title: IgG Control

city: Taichung

first: Hieu-Huy

last: Nguyen-Tran

state: Taichung

address: Xueshi

department: Graduate Institute of Biomedical Sciences

country: Taiwan

institute: China Medical University

data_processing:
Basecalls were performed using bcl2fastq v2.20 for Novaseq (Novaseq X, PE150) output. The adapter sequences of Cut and Tag-Seq reads were removed, and reads with quality score > 25 and length > 140 were retained using fastp v0.22.
Cut and Tag-Seq reads were aligned to the UCSC hg38 genome using Bowtie2 v2.4.5 with parameters : --end-to-end --very-sensitive --no-mixed --no-discordant.
The mapping of insert length between 10-700 bp is retained as mapped fragments. The fragments were then normalized by chromosome size of hg38 genome and converted to bedgraph with bedtools v2.30.0.
Output bedgraph files were called peaks by SEACR v1.3 with stringent model of top 0.01 fraction of peaks based on the total signal within peaks. The called peaks were then annotated by ChIPSeeker v1.34.1.
Differential analysis of the called peaks was performed using DESeq2 v1.38.3. The significant differentially expressed genes were then analyzed for enriched pathways using ClusterProfiler v4.6.2.
Assembly: bigWig files were generated using bamcoverage and the scores were normalized coverage to 1X by the effective genome size of hg38.
Supplementary files format and content: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

growth_protocol: HMEC-1 cells were mantained in MCDB131 medium (Gibco, 10372019) with 10 ng/mL hEGF (Sigma, #E9644), 1 g/mL hydrocortisone (Sigma, #H0888), 10 mM L-glutamine (Gibco, #25030149), and 10% heat inactivated FBS (Gibco, #10437-028).

extract_protocol:
Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903)
Libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit complemented with TruePrep Index Kit V2 (#TD903, Vazyme Biotech, Nanjing, CN). 10^5 cells were used as starting material for Cut and Tag Libraries construction. Libraries were amplified using 12 cycles on the thermocycler. Post amplification libraries were size selected at 250-600bp in length using DNA Clean Beads (#N411, Vazyme Biotech, Nanjing, CN). Using microfluidic electrophoresis to quantify the amount and check the length distribution of the library with DNA-2500 Kit on MultiNA MCE-202 (Shimadzu, Kyoto, JP)

treatment_protocol: 10 ng/mL of rOSM

value: Endothelial cells

tag: chip antibody

value: Rabbit IgG EPR25A

value: IgG Control

value: IgG


title: Ctrl_Z4, RCAS injected, zeugopod

status: Public on Aug 27 2025

type: SRA

city: Shenyang

first: Bai

last: Shibin

address: 120 Dongling Road

country: China

institute: Shenyang Agriculture University

description: control

library_source: transcriptomic

data_processing:
Reads were mapped to the NCBI Gallus gallus genome assembly (bGalGal1.mat.broiler.GRCg7b) with inserted human-Zic3 cDNA sequences using HISAT2 version 2.2.1.
Transcript assembly by StringTie v2.1.7
Use prepDE.py3 script of StringTie to get raw counts and TPM counts
Assembly: bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

molecule: total RNA

organism: Gallus gallus

source_name: hindlimb zeugopod

extract_protocol:
Total RNA was extracted using the RNeasy micro kit (Qiagen, Hilden, Germany), with on-column DNase to remove contaminating genomic DNA. RNA concentration and purity were measured using NanoDrop 2000. (Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit from the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

tag: tissue

value: hindlimb zeugopod

tag: cell line

value: tissue

tag: cell type

tag: genotype

value: RCAS control


title: Modified Sm-RIP human extract, mouse polyA-RNA 1 (hxmr1)

city: Cleveland

first: Anton

middle: James

last: Blatnik III

state: Ohio

address: 2109 Adelbert Road

country: USA

institute: Case Western Reserve University

description:
RNA enriched by Sm-RIP from human S3-iNPC cytoplasmic extract incubated with mouse NSC-34 polyA-RNA
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
B1U28

data_processing:
Adapter sequences were trimmed using Cutadapt. Reads were aligned to both the human GRCh38 and mouse GRCm39 genome assemblies, separately, (Esnembl release 100) using STAR. Reads were counted using FeatureCounts from the subread package, using the fractional argument for reads mapped to multiple loci. The standard use of FeatureCounts is supplied in the '_Sm_counts_master_' files. Additionally, FeatuerCounts was supplied a Simplified Annotation File containing only intronic coordinates and was used to provide count information for intronic reads and is supplied in the '_Sm_counts2intron_master_' processed data files. Unix commands were used combine the counts for each sample into a single master sheet used as an input for Deseq2.
Wald-test comparisons of the FeatureCounts outputs were performed using Deseq2 in RStudio (version 2023.12.1+402) on an Apple 2023 MacBook Pro running macOS Sonoma 14.6.1. For all comparisons, the adjusted p-values from Deseq2 were used. Principal component analysis was performed on the top 1000 genes to ensure proper clustering of samples. Custom R scripts were then written to analyze the data presented within this manuscript and are available upon request.
Assembly: GRCh38, GRCm39
Supplementary files format and content:
Modified FeaturesCount output file for alignment of all samples to human GRCh38 or mouse GRCm39. This file contains a single column of the assigned counts for each sample library and was used as the input for Deseq2.
'2023_n3_Sm_counts2intron_master_human.txt' for GSM8548423-25, GSM8548429-31, GSM8548438-40, and GSM8548444-46
'2023_n3_Sm_counts2intron_master_mouse.txt' for GSM8548426-28, GSM8548432-37, GSM8548441-43

molecule: cytoplasmic RNA

organism: Mus musculus

source_name: S3-iNPC, NSC-34

growth_protocol: Neural stem cell NSC-34 cells were cultured in 12% FBS DMEM supplemented with L-glutamine and PenStrep (12% FBS Atlanta S11550, 10% PenStrep/L-Glutamine Gibco 10378-016, DMEM Gibco 11960077) under 37 °C,  5% CO2 in normoxic conditions. Cells were routinely passaged every 2-3 days by washing twice with Phosphate Buffered Saline lacking divalent cations, and then treating with 0.05% Trypsin-EDTA (Gibco 25300054). S3 fibroblasts were induced to a neural progenitor cell fate as described by Meyer et al (79). To culture neural progenitor cell S3-iNPCs, dishes were coated with fibronectin (Millipore FC010-10MG) and cells were cultured in DMEM/F12+ Glutamax (Gibco 10565-042) supplemented with 10% N2 (Gibco 17502-048), 10% B27 (Gibco 17504-044), 10% Anti-Anti (Gibco 15270-62), and 20 ng/mL FGF2 ( Peprotech 100-18B), under 37 °C, 5% CO2 in normoxic conditions. Cells were routinely passaged every 2-3 days by washing twice with PBS lacking divalent cations and treating with StemPro Accutase (ThermoFisher A1110501).

extract_protocol:
Cytoplasmic cell extracts were generated by scraping and collecting NSC-34 or S3-iNPC cells in cold phosphate buffered saline containing only monovalent cations. Cells were pelleted by centrifugation 400 x g for 4 min. Cells were resuspended in digitoxin lysis buffer (20 mM Tris pH 8, 50 mM KCl, 0.5 MgCl2, 1x eComplete, 200 units/mL RNase-OUT, 50 ug/mL digitonin, in DEPC-treated water) and incubated on ice for a few minutes. Lysates were passaged 6 times through a 27 gauge needle with syringe then centrifuged at 1,500 x g for 1 minute at 4 °C. Supernatant was measured and transferred to a new microfuge tube and supplemented with NP-40 to achieve 0.01% final concentration. Lysates were then centrifuged at 4,000 x g for 15 minutes at 4 °C. Supernatants were then aliquoted into microfuge tubes and frozen in liquid nitrogen.
Three replicates of the four conditions for both species combinations were used to generate sequencing libraries, using 50 ng of captured RNA as input for the Takara SMARTer Stranded Total RNA-Seq Kit v3-Pico Input Mammalian (Takara 634451)

treatment_protocol: Oligo-dT isolation of polyA-RNA - Four 15 cm dishes of NSC-34 or S3-iNPC cell were washed thrice with PBS lacking divalent cations and treated with 8 mL TRIzol Reagent (Invitrogen 15596026) per 15 cm dish. TRIzol samples were pooled and a large scale total RNA isolation and precipitation was performed following manufacturer’s instructions. After purification, isolated RNA was treated with 200 units of Turbo DNase (Invitrogen AM2239) and incubated at 37 °C for 30 minutes with gentle rotation at 350 rpm in Eppendorf Thermomixer R. DNase was removed by phenol:chloroform extraction. RNA was precipitated with 1.5 M final concentration of LiCl and 100% ethanol, centrifuged at > 18,000 x g for 15 minutes. RNA was resupsended in 1 mL nuclease-free water and quantified using Qubit RNA Broad Range Assay (Invitrogen Q10211). PolyA-RNA was isolated using Dynabeads mRNA Purification Kit (Invitrogen 61006). Oligo-dT beads were reused post-polyA-RNA elution to isolate the magnitude of polyA-RNA required for modified Sm-ring assembly reaction and sequencing conditions. After isolation, polyA-RNA was quantified using Qubit RNA Broad Range Assay (Invitrogen Q10211) and RNA integrity (RIN) was quantified by TapeStation analysis performed by the Ohio State Comrpehensive Cancer Center Genomics Core to determine removal of polyA-minus RNAs. For Sm-RIP and modified Sm-ring assembly RIPs, Protein-A DynaBeads (Invitrogen 10001D) were aliquoted 8.6 µL/rxn and washed three times in PBS + 0.1% NP-40. 1.6 µg/rxn Y12 antibody (Novus Biologicals NB600-546) was conjugated to Protein-A DynaBeads by incubating in PBS + 0.1% NP-40 for 1 hour at 4 °C with rotation. Beads were washed 3 more times with PBS + 0.1% NP-40, then three times with RSB-500 + 0.1% NP-40 (RSB-500: 10 mM Tris pH 7.4, 500 mM NaCl, 2.5 mM MgCl2). Beads were finally resuspended in 120 µL/rxn RSB-500 + 0.1% NP-40 supplemented with 2 mg/mL heparin. Sm-ring assembly reactions were scaled up to 250 µg human S3-iNPC and 438 µg mouse NSC-34 total protein cytoplasmic extract, supplemented with 4 µg polyA-RNA (RIN 5-6), and incubated for 1 hour at 30 °C with shake at 750 rpm in the presence or absence of ATP (1 unit/µL RNAse-OUT, 0.25 ug/uL yeast tRNA, 0.01% NP-40, 2.5 mM ATP, 20 mM Tris pH 8, 50 mM KCl, 0.5 MgCl2). Assembly reactions were immunoprecipitated with 120 µL/rxn Y12-conjugated dynabeads, incubated for 1 hour at 30 °C with shaking at 750 rpm. Beads were washed 8 times with RSB-500 + 0.1% NP-40, utilizing magnets to sequester beads. 50 ng of capture RNA was used as input for library preparation including three replicates of four conditions: 1) polyA-RNA only, 2) anti-Sm-RIP, 3) Modified Sm-RIP in which human extract was incubated with mouse polyA-RNA in the absence of ATP (and vice versa), and 4) Modified Sm-RIP in which human extract was incubated with mouse polyA-RNA and ATP (and vice versa). Libraries were pr3pped following = Takara SMARTer Stranded Total RNA-Seq Kit v3-Pico Input Mammalian (Takara 634451) Kit, and sequenced using the NOVA-Seq platform, 150 base-pair paired-end reads.

