title: control bio rep 1, H3K27ac ChIP

description: Library name: control1_ac


title: 004h-miRNAcount

status: Public on Aug 06 2026

type: SRA

city: Toronto

first: Sowmya

last: Viswanathan

address: 60 Leonard Avenue

country: Canada

institute: University Health Network

library_source: transcriptomic

data_processing:
Sequencing data alignment and microRNA counts generation was performed as described by Potla et al. (PMID: 36475076).
Assembly: miRBase v22.1
Supplementary files format and content: raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: bone marrow-derived mesenchymal stromal cells

growth_protocol: Biobanked MSC(M) were thawed and plated on 24-well plates at 50,000 cells/well and cultured for 72 h in proliferation medium.

extract_protocol:
After 24 h, RNA extraction was performed on cell samples using a miRNeasy Mini Kit (Qiagen, Hilden, Germany) and stored at -30°C until analysis.
Libraries of cDNA were prepared using the QIAseq miRNA Library Kit (Qiagen) according to the manufacturer's instructions. The libraries were quantified using a DS-11 Spectrophotometer (DeNovix, Wilmington, USA) and assessed for quality using a high-sensitivity DNA chip on the Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: Cells were then washed with phosphate-buffered saline (PBS) and treated with low-glucose DMEM (Sigma) supplemented with or without synovial fluid. To treat cells with synovial fluid, samples were collected from unrelated late-stage OA patients (KL 3-4) outside of the clinical trial cohort (REB #14–7483), pooled from eight patients, and stored at ‑80°C until use, as previously described (82). For treated wells, DMEM was supplemented with 30% (v/v) synovial fluid.

tag: cell type

tag: treatment

value: Untreated

tag: subject id

value: Cell Donor 4


title: CLP_PBS1

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

country: Japan

institute: Saga University

description: Library name: Sample 1

data_processing:
Obtained FASTQ-formatted data was trimmed using trimmomatic 0.39 and reads were mapped into GRCm38.p4 mus musculus reference genome using hisat 2.1.0, followed by counted using featureCounts 2.0.6  and cuffdiff 2.2.1.
Assembly: GRCm38.p4
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
Cells were lysed with Trizol (thermofisher scientific), and total RNAs were extracted using QuickGene AutoS and AutoS RNA Cultured Cell Kit (KURABO) following manufacturer's protocols.
The cDNA library was constructed using TruSeq stranded mRNA Library Prep kit (illumina), and sequencing was performed using 101-base single-read mode of NovaSeq X plus (illumina).

treatment_protocol: CLP was operated in each mice, and injected EVs or SPLEVs or PBS at tail vein after operation. Ten days after the operation, the mice was dissected and the spleen removed.

tag: tissue

value: Spleen

value: Splenocytes

tag: genotype

value: WT

value: CLP operation and injected PBS


title: MOLM13-DMSO-Replicate3 [RNA-seq]

city: Saarbruecken

first: Gilles

last: Gasparoni

state: Saarland

address: Campus

department: Genetics Department

country: Germany

institute: Saarland University

data_processing:
Quality check with FastQC (v 0.11.2)
Adapter trimming (Q>20) with Trim Galore! (v 0.3.3) using Cutadapt (v 1.4.132)
Reads alignment to hg38 using grape-nf pipeline wrapping STAR (v 2.4.0j33) and RSEM (v 1.2.2134)
Differential analysis was performed with DESeq2 package
Assembly: hg38
Supplementary files format and content: fpm matrix with all samples in one file (MOLM13_DESeq2.fpmMatrix.csv)
Supplementary files format and content: rsem gene.results files with TPM and FPKM values (1 file per sample)

growth_protocol: MOLM-13 cells were cultivated at 37°C in water saturated, CO2-enriched (5 %) atmosphere. RPMI-1640, containing 20 % (v/v) fetal bovine serum (FBS) and 2 mM L-alanyl-L-glutamine were used as growing medium. When reaching a density of 1x106 cells/mL, the cells were routinely passaged to a density of 0.1 x 106 cells/mL.

extract_protocol:
Standard RNA extraction was performed. 100 ng of total RNA were used for RNA-seq library preparations.
RNA-seq libraries were produced with the nebnext ultra ii directional rna library prep kit (New England Bioloabs) including polyA enrichment.

treatment_protocol: For treatment with AzadC or cAzadC, the cells were first passed to a density of 0.1 x 106 cells/mL as well. Cells were then incubated overnight before addition of the respective amounts of AzadC or cAzadC in DMSO and incubation for 72 h.

tag: cell line

value: acute myeloid leukemia cell line

value: DMSO


title: 002SFh-miRNAcount

value: bone marrow-derived mesenchymal stromal cells

value: Synovial fluid-treated

value: Cell Donor 2


title: MOLM13-DMSO-Replicate2 [RNA-seq]


title: Bacteroides thetaiotaomicron & E.coli grown in co-culture (microfluidic device) RNA-seq, replicate 4

city: Wurzburg

first: Elise

last: Bornet

address: Josef-Schneider Strasse 2

institute: Helmholtz Insitute

description: Library name: Mix_4_MF

data_processing:
Sequence reads were trimmed for Nextera adapter and MATQ-Seq primers using bbmap. bbduk.sh -Xmx10g t=20
Trimmed reads were then mapped to the reference genome using bowtie2 version 2.3.4.1. bowtie2 -p 30
features were assigned using featureCounts.
Read counts extraction was performed using feature counts version 2.0.1
Assembly: GCF_000011065.1 for Bacteroides thetaiotaomicron and GCF_904425475.1 for E.coli
Supplementary files format and content: tab delimited text file contains raw counts for each sample

organism:
Escherichia coli
Bacteroides thetaiotaomicron

source_name: Bacteroides thetaiotaomicron VPI-5482 eGFP & E. coli MG1655 Mars Red

growth_protocol: Cells were grown in M9 mininal media comlemented with amylopectin

extract_protocol:
RNA was extracted following the MATQ-seq protocol
MATQ-Seq and ribosomal RNA depletion with DASH. Cells were lysed using mechanical sonication and 5U lysozyme per well. cDNA librairies were obtained using the MATQ-Seq reverse transcription protocol. Ribosomal cDNA was depleted from the cDNA librairies using DASH.

treatment_protocol: 100% RNAlater

value: Bacteroides thetaiotaomicron GFP & E. coli Mars-Red

value: fixed in 100% RNAlater

tag: batch


title: 002h-miRNAcount


title: Bacteroides thetaiotaomicron & E.coli grown in co-culture (microfluidic device) RNA-seq, replicate 3

description: Library name: Mix_3_MF

value: Bacteroides thetaiotaomicron VPI-5482 eGFP & E. coli MG1655 Mars Red


title: MOLM13-DMSO-Replicate1 [RNA-seq]


title: 001SFh-miRNAcount

value: Cell Donor 1


title: MOLM13-CarbocyclicAzaDeoxyCytidine0.5uM-Replicate3 [RNA-seq]

value: 0.5 uM carbocyclic 5-Aza2'-Deoxycytidine


title: 001h-miRNAcount


title: Bacteroides thetaiotaomicron & E.coli grown in co-culture (microfluidic device) RNA-seq, replicate 2

description: Library name: Mix_2_MF


title: MOLM13-CarbocyclicAzaDeoxyCytidine0.5uM-Replicate2 [RNA-seq]


title: Bacteroides thetaiotaomicron & E.coli grown in co-culture (microfluidic device) RNA-seq, replicate 1

description: Library name: Mix_1_MF


title: Bacteroides thetaiotaomicron & E.coli grown in co-culture (liquid medium) RNA-seq, replicate 4

description: Library name: Mix_4_LC


title: MOLM13-CarbocyclicAzaDeoxyCytidine0.5uM-Replicate1 [RNA-seq]


title: Pt013SFh-miRNAcount

value: Cell Donor 13


title: Bacteroides thetaiotaomicron & E.coli grown in co-culture (liquid medium) RNA-seq, replicate 3

description: Library name: Mix_3_LC


title: Pt013h-miRNAcount

value: Untreated


title: Pt012SFh-miRNAcount

value: Cell Donor 12


title: MOLM13-AzaDeoxyCytidine0.5uM-Replicate3 [RNA-seq]

value: 0.5 uM 5-Aza2'-Deoxycytidine


title: Bacteroides thetaiotaomicron & E.coli grown in co-culture (liquid medium) RNA-seq, replicate 2

description: Library name: Mix_2_LC


title: MOLM13-AzaDeoxyCytidine0.5uM-Replicate2 [RNA-seq]


title: Pt012h-miRNAcount


title: Bacteroides thetaiotaomicron & E.coli grown in co-culture (liquid medium) RNA-seq, replicate 1

description: Library name: Mix_1_LC

source_name: Bacteroides thetaiotaomicron VPI-5482 & E. coli MG1655


title: MOLM13-AzaDeoxyCytidine0.5uM-Replicate1 [RNA-seq]


title: MOLM13-DMSO-Replicate3

type: genomic

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina High Scan platform using standard recommended Illumina scanner setting (Methylation NXT).

data_processing:
Raw data (idat files) were imported into RnBeads v2.0 software. Data was normalized using 'swan' algorithm, no background subtraction was applied. Quality filtering was done using the following settings: filtering.greedycut.pvalue.threshold=0.05, filtering.sex.chromosomes.removal = TRUE, filtering.snp = 3, filtering.coverage.threshold = 5, filtering.missing.value.quantile = 0.8, filtering.context.removal=c('CC','CAG','CAH','CTG','CTH','Other').
matrix signal intensities value definition: unmethylated and methylated signal intensities

label: Cy3, Cy5

molecule: genomic DNA

source_name: MOLM-13 acute myeloid leukemia cell line

label_protocol: Standard Illumina labelling protocol

extract_protocol: For the purification of DNA, cells were washed with DPBS and subsequently harvested in 80 % MeCN. The samples were incubated 30 min on ice with occasional vortex and centrifugated 30 min at 4 °C and 10,000 ×g. Genomic DNA was purified using standard procedure.


title: 50 hyphae_rep2

status: Public on Aug 05 2026

city: Athens

first: Michelle

last: Momany

state: GA

address: 120 Carlton Street

department: Plant Biology

country: USA

institute: University of Georgia

description: Library name: 50 hyphae_2

data_processing:
Differential analyses of RNA-seq data were carried out using DESeq2 v.1.50.2 (BiocManager v1.30.27) in R. Low read counts were filtered out (< 5). All parameters were performed according to standard methods. Resulting differentially expressed genes (DEGs) were filtered based upon adjusted p-value (padj < 0.05) and |Log2FoldChange| > 2.
Assembly: Quality-filtered reads were aligned to the A. fumigatus CEA10/A1163 reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file. Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation. Differential analyses of RNA-seq data were carried out using DESeq2 v.1.50.2 (BiocManager v1.30.27) in R. Low read counts were filtered out (< 5). All parameters were performed according to standard methods. Resulting differentially expressed genes (DEGs) were filtered based upon adjusted p-value (padj < 0.05) and |Log2FoldChange| > 2.
Supplementary files format and content: csv files include raw read counts

organism: Aspergillus fumigatus

source_name: 50 hyphae

growth_protocol: A. fumigatus strain CEA10 conidia were sporulated on solid Aspergillus Minimal Medium (AMM) for 3-days at 37C or 50C, harvested, washed, and quantified. RNA-extraction was either carried out immediately on conidia and/ or conidia were used to grow hyphal cells or conidiophores. For hyphae: conidia were grown in liquid AMM for 12 hours at 37C or 50C. For conidiophores: conidia were grown on solid AMM and incubated at 37C for 28-hours or 50C for 38hr.

