title: STINGKO_TL8-2

city: Ithaca

first: Karla

middle: Yvonne

last: García-Martínez

state: NY

address: 930 Campus Rd

department: Microbiology and Immunology

institute: Cornell University

data_processing:
Illumina pipeline software was used for base calling.
Sequenced reads were trimmed for 3' adaptor sequence and low-quality sequence and filtered to remove reads < 50nt with TrimGalore/cutadapt.
Processed reads were mapped to the reference genome/transcriptome with STAR using --quantMode GeneCounts to generate raw counts per gene.
Raw counts were analyzed in R with DEseq2.
Assembly: Matrix table with raw gene counts for every gene and every sample

source_name: Dual THP-1 Cells

growth_protocol: THP1-Dual cells (InvivoGen) were cultured and maintained in RPMI 1640 (Corning) supplemented with 10% FBS, 50 U ml−1 penicillin, 50 µg ml−1 streptomycin, 100 µg ml−1 normocin, and 2 mM L-glutamine. 100 µg ml−1 of zeocin and 10 µg/ml−1 of blasticidin were added to growth medium every other passage to retain the dual reporters.

extract_protocol:
Cells were pelleted and lysed using 1mL trizol LS, RNA was extracted using total RNA extraction protocol by the Cornell Transcriptional Regulation and Expression (TREx) facility, using chloroform extraction. RNA integrity was confirmed by Fragment Analyzer RNA QC (Agilent). RNAseq libraries were constructed by the TREx Facility at Cornell University using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs).
RNA-seq libraries were prepared from 100ng total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial [polyA+ isolation/rRNA depletion].

treatment_protocol: 2x10^6 THP-1 WT or STING cells were treated with DMSO or 500ng/mL H151 for 1 hour, then stimulated with media or 10ug/mL TL8 for 8 hours. After 8 hours RNA was collected using trizol.

value: Dual THP-1 Cells

value: Monocyte cell line

value: STING KO

value: DMSO+10ug/mL TL8


title: B41_65_B_BX_S70

status: Public on Jun 03 2024

type: SRA

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

country: USA

institute: University of North Carolina at Chapel Hill

library_source: transcriptomic

data_processing:
Align the data with STAR 2.7.6a
Quantify the expression with Salmon 1.4.0
QC methods used samtools sort 1.10, Picard 2.22.4, and FastQC 0.11.9
Assembly: hg38
Supplementary files format and content: Salmon gene expression file (tab-delimited)

molecule: total RNA

organism: Homo sapiens

source_name: Breast

extract_protocol:
RNA was extracted from paraffin-embedded baseline tumor samples
ribo-zero RNAseq libraries were made using an Illumina TruSeq Stranded Total RNA kit

tag: tissue

value: Breast

tag: Sex

value: Female

tag: race

value: Black

tag: treatment

value: Untreated


title: B41_42_5_BX_S62


title: BQ6133 Plasma

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: Plasma

extract_protocol:
RNA Isolation method was . RNA Isolation kit was Homebrew Kit.
Library construction kit was Homebrew Kit. Samples were multiplexed. Type of Starting Material was total RNA.

tag: condition

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA


title: Control treated subcutaneous FL8 allograft tumor #5

city: Vienna

first: Julia

last: Arand

address: Schwarzspanierstr. 16

country: Austria

institute: Medical University of Vienna

data_processing:
Raw sequencing reads were also demultiplexed by the vendor to generate approximately 20 million paired-end reads per sample.  Fastq files were trimmed using CutAdapt (v2.10) (Martin et al., 2011 using TruSeq sequencing adapter (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC), and a minimum read length of at least 25. Reads were then aligned to the ENSEMBL mm10 genome using HiSat2 (Kim et al., 2019) using reverse strandedness and discarding unaligned reads. Counts were assigned to genes using featureCounts (Liao et al., 2014) at ENSEMBL gene annotation (v93). Differential expression analysis was conducted using DESeq2 (Love et al., 2014) on R v4.1.2 (https://www.R-project.org/).
Assembly: mm10
Supplementary files format and content: The processed csv file represents countspermillion (post featurecounts is a conversion to CPM)

organism: Mus musculus

source_name: Tumor allograft

growth_protocol: FL8 cells were suspended at concentration of 106 cells/100 µL in 10% w/v methacrylated gelatin (Sigma 276685) and 0.067% w/v LAP (Sigma 900889) suspended in RPMI (Sigma R0883). 200 µL aliquots in 96-well plates were photocrosslinked into solid capsules at 405 nm light (Amazon 0191673174324) for 3 min at room temperature. Capsules were implanted in the subcutaneous flanks of NSG mice.

extract_protocol:
Tumors were frozen down and stored at -80 C before being sent to Novogene for tissue processing and RNA extraction.
Library construction was carried out by Novogene.
PairedEnd150

treatment_protocol: When average tumor size reached 75 mm3 mice were randomized into treatment groups. Mice either received vehicle (0.5% methocel Sigma 94378) or palbociclib (LC Laboratories P-7788) at a dose of 75 mg/kg via oral gavage for 3 consecutive days and given 4 days with no treatment.

value: Tumor allograft

tag: cell line

value: Control Carrier


title: B41_38_A_BX_S60

value: White


title: whole blood, EpiAge I, scBS-seq

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description: Sample 5123

library_source: genomic

data_processing:
scM&T-seq data was processed as described previously (Angermueller et al. 2016). scBS-seq data was processed as described previously; briefly, reads had 6bp removed on their 5’-ends to remove the random primed portion of the reads, and were also adapter- and quality-trimmed using Trim Galore (v0.6.7; options --clip_r1 6). Trimmed reads were  aligned to the bisulfite converted GRCm38 mouse genome using Bismark v0.22.3 in single-end mode (Krueger and Andrews, 2011; options: --non_directional). Methylation calls were extracted after duplicate reads had been removed (deduplicate_bismark).
Assembly: GRCm38
Supplementary files format and content: bismark.cov.gz files are tab separated and contain DNA methylation data with the following columns: chromosome, start, end, methylation, methylated reads, nonmethylated reads.

molecule: genomic DNA

source_name: whole blood

extract_protocol:
scM&T-seq (Angermueller et al 2016, https://doi.org/10.1038/nmeth.3728)
scBS-seq (Clark et al 2017, https://doi.org/10.1038/nprot.2016.187)
scBS-seq

value: whole blood

tag: genotype

value: wild type

tag: cell type

value: whole blood depleted of red blood cells

value: wildtype


title: WT-rep1 [scRNA-Seq]

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
For modified STRT-seq data, raw reads were first split for each cell by specific barcode sequence attached in Read 2.
The TSO sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Reads with adapter contaminants or low-quality bases (N > 10%) were discarded.
Subsequently, we aligned the stripped Read 1 sequences to mm10 mouse transcriptome (UCSC) using tophat2 (version 2.0.12). Uniquely mapped reads were counted by HTSeq package and grouped by the cell-specific barcodes.
Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files with raw gene umi.

source_name: mouse HSC

extract_protocol:
modified STRT-seq
A modified STRT-seq protocol was applied for single-cell RNA-seq. Briefly, sorted single cells in good condition were picked into lysis by mouth pipetting, and the scRNA-seq libraries were constructed based on STRT-seq with some modifications. cDNAs were synthesized using sample-specific 25-nt oligo-dT primer containing 8-nt barcode (TCAGACGTGTGCTCTTCCGATCT-XXXXXXXX-DDDDDDDD-T25, X representing sample-specific barcode while D standing for unique molecular identifiers (UMI).  After reverse transcription and second-strand cDNA synthesis, the cDNAs were amplified by 16 cycles of PCR using ISPCR primer and 3’ Anchor primer. Samples were pooled and purified using Agencourt AMPure XP beads . 4 cycles of PCR were performed to introduce index sequence  and subsequently, 400 ng cDNAs were fragmented to around 300 bp by Covaris S2. After being incubated with Dynabeads MyOneTM Streptavidin C1 beads (Thermo Fisher, 65002) for 1 hour at room temperature, cDNA Libraries were generated using KAPA Hyper Prep Kit (Kapa Biosystems, kk8505). After adaptor ligation, the libraries were amplified by 8 cycles of PCR using QP2 primer and short universal primer. The libraries were sequenced on Illumina Hiseq 4000 platform in 150 bp pair-ended manner

treatment_protocol: FACS-sorted HSC were kept on ice until lysed and reverse transcribed.

value: bone marrow


title: B41_64_A1_BX_S69


title: B41_39_NS01_BX_S61


title: STINGKO_DMSO-2

value: Dual THP-1 Cells

value: Monocyte cell line

value: STING KO

value: DMSO


title: Control-Chow-F_302806-2

city: Milwaukee

first: Justin

middle: L

last: Grobe

address: 8701 W Watertown Plank Road

institute: Medical College of Wisconsin

data_processing:
MAP-RSeq.v3.0
Pipeline included STAR.V2.5.2b, STAR-Fusion, featurCounts(Subread)v1.5.1, FastQC, RSeQC.v3.0.0
Downstream analyses included several R packages: EdgeR and WGCNA
Applied two different methods in EdgeR for Differential Expression Analysis (Pairwise and GLM).
Assembly: mm10
Supplementary files format and content: xlsx files contain RPKM values for each sample

source_name: Brain

growth_protocol: Mice were left of standard chow diet until sacrifice for brain collection at 20 weeks of age or switched to high fat diet for 10 weeks at 10 weeks of age and then sacrificed for brain collection.

extract_protocol:
Trizol and chloroform extraction, aqueous phase saved and RNA precipitated into a pellet with sodium acetate, glycogen, and ispropanol
RNA libraries were prepared using Takara SMART-Seq Ultra Low Input v4

value: Brain

value: Arcuate nucleus of the hypothalamus

value: Control

value: Chow


title: BQ9115 Cerebrospinal fluid

source_name: Cerebrospinal fluid

value: Healthy Subject

value: Entire brain and spinal cord

value: total cell-free biofluid RNA


title: B41_76_A1_BX_S78

value: Breast

value: Female

value: Asian

value: Untreated


title: KO-rep1 [scRNA-Seq]

value: Mat KO


title: Trmt6 WT, scRNA-seq

first: Aiwei

last: Wu

state: Zhejiang

address: 2318 Yuhangtang Road

department: School of Basic Medical Sciences

institute: Hangzhou Normal University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
BM cells were harvested by crushing the bones (Femur, Tibia and Hip). Then, red blood cells were lysed with Ammonium-Chloride-Potassium (ACK) buffer and the remainning cells were washed twice with PBS, lineage depleted using the Lineage Cell Depletion Kit (Miltenyi), labelled with the following antibody cocktail: anti-cKit, anti Sca-1 and anti Flt3 antibodies and FACS sorted   FACS purified HSPCs were loaded 30 min after the sorting onto a Chromium Single Cell Chip and processed with the Chromium Controller (10x Genomics) according to the manufacturer’s instructions for single cell barcoding at a target capture rate of 4000 individual cells per sample. Libraries were prepared using Chromium Single-Cell 3′ Reagent Kits v2 (10x Genomics)  single cell RNAseq library using Chromium Single-Cell 3′ Reagent Kits v2 (10x Genomics)
Library was performed according to the manufacter’s instructions (single cell 3’ protocol, 10x Genomics). Briefly, HSPCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Bone marrow

