title: Plasma,AD,9

description:
Memories_AZM06713_Plasma_S73_R1_001.fastq
miR.Counts_plasma.csv

data_processing:
We used cutadapt (version 1.8.1) to trim adapters and random bases
Data were processed with miRge2 with the latest release of miRbase
Supplementary files format and content: For miR.Counts_serum.csv, each row represents one miRNA, each column represents one serum sample.
Supplementary files format and content: For miR.Counts_plasma.csv, each row represents one miRNA, each column represents one plasma sample.

extract_protocol:
RNAs were isolated using the tRNA/YRNA Depletion Protocol.
Libraries were prepared for sequencing with the automated Gel-Free option in the NEXTFLEX® Small RNA-Seq Kit v3.

value: Plasma

value: Female

value: AD


title: wild type L4 experiment 1rep1

status: Public on Feb 26 2024

type: SRA

city: Bethesda

first: Katherine

last: McJunkin

state: MD

address: 50 South Drive, Building 50 Room 3148

country: USA

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
Small RNA libraries were trimmed using Cutadapt 3.4 (122), then mapped using bowtie2 2.4.4 with settings “--no-unal --end-to-end –sensitive” (123). BAM files were sorted and indexed using samtools 1.13, then assigned to miRNAs using htseq 0.13.5 (124, 125). For genome mapping and miRNA assignment, custom reference files were used which included the spiked in RNA oligos. Statistical analysis was performed using DESeq2 and GraphPad Prism (126). For spike-in normalization (Figure S3), size factors for DESeq2 analysis were calculated by dividing spike-in reads in each sample by the median number of spike-in reads per sample. For all other analyses, default DESeq2 normalization was performed using all endogenous miRNA-mapping reads (spike-in reads were excluded from analysis).
Assembly: genome_c_elegans.PRJNA13758.WS280.genomic_with_spike_mut_mir35.fa
Assembly: cel_mirGeneDB_spikeins_010622.gff
Supplementary files format and content: xlsx file containing counts of reads mapped to miRNA and spike in RNA annotations

molecule: total RNA

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Nematode culture was performed on NGM plates seeded with OP50. Worms were maintained at 20°C except where otherwise noted. Embryo samples were harvested by hypochlorite treatment. For L4 and young adult samples, L1s were hatched overnight in M9 supplemented with cholesterol, then grown on NGM with OP50 for 48h at 20°C (for L4s) or for 44h at 25°C (for young adults).

extract_protocol:
Samples were snap frozen, then resuspended in Trizol and vortexed for 15 minutes at room temperature. Thereafter, total RNA was purified according to the Trizol manufacturer’s instructions (ThermoFisher).
Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37C.

tag: tissue

tag: strain

tag: dev stage

tag: genotype

value: wild type

tag: alias in_text_and_figures

tag: Sex

value: hermaphrodite

value: whole animal


title: Plasma,MCI,14

city: Maastricht

first: Qingfeng

last: Wen

state: Limburg

address: Universiteitssingel 40

department: Department of Toxicogenomics

country: Netherlands

institute: Maastricht University

description:
Memories_AZM06704_Plasma_S3_R1_001.fastq
miR.Counts_plasma.csv

organism: Homo sapiens

source_name: Plasma

tag: age

tag: disease state

value: MCI

tag: subject


title: Plasma,MCI,15

description:
Memories_AZM06708_Plasma_S43_R1_001.fastq
miR.Counts_plasma.csv


title: dmso+pid 1-X per treatment/timepoint group rep 3

city: San Diego

first: Richard

last: Virgen-Slane

state: CA

address: 0777 Science Center Drive, CB4-2131, Pfizer La Jolla

department: Global Computational Safety Science, DSRD

institute: Pfizer

description: pid

data_processing:
aligned sample reads to Ensembl Macaca_fascicularis_6.0 using Salmon v 14.0
Assembly: Crab-eating macaque (Macaca_fascicularis_6.0)
Supplementary files format and content: txt file

organism: Macaca fascicularis

source_name: PBMCs

growth_protocol: PBMCs from immunized monkeys were thawed and washed with CTL Anti-Aggregate WashTM Solution (ImmunoSpot/Cellular Technology Limited), resuspended in CTL-TestTM Media (ImmunoSpot/Cellular Technology Limited), counted, and evaluated for viability

extract_protocol:
RNA isolation was performed using the Qiagen RNeasy Lipid Tissue (Qiagen, #74804) protocol on the Qiacubes according to manufacturer’s instruction
25 ng RNA was used as input for the Lexogen QuantSeq 3’mRNA-Seq Library Preparation kit for Illumina (Forward ) (Lexogen, #015.96) and libraries were prepared according to the manufacturer’s protocol
3' bulk RNAseq

treatment_protocol: AAV9 peptide pool (3 mg/mL/peptide final concentration) or DMSO (negative control) or anti-CD3 (positive control) were added, and cells were cultured for approximately 24 hours at 37oC with 5% CO2

value: PBMCs

value: WT

tag: treatment

value: dmso


title: freshly prepared axillary TN cells with high TTS, biol rep3

city: Ichikawa

first: Takashi

last: Sekiya

state: Chiba

address: 1-7-1 Kohnodai

country: Japan

institute: National Center for Global Health and Medicine

library_source: genomic

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
Generated sequencing reads in FASTQ format were mapped to mm10 reference genome using bowtie2.
Reads mapped to the "black list" regions were removed with intersectBed command, inputting the bed file which denotes the black list region (mm10-blacklist.v2.bed.gz).
Peak calling was performed with MACS14, with default parameters.
Assembly: bedGraph files were generated using MACS14. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak  files were generated using MACS14 with default settings.
Supplementary files format and content: mm10
Supplementary files format and content: bedGraph, narrowPeak

molecule: genomic DNA

organism: Mus musculus

source_name: axillary lymph node

extract_protocol:
5x10^5 cells were suspended in 200 μl Hypotonic buffer (20 mM Tris pH 7.5, 10 mM NaCl, 3 mM ), and incubated for 15 min on ice. Then, 10 μl 10% NP-40 was added to the sample and vortexed for 10 sec at maximum speed. Nuclei were pelleted by centrifugation at 6,000 rpm for 5 min.
Nuclei pelets were suspended in 40 μl 1x Tagmentation buffer. Samples were added with 2 μl Tagment DNA Enzyme 1, and incubated for 30 min at 37 oC. Then, samples were cleaned up with FastGene Gel/PCR clean up kit (Nippon Genetics), and eluted with 20 μl elution buffer. 5 μl of the eluted samples were PCR amplified with index 1 (i7) and index 2 (i5) adapter primers, using PCR Primer Cocktail which was attached to Nextera DNA Library Preparation Kit.

value: axillary lymph node

tag: cell type

value: naive CD4+ T cells

value: no treatment


title: freshly prepared axillary TN cells with low TTS, biol rep2


title: ebax-1(null) young adult experiment 2rep3

description: Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37C.

value: young adult

value: ebax-1(tm2321) IV


title: Plasma,MCI,11

description:
Memories_AZM06695_Plasma_S1_R1_001.fastq
miR.Counts_plasma.csv

value: Male


title: freshly prepared axillary TN cells with high TTS, biol rep2


title: St35_het2

city: New York

first: Ziyan

last: Lin

state: NY

department: Applied Bioinformatics Laboratories

institute: NYU Grossman School of Medicine

data_processing:
NovaSeq 6000 System (RTA Version 3.4.4)
bcl2Fastq v2.20
Trimming, alignment and generating count matrix were all done by using the sns/rna-star pipeline (https://igordot.github.io/sns/routes/rna-star.html)
Assembly: Xentr10.0 (http://ftp.xenbase.org/pub/Genomics/JGI/Xentr10.0/XENTR_10.0_genome.fasta.gz)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: Embryos were grown in NAM until desired stage of collection

extract_protocol:
Pools of 5 embryos were used for RNA extraction via the Qiagen Rneasy Micro Kit
Automated stranded RNA-seq library prep, polyA selection

value: whole embryo

value: Sf3b4 heterozygous


title: freshly prepared mLN TN cells with high TTS, biol rep3

source_name: mesenteric lymph node

value: mesenteric lymph node


title: Plasma,MCI,10

description:
Memories_AZM06694_Plasma_S161_R1_001.fastq
miR.Counts_plasma.csv

value: Plasma

value: Female


title: Y47(mir-243bs_del) young adult experiment 2rep3

value: hermaphrodite


title: Y47(mir-243bs_del); alg-1(AEDH); alg-2(AEDH)  young adult experiment 2rep3

value: whole animal


title: Plasma,MCI,9

description:
Memories_AZM06686_Plasma_S139_R1_001.fastq
miR.Counts_plasma.csv

value: MCI


title: St35_null1

value: Sf3b4 null


title: freshly prepared axillary TN cells with low TTS, biol rep1

value: WT


title: Plasma,MCI,12

description:
Memories_AZM06699_Plasma_S163_R1_001.fastq
miR.Counts_plasma.csv


title: St35_het1


title: alg-1(AEDH); alg-2(AEDH)  young adult experiment 2rep3

value: alg-2(cdb155) II; alg-1(cdb153) X

value: alg-1(AEDH); alg-2(AEDH)


title: freshly prepared axillary TN cells with low TTS, biol rep3

value: axillary lymph node

value: naive CD4+ T cells


title: St35_null2


title: freshly prepared mLN TN cells with high TTS, biol rep1

value: no treatment


title: Plasma,AD,8

description:
Memories_AZM06679_Plasma_S92_R1_001.fastq
miR.Counts_plasma.csv

value: AD


title: wild type young adult experiment 2rep3

value: young adult

value: wild type


title: Plasma,MCI,8

description:
Memories_AZM06675_Plasma_S138_R1_001.fastq
miR.Counts_plasma.csv

value: Male


title: freshly prepared mLN TN cells with low TTS, biol rep3

value: mesenteric lymph node


title: ebax-1(null); alg-1(AEDH); alg-2(AEDH)  young adult experiment 2rep2

value: ebax-1(null); alg-1(AEDH); alg-2(AEDH)


title: Plasma,MCI,7

description:
Memories_AZM06674_Plasma_S117_R1_001.fastq
miR.Counts_plasma.csv

value: Plasma

value: Female


title: ebax-1(null) young adult experiment 2rep2

value: ebax-1(tm2321) IV

value: hermaphrodite

value: whole animal


title: freshly prepared mLN TN cells with low TTS, biol rep2

value: WT


title: St25_null1

value: whole embryo

value: Sf3b4 null


title: freshly prepared mLN TN cells with high TTS, biol rep2


title: Plasma,MCI,6

description:
Memories_AZM06673_Plasma_S95_R1_001.fastq
miR.Counts_plasma.csv

value: MCI


title: Plasma,MCI,5

description:
Memories_AZM06672_Plasma_S89_R1_001.fastq
miR.Counts_plasma.csv


title: Plasma,MCI,4

description:
Memories_AZM06669_Plasma_S144_R1_001.fastq
miR.Counts_plasma.csv


title: St25_het2

value: Sf3b4 heterozygous


title: St25_wt2


title: tau P251L KI, replicate 3, scRNAseq

city: Boston

first: Hassan

last: Bukhari

state: MA

address: 77, Avenue Louise Pasteur

department: Pathology

institute: Brigham and Womens hospital

description: 10 X genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cellranger, version 6.0, 10x Genomics.(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
For Control 1, Control 3 and tauP251L KI 3  libraries were sequenced once with enough sequencing depth. For control 2, tau P251L KI 1 and tau P251L KI 2, the libraries were sequenced twice to get enough sequencing depth.
Assembly: Drosophila Melanogaster
Supplementary files format and content: Tab-separated values files and matrix files

organism: Drosophila melanogaster

source_name: Brain

extract_protocol:
20 male and 20 female Drosophila brain of the appropriate geneotype were dissected were dissected on ice cold Schneider’s medium. After a brief wash with PBS, the brains were incubated with 0.05% trypsin-EDTA (Fisher scientific) for 30 minutes, with continuous pipetting every 5 minutes. The dissociated tissue were filtered through a 10um cell strainer to get a single cell suspension.
10x libraries were constructed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3' Kit v3.1).

