title: C4-2 Cell line, IgG_rep2

last: Li

description:
Library name: Sample 19
IgG_rep2.bw

data_processing:
The raw reads with fastq format were aligned to the human reference genome hg19 from iGenome (https://support.illumina.com/sequencing/sequencing_software /igenome.html) using STAR aligner (v2.7.9a) (1). The count number of mapped reads were calculated by htseq-count (v0.11.2) software (2). After mapping, the software REDItoolDnaRna.py from REDItools (v1.3) (3) was used to detect the RNA editing with the C4-2 genome information using the parameters provided by the published protocol (4). For the whole genome sequencing, the raw fastq files were mapped to the human reference genome hg19 with BWA. Sorted bam file was used as the corresponding genome reference of C4-2 for delectation of RNA editing events.
For eCLIP-seq analysis, both STAR (v2.7.9a)[57] with default parameters and UCSC known genes were firstly employed to map the genome hg19, followed by peak calling using CLIP-seq peak caller Piranha with default parameters and bin size=20[64]. To define the RBP binding peaks in each sample, a P-value cutoff of 0.01 was set up. The homer (v4.8.3) annotatePeaks.pl script[65] was then applied to annotate the peaks from the eCLIP-seq data.
Assembly: hg19
Supplementary files format and content: abundance measurements for RNA-seq sample
Supplementary files format and content: bigwig for IgG sample

growth_protocol: For patient-derived organoid (PDO), PCa PDX MDA-PCa-174 was maintained in immune-deficient, severe combined immunodeficiency (SCID) male mice[60]. Organoids were established using the method described previously[61]. Briefly, tumors were dissected into small pieces and digested with 5 mg/ml collagenase type II in base medium (Advanced DMEM/F12 with 10 mM HEPES and 2 mM Glutamax) at 37°C for 1 hour with gentle shaking. A single tumor cell suspension was obtained after red blood cell lysis. Single cells were then seeded into a 6-well plate in growth factor-reduced Matrigel with complete human prostate organoid culture medium (B27, N-Acetylcysteine 1.25 mM, recombinant human EGF 5 ng/ml, recombinant human Noggin 100 ng/ml, recombinant human R-spondin-1 500 ng/ml, A83-01 500 nM, recombinant FGF-2 5 ng/ml, prostaglandin E2 1 μM, SB202190 10 μM, Nicotinamide 10 mM, DHT 1 nM, Y27632 10 μM in base medium) to form organoids. The human prostate cancer cell line C4-2 was a gift from L. Chung at Cedars-Sinai Medical Center and were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37 °C and 5% CO2 in a humidified atmosphere and were authenticated and routinely screened for Mycoplasma.

extract_protocol:
RNA-seq (n=2 for siCTRL, n=2 for siEZH2, n=2 for siADAR1 and n=2 for siADAR2) was isolated from patient-derived organoid were used to detect RNA editing. To analyze the impact of EZH2 inhibitor on RNA editing, DMSO, EPZ6438 and GSK126 treated C4-2 cells were used to do high depth RNA-seq. eCLIP-seq of igG were profomed to use as additional control for RNA binding target in C4-2. The RNA was isolated using RNeasy Plus Mini Kit (Qiagen) and subjected to admerahealth for library preparation and sequencing using the Novaseq platform.
RNA samples were harvested 72 hours post-second knockdown. RNA was isolated using the Qiagen miRNA isolation kit, and knockdown was confirmed by RT-qPCR before sending samples for sequencing. For high-throughput sequencing of RNA-seq and IgG RNA samples were shipped to Admera for library preparation and sequencing using the Novaseq platform.

treatment_protocol: Knockdown of EZH2, ADAR1, and ADAR2 were achieved by introducing 100 nM of siRNA per well in a 6-well plate, followed by two consecutive knockdowns.

value: C4-2 Cell line

value: prostate cancer

value: anti-IgG


title: NIH/3T3, WT, Serum starvation 24 h, Xap5

status: Public on Nov 15 2025

type: SRA

city: Wuhan

first: Weihua

last: Wang

address: No.8, Sanjiaohu Rd

country: China

institute: Jianghan University

description: Library name: SAMPLE 1

library_source: genomic

data_processing:
Raw reads were assessed for quality with FastQC (v0.11.9) and trimmed with fastp (v0.20.0; parameters: --length_required 15, --n_base_limit 6).
Clean reads were aligned to the Mus musculus reference genome (mm39) using BWA-MEM (v0.7.12; parameters: -k 32, -T 30, -M).
Peak calling was performed using MACS2 (v2.1.0) with a q-value threshold of 0.05 and the following parameters: -f AUTO --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all.
Peak annotation and association with the nearest genes were performed using the ChIPseeker R package.
Assembly: GRCm39
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

growth_protocol: The NIH/3TT3 was cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% calf serum (CS) and 1% penicillin-streptomycin.

extract_protocol:
Following a 24-hour starvation period, NIH/3T3 cells were harvested using 0.25% Trypsin-EDTA. Cell viability was assessed using a hemocytometer with Trypan Blue staining. Only cell suspensions with a viability of 90% or greater were carried forward for CUT&Tag library preparation. A total of 100,000 viable cells were used as input for each CUT&Tag reaction.
CUT&Tag libraries for sequencing were prepared according to the manufacturer’s protocol using Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme).

treatment_protocol: NIH/3T3 cells were seeded at a low density and grown for 24 hours in standard medium, after which the medium was switched to serum-free DMEM for an additional 24 hours of culture.

tag: cell line

tag: cell type

value: mouse embryonic fibroblast

tag: antibody

tag: treatment

value: Serum Starvation for 24 h


title: C4-2 Cell line, IgG_rep1

city: Boston

first: Yanqiang

state: MA

address: 300 Longwood Ave.

department: Cardiology Department

country: USA

institute: Boston Children's Hospital

description:
Library name: Sample 18
IgG_rep1.bw

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: C4-2 Cell line


title: Nnt-wt mouseID=MYW19

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

data_processing:
RNA preparation, library construction, sequencing on NovaSeq 6000 platform and raw data filtering was performed by Novogene (China).
Reads were aligned to the mouse genome (Mus_musculus.GRCm39.108) using STAR  (-runThreadN 2 --genomeDir --readFilesIn  --readFilesCommand gunzip -c --outFileNamePrefix  --outSAMtype BAM SortedByCoordinate --outSAMunmapped None --outSAMattrIHstart 0 --outFilterType BySJout --sjdbGTFfile /Mus_musculus.GRCm39.108.gtf --quantMode TranscriptomeSAM
Reads were quantified using HTSeq
Assembly: Mus_musculus.GRCm39.108
Supplementary files format and content: Raw counts using HTSeq

source_name: Gastrocnemius muscle

extract_protocol:
Mice were killed by cervical dislocation. Gastrocnemius was isolated, snap frozen in liquid nitrogen and stored at -80°C until further analysis. Total RNA was extracted by grinding frozen muscle tissue and dissolving approximately 15 mg in 1 ml Trizol. Further RNA isolation was performed according to manufacture's  instructions (Thermo Fisher). RNA concentration was measured using NanoDrop one spectrophotometer (Thermo Fisher). RNA integrity was measured using RNA Screentape on the 2200 Tapestation (Agilent).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP for directional library. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification(In-house kit: Novogene NGS Stranded RNA Library Prep Set (PT044)). The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms (NovaSeq 6000 platform using S4 flow cells), according to effective library concentration and data amount.

treatment_protocol: Gene expression profiles from gastrocnemius of 24-day-old Nnt-wt and Nnt-mut male mice were compared. Mice were weaned on 21 days and had ad libitum access to chow diet and water. Mice were killed in the first half light phase.

tag: tissue

value: Gastrocnemius muscle

tag: Sex

value: male

tag: strain

tag: genotype

value: Nnt-wt

tag: age

value: 24 days


title: CD8+ Unconventional T cells extracted from the CD8+ full dataset

city: Prague

first: Veronika

last: Niederlova

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Science

description:
Library name: cd8_l2_unconventional.rds
ScRNAseq data from multiple batches and multiple participants. For details please see the metadata of the .rds file or the associated Zenodo and Github repositories.

library_source: transcriptomic single cell

data_processing:
The count matrices were generated by 10x Cell Ranger 5.0.1 Software (count tool) and pre-processed using Seurat 4.3.1 package 114 on R 4.2.1. Any cell that was not marked by any expected combination of hashtags was removed. All cells with more than 10% of genes mapping to mitochondrial genes, those expressing less than 200 genes and those that were marked as doubles according to the V(D)J (more than 2 TCRα or more than 1 productive TCRβ sequence present) were excluded during initial object creation. Mitochondrial genes, ribosomal genes, genes encoding TCR variable segments (any gene symbol containing the TR[AB][VDJ] substring) and genes present in less than 3 cells were removed. Batches were integrated using STACAS. Detailed methods can be found in the publication, all scripts are available on Github: https://github.com/Lab-of-Adaptive-Immunity/dia.
Assembly: GRCh38
Supplementary files format and content: Processed data contain Seurat objects with all metadata.

molecule: polyA RNA

source_name: PBMC

extract_protocol:
Three to ten mL of peripheral blood were collected into EDTA-coated tubes, kept on ice, and transferred from Motol University Hospital to the Institute of Molecular Genetics within two hours. PBMCs were separated using Ficoll-Paque (GE Healthcare) and immediately frozen following a cryopreservation protocol (10x Genomics). PBMCs were then gently thawed by slow, sequential dilution in RPMI medium containing 10% FBS. Cells were labeled with TotalSeq-C hashtags and flow cytometry antibodies. In initial experiments, we sorted CD4+ and CD8+ T cells. In final experiments, non-naïve cells were enriched as follows: from each sample 1 000 naïve (CCR7+ CD45RA+) and 5 000 antigen-experienced cells were sorted into two tubes, one for CD4+ T cells and one for CD8+ T cells. For detailed methods please refer to the publication.
10x Chromium Single Cell 5’ Library & Gel Bead and Chromium Single Cell 5' Feature Barcode Library kits (10x Genomics, #PN-1000014, #PN-1000020, #PN-1000080, #PN-1000009, #PN-1000084)

value: PBMC

value: T cell

value: CD8+ T cell


title: C4-2 Cell line, GSK_rep3

description:
Library name: Sample 17
DMSO_EPZ_GSK.count.txt

value: GSK


title: Nnt-wt mouseID=MYW16


title: C4-2 Cell line, GSK_rep1

description:
Library name: Sample 15
DMSO_EPZ_GSK.count.txt


title: C4-2 Cell line siADAR1_rep1_24h

data_processing:
The raw reads with fastq format were aligned to the human reference genome hg19 from iGenome (https://support.illumina.com/sequencing/sequencing_software /igenome.html) using STAR aligner (v2.7.9a) (1). The count number of mapped reads were calculated by htseq-count (v0.11.2) software (2). After mapping, the software REDItoolDnaRna.py from REDItools (v1.3) (3) was used to detect the RNA editing with the C4-2 genome information using the parameters provided by the published protocol (4). For the whole genome sequencing, the raw fastq files were mapped to the human reference genome hg19 with BWA. Sorted bam file was used as the corresponding genome reference of C4-2 for delectation of RNA editing events.
For eCLIP-seq analysis, both STAR (v2.7.9a)[57] with default parameters and UCSC known genes were firstly employed to map the genome hg19, followed by peak calling using CLIP-seq peak caller Piranha with default parameters and bin size=20[64]. To define the RBP binding peaks in each sample, a P-value cutoff of 0.01 was set up. The homer (v4.8.3) annotatePeaks.pl script[65] was then applied to annotate the peaks from the eCLIP-seq data.
Assembly: hg19
Supplementary files format and content: abundance measurements for each sample
Supplementary files format and content: bigwig for each sample

growth_protocol: The human prostate cancer cell line C4-2 was a gift from L. Chung at Cedars-Sinai Medical Center and were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS). The cells were maintained at 37 °C and 5% CO2 in a humidified atmosphere and were authenticated and routinely screened for Mycoplasma.

