title: snRNA-seq of adult human peripheral lobe region of retina donor_BCM_22_0200

value: peripheral region of retina

tag: assay

value: female

tag: ethnicity

value: Hispanic or Latin American

tag: age

value: 43 years

value: FALSE

tag: donor id

tag: raw matrix_feature_keys

value: gene symbol

tag: raw matrix_cellranger_assay_chemistry

value: GENCODE 32

value: UMI


title: Human1_009

status: Public on Oct 14 2025

type: SRA

city: Leiden

first: Evita

last: van de Steeg

address: Sylviusweg 71

department: Metabolic Health Research

country: Netherlands

institute: TNO

library_source: transcriptomic

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the ensembl reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Human: Homo_sapiens.GRCh38.gencode.v29, Pig: GCF_000003025.6_Sscrofa11.1_genomic
Supplementary files format and content: The count files (.tsv) contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).

molecule: total RNA

organism: Homo sapiens

source_name: liver

extract_protocol:
After total RNA isolation from liver tissue, RNA quality was evaluated using a Fragment Analyzer (tot.RNA conc. & RQN) and RNA integrity was assessed using RNA 6000 Nano LabChip 669 kit and a bioanalyzer 2100 (Agilent Technologies, Amstelveen, the Netherlands). Next Generation Sequencing (NovaSeq6000) was performed at GenomeScan (Leiden, the Netherlands).
Total RNA was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB #E7760S/L , Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 sequencer with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in ~18-26 million read counts per sample.
Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: - Porcine livers (of 6 ~6 months old male pigs, 2.1-2.5 kg/liver) were procured, preserved  and perfused for 360 min at 37°C as previously published*. Standard perfusion protocol consisted of infusion with TCA at a fixed rate of 0.2g/hr (0.39 mmol/hr). Porcine liver samples were taken at t=0min and t=360min for RNAseq analysis. *Stevens LJ, Zhu AZ, Chothe PP, Chowdhury SK, Donkers JM, Vaes WH, Knibbe CA, et al. Evaluation of normothermic machine perfusion of porcine livers as a novel preclinical model to predict biliary clearance and transporter-mediated drug-drug interactions using statins. Drug Metabolism and Disposition 2021;49:780-789.  - Human explanted and discarded livers (from adults, Male & Female, 1 healthy and 5 with various liver diseases, ~2kg/liver) were perfused for 360 min at 37°C as previously published**. Standard perfusion protocol consisted of infusion with TCA at a fixed rate of 0.2g/hr. The samples (perfusate, bile and tissue) used in this research with TCA infusion were derived from a study which was previously published**. Human liver samples were taken at t=0min and t=360min for RNAseq analysis. **Stevens LJ, Dubbeld J, Doppenberg JB, van Hoek B, Menke AL, Donkers JM, Alsharaa A, et al. Novel explanted human liver model to assess hepatic extraction, biliary excretion and transporter function. Clinical Pharmacology & Therapeutics 2023.

tag: tissue

value: liver

tag: subject id

tag: treatment

tag: treatorganism

value: H

tag: treatperfusionhr

tag: treat(non)cirrhotic

value: C

tag: diagn

value: PBC

tag: diagnosis


title: RRBS_RS_S12NSUV2_dTAG_rep3

city: London

first: Aina

middle: Maria

last: Mas

address: Chester Beatty Laboratories, 237 Fulham Rd.

