title: WT_023

city: Baltimore

first: Jin-Young

last: Koh

state: MD

address: 670 W Baltimore Street

department: Otorhinolaryngology-Head & Neck Surgery

institute: University of Maryland, Baltimore

description: Library name: Sample 1

data_processing:
Nanopore sequencing reads were demultiplexed and aligned to the mm10 genome (GRCm38) by Mandalorion (commit c2b369e plus local modification) using BLAT version 35 and GMAP version 2018-07-04.  Mandalorion then quality filtered the aligned reads and used the filtered alignments to define and quantify isoforms.
Assembly: mm10
Supplementary files format and content: PSL file produced by Mandalorion for each sample

source_name: cochlear lateral wall

extract_protocol:
After euthanasia by CO2, the temporal bones were removed and placed into DPBS. The temporal bone was removed and opened under a dissecting microscope to access the cochlear membranous labyrinth. Once the cochlea was accessible, the stria vascularis tissue was extracted from the temporal bone and incubated for 5min at 37°C with collagenase from clostridium histolyticum solution at a working concentration of 0.3mg/500µl. The cell dissociation was completed by gently pipetting up and down. The disrupted stria vascularis tissues were placed under an inverted microscope equipped with 20x and 40x objectives and two 3D micromanipulators, each driving a pulled-glass micropipette attached to a nitrogen gas-powered Pico-Injector to control aspiration pressure. The dissociated cells were examined under the inverted microscope and were aspirated into the first pulled-glass micropipette in a slow and controlled manner then washed in fresh DPBS to remove residual collagenase solution and debris.
Nextera XT DNA sample preparation kits, including Tn5 enzymes for tagmentation, were used together with Nextera XT index kits for multiplexing.

value: cochlear lateral wall

value: root cell

tag: strain


title: Blood neutrophils, 0h,  Healthy Control replicate 10

status: Public on Jul 16 2026

type: SRA

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

description:
Library name: 9-5010
9-5010_hisat2.bam

library_source: transcriptomic

data_processing:
Reads were aligned to the human genome (hg38) using HISAT2 (v2.2.0)
Counts were generated using featureCounts in R (v4.4.1) providing the hg38 GTF file (iGenomes)
Assembly: hg38
Supplementary files format and content: Raw gene counts

molecule: polyA RNA

organism: Homo sapiens

source_name: Neutrophil

growth_protocol: Neutrophils (purity >99%) were isolated from whole blood using HetaSep followed by negative selection with the Stem Cell human neutrophil isilation kit.

extract_protocol:
Trizol:chloroform extraction followed by Qiagen RNAeasy cleanup including on-column DNase digest
NEBNext polyA selection and Ultra II Directional RNA library preparation kits (Paired-end, 2x150 bp sequencing).

treatment_protocol: Neutrophils were suspended in RPMI 1640 media and processed immediately

tag: cell type

value: Neutrophil

tag: genotype

value: Healthy control

tag: treatment

value: 0h no treatment


title: MIA_2

city: Beijing

first: Tang

last: Tianran

address: Chinese PLA General Hospital, No. 28, Fu Xing Road, Haidian District, Beijing 100853, China

country: China

institute: Chinese PLA General Hospital

description: Library name: MIA_2

data_processing:
Raw sequencing reads were quality‑checked using FastQC and trimmed using Trimmomatic to remove adapters and low‑quality bases.
Assembly: GRCm39 (mm39)
Supplementary files format and content: Tab-delimited text file containing raw read counts and FPKM values for all genes across MIA, and MIA_Acu samples.

molecule: total RNA

organism: Mus musculus

source_name: dorsal root ganglia (DRG)

extract_protocol:
Total RNA was extracted from L3‑L5 dorsal root ganglia (DRG) using TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA integrity and concentration were verified using an Agilent 2100 Bioanalyzer with RIN ≥ 8.0.
RNA‑seq libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina. Poly(A) mRNA was purified from total RNA, fragmented, and reverse‑transcribed into cDNA. Double‑stranded cDNA was ligated with adaptors, amplified, and purified to generate the final library.

tag: tissue

value: dorsal root ganglia (DRG)


title: Blood neutrophils, 0h,  Healthy Control replicate 9

description:
Library name: 8-5009
8-5009_hisat2.bam


title: U251 in vitro culture reference [C2B]

status: Public on Jul 17 2026

city: Detroit

first: Tavarekere

last: Nagaraja

state: MI

address: 2799 W. Grand Blvd.

department: Neurosurgery

country: USA

institute: Henry Ford Health

description:
Library name: C2B
Out-of-experiment reference (PCA / clustering)

data_processing:
Raw paired-end reads were sorted into human (graft) and rat (host) streams with xengsort 2.1.0 using GRCh38 and Rattus norvegicus reference k-mer indices.
The human (graft) read stream was quantified with nf-core/rnaseq v3.22.2 (Nextflow 25.10.2; STAR alignment and Salmon 1.10.3 quantification, reverse-stranded) against GRCh38, GENCODE release 44.
Gene-level counts were merged across samples into salmon.merged.gene_counts.tsv.
Differential expression between recurrent (post-LITT) and primary (pre-LITT) tumors was computed with nf-core/differentialabundance v1.5.0 (DESeq2; design ~ Classification).
Assembly: GRCh38 (human graft transcriptome), GENCODE release 44 (GRCh38.primary_assembly.annotation).
Supplementary files format and content: salmon.merged.gene_counts.tsv: tab-delimited matrix; rows = Ensembl gene IDs (column gene_id) with gene symbols (gene_name), columns = samples, values = Salmon-estimated gene-level counts for the human/graft transcriptome.

source_name: in vitro cell culture

growth_protocol: Adult female immune-compromised RNU/RNU rats (Charles River Laboratories) were stereotactically implanted intracerebrally with log-growth-phase U251N human glioblastoma cells (5 x 10^4 cells in 10 uL PBS) under isoflurane anesthesia. A burr hole was drilled 3.50 mm right of bregma (anterio-posterior 0.0); cells were injected at a depth of 2.5 mm at 0.5 uL/10 s and the needle held in place 5 min before withdrawal. IACUC #1509. Tumor establishment was confirmed by MRI/DCE-MRI ~2 weeks after implantation.

extract_protocol:
Tumor-bearing brains were sliced (2 mm), flash-frozen in 2-methylbutane chilled to -40 C on dry ice, and stored at -80 C; tumor tissue was dissected from the frozen slices. Total RNA was extracted by the originating laboratory using the Qiagen RNeasy Total RNA Purification Kit with QIAzol Lysis Reagent for tissue lysis; no separate DNase digestion was performed, as the RNeasy silica-membrane purification efficiently removes most genomic DNA. RNA was provided to the sequencing core already extracted. RNA integrity number (RIN) per sample: C2B 9.2, IL64B 8.7, IL66B 8.8, IL67B 8.9, IL68B 7.8, IL69B 8.9, NL70B 8.6, NL71B 8.1, N168B 6.1, N269B 8.9.
RNA libraries were prepared at the USC Molecular Genomics Core, University of Southern California, using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio, cat# 634411), an rRNA/total-RNA depletion (ribodepletion) based, strand-specific chemistry that preserves the reverse (antisense) strand. Library yield was quantified on a Qubit fluorometer and validated by qPCR (Thermo Fisher QuantStudio 7). Libraries were sequenced on an Illumina NextSeq 2000 in 2x100 bp paired-end configuration; the resulting data are reverse-stranded (Salmon auto-detected library type ISR).

treatment_protocol: Recurrent-arm tumors underwent diffusion-weighted-imaging-guided laser interstitial thermal therapy (DWI-LITT) using the Visualase system under real-time DWI-MRI guidance, performed ~24 h after a localizing MRI; ablation was stopped when it reached the tumor margins and animals were monitored longitudinally for recurrence. Primary-arm tumors were not ablated.

value: in vitro cell culture

tag: cell line

value: glioblastoma

value: none (in vitro reference)


title: Blood neutrophils, 0h,  Healthy Control replicate 8

description:
Library name: 7-5006
7-5006_hisat2.bam


title: snRNA-seq of 4 cochlear samples pooled prior to sequencing

city: New York

first: Xiaohui

last: Ma

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: Mini1_pool
Cochlear samples from four groups (CTRL1, CTRL2, CTRL3, and cKO) were pooled prior to sequencing, and the processed count matrix includes per-cell sample identities.

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed using the Parse Biosciences TrailMaker platform, which implements the split-pipe pipeline for demultiplexing, combinatorial barcode assignment, alignment to the mouse reference genome, and generation of gene-cell count matrices.
Assembly: GRCm38
Supplementary files format and content: Processed single-nucleus RNA-seq data are provided as a gene-by-cell count matrix in Matrix Market format (count_matrix.mtx.gz), with accompanying gene list (all_genes.csv.gz) and cell metadata (cell_metadata.csv.gz) files. These files are fully compatible with Seurat and contain raw UMI counts for each gene in each nucleus.

molecule: nuclear RNA

source_name: Cochlea

extract_protocol:
Nuclei were isolated from freshly dissected cochlear tissues using a detergent-based lysis buffer followed by filtration and centrifugation. Isolated nuclei were washed and prepared for single-nucleus RNA sequencing according to the Parse Biosciences Evercode WT Mini v3 protocol.
Single-nucleus RNA-seq libraries were generated using the Parse Biosciences Evercode WT Mini v3 kit according to the manufacturer's instructions. Briefly, isolated nuclei underwent combinatorial barcoding through multiple rounds of split-pool indexing to uniquely label individual nuclei. Barcoded cDNA was amplified and sequencing libraries were constructed for Illumina paired-end sequencing.

value: Cochlea


title: MIA_1

description: Library name: MIA_1


title: Multiplexed captuere file with DIO2, ND2 and TRF2

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

institute: University of Alabama at Birmingham

description: Library name: D10Day2FB

data_processing:
The de-multiplexing, barcode processing, and cell aggregation were done on Cell Ranger v7.2.0.
Count matrix were integrated  and down stream analyses conducted with Seurat V5
Assembly: Mus musculus
Supplementary files format and content: RNAbarcodes.csv containes the annotated cells and their corresponding barcodes.
Supplementary files format and content: The merge.final.RDS is the final integrated Seurat object.

source_name: kidney

extract_protocol:
Mice were euthanized and kidneys excised and single cell suspensions generated. Cells were also incubated with Total-SeqB hashing antibodies per manufacturer’s directions (Biolegend). the hasing antibodies were: ND samples - B0301 (ACCCACCAGTAAGAC), DIO samples- B0302 (GGTCGAGAGCATTCA) and TRF samples - B0303 (CTTGCCGCATGTCAT). Samples were then FACS sorted for CD45+ cells using the BD S6 6-way sorter. A second set of samples were run without multiplexing, but FACs sorted for CD45+.
10X Genomics

value: kidney

value: CD45+ cells

value: DIO, ND, TRF


title: C27_invitro_GPC_CD140+

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

description: Library name: Sample_C27_CD140_3

data_processing:
Alignment and gene counting were accomplished using STARsolo with the following flags: “--twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --soloType CB_UMI_Simple --soloCBwhitelist 3M-february-2018.txt --soloUMIlen 12 --soloUMIfiltering MultiGeneUMI --soloCBmatchWLtype 1MM_multi_pseudocounts --limitSjdbInsertNsj 2000000”. Samples produced using 10X Genomics scRNA 2.0 chemistry were aligned using the following STARsolo flags: “--twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --soloType CB_UMI_Simple --soloCBwhitelist 737K-august-2016.txt --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 10 --soloBarcodeReadLength 0 --soloUMIfiltering MultiGeneUMI --soloCBmatchWLtype 1MM_multi_pseudocounts --limitSjdbInsertNsj 2000000.”
Assembly: A custom chimeric reference comprised of concatenating GRCh38 ensembl 106 to GRCm39 ensembl 106 and filtering for transcript types: “protein_coding”, “lncRNA”, or “miRNA”.
Supplementary files format and content: Contains two 10X sparse matrixes with gene counts per cell. One for the mouse fraction and one for the human fraction. The mouse fraction of invivo cultures consist of the small subset of genes with homology great enough that the chimeric aligner cannot distinguish them.