extract_protocol:
Total RNA (n=4 for siCTRL, n=4 for siEZH2, n=6 for siADAR1 and n=5 for siADAR2) was isolated from C4-2 cells using RNeasy Plus Mini Kit (Qiagen) and subjected to BGI for library preparation and sequencing using the DNBseq platform. Meanwhile, the genomic DNA was extracted from C4-2 cells using Quick-DNA Kit (Zymo Research) and subjected to BGI for human true PCR-free 30x coverage WGS.
The eCLIP-seq experiment was performed in duplicates following the method described previously[63]. For each sample, a total of 50 million C4-2 cells were crosslinked, lysed and partially digested by RNase I (Thermo Fisher). The resulting lysates were incubated with the antibody of interested RBP and Protein A/G magnetic beads (Pierce) at 4 ºC overnight, followed by washing, end repair and 3′ adaptor ligation. The protein-RNA complexes were then eluted from the beads, resolved by denaturing gel electrophoresis and transferred to a nitrocellulose membrane. Subsequently, the region of interest was cut from membrane and subjected to RNA extraction, cDNA synthesis and library preparation. The cDNA library was further amplified using Q5 PCR Master Mix (NEB) and sent to BGI for sequencing using the DNBseq platform.
For high-throughput sequencing of RNA-seq, DNA-seq, input and CLIP RNA samples were shipped to BGI for library preparation and sequencing using the DNBseq platform.


title: Nnt-wt mouseID=MYW17


title: WT/miR26a-KO lung, before bleomycin administration-01-03

city: Hiroshima

first: Arisa

last: Hamada

state: Hiroshima

address: Kasumi, Minami-ku,

department: Department of Molecular and Internal Medicine

country: Japan

institute: Graduate School of Biomedical and Health Sciences, Hiroshima University

description: Library name: WT/miR26a-KO-d0-01-03

data_processing:
Read1 (barcode read) was extracted by using UMI-tools (ver.1.1.1) with the following command “umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC --read2-stdout ”.
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver. 0.6.7).
Reads were mapped to the GRCm39 reference using HISAT2 (ver. 2.2.1).
Gene count was obtaind by featureCounts(ver.2.0.1) and UMI duplication was ramoved by using UMI tools (ver.1.1.1).
Assembly: GRCm39
Supplementary files format and content: compressed tab separated files(.tsv.gz, .txt.gz)

source_name: lung

extract_protocol:
Total lung RNA of WT and KO mice  were homogenized using 1 mL TRIzol reagent (Life Technologies) and total RNA was extracted using the RNeasy Mini Kit (Qiagen). 180ng of total RNA was used for the construction of sequencing libraries.
Libraries were prepared by BRB-Seq(Alpern D, et al.) method. Individual samples were reverse transcribed using dT primer with unique cell barcodes. Then replicate were mixed and amplified by PCR. 10nt of UMI followedby 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.

value: lung

value: miR-26a KO, WT


title: Nnt-wt mouseID=MYW24


title: C4-2 Cell line, EPZ_rep3

description:
Library name: Sample 14
DMSO_EPZ_GSK.count.txt

value: EPZ


title: C4-2 Cell line, EPZ_rep2

description:
Library name: Sample 13
DMSO_EPZ_GSK.count.txt


title: Nnt-mut mouseID=MYK25

value: Nnt-mut


title: CD4+ Temra cells extracted from the CD4+ full dataset

description:
Library name: cd4_l3_temra.rds
ScRNAseq data from multiple batches and multiple participants. For details please see the metadata of the .rds file or the associated Zenodo and Github repositories.

value: CD4+ T cell


title: C4-2 Cell line, GSK_rep2

description:
Library name: Sample 16
DMSO_EPZ_GSK.count.txt

value: C4-2 Cell line

value: prostate cancer


title: Nnt-wt mouseID=MYW13


title: Nnt-wt mouseID=MYW23


title: Nnt-wt mouseID=MYW18


title: Nnt-wt mouseID=MYW15


title: Nnt-mut mouseID=MYK20


title: Nnt-mut mouseID=MYK24


title: C4-2 Cell line, DMSO_rep3

description:
Library name: Sample 11
DMSO_EPZ_GSK.count.txt

value: DMSO


title: Nnt-wt mouseID=MYW14


title: Nnt-mut mouseID=MYK18


title: patient-derived organoid , PDO_siADAR1_rep1

description:
Library name: Sample 5
PDO_174.count.txt

source_name: patient-derived organoid

value: patient-derived organoid

value: PCa PDX MDA-PCa-174


title: Nnt-mut mouseID=MYK21

value: Gastrocnemius muscle

value: male


title: C4-2 Cell line, DMSO_rep2

description:
Library name: Sample 10
DMSO_EPZ_GSK.count.txt


title: Nnt-mut mouseID=MYK22

value: 24 days


title: patient-derived organoid , PDO_siADAR2_rep1

description:
Library name: Sample 7
PDO_174.count.txt


title: patient-derived organoid , PDO_siADAR1_rep2

description:
Library name: Sample 6
PDO_174.count.txt


title: patient-derived organoid , PDO_siADAR2_rep2

description:
Library name: Sample 8
PDO_174.count.txt


title: Nnt-mut mouseID=MYK19


title: Nnt-mut mouseID=MYK15


title: C4-2 Cell line, EPZ_rep1

description:
Library name: Sample 12
DMSO_EPZ_GSK.count.txt


title: Nnt-mut mouseID=MYK17


title: patient-derived organoid , PDO_siEZH2_rep2

description:
Library name: Sample 4
PDO_174.count.txt


title: C4-2 Cell line, DMSO_rep1

description:
Library name: Sample 9
DMSO_EPZ_GSK.count.txt


title: Nnt-mut mouseID=MYK16


title: patient-derived organoid , PDO_siEZH2_rep1

description:
Library name: Sample 3
PDO_174.count.txt


title: patient-derived organoid , PDO_siCTRL_rep1

description:
Library name: Sample 1
PDO_174.count.txt

value: siCTRL


title: Nnt-mut mouseID=MYK14


title: Nnt-mut mouseID=MYK13


title: T6

city: Lanzhou City

first: Lan

middle: Lan

last: Yu

state: Anning District

address: Northwest Normal University, Shi Street, Anning District, Lanzhou City, Gansu Province, China

department: College of Life Sciences

institute: Northwest Normal University

description: Fusarium sp-S. vaninii co-culture,day6

data_processing:
Raw data (raw reads) were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads
Afterremoving adaptor and low quality sequences, the clean reads were assembled into expressed sequence tag clusters (contigs) and de novo assembled into transcript by using Trinity (vesion:2.4) in paired-end method.
The longest transcript was choose as a unigene based the similarity and length of a sequence for subsequent analysis.
Assembly: De novo RNA-seq
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

organism:
Fusarium sp.
Sanghuangporus vaninii

source_name: fungi

growth_protocol: Fungal–fungal  co-culture were Incubated in dark for 6 days at 28 ℃

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated NanoDrop 2000 spectrophotometer (Thermo Scientific,USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina according to the manufacturer’s instructions. The libraries were finally sequenced using the Illumina Novaseq 6000 platform. 150 bp paired-end reads were generated. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: fungi

value: WT

value: Fungal-fungal co-culture


title: T5

description: Fusarium sp-S. vaninii co-culture,day6


title: patient-derived organoid , PDO_siCTRL_rep2

description:
Library name: Sample 2
PDO_174.count.txt


title: MCF-7 tramadol 1 mg/ml

city: Taipei

first: Zih-Syuan

last: Wu

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 114201, Taiwan

country: Taiwan

institute: National defense medical center

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data. Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1). Expression analysis In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data. Differential expression analysis Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM for each sample

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen, 74104) following the manufacturer’s instructions.
For RNA-seq, 1 μg of total RNA was used for library preparation. Poly(A) mRNA isolation was performed using Oligo(dT) beads. mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using random primers. First-strand cDNA and second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends, and dA-tailing was added in one reaction, followed by T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified via PCR using the P5 and P7 primers, and the PCR products were validated. Libraries with different indices were then multiplexed and loaded on an Illumina HiSeq/Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end configuration according to the manufacturer’s instructions.

value: Breast cancer

value: tramadol 1 mg/ml


title: T4

description: Fusarium sp-S. vaninii co-culture,day6


title: MCF-7 tramadol 0 mg/ml

value: tramadol 0 mg/ml


title: MDA-MB-231 tramadol 0 mg/ml


title: Rat lung - healthy and induced PAH model at 1, 3, 5, and 8 weeks, pool A2, LMO

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
Library name: lung_LMO_A2
MULTIseq barcode sequences

data_processing:
CellRanger (10x Genomics, version 6.1.2) was used to process raw sequencing reads using the Ensembl104 rat transcriptome annotations with additional inclusion of Pecam.
an estimated 37554 cells with 21879 mean reads per cell, 2372 median UMI per cell, and 1118 median genes per cell (first pool) and 35546 cells with 22322 mean reads per cell, 3152 median UMI per cell, and 1370 median genes per cell (second pool)
MULTI-seq barcode sequence libraries were processed using the deMULTIplex R package to identify the samples barcode(s) associated with each cell barcode.
Assembly: rnor_6.0
Supplementary files format and content: Filtered feature-barcode matrices in HDF5 format
Supplementary files format and content: Cell metadata including cell type labels (cell_metadata.tsv) tab-separated text
Supplementary files format and content: Multiplexed sample information (feature_reference.csv) comma-separated text

organism: Rattus norvegicus

source_name: Dissociated lung

extract_protocol:
Animals were perfused with 20ml of 0.9% saline containing 25U/ml heparin (LEO Pharm Inc.) through  the right ventricle, to drain the blood from the lungs. Lung tissue was isolated, minced with scissors and placed in Hank’s Balanced Salt Solution (HBSS, Gibco) on ice. Enzymatic digestion was performed with 2500U Collagenase (Worthington), 30U Neutral Protease (Worthington), and 165U DNase I (Sigma Aldrich) in HBSS, samples were loaded into gentleMACS C tubes (Milltenyi Biotec), and placed on the OctoMACS dissociators (Milltenyi Biotec) using program 37C_LDK_m_1 for ~30min. Samples were immediately placed on ice, filtered through 70µm cell strainers (Falcon), and washed with phosphate buffered saline (PBS, Gibco) with 2mM EDTA (ThermoFischer Scientific) and 0.5% bovine serum albumin (BSA, Wisent) (PEB). Dissociated cell samples were spun at 400g for 5min at 4°C and washed again. Samples were incubated in 1x red blood cell lysis (eBioscience) for 3min, diluted with PEB, and filtered again through 70µm cell strainers (Milltenyi Biotec).
Individual biological samples were barcoded using the MULTI-seq protocol described by McGinnis et al. In brief, single cells were incubated with 1:1 molar ratio of anchor: unique barcode oligonucleotide sequence for 10 min at room temperature with gentle mixing. Followed by addition of the co-anchor to stabilize barcodes within membranes which was incubated for 5min on ice. Barcoded cells were washed in PBS, counted as above, and pooled at an equal ratio of cells per biological replicates. Two aliquots from the pooled library preparation were run on separate channels of the 10X chromium controller.

