title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 325 AG017_NS500289

value: PBMC-derived CD4+ T cells


title: rdd_M_BS

status: Public on Dec 19 2022

type: SRA

city: Shanghai

first: Huiming

last: Zhang

address: No. 3888 Chenhua Road

country: China

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

library_source: genomic

data_processing:
For the WGBS libraries, the sequence reads were mapped to the naturally unmethylated chloroplast genome of Arabidopsis using BSMAP to evaluate the bisulfite non-conversion rate. The libraries with non-conversion rates < 1% were retained for further analysis.
Adapters and low-quality bases in the WGBS reads were trimmed by cutadapt and SolexaQA.
Subsequently,the trimmed reads were unique mapped to each corrected pseudo-reference genome by BSMAP. After filtering the duplicate reads, the methylation information for each cytosine site was extracted and only sites that covered more than four mapped reads were considered. In the binomial test, the non-conversion rate was used as the expected probability.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig file

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 2-week-old plants grown in soil

growth_protocol: Col-0 and rdd triple mutant were grown in half MS medium for 5-6 days and transferred to soil for treatment in a growth room (22°C, 16h light/8h dark).

extract_protocol:
Genomic DNA samples from Col-0 and rdd plants with and without bacterial treatment of YCR-R4 inoculation were extracted by using the DNeasy DNA extraction Plant Mini Kit (Qiagen).
An aliquot with 1 μg of DNA per sample was used for library preparation with NEBNext Ultra II DNA Library Prep Kit for Illumina® (New England BioLabs, E7645L) and Epitect Plus DNA Bisulfite Kit (Qiagen, Cat. No. 59124). All library preparation and subsequent sequencing processes were performed at the Core Facility of Genomics at Shanghai Center for Plant Stress Biology.

treatment_protocol: Seedlings were transferred to soil for 24 hr, and then inoculated with 50 mL of 107–108 CFU/mL bacterial inoculum per soil pot. Bacteria-free 0.45% NaCl saline solution was used for the mock control.

tag: treatment

value: Regular

tag: genotype

value: rdd triple mutant in Col-0 background

tag: tissue

value: full plants


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 325 AG017_NB551203

city: New York

first: Annemieke

last: de Jong

email: ad2952@cumc.columbia.edu, mongaisha4@gmail.com, im2569@cumc.columbia.edu, gwennaelle.monnot@gmail.com

state: NY

address: 1150 st. Nicholas Avenue

department: Department of Dermatology

country: USA

institute: Columbia University Irving Medical Center

description:
CD1a-lysylPG tetramer+ CD4+ T cells from donor 325
all_plates_umi_counts_325.csv
Single-cell RNAseq-Donor_325

library_source: transcriptomic

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
In Bulk RNA-seq files, the trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.BAM files were generated as a result of this step.  In the case of single-cell RNA sequencing, during alignment, reads with more than one mapping were recorded as unmapped using the arguments ‘--outFilterMultimapNmax 1’ and ‘--outSAMunmapped Within’. Alignment counts were generated using Subread’s featureCounts (version 1.6) with default parameters. Reads were assigned to cell and unique molecular indicator (UMI) barcodes using UMI-tools. Rest single-cell data was analyzed using Seuratv4.
For bulk RNAseq, unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. These hit counts were used to perform downstream differential gene expression, and pathway analyses. The differential gene expression analysis was performed by using the  DESeq2 package in Bioconductor. Differential gene expression analysis was performed on the batch corrected data set based on the negative binomial distribution using a significance of FDR<0.05 comparing  Normal control cohort to the each kind of PCA subtype. For single-cell analysis, genes expressed in <3 cells were removed from the analysis, as well as cells that had <200 genes expressed. Moreover, cells that had a total UMI count of less than 200 or more than 5000 or a percentage of mitochondrial reads higher than 11% were removed from the analysis. Contaminating APCs forming a separate cluster and overexpressing DCs markers were also removed from the analysis. The datasets from two donors were merged using Seurat V4 methods of anchoring, and clusters were computed using the “FindClusters” Seurat function. Data was normalized using the Normalizedata function and scaled using the ScaleData function. Logistic regression differential expression test was used via the "FindMarkers" function in Seurat. For data representation, RunPCA and RunUMAP functions were used, as well as DoHeatmap
Gene count files obtained as txt files, UMI counts as csv and DEseq2 in csv format.
Genome_build: GRCh38

molecule: total RNA

organism: Homo sapiens

source_name: PBMCs

growth_protocol: For both bulk and single-cell sequencing,PBMCs were isolated using Ficoll-paque (GE lifesciences - 17-5442-02) and following manufacturer’s instruction. PBMCs were cryopreserved in FBS supplemented with 10% dimethyl sulfoxide (DMSO) and stored in liquid nitrogen.

extract_protocol:
Reverse transcription was performed by adding 7.5 μl of RT mix to each well [containing: 40U Maxima H- (Thermo Fisher Scientific), 2X Maxima H- Buffer (Thermo Fisher Scientific), 4U SUPERaseIN (Thermo Fisher Scientific), 15% polyethylene glycol, 2µM Template Switching Oligo (Integrated DNA Technologies)]. Further sample processing and library preparation was performed by the Single Cell Analysis Core of Columbia University according to published protocol.
For bulk RNAseq, RNA sequencing library preparation used the NEBNext Ultra RNA Library Prep Kit for Illumina by following manufacturer’s recommendations (NEB, Ipswich, MA, USA). The samples were sequenced using a Illumina HiSeq 2x150 Paired End (PE) configuration. The single-cell RNA libraries were prepared for sequencing using Illumina NextSeq 500 using the 75-cycle High Outpit Kit [read lengths 26(R1) × 8(i) × 58(R2)].

treatment_protocol: For single-cell RNAseq, PBMCs were thawed and rested overnight at 37°C. The next day, cell stimulation cocktail (eBioscience 00497003) was added to the cells for 2.5 hours before staining as described in tetramer staining. The gating strategy included: lymphocyte gate, gating out of doublets, dead cells, CD14+, CD19+ cells, and positive selection for CD3+ CD4+. Individual tetramer+ and tetramer- CD4+ T cells were sorted with a BD Influx analyzer into the wells of a 96-well plate, each containing 7.5 µl of lysis buffer [0.2% Triton X-100 (Sigma), SUPERaseIN (1 U/μl) (Thermo Fisher Scientific), 2 mM deoxyribonucleotides (dNTPs) (Thermo Fisher Scientific), and 2 μM reverse transcriptase (RT) primer (Integrated DNA Technologies)]. Primer annealing was performed at 72°C for 3 min.  For bulk RNA sequencing, T cell lines were either untreated (unstim) or treated for 6 hrs with anti-CD3/CD28 before RNA was extracted using RNAeasy

tag: cell type


title: Lyz2Cre+/+Ctnnb1exon3del/wtYFP+/- Alveloar Macrophages 1

city: Buffalo

first: Elliot

middle: David

last: Kramer

state: New York

address: 665 Elm St

department: Immunology

institute: Roswell Park Comprehensive Cancer Center

description: Triple 1

data_processing:
First pass base pairs quality control (QC) was performed using fastqc (v0.10.1)
Spliced alignment was done using Bowtie (v1.0.1) and TopHat (v2.0.13), allowing a maximum of 1 mismatch per read
Read counts were extracted with HTSeq (v0.9.1) using intersection-strict option.
Differential expression analyses were performed using DESeq2 (v1.32.0)
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes raw counts for all samples

organism: Mus musculus

source_name: Lung

growth_protocol: Live singlet CD45+Ly6G-SSChiCD11c+Lyz2-YFPhi alveolar macrophages were isolated by fluorescence-activated cell sorting from the whole dissociated lungs of Lyz2Cre+/+YFP+/- (YFPCtr) and Lyz2Cre+/+Ctnnb1exon3del/wtYFP+/- (Triple) mice in biological triplicate

extract_protocol:
Total RNA was extracted using the miRNeasy mini kit (Qiagen). 5 ng of total RNA was used for the construction of sequencing libraries.
Illumina compatible NGS libraries were generated using the SMARTer Stranded v2 Ultra Pico Input Total RNA Seq kit (Clonetech) following manufacturer's protocols.

value: Lung

tag: strain

value: Alveolar macrophage


title: A5

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads from human brain samples were mapped to hg38 using HISAT2.
Counts of reads mapping to genes were obtained using featureCounts software of Subread package against Ensembl v90 annotation.
Differential expression was done using the DESeq2 package.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files containing raw counts

source_name: Brain

extract_protocol:
Biospecimens were provided by the University of Miami Brain Endowment Bank™, an IRB-approved biorepository that holds frozen brain tissue annotated with demographic information and clinical variables. Postmortem brain specimens were obtained from unaffected control subjects and from cocaine-related deaths that came to routine autopsy. Medicolegal investigations and certifications of the cocaine intoxication deaths were conducted by forensic pathologists to determine the cause and manner of death. The circumstances of death and blood and brain toxicology were reviewed to identify sudden deaths due to the toxic effects of chronic cocaine abuse in persons who met the criteria for cocaine use disorder (n = 25). Drug-free age-matched control subjects (n = 20) were selected from homicides, accidental or natural deaths that had negative urine screens for all common drugs in decedents with no history of licit or illicit drug use before death. The brain samples were matched for sex (male), age, race, smoking history, PMI and brain pH to normalize factors that can affect sample quality. This study used male samples only because of the preponderance of males in the available brain bank. Cocaine use still predominates in males overall and the incidence of cocaine intoxication deaths follows this pattern. Also, the rates of polydrug abuse and psychiatric comorbidity are higher among females, further excluding females based on the criteria for subject inclusion for the present study. To isolate RNA from the samples in Trizol LS, we used the Zymo Directzol RNA miniprep kit (Zymo Research; R2050). We performed DNase treatment on all samples to ensure the removal of genomic DNA before proceeding with library preparation. RNA was analyzed for size distribution and quantity using Bioanalyzer 2000 (Agilent Technologies, USA).
We used the Takara SMARTer Stranded Total RNA-seq library preparation kit to create indexed libraries from ribo-depleted RNA from each sample for sequencing (Takara; 634839). All libraries were generated simultaneously using a multiplexed library preparation strategy to ensure no variation in processing due to batch effects. Resulting libraries were analyzed for size distribution and quantity using the Agilent Bioanalyzer and Tape Station (Life Technologies) prior to sequencing.