value: S3-iNPC, NSC-34

value: Induced neural progenitor cell, Neural stem cell-like hybridoma

value: wild-type

tag: treatment

value: anti-Sm-RNA immunoprecipitation


title: OSM_Rep_2

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

value: OSM-treated

value: 10 ug/mL OSM


title: Org_12 liver spheroids Insphero

city: Los Angeles

first: Ana

middle: C

last: Maretti-Mira

state: CA

address: 1450 Biggy Street, NRT 3514

department: Medicine

institute: USC

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw data processing: Cell by gene count matrices were generated by processing FASTQ files using the Cell Ranger count (version 5.0.1, 10X Genomics) pipeline with the GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics) human genome reference for each sample.
Gene expression data were processed using the R package Seurat (version 4) [PMID: 29608179].
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver spheroids Insphero

growth_protocol: 7 days in low glucose media (media obtained from InSphero)

extract_protocol:
Not extracted, spheroids cells were dissociated for 15min using Trypsin, at 37˚C. Dead cells were removed using Dead Cell Removal Kit (Miltenyi Biotec). Viable cells were particioned using 10x Chromium Controller and kit 3' v3.1.
Library was performed according to the manufacter’s instructions

treatment_protocol: PFAS replenished every 2-3 days with media change

value: liver spheroids Insphero

value: PFHxS


title: Liver_Mut_3

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: Library name: Sample 23

data_processing:
The original FASTQ files were aligned using salmon to a transcriptome reference created using GENCODE vM34
Gene level counts were generated using pytximport and differentially expressed genes were computed using pydeseq2
Assembly: GENCODE vM34
Supplementary files format and content: tab-delimited text files include TPMs for each sample. The TPMs are  transcript level abundance estimates from salmon that can be used to generate estimate gene counts for gene level analysis

source_name: Liver

extract_protocol:
The RNA was extractedusing the MagMAX™-96 Total RNA Isolation Kit (Invitrogen) by the Kingfisher Duo Prime Purification
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

value: Liver

tag: strain

value: Mut


title: Ctrl_Z3, RCAS injected, zeugopod

description: control


title: Ctrl_Z2, RCAS injected, zeugopod

description: control


title: Org_10 liver spheroids Insphero

description: 10X Genomics

value: DMSO


title: CT_Rep_2

value: Endothelial cells

value: Control

value: CT


title: Mouse Sm-RIP 2 (mx2)

description:
RNA enriched by Sm-RIP from mouse NSC-34 and detected by random priming
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
D3U38

value: Neural stem cell-like hybridoma


title: Ctrl_Z1, RCAS injected, zeugopod

description: control

value: hindlimb zeugopod

value: tissue


title: WGBS dac treatment rep2

city: Cambridge

first: Arndt

last: Wallmann

address: Tennis Ct Rd

country: United Kingdom

institute: MRC Toxicology Unit

data_processing:
TrimGalore (version 0.6.6) was used to trim low-quality bases (quality score lower than 20), adapter sequence, and end-repair bases from the 3ʹ end of reads
Bismark (version 0.22.3) was used for alignment to the human hg19 reference genome, deduplication of reads and methylation calling.
Assembly: hg19
Supplementary files format and content: bedGraph and cov file from bismark output

source_name: kidney epithelial

extract_protocol:
DNA was extracted following the instructions for cell extraction of the Dneasy blood and tissue extraction kit (Qiagen)
The libraries were contructed using the Zymo-Seq WGBS library kit (Zymo) instructions.

value: kidney epithelial

value: human embryonic kidney cells

value: WT

value: Decitabine


title: CT_Rep_1


title: Mouse Sm-RIP 1 (mx1)

description:
RNA enriched by Sm-RIP from mouse NSC-34 and detected by random priming
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
D2U37

value: wild-type

value: anti-Sm-RNA immunoprecipitation


title: Ctrl_Z5, RCAS injected, zeugopod

description: control

value: RCAS control


title: WGBS dac treatment rep1


title: Ctrl_A5, RCAS injected, autopod

description: control

source_name: hindlimb autopod

value: hindlimb autopod


title: Mouse polyA-RNA 3 (mr3)

description:
polyA-RNA enriched by oligo-dT purification isolated from mouse NSC-34
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
M3U36

molecule: polyA RNA

value: oligo-dT purified


title: Feathers in Skin, 12 days, scRNAseq

city: New Haven

first: Cody

last: Limber

state: CT

address: 165 Prospect St

department: Ecology and Evolutionary Biology

institute: Yale University

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing, and gene counting and agragation were performed with Cell Ranger version 7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: GRCg6a
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: Feather + Epidermis

extract_protocol:
Dissected samples were placed in PBS on ice and kept for less than 15 minutes before proceeding to single cell or single nuclear isolation. For samples from stage 38 embryos, we gently chopped the tissue with a scalpel before incubating the samples in a solution of Pronase (1mg/1ml PBS) for 60 minutes at 37˚ C. The tissue was then gently passed 20 times though an 18 gauge needle. The resulting cellular suspension was filtered through a 70μm filter and then filtered twice through a 40μm filter to remove larger debris. We then spun down the cell suspension at 300 g for 5 minutes removing the supernatant and resuspended the pellet in calcium and magnesium free PBS containing 1% bovine serum albumin twice to wash the cells. We used Trypan blue to estimate cellular viability with only a ≥ 70% viability used for further processing. We also estimated the cellular concentration on a hemocytometer before diluting the suspension to 1000 cells/μL to submit for 10x library preparation. For samples from stage 39 and 40 embryos, we resorted to nuclear isolation as single cell dissociation was impossible due to the keratinization of cells in these stages. Our protocol was adapted from Sarropoulos et al. 2021.2 Plucked feathers were placed in 2 mL of TST lysis buffer containing 1ml 2x Salt-Tris Buffer (see below for 1x buffer), 60 μL 1% Tween-20, 10 μL 2% bovine serum albumin, and 930 μL nuclease free H2O. We ground the tissue using a dounce homogenizer grinding 20 times with the loose pestle and 20 times with the tight pestle. This suspension was filtered through a 70μm filter and then filtered twice through a 40μm filter. Nuclei were pelleted at 500 g for 5 minutes before being washed with a Salt-Tris Buffer (146 mM NaCL, 1mM CaCL2, 21mM MgCl2, 20mM tris-HCl PH 7.5). The nuclei were then and resuspended in ice cold PBS without calcium or magnesium and containing 1% bovine serum albumin for submission for 10x library preparation.
Library construction was performed according to the manufacturers instructions (single cell 3' v3 protocol, 10x Genomics).

value: Feather + Epidermis

tag: age

value: 12 days

tag: developmental stage

value: H&H stage 38

tag: sample type

value: single cell

tag: chicken breed

value: White Leghorn


title: Ctrl_A4, RCAS injected, autopod

description: control


title: WGBS aza treamtent rep2

value: Azacitidine


title: Mouse polyA-RNA 2 (mr2)

description:
polyA-RNA enriched by oligo-dT purification isolated from mouse NSC-34
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
M2U35

value: Neural stem cell-like hybridoma


title: Plucked Feather, 14 days, scRNAseq

description: 10x Genomics

source_name: Feather

value: Feather

value: 14 days

value: H&H stage 40

value: single nucleus


title: Ctrl_A3, RCAS injected, autopod

description: control

value: tissue


title: Plucked Feather, 13 days, scRNAseq

description: 10x Genomics

value: 13 days

value: H&H stage 39


title: Org_11 liver spheroids Insphero

description: 10X Genomics

value: liver spheroids Insphero

value: PFOA


title: WGBS aza treamtent rep1

value: kidney epithelial

value: human embryonic kidney cells

value: WT


title: Mouse Sm-RIP 3 (mx3)

description:
RNA enriched by Sm-RIP from mouse NSC-34 and detected by random priming
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
D4U39

value: wild-type

value: anti-Sm-RNA immunoprecipitation


title: Ctrl_A2, RCAS injected, autopod

description: control

value: hindlimb autopod

value: RCAS control


title: Mouse polyA-RNA 1 (mr1)

description:
polyA-RNA enriched by oligo-dT purification isolated from mouse NSC-34
2023_n3_Sm_counts_master_human.txt
2023_n3_Sm_counts_master_mouse.txt
M1U34

value: Neural stem cell-like hybridoma

value: oligo-dT purified


title: WGBS control treatment rep2

value: acetic acid/water (1:1)


title: Ctrl_A1, RCAS injected, autopod

description: control


title: HCCLM3 cells, quercetin 100μM, rep3

city: Beijing

first: Lin

last: Chen

address: Chuiyangliunan Road 2

institute: Chuiyangliu Hospital

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by Removing reads containing sequencing adapter;
Removing reads whose low-quality base ratio base  quality less than or equal to 5) is more than 20%
Removing reads whose unknown  base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12)
Assembly: GRCh38.p13
Supplementary files format and content: fpkm, tpm, readcounts

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA)
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. (Note: for FFPE samples, the above two steps can be omitted according to the quality of samples.) Then, First-strand cDNA was generated in First Strand reaction system by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments with adapters were amplified by PCR, and the products were purified by Ampure XP Beads. The library was assessed quality and quantity using the Agilent 2100 bioanalyzer. Then, undergo DSN treatment. The DSN treated library was assessed quality to ensure the high quality of the sequencing data by two methods: checked the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantified the library using real-time quantitative PCR (qPCR). The qualified library was amplified on cBot to generate the cluster on the flowcell. And the amplified flowcell was sequenced single end on the BGI-500 platform (BGI-Shenzhen, China)

value: High metastatic Human hepatocellular Carcinoma Cells

value: quercetin 100μM


title: WGBS control treatment rep1


title: Rhesus Macaque, Sample 06, Submandibular, Male, Left gland, Flash Frozen, RNA

city: Buffalo

first: Charikleia

last: Karageorgiou

state: NY

address: 109 Cooke Hall, Mary Talbert Way

department: Department of Biological Sciences

institute: University at Buffalo

description: Library name: Rhes-06-SM-Mal-L-FF-RNA

data_processing:
Mutltiple tools (FastQC, MultiQC, cutadapt, Hisat2, Kallisto, samtools, featureCounts, DESeq2)
Assembly: GCF_003339765.1; NCBI Macaca mulatta Annotation Release 103
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Macaca mulatta

source_name: Submandibular

extract_protocol:
RNA was isolated from 3 x 30µm sections of tissue using RNAqueous Micro Kit (Ambion) and total RNA samples were DNase-treated (Ambion). Sample yield and integrity was analyzed using a Bioanalyzer (Illumina)."
RNA sequencing was performed by standard operating procedure by GENEWIZ (https://www.genewiz.com/en) using Illumina HiSeq with a 2x150bp configuration.

tag: Sex

value: Male

value: Submandibular

tag: animal id


title: HCCLM3 cells, quercetin 100μM, rep2


title: hZ_Z5, RCAS-hZic3 injected, zeugopod

description: treatment

value: hindlimb zeugopod

value: tissue

value: RCAS-hZic3 overexpression


title: dac treatment rep3

data_processing:
Quality of data in fastq files was assessed using FastQC and low quality bases (quality score lower than 20) and adapter sequences were removed using TrimGalore.
Reads were aligned to the human hg19 reference genome using Hisat2 (version 2.2) and raw read counts were generated using featureCounts.
The data was normalised for composition bias using the calcNormFactors function from the edgeR R package (version 3.36.0), and normalised again and transformed to log2 counts per million reads (CPM) using the voom function from the limma R package ( (version 3.50.3).
Assembly: hg19
Supplementary files format and content: tab-delimited text file with raw counts for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen), 1ug of total RNA was used for the libraries
The libraries were contructed using the QIAseq Fast select rRNA HMR (QIAGEN) kit instructions.

