title: 16s microbiome data for patient 16 as JEB control at week 0

description: Library name: 1985set2_257_AP16Week0-C


title: MITF_SETD6_KO3 cells

status: Public on Aug 20 2025

type: SRA

city: Be'er Sheva

first: Dan

last: Levy

address: David Ben Gurion Blvd 1

country: Israel

institute: Ben-Gurion University

description: Library name: Sample 15

library_source: genomic

data_processing:
Trim Galore v0.4.5 (length= 25, q- 25)
FastQC v0.12.0 was used for reads quality control
BWA Mapper (v0.7.12,  t=20, B= 5) aligned paired-end reads to reference human genome assembly hg38 and to  spike-in control (Escherichia coli) reference genome assembly
SAMtools removed PCR duplicates and created coordinate-sorted BAM files
Bigwig files were created by bamCoverage
Reads that refer to off-chromosome locations were removed with BedClip v377 and sorted by Bedtools v2.30.0
Bigwig files of each sample and corresponding IgG control were created with bedGraphToBigWig v2.8 by deepTools.
Peak calling results by Macs2 and SEACR  are presented as bed files
Assembly: GRCh38
Supplementary files format and content: bed files and bigwig files
Library strategy: CUT&Run

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: SKmel147 cells  were maintained in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum (FBS), penicillin-streptomycin , 2 mg/ml L-glutamine and non-essential amino acids.

extract_protocol:
EpiCypher CUT&RUN Protocol
EpiCypher library kit protocol

tag: cell line

tag: genotype

value: SETD6 KO Cells


title: mutant, -Mg, batch3, rep1

city: Bethesda

first: Hernan

middle: A

last: Lorenzi

state: Maryland

address: 8 Center Dr, Bldg 8A

department: National Institutes of Diabetes and Digestive and Kidney Diseas

country: USA

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
Libraries were sequenced using a HiSeq 2500 sequencer to generate single-end reads.
Sequencing reads were quality trimmed and sequencing adapters removed with fastp (v0.23.2). Trimmed reads were then mapped to the GenBank B. pertussis Tohama I assembly GCF_000195715.1 with STAR (v2.7.10a) and quantification of fragments per gene was carried out with the featureCounts tool from Subread software (v2.0.1) by counting reads falling within gene features.
Assembly: GCF_000195715.1
Supplementary files format and content: Tab-delimited test file with raw read counts per sample per gene.
Supplementary files format and content: BigWig files with RNA-Seq reads mapped to GCF_000195715.1 assembly.

molecule: total RNA

organism: Bordetella pertussis Tohama I

growth_protocol: Bordetella pertussis strains were grown at 37˚C in Bordet Gengou media containing streptomycin (50 µ/mL) in the absence or presence of 50 mM MgSO4. After 3 days, cells were scraped from plates and resuspended in PLB medium without MgSO4 to obtain an initial OD600 between 0.1 and 0.2.  Cells were then incubated at 37°C with shaking at 250 rpm until mid-log phase (OD600 ~ 0.5).

extract_protocol:
Culture aliquots of 7 ml were collected by centrifugation, and total RNA was isolated by the hot-phenol method (Moon et al. 2021).  Total RNA was treated with DNase (Turbo DNA-free kit; Life Technologies, Inc.) for 1 h at 37° C, followed by phenol extraction and ethanol precipitation. rRNA wasremoved using the RiboZero kit.
Strand-specific Illumina DNA libraries were prepared for Illumina sequencing using the ScriptSeq 2.0 kit (Illumina).

tag: tissue

tag: batch number

tag: treatment

value: without Mg


title: RNAseq of porcine: skin woundDay_6_ID1326_Wound_K_edge

city: Santa Cruz

first: Ksenia

last: Zlobina

state: California

address: 1156 High Street

department: Applied Mathematics

institute: University of California Santa Cruz

description:
Library name: G_69_K_E_1
G_69_K_E

data_processing:
The folowings prepared by Novogene: Raw Data, as well as gene counts in raw and normalized format: gene_count.txt and  gene_fkpm.txt
Assembly: Sus scrofa
Supplementary files format and content: gene_count.txt - the readcount list with the annotation of each gene
Supplementary files format and content: gene_fpkm.txt - the FPKM list with the annotation of each gene

organism: Sus scrofa domesticus

source_name: Skin wound tissue

extract_protocol:
mRNA was extracted from these samples with the RNeasy fibrous tissue mini kit (Qiagen)
>200ng mRNA/sample were sent to Novogene for RNA sequencing. The followings were done by Novogene: 1. RNA Sample QC 2. Library Preparation (Poly-A Enrichment) 3. Sequencing (Illumina – PE150 – 20M Paired Reads)

value: Skin wound tissue

tag: time

tag: location

value: edge

tag: anumal id

tag: wound id


title: 16s microbiome data for patient 16 as JEB sample at week 0, rep 2

city: Chicago

first: Ziyou

last: Ren

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

description: Library name: 1985set2_256_AP16Week0-2

data_processing:
Cutadapt v3.5 was used to trim forward and reverse primers from sequences. Reads were also trimmed and filtered for quality using DADA2 v1.32.0, with the following changes from default parameters: acceptable lengths were set to between 100 (minLen) and 1600 bp (maxLen), minimum quality score (minQ) set to 3, maxEE of 2, and rm.phix as FALSE
Error rates were estimated using PacBioErrfun, which is recommended for analysis of PacBio circular consensus reads. To follow, reads were separated into ASVs using dada2’s divisive partitioning machine learning approach. For both error modeling and divisive partitioning, band size was increased to 32 for sequence alignment in order to accommodate for increased rate of insertions and deletions in PacBio sequences.19 Chimeric sequences were identified and removed using the de novo approach included within dada2, with minFoldParentAbundance increased to 3.5.
Assembly: hg38
Supplementary files format and content: Excel file include count value
Library strategy: 16s microbiome

source_name: skin

extract_protocol:
Genomic DNA was extracted using a Maxwell 16 LEV Blood DNA Kit (Promega, Madison, WI) implemented on a Maxwell 16 Instrument, following the manufacturer’s instructions with minor modifications
Genomic DNA was prepared for sequencing on a PacBio Revio sequencer using a two-stage PCR protocol, similar to that described for Illumina amplicon library preparation.15 In the first stage of PCR, DNA was PCR amplified with primers 27F and 1492R (TTTCTGTTGGTGCTGATATTGCAGRGTTYGATYMTGGCTCAG and ACTTGCCTGTCGCTCTATCTTC RGYTACCTTGTTACGACTT, respectively) using domain-level bacterial primers as described by PacBio.
The underlined regions, however, represent Oxford Nanopore Universal sequences for tailing PCR primers’ linker sequences. In the second stage of PCR, amplicons from the first stage were used as a template and amplified with primers that contained PacBio Kinnex adapter sequences, combinatorial dual indices, and the ONT linker sequences at the 3’ ends of the primers . Library preparation was performed using a two-stage PCR amplification protocol but with primers targeting the full 16S rRNA gene

value: skin


title: RNAseq of porcine: skin woundDay_6_ID1326_Wound_K_center

description:
Library name: G_70_K_C_1
G_70_K_C

value: center


title: 16s microbiome data for patient 16 as JEB sample at week 0, rep 1

description: Library name: 1985set2_255_AP16Week0-1


title: mutant, -Mg, batch2, rep2


title: 16s microbiome data for patient 15 as JEB control at week 12

description: Library name: 1985set2_254_AP15Week12-C


title: RNAseq of porcine: skin woundDay_1_ID1324_Wound_A_edge

description:
Library name: B_11_A_E_1
B_11_A_E


title: 16s microbiome data for patient 15 as JEB sample at week 12, rep 2

description: Library name: 1985set2_253_AP15Week12-2


title: mutant, -Mg, batch2, rep1


title: RNAseq of porcine: skin woundDay_6_ID1327_Wound_B_edge

description:
Library name: G_71_B_E_1
G_71_B_E


title: RNAseq of porcine: skin woundDay_6_ID1327_Wound_B_center

description:
Library name: G_72_B_C_1
G_72_B_C


title: BRD4_SETD6_Control2 cells

description: Library name: Sample 9

value: SETD6 CT Cells


title: 16s microbiome data for patient 15 as JEB sample at week 8, rep 2

description: Library name: 1985set2_251_AP15Week8-2


title: mutant, -Mg, batch1, rep2


title: mutant, -Mg, batch1, rep1


title: BRD4_SETD6_Control1 cells

description: Library name: Sample 8


title: IgG_SETD6_Control1B cells

description: Library name: Sample 7


title: RNAseq of porcine: skin woundDay_6_ID1327_Wound_K_center

description:
Library name: G_74_K_C_1
G_74_K_C


title: 16s microbiome data for patient 15 as JEB sample at week 8, rep 1

description: Library name: 1985set2_250_AP15Week8-1


title: BRD4_SETD6_KO3 cells

description: Library name: Sample 11


title: Flag_BRD4_K99R2 cells

description: Library name: Sample 5

value: Parental Cells


title: IgG_SETD6_Control1A cells

description: Library name: Sample 6


title: 16s microbiome data for patient 15 as JEB sample at week 4, rep 1

description: Library name: 1985set2_248_AP15Week4-1


title: Salmonella, delta_relA with Magnesium, biol rep 1

city: FRIBOURG

first: Laurent

last: Poirel

address: Ch. du Musée 18

department: Medicine

country: France

institute: Université de Fribourg

description: Library name: Sample 10

data_processing:
CLC software (Qiagen) version 24 was used to process and analyze the data.
Raw data were paired, trimmed, and mapped against the reference genome of Salmonella enterica serovar Typhimurium (accession numbers CP001362 and CP001363)
Differential expression analysis (DE) and volcano plots were generated using CLC, with a choosen cutoff of log2 fold change and FDR < 0.05 to narrow down the deregulated transcripts.
Unsupervised heatmaps were generated using the mean of Transcript Per Million (TPM) in log10 of each condition and plotted using R package ggplot2
Assembly: Trimmed data were mapped  against the reference genome of Salmonella enterica serovar Typhimurium (accession numbers CP001362 and CP001363)
Supplementary files format and content: csv file include TPM and total count values for each sample
Supplementary files format and content: In addition, protein and gene IDs have been included

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: bacteria

growth_protocol: Salmonella strains (WT or ΔrelA) were grown overnight in MOPS in three biological replicates. Bacteria were then diluted in MOPS (1:50) and grow aerobically for 90 min at 37°C to reach an OD600 of 0.2-0.3 in 50 ml.

extract_protocol:
RNA extraction was performed using the zymo kit for quick RNA extraction. DNase treatment was carried out using the Turbo DNase kit from Invitrogen. After quality checking with a TapeStation (Agilent), RNA samples were sent to Genewiz.
rRNA depletion was performed using NEBNext rRNA Depletion Kit (Bacteria). RNA sequencing library preparation was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, enriched RNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).
The sequencing libraries were multiplexed and loaded on the flowcell on the Illumina NovaSeq X plus instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5. Image analysis and base calling were conducted by the NovaSeq Control Software v1.3.1 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.

treatment_protocol: When needed, media was supplemented with 0.5 MnSO4. After 30 min of stress, bacteria were centrifuged and the pellets froze at -80°C.