extract_protocol:
For invitro samples unsorted PSC and GPC stage cells were incubated in Accutase (Millipore Sigma Cat. A6964) diluted 50% in DPBS for 6 minutes at 37 degrees. Cells were resuspended in DMEM and filtered for FACS. . Cells were selected based on forward and side scatter in addition to negative gating of 4′,6-diamidino-2-phenylindole (DAPI, Thermo Fisher Scientific, D1306) staining to remove dead cells and debri (1 µg ml−1). Cells were then captured for scRNA-seq on a 10X Genomics chromium controller. For Invivo samples the mouse brains were removed and immersed in ice-cold HBSS and their corpora callosa dissected and chopped into small pieces. This tissue was then incubated in a papain/DNase dissociation solution at 37 °C for 50 min. Papain was inactivated with the addition of ovomucoid dissolved in EBSS. A single-cell suspension was then achieved via repeated pipetting. Cells were pelleted, resuspended into MEM, and filtered for FACS. Cells were selected based on forward and side scatter in addition to negative gating of 4′,6-diamidino-2-phenylindole (DAPI, Thermo Fisher Scientific, D1306) staining to remove dead cells and debri (1 µg ml−1). Cells were then captured for scRNA-seq on a 10X Genomics chromium controller.
Libraries were constructed according to manufacturers instructions for either single cell 3' v2 or single cell 3' v3.1 from 10X genomics as noted in the metadata table.

tag: Stage

value: In Vitro - GPC Stage

tag: sort

tag: 10x chemistry


title: Blood neutrophils, 0h,  SLE replicate 11

description:
Library name: 5-6018
5-6018_hisat2.bam

value: SLE


title: Multiplexed gene expression file with DIO2, ND2 and TRF2 samples multiplexed

description: Library name: D10Day2GEX


title: Time restricted feed (TRF) gene expression file

description: Library name: TrfGEX

value: TRF


title: Blood neutrophils, 0h,  SLE replicate 9

description:
Library name: 3-6016
3-6016_hisat2.bam


title: Blood neutrophils, 0h,  SLE replicate 10

description:
Library name: 4-6017
4-6017_hisat2.bam


title: Diet induced obseity (DIO), gene expression file

description: Library name: D10GEX

value: DIO


title: Blood neutrophils, 0h,  SLE replicate 8

description:
Library name: 2-6015
2-6015_hisat2.bam


title: brain cells, FACS sorted, 8month old, Plp1Tg, rep1

city: Bonn

first: Ozgun

last: Gokce

address: Venusberg Campus 1

country: Germany

institute: Uniklinikum Bonn

description:
Library name: Sorted_8m_Plp1Tg_1
10X Genomics

data_processing:
Sequenced scRNA-Seq data were processed using the CellRanger pipeline (v6.0.1/v6.1.2 for 24 week old Plp1Tg, 6 and 12 week cuprizone mice; v7.0.0 for “sorted data”) from 10xGenomics.
Assembly: mm10.98-mm10.98
Supplementary files format and content: Plp1Tg_Acute_Chronic_microglia.rds: Seurat object (v.4.1.3) containing microglia of Plp1Tg, Cuprizone (Acute: 6 weeks, Chronic:12 weeks treatment) and control brains
Supplementary files format and content: sorted_Plp1Tg_4m_8m_microglia.RDS: Seurat object (v.4.1.3) containing microglia from FACS isolated cell from Plp1Tg and control brains (4 months and 8 months old)
Supplementary files format and content: sorted_Plp1Tg_4m_8m_oligodendrocytes.RDS: Seurat object  (v.4.1.3) containing microglia from FACS isolated cell from Plp1Tg and control brains (4 months and 8 months old)

source_name: brain: cortex, hippocampus

extract_protocol:
Mice were anesthetized using ketamine/xylazine and perfused with cold PBS. One hemisphere including cortex and hippocampus but excluding cerebellum and brain stem were dissociated with a previously established protocol using gentleMACS OctoDissector together with the Papain Neural Tissue Dissociation Kit (Miltenyi Biotec) and actinomycin D (catalog no. A1410, Sigma-Aldrich). After dissociation, myelin debris were removed from the single cell suspension using Myelin Removal Beads II (Miltenyi Biotec). The single cells were then resuspended in 0.04% BSA + PBS and counted using an automatic cell counter and trypan blue (BioRad TC20). For generating the sorted scRNA-seq data, 16 weeks and 32 weeks old Plp1Tg mice were anesthetized using ketamine/xylazine and perfused with cold PBS. Following gentleMACS brain hemisphere dissociation, SYTOX Blue-negative cells were sorted into a 2-ml Eppendorf tube with 1 ml of PBS + 5% fetal bovine serum (FBS). Sorted cells were centrifuged at 300g for 10 min at 4 °C. Cell pellets were resuspended in 0.04% bovine serum albumin (BSA) + PBS catching medium at a concentration of 700–900 cells per µl.
Single cell libraries were constructed according to the 10X Genomics instructions (Chromium Single Cell 3' v3.1 (Single Index). Sample processing and library preparation were performed according to the manufacturer’s instructions using AMPure beads (Beckman-Coulter). Sequencing was performed on the Illumina NovaSeq 6000 (BGI Group).

treatment_protocol: For cuprizone treatment: Mice were fed 0.2% w/w cuprizone (Sigma-Aldrich, Germany) in powder chow (ssniff V1120) for 6 weeks or 12 weeks to induce acute or chronic demyelination followed by remyelination. Mice were fed three times a week an exceeding amount of chow by dispenser. Food intake and animal weight was monitored. Age-matched untreated controls were fed standard powder chow (ssniff V1120).

value: brain:cortex, hippocampus

tag: age

value: 8 months

tag: Sex

value: female

tag: pooling


title: Blood neutrophils, 0h,  Healthy Control replicate 6

description:
Library name: 21-5016
21-5016_hisat2.bam

value: Neutrophil

value: Healthy control


title: Blood neutrophils, 0h,  Healthy Control replicate 4

description:
Library name: 19-5014
19-5014_hisat2.bam

value: 0h no treatment


title: brain cells, FACS sorted, 8month old, Plp1Tg, rep2

description:
Library name: Sorted_8m_Plp1Tg_2
10X Genomics


title: brain cells, FACS sorted, 8month old, ctrl, rep3

description:
Library name: Sorted_8m_ctrl_3
10X Genomics


title: Blood neutrophils, 0h,  Healthy Control replicate 5

description:
Library name: 20-5015
20-5015_hisat2.bam


title: Blood neutrophils, 0h,  Healthy Control replicate 3

description:
Library name: 18-5013
18-5013_hisat2.bam


title: Blood neutrophils, 0h,  SLE replicate 7

description:
Library name: 17-6013
17-6013_hisat2.bam


title: brain cells, FACS sorted, 8month old, Plp1Tg, rep3

description:
Library name: Sorted_8m_Plp1Tg_3
10X Genomics


title: brain cells, FACS sorted, 8month old, ctrl, rep1

description:
Library name: Sorted_8m_ctrl_1
10X Genomics


title: Blood neutrophils, 0h,  SLE replicate 6

description:
Library name: 16-6012
16-6012_hisat2.bam


title: brain cells, FACS sorted, 8month old, ctrl, rep2

description:
Library name: Sorted_8m_ctrl_2
10X Genomics


title: brain cells, FACS sorted, 4month old, Plp1Tgl, rep3

description:
Library name: Sorted_4m_Plp1Tg_3
10X Genomics

value: 4 months


title: brain cells, FACS sorted, 4month old, Plp1Tg, rep2

description:
Library name: Sorted_4m_Plp1Tg_2
10X Genomics


title: Blood neutrophils, 0h,  SLE replicate 5

description:
Library name: 1-6014
1-6014_hisat2.bam


title: brain cells, FACS sorted, 4month old, Plp1Tg, rep1

description:
Library name: Sorted_4m_Plp1Tg_1
10X Genomics


title: Blood neutrophils, 0h,  SLE replicate 1

description:
Library name: 12-6008
12-6008_hisat2.bam


title: Blood neutrophils, 0h,  SLE replicate 3

description:
Library name: 14-6010
14-6010_hisat2.bam


title: Blood neutrophils, 0h,  SLE replicate 2

description:
Library name: 13-6009
13-6009_hisat2.bam


title: brain cells, FACS sorted, 4month old, ctrl, rep3

description:
Library name: Sorted_4m_ctrl_3
10X Genomics


title: Blood neutrophils, 0h,  Healthy Control replicate 1

description:
Library name: 10-5011
10-5011_hisat2.bam


title: brain cells, FACS sorted, 4month old, ctrl, rep2

description:
Library name: Sorted_4m_ctrl_2
10X Genomics


title: brain cells, chronic cuprizone treatment (12 weeks), rep1

description:
Library name: Chronic_1
10X Genomics

value: cuprizone (12 weeks)

value: 20 weeks

value: male

value: 2 animals pooled


title: Pan2_2-cell_PAIso-seq2

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

description: Library name: 2-cell_PAIso-seq2

data_processing:
Obtained hifi reads were segmented into single reads according to the concatenating primer, only the reads between successive barcodes were considered as confident reads. And the segmented reads were splitted into samples according to the barcodes, and the UMI sequences for each reads were extracted at the same time. Then the duplicated reads were removed according to the UMI sequence, and the clean reads were aligned to the mm10 genome (gencode, vM25) by using minimap2 (v2.24), and the information of poly(A) tails of mapped clean-reads was extracted and annotated according to the previous pipeline. The polyA length of each gene was calculated as the geometric average of all reads of the gene.
Assembly: mm10
Supplementary files format and content: pA_length.xlsx
Concatenating primer: Sequences
BCA: AGCTTACTTGTGAAGATCTACACGACGCTCTTCCGATCT
BCB: ACTTGTAAGCTGTCTATCTACACGACGCTCTTCCGATCT
BCC: ACTCTGTCAGGTCCGATCTACACGACGCTCTTCCGATCT
BCD: ACCTCCTCCTCCAGAATCTACACGACGCTCTTCCGATCT
BCE: AACCGGACACACTTAGTCTACACGACGCTCTTCCGATCT
BCF: CTCTGCGTTGATACCACTGCTTAGAGTCCAATTCGCAGT
Samples: barcodes
WT_PN3_1: TGCTATCTGAGATACTGTACTCTGCGTTGATACCACTGCTT
WT_PN3_2: GAGTCTCGATATACTAGTACTCTGCGTTGATACCACTGCTT
KO_PN3_1: GCTCTCACGATATCAGGTACTCTGCGTTGATACCACTGCTT
KO_PN3_2: TATATGCTCTGTGTGAGTACTCTGCGTTGATACCACTGCTT
WT_L2C_1: ACACTGACGTCGCGACGTACTCTGCGTTGATACCACTGCTT
WT_L2C_2: CGTCTATATACGTATAGTACTCTGCGTTGATACCACTGCTT
KO_L2C_1: ACACTGACGTCGCGACGTACTCTGCGTTGATACCACTGCTT
KO_L2C_2: CGTCTATATACGTATAGTACTCTGCGTTGATACCACTGCTT

source_name: embryo

extract_protocol:
In brief, total RNA was extracted with TRIzol Reagent and Direct-zol RNA MicroPrep (Zymo Research, Cat. no. R2060), and the barcode containing adapter were ligated to the 3’-end of mRNA. Then the RNA were purified by the RNA Clean & Concentrator-5 kit (Zymo Research, Cat. no. R1016).
After being purified by the RNA Clean & Concentrator-5 kit (Zymo Research, Cat. no. R1016), the RNA were RT into cDNA by the UMI containing template-switching oligo (TSO) primer and the first PCR amplification were proceeded. Then the cDNA from rRNA will be removed by the CRISPR-Cas9 system and the second PCR amplification will be performed to get enough cDNA. Then the cDNA from each sample will be concatenated into long molecules by following the MAS-ISO-seq procedure. Finally, all the samples were mixed up according to the molar ratios of cDNA, and at least 500ng of cDNA was sent for SMRTbell library preparation and sequenced on PacBio Revio platform.

value: embryo


title: BxPC-3 cells, RASA2 overexpression, biol rep 3

city: Shanghai

first: taochen

last: he

address: 180 Fenglin Road, Shanghai, China

institute: Zhongshan Hospital Fudan University

description:
Library name: BxPC-3-OE-3
Column name in gene_count_matrix: BxPC3-OE-3

data_processing:
Raw sequencing reads were subjected to quality control to remove adaptor sequences and low-quality reads. Clean reads were aligned to the human reference genome (GRCh38). Gene-level read counts were quantified and summarized into a gene expression matrix. Differential expression analysis was performed using DESeq2. The processed data file deposited in GEO contains the gene-level count matrix for all samples.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing gene-level raw read counts for all samples. Rows represent genes identified by Ensembl Gene IDs and columns represent individual RNA-seq samples. The count matrix was used for downstream differential expression analysis.