value: kidney epithelial

value: Decitabine


title: Rhesus Macaque, Sample 06, Sublingual, Male, Left gland, Flash Frozen, RNA

description: Library name: Rhes-06-SL-Mal-L-FF-RNA

source_name: Sublingual

value: Sublingual


title: HCCLM3 cells, quercetin 100μM, rep1

value: WT


title: dac treatment rep2

value: human embryonic kidney cells


title: hZ_Z4, RCAS-hZic3 injected, zeugopod

description: treatment


title: Rhesus Macaque, Sample 06, Parotid, Male, Left gland, Flash Frozen, RNA

description: Library name: Rhes-06-PAR-Mal-L-FF-RNA

source_name: Parotid

value: Parotid


title: HCCLM3 cells, quercetin 50μM, rep3

value: quercetin 50μM


title: hZ_Z3, RCAS-hZic3 injected, zeugopod

description: treatment


title: Rhesus Macaque, Sample 06, Pancreas, Male, Flash Frozen, RNA

description: Library name: Rhes-06-PANC-Mal-FF-RNA

source_name: Pancreas

value: Pancreas


title: HCCLM3 cells, quercetin 50μM, rep2


title: aza treamtent rep3

value: Azacitidine


title: hZ_Z1, RCAS-hZic3 injected, zeugopod

description: treatment


title: Rhesus Macaque, Sample 06, Liver, Male, Flash Frozen, RNA

description: Library name: Rhes-06-LIV-Mal-FF-RNA

value: Liver


title: HCCLM3 cells, quercetin 50μM, rep1

value: High metastatic Human hepatocellular Carcinoma Cells


title: aza treamtent rep2


title: HCCLM3 cells, control, rep3

value: control; DMSO


title: Plucked Feather, 12 days, scRNAseq

description: 10x Genomics

value: Feather

value: 12 days

value: H&H stage 38

value: single cell

value: White Leghorn


title: hZ_A5, RCAS-hZic3 injected, autopod

description: treatment

value: hindlimb autopod

value: tissue

value: RCAS-hZic3 overexpression


title: aza treamtent rep1

value: kidney epithelial

value: WT


title: Rhesus Macaque, Sample 05, Sublingual, Male, Left gland, Flash Frozen, RNA

description: Library name: Rhes-05-SL-Mal-L-FF-RNA

value: Male

value: Sublingual


title: hZ_A4, RCAS-hZic3 injected, autopod

description: treatment


title: HCCLM3 cells, control, rep2


title: control treatment rep3

value: human embryonic kidney cells

value: acetic acid/water (1:1)


title: HCCLM3 cells, control, rep1


title: Rhesus Macaque, Sample 05, Parotid, Male, Left gland, Flash Frozen, RNA

description: Library name: Rhes-05-PAR-Mal-L-FF-RNA

value: Parotid


title: hZ_A3, RCAS-hZic3 injected, autopod

description: treatment


title: Rhesus Macaque, Sample 05, Pancreas, Male, Flash Frozen, RNA

description: Library name: Rhes-05-PANC-Mal-FF-RNA

value: Pancreas


title: control treatment rep2


title: dac treatment rep1

value: Decitabine


title: Liver, Fed, LKO 8

city: Toulouse

first: Jean

last: Personnaz

address: CHU Purpan pavillon Lefebvre, av des arènes romaines

department: IRSD

country: France

institute: Inserm

description: Library name: 71_Male_Fed_FGL1_LKO

data_processing:
We used HISAT to align the clean reads to the reference genome. We used Bowtie2 to align the clean reads to the reference genes. Sequencing lenght: PE150
Assembly: mm39
Supplementary files format and content: tab-delimited text file data includes FPKM for all sample

extract_protocol:
RNA was extract using phenol chloroform
RNA library for RNA sequencing were prepared using DNBSEQ stranded specific mRNA library preparation

value: Liver

value: Fgl1 LKO


title: Rhesus Macaque, Sample 05, Liver, Male, Flash Frozen, RNA

description: Library name: Rhes-05-LIV-Mal-FF-RNA


title: hZ_A2, RCAS-hZic3 injected, autopod

description: treatment


title: Rhesus Macaque, Sample 04, Submandibular, Female, Left gland, Flash Frozen, RNA

description: Library name: Rhes-04-SM-Fem-L-FF-RNA

value: Female

value: Submandibular


title: hZ_A1, RCAS-hZic3 injected, autopod

description: treatment


title: Liver, Fed, LKO 7

description: Library name: 70_Male_Fed_FGL1_LKO


title: Rhesus Macaque, Sample 05, Submandibular, Male, Left gland, Flash Frozen, RNA

description: Library name: Rhes-05-SM-Mal-L-FF-RNA


title: Liver, Fed, LKO 6

description: Library name: 63_Male_Fed_FGL1_LKO


title: Rhesus Macaque, Sample 04, Sublingual, Female, Left gland, Flash Frozen, RNA

description: Library name: Rhes-04-SL-Fem-L-FF-RNA


title: WT RNaseH rep2

library_source: other

data_processing:
FastQC was used to assess the overall quality of the samples, and TrimGalore was used to trim low-quality bases and adapter sequences.
Trimmed reads were mapped to UCSC human hg19 genome using Bowtie2 (version 2.4.2)
The mapped reads were deduplicated using the MarkDuplicates command in Picard tools
Assembly: hg19
Supplementary files format and content: bedGraph files for positive and negative strands

molecule: other

extract_protocol:
Trizol extraction of genomic DNA and IP with S9.6 antibody to extract DNA:RNA hybrids. Protocol after Sanz & Chedin (2019) Nature Protocols
The libraries were contructed using the Illumina TruSeq RNA V.2 kit instructions.
DRIPc-seq

tag: anti-body

value: RNaseH


title: Liver, Fed, LKO 3

description: Library name: 55_Male_Fed_FGL1_LKO


title: Liver, Fed, LKO 4

description: Library name: 61_Male_Fed_FGL1_LKO


title: Rhesus Macaque, Sample 04, Pancreas, Female, Flash Frozen, RNA

description: Library name: Rhes-04-PANC-Fem-FF-RNA


title: Rhesus Macaque, Sample 04, Parotid, Female, Left gland, Flash Frozen, RNA

description: Library name: Rhes-04-PAR-Fem-L-FF-RNA


title: p53KO dac dac 2 treatment rep2


title: WT RNaseH rep1


title: Liver, Fed, LKO 5

description: Library name: 62_Male_Fed_FGL1_LKO


title: p53KO dac dac treatment rep2


title: control treatment rep1


title: p53KO dac dac 2 treatment rep1


title: Liver, Fed, WT 8

description: Library name: 72_Male_Fed_WT

value: Fgl1 WT


title: 6D miRNA ADSC TK168 Epi FGFa 060319

type: RNA

city: Barcelona

first: Gemma

last: Arderiu

address: Avda. S. Antoni M. Claret 167

department: Cardiovascular area

country: Spain

institute: Institut de Recerca de l'Hospital de la Santa Creu i Sant Pau IIB-Sant Pau

description: miRNA expression data from ASCs cultured with bFGF

hyb_protocol: Biotin-labeled RNA was hybridized to affymetrix miRNA 4.0 GeneChips for 16 hours (48ºC, 60 rpm) using a GeneChip 645 hybridization oven and washed and stained on the GeneChip Fluidics Station 450 using protocol FS450_0002.

scan_protocol: Scanning of microarrays was performed using the Affymetrix GeneChip 3000 7G scanner. AGGC software was used for scanner images adquisition.

data_processing: Raw data was normalized in Transcriptome Analysis Console (TAC 4.0.2.15) software using RMA-DABG algorithm

label: biotin

source_name: Adipose-derived stem cell

label_protocol: 500 ng of RNA was labeled using Applied Biosystems FlashTag Biotin HSR RNA labeling kit according to manufacturer's instructions.

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM)-Low Glucose (Thermo Fisher Scientific) supplemented with 10% FBS, 100 U/ml penicillin and 0.1 mg/ml streptomycin (Invitrogen) in a humidified environment at 37°C with 5% CO2 and were used between passages 2 and 4.

extract_protocol: miRNA was isolated using a mirVana™ miRNA Isolation Kit with phenol (Life Technologies Corporation) according to the manufacturer's instructions.

treatment_protocol: ASCs were cultured in DMEM-Low Glucose supplemented with 10 ng/ml bFGF (233-FB, R&D Systems). Cells were supplied with fresh medium every 3 days and cultured for a total of 9 days

value: Visceral adipose tissue

tag: categorization

value: obese type 2 diabetes mellitus

tag: state

value: treated


title: p53KO dac dac treatment rep1

value: kidney epithelial


title: Liver, Fed, LKO 2

description: Library name: 50_Male_Fed_FGL1_LKO


title: 6C miRNA ADSC TK132 Epi FGFb 190219


title: Rhesus Macaque, Sample 04, Liver, Female, Flash Frozen, RNA

description: Library name: Rhes-04-LIV-Fem-FF-RNA


title: Rhesus Macaque, Sample 03, Submandibular, Female, Left gland, Flash Frozen, RNA

description: Library name: Rhes-03-SM-Fem-L-FF-RNA


title: p53KO dac control treatment rep2


title: Rhesus Macaque, Sample 03, Sublingual, Female, Left gland, Flash Frozen, RNA

description: Library name: Rhes-03-SL-Fem-L-FF-RNA


title: 6A miRNA ADSC TK106 Epiplon FGFb 050219


title: Rhesus Macaque, Sample 03, Parotid, Female, -RFlash Frozen, RNA

description: Library name: Rhes-03-PAR-Fem-R-FF-RNA


title: 6B miRNA ADSC TK116EP FGFb 070219


title: p53KO dac control treatment rep1


title: Liver, Fed, WT 7

description: Library name: 69_Male_Fed_WT


title: 5D miRNA TK168 Epi 070319

description: miRNA expression data from ASCs

value: basal


title: Liver, Fed, LKO 1

description: Library name: 48_Male_Fed_FGL1_LKO


title: 5B miRNA ADSC TK116 Epiplon 050219

description: miRNA expression data from ASCs


title: p53KO aza aza treatment rep2

value: Azacitidine


title: Rhesus Macaque, Sample 03, Pancreas, Female, Flash Frozen, RNA

description: Library name: Rhes-03-PANC-Fem-FF-RNA


title: 5C miRNA ADSC TK132 epi 260219

description: miRNA expression data from ASCs


title: Liver, Fed, WT 6

description: Library name: 64_Male_Fed_WT


title: OSM_Rep_1

value: Endothelial cells

value: OSM-treated

value: 10 ug/mL OSM


title: p53KO aza aza treatment rep1

value: human embryonic kidney cells


title: Rhesus Macaque, Sample 03, Liver, Female, Flash Frozen, RNA

description: Library name: Rhes-03-LIV-Fem-FF-RNA


title: Liver, Fed, WT 4

description: Library name: 49_Male_Fed_WT


title: Rhesus Macaque, Sample 02, Submandibular, Female, Left gland, Flash Frozen, RNA

description: Library name: Rhes-02-SM-Fem-L-FF-RNA


title: p53KO aza control treatment rep2

value: acetic acid/water (1:1)


title: Rhesus Macaque, Sample 02, Sublingual, Female, Left gland, Flash Frozen, RNA

description: Library name: Rhes-02-SL-Fem-L-FF-RNA

value: Sublingual


title: 4D miRNA ADSC TK168 Sub FGFa 050319

value: Subcutaneous adipose tissue


title: WT dac dac treatment rep2

value: WT

value: Decitabine


title: Rhesus Macaque, Sample 02, Parotid, Female, Left gland, Flash Frozen, RNA

description: Library name: Rhes-02-PAR-Fem-L-FF-RNA

value: Female

value: Parotid


title: Liver, Fed, WT 2

description: Library name: 37_Male_Fed_WT

value: Liver

value: Fgl1 WT


title: Liver, Fed, WT 1

description: Library name: 36_Male_Fed_WT


title: Rhesus Macaque, Sample 02, Pancreas, Female, Flash Frozen, RNA

description: Library name: Rhes-02-PANC-Fem-FF-RNA

value: Pancreas


title: 4B miRNA TK116 subc FGF b 120219

value: obese type 2 diabetes mellitus

value: treated


title: 5A miRNA ADSC TK106EP  070219

description: miRNA expression data from ASCs

value: Visceral adipose tissue

value: basal


title: Rhesus Macaque, Sample 02, Liver, Female, Flash Frozen, RNA

description: Library name: Rhes-02-LIV-Fem-FF-RNA


title: 4C miRNA TK132 subc FGF a  120219


title: WT dac control treatment rep2

value: kidney epithelial


title: 3D miRNA ADSC TK168 Sub 050319

description: miRNA expression data from ASCs


title: 4A miRNA ADSC TK106 sub FGF a 260219


title: Rhesus Macaque, Sample 01, Submandibular, Female, Left gland, Flash Frozen, RNA