value: HSPCs


title: Control treated subcutaneous FL8 allograft tumor #4

value: Tumor allograft

value: Control Carrier


title: KO-Chow-F_302705-5

value: Klf4 KO


title: #2BQ8119 Cerebrospinal fluid


title: Control treated subcutaneous FL8 allograft tumor #2


title: Control-Chow-M_302805-1

value: Brain


title: STINGKO_TL8-3

value: Dual THP-1 Cells

value: Monocyte cell line

value: STING KO

value: DMSO+10ug/mL TL8


title: B41_43_NS01_BX_S63

value: White


title: WT_H151_TL8-3

value: WT


title: B41_62_2_BX_S68

value: Breast


title: WT_H151_2


title: Control treated subcutaneous FL8 allograft tumor #1


title: Control treated subcutaneous FL8 allograft tumor #3


title: WT_DMSO_TL8-3


title: Trmt6 cKO, scRNA-seq

description: 10x Genomics

value: Trmt6fl/fl, MX1-cre


title: AC250 Cerebrospinal fluid

value: Healthy Subject

value: Entire brain and spinal cord

value: total cell-free biofluid RNA


title: Control-HFD-F_303300-1

value: Arcuate nucleus of the hypothalamus

value: Control

value: HFD


title: BQ0422 Cerebrospinal fluid


title: STINGKO_TL8-1


title: AC/BQ265 Cerebrospinal fluid


title: 2BQ0457 Cerebrospinal fluid


title: STINGKO_DMSO-3

value: DMSO


title: AC249 Cerebrospinal fluid


title: WT_H151-3


title: B41_50_B_BX_S66

value: Female

value: Untreated


title: B41_27_A1_BX_S56


title: 2BQ0201 Cerebrospinal fluid


title: AC049 Cerebrospinal fluid


title: STINGKO_DMSO-1

value: Dual THP-1 Cells


title: B41_18_X3_BX_S52


title: WT_H151-2

value: Monocyte cell line


title: BQ258 Cerebrospinal fluid


title: Control-Chow-M_302742-1

value: Brain

value: Chow


title: B41_47_NS01_BX_S56

value: White


title: KO-HFD-F_303264-1

value: Klf4 KO


title: #2BQ6114 Cerebrospinal fluid


title: WT_H151-1

value: WT


title: WT_DMSO-3


title: AC618 Cerebrospinal fluid


title: KO-HFD-F_303262-2


title: BQ11028 Cerebrospinal fluid


title: Vehicle-4

source_name: Cell line

growth_protocol: GT1-7 hypothamic neuronal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin streptomycin with 5% CO2 at 37C

treatment_protocol: GT1-7 cells were transfected with Klf4 siRNA or siRNA scramble in Opti-MEM I and lipofectamine 2000 for 24 hours, vehicle cells were serum starved for 6 hours prior to treatment and then placed in Ca2+ free DMEM with 1% penicillin strepomycin for 1 hour prior to collection

value: Cell line

value: Mouse hypothalamic GnRH neuronal cells

value: Vehicle control

value: Ca2+ free DMEM (vehicle)


title: B41_23_A1_BX_S49

value: Breast


title: BQ9120 Cerebrospinal fluid

value: Healthy Subject

value: Entire brain and spinal cord

value: total cell-free biofluid RNA


title: B41_30_B_BX_S53

value: Female

value: Black


title: Caco2-shP7-8-4

city: Charleston

first: Antonis

last: Kourtidis

state: SC

address: 173 Ashley Avenue

department: Regenerative Medicine and Cell Biology

institute: Medical University of South Carolina

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads (fastq files) were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Secondary analysis was carried out on an OnRamp Bioinformatics Genomics Research Platform (OnRamp Bioinformatics, San Diego, CA). OnRamp’s advanced Genomics Analysis Engine utilized an automated RNAseq workflow to process the data, including data validation and quality control and read alignment to the human genome (hg19) using blastx
The resulting SAM files were sorted and inputted into the Python package HTSeq to generate count data for gene-level differential expression analyses.
Transcript count data from DESeq2 analysis of the samples were sorted according to their adjusted p-value or q-value, which is the smallest false discovery rate (FDR) at which a transcript is called significant.
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited .txt files include DESEQ2 output for each Comparison ...

source_name: colon

growth_protocol: Caco2 colon epithelial cells were cultured in MEM supplemented with 10% FBS, 1 mM sodium pyruvate and 1x non-essential amino-acid supplement.

extract_protocol:
100–200 ng of total RNA was used to prepare RNA-Seq libraries using the TruSeq RNA Sample Prep Kit (Illumina, CA, USA), following the protocol described by the manufacturer. High-throughput sequencing (HTS) was performed using an Illumina HiSeq2500 with each sample sequenced to a minimum depth of ∼ 50 million reads.
To prepare RNA-Seq libraries using the SMART-Seq® v4 RNA-seq kit (Clontech Laboratories, Mountain View, CA), 10 pg–10 ng of total RNA was used following the protocol described by the manufacturer.

treatment_protocol: Caco2 cells were infected with lentiviral vectors carrying non-target (NT) or PLEKHA7-targeting (shP7) shRNAs and seleted (using puromycin) to generate stably expressing populations. Lentiviral shRNAs were derived from the pLKO.1-based TRC1 (Sigma - RNAi consortium) shRNA library (pLKO.1-puro Non-Target shRNA Control: SHC016; shPLEKHA7 #8: TRCN0000146289). Cells were lysed using Trizol (Invitrogen) and total RNA was isolated using the Trizol Plus Total Transcriptome Isolation protocol of the PureLink RNA mini kit (Ambion - Life Technologies)

value: colon

value: shRNA targeting PLEKHA7 (shP7)


title: B41_75_A1_BX_S77

value: Untreated


title: KO-Chow-F_302223-2

value: Brain

value: Arcuate nucleus of the hypothalamus

value: Chow


title: B41_31_A08_BX_S39

value: White


title: WT_H151_TL8-1

value: Dual THP-1 Cells

value: Monocyte cell line

value: WT


title: Caco2-shP7-8-3


title: B41_26_NS01_BX_S55


title: B41_48_A1_BX_S65


title: KO-Chow-M_302932-2

value: Klf4 KO


title: AC/BQ294 Cerebrospinal fluid


title: AC103 Cerebrospinal fluid


title: WT_DMSO_TL8-2

value: DMSO+10ug/mL TL8


title: B41_35_A1_BX_S57

value: Breast


title: BQ/AC0463 Cerebrospinal fluid

value: Healthy Subject

value: Entire brain and spinal cord


title: Vehicle-1

value: Cell line

value: Mouse hypothalamic GnRH neuronal cells

value: Vehicle control

value: Ca2+ free DMEM (vehicle)


title: Control-HFD-F_303262-1

value: Control

value: HFD


title: WT_DMSO_TL8-1


title: B41_36_2_BX_S58

value: Female

value: Untreated


title: BQ6120 Cerebrospinal fluid

value: total cell-free biofluid RNA


title: B41_57_X3_BX_S59

value: White


title: AC/BQ0392 Cerebrospinal fluid


title: Caco2-NT-4

value: colon

value: non-target (NT) shRNA


title: 2BQ0293 Cerebrospinal fluid


title: AC0024 Cerebrospinal fluid


title: Control-HFD-M_303239-3

value: Brain

value: Arcuate nucleus of the hypothalamus


title: Scramble-3

value: Scramble control

value: Scramble


title: B41_46_A1_BX_S64

value: Breast


title: Scramble-2

value: Cell line


title: Control-HFD-M_303239-2


title: Oct4-pull-down replicate 4

city: Gif-sur-yvette

first: Matthieu

last: Gerard

address: Route Nationale

country: France

institute: CEA

description: Unfixed chromatin prepared from mESCs expressing a tagged-histone H3.3 was immunopurified with anti-HA-agarose-beads and centrifugated through a sucrose gradient. The low sedimentation fractions, containing the purified native 50-80 bp subnucleosomes, were incubated with tagged-OCT4 immobilized onto agarose beads. After several washes, the potential OCT4-subnucleosome complexes were eluted by TEV protease cleavage. DNA was extracted from the eluted fraction and deep-sequenced.

data_processing:
Cleaning with fastp=0.20.1, parameters: --length_required 25 --detect_adapter_for_pe --cut_front --cut_tail --cut_window_size 6 --cut_mean_quality 10 --unqualified_percent_limit 40 --n_base_limit 7 --average_qual 0 –overrepresentation_analysis --trim_poly_g
Alignment with bowtie2=2.4.2, default parameters
Marking duplicates reads with picard=2.23.8, parameters: CREATE_INDEX=true VALIDATION_STRINGENCY=STRICT
Filtring with samtools=1.11, parameters: -h -f 1 -F 3852 -q 30
Coverage with deeptools=3.5.0 (for the blacklist : http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm9-mouse/mm9-blacklist.bed.gz), parameters: bamCoverage --outFileFormat bigwig --binSize 1 --numberOfProcessors 5 --effectiveGenomeSize 2652783500 --normalizeUsing RPKM --MNase --minFragmentLength 10 --extendReads --centerReads --maxFragmentLength 500 --ignoreForNormalization chrX chrY chrM --blackListFileName mm9-blacklist.bed.gz
Assembly: mm9
Supplementary files format and content: bigWig

growth_protocol: Mus musculus ES cells were grown on mitomycin C-inactivated  Mus musculus embryonic fibroblasts at 37 °C, 5 % CO2, in DMEM (Sigma) supplemented by leukaemia inhibitory factor (LIF), 1X non-essential amino acids (Invitrogen), 15 % foetal calf serum (Invitrogen), 0.2 % β-mercaptoethanol (Sigma) and 1X penicillin/streptomycin (Invitrogen).

extract_protocol:
Chromatin preparation: ES cells were collected and fixed in D15 culture medium containing 1 % formaldehyde (Sigma) for 10 min at 20°C. We stopped fixation by adding glycine to 125 mM, and the cells were centrifugated and washed three times with PBS. Cells were then permeabilized in Tris-HCl pH 7.5 15 mM, NaCl 15 mM, MgCl2 5 mM, EGTA 0.1 mM, KCl 60 mM, Sucrose 0.3 M, 0.4% IGEPAL CA-630 (I3021, Sigma) during 15 min on ice. We next diluted the cells with two volumes of MNase buffer (Tris-HCl pH 7.5 20 mM, NaCl 20 mM, CaCl2 2 mM, MgCl2 4 mM, KCl 15 mM, 0.1 M sucrose), and chromatin was digested during 10 min at 37 °C with 6 Kunitz units of MNase (New England Biolabs, 200 Kunitz units/µl) per 1 million cells. We stopped MNase digestion by adding a final concentration of 10 mM EDTA. We released chromatin from MNase-treated ES cells by passing the cell suspension 13 times through a 26G syringe. Next, we centrifuged the samples, and the supernatants containing the solubilized chromatin were used directly for ChIP-seq experiments or sucrose gradient centrifugation.
DNA libraries were prepared using MicroPlex Library Preparation Kit v2 or v3 (Diagenode)

treatment_protocol: untreated

value: embryonic stem cells

tag: strain

tag: chip antibody


title: B41_29_A1_BX_S38


title: Caco2-NT-1


title: Oct4-pull-down replicate 2


title: B41_37_A1_BX_S59


title: B41_15_A1_BX_S50


title: B41_24_NS01_BX_S50


title: KO-HFD-M_303240-1

value: Klf4 KO


title: BQ8104 Cerebrospinal fluid

value: Healthy Subject

value: Entire brain and spinal cord


title: BQ211 Cerebrospinal fluid


title: Oct4-pull-down replicate 1


title: WT_DMSO-1

value: Dual THP-1 Cells

value: Monocyte cell line

value: WT

value: DMSO


title: B41_25_1_BX_S54

value: Female

value: White

value: Untreated


title: B41_67_A1_BX_S72


title: Klf4-siRNA-1

value: Mouse hypothalamic GnRH neuronal cells

value: siRNA

value: Klf4 siRNA


title: Vehicle-3

value: Vehicle control

value: Ca2+ free DMEM (vehicle)


title: Histone H3.3-TAG MNase N-ChIP-seq low sedimentation rate (5-6) replicate 4

description: ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of low sedimentation rate fractions (pool of fractions 5, 6) was performed.

value: anti-HA epitope (sigma clone HA-7)


title: Klf4-siRNA-2

value: Cell line


title: WT_DMSO-2


title: KO mouse [Polysome RNA RNA-seq]