tag: library type

value: LMO

value: Dissociated lung


title: Rat lung - healthy and induced PAH model at 1, 3, 5, and 8 weeks, pool A2, GEX

description:
Library name: lung_GEX_A2
10X Genomics 3' RNA

value: mRNA


title: Rat lung - healthy and induced PAH model at 1, 3, 5, and 8 weeks, pool B1, LMO

description:
Library name: lung_LMO_B1
MULTIseq barcode sequences


title: Rat lung - healthy and induced PAH model at 1, 3, 5, and 8 weeks, pool A1, LMO

description:
Library name: lung_LMO_A1
MULTIseq barcode sequences


title: MDA-MB-231 tramadol 1 mg/ml


title: Rat lung - healthy and induced PAH model at 1, 3, 5, and 8 weeks, pool A1, GEX

description:
Library name: lung_GEX_A1
10X Genomics 3' RNA


title: Rat lung - healthy and induced PAH model at 1, 3, 5, and 8 weeks, pool B1, GEX

description:
Library name: lung_GEX_B1
10X Genomics 3' RNA


title: T2

description: Fusarium sp-S. vaninii co-culture,day6


title: Rat lung - healthy and induced PAH model at 1, 3, 5, and 8 weeks, pool B2, LMO

description:
Library name: lung_LMO_B2
MULTIseq barcode sequences


title: T1

description: Fusarium sp-S. vaninii co-culture,day6


title: Nb_cond_pH2_rep3_pitcher

city: Hickory Corners

first: Kadeem

last: Gilbert

state: MI

address: 3700 E Gull Lake Dr

department: Plant Biology

institute: Michigan State University

description:
Nb_salmon.gene.counts.txt
Nb_salmon.gene.TPM.txt
Nb_Trinity.fasta
Nb_Trinity_map.txt
annotatedCounts_N_bicalcarata.txt

data_processing:
Each RNAseq analysis was performed for each species separately. The raw read quality of each paired-end library was tested by FastQC v0.11.9 (Andrews, 2010).
Adapters and low-quality bases were removed with Trimmomatic (Bolger et al., 2014).
Transcriptome de novo assembly was performed using Trinity v2.9.1 (Grabherr et al., 2011) with default settings for each species to treat them all the same.
Reads counts were done with Salmon v1.5.0. Low counts (< 3 TPM) were filtered out and the most highly expressed isoform for each gene was kept. Transdecoder (Haas and Papanicolaou, 2017) was used to identify ORF coding region in all the assemblies.
Annotation was done with Trinotate v4.0.2 (Haas et al., 2013) and EnTAP v1.0.1 using Swissprot and PFAM protein database mainly. Salmon counts were filtered by taxonomy, only genes that were annotated for Viridiplantae taxa were considered.
Assembly: De novo transcriptome assembly without reference genome
Supplementary files format and content: tab-delimited text file includes all raw counts by sample for each species: _salmon.gene.counts.txt
Supplementary files format and content: tab-delimited text file including all normalized TPM gene expression by sample for each species: _salmon.gene.TPM.txt
Supplementary files format and content: fasta file of whole transcript sequence by species: _Trinity.fasta
Supplementary files format and content: tab-delimited text file with transcript to gene map by species: _Trinity_map.txt
Supplementary files format and content: tab-delimited text file with whole annotation of transcripts by species: annotatedCounts_Species.txt

organism: Nepenthes bicalcarata

source_name: Pitcher

growth_protocol:
We acquired seeds of G. arboreum (accession PI 615701), G. hirsutum (accession PI 529181), and B. vulgaris (accession Ames 3060) from the United States Department of Agriculture (USDA) Germplasm Resources Information Network (GRIN). The seeds were planted in Sunshine #4 Soil Mix (Professional growing mix, Sungro horticulture)  and grown in the Pennsylvania State University Department of Entomology headhouse greenhouse under ambient conditions
Because it was not feasible to grow Nepenthes from seed, we attained small adult plants (clonally propagated) of N. bicalcarata (accession BE-3031) and N. rafflesiana (accession BE-3722)  from Borneo Exotics ltd. Supplied by Carnivero (Austin, TX, USA). The Nepenthes were potted in a sphagnum medium and grown in a Conviron reach-in growth chamber with the following settings: 12-hour day-night cycle, daytime temp = 28°C, nighttime temp = 26°, relative humidity = 80%, fluorescent/ incandescent levels = 250 uMol. The Nepenthes pots were also treated with imidacloprid to clear a scale infestation before the start of the experiment. For Nepenthes, we exposed to the pH treatments, two tissues, leaf blade and pitcher leaves separately. In this paper we only used the transcriptome of the leaf lamina for our comparative transcriptomics analysis.
For the plants grown from seed, they were all planted in October 2020 and grown until all species had germinated, emerged, and produced the first two nodes of true leaves (4-6 weeks from being sown).

extract_protocol:
We conducted total RNA extractions using the Spectrum Plant Total RNA kit, according to manufacturer’s protocol with some modifications. First, the leaves were transferred into clean tubes and centrifuged at max speed for 30 seconds to remove remnant RNALater. For the mechanical lysis step, we used a single large steel bead (autoclaved and sterilized with RNAse Away) to homogenize the leaf sample in lysis buffer using a FastPrep machine set to 5.5 m/s for 20 s. Following homogenization, the sample was incubated in a heatblock at 56 C for 5 minutes, and the remaining steps proceeded as per the original protocol.
Our extracted RNA was sent to Novogene for library prep, quality control, and sequencing on an Illumina NovaSeq 6000 PE150 platform.

treatment_protocol: For the pH manipulation experiments, the leaf was sprayed with one of three pH treatments: pH 6.5, 4.0, and 2.0. These sprays were created by mixing distilled deionized water (ddH2O) with the appropriate volume of HCl to reach the target pH level. These pH solutions were stored in inert glass spray bottles to avoid leaching of material or change in pH due to CO2 diffusion. The leaf was sprayed until thoroughly wet (~15 sprays) and collected directly into 2.0 mL DNAse/RNAse-free tubes of RNALater after 5 minutes of exposure.

value: Pitcher

tag: accession

value: pH 2

tag: time (min)


title: Nb_cond_pH2_rep2_pitcher


title: Rat lung - healthy and induced PAH model at 1, 3, 5, and 8 weeks, pool B2, GEX

description:
Library name: lung_GEX_B2
10X Genomics 3' RNA


title: Nb_cond_pH2_rep1_pitcher


title: Nb_cond_pH4_rep3_pitcher

value: pH 4


title: 4MHFA14

city: Lexington

first: Nirmal

last: Verma

state: Kentcuky

address: 900 S Limestone

department: Pharmacology and Nutritional Sciences

institute: University of Kentucky

description: Library name: sample39

data_processing:
The libraries was sequenced in PE150 format on HiseqX10 platform
Supplementary files format and content: text file includes processes data file

source_name: frontal cortex brain

growth_protocol: mice were put on high fat diet for 2 month(WT) and 4 month (WT, Amylin-KO, and human amylin conditional transgenic mice, conditional human amylin expressing mice were injected with either vehicle or tamoxifen and organs brain were collected after 2 months.

extract_protocol:
RNA were isoated from frontal cortex region of the brain and RNA quality was checked on nanodrop and Agilent tapestation
Illumina Truseq Stranded mRNA was used to construct RNA library

treatment_protocol: mice transgenic for human amylin were injected with vehicle or tamoxifen

value: frontal cortex brain

value: brain

value: frontal cortex


title: Nb_cond_pH4_rep1_pitcher


title: 4MHFA13

description: Library name: sample37


title: Nb_cond_pH6_rep3_pitcher


title: Nb_cond_pH6_rep1_pitcher


title: Yeast, mut-NNS-BS, OD1, rep1

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

description: Library name: Rpo21_mut-NNS-BS_Rep1

data_processing:
Raw sequencing outputs were returned as FASTQ files. Hence, after conversion into FASTA format, files were processed using the paired-end (PE) version of the pyCRAC pipeline (Webb et al., 2014). This package demultiplexes barcoded reads and removes adapter sequences applying the previously developed Flexbar tool (Dodt et al., 2012). Having been filtered based on their length and nucleotide quality values (i.e., PHRED scores), remaining reads were aligned to the provided Saccharomyces_cerevisiae.R64-1-1.75 reference genome with the Novoalign tool (version 2.07). Filtered and aligned reads were gathered into BAM outputs and fed into the newly developed DBPeaks.py peak calling script (https://git.ecdf.ed.ac.uk/sgrannem/dbpeaks). Firstly, the countReadsBam function of the DBPeaks script employs the pyReadCounters tool from the pyCRAC package to generate GTF files with read counts and gene mapping locations. Next, the getPeaks function uses the pyCalculateFDRs script from the pyCRAC package to retrieve peaks enriched in each library relative to randomly distributed reads over the same genes. The resulting peak GTF files are then filtered by the filterPeaks function, to remove peaks comprising less reads than the mean coverage of all the intervals in the dataset. Although we used mean, median or mean with one standard deviation can be selected as thresholds. Peak widths were normalised to a minimum length of 10 nucleotides with the adjustPeakWidths function. Afterwards, the mergeGTFintervals applied BEDTools (Quinlan and Hall, 2010) to concatenate intervals or peaks that are present in all replicates. Subsequently, the numberPeaks function assigns a number to each filtered peak to prevent misidentification in downstream steps. The software then performs a pyReadCounters analysis on the BAM files using the new GTF file encompassing the numbered filtered peaks. We then gathered the hit tables outputted by pyReadCounters and combined them using the mergeHittables function. Finally, the runDESeq function automatically performs the statistical analysis to identify differential peaks using the DESeq2 pipeline (Love et al., 2014). By default, DESeq returns results in a TXT file, so we developed two additional functions to extract the calculated fold change and incorporate it into the original peak file. Finally, the getSignificantPeaks function generates a new GTF file containing solely the peaks that were called significant by the DESeq.
Assembly: Saccharomyces_cerevisiae.R64-1-1.75.fa
Supplementary files format and content: Bedgraph files include aligned single-collapsed reads
Supplementary files format and content: DESeq analysis results

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown to OD600 1 in 0.5 L-cultures of SC-Ura containing 1% (w/v) raffinose

extract_protocol:
Following optimised crosslinking (500 mJ UV 254 nm), UV-irradiated pellets were resuspended in a volume of lysis buffer (150 mM NaCl, 50 mM Tris pH 7.8, 0.1% (v/v) Nonidet P-40, 1U/mL of RQ1 RNase-free DNAse (Promega) and 1 EDTA-free protease inhibitor cocktail (Roche)/ 50 mL and 5 mM β-mercaptoethanol) corresponding to twice their mass. Lysates were then transferred to a fresh 50 mL tubes, where they were mixed with 2 volumes of 0.5 mm zirconia beads (Thistle Scientific), and vortexed at maximum speed for five 1-minute intervals alternated with 1-minute incubations on ice. An additional volume of lysis buffer was pipetted into each sample before partitioning the cell debris by centrifugation at 4ºC (4000 rpm, 15 minutes) and spinning down lighter impurities in an additional centrifugation step (10000 rpm, 20 minutes) at 4ºC. Immunoprecipitation of the labelled protein from the supernatant was achieved during a two-hour incubation of the sample with 75 µL of anti-FLAG® M2 magnetic beads (Sigma-Aldrich, M8823-5ML) which had been previously washed three times with 1 mL TN150 buffer. Immobilised beads underwent three 5-minute washes with TN1000 buffer (50 mM Tris pH 7.8, 1 M NaCl, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol) and three additional 5-minute washes in 2 mL TN150 buffer (150 mM NaCl, 50 mM Tris pH 7.8, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol). Afterwards, beads were resuspended in 550 µL of TN150 and incubated with 1 µL of a 1:100 dilution of RNace-It™ for exactly 5 minutes at 37 °C. To prevent overdigestion of co-immunoprecipitated transcripts and elute the bait proteins from the anti-FLAG beads, the solution was mixed with 0.4 g of guanidium hydrochloride (Gu-HCl) and the necessary volume of NaCl and imidazole (pH 8.0) to reach a final concentration of 300 mM and 10 mM respectively. After removing the beads, samples were pipetted onto 50 µL of Ni-NTA agarose resin (Qiagen) equilibrated with wash buffer I (6 M Gu-HCl, 10 mM imidazole, 300 mM NaCl, 50 mM Tris-HCl pH 7.8, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol) and incubated at 4 °C overnight while rotating at 12 rpm.
Upon Ni-NTA binding, beads were transferred to Pierce columns (Thermo Fisher Scientific) and washed twice with 500 µL of wash buffer I before undergoing three additional washes of 500 µL with NP-PNK buffer (10 mM MgCl2, 50 mM Tris-HCl pH 7.8, 0.1% (v/v) Nonidet P-40, 5 mM β-mercaptoethanol). Alkaline phosphatase treatment was performed by resuspending immunoprecipitated RNA-protein conjugates in 80 µL of NP-PNK buffer containing 4 units of FastAP thermosensitive alkaline phosphatase (Thermo Fisher Scientific) and 80 units of RNasin® ribonuclease inhibitor (Promega) and incubating the samples at 37 °C for 1 hour. Dephosphorylation was stopped upon addition of 500 µL of wash buffer. Having equilibrated the Ni-NTA agarose with three washes of 500 µL with NP-PNK, we performed adapter ligation by resuspending the beads 80 µL of reaction mix containing 0.6 µM of the applicable App-PE 3′ adapter (5’App-NAGATCGGAAGAGCACACGTCTG-ddC 3’), 30 units of T4 RNA ligase 2 truncated K227Q (New England Biolabs), 60 units RNasin® (Promega) and 10% (w/v) polyethylene glycol 8000 (PEG 8000). The reaction took place at 25 °C for six hours.  After washing once with 500 µL of wash buffer I and three times with 500 µL of NP-PNK buffer, we 5’end radiolabelled co-immunoprecipitated RNAs by incubating the Ni-NTA resin with 60 µL of NP-PNK buffer containing 30 µCi 32P-γATP (PerkinElmer) and 30 units of T4 polynucleotide kinase (New England Biolabs). After a 40-minute incubation of the reaction at 37ºC, ATP (Roche) was supplemented to a final concentration of 1 mM and the reaction continued for another 20 minutes. The reaction was stopped by washing three times with 500 µL of wash buffer I and three 500 µL washes of NP-PNK buffer followed before the addition of the 5′ linker ligation mix. The reaction took place in a volume of 80 µL of NP-PNK buffer supplemented with 1.25 µM of the fitting adapter, 40 units of T4 RNA ligase 1 (New England Biolabs), 80 units of RNasin® and 10 mM ATP (Roche).  5’ adapter ligation was left to proceed overnight at 16 °C for all bait proteins. The adapter sequences were 5’-ACACGACGCTCTTCCGATCTNNNTAAGCN-3’  and 5’-ACACGACGCTCTTCCGATCTNNNCGCTTAGCN-3’ for PIC2-GFP repeats 1 and 2 respectively; 5’-ACACGACGCTCTTCCGATCTNNNGTGAGCN-3’ and 5’-ACACGACGCTCTTCCGATCTNNNTAGTGCN-3’ for mut-Nab3-BS replicates 1 and 2 respectively;  and 5’-ACACGACGCTCTTCCGATCTNNNACTCAGCN-3’ and 5’-ACACGACGCTCTTCCGATCTNNNGTGACAN-3’ for mut-NNS-BS libraries 1 and 2 respectively. After pooling suitable libraries together, the samples and its corresponding traces were submitted to Novogene, where paired-end sequencing of 150 bp-reads was performed in a NovaSeq 6000 system (Illumina).