country: United Kingdom

institute: Institute of Cancer Research

library_source: genomic

data_processing:
RRBS sequencing reads were trimmed using v0.4.5 of TrimGalore with --rrbs setting enabled to remove 2bp from the 3´end of Read 1 and 5´end of Read 2 in addition to adaptor contamination. Raw reads were filtered for quality and adapter content using TrimGalore with a quality setting of 20 and running v1.15 of Cutadapt and v0.11.5 of FastQC.
Trimmed reads were then aligned to the mm10 in silico bisulfite transformed genome with the bisulfite sequencing aligner Bismark v0.19.0 (https://www.bioinformatics.babraham.ac.uk/ projects/bismark/) using default Bowtie2 (v2.3.4.1) settings within Bismark.
Duplicated reads were discarded, and the remaining alignments were used for cytosine methylation calling by Bismark methylation extractor. Initial visualization with principle component analysis revealed no outliers or batch effects.
Differentially methylated CpGs (DMCs) were identified using DSS R-package v2.42.0 using the dispersion shrinkage method followed by Wald statistical test for beta-binomial distributions. Any CpGs with FDR < 0.05 and methylation percentage differences greater than 10% were considered significant DMCs. Custom annotation was built from the H3K27me3 peak-set using the R-package Annotatr v1.20.0, and DMCs were filtered for direct PRC2 target DMCs. Annotatr was then used to add annotations for CpG-type, gene, and transcriptional rescue groups to each DMC.
Custom DMRs were called by grouping DMCs based on shared identifiers by combining the gene ID with CpG type, resulting in up to 4 DMRs per gene (CpG-island, CpG-shore, CpG-shelf, and CpG-opensea). Mean methylation (%) was then calculated for each DMR
Assembly: mm10
Supplementary files format and content: BigWig coverage and BigWig Methyl

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Mouse embryonic stem cells were cultured in serum/LIF medium (Glasgow Minimum Essential Media (GMEM) supplemented with 10% heat-inactivated Fetal Bovine Serum (HI-FBS), 1% Penicillin/Streptomycin, 2mM L-glutamine, 1 mM Sodium Pyruvate (Gibco), 0.1 mM MEM Non-essential amino acids (Gibco), 100μM ß-Mercaptoethanol (Gibco) and Leukemia Inhibitory Factor (LIF, produced in the lab))

extract_protocol:
DNA was extracted from cells using DNeasy Blood and Tissue kit (Qiagen), and concentrations were quantified with Qubit dsDNA HS assay kit. For each sample, 2ug genomic DNA was spiked with 2ng unmethylated Lambda DNA (Promega) to allow assessment of the bisulfite-conversion reaction efficiency before DNA was ingested for 5 hours at 37°C using a methylation-insensitive restriction enzyme, MspI.
Library preparation was performed using NEXTFLEX Bisulfite-Seq kit (Bioo Scientific) with methylated adaptors (Bioo Scientific) and 1µg input DNA according to manufacturer’s protocol. DNA was quantified again using Qubit dsDNA HS assay kit before bisulfite conversion was performed with EZ DNA Methylation-Lightning kit (Zymo Research). Bisulfite-converted DNA was PCR amplified and purified following the protocol of NEXTFLEX Bisulfite-Seq kit (Bioo Scientific). RRBS libraries were quantified with Qubit dsDNA HS assay kit, and size distributions were analyzed on TapeStation 2200 (Agilent Technologies). Libraries were first pooled based on molar concentrations and then combined with RNA-seq or CUT&RUN samples to compensate for the inherently low ATGC complexity of RBBS libraries. The final library pools were denatured, loaded onto an Illumina Nextseq 550 with SE75 high-output kits, and sequenced as paired-end 36/36 cycles.

treatment_protocol: Cells were treated with either dTAG13 or DMSO for 24hrs. KDM4-specific inhibitor QC6352 treatment for 96hrs

tag: cell line

tag: cell type

value: Mouse embryonic stem cells

tag: genotype

value: RS + S12N:SUV2


title: Wild type mESCs_Replicate 2

description: Library name: WT_R2

data_processing:
RNA sequencing reads were 3’ trimmed for base quality with a setting of 20 and adapter sequences using Trimmomatic and reads were then aligned to mouse assembly mm10 using HISAT2 with default parameters.
Assembly: mm10
Supplementary files format and content: feature counts

molecule: polyA RNA

extract_protocol:
Total RNA was extracted from fresh cell pellets in biological triplicates using RNeasy Plus Mini kit (Qiagen). RNA integrity was assessed on TapeStation 2200 (Agilent Technologies) using High Sensitivity RNA Screentape assay, and RNA was quantified with Qubit RNA HS assay kit
Libraries of mRNA were prepared using NEBNext UltraII Library prep kit according to the manufacturer’s instructions using 1µg input RNA. Libraries were quantified with Qubit dsDNA HS assay kit, and size distributions were analyzed on a Tape Station 2200 (Agilent Technologies). Libraries were pooled based on molar concentrations, denatured, loaded onto an Illumina Nextseq 2000, and sequenced as paired-end 60/60 cycles.

