title: P2 SVZ n2 multiomic data, snRNA-seq

city: Vancouver

first: Freda

last: Miller

state: BC

address: 2185 East Mall

department: Michael Smith Laboratories

institute: University of British Columbia

description: Library name: P2 SVZ n2 RNA

library_source: transcriptomic single cell

data_processing:
Raw data was processed through Cell Ranger ARC v2. Reads were aligned to the wild-type mouse genome (mm10).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and HDF5 files

molecule: nuclear RNA

source_name: Dorsal and lateral ventricular-subventricular zone

extract_protocol:
For single-cell isolation of the embryonic (E14, E17) cortex, the meninges were removed and tissue immediately dorsal to the lateral ventricles—including the cortical layers and the V-SVZ—was collected. For single-cell isolation of the postnatal (P1, P2, P6, P7) V-SVZ, the cortex was removed to expose the lateral ventricles, and the dorsolateral V-SVZ was microdissected out and collected. During dissections, collected tissue was placed in either DMEM (Gibco) or Hibernate A without calcium (BrainBits) supplemented with 2% B27 (Life Technologies) and 500 µM L-glutamine (Cedarlane) and left on ice until subsequent processing steps. For some datasets (E17 cortex multiomic, P2 V-SVZ n2 multiomic, P7 V-SVZ multiomic), tissue collection was immediately followed by an enzymatic digestion step. Samples were incubated in 20 units/mL Papain with 1 mM L-cysteine, 0.5 mM EDTA, and 0.005% DNase I (Worthington) dissolved in Hibernate A medium without calcium (BrainBits) and DRAQ5 (Abcam) diluted 1:3000 for 30 minutes at 37°C to simultaneously enzymatically digest the tissue and label nuclei. Following enzyme treatment, cells were spun down at 300 g for 5 minutes and resuspended in media, either DMEM (Gibco) or Hibernate A medium without calcium, supplemented with 2% B27 (Life Technologies) and 500 µM L-glutamine (Cedarlane). Following enzymatic digestion or immediately following collection, tissue was triturated using blunt needles with sequentially decreasing diameters (McMaster-Carr). Cells were then spun down at 300 g for 5 minutes and resuspended in 0.25% BSA (Jackson) in HBSS, after which the cell suspension was filtered through a 40 µm cell strainer and incubated in 1:1000 propidium iodide (PI) (Abcam) to label dead/damaged cells. Samples were then FACS sorted using a MoFlo Cell Sorter (Beckman Coulter) or Aria Fusion A (Becton Dickinson) to enrich for viable (PI-negative, DRAQ5-positive) cells, which were collected in media, either DMEM or Hibernate A without calcium, supplemented with 2% B27 and 500 µM L-glutamine.
Libraries were constructed according to the manufacturer's instructions (Single Cell Multiome ATAC + Gene Expression v1, 10x Genomics).

tag: age

value: Postnatal day 2

value: Early postnatal ventricular-subventricular zone cell types


title: SC_2

status: Public on Jun 18 2026

type: SRA

city: Auburn

first: Wellison

middle: J. S.

last: Diniz

state: Alabama

address: CASIC Building 559 Devall Drive Auburn University, 205

department: Animal Sciences

country: USA

institute: Auburn University

description: Library name: SC_2

library_source: transcriptomic

data_processing:
The quality control (QC) and read statistics of the raw sequencing data were verified using FastQC v0.11.9  and aggregated with MultiQC v1.12. The quality of the reads was evaluated based on parameters such as average read length, adapter content, over-represented sequences, and Phred sequence quality scores. Reads were mapped with the STAR aligner v2.7.5 to the Ensembl ARS-UCD 1.3 Bos taurus reference genome. The read quantification was performed using the STAR aligner with the -quantMode gene counts flag and annotation file from Ensembl (release 113). Read counts with zero or low count expression were filtered out using the filterByExpr function from edgeR v3.28.1. A principal component analysis (PCA) using the factoextra v1.0.7 R-package was performed for exploratory analysis. The DEGs were identified using DESeq2.
Matrix table with raw gene counts for every gene and every sample
Assembly: ARS-UCD1.3, Ensembl (release 113).
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample. TXT file
Supplementary files format and content: .TXT file

molecule: polyA RNA

organism: Bos taurus

source_name: liver

extract_protocol:
Total RNA isolation was carried out using Trizol in conjunction with an on-column DNase digestion step, as per the manufacturer’s guidelines.
Strand-specific libraries were then constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs®, Ipswich, MA, USA).

tag: tissue

value: liver

tag: treatment

value: S

tag: Sex

value: M


title: WT-7

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto St

department: Environmental and Occupational Health

institute: University of Pittsburgh

description: Library name: F2598

library_source: other

data_processing:
Noncoding RNA library data were aligned and quality checked by STAR (v 2.5.3a) and analyzed with COMPSRA (v 1.0.3) and DESeq2 (v 1.42.1). Selected gene targets were analyzed using TargetScanMouse 8.0.
Assembly: mm10
Supplementary files format and content: Excel spreadsheet containing ncRNA overall reads generated from Compsra COMPSRA (v 1.0.3)

molecule: other

organism: Mus musculus

source_name: plasma-derived EVs

extract_protocol:
pEVs were isolated from 200 µL plasma using the Total Exosome Isolation Kit (#4484450, Invitrogen, Vilnius, Lithuania) following manufacturer’s protocol. EV RNA was extracted using the ExoQuick Exosome RNA Purification Column Kit (EQ808A, SBI, CA).
Small ncRNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set (#E7560S, NEB, MA).

value: plasma-derived EVs

tag: genotype

value: WT


title: IND10, replicate 1, snATAC

city: San Francisco

first: Faranak

last: Fattahi

state: California

department: Cellular and Molecular Pharmacology

institute: University of California San Francisco

description:
Library name: Sample6-IND10-ATAC
10X Genomics Multiome

library_source: genomic single cell

data_processing:
Libraries were pooled and sequenced on an Illumina NovaSeq 6000. Reads were demultiplexed, alignened to the GRCh38 human genome, and quantiifed using CellRanger-ARC (v2.0.2).
The GRCh38 genome was modified to include CRE, GFP, BFP, and NGN2::LHX3 transcripts which were expressed in the FOXN4:Cre and PB-TetO-NGN2::LHX3 lines, respectively.
Assembly: human GRCh38
Supplementary files format and content: Processed data files consist of the fragements output of cellranger-arc counts. The fragments.tsv.gz files consist of BED-like format with each line represented a unique chormatin fragment. The fragments.tsv.gz.tbi file is a tabix index of the fragments.tsv.gz file.

molecule: genomic DNA

organism: Homo sapiens

source_name: PB-TetO-NGN2::LHX3 (WTC11)

extract_protocol:
Nuclei isolation followed the 10X Genomics Demonstrated Protocol GC00365 Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing. The Dnase treatment step was included and the lysis buffer was adjusted to 0.8x strength.
Library construction followed 10X Genomcis Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Protocol (CG000338 Rev E). Final libraries were quality-controlled on an Aligent 5200 Fragment Analyzer.

treatment_protocol: NEP progenitors were achieved by treating stem cells with dual SMAD inhibition in mTeSR Plus media for 5 days. NMP progenitors were differentiated by exchanging mTeSR Plus media for E6 for 24 hours, followed by the addition of 20 ng/mL bFGF for 24 hours, and finally 20 ng/mL bFGF, 3 uM CHIR99021, and 10 uM SB431542 for 48 hours. After NEP or NMP treatment, both populations were differentiated under identical conditions in neural induction media (DMEM:F12 supplemented with N2, NEAA, L-glut, and PenStrep at 1x concentration and 2 ug/mL heparin and 0.4 ug/mL ascorbic acid). For the first 48 hours after NEP or NMP treatment, NIM was supplemented with 10 ng/mL BDNF and 100 nM retinoic acid. This was followed by 12 days of NIM supplemented with 10 ng/mL BDNF, 1 uM DAPT, 100 nM retinoic acid, and 300 nM purmorphamine. At the final day 19 time point, neurons were dissociated with Accutase and cryopreserved in 50% media, 40% FBS, and 10% DMSO.

tag: cell line

value: PB-TetO-NGN2::LHX3 (WTC11)

tag: cell type

value: hPSC-derived neuron

value: IND


title: SC_17

description: Library name: SC_17

value: F


title: IND4, replicate 1, snATAC

description:
Library name: Sample5-IND4-ATAC
10X Genomics Multiome


title: E17 cortex multiomic data, snRNA-seq

country: Canada

description: Library name: E17 cortex RNA

source_name: Dorsal ventricular-subventricular zone and cortex

value: Embryonic day 17

value: Embryonic cortical cell types


title: SC_13

description: Library name: SC_13


title: WT-5

description: Library name: F2608


title: P2 SVZ n2 multiomic data, snATAC-seq

description: Library name: P2 SVZ n2 ATAC

value: Dorsal and lateral ventricular-subventricular zone


title: Mouse heart tissue, untreated, rep3

city: Skövde

first: Jane

last: Synnergren

address: Högskolevägen 1

country: Sweden

institute: University of Skövde

description:
P25704_103
Raw_gene_counts_matrix.tsv
TPM_matrix.tsv

data_processing:
Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.5/RTA v3.4.4) with a 151nt(Read1)-19nt(Index1)-10nt(Index2)-151nt(Read2) setup using 'NovaSeqXp' workflow in 'S4' mode flowcell.
The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite.
The quality scale used is Sanger / phred33 / Illumina 1.8+. Processing of FASTQ files was carried out by the SciLifeLab National Genomics Infrastructure at the Uppsala Multidisciplinary Center for Advanced Computational Science, Sweden.
The processed reads were then aligned to the reference genome of Mus musculus (build GRCm38) with the STAR aligner.
Read counts for genes were generated using the feature Counts library and normalized TPM values calculated with StringTie, and raw gene read counts were generated by Salmon.
Technical documentation on the RNA-seq pipeline can be accessed here: https://github.com/nf-core/rnaseq.
Assembly: Mus musculus (build GRCm38)
Supplementary files format and content: tab-separated text file with raw gene counts for every gene and every sample
Supplementary files format and content: tab-separated text file with transcript-per-million (TPM) values for every gene and every sample

molecule: total RNA

source_name: Heart

extract_protocol:
The mice were sacrificed 6h post injection, and the heart, liver and blood were collected. For the heart, the area of injection in the left ventricle was dissected and separated from the rest of the heart and snap-frozen. The remaining parts of the heart (remote left ventricle, right ventricle and atria) was snap-frozen in a second tube and referred to as remote non-injected area for further analysis. Total RNA were isolated using miRNeasy Mini Kit.
Library construction was performed using Takara SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian kit - V3, which is specifically designed for very low input total RNA samples