treatment_protocol: When SC-Ura cultures containing 1% (w/v) raffinose reached an OD600 of 1, cells were UV cross-linked (254 nm; 500 mJ/cm2) in the Vari-X-linker (UVO3) and rapidly filtered on 0.8 μm membranes (Merck) using a filtration device connected to a vacuum pump. Membranes were collected in 50 mL tubes, flash frozen by submersion into liquid nitrogen and stored at -80ºC until the day of the experiment.

value: mutant

value: mut-NNS-BS, RPO21-HTF

value: 500 mJ UV 254 nm


title: Yeast, mut-Nab3-BS, OD1, rep2

description: Library name: Rpo21_mut-Nab3-BS_Rep2

value: mut-Nab3-BS, RPO21-HTF


title: Yeast, mut-Nab3-BS, OD1, rep1

description: Library name: Rpo21_mut-Nab3-BS_Rep1


title: T3

description: Fusarium sp-S. vaninii co-culture,day6

value: fungi

value: WT

value: Fungal-fungal co-culture


title: Yeast, PIC2-GFP, OD1, rep2

description: Library name: Rpo21_PIC2-GFP_Rep2

value: parental

value: PIC2-GFP, RPO21-HTF


title: Nr_cond_pH2_rep2_pitcher

description:
Nr_salmon.gene.counts.txt
Nr_salmon.gene.TPM.txt
Nr_Trinity.fasta
Nr_Trinity_map.txt
annotatedCounts_N_rafflesiana.txt

organism: Nepenthes rafflesiana


title: Nb_cond_Control_rep3_pitcher

value: Dry control


title: Nr_cond_pH2_rep1_pitcher


title: Nb_cond_Control_rep2_pitcher


title: Yeast, PIC2-GFP, OD1, rep1

description: Library name: Rpo21_PIC2-GFP_Rep1


title: Nr_cond_pH4_rep3_pitcher


title: Nr_cond_pH4_rep1_pitcher


title: Nr_cond_pH4_rep2_pitcher


title: Nb_cond_pH4_rep2_pitcher


title: Nr_cond_pH6_rep2_pitcher


title: Nb_cond_pH2_rep3_lamina

source_name: Leaf blade

value: Leaf blade


title: Nb_cond_Control_rep1_pitcher

value: Pitcher


title: Nb_cond_pH6_rep2_pitcher


title: Nr_cond_Control_rep3_pitcher


title: Nr_cond_Control_rep2_pitcher


title: Nb_cond_pH2_rep2_lamina

value: pH 2


title: Nr_cond_pH6_rep1_pitcher


title: Nr_cond_Control_rep1_pitcher


title: Yeast, mut-NNS-BS, OD1, rep2

description: Library name: Rpo21_mut-NNS-BS_Rep2


title: Nr_cond_pH2_rep3_lamina


title: Nr_cond_pH2_rep1_lamina


title: Bv_cond_pH2_rep3

description:
Bv_salmon.gene.counts.txt
Bv_salmon.gene.TPM.txt
Bv_Trinity.fasta
Bv_Trinity_map.txt
annotatedCounts_Beta_vulgaris.txt

organism: Beta vulgaris

value: Beta vulgaris L. subsp. vulgaris

value: Ames 3060

tag: grin plant_name

value: IDBBNR 4825


title: Nb_cond_pH4_rep3_lamina

value: pH 4


title: Nr_cond_pH2_rep3_pitcher


title: Nb_cond_pH2_rep1_lamina


title: Nb_cond_pH6_rep3_lamina


title: Nb_cond_pH4_rep2_lamina


title: Bv_cond_pH4_rep3


title: Bv_cond_pH2_rep2


title: Nr_cond_pH2_rep2_lamina


title: Nr_cond_pH4_rep1_lamina


title: Bv_cond_pH4_rep2


title: Nb_cond_pH4_rep1_lamina


title: Nr_cond_pH6_rep3_lamina


title: Nr_cond_pH6_rep3_pitcher


title: 4MHFW14

description: Library name: sample24

value: frontal cortex brain

value: brain

value: frontal cortex


title: Bv_cond_pH4_rep1


title: Nr_cond_pH4_rep2_lamina


title: Nr_cond_pH6_rep2_lamina


title: Nb_cond_Control_rep3_lamina


title: Nr_cond_pH4_rep3_lamina


title: Bv_cond_pH2_rep1


title: 4MHFW13

description: Library name: sample21


title: Nr_cond_pH6_rep1_lamina


title: Nb_cond_pH6_rep2_lamina


title: Bv_cond_pH6_rep2


title: Bv_cond_pH6_rep3


title: Nb_cond_Control_rep2_lamina


title: Nr_cond_Control_rep3_lamina


title: Bv_cond_pH6_rep1


title: Bv_cond_Control_rep2


title: E2_ATAC_AP07

first: Marcos

last: Simoes-Costa

state: Massachusetts

address: 300 Longwood Ave

department: Pathology

description: Library name: E2_ATAC_AP07

data_processing:
Trimming of Nextera adapter sequences was performed using cutadapt (version 3.4) using the following parameters: “-a CTGTCTCTTATACACATCT -A AGATGTGTATAAGAGACAG --minimum-length=25”. Trimmed reads were aligned to the galGal6 chicken reference genome using bowtie2 (version 2.4.4) with the following arguments: “--local --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000”.
Assembly: galGal6
Supplementary files format and content: bigwigs

organism: Gallus gallus

source_name: embryonic

growth_protocol: Gastrula stage chicken embryos were obtained from fertilized eggs and dissected in Ringers solution

extract_protocol:
N.A.
After enzymatic tissue dissociation cells were processed using the OMNI-ATAC-Seq protocol (Corces et al., 2017)
Bam alignment files were indexed using samtools (version 1.10), followed by marking of duplicate reads using Picard’s (version 2.26.2) MarkDuplicates function. Duplicate reads were then removed using samtools view with the following arguments: “-F 1804 -f 2”. Peaks were called with macs2 (version 2.2.7.1) using the parameters: “-f BAMPE -g 1e9 -q 0.05 --call-summits”

treatment_protocol: HH5 chicken embryos were hand dissected into equally distributed antero-posterior sections. Position matching sections from 5 embryos were pooled  for ATAC-seq library preparation.

value: embryonic

tag: developmental stage

tag: axis

value: antero-posterior

tag: section


title: Nr_cond_Control_rep2_lamina


title: Nr_cond_Control_rep1_lamina


title: Bv_cond_Control_rep3


title: Nb_cond_pH6_rep1_lamina


title: CK6

description: S. vaninii-S. vaninii  co-culture,day6

organism: Sanghuangporus vaninii

value: fungi

value: WT


title: E2_ATAC_AP05

description: Library name: E2_ATAC_AP05


title: CK5

description: S. vaninii-S. vaninii  co-culture,day6

value: Fungal-fungal co-culture


title: E2_ATAC_AP04

description: Library name: E2_ATAC_AP04


title: E2_ATAC_AP03

description: Library name: E2_ATAC_AP03


title: CK4

description: S. vaninii-S. vaninii  co-culture,day6


title: OE19_Rosiglitazone_1

city: Notre Dame

first: Ian

last: Mersich

state: Indiana

address: 54417 Leahy Dr, Notre Dame, IN 46556

department: Chemistry and Biochemistry

institute: University of Notre Dame

description:
Library name: Sample 7
column name in DESeq2_normalized_counts_all.txt: OE19_Rosiglitazone_1

data_processing:
Raw FASTQ files were quality-checked using FastQC
Reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2 with default parameters
Gene-level read counts were generated using featureCounts
Downstream normalization and differential expression analyses were performed in R using DESeq2.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file includes DESeq2 normalized counts

growth_protocol: OE19 esophageal adenocarcinoma cells were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were maintained at 37°C in a humidified incubator with 5% CO₂ and were routinely passaged at 70–80% confluence to maintain exponential growth.

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini Kit following the manufacturer’s instructions, including on-column DNase digestion to remove genomic DNA contamination. RNA quantity and integrity were assessed by fluorometric quantification and Agilent Bioanalyzer analysis prior to library preparation.
RNA-seq libraries were prepared by the University of Notre Dame Genomics Core using standard poly(A) mRNA-seq workflows. Libraries were constructed according to Illumina protocols and sequenced on the Illumina NextSeq 2000 platform using paired-end 50 bp (PE50) reads, targeting approximately 30 million reads per sample.

treatment_protocol: Cells were plated and allowed to recover overnight before treatment. OE19 cells were treated with halcinonide, methylprednisolone, or rosiglitazone for the indicated duration under standard culture conditions. Untreated cells cultured under identical conditions served as controls. After treatment, cells were washed with PBS and immediately processed for RNA extraction.

value: esophageal cancer cell line

value: 1 µM rosiglitazone

tag: time

value: 24 hours


title: OE19_Rosiglitazone_2

description:
Library name: Sample 8
column name in DESeq2_normalized_counts_all.txt: OE19_Rosiglitazone_2

tag: cell line


title: CK2

description: S. vaninii-S. vaninii  co-culture,day6

tag: cell type


title: E2_ATAC_AP02

description: Library name: E2_ATAC_AP02


title: E2_ATAC_AP01

description: Library name: E2_ATAC_AP01


title: Nb_cond_Control_rep1_lamina

value: Leaf blade

value: Dry control


title: OE19_Halcinonide_2

description:
Library name: Sample 4
column name in DESeq2_normalized_counts_all.txt: OE19_Halcinonide_2

value: 1 µM halcinonide


title: OE19_Halcinonide_1

description:
Library name: Sample 3
column name in DESeq2_normalized_counts_all.txt: OE19_Halcinonide_1


title: Ga_cond_pH2_rep3

description:
Ga_salmon.gene.counts.txt
Ga_salmon.gene.TPM.txt
Ga_Trinity.fasta
Ga_Trinity_map.txt
annotatedCounts_G_arboreum.txt

organism: Gossypium arboreum

value: Gossypium arboreum L.