extract_protocol:
Isolated cells were immediately lysed by resuspending cells in  1xTE buffer (Invitrogen) and 425-600 µM beads (Sigma) by vortexing on high for 2 minutes. RNA extractions were carried out utilizing TRIzol according to the manufacturer's protocol (Invitrogen). RNA-sequencing: RNA-sequencing was performed by Plasmidsaurus on RNA extracted from isolated conidia, hyphae and conidiophores produced at 37°C or 50°C.
Three biological replicates of each condition were sequenced. Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp.

value: 50 hyphae

value: 50 hyphae rep2

value: wildtype

value: 12-hr 50C liquid AMM, shaking


title: MOLM13-DMSO-Replicate1

value: acute myeloid leukemia cell line

value: DMSO


title: 37 hyphae_rep3

description: Library name: 37 hyphae_3

source_name: 37 hyphae

value: 37 hyphae

value: 37 hyphae rep3

value: 12-hr 37C liquid AMM, shaking


title: 37 hyphae_rep2

description: Library name: 37 hyphae_2

value: 37 hyphae rep2


title: 37 hyphae_rep1

description: Library name: 37 hyphae_1

value: 37 hyphae rep1


title: MOLM13-Carbocyclic5Aza2DeoxyCytidine0.5uM-Replicate1


title: MOLM13-Carbocyclic5Aza2DeoxyCytidine0.5uM-Replicate2


title: MOLM13-DMSO-Replicate2


title: 50 conidiophore_rep2

description: Library name: 50 conidiophore_2

source_name: 50 conidiophores

value: 50 conidiophores

value: 50 conidiophores rep2

value: 38-hr 50C on solid AMM


title: 50 conidiophore_rep3

description: Library name: 50 conidiophore_3

value: 50 conidiophores rep3


title: 37 conidiophore_rep3

description: Library name: 37 conidiophore_3

source_name: 37 conidiophores

value: 37 conidiophores

value: 37 conidiophores rep3

value: 28-hr 37C on solid AMM


title: MOLM13-Carbocyclic5Aza2DeoxyCytidine0.5uM-Replicate3

value: 0.5 uM carbocyclic 5-Aza2'-Deoxycytidine


title: 37 conidiophore_rep2

description: Library name: 37 conidiophore_2

value: 37 conidiophores rep2

value: wildtype


title: 50 conidiophore_rep1

description: Library name: 50 conidiophore_1

value: 50 conidiophores rep1


title: 37 conidiophore_rep1

description: Library name: 37 conidiophore_1

value: 37 conidiophores rep1


title: MOLM13-5Aza2DeoxyCytidine0.5uM-Replicate3

value: acute myeloid leukemia cell line

value: 0.5 uM 5-Aza2'-Deoxycytidine


title: MOLM13-5Aza2DeoxyCytidine0.5uM-Replicate1


title: 50 conidia_rep3

description: Library name: 50 conidia_3

source_name: 50 conidia

value: 50 conidia

value: 50 conidia rep3

value: 72-hr 50C on solid AMM


title: 37 conidia_rep2

description: Library name: 37 conidia_2

source_name: 37 conidia

value: 37 conidia

value: 37 conidia rep2

value: 72-hr 37C on solid AMM


title: 50 conidia_rep1

description: Library name: 50 conidia_1

value: 50 conidia rep1


title: 37 conidia_rep3

description: Library name: 37 conidia_3

value: 37 conidia rep3


title: 50 conidia_rep2

description: Library name: 50 conidia_2

value: 50 conidia rep2


title: 37 conidia_rep1

description: Library name: 37 conidia_1

value: 37 conidia rep1


title: 50 hyphae_rep1

description: Library name: 50 hyphae_1

value: 50 hyphae

value: 50 hyphae rep1

value: 12-hr 50C liquid AMM, shaking


title: Ho2 Ho muscle/myoseptal RNA-seq biological replicate 2

city: Jiaxing

first: Jianbo

last: Zheng

state: Zhejiang

address: No. 705 Yatai Road

country: China

institute: Yangtze Delta Region Institute of Tsinghua University Zhejiang

description: Library name: Ho2

data_processing:
Raw reads were filtered to remove adaptor sequences, low-quality reads, and reads containing ambiguous bases.
Clean reads were aligned to the Culter alburnus reference genome GCA_040182925.1.
Gene expression levels were quantified as raw read counts, TPM, and FPKM values.
Differentially expressed genes were identified among Ctrl, He, and Ho groups using pairwise comparisons with |log2 fold change| >= 1 and adjusted P value < 0.01.
Assembly: Culter alburnus reference genome GCA_040182925.1
Supplementary files format and content: CSV file containing gene-level raw read counts and annotation information for all samples.
Supplementary files format and content: CSV files containing gene-level TPM and FPKM expression matrices with annotation information for all samples.

organism: Culter alburnus

source_name: Group: Ho; genotype: runx2b homozygous mutant; developmental stage: two-month-old juvenile; processed matrix column: Ho2

growth_protocol: Two-month-old Culter alburnus juveniles from wild-type, runx2b heterozygous mutant, and runx2b homozygous mutant groups were maintained under the same rearing conditions before sampling.

extract_protocol:
Muscle/myoseptal region tissues associated with intermuscular bone development were dissected, snap-frozen in liquid nitrogen, and stored at -80 degrees C. Total RNA was extracted from each sample and assessed for quantity and integrity before library construction.
Poly(A) mRNA was enriched from total RNA using oligo(dT) magnetic beads, fragmented, reverse-transcribed into cDNA, end-repaired, adaptor-ligated, PCR-amplified, and sequenced as paired-end RNA-seq libraries on an Illumina NovaSeq X Plus platform.

treatment_protocol: No external treatment was applied. Samples were grouped by runx2b genotype: wild type, heterozygous mutant, and homozygous mutant.

value: muscle/myoseptal region

value: runx2b homozygous mutant


title: Ho3 Ho muscle/myoseptal RNA-seq biological replicate 3

description: Library name: Ho3

source_name: Group: Ho; genotype: runx2b homozygous mutant; developmental stage: two-month-old juvenile; processed matrix column: Ho3


title: Ho1 Ho muscle/myoseptal RNA-seq biological replicate 1

description: Library name: Ho1

source_name: Group: Ho; genotype: runx2b homozygous mutant; developmental stage: two-month-old juvenile; processed matrix column: Ho1


title: 50 hyphae _rep3

description: Library name: 50 hyphae _3

value: 50 hyphae rep3

value: wildtype


title: He3 He muscle/myoseptal RNA-seq biological replicate 3

description: Library name: He3

source_name: Group: He; genotype: runx2b heterozygous mutant; developmental stage: two-month-old juvenile; processed matrix column: He3

value: runx2b heterozygous mutant


title: He1 He muscle/myoseptal RNA-seq biological replicate 1

description: Library name: He1

source_name: Group: He; genotype: runx2b heterozygous mutant; developmental stage: two-month-old juvenile; processed matrix column: He1


title: WT3 Ctrl muscle/myoseptal RNA-seq biological replicate 3

description: Library name: WT3

source_name: Group: Ctrl; genotype: wild type; developmental stage: two-month-old juvenile; processed matrix column: WT3

value: wild type


title: He2 He muscle/myoseptal RNA-seq biological replicate 2

description: Library name: He2

source_name: Group: He; genotype: runx2b heterozygous mutant; developmental stage: two-month-old juvenile; processed matrix column: He2


title: WT1 Ctrl muscle/myoseptal RNA-seq biological replicate 1

description: Library name: WT1

source_name: Group: Ctrl; genotype: wild type; developmental stage: two-month-old juvenile; processed matrix column: WT1


title: WT2 Ctrl muscle/myoseptal RNA-seq biological replicate 2

description: Library name: WT2

source_name: Group: Ctrl; genotype: wild type; developmental stage: two-month-old juvenile; processed matrix column: WT2


title: TDP-43ΔNLS transgenic replicate 3

city: Seattle

first: Nicole

last: Liachko

state: WA

address: 1660 Columbian Way S.

department: GRECC

institute: VA Puget Sound Health Care System

description: Library name: NLS151_3

data_processing:
FASTQ files were pre-processed with FASTP (version 0.23.4), aligned with STAR two-pass-mapping (version 2.7.10b),and quantified with featureCounts (version 2.20.0) in R (version 4.4.2) without multi-mapping reads against the C. elegans genome WBcel235 (version 113).
Assembly: WBcel235
Supplementary files format and content: .txt output of featureCounts

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: C. elegans grown from hypochlorite-purified eggs at 20 °C on 5XPEP plates until L4.

extract_protocol:
RNA was extracted from snap-frozen C. elegans pellets using the Thermo Fisher Scientific TRIzol RNA extraction protocol. RNA was resuspended in nuclease free water, run on an agarose gel to assess integrity, and concentration was assessed using a NanoPhotometerNP80 spectrophotometer (Implen GMbH).
RNA was assembled into poly-A enriched libraries as a fee-for-service (Novogene).

value: whole body

tag: developmental stage

value: larval stage 4


title: TDP-43ΔNLS transgenic replicate 4

description: Library name: NLS151_4


title: TDP-43-transgenic replicate 4

description: Library name: CK410_4

value: Psnb-1::TDP-43; Pmyo-2::dsRED


title: TDP-43ΔNLS transgenic replicate 2

description: Library name: NLS151_2


title: TDP-43-transgenic replicate 2

description: Library name: CK410_2


title: TDP-43-transgenic replicate 3

description: Library name: CK410_3


title: TDP-43-transgenic replicate 1

description: Library name: CK410_1


title: TDP-43ΔNLS transgenic replicate 1

description: Library name: NLS151_1


title: non-transgenic wildtype control replicate 4

description: Library name: N2_4

value: wildtype N2


title: non-transgenic wildtype control replicate 3

description: Library name: N2_3


title: MOLM13-5Aza2DeoxyCytidine0.5uM-Replicate2

source_name: MOLM-13 acute myeloid leukemia cell line

value: acute myeloid leukemia cell line

value: 0.5 uM 5-Aza2'-Deoxycytidine


title: non-transgenic wildtype control replicate 2

description: Library name: N2_2


title: non-transgenic wildtype control replicate 1

description: Library name: N2_1


title: RNA-seq of HU-HSA-2 GNE140 rep2

city: Sapporo

first: Keisuke

last: Aoshima

state: Hokkaido

address: Kita 18 Nishi 9

department: Faculty of Veterinary Medicine

institute: Hokkaido University

description: Library name: RNA_H2_GNE140_2

data_processing:
Sequencing reads were mapped to the CanFam4 canine reference genome using STAR.
Expression levels were estimated using RSEM. Differential expression was analyzed with edgeR 3.42.0
Assembly: CanFam4
Supplementary files format and content: tsv file include TPM count in each sample

organism: Canis lupus familiaris

growth_protocol: DMEM as indictated treatment with 10% fetal bovine serum and penicillin–streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using a NucleoSpin RNA isolation kit
mRNA-seq libraries were constructed using a NEBNext Ultra II Directional RNA Library Prep Kit

treatment_protocol: DMSO or (R)-GNE-140 for 72 hours


title: RNA-seq of HU-HSA-2 GNE140 rep3

description: Library name: RNA_H2_GNE140_3


title: RNA-seq of HU-HSA-2 control rep3

description: Library name: RNA_H2_control_3


title: RNA-seq of HU-HSA-2 GNE140 rep1

description: Library name: RNA_H2_GNE140_1


title: RNA-seq of HU-HSA-2 control rep2

description: Library name: RNA_H2_control_2


title: Blanchard-wt-snRNAseq-b

city: New York

first: Joel

middle: W.