value: Wild type


title: Human6_089

value: Nc

value: HL


title: Human5_072

value: ALD


title: RRBS_Rbbp5-FKBP_DMSO_rep3

value: DMSO


title: Human1_001R


title: Wild type mESCs_Replicate 1

description: Library name: WT_R1


title: GSC738, shATP7A, replicate 2

city: PITTSBURGH

first: Fanen

last: Yuan

state: PA

address: 5030 Centra Ave, APT861

country: USA

institute: University of pittsburgh

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as themapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: xls file includes raw counts for each sample

source_name: brain glioma

growth_protocol: Cells were cultured in Neurobasal media (Invitrogen) supplemented with B27 minus vitamin A (Invitrogen), sodium pyruvate, glutamax, and EGF and bFGF (20 ng/mL each; R&D Systems)

extract_protocol:
Total cellular RNA was extracted from cell pellets using Trizol reagent and Direct-zol RNA Miniprep Kits
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.After fragmentation, the first strand cDNA was synthesized using random hexamer primers,followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. It was ready after end repair, A-tailing, adapter ligation, size selection,amplification, and purification.The clustering of the index-coded samples was performed according to the manufacturer’s instructions.After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: ATP7A was knockdown by shRNA in GSC387, GSC3565 and GSC738. And then RNA-seq was performed to investigate the effect of ATP7A knockdown on gene expression.

value: brain glioma

value: glioma stem cells

value: ATP7A knockdown


title: GSC738, shATP7A, replicate 1


title: RNA-seq mESCs+Suz12mAID 48 hours IAA_Replicate 3

description: Library name: 48hrsIAAR3

source_name: TCF

value: TCF

value: 48hrs IAA 50 µM


title: Human5_065


title: RRBS_R-Suz12KO_DMSO_rep3

value: RBBP5-FKBP + Suz12 KO (RS)


title: GSC738, shCONT, replicate 1

value: WT

value: shCONT


title: GSC738, shCONT, replicate 2


title: Human3_033

value: liver

value: H

value: C


title: GSC3565, shATP7A, replicate 1


title: RNA-seq mESCs+Suz12mAID 48 hours IAA_Replicate 1

description: Library name: 48hrsIAAR1

value: Mouse embryonic stem cells


title: RNA-seq mESCs+Suz12mAID 48 hours IAA_Replicate 2

description: Library name: 48hrsIAAR2


title: Human2_017

value: NASH


title: GSC3565, shCONT, replicate 1


title: RRBS_RS_S12NSUV2_DMSO_rep3

value: RS + S12N:SUV2


title: RNAseq_R-Suz12KO_dTAG_rep3

description:
RBBP5_RNAseq_mm10_Counts_Merged.tsv
RBBP5_Table_DESeq2_AllNormalizedCounts_PeakNorm.txt
RBBP5_Table_DESeq2_FilteredNormalizedCounts_PeakNorm.txt

data_processing:
RNA sequencing reads were 3’ trimmed for base quality with a setting of 15 and adapter sequences using TrimGalore v0.4.5 (https://www.bioinformatics.babraham.ac.uk/projects/ trim_galore) and read were then aligned to mouse assembly mm10 using STAR v2.4 with default parameters. Data quality and transcript coverage were assessed using the Picard tool CollectRNASeqMetrics (http://broadinstitute.github.io/picard/).
Read count tables were generated with HTSeq v0.9.1. The DESeq2 R-package was used with default parameters to evaluate normalization and expression dynamics, and potential outliers were assessed by sample grouping in principal component analysis (PCA). Differentially expressed genes were identified from normalized filtered read counts as expression foldchange (FC) > 2 and false discovery rate-adjusted P (FDR) < 0.05 from pairwise contrasts and filtered based on H3K27me3 promoter peaks to identify direct PRC2 target genes.
Assembly: mm10
Supplementary files format and content: Read count files, normalized counts and filtered normalized counts