value: pH 2


title: OE19_Methylprednisolone_1

description:
Library name: Sample 5
column name in DESeq2_normalized_counts_all.txt: OE19_Methylprednisolone_1

value: 1 µM methylprednisolone


title: OE19_Methylprednisolone_2

description:
Library name: Sample 6
column name in DESeq2_normalized_counts_all.txt: OE19_Methylprednisolone_2


title: Bv_cond_Control_rep1

value: Beta vulgaris L. subsp. vulgaris

value: Ames 3060

value: IDBBNR 4825


title: CK3

description: S. vaninii-S. vaninii  co-culture,day6


title: MiaPaca-3

city: Suita

first: Naoko

last: Sekiguchi

department: Gastroenterological surgery

institute: The university of Osaka

description: Library name: GA48632

data_processing:
Sequencing was performed on DNBSEQ-G400 platform in 100+100-base paired-end mode.
The DNBSEQ-G400 control software operated base calling analysis software and delivered raw sequencing data.
Reads were filtered allowing only those with an average base quality of 5 or higher. The processed reads were then mapped to the human reference genome (GRCh38.p13, release 38) using STAR (version 2.7.10a). The output tab-delimited text files list all detected circRNAs, including genomic coordinates, the number of reads spanning the back-splice junction (BSJ), the host gene from which the circRNAs originate, and the circRNA ID assigned by CIRCexplorer2 (v2.4.0).
Assembly: hg19
Supplementary files format and content: tab-delimited text files for each sample

source_name: Tumor tissue of pancreatic cancer

extract_protocol:
Total RNA was extracted from cells with a miRNeasy Mini kit (Qiagen) following the manufacturer’s instruction.
Ribosomal RNA was depleted using Ribo-Zero Plus rRNA Depletion Kit (Illumina).
The linear RNA parts were digested with RNaseR.
According to the manufacturer's instructions, library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) without the poly-A selection step. Libraries were converted to libraries for DNBSEQ using MGIEasy Universal Library Conversion Kit (App-A).

value: Tumor tissue of pancreatic cancer

value: pancreatic cancer cell line


title: E2_ATAC_AP06

description: Library name: E2_ATAC_AP06

value: embryonic

value: antero-posterior


title: CK1

description: S. vaninii-S. vaninii co-culture ,day6

value: fungi

value: WT

value: Fungal-fungal co-culture


title: GR3-3

description: Library name: GA48635

value: gemcitabine-resistant pancreatic cancer cell line


title: GR3-2

description: Library name: GA48634


title: GR3-1

description: Library name: GA48633


title: Ga_cond_pH2_rep2

value: Leaf blade


title: MiaPaca-2

description: Library name: GA48631


title: OE19_Control_2

description:
Library name: Sample2
column name in DESeq2_normalized_counts_all.txt: OE19_Control_2

value: esophageal cancer cell line

value: control (0.1% DMSO)

value: 24 hours


title: Ga_cond_pH2_rep1

value: Gossypium arboreum L.

value: pH 2


title: KMM1_Input ChIPSeq

city: Shimotsuke

first: Sae

last: Matsuoka

state: Tochigi

department: Center for Molecular Medicine

institute: Jichi  Medical  University

data_processing:
Basecalls performed using bcl2Fastq version 2.20
ChIP-seq reads were aligned to the hg38 genome assembly using bwa version 0.7.12
Spike-in protocols and normalization were used. For comparative analysis, the number of test tags are adjusted by a factor that would result in the same number of usable spike-in Drosophila tags for each sample within a normalization group. The normalization is implemented through random deletion of test sample tags (down-sampling). The normalization factor shows the adjustment relative to standard normalized tag numbers (where the usable tags for each sample within a normalization group would be adjusted to the same number).
The two main peak callers used at Active Motif are MACS(v2.1.0) and SICER(v1.1) .MACS is suitable to identify the binding sites of transcription factors that bind to discrete sites (often containing a consensus DNA sequence) as well as many active histone marks and methyl-C enriched regions, while SICER is used to study proteins that bind to extended regions in the genome (such as repressive histone marks or RNA polymerase II).
Assembly: hg38
Supplementary files format and content: bigWig,narrow Peak(except for Input sample)

source_name: Hematopoietic cells

growth_protocol: We cultured KMM1 cells in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol:
Whole cell lysates were clarified from sonicated nuclei and isolated with anti-FOXM1 antibody.
The 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.

treatment_protocol: We fixed KMM1 cells  in 1% formaldehyde at room temperature  for 10 min and isolated  chromatin fractions using enzymatic shearing

value: Hematopoietic cells

value: Multiple Myeloma_KMM1

tag: chip antibody


title: MiaPaca-1

description: Library name: GA48630


title: KMM1_FOXM1 ChIPSeq


title: Ga_cond_pH6_rep3

tag: treatment


title: Ga_cond_pH4_rep1

tag: tissue

value: pH 4


title: BMVECs 24 hours DEVD mIL-36β (100 ng/ml) N3

city: Dublin 2

first: Jeffrey

last: O'Callaghan

state: Dublin

address: Smurfit Institute

country: Ireland

institute: Trinity College, Dublin

description:
Library name: E24
E24

data_processing:
Raw data was processed through fastp software to generate clean data.
Paired end clean reads were aligned to the reference genome using Hisat2 v2.05
The mapped reads of each sample were assembled via StringTie v1.3.3b56 in a reference-based approach
To count the reads numbers mapped to each gene featureCounts v1.50-p3 was used, which then allowed the FPKM to be calculated
Differential expression analysis was performed with DESeq2 v1.38.3 in R. ene Set Enrichment Analysis (GSEA) was carried out using version 4.3.3 of the GSEA software (Broad Institute, https://www.gsea-msigdb.org/gsea/index.jsp)
Assembly: GRCm38
Supplementary files format and content: gene_fkpm.csv: This file contains gene-level expression estimates (FPKM values) from RNA-seq for all samples used in the study. Each row corresponds to a single gene (identified by Ensembl gene ID and annotation), and each column corresponds to a sample. Columns A_0, B_0, D_0: biological replicates at 0 hours. Columns A_24, D_24, E_24: biological replicates at 24 hours. gene_name: official gene symbol. gene_chr, gene_start, gene_end, gene_strand: genomic location (based on reference genome). gene_length: transcript length used for FPKM calculation. gene_biotype: gene classification (e.g., protein_coding, lncRNA). gene_description: functional annotation from Ensembl/MGI.
Supplementary files format and content: heatmap.xls: This file contains gene-level expression values used to generate heatmaps in the manuscript. Each row corresponds to a gene, and each column corresponds to a sample. Columns A_0, B_0, D_0: biological replicates at 0 hours. Columns A_24, D_24, E_24: biological replicates at 24 hours.
Supplementary files format and content: IL36Bvscontrol.up_GOenrich.xls: This file contains results from Gene Ontology (GO) enrichment analysis performed on the set of significantly upregulated genes. Each row corresponds to a GO term enriched in the gene set. Category: GO ontology category (BP = Biological Process, CC = Cellular Component, MF = Molecular Function). GOID: GO accession identifier. Description: GO term name. GeneRatio: proportion of input genes annotated with the term. BgRatio: proportion of background genes annotated with the term. pvalue: raw enrichment p-value. padj: adjusted p-value (multiple testing correction). geneID: Ensembl IDs of genes associated with the GO term. geneName: corresponding gene symbols. Count: number of input genes associated with the term.
Supplementary files format and content: IL36Bvscontrol_deg_all.xls: This file contains differential expression analysis results for all detected genes, comparing 24 h samples vs. 0 h controls. Each row corresponds to a gene (Ensembl ID + annotation). Columns A_0, B_0, D_0: biological replicates at 0 hours. Columns A_24, D_24, E_24: biological replicates at 24 hours. IL36B / control: group labels for comparison. log2FoldChange: differential expression estimate (log2-transformed fold change, 24 h vs. 0 h). pvalue: raw significance from statistical test. padj: adjusted p-value (multiple testing correction). gene_name, gene_chr, gene_start, gene_end, gene_strand, gene_length, gene_biotype, gene_description, tf_family: gene annotation information. _count columns (e.g., A_24_count, A_0_count): raw read counts per sample. _fpkm columns (e.g., A_24_fpkm, A_0_fpkm): normalized expression values (FPKM) per sample.

source_name: Brain

growth_protocol: C57BL/6J mice were sacrificed and the brain was removed. Under sterile conditions the olfactory bulb, cerebellum and meninges were discarded. The remaining brain sections were homogenized and centrifuged at 600 g for 5 minutes at 4°C in working buffer (10 mM HEPES, 0.5% (w/v) bovine serum albumin (BSA), 100 U/ml penicillin, 100 μg/ml streptomycin in Hank’s balanced salt solution (HBSS)). The resulting pellet was resuspended in 22% (w/v) BSA and centrifuged at 1,000 g for 20 minutes. The myelin plug was recovered, resuspended in fresh 22% (w/v) BSA and centrifuged again to increase vessel yield. The supernatant was discarded, pellet resuspended in complete digestion media (1 mg/ml collagenase/dispase, 20 μg/ml DNase I, 0.147 µg/ml TLCK, 100 U/ml penicillin, 100 μg/ml streptomycin in HBSS) and incubated at 37°C for 1 hour and 15 minutes, with frequent shaking. Following digestion, the cell suspension was centrifuged at 600 g for 5 minutes, the supernatant removed, and pellet washed once by resuspending in PBS and centrifuging as before. The vessel fragments were resuspended in EGM-MV2 media (PromoCell) with all supplements along with puromycin (5 µg/ml) and seeded on to plates that had been coated with collagen IV (100 µg/ml) and fibronectin (50 µg/ml) (both Sigma- Aldrich). After 24 hours of incubation, the media was replaced for a further 24 hours. On day 3 post seeding, the puromycin-containing media was removed and replaced with EGM-MV2 growth media without puromycin for 5 days until the cells became confluent.

extract_protocol:
RNA was harvested using E.Z.N.A® total RNA kit I (Omega Bio-tek).
Libraries were prepped using TrueSeq Stranded mRNA (Illumina) with input of 0.1 to 1 µg total RNA and sequenced using a NextSeq 500 output kit v2.5 (Illumina) with the Illumina NextSeq 500 platform

treatment_protocol: BMVECs were treated with processed DEVDmIL-36β (100 ng/ml) for 24 hours or left untreated as controls.

value: Brain

value: Microvascular endothelial cells

value: DEVD mIL-36β (100 ng/ml)


title: Yeast, KO, OD1, rep2

description: Library name: Nab3_KO_Rep2

data_processing:
Raw sequencing outputs were returned as FASTQ files. Hence, after conversion into FASTA format, files were processed using the paired-end (PE) version of the pyCRAC pipeline (Webb et al., 2014). This package demultiplexes barcoded reads and removes adapter sequences applying the previously developed Flexbar tool (Dodt et al., 2012). Having been filtered based on their length and nucleotide quality values (i.e., PHRED scores), remaining reads were aligned to the provided Saccharomyces_cerevisiae.R64-1-1.75 reference genome with the Novoalign tool (version 2.07). Filtered and aligned reads were gathered into BAM outputs and fed into the newly developed DBPeaks.py peak calling script (https://git.ecdf.ed.ac.uk/sgrannem/dbpeaks). Firstly, the countReadsBam function of the DBPeaks script employs the pyReadCounters tool from the pyCRAC package to generate GTF files with read counts and gene mapping locations. Next, the getPeaks function uses the pyCalculateFDRs script from the pyCRAC package to retrieve peaks enriched in each library relative to randomly distributed reads over the same genes. The resulting peak GTF files are then filtered by the filterPeaks function, to remove peaks comprising less reads than the mean coverage of all the intervals in the dataset. Although we used mean, median or mean with one standard deviation can be selected as thresholds. Peak widths were normalised to a minimum length of 10 nucleotides with the adjustPeakWidths function. Afterwards, the mergeGTFintervals applied BEDTools (Quinlan and Hall, 2010) to concatenate intervals or peaks that are present in all replicates. Subsequently, the numberPeaks function assigns a number to each filtered peak to prevent misidentification in downstream steps. The software then performs a pyReadCounters analysis on the BAM files using the new GTF file encompassing the numbered filtered peaks. We then gathered the hit tables outputted by pyReadCounters and combined them using the mergeHittables function. Finally, the runDESeq function automatically performs the statistical analysis to identify differential peaks using the DESeq2 pipeline (Love et al., 2014). By default, DESeq returns results in a TXT file, so we developed two additional functions to extract the calculated fold change and incorporate it into the original peak file. Finally, the getSignificantPeaks function generates a new GTF file containing solely the peaks that were called significant by the DESeq.
Assembly: Saccharomyces_cerevisiae.R64-1-1.75.fa
Supplementary files format and content: Bedgraph files include aligned single-collapsed reads
Supplementary files format and content: GTF files contain peaks (called and filtered with DBPeaks.py) and an adjusted p-value resulting from the statistical comparison of their coverage in the parental referrence and the mutant strain.

