title: Naïve ear  [mid.W6.Naive]

city: Milwaukee

first: Yu-Chieh

state: WI

address: 8701 Watertown Plank Rd.,

department: Dermatology and Cancer

institute: Medical College of Wisconsin

data_processing:
Demultiplexed fastq files were analyzed with the 10x Genomics Cell Ranger 3.0.2 count function for sequence alignment and gene counting
The UCSC mm10 reference mouse transcriptome
Seurat was used to pre-process the raw counts generated by cellranger count to filter cells with low quality cells, cell doublets, and cells with high percentage of mitochondrial genes
Filtered cells that have unique feature counts over more the 75th percentile plus 1.5 times the interquartile range (IQR) or less than the 25th percentile minus 1.5 time the IQR. Additionally, filtered cells with mitochondrial counts falling outside the same range with respect to mitochondrial gene percentage
Counts were normalized using the LogNormalize method, which normalizes the feature expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000 by default), and log-transforms the result using the natural log.
The 5000 highest variable features were selected. The data was then scaled by a linear transformation and PCA performed on the scaled data. A JackStraw procedure was implemented to determine the significant PCA components that have a strong enrichment of low p-value features
A graph-based clustering approach was then applied to embed cells in a graph structure with edges drawn between cells with similar feature expression patterns, and then attempt to partition this graph into highly interconnected ‘quasi-cliques’ or ‘communities’. To this end, we employed Uniform Manifold Approximation and Projection (UMAP) (41), a non-linear dimensional reduction technique to visualize and explore the results using Seurat.
Seurat FindNeighbors and FindClusters functions were optimized to label clusters based on the visual clustering in the projections and cell types assigned
Differential expression analysis was performed using MAST, a GLM-framework that treats cellular detection rate as a covariate
Genome_build: The UCSC mm10 reference mouse transcriptome
Supplementary_files_format_and_content: .zip file containing following files: barcodes.tsv.gz,features.tsv.gz,matrix.mtx.gz
Supplementary_files_format_and_content: .tar.gz file containing following files combined.qc.barcodes.tsv.gz combined.qc.counts.tsv.gz combined.qc.metadata.tsv.gz

source_name: uninfected control medium sequence depth

growth_protocol: Leishmania major (WHO/MHOM/IL/80/Friedlin) was used. Parasites were maintained in vitro in Schneider's Drosophilia medium supplemented with 20% heat-inactivated FBS, 2mM L-glutamine, 100U/mL penicillin, and 100 mg/ml streptomycin. Metacyclic stationary phase promastigotes were isolated from 4-5 days cultures by Ficoll density gradient seperation.

extract_protocol:
At 4 week, with or without infection, mice ears were excised and enzymatically digested using 0.25 mg/ml Liberase and 10 mg/ml Dnase-I in incomplete RPMI 1640 for 90 minutes at 370 C. After digesting, ears were minced manually to obtain cellular content in single cell suspensions. The total RNA was isolated from the cell lysate of naive and infected ears by using RNeasy plus mini kit according to the manufacturer's instruction.
Single cell 3’ library generation was performed using a 10X Genomics Chromium Controller and the v3 reagent kit (10x Genomics) according to the manufacturer’s protocol.  Cell suspensions were loaded on to the middle four channels of a Chromium Single Cell A Chip according to the manufacturer’s instructions, aiming for 10,000 cells per channel.  Following generation of single-cell gel bead-in-emulsions (GEM), reverse transcription, fragmentation and cDNA amplification, library preparations and bar coding were performed using the Illumina TruSeq Stranded mRNA Sample Preparation Kit v2 as per manufacturer’s instructions
200pM of each library was pooled for sequencing on the Illumina NextSeq 500 platform using a high output flow cell (100 cycles) to generate approximately 25 million 75 base reads per sample.

treatment_protocol: For ear dermal infections, 2x106 L. major promastigote parasites in 10 µl PBS were injected intradermally into the ear.

value: Ears

value: wild type

tag: infection status

value: uninfected control


title: H3K27Ac ChIP 18h Rn7sk rep 3

status: Public on Aug 12 2021

type: SRA

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

country: USA

institute: Washington University School of Medicine

description: ChIPseq

library_source: genomic

data_processing:
Single-end ChIP-seq reads for PolII, H3K27ac, H3K4me1 ChIP, and WCE (whole cell extract) were quality-trimmed using Trim Galore!, and reads were mapped to the human reference genome (GRCh37/hg19) using bowtie with the parameters “-m 1 –v 2” to generate unique sequence alignments. Potential PCR duplicates were removed with MACS2 ‘filterdup’.
Genome-wide ChIP-seq read coverage was calculated using 'bedtools genomeCoverageBed', and the genome coverage files in BedGraph format were compressed to bigwig using the UCSC tool 'bedGraphToBigWig'
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Genome-wide ChIP-seq coverage in BigWig format.

molecule: genomic DNA

organism: Homo sapiens

source_name: Human primary keratinocytes

growth_protocol: Human keratinocytes were grown in KGM gold with 0.06mM Calcium, without antibiotics

extract_protocol:
18 hours after transfection cells were fixed with 1% formaldehyde for 10 minutes at room temperature. Chromatin was isolated and sonicated for 17 cycles of 30 seconds with an output of 30W, using an automated sonicator (3000; Misonix). Immunoprecipitation was carried out overnight at 4°C using 5μg of H3K4Me1 (Abcam) or 10μg of H3K27Ac (Abcam) or RNA Pol II N20 (Santa Cruz) antibodies previously bound to Dynabeads protein G (Thermo Fisher Scientific). DNA-protein complexes were eluted in 200μl of elution buffer (50mM Tris pH 8, 1mM EDTA, 1% SDS) by incubating at 65°C with brief agitation every 2-3 minutes. Cross-links were reverted both in the immunoprecipitated samples and the whole cell extract, separated from the sonicated material before immunoprecipitation, by incubating overnight at 65°C. DNA was then purified by phenol-chloroform extraction.
Libraries were prepared using NEXTflex Rapid DNA-Seq Kit (Bioo Scientific)

treatment_protocol: Cells were transfected with siRNAs, control or agains Rn7SK, using Lipofectamine RNAi and collected 18h later

tag: developmental stage

value: Neonatal

tag: time point after transfection


title: H3K27Ac ChIP 18h control rep 2

description: ChIPseq


title: RNA Pol II ChIP 18h Rn7sk rep 3

description: ChIPseq


title: G2CA-E

city: Philadelphia

first: Junnan

last: Wu

state: Pennsylvania

address: 12-188Smilow Center for Translational Research 3400 Civic Center Blvd

institute: University of Pennsylvania

description: G2CA-E 4913-ZM-3_S1

library_source: transcriptomic

data_processing:
Raw fastq files were aligned to the mm10 (Ensembl GRCm38.93) reference genome and quantified using CellRanger v3.1.0
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: kidney

extract_protocol:
single cell isolation
10xGenomics

treatment_protocol: untreated mice

tag: strain

value: FVB

tag: genotype

value: G2APOL1 transgenetic

tag: tissue

value: kidney


title: H3K4Me1 ChIP 18h control rep 3

description: ChIPseq


title: Cdc42-/-1

city: Cincinnati

first: Fukun

last: Guo

state: OH

address: 3333 Burnet Avenue

institute: Children's Hospital Medical Center

data_processing:
75bp single-end sequencing was performed on an Illumina Hi-Seq 2500.
Sequenced reads were psuedo-aligned to mm10 using the TopHat aligner.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are in text format. They contain gene ID, symbol, name, base mean, fold change, log2fold change, p value, adjusted p value, and reads for each sample

source_name: Spleen

extract_protocol:
Spleen was smashed with syringe plungers. Single cells were obtained by filtering smashed spleen with cell strainer. Red blood cells were removed by using red blood cell lysis buffer. The splenocytes were then enriched of CD4+ T cells by MACS sorting followed by FACS sorting of CD4+YFP+ Treg cells.  Total RNA was extracted using a Qiagen RNeasy Mini kit. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2101) was used with a minimum of 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: Treg cells

value: Homozygous Cdc42 knockout


title: G2CA-C

description: G2CA-C 4913-ZM-4_S1

value: WT


title: H3K4Me1 ChIP 18h Rn7sk KD rep 1

description: ChIPseq


title: Naïve ear  [high.W6.Naive]

last: Wang

source_name: uninfected control higher sequencing depth


title: Infected ear [high.W2.Inf]

source_name: L. major promastigote parasite infected higher sequencing depth

value: L. major promastigote parasite infected


title: Naïve ear  [mid.W5.Naive]


title: Infected ear [mid.W2.Inf]

source_name: L. major promastigote parasite infected medium sequence depth


title: Infected ear [high.W1.Inf]


title: 60 dpi Memory 3

city: Coralville

first: Alan

middle: Jacob

last: Sariol

state: IA

address: 2868 Coral Ct., Apt 201

department: Microbiology and Immunology

institute: University of Iowa

data_processing:
Libraries were loaded onto a NextSeq 550 (single read, Illumina) cartridge, where clustering occurred on-board the instrument. After clustering, sequencing was commenced using Illumina’s 2-color SBS chemistry. Following sequencing, Base call (.bcl) files for each cycle of sequencing were generated by Illumina Real Time Analysis software. Primary analysis and de-multiplexing were performed using Illumina’s CASAVA software 1.8.2. The end result of the CASAVA workflow was de-multiplexed FASTQ files for subsequent analysis.
75bp FastQ single-end reads (19.7-25.9 million reads per sample) were trimmed using Trimmomatic (version 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30. Quality control of raw sequence data for each sample was performed using FastQC. Read mapping was performed via Hisat2 (v2.1.0) using the mouse genome (mm10) as reference. Gene quantification was performed using Feature Counts for raw read counts. Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen) using raw read counts. We filtered the generated list on the basis of a minimum 2 absolute fold change after log2 transformation and an FDR corrected p value < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Excel

source_name: Spleen_60 dpi Memory

extract_protocol:
Tregs were isolated by FACS-sorting. Total RNA was extracted by RNeasy Micro Kit (Qiagen) per manufacturer's instructions
Libraries were prepared using a SMARTer Stranded Total RNA-Seq v2 – Pico Mammalian kit (Takara) per manufacturer's instructions. Briefly, between 250pg-10ng of total RNA was fragmented and then reverse transcribed into cDNA using random primers, with a template switching oligo incorporated during cDNA synthesis to allow for full length cDNA synthesis and retain strand specificity. Illumina sequencing adapters and barcodes were then added to the cDNA by PCR, followed by cleavage of ribosomal cDNA. Uncleaved fragments were then enriched by PCR for 12-16 cycles. Final library size distribution was again validated using capillary electrophoresis and quantified using fluorimetry (PicoGreen). Indexed libraries were then normalized and pooled for sequencing.

treatment_protocol: Tregs were sorted from M133 transgenic mice by FACS on the basis of Foxp3-GFP expression and used as naïve controls or adoptively transferred to naïve B6 mice and infected with JHMV. 60 days post-infection, Tregs were again sorted by FACS on the basis of Foxp3-GFP and Thy1.1 expression.

tag: age

value: 4 months

value: infected

value: Spleen


title: 60 dpi Memory 4


title: H3K4Me1 ChIP 18h Rn7sk KD rep 3

description: ChIPseq


title: 103593-001-068

city: Rijswijk

first: Eveline

last: Gart

state: Zuid-Holland

address: Van vredenburchweg 659

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NextSeq 500 V2.5 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (only in case of Paired-end reads) and aligned to the reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Genome_build: Homo_sapiens.GRCh38.gencode.v29
Supplementary_files_format_and_content: The count files contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package.

source_name: eWAT

growth_protocol: All animal experiments were performed in accordance with the Animal Care and Use Committee and ethical approval by an independent Animal Welfare Body (IVD TNO; approval number 3682/TNO-274). Male Ldlr-/-.Leiden mice were obtained from the breeding facility of TNO Metabolic Health Research, Leiden, the Netherlands. All mice were group-housed in an AAALAC-accredited animal facility (relative humidity 50-60%, temperature ~21˚C, light cycle 7 am to 7 pm) and had ad libitum access to food and water.