last: Blanchard

state: NY

address: 619 W54th Street, 8th Floor

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Blanchard-wt-snRNAseq-b
NovaSeq X platform (Illumina)

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were aligned to the human reference genome (GRCh38) and per-nucleus count matrices generated using Cell Ranger (10x Genomics, v9.0.1). Six libraries were processed two replicates each for Control, A53T-APOE E3, and A53T-APOE E4 conditions. Nuclei were filtered out if they had unique molecular identifier (UMI) counts or number of detected genes outside ±4 median absolute deviations (MADs) from the sample median, or if the fraction of mitochondrial reads exceeded 5%. Doublets were identified and removed using the simulation-based inference implemented in pegasus v1.10.0,, stratified by sample, prior to final clustering. Library-size normalization followed by log(x+1) transformation was then applied using scanpy v1.9.8.. Highly variable genes (HVGs) were identified using a Cell Ranger-flavored dispersion method using scanpy
Assembly: GRCh38
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: miBRAIN

extract_protocol:
miBrains were cultured in standard conditions for 18 days, rinsed with PBS and frozen without media. Fresh frozen miBrains were processed using the Chromium Nuclei Isolation Kit (10x Genomics), with RNase inhibitors. Nuclei were quantified via DAPI staining using a Countess II FL automated cell counter (Life Technologies). 20,000 nuclei per sample were processed using 3’ GemX v4 reagents (10x Genomics), and libraries prepared according to the manufacturer’s instructions. All libraries were sequenced at Azenta using the NovaSeq X platform (Illumina).
Libraries were prepared according to the manufacturer’s instructions (10xgenomics.com). All libraries were sequenced at Azenta using the NovaSeq X platform (Illumina).

value: iPSC-derived brain cells

value: miBRAIN


title: Blanchard-A53T-E4-snRNAseq-a

description:
Library name: Blanchard-A53T-E4-snRNAseq-a
NovaSeq X platform (Illumina)


title: RNA-seq of HU-HSA-2 control rep1

description: Library name: RNA_H2_control_1


title: Blanchard-wt-snRNAseq-a

description:
Library name: Blanchard-wt-snRNAseq-a
NovaSeq X platform (Illumina)


title: Blanchard-A53T-E4-snRNAseq-b

description:
Library name: Blanchard-A53T-E4-snRNAseq-b
NovaSeq X platform (Illumina)


title: Blanchard-A53T-E3-snRNAseq-b

description:
Library name: Blanchard-A53T-E3-snRNAseq-b
NovaSeq X platform (Illumina)


title: iMGL, LACTBKO, clone C, differentiation 2

city: New York City

first: Carmen

last: Romero Molina

address: 1 Gustave L. Levy Pl

department: Genetics and Genomic Science

description:
Library name: BKOC2
column name in WTC11_img_bulkRNAseq_raw_counts.tsv: BKOC2

data_processing:
Raw base call files were converted to FASTQ format and processed using the nf-core/rnaseq pipeline (DOI: 10.5281/zenodo.1400710).
Reads were quality controlled, adapter-trimmed, and aligned to the human reference genome (GRCh38). Gene-level quantification was performed within the nf-core/rnaseq pipeline using standard parameters.
Gene-level count matrices were imported into R (v4.3.3) for downstream analysis. Differential gene expression analysis was performed using the DREAM method implemented in the variancePartition package (v1.23.1), applying linear mixed-effects models.
Assembly: hg38
Supplementary files format and content: tab-separated values (tsv) file containing raw counts for each sample

growth_protocol: We CRISPR-edited the WTC11 line to generate control (WT) and LACTB KO isogenic clonal lines (3 independent clones per genotype) at the Stem Cell Core at Ichan School of Medicine at Mount Sinai. iPSC lines were differentiated to hematopoietic precursor cells (HPCs) using StemDiff kit (StemCell Technologies). HPCs were plated and differentiated for 24 days to microglia (iMGL) in iMGL media (DMEM/F12, B27, 0.5xN2, 2xITSG, 400uM monothioglycerol, 5ug/ml insulin, 1xNEAA, 1xGlutaMax) supplemented with three factors (IL34 (100ng/ml), TGFb (50ng/ml), and MCSF (25ng/ml). iMGLs were fed Monday, Wednesday and Friday with 1ml of iMGL media with three factors. Cells were splitted in 1:2 ratio if too confluent. At day 24 iMGLs were lifted with gentle pipetting and Accutase and plated in fresh media iMGL media with three factors supplemented additionally with two factors (CX3CL1 and CD200 100ng/ml each) for 3 additional days (day 25, day 26,  day 27). At day 26 of iMGL differentiation. Cells were collected at day 27.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, 74136) according to the manufacturer’s instructions. RNA quantity was assessed using NanoDrop 8000 (Thermo Fisher Scientific). RNA integrity was evaluated by Azenta using Qubit and BioAnalyzer, with all samples demonstrating RNA integrity number (RIN) > 9.0 prior to library preparation.
RNA-seq libraries were prepared by Azenta (New Jersey, USA) using the TruSeq RNA Sample Preparation Kit v2 (Illumina) according to the manufacturer’s protocol. Libraries were paired-end sequenced on an Illumina HiSeq2500 platform with 150 bp read length, generating approximately 20–30 million mapped fragments per sample.

treatment_protocol: No additional treatments were added

value: iPSC-derived microglia

value: LACTBKO

value: no treatment


title: iMGL, LACTBKO, clone C, differentiation 1

description:
Library name: BKOC1
column name in WTC11_img_bulkRNAseq_raw_counts.tsv: BKOC1


title: Blanchard-A53T-E3-snRNAseq-a

description:
Library name: Blanchard-A53T-E3-snRNAseq-a
NovaSeq X platform (Illumina)


title: iMGL, LACTBKO, clone B, differentiation 2

description:
Library name: BKOB2
column name in WTC11_img_bulkRNAseq_raw_counts.tsv: BKOB2


title: iMGL, LACTBKO, clone A, differentiation 2

description:
Library name: BKOA2
column name in WTC11_img_bulkRNAseq_raw_counts.tsv: BKOA2


title: iMGL, LACTBKO, clone B, differentiation 1

description:
Library name: BKOB1
column name in WTC11_img_bulkRNAseq_raw_counts.tsv: BKOB1


title: iMGL, LACTBKO, clone A, differentiation 1

description:
Library name: BKOA1
column name in WTC11_img_bulkRNAseq_raw_counts.tsv: BKOA1


title: iMGL, WT, clone L, differentiation 2

description:
Library name: SCRL2
column name in WTC11_img_bulkRNAseq_raw_counts.tsv: SCRL2

value: WT


title: iMGL, WT, clone L, differentiation 1

description:
Library name: SCRL1
column name in WTC11_img_bulkRNAseq_raw_counts.tsv: SCRL1


title: iMGL, WT, clone K, differentiation 2

description:
Library name: SCRK2
column name in WTC11_img_bulkRNAseq_raw_counts.tsv: SCRK2


title: iMGL, WT, clone K, differentiation 1

description:
Library name: SCRK1
column name in WTC11_img_bulkRNAseq_raw_counts.tsv: SCRK1


title: THP1 macrophages, LACTB KD, differentiation e

description:
Library name: siLACTB-e
column name in THP1_bulkRNAseq_raw_counts.tsv: siLACTB.e

growth_protocol: The monocytic human immortalized cell line THP1 was treated with phorbol 12-myristate 13-acetate (PMA, 25 ng/ml) for 72 hours to differentiate into macrophages. Cells were grown in RPMI medium supplemented with 10% FBS, 1x Penicillin Streptomycin and 10 mM HEPES.

treatment_protocol: We used small-interfering RNA (siRNA, 40 nM) for 6 days (before and after PMA addition) to reduce LACTB expression. This treatment reduced LACTB expression 90% at the mRNA level and 60% at the protein level.

value: Human monocytes

value: LACTB knockdown

value: Differentiation to macrophages

value: e


title: iMGL, WT, clone J, differentiation 2

description:
Library name: SCRJ2
column name in WTC11_img_bulkRNAseq_raw_counts.tsv: SCRJ2


title: iMGL, WT, clone J, differentiation 1

description:
Library name: SCRJ1
column name in WTC11_img_bulkRNAseq_raw_counts.tsv: SCRJ1


title: THP1 macrophages, LACTB KD, differentiation d

description:
Library name: siLACTB-d
column name in THP1_bulkRNAseq_raw_counts.tsv: siLACTB.d

value: d


title: THP1 macrophages, LACTB KD, differentiation b

description:
Library name: siLACTB-b
column name in THP1_bulkRNAseq_raw_counts.tsv: siLACTB.b

value: b


title: THP1 macrophages, scrambled, differentiation e

description:
Library name: scr-e
column name in THP1_bulkRNAseq_raw_counts.tsv: scr.e

value: SCR


title: THP1 macrophages, LACTB KD, differentiation c

description:
Library name: siLACTB-c
column name in THP1_bulkRNAseq_raw_counts.tsv: siLACTB.c

value: c


title: THP1 macrophages, LACTB KD, differentiation a

description:
Library name: siLACTB-a
column name in THP1_bulkRNAseq_raw_counts.tsv: siLACTB.a

value: a


title: THP1 macrophages, scrambled, differentiation c

description:
Library name: scr-c
column name in THP1_bulkRNAseq_raw_counts.tsv: scr.c


title: THP1 macrophages, scrambled, differentiation b

description:
Library name: resub-scr-b
column name in THP1_bulkRNAseq_raw_counts.tsv: resub.scr.b


title: THP1 macrophages, scrambled, differentiation d

description:
Library name: scr-d
column name in THP1_bulkRNAseq_raw_counts.tsv: scr.d


title: THP1 macrophages, scrambled, differentiation a

description:
Library name: scr-a
column name in THP1_bulkRNAseq_raw_counts.tsv: scr.a


title: DrpZ39-44C-C-4

city: Richardson

first: Marisol

last: Mancilla Moreno

address: 800 w. Campbell Road

institute: University of Texas at Dallas

description:
Library name: UTD-MF-DrpZ39-44C-C-VIS8
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.