description: Library name: Rhes-01-SM-Fem-L-FF-RNA

value: Submandibular


title: PAT, rep2, rep3, CITE-seq

city: Incheon

first: Mijoo

last: Ahn

state: Yeonsu-gu

address: 155 Gaetbeol-ro

country: South Korea

institute: Gachon University

description: 10x Genomics

data_processing:
Fastq files containing cDNA and HTO data were separated with splitBarcode v.2.0.0 (MGI) by sample index sequences.
The reads of Fastq files were trimmed with Trimmomatic v.0.39.
Single-cell ATAC- and RNA-seq data were aligned and counted using cellranger-arc count v.2.0.2 (10x Genomics).
HTO data were preprocessed using CITE-seq-Count v.1.4.5.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: BED files for scATAC-seq peaks
Library strategy: CITE-seq

source_name: Perigonadal adipose tissue

extract_protocol:
Nuclei isolation from frozen mouse adipose tissue was performed following a modified protocol for single-cell multiome ATAC analysis. Briefly, frozen mouse adipose tissues were minced to prepare <0.5 cm pieces on dry ice. The pieces were transferred to a gentleMACS C tube (Miltenyi Biotec, Bergisch Gladbach, Germany) with chilled TST buffer, containing 0.03% Tween20, 0.01% BSA, 146 mM NaCl, 1 mM CaCl2, 21 mM Mg Cl2, and 10 mM Tris-HCl pH 7.5 prepared in ultrapure water. Tissues were then dissociated using the gentleMACS Dissociator (Miltenyi Biotec) by running the mr_adipose_01 program twice. The homogenates were incubated on ice for 10 min and filtered through a 40-µm cell strainer, with washing into a single-nucleus suspension. Nuclei were centrifuged at 500 ×g for 5 min at 4 °C. Each pellet was resuspended in an appropriate volume of chilled nuclei resuspension buffer, containing 0.04% BSA and 0.2 U/μL RNase inhibitor in PBS. Nuclei were further purified and enriched using anti-nucleus microbeads (Miltenyi Biotec). Viability and concentration of nuclei were determined using Countess 3 (Thermo Fisher Scientific) with trypan blue staining.
The nuclei of each sample were incubated with a specific hash-tag antibody (TotalSeq™-A0451~8, BioLegend) for 20 min on ice and then washed thrice with staining buffer. The hash-tagged nuclei were resuspended in the appropriate buffer for downstream analysis and combined to multiplex three or four samples, each containing an equal number of nuclei. Single-cell RNA and ATAC-seq were performed using a Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (cat# CG000338, 10x Genomics, Pleasanton, CA, USA) following the manufacturer's instructions. Briefly, following reverse transcription and cleanup, barcoded ATAC fragments, cDNA, and HTO were amplified with the pre-amplification mix with 1 µL of 0.2 µM HTO-targeting additive primer. Each sample was divided and used separately as input for ATAC and cDNA/HTO. ATAC and cDNA libraries were constructed following the manufacturer's protocol. For the HTO-derived cell hashing library, cDNA/HTO products, which were amplified with cDNA primers and HTO-targeting additive primer, were selected with SPRIselect reagent for subsequent library construction. ATAC, cDNA, and HTO libraries were processed using the MGIEasy Universal Library Conversion Kit (App-A) (cat# 1000004155, MGI, Shenzhen, China) following the manufacturer's instructions. The converted libraries were sequenced using a DNBSEQ-G400 (MGI).

value: Perigonadal adipose tissue


title: WT dac control treatment rep1

value: human embryonic kidney cells

value: acetic acid/water (1:1)


title: WT aza aza treatment rep2

value: Azacitidine


title: Liver, Fed, WT 5

description: Library name: 60_Male_Fed_WT


title: p53KO aza control treatment rep1


title: Liver, Fed, WT 3

description: Library name: 38_Male_Fed_WT


title: Rhesus Macaque, Sample 01, Sublingual, Female, Left gland, Flash Frozen, RNA

description: Library name: Rhes-01-SL-Fem-L-FF-RNA

value: Sublingual


title: mf-lon TopA-PDT, 4h P.I. (AtC)

city: Paris Cedex 05

first: Celine

last: Borde

address: 11 place Marcelin Berthelot

department: CIRB

institute: College de france

data_processing:
Rockhopper software
Sequences were mapped to E.coli MG1655 (NC_000913.3) and read counts were extracted using Rockhopper. RPKMs were calculated based on the total number of reads without rRNAs.
Assembly: E.coli MG155 genome used was NC_000913.3.
Supplementary files format and content: tab delimited text file includes raw counts and RPKM values for each sample

organism: Escherichia coli

growth_protocol: Bacteria were grown in rich medium,LB, at 30°C with agitation.

extract_protocol:
Total RNA was extracted by an aqua-phenol extraction and ethanol precipitation.
Depletions of rRNA were realized with NEBNext rRNA Depletion kit and RNA librairies were prepared with TruSeq Stranded total RNA library Prep Gold kit and sequenced by Macrogen Europe.

treatment_protocol: Exponential growth cultures were diluted in LB and were induced for 4h with 50ng/mL AtC.

value: AtC 50ng/mL

tag: time

value: 4H P.I.


title: Rhesus Macaque, Sample 01, Parotid, Female, Left gland, Flash Frozen, RNA

description: Library name: Rhes-01-PAR-Fem-L-FF-RNA

value: Female

value: Parotid


title: WT aza aza treatment rep1

value: WT


title: 3B miRNA TK116 subc  120219

description: miRNA expression data from ASCs

value: Subcutaneous adipose tissue


title: WT dac dac treatment rep1

value: Decitabine


title: 3C miRNA ADSC TK132 sub 260219

description: miRNA expression data from ASCs

value: obese type 2 diabetes mellitus


title: 3A miRNA TK106 sub 290319

description: miRNA expression data from ASCs


title: mf-lon WT, 4h P.I. (AtC)

value: MG1655pro lacZ::PLtetO-mf-lon


title: PAT, rep1, scATAC-seq

description: 10x Genomics

library_source: genomic single cell

data_processing:
Fastq files containing cDNA and HTO data were separated with splitBarcode v.2.0.0 (MGI) by sample index sequences.
The reads of Fastq files were trimmed with Trimmomatic v.0.39.
Single-cell ATAC- and RNA-seq data were aligned and counted using cellranger-arc count v.2.0.2 (10x Genomics).
HTO data were preprocessed using CITE-seq-Count v.1.4.5.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: BED files for scATAC-seq peaks


title: 8wk_bl6_fat depots_experiment 2

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: 8 samples were hashed together into a single 10X scRNA-seq run

data_processing:
Sequenced reads were demultiplexed, aligned, assigned to cells, and output as count matrices using Cell Ranger (10x Genomics) and  bcl2fastq Conversion (Illumina)
Hash-by-cell matrices were computed using CITE-seq-count.
Cells with no or multiple hashes, high mitochondrial content, low gene number, low UMI number, or lineage markers of contaminants were filtered out in Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: BAT, SAT, VAT, Spleen

extract_protocol:
CD4 T cells were isolated from fat tissue depots via a mechanical and enzymatic/collagenase II digestion protocol. Spleen samples were isolated by mechanical digestion. All samples were treated with red blood cell lysis buffer and filtered through 70 uM filter.
10x Genomics library prep, 3' v3 chemistry

value: BAT, SAT, VAT, Spleen

value: Male

tag: hashid

value: BAT1 (TSA-H2); BAT2 (TSA-H12); SAT1 (TSA-H4); SAT2 (TSA-H7); VAT1( TSA-H8); VAT2 (TSA-H9); SPLN1 (TSA-H10); SPLN2 (TSA-H11)


title: Rhesus Macaque, Sample 01, Liver, Female, Flash Frozen, RNA

description: Library name: Rhes-01-LIV-Fem-FF-RNA

tag: tissue

value: Liver


title: PAT, rep1, scRNA-seq

description: 10x Genomics

molecule: nuclear RNA

value: Perigonadal adipose tissue


title: 8wk_bl6_fat depots_experiment 1

value: BAT1 (TSA-H2); BAT2 (TSA-H5); SAT1 (TSA-H6); SAT2 (TSA-H7); VAT1( TSA-H8); VAT2 (TSA-H9); SPLN1 (TSA-H10); SPLN2 (TSA-H11)


title: WT aza control treatment rep1

value: kidney epithelial

tag: cell line

value: human embryonic kidney cells

value: acetic acid/water (1:1)


title: PAT, rep2, rep3, scATAC-seq

description: 10x Genomics


title: hPSC, shPIN1, untreated, rep3

status: Public on Aug 26 2025

city: Portland

first: Ellen

last: Langer

state: Oregon

address: 2720 S Moody Ave

department: CEDAR

institute: OHSU

description: Library name: PSCPINU3

data_processing:
Base calling using bcl2fastq
Adapter trimming and quality filtering were performed using Trimmomatic v0.39. Reads shorter than 36 bases after trimming were discarded.
Trimmed reads were aligned to the GRCh38 human reference genome using STAR v2.7.11b with default parameters.
Aligned BAM files were subsequently processed with featureCounts v2.0.8 to generate gene-level count matrices. All downstream differential expression analyses were performed using DESeq2 v1.46.0.
Assembly: GRCh38
Supplementary files format and content: Knockdown_proteincoding_fpkm.txt (FPKM  of all protein coding genes, text file, Genes exhibiting zero counts across all samples were filtered out prior to downstream analysis.)
Supplementary files format and content: Knockdown_COUNTS.txt (text file, counts table)

source_name: pancreatic stellate cells

growth_protocol: Primary human pancreatic stellate cells were purchased from Sciencell and grown in 2D in Stellate Cell Media.

extract_protocol:
Qiagen Rneasy kit
For paired end RNA-seq, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library then underwent end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and RT-PCR for quantification and bioanalyzer for size distribution. Quantified libraries were pooled and sequenced on an Illumina NovoSeq X plus. For single end RNA-seq, sequencing libraries were constructed using a TruSeq Stranded mRNA kit (Illumina, San Diego, CA). Briefly, poly(A)+ RNA was isolated using oligo-dT-coated magnetic beads. The recovered RNA was then chemically fragmented. First strand cDNA was generated using random hexamers as primers for reverse transcriptase. Strand-specific second strand cDNA synthesis was performed and a single ‘A’ nucleotide was then added to each end. Illumina adaptors were ligated to the cDNAs. Limited-round (15-cycle) PCR was used to amplify the material to yield the final libraries. Library concentration was determined using real-time PCR with primers complementary to the Illumina adaptors. Sample libraries were diluted and applied to an IlluminaNextSeq500 HiOutput flow cell. Llibraries were prepared with indexing barcodes to permit multiplexing in a single lane. The 75-cycle single read sequencing was used to assemble the reads into standard fastq formatted data.

treatment_protocol: PSCs were infected with an shSCR (control) or shPIN1 (knockdown) lentivirus and stable pools selected with puromycin. Cells were plated overnight, and then treated +/- 5 ng/mL TGFB for 24 hours prior to collection.

tag: cell type

value: pancreatic stellate cells

tag: shRNA

value: Untreated

tag: batch


title: hPSC, shSCR, TGFB, rep3

description: Library name: PSCSCRT3

value: shSCR

tag: treatment

value: TGFB


title: hPSC, shPIN1, untreated, rep2

description: Library name: PSCPINU2


title: hPSC, shSCR, TGFB, rep2

description: Library name: PSCSCRT2


title: hPSC, shPIN1, TGFB, rep1

description: Library name: PSCPINT1


title: hPSC, shSCR, untreated, rep2

description: Library name: PSCSCRU2


title: hPSC, shSCR, TGFB, rep1

description: Library name: PSCSCRT1


title: PAT, rep2, rep3, scRNA-seq

description: 10x Genomics


title: hPSC, shPIN1, untreated, rep1

description: Library name: PSCPINU1


title: hPSC, ATRA, TGFB, rep3

description: Library name: PSC_A_T3

data_processing:
Base calling using bcl2fastq
Adapter trimming and quality filtering were performed using Trimmomatic v0.39. Reads shorter than 36 bases after trimming were discarded.
Trimmed reads were aligned to the GRCh38 human reference genome using STAR v2.7.11b with default parameters.
Aligned BAM files were subsequently processed with featureCounts v2.0.8 to generate gene-level count matrices. All downstream differential expression analyses were performed using DESeq2 v1.46.0.
Assembly: GRCh38
Supplementary files format and content: inhibitor_proteincoding_fpkm.txt(FPKM for all protein coding genes, tab delimited text, Genes exhibiting zero counts across all samples were filtered out prior to downstream analysis.)
Supplementary files format and content: final_counts_inhibitor.txt (text file, counts table)

extract_protocol:
Qiagen Rneasy kit
For paired end RNA-seq, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library then underwent end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and RT-PCR for quantification and bioanalyzer for size distribution. Quantified libraries were pooled and sequenced on an Illumina NovoSeq X plus.