growth_protocol: BxPC-3 pancreatic ductal adenocarcinoma cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and maintained at 37°C in a humidified incubator containing 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen, USA) according to the manufacturer's instructions. RNA quantity and integrity were assessed using NanoDrop spectrophotometry and Agilent 2100 Bioanalyzer.
RNA sequencing libraries were prepared from high-quality total RNA using a standard mRNA library preparation kit according to the manufacturer's instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform to generate paired-end 150 bp reads.

treatment_protocol: BxPC-3 cells were transduced with lentiviral vectors expressing human RASA2 or empty vector control to establish stable cell lines. Cells were harvested at approximately 80% confluence for RNA extraction.

value: pancreatic cancer cell

value: RASA2 overexpression


title: Pan2_RS_PAIso-seq2

description: Library name: Pan2_RS_PAIso-seq2

data_processing:
Obtained hifi reads were segmented into single reads according to the concatenating primer, only the reads between successive barcodes were considered as confident reads. And the segmented reads were splitted into samples according to the barcodes, and the UMI sequences for each reads were extracted at the same time. Then the duplicated reads were removed according to the UMI sequence, and the clean reads were aligned to the mm10 genome (gencode, vM25) by using minimap2 (v2.24), and the information of poly(A) tails of mapped clean-reads was extracted and annotated according to the previous pipeline. The polyA length of each gene was calculated as the geometric average of all reads of the gene.
Assembly: mm10
Supplementary files format and content: pA_length.xlsx

source_name: sperm

value: sperm


title: BxPC-3 cells, RASA2 overexpression, biol rep 2

description:
Library name: BxPC-3-OE-2
Column name in gene_count_matrix: BxPC3-OE-2


title: E. coli pBAD FLAG-sp-HA, 37°C, rep 3

city: Taipei

first: Sue

last: Lin-Chao

address: 128 Academia Road, Section 2, Nankang,

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

description: Library name: FHIP373_22HNHTLT4

library_source: other

data_processing:
For RNA sequencing analysis of samples obtained by RNA crosslinking and immunoprecipitation, quality filtering and adapter trimming of the raw paired-end reads were performed using fastp (v 0.20.0). The trimmed reads were subsequently aligned to the reference genome and transcriptome of E. coli K-12 MG1655* (GCF_000146735.1; ASM14673v1) using STAR (v 2.7.11b). Alignment successfully recovered between 10 to 16 million paired-aligned reads from each RNA-seq library. Then, peak calling was performed using PEAKachu, configured in adaptive mode, with a MAD multiplier of 0 and a maximum insert size of 200 base-pairs. Peaks with a log2 fold change ≥ 2.0 and an adjusted FDR p-value ≤ 0.05 were considered significantly enriched in E. coli carrying pBAD FLAG-PNPase D492G or pBAD FLAG-CsdA compared to pBAD FLAG-sp-HA.
Assembly: Escherichia coli (GCF_000146735.1; ASM14673v1)
Supplementary files format and content: tab-deliminated tsv file includes  normalized gene expression for each peak in a sample

molecule: other

organism: Escherichia coli

source_name: bacteria

growth_protocol: E. coli MG1655* Rned500 Δpnp ΔdbpA ΔrhlB ΔrhlE ΔsrmB carrying pBAD FLAG-PNPase D492G, pBAD FLAG-CsdA or pBAD FLAG-sp-HA were separately cultured in LB medium with 100 µg/mL ampicillin at 37 ºC and 200 rpm for 24 hours. Then cultures were diluted to an OD600 of 0.1 in 1 L flasks containing 200 mL of the same medium. Expression of the tagged proteins was induced in the cells by addition of arabinose to a final concentration of 0.2 % and the cultures were incubated for until they reached an OD600 of 0.6.

extract_protocol:
Following de-crosslinking, RNA was isolated as previously described [S. Lin-Chao, S. N. Cohen, The rate of processing and degradation of antisense RNAI regulates the replication of ColE1-type plasmids in vivo. Cell 65, 1233–1242 (1991)]
RNA quality was determined using an Agilent 5200 Fragment Analyzer and only samples with an RNA Quality Number of 8.0 or higher were used for subsequent steps. Before rRNA depletion, ERCC ExFold RNA Spike-In Mix (Thermo Fisher Scientific, Cat. No. 4456739) was added to each sample for later normalization. Ribosomal RNA was depleted using the RiboMinus Bacteria 2.0 Transcriptome Isolation Kit (Thermo Fisher Scientific, Cat. No. A47335) following manufacturer's instructions. Next, cDNA synthesis and library preparation were performed using KAPA mRNA HyperPrep Kit (Roche, Cat. No. KK8581) following the manufacturer's protocol. Briefly, rRNA-depleted samples were fragmented into 200–300 bp fragments, then cDNA was synthesized and A-tailed. Then, Illumina TruSeq RNA UD Index V2 dual indexed adapters (IDT, Cat. No. 20042114) were ligated to the A-tailed cDNA and amplified by 12 PCR cycles. Library concentration was measured using a Qubit dsDNA HS Assay Kit (Invitrogen, Cat. No. Q32854) on a Qubit 3.0 Fluorometer (Invitrogen, Cat. No. Q32866). Final library quantification was performed with a qPCR-based method using the KAPA Library Quantification Kit (Roche, Cat. No. KK4824) on a BioRad CFX Opus 96 real-time PCR machine. The strand-specific RNA-sequencing libraries were pooled and sequenced on an Illumina NovaSeq X Plus sequencer with paired-end, 150 cycle reads, with an average of 5 million reads per sample.

treatment_protocol: The crosslinker formaldehyde was added into each flask to a final concentration of 0.5 %. Each flask was incubated for 10 min, and then glycine (pH 7) was added to a final concentration of 125 mM to stop the crosslinking reaction. The flasks were incubated for 5 min at room temperature without shaking and then the cultures were centrifuged for 10 min at 4000 g and 4 ºC. The resulting pellets were resuspended in 2 mL of a solution containing 50 mM Tris, 300 mM NaCl, 10 % glycerol and 1 mM PMSF. Then, cell suspensions were treated with cOmplete protease inhibitor cocktail tablets (Roche, Cat. No. 04693132011) and RNasin Plus RNase Inhibitor (Promega, Cat. No. N2611) by following the manufacturer's instructions. Cell lysis was carried out by using a French press at 35 Kpsi and the cell debris was separated by centrifugation for 10 min at 14000 g and 4 ºC.  Clear cell lysates were incubated with Anti-FLAG M2 Magnetic Beads (Sigma, Cat. No. M8823) and a DynaMag Spin Magnet separator (Invitrogen, Cat. No. 12320D) following manufacturer’s instructions. De-crosslinking from the beads was carried out by incubation in a buffer containing 50 mM Tris, 5 mM EDTA, 10 mM DTT and 1% SDS (pH 7.0) for 40 min at 70 ºC.

value: bacteria

value: Rned500 deletion-rhlB deletion-rhlE deletion-srmB deletion-dbpA deletion-pnp

tag: batch


title: brain cells, acute cuprizone treatment (6 weeks), rep2

description:
Library name: Acute_2
10X Genomics

value: brain:cortex, hippocampus

value: cuprizone (6 weeks)

value: 14 weeks


title: E. coli pBAD FLAG-sp-HA, 37°C, rep 2

description: Library name: FHIP372_22HNHTLT4


title: BxPC-3 cells, RASA2 overexpression, biol rep 1

description:
Library name: BxPC-3-OE-1
Column name in gene_count_matrix: BxPC3-OE-1


title: E. coli pBAD FLAG-sp-HA, 37°C, rep 1

description: Library name: FHIP371_22HNHTLT4


title: brain cells, acute cuprizone treatment (6 weeks), rep1

description:
Library name: Acute_1
10X Genomics


title: E. coli pBAD FLAG-PNP(D492G), 37°C, rep 3

description: Library name: PNPKOIP374_22HNHTLT4


title: BxPC-3 cells, vector control, biol rep 3

description:
Library name: BxPC-3-vector-3
Column name in gene_count_matrix: BxPC3-vector-3

value: Empty vector


title: E. coli pBAD  FLAG-PNP(D492G), 37°C, rep 1

description: Library name: PNPKOIP372_22HNHTLT4


title: BxPC-3 cells, vector control, biol rep 2

description:
Library name: BxPC-3-vector-2
Column name in gene_count_matrix: BxPC3-vector-2


title: brain cells, Plp1Tg, rep1

description:
Library name: Plp1Tg_1
10X Genomics

value: 24 weeks


title: E. coli pBAD FLAG-CsdA, 37°C, rep 3

description: Library name: CSIP373_22HNHTLT4


title: E. coli pBAD FLAG-CsdA, 37°C, rep 2

description: Library name: CSIP372_22HNHTLT4


title: BxPC-3 cells, vector control, biol rep 1

description:
Library name: BxPC-3-vector-1
Column name in gene_count_matrix: BxPC3-vector-1


title: E. coli Δrnb Δrnr Δfbp, 8 min, rep6

description: Library name: d3-8min-6

data_processing:
Paired-end raw sequencing reads were aligned to the Escherichia coli reference genome and transcriptome (GCF_000005845.2; ASM584v2) using STAR (v 2.7.11b)
Transcript abundance for 4,731 genes, including 92 exogenous ERCC spike-in RNAs, was then estimated by RSEM (v1.3.3)
Read-count-per-gene measurements were normalized across all samples using the ERCC spike-in RNAs according to the method described by Potts et al. Normalization factors (k values) were calculated from the sample at time 0 using the 24 most abundant ERCC spike-in RNAs (top 6 abundances from each A, B, C, and D group).
The geometric average of these k values served as the library normalization factor. Finally, normalized read counts were obtained by dividing the raw read counts for each sample by its corresponding library normalization factor.
Assembly: Escherichia coli (GCF_000005845.2; ASM584v2)
Supplementary files format and content: tab-deliminated text file includes log10-transformed and ERCC-normalized gene expression for each sample

growth_protocol: To study the effects of fbp deletion on the RNA half-life of PNPase-essential strains, E. coli MG1655 Δrnb Δrnr, and MG1655 Δrnb Δrnr Δfbp were cultured in 2 L flasks containing 400 mL of M9 supplemented with 0.2 % glucose and 0.4 % CAA at 37 ºC and 200 rpm.

extract_protocol:
Following rifampicin treatment, RNA was isolated as previously described [S. Lin-Chao, S. N. Cohen, The rate of processing and degradation of antisense RNAI regulates the replication of ColE1-type plasmids in vivo. Cell 65, 1233–1242 (1991)]
RNA quality was determined using an Agilent 5200 Fragment Analyzer and only samples with an RNA Quality Number of 8.0 or higher were used for subsequent steps. Before rRNA depletion, ERCC ExFold RNA Spike-In Mix (Thermo Fisher Scientific, Cat. No. 4456739) was added to each sample. In brief, 2 µg of total RNA was combined with 4 µL of a 1:100 dilution of the ERCC RNA spike-in in a final volume of 50 µL. Ribosomal RNA was depleted using the RiboMinus Bacteria 2.0 Transcriptome Isolation Kit (Thermo Fisher Scientific, Cat. No. A47335) following manufacturer's instructions. Next, cDNA synthesis and library preparation were performed using KAPA mRNA HyperPrep Kit (Roche, Cat. No. KK8581) following the manufacturer's protocol. Briefly, rRNA-depleted samples were fragmented into 200–300 bp fragments, and cDNA was synthesized and A-tailed. Then, Illumina TruSeq RNA UD Index V2 dual indexed adapters (IDT, Cat. No. 20042114) were ligated to the A-tailed cDNA and amplified by 12 PCR cycles. Library concentration was measured using a Qubit dsDNA HS Assay Kit (Invitrogen, Cat. No. Q32854) on a Qubit 3.0 Fluorometer (Invitrogen, Cat. No. Q32866). Final library quantification was performed with a qPCR-based method using the KAPA Library Quantification Kit (Roche, Cat. No. KK4824) on a BioRad CFX Opus 96 real-time PCR machine. The strand-specific RNA-sequencing libraries were pooled and sequenced on an Illumina NovaSeq X Plus sequencer with paired-end, 150 cycle reads, with an average of 5 million reads per sample.

treatment_protocol: When OD460 reached approximately 0.450 rifampicin (Sigma, Cat. No. R3501) was added to the cultures to a final concentration of 0.5 mg/mL and aliquots were withdrawn after different time points, a time point zero was used as a control before treatment.