data_processing:
Raw data were processed with the 10X SpaceRanger pipeline
Assembly: Macaca_fascicularis_6.0 (GCA_011100615.1), Panubis1.0 GCA_008728515.1, Mmul_10 (GCA_003339765.3)
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: lis of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png:low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifuing spots
Supplementary files format and content: spatial_enrichment.csv: list of gene enrishment in specific locations of the tissue
Library strategy: Spatial Transcriptomics

organism: Macaca fascicularis

source_name: dorsal root ganglia

extract_protocol:
Fresh frozen non-human primate were collected from Worldwide Primates, inc.
Fresh frozen non-human primate dorsal root ganglia underwent Visium tissue optimization and spatial gene expression. Protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain.

value: dorsal root ganglia

tag: Sex

value: Male


title: DrpZ39-44C-C-3

description:
Library name: UTD-MF-DrpZ39-44C-C-VIS7
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: DrpZ39-44C-C-2

description:
Library name: UTD-MF-DrpZ39-44C-C-VIS4
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: DrpZ41-6C-B-3

description:
Library name: UTD-MF-DrpZ41-6C-B-VIS5
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.

value: Female


title: DrpZ41-6C-B-4

description:
Library name: UTD-MF-DrpZ41-6C-BVIS6
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: DrpZ41-6C-B-2

description:
Library name: UTD-MF-DrpZ41-6C-B-VIS2
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: DrpZ39-44C-C-1

description:
Library name: UTD-MF-DrpZ39-44C-C-VIS3
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: DrpZ41-6C-B-1

description:
Library name: UTD-MF-DrpZ41-6C-B-VIS1
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: 7278437832-4

description:
Library name: UTD-MF7278437832-VIS8
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: 7278437832-3

description:
Library name: UTD-MF-7278437832-VIS7
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: 1611266-4

description:
Library name: UTD-MF-1611266-VIS6
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: 1611266-3

description:
Library name: UTD-MF-1611266-VIS5
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: 7278437832-1

description:
Library name: UTD-MF-7278437832-VIS3
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: Cu24_Fcol_24h_fish biological rep6

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

data_processing:
Base-calling and demultiplexing were performed using the native Illumina software by the sequencing service provider.
Raw reads were processed for quality control using the TrimGalore! software version 0.5.0. This software was used to trim low-quality ends from reads and for Illumina adapter removal.
Bowtie2 version 2.3.4.3 was used for alignment of reads to the channel catfish transcriptome using the alignment parameters as recommended by the eXpress software.
Alignment files were piped into the eXpress version 1.5.1 software using the default parameters, but including the strand information, to generate read-counts.
Effective read counts output from the eXpress version 1.5.1 software were used to calculate fold-change using the DESeq2 package 1.24.0 in R-Bioconductor Release 3.6.1.
Genome_build: All cDNA transcripts from the channel catfish genome (assembly IpCoco_1.2) in Ensembl
Supplementary_files_format_and_content: tab-delimited text files of effective read counts, rounded to the nearest whole number

organism: Ictalurus punctatus

source_name: gill

extract_protocol:
Tissue samples were placed in RNAlater and stored at -80°C until usage. Total RNA was extracted with the Qiagen RNeasy Mini Kit per the manufacturer's recommendation. Total RNA was treated with Amplification Grade DNase I from Sigma-Aldrich and then precipitated prior to library construction.
Total RNA was standardized to 100 ng each sample. Sequencing libraries were then prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with the NEBNext Poly(A) mRNA Magnetic Isolation Module. Barcodes used were the NEBNext Multiplex Oligos for Illumina (Index Primers Sets 1 and 2).

value: gill

tag: time post f.columnare challenge

value: exposed to copper sulfate for 24h and then challenged with Fcolumnare


title: 7278437832-2

description:
Library name: UTD-MF-7278437832-VIS4
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: Cu24_Fcol_24h_fish biological rep5


title: UTD-PA-001-1

description:
Library name: UTD-PA-001-VIS1
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.

organism: Papio anubis


title: 1611266-2

description:
Library name: UTD-MF-1611266-VIS2
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: UTD-PA-001-2

description:
Library name: UTD-PA-001-VIS2
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: Cu24_Fcol_24h_fish biological rep4


title: Cu24_Fcol_24h_fish biological rep3


title: 1611266-1

description:
Library name: UTD-MF-1611266-VIS1
Fresh frozen DRGs were bought from Worldwide Primates, inc. and cryosectioned onto SuperFrost Plus charged slides at 10µm. To sample a larger subset of neurons, at least two sections were utilized from each DRG and each 10µm section was 100µm apart. Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://www.10xgenomics.com/) using Haematoxylin and Eosin as the counterstain. Optimal permeabilization time was obtained at 12 min incubation with permeabilization enzyme. mRNA library preparation and sequencing were done at the Genome Center in the University of Texas at Dallas Research Core Facilities.


title: Cu24_Fcol_4h_fish biological rep6


title: Cu24_Fcol_24h_fish biological rep2


title: Cu24_Fcol_4h_fish biological rep5


title: Cu24_Fcol_24h_fish biological rep1


title: Cu24_Fcol_4h_fish biological rep4


title: Cu24_Fcol_4h_fish biological rep3


title: Cu24_Fcol_4h_fish biological rep1


title: Cu24_Fcol_4h_fish biological rep2


title: Cu24_Fcol_1h_fish biological rep4


title: Cu24_Fcol_1h_fish biological rep3


title: Cu24_Fcol_1h_fish biological rep6


title: Cu24_Fcol_1h_fish biological rep1


title: Cu24_Fcol_1h_fish biological rep2


title: Cu24_Fcol_1h_fish biological rep5


title: Cu0_Fcol_24h_fish biological rep6

value: exposed to copper sulfate and then immediately challenged with Fcolumnare


title: Cu0_Fcol_24h_fish biological rep5


title: Cu0_Fcol_24h_fish biological rep3


title: Cu0_Fcol_24h_fish biological rep4


title: Cu0_Fcol_24h_fish biological rep2


title: Cu0_Fcol_24h_fish biological rep1


title: Cu0_Fcol_4h_fish biological rep6


title: Subject P165 (P165-T1F)

type: protein

city: Stanford

first: Paul

middle: Joseph

last: Utz

state: California

address: 269 Campus Dr

institute: Stanford University School of Medicine

description:
reason for sample removal: NA
Antibodies in samples bind to barcoded beads conjugated to antigens. Antibody reactivity was quantified by the fluorescence measured as MFI from the secondary antibody.
Luminex™ FLEXMAP 3D™

hyb_protocol: A fluorescent secondary antibody was added to a PBS solution containing conjugated beads bound to antibodies.

scan_protocol: A Luminex FlexMAP 3D instrument was used to quantify autoantibody levels in each sample by measuring fluorescence (in MFI) from each barcoded bead.

data_processing: See methods section for detailed description. MFI values for unconjugated beads were subtracted from MFI values for antigen conjugated bead IDs, with MFI averages calculated after background subtraction.

label: R-PE conjugated goat anti-human IgG secondary antibody

molecule: protein

source_name: Serum/Plasma

label_protocol: Secondary antibody with a conjugated fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.

extract_protocol: Blood was collected from patients and healthy controls. Blood was then processed into serum or plasma.

value: Serum/Plasma

tag: condition

value: Patient


title: Cu0_Fcol_4h_fish biological rep5


title: 1103-2 #2 P2_3

city: Seattle,

first: Stephanie

last: Osmond

address: 1201 9th Ave

institute: Benaroya Research Institute

description: Library name: lib105936

data_processing:
Base-calling was performed automatically with Illumina RTA (v. 1.18.66.3).
The FASTQs were aligned to the University of California Santa Cruz (UCSC) Human genome assembly version 19, using STAR v.2.4.2a and gene counts were generated using HTSeq-count (v0.4.1) (57, 58). Quality metrics were compiled from PICARD (v1.134FASTQC (v0.11.3) Samtools (v1.2)8, and HTSeq-count.
Assembly: Homo sapiens GRCh38.77 (version 77)
Supplementary files format and content: Gene count matrix with genes in columns and samples in rows

source_name: airway epithelial cells

extract_protocol:
Airway epithelial cells from airway brushings pediatric patients  were cultured in room air or hyperoxia conditions
We generated full-length cDNA from total RNA (0.5 ng). We amplified cDNA using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) and constructed sequencing libraries using the NexteraXT DNA Library prep kit (Illumina).

value: airway epithelial cells

value: RA

value: female

tag: donorid

tag: studygroup

value: BPD

tag: collection timepoint

tag: cell morphology

value: AEC


title: mESC, H2AK119ub1, Control 1

city: Mexico City

first: Víctor

middle: Julián

last: Valdés

state: Mexico City

address: Circuito Exterior s/n, Ciudad Universitaria

department: Departamento de Biología Celular y Desarrollo

country: Mexico

institute: Instituto de Fisiología Celular (IFC), Universidad Nacional Autónoma de México (UNAM)

description: Library name: Control_UB_1

library_source: genomic

data_processing:
The peaks obtained from the processing of our auxin induced experiment were merged into non-redundant union sets for each of the immunoprecipitation antibodies with Bedtools v2.30.0, Peak calling was performed per replicate using MACS2 v2.2.7.1
To create visualization files and plots such as BigWig and heatmaps, we calculate scaling factors for all sam-ples for each immunoprecipitation condition with deepTools 3.5.0.
Assembly: mm10
Supplementary files format and content: bigWig, broad peak

source_name: Mouse embryonic stem cells, mESC

growth_protocol: J1 mouse embryonic stem cells (mESC) were cultured under standard conditions on 0.1% gelatin-coated plates and in ES medium: DMEM High Glucose supplemented with 15% FBS (Biowest L0101-500), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM MEM non-essential amino acids (NEAA), 1% nucleoside mix, 50 U/mL Penicillin/Streptomycin (P/S), Leukemia inhibitory factor (LIF, made in house) and 2i inhibitors: 1 μM PD0325901 and 3 μM CHIR99021. Cells were passed every other day using 0.05% Trypsin/EDTA. All cells were grown at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Cells were dissociated with 0.05% trypsin, fixed with 1% formaldehyde solution for 10 min at room temperature (RT), and quenched with fresh 125 mM glycine for 5 min RT. After PBS washed, nuclei were isolated using sequential lysis buffers: B1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x protease inhibi-tors; 10 min at 4°C), B2 (10 mM Tris-HCL, pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 1x pro-tease inhibitors; 10 min at 4°C), and B3 (10 mM Tris-HCL, pH 8, at 4 C, 100 mM NaCl,1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-Lauroylsarcosine sodium salt, and 1x protease inhibitors). Chromatin was fragmented to an average size of 250-500 bp using a Diagenode Bioruptor and triton X-100 was added to a final concentration of 1%. ChIP was performed using 1 ug of antibody per 2 million of cells incubated and rotated overnight at 4 ºC. Antibodies: rabbit anti-H2AK119ub1 (Cell signaling, 8240). Dynabeads (10 µL pero µg Ab) were pre-washed in PBS + 0.5% BSA and rotated for 2 hours at 4 ºC before adding to the IPs.  Then washes X5 with ChIP RIPA buffer 4°C (50mM HEPES-KOH, pH 7.5 at 4 °C, 500 mM LiCl, 1 mM EDTA, 1% NP-40, and 0.7% Na-deoxycholate) and one wash with TE + 50 mM NaCl. DNA was eluted in freshly prepared elution buffer (50 mM Tris, pH 8, 10 mM EDTA, 1% SDS) at 65 °C for 20 min and then de-crosslinked overnight at 65 °C. Samples were treated with RNase A and proteinase K and DNA was purified by phenol:chloroform:isoamyl alcohol (P:C:IA).
Libraries were pre-pared using NEBNext Ultra II DNA Library Prep Kit (NEB), quantified by Qubit dsDNA HS Assay, quality-checked with Aligent Bioanalyzer HS DNA chip. Libraries were sequenced as 150 pb paired-end reads on the Illumina HiSeq platform.