value: bacteria

value: relA knockdown

value: addition of Manganese

tag: batch

value: 8th of September 2024


title: RNAseq of porcine: skin woundDay_5_ID1325_Wound_K_center

description:
Library name: F_66_K_C_1
F_66_K_C


title: Salmonella, delta_relA with Magnesium, biol rep 3

description: Library name: Sample 12


title: 16s microbiome data for patient 15 as JEB sample at week 4, rep 2

description: Library name: 1985set2_249_AP15Week4-2


title: Salmonella, delta_relA with Magnesium, biol rep 2

description: Library name: Sample 11


title: RNAseq of porcine: skin woundDay_6_ID1328_Wound_K_center

description:
Library name: G_78_K_C_1
G_78_K_C


title: Salmonella, delta_relA without treatment, biol rep 3

description: Library name: Sample 9


title: Flag_BRD4_K99R1 cells

description: Library name: Sample 4


title: 16s microbiome data for patient 15 as JEB control at week 0

description: Library name: 1985set2_247_AP15Week0-C


title: 16s microbiome data for patient 15 as JEB sample at week 0, rep 2

description: Library name: 1985set2_246_AP15Week0-2


title: BRD4_SETD6_KO1 cells

description: Library name: Sample 10


title: Salmonella, delta_relA without treatment, biol rep 2

description: Library name: Sample 8


title: Flag_BRD4_WT1 cells

description: Library name: Sample 2


title: RNAseq of porcine: skin woundDay_6_ID1327_Wound_K_edge

description:
Library name: G_73_K_E_1
G_73_K_E


title: RNAseq of porcine: skin woundDay_7_ID1323_Wound_E_edge

description:
Library name: H_79_E_E_1
H_79_E_E


title: 16s microbiome data for patient 15 as JEB sample at week 12, rep 1

description: Library name: 1985set2_252_AP15Week12-1


title: Salmonella, delta_relA without treatment, biol rep 1

description: Library name: Sample 7


title: Flag_Empty cells

description: Library name: Sample 1


title: RNAseq of porcine: skin woundDay_7_ID1323_Wound_E_center

description:
Library name: H_80_E_C_1
H_80_E_C


title: RNAseq of porcine: skin woundDay_1_ID1324_Wound_A_center

description:
Library name: B_12_A_C_1
B_12_A_C


title: 16s microbiome data for patient 14 as DEB sample at week 12, rep 2

description: Library name: 1985set2_244_AP14Week12-2


title: RNAseq of porcine: skin woundDay_6_ID1328_Wound_B_edge

description:
Library name: G_75_B_E_1
G_75_B_E


title: SETD6_KO4-clone9

description: Library name: Sample 6

data_processing:
Raw sequences were quality trimmed and filtered using Trim Galore (version 0.4.5) (quality cutoff=25, length cutoff=25) and cutadapt (version 1.15)
Alignment of the reads to the human genome (Homo_sapiens.GRCh38) was done with RSEM (version 1.2.28 option ‘bowtie2’) and calculation of number of reads per gene per sample was also done with RSEM
Assembly: GRCh38
Supplementary files format and content: Gene count matrix

molecule: polyA RNA

growth_protocol: SKmel147  were maintained in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum (FBS), penicillin-streptomycin , 2 mg/ml L-glutamine and non-essential amino acids.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA Kit (Macherey-Nagel)
mRNA library preparation (poly A enrichment)

value: SETD6 KO


title: Salmonella, wild-type with Magnesium, biol rep 2

description: Library name: Sample 5

value: wild-type


title: 16s microbiome data for patient 14 as DEB sample at week 12, rep 1

description: Library name: 1985set2_243_AP14Week12-1


title: RNAseq of porcine: skin woundDay_7_ID1323_Wound_H_edge

description:
Library name: H_81_H_E_1
H_81_H_E


title: SETD6_KO3-clone21

description: Library name: Sample 5


title: Salmonella, wild-type with Magnesium, biol rep 1

description: Library name: Sample 4


title: RNAseq of porcine: skin woundDay_7_ID1323_Wound_H_center

description:
Library name: H_82_H_C_1
H_82_H_C


title: SETD6_KO2-clone8

description: Library name: Sample 4


title: 16s microbiome data for patient 14 as DEB control at week 8

description: Library name: 1985set2_242_AP14Week8-C


title: Salmonella, wild-type without treatment, biol rep 3

description: Library name: Sample 3


title: RNAseq of porcine: skin woundDay_7_ID1324_Wound_E_edge

description:
Library name: H_83_E_E_1
H_83_E_E


title: Flag_BRD4_WT2 cells

description: Library name: Sample 3


title: 16s microbiome data for patient 14 as DEB sample at week 8, rep 2

description: Library name: 1985set2_241_AP14Week8-2


title: Salmonella, wild-type without treatment, biol rep 2

description: Library name: Sample 2


title: SETD6_KO1-clone4

description: Library name: Sample 3


title: RNAseq of porcine: skin woundDay_7_ID1324_Wound_H_edge

description:
Library name: H_85_H_E_1
H_85_H_E


title: SETD6_Control2

description: Library name: Sample 2

value: SETD6 Control


title: 16s microbiome data for patient 15 as JEB sample at week 0, rep 1

description: Library name: 1985set2_245_AP15Week0-1


title: Salmonella, wild-type with Magnesium, biol rep 3

description: Library name: Sample 6


title: 16s microbiome data for patient 14 as DEB sample at week 8, rep 1

description: Library name: 1985set2_240_AP14Week8-1


title: Salmonella, wild-type without treatment, biol rep 1

description: Library name: Sample 1


title: SETD6_Control1

description: Library name: Sample 1


title: RNAseq of porcine: skin woundDay_7_ID1324_Wound_E_center

description:
Library name: H_84_E_C_1
H_84_E_C


title: RNAseq of porcine: skin woundDay_6_ID1328_Wound_B_center

description:
Library name: G_76_B_C_1
G_76_B_C


title: 16s microbiome data for patient 14 as DEB sample at week 4, rep 1

description: Library name: 1985set2_238_AP14Week4-1


title: Isotype control, 10 mg/kg, replicate 4

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

description: Library name: HSA-000035801

data_processing:
Raw data (FASTQ files)  were processed using nf-core/rnaseq v3.11.2 (doi: https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020) with genome sequences and gene annotations from Gencode version M31. To deduplicate unique molecular identifiers, the following umitools_bc_pattern was used: ^(?P.{6})(?P.{4}).*
To account for the fact that the QuantSeq 3' mRNA-Seq library protocol only captures a 3' tag from each transcript, the following custom argument was included in the nf-core/rnaseq workflow: extra_star_align_args: --alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterType BySJout --outFilterMismatchNoverLmax 0.1 --clip3pAdapterSeq AAAAAAAA
Similarly, the following custom arguments were passed to the salmon quantitation step of the workflow: extra_salmon_quant_args: --noLengthCorrection
The nf-core/rnaseq workflow produces a SummarizedExperiment R object that is serialized to disk. To generate the processed data file, this object was read into an R session (using R 4.4.1), library sizes were estimated with the edgeR::normLibSizes function (version 4.2.0) using the TMM method and counts per million were returned with the edgeR::cpm function.
Assembly: GRCm39
Supplementary files format and content: File raw_and_normalized_counts.xlsx is a microsoft excel file with three worksheets: 1. sample information 2. raw count table 3. normalized count table (counts per million)

organism: Mus musculus

source_name: brain

growth_protocol: APP-SAA ki/ki x hTfR ki/ki mice were acquired from Jackson Laboratories or bred homozygously in our in-house mouse facility and maintained on a C57BL/6J background. Shipped mice were acclimated for a minimum of two weeks before entering experiments. All mice were housed in standard sized individually ventilated cages (IVC), maximum 5 mice per cage, with enriched environment and ad libitum access to food and water, on a 12-hour light/dark cycle. All experiments and handling of mice was performed in compliance with the German animal welfare law and with approval from the Government of Upper Bavaria (animal license: ROB-55.2-2532.Vet_02-18-32).

extract_protocol:
RNA was extracted from ~100,000 CD11b+ microglia per sample with the RNeasy Plus Micro Kit (Qiagen, Ref #74034) and resuspended in nuclease-free water for RNAseq library preparation.
Libraries were generated using the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD (Lexogen 193.384) with the UMI second strand synthesis module, following the protocol defined by the manufacturer. Library quantity and quality were assessed with TapeStation D1000 screentape (Agilent 5067-5582). Libraries were pooled in equimolar ratios for sequencing on one lane of an Illumina NovaSeq X 10B flowcell; 100 bp, single end reads were generated.

treatment_protocol: Mice were randomly assigned to a treatment arm: isotype antibody (10 mg/kg) or mAducanumab (1, 3 or 10 mg/kg) and treated by weekly intraperitoneal injection from 4.5 months of age until 8.5 months of age (16 weeks). Mice were sacrificed 7 days after the last antibody injection. Before perfusion, mice were anesthetized using a mix of medetomidine [0.5 mg/kg], midazolam [5 mg/kg], and fentanyl [0.05 mg/kg] (MMF) and CSF was collected from the cisterna magna. Blood was collected using cardiac puncture followed by perfusion using ice cold PBS. Mouse brains were harvested and kept in HBBS (Gibco, 14025092) + 7 mM HEPES (Gibco, 15630080) + 2x Glutamax (Gibco, 35050061) on ice. Olfactory bulb, cerebellum, pons and meninges were removed and remaining brain tissue was dissociated using the Neural Tissue Dissociation Kit (Miltenyi, 130-092-628), supplemented with 5µM Actinomycin D (Cell Signaling Technology, 15021) and 2µM Anisomycin (Cell Signaling Technology, 2222) following manufacturer's instructions. After straining and centrifugation, pelleted cells were resuspended in 0.25% fatty acid free BSA (Sigma-Aldrich, A8806) in HBSS, incubated with magnetic Cd11b Microbeads (Miltenyi, 130-093-634) and run twice over MS columns (Miltenyi, 130-042-201). Cells were eluted from columns, counted, aliquoted, centrifugated and snap frozen in liquid nitrogen until further processing.

value: brain

tag: Sex

value: female

tag: cell type

value: primary microglia

value: APP-SAA KI/KI x hTfR KI/KI

value: Isotype control

tag: dose

value: 10 mg/kg

tag: age

value: 8 months


title: RNAseq of porcine: skin woundDay_6_ID1328_Wound_K_edge

description:
Library name: G_77_K_E_1
G_77_K_E

value: Skin wound tissue

value: edge


title: Isotype control, 10 mg/kg, replicate 3

description: Library name: HSA-000035800

value: male


title: 16s microbiome data for patient 14 as DEB control at week 0

description: Library name: 1985set2_237_AP14Week0-C

value: skin


title: Isotype control, 10 mg/kg, replicate 2

description: Library name: HSA-000035799


title: RNAseq of porcine: skin woundDay_7_ID1325_Wound_E_center

description:
Library name: H_88_E_C_1
H_88_E_C

value: center


title: Sweat gland duct Rep1

city: Cleveland

first: Katreya

last: Lovrenert

address: 10900 Euclid Avenue

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

description: Library name: AH920 Sweat gland duct replica 1 ATAC-Seq

data_processing:
Libraries were processed using the ENCODE‐DCC/atac‐seq‐pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline)
Assembly: Oviari4 for all sheep gall bladder epithelial cell libraries, hg19 for all other libraries
Supplementary files format and content: bigWig

source_name: Human sweat gland duct epithelial cells

growth_protocol: Cell lines were grown by standard protocols as per ATCC. Cholangiocyte organoids were grown as per https://pubmed.ncbi.nlm.nih.gov/34764255/ ; Sweat gland duct cells were grown as per https://pubmed.ncbi.nlm.nih.gov/38969603/

extract_protocol:
Cells were lysed and isolated nuclei transposed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962.
Libraries were constructed using published protocol: Corces, M.R., et al. (2017) An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods, 14, 959-962. With the following exceptions: Final libraries were purified with Agencourt AMPure XP magnetic beads (Beckman-Coulter) at a sample to bead ratio of 1:1.2, following the manufacturer’s protocol, and eluted into 20 μL Buffer EB (Qiagen).

treatment_protocol: 50,000 cells were isolated prior to lysing/transpostion.

value: Human sweat gland duct epithelial cells


title: Sweat gland coil Rep2

description: Library name: AH923 Sweat gland coil replica 2 ATAC-Seq

source_name: Human sweat gland coil epithelial cells

value: Human sweat gland coil epithelial cells


title: RNAseq of porcine: skin woundDay_7_ID1325_Wound_H_edge

description:
Library name: H_89_H_E_1
H_89_H_E


title: RNAseq of porcine: skin woundDay_7_ID1325_Wound_H_center

description:
Library name: H_90_H_C_1
H_90_H_C


title: Sweat gland coil Rep1

description: Library name: AH922 Sweat gland coil replica 1 ATAC-Seq


title: hPSC-Cholangiocytes (organoid) Rep2

description: Library name: AH917 hPSC-Cholangiocytes (organoid) replica 2 ATAC-Seq

source_name: Human hPSC-Cholangiocyte organoids

value: Human hPSC-Cholangiocyte organoids


title: RNAseq of porcine: skin woundDay_9_ID1328_Wound_E_center

description:
Library name: I_100_E_C_1
I_100_E_C


title: Untreated, replicate 6

description: Library name: HSA-000035795

value: Untreated

value: 0 mg/kg

value: 4 months


title: 16s microbiome data for patient 13 as DEB sample at week 12, rep 1

description: Library name: 1985set2_232_AP13Week12-1


title: 16s microbiome data for patient 13 as DEB sample at week 12, rep 2

description: Library name: 1985set2_233_AP13Week12-2


title: 16s microbiome data for patient 14 as DEB sample at week 4, rep 2

description: Library name: 1985set2_239_AP14Week4-2


title: 16s microbiome data for patient 13 as DEB control at week 12

description: Library name: 1985set2_234_AP13Week12-C


title: Isotype control, 10 mg/kg, replicate 6

description: Library name: HSA-000035797

value: brain

value: female


title: HUDEP2, H3K27me3, ko, CUT&RUN

city: Omaha

first: Meg

last: Schaefer

state: Nebraska

address: 985805 Nebraska Medical Center

department: Genetics Cell Biology and Anatomy

institute: University of Nebraska Medical Center

description:
HUDEP2_H3K27me3_ko
H3K27me3_ko_HUDEP2.bw

data_processing:
Adapters were clipped using Cutadapt, and paired-end Homo sapien reads were mapped to UCSC Hg38 using Bowtie2. Spike-in S. cerevisiae reads were mapped to repeat-masked sacCer3/V64.
Continuous-valued data tracks (bedGraph and bigWig) were generated using genomecov in bedtools v2.30.0 (-bg option) and bedGraphtoBigWig and normalized using a total number of spike-in reads.
Top 0.5% of peaks were called by SEACR (v.1.3) using the non and stringent settings. Alternatively, histone methylation peaks were called using MACS3 with --nolambda --nomodel  --extsize 200 parameters.
Assembly: hg38
Supplementary files format and content: bigWig, bed (excluding histone marks and IgG), narrowPeak (H3K4me2 and H3K4me3 only)
Library strategy: CUT&RUN

growth_protocol: Serum free expansion media, 2% Pen/Strep, 0.4 μg/mL dexamethasone, 50 ng/mL recombinant human SCF, 3 U/mL erythropoietin, and 1 μg/mL doxycycline.

