title: Mouse LGN 8 hour stim rep 3

description:
LC_DEG_Stim8vs0_downregulated.xlsx
LC_DEG_Stim8vs0_upregulated.xlsx

extract_protocol:
Mice were euthanized following dark-rearing between P20 and P27 then re-exposure to light for 0, 1, or 8 hours. Each time point includes data from three mice total processed as three independent samples.  After isoflurane anesthetization, mice were decapitated and the brain was isolated. Mouse brains were dissected and 300 um coronal sections were made on a Leica VT1000S vibratome. The dorsal LGNs were then microdissected in ice cold PBS after visual identification using a Nikon SMZ-10A brightfield dissection microscope, and flash frozen. Total RNA was trizol-extracted and purified using the Qiagen RNeasy Micro kit.
After RNA extraction, total RNA was depleted of ribosomal RNA, heat-fragmented to ~350 bp using the NEBNext kit, and processed with adapters to allow nonspecific sequencing on an Illumina NextSeq 500 System.

value: dark-reared


title: Mouse LGN 1 hour stim rep 3

status: Public on Jul 12 2021

type: SRA

city: Boston

first: Lucas

middle: Martin

last: Cheadle

state: MA

address: 220 Longwood Ave; Goldenson Bldg 413

department: Neurobiology

country: USA

institute: Harvard Medical School

description:
LC_DEG_Stim1vs0_downregulated.xlsx
LC_DEG_Stim1vs0_upregulated.xlsx

library_source: transcriptomic

data_processing:
Reads of fragment ends were nominally 75 bp in all cases, although for about one third of the reads not all sequencing cycles were completed.  Generally, over 99.9% of reported sequences were at least 70 bp long, so longer reads were uniformly 3ʹ-trimmed to that length and shorter ones were discarded, as were reads having any base with a sequencing Phred score below 13.  Most samples yielded a population of 35–80 million 70-bp reads.
Reads were aligned to the mouse genome (GRCm38/mm10 assembly, Dec. 2011) using the Burrows-Wheeler Aligner (bwa) tool.  Two sets of target sequences were incorporated into the bwa index in addition to the usual 21 chromosomal targets:  (1) the 16,299-bp mouse mitochondrial genome (GenBank accession NC_005089.1) and (2) a set of ~ 8 million short (≤ 138 bp) exon-exon splice-junction sequences (see below).  Typically ~70–75% of all LDR reads and ~80–90% of all developmental reads were mappable in each sample, allowing up to 2 mismatches, and of these ~75–90% aligned uniquely.
An in-house software tool, MAPtoFeatures, was used to quantify expression levels for individual genes as follows (Gray et al., 2014):  a database of genic features (CDSs and UTRs) was constructed from 95,023 genomic and 37 mitochondrial transcripts annotated in RefSeq for GRCm38.  Merged genes were constructed by unioning all exons in all transcripts assigned to each distinct gene; the resulting segments defined the gene’s exonic coordinates used here (with the gaps between them defining introns).  Genes with zero CDS exons were labeled “noncoding”.  These 33,102 genes were supplemented with 1,563 additional noncoding genes specified by the loci of all ribosomal RNA genes obtained from RepeatMasker (where the options Variations and Repeats, rmsk.repFamily=“rRNA” yielded 480 LSU-rRNA_Hsa elements; 45 SSU-rRNA_Hsa; and 1,038 5S).  The purpose of this step was to allow the filtering out of reads stemming from transcription of repeats and rRNA genes, which tend to get populated to inconsistent degrees from sample to sample depending on variability in the quality of rRNA depletion.
The splice-junction target sequences were based on the NCBI RefSeq database for GRCm38.  For each annotated transcript, we noted all subsets of two or more exons, ordered but not necessarily consecutive, that could be spliced together to produce a sequence at least as long as the read length (70 bp).  Each of these sequences was then trimmed to the maximum number of bases such that a read mapping to the sequence would necessarily cross these exons’ splice junction(s).  This procedure produced a library of all unique sets of exons whose intragenic splice junctions could possibly be covered by a read of the given length, based on the RefSeq annotation of exonic loci.  Aligned reads thus had the opportunity to align either to genomic (chromosomal) sequences or to exon-junction-crossing sequences found only in mature mRNA.  Multiple reads whose 5ʹ ends were assigned to the same locus on the same strand were not flattened to a single count.
For the developmental time course, our differential expression analysis calculated mean fold change ratios and their significance between (adjacent) pairs of time points for every expressed gene.  For the late-dark-rear study, we compared samples from mice re-exposed to light for one or eight hours to the unstimulated control using the three replicates for each pair. Statistical significance of each fold change was evaluated by Benjamini-Hochberg (BH) corrected p-values of all genes based on the biological variability implied by the replicates for each pair of conditions, with a significance threshold consistent with a false discovery rate of 5% (FDR=0.05). Differential-expression between sets of replicates was analyzed using the R Bioconductor package edgeR (version 3.14.0) (McCarthy et al., 2012).
Genome_build: Reads were aligned to the mouse genome (GRCm38/mm10 assembly, Dec. 2011) using the Burrows-Wheeler Aligner (bwa) tool
Supplementary_files_format_and_content: Excel tables for the developmental time course and the late-dark-rear study document differential expression (DE) analyses between a pair of time points, each with multiple biological replicates.  Files labeled AvsB for times A and B report fold changes A/B.  Each row reports data for one merged gene (see above), excluding rRNA genes; only those genes are shown that meet a minimum threshold of 4 reads total over all listed samples, fewer being insufficiently informative for edgeR to meaningfully assess DE.  Columns include gene name and Entrez GeneID, genomic locus, exon number and total exonic (i.e., mRNA) length, and whether a coding gene; edgeR-calculated fold-change (FC>=1 for upregulated genes, FC<1 for downregulated), average expression level (Counts Per Million), unadjusted p value, and Benjamini-Hochberg-adjusted q value (FDR); read counts per sample (frds...), used as the input to edgeR; and normalized expression levels per sample (Dens...; units of Density = 0.35*RPKM).

molecule: total RNA

organism: Mus musculus

tag: age

tag: treatment

tag: time post-light stim

tag: replicate


title: Mouse LGN 8 hour stim rep 1


title: Mouse LGN 8 hour stim rep 2


title: Mouse LGN E18 control rep 1

description:
LC_DEG_DevP4vsE18_downregulated.xlsx
LC_DEG_DevP4vsE18_upregulated.xlsx

extract_protocol:
Mice were euthanized on E18, P4, P10, P16, P20, P27 or P32. Each time point includes data from four mice total, processed as four independent samples.  After isoflurane anesthetization, mice were decapitated and the brain was isolated. Mouse brains were dissected and 300 um coronal sections were made on a Leica VT1000S vibratome. The dorsal LGNs were then microdissected in ice cold PBS after visual identification using a Nikon SMZ-10A brightfield dissection microscope, and flash frozen. Total RNA was trizol-extracted and purified using the Qiagen RNeasy Micro kit.
After RNA extraction, total RNA was depleted of ribosomal RNA, heat-fragmented to ~350 bp using the NEBNext kit, and processed with adapters to allow nonspecific sequencing on an Illumina NextSeq 500 System.

value: control (standard housing)


title: Mouse LGN 1 hour stim rep 1


title: Mouse LGN 0 hour stim rep 3

description:
LC_DEG_Stim1vs0_downregulated.xlsx
LC_DEG_Stim1vs0_upregulated.xlsx
LC_DEG_Stim8vs0_downregulated.xlsx
LC_DEG_Stim8vs0_upregulated.xlsx


title: Mouse LGN 0 hour stim rep 1


title: Mouse LGN 1 hour stim rep 2


title: Mouse LGN 0 hour stim rep 2


title: D63_TC1

city: Beijing

first: Jun

last: Zhu

address: No.52 Fucheng Road, Haidian District

country: China

institute: Department of Lymphoma, Peking University Cancer Hospital & Institute

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low complexity or low-quality sequence, then mapped to hg 19 whole genome using bowtie v0.12.2 with parameters.
Reads per kilobase of exon per megabase of library size(RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research,2009.
Genome_build: hg 19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

organism: Homo sapiens

source_name: SU-DHL6_SHR2554+HBI8000 for 48h

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

tag: cell type

value: diffuse large B cell lymphoma (DLBCL) cell line


title: D64_TC2

source_name: SU-DHL6_SHR2554+HBI8000 for 60h


title: D63_TH

source_name: SU-DHL6_HBI8000 for 48h


title: D64_TH


title: U24_TC2


title: D64_TCT

value: DMSO


title: U24_TC1


title: D63_TS

source_name: SU-DHL6_SHR2554 for 48h


title: D63_TC2


title: U24_TH


title: D63_TCT


title: U23_TH


title: U23_TC1


title: U23_TS


title: U24_TS


title: U23_TC2


title: U24_TCT


title: D64_TS


title: Mouse LGN snRNAseq 0 -8  hour stim rep 1-4 (12 samples)

description: see README_snRNAseq.pdf for sample barcodes

data_processing:
Transcripts were processed according to the pipeline in Macosko et al. (2015). Briefly, this pipeline was used to build a custom transcriptome from Ensembl GRCm38 genome and GRCm38.84 annotation using Bowtie 1.1.1, after filtering the annoatation gtf file (gencode.v17.annotation.gtf filtered for feature_type=îgeneî, gene_type="protein_coding" and gene_status="KNOWN"). Read quality control and mapping against this transcriptome was performed. Unique molecular identifiers (UMIs) were used to link sequence reads back to individual captured molecules. All steps of the pipeline were run using default parameters unless explicitly stated.
All cells were combined into a single dataset. Nuclei with >10% mitochondrial content were excluded from the dataset. Cells with fewer than 500 or more than 15,000 UMI counts were excluded. Cells were then clustered using the Seurat R package (Satija et al., 2015). The data were log normalized and scaled to 10,000 transcripts per cell. Variable genes were identified using the following parameters: x.low.cutoff = 0.0125, x.high.cutoff = 3, y.cutoff = 0.5. We limited the analysis to the top 30 principal components (PCs). Clustering resolution was set to 0.6. Clusters containing fewer than 100 cells were discarded. The expression of known marker genes was used to assign each cluster to one of the main cell types. Snap25, Olig1, Aqp4, Cx3cr1, Cldn5, and Vtn were used to identify neurons, oligodendrocytes, astrocytes, microglia, endothelial cells, and pericytes, respectively. Slc17a6 and Gad1 were used to distinguish excitatory and inhibitory neurons, respectively, which comprised the majority of cells analyzed. Clusters with significant expression of two or more markers were removed, as they likely represented doublet clusters resulting from simultaneous capture of two or more nuclei in a single droplet. In total, the final dataset included 8,398 excitatory neurons and 4,987 inhibitory neurons.
Genome_build: Custom transcriptome from Ensembl GRCm38 genome and GRCm38.84 annotation using Bowtie 1.1.1
Supplementary_files_format_and_content: The tsv files are tables showing transcript counts per cell for every gene.