treatment_protocol: Auxin (indole-3-acetic acid, IAA; Sigma, catalog no. I5148) was dissolved in water to a 200 mM stock solution and stored at -20 ºC. For AID-mediated degradation, auxin was titrated and used at a final concentration of 50 μM in culture media. Auxin treatment last 96 hours. Washout reintroduction treatment last 4.5 h.

value: Mouse embryonic stem cells, mESC


title: mESC, H2AK119ub1, Control 2

description: Library name: Control_UB_2


title: mESC, H2AK119ub1, Re-introduction 1

description: Library name: Re-introduction _UB_1

value: Auxin washout


title: Cu0_Fcol_4h_fish biological rep4


title: mESC, H2AK119ub1, Auxin 1

description: Library name: Auxin_UB_1

value: Auxin


title: Cu0_Fcol_4h_fish biological rep3


title: Cu0_Fcol_4h_fish biological rep1


title: mESC, H2AK119ub1, Auxin 2

description: Library name: Auxin_UB_2


title: Subject P146 (P146-T1F)


title: Nkx2-5Cre;Lmnb1Flox/+, P0.5 Heart, scRNA, Rep1

city: Baltimore

first: Yixian

state: MD

address: 3520 San Martin Dr

institute: Carnegie Institution of Washington

description: Library name: KB4_LB1Fplus_P0_5_scRNA_rep1

data_processing:
Reads were processed using Cell Ranger (v8.0.1) following the 10x Genomics protocol. The Mus musculus reference genome (mm10, version 3.0.0) was used for alignment and gene quantification. Downstream analyses were performed in R (v4.1.2) using the Seurat package (v5.4.0) following standard workflows from the Satija lab. Gene–cell count matrices from four samples were imported and converted into Seurat objects. Cells expressing fewer than 100 genes or more than 8,000 genes, as well as cells with greater than 30% mitochondrial transcript content, were excluded from further analysis. Filtered datasets were then merged and normalized. Data was log-normalized and highly variable features were identified, followed by scaling and principal component analysis (PCA). To improve normalization and integration across samples, SCTransform was applied, and datasets were integrated using canonical correlation analysis (CCA)-based integration. Dimensionality reduction was performed using PCA, and the first 17 principal components were used to construct a shared nearest neighbor graph. Cells were clustered using a resolution of 0.5 and visualized using Uniform Manifold Approximation and Projection (UMAP). Rdata files from public data sets were downloaded and preprocessed with the workflow prior to integration. Cell-type populations were identified based on the expression of canonical marker genes, as previously described by Shen J et al. Data was integrated both with all populations to assess heart population composition and non-ventricular cardiomyocytes populations excluded to enable focused analyses of cardiomyocyte-specific transcriptional programs.  Each filtered dataset was independently normalized using SCTransform to account for technical variation and improve data comparability. Following normalization, integration anchors were identified across the three datasets using canonical correlation analysis (CCA) with the first 12 principal components. These anchors were then used to integrate the datasets into a single combined object. The integrated dataset was subsequently scaled, and principal component analysis (PCA) was performed using the same 12 dimensions. A shared nearest neighbor graph was constructed based on these principal components, and unsupervised clustering was carried out with a resolution of 0.5. For visualization, Uniform Manifold Approximation and Projection (UMAP) was applied using the first 12 principal components to generate a two-dimensional representation of the data.
Assembly: GRCm38
Supplementary files format and content: Cell ranger outputs include the barcode.tsv, features.tsv and matrix.mtx. The integrated datasets containing only cardiomyocyte clusters were included as a R Data Serialization (.rds) file.

source_name: Heart

extract_protocol:
Hearts from P0.5 hearts were dissociated using the Pierce Primary Cardiomyocyte Isolation Kit from ThermoFisher Scientific.
Samples were processed with the Chromium GEM-X Single Cell 3' Kit v4 kit and associated library components as per manufacturer directions.

value: Heart

value: All heart cells

value: Nkx2-5Cre; Lmnb1 Flox/+

tag: timepoint


title: Cu0_Fcol_4h_fish biological rep2


title: Nkx2-5Cre;Lmnb1Flox/-, P0.5 Heart, scRNA, Rep2

description: Library name: KB3_LB1Fminus_P0_5_scRNA_rep2

value: Nkx2-5Cre; Lmnb1 Flox/-


title: Nkx2-5Cre;Lmnb1Flox/-, P0.5 Heart, scRNA, Rep1

description: Library name: KB2_LB1Fminus_P0_5_scRNA_rep1


title: non-Hoxa10+, non-Hoxa10 lineage, skeletal (Control&Mutant from Homeostasis, 5d and 14d post-fracture)

first: Philipp

last: Leucht

state: New York

address: 540 1st Avenue, RB 4-530

department: Orthopedic Surgery

institute: NYU Langone Health

description: Library name: Stromal

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using Cell Ranger software v2.1.1
Assembly: Mouse mm10
Supplementary files format and content: rds

source_name: Tibia

extract_protocol:
Skeletal elements were crushed once using a mortar and pestle, then cut into small pieces with scissors. Half of each sample was subjected to two rounds of enzymatic digestions with 0.25% Trypsin (powder; Millipore Sigma, T4799) and 0.8% collagenase type II (ThermoFisher Scientific, 17101015) at 37 °C under agitation for 20 minutes each.  The other half of each sample was subjected to 1 round of enzymatic digestion with 0.1% collagenase type I (Sigma, C3867) and 0.1% collagenase type IV (ThermoFisher Scientific, 17104019) followed by two rounds of digestion with 0.2% collagenase type II, at 37 °C under agitation for 20 minutes each. The resulting cell suspensions were filtered through a 70 μm strainer and centrifuged at 1500 rpm for 5 minutes at 4 °C. Red blood cells were lysed with NH4Cl (StemCell Technologies) for 10 minutes on ice, washed with staining medium (HBSS containing 2% fetal bovine serum (Life Technologies, 10437-028), 1% HEPES (10 mmol·L−1; Thermo Fisher Scientific) and 1% penicillin–streptomycin (Thermo Fisher Scientific)), and resuspended in HBSS. Samples were stained for CD45 (hematopoietic), TIE2 (endothelial), and TER-119 (erythroid). The six samples were then multiplexed using MULTI-seq (Sigma, LMO001-30RXN) according to the manufacturer’s instructions and then pooled. Nonhematopoietic/non-endothelial (CD45-Ter119-TIE2-) Hoxa10+ (GFP+Tomatovariable), Hoxa10 Lineage (GFP-Tomato+), and other stromal (GFP-Tomato-) cells were then separately isolated by flow cytometry from each of the 6 groups.
Nonhematopoietic/non-endothelial (CD45-Ter119-TIE2-) Hoxa10+ (GFP+Tomatovariable), Hoxa10 Lineage (GFP-Tomato+), and other stromal (GFP-Tomato-) cells were then separately isolated by flow cytometry from each of the 6 groups. The 3 sorted cell populations were then submitted to NYU Langone’s Genome Technology Center for 3 separate PIP-seq preparations (with each preparation containing a combination of the 6 multiplexed mouse groups).

treatment_protocol: Tibial fracture

value: Tibia

value: skeletal cells

value: Hoxa10 control and Hoxa10 homozygous mutant

value: Homeostasis, 5d-, 14d-postfracture


title: Hoxa10 lineage cells (Hoxa10 Control and Mutant from Homeostasis, 5d, and 14d post-fracture)

description: Library name: Tomato


title: Nkx2-5Cre;Lmnb1F/-, P7.5 Heart, bulk RNA-seq, Rep3

description: Library name: P7.5_LB1Fminus_Nkx2_5Cre_bulk_RNA_rep3

data_processing:
Reads were first adapter- and quality-trimmed using Cutadapt (removing 10 bases from the 5′ end and 5 bases from the 3′ end). The processed reads were then aligned to the mouse mm10 reference genome using HISAT2. The resulting alignments were converted to BAM format, sorted, and indexed using SAMtools. FeatureCounts was used to covert BAM files to a tab-delimited text file countaing the raw counts for each sample.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample.

extract_protocol:
Whole hearts were diseccted out of P7.5 pups and dipped in liquid nitrogen for 10 seconds before being crushed with a mortar and pestle. RNA was harvested with Rneasy Fibrous Tissue Mini kit.
Library was prepared Bulk using the Illumina TruSeq Stranded mRNA Library Prep kit.


title: Cu0_Fcol_1h_fish biological rep4

value: gill

value: exposed to copper sulfate and then immediately challenged with Fcolumnare


title: Cu0_Fcol_1h_fish biological rep5


title: Nkx2-5Cre;Lmnb1F/-, P7.5 Heart, bulk RNA-seq, Rep1

description: Library name: P7.5_LB1Fminus_Nkx2_5Cre_bulk_RNA_rep1


title: Hoxa10+ cells (Hoxa10 Control and Mutant from Homeostasis, 5d, and 14d post-fracture)

description: Library name: GFP-Positive


title: Nkx2-5Cre;Lmnb1F/+, P7.5 Heart, bulk RNA-seq, Rep4

description: Library name: P7.5_LB1Fplus_Nkx2_5Cre_bulk_RNA_rep4


title: Nkx2-5Cre;Lmnb1F/+, P7.5 Heart, bulk RNA-seq, Rep3

description: Library name: P7.5_LB1Fplus_Nkx2_5Cre_bulk_RNA_rep3


title: UCN_2

city: Nantong

first: Ling-Jie

last: Ma

state: Jiangsu

address: Seyuan Road 9

institute: Nantong University

description:
Library name: Sample 10
U3

data_processing:
Raw reads were processed to remove adapters and low-quality sequences. Clean reads were then aligned to the mouse reference genome using STAR. Gene-level counts were obtained from the uniquely aligned reads using HTSeq. Gene expression was quantified as FPKM values for visualization, whereas differential expression analysis was performed using raw read counts with DESeq2.
Assembly: Mus_musculus.GRCm39.109
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: trigeminal ganglion

