title: 31RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_05.RCC

value: Recombinant antigen


title: participant_4K

status: Public on Dec 21 2022

type: genomic

city: Berlin

first: Anna-Lena

last: Lang

address: Charitéplatz 1

department: Institute of Neuropathology

country: Germany

institute: Charité – Universitätsmedizin Berlin

description: Illumina EPIC 850k methylation data from FFPE brain tissue

hyb_protocol: Hybridization to the Illumina 850k BeadChip was carried out as per manufacturers protocol.

scan_protocol: Scanning was carried out as per manufacturers protocol using the Illumina iScan System.

data_processing:
Bulk data processing description:
Data was normalized using noob implemented by minfi and BMIQ implemented by ChAMP. We kept the first processed sample and removed all replicates from the datasets after normalization. Processed average beta values from bulk data for each of the eight brain regions is available.
Cell type specific data processing description:
To estimate cell type heterogeneity in our bulk data, we used an existing cell type-specific DNA methylation reference matrix for brain tissue from EpiSCORE. Bulk data was processed for each brain region separately. First, CpGs were mapped to Entrez IDs using the constAvBetaTSS function from the EpiSCORE package. Cell type proportions were estimated using the wRPC function, using weights in the regression, setting the threshold on the weights to select the most informative genes to 0.4 and the maximum number of iterations in the robust linear regression to 300. The brain reference matrix for EpiSCORE can be used to estimate cell type proportions for neurons, astrocytes, endothelial cells, microglia, oligodendrocytes, and oligodendrocyte precursor cells (OPCs). Because we detected relatively small proportions for oligodendrocytes and OPCs and the cell types are highly related, we combined those proportions into one value for oligodendrocytes/OPCs (olig/OPC). The resulting estimated cell type proportions for the five cell types served as input for cell type deconvolution. Cell type deconvolution was performed using the Tensor Composition Analysis (TCA) package in R. Given the estimated cell type proportions, TCA uses a tensor generalization of matrix factorization to estimate CTS methylation profiles for each of the five cell types we considered. The resulting deconvolved data consists of a CTS methylation value for each CpG and sample. We deconvolved the five cell types within each of the eight brain regions separately. Given that some cell types had very low abundancy in some brain regions, 37 datasets with cell type specific processed average beta values is available.
Bulk CSV data:
Normalized average beta values (Data was normalized using noob implemented by minfi and BMIQ implemented by ChAMP) from bulk data including detection p-values.
Cell type specific CSV data:
Normalized average beta values (see definition above) were followed by cell type deconvolution using EpiSCORE and TCA. Cell type specific data is available for all brain regions. File name abbreviations follow cell descriptions documented in legend of the metadata file.
Additional data processing in the paper, data not available on GEO:
Within each CTS methylation profile, we further collapsed probe-level methylation to three genomic region types (promoters, genes, and CpG islands) using the RnBeads annotations, by calculating the average methylation value across all CpGs within the respective genomic region. These datasets were not uploaded to GEO, but can be easily reproduced using the code available on GitHub https://github.com/anna-lena-lang/90plus_brain_methylation.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Depending on DNA concentration, 250ng to 1000ng of high-quality DNA were bisulfite converted using the Zymo EZ DNA Methylation Kit (Zymo Research, Orange, CA, USA). After bisulfite conversion, the entire yield (8 µl) was restored with the Infinium HD FFPE DNA Restore Kit. Samples were further processed as per the manufacturer’s standard protocol for FFPE samples on the Illumina Infinium Human MethylationEPIC BeadChip  (Illumina, USA).

extract_protocol: Cores were extracted from FFPE blocks with a biopsy punch needle 1 to 1.5mm in diameter and 2-3mm in length, assuring accurate dissection of very fine regions from FFPE. DNA was extracted from FFPE cores using the Zymo Research Quick DNA FFPE Miniprep kit following the manufacturer's instructions with one minor modification. During overnight digestion with proteinase K at 55°C, intermittent vortexing every 20 minutes at 2000rpm for 1 minute was used to facilitate more complete digestion of tissue chunks.

treatment_protocol: All brain tissue used for this study was formaline fixed, paraffine embedded (FFPE).

value: SN

value: substantia nigra

tag: batch

tag: Sex

value: female

tag: age

tag: education

tag: genotype

tag: flanitot

tag: niaaaascore

tag: niaaabscore

tag: niaaacscore

tag: adseverityscore


title: shAlox12b.728_3bulkRNAseq

type: SRA

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

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

country: China

institute: Sichuan University

library_source: transcriptomic

data_processing:
Illumina sequencing workflow
Sequenced reads were mapped to GRCm38 whole genome using STAR v2.6.0 .
Transcripts Per Kilobase Million of library size (TPM) were calculated .
Genome_build: GRCm38
Supplementary_files_format_and_content: xlsx  file includes TPM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: pre B cells

extract_protocol: PreB cells from WT mice were harvested and transduced with shRNAs targeting either shAlox15b or shAlox12b, fluorescence activated cell sorting of transduced cells were conducted 48h post-infection and RNA was harvested using Trizol reagent.

tag: strain

tag: cell type

value: pre B cells


title: Pt2a Hi-C rep 1

city: San Francisco

first: Katherine

middle: S

last: Pollard

state: CA

address: 1650 Owens St

department: Institute of Data Science and Biotechnology

country: USA

institute: Gladstone Institutes

library_source: genomic

data_processing:
Adapters were trimmed from raw FASTQ files using TrimGalore [v0.6.5] with options --illumina --paired.
The data were then processed from adapter-trimmed FASTQ files to Hi-C contacts as cooler files using Distiller [v0.3.3] (65). This processing includes read mapping with BWA-MEM (66), filtering (MAPQ >= 30), contact pair processing with pairtools (67) and normalization via matrix balancing (68). Samples were processed both per replicate, per individual and per species. For easier comparison of samples in some analyses, we mapped the data from each species to the reference genome of the other species (human to pantro6 and chimp to hg38).
Genome_build: hg38, panTro6
Supplementary_files_format_and_content: Cooler (Hi-C contact matrices)

organism: Pan troglodytes

growth_protocol: Two human (WTC11 and HS1) and two chimpanzee (C3649 and Pt2a) induced pluripotent cell lines (iPSCs) were cultured in Matrigel-coated plates with mTeSR media (WTC11 and C3649 were cultured in StemFlex) in an undifferentiated state. Cells were propagated at a 1:3 ratio by treatment with 200 U/mL collagenase IV (or PBS-EDTA) and mechanical dissection.   WTC11 and C3649 iPSCs were differentiated to neural progenitor cells (NPCs) as previously described (64). Briefly, 2-2.5×10⁵ cells per cm² were seeded on Matrigel-coated wells in StemFlex containing 2 μM Thiazovivin. The following day (Day 0), medium was replaced with E6 containing 500 nM LDN193189 (Selleckchem), 10 μM SB431542 (Selleckchem), and 5 μM XAV-939 (Selleckchem). Starting on Day 3, medium was replaced with E6 containing 500 nM LDN193189 and 10 μM SB431542 every 48 hrs. Starting on Day 12, medium was replaced with Neurobasal containing 2 mM GlutaMAX, 60 μg per ml L-Ascorbic acid 2-phosphate, N2, and B27 without Vitamin A every 48 hours. Around Day 16, cells were washed with PBS, dissociated with Accutase, pelleted and resuspended in Neurobasal containing 2 mM GlutaMAX, 60 μg per ml L-Ascorbic acid 2-phosphate, N2, and B27 without Vitamin A, 10 ng per ml fibroblast growth factor 2, and 10 ng per ml epidermal growth factor, and seeded on poly-L-ornithine-, fibronectin-, and laminin-coated wells. Cells were collected for HiC at passage 5-7.  To differentiate HS1 and Pt2a iPSCs into NPCs, cells were split with EDTA at 1:5 ratios in culture dishes coated with matrigel and culture in N2B27 medium (comprised of DMEM/F12 medium (Invitrogen) supplemented with 1% MEM-nonessential amino acids (Invitrogen), 1 mM L-glutamine, 1% penicillin-streptomycin, 50 ng/mL bFGF (FGF-2) (Millipore), 1x N2 supplement, and 1 x B27 supplement without Vitamin A (Invitrogen)) supplemented with 100 ng/ml mouse recombinant Noggin (R&D systems). Cells at passages 1-3 were split by collagenase into small clumps, and continuously cultured in N2B27 medium with Noggin. After passage 3, cells were plated at the density of 5×10⁵ cells/cm² after disassociation by TrypLE express (Invitrogen) into single-cell suspension, and cultured in N2B27 medium supplemented with 20 ng/mL bFGF and EGF. Cells were maintained and collected at passage 18-20. Our use of two differentiation protocols reflects rapid progress in stem cell research during the course of this study.

treatment_protocol: Hi-C was performed using the Arima Hi-C kit (Arima Genomics) according to the manufacturer’s instructions. 10 million cells were used. The sequencing library was prepared using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) according to the manufacturer's protocol. Two independent biological replicates were prepared for each cell line. In total eight libraries were pooled and sequenced with paired-end 150-bp reads using two lanes of a NovaSeq6000 S2 (Illumina) at the Chan Zuckerberg Biohub.

tag: cell line

value: iPS-derived neural progenitor cells


title: ZEB D #15

type: RNA

city: Milano

first: Barbara

last: Bassani

address: via G. Antonio Amadeo, 42

department: Department of Research

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori di Milano

description: Gene expression data from C1498 cells expressing the ZEB-1 seq D shRNA construct

hyb_protocol: Hybridization was performed according to manufacturer's standard protocols

scan_protocol: Gene microarrays were scanned with the Gene Chip System 3000 Scanner

data_processing: Raw data were pre-processed using the sst-RMA algorithm implemented in the Transcriptome Analysis Console software (Thermo Fisher Scientific).

label: biotin

label_protocol: RNA was labeled according to manufacturer's recommended protocols

growth_protocol: C1498 cells were cultured in DMEM (Dulbecco's modified Eagle's medium) supplemented with 10 % fetal bovine serum, 1 % antibiotics, 2 mM glutamine, 1 mM sodium pyruvate, 1 mM HEPES and 1X Minimum Essential Medium (MEM) Non-Essential Amino Acids Solution, in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol: Total RNA was extracted using the Quick RNA micro prep kit (Zymo Research).

