: Birmingham

first: Marco

last: Saponaro

address: Vincent Drive

department: Institute of Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

library_source: genomic

data_processing:
Single-end ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie 2 v.2.3.3.1 (Langmead et al., 2012).
BAM files were sorted and indexed using SAMtools v.1.4 (Li et al., 2009).
The reads that mapped to region DAC blacklisted for mappability by the ENCODE project were removed.
Metagene were generated using the function “average” in EaSeq
Assembly: hg38
Supplementary files format and content: .txt, containing the quantifications over each gene as above described

molecule: genomic DNA

organism: Homo sapiens

source_name: skin; foreskin

growth_protocol: Human immortalized fibroblasts (BJ-hTERT cells) were cultured in DMEM (Sigma-Aldrich) supplemented with 10 % FBS, 2 mM L-glutamine and penicillin/streptomycin in 5 % CO2 at 37°C.

extract_protocol:
Cells were fixed in 1 % formaldehyde for 10 min at room temperature. Then, glycine was added to a final concentration of 0.125 M and the reaction was incubated for 5 min at room temperature. Fixed cells were washed twice with ice-cold PBS, and lysed for 5 min in ice-cold ChIP cell lysis buffer (5 mM HEPES pH 8.0, 85 mM KCl, 0.5 % NP-40 alternative, protease inhibitors). Nuclei were pelleted by centrifugation at 3900 g for 5 min at 4ºC, and lysed for 5 min in ChIP nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS, protease inhibitors) and incubated 5 minutes on ice. Lysates were sonicated using VCX130 (Sonics & Materials, Inc) with the following settings: 8 cycles, 30 % Amp, 15 s ON, 25 s OFF. Sonicated chromatin was centrifuged at 17000 g at 4ºC for 10 min and the supernatant was stored at -80ºC until immunoprecipitation. Before immunoprecipitation, 15 µl of Dynabeads Protein A was washed twice with 900 µl 5 mg/ml BSA in PBS and reacted for 1 h or more with 3 µg of the corresponding antibody (Phospho-Histone H2A.X: ab2893, Abcam; H3: ab1791, Abcam) in 500 µl of 5 mg/ml BSA in PBS at room temperature. The beads were washed again with 900 µl 5 mg/ml BSA in PBS before use. The concentration of sonicated chromatin was quantified by using Quick Start Bradford protein 1x dye reagent (Bio-Rad). 50 µl chromatin were used as Input. 0.6 mg of chromatin was 1:5 diluted with ChIP dilution buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, protease inhibitors), and incubated with prepared beads overnight at 4ºC with rotation. Chromatin bound to beads was washed twice in ChIP low salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), twice in ChIP high salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl),  twice in ChIP LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 % NP40 alternative, 1 % sodium deoxycholate, 1 mM EDTA), and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA). Most of the TE buffer was removed after the beads were centrifuged at 3000 rpm for 3 min and put on Magnet. The remaining TE was removed after the beads were centrifuged again at 13200 rpm for 1 min and put on Magnet. The beads were resuspended in 50 µl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS) and incubated at 65°C for 10 min followed by centrifugation at 12000 rpm for 1 min. The supernatant was transferred to a new DNA low binding tube (Sarstedt) and incubated at 65°C overnight for de-crosslinking. Reverse cross-linked supernatant was mixed with 50 µl of TE and incubated with RNase A at 37°C for 1 h. The supernatant was further incubated with 0.7 mg/ml proteinase K at 55°C for 2 h. DNA was purified by DNA Clean & Concentrator-5 and eluted with 8 µl EB (10 mM Tris-HCl pH 8.5). The purified DNA was quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). 1 ng of DNA was used to construct DNA library according to Illumina's Nextera XT DNA Library Preparation Kit protocol. After being cleaned up, indexed libraries were quantified, normalized and pooled, sequenced on Illumina NextSeq system
NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads following manufacturer’s protocol
single end on 4 lanes (L1-L4)

tag: condition

value: 16h total ATRi

tag: tissue

value: skin; foreskin

value: BJ hTERT

value: fibroblasts

tag: chip antibody

value: Rpb1 NTD antibody, Cell Signaling


title: HeLa_siGL2_1

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: HeLa

growth_protocol: HeLa cells were cultured in Iscove's modified Dulbecco's medium supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was collected using the MagNA pure compact RNA isolation kit (Roche Diagnostics)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Cells were incubated in Iscove's modified Dulbecco's medium supplemented with 10% FBS and 1% penicillin-streptomycin. HeLa cells were transfected with 4ug FLAG vector for non-target, FIR-FLAG, FIRΔexon2-FLAG, or untreated samples using Lipofectamine 2000, and they were exposed to 2 days for selection.  HeLa cells were transfected with each 25uM siRNAs using Lipofectamine 2000, and they were exposed to 2 days for selection.

value: HeLa

value: sicontrol


title: DMSO 2, Dual ZF, 1

description:
Library name: DMSO 2 Dual ZF 1
ALV2_processed.txt


title: RNAPII 14h Ser2 ChIP-Seq

value: 14h Ser2

value: Ser2-RPB1, Abcam


title: Porcine brain RNA-Seq sample 22122XR-01-12, uninfected untreated, clear, parenchymal

description:
Library name: 22122XR-01-12
Column name in Counts_AllSamples.txt: 22122XR-01-12

value: Untreated

value: Not applicable


title: RNAPII 16h total DMSO ChIP-Seq

value: 16h total DMSO


title: ISCs_67_DAE

city: Shanghai

first: Yonghao

last: Li

address: Siping Road No.1239

department: School of Life Sciences and Technology

country: China

institute: Tongji University

data_processing:
Cellranger(v3.0.2) used for calling 10X genomics single-cell RNA-seq UMI counts matrix
Genome_build: dm6
Supplementary_files_format_and_content: standard 10X genomics UMI counts matrix ziped by .tar.gz for each sample

organism: Drosophila melanogaster

source_name: midgut

growth_protocol: The stocks were routinely maintained at 25 °C, with 12/12 h dark/light cycles in humidity controlled incubators.

extract_protocol:
Each adult fly midguts were dissected in ice-cold 1XPBS/1%BSA solution.sample were washed for 2 times on ice with 1xPBS/1%BSA. 500 μL of 0.5%Trypsin-EDTA solution was add.Samples were  incubated by gentle rotating at room temperature for 20 min.The cells in suspension were carefully removed and filtered through a 40 µm nylon mesh into a fresh tube. The cells were spined down at 100 x g for 5 min at 4 °C, and finally resuspended in PBS with 0.04% BSA at a concentration of approximately 500 cells/µl.
The libraries of single cells were prepared using  Gel Bead Kit v2 Chip Kit (10x genomics). RNA sequencing was performed on an Illumina XTEN.
Single-cell RNA-Seq

value: intestine stem cell

value: intestine

tag: age

value: 67 days after eclosion

tag: strain

value: esg-Gal4 UAS-GFP/CyO


title: Porcine brain RNA-Seq sample 22122XR-01-13, infected treated 120h, blue capsule, parenchymal

description:
Library name: 22122XR-01-13
Column name in Counts_AllSamples.txt: 22122XR-01-13

value: brain tissue

value: Albendazole plus praziquantel

value: 120 h post-treatment


title: Pomalidomide, 15uM, Dual ZF, 3

description:
Library name: Pomalidomide 15 Dual ZF 3
Dual_Pomalidomide_processed.txt

value: Pomalidomide5uM, Dual ZF


title: RNAPII 14h total ChIP-Seq

value: 14h total

value: skin; foreskin

value: BJ hTERT

value: fibroblasts


title: ISCs_37_DAE

value: 37 days after eclosion


title: Pomalidomide, 15uM, Dual ZF, 2

description:
Library name: Pomalidomide 15 Dual ZF 2
Dual_Pomalidomide_processed.txt


title: Porcine brain RNA-Seq sample 22122XR-01-11, uninfected untreated, clear, parenchymal

description:
Library name: 22122XR-01-11
Column name in Counts_AllSamples.txt: 22122XR-01-11


title: ISCs_7_DAE

value: 7 days after eclosion


title: ISC_PA14_roX2_RNAi

data_processing:
Cellranger(v6.0.2) used for calling 10X genomics single-cell RNA-seq UMI counts matrix
Genome_build: dm6
Supplementary_files_format_and_content: Zipped UMI counts matrix processed by cellranger

source_name: intestinal stem cells

extract_protocol:
Using single cell 3 'Library and Gel Bead Kit V3.1 the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°C for 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200 (performed by CapitalBio Technology, Beijing).
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3.1. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

value: stem cells

value: PA14 treated

tag: genotype

value: roX2 RNAi


title: Porcine brain RNA-Seq sample 22122XR-01-10, uninfected untreated, clear, parenchymal

description:
Library name: 22122XR-01-10
Column name in Counts_AllSamples.txt: 22122XR-01-10

value: Untreated

value: Not applicable


title: ISC_PA14_CTRL

value: intestine

value: WT


title: R5WT_MA9_29

city: Suzhou

first: Peng

last: Xu

state: Jiangsu

address: Office3625 Building703, RENAI ROAD No.199, INDUSTRIAL PARK DISTRICT

department: Suzhou Medical College

institute: Soochow University

description: Library name: Sample 6

data_processing:
Raw counts of gene transcripts were derived from raw fastq files using the alignment-independent quantification tool, Salmon (https://combine- lab.github.io/salmon/), with standard settings. The raw count matrix was then imported into R-studio and utilized as input for Limma_voom analysis following the vignette of the package for normalization, differential gene expression analysis, and unbiased clustering analysis, including principal component analysis. The output of Limma_voom was used as the input for pre-ranked-based GSEA to enrich functional pathways and gene signatures (https://www.gsea-msigdb.org/gsea/index.jsp).
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file includes Row counts for each sample

organism: Mus musculus

source_name: bone marrow

extract_protocol:
RNA samples of three independent replicates were extracted from whole bone marrow, using TRIzol (Ambion by Life technologies, 343,911), following the manufacturer’s instructions. RNA was then sent out for library preparation and next-generation sequencing to a commercial company, Novogene (CA, USA).
According to the manufacturer's instructions, three biologically duplicated RNA samples were extracted from cultured cells using TRIZOL (Ambion by Life technologies, 343911). RNA sample quality was analyzed, and library were prepared and next-generation sequenced by a commercial company, Novogene (California, USA).

