title: Mild MASLD sample 2, female, Foxa2 ChIP

description:
Foxa2_H_F_mild_MASLD.bed
H F Foxa2 mild MASLD 2

value: Liver


title: 54_RNAseq Lung_HDM/SAL

status: Public on Aug 06 2025

type: SRA

city: Chapel Hill

first: Lanazha

last: Belfield-Simpson

address: 125 Mason Farm Rd

country: USA

institute: Univeristy of North Carolina at Chapel Hill

library_source: transcriptomic

data_processing:
Raw data in fastq files were mapped to reference genome/transcriptome using STAR aligner to generate .BAM files.
Gene expression was estimated based on the BAM file with transcript assembler, StringTie v2, and saved as count and TPM values.
Assembly: GRCm39 and Gencode vM33
Supplementary files format and content: Estimated raw count in tab-delimited text.
Supplementary files format and content: Estimated TPM (transcripts per million mapped reads) in tab-delimited text.

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
Total RNA was isolated from Whole Lung using the Quick-RNA Microprep kit (Zymo Research).
Standard RNA-seq with PolyA selection, 20M paired end reads per sample, Illumina, 2x150bp.

treatment_protocol: Male wild type (C57Bl/6;stock no. 000664, Bar Harbor, Maine) mice between 7-8 weeks of age were utilized for all studies. Mice received five oropharyngeal instillations of 10 µg HDM (Greer, catalog number: XPB70D3A2.5) in 50µl (HDM mice) or PBS (Ca2+, Mg2+ free, 50µl) (PBS mice) at 2-3 day intervals. Twenty-four hours after the fifth instillation of HDM (HDM mice) or PBS (PBS mice), mice received 100 µL of 2 mg Combustion Products (CP)/ml saline or 100 µL saline (controls) by oropharyngeal instillation. At 24 hours post instillation, animals were euthanized by isoflurane overdose immediately prior to lung harvest. Lungs were flash frozen and stored at -80*C prior to RNA isolation.

tag: tissue

value: Lung

tag: genotype

tag: treatment

value: HDM and Saline


title: SA55_rep2

city: Beijing

first: Yihan

last: Lin

address: No.5 Yiheyuan Road, Haidian

country: China

institute: Peking University

description: Library name: Sample 21

data_processing:
Trimmomatic 0.39 was used to remove the 5' end 15-bp low quality sequence of the FASTQ file. BWA 0.7.17-r1188 was employed to map the resulting cleaned reads to the reference sequence. The resulting bam files were processed using a command mpileup from samtools to generate bcf file. To precisely profile the mutational frequency, nucleotides with sequencing quality score below Q30 were discarded. Then, custom Bash and Python scripts were used to extract the mutation information and calculate the mutation frequency.
Assembly: trVLP-ASV genome sequence
Supplementary files format and content: An Excel file for each sample, containing the mutation frequency information for each type of mutation in the RBD region.

organism: Mesocricetus auratus

source_name: kidney

growth_protocol: BHK-21 cells were cultivated in Minimum Essential Medium with Earle's Balanced Salts (MEM/EBSS) supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, 100 μg/ml streptomycin, and 1% MEM Non-Essential Amino Acids Solution (Gibco, #11140050) in a humidified 37℃ incubator with 5% CO2.

extract_protocol:
For each sample, supernatants containing trVLPs were collected, and RNA was extracted using TRIzol LS Reagent (HaiGene, #B1901), and the RNA was extracted following the manufacturer's protocol.
Approximately 100 ng of RNA was reverse transcribed into cDNA using the HiScript III First-Strand cDNA Synthesis Kit (Vazyme, R312-02) with sequence-specific primer (Sindis-gsp-R2: tgcgcctcctcggaaatacg). Subsequently, 5 µL of the cDNA was used as a template for PCR amplification in a 50 µL reaction volume with KOD One PCR Master Mix. The PCR was performed for 28 cycles using primers designed to target specific regions of the trVLP genome, such as the RBD region. The PCR products were sequenced using the Fast Next-Generation Sequencing (NGS) service by a Miseq merchine from Tsingke Biotechnology.

treatment_protocol: trVLP-ASV transduction and antibody treatment

value: kidney

tag: cell line

value: BHK-21 cells

tag: cell type

value: fibroblast cells

value: expressing nsP4 and human ACE2

value: SA55 antibody

tag: batch


title: SA55_rep1_JN.1

description: Library name: Sample 20


title: 52_RNAseq Lung_HDM/SAL


title: T-ALL PDX 2

city: Gent

first: Igor

last: Fijalkowski

address: Sint-Pietersnieuwstraat 33

country: Belgium

institute: Ugent

description:
T-ALL PDX 2
TALL_Thymus_normalized_counts.tsv

data_processing:
Data was mapped to the reference genome (GRCh38.105 assembly) using STAR (version STAR/2.7.11b) and differential expression analysis was performed with DESeq2 (version 1.42.1).
Assembly: hg38
Supplementary files format and content: DESeq2 normalized counts, .csv format

molecule: polyA RNA

organism: Homo sapiens

source_name: blood

growth_protocol: RPMI 20%FBS

extract_protocol:
RNA was extracted using ‘miRNeasy Mini’ (217004, Qiagen Benelux BV, Venlo, The Netherlands) or ‘miRNeasy Micro’ (217084, Qiagen Benelux BV) kits, and DNA digestion was done on-column according to the manufacturer’s protocol.
RNA extracted as described above was further used for full length RNA sequencing utilizing the Watchmaker total mRNA library preparation kit (7BK0001-096, Watchmaker Genomics, Boulder, CO, USA) according to manufacturer’s instructions). Prepared libraries were further sequenced using the AVITI sequencer (Element Biosciences, San Diego, USA) using the AVITI 2x150 High Output Sequencing Kit (860-00001, Element Biosciences, San Diego, USA).

value: blood

value: T-ALL blasts

value: Leukemic blasts

value: WT


title: T-ALL PDX 1

description:
T-ALL PDX 1
TALL_Thymus_normalized_counts.tsv


title: Mild MASLD sample 1, female, Foxa2 ChIP

city: Pittsburgh

first: Irina

middle: M

last: Bochkis

state: PA

address: 707A Scaife Hall, 3550 Terrace Street

department: Department of Pathology

institute: University of Pittsburgh

description:
Foxa2_H_F_mild_MASLD.bed
H F Foxa2 mild MASLD 1

library_source: genomic

data_processing:
Reads were aligned to human genome (hg19; NCBI build 37) using BWA v0.7.12 (Li and Durbin 2009). Duplicate reads were removed using Picard v 1.134 (http://picard.sourceforge.net). Reads (Phred score ≥ 30) that aligned uniquely were used for subsequent analysis. Data from three human patients were merged for FOXA2 and lamin B1 binding (three normal and three MASLD). Epic peak caller 16 (https://github.com/biocore-ntnu/epic2) was used to determine lamin B1–associated domains in human patients (hg19 as species, window size of 10 kb, gap size of three, FDR 5%). PeakSeq 17 was used to identify FOXA2 bound peaks against input Normals (FDR 5%, Q-value < 0.07).
Assembly: hg19
Supplementary files format and content: bed files with peak calls from PeakSeq with the following columns: chromosome, begin coordinate, end coordinate, q-value

molecule: genomic DNA

source_name: Liver

extract_protocol:
Snap-frozen mouse or human liver (100 mg) was used to prepare chromatin. Briefly, liver tissue was minced in cold PBS and cross-linked in 1% formaldehyde/PBS for 15 min with constant rotation in a Labquake tube rotator. Cross-linking was quenched by adding glycine to a final concentration of 0.125M. Nuclear lysate was sonicated using a Diagenode Bioruptor Pico for 14 cycles (30 sec on/30 sec off). FOXA2- specific rabbit antiserum (Seven Hills Bioreagents WRAB-1200) and rabbit antibody to lamin B1 (Abcam Ab16048), were used for immunoprecipitation.
Libraries were made according to standard Illumina protocol (end-repair of ChIP DNA, addition of A base to the 3′-ends, adapter ligation, and amplification). We used multiplex adapters for sequencing and Kapa HiFi DNA polymerase (Kapa Biosystems) for PCR amplification (16 cycles). Library fragments were isolated using Pippin HT agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina NextSeq 500 and NextSeq 2000 instruments following the manufacturer’s protocols.

tag: subject status

value: Mild MASLD

tag: chip antibody

value: Foxa2 ChIP


title: 64_RNAseq Lung_PBS/SAL

value: PBS and Saline


title: Normal Liver sample 3, female, Foxa2 ChIP

description:
Foxa2_H_F_normal_liver.bed
H F Foxa2 Normal 3

value: healthy


title: 50_RNAseq Lung_HDM/SAL


title: SA55_rep1

description: Library name: Sample 19


title: CUTTL1 cells STM2457, rep4

description:
STM2457_4
DMSOvsSTM2457_normalized_counts.tsv

value: T-ALL


title: VIR-7831_rep2

description: Library name: Sample 24

value: VIR-7831 antibody


title: Thymocytes 3

description:
Thymocytes 3
TALL_Thymus_normalized_counts.tsv

source_name: Thymus

value: Thymus

value: Thymocytes


title: Normal Liver sample 2, female, Foxa2 ChIP

description:
Foxa2_H_F_normal_liver.bed
H F Foxa2 Normal 2

value: Liver


title: CUTTL1 cells STM2457, rep3

description:
STM2457_3
DMSOvsSTM2457_normalized_counts.tsv


title: REGN10987_rep2

description: Library name: Sample 18

value: kidney

value: BHK-21 cells

value: REGN10987 antibody


title: 57_RNAseq Lung_PBS/CP

value: Lung

value: PBS and CP


title: Normal Liver sample 1, female, Foxa2 ChIP

description:
Foxa2_H_F_normal_liver.bed
H F Foxa2 Normal 1


title: 49_RNAseq Lung_HDM/CP

value: HDM and CP


title: REGN10987_rep1

description: Library name: Sample 17

value: fibroblast cells

value: expressing nsP4 and human ACE2


title: THESC, hormone induced decidualization, Day3, rep3

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road, Oxford, OX3 7LD, UK

country: United Kingdom

institute: University of Oxford

description:
raw_count_matrix.txt
TPM_count_matrix.txt

data_processing:
For long-read sequencing, base calling of fast5 files was done by Guppy and converted to fastq format.
Fastq files were processed by the pipeline (pipeline_count) implemented in the workflow TallyTriN (https://github.com/cribbslab/TallyTriN/tree/main) and raw count matrix for PCA analysis was then generated.
For isoform-level analysis, reads of each sample were then aligned to hg38 genome by Minimap2 with - - MD flag enabled and output as SAM format.
The SAM file of each sample was then processed by TALON and visualized by Swan.
For short-read sequencing, reads were initially assessed for quality using FastQ Screen v0.14.0, FastQC v0.11.9 and MulitQC v1.5.dev0.
Raw reads of each sample were then merged into a single file and pseudo-aligned to the human genome hg38 with Kallisto 0.46.0.
Using the count matrix produced by Kallisto, differential expression analysis was performed by DESeq2 v1.35.0
Assembly: Human genome hg38
Supplementary files format and content: raw count matrix for each sample (including short and long-read sequencing data)

source_name: THESC

growth_protocol: THESC cell line was incubated in DMEDM/F-12 with bicarbonate and HEPES (Sigma Cat# D 2906) supplemented with 10% fetal bovine serum (FBS, Charcoal stripped F6765-500ML), puromycin (500 ng/ml), and 1% ITS Premix Universal Culture Supplement (Corning 354350).

extract_protocol:
Cells were harvested using Direct-zol RNA MiniPrep kit (Cambridge Bioscience, R2052)
For long-read sequencing, 50 ng RNA of each sample were reverse transcribed and barcoded by using the PCR-cDNA barcoding kit (SQK-PCB111.24) and NEBNext Companion Module (NEB E7180L).
For short-read sequencing, Approximately 100 ng of each RNA sample was used to create Illumina sequencing libraries using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) according to the manufacturer’s instructions.