treatment_protocol: 104 C1498 cells were treated overnight with lentiviral particles containing plasmid expressing a short hairpin RNA (shRNA) sequence against ZEB-1 (or a negative control construct) and green fluorescence protein (GFP). Two weeks after infection, GFP+ cells were isolated.


title: shAlox12b.728_2bulkRNAseq


title: 31A,W0

city: Lincoln

first: Paul

last: Maclean

address: Cnr Springs Road and Gerald Street

country: New Zealand

institute: AgResearch NZ LTD

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_04.RCC

hyb_protocol: Hybrdization reactions were performed in final voulme of 15µl according to the manufacturer's instructions (MAN-10040-06). All hybridization reactions were incubated at 67°C for a minimum of 18 h

scan_protocol: Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer’s instructions. For each assay, a high-density scan (600 fields of view) was performed

data_processing: The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using vsn normalization

label: Fluorescently labeled target sequences

organism: Bos taurus

source_name: Leukocytes

label_protocol: 1.1 µg of purified RNA in 7µl was added to tubes containing 8 µl of PlexSet master mix (Probe A & B as well as Reporter probes with flouresenct tags and Capture  probes) according to the manufacturer's instructions (MAN-10040-06).

extract_protocol: Total RNA was isolated from the samples using RNeasy kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany).

treatment_protocol: Briefly, 3 mL of blood was transferred into a 50 mL falcon tube and 13.5 mL of chilled water was added (4.5 mL/ml of blood) to lyse the red blood cells. The tubes were quickly mix for 15 sec and 1.5 mL of 10X DPBS (500 µL/mL of blood) (Thermo Fisher Scientific, New Zealand) was added to equilibrate the sample. Subsequently, the cells were centrifuged at 250 μg for 10 min at 4°C, washed with PBS (10 mM, pH-7.3) and the cells were re-suspended in 0.5 mL of RPMI-1640 containing 10% fetal bovine serum (Thermo Fisher Scientific, New Zealand). Cell number and viability was measured by trypan blue exclusion method using TC20 cell counter (BioRad). A total of 2x106 cells were added to each well in a U-bottom 96-well tissue culture plate (Nunc(TM)) and stimulated with either media alone (un-stimulated), PPDA (24 μg/mL) or RA (10 µg/mL) at 37°C for 24 h. After incubation, plates were centrifuged in a swing out rotor at 350 μg for 10 min at room temperature. The supernatant was removed and 150 µL of a commercial lysis buffer for RNA preparation was added (RLT buffer, Qiagen, Hilden, Germany) to the samples and the plates were stored at –80°C until RNA isolation.

tag: nanostring plexset set in rcc files

tag: time

value: Week 0

tag: antigen

value: PPBDA

tag: vaccine

value: Leukocytes


title: 32RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_08.RCC


title: shAlox12b.728_1bulkRNAseq


title: 32A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_07.RCC


title: participant_3J2

value: EC

value: entorhinal cortex

tag: batch

value: male


title: DMNT treted_3

city: Hefei

first: Chen

last: Hongyi

address: 130 Changjiang West Road

institute: Anhui Agricultural University

data_processing:
Illumina Novaseq™ 6000
A cDNA library constructed by technology from the pooled RNA from brain samples of pig was sequenced run with Illumina Novaseq™ 6000 sequence platform. Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon paired-end reads of bp length. This yielded gigabases (Gb) of sequence. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed .After that, a total of G bp of cleaned ,paired-end reads were produced. The raw sequence data have been submitted to the NCBI Short Read Archive with accession number .
we aligned reads of sample A and sample B to the UCSC (http://genome.ucsc.edu/) homo sapiens reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.HISAT build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package.
Genome_build: GCA_000330985.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Plutella xylostella

source_name: whole body

growth_protocol: 2th instar larva

extract_protocol:
Total RNA of P. xylostalla larva was extracted with TRIzol RNA preparation method (Invitrogen, CA, USA),and then construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2th instar larva after DMNT treatment at 12h

tag: developmental stage

value: 2th instar larva


title: 30RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200729_cJD immune Run-3 555_01_02.RCC


title: participant_3F

value: CG

value: cingulate gyrus

tag: Sex

tag: age


title: participant_3DEN_redoBatch9fail

value: DG

value: dentate gyrus

tag: education

tag: genotype


title: 30A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200729_cJD immune Run-3 555_01_01.RCC


title: Control_3


title: DMNT treted_1


title: participant_3CA1

tag: flanitot

tag: niaaaascore


title: ZEB D #14

source_name: C1498 cells expressing the ZEB-1 seq D shRNA construct


title: ZEB C #12

description: Gene expression data from C1498 cells expressing the ZEB-1 seq C shRNA construct


title: ZEB C #10

source_name: C1498 cells expressing the ZEB-1 seq C shRNA construct


title: 32RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_12.RCC

value: Week 6

value: Recombinant antigen


title: 32N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_10.RCC

value: PBS


title: participant_3L

value: LC

value: locus coeruleus

tag: niaaabscore

tag: niaaacscore


title: Control_2


title: ZEB C #11


title: ZEB D #13


title: Heart tissue, POR knockout, N3 [Heart_POR-KO_N3]

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

institute: Goethe Universität Frankfurt am Main

data_processing:
FastQC (0.11.9)
Salmon (1.9.0)
DESeq2 (1.36.0)
Assembly: mm10
Supplementary files format and content: xlsx, DESeq2 differential gene expression results

source_name: Heart

extract_protocol:
Cardiac endothelial cells were isolated from LV of ecPOR-/- and CTL mice using magnetic activated cell sorting. The remaining myocardial tissue was designated as cardiac fraction. Briefly, two LVs per genotype were pooled in Hank’s balanced salt solution (HBSS, 1mL) and cut into small pieces (1 mm). Minced tissue was transferred to 50 mL Falcon tubes containing enzyme mix (10 mL Dulbecco’s modified Eagle’s (DMEM, Gibco Life Technologies, Carlsbad, US) containing dispase (1.2 U/mL, #39307800, Roche Diagnostics, Mannheim, Germany), collagenase II (2 mg/mL, #LS004177, Worthington, Lakewood, US), elastase (0.03 mg/mL, #2292, Worthington, Lakewood, US) and digested for 20 minutes at 37 °C. Digestion was stopped with DMEM containing 10% FCS. Undigested tissue was removed by filtration through strainers (100 µm and 70 µm). Cells were spun down (10 min, 500 xg, 4 °C) and the pellet was resuspended in 10 mL RBC (redo blood cells) lysis buffer (J62150, Alfa Aesar, Kandel, Germany)
RNA and library preparation integrity were verified with LabChip Gx Touch 24 (Perkin Elmer). For the cardiac fraction 4 µg of total RNA was used as input for VAHTS Stranded mRNA-seq Library preparation following manufacture’s protocol (Vazyme). For EC samples RNA was used for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio).

treatment_protocol: Endothelial cell-specific, tamoxifen inducible POR knockout mice (ecPOR-/-) were generated as previously described (Malacarne et al. 2022). Briefly, Porflox/flox mice (Portm1Ding) (Wu et al. 2003) were crossed with Cdh5-CreERT2 (Tg(Cdh5-CreERT2)1Rha) (Wang et al. 2010) mice. POR deletion was induced by tamoxifen feeding (CreActive TAM400, #D.T400.R1, Laval, France, 1 mg/mouse/day, 10 days) when mice were at least 8 weeks old followed by a “wash-out period” of at least 30 days. Porflox/flox-Cdh5-CreERT20/0 littermates (no cre expression) with tamoxifen treatment served as control (CTL). Animals were housed in groups with free access to chow and water in a specified pathogen-free facility with a 12h-day/12h-night cycle. All animal experiments were performed in accordance with the German animal protection law and were carried out after approval by the local authorities (FU1188). Unless specified, all animal experiments were performed 30 days after inducing the knockout.

tag: tissue

value: Heart

value: Whole tissue

tag: strain background

value: ecPOR-/- (Portm1Ding x Tg(Cdh5-CreERT2)1Rha)

value: POR knockout


title: participant_3K

value: SN

value: substantia nigra

tag: adseverityscore


title: 31N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200729_cJD immune Run-3 555_01_03.RCC

tag: nanostring plexset set in rcc files

value: Week 0

tag: cell type

value: Leukocytes


title: participant_3B

value: MFG

value: middle frontal gyrus

value: male


title: Control_1

value: 2th instar larva


title: 31RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_09.RCC

tag: time

value: Week 6

tag: antigen


title: participant_2N

value: CBM

value: cerebellar cortex

tag: batch

value: female


title: DMNT treted_2

tag: developmental stage


title: SCR #7

description: Gene expression data from C1498 cells expressing the negative control construct

tag: cell line


title: SCR #8

source_name: C1498 cells expressing the negative control construct


title: Heart tissue, POR knockout, N2 [Heart_POR-KO_N2]


title: participant_2F

value: CG

value: cingulate gyrus

tag: Sex

tag: age


title: Heart tissue, Wild-type, N2 [Heart_WT_N2]

value: Heart

value: Whole tissue

tag: genotype

value: Control


title: Heart tissue, Wild-type, N3 [Heart_WT_N3]


title: Heart tissue, POR knockout, N1 [Heart_POR-KO_N1]

value: ecPOR-/- (Portm1Ding x Tg(Cdh5-CreERT2)1Rha)

value: POR knockout


title: 32A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_11.RCC

value: PPBDA

tag: vaccine


title: HPUra38+4h

city: Cambridge

first: Alan

last: Grossman

state: MA

address: 31 Ames St.

department: Biology

institute: MIT

data_processing:
Reads were trimmed to remove sequence from the transposon
Sequences adjacent to the transposon were mapped to AG174 genome using Bowtie2
Wiggle files were generated from the Bowtie output using in-house R scripts
Assembly: AG174 (GenBank #CP007800.1)
Supplementary files format and content: Wiggle track, variableStep format
Library strategy: Tn-Seq

organism: Bacillus subtilis subsp. subtilis

source_name: JMA222-based transposon insertion library

growth_protocol: A suspension culture of the transposon insertion library was grown in defined minimal medium at 37°C

extract_protocol:
Total DNA was extracted using Qiagen DNeasy Blood and Tissue kit using the protocol for Gram-positive bacteria.
Transposon insertions were prepared for sequencing as described in Johnson, C. M. & Grossman, A. D. Identification of host genes that affect acquisition of an integrative and conjugative element in Bacillus subtilis. Mol Microbiol 93, 1284–1301 (2014).