extract_protocol:
Next generation sequencing (NGS) was performed was performed on liver and eWAT tissue samples. Briefly, total RNA was extracted from was extracted from eWAT using an Ambion RNAqueous total RNA isolation kit (Thermo Fisher Scientific, Waltman, USA) and from liver using the RNA-Bee total-RNA isolation kit.
To assess the quality of the samples, the concentration of the sample was determined using the Fragment Analyzer. The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer (see appendices). The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).
Clustering and DNA sequencing using the NextSeq 500 V2.5 was performed according to manufacturer's protocols. A concentration of 1.6 pM of DNA was used yielding single end reads (1x 75bp). NextSeq control software 2.2.0 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: At the start of the study, mice were matched into 3 groups based on body weight and blood glucose. Two groups (n=15 each) were treated with an energy-dense high-fat diet (HFD; D12451, Research Diets Inc.; 20 kcal% protein, 35 kcal% carbohydrate, 45 kcal% lard fat), or KrO in which 3% of lard (w/w of total diet) was replaced with KrO con-taining EPA ≥150 mg/g, DHA ≥70 mg/g and ≥560 mg/g phospholipids, of which ≥480 mg is phosphatidylcholine (3% w/w KrO, Superba, Aker BioMarine Antarctic ASA, Norway). At an expected average daily intake of 3 g diet per mouse, the dietary intake of KrO is on average 0.02 g/mouse/day. HFD and KrO diets were isocaloric. A reference group remained on a low-fat control chow diet (n=6), (chow; Ssniff-Spezialdiäten GmbH, Soest, Germany). In week 28, animals were terminated after 5h fasting by gradual-fill CO2 asphyxiation and a terminal blood sample was collected by cardiac puncture. Isolated adipose and liver tissues were snap-frozen and stored at -80°C for gene expression.

value: HighFatDiet+KrillOil

tag: mousenr


title: 60 dpi Memory 2


title: 150_4hr3

city: New York

first: Justin

middle: Shaun Arnold

last: Perry

state: New York

address: 408 East 69th Street, 408-15

department: Immunology Program

institute: Sloan Kettering Institute for Cancer Research

description:
UV7
150_4hr_3_S23

data_processing:
Adapter trimming via FastX 0.0.14 and cutadapt 1.15
ShortRead 1.36.0 package from Bioconductor, Removal of contaminants: Using bowtie 2.3.3.1
Alignment with Tophat v2.1.1
Quantitation via featureCounts featureCounts 1.5.3
Genome_build: Salmonella Typhimurium SL1344, ASM21085v2, EnsEMBL 39
Supplementary_files_format_and_content: .XLS file with correct gene names, generated using DESeq2, with normalized read counts and differential expression statistics

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella

growth_protocol: Culture supernatants were McCoy's 5A + 10% serum

extract_protocol:
Total RNA was extracted using Qiagen RNA isolation kit
mRNA library was prepared using the Illumina TruSeq platform; 75bp, single end sequencing

tag: culture condition

value: HCT116 apoptotic (UV) supernatants, 24 hours post apoptosis, mid log growth


title: 150_4hr4

description:
UV8
150_4hr_4_S24


title: Infected ear [mid.W1.Inf]


title: 103593-001-070


title: 103593-001-067


title: H3K4Me1 ChIP 18h control rep 2

description: ChIPseq


title: 60 dpi Memory 1


title: Naïve ear  [high.W5.Naive]


title: H3K4Me1 ChIP 18h control rep 1

description: ChIPseq


title: Naïve Control 4

source_name: Spleen_Naïve Control

value: naïve


title: media_4hr4

description:
M8
Media_4hr_4_S8

value: fresh media controls, mid log growth


title: 103593-001-066


title: H3K4Me1 ChIP 18h control rep 4

description: ChIPseq


title: 103593-001-069


title: Naïve Control 3


title: 150_4hr2

description:
UV6
150_4hr_2_S22


title: 150_4hr1

description:
UV5
150_4hr_1_S21


title: media_4hr2

description:
M6
Media_4hr_2_S6


title: Naïve Control 1


title: media_4hr3

description:
M7
Media_4hr_3_S7


title: media_4hr1

description:
M5
Media_4hr_1_S5


title: 103593-001-064


title: 103593-001-065


title: Naïve Control 2


title: CT26:FADD + QVD, rep2

data_processing:
Adapter trimming via ea-utils.1.1.2-537
FastQC for read quality check
Alignment with STAR -RNAseq Data (variables P=24; BAMRAM=$(($P*8 * 1000000000 - (30*1000000000))); INDEX=INDEX; GTF=GTF)
Quantitation via featureCounts (featureCounts -a GTF -o counts.txt -p -B -T 16 -t exon -g gene_id *.bam)
Genome_build: Salmonella Typhimurium SL1344, ASM21085v2, EnsEMBL 39
Supplementary_files_format_and_content: .XLS file with correct gene names, generated using DESeq2, with normalized read counts and differential expression statistics

source_name: CT26:FADD + QVD

growth_protocol: Culture supernatants were DMEM + 10% serum

extract_protocol:
Total RNA was extracted using Qiagen RNA isolation kit
mRNA library was prepared using the Illumina TruSeq platform
RNA-seq, 75bp, paired-end sequencing

tag: growth protocol

value: CT26 apoptotic (FADD) supernatants + caspase inhibitor, 5 hours post apoptosis, mid log growth

tag: condition

value: QVD


title: 103593-001-063


title: CT26:FADD + QVD, rep4


title: 103593-001-062

value: HFD

value: HighFatDiet


title: 103593-001-061


title: CT26:FADD + QVD, rep3


title: CT26:FADD + QVD, rep1


title: 103593-001-059


title: CT26:FADD, rep4

value: CT26 apoptotic (FADD) supernatants, 5 hours post apoptosis, mid log growth

value: Dead


title: CT26:FADD, rep2


title: 103593-001-060


title: 103593-001-057


title: 103593-001-056


title: 103593-001-055


title: CT26:FADD, rep3


title: 103593-001-054


title: CT26:FADD, rep1


title: 103593-001-053


title: Panicle, 58CRIS-1

city: Beijing

first: Liping

last: Shen

address: Yanyuan

country: China

institute: Peking University

data_processing:
The reads from RNA-seq experiments were mapped into the rice genome (MSU v7.0) with the guided of gene annotation using Hisat (v2.1.0) with the option of "--dta"
The gene expression levels for each sample were calculated using Stringtie (v1.3.3b) with the options of "-B -e".
Genome_build: MSU v7.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Oryza sativa

source_name: Panicle

extract_protocol:
Panicles were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Panicle

tag: length


title: Panicle, 58Z-5b


title: Panicle, 58CRIS-2


title: 103593-001-052


title: input background for Bmal1

city: Gainesville

first: Karyn

middle: A

last: Esser

state: Florida

address: 1345 Center Drive

department: PHYSIOLOGY & FUNCTIONAL GENOMICS

institute: University of Florida

data_processing:
quality of the fastq files were assessed by fastqQC, and the data quality was great
fastq files were aligned to mm10 using bowtie2
biological replicates of the resulting sam files were merged
homer was use for peak calling, using input as background
bigwig files were generated for UCSC genomebrowswer visualization purpose
Genome_build: mm10
Supplementary_files_format_and_content: peak.txt contains identified peaks; bigWig contains binary data to display ChIP-Seq data in Genome Browswer

source_name: input background for Bmal1

growth_protocol: 12 wks old C57BL/6J mice - Gastrocnemius muscles were collected.

extract_protocol:
muscle nuclei were isolated by homogenization and and centrifugation. ChIP DNA was recovered after sonication and centrifugation.
ChIPseq library was prepared by using NEBNext Ultra DNA library prep kit for Illumina.
A 2 X 100 run was conducted on HiSeq 3000 Illumina sequencing system

treatment_protocol: for CLOCK Ab ChIPseq,muscle samples were sequentially treated with EGS and formaldehyde. For BMAL1 Ab ChIPseq, muscle samples were treated with formaldehyde.

tag: Sex

value: male

tag: time

value: gastrocnemius muscles

tag: chip antibody


title: input background for Clock

source_name: input background for Clock


title: Panicle, 58Z-4b


title: Panicle, 58Z-2


title: Clock_bioRep2

source_name: gastrocnemius muscles_Clock


title: Bmal1_bioRep2

source_name: gastrocnemius muscles_Bmal1


title: Panicle, 58Z-1


title: 103593-001-045

value: Chow

value: ControlHealthyDiet


title: 103593-001-046


title: Bmal1_bioRep1


title: Astrocyte TNF/Smac/zVAD/Nec-1s rep3

city: Framingham

first: Dimitry

last: Ofengeim

address: 49 New York Avenue

institute: Sanofi

data_processing:
The raw RNA-seq data were uploaded, processed and analyzed with the RNA-seq process pipeline in OmicSoft Array Studio software (version 10.1.1.3), including data quality control, alignment, quantification, normalization and log2 transformation to obtain the expression values (log2 FPKM) for each sample.
Genome_build: Human B38
Supplementary_files_format_and_content: HumanAstrocyteQuantLog2.txt: Tab-delimited text file includes FPKM values for each Sample.
Supplementary_files_format_and_content: HumanAstrocyteQuantLog2_Annotation.txt: Tab-delimited text file includes gene annotation.

source_name: Human Astrocytes

growth_protocol: Fetal-derived human astrocytes from Gibco (K1884) were plated in Matrigel-coated plates 6-well plates 2x10^5 cells/well and rested for 48 hours prior to treatment in DMEM-GlutaMAX media with 10% FBS and N2 supplement.

extract_protocol:
Cells were lysed in 350uL RLT Plus Lysis Buffer and RNA was extracted with the Qiagen RNeasy Plus Mini Kit according to manufacturer's instructions.
Astrocytes (BGI): we captured mRNA with oligo dT and constructed mRNA-seq library by strand-specific protocol. Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA were fragmented into small pieces (200-350bp) with fragment buffer at appropriate temperature. Then First-strand cDNA is generated in First Strand reaction system by random hexamer-primed reverse transcription, and the second-strand cDNA was generated with dNTP (dTTP replaced by dUTP). Adapters were added by incubating to end repair. After degradation of the second-strand cDNA, the first Strand were amplified by PCR. Products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on DNBseq platform.

treatment_protocol: Astrocytes were treated with (1) DMSO, (2) Nec-1s, (3) TNF/Smac/zVAD or (4) TNF/Smac/zVAD/Nec-1s for 4 hours prior to lysis and RNA extraction.

value: Astrocytes

tag: treatment


title: Clock_bioRep1


title: 103593-001-048


title: Panicle, WT-3

value: wild type


title: Astrocyte TNF/Smac/zVAD/Nec-1s rep1


title: FFPE_ATAC_on_Cereblum_rep2_trim

city: Uppsala

first: xingqi

last: chen

address: Uppsala Biomedical Center C10:2, Husargatan 3

department: IGP

country: Sweden

institute: Uppsala University

data_processing:
Reads were aligned to the mm9 genome/hg19 genome using bowtie2
duplicate reads were removed with Picard
MACS2 was used call narrow peak
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: peak text files

source_name: Cerebellum

extract_protocol:
RNA is synthesized after in vitro transcription from tagmented DNA with T7-Tn5. And cDNA is synthesized after reverse transcription.
dsDNA was tagmented with Tn5, then PCR is performed using primers with barcode.

treatment_protocol: Samples were fixed with 4% paraformaldehyde overnight, and then washed with phosphate-buffered saline (PBS) and kept in 70% ethanol for paraffin embedding.

value: FVBN

value: FFPE

value: Cerebellum


title: Astrocyte TNF/Smac/zVAD/Nec-1s rep2


title: 103593-001-042


title: Astrocyte TNF/Smac/zVAD rep3

value: TNF/Smac/zVAD


title: 103593-001-043


title: FFPE_ATAC_on_Rectum2_rep2_trim

source_name: Rectum

value: Rectum


title: Panicle, WT-1


title: Blood_TOL_rep2

type: genomic

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description: Bisulfite-converted DNA

hyb_protocol: Infinium HD Assay Methylation Protocol, Illumina Inc.