value: deletion-rnb deletion-rnr deletion-fbp

value: rifampicin

tag: time

value: 8 min


title: E. coli Δrnb Δrnr Δfbp, 8 min, rep4

description: Library name: d3-8min-4


title: brain cells, ctrl, rep1

description:
Library name: Ctrl_1
10X Genomics

value: 18 weeks


title: E. coli Δrnb Δrnr Δfbp, 8 min, rep3

description: Library name: d3-8min-3


title: Spatial transcriptomics (Visium) of Human Lung Cancer Capture 1 (NSCLC_936_1)

first: Laszlo

last: Halasz

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

description:
Library name: NSCLC_936_1
V11A12-042_C1

data_processing:
Raw sequences were processed and aligned to hg38 using Space Ranger 1.3 with defaut options.
Assembly: hg38
Supplementary files format and content: Processed results from spaceranger, including count matrix and image.
Library strategy: Spatial Transcriptomics

source_name: Lung

extract_protocol:
Prior to processing Visium gene expression samples, DV200 was measured on RNA isolated from Formalin-fixed paraffin-embedded (FFPE) blocks to assess RNA integrity. Samples with a DV200 greater than 50% were selected for subsequent steps. After quality control, blocks were trimmed and 5-µm tissue sections were cut and placed on the capture area of a Visium Spatial Gene Expression for FFPE slide (10X Genomics). The slide was incubated in a thermal cycler at 42 °C for 3 h, and then placed in a desiccator overnight at room temperature. Subsequent steps covering tissue staining and library preparation were performed according to the manufacturer’s instructions (CG000407_VisiumSpatialGeneExpressionforFFPE_RevC).
The quality of the libraries was assessed using an Agilent 4200 TapeStation. Libraries were sequenced using the NovaSeq 6000 platform with 150 paired-end configuration on a NovaSeq SP flowcell.

value: Lung


title: Blood neutrophils, 0h,  Healthy Control replicate 7

description:
Library name: 6-5008
6-5008_hisat2.bam

value: Neutrophil

value: Healthy control

value: 0h no treatment


title: Spatial transcriptomics (Visium) of Human Liver Cancer Capture 1 (HCC_204_1)

description:
Library name: HCC_204_1
V11A19-107_C1

source_name: Liver

value: Liver


title: Normal diet (ND) gene expression file

description: Library name: NDGEX

value: kidney

value: CD45+ cells

value: ND


title: E. coli Δrnb Δrnr Δfbp, 4 min, rep3

description: Library name: d3-4min-3

value: bacteria

value: 4 min


title: Spatial transcriptomics (Visium) of Human Colorectal Cancer Capture 2 (CRC_BIC31_2)

description:
Library name: CRC_BIC31_2
V12Y31-335_D1

source_name: Colon

value: Colon


title: DSP-1012550011232-E-A05

city: Osong-eup, Heungdeok-gu

first: WANG

last: FENG

state: Cheongju-si, Chungcheongbuk-do

address: Osongsaengmyeong ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungcheongbuk-do, Republic of Korea

country: South Korea

institute: chungbun national university

description:
Library name: ROI_004_Albumin
FFPE samples from 24-week-old mice on NCD and FFD diets liver tissues

data_processing:
Morphology markers: Albumin and Nuclear stain morphology markers Segment ROI (Alb)
Differential Expression Analysis: Differentially expressed genes (DEGs) were identified based on read counts. TMM+CPM normalization was applied using EdgeR within the R/Bioconductor framework, ensuring accurate expression level comparisons.
Assembly: The mouse genome assembly GRCm38
Supplementary files format and content: Processed data file is in format of text file containing ID, Gene Symbol, NCD/FFD Group
Library strategy: Spatial Transcriptomics

extract_protocol:
Sequencing Saturation is a measure of sequencing depth for a sample [1 – % Unique reads]. Below 50% the counts become less reliable. Sensitivity for low expressing genes is depressed with lower sequencing saturation.  We use Q3 normalization as we find it consistently outperforms other methods like Negative Probe, which can over-normalize small regions and Housekeeper Normalization, which is susceptible to inconsistency in experiments investigating disparate sample types that often have different expression levels.
Using a patented DNA barcoding technology, synthetic DNA oligonucleotide barcodes are attached to antibodies for protein detection, and In Situ Probes for mRNA detection via a UV photocleavable linker. A single tissue section is labeled with a cocktail of these probes and 4 fluorescently labeled morphology markers. Regions of interest for molecular profiling are selected based on the fluorescent images, and UV light illuminates each region independent, which releases the barcodes from that region for subsequent counting. Molecular counts for each target in the panel can then be mapped back to distinct regions of interest and comparisons made within and between samples. The workflow is simple with many aspects of it automated in the system.  Staining can be done on an Autostainer, or manually on the bench.  The system first scans the fluorescence, and ROI selection is done right through the software.  Once ROIs are selected, the system goes through and picks from each region one at a time.  As barcodes are released, a microcapillary system sips up the tags, and dispenses them into a 96 well microtiter plate.  Those barcodes can then be read out on our nCounter platform, or an Illumina sequencer.

value: FFD


title: E. coli Δrnb Δrnr Δfbp, 2 min, rep6

description: Library name: d3-2min-6

value: 2 min


title: Spatial transcriptomics (Visium) of Human Colorectal Cancer Capture 1 (CRC_BIC31_1)

description:
Library name: CRC_BIC31_1
V12Y31-062_D1


title: E. coli Δrnb Δrnr Δfbp, 2 min, rep4

description: Library name: d3-2min-4

value: deletion-rnb deletion-rnr deletion-fbp


title: DSP-1012550011232-E-A04

description:
Library name: ROI_003_Albumin
FFPE samples from 24-week-old mice on NCD and FFD diets liver tissues

value: NCD


title: E. coli Δrnb Δrnr Δfbp, 2 min, rep3

description: Library name: d3-2min-3

value: rifampicin


title: Spatial transcriptomics (Visium) of Human Colorectal Cancer Capture 2 (CRC_BIC18_2)

description:
Library name: CRC_BIC18_2
V12Y31-038_C1


title: E. coli Δrnb Δrnr Δfbp, 2 min, rep2

description: Library name: d3-2min-2


title: DSP-1012550011232-E-A03

description:
Library name: ROI_002_Albumin
FFPE samples from 24-week-old mice on NCD and FFD diets liver tissues


title: E. coli Δrnb Δrnr Δfbp, 16 min, rep6

description: Library name: d3-16min-6

value: 16 min


title: Spatial transcriptomics (Visium) of Human Colorectal Cancer Capture 1 (CRC_BIC18_1)

description:
Library name: CRC_BIC18_1
V12Y31-038_B1


title: E. coli Δrnb Δrnr Δfbp, 16 min, rep4

description: Library name: d3-16min-4


title: DSP-1012550011232-E-A02

description:
Library name: ROI_001_Albumin
FFPE samples from 24-week-old mice on NCD and FFD diets liver tissues


title: E. coli Δrnb Δrnr Δfbp, 16 min, rep3

description: Library name: d3-16min-3


title: Homo sapiens HepG2 hepatocellular carcinoma cells with pGEM, replicate 5.

city: Rehovot

first: Amir

last: Szitenberg

address: 234 Herzl St

department: INCPM

country: Israel

institute: Weizmann Institute

description: Library name: Y_EV_pGEM_5

data_processing:
Quality and adaptor trimming with cutadapt
Read mapping with STAR
Read counting and UMI counting with HTSeq
Assembly: GRCm38
Supplementary files format and content: TSV matrix raw counts
Supplementary files format and content: TSV matrix umi corrected counts

extract_protocol:
RNA was extracted using NucleoSpin RNA kit (Macherey-Nagel, 740955) according to manufacturer’s instructions
INCPM Bulk-MARSSeq: RNA-seq libraries were prepared at the Crown Genomics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science. A bulk adaptation of the MARS-Seq protocol (Jaitin et al., Science, 2014; Keren-Shaul et al., Nature Protocols, 2019) was used to generate RNA-Seq libraries for expression profiling of XXX. Briefly, (30 ng of input) RNA from each sample was barcoded during reverse transcription and pooled. Following Agencourct Ampure XP beads cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.  Libraries were quantified by Qubit and TapeStation as well as by qPCR  as previously described (Jaitin et al., Science, 2014; Keren-Shaul et al., Nature Protocols, 2019).

value: pGEM


title: DSP-1012550011232-E-A01

description:
Library name: No template control A
FFPE samples from 24-week-old mice on NCD and FFD diets liver tissues

value: control


title: E. coli Δrnb Δrnr Δfbp, 0 min, rep6

description: Library name: d3-0min-6

value: 0 min


title: Homo sapiens HepG2 hepatocellular carcinoma cells with pGEM, replicate 4.

description: Library name: Y_EV_pGEM_4


title: E. coli Δrnb Δrnr Δfbp, 0 min, rep4

description: Library name: d3-0min-4


title: Homo sapiens HepG2 hepatocellular carcinoma cells with pGEM, replicate 3.

description: Library name: Y_EV_pGEM_3


title: E. coli Δrnb Δrnr Δfbp, 0 min, rep2

description: Library name: d3-0min-2


title: TG2KO_Inj_K9_rep1

first: Benjamin

last: Weekley

address: 310 E 92nd St

department: Neuroscience

institute: Mount Sinai

description: Library name: KO_Inj_1_K9_S3

library_source: genomic

data_processing:
Raw sequencing files were demultiplexed using bcl2fastq2 (Illumina, v.2.20). Between 20 and 100 million total reads were achieved for each replicate (average, 42.6 million). The samples were aligned to the mm10 genome using bowtie2 (v.2.5.0) [84], with the following parameters: --local --very-sensitive-local --phred33 -I 10 -X 700 --dovetail --no-unal --no-mixed --no-discordant [82]. Low-quality reads were filtered out using Samtools (v.1.9) with a cut-off MAPQ score of 30, and only unique reads were retained for further processing [85]. Unique read files for each replicate/timepoint/antibody were merged and used for peak calling using MACS2 (v.3.0.0a6) with the callpeak function and the options -f BAMPE -q 0.05 --broad --broad-cutoff .05, using the corresponding IgG sample as the -c. For visualization, each sample was normalized by scaling the samples based on the E. coli spike-in DNA. Each sample was aligned to the E. coli genome (MG1655), and the uniquely aligned reads were counted. The number of E. coli reads for each replicate between timepoints was compared, with the sample with the lowest number of E. coli reads set at a scaling factor of 1×. The other samples were scaled down by a scaling factor that was computed by dividing the lowest number of E. coli reads by the sample number of E. coli reads.  Genome coverage tracks (bigwig files) were produced using the deepTools (v.3.5.1) bamCoverage function with the options --binSize 10 --smoothLength 30 --normalizeUsing None --scaleFactor # (derived from E. coli spike in) and using an ENCODE mm10 blacklist file (https://doi.org/10.1038/s41598-019-45839-z, v2) to discard regions with consistently non-specific signal [86]. Deeptools multibigwigSummary was run genome wide using a sliding window (window size 500 basepairs, offset by -450 basepairs), and the significant regions identified by comparison to the IgG controls (using a minimum cutoff of 20 reads for H3K9ac and 10-fold increase over IgG). Overlapping and neighboring regions were merged using Bedtools (merge -d 501). Then, the average number of H3K9ac reads per peak was calculated using multibigwigSummary. Overlap of various peaks and TSSs was achieved using bedtools intersect (v.2.31). Heatmaps were made using Deeptools (v.3.5.5) computeMatrix and plotHeatmap in reference-point mode, centered over TSSs or peak centres, using binSize 10 and --sortUsing mean, sorted in descending order. TSSs were downloaded from the UCSC (mm10) table browser using the canonically annotated transcript for each gene. The resulting matrix files were analyzed in R using dplyr (v.1.1.4), calculating the ratio between sham and injured animals in both genotypes. Genes with ≥ 1.5 and < 1.5-fold change comparing sham to TBI samples were plotted as heatmaps using the same deeptools parameters as above.
Assembly: mm10
Supplementary files format and content: bigwigs and peaks
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Brain astrocytes