treatment_protocol:
For the three days experiment of decidualization, cells were seeded at 6-well plates for 40,000 cells per well and incubated overnight.
At the next day (Day 0), the decidualization were induced by adding the following reagents into cell medium: Medroxyprogesterone 17-acetate (Sigma, M1629; final conc. 1.0 µM), E2 (estradiol, final conc. 10 nM; Sigma E1024), 8-Br cAMP (8-Bromoadenosine 3′,5′-cyclic monophosphate, final conc. 500 µM; Sigma B6386-100mg).
In addition to stimulation for decidualization, cells were further treated with DMSO as mock, TGF-beta (10 ng/ml; Millipore GF346) together with or without MEK inhibitor (BAY 1076672, 100 ng/ml) since Day 0, depending on the experimental design.

value: THESC

value: Endometrial Stromal Cells

value: hTERT-immortalized

value: hormone induced decidualization

tag: time


title: CUTTL1 cells STM2457, rep2

description:
STM2457_2
DMSOvsSTM2457_normalized_counts.tsv

value: blood

value: T-ALL

value: WT


title: Control mouse DRG 7

city: Baltimore

first: Pang-Yen

last: Tseng

state: MD

address: 655 W. Lombard St.

department: Pain and Translational Symptom Science

institute: University of Maryland Baltimore

description:
Library name: ADAM17WT7
ADAM17_TPM.csv
ADAM17_counts.csv

data_processing:
Sequencing reads were aligned to reference transcriptomes using kallisto
Assembly: Ensembl mouse reference transcriptome GRCm38.v98; NCBI Macaca nemestrina Annotation Release 101, Mnem_1.0 (GCF_000956065.1)
Supplementary files format and content: Transcript per million (TPM)
Supplementary files format and content: counts

source_name: DRG

extract_protocol:
The total RNA from fresh frozen mouse or monkey DRG were purified with Direct-zol RNA Miniprep kit (Zymo Research)
RNA-sequencing libraries were prepared and sequenced at NIDCD/NIDCR Genomics and Computational Biology Core

value: DRG

value: ADAM17 flox


title: THESC, hormone induced decidualization, Day3, rep2


title: Control mouse DRG 6

description:
Library name: ADAM17WT6
ADAM17_TPM.csv
ADAM17_counts.csv


title: CUTTL1 cells DMSO control, STM2457_matched, rep4

description:
DMSO_4
DMSOvsSTM2457_normalized_counts.tsv

value: DMSO


title: REGN10933_rep2

description: Library name: Sample 16

value: kidney

value: BHK-21 cells

value: REGN10933 antibody


title: Negative_control_rep2

description: Library name: Sample 14

value: No


title: Control mouse DRG 5

description:
Library name: ADAM17WT5
ADAM17_TPM.csv
ADAM17_counts.csv


title: CUTTL1 cells DMSO control, STM2457_matched, rep3

description:
DMSO_3
DMSOvsSTM2457_normalized_counts.tsv


title: THESC, no hormone induction, Day0, biol rep3

value: before hormone induced decidualization


title: THESC, no hormone induction, Day0, biol rep2


title: CUTTL1 cells DMSO control, STM2457_matched, rep2

description:
DMSO_2
DMSOvsSTM2457_normalized_counts.tsv


title: THESC, hormone induced decidualization, Day3, rep1


title: 45_RNAseq Lung_HDM/CP

value: Lung

value: HDM and CP


title: THESC, no hormone induction, Day0, biol rep1

value: THESC


title: Negative_control_rep1

description: Library name: Sample 13

value: fibroblast cells

value: expressing nsP4 and human ACE2


title: CUTTL1 cells DMSO control, STM2457_matched, rep1

description:
DMSO_1
DMSOvsSTM2457_normalized_counts.tsv


title: Control mouse DRG 3

description:
Library name: ADAM17WT3
ADAM17_TPM.csv
ADAM17_counts.csv


title: Control mouse DRG 2

description:
Library name: ADAM17WT2
ADAM17_TPM.csv
ADAM17_counts.csv


title: LY-CoV555_rep2

description: Library name: Sample 12

value: LY-CoV555 antibody


title: CUTTL1 cells HNRNPC KD, 7days, rep2

description:
HNRNPC_KD_sh482_7d_2
HNRNPC_KD_normalized_counts.tsv

value: blood


title: Control mouse DRG 1

description:
Library name: ADAM17WT1
ADAM17_TPM.csv
ADAM17_counts.csv


title: LY-CoV555_rep1

description: Library name: Sample 11


title: CUTTL1 cells STM2457, rep1

description:
STM2457_1
DMSOvsSTM2457_normalized_counts.tsv

value: T-ALL


title: CUTTL1 cells HNRNPC KD, 7days, rep3

description:
HNRNPC_KD_sh482_7d_3
HNRNPC_KD_normalized_counts.tsv


title: Cre_3

city: Dallas

first: Qiyu

last: Zeng

address: 5323 Harry Hines Blvd

institute: UTSW

description: Library name: Sample_18

data_processing:
CLC genomic workbench
Assembly: mm10
Supplementary files format and content: tab-delimited text file incluindg raw counts for each samples

source_name: liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared follow the NEBNest ultra II Directional RNA library prep kit for illumina

value: liver

value: cidebfl/fl injected with AAV-TBG-Cre

value: CDA-HFD for  3 months


title: LY-CoV1404_rep1

description: Library name: Sample 9

value: LY-CoV1404 antibody


title: CUTTL1 cells HNRNPC KD, 7days, rep1

description:
HNRNPC_KD_sh482_7d_1
HNRNPC_KD_normalized_counts.tsv


title: REGN10933_rep1

description: Library name: Sample 15

value: kidney


title: Cre_5

description: Library name: Sample_20


title: ADAM17 knockout mouse DRG 7

description:
Library name: ADAM17KO7
ADAM17_TPM.csv
ADAM17_counts.csv

value: DRG

value: ADAM17 KO


title: ADAM17 knockout mouse DRG 6

description:
Library name: ADAM17KO6
ADAM17_TPM.csv
ADAM17_counts.csv


title: Cre_4

description: Library name: Sample_19


title: LY-CoV016_rep2

description: Library name: Sample 8

value: BHK-21 cells

value: LY-CoV016 antibody


title: Control mouse DRG 4

description:
Library name: ADAM17WT4
ADAM17_TPM.csv
ADAM17_counts.csv

value: ADAM17 flox


title: Cre_2

description: Library name: Sample_17


title: CUTTL1 cells shControl, 7days, rep3

description:
NEG_shCTR_7d_3
HNRNPC_KD_normalized_counts.tsv

value: WT


title: ADAM17 knockout mouse DRG 5

description:
Library name: ADAM17KO5
ADAM17_TPM.csv
ADAM17_counts.csv


title: LY-CoV016_rep1

description: Library name: Sample 7


title: CUTTL1 cells shControl, 7days, rep2

description:
NEG_shCTR_7d_2
HNRNPC_KD_normalized_counts.tsv


title: Cre_1

description: Library name: Sample_16


title: LY-CoV1404_rep2

description: Library name: Sample 10


title: CUTTL1 cells shControl, 7days, rep1

description:
NEG_shCTR_7d_1
HNRNPC_KD_normalized_counts.tsv


title: DXP-593_rep2

description: Library name: Sample 6

value: DXP-593 antibody


title: ADAM17 knockout mouse DRG 4

description:
Library name: ADAM17KO4
ADAM17_TPM.csv
ADAM17_counts.csv


title: GFP_5

description: Library name: Sample_15

value: cidebfl/fl injected with AAV-TBG-GFP


title: CUTTL1 cells HNRNPC KD, 3days, rep3

description:
HNRNPC_KD_sh482_3d_3
HNRNPC_KD_normalized_counts.tsv


title: ADAM17 knockout mouse DRG 3

description:
Library name: ADAM17KO3
ADAM17_TPM.csv
ADAM17_counts.csv


title: DXP-593_rep1

description: Library name: Sample 5

value: fibroblast cells

value: expressing nsP4 and human ACE2


title: BRII-196_rep2

description: Library name: Sample 4

value: BRII-196 antibody


title: CUTTL1 cells HNRNPC KD, 3days, rep2

description:
HNRNPC_KD_sh482_3d_2
HNRNPC_KD_normalized_counts.tsv

value: blood

value: T-ALL


title: GFP_4

description: Library name: Sample_14

value: liver


title: GFP_3

description: Library name: Sample_13

value: CDA-HFD for  3 months


title: ADAM17 knockout mouse DRG 1

description:
Library name: ADAM17KO1
ADAM17_TPM.csv
ADAM17_counts.csv


title: ADAM17 knockout mouse DRG 2

description:
Library name: ADAM17KO2
ADAM17_TPM.csv
ADAM17_counts.csv


title: BRII-196_rep1

description: Library name: Sample 3


title: AZD8895_rep2

description: Library name: Sample 2

value: AZD8895 antibody


title: GFP_1

description: Library name: Sample_11


title: AZD8895_rep1

description: Library name: Sample 1

value: kidney


title: After selection, transposon orientation 2

city: Beverly

first: Hoong Chuin

last: Lim

state: MA

address: 44 Dunham Ridge Road

institute: New England Biolabs

description: Library name: Reverse_After

data_processing:
Trim barcodes and transposon sequences using fastp
Trim barcode and poly-G sequence using fastp
Map reads to reference genome using minimap2
Mapped reads were either binned (bin size 100) or unbinned (bin size 1)
Assembly: E. coli MG1655 (NC_000913) with reporter inserted at 4088112 bp
Supplementary files format and content: Table tabulating the reads mapped to each bin and strand direction

organism: Escherichia coli

growth_protocol: Lysogeny broth (1% tryptone, 0.5% yeast extract, 1% NaCl) + 0.2% arabinose liquid culture over 8 hours. "Before" samples were extracted. Remaining cells were plated on solid lysogeny broth + 25 µg/mL kanamycin for selection of "After" samples.

extract_protocol:
Genomic DNA was extracted as per the NEB Genomic DNA preparation kit (T3010) for gram negative bacteria.
Genomic DNA was sheared using Covaris ML230 into ~1 kb fragments. End repaired using NEB end repair kit (E6050). Poly-C tailed using NEB terminal transferase (M0315) and dCTP. Purified with sample purification beads and region amplified using primers specific to the transposon paired with a poly-G primer that introduces a known sequence to the other end. A second, nested PCR was done to introduce illumina barcode handles.

value: Kanamycin selection


title: CUTTL1 cells shControl, 3days, rep3

description:
NEG_shCTR_3d_3
HNRNPC_KD_normalized_counts.tsv


title: GFP_2

description: Library name: Sample_12


title: After selection, transposon orientation 1

description: Library name: Forward_After


title: CUTTL1 cells shControl, 3days, rep2

description:
NEG_shCTR_3d_2
HNRNPC_KD_normalized_counts.tsv


title: Before selection, transposon orientation 2

description: Library name: Reverse_Before

value: Control


title: Cre_WD_5

description: Library name: Sample_10

value: cidebfl/fl injected with AAV-TBG-Cre

value: Western diet for 3 months


title: Patient 10, run 1

type: RNA

city: Houston

first: Kelli

last: McCord

state: TX

address: 1 Baylor Plz

institute: Baylor College of Medicine

description: 10X Xenium V1 in situ sequencing

hyb_protocol: Probes from the predesigned Xenium Human Multi-Tissue and Cancer Gene Expression and hMulti_v1 design (chemistry v1: 10x Genomics), consisting of 377 genes as well as an additional 100 custom gene panel containing key T cell, tumor cell, and TCR-targeting probes were used for gene detection.

scan_protocol: Samples were run on Xenium Analyzer. April 13th 2024 run used intrument software version 2.0.0.0, analysis version xenium-2.0.0.10. May 6th 2024 run used instrument software version 2.0.1.0 and analysis version xenium-2.0.0.10. September 11th 2024 run used instrument software version 3.0.2.0 and analysis version xenium-2.0.1.1. November 21st 2024 run used instrument software version 3.1.0.0 and analysis version xenium-2.0.2.0

source_name: Ameloblastoma

label_protocol: Patient numbers (in title) were assigned to sample name for simplicity.

growth_protocol: Immediate following tumor resection, tumor samples were embedded in optimal cutting temperature (OCT) compound and flash frozen in a dry ice/isopentane bath before being stored in the vapor phase of liquid nitrogen.