scan_protocol: HiScan, Illumina Inc.

data_processing: HCFIS-15_mIN_raw.txt, Raw data were decoded by GenomeStudio Illumina Inc. and, normalization was done (1) forcePositive background correction, (2) log2 transformation, (3) quantile adjusted for color balance and (4) quantile normalization

label: Cy3 & Cy5

source_name: Peripheral Blood Mononuclear Cells, operational tolerance

extract_protocol: Mononuclear cells were isolated from peripheral blood by density gradient. DNA was extracted using an ATP Genomic DNA Mini Kit (ATP Biotech) following manufacturer instructions, and then quantified with a Qubit 2.0 Fluorometer (Life Technologies). DNA integrity was evaluated in TAE agarose gels.

value: Peripheral Blood Mononuclear Cells

tag: clinical trait

value: Operational tolerance


title: Panicle, WT-2


title: 103593-001-029

source_name: liver

value: HighFatDiet+KrillOil


title: Astrocytes TNF/Smac/zVAD/Nec-1s rep3

description:
mouse_astrocyte_12_samples_gene_exp_norm_log.txt
12A

data_processing:
The raw RNA-seq data were uploaded, processed and analyzed with the RNA-seq process pipeline in OmicSoft Array Studio software (version 10.1.1.3), including data quality control, alignment, quantification, normalization and log2 transformation to obtain the expression values (log2 FPKM) for each sample
Genome_build: MouseB38
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text file including gene annoation

source_name: Astrocytes

growth_protocol: Brains from 2-4 day old C57BL/6 mice were harvested and pooled in DMEM/F12-Glutamax media with 10% FBS transferred into warm 0.25% trypsin (2mL/brain) and incubated at 37ºC while rotating for 30 minutes.  The tissues were dissociated and filtered through a 70µM cell strainer.  The single-cell suspension was plated in T150 tissue culture flasks (1 flask/mouse) and the mixed gilal cells were cultured and fed for 12 days. On day 12 mixed glial cells were trypsinized and the single cell suspensions were counted. To isolate primary murine microglia, the EasySep Mouse CD11b Positive Selection Kit (StemCell #18970) was used with EasySep Magnets (StemCell #18000) according to manufacturer’s instructions. Primary murine astrocytes were isolated from the microglia negative fraction, with the EasySep Mouse APC Positive Selection Kit (StemCell #18452) and plated in DMEM high glucose with 10% FBS and N2 supplement (1:100 dilution; Thermo Fisher Scientific #17502-048). Isolated microglia were seeded at 2x10^6 cells/well and astrocytes at 1x10^6 cells/well in 6-well plates and rested for 24-48 hours prior to treatment

extract_protocol:
Cells were lysed in 350uL RLT Plus Lysis Buffer and RNA was extracted with the Qiagen Rneasy Plus Mini Kit according to manufacturer's instructions
Microglia (Genewiz): RNAseq library preparation consists of (A) mRNA enrichment, mRNA fragmentation and random priming; (B) first and second strand cDNA synthesis; (C) end repaire, 5'phophorylation and dA-tailing and (D) adaptor ligation and PCR enrichment and sequencing. Astrocytes (BGI): we captured mRNA with oligo dT and  constructed mRNA-seq library by strand-specific protocol. Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA were fragmented into small pieces (200-350bp) with fragment buffer at appropriate temperature. Then First-strand cDNA is generated in First Strand reaction system by random hexamer-primed reverse transcription, and the second-strand cDNA was generated with dNTP (dTTP replaced by dUTP). Adapters were added by incubating to end repair. After degradation of  the second-strand cDNA, the first Strand were amplified by PCR. Products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on DNBseq platform

treatment_protocol: Microglia and astrocytes were treated with (1) DMSO, (2) Nec-1s, (3) TNF/5z-7 (microglia only), (4) TNF/Smac/zVAD, (5) TNF/5z-7/Nec-1s (microglia only), and (6) TNF/Smac/zVAD/Nec-1s for 4 hours prior to lysis and RNA extraction


title: FFPE_ATAC_on_Cereblum_rep1_trim


title: Astrocytes TNF/Smac/zVAD/Nec-1s rep2

description:
mouse_astrocyte_12_samples_gene_exp_norm_log.txt
11A


title: Astrocyte TNF/Smac/zVAD rep2


title: Blood_TOL_rep3

description: Bisulfite-converted DNA

label_protocol: Infinium HD Assay Methylation Protocol, Illumina Inc.


title: Blood_CR_rep3

description: Bisulfite-converted DNA

source_name: Peripheral Blood Mononuclear Cells, healthy volunteer

value: Chronic rejection


title: Blood_HV_rep1

description: Bisulfite-converted DNA

source_name: Peripheral Blood Mononuclear Cells , healthy volunteer

value: Healthy volunteer


title: Blood_TOL_rep7

description: Bisulfite-converted DNA


title: 103593-001-028


title: Blood_CR_rep6

description: Bisulfite-converted DNA


title: Blood_TOL_rep5

description: Bisulfite-converted DNA


title: Astrocyte TNF/Smac/zVAD rep1


title: Blood_TOL_rep9

description: Bisulfite-converted DNA


title: Blood_HV_rep3

description: Bisulfite-converted DNA


title: Blood_CR_rep5

description: Bisulfite-converted DNA


title: Blood_TOL_rep8

description: Bisulfite-converted DNA


title: Blood_HV_rep6

description: Bisulfite-converted DNA


title: FFPE_ATAC_on_Rectum2_rep1_trim


title: 103593-001-024


title: Astrocytes TNF/Smac/zVAD/Nec-1s rep1

description:
mouse_astrocyte_12_samples_gene_exp_norm_log.txt
10A


title: Astrocyte Nec-1s rep1


title: Astrocytes TNF/Smac/zVAD rep2

description:
mouse_astrocyte_12_samples_gene_exp_norm_log.txt
8A


title: FFPE_ATAC_on_Rectum1_rep2_trim


title: 103593-001-026


title: Astrocyte Nec-1s rep2


title: Blood_CR_rep1

description: Bisulfite-converted DNA


title: Astrocyte DSMO rep3

value: DSMO


title: Astrocytes TNF/Smac/zVAD rep1

description:
mouse_astrocyte_12_samples_gene_exp_norm_log.txt
7A


title: Blood_HV_rep7

description: Bisulfite-converted DNA


title: FFPE_ATAC_on_Colon5_rep1_trim

source_name: Colon

value: Colon


title: Astrocytes TNF/Smac/zVAD rep3

description:
mouse_astrocyte_12_samples_gene_exp_norm_log.txt
9A


title: Blood_CR_rep4

description: Bisulfite-converted DNA


title: FFPE_ATAC_on_Colon5_rep2_trim


title: 103593-001-021


title: Blood_HV_rep5

description: Bisulfite-converted DNA


title: Blood_TOL_rep4

description: Bisulfite-converted DNA


title: Blood_HV_rep4

description: Bisulfite-converted DNA


title: 103593-001-023


title: Blood_HV_rep2

description: Bisulfite-converted DNA


title: FFPE_ATAC_on_Colon4_rep1_trim


title: 103593-001-027


title: Blood_TOL_rep1

description: Bisulfite-converted DNA


title: Blood_TOL_rep6

description: Bisulfite-converted DNA


title: Astrocyte DSMO rep2


title: Astrocytes Nec-1s rep1

description:
mouse_astrocyte_12_samples_gene_exp_norm_log.txt
4A


title: Blood_CR_rep2

description: Bisulfite-converted DNA


title: ACJ4

city: Ås

first: Byron

last: Morales Lange

address: Arboretveien 6

country: Norway

institute: Norwegian University of Life Sciences

data_processing:
Raw reads were cleaned by BBDuk (v34.56) to trim/remove low quality reads, adapter sequences and PhiX (Illumina spike-in) using: ktrim = r, k = 23, mink = 11, hdist = 1, tbo, tpe, qtrim = r, trimq = 15, maq = 15, minlen = 36, forcetrimright = 149.
Cleaned reads were aligned to Salmo salar genome ICSASG_v2 (RefSeq assembly accession: GCF_000233375.1) by HISAT (v2.1.0).
Fragments mapping were counted using featureCounts (v1.4.6-p1)
Differentially expressed genes (DEGs) were estimated between diets using SARTools R package (v1.7.3). Significant DEGs were determined when the adjusted p value (padj) was < 0.05.
Genome_build: ICSASG_v2 (RefSeq assembly accession: GCF_000233375.1
Supplementary_files_format_and_content: Counts of sequencing reads for the features of interest (.counts)

organism: Salmo salar

source_name: Spleen, ACJ

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the supplier's instructions. Then, each total RNA sample was quantified using a NanoDrop TM 8000 spectrophotometer (Nanodrop Technologies). RNA integrity was determined using Agilent Bioanalyzer 2100. All samples showed a RIN value ≥ 8.
Library preparation and RNA-sequencing were performed by the Norwegian Sequencing Center, using TruSeq Stranded mRNA library prep and Illumina HiSeq 4000 System (150 bp paired-end)

treatment_protocol: Atlantic salmon with an average starting weight of 5.71 ± 0.06 g were sorted (at an initial stocking density of 3.21 kg/m3) into 100 L tanks exposed to a 24 h-light regime and recirculated fresh water (15 °C). In each tank, fish were fed for 37 days using one of the four experimental diets: fishmeal diet as a control diet (FM), 40% soybean meal diet as a challenging diet (SBM), and two diets with 40% SBM and 5% inclusion of C. jadinii after different downstream processes: heat-inactivated (ICJ) or autolysed (ACJ)

tag: diet

value: Autolysed-Cyberlindnera jadinii

tag: group

value: ACJ

tag: feeding time

value: spleen


title: 103593-001-018

value: HFD

value: HighFatDiet


title: ACJ3


title: 103593-001-020


title: Astrocytes Nec-1s rep3

description:
mouse_astrocyte_12_samples_gene_exp_norm_log.txt
6A

tag: strain

value: Astrocytes


title: FFPE_ATAC_on_Colon4_rep2_trim

value: FVBN

value: FFPE

tag: tissue


title: FFPE_ATAC_on_Colon2_rep2_trim


title: FFPE_ATAC_on_Colon2_rep1_trim


title: Astrocytes Nec-1s rep2

description:
mouse_astrocyte_12_samples_gene_exp_norm_log.txt
5A

tag: cell type


title: 103593-001-019


title: Astrocytes DSMO rep3

description:
mouse_astrocyte_12_samples_gene_exp_norm_log.txt
3A


title: Astrocyte Nec-1s rep3


title: 103593-001-015


title: 103593-001-012


title: Astrocyte DSMO rep1


title: 103593-001-017


title: Astrocytes DSMO rep2

description:
mouse_astrocyte_12_samples_gene_exp_norm_log.txt
2A


title: ACJ1


title: artery wildtype

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

country: Germany

institute: University of Ulm

description:
CO_Artery_0
vein_artery_wildtype_dbdb_fpkm.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Alignment was done using Hisat2
Cufflinks was used to assemble the transcripts
Cuffmerge was used to merged all the transcripts
Cuffdiff was for differential expression analysis
Genome_build: mm10/hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: artery

extract_protocol:
Total RNA from skin was isolated using Rneasy kit (Qiagen)
rRNA removal was performed by Ribominus Eukaryotic system v2 kit (ThermoFisher Scientific). rRNA depleted RNA was subjected to preparation of Illumina compatible RNA-seq libraries using NEBNext Ultra II Directional RNA Library Prep Kit (NEB).