treatment_protocol: C57BL/6Ncrl mice at 10-12 weeks of age and weight of ~25 g purchased from Charles river. The mice were subjected to a left thoracotomy at the fourth intercostal space ~2 to 3 mm to the left of the sternum. A rib spreader was used to keep the incision open. The pericardium was opened, the heart was held using an USP 8-0 suture and 40 µL of EVs, LNPs, naked RNA or PBS (no mRNA) treatments were injected in one single site in the myocardium of the left ventricle using an insulin syringe

value: Heart

value: Untreated


title: WT-6

description: Library name: F2719


title: E. coli WCAD grown in a minimal medium at 24 h, replicate 1

city: Incheon

first: Hyungyu

last: Lim

address: Inha ro 100

country: South Korea

institute: Inha University

description: Library name: WT_1

data_processing:
Raw read data was processed by running a bacterial transcriptome profiling pipeline utilizing Bowtie2, summarizeOverlaps, and DEseq2 to obtain transcripts per million (TPM) values for each gene. A reference genome was created to include two heterologous genes (i.e., phlF and cad) based on the E. coli W chromosome and its two native plasmids obtained from GenBank.
Assembly: CP002185, CP002186, CP002187
Supplementary files format and content: csv

organism: Escherichia coli W

source_name: bacteria

growth_protocol: E. coli W single colonies of each strain were inoculated into 5 mL of medium in a 15 mL test tube. After 18 h of cultivation, the seed culture was re-inoculated into 150 mL of fresh medium in the 400-mL Erlenmeyer flasks at an optical density at 600 nm (OD600) of 0.05. In case of itaconate production, isopropyl-β-D-thiogalactopyranoside (IPTG) was added to the medium at 10 mM to induce the expression of cad. Cell cultivations were carried out in a shaker at 220 rpm and 30 °C. pH was monitored using an Orion™ 8103BN ROSS™ pH meter (Thermo Scientific) and 5 M HCl was added to maintain the pH below 7.0. All experiments were conducted in triplicate.

extract_protocol:
Cells were treated using the Qiagen RNA-protect bacterial reagent (Hilden, Germany) according to the instruction from the manufacturer. Pelleted cells were stored at -80oC, and after cell resuspension and partial lysis, they were ruptured with a beat beater. Subsequently, the total RNA was extracted using a Qiagen RNA purification kit. After total RNA extraction, ribosomal RNA was removed.
Prepared RNA libraries were prepard by using a TruSeq Stranded Total RNA kit (Illumina, San Diego, CA, USA) and were sequenced by using an Illumina NovaSeq X machine.

value: bacteria

value: W / pCAD


title: NMP, replicate 2, snATAC

description:
Library name: Sample4-FC-NMP-ATAC
10X Genomics Multiome

source_name: FOXN4:CRE (WTC11)

value: FOXN4:CRE (WTC11)

value: NMP


title: WT-7

description: Library name: F2598

source_name: brain

extract_protocol:
10 mg of frozen prefrontal cortex was dissociated in RLT buffer (#74106, Qiagen RNeasy Mini Kit, Germany) with 10% beta-mercaptoethanol and ncRNA was isolated using the Norgen MicroRNA Isolation Kit (#21300, Canada) according to manufacturer's protocol.
Small ncRNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set (#E7560S, NEB, MA).

value: brain


title: E17 cortex multiomic data, snATAC-seq

description: Library name: E17 cortex ATAC

value: Dorsal ventricular-subventricular zone and cortex


title: WT-4

description: Library name: G0813

value: plasma-derived EVs


title: SC_11

description: Library name: SC_11

value: liver

value: S

value: M


title: NMP, replicate 1, snATAC

description:
Library name: Sample3-WTC-NMP-ATAC
10X Genomics Multiome

value: hPSC-derived neuron


title: E14 cortex multiomic data, snRNA-seq

description: Library name: E14_cortex_RNA

value: Embryonic day 14


title: WT-4

description: Library name: G0813

value: WT


title: WT-3

description: Library name: A2796


title: NN_8

description: Library name: NN_8

value: N

value: F


title: WT-3

description: Library name: A2796


title: NN_6

description: Library name: NN_6


title: NEP, replicate 2, snATAC

description:
Library name: Sample2-FC-NEP-ATAC
10X Genomics Multiome

value: NEP


title: E14 cortex multiomic data, snATAC-seq

description: Library name: E14 cortex ATAC

value: Embryonic cortical cell types


title: WT-1

description: Library name: F2702


title: WT-2

description: Library name: G0698


title: 10 Day CON-BDEV 2

city: Atlanta

first: Samantha

middle: Reed

last: Lynn

state: GA

address: 615 Michael St

department: Department of Human Genetics

institute: Emory University

description: Library name: Sample 3

data_processing:
Small RNA-sequencing data was mapped to the mouse miRNA database with miRge 2.0
Differential expression analysis of miRNAs was performed by DESeq2 (FDR < 0.05)
Assembly: mm9
Supplementary files format and content: 10day_miRNA_RPM.csv file includes reads per million mapped reads for all samples
Supplementary files format and content: 10day_miRNA_Deseq2.cvs includes differential expression analysis comparing miRNA abundence in SE-BDEVs and CON-BDEVs

source_name: Brain-Derived Extracellular Vesicles

extract_protocol:
miRNeasy Micro Kit (Qiagen 21708) with DNase treatment (Qiagen 79254)
QIAseq miRNA Library Kit

value: Brain-Derived Extracellular Vesicles


title: NEP, replicate 1, snATAC

description:
Library name: Sample1-WTC-NEP-ATAC
10X Genomics Multiome


title: Tau-8

description: Library name: G0741


title: Liver portal messenchymal cells from WT 014

city: Paris

first: Wenrui

last: Gao

address: 27 rue Chaligny

country: France

institute: Centre de Recherche Saint Antoine

description: Library name: WT 014

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mouse mm10
Supplementary files format and content: h5 files containing features, barcodes and matrix

source_name: Liver

extract_protocol:
The bilio‐vascular tree is isolated from WT mouse liver by an enzyme digestion-based protocol. Liver is perfused with a mixture of collagenase in vivo and then explanted and further processed. A series of filter is then applied to collect portal tract cells. After cell isolation, we sort cells by FACS to collect lineage negative cells (gated as epithelial cell adhesion molecule Epcam-, CD31-, CD45-, CD11b- cells), to enrich mesenchymal cells.
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, messenchymal cells were resuspended in the master mix and loadedtogether with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an lumina R1 primer sequence, UniqueMolecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction lumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Liver

value: Messenchymal cells


title: NN_3

description: Library name: NN_3


title: Tau-7

description: Library name: G0742


title: WT-1

description: Library name: F2702


title: PSN-1_NC

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA61266

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101 base single-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the human reference genome sequences (hg19) using TopHat, version 2.1.1.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cuffdiff 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Tumor tissue of pancreas

extract_protocol:
Total RNA was isolated with miRNeasy Micro Kit (QIAGEN) according to the manufacturer’s instructions.
Sequencing libraries were constructed with the TruSeq stranded mRNA Library Prep kit (Illumina).

value: Tumor tissue of pancreas

value: epithelial cell line

value: negative control (scramble) oligonucleotide


title: Tau-8

description: Library name: G0741

value: plasma-derived EVs


title: Liver portal messenchymal cells from WT 007

description: Library name: WT 007


title: Tau-6

description: Library name: G0740

value: brain


title: NN_14

description: Library name: NN_14

value: liver


title: PSN-1_4800-3p_OE

description: Library name: GA61265


title: Batch2_KO5_plus6_tumor

city: Duarte

first: Zhen

last: Chen

state: CA

address: 1500 E Duarte Rd

department: DMRI

institute: City of Hope

description:
Library name: COHP_56501
Sequencing run was performed on the NovaSeq X Series platform with 10B reagent kit (300 Cycle). NovaSeq Control Software 1.2.0.28691 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

data_processing:
The demultiplexing, barcoding processing, gene counting and aggregation were made using CellRanger software 7.1.0.
Assembly: Mouse mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Briefly, the tumor was dissected from the mammary fat pad of the mouse after 21 days. The tumor was then minced in a collagenase-hyaluronidase in 5% FBS/DMEM (High glucose) and incubated at 37 C for 30 min at 200 RPM. Cells were washed and resuspended in cold DBPS and the supernatant was discarded after spinning. A 0.25% trypsin, EDGA, polyvinyl alcohol solution in DPBS was added and incubated for 1 min at 37 C in water bath. Samples were neutralized with 2% FBS/DPBS and Dispase solution was added and incubated for 5 min at 37C. ACK lysis solution was used and pellets were kept in cold 2% FBS.PBS and stored. Cell viability was assessed prior to sequencing.
Library was performed according to the manufacturer's instructions (single cell 3' v3 protocol, 10X genomics) using the 10XGenomics Chromium Controller.

treatment_protocol: Tumor

value: Tumor

value: KO

tag: batch


title: NN_10

description: Library name: NN_10


title: HL-60 cells, CD68 OE1

city: Gent

first: Laurens

last: Van Camp

address: C. Heymanslaan 10

country: Belgium

institute: Ghent University

description:
Library name: Sample 6
Column name in processed_data_OE_CD68.xlsx:  OE1

data_processing:
R, DEseq2 package
Assembly: NCBI hg38
Supplementary files format and content: csv files include RPKM values for each sample

growth_protocol: cell culture according to standard guidelines

extract_protocol:
To overexpress CD68, a constitutive Lenti-hCMV-ORF-P2A-eGFP-IRES-Puromycin vector was used with an empty lentiviral open reading frame vector as a control, both provided as a bacterial glycerol stocks (Transomic). For the knockdown models, three shERWOOD UltramiR short hairpin RNA targeting CD68, and one non-targeting shRNA (NTC), were purchased as glycerol stocks at Transomic (TLHSU1452). The OE and KD vector backbones allowed for selection of retroviral integration based on GFP and mCherry fluorescent expression, respectively, and puromycin-enriched medium. Plasmid DNA (pDNA) was extracted from bacterial cultures started from the glycerol stock of the constructs using a DNA Midiprep extraction kit (Qiagen) following manufacturer’s guidelines. The pDNA concentrations were measured by Nanodrop (ThermoFisher Scientific BVBA, Merelbeke, Belgium) and DNA quality cutoff values were set at a 260/230 ratio of 1.80 and a 280/230 ratio of 2. HEK293T cells were transfected using JetPEI reagens (Polyplus transfection, Illkirch, France) and the following plasmids: KD or OE vector (3µg), a pCMV-VSV-G envelope (0.3µg), and the packaging vector p8.91 (2.7µg) in 250µL NaCl. The third day after transfection, virus was harvested and concentrated by adding PEG-it virus precipitation solution (Sanbio) and centrifugating the mix after >12h of incubation at 4°C. Concentrated virus was aliquoted and stored at −80 °C. Leukemic cells were spin-infected in a centrifuge at 32° for 90 min at 2300 rpm and puromycin selection (0.5 µg/mL) was initiated 24 hours after transduction. After incubation with puromycin selection of 48h, transduction efficacy was measured through GFP or mCherry fluorescence by flow cytometry (BD Lyrica), using the parental non-transduced cell lines (HL-60 and THP-1) as a control. Puromycin selection was continued in case the transduction efficacy was less than 95%.
Total RNA of the CD68 OE HL-60 cell line (HL-60CD68 OE) and an empty vector control HL-60 cell line (HL-60mock) as well as the CD68 KD THP1 cell line (THP-1CD68 KD) the NTC THP-1 cell line (THP-1NTC) were checked for purity and integrity on a electrophoresis gel. RNA sequencing was done in triplicate for every cell line by Eurofins (Eurofins Genomics, Ebersberg, Germany).