extract_protocol:
Total RNA was extracted from fresh cell pellets in biological triplicates using RNeasy Plus Mini kit (Qiagen). RNA integrity was assessed on TapeStation 2200 (Agilent Technologies) using High Sensitivity RNA Screentape assay, and RNA was quantified with Qubit RNA HS assay kit
Libraries of mRNA were prepared using Illumina TruSeq RNA Sample Prep v.2 kit according to the manufacturer’s instructions using 0.5µg input RNA. Libraries were quantified with Qubit dsDNA HS assay kit, and size distributions were analyzed on a Tape Station 2200 (Agilent Technologies). Libraries were pooled based on molar concentrations, denatured, loaded onto an Illumina Nextseq 550 with SE75 high-output kits, and sequenced as paired-end 36/36 cycles.


title: RNAseq_R-Suz12KO_dTAG_rep2


title: RNA-seq mESCs+Suz12mAID 24 hours IAA_Replicate 3

description: Library name: 24hrsIAAR3

value: 24hrs IAA 50 µM


title: GSC3565, shATP7A, replicate 2


title: GSC387, shATP7A, replicate 1


title: RNA-seq mESCs+Suz12mAID 24 hours IAA_Replicate 2

description: Library name: 24hrsIAAR2


title: GSC3565, shCONT, replicate 2


title: RNAseq_R-Suz12KO_dTAG_rep1


title: GSC387, shCONT, replicate 1


title: GSC387, shCONT, replicate 2


title: RNA-seq mESCs+Suz12mAID 24 hours IAA_Replicate 1

description: Library name: 24hrsIAAR1


title: RNAseq_R-Suz12KO_DMSO_rep3


title: RNAseq_R-Suz12KO_DMSO_rep2


title: RNA-seq mESCs+Suz12mAID 8 hours IAA_Replicate 3

description: Library name: 8hrsIAAR3

value: 8hrs IAA 50 µM


title: 19_D008_Nu

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

library_source: transcriptomic single cell

data_processing:
The raw count matrix processed data files were processed with Cell Ranger count v7.0.1 using reference packagerefdata-gex-GRCh38-2020-A.tar.gz, include_introns = TRUE, value_scale=linear, background_barcodes_included=FALSE
Assembly: GRCh38
Supplementary files format and content: hdf5, count matrix

source_name: peripheral region of retina

extract_protocol:
Samples included in this study were retinal tissues of 22 postmortem donors from the Utah Lions Eye Bank. All donors were screened for medical history, and only the ones with no of retinal diseases were used in this study. Post-mortem phenotyping with OCT were performed to confirm that there were no drusen, atrophy, or any other disease phenotypes on retina. One eye was collected from each donor. All eye tissues were collected and dissected within 6 hours post-mortem. With 4mm and 6mm disposable biopsy punches, macula and peripheral retina were collected and flash frozen in liquid nitrogen, and stored at -80°C before nuclei isolation.  Nuclei for snRNA-seq were isolated by fresh-made pre-chilled RNase-free lysis buffer. The frozen tissue was resuspended and triturated in lysis buffer and homogenized with a WheatonTM Dounce Tissue Grinder.
Single cell Gene Expression Library was prepared according to Chromium Next GEM Single Cell 500 3' Reagent Kits v3.1 (10x Genomics).  Single cell ATAC Library was prepared according to Chromium Next GEM Single cell ATAC 511 Reagent kit v1.1 (10x Genomics).

value: peripheral region of retina

tag: assay

tag: Sex

value: female

value: Hispanic or Latin American

value: 64 years

value: FALSE

value: gene symbol

tag: raw matrix_genome_annotation

value: GENCODE 32

tag: raw matrix_value_units

value: UMI

tag: raw matrix_assays

value: snRNA-seq


title: RNA-seq mESCs+Suz12mAID 8 hours IAA_Replicate 2

description: Library name: 8hrsIAAR2

value: TCF


title: RNAseq_R-Suz12KO_DMSO_rep1

value: RBBP5-FKBP + Suz12 KO (RS)