value: bone marrow

value: whole bone marrow

value: Rbm5 WT


title: Pomalidomide, 0.5uM, Dual ZF, 3

description:
Library name: Pomalidomide 0.5 Dual ZF 3
Dual_Pomalidomide_processed.txt

value: Pomalidomide, 0.5uM, Dual ZF


title: HeLa_FLAG_1

value: HeLa

value: control vector


title: Porcine brain RNA-Seq sample 22122XR-01-09, infected untreated, clear capsule, parenchymal

description:
Library name: 22122XR-01-09
Column name in Counts_AllSamples.txt: 22122XR-01-09

value: brain tissue


title: R5WT_MA9_27

description: Library name: Sample 5


title: Pomalidomide, 0.5uM, Dual ZF, 2

description:
Library name: Pomalidomide 0.5 Dual ZF 2
Dual_Pomalidomide_processed.txt


title: CRC_08_Tumor

city: Duarte

first: David

middle: Wesley

last: Craig

state: CA

address: 1500 East Duarte Road

department: Integrated Translational Sciences

country: USA

institute: City of Hope

description:
Library name: CRC_08_Tumor
FFPE spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using SpaceRanger (v3.1.3) and aligned to a custom reference genome generated using SpaceRanger mkref and composed of GRCh38 (refdata-gex-GRCh38-2020-A) appended with microbial probe target sequences as artificial chromosomes
Gene expression levels were quantified using default SpaceRanger parameters
Assembly: GRCh38 with custom microbial probe sequences added
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene ids
Supplementary files format and content: matrix.mtx.gz: gene expression counts in matrix format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_hires_image.png: high resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png: low resolution image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and corresponding positions
Library strategy: Spatial Transcriptomics

source_name: Colorectal Cancer, Adenocarcinoma

extract_protocol:
FFPE colorectal tissue blocks were sectioned at 10 μm thickness
Samples were processed using the Visium CytAssist Gene Expression platform (10x Genomics #1000443) following the standard manufacturer protocol for FFPE tissue.

value: Colorectal Cancer, Adenocarcinoma


title: R5WT_MA9_25

description: Library name: Sample 4


title: Porcine brain RNA-Seq sample 22122XR-01-07, infected untreated, clear capsule, parenchymal

description:
Library name: 22122XR-01-07
Column name in Counts_AllSamples.txt: 22122XR-01-07


title: CRC_08_Normal

description:
Library name: CRC_08_Normal
FFPE spatial transcriptome sequencing

source_name: Colon Normal/Benign

value: Colon Normal/Benign


title: Pomalidomide, 0.5uM, Dual ZF, 1

description:
Library name: Pomalidomide 0.5 Dual ZF 1
Dual_Pomalidomide_processed.txt


title: R5KO_MA9_40

description: Library name: Sample 3

value: Rbm5 KO


title: Porcine brain RNA-Seq sample 22122XR-01-04, infected untreated, clear capsule, parenchymal

description:
Library name: 22122XR-01-04
Column name in Counts_AllSamples.txt: 22122XR-01-04


title: CRC_07_Tumor

description:
Library name: CRC_07_Tumor
FFPE spatial transcriptome sequencing


title: DMSO, Dual ZF, 3

description:
Library name: DMSO Dual ZF 3
Dual_Pomalidomide_processed.txt

value: DMSO, Dual ZF


title: Porcine brain RNA-Seq sample 22122XR-01-06, infected untreated, clear capsule, parenchymal

description:
Library name: 22122XR-01-06
Column name in Counts_AllSamples.txt: 22122XR-01-06


title: CRC_06_Normal

description:
Library name: CRC_06_Normal
FFPE spatial transcriptome sequencing


title: R5KO_MA9_32

description: Library name: Sample 2


title: DMSO, Dual ZF, 2

description:
Library name: DMSO Dual ZF 2
Dual_Pomalidomide_processed.txt


title: Porcine brain RNA-Seq sample 22122XR-01-03, infected untreated, clear capsule, parenchymal

description:
Library name: 22122XR-01-03
Column name in Counts_AllSamples.txt: 22122XR-01-03


title: R5KO_MA9_31

description: Library name: Sample 1


title: CRC_03_Tumor

description:
Library name: CRC_03_Tumor
FFPE spatial transcriptome sequencing


title: DMSO, Dual ZF, 1

description:
Library name: DMSO Dual ZF 1
Dual_Pomalidomide_processed.txt


title: Porcine brain RNA-Seq sample 22122XR-01-01, infected untreated, clear capsule, parenchymal

description:
Library name: 22122XR-01-01
Column name in Counts_AllSamples.txt: 22122XR-01-01


title: Pomalidomide, 15uM, Dual ZF, 1

description:
Library name: Pomalidomide 15 Dual ZF 1
Dual_Pomalidomide_processed.txt

value: Pomalidomide5uM, Dual ZF


title: APOEε4-Vehivle brain organoids, day 60

status: Public on Jun 07 2026

city: seoul

first: Dakyung

last: Lee

address: 101 Daehakro

country: South Korea

institute: University

description: Library name: Sample2

library_source: transcriptomic single cell

data_processing:
Base call files were processed with Cell Ranger (10x Genomics) using the GRCh38 reference to generate gene–barcode matrices. To reduce background contamination from ambient RNA, raw feature-barcode matrices were processed using CellBender remove-background prior to downstream analysis.
Assembly: GRCh38
Supplementary files format and content: No processed data files are attached

molecule: polyA RNA

source_name: hiPSC (APOE4)

growth_protocol: hiPSCs were aggregated into embryoid bodies in AggreWell plates, then sequentially patterned in serum-containing and neural media with dual-SMAD inhibitors, followed by EGF/bFGF and later BDNF/NT-3 to promote brain organoid formation. After ~day 42, organoids were maintained in Neurobasal-A without Matrigel or growth factors.

extract_protocol:
For single-cell dissociation, three brain organoids per sample were pooled. The culture medium was removed, and the organoids were washed with 0.5 mM EDTA in PBS and incubated for 2 minutes at room temperature; this washing step was repeated once. Subsequently, the organoids were dissociated using ACCUMAX (Innovative Cell Technologies, San Diego, CA, USA). The samples were incubated at 37°C for 4 minutes, gently agitated, and incubated for an additional 4 minutes at 37°C. Mechanical dissociation was performed by pipetting until a single-cell suspension was achieved. To remove cell clumps and debris, the suspension was filtered through a 40 µm Flowmi cell strainer. The cells were centrifuged at 200 × g for 5 minutes at 4°C. The supernatant was discarded, and the cell pellet was washed and resuspended in PBS containing 0.04% BSA. The washing step was repeated to ensure high sample quality for library preparation.
Each sample was loaded into one lane of a 10x Genomics microfluidic chip (Chromium Next GEM-X 3′ Chip) at a concentration adjusted to live cell counts, according to the manufacturer’s instructions.

treatment_protocol: Brain organoids were seeded into 96-well plates and cultured, after which Ceria-TPP was added to each well to a final concentration of 150 μM, followed by incubation for 24 hours.

value: hiPSC (APOE4)

value: hiPSC-derived brain organoids (3D)

value: Neurons

value: Vehicle


title: APOEε4-Ceria-TPP brain organoids, day 60

description: Library name: Sample3

value: Ceria-TPP (150 uM, 24 h)


title: CRC_03_Normal

description:
Library name: CRC_03_Normal
FFPE spatial transcriptome sequencing


title: APOEε3-Vehicle brain organoids, day 60

description: Library name: Sample1

source_name: hiPSC (APOE3)

value: hiPSC (APOE3)


title: APOEε4-Ceria-TPP human iPSC-derived neurons 1, day 19

description: Library name: ApoE414_C-iN1

data_processing:
RNA sequencing data were processed using RSEM, which employs the STAR aligner to map reads to the GRCh38 human reference genome.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

growth_protocol: NPCs were dissociated into single cells and replated on Geltrex-coated plates, then cultured in neuronal differentiation medium containing neurotrophic factors and supplements. Neuronal induction was driven by doxycycline, which was gradually reduced every 48 h and fully withdrawn by days 7–8, with media changes every other day. To suppress non-neuronal proliferation, 50 nM Ara-C was added from days 6 to 19.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Favorgen, Pingtung, Taiwan)
TruSeq RNA

treatment_protocol: Human iPSC-derived neurons were seeded into 12-well plates and cultured, after which Ceria-TPP was added to each well to a final concentration of 95 μM, followed by incubation for 24 hours.

value: hiPSC-derived neurons (2D)

value: APOE 4

value: Ceria-TPP (95 uM, 24 h)+Aβ


title: APOEε4-Ceria-TPP human iPSC-derived neurons 2, day 19

description: Library name: ApoE414_C-iN2

value: Ceria-TPP (95 uM, 25 h)+Aβ


title: APOEε4-Ceria-TPP human iPSC-derived neurons 3, day 19

description: Library name: ApoE414_C-iN3

value: Ceria-TPP (95 uM, 26 h)+Aβ


title: APOEε4-Vehicle human iPSC-derived neurons 4, day 19

description: Library name: ApoE414-iN4

value: Aβ


title: APOEε4-Ceria-TPP human iPSC-derived neurons 4, day 19

description: Library name: ApoE414_C-iN4

value: Ceria-TPP (95 uM, 27 h)+Aβ


title: APOEε4-Vehicle human iPSC-derived neurons 2, day 19

description: Library name: ApoE414-iN2


title: APOEε4-Vehicle human iPSC-derived neurons 3, day 19

description: Library name: ApoE414-iN3


title: APOEε3-Vehicle human iPSC-derived neurons 4, day 19

description: Library name: ApoE313-iN4

value: APOE 3


title: APOEε3-Vehicle human iPSC-derived neurons 3, day 19

description: Library name: ApoE313-iN3


title: APOEε4-Vehicle human iPSC-derived neurons 1, day 19

description: Library name: ApoE414-iN1


title: Circadian profiling,iso31, Second day LD ZT8,rep-3

city: Ann Arbor

first: Ravi

last: Allada

state: Michigan

address: 2800 Plymouth Rd

department: Michigan neuroscience Institute

institute: university of michigan

description: Library name: ZT_8_3

data_processing:
RNA-seq reads were pseudo-aligned and quantified using Kallisto (v0.46.1)  against a pre-built index generated from the Ensembl reference transcriptome (release 96). Paired-end reads were processed with 10 bootstrap samples to estimate technical uncertainty.
Gene-level abundance estimates were obtained using the tximport package  by summing transcript-level TPM values for all isoforms corresponding to each gene.
Assembly: Ensembl reference transcriptome (release 96)
Supplementary files format and content: Comma-separated values  (csv) file, TPM for all samples

source_name: Whole Brain

extract_protocol:
At the appointed time (usually immediately after sleep deprivation at ZT0 or immediately after sleep promotion at ZT12), flies were removed from the incubator and brains were dissected in dissecting saline with channel blockers. Likewise, circadian profiling occurred in the same way at the appropriate time point. 15 brains per sample were pooled, transferred to lysis buffer from the PicoPure RNA Isolation kit, vortexed for 30 seconds, then incubated at 42C for 30 min before freezing. Once all samples were collected, the RNA was isolated using the PicoPure RNA Isolation kit and used for library prep.
Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (Cat #: E7770) following manufacturer instructions.