extract_protocol:
Following optimised crosslinking (500 mJ UV 254 nm), UV-irradiated pellets were resuspended in a volume of lysis buffer (150 mM NaCl, 50 mM Tris pH 7.8, 0.1% (v/v) Nonidet P-40, 1 EDTA-free protease inhibitor cocktail (Roche) per 50 mL and 5 mM β-mercaptoethanol) corresponding to twice their mass. Lysates were then transferred to a fresh 50 mL tubes, where they were mixed with 2 volumes of 0.5 mm zirconia beads (Thistle Scientific), and vortexed at maximum speed for five 1-minute intervals alternated with 1-minute incubations on ice. An additional volume of lysis buffer was pipetted into each sample before partitioning the cell debris by centrifugation at 4ºC (4000 rpm, 15 minutes) and spinning down lighter impurities in an additional centrifugation step (10000 rpm, 20 minutes) at 4ºC. Immunoprecipitation of the labelled protein from the supernatant was achieved during a two-hour incubation of the sample with 75 µL of anti-FLAG® M2 magnetic beads (Sigma-Aldrich, M8823-5ML) which had been previously washed three times with 1 mL TN150 buffer. Immobilised beads underwent three 5-minute washes with TN1000 buffer (50 mM Tris pH 7.8, 1 M NaCl, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol) and three additional 5-minute washes in 2 mL TN150 buffer (150 mM NaCl, 50 mM Tris pH 7.8, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol). Afterwards, beads were resuspended in 550 µL of TN150 and incubated with 1 µL of a 1:100 dilution of RNace-It™ for exactly 5 minutes at 37 °C. To prevent overdigestion of co-immunoprecipitated transcripts and elute the bait proteins from the anti-FLAG beads, the solution was mixed with 0.4 g of guanidium hydrochloride (Gu-HCl) and the necessary volume of NaCl and imidazole (pH 8.0) to reach a final concentration of 300 mM and 10 mM respectively. After removing the beads, samples were pipetted onto 50 µL of Ni-NTA agarose resin (Qiagen) equilibrated with wash buffer I (6 M Gu-HCl, 10 mM imidazole, 300 mM NaCl, 50 mM Tris-HCl pH 7.8, 0.1% (v/v) Nonidet P-40 and 5 mM β-mercaptoethanol) and incubated at 4 °C overnight while rotating at 12 rpm.
Upon Ni-NTA binding, beads were transferred to Pierce columns (Thermo Fisher Scientific) and washed twice with 500 µL of wash buffer I before undergoing three additional washes of 500 µL with NP-PNK buffer (10 mM MgCl2, 50 mM Tris-HCl pH 7.8, 0.1% (v/v) Nonidet P-40, 5 mM β-mercaptoethanol). Alkaline phosphatase treatment was performed by resuspending immunoprecipitated RNA-protein conjugates in 80 µL of NP-PNK buffer containing 4 units of FastAP thermosensitive alkaline phosphatase (Thermo Fisher Scientific) and 80 units of RNasin® ribonuclease inhibitor (Promega) and incubating the samples at 37 °C for 1 hour in the case of Nab3 and Nrd1, or 15 minutes for Sen1. Dephosphorylation was stopped upon addition of 500 µL of wash buffer. Having equilibrated the Ni-NTA agarose with three washes of 500 µL with NP-PNK, we performed adapter ligation by resuspending the beads 80 µL of reaction mix containing 0.6 µM of the applicable App-PE 3′ adapter (5’App-NAGATCGGAAGAGCACACGTCTG-ddC 3’), 30 units of T4 RNA ligase 2 truncated K227Q (New England Biolabs), 60 units RNasin® (Promega) and 10% (w/v) polyethylene glycol 8000 (PEG 8000). The reaction took place at 25 °C for six hours.  After washing once with 500 µL of wash buffer I and three times with 500 µL of NP-PNK buffer, we 5’end radiolabelled co-immunoprecipitated RNAs by incubating the Ni-NTA resin with 60 µL of NP-PNK buffer containing 30 µCi 32P-γATP (PerkinElmer) and 30 units of T4 polynucleotide kinase (New England Biolabs). After a 40-minute incubation of the reaction at 37ºC, ATP (Roche) was supplemented to a final concentration of 1 mM and the reaction continued for another 20 minutes. The reaction was stopped by washing three times with 500 µL of wash buffer I and three 500 µL washes of NP-PNK buffer followed before the addition of the 5′ linker ligation mix. The reaction took place in a volume of 80 µL of NP-PNK buffer supplemented with 1.25 µM of the fitting adapter, 40 units of T4 RNA ligase 1 (New England Biolabs), 80 units of RNasin® and 10 mM ATP (Roche).  5’ adapter ligation was left to proceed overnight at 16 °C for all bait proteins. The adapter sequences were 5’-ACACGACGCTCTTCCGATCTNNNCGCTTAGCN-3’ and 5’-ACACGACGCTCTTCCGATCTNNNGACTTAGCN-3’ or 5’-ACACGACGCTCTTCCGATCTNNNTAAGCN-3’ for PIC2-GFP repeats 1 and 2 respectively; 5’-ACACGACGCTCTTCCGATCTNNNCACTAGCN-3’ and 5’-ACACGACGCTCTTCCGATCTNNNACTCAGCN-3’ for mut-Nab3-BS replicates 1 and 2 respectively;  and 5’-ACACGACGCTCTTCCGATCTNNNGTGACAN-3’ for both mut-NNS-BS libraries. After pooling suitable libraries together, the samples and its corresponding traces were submitted to Novogene, where paired-end sequencing of 150 bp-reads was performed in a NovaSeq 6000 system (Illumina).

value: mutant

value: KO, NAB3-HTF

value: 500 mJ UV 254 nm


title: BMVECs 24 hours DEVD mIL-36β (100 ng/ml) N2

description:
Library name: D24
D24

value: WT


title: Ga_cond_pH6_rep2


title: OE19_Control_1

description:
Library name: Sample 1
column name in DESeq2_normalized_counts_all.txt: OE19_Control_1


title: Yeast, pTEF1-PIC2, OD1, rep2

description: Library name: Nab3_pTEF1-PIC2_Rep2

value: pTEF1-PIC2, NAB3-HTF


title: Ga_cond_pH4_rep2

value: Leaf blade


title: BMVECs Untreated N3

description:
Library name: D0
D0

value: Untreated


title: Yeast, WT, OD1, rep2

description: Library name: Nab3_WT_Rep2

value: parental

value: PIC2-GFP, NAB3-HTF


title: Yeast, KO, OD1, rep1

description: Library name: Nab3_KO_Rep1


title: Ga_cond_pH6_rep1

value: Gossypium arboreum L.


title: Ga_cond_pH4_rep3


title: Ga_cond_Control_rep3

value: Dry control


title: BMVECs Untreated N2

description:
Library name: B0
B0


title: Ga_cond_Control_rep2


title: Yeast, WT, OD1, rep1

description: Library name: Nab3_WT_Rep1


title: BMVECs Untreated N1

description:
Library name: A0
A0


title: Yeast, pTEF1-PIC2, OD1, rep1

description: Library name: Nab3_pTEF1-PIC2_Rep1


title: Ga_cond_Control_rep1


title: Exp09 TCR T cells

status: Public on Nov 14 2025

city: Rochester

first: Abhinav

last: Jain

address: 200 1st ST SW

institute: Mayo Clinic

description: Library name: Exp09_TCR

data_processing:
The FASTQ files reads were assessed using FastQC v0.11.9. Following quality assessment, the raw reads were aligned to the GRCh38 human genome using Cell Ranger multi v7.1.0 (10x Genomics). The cellranger multi pipeline was employed to quantify libraries of antibody-derived tags (ADT) and identify hashtagged samples from pooled CITE-seq libraries. Seurat v4.2.1 was used for downstream analysis following data preprocessing. Quality control was conducted to exclude low-quality cells based on the following thresholds: cells with fewer than 200 or more than 4000 genes, UMIs > 10% mapping to mitochondrial-encoded transcript, or more than 20,000 ADT UMIs. DoubletFinder was applied to identify and remove cell doublets.
We have identified CD4+ and CD8+ T cells based on their CD4 and CD8 gene and protein expression and processed them separately. For RNA normalization, individual samples were processed using SCTransform PMID:31870423, regressing out mitochondrial gene expression, while ADT counts were normalized using centralized log-ratio (CLR) transformation.
Further samples across experiments were integrated using diagonalized Canonical Correlation Analysis (CCA) to identify mutual nearest neighbors that act as anchors employing the FindTransferAnchors and IntegrateData functions PMID:31178118.
The Integrated RNA and ADT matrices were scaled and PCA were calculated. A weighted nearest-neighbor (WNN) graph was subsequently constructed using the FindMultiModalNeighbors function to integrate the modalities effectively PMID:34062119. The WNN graph is utilized to generate the UMAP embeddings, facilitating the visualization for both the modalities. Clustering was performed based on WNN using a smart local moving algorithm, revealing populations enriched in gE-stimulated versus control cultures.
Assembly: GRCh38
Supplementary files format and content: CellRanger Output Files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: scTCR-Seq

source_name: Blood

extract_protocol:
Forty-two hours after peptide stimulation, cultures were pre-purified with EasySep Human T Cell Isolation Kit (using 20% of the recommended reagents, Stemcell Technologies, # 17951). T cells were stained with hashtag TotalSeq-B antibodies and subjected to FACS. Live, single CD3+ CD8+ or CD3+ CD4+ cells that were CD69hi and/or CD137+ were collected. After FACS, cells were counted and pooled into one sample across T cell subsets and donors at similar cell numbers, if possible. The pooled sample was stained with diluted TotalSeq-B cell surface marker antibodies (BioLegend) in PBS containing 2% FBS for 30 minutes at 4C. Cells were washed twice with PBS containing 2% FBS, and cell viability was determined with Trypan Blue which was consistently >90%.
Cells were subjected to high-throughput single cell capture via the Chromium controller (10x genomics), Chromium Next GEM Single Cell 3' Kit v3.1 (Single Index, 10x genomics, #PN-1000121) and gel beads (10x genomics, #1000376). About 20,000 cells per pooled samples were targeted for cell capture. 3’ gene expression as well as antibody-derived tags (ADT) for TotalSeq-B antibodies including hashtag antibodies and cell surface marker (3' Feature Barcode Library Kit, 10x genomics, #PN-1000079) collective known as CITE-seq, were generated from each captured sample.

treatment_protocol: Lymphoprep was used to purify PBMCs of vaccine recipients by density centrifugation according to the manufacturer’s instructions. Cells were used fresh in all experiments and cultured in RPMI 1640 medium supplemented with 5% filtered human AB serum (Sigma Aldrich, #H4522), 100 U/mL penicillin, and 100 U/mL streptomycin (Sigma Aldrich, #P0781) in an incubator with 5% CO2 and atmospheric O2. We employed activation-induced marker (AIM) assays to collect VZV gE-responsive T cells. Briefly, PBMCs were seeded at 20x10^6 per 12-well and stimulated with 1 ug/ml of a VZV glycoprotein E (gE) peptide pool diluted in 0.2% DMSO (15-mer peptides with 11 amino acids overlap, total of 153 peptides; # PM-VZV-gE, JPT Peptide Technologies). Ultra-LEAF anti-CD28 stimulation antibody was added at 1 ug/ml (clone 28.2, BioLegend, #302943) as well anti-CD40 blocking antibody at 1 ug/ml (clone HB14, Miltenyi, #130-094-133). Parallel control PBMC cultures of the same individuals, received 0.2% DMSO instead of the VZV gE peptide mix. PBMCs were spun in plates at 300×g for 3 min before culturing for 42 hours to allow activation of antigen-specific T cells before further sample processing.

value: Blood

value: T cell

value: Activation through VZV gE peptide stimulation, or DMSO background stimulation

value: DMSO_V_Y_IMAG001M_Exp09 (29y) DMSO_V_Y_IMAG047F_Exp09 (26y) DMSO_V_Y_IMAG049M_Exp09 (25y) gE_V_Y_IMAG001M_Exp09 (29y) gE_V_Y_IMAG047F_Exp09 (26y) gE_V_Y_IMAG049M_Exp09 (25y)

tag: t cell_subset

value: VZV gE-responsive CD4 and CD8 T cells, DMSO-reactive CD4 and CD8 T cells


title: Exp06 TCR T cells

description: Library name: Exp06_TCR


title: Endometrial mesenchymal stromal/stem cells, dECM, rep3

city: Saint Petersburg

first: Roman

middle: E.