value: Brain

tag: brain region

value: Caudate nucleus

tag: group

value: Cocaine

tag: race

value: Black

tag: Sex

value: male

tag: age

tag: pmi


title: Lyz2Cre+/+Ctnnb1exon3del/wtYFP+/- Alveloar Macrophages 2

description: Triple 2


title: Col-0_M_BS

value: wild type Col-0


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 325 AG016_NS500289


title: Lyz2Cre+/+YFP+/- Alveloar Macrophages 3

description: YFPCtr 3


title: G4


title: Lyz2Cre+/+YFP+/- Alveloar Macrophages 2

description: YFPCtr 2


title: F4


title: Lyz2Cre+/+YFP+/- Alveloar Macrophages 1

description: YFPCtr 1


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 325 AG015_NS500289


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 325 AG016_NB551203


title: E4


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 325 AG015_NB551203


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 325 AG018_NB551203


title: KO_St_ATAC_rep1

city: Toronto

first: Tae-Hee

last: Kim

state: Ontario

address: 686 Bay St.

department: Development and Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

description:
eed_st_merged_atac.bg
eed_st_peaks.broadPeak
int_st_merged.counts

data_processing:
basecalling: bcl2fastq v2.17
trimming: trimmomatic v0.32
alignment: bwa mem v0.7.8 (ATAC); STAR v2.5.1b (RNA)
filtering + peak calling (ATAC): ataqv v0.9.1 + MACS2 v2.1.2
read counting: featureCounts v2.5.0/v2.5.3
Genome_build: mm10; GENCODEvM4
Supplementary_files_format_and_content: bedgraph, peak, counts

source_name: E13.5 Stomach Mesenchyme

extract_protocol:
Omni-ATAC
Illumina Tn5 (15027865) + buffer (15027866)

treatment_protocol: Stomachs and intestines of each animal were separated through microdissection and placed in 2% Fetal Bovine Serum (Sigma Aldrich, F1051) in ultra-pure PBS. Samples were then centrifuged at 4°C for 5 minutes at 400 RCF. Samples were digested in 3ml of a 2:1 ratio of TrypLE Express (Gibco, 12604021) to ultrapure PBS until tissues clumped together (approximately 10 minutes). Tissue were then subject to manual dissociation with a p200 pipette until a single-cell solution was observed. Samples were then neutralized with and equal volume of 2% FBS in ultrapure PBS and centrifuged at the conditions described above. Samples were washed in ultrapure 2% FBS and centrifuged again. After decanting the solution, cells were resuspended in ultrapure 2% FBS containing a 1:5000 dilution of Sytox Blue (Invitrogen, S34857), and filtered through 35µm mesh (Fisher Scientific, 352235) into a polypropylene tube (Fisher Scientific, 352063) in preparation for FACS using the Sony SH800 BRV instrument. Isolation of BAPX1-positive mesenchymal cells was achieved through sorting of GFP-expressing cells in Bapx1-cre;Rosa26mTmG  and Eedfl/fl;Bapx1-cre;Rosa26mTmG via FACS.


title: Col-0_T_BS

value: Treated with YC4-R4 in soil


title: 30_Days_Crush

city: Paris

first: Lorenzo

last: Giordani

address: 105 bld de l'hôpital

department: Centre de Recherche en Myologie - UMRS974 Sorbonne Université

country: France

institute: INSERM

data_processing:
creation of count-matrices using Space Ranger 1.1.0
Dataset integration  Seurat 4 (Hao and Hao et al. 2021)
Assembly: mm10

source_name: Tibialis Anterior & Extensor digitorum longus muscles

extract_protocol:
TA muscles were isolated, embedded in OCT  (VWR), and flash frozen in liquid nitrogen
Spatially tagged cDNA libraries were built using a Visium Spatial Gene Expression 3′ Library Construction v1 Kit  (10x Genomics, PN-1000187; Pleasanton, CA)

treatment_protocol: Unilateral hindlimb denervation was performed by clamping the left sciatic nerve under anesthesia

tag: condition

value: 30 days post Nerve Crush

value: muscle


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 325 AG014_NS500289


title: C4

value: White


title: WT_St_ATAC_rep1

description:
ctl_st_merged_atac.bg
ctl_st_peaks.broadPeak
int_st_merged.counts


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 325 AG014_NB551203


title: 3_Days_Crush

value: 3 days post Nerve Crush


title: D4


title: H4


title: KO_Int_ATAC_rep2

description:
eed_int_merged_atac.bg
eed_int_peaks.broadPeak
int_int_merged.counts

source_name: E13.5 Intestinal Mesenchyme


title: B4


title: KO_Int_ATAC_rep1

description:
eed_int_merged_atac.bg
eed_int_peaks.broadPeak
int_st_merged.counts


title: KO_St_ATAC_rep2


title: A4


title: Cardiac myofibroblasts_siVgll3

city: Fukuoka

first: Michio

last: Nakaya

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Pharmacology and Toxicology

country: Japan

institute: Kyushu University Graduate School of Pharmaceutical Science

data_processing:
Sequence reads were treated with FastQC and the adapter sequence, low quality bases and reads with length shorter than 36bp were removed by using Trimmomatic program.
Trimmed sequenced reads were mapped to the mouse reference gene (mm10) using HISAT2.
Known genes and transcripts were assembled with StringTie and calculated in the read count and normalized value as FPKM and TPM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM for each Sample

source_name: Cardiac myofibroblasts

growth_protocol: Isolated cardiac myofibroblasts were grown in DMEM with 10% FBS and 1% penicillin–streptomycin and cultured in a 5 % CO2 incubator at 37°C.

extract_protocol:
Total RNA from cardiac myofibroblasts treated with siRNA was extracted using the QIAGEN RNeasy plus Mini Kit (Qiagen) according to manufacturer’s protocol. Library construction was performed by Macrogen Japan, using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) and the libraries read on the Illumina NovaSeq 6000.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cardiac myofibroblasts were transfected with 12.5 nM of siRNA [siControl (ambion #4390844) or siVgll3 (ambion #s91840)] using Lipofectamine RNAiMAX (Invitrogen) and cultured for 72 hours.

value: Cardiac myofibroblasts isolated 3-days after myocardial infarction


title: WT_Int_ATAC_rep2

description:
ctl_int_merged_atac.bg
ctl_int_peaks.broadPeak
int_st_merged.counts


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 921 AG012_NB551203

description:
CD1a-lysylPG tetramer+ CD4+ T cells from donor 921
umi_counts_921_2.csv
Single-cell RNAseq-Donor_921

value: PBMC-derived CD4+ T cells


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 921 AG011_NS500277


title: Sample 3

city: Saint Louis

first: Joseph

middle: B

last: Lin

state: MO

address: 660 South Euclid Ave, MSC-8096-06-07

department: Ophthalmology & Visual Sciences

institute: Washington University School of Medicine

data_processing:
We used Cell Ranger (5.0.0 or 6.0.1) to align reads to the mm10 reference genome and generate filtered feature-barcode matrices.
The filtered Cell Ranger data matrices for each sample were then imported into Seurat v4 and merged for quality control filtering and additional analyses.
We log-normalized and scaled the data using built-in Seurat functions.
We ran PCA, applied harmony (1.0) integration, and then used harmony reduction to run UMAP (dims = 1:19).
Clusters were identified using the Louvain algorithm (resolution = 0.8).
Genome_build: mm10
Supplementary_files_format_and_content: Merged count matrix (genes-by-cells).
Supplementary_files_format_and_content: Cell-level metadata including sample, cell type annotations, and UMAP coordinates.

molecule: polyA RNA

source_name: corneal epithelium

extract_protocol:
We isolated mouse corneas which were then digested first with enzyme G (Miltenyi 130-095-928) to separate the epithelium. Then, 0.25% trypsin was used to dissociate the epithelial sheets into single cells.
We constructed libraries using the Chromium Next GEM Single Cell 3ʹ Kit v3.1, according to the manufacturer's recommended protocols.

value: corneal epithelium

value: 10 weeks

tag: corneas/mice pooled

value: 7 corneas/7 mice


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 921 AG011_NB551203


title: H3


title: Sample 2

value: 11 weeks

value: female

value: 4 corneas/2 mice


title: KO_St_RNA_rep2

description:
PolyA mRNA
eed_st_merged_rna.bg
EEDKO_REP2_St.counts

extract_protocol:
RNeasy Micro Kit (Qiagen, 74004)
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina + SIRV Set 3 Spike-In


title: WT_St_ATAC_rep2


title: G3

value: Brain

value: Caudate nucleus

value: Cocaine


title: F3

value: male


title: KO_St_RNA_rep1

description:
PolyA mRNA
eed_st_merged_rna.bg
EEDKO_REP1_St.counts


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 921 AG010_NS500277


title: Sample 1

value: 20 weeks


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 921 AG010_NB551203


title: WT_Int_ATAC_rep1


title: WT_St_RNA_rep2

description:
PolyA mRNA
ctl_st_merged_rna.bg
WT_REP2_St.counts


title: Dry Eye Disease

data_processing:
We used Cell Ranger (6.0.1) to align reads to the mm10 reference genome and generate filtered feature-barcode matrices.
The filtered Cell Ranger data matrices for each sample were then imported into Seurat v4 and merged for quality control filtering and additional analyses.
We log-normalized and scaled the data using built-in Seurat functions.
We ran PCA, applied harmony (1.0) integration, and then used harmony reduction to run UMAP (dims = 1:22).
Clusters were identified using the Louvain algorithm (resolution = 0.8).
Genome_build: mm10
Supplementary_files_format_and_content: Merged count matrix (genes-by-cells).
Supplementary_files_format_and_content: Cell-level metadata including sample, cell type annotations, and UMAP coordinates.