treatment_protocol: For sleep deprivation, treatment involved either mechanical sleep deprivation or thermogenetic sleep deprivation. Mechanical sleep deprivation of varying lengths of time was accomplished by using a vortexer to deliver vibrations for 2 seconds every 20 seconds at random throughout the deprivation length. Thermogenetic sleep deprivation used temperature and a temperature sensitive ion channel to activate different wake-promoting sets of neurons. Thermogenetically sleep deprived flies were kept at 21C except for a 3 hr shift to 29C at the end of the night before dissection. Sleep promotion relied on thermogenetic activation of sleep promoting neurons for 12 hr during the daytime before dissection at lights off. Thermogenetic experiments also included controls lacking a UAS-TrpA1 transgene but exposed to a 29C shift or controls with both GAL4 and UAS-TrpA1 that were kept at 21C to avoid activation. Circadian profiling took place using flies kept in a light/dark cycle at 25C.

value: Whole Brain


title: APOEε3-Vehicle human iPSC-derived neurons 1, day 19

description: Library name: ApoE313-iN1


title: Circadian profiling, iso31, Second day LD ZT4,rep-3

description: Library name: ZT_4_3


title: APOEε3-Vehicle human iPSC-derived neurons 2, day 19

description: Library name: ApoE313-iN2


title: Circadian profiling, iso31, Second day LD ZT4,rep-2

description: Library name: ZT_4_2


title: Circadian profiling,iso31, Second day LD ZT8,rep-2

description: Library name: ZT_8_2


title: Circadian profiling, iso31, Second day LD ZT4,rep-1

description: Library name: ZT_4_1


title: Circadian profiling, iso31, Second day LD ZT8,rep-1

description: Library name: ZT_8_1


title: Circadian profiling, iso31, Second day LD ZT20,rep-3

description: Library name: ZT_20_3


title: Circadian profiling, iso31, Second day LD ZT20,rep-2

description: Library name: ZT_20_2


title: Circadian profiling, iso31, Second day LD ZT20,rep-1

description: Library name: ZT_20_1


title: Circadian profiling, iso31, Second day LD ZT16,rep-3

description: Library name: ZT_16_3


title: Circadian profiling, iso31, Second day LD ZT16,rep-2

description: Library name: ZT_16_2


title: Circadian profiling, iso31, Second day LD ZT16,rep-1

description: Library name: ZT_16_1


title: Circadian profiling, iso31, Second day LD ZT12,rep-3

description: Library name: ZT_12_3


title: Circadian profiling, iso31, Second day LD ZT12,rep-2

description: Library name: ZT_12_2


title: Circadian profiling, iso31, Second day LD ZT0,rep-3

description: Library name: ZT_0_3


title: Circadian profiling, iso31, Second day LD ZT12,rep-1

description: Library name: ZT_12_1


title: Circadian profiling, iso31, Second day LD ZT0,rep-2

description: Library name: ZT_0_2


title: Circadian profiling, iso31, Second day LD ZT0,rep-1

description: Library name: ZT_0_1


title: R85C10, Tempearture 21, TrpA1, ZT12,Thermogenetic Sleep Deprivation,rep-3

description: Library name: R85C10_TrpA1_21_3


title: R85C10, Tempearture 29, TrpA1, ZT12,Thermogenetic Sleep Deprivation,rep-3

description: Library name: R85C10_TrpA1_29_3


title: R85C10, Tempearture 29, TrpA1, ZT12,Thermogenetic Sleep Deprivation,rep-1

description: Library name: R85C10_TrpA1_29_1


title: R85C10, Tempearture 21, TrpA1, ZT12,Thermogenetic Sleep Deprivation,rep-2

description: Library name: R85C10_TrpA1_21_2


title: R85C10, Tempearture 29, TrpA1, ZT12,Thermogenetic Sleep Deprivation,rep-2

description: Library name: R85C10_TrpA1_29_2


title: R85C10, Tempearture 21, TrpA1, ZT12,Thermogenetic Sleep Deprivation,rep-1

description: Library name: R85C10_TrpA1_21_1


title: R85C10, Tempearture 29, Gal4+, Control, ZT12, Thermogenetic Sleep Deprivation,rep-3

description: Library name: R85C10_29_3


title: R85C10, Tempearture 29, Gal4+, Control, ZT12, Thermogenetic Sleep Deprivation,rep-2

description: Library name: R85C10_29_2


title: R65H02, Tempearture 29, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-3

description: Library name: R65H02_TrpA1_29_3


title: R65H02, Tempearture 29, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-2

description: Library name: R65H02_TrpA1_29_2


title: R65H02, Tempearture 29, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-1

description: Library name: R65H02_TrpA1_29_1


title: R65H02, Tempearture 21, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-2

description: Library name: R65H02_TrpA1_21_2


title: R65H02, Tempearture 21, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-3

description: Library name: R65H02_TrpA1_21_3


title: R65H02, Tempearture 21, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-1

description: Library name: R65H02_TrpA1_21_1


title: R65H02, Tempearture 29, Gal4+, Control, ZT0, Thermogenetic Sleep Deprivation,rep-2

description: Library name: R65H02_29_2


title: R65H02, Tempearture 29, Gal4+, Control, ZT0, Thermogenetic Sleep Deprivation,rep-1

description: Library name: R65H02_29_1


title: R60F09,Tempearture 29, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-2

description: Library name: R60F09_TrpA1_29_2


title: R60F09, Tempearture 29, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-3

description: Library name: R60F09_TrpA1_29_3


title: R60F09, Tempearture 21, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-2

description: Library name: R60F09_TrpA1_21_2


title: R60F09, Tempearture 29, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-1

description: Library name: R60F09_TrpA1_29_1


title: R60F09, Tempearture 21, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-3

description: Library name: R60F09_TrpA1_21_3


title: R60F09, Tempearture 21, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-1

description: Library name: R60F09_TrpA1_21_1


title: R60F09, Tempearture 29, Gal4+, Control, ZT0, Thermogenetic Sleep Deprivation,rep-3

description: Library name: R60F09_29_3


title: R60F09, Tempearture 29, Gal4+, Control, ZT0, Thermogenetic Sleep Deprivation,rep-2

description: Library name: R60F09_29_2


title: R60F09, Tempearture 29, Gal4+, Control, ZT0, Thermogenetic Sleep Deprivation,rep-1

description: Library name: R60F09_29_1


title: R21H11, Tempearture 29, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-2

description: Library name: R21H11_TrpA1_29_2


title: R21H11, Tempearture 21, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-2

description: Library name: R21H11_TrpA1_21_2


title: R21H11, Tempearture 21, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-1

description: Library name: R21H11_TrpA1_21_1


title: R21H11, Tempearture 29, Gal4+, Control, ZT0, Thermogenetic Sleep Deprivation,rep-3

description: Library name: R21H11_29_3


title: R21H11, Tempearture 29, Gal4+, Control, ZT0, Thermogenetic Sleep Deprivation,rep-1

description: Library name: R21H11_29_1


title: iso31,SD amount 6hr,ZT0,Mechanical sleep deprivation,rep-3

description: Library name: MechSD6hr_3


title: iso31,SD amount 6hr,ZT0,Mechanical sleep deprivation,rep-2

description: Library name: MechSD6hr_2


title: iso31,SD amount 6hr,ZT0,Mechanical sleep deprivation,rep-1

description: Library name: MechSD6hr_1


title: iso31,SD amount 3hr,ZT0,Mechanical sleep deprivation,rep-3

description: Library name: MechSD3hr_3


title: iso31,SD amount 12hr,ZT0,Mechanical sleep deprivation,rep-3

description: Library name: MechSD12hr_3


title: iso31,SD amount 3hr,ZT0,Mechanical sleep deprivation,rep-1

description: Library name: MechSD3hr_1


title: iso31,SD amount 3hr,ZT0,Mechanical sleep deprivation,rep-2

description: Library name: MechSD3hr_2


title: iso31,SD amount 12hr,ZT0,Mechanical sleep deprivation,rep-2

description: Library name: MechSD12hr_2


title: iso31,SD amount 12hr,ZT0,Mechanical sleep deprivation,rep-1

description: Library name: MechSD12hr_1


title: Hot cell, Tempearture 29, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-2

description: Library name: HC_TrpA1_29_2


title: Hot cell, Tempearture 29, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-3

description: Library name: HC_TrpA1_29_3


title: Hot cell, Tempearture 21, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-2

description: Library name: HC_TrpA1_21_2


title: Hot cell, Tempearture 29, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-1

description: Library name: HC_TrpA1_29_1


title: Hot cell, Tempearture 21, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-3

description: Library name: HC_TrpA1_21_3


title: Hot cell, Tempearture 21, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-1

description: Library name: HC_TrpA1_21_1


title: Hot cell, Tempearture 29, Gal4+, Control, ZT0, Thermogenetic Sleep Deprivation, rep-2

description: Library name: HC_29_2


title: Hot cell, Tempearture 29, Gal4+, Control, ZT0, Thermogenetic Sleep Deprivation,rep-1

description: Library name: HC_29_1


title: PDX human in mouse tumor resection sample, ATAC modality [PDX1_atac]