extract_protocol:
Mice were euthanized following dark-rearing between P20 and P27 then re-exposure to light for 0, 1, or 8 hours. The LGNs from 3-4 mice of each condition were pooled to represent one bioreplicate, and four bioreplicates were included in the analysis. After isoflurane anesthetization, mice were decapitated and the brain was isolated. Mouse brains were dissected and 300 um coronal sections were made on a Leica VT1000S vibratome. The dorsal LGNs were then microdissected in ice cold PBS after visual identification using a Nikon SMZ-10A brightfield dissection microscope, and flash frozen.
Individual cells were captured and barcoded using the inDrops platform as previously described. Briefly, single-cell suspensions were fed into a microfluidic device that packaged the cells with barcoded hydrogel microspheres and reverse transcriptase/lysis reagents. After cell encapsulation, primers were photo-released by UV exposure. Two libraries of approximately 3000 cells each were collected for each sample. Indexed libraries were pooled and sequenced on a Nextseq 500 (Illumina).
single-nucleus RNA-sequencing

value: 1 to 4

tag: sample type

value: mixed


title: U23_TCT


title: KO_Th17_rep2 [RNA-seq]

city: Chicago

first: Yuan

last: Qian

state: ILLINOIS

address: 303 E Superior St

institute: Northwestern University

data_processing:
Reads were aligned using STAR, gene speciﬁc transcripts were quantified using HT-Seq, and differentially expressed transcripts were identified using DE-Seq2.
Time-course analyses were performed using maSigPro.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: htseq-counts

source_name: Naïve CD4+ T cells

growth_protocol: Human naïve CD4+ T cells were isolated from PBMC and placed into Th0, Th1 and Th17 differentiation conditions for 3 days or 5 days; Time-course: human naïve CD4+ T cells were isolated from PBMC and placed into Th17 differentiation condition for 12, 24, 48 and 72 h; Mouse naive CD4+ T cells were isolated from spleens of wild type or CD4creZEB1f/f mice and placed into Th0, Th1 and Th17 differentiation conditions for 4 days.

extract_protocol:
RNA from human T cells (5 × 10^5 cells) and mouse T cells (5 × 10^5 cells) was isolated with the RNeasy Micro kit (Qiagen) according to the manufacturer’s protocol.
RNA libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen).

treatment_protocol: Human naïve CD4+ T cells were transfected with siCTL or siZEB1 before differentiation.

value: In vitro differentiated Th17 cells

tag: donor

tag: genotype


title: KO_Th1_rep3 [RNA-seq]

value: In vitro differentiated Th1 cells


title: KO_Th0_rep2 [RNA-seq]

value: In vitro differentiated Th0 cells


title: KO_Th0_rep1 [RNA-seq]


title: KO_Th17_rep1 [RNA-seq]


title: D64_TC1


title: KO_Th0_rep3 [RNA-seq]


title: KO_Th1_rep1 [RNA-seq]


title: WT_Th17_rep3 [RNA-seq]

value: wild type


title: WT_Th17_rep2 [RNA-seq]


title: WT_Th1_rep2 [RNA-seq]


title: WT_Th0_rep2 [RNA-seq]


title: WT_Th1_rep3 [RNA-seq]


title: WT_Th17_rep1 [RNA-seq]


title: WT_Th1_rep1 [RNA-seq]


title: WT_Th0_rep3 [RNA-seq]


title: WT_Th0_rep1 [RNA-seq]


title: KO_Th17_rep3 [RNA-seq]


title: B220low CD138+ rep1

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

data_processing:
Reads were trimmed using Trim Galore and mapped to mouse genome GRCm38 using HiSat2 (2.1.0), including known splice sites from the Ensembl annotation release 90
Read counts over mRNA features were then quantified using Seqmonk (https://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), using the Ensembl Mouse GRCm38.97 annotation release, merging transcript isoforms for each gene
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file showing names, IDs and coordinates of genes together raw counts for each sample, quantified using Seqmonk over mRNA features with merged isoforms from the Ensembl Mouse GRCm38.97 annotation release

source_name: Naïve B cells cultured in iGB conditions

growth_protocol: Naive B cells from the spleens of 10-week-old female mice were grown in in vitro induced germinal centre B cell (iGB) cultures: Irradiated (~120Gγ) 40LB cells were seeded at 80x10^3 cells per well in a 12-well plate in supplemented RPMI-1640 media. The next day, naïve splenic B cells were isolated with a B cell isolation kit (Miltenyi Biotec: 130-090-862) and cultured on the irradiated 40LB cells with IL-4 in supplemented RPMI-1640 media (final: 10% FBS, 1x GlutaMAX™, 50µM 2-mercaptoethanol Thermo Scientific™: 31350-010, 100 units/ml penicillin, and 100μg/ml streptomycin Thermo Scientific™: 15140, 10ng/ml mIL-4 PeproTech 214-14). On day 4 B cells were reseeded on freshly irradiated 40LB cells with IL-21 in supplemented RPMI-1640 media (final: 10% FBS, 1x GlutaMAX™, 50µM 2-mercaptoethanol, 100 units/ml penicillin, and 100μg/ml streptomycin, 10ng/ml mIL-21 PeproTech 210-21) and cultured up to day 8.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen)
cDNA was generated from polyadenylated transcripts using SMART-Seq® v4 Ultra® Low Input RNA Kit (cat # 634891, Takara Bio). mRNAseq libraries were prepared with Nextera XT DNA Library Preparation Kit (cat# FC-131–1096, Illumina) and quantified using KAPA library quantification kit (Roche). mRNA-seq libraries were run on a HiSeq 2500 RapidRun generating 50bp single-end reads.

treatment_protocol: On day 8, iGB cells were harvested and sorted by FACS based on expression of CD19, B220 and CD138, together with the eF780 viability dye

tag: strain

value: 10 weeks

tag: Sex

value: female

tag: tissue

value: spleen

tag: flow cytometry markers


title: B220+ CD138- rep1


title: B220+ CD138- rep2


title: B220low CD138+ rep2


title: B220+ CD138- rep3


title: KO_Th1_rep2 [RNA-seq]


title: B220low CD138+ rep3


title: P0320 (SEPTIC T1)

type: RNA

city: Gainesville

first: Azra

last: Bihorac

state: FL

address: 1600 SW Archer Road

department: Medicine

institute: University of Florida

description: WITHIN 12 HRS OF SEPSIS ONSET

hyb_protocol: Labeled cDNA was hybridized to GeneChip™ Human Transcriptome 2.0 arrays according to ThermoFisher Scientific instructions, 16 hours at 45C at 60 rpm.

scan_protocol: Arrays were scanned GeneChip Scanner 3000 7G using AGCC software

data_processing: Background Correction, Normalization and Summarization were done by RMA using Transcriptome Analysis Console (TAC) software provided by Affymetrix. Statistical comparison was done using empirical Bayes method in Linear Models for Microarray Analysis (LIMMA) using TAC. Significance threshold was adjusted for multiple testing using Benjamini-Hochberg false discovery rate (FDR).

label: biotin

source_name: SEPTIC T1

label_protocol: cDNA was amplified using GeneChip™ WT PLUS Reagent Kit, from ThermoFisher Scientific following manufacturers instructions. Amplified cDNA was fragmented with UDG and APE1 enzymes according to ThermoFisher Scientific instructions. Labeling was performed with TdT with biotin reagent followed by streptavidin/phycoerythrin.

extract_protocol: total RNA was extracted from the urine of patients using Qiagen RNeasy mini kit (250) Catalog Number - 74106 according the manufacturer's protocol.

treatment_protocol: Approximately 50mL Urine was spun down at 1500g for 30 min at 4 degrees Celsius. Pellet was collected, lysed using 1mL RLT lysis buffer with 10uL β-mercaptoethanol from the kit and processed according the manufacturer's protocol.

tag: disease state

value: Sepsis

tag: gender

value: Female

value: Urine


title: P0327 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0322 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET

value: Male


title: P0332 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0323 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0254 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0283 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0324 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0314 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0302 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0251 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0282 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0309 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0279 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0318 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0296 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0298 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0304 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0276 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0308 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0287 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0292 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0264 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0315 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0253 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0284 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0310 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0255 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0273 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0300 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Wildtype sample, set3

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
single cell RNA
Separated intestinal cells from WT mice - set3

data_processing:
Sequencing was demultiplexed, aligned to the genome, and quality checked using 10X Genomics Cell Ranger software.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data contains barcodes, gene list, and counts matrix.

source_name: wildtype small intestine

extract_protocol: Libraries were prepped according to 10X Genomics Chromium Single Cell 3' kits (v2 chemistry)

value: small intestine

value: wildtype


title: Wildtype sample, set1

description:
single cell RNA
Separated intestinal cells from WT mice - set1


title: siZEB1_Th17_donor3 [miRNA-seq]

data_processing:
miRNA-seq data was firstly trimmed with Cutadapt default parameters and then aligned with miRDeep2 and Bowtie.
miRNA expression quantification was performed with miRDeep2. Differentially expressed miRNAs were determined by DE-Seq2.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: normalized_counts.txt: Normalized counts of miRNAs.