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 921 AG009_NS500277


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 921 AG012_NS500277


title: D3

value: Control

value: Black


title: Control (corneal epithelium in dry eye disease)


title: WT_TA

value: Unperturbed

value: muscle


title: WT_St_RNA_rep1

description:
PolyA mRNA
ctl_st_merged_rna.bg
WT_REP1_St.counts


title: Cardiac myofibroblasts_siCtrl

value: Cardiac myofibroblasts isolated 3-days after myocardial infarction

value: siControl


title: C3


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 921 AG009_NB551203

value: PBMC-derived CD4+ T cells


title: KO_Int_RNA_rep2

description:
PolyA mRNA
eed_int_merged_rna.bg
EEDKO_REP2_Int.counts


title: Diabetic

data_processing:
We used Cell Ranger (5.0.0) to align reads to the mm10 reference genome and generate filtered feature-barcode matrices.
The filtered Cell Ranger data matrices for each sample were then imported into Seurat v4 and merged for quality control filtering and additional analyses.
We log-normalized and scaled the data using built-in Seurat functions.
We ran PCA, applied harmony (1.0) integration, and then used harmony reduction to run UMAP (dims = 1:18).
Clusters were identified using the Louvain algorithm (resolution = 0.8).
Genome_build: mm10
Supplementary_files_format_and_content: Merged count matrix (genes-by-cells).
Supplementary_files_format_and_content: Cell-level metadata including sample, cell type annotations, and UMAP coordinates.

value: corneal epithelium

tag: disease

value: Diabetic


title: B3

value: White


title: Control


title: KO_Int_RNA_rep1

description:
PolyA mRNA
eed_int_merged_rna.bg
EEDKO_REP1_Int.counts


title: WT_Int_RNA_rep2

description:
PolyA mRNA
ctl_int_merged_rna.bg
WT_REP2_Int.counts


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 921 AG008_NB551203


title: H2


title: Young

data_processing:
We used Cell Ranger (5.0.0) to align reads to the mm10 reference genome and generate filtered feature-barcode matrices.
The filtered Cell Ranger data matrices for each sample were then imported into Seurat v4 and merged for quality control filtering and additional analyses.
We log-normalized and scaled the data using built-in Seurat functions.
We ran PCA, applied harmony (1.0) integration, and then used harmony reduction to run UMAP (dims = 1:25).
Clusters were identified using the Louvain algorithm (resolution = 1.0).
Genome_build: mm10
Supplementary_files_format_and_content: Merged count matrix (genes-by-cells).
Supplementary_files_format_and_content: Cell-level metadata including sample, cell type annotations, and UMAP coordinates.

value: 11 weeks


title: E3


title: WT_Int_RNA_rep1

description:
PolyA mRNA
ctl_int_merged_rna.bg
WT_REP1_Int.counts


title: G2


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 921 AG007_NS500277


description:
CD4+ polyclonal CD1a-lysylPG-reactive T cell lines-donor 966-unstimulated
6-966-unstim.counts.txt
Bulk-RNAseq


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 921 AG007_NB551203


title: A1_GLO

city: LYON

first: Julie

last: CARAMEL

address: 28 Rue Laennec

institute: Cancer Research Center of Lyon

data_processing:
After demultiplexing and trimming, trimmed reads were mapped using TopHat 2.1.00b (Trapnell et al., 2009) against Human genome (hg19, GRCh37 Feb. 2009 from UCSC) in order to identify expressed genes
Mapped reads for each samples were counted and normalized using FPKM method (Fragments Per Kilobase of exon per Milion of mapped reads).
Assembly: GRCh37
Supplementary files format and content: txt file with normalized expression (FPKM)

source_name: GLO

growth_protocol: Cells were seeded in 6 well plates

extract_protocol:
Total RNA was isolated using the RNeasy Kit (QIAGEN) following to manufacturer's recommandations. RNA was quantified and integrity was mesured by optic density using a 2100 BioAnalyzer
Libraries were prepared with the NextFlex Rapid Directional mRNA-Seq kit (Bioo-Scientific) with polyA+ mRNA enrichment

tag: cell line

value: GLO

tag: vector

value: Melanoma short-term cultures


title: Old

value: 18 months


title: A3_GLOR

source_name: GLO-R

value: GLO-R


title: F2

value: Brain

value: Caudate nucleus

value: male


title: H/R_siNC-Rep1

city: Beijing

first: Jianwen

last: Chen

state: Beijing

address: 28th, Fu Xing road, Hai Dian district

institute: First Medical Center of Chinese PLA General Hospital

data_processing:
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
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

source_name: kidney

growth_protocol: We grew mouse primary renal tubular epithelial cells to approximately 50% confluence.

extract_protocol:
Cells were then collected by 1ml TRIzol (Invitrogen, Carlsbad), and sent to Annoroad Corporation (Beijing, China) for high throughout Illumina NovaSeq 6000 sequencing (GPL24247) (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected using EndoFectin™ Max (GeneCopoeia, China) 12h before suffering to H/R injury. H/R was used to mimic IRI in vitro. Briefly, cells were incubated in glucose-free medium in a tri-gas incubator (94% N2, 5% CO2 and 1.0% O2) at 37 °C for 6 hours. Subsequently, cells were incubated in complete medium under normal conditions for 18 hours for reoxygenation.

value: kidney

tag: sirna

value: siNC

value: mice primary renal tubular epithelial cells

value: hypoxia/reoxygenation (H/R)


title: B3_GLOR

tag: treatment


title: H/R_siNC-Rep2


description:
CD4+ polyclonal CD1a-lysylPG-reactive T cell lines-donor 966-stimulated (anti-CD3/CD28)
5-966-stim.counts.txt
Bulk-RNAseq


title: CD4+ polyclonal CD1a-lysylPG-reactive T cell lines-donor 921a-stimulated (anti-CD3/CD28) 4-921a-AdJ-stim

description:
CD4+ polyclonal CD1a-lysylPG-reactive T cell lines-donor 921a-stimulated (anti-CD3/CD28)
4-921-AdJ-stim.counts.txt
Bulk-RNAseq


title: A3

value: Control


title: E2

value: Black


title: B1_GLO


title: CD1a-lysylPG tetramer+ CD4+ T cells from donor 921 AG008_NS500277

value: PBMC-derived CD4+ T cells


title: H/R_siSox9-Rep3


title: D2


title: CD4+ polyclonal CD1a-lysylPG-reactive T cell lines-donor 921b-stimulated (anti-CD3/CD28) 2-921b-stim

description:
CD4+ polyclonal CD1a-lysylPG-reactive T cell lines-donor 921b-stimulated (anti-CD3/CD28)
2-921-stim.counts.txt
Bulk-RNAseq


title: H/R_siNC-Rep3


title: EGR1OV-Rep3

treatment_protocol: We grew mouse primary renal tubular epithelial cells to approximately 50% confluence, transfected using EndoFectin™ Max (GeneCopoeia, China). H/R was used to mimic IRI in vitro. Briefly, cells were incubated in glucose-free medium in a tri-gas incubator (94% N2, 5% CO2 and 1.0% O2) at 37 °C for 6 hours. Subsequently, cells were incubated in complete medium under normal conditions for 18 hours for reoxygenation.

tag: genotype

value: Egr1 overexpression plasmid transfection


title: H/R_siSox9-Rep1

tag: tissue


title: B2


title: CD4+ polyclonal CD1a-lysylPG-reactive T cell lines-donor 921b-unstimulated 1-921b-unstim

description:
CD4+ polyclonal CD1a-lysylPG-reactive T cell lines-donor 921b-unstimulated
1-921-unstim.counts.txt
Bulk-RNAseq

tag: cell type


title: A2


title: H1


title: CD4+ polyclonal CD1a-lysylPG-reactive T cell lines-donor 921a-unstimulated 3-921a-AdJ-unstim

description:
CD4+ polyclonal CD1a-lysylPG-reactive T cell lines-donor 921a-unstimulated
3-921-AdJ-unstim.counts.txt
Bulk-RNAseq


title: EGR1OV-Rep2

tag: strain


title: C2

tag: brain region

value: White


title: G1

tag: group


title: EGR1OV-Rep1


title: H/R-Rep3

value: H/R


title: H/R_siSox9-Rep2


title: F1

tag: race


title: E1

tag: Sex


title: D1

tag: age


title: H/R-Rep2


title: C1

tag: pmi


title: H/R-Rep1


title: mouse_heart_ infarct

type: RNA

city: Kumamoto

first: Soken

last: Tsuchiya

address: 5-1 Oe-honmachi, Chuo-ku

institute: Kumamoto University

description: Gene expression data from myocardial infarcted mouse hearts at the three days after the operation

hyb_protocol: According to manufacture’s instructions, fragmented cRNA were hybridized for 16 hours at 45°C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA (quantile) using Affymetrix default analysis settings.

label: biotin

source_name: infarcted hearts, three days

label_protocol: Biotinylated cRNA were prepared from 2 µg of total RNA according to manufacture’s instructions.

growth_protocol: 8-10 weeks old male mice (C57BL/6J background) were housed in climate-controlled (25°C) pathogen-free facilities with a 12 h light-dark cycle, with free access to standard diet (CE2; CLEA Japan) and water.

extract_protocol: Total RNA samples from sham- or infarcted mouse heart tissues were extracted using ISOGEN (Nippon Gene, Tokyo, Japan) and purified using the RNeasy Mini Kit (Qiagen, Hilden, Germany).

treatment_protocol: C57BL/6J mice (male, 10 weeks old) were subjected to permanent left anterior descending coronary artery ligation under anaesthesia. In sham-operated mice, the same procedure was performed, but the coronary artery was not ligated.

value: heart

value: 10 weeks old


title: B1


title: Sham-Rep3

value: Sham


title: Sham-Rep2


title: A1


title: siHLADPA 1

city: Pittsburgh

first: Neha

last: Hafeez

address: E1240 BST, 200 Lothrop Street

institute: University of Pittsburgh

description: Total human PAEC RNA treated with siRNA against HLA-DPA1

hyb_protocol: Following fragmentation, cRNA was hybridized for at 45C on GeneChip Whole Transcript Expression Array (Catalog #902280 and 902281).

scan_protocol: GeneArrays were processed per standard Clariom S protocol by University of Pittsburgh Sequencing Core.

data_processing: The data were analyzed with Transcriptome Analysis Console.

label: Biotin

source_name: Human Pulmonary Arterial Endothelial Cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Clariom S Assay, Human, Catalog #902927)

growth_protocol: Human pulmonary artery endothelial cells (Lonza, CC-2530) and were cultured in EBM-2 endothelial cell growth basic medium (Lonza, CC-3121) supplemented with growth factors (Lonza, CC-3202).  All cells were maintained in a humidified chamber at 37C and 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions

treatment_protocol: Human pulmonary artery endothelial cells were cultured as above and then treated with silencer select siRNA against ACTN4, HLADPA1, and negative control.


title: siACTN 2

description: Total human PAEC RNA treated with siRNA against ACTN4


title: Hippocampal brain tissue, Trpc4 knock out, P56, rep2

city: Seoul

first: Jeeyoung

last: Seo

address: 222, Wangsimni-ro

country: South Korea

institute: Hanyang university

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Mouse 2.0 Array (Affymetrix, Santa Clara, CA) containing 698,000 unique 25-mer oligonucleotides constituting over 33,000 gene-level probe sets at 45 °C for 16 h.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix)

data_processing: The data were summarized and normalized with the robust multi-average (RMA) method implemented in Affymetrix® Power Tools (APT).

source_name: Hippocampus of Trpc4 deletion mice

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal  labeling kit.

