title: p77026: serum sample 23

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
Sequencing was performed on a Illumina HiSeq 2500 with 50 bp single-end runs. Overall quality of the next-generation sequencing data was evaluated automatically and manually with fastQC v0.11.8 (Andrews 2010) and multiQC v1.7 (Ewels et al. 2016 ). Reads from all passing samples were adapter trimmed and quality filtered using cutadapt v2.3 (Martin 2011 ) and filtered for a minimum length of 17nt. Mapping steps were performed with bowtie v1.2.2 (Langmead  et al. 2009) and miRDeep2 v2.0.1.2 (Friedländer et al. 2012 ), whereas reads were mapped first against the genomic reference GRCh38.p12 provided by Ensembl (Zerbino et al. 2018 ) allowing for two mismatches and subsequently miRBase v22.1 (Griffiths-Jones 2004 ), filtered for miRNAs of hsa only, allowing for one mismatch. For a general RNA composition overview, non-miRNA mapped reads were mapped against RNAcentral (Sweeney et al. 2019 ) and then assigned to various RNA species of interest.
Genome_build: GRCh38.p12

source_name: serum

growth_protocol: Eight healthy participants were enrolled in this study. All voluntary participants were recruited and included at the University Clinic Düsseldorf after written informed consent. The study was conducted in accordance with the Declaration of Helsinki. The study protocol was approved by the German Ethics Committee (Medical Faculty of the University Hospital Duesseldorf, Germany) and by the French Ethics Committee (Medical Faculty of the University of Caen). The inclusion criteria were defined as: age >18 years; airworthiness; cardiorespiratory health; spontaneous circulation; signed informed consent. The exclusion criteria were defined as: history of primary cardiovascular and respiratory diseases or regular intake of medication except for oral contraceptives, missing or withdrawal of informed consent, insufficient requirements for airworthiness and pregnancy. Further details  have been published in a study-outline paper (21).

extract_protocol:
Serum samples were thawed at room temperature followed by centrifugation at 12,000xg for 5 minutes at 4°C to remove any cellular debris. Extraction was conducted by use of the miRNA easy QIAgen kit. For homogenization, 200 µL of serum were mixed with 1000 µL Qiazol and 1 µL of a mix of 3 synthetic spike-in controls (Qiagen, Germany). After a 10-minute incubation at room temperature, 200 µL chloroform were added to the lysates followed by cooled centrifugation at 12,000g for 15 minutes at 4°C. Precisely 650 µL of the upper aqueous phase were mixed with 7 µL glycogen (50mg/mL) to enhance precipitation. Samples were transferred to a miRNeasy mini column, and RNA was precipitated with 750 µL ethanol followed by automated washing with RPE and RWT buffer in a QiaCube liquid handling robot. Finally, total RNA was eluted in 30 µL nuclease free water and stored at -80°C until further analysis.
Equal volumes of total RNA (2 µl) were used for small RNA library preparation using the CleanTag smallRNA library preparation kit (TriLink Biotechnologies, US). Adapter-ligated libraries were amplified using barcoded Illumina reverse primers in combination with the Illumina forward primer. A pool consisting of all 24 sequencing libraries was prepared by mixing samples at equimolar rates on the basis of a DNA-1000 high-sensitivity bioanalyzer results (Agilent, CA). The DNA library pool was gel-purified to enrich for microRNA insert sizes at around 145bp.

treatment_protocol: The term “Parabolic flight” denominates a special aerial manoeuvre, in which the aircraft follows the trajectory of a parabola. By means of this manoeuvre, short phases of weightlessness and hypergravity can be induced. After starting at steady flight (1g), an up to 47° ascent initiates a phase of hypergravity (1,8 g). After the climb, the plane is decelerated and directed into descent to follow the trajectory. In this state, a phase of weightlessness is achieved (0g). With the plane tilting forward, an up to 45° descent is initiated, again inducing a phase of hypergravity (1.8g), before re-entering the steady flight (1g) (22). Each of the phases averages 20-25 seconds respectively. The present study performed in the course of the 31st Parabolic Flight Campaign (PFC) of the German space agency (Deutsches Zentrum für Luft- und Raumfahrt - DLR) conducted by the company NoveSpace, which took place from February 26th to March 11th, 2018 in Bordeaux, France. The aircraft used in this campaign was a modified Airbus A-310. The PFC consisted of 4 flight days, with 31 parabolic flight manoeuvres per flight day. Each study subject participated in one complete flight day. In all participants serum samples were withdrawn before entering the plane 1 hour prior to take off (baseline – XX:XX), one hour after exposure to weightlessness (XX:XX) and 24 hours after exposure to weightlessness (XX:XX). At each of the time points, serum samples were collected with individual punctures. For each blood withdraw, the following materials were used: BD vacutainer tubes (Becton Dickinson, Mountain View, CA), 3 SST tubes (Reference # 367957, Tube size: 75×13mm, draw volume: 3,5ml), 1 SST tube (Reference # 367955, Tube size: 100×13mm, Draw volume: 5ml. After completion of each blood-draw, serum samples aliquots were frozen and stored at -80 C° until further analysis.

value: serum

tag: subject id (donor)

tag: time point


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D12_AD001

status: Public on Nov 16 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: strain

tag: age

tag: tissue

value: brain

tag: source

value: ACA

tag: target

value: STR

tag: gender

value: male


title: KMT2D Mutant H3K27ac_ChIPseq

city: Houston

first: Mahinur

last: Mattohti

state: TX

address: 6670 Bertner Ave

department: Surgery

institute: Houston Methodist Research Institute

data_processing:
ChIPseq reads were aligned to mm9 genome using bowtie1 with max 1 mismatch, duplicated reads were removed
peaks were called using MACS14 and MACS2 using pvalue cutoff of 1e-5, and was further filtered for downstream analysis using a more stringent cutoff of 1e-9
bigwig files were generated by deeptools bamCoverage normalized by RPKM
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contains the ChIPseq signal normalized by RPKM. Bed files contain the peaks called by MACS14

source_name: KMT2D Mutant

growth_protocol: Cells were maintained in DMEM, high glucose, GlutaMAX™ Supplement, HEPES and 1% antibiotic-antimycotic.

extract_protocol:
Crosslinked KMT2D WT and Mutant samples were thawed on ice and resuspended in RIPA lysis buffer supplemented with protease inhibitor, lysed the cells on ice then sheared the chromatin by sonication. After centrifuge, the clean sonicated cell lysate mixed with protein G magnetic dynabeads (Invitrogen) coupled to antibodies described above and incubated over night at 4 degrees. Samples was washed 5 times with cold RIPA, twice with high salt RIPA, twice with LiCl buffer, twice with TE, and then eluted in elution buffer. The eluate was reverse crosslinked at 65C. Solid-phase reversible immobilization (SPRI) cleanup steps were performed. Beads were washed twice on the magnet with 70% ethanol and then air-dried. The DNA was eluted in EB buffer.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.

treatment_protocol: KMT2D mutant mice were crossed with iBIP mice (iBIP = Tyr-CreERT2, Rosa26-rtta, TetO-BRAFV600E, PTENL/L, INK/ARFL/L; mixed genetic background of FVB and B6 (REF)) to generate iBIP;KMT2DL/+ genotype containing mice (as assessed by genotyping for all alleles). The iBIP;KMT2DL/+ males and females were mated to generate iBIP;KMT2D+/+, iBIP;KMT2DL/+, and iBIP;KMT2DL/L genotype containing cohorts. They were put on doxycycline and 4-OHT (1uM) was applied on the ears to generate auricular tumor. KMT2D WT and KO murine cells isolated from iBIP;KMT2D+/+ and iBIP;KMT2DL/L mice.