treatment_protocol: HPUra (38 µg/ml) was added to arrest replication, and a duplicate culture was untreated. After 1 h at 37°C, cells from both cultures were harvested by centrifugation, washed, and resuspended in fresh minimal medium. They were allowed to recover for 4 h, and aliquots were harvested every hour during this time.

value: JMA222 is ICEBs1(0) pheA1 trpC2

tag: treatment

value: 4 hours after washing out HPUra


title: HPUra38+2h

value: 2 hours after washing out HPUra


title: HPUra38+3h

value: 3 hours after washing out HPUra


title: 31A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_08.RCC

value: Leukocytes


title: 31N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_07.RCC

value: Week 6

value: PBS


title: 30RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_06.RCC

value: Recombinant antigen


title: HPUra38+1h

value: 1 hour after washing out HPUra


title: Heart tissue, Wild-type, N1 [Heart_WT_N1]


title: 30A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_05.RCC


title: Endothelial cells, POR knockout, N3 [EC_POR-KO_N3]

source_name: Primary cells

value: Primary cells

value: Cardiac endothelial cells


title: HPUra38+0h

value: immediately after washing out HPUra


title: SCR #9


title: participant_2CA1_redoBatch9fail

description: Illumina EPIC 850k methylation data from FFPE brain tissue

value: female

tag: education

tag: flanitot

tag: niaaaascore

tag: niaaabscore


title: participant_2DEN

value: DG

value: dentate gyrus

tag: niaaacscore

tag: adseverityscore


title: control-4h

value: untreated sample 4 hours after HPUra washout


title: participant_2L

value: LC

value: locus coeruleus


title: participant_2B

value: MFG

value: middle frontal gyrus


title: Endothelial cells, POR knockout, N2 [EC_POR-KO_N2]

tag: tissue

tag: cell type

tag: strain background

value: ecPOR-/- (Portm1Ding x Tg(Cdh5-CreERT2)1Rha)

value: POR knockout


title: participant_1N

value: CBM

value: cerebellar cortex

tag: batch


title: Endothelial cells, POR knockout, N1 [EC_POR-KO_N1]


title: control-3h

value: JMA222 is ICEBs1(0) pheA1 trpC2

value: untreated sample 3 hours after HPUra washout


title: 30N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_04.RCC

tag: nanostring plexset set in rcc files

tag: time

value: Week 6

tag: antigen

value: PBS

value: Leukocytes


title: 29A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_02.RCC

value: PPBDA


title: 29RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_03.RCC

value: Recombinant antigen


title: participant_2K_redoBatch9fail

value: SN

value: substantia nigra

tag: Sex

value: female

tag: age


title: participant_1L

value: LC

value: locus coeruleus

tag: genotype


title: Endothelial cells, Wild-type, N3 [EC_WT_N3]

value: Primary cells

value: Cardiac endothelial cells

value: Control


title: Endothelial cells, Wild-type, N2 [EC_WT_N2]


title: Endothelial cells, Wild-type, N1 [EC_WT_N1]


title: control-2h

tag: treatment

value: untreated sample 2 hours after HPUra washout


title: control-1h

value: untreated sample 1 hour after HPUra washout


title: control-0h

value: JMA222 is ICEBs1(0) pheA1 trpC2

value: untreated sample at time of HPUra washout


title: participant_1J2

value: EC

value: entorhinal cortex

tag: education


title: participant_1K

tag: flanitot


title: 28RA,W3

value: Week 6

tag: vaccine

value: Protein particle displaying MAP fusion protein

value: Leukocytes


title: 28A,W3

value: PPBDA


title: Tumor-bearing mouse injected IV, mouse 4

city: Pamplona

first: Jose

last: Gonzalez

state: Navarra

address: C/PIO XII s/n

country: Spain

institute: FIMA

description:
Tumor-bearing omentum mouse 3
IV 4

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to mm39 whole genome using STAR v2.7.9
Read summarization were obtained using featureCounts.
Normalization were performed in R statistical environment following the limma-voom pipeline
Genome_build: mm39
Supplementary_files_format_and_content: Tab-delimited text file includee log2(cpm) values for each gene and every Sample
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts for every gene and every sample

source_name: Omentum of mouse challenged with tumor and injected with OT-1-IL-12 intravenously on day 6

growth_protocol: 7-10-old week C57BL/6 mice were injected with 500,000 cells of B16-OVA cell line IP on day 0. On day 6 mice were randomized.

extract_protocol:
18h after OT-I T cells injection, mice were euthanized and omenta were extracted and stored in RNAlater solution at -80C. RNA extraction was performed using the RNeasy Mini Kit (Qiagen, Hilden, Germany)
Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB) following the manufacturer’s protocol. All sequencing libraries were constructed from 100 ng of total RNA according to the manufacturer's instructions
Briefly, the protocol selects and purifies poly(A) containing RNA molecules using magnetic beads coated with poly(T) oligos. Poly(A)-RNAs are fragmented and reverse transcribed into first cDNA strand using random primers. The second cDNA strand is synthesized in the presence of dUTP to ensure strand specificity. Resulting cDNA fragments are purified with NEBNext purification beads, adenylated at 3′ ends and then ligated with uniquely indexed sequencing adapters. Ligated fragments are purified and PCR amplified to obtain the final libraries. The quality and quantity of the libraries were verified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and 4200 Tapestation with High Sensitivity D1000 ScreenTape (Agilent Technologies). Libraries were then sequenced using a NextSeq2000 sequencer (Illumina). 40 million pair-end reads (100 bp; Rd1:51; Rd2:51) were sequenced for each sample and demultiplexed using Cutadapt. RNA-Seq was carried out at the Genomics Unit of the Center for Applied Medical Research (CIMA, Universidad de Navarra).

treatment_protocol: On day 6 mice were either injected with PBS, or treated with OVA-specific T lymphocytes electroporated with IL-12 mRNA either IP or IV.

tag: strain

tag: cell line

value: IL-12-coding mRNA, intravenously

value: Omentum


title: 28N,W3

value: PBS


title: Tumor-bearing mouse injected IV, mouse 2

description:
Tumor-bearing omentum mouse 2
IV 2


title: participant_1DEN

value: DG

value: dentate gyrus

value: female

tag: niaaaascore

tag: niaaabscore

tag: niaaacscore

tag: adseverityscore


title: 27RA,W3

value: Recombinant antigen

tag: cell type


title: Mouse 2 Tcon

city: Hamburg

first: Roberta

last: Kurelic

address: Martinistrasse 52

department: Institute of Experimental Cardiovascular Research

institute: UKE

description: non-activated T cells

hyb_protocol: custom-made CodeSet for 36 genes was hybridized to total RNA of individual sample for approx. 16 hours at 67°C and cooled down to 4°C afterward

scan_protocol: RNA expression was measured with the NanoString nCounter FLEX Analysis System (NanoString Technologies)

data_processing: expression data were analyzed using the NanoString nSolver Analysis Software 4.0. according to nSolver 4.0 User Manual and in addition to default settings and algorithms within the nSolver Analysis software

label: unique fluorescent barcodes (CodeSet design details)

source_name: murine CD4+ T cells

label_protocol: up to 30 ng of total RNA per sample was used for the hybridization process

growth_protocol: freshly isolated cells were used to isolate total RNA of individual samples

extract_protocol: total RNA of sorted samples was isolated using RNeasy Mini Kit (Qiagen)

treatment_protocol: lymph nodes (superficial cervical, axillary, brachial, inguinal) and spleen from C57BL/6 mice were used for staining of T cell surface markers and afterward FACS-sorting of Tcon and Treg subsets

value: male

tag: age (in weeks)

value: murine CD4+ T cells


title: Tumor-bearing mouse injected IV, mouse 1

description:
Tumor-bearing omentum mouse 1
IV 1

tag: tissue


title: 27A,W3

tag: nanostring plexset set in rcc files

tag: time

tag: antigen


title: 27N,W3


title: Mouse 6 Treg

description: non-activated T cells

tag: Sex


title: Mouse 6 Tcon

description: non-activated T cells


title: Mouse 5 Treg

description: non-activated T cells


title: 29N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_01.RCC


title: Tumor-bearing mouse injected IP, mouse 4

description:
Tumor-bearing omentum mouse 3
IP 4

source_name: Omentum of mouse challenged with tumor and injected with OT-1-IL-12 intraperitoneally on day 6

tag: treatment

value: IL-12-coding mRNA, intraperitoneally


title: 26RA,W3


title: Mouse 5 Tcon

description: non-activated T cells


title: Tumor-bearing mouse injected IP, mouse 3

description:
Tumor-bearing omentum mouse 2
IP 3


title: participant_1F

value: CG

value: cingulate gyrus

tag: batch

tag: age

tag: education

tag: genotype


title: Tumor-bearing mouse injected with PBS, mouse 3

description:
Tumor-bearing omentum mouse 3
PBS3

source_name: Omentum of mouse challenged with tumor and injected with saline solution on day 6

tag: strain

tag: cell line

value: saline solution


title: 26A,W3

value: Week 6

tag: vaccine


title: Mouse 4 Tcon

description: non-activated T cells


title: 25RA,W3

value: Protein particle displaying MAP fusion protein


title: Tumor-bearing mouse injected with PBS, mouse 1

description:
Tumor-bearing omentum mouse 1
PBS1


title: 25A,W3

value: Leukocytes


title: Mouse 3 Treg

description: non-activated T cells


title: Mouse 3 Tcon

description: non-activated T cells


title: Mouse 2 Treg

description: non-activated T cells


title: Mouse1 Treg

description: non-activated T cells


title: Tumor-bearing mouse injected IP, mouse 2

description:
Tumor-bearing omentum mouse 1
IP 2


title: 24A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_11.RCC

value: PPBDA

value: Recombinant MAP fusion protein


title: 24RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_12.RCC


title: Mouse1 Tcon

description: non-activated T cells


title: 26N,W3


title: INPUT_Z4ChIP_Rep2_2hr

city: Oxford

first: Emilia

last: Dimitrova

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
For cChIP-seq, paired-end reads were aligned to the concatenated mouse mm10 and spike-in genomes (mm10+dm6 for Native cChIP and mm10+hg19 for cross-linked cChIP) using Bowtie2 with the ‘-no-mixed’ and ‘-no-discordant’ options. Reads that mapped more than once were discarded and PCR duplicates were removed using Sambamba.
ZC3H4-T7 ChIP-seq was performed without spike-in normalisation. T7-SET1A, H3K4me3 and RNA Pol II sequencing datasets were calibrated to the spike-in Drosophila or human genomes, as described previously (Fursova et al. 2019). For cChIP-seq, the number of mm10 reads were randomly downsampled to reflect the total number of dm6 or hg19 reads in that sample. Furthermore, to adjust for any variation in cell mixing, each sample was adjusted using the percentage of dm6 reads relative to mm10 reads in the relevant input sample. After normalisation, read coverages for individual biological replicates were compared across regions of interest using the multiBamSummary and plotCorrelation functions from deepTools. Biological replicates correlated well with each other and were merged for subsequent analysis. Genome coverage tracks were generated using the pileup function from MACS2.
Assembly: mm10; dm6; hg19
Supplementary files format and content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.