growth_protocol: Brain hippocampus of P56 mice

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Trpc4 wildtype and Trpc4 deletion gene

tag: strain background

value: Trpc4 knock out

value: hippocampus


title: siHLADPA 3


title: Hippocampal brain tissue, Trpc4 wild type, P56, rep2

source_name: Hippocampus of Trpc4 mice

value: Trpc4 wild type


title: siACTN 1


title: siHLADPA 2


title: Sham-Rep1


title: mouse_heart_sham

description: Gene expression data from sham-operated mouse hearts at the three days after the operation

source_name: sham-operated hearts, three days


title: Hippocampal brain tissue, Trpc4 wild type, P56, rep1

value: male


title: Hippocampal brain tissue, Trpc4 knock out, P56, rep3


title: Hippocampal brain tissue, Trpc4 wild type, P56, rep3


title: siACTN 3


title: siNC 3

description: Total human PAEC RNA treated with siRNA against negative control


title: Hippocampal brain tissue, Trpc4 knock out, P56, rep1


title: IFNg rep3 (RNA-seq)

status: Public on Dec 18 2022

city: Vienna

first: Laura

last: Boccuni

address: Dr-Bohr-Gasse, 9

department: Department of Microbiology, Immunobiology and Genetics

country: Austria

institute: University of Vienna

data_processing:
Adapter trimming via trimmomatic (using catalogue of known contaminant sequences)
Alignment via Bowtie 1 to cDNA (from Ensembl)
Transcript quantification via bitSeq https://github.com/databio/rnapipe/blob/master/src/rnaBitSeq.py
For visualization only: adapter trimming via trimmomatic (using catalogue of known contaminant sequences)
Alignment via TopHat 2 to DNA
Generation of BigWig / TrackHub with rnaTopHat (https://github.com/databio/rnapipe/blob/master/src/rnaTopHat.py)
Differential expression was assessed with DESeq2 v. 1.24.0  (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: comma-separated-value (csv) files holding the name of every gene and their basemean, Log2FC, log fold change standard error (lfcSE), p-value and adjusted p-value for comparison with UT samples of three biological replicates.

source_name: WT IFNg, BMDM

growth_protocol: Bone marrow-derived macrophages (BMDMs) were differentiated from bone marrow isolated from femurs and tibias of 8- to 12-week-old mice. Femur and tibia were separated by cutting at the knee joint. Bones were flushed with Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich) using a 5-mL syringe and a 25-gauge needle. Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich) supplemented with 10% of fetal calf serum (FCS) (Sigma-Aldrich), recombinant M-CSF, 100 units/ml penicillin, and 100 ng/ml streptomycin (Sigma-Aldrich). Cells were kept at 37°C and 5% CO2 and differentiated for 10 days.

extract_protocol:
Cells were harvested after treatments and RNA was isolated using the Qiagen AllPrep DNA/RNA Mini Kit according to the manufacturer's guidelines. RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.
Library was performed at the Biomedical Sequencing Facility (https://www.biomedical-sequencing.org/) with PolyA capture to obtain mRNA molecules

treatment_protocol: 1 x 10^7 cells were seeded with 90 % confluency on 15 cm dishes, respectively. The next day cells were stimulated for 140 minutes with Anisomycin (Sigma-Aldrich) alone, or either with 10 ng/ml murine interferon gamma (IFN-γ; A kind gift from G. Adolf, Boehringer Ingelheim, Vienna) or 250 IU/mL of IFNβ (PBL interferon source) alone for 120 minutes or with Anisomycin (20 minutes pre-treatment) followed by 120 minutes stimulation with either IFN types.

value: wildtype

value: 8-12 weeks

value: IFNg

value: Bone marrow derived macrophage (BMDM)


title: siNC 1

value: siNC


title: re-adherent

description: Gene expression data from cardiac myofibroblasts cultured on plastic plates after suspension culture

hyb_protocol: 0.6 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes using the Gene Expression Hybridization Kit (Agilent Technologies) following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse Gene Expression 8x60K Microarray (G4852A) for 17 hours at 65°C.  After hybridization, microarrays were washed using the Gene Expression Wash Buffers Pack (Agilent Technologies).

scan_protocol: Slides were scanned using the Agilent DNA Microarray Scanner (G2565CA).

data_processing: The scanned images were analyzed with Agilent Feature Extraction (Agilent Technologies) using default parameters.

source_name: Cardiac myofibroblast, cultured on plastic plates after suspension culture

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 µg RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) according to the manufacturer's instructions.

extract_protocol: Total RNA samples were prepared using the QIAzol Lysis Reagent (Qiagen, Hilden, Germany)and purified using the RNeasy Mini Kit (Qiagen). The quality of RNA was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: C57BL/6J mice (male, 10 weeks old) were subjected to permanent left anterior descending coronary artery ligation under anaesthesia. 3 days after the ligation, the infarcetd mouse hearts were collected and  immediately digested in phosphate-buffered saline (PBS) containing 0.1% collagenase type II and 0.01% elastase. Digested cardiac cells were suspended with culture medium DMEM with 10% FBS and 1% penicillin–streptomycin) and allowed to attach to plastic culture plates overnight to remove debris.The attached cardiac cells were separated using an MS column and MiniMACS separator.CD45-negative cells were defined as myofibroblasts.

tag: gender

value: 8 weeks old


title: non-adherent

description: Gene expression data from cardiac myofibroblasts cultured in suspension

source_name: Cardiac myofibroblast, cultured in suspension


title: adherent

description: Gene expression data from cardiac myofibroblasts cultured on plastic plates

source_name: Cardiac myofibroblast, cultured on plastic plates


title: An_IFNb rep3 (RNA-seq)

source_name: WT An+IFNb, BMDM


title: IFNb rep3 (RNA-seq)

source_name: WT IFNb, BMDM

value: IFNb


title: An rep3 (RNA-seq)

source_name: WT An, BMDM

value: Anisomycin


title: IFNg rep2 (RNA-seq)


title: An_IFNg rep2 (RNA-seq)

source_name: WT An_IFNg, BMDM


title: UT rep3 (RNA-seq)

source_name: WT UT, BMDM

value: untreated


title: siNC 2


title: An rep2 (RNA-seq)


title: UT rep2 (RNA-seq)


title: IFNb rep1 (RNA-seq)


title: IFNb rep2 (RNA-seq)


title: An_IFNg rep1 (RNA-seq)


title: UT rep1 (RNA-seq)


title: An_IFNb rep2 (RNA-seq)


title: An rep1 (RNA-seq)


title: An_IFNb rep1 (RNA-seq)


title: IFNg rep1 (RNA-seq)


title: sample123

city: Vancouver

first: Robert

middle: E W

last: Hancock

state: British Columbia

address: Room 232 – 2259 Lower Mall Research Station

department: Microbiology and Immunology

institute: University of British Columbia

data_processing:
Quality control using fastqc (v0.11.9) and multiqc (v1.6)
Alignment to the human genome using STAR (v2.7.9a)
Read count assessments using htseq-count (v0.11.3)
Assembly: GRCh38.104
Supplementary files format and content: count files, which are text files with counts per gene for each sample

source_name: Whole Blood

extract_protocol:
2.5mL of whole blood was collected into PAXgene Blood RNA tubes (BD Biosciences; San Jose, CA, USA) and total RNA was extracted using the PAXgene Blood RNA Kit (Qiagen; Germantown, MD, USA)
Poly-adenylated RNA was captured using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; Ipswich, USA) and cDNA libraries were prepared using the NEBNext RNA First Strand Synthesis Module, NEBNext Ultra Directional RNA Second Strand Synthesis Module, and NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB; Ipswich, USA)

value: Whole Blood

tag: disease state

tag: batch

value: two

tag: sampling group

value: late

tag: predicted endotype

value: IHD

tag: additional metadata

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: sample121

value: early

value: IFN


title: sample117

value: NPS


title: sample116


title: sample115

value: INF


title: sample118


title: sample124


title: sample122


title: sample113


title: sample114


title: sample120

value: ADA


title: sample112


title: sample111


title: sample110


title: sample107


title: sample109


title: sample104


title: sample106


title: sample108


title: sample105


title: sample100


title: sample102


title: sample099


title: sample098


title: sample119


title: sample103


title: An_IFNg rep3 (RNA-seq)

tag: genotype

value: wildtype

value: 8-12 weeks

tag: treatment


title: sample097

tag: tissue


title: sample096


title: sample089


title: sample088


title: sample090


title: sample093


title: sample092


title: sample087


title: sample101


title: sample095


title: T in PBMC

first: Yuetong

last: Wang

address: 320 Yue Yang Road, Room 713

department: Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences

institute: Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to 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: hg38
Supplementary_files_format_and_content: TPMs

source_name: Blood

extract_protocol:
Cells were sorted by CD3 positive staining and then whole cell mRNA were extracted by trizol as previously reported
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Blood

tag: cell type

value: T in PBMC cells


title: sample086


title: sample080


title: sample081


title: sample083


title: sample078

value: one


title: sample082


title: sample091


title: C9ORF72 ALS/FTD 1 iPSC-derived motor neurons treated with Apilimodreplicate 2

city: Los Angeles

first: Justin

last: Ichida

state: CA

address: 1425 San Pablo Street, BCC 305

department: Department of Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

description:
C9-ALS/FTD 1_AP_rep2
g8_a_6769_2_S8

data_processing:
Reads were aligned to the hg38 transcriptome using aligner HISAT2 (v.2.1.0).
A gene count table was obtained using Partek E/M with Partek® Flow® software, v10.0
Differential expression analysis was performed using DESeq2 (v.1.18.1).
Pathway enirchment analysis was performed using Ingenuity Pathway Analysis (Qiagen)
Computations were performed on the High Performing-Computing Cluster supported by the University of Southern California.
Assembly: hg38
Supplementary files format and content: Reference files of the human genome build hg38 (Assembly provider ID: GRCh38), corresponding transcript annotation files (ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/grch38_snp.tar.gz), as well as FeatureCounts (v.1.6.1) build-in Gene ID annotations, which were later translated into EntrezID.

source_name: neural

growth_protocol: Glia-free induced motor neurons were cultured in NeuroDiff media (NDM).

extract_protocol:
mRNA was extracted using NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer's instructions
3'-Digital Gene Expression RNAseq Library Kit (3’-DGE)
3' RNA-seq libraries were generated using the3'-Digital Gene Expression RNAseq Library Kit at Amaryllis Nucleics, according to the manufacturers’ directions. Libraries were sequenced at the Amarillis Nucleics on a Illumina NextSeq 500 sequencer. A total of 10–25 million 80 bp, single end reads were obtained for each sample.

treatment_protocol: iPSC-derived  iPSC-derived motor neurons treated with 3 μM of DMSO or Apilimod for 24 hours.