treatment_protocol: PSCs were treated with DMSO, 10 uM ATRA, or 10 uM KPT-6566 for 48 hours. Media was then changed, replenishing the inhibitor treatment and cells were also treated +/- 5 ng/mL TGFB1. Cells were collected 24 hours after TGFB treatment.

tag: agent

value: 10uM ATRA


title: hPSC, shSCR, untreated, rep1

description: Library name: PSCSCRU1


title: WT aza control treatment rep2

tag: genotype

value: WT


title: hPSC, KPT, untreated, rep3

description: Library name: PSC_K_U3


title: hPSC, ATRA, untreated, rep3

description: Library name: PSC_A_U3


title: hPSC, KPT, TGFB, rep3

description: Library name: PSC_K_T3


title: Rhesus Macaque, Sample 01, Pancreas, Female, Flash Frozen, RNA

description: Library name: Rhes-01-PANC-Fem-FF-RNA

value: Female

value: Pancreas


title: PAT, rep1, CITE-seq

description: 10x Genomics


title: hPSC, DMSO, TGFB, rep3

description: Library name: PSC_D_T3

value: DMSO


title: hPSC, shPIN1, TGFB, rep3

description: Library name: PSCPINT3


title: hPSC, shPIN1, TGFB, rep2

description: Library name: PSCPINT2


title: hPSC, ATRA, untreated, rep2

description: Library name: PSC_A_U2


title: hPSC, KPT, TGFB, rep2

description: Library name: PSC_K_T2


title: hPSC, ATRA, TGFB, rep1

description: Library name: PSC_A_T1


title: hPSC, DMSO, untreated, rep2

description: Library name: PSC_D_U2


title: hPSC, DMSO, TGFB, rep2

description: Library name: PSC_D_T2


title: hPSC, KPT, untreated, rep2

description: Library name: PSC_K_U2


title: hPSC, KPT, untreated, rep1

description: Library name: PSC_K_U1


title: hPSC, DMSO, TGFB, rep1

description: Library name: PSC_D_T1


title: hPSC, shSCR, untreated, rep3

description: Library name: PSCSCRU3


title: hPSC, ATRA, untreated, rep1

description: Library name: PSC_A_U1


title: hPSC, ATRA, TGFB, rep2

description: Library name: PSC_A_T2


title: hPSC, DMSO, untreated, rep1

description: Library name: PSC_D_U1


title: DNA_IMR90_A_097

city: Tsu-shi

first: Rawin

last: Poonperm

state: Mie

address: 1577 Kurimamachiya

department: Graduate School of Bioresources

country: Japan

institute: Mie University

data_processing:
Computation associated with the transcriptome profiling of (scRNA-seq) single cells: All RNA-seq, scRNA-seq, and scRR-seq-RNA data were analyzed using a complete nextflow pipeline, ramdaq v.1.9.2 (Yoshimura, M., Ozaki, H. & Kelly, T. ramdaq. Dataset on Zenodo (2023). doi:10.5281/zenodo.7655298). Human gencode v38 and mouse gencode vM25 were used as references.  Computation associated with the RT profiling (scRepli-seq) of single cells: For non-haplotype/allele-specific analyses, we followed our established pipeline for scRepli-seq RT analysis as described (Takahashi et al., Nat Genet 2019). We mapped scRR-seq-DNA data to hg38 and mm10 reference genomes for human and mouse cells, respectively, using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 40-kb nonoverlapping bins (or 80-kb bins as indicated) using AneuFinder (v.1.2.1). For binarization, different options were applied to each cell depending on their FACS sorting gates (2-HMM option for G1 FACS gate: most.frequent.state = ‘1-somy’; 2-HMM option for S-phase FACS gates: most.frequent.state = ‘2-somy’).  Computation associated with the detection of CNVs in single cells: We mapped G1 IMR-90 scRR-seq-DNA data to hg38 reference genome using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 50-kb, 100-kb, 200-kb, and 500-kb nonoverlapping bins. Using AneuFinder (v.1.2.1), we analyzed CNVs using Aneufinder wrapper with the following parameters: method=‘dnacopy’, correction.method = ‘mappability’, blacklist = ENCODE Blacklist version 231, mappability.reference = merged G1 reads).
Assembly: hg38
Supplementary files format and content: txt
Library strategy: scRepli-seq

extract_protocol:
Single cells were collected into 0.2 ml PCR tubes by cell sorter or manually picked and lysed in RamDA-seq lysis buffer (TOYOBO, #RMD-101) containing 2 mg/ml Dynabeads™ MyOne™ Carboxylic Acid (Invitrogen, #65011). Genomic DNA was trapped on the beads, while RNA was released into the lysis buffer. The isolated DNA on magnetic beads was subjected to whole-genome amplification (WGA) and Next-Generation Sequencing (NGS) library preparation, as described in scRepli-seq (Takahashi et al., Nat Genet 2019). The DNA-seq (scRepli-seq) data was used to assess genome-wide DNA copy numbers, karyotype G1-phase cells, and analyze the replication state of S-phase cells. In parallel, the RNA isolated in the supernatant was subjected to scRamDA-seq (Hayashi et al., Nat Commun 2018) using the GenNext®RamDA-seq™ Single Cell Kit (TOYOBO, #RMD-101) according to the manufacturer’s instructions with modifications.
Sample and library preparation for scRR-seq-DNA (scRepli-seq): Genomic DNA was subjected to WGA with a SeqPlex kit (Sigma, SEQXE) in a 30-µl reaction volume, per the manufacturer’s instructions. Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads (1.7× reaction volume), and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The gDNA was then purified with Agencourt AMPure XP SPRI beads (2.0× reaction volume) and eluted in 20 µl of 1/10× Elution Buffer (Qiagen). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu). We could easily distinguish single cells from zero or two cells by quantification of DNA with MultiNA, which provided reassurance that the gDNA was indeed derived from single cells. Then NGS libraries were constructed using the NGS LTP Library Preparation Kit (KAPA, KK8232) with a SeqCap adapter kit A/B (Roche, 07141530001/07141548001) or NEXTflex DNA barcode (Bio Scientific, NOVA), or the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England BioLabs , #E7645) with NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1, Set 2) (New England BioLabs , #E7600S, #E7780S ) or NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1, Set 2, Set 3, Set 4) (New England BioLabs , #E7355L, E7500L, E7710L, E7730L). Finally, the samples were subjected to NGS on an Illumina HiSeq X Ten system or Novaseq X Plus system (150-bp length, paired-end read).  Library preparation for scRR-seq-RNA scRamDA-seq NGS libraries were generated by using the Nextera® XT Library Prep Kit 24 Samples (illumina, #15032350, #15032352) with Nextera® XT Index Kit v2 Set A 96 indexes-samples (Illumina, #15052163) according to the manufacturer’s instructions with modifications. Finally, the samples were subjected to NGS on an Illumina HiSeq X Ten system or Novaseq X Plus system (150-bp length, paired-end read).

value: Aphidicolin treatment


title: DNA_IMR90_C_010

value: Control


title: DNA_IMR90_A_128


title: DNA_IMR90_A_098


title: DNA_IMR90_C_001


title: hPSC, DMSO, untreated, rep3

description: Library name: PSC_D_U3


title: DNA_IMR90_A_126


title: DNA_IMR90_A_127


title: DNA_IMR90_A_119


title: DNA_IMR90_A_117


title: DNA_IMR90_A_115


title: DNA_IMR90_A_125


title: DNA_IMR90_A_122


title: DNA_IMR90_A_112


title: DNA_IMR90_A_107


title: DNA_IMR90_A_103


title: hPSC, KPT, TGFB, rep1

description: Library name: PSC_K_T1


title: DNA_IMR90_A_110


title: DNA_IMR90_A_108


title: DNA_IMR90_A_100


title: DNA_IMR90_A_106


title: RNA_IMR90_A_122

data_processing:
Computation associated with the transcriptome profiling of (scRNA-seq) single cells: All RNA-seq, scRNA-seq, and scRR-seq-RNA data were analyzed using a complete nextflow pipeline, ramdaq v.1.9.2 (Yoshimura, M., Ozaki, H. & Kelly, T. ramdaq. Dataset on Zenodo (2023). doi:10.5281/zenodo.7655298). Human gencode v38 and mouse gencode vM25 were used as references.  Computation associated with the RT profiling (scRepli-seq) of single cells: For non-haplotype/allele-specific analyses, we followed our established pipeline for scRepli-seq RT analysis as described (Takahashi et al., Nat Genet 2019). We mapped scRR-seq-DNA data to hg38 and mm10 reference genomes for human and mouse cells, respectively, using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 40-kb nonoverlapping bins (or 80-kb bins as indicated) using AneuFinder (v.1.2.1). For binarization, different options were applied to each cell depending on their FACS sorting gates (2-HMM option for G1 FACS gate: most.frequent.state = ‘1-somy’; 2-HMM option for S-phase FACS gates: most.frequent.state = ‘2-somy’).  Computation associated with the detection of CNVs in single cells: We mapped G1 IMR-90 scRR-seq-DNA data to hg38 reference genome using bwa (v.0.7.17-r1188). We then analyzed scRR-seq-DNA data of the whole genome for each single cell in 50-kb, 100-kb, 200-kb, and 500-kb nonoverlapping bins. Using AneuFinder (v.1.2.1), we analyzed CNVs using Aneufinder wrapper with the following parameters: method=‘dnacopy’, correction.method = ‘mappability’, blacklist = ENCODE Blacklist version 231, mappability.reference = merged G1 reads).
Assembly: hg38
Supplementary files format and content: txt


title: RNA_IMR90_C_010


title: RNA_IMR90_A_097


title: DNA_IMR90_A_102


title: DNA_IMR90_A_101


title: DNA_IMR90_A_109


title: RNA_IMR90_A_115


title: RNA_IMR90_A_113


title: RNA_IMR90_A_128


title: RNA_IMR90_A_127


title: RNA_IMR90_A_126


title: RNA_IMR90_A_125


title: RNA_IMR90_A_117


title: RNA_IMR90_A_119


title: RNA_IMR90_A_112


title: RNA_IMR90_A_108


title: RNA_IMR90_A_110


title: RNA_IMR90_A_109


title: DNA_IMR90_A_113


title: RNA_IMR90_A_107


title: RNA_IMR90_C_001


title: RNA_IMR90_A_098


title: RNA_IMR90_A_103


title: RNA_IMR90_A_100


title: Multiome, D6 Z2KO AntNPCs, ATAC

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

institute: Institute of Biomedicine and Biotechnology of Cantabria

description:
Library name: Z2KO_D6_snATAC
ATAC (10x Genomics). Read 1: contains cell barcode and UMI; Read 2: contains sequence of the DNA fragment adjacent to one Tn5 integration site; Read 3: contains the sequence from the opposite end of the same fragment (other Tn5 integration site).