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen). 1.5 μg of RNA was used to construct sequencing libraries.
Sequencing libraries for RNA-seq were prepared with the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: trigeminal ganglion


title: Cu0_Fcol_1h_fish biological rep3


title: Nkx2-5Cre;Lmnb1F/+, P7.5 Heart, bulk RNA-seq, Rep2

description: Library name: P7.5_LB1Fplus_Nkx2_5Cre_bulk_RNA_rep2


title: Nkx2-5Cre;Lmnb1F/+, P7.5 Heart, bulk RNA-seq, Rep1

description: Library name: P7.5_LB1Fplus_Nkx2_5Cre_bulk_RNA_rep1


title: Cu0_Fcol_1h_fish biological rep2


title: PBS_2

description:
Library name: Sample 8
P3


title: 1113-2 #2 P2

description: Library name: lib114835

value: airway epithelial cells

value: female

tag: study group


title: TART15

description: Library name: lib114834

tag: cell type

value: male

value: control

value: AEC


title: EED-Mutant RPR2 tumor 1260-2

city: Boston

first: Yixiang

last: Li

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: Library name: EED-Mutant 1260-2

data_processing:
Sequence tags were aligned with Burrows-Wheeler Aligner (BWA) to build mm10 and uniquely mapped, non-redundant reads were retained. These reads were used to generate binding sites with Model-Based Analysis of ChIP-Seq 2 (MACS v2.1.1.20160309), with narrow peak option and a q-value (FDR) threshold of 0.01.
Assembly: mm10
Supplementary files format and content: bw file

source_name: Lung tumor

growth_protocol: Tumors were harvested at necropsy and were flash-frozen

extract_protocol:
Nuclei isolation for ATAC-sequencing on mouse tumor tissue was performed using ATAC-Seq Kit (ActiveMotif, cat# 53150) following manufacture’s instruction. Briefly, 30mg frozen mouse RPR2 lung tumor tissues were minced with a razor blade and homogenized in ATAC-seq Lysis Buffer in a dounce homogenizer. Lysates were then filtered through a 40 μm cell strainer and Trypan blue at 0.4% was used to count 100,000 nuclei which were subsequently rinsed with ice-cold PBS and resuspended in ice-cold ATAC-seq Lysis Buffer.
After mixing with Tagmentation Master Mix, tagmentation reactions were incubated at 37 ºC and shaken at 800 RPM for 30 minutes on a thermomixer. Transposed DNA was purified using columns and libraries were amplified following manufacture’s manual. 50 million paired-end reads, where each read is 150 base pairs long, were sequenced on a NextSeq instrument (Illumina).

value: Lung tumor


title: Cu0_Fcol_1h_fish biological rep1

tag: treatment


title: Cu24_fish biological rep6

value: exposed to copper sulfate for 24h and then sampled


title: PBS_1

description:
Library name: Sample 7
P1


title: EED-Mutant RPR2 tumor 1257

description: Library name: EED-Mutant 1257


title: Cu24_fish biological rep5


title: UCN_1

description:
Library name: Sample 9
U1


title: Nkx2-5Cre;Lmnb1F/-, P7.5 Heart, bulk RNA-seq, Rep4

description: Library name: P7.5_LB1Fminus_Nkx2_5Cre_bulk_RNA_rep4

value: Heart

value: All heart cells


title: EED-Mutant RPR2 tumor 1256

description: Library name: EED-Mutant 1256


title: pIONT_3

description:
Library name: Sample 6
pIONT_3


title: pIONT_2

description:
Library name: Sample 5
pIONT_2


title: WT EED RPR2 tumor 1267-2

description: Library name: EED-WT 1267-2


title: Cu24_fish biological rep4


title: WT EED RPR2 tumor 1262

description: Library name: EED-WT 1262


title: WT EED RPR2 tumor 1267-1

description: Library name: EED-WT 1267-1


title: Cu24_fish biological rep3


title: Input of EED-Mutant RPR2 tumor 1254

description: Library name: 1254_Input

data_processing:
All samples were processed through the computational pipeline developed at the Dana-Farber Cancer Institute Center for Functional Cancer Epigenetics (CFCE) using primarily open-source programs. Sequence tags were aligned with Burrows-Wheeler Aligner (BWA) to build mm9 and uniquely mapped, non-redundant reads were retained. These reads were used to generate binding sites with Model-Based Analysis of ChIP-Seq 2 (MACS v2.1.1.20160309), with a q-value (FDR) threshold of 0.01. We evaluated multiple quality control criteria based on alignment information and peak quality: (i) sequence quality score; (ii) uniquely mappable reads (reads that can only map to one location in the genome); (iii) uniquely mappable locations (locations that can only be mapped by at least one read); (iv) peak overlap with Velcro regions, a comprehensive set of locations – also called consensus signal artifact regions – in the genome that have anomalous, unstructured high signal or read counts in next-generation sequencing experiments independent of cell line and of type of experiment; (v) number of total peaks (the minimum required was 1,000); (vi) high-confidence peaks (the number of peaks that are tenfold enriched over background); (vii) percentage overlap with known DHS sites derived from the ENCODE Project (the minimum required to meet the threshold was 80%); and (viii) peak conservation (a measure of sequence similarity across species based on the hypothesis that conserved sequences are more likely to be functional).
Assembly: mm9
Supplementary files format and content: bw files except for input samples

extract_protocol:
Frozen mouse tumor tissue was dry pulverized in liquid nitrogen until it was finely powdered. Pulverized tissue was resuspended for crosslinking in 2 mM of disuccinimidyl glutarate (DSG, Pierce) for 45 minutes at room temperature. The crosslinked material was pelleted by centrifugation at 2500 RCF for 5 min and resuspended in 1 ml of 1% formaldehyde for 10 minutes. Formaldehyde was quenched with 0.125 M glycine for 5 minutes at room temperature and then the crosslinked material washed with PBS. Washed cells were now pelleted and resuspended in 500 μl of 1% SDS (50 mM Tris-HCl pH 8, 10 mM EDTA) and sonicated for 10 minutes using Covaris E220 sonicator at the following settings: 140 peak incident power, 5% duty factor and 200 cycles per burst) in 1 ml AFA fiber millitubes. Chromatin was immunoprecipitated with 5 μg of antibody (EED Cell Signaling E4L6E; H3K27ac Diagenode C15410196; H3K27me3 Active Motif 61018; H3K4me3 Abcam ab8580). 5 μg of chromatin was used for histone mark ChIPs, and 40 μg of chromatin was used for EED ChIPs. Imunoprecipitated Chromatin was pulled down using Protein A/G beads (Invitrogen Dynabeads 1000-2D and 1000-4D). Chromatin antibody complex immobilized on beads was washed 6X with RIPA buffer and eluted in 1% SDS and 0.1M Sodium bicarbonate. ChIP-ed DNA was crosslinked with Proteinase K and column purified.
ChIP-seq libraries were made using Swift DNA Library Prep Kit (Swift Biosciences 10024). 75bp paired end reads were sequenced on a NextSeq instrument (Illumina).


title: pIONT_1

description:
Library name: Sample 4
pIONT_1


title: Cu24_fish biological rep2


title: sham_3

description:
Library name: Sample 3
sham_3


title: Input of EED-Mutant RPR2 tumor 1261

description: Library name: 1261_Input


title: Input of EED-Mutant RPR2 tumor 1260-4

description: Library name: 1260-4_Input


title: Input of EED-Mutant RPR2 tumor 1260-2

description: Library name: 1260-2_Input


title: Cu24_fish biological rep1


title: Input of EED-Mutant RPR2 tumor 1257

description: Library name: 1257_Input


title: sham_2

description:
Library name: Sample 2
sham_2


title: Input of EED-Mutant RPR2 tumor 1256

description: Library name: 1256_Input


title: Cu0_fish biological rep6

value: exposed to copper sulfate and then immediately sampled


title: Input of EED-WT RPR2 tumor 1262

description: Library name: 1262_Input


title: sham_1

description:
Library name: Sample 1
sham_1


title: Input of EED-WT RPR2 tumor 1267-2

description: Library name: 1267-2_Input


title: mESC, H2AK119ub1, Re-introduction 2

description: Library name: Re-introduction _UB_2

value: Mouse embryonic stem cells, mESC

value: Auxin washout


title: LSCR-treated MASLD mouse, liver, rep9

city: Qingdao

first: Liangxiu

last: Xing

state: Shandong

address: Laoshan

institute: Qingdao University

description:
Library name: LNP_09
bulk_LNP_all_counts.xlsx

data_processing:
Raw reads were filtered using fastp (v1.3.3).
Reads were aligned to the mm10 reference genome using Hisat2 (v2.2.1).
Gene-level counts were generated using featureCounts implemented in the Subread package (v2.0.2) based on the vM25 annotation, producing a gene-by-sample count matrix.
Genes with counts more than 10 in at least 20% of samples were retained. TPM values were calculated based on the vM25 annotation
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Liver

growth_protocol: Male C57BL/6 mouse were housed under specific pathogen-free conditions with a 12-h light/dark cycle, controlled temperature and humidity, and free access to food and water. Mice were started on a high-fat diet (HFD) at 4 weeks of age and fed the HFD for 18 weeks.

extract_protocol:
Total RNA was extracted from liver tissues using TRIzol reagent (TIANGEN, Cat# DP424) according to the manufacturer's instructions. RNA concentration was measured using a Qubit Fluorometer (Thermo Fisher Scientific), and RNA integrity was assessed using the RNA Nano 6000 Assay Kit on a Bioanalyzer 5400 system (Agilent Technologies, Cat# DNF-471).
RNA libraries were prepared using the Fast RNA-seq Lib Prep Kit V2 (ABclonal, Cat# RK20306) following the manufacturer's protocol.

treatment_protocol: Bulk RNA-seq was performed on three groups: Control (untreated HFD-fed mice, n=9), Exosome (HFD-fed mice treated with UCMSC-Exos, n=9), and LSCR (HFD-fed mice treated with LSCR, n=9). UCMSC-Exos and LSCR were administered via tail-vein injection every 72 hours for 8 weeks at a dose of 5×108 particles/g body weight.

