title: 52w-AR113Q1

description:
Library name: 07587-ZY-17
07587-ZY_gene_expected_count.csv


title: 252800524040_2_2_FP44C_6_hours

status: Public on Apr 15 2026

type: RNA

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

country: USA

institute: WRAIR

hyb_protocol: Hybridizations were performed using Agilent SurePrint G3 Mouse GE 8x60K microarrays following Agilent's Two-Color Microarray-Based Gene Expression protocol.

scan_protocol: Arrays were scanned using Agilent SureScan Microarray Scanner and features were extracted using Agilent Feature Extraction Software (v10.7).

data_processing: Data were processed using Feature Extraction Software. Log2 transformation and quantile normalization were applied where applicable.

molecule: total RNA

organism: Mus musculus

source_name: Agilent Universal Mouse Reference RNA

label_protocol: Purified RNA samples were labeled with Cy5 using the Agilent Low Input Quick Amp Labeling Kit. The reference RNA was labeled with Cy3.

extract_protocol: Total RNA was extracted from tissue samples using TRIzol reagent and miRNeasy Mini Kit (QIAGEN) following the manufacturer's instructions. Quality was assessed using NanoDrop, Qubit, and Tapestation 2200.

tag: time point

tag: treatment

value: Sham

source_name: Cortex

value: Fentanyl

tag: tissue

value: Cortex


title: hCO, d1tic, rep2

type: SRA

city: Atlanta

first: Emily

middle: Jane

last: Hill

state: Georgia

address: 615 Michael Street

department: School of Medicine

institute: Emory University

description: Library name: Sample 5

library_source: transcriptomic

data_processing:
Bulk sequencing of 40 million paired-end reads per sample was completed using the Illumina-based platform. FASTQ files were evaluated for quality using FastQC and then mapped to the human genome (hg19), using the Spliced Transcripts Alignment to a Reference (STAR) aligner with the paired-end option. The featureCounts package was used to generate a raw counts data matrix from mapped reads. After generating the filtered, raw counts data matrices, we used DESeq2 to normalize the matrices and perform differential gene expression-based statistics. scRNAseq: Fastq sequencing files were processed through CellRanger.
Assembly: hg19
Supplementary files format and content: Bulk RNAseq: tab-delimited/comma-delimited text file that includes raw counts for each sample and .bam files.
Supplementary files format and content: scRNAseq: matrix, barcode, and features files for each sample

organism: Homo sapiens

source_name: human cortical organoid

growth_protocol: Human cortical organoids (hCOs): Following 3D formation, hCOs were treated daily in neural induction media (DMEM/F12, KSR, NEAA, Glutamax, Pen/Strep, Beta-mercaptoethanol) supplemented with Dorsomorphin (Sigma, Cat. 142  P5499-25MG, 5 μM) and SB-431542 (Selleck Chemicals, Cat. S1067, 10 μM) for 6 days.  Following this treatment, hCOs were treated daily with neural media supplemented with EGF (R&D Systems, Cat. 236-EG-01M, 20 ng/mL) and FGF2 (R&D Systems, Cat. 233-FB-01M, 20 ng/mL) for 10 days, and every other day for days 16-24. At day 25, hCOs were treated every other day with neural media supplemented with BDNF (PeproTech, Cat. 450-02- 1mg, 20 ng/mL) and NT-3 (R&D Systems, Cat. 267-N3-005/CF, 20 ng/mL) to promote differentiation of progenitors. From day 43 onwards, hCOs were fed every 3 days with neural media only. hCOs were cultured in Neurobasal-A media supplemented with B27-A, 1% penicillin-streptomycin, and 1% GlutaMAX. hCOs were incubated in 10cm low-adherence cell culture dish at 37°C and 5% CO2.

extract_protocol:
Bulk RNAseq: RNA was extracted from the cells using a RNeasy Micro Kit (Qiagen, 74004) following the manufacturer’s instructions. scRNAseq: hCOs were dissociated and cells were prepared for library creation according to the 10X Genomics Chromium Next-GEM Single Cell 3' kit manufacturer's protocol (10X Genomics, 1000268). scRNAseq: hCOs were dissociated and cells were prepared for library creation according to the 10X Genomics Chromium Next-GEM Single Cell 3' kit manufacturer's protocol (10X Genomics, 1000268).
Bulk RNAseq: The SMART-Seq® v4 PLUS Kit (Takara Bio) was used following the manufacturer's instructions. scRNAseq: Libraries were created according to the 10X Genomics Chromium Next Gem Single Cell 3' kit manufacturer's protocol.

treatment_protocol: hCOs were treated with either control Neurobasal-A media or Neurobasal-A supplemented with TNF-α (30ng/mL, Cell Signaling Technology, 16769S), IL-1α (3ng/mL,Sigma-Aldrich, I2778), and C1q (400ng/mL, EMD Millipore, 204876).

value: human cortical organoid

tag: cell line

tag: cell type

value: astrocyte

value: TIC

tag: batch


title: G118E-E2KO; Clone#21; 2month; technical replicate 2

city: Houston

first: Hu

last: Chen

state: TX

address: 1250 Moursund St,

department: Pediatrics

institute: Baylor College of Medicine

data_processing:
Adapter sequences were removed from raw sequencing reads using Trimmomatic v0.39 at default parameters.
Trimmed reads were aligned to GRCh38.p12 version 28 human genome assembly from GENCODE using STAR v2.7.9.a using all default parameters except –sjdbOverhang149.
Finally, differential gene expression analyses on the read counts were performed using DESeq2 in R environment.
Assembly: GRCh38
Supplementary files format and content: The number of reads mapped to each gene using the "--quantMode GeneCounts" option in STAR during mapping.

molecule: polyA RNA

source_name: iPSC-derived neurons

growth_protocol: iPSC-derived neurons (NGN2- and NPC-derived) were cultured on Matrigel-coated 24-well plates in Neuronal Differentiation Media (NDM) until the time of harvesting for RNA extraction

extract_protocol:
RNA was extracted from iPSC-derived neurons using the Rneasy Mini Kit (Qiagen, Cat #74106) and 1ug was sent for RNA-sequencing library prep
Librabry prep was performed by Azenta/Genewiz using polyA selection

value: iPSC-derived neurons

value: iPSC-derived NGN2-iNeurons

tag: genotype


title: hCO, d7tic, rep1

description: Library name: Sample 7


title: 252800524040_1_2_FP73C_6_hours


title: 252800524040_1_4_FP55C_0_hour_(40_mins_post)


title: 52w-WT3

city: Ann Arbor

first: Andrew

middle: P

last: Lieberman

state: MI

address: 1150 W Medical Center Dr.

institute: University of Michigan

description:
Library name: 07587-ZY-15
07587-ZY_gene_expected_count.csv

data_processing:
Reads trimmed using CutAdapt v2.3 (files with 07587-ZY*) or v4.8 (all others).
FastQC v0.11.8 used to ensure data quality.
Fastq Screen v0.15.3 used to screen for various types of contamination.
Reads mapped to GRCm38 using STAR v2.7.8a and assigned count estimates to genes with RSEM v1.3.3.
Assembly: GRCm38 (ENSEMBL)
Supplementary files format and content: .csv files have compiled RSEM counts with gene name annotation, separated by timepoint (5, 26, or 52 weeks were all distinct sequencing projects).

source_name: Tibialis anterior

growth_protocol: Mice aged to 5 weeks (files starting with 12625-CK*), 26 weeks (files starting with 11413-CK*), or 52 weeks (files starting with 07587-ZY*) prior to tissue collection. Library titles named reflecting age of tissue collection (5w, 26w, or 52w).

extract_protocol:
Mice were euthanized at 5, 26, or 52 weeks, and tibialis anterior was dissected and flash-frozen. Total RNA was then extracted using TRIzol, chloroform, and isopropanol. 500 ng RNA per sample was used for library prep and sequencing.
RNA libraries for RNA-seq were prepared by the University of Michigan Advanced Genomics Core, using the Illumina platform with manufacturer's protocols for polyA-enrichment.

treatment_protocol: For 52w project only (files starting with 07587-ZY*): Male wild-type C57BL6/J mice were treated between weeks 26 and 52 of age, once weekly, with subcutaneous injection of 25 mg/kg AR-directed anti-sense oligonucleotide (ASO) dissolved in sterile PBS, or vehicle.

value: Tibialis anterior

value: Skeletal muscle

value: wild-type

value: vehicle

tag: age


title: 52w-WT2

description:
Library name: 07587-ZY-14
07587-ZY_gene_expected_count.csv


title: G118E;Clone#20;2month; technical replicate 4


title: hCO, d1tic, rep1

description: Library name: Sample 4


title: hCO, d1con, rep3

description: Library name: Sample 3

value: control


title: G118E-E2KO; Clone#21; 2month; technical replicate 1


title: 52w-WT1

description:
Library name: 07587-ZY-13
07587-ZY_gene_expected_count.csv


title: 252800524040_2_1_FP96C_0_hour_(40_mins_post)


title: 252800524040_1_1_FP33C_6_hours


title: Total chromatin (pooled input)

description:
Library name: Pooled input
Sequencing files from total input

library_source: genomic

data_processing:
Reads were aligned to the mouse genome (mm10) using the BWA algorithm (v0.7.17, default settings). Duplicate reads were removed; only uniquely mapped reads were used for further analysis.
Alignments were normalized using the CPM (Counts Per Million) method, and the resulting histograms (genomic “signal maps”) were stored in BigWig files.
Peaks were identified using the MACS (v2.2.7) algorithm at a cutoff of q-value 0.1. Peaks that were on the ENCODE blacklist were removed.
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: Male mice of either WT or AR113Q genotype were aged to 26 weeks, at which point tibialis anterior was collected and flash frozen. Pooled muscle totaling 200mg per genotype was sent to Active Motif Services (Carlsbad, CA, USA) for chromatin extraction and processing.

extract_protocol:
Tissue was pulverized with mortar and pestle in liquid nitrogen and then fixed in PBS + 1% formaldehyde at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). Chromatin was isolated by adding lysis buffer and sonicating using the PIXUL® Multi-Sample Sonicator (Active Motif, Catalog #53130) to shear DNA to an average fragment size of 200–1000 bp. Aliquots of chromatin were precleared with protein G agarose beads (Invitrogen). Immunoprecipitations were performed using an antibody specific to PGC-1α (Novus NBP1-04676). After washing, immune complexes were eluted from the beads using SDS buffer, treated with RNase and proteinase K, and de-crosslinked by overnight incubation at 65°C. ChIP DNA was then purified using phenol-chloroform extraction and ethanol precipitation.
ChIP DNA libraries were prepared using either the PrepX DNA Library Kit (Takara Bio) on the Apollo automation platform or the NEB DNA Library Prep Kit, following the manufacturers' protocols. Libraries were sequenced on the Illumina platform and the resulting data were analyzed using standard ChIP-Seq workflows.