data_processing:
Multiome scRNA-Seq and scATAC-Seq derived sequencing files for D3 WT, D3 Zic2-/-, D6 WT and D6 Zic2-/- were processed independently with the Cell Ranger ARC (2.0.2) software. More specifically, cellranger-arc count was employed taking as reference genome the 10X Genomics pre-built version for mm10 (refdata-cellranger-arc-mm10-2020-A-2.0.0). Next, data from WT and Zic2-/- cells, considering each differentiation timepoint independenly (D3 and D6), were loaded into R with the help of Seurat and Signac packages. Regarding the scATAC-seq data, a unified set of consensus peaks per differentiation time-point was defined by combining the peaks called in WT and Zic2-/- by Cell Ranger ARC, using reduce() from GenomicRanges followed by the selection of peaks with a width between 20 and 10000 bps and the re-calculation of read counts in this new set of peaks with the help of Signac FeatureMatrix(). Subsequently, only cells meeting the following requirements were kept (i) RNA metrics: 200 < nFeature_RNA < 8000, 500 < nCount_RNA < 50000 and percent.mt < 40 and (ii) ATAC metrics: 200 < nFeature_ATAC < 60000, TSS.enrichment > 1 and nucleosome_signal < 2.
With respect to the scRNA-Seq data, count matrices were normalised with the "LogNormalize" option (available in the Seurat NormalizeData() method) and scaled. Next, PCAs were performed based on the top 2000 most variable features. To mitigate potential batch effects, gene expression data from WT and Zic2-/- cells were integrated applying Seurat’s Canonical Correlation Analysis (CCA) integration method (available in the IntegrateLayers function). The integration was performed on the PCA embeddings. Then, UMAPs were generated using the first 40 dimensions of the integrated embeddings.
With respect to the scATAC-Seq data, the peak count matrix was normalized through Latent Semantic Indexing (LSI). This involved applying the term frequency-inverse document frequency (TF-IDF) normalization followed by singular value decomposition (SVD) (50 singular values were computed). The first LSI component was not considered in downstream analyses given its expected high correlation with sequencing depth. Next, following an integration strategy analogous to the CCA for scRNA-Seq data, scATAC-Seq data from WT and Zic2-/- cells was integrated applying Reciprocal Latent Semantic Indexing (RLSI). First, integration anchors between the datasets were calculated with the FindIntegrationAnchors() Seurat function, by specifying reduction ="rlsi" and using dimensions 2-30. Next, a batch-corrected low-dimensional representation was obtained with the IntegrateEmbeddings() function, taking profit of the calculated anchors and the previously computed LSI embeddings. Then, UMAPs were generated using dimensions 2-30 of the integrated LSI embeddings.
Assembly: mm10
Supplementary files format and content: CellRanger output files: filtered_feature_bc_matrix.h5; atac_fragments.tsv.gz

source_name: Z2KO E14Tg2a D6 AntNPCs

growth_protocol: For the AntNPC differentiation, mESCs were plated at 20.000 cells/cm2 on geltrex-coated plates (ThermoFisher, A1413302) and grown in N2B27 medium: Advanced Dulbecco’s Modified Eagle Medium F12 (Life Technologies, 21041025) and Neurobasal medium (Life Technologies,12348017) (1:1), supplemented with 1 × N2 (R&D Systems, AR009), 1 × B27 (Life Technologies, 12587010), 2mM l-glutamine (Life Technologies, 25030024) and 0.1 mM 2-mercaptoethanol (Life Technologies, 31350010)). During the six days of differentiation, the N2B27 medium was additionally supplemented with the following components: bFGF (ThermoFisher Scientific, PHG0368) 10 ng/ml from day 0 to day 2, Xav939 (Sigma-Aldrich, X3004-5MG) 5 µM from day 2 to day 6, BSA (ThermoFisher Scientific, 15260037) 1 mg/ml at day 0 and 40 µg/mL the remaining days.

extract_protocol:
Nuclei isolation from WT and Z2KO D3 progenitor cells and D6 AntNPCs was performed by washing cells twice with PBS before detaching them from the tissue culture plate with Stempro™ Accutase™ Cell Dissociation Reagent (Thermo Scientific, A1110501). The Accutase incubation times were adjusted to the cell type (6 min for D3 progenitors and 10 min for D6 AntNPCs). Next, Accutase was inactivated with BSA 0.04% in PBS. Cell clumps were disrupted by gently pipetting up and down the cell suspension in the collection tubes. Cell suspension was then centrifuged for 5 min at 300 rcf. The supernatant was aspirated without disrupting the cell pellet and cells were washed twice in BSA 0.04% in PBS. Then, cells were diluted 1/10 in BSA 0.04% in PBS and counted. Next, 106 cells were transferred to a DNA LoBind® 1.5 ml microtube (Eppendorf, 0030108051). Cells were centrifuged again at 300 rcf for 5 min at 4ºC. Next, the supernatant was carefully aspirated and cells were lysed by adding 175 µl of pre-chilled Lysis Buffer (10X Genomics) to the pellet while smoothly pipetting up and down 10 times. After incubation for 4 min on ice, suspension was centrifuged at 500 rcf for 5 min at 4º C. Then, supernatant was completely removed without disrupting the nuclei pellet. Nuclei suspension was cleaned up by adding Wash Buffer (10X Genomics) followed by centrifugation (500 rcf, 5 min at 4ºC). Assuming ~50% nuclei loss during cell lysis, cells were resuspended in chilled Diluted Nuclei Buffer (10X Genomics) to achieve the desired final nuclei concentration. The rest of the steps of the scATAC-seq and scRNA-seq coupled protocol were performed exactly as indicated in the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide CG000338 Rev F.
Single-cell 3′ gene expression libraries were prepared using the Chromium Next GEM Multiome ATAC + Gene Expression kit (10x Genomics) according to the manufacturer’s protocol. Briefly, nuclei were isolated and loaded into the Chromium Next GEM Chip J, where individual nuclei were partitioned into Gel Bead-In-Emulsions (GEMs) together with a barcoded oligonucleotide gel bead and reverse transcription reagents. Within each GEM, mRNA transcripts were reverse transcribed to generate barcoded cDNA containing both a unique cell barcode and a unique molecular identifier (UMI). After breaking the emulsions, cDNA was recovered, amplified by PCR, and purified. Final 3′ gene expression libraries were constructed through enzymatic fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR, followed by quality control and quantification. ATAC libraries were prepared from the same nuclei using the Chromium Next GEM Multiome ATAC + Gene Expression kit (10x Genomics) following the manufacturer’s protocol. Isolated nuclei were transposed with Tn5 transposase, which inserted sequencing adapters at accessible chromatin sites. Transposed DNA was then loaded into the Chromium Next GEM Chip J with barcoded gel beads and amplification reagents. In GEMs, DNA fragments were amplified with primers containing a cell barcode and UMI, enabling single-nucleus resolution. Following GEM breakage, libraries underwent additional amplification and enrichment PCR steps to incorporate sequencing adapters and sample indices. Libraries were purified, quality-checked, and quantified prior to sequencing.

value: Z2KO E14Tg2a D6 AntNPCs


title: RNA_IMR90_A_101


title: RNA_IMR90_A_106


title: Multiome, D6 WT AntNPCs, ATAC

description:
Library name: WT_D6_snATAC
ATAC (10x Genomics). Read 1: contains cell barcode and UMI; Read 2: contains sequence of the DNA fragment adjacent to one Tn5 integration site; Read 3: contains the sequence from the opposite end of the same fragment (other Tn5 integration site).

source_name: E14Tg2a D6 AntNPCs

value: E14Tg2a D6 AntNPCs


title: Multiome, D3 E14Tg2a Z2KO cells, ATAC

description:
Library name: Z2KO_D3_snATAC
ATAC (10x Genomics). Read 1: contains cell barcode and UMI; Read 2: contains sequence of the DNA fragment adjacent to one Tn5 integration site; Read 3: contains the sequence from the opposite end of the same fragment (other Tn5 integration site).

source_name: Z2KO E14Tg2a D3 cells

value: Z2KO E14Tg2a D3 cells


title: Multiome, D3 E14Tg2a Z2KO cells, GEX

description:
Library name: Z2KO_D3_snRNA
3' mRNA (10x Genomics). Read 1: contains cell barcode and UMI; Read 2 contains transcript sequence.


title: RNA_IMR90_A_102


title: Multiome, D3 E14Tg2a WT cells, GEX

description:
Library name: WT_D3_snRNA
3' mRNA (10x Genomics). Read 1: contains cell barcode and UMI; Read 2 contains transcript sequence.

source_name: E14Tg2a D3 cells

value: E14Tg2a D3 cells


title: Multiome, D6 Z2KO AntNPCs, GEX

description:
Library name: Z2KO_D6_snRNA
3' mRNA (10x Genomics). Read 1: contains cell barcode and UMI; Read 2 contains transcript sequence.


title: Multiome, D6 WT AntNPCs, GEX

description:
Library name: WT_D6_snRNA
3' mRNA (10x Genomics). Read 1: contains cell barcode and UMI; Read 2 contains transcript sequence.


title: Z2KO_D3_ATAC_rep1

description: Library name: Sample 9

data_processing:
Reads quality control and removal of low quality regions and/or adapters was performed with fastqc, MultiQC and Trimmomatic . Next, reads were mapped to the mouse reference assembly (mm10) using Bowtie2. Subsequently, reads with a mapping quality below 10 and duplicated reads were discarded with Samtools. In addition, ATAC-seq BigWigs were generated applying a quantile normalization between samples of the same differentiation timepoint  (e.g., quantile normalization applied between all D3 ATAC-seq samples, including WT and Zic2 -/-). In order to generate them, the mm10 genome was split in bins of 100 bps with bedtools makeWindows and the resulting coordinates were converted into saf (simplified annotation format) format, to be accepted as an annotation file in featureCounts. Next, for each sample, considering their bam file and the saf file, the number of reads in each of the 100 bp genome windows was counted with featureCounts. The resulting counts matrix was loaded in R where two main steps were applied. In the first one, read counts per bin were converted to RPKMs. Next, the resulting values were quantile normalized among samples using the function normalize.quantiles() from the preprocessCore package. Then, bedgraphs with the quantile normalized values per 100 bp window were generated and subsequently converted to BigWigs with the usage of UCSC bedGraphToBigWig tool. Finally, a reference BigWig file per condition was created averaging the information of both replicates with Wiggletools mean and bedGraphToBigWig tools.
Assembly: mm10
Supplementary files format and content: BigWig

source_name: Z2KO E14Tg2a D3

growth_protocol: mESC maintenance and AntNPCs differentiation protocol. E14Tg2a (E14) mouse ESC were cultured on gelatin-coated plates using Knock-out DMEM (Life Technologies, 10829018) supplemented with 15% FBS (Life Technologies, 10082147), leukemia inhibitory factor (LIF), antifungal and antibiotics (Sigma-Aldrich, A5955), β-mercaptoethanol (ThermoFisher Scientific, 21985023), Glutamax (ThermoFisher Scientific, 35050038) and MEM NEAA (ThermoFisher Scientific, 11140035). Cells were cultured at 37°C with 5% CO2. For the AntNPC differentiation, mESCs were plated at 20.000 cells/cm2 on geltrex-coated plates (ThermoFisher, A1413302) and grown in N2B27 medium: Advanced Dulbecco’s Modified Eagle Medium F12 (Life Technologies, 21041025) and Neurobasal medium (Life Technologies,12348017) (1:1), supplemented with 1 × N2 (R&D Systems, AR009), 1 × B27 (Life Technologies, 12587010), 2mM l-glutamine (Life Technologies, 25030024) and 0.1 mM 2-mercaptoethanol (Life Technologies, 31350010)). During the six days of differentiation, the N2B27 medium was additionally supplemented with the following components: bFGF (ThermoFisher Scientific, PHG0368) 10 ng/ml from day 0 to day 2, Xav939 (Sigma-Aldrich, X3004-5MG) 5 µM from day 2 to day 6, BSA (ThermoFisher Scientific, 15260037) 1 mg/ml at day 0 and 40 µg/mL the remaining days.