extract_protocol:
Phenol-chloroform DNA extraction.
Libraries were prepared for Illumina sequencing with UDI adapters, without size selection, and following the KAPA DNA polymerase library preparation kit protocol.

tag: condition

value: SAMD1 knockout

tag: cut&run antibody

value: H3K27me3 (CST)


title: Sweat gland duct Rep2

description: Library name: AH921 Sweat gland duct replica 2 ATAC-Seq


title: Untreated, replicate 2

description: Library name: HSA-000035794

value: primary microglia

value: APP-SAA KI/KI x hTfR KI/KI


title: hPSC-Cholangiocytes (organoid) Rep1

description: Library name: AH916 hPSC-Cholangiocytes (organoid) replica 1 ATAC-Seq


title: 16s microbiome data for patient 13 as DEB sample at week 8, rep 2

description: Library name: 1985set2_231_AP13Week8-2


title: RNAseq of porcine: skin woundDay_9_ID1328_Wound_H_edge

description:
Library name: I_101_H_E_1
I_101_H_E

value: Skin wound tissue


title: RNAseq of porcine: skin woundDay_1_ID1324_Wound_L_edge

description:
Library name: B_13_L_E_1
B_13_L_E

value: edge


title: HUDEP2, H3K27me3, ctrl, CUT&RUN

description:
HUDEP2_H3K27me3_ctrl
H3K27me3_ctrl_HUDEP2.bw

value: Scramble


title: Untreated, replicate 5

description: Library name: HSA-000035793

value: male


title: 16s microbiome data for patient 14 as DEB sample at week 0, rep 2

description: Library name: 1985set2_236_AP14Week0-2

value: skin


title: RNAseq of porcine: skin woundDay_9_ID1328_Wound_H_center

description:
Library name: I_102_H_C_1
I_102_H_C

value: center


title: RNAseq of porcine: skin woundDay_9_ID1326_Wound_E_edge

description:
Library name: I_91_E_E_1
I_91_E_E


title: Aducanumab, 3 mg/kg, replicate 5

description: Library name: HSA-000035792

value: Aducanumab

value: 3 mg/kg

value: 8 months


title: Isotype control, 10 mg/kg, replicate 1

description: Library name: HSA-000035798

value: Isotype control

value: 10 mg/kg


title: 16s microbiome data for patient 14 as DEB sample at week 0, rep 1

description: Library name: 1985set2_235_AP14Week0-1


title: Isotype control, 10 mg/kg, replicate 5

description: Library name: HSA-000035796

value: brain


title: HUDEP2, IgG, ko1, CUT&RUN

description:
HUDEP2_IgG_ko1
IgG_ko_merged_HUDEP2.bw

value: IgG


title: Aducanumab, 3 mg/kg, replicate 2

description: Library name: HSA-000035791


title: 16s microbiome data for patient 13 as DEB sample at week 0, rep 2

description: Library name: 1985set2_226_AP13Week0-2


title: Aducanumab, 3 mg/kg, replicate 6

description: Library name: HSA-000035789

value: female


title: RNAseq of porcine: skin woundDay_13_ID1326_Wound_J_center

description:
Library name: K_118_J_C_1
K_118_J_C


title: RNAseq of porcine: skin woundDay_13_ID1327_Wound_C_edge

description:
Library name: K_119_C_E_1
K_119_C_E


title: RNAseq of porcine: skin woundDay_11_ID1324_Wound_J_edge

description:
Library name: J_109_J_E_1
J_109_J_E


title: HUDEP2, IgG, ctrl1,CUT&RUN

description:
HUDEP2_IgG_ctrl1
IgG_ctrl_merged_HUDEP2.bw


title: HUDEP2, IgG, ctrl2, CUT&RUN

description:
HUDEP2_IgG_ctrl2
IgG_ctrl_merged_HUDEP2.bw


title: HUDEP2, H3K4me3, ko1, CUT&RUN

description:
HUDEP2_H3K4me3_ko1
H3K4me3_ko_merged_HUDEP2.bw
H3K4me3_ko_merged_peaks.narrowPeak

value: SAMD1 knockout

value: H3K4me3 (CST)


title: Aducanumab, 3 mg/kg, replicate 3

description: Library name: HSA-000035788

value: primary microglia

value: APP-SAA KI/KI x hTfR KI/KI


title: 16s microbiome data for patient 13 as DEB sample at week 0, rep 1

description: Library name: 1985set2_225_AP13Week0-1


title: RNAseq of porcine: skin woundDay_13_ID1326_Wound_J_edge

description:
Library name: K_117_J_E_1
K_117_J_E

value: Skin wound tissue

value: edge


title: Aducanumab, 3 mg/kg, replicate 1

description: Library name: HSA-000035790

value: male


title: HUDEP2, H3K4me3, ko2, CUT&RUN

description:
HUDEP2_H3K4me3_ko2
H3K4me3_ko_merged_HUDEP2.bw
H3K4me3_ko_merged_peaks.narrowPeak


title: Aducanumab, 10 mg/kg, replicate 5

description: Library name: HSA-000035786


title: 16s microbiome data for patient 12 as EBS sample at week 12, rep 1

description: Library name: 1985set2_223_AP12Week12-1

value: skin


title: 16s microbiome data for patient 13 as DEB sample at week 4, rep 2

description: Library name: 1985set2_228_AP13Week4-2


title: 16s microbiome data for patient 12 as EBS sample at week 12, rep 2

description: Library name: 1985set2_224_AP12Week12-2


title: 16s microbiome data for patient 13 as DEB sample at week 4, rep 1

description: Library name: 1985set2_227_AP13Week4-1


title: HUDEP2, H3K4me3, ctrl1, CUT&RUN

description:
HUDEP2_H3K4me3_ctrl1
H3K4me3_ctrl_merged_HUDEP2.bw
H3K4me3_ctrl_merged_peaks.narrowPeak

value: Scramble


title: HUDEP2, H3K4me3, ctrl2, CUT&RUN

description:
HUDEP2_H3K4me3_ctrl2
H3K4me3_ctrl_merged_HUDEP2.bw
H3K4me3_ctrl_merged_peaks.narrowPeak


title: HUDEP2, IgG, ko2, CUT&RUN

description:
HUDEP2_IgG_ko2
IgG_ko_merged_HUDEP2.bw


title: RNAseq of porcine: skin woundDay_1_ID1325_Wound_L_center

description:
Library name: B_18_L_C_1
B_18_L_C

value: center


title: RNAseq of porcine: skin woundDay_19_ID1327_Wound_I_edge

description:
Library name: N_141_I_E_1
N_141_I_E


title: 16s microbiome data for patient 13 as DEB control at week 4

description: Library name: 1985set2_229_AP13Week4-C


title: 16s microbiome data for patient 13 as DEB sample at week 8, rep 1

description: Library name: 1985set2_230_AP13Week8-1


title: Aducanumab, 10 mg/kg, replicate 2

description: Library name: HSA-000035785

value: Aducanumab


title: RNAseq of porcine: skin woundDay_19_ID1326_Wound_I_center

description:
Library name: N_140_I_C_1
N_140_I_C


title: Aducanumab, 3 mg/kg, replicate 4

description: Library name: HSA-000035787

value: 3 mg/kg

value: 8 months


title: HUDEP2, H3K4me2, ko2, CUT&RUN

description:
HUDEP2_H3K4me2_ko2
H3K4me2_ko_merged_HUDEP2.bw
H3K4me2_ko_merged_peaks.narrowPeak

value: H3K4me2 (CST)


title: RNAseq of porcine: skin woundDay_19_ID1327_Wound_I_center

description:
Library name: N_142_I_C_1
N_142_I_C


title: RNAseq of porcine: skin woundDay_13_ID1326_Wound_C_center

description:
Library name: K_116_C_C_1
K_116_C_C


title: Aducanumab, 10 mg/kg, replicate 1

description: Library name: HSA-000035784

value: brain

value: 10 mg/kg


title: HUDEP2, H3K4me2, ko1, CUT&RUN

description:
HUDEP2_H3K4me2_ko1
H3K4me2_ko_merged_HUDEP2.bw
H3K4me2_ko_merged_peaks.narrowPeak


title: 16s microbiome data for patient 12 as EBS sample at week 4, rep 1

description: Library name: 1985set2_219_AP12Week4-1


title: RNAseq of porcine: skin woundDay_1_ID1325_Wound_A_center

description:
Library name: B_16_A_C_1
B_16_A_C


title: HUDEP2, H3K4me2, ctrl1, CUT&RUN

description:
HUDEP2_H3K4me2_ctrl1
H3K4me2_ctrl_merged_HUDEP2.bw
H3K4me2_ctrl_merged_peaks.narrowPeak


title: Aducanumab, 10 mg/kg, replicate 3

description: Library name: HSA-000035782

value: female


title: 16s microbiome data for patient 12 as EBS sample at week 4, rep 2

description: Library name: 1985set2_220_AP12Week4-2


title: RNAseq of porcine: skin woundDay_21_ID1323_Wound_I_center

description:
Library name: O_146_I_C_1
O_146_I_C


title: Aducanumab, 1 mg/kg, replicate 5

description: Library name: HSA-000035780

value: 1 mg/kg


title: HUDEP2, LSD1, ko2, CUT&RUN

description:
HUDEP2_LSD1_ko2
LSD1_ko_merged_HUDEP2.bw
LSD1_ko_peaks.bed

value: SAMD1 knockout

value: LSD1 (abcam)


title: 16s microbiome data for patient 12 as EBS sample at week 8, rep 2

description: Library name: 1985set2_222_AP12Week8-2


title: Aducanumab, 1 mg/kg, replicate 6

description: Library name: HSA-000035781

value: primary microglia

value: APP-SAA KI/KI x hTfR KI/KI


title: RNAseq of porcine: skin woundDay_21_ID1324_Wound_I_edge

description:
Library name: O_147_I_E_1
O_147_I_E

value: Skin wound tissue

value: edge


title: Untreated, replicate 1

description: Library name: HSA-000035779

value: male

value: Untreated

value: 0 mg/kg

value: 4 months


title: 16s microbiome data for patient 12 as EBS sample at week 0, rep 2

description: Library name: 1985set2_217_AP12Week0-2

value: skin


title: HUDEP2, LSD1, ko1, CUT&RUN

description:
HUDEP2_LSD1_ko1
LSD1_ko_merged_HUDEP2.bw
LSD1_ko_peaks.bed


title: Untreated, replicate 4

description: Library name: HSA-000035778


title: RNAseq of porcine: skin woundDay_21_ID1324_Wound_I_center

description:
Library name: O_148_I_C_1
O_148_I_C

value: center


title: HUDEP2, LSD1, ctrl2, CUT&RUN

description:
HUDEP2_LSD1_ctrl2
LSD1_ctrl_merged_HUDEP2.bw
LSD1_ctrl_peaks.bed

value: Scramble


title: 16s microbiome data for patient 12 as EBS sample at week 0, rep 1

description: Library name: 1985set2_216_AP12Week0-1


title: RNAseq of porcine: skin woundDay_21_ID1325_Wound_I_center

description:
Library name: O_150_I_C_1
O_150_I_C


title: 16s microbiome data for patient 12 as EBS sample at week 8, rep 1

description: Library name: 1985set2_221_AP12Week8-1


title: HUDEP2, H3K4me2, ctrl2, CUT&RUN

description:
HUDEP2_H3K4me2_ctrl2
H3K4me2_ctrl_merged_HUDEP2.bw
H3K4me2_ctrl_merged_peaks.narrowPeak

value: H3K4me2 (CST)