treatment_protocol: lentiviral transduction

value: myeloid cells

value: CD68 OE


title: CON-BDEV 3

description: Library name: Sample E

data_processing:
Small RNA-sequencing data was mapped to the mouse miRNA database with miRge 2.0
Differential expression analysis of miRNAs was performed by DESeq2 (FDR < 0.05)
Assembly: mm9
Supplementary files format and content: 24hr_miRNA_RPM.csv file includes reads per million mapped reads for all samples
Supplementary files format and content: 24hr_miRNA_Deseq2.cvs includes differential expression analysis comparing miRNA abundence in SE-BDEVs and CON-BDEVs


title: Tau-7

description: Library name: G0742


title: MIAPaCa-2_NC

description: Library name: GA60928

value: MIA PaCa-2


title: Batch2_KO4_tumor

description:
Library name: COHP_56500
Sequencing run was performed on the NovaSeq X Series platform with 10B reagent kit (300 Cycle). NovaSeq Control Software 1.2.0.28691 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.


title: NC_7

description: Library name: NC_7

value: N

value: F


title: Tau-6

description: Library name: G0740


title: NC_5

description: Library name: NC_5

value: M


title: MIAPaCa-2_4800-3p_OE

description: Library name: GA60927


title: Tau-5

description: Library name: G0722


title: Batch2_KO2_plus3_tumor

description:
Library name: COHP_56499
Sequencing run was performed on the NovaSeq X Series platform with 10B reagent kit (300 Cycle). NovaSeq Control Software 1.2.0.28691 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.


title: IND10, replicate 1, snRNA

description:
Library name: Sample6-IND10-RNA
10X Genomics Multiome

data_processing:
Libraries were pooled and sequenced on an Illumina NovaSeq 6000. Reads were demultiplexed, alignened to the GRCh38 human genome, and quantiifed using CellRanger-ARC (v2.0.2).
The GRCh38 genome was modified to include CRE, GFP, BFP, and NGN2::LHX3 transcripts which were expressed in the FOXN4:Cre and PB-TetO-NGN2::LHX3 lines, respectively.
Assembly: human GRCh38
Supplementary files format and content: Processed data files consist of the raw feature, barcode, and matrix files ouput by running cellranger-arc count.

value: PB-TetO-NGN2::LHX3 (WTC11)

value: hPSC-derived neuron

value: IND


title: Tau-4

description: Library name: G0522


title: Batch2_KO1_tumor

description:
Library name: COHP_56498
Sequencing run was performed on the NovaSeq X Series platform with 10B reagent kit (300 Cycle). NovaSeq Control Software 1.2.0.28691 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.


title: NC_20

description: Library name: NC_20


title: IND4, replicate 1, snRNA

description:
Library name: Sample5-IND4-RNA
10X Genomics Multiome


title: Tau-3

description: Library name: G0725


title: NC_19

description: Library name: NC_19


title: Batch2_WT5_tumor

description:
Library name: COHP_56497
Sequencing run was performed on the NovaSeq X Series platform with 10B reagent kit (300 Cycle). NovaSeq Control Software 1.2.0.28691 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: WT


title: NMP, replicate 2, snRNA

description:
Library name: Sample4-FC-NMP-RNA
10X Genomics Multiome

source_name: FOXN4:Cre (WTC11)

value: FOXN4:Cre (WTC11)

value: NMP


title: Batch2_WT4_tumor

description:
Library name: COHP_56496
Sequencing run was performed on the NovaSeq X Series platform with 10B reagent kit (300 Cycle). NovaSeq Control Software 1.2.0.28691 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.


title: NC_16

description: Library name: NC_16


title: THP-1 cells, NTC2

description:
Library name: Sample 4
Column name in processed_data_KD_CD68.xlsx:  NTC2

value: non targetable control


title: Tau-2

description: Library name: G0712

value: plasma-derived EVs


title: Lung of OVA-induced  Rab44-KO mice

city: Nagasaki

first: Takayuki

last: Tsukuba

state: Nagasaki

address: 1-7-1 Sakamoto

department: Dental Pharmacology

institute: Nagasaki University

description: Library name: Ind_KO

data_processing:
RNA-seq libraries were prepared following the manufacturer’s protocol and sequenced on an Illumina NovaSeq X Plus platform to generate 150-bp paired-end reads.
Raw sequencing reads were subjected to quality control and trimming, and the processed reads were aligned to the mouse reference genome (GRCm38) using the HISAT2 software.
The gene expression levels were quantified using Feature Counts software.
Differentially expressed gene (DEG) analysis was performed using DESeq2, and genes with an adjusted p-value < 0.05 were considered significantly differentially expressed.
Supplementary files format and content: raw_counts.txt, normalized_counts.txt, DEG_results.xlsx
Supplementary files format and content: csv files includes FPKM and TPM

source_name: lung

extract_protocol:
Total RNA was isolated from the lungs of normal and OVA-induced WT and KO mice 21 days after OVA-treatment.
RNA was extracted using the NEBNext Ultra II Directional RNA Library Prep Kit(New England Biolabs) according to the manufacturer’s instructions.

treatment_protocol: Wild type (WT) and Rab44-knockout (KO) mice were intraperitoneally injected with ovalbumin (OVA) and aluminum hydroxide (alum) (100 μg) on days 0, 7, and 14; subsequently they were intranasally challenged with 50 μL OVA (100 μg) or 50 μL PBS for 4 days.

value: lung

value: Rab44 KO

value: OVA-induction


title: Batch2_WT3_tumor

description:
Library name: COHP_56495
Sequencing run was performed on the NovaSeq X Series platform with 10B reagent kit (300 Cycle). NovaSeq Control Software 1.2.0.28691 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.

value: Tumor


title: NMP, replicate 1, snRNA

description:
Library name: Sample3-WTC-NMP-RNA
10X Genomics Multiome


title: Tau-1

description: Library name: G0720


title: NEP, replicate 2, snRNA

description:
Library name: Sample2-FC-NEP-RNA
10X Genomics Multiome

value: NEP


title: Lung of  OVA-induced  WT mice

description: Library name: Ind_Wt


title: WT-8

description: Library name: A2536_BmRNA_S16

data_processing:
Rsubread (v2.16.1)
edgeR (v4.0.16)
Assembly: mm10
Supplementary files format and content: normalized CPM matrix

extract_protocol:
10 mg of frozen prefrontal cortex was dissociated in RLT buffer (#74106, Qiagen RNeasy Mini Kit, Germany) with 10% beta-mercaptoethanol and mRNA was isolated using the Norgen MicroRNA Isolation Kit (#21300, Canada) according to manufacturer's protocol.
mRNA libraries were generated using the SMART-Seq mRNA Kit (#634773, Takara, CA) combined with the Nextera XT DNA Library Preparation Kit (#FC-131-1096, Illumina, CA) and Illumina DNA/RNA UD Indexes Set A (#20091654, Illumina, CA).

value: brain


title: Batch2_WT1_tumor

description:
Library name: COHP_56493
Sequencing run was performed on the NovaSeq X Series platform with 10B reagent kit (300 Cycle). NovaSeq Control Software 1.2.0.28691 was used for sequencing and Illumina BCL Convert v3.9.3 to convert base call (BCL) files into FASTQ files.


title: NEP, replicate 1, snRNA

description:
Library name: Sample1-WTC-NEP-RNA
10X Genomics Multiome


title: CCL4

city: Wenzhou

first: Weiwei

last: Zhu

address: Wenzhou Medical University, University Town, Chashan

country: China

institute: Wenzhou Medical University

description:
Library name: Sample 3
10X Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics official pipeline Cell Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) for quality filtering, genome alignment, transcript quantification, and cell barcode identification, resulting in a gene expression matrix for each cell. Subsequent analyses, including further cell filtering, normalization of gene expression, cell clustering, differential gene expression analysis, and marker gene identification, were performed using the Seurat package (https://satijalab.org/seurat/).
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Primary isolated hepatic cell

extract_protocol:
Primary hepatocytes and non-parenchymal liver cells were isolated using a two-step in situ perfusion method. Briefly, mice were anesthetized and subjected to portal vein cannulation for liver perfusion. The liver was first perfused with pre-warmed (37°C) calcium-free HBSS containing 0.5 mM EGTA for 5 minutes to disrupt tight junctions, followed by perfusion with HBSS containing 0.05–0.1% collagenase IV and 5 mM CaCl₂ for 10–12 minutes until the liver became visibly swollen and soft. The liver was then excised, minced, and filtered through 100 μm and 70 μm strainers. The cell suspension was centrifuged at 50 × g for 3 minutes at 4°C to pellet hepatocytes. The supernatant, containing non-parenchymal cells (NPCs), was collected and further purified by 40% Percoll density gradient centrifugation at 800 × g for 20 minutes without brake. Isolated cells were kept on ice throughout the procedure unless otherwise indicated, and viability was assessed by trypan blue exclusion. After cell counting, hepatocytes and non-parenchymal cells were mixed at a 1:1 ratio to generate a final cell suspension, which was used for single-cell RNA-seq library construction and sequencing.
Single-cell RNA-seq libraries were generated using the 10x Genomics Chromium Next GEM Single Cell 3’ Kit v3.1. Cell suspensions (700–1200 cells/μL), barcoded gel beads, and partitioning oil were loaded into separate lanes of a Chromium Chip G to form Gel Beads-in-Emulsions (GEMs). Most GEMs contained either no cell or a single cell. Inside each GEM, gel beads dissolved, releasing barcoded oligos for reverse transcription of mRNA from lysed cells. After GEMs were broken, cDNA was amplified, purified, and used for library construction, including fragmentation, end-repair, A-tailing, adaptor ligation, and PCR enrichment. The final library contained a 16 bp cell barcode, 12 bp UMI, and cDNA insert flanked by Illumina adapters. Sequencing was performed using paired-end reads (Read 1: 28 bp for barcode and UMI; Read 2: 91 bp for transcript information) on an Illumina platform.