value: pooled

tag: chip antibody


title: G118E;Clone#20;2month; technical replicate 2


title: PBNK, Feeder-expanded, day 35 stimulated, biol rep 4

city: Minneapolis

first: Samira

last: Azarin

state: Minnesota

address: 421 Washington Avenue Southeast, 151, Amundson Hall

department: Chemical Engineering and Materials Science

institute: University of Minnesota

description: Library name: Donor 8_day 35

data_processing:
Low quality ends and adapter sequences were trimmed from the Illumina reads using Trimmomatic. Processed reads were mapped and aligned to the human reference genome (GRCh38.91) using Spliced Transcripts Alignment to a Reference (STAR) with default ENCODE parameter settings, except for ‘--runThreadN 16 --sjdbOverhang 76’.  Reads Per Kilobase of transcript, per Million mapped reads, (RPKM) values were computed using Cufflinks and then normalized to transcripts per million (TPM). Using R Studio, TPM was then log2-transformed before performing hierarchical clustering using the Euclidean distance and centroid linkage (UPGMC) method. Principal component analysis (PCA) was performed using the ‘ggplot2’ package in statistical software R (v 3.3.3).
Differential gene expression analysis was performed in R. Python software ‘htseq-counts’ was utilized to extract the necessary raw read counts to upload into the ‘EdgeR’ package to determine differential gene expression. Gene expression was normalized with trimmed mean of M-values (TMM) to adjust for falsely positive downregulated genes after lowly expressed genes (less than 6-7 counts) were filtered out. Negative binomial generalized linear models were then fitted prior to either implementing the quasi-likelihood (QL) F-test or likelihood ratio test for verifying differential gene expression. Transcripts which met the threshold P-value with additional criteria of FDR ≤ 0.05 and fold change ≥ 2 were identified as differentially expressed in various pair-wise comparisons. Gene Ontology (GO) analysis of the differentially expressed genes was performed using DAVID v6.8. Further visualizations of the data including the PCA plot and quadrant analysis for comparative analysis of pair-wise comparisons were completed using the TIBCO Spotfire v7.6.1 OmicsOffice package.
Assembly: human reference genome (GRCh38.91)
Supplementary files format and content: Excel (.xlsx) provide TPM values for each sample

source_name: Peripheral blood NK cell

growth_protocol: Peripheral blood mononuclear cells were obtained from Memorial Blood Center (Minneapolis, MN) using Ficoll-Paque Premium (GE Healthcare). NK cell isolation was performed using negative selection with the EasySep Human NK Cell Enrichment Kit (STEMCELL Technologies). Peripheral blood-derived natural killer cells (PBNK) were cultured overnight in B0 medium supplemented with 100 U/mL IL-2 (Proleukin) to recover from magnetic bead sorting. B0 medium formulation included 2:1 (vol:vol) mix of Dulbecco’s Modification of Eagle’s Medium (DMEM) with 4.5 g/L glucose, L-glutamine, and sodium pyruvate and Ham’s F12 Medium (Corning). Supplements included 20 μM 2-mercaptoethanol (Gibco), 50 μM ethanolamine (Sigma), 10 μg/mL ascorbic acid (Sigma), 1.6 ng/mL sodium selenite (Sigma), 1% penicillin/streptomycin, and 20% heat-inactivated human AB serum (Valley Biomedical).

extract_protocol:
Total RNA was isolated from feeder-expanded NK cells harvested from the culture process at day 0, 7, and 35 using the Qiagen™ RNeasy Mini Kit.
The Illumina TruSeq® Stranded mRNA Sample Prep Kit protocol was used to purify poly-A containing mRNA molecules from the total RNA and create sequence libraries. Sequence libraries of each sample were pooled and sequenced using the Illumina HiSeq 2500 instrument (High Output, 125 bp, Paired Reads, v4) at the University of Minnesota Genomics Center.

treatment_protocol: NK cells from 4 donors (Donor 5, 6, 7, and 8, labeled biol rep 1, 2, 3, and 4) were stimulated with a 1:2 ratio of NK cells to irradiated K562 feeder cells in B0 medium supplemented with 50 U/mL IL2 (feeder-expanded). Seven days after initial stimulation, and weekly thereafter, serial stimulation was conducted by re-seeding NK cells at 1.25x10^5 cell/mL in fresh medium and re-stimulating with K562 feeder cells at a 1:1 ratio. In the first week of culture, half-medium changes were performed at day 3 and day 5, and during subsequent weeks cells were re-seeded to 2.5e5 cells/mL every 2-3 days between rounds of stimulation.

value: Peripheral blood NK cell

value: Stimulated day 35


title: G118E;Clone#20;2month; technical replicate 3


title: hCO, d1con, rep2

description: Library name: Sample 2


title: hCO, d1con, rep1

description: Library name: Sample 1


title: Isogenic WT Control; Clone#42;2month; technical replicate 4


title: PBNK, Feeder-expanded, day 35 stimulated, biol rep 3

description: Library name: Donor 7_day 35


title: WT pooled, PGC-1a (ChIP)

description:
Library name: 16_0JZB_02NUUMichigan_WT9-double_PGC1-alpha-PPARGC1A_mm_i08-3
Sequencing files from pooled chromatin from WT mice

value: WT

value: PGC-1a (Novus, NBP1-04676)


title: AR113Q pooled, PGC-1a (ChIP)

description:
Library name: 09_0K2X_02NUUMichigan_AR113Q1-double_PGC1-alpha-PPARGC1A_mm_i18-10
Sequencing files from pooled chromatin from AR113Q mice


title: 252800524039_2_2_FP38C_6_hours

value: Sham

value: Fentanyl


title: G118E;Clone#20;2month; technical replicate 1


title: PBNK, Feeder-expanded, day 35 stimulated, biol rep 2

description: Library name: Donor 6_day 35


title: 252800524039_2_1_FP86C_6_hours

value: Cortex


title: 252800524039_2_4_FP64C_24_hours


title: Tumor tissue from the anti-PD-1 antibody model

city: Hiroshima

first: Masahiko

last: Sumii

address: 1-2-3 Kasumi, Minami-ku,

country: Japan

institute: Hiroshima University Hospital

description:
Library name: PD_1_treatment
10x Genomics

library_source: transcriptomic single cell

data_processing:
Data were processed by Cell Ranger software (V.7.0.1) by 10x Genomics.
Assembly: Mouse mm10
Supplementary files format and content: 10x Genomics Chromium Raw Gene BC Cellular Barcodes
Supplementary files format and content: 10x Genomics Chromium Raw Gene BC Cellular Genes
Supplementary files format and content: 10x Genomics Chromium Raw Gene BC Cellular Matrix

source_name: subcutaneous tumor

extract_protocol:
Tumor tissue was removed from the LLC tumor-bearing mice in the control model and anti-PD-1antibody model.Subsequently, RNA libraries were prepared with the  GEM-X Flex sample preparation v2 kit (10x Genomics) .
Library was performed according to the manufacter's instructions (Single cell 3' V3.1 protocol, 10x Genomics)

value: subcutaneous tumor

value: Lewis Lung carcinoma

value: anti-PD-1 antibody


title: Isogenic WT Control; Clone#42;2month; technical replicate 3

value: iPSC-derived neurons

value: iPSC-derived NGN2-iNeurons


title: Isogenic WT Control; Clone#42;2month; technical replicate 2


title: PBNK, Feeder-expanded, day 0 unstimulated, biol rep 2

description: Library name: Donor 6_day 0

value: Unstimulated day 0


title: JVT_6

city: Stanford

first: Meena

last: Easwaran

state: California

address: 240 Pasteur Dr, BMI 1400

institute: Stanford University

description:
Library name: Sample 18
Column name in Readcount_allsamples_genename.csv: JVT_6

data_processing:
Initial data processing including mapping and quantification was performed by Novogene Inc. Trimmed sequencing reads were mapped to GRCm38/mm10 reference genome using Spliced Transcripts Alignment to a Reference (STAR) software (v2.6.1d), with a mismatch parameter as 2. Read count extraction was performed featureCounts (v1.5.0-p3) with deafult parameters.
Assembly: GRCm38/mm10
Supplementary files format and content: csv file includes read counts for each Sample

source_name: Larynx

extract_protocol:
Total RNA was extracted from whole mouse larynges using the PureLink™ RNA Mini Kit ( Invitrogen, CA, USA) as per the manufacturer's instructions.
Library construction was performed by Novogene Inc. using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA), following the manufacturer’s instructions. 1 µg of total RNA per sample was used as the input material for the construction of sequencing libraries.

treatment_protocol: Individual mice in each experimental group were exposed to either room air, 3R4F cigarette smoke, or JUUL Virginia tobacco E-Cigarette aerosol using the inEXPOSE whole-body inhalation chamber for 1 hour/day,  5 days/week, over a period of 4 weeks.

value: Larynx

value: Sample exposed to JUUL Virgina tobacco E-Cigarette aerosol

tag: Sex

value: Male

value: 8-9 weeks

tag: strain


title: Isogenic WT Control; Clone#42;2month; technical replicate 1


title: Tumor tissue from the Control model

description:
Library name: Control
10x Genomics

value: IgG2a isotype control antibody


title: PBNK, Feeder-expanded, day 7 stimulated, biol rep 2

description: Library name: Donor 6_day 7

value: Peripheral blood NK cell

value: Stimulated day 7


title: Isogenic WT Control; Clone#32;2month; technical replicate 3


title: PBNK, Feeder-expanded, day 35 stimulated, biol rep 1

description: Library name: Donor 5_day 35

value: Stimulated day 35


title: Isogenic WT Control; Clone#32;2month; technical replicate 4


title: JVT_5

description:
Library name: Sample 17
Column name in Readcount_allsamples_genename.csv: JVT_5


title: JVT_4

description:
Library name: Sample 16
Column name in Readcount_allsamples_genename.csv: JVT_4


title: PBNK, Feeder-expanded, day 7 stimulated,  biol rep 1

description: Library name: Donor 5_day 7


title: 252800524039_1_3_FP59C_7_days

value: Sham


title: JVT_3

description:
Library name: Sample 15
Column name in Readcount_allsamples_genename.csv: JVT_3


title: PBNK, Feeder-expanded, day 0 unstimulated, biol rep 1

description: Library name: Donor 5_day 0


title: 252800524039_2_3_FP93C_24_hours

value: Fentanyl


title: Isogenic WT Control; Clone#32;2month; technical replicate 2


title: WT_72H_rep3

city: Chengdu

first: chen

last: li

address: Renmin South Road

country: China

institute: Sichuan Univercity

description: Library name: Sample 12

data_processing:
Sequence reads were trimmed for adaptor and low-quality sequences using fastp (v0.21.0), with 10 bases trimmed from the 5′ end of each read
Trimmed reads were aligned to the Homo sapiens genome (GRCh38.93) using STAR (v2.7.1a) with default settings and additional filters to restrict multimapping reads and improve splice junction detection
Read counts were extracted using the GenomicAlignments R package (v1.24.0)
Read count extraction were normalization using DESeq2 (v1.24.0)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file contains raw counts, with genes as rows and samples as columns

source_name: Lung

growth_protocol: Calu-3 were maintained in Eagle’s minimal essential medium (EMEM; Lonza, #BE12-136F), further supplemented with 8% FBS (Thermo Fisher, #A3382001), 2 mM L-glutamine (Sigma-Aldrich, #G7513), 100 IU/ml of penicillin and 100 µg/mL of streptomycin (Sigma-Aldrich, #P4458), 1×non-essential amino acids (NEAA; Lonza, #BE13-114E), 1mM of Sodium Pyruvate (Thermo Fisher, #11360039)

extract_protocol:
Total RNA was isolated from cell pellets using TriPure (Roche) isolation reagent according to the manufacturer’s instruction. mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic beads according to the manufacturer’s instruction.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer’s instruction.

treatment_protocol: Calu-3 cells were infected with SARS-CoV-2 virus (BetaCoV/Wuhan/IVDC-HB-01/2019 strain) at an MOI of 2 during 1 hr at 37 °C with shaking. After removal of the inoculum, cells were washed twice with PBS and maintained in EMEM with 2% FCS, L-glutamine, NEAA and antibiotics. Supernatants and cells were collected at 6, 24, 48 and 72 hpi for RNA extraction.