extract_protocol:
Assay for Transposase Accessible Chromatin (ATAC-Seq). Tn5 transposase (produced in house at EMBL Heidelberg Protein Expression and Purification Core Facility) was pre-loaded with sequencing adaptors (see Supplementary Data 4) by mixing one volume of Tn5 enzyme with half volumes of annealed R1N:ME and R2N:ME oligos (e.g., 2µl Tn5, 1µl R1N:ME, 1µl R2N:ME). The assembly reaction was incubated at room temperature for 30–60 min. ATAC-seq was performed using 20.000 nuclei per reaction. The transposition mix (containing 16 µl Transposition buffer- 38.8 mM Tris-Acetate, 77.6 mM Na-Acetate, 11.8 mM Mg-Acetate, 18.8% DMF 0.12% NP40, 0.005X Protease Inhibitor Cocktail, Nucleasefree H2O, 2 µl Assembled Tn5 + oligos and 2 µl of Nuclei suspension) was incubated at 37°C for 60 min with shaking at 500 rpm. DNA was purified using the MinElute Reaction Cleanup Kit (Qiagen, 28204), eluting in 22 µl of elution buffer. Samples were stored at -20°C prior to library preparation.
To enable multiplexed sequencing, each sample (WT and Zic2-/- (Z2KO) at D0, D3, and D6) was uniquely barcoded with non-overlapping index combinations. For each sample, 20 µl of tagmented DNA were mixed with 30 µl of amplification mix and preamplified in a Veriti™ thermocycler (Applied Biosystems). To determine the optimal number of cycles, 2.5 µl of the preamplified product were subjected to RT-qPCR using 12.5 µl of qPCR mix. Based on amplification curves, the remaining PCR was completed with the minimal number of additional cycles to avoid overamplification. Amplified libraries underwent double-sided size selection using SPRIselect reagent (Beckman Coulter, B23317) at a 1.4× bead ratio, eluting in 22 µl of Elution Buffer. DNA concentrations were measured using the Qubit™ dsDNA High Sensitivity Assay Kit (Thermo Scientific, Q32854), and fragment size distribution was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent, 5067-4626). Barcoded libraries were pooled and sequenced on an Illumina NextSeq2000 platform using paired-end reads and ~40 million reads per sample.

treatment_protocol: Zic2 deletions using CRISPR-Cas9.Pairs of sgRNAs were designed to flank Zic2 coding region using Benchling’s genome engineering toolbox (https://www. benchling.com/). Guides were selected for high on target efficiency and minimal off target potential. Complementary oligonucleotides containing BbsI (NEB, R0539L) overhangs were synthesized and annealed (see Supplementary Data 4) by heating to 95°C for 5 min, followed by gradual cooling down to 25°C at -5 °C/min. Annealed oligos were ligated into BbsI-digested pX330A-hCas9-longchimeric-gRNA-G2P vector using T4 DNA ligase (NEB, M0202L) and transformed into chemically competent E. coli (TOP10) via heat shock. Colonies were plated on LB-ampicillin agar and screened by colony PCR to confirm the presence of the desired insert (see Colony PCR section). Plasmids were purified using the NZY Miniprep Kit (NZYTech, MB01001) and verified by Sanger sequencing with the pX330A_R primer (see Supplementary Data 4). Verified clones were stored as glycerol stocks at -140°C. mESCs were plated on gelatin-coated 12- or 6-well plates and co-transfected with Lipofectamine 3000 transfection reagent (Thermo Fisher Scientific, L3000001) and one or two sgRNA-expressing pX330A vectors. For 12-well plates, 150.000 mESC were transfected with 1.5 µl of Lipofectamine 3000. Transfection efficiency was assessed via GFP fluorescence 24 h later. Cells with 70–90% transfection efficiency underwent puromycin (Sigma-Aldrich, P8833-25MG) selection (2 µg puromycin/ml during 48 h). Puromycin-resistant cells were serially diluted and plated in 96-well plates for clonal expansion. After 10–12 days, individual colonies were split into duplicate wells: one for gDNA extraction and PCR based genotyping and another for expansion and maintenance of each clone. Positive Zic2 knock-out mESC clones were expanded and cryopreserved at -140 °C for future use.

value: Z2KO E14Tg2a D3

value: Differentiation to AntNPCs (sample collection at D3); Assay for Transposase-Accessible Chromatin


title: infarct tissue, day 28, type 2 diabetic, rep 10

city: Jackson

first: Alan

middle: J

last: Mouton

state: Mississippi

address: 2500 North State Street

department: Physiology and Biophysics

institute: University of Mississippi Medical Center

description: Library name: 62_4_lo_STZ_HFFD_1481_S31

data_processing:
FastQ files were generated, and alignment and differential expression using DESeq2 was performed on the Cloud Computing Platform (Basespace).
Assembly: mm39
Supplementary files format and content: tab delimited text file including raw counts for each sample

source_name: left ventricular infarct

extract_protocol:
RNA was extracted with the PureLink RNA Mini Kit.
cDNA libraries developed with the TruSeq Stranded RNA-mRNA kit (Illumina).

value: left ventricular infarct

value: myocardial infarction

value: day 28


title: Z2KO_D6_ATAC_rep1

description: Library name: Sample 11

source_name: Z2KO E14Tg2a AntNPCs D6

value: Z2KO E14Tg2a AntNPCs D6

value: Differentiation to AntNPCs (sample collection at D6); Assay for Transposase-Accessible Chromatin


title: Z2KO_D0_ATAC_rep2

description: Library name: Sample 8

source_name: Z2KO E14Tg2a mESC D0

value: Z2KO E14Tg2a mESC D0

value: Culture in S+LIF; Assay for Transposase-Accessible Chromatin


title: WT_D6_ATAC_rep1

description: Library name: Sample 5

source_name: E14Tg2a AntNPCs D6

value: E14Tg2a AntNPCs D6

value: WT


title: WT_D6_ATAC_rep2

description: Library name: Sample 6


title: WT_D3_ATAC_rep1

description: Library name: Sample 3

source_name: E14Tg2a D3

value: E14Tg2a D3


title: WT_D3_ATAC_rep2

description: Library name: Sample 4


title: Z2KO_D0_ATAC_rep1

description: Library name: Sample 7


title: WT_D0_ATAC_rep1

description: Library name: Sample 1

source_name: E14Tg2a mESC D0

value: E14Tg2a mESC D0


title: WT_D0_ATAC_rep2

description: Library name: Sample 2


title: Z2KO_D6_ATAC_rep2

description: Library name: Sample 12


title: infarct tissue, day 28, type 2 diabetic, rep 9

description: Library name: 62_2_lo_STZ_HFFD_1481_S30


title: infarct tissue, day 28, type 2 diabetic, rep 8

description: Library name: 62_1_lo_STZ_HFFD_1481_S29


title: F12

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Library name: Sample 75

data_processing:
The fastq sequences were mapped with a standard STAR pipeline (version: 2.7.3a). The duplicated reads were filtered out using UMI-tools (version: 1.1.4). The gene expression counts summary was calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Assembly: mm10
Supplementary files format and content: Tab-seprated values files

source_name: Kidney

extract_protocol:
Kidney tissue was lysed in RLT buffer and homogenized. RNAeasy Micro or Mini kit (Qiagen) was used to extract mRNA according to the manufacturer’s protocol.
Library preparation and sequencing was performed as described previously (Hagemann-Jensen M, et al. Single-cell RNA counting at allele and isoform resolution using Smart-seq3. Nature biotechnology. 2020;38(6):708-14.).

value: Kidney

tag: age

value: adult

value: PbKO

tag: treatment group

value: UUO


title: Multiome, D3 E14Tg2a WT cells, ATAC

description:
Library name: WT_D3_snATAC
ATAC (10x Genomics). Read 1: contains cell barcode and UMI; Read 2: contains sequence of the DNA fragment adjacent to one Tn5 integration site; Read 3: contains the sequence from the opposite end of the same fragment (other Tn5 integration site).

value: E14Tg2a D3 cells


title: infarct tissue, day 28, type 2 diabetic, rep 7

description: Library name: 50_3_lo_STZ_HFFD_1481_S28


title: E11

description: Library name: Sample 73


title: A12

description: Library name: Sample 74


title: infarct tissue, day 28, type 2 diabetic, rep 6

description: Library name: 50_1_lo_STZ_HFFD_1481_S27


title: Z2KO_D3_ATAC_rep2

description: Library name: Sample 10

value: Z2KO E14Tg2a D3

value: Differentiation to AntNPCs (sample collection at D3); Assay for Transposase-Accessible Chromatin