value: Liver

value: Primary isolated hepatic cell

value: wild-type


title: Lung of control Rab44- KO mice

description: Library name: Cont_KO

value: No treatment


title: WT-7

description: Library name: F2598_BmRNA_S15


title: R10

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description: Library name: R10

library_source: genomic

data_processing:
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated using a copy number aware UMI deduplicator. Pipeline available at https://github.com/laurabiggins/TrAEL-seq Samples were imported into Seqmonk v1.49.1, truncated to a single base, then quantified either as total read count or as strand bias (R-F)/(R+F) equivalent to RFD. Assembly: GRCm38
Assembly: GRCh38
Supplementary files format and content: Replication Fork Direction and was calculated in 20KB windows spaced 10kb

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with GlutaMAX (Gibco, 61870-010), 10% fetal bovine serum (Gibco, A5256701), and 100 IU/mL penicillin–streptomycin (Sigma-Aldrich, P4333-100ML). Cells were maintained at 37°C in a humidified incubator with 5% CO₂ and passaged at 70–80% confluence using 0.25% trypsin–EDTA (Gibco, 25200056). Cells were thawed from authenticated master stocks and used within 10–12 passages. Mycoplasma contamination was excluded by routine PCR-based testing. All experiments were performed using cells in logarithmic growth phase unless otherwise stated

extract_protocol:
1-2x10^6 cells were washed once in 5 ml L buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl) and resuspended in 60 µl L buffer in a 2 ml tube. Samples were heated to 50°C for 2-3 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl digestion buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl, 1% sodium N-lauroyl sarcosine, 0.1 mg/ml Proteinase K) and incubated overnight at 50°. Plugs were washed three times with 1 ml TE for 1-2 hours at room temperature with rocking, 10 mM PMSF was added to the second and third washes from 100 mM stock (Merck 93482). Plugs were then digested 1 h at 37°C with 1 µl 1000 U/ml RNase T1 (Thermo EN0541) in 200 µl TE. ½ an agarose plug of cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µl multiplexed TrAEL-seq adaptor 1 ([App]YYYYNNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUAGCA/iBiodT/TGCUACACTCTTTCCCTACACGACGCTCTTCCG) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs were pooled, equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added per plug. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl per plug β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol per plug and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2µl 10 mM dNTPs and 1µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined. An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA chip (Agilent 5067-4626). Ideal cycle number should bring final library to final concentration of 1-3 nM, noting that the final library will be 3 cycles more concentrated than the test anyway. 21 µl of library was then amplified with 2 µl each of NEBNext Universal and chosen Index primer and 25 µl NEBNext Ultra II Q5 PCR master mix using same conditions as above for calculated cycle number. Amplified library was cleaned with 40 µl AMPure XP beads (Beckman A63881) and eluted with 26 µl 0.1x TE, then 25 µl of this was again purified with 20µl AMPure XP beads and eluted with 11µl 0.1x TE.

treatment_protocol: Cells were continuously exposed to 500 nM osimertinib dissolved in DMSO for up to 28 days. Media containing drug or vehicle was replaced every 3–4 days. Final DMSO concentration did not exceed 0.1% (v/v).

value: NSCLC

value: Maintained in 500 nm osimertinib


title: HFD

description:
Library name: Sample 2
10X Genomics


title: Lung of contorl  WT mice

description: Library name: Cont_Wt

value: WT


title: R5

description: Library name: R5


title: WT-5

description: Library name: F2608_BmRNA_S13


title: CON

description:
Library name: Sample 1
10X Genomics


title: Mulitome, SCNT, E14.5, rep2, ATAC

city: Shanghai

first: Shanshan

last: Yi

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: College of Life Science and Technology

institute: Tongji University

description:
Library name: SCNT145-2_ATAC
10x Genomics Multiome ATAC: Read1 contains ATAC sequences; Read2 contains cell barcode; Read3 contains ATAC sequences

data_processing:
The 10X Genomics CellRanger-ARC (v2.0.2) pipeline were used to process multiome data. The raw fastq files of RNA-seq and ATAC-seq libraries from the sample were aligned to UCSC mouse genome (mm10) and quantified using 'cellranger-arc count'.
Assembly: mm10
Supplementary files format and content: h5 file: contains both RNA-seq counts and ATAC-seq counts; tsv.gz: fragments file for ATAC-seq; tsv.gz.tbi: fragment file index for ATAC-seq

source_name: placenta

growth_protocol: For natural fertilization, female C57BL/6n mice were mated with male PWK/PhJ mice, followed by placental tissue collection at specified developmental stages. For nuclear transfer, cumulus cells from BPF1 (female C57BL/6n×male PWK/PhJ) female mice were injected into enucleated oocytes. The reconstructed oocytes were then incubated in CZB medium for 1 h before activation. Activation was performed by incubation in Ca2+-free CZB medium containing 1 mM SrCl2 and 5 mg/mL CB for 6 h, and then the oocytes were thoroughly washed and cultured in G-1 PLUS medium (Vitrolife) at 37℃ under 5% CO2. The SCNT embryos were transplanted into the uterus of pseudopregnant recipients at the stage of 2-cell development, and the samples were collected at the appropriate day.

extract_protocol:
Placental samples were collected from SCNT and naturally fertilized pregnant mice. Pregnant ICR mice at E12.5, E14.5 and E18.5 were humanely sacrificed and their placenta were dissected. Placentas were washed with PBS to remove blood and blotted dry with absorbent paper. The treated placentas were snap-frozen in liquid nitrogen and stored to a liquid nitrogen tank. Placental tissue was thoroughly washed in ice-cold PBS to eliminate blood contaminants and precisely weighed (2-3 g). The tissue was then carefully minced into ~1 mm³ fragments using sterile scissors before enzymatic digestion in pre-warmed DMEM/F12 medium (Gibco) containing 0.5 mg/mL collagenase IV (Thermo Fisher Scientific, 17104019) and 0.2 mg/mL DNase I (Roche 10104159001). The digestion was performed at 37°C for 20 minutes in a shaking water bath with gentle manual inversion every 10 minutes.
Libraries were constructed by following the 10X Genomics Chromiun Next GEM Sing Cell Multiome ATAC + Gene Expression protocol (CG000338).

treatment_protocol: Small molecule treatments were performed with 50nM Farrerol for 16h starting after activation.

value: placenta

tag: developmental stage

value: embryonic day (E) 14.5

tag: group

value: Somatic cell nuclear transfer

tag: strain

value: C57BL/6n x PWK/PhJ

tag: library type

value: ATAC


title: WT-6

description: Library name: F2719_BmRNA_S14


title: Tau-1

description: Library name: G0720


title: D28 R4

description: Library name: D28 R4

value: 7 days 500 nM osimertinib


title: Mulitome, SCNT, E14.5, rep2, GEX

description:
Library name: SCNT145-2_GEX
10x Genomics Multiome GEX: Read1 contains cell barcode and UMI; Read2 contains transcript sequences

value: mRNA


title: WT S. aureus, 100μM Copper cholride, bio rep 3

city: Leicester

first: Sean

middle: Cathal

last: Brennan

address: Univeristy Road

department: Division of Microbiology and Infection

institute: University of LEicester

description: Library name: WTCHG_724336_71315203

data_processing:
RNA integrity was assessed using an Agilent 2100 Bioanalyzer and samples with RIN ≥9 were used for library preparation. Library preparation and sequencing were performed by the Oxford Genomics Centre. Libraries were sequenced on an Illumina NovaSeq 6000 platform to a depth of approximately 20 million paired-end reads per sample following ribosomal RNA depletion. Raw reads were assessed using FastQC. Adapter trimming was performed using Trimmomatic v0.36. Reads were aligned to the Staphylococcus aureus USA300 FPR3757 reference genome (NC_007793.1) using HISAT2 v2.1.0. Transcript assembly and quantification were performed using StringTie v1.3.3b. Differential expression analysis was conducted using DESeq2 in R.
Quality control performed using FastQC
Adapter trimming performed using Trimmomatic v0.36
Alignment performed using HISAT2 v2.1.0 against NC_007793.1
Transcript quantification performed using StringTie v1.3.3b.
Assembly: S. aureus USA300 FPR3757  reference genome (accession no. NC_007793.1)
Supplementary files format and content: CSV file containing raw gene counts for all samples used for differnetial expression analysis

organism: Staphylococcus aureus

source_name: Staphylococcus aureus USA300 JE2 wild-type

growth_protocol: RNAseq profiling of S. aureus USA300 JE2 wild-type and copL copper resistance lipoprotein mutant. Overnight cultures of S. aureus WT and copL strains were grown in RPMI-A for 16 hours at 37 °C in 5 % CO2. To collect and extract RNA, the bacteria were subcultured into fresh pre-warmed RPMI-A and grown to mid-exponential phase in the presence or absence of 100μM CuCl2. RNA was stabilised using RNAprotect Bacteria Reagent (Qiagen; 76104) according to the manufacturer’s instructions and were stored at -80°C.

extract_protocol:
Cells were lysed in 200µL TE buffer (10 mM TRIS-HCL pH 7.5, 10 mM EDTA) containing lysostaphin (10mg/mL; Sigma-Aldrich; L7386) for 30 min at 37 °C, followed by 10 µL of proteinase K treatment (10 mg/mL; Sigma-Aldrich; 1245680500) for 10 minutes. Lysates were transferred to Lysing Matrix B tubes (MP Biomedicals; 1169110-CF) and were homogenised in 600 µL of TRIzol reagent (Invitrogen; 15596026), using a FastPrep Instrument at 5m/s for 20 seconds. RNA was purified using an RNeasy Mini Kit (Qiagen; 74106), including an on-column DNase digestion and a subsequent Turbo DNA-free treatment (Invitrogen; AM1907).
Ribosomal RNA was depleted using the NEBNext Bacterial rRNA Depletion Kit v2. Libraries were prepared using a strand-specific protocol in which second-strand cDNA synthesis incorporated dUTP. cDNA was end repaired, A-tailed, and adapter ligated. Uracil digestion was performed prior to library amplification to preserve strand specificity. Libraries were size selected, multiplexed, quality assessed, and sequenced as paired-end reads on an Illumina NovaSeq 6000 platform.