value: Lung

value: Calu-3 cells

value: epithelial cell

value: WT

value: SARS-CoV-2 (BetaCoV/Wuhan/IVDC-HB-01/2019 strain) infection


title: 252800524039_1_4_FP56C_24_hours

value: Cortex


title: 252800524038_2_4_FP21C_0_hour_(40_mins_post)


title: Isogenic WT Control; Clone#32;2month; technical replicate 1

value: iPSC-derived neurons

value: iPSC-derived NGN2-iNeurons


title: 252800524039_1_1_FP51C_24_hours


title: JVT_2

description:
Library name: Sample 14
Column name in Readcount_allsamples_genename.csv: JVT_2

value: Larynx

value: Sample exposed to JUUL Virgina tobacco E-Cigarette aerosol


title: WT_72H_rep2

description: Library name: Sample 11


title: 252800524039_1_2_FPB2C_6_hours


title: G118E;Clone#15;2month; technical replicate 4


title: CSE_6

description:
Library name: Sample 12
Column name in Readcount_allsamples_genename.csv: CSE_6

value: Sample exposed to 3R4F CS

value: Male

value: 8-9 weeks


title: JVT_1

description:
Library name: Sample 13
Column name in Readcount_allsamples_genename.csv: JVT_1


title: 252800524038_2_2_FP53C_7_days


title: WT_72H_rep1

description: Library name: Sample 10


title: WT_48H_rep3

description: Library name: Sample 9


title: CSE_5

description:
Library name: Sample 11
Column name in Readcount_allsamples_genename.csv: CSE_5


title: G118E;Clone#15;2month; technical replicate 3


title: G118E;Clone#15;2month; technical replicate 2


title: 252800524038_2_3_FP66C_24_hours


title: RFP

city: Amsterdam

first: Elzo

last: de Wit

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description: Library name: RFP

data_processing:
Sequencing reads were aligned to the mm10 genome using Bismark (v0.22.3).
Two single nucleotide polymorphisms within the amplicon were used to assign aligned reads into CAST or 129 specific reads.
Bismark was used to perform methylation calling on allele-specific reads.
Assembly: mm10
Supplementary files format and content: txt files contain CpG methylation calls

source_name: Embryo

growth_protocol: Mouse embryonic stem cell lines were cultured as described previously (Liu et al., 2021, 2025; van Schaik et al., 2022). Briefly, the 129/Castaneus F1 hybrid methylation reporter cell lines were cultured on 0.1% gelatin-coated plates in serum-free DMEM/F12 (Gibco) and Neurobasal (Gibco) medium (1:1) supplemented with N-2 (Gibco), B-27 (Gibco), BSA (0.05%, Gibco), 10 4 U of Leukaemia Inhibitory Factor (LIF) (Millipore), MEK inhibitor PD0325901 (1 μM, Selleckchem), GSK3-β inhibitor CHIR99021 (3 μM, Cayman Chemical) and 1-Thioglycerol (1.5 × 10-4 M, Sigma-Aldrich). The cell lines were passaged every 2  days in daily culture.

extract_protocol:
Genomic DNA was extracted from each sorted population (200,000 cells per condition), which served as input for bisulfite conversion, carried out using the EpiJET Bisulfite Conversion Kit (Thermo K1461), following the manufacturer’s instructions.
Sox2 SCR region containing 7xCpG was amplified by PCR. Amplified products were gel-purified and submitted for sequencing with MiSeq Nano.

value: Embryo

value: 129/CAST F1 hybrid SCR methylation reporter mESC

value: Embryonic stem cells


title: CSE_3

description:
Library name: Sample 9
Column name in Readcount_allsamples_genename.csv: CSE_3


title: G118E;Clone#15;2month; technical replicate 1


title: WT_48H_rep2

description: Library name: Sample 8


title: 252800524038_1_2_FP81C_7_days

value: Sham

value: Fentanyl


title: 252800524038_1_3_FP84C_7_days


title: 252800524038_2_1_FP94C_24_hours


title: GFP

description: Library name: GFP


title: DP

description: Library name: DP


title: CSE_2

description:
Library name: Sample 8
Column name in Readcount_allsamples_genename.csv: CSE_2


title: WT_48H_rep1

description: Library name: Sample 7

value: Lung

value: Calu-3 cells


title: CSE_1

description:
Library name: Sample 7
Column name in Readcount_allsamples_genename.csv: CSE_1


title: WT_24H_rep3

description: Library name: Sample 6

value: epithelial cell

value: WT


title: leaves_ZT110_replicate2

city: La Jolla

first: Jose

middle: Luis

last: Pruneda-Paz

state: CA

address: 9500 Gilman Dr Biology #3125 Biology #3125

department: Cell and Developmental Biology

institute: University of California San Diego

description:
Library name: leaf_mock_t6_rep2
Column name in fpkm_values_shoot-apex_leaves_All_samples: leaf_mock_t6_rep2

data_processing:
mRNA-seq reads mapped to the TAIR10 reference genome using STAR v2.5.0c
Sorted .bam files used to generate HOMER Tag Directories
UCSC format tracks generated using the makeUCSCfile script
Raw read counts and normalized values (FPKM) obtained using the HOMER analyzeRepeats.pl program
Assembly: TAIR10
Supplementary files format and content: .csv file includes Arabidopsis Gene Identification number (AGI) in the first column and fpkm values for each sample in the subsequent columns

organism: Arabidopsis thaliana

source_name: Leaves

growth_protocol: Arabidopsis seeds were stratified for 2-3 days at 4oC in a tube containing a 0.15% agar solution and then pipetted onto growth trays containing 2.5” square pots (8x4 divider) filled with autoclaved soil (Berger, BM2). Plants were grown at 22oC under light-dark cycles: 12 hours light (~100 μmol m-2 s-1)/12 hours dark for 14 days. Trays were transferred to constant light (~60 μmol m-2 s-1) and plants collected 90, 94, 98, 102, 106, and 110 hours after (6 total time points).

extract_protocol:
For each sample 6-10 seedlings were snap frozen in liquid nitrogen and then cryodissected to isolate the shoot apex and true leaves.Total RNA was isolated from each sample using the RNeasy Plant Mini kit (Qiagen, Cat# 74904) and mRNAs were purified from 0.46µg of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Cat# E7490) before library preparation.
Library was prepared according to the Library Prep Kit (New England Biolabs, Cat# E7770). Sera-Mag Magnetic SpeedBeads (Thermo Scientific, Cat# 65152105050250) were used for all size selection and clean-up steps, and the resulting libraries were pooled and sequenced (single end 50 bp, SE50) on a HiSeq 2500 machine (Illumina).

value: Leaves

tag: time

value: Zeitgeber Time (ZT) 110


title: G118E-E2KO; Clone#25; 1month; technical replicate 4

value: iPSC-derived neurons

value: iPSC-derived NGN2-iNeurons


title: CSE_4

description:
Library name: Sample 10
Column name in Readcount_allsamples_genename.csv: CSE_4

value: Larynx


title: G118E-E2KO; Clone#25; 1month; technical replicate 2


title: WT_24H_rep1

description: Library name: Sample 4

value: SARS-CoV-2 (BetaCoV/Wuhan/IVDC-HB-01/2019 strain) infection


title: leaves_ZT106_replicate2

description:
Library name: leaf_mock_t5_rep2
Column name in fpkm_values_shoot-apex_leaves_All_samples: leaf_mock_t5_rep2

value: Zeitgeber Time (ZT) 106


title: G118E-E2KO; Clone#25; 1month; technical replicate 3


title: G118E-E2KO; Clone#25; 1month; technical replicate 1


title: TRC_5

description:
Library name: Sample 5
Column name in Readcount_allsamples_genename.csv: TRC_5

value: Control sample exposed to room air

value: Male

value: 8-9 weeks


title: TRC_6

description:
Library name: Sample 6
Column name in Readcount_allsamples_genename.csv: TRC_6


title: 252800524038_1_1_FP20C_0_hour_(40_mins_post)

value: Cortex


title: leaves_ZT110_replicate1

description:
Library name: leaf_mock_t6_rep1
Column name in fpkm_values_shoot-apex_leaves_All_samples: leaf_mock_t6_rep1


title: 252800524038_1_4_FP78C_6_hours

value: Sham


title: TRC_4

description:
Library name: Sample 4
Column name in Readcount_allsamples_genename.csv: TRC_4


title: WT_6H_rep2

description: Library name: Sample 2


title: leaves_ZT102_replicate2

description:
Library name: leaf_mock_t4_rep2
Column name in fpkm_values_shoot-apex_leaves_All_samples: leaf_mock_t4_rep2

value: Zeitgeber Time (ZT) 102


title: WT_6H_rep3

description: Library name: Sample 3

value: Lung


title: G118E-E2KO; Clone#21; 1month; technical replicate 3


title: WT_24H_rep2

description: Library name: Sample 5

value: Calu-3 cells


title: G118E-E2KO; Clone#21; 1month; technical replicate 4


title: WT_6H_rep1

description: Library name: Sample 1

value: epithelial cell


title: G118E-E2KO; Clone#21; 1month; technical replicate 2


title: TRC_2

description:
Library name: Sample 2
Column name in Readcount_allsamples_genename.csv: TRC_2


title: Liver_Healthy :CT_13

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

data_processing:
Raw reads data were converted into FASTQ format and quality control was performed using the FASTQC software (Babraham Bioinformatics).
After trimming for adapters using trim_galore (Babraham Bioinformatics), mapping of the reads were obtained using the STAR program against human genome (gencode.v26) and the quantification of genes and transcripts were done with the RSEM program using ENSEMBL v91.
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Assembly: Homo Sapiens genome hg38 (gencode.v26)
Supplementary files format and content: RSEM expected counts

source_name: Liver

extract_protocol:
Tissues were snap-frozen and minced with a mortar and pestle under liquid nitrogen. The resulting tissue powder was dissolved in Trizol (Invitrogen 15596-018). RNA was separated from DNA and proteins with a Trizol-Chloroform centrifugation and was subsequently precipitated with isopropanol. The RNA pellet was then resuspended in nuclease-free water.
Sequencing libraries were prepared following the protocol included with the kit TruSeq Stranded mRNA Sample Preparation Guide (Part #15031047 Rev. E)

value: Liver

tag: disease state

value: Healthy


title: TRC_3

description:
Library name: Sample 3
Column name in Readcount_allsamples_genename.csv: TRC_3


title: Liver_Healthy :CT_12


title: G118E-E2KO; Clone#21; 1month; technical replicate 1


title: G118E;Clone#20;1month; technical replicate 4


title: leaves_ZT98_replicate1

description:
Library name: leaf_mock_t3_rep1
Column name in fpkm_values_shoot-apex_leaves_All_samples: leaf_mock_t3_rep1

value: Leaves

value: Zeitgeber Time (ZT) 98


title: leaves_ZT102_replicate1

description:
Library name: leaf_mock_t4_rep1
Column name in fpkm_values_shoot-apex_leaves_All_samples: leaf_mock_t4_rep1


title: leaves_ZT94_replicate2

description:
Library name: leaf_mock_t2_rep2
Column name in fpkm_values_shoot-apex_leaves_All_samples: leaf_mock_t2_rep2

value: Zeitgeber Time (ZT) 94


title: TRC_1

description:
Library name: Sample 1
Column name in Readcount_allsamples_genename.csv: TRC_1

value: Larynx


title: G118E;Clone#20;1month; technical replicate 2

value: iPSC-derived neurons

value: iPSC-derived NGN2-iNeurons


title: Liver_Healthy :CT_11


title: leaves_ZT106_replicate1

description:
Library name: leaf_mock_t5_rep1
Column name in fpkm_values_shoot-apex_leaves_All_samples: leaf_mock_t5_rep1

value: Zeitgeber Time (ZT) 106


title: leaves_ZT98_replicate2

description:
Library name: leaf_mock_t3_rep2
Column name in fpkm_values_shoot-apex_leaves_All_samples: leaf_mock_t3_rep2


title: Mouse heart left ventricle, MI with BAT transplantation, Day3, biol rep 3

city: Shanghai

first: YANG

last: Xingbo

address: Shanghai siping road 1239

institute: Tongji

description:
Library name: Sample 6
Column name in Processed_data_TPMs_allSamples.csv : MBT_3

data_processing:
The clean reads were mapped to the reference genome using HISAT2
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
PCA analysis and GO pathway analysis were performed using R (v 3.2.0)
Differential expression analysis was performed using the DESeq2 (Q value<0.05, Fold change >2 or <0.5)
Assembly: NCBI_GRCm39
Supplementary files format and content: csv file includes TPM values for each sample

source_name: Heart left ventricle

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Mouse myocardial infarction model was estabolished by left anterior descending coronary artery ligation.