extract_protocol:
Cortical astrocytes were isolated from sham and TBI mice 1 month after the rmTBI protocol, following MRI. Magnetic-activated cell sorting (MACS) was used with anti-ASCA2-micro magnetic beads (Miltenyi, 130-097-678) to select for astrocytes, modified from a validated protocol. Briefly, mice were anesthetized by isoflurane and rapidly decapitated. Brains were extracted and cortical tissue was dissected out from the rest of the brain and minced to roughly 1 cubic millimeter pieces. Tissue dissociation was performed using papain (Worthington Biochemical, LK003178) diluted in homemade artificial cerebral spinal fluid (aCSF) (125 mM NaCl, 5 mM KCl, 2 mM MgSO4, 24 mM NaHCO3, 1.25 mM NaH2PO4, 2 mM CaCl2, 10 mM glucose, pH 7.4), plus Dnase I (Sigma, D5025), followed by gentle trituration, centrifugation, supernatant removal, and resuspension with aCSF buffer containing ovomucoid inhibitor (Worthington Biochemical, 50-592-496). Tissue was further triturated, centrifuged, supernatant was removed, and the pellet was resuspended in 5% BSA in PBS. The suspensions were filtered through 40 µm cell strainers followed by MACS protocol for astrocyte isolation using LS columns (Miltenyi, 130-042-401). Astrocytes were eluted from MACS LS columns in aCSF, pelleted, and frozen at -80oC for CUT&RUN, proteomic, and metabolomic analyses. Each isolated astrocyte sample (n= 2 per group) was resuspended in 500 μl of nuclear extract (NE) buffer (20mM HEPES-KOH, pH 7.9, 10mM KCl, 0.5mM Spermidine, 0.1% TritonX-100, 20% glycerol, freshly added protease inhibitors (Halt Protease and Phosphatase Inhibitor Cocktail, 78446)) [81] for nuclear isolation in DNA LoBind 1.5 ml microfuge tubes (Eppendorf, 13-698-791). Sodium butyrate (10mM) was added to buffers including protease inhibitors to inhibit histone deacetylase activity during processing. Nuclei were pelleted at 1,100g for 5 min at 4 °C in a swinging-bucket rotor and supernatant discarded. Nuclei were washed again in 500 μl NE buffer and counted using a hemocytometer. In total, 100,000 nuclei were used per biological replicate. BioMag Plus Concanavalin A beads (Polysciences, 86057) were prepared (15 μl bead slurry per reaction) by washing three times in 500 μl binding buffer (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2) and resuspending to 500 μl binding buffer [81-83]. For all CUT&RUN reactions, including IgG negative controls, 15 μl of the resuspension was aliquoted into 1.5 ml DNA LoBind tubes (Eppendorf, 022431021) and 500 μl NE buffer was added to each tube. 100,000 isolated nuclei from cells were added to each tube, and rotated end over end at room temperature for 10 min. The bead-bound nuclei were washed with 1 ml wash buffer (WB: 20 mM HEPES, pH 7.5, 150 mM NaCl, 0.1% Triton X-100, 0.1% Tween-20, 0.5 mM spermidine, 0.1% BSA, freshly added protease inhibitors, 10mM sodium butyrate) three times. All washes were done with minimal pipetting, and beads were mixed by inversion and light flicking of the tube. Beads were resuspended in 100 μl of antibody buffer (1 ml wash buffer with 2 mM EDTA) and mixed by flicking. Two microliters of H3K9ac antibody (Millipore Sigma, 07-352) or CUTANA IgG negative control (EpiCypher, 13-0042) (1:50) were added to their corresponding tubes and mixed by flicking. Bead-bound nuclei were incubated on a mixer (tubes on their side at ~20-degree upward angle) with primary antibodies overnight at 4 °C. Nuclei were washed twice the next day with 1 ml of cold WB. Nuclei were resuspended in 50 μl of cold wash buffer by flicking, and 2.5 μl of pAG-MNase (Epicypher, 15-1016) was added and mixed by flicking and incubated for 1 h at 4 °C on the same mixer. Nuclei were then washed three times with 1 ml ice-cold wash buffer, followed by one wash in 1 ml low-salt rinse buffer (20 mM HEPES, pH 7.5, 0.5 mM spermidine, 0.1% Tween-20 and 0.1% Triton X-100). Nuclei were resuspended in ice-cold calcium incubation buffer (3.5 mM HEPES, pH 7.5, 10 mM CaCl2, 0.1% Tween-20, 0.1% Triton X-100) and immediately placed into an ice-cold metal block on ice to maintain the temperature. The samples were incubated for 30 min, and then 100 μl of 2× stop buffer (340 mM NaCl, 20 mM EDTA, 5 mM EGTA, 0.1% Tween-20, 0.1% Triton X-100, 25 μg/ml RNase A (Thermo Fisher Scientific, EN0531)) and 0.1 ng per 100 μl of E. coli spike-in DNA (Epicypher, 18-1401) was added, and the beads were mixed by flicking. Nuclei were incubated at 37 °C for 15 min with no shaking to allow for release of chromatin and digestion of RNA. Beads were placed onto a magnet, and the supernatant (200 μl) was collected. The supernatant was treated with proteinase K for 1 hour at 50oC to degrade all proteins. DNA was isolated using the Zymo ChIP DNA Clean & Concentrator kit (D5205) and eluted in 30 μl and frozen at −20 °C for library preparation [40].
Library preparation was performed using the NEBnext Ultra II DNA library kit (E7645L) with multiplexed adapters with minor modifications. CUT&RUN DNA underwent end repair and adapter ligation according to the manufacturer’s protocol (1:15 adapter dilution was used). DNA was amplified using 16 PCR cycles with 10 s of extension time per cycle. Libraries were quantified using the Qubit fluorometer (Thermo Fisher Scientific) DNA high sensitivity kit, and the library size distribution was checked using the Tapestation DNA High Sensitivity ScreenTape (Agilent). Libraries were pooled at an equimolar concentration and sequenced on the Illumina NovaSeq X+ sequencer by the NYU Genome Technology Center (paired-end, 100 cycles).

treatment_protocol: Male wild type and TG2-/- mice, 10-12 weeks old, were used for rmTBI. A modified weight drop model was used deliver mTBIs as previously characterized [47]. In brief, mice were anesthetized with 3% isoflurane, placed on a sterile pad over a foam platform, secured with two elastic straps, and a 444 g weight was dropped, hitting the impactor, which is installed with a Teflon tip that diffuses the impact force over the skull. Anatomical bregma was targeted by positioning the center of the impactor at the midline point at the anterior base of the ears. The impactor was driven downward into the skull at 3.1m/s velocity, delivering an approximate force/area of 3.3 N/mm2. Following the impact, a spring and solenoid piston work in concert to “catch” the weight, allowing the animal’s skull to rapidly return to its original position, producing a whiplash effect with combined linear and angular accelerations, which were quantified from both an accelerometer fixed to the weight sled and high-speed videos taken of every impact [47]. Immediately after the impact the mice were placed in separate cages in supine position until recovery. The time to right themselves from the supine position was recorded.

value: Brain astrocytes

value: TBI+28 days


title: E. coli Δrnb Δrnr Δfbp, 16 min, rep2

description: Library name: d3-16min-2


title: E. coli Δrnb Δrnr, 8 min, rep6

description: Library name: d2-8min-6

value: deletion-rnb deletion-rnr

value: 8 min


title: Homo sapiens HepG2 hepatocellular carcinoma cells with pGEM, replicate 2.

description: Library name: Y_EV_pGEM_2


title: E. coli Δrnb Δrnr, 8 min, rep4

description: Library name: d2-8min-4


title: TG2KO_Inj_K9_rep2

description: Library name: KO_Inj_2_K9_S4


title: Blood neutrophils, 0h,  SLE replicate 4

description:
Library name: 15-6011
15-6011_hisat2.bam

value: Neutrophil

value: SLE

value: 0h no treatment


title: TG2KO_Inj_IgG

description: Library name: KO_Inj_Ig_S20


title: E. coli Δrnb Δrnr Δfbp, 0 min, rep3

description: Library name: d3-0min-3

value: bacteria


title: Blood neutrophils, 0h,  Healthy Control replicate 2

description:
Library name: 11-5012
11-5012_hisat2.bam

value: Healthy control


title: brain cells, chronic cuprizone treatment (12 weeks), rep2

description:
Library name: Chronic_2
10X Genomics

value: brain:cortex, hippocampus

value: cuprizone (12 weeks)

value: 20 weeks

value: male

value: 2 animals pooled


title: brain cells, FACS sorted, 4month old, ctrl, rep1

description:
Library name: Sorted_4m_ctrl_1
10X Genomics

value: 4 months

value: female


title: E. coli Δrnb Δrnr, 8 min, rep3

description: Library name: d2-8min-3

value: rifampicin


title: E. coli Δrnb Δrnr, 8 min, rep2

description: Library name: d2-8min-2


title: Homo sapiens HepG2 hepatocellular carcinoma cells with pGEM, replicate 1.

description: Library name: Y_EV_pGEM_1

value: pGEM


title: TG2KO_Sham_K9_rep2

description: Library name: KO_Sh_2_K9_S8

value: Brain astrocytes

value: Sham


title: E. coli Δrnb Δrnr Δfbp, 8 min, rep2

description: Library name: d3-8min-2

value: deletion-rnb deletion-rnr deletion-fbp

value: 8 min


title: TG2KO_Sham_K9_rep1

description: Library name: KO_Sh_1_K9_S7


title: E. coli Δrnb Δrnr, 4 min, rep6

description: Library name: d2-4min-6

value: deletion-rnb deletion-rnr

value: 4 min


title: E. coli Δrnb Δrnr, 4 min, rep4

description: Library name: d2-4min-4

value: bacteria


title: Homo sapiens HepG2 hepatocellular carcinoma cells with FoxA2, replicate 5.

description: Library name: Y_FoxA2_P1P2_5


title: E. coli pBAD FLAG-PNP(D492G), 37°C, rep 2

description: Library name: PNPKOIP373_22HNHTLT4

value: Rned500 deletion-rhlB deletion-rhlE deletion-srmB deletion-dbpA deletion-pnp


title: brain cells, Plp1Tg, rep2

description:
Library name: Plp1Tg_2
10X Genomics

value: brain:cortex, hippocampus

value: 24 weeks


title: E. coli Δrnb Δrnr, 4 min, rep3

description: Library name: d2-4min-3


title: E. coli Δrnb Δrnr, 4 min, rep2

description: Library name: d2-4min-2


title: Homo sapiens HepG2 hepatocellular carcinoma cells with FoxA2, replicate 4.

description: Library name: Y_FoxA2_P1P2_4


title: TG2KO_Sham_IgG

description: Library name: KO_Sh_Ig_S18


title: E. coli Δrnb Δrnr, 2 min, rep6

description: Library name: d2-2min-6

value: 2 min


title: E. coli Δrnb Δrnr, 2 min, rep3

description: Library name: d2-2min-3


title: E. coli Δrnb Δrnr, 2 min, rep4

description: Library name: d2-2min-4


title: WT_Inj_K9_rep2

description: Library name: WT_Inj_2_K9_S2

value: Wild type

value: TBI+28 days


title: Homo sapiens HepG2 hepatocellular carcinoma cells with FoxA2, replicate 3.

description: Library name: Y_FoxA2_P1P2_3


title: brain cells, ctrl, rep2

description:
Library name: Ctrl_2
10X Genomics

value: 18 weeks

value: male

value: 2 animals pooled


title: Homo sapiens HepG2 hepatocellular carcinoma cells with FoxA2, replicate 2.

description: Library name: Y_FoxA2_P1P2_2


title: Spatial transcriptomics (Visium) of Human Lung Cancer Capture 1 (NSCLC_41485_2)

description:
Library name: NSCLC_41485_2
V11T30-021_C1

value: Lung


title: E. coli pBAD FLAG-CsdA, 37°C, rep 1

description: Library name: CSIP371_22HNHTLT4


title: E. coli Δrnb Δrnr, 2 min, rep2

description: Library name: d2-2min-2

value: rifampicin


title: WT_Inj_K9_rep1

description: Library name: WT_Inj_1_K9_S1

value: Brain astrocytes


title: Homo sapiens HepG2 hepatocellular carcinoma cells with FoxA2, replicate 1.

description: Library name: Y_FoxA2_P1P2_1


title: E. coli Δrnb Δrnr, 16 min, rep6

description: Library name: d2-16min-6

value: 16 min


title: E. coli Δrnb Δrnr, 16 min, rep4

description: Library name: d2-16min-4


title: WT_Inj_IgG

description: Library name: WT_Inj_Ig_S19


title: Homo sapiens HepG2 hepatocellular carcinoma cells with FoxA2P2, replicate 5.