value: 100μM Copper cholride


title: WT-3

description: Library name: A2796_BmRNA_S7


title: D28 R3

description: Library name: D28 R3


title: copL mutant 100𝝻M copper chloride, bio rep 3

description: Library name: WTCHG_724336_71325204

source_name: Staphylococcus aureus USA300 JE2 copL mutant


title: WT-4

description: Library name: G0813_BmRNA_S8


title: copL mutant 0𝝻M copper chloride, bio rep 3

description: Library name: WTCHG_724336_71305202

value: Staphylococcus aureus USA300 JE2 copL mutant

value: 0μM Copper cholride


title: D0 R3

description: Library name: D0 R3

value: Untreated


title: Mulitome, WT, E14.5, rep2, ATAC

description:
Library name: WT145-2_ATAC
10x Genomics Multiome ATAC: Read1 contains ATAC sequences; Read2 contains cell barcode; Read3 contains ATAC sequences

value: Naturally fertilized


title: SC_4

description: Library name: SC_4

data_processing:
The quality control (QC) and read statistics of the raw sequencing data were verified using FastQC v0.11.9  and aggregated with MultiQC v1.12. The quality of the reads was evaluated based on parameters such as average read length, adapter content, over-represented sequences, and Phred sequence quality scores. Reads were mapped with the STAR aligner v2.7.5 to the Ensembl ARS-UCD 1.3 Bos taurus reference genome. The read quantification was performed using the STAR aligner with the -quantMode gene counts flag and annotation file from Ensembl (release 113). Read counts with zero or low count expression were filtered out using the filterByExpr function from edgeR v3.28.1. A principal component analysis (PCA) using the factoextra v1.0.7 R-package was performed for exploratory analysis. The DEGs were identified using DESeq2.
Matrix table with raw gene counts for every gene and every sample
Assembly: ARS-UCD1.3, Ensembl (release 113).
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample. TXT file
Supplementary files format and content: .TXT file

source_name: liver

extract_protocol:
Total RNA isolation was carried out using Trizol in conjunction with an on-column DNase digestion step, as per the manufacturer’s guidelines.
Strand-specific libraries were then constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs®, Ipswich, MA, USA).

value: liver

value: S

value: M


title: WT-2

description: Library name: G0698_BmRNA_S6

value: brain


title: WT S. aureus, 0μM Copper cholride, bio rep 3

description: Library name: WTCHG_724336_71295201

value: Staphylococcus aureus USA300 JE2 wild-type


title: Mulitome, WT, E14.5, rep2, GEX

description:
Library name: WT145-2_GEX
10x Genomics Multiome GEX: Read1 contains cell barcode and UMI; Read2 contains transcript sequences

value: placenta


title: Day 28 S clone 1

description: Library name: Day 28 S clone 1

data_processing:
Trimmed reads were aligned with HISAT2 (v2.1.0). Gene-level counts preformed in SeqMonk (v1.48.1) were imported into DESeq2 for differential expression analysis (Benjamini–Hochberg FDR < 0.05). Principal component analysis confirmed replicate clustering by condition. Gene ontology enrichment was performed using Gorilla (41).
Assembly: GRCh38
Supplementary files format and content: Reads on opposite strand to gene annotations were quantified and datasets size factor normalised.

growth_protocol: PC9 cells were engineered to stably express the FUCCI4 reporter (Addgene #83841) containing mKO2-CDT1 or Clover-GMNN marker proteins. Cells were cultured in RPMI-1640 medium supplemented with GlutaMAX (Gibco, 61870-010), 10% fetal bovine serum (Gibco, A5256701), and 100 IU/mL penicillin–streptomycin (Sigma-Aldrich, P4333-100ML). Cells were maintained at 37°C in a humidified incubator with 5% CO₂ and passaged at 70–80% confluence using 0.25% trypsin–EDTA (Gibco, 25200056). Cells were thawed from authenticated master stocks and used within 10–12 passages. Mycoplasma contamination was excluded by routine PCR-based testing. All experiments were performed using cells in logarithmic growth phase unless otherwise stated

extract_protocol:
Cells were fixed with glyoxal as described to preserve RNA integrity during sorting (39). Following fixation cells were saponin-permeabilized and using FACS were sorted into G1, S, and G2 populations. Cells were first gated based on DAPI content, followed by refinement using mKO2-CDT1 and Clover-GMNN marker expression, and were collected directly into TRI Reagent for RNA extraction. Total RNA was extracted using TRI Reagent (Sigma, T9424) followed by organic phase separation and isopropanol precipitation. RNA purity was assessed by spectrophotometry.
Poly(A)+ RNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S). Strand-specific libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760S). Libraries were amplified for 10–18 PCR cycles based on test amplifications carried out on a small portion of the sample. Following AMPure XP bead purification, libraries were quality assessed by Agilent Bioanalyzer, quantified by KAPA Library Quantification Kit. Sequencing was performed (75 bp single-end) to an average depth of ~24 million reads per sample.

treatment_protocol: Cells were continuously exposed to 500 nM osimertinib dissolved in DMSO for 28 days. Media containing drug or vehicle was replaced every 3–4 days. Final DMSO concentration did not exceed 0.1% (v/v).

value: NSCLC

value: 500nM Osimertinib

tag: time point

value: Day 28 S


title: Vehicle liposomes

city: suzhou

first: Yan

last: Lei

address: No. 199, Ren'ai Road

institute: soochow university

description:
Library name: Sample2
P15.5 dental tissue single-cell suspension, vehicle liposome treated

data_processing:
10X Genomics Cell Ranger software (version 3.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification. Briefly, reads with low-quality barcodes and UMIs were filtered out and then mapped to the reference genome. Reads uniquely mapped to the transcriptome and intersecting an exon at least 50% were considered for UMI counting. Before quantification, the UMI sequences would be corrected for sequencing errors, and valid barcodes were identified based on the EmptyDrops method.The cell by gene matrices were produced via UMI counting and cell barcodes calling. The cell by gene matrices for each sample were individually imported to Seurat version 3.1.1 for downstream analysis. Cells with unusually high number of UMIs (≥92000) or mitochondrial gene percent (≥10%) were filtered out. We also excluded cells with less than 500 or more than 2900 genes detected. Additionally, doublet GEMs also should be filtered out. It was achieved by using the tool Doublet Finder (v2.0.3) by the generation of artificial doublets, using the PC distance to find each cell’s proportion of artificial k nearest neighbors (pANN) and ranking them according to the expected number of doublets. After removing unwanted cells from the dataset, we employed a global-scaling normalization method “LogNormalize” that normalizes the gene expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000 by default), and log-transforms the results. The formula is shown as follows: A gene expression level= log (1+UMIA/UMITotal ×10000).
Assembly: GRCm39 (mm39)
Supplementary files format and content: Processed data files consist of filtered gene-barcode count matrices generated by Cell Ranger. The data are provided in Matrix Market format (.mtx) along with accompanying gene annotation (genes.tsv) and cell barcode (barcodes.tsv) files.

source_name: Dental tissues

extract_protocol:
To obtain single-cell transcriptomes, first mandibular molars and its surrounding tissues at PN15.5 were digested with 4 mg/mL Dispase (Roche) and 2 mg/mL Collagenase I (Gibco) at 37°C for 30 minutes on a thermomixer (Eppendorf). The resulting cell suspension was filtered through a 40 μm strainer (Corning, 352350) and centrifuged at 400 g for 5 minutes. Cell viability and counts were assessed using an automated cell counter.
R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A tailing, Adaptor Ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification.

value: Dental tissues

value: Primary tissue

value: Mixed cells

value: Vehicle liposome injection


title: Day 28 G2 clone 1

description: Library name: Day 28 G2 clone 1

value: Day 28 G2


title: copL mutant 100𝝻M copper chloride, bio rep 2

description: Library name: WTCHG_724336_71285200

value: Staphylococcus aureus USA300 JE2 copL mutant

value: 100μM Copper cholride


title: Clodronate liposomes

description:
Library name: Sample1
P15.5 dental tissue single-cell suspension, clodronate liposome treated

value: Clodronate liposome injection


title: Day 28 G1 clone 7

description: Library name: Day 28 G1 clone 7

value: Day 28 G1


title: Tau-7

description: Library name: G0742_BmRNA_S11


title: copL mutant 0𝝻M copper chloride, bio rep 2

description: Library name: WTCHG_724336_71265198

value: 0μM Copper cholride


title: WT S. aureus, 100μM Copper cholride, bio rep 2

description: Library name: WTCHG_724336_71275199


title: Tau-8

description: Library name: G0741_BmRNA_S12


title: Tau-6

description: Library name: G0740_BmRNA_S10


title: Day 0 G2 clone 1

description: Library name: Day 0 G2 clone 1

value: untreated

value: Day 0 G2


title: Tau-5

description: Library name: G0722_BmRNA_S9

value: brain


title: PPARr2 K382R expressing mouse scWAT SVF cell line, day 2 post differentiation, biol rep1

city: Kumamoto

first: Tomonori

last: Tsuyama

state: Kumamoto

address: 1-1-1, Honjo Chuo-ku

department: Faculty of Life Sciences

institute: Kumamoto university

description: Library name: KR1

data_processing:
Reads were trimmed for Illumina adaptors with TrimGaloreand then mapped to GRCm39 with HISAT2. Gene assembly and quantification were performed with Stringtie.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file containing TPM value for each samples

source_name: mouse scWAT SVF cell line

growth_protocol: Mouse scWAT SVF cell lines were maintained in Dulbecco's Modified Eagles Medium (DMEM; high Glucose with L-glutamine, Phenol red and without sodium pyruvate) supplemented with 10% FBS and 100 U/mL penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37 degrees Celsius.

extract_protocol:
RNA was extracted with the RNeasy Micro Kit (74004, QIAGEN) according to the manufacturer’s instructions.
Sequencing libraries were prepared with a NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs)

treatment_protocol: For differentiation into beige adipocytes, cells grown to 90-95% confluence (day 0) were exposed to induction medium (complete medium containing 500 μM isobutylmethylxanthine (Sigma-Aldrich), 125 μM indomethacin (Sigma-Aldrich), 2 μg/mL dexamethasone (Sigma-Aldrich), 5 μg/mL insulin (Fujifilm Wako Pure Chemical Corp.), 1 nM T3 (Sigma-Aldrich), and 0.5 μM rosiglitazone (Sigma-Aldrich).