value: db/db


title: FFPE_ATAC_on_Rectum1_rep1_trim

value: Rectum


title: ACJ2


title: EAE-RIPK1inh. microglia rep1

source_name: spinal cord microglia

extract_protocol:
Mice were sacrificed and perfused with PBS. Spinal cords were extracted, chopped in Accutase (1mL/sample; Sigma), and homogenized with a 19-gauge needle. Samples were incubated at 4°C for a total of 20 minutes and homogenized with a 21-gauge needle at intervals of 10 minutes. Cells were then filtered through a 100µm cell strainer. Samples were pelleted, resuspended in 3mL PBS and 4mL 25% BSA in PBS, and centrifuged (1200g, 10 minutes). Supernatants were aspirated to remove excess myelin and samples were resuspended in 5mL 25% BSA. The spin was repeated, and supernatants discarded. Cells were resuspended in 100µL FACS staining buffer (2% FBS, 2mM EDTA, 1% P/S in PBS) and treated with Fc block (CD16/32, 1:100; BD Biosciences, #553142) for 5 minutes. Cells were stained for FACS sorting at 4°C for 45 minutes with the following antibodies: anti-CD45 BUV395 (1:50; BD Biosciences #564279, clone 30-F11), anti-CD11b BV421 (1:50; BD Biosciences #562605, clone M1/70), anti-CX3CR1 BV711 (1:50; Biolegend, #149031, clone SA011F11), anti-CD140a PE (1:50; Biolegend, #135905, clone APA5), and anti-GLAST APC (1:10; Miltenyi Biotec, #130-095-822, clone ASCA-1). Astrocytes were defined as GLAST+CD11b-CD45-CD140a- while microglia were defined as CD11b+CD45intCX3CR1+. Sorted cells were collected in Qiazol or RLT Plus Lysis buffer and frozen prior to RNA extraction with standard protocols.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Then First-strand cDNA is generated directly by MMLVRT Reverse transcriptase (SMRT seq2 method: Mmurine Leukemia Reverse Sivia, MMLVRT). Then the cDNA was amplificated by PCR. Finally, the cDNA was fragmented into small pieces (200-350bp) with Tn5 transposase enzymes. Products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on DNBseq platform (BGI)

treatment_protocol: Female C57BL/6 mice were immunized with MOG35-55 peptide to induce EAE. Upon reaching a clinical score of around 1, mice were dosed for 3 days with vehicle (20% Captisol) or RIPK1 inhibitor (GSK'547, 50mg/kg) twice a day by oral gavage

value: spinal cord microglia

value: EAE - GSK'547 (RIPK1 inhibitor)


title: 103593-001-007


title: vein db/db

description:
DBDB_Vein_0
vein_artery_wildtype_dbdb_fpkm.txt

source_name: vein


title: Astrocytes DSMO rep1

description:
mouse_astrocyte_12_samples_gene_exp_norm_log.txt
1A


title: SBM3

source_name: Spleen, SBM

value: Soybean meal

value: SBM


title: 103593-001-014


title: ICJ4

source_name: Spleen, ICJ

value: Inactivated-Cyberlindnera jadinii

value: ICJ


title: FFPE_ATAC_on_Colon1_rep2_trim

value: Colon


title: vein wildtype

description:
CO_Vein_0
vein_artery_wildtype_dbdb_fpkm.txt


title: FFPE_ATAC_on_Colon3_rep2_trim


title: EAE-RIPK1inh. microglia rep5


title: 103593-001-013


title: EAE-RIPK1inh. microglia rep4


title: FFPE_ATAC_on_Colon3_rep1_trim


title: EAE-vehicle microglia rep5

value: EAE - vehicle


title: ICJ2


title: ICJ3


title: artery db/db

description:
DBDB_Artery_0
vein_artery_wildtype_dbdb_fpkm.txt


title: CDDP_STING_KO3

city: Nanjing

first: Lintao

state: Jiangsu

address: Long Mian Da Dao

institute: China Pharmaceutical University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: heart

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cisplatin (6 mg/kg) in 0.9% normal saline was administered by intraperitoneal injection on 1th day, 8th day and 15th day

value: heart

value: treated with CDDP on 1st, 8th and 15th Day

tag: genotype


title: 103593-001-005

value: Chow

value: ControlHealthyDiet

tag: mousenr


title: EAE-RIPK1inh. microglia rep3


title: FFPE_ATAC_on_Colon1_rep1_trim


title: 103593-001-010

value: HFD

value: HighFatDiet


title: SBM1

value: spleen


title: CDDP_STING_KO2


title: 103593-001-004


title: ICJ1


title: EAE-RIPK1inh. microglia rep2


title: 103593-001-003


title: 103593-001-009


title: EAE-vehicle microglia rep2


title: STING_KO3

value: untreated


title: SBM4


title: FM2

source_name: Spleen, FM

value: Fish meal

value: FM


title: SBM2


title: EAE-vehicle microglia rep6

value: spinal cord microglia


title: EAE-vehicle microglia rep4


title: EAE-vehicle microglia rep3


title: CDDP3

value: wild type


title: Pool_12

city: San Francisco

first: Yang

last: Sun

state: CA

address: 513 Parnassus Ave

department: Rheumatology

institute: UCSF

description:
mixture of stimulated PBMCs from healthy donors,  stained with oligo-conjugated antibodies
aggr_raw_feature_bc_matrix.h5

data_processing:
Base-calling and read demultiplexing was done using the bcl2fastq conversion tool.
FASTQs were aligned and unique-molecular identifiers were counted using 10x Genomics' cellranger v3.0.1 using the standard hg38 reference. This produces 1 binary sequence alignment map (BAM) file per droplet sequencing lane.
BAMs were inputted into dsc-pileup, which generates intermediate pileup files. These pileup files were then merged and a single aggregated file set was input into freemuxlet for genotype clustering. The output was used to annotate filtered barcodes as either singlets or doublets and assign cell-containing droplets to nameless cell donors. This generates a VCF with nameless donors.
The freemuxlet-generated VCF with nameless donors was deconvoluted using the pooling framework scheme, which enabled unambiguous assignment of freemuxlet clusters to individual donors, attaching donor ids and other individual covariates.
Genome_build: hg38
Supplementary_files_format_and_content: File formats are (1) Hierarchical Data Format (HDF) files with suffix .h5, and (2) HDF files formatted using the AnnData standard. The h5 files with the names of individual well have the raw output of the protein counts only, while the h5 files with the "aggr" label contains the aggregated matrix (across all wells) for the RNA transcript counts. The content of the h5ad files are count matrices with filtered cell barcodes across all wells, both RNA and protein with attached individual covariates located in the ".obs" attribute. The h5ad labeles raw has the raw integer counts, while the one without the raw label contains counts that have been normalized, log transformed and scaled.

molecule: polyA RNA

source_name: Human PBMC

growth_protocol: PBMCs were isolated from blood samples by Ficoll-PaqueTM PLUS density gradient centrifugation and frozen in fetal bovine serum containing 10% (vol/vol) dimethyl sulfoxide. Cells were frozen and not thawed until the day of the experiment when they were used directly for in vitro stimulation.

extract_protocol:
Pools were loaded onto the 10x Genomics controller using 1 lane per pool, and processed using standard protocols, including cell lysis, reverse transcription, amplification and library generation.
Libraries were constructed using standard protocols from 10x Genomics.

treatment_protocol: Cells were stimulated with 5 soluble immunomodulatory agonists: tumor necrosis factor alpha (TNF-ɑ, 50 ng/mL), interferon beta (IFN-β, 500 IU/mL), interferon gamma (IFN-γ, 100 IU/mL), Resiquimod (R-848, 1 μg/mL), and phorbol myristate acetate with ionomycin (PMA/I, 81 nM PMA/1.33μM Ionomycin) for 9 hours at 37°C, 5% CO2. Unstimulated PBMCs were incubated under identical conditions to reduce any confounding from incubation conditions other than stimulation. After incubation, cells were counted and mixed according to the compressed pooling framework. Cells were blocked with Fc block and stained with a cocktail of antibodies targeting 89 surface proteins, then washed and counted.

tag: organ

value: PBMC


title: Naïve microglia rep2

value: naïve


title: Naïve microglia rep3


title: Pool_11


title: RGFP_CD4_2

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

data_processing:
Sequence reads were mapped to mouse GRCm38/mm10 genome with TopHat2 in very-sensitive settings for Bowtie2 and EnsEMBL annotation release 67.
Gene expression was quantified by feature featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for genes.

source_name: small intestinal lamina propria

extract_protocol:
isolation protocol: Intestines were isolated and PPs were removed. Tissue was cleaned, longitudinally opened and chopped into pieces of 2 cm, followed by two rounds à 15 min at 37°C epithelial cell dissociation using Hank’s balanced salt solution without calcium and magnesium (HBSS-/-, Gibco) supplemented with 2% FCS, 10 mM HEPES buffer (Sigma), 1 mM DTT (ThermoFisher) and 5 mM EDTA (Sigma). After washing with HBSS-/-, tissues were digested using a lamina propria dissociation kit (Miltenyi) according to the manufacturer’s instructions. Lymphocytes were further enriched on a 40%/80% Percoll (GE Healthcare) gradient.  Cells were sorted on a BD Aria II machine.
FACS sort: Viable Lineage (CD19, CD11c, CD11b, F4/80,FceRIa, Gr-1)-CD45+CD3-RORgt-GFP+  expressing either NKp46 or CD4
RNA isolation protocol: RNA of cells was extracted using RNeasy Plus Micro Kit (Qiagen) and RNA quality was assessed by an Agilent 2100 Bioanalyzer.
SMART-SeqII (ultra-low input RNA) libraries were prepared using Nextera XT DNA sample preparation kit (Illumina).

value: C57BL/6J background

tag: genotypes

value: RorcGFP/wt

tag: age

value: 4 weeks

tag: sorting strategy

value: viable Lineage (CD19, CD11c, CD11b, F4/80,FceRIa, Gr-1)-CD45+CD3-RORgt-GFP+  CD4+


title: 103593-001-006


title: CDDP_STING_KO1

value: heart

value: treated with CDDP on 1st, 8th and 15th Day


title: FM4


title: Pool_9


title: CDDP1


title: Naïve microglia rep1


title: FM3


title: WT2


title: STING_KO2


title: EAE-vehicle microglia rep1

value: EAE - vehicle


title: RKO_NKp46_1

value: RorcGFP/GFP

value: viable Lineage (CD19, CD11c, CD11b, F4/80,FceRIa, Gr-1)-CD45+CD3-RORgt-GFP+  NKp46+


title: Pool_7


title: 103593-001-002

value: Chow

value: ControlHealthyDiet


title: EAE-RIPK1inh. astrocyte rep3

source_name: spinal cord astrocytes

value: spinal cord astrocytes

value: EAE - GSK'547 (RIPK1 inhibitor)


title: Naïve microglia rep4

value: spinal cord microglia


title: RGFP_NKp46pos_3


title: E18_SI

data_processing:
The Cell Ranger Single Cell Software Suite 3.0.2 was used to perform sample demultiplexing, barcode processing, and single cell 3’ v3 gene counting with refdata-cellranger-mm10-1.2.0 as reference and expected cell number of 3000.
Antibody- and hashtag-barcodes were demultiplexed and quantified by CITE-seq-count using the undetermined reads.
Genome_build: mm10
Supplementary_files_format_and_content: Barcoded BAM, with Chromium cellular and molecular barcode information for each read, stored as TAG fields; h5: aggregated gene count matrix in hdf5 format. txt: tab-delimeted text file including antibody and hashtag UMI counts with cellular barcodes corresponding to the transcriptome sequencing.