value: Heart left ventricle

value: WT

value: myocardial infarction D3


title: Mouse heart left ventricle, MI with BAT transplantation, Day3, biol rep 2

description:
Library name: Sample 5
Column name in Processed_data_TPMs_allSamples.csv : MBT_2


title: leaves_ZT94_replicate1

description:
Library name: leaf_mock_t2_rep1
Column name in fpkm_values_shoot-apex_leaves_All_samples: leaf_mock_t2_rep1


title: Mouse heart left ventricle, MI with BAT transplantation, Day3, biol rep 1

description:
Library name: Sample 4
Column name in Processed_data_TPMs_allSamples.csv : MBT_1


title: Liver_Healthy :CT_09


title: Liver_Healthy :CT_08


title: G118E;Clone#20;1month; technical replicate 1


title: G118E;Clone#20;1month; technical replicate 3


title: leaves_ZT90_replicate1

description:
Library name: leaf_mock_t1_rep1
Column name in fpkm_values_shoot-apex_leaves_All_samples: leaf_mock_t1_rep1

value: Zeitgeber Time (ZT) 90


title: leaves_ZT90_replicate2

description:
Library name: leaf_mock_t1_rep2
Column name in fpkm_values_shoot-apex_leaves_All_samples: leaf_mock_t1_rep2


title: Mouse heart left ventricle, MI, Day3, biol rep 2

description:
Library name: Sample 2
Column name in Processed_data_TPMs_allSamples.csv : MI_2


title: Isogenic WT Control; Clone#42;1month; technical replicate 4


title: Liver_Healthy :CT_05


title: Liver_Healthy :CT_06


title: Isogenic WT Control; Clone#42;1month; technical replicate 3


title: Mouse heart left ventricle, MI, Day3, biol rep 3

description:
Library name: Sample 3
Column name in Processed_data_TPMs_allSamples.csv : MI_3


title: shoot apex_ZT110_replicate2

description:
Library name: apex_mock_t6_rep2
Column name in fpkm_values_shoot-apex_leaves_All_samples: apex_mock_t6_rep2

source_name: shoot apex

value: shoot apex

value: Zeitgeber Time (ZT) 110


title: Mouse heart left ventricle, MI, Day3, biol rep 1

description:
Library name: Sample 1
Column name in Processed_data_TPMs_allSamples.csv : MI_1


title: Isogenic WT Control; Clone#42;1month; technical replicate 2


title: Liver_Healthy :CT_04


title: shoot apex_ZT110_replicate1

description:
Library name: apex_mock_t6_rep1
Column name in fpkm_values_shoot-apex_leaves_All_samples: apex_mock_t6_rep1


title: Liver_Healthy :CT_03


title: Isogenic WT Control; Clone#42;1month; technical replicate 1


title: shoot apex_ZT106_replicate2

description:
Library name: apex_mock_t5_rep2
Column name in fpkm_values_shoot-apex_leaves_All_samples: apex_mock_t5_rep2


title: shoot apex_ZT106_replicate1

description:
Library name: apex_mock_t5_rep1
Column name in fpkm_values_shoot-apex_leaves_All_samples: apex_mock_t5_rep1


title: Test,Female,Rep2

city: Seongbuk-gu, Seoul

first: Seoyeon

last: Kim

address: 145, Anam-ro

country: South Korea

institute: Korea University

description: Library name: Test_F_Rep2

data_processing:
Reads were aligned to the pre-built 10X mouse reference and collapsed into unique molecular identifier (UMI) counts using CellRanger (v6.1.2).
Assembly: refdata-gex-mm10-2020-A (GRCm38)
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: nuclear RNA

source_name: Subcortex, Thalamus, Hippocampus

extract_protocol:
Fresh-frozen tissue samples were used for snRNAseq analysis. Tissue blocks embedded in optimal cutting temperature (OCT) compound (Tissue-Tek, Sankura; #4583) were sectioned into 20 µm thick curls (4–5 per sample) using a Leica CM1950 cryostat (Leica, Wetzlar, Germany). The sections were transferred into 5 mL tubes (Eppendorf, Hamburg, Germany), washed with ice-cold PBS (Thermo Fisher, #10010023), centrifuged at 400 × g for 2 minutes, and the supernatant was removed. The tissue was then resuspended in 1 mL ST buffer [146 mM NaCl, 10 mM Tris-HCl (pH 7.5), 1 mM CaCl2, and 21 mM MgCl2 in ultrapure water] containing 0.03% Tween-20 (Sigma Aldrich, #p-7949) and 0.1% BSA (New England Biolabs, B9000S), with or without 40 U/mL RNAse inhibitor (RNAse OUT, Thermo Fisher). The suspension was mechanically dissociated by pipetting 15 times with a 1 mL pipette, followed by a 5-minute incubation on ice. After the incubation, pipetting was repeated, and the reaction was stopped by adding 4 mL ST buffer (with or without RNAse inhibitor). The suspension was filtered twice through pre-wetted 70 µm mesh filters into a 50 mL conical tube, and the filter was washed with 5 mL ST buffer. The filtered sample was centrifuged at 500 × g for 5 minutes, and the pellet containing dissociated nuclei was resuspended in 100–400 µL ST buffer. The suspension was then passed through a 40 µm mesh filter, and nuclei were counted using a Neubauer chamber (Bulldog Bio, Portsmouth, NH) after staining with 50 µg/mL Hoechst 33342 (Thermo Fisher, H3570).
A total of 0.9–1.5 × 10³ nuclei were loaded into ST buffer without RNAse inhibitor using a Chromium controller and Chromium reagents (10X Genomics). cDNA libraries were prepared following the manufacturer’s instructions, with an additional cycle of cDNA amplification to account for the lower RNA content in nuclei compared to whole cells. The final sequencing libraries were quantified using the 2200 TapeStation system with D1000 and D5000 reagents (Agilent). The libraries were pooled and sequenced to achieve a target depth of >20,000 reads per cell for gene expression libraries, using NovaSeq 6000 (Illumina, San Diego, CA) with a minimum read length of 2 × 100 bp.

value: Subcortex, Thalamus, Hippocampus

value: 5xFAD +/-

value: Female

value: ANGPT2 AAV

value: Replicate 2


title: Isogenic WT Control; Clone#32;1month; technical replicate 4


title: Test,Male,Rep2

description: Library name: Test_M_Rep2

value: Male


title: Control,Male,Rep2

description: Library name: Control_M_Rep2

value: Control AAV


title: Liver_Healthy :CT_02

value: Liver

value: Healthy


title: Isogenic WT Control; Clone#32;1month; technical replicate 3

value: iPSC-derived neurons

value: iPSC-derived NGN2-iNeurons


title: shoot apex_ZT102_replicate2

description:
Library name: apex_mock_t4_rep2
Column name in fpkm_values_shoot-apex_leaves_All_samples: apex_mock_t4_rep2

value: Zeitgeber Time (ZT) 102


title: Isogenic WT Control; Clone#32;1month; technical replicate 2


title: Test,Female,Rep1

description: Library name: Test_F_Rep1

value: Replicate 1


title: Liver_Healthy :CT_01


title: shoot apex_ZT102_replicate1

description:
Library name: apex_mock_t4_rep1
Column name in fpkm_values_shoot-apex_leaves_All_samples: apex_mock_t4_rep1


title: Liver_Cirrhotic :CH_13

value: Cirrhotic


title: Liver_Cirrhotic :CH_12


title: Test,Male,Rep1

description: Library name: Test_M_Rep1


title: Isogenic WT Control; Clone#32;1month; technical replicate 1


title: shoot apex_ZT98_replicate2

description:
Library name: apex_mock_t3_rep2
Column name in fpkm_values_shoot-apex_leaves_All_samples: apex_mock_t3_rep2

value: Zeitgeber Time (ZT) 98


title: Liver_Cirrhotic :CH_11


title: Control,Female,Rep1

description: Library name: Control_F_Rep1


title: shoot apex_ZT98_replicate1

description:
Library name: apex_mock_t3_rep1
Column name in fpkm_values_shoot-apex_leaves_All_samples: apex_mock_t3_rep1

value: shoot apex


title: shoot apex_ZT94_replicate2

description:
Library name: apex_mock_t2_rep2
Column name in fpkm_values_shoot-apex_leaves_All_samples: apex_mock_t2_rep2

value: Zeitgeber Time (ZT) 94


title: Liver_Cirrhotic :CH_10


title: scRNA-seq of Mus Muculus-random

city: KunMing

first: Xue

last: Lv

state: Yunnan

address: No.17 Longxin Road

institute: Kunming Institute of Zoology, CAS

data_processing:
Split-seq data were pre-processed by dropEst 0.8.6, 10x data were pre-processed by cellranger 6.1.1
Assembly: PRJNA1048078
Supplementary files format and content: tab-delimited text file including raw matrix of geneXcell
Supplementary files format and content: tab-delimited text file including gene names, cell barcodes and counts matrix.

source_name: limb

extract_protocol:
Each sample was homogenized using Dounce homogenizers (Wheaton) with a loose pestle for 10 rounds followed by 20 rounds with a tight pestle.  The resulting homogenate was processed to obtain a uniform nuclear solution.  Subsequently, the nuclear extract was filtered through a 40 μm cell strainer (Corning) into 1.5 ml tubes, which were then centrifuged to isolate the nuclei.
The purified nuclei were then diluted to 1×106 nuclei/ml after quantification using a hemocytometer.  The nuclei were evenly distributed among 48 wells of a 96-well plate, with each well containing 9,000 ~ 12,000 nuclei.  Subsequently, random hexamer and anchored poly(dT)15 barcoded reverse transcription (RT) primers were added to each of the 48 wells, respectively.  The cells were then combined and split twice.  Following this, the second- and third-round barcodes were attached.
16 libraries were generated and subjected to sequencing on the Illumina platform to produce 150 bp pair-end reads.