title: HUDEP2, LSD1, ctrl1, CUT&RUN

description:
HUDEP2_LSD1_ctrl1
LSD1_ctrl_merged_HUDEP2.bw
LSD1_ctrl_peaks.bed


title: 16s microbiome data for patient 11 as JEB sample at week 12, rep 2

description: Library name: 1985set2_215_AP11Week12-2


title: Untreated, replicate 3

description: Library name: HSA-000035777

value: brain


title: Aducanumab, 10 mg/kg, replicate 6

description: Library name: HSA-000035783

value: female

value: Aducanumab

value: 10 mg/kg

value: 8 months


title: RNAseq of porcine: skin woundDay_21_ID1325_Wound_I_edge

description:
Library name: O_149_I_E_1
O_149_I_E


title: HUDEP2, SAMD1, ko2, CUT&RUN

description:
HUDEP2_SAMD1_ko2
SAMD1_ko_merged_HUDEP2.bw
SAMD1_ko_peaks.bed

value: SAMD1 knockout


title: Aducanumab, 10 mg/kg, replicate 4

description: Library name: HSA-000035776

value: primary microglia

value: APP-SAA KI/KI x hTfR KI/KI


title: 16s microbiome data for patient 12 as EBS control at week 0

description: Library name: 1985set2_218_AP12Week0-C


title: 16s microbiome data for patient 11 as JEB sample at week 12, rep 1

description: Library name: 1985set2_214_AP11Week12-1


title: Aducanumab, 1 mg/kg, replicate 3

description: Library name: HSA-000035775

value: 1 mg/kg


title: RNAseq of porcine: skin woundDay_1_ID1323_Wound_A_center

description:
Library name: B_8_A_C_1
B_8_A_C

value: Skin wound tissue


title: Aducanumab, 1 mg/kg, replicate 2

description: Library name: HSA-000035774

value: male


title: 16s microbiome data for patient 11 as JEB control at week 8

description: Library name: 1985set2_213_AP11Week8-C


title: RNAseq of porcine: skin woundDay_1_ID1323_Wound_A_edge

description:
Library name: B_7_A_E_1
B_7_A_E

value: edge


title: 16s microbiome data for patient 11 as JEB sample at week 8, rep 2

description: Library name: 1985set2_212_AP11Week8-2


title: 16s microbiome data for patient 11 as JEB sample at week 8, rep 1

description: Library name: 1985set2_211_AP11Week8-1


title: HUDEP2, SAMD1, ctrl2, CUT&RUN

description:
HUDEP2_SAMD1_ctrl2
SAMD1_ctrl_merged_HUDEP2.bw
SAMD1_ctrl_peaks.bed


title: HUDEP2, SAMD1, ko1, CUT&RUN

description:
HUDEP2_SAMD1_ko1
SAMD1_ko_merged_HUDEP2.bw
SAMD1_ko_peaks.bed


title: HUDEP2, SAMD1, ctrl1, CUT&RUN

description:
HUDEP2_SAMD1_ctrl1
SAMD1_ctrl_merged_HUDEP2.bw
SAMD1_ctrl_peaks.bed


title: RNAseq of porcine: skin woundDay_1_ID1323_Wound_L_edge

description:
Library name: B_9_L_E_1
B_9_L_E


title: Aducanumab, 1 mg/kg, replicate 1

description: Library name: HSA-000035773


title: RNAseq of porcine: skin woundDay_2_ID1326_Wound_A_edge

description:
Library name: C_19_A_E_1
C_19_A_E


title: Biol rep 4 RNAPII UNC1999 treated

city: Grand Forks

first: Barry

last: Milavetz

state: North Dakota

address: 1301 N Columbia Rd Stop 9037 RM W129

institute: University of North Dakota School of Medicine and Health Sciences

data_processing:
Adapters were trimmed from fastq files with Cutadapt (V2.3)
Trimmed reads were aligned to the SV40 genome with STAR (V2.7.1a)
Aligned reads were filtered for properly paired reads and sorted with Samtools (1.10 using htslib V1.10)
Secondary reads were removed and the reads were sorted to position with Samtools (1.10 using htslib V1.10)
Duplicate reads were removed with Picard MarkDuplicates (V2.20.2 SNAPSHOT)
Fragments below 100bp or greater than 150bp were removed with Samtools (1.10 using htslib V1.10)
Bam files were indexed with Samtools (1.10 using htslib V1.10)
Bam files were normalized and bedgraphs were created with bamCoverage (V3.3.0)
Per basepair bedgraph files were created with R (V4.0.1 (2020-06-06) -- "See Things Now")
Replicate per basepair bedgraph files were merged with bedtools (V2.29.0) and averages of the replicates were calculated
heatmaps from the merged and averaged replicate samples were created in Python (V3.8)
Assembly: Reads were aligned to the SV40 genome (RefSeq Acc: NC_001669.1) cut at nucleotide (nt) 2666
Supplementary files format and content: bedgraph

organism: Betapolyomavirus macacae

source_name: BSC-1 ATCC CCL-26

extract_protocol:
Chromatin immunoprecipitation (ChIP) analyses of the SV40 chromosomes obtained by treatment with DMSO, or inhibitor were performed according to the detailed description of the procedures previously described (Balakrishnan and Milavetz, 2017b;a). All the antibodies used were ChIP validated by their respective vendors. Antibodies (and their vendors) included: acetyl-H3 (06-599, Millipore), acetyl-H4 (06-866, Millipore), H3K9me1 (ab9045, Abcam), H3K27me3 (17-622 Millipore), and RNAPII (05-623-25G, Millipore). ChIPs were performed using Millipore kit Cat. No. 17-295 according to the supplier’s protocol. In a standard ChIP, 10 µl of antibody (10 µg) was incubated with the SV40 chromosomes being analyzed for 4 hours at 40C. A mixture of magnetic beads containing protein A and protein G was added (15 µl each) to each sample and incubated overnight. The next morning the magnetic beads and associated antibody bound chromatin was purified according to the protocol present in the kit.
The remaining DNA sample 25 µl was used for the preparation of a sequencing library. Libraries were prepared using the New England Biolabs Next UltraII kit according to the protocol supplied with the kit with one exception. All reagent volumes were reduced by half for the preparation of libraries with no apparent effect on library quality or quantity. Following its preparation, the library was purified AMPure magnetic beads in a two-step process. First, 7.5 µl of AMPure was added to the library (50 µl) in a 1.4 ml Eppindorf tube and incubated for 10 minutes to bind the DNA. The tube was incubated for 5 minutes in a magnetic rack and the liquid transferred to a new Eppendorf tube. An additional 20 µl of AMPure was added and incubated for 10 minutes. The tube was again placed on the magnetic rack and after a 5-minute incubation the liquid was removed and discarded. The magnetic beads were washed twice with 400 µl 70% ethanol, dried for 10 minutes, and resuspended in 20 µl nuclease-free water. In preliminary studies we found that this two-step purification yielded libraries enriched for nucleosome-sized insert DNA while also removing residual adapter from the library preparation. The size-selected library from each sample, 5 µl, was amplified by PCR using indices from New England Biolabs and purified on AMPure as previously described with minor modification (Balakrishnan and Milavetz, 2017a). Following PCR the amplification products, 170 µl were again purified in a two-step AMPure procedure. In the first step 60 µl of AMPure was added, the beads bound to a magnetic rack and the liquid transferred to a new tube. AMPure, 40 µl, was added to the liquid and the purification continued as previously described. This two-step process yielded a final sequencing library that was primarily in the size range of 150 to 300 base pairs in length including the adapter sequences from the library preparation.
ChIP samples for library preparation for ChIP-Seq was performed as above until the final elution step. Instead of eluting the intact SV40 chromatin bound to magnetic beads, the chromatin bound to beads was sonicated to fragment the chromatin and the fragments bound to the beads separated from the unbound fragments. The beads were washed twice with TE buffer from the Millipore kit. The DNA in the chromatin fragments still bound to the magnetic beads was removed by incubation for 15 minutes in the DNA binding buffer found in the NEB Monarch PCR and DNA Cleanup Kit. The DNA present in binding buffer was then purified according to the protocol found in the Monarch kit. In the final purification step with the kit, the DNA was eluted in 26 μl nuclease-free H2O. In order to estimate the amount of SV40 DNA present in the eluate, 1 µl was amplified along with a 1 µl sample of the SV40 chromatin used in the original ChIP using the early primers.

value: BSC-1 ATCC CCL-26

value: RNAPII UNC1999 treated


title: 16s microbiome data for patient 11 as JEB sample at week 4, rep 2

description: Library name: 1985set2_210_AP11Week4-2

value: skin


title: Aducanumab, 1 mg/kg, replicate 4

description: Library name: HSA-000035772


title: RNAseq of porcine: skin woundDay_21_ID1323_Wound_I_edge

description:
Library name: O_145_I_E_1
O_145_I_E


title: 16s microbiome data for patient 11 as JEB sample at week 4, rep 1

description: Library name: 1985set2_209_AP11Week4-1


title: N279_BMT_Stroma

city: Providence

first: Patrycja

middle: M

last: Dubielecka

state: RI

address: 1 Hoppin St., Coro West, 5th Fl., Suite 5.36

department: Division of Hematology/Oncology, Department of Medicine

institute: Warren Alpert Medical School of Brown University and Rhode Island Hospital

description:
Libraries were run twice on Novaseq X
Stroma_15

data_processing:
Adapter and quality read trimming was performed using Skewer (version 0.2.1) and alignments were performed using Star Aligner (v2.7.3a) against the murine primary assembly transcriptome (GRCm39 v110). Counts tables were then generated using featureCounts (subread v1.6.2).
For only the stroma samples, since these libraries were run twice (technical replicates), the total counts from the two runs were combined for the raw counts table.
Assembly: GRCm39 v110
Supplementary files format and content: tab-delimited text file includes raw counts

source_name: Bone Marrow

extract_protocol:
RNA was isolated using guanidinium thiocyanate-phenol-chloroform extraction (TRIzol®) from sorted BM samples. Due to the low numbers of cells isolated from the sorted bone marrow stroma RNA, samples was concentrated using SPRIselect magnetic beads (Beckman Coulter).
For the hematopoietic samples: 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. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina NovaSeq6000 at PE150. Each library was sequenced to 6G (20 million paired-end reads).  For the Stromal Samples: Libraries were created using the NEBNext Low Input RNA Library Prep Kit (E6420S, New England Biolabs) and indexed using the NEBNext Multiplex Oligos dual index primers (E6440S, New England Biolabs). Libraries were sequenced at Novogene (Sacramento, CA) using the NovaSeq X system to generate 150bp paired end reads.

treatment_protocol: To isolate bone marrow (BM) from bone marrow transplant (BMT) recipients and donor animals they were euthanized via CO2 administration and secondary cervical dislocation. Bones were isolated, manually cleaned with sterile gauze, and stored in 4C dissection media (phosphate buffered saline without calcium and magnesium (1x PBS, Corning), 0.5% albumin bovine fraction V (BSA, RPI research products international), and 2mM EDTA (Invitrogen)).  Bones included were pelvic (2x), fibula (2x), tibia (2x), femur (1x), humerus (2x), scapula (2x), and sternum (1x).  After extraction of bones from euthanized animals, they were lightly crushed once in a mortar and pestle and collected into 3ml of Liberace TM (0.2 mg/ml), DNase I (200 U/ml, benzonase) and 1x PBS. Bones and cell suspension were then allowed to digest in an incubator at 37°C for 60 min on a tube rotator in a 5mL conical tube. Contents were then poured through a 70µm filter on a 50mL conical tube and washed with additional 45ml dissection media to collect released BM cells and quench the digestion. This was followed by peleting the cells at 485g for 10 minutes at 4C. Supernatant was discarded, and the cell pellet was resuspended into 7mL of  RBC lysis buffer for mouse (Boston BioProducts) and incubated on a tube rotator (Rotator Genie) for 15 minutes at room temperature. RBC lysis was quenched with the addition of 43mL of dissection media, tubes were lightly inverted to mix, and the suspension was spun down again at 485g for 5-10 minutes at 4C. Cells were resuspended into 3ml 1x PBS + 1µL/mL benzonase and counted to determine concentration.  Once cells were counted, they were concentrated into 1mL of 1x PBS where they were stained with zombie violet viability dye for 10 minutes at room temperature in the dark followed by quenching in FACS buffer (0.5% FBS in 1X PBS) and pelleted at 300g at 4C for 5 minutes. Cells were then resuspended into 15ml conical tubes at concentrations of 2.0x10^6 cells/100µL and blocked with Rat anti-mouse CD16/CD32 (Fc Block, BD Biosciences) for 10 minutes at room temperature in the dark on a tube revolver (FisherBrand). The samples were then diluted with an antibody cocktail to a concentration of 1.0x10^6 cells/100µL. This cocktail contained anti-CD45.1 (A20)-FITC (BioLegend), and anti-CD45.2 (104)-APC (BioLegend) along with biotinylated lineage markers: anti-B220 (RA3-6B2, BioLegend), CD4, (GK1.5, BioLegend), CD8 (53-6.7, BioLegend), NK1.1 (PK136, BioLegend), Ly-6G/Ly-6C (RB6-8C5, BioLegend), TER119 (BioLegend), and CD11b (M1/70, BioLegend).  Cell suspension was allowed to incubate on a tube revolver in the dark at room temperature for 30 minutes. Cells were then spun down (300g for 5min) and washed. Cells were spun down again and resuspended at 1.0x10^6 cells/100µL of FACs buffer with PE streptavidin (BD Biosciences) and allowed to incubate at room temperature on a rotator in the dark for 15 minutes. Cells were again spun down, washed, and resuspended into FACs buffer for sorting. Matched unstained BM was also kept aside to be run alongside the stained BM during sorting. Stained BM was then put through FACs tube 35µm strainer caps (Alkali Scientific) just prior to cell sorting. All sorted cells were collected into collection media. The workflow for sorting the BM proceeded as follows. To isolate hematopoietic BM, live singlets were sorted using gates that isolated CD45.2 donor-derived (FITC-positive/APC-negative) or CD45.1 recipient-derived (FITC-negative/APC-positive) BM. Concurrently, CD45.1/CD45.2 double negative cells were gated to observe the PE-stained combined lineage makers. A sorting gate was then used to collect the lineage-negative stromal-enriched cells. While performing the sorting only two populations were being isolated at a time to reduce the chance of contamination by positioning the collection tubes on either side of the sorting stream. The stromal isolation tube was always present during the sorting on one side since the frequency was always very low, while the other side would be used for the hematopoietic donor- or recipient-derived collection tubes. Starting with the recipient-derived material we would sort until 5.0x106 cells were collected before pausing the sorting and switching out collection tubes to collect 4.0-5.0x106 donor-derived cells. Wild-type no-BMT cells were sorted with the same gating paradigm but no CD45.2 cells were collected. Once isolated, cells were pelleted down (300g for 10 minutes) and resuspended into 1mL of TRIZOL and stored at -80C until RNA isolation.