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data were trimmed with trimmomatic and then were filtered out any reads could map to rRNA (Genebank: BK000964.3) using SortMeRNA (2.1b)
Clean data were aligned to the mouse reference genome GRCm38 by HISAT2 (2.1.0) with default setting.
Genes counts were quantified by HTSeq (0.11.2)[9] with parameter “--mode intersection-strict --stranded no --minaqual 1”.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files with raw gene counts for every gene and every sample

source_name: bone marrow cells

extract_protocol: WT/KO BM cells (4× 107) were incubated with 100 μg/ml of cycloheximide(Cell Signaling Technology) for 10 minutes at 37°C, washed with cold PBS containing100 μg/ml of cycloheximideand lysed as 50 mM HEPES, 2mM MgCl2, 100 mM KCl, 1% Triton X-100, 1mM DTT, 100 μg/ml cycloheximide, 20U/ml RNase Inhibitor(EDTA free) and 1× Complete Protease Inhibitor, EDTA-free (Roche). Polysomal RNA was separated on 10.5mL 10%-50% linear sucrose gradients containing 10mM Tris-HCl (pH 7.5), 5mM MgCl2, and 100mM NaCl, and centrifuged in a SW41 rotor at 38,000rpm for 3 hours. Gradients were then measured of absorbance at 254 nm and fractionated using a Gradient Station fractionator.

value: bone marrow

value: Mat KO


title: Histone H3.3-TAG MNase N-ChIP-seq low sedimentation rate (5-6) replicate 3

value: embryonic stem cells


title: B41_22_NS01_BX_S53

value: Breast


title: Vehicle-2


title: Histone H3.3-TAG MNase N-ChIP-seq low sedimentation rate (5-6) replicate 2


title: B41_40_B_BX_S54


title: WT mouse rep1 [Polysome RNA RNA-seq]

value: wildtype


title: Caco2-shP7-8-1

value: colon

value: shRNA targeting PLEKHA7 (shP7)


title: B41_56_A1_BX_S67

value: Female


title: B41_51_A_BX_S57

value: White


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) Oct4-depleted ZHBTc4 replicate2

value: treated with DOX for 20 hours

value: histone H3 (Abcam ab1791)


title: Scramble-4

value: Mouse hypothalamic GnRH neuronal cells

value: Scramble control

value: Scramble


title: B41_69_E_BX_S73

value: Unknown

value: Untreated


title: Caco2-NT-3

value: non-target (NT) shRNA


title: AC\BQ0264 Cerebrospinal fluid

value: Healthy Subject

value: Entire brain and spinal cord

value: total cell-free biofluid RNA


title: B41_16_1_BX_S51

value: Breast


title: Scramble-1

value: Cell line


title: AC167 Cerebrospinal fluid


title: CT20_SD-2_Kidney

city: Shanghai

first: Renrui

last: Chen

address: No. 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (parameter:--phred33 --length 50 --stringency 3 --paired)
Trimmed sequence reads were mapped to GrCM38/mm10 using  HISAT2 (parameters-  -t -p 8 --dta --rna-strandness RF)
Read count extraction and normalization were performed using Samtools (parameters view -b -q 60) and featureCounts(parameters -T 16 -p -s 2)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Kidney

extract_protocol:
We extracted total RNA from tissue samples using Trizol (Invitrogen). After separating the RNA, DNA, and protein layers with chloroform, we precipitated the RNA using a standard isopropanol/ethanol procedure. The resulting RNA pellet was washed, and then resuspended in RNase-free water.
We assessed the quantity and quality of the total RNA using the Qubit RNA HS Assay (Life Technologies) and RNA 6000 Nano Assay on a Bioanalyzer 2100 (Agilent). For RNA-seq library construction, we followed the Illumina TruSeq Total RNA stranded protocol.

value: Kidney

value: WT

value: control

tag: time point


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) Control ZHBTc4 replicate2

description: ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of low sedimentation rate fractions (pool of fractions 2, 3, 4) was performed.

value: embryonic stem cells


title: Gastruloid

city: San Francisco

first: Chang

last: Kim

address: 505 Parnassus Ave

institute: UCSF

data_processing:
cellranger mkfastq to generate fastqs
cellranger-6.0.0 count
Assembly: hg38
Supplementary files format and content: Filtered matrix output of cellranger count

molecule: polyA RNA

source_name: ipsc

extract_protocol:
Gastruloids were dissociated into single cell suspensions and loaded on the 10x Chromium controller
Library construction was done according to the 10X Genomics V3.1 3' protocol

value: ipsc


title: B41_63_A_BX_S60

value: Female

value: White


title: B41_19_15_BX_S37


title: Oct4-pull-down replicate 3


title: BQ11002 Cerebrospinal fluid


title: CT20_SD-1_Kidney


title: Klf4-siRNA-3

value: Mouse hypothalamic GnRH neuronal cells

value: siRNA

value: Klf4 siRNA


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) Control ZHBTc4 replicate1

value: Untreated

value: histone H3 (Abcam ab1791)


title: HepG2_8_SP2509_H3K27ac_CUTTAG

first: Boshi

address: No.800 Dongchuan Road

institute: Shanghai Cancer Institute

data_processing:
The sequencing reads obtained from the Illumina platform were subjected to quality control using FastQC (v0.11.9) to assess the quality of the reads.
Adapter trimming and read filtering were performed using Trim-galore (0.6.5-1).
The filtered reads were then aligned to the human genome (UCSC hg38) using Bowtie2 version 2.2.6 with parameters.
The aligned reads were processed by MACS2 (v2.2.7.1) to call peaks and transformed to bigwig formatted files by bamCoverage function in Deeptools (v3.5.1) with default parameters.
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: liver

extract_protocol:
The CUT&Tag experiments were performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech Co., Ltd., TD903) according to the manufacturer’s instructions.
The library was constructed by TruePrep® Index Kit V2 for Illumina kit and PCR amplification

value: liver

value: HCC

tag: cut&tag antibody

value: H3K27ac ab4729 Abcam


title: Klf4-siRNA-4


title: CT16_SD-2_Kidney


title: BQ0497 Cerebrospinal fluid

value: Healthy Subject

value: Entire brain and spinal cord

value: total cell-free biofluid RNA


title: BQ/2AC0245 Cerebrospinal fluid


title: HepG2_7_ctr_H3K27ac_CUTTAG

value: Control


title: B41_70_B1_BX_S74

value: Breast


title: Sox2 (sc-17320) MNase ChIP-seq low sedimentation rate (5-6) replicate 2

value: embryonic stem cells

value: Sox2 (Santa Cruz Biotechnology sc-17320)


title: BQ8123 Cerebrospinal fluid


title: Sox2 (sc-17320) MNase ChIP-seq low sedimentation rate (5-6) replicate 1


title: WT mouse rep2 [Polysome RNA RNA-seq]

value: bone marrow

value: wildtype


title: AC094 Cerebrospinal fluid


title: Histone H3.3-TAG MNase N-ChIP-seq low sedimentation rate (5-6) replicate 1

value: anti-HA epitope (sigma clone HA-7)


title: CT24_SD-2_Kidney

value: Kidney

value: WT

value: Sleep deprivation


title: BQ11045 Cerebrospinal fluid


title: HepG2_3_ctr_H3K4me2_CUTTAG

value: H3K4me2 ab32356 Abcam


title: AC085 Cerebrospinal fluid


title: CT24_SD-1_Kidney


title: SimB11137 Cerebrospinal fluid


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) Oct4-depleted ZHBTc4 replicate1

value: treated with DOX for 20 hours

value: histone H3 (Abcam ab1791)


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6-7) replicate 1

description: ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of low sedimentation rate fractions (pool of fractions 5, 6, 7) was performed.

value: treated with auxin for 20 hours

value: Oct4 (Santa Cruz Biotechnology sc-5279)


title: SimB11199-05/29/12 Cerebrospinal fluid

value: Healthy Subject

value: Entire brain and spinal cord


title: CCT068127-D3

city: WEST LAFAYETTE

first: Majid

last: Kazemian

state: IN

address: 201 S. University Street

department: Biochemistry and Computer Science

institute: Purdue University

description:
all_sample_read_count.txt
all_sample_tpm.txt

data_processing:
Sequence reads were aligned to hg38 using rsem with parameters: rsem-calculate-expression --bowtie-n 1 --bowtie-m 100 --seed-length 28 --bowtie-chunkmbs 1000
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw read count for each sample
Supplementary files format and content: tab-delimited text files include TPM for each sample

source_name: T-24, Human urinary bladder cancer cell line

extract_protocol:
RNA isolation: T-24 cells (approximately 1x106 per well) were seeded in a 6 well plate. Next day, cells were treated with either vehicle (DMSO) control or CCT068127 at 1micro molar concentration for 48 hours. Cells were stored with TRI Reagent (ZYMO Research International, Tustin, CA) at -80 freezer. Genomic RNA was extracted from cells using a Direct-zol RNA MiniPrep Plus (ZYMO Research International, Tustin, CA).
500 ng total RNA for each sample was subjected to NEBNext Poly(A) mRNA Magnetic Isolation (E7490) and resulting mRNA libraries were prepared for RNA-seq by NEB Ultra II kit (New England Biolabs) following manufacturer's protocols and sequenced by NovaSeq (Illumina).

value: Epithelial adherant cell

value: CCT068127 treated

tag: treatment duration

value: 48 hours


title: SimB11198-06/11/12 Cerebrospinal fluid

value: total cell-free biofluid RNA


title: CT4_SD-2_Kidney

value: control


title: B41_66_NS01_BX_S71

value: Breast

value: Female

value: White

value: Untreated


title: SimB11172-12/27/11 Cerebrospinal fluid


title: Sox2 (sc-17320) MNase ChIP-seq low sedimentation rate (2-3-4) replicate 2

value: embryonic stem cells

value: Sox2 (Santa Cruz Biotechnology sc-17320)


title: TBI478-01/08/15 Cerebrospinal fluid


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6-7) - Smarca4-depleted auxin 20h replicate 1


title: CT16_SD-1_Kidney

value: Kidney

value: WT


title: HepG2_6_SP2509_H3K9me2_CUTTAG

value: liver

value: HCC

value: H3K9me2 ab1220 Abcam


title: TBI11268-12/22/15 Cerebrospinal fluid

value: Healthy Subject

value: Entire brain and spinal cord


title: CT12_SD-2_Kidney


title: HepG2_5_ctr_H3K9me2_CUTTAG

value: Control


title: Sox2 (sc-17320) MNase ChIP-seq low sedimentation rate (2-3-4) replicate 1


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6-7) - Brd9-depleted auxin 20h replicate 2

value: treated with auxin for 20 hours

value: Oct4 (Santa Cruz Biotechnology sc-5279)


title: DMSO-D3

value: T-24, Human urinary bladder cancer cell line

value: Epithelial adherant cell

value: DMSO

value: 48 hours


title: SimB11103 Cerebrospinal fluid

value: total cell-free biofluid RNA


title: CT12_SD-1_Kidney

value: control


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6-7) - Brd9-depleted auxin 20h replicate 1

value: embryonic stem cells


title: CT20_CON-2_Kidney

value: Kidney


title: DMSO-D1

value: WT


title: HepG2_4_SP2509_H3K4me2_CUTTAG

value: liver

value: H3K4me2 ab32356 Abcam


title: SimB11201-07/30/12 Cerebrospinal fluid


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6-7) - Pbrm1-depleted auxin 20h replicate 1


title: TBI11231 Cerebrospinal fluid


title: E753-S: Patient 105 HTS

first: James

middle: William

last: MacDonald

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

data_processing:
Our processing pipeline consists of the following elements: (1) base calls generated in real-time on the NovaSeq6000 instrument (RTA 3.1.5); (2) demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4); (3) sequence read and base quality are checked using the FASTX-toolkit (v0.0.13); (4) sequences are aligned to GRCh38 with reference transcriptome GENCODE release 26 (GRCh38.p10) using STAR (v2.5.3a).
Counts per gene were generated using the Bioconductor Rsubread package version 1.32.4, using the inbuilt hg38 gene annotations
Genes were filtered using the Bioconductor edgeR package version 3.24.3, using the filterByExpr function to remove unexpressed or unreliable genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table containing raw gene counts per sample. Column names correspond to the raw file names and the row names correspond to the NCBI Gene ID

source_name: Skin

extract_protocol:
RNA was isolated from 108 human samples comprising of uninjured skin (n=26), acute burn wounds (n=54), and hypertrophic scars (HTS) (n=30). Frozen tissue was pulverized using mortar and pestle in liquid nitrogen to maintain temperature during processing. Total RNA, including small RNAs such as microRNAs, non-coding RNA, messenger RNA, and ribosomal RNA was isolated using the MagMAX™ mirVana™ Total RNA Isolation Kit (Applied Biosystems) followed by DNAse digestion on Purelink RNA mini kit spin columns (Thermo Fisher Scientific).
Total RNA is normalized to 7.5ng/ul in a total volume of 50ul on the Perkin Elmer Janus Workstation (Perkin Elmer, Janus II). Poly-A selection and cDNA synthesis are performed using the TruSeq Stranded mRNA kit as outlined by the manufacturer (Illumina, cat#RS-122-2103). All steps are automated on the Perkin Elmer Sciclone NGSx Workstation to reduce batch to batch variability and to increase sample throughput. Final RNASeq libraries are quantified using the Quant-it dsDNA High Sensitivity assay, and library insert size distribution is checked using a fragment analyzer (Advanced Analytical; kit ID DNF474). Samples where adapter dimers constitute more than 4% of the electropherogram area are failed prior to sequencing. Technical controls (K562,Thermo Fisher Scientific, cat# AM7832), are compared to expected results to ensure that batch to batch variability is minimized. Successful libraries are normalized to 10nM for submission to sequencing.