value: Brain

value: Brain cells

value: elav-tau P251L KI

value: Tau P251L mutant


title: ebax-1(null) young adult experiment 2rep1

value: young adult


title: ebax-1(null); alg-1(AEDH); alg-2(AEDH)  young adult experiment 2rep1


title: freshly prepared mLN TN cells with low TTS, biol rep1

value: mesenteric lymph node

value: naive CD4+ T cells

value: no treatment


title: St15_wt2


title: St25_het1


title: freshly prepared spleen TN cells with high TTS, biol rep2

source_name: Spleen

value: Spleen


title: freshly prepared spleen TN cells with high TTS, biol rep3


title: Plasma,MCI,3

description:
Memories_AZM06639_Plasma_S42_R1_001.fastq
miR.Counts_plasma.csv

value: Plasma

value: Male


title: freshly prepared spleen TN cells with low TTS, biol rep3


title: St25_wt1


title: St15_wt1


title: tau P251L KI, replicate 1, scRNAseq

description: 10 X genomics


title: Plasma,AD,6

description:
Memories_AZM06591_Plasma_S17_R1_001.fastq
miR.Counts_plasma.csv

value: Female

value: AD


title: Plasma,AD,7

description:
Memories_AZM06666_Plasma_S65_R1_001.fastq
miR.Counts_plasma.csv


title: tau P251L KI, replicate 2, scRNAseq

description: 10 X genomics


title: freshly prepared spleen TN cells with low TTS, biol rep2

value: WT


title: Control, replicate 3, scRNAseq

description: 10 X genomics

value: wild type


title: St25_null2

value: whole embryo

value: Sf3b4 null


title: Plasma,MCI,2

description:
Memories_AZM06569_Plasma_S97_R1_001.fastq
miR.Counts_plasma.csv

value: MCI


title: St15_het2

value: Sf3b4 heterozygous


title: freshly prepared spleen TN cells with low TTS, biol rep1


title: Plasma,MCI,1

description:
Memories_AZM06542_Plasma_S49_R1_001.fastq
miR.Counts_plasma.csv


title: St15_het1


title: Control, replicate 2, scRNAseq

description: 10 X genomics

value: Brain

value: Brain cells


title: freshly prepared spleen TN cells with high TTS,biol  rep1


title: AI04-2

status: Public on Feb 25 2024

type: RNA

city: Montreal

first: Jo Anne

last: Stratton

address: 3801 Rue University

country: Canada

institute: McGill University

description: merscope instrument

data_processing:
Following generation of MERSCOPE outputs and cell segmentation via Cellpose, gene count matrices and cell centroid definitions were defined using squidpy (v1.3.1).
Cells were categorized as within our outside the heart for the purpose of this study via their spatial position, utilizing user input to define a bounding box around the heart.
Data and metadata generated previously was then analyzed using the Seurat library (v5.0.1), conducting blind clustering to determine cell identities, then determining DEGs between experimental conditions for relevant conditions.
processed data files format and content
*-mat.tar.gz: gzipped tar archive folder containing 3 files: bb.csv, a table defining the bounding box used to categorize cells as outside or within the heart; centroids.csv, a table containing x and y coordinates for centroids defining each cell boundary; counts.csv, a table containing raw counts of RNA levels for each cell (rows - gene symbols, columns - cell IDs)
metadata.csv: table defining per-cell metadata values, including clustering assignments, sample name, localization

extract_protocol: Vizgen provided protocols for requisite tissue type were utilized to conduct data acquisition


title: AH59-2

description: merscope instrument


title: AH59-5

description: merscope instrument


title: AH50-1

description: merscope instrument


title: AH59-6

description: merscope instrument


title: AI13-3

description: merscope instrument


title: St15_null1


title: circRNA_Control29

city: Amsterdam

first: Silvia

last: D'Ambrosi

address: De Boelelaan 1118

institute: Amsterdam UMC

description: RNA hybridization with 78-circRNA panel

hyb_protocol: Two different nCounter panels for the analysis of platelet-derived RNA. The Human Immunology V2 Panel (NanoString Technologies) targets 594 genes involved in the immune response such as cytokines, enzymes, interferons, and their receptors. For each sample, 6 ng of total platelet RNA was hybridized with the biotinylated capture probe and the reporter probe attached to color-barcode tags for 18 hours at 65°C. The second panel was a custom-made panel targeting 78 circRNAs (78-circRNA Panel), 6 linear reference genes and 4 mRNAs. For this analysis, 8 ng of total platelet RNA from each sample was hybridized with the capture and reporter probes for 18 hours at 67°C.

scan_protocol: The automated nCounter® Prep Station was used to process the samples. The samples were purified and immobilized in a sample cartridge for data collection, where the target mRNA and circRNA in each hybridized sample were quantified, using the nCounter Digital Analyzer.

data_processing:
Pre-processing and normalization of the data were performed using R (version 4.0.3) and Rstudio as graphical interface (version 2022.02.2). The quality of the raw RCC proprietary format data was initially assessed by using the NanoStringQCPro (version 1.22.0) package. Standard control metrics embedded by NanoString, such as Imaging, Binding Density, Positive Control Linearity, and Limit of Detection, were used to search for any potential outlier samples.
Additionally, all samples were also subjected to supplementary exploratory examination, including Principal Component Analysis (PCA) and Inter Quartile Range (IQR) method for outlier detection. Samples higher than the upper bound (Q3 + 1.5 * IQR) or lower than the lower bound (Q1 - 1.5 * IQR) were excluded from subsequent analysis.
Prior to normalization, negative control probes embedded to each panel were used to filter out targets with poor expression and high background noise. Consequently, the background values were firstly calculated, by taking the mean of each sample’s Negative Controls increased by two times the standard deviation, and then removed from each sample. Any transcript that indicated a score of less or equal to 0 in more than 75% of the examined samples, was excluded from further examination. After this filtering steps, the data was again evaluated using a PCA plot. Two different packages were compared for the normalization of the data: DESeq2 (version 1.30.1) and edgeR (version 3.32.1). The normalization performance was assessed using the standard relative log expression (RLE) plot. DESeq2 was chosen as default to perform the normalization of the data. Differential expression (DE) analysis was performed to find significantly differentially (|FC|>0.5 and p-adj < 0.05) expressed genes between the cancer and control groups.

label: biotin

source_name: platelets

label_protocol: According to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA).

extract_protocol: Platelets isolation from the whole blood specimens was performed by separating platelet-rich plasma (PRP) and nucleated blood cells, by centrifugation at 120 g for 20 minutes, followed by PRP centrifugation at 360 g for 20 minutes at room temperature. Resulting platelets pellet was re-suspended in RNAlater. Total RNA isolation was carried out using the mirVana RNA isolation kit according to the manufacturer's instructions (Ambion, Thermo Scientific, cat. no. AM1560). Extracted RNA was eluded in 30 μl of mirVana buffer

value: control

tag: Stage

value: platelets

value: whole blood

tag: fraction

value: circRNA


title: circRNA_Control30

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control25

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control23

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control27

description: RNA hybridization with 78-circRNA panel

value: nodules


title: circRNA_Control24

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control28

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control20

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control22

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control19

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control17

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control18

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control15

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control21

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control16

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer30

description: RNA hybridization with 78-circRNA panel

value: lung cancer


title: circRNA_Cancer29

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer26

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer25

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control26

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer27

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer24

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer23

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control13

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control14

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer22

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control12

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer21

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control11

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer18

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control9

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer16

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer15

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer17

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control8

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer28

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control7

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control10

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer9

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer8

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer7

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer14

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer19

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer13

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control6

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer12

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer11

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control3

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer20

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control2

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer3

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control1

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer2

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer4

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer1

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer10

description: RNA hybridization with 78-circRNA panel


title: circRNA_Control5

description: RNA hybridization with 78-circRNA panel


title: circRNA_Cancer6

description: RNA hybridization with 78-circRNA panel


title: Infection with Fusarium and treated with pulsed light (12J), rep 2

city: Rio de Janeiro

first: Luis

middle: Willian

last: Pacheco Arge

state: Rio de Janeiro

address: Av. Carlos Chagas Filho, 373

department: Genetica

country: Brazil

institute: UFRJ

data_processing:
The cleaning step was performed with Trimmomatic v.0.39, with the following parameters: PE, ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 to remove possible adapters; SLIDINGWINDOW:4:15 to remove bases with quality (Q) < 15 in a 4-base window; and, MINLEN:36 to maintain reads with at least 36 bases.
Read mapping step was performed against the Cucumis melo (build 3.6.1) genome with annotation Ver. 4.0 using the software Star Ver. 2.5.3a with default parameters.
Mapped reads were counted using HTSeq Ver. 0.9.1.
Genes with low expression values (CPM<1) were removed from differential expression analysis.
Differential expression analysis was performed using EdgeR Ver. 3.9 (FDR<0.05).
Assembly: Cucumis melo (build 3.6.1) genome with annotation Ver. 4.0
Supplementary files format and content: Tab-delimited text file includes raw counts for each library
Supplementary files format and content: Tab-delimited text file includes TPM values for each library

organism: Cucumis melo

source_name: Epicarp

extract_protocol:
The RNA extraction was carried out using CTAB-pBIOZOL protocol. The quality and quantity of RNA were assessed using both NanoDrop and Agilent 2100 bioanalyzer systems.
For RNA-seq library preparation, the TruSeq RNA Library Prep Kit v2 was employed following the manufacturer's instructions. Subsequently, the libraries were sequenced using the Illumina HiSeq 3000 platform.

value: Epicarp

tag: cell line

value: fruit

value: Goldex

value: Infection with Fusarium + pulsed light (12J)


title: No infection and treated with pulsed light (9J), rep 3

value: No infection + PL (9J)


title: No infection and treated with pulsed light (0J), rep 1

value: No infection + PL (0J)


title: No infection and treated with pulsed light (0J), rep 2


title: No infection and treated with pulsed light (0J), rep 3


title: No infection and treated with pulsed light (9J), rep 1


title: Infection with Fusarium and treated with pulsed light (12J), rep 1


title: Infection with Fusarium and treated with pulsed light (9J), rep 3

value: Infection with Fusarium + pulsed light (9J)


title: Infection with Fusarium and treated with pulsed light (9J), rep 2


title: circRNA_Control4

description: RNA hybridization with 78-circRNA panel


title: Infection with Fusarium and treated with pulsed light (9J), rep 1


title: Infection with Fusarium and treated with pulsed light (6J), rep 3

value: Infection with Fusarium + pulsed light (6J)


title: Infection with Fusarium and treated with pulsed light (0J), rep 3

value: Infection with Fusarium + pulsed light (0J)


title: Infection with Fusarium and treated with pulsed light (0J), rep 2


title: Infection with Fusarium and treated with pulsed light (6J), rep 1


title: circRNA_Cancer5

description: RNA hybridization with 78-circRNA panel


title: Infection with Fusarium and treated with pulsed light (0J), rep 1


title: No infection and treated with pulsed light (9J), rep 2


title: Horse 6, naïve

city: Raleigh

first: Lauren

middle: V.