extract_protocol: Xenium slides were prepared following the Xenium In Situ for Fresh Frozen Tissues User Guides CG000579, CG000581, CG000760, and CG000613 from 10x Genomics.

treatment_protocol: For each tumor sample, 10 µm sections were mounted onto Xenium V1 slides and stored at -80ºC for under one week prior to initiating the Xenium experiment.

tag: p16 status

tag: recurrence

value: Primary

tag: pack years

tag: site of tumor resection

value: Oral Cavity


title: CUTTL1 cells shControl, 3days, rep1

description:
NEG_shCTR_3d_1
HNRNPC_KD_normalized_counts.tsv

value: WT


title: Cre_WD_4

description: Library name: Sample_9


title: Patient 28, run 2

description: 10X Xenium V1 in situ sequencing

data_processing: Samples were run on Xenium Analyzer. April 13th 2024 run used intrument software version 2.0.0.0, analysis version xenium-2.0.0.10. May 6th 2024 run used instrument software version 2.0.1.0 and analysis version xenium-2.0.0.10. September 11th 2024 run used instrument software version 3.0.2.0 and analysis version xenium-2.0.1.1. November 21st 2024 run used instrument software version 3.1.0.0 and analysis version xenium-2.0.2.0

source_name: HNSCC tumor

value: Positive

value: Recurrent

value: Oropharynx


title: CUTTL1 cells CS1 treatment, rep3

description:
6_4uM_CS_1
DMSOvsCS1_normalized_counts.tsv


title: Cre_WD_3

description: Library name: Sample_8


title: Arrangement 3 replicate 3

description: Library name: TR3_c

library_source: other

data_processing:
Reads mapped to reference sequence using minimap2 aligner
Frequency of mismatch at adenine residues recorded and grouped within context of sequence
Assembly: TR1: CAGTACAACGATTAGAAATATGACCACCATAAGGAG; TR2: TAGAAATATGACCACCATAAGGAGCAGTACAACGAT; TR3: CACCATAAGGAGCAGTACAACGATTAGAAATATGAC
Supplementary files format and content: Table showing percent misincorporation rate at adenine residues in sequence context

molecule: other

growth_protocol: Lysogeny broth (1% tryptone, 0.5% yeast extract, 1% NaCl) + 0.2% arabinose liquid culture for 2 hours.

extract_protocol:
Total RNA (no Dnase treatment step) using Monarch Total RNA Extraction kit (NEB, T2010).
PCR to amplify region of interest. A second, nested PCR was done to introduce Illumina barcode handles.


title: Patient 28, run 1

description: 10X Xenium V1 in situ sequencing


title: CUTTL1 cells CS1 treatment, rep 2

description:
5_4uM_CS_1
DMSOvsCS1_normalized_counts.tsv


title: Cre_WD_2

description: Library name: Sample_7


title: Patient 23, run 1

description: 10X Xenium V1 in situ sequencing


title: CUTTL1 cells CS1 treatment, rep1

description:
4_4uM_CS_1
DMSOvsCS1_normalized_counts.tsv


title: CUTTL1 cells HNRNPC KD, 3days, rep1

description:
HNRNPC_KD_sh482_3d_1
HNRNPC_KD_normalized_counts.tsv


title: Cre_WD_1

description: Library name: Sample_6


title: Arrangement 3 replicate 2

description: Library name: TR3_b


title: Arrangement 3 replicate 1

description: Library name: TR3_a


title: CUTTL1 cells DMSO control, rep3

description:
3_DMSO_3
DMSOvsCS1_normalized_counts.tsv

value: DMSO


title: Arrangement 2 replicate 3

description: Library name: TR2_c


title: Patient 20, run 1

description: 10X Xenium V1 in situ sequencing

value: Negative

value: Hypopharynx


title: CUTTL1 cells DMSO control, rep 2

description:
2_DMSO_2
DMSOvsCS1_normalized_counts.tsv

value: blood

value: T-ALL


title: Patient 20, run 2

description: 10X Xenium V1 in situ sequencing


title: Patient 19, run 2

description: 10X Xenium V1 in situ sequencing

value: Larynx


title: CUTTL1 cells DMSO control, rep1

description:
1_DMSO_1
DMSOvsCS1_normalized_counts.tsv


title: GFP_WD_5

description: Library name: Sample_5

value: liver

value: cidebfl/fl injected with AAV-TBG-GFP


title: GFP_WD_4

description: Library name: Sample_4


title: Arrangement 2 replicate 2

description: Library name: TR2_b


title: Arrangement 2 replicate 1

description: Library name: TR2_a


title: Patient 19, run 1

description: 10X Xenium V1 in situ sequencing


title: GFP_WD_2

description: Library name: Sample_2


title: GFP_WD_3

description: Library name: Sample_3


title: Before selection, transposon orientation 1

description: Library name: Forward_Before

value: Control


title: Arrangement 1 replicate 3

description: Library name: TR1_c


title: Patient 17, run 2

description: 10X Xenium V1 in situ sequencing


title: Zebrafish, rep1, snATAC

city: Huntsville

first: J.

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description:
Library name: ZF1_snATAC
ZF1_filtered_feature_bc_matrix.h5

library_source: genomic single cell

data_processing:
Data was processed using cellranger-arc (v2.0.0).
Assembly: Rattus rattus (rat) assembly: mRatBN7.2 (rn7), annotation: Ensembl release 111; Oryctolagus cuniculus (rabbit) assembly: OynCun2, annotation: Ensembl release 111; Bos taurus (cow) assembly: bosTau9, annotation: GCF_002263795.2; Equus caballus (horse) assembly: equCab3, annotation: GCA_002863925.1; Danio rerio (zebrafish) assembly: danRer11, annotation: Ensembl release 109.
Supplementary files format and content: h5 files contain all snRNA and snATAC-seq counts for each sample. Fragment files included for snATAC-seq.

organism: Danio rerio

source_name: cortex

extract_protocol:
At least 10 – 20 mg of frozen tissue was obtained from each sample using a metallic block and hammer to take a portion of the dissected cortex tissue. The tissue was then sealed inside of a Covaris Tissue TUBE (Covaris, cat. Nos. 520021 and 520023) and thoroughly pulverized using the chilled hammer and metallic block, with intermittent submerging into liquid nitrogen to maintain cold temperature and brittleness. Using a clean, pre-chilled scoopula, pulverized tissue was then transferred to a pre-chilled 2 mL DNA LoBind tube. RNA was isolated using the miRNeasy Mini Kit according to manufacturer instructions (QIAGEN, cat. no. 217084). RIN scores were calculated by a 2100 BioAnalzyer (Agilent) using the RNA 6000 Nano Kit following manufacturer instructions (Agilent cat. no. 50671511) .
Transposition, nuclei isolation, barcoding, and library preparation were performed according to the 10X Genomics Chromium Next GEM Single Cell Multiome protocol CG000338 Rev E with the following alterations. Each sample was loaded on one lane of the Chromium Next GEM Chip J. Nuclei were loaded according to manufacturer’s recommendations to target recovery of 10,000 nuclei per lane.

value: cortex


title: GFP_WD_1

description: Library name: Sample_1

value: Western diet for 3 months


title: Zebrafish, rep2, snRNA

description: Library name: ZF2_snRNA

library_source: transcriptomic single cell


title: Arrangement 1 replicate 1

description: Library name: TR1_a


title: Patient 15, run 1

description: 10X Xenium V1 in situ sequencing

value: Primary


title: Zebrafish, rep1, snRNA

description: Library name: ZF1_snRNA


title: mature cDCs-3 from T-all spleen

city: Tianjin

first: cui

last: xiaoxi

address: 288 Nanjing Road

institute: Peking Union Medical College

description:
Library name: T_DC_hi_3
T_DC_hi_3

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse genes.
Assembly: mouse mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: spleen

extract_protocol:
sorted DCs were harvested and resuspended in 350ul RLT and 3.5ul β-Me.Total RNA is exacted by QIAGEN Rneasy Mini Kit(CAT 74103). 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD11c+MHCIIlo, mature cDCs from healthy and T-all mice as T-DCs, N-mDCs and T-mDCs

value: spleen

value: ns

value: Dendritic cell


title: Patient 13, run 2

description: 10X Xenium V1 in situ sequencing

value: Positive

value: Recurrent


title: mature cDCs-2 from T-all spleen

description:
Library name: T_DC_hi_2
T_DC_hi_2


title: mature cDCs-1 from T-all spleen

description:
Library name: T_DC_hi_1
T_DC_hi_1


title: Fungus cells, Deletion_MtHac-1, Avicel medium, rep 2

city: Auckland

first: Yapeng

last: Lai

address: 55 Wellesley Street East,  Auckland Central

department: School of Science

country: New Zealand

institute: Auckland University of Technology

description: Library name: Deletion_MtHac-1_2

data_processing:
Raw reads containing adapters or low quality bases  were further filtered by fastp (version 0.18.0). An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Gene differential expression analysis was performed by DESeq2 software between two different groups.
Assembly: The Reference genome is ASM22609v1
Supplementary files format and content: FPKM values for each sample

organism: Thermothelomyces thermophilus ATCC 42464

source_name: Fungus cells

growth_protocol: For analysis of MtHac-1-specific transcriptomes, conidia from the wild type (WT) and ΔMthac-1 strains of M. thermophila were pre-grown in liquid glucose medium, and then transferred the washed mycelia into liquid medium containing 2% (w/v) Avicel as the carbon source for 48 h.

extract_protocol:
Total fungal RNAs were extracted from fresh mycelia harvested from 2% (w/v) Avicel media through vacuum filtration.Total RNAs were isolated using an RNA extraction kit TransZol Up (TransGen Biotech, Beijing, China) following the manufacturer’s protocols, and RNA extracts were assessed by electrophoresis and quantified using the NanoDrop 2000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA).
After total RNA was obtained, the mRNA for each sample was enriched by Oligo (dT) beads and reversely transcribed into cDNA via the aid of NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA).

value: Fungus cells

value: MtHac-1 deletion


title: Fungus cells, Deletion_MtHac-1, Avicel medium, rep 3

description: Library name: Deletion_MtHac-1_3


title: Patient 12, run 2

description: 10X Xenium V1 in situ sequencing

value: Oropharynx


title: Zebrafish, rep2, snATAC

description:
Library name: ZF2_snATAC
ZF2_filtered_feature_bc_matrix.h5


title: Strong promoter on leading strand replicate 2

description: Library name: Strong_LE_b

data_processing:
merge paired ends with BBMap bbmerge
take only the VR region by removing primer binding sites and before and after sequences with cutadapt
i. count the A mutations (among G>T reads to make sure they are result of DGR editing) with custom python script ii. map to original VR sequence with minimap2, get sorted primary alignments with samtools, count A mutations with location information with samtools mpileup
in either case normalize to total read number
Assembly: Custom sequence
Supplementary files format and content: Table tabulating the number of mutations at each site
Supplementary files format and content: Table tabulating the total number of mutations per sample

growth_protocol: Lysogeny broth (1% tryptone, 0.5% yeast extract, 1% NaCl) + 0.2% arabinose liquid culture over 8 hours.

extract_protocol:
PCR of the genomic region around the reporter.
A second, nested PCR was done to introduce illumina barcode handles.