value: Bone Marrow

value: FEMALE

tag: animal id

tag: source

value: BMT Stromal Cells

value: Bone Marrow Transplant

tag: euthanasia date

tag: final peripheral_blood_chimerism


title: 16s microbiome data for patient 11 as JEB control at week 0

description: Library name: 1985set2_208_AP11Week0-C

tag: tissue


title: Biol rep 2 RNAPII UNC1999 treated

tag: cell line

tag: treatment


title: N203_BMT_Stroma

description:
Libraries were run twice on Novaseq X
Stroma_14

value: MALE


title: RNAseq of porcine: skin woundDay_0_ID1325

description:
Library name: A_3_1325_1
A_3_1325

tag: time


title: RNAseq of porcine: skin woundDay_2_ID1326_Wound_L_edge

description:
Library name: C_21_L_E_1
C_21_L_E

tag: location

tag: anumal id


title: 16s microbiome data for patient 11 as JEB sample at week 0, rep 2

description: Library name: 1985set2_207_AP11Week0-2


title: Biol rep 1 RNAPII UNC1999 treated


title: 16s microbiome data for patient 11 as JEB sample at week 0, rep 1

description: Library name: 1985set2_206_AP11Week0-1


title: N032_BMT_Stroma

description:
Libraries were run twice on Novaseq X
Stroma_13


title: RNAseq of porcine: skin woundDay_2_ID1326_Wound_L_center

description:
Library name: C_22_L_C_1
C_22_L_C

value: center

tag: wound id


title: Biol rep 4 RNAPII A366 treated

value: RNAPII A366 treated


title: RNAseq of porcine: skin woundDay_2_ID1327_Wound_A_edge

description:
Library name: C_23_A_E_1
C_23_A_E


title: 16s microbiome data for patient 10 as DEB control at week 0

description: Library name: 1985set2_205_AP10Week0-C


title: Biol rep 3 RNAPII UNC1999 treated


title: RNAseq of porcine: skin woundDay_9_ID1326_Wound_E_center

description:
Library name: I_92_E_C_1
I_92_E_C


title: Biol rep 2 RNAPII A366 treated


title: RNAseq of porcine: skin woundDay_7_ID1324_Wound_H_center

description:
Library name: H_86_H_C_1
H_86_H_C


title: Biol rep 1 RNAPII A366 treated


title: N005_BMT_Stroma

description:
Libraries were run twice on Novaseq X
Stroma_09

tag: Sex


title: Biol rep 3 RNAPII A366 treated


title: N269_BMT_Stroma

description:
Libraries were run twice on Novaseq X
Stroma_10


title: N204_BMT_Stroma

description:
Libraries were run twice on Novaseq X
Stroma_12


title: RNAseq of porcine: skin woundDay_7_ID1325_Wound_E_edge

description:
Library name: H_87_E_E_1
H_87_E_E


title: 16s microbiome data for patient 09 as DEB control at week 4

description: Library name: 1985set2_202_AP09Week4-C


title: 16s microbiome data for patient 10 as DEB sample at week 0, rep 2

description: Library name: 1985set2_204_AP10Week0-2


title: Biol rep 5 RNAPII Gsk_LSD1 treated

value: RNAPII Gsk_LSD1 treated


title: 16s microbiome data for patient 10 as DEB sample at week 0, rep 1

description: Library name: 1985set2_203_AP10Week0-1


title: N283_Control_Stroma

description:
Libraries were run twice on Novaseq X
Stroma_08

value: Wild-type Control Stromal Cells

value: Wild-Type Control


title: 16s microbiome data for patient 09 as DEB sample at week 4, rep 2

description: Library name: 1985set2_201_AP09Week4-2


title: RNAseq of porcine: skin woundDay_9_ID1327_Wound_E_edge

description:
Library name: I_95_E_E_1
I_95_E_E


title: Biol rep 4 RNAPII Gsk_LSD1 treated


title: 16s microbiome data for patient 09 as DEB sample at week 4, rep 1

description: Library name: 1985set2_200_AP09Week4-1


title: N002_Control_Stroma

description:
Libraries were run twice on Novaseq X
Stroma_07


title: RNAseq of porcine: skin woundDay_9_ID1327_Wound_E_center

description:
Library name: I_96_E_C_1
I_96_E_C


title: N280_Control_Stroma

description:
Libraries were run twice on Novaseq X
Stroma_06


title: Biol rep 3 RNAPII Gsk_LSD1 treated


title: N014_BMT_Stroma

description:
Libraries were run twice on Novaseq X
Stroma_11


title: N051_Control_Stroma

description:
Libraries were run twice on Novaseq X
Stroma_05


title: RNAseq of porcine: skin woundDay_9_ID1327_Wound_H_edge

description:
Library name: I_97_H_E_1
I_97_H_E


title: 16s microbiome data for patient 09 as DEB control at week 0

description: Library name: 1985set2_199_AP09Week0-C


title: RNAseq of porcine: skin woundDay_0_ID1324

description:
Library name: A_2_1324_1
A_2_1324


title: 16s microbiome data for patient 09 as DEB sample at week 0, rep 2

description: Library name: 1985set2_198_AP09Week0-2


title: Biol rep 1 RNAPII Gsk_LSD1 treated


title: Biol rep 2 RNAPII Gsk_LSD1 treated


title: N288_Control_Stroma

description:
Libraries were run twice on Novaseq X
Stroma_04


title: RNAseq of porcine: skin woundDay_1_ID1324_Wound_L_center

description:
Library name: B_14_L_C_1
B_14_L_C


title: 16s microbiome data for patient 09 as DEB sample at week 0, rep 1

description: Library name: 1985set2_197_AP09Week0-1


title: Biol rep 4 RNAPII DMSO treated

value: RNAPII DMSO treated


title: N208_Control_Stroma

description:
Libraries were run twice on Novaseq X
Stroma_03


title: 16s microbiome data for patient 08 as DEB sample at week 12, rep 2

description: Library name: 1985set2_196_AP08Week12-2


title: 16s microbiome data for patient 08 as DEB sample at week 12, rep 1

description: Library name: 1985set2_195_AP08Week12-1


title: RNAseq of porcine: skin woundDay_9_ID1327_Wound_H_center

description:
Library name: I_98_H_C_1
I_98_H_C

value: Skin wound tissue


title: N277_Control_Stroma

description:
Libraries were run twice on Novaseq X
Stroma_02


title: Biol rep 3 RNAPII DMSO treated


title: RNAseq of porcine: skin woundDay_9_ID1328_Wound_E_edge

description:
Library name: I_99_E_E_1
I_99_E_E


title: N093_Control_Stroma

description:
Libraries were run twice on Novaseq X
Stroma_01


title: Biol rep 2 RNAPII DMSO treated


title: RNAseq of porcine: skin woundDay_11_ID1323_Wound_C_edge

description:
Library name: J_103_C_E_1
J_103_C_E


title: 16s microbiome data for patient 08 as DEB sample at week 8, rep 2

description: Library name: 1985set2_194_AP08Week8-2


title: Biol rep 1 RNAPII DMSO treated


title: 16s microbiome data for patient 08 as DEB sample at week 8, rep 1

description: Library name: 1985set2_193_AP08Week8-1


title: RNAseq of porcine: skin woundDay_11_ID1323_Wound_J_edge

description:
Library name: J_105_J_E_1
J_105_J_E


title: BMMs, K7M2 CM, DTM, 48 h, rep3

city: Nangning

first: Keyi

last: Wang

address: No. 22 Shuangyong Road, Qingxiu District

country: China

institute: Guangxi Medical University

description: Library name: TD3

data_processing:
Sequencing datasets underwent quality control processing with Trimmomatic (v0.36) and FastQC (v0.11.2) for adapter trimming and read visualization. A representative subset of 10,000 high-quality reads was randomly subsampled for taxonomic profiling using blastn against the NCBI NT database. Genome-guided alignment was subsequently executed via HISAT2 (v2.1.0) with GRCh38 reference genome, followed by alignment quality metrics computation using RSeQC (v2.6.1). Gene expression quantification was conducted via transcripts per million (TPM) normalization. Differential expression profiling employed DESeq2 (v1.12.4) with stringent thresholds (FDR <0.05, absolute log2FC >2). Significantly altered genes underwent functional annotation through: STRING database (v11.5) for protein-protein Interaction Networks (PPI) network reconstruction; topGO (v2.24.0) for Gene ontology (GO) enrichment; clusterProfiler (v3.0.5) for KOG and KEGG analysis.
Assembly: mm39
Supplementary files format and content: .xlsx file includes raw counts for each Sample

source_name: BMMs

extract_protocol:
RNA isolation from BMMs conditioned with K7M2 secretome and untreated counterparts using TRIzol™ Reagent
RNA-seq libraries were assembled with Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit (Yeasen, Shanghai, China), followed by DNBSEQ-T7 platform (MGI Tech, Shenzhen, China) sequencing (n=3).

tag: cell type

value: BMMs


title: 16s microbiome data for patient 08 as DEB sample at week 4, rep 2

description: Library name: 1985set2_192_AP08Week4-2


title: RNAseq of porcine: skin woundDay_9_ID1326_Wound_H_edge

description:
Library name: I_93_H_E_1
I_93_H_E

value: edge


title: Biol rep 4 MMH3K9 UNC1999 treated

value: BSC-1 ATCC CCL-26

value: MMH3K9 UNC1999 treated


title: BMMs, K7M2 CM, DTM, 48 h, rep2

description: Library name: TD2


title: Biol rep 3 MMH3K9 UNC1999 treated


title: BMMs, K7M2 CM, DTM, 48 h, rep1

description: Library name: TD1


title: RNAseq of porcine: skin woundDay_9_ID1326_Wound_H_center

description:
Library name: I_94_H_C_1
I_94_H_C


title: BMMs, K7M2 CM, 48 h, rep3

description: Library name: T3


title: Biol rep 2 MMH3K9 UNC1999 treated


title: RNAseq of porcine: skin woundDay_11_ID1324_Wound_J_center

description:
Library name: J_110_J_C_1
J_110_J_C


title: Biol rep 1 MMH3K9 UNC1999 treated


title: 16s microbiome data for patient 08 as DEB control at week 0

description: Library name: 1985set2_190_AP08Week0-C

value: skin


title: RNAseq of porcine: skin woundDay_1_ID1325_Wound_A_edge

description:
Library name: B_15_A_E_1
B_15_A_E


title: BMMs, K7M2 CM, 48 h, rep2

description: Library name: T2


title: 16s microbiome data for patient 08 as DEB sample at week 0, rep 2

description: Library name: 1985set2_189_AP08Week0-2


title: Biol rep 5 MMH3K9 GSK-LSD1 treated

value: MMH3K9 GSK-LSD1 treated


title: 16s microbiome data for patient 08 as DEB sample at week 0, rep 1

description: Library name: 1985set2_188_AP08Week0-1


title: BMMs, control，rep3

description: Library name: B3


title: BMMs, K7M2 CM, 48 h, rep1

description: Library name: T1


title: RNAseq of porcine: skin woundDay_11_ID1325_Wound_C_center

description:
Library name: J_112_C_C_1
J_112_C_C


title: 16s microbiome data for patient 07 as JEB sample at week 0, rep 2

description: Library name: 1985set2_187_AP07Week0-2


title: Biol rep 4 MMH3K9 GSK-LSD1 treated


title: BMMs, control，rep2

description: Library name: B2


title: RNAseq of porcine: skin woundDay_11_ID1325_Wound_J_center

description:
Library name: J_114_J_C_1
J_114_J_C


title: 16s microbiome data for patient 07 as JEB sample at week 0, rep 1

description: Library name: 1985set2_186_AP07Week0-1


title: Biol rep 3 MMH3K9 GSK-LSD1 treated


title: BMMs, control，rep1

description: Library name: B1


title: RNAseq of porcine: skin woundDay_13_ID1327_Wound_C_center

description:
Library name: K_120_C_C_1
K_120_C_C


title: 16s microbiome data for patient 08 as DEB sample at week 4, rep 1

description: Library name: 1985set2_191_AP08Week4-1


title: Biol rep 2 MMH3K9 GSK-LSD1 treated


title: M18

city: Macau

first: Chen

last: Huang

address: Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau

description: Library name: Sample 24

data_processing:
The DNB was then loaded to flowcell, and sequenced by DNBSEQ Platform.
Assembly: GRCm39
Supplementary files format and content: csv file contains the count value of each sample

source_name: steatohepatitis model mice

extract_protocol:
RNA was extracted using the Trizol method, and qualified RNA was used to construct a sequencing library.
After Sample QC, the mRNA was hybridized with Oligo（dT）probe and Captured by Magnetic Beads. The mRNA was then reverse-transcripted to first strand DNA. First strand DNA was used as template to synthesis second strand DNA, obtaining dsDNA. The dTTP tailed adaptor was ligated to both ends of the dsDNA fragments. The ligation product was amplified by PCR, and circularized to get single-stranded circular(ssCir) library. The ssCir library was then amplified through rolling circle amplification (RCA) to obtain DNA nanoball(DNB).