last: Schnabel

state: NC

address: 1060 William Moore Dr

department: Clinical Sciences

institute: North Carolina State University

description: NaiveSassy

data_processing:
Sequence reads were trimmed to remove possible adaptor sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the EquCab 3.0 reference genome available on ENSEMBL using the STAR aligner v2.5.2b.
Unique gene hit counts were calculated using featureCounts from the Subread package v1.5.2.
Read count extraction and normalization were performed using DESeq2.
Assembly: EquCab 3.0
Supplementary files format and content: tab-deliniated text file containing normalized gene expression data

organism: Equus caballus

source_name: mesenchymal stem cells

growth_protocol: Primary equine bone marrow-derived mesenchymal cells were maintained in low glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using the Rneasy Mini Kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
PolyA selection

treatment_protocol: MSCs were seeded at 0.163x10^6 cells per 100 mm plate and grown for 72 hours in standard MSC media or media containing 2 ng/ml recombinant human IL-1b + 1 ng/ml recombinant human TGF-b2

tag: source

value: Bone marrow

value: mesenchymal stem cells

value: Naive


title: Horse 6, licensed

description: DualSassy

value: IL-1beta + TGF-beta2


title: Horse 4, naïve

description: NaiveHannah


title: Horse 5, licensed

description: DualHerman


title: Infection with Fusarium and treated with pulsed light (12J), rep 3


title: Horse 5, naïve

description: NaiveHerman


title: Horse 4, licensed

description: DualHannah


title: Horse 3, naïve

description: NaiveGlorioso


title: Horse 2, naïve

description: NaiveElle


title: Horse 1, naïve

description: NaiveDrusco


title: Horse 2, licensed

description: DualElle


title: 66cl4_chitin+anti-PD-1_tumor5

city: Merelbeke

first: Jonas

last: Steenbrugge

address: Salisburylaan 133

department: Veterinary and Biosciences

country: Belgium

institute: Ghent University

data_processing:
Reads were mapped to the mouse reference genome (mm10) using HISAT2.
Read counts were generated using the summariseOverlaps function from the BioConductor package GenomicAlignments.
Raw counts were VST-normalized and up- or downregulated expression of selected genes associated with innate immunity, T-cell exhaustion, T-cell activation and inflammation in the different treatment groups was evaluated.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including VST-normalized read counts for samples from all treatment groups, derived from both the 4T1- and 66cl4-based model.

source_name: 66cl4 primary tumor

extract_protocol:
Primary tumors were removed, flash frozen in liquid nitrogen, and RNA was isolated using the Rneasy Mini Kit (QiAgen, Valencia, CA, USA) according to the manufacturer's instructions. 250 ng of total RNA was subjected to a stranded library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Individually-caged mice were assigned to a group and provided with treatment, single-blinded (up to the end of the study) in a climate-controlled animal facility. Systemic administration of 1 mg chitin (1-10 µm particle size)/mouse was established through intraperitoneal (i.p.) injection of 100 µl of a 10 mg/ml chitin mixture. Anti-mPD-1-mIgG1e3 InvivoFit™ (Invivogen, San Diego, USA) derived from clone RMP1-14 was used for anti-PD-1 ICB through i.p. injection at 200 µg/mouse.

value: 66cl4 primary tumor

value: WT female BALB/c


title: Infection with Fusarium and treated with pulsed light (6J), rep 2


title: 66cl4_chitin+anti-PD-1_tumor4


title: Horse 1, licensed

description: DualDrusco


title: 66cl4_chitin+anti-PD-1_tumor3


title: 66cl4_chitin+anti-PD-1_tumor2


title: 66cl4_chitin_tumor4

value: chitin


title: 66cl4_chitin_tumor5


title: 66cl4_chitin_tumor3


title: DIP_INPUT

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

institute: mie university

data_processing:
Reads were mapped on the P. berghei genome using Bowtie 2.0 with default settings. The reads mapped onto multiple sites were removed using grep command. The SAM files were sorted using samtools to produce BAM files. The mapping data were analyzed with the MACS2 peak-calling algorithm.
Assembly: PlasmoDB, version 3
Supplementary files format and content: Peak-calling, text.

organism: Plasmodium berghei ANKA

source_name: ANKA

extract_protocol:
Recombinant homeodomain fused with GST  was incubated with P. berghei ANKA genomic DNA fragments in binding/washing buffer (10 μM ZnSO4, 2 mM MgCl2, 2 mM Tris-HCl at pH 7.4, 100 mM KCl, and 10% glycerol) for 30 min. The protein/DNA solution was further mixed with glutathione-sepharose resin and incubated for 30 min. After incubation, the resin was washed three times with binding/washing buffer, and bound protein-DNA complexes were eluted with 10 mM glutathione solution.
Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems),

value: ANKA


title: Horse 3, licensed

description: DualGlorioso


title: 66cl4_chitin_tumor2


title: 66cl4_anti-PD-1_tumor4


title: 66cl4_anti-PD-1_tumor5


title: 66cl4_anti-PD-1_tumor3


title: Kat6a_WT_Kat6b_DECDEC_C57Bl6_2

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Thebase calling and quality scoring were determined using Real-Time Analysis on board software v2.4.6
Reads were aligned to the mouse genome by Rsubread version 2.4.3
Fragment (read-pair) counts were summarized by Ensembl Gene ID using the Rsubread featureCounts function
Genes were identified using Gencode annotation to the mm10 genome, version M25
Assembly: mm10
Supplementary files format and content: tab-delimited text files wre written from the R prompt; columns represent Ensembl Gene ID, total gene length (total base count of all exons) and the number of fragments mapping to that gene

molecule: polyA RNA

source_name: Foetal Liver

growth_protocol: Cells were used ex vivo immediately after FACS isolation from E14.5 fetal livers. They were not grown in culture.

extract_protocol:
RNA was isolated using the Qiagen RNeasy micro kit (Qiagen, 74004) and RNA quality and concentration determined using the High Sensitivity 4200 Tapestation (Agilent).
50 ng RNA was used to generate RNA libraries using the Illumina TruSeq RNA library kit (Illumina).

treatment_protocol: The experimental groups were LSK cells isolated from mice distinguished by genotype: on a C57BL/6 genetic background: wild-type, Kat6b–/– null, Kat6a+/– single heterozygous and Kat6a+/–Kat6b+/– double heterozygous; on a FVBxBALB/c mixed genetic background: wild-type and Tg(Kat6b) overexpressing.Animals and cells were not treated.

value: Foetal Liver

tag: kat6a genotype

value: WT

tag: kat6b genotype

value: DEC/DEC

value: Male

tag: litter


title: Kat6a_WT_Kat6b_DECDEC_C57Bl6_1

tag: tissue

tag: strain


title: Kat6a_WT_Kat6b_DECDEC_C57Bl6_4


title: 66cl4_chitin+anti-PD-1_tumor1

tag: genotype


title: Kat6a_WT_Kat6b_WT_C57Bl6_4

value: Female


title: Kat6a_WT_Kat6b_DECDEC_C57Bl6_3


title: 66cl4_anti-PD-1_tumor2


title: Kat6a_WT_Kat6b_WT_C57Bl6_3


title: microglia_cko_EAE_rep3

city: Harbin

first: Jiahui

last: Zhu

state: HEILONGJIANG SHENG

address: No.157 Baojian Road, Nangang District

department: Neurobiology

country: China

institute: Harbin Medical University

description: Gene expression data of brian microglia from cko mice at EAE peak stage

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on  Affymetrix Mouse Transcriptome Array 1.0 in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip 3000 7G (Thermo Fisher Scientific, USA).

data_processing: Expression data were generated by GeneChip Operating Software and normalized by the RMA(Robust Multi-chip Average ) method.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol by using GeneChip® WT PLUS Reagent Kit

growth_protocol: Mice were kept on 7:30-19:30 light cycle in a humidity (40-70%) and temperature (22-25°C) controlled environment. They were group-housed (4-6/cage) throughout the experimental period with ad libitum access to food and water. Mice were bred and maintained in a specific-pathogen-free room at Harbin Medical University.

extract_protocol: Total RNA of brain microglia was extracted with TRIzol reagent (Generay Biotech, Shanghai, China) according to the manufacturer’s recommendations and quantified using spectrophotometry.

treatment_protocol: Mice were each immunized subcutaneously on the back with 100 μg recombinant MOG (rMOG, Chinapeptides, Shanghai, China) in 100 μL IFA. Mice received intravenous 300 ng injections of pertussis toxin (List Biological Laboratories, Inc., Campbell, CA) on the day of immunization and 48 h later. Mice were euthanized at peak stage of EAE to collect microglia from the brain.

tag: gender

value: female

tag: genotype/variation

value: B cell conditional knock-out

tag: tissue/cell type

value: brain microglia at EAE peak stage


title: 66cl4_anti-PD-1_tumor1


title: Kat6a_WT_Kat6b_WT_C57Bl6_2

tag: Sex


title: Kat6a_WT_Kat6b_WT_C57Bl6_1


title: microglia_ctrl_EAE_rep3

description: Gene expression data of brian microglia from control mice at EAE peak stage

value: control


title: HDP1_DIP


title: microglia_cko_EAE_rep1


title: microglia_ctrl_EAE_rep1


title: microglia_cko_EAE_rep2


title: microglia_ctrl_EAE_rep2


title: 66cl4_untreated_tumor4

value: untreated


title: Kat6a_CFD_Kat6b_DEC_C57Bl6_3

value: CFD/+

value: DEC/+


title: 66cl4_untreated_tumor3


title: Kat6a_CFD_Kat6b_DEC_C57Bl6_4


title: 66cl4_chitin_tumor1


title: 66cl4_untreated_tumor2


title: Kat6a_CFD_Kat6b_DEC_C57Bl6_2


title: 66cl4_untreated_tumor1


title: Kat6a_CFD_Kat6b_DEC_C57Bl6_1


title: 4T1_chitin+anti-PD-1_tumor5

source_name: 4T1 primary tumor

value: 4T1 primary tumor


title: Kat6a_CFD_Kat6b_WT_C57Bl6_4


title: Kat6a_CFD_Kat6b_WT_C57Bl6_3


title: 4T1_chitin+anti-PD-1_tumor3


title: 66cl4_untreated_tumor5

value: 66cl4 primary tumor


title: 4T1_chitin+anti-PD-1_tumor4

value: WT female BALB/c


title: 4T1_chitin+anti-PD-1_tumor2


title: Kat6a_CFD_Kat6b_WT_C57Bl6_2


title: 4T1_chitin+anti-PD-1_tumor1


title: Kat6a_CFD_Kat6b_WT_C57Bl6_1


title: 4T1_chitin_tumor4

value: chitin


title: 4T1_chitin_tumor5


title: 4T1_chitin_tumor3


title: Kat6a_WT_Kat6b_TG_FvBxBalbC_2

value: Transgenic

value: FvBxBalbC


title: Kat6a_WT_Kat6b_WT_FvBxBalbC_4

value: Foetal Liver

value: WT


title: 4T1_chitin_tumor2


title: Kat6a_WT_Kat6b_TG_FvBxBalbC_4

value: Male


title: Kat6a_WT_Kat6b_TG_FvBxBalbC_3


title: Kat6a_WT_Kat6b_WT_FvBxBalbC_3


title: 4T1_chitin_tumor1


title: Kat6a_WT_Kat6b_TG_FvBxBalbC_1


title: 4T1_anti-PD-1_tumor5


title: 4T1_anti-PD-1_tumor3


title: 4T1_anti-PD-1_tumor4


title: Kat6a_WT_Kat6b_WT_FvBxBalbC_2


title: Kat6a_WT_Kat6b_WT_FvBxBalbC_1


title: Non-Carrier16_Heart_CCR2n

city: Freiburg

first: Ingo

last: Hilgendorf

address: Hugstetter Straße 55

department: Department of Cardiology and Angiology

country: Germany

institute: UNIVERSITY HOSPITAL FREIBURG University Heart Center Freiburg-Bad Krozingen

data_processing:
Paired-end reads were trimmed to remove the adaptors and low-quality ends.
Trimmed reads were aligned to the human genome (protein-coding genes) using STAR.
Primary aligned reads were annotated and quantified as counts of features (exon) using FeatureCounts.
Assembly: GRCh38 assembly (hg38)
Supplementary files format and content: tab-delimited text files including feature counts of each sample

source_name: Heart

extract_protocol:
Cells were directly sorted in RLT-plus lysis buffer with 1% beta-mercaptoethanol. DNA and RNA were extracted using AllPrep DNA/RNA micro kit (Quigen)
The RNA library was made using NEBNext® Single Cell/Low Input RNA Library Prep Kit (New England BioLabs) and sequenced on Illumina NextSeq Instrument.