tag: cell type

value: iBiP melanoma mouse model tumor cell

tag: chip antibody

tag: genotype/variation

value: mutant


title: p77027: serum sample 24

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: BL


title: elST_3

city: Beijing

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

country: China

institute: Peking Union Medical College

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
fragments per kilobaseof exon per million fragments mapped (FPKM) were calculated using StringTie
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Testis

extract_protocol:
6 distinct germ cells were isolated from the testes of male mice based on STA-PUT velocity sedimentation.RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: elST

value: ICR

value: post natal day 56


title: KMT2D Mutant H3K4me1_ChIPseq


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D10_AD010

value: AI

value: female


title: KMT2D WT Input DNA

source_name: KMT2D WT

value: wild type


title: p77024: serum sample 21


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D10_AD007


title: elST_1

value: Testis


title: rST_3

value: rST

value: post natal day 35


title: KMT2D WT H3K27me3_ChIPseq


title: p77023: serum sample 20

value: serum


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D10_AD006

value: brain


title: rST_2


title: MAX IP in sgMGA transduced A549 cells set#1

city: Seattle

first: Haritha

last: Mathsyaraja

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutch

data_processing:
Library strategy: CUT&RUN
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Alignment to hg38 with Bowtie 2,  reads >700bp filtered out, samples spike-in normalized
BigWigs were created using bedtools (genomecov) and WigToBigWig scripts
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: A549 lung adenocarcinoma

growth_protocol: Human lung adenocarcinoma line A549 cells were cultured in 10% FBS containing DMEM. They were transduced with vectors (lentiCRISPRv2 Empty and sgMGA). Cells were selected using puromycin.

extract_protocol: CUT&RUN libraries were prepared for sequencing using custom protocols

treatment_protocol: Cells were bound to ConA beads and incubated with antibodies (1 million cells per antibody)

value: lung adenocarcinoma

tag: cell line

tag: antibody

value: MAX IP

tag: transduction

value: sgMGA


title: KMT2D WT H3K4me3_ChIPseq

value: iBiP melanoma mouse model tumor cell


title: m_15733_wt

city: Montreal

first: André

last: Veillette

state: QC

address: 110 Des Pins Ouest Rm1065

department: Molecular Oncology

country: Canada

institute: IRCM

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to the reference mouse genome version GRCm38 (gene annotation Ensembl v98) using STAR version 2.5
Gene expressions are obtained with featureCounts v1.5
DESeq2 version 1.14.1 was used to normalize raw counts and compute differential expression between wt and ko conditions.
Genome_build: GRCm38
Supplementary_files_format_and_content: normalized count matrix from DESeq2

source_name: Germinal center B cells

growth_protocol: AID-GFP reporter mice

extract_protocol:
GFP+ cells were sorted for total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Immunized with NP(18)OVA + alum, splenocytes isolated on Day 9

value: Germinal center B cells

tag: cell population

value: AID-GFP+ cells

tag: genotype

value: wildtype

tag: treatment

value: Immunized, on Day 9


title: p77022: serum sample 19

tag: subject id (donor)


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D10_AD004

value: ACA

value: STR


title: KMT2D WT H3K79me2_ChIPseq


title: rST_1

value: ICR


title: p77021: serum sample 18

tag: time point

value: BL


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D10_AD002

tag: strain

value: male


title: pacSC_3

value: pacSC

value: Testis

tag: age

value: post natal day 21


title: p77020: serum sample 17

tag: tissue

value: serum


title: p77025: serum sample 22


title: KMT2D WT H3K27ac_ChIPseq

value: wild type


title: pacSC_2


title: elST_2

value: elST

value: post natal day 56


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C9_AD012

value: brain

tag: source

value: AI

value: female


title: KMT2D WT H3K4me1_ChIPseq

value: iBiP melanoma mouse model tumor cell


title: pacSC_1


title: p77018: serum sample 15


title: TMEV + miR-219 [AM-300]

city: Chicago

first: Ana

middle: Lis

last: Moyano

state: IL

address: 808 South Wood Street

department: Anatomy and Cell Biology

institute: University of Illinois at Chicago

description:
AM-300_S22
AM.300#1

data_processing:
Raw reads were aligned to the reference genome using BWA MEM (Li and Durbin, Bioinfomatics, 2010)
Gene expression levels  were quantified using FeatureCounts (Liao etal., Bioinformatics, 2014), first as raw read counts suitable for differential expression analyses, and also normalized to reads-per-million for direct comparison between samples. Differential expression statistics (fold-change and p-value) were computed using edgeR (McCarthy et al., Nucleic Acids Res, 2012 and Rppbinson et al. Bioinformatics, 2009) on raw expression.
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements normalized

source_name: TMEV + miR-219

extract_protocol:
Total RNA (including small RNAs) was purified from tissues or cell cultures using the miRVana™ miRNA isolation kit per manufacturer’s instructions (Life technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SJL

tag: Sex

tag: tmev infection

value: YES

value: Cervical spinal cord


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C9_AD006

value: ACA

tag: target

value: STR

tag: gender


title: plpSC_3

tag: cell type

value: plpSC

value: ICR

value: post natal day 14


title: p77017: serum sample 14


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C9_AD004


title: TMEV + veh [AM-233]

description:
AM-233_S9
AM.233#1

source_name: TMEV + veh


title: p77016: serum sample 13


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C9_AD002

value: male


title: TMEV + miR-scr [AM-228]

description:
AM-228_S8
AM.228#1

source_name: TMEV + miR-scr


title: p77015: serum sample 12

value: serum

value: BL


title: plpSC_1

value: Testis


title: priSG-B_3

value: priSG-B

value: post natal day 9


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C9_AD001

value: brain


title: TMEV + miR-scr [AM-226]

description:
AM-226_S4
AM.226#1

value: female


title: p77014: serum sample 11


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_D10_AD001


title: p77019: serum sample 16


title: TMEV + miR-219 [AM-188]

description:
AM-188_S18
AM.188#1


title: p77013: serum sample 10


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C8_AD010

value: AI


title: TMEV + miR-219 [AM-187]

description:
AM-187_S11
AM.187#1

value: SJL


title: p77012: serum sample 9


title: priSG-B_1


title: priSG-B_2


title: priSG-A_3

value: priSG-A

value: post natal day 6


title: control [AM-296]

description:
AM-296_S30
AM.296#1

source_name: control

value: NO

value: Cervical spinal cord


title: plpSC_2

value: plpSC


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C8_AD008

value: STR


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C8_AD007


title: TMEV + veh [AM-139]

description:
AM-139_S29
AM.139#1

value: YES


title: priSG-A_2

value: ICR


title: p77010: serum sample 7

value: serum


title: p77011: serum sample 8


title: TMEV + veh [AM-140]

description:
AM-140_S27
AM.140#1


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C8_AD004

value: ACA


title: priSG-A_1

value: Testis


title: control [AM-138]

description:
AM-138_S19
AM.138#1


title: p77009: serum sample 6


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C8_AD012


title: control [AM-134]

description:
AM-134_S21
AM.134#1


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C8_AD001

value: male


title: Sample_Liver-LU-8

city: Daegu

first: Ri

last: Ryu

address: 80 Daehak-ro

department: Food Science and Nutrition

country: South Korea

institute: Kyungpook National University

description: LU added high-fat diet_mRNA

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence
Mapped to M. musculus whole genome using the aligner bowtie2 version 2.2.3 with tophat 2.0.12
Transcripts were assembled and quantitated using Cufflinks v2.2.1
Genome_build: M. musculus Ensembl 77
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for "ND","HFD", "CLE" and "LU" sample.

source_name: Mouse liver tissue

growth_protocol: Forty male C57BL/6J mice (four-week-old, male) were obtained from the Jackson Laboratories (Bar Harbor, ME, USA). All mice were individually housed under a constant temperature (24°C) and 12-h light/dark cycle and, fed a normal chow diet for acclimation for 1 week after arrival.

extract_protocol:
Total RNA was extracted from liver tissue using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.
Libraries were constructed from mRNA using the Illumina TruSeq RNA Sample Prep Kit following  manufacturer's protocols.

treatment_protocol: At 5 weeks of age, they were randomly divided into 4 groups and fed a normal diet (ND), high-fat diet (HFD), HFD + 1.5% (w/w) chrysanthemum leaf ethanol extract (CLE), HFD + 0.003% (w/w) luteolin (LU) for 16 weeks

value: 21 weeks

value: Liver


title: Sample_Liver-LU-3

description: LU added high-fat diet_mRNA


title: BT12 cells, IPAc, mithramycin 18h_F, ChIP-seq

city: Philadelphia

first: Patrick

last: Grohar

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Libraries were sequenced using 2x50 bp sequencing on the Illumina NovaSeq platform at the Van Andel Research Institute. Data were demultplexed using bcl2fastq v2.20.0.
Reads were aligned using bwa mem, duplicate marked with samblaster, and filtered and converted to BAM format using samtools. Aligned reads were retained if they were aligned and had a minimum mapping quality of 20 (e.g. -F 4 -q 20 flags in samtools). BAMs were ingested into R (v3.6.1) and processed using csaw (v1.18.0). Briefly, a 150 bp sliding window with a 50 bp step-size was used to summarize the read counts with a maximum fragment size set to 800 bp. Next, the background was estimated using a 5kb sliding window where reads were binned and summarized. Regions were excluded if they overlapped known blacklist regions in hg19. Regions having signal greater than log2(3) fold-change over background were retained for differential binding analysis. The first principal component was regressed out of the data due to a batch effect being present prior to downstream analysis. Differential binding analysis was carried out using csaw and edgeR, fitting a quasi-likelihood (QL) negative binomial generalized log-linear model that estimates the prior QL dispersion distribution robustly. Differences were tested using an anova-like test or individual contrasts to generate initial differentially bound regions (DBR). Windows were merged with a maximum width of 5kb and a tolerance of 100bp between adjacent windows to consider being combined. Next, p-values were combined across clustered sites using Simes’ method to control the cluster false discovery rate as implemented in the combineTests function in csaw. Finally, clustered DBRs were defined as having a q < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files for raw and lambda corrected (pc1_corrected) peaks from all samples.