value: Liver tissue


title: RNAseq of porcine: skin woundDay_13_ID1326_Wound_C_edge

description:
Library name: K_115_C_E_1
K_115_C_E


title: M17

institute: Macau University of Science and Technology

description: Library name: Sample 23


title: Biol rep 6 MMH3K9 GSK-LSD1 treated


title: Biol rep 1 MMH3K9 GSK-LSD1 treated


title: 16s microbiome data for patient 06 as DEB sample at week 12, rep 1

description: Library name: 1985set2_184_AP06Week12-1


title: RNAseq of porcine: skin woundDay_11_ID1325_Wound_C_edge

description:
Library name: J_111_C_E_1
J_111_C_E


title: Biol rep 5 MMH3K9 A366 treated

value: MMH3K9 A366 treated


title: M16

description: Library name: Sample 22


title: 16s microbiome data for patient 06 as DEB sample at week 8, rep 2

description: Library name: 1985set2_183_AP06Week8-2


title: Biol rep 4 MMH3K9 A366 treated


title: M15

description: Library name: Sample 21


title: RNAseq of porcine: skin woundDay_13_ID1328_Wound_J_center

description:
Library name: K_126_J_C_1
K_126_J_C


title: Biol rep 3 MMH3K9 A366 treated


title: 16s microbiome data for patient 06 as DEB sample at week 4, rep 2

description: Library name: 1985set2_181_AP06Week4-2


title: M14

description: Library name: Sample 20


title: RNAseq of porcine: skin woundDay_13_ID1327_Wound_J_center

description:
Library name: K_122_J_C_1
K_122_J_C


title: 16s microbiome data for patient 06 as DEB sample at week 8, rep 1

description: Library name: 1985set2_182_AP06Week8-1


title: RNAseq of porcine: skin woundDay_15_ID1323_Wound_D_edge

description:
Library name: L_127_D_E_1
L_127_D_E


title: 16s microbiome data for patient 06 as DEB sample at week 4, rep 1

description: Library name: 1985set2_180_AP06Week4-1


title: Biol rep 2 MMH3K9 A366 treated


title: 16s microbiome data for patient 06 as DEB sample at week 0, rep 2

description: Library name: 1985set2_179_AP06Week0-2


title: 16s microbiome data for patient 06 as DEB sample at week 12, rep 2

description: Library name: 1985set2_185_AP06Week12-2


title: RNAseq of porcine: skin woundDay_13_ID1327_Wound_J_edge

description:
Library name: K_121_J_E_1
K_121_J_E


title: M13

description: Library name: Sample 19


title: RNAseq of porcine: skin woundDay_11_ID1325_Wound_J_edge

description:
Library name: J_113_J_E_1
J_113_J_E


title: 16s microbiome data for patient 06 as DEB sample at week 0, rep 1

description: Library name: 1985set2_178_AP06Week0-1


title: M11

description: Library name: Sample 17


title: Biol rep 4 MMH3K9 DMSO treated

value: MMH3K9 DMSO treated


title: M12

description: Library name: Sample 18


title: RNAseq of porcine: skin woundDay_11_ID1323_Wound_C_center

description:
Library name: J_104_C_C_1
J_104_C_C


title: Biol rep 1 MMH3K9 A366 treated


title: 16s microbiome data for patient 05 as DEB control at week 12

description: Library name: 1985set2_177_AP05Week12-C


title: RNAseq of porcine: skin woundDay_13_ID1328_Wound_C_center

description:
Library name: K_124_C_C_1
K_124_C_C


title: RNAseq of porcine: skin woundDay_13_ID1328_Wound_C_edge

description:
Library name: K_123_C_E_1
K_123_C_E


title: Biol rep 3 MMH3K9 DMSO treated


title: 16s microbiome data for patient 05 as DEB sample at week 12, rep 2

description: Library name: 1985set2_176_AP05Week12-2


title: Biol rep 2 MMH3K9 DMSO treated


title: M9

description: Library name: Sample 15


title: 16s microbiome data for patient 05 as DEB sample at week 12, rep 1

description: Library name: 1985set2_175_AP05Week12-1


title: 16s microbiome data for patient 05 as DEB control at week 8

description: Library name: 1985set2_174_AP05Week8-C


title: Biol rep 1 MMH3K9 DMSO treated


title: M7

description: Library name: Sample 13


title: M10

description: Library name: Sample 16


title: Biol rep 5 TMH3K27 UNC1999 treated

value: TMH3K27 UNC1999 treated


title: RNAseq of porcine: skin woundDay_15_ID1325_Wound_D_edge

description:
Library name: L_131_D_E_1
L_131_D_E


title: M8

description: Library name: Sample 14


title: RNAseq of porcine: skin woundDay_13_ID1328_Wound_J_edge

description:
Library name: K_125_J_E_1
K_125_J_E


title: 16s microbiome data for patient 05 as DEB sample at week 8, rep 2

description: Library name: 1985set2_173_AP05Week8-2


title: RNAseq of porcine: skin woundDay_16_ID1326_Wound_D_edge

description:
Library name: M_133_D_E_1
M_133_D_E


title: M6

description: Library name: Sample 12


title: Biol rep 4 TMH3K27 UNC1999 treated


title: 16s microbiome data for patient 05 as DEB sample at week 8, rep 1

description: Library name: 1985set2_172_AP05Week8-1


title: Biol rep 3 TMH3K27 UNC1999 treated


title: M5

description: Library name: Sample 11


title: RNAseq of porcine: skin woundDay_16_ID1326_Wound_D_center

description:
Library name: M_134_D_C_1
M_134_D_C

value: center


title: M4

description: Library name: Sample 10


title: RNAseq of porcine: skin woundDay_11_ID1324_Wound_C_edge

description:
Library name: J_107_C_E_1
J_107_C_E


title: RNAseq of porcine: skin woundDay_16_ID1327_Wound_D_center

description:
Library name: M_136_D_C_1
M_136_D_C


title: Biol rep 1 TMH3K27 UNC1999 treated


title: 16s microbiome data for patient 05 as DEB sample at week 4, rep 1

description: Library name: 1985set2_169_AP05Week4-1


title: 16s microbiome data for patient 05 as DEB sample at week 4, rep 2

description: Library name: 1985set2_170_AP05Week4-2


title: M2

description: Library name: Sample 8


title: M3

description: Library name: Sample 9


title: RNAseq of porcine: skin woundDay_15_ID1325_Wound_D_center

description:
Library name: L_132_D_C_1
L_132_D_C


title: Biol rep 5 TMH3K27 A366 treated

value: TMH3K27 A366 treated


title: RNAseq of porcine: skin woundDay_16_ID1328_Wound_D_edge

description:
Library name: M_137_D_E_1
M_137_D_E


title: M1

description: Library name: Sample 7


title: Biol rep 4 TMH3K27 A366 treated


title: RNAseq of porcine: skin woundDay_15_ID1324_Wound_D_edge

description:
Library name: L_129_D_E_1
L_129_D_E


title: Biol rep 3 TMH3K27 A366 treated


title: 16s microbiome data for patient 05 as DEB sample at week 0, rep 2

description: Library name: 1985set2_167_AP05Week0-2


title: C6

description: Library name: Sample 6

source_name: normal control mice


title: 16s microbiome data for patient 05 as DEB sample at week 0, rep 1

description: Library name: 1985set2_166_AP05Week0-1


title: Biol rep 2 TMH3K27 A366 treated


title: C5

description: Library name: Sample 5


title: RNAseq of porcine: skin woundDay_19_ID1326_Wound_I_edge

description:
Library name: N_139_I_E_1
N_139_I_E


title: 16s microbiome data for patient 05 as DEB control at week 4

description: Library name: 1985set2_171_AP05Week4-C


title: 16s microbiome data for patient 04 as DEB control at week 12

description: Library name: 1985set2_165_AP04Week12-C


title: C4

description: Library name: Sample 4


title: Biol rep 2 TMH3K27 UNC1999 treated


title: 16s microbiome data for patient 04 as DEB sample at week 12, rep 2

description: Library name: 1985set2_164_AP04Week12-2


title: RNAseq of porcine: skin woundDay_15_ID1324_Wound_D_center

description:
Library name: L_130_D_C_1
L_130_D_C


title: C3

description: Library name: Sample 3


title: Biol rep 5 TMH3K27 GSK-LSD1 treated

value: TMH3K27 GSK-LSD1 treated


title: RNAseq of porcine: skin woundDay_1_ID1325_Wound_L_edge

description:
Library name: B_17_L_E_1
B_17_L_E


title: 16s microbiome data for patient 04 as DEB sample at week 12, rep 1

description: Library name: 1985set2_163_AP04Week12-1


title: 16s microbiome data for patient 05 as DEB control at week 0

description: Library name: 1985set2_168_AP05Week0-C


title: RNAseq of porcine: skin woundDay_15_ID1323_Wound_D_center

description:
Library name: L_128_D_C_1
L_128_D_C


title: Biol rep 3 TMH3K27 GSK-LSD1 treated


title: C2

description: Library name: Sample 2


title: 16s microbiome data for patient 04 as DEB sample at week 8, rep 2

description: Library name: 1985set2_162_AP04Week8-2


title: RNAseq of porcine: skin woundDay_11_ID1323_Wound_J_center

description:
Library name: J_106_J_C_1
J_106_J_C


title: 16s microbiome data for patient 04 as DEB sample at week 8, rep 1

description: Library name: 1985set2_161_AP04Week8-1


title: Biol rep 2 TMH3K27 GSK-LSD1 treated


title: RNAseq of porcine: skin woundDay_16_ID1328_Wound_D_center

description:
Library name: M_138_D_C_1
M_138_D_C


title: RNAseq of porcine: skin woundDay_19_ID1328_Wound_I_edge

description:
Library name: N_143_I_E_1
N_143_I_E


title: 16s microbiome data for patient 04 as DEB sample at week 4, rep 2

description: Library name: 1985set2_160_AP04Week4-2


title: 3LL_tumor_K0N0_B4

city: Sendai

first: Takafumi

last: Suzuki

state: Miyagi

address: 2-1 Seiryo-machi, Tohoku University

country: Japan

institute: Tohoku University

description: Library name: 3LL_tumor_K0N0_B4

data_processing:
Transcript per million (TPM) normalized read counts were generated using Salmon quant script (Galaxy version 1.5.1+galaxy0) with mouse reference transcript sequences (version 35)
Assembly: transcript sequences (version 35)
Supplementary files format and content: tab-delimited text file inculde raw counts for each Sample

source_name: tumor tissue

extract_protocol:
Total RNA was extracted from livers of male mice using Sepasol®-RNA I Super G (09379-97; Nacalai Tesque).
Double-stranded DNA (dsDNA) libraries were created from the rRNA-depleted eluate using an MGIEasy RNA directional library prep kit (MGI).