treatment_protocol: Blood monocytes, plaque macrophages, heart monocytes, heart CCR2+ macrophages, and heart CCR2- macrophages  were isolated by fluorescent activated cell sorting from freshly processed patient blood or cardiovascular tissue samples.

value: Heart

value: CCR2- macrophage


title: Non-Carrier16_Heart_mono

value: Monocyte


title: Non-Carrier16_Heart_CCR2p

value: CCR2+ macrophage


title: 4T1_anti-PD-1_tumor1


title: 4T1_anti-PD-1_tumor2


title: 4T1_untreated_tumor5


title: Non-Carrier16_Blood_mono

source_name: Blood

value: Blood


title: Non-Carrier15_Heart_CCR2n


title: Non-Carrier15_Heart_CCR2p


title: 4T1_untreated_tumor2

value: untreated


title: 4T1_untreated_tumor3


title: Non-Carrier14_Heart_CCR2n


title: 4T1_untreated_tumor1


title: PLLB_miRNA

city: Urumqi

first: Zengru

last: Xie

state: Xinjiang

address: 137 Liyushan South Road

institute: The First Affiliated Hospital of Xinjiang Medical University

data_processing:
1.mRNA data quality control: FastQC software and R were used to evaluate the quality of raw sequencing data；2. mRNA reference genome alignment, using STAR software to align the filtered reads with the reference database；3.mRNA analysis, using Stringtie's analysis workflow to quantify the expression of known genes and transcripts, using Deseq2 software to analyze differential genes, and significantly differentially differentiated gene GO and KEGG enrichment analysis
Assembly: mm39
Supplementary files format and content: raw_counts.txt

source_name: Bonemarrow

extract_protocol:
The concentration of RNA samples was ≥ 100 ng/μL, the total amount was > 2 μg, the OD value was between 1.8~2.2, the OD was ≥ 2.0, and Agilent 2100 was required The Bioanalyzer assays RIN ≥ 6.5 to ensure the construction of downstream high-quality mRNA-seq libraries
Library concentration and fragment length distributions were measured using Qubit and Agilent 2100 Bioanalyzers, respectively. The concentration is required to be >5ng/μl and the fragment length is concentrated Between 300-400 bp

value: Bonemarrow

value: Mesenchymalstemcells(MSCs)

value: Antigenintervention


title: PLLC_miRNA


title: Non-Carrier13_Heart_CCR2n


title: Non-Carrier14_Blood_mono


title: PLLA_miRNA


title: Non-Carrier14_Heart_CCR2p


title: Non-Carrier15_Blood_mono


title: NYB_miRNA


title: NYA_miRNA


title: Non-Carrier13_Heart_CCR2p


title: Non-Carrier13_Heart_mono


title: aFMC_miRNA


title: NYC_miRNA


title: Non-Carrier13_Blood_mono


title: Non-Carrier14_Heart_mono


title: aFMA_miRNA


title: DZC_miRNA


title: Non-Carrier12_Plaque_macro

source_name: Plaque

value: Plaque

value: Macrophage


title: 4T1_untreated_tumor4

value: 4T1 primary tumor

value: WT female BALB/c


title: Non-Carrier12_Blood_mono


title: aFMB_miRNA


title: Non-Carrier11_Plaque_macro


title: Non-Carrier15_Heart_mono


title: DZB_miRNA


title: DZA_miRNA


title: Non-Carrier11_Blood_mono


title: PLL_3


title: Non-Carrier10_Plaque_macro


title: PLL_2


title: Non-Carrier10_Blood_mono


title: PLL_1


title: NY_3


title: NY_2


title: Non-Carrier8_Heart_CCR2p

data_processing:
Paired-end reads were trimmed to remove the adaptors and low-quality ends.
Trimmed reads were aligned to the human genome (protein-coding genes) using STAR.
Primary aligned reads were annotated and quantified as counts of features (exon) using FeatureCounts.
Assembly: GRCh38 assembly (hg38)
Supplementary files format and content: tab-delimited text files including single-cell feature counts of each sample


title: Non-Carrier9_Blood_mono


title: Non-Carrier8_Heart_CCR2n


title: NY_1


title: Non-Carrier8_Heart_mono


title: Non-Carrier9_Plaque_macro


title: FM2


title: Non-Carrier8_Blood_mono


title: FM1


title: FM3


title: CONC


title: Non-Carrier7_Heart_CCR2p


title: CONB


title: CONA


title: Non-Carrier7_Heart_mono


title: Non-Carrier6_Heart_CCR2n


title: Non-Carrier7_Blood_mono


title: Non-Carrier6_Heart_CCR2p


title: CON2


title: CON1


title: Non-Carrier6_Heart_mono


title: CON_3


title: CON3


title: Non-Carrier6_Blood_mono


title: CON_2


title: Non-Carrier5_Heart_CCR2n


title: aFMB


title: Non-Carrier4_Plaque_macro


title: Non-Carrier5_Heart_CCR2p


title: Non-Carrier5_Heart_mono


title: Non-Carrier7_Heart_CCR2n


title: aFMC


title: aFM_1


title: Non-Carrier5_Blood_mono


title: Non-Carrier3_Plaque_macro


title: SQ23071771-ZNa-I6, BMDM, APT2-/-, LFn-Rod

city: Shanghai

first: Zhang

state: Shanghai

address: 100 Haike Rd, Building 13 Pudong New Area

institute: Chinese Academy of Sciences

data_processing:
Sequencing reads were mapped to the reference genome mm10 (GRCm38) from Gencode with hisat2 by default parameter.
The read counts for each gene were calculated by featureCounts58.
The count files were used as input to R package DESeq2 (v1.26.0)59 for normalization.
The count files were used as input to R package DESeq2 (v1.26.0)59 for differential expression genes.
Use GraphPad Prism 8.0 software to map volcanoes plot.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes read counts for each Sample

source_name: Bone marrow

growth_protocol: Primary BMDMs were obtained from the rear leg bone marrow of 2-month-old littermate and sex-matched mice and differentiated into macrophages for 6 days with 20% filtered L929 cell conditional medium (a source of macrophage colony-stimulating factor). Primary BMDMs were maintained in DMEM supplemented with 15% FBS and 100 units/ml penicillin/streptomycin.

extract_protocol:
Total RNA was extracted and purified using RNAiso Plus (TaKaRa)
RNA libraries were prepared according to instructions of Abclonal Fast RNA-seq Lib Prep Kit V2 (RK20306)

treatment_protocol: Primary BMDMs were treated with LFn-Rod (100ng/ml, 1.5h) plus protective antigen (1μg/ml) followed by treatment with 2-BP (50 μM) for 0.5 hours.

value: Bone marrow

value: Bone marrow derived macrophage

value: LFn-Rod


title: aFM_3


title: Non-Carrier4_Blood_mono

value: WT


title: aFMA


title: Non-Carrier2_Plaque_macro


title: SQ23071771-ZNa-I5, BMDM, APT2-/-, LFn-Rod


title: Non-Carrier2_Blood_mono


title: Non-Carrier1_Blood_mono


title: SQ23071771-ZNa-I2, BMDM, APT2+/+, LFn-Rod


title: SQ23071771-ZNa-I3, BMDM, APT2+/+, LFn-Rod


title: Non-Carrier3_Blood_mono


title: SQ23071771-ZNa-I1, BMDM, APT2+/+, LFn-Rod


title: Non-Carrier1_Plaque_macro


title: Carrier8_Heart_CCR2p

value: Heart

value: DNMT3A R729W


title: CON_1


title: SQ23071771-ZNa-H6, BMDM, Dhhc7-/-, LFn-Rod


title: aFM_2


title: Carrier8_Blood_mono

value: Monocyte


title: Carrier7_Heart_CCR2p

value: CCR2+ macrophage

value: DNMT3A R736L


title: SQ23071771-ZNa-H3, BMDM, Dhhc7+/+, LFn-Rod


title: SQ23071771-ZNa-H4, BMDM, Dhhc7-/-, LFn-Rod


title: Carrier7_Heart_mono


title: Carrier7_Heart_CCR2n

value: CCR2- macrophage


title: SQ23071771-ZNa-H2, BMDM, Dhhc7+/+, LFn-Rod


title: Carrier7_Blood_mono

value: Blood


title: SQ23071771-ZNa-H1, BMDM, Dhhc7+/+, LFn-Rod


title: SQ23071771-ZNa-I4, BMDM, APT2-/-, LFn-Rod


title: Carrier6_Heart_CCR2p

value: DNMT3A V563M


title: Carrier6_Heart_CCR2n


title: Carrier6_Heart_mono


title: SQ23071771-ZNa-G5, BMDM, WT, LFn-Rod+2-BP


title: Carrier8_Heart_CCR2n


title: SQ23071771-ZNa-G6, BMDM, WT, LFn-Rod+2-BP


title: SQ23071771-ZNa-G3, BMDM, WT, LFn-Rod


title: Carrier5_Heart_CCR2n


title: Carrier6_Blood_mono


title: SQ23071771-ZNa-G1, BMDM, WT, LFn-Rod


title: Carrier5_Heart_CCR2p


title: SQ23071771-ZNa-G2, BMDM, WT, LFn-Rod


title: SQ23066899-Zna-F8, BMDM, APT2-/-, Vehicle

growth_protocol: Primary BMDMs were obtained from the rear leg bone marrow of 2-month-old littermate and sex-matched mice and differentiated into macrophages for 6 days with 20% filtered L929 cell conditional medium (a source of macrophage colony-stimulating factor). Primary BMDMs were maintained in DMEM supplemented with 15% FBS and 100 units/ml penicillin/streptomycin; All animals were maintained in a specific pathogen-free environment, and animal experiments were conducted according to the protocols approved by the Standing Animal Care Committee at the Interdisciplinary Research Center on Biology and Chemistry.

treatment_protocol: Primary BMDMs were primed with LPS (100 ng/ml, 3h) followed by treatment with 2-BP (50 μM) for 0.5 hours; Mice aged 8-10 weeks were injected intraperitoneally with 54 mg LPS (E. coli O111:B4, Sigma)/kg body weight and 50 mg 2-BP (sigma)/kg body weight for 6 hours and sacrificed  for RAN-seq.