description: Library name: Y_FoxA2P2_5


title: E. coli Δrnb Δrnr, 16 min, rep3

description: Library name: d2-16min-3


title: WT_Sham_K9_rep2

description: Library name: WT_Sh_2_K9_S6

value: Sham


title: E. coli Δrnb Δrnr Δfbp, 4 min, rep4

description: Library name: d3-4min-4

value: deletion-rnb deletion-rnr deletion-fbp


title: Homo sapiens HepG2 hepatocellular carcinoma cells with FoxA2P2, replicate 4.

description: Library name: Y_FoxA2P2_4


title: E. coli Δrnb Δrnr, 16 min, rep2

description: Library name: d2-16min-2

value: deletion-rnb deletion-rnr


title: E. coli Δrnb Δrnr, 0 min, rep6

description: Library name: d2-0min-6

value: bacteria

value: 0 min


title: WT_Sham_K9_rep1

description: Library name: WT_Sh_1_K9_S5


title: E. coli Δrnb Δrnr, 0 min, rep3

description: Library name: d2-0min-3


title: Homo sapiens HepG2 hepatocellular carcinoma cells with FoxA2P2, replicate 3.

description: Library name: Y_FoxA2P2_3


title: rat C6 IgG - 100K cells - Replicate 3

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8797 Watertown Plank Rd

department: Stem Cell Transriptional Regulation

institute: Versiti Blood Research Institte

description: Library name: R100K_IgG_R3

data_processing:
For each of the mESCs and rat C6 CUT&Tag samples, the adaptors and low-quality sequences (> 20 bp) were trimmed by Cutadapt using this criterion ‘-a CTGTCTCTTATACACATCT -m 20 -q 20’.
Then all the raw reads were aligned to their respective genome (mm10 for mESC samples, and rn7 for rat C6 samples) using bowtie2 --end-to-end --very-sensitive --no-mixed --no-discordant. The PCR duplicate reads were removed using Picard. After removing PCR duplicates, replicate alignment files for each sample were merged and sorted by using $PICARD MergeSamFiles.
These merged alignment files were used for peak calling by MACS2 (2.2.9.1). We called the ‘broad’ Peak for H3K27me3, and for CTCF, ‘narrow’ peaks were called.
These merged alignment files were used to generate bigwig files (CPM normalization).
Assembly: mm10 and rn7
Supplementary files format and content: .bw file for normalized signal files for visualization
Library strategy: CUT&Tag

organism: Rattus norvegicus

growth_protocol: mESC cells were cultured in mouse ES cell media and Rat C6 were cultured in DMEM, both media supplemented with 15% and 10% FBS, respectively.

extract_protocol:
Genomic DNA of mESCs and rat C6 was extracted to perform CUT&Tag using CUT&Tag-direct with CUTAC V.3 (Steven Henikoff, Jorja Henikoff, Kami Ahmad 2021. CUT&Tag-direct with CUTAC. protocols.io https://dx.doi.org/10.17504/protocols.io.bqwvmxe6).
CUT&Tag libraries for CTCF, H3K27me3, IgG were then prepared based on the before-mentioned protocol and sent all mESCs and RatC6 samples to the Novogene (illumina Novaseq 6000) for sequencing.

treatment_protocol: Both mESC and rat C6 cells were grown up to ~80% confluency before collecting cells for CUT&Tag experiment.

value: rat C6 Glial Cell Line

value: WT


title: Homo sapiens HepG2 hepatocellular carcinoma cells with FoxA2P2, replicate 2.

description: Library name: Y_FoxA2P2_2


title: WT_Sham_IgG

description: Library name: WT_Sh_Ig_S17


title: mESC IgG - 100K cells - Replicate 4

description: Library name: M100K_IgG_R4

data_processing:
For each of the mESCs and OCIAML3 CUT&Tag samples, the adaptors and low-quality sequences (> 20 bp) were trimmed by Cutadapt using this criterion ‘-a CTGTCTCTTATACACATCT -m 20 -q 20 ’.
Then all the raw reads were aligned to their respective genome (mm10 for mESC samples, and hg38 for OCI-AML3 samples) using bowtie2 --end-to-end --very-sensitive --no-mixed --no-discordant. The PCR duplicate reads were removed using Picard. After removing PCR duplicates, replicate alignment files for each sample were merged and sorted by using $PICARD MergeSamFiles.
These merged alignment files were used for peak calling by MACS2 (2.2.9.1). We called the ‘broad’ Peak for H3K9me3, and H3K36me3 and for RAD21, H3K27Ac, and H3K4me3 ‘narrow’ peaks were called.
These merged alignment files were used to generate bigwig files (CPM normalization)
Assembly: mm10 and hg38
Supplementary files format and content: .bw file for normalized signal files for visualization
Library strategy: CUT&Tag

source_name: mESC

growth_protocol: mESC cells were cultured in mouse ES cell media and OCIAML3 were cultured in MEM Alpha, both media supplemented with 15% and 20% FBS, respectively

extract_protocol:
Genomic DNA of mESCs and OCIAML3 was extracted to perform CUT&Tag using CUT&Tag-direct with CUTAC V.3 (Steven Henikoff, Jorja Henikoff, Kami Ahmad 2021. CUT&Tag-direct with CUTAC. protocols.io https://dx.doi.org/10.17504/protocols.io.bqwvmxe6)
CUT&Tag libraries for H3K4me3, H3K27ac, H3K9me3, H3K36me3, RAD21, and IgG were then prepared based on the before-mentioned protocol and sent all mESCs and OCIAML3 samples to the Novogene (illumina Novaseq 6000) for seuencing.

treatment_protocol: Both mESC and OCIAML3 cells were grown up to ~80% confluency before collecting cells for CUT&Tag experiment

value: mESC

value: murine Embryonic Stem Cells (mESC)


title: rat C6 IgG - 100K cells - Replicate 1

description: Library name: R100K_IgG_R1


title: Homo sapiens HepG2 hepatocellular carcinoma cells with FoxA2P2, replicate 1.

description: Library name: Y_FoxA2P2_1


title: rat C6 IgG - 50K cells - Replicate 3

description: Library name: R50K_IgG_R3


title: Homo sapiens HepG2 hepatocellular carcinoma cells with FoxA2P1, replicate 5.

description: Library name: Y_FoxA2P1_5


title: rat C6 IgG - 50K cells - Replicate 2

description: Library name: R50K_IgG_R2


title: mESC IgG - 100K cells - Replicate 2

description: Library name: M100K_IgG_R2


title: mESC IgG - 100K cells - Replicate 3

description: Library name: M100K_IgG_R3


title: rat C6 IgG - 50K cells - Replicate 1

description: Library name: R50K_IgG_R1


title: rat C6 IgG - 10K cells - Replicate 2

description: Library name: R10K_IgG_R2


title: mESC IgG - 100K cells - Replicate 1

description: Library name: M100K_IgG_R1


title: Homo sapiens HepG2 hepatocellular carcinoma cells with FoxA2P1, replicate 3.

description: Library name: Y_FoxA2P1_3


title: mESC H3K9me3 - 100K cells - Replicate 3

description: Library name: M100K_H3K9me3_R3


title: rat C6 IgG - 1K cells - Replicate 2

description: Library name: R1K_IgG_R2


title: rat C6 IgG - 1K cells - Replicate 1

description: Library name: R1K_IgG_R1


title: mESC H3K9me3 - 100K cells - Replicate 2

description: Library name: M100K_H3K9me3_R2


title: rat C6 CTCF - 100K cells - Replicate 3

description: Library name: R100K_CTCF_R3


title: rat C6 CTCF - 100K cells - Replicate 2

description: Library name: R100K_CTCF_R2


title: mESC H3K9me3 - 100K cells - Replicate 1

description: Library name: M100K_H3K9me3_R1


title: rat C6 CTCF - 100K cells - Replicate 1

description: Library name: R100K_CTCF_R1


title: rat C6 CTCF - 50K cells - Replicate 3

description: Library name: R50K_CTCF_R3


title: SF12930 (G2)

city: San Francisco

first: Joanna

last: Phillips

address: 1450 Third Street, Room HD492B

institute: University of California San Francisco

description:
Library name: sample 10
G2

data_processing:
The demultiplexing, barcode processing,and gene counting and aggregation were made using 10X Genomics CellRanger software v3.0.2. using default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: Brain

extract_protocol:
Single-nucleus capture, reverse transcription, cell lysis for snRNA-seq were performed on the 10x Genomics platform as per manufacturer’s protocol. Approximately 15,000 nuclei were loaded per capture.
snRNA-seq library prepration were performed on the 10x Genomics platform as per manufacturer’s protocol.

value: Brain


title: rat C6 CTCF - 50K cells - Replicate 2

description: Library name: R50K_CTCF_R2


title: rat C6 CTCF - 50K cells - Replicate 1

description: Library name: R50K_CTCF_R1


title: SF12337 (G3)

description:
Library name: sample 9
G3


title: mESC H3K36me3 - 100K cells - Replicate 1

description: Library name: M100K_H3K36me3_R1


title: rat C6 CTCF - 10K cells - Replicate 3

description: Library name: R10K_CTCF_R3


title: SF12183 (G3)

description:
Library name: sample 8
G3


title: mESC H3K4me3 - 100K cells - Replicate 3

description: Library name: M100K_H3K4me3_R3


title: rat C6 IgG - 100K cells - Replicate 2

description: Library name: R100K_IgG_R2


title: SF11733 (G3)

description:
Library name: sample 7
G3


title: mESC H3K4me3 - 100K cells - Replicate 2

description: Library name: M100K_H3K4me3_R2


title: rat C6 CTCF - 10K cells - Replicate 1

description: Library name: R10K_CTCF_R1


title: Homo sapiens HepG2 hepatocellular carcinoma cells with FoxA2P1, replicate 2.

description: Library name: Y_FoxA2P1_2


title: mESC H3K4me3 - 100K cells - Replicate 1

description: Library name: M100K_H3K4me3_R1


title: Liver, sepsis sample, rep 11

city: Gent

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description: Library name: P011

data_processing:
Reads were quality checked with fastQC and no further processing was required
Reads were mapped to the ROS_Cfam_1.0 reference genome with STAR (2.7.10b). Read counts were directly obtained using the the featurecounts package
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: ROS_Cfam_1.0
Supplementary files format and content: tab delimited count matrix

organism: Canis lupus familiaris

source_name: liver

growth_protocol: All biological samples wee obtained from liver biospes from dogs diagnosed with peritonitic sepsis, control samples were obteind from non-sepsis dogs that required abdominal surgery for other reasons.

extract_protocol:
Total RNA was isolated with Aurum Total RNA mini Kit (Bio-Rad) following the manufacturer’s instructions
Library preparation was done using the illumina truseq stranded library kit for sequencing with a Cloudbreak sequencing kit on the element AVITI according the the manufacturer's instructions. Reads were sequenced paired end for 150 cycles

treatment_protocol: A liver biopsy was taken and stored in RNAlaer

value: liver

tag: breed

value: Shiba Inu

value: female

tag: weight (kg)


title: rat C6 CTCF - 1K cells - Replicate 3

description: Library name: R1K_CTCF_R3


title: mESC H3K27ac - 100K cells - Replicate 3

description: Library name: M100K_H3K27ac_R3


title: Liver, sepsis sample, rep 10

description: Library name: P010

value: Labrado

value: male


title: Liver, sepsis sample, rep 12

description: Library name: P012

value: Small Munsterlander


title: SF10348 (G3)

description:
Library name: sample 4
G3


title: SF11640 (G3)

description:
Library name: sample 6
G3


title: 3276418_3D11_RabIgG_003

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

description:
Library name: 3276418_3D11_RabIgG_003
Spike-in species: Drosophila melanogaster

data_processing:
Raw sequencing reads were quality-filtered and adapter-trimmed using Trim Galore (v0.4.4) with cutadapt (Q20 quality cutoff).
Trimmed reads were aligned to a combined human-Drosophila hybrid reference genome (GRCh38.p12 + dm6) using BWA (v0.7.12-r1039). Alignments were converted to BAM format using samtools (v1.2), and duplicate reads were marked using biobambam2 (v2.0.87).
Spike-in normalization factors were calculated based on the fraction of reads mapping to the Drosophila (dm6) genome relative to all mapped reads. For downstream analyses, only reads mapping to the human genome were retained. Alignments were filtered to uniquely mapped reads (MAPQ ≥1), excluding low-quality, secondary, and supplementary alignments.
Filtered BAM files were name-sorted and converted to paired-end fragment representations (BEDPE) using bedtools (v2.17.0), retaining properly paired fragments. Genome-wide coverage tracks were generated from fragments shorter than 2 kb by extracting the central 80 bp of each fragment (midpoint ±40 bp). Coverage was computed using bedtools genomecov and converted to bigWig format using UCSC bedGraphToBigWig. Coverage tracks were normalized to 10 million fragments and additionally scaled by the spike-in normalization factor.
Peak calling was performed using MACS2 with matched IgG controls. Broad histone targets (H3K4me1) were called with SICER (v1.1; p‑value 1e‑5). Peaks overlapping ENCODE blacklist regions were removed using bedtools.
Assembly: hg38
Supplementary files format and content: Processed data include peak files in narrowPeak BED, for targets with narrow peak profile, and BED format for broad targets; BigWig files containing sample level normalized genome-wide signal tracks and condition level signals (samples average).
Library strategy: CUT&Run

source_name: CMY

growth_protocol: Cmy cells and isogenic clones were cultured in RPMI (Gibco) supplemented with heat-inactivated fetal bovine serum (10%) and 1× penicillin/streptomycin at 37 °C with 5% CO₂. Cells were passaged every 2–5 days and confirmed to be mycoplasma-free and authenticated prior to experiments.