value: neural

tag: cell line

value: induced neurons

value: motor neurons

value: C9ORF72 ALS/FTD

value: Apilimod


title: C9ORF72 ALS/FTD 1 iPSC-derived motor neurons treated with Apilimod replicate 3

description:
C9-ALS/FTD 1_AP_rep3
g12_a_6769_3_S12


title: C9ORF72 ALS/FTD 1 iPSC-derived motor neurons treated with Apilimod replicate 1

description:
C9-ALS/FTD 1_AP_rep1
g4_a_6769_1_S4


title: sample094

value: Whole Blood

value: two

value: late


title: C9ORF72 ALS/FTD 1 iPSC-derived motor neurons treated with DMSO replicate 3

description:
C9-ALS/FTD 1_DMSO_rep3
g35_d_6769_3_S35

value: DMSO


title: C9ORF72 ALS/FTD 1 iPSC-derived motor neurons treated with DMSO replicate 2

description:
C9-ALS/FTD 1_DMSO_rep2
g34_d_6769_2_S34


title: sample077

value: early

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: C9ORF72 ALS/FTD 1 iPSC-derived motor neurons treated with DMSO replicate 1

description:
C9-ALS/FTD 1_DMSO_rep1
g33_d_6769_1_S33


title: sample085

value: ADA


title: IFNg-treated batch 3

city: Maastricht

first: Han

last: Jin

address: P. Debyelaan 25

country: Netherlands

institute: Maastricht University

data_processing:
Quality of raw sequences was inspected with FastQC (v0.11.8).
All sequencing data were aligned to the reference human genome sequence GRCh38 primary assembly version and its corresponding annotation on GTF file (https://www.gencodegenes.org/human/) using STAR (v2.4.0.1).
Gene expression from aligned sequences to read counts was quantified using HTSeq (v0.11.1).
Genes with an average count < 5 were removed from the analysis.
Assembly: GRCh38 primary assembly
Supplementary files format and content: exp_counts.tsv
Supplementary files format and content: tab-delimited text files include read count values for each sample

source_name: primary CD14+-derived macrophages

growth_protocol: Primary monocytes were isolated from human PBMCs by CD14+ beads and differentiated into macrophages using RPMI1640 (Thermofisher) supplemented with 10% FCS (Gibco) and 1% PenStrep (Gibco) and recombinant human M-CSF 100ng/ml for seven days with one medium change, in an incubator at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated from macrophages exposed to stimulus for 24h (n=4-6 wells per condition) using the Micro RNeasy kit (Qiagen) according to the <100,000 cells protocol. RNA quality and integrity was assessed on a 2100 BioAnalyser Picochip (Agilent Technologies).
mRNA was converted into libraries of double stranded cDNA molecules as a template for high throughput sequencing following the SMART-Seq2 protocol as described by Picelli et al. Shortly, mRNA was primed for SMART reverse transcription from 5 ng of total RNA using poly-T oligos. Resulting cDNA was pre-amplified by SMART ISPCR. Fragmentation was carried out using the Illumina Nextera XT kit, followed by PCR amplification and indexing. Size selection and purification of library fragments with preferentially 300-400 bp in length was performed using SPRIBeads (Beckman-Coulter). The size-distribution of cDNA libraries was measured using the Agilent high sensitivity D5000 assay on a Tapestation 4200 system (Agilent). cDNA libraries were quantified using a Qubit high sensitivity dsDNA assay. 75 bp single-end sequencing was performed on a NextSeq500 system using High Output v2.5 chemistry.

treatment_protocol: 24 hrs, stimulus directly added in growth medium of fully differentiated macrophages

value: primary CD14+-derived macrophages

value: 24hrs human recombinant IFNgamma 200IU/ml


title: sample084

value: IFN


title: TIL

source_name: Ovarian tumor

value: Ovarian tumor

value: tumor infiltrating lymphocytes (TIL)


title: Non-treated plant Rep 4

city: La Creueta

first: Mélina

last: Ramos

state: Girona

address: Edifici Jaume Casademont. Porta E, Carrer Pic de Peguera, 15, 4t,

country: Spain

institute: University of Girona

data_processing:
Illumina CASAVA v1.8.2 was used for base-calling
Raw sequence files were subjected to quality control analysisis using FastQC v0.10.1
Raw sequence files were trimmed and adapters were removed with BBDuk (minimum base quality of 25 and a minimum read length of 35 bp)
Reads were mapped against the Vitis vinifera genome with STAR v2.6
Raw expression counts were obtained with FeatureCounts v1.6.1 for each annotated gene using only uniquely mapping reads (MAPQ ≥ 30).
Assembly: Vitis vinifera L. genome (Vitis vinifera cv. Pinot noir var. PN40024) (version 12X Ensembl)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Vitis vinifera

source_name: Finely grounded frozen leaves

growth_protocol: Garnacha Blanca grapevine cultivars (Vitis vinifera L.) grafted on rootstock 110R, were obtained from commercial nurserie (Agromillora Iberica, Spain). One-year-old bench-grafted grapevine rootlings were planted in a 2 L pot with 80% of the growing media (Prodeasa BV35, Burés Profesional, Spain), 20% of perlite (A-13, Agroteibe, Spain), and 4 g of the fertilizer (Osmocote® Exact Mini 3-4M, ICL Specialty Fertilizers, France). Bench-grafted grapevines were grown in a greenhouse at 25 ± 2ºC, 60 ± 10% relative humidity and a 16:8 h light:dark photoperiod. Young stocks with at least about 4 to 6 expanded leaves were used for the experiments.

extract_protocol:
Sampling was carried out 24 h after spraying plants with the products. Four biological replicates were sampled for each treatment for RNA-sequencing analysis (RNA-seq), and three biological replicates for reverse transcription quantitative PCR (RT-qPCR) analysis. Two leaves from each plant (5 plants per repetition) were harvested, grounded, and soaked in liquid nitrogen. Each ground leaf sample was added to 2 mL tubes containing two borosilicate glass beads in order to obtain a fine powder using Tissuelyzer II system (Qiagen, USA) for 1 min at 30 Hz. For total RNA isolation from grapevine leaves, the commercial kit SpectrumTM Plant Total RNA Kit (Sigma-Aldrich, USA) was used  following manufacturer’s instructions. Residual DNA was removed using Invitrogen™ TURBO DNA-free™ Kit (Applied Biosystems, USA).
The RNA-seq transcriptome library was prepared using the TruSeq Stranded mRNA Sample Prep kit (Illumina, USA) following the manufacturer’s instructions using 1-2 µg of good quality RNA (R.I.N. > 7) as input. The RNA was fragmented 3 minutes at 94°C and every purification step was performed by using 0.81X Agencourt AMPure XP beads. Final libraries were quantified by using the Qubit 2.0 Fluorometer (Invitrogen, USA) and quality tested by Agilent 2100 Bioanalyzer RNA Nano assay (Agilent technologies, USA). Libraries were then processed with Illumina cBot for cluster generation on the flowcell, following the manufacturer’s instructions and sequenced on paired-end (2x150 bp, 30M reads per sample) at the multiplexing level requested on NovaSeq6000 (Illumina). The CASAVA 1.8.2 version of the Illumina pipeline was used to processed raw data for both format conversion and de-multiplexing.

treatment_protocol: The treatments consisted of Akivi at 0.521 g L-1 (Aki), and Bacillus UdG at 108 CFU mL-1 lyophilized (BL) and fresh (BF). A non-treated control (NTC) was included in all the experiments. The products were sprayed on adaxial and abaxial leaf surfaces using an airbrush until near run-off. The experimental design consisted in 4 randomized blocks corresponding to the different treatment modalities (Aki, BL, BF, and NTC), each block was composed of 4 biological replicates of 5 plants.

tag: organ

value: leaf

tag: cultivar

value: Garnacha Blanca

tag: treatment group

value: not treated


title: Non-treated plant Rep 3


title: Untreated batch 3

value: untreated control


title: Non-treated plant Rep 2


title: PGE2-treated batch 3

value: 24hrs human recombinant PGE2 1 microg/ml


title: sample079

value: Whole Blood

value: IHD


title: sample075

value: one


title: IL4-treated batch 3

value: 24hrs human recombinant IL4, 50ng/ml


title: IFNg-treated batch 2

value: 24hrs human recombinant IFNgamma 200 IU/ml


title: PGE2-treated batch 2


title: Non-treated plant Rep 1


title: sample074

value: early

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: IL4-treated batch 2

value: primary CD14+-derived macrophages


title: BL-treated plant Rep 4

value: BL


title: PGE2-treated batch 1


title: BL-treated plant Rep 3


title: sample073

value: ADA


title: sample072

value: IFN


title: sample071

value: late


title: IFNg-treated batch 1


title: Untreated batch 1


title: IL4-treated batch 1


title: AMI patient 49

description:
P49
Processed_data.tsv

data_processing:
FastQC (v0.11.8) was used to inspect the quality of the raw sequences. All data passed quality control, and no overrepresented adaptors could be detected.
All sequencing data were aligned using STAR (v2.4.0.1) to the reference human genome sequence GRCh38 primary assembly version and its corresponding annotation GTF file.
Read counts were quantified by HTseq (v0.11.1).
Low-expressed genes having less than 10 counts in more than 90% of the samples were removed.
Read counts were normalized by using variance-stabilizing transformation provided by R package DESeq2 (v1.24.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data.tsv: Tab-delimited text file containing variance-stabilizing transformed gene expression values for each sample.

source_name: primary macrophages

growth_protocol: Human primary macrophages were routinely generated. Briefly, CD14+ monocytes were isolated from frozen human PBMCs by positive magnetic bead selection (Miltenyi), plated at 75000 cells/96-well and differentiated in a humidified 5%CO2 incubator at 37 degrees Celsius using recombinant human M-CSF at a concentration of 100ng/ml for 7 days. Medium was refreshed at day 4. For each sample, monocytes from 6-8 human blood donors were pooled.

extract_protocol:
To ensure sufficient input material, human primary macrophages were stimulated in 4- to 6-plo replicate wells with serum samples. Total RNA was isolated from 24 hrs AMI- or control sera stimulated macrophages using the Micro RNeasy kit (Qiagen) following the <100 000 cells protocol. RNA quality and integrity were assessed on a 2100 BioAnalyzer Picochip (Agilent Technologies). Average RIN value was 7.5 (95% confidence interval 7.3-7.7).
Quality controlled total RNA was enriched for the Poly(A) RNA fraction by use of the NEBNext Poly(A) mRNA Magnetic Isolation Modul (NEB). Subsequent cDNA library preparation was carried out using the NEBNExt Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer´s instructions. The size of the resulting library was checked (Agilent Tape Station) and quantified by qPCR (NEBNExt Library Quant Kit for Illumina, NEB). Equimolar pooled libraries were sequenced in a single read mode (75 cycles) on a NextSeq500 system (Illumina) and v2.5 chemistry at a depth of about 10M reads per sample.

treatment_protocol: Human serum was added directly to the culture medium of fully differentiated human primary macrophages to obtain a 1:5 dilution. Blood samples were collected into endotoxin-free tubes without additives and centrifuged at 2100 g for 15 minutes after full coagulation at room temperature. Immediately following centrifugation, serum was collected and stored at -80°C in multiple aliquots until analyses. Serum samples were thawed only once before use.