source_name: Input sample for ZC3H4-T7 ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B.

growth_protocol: Mouse embryonic stem cells were grown in Dulbecco’s Modified Eagle Medium (Thermo Fisher Scientific) supplemented with  fetal bovine serum (FBS, 15% Biosera or 10% Sigma), 1x non-essential amino acids (Thermo Fisher Scientific), 2 mM L-glutamine (Thermo Fisher Scientific), 1x penicillin/streptomycin (Thermo Fisher Scientific), 0.5 mM beta-mercaptoethanol (Thermo Fisher Scientific), and 10 ng/ml leukaemia inhibitory factor (produced in-house). ESCs were grown on gelatinised plates at 37⁰C and 5% CO2.

extract_protocol:
Native cChIP-seq was performed as described previously (Fursova et al. 2019). In brief, 5 x 107 ESCs were mixed with 2 x 107 Drosophila SG4 cells and nuclei were released by resuspending in RSB (10 mM Tris HCl pH 8, 10 mM NaCl, 3 mM MgCl2) with 0.1% NP40. Nuclei were pelleted at 1500xg for 5 min and then washed and resuspended in 1 ml MNase digestion buffer (RSB with 0.25 M Sucrose, 3 mM CaCl2, 1x PIC). Each sample was incubated with 200 units of MNase (Fermentas) at 37⁰C for 5 minutes, with gentle inversion. Digestion was stopped by addition of 4 mM EDTA. Following centrifugation at 1500xg for 5 min, the supernatant (S1 fraction) was retained and the remaining pellet was resuspended in 300 μl nucleosome release buffer (10 mM Tris HCl pH 7.5, 10 mM NaCl, 0.2 mM EDTA, 1x PIC), rotated at 4⁰C for 1 hr and then passed five times through a 27G needle using a 1 ml syringe. Following centrifugation at 1500xg for 5 min, the supernatant (S2) was combined with S1 fraction, aliquoted, snap frozen and stored at -80°C. For each IP, 100 μl S1/S2 nucleosomes were diluted to 1 ml total volume in native ChIP incubation buffer (70 mM NaCl, 10 mM Tris HCl, pH 7.5, 2 mM MgCl2, 2 mM EDTA, 0.1 % Triton-X100, 1x PIC) and immunoprecipitated with 3 µl H3K4me3 antibody (Klose Lab) overnight at 4⁰C. IPs were all set up in duplicate for each sample. 100 μl diluted chromatin was also set aside as an input sample. Protein A agarose beads (Repligen) were blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA in native ChIP incubation buffer, overnight at 4⁰C. 40 μl slurry of pre-blocked agarose beads were used to capture antibody-bound nucleosomes at 4⁰C for 1 hr. Beads were then washed 4x with Native ChIP wash buffer (20 mM Tris HCl, pH 7.5, 2 mM EDTA, 125 mM NaCl, 0.1 % Triton-X100, 1x PIC) and 1x TE buffer, pH 8. DNA was eluted by vortexing for 30 min in elution buffer (1% SDS and 0.1 M NaHCO3) and DNA was purified using a ChIP DNA Clean & Concentrator kit (Zymo Research). For each ChIP, DNA from the matched input control (10% of the IP) was also purified. Purified DNA was analysed using ChIP-qPCR.    For double cross-linked T7-SET1A ChIP and ZC3H4-T7 ChIP, 5 x 107 ESCs were fixed with 2 mM DSG (disuccinimidyl glutarate, Thermo Fisher Scientific) for 50 min at 25⁰C and then 1% formaldehyde (methanol-free, Thermo Fisher Scientific) for 10 min. Alternatively, for single cross-linked RNA Pol II ChIP, 5 x 107 ESCs were fixed with 1% formaldehyde for 10 min at 25⁰C. Fixation was quenched using glycine added to 125 mM. Cells were then pelleted at 1000xg for 5 min and washed with PBS. Cross-linked ESCs were mixed with 1 x 105 cross-linked HEK 293T/T7-SCC1 cells (1% formaldehyde, 15 min for SET1A ChIP; a gift from Martin Houlard, Nasmyth lab) or 2 x 106 cross-linked HEK 293T cells (1% formaldehyde, 10 min for RNA Pol II ChIP). Chromatin was prepared by incubation in 1 ml FA-lysis buffer (50 mM HEPES pH 7.9, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.5% NP-40, 0.1% Na-deoxycholate, 0.1% SDS, 1x PIC, 1 mM AEBSF. For RNA Pol II ChIP, EDTA concentration was increased to 2 mM and 10 mM NaF was added fresh) on ice for 10 min. Chromatin was sonicated using a BioRuptor Pico sonicator (Diagenode) at 4⁰C. Sonication was performed using 23-30 cycles of 30s on/30s off at full power, shearing genomic DNA to an average size of 0.5 kb. The sonicated material was pelleted at 20,000xg for 20 min, and the supernatant taken as sonicated chromatin. 300 μg chromatin was used per IP. Chromatin was diluted to 1 ml total volume per IP in FA-lysis buffer. An additional volume of diluted chromatin was taken to use as an input sample. Protein A agarose beads (Repligen) were blocked with 1 mg/ml BSA and 1 mg/ml yeast tRNA in 1x TE buffer at 4⁰C for 1 hr. Chromatin was pre-cleared with agarose beads (40 μl slurry beads per ChIP) at 4⁰C for 1 - 2 hr. The input sample was taken from the pre-cleared chromatin, and the remainder was immunoprecipitated overnight at 4⁰C with the appropriate amount of antibody: T7 (Cell Signalling, D9E1X, 10µl) or RNA Pol II N-terminal domain (Cell Signalling, D8L4Y, 15µl). Antibody-bound chromatin was precipitated for 3 hr at 4⁰C using 40 μl slurry of blocked Protein A agarose beads. Washes were carried out for 5 min each at 4⁰C, using FA-lysis buffer, FA-lysis buffer with 500 mM NaCl, 1x DOC buffer (10 mM Tris HCl, pH 8, 250 mM LiCl, 1 mM EDTA (2 mM EDTA for RNA Pol II ChIP), 0.5% NP-40, 0.5% Na-deoxycholate), and 2 washes with TE buffer (1x PIC and 1 mM AEBSF were added fresh to all wash buffers. 10 mM NaF was also added for RNA Pol II ChIP). DNA was eluted by vortexing for 30 min in elution buffer (1% SDS and 0.1 M NaHCO3). Cross-links were reversed for ChIPs and inputs at 65⁰C overnight with 200 mM NaCl and 2 μl RNase A (Sigma). Samples were then incubated with 20 μg Proteinase K for 1 hr at 45⁰C. DNA for ChIPs and inputs was purified using a ChIP DNA Clean & Concentrator kit (Zymo Research). Purified DNA was analysed using ChIP-qPCR.
cChIP-seq libraries for both ChIP and Input samples were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina, following manufacturer’s guidelines. Samples were indexed using NEBNext Multiplex Oligos. The average size and concentration of all libraries were analysed using the 2100 Bioanalyzer High Sensitivity DNA Kit (Agilent) followed by qPCR quantification using SensiMix SYBR (Bioline, UK) and KAPA Illumina DNA standards (Roche). Libraries were sequenced as 40 bp paired-end reads in biological triplicate on Illumina NextSeq 500 platform.

treatment_protocol: Cell lines expressing dTAG fusion proteins were treated with 100 nM dTAG-13 (produced by Behnam Nabet and Nathanael Gray1 or Carole Bataille and Angela Russell) to induce protein depletion.

value: 100 nM dTAG13

tag: treatment time

tag: replicate

tag: type of chip

value: cross-linked

tag: ChIP

value: Input

tag: antibody


title: 25N,W3

tag: nanostring plexset set in rcc files

value: PBS

tag: cell type


title: INPUT_Z4ChIP_Rep1_2hr


title: 23RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_10.RCC

tag: time

tag: antigen


title: Mouse 4 Treg

description: non-activated T cells

tag: Sex

value: female

tag: age (in weeks)


title: CN32_RpoN_2

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

institute: Twincore

description:
geographical location: Germany: Gießen
Cells were grown in LB to an OD600 =0.5 at 30C and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.

data_processing:
mRNA reads were trimmed using the tool ‘cutadapt’ (version 3.5) with default settings and mapped to the NC_009438.1 (Shewanella putrefaciens CN-32) reference genome from NCBI using ‘bowtie2’ (version 2.3.5.1) with default settings for single-end sequencing.
Assembly: NC_009438.1 (Shewanella putrefaciens CN-32)
Supplementary files format and content: raw unique gene reads.

organism: Shewanella putrefaciens

source_name: CN-32 RpoN mutant

growth_protocol: cell were grown in LB to an OD600 =0.d at 30C

extract_protocol:
The RNeasy Mini Kit (Qiagen) in combination with Qiashredder columns (Qiagen) was used according to the manufacturer’s instruction
The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina).