city: Brussels

first: Cedric

last: Blanpain

address: Route de Lennik 808

country: Belgium

institute: ULB

description: Library name: PDX1_atac

library_source: genomic single cell

data_processing:
The raw reads from Multiome sequencing outputs with single cell ATAC and single cell gene expression were aligned to both the hg38 human and mm10 mouse reference genome to correctly identify species transcripts, and then quantified by the CellRanger pipeline and human reads were thus seperated from mouse reads.
Assembly: hg38 and mm10
Supplementary files format and content: PDX2_sample_filtered_feature_bc_matrix.h5

source_name: PDX

extract_protocol:
PDX tumors from NOD/SCID mice were dissected, minced and digested in collagenase type I (Sigma) at 3.5 mg/ml in HBSS (Gibco) for 30 minutes and in DNase, trypsin and EDTA (5 mM) for other 30 minutes, at 37°C on a rocking plate. The digestion was stopped by adding FBS. The cell suspensions were rinsed in PBS supplemented with 10% FBS, filtered through a 70-μm cell strainer (BD Bioscience) and centrifuged at 1.000 rpm for 10 minutes at 4ºC. For antibody incubation, cells were resuspended in PBS supplemented with 2% FBS. Cells were incubated with FITC-conjugated anti-CD31 (rat, clone MEC 13.3, BD, 553372, dilution 1:100), FITC-conjugated anti-CD45 (rat, clone 30-F11, BD, 553079, dilution 1:100), FITC-conjugated anti-CD13 (rat, clone R3-242, BD, 558744, dilution 1:100), FITC-conjugated anti-CD45 (mouse, clone HI30, BD, 555482, dilution 1:50), APC-conjugated anti-EPCAM (mouse, clone EBA-1, BD, 347200, dilution 1:50), PE/Cy7- conjugated anti-CD298 (mouse, clone LNH-94, Biolegend, 341707, dilution 1:50) antibodies for 30 min at 4ºC protected from light.  After antibody staining, cell suspensions were washed with PBS supplemented with 2% FBS and centrifuged for 5 minutes. Cells were then resuspended in Hoechst 33342 trihydrochloride trihydrate (Invitrogen, H3570, dilution 1:4.000) and filtered through a 40-μm cell strainer (BD Bioscience). Living single tumor cells were selected by forward and side scatter, doublet discrimination and Hoechst dye exclusion. Tumor cells were selected based on CD298 expression and the exclusion of CD45, CD31 and CD13. EPCAM expression in tumor cells was then assessed on the CD298+ CD45- CD31- CD13- population.
PDX tumors were sorted as 100% CD298+ CD45- CD31- CD13-. 200.000 cells were collected in PBS, 0,04% filtered BSA using low binding 1.5 ml tubes (Eppendorf). For nuclei isolation, buffers were prepared following manufacturer’s instructions (adapted from protocol CG000365 Rev C, 10x Genomics): nuclei buffer: 10X Nuclei Buffer 1X, 1 mM DTT, 1 U/ul RNase inhibitor, nuclease free water; wash buffer: 10 mM Tris-HCl (ph 7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0,1% Tween-20, 1 mM DTT, 1 U/ul RNase inhibitor, nuclease free water; lysis buffer: 10 mM Tris-HCl (ph 7.4), 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0,1% Tween-20, 0,1% Nonidet P40 Substitute, 0,01% digitonin, 1 mM DTT, 1 U/ul RNase inhibitor, nuclease free water.  Sorted cells were centrifuged at 300g, 5 min at 4ºC and supernatant was carefully removed. Chilled lysis buffer (100 μl) was added, pipette mixed 10 times and incubated on ice for 3 minutes and 30 seconds. Wash buffer (800 μl) was added to the lysed cells and pipette mixed 5 times. Lysed cells were centrifuged at 500g, 5 min at 4ºC, followed by a second washing step. Nuclei were resuspended in nuclei buffer, counted and loaded on Chromium Next GEM Single Cell Multiome, ATAC + Gene Expression microfluidic chips (10x Genomics) was employed for Multiome. The libraries were prepared using the Chromium Single Cell 3′ Library Kit (V2-chemistry, 10x Genomics), quantified using a low coverage Illumina NextSeq 550 run and sequenced on an Illumina NovaSeq.

value: PDX

value: tumor

value: PDX model - patient tumor grafted into NOD/SCID mouse

tag: library

value: ATAC


city: La Jolla

first: Pandurangan

last: Vijayanand

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description:
Library name: HIPC-1_LN02_Hu_2_6D
Pooled 10x single-cell library of lung-draining lymph node (LN) from multiple donors (HTO-labeled): L035;L037

data_processing:
Processing of scRNA-seq libraries: Sequencing reads from single-cell (sc)RNA-seq data were demultiplexed using Cell Ranger (v7.1.0, 10x Genomics) with the mkfastq module and aligned to the GRCh38 reference genome (pre-built reference “2020-A”) with the count module. This generated UMI-collapsed gene expression matrices for 46 single-cell libraries. Independent gene expression libraries were aggregated into combined datasets using the aggr module, yielding a dataset of lung CD3⁺ T cells from 40 donors and a dataset of lung-draining LN CD3⁺ T cells from 8 donors. Aggregated datasets were processed in R (v3.6.1) using Seurat (v3.2.3; Stuart et al., Cell, 2019). Genes expressed in fewer than 0.1% of cells were excluded. To minimize doublets and eliminate low-quality transcriptomes while still allowing for variability in the distribution of UMI and gene counts, we excluded cells that did not meet the following lenient criteria: 500≤ UMI count ≤10,000; 400≤ gene count ≤3,000; and mitochondrial UMI percentage ≤15%. Data normalization was performed using NormalizeData with default parameters. Highly variable genes (HVGs) were identified with the FindVariableFeatures function using the vst method and default settings; selection was restricted to genes with a mean expression >0.01 and contributing 30% of the standardized variance. Gene-wise scaling was performed using ScaleData, with regression of total UMI counts and mitochondrial UMI percentages (vars.to.regress argument), while retaining default settings for other arguments. Dimensionality reduction was performed via principal component analysis (PCA), followed by UMAP embedding using RunUMAP with the top 40 PCs, 15 neighbors (n.neighbors = 15), and a minimum distance of 0.1 (min.dist = 0.1). Unsupervised clustering was conducted with FindNeighbors and FindClusters, with a defined resolution and 30 PCs specified per iteration and all other parameters left unchanged. For the last iteration, 0.2 and 0.3 were chosen as the resolution values for lung and LN T cells, respectively, and irrespective of lineage. Lineage-specific subsets of CD4⁺ and CD8⁺ T cells were defined through iterative rounds of clustering and phenotype-guided filtering. In each round, contaminant clusters were reassigned to the appropriate lineage-specific dataset for further refinement. A total of 16 and 10 rounds of deconvolution were performed for lung and LN T cells, respectively, at which point no lineage contaminating clusters could be discerned.
Processing of hashtag oligonucleotide (HTO)-seq libraries: In the study cohort, hashtag barcoding was used in a subset of libraries to pool cells from multiple donors prior to sequencing. Specifically, 5 coupled scRNA-seq and scTCR-seq libraries included pooled samples and required demultiplexing during analysis. In the resource cohort, all scTCR-seq libraries consisted of pooled, hashtag-barcoded samples that were also demultiplexed during analysis. Reads from hashtag oligonucleotide (HTO) feature barcoding were demultiplexed using Cell Ranger mkfastq (v7.1.0, 10x Genomics) and processed with the count module adapted for feature barcoding (v7.1.0). For each library, cell calling was performed, and barcodes were demultiplexed into separate samples and donor identities with Seurat’s MULTIseqDemux function (v3.2.3; McGinnis et al., Nat. Methods, 2019), as detailed previously (Meckiff et al., Cell, 2020; Kusnadi et al., Science Immunol., 2021). Barcodes classified as doublets were removed from downstream analyses at the initial round of clustering.
Processing of single-cell T-cell receptor (TCR)-seq libraries: Reads from single-cell TCR sequencing (scTCR-seq) data were processed using cellranger vdj (v7.1.0) with the pre-built GCRh38 reference (“vdj-GRCh38-alts-ensembl-7.1.0”) and aggregated following previously described workflows (Meckiff et al., Cell, 2020; Kusnadi et al., Science Immunol., 2021). For the study cohort, one aggregated dataset was generated for lung CD3+ T cells (n=40 libraries, one per donor) and another for lung-draining LN CD3+ T cells (n=6 libraries spanning 8 donors). For the resource cohort, 45 libraries derived from putative pathogen-specific CD4+ T cells were aggregated into a single TCR dataset. For this type of data (single-cell resolution), a clonotype was defined as a unique set of CDR3 α and β sequences and the V and J gene segments encompassing each of them.
Clonotype group-bias assignment problem: Given a clonotype observed across n groups (n>1), let f_g denote its absolute frequency in group g, and let r_g denote its relative frequency in that group, computed as f_g normalized by the total clonotype counts within group g. The task is to classify each clonotype as either biased toward a particular group or unbiased across groups. Proposed solution: First, sort all groups by the clonotype’s relative frequency r_g, identifying the top-ranked group (g_1) and the second-ranked group (g_2). Compute the bias ratio as: bias_ratio=r_(g_1 )/r_(g_2 ) . A clonotype is then assigned as biased to group g_1 if and only if: (i) f_(g_1 )>2 and (ii) bias_ratio>2.
Assignment of uniquely defined antigen specificities to TCR clonotypes: In this study, the ARTE assay was employed to capture antigen-specific T cells, with concomitant TCR repertoires profiled at single-cell resolution. These data have : (i) a readout consisting of CDR3 sequences and the V and J gene segments that encompass them; (ii) clonotypes with an absolute frequency of 1 unit—with cell barcodes as units, referred to as singletons—represented a substantial proportion across the board; (iii) a division of expanded (non-singleton) clonotypes into two classes with regard to antigen specificity—those that were detected with a single peptide MP (unambiguous) and those that were detected with multiple peptide MPs (ambiguous); and (iv) for ambiguous clonotypes, when their associated peptide MPs were ranked by relative frequency and the ratio of the top-to-the-second-highest ranked MP was calculated (reminiscent of the bias_ratio), the resulting distributions were highly similar between assays and data types. Unambiguous clonotypes were directly deemed specific to the antigen corresponding to the peptide MP with which they were detected. In contrast, the assignment of unique specificities to ambiguous clonotypes can be framed as an instance of the clonotype group-bias assignment problem described above. The proposed solution was implemented as a common framework, such that an ambiguous clonotype was defined as specific to antigen g_1 when (i) f_(g_1 )>2, where f_(g_1 ) denotes its absolute frequency for that antigen and (ii) bias_ratio>2.
Assembly: GRCh38 (2020-A reference prebuilt and provided by 10x cellranger).
Supplementary files format and content: This submission includes seurat objects (v3.2.3; Stuart et al., Cell, 2019) created as described above for the sets of CD4+ (HIPC-1_LG-CD4-ALL_SeuratObject.RDS) and CD8+ (HIPC-1_LG-CD8-ALL_SeuratObject.RDS) lung T cells and the sets of CD4+ (HIPC-1_LN-CD4-ALL_SeuratObject.RDS) and CD8+ (HIPC-1_LN-CD8-ALL_SeuratObject.RDS) lung-draining LN T cells.
Supplementary files format and content: TCR clonotype metadata including CDR3 sequences and V and J gene usage, as well as antigen specificity-associated metrics, are provided in file: DICE-TCR_BL-CD4-ALL_ProcessedObject.csv