value: mouse scWAT SVF cell line

value: stromal vascular fraction

value: PPARr2 K382R

value: Beige adipogenic differentiation


title: Day 0 S clone 7

description: Library name: Day 0 S clone 7

value: NSCLC

value: Day 0 S


title: copL mutant 100𝝻M copper chloride, bio rep 1

description: Library name: WTCHG_724336_71245196


title: PPARr2 K382R expressing mouse scWAT SVF cell line, day 2 post differentiation, biol rep2

description: Library name: KR2


title: PPARr2 K382Q expressing mouse scWAT SVF cell line, day 2 post differentiation, biol rep3

description: Library name: KQ3

value: PPARr2 K382Q


title: Tau-4

description: Library name: G0522_BmRNA_S4


title: WT S. aureus, 100μM Copper cholride, bio rep 1

description: Library name: WTCHG_724336_71235195

value: Staphylococcus aureus USA300 JE2 wild-type


title: Day 0 S clone 1

description: Library name: Day 0 S clone 1


title: Day 0 G1 clone 7

description: Library name: Day 0 G1 clone 7

value: Day 0 G1


title: PPARr2 K382Q expressing mouse scWAT SVF cell line, day 2 post differentiation, biol rep2

description: Library name: KQ2


title: PPARr2 K382Q expressing mouse scWAT SVF cell line, day 2 post differentiation, biol rep1

description: Library name: KQ1


title: copL mutant 0𝝻M copper chloride, bio rep 1

description: Library name: WTCHG_724336_71225194

value: Staphylococcus aureus USA300 JE2 copL mutant


title: Tau-3

description: Library name: G0725_BmRNA_S3


title: Tau-1

description: Library name: G0720_BmRNA_S1


title: Day 0 G1 clone 1

description: Library name: Day 0 G1 clone 1


title: Tau-2

description: Library name: G0712_BmRNA_S2


title: WT S. aureus, 0μM Copper cholride, bio rep 1

description: Library name: WTCHG_724336_71215193


title: elav[WDd]_rep3

city: New York

first: David

middle: W. J.

last: McQuarrie

state: NY

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medicine, Cornell University

description: Library name: Sample12

data_processing:
Sequencing quality was assessed using a standard quality-control pipeline. Adapter sequences were removed with Trim Galore (v0.6.7), and reads were aligned to the D. melanogaster dm6 reference genome using STAR (v2.7.11a). Gene-level counts were generated with FeatureCounts (v2.0.8) and used for differential gene expression analysis with DESeq2 (v1.40.2) under default parameters.
Assembly: dm6
Supplementary files format and content: tab-delimited text file with counts for each sample replicate

organism: Drosophila melanogaster

source_name: Embryo

extract_protocol:
RNA was extracted with Trizol followed by phenol chloroform extraction.
mRNA was enriched from total RNA by poly(A) selection. Sequencing libraries were constructed by Novogene (UK) Company Limited using their standard Illumina-compatible mRNA library preparation protocol (Plant and Animal Eukaryotic mRNA, WOBI) and sequenced on an Illumina NovaSeq X Plus system.

value: Embryo

value: elav[WDd] rep3


title: 16 day old embryo of Hu sheep - E16 of HS

city: Inner Mongolia

first: Hong

last: Su

state: Inner Mongolia

address: No. 306, Zhaowuda Road, Saihan District, Hohhot, Inner Mongolia Autonomous Region

institute: Inner MongoliaAgricultural University

description:
Library name: hu490-3LIB
10x Genomics

data_processing:
The fastq data obtained from sequencing were analyzed using the Ovis_aries-genome-v1.0 genome of sheep as the reference genome, and the Cell Ranger (v6.1.2) standard procedure was performed to obtain the gene expression matrix. The output expression matrix was further analyzed using R software (v4.1.2) and Seurat package (v4.1.1). Use a custom R script to integrate gene expression data and metadata from two samples. Load the integrated gene expression matrix and metadata matrix together into a Seurat object for downstream processing. Calculate the percentage (percentage. mt) of mitochondrial transcripts for each cell and add it as metadata to the Seurat object. Before dimensionality reduction, further filtering is performed on the cells to retain only those with a gene count greater than 200 and a percentage. mt of less than 10%. Use the NormalizeData function to scale gene expression values to 10000 transcripts per cell and perform log transformation, with parameters selected as normalization.method = “LogNormalize”, scale.factor = 10000。 Use the magic_op. fit_transform (magic_op=magic. MAGIC()) function in the magic package (v3.0.0) to process missing values in the data, with the parameter set to genes='all_genes'. Use the indVariableFeatures function to calculate highly variable genes, with corresponding parameters set to selection.method="vst" and nfeatures=2000. Use the ScaleData function (vars. to. regress="percentage. mt") to evaluate the impact of variables (percentage. mt) and perform regression, and use scaled and centered residuals for dimensionality reduction and clustering.
Assembly: Ovis_aries_genome_v1.0
Supplementary files format and content: matrix table with gene counts for every gene and every cell

organism: Ovis aries

source_name: embryo

extract_protocol:
Sheep embryos were digested in calc-Mg-free HBSS containing collagenase Ⅱ (Thermo Fisher Scientific, 17101015, 100 U/ul) and collagenase Ⅳ (Thermo Fisher Scientific,17104019,100 U/ul) at 37℃, and the optimal digestion time was determined to be 15 min through pre-experiment. After digestion for 15 min, the dissociated cells were passed through a 70μm filter, centrifuged at 400g at 4℃ for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi) and incubated on ice for 5 min to lyse red blood cells. After cracking red, the reaction was terminated with PBS+2%FBS. Centrifuged at 400g at 4℃ for 5 min. Then discard the supernatant and re-suspend, centrifuged at 300g at 4℃ for 5 min, discard the supernatant and re-suspend, the dissociated cells were passed through a 40μm filter element, and counted by Countstar automatic counter (Countstar Rigel S5).
Approximately 17,000 cells were loaded into the 10x Chromium Controller. Library preparation was performed using the Single-Cell 3′ Reagent Kit v3.1 following the manufacturer's protocol. GEM-Reverse Transcription (GEM-RT) was carried out in a thermal cycler under the following conditions: 53°C for 45 minutes, followed by 85°C for 5 minutes, and finally held at 4°C.  After reverse transcription and cell barcoding, emulsions were broken, and cDNA was isolated and purified using a Cleanup Mix containing DynaBeads and SPRIselect reagent (Thermo Fisher Scientific). The purified cDNA was subsequently amplified by PCR. cDNA quality was assessed using the Agilent Bioanalyzer. For library construction, amplified cDNA was fragmented and end-repaired, followed by double-sided size selection. The library was then PCR-amplified with sample indexing primers and subjected to an additional double-sided size selection step.  The final libraries were purified and quality assessed according to the manufacturer's guidelines.

value: embryo


title: Mulitome, Farrerol, SCNT, E12.5, GEX

description:
Library name: F-SCNT125_GEX
10x Genomics Multiome GEX: Read1 contains cell barcode and UMI; Read2 contains transcript sequences
F-SCNT125_filtered_feature_bc_matrix.h5
scMutiomics_GEX_counts_matrix.txt.gz
scMutiomics_Metadata.txt.gz

value: placenta

value: embryonic day (E) 12.5

tag: origin

value: Somatic cell nuclear transfer

value: Farrerol

value: C57BL/6n x PWK/PhJ

value: mRNA


title: elav[WDd]_rep2

description: Library name: Sample11

value: elav[WDd] rep2


title: 19 day old embryo of Hu sheep - E19 of HS

description:
Library name: HY-3LIB
10x Genomics


title: Mulitome, SCNT, E18.5, ATAC

description:
Library name: SCNT185_ATAC
10x Genomics Multiome ATAC: Read1 contains ATAC sequences; Read2 contains cell barcode; Read3 contains ATAC sequences
SCNT185_filtered_feature_bc_matrix.h5
scMutiomics_Metadata.txt.gz

value: embryonic day (E) 18.5

value: ATAC


title: Cerebellum, Exercise SCA, 198

city: Albany

first: J

middle: Andrew

last: Berglund

address: 1400 Washington Avenue

department: Biology

institute: University at Albany, State University of New York

description: Library name: 198

data_processing:
After sequencing the quality of the fastq files were checked using the program FastQC (version 0.11.9).
FASTQ files with >20% adapter content were trimmed using fastp (version 0.24.0) and quality re-confirmed using FastQC
STAR (version 2.7.10a) was used to align the fastq files to the GRcm39/mm39 genome with the --quantModeGeneCounts option added to count the reads per gene.
Assembly: GRCm39/mm39
Supplementary files format and content: Tab-delimited text files contain the raw read count abundances for each sample.

source_name: Cerebellum

extract_protocol:
Total RNA was extracted from the cerebellum using TRIzol reagent (Invitrogen). The tissues were first homogenized with RNase-free beads and then processed using the RNeasy kit (Qiagen), followed by DNase treatment.
The NEBNext Ultra II Directional RNA Library Prep Kit (Illumina) with NEBNext rRNA Depletion Kit (New England Biolabs) was used to prepare RNA-seq libraries, with a total of 250 ng input RNA from each sample. The manufacturer’s protocols were followed, with the following exceptions: 40× adaptor dilutions were used, and 13 cycles of library amplification were performed. The resulting libraries were pooled in equimolar amounts, quantified using the NEBNext Library Quant Kit for Illumina (New England Biolabs), quality checked via capillary electrophoresis on the 5300 fragment analyzer (Agilent Bioanalzyer) using the DNF-474 HS NGS kit (Agilent). Libraries with sufficient quantity were loaded into P2 flow cell 1000/2000 by Illumina and were sequenced using paired-end, 151 base pair sequencing on the Illumina NextSeq 2000 sequencer at the University at Albany RNA Institute. All datasets had total read depths greater than 90 million paired-end reads.

value: Cerebellum

value: Het

value: Exercise


title: 19 day old embryo of Hulunbuir Short-tailed sheep - E19 of HSTS

description:
Library name: DWY-3LIB
10x Genomics


title: Mulitome, SCNT, E18.5, GEX

description:
Library name: SCNT185_GEX
10x Genomics Multiome GEX: Read1 contains cell barcode and UMI; Read2 contains transcript sequences
SCNT185_filtered_feature_bc_matrix.h5
scMutiomics_GEX_counts_matrix.txt.gz
scMutiomics_Metadata.txt.gz


title: elav[null]_fne[null]_rep3

description: Library name: Sample9

value: elav[null] fne[null] rep3


title: P2 n3 Xenium

type: RNA

city: Vancouver

first: Freda

last: Miller

address: 2185 East Mall

institute: University of British Columbia

hyb_protocol: Samples were incubated in a probe solution for 16-24 hours at 50°C. For all datasets, the solution contained the same set of 347-gene targeting probes: 247 from the 10x Genomics predesigned mouse brain panel, and 100 from a custom add-on that allowed better resolution of key cell types within the ventricular-subventricular zone. Nonspecific probe binding was next washed off via PBS-T, a 30-minute incubation in post-hybridization buffer at 37°C, and additional PBS-T washes. Ligation of the hybridized probes was performed by incubating the samples in ligation enzymes for 2 hours at 37°C. After a series of PBS-T washes, the ligated probes were amplified via rolling circle amplification; to achieve this, samples were incubated with amplification enzyme for 2 hours at 30°C. These steps were next followed by autoflorescence quenching and nuclear staining.