value: DMSO


title: GSC387, shATP7A, replicate 2

value: brain glioma

value: glioma stem cells

value: ATP7A knockdown


title: 10xATAC_19_D010_Mac_NeuN_3

library_source: genomic single cell

source_name: macula lutea

tag: enrichment protocol

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

tag: suspension enrichment_factors

value: NeuN

value: macula lutea

value: 10x scATAC-seq

tag: ethnicity

value: European

tag: age

value: 88 years

tag: donor id

tag: raw matrix_feature_keys

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: RNAseq_RS_S12NSUV2_dTAG_rep3

value: Mouse embryonic stem cells

value: RS + S12N:SUV2

tag: treatment


title: Pig5_073

organism: Sus scrofa domesticus

tag: tissue

value: liver

value: male

tag: subject id

tag: treatorganism

value: P

tag: treatperfusionhr

tag: treat(non)cirrhotic

value: Nc

tag: diagn

value: HL


title: 10xATAC_19_D010_Mac_NeuN_2

tag: assay

tag: Sex

value: female

value: FALSE


title: RNA-seq mESCs+Suz12mAID 8 hours IAA_Replicate 1

description: Library name: 8hrsIAAR1

tag: cell line

value: TCF

tag: cell type

tag: genotype

value: 8hrs IAA 50 µM


title: 10x3v31_19D008_Mac_NeuN_T

tag: enrichment protocol

value: To enrich the retinal ganglion cell nuclei, isolated macular retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle). The nuclei group with strongest 5% FITC signal was collected for RGC enrichment.