value: Vehicle


title: Carrier5_Blood_mono


title: SQ23066899-Zna-F9, BMDM, APT2-/-, Vehicle


title: Carrier8_Heart_mono


title: SQ23071771-ZNa-H5, BMDM, Dhhc7-/-, LFn-Rod


title: SQ23066899-Zna-F7, BMDM, APT2-/-, Vehicle


title: Carrier4_Plaque_macro

value: Plaque

value: DNMT3A W297G


title: Carrier4_Blood_mono


title: SQ23066899-Zna-F3, BMDM, APT2+/+, Vehicle


title: Carrier3_Blood_mono


title: SQ23066899-Zna-F2, BMDM, APT2+/+, Vehicle


title: SQ23066899-Zna-E8, BMDM, Dhhc7-/-, Vehicle


title: SQ23066899-Zna-F1, BMDM, APT2+/+, Vehicle


title: SQ23071771-ZNa-G4, BMDM, WT, LFn-Rod+2-BP


title: SQ23066899-Zna-E9, BMDM, Dhhc7-/-, Vehicle


title: Carrier2_Plaque_macro

value: Macrophage

value: DNMT3A C557*


title: SQ23066899-Zna-E2, BMDM, Dhhc7+/+, Vehicle

value: Bone marrow


title: Carrier1_Plaque_macro

value: DNMT3A G800S


title: SQ23066899-Zna-E1, BMDM, Dhhc7+/+, Vehicle

value: Bone marrow derived macrophage


title: benzo(a)pyrene, biological replicate 3

city: RENNES

first: Lydie

last: SPARFEL

address: 2 avenue du Pr Léon Bernard

department: IRSET U1085

country: France

institute: Inserm

data_processing:
After filtering low-quality reads and adaptor sequences, Fastq files were aligned using the Qiagen pipeline (QIAseq® miRNA Primary Quantification). The number of differentially expressed miRNAs between the two conditions was determined with the DESeq2 package (DESeq2_1.26.0). The standard DESq2 normalization method (DESeq2’s median of ratios with the DESeq2 function) was used, with a pre-filter of reads and miRNAs (reads uniquely mapped on the genome, and up to 10 different loci with a count adjustment, and miRNAs with at least 10 reads in at least 3 different samples). Following the package recommendations, the Wald test was used with the contrast function and the Benjamini-Hochberg False Discovery Rate control procedure to identify differentially expressed miRNAs.
Assembly: R scripts and parameters are available on GitHub (https://github.com/BSGenomique/genomic-rnaseq-pipeline/releases/tag/v1.0420).
Supplementary files format and content: Tabulated file with raw count from the Qiaseq Pipeline

source_name: Evs from PBMC

growth_protocol: EVs were isolated from conditioned media of independent PBMC cultures derived from blood donor buffy coats (written consent for the use of blood samples for the research protocol obtained according to the regulation for blood transfusion of the French blood organization Etablissement Français du Sang, Rennes (France)) by Ficoll (Eurobio, Les Ulis, France) gradient centrifugation

extract_protocol:
Isolation of small RNAs from PBMCs was performed using the total exosome RNA and protein isolation kit (Thermo Fisher Scientific).
To construct the libraries, 12 EVs isolated from independent PBMC cultures each grown in untreated (DMSO) and 2 µM B[a]P-treated conditions for 48 h, were combined in 3 equal pools (with 4 separate blood donors per pool) for each condition. 5 µL of each pool were used to isolate the small RNA fraction and processed using Qiaseq miRNA library prep kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: PBMCs were cultivated at 37°C with 5% CO2 in RPMI medium (Eurobio) supplemented with 20 IU/mL penicillin, 20 μg/mL streptomycin, and 10% decomplemented fetal calf serum (Lonza, Bale, Swiss) and exposed to PAHs, stocked in DMSO. The final concentration of DMSO in the culture medium was always < 0.2% v/v and control cultures received the same dose of DMSO as treated cultures. EVs were isolated from conditionned media.

value: Evs from PBMC

value: primary culture from blood donors

value: conditionned media

value: benzo(a)pyrene


title: Carrier5_Heart_mono

value: Heart

value: Monocyte


title: benzo(a)pyrene, biological replicate 2


title: Carrier1_Blood_mono


title: benzo(a)pyrene, biological replicate 1


title: SQ23066899-Zna-D9, BMDM, WT, 4-BP

value: WT


title: SQ23066899-Zna-D8, BMDM, WT, 3-BP


title: SQ23066899-Zna-D3, BMDM, WT, Vehicle


title: I500_Z5_2

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

description:
Transgenic
I500Z5_all_remap.mcool

data_processing:
Micro-C data was analyzed using the 4D Nucleome Hi-C analysis pipeline. Briefly, paired-end reads were mapped to either the dm6 reference genome, or a reconfigured genome with the transgene inserted into the -142kb attP site, using BWA v0.7.17 [Li and Durbin, 2009], and alignments were filtered using pairtools v0.2.2 to retain only uniquely-mapping reads with alignment quality ≥3. Reads were assigned to 100bp genomic bins, and “inward”/”outward” reads assigned to adjacent bins (separated by less than 50bp) were removed. Matrix aggregation and normalization were performed using Cooler v0.8.3 [Abdennur and Mirny 2019], using the built-in ICE balancing method. Matrices were visualized using HiGlass [Kerpedjiev et al. 2018]. Visual inspection of contact matrices showed high concordance between biological duplicates, which were therefore pooled to generate final high-coverage contact matrices for each genotype.
Assembly: dm6/custom
Supplementary files format and content: cool, valid pairs
Library strategy: Micro-C

source_name: Embryo

growth_protocol: Embryos were collected on yeasted apple juice plates at 25˚C. Embryos were collected for 4 hrs and subsequently incubated at 25˚C for 12 hrs.

extract_protocol:
Chromatin was digested with a pre-determined amount of Micrococcal Nuclease (Worthington Biochem) to yield a 90% mononucleosome / 10% dinucleosome ratio given the appropriate number of embryos.
Micro-C libraries were constructed as previously described [Hsieh et al. 2020], with the following modifications.
Libraries were barcoded, pooled and subjected to paired-end sequencing on an Illumina Novaseq S1 100nt Flowcell (read length 50 bases per mate, 6-base index read).

treatment_protocol: Embryos were collected in nylon mesh sieves, dechorionated for 3 mins in 3% sodium hypochlorite, rinsed with deionized water, and transferred to glass scintillation vials containing 6 mL PBST (0.1% Triton-X in PBS), 7.5 mL N-heptane, and 1.5 mL fresh 16% formaldehyde. Crosslinking was carried out at room temperature for exactly 15 mins on an orbital shaker at 250rpm, followed by addition of 5.5 mL 2M Tris-HCl pH7.5 and shaking for 5 mins to quench the reaction. Embryos were washed twice with >15mL PBST and stored at 4˚C while an additional 2-3 collection rounds were carried out (45 mins each). Pooled embryos were subjected to a secondary crosslinking in 15 mL DSG+EGS (ThermoFisher, 3 mM each) at room temperature for 45 mins on a rotating mixer. Following quenching by addition of 5.5 mL 2M Tris-HCl pH7.5 and rotation for 5 mins, the embryos were washed twice with PBST and stored at 4˚C overnight. Samples were hand-sorted the following day under a dissection microscope to remove inappropriately staged embryos, snap-frozen in liquid nitrogen and stored at -80˚C.

value: Embryo


title: I500_Z5_1

description:
Transgenic
I500Z5_all_remap.mcool


title: SQ23066899-Zna-D2, BMDM, WT, Vehicle


title: CTR (dimethylsulfoxide), biological replicate 3

value: DMSO


title: Carrier3_Plaque_macro


title: CTR (dimethylsulfoxide), biological replicate 2


title: SQ23066899-Zna-D1, BMDM, WT, Vehicle

value: Vehicle


title: Carrier2_Blood_mono

value: Blood


title: SQ23066899-Zna-F12, BMDM, APT2-/-, LPS

value: LPS


title: SQ23066899-Zna-F10, BMDM, APT2-/-, LPS


title: SQ23066899-Zna-E3, BMDM, Dhhc7+/+, Vehicle


title: CTR (dimethylsulfoxide), biological replicate 1


title: CDEF_Z5

description:
Transgenic
CDEF_Z5all_remap.mcool


title: SQ23066899-Zna-E7, BMDM, Dhhc7-/-, Vehicle


title: FEDC_5Z2

description:
Transgenic
FEDC_5Zall.mcool


title: SQ23066899-Zna-F11, BMDM, APT2-/-, LPS


title: SQ23066899-Zna-F6, BMDM, APT2+/+, LPS


title: FEDC_5Z1

description:
Transgenic
FEDC_5Zall.mcool


title: JHH-DIPG-1-DAC-3

city: Baltimore

first: Michael

middle: A

last: Koldobskiy

address: 855 N. Wolfe St.

department: Center for Epigenetics

institute: Johns Hopkins University

description: RNA-Seq

data_processing:
We aligned reads to GRCh37 using STAR version 2.4.2a [8] with the following options --readFilesCommand zcat --outSAMtype BAM Unsorted SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts. We generated summarized experiment (se) objects using the gtf file Homo_sapiens.GRCh37.75.gtf and the following command from the Bioconductor package ‘GenomicAlignments’: summarizeOverlaps(features=exonsByGene, reads=bamfiles, mode="Union", singleEnd=FALSE, ignore.strand=FALSE, fragments=TRUE).
Assembly: hg19

source_name: diffuse midline glioma

growth_protocol: Cell lines were cultured in DMEM/F12 human neurosphere proliferation medium (30% Hams F12 [Gibco 11765-062], 70% DMEM [Gibco 11965-118], 1% PSA [Gibco-BRL 15420-062], 2% B27 [Gibco-BRL 17504-044], 20 ng/ml EGF [Peprotech AF-100-15], 20 ng/ml FGF-2 [Peprotech 100-18B], and 5 ug/ml of heparin [Millipore Sigma H3149].

extract_protocol:
RNA extraction was carried out using the RNeasy Mini kit (Qiagen), including on-column DNase I digestion (Invitrogen). Integrity of genomic DNA was confirmed by gel electrophoresis. RNA was assessed on an Agilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano kit.
Strand specific mRNA libraries were generated using the NEBNext Ultra II Directional RNA library prep Kit for Illumina (New England BioLabs #E7760), mRNA was isolated using Poly(A) mRNA magnetic isolation module (New England BioLabs #E7490). Preparation of libraries followed the manufacturer’s protocol (Version 1.0 4/17).  Input was 1000ng and samples were fragmented for 15 min for RNA insert size of ~200 bp.  The following PCR cycling conditions were used: 98°C 30s / 8 cycles: 98°C 10s, 65°C 75s / 65°C 5 min. Stranded mRNA libraries were sequenced on an Illumina HiSeq4000 instrument,  using 47bp paired-end dual indexed reads and 1% PhiX control.

treatment_protocol: Cells were treated with 100 nm DAC or DMSO for 5 days, with media and drug change every 24 hours. For the RNA-Seq and WGBS experiments, the DMSO and DAC treated cells were harvested at the 72 hour time point (day 8).