scan_protocol: Image processing, decoding, quality score generation, and DAPI-based cell segmentation was automatically performed by the Xenium Analyzer system. Data was acquired on instrument software versions 2.0.1.0 to 3.1.0.0, and onboard analysis versions 2.0.0.10 to 3.1.0.4.

data_processing: Following on-instrument analysis, all datasets were run through 10x Genomics Xenium Ranger v3 software (xeniumranger resegment function) with settings as recommended by the manufacturer to assign transcripts to the closest nucleus within a maximum distance of 2 µm.

label: Xenium probe set

source_name: Brain (postnatal coronal brain sections containing the lateral ventricles)

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Brain tissue was collected from mice at E15, E18, and P2. Samples were fixed in 4% paraformaldehyde (Electron Microscopy Sciences) for 24 hours at 4°C and subsequently cryopreserved in 30% sucrose for 48 hours. Samples were embedded in O.C.T. (Tissue-Tek) and cryosectioned coronally onto Xenium slides (chemistry v1) at a thickness of 10 μm. Afterwards, all samples were processed as per the Xenium worflow for fixed frozen tissue, which involved washes in PBS, water, 100% ethanol, and 70% ethanol, followed by decrosslinking.

treatment_protocol: E15 samples were collected from pregnant mice that were intraperitoneally administered 200 µL of 0.1% BSA in PBS 48 hours prior to collection.

tag: tissue preservation method

value: Other

tag: preservation method

value: Fixed frozen


title: Mulitome, SCNT, E14.5, ATAC

description:
Library name: SCNT145_ATAC
10x Genomics Multiome ATAC: Read1 contains ATAC sequences; Read2 contains cell barcode; Read3 contains ATAC sequences
SCNT145_filtered_feature_bc_matrix.h5
scMutiomics_Metadata.txt.gz

value: embryonic day (E) 14.5


title: Cerebellum, Sedentary SCA, 195

description: Library name: 195

value: Sedentary


title: elav[null]_fne[null]_rep2

description: Library name: Sample8

value: Embryo

value: elav[null] fne[null] rep2


title: P2 n2 Xenium

value: Brain (postnatal coronal brain sections containing the lateral ventricles)


title: Cerebellum, Sedentary SCA, 194

description: Library name: 194


title: Mulitome, SCNT, E14.5, GEX

description:
Library name: SCNT145 _GEX
10x Genomics Multiome GEX: Read1 contains cell barcode and UMI; Read2 contains transcript sequences
SCNT145_filtered_feature_bc_matrix.h5
scMutiomics_GEX_counts_matrix.txt.gz
scMutiomics_Metadata.txt.gz

value: placenta

value: Somatic cell nuclear transfer


title: Mulitome, SCNT, E12.5, ATAC

description:
Library name: SCNT125_ATAC
10x Genomics Multiome ATAC: Read1 contains ATAC sequences; Read2 contains cell barcode; Read3 contains ATAC sequences
SCNT125_filtered_feature_bc_matrix.h5
scMutiomics_Metadata.txt.gz

value: embryonic day (E) 12.5

value: C57BL/6n x PWK/PhJ


title: P2 n1 Xenium


title: Cerebellum, Sedentary Wt, 192

description: Library name: 192

value: Wt


title: Con_30h_Sample30_batch2

city: Newton

first: Matt

last: Kanke

state: MA - Massachusetts

address: 112 Harding Street

institute: Amgen

description: Library name: 30160_C_Colon_Adcrcnma_Trtd

data_processing:
Raw sequencing reads were aligned to the human genome reference (Human.B38) using the OSA aligner (Qiagen Omicsoft). Aligned reads were collapased into gene-level counts using Omicsoft’s RSEM implementation and the genomic locations in the GENCODE v33 gene model. Data analysis was performed using the Ingenuity Pathway Analysis (IPA) package (Qiagen).
Assembly: Human.B38 Gencode v33
Supplementary files format and content: batch1_primary_count_gene.Counts.Table.txt
Supplementary files format and content: batch2_primary_count_gene.Counts.Table.txt

growth_protocol: The human colorectal adenocarcinoma cell line Caco-2 expressing Cas9 was purchased from UBIGENE Biosciences Co., Ltd (Guangzhou, China). Cells were maintained in 77% minimum essential media (Gibco) supplemented with 20% heat inactivated fetal bovine serum (Sigma Aldrich), 1% Glutamax, 1% Sodium pyruvate, 1% non-essential amino acids (Gibco) and 100 μg/ml hygromycin (Gibco) in a humidified atmosphere (37⁰C and 5% CO2). For differentiation, cells were seeded at 8x104 cells/200μl on 0.4μm pores polyester HTS transwell membrane (Corning-Costar, Acton, MA) and grown as monolayers.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions and 800ng of RNA was reverse transcribed with cDNA synthesis master mix (Legene Biosciences,CA, USA).
Sequencing libraries were constructed using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) and IDT for Illumina-TruSeq RNA UD Indexes. Libraries were sequenced on a NovaSeqX to a minimum depth of 35 million reads.

treatment_protocol: After 12 days, recombinant human TNF-α and human IFN-γ were treated to both apical and basal chamber for 0h (N = 4 per group), 6h (N=7~8 per group), 9h (N=7 per group), 18h (N=4 per group), 30h (N=8 per group) and 54h (N=8 per group). For 3D microfluidic model system, OrganoReady Colon Caco-2 (Mimetas BV, The Netherlands) comprising 64 ready-to-use Caco-2 seeded against collagen I was used.


title: Mulitome, SCNT, E12.5, GEX

description:
Library name: SCNT125_GEX
10x Genomics Multiome GEX: Read1 contains cell barcode and UMI; Read2 contains transcript sequences
SCNT125_filtered_feature_bc_matrix.h5
scMutiomics_GEX_counts_matrix.txt.gz
scMutiomics_Metadata.txt.gz

value: mRNA


title: WT-1

city: Pittsburgh

first: Iliya

last: Lefterov

address: 130 De Soto St

institute: University of Pittsburgh

description: Library name: F2702_BmRNA_S5

source_name: brain

value: brain

value: WT


title: E18 n4 Xenium

source_name: Brain (embryonic coronal brain sections containing the lateral ventricles)


title: Cerebellum, Exercise SCA, 122

description: Library name: 122

value: Cerebellum

value: Het

value: Exercise


title: Cerebellum, Exercise Wt, 121

description: Library name: 121


title: Mulitome, WT, E18.5, ATAC

description:
Library name: WT185_ATAC
10x Genomics Multiome ATAC: Read1 contains ATAC sequences; Read2 contains cell barcode; Read3 contains ATAC sequences
WT185_filtered_feature_bc_matrix.h5
scMutiomics_Metadata.txt.gz

value: embryonic day (E) 18.5

value: Naturally fertilized

value: ATAC


title: elav[null]_rep3

description: Library name: Sample6

value: Embryo

value: elav[null] rep3


title: elav[null]_rep1

description: Library name: Sample4

value: elav[null] rep1


title: PPARr2 K382R expressing mouse scWAT SVF cell line, day 2 post differentiation, biol rep3

description: Library name: KR3

value: mouse scWAT SVF cell line

value: stromal vascular fraction

value: PPARr2 K382R

value: Beige adipogenic differentiation


title: WT S. aureus, 0μM Copper cholride, bio rep 2

description: Library name: WTCHG_724336_71255197

value: Staphylococcus aureus USA300 JE2 wild-type

value: 0μM Copper cholride


title: Mulitome, WT, E18.5, GEX

description:
Library name: WT185_GEX
10x Genomics Multiome GEX: Read1 contains cell barcode and UMI; Read2 contains transcript sequences
WT185_filtered_feature_bc_matrix.h5
scMutiomics_GEX_counts_matrix.txt.gz
scMutiomics_Metadata.txt.gz

value: placenta

value: C57BL/6n x PWK/PhJ

value: mRNA


title: Cerebellum, Sedentary Wt, 117

description: Library name: 117

value: Cerebellum

value: Wt

value: Sedentary


title: E18 n2 Xenium

value: Brain (embryonic coronal brain sections containing the lateral ventricles)

value: Other

value: Fixed frozen


title: Mulitome, WT, E14.5, ATAC

description:
Library name: WT145_ATAC
10x Genomics Multiome ATAC: Read1 contains ATAC sequences; Read2 contains cell barcode; Read3 contains ATAC sequences
WT145_filtered_feature_bc_matrix.h5
scMutiomics_Metadata.txt.gz

value: embryonic day (E) 14.5

value: Naturally fertilized

value: ATAC


title: E18 n1 Xenium


title: WT_rep2

description: Library name: Sample2

value: Embryo

value: Wild type control (elav[e5]/FM7) rep2


title: E15 n3 Xenium

value: Pregnant mice were intraperitoneally administered 200 µL of 0.1% BSA in PBS 48 hours prior to collection.