treatment_protocol: Samples were collected from patients admitted to the UW Medicine Regional Burn Center and undergoing an operation for burn injury from 2002 to 2018. Samples consisted of discarded burn wounds, scars, and donor skin that were stored as part of an IRB exempt human tissue repository. All samples were de-identified upon collection. Specific to the wound samples, when able, samples were collected at periphery of the burn wound to include the epithelial edge where the transition from wound to normal tissue exists as previously described.[8] Tissue samples were minced and placed in cryogenic vials for either snap freezing in liquid nitrogen within 20 minutes of collection or placement in RNALater (Invitrogen, Carlsbad, CA) and stored in 4°C overnight to allow the solution to penetrate the tissue. All samples were transferred to -80°C for long term storage.

tag: subject

value: Patient 105

value: Skin

tag: wound type

value: HTS

tag: days since injury

tag: age

value: female

tag: hispanic

value: unknown

value: asian

tag: burn type

value: scar

tag: location

value: ear


title: CT8_SD-2_Kidney

tag: tissue

tag: treatment


title: SimB11151-08/25/11 Cerebrospinal fluid

tag: condition

value: Healthy Subject

tag: anatomical location

value: Entire brain and spinal cord

tag: rna source


title: TBI11266-07/31/14 Cerebrospinal fluid

value: total cell-free biofluid RNA


title: CT16_CON-2_Kidney

tag: strain

tag: genotype

value: control


title: CCT068127-D2

tag: cell line

value: T-24, Human urinary bladder cancer cell line

tag: cell type

value: Epithelial adherant cell

value: CCT068127 treated

value: 48 hours


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6-7) - Smarca4-depleted auxin 20h replicate 2

value: embryonic stem cells

value: treated with auxin for 20 hours

tag: chip antibody

value: Oct4 (Santa Cruz Biotechnology sc-5279)


title: E752-S: Patient 105 HTS

tag: subject

value: Patient 105

value: Skin

value: HTS

tag: Sex

tag: race

value: sternum


title: CT8_SD-1_Kidney

value: Kidney

value: WT

tag: time point


title: SimB381 Cerebrospinal fluid

value: Healthy Subject


title: CCT068127-D1

tag: treatment duration


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6-7) - Brd7-depleted auxin 20h replicate 1


title: TBI11178-03/13/12 Cerebrospinal fluid

value: Entire brain and spinal cord


title: SimB11171-12/22/11 Cerebrospinal fluid

value: total cell-free biofluid RNA


title: E746-S: Patient 106 HTS

value: Patient 106

tag: wound type

tag: days since injury

tag: age

value: male

tag: hispanic

value: unknown

value: white

tag: burn type

value: scar


title: TBI11149-02/23/15 Cerebrospinal fluid

tag: condition

tag: anatomical location


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6-7) - Arid1a-depleted auxin 20h replicate 2

value: embryonic stem cells

tag: treatment

tag: strain


title: CT4_SD-1_Kidney

tag: tissue

tag: genotype

value: control


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6-7) - Pbrm1-depleted auxin 20h replicate 2

tag: cell line

tag: cell type

value: treated with auxin for 20 hours

tag: chip antibody

value: Oct4 (Santa Cruz Biotechnology sc-5279)


title: CT24_CON-1_Kidney


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6-7) - Arid1a-depleted auxin 20h replicate 1


title: E742-S: Patient 104 HTS

tag: subject

value: Patient 104

value: Skin

tag: Sex

tag: race

tag: location

value: neck


title: DMSO-D2

value: T-24, Human urinary bladder cancer cell line

value: Epithelial adherant cell

value: DMSO

tag: treatment duration

value: 48 hours


title: CT24_CON-2_Kidney

value: Kidney

value: WT

tag: time point


title: CT20_CON-1_Kidney


title: TBI11208 Cerebrospinal fluid

value: Healthy Subject

value: Entire brain and spinal cord

tag: rna source

value: total cell-free biofluid RNA


title: E741-S: Patient 103 HTS

value: Patient 103

tag: wound type

value: HTS

tag: days since injury

tag: age

value: female

tag: hispanic

value: unknown

value: white

tag: burn type

value: scar

value: upper extremity


title: SimB11125 Cerebrospinal fluid

tag: condition

tag: anatomical location


title: SimB11160-10/17/11 Cerebrospinal fluid


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6-7) - Brd7-depleted auxin 20h replicate 2

tag: cell line

value: embryonic stem cells

tag: treatment

value: treated with auxin for 20 hours

tag: strain

value: Oct4 (Santa Cruz Biotechnology sc-5279)


title: CT16_CON-1_Kidney

tag: tissue

tag: genotype

value: control


title: E751-S: Patient 105 HTS

tag: subject

value: Patient 105

value: Skin

tag: Sex

tag: race

value: asian

value: face


title: E738-S: Patient 102 HTS

value: Patient 102

value: male

tag: location


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6-7) - Smarcb1-depleted auxin 20h replicate 1

tag: cell type

tag: chip antibody


title: SimB400 Cerebrospinal fluid

value: Healthy Subject

value: Entire brain and spinal cord

tag: rna source

value: total cell-free biofluid RNA


title: SimB11144 Cerebrospinal fluid


title: E735-S: Patient 100 HTS

value: Patient 100

tag: wound type

value: HTS

tag: days since injury

tag: age

value: unknown


title: SimB11224 Cerebrospinal fluid

tag: condition


title: CT12_CON-2_Kidney

value: Kidney

value: WT

tag: time point


title: CT12_CON-1_Kidney


title: CT24_SD-2_Liver

source_name: Liver

value: Liver

value: Sleep deprivation


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6-7) replicate 2

tag: cell line

value: embryonic stem cells

value: treated with auxin for 20 hours

value: Oct4 (Santa Cruz Biotechnology sc-5279)


title: TBI11283 Cerebrospinal fluid

tag: anatomical location


title: E733-S: Patient 99 HTS

value: Patient 99

value: Skin

tag: hispanic

value: white

tag: burn type

value: scar

value: lower extremity


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) replicate 5

description: ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed.

tag: treatment

tag: strain

value: histone H3 (Abcam ab1791)


title: CT24_SD-1_Liver

tag: tissue

tag: genotype


title: SimB11140-08/04/11 Cerebrospinal fluid

value: Healthy Subject

value: Entire brain and spinal cord

value: total cell-free biofluid RNA


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) - Brd9-depleted auxin 20h replicate 2


title: SimB11157-10/13/11 Cerebrospinal fluid


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6-7) - Smarcb1-depleted auxin 20h replicate 2


title: E731-S: Patient 98 HTS

tag: subject

value: Patient 98

value: HTS

tag: Sex

value: female

value: unknown

tag: race

tag: location


title: SimB11100 Cerebrospinal fluid

tag: rna source


title: E728-W: Patient 97 Late wound

value: Patient 97

tag: wound type

value: Late wound

tag: days since injury

value: wound

value: abdomen


title: SimB11230 Cerebrospinal fluid

tag: condition


title: E725-S: Patient 96 HTS

value: Patient 96

tag: age

value: male

value: sternum


title: CT4_CON-2_Kidney

value: Kidney

value: WT

value: control

tag: time point


title: E736-S: Patient 101 HTS

value: Patient 101

value: Skin

value: black

value: scar

value: upper extremity


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) – PBRM1-depleted auxin 20h replicate 2

tag: cell line

tag: cell type

value: embryonic stem cells

value: treated with auxin for 20 hours

tag: chip antibody

value: histone H3 (Abcam ab1791)


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) replicate 6

tag: treatment


title: CT4_CON-1_Kidney

tag: strain


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) - Brd9-depleted auxin 20h replicate 1


title: CT8_CON-2_Kidney

tag: tissue


title: CT12_SD-2_Liver

value: Liver

tag: genotype

value: Sleep deprivation


title: E717-S: Patient 94 HTS

tag: subject

value: Patient 94

value: HTS

tag: hispanic

value: unknown

tag: burn type

value: hand


title: CT20_SD-2_Liver


title: SimB11174-01/11/12 Cerebrospinal fluid

value: Healthy Subject

tag: anatomical location

value: Entire brain and spinal cord

value: total cell-free biofluid RNA


title: SimB268 Cerebrospinal fluid

tag: rna source


title: CT12_SD-1_Liver

value: WT


title: CT8_CON-1_Kidney

value: Kidney

value: control


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) – BRD7-depleted auxin 20h replicate 2


title: CT20_SD-1_Liver


title: E722-S: Patient 95 HTS

value: Patient 95

value: Skin

tag: wound type

tag: Sex

value: female

tag: race

value: asian

value: scar

tag: location


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) – BRD7-depleted auxin 20h replicate 1

value: embryonic stem cells

value: treated with auxin for 20 hours

value: histone H3 (Abcam ab1791)


title: SimB11209 Cerebrospinal fluid

tag: condition


title: E724-D: Patient 96 Normal skin

value: Patient 96

value: Normal skin

tag: days since injury

tag: age

value: male

value: white

value: uninjured

value: back


title: CT16_SD-2_Liver

value: Liver

value: WT

value: Sleep deprivation

tag: time point


title: SimB11240 Cerebrospinal fluid

value: Healthy Subject

value: Entire brain and spinal cord

value: total cell-free biofluid RNA


title: CT16_SD-1_Liver

tag: treatment


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) - Arid1a-depleted auxin 20h replicate 2

tag: cell line

tag: cell type

tag: strain

tag: chip antibody


title: E714-S: Patient 92 HTS

tag: subject

value: Patient 92

tag: tissue

value: Skin

value: HTS

tag: hispanic

value: unknown

value: neck


title: CT8_SD-2_Liver

tag: genotype


title: CT8_SD-1_Liver


title: SimB11263 Cerebrospinal fluid

tag: anatomical location

tag: rna source


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) – PBRM1-depleted auxin 20h replicate 1

value: embryonic stem cells

value: treated with auxin for 20 hours

value: histone H3 (Abcam ab1791)