extract_protocol:
isolation protocol: Small intestines from fetal mice were isolated from embryos under a dissecting microscope. Surrounding mesenteric tissue was removed under further magnification and cut open longitudinally. Tissue was incubated for 30 min at 37°C under agitation in HBSS containing calcium and magnesium (HBSS+/+), 2% FCS, 10 mM HEPES, 0.2 U/mL Liberase DL (Sigma) and 50 µg/mL DNaseI (Sigma). Leftover tissue was dissociated using a 22G needle and cell suspension was passed through a 70 µm strainer and washed in PBS/BSA. Cells were subsequently surface stained for FACS and in the second step with Total-Seq antibodies (BioLegend) according to manufacturer's instructions. Cells were sorted on a BD Aria II machine.
FACS sort and CITE-Seq staining: Cells sorted according to viable Lineage(CD19, CD3, CD5, F4/80,FceRIa, Gr-1)-CD45+CD122+ and/or CD127+. Cells were furthermore stained with the following TotalSeq A antibodies (BioLegend) according to the manufacturer's instructions: CD4, CD49b, NK11, DNAM1, CD3, CCR6, NKp46, cKit, Nrp1, NKG2D, TCRgd, TCRb, CD49a, CXCR5, CD27, CD200R1, PD1, CD127, a4b7, ICOS, Sca1, ST2, CD25 and KLRG1 antibodies. Genotypes were hashtagged using TotalSeq A hashtags 1-3.
library construction protocol: A total of 8000 cells were loaded in the ChromiumTM Controller for partitioning single cells into nanoliter-scale Gel Bead-In-Emulsions (GEMs). Single Cell 3′ reagent kit v3.1 was used for reverse transcription, cDNA amplification and library construction of gene expression libraries (10x Genomics) according to the manufacturer’s instructions. TotalSeqTM-A libraries were prepared following the protocol for 10x Single Cell 3′ Reagent Kit v3.1 provided by BioLegend, including primer sequences and reagent specifications. All libraries were quantified using a QubitTM 2.0 Fluorometer (ThermoFisher) and quality was tested on a 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent). Sequencing was performed using the NextSeq500/550 HighOutput Kit v2.5 (150 cycles) on a NextSeq500 sequencer (Illumina). Antibody and hashtag libraries were amplified using the KAPA HiFi ready mix with primers containing Illumina Small RNA RPIx sequences and Truseq D70x_s, respectively.
Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1

value: RorcGFP, RorcKO, RorcTbxDKO

value: embryonic day E18.5

value: Lin-CD45+CD122+and/orCD127+ ILCs


title: STING_KO1

value: untreated


title: FM1

value: Fish meal

value: FM

value: spleen


title: EAE-RIPK1inh. astrocyte rep2


title: Pool_5

value: PBMC


title: DKO_CD4_2

value: C57BL/6J background

value: RorcGFP/GFP x Tbx21-/-

value: 4 weeks

value: viable Lineage (CD19, CD11c, CD11b, F4/80,FceRIa, Gr-1)-CD45+CD3-RORgt-GFP+  CD4+


title: DKO_CD4_1


title: WT1

value: heart

value: wild type


title: EAE-RIPK1inh. astrocyte rep5

value: spinal cord astrocytes


title: 12_week

city: MILWAUKEE

first: Yi-Guang

last: Chen

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

data_processing:
Raw sequencing data was downloaded using the Python Run Downloader (Illumina).
Demultiplexing was done using the mkfastq function in Cell Ranger (version 1.3.1) (10x Genomics)
Alignment and conversion to gene-barcode matrices was done using the count function in Cell Ranger (version 1.3.1) (10xGenomics)
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx: filtered gene-barcode matrix in MEX format

extract_protocol:
CD45.1+ cells were sorted from the pancreatic islets of 7 or 12-week old female NOD mice by flow cytometry
Single cell cDNA libraries were prepared according to the 10x Genomics Chromium Single Cell 3' Reagent Kit protocol

value: NOD/ShiLtJ

tag: Sex

value: female

tag: time point

value: 12 weeks old

value: immune cells isolated from pancreatic islets

tag: cell population

value: CD45.1+ cells


title: CDDP2

tag: treatment

value: treated with CDDP on 1st, 8th and 15th Day


title: RGFP_CD4_1

value: RorcGFP/wt


title: RKO_NKp46_2

value: RorcGFP/GFP

value: viable Lineage (CD19, CD11c, CD11b, F4/80,FceRIa, Gr-1)-CD45+CD3-RORgt-GFP+  NKp46+


title: Pool_10

value: PBMC


title: EAE-RIPK1inh. astrocyte rep4

value: EAE - GSK'547 (RIPK1 inhibitor)


title: Pool_8


title: WT3

value: untreated


title: BCR Sample 3

city: Guang Zhou

first: Siyu

last: Yang

address: outer ring road 384

institute: South China University of Technology

data_processing:
The Cell Ranger software pipeline(version 5.0.0) provided by 10x Genomics was used to demultiplex cellular barcodes, map reads to the reference genome
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: murine spleen and peritoneal cavity

extract_protocol:
Single cells were suspended with PBS + 0.04% BSA and loaded to 10× chromium controller to generated Gel beads in emulsion using 10× genomics Single Cell 5’ Library & Gel Bead Kit
RNA libraries were prepared using Chromium Single Cell V(D)J Reagent Kits with Feature Barcoding technology for Cell Surface Protein according to the instructions of 10x genomics.

value: 10 weeks

value: spleen and peritoneal cavity

value: CD19+B220+ cells

tag: feature type

value: vdj-b


title: Pool_2


title: EA.hy.control.rep1

city: Kuopio

first: Minna

last: Kaikkonen-Määttä

country: Finland

institute: A. I. Virtanen Institute

description:
total RNA, rRNA depleted
Clones
EA.hy.control.rep1 FPKM

data_processing:
Raw reads were trimmed and filtered using Trim Galore (v.0.4.4) with Phred quality score cutoff 30.
Processed reads were aligned to the GRCh37 genome assembly using STAR version 2.5.4b (Dobin et al. 2013) with options --outFilterMismatchNoverLmax 0.04 and --outFilterMultimapNmax 10.
Aligned reads mapping to features were assigned using featureCounts (Rsubread 1.32.4) with the Gencode V19 GTF.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bedGraphs
Supplementary_files_format_and_content: RNA-Seq_EA.hy9268_DeltaSE2_DeltaSE_E2_rpkm.txt

growth_protocol: EA.hy926 (ATCC; CRL-2922) were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM)-high glucose (D5671, Sigma) supplemented with 10% Fetal Bovine Serum (FBS) and 1% penicillin-streptomycin.

extract_protocol:
RNA-Seq: Total RNA was isolated from the cells using RNeasy Mini kit (74104; QIAGEN) and DNase treated with RNase-Free DNase Set (79254; QIAGEN).
RNA-Seq: Prior to RNA library preparation, the quality of the input RNA was assessed by Fragment Analyzer (Agilent) using the RNA Kit (DNF-471; Agilent) and a threshold of RQN>9. RNA library preparation was carried out using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7765; New Englands BioLabs) according to manufacturer instructions. Briefly, 0.5 ug of DNase-treated RNA was subjected to ribosomal RNA (rRNA) depletion, followed by RNA fragmentation, cDNA synthesis and 11 cycles of PCR amplification. The resultant library was quantified using Qubit dsDNA HS Assay Kit (Q32851; ThermoFisher Scientific) and its quality was checked with Bioanalyzer (Agilent). Individual libraries were pooled in equimolar amount (4 nM for each) and sequenced with the Nextseq 550 (Illumina) using single end 75 cycles for 10 million reads per sample.

treatment_protocol: CRISPR/Cas9-mediated deletion of target regions were performed using the Alt-R CRISPR-Cas9 System (Integrated DNA technology; IDT).

tag: cell line

tag: genotype/variation

value: Control


title: Pool_6


title: Pool_1


title: EAE-RIPK1inh. astrocyte rep1

value: spinal cord astrocytes


title: Pool_4


title: EAE-vehicle astrocyte rep6

value: EAE - vehicle


title: Gene expression Sample 2

source_name: murine mesenteric lymph nodes

value: wild type

value: mesenteric lymph nodes

value: gene expression


title: EAE-vehicle astrocyte rep3


title: 7_week

value: NOD/ShiLtJ

value: female

value: 7 weeks old

value: immune cells isolated from pancreatic islets

value: CD45.1+ cells


title: BCR Sample 1

source_name: murine liver and spleen tissue

value: liver and spleen tissue


title: EA.hy.control.rep2

description:
total RNA, rRNA depleted
Clones
EA.hy.control.rep2 FPKM


title: RGFP_NKp46pos_1

value: C57BL/6J background

value: RorcGFP/wt

value: 4 weeks

value: viable Lineage (CD19, CD11c, CD11b, F4/80,FceRIa, Gr-1)-CD45+CD3-RORgt-GFP+  NKp46+


title: EAE-vehicle astrocyte rep5


title: Pool_3

value: PBMC


title: HUVEC co-culture with db/db MDF 3

description:
DBDB_EC_5D_cocul_2
huvec_coculture_fpkm_replicates.txt

source_name: HUVEC

value: Endothelial cells

tag: co-culture

value: db/db MDF


title: Gene expression Sample 3

tag: strain

value: 10 weeks

value: spleen and peritoneal cavity

value: CD19+B220+ cells


title: EAE-vehicle astrocyte rep1

value: spinal cord astrocytes

value: EAE - vehicle


title: Gene expression Sample 1

value: wild type

tag: tissue

value: gene expression


title: EAE-vehicle astrocyte rep4

tag: cell type


title: BCR Sample 2

tag: genotype

value: mesenteric lymph nodes

value: vdj-b


title: HUVEC co-culture with db/db MDF 1

description:
DBDB_EC_5D_cocul_0
huvec_coculture_fpkm_replicates.txt


title: Naïve astrocyte rep4

value: naïve


title: 16234X1 Old Ambulatory Control

city: Salt Lake City

first: Micah

middle: J

last: Drummond

state: Utah

address: 520 Wakara Way

department: Physical Therapy and Athletic Training

institute: The University of Utah

data_processing:
Sequencing reads were demulitplexed with 10x cellranger mkfastq version 3.1.0
Reads were aligned to the mouse genome (refdata-cellranger-mm10-3.0.0 from 10X Genomics) and count barcodes and UMIs were generated using cellranger count 3.1.0 with expected-cells set to 6000 per library
High and low mitochondrial read count cells were filtered from the data set prior to analysis
Data was next analyzed using R software with Seurat and CIPR cluster analysis packages
Genome_build: mm10
Supplementary_files_format_and_content: Filtered feature-barcode matrices in TSV and MEX format from cellranger count.

source_name: CD45+ Cells From FACS

extract_protocol:
Solei were extracted from mice, pooled for each respective treatment group finely minced and homogenzied using GentleMACS machine, blocked with FC receptor antibody sorted for CD45+ DAPI- cells via FACS and then analyzed through scRNAseq
10X Chromium Single Cell Gene Expression Solution with 3’ chemistry, version 3

treatment_protocol: Control, Hindlimb Unloading, Reloading

tag: strain background

value: male

value: Ambulatory Control

value: Skeletal Muscle (Soleus)

value: CD45+ Cells From FACS


title: EA.hy.RNA.DeltaSE12313-b.rep2

description:
total RNA, rRNA depleted
Clones
EA.hy.RNA.?E12313-b.rep2 FPKM

value: SE12313-b knock-out


title: EA.hy.RNA.DeltaSE12313-b.rep1

description:
total RNA, rRNA depleted
Clones
EA.hy.RNA.?E12313-b.rep1 FPKM


title: Naïve astrocyte rep3


title: HUVEC co-culture with wildtype MDF 3

description:
Co_EC_5D_cocul_2
huvec_coculture_fpkm_replicates.txt

value: Endothelial cells

value: wildtype MDF


title: EA.hy.RNA.DeltaE2.rep2

description:
total RNA, rRNA depleted
Clones
EA.hy.RNA.?E2.rep2 FPKM

value: E2 knock-out


title: Naïve astrocyte rep2


title: 17390X1 Young Hindlimb Unloading

description: 17390X1_191004_A00421_0117_BHL3GGDMXX_S4

value: Young (4-5 mo)