value: limb


title: Control,Male,Rep1

description: Library name: Control_M_Rep1

value: Subcortex, Thalamus, Hippocampus

value: 5xFAD +/-


title: G118E;Clone#15;1month; technical replicate 3


title: G118E;Clone#15;1month; technical replicate 4


title: Liver_Cirrhotic :CH_09


title: G118E;Clone#15;1month; technical replicate 2


title: shoot apex_ZT94_replicate1

description:
Library name: apex_mock_t2_rep1
Column name in fpkm_values_shoot-apex_leaves_All_samples: apex_mock_t2_rep1


title: scRNA-seq of Mus Muculus-dT


title: G118E;Clone#15;1month; technical replicate 1


title: Liver_Cirrhotic :CH_07


title: NEC2, snATAC-seq

city: Beijing

first: Yi

last: Xiong

address: 2 Yabao Rd

institute: Children's Hospital of Capital Institute of Pediatrics

description: 10x genomics

library_source: other

data_processing:
FASTQ sequence data were processed to obtain UMI counts in each cell using Cell Ranger (v7.2.0). The raw FASTQ data for each sample were processed using CellRanger for read filtering and alignment, barcode counting, identification of transposase cut sites, detection of accessible chromatin peaks, and cell calling, using the "cellranger-atac count" function (v2.1.0).
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for read counts

molecule: other

source_name: Intestinal tissues at postnatal day 9

extract_protocol:
The nuclei suspension was loaded onto the Chromium Next GEM Chip M (10X Genomics, Cat. No. 1000349), and single-cell gel beads were generated in the Gel Bead-in-emulsion (GEMs) (10X Genomics, Cat. No. 1000350) using the Chromium X system, following the manufacturer's recommendations. Single-cell libraries for snATAC-seq were generated using the GemCode Single-Cell Instruments and the Single Cell ATAC Library & Gel Bead Kit and ChIP Kit from 10X Genomics, following the manufacturer’s instructions.
All libraries were sequenced in paired-end mode (PE150) for 150 bp reads on a NovaSeq 6000 platform (Illumina)

treatment_protocol: Five-day-old C57BL/6 mice were separated from their mothers to prevent breastfeeding and NEC was induced by exposure to hypoxia (5% O2 for 10 minutes, 4 times a day), gavage feeding of formula milk (15 g Similac + 75 mL Esbilac, 50 μl/g, 4 times a day), and oral administration of lipopolysaccharide (LPS, Sigma#L2880) (4 mg/kg/day on postnatal days 6 and 8) from postnatal days 5 to 9

value: Intestinal tissues at postnatal day 9

value: NEC


title: Liver_Cirrhotic :CH_06


title: MDA-MB-231A tumor cells, ITGB1KD-3 [NS_06]

city: LOS ANGELES

first: NUOZI

last: SONG

state: CALIFORNIA

address: City of Hope 1500 E Duarte Rd INTL Stud

institute: city of hope

data_processing:
RNA-seq raw data were processed using Partek Flow
The aligned sequencing reads to human genome utilizing the Spliced Transcripts Alignment to a Reference (STAR 2.5.3a) tool
The aligned reads were subsequently quantified to the transcriptome, referencing hg38 for humans (Ensembl Transcripts release 109).
The data then underwent Median Ratio normalization. For differential gene expression analysis, we employed DESeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw rounts for each sample
Supplementary files format and content: tab-delimited text file includes P-value, FDR, Ratio, Log2 and Foldchange for each sample

source_name: tumor cells

extract_protocol:
Total RNA was subsequently extracted using a Qiagen RNA extraction kit and prepped for sequencing. 200ng of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols

value: tumor cells

value: breast cancer (TNBC) cell line


title: shoot apex_ZT90_replicate1

description:
Library name: apex_mock_t1_rep1
Column name in fpkm_values_shoot-apex_leaves_All_samples: apex_mock_t1_rep1

value: Zeitgeber Time (ZT) 90


title: MDA-MB-231A tumor cells, CtrlKD-3 [NS_05]


title: Control2, snATAC-seq

description: 10x genomics

value: Control


title: Liver_Cirrhotic :CH_05

value: Liver


title: NEC1, snRNA-seq

description: 10x genomics


title: Ogg1Tg 3, Gastroc, 20wks

city: New Brunswick

first: Sai Santosh Babu

last: Komakula

state: New Jersey

address: 61 Dudley Rd

department: Department of Nutritional Sciences

institute: Rutgers University

data_processing:
Quality trim and adaptor removal using "Trimmomatic"
reads were mapped to mouse genome - mm10
Genes assigned to reads using "Samtools"
Post mapping QC using RSeQC
Counts read using "HTSeq-count"
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing FPKM values for each sample

source_name: Gastrocnemius muscle

growth_protocol: Chow diet

extract_protocol:
Total RNA was isolatred using RNeasy mini kit (QIAGEN, USA)
Library construction was performed using the NuGen Ovation Universal RNA-Seq system according to manufacturer’s protocol

treatment_protocol: no treatment

value: Gastrocnemius muscle

value: male

tag: strain background

value: Chow diet


title: Ogg1Tg 2, Gastroc, 20wks


title: MDA-MB-231A tumor cells, ITGB1KD-2 [NS_04]


title: Liver_Cirrhotic :CH_04

value: Cirrhotic


title: Control1, snRNA-seq

description: 10x genomics


title: Liver_Cirrhotic :CH_03


title: shoot apex_ZT90_replicate2

description:
Library name: apex_mock_t1_rep2
Column name in fpkm_values_shoot-apex_leaves_All_samples: apex_mock_t1_rep2


title: MDA-MB-231A tumor cells, ITGB1KD-1 [NS_02]

value: CtrlKD


title: Ogg1Tg 1, Gastroc, 20wks


title: DiI positive population of nociceptors,D4 after challenge

city: Toulouse

first: Lilian

last: Basso

address: INSERM UMR1291 – CNRS UMR5051 - University Toulouse III CHU Purpan – BP 3028

country: France

institute: INFINITY INSERM U1291

data_processing:
scRNA sequencing count tables were generated for each dataset using CellRanger pipeline (v-6.1.1)
Assembly: GrCh38
Supplementary files format and content: Tab-separated values files and  matrix files

source_name: DRG

extract_protocol:
DRG were collected from 6- to 8-week old mice and enzymatically dissociated in HBSS with collagenase type I (2 mg/ml) and dispase (4 mg/ml) for 45 minutes at 37 °C
Libraries were generated according to the manufacturer’s protocol using the GemCode Single Cell Instrument and Single Cell 3′ Library & Gel Bead Kit v3 and B Chip Kit (10X Genomics).

value: DRG

value: Neurons+Glial

value: DNFB, chalenge


title: Liver_Cirrhotic :CH_02


title: MDA-MB-231A tumor cells, CtrlKD-2 [NS_03]


title: DiI positive population of nociceptors,D1 after challenge


title: MDA-MB-231A tumor cells, CtrlKD-1 [NS_01]


title: Control 3, Gastroc, 20wks


title: Control 2, Gastroc, 20wks


title: Liver_Cirrhotic :CH_01


title: Non-Responder 4, scRNAseq

city: Erlangen

first: Christian

last: Büttner

address: Schwabachanlage 10

department: Institut of Human Genetics

country: Germany

institute: University Hospital Erlangen

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, alignment and generation of gene count matrices were made using the 10x Genomics Cellranger v4.0.0.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: intestinal biopsies

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). The poly-A RNA of the single GEM wells was retrotranscripted to cDNA. Library Prep included Unique Molecular Identifiers and the 10x Cell Barcode in R1 and the transcriptome in R2.

value: Lamina propria mononuclear cells

value: intestinal biopsies

tag: phenotype

value: non-responder


title: MDA-MB-231A cells, ITGB1KD-3 [NS_C6]

source_name: cell line

value: cell line


title: DiI positive population of nociceptors,senzitized

value: DNFB, senzitization


title: DiI positive population of nociceptors,steady state

value: NO


title: Non-Responder 3, scRNAseq

description: 10x Genomics


title: Control 1, Gastroc, 20wks


title: MDA-MB-231A cells, ITGB1KD-1 [NS_C4]

value: breast cancer (TNBC) cell line


title: LAD2_Extracellular_Vesicle_R2

city: Bloomington

first: Heather

last: O'Hagan

state: IN

address: 1001 E 3RD ST

institute: Indiana University

description: Library name: Sample 2

data_processing:
Sequencing read quality control for all samples was assessed with FastQC (v0.11.5)
An index of the hg38 genome was created, and reads were aligned with STAR (v2.6.1a)
Raw read counts were obtained with Rsubread (v1.24.2)
Assembly: hg38
Supplementary files format and content: Each processed file contains one sample column with gene counts

source_name: Extracellular Vesicles

growth_protocol: LAD2 cells were maintained in SP34 media supplemented with SP34 nutrients and stem cell factor in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mico kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEB NextUltra DNA Library following the manufacturer's protocol.

treatment_protocol: LAD2 cell-derived extracellular vesicles were collected after 4 days of culture.

value: Extracellular Vesicles

value: Mast cell line


title: MDA-MB-231A cells, CtrlKD-2 [NS_C2]


title: Non-Responder 2, scRNAseq

description: 10x Genomics


title: LAD2_Extracellular_Vesicle_R1

description: Library name: Sample 1


title: MDA-MB-231A cells, ITGB1KD-2 [NS_C5]


title: PBS_rep3

city: Chicago

first: Francisco

last: Silva

state: Illinois

address: 420 E Superior street #9

department: Microbiology-Immunology

institute: Northwestern University

description:
Library name: Sample 51
Column name in raw_counts.txt: PBS_rep3
Correspondence to fastq: PBS_3

data_processing:
Assembly: Filtered reads were aligned to the human reference genome UCSC hg38
Raw sequencing reads were quality-checked and trimmed to remove adapters and low-quality bases. Reads were aligned to the human reference genome, and gene-level counts were generated. Differential gene expression analysis was performed using standard statistical methods in R with an adjusted p-value < 0.05 and |log2 fold-change| ≥ 1.
Supplementary files format and content: Tab-delimited text files containing gene-level raw counts for all samples (raw_counts.txt) and corresponding sample metadata (Column_data.txt), including sample identifiers, conditions, and biological replicates.

extract_protocol:
Total RNA was extracted from intestinal epithelial cells following 110 minutes of infection with Vibrio vulnificus strains or PBS control. Cells were lysed and RNA was isolated using a standard column-based RNA purification method according to the manufacturer’s instructions.
RNA-seq libraries were prepared from total RNA using a poly(A) selection protocol to enrich for mRNA, followed by fragmentation, cDNA synthesis, adapter ligation, and PCR amplification according to the manufacturer’s instructions.