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) - Arid1a-depleted auxin 20h replicate 1


title: E711-S: Patient 90 HTS

value: Patient 90

tag: wound type

tag: Sex

value: male

value: yes

tag: race

tag: burn type

value: scar

value: sternum


title: E716-S: Patient 93 HTS

value: Patient 93

tag: days since injury

tag: age

value: white

tag: location


title: E710-W: Patient 89 Late wound

value: Patient 89

value: Late wound

value: native american

value: wound

value: lower extremity


title: SimB11175-01/12/12 Cerebrospinal fluid

tag: condition

value: Healthy Subject

value: Entire brain and spinal cord

value: total cell-free biofluid RNA


title: CT4_SD-1_Liver

value: Liver

value: WT

tag: treatment

value: Sleep deprivation

tag: time point


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) - Smarcb1-depleted auxin 20h replicate 2

tag: cell line

tag: cell type

value: embryonic stem cells

value: treated with auxin for 20 hours

tag: strain

tag: chip antibody

value: histone H3 (Abcam ab1791)


title: E708-W: Patient 88 Late wound

tag: subject

value: Patient 88

tag: tissue

value: Skin

value: male

tag: hispanic

value: unknown

value: sternum


title: CT4_SD-2_Liver

tag: genotype


title: SimB11130 Cerebrospinal fluid

tag: anatomical location

tag: rna source


title: TBI11180-03/15/12 Cerebrospinal fluid


title: E707-W: Patient 87 Late wound

value: Patient 87

tag: wound type

value: Late wound

tag: Sex

tag: race

value: native american

tag: burn type


title: DRGs_PGE2_Treated_3

city: Austin

first: Husniye

last: Kantarci

state: TX

address: NHB Building,, 100 E 24TH ST, Room 4.358

department: Neuroscience

institute: UT Austin

data_processing:
Sequenced reads were aligned to the rat reference genome (Rnor_6.0) using Geneious Prime 2021.0.1 (https://www.geneious.com).
Assembly: Rnor 6.0
Supplementary files format and content: Excel file includes FPKM values for each sample

organism: Rattus norvegicus

source_name: Dorsal Root Ganglion

extract_protocol:
Total RNA from DIV14 immunopanned DRG neurons (untreated [n=3], SCCM [n=4] or PGE2 [n=4] treated) was purified using RNeasy Plus mini kit (Cat # 74134). Genomic DNA was eliminated using eliminator spin columns provided by the manufacturer. RNA quality and quantity were assessed using Agilent 2100 Bioanalyzer system, samples with high RNA integrity numbers (>8) were used for further analysis.
KAPA/Roche Stranded mRNA-Seq kit KK8420 (Cat # 07962193001) was used to prepare poly-A enriched mRNA libraries.

value: Dorsal Root Ganglion

value: Sprague-Dawley

value: Dorsal root ganglion neurons

value: wild type

value: 1 microM PGE2


title: CT24_CON-1_Liver

value: Liver

value: WT

value: control


title: SimB11153-08/30/11 Cerebrospinal fluid

tag: condition

value: Healthy Subject

value: Entire brain and spinal cord

value: total cell-free biofluid RNA


title: SimB11127 Cerebrospinal fluid


title: CT24_CON-2_Liver

tag: treatment


title: DRGs_PGE2_Treated_2


title: E706-S: Patient 86 HTS

value: Patient 86

value: Skin

value: HTS

tag: days since injury

tag: age

value: male

value: scar

tag: location

value: neck


title: DRGs_SCCM_Treated_3

value: Dorsal Root Ganglion

tag: strain

tag: cell type

value: Schwann cell conditioned media


title: Histone H3 MNase ChIP-seq low sedimentation rate (5-6) - Smarcb1-depleted auxin 20h replicate 1

tag: cell line

value: embryonic stem cells

value: treated with auxin for 20 hours

tag: chip antibody

value: histone H3 (Abcam ab1791)


title: SimB11272 Cerebrospinal fluid


title: 88-W: Patient 83 Early Wound

tag: subject

value: Patient 83

tag: tissue

value: Early Wound

value: female

tag: hispanic

value: unknown

value: flame

value: wound

value: shoulder


title: DRGs_PGE2_Treated_1

value: Sprague-Dawley

value: Dorsal root ganglion neurons

tag: genotype

value: wild type

value: 1 microM PGE2


title: SimB11204-07/10/12 Cerebrospinal fluid

value: Healthy Subject

tag: anatomical location

value: Entire brain and spinal cord

tag: rna source

value: total cell-free biofluid RNA


title: CT20_CON-2_Liver

value: Liver

value: WT

value: control

tag: time point


title: CT16_CON-2_Liver


title: SimB11143 Cerebrospinal fluid


title: 87-W: Patient 84 Chronic wound

value: Patient 84

value: Skin

tag: wound type

value: Chronic wound

tag: Sex

value: no

tag: race

value: white

tag: burn type

value: back


title: E705-S: Patient 85 HTS

value: Patient 85

value: HTS

tag: days since injury

tag: age

value: female

value: unknown

value: asian

value: scar

value: lower extremity


title: TBI11206-07/31/12 Cerebrospinal fluid

tag: condition

value: Healthy Subject

value: Entire brain and spinal cord

value: total cell-free biofluid RNA


title: CT20_CON-1_Liver

value: Liver

tag: strain

value: WT

tag: treatment

value: control


title: DRGs_SCCM_Treated_2

value: Dorsal Root Ganglion

value: Sprague-Dawley

tag: cell type

value: Dorsal root ganglion neurons

value: wild type

value: Schwann cell conditioned media


title: DRGs_PGE2_Treated_4

value: 1 microM PGE2


title: DRGs_SCCM_Treated_1


title: DRGs_SCCM_Treated_4


title: TBI11288-08/05/14 Cerebrospinal fluid


title: 87-D: Patient 84 Normal skin

tag: subject

value: Patient 84

value: Skin

value: Normal skin

value: female

value: no

value: white

value: flame

value: uninjured

tag: location


title: SimB11139 Cerebrospinal fluid

value: Healthy Subject

value: Entire brain and spinal cord

value: total cell-free biofluid RNA


title: DRGs_Untreated_3

tag: tissue

value: Dorsal Root Ganglion

value: No Treatment


title: 85-W1: Patient 82 Early Wound

value: Patient 82

value: Early Wound

tag: hispanic

value: unknown

value: wound

value: shoulder


title: CT12_CON-1_Liver

value: Liver

tag: genotype

value: WT

value: control


title: CT12_CON-2_Liver


title: SimB11164-11/15/11 Cerebrospinal fluid

tag: anatomical location

tag: rna source


title: 84-S: Patient 81 HTS

value: Patient 81

value: Skin

tag: wound type

value: HTS

value: male

value: no

value: contact

value: scar

value: lower extremity


title: 83-WE3: Patient 80 Late wound

value: Patient 80

value: Late wound

tag: Sex

value: female

value: black

value: flame


title: DRGs_Untreated_2

value: Dorsal Root Ganglion

value: Sprague-Dawley

value: Dorsal root ganglion neurons

value: wild type

value: No Treatment


title: SimB11173-01/24/12 Cerebrospinal fluid

value: Healthy Subject

value: Entire brain and spinal cord

value: total cell-free biofluid RNA


title: ZKC_S2_Ptges3 cKO p4

description: 10 X genomics

data_processing:
Initial gene expression tables for barcodes were generated using CellRanger version 5.0.1 (10X genomics) using default parameters. Gene expression tables were than imported to Phyton and analyzed using Scanpy using scanpy tutorials.
Assembly: mm10-2020-A
Supplementary files format and content: tab seperated matrix files

source_name: Dorsal root ganglia

extract_protocol:
DRG ganglia from all axial levels were dissected from Ptges3-Flox or Ptges3-cKO mice at P4 postnatal stage and placed in Neurobasal medium supplemented with 12.5 mM D-glucose and 100 U/mL +penicillin and 0.1 mg/mL streptomycin [GibcoTM, 15140122]). Next, dissected DRG ganglia were placed in a collagenase/dispase cocktail composed of 1 mg/mL collagenase (Roche, 10103578001), 2.9 mg/mL dispase (Roche, 101103578001), 40 U of papain (Worthington LS003126), 100  µl DNAse (0.02 mg/mL) in 1X HEPES buffered saline solution (Sigma-Aldrich, 51558) and placed in 37 C for 20 minutes. DRG ganglia were dissociated in Lo-ovomucoid inhibitor solution in PBS. Cells were counter-stained with trypan blue counted under a hemocytometer to assess cell density and health (cell viability was measured as greater than 92%), and subsequently resuspended in Neurobasal medium supplemented with 12.5 mM D-glucose and 100 U/mL +penicillin and 0.1 mg/mL streptomycin [GibcoTM, 15140122]) as 1000 cells per  µl.
Libraries were prepared using the Single Cell 3ʹ v.3.1 according to the manufacturer’s protocol (10x Genomics), targeting 10,000 cells per sample. 12 cycles of cDNA amplification were done for all samples. Individual libraries were quality checked on an Agilent 4200 Tapestation 827 using D5000 screen tape. Next, KAPA library quantification kit (#KK4923) was used for qPCR on a BioRad CFX96 RT PCR thermal cycler.

value: Dorsal root ganglia

value: Dorsal root ganglion cells

value: Dhh CRE+, Ptges3 flox/flox


title: CT8_CON-2_Liver

value: Liver

value: WT

value: control

tag: time point


title: SimB11192-05/02/12 Cerebrospinal fluid


title: DRGs_Untreated_1


title: 83-W3: Patient 80 Late wound

value: Patient 80

value: Skin

value: Late wound

value: female

value: no

tag: race

tag: burn type

value: wound

value: lower extremity


title: CT8_CON-1_Liver


title: CT16_CON-1_Liver


title: SimB11201-07/30/12 Plasma

source_name: Plasma

value: Entire cardiovascular system

tag: rna isolation kit

value: Homebrew Kit


title: 81-D: Patient 78 Normal skin

value: Patient 78

value: Normal skin

tag: days since injury

tag: age

value: male

value: white

value: flame

value: uninjured


title: ZC_S1_Ptges3 Flox p4

description: 10 X genomics

value: Dorsal root ganglia

value: Dorsal root ganglion cells

value: Ptges3 flox/flox


title: section3_infected_control_24h

city: Stockholm

first: Franziska

last: Hildebrandt

address: Svante Arrhenius Väg 20C, Stockholm

country: Sweden

institute: Stockholm University

data_processing:
Raw sequencing data (.fastq) were processes using the stpipeline to generate count matrices
H&E and CY3 images were aligned using the spotdetector tool
Assembly: mm10 (GRCm38.101), PlasmoDB-48_PbergheiANKA
Supplementary files format and content: stdata.tsv.gz: gene expression count-data
Supplementary files format and content: spotfiles_0.1.tsv.gz, spot-coordinate data
Supplementary files format and content: .jpg, images from spatial transcrptomics analysis (Fluoercence or Hematoxylin&Eosin)

organism:
Plasmodium berghei ANKA
Mus musculus

extract_protocol:
Livers were dissected at the respective timepoints, divided into approxmately 6x6mm large pieces and frozen in Methylbutane at -30°C for 5-10 seconds and embedded in OCT before sectioning them in 10µm thick sections.
Libraries were constructed as previously described in Hildebrandt et al. (2021), https://doi-org.ezp.sub.su.se/10.1038/s41467-021-27354-w
Spatial Transcriptomics

value: liver

tag: timepoint

tag: treatment

value: infected and control


title: section4_infected_control_38h


title: 81-W: Patient 78 Late wound

tag: subject

value: Skin

value: Late wound


title: SimB11272 Plasma

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

extract_protocol:
RNA Isolation method was . RNA Isolation kit was Homebrew Kit.
Library construction kit was Homebrew Kit. Samples were multiplexed. Type of Starting Material was total RNA.