growth_protocol: Human naïve CD4+ T cells were isolated from PBMC and placed into Th0 or Th17 differentiation conditions.

extract_protocol:
Total RNA of human T cells transfected with siCTL or siZEB1 (5 × 10^5 cells, day 3 of Th17 differentiation) was isolated with the miRNeasy mini kit (Cat: #217004, Qiagen) according to the manufacturer’s protocol.
RNA libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina. 6% PAGE gel, followed by ethanol precipitation, was performed post library prep to purify small RNA library.

value: transfected with siZEB1


title: siZEB1_Th17_donor2 [miRNA-seq]


title: Wildtype sample, set2

description:
single cell RNA
Separated intestinal cells from WT mice - set2


title: siZEB1_Th0_donor3 [miRNA-seq]


title: siZEB1_Th0_donor2 [miRNA-seq]


title: siCTL_Th17_donor3 [miRNA-seq]

value: transfected with siCTL


title: siCTL_Th17_donor2 [miRNA-seq]


title: siZEB1_Th17_donor1 [miRNA-seq]


title: P0244 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th17_donor1 [miRNA-seq]


title: P0272 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0270 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th0_donor3 [miRNA-seq]


title: P0242 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0232 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0236 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0237 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siZEB1_Th0_donor1 [miRNA-seq]


title: P0095 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th0_donor2 [miRNA-seq]


title: P0068 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th0_donor1 [miRNA-seq]


title: P0247 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0235 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0245 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0271 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0230 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0240 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0233 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siZEB1_Th17_72h_donor2 [RNA-seq]


title: siZEB1_Th17_48h_donor4[RNA-seq]


title: siZEB1_Th17_72h_donor1 [RNA-seq]


title: siZEB1_Th17_72h_donor4[RNA-seq]


title: P0229 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siZEB1_Th17_48h_donor2 [RNA-seq]


title: siZEB1_Th17_48h_donor3 [RNA-seq]


title: P0228 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0225 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0222 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0220 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0218 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siZEB1_Th17_48h_donor1 [RNA-seq]


title: siZEB1_Th17_24h_donor2 [RNA-seq]


title: siZEB1_Th17_12h_donor4[RNA-seq]


title: siZEB1_Th17_24h_donor3 [RNA-seq]


title: siZEB1_Th17_24h_donor1 [RNA-seq]


title: siZEB1_Th17_12h_donor2 [RNA-seq]


title: P0214 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0216 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0224 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0217 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th17_72h_donor4[RNA-seq]


title: siCTL_Th17_72h_donor3 [RNA-seq]


title: P0211 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th17_72h_donor2 [RNA-seq]


title: siCTL_Th17_72h_donor1 [RNA-seq]


title: siCTL_Th17_48h_donor3 [RNA-seq]


title: siCTL_Th17_48h_donor4[RNA-seq]


title: siZEB1_Th17_12h_donor3 [RNA-seq]


title: P0213 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0210 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0207 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th17_48h_donor2 [RNA-seq]


title: P0200 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th17_24h_donor4[RNA-seq]


title: siCTL_Th17_48h_donor1 [RNA-seq]


title: P0208 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0204 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th17_24h_donor2 [RNA-seq]


title: P0203 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0205 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th17_24h_donor3 [RNA-seq]


title: P0202 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0190 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th17_24h_donor1 [RNA-seq]


title: P0188 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th17_12h_donor4[RNA-seq]


title: P0189 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0186 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0187 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0197 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th17_12h_donor3 [RNA-seq]


title: siCTL_Th17_12h_donor1 [RNA-seq]


title: P0184 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0177 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0176 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th17_12h_donor2 [RNA-seq]


title: siZEB1_Th17_donor3 [RNA-seq]


title: P0174 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siZEB1_Th17_donor2 [RNA-seq]


title: siZEB1_Th17_donor1 [RNA-seq]


title: siZEB1_Th1_donor3 [RNA-seq]


title: siZEB1_Th1_donor2 [RNA-seq]


title: P0175 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: CRTH2-KO sample, set1

description:
single cell RNA
Separated intestinal cells from CRTH2-KO mice - set1

source_name: CRTH2-KO small intestine


title: siZEB1_Th1_donor1 [RNA-seq]


title: siZEB1_Th0_donor3 [RNA-seq]


title: P0168 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siZEB1_Th0_donor2 [RNA-seq]


title: siZEB1_Th0_donor1 [RNA-seq]


title: P0246 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0162 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0166 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0158 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0167 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th17_donor3 [RNA-seq]


title: siCTL_Th17_donor1 [RNA-seq]


title: siCTL_Th17_donor2 [RNA-seq]


title: P0159 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0156 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0157 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0147 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0152 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0149 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siCTL_Th1_donor3 [RNA-seq]


title: siCTL_Th1_donor2 [RNA-seq]


title: siCTL_Th0_donor2 [RNA-seq]


title: siCTL_Th0_donor1 [RNA-seq]

value: in vitro differentiated Th0 cells


title: VDJ_siZEB1 [scRNA-seq]

data_processing:
Alignment, filtering, barcode counting, and unique molecular identifier counting were performed using Cell Ranger v.2.1.0.
Data were further analyzed using Seurat v.3.0. Briefly, cells with a percentage of mitochondrial genes below 5% were included. Cells with the number of detected genes lower than 200 were excluded.
Cells were filtered for feature counts more than 1000 and less than 7000. Then data was normalized to unique molecular identifier count per million total counts and log-transformed. Then, 2000 variable genes were selected per dataset.
HashTags: siCTL_day1 (GTCAACTCTTTAGCG); siCTL_day5 (TGATGGCCTATTGGG); siZEB1_day1 (TTCCGCCTCTCTTTG); siZEB1_day5 (AGTAAGTTCAGCGTA).
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx file is count matrix in sparse matrix format; barcodes.tsv is list of barcodes for each sample; features.tsv is list of genes detected in samples.

growth_protocol: Human naïve CD4+ T cells were isolated from PBMC and placed into Th17 differentiation condition for 1 day or 5 days.

extract_protocol:
Live cells were isolated using dead cell removal kit (Miltenyi), and cells harvested at day 1 and day 5 of differentiation were pooled respectively for siCTL and siZEB1.
Library preparation was performed using 10x Genomics Single Cell 5’ v1 workflow and processed according to the manufacturer’s instructions. For additional VDJ and hashtag libraries the Chromium Single Cell V(D)J Enrichment Kit, Human T Cell (10x Genomics) and the Chromium Single Cell 5’ Feature Barcode Library Kit (10x Genomics) were used respectively.

treatment_protocol: Human naïve CD4+ T cells were transfected with siCTL or siZEB1 before Th17 differentiation.

tag: time point

value: Day 1 and Day 5 of differentiation


title: VDJ_siCTL [scRNA-seq]

value: In vitro differentiated Th17 cells


title: P0141 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: siZEB1_Th17 [scRNA-seq]


title: siCTL_Th1_donor1 [RNA-seq]

value: In vitro differentiated Th1 cells


title: siCTL_Th17 [scRNA-seq]


title: siCTL_Th0_donor3 [RNA-seq]

value: In vitro differentiated Th0 cells


title: BC11

city: CDMX

first: Luis

middle: Alonso

last: Herrera Montalvo

state: CDMX

address: Av. San Fernando 22

department: Investigación

country: Mexico

institute: Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas

data_processing:
The quality of the sequencing files was determined with the reports generated with the FastQC
Filtering of low-quality reads and adapter removal was performed with trimmomatic v.0.39
Reads were mapped to the human reference with STAR aligner v.2.7.1a
Gene expression quantification was done with featureCounts from the rsubread package on the STAR bam files
Gene expression quantification was also done by aligning to the transcriptome with Salmon v.0.14.1 l
All gene quantifications were done on gencode v31 annotations
Differential expression analysis was performed with DEseq2
Genome_build: Reads were mapped to the human reference genome assembly version hg38
Supplementary_files_format_and_content: Differential expression tables from DESeq2 are included in .csv format. There are 2 tables from 2 different counting pipelines: STAR aligner v.2.7.1a and Salmon v.0.14.1 for comparison and validation

molecule: polyA RNA

source_name: Biopsy from primary mammary adenocarcinoma (thick needle)

extract_protocol:
RNA was isolated using the AllPrep kit (QIAGEN, No. 80204); RNA concentration and quality analysis (RIN value) were performed by Tape Station 2200 bioanalyzer (Agilent Technologies)
1 ug of RNA with RIN associated greater than 8.0 were used to generate sequencing libraries using the TruSeq Stranded mRNA library prep kit from illumina according to the manufacturer’s instruction

value: Neoadjuvant Chemotherapy

tag: disease

value: Breast Cancer

tag: molecular subtype

value: Luminal B

tag: group

value: Responder


title: P0135 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET

value: Sepsis

tag: age


title: siZEB1_Th17_72h_donor3 [RNA-seq]

tag: treatment


title: BC10


title: P0129 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET

value: Female


title: P0133 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET

value: Urine


title: P0142 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET

value: Male


title: P0125 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: BC9


title: P0116 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0140 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0134 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0121 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0111 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0104 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0120 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0102 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0107 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0076 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: BC6

value: Nonresponder


title: BC5


title: BC12


title: BC3


title: BC4


title: P0072 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: BC2


title: BC7


title: BC1


title: Skater 7 - before exercise

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

institute: Wellcome Sanger Institute

data_processing:
Raw sequencing reads were aligned to full human genome and transcriptome using STAR v2.5.3a splice-aware alignment software. Primary part of GRCh38.p10 human genome assembly and Gencode v26 annotation were used to generate the genomic and transcriptomic reference index.
The resulting transcriptome-aligned sequences were used for expression quantification with RSEM v1.2.31 with “--strandedness reverse” option.
Genome_build: primary GRCh38.p10
Supplementary_files_format_and_content: expression table of transcripts per million (TPM) per gene, with additional gene annotation (Ensembl, symbol, type of a gene)
Supplementary_files_format_and_content: expression table of raw read counts per gene, with additional gene annotation (Ensembl, symbol, type of a gene)

source_name: whole blood (globin-depleted)

extract_protocol:
Total RNA was extracted from blood using PureLink RNA Mini Kit (Thermo Fisher Scientific, Inc.) and «BioMaxi™ Precipitation Buffer» (Biomatrica, USA), according to the manufacturer’s protocol. RNA concentration was measured using Quantus Fluorometer TM with QuantiFluor RNA System kit (Promega, USA). RNA quality control was performed using capillary gel electrophoresis on a QIAxcel Advanced System (Qiagen, Germany). Total RNA was depleted of globin mRNA with GLOBINclear - Human Kit (Invitrogen, USA) according to the manufacturer’s protocol.
PolyA-enriched transcriptome libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc., USA) according to the TruSeq Stranded mRNA Sample Preparation Guide, Document # 15031047 E (Illumina, USA). Validation of the libraries was performed on the QIAxcel Advanced System (Qiagen, Germany). Library quantification was performed using Quantus Fluorometer with QuantiFluor dsDNA System kit (Promega, USA). Paired-end sequencing of the libraries was performed on HiSeq 4000 System with a reading length of 2x150 bp using HiSeq 3000/4000 PE Cluster Kit and HiSeq 3000/4000 SBS Kit (300 cycle) (Illumina, USA).