value: sbcB::frt mutS::frt


title: Fungus cells, Deletion_MtHac-1, Avicel medium, rep 1

description: Library name: Deletion_MtHac-1_1


title: Weak promoter on leading strand replicate 3

description: Library name: Weak_LE_c


title: immature DCs-2 from T-all spleen

description:
Library name: T_DC_lo_2
T_DC_lo_2

value: T-ALL


title: Fungus cells, WT, Avicel medium, rep 3

description: Library name: WT_3

value: WT


title: immature DCs-1 from T-all spleen

description:
Library name: T_DC_lo_1
T_DC_lo_1


title: Strong promoter on leading strand replicate 1

description: Library name: Strong_LE_a


title: Weak promoter on leading strand replicate 2

description: Library name: Weak_LE_b


title: Patient 12, run 1

description: 10X Xenium V1 in situ sequencing


title: Patient 9, run 2

description: 10X Xenium V1 in situ sequencing


title: Fungus cells, WT, Avicel medium, rep 2

description: Library name: WT_2


title: mature cDCs-3 from normal spleen

description:
Library name: N_DC_hi_3
N_DC_hi_3


title: Arrangement 1 replicate 2

description: Library name: TR1_b


title: Patient 17, run 1

description: 10X Xenium V1 in situ sequencing

value: Oral Cavity


title: Weak promoter on leading strand replicate 1

description: Library name: Weak_LE_a


title: Strong promoter on leading strand replicate 3

description: Library name: Strong_LE_c


title: Fungus cells, WT, Avicel medium, rep 1

description: Library name: WT_1


title: mature cDCs-2 from normal spleen

description:
Library name: N_DC_hi_2
N_DC_hi_2


title: Patient 1, run 1

description: 10X Xenium V1 in situ sequencing


title: immature DCs-3 from T-all spleen

description:
Library name: T_DC_lo_3
T_DC_lo_3


title: Patient 9, run 1

description: 10X Xenium V1 in situ sequencing


title: Strong promoter on lagging strand replicate 3

description: Library name: Strong_LA_c


title: Patient 13, run 1

description: 10X Xenium V1 in situ sequencing


title: Sample 14

city: San Francisco

first: Susanna

last: Rosi

state: CA

address: 2200 Island Dr

institute: Altos labs

description: Library name: Sample 14

data_processing:
Sample demultiplexing, barcode processing, and single-cell counting were performed using the Cell Ranger Single-Cell Software Suite (10x Genomics). The cellranger count command was used to align reads to the human reference genome (hg38).
Raw sequencing reads were aligned to the GRCh38 human reference genome using the Cell Ranger pipeline (v.8.0.0) to generate the raw RNA count matrix. The resulting count matrix was further processed using the Seurat R package (v5.2.0) for downstream quality control, normalization, and dimensionality reduction. To ensure high data quality, filtering was performed using PopsicleR (v0.2.1) with strict thresholds. The criteria included: 1) A minimum of 500 and maximum 12000 detected genes per cell (G_RNA_low=500, G_RNA_hi=12000). 2) The number of unique molecules per cell was required to fall within a reasonable range (U_RNA_low=1500, U_RNA_hi=37000). 3) Cells exceeding the upper limits for mitochondrial, ribosomal, and dissociation gene percentages (percent_mt_hi=5, percent_ribo_hi=100, percent_disso_hi=100)vwere removed. After filtering, 98,492 cells met the inclusion criteria for analysis. The dataset had an average read depth of 9,226 unique RNA molecules per cell, with an average of 3,312 unique genes detected per cell. Doublets were detected and removed using the CalculateDoublets function within PopsicleR. RNA normalization was performed using the log-normalization method within Seurat’s NormalizeData function, followed by scaling using ScaleData. This was followed by Principal Component Analysis (PCA), on the top 2,000 highly variable features, retaining the first 30 principal components for downstream clustering and visualization. For cell type annotation, we utilized Azimuth (v0.5.0) for reference-based mapping, using the humancortexref reference dataset to assign cell identities. The classification was performed at two hierarchical levels: Level 1: Broad categorization into GABAergic neurons, Glutamatergic neurons, and non-neuronal populations. Level 2: Further refinement into specific neuronal and non-neuronal subtypes.
Assembly: GRCh38
Supplementary files format and content: Counts, barcodes, and metadata for all samples in 10X format.

source_name: Brain

extract_protocol:
Frozen human brain tissues were homogenized in a Dounce homogenizer using Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.025% NP-40) and incubated on ice for 15 minutes. The homogenate was filtered through a 30-μm mesh to remove debris and centrifuged at 500g for 5 minutes at 4°C to pellet the nuclei. Nuclei were then washed and filtered twice using Nuclei Wash Buffer (1% BSA in PBS with 0.2 U/μl RNasin, Promega). For myelin debris removal, the nuclei were resuspended in 500 μl of Nuclei Wash Buffer, mixed with 900 μl of 1.8 M sucrose, and carefully layered over 500 μl of 1.8 M sucrose. This gradient was centrifuged at 13,000g for 45 minutes at 4°C.
The isolated nuclei were then resuspended in Nuclei Wash Buffer at a final concentration of 1,000 nuclei/μl and passed through a 40-μm FlowMi Cell Strainer for further purification. Isolated human nuclei were processed using the Chromium Single Cell 5′ Reagent Kits (10x Genomics) for droplet-based 5′ end massively parallel single-cell RNA sequencing. Sequencing libraries were generated and run on Illumina sequencers at the McDonnell Genome Institute.

value: Brain

tag: tbi

value: Yes

tag: Sex

value: Male

tag: age at_death

value: 52 years


title: mature cDCs-1 from normal spleen

description:
Library name: N_DC_hi_1
N_DC_hi_1


title: Strong promoter on lagging strand replicate 2

description: Library name: Strong_LA_b


title: DMS_SA55_treatment_rep2

description: Library name: Sample 3

data_processing:
A custom Python script was used to extract the mutation information for each sequence and calculate the mutant counts.
Assembly: trVLP-ASV genome sequence
Supplementary files format and content: An Excel file containing the mutation information for each mutant in the DMS library for every sample.

extract_protocol:
For each sample, supernatants containing trVLPs were collected, and RNA was extracted using TRIzol LS Reagent (HaiGene, #B1901), and the RNA was extracted following the manufacturer's protocol.
Approximately 1000 ng of RNA was reverse transcribed into cDNA using the HiScript III First-Strand cDNA Synthesis Kit (Vazyme, R312-02) with sequence-specific primer (Sindis-gsp-R2: tgcgcctcctcggaaatacg). Subsequently, 5 µL of the cDNA (or 1000 ng plasmid DNA) was used as a template for PCR amplification in a 50 µL reaction volume with KOD One PCR Master Mix. The PCR was performed for 28 cycles using primers designed to target specific regions of the trVLP genome, such as the mCherry region. The PCR products were sequenced using the Fast Next-Generation Sequencing (NGS) service by a Miseq merchine from Tsingke Biotechnology.

treatment_protocol: trVLP-ASV transduction and SA55 antibody treatment

value: kidney

value: BHK-21 cells

value: fibroblast cells

value: expressing nsP4 and human ACE2

value: SA55 antibody


title: Sample 13

description: Library name: Sample 13

value: No

value: 50 years


title: Strong promoter on lagging strand replicate 1

description: Library name: Strong_LA_a


title: CR-Hlg300

city: Jinan

first: Wenhao

last: Hou

address: xingfu

institute: Shandong First Medical University

description: Library name: Sample 10

data_processing:
Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq, depends on project) according to the manufacturer’s instructions.
Assembly: GRCh38
Supplementary files format and content: tsv,mtx and rds files

extract_protocol:
The tissues were surgically removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 1 mg/mL collagenase I (Gibco)，1 mg/mL collagenase II，60U/mL Hyaluronidase (Sigma), 10U/mL Liberase (Roche) and 0.02mg/mL DNase I (Roche) for 90 min at 37°C, with agitation . After digestion, samples were sieved through a 100µm and 40µm cell strainer, and centrifuged at 300g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Gibco) to lyse red blood cells.  After washing with DPBS containing 0.5% BSA, the cell pellets were re-suspended in DPBS containing 0.5% BSA，stained and counted.
The Chromium instrument and the Single Cell 3’ Reagent kit V3.1 (Dual Index) was used to prepare individually barcoded single-cell RNA-Seq libraries following the manufacturer’s protocol (10X Genomics). Briefly, sample partitioning and molecular barcoding were done on the Chromium Controller (10x Genomics), where we loaded cellular suspensions together with the Single-cell 3’ Gel Beads on a Single-cell 3’ chip, in which gel beads in emulsion (GEM) generation took place. RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell reagent kit V3.1 (10X Genomics).

value: Noncancerous liver tissue

value: Hepatocyte

tag: patient id

value: patient 1

tag: gender

value: Female

tag: age

tag: chlid-pugh

value: A

tag: cirrhosis

tag: hbv/hcv infection

tag: afp(ng/ml)


title: Sample 12

description: Library name: Sample 12

tag: tissue

value: 49 years


title: CR-Hlg299

description: Library name: Sample 9

value: Primary hepatocellular carcinoma tissue

tag: cell type

tag: tumor type

value: Primary hepatocellular carcinoma

tag: bclc stage

tag: distant metastasis

tag: number of tumors

tag: size(cm)

tag: microvascular invasion


title: Weak promoter on lagging strand replicate 2

description: Library name: Weak_LA_b

tag: cell line

tag: genotype

value: sbcB::frt mutS::frt


title: Sample 11

description: Library name: Sample 11

value: Brain

tag: tbi

value: Yes

tag: Sex

value: Male

tag: age at_death

value: 59 years


title: Weak promoter on lagging strand replicate 3

description: Library name: Weak_LA_c


title: Sample 9

description: Library name: Sample 9

value: 60 years


title: CR-Hlg296

description: Library name: Sample 6

tag: patient id

value: patient 4

tag: gender

tag: age

tag: chlid-pugh


title: CR-Hlg298

description: Library name: Sample 8

tag: tissue

value: patient 2

tag: cirrhosis

tag: hbv/hcv infection

tag: afp(ng/ml)


title: After selection replicate 1

description: Library name: After A

data_processing:
Trim barcodes and transposon sequences using CutAdapt
Trim barcode and poly-G sequence using CutAdapt
Map reads to reference genome using Bowtie version 1.0.0
Count reads by gene
Calculate fold change between the sample conditions
Assembly: E. coli MG1655 (NC_000913) with reporter inserted at 4088112 bp
Supplementary files format and content: Table tabulating the reads mapped to each gene and calculated fold change and significance score.

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: Lennox broth (1% tryptone, 0.5% yeast extract, 0.5% NaCl) + 0.2% arabinose liquid culture over 16 hours. "Before" samples were extracted. Remaining cells were plated on solid Lennox broth + 25 µg/mL kanamycin for selection of "After" samples.

tag: strain

tag: treatment

value: Kanamycin selection

tag: batch


title: After selection replicate 2

description: Library name: After B


title: Weak promoter on lagging strand replicate 1

description: Library name: Weak_LA_a


title: TdTomato+ and TdTomato- cells (50:50) from Ptbp1 fl/fl;Aldh1l1+;tdT+/- 17 weeks old mouse brain

city: Riverside

first: Sika

last: Zheng

address: University Ave 900

department: School of Medicine

institute: University of California, Riverside

description: Library name: KO

data_processing:
For quantification of unique molecular identifiers (UMIs) in our single-cell RNA-seq (scRNA-seq) reads from Ptbp1 knockout samples, we employed the Snakemake workflow "kb-nac.smk" from SnakeNgs (version 0.2.0). This workflow internally executes kb-python, a wrapper of kallisto and bustools, to obtain UMI count matrix. We ran this workflow with customized genome and transcript annotation files that contain tdTomato and Cre gene sequences as well as the reference Gencode mouse genes. The UMI count matrix was then processed by Scanpy (version 1.9.5). We used Scrublet for cell doublets detection and Harmony for batch-effect correction. Cell types were manually assigned based on the expression level of marker genes.
Assembly: mm10
Supplementary files format and content: UMI count matrix in anndata format

source_name: Cortex

extract_protocol:
Mouse brain cortices were collected 12 weeks after tamoxifen injection and subjected to single cell isolation. After cell sorting, the single cell suspension of tdT+ cells were approximately adjusted to 1000 cells/ul. To enrich the tdT+ cells, for each animal, the cells subjected to 10x procedure were mixed as 1:1 ratio of tdT+ and tdT- from the same animal.
The procedures were carried out according to the manufacturer’s instructions for Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (10x Genomics # 1000128).