source_name: Atypical Teratoid/Rhabdoid Tumor

growth_protocol: BT12 cells were grown in RPMI-1640 medium (Invitrogen) supplemented with 10% fetal bovine serum (Gemini Bio-Products), 2 mM L-glutamine (Invitrogen), 100 U/mL penicillin and 100 μg/mL streptomycin (Invitrogen). Cell lines were maintained at less than 80% confluency at 37°C and 5% CO2 and confirmed to be mycoplasma negative every 6-months.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Sequencing libraries were prepared using the Kapa Biosystems Hyper Prep kit for the Illumina platform.

treatment_protocol: BT12 cells were treated with 100nM mithramycin for 8-hours or 18-hours continous treatment then collected.

tag: cell line

value: Mithramycin

tag: timepoint

tag: replicate

tag: chip antibody

value: H3K27ac (Active Motif 39135)


title: p77007: serum sample 4


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C7_AD012

value: brain

value: AI

value: female


title: Sample_Liver-LU-2

description: LU added high-fat diet_mRNA


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C7_AD010


title: BT12 cells, IPAc, mithramycin 18h_D, ChIP-seq


title: p77006: serum sample 3


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C7_AD008


title: Sample_Liver-CLL-11

description: CLE added high-fat diet_mRNA


title: Sample_Liver-CLL-4

description: CLE added high-fat diet_mRNA


title: p77004: serum sample 1


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C7_AD007


title: BT12 cells, IPAc, mithramycin 8h_E, ChIP-seq


title: Sample_Liver-CLL-2

description: CLE added high-fat diet_mRNA


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C7_AD006


title: Sample_Liver-HFD-18

description: High-fat diet_mRNA


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C8_AD002


title: BT12 cells, IPAc, mithramycin 8h_D, ChIP-seq


title: p77008: serum sample 5


title: nrpe1_WGBS_rep2

city: Ann Arbor

first: Shriya

last: Sethuraman

state: MI

address: 5164 Biological Sciences Building, 1105 N. University Ave.

department: Bioinformatics

institute: University of Michigan

data_processing:
UMI was extracted from the read 2 and appended to read 1 name using umi_tools.
The reads were then trimmed for the 3' adapters and poly(A) sequences using cutadapt with a maximum allowed error-rate of 0.05 and a minimum length cut-off of 20bps.
The trimmed reads were then mapped to the TAIR10 genome using bowtie2 allowing one mismatch.
The mapped reads were then sorted followed by removal of PCR duplicates using the umi_tools_dedup command.
The hmmlearn python package was used to split the genome based on Pol V IPARE enrichment in Col-0 compared to nrpe1 and CHHme difference between Col-0 and nrpe1, and IPARE strand bias.
The HMM output states were then filtered further to produce 3 final groups: RdDM_PolV_transcribed; nonRdDM_PolV_transcribed; nonPolV_transcribed.
The WGBS reads were mapped using Bismark allowing no mismatches. The methylation information was extracted using bismark_methylation_extractor.
genome build: TAIR10.
processed data files format and content: RdDM_PolV_transcribed_HMM_bins.bed : tab delimited bed file with the filtered HMM bins identified as RdDM-PolV transcribed.
processed data files format and content: nonRdDM_PolV_transcribed_HMM_bins.bed : tab delimited bed file with the filtered HMM bins identified as nonRdDM-PolV transcribed.
processed data files format and content: nonPolV_transcribed_HMM_bins.bed : tab delimited bed file with the filtered HMM bins identified as nonPolV transcribed.
processed data files format and content: 200bp_150bp_sliding_windows_allDatasets_coverages.bed : tab delimited bed file with the read coverages and average methylation of all datasets in each 200bp-150bp sliding window. The "NA" in methylation columns suggests there weren't sufficient reads to calculate methylation ratios (#converted Cs/Total number of Cs).

organism: Arabidopsis thaliana

source_name: 3.5 week old leaves

growth_protocol: Arabidopsis thaliana plants were grown in at 22ºC under white fluorescent light in 16h/8h day/dark cycle.

extract_protocol:
Immunoprecipitation followed by Analysis of RNA Ends (IPARE) was performed as described in the associated publication. Briefly, RNA was immunoprecipitated using an anti-NRPE1 antibody and the high throughput sequencing library was prepared using a modified template switching NanoPARE protocol.
WGBS samples: Genomic DNA was extracted from 3.5-week old Arabidopsis leaves using Dneasy Plant Mini Kit.
Library was prepared by a modified version of NanoPARE protocol (PMID: 30355603). RNA was polyadenylated with Poly(A) polymerase. The polyadenylated RNA was EtOH-precepitated. The deadenylated RNA was DNase treated with TURBO DNase. The RNA was EtOH precepitated. The RT, template switching, pre-amplification and 2nd PCR were performed as NanoPARE.
The DNA extracted for WGBS were processed with bisulfite treatment followed by 100 bp paired-end sequencing.
RIP-seq with modified NanoPARE : IPARE and WGBS

tag: ecotype

value: Columbia

tag: genotype

tag: development stage

value: 3.5 week old leaves


title: Col-0_WGBS_rep2

description: 200bp_150bp_sliding_windows_allDatasets_coverages.bed

value: Col-0 (wild-type)


title: Sample_Liver-HFD-15

description: High-fat diet_mRNA


title: nrpe1_WGBS_rep1


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C7_AD004

value: STR


title: BT12 cells, IPAc, Solv_F, ChIP-seq

tag: treatment

value: Solvent


title: Sample_Liver-HFD-12

description: High-fat diet_mRNA

tag: strain


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C7_AD002

tag: age


title: Col-0_WGBS_rep1


title: BT12 cells, IPAc, Solv_E, ChIP-seq


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C7_AD001

tag: tissue


title: BT12 cells, IPAc, mithramycin 18h_E, ChIP-seq


title: Sample_Liver-ND-4

description: Normal diet_mRNA


title: p77005: serum sample 2

tag: subject id (donor)

tag: time point

value: BL


title: BT12 cells, IPAc, Solv_D, ChIP-seq


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C6_AD008

tag: source


title: Sample_Liver-ND-3

description: Normal diet_mRNA


title: BT12 cells, IPAc, mithramycin 8h_F, ChIP-seq


title: srn2050-deleted Aus0004 mutant with recombinant pAT29Wsrn2050 plasmid - sample 1

city: Rennes

first: Vincent

last: Cattoir

address: 2 rue Henri Le Guilloux

country: France

institute: CHU de Rennes

data_processing:
The reads were mapped against the genomic sequence of E. faecium Aus0004 (Genbank accession no. CP003351) and counted using the CLC Genomics Workbench software v10.0.1 (Qiagen).
The expression of genes in different RNA-seq samples was compared using the R package DESeq2 R package.
Genome_build: E. faecium Aus0004 (Genbank accession no. CP003351)
Supplementary_files_format_and_content: Tab-delimited text files generated using the CLC Genomics Workbench software v10.0.1 (Qiagen).

organism: Enterococcus faecium

source_name: Bacteria

growth_protocol: Bacterial cells of E. faecium Aus0004 were cultured at 37°C to the late-exponential-growth phase in BHI broth

extract_protocol:
Total RNA was extracted from using the phenol/chloroform method. Residual chromosomal DNA was removed by treating samples with the TURBO DNA-free kit (Life Technologies).
The strand-specific library preparation was performed using the Ovation Universal Prokaryotic RNA-Seq kit (Nugen) with custom depletion (Anydeplete rRNA design Enterococcus faecium) and the samples were sequenced using the Illumina NextSeq500 instrument (multiplex protocol, single-end 75-bp reads).