value: cell line


title: SQ23066899-Zna-D7, BMDM, WT, 2-BP


title: JHH-DIPG-1-DAC-2

description: RNA-Seq


title: JHH-DIPG-1-DMSO-3

description: RNA-Seq


title: FEDC_3Z1

description:
Transgenic
FEDC_3Zall_remap.mcool


title: SQ23066899-Zna-F4, BMDM, APT2+/+, LPS


title: SQ23066899-Zna-E12, BMDM, Dhhc7-/-, LPS


title: CDEF_3Z

description:
Transgenic
CDEF_3Z_remap.mcool


title: FEDC_3Z2

description:
Transgenic
FEDC_3Zall_remap.mcool


title: JHH-DIPG-1-DAC-1

description: RNA-Seq


title: JHH-DIPG-1-DMSO-1

description: RNA-Seq


title: JHH-DIPG-1-DMSO-2

description: RNA-Seq


title: SQ23066899-Zna-E11, BMDM, Dhhc7-/-, LPS


title: SQ23066899-Zna-E10, BMDM, Dhhc7-/-, LPS


title: HSJD-DIPG-007-DAC-3

description: RNA-Seq


title: SK-N-SH cells_24hr_uninfected_rep3

city: Hangzhou

first: Jia

last: Wang

state: Zhejiang province

address: 568 Mingshi Road, Jianggan District, Hangzhou

institute: Hangzhou Center for Disease Control and Prevention

description: Gene expression after 24hr in SK-N-SH cells  uninfected with  Toxoplasma gondii

hyb_protocol: Add 500 ng of total RNA to a 1.5-mL microcentrifuge tube. Add 2 μL of CIP (Calf Intestinal Phosphatase) Master Mix and incubate the reaction at 37°C for 30 minutes. Add 2.8 μL of DMSO to each sample and incubate at 100°C for 5 to10 minutes.Immediately transfer to ice-water bath.Add 4.5 μL Ligation Master Mix (1 μL 10×T4 RNA ligase buffer, 3.0 μLCyanine 3-pCp, 0.5 μL T4 RNA ligase) and incubate at 16°C for 2 hours.Open the cadboard box with the cubitainer of wash buffer and carefully remove the outer and inner caps from cubitainer.Use a pipette to add 2 ml of provided Triton S-102 (10%) into the wash buffer  in the cubitainer.Replace the original inner and outer caps and mix the buffer carefully but thoroughly by inverting the container 5 to 6 times.Prewarm slide-staining dish # 3 and enough volume of Gene Expression Wash Buffer 2 to 37°C.Add the slide rack and stir bar to the staining dish.Transfer the staining dish with the slide rack and stir bar to a magnetic stir plate.Fill the staining dish with 100% acetonitrile.Turn on the magnetic stir plate and adjust the speed to a setting of 4 (medium speed).Wash for 5 minutes.Discard the acetonitrile as is appropriate for your site.Repeat step 5 to step 10.Air dry the staining dish in the vented fume hood.Wash all dishes, racks, and stir bars with Milli-Q water.   Completely fill slide-staining dish #1 with Gene Expression Wash Buffer 1 at room temperature.Place a slide rack into slide-staining dish #2. Add a magnetic stir bar. Fill slide-staining dish #2 with enough Gene Expression Wash Buffer 1 at room temperature to cover the slide rack. Place this dish on a magnetic stir plate.Put the prewarmed 1.5 L glass dish filled with water and containing slide-staining dish # 3 on a magnetic stir plate with heating element. Fill the slide-staining dish # 3 approximately three-fourths full with Gene Expression Wash Buffer 2. Add a magnetic stir bar. Turn on the heating element and maintain temperature of Gene Expression Wash Buffer 2 at 37°C.Prepare the hybridization chamber disassembly.With the sandwich com[lately submerged in Gene Expression Wash Buffer 1, pry the sandwich open from the barcode end only.Repeat step 17 through step 18 for up to seven additional slides in the group.When all slides in the group are p;aced into the silde rack in slide-staining dish # 2, stir using setting 4 to 5 minutes.Transfer slide rack to slide-staining dish # 3 that containing Gene Expression Wash Buffer 2 at evevated temperature. Stir using setting 4, or a moderate speed setting, for 5 minutes.Slowly remove the slide rack minimizing droplets on the slides.Discard used Gene Expression Wash Buffer 1 and Gene Expression Wash Buffer 2.Put the slides in a slide holder.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The array images acquired were then analyzed using Agilent Feature Extraction software (version 11.0.1.1; Agilent Technologies, Inc.). The median values of the raw data were normalized and subsequent data processing was performed using the GeneSpring GX v14.9 software package (Agilent Technologies, Inc.).

label: Agilent miRNA Microarray Systemwith miRNA Complete Labeling and Hyb Kit

source_name: SK-N-SH cells ATCC

label_protocol: MicroRNA was prepared from 0.5 ug RNA using the miRNA Complete Labeling and Hyb Kit (Agilent) according to the manufacturer's instructions.  RNA quantification and quality assurance were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The total RNA was harvested using Trizol reagent (Invitrogen, SF, USA) and an miRNeasy Mini kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer .RNA intergrity and gDNA contamination was tested by Denaturing Agarose Gel Electrophoresis

treatment_protocol: Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The amount of TRIzol Reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present. Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization.

tag: age

value: development stage

value: SK-N-SH

value: 24hr uninfected


title: HSJD-DIPG-007-DAC-2

description: RNA-Seq


title: SK-N-SH cells_24hr_uninfected_rep2

tag: treatment


title: SQ23066899-Zna-E6, BMDM, Dhhc7+/+, LPS

value: Bone marrow

tag: cell type

value: Bone marrow derived macrophage


title: SQ23066899-Zna-E4, BMDM, Dhhc7+/+, LPS


title: SQ23066899-Zna-E5, BMDM, Dhhc7+/+, LPS


title: HSJD-DIPG-007-DAC-1

description: RNA-Seq


title: HSJD-DIPG-007-DMSO-3

description: RNA-Seq


title: SQ23066899-Zna-F5, BMDM, APT2+/+, LPS


title: SK-N-SH cells_24hr_uninfected_rep1


title: SQ23066899-Zna-D12, BMDM, WT, LPS+2-BP


title: SK-N-SH cells_24hr_RH tachyzoites_rep3

description: Gene expression after 24hr in SK-N-SH cells  infected with  Toxoplasma gondii

value: 24hr RH tachyzoites


title: HSJD-DIPG-007-DMSO-2

description: RNA-Seq


title: SQ23066899-Zna-D11, BMDM, WT, LPS+2-BP


title: HSJD-DIPG-007-DMSO-1

description: RNA-Seq


title: SK-N-SH cells_24hr_RH tachyzoites_rep2


title: SK-N-SH cells_24hr_RH tachyzoites_rep1


title: Normal WT P13, scRNAseq

first: Emil

last: Kriukov

address: 20 Staniford St

institute: Schepens Eye Research Institute

description:
Pool84-4_3
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: *.tar: Tar archives include tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx) and .h5 files.
Supplementary files format and content: h5ad files
Supplementary files format and content: rds files

source_name: Retina

extract_protocol:
The fresh retinas were isolated from mouse eyes and the single cells were generated by Papain Dissociation System (Worthington-biochem LK003150). Retina myeloid cells were incubated with FITC-CD45 antibody for 30 min on ice in the dark box. Wash the cells 3 times by centrifugation at 1000 rpm for 3 minutes and resuspend cells in ice-cold FACS buffer for sorting. Dead cells were removed during sorting.
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Wild type and myeloid Socs3 knockout mice were subjected to oxygen-induced retinopathy and the retinas were collected at postnatal day 13 for sequencing.

value: Retina

value: CD45+ cells

value: Socs3 flox/flox

value: postnatal day 13


title: SQ23066899-Zna-D10, BMDM, WT, LPS+2-BP

value: WT


title: OIR Socs3 cKO P13, scRNAseq

description:
Pool84-4_2
10x Genomics

value: Socs3 flox/flox-LysMCre

value: oxygen-induced retinopathy


title: SU-DIPG-XIII-DAC-2

description: RNA-Seq


title: OIR WT P13, scRNAseq

description:
Pool84-4_1
10x Genomics


title: SQ23066899-Zna-D5, BMDM, WT, LPS


title: RPMI multiple myeloma cells without co-culture of J3 stromal cells [RNA-Seq]

first: Mehmet

middle: K.

last: Samur

address: 440 Brookline Avenue

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Perform pre-alignment quality control (FastQC v0.11.9)
Trim reads for quality (Trim Galore v0.5.0)
Adapter removal (Cutadapt v1.18)
Align to GRCh38 reference genome (STAR v2.5.4b)
Perform post-alignment quality control (FastQC v0.11.9)
Call transcripts (featureCounts v2.0.1)
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw transcript counts for each sample

source_name: Hematopoietic

growth_protocol: The human multiple myeloma cell lines MM.1S, RPMI-8226, INA-6, and the human stromal cell line HS5 were cultured in RPMI-1640 medium supplemented with complete medium (10% fetal bovine serum, 100 units/mL penicillin, 100 µg/mL streptomycin, and 2 mM L-glutamine) at 37°C and 5% CO2. Recombinant human IL-6 at a concentration of 1 ng/mL (R&D Systems, Minneapolis, United States) was added to INA-6 culture medium.

extract_protocol:
Cells were counted and viability was assessed. CD138+ plasma cells were then purified using anti-CD138 microbeads (Miltenyi Biotech, Auburn, United States). CD138+ multiple myeloma cells were then aliquoted separately to perform RNA extraction. RNA was extracted from CD138+ multiple myeloma cells using the RNeasy MiniKit (Qiagen, Germantown, United States). RNA quantity was evaluated using the Qubit RNA Assay Kit (Life Technologies, Carlsbad, United States) and RNA quality was determined on the Bioanalyzer using the RNA Pico Kit (Agilent, Santa Clara, United States). We used at least 500 ng of total RNA for each sample.
Next, library preparation was done with NEBNext Ultra RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, United States), was converted into a DNA library following the manufacturer’s protocol. Library quantity was determined using the Qubit High Sensitivity DNA Kit and library size was determined using the Bioanalyzer High Sensitivity Chip Kit (Agilent). Finally, libraries were put through quantitative PCR using the Universal Library Quantification Kit for Illumina (Kapa Biosystems, Wilmington, United States) and run on the 7900HT Fast quantitative PCR machine (ABI, Grand Island, NY). Libraries passing quality control were diluted to 2 nM using sterile water, and then sequenced

treatment_protocol: For co-culture experiments, the multiple myeloma cell lines and HS5 were passaged and cultured separately for 24 hours in a 75 cm2 flask. After 24 hours of culture and once HS5 50% confluency was observed, the multiple myeloma cells were manually counted and 10 million multiple myeloma cells with 90% or greater viability (assessed using Tryptan Blue staining), were transposed into 20 ml of fresh RPMI-1640 medium and either added into a 75 cm2 flask containing HS5 cells or cultured alone in a new flask. After 72 hours of culture, total cells were collected from each condition using adherent culture protocol and Trypsin-EDTA to remove attached cells.