tag: source

value: CD14+ monocytes from healthy volunteers

value: Primary monocyte-derived macrophages

tag: culture medium

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum AMI patient 49


title: AMI patient 48

description:
P48
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 48


title: sample076

value: Whole Blood

value: two


title: sample070

value: one

value: INF


title: BL-treated plant Rep 1

value: leaf

value: Garnacha Blanca


title: sample069

value: early

value: NPS

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: B-treated plant Rep 4

value: B


title: AMI patient 46

description:
P46
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 46


title: AMI patient 47

description:
P47
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 47


title: Untreated batch 2

value: primary CD14+-derived macrophages

value: untreated control


title: sample068


title: AMI patient 45

description:
P45
Processed_data.tsv

value: CD14+ monocytes from healthy volunteers

value: Primary monocyte-derived macrophages

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum AMI patient 45


title: AMI patient 44

description:
P44
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 44


title: AMI patient 43

description:
P43
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 43


title: B-treated plant Rep 3


title: sample067

value: Whole Blood

value: one

value: INF


title: B-treated plant Rep 2

value: leaf

value: Garnacha Blanca


title: AMI patient 41

description:
P41
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 41


title: sample066

value: late

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: AMI patient 37

description:
P37
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 37


title: B-treated plant Rep 1

value: B


title: AMI patient 34

description:
P34
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 34


title: AMI patient 36

description:
P36
Processed_data.tsv

value: CD14+ monocytes from healthy volunteers

value: 24h 1:5 human serum AMI patient 36


title: AMI patient 39

description:
P39
Processed_data.tsv

value: Primary monocyte-derived macrophages

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum AMI patient 39


title: sample065

value: two

value: IHD


title: A-treated plant Rep 4

value: A


title: sample064

value: Whole Blood

value: one

value: IFN


title: BL-treated plant Rep 2

value: leaf

value: Garnacha Blanca

value: BL


title: AMI patient 40

description:
P40
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 40


title: A-treated plant Rep 3


title: sample063

value: early

value: NPS

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: AMI patient 35

description:
P35
Processed_data.tsv

value: CD14+ monocytes from healthy volunteers

value: 24h 1:5 human serum AMI patient 35


title: AMI patient 32

description:
P32
Processed_data.tsv

value: Primary monocyte-derived macrophages

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum AMI patient 32


title: AMI patient 31

description:
P31
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 31


title: AMI patient 29

description:
P29
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 29


title: AMI patient 30

description:
P30
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 30


title: A-treated plant Rep 1

value: A


title: AMI patient 28

description:
P28
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 28


title: AMI patient 26

description:
P26
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 26


title: sample062

value: Whole Blood

value: one

value: late


title: AMI patient 27

description:
P27
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 27


title: AMI patient 25

description:
P25
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 25


title: sample060

value: ADA

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: A-treated plant Rep 2

value: leaf

value: Garnacha Blanca


title: Blastocyst, sgNprl2+sgTsc2 ovariectomy, E5.5, rep1 [sgN2T2_1]

city: Shanghai

first: Jiajia

last: Ye

address: Qiangye road 500

description: FPKM and count are in K and AG column respectively

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/, version: cutadapt-1.9)
Cutadapt software was used to remove the reads that contained adaptor contamination. And after removed the low quality bases and undetermined bases, we used HISAT2 software (https://daehwankimlab.github.io/hisat2/, version: hisat2-2.0.4) to map reads to the genome
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version: stringtie-1.3.4d).
The expression levels of all transcripts were estimated and performed as calculating FPKM (FPKM = [total exon fragments / mapped reads (millions) × exon length (kB)] ).
Assembly: Mus_musculus.GRCm38 v101
Supplementary files format and content: FPKM and count

source_name: Blastocyst

extract_protocol:
RNA was harvested using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, Japan)  and Total RNA Purification Kit, TRK1001 (LC Science, Houston, TX)
cDNA was fragmented by dsDNA Fragmentase(NEB, M0348S) by incubate at 37°C for 30min.Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand,indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR.

value: Blastocyst

value: Nprl2 and Tsc2 knockout

tag: strain background

value: B6D2F1 (mixed C57BL/6 and DBA2J)

value: ovariectomy


title: Blastocyst, sgNprl2+sgTsc2 ovariectomy, E5.5, rep2 [sgN2T2_2]

description: FPKM and count are in L and AH column respectively


title: AMI patient 33

description:
P33
Processed_data.tsv

value: CD14+ monocytes from healthy volunteers

value: Primary monocyte-derived macrophages

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum AMI patient 33


title: Blastocyst, KSOM reduced the concentration of Arg, Leu, Ile, Lys, Glc, and lactate , E5.5, rep2 [K_PG_0_02_2]

description:
Blastocyst, KSOM reduced the concentration of arginine, leucine, isoleucine, lysine, glucose, and lactate , E5.5, rep2 [K_PG_0_02_2]
FPKM and count are in N and Y column respectively

value: WT

value: in vitro cuture in KSOM reduced the concentration of arginine, leucine, isoleucine, lysine, glucose, and lactate


title: sample057

value: Whole Blood

value: one

value: early

value: IFN


title: sample058

value: NPS

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: AMI patient 21

description:
P21
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 21


title: Blastocyst, KSOM reduced the concentration of Arg, Leu, Ile, Lys, Glc, and lactate , E5.5, rep3 [K_PG_0_02_3]

description:
Blastocyst, KSOM reduced the concentration of arginine, leucine, isoleucine, lysine, glucose, and lactate , E5.5, rep3 [K_PG_0_02_3]
FPKM and count are in O and Z column respectively

value: Blastocyst


title: AMI patient 24

description:
P24
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 24


title: AMI patient 22

description:
P22
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 22


title: AMI patient 23

description:
P23
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 23


title: sample059

value: ADA


title: AMI patient 20

description:
P20
Processed_data.tsv

value: CD14+ monocytes from healthy volunteers

value: Primary monocyte-derived macrophages

value: 24h 1:5 human serum AMI patient 20


title: AMI patient 19

description:
P19
Processed_data.tsv

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum AMI patient 19


title: sample056

value: Whole Blood


title: AMI patient 16

description:
P16
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 16


title: Blastocyst, KSOM without protein and carbohydrate components, E5.5, rep1 [K_PG_1]

description: FPKM and count are in P and AA column respectively

value: WT

value: B6D2F1 (mixed C57BL/6 and DBA2J)

value: in vitro cuture in KSOM without protein and carbohydrate components


title: sample054

value: one

value: early

value: INF

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: AMI patient 18

description:
P18
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 18


title: Blastocyst, KSOM without protein and carbohydrate components, E5.5, rep2 [K_PG_2]

description: FPKM and count are in Q and AB column respectively

value: Blastocyst


title: AMI patient 17

description:
P17
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 17


title: sample055

value: IFN


title: AMI patient 15

description:
P15
Processed_data.tsv

value: CD14+ monocytes from healthy volunteers

value: Primary monocyte-derived macrophages

value: 24h 1:5 human serum AMI patient 15


title: sample061


title: Blastocyst, starvation, E5.5, rep1 [Sta_1]

description: FPKM and count are in R and AE column respectively

value: starvation


title: sample053

value: Whole Blood

value: NPS


title: Blastocyst, KSOM reduced the concentration of Arg, Leu, Ile, Lys, Glc, and lactate , E5.5, rep1 [K_PG_0_02_1]

description:
Blastocyst, KSOM reduced the concentration of arginine, leucine, isoleucine, lysine, glucose, and lactate , E5.5, rep1 [K_PG_0_02_1]
FPKM and count are in M and X column respectively

value: WT

value: in vitro cuture in KSOM reduced the concentration of arginine, leucine, isoleucine, lysine, glucose, and lactate


title: AMI patient 13

description:
P13
Processed_data.tsv

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum AMI patient 13


title: sample051

value: one

value: late

value: ADA


title: Blastocyst, ovariectomy, E5.5, rep2 [DIA_E5_5_2]

description: FPKM and count are in U and AD column respectively

value: B6D2F1 (mixed C57BL/6 and DBA2J)

value: ovariectomy


title: AMI patient 12

description:
P12
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 12


title: sample050

value: early

value: INF

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: sample052


title: NCI-H1299, si3-LRRK1-CAPT-rep1

city: shanghai

first: xiaomeng

last: cheng

state: Shanghai

address: Jiangwan Campus of Fudan University, 2205 Songhu Road, Yangpu District, Shanghai, China

institute: Fudan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore with default settings
Trimmed sequence reads were mapped to hg38 using STAR with default settings
Read count extraction were performed using featurecounts with default settings
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes read counts for each Sample

source_name: lung cancer

extract_protocol:
We constructed the dUTP-based strand-specific RNA-seq library by RNA HyperPrep Kit (KAPA). 500 ng purified total RNA of each sample were processed for poly (A)-enrichment and fragmentation. Then 1st strand cDNA and 2st strand cDNA were synthesized from fragmented RNA, followed by A-tailing and adapter ligation. Finally, adapter ligated library DNA was amplified by PCR.
Library concentration was determined by Qubit dsDNA HS Assay Kit (Invitrogen) according to manufacturers instructions

value: lung cancer

value: epithelial-like cell

value: LRRK1-CAPT knckdown

tag: protocol

value: cell differentiation


title: NCI-H1299, si3-LRRK1-CAPT-rep2


title: NCI-H1299, si2-LRRK1-CAPT-rep2


title: Blastocyst, normal diet, E4.5, rep2 [E4_5_2]

description: FPKM and count are in J and K column respectively

value: Blastocyst

value: WT

value: normal diet


title: Blastocyst, ovariectomy, E5.5, rep1 [N_DIA1_1]

description: FPKM and count are in T and AC column respectively


title: NCI-H1299, si2-LRRK1-CAPT-rep1


title: AMI patient 10

description:
P10
Processed_data.tsv

value: CD14+ monocytes from healthy volunteers

value: Primary monocyte-derived macrophages

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum AMI patient 10


title: sample049

value: Whole Blood

tag: disease state

value: one

value: ADA


title: sample048

tag: batch

value: late

value: IFN


title: Blastocyst, normal diet, E4.5, rep1 [E4_5_1]

description: FPKM and count are in I and V column respectively

value: B6D2F1 (mixed C57BL/6 and DBA2J)


title: Blastocyst, starvation, E5.5, rep2 [Sta_3]

description: FPKM and count are in S and AF column respectively

value: starvation


title: JNKi_p38i_An_IFNg_IgG (ChIP-seq)

data_processing:
Raw data were processed using the ChIP-seq pipeline from the nf-core framework (nfcore/ChIP-seq v.1.2.2; Ewels et al., 2020; https://zenodo.org/record/3529400#.YA8YGmRKjZk) in conjunction with Docker (version 20.10.8; Merkel, 2014).
The command used was " nextflow run nf-core/chipseq --input design.csv  --genome GRCm38  -profile docker --min_reps_consensus 2 -r 1.2.2 --narrow_peak" .
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/chipseq).
Assembly: mm10
Supplementary files format and content: Normalised genome-wide bigWig coverage files generated from merged BAM files with bamCompare from deeptools version 3.4.3 (https://zenodo.org/record/3965985#.Yh-DPejMJPZ) with  --scaleFactorsMethod readCount as method to scale the samples.
Supplementary files format and content: Peak .narrowPeak file were generated from the nfcore pipeline

source_name: JNKi_p38i_An_IFNg_IgG, BMDM

extract_protocol:
Cells were washed 2x with ice cold PBS and crosslinked for 10 minutes at room temperature in 1% formaldehyde PBS (ThermoFisher #28906). The cross-linked chromatin was sheared by sonication, providing fragments of 200 - 1000 base pairs in length. Protein-DNA complexes were selectively immunoprecipitated using CREB,c-Jun and igG antibodies. The immunoprecipitated complexes were washed to remove non-specifically bound chromatin, the protein-DNA cross-link was reversed and proteins were removed by proteinase K digest. At least three IPs were pooled for each sample of the three biological replicates, in order to obtain enough DNA precipitated. The DNA associated with the complex was furthermore purified and used for ChIP-seq.
The library generation was carried out by the VBCF NGS facility (https://www.viennabiocenter.org/vbcf/next-generation-sequencing/). The chromatin quality was analyzed on an Agilent 2100 Bioanalyzer and a size selection of 200-1000bp was carried out.