tag: plasmid

value: recombinant pAT29Wsrn2050 plasmid


title: Sample_Liver-ND-2

description: Normal diet_mRNA


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C6_AD007

tag: target

tag: gender


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C6_AD006

value: ACA


title: WAT ENT m6A IP

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

data_processing:
Reads were aligned to the mm10 genome assembly using TopHat v2.1.1
m6A peaks in two biological replicates m6A-immunoprecipitation sample were identified by MACS2 peak-calling software (version 2.1.1) with the corresponding input sample serving as control.
Genome_build: mm10
Supplementary_files_format_and_content: txt, input reads count and m6A peaks in Vehicle/Entacapone(ENT) treated inguinal White Adipose Tissue(iWAT) of DIO mouse.

source_name: White Adipose Tissue

extract_protocol:
RNA was isolated from mouse White Adipose Tissue using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen) , fragmented and ethanol precipitated mRNA (5 μg) was incubated with 10 μg of anti-m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer (150 mM NaCl, 0.1% NP-40, and 10 mM Tris-HCl [pH 7.4]) for 2 hr with rotatin at 4°C. The mixture was then immunoprecipitated by incubation with 50 μl protein-A beads (Sigma, P9424) at 4°C for an additional 2 hr. After being washed three times, bound RNA was eluted from the beads with 0.5 mg/ml N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted by Trizol. The remaining RNA was re-suspended in H2O and used for library generation with TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq 2500 (Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.
Approximately 100 ng of recovered RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in single-read or paired-read mode, creating reads with a length of 101 bp.

value: 23 weeks

value: White Adipose Tissue

value: Entacapone

tag: phenotype

value: high fat diet-induced-obesity (DIO)


title: srn2050-deleted Aus0004 mutant with empty pAT29 plasmid - sample 1

value: empty pAT29 plasmid


title: WAT ENT m6A input

value: male


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C6_AD004

value: brain


title: srn2050-deleted Aus0004 mutant - sample 2


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C6_AD002


title: WAT vehicle m6A IP

value: vehicle


title: srn2050-deleted Aus0004 mutant - sample 1


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C6_AD001


title: WAT vehicle m6A input


title: srn2050-deleted Aus0004 mutant with recombinant pAT29Wsrn2050 plasmid - sample 2


title: WAT ENT T RNA-seq

data_processing:
Reads were aligned to the mm10 genome assembly using TopHat v2.1.1
For each sample, reads counts of all genes were computed using HTSeq v0.6.0. Differentially-expressed genes between vehicle and ENT were determined  using the R-package DEGseq with the method MARS (MA-plot-based method with random sampling model).
Genome_build: mm10
Supplementary_files_format_and_content: Reads count for each gene in two biological replicates for mouse white adipose tissue.

extract_protocol:
For RNA-seq, RNA was isolated from was isolated from White Adipose Tissue as mentioned above using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen). For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100.
Approximately 100ng of mRNA was used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq 2500 (Illumina) in single-read or paired-read mode, creating reads with a length of 101 bp.


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C5_AD012

value: AI

value: female


title: Aus0004 wild-type strain - sample 1

value: wild type


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C5_AD008


title: WAT vehicle T RNA-seq


title: srn2050-deleted Aus0004 mutant with empty pAT29 plasmid - sample 2


title: Aus0004 wild-type strain - sample 2


title: Whole blood, Day 31, PID 63

status: Public on Nov 15 2020

type: RNA

city: Rixensart

first: Robbert

middle: Gerrit

last: van der Most

address: 89, rue de l'Institut

country: Belgium

institute: GSK

description: 1 day after 2nd vaccination

hyb_protocol: After fragmentation, 3.75 ug of cDNA were hybridized for 16 hr at 45C on GeneChip_ Human Genome U133 Plus 2.0 arrays following standard procedures.

scan_protocol: Data acquisition was performed using GeneChip Operating Software (Affymetrix).

data_processing: The data were analyzed with R/Bioconductor using GCRMA as summarization/normalization method

label: Biotin

source_name: Whole blood samples from subject 63 at Day 31

label_protocol: Biotinylated cDNA were prepared according to NuGen Ovation WB amplification protocol from 50ng total RNA

extract_protocol: Total RNA was isolated by PAXgene Blood RNA kit (Qiagen) according to the manufacturer’s protocol. A DNAse treatment was applied on the PAXgene RNA spin column to avoid genomic DNA contamination. RNA was quantified by UV-spectrophotometry.

treatment_protocol: PAXgene preserved whole blood samples were centrifuged, resuspended in lysis buffer and treated with proteinase K.

tag: adjuvant

tag: subject id

tag: time (sample day)


title: Whole blood, Day 30 post, PID 63

description: 30 post

source_name: Whole blood samples from subject 63 at Day 30 post


title: Whole blood, Day 30 pre, PID 34

description: day of 2nd vaccination, before vaccination

source_name: Whole blood samples from subject 34 at Day 30, pre vaccination


title: Whole blood, Day 31, PID 61

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 61 at Day 31

value: Alum


title: Whole blood, Day 30 pre, PID 63

source_name: Whole blood samples from subject 63 at Day 30, pre vaccination


title: Whole blood, Day 33, PID 63

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 63 at Day 33


title: Whole blood, Day 1, PID 107

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 107 at Day 1


title: Whole blood, Day 14, PID 104

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 104 at Day 14


title: Whole blood, Day 14, PID 29

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 29 at Day 14


title: Whole blood, Day 33, PID 44

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 44 at Day 33


title: Whole blood, Day 1, PID 104

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 104 at Day 1


title: Whole blood, Day 0 post, PID 86

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 86 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 14, PID 86

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 86 at Day 14


title: Whole blood, Day 14, PID 103

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 103 at Day 14


title: Whole blood, Day 1, PID 63

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 63 at Day 1


title: Whole blood, Day 30 pre, PID 103

source_name: Whole blood samples from subject 103 at Day 30, pre vaccination


title: Whole blood, Day 31, PID 104

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 104 at Day 31


title: Whole blood, Day 14, PID 61

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 61 at Day 14


title: Whole blood, Day 30 post, PID 103

description: 30 post

source_name: Whole blood samples from subject 103 at Day 30 post


title: Whole blood, Day 1, PID 32

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 32 at Day 1


title: Whole blood, Day 37, PID 63

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 63 at Day 37


title: Whole blood, Day 31, PID 3

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 3 at Day 31


title: Whole blood, Day 30 pre, PID 36

source_name: Whole blood samples from subject 36 at Day 30, pre vaccination


title: Whole blood, Day 30 pre, PID 29

source_name: Whole blood samples from subject 29 at Day 30, pre vaccination


title: Whole blood, Day 33, PID 110

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 110 at Day 33


title: Whole blood, Day 0 pre, PID 61

description: day of 1st vaccination, before vaccination

source_name: Whole blood samples from subject 61 at Day 0, pre vaccination


title: Whole blood, Day 0 pre, PID 104

source_name: Whole blood samples from subject 104 at Day 0, pre vaccination


title: Whole blood, Day 1, PID 23

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 23 at Day 1


title: Whole blood, Day 0 post, PID 104

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 104 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 1, PID 3

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 3 at Day 1


title: Whole blood, Day 30 pre, PID 62

source_name: Whole blood samples from subject 62 at Day 30, pre vaccination


title: Whole blood, Day 30 pre, PID 3

source_name: Whole blood samples from subject 3 at Day 30, pre vaccination


title: Whole blood, Day 0 pre, PID 111

source_name: Whole blood samples from subject 111 at Day 0, pre vaccination


title: Whole blood, Day 1, PID 36

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 36 at Day 1


title: Whole blood, Day 0 pre, PID 103

source_name: Whole blood samples from subject 103 at Day 0, pre vaccination


title: Whole blood, Day 33, PID 104

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 104 at Day 33


title: Whole blood, Day 0 post, PID 3

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 3 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 37, PID 61

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 61 at Day 37


title: Whole blood, Day 0 post, PID 110

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 110 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 37, PID 103