treatment_protocol: For each participant, 2.5 mL whole blood sample was collected before and after the exercise using the RNAgard Blood Tubes (Biomatrica, USA) according to the manufacturer’s protocol and then stored at −20 °C until further processing.

value: whole blood (globin-depleted)

value: before exercise


title: Skater 6 - after exercise

value: after exercise


title: Skater 7 - after exercise


title: Skater 6 - before exercise


title: Skater 5 - after exercise


title: Skater 5 - before exercise


title: P0062 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Skater 4 - before exercise


title: Skater 4 - after exercise


title: P0056 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0060 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Skater 3 - after exercise


title: P0074 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0094 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0089 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0087 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Skater 2 - after exercise


title: P0085 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0091 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0073 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0053 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0066 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0101 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0100 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0077 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Skater 1 - after exercise


title: Skater 2 - before exercise


title: Skater 1 - before exercise


title: P0052 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Skater 3 - before exercise


title: Sorted Purkinje cells [ww45_0]

first: Kellen

last: Winden

address: 300 Longwood Ave

department: Neurology

institute: Boston Children's Hospital

description:
processed data file: gene.count_table
20160401-45-MS2872_S1

data_processing:
Trim adapters using trimmomatic (v0.39)
Align to genome using STAR (v2.7.0f)
Assemble transcriptome using data from sorted PCs using cufflinks (v2.2.1)
Quantify genes/transcripts using cufflinks (v2.2.1)
Genome_build: GRCm38

source_name: Purkinje cells_WW

extract_protocol:
FACS: Qiagen RNAeasy for RNA isolation
TRAP: IP of GFP labeled ribosomes; Trizol/Qiagen RNAeasy for RNA isolation
SmartSeqv4 RNASeq kit, Clontech

tag: strain background

value: WW

value: Purkinje cells


title: Sorted Purkinje cells [ww48_0]

description:
processed data file: gene.count_table
20160401-48-MS2872_S2

tag: cell type


title: Sorted Purkinje cells [ww176_0]

description:
processed data file: gene.count_table
20160503-176-MS3005_S4


title: P0049 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Sorted Purkinje cells [ww144b_0]

description:
processed data file: gene.count_table
20160401-144-MS2872_S3


title: P0046 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Sorted Purkinje cells [cc74_0]

description:
processed data file: gene.count_table
20160226-74-MS2723_S5

source_name: Purkinje cells_CC

value: CC


title: P0078 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Sorted Purkinje cells [ww144a_0]

description:
processed data file: gene.count_table
20160503-144-MS3005_S2


title: P0045 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Sorted Purkinje cells [cc61_0]

description:
processed data file: gene.count_table
20160226-61-MS2723_S4


title: Sorted Purkinje cells [cc191_0]

description:
processed data file: gene.count_table
20160503-191-MS3005_S6


title: Sorted Purkinje cells [cc167_0]

description:
processed data file: gene.count_table
20160503-167-MS3005_S3


title: Sorted Purkinje cells [cc103_0]

description:
processed data file: gene.count_table
20160226-103-MS2723_S7


title: P0044 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: CDK8_C8 ATRi L7 [SLX-17508.NEBNext12.H5JGFBBXY.s_7]

first: Rebecca

middle: L

last: Lloyd

address: Tennis Court Road

department: University of Cambridge

institute: Wellcome/CRUK Gurdon Institute

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext12.H5JGFBBXY.s_7

data_processing:
Base-calling performed with the standard Illumina pipeline
Adaptors removed with Trimmomatic 0.38, specifying the TruSeq3-SE.fa:2:30:10 adapters in the ILLUMINACLIP argument
Trimmed sequences  were aligned to the reference Mus musculus genome and annotation (build GRCm38.p6, NCBI:GCA_000001635.8) using HISAT2 (version 2.1.0) with default settings
Gene level expression was quantified using featureCounts (version 2.0.1) with the options --ignoreDup and -s 2
R package DESeq2 was used to normalise the count matrices, using the "rlog" function
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: For two independent sequencing runs (SLX-17502 and SLX-17508), raw count matrices and rlog normalised expression matrices are provided. Rows correspond to genes labelled with their Ensembl Gene ID, and columns correspond to samples, labelled according to the FASTQ file name

growth_protocol: mESCs were cultured in a standard humidified incubator at 37C and 5% CO2. Cell lines were passaged every 48 h and were not kept in culture for longer than 4 weeks. Tissue culture flasks were coated with 0.1% gelatin for at least 15 min at RT prior to seeding. Culture media was DMEM supplemented with 15% FBS, 1% PSQ, 1% sodium pyruvate, 1% non-essential amino acids, 60 mio units of mouse LIF, and 0.8% beta-mercaptoethanol

extract_protocol:
RNA was extracted using a RNeasy kit with on column DNase digestion according to the manufacturer’s protocol (Qiagen, 74106). RNA integrity was confirmed using Agilent Tapestation RNA screentape, showing 2 sharp peaks representing the 18S and 28S ribosomal subunits, with a 28S:18S ratio of approximately 2. Using 5 mg input RNA, mRNA was isolated from ribosomal RNA using the NEBNext Poly(A) mRNA magnetic isolation module (E7490) according to the manufacturer’s instructions. Following two rounds of enrichment, successful isolation and sample integrity (RINe 2-3) were confirmed using high sensitivity Agilent Screen tape.
Library preparation was performed using the NEBNext Ultra II directional library prep kit (E7760) according to the manufacturer’s instructions for “purified RNA or clean RNA”. cDNA concentration was measured using the Qubit dsDNA assay kit (Q32854), and molar concentrations calculated using the average DNA fragment size following analyses on the Agilent Tapestation with high sensitivity DNA screentape (D1000). Equal molar concentrations were multiplexed at a final concentration of 15 nM and sequenced using Illumina Nextera Truseq single-ended reads. Due to limitations in the number of samples that could be combined in a single multiplex for sequencing, WT samples were independently multiplexed with Ccnc KO samples, and again with Cdk8 KO samples, in order to eliminate any sequencing-run bias.

treatment_protocol: For each clone or replicate, one sample was treated with DMSO and the other with 900nM AZD6738 for 4 hours prior to sample collection.

value: Mouse Embryonic Stem Cells (mESCs)

tag: clone

value: ATRi

tag: lane


title: CDK8_H4 ATRi L8 [SLX-17508.NEBNext11.H5JGFBBXY.s_8]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext11.H5JGFBBXY.s_8

tag: genotype


title: CDK8_C8 ATRi L8 [SLX-17508.NEBNext12.H5JGFBBXY.s_8]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext12.H5JGFBBXY.s_8


title: P0032 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0011 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: CDK8_H4 ATRi L7 [SLX-17508.NEBNext11.H5JGFBBXY.s_7]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext11.H5JGFBBXY.s_7


title: P0020 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0025 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0023 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0008 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: CDK8_B9 ATRi L8 [SLX-17508.NEBNext10.H5JGFBBXY.s_8]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext10.H5JGFBBXY.s_8


title: P0027 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: CDK8_B9 ATRi L7 [SLX-17508.NEBNext10.H5JGFBBXY.s_7]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext10.H5JGFBBXY.s_7


title: P0015 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0010 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0031 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0029 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0017 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0024 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: CDK8_C8 DMSO L8 [SLX-17508.NEBNext09.H5JGFBBXY.s_8]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext09.H5JGFBBXY.s_8

value: DMSO


title: P0006 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: CDK8_C8 DMSO L7 [SLX-17508.NEBNext09.H5JGFBBXY.s_7]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext09.H5JGFBBXY.s_7


title: P0004 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: CDK8_H4 DMSO L8 [SLX-17508.NEBNext08.H5JGFBBXY.s_8]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext08.H5JGFBBXY.s_8


title: CDK8_H4 DMSO L7 [SLX-17508.NEBNext08.H5JGFBBXY.s_7]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext08.H5JGFBBXY.s_7


title: P0019 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0002 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: CDK8_B9 DMSO L7 [SLX-17508.NEBNext07.H5JGFBBXY.s_7]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext07.H5JGFBBXY.s_7


title: WT_2 ATRi L8 [SLX-17508.NEBNext05.H5JGFBBXY.s_8]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext05.H5JGFBBXY.s_8

value: WT


title: N058 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY

source_name: SIRS

value: Systemic inflammatory response syndrome (SIRS)


title: WT_1 ATRi L8 [SLX-17508.NEBNext04.H5JGFBBXY.s_8]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext04.H5JGFBBXY.s_8