value: Liver

tag: sample group

value: LSCR-treated MASLD mouse


title: Input of EED-WT RPR2 tumor 1267-1

description: Library name: 1267-1_Input

tag: tissue


title: Cu0_fish biological rep5

value: gill


title: EED ChIP-seq on EED-WT RPR2 tumor 1267-2

description: Library name: 1267-2EED

tag: genotype

tag: chip antibody

value: EED Cell Signaling E4L6E


title: Cu0_fish biological rep4


title: EED ChIP-seq on EED-WT RPR2 tumor 1267-1

description: Library name: 1267-1EED


title: Extra Hoxa10+ cells (Hoxa10 Control, 5d post-fracture)

description: Library name: DP15GFP-102125

value: Tibia

value: skeletal cells

value: Hoxa10 control and Hoxa10 homozygous mutant

value: Homeostasis, 5d-, 14d-postfracture


title: LSCR-treated MASLD mouse, liver, rep8

description:
Library name: LNP_08
bulk_LNP_all_counts.xlsx


title: LSCR-treated MASLD mouse, liver, rep7

description:
Library name: LNP_07
bulk_LNP_all_counts.xlsx


title: Cu0_fish biological rep3


title: H3K27me3 ChIP-seq on EED-WT RPR2 tumor 1267-1

description: Library name: 1267-1_K27me3

value: H3K27me3 Active Motif 61018


title: H3K27me3 ChIP-seq on EED-WT RPR2 tumor 1267-2

description: Library name: 1267-2_K27me3


title: Cu0_Fcol_1h_fish biological rep6

value: exposed to copper sulfate and then immediately challenged with Fcolumnare


title: Cu0_fish biological rep2


title: H3K27me3 ChIP-seq on EED-WT RPR2 tumor 1262

description: Library name: 1262_K27me3

value: Lung tumor


title: EED ChIP-seq on EED-WT RPR2 tumor 1262

description: Library name: 1262EED


title: Cu0_fish biological rep1


title: Nkx2-5Cre;Lmnb1F/-, P7.5 Heart, bulk RNA-seq, Rep2

description: Library name: P7.5_LB1Fminus_Nkx2_5Cre_bulk_RNA_rep2

value: Nkx2-5Cre; Lmnb1 Flox/-


title: H3K4me3 ChIP-seq on EED-WT RPR2 tumor 1267-1

description: Library name: 1267_1_K4me3

value: H3K4me3 Abcam ab8580


title: H3K4me3 ChIP-seq on EED-WT RPR2 tumor 1267-2

description: Library name: 1267_2_K4me3


title: LSCR-treated MASLD mouse, liver, rep5

description:
Library name: LNP_05
bulk_LNP_all_counts.xlsx


title: H3K4me3 ChIP-seq on EED-WT RPR2 tumor 1262

description: Library name: 1262_K4me3


title: control_fish biological rep6

value: no treatment control


title: H3K27ac ChIP-seq on EED-Mutant RPR2 tumor 1254

description: Library name: 1254K27ac

value: H3K27ac Diagenode C15410196


title: LSCR-treated MASLD mouse, liver, rep4

description:
Library name: LNP_04
bulk_LNP_all_counts.xlsx


title: H3K27ac ChIP-seq on EED-Mutant RPR2 tumor 1261

description: Library name: 1261K27ac


title: LSCR-treated MASLD mouse, liver, rep3

description:
Library name: LNP_03
bulk_LNP_all_counts.xlsx


title: control_fish biological rep5


title: H3K27ac ChIP-seq on EED-Mutant RPR2 tumor 1260-2

description: Library name: 1260-2K27ac


title: H3K27ac ChIP-seq on EED-Mutant RPR2 tumor 1260-4

description: Library name: 1260-4K27ac


title: control_fish biological rep4


title: H3K27ac ChIP-seq on EED-Mutant RPR2 tumor 1257

description: Library name: 1257K27ac


title: LSCR-treated MASLD mouse, liver, rep2

description:
Library name: LNP_02
bulk_LNP_all_counts.xlsx


title: H3K27ac ChIP-seq on EED-Mutant RPR2 tumor 1256

description: Library name: 1256K27ac


title: H3K27ac ChIP-seq on EED-WT RPR2 tumor 1262

description: Library name: 1262K27ac


title: EED-Mutant RPR2 tumor 1261

description: Library name: EED-Mutant 1261


title: EED-Mutant RPR2 tumor 1260-4

description: Library name: EED-Mutant 1260-4


title: LSCR-treated MASLD mouse, liver, rep1

description:
Library name: LNP_01
bulk_LNP_all_counts.xlsx


title: control_fish biological rep3


title: H3K27ac ChIP-seq on EED-WT RPR2 tumor 1267-2

description: Library name: 1267-2K27ac


title: H3K27ac ChIP-seq on EED-WT RPR2 tumor 1267-1

description: Library name: 1267-1K27ac


title: UCMSC-Exos-treated MASLD mouse, liver, rep9

description:
Library name: Treat_09
bulk_Con&Exo_all_counts.txt

value: UCMSC-Exos-treated MASLD mouse


title: control_fish biological rep2


title: EED-Mutant RPR2 tumor 1254

description: Library name: EED-Mutant 1254


title: B cells FB donors S6, S7, S8, S9, H9, H10, H11, H12, H13, H14, H15 multiplex, replicate 4

city: Phnom Penh

first: Sivyi

last: Chhay

address: Monivong 5

department: BAIA

country: Cambodia

institute: Institut Pasteur du Cambodge

description:
Library name: S6_S7_S8_S9_H9_H10_H11_H12_H13_H14_H15-FB-4
FB: read1 file contains cell barcode and UMI, read2 file contains transcript, I1 and I2 files contain Illumina sample indices

data_processing:
cellranger multi (Cell Ranger, 10X Genomics, v.7.1.0) was run to separate the single GEX libraries based on the FB libraries content
reads from each GEX library were extracted from the results bamtofastq contained in the Cell Ranger suite, 10X Genomics, v.7.1.0
the final transcript and VDJ counts were obtained running cellranger multi (Cell Ranger, 10X Genomics, v.7.1.0) on the extracted GEX reads, including the VDJ libraries in the command configuration
Assembly: 10X human reference refdata-gex-GRCh38-2020-A
Assembly: refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0
Supplementary files format and content: Demultiplexed cellranger multi output mRNA count matrix and VDJ information

source_name: filtered B cells

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from venous blood samples by density gradient centrifugation and used fresh. PBMCs were stained with biotinylated sE-dimer protein complexed with fluorescent barcoded Klickmers (Dcode Klickmer, APC or PE; Immudex), followed by switched memory B-cell markers. To increase the yield of sE-dimer-binding cells, samples were pooled prior to sorting (4, 9, or 11 donors per pool). sE-dimer-binding B cells were FACS-sorted (FACSAria Fusion, BD Biosciences) into PBS supplemented with 0.2% BSA from 9 subclinical individuals and 15 hospitalized patients.
Single-cell RNA sequencing libraries were prepared using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 with dual indexing and Feature Barcoding technology (10x Genomics), according to the manufacturer’s protocol. Three types of libraries were generated: 5’ gene expression (GEX), B-cell receptor (BCR) V(D)J, and Feature Barcode libraries.

value: filtered B cells

value: B cells


title: control_fish biological rep1


title: B cells VDJ donors S6, S7, S8, S9, H9, H10, H11, H12, H13, H14, H15 multiplex

description:
Library name: S6_S7_S8_S9_H9_H10_H11_H12_H13_H14_H15-VDJ
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript, I1 and I2 files contain Illumina sample indicess: processed data for demultiplexed samples


title: UCMSC-Exos-treated MASLD mouse, liver, rep8

description:
Library name: Treat_08
bulk_Con&Exo_all_counts.txt

value: Liver


title: B cells FB donors S6, S7, S8, S9, H9, H10, H11, H12, H13, H14, H15 multiplex, replicate 3

description:
Library name: S6_S7_S8_S9_H9_H10_H11_H12_H13_H14_H15-FB-3
FB: read1 file contains cell barcode and UMI, read2 file contains transcript, I1 and I2 files contain Illumina sample indices


title: B cells FB donors S6, S7, S8, S9, H9, H10, H11, H12, H13, H14, H15 multiplex, replicate 2

description:
Library name: S6_S7_S8_S9_H9_H10_H11_H12_H13_H14_H15-FB-2
FB: read1 file contains cell barcode and UMI, read2 file contains transcript, I1 and I2 files contain Illumina sample indices


title: HepG2 Cells_GenX (100 µM)_2

city: Winston-Salem

first: Sarah

last: Adjei-Fremah

state: North Carolina

address: 601 S Martin Luther King Jr Dr

department: Biological Sciences

institute: Winston-Salem State University

description:
Library name: Sample_G100_replicate 2
GenX (10 0µM) replicate 2

data_processing:
Raw reads were quality-checked using FastQC.
Reads were aligned to the human genome (GRCh38) using STAR aligner.
Counts were generated using feature Counts, and differential expression analysis was performed with DESeq2.
Assembly: Human reference genome GRCh38 (GENCODE release 42, Ensembl annotation) was used for read alignment and gene annotation.
Supplementary files format and content: Raw counts of mitochondrial genes per sample

source_name: liver

growth_protocol: HepG2 cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C with 5% CO₂.

extract_protocol:
After treatment, mitochondria were isolated using the Fisher Scientific Mitochondria Isolation Kit per manufacturer’s protocol. Total mitochondrial RNA was extracted using the TRIzol method. RNA concentration and purity were measured using Nanodrop; integrity was confirmed with Agilent Bioanalyzer (RIN > 7).
Ribosomal RNA-depleted libraries were constructed from 2 µg of total RNA using Azenta’s stranded total RNA-Seq workflow.

treatment_protocol: Cells were treated with GenX at final concentrations of 10 µM or 100 µM for 48 hours. Control samples received vehicle (DMSO) only.

value: liver

tag: cell line

value: Epithelial

value: WT

tag: batch


title: UCMSC-Exos-treated MASLD mouse, liver, rep7

description:
Library name: Treat_07
bulk_Con&Exo_all_counts.txt


title: B cells FB donors S6, S7, S8, S9, H9, H10, H11, H12, H13, H14, H15 multiplex, replicate 1

description:
Library name: S6_S7_S8_S9_H9_H10_H11_H12_H13_H14_H15-FB-1
FB: read1 file contains cell barcode and UMI, read2 file contains transcript, I1 and I2 files contain Illumina sample indices


title: UCMSC-Exos-treated MASLD mouse, liver, rep6

description:
Library name: Treat_06
bulk_Con&Exo_all_counts.txt


title: B cells GEX donors S6, S7, S8, S9, H9, H10, H11, H12, H13, H14, H15 multiplex

description:
Library name: S6_S7_S8_S9_H9_H10_H11_H12_H13_H14_H15-GEX
GEX (5’ mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript, I1 and I2 files contain Illumina sample indicess: processed data for demultiplexed samples


title: B cells VDJ donors S1, S2, S3, S4, S5, H5, H6, H7, H8 multiplex, replicate 3

description:
Library name: S1_S2_S3_S4_S5_H5_H6_H7_H8-VDJ-3
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript, I1 and I2 files contain Illumina sample indicess: processed data for demultiplexed samples


title: HepG2 Cells_GenX (10 µM)_2

description:
Library name: Sample _G10_replicate 2
GenX (10 µM) replicate 2

value: 10 µM


title: HepG2 Cells_GenX (100 µM)_1

description:
Library name: Sample_G100_replicate 1
GenX (100 µM) replicate 1


title: B cells VDJ donors S1, S2, S3, S4, S5, H5, H6, H7, H8 multiplex, replicate 2

description:
Library name: S1_S2_S3_S4_S5_H5_H6_H7_H8-VDJ-2
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript, I1 and I2 files contain Illumina sample indicess: processed data for demultiplexed samples


title: UCMSC-Exos-treated MASLD mouse, liver, rep5

description:
Library name: Treat_05
bulk_Con&Exo_all_counts.txt


title: HepG2 Cells_GenX (10 µM)_1

description:
Library name: Sample _G10_replicate 1
GenX (10 µM) replicate 1


title: B cells FB donors S1, S2, S3, S4, S5, H5, H6, H7, H8 multiplex

description:
Library name: S1_S2_S3_S4_S5_H5_H6_H7_H8-FB
FB: read1 file contains cell barcode and UMI, read2 file contains transcript, I1 and I2 files contain Illumina sample indices