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 103 at Day 37


title: Whole blood, Day 30 post, PID 107

description: 30 post

source_name: Whole blood samples from subject 107 at Day 30 post


title: Whole blood, Day 0 post, PID 107

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 107 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 30 pre, PID 104

source_name: Whole blood samples from subject 104 at Day 30, pre vaccination


title: Whole blood, Day 30 post, PID 3

description: 30 post

source_name: Whole blood samples from subject 3 at Day 30 post


title: Whole blood, Day 0 pre, PID 23

source_name: Whole blood samples from subject 23 at Day 0, pre vaccination


title: Whole blood, Day 1, PID 110

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 110 at Day 1


title: Whole blood, Day 30 pre, PID 69

source_name: Whole blood samples from subject 69 at Day 30, pre vaccination


title: Whole blood, Day 14, PID 23

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 23 at Day 14


title: Whole blood, Day 1, PID 44

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 44 at Day 1


title: Whole blood, Day 37, PID 36

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 36 at Day 37


title: Whole blood, Day 30 pre, PID 86

source_name: Whole blood samples from subject 86 at Day 30, pre vaccination


title: Whole blood, Day 0 pre, PID 63

source_name: Whole blood samples from subject 63 at Day 0, pre vaccination


title: Whole blood, Day 0 pre, PID 44

source_name: Whole blood samples from subject 44 at Day 0, pre vaccination


title: Whole blood, Day 30 post, PID 98

description: 30 post

source_name: Whole blood samples from subject 98 at Day 30 post


title: dCAR1-Ag

type: genomic

first: Wang

last: Yao

address: No. 28, fuxing street

institute: Chinese general PLA hospital

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
R software v3.5
The signal_intensities.txt contains Unmethylated and methylated signal intensities.

label: Cy3, Cy5

source_name: CD19-CAR T cells treated by Decitabine after co-culture with Raji cells

label_protocol: Standard Illumina Protocol

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were collected from patients by leukapheresis. Primary T cells derived from the PBMCs were activated using Dynabeads Human T-Activator CD3/CD28 magnetic beads (Invitrogen) at a 1:1 bead:cell ratio and cultured in X-VIVO 15 medium (Lonza) supplemented with 300 U/ml recombinant human IL-2 (PeproTech). After 2 days, RetroNectin-coated plates (Takara) were loaded with viral supernatants by centrifuging the plates at 2,000 g for 2 h at 32 °C. Activated T cells were added to the plates and centrifuged at 800 g for 10 min, and Polybrene (Sigma) was added to increase infection efficiency. The following day, the transduced cells were collected and transferred to new flasks for further expansion. The Dynabeads were magnetically removed 2 days after initiating T cell transduction, and the cells were cultured at 106 cells per ml in X-VIVO 15 medium supplemented with 300 IU/mL IL-2, with fresh IL-2-containing medium added every 2 days until the cells were harvested on days 8-10.

extract_protocol: T cells were resuspended in 250ul PBS and placed in 750ul TRIzol LS (Invitrogen). RNA was extracted using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol. Total RNA integrity was checked using the Bioptic Qsep100 (BIOptic) and quantified using a Synergy H1 (BioTek).

treatment_protocol: dCAR and CAR T cells were cocultured with Raji cells for 24 h, followed by magnetic selection of CD3+ cells (Miltenyi Biotec).

tag: cell type

value: CD19-CAR T cells


title: CAR2-Ag

source_name: CD19-CAR T cells after co-culture with Raji cells

value: after co-culture with Raji cells


title: CAR1

source_name: CD19-CAR T cells


title: dCAR2

source_name: CD19-CAR T cells treated by Decitabine

value: treated by Decitabine


title: dCAR2-Ag

value: treated by Decitabine after co-culture with Raji cells


title: CAR1-Ag


title: dCAR1


title: Whole blood, Day 0 post, PID 63

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 63 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 30 post, PID 62

description: 30 post

source_name: Whole blood samples from subject 62 at Day 30 post


title: Whole blood, Day 30 post, PID 32

description: 30 post

source_name: Whole blood samples from subject 32 at Day 30 post


title: CAR2


title: Whole blood, Day 31, PID 44

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 44 at Day 31


title: Whole blood, Day 31, PID 23

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 23 at Day 31


title: Whole blood, Day 0 post, PID 62

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 62 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 0 post, PID 44

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 44 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 1, PID 69

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 69 at Day 1


title: Whole blood, Day 31, PID 32

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 32 at Day 31


title: Whole blood, Day 14, PID 44

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 44 at Day 14


title: Whole blood, Day 33, PID 86

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 86 at Day 33


title: Whole blood, Day 37, PID 86

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 86 at Day 37


title: Whole blood, Day 33, PID 32

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 32 at Day 33


title: Whole blood, Day 30 post, PID 61

description: 30 post

source_name: Whole blood samples from subject 61 at Day 30 post


title: Whole blood, Day 30 post, PID 104

description: 30 post

source_name: Whole blood samples from subject 104 at Day 30 post


title: Whole blood, Day 1, PID 111

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 111 at Day 1


title: Whole blood, Day 1, PID 42

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 42 at Day 1


title: Whole blood, Day 0 pre, PID 110

source_name: Whole blood samples from subject 110 at Day 0, pre vaccination


title: Whole blood, Day 0 pre, PID 69

source_name: Whole blood samples from subject 69 at Day 0, pre vaccination


title: Whole blood, Day 1, PID 86

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 86 at Day 1


title: Whole blood, Day 0 pre, PID 98

source_name: Whole blood samples from subject 98 at Day 0, pre vaccination


title: Whole blood, Day 31, PID 107

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 107 at Day 31


title: Whole blood, Day 14, PID 111

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 111 at Day 14


title: Whole blood, Day 31, PID 29

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 29 at Day 31


title: Whole blood, Day 30 post, PID 29

description: 30 post

source_name: Whole blood samples from subject 29 at Day 30 post


title: Whole blood, Day 30 pre, PID 61

source_name: Whole blood samples from subject 61 at Day 30, pre vaccination


title: Whole blood, Day 37, PID 98

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 98 at Day 37


title: Whole blood, Day 37, PID 104

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 104 at Day 37


title: Whole blood, Day 0 pre, PID 73

source_name: Whole blood samples from subject 73 at Day 0, pre vaccination


title: Whole blood, Day 30 post, PID 78

description: 30 post

source_name: Whole blood samples from subject 78 at Day 30 post


title: Whole blood, Day 1, PID 96

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 96 at Day 1


title: Whole blood, Day 0 post, PID 49

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 49 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 30 post, PID 73

description: 30 post

source_name: Whole blood samples from subject 73 at Day 30 post


title: Whole blood, Day 30 post, PID 108

description: 30 post

source_name: Whole blood samples from subject 108 at Day 30 post


title: Whole blood, Day 0 post, PID 61

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 61 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 31, PID 103

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 103 at Day 31


title: Whole blood, Day 30 pre, PID 32

source_name: Whole blood samples from subject 32 at Day 30, pre vaccination


title: Whole blood, Day 14, PID 14

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 14 at Day 14


title: Whole blood, Day 31, PID 14

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 14 at Day 31


title: Whole blood, Day 37, PID 96

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 96 at Day 37


title: Whole blood, Day 14, PID 63

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 63 at Day 14


title: Whole blood, Day 14, PID 43

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 43 at Day 14


title: Whole blood, Day 31, PID 86

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 86 at Day 31


title: Whole blood, Day 1, PID 49

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 49 at Day 1


title: Whole blood, Day 0 post, PID 80

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 80 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 30 post, PID 49

description: 30 post

source_name: Whole blood samples from subject 49 at Day 30 post


title: Whole blood, Day 0 post, PID 29

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 29 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 0 pre, PID 78

source_name: Whole blood samples from subject 78 at Day 0, pre vaccination


title: Whole blood, Day 0 post, PID 16

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 16 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 0 post, PID 67

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 67 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 1, PID 103