tag: suspension enrichment_factors

value: NeuN

value: macula lutea

value: Hispanic or Latin American

value: 64 years

value: gene symbol

tag: raw matrix_cellranger_assay_chemistry

tag: raw matrix_genome_annotation

value: GENCODE 32

tag: raw matrix_value_units

value: UMI

tag: raw matrix_assays

value: snRNA-seq


title: RNA-seq mESCs+Suz12mAID 4 hours IAA_Replicate 3

description: Library name: 4hrsIAAR3

value: Mouse embryonic stem cells

tag: treatment

value: 4hrs IAA 50 µM


title: RNA-seq mESCs+Suz12mAID 4 hours IAA_Replicate 2

description: Library name: 4hrsIAAR2


title: RNAseq_RS_S12NSUV2_dTAG_rep2

value: RS + S12N:SUV2


title: Pig5_066

tag: tissue

value: liver

value: male

tag: subject id

value: P

value: Nc

value: HL

tag: diagnosis


title: 19_D019_Nu

value: peripheral region of retina

value: female

tag: ethnicity

value: European

tag: age

value: 82 years

value: FALSE

tag: donor id

tag: raw matrix_feature_keys


title: D28_13_Nu

tag: assay

tag: Sex

value: 67 years

value: gene symbol


title: RNA-seq mESCs+Suz12mAID 4 hours IAA_Replicate 1

description: Library name: 4hrsIAAR1

tag: cell line

value: TCF

tag: cell type

tag: genotype


title: Pig4_050

tag: treatorganism

tag: treatperfusionhr

tag: treat(non)cirrhotic

tag: diagn


title: RNAseq_RS_S12NSUV2_DMSO_rep3

tag: treatment

value: DMSO


title: D27_13_NeuN

tag: enrichment protocol

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

tag: suspension enrichment_factors

value: NeuN

tag: tissue

value: 77 years

tag: raw matrix_cellranger_assay_chemistry

tag: raw matrix_genome_annotation

value: GENCODE 32

tag: raw matrix_value_units

value: UMI

tag: raw matrix_assays

value: snRNA-seq


title: RNAseq_RS_S12NSUV2_dTAG_rep1

value: Mouse embryonic stem cells

value: RS + S12N:SUV2


title: D005_13_NeuN

value: peripheral region of retina

tag: assay

value: male

tag: ethnicity

tag: age

value: 80 years

tag: donor id

tag: raw matrix_feature_keys


title: Pig3_041

value: liver

tag: Sex

tag: subject id

tag: treatorganism

value: P

value: Nc

value: HL

tag: diagnosis


title: 19_D006_Nu

value: European

value: >89 years

value: FALSE

value: gene symbol


title: RNA-seq mESCs+Suz12mAID 2 hours IAA_Replicate 3

description: Library name: 2hrsIAAR3

tag: cell line

value: TCF

tag: cell type

tag: genotype

tag: treatment

value: 2hrs IAA 50 µM


title: Pig3_034

tag: tissue

tag: treatperfusionhr

tag: treat(non)cirrhotic

tag: diagn


title: RNAseq_RS_S12NSUV2_DMSO_rep2

value: DMSO


title: RNA-seq mESCs+Suz12mAID 2 hours IAA_Replicate 2

description: Library name: 2hrsIAAR2


title: RNAseq_RS_S12NSUV2_DMSO_rep1


title: RNAseq_Rbbp5_FKBP_dTAG_rep3


title: Pig4_058


title: RNA-seq mESCs+Suz12mAID DMSO_Replicate 3

description: Library name: 0hrsIAAR3

value: 48hrs DMSO


title: Pig2_026


title: Pig2_018


title: 19_D005_NeuN

tag: enrichment protocol

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

tag: suspension enrichment_factors

value: NeuN

tag: assay

value: Hispanic or Latin American

value: 53 years

tag: raw matrix_cellranger_assay_chemistry

tag: raw matrix_genome_annotation

value: GENCODE 32

tag: raw matrix_value_units

value: UMI

tag: raw matrix_assays

value: snRNA-seq


title: D026_13_NeuN

value: peripheral region of retina

tag: Sex

value: male

tag: ethnicity

tag: age

value: 81 years

tag: donor id

tag: raw matrix_feature_keys


title: 10xATAC_19_D3_Mac_NeuN_1

value: macula lutea

value: 10x scATAC-seq

value: European

value: 86 years

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: RNA-seq mESCs+Suz12mAID 2 hours IAA_Replicate 1

description: Library name: 2hrsIAAR1

tag: cell line

value: TCF

tag: cell type

value: Mouse embryonic stem cells

tag: genotype

tag: treatment

value: 2hrs IAA 50 µM


title: RNAseq_Rbbp5_FKBP_dTAG_rep2


title: D21_13_NeuN

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

value: NeuN

tag: tissue

value: FALSE

value: gene symbol


title: 10xATAC_19_D6_Mac_NeuN_2

tag: enrichment protocol

value: >89 years


title: RNA-seq mESCs+Suz12mAID DMSO_Replicate 1

description: Library name: 0hrsIAAR1

value: 48hrs DMSO


title: RNAseq_Rbbp5_FKBP_DMSO_rep3

value: DMSO


title: RBBP5-dTAG, Suz12 KO, S12N:SD2 expressing ES line (set) treated with dTAG-13, replicate 3

description: Library name: mrna_set_dtag_Rep3

data_processing:
Galaxy server (usegalaxy.org), version 24.2
Trim Galore! (Galaxy Version 0.6.7+galaxy0) was used to trim for the base quality with a phred score thresold of 20 and adapter sequences. Trimmed reads were aligned to mm10 mouse genome using HISAT2 (Galaxy Version 2.2.1+galaxy1) with default parameters.
Read counts were computed using featureCounts (Galaxy Version 2.0.8+galaxy0) using built-in gene annotations. Read count tables from featureCounts were used as input for differential expression analysis by DESeq2 (1.46.0) in R environment. In pair-wise comparisions, genes that are differentially expressed with a fold change (FC) >2 and adjusted p value <0.05 were regarded as significantly differentially expressed genes (DEGs). Promoter-associated H3K27me3 peaks were used to identify direct targets of PRC2.
Deseq2
Assembly: mm10
Supplementary files format and content: count table, unnormalized counts from featureCounts, one column per sample with Gene_id

growth_protocol: Cells were grown in GMEM (Gibco) suplemented with 10% heat-inactivated FBS, 1 × non-essential amino acids, 1 × sodium pyruvate, 1 × Glutamax,  1 × penicillin/stretomycin, 55 mM β-merchaptoethanol, LIF (in-house) on 0.2% gelatin-coated TC treated plates. Cultures were maintained in humidified atmosphere at 37ºC with 5% CO2.