title: WT_1 ATRi L7 [SLX-17508.NEBNext04.H5JGFBBXY.s_7]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext04.H5JGFBBXY.s_7


title: WT_2 ATRi L7 [SLX-17508.NEBNext05.H5JGFBBXY.s_7]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext05.H5JGFBBXY.s_7


title: WT_2 DMSO L8 [SLX-17508.NEBNext02.H5JGFBBXY.s_8]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext02.H5JGFBBXY.s_8


title: CDK8_B9 DMSO L8 [SLX-17508.NEBNext07.H5JGFBBXY.s_8]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext07.H5JGFBBXY.s_8


title: N057 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: WT_1 DMSO L8 [SLX-17508.NEBNext01.H5JGFBBXY.s_8]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext01.H5JGFBBXY.s_8


title: WT_2 DMSO L7 [SLX-17508.NEBNext02.H5JGFBBXY.s_7]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext02.H5JGFBBXY.s_7


title: CCNC_H5 ATRi L6 [SLX-17502.NEBNext12.H5J7KBBXY.s_6]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext12.H5J7KBBXY.s_6


title: WT_1 DMSO L7 [SLX-17508.NEBNext01.H5JGFBBXY.s_7]

description:
processed data file:
SLX-17508_gene_count_matrix.csv
SLX-17508_gene_count_matrix_rlog.csv
SLX-17508.NEBNext01.H5JGFBBXY.s_7


title: CCNC_H5 ATRi L5 [SLX-17502.NEBNext12.H5J7KBBXY.s_5]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext12.H5J7KBBXY.s_5


title: P0042 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: N056 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N055 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: CCNC_G2 ATRi L6 [SLX-17502.NEBNext11.H5J7KBBXY.s_6]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext11.H5J7KBBXY.s_6


title: N051 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N054 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N053 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N048 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: CCNC_D1 ATRi L6 [SLX-17502.NEBNext10.H5J7KBBXY.s_6]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext10.H5J7KBBXY.s_6


title: N052 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N043 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N047 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N044 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N041 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: CCNC_G2 ATRi L5 [SLX-17502.NEBNext11.H5J7KBBXY.s_5]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext11.H5J7KBBXY.s_5


title: CCNC_H5 DMSO L5 [SLX-17502.NEBNext09.H5J7KBBXY.s_5]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext09.H5J7KBBXY.s_5


title: CCNC_D1 ATRi L5 [SLX-17502.NEBNext10.H5J7KBBXY.s_5]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext10.H5J7KBBXY.s_5


title: CCNC_H5 DMSO L6 [SLX-17502.NEBNext09.H5J7KBBXY.s_6]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext09.H5J7KBBXY.s_6


title: N045 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N046 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: CCNC_D1 DMSO L6 [SLX-17502.NEBNext07.H5J7KBBXY.s_6]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext07.H5J7KBBXY.s_6


title: CCNC_G2 DMSO L5 [SLX-17502.NEBNext08.H5J7KBBXY.s_5]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext08.H5J7KBBXY.s_5


title: CCNC_D1 DMSO L5 [SLX-17502.NEBNext07.H5J7KBBXY.s_5]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext07.H5J7KBBXY.s_5


title: CCNC_G2 DMSO L6 [SLX-17502.NEBNext08.H5J7KBBXY.s_6]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext08.H5J7KBBXY.s_6


title: N042 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N036 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N031 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N029 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: WT_2 ATRi L5 [SLX-17502.NEBNext05.H5J7KBBXY.s_5]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext05.H5J7KBBXY.s_5


title: WT_2 ATRi L6 [SLX-17502.NEBNext05.H5J7KBBXY.s_6]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext05.H5J7KBBXY.s_6


title: N028 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N039 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N034 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: WT_2 DMSO L6 [SLX-17502.NEBNext02.H5J7KBBXY.s_6]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext02.H5J7KBBXY.s_6


title: WT_1 ATRi L5 [SLX-17502.NEBNext04.H5J7KBBXY.s_5]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext04.H5J7KBBXY.s_5


title: WT_1 ATRi L6 [SLX-17502.NEBNext04.H5J7KBBXY.s_6]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext04.H5J7KBBXY.s_6


title: N035 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N040 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N032 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N027 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: WT_2 DMSO L5 [SLX-17502.NEBNext02.H5J7KBBXY.s_5]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext02.H5J7KBBXY.s_5


title: WT_1 DMSO L6 [SLX-17502.NEBNext01.H5J7KBBXY.s_6]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext01.H5J7KBBXY.s_6


title: WT_1 DMSO L5 [SLX-17502.NEBNext01.H5J7KBBXY.s_5]

description:
processed data file:
SLX-17502_gene_count_matrix.csv
SLX-17502_gene_count_matrix_rlog.csv
SLX-17502.NEBNext01.H5J7KBBXY.s_5


title: N020 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N025 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N017 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N009 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N014 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N011 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N016 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N005 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N023 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N002 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: P0443 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0425 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: N008 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: P0441 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: N018 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: P0402 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0435 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0417 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0404 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0403 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0434 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0418 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: N004 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: P0432 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0428 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0419 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0438 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0440 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0436 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0420 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Liver of Leishmania-infected Balb/c mice (10R6RH: MODEL)

city: La Laguna

first: Emma

last: Carmelo

state: SANTA CRUZ DE TENERIFE

address: C/ Astrofisico Francisco Sanchez s/n, Campus de Anchieta

department: University Institute of Tropical Diseases and Public Health

country: Spain

institute: University of La Laguna

description: TEST 10 DAYS

data_processing:
Cq values from the 48 samples analyzed were exported for normalization using GenEx (GenEx software (MultiD)). Genes that showed no expression in any sample mice were excluded for normalization.  Two genes showed the most stable expression (Lta4h and P38mapk) and were used for normalization to obtain NRQ values (Normalized Relative Quantities).
No data has been introduced under “Fold Change template” tab, since no fold-changes have been calculated between different conditions in our manuscript.

label: FAM

source_name: LIVER

label_protocol: The reverse transcription was performed with 2 ug of RNA with random hexamers using the High Capacity cDNA Reverse Transcription Kit (Life Technologies, Carlsbad, CA) according to manufacturer's instructions.

growth_protocol: 48 BALB/c (purchased to Charles River Laboratories, France) mice (14-15 weeks old) were used  in this study. Mice were randomly separated in two groups: (i) 24 control mice and (ii) 24 mice  that were infected with 10^6 stationary-phase L. infantum promastigotes via tail vein. Mice were euthanized by cervical dislocation and spleens were removed and immediately stored in RNAlater at -70°C (Sigma-Aldrich, St. Louis, USA).

extract_protocol: Total RNA isolation from livers (7-10 mg) was performed by cell disruption using FastPrep  System (ProScientific, Cedex, France) and Lysing Matrix D (MP Biomedicals, Solon, USA) in TRI-Reagent (Sigma-Aldrich, St. Louis, USA). RNeasy Mini Kit (Qiagen) was subsequently used for mRNA enrichment following manufacturer's instructions

treatment_protocol: 24 out of the 48 mice were infected with 10^6 stationary-phase L. infantum promastigotes via tail vein.

tag: strain

value: Balb/c


title: Liver of Leishmania-infected Balb/c mice (10R5RH: MODEL)

description: TEST 10 DAYS


title: Liver of Leishmania-infected Balb/c mice (10R4RH: MODEL)

description: TEST 10 DAYS


title: Liver of Leishmania-infected Balb/c mice (10R3RH: MODEL)

description: TEST 10 DAYS


title: Liver of Leishmania-infected Balb/c mice (10R1RH: MODEL)

description: TEST 10 DAYS


title: Liver of non-infected Balb/c mice (10R3NRH: MODEL)

description: CONTROL 10 DAYS


title: Liver of non-infected Balb/c mice (10R5NRH: MODEL)

description: CONTROL 10 DAYS


title: Liver of Leishmania-infected Balb/c mice (5R6RH: MODEL)

description: TEST 5 DAYS


title: Liver of non-infected Balb/c mice (10R2NRH: MODEL)

description: CONTROL 10 DAYS


title: Liver of non-infected Balb/c mice (10R1NRH: MODEL)

description: CONTROL 10 DAYS


title: Liver of Leishmania-infected Balb/c mice (5R5RH: MODEL)

description: TEST 5 DAYS


title: P0392 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET

value: Sepsis


title: P0390 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0396 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0383 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0375 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET

value: Female


title: P0398 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET

value: Urine


title: P0385 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0387 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET

value: Male


title: P0389 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Liver of Leishmania-infected Balb/c mice (10R2RH: MODEL)

description: TEST 10 DAYS


title: P0382 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0381 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0341 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0401 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0380 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0362 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0364 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Liver of non-infected Balb/c mice (10R6NRH: MODEL)

description: CONTROL 10 DAYS


title: Liver of non-infected Balb/c mice (10R4NRH: MODEL)

description: CONTROL 10 DAYS


title: Liver of Leishmania-infected Balb/c mice (5R3RH: MODEL)

description: TEST 5 DAYS


title: Liver of Leishmania-infected Balb/c mice (5R4RH: MODEL)

description: TEST 5 DAYS


title: Liver of non-infected Balb/c mice (5R4NRH: MODEL)

description: CONTROL 5 DAYS


title: Liver of non-infected Balb/c mice (5R2NRH: MODEL)

description: CONTROL 5 DAYS


title: Liver of non-infected Balb/c mice (5R3NRH: MODEL)

description: CONTROL 5 DAYS


title: Liver of non-infected Balb/c mice (5R6NRH: MODEL)

description: CONTROL 5 DAYS


title: Liver of non-infected Balb/c mice (5R5NRH: MODEL)

description: CONTROL 5 DAYS


title: Liver of Leishmania-infected Balb/c mice (5R2RH: MODEL)

description: TEST 5 DAYS


title: Liver of Leishmania-infected Balb/c mice (5R1RH: MODEL)