value: Cortex

value: Ptbp1 fl/fl;Aldh1l1+;tdT+/-


title: Sample 8

description: Library name: Sample 8

value: 47 years


title: CR-Hlq297

description: Library name: Sample 7

tag: cell type

value: Hepatocyte

tag: tumor type

tag: bclc stage

tag: distant metastasis

tag: number of tumors

tag: size(cm)

tag: microvascular invasion


title: CR-Hlg295

description: Library name: Sample 5

tag: patient id

tag: gender

value: A

value: B

value: many


title: TdTomato+ and TdTomato- cells (50:50) from +/+;Aldh1l1+;tdT+/- 17 weeks old mouse brain

description: Library name: Ctrl

tag: genotype


title: Before selection replicate 2

description: Library name: Before B

value: Control


title: DMS_SA55_treatment_rep1

description: Library name: Sample 2

tag: tissue

value: kidney

tag: cell line

value: BHK-21 cells

value: fibroblast cells

value: expressing nsP4 and human ACE2

value: SA55 antibody


title: Sample 7

description: Library name: Sample 7

value: Brain

tag: tbi

value: No

tag: Sex

value: Male

tag: age at_death

value: 38 years


title: CR-Hlg294

description: Library name: Sample 4

value: Noncancerous liver tissue

value: patient 3

tag: age

tag: chlid-pugh

tag: cirrhosis

tag: hbv/hcv infection

tag: afp(ng/ml)


title: Sample 6

description: Library name: Sample 6

value: Yes

value: 40 years


title: DMS_DNA_library

description: Library name: Sample 1

tag: cell type

tag: treatment

tag: batch


title: liver-specific conditional knockout of the G3BP1 mouse liver on HFD, replicate3

city: beijing

first: qinqin

last: ouyang

state: beijing

address: No. 10 Tianxiu Road, Haidian District, Beijing

department: department of nutrition and health

institute: China agricultural university

description: Library name: C57_G3BP1_KO_HFD_3

data_processing:
Data filtering:The raw data was filtered with SOAPnuke(v1.4.0) by 1) Removing readscontaining adapters (adapter contamination); 2) Removing reads whose unknown base('N' base) ratio is more than 5%; 3) Removing reads whose low-quality base ratio(Base quality less than or equal to 15) is more than 20%, afterwards clean reads wereobtained and stored in FASTQ format.
De novo assembly and quality assessment:Trinity (v2.0.6) was used to assemble the clean reads and BUSCO to assess theassembly quality.
Reference gene mapping:Clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5) and the expression level of genes was calculated by RSEM (v1.2.8)
CDS and SSR forecast:The candidate coding regions in Unigene were identified by the softwareTransdecoder (v3.0.1), the regions were aligned to SwissProt by BLAST. Thehomologous sequences of the Pfam protein and the coding regions were respectivelysearched and predicted by Hmmscan. Unigene was detected with MISA was used forUnigene detection (v1.0)and Primer3 (v2.2.2)designed primer for SSRdetection.
Gene Annotation:Annotating assembled Unigene with seven major functional databases (KEGG, GO,NR, NT, SwissProt, Pfam, and KOG), and predicting the transcription factors.
Time Series and WGCNA analysis:Time Series analysis was performed by Mfuzz (v2.34.0), and gene co-expressionnetwork analysis was performed by WGCNA (v1.48).
Differential Gene Expression:Within-group differential gene analysis was performed using DESeq under theconditions of Fold Change ≥ 2 and Adjusted Pvalue ≤ 0.001. PossionDis wasperformed between-group differential gene analysis under the conditions of FoldChange ≥ 2 and FDR ≤ 0.001. Using the pheatmap function on the differential geneset to draw a heatmap of differential gene clusters. According to the GO and KEGGannotation results and official classifications, the differentially expressed genes werefunctionally classified, and the phyper in R software was used for KEGG enrichmentanalysis, and the TermFinder package was used for GO Enrichment analysis(https://metacpan.org/pod/GO::TermFinder). With a Q value of ≤ 0.05 as thethreshold, candidate genes that met this condition was defined as being significantlyenriched.
Assembly: GRCm38
Supplementary files format and content: The quant.sf file is a tab-delimited text file that provides detailed abundance information for each transcript or gene. Key columns include Name (the transcript or gene ID), Length (the transcript's effective length), TPM (Transcripts Per Million, a normalized measure of expression abundance), and NumReads (the raw number of reads mapped to the transcript).

growth_protocol: Male 8-week-old WT and G3BP1 LKO mice were maintained under specific pathogen-free conditions (22±2°C, 12-hour light/dark cycle) with ad libitum access to either HFD for 20 weeks to establish MASLD

extract_protocol:
The process begins with tissue lysis, where the liver sample is ground using a grinding machine, then transferred to a tube containing 1.5 mL of TRIzol lysis buffer. The mixture is ground for 30 seconds and left to stand for 5 minutes to ensure complete tissue cell lysis. Following lysis, the sample is centrifuged at 12000×g for 5 minutes at 4℃ to pellet cellular debris. The resulting supernatant is then transferred to a new tube, mixed thoroughly with 300 μL of Chloroform/isoamyl alcohol (24:1), and centrifuged again at 12000×g for 8 minutes at 4℃ to separate the phases. The aqueous supernatant, containing the target molecules, is carefully transferred to a fresh tube. To this, 2/3 volume of Isopropyl alcohol is added (with optional glycogen for low-input samples), and the mixture is gently inverted and incubated at -20℃ for over 2 hours to precipitate the molecules. After precipitation, the sample is centrifuged at 17500×g for 25 minutes at 4℃ to form a pellet. The supernatant is discarded, and the pellet is washed with 0.9 mL of 75% ethanol by inversion. A final centrifugation at 17500×g for 3 minutes at 4℃is performed to remove the remaining wash buffer. The final pellet is air-dried for 3-5 minutes to remove residual ethanol and then dissolved in 20-200 μL of DEPC-H2O or RNase-free water for downstream analysis.
The protocol begins with a quality control check of the initial RNA sample to ensure it meets product specifications. Next, mRNA is isolated by denaturing the RNA sample at an appropriate temperature to disrupt its secondary structure, followed by enrichment using oligo(dT) magnetic beads. The purified mRNA is then fragmented into smaller pieces using a fragmentation reagent at a suitable temperature. This is followed by cDNA synthesis, where a reaction system is prepared and programmed to synthesize the first cDNA strand, and then a separate reaction system is used to synthesize the second strand. The double-stranded cDNA then undergoes end repair to create blunt ends, followed by the addition of an "A" base to the 3' end. Adapter ligation is performed by preparing a reaction mixture and program to attach adapters to the cDNA fragments. The resulting product is then amplified using PCR with a prepared reaction system and program. The amplified library is then subjected to a quality control check. In the cyclization step, the PCR product is denatured into single strands, and a cyclization reaction is performed to create single-stranded circular DNA molecules, with unligated linear DNA molecules digested away. Finally, for sequencing, the single-stranded circular DNA molecules undergo rolling circle replication to form DNA nanoballs (DNBs). These DNBs are loaded onto a high-density DNA nan chip and sequenced using combinatorial probe-anchor synthesis (cPAS) technology.

value: liver

value: Alb-cre; G3BP1f/f

value: high fat diet


title: yw_rep2, dme ovary, smallRNA-seq

city: Moscow

first: Anastasiya

last: Kobelyatskaya

address: Vavilov str, 32

country: Russia

institute: Engelhardt Institute of Molecular Biology, RAS

description: Library name: yw_rep2

data_processing:
FastQC and Trimmomatic were used for the quality control and trimming of reads. Small RNA reads that passed quality control and minimal length filter (>18 nt) were mapped to the reference genome (BDGP assembly R6/dm6), and miRNAs sequences of miRbase by bowtie2. To identify piRNAs, we used reads with a length from 24 to 29 nt. The Rsamtools package was used to process bam files. FeatureCounts was used to calculate the read counts.
Assembly: dme6
Supplementary files format and content: tab-delimited text files include counts for each Sample

organism: Drosophila melanogaster

source_name: ovary

extract_protocol:
Total RNA from Drosophila ovaries was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (20-29 nt).
TruSeq Small RNA Library Preparation Kit (Illumina, USA)

value: ovary


title: CR-Hlg293

description: Library name: Sample 3

value: Primary hepatocellular carcinoma tissue

value: Hepatocyte

tag: tumor type

value: Primary hepatocellular carcinoma

value: A

tag: bclc stage

tag: distant metastasis

tag: number of tumors

tag: size(cm)

tag: microvascular invasion


title: yw_rep1, dme ovary, smallRNA-seq

description: Library name: yw_rep1

tag: tissue

tag: genotype


title: Sample 10

description: Library name: Sample 10

tag: tbi

tag: Sex

tag: age at_death

value: 54 years


title: CR-Hlg292

description: Library name: Sample 2

tag: patient id

value: patient 5

tag: gender

tag: age

tag: chlid-pugh

tag: cirrhosis


title: BeafKOhomo_rep2, dme ovary, smallRNA-seq

description: Library name: BeafKOhomo_rep2

value: BEAF AB-KO strain, homozygotes BEAF AB-KO/BEAF AB-KO  (Roy, Gilbert and Hart 2007)


title: liver-specific conditional knockout of the G3BP1 mouse liver on HFD, replicate2

description: Library name: C57_G3BP1_KO_HFD_2

tag: treatment


title: liver-specific conditional knockout of the G3BP1 mouse liver on HFD, replicate1

description: Library name: C57_G3BP1_KO_HFD_1


title: BeafKOhomo_rep1, dme ovary, smallRNA-seq

description: Library name: BeafKOhomo_rep1


title: Sample 4

description: Library name: Sample 4

value: Brain

value: Male

value: 66 years


title: Wild-type mouse liver on HFD, replicate 3

description: Library name: C57_HFD_3


title: human corneal endothelial cells, AMF30a, Day1

city: Seoul

first: Young joo

last: Shin

state: Seoul

address: 665-3 shiheungdaero, Shinkwan2dong

country: South Korea

institute: Hallym University

description: Library name: AMF

data_processing:
HISAT2
TruSeq Stranded mRNA Library Prep Kit
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: human corneal endothelial cells

growth_protocol: Opti-MEM I

extract_protocol:
RNA was harvested using RNA extraction kit (Bioneer). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: AMF30a (5uM)

tag: cell type

value: human corneal endothelial cells

value: WT

tag: batch

value: Day 1


title: Sample 3

description: Library name: Sample 3

value: No

value: 29 years


title: BeafKOhetero_rep2, dme ovary, smallRNA-seq

description: Library name: BeafKOhetero_rep2

value: BEAF AB-KO strain, heterozygotes BEAF AB-KO/Cy  (Roy, Gilbert and Hart 2007)


title: Sample 2

description: Library name: Sample 2

value: Yes

value: 46 years


title: Before selection replicate 1

description: Library name: Before A

tag: strain

value: Control


title: Wild-type mouse liver on HFD, replicate 2

description: Library name: C57_HFD_2

value: liver

value: high fat diet


title: human corneal endothelial cells, Control, Day1

description: Library name: control

value: control


title: Sample 1

description: Library name: Sample 1

value: 24 years


title: Wild-type mouse liver on HFD, replicate 1

description: Library name: C57_HFD_1


title: BeafKOhetero_rep1, dme ovary, smallRNA-seq

description: Library name: BeafKOhetero_rep1

value: ovary

value: BEAF AB-KO strain, heterozygotes BEAF AB-KO/CyO  (Roy, Gilbert and Hart 2007)


title: Sample 5

description: Library name: Sample 5

value: Brain

value: Male

value: 55 years


title: DAHB+Cyc-treated rep2

status: Public on Aug 05 2025

city: New York

first: Craig

last: Thompson

state: NY

address: 411 East 67th Street RRL 469

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: DAHB+Cyc2
ATAC-seq on CD8+ T cells

data_processing:
FASTQ files were uploaded to Galaxy and processed on the public server at usegalaxy.org. BAM files were generated using Bowtie2, aligned to mm10 with "very sensitive local" preset. BigWig files for track viewing were generated using the bamCoverage tool with normalization set to 1x genome coverage.
Assembly: mm10
Supplementary files format and content: BigWig files representing genome-wide ATAC-seq signal tracks.

source_name: Spleen and lymph nodes

extract_protocol:
100,000 CD8 T cells were obtained from spleen/lymph nodes of mice and were activated with anti-CD3/anti-CD28 and treated as indicated.
Nuclei were isolated and Tn5 transposition was performed per manufacturer's instructions (Active Motif ATAC-Seq Kit). Libraries were PCR-amplified with Nextera-compatible i5/i7 primers. Libraries which passed QC (Bioanalyzer or Tapestation) were sequenced on Illumina NextSeq 2000 by the MSKCC Integrated Genomics Core.