tag: condition

value: Healthy Subject

value: total cell-free biofluid RNA


title: CT4_CON-1_Liver

tag: tissue

value: Liver

tag: strain

value: WT

value: control


title: SimB11137 Plasma

value: Entire cardiovascular system

value: Homebrew Kit


title: CT24_SD-2_forebrain

source_name: Forebrain

value: Forebrain

tag: genotype

value: Sleep deprivation


title: SimB11139 Plasma

tag: anatomical location


title: 80-WE: Patient 77 Early Wound

value: Patient 77

value: Early Wound

value: female

tag: hispanic

value: no

value: white

value: flame

value: wound

tag: location

value: sternum


title: CT4_CON-2_Liver


title: CT24_SD-1_forebrain


title: section2_infected_control_12h

value: liver

value: infected and control


title: section5_control_38h

tag: sample id


title: SimB11230 Plasma

value: Healthy Subject

tag: rna source

value: total cell-free biofluid RNA


title: SimB11173-01/24/12 Plasma


title: CT16_SD-1_forebrain

value: WT

tag: time point


title: CT16_SD-2_forebrain


title: 80-D: Patient 77 Normal skin

value: Skin

tag: wound type

value: Normal skin

tag: Sex

tag: race

tag: burn type

value: uninjured


title: CT12_SD-2_forebrain

value: Forebrain

value: Sleep deprivation


title: 78-D: Patient 75 Normal skin

value: Patient 75

tag: days since injury

tag: age

value: native american

value: contact


title: CT12_SD-1_forebrain

tag: treatment


title: section2_control_24h

tag: timepoint

value: control


title: section6_control_12h

tag: tissue


title: TBI11288-08/05/14 Plasma

tag: condition

value: Entire cardiovascular system

tag: rna isolation kit

value: Homebrew Kit


title: 79-W3: Patient 76 Late wound

tag: subject

value: Patient 76

value: Late wound

value: female

value: no

value: white

value: wound

value: abdomen


title: 83-D: Patient 80 Normal skin

value: Patient 80

value: Skin

value: Normal skin

tag: hispanic

value: black

value: flame


title: section1_infected_control_38h

value: liver

value: infected and control


title: CT8_SD-1_forebrain

value: Forebrain

tag: strain

tag: genotype

value: WT

value: Sleep deprivation


title: CT20_SD-1_forebrain


title: SimB11103 Plasma

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

value: Homebrew Kit


title: CT20_SD-2_forebrain

tag: time point


title: section5_control_12h

value: control

tag: sample id


title: 76-D: Patient 73 Normal skin

value: Patient 73

tag: wound type

tag: Sex

value: male

value: no

tag: race

value: native american

value: scald

value: uninjured

tag: location


title: section4_control_38h

tag: treatment


title: 78-W2: Patient 75 Early Wound

value: Patient 75

value: Skin

value: Early Wound

tag: days since injury

tag: age

value: female

tag: burn type

value: contact

value: wound

value: abdomen


title: section4_control_12h

tag: tissue

value: liver

tag: timepoint


title: section3_control_24h


title: section3_control_38h


title: TBI11283 Plasma

tag: condition

value: Healthy Subject

value: Entire cardiovascular system

value: total cell-free biofluid RNA

tag: rna isolation kit


title: section3_control_12h

value: control


title: 79-W1: Patient 76 Late wound

tag: subject

value: Patient 76

value: Late wound

tag: hispanic

value: white

value: lower extremity


title: SimB11175-01/12/12 Plasma

tag: anatomical location

tag: rna source

value: Homebrew Kit


title: TBI478-01/08/15 Plasma


title: CT8_SD-2_forebrain

value: Forebrain

tag: strain

tag: genotype

value: WT

value: Sleep deprivation

tag: time point


title: CT4_SD-1_forebrain


title: 79-D: Patient 76 Normal skin

value: Skin

tag: wound type

value: Normal skin

tag: Sex

value: female

value: no

tag: race

value: uninjured


title: SimB11240 Plasma

value: Healthy Subject


title: 76-S: Patient 73 HTS

value: Patient 73

value: HTS

tag: days since injury

value: male

value: native american

value: scald

value: scar

tag: location

value: face


title: SimB11153-08/30/11 Plasma

value: Entire cardiovascular system

value: total cell-free biofluid RNA

value: Homebrew Kit


title: CT4_SD-2_forebrain

value: Forebrain

value: WT

tag: treatment

value: Sleep deprivation


title: 74-D: Patient 71 Normal skin

value: Patient 71

tag: tissue

value: Skin

value: Normal skin

tag: age

value: white

tag: burn type

value: unknown


title: SimB381 Plasma

tag: condition

value: Healthy Subject

tag: rna isolation kit


title: section7_infected_38h

value: liver

tag: timepoint

value: infected

tag: sample id


title: CT24_CON-1_forebrain

value: control


title: SimB11174-01/11/12 Plasma

tag: anatomical location

tag: rna source


title: CT20_CON-2_forebrain

tag: strain

tag: genotype


title: 73-W: Patient 70 Late wound

tag: subject

value: Patient 70

tag: wound type

value: Late wound

value: male

tag: hispanic

value: no

value: scald

value: wound

value: lower extremity


title: TBI11206-07/31/12 Plasma

value: Entire cardiovascular system

value: total cell-free biofluid RNA

value: Homebrew Kit


title: section2_control_12h


title: 70-W: Patient 68 Late wound

value: Patient 68

value: Skin

tag: days since injury

tag: Sex

value: female

tag: race


title: 68-W: Patient 66 Late wound

value: Patient 66

tag: tissue

value: white

value: flame

tag: location


title: section6_infected_38h

value: liver

tag: treatment

value: infected


title: 74-W: Patient 71 Late wound

value: Patient 71

value: Late wound

tag: age

tag: burn type

value: unknown


title: CT20_CON-1_forebrain

value: Forebrain

value: WT

value: control

tag: time point


title: CT16_CON-2_forebrain


title: CT24_CON-2_forebrain


title: 64-W: Patient 63 Early Wound

value: Patient 63

value: Early Wound

value: male

value: no

value: other

value: wound

value: lower extremity


title: SimB11204-07/10/12 Plasma

tag: condition

value: Healthy Subject

value: Entire cardiovascular system

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Homebrew Kit


title: section5_infected_38h

value: liver

tag: timepoint

value: infected

tag: sample id


title: SimB400 Plasma

tag: anatomical location

tag: rna source


title: section3_infected_38h


title: 62-W2: Patient 61 Early Wound

tag: subject

value: Patient 61

value: Skin

tag: wound type

value: white

value: flame

value: back


title: CT16_CON-1_forebrain

value: Forebrain

tag: strain

tag: genotype

value: WT

value: control


title: section4_infected_38h


title: section7_infected_24


title: 63-S: Patient 62 HTS

value: Patient 62

value: HTS

tag: days since injury

tag: Sex

value: female

tag: hispanic

value: yes

tag: race

value: unknown

value: scar

value: hand


title: CT12_CON-2_forebrain

tag: tissue

tag: treatment


title: SimB11127 Plasma

value: Healthy Subject

value: Entire cardiovascular system

value: total cell-free biofluid RNA

value: Homebrew Kit


title: TBI11231 Plasma


title: CT12_CON-1_forebrain

tag: time point


title: 62-W: Patient 61 Early Wound

value: Patient 61

value: Skin

value: Early Wound

tag: age

value: male

value: no

value: white

tag: burn type

value: wound

tag: location

value: upper extremity


title: section5_infected_24

value: liver

tag: timepoint

value: infected

tag: sample id


title: CT8_CON-1_forebrain

value: Forebrain

value: WT

value: control


title: 62-D: Patient 61 Normal skin

value: Normal skin

value: flame

value: uninjured


title: section6_infected_24


title: SimB11224 Plasma

tag: condition

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Homebrew Kit


title: SimB11192-05/02/12 Plasma


title: CT4_CON-2_forebrain

tag: strain

tag: genotype


title: 67-W: Patient 65 Early Wound

tag: subject

value: Patient 65

value: Skin

tag: wound type

value: Early Wound

tag: days since injury

tag: Sex

value: male

value: lower extremity


title: 60-W: Patient 59 Late wound

value: Patient 59

tag: tissue

value: Late wound

value: female

tag: hispanic

value: no

tag: race

value: white

value: wound

value: abdomen


title: SimB11164-11/15/11 Plasma


title: section4_infected_24

value: liver

tag: treatment

value: infected


title: SimB268 Plasma

value: Healthy Subject

value: Entire cardiovascular system


title: 61-W: Patient 60 Chronic wound

value: Patient 60

value: Chronic wound

tag: age

tag: burn type

value: flame

tag: location

value: back


title: 59-W: Patient 58 Early Wound

value: Patient 58

value: Skin

value: Early Wound

value: male

value: unknown


title: section2_infected_24h

tag: timepoint

tag: sample id


title: section8_infected_12h


title: TBI11268-12/22/15 Plasma

tag: condition

tag: anatomical location

tag: rna source

value: total cell-free biofluid RNA

value: Homebrew Kit


title: SimB11125 Plasma

tag: rna isolation kit


title: CT8_CON-2_forebrain

value: Forebrain

tag: strain

tag: genotype

value: WT

value: control

tag: time point


title: 58-S: Patient 57 HTS

tag: subject

value: Patient 57

tag: wound type

value: HTS

tag: days since injury

tag: Sex

value: female

value: no

value: black

value: contact

value: scar

value: neck


title: section1_infected_24h

tag: tissue

value: liver

tag: treatment

value: infected


title: section7_infected_12h


title: SimB11199-05/29/12 Plasma

value: Healthy Subject

value: Entire cardiovascular system


title: CT20_SD-1_Cerebellum

source_name: Cerebellum

value: Cerebellum

value: Sleep deprivation


title: TBI11266-07/31/14 Plasma

value: total cell-free biofluid RNA

value: Homebrew Kit


title: CT20_SD-2_Cerebellum

value: WT


title: section4_infected_12h


title: SimB11100 Plasma


title: SimB11209 Plasma


title: 56-W2: Patient 55 Early Wound

value: Patient 55

value: Skin

value: Early Wound

tag: age

value: male

tag: hispanic

tag: race

value: white

tag: burn type

value: flame

value: wound

value: hand


title: 58-WE: Patient 57 Early Wound

value: Patient 57

value: female

value: no

value: black

value: contact

tag: location

value: upper extremity


title: section5_infected_12h

value: liver

tag: timepoint

value: infected

tag: sample id


title: CT24_SD-2_Cerebellum

value: Cerebellum

value: WT

value: Sleep deprivation


title: SimB11198-06/11/12 Plasma

tag: condition

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Homebrew Kit


title: CT16_SD-1_Cerebellum

tag: strain

tag: genotype

tag: time point


title: CT24_SD-1_Cerebellum


title: 56-W1: Patient 55 Early Wound

tag: subject

value: Patient 55

value: Skin

tag: wound type

value: Early Wound

tag: days since injury

tag: Sex

value: male

value: white

value: flame

value: wound


title: CT12_SD-2_Cerebellum

tag: tissue

tag: treatment


title: 57-W: Patient 56 Late wound

value: Patient 56

value: Late wound

tag: age

value: female

tag: hispanic

value: no

tag: race

tag: burn type

value: hand


title: section6_infected_12h

value: liver

tag: timepoint

value: infected

tag: sample id


title: CT4_CON-1_forebrain

value: Forebrain

value: WT

value: control


title: CT12_SD-1_Cerebellum

value: Cerebellum

value: Sleep deprivation


title: SimB11172-12/27/11 Plasma

tag: condition

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

value: Homebrew Kit


title: 55-W: Patient 54 Early Wound

value: Patient 54

value: Skin

value: Early Wound

value: male

value: white

value: flame

value: wound

tag: location


title: TBI11149-02/23/15 Plasma

tag: rna isolation kit


title: SimB11151-08/25/11 Plasma


title: P. berghei Infected murine liver, 38h post infection, snRNAseq

first: Miren

last: Urrutia Iturritza

address: Svante Arrhenius väg 20C

department: The Department of Molecular Biosciences, The Wenner-Gren Institute (MBW)