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 103 at Day 1


title: Whole blood, Day 0 pre, PID 64

source_name: Whole blood samples from subject 64 at Day 0, pre vaccination


title: Whole blood, Day 31, PID 108

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 108 at Day 31


title: Whole blood, Day 37, PID 18

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 18 at Day 37


title: Whole blood, Day 0 post, PID 64

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 64 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 0 pre, PID 107

source_name: Whole blood samples from subject 107 at Day 0, pre vaccination


title: Whole blood, Day 1, PID 16

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 16 at Day 1


title: Whole blood, Day 33, PID 61

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 61 at Day 33


title: Whole blood, Day 30 post, PID 44

description: 30 post

source_name: Whole blood samples from subject 44 at Day 30 post


title: Whole blood, Day 1, PID 43

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 43 at Day 1


title: Whole blood, Day 14, PID 55

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 55 at Day 14


title: Whole blood, Day 1, PID 34

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 34 at Day 1


title: Whole blood, Day 30 pre, PID 55

source_name: Whole blood samples from subject 55 at Day 30, pre vaccination


title: Whole blood, Day 31, PID 16

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 16 at Day 31


title: Whole blood, Day 37, PID 107

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 107 at Day 37


title: Whole blood, Day 37, PID 83

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 83 at Day 37


title: Whole blood, Day 37, PID 44

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 44 at Day 37


title: Whole blood, Day 30 post, PID 59

description: 30 post

source_name: Whole blood samples from subject 59 at Day 30 post


title: Whole blood, Day 0 pre, PID 29

source_name: Whole blood samples from subject 29 at Day 0, pre vaccination


title: Whole blood, Day 14, PID 108

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 108 at Day 14


title: Whole blood, Day 33, PID 29

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 29 at Day 33


title: Whole blood, Day 0 post, PID 106

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 106 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 0 pre, PID 87

source_name: Whole blood samples from subject 87 at Day 0, pre vaccination


title: Whole blood, Day 33, PID 80

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 80 at Day 33


title: Whole blood, Day 37, PID 91

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 91 at Day 37


title: Whole blood, Day 30 post, PID 43

description: 30 post

source_name: Whole blood samples from subject 43 at Day 30 post


title: Whole blood, Day 1, PID 29

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 29 at Day 1


title: Whole blood, Day 37, PID 80

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 80 at Day 37


title: Whole blood, Day 30 post, PID 96

description: 30 post

source_name: Whole blood samples from subject 96 at Day 30 post


title: Whole blood, Day 14, PID 83

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 83 at Day 14


title: Whole blood, Day 0 pre, PID 96

source_name: Whole blood samples from subject 96 at Day 0, pre vaccination


title: Whole blood, Day 33, PID 46

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 46 at Day 33


title: Whole blood, Day 30 pre, PID 16

source_name: Whole blood samples from subject 16 at Day 30, pre vaccination


title: Whole blood, Day 30 post, PID 18

description: 30 post

source_name: Whole blood samples from subject 18 at Day 30 post


title: Whole blood, Day 1, PID 64

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 64 at Day 1


title: Whole blood, Day 1, PID 14

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 14 at Day 1


title: Whole blood, Day 31, PID 67

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 67 at Day 31


title: Whole blood, Day 14, PID 78

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 78 at Day 14


title: Whole blood, Day 14, PID 16

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 16 at Day 14


title: Whole blood, Day 37, PID 78

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 78 at Day 37


title: Whole blood, Day 30 pre, PID 58

source_name: Whole blood samples from subject 58 at Day 30, pre vaccination


title: Whole blood, Day 0 pre, PID 16

source_name: Whole blood samples from subject 16 at Day 0, pre vaccination


title: Whole blood, Day 33, PID 16

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 16 at Day 33


title: Whole blood, Day 0 pre, PID 59

source_name: Whole blood samples from subject 59 at Day 0, pre vaccination


title: Whole blood, Day 0 post, PID 55

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 55 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 1, PID 61

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 61 at Day 1


title: Whole blood, Day 0 pre, PID 28

source_name: Whole blood samples from subject 28 at Day 0, pre vaccination


title: Whole blood, Day 37, PID 43

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 43 at Day 37


title: Whole blood, Day 31, PID 18

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 18 at Day 31


title: Whole blood, Day 30 pre, PID 108

source_name: Whole blood samples from subject 108 at Day 30, pre vaccination


title: Whole blood, Day 1, PID 108

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 108 at Day 1


title: Whole blood, Day 31, PID 64

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 64 at Day 31


title: Whole blood, Day 33, PID 78

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 78 at Day 33


title: Whole blood, Day 33, PID 108

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 108 at Day 33


title: Whole blood, Day 30 post, PID 80

description: 30 post

source_name: Whole blood samples from subject 80 at Day 30 post


title: Whole blood, Day 0 post, PID 96

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 96 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 14, PID 67

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 67 at Day 14


title: Whole blood, Day 33, PID 67

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 67 at Day 33


title: Whole blood, Day 31, PID 80

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 80 at Day 31


title: Whole blood, Day 37, PID 55

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 55 at Day 37


title: Whole blood, Day 14, PID 49

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 49 at Day 14


title: Whole blood, Day 31, PID 73

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 73 at Day 31


title: Whole blood, Day 30 pre, PID 67

source_name: Whole blood samples from subject 67 at Day 30, pre vaccination


title: Whole blood, Day 0 pre, PID 14

source_name: Whole blood samples from subject 14 at Day 0, pre vaccination


title: Whole blood, Day 0 pre, PID 49

source_name: Whole blood samples from subject 49 at Day 0, pre vaccination


title: Whole blood, Day 31, PID 78

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 78 at Day 31


title: Whole blood, Day 30 post, PID 91

description: 30 post

source_name: Whole blood samples from subject 91 at Day 30 post


title: Whole blood, Day 37, PID 67

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 67 at Day 37


title: Whole blood, Day 30 pre, PID 73

source_name: Whole blood samples from subject 73 at Day 30, pre vaccination


title: Whole blood, Day 37, PID 49

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 49 at Day 37


title: Whole blood, Day 30 pre, PID 107

source_name: Whole blood samples from subject 107 at Day 30, pre vaccination


title: Whole blood, Day 30 pre, PID 64

source_name: Whole blood samples from subject 64 at Day 30, pre vaccination


title: Whole blood, Day 30 pre, PID 96

source_name: Whole blood samples from subject 96 at Day 30, pre vaccination


title: Whole blood, Day 0 pre, PID 55

source_name: Whole blood samples from subject 55 at Day 0, pre vaccination


title: Whole blood, Day 14, PID 73

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 73 at Day 14


title: Whole blood, Day 1, PID 73

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 73 at Day 1


title: Whole blood, Day 30 pre, PID 99

source_name: Whole blood samples from subject 99 at Day 30, pre vaccination


title: Whole blood, Day 30 post, PID 64

description: 30 post

source_name: Whole blood samples from subject 64 at Day 30 post


title: Whole blood, Day 33, PID 55

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 55 at Day 33


title: Whole blood, Day 37, PID 14

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 14 at Day 37


title: Whole blood, Day 1, PID 78

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 78 at Day 1


title: Whole blood, Day 33, PID 49

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 49 at Day 33


title: Whole blood, Day 37, PID 108

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 108 at Day 37


title: Whole blood, Day 0 post, PID 14

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 14 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 30 pre, PID 44

source_name: Whole blood samples from subject 44 at Day 30, pre vaccination


title: Whole blood, Day 30 pre, PID 14

source_name: Whole blood samples from subject 14 at Day 30, pre vaccination


title: Whole blood, Day 37, PID 64

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 64 at Day 37


title: Whole blood, Day 33, PID 64

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 64 at Day 33


title: Whole blood, Day 14, PID 96

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 96 at Day 14


title: Whole blood, Day 0 pre, PID 108

source_name: Whole blood samples from subject 108 at Day 0, pre vaccination


title: Whole blood, Day 31, PID 55

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 55 at Day 31


title: Whole blood, Day 30 post, PID 16

description: 30 post

source_name: Whole blood samples from subject 16 at Day 30 post


title: Whole blood, Day 30 post, PID 67

description: 30 post

source_name: Whole blood samples from subject 67 at Day 30 post


title: Whole blood, Day 14, PID 107

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 107 at Day 14


title: Whole blood, Day 14, PID 91

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 91 at Day 14


title: Whole blood, Day 30 post, PID 86

description: 30 post

source_name: Whole blood samples from subject 86 at Day 30 post


title: Whole blood, Day 30 pre, PID 78

source_name: Whole blood samples from subject 78 at Day 30, pre vaccination


title: Whole blood, Day 0 pre, PID 106

source_name: Whole blood samples from subject 106 at Day 0, pre vaccination


title: Whole blood, Day 14, PID 12

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 12 at Day 14


title: Whole blood, Day 30 post, PID 55

description: 30 post

source_name: Whole blood samples from subject 55 at Day 30 post


title: Whole blood, Day 14, PID 64

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 64 at Day 14


title: Whole blood, Day 37, PID 73

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 73 at Day 37


title: Whole blood, Day 30 post, PID 14

description: 30 post

source_name: Whole blood samples from subject 14 at Day 30 post


title: Whole blood, Day 30 post, PID 52

description: 30 post

source_name: Whole blood samples from subject 52 at Day 30 post


title: Whole blood, Day 30 pre, PID 111

source_name: Whole blood samples from subject 111 at Day 30, pre vaccination


title: Whole blood, Day 33, PID 73

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 73 at Day 33


title: Whole blood, Day 31, PID 41

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 41 at Day 31


title: Whole blood, Day 30 post, PID 12

description: 30 post

source_name: Whole blood samples from subject 12 at Day 30 post


title: Whole blood, Day 33, PID 93

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 93 at Day 33


title: Whole blood, Day 33, PID 12

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 12 at Day 33


title: Whole blood, Day 37, PID 99

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 99 at Day 37


title: Whole blood, Day 33, PID 58

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 58 at Day 33


title: Whole blood, Day 31, PID 99

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 99 at Day 31


title: Whole blood, Day 0 post, PID 23

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 23 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 31, PID 98