value: Spleen and lymph nodes

value: CD8 T cells

value: Wild-type

value: DAHB+Cyc


title: NaCl-treated rep2

description:
Library name: Ctrl2
ATAC-seq on CD8+ T cells

value: NaCl


title: NaCl-treated rep1

description:
Library name: Ctrl1
ATAC-seq on CD8+ T cells


title: DAHB+Cyc-treated rep1

description:
Library name: DAHB+Cyc1
ATAC-seq on CD8+ T cells


title: DAHB-treated rep1

description:
Library name: DAHB1
ATAC-seq on CD8+ T cells

value: DAHB


title: CIH_mm10_vM23

city: Quebec

first: Vincent

last: Joseph

state: Quebec

address: 2725, chemin Sainte-Foy

country: Canada

institute: Université Laval / IUCPQ

description:
Library name: CIH_Sample
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Software v. 7.1.0. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Raw BCL files were demultiplexed into FASTQ files using cellranger mkfastq (10x Genomics, version 7.1.0), which wraps Illumina's bcl2fastq v2.20 with default parameters.
Reads were aligned to the mouse reference genome (mm10-2020-A, provided by 10x Genomics) using the cellranger count pipeline (10x Genomics, version 7.1.0).
The reference transcriptome was built using Ensembl gene annotation (GRCm38/mm10).
Sequencing reads were processed with the following default structure: Read 1 (28 bp): cell barcode and UMI, Read 2 (91 bp): cDNA (transcript) read, Index read (i7, 8 bp): sample index
The chemistry was specified as --chemistry=SC3Pv3 (Chromium Single Cell 3' v3).
The --include-introns flag was set to true to improve quantification of nuclear transcripts, as recommended for partially lysed or frozen samples.
Cell Ranger’s internal cell calling algorithm was used to distinguish high-quality cells from background RNA.
Only barcodes with sufficient UMI complexity and transcript count were retained.
The final filtered gene-barcode matrices (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz) represent high-confidence single-cell transcriptomes.
Approximately 213 million and 262 million reads were generated for the Nx and IH libraries respectively, Sequencing saturation was 51% for Nx and 62% for IH, Mean depth was approximately 23,000 reads/cell (Nx) and 33,000 reads/cell (IH).
Assembly: GRCm38 (Mouse mm10)
Supplementary files format and content: Tab-separated text and plain text (.tsv, gzipped), and matrix files (.mtx, gzipped)

source_name: Lung

growth_protocol: Animals were housed 3 per cages, had ad-libitum access to food and water and were maintained on a 12/12 h light/dark cycle.

extract_protocol:
Immediately after dissection, the lungs were pooled (3 mice for each group) and then minced mechanically before dissociation with a protease mix, filtered, washed, and counted for viability.
Library was performed according to the manufacturer's instructions, (Chromium Single Cell 3' v3.1 kit.). Briefly, single-cell suspensions were loaded onto 10x Genomics Chromium Next GEM Chip G and partitioned into droplets with barcoded gel beads using the Chromium Controller. Reverse transcription tagged mRNAs with cell barcodes and UMIs. cDNA was amplified, fragmented, and converted into sequencing libraries using the Chromium Single Cell 3' v3.1 kit. Libraries were sequenced paired-end on Illumina NovaSeq 2000 (28 bp R1, 8 bp i7, 91 bp R2).

treatment_protocol: Exposition to intermittent hypoxia from 6 am to 6 pm for 14 days. Oxygen dropped from 21% to 6% in 75 seconds then returned to 21% in 45 seconds, for a total cycle length of 120 seconds and a frequency of 30 cycles/h. Mice have been euthanized at 9 am, while still being exposed to IH following the normal schedule. Control mice are kept in normoxia (21%O2) at all time.

value: Lung

value: 8-12 weeks

value: male

value: Intermittent hypoxia


title: NX_mm10_vM23

description:
Library name: NX_Sample
10X Genomics

value: Normoxia


title: CR-Hlg291

description: Library name: Sample 1

value: Primary hepatocellular carcinoma tissue

value: Hepatocyte

value: patient 5

tag: tumor type

value: Primary hepatocellular carcinoma

value: A

tag: bclc stage

tag: distant metastasis

tag: number of tumors

tag: hbv/hcv infection

tag: afp(ng/ml)


title: GMT + Hand2 Day 6 biol rep 2

first: Nikhil

last: Munshi

department: Cardiology

institute: UT Southwestern

data_processing:
UTSW BioHPC NGS pipeline
Raw FASTQ files were analyzed using FastQC v0.11.2
reads were quality-trimmed using fastq-mcf. (ea-utils/1.1.2–806)
The trimmed reads were mapped to the mm9 assembly using Tophat
RNA counts generated from HT_seq Count
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes the raw counts for each Sample

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Roughly 150-200k cells were seeded in 1 well of a 6 well dish in 2 mL of DMEM supplemented with 10% FBS and 5% CO2 at 37C

extract_protocol:
RNA was isolated using Trizol reagent following standard protocol
RNA libraries for RNA-seq were created using Illumina TruSeq Stranded RNA kit

treatment_protocol: One day after plating cells were infected with retrovirus encoding each of the reprogramming cocktails described in the sample header. The cells received a second round of virus one day after the first infection. The cells were then changed to fresh 18s media to promote differentiation. The cells were then grown for 6 days in 18s media prior to RNA extraction.

tag: cell line

value: Mouse Embryonic Fibroblasts

value: Fibroblasts

tag: genotype

value: HCN4-GFP reporter

value: GMT + Hand2


title: Sham_2

city: kunming

first: youjun

last: zhou

state: yunnan

address: No,245, renmin eastroad

department: 1Department of Nuclear Medicine

institute: The Affiliated Yan’an Hospital of Kunming Medical University

description: sham group, replicate biosample 2

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software （version10.7.1.1, Agilent Technologies）using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The MI model mice were established by ligation of the left anterior descending (LAD) coronary artery, as described in previous methods44. In brief, the mice were anaesthetised, and their chests were opened.

extract_protocol: The total RNA sample was quantified using the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed with the Agilent Mouse ceRNA Microarray 2019(4*180K,Design ID:086242).

treatment_protocol: 7-0 nylon was used to suture LAD surgically, and the Sham group mice underwent the same surgery

tag: tag

value: heart


title: Sham_1

description: sham group, replicate biosample 1


title: GMT + N- D+ Day 6 biol rep 1

value: GMT + N- D+


title: GMT + N- D- Day 6 biol rep 1

value: GMT + N-D-


title: GMT + Hand2 Day 6 biol rep 1


title: GMT + N- D+ Day 6 biol rep 2


title: Sham_3

description: sham group, replicate biosample 3


title: MI_2

description: MI group, replicate biosample 2


title: MEF Day 6 biol rep 1

value: WT


title: DAHB-treated rep2

description:
Library name: DAHB2
ATAC-seq on CD8+ T cells

tag: tissue

value: Spleen and lymph nodes

value: CD8 T cells

value: Wild-type

value: DAHB


title: DAHB+BRM-treated rep1

description:
Library name: DAHB+BRM1
ATAC-seq on CD8+ T cells

value: DAHB+BRM


title: NaCl-treated rep2

value: NaCl


title: GMT + N+ D- Day 6 biol rep 2

value: GMT + N+D -


title: GMT Day 6 biol rep 2

value: GMT


title: GMT + N+ D- Day 6 biol rep 1


title: NaCl-treated rep1


title: GMT Day 6 biol rep 1


title: HEK cells transfected with control scramble sequence, replicate 3

city: Boston

first: Guoping

last: Li

address: Cardiovascular Research Center, 185 Cambridge St, Simches 3.5000

department: CVRC

institute: Massachusetts General Hospital

description: Library name: Ctrl_3

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt (v2.10) and aligned to the Gencode GRCh38.p13 genome using STAR (v2.7.8a). Gencode v38 gene annotations were provided to STAR to improve the accuracy of mapping. Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.11.9) (www.bioinformatics.babraham.ac.uk/projects/fastqc). featureCounts (v2.0.2) was used to count the number of mapped reads to each gene. Heatmap3 was used for cluster analysis and visualization. Significantly differential expressed genes with absolute fold change >= 1.5 and FDR-adjusted p-value <= 0.05 were detected by DESeq2 (v1.30.1).
Assembly: hg38
Supplementary files format and content: txt, raw read counts

growth_protocol: Human embryonic kidney 293 (HEK) cells were purchased from ATCC (ATCC, CRL-1573) and cultured in D10 medium, which consisted of DMEM with high glucose and pyruvate (Thermo Fisher, Cat# 11995073) supplemented with 10% fetal bovine serum (FBS) (ThermoFisher, Cat# 16000044) and 1% Penicillin/Streptomycin (Thermo Fisher, Cat# 15140122).

extract_protocol:
Total RNA was extracted following TRIzol protocol.
Libraries were prepared using  the SMARTer Stranded Total RNA-Seq Kit v2 Pico Input Mammalian (Takara Bio, San Jose, CA, USA)

treatment_protocol: HEK cells were transfected with 50nM tRNA-Asp-GTC-3'tDR or scramble control mimics with Lipofectamine RNAiMax. Cells were collected 48 hours after transfection.

value: transfected with control scramble mimics


title: HEK cells transfected with tRNA-Asp-GTC 3' tDR, replicate 3

description: Library name: tDR_3

value: transfected with tRNA-Asp-GTC 3' tDR mimics


title: HEK cells transfected with tRNA-Asp-GTC 3' tDR, replicate 2

description: Library name: tDR_2


title: MEF Day 6 biol rep 2

value: Mouse Embryonic Fibroblasts

value: Fibroblasts


title: MI_1

description: MI group, replicate biosample 1


title: HEK cells transfected with control scramble sequence, replicate 4

description: Library name: Ctrl_4


title: Aorta_pericyte_nanofiber_Day21

city: Pittsburgh

first: Julie

middle: A

last: Phillippi

address: 450 Technology Drive, Suite 300

department: Cardiothoracic Surgery

institute: University of Pittsburgh

description: Library name: Nano_Day21

data_processing:
Quality control reports were performed for raw, untrimmed sequences and again after sequence trimming. Sequences were trimmed per default settings in the CLC Genomics software with Molecular Bio plugin (QIAgen), with an additional requirement for a minimum length of 10 nucleotides. Trimmed sequences were then aligned to GRCh38 human genome reference and a mapping quality control report was reviewed.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

growth_protocol: Adventitial tissue was delaminated from the medial layer and digested in 0.5mg/mL collagenase and 0.25mg/mL elastase, with the resulting slurry passed through a 70 µm strainer. This single cell suspension was then cultured on type I collagen coated flasks in StemMACS MSC Expansion Medium, human (Miltenyi Biotec) until ~85-90% confluent. Cells were then enriched using magnetic bead separation to achieve a CD31-/CD146+ phenotype (Miltenyi Biotec), subcultured once and infected with lentiviral HPV for immortalization (Applied Biological Materials). Immortalized cells were serially passaged to select for cells that incorporated the HPV vector for 4-5 passages and phenotype was confirmed prior to experimentation beginning. Cells were incubated at 37°C in 5% CO2 at all time.

extract_protocol:
Monolayer cells and spheroids formed on nanofiber scaffolds were collected in Buffer RA1 (Takara Bio) +1% beta-mercaptoethanol (Fisher Scientific). NucleoSpin RNA kit from Takara Clontech was used for RNA extraction, 50ng input RNA used for library construction.
RNA was assessed for quality using an Agilent TapeStation 4150/Fragment Analyzer 5300 and RNA concentration was quantified on a Qubit FLEX fluorometer. Libraries were generated with the Illumina Stranded Total Library Prep kit (Illumina: 20040529) according to the manufacturer’s instructions. Briefly, 6 ng of input RNA was used for each sample. Following adapter ligation, 15 cycles of indexing PCR were completed, using Illumina RNA UD Indexes. Library quantification and assessment was done using a Qubit FLEX fluorometer and an Agilent TapeStation 4150/Fragment Analyzer 5300. Libraries were normalized and pooled to 2 nM by calculating the concentration based off the fragment size (base pairs) and the concentration (ng/ml) of the libraries. Sequencing was performed on an Illumina NextSeq 2000, using a P3 flow cell. The pooled library was loaded at 750 pM and sequencing was carried out with read lengths of 2x101 bp, with a target of 40 million reads per sample. Sequencing data was demultiplexed by the on-board Illumina DRAGEN FASTQ Generation software.