value: Hematopoietic

value: RPMI

value: Plasma Cell

value: 46XY, KRAS p.Gly12Ala, TP53 p.Glu285Lys, TRAF3 p.Lys191Leufs*60, EGFR p.Thr751Ile


title: SQ23066899-Zna-D4, BMDM, WT, LPS

value: LPS


title: RPMI multiple myeloma cells co-cultured with HS5 stromal cells for 72 hours [RNA-Seq]

value: Co-Culture with J3 bone marrow stromal cells


title: SU-DIPG-XIII-DAC-1

description: RNA-Seq

value: cell line


title: SQ23066899-Zna-CS6, Spleen, APT2-/-, i.p. LPS

source_name: Spleen

value: Spleen

value: i.p. LPS


title: SU-DIPG-XIII-DMSO-2

description: RNA-Seq


title: SQ23066899-Zna-CS5, Spleen, APT2-/-, i.p. LPS


title: SU-DIPG-XIII-DMSO-1

description: RNA-Seq


title: INA6 multiple myeloma cells without co-culture of HS5 stromal cells [RNA-Seq]

value: 46XY, NRAS p.Gly12Asp, TP53 p.Lys132Met , TP53 p.Gln331Ter


title: SF7761-DAC-3

description: RNA-Seq


title: SQ23066899-Zna-CS4, Spleen, APT2-/-, i.p. LPS


title: MM1S multiple myeloma cells co-cultured with HS5 stromal cells for 72 hours [RNA-Seq]

value: 45XX, KRAS p.Gly12Ala, TRAF3 p.Val536_Asn545delValPheValAlaGlnThrValLeuGluAsninsAsp

value: Co-Culture with HS5 bone marrow stromal cells


title: SU-DIPG-XIII-DMSO-3

description: RNA-Seq


title: SQ23066899-Zna-CS3, Spleen, Dhhc7-/-, i.p. LPS


title: SF7761-DAC-2

description: RNA-Seq


title: INA6 multiple myeloma cells co-cultured with HS5 stromal cells for 72 hours [RNA-Seq]


title: SU-DIPG-XIII-DAC-3

description: RNA-Seq


title: SF7761-DAC-1

description: RNA-Seq


title: SF7761-DMSO-3

description: RNA-Seq


title: SQ23066899-Zna-D6, BMDM, WT, LPS

value: Bone marrow

value: Bone marrow derived macrophage


title: SQ23066899-Zna-CS1, Spleen, Dhhc7-/-, i.p. LPS


title: SQ23066899-Zna-CL6, Liver, APT2-/-, i.p. LPS

source_name: Liver

value: Liver


title: SF7761-DMSO-2

description: RNA-Seq


title: HC10

first: Shanshan

last: Sun

state: Zhejiang

address: Qingchun Road, No 79

department: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample,Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Peripheral whole blood was drawn via venepuncture. Neutrophils were isolated using Polymorphprep (Axis-Shield PoC AS, Norway) by density centrifugation according to the manufacturer's instructions.Total RNA was extracted from freshly isolated neutrophils using TRIzol reagent (Invitrogen, CA, USA). The sequencing library was established using an NEBNext® Ultra™ RNA Library Prep kit for Illumina® (NEB, USA) and then sequenced on the Illumina HiSeq 2000 platform according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Peripheral whole blood

value: circulating neutrophils

tag: group

value: HC


title: HC9


title: HC8


title: HC7


title: SF7761-DMSO-1

description: RNA-Seq


title: SQ23066899-Zna-CL5, Liver, APT2-/-, i.p. LPS


title: SQ23066899-Zna-CL4, Liver, APT2-/-, i.p. LPS


title: MM1S multiple myeloma cells without co-culture of HS5 stromal cells [RNA-Seq]

value: Hematopoietic


title: HC6


title: gastric cancer tissues-#3

city: Nanjing

first: Duochen

last: Jin

address: No. 300 of Guangzhou Road, Nanjing 210029, China.

institute: the First Affiliated Hospital of Nanjing Medical University

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs.
 The reads were aligned to the reference genome/transcriptome with bowtie2 software and circRNAs were detected and identified with find_circ software.
Raw junction reads for all samples were normalized by total reads number and log2 transformed.
Differentially expressed circRNAs were identified by ttest between two groups, and fold change between two samples.
Genome_build: hg19

source_name: gastric tissues

extract_protocol:
Total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, USA). 10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

value: Gastric cancer


title: SQ23066899-Zna-CL3, Liver, Dhhc7-/-, i.p. LPS


title: HC5


title: SQ23066899-Zna-CS2, Spleen, Dhhc7-/-, i.p. LPS


title: SQ23066899-Zna-CL2, Liver, Dhhc7-/-, i.p. LPS


title: HC4


title: SQ23066899-Zna-CL1, Liver, Dhhc7-/-, i.p. LPS


title: gastric cancer tissues-#2


title: HC3


title: SQ23066899-Zna-BS6, Spleen, APT2+/+, i.p. LPS


title: HC2


title: SQ23066899-Zna-BS5, Spleen, APT2+/+, i.p. LPS


title: gastric cancer tissues-#1


title: HC1


title: Adjacent normal gastric tissues-#1

value: Normal tissue adjacent to gastric cancer


title: SQ23066899-Zna-BS4, Spleen, APT2+/+, i.p. LPS


title: SQ23066899-Zna-BS3, Spleen, Dhhc7+/+, i.p. LPS


title: CLC10

value: CLC


title: SQ23066899-Zna-BS2, Spleen, Dhhc7+/+, i.p. LPS


title: CLC8


title: SQ23066899-Zna-BS1, Spleen, Dhhc7+/+, i.p. LPS


title: Mutant 30 hours post-fertilization Zebrafish Embryo bulk RNA-Seq - Replicate 2

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

institute: University of Calgary

data_processing:
For bulk RNASeq, quality control evaluations performed by FastQC v0.11.9 revealed that the reads were of high quality and required no trimming step. Consequently, the reads were mapped to the reference genome danRer11 obtained from UCSC and gene annotation file Zebrafish ENSEMBL Lawson v4.3.2 using the splice-aware alignment tool, STAR v2.7.8a. STAR was run on default settings with the additional optional command ‘--quantMode GeneCounts’ to generate the gene counts files. The gene counts files were filtered for genes with less than 10 counts and normalized to the median ratio using DESeq2 v1.34.0. Differentially expressed genes were identified as genes with FDR-adjusted p-value < 0.05 and log2(fold-change) < -0.5 or log2(foldchange) > 0.5. Volcano plots of differentially expressed genes was generated using Enhanced Volcano v1.12.0.
Assembly: GRCz11 obtained from UCSC and gene annotation file Zebrafish ENSEMBL Lawson v4.3.2
Supplementary files format and content: DESeq2 output

organism: Danio rerio

extract_protocol:
30 hpf nkx3.1ca116 mutant and wild type embryos were collected and RNA prepared using Trizol (ThermoFisher, Waltham MA).
Libraries were prepared from total mRNA per sample using the Illumina Ultra II directional RNA library prep (SanDiego, CA), and sequenced via the NovaSeq SP 100 cycle v 1.5 sequencing run with 33 million reads per sample. 4 replicates were sequenced per condition.

tag: transgenic strain

tag: background

value: TL background


title: CLC7


title: SQ23066899-Zna-BL6, Liver, APT2+/+, i.p. LPS


title: Adjacent normal gastric tissues-#3


title: WT 30 hours post-fertilization Zebrafish Embryo bulk RNA-Seq - Replicate 4


title: NA2

first: Meng

last: Xia

address: 866 Yuhangtang ROAD

institute: Zhejiang University

description: CD4 T cells activated in No arginine-biol rep 2

data_processing:
2×150bp paired-end sequencing (PE150) was performed on an illumina Novaseq™ 6000 to generate the raw RNA-seq data with FASTQ format, following the manufacturer’s protocol.
The FastQC software was used to remove the reads that contained adaptor contamination, low quality bases, or undetermined bases, as a default parameter. Remaining reads were mapped to the reference genome of Homo sapiens GRCh38 with HISAT2 to obtain Bam files. The mapped reads were assembled using StringTie and the final transcriptome was generated using GFFCompare. StringTie was used to show expression level for transcripts by calculating FPKM (FPKM = [total exon fragments/mapped reads (millions) × exon length (kB)]). The differentially expressed transcripts from different groups were selected with criteria of |log2(fold change)| >1 and p value <0.05 by R package. Hierarchical clustering and KEGG analysis were conducted using the R package stats (commands: hclust, kmeans and prcomp) and the DAVID software, respectively.
Assembly: hg18
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: CD4+ T cells

extract_protocol:
Total RNA from 1million human CD4+ T cells cultured under different arginine conditions (FULL, LOW, NA) for 7 days were extracted using TRIzol (Takara) following the manufacturer’s procedure.
The quantity and quality of RNA were assessed by using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA) and Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Approximately 2ug of total RNA was used to remove ribosomal RNA. Following purification, the ribominus RNA was fragmented and reverse-transcribed to create the cDNA by SuperScriptTM II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesize U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR. The average insert size for the final cDNA library was 300±50 bp.

value: CD4+ T cells

value: CD4 T cells activated in No arginine


title: NA3

description: CD4 T cells activated in No arginine-biol rep 3


title: CLC6


title: WT 30 hours post-fertilization Zebrafish Embryo bulk RNA-Seq - Replicate 3


title: SQ23066899-Zna-BL4, Liver, APT2+/+, i.p. LPS

value: i.p. LPS


title: LOW3

description: CD4 T cells activated in Low arginine-biol rep 3

value: CD4 T cells activated in Low arginine


title: Adjacent normal gastric tissues-#2


title: CLC4


title: SQ23066899-Zna-BL5, Liver, APT2+/+, i.p. LPS


title: WT 30 hours post-fertilization Zebrafish Embryo bulk RNA-Seq - Replicate 2


title: CLC9


title: Mutant 30 hours post-fertilization Zebrafish Embryo bulk RNA-Seq - Replicate 4


title: CLC3


title: SQ23066899-Zna-BL3, Liver, Dhhc7+/+, i.p. LPS


title: LOW2

description: CD4 T cells activated in Low arginine-biol rep 2


title: WT 30 hours post-fertilization Zebrafish Embryo bulk RNA-Seq - Replicate 1


title: Mutant 30 hours post-fertilization Zebrafish Embryo bulk RNA-Seq - Replicate 3


title: CLC2


title: Mutant 30 hours post-fertilization Zebrafish Embryo bulk RNA-Seq - Replicate 1


title: Wildtype 30 hours post-fertilization Zebrafish Embryo - Replicate 2

description: Recovered cells: 3,253 cells

data_processing:
All raw FASTQs reads were aligned to Danio rerio (zebrafish) (GRCz11) genome using the STAR algorithm. The sample was quantified through the 10X Genomics Cellranger v.6.1.2 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat R toolkit for quality control and downstream analysis.
Assembly: Samples aligned to a custom Zebrafish Genome Assembly GRCz11 (version 4.3.2) (Lawson et al, eLife (2020)) which is included in the GEO submission.
Supplementary files format and content: Filtered gene - barcode matrix output from CellRanger

extract_protocol:
Wildtype zebrafish embryos, expressing the Tg(nkx3.1:Gal4;UAS:NTR-mCherry)ca101 transgene, were dissociated, assessed for viability, processed, resuspended in a designated solution, and subsequently sorted via fluorescence-activated cell sorting to isolate red fluorescent nkx3.1-transgene expressing cells.
The sample was prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3 Chemistry. Briefly, single cells were sorted into 0.1% BSA–HBSS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using Illumina NovaSeq S2 flow cell at the Center for Health Genomics and Informatics at the University of Calgary.

value: embryo

value: 30 hpf

tag: facs strategy

value: nkx3.1-transgene expressing cells. Dead cells excluded using the forward/side scatter gating and viability dye (Fixable Viability Dye eFluor™ 780)

tag: library preparation

value: 10X Genomics Single Cell RNAseq v3


title: LOW1

description: CD4 T cells activated in Low arginine-biol rep 1


title: CLC1


title: FULL3

description: CD4 T cells activated in Full arginine-biol rep 3

value: CD4 T cells activated in Full arginine


title: SQ23066899-Zna-BL2, Liver, Dhhc7+/+, i.p. LPS

value: Liver


title: CLC5

value: Peripheral whole blood

value: circulating neutrophils


title: NA1

description: CD4 T cells activated in No arginine-biol rep 1


title: Wildtype 30 hours post-fertilization Zebrafish Embryo - Replicate 1

description: Recovered cells: 2,058 cells


title: SQ23066899-Zna-A12, Spleen, WT, i.p. LPS+2-BP

value: Spleen

value: WT

value: i.p. LPS+2-BP


title: ACLF10

value: ACLF


title: FULL2

description: CD4 T cells activated in Full arginine-biol rep 2


title: SQ23066899-Zna-A11, Spleen, WT, i.p. LPS+2-BP


title: WT rat

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
For the raw sequencing data, the Cell Ranger (v3.1.0; 10× Genomics) was used for reads alignment, deduplication and quantification of gene expression with default parameters. Raw reads were aligned to the two-species reference genome (Mus musculus, GRCm38.p6 and Rattus norvegicus, Rnor_6.0) and quality checked. The filtered feature-barcode matrices were constructed by the Cell Ranger (v3.1; 10× Genomics) and used for the downstream analysis.
As quality control, cells were included if they passed the following filters: 1) the number of counts was more than 25,000, 2) the number of unique detected genes was more than the half of the average unique detected genes across the cells within the same sample and 3) the percentage of counts from the mitochondrial genome was less than 10%.
Genome_build: GRCm38.p6 and Rnor_6.0
Supplementary_files_format_and_content: Hierarchical Data Format (HDF5 or H5) files contains gene expression values  (counts).