treatment_protocol: directly after cultivation the cells were treated with one volume of RNAprotect (Qiagen), incubated for 10 minutes at room temperature, centrifuged at 10.000 rpm and cell pellets were frozen at -80°C

value: CN-32 RpoN mutant

tag: geographical location


title: INPUT_Z4ChIP_Rep3_2hr

tag: treatment


title: Tumor-bearing mouse injected with PBS, mouse 2

description:
Tumor-bearing omentum mouse 2
PBS2

tag: tissue

value: Omentum


title: Z4ChIP_Rep3_2hr

source_name: Mouse embryonic stem cells. ZC3H4-T7 ChIP-seq in dTAG-SET1A/B cells depleted of dTAG-SET1A and dTAG-SET1B.

value: anti-T7 (Cell Signalling D9E1X)


title: 23A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_09.RCC


title: CN32_RpoN_1

tag: genotype


title: Z4ChIP_Rep2_2hr

tag: cell line


title: CN32_flrAn_2

source_name: CN-32 flrAn mutant

value: CN-32 flrAn mutant


title: Z4ChIP_Rep1_2hr


title: CN32_flrAn_1


title: 23N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_08.RCC

tag: vaccine


title: 22RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_07.RCC

value: Recombinant antigen


title: M_4_pos

city: Worcester

first: Filiz

last: Korkmaz

address: 364 Plantation St.

institute: UMass Chan Medical School

description: LOX-1+ neutrophils obtained from animals with pneumonia

data_processing:
FASTQ files were aligned to mouse genome build mm10 using STAR (version 2.6.0c).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 1.6.2) and Ensembl annotation build 99 (uniquely aligned proper pairs, same strand).
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Variance-stabilizing transformation (VST) was accomplished using the varianceStabilizingTransformation function in the DESeq2 R package (version 1.22.1).
Differential expression was assessed using the Wald test implemented in the DESeq2 R package (version 1.22.1).
Assembly: All analyses were performed using the R environment for statistical computing (version 3.5.1).
Supplementary files format and content: N/A

source_name: Neutrophils

growth_protocol: Mice were kept in a specific pathogen-free environment, on a 12h light-dark cycle with food and water provided ad libitum. Experimental pneumonia was induced by intratracheal instillation of bacteria for 24h, after which mice were humanely euthanized by isofluorane overdose

extract_protocol:
After FACS-isolation, cells were collected in RPMI containing 10% FBS, immediately spun down & resuspended in Buffer RLT (Lysis Buffer, Qiagen). Lysates were stored in -80C until RNA extraction with the Qiagen RNA Micro Kit performed per manufacturer's instructions.
Library construction performed by BUMSR lab.

treatment_protocol: Alveolar macrophages and neutrophils were collected by bronchoalveolar lavage 24h post-intratracheal instillation of antibody (anti-LOX-1 or control) & 1-3 x 10^6 CFU E. coli & isolated from other cells by fluorescence activated cell sorting (FACS)


title: 22A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_06.RCC

source_name: Leukocytes


title: M_4_neg

description: LOX-1-  neutrophils obtained from animals with pneumonia


title: CN32_fliAn_2

source_name: CN-32 fliAn mutant

value: CN-32 fliAn mutant


title: 22N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_05.RCC


title: CN32_WT_2

source_name: CN-32 WT

value: CN-32 WT


title: 21A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_03.RCC

value: Week 6


title: 21RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_04.RCC


title: CN32_fliAn_1


title: M_3_neg


title: M_2_neg


title: M_3_pos


title: CN32_WT_1


title: 21N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_02.RCC


title: M_2_pos


title: M_1_neg


title: IR10 (array)

city: Memphis

first: Jason

last: Chiang

state: Tennessee

address: 262 Danny Thomas Pl

department: Pathology

institute: St. Jude Children's Research Hospital

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Raw signal intensities from IDAT files were normalized using the functional normalization method implemented in minfi (v.1.38.0). Poor quality (P > 0.01) and failed probes were removed from the downstream analysis. The probes targeting the X and Y chromosomes, containing single-nucleotide polymorphism, and not mapping uniquely to the human reference genome (hg19) were also filtered out.
Identification of differentially methylated probes and regions were performed using limma (v3.48.0) and bumphunter.
Genes within differentially methylated regions were queried against MSigDB v7.4.

label: Cy3 and Cy5

source_name: FFPE brain tumor sample

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was prepared following the instructions of a QIAamp DNA FFPE Tissue Kit.

tag: disease state

value: unresectable, non-NF1-associated, hypothalamic/optic pathway pilocytic astrocytoma

value: Brain

tag: tumor stage

value: tumor

tag: ffpe (yes/no)

value: yes

tag: age (yr)

value: non-treated

tag: tumor grade

value: low-grade

tag: risk (low/intermediate/high)

value: intermediate

tag: outcome

value: not progressed after RT


title: as2-1 10H-CPT

city: Kanazawa

first: Hiro

last: Takahashi

state: Ishikawa

address: Kakuma-machi

country: Japan

institute: Kanazawa University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip ATH1. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChipR Scanner 3000 7G system.

data_processing: The data were analyzed with MAS5.0 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 200.

organism: Arabidopsis thaliana

source_name: Shoot apices

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Col-0 (wild-type), as2-1 mutant plants were grown on Murashige and Skoog (MS) agar medium with and without 10-hydroxyl substituted camptothecin (10H-CPT), which was dissolved in DMSO, under long day condition (16 hours light and 8 hours dark) for 14 days.

extract_protocol: Total RNAs were extracted using RNeasy (QIAGEN).

treatment_protocol: Shoot apices were harvested.

tag: ecotype/background

tag: genotype/variation

value: as2-1 mutant

value: Shoot apex


title: as2-1 DMSO

value: DMSO


title: HR25 (array)

tag: Sex

value: male

value: high

value: progressed after RT


title: M_1_pos


title: 20A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_12.RCC

tag: nanostring plexset set in rcc files

tag: time

tag: antigen

value: PPBDA

value: Recombinant MAP fusion protein

tag: cell type

value: Leukocytes


title: IR19 (array)

value: unresectable, non-NF1-associated, hypothalamic/optic pathway pilocytic astrocytoma

tag: tissue

value: female

tag: treatment


title: Col-0 10H-CPT

value: Wild-type


title: 20N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_11.RCC

value: Week 6

value: PBS

tag: vaccine


title: HR33 (array)

tag: disease state

value: Brain

value: tumor

value: yes

value: non-treated

value: low-grade

value: dead, presumably died of disease


title: 20RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_01.RCC

value: Recombinant antigen


title: 9-11 anti-LOX1 6

description: Alveolar macrophages obtained from animals with pneumonia and treated with anti-LOX1 antibody.

source_name: Alveolar macrophages


title: IR06 (array)

tag: tumor stage

value: male

value: intermediate

value: not progressed after RT


title: IR04 (array)

tag: ffpe (yes/no)


title: BMDM_PRX_LPS24h_rep2

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

description: PRX-treated, LPS-treated

data_processing:
Reads were aligned to the mm9 mouse genome using STAR.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were generated using Homer.

source_name: Bone marrow-derived macrophage

growth_protocol: Bone marrow cells were flushed from femurs and tibias of male mice between 6 and 9 weeks of age, and were grown in RPMI (Nacalai Tesque) supplemented with 10% FBS (HyClone), 1% penicillin–streptomycin (Thermo Fisher), 1% L-glutamine (Thermo Fisher), and 40 ng/ml of recombinant mouse M-CSF (576406; BioLegend) for 7-8 days. The medium was changed every 3 days. Differentiated BMDMs were detached from plates using PBS supplemented with 2% EDTA and replated into 12-well tissue culture dishes at a density of 5 x 105 cells per well prior to cell stimulation.

extract_protocol: Poly-A mRNA was extracted from total RNA by using an NEBNext Poly(A) mRNA magnetic Isolation module (NEB), after which RNA-seq libraries were prepared using a NEBNext UltraII RNA Library Prep kit for Illumina (NEB) according to the manufacturer’s protocol.

treatment_protocol: For LPS treatment, 100 ng/ml of LPS (Sigma-Aldrich) was added to the medium.

tag: strain


title: IR18 (array)

tag: age (yr)

tag: tumor grade


title: Col-0 DMSO

value: Shoot apex

value: DMSO


title: 19RA,W3

value: Recombinant MAP fusion protein

value: Leukocytes


title: 19N,W3


title: HR34 (array)

value: unresectable, non-NF1-associated, hypothalamic/optic pathway pilocytic astrocytoma

tag: risk (low/intermediate/high)

value: high

tag: outcome

value: progression after RT


title: 8-23 anti-LOX1 6


title: 19A,W3

value: Week 6

value: PPBDA


title: IR21 (array)

value: Brain

value: tumor

value: yes

value: female


title: HR03 (array)

value: non-treated

value: low-grade

value: dead after one chemo


title: BMDM_PRX_LPS24h_rep3

description: PRX-treated, LPS-treated


title: IR22 (array)

value: male

value: intermediate

value: not progressed after RT


title: BMDM_PRX_LPS8h_rep2

description: PRX-treated, LPS-treated


title: 9-11 anti-LOX1 4


title: 8-23 IgG 7

description: Alveolar macrophages obtained from animals with pneumonia and treated with IgG.