treatment_protocol: All culturing of pericytes was performed in  StemMACS MSC Expansion Medium (Miltenyi Biotec). Monolayer culture occurred on fibronectin-coated six-well plates. Spheroids were formed on nanofiber scaffolds (hollow metal scaffolds using non-electrospinning Spinneret based Tunable Engineered Parameters (STEP) technique) at Day 1, Day 7 and Day 21 post seeding. Specific scaffold parameters are ~2 µm thick ‘base’ fibers spaced ~350 µm apart, over which orthogonal layers of a parallel array of ~200 nm ‘aligned’ fibers with ~10 µm spacing were deposited.

value: Pericyte


title: HEK cells transfected with control scramble sequence, replicate 1

description: Library name: Ctrl_1


title: HEK cells transfected with tRNA-Asp-GTC 3' tDR, replicate 4

description: Library name: tDR_4


title: Aorta_pericyte_nanofiber_Day1

description: Library name: Nano_Day1


title: HEK cells transfected with control scramble sequence, replicate 2

description: Library name: Ctrl_2


title: Aorta_pericyte_monolayer_Day7

description: Library name: 2D_Day7

value: Monolayer


title: non-OA/RA44

city: Detroit

first: Shabana Amanda

last: Ali

state: Michigan

address: Integrative Biosciences Center, 6135 Woodward Avenue

department: Bone and Joint Center

institute: Henry Ford Health + Michigan State University Health Sciences

description:
Library name: Sample 62
Column name in allsamples_raw_counts.csv: non-OA/RA44

data_processing:
The raw microRNA sequences obtained after sequencing were aligned to miRBase v22.1 and the human reference genome (vGRCh38).
Abundant microRNAs, defined as those with at least 10 counts-per-million (CPM) in two or more samples, were selected, and the counts were normalized to total counts.
Differential expression analysis between groups was performed in a pairwise manner using a quasi-likelihood negative binomial model with trended dispersions, implemented in the edgeR package (v3.40.2).
Novel microRNA sequences were identified using miRDeep2.
Assembly: vGRCh38
Supplementary files format and content: allsamples_raw_counts cvs file includes raw counts for each sample

source_name: Plasma

growth_protocol: No growth

extract_protocol:
Blood samples were collected in EDTA-coated vacutainers and fractionated by centrifugation. RNA was isolated from 250 μL plasma using the miRNeasy Serum/Plasma Advanced Kit (QIAGEN Inc.), following the manufacturer's instructions.
Library construction followed the QIAseq miRNA Library Kit (QIAGEN Inc.) protocol.

treatment_protocol: No treatment

value: Plasma

tag: disease

value: Non-OA/RA


title: Aorta_pericyte_monolayer_Day1

description: Library name: 2D_Day1


title: MI_3

description: MI group, replicate biosample 3

value: heart


title: Aorta_pericyte_monolayer_Day21

description: Library name: 2D_Day21


title: non-OA/RA42

description:
Library name: Sample 60
Column name in allsamples_raw_counts.csv: non-OA/RA42


title: HEK cells transfected with tRNA-Asp-GTC 3' tDR, replicate 1

description: Library name: tDR_1


title: non-OA/RA40

description:
Library name: Sample 58
Column name in allsamples_raw_counts.csv: non-OA/RA40


title: non-OA/RA36

description:
Library name: Sample 54
Column name in allsamples_raw_counts.csv: non-OA/RA36


title: non-OA/RA37

description:
Library name: Sample 55
Column name in allsamples_raw_counts.csv: non-OA/RA37


title: non-OA/RA39

description:
Library name: Sample 57
Column name in allsamples_raw_counts.csv: non-OA/RA39


title: non-OA/RA43

description:
Library name: Sample 61
Column name in allsamples_raw_counts.csv: non-OA/RA43


title: non-OA/RA38

description:
Library name: Sample 56
Column name in allsamples_raw_counts.csv: non-OA/RA38


title: non-OA/RA33

description:
Library name: Sample 51
Column name in allsamples_raw_counts.csv: non-OA/RA33


title: non-OA/RA34

description:
Library name: Sample 52
Column name in allsamples_raw_counts.csv: non-OA/RA34


title: non-OA/RA31

description:
Library name: Sample 49
Column name in allsamples_raw_counts.csv: non-OA/RA31


title: Aorta_pericyte_nanofiber_Day7

description: Library name: Nano_Day7


title: non-OA/RA30

description:
Library name: Sample 48
Column name in allsamples_raw_counts.csv: non-OA/RA30


title: non-OA/RA29

description:
Library name: Sample 47
Column name in allsamples_raw_counts.csv: non-OA/RA29


title: non-OA/RA28

description:
Library name: Sample 46
Column name in allsamples_raw_counts.csv: non-OA/RA28


title: non-OA/RA27

description:
Library name: Sample 45
Column name in allsamples_raw_counts.csv: non-OA/RA27


title: non-OA/RA26

description:
Library name: Sample 44
Column name in allsamples_raw_counts.csv: non-OA/RA26


title: non-OA/RA23

description:
Library name: Sample 41
Column name in allsamples_raw_counts.csv: non-OA/RA23


title: non-OA/RA20

description:
Library name: Sample 38
Column name in allsamples_raw_counts.csv: non-OA/RA20


title: non-OA/RA24

description:
Library name: Sample 42
Column name in allsamples_raw_counts.csv: non-OA/RA24


title: non-OA/RA25

description:
Library name: Sample 43
Column name in allsamples_raw_counts.csv: non-OA/RA25


title: non-OA/RA22

description:
Library name: Sample 40
Column name in allsamples_raw_counts.csv: non-OA/RA22


title: non-OA/RA41

description:
Library name: Sample 59
Column name in allsamples_raw_counts.csv: non-OA/RA41


title: non-OA/RA19

description:
Library name: Sample 37
Column name in allsamples_raw_counts.csv: non-OA/RA19


title: non-OA/RA35

description:
Library name: Sample 53
Column name in allsamples_raw_counts.csv: non-OA/RA35


title: non-OA/RA32

description:
Library name: Sample 50
Column name in allsamples_raw_counts.csv: non-OA/RA32


title: non-OA/RA18

description:
Library name: Sample 36
Column name in allsamples_raw_counts.csv: non-OA/RA18


title: non-OA/RA21

description:
Library name: Sample 39
Column name in allsamples_raw_counts.csv: non-OA/RA21


title: non-OA/RA17

description:
Library name: Sample 35
Column name in allsamples_raw_counts.csv: non-OA/RA17


title: non-OA/RA16

description:
Library name: Sample 34
Column name in allsamples_raw_counts.csv: non-OA/RA16


title: mouse,pre-hepatectomy,anti-RPB1(nano-CUT&Tag)

city: Xiamen

first: yongyou

last: zhang

state: Fujian

address: Xiang'an South Road

institute: Xiamen University

description: Library name: pre-hepatectomy_anti-RPB1

data_processing:
Raw reads were filtered to remove adapter sequences and low-quality sequences using fastp (version 0.20).
Clean reads were mapped to the mouse mm10 or human hg19 reference genome using Bowtie2 (version 2.4) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -l 10 -X 700.
Duplicate reads were removed using Picard MarkDuplicates (version 2.27). Mitochondrial reads, unmapped reads, and reads with mapping quality <30 were filtered out using SAMtools (version 1.15).
BigWig files were generated using deepTools bamCoverage (version 3.3.1) with options: --binSize 10 --normalizeUsing RPGC.
Peaks were called for each sample using MACS2 callpeak (version 2.2) with options: --bdg --SPMR --gsize hs --keepdup all --gvalue 0.05 --shift -75 --extsize 150 --nomodel --call-summits --nolambda.
Assembly: hg19,mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
For cell samples, digestion followed by permeabilization is sufficient. For mouse liver tissue, 0.1-0.2 g of liver tissue was excised and washed with 2 mL of swelling buffer (10 mM Tric-HCl pH 7.5, 2 Mm MgCl2, 3 mM CaCl2, 1×Protease inhibitor cocktail). The liver was then dounced in 1 ml of swelling buffer (dounced 10 times, piston A) and incubated at 4°C for 20 min. Afterward, the liver was dounced again 20 times (piston B), and 1 mL of swelling buffer was added. The cells were filtered using a 100 μm cell strainer and spun at 400×g at 4°C for 10 min. The supernatant was removed, and the cells were resuspended in 0.5 ml of swelling buffer + 10% glycerol. Slowly vortex while adding drop by drop 0.5 mL of lysis buffer (Swelling buffer + 10% glycerol + 1% NP-40). Incubate for 5 min at 4°C and add 1.5 mL of lysis buffer. Spin at 600×g at 4°C for 5 min, remove the supernatant, and wash the nuclei again with 1.5 mL of lysis buffer. Spin at 600 g at 4°C for 5 min, remove the supernatant, and resuspend the nuclei in 1 mL of freezing buffer. Finally, the nuclei were stained with DAPI and counted.
Following cell or nucleus counting, permeabilization is performed without the addition of antibodies. The permeabilized samples are incubated with LgBiT-Tn5 or NbALFA-Tn5, and unbound proteins are subsequently removed. A transposition activation reaction is then conducted to fragment intracellular DNA, which is extracted for downstream library preparation. Indexed libraries are generated using universal i5 primers and unique barcoded i7 primers, with each sample assigned a distinct barcode. The libraries are amplified through 15 cycles of PCR, and the resulting DNA is purified for high-throughput sequencing.

value: liver


title: non-OA/RA15

description:
Library name: Sample 33
Column name in allsamples_raw_counts.csv: non-OA/RA15


title: mouse,post-hepatectomy,anti-RPB1(nano-CUT&Tag)

description: Library name: post-hepatectomy_anti-RPB1


title: non-OA/RA14

description:
Library name: Sample 32
Column name in allsamples_raw_counts.csv: non-OA/RA14


title: [38] Aged (20-21 months old); Obese (60% Kcal fat diet)

city: Fayetteville

first: Eleanor

last: Schrems

state: Arkansas

address: 155 Stadium Dr.

department: Health, Human Performance, and Recreation

institute: University of Arkansas

description: Library name: Sample 38

data_processing:
FASTQ files were aligned using STAR 2.78a index alignment – RefSeq: mus musculus (mouse) – mm39 GeneBank assembly. Pre-alignment QA/QC was done prior to STAR alignment and after to ensure the quality of raw, unaligned sequencing reads (quality score ~35.66). Samples were normalized by using the median ratio for DESeq2 in Partek, and a filter of 10 minimum reads across all samples was applied. Analysis of differentially expressed genes (DEGs) was done using DESeq2. In order to gain insight to the effects of obesity and age alone, as well as those purely unique to aged obesity (SO), DESeq2 was performed with separate comparisons of YO, AL, and AO groups against YL. Additional DESeq2 was performed for comparisons of AO against AL to gain insight to the effects of obesity in an aged condition. Finally, DESeq2 comparisons were made between AO and YO to gain insight to the effects of ageing with obesity, indicative of lifelong obesity.
Assembly: mm39 GeneBank Assembly
Supplementary files format and content: File Type: xlsx; Contents: Data for each individual sample, normalized by using the median ratio for DeSeq2 in Partek. Normalization was done following a filtering step to include genes with a minimum of 10 counts.