organism: Rattus norvegicus

source_name: Rat Forebrain Cells

extract_protocol:
Cell isolation for 10× single cell RNA-seq was conducted as described.
Sample loading and library construction were performed according to the manufacturer’s protocol, Chromium Single Cell 3' Reagent Kits User Guide (v3 Chemistry).

value: Sprague-Dawley

value: wild type

value: forebrain


title: FULL1

description: CD4 T cells activated in Full arginine-biol rep 1

value: CD4+ T cells


title: ACLF8


title: ACLF9


title: SQ23066899-Zna-A10, Spleen, WT, i.p. LPS+2-BP


title: SQ23066899-Zna-A8, Liver, WT, i.p. LPS+2-BP


title: ACLF7


title: SQ23066899-Zna-BL1, Liver, Dhhc7+/+, i.p. LPS

value: i.p. LPS


title: 2855-0h

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

institute: BIH at Charité

data_processing:
Fastq files generation and demultiplexing were performed using bcl2fastq v2.20.0. ; residual adapter sequences, ambiguous bases, low quality reads and reads with a length below 25 were removed by AdapterRemoval (version 2.2.3 )
alignment: tophat 2.1.0 with bowtie2 2.2.5 and samtools 0.1.19 (--no-novel-juncs)
Reads were summarized per gene using the featureCount algorithm implemented in the R package Rsubread (v1.16.1).
Raw counts of protein-coding genes were normalized either using normTransform function (pseudocount=1, log2-transformation) or variancestabilising transformation of the DESeq2 package (v1.6.3)
Genome_build: GRCm38 Ensembl version (mm10)
Supplementary_files_format_and_content: raw_counts - tab-deliminated file with reads summerized per gene.
Supplementary_files_format_and_content: norma_data - tab-deliminated file with normalized data of protein-coding genes
Supplementary_files_format_and_content: vst_data - tab-deliminated file with variancestabilising transformed data of protein-coding genes
Supplementary_files_format_and_content: fpkm - tab-deliminated file with fpkm values of protein-coding genes

source_name: CD8+ T lymphocytes

growth_protocol: Naive CD8+ T cells were isolated by magnetically depletion of non-target cells from single cell suspensions of spleen and lymph nodes of indicated mice.

extract_protocol:
Cells were harvested after culture and RNA was isolated using Macherey&Nagel RNA isolation kit according to the manufacturers protocol. Samples concentration was measured with Qubit Fluorometer (ThermoFischer). RNA integrity was assessed using Agilent 2100 BioAnalyser. RIN values were between 7.7 and 9.4.
mRNA-Seq libraries were prepared from 100ng of input total RNA samples using TruSeq stranded mRNA kit (Illumina). Barcoded and pooled libraries were sequenced on 5,5 lanes of Illumina HiSeq 4000 platform (HCS version 3.3.76, RTA version 2.7.6) in a paired-end 2x75 nt sequencing mode.

treatment_protocol: Isolated naive CD8+ T cells were polyclonally stimulated with 2 µg/ ml plate bound αCD3 (145-2C11, eBioscience) and 1 µg/ ml soluble αCD28 (37.51, eBioscience) for 24 - 48 hours.

tag: line

value: Tcaim KO Cd4Cre

value: hocre

tag: activation status

value: naive

tag: mouse

value: female

tag: experiment


title: 2855-48h

tag: genotype

value: 48h polyclonally activated


title: ACLF6

tag: tissue


title: SQ23066899-Zna-A9, Liver, WT, i.p. LPS+2-BP

value: Liver


title: 2874-48h

value: Tcaim KI Cd4Cre

value: wtcre


title: 2874-24h

value: 24h polyclonally activated


title: SQ23066899-Zna-A7, Liver, WT, i.p. LPS+2-BP

value: WT


title: ACLF5

value: Peripheral whole blood

value: circulating neutrophils


title: SQ23066899-Zna-A6, Spleen, WT, i.p. LPS

value: Spleen


title: OA8-2_Condition_WB_Rep8

city: Xi'an

first: Yue

last: Fan

address: Yanta West Road No.76

institute: Xi'an Jiaotong University

data_processing:
Unique molecular identifier (UMI) counts were obtained by aligning FASTQ files to the human reference genome (GRCh38 3.0.0) through Cell Ranger (version 4.0) software from the 10X Genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references). Gene expression raw count matrices were used for downstream analyses. Specifically, for each scRNA-seq dataset, the quality control steps included low-quality cell removal and mitochondrial count filtering. We performed the doublets removal step using the DoubletFinder (version 2.0.3) when the captured cell was larger than 10,000, with pK (the principal component neighbourhood size used to calculate pANN) set to 0.09, nEXP (the total number of doublet predictions produced) set to 0.075, and other parameters as the default settings.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: comma-delimited text file includes annotation information for each Sample

source_name: Cartilage

extract_protocol:
Cartilage was harvested within an hour after surgery, washed twice with phosphate-buffered saline (PBS) buffer containing penicillin and streptomycin, and cut into 1 mm3 pieces. Samples were then subjected to pretreatment with 0.25% Trypsin (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in an incubator with 5% CO2 for 30 minutes. The cartilage fragment was then centrifuged at 350×g for 5 minutes and the supernatant was discarded completely, followed by digestion in basal Dulbecco's modified Eagle's medium/F12 media (Gibico, Grand Island, NY, USA) supplemented with 0.2% type II collagenase (Gibico, Grand Island, NY, USA) at 37 °C for 10-12 hours. Cell count and viability were estimated using a fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after the removal of erythrocytes (Miltenyi 130-094-183). Debris and dead cells removal was performed according to the recommended manuals (Miltenyi 130-109-398/130-090-101). For the 10X Genomics protocol, isolated chondrocytes were filtered through a 70 μm cell strainer, washed twice with PBS buffer, and directly subjected to cDNA library construction. Articular cartilage tissue was dissociated into single cells by enzymatic methods according to standard procedures. Briefly, the cells were washed with PBS and resuspended in 500 μL PBS, and single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA).
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3’ Library v3 Reagent Kit (10x Genomics, Pleasanton, CA, USA). Sequencing was performed on an by Illumina NovaSeq 6000.

value: Cartilage


title: OA7-2_Condition_WB_Rep7


title: 2874-0h


title: OA8-1_Condition_NWB_Rep8


title: OA7-1_Condition_NWB_Rep7


title: ACLF4

value: ACLF


title: OA6-2_Condition_WB_Rep6


title: SQ23066899-Zna-A5, Spleen, WT, i.p. LPS


title: ACLF3


title: 2873-48h


title: SQ23066899-Zna-A4, Spleen, WT, i.p. LPS


title: SQ23066899-Zna-A3, Liver, WT, i.p. LPS


title: ACLF2


title: OA6-1_Condition_NWB_Rep6


title: 2873-24h


title: ACLF1


title: OA5-2_Condition_WB_Rep5


title: OA5-1_Condition_NWB_Rep5


title: 2754-48h

value: male


title: 2873-0h


title: SQ23066899-Zna-A2, Liver, WT, i.p. LPS

value: i.p. LPS


title: 2754-24h


title: OA4-2_Condition_WB_Rep4


title: SQ23066899-Zna-A1, Liver, WT, i.p. LPS


title: mouse 4-6, FAC-Sorted, scRNAseq

first: Yuejun

last: Chen

address: 320 Yueyang Road

institute: Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences

description:
10x Genomics
pfc_exn.Robj
pfc_exn_meta.csv

data_processing:
ScRNA-seq data were aligned with the modified mouse reference genome mm10-3.0.0 adding five projection barcodes as separate genes.ScRNA-seq data was demultiplexed using the default parameters of Cellranger software (10X Genomics, v3.0.2). Obtained filtered transcription count matrix was used for downstream analysis.The filtered count matrix was analyzed and processed using Seurat (v3.1.4) and Scanpy (v3.0.46), including data filtering, normalization, highly variable genes selection, scaling, dimension reduction, and clustering.
Supplementary files format and content: Output files of cellranger: Filtered feature-barcode matrix.
Supplementary files format and content: pfc_exn.Robj: R object which contain all excitatory neurons.
Supplementary files format and content: pfc_exn_meta.csv: metadata file containing clustering and annotation results of pfc_exn.Robj.
Assembly: mm10-3.0.0

source_name: retrograde labeled vmPFC neurons

extract_protocol:
For mice without FAC-sorting, three mice that had been injected with virus were anaesthetized and then subjected to transcranial perfusion with ice-cold oxygenated self-made dissection buffer (in mM: 92 Choline chloride, 2.5 KCl, 1.2 NaH2PO4, 30 NaHCO3, 20 HEPES, 25 Glucose, 5 Sodium ascorbate, 2 Thiourea, 3 Sodium pyruvate, 10 MgSO4.7H2O, 0.5 CaCl2.2H2O, 12 N-Acetyl-L-Cysteine). The brain was removed, 300 µm vibratome sections were collected, and the PrL and IL regions were microdissected under a stereo microscope with a cooled platform. Brain slices were incubated in dissection buffer with 10 µM AMPA receptor antagonist CNQX (Abcam, Cat #ab120017) and 50 µM NMDA receptor antagonist D-AP5 (Abcam, Cat #ab120003) at 33°C for 30 min. The pieces were dissociated first using the ice-cold oxygenated dissection buffer added papain (20 units/ml, Worthington, Cat #LS003126), 0.067 mM 2-mercaptoethanol (Sigma, Cat #M6250), 1.1 mM EDTA (Invitrogen, Cat #15575020), L-Cysteine hydrochloride monohydrate (Sigma, Cat #C7880) and Deoxyribonuclease I (Sigma, Cat #D4527), with 30-40 min enzymatic digestion at 37°C, followed by 30 min 1 mg/ml protease (Sigma, Cat #P5147) and 1 mg/ml dispase (Worthington, Cat #LS02106) enzymatic digestion at 25°C. Supernatant was removed and digestion was terminated using dissection buffer containing 2% fetal bovine serum (FBS, Bioind, Cat #04-002-1A). Single-cell suspension was generated by manual trituration using fire-polishing pasteur pipettes and filtered through a 35 µm DM-equilibrated cell strainer (Falcon, Cat #352052). Cells were then pelleted at 400 g for 5 min. The supernatant was carefully removed and resuspended in 1-2 ml dissection buffer containing 2% FBS. The suspension was then subjected to the debris removal step using the Debris Removal Solution (Miltenyi, Cat #130-109-398). Cell pellets were resuspended and 48,000 cells were loaded into 3 lanes to perform 10X Genomics sequencing. For mice with FAC-sorting, PrL and IL regions were microdissected and dissociated as mice without FAC-sorting, cells were sorted to enrich for EGFP-positive retro-AAV-labeled cells. About 4893 EGFP-positive cells were captured and loaded to perform 10X Genomics sequencing.
Chromium Single Cell 3' Reagent Kits (v3) were used for library preparation (10X Genomics). Libraries were sequenced on an Illumina Novaseq 6000 system.

value: retrograde labeled vmPFC neurons

tag: strain

value: Male

value: 8 weeks


title: OA3-2_Condition_WB_Rep3