value: Hindlimb Unloading


title: EA.hy.RNA.DeltaSE12313-b.rep3

description:
total RNA, rRNA depleted
Clones
EA.hy.RNA.?E12313-b.rep3 FPKM


title: EA.hy.RNA.DeltaE2.rep1

description:
total RNA, rRNA depleted
Clones
EA.hy.RNA.?E2.rep1 FPKM


title: Naïve astrocyte rep1

value: spinal cord astrocytes


title: 16234X2 Young Ambulatory Control


title: HUVEC co-culture with db/db MDF 2

description:
DBDB_EC_5D_cocul_1
huvec_coculture_fpkm_replicates.txt

value: db/db MDF


title: Irpex lacteus, aspen rep2

status: Public on Aug 11 2021

city: Marseille

first: Marie-Noëlle

last: Rosso

address: 163 avenue de Luminy

department: Biodiversity and Biotechnology of Fungi - BBF

country: France

institute: INRAE - Aix Marseille University

data_processing:
Raw fastq file reads were filtered and trimmed using the JGI QC pipeline.
QCed reads from each library were aligned to the  genome of Irpex lacteus CCBAS Fr. 238 617/93, available via Mycocosm JGI portal, using TopHat2 (Kim et al. 2013. Genome Biol. 14(4):R36) with only unique mapping allowed.
Read counts were determined by HTSeq (Anders S, Pyl PT, Huber W. 2015. Bioinformatics. 31(2):166-169)
Read counts were normalized using ddsNorm from the DESeq Bioconductor package (version 1.5; Love MI, Huber W, Anders S. 2014. Genome Biol. 15:550)
The mean normalized read counts for each gene were calcuated from the normalized read counts of three replicates for each growth condition, except for pine wood for which only two replicates were considered.
The mean normalized counts of CAZyme coding genes were log2 converted and retrieved
Supplementary_files_format_and_content: The Excel file includes the mean normalized log2 read count values for each CAZyme coding gene in each growth condition

organism: Irpex lacteus

source_name: mycelium

growth_protocol: Culture for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.( g.l-1), 1 mm Wiley-milled aspen (15 g.l-1 )

extract_protocol:
Total RNA was extracted from 100 mg tissue ground with FastPrep Lysis Matrix A (MP Biomedicals) in 1 ml TRIZOL (Ambion). Nucleic acids were precipitated with isopropanol, resuspended in water and treated with RNase-Free DNase I (QIAGEN). Total RNA was precipitated with LiCl and resuspended in DEPC-treated water. RNA quantity and quality were determined using the Experion RNA StdSens kit (QIAGEN).
Double stranded cDNAs were synthesized from Poly A RNA and fragmented (200-300bp) before construction of the sequencing libraries (Kapa Library Amplification Kit ; Kapa Biosystems).
Illumina HiSeq 2500 JGI platform generating paired end reads of 150bp each.

treatment_protocol: Mycelium and remaining solid substrate were immediately frozen in liquid nitrogen and stored at -80°C before RNA extraction.

tag: substrate

value: aspen

tag: time

value: day 3


title: EAE-vehicle astrocyte rep2

value: EAE - vehicle


title: Irpex lacteus, pine rep2

growth_protocol: Culture for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and sifted pine wood fragments < 2 mm (15 g.l-1)

value: pine


title: Irpex lacteus, pine rep1


title: Irpex lacteus, wheat straw rep2

growth_protocol: Culture for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and sifted wheat straw fragments < 2 mm (15 g.l-1)

value: wheat straw


title: 17320X2 Old Reloading Day 4

description: 17320X2_191004_A00421_0117_BHL3GGDMXX_S1

tag: age

value: male

value: Reloading (4 Day)


title: 17390X2 Old Hindlimb Unloading

description: 17390X2_191004_A00421_0117_BHL3GGDMXX_S3

value: Skeletal Muscle (Soleus)


title: Irpex lacteus, maltose rep2

growth_protocol: Culture for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (20 g.l-1)

value: maltose


title: Irpex lacteus, cellulose rep2

growth_protocol: Culture for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and Avicel (15 g.l-1)

value: avicel


title: HUVEC co-culture with wildtype MDF 1

description:
Co_EC_5D_cocul_0
huvec_coculture_fpkm_replicates.txt

value: Endothelial cells


title: 17320X1 Young Reloading Day 4

description: 17320X1_191004_A00421_0117_BHL3GGDMXX_S2

value: CD45+ Cells From FACS


title: 3D_rne_dCT

city: Burnaby

first: Travis

last: Blimkie

state: British Columbia

address: 8888 University Drive

department: MBB

country: Canada

institute: Simon Fraser University

description: Mutation in the rne gene

data_processing:
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq 2500
Fastq file quality control was performed using FastQC v0.11.7
Fastq files were aligned to the B. pertussis genome using STAR v2.6.1a
BAM files were sorted as part of read alignment with STAR
Read count tables were generated using htseq-count v0.9.1
Genome_build: B. pertussis sp. Tohama I reference genome: https://www.ncbi.nlm.nih.gov/assembly/GCF_000195715.1
Supplementary_files_format_and_content: Tab delimited files containing uniquely mapped reads per gene for each sample

organism: Bordetella pertussis

source_name: Bacterial

growth_protocol: Wild type and mutant cells were grown to an OD600 0.6-0.7 in SS broth.

extract_protocol:
RNA was extracted from cell pellets using RNAqueous RNA extraction kit (Ambion) following kit instructions, and DNA was removed using the TurboDNAse kit. Ribosomal RNA depletion was completed using the RiboZero Bacteria Kit (Illumina).
The KAPA Stranded Total RNA Kit (KAPA Biosystems) was used for library construction (single end reads).

treatment_protocol: 2ml of cells harvested into 4ml RNA protect Bacteria (Qiagen)


title: EA.hy.RNA.DeltaE2.rep3

description:
total RNA, rRNA depleted
Clones
EA.hy.RNA.?E2.rep3 FPKM

value: E2 knock-out


title: HUVEC co-culture with wildtype MDF 2

description:
Co_EC_5D_cocul_1
huvec_coculture_fpkm_replicates.txt

value: wildtype MDF


title: 3B_rne_dCT

description: Mutation in the rne gene


title: 3C_rne_dCT

description: Mutation in the rne gene


title: Irpex lacteus, aspen rep3


title: Irpex lacteus, cellulose rep3


title: Irpex lacteus, wheat straw rep1


title: 2B_rncD45A

description: Mutation in the rnc gene


title: 2A_rncD45A

description: Mutation in the rnc gene


title: Irpex lacteus, maltose rep3


title: Irpex lacteus, cellulose rep1


title: 1A_wild_type

description: Wild type B. pertussis


title: Irpex lacteus, maltose rep1


title: Irpex lacteus, aspen rep1


title: 3E_rne_dCT

description: Mutation in the rne gene


title: 3A_rne_dCT

description: Mutation in the rne gene


title: 2D_rncD45A

description: Mutation in the rnc gene


title: 2E_rncD45A

description: Mutation in the rnc gene


title: 2C_rncD45A

description: Mutation in the rnc gene


title: 1E_wild_type

description: Wild type B. pertussis


title: 1D_wild_type

description: Wild type B. pertussis


title: Irpex lacteus, wheat straw rep3


title: Ti Rep2

city: Portici

first: Daniela

last: D'Esposito

address: Via Università 100

department: Department of Agriculture

country: Italy

institute: University of Naples Federico II

data_processing:
Base calling was performed with CASAVA
Data filtering (trimming and clipping) was performed with Trimmomatic (minimum quality 35 and minimum length 25bp)
Read alignment was performed with TopHat2.
Read count was performed usign FeatureCounts
Differential expression analysis was performed using the R package edgeR
Genome_build: Solanum lycopersicum reference genome SL2.50
Supplementary_files_format_and_content: tab-delimited text files including raw read counts for the sample Tni (Rep1 and Rep 2), Ti (Rep1 and Rep2), Sni (Rep 1 and Rep 2), Si (Rep1 and Rep2)

organism: Solanum lycopersicum

source_name: Leaf

growth_protocol: Plants were grown in greenhouse

extract_protocol:
Total RNA purification was performed using Spectrum™Plant Total RNA Kit (Sigma Aldrich), according to manufacturer’s protocol.
strand-specific library

treatment_protocol: Infested plants, 4 weeks old, were exposed to 100 females and 100 males of T. absoluta

value: Tolerant/partially resistant to Tuta absoluta

value: infested with Tuta absoluta

value: Leaf


title: Tni Rep1

value: not infested with Tuta absoluta


title: Sni Rep2

value: Susceptible to Tuta absoluta


title: Ti Rep1


title: Si Rep2


title: Sni Rep1


title: 1B_wild_type

description: Wild type B. pertussis


title: 1C_wild_type

description: Wild type B. pertussis


title: HD1 unstim

city: Freiburg

first: Baerbel

last: Keller

department: Department of Rheumatology and clinical immunology

institute: University Medical Center Freiburg

data_processing:
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:3 TRAILING:10 MINLEN:25
Alignments and gene count tables were obtained for each sample using STAR (version 2.4.2a) on GRCh38 genome and annotation (GRCh38.p7).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited txt file including read count per gene for each sample

source_name: primary cells

extract_protocol:
Total RNA was purified from in vitro cultivated naive B cells using the Qiagen Rneasy Microkit according to the manufacturer’s instructions (Qiagen)
Samples were processed using the NEBNext Directional Ultra RNA 2 (NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina, cat # E7760L) protocol from NEB, with 10 ng of input total RNA and with 15 PCR cycles. Samples were sequenced 84-bases long on 2 lanes of NextSeq® 550 with high output flowcell (NextSeq® 500/550 High Output Kit v2).

treatment_protocol: 50.000 isolated naive B cells were either left untreated or stimulated with 5ug/ml anti-IgM and 50ng/ml IFNg

value: naive B cells

value: unstimulated

tag: healthy donor


title: HD2 IgM IFNg

value: IgM IFNg


title: HD2 unstim


title: Capan-1 RNA-seq Rep3

city: Beijing

first: Bo

last: Ren

address: Shuaifuyuan #1

department: General Surgery

institute: Peking Union Medical College Hospital

data_processing:
Raw Hi-C fastq files were processed by HiC-Pro for filtering, mapping and creating raw contact count matrices. The matrices were normalized by using the iterative correction method and converted to hic format which can be visualized by Juicebox.
ChIP-seq reads were aligned to the human hg19 by Bowtie ver 2.1.0 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Peak calling was performed by MACS2 ver 2.1.1 (https://github.com/taoliu/MACS/), and followed by peak annotation by using bedtools ver 2.20.1 (http://bedtools.readthedocs.io/en/latest). We used bamCompare module of deeptools to generate bigwig files, considering the input libraries as the control.
ATAC-seq was mapped to human h19 genome by Bowtie2. Peaks corresponding to the open region were called by MACS2 using the default parameters.
RNA-seq reads were mapped to human hg19 using HISAT2 ver 2.1.0 (https://github.com/DaehwanKimLab/hisat2). Expression levels of genes in each sample were quantified by HTSeq ver 0.6.1 (https://github.com/simon-anders/htseq) and normalized by FPKM method (Supplementary Data 2). Differential expressed genes were identified by DESeq2. The p-value was calculated by Wald test and corrected by Benjamini and Hochberg’s method as q-value. Genes with adj. p≤0.05 and |log2(Fold Change)| ≥1 were identified as differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C: hic format containing interaction matrices; ChIP-seq & ATAC-seq: bigwig format with peaks information; RNA-seq: xls format containing FPKM values of each library.

source_name: Liver metastasis of pancreatic cancer

growth_protocol: HPNE, PANC-1, and Capan-1 were obtained from America Type Culture Collection (ATCC, https://www.atcc.org/). All of them were cultured under recommended conditions.