value: tumor tissue

value: Male

value: subcutaneous transplantation

tag: genotype


title: Biol rep 1 TMH3K27 GSK-LSD1 treated


title: 3LL_tumor_K0N0_B3

description: Library name: 3LL_tumor_K0N0_B3


title: RNAseq of porcine: skin woundDay_19_ID1328_Wound_I_center

description:
Library name: N_144_I_C_1
N_144_I_C

value: Skin wound tissue


title: Biol rep 1 TMH3K27 A366 treated


title: Biol rep 6 TMH3K27 DMSO treated

value: TMH3K27 DMSO treated


title: RNAseq of porcine: skin woundDay_16_ID1327_Wound_D_edge

description:
Library name: M_135_D_E_1
M_135_D_E

value: edge


title: 16s microbiome data for patient 04 as DEB sample at week 0, rep 2

description: Library name: 1985set2_158_AP04Week0-2


title: Biol rep 5 TMH3K27 DMSO treated

value: BSC-1 ATCC CCL-26


title: 3LL_tumor_K0N0_B2

description: Library name: 3LL_tumor_K0N0_B2


title: Biol rep 4 TMH3K27 GSK-LSD1 treated


title: 16s microbiome data for patient 04 as DEB sample at week 4, rep 1

description: Library name: 1985set2_159_AP04Week4-1


title: 3LL_tumor_K0N0_B1

description: Library name: 3LL_tumor_K0N0_B1


title: RNAseq of porcine: skin woundDay_11_ID1324_Wound_C_center

description:
Library name: J_108_C_C_1
J_108_C_C


title: C1

description: Library name: Sample 1


title: 16s microbiome data for patient 04 as DEB sample at week 0, rep 1

description: Library name: 1985set2_157_AP04Week0-1


title: Biol rep 4 TMH3K27 DMSO treated


title: 16s microbiome data for patient 03 as DEB sample at week 12, rep 2

description: Library name: 1985set2_156_AP03Week12-2


title: 3LL_tumor_K0_B4

description: Library name: 3LL_tumor_K0_B4


title: RNAseq of porcine: skin woundDay_2_ID1327_Wound_A_center

description:
Library name: C_24_A_C_1
C_24_A_C


title: RNAseq of porcine: skin woundDay_2_ID1327_Wound_L_edge

description:
Library name: C_25_L_E_1
C_25_L_E


title: 16s microbiome data for patient 03 as DEB sample at week 12, rep 1

description: Library name: 1985set2_155_AP03Week12-1


title: RNAseq of porcine: skin woundDay_2_ID1327_Wound_L_center

description:
Library name: C_26_L_C_1
C_26_L_C


title: Biol rep 2 TMH3K27 DMSO treated


title: 3LL_tumor_K0_B3

description: Library name: 3LL_tumor_K0_B3


title: 16s microbiome data for patient 03 as DEB control at week 8

description: Library name: 1985set2_154_AP03Week8-C


title: RNAseq of porcine: skin woundDay_2_ID1328_Wound_A_edge

description:
Library name: C_27_A_E_1
C_27_A_E


title: 16s microbiome data for patient 03 as DEB sample at week 8, rep 2

description: Library name: 1985set2_153_AP03Week8-2


title: Biol rep 4 Acetyl-H4 UNC1999 treated

value: Acetyl-H4 UNC1999 treated


title: 16s microbiome data for patient 03 as DEB sample at week 8, rep 1

description: Library name: 1985set2_152_AP03Week8-1

value: skin


title: 3LL_tumor_K0_A3

description: Library name: 3LL_tumor_K0_A3


title: RNAseq of porcine: skin woundDay_2_ID1328_Wound_A_center

description:
Library name: C_28_A_C_1
C_28_A_C


title: Biol rep 3 Acetyl-H4 UNC1999 treated


title: Biol rep 2 Acetyl-H4 UNC1999 treated


title: RNAseq of porcine: skin woundDay_2_ID1326_Wound_A_center

description:
Library name: C_20_A_C_1
C_20_A_C


title: 16s microbiome data for patient 03 as DEB sample at week 4, rep 2

description: Library name: 1985set2_150_AP03Week4-2


title: 3LL_tumor_K0_A2

description: Library name: 3LL_tumor_K0_A2


title: RNAseq of porcine: skin woundDay_2_ID1328_Wound_L_edge

description:
Library name: C_29_L_E_1
C_29_L_E


title: Biol rep 1 Acetyl-H4 UNC1999 treated


title: Biol rep 3 TMH3K27 DMSO treated


title: 3LL_tumor_K0_A1

description: Library name: 3LL_tumor_K0_A1


title: 16s microbiome data for patient 03 as DEB sample at week 4, rep 3

description: Library name: 1985set2_151_AP03Week4-3


title: 16s microbiome data for patient 03 as DEB sample at week 4, rep 1

description: Library name: 1985set2_149_AP03Week4-1


title: 3LL_tumor_K0_B1

description: Library name: 3LL_tumor_K0_B1


title: 3LL_tumor_WT_A4

description: Library name: 3LL_tumor_WT_A4

value: wild-type


title: 3LL_tumor_K0_B2

description: Library name: 3LL_tumor_K0_B2


title: RNAseq of porcine: skin woundDay_3_ID1323_Wound_F_edge

description:
Library name: D_31_F_E_1
D_31_F_E


title: Biol rep 1 TMH3K27 DMSO treated


title: 16s microbiome data for patient 03 as DEB sample at week 0, rep 2

description: Library name: 1985set2_148_AP03Week0-2


title: Biol rep 5 Acetyl-H4 GSK-LSD1 treated

value: Acetyl-H4 GSK-LSD1 treated


title: 3LL_tumor_WT_A3

description: Library name: 3LL_tumor_WT_A3


title: RNAseq of porcine: skin woundDay_0_ID1326

description:
Library name: A_4_1326_1
A_4_1326


title: RNAseq of porcine: skin woundDay_3_ID1323_Wound_F_center

description:
Library name: D_32_F_C_1
D_32_F_C


title: 16s microbiome data for patient 03 as DEB sample at week 0, rep 1

description: Library name: 1985set2_147_AP03Week0-1


title: 3LL_tumor_K0_A4

description: Library name: 3LL_tumor_K0_A4


title: Biol rep 3 Acetyl-H4 GSK-LSD1 treated


title: Biol rep 2 Acetyl-H4 GSK-LSD1 treated


title: 3LL_tumor_WT_A1

description: Library name: 3LL_tumor_WT_A1


title: 16s microbiome data for patient 02 as DEB sample at week 12, rep 2

description: Library name: 1985set2_146_AP02Week12-2


title: 3LL_cell_K0N0_4

description: Library name: 3LL_cell_K0N0_4

source_name: cell line

value: cell line

value: cultivation


title: RNAseq of porcine: skin woundDay_3_ID1324_Wound_F_edge

description:
Library name: D_35_F_E_1
D_35_F_E


title: 3LL_cell_K0N0_3

description: Library name: 3LL_cell_K0N0_3


title: Biol rep 1 Acetyl-H4 GSK-LSD1 treated


title: 16s microbiome data for patient 02 as DEB sample at week 12, rep 1

description: Library name: 1985set2_145_AP02Week12-1


title: RNAseq of porcine: skin woundDay_3_ID1324_Wound_F_center

description:
Library name: D_36_F_C_1
D_36_F_C


title: 16s microbiome data for patient 02 as DEB sample at week 8, rep 1

description: Library name: 1985set2_143_AP02Week8-1


title: 3LL_cell_K0N0_2

description: Library name: 3LL_cell_K0N0_2


title: RNAseq of porcine: skin woundDay_3_ID1324_Wound_G_edge

description:
Library name: D_37_G_E_1
D_37_G_E


title: 3LL_cell_K0N0_1

description: Library name: 3LL_cell_K0N0_1


title: 16s microbiome data for patient 02 as DEB sample at week 4, rep 3

description: Library name: 1985set2_142_AP02Week4-3


title: Biol rep 4 Acetyl-H4 GSK-LSD1 treated


title: 16s microbiome data for patient 02 as DEB sample at week 4, rep 2

description: Library name: 1985set2_141_AP02Week4-2


title: Biol rep 5 Acetyl-H4 24 h infection

value: Acetyl-H4 24 h infection


title: 16s microbiome data for patient 02 as DEB sample at week 8, rep 2

description: Library name: 1985set2_144_AP02Week8-2


title: RNAseq of porcine: skin woundDay_4_ID1327_Wound_G_edge

description:
Library name: E_49_G_E_1
E_49_G_E


title: 3LL_cell_K0_4

description: Library name: 3LL_cell_K0_4


title: 16s microbiome data for patient 02 as DEB sample at week 4, rep 1

description: Library name: 1985set2_140_AP02Week4-1


title: Biol rep 2 Acetyl-H4 24 h infection


title: Biol rep 4 Acetyl-H4 24 h infection


title: Biol rep 1 Acetyl-H4 24 h infection


title: RNAseq of porcine: skin woundDay_3_ID1323_Wound_G_edge

description:
Library name: D_33_G_E_1
D_33_G_E


title: 3LL_tumor_WT_A2

description: Library name: 3LL_tumor_WT_A2


title: RNAseq of porcine: skin woundDay_3_ID1324_Wound_G_center

description:
Library name: D_38_G_C_1
D_38_G_C

value: center


title: RNAseq of porcine: skin woundDay_3_ID1323_Wound_G_center

description:
Library name: D_34_G_C_1
D_34_G_C


title: 16s microbiome data for patient 02 as DEB sample at week 0, rep 2

description: Library name: 1985set2_139_AP02Week0-2


title: 16s microbiome data for patient 02 as DEB sample at week 0, rep 1

description: Library name: 1985set2_138_AP02Week0-1


title: RNAseq of porcine: skin woundDay_2_ID1328_Wound_L_center

description:
Library name: C_30_L_C_1
C_30_L_C


title: 3LL_cell_K0_2

description: Library name: 3LL_cell_K0_2


title: 3LL_cell_K0_1

description: Library name: 3LL_cell_K0_1


title: Biol rep 3 Acetyl-H4 24 h infection


title: RNAseq of porcine: skin woundDay_3_ID1325_Wound_F_center

description:
Library name: D_40_F_C_1
D_40_F_C


title: 16s microbiome data for patient 01 as DEB sample at week 12, rep 2

description: Library name: 1985set2_137_AP01Week12-2


title: 3LL_cell_WT_4

description: Library name: 3LL_cell_WT_4


title: RNAseq of porcine: skin woundDay_3_ID1325_Wound_G_center

description:
Library name: D_42_G_C_1
D_42_G_C


title: 3LL_cell_WT_3

description: Library name: 3LL_cell_WT_3


title: 16s microbiome data for patient 01 as DEB sample at week 8, rep 2

description: Library name: 1985set2_135_AP01Week8-2


title: Biol rep 3 Acetyl-H4 A366 treated

description: HH4_48_hour_infections_A366_inhibtor_23_27_7

value: Acetyl-H4 A366 treated


title: 16s microbiome data for patient 01 as DEB sample at week 12, rep 1

description: Library name: 1985set2_136_AP01Week12-1


title: Biol rep 2 Acetyl-H4 A366 treated

description: HH4_48_hour_infections_A366_inhibtor_23_94_9


title: 3LL_cell_WT_2

description: Library name: 3LL_cell_WT_2


title: Biol rep 1 Acetyl-H4 A366 treated

description: HH4_48_hour_infections_A366_inhibtor_23_17_9


title: RNAseq of porcine: skin woundDay_4_ID1326_Wound_F_center

description:
Library name: E_44_F_C_1
E_44_F_C


title: RNAseq of porcine: skin woundDay_4_ID1326_Wound_F_edge

description:
Library name: E_43_F_E_1
E_43_F_E


title: 3LL_cell_WT_1

description: Library name: 3LL_cell_WT_1


title: Biol rep 6 Acetyl-H4 DMSO treated

description: HH4_48_hour_infections_DMSO_Control_23_94_1

value: Acetyl-H4 DMSO treated


title: RNAseq of porcine: skin woundDay_3_ID1325_Wound_F_edge

description:
Library name: D_39_F_E_1
D_39_F_E


title: 3LL_cell_K0_3

description: Library name: 3LL_cell_K0_3


title: 16s microbiome data for patient 01 as DEB sample at week 4, rep 3

description: Library name: 1985set2_133_AP01Week4-3


title: Biol rep 5 Acetyl-H4 DMSO treated

description: HH4_48_hour_infections_DMSO_Control_23_94_22


title: RNAseq of porcine: skin woundDay_4_ID1326_Wound_G_edge

description:
Library name: E_45_G_E_1
E_45_G_E


title: Lung, OMA.14, 12hours, rep3

city: Nagasaki

first: Naoki

last: Iwanaga

address: Sakamoto, 1-7-1

institute: Nagasaki University

data_processing:
RNA-seq libraries were sequenced using paired end reads (150nt of read1 and read2) on a DNBSEQ-G400RS instrument (MGI Tech).
Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.4.4), Trimmomatic (version 0.36), and cutadapt (version 1.16) software.
Trimmed reads were then mapped to the human GRCh38 genome using STAR (version 2.7.2b). Reads on annotated genes were counted using featureCounts (version 1.6.1).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: lungs

extract_protocol:
RNA was harvested using Rneasy miini plus kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit (Clontech, 634442) and MGIEasy Universal Library Conversion Kit (App-A) (MGI, 1000004155) according to the manufacturer’s instruction..