source_name: lung-draining lymph node (LN)

growth_protocol: Study cohort samples: A total of 40 individuals undergoing standard-of-care surgical resection for primary lung non-small cell lung cancer (NSCLC) at Liverpool Heart and Chest NHS Foundation Trust Hospital were enrolled. The cohort included 16 men and 24 women, all of White British ethnicity, with a median age of 70 years (range: 61–83). Background lung tissue, along with matched peripheral blood and LLNs, was collected intraoperatively. Background lung samples were obtained from macroscopically uninvolved, non-tumor-bearing regions of the parenchyma, typically distant from the primary tumor. All samples were de-identified and cryopreserved in freezing medium (90% fetal bovine serum (FBS) and 10% DMSO) prior to downstream processing. Reference cohort samples: Peripheral blood mononuclear cells (PBMCs) were obtained from a total of 61 healthy donors through the San Diego Blood Bank (SDBB) between December 2021 and February 2022. Each donor provided approximately 8 mL of LRS-WBC (Leukoreduction System - Whole Blood Collection) material. Donor ages ranged from 27 to 79 years (median of 65). Of the 61 donors, 47 were male, 12 were female, and 2 had unspecified sex information. No clinical or immunological abnormalities were reported for these donors at the time of collection. PBMCs were isolated and cryopreserved according to standard protocols for downstream immunological assays.

extract_protocol:
Single-cell (sc)RNA-seq library preparation was performed alongside TCR repertoire immune profiling (scTCR-seq) and cell surface protein technology to enable hashtag oligonucleotide (HTO) -based sample demultiplexing. Up to 100,000 CD3⁺ T cells from each of 40 lung samples, up to 100,000 CD3+ T cells of 8 LLN samples—from a single- or 2-donor pools—, and up to 120,000 circulating,  pathogen-specific CD4+ T cells—from up to 16 pooled donors—were processed using the 10x Genomics Chromium Next GEM Single Cell 5′ HT Reagent Kit v2 (Dual Index), following the manufacturer’s instructions.
Initial amplification of cDNA (concomitantly, for gene expression library preparation) was carried out with 13 cycles of amplification; scTCR and HTO libraries were both generated with 8 cycles of amplification. All libraries were quantified and pooled according to equivalent molar concentrations. Libraries from lung CD3+ T cells and circulating, pathogen-specific CD4+ T cells were sequenced on an Illumina NovaSeq6000 sequencing instrument (read 1 and read 2 – 100 cycles; i5 and i7 index - 10 cycles). Libraries from LLN CD3+ T cells were sequenced on an Illumina NovaSeq X instrument (150 x 150 cycle paired-end configuration with index reads ).

treatment_protocol: Study cohort samples: Human lung tissue and LLN samples were thawed in a 37°C water bath for ~5 minutes until only a small ice fragment remained, followed by washing with FBS and dilution in MACS buffer to reduce DMSO concentration. The thawed tissue suspension was filtered through a 70 µm strainer, with retained tissue pieces collected and finely diced using a scalpel (this step only in case of lung tissue). The minced tissue was transferred to a gentleMACS C tube (Miltenyi Biotec,130-096-334) and supplemented with RPMI, after which enzymatic digestion was initiated by adding DNase I (Sigma, D4527-200K) and Liberase (Sigma, 5401127001). The sample underwent mechanical and enzymatic dissociation using an OctoDissociator (Miltenyi Biotec) set at 37°C for 15 minutes. Following dissociation, the cell suspension was filtered through a MACS SmartStrainer, gently pressing residual tissue to maximize cell yield. The resulting cell suspension was centrifuged, and the pellet resuspended in MACS buffer containing FcR Blocking Reagent, followed by the addition of Cell-hashtag TotalSeq-C antibody (1 μg/condition) to enable hashtag oligonucleotide (HTO)-based sample deconvolution at the analysis stage. Cells were then stained with a panel of antibodies optimized to sort for CD3+ T cells while incubating at 4°C. After washing, the cells were underlaid with FBS and centrifuged again. The final cell pellet was resuspended in cold MACS buffer supplemented with DAPI for viability staining and sorted for CD3+ T cells on a FACSAria Fusion Cell Sorter (Becton Dickinson). Resource cohort samples: The enrichment and FACS sort of pathogen-specific CD4+ memory T cells from the PBMC samples of the resource cohort (n=61 donors) was performed using a modified protocol based on Bacher et al., J Immunol., 2016. PBMCs from donors were thawed, washed, and cultured overnight (5% CO2, 37 °C) in serum-free TexMACS medium at a concentration of 10 × 10^6 cells/mL. The cells were then stimulated with pathogen peptide MPs (1ug/ml) for 6 hours, with a CD40 blocking antibody (1 μg/mL; Miltenyi Biotec) present. To enrich CD154+ cells, a series of staining steps were carried out, including surface antibodies, Cell-hashtag TotalSeq-C antibody (1ug/condition), and a biotin-conjugated CD154 antibody, followed by anti-biotin microbeads. The labeled cells underwent positive selection using MS columns, with the CD154+ cells being eluted for subsequent FACS sorting. The enriched populations were immediately sorted using a FACSAria Fusion Cell Sorter (Becton Dickinson) based on dual expression of CD154 and CD69.

value: lung-draining lymph node (LN)

value: CD3+ T cells

value: Ex-vivo


description:
Library name: HIPC-1_LN01_4
10x single-cell library of lung-draining lymph node (LN) sample from donor L004


description:
Library name: HIPC-1_LN02_Hu_1_6D
Pooled 10x single-cell library of lung-draining lymph node (LN) from multiple donors (HTO-labeled): L003;L009


description:
Library name: HIPC-1_LN01_5
10x single-cell library of lung-draining lymph node (LN) sample from donor L005


description:
Library name: HIPC-1_LN01_14
10x single-cell library of lung-draining lymph node (LN) sample from donor L014


description:
Library name: HIPC-1_12_Hu_TL40_6D
10x single-cell library of lung sample from donor L040

source_name: lung

value: lung


description:
Library name: HIPC-1_12_Hu_TL39_6D
10x single-cell library of lung sample from donor L039


title: CTR siRNA1-BrdU-Seq

data_processing:
Paired-end BrdU-seq reads were aligned to the hg38 genome assembly using Bowtie 2 v.2.3.3.1 (Langmead et al., 2012).
BAM files were sorted and indexed using SAMtools v.1.4 (Li et al., 2009).
The reads that mapped to region DAC blacklisted for mappability by the ENCODE project were removed.
Coverage calcualtion was done using the function “quantify” in EaSeq, from the start to the end of the gene of all annotated genes
Assembly: hg38
Supplementary files format and content: .txt, containing the quantifications over each gene as above described

extract_protocol:
Cells were fixed in 1 % formaldehyde for 10 min at room temperature. Then, glycine was added to a final concentration of 0.125 M and the reaction was incubated for 5 min at room temperature. Fixed cells were washed twice with ice-cold PBS, and lysed for 5 min in ice-cold ChIP cell lysis buffer (5 mM HEPES pH 8.0, 85 mM KCl, 0.5 % NP-40 alternative, protease inhibitors). Nuclei were pelleted by centrifugation at 3900 g for 5 min at 4ºC, and lysed for 5 min in ChIP nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS, protease inhibitors) and incubated 5 minutes on ice. Lysates were sonicated using VCX130 (Sonics & Materials, Inc) with the following settings: 8 cycles, 30 % Amp, 15 s ON, 25 s OFF. Sonicated chromatin was centrifuged at 17000 g at 4ºC for 10 min and the supernatant was stored at -80ºC until immunoprecipitation. Before immunoprecipitation, 15 µl of Dynabeads Protein A was washed twice with 900 µl 5 mg/ml BSA in PBS and reacted for 1 h or more with 3 µg of the corresponding antibody (Phospho-Histone H2A.X: ab2893, Abcam; H3: ab1791, Abcam) in 500 µl of 5 mg/ml BSA in PBS at room temperature. The beads were washed again with 900 µl 5 mg/ml BSA in PBS before use. The concentration of sonicated chromatin was quantified by using Quick Start Bradford protein 1x dye reagent (Bio-Rad). 50 µl chromatin were used as Input. 0.6 mg of chromatin was 1:5 diluted with ChIP dilution buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, protease inhibitors), and incubated with prepared beads overnight at 4ºC with rotation. Chromatin bound to beads was washed twice in ChIP low salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), twice in ChIP high salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl),  twice in ChIP LiCl buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 % NP40 alternative, 1 % sodium deoxycholate, 1 mM EDTA), and once in TE buffer (10 mM Tris-HCl, 1 mM EDTA). Most of the TE buffer was removed after the beads were centrifuged at 3000 rpm for 3 min and put on Magnet. The remaining TE was removed after the beads were centrifuged again at 13200 rpm for 1 min and put on Magnet. The beads were resuspended in 50 µl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS) and incubated at 65°C for 10 min followed by centrifugation at 12000 rpm for 1 min. The supernatant was transferred to a new DNA low binding tube (Sarstedt) and incubated at 65°C overnight for de-crosslinking. Reverse cross-linked supernatant was mixed with 50 µl of TE and incubated with RNase A at 37°C for 1 h. The supernatant was further incubated with 0.7 mg/ml proteinase K at 55°C for 2 h. DNA was purified by DNA Clean & Concentrator-5 and eluted with 8 µl EB (10 mM Tris-HCl pH 8.5). The purified DNA was quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) using a Qubit 3.0 Fluorometer (Thermo Fisher Scientific). 1 ng of DNA was used to construct DNA library according to Illumina's Nextera XT DNA Library Preparation Kit protocol. After being cleaned up, indexed libraries were quantified, normalized and pooled, sequenced on Illumina NextSeq system
NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads following manufacturer’s protocol
paired end on 4 lanes (L1-L4)