treatment_protocol: 1.5 x 10^7 cells were seeded with 90 % confluency on 15 cm dishes, respectively. The next day cells were stimulated for 140 minutes with Anisomycin, or with with 10 ng/ml murine IFN-γ (a kind gift from G. Adolf, Boehringer Ingelheim, Vienna) for 120 minutes alone or in combination with 1 µM p38 inhibitor (PH-797804; Selleckchem) and 20µM JNK inhibitor (SP600125; Sigma Aldrich) for 60min pre-treatment followed by 20 minutes Anisomycin pre-treatment or the combination of the two inhibitors alone.

tag: strain

tag: age

value: 8-12 weeks

value: JNK inhibitor + p38 inhibitor + Anisomycin + IFNg

tag: chip antibody

value: IgG

value: Bone marrow derived macrophage (BMDM)


title: NCI-H1299, siControl-rep1

value: lung cancer

value: epithelial-like cell

value: siControl

tag: genotype

value: WT

value: cell differentiation


title: AMI patient 14

description:
P14
Processed_data.tsv

value: CD14+ monocytes from healthy volunteers

value: Primary monocyte-derived macrophages

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

tag: treatment

value: 24h 1:5 human serum AMI patient 14


title: AMI patient 9

description:
P9
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 9


title: Macrophages, TSN 3

city: Philadelphia

first: Yi

last: Fan

state: PA

address: 3400 Civic Center Blvd, SCTR 8-168

department: Radiation Oncology

institute: University of Pennsylvania

data_processing:
Kallisto quantification was performed for the RNA-Seq data using Kallisto version 0.45.1 obtained from github. Kallisto index was built with reference transcriptome GRCh38.
The gene expression was normalized and calculated as counts per million (CPM) values by EdgeR (version 3.14.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: cpm.filtered.norm.csv

source_name: PBMC-derived monocytes

growth_protocol: Monocytes were cultured in RPMI-1640 medium supplemented with 10% FBS, and treated with 10 ng/ml CSF-1 (BioLegend, 574806) to induce macrophage differentiation

extract_protocol:
Peripheral blood mononuclear cell (PBMC)-derived monocytes were provided from healthy human volunteer donors by Human Immunology Core at the University of Pennsylvania. Blood samples were obtained for research purpose with informed consent by each donor, and the respective regulations were followed under a University Institutional Review Board-approved protocol.
Library was constructed with a TruSeq mRNA Stranded Kit (Illumina) followed by quality analyzing with DNA nano assay chips using a 2100 bioanalyzer (Agilent), and was subjected to next-generation sequencing (HiSeq2500) at PSOM Next-Generation Sequencing Core of University of Pennsylvania

treatment_protocol: Macrophages were treated with conditioned medium collected from human GBM patient-derived tumor ECs in the presence of 50 nM TSN (Carbosynth, FT65803)

value: Monocytes

value: toosendanin (TSN)


title: AMI patient 8

description:
P8
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 8


title: Macrophages, TSN 2


title: sample047

tag: tissue

value: Whole Blood

value: one

tag: sampling group

value: early

tag: predicted endotype

value: IHD

tag: additional metadata

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: An_IFNg_IgG (ChIP-seq)

source_name: An_IFNg_IgG, BMDM

value: 8-12 weeks

value: Anisomycin + IFNg

value: IgG

tag: cell type

value: Bone marrow derived macrophage (BMDM)


title: NCI-H1299, siControl-rep2

value: lung cancer

tag: cell line

value: epithelial-like cell

value: siControl

value: WT

value: cell differentiation


title: AMI patient 11

description:
P11
Processed_data.tsv

tag: source

value: CD14+ monocytes from healthy volunteers

value: Primary monocyte-derived macrophages

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum AMI patient 11


title: Macrophages, TSN 1

value: Monocytes

value: toosendanin (TSN)


title: sample046

value: Whole Blood

value: one

value: early

value: INF


title: IFNg_IgG (ChIP-seq)

source_name: IFNg_IgG, BMDM

value: 8-12 weeks

value: IFNg

value: IgG


title: AMI patient 6

description:
P6
Processed_data.tsv

tag: culture medium

value: 24h 1:5 human serum AMI patient 6


title: Macrophages, Control 3

value: Control


title: sample045

value: NPS

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: AMI patient 5

description:
P5
Processed_data.tsv

value: CD14+ monocytes from healthy volunteers

value: 24h 1:5 human serum AMI patient 5


title: AMI patient 4

description:
P4
Processed_data.tsv

value: Primary monocyte-derived macrophages

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum AMI patient 4


title: sample044

value: IHD


title: JNKi_IgG (ChIP-seq)

source_name: JNKi_p38i_IgG, BMDM

value: JNK inhibitor + p38 inhibitor

value: Bone marrow derived macrophage (BMDM)


title: An_IgG (ChIP-seq)

source_name: An_IgG, BMDM

value: Anisomycin


title: UT_IgG (ChIP-seq)

source_name: UT_IgG, BMDM

value: untreated


title: AMI patient 3

description:
P3
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 3


title: AMI patient 2

description:
P2
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 2


title: sample041

value: Whole Blood

value: one

value: early

value: IFN


title: JNKi_p38i_An_IFNg_CREB1_rep3 (ChIP-seq)

source_name: JNKi_p38i_An_IFNg_CREB1, BMDM

value: 8-12 weeks

value: JNK inhibitor + p38 inhibitor + Anisomycin + IFNg


title: Liv_Antibiotics3

city: Changsha

first: Qing

last: Li

state: Hunan

address: 110 Xiangya Road

department: Department of Clinical Pharmacology, Xiangya Hospital

institute: Central South University

data_processing:
Basecalls performed using CASAVA version 1.4
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Differential expression analysis of two groups was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: rattus norvegicus ENSEMBL genome release-99
Supplementary files format and content: EXCEL files containing raw gene Counts and FPKM values for differential gene expression

organism: Rattus norvegicus

source_name: liver

growth_protocol: All rats were housed in the SPF animal facilities of Animal Experimental Center of Central South University, and provided a 12-hour light/dark cycle environment, with temperature controlled at 20-25 °C and humidity controlled at 50±10%.

extract_protocol:
Total RNA was isolated from liver and jejunum tissues using Trizol.
Library preparation for Transcriptome sequencing  A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.   Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.   Clustering and sequencing (Novogene Experimental Department)  The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: Wistar rats were randomly divided into antibiotics-treated group and wild-type group. The antibiotics-treated group was given a mixture of antibiotics (ampicillin 20 g/L, neomycin sulfate 20 g/L, vancomycin 10 g/L, metronidazole 20 g/L, and amphotericin B 0.2 g/L) for 2 weeks to deplete intestinal flora of recipient rats, while the wild-type group was given the same amount of normal saline. The dosage of intragastric liquid was 5 mL/kg. Mix the antibiotic mixture solution thoroughly before each intragastric administration.

value: Wistar Han Rat

value: liver

value: treated with antibiotics for 2 weeks


title: sample042

source_name: Whole Blood

value: two

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: AMI patient 7

description:
P7
Processed_data.tsv

value: CD14+ monocytes from healthy volunteers

value: Primary monocyte-derived macrophages

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum AMI patient 7


title: Macrophages, Control 1

value: Monocytes

value: Control


title: Liv_Antibiotics2


title: sample040

value: Whole Blood

value: late

value: IHD


title: AMI patient 1

description:
P1
Processed_data.tsv

value: 24h 1:5 human serum AMI patient 1


title: Liv_Antibiotics1


title: sample039

value: one

value: INF


title: An_IFNg_CREB1_rep3 (ChIP-seq)

source_name: An_IFNg_CREB1, BMDM

value: 8-12 weeks

value: Anisomycin + IFNg

value: Bone marrow derived macrophage (BMDM)


title: control 20

description:
C20
Processed_data.tsv

value: 24h 1:5 human serum control patient 20


title: Liv_Wild type3

value: Wistar Han Rat

value: liver

value: treated with the same amount of normal saline for 2 weeks


title: Macrophages, Control 2


title: sample043

value: early

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: JNKi_p38i_CREB1_rep3 (ChIP-seq)

source_name: JNKi_p38i_CREB1, BMDM

value: JNK inhibitor + p38 inhibitor


title: control 19

description:
C19
Processed_data.tsv

value: CD14+ monocytes from healthy volunteers

value: Primary monocyte-derived macrophages

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum control patient 19


title: sample038

value: Whole Blood

value: late

value: IFN


title: Liv_Wild type2


title: An_CREB1_rep3 (ChIP-seq)

source_name: An_CREB1, BMDM

value: 8-12 weeks

value: Anisomycin


title: sample037

value: two

value: IHD


title: control 18

description:
C18
Processed_data.tsv

value: 24h 1:5 human serum control patient 18


title: Liv_Wild type1

value: Wistar Han Rat

value: liver


title: control 17

description:
C17
Processed_data.tsv

value: 24h 1:5 human serum control patient 17


title: UT_CREB1_rep3 (ChIP-seq)

source_name: UT_CREB1, BMDM

value: untreated

value: Bone marrow derived macrophage (BMDM)


title: sample036

value: one

value: early

value: ADA

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: sample035

value: Whole Blood

value: INF


title: control 15

description:
C15
Processed_data.tsv

source_name: primary macrophages

value: CD14+ monocytes from healthy volunteers

value: Primary monocyte-derived macrophages

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum control patient 15


title: An_IFNg_CREB1_rep2 (ChIP-seq)

value: 8-12 weeks

value: Anisomycin + IFNg


title: IFNg_CREB1_rep3 (ChIP-seq)