value: lungs

value: 12 hours post infection with S. anginosus and the supernatants of Prevotella intermedia


title: RNAseq of porcine: skin woundDay_4_ID1326_Wound_G_center

description:
Library name: E_46_G_C_1
E_46_G_C


title: Biol rep 5 Acetyl-H4 A366 treated

description: HH4_48_hour_infections_A366_inhibtor_23_81_4


title: Biol rep 4 Acetyl-H4 A366 treated

description: HH4_48_hour_infections_A366_inhibtor_23_81_3


title: 16s microbiome data for patient 01 as DEB sample at week 4, rep 2

description: Library name: 1985set2_132_AP01Week4-2


title: 16s microbiome data for patient 01 as DEB sample at week 4, rep 1

description: Library name: 1985set2_131_AP01Week4-1


title: Lung, OMA.14, 12hours, rep2


title: Biol rep 4 Acetyl-H4 DMSO treated

description: HH4_48_hour_infections_DMSO_Control_23_81_1


title: RNAseq of porcine: skin woundDay_4_ID1327_Wound_F_edge

description:
Library name: E_47_F_E_1
E_47_F_E


title: RNAseq of porcine: skin woundDay_4_ID1327_Wound_F_center

description:
Library name: E_48_F_C_1
E_48_F_C


title: Lung, OMA.14, 12hours, rep1


title: Biol rep 3 Acetyl-H4 DMSO treated

description: HH4_48_hour_infections_DMSO_Control_23_27_6


title: 16s microbiome data for patient 01 as DEB control at week 0

description: Library name: 1985set2_130_AP01Week0-C


title: 16s microbiome data for patient 01 as DEB sample at week 8, rep 1

description: Library name: 1985set2_134_AP01Week8-1


title: 16s microbiome data for patient 01 as DEB sample at week 0, rep 2

description: Library name: 1985set2_129_AP01Week0-2


title: Lung, GAM, 12hours, rep3

value: 12 hours post infection with S. anginosus and control medium


title: RNAseq of porcine: skin woundDay_0_ID1327

description:
Library name: A_5_1327_1
A_5_1327

value: Skin wound tissue


title: Biol rep 4 TMH3K27 24 h infection

value: TMH3K27 24 h infection


title: RNAseq of porcine: skin woundDay_3_ID1325_Wound_G_edge

description:
Library name: D_41_G_E_1
D_41_G_E

value: edge


title: Biol rep 1 Acetyl-H4 DMSO treated

description: HH4_48_hour_infections_DMSO_Control_23_17_7

value: BSC-1 ATCC CCL-26


title: Lung, GAM, 12hours, rep2


title: 16s microbiome data for patient 01 as DEB sample at week 0, rep 1

description: Library name: 1985set2_128_AP01Week0-1


title: Biol rep 3 TMH3K27 24 h infection


title: Haemophilus influenzae RdKW20, dam mutant, anaerobic, rep3

city: Mutilva Baja

first: Junkal

last: Garmendia

address: Pamplona, 123

country: Spain

institute: Instituto de Agrobiotecnologia, Consejop Superior de Investigaciones Científicas

data_processing:
The adapters were removed from the sequenced libraries by TrimGalore v0.6.10 (www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters for paired-end Illumina reads and reads <20 bps and/or error rate (TrimGalore option “-e”) higher than 0.1 were discarded.
Previously to the mapping step, the genome was indexed with STAR v2.7.10 with the parameters –runMode genomeduplicated reads were marked with Picard tools v3.2 (https://broadinstitute.github.io/picard/)Generate –genomeSAindexNbases 9.4. The remaining reads were mapped to the H. influenzae RdKW20 (GCA_000027305.1) genome using STAR using default parameters with the following exceptions: “–outputMultimapperOrder random” and “–twopassMode basic.”
duplicated reads were marked with Picard tools v3.2 (https://broadinstitute.github.io/picard/)
Quantification was done by HTSeq-count included into HTSeq v.2.0.5, using the NCBI annotation in GTF format with the option “–stranded no.”
Statistical analysis and FPKM calculation were done using DESeq2 v1.44.0 (R package). Expression tracks were generated with the function bamCoverage included into the software deepTools v3.5.2. with the parameter –normalizeUsing RPKM.
Assembly: GCA_000027305.1
Supplementary files format and content: Genome broser tracks are provided with BigWig format
Supplementary files format and content: Tabular-text files with gene counts are provided.

organism: Haemophilus influenzae

growth_protocol: H. influenzae clinical strains were recovered from COPD respiratory samples (BioProject accession number PRJNA282520). H. influenzae strains were grown at 37ºC on PolyViteX (PVX) agar (bioMérieux, 43101), on brain-heart infusion (BHI, Condalab, 1400.10) agar supplemented with 10 μg/mL hemin (Merck, H9039) and 10 μg/mL nicotinamide adenine dinucleotide (NAD, Merck, N0632), referred to as sBHI agar, or on supplemented Haemophilus Test Medium agar (HTM, Oxoid, CM0898), referred to as sHTM agar. H. influenzae liquid cultures were grown at 37ºC in sBHI. Solid and liquid cultures were grown aerobically in 5% CO2, or under static anaerobic conditions in an anaerobic workstation (Don Withlety A25). To monitor growth, H. influenzae strains were grown on PVX agar for 12 h in aerobiosis or anaerobiosis in all cases. Erythromycin 11 μg/mL (Erm11) or Spectinomycin 50 μg/mL (Spec50) were used when required.

extract_protocol:
RNA for sequencing was isolated from bacteria grown in sBHI to OD600=0.3. H. influenzae was grown for 12 h on PVX agar. Two to five colonies were inoculated into 10 mL sBHI, grown for 12 h at 90 r.p.m., diluted into 20 mL fresh sBHI to OD600=0.05, and grown to OD600=0.3 at 180 r.p.m. Next, 7 mL bacterial cultures were recovered, pelleted (4,000 r.p.m, 4 min), flash frozen, and stored at -80ºC. Bacterial RNA was isolated using NucleoSpin RNA kit (Macherey-Nagel). Alternatively, bacterial suspensions collected from PVX agar anaerobic growth were normalized to OD600=0.4 in sBHI, 5 mL aliquots were transferred to 50 mL-Falcon tubes with 20 mL sBHI and grown to OD600=0.3 also in static anaerobiosis. Next, 25 mL bacterial cultures were recovered, pelleted (4,000 r.p.m, 4 min), flash frozen, and stored at -80ºC.
Total RNA was isolated using TRIzol reagent (Invitrogen). In both cases, to prevent any DNA interference, a second DNase digestion was performed using RNase-free DNase and cleaning on a RNeasy Mini column (Qiagen). Purified RNA was quantified on a Nanodrop OneC (Thermofisher Scientific), libraries were checked for quality control with RNA 6000 Nano LabChips (Agilent 2,100 Bioanalyzer), and sequenced by Admera Health on an Illumina HiSeq platform with 2×150 bp reads, estimated 20M PE reads per sample, 10M in each direction. Three replicates per sample type were sequenced.

tag: strain

value: anaerobic


title: LgA-HL-09

city: Baltimore

first: Atul

last: Daiwile

state: MD

address: 251 Bayview Blvd,

department: MNRB

institute: NIDA

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Rattus norvegicus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts were added to the table
Assembly: Rattus norvegicus Rnor6.0
Supplementary files format and content: Txt file and counts

organism: Rattus norvegicus

source_name: Dorsal striatum

extract_protocol:
RNA was extracted using the protocol from RNeasy Mini Handbook (Qiagen)
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered on two flowcell lanes. After clustering, the flowcells were loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration.

treatment_protocol: Rats (n = 41) were randomly assigned to different groups: Saline (Sal) (n =8), Short-access (ShA) (n = 10), or Long-access (LgA) (n=23). On each training day, Long-access (LgA) and Sal rats were trained to self-administer for three sessions: one 3-h session during days 1–5, followed by two 3-h sessions during days 8–14, and then for three 3-h sessions during the rest of the study (days 15–20). Short-access (ShA) rats were trained to self-administer oxycodone for only one 3-h session for the entirety of the study (days 1–20). Rats were trained to self-administer oxycodone or saline for 20 days.

value: Dorsal striatum

value: Neural tissue

value: Sprague Dawley

value: wild type

value: Oxycodone SA Long-access high (LgA-H)


title: Haemophilus influenzae RdKW20, dam mutant, anaerobic, rep2

tag: condition


title: RNAseq of porcine: skin woundDay_4_ID1327_Wound_G_center

description:
Library name: E_50_G_C_1
E_50_G_C


title: LgA-HL-08


title: Lung, GAM, 12hours, rep1


title: KYSE510 cells, shRNH1 biol rep 3

city: Shanghai

first: He

last: Zhang

state: Shanghai

address: Tongji University, 1239 Siping Road, Yangpu District, Shanghai

institute: School of Life Science and Technology, Tongji University

data_processing:
Reads were trimmed using SOAPnuke
Raw reads were aligned to the reference genome (GRCh38) using HISAT2
Read counts were calculated using StringTie
Differentially expressed genes were analyzed using DEseq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene-level read counts and transcript-level read counts for each Sample

growth_protocol: cells are cultured with 1640 with 10%FBS

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Total RNA was processed by mRNA enrichment. mRNA enrichment: mRNA with a polyA tail was enriched with magnetic beads with OligodT. The obtained RNA was fragmented with an interruption buffer, reverse transcribed with a random N6 primer, and then the cDNA second strand was synthesized to form a double-stranded DNA. The ends of the synthesized double-stranded DNA are flattened and phosphorylated at the 5' end, and a sticky end with an "A" protruding from the 3' end is joined to a bulbous joint with a protruding "T" at the 3' end. The ligated product is amplified by PCR with specific primers, and the PCR product is heat denatured to a single strand, and a bridge primer is used to loop the single-stranded DNA to obtain a single-stranded circular DNA library. The constructed library is quality checked and sequenced after passing the test.

treatment_protocol: The medium was discarded. Cells were rinsed with PBS and placed on ice in the Trizol solution (Invitrogen)

value: esophageal squamous cell carcinoma

value: RNH1 knockdown


title: KYSE510 cells, shRNH1 biol rep 2


title: Biol rep 1 TMH3K27 24 h infection


title: Haemophilus influenzae RdKW20, dam mutant, anaerobic, rep1


title: Biol rep 2 TMH3K27 24 h infection


title: LgA-HL-06


title: Biol rep 2 Acetyl-H4 DMSO treated

description: HH4_48_hour_infections_DMSO_Control_23_94_7


title: Haemophilus influenzae RdKW20, WT, anaerobic, rep3

value: WT


title: LgA-HL-05


title: Haemophilus influenzae RdKW20,WT, anaerobic, rep2


title: Biol rep 4 Acetyl-H3 24 h infection

value: Acetyl-H3 24 h infection


title: Biol rep 5 Acetyl-H3 24 h infection


title: KYSE510 cells, shControl biol rep 3


title: Haemophilus influenzae RdKW20, WT, anaerobic, rep1


title: KYSE510 cells, shControl biol rep 2


title: Biol rep 3 Acetyl-H3 24 h infection


title: KYSE510 cells, shRNH1 biol rep 1


title: KYSE510 cells, shControl biol rep 1


title: LgA-HL-02


title: Haemophilus influenzae RdKW20, dam mutant, aerobic, rep2

value: aerobic


title: LgA-LL-11

value: Oxycodone SA Long-access low (LgA-L)


title: Biol rep 1 Acetyl-H3 24 h infection


title: SW480 cells, sgHSPB1, biol rep2, , tech rep1

city: shanghai

first: Songguo

last: Zheng

address: No.621 Zhongshan 2nd Road, Songjiang District, Shanghai

institute: Shanghai Jiaotong University

description: Library name: sg1-3-2

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2(v2.0.4) . Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set， then expression level of gene was calculated by StringTie (v2.1.2)
Assembly: GRCh38
Supplementary files format and content: .txt include FPKM value for each sample

extract_protocol:
Total RNA was isolated from cell pellets, using the TRIzol.
Strand-specific libraries were generated using the VAHTS Universal V6 RNA-seq Library Prep Kit for MGI (NRM604-01) according to the manufacturer's instructions.

value: CRC cell


title: SW480 cells, sgHSPB1, biol rep2, tech rep2

description: Library name: sg1-3-3


title: LgA-HL-03


title: Haemophilus influenzae RdKW20, dam mutant, aerobic, rep1


title: LgA-LL-07


title: LgA-LL-011


title: Biol rep 4 Acetyl-H3 UNC1999 treated

value: Acetyl-H3 UNC1999 treated


title: SW480 cells, sgHSPB1, biol rep2

description: Library name: sg1-3-1


title: Haemophilus influenzae RdKW20, dam mutant, aerobic, rep3


title: Biol rep 3 Acetyl-H3 UNC1999 treated


title: LgA-LL-05


title: Haemophilus influenzae RdKW20, WT, aerobic, rep3


title: Biol rep 2 Acetyl-H3 UNC1999 treated


title: Haemophilus influenzae RdKW20,WT, aerobic, rep2


title: LgA-LL-04


title: SW480 cells, sgHSPB1, biol rep1, tech rep2

description: Library name: sg1-2-3


title: Biol rep 1 Acetyl-H3 UNC1999 treated