value: Human Intestinal epithelial cells (IECs)

value: Wild type

value: Vibrio vulnificus intoxication

tag: group

value: PBS


title: Non-Responder 1, scRNAseq

description: 10x Genomics


title: WT->WT2 NTSN snRNAseq

city: Graz

first: Katharina

last: Artinger

address: Auenbruggerplatz 27

department: Division of Nephrology, Department of Internal Medicine

country: Austria

institute: Medical University of Graz

data_processing:
Sequencing datawere processedusing the Cell Ranger Single Cell software suite 7.0.1 (10x Genomics)
Assembly: mm10
Supplementary files format and content: barcodes, features, matrix files

source_name: kidney

extract_protocol:
Chromium Nuclei Isolation Kit (10xGenomics)
Library was performed according to the manufacter´s instructions (Chromium Single Cell 3´Reagent kit (v3.1 Chemistry)

value: kidney

value: WT->WT


title: KO->WT2 NTSN snRNAseq

value: ACKR1-/- -> WT


title: Responder 3, scRNAseq

description: 10x Genomics

value: responder


title: PBS_rep2

description:
Library name: Sample 50
Column name in raw_counts.txt: PBS_rep2
Correspondence to fastq: PBS_2


title: MDA-MB-231A cells, CtrlKD-3 [NS_C3]

value: CtrlKD


title: KO->WT1 NTSN snRNAseq


title: MDA-MB-231A cells, CtrlKD-1 [NS_C1]


title: WT->WT1 NTSN snRNAseq


title: PBS_rep1

description:
Library name: Sample 49
Column name in raw_counts.txt: PBS_rep1
Correspondence to fastq: PBS_1


title: 18-month-old brain (n = 3),  sgsh wild type, rep3

status: Public on Apr 14 2026

city: Melbourne

first: Jan

last: Kaslin

state: Victoria

address: 15 Innovation Walk

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

description: Library name: WTold3

data_processing:
SOAPnuke was used for adaptor removal and low-quality read filtration, and genome mapping was performed with HISAT2 for SNP analysis and novel transcript detection. Clean reads were mapped to the reference genome using Bowtie2, and gene expression levels were calculated with RSEM.
Assembly: GRCz11 INSDC Assembly GCA_000002035.6, May 2017
Supplementary files format and content: TSV or tab-separated text files containing raw counts for each sample

organism: Danio rerio

source_name: Brain

growth_protocol: 24 hpf embryos and 5 dpf larvae were raised in E3 medium at 28.5 °C. Juvenile and adult zebrafish were raised in system water under standard housing conditions

extract_protocol:
Prior to total RNA extraction: - 24 hpf embryos were manually dechorionated in E3 medium, then transferred to Eppendorf tubes on ice. - 5 dpf larvae were euthanised by tricaine overdose, then immediately decapitated in ice-cold 1x PBS. Heads were collected into an Eppendorf tube on ice. - Adult zebrafish were euthanised in an ice-water slurry, then exsanguinated by tail resection on ice. Following exsanguination, whole brains were dissected from the neurocranium, rinsed in fresh ice-cold PBS, then transferred to an Eppendorf tube on ice.  Extraction method: Total RNA from all samples were harvested in TRIzol (Sigma) per the manufacturer's protocol.
Libraries for 150 bp paired-end RNA-sequencing were prepared by BGI using the DNBSEQ method.

value: Brain

value: WT

tag: genetic modification

tag: developmental stage

value: 18 months


title: Responder 2, scRNAseq

description: 10x Genomics

value: Lamina propria mononuclear cells

value: intestinal biopsies


title: 18-month-old brain (n = 3),  sgsh wild type, rep2

description: Library name: WTold2


title: DiI negative population of nociceptors,steady state

value: DRG

value: Neurons+Glial

tag: treatment

value: NO


title: Responder 1, scRNAseq

description: 10x Genomics

tag: tissue


title: 18-month-old brain (n = 3),  sgshΔex5-6 homozygous, rep2

description: Library name: sgshold2


title: 3-month-old brain (n = 3),  sgsh wild type, rep2

description: Library name: WTyoung2

value: 3 months


title: 18-month-old brain (n = 3),  sgsh wild type, rep1

description: Library name: WTold1


title: 3-month-old brain (n = 3),  sgsh wild type, rep3

description: Library name: WTyoung3


title: 3-month-old brain (n = 3),  sgsh wild type, rep1

description: Library name: WTyoung1


title: small cell lung cancer tissue, treated with OSI906

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

institute: Sichuan University

description: Library name: OSI906

data_processing:
Single-cell RNA sequencing libraries were generated using the Chromium Single Cell 3′ Reagent Kits v3 (10x Genomics) according to the manufacturer’s instructions. Libraries were sequenced on the NovaSeq X Plus platform. To distinguish tumor cells from non-tumor cells, exogenous sequences, including sgRNA and Myc expression constructs, were added to the reference genome. Cleaned reads were then aligned to the mm10 mouse reference genome using Cell Ranger (v7.0.1).
Assembly: mm10
Supplementary files format and content: mtx files and tsv files

source_name: Mus small cell lung cancer tissue

extract_protocol:
Tumor tissues were dissected into 5 mm3 pieces and incubated in a digestion buffer containing 1.0 mg/ml collagenase I (Gibco, 17100–017) and 0.5 mg/ml collagenase IV (Gibco, 17104–019) in DMEM/F12 (Gibco, C11330500BT). The tissues were mechanically pipetted at 10-minute intervals and gently agitated at 37°C for 30 minutes. Subsequently, the resulting mixture was filtered through 100 µm cell strainers. Following red blood cell lysis with ammonium-chloride-potassium (ACK) lysis buffer, cells were collected for subsequent single-cell RNA-seq library preparation.
Single-cell RNA libraries were constructed using the Chromium Single Cell 3′ Reagent Kits v3 according to the manufacturer’s instructions (10x Genomics).

value: Mus small cell lung cancer tissue


title: 3-month-old brain (n = 3),  sgshΔex5-6 homozygous, rep2

description: Library name: sgshyoung2


title: 18-month-old brain (n = 3),  sgshΔex5-6 homozygous, rep3

description: Library name: sgshold3


title: 3-month-old brain (n = 3),  sgshΔex5-6 homozygous, rep3

description: Library name: sgshyoung3


title: small cell lung cancer tissue, treated with OSI906 and anti-PD1

description: Library name: OSI906_antiPD1


title: 3-month-old brain (n = 3),  sgshΔex5-6 homozygous, rep1

description: Library name: sgshyoung1


title: 18-month-old brain (n = 3),  sgshΔex5-6 homozygous, rep1

description: Library name: sgshold1


title: small cell lung cancer tissue, sgScr, treated with anti-PD1

description: Library name: antiPD1_sgScr


title: pachytene spermatocytes, Hsf5 knockdown, biol rep2

city: Wuhan

first: shen

last: jin

state: Hubei

address: No. 299, Bayi Road, Wuchang District, Wuhan City

institute: Wuhan university

description:
Library name: SAMPLES4
Hsf5_2

data_processing:
For analysis of differentially expressed genes , raw sequence reads were trimmed using Trim Galore (0.6.10, parameters:–paired–length 25--stringency 4--clip_R1 10 --clip_R2 10 ). Then, clean sequence reads were mapped to the UCSC mm39 genome  with default parameters using HISAT2(2.2.1) , mapped reads per gene were counted with FeatureCount (1.5.3), providing a GTF file, and differential expression analysis was performed by DESeq2(1.46.0).
Assembly: UCSC mm39
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

source_name: testis

extract_protocol:
The animal total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA). RNA concentration and purity was measured using NanoDrop 2000                                                                                (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: testis

value: meiotic cells

value: Hsf5 knockdown


title: pachytene spermatocytes, Hsf5 knockdown, biol rep1

description:
Library name: SAMPLES3
Hsf5_1


title: 24 hpf whole embryo pool (n = 50), sgsh wild type, rep2

description: Library name: WT24h2

source_name: Whole embryo

value: Whole embryo

value: 24 hpf


title: 24 hpf whole embryo pool (n = 50), sgshΔex5-6 homozygous, rep3

description: Library name: sgsh24h3


title: 24 hpf whole embryo pool (n = 50), sgsh wild type, rep1

description: Library name: WT24h1


title: pachytene spermatocytes, Wild type, biol rep2

description:
Library name: SAMPLES2
Control_2


title: pachytene spermatocytes, Wild type, biol rep1

description:
Library name: SAMPLES1
Control_1


title: 24 hpf whole embryo pool (n = 50), sgsh wild type, rep3

description: Library name: WT24h3


title: lung, PD-1-Deficient Mice, MAB infection, day 21, rep5

city: Chongqing

first: Xiaowen

last: Yu

address: No. 6, Panxi 7th Branch Road, Jiangbei District

department: Basic Research Laboratory of Traditional Chinese Medicine

institute: Chongqing Traditional Chinese Medicine Hospital

description:
Library name: P5
P5

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NCBI reference genome of WT C57BL/6 mice
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: CSV files include FPKM values for each Sample

source_name: lung

extract_protocol:
Total RNA was extracted and purified from mouse lung tissue, and 1 μg of the purified RNA was used to construct the sequencing library.
The synthesized double stranded cDNA fragments were then adapter-ligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system.

value: lung

value: PD-1 Deficiency C57 mouse

value: Mycobacterium abscessus


title: lung, PD-1-Deficient Mice, MAB infection, day 21, rep3

description:
Library name: P3
P3


title: lung, PD-1-Deficient Mice, MAB infection, day 21, rep4

description:
Library name: P4
P4


title: 24 hpf whole embryo pool (n = 50), sgshΔex5-6 homozygous, rep1

description: Library name: sgsh24h1


title: lung, PD-1-Deficient Mice, MAB infection, day 21, rep2

description:
Library name: P2
P2


title: Lemna minor, NodeTract region, replicate 2

city: Sutton Bonington

first: Alexander

middle: George

last: Ware

state: Leicestershire

address: Sutton Bonington Campus

country: United Kingdom

institute: University of Nottingham

description:
Library name: Lemna_NodeTract_2
RNA-seq of Lemna NodeTract region, biological replicate 2

data_processing:
Salmon v1.10.0
Reads were pseudo-aligned and quantified using Salmon v1.10.0 with --validateMappings against a gentrome index built from the species-specific reference transcriptome and genome as decoys.
TPM values were extracted from Salmon quant.sf output files and assembled into gene x sample matrices.
Genes were filtered to remove those where max organ-averaged TPM was not at least 2.0 in at least one organ.
Assembly: Lemna minor: Le_minor_7210-REF-CSHL-1.0 (lemna.org); Spirodela polyrhiza: Sp_polyrhiza_9509-REF-OXFORD-3.0 (lemna.org); Colocasia esculenta (cngdb.com)
Supplementary files format and content: CSV files containing TPM (Transcripts Per Million) values for each gene across all samples per species

organism: Lemna minor

source_name: NodeTract

extract_protocol:
Duckweed samples: Samples were recovered from RNAlater by sieving through 70uM cell strainers, blotted from underneath with tissue paper to remove excess RNAlater, and snap frozen. Samples were ground on liquid nitrogen in 1.5ml Eppendorf tubes with plastic pestles. RNA was extracted using a RNeasy UCP Micro Kit (Qiagen) as per manufacturer's instructions.
Taro leaf-derived tissue (Apical, Basal regions): Tissue was ground to fine powder using a mortar and pestle on liquid nitrogen. 3 replicate aliquots of approximately 100mg were taken, added to 450ul buffer RLT and snap frozen. RNA extraction was performed on a single aliquot using the RNeasy Mini Kit (Qiagen) as per manufacturer's instructions with an additional RPE wash step.
Taro sheath and petiole tissue: Tissue was ground to fine powder using a mortar and pestle on liquid nitrogen. 3 replicate aliquots of approximately 100mg were taken, added to 450ul buffer RLT and snap frozen. All three aliquots were extracted using the RNeasy Mini Kit (Qiagen), then pooled and cleaned up using the RNeasy PowerClean Pro Cleanup Kit as per manufacturer's instructions.
RNA integrity was assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 2100 (Agilent Technologies). Library preparation and sequencing were performed by Novogene. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was performed using DNA Polymerase I and RNase H. After adenylation of 3' ends, adaptors with hairpin loop structure were ligated. Library fragments of 370-420 bp were purified with AMPure XP system (Beckman Coulter). PCR was performed with Phusion High-Fidelity DNA polymerase. Clustering was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina). Libraries were sequenced on an Illumina NovaSeq platform generating 150 bp paired-end reads.