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation steps were carried out using the Cell Ranger software v3.1.0
Assembly: custom reference genome combining Mus musculus (GRCm38.101) and Plasmodium berghei (PlasmoDB-48_PbergheiANKA)
Supplementary files format and content: Matrix files

extract_protocol:
The livers were collected, and lobes were separated. Each lobe was segmented and  frozen in -30°C 2-Methylbutane.  Frozen liver tissues were homogenized using the Kimble Dounce grinder in homogenization buffer with RNAse inhibitors.  Nuclei were isolated from snap frozen liver tissue with a sucrose gradient.  Homogenized tissue was then subjected to density gradient (29% cushion – Optiprep) ultracentrifugation. Nuclei were resuspended and 2 biological replicates of each condition were pooled before nuclei were stained using DAPI. Intact nuclei were FACS-purified from remaining debris and sorted into BSA coated tubes. The sorted nuclei were pelleted by centrifugation and then resuspended in PBS with 0.04% BSA.
Nuclei suspensions were loaded on a GemCode Single-Cell Instrument (10x Genomics) to generate single-cell Gel Bead-in-Emulsions (GEMs). Single-cell RNA-Seq libraries were prepared using GemCode Single-Cell 3ʹGel Bead and Library Kit (10x Genomics, V2 and V3 technology) according to the manufacturer’s instructions. Briefly, GEM-RT was performed in a 96-Deep Well Reaction Module. After RT, GEMs were broken down and the cDNA was cleaned up with DynaBeads MyOne Silane Beads and SPRIselect Reagent Kit. cDNA was amplified with 96-Deep Well Reaction Module. Amplified cDNA product was cleaned up with SPRIselect Reagent Kit prior to enzymatic fragmentation. Indexed sequencing libraries were generated using the reagents in the GemCode Single-Cell 3ʹ Library Kit with the following intermediates: (1) end repair; (2) A-tailing; (3) adapter ligation; (4) post-ligation SPRIselect cleanup and (5) sample index PCR. Pre-fragmentation and post-sample index PCR samples were analyzed using the Agilent 2100 Bioanalyzer. snRNA-seq libraries were pooled in equal ratios and loaded on a S4 lane Illumina NovaSeq 6000, resulting in 2500 - 3000 million read-pairs.
single-nuclei RNA sequencing

value: Liver

value: P. berghei infected

tag: time

value: 38h post infection


title: 56-D2: Patient 55 Normal skin

tag: subject

value: Patient 55

tag: wound type

value: Normal skin

value: no

value: uninjured


title: section3_infected_12h

value: liver

value: infected


title: 55-D: Patient 54 Normal skin

tag: days since injury

tag: Sex


title: TBI11178-03/13/12 Plasma

value: Healthy Subject

value: Entire cardiovascular system

value: total cell-free biofluid RNA

value: Homebrew Kit


title: P. berghei Infected murine liver, 12h post infection, snRNAseq

description: 10x Genomics

tag: tissue

tag: treatment

value: 12h post infection


title: F2023_RNA_Seq

city: Boston

first: Pinzhu

last: Huang

state: MA

address: 330 Brookline Ave

department: Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition

institute: Beth Israel Deaconess Medical Center

data_processing:
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate P values and Log2 fold changes. Genes with adjusted P values < 0.05 and absolute log2 fold changes >1 were called as differentially expressed genes for each comparison
Assembly: mm39
Supplementary files format and content: .csv files of raw_counts
Supplementary files format and content: .csv files of TPM_values

source_name: nontumor-bearing healthy liver tissues

extract_protocol:
Total RNA extraction was conducted at Azenta Life Sciences (South Plainfield, NJ, USA) using Qiagen Rneasy Plus Mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
Samples were initially treated with TURBO DNase (Thermo Fisher Scientific, Waltham, MA, USA) to remove DNA contaminants. rRNA depletion was performed by using QIAGEN FastSelect rRNA Bacteria Kit (Qiagen, Hilden, Germany). RNA sequencing libraries were prepared using NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters are ligated to cDNA fragments, followed by index addition and library enrichment with limited cycle PCR. Sequencing libraries were validated using the Agilent Tapestation 4200 (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA, USA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The sequencing libraries were multiplexed and clustered onto a flowcell on the Illumina NovaSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

value: nontumor-bearing healthy liver tissues

tag: genotype

value: wild-type


title: TBI11180-03/15/12 Plasma

first: Kai

address: 401 Terry Ave N


title: 51-W: Patient 50 Late wound

value: Patient 50

value: Skin

value: Late wound

tag: age

value: male

tag: hispanic

tag: race

value: white

value: flame

value: wound

value: lower extremity


title: CT4_SD-2_Cerebellum

value: Cerebellum

tag: strain

value: WT

value: Sleep deprivation

tag: time point


title: 53-WE: Patient 52 Early Wound

value: Patient 52

value: Early Wound

value: no

tag: burn type

value: sternum


title: CT4_SD-1_Cerebellum


title: SimB11171-12/22/11 Plasma

tag: condition

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

value: Homebrew Kit


title: CT8_SD-1_Cerebellum


title: SimB11140-08/04/11 Plasma

tag: rna isolation kit


title: P. berghei Infected murine liver, 24h post infection, snRNAseq

description: 10x Genomics

value: Liver

value: P. berghei infected

tag: time

value: 24h post infection


title: F1901_RNA_Seq

value: nontumor-bearing healthy liver tissues

value: wild-type


title: CT16_SD-2_Cerebellum


title: TBI11208 Plasma


title: 54-W: Patient 53 Late wound

tag: subject

value: Patient 53

value: Skin

tag: wound type

value: Late wound

value: male

value: multiracial

value: scald

value: wound

tag: location

value: upper extremity


title: 49-S: Patient 48 HTS

value: Patient 48

tag: tissue

value: HTS

tag: days since injury

tag: Sex

value: female

value: no

value: asian

value: contact

value: scar


title: F1899_RNA_Seq

value: nontumor-bearing healthy liver tissues

tag: genotype

tag: treatment


title: F1755_RNA_Seq

value: wild-type


title: 50-D: Patient 49 Normal skin

value: Patient 49

value: Normal skin

tag: age

tag: hispanic

value: yes

tag: race

value: white

value: flame

value: uninjured


title: SimB11160-10/17/11 Plasma

value: Healthy Subject

value: Entire cardiovascular system

value: total cell-free biofluid RNA

value: Homebrew Kit


title: CT24_CON-1_Cerebellum

value: Cerebellum

tag: strain

value: WT

value: control

tag: time point


title: SimB11157-10/13/11 Plasma

tag: condition

tag: anatomical location


title: 48-WE: Patient 47 Early Wound

value: Patient 47

value: Skin

value: Early Wound

value: male

tag: burn type

value: other

value: wound

value: hand


title: CT20_CON-2_Cerebellum


title: F1754_RNA_Seq

value: nontumor-bearing healthy liver tissues

value: wild-type


title: 47-S: Patient 46 HTS

value: Patient 46

value: HTS

value: no

value: black

value: flame

value: scar

value: upper extremity


title: CT8_SD-2_Cerebellum

value: Cerebellum

value: WT

value: Sleep deprivation


title: F3021_RNA_Seq

source_name: tumor-bearing wild-type liver tissues

value: tumor-bearing wild-type liver tissues


title: 46-WE: Patient 45 Early Wound

value: Patient 45

value: Skin

value: Early Wound

value: male

value: white

value: contact

value: foot


title: CT16_CON-2_Cerebellum

value: control


title: 46-D: Patient 45 Normal skin

value: Normal skin

value: no

value: uninjured


title: F1900_RNA_Seq

value: nontumor-bearing healthy liver tissues

value: wild-type


title: CT20_CON-1_Cerebellum

value: Cerebellum


title: CT24_CON-2_Cerebellum

value: WT


title: SimB11144 Plasma

value: Healthy Subject

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

tag: rna isolation kit

value: Homebrew Kit


title: CT12_CON-2_Cerebellum


title: CT16_CON-1_Cerebellum


title: F2479_RNA_Seq

value: tumor-bearing wild-type liver tissues


title: F2480_RNA_Seq


title: 46-WE2: Patient 45 Early Wound

tag: subject

value: Patient 45

value: Skin

tag: wound type

value: Early Wound

value: male

value: wound

value: lower extremity


title: 45-W: Patient 44 Chronic wound

value: Patient 44

tag: tissue

value: Chronic wound

value: no

value: white

value: flame

tag: location

value: shoulder


title: F2478_RNA_Seq

value: wild-type


title: SimB11130 Plasma

value: Healthy Subject

value: Entire cardiovascular system


title: CT12_CON-1_Cerebellum

value: Cerebellum

value: WT

value: control


title: 45-S: Patient 44 HTS

value: Skin

value: HTS

tag: days since injury

tag: Sex

value: scar

value: ear


title: F2477_RNA_Seq

value: tumor-bearing wild-type liver tissues

tag: genotype

tag: treatment


title: SimB11263 Plasma

value: total cell-free biofluid RNA

value: Homebrew Kit


title: CAR 1 Day 34 Biological Replicate 2

city: Besancon

first: Evan

last: Seffar

address: 8 rue du Dr JFX Girod

institute: UMR INSERM 1098

data_processing:
Mapping using STAR v2.7.9a
Read count matrix produced with FeatureCounts v2.0.1
Differential gene expression performed with DESEQ2 v1.32.0
Poorly expressed genes were eliminated based on the criteria of a minimum sum of read counts >= 20 for all samples
Only Protein Coding Genes were kept for the analysis using biomaRt v2.48.3
Assembly: GENCODE Human Release 39 (GRCh38.p13)
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: CAR T Cells

extract_protocol:
RNA was harvested using Rneasy Mini Kit Qiagen fir RNA isolation
RNA libraries were performed at Plateforme Oncologie Moleculaire, Centre Georges François Leclerc

tag: cell type

value: CAR T Cells

value: CAR 1

tag: time

value: Day 34


title: CT8_CON-2_Cerebellum

tag: strain


title: CAR 1 Day 34 Biological Replicate 1


title: F2879_RNA_Seq

source_name: nontumor-bearing Mdr2-/- liver tissues

value: nontumor-bearing Mdr2-/- liver tissues


title: 44-D: Patient 43 Normal skin

value: Patient 43

value: Normal skin

tag: age

value: female

tag: hispanic

value: no

tag: race

value: white

value: flame

value: uninjured


title: CT8_CON-1_Cerebellum

value: Cerebellum

value: WT

value: control

tag: time point


title: CT4_CON-2_Cerebellum


title: F3020_RNA_Seq

value: tumor-bearing wild-type liver tissues

value: wild-type


title: SimB11143 Plasma

last: Wang

institute: Institute for Systems Biology

tag: condition

value: Healthy Subject

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: total cell-free biofluid RNA

value: Homebrew Kit


title: 44-WE: Patient 43 Late wound

tag: subject

value: Skin

tag: wound type

value: Late wound

tag: burn type

value: wound

value: upper extremity


title: F2878_RNA_Seq

tag: tissue

value: nontumor-bearing Mdr2-/- liver tissues


title: 43-WE2: Patient 42 Late wound

value: Patient 42

tag: days since injury

tag: Sex

value: male

value: no

value: white

tag: location

value: hand


title: F1882_RNA_Seq

tag: genotype

tag: treatment


title: CAR 1 Day 0 Biological Replicate 2

tag: cell type

value: CAR T Cells

value: CAR 1

tag: time

value: Day 0


title: 43-WE: Patient 42 Late wound

tag: age

tag: hispanic

value: flame


title: CAR 1 Day 0 Biological Replicate 1


title: F1762_RNA_Seq


title: 43-W2: Patient 42 Late wound

tag: race


title: Kidney,DD20-4,WT

value: Kidney

tag: strain

value: WT

tag: time point


title: CAR 4 Day 34 Biological Replicate 2

value: CAR 4

value: Day 34


title: Kidney,DD20-3,WT


title: 43-D: Patient 42 Normal skin

value: Skin

value: Normal skin

value: uninjured


title: CAR 4 Day 0 Biological Replicate 1


title: F1712_RNA_Seq

value: nontumor-bearing Mdr2-/- liver tissues


title: 42-WE: Patient 41 Early Wound

value: Patient 41

value: Early Wound

value: wound

value: lower extremity


title: mouse ZFTA-RELA ependymoma tumor, ChIP-ETV5

city: Houston

first: Hsiao-Chi

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Quality control was performed using fastQC (v0.11.7) and MultiQC (v1.6).
Reads were mapped to the mouse genome mm10 assembly using bowtie2
Using the HOMER software suite, bedgraph files and tag directories were made
MACS2 was used for histone serotonylation and findPeaks command in histone (for H3K27ac and H3K27me3) were used to filter ChIP peaks enriched over Input control
MACS2 was used for filter ChIP peaks in ETV5 ChIP
Annotation of enriched peaks was performed using annotatePeaks with mm10 assembly
Integrated Genome Browser compatible files were made using samtools, sort and index, deepTools bamCompare
Assembly: mm10
Supplementary files format and content: bw

source_name: mouse ZFTA-RELA ependymoma tumor

extract_protocol:
Tissue was dissociated, crosslinked with 1.1% formaldehyde for 10 min, quenched and frozen. After thawing, cells were lysed, followed by nuclear lysis. Lysates were sonicated using a Diagenode Bioruptor.
ChIP-Seq libraries were generated from the ChIP-DNA using a custom Illumina library type on an automated system (Apollo 342, Wafergen Biosystems/Takara). ChIP-Seq libraries were sequenced on Illumina NextSeq 500 as 75-nt single end reads

value: mouse ZFTA-RELA ependymoma tumor

value: control

tag: chip antibody

value: anti-ETV5, Abcam #ab102010


title: Kidney,DD20-2,WT


title: Kidney,DD20-1,WT


title: 41-WE: Patient 40 Early Wound

tag: subject

value: Patient 40

value: female

value: no

value: white

value: hand


title: F1761_RNA_Seq


title: CAR 4 Day 34 Biological Replicate 1

value: CAR T Cells

value: CAR 4

value: Day 34


title: 41-D: Patient 40 Normal skin

value: Skin

tag: wound type

value: Normal skin

value: flame

value: uninjured


title: mouse ZFTA-RELA ependymoma tumor, ETV5 overexpression, ChIP-H3K27me3, rep2

data_processing:
Quality control was performed using fastQC (v0.11.7) and MultiQC (v1.6).
Reads were mapped to the mouse genome mm10 assembly using bowtie2
Using the HOMER software suite, bedgraph files and tag directories were made
MACS2 was used for histone serotonylation and findPeaks command in histone (for H3K27ac and H3K27me3) were used to filter ChIP peaks enriched over Input control
Annotation of enriched peaks was performed using annotatePeaks with mm10 assembly
Integrated Genome Browser compatible files were made using samtools, sort and index, deepTools bamCompare
Assembly: mm10
Supplementary files format and content: bw

extract_protocol:
Tissue was dissociated, crosslinked with 1.1% formaldehyde for 10 min, quenched and frozen. After thawing, cells were lysed, followed by nuclear lysis. Lysates were sonicated using a Diagenode Bioruptor.
ChIP-seq libraries were prepared using the TruSeq ChIP Library Preparation Kit (Illumina, IP-202-1012). 10 ng of DNA was used as starting material. Libraries ranging from 250-350 bp were extracted from agarose gel incisions and PCR amplified for 18 cycles. Libraries were purified using AMPure XP beads and quality assessed using a Standard Sensivity NGS Fragment Analysis Kit.