last: Ushakov

address: Tikhoretsky av., 4

country: Russia

institute: Institute of Cytology of the Russian Academy of Sciences

description: Library name: Sample 6

data_processing:
Sequence reads were trimmed using cutadapt v. 3.1 (parameters --trim-n -n 5 -m 14)
Reads were aligned to reference genome (GRCh38) using bowtie v. 1.0.1 (parameter -n 0 (without mismatches))
Reads were counted using featureCounts
Assembly: GRCh38
Supplementary files format and content: .xlsx file includes raw counts for each Sample

source_name: mesenchymal stromal/stem cells

growth_protocol: Mesenchymal stromal/stem cells derived from desquamated endometrium of menstrual blood were maintained in DMEM/F12 supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 1% GlutaMax in humidified incubator at +37 C and 5% CO2.

extract_protocol:
RNA was isolated using miRNeasy kit (Qiagen) (combined phenol guanidine thyocyanate solution and silica membrane-based purification).
Libraries for miRNA-seq were prepared using NEBNext® Multiplex Small RNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s instructions.

treatment_protocol: Prior to RNA extraction cells were cultured for 72 hours on plastic (polystyrene) dishes and decellularized extracellular matrix (dECM)-coated dishes. dECM was deposited by Wharton's jelly mesenchymal stromal/stem cells.

value: mesenchymal stromal/stem cells


title: Endometrial mesenchymal stromal/stem cells, dECM, rep1

description: Library name: Sample 4


title: Endometrial mesenchymal stromal/stem cells, dECM, rep2

description: Library name: Sample 5


title: Exp01 TCR T cells

description: Library name: Exp01_TCR

value: gE_V_Y_IMAG002F_Exp01 (24y) gE_V_Y_IMAG003F_Exp01 (23y) gE_V_Y_IMAG004M_Exp01 (25y)

value: VZV gE-responsive CD4 and CD8 T cells


title: Exp02 TCR T cells

description: Library name: Exp02_TCR


title: Endometrial mesenchymal stromal/stem cells, plastic, rep3

description: Library name: Sample 3


title: BMVECs 24 hours DEVD mIL-36β (100 ng/ml) N1

description:
Library name: A24
A24

value: Brain

value: Microvascular endothelial cells

value: DEVD mIL-36β (100 ng/ml)


title: Endometrial mesenchymal stromal/stem cells, plastic, rep1

description: Library name: Sample 1


title: pLJM1-SF3A3-1

city: Hangzhou

first: Wei

state: Zhejiang

address: 268 Kaixuan Road

department: Institute of Translational Medicine

institute: Zhejiang University

description: Library name: Sample4

data_processing:
Raw sequencing data were processed using fastp v0.23.4 to filter out low-quality and low-complexity reads and remove adapter sequences. Cleaned reads were aligned to the hg38 reference genome in paired-end mode using bowtie2 (v2.5.1). The resulting BAM files were converted to bigWig format using bamCoverage from deeptools (v3.5.3) for chromosome coverage visualization. Custom R scripts were utilized to generate chromosome coverage plots.
Metagene plots were created using computeMatrix and plotProfile functions from deeptools (v3.5.3). Peak calling was performed with MACS2 (v2.2.9.1) using the callpeak function, and highly reproducible peaks across replicates were identified using IDR (v2.0.4.2). After quality control checks, data from replicates were merged to generate a combined set of peaks for each group.
The overlap and intersection of peaks between cell lines were assessed using Venn diagrams generated by the intersect function in bedtools (v2.27.1). Motif analysis was conducted with MEME (v5.0.2), restricting motif length to 6–10 bp and retaining motifs with significant E-values (< 10-3). Peak annotation, including overlapping gene locations, was performed with bedtools (v2.27.1) and reference gene annotation data from encode regions. Functional annotation of genes was done using the DAVID online database (https://david.ncifcrf.gov/; last accessed October 2023), focusing on cell cycle, apoptosis, resistant to cisplatin and transcription regulation-related genes. Genomic distribution of peaks was visualized using IGV (v2.16.2).
Assembly: hg38
Supplementary files format and content: xlsx file include FPKM values for each sample

source_name: cell line

growth_protocol: KLE cells were maintained in DF12 supplemented with 10 fetal fetal bovine serum (FBS) and antibiotics in humidfied atmosphere with 5% CO2 at 37 ℃

extract_protocol:
10 million cells were collected and lysed in RIP buffer (20 mM Tris-HCl pH=7.4, 100 mM KCl, 1.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40, 100U RNase inhibitor, 1×cocktail), and lysates were incubated withGFP-beads (AlpalifeBio, ktsm1301) overnight at 4°C. Immunocomplexes were washed with washing buffer for 3 times (20 mM Tris-HCl pH=7.4, 100 mM KCl, 1.5 mM MgCl2, 0.2 mM EDTA), treated with proteinase K, and RNA was extracted using phenol/chloroform/isoamyl alcohol (125:24:1). Clean reads were aligned to the hg38 genome using bowtie2 (v2.5.1). Both input and RIP samples were prepared for next-generation sequencing.
RIP sequencing libraries were prepared using Illumina TruSeq-stranded-mRNA following manufactors' protocols.

treatment_protocol: We overexpressed GFP-SF3A3 in KLE cells and extracted the RNA bound to SF3A3 protein through IP experiments

value: cell line

value: KEL cell

value: Human endometrial cancer cells

value: Transfection of SF3A3- EGFP plasmid


title: pLJM1-EGFP-2

description: Library name: Sample2

value: WT

value: Transfection of plj EGFP plasmid


title: pLJM1-SF3A3-2

description: Library name: Sample5

value: Transfection of SF3A4- EGFP plasmid


title: Endometrial mesenchymal stromal/stem cells, plastic, rep2

description: Library name: Sample 2


title: pLJM1-SF3A3-3

description: Library name: Sample6

value: Transfection of SF3A5- EGFP plasmid


title: pLJM1-EGFP-3

description: Library name: Sample3


title: 45F; FEMALE, ENVIRONMENTALLY ENRICHED, LPS

city: New York

first: Jordan

last: Marrocco

state: NY

address: 3 Times Sq, Office 752

department: Biology

institute: Touro University

description:
Library name: 45F
Illumina NextSeq 2000

data_processing:
The raw sequence reads were quality, adapter trimmed and quantified using quantify miRNA tool in CLC Genomics workbench 20.0.4.
Trimmed reads with a length of 15 to 31 bp were retained.
Trimmed reads were compared to, and annotated with, the small RNA database miRbase 22.
Hit counts for each small RNA were used as expression values and quantile normalization and log2-transformation were performed.
Differentially expressed annotated small RNAs were identified via empirical analysis using the Fisher’s exact test. Differentially expressed miRNAs were considered statistically significant if p<0.01 and fold-change of normalized expression values >2. Benjamini–Hochberg false discovery rate corrected (FDR) p<0.05 and absolute fold-changes of normalized expression values >2 was used to find differentially expressed miRNAs that met this level of statistical significance. The miRNA-mRNA targets (target score>80) were predicted using miRDB (https://mirdb.org/) or miRDeep2 for Novel miRNAs.
Assembly: mRatBN7.2
Supplementary files format and content: .xlsx file includes raw counts for each sample

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from P12 hippocampal tissues using the RNeasy Lipid Tissue Mini Kit (74804, Qiagen)
Small RNA sequencing libraries were prepared by using Illumina TruSeq Small RNA Library Prep Kit (Illumina).