extract_protocol:
For in situ Hi-C, the experiments were performed following the protocol provided by Rao et al with minor modifications. Briefly, the cells were crosslinked by 1% formaldehyde, and then were resuspended in lysis buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% Igepal CA-630, 1/10 vol. of proteinase inhibitor cocktail (Sigma)). The genome was then digested by 4 cutter restriction enzyme MboI, and the DNA ends were marked by biotin-14-dCTP and ligated by ligation enzyme. Next, the nuclear complexes were treated by proteinase K at 65℃ for reverse crosslink and DNA was purified by phenol-chloroform extraction. For ChIP-seq, the experiments were performed by following the protocol of SimpleChIP®Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology #9005). Per 10μg chromatin of 3 cell lines was precipitated by the corresponding 10μL antibody. For ATAC-seq, around 50,000 living cells were taken for library construction. The cells were lysed in 1 × lysis buffer to obtain the nuclei. RNA was extracted using Trizol reagent (Cat # 15596-018; Thermo Fisher Scientific, NY, USA).
For Hi-C, fragment ends were repaired by the mixture of T4 DNA polymerase,T4 polynucleotide kinase and Klenow DNA polymerase. Biotin labeled Hi-C sample were specifically enriched using streptavidin C1 magnetic beads. The fragment ends were adding A-tailing by Klenow(exo-) and then adding Illumina paired-end sequencing adapter by ligation mix. Finally, the Hi-C libraries were amplified by 12-14 cycles PCR. For ChIP-seq,  the libraries were constructed by DNA fragmentation, end repairing, dA-Tailing, adaptor ligation and PCR amplification. For ATAC-seq, the transposase-treated libraries were constructed by TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme Biotech, China) and using PCR for amplification of libraries. For RNA-seq, sequencing libraries were constructed by NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA).

value: Pancreatic cancer cells derived from liver metastasis


title: HD3 IgM IFNg


title: Si Rep1


title: Capan-1 RNA-seq Rep1


title: Capan-1 input

tag: chip antibody

value: none (input)


title: Capan-1 RNA-seq Rep2


title: HD5 IgM IFNg


title: HD4 IgM IFNg


title: Tni Rep2


title: HD3 unstim


title: HD1 IgM IFNg


title: Capan-1 H3K27me3 ChIP-seq Rep1

value: H3K27me3 Cell Signaling Technology #9733S


title: Capan-1 H3K9me3 ChIP-seq Rep2

value: H3K9me3 Cell Signaling Technology #13970S


title: TMS_2

city: New York City

first: Franck

last: Rapaport

state: NY

address: 1230 York Ave

institute: Rockefeller University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were aligned to hg19 and the HPV2 genomes using STAR 2.7.2b
Read counts were calculated using HTSeq.scripts.count with the options --nonunique all —stranded=no
Genome_build: hg19, HPV2
Supplementary_files_format_and_content: Tab-delimited files including raw read counts for each file

organism:
Homo sapiens
Human papillomavirus type 2

source_name: Back

extract_protocol:
Two tree-man syndrome lesions immersed in RNA later were snap-frozen in liquid nitrogen and crushed with a tissue pulverizer kit (Cell crusher) according to the manufacturer’s instructions. Total RNA was extracted with the RNeasy Fibrous Tissue Mini Kit (QIAGEN), according to the manufacturer’s instructions. The procedure included a DNAse digestion step or an additional column to remove contaminating DNA. The concentration and purity of the total RNA extracted were measured by spectrometry with an Xpose (Trinean). RNA integrity was evaluated by capillary electrophoresis with a Tape Station (Agilent). The Ovation Universal RNA-Seq System from NUGEN was used to prepare the RNA-seq libraries from100 ng of total RNA, as recommended by the manufacturer. This type of RNAseq kit is less sensitive to total RNA degradation (the RNA integrity number (RIN) of the two samples was quite low: 3.9 for one sample and 5 for the other). This kit constructs strand-specific RNA-seq libraries from 10 to 100 ng of total RNA and uses Insert-Dependent Adaptor Cleavage(InDA-C) technology to remove the ribosomal RNA transcripts.
The RNA is subjected to reverse transcription and the second strand is synthesized and a fragmentation step is then performed before Illumina-compatible indexed adaptator ligation. This ligation is followed by a strand-selection enzymatic reaction to provide information about the sense of the transcripts. Insert-dependent adaptor cleavage (InDA-C)-specific primers were then used for the targeted depletion of human ribosomal RNA sequencing transcripts before PCR enrichment. We ensure that no excess amplification occurred during the final PCR step, by evaluating the number of PCR cycles to be applied to each sample in a preliminary Q-PCR test with EvaGreen. An equimolar pool of the final indexed RNA-Seq libraries was sequenced on an Illumina NovaSeq6000 (paired-end reads, 100 bases + 100 bases) and ~50 million paired-end reads per library were produced.

tag: hpv strain

tag: disease

value: tree-man syndrome


title: Capan-1 H3K27me3 ChIP-seq Rep2

value: H3K27me3 Cell Signaling Technology #9734S


title: Capan-1 H3K36me3 ChIP-seq Rep2

value: H3K36me3 Cell Signaling Technology #4909S


title: Capan-1 H3K36me3 ChIP-seq Rep1


title: Capan-1 H3K27ac ChIP-seq Rep2

value: H3K27ac Cell Signaling Technology #8173S


title: Capan-1 H3K4me3 ChIP-seq Rep1

value: H3K4me3 Cell Signaling Technology #9751S


title: Capan-1 CTCF ChIP-seq Rep1

value: CTCF Cell Signaling Technology #3418


title: Capan-1 CTCF ChIP-seq Rep2

value: CTCF Cell Signaling Technology #3419


title: TMS_1

source_name: Arm


title: Capan-1 H3K27ac ChIP-seq Rep1


title: Capan-1 in situ Hi-C Rep4


title: Capan-1 H3K9me3 ChIP-seq Rep1

value: H3K9me3 Cell Signaling Technology #13969S


title: Capan-1 in situ Hi-C Rep2


title: Capan-1 in situ Hi-C Rep1


title: PANC-1 CTCF ChIP-seq Rep2

source_name: Primary pancreatic cancer

value: Primary pancreatic cancer cells


title: Capan-1 in situ Hi-C Rep3


title: PANC-1 H3K9me3 ChIP-seq Rep1


title: PANC-1 RNA-seq Rep1


title: PANC-1 RNA-seq Rep3


title: Capan-1 H3K4me3 ChIP-seq Rep2


title: PANC-1 input


title: PANC-1 RNA-seq Rep2


title: PANC-1 H3K27me3 ChIP-seq Rep2


title: PANC-1 H3K27me3 ChIP-seq Rep1


title: PANC-1 CTCF ChIP-seq Rep1


title: PANC-1 H3K36me3 ChIP-seq Rep1


title: PANC-1 H3K9me3 ChIP-seq Rep2


title: PANC-1 H3K36me3 ChIP-seq Rep2


title: Capan-1 ATAC-seq Rep1


title: Capan-1 ATAC-seq Rep2


title: PANC-1 H3K27ac ChIP-seq Rep2


title: PANC-1 H3K27ac ChIP-seq Rep1


title: PANC-1 H3K4me3 ChIP-seq Rep1


title: PANC-1 ATAC-seq Rep2


title: PANC-1 ATAC-seq Rep1


title: PANC-1 in situ Hi-C Rep3


title: UvCGBP1GFP1_ChIPSeq

city: Wuhan

first: Zhou

last: Jian

address: Wuhan China

institute: AJBK

description: Repet 1

data_processing:
Basecalls performed using CASAVA version 1.5
ChIP-seq reads were aligned to the Ustilaginoidea_virens genome assembly using MACS2 with the default configurations…
Data were filtered using fastp,samtools rmduplicates specifications
peaks were called using MACS version 2.2 with the default setting
Genome_build: Ustilaginoidea_virens JHTR01000001.1
Supplementary_files_format_and_content: peak

organism: Ustilaginoidea virens

source_name: Hyphae

growth_protocol: The UvCGBP1-GFP expression of Ustilaginoidea virens strain was cultured in potato sucrose broth  medium at 28 °C, after shaking at 180 rpm for 7 days.

extract_protocol:
1000 millions of cells was washed twice in cold PBS buffer and proteins were cross-linked to DNA by incubating the sampels with formaldehyde at a final concentration of 1%. Afterwards, samples were lysed and chromatins were obtained on ice. Chromatins were sonicated to get soluble sheared chromatin (average DNA length of 200–500 bp). One part of the soluble chromatin was saved at –20°C for input DNA, and the remainder was used for immunoprecipitation by antibody.
DNA from chromatin immunoprecipitation was used to construct sequencing libraries following the protocol provided by the Illumina TruSeqChIP Sample Prep Set A and sequenced on Illumina Xten with PE 150 method.

treatment_protocol: Seven-day-old mycelia of the UvCGBP1-GFP collected from potato sucrose broth  medium was use for Chromatin immunoprecipitation (ChIP)

tag: treatment

value: Normal growth

value: Anti-GFP (Abcam, MA)

tag: sample type

value: IP library


title: AdV_hEPO_rep2

city: Tsukubashi

first: Takeito

last: Sugasawa

state: Ibarakiken

address: Igakukei Gakukeitou 236, 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly using CLC genomics workbench 20.0.4 with the default settings.
A statistical differential expression test was used The Differential Expression in Two Groups tool in CLC genomics workbench.
Differentially expressed genes were filtered by FDR < 0.01 and minimum fold change cutoff 3.0.
Low expression genes were filtered by 0 in all samples for downstream analysis and data visalizations.
Supplementary_files_format_and_content: Excel file of statistic test and expression data

source_name: Blood

growth_protocol: Standard protocol.

extract_protocol:
RNA were extracted from whole blood, using RNAiso Blood (Cat#9112; Takara Bio)
Llibrary was constracted using NEBNext Ultra II RNA Library Prep Kit for Illumina and NEBNext rRNA Depletion Kit v2 (Cat# E7770S and E7400L; New England Biolabs).

treatment_protocol: Mice were injected recombinant adenoviral vector including hEPO gene.

value: ICR

value: Blood

value: Wild type


title: PANC-1 in situ Hi-C Rep1


title: UvCGBP1GFP2_ChIPSeq

description: Repet 2


title: AdV_hEPO_rep1


title: HPNE RNA-seq Rep2

source_name: Immortalized normal pancreatic ductal epithelium

value: Normal pancreatic cells


title: AdV_hEPO_rep3


title: HPNE CTCF ChIP-seq Rep2


title: AdV_hEPO_rep4


title: HPNE input

value: none (input)


title: HPNE H3K9me3 ChIP-seq Rep2

value: H3K9me3 Cell Signaling Technology #13970S


title: HPNE H3K27me3 ChIP-seq Rep2

value: H3K27me3 Cell Signaling Technology #9734S


title: PANC-1 in situ Hi-C Rep4


title: HPNE H3K27me3 ChIP-seq Rep1

value: H3K27me3 Cell Signaling Technology #9733S


title: PANC-1 H3K4me3 ChIP-seq Rep2


title: Control_rep1

value: control


title: Control_rep3


title: Control_rep4


title: Control_rep2


title: input1 DNA

description: Repet 1

value: Input library


title: PANC-1 in situ Hi-C Rep2


title: HPNE RNA-seq Rep3


title: HPNE H3K36me3 ChIP-seq Rep2

value: H3K36me3 Cell Signaling Technology #4909S


title: HPNE RNA-seq Rep1


title: HPNE H3K36me3 ChIP-seq Rep1


title: HPNE H3K27ac ChIP-seq Rep2

value: H3K27ac Cell Signaling Technology #8173S


title: HPNE CTCF ChIP-seq Rep1

value: CTCF Cell Signaling Technology #3418


title: HPNE H3K9me3 ChIP-seq Rep1

value: H3K9me3 Cell Signaling Technology #13969S


title: HPNE H3K4me3 ChIP-seq Rep2

value: H3K4me3 Cell Signaling Technology #9751S


title: HPNE H3K4me3 ChIP-seq Rep1


title: HPNE ATAC-seq Rep2


title: HPNE in situ Hi-C Rep4


title: HPNE in situ Hi-C Rep1


title: HPNE ATAC-seq Rep1


title: Male Ethanol Rep2

city: Greenwood

first: Vijay

last: Shankar

state: South Carolina

address: 115 Milford Pines Drive

institute: Clemson University

data_processing:
The mkfastq pipeline within Cell Ranger v3.1 (10X Genomics, Pleasanton, CA) was used to convert BCL files from the sequence run folder to demultiplexed FASTQ files. Release 6 version of the Drosophila melanogaster reference GCA_000001215.4 from NCBI Genbank was indexed using the mkref pipeline and used for alignment using the count pipeline within Cell Ranger v3.1 with the expected cell count parameter set to 5,000 cells.
Raw expression counts output for each sample from the Cell Ranger pipeline was imported and analyzed using the Seurat v3 package in R. Each sample was filtered to remove genes that are expressed in less than 5 cells and to remove cells with fewer than 300 or greater than 2,500 RNA features. Counts were normalized by regularized negative binomial regression using the scTransform pipeline.
Integration of all samples was performed using the SCT method. RunUMAP and FindNeighbors functions were used with 10 dimensions to ordinate expression space and reduce data dimensionality. To identify the cell-type clusters within the dataset, unsupervised clustering using the FindClusters function and a resolution of 0.9 was used. The resolution value was selected by iterating from 0.4 to 2.0 and identifying the value at which there is significant change in the granularity of cluster assignment. In order to identify marker genes for each cluster, DefaultAssay was set to “RNA”, values were normalized using the NormalizeData function, the function FindAllMarkers run on the integrated set. The top three genes with positive expression for each cluster were extracted and used for cell-type characterization.
Genome_build: GCA_000001215.4 R6.13
Supplementary_files_format_and_content: UMI barcodes, feature set and counts matrix