extract_protocol:
Nuclei were isolated from intact cells and chromatin-bound proteins were selectively released using micrococcal nuclease (MNase) digestion following the Epicypher CUTANA CUT&RUN protocol. MNase digestion time was modified to 1.5 hours.
CUT&RUN libraries were prepared using the CUTANA CUT&RUN Library Prep Kit (Epicypher; Cat#14-1001) according to the manufacturer’s protocol following antibody-directed MNase digestion. Libraries were indexed, pooled, and sequenced on an Illumina NovaSeq platform.

treatment_protocol: No chemical treatment was applied prior to CUT&RUN. Genome-edited cell lines were generated by CRISPR-Cas9 nucleofection and clonally expanded prior to chromatin profiling.

value: CMY

value: Myeloid leukemia of Down syndrome (ML-DS) cell line

value: RAD21 WT

tag: antibody

value: Epicypher 13-0042K


title: E. coli Δrnb Δrnr, 0 min, rep4

description: Library name: d2-0min-4

value: bacteria

tag: strain

value: deletion-rnb deletion-rnr


title: rat C6 CTCF - 1K cells - Replicate 2

description: Library name: R1K_CTCF_R2

tag: cell type

value: rat C6 Glial Cell Line


title: mESC H3K27ac - 100K cells - Replicate 2

description: Library name: M100K_H3K27ac_R2

tag: genotype

value: WT


title: Liver, sepsis sample, rep 9

description: Library name: P009

value: German Wirehaired Pointer


title: SF10304 (G2)

description:
Library name: sample 3
G2


title: mESC H3K27ac - 100K cells - Replicate 1

description: Library name: M100K_H3K27ac_R1

value: mESC

value: murine Embryonic Stem Cells (mESC)


title: rat C6 CTCF - 1K cells - Replicate 1

description: Library name: R1K_CTCF_R1


title: SF10786 (G2)

description:
Library name: sample 5
G2

value: Brain


title: Liver, sepsis sample, rep 8

description: Library name: P008

value: liver

value: Beagle


title: rat C6 H3K27me3 - 100K cells - Replicate 3

description: Library name: R100K_H3K27me3_R3


title: mESC IgG - 10K cells - Replicate 4

description: Library name: M10K_IgG_R4


title: Liver, sepsis sample, rep 7

description: Library name: P007

value: Bouvier des Flandres


title: SF5563 (G3)

description:
Library name: sample 1
G3


title: rat C6 H3K27me3 - 100K cells - Replicate 2

description: Library name: R100K_H3K27me3_R2


title: mESC IgG - 10K cells - Replicate 3

description: Library name: M10K_IgG_R3


title: E. coli Δrnb Δrnr, 0 min, rep2

description: Library name: d2-0min-2

tag: treatment

value: 0 min


title: AAK_D90_S2

city: Izmir

first: Burak

last: Kahveci

address: Izmir

country: Turkey

institute: Izmir Biomedicine and Genome Center

description: Library name: Sample 9

data_processing:
R statistical computing environment
Assembly: Homo_sapiens.GRCh38.112
Supplementary files format and content: comma-delimited csv file

source_name: Cornea

growth_protocol: iPSCs were cultivated using feeder-free conditions in mTeSR1 (StemCell Technologies) on hESC-qualified Matrigel (Corning) coated plates. hiPSCs were passaged every 5-7 days at a ratio of up to 1:10 using ReleSR (STEMCELL Technologies).

extract_protocol:
Total RNA extraction of undifferentiated hiPSCs and hiPSC-derived organoids were performed with TRIzol reagent, and samples were kept at -80 °C until further processing. Following the manufacturer’s instructions, RNA was isolated using the Macherey-Nagel Nucleospin RNA isolation kit.
Library preparation is made by SZAOMİCS using the Illumina Stranded total RNA Prep (Ribo-Zero Plus) Kit. The total-RNA samples are depleted from abundant transcripts, such as ribosomal RNA, using Ribo-Zero Plus depletion reagents. The samples are then chemically fragmented and turned into cDNA using reverse transcriptase, while subsequent ligation and amplification steps add the Illumina index-adapters for clustering and sequencing.

tag: tissue

value: Cornea

value: Induced Pluripotent Stem Cells

value: iPSCs


title: Liver, sepsis sample, rep 6

description: Library name: P006

value: Chihuahua

value: female


title: mESC IgG - 10K cells - Replicate 2

description: Library name: M10K_IgG_R2

tag: cell line


title: rat C6 H3K27me3 - 100K cells - Replicate 1

description: Library name: R100K_H3K27me3_R1


title: Liver, sepsis sample, rep 5

description: Library name: P005

value: American Cocker Spaniel


title: rat C6 IgG - 10K cells - Replicate 3

description: Library name: R10K_IgG_R3


title: AAK_D90_S1

description: Library name: Sample 8


title: Homo sapiens HepG2 hepatocellular carcinoma cells with FoxA2P1, replicate 4.

description: Library name: Y_FoxA2P1_4


title: rat C6 H3K27me3 - 50K cells - Replicate 3

description: Library name: R50K_H3K27me3_R3


title: mESC IgG - 10K cells - Replicate 1

description: Library name: M10K_IgG_R1


title: rat C6 IgG - 10K cells - Replicate 1

description: Library name: R10K_IgG_R1


title: Liver, sepsis sample, rep 4

description: Library name: P004

value: Chinese Crested Dog


title: rat C6 IgG - 1K cells - Replicate 3

description: Library name: R1K_IgG_R3

value: rat C6 Glial Cell Line


title: WT_Control_D90

description: Library name: Sample 7


title: rat C6 H3K27me3 - 50K cells - Replicate 2

description: Library name: R50K_H3K27me3_R2

value: WT


title: mESC H3K9me3 - 10K cells - Replicate 3

description: Library name: M10K_H3K9me3_R3


title: Liver, sepsis sample, rep 3

description: Library name: P003

value: Labrador

value: male


title: rat C6 H3K27me3 - 50K cells - Replicate 1

description: Library name: R50K_H3K27me3_R1


title: mESC H3K9me3 - 10K cells - Replicate 2

description: Library name: M10K_H3K9me3_R2

value: mESC

value: murine Embryonic Stem Cells (mESC)


title: AAK_D30_S2

description: Library name: Sample 6


title: Liver, sepsis sample, rep 2

description: Library name: P002

value: liver

value: Bernese Mountain Dog


title: Homo sapiens HepG2 hepatocellular carcinoma cells with FoxA2P1, replicate 1.

description: Library name: Y_FoxA2P1_1


title: AAK_D30_S1

description: Library name: Sample 5


title: Liver, sepsis sample, rep 1

description: Library name: P001

value: American Staffordshire Terrier


title: rat C6 H3K27me3 - 10K cells - Replicate 3

description: Library name: R10K_H3K27me3_R3


title: mESC H3K9me3 - 10K cells - Replicate 1

description: Library name: M10K_H3K9me3_R1


title: WT_Control_D30

description: Library name: Sample 4


title: rat C6 H3K27me3 - 10K cells - Replicate 2

description: Library name: R10K_H3K27me3_R2


title: mESC H3K36me3 - 100K cells - Replicate 2

description: Library name: M100K_H3K36me3_R2


title: Liver, control sample, rep 9

description: Library name: C009

value: Belgian Shepherd


title: AAK_iPSC_S2

description: Library name: Sample 3

value: Cornea


title: mESC H3K36me3 - 10K cells - Replicate 3

description: Library name: M10K_H3K36me3_R3


title: rat C6 H3K27me3 - 10K cells - Replicate 1

description: Library name: R10K_H3K27me3_R1


title: mESC H3K36me3 - 10K cells - Replicate 2

description: Library name: M10K_H3K36me3_R2


title: Liver, control sample, rep 8

description: Library name: C008

value: Dalmatian


title: Liver, sepsis sample, rep 14

description: Library name: P014

value: Pomeranian


title: AAK_iPSC_S1

description: Library name: Sample 2

value: Induced Pluripotent Stem Cells

value: iPSCs


title: rat C6 H3K27me3 - 1K cells - Replicate 3

description: Library name: R1K_H3K27me3_R3


title: Liver, control sample, rep 7

description: Library name: C007

value: Mixed Breed


title: mESC H3K36me3 - 10K cells - Replicate 1

description: Library name: M10K_H3K36me3_R1


title: control_ipsc

description: Library name: Sample 1


title: rat C6 H3K27me3 - 1K cells - Replicate 1

description: Library name: R1K_H3K27me3_R1


title: Liver, control sample, rep 6

description: Library name: C006

value: Shetland Sheepdog


title: mESC H3K4me3 - 10K cells - Replicate 3

description: Library name: M10K_H3K4me3_R3


title: DSP-1012550005943-G-H01

description:
Library name: TMA_MASH|044|CK8_18+
FFPE samples from human liver samples

data_processing:
Morphology markers: CK8/18 and Nuclear stain morphology markers Segment ROI (CK8/18+)
Differential Expression Analysis: Differentially expressed genes (DEGs) were identified based on read counts. TMM+CPM normalization was applied using EdgeR within the R/Bioconductor framework, ensuring accurate expression level comparisons.
Assembly: The human genome assembly GRCh38
Supplementary files format and content: Processed data file is in format of text file containing ID, Gene Symbol, Healthy/MASH Group
Library strategy: Spatial Transcriptomics

value: Liver

value: MASH


title: mESC H3K4me3 - 10K cells - Replicate 2

description: Library name: M10K_H3K4me3_R2

value: WT


title: eye-brain complex, WT, Rep2, NovaSeq 6000

city: St. Louis

first: Helen

last: McNeill

state: Missouri

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine in St. Louis

description:
Library name: w1118_eyebrain_R2
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: w1118_eyebrain_R2

data_processing:
Quality control of reads was performed using FastQC v.0.10.
Sequence reads were trimmed for adapter sequence/low-quality sequence using Trimmomatic v.0.33.
Trimmed sequence reads were mapped to dm6 using Salmon v.1.80 with default parameters
Read count extraction and normalization were performed using edgeR.
Assembly: dm6
Supplementary files format and content: tab-delimited text files include raw gene counts for each Sample

organism: Drosophila melanogaster

source_name: Eye-brain complex

growth_protocol: Larvae from a ubi-Gal4; UAS-FtICD-3xFLAG (Ft overexpression) stock, ft^fd5-5/ft^X13 (Ft null), and w^1118 (wild-type)  were grown in standard Drosophila media at 25C and tissues dissected in ice cold PBS. Embryos were collected and aged at 25 C on grape agar plates.