source_name: Gastrocnemius muscle

extract_protocol:
Given the gastrocnemius is a muscle with a mixed fiber type and atrophied the most in the aged-obese (SO) animal group (Table 1), RNA from this muscle was chosen for sequencing. mRNA was isolated from the gastrocnemius muscle, where the muscle tissue was homogenized with Trizol (Life Technologies, Grand Island, NY, USA), and phenol–chloroform extraction was performed following homogenization. RNA was ethanol-precipitated and diluted in 70% of diethyl pyro carbonate-treated ethanol. Total RNA was isolated using an Invitro-gen PureLinkTM RNA Mini Kit (Invitrogen, Waltham, MA, USA; 12183018A). Total RNA was eluted in RNase-free water. RNA concentration and purity were measured using a BioTek Take3 micro-volume microplate with a BioTek Synergy HTX Multi-Mode Microplate Reader, IVD (Fisher Scientific, Waltham, MA, USA; BTS1LASI). A 260/280 nm ratio of >2 was utilized as an initial quality assessment(28). RNA concentration was assessed using a Qubit Fluorimeter, Fragment Analyzer, Nano Drop, and Microplate reader. RNA integrity and quality were assessed by quantifying the RNA integrity number (RIN) and the RNA quality number (RQN) using Agilent 2100 Bioanalyzer and Fragment Analyzer. RIN scores below 7 were excluded from subsequent analysis.
Single-end mRNA sequencing was completed at the BGI Hong Kong Tech Solution NGS Lab (Hong Kong, China) using MGISeq 2000 Transcriptome for library preparation.

value: Gastrocnemius muscle

value: Male

value: 20-21 months old

value: 60% Kcal from fat diet


title: [37] Aged (20-21 months old); Obese (60% Kcal fat diet)

description: Library name: Sample 37


title: [39] Aged (20-21 months old); Obese (60% Kcal fat diet)

description: Library name: Sample 39


title: non-OA/RA11

description:
Library name: Sample 29
Column name in allsamples_raw_counts.csv: non-OA/RA11


title: [36] Aged (20-21 months old); Obese (60% Kcal fat diet)

description: Library name: Sample 36


title: non-OA/RA10

description:
Library name: Sample 28
Column name in allsamples_raw_counts.csv: non-OA/RA10


title: GMT + N- D- Day 6 biol rep 2

city: Dallas

address: 5323 Harry Hines Blvd

value: HCN4-GFP reporter

value: GMT + N-D-


title: [35] Aged (20-21 months old); Obese (60% Kcal fat diet)

description: Library name: Sample 35


title: non-OA/RA9

description:
Library name: Sample 27
Column name in allsamples_raw_counts.csv: non-OA/RA9


title: [34] Aged (20-21 months old); Lean (12% Kcal fat diet)

description: Library name: Sample 34

value: 12% Kcal from fat diet


title: non-OA/RA7

description:
Library name: Sample 25
Column name in allsamples_raw_counts.csv: non-OA/RA7


title: non-OA/RA8

description:
Library name: Sample 26
Column name in allsamples_raw_counts.csv: non-OA/RA8


title: [31] Aged (20-21 months old); Lean (12% Kcal fat diet)

description: Library name: Sample 31


title: non-OA/RA5

description:
Library name: Sample 23
Column name in allsamples_raw_counts.csv: non-OA/RA5


title: [33] Aged (20-21 months old); Lean (12% Kcal fat diet)

description: Library name: Sample 33


title: non-OA/RA6

description:
Library name: Sample 24
Column name in allsamples_raw_counts.csv: non-OA/RA6


title: non-OA/RA3

description:
Library name: Sample 21
Column name in allsamples_raw_counts.csv: non-OA/RA3


title: [28] Young (6 months old); Obese (60% Kcal fat diet)

description: Library name: Sample 28

value: 6 months old


title: [29] Young (6 months old); Obese (60% Kcal fat diet)

description: Library name: Sample 29


title: [32] Aged (20-21 months old); Lean (12% Kcal fat diet)

description: Library name: Sample 32


title: non-OA/RA13

description:
Library name: Sample 31
Column name in allsamples_raw_counts.csv: non-OA/RA13


title: [25] Young (6 months old); Obese (60% Kcal fat diet)

description: Library name: Sample 25


title: [30] Aged (20-21 months old); Lean (12% Kcal fat diet)

description: Library name: Sample 30


title: [26] Young (6 months old); Obese (60% Kcal fat diet)

description: Library name: Sample 26


title: earlyOA11

description:
Library name: Sample 17
Column name in allsamples_raw_counts.csv: earlyOA11

value: Early OA


title: non-OA/RA1

description:
Library name: Sample 19
Column name in allsamples_raw_counts.csv: non-OA/RA1


title: earlyOA12

description:
Library name: Sample 18
Column name in allsamples_raw_counts.csv: earlyOA12


title: [24] Young (6 months old); Lean (12% Kcal fat diet)

description: Library name: Sample 24


title: non-OA/RA12

description:
Library name: Sample 30
Column name in allsamples_raw_counts.csv: non-OA/RA12


title: non-OA/RA4

description:
Library name: Sample 22
Column name in allsamples_raw_counts.csv: non-OA/RA4


title: [27] Young (6 months old); Obese (60% Kcal fat diet)

description: Library name: Sample 27


title: earlyOA10

description:
Library name: Sample 16
Column name in allsamples_raw_counts.csv: earlyOA10


title: 19-222, 2N, ChP, Batch 3, Medial Septal Neurons

city: Orangeburg

first: Stephen

middle: D.

last: Ginsberg

state: New York

address: 140 Old Orangeburg Road

department: Centre for Dementia Research

institute: Research Foundation for Mental Hygiene

description: Library name: 19-222

data_processing:
Quality Control was performed, and reads with any adapter contamination are trimmed using trimmomatic 0.39. The sequences are then decontaminated using Kraken2 to ensure host specificity.
The decontaminated sequences are then aligned to a reference genome using the STAR aligner. Gene counts were extracted using RSEM.
Downstream analysis was performed using R with the gene counts obtained from RSEM. Genes with over 0.1 counts per million were retained followed by TMM normalization.
Batch correction was performed using three different approaches then differential expression analysis was performed separately for each method, and DEGs common in 2 or more approaches are used for Downstream interpretation.
Assembly: GRCm39
Supplementary files format and content: tab delimited text files with gene counts of all samples in one file
Supplementary files format and content: tab delimited text files with gene counts of one sample per one file

source_name: Brain, basal forebrain

growth_protocol: Breeder pairs (female Ts65Dn and male C57Bl/6J Eicher x C3H/HeSnJ F1 mice) were purchased from Jackson Laboratories (Bar Harbor, ME, USA) and mated at the Nathan Kline Institute. Breeder pairs were assigned to receive one of two choline-controlled experimental diets: i) control rodent diet containing 1.1 g/kg choline chloride (AIN-76A; Dyets Inc., Bethlehem, PA), or ii) choline-supplemented diet containing 5.0 g/kg choline chloride (AIN-76A; Dyets Inc.). Tail clips were taken and genotyped  at weaning and mice were aged to ~10-12 MO, with the average age of ~11 MO.

extract_protocol:
A rapid staining protocol utilizing antibody against choline acetyltransferase (ChAT) (AB144P, Millipore, Burlington MA) was performed to detect cholinergic positive neurons while preserving intact RNA in the unfixed tissue. ChAT-immunoreactive (ir) neurons were identified within the medial septal (MS) region and isolated by LCM (LMD7000)RNA from ~500 MS neukrons was purified using miRNeasy Micro kit (Qiagen) according to manufacturers’ specifications. A DNase digestion was performed twice sequentially before the final washes and RNA purification. . Approximately 500 ChAT-ir neurons were isolated per brain before proceeding to RNA isolation and RNA-seq library preparation.
The SMARTer Stranded Total RNA-Seq kit-Pico input Mammalian (v1, Takara Bio, Mountain View, CA) was employed with minor modifications during step A to utilize full volume of isolated RNA. Samples were quantified (Agilent 2100 HS DNA kit), with samples showing no peak between 300-500bp re-isolated by LCM, with RNA isolation and library preparation repeated.  Samples were isolated and processed in three independent batches, batch 1 (2N, n=3; 2N+, n=5; Ts n=4, Ts+ n=5), batch 2 (2N, n=2; 2N+, n=2; Ts n=4, Ts+ n=2), batch 3 (2N, n=6; 2N+, n=5; Ts n=3, Ts+ n=3).  For each sample run (Batch 1, 2 and 3), library samples were pooled in equimolar concentrations and assayed on an HiSeq-4000 (Illumina, San Diego, CA) using a single read 50 cycle protocol at NYUGSOM Genome Technology Center (GTC).

treatment_protocol: see growth protocol.

value: Brain, basal forebrain

value: cholinergic neurons

value: Medial Septal Neurons

value: ChP

value: Batch 3


title: non-OA/RA2

description:
Library name: Sample 20
Column name in allsamples_raw_counts.csv: non-OA/RA2

value: Plasma

value: Non-OA/RA


title: [22] Young (6 months old); Lean (12% Kcal fat diet)

description: Library name: Sample 22


title: earlyOA9

description:
Library name: Sample 15
Column name in allsamples_raw_counts.csv: earlyOA9


title: 19-201, 2N, ChP, Batch 3, Medial Septal Neurons

description: Library name: 19-201


title: 15-54, 2N, ChN, Batch 3, Medial Septal Neurons

description: Library name: 15-54

value: ChN


title: HDAC5_KO4

first: Zheng

last: Kuang

address: 4400 Fifth Avenue

department: Biological Sciences

institute: Carnegie Mellon University

description: Library name: HDAC5KO4

data_processing:
Sequences were joined, depleted of barcodes then sequences <150bp removed, sequences with ambiguous base calls removed.  Sequences were denoised, OTUs generated and chimeras removed.  Operational taxonomic units (OTUs) were defined by clustering at 3% divergence (97% similarity).  Final OTUs were taxonomically classified using BLASTn against a curated database derived from RDPII and NCBI (www.ncbi.nlm.nih.gov, http://rdp.cme.msu.edu).
Assembly: RDPII and NCBI
Supplementary files format and content: Tab-delimited file with OTU counts for each sample
Library strategy: 16S rRNA-seq

organism: feces metagenome

source_name: mouse feces

extract_protocol:
Fecal DNA was extracted and purified from freshly collected feces using the FastDNA Spin Kit (MP Biomedicals 116560-200)
To generate sequencing libraries, the V3–V4 variable regions of the 16S rRNA gene were amplified using HotStarTaq Plus Master Mix (Qiagen) and region-specific primers

value: mouse feces

tag: Sex

value: female

value: Mice were co-housed


title: HDAC5_KO3

description: Library name: HDAC5KO3


title: HDAC5_KO1

description: Library name: HDAC5KO1


title: 15-53, TS, ChN, Batch 3, Medial Septal Neurons

description: Library name: 15-53

value: TS


title: earlyOA7

description:
Library name: Sample 13
Column name in allsamples_raw_counts.csv: earlyOA7


title: HDAC5_WT4

description: Library name: WT4


title: HDAC5_WT2

description: Library name: WT2


title: [23] Young (6 months old); Lean (12% Kcal fat diet)

description: Library name: Sample 23

value: Gastrocnemius muscle

value: Male


title: HDAC5_KO2

description: Library name: HDAC5KO2


title: earlyOA6

description:
Library name: Sample 12
Column name in allsamples_raw_counts.csv: earlyOA6


title: earlyOA4

description:
Library name: Sample 10
Column name in allsamples_raw_counts.csv: earlyOA4


title: HDAC5_WT1

description: Library name: WT1


title: earlyOA3

description:
Library name: Sample 9
Column name in allsamples_raw_counts.csv: earlyOA3


title: HDAC5_WT3

description: Library name: WT3


title: 15-52, 2N, ChN, Batch 3, Medial Septal Neurons

description: Library name: 15-52


title: 15-309, TS, ChP, Batch 3, Medial Septal Neurons

description: Library name: 15-309


title: earlyOA5

description:
Library name: Sample 11
Column name in allsamples_raw_counts.csv: earlyOA5


title: DAHB+BRM-treated rep2

description:
Library name: DAHB+BRM2
ATAC-seq on CD8+ T cells

value: Spleen and lymph nodes

value: CD8 T cells

value: Wild-type

value: DAHB+BRM


title: 15-276, TS, ChN, Batch 3, Medial Septal Neurons

description: Library name: 15-276

value: Brain, basal forebrain

value: cholinergic neurons