organism: Drosophila melanogaster

source_name: Drosophila brains

extract_protocol:
For single cell RNA sequencing we collected duplicate samples of 20 brains for each sex from flies reared on regular medium or on ethanol-supplemented medium.  We dissociated the brains as in previously published work after incubation with 450 l of collagenase solution (50 ul of fresh 25mg/ml collagenase (Gibco) in sterile water + 400 l of Schneider s medium for 30 minutes followed by stepwise trituration - P200 pipette 5 times, 23G needle pre-wetted with PBS + BSA 5 times, and 27G pre-wetted needle 5 times (19). The resulting suspension was passed through a pre-wetted 10 m strainer (Celltrics, G rlitz, Germany) with gentle tapping. We counted live cells using a hemocytometer with trypan blue exclusion and proceeded with GEM generation using the Chromium controller (10X Genomics, Pleasanton, CA) for samples with > 500 live cells/ l.
We made libraries after GEM generation in accordance with 10X Genomics v3.1 protocols. We determined fragment sizes using Agilent Tapestation kits (Agilent, Santa Clara, CA) - d5000 for amplified cDNA and d1000 for libraries. However, the samples were not diluted at either step since these were not high concentration libraries. We measured the concentrations of amplified cDNA and the final libraries using a Qubit 1X dsDNA HS kit, also without dilution. In addition to Qubit, we quantified the final library concentrations using a qPCR based library quantification kit (KAPA Biosystems, Roche, Basel, Switzerland) in order to measure the concentration of fragment sizes of interest in accordance with the manufacturer’s recommendations. We used 12 cycles for the cDNA amplification and 14 cycles for indexing PCR. We sequenced the final libraries on an S1 flow cell using a Novaseq (Illumina, Inc., San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: D. melanogaster of the standard laboratory Canton S (B) strain were maintained on standard cornmeal/yeast/molasses-agar supplemented with yeast at 25°C on a 12h light:dark cycle with 50% humidity in controlled adult density vials to prevent overcrowding. We allowed 5 males and 5 females to mate for two days and aged their progeny for 3-5 days after eclosion.  We then placed 50 males and 50 females into large egg collection cages on grape juice agar and yeast paste. We acclimatized the flies to the cages for 24 hours with grape juice plate changes every 12 hours and collected up to 12-hour old eggs with a blunt metal needle. We placed the eggs on regular fly food or fly food that contained 10% (v/v) ethanol without yeast. We collected 50 eggs per vial and set up 10-15 vials per condition per collection week over a 48-hour period. After eclosion, flies were collected onto regular fly food without yeast and aged as indicated for the relevant experiments. Unless otherwise indicated, all behavioral assays were performed in a controlled environment at 25oC between 8:30am and 11:30am.

value: Brains

tag: Sex

value: Male

value: Ethanol supplemented

value: CantonSB

value: 3-5 days post-eclosion


title: HPNE H3K27ac ChIP-seq Rep1

value: Normal pancreatic cells


title: HPNE in situ Hi-C Rep2


title: HPNE in situ Hi-C Rep3


title: Male Ethanol Rep1


title: IL-22Fc + IL-1B SAM16771471

type: RNA

city: South San Francisco

first: Kevin

last: Huang

state: California

address: 1 DNA Way

department: Bioinformatics

institute: Genentech

description: IL-22Fc + IL-1B SAM16771471

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data were analyzed with standard Bioconductor packages

source_name: RNA from HT-29 cell line

label_protocol: standard Affymetrix protocol

extract_protocol: none provided by the submitter

value: IL-22Fc + IL-1B


title: Male Reference Rep2

value: Reference media


title: Male Reference Rep1


title: IL-22Fc + IL-1B SAM16771469

description: IL-22Fc + IL-1B SAM16771469


title: Female Reference Rep2

value: Female


title: Female Ethanol Rep2


title: Female Ethanol Rep1


title: B-cells (CD19+)_899

city: Linköping

first: Shumaila

last: Sayyab

address: Campus US, Building 420, Entrance 68

department: Biomedical and Clinical Sciences (BKV)

institute: Linköping University

data_processing:
*** Raw data not provided due to patient privacy concerns ***
Filtering or Preprocess:The raw RNA-seq reads were pre-processed using cutadopt v3.1
Alignment: The RNA reads were aligned to reference genome hg19 using STAR v2.7.2.
Processing data: Gene expression levels in fragments per kilobase per million mapped reads (FPKM) was calculated using Cufflinks v2.2.0, and Cuffdiff was used to detect differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file include FPKM values for each Sample.

source_name: Peripheral Blood

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Healthy control

value: Peripheral Blood

tag: rna prep

value: ScriptSeq

tag: source

value: Marincevic-Zuniga et al., 2017.


title: IL-6 + IL-1B SAM16771472

description: IL-6 + IL-1B SAM16771472

value: IL-6 + IL-1B


title: Female Reference Rep1

tag: tissue

tag: strain


title: IL-6 + IL-1B SAM16771474

description: IL-6 + IL-1B SAM16771474


title: IL-6 SAM16771462

description: IL-6 SAM16771462


title: IL-6 SAM16771460

description: IL-6 SAM16771460


title: T-cells (CD3+)_867


title: T-cells (CD3+)_858


title: Media SAM16771458

description: Media SAM16771458

value: Media


title: IL-1B SAM16771463

description: IL-1B SAM16771463


title: IL-22Fc SAM16771467

description: IL-22Fc SAM16771467


title: IL-1B SAM16771464

description: IL-1B SAM16771464


title: IL-6 + IL-1B SAM16771473

description: IL-6 + IL-1B SAM16771473


title: Media SAM16771459

description: Media SAM16771459


title: B-cells (CD19+)_858


title: IL-22Fc SAM16771468

description: IL-22Fc SAM16771468


title: IL-22Fc SAM16771466

description: IL-22Fc SAM16771466


title: IL-22Fc + IL-1B SAM16771470

description: IL-22Fc + IL-1B SAM16771470


title: Media SAM16771457

description: Media SAM16771457


title: IL-6 SAM16771461

description: IL-6 SAM16771461


title: IL-1B SAM16771465

description: IL-1B SAM16771465


title: T-cells (CD3+)_845


title: Fndc5 knock-out mouse 2

city: Charlestown

first: Christiane

last: Wrann

state: MA

address: 149 13th Street

institute: Massachusetts General Hospital

data_processing:
Sequenced reads were aligned to the UCSC mm10 reference genome assembly
Gene counts were quantified using STAR (v2.5.1b)
Normalized read counts (FPKM) were calculated using cufflinks (v2.2.1)
RNAseq analysis was performed using the VIPER snakemaker pipeline
Genome_build: mm10
Supplementary_files_format_and_content: STAR normalized counts for all mice in different groups and all genes.

source_name: microdisected dentate gyrus sample_KO

extract_protocol:
Dentate gyri were micro-dissected and the RNA was isloated using trizol and the Qiagen RNAeasy mini kit.
Libraries were prepared from 500 ng of purified total RNA using the Illumina TruSeq stranded mRNaseq kit according to the manufacturer’s protocol. Pooled, uniquely indexed libraries were sequenced on an Illumina NextSeq500 with single-end 75-bp reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

tag: genotype/variation

value: Global Fndc5 Knock out

value: Dentate Gyrus


title: Fndc5 knock-out mouse 4

tag: strain background


title: B-cells (CD19+)_845


title: T-cells (CD3+)_817


title: ALL_680r1

source_name: Bone marrow

value: first relapse

value: Bone marrow


title: Wild-type mouse 3

source_name: microdisected dentate gyrus sample_WT

value: Wild-type


title: B-cells (CD19+)_817


title: Wild-type mouse 2


title: ALL_827r1

value: TruSeq stranded total RNA

value: Current study


title: Wild-type mouse 4


title: ALL_464r1


title: Prmt1_KO rep2

city: Daejeon

first: Byoung-Ha

last: Yoon

address: Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea

country: South Korea

institute: KRIBB

data_processing:
Illumina Casava software used for basecalling.
The FastQC (FastQC v0.11.3) and cut-adapt (v1.1) were used to filter sequencing reads of low quality.
Then reads were mapped to mouse genome build mm10 using STAR with default parameters. The HTseq (v0.9.1) was used for raw read counts. The DESeq2 (DESeq2 v3.1) was used for selecting differentially expressed genes (DEGs).
Genome_build: mm10
Supplementary_files_format_and_content: generation of raw abundance measurements, txt file

source_name: testes

extract_protocol:
RNA was extracted from testes from P8 mice (WT and PRMT1 KO) using the TRIzol reagent (#15596018, Life Technologies, CA, USA) and the quality of the extracted total RNA samples was checked with RNA 6000 Nano Kit (#5067-1511, Agilent, CA, USA) on an Agilent 2100 bioanalyzer, confirming RIN values were above 7.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: testes

tag: genotype


title: Prmt1_WT rep2

value: WT


title: ALL_827

value: diagnosis


title: Prmt1_KO rep1


title: Fndc5 knock-out mouse 1


title: Wild-type mouse 1


title: ALL_388


title: ALL_464


title: KO-sedentary group mouse 3

source_name: microdisected hippocampus sample

extract_protocol:
Hippocampi were micro-dissected, flash frozen on dry ice, and the nuclei were isolated. The isolated nuclei were stained woth Vybrant Ruby dye and Ruby+/GFP+ nuclei were FACS-sorted.
The cDNA was synthesized from sorted cells using Takara SmartSeq v4 reagents according to manufacturer's protocol with modification: 1μl of 2X Reaction buffer was used with 1μl of CDS primer and 18 cycles of PCR were used for the cDNA amplification step. Full length cDNA was fragmented to a mean size of 150bp with a Covaris M220 ultrasonicator and Illumina libraries were prepared from 2ng of sheared cDNA using Rubicon Genomics Thruplex DNAseq reagents according to manufacturer’s protocol. Uniquely indexed libraries were pooled in equimolar ratios and sequenced with single-end 75bp reads on an Illumina NextSeq500 run by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

value: Global Fndc5 Knock out mice (C57BL/6 background)

value: Knock-out

value: Injected with GFP-reporter retrovirus

tag: running or sedentary

value: Sedentary group

value: Hippocampus


title: Prmt1_WT rep1

tag: age


title: KO-sedentary group mouse 5


title: ALL_380

value: ScriptSeq

value: Marincevic-Zuniga et al., 2017.


title: KO-sedentary group mouse 2


title: KO-sedentary group mouse 1


title: Wild-type mouse 5


title: ALL_317r1

value: TruSeq RNA Access


title: ALL_358