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 98 at Day 31


title: Whole blood, Day 33, PID 36

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 36 at Day 33


title: Whole blood, Day 31, PID 83

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 83 at Day 31


title: Whole blood, Day 31, PID 28

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 28 at Day 31


title: Whole blood, Day 31, PID 49

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 49 at Day 31


title: Whole blood, Day 33, PID 28

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 28 at Day 33


title: Whole blood, Day 30 post, PID 41

description: 30 post

source_name: Whole blood samples from subject 41 at Day 30 post


title: Whole blood, Day 31, PID 62

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 62 at Day 31


title: Whole blood, Day 33, PID 111

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 111 at Day 33


title: Whole blood, Day 37, PID 28

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 28 at Day 37


title: Whole blood, Day 30 post, PID 88

description: 30 post

source_name: Whole blood samples from subject 88 at Day 30 post


title: Whole blood, Day 0 pre, PID 65

source_name: Whole blood samples from subject 65 at Day 0, pre vaccination


title: Whole blood, Day 14, PID 41

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 41 at Day 14


title: Whole blood, Day 0 post, PID 12

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 12 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 0 post, PID 103

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 103 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 0 post, PID 4

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 4 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 37, PID 62

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 62 at Day 37


title: Sulfolobus acidocaldarius DSM 639 under sugar-rich condition

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

institute: Pusan National University

data_processing:
The filtered reads of raw data were processed using the BWA-MEM algorithm with default parameters.
SAM files were converted to BAM files of binary format, and then sorted by chromosomal coordinates using the SAMtools program.
Mapped reads per annotated gene were counted by Bamtoreadcount.
Reads per kilobase of exon per million mapped sequence reads were calculated for normalization.
Genome_build: Sulfolobus acidocaldarius DSM 639 ASM1228v1
Supplementary_files_format_and_content: txt: tab-delimited text files include RPKM values for each Sample

organism: Sulfolobus acidocaldarius

source_name: Archaea culture under basal medium with glucose

growth_protocol: Sulfolobus acidocaldarius DSM 639 was grown in basal medium at 77 °C. To make the sugar-free medium, Brock’s medium was supplemented with 0.1% (w/v) tryptone, 0.005% (w/v) yeast extract and pH was adjusted to 3.3 with 6 M H2SO4. For the sugar-rich medium, 0.2% (w/v) glucose was added.

extract_protocol:
Sulfolobus acidocaldarius DSM 639 cells grown in each condition were harvested at early exponential phase and total RNA was extracted from the cell using RiboEX (GeneAll, Republic of Korea). The grown cells were harvested and disrupted with TEN (20 mM Tris-HCl, pH 8.0, 1 mM EDTA, and 100 mM NaCl) and TENST (TEN buffer with 1.6% SDS and 0.12% Tween 20) buffer. Total RNA was extracted with RiboEX, chloroform and isopropanol. The RNA which was further washed with ethanol was resuspended with TE buffer. Residual DNA in RNA extract was degraded by DNase I (ThermoFisher Scientific, MA, USA) treatment for 30 min at 37 °C.
RNA-Seq libraries were prepared using an Illumina TruSeqTM RNA sample prep kit (Illumina, SD, USA) according to the standard low-throughput protocol.

value: DSM 639

tag: condition

value: sugar-rich medium

tag: glucose concentration (w/v)


title: Whole blood, Day 30 pre, PID 109

source_name: Whole blood samples from subject 109 at Day 30, pre vaccination


title: Sulfolobus acidocaldarius DSM 639 under sugar-free condition

source_name: Archaea culture under basal medium (yeast extract and tryptone)

value: sugar-free medium

value: not applicable


title: TKO_HFD

first: Xiang

last: Zhang

address: Tsinghuayuan Street

institute: Tsinghua University

description: high fat diet

data_processing:
Data were filtered by fastp to get clean data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Gene expression levels were quantified using featureCounts v1.5.0-p3
FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene.
Genome_build: mouse (mm10)
Supplementary_files_format_and_content: Excel file contains gene expression levels as FPKM.

molecule: polyA RNA

source_name: Macrophages

extract_protocol:
RNA was isolated with TRIzol reagent and total RNA was polyA enriched.
1. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X).   2. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H).   3. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.   4. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities.   5. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization.   6. The library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA) and then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR.   7. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.   8. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: TKO mice were fed with high fat diet for 8 weeks

value: Adipose tissue macrophages

tag: genotype


title: Non-myelinating Corneal Schwann Cells scRNA-seq

city: Farmington

first: Royce

last: Mohan

state: Connecticut

address: 263 Farmington Avenue

department: Neuroscience

institute: University of Connecticut Health Center

data_processing:
Illumina basecall files (*.bcl) were converted to FASTQs using CellRanger v3.0.1.
FASTQ files were then aligned to the rabbit reference genome (OryCun2, version 3.0.2) and transcriptome using the CellRanger v3.0.1 with default parameters, as described in (Zheng et al., 2017)).
total UMIs per cell were divided by the count depth of that cell and multiplied by the median count depth of the dataset; the result plus a pseudo-count of 1 was then log-transformed.
Differential expression was performed using Monocle3
Genome_build: OryCun2, version 3.0.2
Supplementary_files_format_and_content: Excel files include raw counts and normalized expression (NE)

organism: Oryctolagus cuniculus

source_name: Central corneal tissue

growth_protocol: New Zealand white rabbits (NCBI:txid9986; 3.2 to 4 kg; male; Envigo, Denver, PA)

extract_protocol:
Corneal buttons from central aspect of the tissue from young adult male rabbits (after mechanical removal of endothelial cell layer and trypsin digeston for partial removal of epithelium) were dissociated into single cell suspension, filtered, centrifuged , and resuspended in ice-cold 1X PBS with 0.05% BSA and immediately processed for scRNA-seq analysis.
scRNA libraries were prepared for sequencing using Chromium system (10x Genomics; (Zheng et al., 2017)) for droplet-based single cell library generation with v3 Chromium chemistry and processed for cDNA library construction and subsequent scRNA-seq analysis (Rheaume et al., 2018)

value: Nonmyelinating Corneal Schwann Cells

tag: treatment

value: No treatment


title: Whole blood, Day 0 pre, PID 88

source_name: Whole blood samples from subject 88 at Day 0, pre vaccination


title: TKO

data_processing:
Data were filtered by fastp to get clean data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Gene expression levels were quantified using featureCounts v1.5.0-p3
1. Differential expressed genes between WT and TKO ATMs were defined as p-value ≤ 0.05, (FPKM +1) fold changes (TKO/WT) ≥ 1.5 for upregulated genes and (FPKM +1) fold changes (TKO/WT) ≤ 0.6 for downregulated genes.   2. Differential expressed genes between WT_HFD and WT ATMs were defined as P-value ≤0.05 and absolute  log2 ratio (WT-HFD/WT) ≥ 1.
Genome_build: mouse (mm10)
Supplementary_files_format_and_content: Excel file contains quantified gene expression level as FPKM and P-value for differential expression analysis.

treatment_protocol: WT mice were fed with high fat diet for 8 weeks

tag: strain background

tag: genotype/variation

value: regular chow diet

value: adipose tissue macrophages (ATMs)


title: WT


title: Whole blood, Day 33, PID 98

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 98 at Day 33


title: Whole blood, Day 31, PID 42

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 42 at Day 31


title: Whole blood, Day 31, PID 88

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 88 at Day 31


title: Whole blood, Day 30 pre, PID 87

source_name: Whole blood samples from subject 87 at Day 30, pre vaccination


title: Whole blood, Day 37, PID 23

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 23 at Day 37


title: S6LaAPLV

city: Boise

first: Matthew

last: Goelzer

state: Idaho

address: 1910 University Drive

department: Materials Science and Engineering

institute: Boise State University

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on FASTQ files using FastQC
Paired end reads were aligned by STAR
Gene counts generated by DESEQ2
Genome_build: mm10
Supplementary_files_format_and_content: Files include raw counts and RPKM log2Fold Change for each gene per sample. Log2Fold for specific sample comparisons.