value: IgG


title: 9-11 anti-LOX1 1


title: 18A,W3

value: Recombinant MAP fusion protein

value: Leukocytes


title: IR24 (array)

value: unresectable, non-NF1-associated, hypothalamic/optic pathway pilocytic astrocytoma


title: HR28 (array)

value: high

value: 3+ chemo


title: 8-23 IgG 3


title: BMDM_PRX_LPS8h_rep1

description: PRX-treated, LPS-treated


title: 9-11 IgG 2


title: BMDM_PRX_LPS8h_rep3

description: PRX-treated, LPS-treated


title: 18N,W3

value: Week 6

value: PBS


title: 18RA,W3

value: Recombinant antigen


title: IR17 (array)

value: Brain

value: tumor

value: yes


title: BMDM_PRX_LPS4h_rep3

description: PRX-treated, LPS-treated


title: HR29 (array)

value: female

value: non-treated

value: low-grade


title: HR26 (array)

value: male

value: metastatic


title: 17RA,W3


title: IR13 (array)

value: intermediate

value: not progressed after RT


title: 8-23 IgG 1

value: IgG


title: BMDM_PRX_LPS24h_rep1

description: PRX-treated, LPS-treated


title: BMDM_PRX_LPS4h_rep2

description: PRX-treated, LPS-treated


title: HR27 (array)

value: unresectable, non-NF1-associated, hypothalamic/optic pathway pilocytic astrocytoma

value: 3+ chemo, progressed after RT


title: IR11 (array)


title: scRNASeq (10X), 6 populations from a pool of 33 C57BL/6 yolk sacs

city: Melbourne

first: Samir

last: Taoudi

address: 1G Royal Parade

country: Australia

institute: The Walter and Eliza Hall Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
For -rds file: data will filtered  with the following criteria: >3000 UMI, >1000 features <5% mitochodrial RNA. Gene counts were scaled with scTransform. Hashtag data (MultiSeq) was integrated and multiplets removed. Seurat clustering was perfomed
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: fully processed file with Seurat clusters and annotation (.rds)

source_name: E10.5 yolk sac

extract_protocol:
Freshly collected yolk sacs were dissociated and separated into 6 pools that were hashtagged using MultiSeq reagents. 6 populations were sorted for those 6 pools, each with a unique hashtag. Populations were combined to run in a single 10X experiment.
Library was performed according to the manufactorer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: E10.5 yolk sac

value: blood (erythocytes, macrophages, haematopoietic progenitors, megakaryocytes), endothelium, mesenchyme

tag: genotype

value: tissue was dissociated with liberase


title: BMDM_PRX_LPS2h_rep3

description: PRX-treated, LPS-treated


title: INPUT_Z4ChIP_Rep2

data_processing:
For cChIP-seq, paired-end reads were aligned to the concatenated mouse mm10 and spike-in genomes (mm10+dm6 for Native cChIP and mm10+hg19 for cross-linked cChIP) using Bowtie2 with the ‘-no-mixed’ and ‘-no-discordant’ options. Reads that mapped more than once were discarded and PCR duplicates were removed using Sambamba.
Sequencing datasets were calibrated to the spike-in Drosophila or human genomes, as described previously (Fursova et al. 2019). For cChIP-seq, the number of mm10 reads were randomly downsampled to reflect the total number of dm6 or hg19 reads in that sample. Furthermore, to adjust for any variation in cell mixing, each sample was adjusted using the percentage of dm6 reads relative to mm10 reads in the relevant input sample. After normalisation, read coverages for individual biological replicates were compared across regions of interest using the multiBamSummary and plotCorrelation functions from deepTools. Biological replicates correlated well with each other and were merged for subsequent analysis. Genome coverage tracks were generated using the pileup function from MACS2.
Assembly: mm10; dm6; hg19
Supplementary files format and content: bigWig files showing the genome coverage for merged spike-in normalised biological replicates were generated using the pileup function from MACS2.

source_name: Input sample for ZC3H4-T7 ChIP-seq in mouse embryonic stem cells.

tag: cell line

value: ESCs

tag: condition

value: untreated

tag: treatment time

tag: replicate

tag: type of chip

value: cross-linked

tag: ChIP

value: Input

tag: antibody


title: INPUT_Z4ChIP_Rep3

value: Input sample for ZC3H4-T7 ChIP-seq in mouse embryonic stem cells.

tag: treatment


title: T23

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Probes were hybridized to microarray slide and incubated at 55°C for 20 hours.

scan_protocol: Microarrays were washed and scanned using the Agilent Microarray Scanner G2505C with Surescan High Resolution Technology.

data_processing:
Feature Extraction v10.7.3.1 software was utilized for feature extraction.
Bioconductor AgiMicroRna R package was applied to retrieve log2-transformed normalized expression for miRNAs annotated on miRBase 19.0

label_protocol: 100 ng of total RNA from each sample were labeled according to the manufacturer’s protocol.

extract_protocol: RNA was extracted with QIAGEN FFPE RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: group

tag: patient diagnosis

value: diffuse intrinsic pontine glioma

tag: tissue

value: serum

tag: gender

value: M

tag: age


title: V24

value: F


title: 17A,W3

tag: nanostring plexset set in rcc files

tag: time

value: Week 6

tag: antigen

value: PPBDA

tag: vaccine

value: Recombinant MAP fusion protein

tag: cell type

value: Leukocytes


title: 16RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_01.RCC

value: Recombinant antigen

value: Silirum®


title: 17N,W3

value: PBS


title: T22


title: BMDM_PRX_LPS2h_rep2

description: PRX-treated, LPS-treated

tag: strain


title: INPUT_Z4ChIP_Rep1

tag: cell line

tag: condition

tag: treatment time


title: BMDM_PRX_LPS4h_rep1

description: PRX-treated, LPS-treated


title: HR16 (array)

tag: disease state

value: unresectable, non-NF1-associated, hypothalamic/optic pathway pilocytic astrocytoma

value: Brain

tag: tumor stage

value: tumor

tag: ffpe (yes/no)

value: yes

tag: age (yr)

tag: Sex

value: male

value: non-treated

tag: tumor grade

value: low-grade

tag: risk (low/intermediate/high)

value: high

tag: outcome

value: progressed after RT, mets, dead


title: 16A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_12.RCC

tag: nanostring plexset set in rcc files


title: 16N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_11.RCC

tag: time


title: Z4ChIP_Rep3

source_name: ZC3H4-T7 ChIP-seq in mouse embryonic stem cells.

value: ESCs

tag: treatment

value: untreated

tag: replicate

tag: type of chip

value: cross-linked

tag: ChIP

tag: antibody

value: anti-T7 (Cell Signalling D9E1X)


title: V23

tag: group

tag: patient diagnosis

value: diffuse intrinsic pontine glioma

tag: tissue

value: serum

tag: gender

value: M

tag: age


title: BMDM_PRX_LPS1h_rep3

description: PRX-treated, LPS-treated

tag: strain


title: Z4ChIP_Rep2

tag: cell line

tag: condition

value: ZC3H4-T7 ChIP-seq in mouse embryonic stem cells.

tag: treatment time


title: Z4ChIP_Rep1


title: BMDM_PRX_LPS1h_rep2

description: PRX-treated, LPS-treated


title: 15RA,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_10.RCC

value: Week 6

tag: antigen

value: Recombinant antigen

tag: vaccine

value: Silirum®

tag: cell type

value: Leukocytes


title: V22

value: F


title: 15A,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_09.RCC

tag: nanostring plexset set in rcc files

tag: time

value: PPBDA


title: 15N,W3

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Silirum®, sample taken 6 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_08.RCC

value: PBS


title: T21


title: V21


title: BMDM_PRX_LPS0h_rep3

description: PRX-treated, LPS-untreated


title: Parg mutant Biological replicate 3

city: Grand Forks

first: Alexei

last: Tulin

state: North Dakota

address: 501 N Columbia Rd Stop 9061

department: Epigenetics Department

institute: University of North Dakota

data_processing:
Illumina FQ sequencing were analyzed with CLC Genomics Workbench, version 12.0.
The reads were trimmed to remove adapters, then mapped to the Dm6 Drosophila melanogaster genome using CLC’s default settings (mismatch cost = 2, Insertion cost = 3, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, auto-detect paired distances, maximum number of hits for a read = 10).
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: dm6
Raw data are provided in the excel spreadsheet named "dPARG27.1_RNAseq_L3ps7-9_Raw_data.xlsx". Column A indicates gene name. Column B indicates the chromosome. Column C indicates the begining of the position of the 5' of the gene and Column D the position of the 3'. Column E indicates the Flybase ID of the gene. Column F indicates the Max group mean between parg mutant and control group. Column G indicates the Fold change while Column H indicates the log2 fold change. Column I indicates t-test p-value while Column J indicates FDR-corrected p-value. Column K to V indicate total read count and RPKM for each samples.

organism: Drosophila melanogaster

growth_protocol: parg mutants larvae were obtained by crossing parg27.1/FM7iG females with FM7iG/Y males. Twelve GFP negative larvae were selected at L3 larva puffstage 7-9. All the GFP negative larvae were males (parg27.1/Y). Control larvae were generating by crossing w1118, y1/FM7iG females with FM7iG/Y males. Twelve GFP negative larvae at L3 larva puffstage 7-9 stage were selected. All GFP negative larvae are males (w1118, y1/Y).

extract_protocol:
Total RNA was purified from whole organism using the QIAshredder column and RNeasy Mini kit (Qiagen, Valencia, CA).
The quality of RNA was determined by Bioanalyzer with the integrity value ranging from 7 to 7.3 between samples. mRNA was enriched based on a Poly(A) selection. Libraries were prepared using NEB’s Ultra II RNA library kit.
Sequencing was performed on the NovaSeq 6000 system (Illumina, USA).