value: NodeTract


title: Lemna minor, NodeTract region, replicate 3

description:
Library name: Lemna_NodeTract_3
RNA-seq of Lemna NodeTract region, biological replicate 3


title: Lemna minor, NodeTract region, replicate 1

description:
Library name: Lemna_NodeTract_1
RNA-seq of Lemna NodeTract region, biological replicate 1


title: Lemna minor, NodeTract region, replicate 4

description:
Library name: Lemna_NodeTract_4
RNA-seq of Lemna NodeTract region, biological replicate 4


title: 24 hpf whole embryo pool (n = 50), sgshΔex5-6 homozygous, rep2

description: Library name: sgsh24h2


title: VisiumHD_C57BL_P25

city: Houston

first: Taishi

last: Komori

address: 7500 Cambridge St #1210

institute: The University of Texas Health School of Dentistry

description: Library name: VisiumHD

data_processing:
Spatial data was processed with Space Ranger v3 (10x Genomics Cloud analysis) using the Mouse (mm10) reference (2020-A) and the corresponding 10x Genomics Mouse probe set.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics

source_name: Molars

extract_protocol:
Mandibles were collected from C57BL/6J mice at P25. After removing the soft tissues, samples were fixed overnight with RNase-free 4% PFA . Samples were decalcified with RNase-free 0.5 M EDTA for 3 days. Decalcified samples were cryoprotected in 30% sucrose/PBS solutions and then in 30% sucrose/PBS: OCT (1:1) solutions, each for at least overnight at 4 °C. Samples were embedded in an OCT compound under a stereomicroscope and transferred on a sheet of dry ice to solidify the compound.
The library preparation followed the protocol (CG000685). The quality of the final libraries was examined using the Agilent High-Sensitivity DNA Kit (#5067-4626) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). The qualified libraries were sequenced using the paired-end sequencing on an Illumina NovaSeq X Plus (Illumina, Inc., USA)

value: Molars

value: Cells composing the periodontal tissues


title: small cell lung cancer tissue, sgIgfbp5, treated with anti-PD1

description: Library name: antiPD1_sgIGFBP5


title: Lemna minor, Basal region, replicate 4

description:
Library name: Lemna_Basal_4
RNA-seq of Lemna Basal region, biological replicate 4

source_name: Basal

value: Basal


title: lung, PD-1-Deficient Mice, MAB infection, day 21, rep1

description:
Library name: P1
P1


title: lung, WT mice, MAB infection, day 21, rep4

description:
Library name: W9
W9

value: WT C57 mouse


title: Lemna minor, Basal region, replicate 3

description:
Library name: Lemna_Basal_3
RNA-seq of Lemna Basal region, biological replicate 3


title: Lemna minor, Basal region, replicate 2

description:
Library name: Lemna_Basal_2
RNA-seq of Lemna Basal region, biological replicate 2


title: Lemna minor, LowerWall region, replicate 4

description:
Library name: Lemna_LowerWall_4
RNA-seq of Lemna LowerWall region, biological replicate 4

source_name: LowerWall

value: LowerWall


title: Lemna minor, Basal region, replicate 1

description:
Library name: Lemna_Basal_1
RNA-seq of Lemna Basal region, biological replicate 1


title: lung, WT mice, MAB infection, day 21, rep2

description:
Library name: W7
W7


title: Lemna minor, LowerWall region, replicate 2

description:
Library name: Lemna_LowerWall_2
RNA-seq of Lemna LowerWall region, biological replicate 2


title: lung, WT mice, PBS treatment, day 21, rep5

description:
Library name: W5
W5

value: PBS


title: Lemna minor, Apical region, replicate 4

description:
Library name: Lemna_Apical_4
RNA-seq of Lemna Apical region, biological replicate 4

source_name: Apical

value: Apical


title: lung, WT mice, MAB infection, day 21, rep1

description:
Library name: W6
W6


title: Lemna minor, Apical region, replicate 3

description:
Library name: Lemna_Apical_3
RNA-seq of Lemna Apical region, biological replicate 3


title: lung, WT mice, PBS treatment, day 21, rep4

description:
Library name: W4
W4


title: lung, WT mice, MAB infection, day 21, rep3

description:
Library name: W8
W8


title: Lemna minor, Apical region, replicate 2

description:
Library name: Lemna_Apical_2
RNA-seq of Lemna Apical region, biological replicate 2


title: lung, WT mice, MAB infection, day 21, rep5

description:
Library name: W10
W10


title: lung, WT mice, PBS treatment, day 21, rep2

description:
Library name: W2
W2


title: lung, WT mice, PBS treatment, day 21, rep3

description:
Library name: W3
W3


title: Lemna minor, Apical region, replicate 1

description:
Library name: Lemna_Apical_1
RNA-seq of Lemna Apical region, biological replicate 1


title: Human corneal epithelial cells cultured in defined special medium

city: Taipei

first: CHO-YI

last: CHEN

address: No.155, Sec.2, Linong St.

country: Taiwan

institute: National Yang Ming Chiao Tung University

description:
Library name: SP
Pooled RNA from three independent biological replicates of HCECs cultured in defined special medium. Column names in gene_counts.txt and TPM_matrix.txt: SP

data_processing:
Raw reads were assessed using FastQC (v0.11.9) and trimmed using fastp (v0.20.0).
Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 (v2.1.0) with GENCODE v43 annotation.
Gene-level expression was quantified using RSEM. Gene expression levels were normalized to transcripts per million (TPM).
Assembly: GRCh38
Supplementary files format and content: gene_counts.txt: Tab-delimited text file containing RSEM expected counts per gene (gene_symbol, ensembl_id, KSFM, SP) for 26,506 genes.
Supplementary files format and content: TPM_matrix.txt: Tab-delimited text file containing TPM-normalized expression values per gene (gene_symbol, ensembl_id, KSFM, SP) for 26,506 genes.

source_name: cornea

growth_protocol: Human corneal epithelial cells (HCECs, ATCC CRL-11515) were cultured at 37°C with 5% CO2. Cells were maintained either in keratinocyte serum-free medium (KSFM; Thermo Fisher) or a defined special medium consisting of DMEM/F12 supplemented with 1 mM CaCl2, 10% fetal bovine serum, 10 ng/mL EGF, and 1x antibiotic/antimycotic. Cells were cultured for 72 hours prior to RNA extraction.

extract_protocol:
Total RNA was extracted using the Qiagen RNA isolation kit (#74104) according to the manufacturer's protocol. RNA quality was assessed, and samples with RNA integrity number (RIN) >= 7.0 and OD260/280 ratios between 1.8-2.1 were used.
RNA sequencing libraries were prepared from poly(A)-selected RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina).

value: cornea

tag: cell line

value: ATCC CRL-11515

value: human corneal epithelial cell

value: Defined special medium (DMEM/F12, 1mM CaCl2, 10% FBS, 10ng/mL EGF, 1x antibiotic/antimycotic)


title: lung, WT mice, PBS treatment, day 21, rep1

description:
Library name: W1
W1


title: ES2_YY-15

city: Wenzhou

first: Yeying

last: He

address: Chashan

institute: Wenzhou Medical University

description:
Library name: sample2
with YY-15

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Human ovarian cancer cells ES2

growth_protocol: Cells were incubated at 37 ℃ in 5% CO2 and maintained in 5A medium with 10% FBS and 100 U/mL penicillin and streptomycin.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

treatment_protocol: SKOV3 and ES2 cells (3×10^5 cells per well, placed in 6-well plates) were treated with YY-15 for 48 hours. After the treatment, the cells were collected and total RNA was extracted from each group using TRIzol (TaKaRa Company, Japan). Finally, paired-end sequencing was performed on the Illumina HiSeq 4000 platform at LC-BIO Technology Company (Hangzhou, China).

value: Human ovarian cancer cells ES2

value: Epithelial cell

tag: cell type

value: WT

value: cell line

value: total RNA

value: paired-end


title: ES2_Control

description:
Library name: sample1
without any drugs

tag: batch


title: lung, PD-1-Deficient Mice, MAB infection, day 14, rep4

description:
Library name: p3-4
p3-4

data_processing:
CLC Genomics Workbench 11. 0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
mm10
Assembly: NCBI reference genome of WT C57BL/6 mice
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: CSV files include FPKM values for each Sample

value: lung

tag: genotype

value: PD-1 Deficiency C57 mouse

value: Mycobacterium abscessus

value: day 14


title: lung, PD-1-Deficient Mice, MAB infection, day 14, rep1

description:
Library name: p3-1
p3-1


title: lung, PD-1-Deficient Mice, MAB infection, day 14, rep2

description:
Library name: p3-2
p3-2


title: lung, PD-1-Deficient Mice, MAB infection, day 7, rep5

description:
Library name: p2-5
p2-5

value: day 7


title: lung, PD-1-Deficient Mice, MAB infection, day 14, rep5

description:
Library name: p3-5
p3-5


title: lung, PD-1-Deficient Mice, MAB infection, day 14, rep3

description:
Library name: p3-3
p3-3


title: Ileum

city: Los Angeles

first: Hitomi

last: Hosoya

address: 116 N Robertson Blvd

institute: Cedars-Sinai Medical Center

description:
Library name: Lib816
10x Genomics

data_processing:
Demultiplexing of bulk sequencing FASTQs was performed using internal pipelines. Barcode processing, gene counting, and aggregation were accomplished using Cell Ranger 6.1.2 and 7.0.1 (10x Genomics).
Assembly: hg38
Supplementary files format and content: Tab-delimited gzipped value files (*barcodes.tsv.gz, *features.tsv.gz), gzipped matrix files (*matrix.mtx.gz)

source_name: Ileum

extract_protocol:
Fresh peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using Ficoll-Paque density-gradient centrifugation and cryopreserved. At a later time, PBMCs were thawed. Gastrointestinal biopsies were dissociated into single cell suspensions using gentleMACS Tumor Dissociation Kit (Miltenyi Biotec). For both PBMC and GI samples, dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec). Viable cells were resuspended in 0.04% BSA in DPBS (no Ca2+/Mg2+).
Library construction was performed according to the manufacturer's instructions (Single Cell Next GEM 5' v2 protocol, 10x Genomics). Briefly, PBMCs were resuspended in the master mix and loaded with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contained an Illumina R1 primer sequence, 10x barcode, and unique molecular identifier (UMI). The pooled barcoded DNA was then cleaned up using Silane Dynabeads, amplified by PCR, and then the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, Illumina R2 primer sequences, paired-end constructs with P5 and P7 sequences, and a sample index were added.

value: Ileum


title: Human corneal epithelial cells cultured in KSFM

description:
Library name: KSFM
Pooled RNA from three independent biological replicates of HCECs cultured in KSFM. Column names in gene_counts.txt and TPM_matrix.txt: KSFM

value: Keratinocyte serum-free medium (KSFM)


title: Stomach

description:
Library name: Lib814
10x Genomics

source_name: Stomach

value: Stomach


title: lung, PD-1-Deficient Mice, MAB infection, day 7, rep1

description:
Library name: p2-1
p2-1


title: SKOV3_Control

description:
Library name: sample3
without any drugs

source_name: Human ovarian cancer cells SKOV3

value: Human ovarian cancer cells SKOV3


title: lung, PD-1-Deficient Mice, MAB infection, day 7, rep2

description:
Library name: p2-2
p2-2


title: lung, PD-1-Deficient Mice, MAB infection, day 7, rep4

description:
Library name: p2-4
p2-4


title: lung, PD-1-Deficient Mice, MAB infection, day 3, rep5

description:
Library name: p1-5
p1-5

value: day 3


title: SKOV3_YY-15

description:
Library name: sample4
with YY-15


title: fr34227609

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

description: Library name: fr34227609

data_processing:
Binary base call output was converted to fastq files using bclconvert
Fastq files were normalized to transcript per million by Hartwig Medical Foundation's isofox algorithm
the normalized count data were corrected for RIN value (continuous covariate) using the ‘removeBatchEffect’ (limma package, R)
Assembly: ch37
Supplementary files format and content: text file contains isofox-normalized count data for each sample
Supplementary files format and content: reference genome: ensh37 , version 75, log2 transformed

source_name: Pancreatic ductal adenocarcinoma

extract_protocol:
Tumor RNA was isolated from 40x10um slides according to the protocol of Qiagen AllPrep DNA/RNA/miRNA kit 50 (80224). 50-100 ng RNA was used as input
RNA was fragmented to a targeted fragment length of 300bp.
Library preparation was performed with KAPA RNA HyperPrep Kit with RiboErase (Human/Mouse/Rat) (Roche).