extract_protocol:
RNA was harvested using ReliaPrep RNA Tissue Miniprep System (Promega).
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds.  cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq X Plus and NovaSeq 6000 using paired end reads extending 150 bases

value: Eye-brain complex


title: Liver, control sample, rep 5

description: Library name: C005

value: male


title: Liver, sepsis sample, rep 13

description: Library name: P013

value: Pug


title: DSP-1012550005943-G-G12

description:
Library name: TMA_MASH|043|CK8_18+
FFPE samples from human liver samples


title: mESC H3K4me3 - 10K cells - Replicate 1

description: Library name: M10K_H3K4me3_R1

value: mESC

value: murine Embryonic Stem Cells (mESC)


title: eye-brain complex, WT, Rep1, NovaSeq 6000

description:
Library name: w1118_eyebrain_R1
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: w1118_eyebrain_R1


title: Liver, control sample, rep 4

description: Library name: C004

value: liver

value: Beagle

value: female


title: E. coli Δrnb Δrnr Δfbp, 4 min, rep2

description: Library name: d3-4min-2

value: bacteria

value: deletion-rnb deletion-rnr deletion-fbp

value: rifampicin

value: 4 min


title: eye-brain complex, Ubi>FtC, Rep3, NovaSeq 6000

description:
Library name: ubiFtICD_eyebrain_R3
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: ubiFtICD_eyebrain_R3

value: Ubi>FtICD


title: DSP-1012550005943-G-G11

description:
Library name: TMA_MASH|042|CK8_18+
FFPE samples from human liver samples


title: mESC H3K27ac - 10K cells - Replicate 3

description: Library name: M10K_H3K27ac_R3


title: DSP-1012550005943-G-G09

description:
Library name: TMA_MASH|041|CK8_18+
FFPE samples from human liver samples


title: eye-brain complex, Ubi>FtC, Rep2, NovaSeq 6000

description:
Library name: ubiFtICD_eyebrain_R2
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: ubiFtICD_eyebrain_R2


title: Liver, control sample, rep 3

description: Library name: C003

value: Standard Poodle


title: rat C6 CTCF - 10K cells - Replicate 2

description: Library name: R10K_CTCF_R2

value: rat C6 Glial Cell Line


title: mESC H3K27ac - 10K cells - Replicate 2

description: Library name: M10K_H3K27ac_R2


title: Liver, control sample, rep 2

description: Library name: C002


title: DSP-1012550005943-G-G05

description:
Library name: TMA_MASH|038|CK8_18+
FFPE samples from human liver samples

value: Liver

value: MASH


title: eye-brain complex, Ubi>FtC, Rep1, NovaSeq 6000

description:
Library name: ubiFtICD_eyebrain_R1
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: ubiFtICD_eyebrain_R1

value: Eye-brain complex


title: mESC H3K27ac - 10K cells - Replicate 1

description: Library name: M10K_H3K27ac_R1

value: WT


title: Liver, control sample, rep 1

description: Library name: C001

value: male


title: DSP-1012550005943-G-G03

description:
Library name: TMA_MASH|037|CK8_18+
FFPE samples from human liver samples


title: imaginal wing disc, WT, Rep3, NovaSeq 6000

description:
Library name: w1118_wing_R3
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: w1118_wing_R3

source_name: Imaginal wing disc

value: Imaginal wing disc


title: Myeloid cells, E0771 tumour, CD1d knockout, rep3 (KO_R3)

city: London

first: Patricia

last: Barral

address: Great Maze Pond

department: CIBCI

institute: King's College London

description:
Library name: PB6
10x Genomics Chromium Single Cell 3' v3.1

data_processing:
Raw FASTQ files were processed using Cell Ranger v9.0.1 (10x Genomics) with mouse reference genome GRCm39 (2024-A) to generate feature-barcode matrices
Assembly: GRCm39
Supplementary files format and content: HDF5 files containing filtered fature-barcode matrices from 10x Genomics Cell Ranger v9.0.1 Each file contains raw UMI countws for one biological sample

source_name: Breast tumour

growth_protocol: E0771 breast tuour cells were orthotopically injected into the mammary fat pads of C57BL/6  WT and CD1d knockout mice. Tumours were hsversted at day 15 post-injection

extract_protocol:
Tumours were mechanically and enzynatically dissociated using Mouse Tumor Dissoaciation Kit (Miltenyi Biotec). CD45+ immune infiltrates were positively selected uing CD45 MicroBeads. Myeloid cells were sorted as CD11+ and/or CD11c+ CD45+ NK1.1- CD19- CD3- LY6G- SiglecF- Zombie- using BD FACSAria II. Cell viability exceeded 80% for all samples prior to loading
Single-cell libraries were prepared using 10x Genoics Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (Dual Index) with approximmately 10,000 loaded per channel onto Chromium Chip G according to the manufacturer's protocol

value: Breast tumour

value: Myeloid cells

value: CD1d knockout


title: 2D-BR2

city: Houston,

first: Hari Krishna

last: Yalamanchili

state: TX

address: 1250 Moursund St #1125,

institute: Baylor College of Medicine

description: Library name: Sample 6

data_processing:
Illumina basespace software was used to demultiplex and convert bcl files to fastq files.
The paired-end reads were mapped to the mm10 mouse genome (UCSC mm10) using the software STAR, with NCBI RefSeq genes as the reference.
STAR generated read counts for each gene, which were used as the measurements of gene expression.
DESeq2 was then used to analyze the gene-level read counts.
Assembly: mm10
Supplementary files format and content: Tab separated text file with raw counts.

extract_protocol:
Total RNA was extracted using an Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad) following the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Mef2c-AHF+ cells differentiated for 2 days (2D) using either standard brown adipogenic induction medium (IM) containing IBMX, dexamethasone, insulin, and T3, or a combination of Bmp7 and Rosiglitazone (BR)

value: mesencMef2c-anterior heart field (AHF)-marked hymal stem cells

tag: group

value: BR

value: Bmp7 and Rosiglitazone (BR)


title: DSP-1012550005943-G-G01

description:
Library name: TMA_MASH|036|CK8_18+
FFPE samples from human liver samples


title: imaginal wing disc, WT, Rep2, NovaSeq 6000

description:
Library name: w1118_wing_R2
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: w1118_wing_R2


title: Myeloid cells, E0771 tumour, CD1d knockout, rep2 (KO_R2)

description:
Library name: PB5
10x Genomics Chromium Single Cell 3' v3.1

value: female


title: 2D-BR1

description: Library name: Sample 5


title: imaginal wing disc, WT, Rep1, NovaSeq 6000

description:
Library name: w1118_wing_R1
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: w1118_wing_R1


title: Myeloid cells, E0771 tumour, CD1d knockout, rep1 (KO_R1)

description:
Library name: PB4
10x Genomics Chromium Single Cell 3' v3.1


title: imaginal wing disc, Ubi>FtC, Rep3, NovaSeq 6000

description:
Library name: ubiFtICD_wing_R3
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: ubiFtICD_wing_R3


title: 2D-M2

description: Library name: Sample 4

value: IM

value: Induction medium (IM)


title: Myeloid cells, E0771 tumour, wild-type, rep3 (WT_R3)

description:
Library name: PB3
10x Genomics Chromium Single Cell 3' v3.1


title: DSP-1012550005943-G-F05

description:
Library name: TMA_MASH|032|CK8_18+
FFPE samples from human liver samples


title: 2D-M1

description: Library name: Sample 3


title: DSP-1012550005943-G-F03

description:
Library name: TMA_MASH|031|CK8_18+
FFPE samples from human liver samples


title: imaginal wing disc, Ubi>FtC, Rep2, NovaSeq 6000

description:
Library name: ubiFtICD_wing_R2
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: ubiFtICD_wing_R2

value: Ubi>FtICD


title: Myeloid cells, E0771 tumour, wild-type, rep2 (WT_R2)

description:
Library name: PB2
10x Genomics Chromium Single Cell 3' v3.1


title: imaginal wing disc, Ubi>FtC, Rep1, NovaSeq 6000

description:
Library name: ubiFtICD_wing_R1
Column name in McNeill_UbiFtICD_raw_gene_counts.txt: ubiFtICD_wing_R1


title: 2D-C2

description: Library name: Sample 2

value: Control


title: Myeloid cells, E0771 tumour, wild-type, rep1 (WT_R1)

description:
Library name: PB1
10x Genomics Chromium Single Cell 3' v3.1


title: 2D-C1

description: Library name: Sample 1


title: OR_50C;head;Oregon-R;Old group;50 days old;rep3

city: changsha

first: Jun

last: Wang

state: HuNan

address: Lushan

department: College of Life Science

institute: Hunan Normal University

description: Library name: OR_50C

data_processing:
Raw reads of FASTQ format were firstly processed using fastp and the low-quality reads were removed to obtain the clean reads that were mapped to the reference genome using HISAT2.FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: BDGP6.46
Supplementary files format and content: csv file includes raw counts for each Sample

source_name: head

growth_protocol: growth with standard food

extract_protocol:
Total RNA was extracted from heads of females for RNA-seq analysis. Fly heads were dissected in ice-cold PBS, transferred into RNAiso Plus (TaKaRa #9109), and homogenized with the Precellys Evolution Homogenizer (Bertin Technologies). 20 heads were used for each sample in biological triplicates. Total RNA extraction was performed as previously described 84. RNA concentration was measured by Nanodrop One (Thermo Fisher Scientific). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies).
Then, the sequencing libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Vazyme) and sequenced on an Illumina Novaseq 6000 platform with 150 bp paired-end reads.

treatment_protocol: (i) Diet group: 7-days-old w1118 iso (iso31) females raised on CD followed by 2 days with either a control diet (2% sucrose) or a protein-rich diet (2% sucrose + 3.3% yeast extract) at 25ºC; (ii) Age group: 3-day-old (as Young) and 50-day-old (as Old) Oregon-R flies raised on CD at 25°C; (iii) Lsp2 and Rheb overexpression: flies with fat body specific overexpression of Lsp2 or Rheb by LppTS and respective control raised on CD for 3 days prior to a sugar-only diet (5% sucrose) for 2 days at 29°C.

value: head

value: OR

value: 50 days old


title: DSP-1012550005943-G-E11

description:
Library name: TMA_MASH|029|CK8_18+
FFPE samples from human liver samples

value: Liver

value: MASH


title: inv(16);Smc3 wt PIPC 3

description: Library name: Smc3Wt-PIPC5

data_processing:
Mapping was done with Bowtie2 to mm10 using end-to-end, very-sensitive, and phred33 settings
Only mapped reads and non-mitochondrial reads were kept.
Peaks were called using MACS2 with BAMPE parameters and a q-value cutoff of 0.05
Assembly: mm10
Supplementary files format and content: Excel Spreadsheet and Called Peaks

source_name: Bone marrow

growth_protocol: mouse, in vivo

treatment_protocol: PIPC treatment

value: Bone marrow

value: HSPC

value: PIPC


title: mESC IgG - 100K cells - Replicate 3

description: Library name: M100K_IgG_R3

value: mESC

value: murine Embryonic Stem Cells (mESC)

value: WT


title: DSP-1012550005943-G-E05

description:
Library name: TMA_MASH|026|CK8_18+
FFPE samples from human liver samples

value: Healthy


title: OR_50B;head;Oregon-R;Old group;50 days old;rep2

description: Library name: OR_50B


title: inv(16);Smc3 wt PIPC 2

description: Library name: Smc3Wt-PIPC4


title: DSP-1012550005943-G-E03

description:
Library name: TMA_MASH|025|CK8_18+
FFPE samples from human liver samples


title: OR_50A;head;Oregon-R;Old group;50 days old;rep1

description: Library name: OR_50A


title: mESC IgG - 100K cells - Replicate 2

description: Library name: M100K_IgG_R2


title: mESC IgG - 100K cells - Replicate 1

description: Library name: M100K_IgG_R1


title: inv(16);Smc3 wt PIPC 1

description: Library name: Smc3Wt-PIPC3


title: DSP-1012550005943-G-E01

description:
Library name: TMA_MASH|024|CK8_18+
FFPE samples from human liver samples


title: OR_3C;head;Oregon-R;Young group;3 days old;rep3

description: Library name: OR_3C

value: 3 days old


title: mESC IgG - 50K cells - Replicate 3

description: Library name: M50K_IgG_R3


title: inv(16);Smc3 het PIPC 2

description: Library name: Smc3Het-PIPC2

value: Mx1-Cre+, inv(16);Smc3 D/+


title: DSP-1012550005943-G-D11

description:
Library name: TMA_MASH|023|CK8_18+
FFPE samples from human liver samples


title: mESC IgG - 50K cells - Replicate 2

description: Library name: M50K_IgG_R2


title: inv(16);Smc3 het PIPC 1

description: Library name: Smc3Het-PIPC1


title: OR_3B;head;Oregon-R;Young group;3 days old;rep2

description: Library name: OR_3B


title: DSP-1012550005943-G-D09

description:
Library name: TMA_MASH|022|CK8_18+
FFPE samples from human liver samples


title: mESC IgG - 50K cells - Replicate 1

description: Library name: M50K_IgG_R1


title: OR_3A;head;Oregon-R;Young group;3 days old;rep1

description: Library name: OR_3A


title: DSP-1012550005943-G-D07

description:
Library name: TMA_MASH|021|CK8_18+
FFPE samples from human liver samples