source_name: Bone marrow derived MSC

extract_protocol:
TRIzol reagent (Invitrogen), extraction comleted by Novogene sequencing company.
mRNA version 2 library prep kit (Illumina)

value: MSC

tag: passage

value: Passage 10

tag: media

value: Adipogenic

tag: sirna

value: siLamin

tag: mechanical force

value: LIV

value: Adipogenic with LIV (APLV)


title: Whole blood, Day 30 post, PID 93

description: 30 post

source_name: Whole blood samples from subject 93 at Day 30 post


title: S6LaAP

value: Adipogenic only (AP)


title: S5CnAPLV

value: SiCntl


title: Whole blood, Day 37, PID 32

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 32 at Day 37


title: S4LaAPLV


title: S5CnAP


title: Whole blood, Day 0 post, PID 73

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 73 at Day 0, 3 to 6 hours post vaccination

value: Alum


title: S4LaAP


title: Whole blood, Day 31, PID 65

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 65 at Day 31


title: Whole blood, Day 0 pre, PID 41

source_name: Whole blood samples from subject 41 at Day 0, pre vaccination


title: Whole blood, Day 30 post, PID 99

description: 30 post

source_name: Whole blood samples from subject 99 at Day 30 post


title: Whole blood, Day 31, PID 93

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 93 at Day 31


title: S3CnAPLV


title: S3CnAP


title: S2LaAPLV


title: Whole blood, Day 33, PID 41

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 41 at Day 33


title: Whole blood, Day 0 pre, PID 58

source_name: Whole blood samples from subject 58 at Day 0, pre vaccination


title: Whole blood, Day 14, PID 65

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 65 at Day 14


title: S2LaNAL

value: Growth

value: No Treatment (NAL)


title: S1CnAP


title: S2LaAP


title: Whole blood, Day 31, PID 87

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 87 at Day 31


title: Whole blood, Day 30 post, PID 87

description: 30 post

source_name: Whole blood samples from subject 87 at Day 30 post


title: Whole blood, Day 0 post, PID 87

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 87 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 33, PID 23

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 23 at Day 33


title: S1CnNAL


title: Whole blood, Day 37, PID 31

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 31 at Day 37


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C5_AD007

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J P56 Mouse Brain

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

tag: strain

tag: age

tag: tissue

value: brain

tag: source

value: AI

tag: target

value: STR

value: male


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C5_AD004

value: ACA

tag: gender

value: female


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C3_AD010


title: Whole blood, Day 37, PID 70

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 70 at Day 37

tag: adjuvant

tag: subject id

tag: time (sample day)


title: Whole blood, Day 37, PID 109

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 109 at Day 37


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C3_AD008


title: Whole blood, Day 14, PID 24

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 24 at Day 14


title: S1CnAPLV

source_name: Bone marrow derived MSC

tag: cell type

value: MSC


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C3_AD007


title: Whole blood, Day 33, PID 42

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 42 at Day 33


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C3_AD006


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C3_AD004


title: Whole blood, Day 30 post, PID 94

description: 30 post

source_name: Whole blood samples from subject 94 at Day 30 post


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C3_AD001


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C2_AD008


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C3_AD002


title: Whole blood, Day 0 pre, PID 46

source_name: Whole blood samples from subject 46 at Day 0, pre vaccination


title: Whole blood, Day 30 post, PID 42

description: 30 post

source_name: Whole blood samples from subject 42 at Day 30 post


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C2_AD007


title: Whole blood, Day 14, PID 94

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 94 at Day 14


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C2_AD004


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C2_AD001


title: Whole blood, Day 0 post, PID 42

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 42 at Day 0, 3 to 6 hours post vaccination


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C2_AD002


title: Whole blood, Day 1, PID 70

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 70 at Day 1


title: Whole blood, Day 0 post, PID 111

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 111 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 14, PID 52

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 52 at Day 14


title: Whole blood, Day 30 post, PID 6

description: 30 post

source_name: Whole blood samples from subject 6 at Day 30 post


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C1_AD010


title: Whole blood, Day 14, PID 32

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 32 at Day 14


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C1_AD008


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C1_AD006


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C1_AD007


title: Whole blood, Day 30 post, PID 28

description: 30 post

source_name: Whole blood samples from subject 28 at Day 30 post


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C1_AD004

source_name: C57BL/6J P56 Mouse Brain


title: Whole blood, Day 0 pre, PID 42

source_name: Whole blood samples from subject 42 at Day 0, pre vaccination


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C12_AD010


title: Whole blood, Day 30 pre, PID 28

source_name: Whole blood samples from subject 28 at Day 30, pre vaccination


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C12_AD008


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C1_AD001


title: Whole blood, Day 31, PID 12

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 12 at Day 31


title: Whole blood, Day 0 pre, PID 93

source_name: Whole blood samples from subject 93 at Day 0, pre vaccination


title: Whole blood, Day 31, PID 111

description: 1 day after 2nd vaccination

source_name: Whole blood samples from subject 111 at Day 31


title: Whole blood, Day 0 pre, PID 51

source_name: Whole blood samples from subject 51 at Day 0, pre vaccination


title: Whole blood, Day 0 post, PID 93

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 93 at Day 0, 3 to 6 hours post vaccination


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C12_AD004


title: Whole blood, Day 14, PID 99

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 99 at Day 14


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C1_AD002


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C12_AD002


title: Whole blood, Day 1, PID 28

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 28 at Day 1


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C12_AD006


title: Whole blood, Day 0 post, PID 28

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 28 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 30 post, PID 110

description: 30 post

source_name: Whole blood samples from subject 110 at Day 30 post


title: Whole blood, Day 0 post, PID 41

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 41 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 30 pre, PID 12

source_name: Whole blood samples from subject 12 at Day 30, pre vaccination


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C10_AD012


title: Whole blood, Day 37, PID 52

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 52 at Day 37


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C10_AD006


title: Whole blood, Day 0 post, PID 99

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 99 at Day 0, 3 to 6 hours post vaccination


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C12_AD001


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C11_AD012


title: Whole blood, Day 14, PID 62

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 62 at Day 14


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C10_AD002

source_name: C57BL/6J P56 Mouse Brain


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C10_AD001


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_B9_AD012


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_B9_AD010


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_B9_AD008


title: Whole blood, Day 30 post, PID 23

description: 30 post

source_name: Whole blood samples from subject 23 at Day 30 post


title: Whole blood, Day 1, PID 58

description: 1 day after 1st vaccination

source_name: Whole blood samples from subject 58 at Day 1


title: Whole blood, Day 0 post, PID 98

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 98 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 14, PID 88

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 88 at Day 14


title: Whole blood, Day 30 post, PID 36

description: 30 post

source_name: Whole blood samples from subject 36 at Day 30 post


title: Whole blood, Day 33, PID 69

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 69 at Day 33


title: Whole blood, Day 14, PID 80

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 80 at Day 14


title: Whole blood, Day 33, PID 106

description: 3 days after 2nd vaccination

source_name: Whole blood samples from subject 106 at Day 33


title: Whole blood, Day 0 post, PID 81

description: 3 to 6 hours after 1st vaccination

source_name: Whole blood samples from subject 81 at Day 0, 3 to 6 hours post vaccination


title: Whole blood, Day 37, PID 69

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 69 at Day 37


title: Whole blood, Day 37, PID 111

description: 7 days after 2nd vaccination

source_name: Whole blood samples from subject 111 at Day 37


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_C10_AD004


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_B9_AD007


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_B9_AD002


title: WT_HFD

source_name: Macrophages

tag: treatment

value: high fat diet

value: adipose tissue macrophages (ATMs)


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_B8_AD012


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_B8_AD010


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_B9_AD004


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_B8_AD007


title: Whole blood, Day 14, PID 93

description: 14 days after 1st vaccination

source_name: Whole blood samples from subject 93 at Day 14


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_B8_AD004


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_B8_AD001


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_B8_AD002


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_B8_AD006


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_B7_AD008


title: 180221_CEMBA_mm_P56_P63_RS2_180221_P3_180221_P4_B7_AD010