description: TEST 5 DAYS


title: P0359 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0357 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0353 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Liver of non-infected Balb/c mice (5R1NRH: MODEL)

description: CONTROL 5 DAYS


title: Liver of Leishmania-infected Balb/c mice (3R6RH: MODEL)

description: TEST 3 DAYS


title: P0348 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Liver of Leishmania-infected Balb/c mice (3R4RH: MODEL)

description: TEST 3 DAYS


title: Liver of Leishmania-infected Balb/c mice (3R5RH: MODEL)

description: TEST 3 DAYS


title: Liver of Leishmania-infected Balb/c mice (3R3RH: MODEL)

description: TEST 3 DAYS


title: Liver of non-infected Balb/c mice (3R6NRH: MODEL)

description: CONTROL 3 DAYS


title: Liver of non-infected Balb/c mice (3R5NRH: MODEL)

description: CONTROL 3 DAYS


title: Liver of Leishmania-infected Balb/c mice (3R2RH: MODEL)

description: TEST 3 DAYS


title: Liver of Leishmania-infected Balb/c mice (3R1RH: MODEL)

description: TEST 3 DAYS


title: Liver of non-infected Balb/c mice (3R3NRH: MODEL)

description: CONTROL 3 DAYS


title: Liver of non-infected Balb/c mice (3R4NRH: MODEL)

description: CONTROL 3 DAYS


title: Liver of non-infected Balb/c mice (3R2NRH: MODEL)

description: CONTROL 3 DAYS


title: Liver of non-infected Balb/c mice (3R1NRH: MODEL)

description: CONTROL 3 DAYS


title: Liver of Leishmania-infected Balb/c mice (1R6RH: MODEL)

description: TEST 1 DAY


title: Liver of Leishmania-infected Balb/c mice (1R4RH: MODEL)

description: TEST 1 DAY


title: Liver of Leishmania-infected Balb/c mice (1R5RH: MODEL)

description: TEST 1 DAY


title: Liver of Leishmania-infected Balb/c mice (1R3RH: MODEL)

description: TEST 1 DAY


title: P0344 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: P0352 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Liver of Leishmania-infected Balb/c mice (1R1RH: MODEL)

description: TEST 1 DAY


title: P0343 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: Liver of non-infected Balb/c mice (1R6NRH: MODEL)

description: CONTROL 1 DAY


title: N024 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N022 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N037 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: Liver of non-infected Balb/c mice (1R5NRH: MODEL)

description: CONTROL 1 DAY


title: P0347 (SEPTIC T1)

description: WITHIN 12 HRS OF SEPSIS ONSET


title: N059 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: Liver of non-infected Balb/c mice (1R4NRH: MODEL)

description: CONTROL 1 DAY


title: N049 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N021 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: Liver of non-infected Balb/c mice (1R3NRH: MODEL)

description: CONTROL 1 DAY


title: N019 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: LT2

city: Wuhan

first: Jie

last: Wu

state: Hubei

address: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1277

department: Department of Cardiovascular Surgery

description: peritoneal-derived macrophages were treated with trametinib (100nM)  for 2h, and then challenged by LPS (100ng/ml) for 12h (rep 2)

data_processing:
Clean reads were mapped to the mm10 (UCSC) mouse genome with  HISAT2 (v2.1.0) with default parameters.
Transcripts were assembled Expression quantitation using featureCounts(v1.6.4) with mouse annotation(release_M21) from Gencode
Differential gene expression was calculated using the DESeq2 package (v1.24.0) package of the R (version 3.6.0) software
Genome_build: mm10
Supplementary_files_format_and_content: Comma-Separated Row counts for each sample

source_name: peritoneal-derived macrophages

growth_protocol: We injected three mice with thioglycollate broth intraperitoneally. Three days later, the mice were injected with 5 ml of cold PBS into the peritoneal cavity and gently massaged. Then, the peritoneal fluid was collected, centrifuged, and the cell pellet was resuspended in DMEM supplemented with 10% FBS and cultured in 6-well-plate at 37℃. After adhering for 1h, the cells were gently washed with warm PBS for 3 times to remove non-adherent cells and then cultured with fresh medium.

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
DNase I was used to digest double-stranded and single-stranded DNA in total RNA, then, magnetic beads were purified to recover the reaction products, RNase H or Ribo-Zero method (human, mouse, plants) (Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to carry out end repair. The cDNA fragments with adapters were amplyfied by PCR, and the products were purified by Ampure XP Beads. Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products above were heated denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGISEQ500 platform (BGI Shenzhen, China).

treatment_protocol: After additional 24h of culture, these cells were treated with trametinib (100nM) or vehicle (DMSO) for 2h, and then challenged by LPS (100ng/ml) for 12h.

value: wild type

value: 8 weeks


title: LT3

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

description: peritoneal-derived macrophages were treated with trametinib (100nM)  for 2h, and then challenged by LPS (100ng/ml) for 12h (rep 3)


title: Liver of non-infected Balb/c mice (1R1NRH: MODEL)

description: CONTROL 1 DAY


title: Liver of non-infected Balb/c mice (1R2NRH: MODEL)

description: CONTROL 1 DAY


title: LT1

description: peritoneal-derived macrophages were treated with trametinib (100nM)  for 2h, and then challenged by LPS (100ng/ml) for 12h (rep 1)


title: LD3

description: peritoneal-derived macrophages were treated with vehicle (DMSO) for 2h, and then challenged by LPS (100ng/ml) for 12h (rep 3)


title: LD2

description: peritoneal-derived macrophages were treated with vehicle (DMSO) for 2h, and then challenged by LPS (100ng/ml) for 12h (rep 2)


title: Liver of Leishmania-infected Balb/c mice (1R2RH: MODEL)

description: TEST 1 DAY


title: LD1

description: peritoneal-derived macrophages were treated with vehicle (DMSO) for 2h, and then challenged by LPS (100ng/ml) for 12h (rep 1)


title: Wild type Sulfur Starvation Biological Replicate 3

city: Ithaca

first: Lori

middle: B

last: Huberman

address: 236 Tower Rd.

department: Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science

data_processing:
Illumina Casava1.8 software used for base calling
Sequence reads were trimmed for adaptor sequence and aligned to the predicted transcripts from the N. crassa OR74A genome (v12) with HiSat2 v2.1.0 with the parameters --max-intronlen 5000 --dta-cufflinks
Fragments per kilobase of transcript per million mapped reads (FPKM) were calculated using Cufflinks v2.2.1 with the parameters --library-type fr-unstranded -u -b -G --compatible-hits-norm --max-bundle-frags=10000000
FPKMs in the FPKM_Metafile.xlsx were generated by running all samples through cuffmerge v2.2.1; then cuffquant v2.2.1 with the parameters --library-type fr-unstranded --max-bundle-frags=10000000; then cuffnorm v2.2.1 with the parameters --library-type fr-unstranded.
Genome_build: Neurospora crassa OR74A genome v12
Supplementary_files_format_and_content: tab-deliminated text files include FPKM values for each sample

organism: Neurospora crassa

source_name: Wild type Sulfur Starvation

growth_protocol: N. crassa conidia were inoculated into 3ml of Vogel's minimal media + 500mg/L methionine and incubated at 25C in constant light with constant shaking at 200rpm for 24h

extract_protocol:
Mycelia were filtered using Whatman paper #1 and flash frozen using liquid nitrogen. RNA was isolated by bead beating in Trizol reagent and then cleaned up using the Qiagen RNeasy kit.
RNA were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mycelia were washed in media lacking sulfur and then transferred to 3ml of Vogel's minimal media with either 24uM sulfate or no sulfur source and incubated at 25C in constant light with constant shaking at 200rpm for 4h prior to harvesting for RNAseq.

value: FGSC 4200

tag: medium

value: Vogel's minimal medium with no sulfur

value: mycelia


title: Δcys-3 Sulfur Starvation Biological Replicate 1

source_name: Δcys-3 Sulfur Starvation

tag: tissue


title: Δcys-3 Sulfur Starvation Biological Replicate 2


title: N013 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N007 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: Wild type Sulfur Starvation Biological Replicate 2


title: N012 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N010 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: Δcys-3 24uM Sulfate Biological Replicate 1

source_name: Δcys-3 24uM Sulfate

value: Vogel's minimal medium with 24uM sulfate


title: Wild type Sulfur Starvation Biological Replicate 1


title: Δcys-3 24uM Sulfate Biological Replicate 2


title: N006 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: Wild type 24uM Sulfate Biological Replicate 3

source_name: Wild type 24uM Sulfate


title: Wild type 24uM Sulfate Biological Replicate 2


title: Wild type 24uM Sulfate Biological Replicate 1


title: Δcys-3 Sulfur Starvation Biological Replicate 3


title: Gja5-Cd44+ YS

first: Gong

last: Yandong

address: DongDaJie #8

institute: the Fifth Medical Center of the PLA General Hospital

data_processing:
not provided
Genome_build: mm10
Supplementary_files_format_and_content: txt, rawdata for gene expression

source_name: Endothelial cells

extract_protocol: Sequencing libraries were prepared following a modified single-cell tagged reverse  transcription (STRT) protocol as previously reported (Li et al., 2017; Picelli et al.,  2013). The cells were first judged by morphology to assess their state, with cells in  good condition being picked and directly placed into lysis buffer. The reverse  transcription reaction was performed using a sample-specific 25-nucleotide (nt) oligo  dT primer containing an 8-nt barcode (TCAGACGTGTGCTCTTCCGATCTXXXXXXXX-  DDDDDDDD-T25, where X represents the sample-specific barcode,  and D stands for the unique molecular identifier (UMI)). After reverse transcription and  second-strand cDNA synthesis, the cDNAs were amplified by 16 cycles of PCR. The barcoded DNAs were then pooled together and purified using AMPure XP beads.  Biotinylated pre-indexed primers were used to further amplify the PCR product by an  additional four cycles of PCR to introduce biotin tags to the 3′ ends of the amplified  cDNAs. Approximately 300 ng cDNA was sonicated into 300-bp fragments using the  Covaris S2 system and enriched with Dynabeads MyOneTM Streptavidin C1 beads.  Libraries were constructed using a Kapa Hyper Prep Kit (Kapa Biosystems) and were  then submitted to150-bp paired-end sequencing on an Illumina Hiseq X Ten  platform(Novogene).