title: Cerebellum, Exercise SCA, 55

description: Library name: 55

value: Het

value: Exercise


title: WT_rep1

description: Library name: Sample1

value: Wild type control (elav[e5]/FM7) rep1


title: E15 n2 Xenium


title: Mulitome, WT, E12.5, ATAC

description:
Library name: WT125_ATAC
10x Genomics Multiome ATAC: Read1 contains ATAC sequences; Read2 contains cell barcode; Read3 contains ATAC sequences
WT125_filtered_feature_bc_matrix.h5
scMutiomics_Metadata.txt.gz

value: placenta

value: embryonic day (E) 12.5

value: C57BL/6n x PWK/PhJ


title: Cerebellum, Sedentary SCA, 16

description: Library name: 16

value: Cerebellum


title: 8 dpf pax9 mutant tail

city: Cincinnati

first: Lindsey

last: Barske

state: OH

address: 3333 Burnet Ave MLC 7016

department: Human Genetics

institute: Cincinnati Children's Hospital Medical Center

description:
Library name: MUT-8dpf
10x Genomics

data_processing:
Raw data were processed into feature-barcode matrices using CellRanger v9.0.1 in the 10x Genomics Cloud Analysis platform.
Assembly: Danio rerio genome annotation release 106 (GRCz11)
Supplementary files format and content: standard CellRanger output (barcode, feature, matrix), as .csv files

organism: Danio rerio

source_name: tail

extract_protocol:
Tails were pooled for the pax9 mutant and wild-type samples, then dissociated into a single-cell suspension largely as described (Bresciani et al., 2018), with Liberase substituting for collagenase. Tail biopsies were washed in PBS, then incubated in a sterile dish with a pre-warmed dissociation mixture of Liberase and Trypsin-EDTA (40 μl/8% 25x Liberase: 460 μl Trypsin-EDTA) in a standard incubator set at 30°C with the plate placed directly on a heat block. Dissociation progress was monitored over 15-20 minutes, and gentle trituration was performed every 3 minutes through a P200 pipette tip against the bottom of the dish, being careful to avoid bubbles and aggressive pipetting. Once a single-cell suspension was achieved, a stop solution of Leibovitz's media containing 10% FBS was added to halt dissociation. Pellets were washed in PBS containing 1% fetal bovine serum, filtered, and resuspended in 50 µl of 1% FBS/PBS. Samples were kept on ice for transfer to the core facility, where cell viability was confirmed at over 79%.
Libraries were prepared using the Chromium GEM-X 3' Kit v4 according to the manufacturer's instructions

value: tail

value: all cell types in tail

value: pax9^el622 mutant


title: Mulitome, WT, E12.5, GEX

description:
Library name: WT125_GEX
10x Genomics Multiome GEX: Read1 contains cell barcode and UMI; Read2 contains transcript sequences
WT125_filtered_feature_bc_matrix.h5
scMutiomics_GEX_counts_matrix.txt.gz
scMutiomics_Metadata.txt.gz

value: mRNA


title: 8 dpf wild-type tail

description:
Library name: WT-8dpf
10x Genomics

value: wild-type


title: strep_JCC341_plus-glucose_6.5h_rep3

city: Chicago

first: Hoang Anh

middle: V

last: Tran

state: IL

address: 5801 S Ellis Ave

institute: University of Chicago

description: Library name: Sample S24

data_processing:
[Sample T1-T16] The methods of the previously published pipeline (PMID 30559359) were used with some modifications. Raw paired-end sequence reads of 75 or 100 nucleotides were processed by Illumina-utils (PMID 23799126). Inserts contained a 7 nucleotide sample barcode and a random 6 nucleotide unique molecular identifier (UMI). Given that tRNA molecules range in length from 74-96 nucleotides, forward and reverse 100 nucleotide reads fully covered some tRNA sequences and partially overlapped for others. We upgraded the Illumina-utils ‘iu-merge-pairs’ command to merge both fully and partially overlapping reads, while trimming overhanging adapter sequences in the case of more than full overlap (the command line flag, ‘--marker-gene-stringent’, enables consideration of full as well as partial overlap). We minimized erroneous base calls, important for our analysis of modification-induced mutations, by retaining reads that matched with zero mismatches in the overlapping region (option ‘--max-num-mismatches 0’)
[Sample T1-T16] The procedure for de novo profiling of full-length and fragmentary tRNA reads introduced in tRNA-seq-tools (PMID 30559359) was modified as follows. tRNA structural features were identified from the 3’ end of the read. The minimum criteria for tRNA identification were the correct distance to the 7 canonically conserved nucleotides in the T arm, of which 5 must be found, and base pairing in of the T stem. A full-length read must contain a base-paired acceptor stem and all features in between.
[Sample S1-S24] Raw sequences reads were demultiplexed using Je to detect encoded barcode reads. Following this, reads were aligned to a curated Streptococcus mutans tRNA, rRNA and reference genome.
[Sample S1-S24] The aligned reads were then used to determine RNA sequence abundance using custom python script. RNA modifications were detected based on aligned reads using samtools sort (http://www.htslib.org/, Li et al., 2009) feature sort the reads in a bam file format. Then IGVtools count (https://software.broadinstitute.org/software/igv/igvtools) count feature was utilized to output a wig files using the following parameters: -z 5 -w 1 -e 250 —bases. The resulting wig files were processed using a custom python script to identify nucleotide mutations as well as coverage of aligned reads.
Assembly: [Sample T1-T16] tRNA sequences were taxonomically annotated by using the Global Alignment for Sequence Taxonomy (GAST) tool (PMID 19023400) to search a set of reference tRNA sequences that tRNAscan-SE (v1.3.1) (PMID 9023104) identified from 4,235 gold-standard bacterial genomes (non-endosymbiont genomes with an assembly level of “chromosome”) stored in the Ensembl Genomes 2016 database (PMID 26553803).
Assembly: [Sample S1-S24] ASM746v2
Supplementary files format and content: [Sample T1-T16] .tsv files with family taxonomy and tRNA anticodon counts per sample
Supplementary files format and content: [Sample S1-S24] .tsv files with gene name and abundance per sample
Supplementary files format and content: [Sample S1-S24] .sam.tsv files with mutation, deletion, coverage for each gene position per sample

organism: Streptococcus mutans

source_name: bacterial cells

growth_protocol: [Sample S1-S24] S. mutans strains were cultured in Brain Heart Infusion Broth without Dextrose (BHI-D; Alpha Biosciences) at 37°C.

extract_protocol:
[Sample T1-T16] The tongue dorsum scrapings were combined with RNAlater Stabilization solution (Invitrogen) and stored at −80°C. For extraction, RNAlater was first removed by centrifugation. Pelleted material was lysed in 0.3M NaOAc/HOAc,10mM EDTA, pH 4.8 with an equal volume of acetate-saturated phenol:chloroform pH 4.5 (Invitrogen). After addition of 1.0 mm glass lysing beads (Bio-Spec Products) in a 1:1 ratio (bead:sample weight), samples were placed in a reciprocating bead beater (Mini-Beadbeater-16, Bio-Spec Products) for two 1-min intervals on maximum intensity. Samples were centrifuged before re-extraction and isopropanol precipitation of total RNA. Pellets were washed with 75% ethanol before resuspension in an acid-buffered elution buffer (10mM NaOAc, 1mM EDTA, pH 4.8). 1 ug of total RNA was used for the construction of sequencing libraries. RNA quality and quantity were assessed using the Agilent bio-analyzer.
[Sample S1-S24] RNA was isolated using the Quick-RNA Fungal/Bacterial Microprep Kit (Zymo) and treated with DNAse I according to the DNAfree kit (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries. RNA quality and quantity were assessed using the Agilent bio-analyzer.
MSR-seq (PMID 35513407)
[Sample T1-T16] Standard MSR-seq protocol was used with additional chemical treatment. Specifically, after the first ligation and streptavidin bead binding of all CHO, samples were split in two: one mock-treated, and the other subjected to AlkB demethylase reaction (PMID 35513407).

treatment_protocol: [Sample S1-S24] A starter culture for each strain was thawed, resuspended in BHI-D, and used to inoculate BHI-D or BHI-D + 0.15% glucose before incubation. Cells were harvested by centrifugation at 1 h and at early stationary phase (3 h for BHI-D, or 6.5 h for BHI-D + 0.15% glucose).

value: bacterial cells

value: plus-glucose, 6.5h


title: FGSCs, 917KO-2

first: Ji

last: Wu

address: No.800, Dongchuan Road

institute: Shanghai Jiao Tong University

description: Library name: 917KO-2

data_processing:
The reads were first mapped to the GENCODE(mouse-mm10) or Ensembl gene set using Bowtie2 version 2.1.0
the gene expression level was estimated using RSEM v1.2.28.
TMM (trimmed mean of M-values) was used to normalize the gene expression. Differentially expressed genes were identified using the edgeR program
Assembly: MM10
Supplementary files format and content: Tab-delimited text files include the number of reads, relative RPKM values, and P-values for control and experimental group Sample.

source_name: Ovary

extract_protocol:
Total RNA was extracted from shnc and shGm26917 FGSCs using Takara RNAiso Plus.
Next, 1000 ng of the digested RNA was used for the  GENESEED®RNA-seq Library Prep Kit for Illumina, and sequencing libraries were created according to the manufacturer's protocol.

value: Ovary

value: FGSCs

value: germ stem cells

value: shGm26917 group


title: CNTL_inj

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: Library name: CNTL_inj

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8.0.0 with –force-cells 10k option.
Data matrixes were imported into Seurat v4.3.0 (Satija, et al. 2015) in the R v4.2.3 statistical environment. Initial matrix filtering of >5 cells per gene, >500 features per cell, and cells with mitochindria reads <20% was perfomed.
Sample count matrixes were merged and ambiant RNA was removed using decontX function in the celda v1.14.2 package.
Sample decontX adjusted count matrixes were normalized and variance stabalized using SCTransform v2 (Choudhary and Satija, 2022). PCA (50 dimensions), FindNeighbors (30 dimensions), RunUMAP (30 dimensions), and FindClusters were performed using Seurat.
Cell types were assigned using scType (https://github.com/IanevskiAleksandr/sc-type) with sctype 'eye' database "Astrocytes", "Fibroblasts", "Extracellular matrix cells, "Retinal pigment epithelial cells", and custom cell type gene lists (https://github.com/MBrooks313/scRNA-seq/blob/main/Retina_Cell_type_MB_v4.xlsx). High resolution clustering was perfomed to assess and remove clusters exhibiting expression of canonical cell type markers from more than one cell type.
Assembly: GRCm38.p6/ENSEMBL v98
Supplementary files format and content: HDF5 file of filtered CellRanger output
Supplementary files format and content: Seurat object of final data

source_name: Retina

extract_protocol:
CD-1 mouse retinas were dissected, GFP-positive punches extracted, and retina dissociated as previously described (Fadl, et al. Mol Vis 2020). One sample from each condition was used. Dissociate was used as input for 10X Genomics Chromium controller using v3.1 (Chromium Next GEM Single Cell 3ʹ GEM, Library and Gel Bead Kit v3.1) chemistry. Approximately 17,000 live cells per sample were loaded into the Chromium chip following the Cell Suspension Volume Calculator Table to capture transcripts from approximately 10,000 cells.
Libraries were performed according to the manufacter’s instructions (Single Cell 3’ v3.1 protocol, 10x Genomics)

value: Retina

value: whole retina

value: male


title: 3 dpf pax9 mutant tail

description:
Library name: MUT-3dpf
10x Genomics


title: strep_JCC341_plus-glucose_6.5h_rep2

description: Library name: Sample S23


title: FGSCs, 917KO-1

description: Library name: 917KO-1


title: 3 dpf wild-type tail

description:
Library name: WT-3dpf
10x Genomics


title: BACH1

description: Library name: BACH1


title: strep_JCC341_plus-glucose_6.5h_rep1

description: Library name: Sample S22


title: FGSCs, 917NC-2

description: Library name: 917NC-2

value: shnc group


title: ATF4

description: Library name: ATF4