title: B cells VDJ donors S1, S2, S3, S4, S5, H5, H6, H7, H8 multiplex, replicate 1

description:
Library name: S1_S2_S3_S4_S5_H5_H6_H7_H8-VDJ-1
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript, I1 and I2 files contain Illumina sample indicess: processed data for demultiplexed samples


title: UCMSC-Exos-treated MASLD mouse, liver, rep3

description:
Library name: Treat_03
bulk_Con&Exo_all_counts.txt


title: B cells GEX donors S1, S2, S3, S4, S5, H5, H6, H7, H8 multiplex

description:
Library name: S1_S2_S3_S4_S5_H5_H6_H7_H8-GEX
GEX (5’ mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript, I1 and I2 files contain Illumina sample indicess: processed data for demultiplexed samples


title: HepG2 Cells_Control (0 µM)_2

description:
Library name: Sample _Control_replicate 2
Control replicate 2

value: 0 µM


title: UCMSC-Exos-treated MASLD mouse, liver, rep2

description:
Library name: Treat_02
bulk_Con&Exo_all_counts.txt


title: B cells FB donors H1, H2, H3, H4 multiplex

description:
Library name: H1_H2_H3_H4-FB
FB: read1 file contains cell barcode and UMI, read2 file contains transcript, I1 and I2 files contain Illumina sample indices


title: HepG2 Cells_Control (0 µM)_1

description:
Library name: Sample _Control_replicate 1
Control replicate 1


title: B cells GEX donors H1, H2, H3, H4 multiplex

description:
Library name: H1_H2_H3_H4-GEX
GEX (5’ mRNA): read1 file contains cell barcode and UMI, read2 file contains transcript, I1 and I2 files contain Illumina sample indices: processed data for demultiplexed samples


title: B cells VDJ donors H1, H2, H3, H4 multiplex

description:
Library name: H1_H2_H3_H4-VDJ
VDJ-B: read1 file contains cell barcode and UMI, read2 file contains transcript, I1 and I2 files contain Illumina sample indicess: processed data for demultiplexed samples


title: UCMSC-Exos-treated MASLD mouse, liver, rep1

description:
Library name: Treat_01
bulk_Con&Exo_all_counts.txt


title: Human U2OS cells, 50 μM CCCP for 30 min followed by 6 h washout (W6H), Biol. Rep. 3

city: Hangzhou

first: Nuo

last: Chen

address: 866 Yuhangtang Rd, Hangzhou 310058, P.R. China

institute: Zhejiang University

description:
Library name: W6H3
Column name in Processed data.xls: W6H3

data_processing:
Raw FASTQ reads were processed using fastp software to remove adapter sequences, poly-N reads, and low-quality reads, yielding clean reads. Clean reads were aligned to the human reference genome (GRCh38) using HISAT2 v2.0.5. Gene expression levels were quantified using featureCounts v1.5.0-p3, and FPKM values were calculated for each gene. Differential expression analysis was performed using DESeq2 R package (1.20.0), with genes showing adjusted p-value ≤ 0.05 considered differentially expressed.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data.xls: Excel file containing count and FPKM values for all 12 samples (4 conditions × 3 biological replicates), with genes as rows and samples as columns.

source_name: Human U2OS cells

growth_protocol: U2OS cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. The library was prepared after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Library quality was assessed using Qubit, real-time PCR, and Bioanalyzer.

treatment_protocol: Cells were treated with 50 μM CCCP (carbonyl cyanide 3-chlorophenylhydrazone) for 30 minutes, followed by washout with fresh DMEM medium for 0, 1, or 6 hours. Control cells were treated with an equivalent volume of DMSO.

value: Human U2OS cells

value: Osteosarcoma cells


title: Human U2OS cells, 50 μM CCCP for 30 min followed by 6 h washout (W6H), Biol. Rep. 2

description:
Library name: W6H2
Column name in Processed data.xls: W6H2


title: MASLD mouse, liver, rep9

description:
Library name: CTRL_09
bulk_Con&Exo_all_counts.txt

value: MASLD mouse


title: with APX2009 treatment 3

city: Miami

first: Wael

last: El-Rifai

state: FL

address: Griffin Cancer Research Building,1425 NW 10th Ave

department: Department of Surgery and Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

description: Library name: PA3

data_processing:
Raw paired-end reads were trimmed to remove adapter sequences and low-quality nucleotides using Trimmomatic v0.36. The trimmed reads were aligned to the Homo sapiens GRCh38 reference genome supplemented with ERCC sequences, available from Ensembl, using STAR v2.5.2b. Unique gene-level read counts were generated using featureCounts from the Subread package v1.5.2. Counts were summarized using the gene_id feature in the annotation file, and only uniquely mapped reads falling within annotated exon regions were counted.
Assembly: GRCh38
Supplementary files format and content: The processed data file, OE33_parental_cells_APX2009_RNAseq_GeneWiz_2026_6samples_count_matrix.tsv.gz, is a gzip-compressed, tab-delimited gene-level raw-count matrix. Rows represent gene_id features from the GRCh38-with-ERCC annotation, columns represent the 6 biological samples, and values are unnormalized integer read counts.

source_name: esophageal adenocarcinoma (EAC)

growth_protocol: OE33 cells were cultured RPMI1640 supplemented with 10% FBS,  and 1% Pen-Step with 5% CO2 at 37C.

extract_protocol:
RNA was extracted from cells using RLT buffer (RNeasy Kit Qiagen)
Standard RNA-sequencing (mRNA-Seq) in eukaryotic samples. Polyadenylated mRNA is selectively enriched from total RNA using oligo(dT) magnetic beads. High-temperature thermal treatment in divalent cation buffer fragments the mRNA to ~250–300 bp.

treatment_protocol: Cells were treated with 15µM APX2009, APE1-redox-specific inhibitor, for 24h before collection. Untreated cells work as control.

value: esophageal adenocarcinoma (EAC)


title: Human U2OS cells, 50 μM CCCP for 30 min followed by 6 h washout (W6H), Biol. Rep. 1

description:
Library name: W6H1
Column name in Processed data.xls: W6H1


title: with APX2009 treatment 2

description: Library name: PA2


title: Human U2OS cells, 50 μM CCCP for 30 min followed by 1 h washout (W1H), Biol. Rep. 2

description:
Library name: W1H2
Column name in Processed data.xls: W1H2


title: Human U2OS cells, 50 μM CCCP for 30 min followed by 1 h washout (W1H), Biol. Rep. 3

description:
Library name: W1H3
Column name in Processed data.xls: W1H3


title: with APX2009 treatment 1

description: Library name: PA1


title: Human U2OS cells, 50 μM CCCP for 30 min followed by 1 h washout (W1H), Biol. Rep. 1

description:
Library name: W1H1
Column name in Processed data.xls: W1H1


title: MASLD mouse, liver, rep7

description:
Library name: CTRL_07
bulk_Con&Exo_all_counts.txt


title: Human U2OS cells, 50 μM CCCP for 30 min (CCCP), Biol. Rep. 3

description:
Library name: CCCP3
Column name in Processed data.xls: CCCP3

value: 50 μM CCCP for 30 min (CCCP)


title: Untreated control 3

description: Library name: P3

value: untreated


title: Human U2OS cells, 50 μM CCCP for 30 min (CCCP), Biol. Rep. 1

description:
Library name: CCCP1
Column name in Processed data.xls: CCCP1


title: Untreated control 2

description: Library name: P2


title: MASLD mouse, liver, rep6

description:
Library name: CTRL_06
bulk_Con&Exo_all_counts.txt


title: Human U2OS cells, 50 μM CCCP for 30 min (CCCP), Biol. Rep. 2

description:
Library name: CCCP2
Column name in Processed data.xls: CCCP2


title: Human U2OS cells, untreated control (WT), Biol. Rep. 2

description:
Library name: WT2
Column name in Processed data.xls: WT2

value: untreated control (WT)


title: MASLD mouse, liver, rep5

description:
Library name: CTRL_05
bulk_Con&Exo_all_counts.txt


title: MASLD mouse, liver, rep4

description:
Library name: CTRL_04
bulk_Con&Exo_all_counts.txt


title: Human U2OS cells, untreated control (WT), Biol. Rep. 1

description:
Library name: WT1
Column name in Processed data.xls: WT1


title: Untreated control 1

description: Library name: P1


title: Osteoporosis sample 7

city: México city

first: Rogelio Frank

last: Jiménez-Ortega

state: Alcaldía Tlalpan

address: Calzada México-Xochimilco No. 289

department: Subdirección de investigación Biomédica

institute: Instituto Nacional de Rehabilitación

description:
Library name: ID-14
Condition: Osteoporosis; source: peripheral blood CD14-positive monocytes; batch/source folder: 20170821_14; processed matrix column: ID-14.

data_processing:
FASTQ files were evaluated with FastQC. Seqtk was used to remove the first three bases from each read, stretches of more than 15 adenines, and Illumina small RNA adapter sequence was removed with reaper.
Small RNA-seq reads were processed with the exceRpt pipeline. Low-quality or contaminant reads were filtered, and surviving reads were aligned to miRBase v21, transcriptome, and genome using STAR against GRCh38.
Processed matrix OP_gene_raw_counts_matrix.tsv.gz contains raw gene-level counts for all 14 libraries.
Processed matrix OP_gene_TPM_normalized_matrix.tsv.gz contains TPM-normalized expression values for all 14 libraries.
Library identifiers in the processed matrices correspond to library names ID-1 through ID-14 in the SAMPLES section.
Differential expression was evaluated using TMM normalization, voomWithQualityWeights, and limma-based linear modeling.
Assembly: Homo sapiens GRCh38/hg38
Supplementary files format and content: OP_gene_raw_counts_matrix.tsv.gz: tab-delimited raw count matrix; rows are gene identifiers and columns are library names ID-1 through ID-14.
Supplementary files format and content: OP_gene_TPM_normalized_matrix.tsv.gz: tab-delimited TPM-normalized expression matrix; rows are gene identifiers and columns are library names ID-1 through ID-14.

source_name: peripheral blood

growth_protocol: Not applicable; primary human peripheral blood samples were analyzed.

extract_protocol:
Peripheral blood was collected in CPT tubes. Peripheral blood mononuclear cells were obtained and CD14-positive monocytes were enriched using an EasySep negative-selection kit. Total RNA was purified using the miRNeasy Mini Kit (QIAGEN). RNA quantity and integrity were assessed using a Qubit 3.0 Fluorometer and an Agilent 2100 Bioanalyzer.
Small RNA sequencing libraries were prepared from total RNA using the SMARTer small RNA-Seq Kit for Illumina (Clontech). Libraries were prepared by polyadenylation, cDNA synthesis, adapter incorporation, PCR amplification with Illumina adapters, size selection with Agencourt AMPure XP beads, and sequencing for 50 cycles on an Illumina NextSeq 500.

treatment_protocol: No in vitro treatment was applied. Samples were classified according to clinical/densitometric status as non-osteoporotic control or osteoporosis.

value: peripheral blood

value: CD14-positive monocyte

value: Osteoporosis