value: Pancreatic ductal adenocarcinoma


title: fr34227608

description: Library name: fr34227608


title: fr34227605

description: Library name: fr34227605


title: lung, PD-1-Deficient Mice, MAB infection, day 7, rep3

description:
Library name: p2-3
p2-3


title: Duodenum

description:
Library name: Lib812
10x Genomics

source_name: Duodenum

value: Duodenum


title: lung, PD-1-Deficient Mice, MAB infection, day 3, rep2

description:
Library name: p1-2
p1-2


title: lung, PD-1-Deficient Mice, MAB infection, day 3, rep3

description:
Library name: p1-3
p1-3


title: fr34227607

description: Library name: fr34227607


title: lung, PD-1-Deficient Mice, MAB infection, day 3, rep1

description:
Library name: p1-1
p1-1


title: lung, PD-1-Deficient Mice, MAB infection, day 3, rep4

description:
Library name: p1-4
p1-4


title: fr34227600

description: Library name: fr34227600


title: fr34227599

description: Library name: fr34227599


title: fr34227597

description: Library name: fr34227597


title: fr34227604

description: Library name: fr34227604


title: fr34227593

description: Library name: fr34227593


title: lung, WT mice, MAB infection, day 14, rep2

description:
Library name: w3-2
w3-2

value: WT C57 mouse


title: lung, WT mice, MAB infection, day 14, rep3

description:
Library name: w3-3
w3-3


title: fr34227601

description: Library name: fr34227601


title: fr34227592

description: Library name: fr34227592


title: lung, WT mice, MAB infection, day 14, rep4

description:
Library name: w3-4
w3-4


title: fr34227591

description: Library name: fr34227591


title: lung, WT mice, MAB infection, day 14, rep1

description:
Library name: w3-1
w3-1


title: fr34227590

description: Library name: fr34227590


title: lung, WT mice, MAB infection, day 7, rep3

description:
Library name: w2-3
w2-3


title: fr34227588

description: Library name: fr34227588


title: lung, WT mice, MAB infection, day 14, rep5

description:
Library name: w3-5
w3-5


title: lung, WT mice, MAB infection, day 7, rep1

description:
Library name: w2-1
w2-1


title: fr34227584

description: Library name: fr34227584


title: fr34227586

description: Library name: fr34227586


title: lung, WT mice, MAB infection, day 7, rep2

description:
Library name: w2-2
w2-2


title: fr34227596

description: Library name: fr34227596


title: lung, WT mice, MAB infection, day 3, rep4

description:
Library name: w1-4
w1-4


title: lung, WT mice, MAB infection, day 3, rep5

description:
Library name: w1-5
w1-5


title: lung, WT mice, MAB infection, day 7, rep5

description:
Library name: w2-5
w2-5


title: lung, WT mice, MAB infection, day 7, rep4

description:
Library name: w2-4
w2-4


title: fr34227583

description: Library name: fr34227583


title: fr34227585

description: Library name: fr34227585


title: fr34227582

description: Library name: fr34227582


title: lung, WT mice, MAB infection, day 3, rep1

description:
Library name: w1-1
w1-1


title: fr34227576

description: Library name: fr34227576


title: fr34227577

description: Library name: fr34227577


title: fr34227578

description: Library name: fr34227578


title: fr34227574

description: Library name: fr34227574


title: lung, WT mice, MAB infection, day 3, rep3

description:
Library name: w1-3
w1-3


title: fr34227573

description: Library name: fr34227573


title: lung, WT mice, MAB infection, day 3, rep2

description:
Library name: w1-2
w1-2


title: MDP-Monocytes from infected dura and brain, replicates 1-4 [VG1_MDP_Cellplex]

city: Freiburg

first: Vitka

last: Gres

address: Breisacherstraße 115b

department: Institute for Infection Prevention and Control

institute: University of Freiburg

description:
Library name: VG1_MDP_Cellplex
10X Genomics

data_processing:
Fastq files were aligned to prebuilt CellRanger reference refdata-gex-GRCm39-2024-A using the CellRanger version 9.0.1.
Downstream analyses were conducted in R version 4.5.1 programming environment using the Seurat package version 5.3.1. Cells were retained only if the mitochondrial gene content was below 20% and we restricted the number of detected genes per cell to be between 300 and 6,000. Furthermore, total UMI counts per cell were required to exceed 500.
Assembly: GRCm39
Supplementary files format and content: Processed data are provided as gzipped sparse gene-expression matrices in 10x Genomics Matrix Market format, separately for dura.mdp and dura.gmp samples. They include .barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz.

source_name: Dura mater and brain

extract_protocol:
Dura mater was peeled using forceps from calvaria and placed into a digestion solution (2.5 mg/ml collagenase IV in RPMI) and incubated for 20 min at 37°C shaking, after which the solution was filtered through 70 µm strainer (BD) and washed with FACS buffer.
Sorted samples were processed using the 10X Chromium Next GEM Single Cell 3’ Kit v3.1 (PN-1000269) and 3´ Feature Barcode Kit (PN-1000262). Single cell droplets were generated using Chromium Next GEM Chip G Single Cell Kit (PN-1000127) and Chromium Controller for 3’ gene expression and cell multiplexing libraries were generated according to the manufacturer’s specifications. Library quality was assessed using Agilent High Sensitivity DNA Kit (cat. no. 5067-4626). The single cell libraries were sequenced using Ilumina NovaSeq X Plus, with a minimum targeted sequencing depth of 20,000 reads per cell.

treatment_protocol: A total of 50 µl (5 x 107 CFU) suspension of GBS was injected into the retro-orbital venous plexus. Mice were sacrificed 2 days post infection.

value: Dura mater and brain

value: MDP-Monocytes

value: GBS


title: MDP-Monocytes from infected dura and brain, replicates 1-4 [VG1_MDP_GEX]

description:
Library name: VG1_MDP_GEX
10X Genomics


title: CD8+ T cell, IgG, untreat, rep3

city: Beijing

first: Zhidong

last: Gao

address: No.11 Xizhimen South Street

institute: Peking University People’s Hospital

description: Library name: IgG_UN_3

data_processing:
Raw sequencing reads were assessed using FastQC to evaluate base quality, duplication levels, and adapter content.
Adapters and low-quality bases were removed using Trim Galore (v0.6.10) with paired-end mode and other default parameters.
Trimmed reads were aligned to the mm10 reference genome using Bowtie2 with --very-sensitive preset and maximum insert size of 2000 bp.
Properly paired reads with MAPQ >= 30, excluding secondary, supplementary, and duplicate alignments were retained, mitochondrial reads (chrM) were removed, and duplicate reads were removed using SAMtools (v1.17) pipeline.
Final BAM files were coordinate-sorted and indexed using SAMtools.
bigWig coverage tracks were generated using deepTools bamCoverage (v3.5.3) with 10 bp bin size and RPGC normalization (effective genome size: 2,652,783,500). chrX were excluded from normalization, and reads were extended to the estimated fragment size.
bigWig files from biological replicates were merged using bigWigMerge (v2) and bedGraphToBigWig (v2.10) with default parameters.
Peaks were called uing MACS v2.1.0 with a p-value threshold of 0.05.
Peak annotation was performed with ChlPseeker, GenomicFeatures and org.Mm.eg.db packages. Peaks heatmaps and differential peak analysis were performed with the DiffBind package.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: CD8+ T cells

growth_protocol: HA-tagged Arid3b-overexpressing CD8+ T cells were cultured in complete RPMI-1640 medium (containing 10% fetal bovine serum, 1% penicillin/streptomycin, 1% non-essential amino acids, 20 mM HEPES, 1 mM sodium pyruvate, and 0.05 mM 2-mercaptoethanol) supplemented with 20 ng/mL IL-2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 8 minutes. After quenching and cell lysis, chromatin was sonicated using a Qsonica Q800R3 sonicator.
ChIP-seq libraries were prepared using the VAHTS Universal Pro DNA Library Prep Kit for Illumina complemented with VAHTS Multiplex Oligos Set 4/5 for Illumina from Vazyme. 10 ng of DNA was used as starting material for per sample. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using VAHTS DNA Clean Beads from Vazyme. Libraries were validated using the Agilent 4150 Tape Station System.

treatment_protocol: CD8+ T cells were treated with or without 100ng/mL OVA antigen peptide for 4 hours.

value: CD8+ T cells

value: IgG (Cell Signaling Technology, 2729)


title: fr34227580

description: Library name: fr34227580


title: GMP-Monocytes from infected dura and brain, replicates 1-4 [VG2_GMP_GEX]

description:
Library name: VG2_GMP_GEX
10X Genomics

value: GMP-Monocytes


title: fr34227570

description: Library name: fr34227570


title: CD8+ T cell, IgG, untreat, rep2

description: Library name: IgG_UN_2


title: fr34227572

description: Library name: fr34227572


title: GMP-Monocytes from infected dura and brain, replicates 1-4 [VG2_GMP_Cellplex]

description:
Library name: VG2_GMP_Cellplex
10X Genomics


title: CD8+ T cell, IgG, untreat, rep1

description: Library name: IgG_UN_1


title: fr34227569

description: Library name: fr34227569


title: CD8+ T cell, HA, untreat, rep3

description: Library name: HA_UN_3

value: HA (Cell Signaling Technology, 3724)


title: fr34227575

description: Library name: fr34227575


title: CD8+ T cell, HA, untreat, rep1

description: Library name: HA_UN_1


title: fr34227567

description: Library name: fr34227567


title: fr34227568

description: Library name: fr34227568


title: CD8+ T cell, HA, untreat, rep2

description: Library name: HA_UN_2


title: CD8+ T cell, IgG, OVA treatment, rep3

description: Library name: IgG_OVA_3

value: CD8+ T cells were treated with 100ng/mL OVA antigen peptide for 4 hours.


title: CD8+ T cell, IgG, OVA treatment, rep2

description: Library name: IgG_OVA_2


title: fr34227566

description: Library name: fr34227566


title: CD8+ T cell, IgG, OVA treatment, rep1

description: Library name: IgG_OVA_1


title: fr23588437

description: Library name: fr23588437


title: fr34227564

description: Library name: fr34227564


title: fr23588436

description: Library name: fr23588436


title: CD8+ T cell, HA, OVA treatment, rep2

description: Library name: HA_OVA_2


title: fr34227565

description: Library name: fr34227565


title: fr23588434

description: Library name: fr23588434


title: CD8+ T cell, HA, OVA treatment, rep1

description: Library name: HA_OVA_1


title: CD8+ T cell, HA, OVA treatment, rep3

description: Library name: HA_OVA_3


title: Spirodela polyrhiza, Stipe region, replicate 4

description:
Library name: Spirodela_Stipe_4
RNA-seq of Spirodela Stipe region, biological replicate 4

organism: Spirodela polyrhiza

source_name: Stipe

value: Stipe


title: Spirodela polyrhiza, Stipe region, replicate 2

description:
Library name: Spirodela_Stipe_2
RNA-seq of Spirodela Stipe region, biological replicate 2


title: fr23588433

description: Library name: fr23588433


title: fr23588429

description: Library name: fr23588429


title: fr23588428

description: Library name: fr23588428