tag: sample type

value: 12 male larvae at L3 larva puffstage 7-9

tag: fraction

value: Whole organism


title: HR13 (array)

tag: disease state

value: unresectable, non-NF1-associated, hypothalamic/optic pathway pilocytic astrocytoma

value: Brain

tag: tumor stage

value: tumor

tag: ffpe (yes/no)

value: yes

tag: age (yr)

tag: Sex

value: male

tag: treatment

value: non-treated

tag: tumor grade

value: low-grade

tag: risk (low/intermediate/high)

value: high

tag: outcome

value: 3+ chemo, metastatic


title: Parg mutant Biological replicate 2

tag: strain


title: BMDM_PRX_LPS2h_rep1

description: PRX-treated, LPS-treated


title: 30N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_07.RCC

value: Week 0

tag: antigen


title: BMDM_PRX_LPS0h_rep2

description: PRX-treated, LPS-untreated


title: HR20 (array)

tag: tissue

value: female

value: progressed after RT


title: 29RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_06.RCC

value: Recombinant antigen

tag: vaccine

tag: cell type

value: Leukocytes


title: T20

tag: group

tag: patient diagnosis

value: diffuse intrinsic pontine glioma

value: serum

tag: gender

value: M

tag: age


title: HR11 (array)

tag: disease state

value: unresectable, non-NF1-associated, hypothalamic/optic pathway pilocytic astrocytoma

tag: tumor stage

value: progression after RT, dead


title: HR15 (array)

value: Brain

value: tumor

tag: ffpe (yes/no)

tag: age (yr)

value: metastatic at diagnosis


title: Control Biological replicate 3

tag: sample type

value: 12 male larvae at L3 larva puffstage 7-9

tag: fraction

value: Whole organism


title: BMDM_PRX_LPS0h_rep1

description: PRX-treated, LPS-untreated


title: V20


title: 29A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_05.RCC

tag: nanostring plexset set in rcc files

tag: time

value: PPBDA


title: BMDM_Veh_LPS24h_rep3

description: Vehicle-treated, LPS-treated

tag: strain


title: T19


title: V19


title: HR10 (array)

value: yes

tag: Sex

value: male

tag: treatment

value: non-treated

tag: tumor grade

value: low-grade

tag: risk (low/intermediate/high)

value: high

tag: outcome

value: 3+ chemo


title: Parg mutant Biological replicate 1


title: 29N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_04.RCC

value: Week 0

tag: antigen

value: PBS

tag: vaccine

tag: cell type

value: Leukocytes


title: Control Biological replicate 2


title: BMDM_Veh_LPS24h_rep2

description: Vehicle-treated, LPS-treated


title: Control Biological replicate 1


title: BMDM_Veh_LPS24h_rep1

description: Vehicle-treated, LPS-treated


title: 28RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_03.RCC

value: Recombinant antigen


title: 28A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_02.RCC


title: HR06 (array)

tag: disease state

value: unresectable, non-NF1-associated, hypothalamic/optic pathway pilocytic astrocytoma

tag: tissue

value: 3+ chemo, metastatic


title: 28N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_01.RCC


title: BMDM_Veh_LPS8h_rep3

description: Vehicle-treated, LPS-treated


title: HR07 (array)

value: Brain

tag: tumor stage

value: tumor

tag: ffpe (yes/no)

value: progressed after RT


title: T18

tag: group

tag: patient diagnosis

value: diffuse intrinsic pontine glioma

value: serum

tag: gender

value: F

tag: age


title: Liver,high, day7, rep4

city: Aberdeen Proving Ground

first: Jennifer

last: Sekowski

state: MD

address: 5183 Blackhawk Rd.

department: BioSciences Division

institute: US Army DEVCOM Chemical Biological Center

data_processing:
Reads were trimmed for adapter sequences using Trimmomatic and filtered for quality using FASTQC. The reads were then aligned to the human genome using HISAT2. Next, to assemble transcripts and estimate their abundances, we processed the date through CuffLinks. The resulting Fragments Per Kilobase of transcript per million mapped reads (FPKM) data was later analyzed with Qlucore Omics Explorer 3.7 software.
Supplementary files format and content: CSV file containing FPKM values for each sample

source_name: liver

growth_protocol: Hepatocyte Seeding- Emulate chips were equilibrated to room temperature and washed 3X with 200 µL of Complete Hepatocyte Seeding Media. The final wash was left in the top and bottom channels of the chips. Human hepatocytes were removed from liquid nitrogen storage and the cryovial was quick thawed in a 37 ֯C water bath. The thawed cell solution was quickly added to 3 mL of warm Complete Hepatocyte Seeding Medium in a 50 mL conical tube. The vial was rinsed with 1 mL of medium, which was then transferred to the 50 mL conical tube.  Complete Hepatocyte Seeding Medium was slowly added to the 50 mL conical tube until the volume was brought to 35 mL. Then, 15 mL of 90% Percoll solution (Sigma Aldrich) in 1X DPBS was slowly layered on top of the 35 mL of cell solution. The cells were centrifuged at 96 x g for 6 minutes at room temperature. The supernatant was carefully aspirated leaving 3 to 5 mL and the pellet undisturbed. The cell pellet was gently resuspended by tilting and rotating the 50 mL conical tube. Complete Hepatocyte Seeding Medium was added to the 50 mL conical tube until the total volume was 50 mL, and the cell solution was centrifuged at 72 x g for 4 minutes at room temperature. The supernatant was carefully removed until the volume was down to 1-2 mL; the pellet was then carefully resuspended as described above. The human hepatocytes were counted in trypan blue solution using a hemocytometer and resuspended to a final cell density of 3.5 x 106 cells/mL in Complete Hepatocyte Seeding Medium. The hepatocyte suspension (50 µL) was then carefully added to the top channel of each chip. After adding the cells, the chips were incubated at 37 ֯C with 5% CO2 for 3 hours (or until the hepatocytes have fully attached). Once the hepatocytes have successfully attached to the channel, a gravity wash was performed on each chip by gently dropping 200 µL of Complete Hepatocyte Seeding Medium on top of both inlet ports of the top and bottom channels. The chips were then incubated overnight at 37 ֯C with 5% CO2.

extract_protocol:
Cell lysates were prepared on ice, using on-chip lysis using lysis buffer (QIAGEN Buffer RLT with 1% Betamercaptoethanol). Briefly, 175 µL of the lysis buffer was added to each of upper and lower channels and allowed to incubate on ice for 1 min. Lysates were then quickly removed from the two channels, combined in RNAse-free cryotubes, and frozen at -80 °C until further processing. RNA was extracted from these samples using the Rneasy® Mini Kit (QIAGEN; Frederick, MD), according to manufacturer’s instructions with minor modifications. Briefly, centrifugation was carried out at 10,000 x g and spun for 30s. On-column extraction was performed by incubating 30 µL RNase-free water directly on the spin column membrane for 2 min, followed by elution at 10,000 x g for 1 min. The eluate was run through the column again using the above centrifugation parameters and then stored at -80 °C for later analysis. The extracted samples were then quantified on a Qubit™ 4 Fluorometer using the Qubit™ RNA High Sensitivity (HS) Assay Kit following the recommended protocol in the Qubit Assay Kit User Guide. Further quantification and qualification was performed on a 2100 Agilent Bioanalyzer according to the Agilent RNA 6000 Nano Kit Guide. All samples with a RNA Integrity Number (RIN) higher than 8 were used in further analysis.
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit was used for library generation. The protocol and corresponding calculations were carried out following the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus Reference Guide with minor modifications. Centrifugation steps were at 280 x g for 1 min as opposed to the recommended 10 s due to plate centrifuge limitations. Library samples were then quantified using the Qubit 1X dsDNA High-Sensitivity (HS) Assay Kit and measured on a Qubit™ 4 Fluorometer, using manufacturer’s recommended parameters. To assess the quality and quantity during the preparation steps, library samples were measured on a 2100 Agilent Bioanalyzer according to the Agilent High Sensitivity DNA Kit Guide.

treatment_protocol: VX was synthesized and purified (99.1 %) by U.S. Army DEVCOM CBC in accordance with international regulations. Neat VX was then diluted into a working stock of 1 mg/mL in DMSO. Experimental VX dilutions were prepared from working stocks by diluting agent in NPC Maintenance Medium without FBS to final concentrations of 6.25 µM, 12.5 µM, and 25 µM. A vehicle control was also prepared by diluting cell culture grade DMSO in NPC Maintenance Medium to a final concentration of 0.6 %. The bottom channel inlet reservoir medium was aspirated and replaced with 3 mL of medium containing either VX or vehicle control (DMSO), so that the experimental compound would be introduced on the endothelial channel (similar to a potential in vivo exposure). The Pods were returned to the Zoë and the VX exposure was initiated by increasing the flow rate of the Zoë to 600 µL/h for 5 minutes. The flow rate was then returned to 30 µL/h. After 24 hours, the cells from 12 of the chips were trypsinized, pelleted, and flash frozen in liquid N2. Cell pellets were stored at -80 °C before protein, metabolite, and RNA extractions were performed.

value: liver

value: male

tag: day

value: VX


title: BMDM_Veh_LPS8h_rep2

description: Vehicle-treated, LPS-treated

tag: strain


title: Liver,high, day7, rep3

tag: treatment


title: Liver,high, day7, rep2


title: BMDM_Veh_LPS4h_rep3

description: Vehicle-treated, LPS-treated


title: Liver,high, day7, rep1


title: HR14 (array)

value: yes

tag: age (yr)

tag: Sex

value: non-treated

tag: tumor grade

value: low-grade

value: high

value: metastatic, dead


title: T17

value: M


title: V18


title: Liver, medium, day7, rep4


title: V16


title: 27A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_11.RCC

data_processing: The data were normalized for lane-to-lane variation with a dilution series of six spike-in positive controls using vsn normalization

tag: nanostring plexset set in rcc files

tag: time

value: Week 0

tag: antigen

value: PPBDA

value: Leukocytes


title: 27RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_12.RCC

value: Recombinant antigen

tag: vaccine

tag: cell type


title: 27N,W0_rep1

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_10.RCC

value: PBS


title: T16

value: diffuse intrinsic pontine glioma

tag: tissue


title: V17

value: serum


title: HR08 (array)

tag: disease state

value: unresectable, non-NF1-associated, hypothalamic/optic pathway pilocytic astrocytoma

value: Brain

tag: tumor stage

value: tumor

tag: ffpe (yes/no)

value: female

tag: risk (low/intermediate/high)

tag: outcome

value: 3+ chemo


title: 26RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_09.RCC


title: Liver, medium, day7, rep3

value: liver

tag: gender

value: male

tag: day

value: VX


title: V15

tag: group

tag: patient diagnosis

value: F

tag: age


title: BMDM_Veh_LPS8h_rep1

description: Vehicle-treated, LPS-treated

tag: strain


title: Liver, medium, day7, rep2

tag: treatment


title: BMDM_Veh_LPS4h_rep1

description: Vehicle-treated, LPS-treated


title: T15

value: M


title: 26A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Protein particle displaying MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_08.RCC