value: Hippocampus

tag: strain

value: Sprague-Dawley

tag: Sex

value: Female

value: Wild type

value: Environmentally Enriched LPS


title: pLJM1-EGFP-1

description: Library name: Sample1

tag: genotype


title: 3F; FEMALE, ENVIRONMENTALLY ENRICHED, LPS

description:
Library name: 3F
Illumina NextSeq 2000

tag: age


title: 33F; FEMALE, ENVIRONMENTALLY ENRICHED, LPS

description:
Library name: 33F
Illumina NextSeq 2000


title: 50F; FEMALE, ENVIRONMENTALLY ENRICHED, SALINE

description:
Library name: 50F
Illumina NextSeq 2000

value: Environmentally Enriched Saline


title: 9F; FEMALE, ENVIRONMENTALLY ENRICHED, LPS

description:
Library name: 9F
Illumina NextSeq 2000


title: 46F; FEMALE, ENVIRONMENTALLY ENRICHED, SALINE

description:
Library name: 46F
Illumina NextSeq 2000


title: 5F; FEMALE, ENVIRONMENTALLY ENRICHED, LPS

description:
Library name: 5F
Illumina NextSeq 2000


title: 10F; FEMALE, ENVIRONMENTALLY ENRICHED, SALINE

description:
Library name: 10F
Illumina NextSeq 2000


title: 7F; FEMALE, ENVIRONMENTALLY ENRICHED, LPS

description:
Library name: 7F
Illumina NextSeq 2000


title: 4F; FEMALE, ENVIRONMENTALLY ENRICHED, SALINE

description:
Library name: 4F
Illumina NextSeq 2000


title: 2F; FEMALE, ENVIRONMENTALLY ENRICHED, SALINE

description:
Library name: 2F
Illumina NextSeq 2000


title: 8F; FEMALE, ENVIRONMENTALLY ENRICHED, SALINE

description:
Library name: 8F
Illumina NextSeq 2000


title: 55F; FEMALE, STANDARD HOUSED, LPS

description:
Library name: 55F
Illumina NextSeq 2000

value: Standard housed LPS


title: 19F; FEMALE, STANDARD HOUSED, LPS

description:
Library name: 19F
Illumina NextSeq 2000


title: 68F; FEMALE, STANDARD HOUSED, SALINE

description:
Library name: 68F
Illumina NextSeq 2000

value: Standard housed Saline


title: 17F; FEMALE, STANDARD HOUSED, LPS

description:
Library name: 17F
Illumina NextSeq 2000


title: 67F; FEMALE, STANDARD HOUSED, LPS

description:
Library name: 67F
Illumina NextSeq 2000


title: 42F; FEMALE, STANDARD HOUSED, SALINE

description:
Library name: 42F
Illumina NextSeq 2000


title: 66F; FEMALE, STANDARD HOUSED, SALINE

description:
Library name: 66F
Illumina NextSeq 2000


title: 15F; FEMALE, STANDARD HOUSED, LPS

description:
Library name: 15F
Illumina NextSeq 2000


title: 16F; FEMALE, STANDARD HOUSED, SALINE

description:
Library name: 16F
Illumina NextSeq 2000


title: 32F; FEMALE, STANDARD HOUSED, SALINE

description:
Library name: 32F
Illumina NextSeq 2000


title: 45M; MALE, ENVIRONMENTALLY ENRICHED, LPS

description:
Library name: 45M
Illumina NextSeq 2000

value: Male


title: 14F; FEMALE, STANDARD HOUSED, SALINE

description:
Library name: 14F
Illumina NextSeq 2000


title: 7M; MALE, ENVIRONMENTALLY ENRICHED, LPS

description:
Library name: 7M
Illumina NextSeq 2000


title: 33M; MALE, ENVIRONMENTALLY ENRICHED, LPS

description:
Library name: 33M
Illumina NextSeq 2000


title: 9M; MALE, ENVIRONMENTALLY ENRICHED, LPS

description:
Library name: 9M
Illumina NextSeq 2000


title: 5M; MALE, ENVIRONMENTALLY ENRICHED, LPS

description:
Library name: 5M
Illumina NextSeq 2000


title: 46M; MALE, ENVIRONMENTALLY ENRICHED, SALINE

description:
Library name: 46M
Illumina NextSeq 2000


title: 50M; MALE, ENVIRONMENTALLY ENRICHED, SALINE

description:
Library name: 50M
Illumina NextSeq 2000


title: 2M; MALE, ENVIRONMENTALLY ENRICHED, SALINE

description:
Library name: 2M
Illumina NextSeq 2000


title: 67M; MALE, STANDARD HOUSED, LPS

description:
Library name: 67M
Illumina NextSeq 2000


title: 55M; MALE, STANDARD HOUSED, LPS

description:
Library name: 55M
Illumina NextSeq 2000


title: 65F; FEMALE, STANDARD HOUSED, LPS

description:
Library name: 65F
Illumina NextSeq 2000


title: 8M; MALE, ENVIRONMENTALLY ENRICHED, SALINE

description:
Library name: 8M
Illumina NextSeq 2000


title: 4M; MALE, ENVIRONMENTALLY ENRICHED, SALINE

description:
Library name: 4M
Illumina NextSeq 2000


title: 3M; MALE, ENVIRONMENTALLY ENRICHED, LPS

description:
Library name: 3M
Illumina NextSeq 2000


title: 10M; MALE, ENVIRONMENTALLY ENRICHED, SALINE

description:
Library name: 10M
Illumina NextSeq 2000


title: 65M; MALE, STANDARD HOUSED, LPS

description:
Library name: 65M
Illumina NextSeq 2000


title: 17M; MALE, STANDARD HOUSED, LPS

description:
Library name: 17M
Illumina NextSeq 2000


title: 19M; MALE, STANDARD HOUSED, LPS

description:
Library name: 19M
Illumina NextSeq 2000


title: 68M; MALE, STANDARD HOUSED, SALINE

description:
Library name: 68M
Illumina NextSeq 2000


title: 15M; MALE, STANDARD HOUSED, LPS

description:
Library name: 15M
Illumina NextSeq 2000


title: 42M; MALE, STANDARD HOUSED, SALINE

description:
Library name: 42M
Illumina NextSeq 2000


title: 66M; MALE, STANDARD HOUSED, SALINE

description:
Library name: 66M
Illumina NextSeq 2000


title: 16M; MALE, STANDARD HOUSED, SALINE

description:
Library name: 16M
Illumina NextSeq 2000


title: 14M; MALE, STANDARD HOUSED, SALINE

description:
Library name: 14M
Illumina NextSeq 2000


title: 32M; MALE, STANDARD HOUSED, SALINE

description:
Library name: 32M
Illumina NextSeq 2000


title: DRG, Male, 1W, IL, rep 4

city: Würzburg

first: Robert

last: Blum

address: Josef-Schneider-Str. 11

department: Department of Neurology

country: Germany

institute: University Hospital Würzburg

description:
DRG_M_1W_IL_R4
CCI_1W_L4_IL_R4
Raw_count_table_1.csv

data_processing:
Base calling with Illumina NextSeq RTA v2.11.3 (NextSeq 500) and v3.9.25/v3.10.30 (NextSeq 2000)
FASTQ conversion with bcl2fastq v2.20.0.422/bcl-convert v4.0.3
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) v2.5 (parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) except for Male, 5W samples where read 3' ends were initially trimmed by 25 bases (parameters: -u -25 --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) to allow fair comparison with Male, 1W samples at 76 nt read length.
Alignment of trimmed reads to rat genome using STAR (Dobin et al., 2013) v2.7.2b with default parameters except for including transcript annotations from RefSeq annotation version 108 for mRatBN7.2
Calculation of read counts on exon level summarized for each gene (RefSeq annotation version 108 for mRatBN7.2) using featureCounts v1.6.4 from Subread package (Liao et al., 2014) (parameters: -s 2 -t exon -M -O --fraction)
Assembly: GCF_015227675.2/mRatBN7.2
Supplementary files format and content: Character (TAB) separated value file containing raw read counts

source_name: dorsal root ganglion (DRG)

extract_protocol:
Arturus PicoPure kit (with lysis at 30Hz for 2 mins in a Retsch Bead Mill)
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was ≥ 7,5. DNA libraries suitable for sequencing were prepared from 300-500 ng of total RNA with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions (1/2 volume). After 13-15 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~310 bp by electrophoresis on Agilent DNA 1000 Bioanalyzer microfluidic chips. Sequencing of pooled libraries, spiked with 1% PhiX control library, was performed at ~25 million reads/sample in single-end mode with 75 nt read length on the NextSeq 500 platform (Illumina) or 100 nt read lenght on the NextSeq 2000 platform (Illumina).

value: dorsal root ganglion (DRG)

value: male

value: 1 week

value: Chronic Constriction Injury (CCI), ipsilateral side

tag: replicate

value: rep 4


title: DRG, Male, 1W, IL, rep 5

description:
DRG_M_1W_IL_R5
CCI_1W_L4_IL_R5
Raw_count_table_1.csv

value: rep 5


title: DRG, Male, 1W, IL, rep 3

description:
DRG_M_1W_IL_R3
CCI_1W_L4_IL_R3
Raw_count_table_1.csv

value: rep 3


title: DRG, Male, 1W, IL, rep 2

description:
DRG_M_1W_IL_R2
CCI_1W_L4_IL_R2
Raw_count_table_1.csv

value: rep 2


title: DRG, Male, 1W, CL, rep 7

description:
DRG_M_1W_CL_R7
CCI_1W_L4_CL_R7
Raw_count_table_1.csv

value: Chronic Constriction Injury (CCI), contalateral side

value: rep 7


title: DRG, Male, 1W, CL, rep 6

description:
DRG_M_1W_CL_R6
CCI_1W_L4_CL_R6
Raw_count_table_1.csv

value: rep 6


title: DRG, Male, 1W, CL, rep 5

description:
DRG_M_1W_CL_R5
CCI_1W_L4_CL_R5
Raw_count_table_1.csv


title: DRG, Male, 1W, IL, rep 7

description:
DRG_M_1W_IL_R7
CCI_1W_L4_IL_R7
Raw_count_table_1.csv


title: DRG, Male, 1W, CL, rep 4

description:
DRG_M_1W_CL_R4
CCI_1W_L4_CL_R4
Raw_count_table_1.csv


title: DRG, Male, 1W, CL, rep 3

description:
DRG_M_1W_CL_R3
CCI_1W_L4_CL_R3
Raw_count_table_1.csv


title: DRG, Male, 1W, CL, rep 1

description:
DRG_M_1W_CL_R1
CCI_1W_L4_CL_R1
Raw_count_table_1.csv

value: rep 1


title: DRG, Male, 1W, CL, rep 2

description:
DRG_M_1W_CL_R2
CCI_1W_L4_CL_R2
Raw_count_table_1.csv


title: h2184_PDX_Early_Relapse_VTP_3729_r3

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

description: Library name: L21

data_processing:
Star aligner and kallisto to get alignment file and TPM per transcript
DEseq2 as the tool to identify over/under expressed genes at FDR less than 0.05
Assembly: HG38
Supplementary files format and content: tab separated TPM per sample

source_name: bone marrow

growth_protocol: 6-8 week old NSG (NOD-scid IL2Rgnull) mice were obtained from Jackson laboratories® and maintained under specific pathogen free conditions. 24-48 hours prior to transplantation, mice were conditioned with 25 mg/kg busulfan i.p. Previously banked patient leukemia samples were thawed, resuspended in PBS and injected into the tail vein.

extract_protocol:
RNA was extracted using the RNeasy mini kit from QIAGEN
RNA-Seq libraries were prepared from PolyA selected mRNA (eukaryotic) using the NEBNext Ultra II RNA Library Prep Kit for Illumina 24. Multiplexed sequencing was conducted on a NovaSeq 6000  using the NovaSeq 6000 SP Reagent Kit v1.5, paird end to a read depth of 20-30 million per sample.

treatment_protocol: Mice underwent monitoring for leukemia development using weekly serial bleeds. Treatment with VTP-50469 0.1% chow was started once peripheral blood engraftment in the range of 1-5% was seen (day 14 for sample 5.1, and day 7 for sample 5.2). After three weeks of treatment, mice were sacrificed and leukemia cells were isolated by and sorted on live (FSC vs SSC and DAPI negative), human CD45+, mouse CD45-.

value: bone marrow

value: patient derived xenograft

value: leukemia

value: Sample # 5.1 (early)

tag: batch


title: h2184_PDX_Early_Relapse_VTP_3727_repeat_r5

description: Library name: L23


title: h2184_PDX_Early_Relapse_VTP_3727_r1

description: Library name: L19


title: h2184_PDX_Early_Relapse_VTP_3730_r4

description: Library name: L22


title: h2184_PDX_Early_Relapse_VTP_3728_repeat_r6

description: Library name: L24


title: h2184_PDX_Early_Relapse_Con_3736_repeat_r6

description: Library name: L18

value: control chow


title: h2184_PDX_Early_Relapse_VTP_3728_r2

description: Library name: L20


title: h2184_PDX_Early_Relapse_Con_3790_r3

description: Library name: L15


title: h2184_PDX_Early_Relapse_Con_3716_r2

description: Library name: L14


title: h2184_PDX_Early_Relapse_Con_3716_repeat_r5

description: Library name: L17


title: h2184_PDX_Early_Relapse_Con_3792_r4

description: Library name: L16


title: h2184_PDX_Early_Relapse_Con_3736_r1

description: Library name: L13


title: h2263_PDX_Lineage_switch_VTP_1580_r4

description: Library name: L10

value: Sample # 5.2 (late)


title: DRG, Male, 1W, IL, rep 1

description:
DRG_M_1W_IL_R1
CCI_1W_L4_IL_R1
Raw_count_table_1.csv

value: dorsal root ganglion (DRG)

value: male


title: h2263_PDX_Lineage_switch_VTP_1576_repeat_r5

description: Library name: L11


title: DRG, Male, 1W, IL, rep 6

description:
DRG_M_1W_IL_R6
CCI_1W_L4_IL_R6
Raw_count_table_1.csv

value: 1 week

value: Chronic Constriction Injury (CCI), ipsilateral side


title: h2263_PDX_Lineage_switch_VTP_1576_r3

description: Library name: L9


title: h2263_PDX_Lineage_switch_VTP_1549_r2

description: Library name: L8


title: h2263_PDX_Lineage_switch_VTP_1548_r1

description: Library name: L7


title: h2263_PDX_Lineage_switch_Con_1536_repeat_r6

description: Library name: L6


title: h2263_PDX_Lineage_switch_Con_1535_repeat_r5

description: Library name: L5


title: h2263_PDX_Lineage_switch_Con_1535_r1

description: Library name: L1


title: h2263_PDX_Lineage_switch_Con_1536_r2

description: Library name: L2


title: h2263_PDX_Lineage_switch_Con_1537_r3

description: Library name: L3


title: corresponding adjacent tissues of patient 3

city: Changchun

first: Xiaosong

last: Wang

state: Jilin

address: No.519 Dongminmin Street Changchun 130021, China

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

description: Library name: ATN03

data_processing:
The BD Resolve analysis pipeline was used to process sequencing data (fastq files). Raw data (raw reads) of fastq format were first processed to obtain clean data (clean reads). All the downstream analyses were based on the clean data with high quality. The p values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate (FDR). Gene with an adjusted p value < 0.05 was assigned as differentially expressed. Using Seurat 3.0(R package) analyses included identification of highly variable genes, data dimension reduction (PCA, T-SNE), cell clustering, identification of differentially expressed genes and markers.  Functional analysis including GO enrichment, KEGG enrichment, Reactome enrichment and Disease enrichment (human only) was performed on the genes with top20 differences in each Cluster. Protein-protein interaction was obtained from STRING database with combine_score >=700. Transcription Factors were predicted within 2000 bp upstream and 500 bp downstream of TSS for top 20 marker genes of each cluster using TFBSTools and JASPAR database. GSEA was performed by using GSEA software version 2.2.2.4, which uses predefined gene sets from the Molecular Signatures Database (MSigDB v6.2). Single-cell trajectories were built with Monocle (R package).
Assembly: GRCh38
Supplementary files format and content: Tap-separated values files and matrix files

source_name: corresponding adjacent tissues

extract_protocol:
cervical squamous cell carcinoma tissues and corresponding adjacent tissues were taken by pathologists from normal and tumor regions. Tissues were washed by PBS and put into a gentle Tube full of MACS Tissue Storage solution
The cell suspension was loaded onto the Rhapsody™ Cartridge (BD) to generate single-cell magnetic beads in the microwells according to the manufacturer’s protocol. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual microwells.     The cDNA was generated and then amplified, the quality assessed using an Agilent 4200 (performed by CapitalBio Technology, Beijing). Whole transcriptome libraries were prepared using the BD Resolve single cell whole transcriptome amplification workflow. The libraries were sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 50,000 reads per cell with pair-end 150 bp (PE150) reading strategy

value: corresponding adjacent tissues

value: tissue

value: corresponding adjacent tissue cell


title: cervical squamous cell carcinoma tissues of patient 3

description: Library name: CC03

value: cervical squamous cell carcinoma cell


title: corresponding adjacent tissues of patient 1

description: Library name: ATN01


title: cervical squamous cell carcinoma tissues of patient 1

description: Library name: CC01