value: human variant ETV5 overexpression

value: anti-H3K27me3, ActiveMotif, #39055


title: F2485_RNA_Seq

source_name: tumor-bearing Mdr2-/- liver tissues

value: tumor-bearing Mdr2-/- liver tissues


title: CT4_CON-1_Cerebellum

value: Cerebellum

value: WT

value: control


title: mouse ZFTA-RELA ependymoma tumor, ETV5 overexpression, input (for H3K27me3), rep2

value: mouse ZFTA-RELA ependymoma tumor


title: Kidney,DD16-3,WT

source_name: Kidney

value: Kidney


title: CAR 4 Day 0 Biological Replicate 2

value: Day 0


title: 40-WE: Patient 39 Late wound

value: Patient 39

value: Late wound

value: male

value: no

value: white

tag: burn type

value: wound

value: abdomen


title: mouse ZFTA-RELA ependymoma tumor, ETV5 overexpression, ChIP-H3K27me3, rep1


title: Kidney,DD16-4,WT

tag: tissue


title: 38-WE: Patient 37 Early Wound

value: Patient 37

value: Skin

value: Early Wound

tag: days since injury

value: yes

value: scald

value: lower extremity


title: 38-D: Patient 37 Normal skin

value: Normal skin

tag: Sex

value: uninjured


title: 37-W: Patient 36 Late wound

value: Patient 36

value: contact

tag: location

value: upper extremity


title: F1711_RNA_Seq

value: tumor-bearing Mdr2-/- liver tissues

tag: genotype


title: mouse ZFTA-RELA ependymoma tumor, ChIP-H3K27me3, rep2

value: mouse ZFTA-RELA ependymoma tumor

value: control

value: anti-H3K27me3, ActiveMotif, #39055


title: F1758_RNA_Seq

tag: treatment


title: 36-S: Patient 35 HTS

value: Patient 35

value: HTS

value: female

value: no

value: white

value: flame

value: scar


title: F1461_RNA_Seq


title: Kidney,DD12-4,WT

value: Kidney

value: WT


title: Kidney,DD12-2,WT


title: Kidney,DD16-2,WT


title: mouse ZFTA-RELA ependymoma tumor, input (for H3K27me3), rep2

tag: cell type


title: mouse ZFTA-RELA ependymoma tumor, ETV5 overexpression, input (for H3K27me3), rep1

value: human variant ETV5 overexpression


title: Kidney,DD12-3,WT


title: F2484_RNA_Seq


title: mouse ZFTA-RELA ependymoma tumor, input (for H3K27me3), rep1


title: primary endometrial stromal cells,siASPM_1

city: Liuzhou

first: Fengque

last: Zheng

state: Guangxi

address: NO.156 Heping Road, Liunan District

department: Department of Gynecology

institute: The Fourth Affiliated Hospital of Guangxi Medical University

data_processing:
RNA sequencing was performedconducted by BGI Technology Co.
Assembly: tab-delimited text fle includes raw counts for each
Supplementary files format and content: Sampletab-delimited text fles include fpkm, tpm, read count values for each Sample

source_name: endometrium

growth_protocol: Proliferating endometrial tissues were obtained from patients with endometriosis and patients without endometriosis , immediately preserved in Dulbecco’s modified Eagle medium (DMEM)/F12 medium (Gibco, Grand Island, NY, USA) afterfollowing isolation, and subsequently transferred to the laboratory at the earliest convenience. The Endometrial endometrial tissue was washed thricethree times with phosphate-buffered saline (PBS) (;Gibco, Grand Island, NY, USA) containing a mixture of penicillin and streptomycin to remove blood from the tissue. The endometrial tissue was cut into 0.5 cm × 0.5 cm pieces and digested using trypsin (Gibco, Grand Island, NY, USA) for 1.5–2 h. Stromal cells were obtained after removing tissue debris and epithelial cells with a 100-μm and 40-μm filter, respectively. Cells were resuspended in DMEM/F12 medium containing 10% fetal bovine serum (FBS) (;Gibco, Auckland, NZ) and a 1% penicillin-streptomycin mixture and incubated in an atmosphere of 5% CO2 at 37°C.

extract_protocol:
RNA was extracted from cells that were transfected with a si-NC or si-ASPM siRNA,either si-NC or si-ASPM, with three replicate samples perfor each group.
Total RNA was extracted from endometrial tissues and ESCs using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: ESCs (1×106) were placed in six-well plates 1 day prior to transfection. ESCs were transfected with 30 pmol of the Control control or ASPM siRNA usingwas transfected into ESCs with Lipofectamine RNAiMAX (Invitrogen, Carlsbad, CA, USA) at a concentration of 30 pmol. The GV230-ASPM plasmid was constructed by GeneChem (Shanghai, China). The cells were transfected with 2.5 μg of control or GV230-ASPM plasmids using with Optimi Lipofectamine 3000 (Invitrogen, Carlsbad, CA, USA) mixed with 2.5 μg of control or GV230-ASPM plasmid suspensions. ESCs were collected 48 h after transfection.

value: endometrium

value: primary endometrial stromal cells

value: siASPM


title: primary endometrial stromal cells,siASPM_3


title: F2461_RNA_Seq

value: tumor-bearing Mdr2-/- liver tissues


title: primary endometrial stromal cells,siControl_3

value: siControl


title: Kidney,DD8-4,WT


title: 33-WE1: Patient 32 Late wound

value: Patient 32

value: Skin

value: Late wound

value: wound

value: sternum


title: Kidney,DD16-1,WT


title: mouse ZFTA-RELA ependymoma tumor, ETV5 overexpression, ChIP-H3K27ac, rep1

value: mouse ZFTA-RELA ependymoma tumor

value: anti-H3K27ac, Abcam #ab4729


title: 35-D: Patient 34 Normal skin

value: Patient 34

value: Normal skin

value: male

value: no

value: white

value: contact

value: uninjured


title: primary endometrial stromal cells,siASPM_2

value: endometrium

value: primary endometrial stromal cells

value: siASPM


title: Kidney,DD12-1,WT

value: Kidney

value: WT


title: 34-D: Patient 33 Normal skin

value: Patient 33

value: Skin

value: unknown

value: other


title: Kidney,DD8-3,WT


title: primary endometrial stromal cells,siControl_2

value: siControl


title: mouse ZFTA-RELA ependymoma tumor, ChIP-H3K27me3, rep1

value: mouse ZFTA-RELA ependymoma tumor

value: control

value: anti-H3K27me3, ActiveMotif, #39055


title: 33-W1: Patient 32 Late wound

value: Patient 32

value: Late wound

value: female

value: no

value: flame

value: wound

value: upper extremity


title: mouse ZFTA-RELA ependymoma tumor, ETV5 overexpression, input (for H3K27ac), rep1

value: human variant ETV5 overexpression


title: Kidney,DD8-2,WT

value: Kidney

value: WT


title: 33-D: Patient 32 Normal skin

value: Skin

value: Normal skin

value: white

value: uninjured


title: primary endometrial stromal cells,siControl_1

value: endometrium

value: primary endometrial stromal cells

value: siControl


title: Kidney,DD8-1,WT


title: mouse ZFTA-RELA ependymoma tumor, ETV5 overexpression, input (for H3K27ac), rep2

value: mouse ZFTA-RELA ependymoma tumor


title: mouse ZFTA-RELA ependymoma tumor, ChIP-H3K27ac, rep2

value: control

value: anti-H3K27ac, Abcam #ab4729


title: 32-D: Patient 31 Normal skin

value: Patient 31

value: male

value: no


title: Kidney,DD4-3,WT


title: Kidney,DD4-4,WT


title: Aedes aegypti, Naïve-infected, Day7, Rep2

city: Taipei

first: Yu-Ning

address: No.1 Jen Ai road section 1

department: Biochemistry and molecular biology

country: Taiwan

institute: National Taiwan University

data_processing:
The bcl2fastq conversion software v2.20 was used to convert BCL files from all Illumina sequencing platforms into FASTQ reads.
Sequence reads were trimmed for adaptor sequence/low-quality sequence with Trimmomatic v0.36 with a sliding-window approach (parameter: Q20)
Trimmed sequence reads were aligned to AaegL5.0 using HISAT2
Cuffdiff (cufflinks v2.2.1) with genome bias detection/correction and Welgene Biotech's in-house pipeline were used to perform differential expression analysis.
Assembly: AaegL5.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Aedes aegypti

source_name: Higgs

growth_protocol: The mosquitoes were kept in 75%–80% humidity at 28℃ and were given 10% sucrose. Light and dark periods were 12:12 h.

extract_protocol:
RNA was harvested using RNA extraction kit (ZYMO Research, catalog E1011-A). Five ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Agilent's SureSelect Strand-Specific RNA Library Preparation Kit.

treatment_protocol:
The female mosquitoes at 7 to 14 days post eclosion were used for the experiments. The mice were tail-vein injected with DENV TW-2015 or PBS as naïve infection. After 3-4 days, the female mosquitoes were feed with DENV- or naïve- infected mice.
After taking the blood meal, the mosquitoes were supplied with 10% sucrose until whole body harvesting for RNA-seq.

value: Higgs

value: Naïve infection

tag: time

value: Day 7


title: Aedes aegypti, Naïve-infected, Day7, Rep1


title: mouse ZFTA-RELA ependymoma tumor, input (for H3K27ac), rep2


title: Aedes aegypti, Naïve-infected, Day2, Rep3

value: Day 2


title: 31-W2: Patient 30 Late wound

city: Seattle

value: Patient 30

value: Skin

value: Late wound

tag: age

value: asian

value: flame

value: wound

value: hand


title: mouse ZFTA-RELA ependymoma tumor, ChIP-H3K27ac, rep1

value: mouse ZFTA-RELA ependymoma tumor


title: 31-W1: Patient 30 Late wound

tag: hispanic

value: upper extremity


title: Aedes aegypti, Naïve-infected, Day2, Rep2


title: Kidney,DD4-1,WT

value: Kidney

value: WT


title: Kidney,DD4-2,WT


title: 30-W4: Patient 29 Late wound

value: Patient 29

value: male

tag: race

value: native american


title: 31-D: Patient 30 Normal skin

value: Normal skin

value: no

value: uninjured


title: mouse ZFTA-RELA ependymoma tumor, input (for H3K27ac), rep1

value: control


title: mouse ZFTA-RELA ependymoma tumor, ChIP-5HTH3, rep3

value: anti-H3K4me3Q5ser, EMD #ABE2580