tag: nanostring plexset set in rcc files

tag: time

value: Week 0


title: BMDM_Veh_LPS4h_rep2

description: Vehicle-treated, LPS-treated


title: Liver, medium, day7, rep1


title: 26N,W0

tag: antigen

tag: vaccine

value: Protein particle displaying MAP fusion protein


title: BMDM_Veh_LPS2h_rep3

description: Vehicle-treated, LPS-treated


title: Liver, low, day7, rep4

tag: tissue


title: V14


title: BMDM_Veh_LPS2h_rep1

description: Vehicle-treated, LPS-treated


title: Liver, low, day7, rep3


title: 25RA,W0

tag: cell type

value: Leukocytes


title: T14


title: BMDM_Veh_LPS1h_rep3

description: Vehicle-treated, LPS-treated


title: BMDM_Veh_LPS1h_rep2

description: Vehicle-treated, LPS-treated


title: Liver, low, day7, rep2


title: 25A,W0

value: PPBDA


title: 25N,W0

value: PBS


title: BMDM_Veh_LPS1h_rep1

description: Vehicle-treated, LPS-treated


title: T13

value: diffuse intrinsic pontine glioma


title: V13

value: serum


title: 24RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_03.RCC

value: Recombinant antigen

value: Recombinant MAP fusion protein


title: Liver, low, day7, rep1


title: T12


title: 24N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_01.RCC


title: 24A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_02.RCC


title: BMDM_Veh_LPS2h_rep2

description: Vehicle-treated, LPS-treated


title: Liver, control, day7, rep3

value: control


title: BMDM_Veh_LPS0h_rep3

description: Vehicle-treated, LPS-untreated


title: BMDM_Veh_LPS0h_rep2

description: Vehicle-treated, LPS-untreated


title: V11


title: 23RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_12.RCC


title: BMDM_PRX_LPS1h_rep1

description: PRX-treated, LPS-treated


title: Liver, control, day7, rep2


title: V12


title: BMDM_Veh_LPS0h_rep1

description: Vehicle-treated, LPS-untreated


title: Liver, control, day7, rep1


title: Liver, control, day7, rep4


title: 23A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_11.RCC


title: Liver,high, day1, rep4


title: V10


title: 22RA,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_09.RCC


title: 23N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_10.RCC


title: Liver,high, day1, rep3


title: T10


title: GRTH-KO (KO)

city: BETHESDA

first: Veronica

last: Gomez-Lobo

address: 10 Central Dr. Bldg10, Rm 8N248

institute: NIH

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Testis

extract_protocol:
Testicular cells were prepared individually from three different adult mice (WT, KO and KI) following two-step enzymatic digestion. Testes from each mouse were dissected and tunica albuginea was removed. The seminiferous tubules were treated with collagenase type-I in M199 medium containing 0.1% bovine serum albumin (BSA) for 10 mins at 35°C and dispersed by gently shaking in between. The collagenase treated tubules were minced and incubated in M199 with 0.1% BSA and 0.1% trypsin for 10 mins at 35°C in rotation at 100 rpm to obtain dispersed cell suspension. The trypsin digestion was stopped by adding 0.02% of trypsin inhibitor (Sigma) to the sample. Cells were filtered through 100 µm and then with 40 µm cell strainer (Millipore) to obtain single cell suspension fraction, pelleted at 800g for 2 mins, washed and resuspended in cold M199 with 0.1% BSA for scRNA-seq.
scRNA-seq libaray of testicular cells was prepared according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). In brief, freshly prepared cell suspension (7,000 cell for each sample) was loaded into Chromium microfluidic chips used to generate single-cell gel bead emulsions using the 10X Genomics Chromium controller as per manufacturer’s protocol. Each scRNA-seq library was constructed following the manufacturer’s instructions. Sequencing of libraries was performed for 100 cycle paired-end run on an Illumina HiSeq 2500 instrument.

value: Testicular cells

value: Testis

value: 8 weeks old


title: GRTH-KI (KI)

description: 10x Genomics


title: Wild Type (WT)

description: 10x Genomics


title: T11


title: Liver,high, day1, rep1

value: liver

value: male


title: Liver, medium, day1, rep4

value: VX


title: T09

value: F


title: V09


title: V08

value: M


title: T08


title: 21RA,W0

city: Lincoln

first: Paul

last: Maclean

address: Cnr Springs Road and Gerald Street

institute: AgResearch NZ LTD

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with Recombinant antigen antigen
20200724_cJD Immune Run-2 555_01_06.RCC

extract_protocol: Total RNA was isolated from the samples using RNeasy kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany).

value: Week 0


title: DC+MTX 4

city: Gent

first: Dmitri

last: Krysko

address: C. Heymanslaan 10, 4B3

department: Department of Human Structure and Repair

country: Belgium

institute: Ghent University

data_processing:
Read quality was checked for each sample using FastQC v0.11.5.
Then the paired-end reads were mapped to the Ensembl Mus musculus GRCm39 genome using the BWA-MEM v.0.7.17.
Gene quantification was calculated by using featureCounts v2.0.1.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: BMDCs

growth_protocol: Murine glioma GL261 cells were cultured at 37°C under 5% CO2 in DMEM containing 4.5 g/L glucose and supplemented with 2 mM glutamine, 100 µM sodium pyruvate, 100 units/ml penicillin, 100 µg/L streptomycin and 10% fetal bovine serum, all purchased from Thermo Fisher Scientific.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (QIAGEN).
The TruSeq Stranded mRNA kit (Illumina) was used to prepare a RNA-seq library according to the manufacturer’s protocol, followed by PE100 cycles sequencing on one lane of a NovaSeq 6000 S1 run (Illumina).

treatment_protocol: Cell death was induced by photosens (PS)-based PDT or mitoxantrone (MTX, Sigma Aldrich). For PS-PDT, GL261 cells were first incubated with 1.4 µM PS in serum-free DMEM for 4 h and then irradiated with a light dose of 20 J/cm2 in photosensitizer-free media. After PDT, the cells were cultured in complete DMEM for 24 h. For MTX induction, the cells were cultured in full medium with 2.0 µM MTX for 24 h. Cells loaded with PS or MTX were handled in the dark or in subdued light. DCs isolated from four C57BL/6J mice were used for each experimental group. DCs were cocultured for 6 h with dying/dead glioma GL261 cells in a ratio of 1:5. There were three experimental groups: DCs alone (negative control), DCs cocultured with glioma GL261 cells pulsed with PS-PDT (PS at a dose of 1.4 µM, 24 h) or MTX (positive control, 2 µM, 24 h).

value: BMDCs

tag: cell line

value: glioma

tag: genotype

value: wild type

value: MTX 2.0 microM


title: 22N,W0_rep1

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_07.RCC

value: PBS

value: Leukocytes


title: Liver, medium, day1, rep3


title: DC+MTX 3


title: DC+MTX 2


title: V07

value: diffuse intrinsic pontine glioma

value: serum


title: Liver, medium, day1, rep2


title: Liver,high, day1, rep2


title: 21A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_05.RCC

value: PPBDA

value: Recombinant MAP fusion protein


title: 21N,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PBS antigen
20200724_cJD Immune Run-2 555_01_04.RCC


title: T07


title: DC+MTX 1


title: 20RA,W0

value: Recombinant antigen


title: DC+PS-PDT 4

value: PS 1.4 microM


title: Liver, low, day1, rep4

value: liver

value: male


title: 22A,W0

description:
Leukocytes from heparinized blood samples, from animal vaccinated with Recombinant MAP fusion protein, sample taken 0 weeks after vaccination, stimulated with PPBDA antigen
20200724_cJD Immune Run-2 555_01_08.RCC


title: V06


title: DC+PS-PDT 3


title: BM_Control

city: Ottawa

first: David

last: Cook

state: ON

address: 501 Smyth Rd

department: Cancer Therapeutics Program

country: Canada

institute: Ottawa Hospital Research Institute

description: 10x Genomics

data_processing:
Transcripts were quantified from sequencing files using Cellranger (v7.0.0) with default parameters
Assembly: mm10 (GRCm38)
Supplementary files format and content: UMI count matrix

source_name: Bone marrow

extract_protocol:
Femur and tibiae were collected from 2 mice and flushed with 5mL of cold complete media (RPMI +Glutamax, 10% fetal bovine serum (FBS), 1% PenStrep) per mouse. Bone marrow was subsequently passed through a 70µm cell strainer, and collected cells were washed in 25mL of complete media and centrifuged at 600g for 4 minutes at 4˚C. Red blood cell lysis was then performed in 3mL of ACK Lysis Buffer (A1049201, Gibco) for 3-5 minutes at room temperature. Cells were washed with 25mL complete media and cryopreserved at -80˚C in freezing medium containing 15% DMSO, 20% FBS and 65% complete media at a final concentration of 1.0 x 107 cells/mL.
Barcoding of individual biological samples was performed as described by McGinnis et.al.(2019). Thawed cells were suspended in 150 μLs solution containing a 1:1 molar ratio (200nM) of anchor and barcode oligonucleotide containing a unique sequence for each sample to be processed. Samples were incubated for 10 minutes at room temperature with gentle mixing every 3-5 minutes. Next, a co-anchor (200nM) was added to stabilize the barcodes within the cell membrane and incubated for additional 5 minutes. Cells were washed twice in PBS,  cell counts were measured using a Countess(TM) automated counter (Thermofischer Scientific, Burlington, ON, Canada), and viability was measured based on the ratio of cells staining with trypan blue (Thermofischer Scientific, Burlington, ON, Canada). An equal number of cells from each sample was pooled and 1000 cells/μL were further processed using the 10x Genomics Chromium scRNA-seq 3' v3 kit.

value: Bone marrow


title: Liver, low, day1, rep2

value: VX


title: DC+PS-PDT 2


title: T06

value: F


title: 19RA,W0

value: Week 0


title: 20N,W0


title: 19A,W0


title: Liver, low, day1, rep1


title: Liver, medium, day1, rep1


title: DC 4

value: BMDCs

value: untreated


title: T05


title: V04


title: Liver, control, day1, rep3

value: control


title: 19N,W0

value: PBS


title: 18RA,W0

value: Leukocytes


title: DC 3

value: wild type


title: V05

value: diffuse intrinsic pontine glioma

value: serum


title: DC 1


title: Liver, low, day1, rep3


title: 20A,W0

value: PPBDA

value: Recombinant MAP fusion protein


title: T04


title: 18A,W0


title: V02

value: M


title: 18N,W0


title: T03


title: Liver, control, day1, rep1

value: liver


title: DC+PS-PDT 1

value: glioma

value: PS 1.4 microM


title: Liver, control, day1, rep4

value: male