value: CTR siRNA1

value: skin; foreskin

value: BJ hTERT

value: fibroblasts

value: anti-BrdU antibody, Sigma-Aldrich


description:
Library name: HIPC-1_12_Hu_TL38_6D
10x single-cell library of lung sample from donor L038


description:
Library name: HIPC-1_12_Hu_TL37_6D
10x single-cell library of lung sample from donor L037


description:
Library name: HIPC-1_12_Hu_TL35_6D
10x single-cell library of lung sample from donor L035


description:
Library name: HIPC-1_12_Hu_TL36_6D
10x single-cell library of lung sample from donor L036


description:
Library name: HIPC-1_11_Hu_TL34_6D
10x single-cell library of lung sample from donor L034


description:
Library name: HIPC-1_11_Hu_TL31_6D
10x single-cell library of lung sample from donor L031


description:
Library name: HIPC-1_11_Hu_TL30_6D
10x single-cell library of lung sample from donor L030


description:
Library name: HIPC-1_11_Hu_TL32_6D
10x single-cell library of lung sample from donor L032


description:
Library name: HIPC-1_11_Hu_TL29_6D
10x single-cell library of lung sample from donor L029


description:
Library name: HIPC-1_10_Hu_TL28_6D
10x single-cell library of lung sample from donor L028


description:
Library name: HIPC-1_10_Hu_TL27_6D
10x single-cell library of lung sample from donor L027


description:
Library name: HIPC-1_10_Hu_TL26_6D
10x single-cell library of lung sample from donor L026


description:
Library name: HIPC-1_10_Hu_TL25_6D
10x single-cell library of lung sample from donor L025


description:
Library name: HIPC-1_09_Hu_TL22_4D
10x single-cell library of lung sample from donor L022


description:
Library name: HIPC-1_10_Hu_TL24_6D
10x single-cell library of lung sample from donor L024


description:
Library name: HIPC-1_10_Hu_TL23_6D
10x single-cell library of lung sample from donor L023


description:
Library name: HIPC-1_09_Hu_TL21_4D
10x single-cell library of lung sample from donor L021


description:
Library name: HIPC-1_09_Hu_TL20_4D
10x single-cell library of lung sample from donor L020


description:
Library name: HIPC-1_07_Hu_TL17_4D
10x single-cell library of lung sample from donor L017


description:
Library name: HIPC-1_07_Hu_TL18_4D
10x single-cell library of lung sample from donor L018


description:
Library name: HIPC-1_07_Hu_TL15_4D
10x single-cell library of lung sample from donor L015


description:
Library name: HIPC-1_07_Hu_TL16_4D
10x single-cell library of lung sample from donor L016


description:
Library name: HIPC-1_06_Hu_TCL14_2D
10x single-cell library of lung sample from donor L014


description:
Library name: HIPC-1_06_Hu_TCL13_2D
10x single-cell library of lung sample from donor L013


description:
Library name: HIPC-1_06_Hu_TCL12_2D
10x single-cell library of lung sample from donor L012


description:
Library name: HIPC-1_05_Hu_TCL9_2D
10x single-cell library of lung sample from donor L009


description:
Library name: HIPC-1_06_Hu_TCL11_2D
10x single-cell library of lung sample from donor L011


description:
Library name: HIPC-1_04_Hu_TL8_2D
10x single-cell library of lung sample from donor L008


description:
Library name: HIPC-1_05_Hu_TCL10_2D
10x single-cell library of lung sample from donor L010


description:
Library name: HIPC-1_03_Hu_TCL5_5D
10x single-cell library of lung sample from donor L005


description:
Library name: HIPC-1_02_Hu_TCL4_2D
10x single-cell library of lung sample from donor L004


description:
Library name: HIPC-1_01_Hu_1_2D
10x single-cell library of lung sample from donor L001


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to PIV (4)

description:
Library name: DICE-TCR_028_Hu_RSPV_1_17D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the PIV peptide megapool (MP)

source_name: Blood

value: Blood

value: PIV-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+

value: Antigen-reactive T cell enrichment (ARTE) assay


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to CMV (8)

description:
Library name: DICE-TCR_028_Hu_CMV_2_17D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the CMV peptide megapool (MP)

value: CMV-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to Aspergillus (3)

description:
Library name: DICE-TCR_026_Hu_ASP_1_16D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the Aspergillus peptide megapool (MP)

value: Aspergillus-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+


title: CON

city: Guizhou

first: Dengwang

last: Chen

address: No. 6, Xuefu West Road, Xinpu Subdistrict, Xinpu New District

institute: Department of Histology and Embryology, Zunyi Medical University

description:
Library name: CON
control sample

data_processing:
Raw reads were filtered with fastp, aligned to mouse genome mm10 using Bowtie2, and peaks called with MACS2. Enrichment was visualized with deepTools.
Assembly: mm10
Supplementary files format and content: tab-delimited text fie includes the peak for each sample
Library strategy: CUT&Tag

source_name: cell culture

extract_protocol:
Cells were harvested, washed with PBS, and directly processed for CUT&Tag using the Hyperactive pA Tn5 kit (Vazyme).
For library amplification, 15 μL of extracted DNA was mixed with 25 μL of 2 × CAM, P5 Primer, and P7 Primer. The H3K27ac library was amplified for 13 cycles, while the H3K4me1 and H3K4me3 libraries were amplified for 11 cycles. To purify the PCR products, 2 × VAHTS DNA Clean Beads was added, followed by incubation at room temperature for 5 min. After purification, paired-end sequencing was performed on the NovaSeq 6000 platform with three biological replicates at Novogene Biotech Co., Ltd.

value: cell culture


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to Aspergillus (2)

description:
Library name: DICE-TCR_025_Hu_ASP_2_17D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the Aspergillus peptide megapool (MP)


title: VB6

description:
Library name: VB6
Cells were cultured in EB medium (without LIF) for 7 days. VB6 group received 20 µM pyridoxine freshly added every 24 h.


title: ES3

description:
Library name: ES3
Mouse embryonic stem cells (mESCs) maintained under standard culture conditions, no treatment.

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

extract_protocol:
RNA was extracted from cell culture using TRIzol reagent. Briefly, cell culture were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an Illumina flow cell.

value: embryonic stem cells


description:
Library name: HIPC-1_03_Hu_TCL6_5D
10x single-cell library of lung sample from donor L006


description:
Library name: HIPC-1_02_Hu_TCL3_2D
10x single-cell library of lung sample from donor L003


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to PIV (3)

description:
Library name: DICE-TCR_023_Hu_RSPV_13D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the PIV peptide megapool (MP)


description:
Library name: HIPC-1_01_Hu_2_2D
10x single-cell library of lung sample from donor L002


title: ES2

description:
Library name: ES2
Mouse embryonic stem cells (mESCs) maintained under standard culture conditions, no treatment.


title: R85C10, Tempearture 29, Gal4+, Control, ZT12, Thermogenetic Sleep Deprivation,rep-1

description: Library name: R85C10_29_1

value: Whole Brain


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to MPV (4)

description:
Library name: DICE-TCR_023_Hu_MPV_13D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the MPV peptide megapool (MP)

value: MPV-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+


title: ES1

description:
Library name: ES1
Mouse embryonic stem cells (mESCs) maintained under standard culture conditions, no treatment.


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to Aspergillus (4)

description:
Library name: DICE-TCR_027_Hu_ASP_2_11D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the Aspergillus peptide megapool (MP)


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to MPV (3)

description:
Library name: DICE-TCR_022_Hu_hMPV_2_17D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the MPV peptide megapool (MP)


title: V_D7_3

description:
Library name: V_D7_3
Mouse embryonic stem cells (mESCs) treated with 20 uM vitamin B6 (pyridoxine) for 7 days.


title: R65H02, Tempearture 29, Gal4+, Control, ZT0, Thermogenetic Sleep Deprivation,rep-3

description: Library name: R65H02_29_3


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to PIV (2)

description:
Library name: DICE-TCR_022_Hu_RSPV_1_17D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the PIV peptide megapool (MP)


title: V_D7_2

description:
Library name: V_D7_2
Mouse embryonic stem cells (mESCs) treated with 20 uM vitamin B6 (pyridoxine) for 7 days.


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to MPV (2)

description:
Library name: DICE-TCR_021_Hu_hMPV_17D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the MPV peptide megapool (MP)


title: V_D7_1

description:
Library name: V_D7_1
Mouse embryonic stem cells (mESCs) treated with 20 uM vitamin B6 (pyridoxine) for 7 days.


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to PIV (1)

description:
Library name: DICE-TCR_021_Hu_RSPV_17D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the PIV peptide megapool (MP)


title: R21H11 Tempearture 29, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-3

description: Library name: R21H11_TrpA1_29_3


title: V_D5_3

description:
Library name: V_D5_3
Mouse embryonic stem cells (mESCs) treated with 20 uM vitamin B6 (pyridoxine) for 5 days.


title: R21H11, Tempearture 21, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-3

description: Library name: R21H11_TrpA1_21_3


title: R21H11, Tempearture 29, TrpA1, ZT0,Thermogenetic Sleep Deprivation,rep-1

description: Library name: R21H11_TrpA1_29_1


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to MPV (1)

description:
Library name: DICE-TCR_020_Hu_hMPV_17D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the MPV peptide megapool (MP)


title: R21H11, Tempearture 29, Gal4+, Control, ZT0, Thermogenetic Sleep Deprivation,rep-2

description: Library name: R21H11_29_2


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to RSV (4)

description:
Library name: DICE-TCR_019_Hu_RSV_13D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the RSV peptide megapool (MP)

value: RSV-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+


title: V_D5_2

description:
Library name: V_D5_2
Mouse embryonic stem cells (mESCs) treated with 20 uM vitamin B6 (pyridoxine) for 5 days.


title: V_D5_1

description:
Library name: V_D5_1
Mouse embryonic stem cells (mESCs) treated with 20 uM vitamin B6 (pyridoxine) for 5 days.