source_name: IFNg_CREB1, BMDM

value: IFNg


title: Jej_Antibiotics1

source_name: jejunum

value: Wistar Han Rat

value: jejunum

value: treated with antibiotics for 2 weeks


title: Jej_Antibiotics3


title: Jej_Wild type3

value: treated with the same amount of normal saline for 2 weeks


title: Jej_Wild type2


title: control 13

description:
C13
Processed_data.tsv

value: 24h 1:5 human serum control patient 13


title: JNKi_p38i_CREB1_rep2 (ChIP-seq)

value: JNK inhibitor + p38 inhibitor

value: Bone marrow derived macrophage (BMDM)


title: control 12

description:
C12
Processed_data.tsv

value: 24h 1:5 human serum control patient 12


title: JNKi_p38i_An_IFNg_CREB1_rep2 (ChIP-seq)

value: JNK inhibitor + p38 inhibitor + Anisomycin + IFNg


title: Jej_Antibiotics2


title: control 16

description:
C16
Processed_data.tsv

value: 24h 1:5 human serum control patient 16


title: sample034

value: Whole Blood

value: one

value: early

value: IHD

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: Jej_Wild type1


title: control 14

description:
C14
Processed_data.tsv

value: CD14+ monocytes from healthy volunteers

value: Primary monocyte-derived macrophages

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum control patient 14


title: IFNg_CREB1_rep2 (ChIP-seq)

value: 8-12 weeks

value: IFNg


title: sample033

value: late


title: sample029

value: two

value: IFN


title: sample032


title: An_CREB1_rep2 (ChIP-seq)

value: Anisomycin

value: Bone marrow derived macrophage (BMDM)


title: JNKi_p38i_An_IFNg_CREB1_rep1 (ChIP-seq)

value: JNK inhibitor + p38 inhibitor + Anisomycin + IFNg


title: control 9

description:
C9
Processed_data.tsv

value: 24h 1:5 human serum control patient 9


title: An_IFNg_CREB1_rep1 (ChIP-seq)

value: Anisomycin + IFNg


title: IFNg_CREB1_rep1 (ChIP-seq)


title: control 8

description:
C8
Processed_data.tsv

value: 24h 1:5 human serum control patient 8


title: control 6

description:
C6
Processed_data.tsv

value: 24h 1:5 human serum control patient 6


title: An_CREB1_rep1 (ChIP-seq)


title: sample026

value: Whole Blood

value: one

value: early

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: sample031

value: ADA


title: sample027


title: sample025

value: IHD


title: UT_CREB1_rep1 (ChIP-seq)

value: 8-12 weeks

value: untreated


title: control 5

description:
C5
Processed_data.tsv

value: CD14+ monocytes from healthy volunteers

value: Primary monocyte-derived macrophages

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum control patient 5


title: control 11

description:
C11
Processed_data.tsv

value: 24h 1:5 human serum control patient 11


title: control 3

description:
C3
Processed_data.tsv

value: 24h 1:5 human serum control patient 3


title: JNKi_p38i_An_IFNg_c-Jun_rep3 (ChIP-seq)

source_name: JNKi_p38i_An_IFNg_cJun, BMDM

value: JNK inhibitor + p38 inhibitor + Anisomycin + IFNg

value: c-Jun

value: Bone marrow derived macrophage (BMDM)


title: sample022

value: Whole Blood


title: control 10

description:
C10
Processed_data.tsv

value: 24h 1:5 human serum control patient 10


title: UT_CREB1_rep2 (ChIP-seq)


title: sample030

value: one

value: early

value: NPS


title: An_IFNg_c-Jun_rep3 (ChIP-seq)

source_name: An_IFNg_cJun, BMDM

value: Anisomycin + IFNg


title: IFNg_c-Jun_rep3 (ChIP-seq)

source_name: IFNg_cJun, BMDM

value: 8-12 weeks

value: IFNg


title: sample023

value: IHD

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: control 2

description:
C2
Processed_data.tsv

value: CD14+ monocytes from healthy volunteers

value: Primary monocyte-derived macrophages

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum control patient 2


title: sample024

value: INF


title: sample021

value: IFN


title: sample028

value: late


title: JNKi_p38i_CREB1_rep1 (ChIP-seq)

value: JNK inhibitor + p38 inhibitor

value: Bone marrow derived macrophage (BMDM)


title: JNKi_p38i_c-Jun_rep3 (ChIP-seq)

source_name: JNKi_p38i_cJun, BMDM

value: c-Jun


title: An_c-Jun_rep3 (ChIP-seq)

source_name: An_cJun, BMDM

value: Anisomycin


title: sample020

value: Whole Blood

value: one

value: early

value: NPS


title: control 1

description:
C1
Processed_data.tsv

value: 24h 1:5 human serum control patient 1


title: UT_c-Jun_rep3 (ChIP-seq)

source_name: UT_cJun, BMDM

value: 8-12 weeks

value: untreated


title: control 4

description:
C4
Processed_data.tsv

value: CD14+ monocytes from healthy volunteers

value: Primary monocyte-derived macrophages

value: 24h 1:5 human serum control patient 4


title: sample017

value: INF

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: JNKi_p38i_An_IFNg_c-Jun_rep2 (ChIP-seq)

value: JNK inhibitor + p38 inhibitor + Anisomycin + IFNg


title: control 7

description:
C7
Processed_data.tsv

value: RPMI 10% FCS 1% P/S + 100ng/ml rh-M-CSF

value: 24h 1:5 human serum control patient 7


title: IFNg_c-Jun_rep2 (ChIP-seq)

value: IFNg

value: c-Jun

value: Bone marrow derived macrophage (BMDM)


title: C57BL/6 Mouse, Liver, Tangerine, 226

city: Houston

first: Michael

middle: P.

last: Dzakovich

state: TX

address: 1100 Bates Ave.

department: Pediatrics

institute: USDA-ARS Children's Nutrition Research Center

description: Column name of samples listed in total counts file: NM-15-226

data_processing:
Checked data quality using FASTQC
Removed adapters and trimmed low quality reads using Trimmomatic (ILLUMINACLIP: TruSeq3-PE-2.fa:20:30:10; MAXINFO: 40:0.7; MINLEN: 36; AVGQUAL: 20)
Aligned reads to mouse genome (GRCm38.p6) using the default settings of Rsubread
Checked for potential lane effects using multidimensional scaling and merged counts from both lanes using BAMtools
Genes with less than 0.37 counts per million (10/library size) and present in less than 11 samples total excluded from analysis
Resulting DGElist was TMM normalized and used for differential expression analysis in edgeR
Assembly: GRCm38.p6
Supplementary files format and content: Comma delimited CSV file of raw counts for each sample

source_name: Liver

growth_protocol: Male C57BL/6 mice were reared according to standards set by the American Association for Accreditation of Laboratory Animal Care (protocol #2010A00000095).

extract_protocol:
10 mg (± 2 mg) of preserved tissue was extracted with QIAshredders and RNEasy kits (Qiagen) according to manufacturer's directions
One µg of RNA was used to generate cDNA libraries which were prepared using the NEXTflex Rapid Directional RNA-Seq kit (PerkinElmer)

treatment_protocol: At four weeks of age, mice were randomly assigned treatment groups (n=11-12/group) and fed either a control diet, a diet supplemented with 10% (w/w) red tomato powder, or a diet supplemented with 10% (w/w) tangerine tomato powder.

value: Liver

value: 10 weeks

tag: Sex

value: Male

value: AIN93G diet + 10% tangerine tomato powder


title: C57BL/6 Mouse, Liver, Control, 240

description: Column name of samples listed in total counts file: NM-15-240

value: AIN93G diet


title: C57BL/6 Mouse, Liver, Tangerine, 242

description: Column name of samples listed in total counts file: NM-15-242


title: C57BL/6 Mouse, Liver, Tangerine, 225

description: Column name of samples listed in total counts file: NM-15-225


title: sample018

value: Whole Blood

value: two

value: early


title: sample019

value: one

value: IFN


title: sample016

value: late

value: INF

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: C57BL/6 Mouse, Liver, Control, 245

description: Column name of samples listed in total counts file: NM-15-245


title: sample014

value: ADA


title: JNKi_p38i_c-Jun_rep2 (ChIP-seq)

value: 8-12 weeks

value: JNK inhibitor + p38 inhibitor


title: An_c-Jun_rep2 (ChIP-seq)

value: Anisomycin

value: c-Jun

value: Bone marrow derived macrophage (BMDM)


title: C57BL/6 Mouse, Liver, Tangerine, 217

description: Column name of samples listed in total counts file: NM-15-217

value: Liver

value: 10 weeks

value: Male


title: C57BL/6 Mouse, Liver, Tangerine, 216

description: Column name of samples listed in total counts file: NM-15-216

value: AIN93G diet + 10% tangerine tomato powder


title: sample015

value: Whole Blood


title: sample013

value: two


title: UT_c-Jun_rep2 (ChIP-seq)

value: untreated


title: C57BL/6 Mouse, Liver, Tangerine, 215

description: Column name of samples listed in total counts file: NM-15-215


title: sample012

value: one

value: NPS


title: C57BL/6 Mouse, Liver, Control, 208

description: Column name of samples listed in total counts file: NM-15-208

value: AIN93G diet


title: An_IFNg_c-Jun_rep1 (ChIP-seq)

value: Anisomycin + IFNg


title: JNKi_p38i_An_IFNg_c-Jun_rep1 (ChIP-seq)

value: JNK inhibitor + p38 inhibitor + Anisomycin + IFNg


title: An_IFNg_c-Jun_rep2 (ChIP-seq)

value: 8-12 weeks


title: C57BL/6 Mouse, Liver, Red, 204

description: Column name of samples listed in total counts file: NM-15-204

value: AIN93G diet + 10% red tomato powder


title: sample011

value: late

value: IHD

value: Additional metadata is accessible at the BQC19 Biobank:https://en.quebeccovidbiobank.ca/acceder-au-materiel-de-la-bqc19


title: C57BL/6 Mouse, Liver, Red, 203

description: Column name of samples listed in total counts file: NM-15-203

value: Liver


title: sample010


title: sample009

value: ADA


title: IFNg_c-Jun_rep1 (ChIP-seq)

value: IFNg

value: c-Jun

value: Bone marrow derived macrophage (BMDM)


title: sample008

value: Whole Blood

value: early

value: INF


title: JNKi_p38i_c-Jun_rep1 (ChIP-seq)

value: JNK inhibitor + p38 inhibitor


title: sample007

value: one


title: C57BL/6 Mouse, Liver, Red, 199

description: Column name of samples listed in total counts file: NM-15-199

value: 10 weeks

value: Male


title: UT_c-Jun_rep1 (ChIP-seq)

value: 8-12 weeks

value: untreated