tag: developmental stage

value: Gja5-Cd44+ YS


title: Gja5+Cd44+ YS

value: Gja5+Cd44+ YS


title: Gja5+Cd44+ CR

value: Gja5+Cd44+ CR


title: batch40

value: yolk sac,E8.0


title: N003 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY

tag: disease state


title: Δcys-3 24uM Sulfate Biological Replicate 3


title: batch36

value: yolk sac,E9.5


title: batch38

value: yolk sac,E9.0


title: batch35


title: batch39


title: N094 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY

value: Systemic inflammatory response syndrome (SIRS)

tag: gender


title: batch34

value: yolk sac,E10.0


title: batch33

value: yolk sac,E8.5


title: N001 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY

value: Urine


title: batch32


title: batch30


title: N093 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY

value: Male


title: N090 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: batch29


title: batch26


title: batch28


title: batch27


title: N091 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N092 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY

value: Female


title: batch37


title: batch25


title: N089 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N085 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N086 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N084 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N083 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N082 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: batch31


title: N081 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: batch21


title: batch23


title: batch20


title: batch24


title: N079 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: batch17


title: batch22


title: batch19


title: batch15


title: batch18


title: batch14


title: batch11


title: N078 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: batch13


title: batch12


title: N077 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N080 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: batch10


title: N075 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: batch6


title: batch7


title: N074 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N073 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: batch8


title: batch5


title: batch16


title: batch4


title: batch2


title: macrophages treated with IL-36gammma

first: Jiao

last: Fan

address: Fuxing road

institute: 301 hospital

data_processing:
The quality control of RNA-seq data was done by FastQC (v0.11.8).
The RNA-seq data was trimmed by Trim Galore (v0.6.1) with default parameters for pair-end data to remove the low-quality reads and adaptors.
The trimmed RNA-seq data were aligned to the mm10 mouse transcriptome using STAR (v2.5.0a) with default parameters.
Gene expression was quantified as fragments per kilobase of transcript per million mapped reads (FPKM) using HTSeq.
Supplementary_files_format_and_content: raw counts

source_name: macrophages

extract_protocol:
Macrophages treated with or without IL-36 gamma were collected, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow derived macrophages (BMDMs)

value: IL-36 gamma


title: batch1


title: macrophages-control


title: High-Fli1+, rep2

city: Edinburgh

first: Gianfranco

last: Matrone

address: 47 Little France Cresc

institute: University of Edinburgh

data_processing:
Illumina Illumina Hi-Seq 2500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to dr10 whole genome
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated.
Genome_build: danio rerio10
Supplementary_files_format_and_content: Text files with FPKM values for each sample were grouped in a single excel file

organism: Danio rerio

extract_protocol:
100 ng of total RNA was subjected to library synthesis
Total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA.

tag: cell population


title: Low-Fli1+, rep2


title: High-Fli1+, rep1


title: WT_D_rep2

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

data_processing:
In total, we yielded paired-end reads of 2x150bp for 24 libraries of methylated RNA immunoprecipitation sequencing (MeRIP-seq), which included wild type and mutation under dark and blue with three biological repeats from immunoprecipitated (IP) and input samples, respectively. The fastx_clipper script from FASTXtoolkit (http://hannonlab.cshl.edu/fastx_toolkit) was used for adapter sequence trimming of FASTQ files from input and IP samples using following parameters: -l 20 -d 0 -n -v -M 6. Then above clean reads were aligned to the Arabidopsis reference genome (TAIR10) using TopHat v2.0.11 with following parameters: -a 8 -m 0, which required the min anchor length and maximum number mismatches for junction reads was 8 and 0, respectively. Reads aligned to multiple genome regions were discarded.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

organism: Arabidopsis thaliana

source_name: m6A-IP sample of dark-grown WT seedlings, repeat 2

growth_protocol: Arabidopsis WT and crycry2 seedlins grown in the dark or continuous blue light for 6 days were used to isolated total RNA for m6A-IP-seq

extract_protocol:
The total RNA was extracted using TRIZOL reagent.
anti-m6A antibody for MeRIP-seq

value: seedlings

tag: Stage

value: WT

tag: light condition

value: dark grown

tag: rip antibody


title: WT_D_rep1

source_name: m6A-IP sample of dark-grown WT seedlings, repeat 1


title: Low-Fli1+, rep1


title: batch9


title: N072 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY

tag: age


title: N076 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: WT_D_input_rep3

source_name: Input sample of dark-grown WT seedlings, repeat 3

value: none (input)


title: Fli1-, rep2


title: Fli1-, rep1


title: N071 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N070 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N069 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: N068 (SIRS)

description: WITHIN 4 HRS AFTER VASCULAR SURGERY


title: WT_D_input_rep2

source_name: Input sample of dark-grown WT seedlings, repeat 2


title: batch3


title: WT_D_input_rep1

source_name: Input sample of dark-grown WT seedlings, repeat 1


title: WT_D_rep3

source_name: m6A-IP sample of dark-grown WT seedlings, repeat 3


title: WT_B_rep3

source_name: m6A-IP sample of blue light-grown WT seedlings, repeat 3

value: blue light-grown


title: WT_B_rep2

source_name: m6A-IP sample of blue light-grown WT seedlings, repeat 2


title: PTENα_2

first: Yizhe

last: Sun

state: Beijing

address: No.38, Xueyuan Road ,Haidian District

institute: Peking University Health Science Center

data_processing:
The Cell ranger software pipeline (version 6.0.1) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.0.1) was used for generation of Seurat object.
Low-quality cells with UMI numbers greater than 5000 or less than 300, or having over 10% mitochondrial-derived UMI counts were removed.
The count matrix was normalized with SCTransform function.
IntegrateData function was used to integrate data and create a new matrix with 3000 features.
PCA was performed by R package Seurat (version 4.0.1). Top 30 PCs were used for tSNE and UMAP.
tSNE and UMAP were performed by R package Seurat (version 4.0.1).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.

source_name: murine tumor infiltration lymphocytes

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.
10x scRNA-Seq

value: tumor


title: OB_2dpi_1

first: Rui-Ting

last: Li

address: No.20 Dongda Street, Fengtai District

department: State Key Laboratory of Pathogen and Biosecurity

institute: Beijing Institute of Microbiology and Epidemiology

data_processing:
After sequencing, perl script was used to filter the original data (Raw Data) to clean reads by removing contaminated reads for adapters and low-quality reads.
Clean reads were aligned to the mouse genome (Mus_musculus.GRCm38.99) using Hisat2 v2.1.0. The number of reads mapped to each gene in each sample was counted by HTSeq v0.6.0 and FPKM was then calculated  to estimate the expression level of genes in each sample.
Genome_build: Mus_musculus.GRCm38.99
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: lung

extract_protocol:
Total RNA from lung  were extracted using TRIzol (Invitrogen, Carlsbad, CA, USA)  and DNase I (NEB, USA) treated, respectively.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations

value: Olfactory Bulb

value: 6-8 weeks

tag: treatment

value: SARS-CoV-2 infected


title: WT_B_rep1

source_name: m6A-IP sample of blue light-grown WT seedlings, repeat 1


title: OB_4dpi_1


title: OB_4dpi_2


title: OB_mock_3

value: mock


title: OB_2dpi_2


title: OB_4dpi_3


title: WT_B_input_rep3

source_name: Input sample of blue light-grown WT seedlings, repeat 3


title: OB_mock_2


title: WT_B_input_rep2

source_name: Input sample of blue light-grown WT seedlings, repeat 2


title: OE_4dpi_3

value: Olfactory Epithelium


title: WT_B_input_rep1

source_name: Input sample of blue light-grown WT seedlings, repeat 1


title: PTENα_1


title: OE_4dpi_1


title: OE_4dpi_2


title: Cry_D_rep3

source_name: m6A-IP sample of dark-grown cry1cry2 seedlings, repeat 3


title: OE_2dpi_2


title: Cry_D_rep2

source_name: m6A-IP sample of dark-grown cry1cry2 seedlings, repeat 2


title: Mock_1


title: Mock_2


title: OE_2dpi_3


title: OE_mock_3


title: OB_2dpi_3


title: OE_2dpi_1


title: Cry_D_rep1

source_name: m6A-IP sample of dark-grown cry1cry2 seedlings, repeat 1


title: Cry_D_input_rep3

source_name: Input sample of dark-grown cry1cry2 seedlings, repeat 3


title: OE_mock_2


title: OE_mock_1


title: Cry_D_input_rep2

source_name: Input sample of dark-grown cry1cry2 seedlings, repeat 2


title: Cry_D_input_rep1

source_name: Input sample of dark-grown cry1cry2 seedlings, repeat 1


title: Cry_B_rep3

source_name: m6A-IP sample of blue light-grown cry1cry2 seedlings, repeat 3


title: female_old_4dpi_3

value: BALB/c

value: lung

value: 38 weeks

value: MASCp36 infected

value: female


title: female_old_4dpi_2


title: OB_mock_1


title: Cry_B_rep2

source_name: m6A-IP sample of blue light-grown cry1cry2 seedlings, repeat 2


title: Cry_B_rep1

source_name: m6A-IP sample of blue light-grown cry1cry2 seedlings, repeat 1


title: female_old_1dpi_3


title: Cry_B_input_rep2

source_name: Input sample of blue light-grown cry1cry2 seedlings, repeat 2


title: female_old_4dpi_1


title: PK-048: Pax_RNA_Pancreatic_cancer patient_48

city: Kanazawa

first: Yoshio

last: Sakai

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Gastroenterology

country: Japan

institute: Kanazawa University

description: Gene expression about Pancreatic cancer patient blood

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to DNA microarray Whole Human Genome 4×44K Array kit G4112F (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air dry.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slide