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to CMV (7)

description:
Library name: DICE-TCR_018_Hu_CMV2_17D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the CMV peptide megapool (MP)


title: V_D3_3

description:
Library name: V_D3_3
Mouse embryonic stem cells (mESCs) treated with 20 uM vitamin B6 (pyridoxine) for 3 days.


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to CMV (6)

description:
Library name: DICE-TCR_018_Hu_CMV1_17D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the CMV peptide megapool (MP)


title: V_D3_2.

description:
Library name: V_D3_2.
Mouse embryonic stem cells (mESCs) treated with 20 uM vitamin B6 (pyridoxine) for 3 days.


title: V_D3_1

description:
Library name: V_D3_1
Mouse embryonic stem cells (mESCs) treated with 20 uM vitamin B6 (pyridoxine) for 3 days.


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to RSV (2)

description:
Library name: DICE-TCR_016_Hu_RSV_17D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the RSV peptide megapool (MP)


title: C_D7_2

description:
Library name: C_D7_2
Mouse embryonic stem cells (mESCs) cultured with vehicle control for 7 days.


title: C_D7_3

description:
Library name: C_D7_3
Mouse embryonic stem cells (mESCs) cultured with vehicle control for 7 days.


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to RSV (1)

description:
Library name: DICE-TCR_015_Hu_1_17D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the RSV peptide megapool (MP)


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to B. pertussis-aP (4)

description:
Library name: DICE-TCR_014_Hu_2_14
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the B. pertussis-aP peptide megapool (MP)

value: B. pertussis-aP-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+


title: Hot cell, Tempearture 29, Gal4+, Control, ZT0,Thermogenetic Sleep Deprivation, rep-3

description: Library name: HC_29_3


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to Aspergillus (1)

description:
Library name: DICE-TCR_024_Hu_ASP_1_16D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the Aspergillus peptide megapool (MP)


title: C_D7_1

description:
Library name: C_D7_1
Mouse embryonic stem cells (mESCs) cultured with vehicle control for 7 days.


title: C_D5_3

description:
Library name: C_D5_3
Mouse embryonic stem cells (mESCs) cultured with vehicle control for 5 days.


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to B. pertussis-R (4)

description:
Library name: DICE-TCR_014_Hu_1_14
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the B. pertussis-R peptide megapool (MP)

value: B. pertussis-R-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to B. pertussis-aP (3)

description:
Library name: DICE-TCR_013_Hu_2_14D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the B. pertussis-aP peptide megapool (MP)


title: PDX human in mouse tumor resection sample, GEX modality [PDX1_rna]

description: Library name: PDX1_rna

molecule: nuclear RNA

value: PDX

value: tumor

value: PDX model - patient tumor grafted into NOD/SCID mouse

value: mRNA


title: C_D5_2

description:
Library name: C_D5_2
Mouse embryonic stem cells (mESCs) cultured with vehicle control for 5 days.


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to B. pertussis-R (3)

description:
Library name: DICE-TCR_013_Hu_1_14D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the B. pertussis-R peptide megapool (MP)


title: C_D3_3

description:
Library name: C_D3_3
Mouse embryonic stem cells (mESCs) cultured with vehicle control for 3 days.


title: C_D5_1

description:
Library name: C_D5_1
Mouse embryonic stem cells (mESCs) cultured with vehicle control for 5 days.


title: C_D3_2

description:
Library name: C_D3_2
Mouse embryonic stem cells (mESCs) cultured with vehicle control for 3 days.


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to B. pertussis-aP (1)

description:
Library name: DICE-TCR_011_Hu_VAX_17D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the B. pertussis-aP peptide megapool (MP)


title: C_D3_1

description:
Library name: C_D3_1
Mouse embryonic stem cells (mESCs) cultured with vehicle control for 3 days.


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to B. pertussis-R (1)

description:
Library name: DICE-TCR_011_Hu_R_17D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the B. pertussis-R peptide megapool (MP)


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to SARS-CoV-2 (4)

description:
Library name: DICE-TCR_010_Hu_SC2_CD4_13D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the SARS-CoV-2 peptide megapool (MP)

value: SARS-CoV-2-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to EBV (4)

description:
Library name: DICE-TCR_010_Hu_EBV_CD4_13D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the EBV peptide megapool (MP)

value: Blood

value: EBV-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to SARS-CoV-2 (3)

description:
Library name: DICE-TCR_009_Hu_SC2_CD4_16D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the SARS-CoV-2 peptide megapool (MP)

value: Antigen-reactive T cell enrichment (ARTE) assay


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to SARS-CoV-2 (2)

description:
Library name: DICE-TCR_008_Hu_SC2_CD8_16D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the SARS-CoV-2 peptide megapool (MP)


title: Single-cell RNA sequencing of mouse tissue with WT EVs treated, B2

city: Wuhan

first: Zheng

last: Zhang

address: Jiefang Road 1095

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: Library name: B2_EmptyDrops_CR_282920_matrix

data_processing:
Raw sequencing data were processed using CeleScope v3.0.1 (Singleron Biotechnologies) with default settings. Cell barcodes and unique molecular identifiers (UMIs) were extracted and corrected from Read 1, while Read 2 was trimmed to remove adapter sequences and poly(A) tails. The trimmed reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR v2.6.1b. Uniquely mapped reads were assigned to exons using FeatureCounts v2.0.1, and UMIs with identical cell barcodes and gene annotations were collapsed to generate the final gene expression matrix.
Assembly: Mus musculus GRCm38 (mm10)
Supplementary files format and content: Each processed data file (.tar) contains the filtered single-cell expression matrix generated by CeleScope, including matrix.mtx, features.tsv, and barcodes.tsv files in Matrix Market format. File names correspond to individual samples.

source_name: epidural scar

extract_protocol:
Fresh tissues were preserved in sCelLiveTM Tissue Preservation Solution (Singleron) on ice within 30 min post-surgery. Specimens were washed with HBSS, minced, and digested with 3 mL sCelLiveTM Dissociation Solution (Singleron) (37°C, 15 min) using Singleron PythoN™ Tissue Dissociation System. After filtration (40 μm strainer), red blood cells were lysed with GEXSCOPE® RCLB (1:2 ratio, 5-8 min, RT). The mixture was then centrifuged at 300 × g 4 ℃ for 5 mins to remove supernatant, followed by PBS resuspension. Cell viability was assessed via Trypan Blue staining
Single-cell suspensions (2×105 cells/mL in PBS) were loaded onto a microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads were collected from the chip, and reverse transcription was performed to generate cDNA from captured mRNA, followed by PCR amplification. The amplified cDNA was fragmented, ligated with sequencing adapters, and libraries were constructed using GEXSCOPE® Single Cell RNA Library Kits (Singleron)

value: epidural scar

value: WT EVs


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to EBV (2)

description:
Library name: DICE-TCR_008_Hu_EBV_CD8_16D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the EBV peptide megapool (MP)


title: Single-cell RNA sequencing of mouse tissue with WT EVs treated, B1

description: Library name: B1_EmptyDrops_CR_282922_matrix


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to SARS-CoV-2 (1)

description:
Library name: DICE-TCR_007_Hu_SC2_CD4_16D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the SARS-CoV-2 peptide megapool (MP)


title: Single-cell RNA sequencing of mouse tissue with BiTE EVs treated, A3

description: Library name: A3_EmptyDrops_CR_282293_matrix

value: BiTE EVs


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to EBV (1)

description:
Library name: DICE-TCR_007_Hu_EBV_CD4_16D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the EBV peptide megapool (MP)


title: Single-cell RNA sequencing of mouse tissue with BiTE EVs treated, A2

description: Library name: A2_EmptyDrops_CR_282921_matrix


title: Single-cell RNA sequencing of mouse tissue with BiTE EVs treated, A1

description: Library name: A1_EmptyDrops_CR_282923_matrix


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to CMV (5)

description:
Library name: DICE-TCR_004_Hu_CMV_CD4_16D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the CMV peptide megapool (MP)

value: CMV-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to IAV (4)

description:
Library name: DICE-TCR_003_Hu_FLU_CD4_16D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the IAV peptide megapool (MP)

value: IAV-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+


title: MU4

description:
Library name: mu8
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v7.0.1).
Data was processed with Scanpy v1.10.2, soupX v1.6.2, scDBLfinder v3.20 and scVI v1.1.4
Only cells that met the following criteria were included in the subsequent analysis: more than 700 uniquely expressed genes, and less than 20% and 30% of unique molecular identifier counts mapping to mitochondrial and ribosomal sequence. In addition only cells that exhibit enrichment of the YFP transgene, the presence of KrasG12D and Trp53 mutations, and a higher number of copy number aberrations (inferred using inferCNV v1.22.028) were considered for downstream analysis
Assembly: Mouse mm10
Supplementary files format and content: Scanpy processed data for all the samples in Seurat format

source_name: skin

extract_protocol:
10,000 single cells from the LKPR tumour were loaded onto each channel of the Chromium Single Cell 3′ microfluidic chips (V2-chemistry, PN-120232, 10X Genomics) and barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics). RNA from the barcoded cells was subsequently reverse transcribed, followed by amplification, shearing 5′ adaptor and sample index attachment. The libraries were prepared using the Chromium Single Cell 3′ Library Kit (V3-chemistry, PN-120233, 10X Genomics) and sequenced on an Illumina Novaseq 6000 (paired-end 100bp reads).
scRNA-seq

value: skin

value: LKPR tumor cell


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to CMV (4)

description:
Library name: DICE-TCR_003_Hu_CMV_CD4_16D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the CMV peptide megapool (MP)


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to IAV (3)

description:
Library name: DICE-TCR_002_Hu_FLU_CD4_16D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the IAV peptide megapool (MP)


title: MU2

description:
Library name: mu4
10x Genomics


title: MU1

description:
Library name: mu3
10x Genomics


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to CMV (3)

description:
Library name: DICE-TCR_002_Hu_CMV_CD4_16D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the CMV peptide megapool (MP)