title: infarct tissue, day 28, type 2 diabetic, rep 5

description: Library name: 49_4_lo_STZ_HFFD_1481_S26

value: left ventricular infarct

value: myocardial infarction


title: infarct tissue, day 28, type 2 diabetic, rep 4

description: Library name: 49_2_lo_STZ_HFFD_1481_S25

value: day 28


title: infarct tissue, day 28, type 2 diabetic, rep 2

description: Library name: 38_3_lo_STZ_HFFD_1481_S23


title: infarct tissue, day 28, type 2 diabetic, rep 3

description: Library name: 49_1_lo_STZ_HFFD_1481_S24


title: D12

description: Library name: Sample 71

value: PbWT


title: C12

description: Library name: Sample 70


title: D11

description: Library name: Sample 69


title: B11

description: Library name: Sample 68


title: infarct tissue, day 28, type 1 diabetic, rep 10

description: Library name: 69_4_hi_STZ_1481_S21


title: infarct tissue, day 28, type 1 diabetic, rep 9

description: Library name: 69_3_hi_STZ_1481_S20


title: infarct tissue, day 28, type 2 diabetic, rep 1

description: Library name: 37_3_lo_STZ_HFFD_1481_S22


title: D10

description: Library name: Sample 65

value: CL


title: B5

description: Library name: Sample 63


title: infarct tissue, day 28, type 1 diabetic, rep 5

description: Library name: 68_1_hi_STZ_1481_S16


title: infarct tissue, day 28, type 1 diabetic, rep 6

description: Library name: 68_2_hi_STZ_1481_S17


title: E10

description: Library name: Sample 66


title: B10

description: Library name: Sample 64


title: infarct tissue, day 28, type 1 diabetic, rep 7

description: Library name: 68_4_hi_STZ_1481_S18


title: A11

description: Library name: Sample 67


title: infarct tissue, day 28, type 1 diabetic, rep 4

description: Library name: 67_5_hi_STZ_1481_S15


title: F10

description: Library name: Sample 72


title: F4

description: Library name: Sample 61


title: infarct tissue, day 28, type 1 diabetic, rep 3

description: Library name: 65_3_hi_STZ_1481_S14


title: infarct tissue, day 28, type 1 diabetic, rep 1

description: Library name: 65_1_hi_STZ_1481_S12


title: E4

description: Library name: Sample 60


title: H_8

description: Library name: Sample 59

value: VeKO


title: infarct tissue, day 28, type 1 diabetic, rep 2

description: Library name: 65_2_hi_STZ_1481_S13


title: A5

description: Library name: Sample 62


title: H_7

description: Library name: Sample 58


title: infarct tissue, day 28, type 1 diabetic, rep 8

description: Library name: 68_5_hi_STZ_1481_S19


title: infarct tissue, day 28, non-diabetic, rep 11

description: Library name: 4_1_Ctrl_1481_S11


title: H_1

description: Library name: Sample 56


title: infarct tissue, day 28, non-diabetic, rep 10

description: Library name: 3_5_Ctrl_1481_S10


title: E9

description: Library name: Sample 55


title: infarct tissue, day 28, non-diabetic, rep 9

description: Library name: 2_5_Ctrl_1481_S9


title: H_2

description: Library name: Sample 57


title: infarct tissue, day 28, non-diabetic, rep 7

description: Library name: 2_2_Ctrl_1481_S7


title: G8

description: Library name: Sample 54


title: infarct tissue, day 28, non-diabetic, rep 8

description: Library name: 2_3_Ctrl_1481_S8


title: D8

description: Library name: Sample 53


title: H_6

description: Library name: Sample 51

value: VeWT


title: infarct tissue, day 28, non-diabetic, rep 5

description: Library name: 1_5_Ctrl_1481_S5


title: C8

description: Library name: Sample 52


title: infarct tissue, day 28, non-diabetic, rep 6

description: Library name: 2_1_Ctrl_1481_S6


title: infarct tissue, day 28, non-diabetic, rep 4

description: Library name: 1_4_Ctrl_1481_S4


title: infarct tissue, day 28, non-diabetic, rep 3

description: Library name: 1_3_Ctrl_1481_S3


title: H_4

description: Library name: Sample 49


title: infarct tissue, day 28, non-diabetic, rep 2

description: Library name: 1_2_Ctrl_1481_S2


title: H_3

description: Library name: Sample 48


title: infarct tissue, day 28, non-diabetic, rep 1

description: Library name: 1_1_Ctrl_1481_S1


title: H9

description: Library name: Sample 47


title: infarct tissue, day 7, type 2 diabetic, rep 7

description: Library name: 26_2_lo_STZ_HFFD_1443_S23

value: day 7


title: C9

description: Library name: Sample 45


title: infarct tissue, day 7, type 2 diabetic, rep 8

description: Library name: 26_3_lo_STZ_HFFD_1443_S24


title: G9

description: Library name: Sample 46


title: infarct tissue, day 7, type 2 diabetic, rep 6

description: Library name: 26_1_lo_STZ_HFFD_1443_S22


title: G_4

description: Library name: Sample 43


title: H8

description: Library name: Sample 44


title: infarct tissue, day 7, type 2 diabetic, rep 4

description: Library name: 14_2_lo_STZ_HFFD_1443_S20


title: infarct tissue, day 7, type 2 diabetic, rep 5

description: Library name: 14_4_lo_STZ_HFFD_1443_S21


title: infarct tissue, day 7, type 2 diabetic, rep 3

description: Library name: 14_1_lo_STZ_HFFD_1443_S19


title: G_2

description: Library name: Sample 41


title: G_3

description: Library name: Sample 42


title: infarct tissue, day 7, type 2 diabetic, rep 2

description: Library name: 2_2_lo_STZ_HFFD_1443_S18


title: infarct tissue, day 7, type 2 diabetic, rep 1

description: Library name: 1_2_lo_STZ_HFFD_1443_S17


title: infarct tissue, day 7, type 1 diabetic, rep 6

description: Library name: 51_3_hi_STZ_1443_S14


title: infarct tissue, day 7, type 1 diabetic, rep 8

description: Library name: 52_3_hi_STZ_1443_S16


title: H_5

description: Library name: Sample 50


title: E7

description: Library name: Sample 38


title: infarct tissue, day 7, type 1 diabetic, rep 7

description: Library name: 52_2_hi_STZ_1443_S15


title: infarct tissue, day 7, type 1 diabetic, rep 5

description: Library name: 39_1_hi_STZ_1443_S13


title: G_8

description: Library name: Sample 37


title: B8

description: Library name: Sample 39


title: G_1

description: Library name: Sample 40


title: G_7

description: Library name: Sample 36


title: infarct tissue, day 7, type 1 diabetic, rep 4

description: Library name: 16_2_hi_STZ_1443_S12


title: G_5

description: Library name: Sample 34


title: A8

description: Library name: Sample 32


title: F3

description: Library name: Sample 31


title: O_12

description: Library name: Sample 30

value: ABT


title: infarct tissue, day 7, type 1 diabetic, rep 1

description: Library name: 4_3_hi_STZ_1443_S9


title: infarct tissue, day 7, type 1 diabetic, rep 2

description: Library name: 4_4_hi_STZ_1443_S10


title: infarct tissue, day 7, type 1 diabetic, rep 3

description: Library name: 15_1_hi_STZ_1443_S11


title: F9

description: Library name: Sample 33


title: infarct tissue, day 7, non-diabetic, rep 8

description: Library name: 7_1_Ctrl_1443_S8


title: G6

description: Library name: Sample 26


title: infarct tissue, day 7, non-diabetic, rep 3

description: Library name: 6_3_Ctrl_1443_S3


title: infarct tissue, day 7, non-diabetic, rep 2

description: Library name: 6_2_Ctrl_1443_S2


title: G5

description: Library name: Sample 24


title: O_11

description: Library name: Sample 29


title: P_7

description: Library name: Sample 22

value: IgG


title: multiplexed single cell pool, 3x WT, Round1

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: Library name: sample3

data_processing:
Reads were aligned against the mouse genome (mm10) and counted by StarSolo.
Preprocessed counts were further analysed using Scanpy.
Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 1541  cells in total that did not express more than 300 genes or had a mitochondrial content greater than 8%. Furthermore, we filtered 14472  genes if they were detected in less than 30 cells (<0.01%).
Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA, retaining 50 principal components. Subsequent steps, like low-dimensional UMAP embedding and cell clustering via community detection, were based on the initial PCA.
Final data visualization was done by scanpy and cellxgene packages.
Assembly: mm10
Supplementary files format and content: starsolo outputs

extract_protocol:
The islets were dissociated using Accutase solution at 37 °C for a duration of 30 minutes. Thereafter, the reaction was halted by the addition of complete culture media, and the solution was filtered through a 40 µm cell strainer. Centrifugation at 200 g for 3 minutes 30 seconds at room temperature was then performed, with the resultant supernatant being discard. For antibody-based cell hashing, cell pellets were carefully suspended in staining buffer (PBS containing 2% BSA and 0.02% Tween). Subsequently, 1 µg of the designated rat anti-mouse hashing antibodies (Biolegend, TotalSeq™ anti-mouse Hashtag reagents) were incorporated and incubated for a duration of 30 minutes at 4 °C. And then 2 ml of neutralizing solution (complete culture media/PBS, v/v 2:1) was added to the cell suspension, filtered through a 40 µm cell strainer, and sorted by BD FACSMelody for DAPI-based dead exclusion as well as doublet discrimination.
The sorted cell suspensions were counted with a Moxi cell counter and diluted according to the manufacturer’s protocol to obtain 10.000 single-cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10xGenomics). Single-cell RNAseq library preparation was done using a standard protocol.

tag: Sex

value: male

value: pancreatic islet cells, primary mouse

value: Control

value: 16 weeks  high fat diet


title: O_9

description: Library name: Sample 28

value: Kidney

value: adult

value: UUO


title: infarct tissue, day 7, non-diabetic, rep 6

description: Library name: 30_2_Ctrl_1443_S6

value: left ventricular infarct


title: infarct tissue, day 7, non-diabetic, rep 7

description: Library name: 5_4_Ctrl_1443_S7

value: myocardial infarction


title: infarct tissue, day 7, non-diabetic, rep 5

description: Library name: 18_3_Ctrl_1443_S5


title: infarct tissue, day 7, non-diabetic, rep 4

description: Library name: 17_4_Ctrl_1443_S4


title: P_8

description: Library name: Sample 23


title: G_6

description: Library name: Sample 35


title: infarct tissue, day 7, non-diabetic, rep 1

description: Library name: 5_1_Ctrl__1443_S1


title: multiplexed single cell pool, 2x KO, Round2

description: Library name: sample2


title: D7

description: Library name: Sample 19


title: P_5

description: Library name: Sample 20


title: H6

description: Library name: Sample 18


title: D6

description: Library name: Sample 17


title: P_6

description: Library name: Sample 21


title: C7

description: Library name: Sample 27


title: H5

description: Library name: Sample 25


title: multiplexed single cell pool, 3x WT, Round2

description: Library name: sample4


title: C6

description: Library name: Sample 16


title: N_12

description: Library name: Sample 15


title: N_11

description: Library name: Sample 14


title: CTRL_1

description: Library name: Sample 1

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl mouse genome version mm10 (Ensembl release 101) with STAR 2.7.9a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.25.5 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.2 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.30.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Assembly: mm10
Supplementary files format and content: The tab-delimited matrix shows DESeq normalized counts.

source_name: pancreatic beta cells, primary mouse

extract_protocol:
For RNA-seq, RNA was isolated by miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA. RNA and library preparation integrity were verified with LabChip Gx Touch (Perkin Elmer).
RNA amounts were normalized and 1µg of total RNA was used as input for VaZyme_VAHTS Universal Stranded mRNA-seq - V6 (Vazyme). Sequencing was performed on the NextSeq2000 platform (Illumina) using P3 flowcell with 72bp single-end setup.

value: pancreatic beta cells, primary mouse

value: 12-14 wks old


title: KO_1

description: Library name: Sample 4


title: CTRL_3

description: Library name: Sample 3


title: KO_2

description: Library name: Sample 5


title: CTRL_2

description: Library name: Sample 2


title: Dex, KO, 24h, Rep3

city: Rozzano

first: Massimo

last: Locati

state: Milano

address: Via Alessandro Manzoni, 56

country: Italy

institute: IRCCS Humanitas Research Hospital

description: Library name: BMDM_125

data_processing:
Reads were trimmed for adapter sequences using fastp.
Trimmed reads were mapped to GRCm38 using HISAT2 and transcript-level quantification was performed using Salmon.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes normalized counts per each sample.

source_name: Macrophages

growth_protocol: Murine bone marrow-derived macrophages (BMDMs) were generated by 6 days of culture with 50 ng/ml recombinant murine (rm) M-CSF in Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 10% FBS, 1% Penicillin/Streptomycin, and 1% L-Glutamine in 100 mm dishes.

extract_protocol:
At the end of the treatment, the medium was removed, and cells were washed with 1X PBS and lysed with Trizol. RNA was extracted using the ReliaPrep™ RNA Cell Miniprep System (Promega – Z6012) according to the manufacturer's instructions.
RNA-seq libraries were prepared using SMART-Seq® mRNA LP kit (Takara Bio) following the manufacturer’s protocol.

treatment_protocol: At the end of the differentiation, BMDMs were detached with Accutase and plated in 12-well plates. The following day, cells were stimulated with or without 1 µM Dexamethasone for 2 h, 8 h, and 24 h.

value: Macrophages

value: MS4A4A KO

value: Dex

tag: timepoint


title: N_9

description: Library name: Sample 13

value: CL


title: vehicle, KO, 24h, Rep3

description: Library name: BMDM_124

value: vehicle


title: F6

description: Library name: Sample 12

value: ABT


title: Dex, WT, 24h, Rep3

description: Library name: BMDM_120

value: WT


title: multiplexed single cell pool, 2x KO, Round1

description: Library name: sample1

value: male

value: pancreatic islet cells, primary mouse


title: E6

description: Library name: Sample 11


title: F5

description: Library name: Sample 10


title: vehicle, KO, 8h, Rep3

description: Library name: BMDM_114


title: Dex, KO, 8h, Rep3

description: Library name: BMDM_115


title: E3

description: Library name: Sample 9


title: P_3

description: Library name: Sample 7

value: IgG


title: vehicle, WT, 8h, Rep3

description: Library name: BMDM_109


title: P_4

description: Library name: Sample 8

value: Kidney


title: Dex, WT, 8h, Rep3

description: Library name: BMDM_110


title: Dex, KO, 2h, Rep3

description: Library name: BMDM_105


title: P_2

description: Library name: Sample 6

value: adult


title: P_1

description: Library name: Sample 5


title: vehicle, KO, 2h, Rep3

description: Library name: BMDM_104


title: B7

description: Library name: Sample 4


title: Dex, WT, 2h, Rep3

description: Library name: BMDM_100


title: vehicle, WT, 2h, Rep3

description: Library name: BMDM_99


title: B6

description: Library name: Sample 3


title: Untr, WT, 0_baseline, Rep3

description: Library name: BMDM_97

value: Untr


title: vehicle, WT, 24h, Rep3

description: Library name: BMDM_119


title: Untr, KO, 0_baseline, Rep3

description: Library name: BMDM_98


title: A6

description: Library name: Sample 2


title: Untr, WT, 0_baseline, Rep2

description: Library name: BMDM_63


title: 293T_Control,RRBS

city: Shanghai

first: Yifan

last: Guo

address: Dongan Road No.150

institute: Fudan university, Shanghai, China

description: Library name: 293T_Control,RRBS

data_processing:
Sequencing was performed on an Illumina HiSeq/NovaSeq platform, generating 150 bp paired-end reads. Raw sequencing data were processed to remove adapter sequences and low-quality bases using Trimmomatic (v0.36). Quality assessment of the trimmed reads was conducted using FastQC (v0.11.5) to ensure data integrity. The trimmed reads were aligned to the mouse reference genome (GRCm38/mm10, sourced from Ensembl), and duplicate reads were removed to mitigate PCR amplification bias.
Assembly: GRCh38.p13
Supplementary files format and content: bigwig

extract_protocol:
Genomic DNA was extracted using the DNA Extraction Kit (DP304, Tiangen).
DNA was digested with the restriction enzyme MspI to enrich for CpG-rich regions, followed by end-repair, A-tailing, and ligation with methylated adapters to preserve methylation information during subsequent steps. Size-selected fragments were then subjected to bisulfite conversion using the EZ DNA Methylation-Gold Kit (Zymo Research) to convert unmethylated cytosines to uracil. Adapter-ligated fragments were amplified by PCR to generate the final RRBS libraries, which were quality-checked prior to sequencing.


title: siSNRPA,RRBS

description: Library name: siSNRPA,RRBS


title: siZFPM2AS1,RRBS

description: Library name: siZFPM2AS1,RRBS