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014850_D_20070207)to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Peripheral Blood, Pancreatic cancer patient No.48

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug total RNA using Quick Amp Labeling kit, One-Color (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from PAXgene blood RNA tube using PAXgene Blood RNA Kit (PreAnalytix, Hombrechtikon, Switzerland) in accordance with the manufacturer’s protocol. total RNA was quantified using a NanoDrop-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA).

tag: diagnosis

value: pancreatic cancer

value: whole blood

value: male


title: PK-046: Pax_RNA_Pancreatic_cancer patient_46

source_name: Peripheral Blood, Pancreatic cancer patient No.46


title: female_old_1dpi_2

source_name: lung


title: female_old_mock_3


title: Cry_B_input_rep1

source_name: Input sample of blue light-grown cry1cry2 seedlings, repeat 1

value: seedlings


title: female_old_1dpi_1


title: PK-040: Pax_RNA_Pancreatic_cancer patient_40

source_name: Peripheral Blood, Pancreatic cancer patient No.40


title: female_old_mock_2


title: PK-037: Pax_RNA_Pancreatic_cancer patient_37

source_name: Peripheral Blood, Pancreatic cancer patient No.37


title: PK-043: Pax_RNA_Pancreatic_cancer patient_43

source_name: Peripheral Blood, Pancreatic cancer patient No.43


title: PK-041: Pax_RNA_Pancreatic_cancer patient_41

source_name: Peripheral Blood, Pancreatic cancer patient No.41


title: PK-027: Pax_RNA_Pancreatic_cancer patient_27

source_name: Peripheral Blood, Pancreatic cancer patient No.27


title: PK-032: Pax_RNA_Pancreatic_cancer patient_32

source_name: Peripheral Blood, Pancreatic cancer patient No.32


title: PK-036: Pax_RNA_Pancreatic_cancer patient_36

source_name: Peripheral Blood, Pancreatic cancer patient No.36


title: col_cBL_rep3

data_processing:
The RNA-seq reads were aligned to the arabidopsis genome (TAIR10) using tophat-2.0.11 (Trapnell et al., 2009) with anchor length more than 8nt for spliced alignments. Only uniquely mapped reads were retained for subsequent analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig

source_name: blue light-grown WT  seedlings, repeat 3

growth_protocol: the seedling were grown in greenhouse

extract_protocol:
The total RNA was extracted using TRIZOL reagent.
Strand-specific RNA-Seq libraries generated from samples above were constructed using dUTP method (Parkhomchuk et al., 2009) and sequenced on Illumina Hiseq 2500.

treatment_protocol: continue  blue light

value: seedling

value: WT


title: col_cBL_rep2

source_name: blue light-grown WT  seedlings, repeat 2


title: PK-016: Pax_RNA_Pancreatic_cancer patient_16

source_name: Peripheral Blood, Pancreatic cancer patient No.16


title: female_old_mock_1


title: col_cBL_rep1

source_name: blue light-grown WT  seedlings, repeat 1


title: male_young_4dpi_3

value: 6 weeks


title: Cry_B_input_rep3

source_name: Input sample of blue light-grown cry1cry2 seedlings, repeat 3

value: blue light-grown

value: none (input)


title: c1c2_cBL_rep3

source_name: blue light-grown cry1cry2 seedlings, repeat 3


title: male_young_4dpi_2


title: male_young_4dpi_1


title: PK-015: Pax_RNA_Pancreatic_cancer patient_15

source_name: Peripheral Blood, Pancreatic cancer patient No.15


title: c1c2_cBL_rep2

source_name: blue light-grown cry1cry2 seedlings, repeat 2


title: PK-020: Pax_RNA_Pancreatic_cancer patient_20

source_name: Peripheral Blood, Pancreatic cancer patient No.20


title: male_young_1dpi_3

source_name: lung


title: c1c2_cBL_rep1

source_name: blue light-grown cry1cry2 seedlings, repeat 1


title: PK-012: Pax_RNA_Pancreatic_cancer patient_12

source_name: Peripheral Blood, Pancreatic cancer patient No.12


title: male_young_1dpi_2


title: Tendon_horse20

city: Copenhagen

first: Peter

last: Schjerling

address: Bispebjerg Bakke 23, M81

department: Institute of Sports Medicine Copenhagen, ISMC

country: Denmark

institute: Bispebjerg Hospital

data_processing:
Reads were filtered using SOAPnuke v1.5.2 and parameters: -n 0.01 -l 15 -q 0.5 -A 0.25 -Q 2
Clean reads were mapped to the horse genome (EquCab3.0) using Rsubread v2.0.0 and parameters: unique=TRUE
Clean reads were mapped to reference RNA using Rsubread v2.0.0 and parameters: countMultiMappingReads = FALSE
Expression levels were normalized with DESeq2 v1.26.0 resulting in rlog normalized values ("Count and rlog values.xlsx"). Only transcripts with count in at least 5 of the 15 samples were included.
Furthermore, increases in MTJ samples ("MTJ_changes.xlsx") were calculated by considering the background level of MTJ samples as a mix from muscle and tendon which can be estimated from muscle and tendon specific transcripts ("Reference genes for MTJ prediction.xlsx"), see article.
Genome_build: EquCab3.0
Supplementary_files_format_and_content: "Count and rlog values.xlsx" contains transcript read counts and DESeq2 regularized log transformation values.  "Reference genes for MTJ prediction.xlsx" contains muscle and tendon specific transcripts used for predicting muscle and tendon contribution to the MTJ samples, see article.  "MTJ_changes.xlsx" contains log2FC differences between measured and predicted counts in the MTJ samples.  All three files in Microsoft Excel Open XML format.

organism: Equus caballus

source_name: superficial digital muscle

extract_protocol:
Total RNA was purified with TriReagent
RNA was submitted to BGI Europa and analyzed according to their standard procedure:   1)mRNA enrichment: Oligo dT Selection or rRNA depletion;  2)RNA fragment and reverse transcription: Fragment the RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random  primer;  3) End repair, add A tailing and adaptor ligation: The synthesized cDNA was subjected to end-repair  and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA  fragments;  4)PCR amplification:The ligation products were purified and many rounds of PCR amplification  were performed to enrich the purified cDNA template using PCR primer;  5)Denature and cyclization:Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and  DNA ligase;  6) Sequencing on DNBseq platform.

treatment_protocol: These samples were obtained from the front limb of euthanized horses from which the SDF muscle was dissected and small samples of muscle with attached tendon were punched out using a 4 mm diameter biopsy puncher. The samples were mounted in TissueTeK (Sakura, Netherlands), tendon side down, frozen in liquid nitrogen-cooled isopentane, and stored at -80 °degrees C until analysis. By cryosectioning muscle, MTJ and tendon specific samples were obtained (approx. 200 micrometer each) and RNA purified using TriReagent.

value: Tendon

tag: horse number

tag: age (years)

value: Gelding

tag: training

value: Trained


title: RKO_Dex

city: Shanghai

first: Zhen

last: Xiang

state: Shanghai

address: No. 197, Ruijin er Road

institute: Department of Surgery of Ruijin Hospital

data_processing:
Raw sequence reads were initially processed by FASTQC for quality control, and then adapter sequences and poor quality reads were removed by using CUTADAPT
Quality filtered reads were then mapped to grape genome using STAR
Read counts were calculated by using htseq-count
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Colorectal cancer cell line

growth_protocol: Cancer cell lines were cultured in RPMI-1640 containing 10% FBS and 1% Penicillin-Streptomycin, and incubated at 37 °C in a humidified incubator at 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cancer cell lines were treated by DMSO or Dex for 48 hours.

tag: cell line

value: RKO

tag: cell type

value: Colorectal cancer cell line

value: dexamethasone (Dex)


title: MV3_Dex

source_name: Melanoma cell line

value: Melanoma cell line


title: MTJ_horse20

value: MTJ


title: Muscle_horse20

value: Muscle


title: male_young_mock_3

tag: strain

value: BALB/c

value: lung

value: mock


title: Tendon_horse18

description:
H18T
Mare

tag: tissue

value: Female


title: PK-010: Pax_RNA_Pancreatic_cancer patient_10

source_name: Peripheral Blood, Pancreatic cancer patient No.10

value: pancreatic cancer

value: whole blood

value: female


title: BxPC3_Dex

source_name: Pancreatic cancer cell line

value: Pancreatic cancer cell line


title: N-028: Pax_RNA_Normal_28

description: Gene expression about healthy volunteer blood

source_name: Peripheral Blood, healthy volunteer No.28

value: healthy


title: male_young_mock_2

value: 6 weeks

value: male


title: MTJ_horse18

description:
H18MT
Mare

value: Trained


title: PK-008: Pax_RNA_Pancreatic_cancer patient_8

source_name: Peripheral Blood, Pancreatic cancer patient No.8


title: PK-009: Pax_RNA_Pancreatic_cancer patient_9

source_name: Peripheral Blood, Pancreatic cancer patient No.9


title: PK-014: Pax_RNA_Pancreatic_cancer patient_14

source_name: Peripheral Blood, Pancreatic cancer patient No.14


title: N-026: Pax_RNA_Normal_26

source_name: Peripheral Blood, healthy volunteer No.26


title: male_young_mock_1


title: NCIH-747_Dex

value: Colorectal cancer cell line


title: Muscle_horse18

description:
H18M
Mare


title: N-024: Pax_RNA_Normal_24

source_name: Peripheral Blood, healthy volunteer No.24


title: male_old_4dpi_3

value: 38 weeks

value: MASCp36 infected


title: MKN-45_Dex

source_name: Gastric cancer cell line

value: Gastric cancer cell line

value: dexamethasone (Dex)


title: N-023: Pax_RNA_Normal_23

source_name: Peripheral Blood, healthy volunteer No.23


title: Tendon_horse17

description:
H17T
Mare

value: Tendon

value: Sedentary


title: male_old_4dpi_2

value: BALB/c

value: lung


title: male_young_1dpi_1


title: SGC-7901_Dex