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to IAV (2)

description:
Library name: DICE-TCR_001_Hu_FLU_2_12D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the IAV peptide megapool (MP)


title: SC8

description:
Library name: sc46
10x Genomics


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to IAV (1)

description:
Library name: DICE-TCR_001_Hu_FLU_1_12D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the IAV peptide megapool (MP)


title: SC7

description:
Library name: sc43
10x Genomics


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to CMV (2)

description:
Library name: DICE-TCR_001_Hu_CMV_2_12D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the CMV peptide megapool (MP)


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to CMV (1)

description:
Library name: DICE-TCR_001_Hu_CMV_1_12D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the CMV peptide megapool (MP)


title: SC5

description:
Library name: sc33
10x Genomics


title: HK2-TBOEP3

city: Changzhou

first: Shuai

address: 68 Gehu Rd, Wujin District

institute: The Affiliated Changzhou NO.2 People’s Hospital of Nanjing Medical University

description:
Library name: sample6
HK2-TBOEP3

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences. In order to get high-quality reads that could be used for later analysis, raw reads needed to be further quality filtered. Trimmomatic software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.Using hisat2 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
Assembly: Homo_sapiens_Ensembl_110
Supplementary files format and content: 1processed data.xlsx

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded Total

value: human kidney cell

value: TBOEP


title: HK2-TBOEP2

description:
Library name: sample5
HK2-TBOEP2


title: SC1

description:
Library name: sc15
10x Genomics


title: SC3

description:
Library name: sc2b3
10x Genomics


title: HK2-TBOEP1

description:
Library name: sample4
HK2-TBOEP1


title: HK2-NC3

description:
Library name: sample3
HK2-NC3

value: DMSO


title: SC2

description:
Library name: sc2b1
10x Genomics


title: HK2-NC2

description:
Library name: sample2
HK2-NC2


title: HK2-NC1

description:
Library name: sample1
HK2-NC1


title: OE_5

city: taiyuan

first: Yutong

state: Shanxi

address: NO.56 Xinjian South Road

institute: Shanxi Medical University

description:
processed data file: Processed_data_files_2.txt
processed data file header: OE_2

data_processing:
Illumina Casava 1.8 software was used for basecalling.
Raw data (raw reads) in fastp format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and reads with low quality. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were conducted using the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Differential expression analysis of two groups (five biological replicates per group) was performed using the DESeq2 R package (1.20.0).
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include FPKM values and read count numbers for each sample.

extract_protocol:
The total RNA samples for RNA-seq were extracted using TRIzol reagent and then treated with DNaseⅠ in order to eliminate the DNA contamination. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used to prepared the RNA-seq libraries according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: PTCSC3-AS1 overexpression


title: mBMSCs，siRIOK3-_1

city: Hefei

first: shengqian

address: No. 218, Ji-xi Road

institute: the First Affiliated Hospital of Anhui Medical University

data_processing:
MultiQC Version v1.11
Sequence reads were trimmed for adaptor sequence/low-quality sequence using MultiQC Version v1.11
Trimmed sequence reads were mapped to GRCm39 using HISAT2
FPKM=total exon fragments/(uniquely mapped reads*exon length)
Assembly: GRCm39
Supplementary files format and content: expressed_gene_FPKM file includes raw counts for each sample
Supplementary files format and content: expressed_gene_reads file includes raw counts for each sample

source_name: bone marrow mesenchymal stem cells

extract_protocol:
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.
PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: bone marrow mesenchymal stem cells

value: RIOK3 knockdown


title: OE_4

description:
processed data file: Processed_data_files_2.txt
processed data file header: OE_1


title: mBMSCs，siNC_3

value: WT


title: OE_3

description:
processed data file: Processed_data_files_1.txt
processed data file header: EST_OE_3


title: SC4

description:
Library name: sc32
10x Genomics


title: mBMSCs，siNC_2


title: OE_2

description:
processed data file: Processed_data_files_1.txt
processed data file header: EST_OE_2


title: mBMSCs，siNC_1


title: OE_1

description:
processed data file: Processed_data_files_1.txt
processed data file header: EST_OE_1


title: mBMSCs，siRIOK3-_3


title: Vigna radiata T2 48h WGBS rep3

city: Jinan

first: Zhi-Wei

last: Wang

address: No. 23788, Industrial North Road, Licheng District

institute: Shandong Academy of Agricultural Sciences

description:
Library name: Meth_T2H48_rep3
WGBS of T2 H48 leaf

data_processing:
Raw reads were trimmed using fastp (v1.0.1). Clean reads were aligned to the Vigna radiata reference genome using Bismark (v0.25.1, --non_directional). PCR duplicates were removed with samtools (v1.22.1), retaining uniquely mapped reads with ≥ 4× coverage. Cytosine methylation ratios (CpG/CHG/CHH) were calculated using BatMeth2 with sliding-window analysis for DMR detection. Differential methylation analysis was performed using methylKit (v1.34.0), defining DMRs as |Δmeth| ≥ 20% and FDR < 0.05. Methylation levels were integrated with RNA-seq expression profiles by stratifying genes into expression quantiles. Genome-wide methylation landscapes and gene-centric profiles were visualized in R (v4.4.3) using ggplot2 and pheatmap.
Assembly: Vigna radiata (Weilv 9) reference genome
Supplementary files format and content: Methylation_methylation_matrix.txt

organism: Vigna radiata

source_name: Leaf

growth_protocol: Mung bean (Vigna radiata cv. Weilv 9) seeds were surface‑sterilized and germinated on moist filter paper for 2 days. Uniform seedlings were transferred to seedling trays and grown for 3 days, then moved to hydroponic containers containing half‑strength Murashige and Skoog (1/2 MS) nutrient solution. Plants were cultivated under controlled conditions: 25°C, 12,000 lux light intensity, 16 h light/8 h dark photoperiod, and 70% relative humidity.

extract_protocol:
Genomic DNA was extracted from frozen leaf tissues using the DNeasy Plant Maxi Kit (Qiagen, USA) following the manufacturer’s protocol. DNA integrity and concentration were assessed using a NanoDrop spectrophotometer and agarose gel electrophoresis. Only samples with A260/280 ratios between 1.8 and 2.0 and high‑molecular‑weight bands were used for library construction.
Whole‑genome bisulfite sequencing (WGBS) libraries were prepared using the TruSeq DNA Methylation Kit (Illumina, USA). Libraries were sequenced on the Illumina NovaSeq 6000 platform to generate 150 bp paired‑end reads. Library quality and insert size distribution were confirmed using a Bioanalyzer.

treatment_protocol: Two experimental treatments were applied. T1: seedlings were exposed to 100 mM NaCl for 24 h, followed by 48 h recovery in NaCl‑free 1/2 MS solution, then subjected to a second 100 mM NaCl treatment. T2: seedlings were directly exposed to 100 mM NaCl without preconditioning. The first fully expanded true leaves were harvested at 0, 6, and 48 h after the onset of the final salt treatment.

value: Leaf

value: Weilv 9

value: Direct salt stress


title: EV_5

description:
processed data file: Processed_data_files_2.txt
processed data file header: EV_2

value: Empty vector


title: Vigna radiata T2 48h WGBS rep2

description:
Library name: Meth_T2H48_rep2
WGBS of T2 H48 leaf


title: mBMSCs，siRIOK3-_2


title: EV_4

description:
processed data file: Processed_data_files_2.txt
processed data file header: EV_1


title: Vigna radiata T2 48h WGBS rep1

description:
Library name: Meth_T2H48_rep1
WGBS of T2 H48 leaf


title: EV_3

description:
processed data file: Processed_data_files_1.txt
processed data file header: Empty_Vector_3


title: Vigna radiata T2 6h WGBS rep3

description:
Library name: Meth_T2H6_rep3
WGBS of T2 H6 leaf


title: EV_2

description:
processed data file: Processed_data_files_1.txt
processed data file header: Empty_Vector_2


title: Vigna radiata T2 6h WGBS rep2

description:
Library name: Meth_T2H6_rep2
WGBS of T2 H6 leaf


title: Pooled 10x single-cell library of PBMC samples (HTO-labeled), CD4+ T cells specific to RSV (3)

description:
Library name: DICE-TCR_017_Hu_RSV_17D
Pooled 10x single-cell library of PBMC samples from multiple donors (HTO-labeled), CD4+ T cells specific to antigens in the RSV peptide megapool (MP)

value: Blood

value: RSV-specific CD4+ T cells:CD3+ CD4+ CD154+ CD69+

value: Antigen-reactive T cell enrichment (ARTE) assay


title: EV_1

description:
processed data file: Processed_data_files_1.txt
processed data file header: Empty_Vector_1


title: nonSMA41

city: Albuquerque

first: Douglas

middle: Jay

last: Perkins

state: NM

address: MSC10 5550, 1 University of New Mexico

department: Center for Global Health

institute: University of New Mexico

description: Library name: s9b

data_processing:
Raw data were quality-controlled and filtered using fastp
Sequences were aligned to the Plasmodium falciparum Kenya isolate pfKE01 reference genome using Bowtie 2.
HTSeq v0.6.1 was used to generate read counts mapped to each gene.
Differential expression analysis of the two clinical conditions (non-SMA vs SMA) was performed using EdgeR (3.16.5) package, utilizing a negative binomial (NB) based statistical model
Assembly: GCA_900631975.1
Supplementary files format and content: excel files includes Mapped reads stats for each sample
Supplementary files format and content: excel  files includes raw read counts for each sample
Supplementary files format and content: excel  files includes Quality control summary for each sample

organism: Plasmodium falciparum

source_name: blood

extract_protocol:
Total RNA was batch-isolated using E.Z.N.A® Total RNA Kit (Omega Bio-Tek Inc.), treated with RNase-free DNase I (New England Biolabs Inc.), and further processed using RNA Clean & Concentrator (ZYMO Research Corp.).
Only samples with RNA integrity number (RIN) >8 were used for library preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s protocol.

value: blood

value: Day 0

tag: sample group

value: nonSMA


title: Vigna radiata T2 6h WGBS rep1

description:
Library name: Meth_T2H6_rep1
WGBS of T2 H6 leaf


title: Vigna radiata T2 0h WGBS rep3

description:
Library name: Meth_T2H0_rep3
WGBS of T2 H0 leaf


title: nonSMA40

description: Library name: s95b


title: Vigna radiata T2 0h WGBS rep2

description:
Library name: Meth_T2H0_rep2
WGBS of T2 H0 leaf


title: nonSMA39

description: Library name: s92b