extract_protocol:
Trizol extracts were procesed as per manufacturer's recommendation.
Libraries were prepared from 1 µg total RNA using NEBNext Ultra II RNA Library Prep kit for illumina (NEB #E7770S) together with poly(A) mRNA magneticisolation module (NEB #E7490) as manufacturer's recommendations.

treatment_protocol: Forty thousands cells were plated per well of a 6-well plate one day before the treatment with 500 nM dTAG-13 or 0.1% DMSO for 24 hours. At the end of the treatment period, culture medium was removed and cells were lysed in Trizol and extracts were stored at -80ºC

value: mouse embryonic stem cell

value: RBBP5-FKBP12 knock-in, Suz12 knockout, S12N-SD2 fusion expression


title: RNAseq_Rbbp5_FKBP_DMSO_rep2


title: 10x3v31_19_D011_Macular_NeuN_T

value: To enrich the retinal ganglion cell nuclei, isolated macular retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle). The nuclei group with strongest 5% FITC signal was collected for RGC enrichment.

tag: suspension enrichment_factors

value: macula lutea

value: female

value: European

value: GENCODE 32

value: UMI

value: snRNA-seq


title: PSC-sEV injection treatment, replicate 3, scRNAseq

city: Chengdu

first: Ruiqi

last: Hua

address: Sichuan, Chengdu, Huimin Road 211

country: China

institute: Sichuan Agricultural University

data_processing:
Raw reads were aligned against the genome,dmultiplexing UMI，barcoded processing, gene counting and aggregation were made using BSCMatrix software.
Assembly: GRCm38
Supplementary files format and content: Tab-separated barcodes files, Tab-separated genes files,and matrix files

extract_protocol:
After anesthesia, mice were weighed before cutting the portal vein and perfusion with pre-digestion buffer (1 mM HEPS, 0.5 mM EGTA, 1 g/L D-Glucose) to reduce blood via inferior vena cava. Next, fresh livers were removed from the body, washed with DPBS, and cut into small pieces. Liver pellets were incubated within digestion buffer (DMEM with Mg2+/Ca2+ supplemented with 0.5 mg/ml collagenase type IV and 7.5 mg/ml DNase I, containing 1 % penicillin/streptomycin) in a shaking incubator at 37 °C for 30 mins. At the end of the incubation time, DMEM with 10 % FBS was added and the cell suspension was filtered through a 70 mm cell strainer and centrifuged at 300 g for 3 minutes. The obtained pellet was resuspended in DMEM with 10 % FBS and filtered through a 40 mm cell strainer. Samples were centrifuged at 300 g for 3 minutes and re-suspended for cell viability assay.
The isolated single cells were immediately loaded onto DG1000 platform, and then partitioned into nanoliter-scale Gel Beads-In-Emulsion (GEMs). Cells in GEMs were lysed, and RNAs released from cells were immediately captured by barcoded beads in the same GEMs, followed by reverse transcription, amplification, fragmentation, adaptor ligation and index PCR. Libraries were constructed using BMKMANU DG1000-3’ Gel Beads Kits (Biomarker, China). Sequencing was performed on BGISEQ-500 sequencing platform, BGI, China.

value: 35-38 weeks old

tag: parasite genotype

value: liver

value: PSC-sEV injection via tail vein

tag: strain


title: PSC-sEV injection treatment, replicate 2, scRNAseq


title: 10x3V31_19_D017_Macular_NeuN_T

value: NeuN

tag: assay

value: male

value: 71 years

value: FALSE

tag: raw matrix_cellranger_assay_chemistry

tag: raw matrix_genome_annotation


title: RNAseq_Rbbp5_FKBP_DMSO_rep1

value: Mouse embryonic stem cells

value: DMSO


title: RBBP5-dTAG, Suz12 KO, S12N:SD2 expressing ES line (set) treated with dTAG-13, replicate 2

description: Library name: mrna_set_dtag_Rep2

value: mouse embryonic stem cell

value: RBBP5-FKBP12 knock-in, Suz12 knockout, S12N-SD2 fusion expression


title: RNAseq_Suz12KO_rep3

description:
RNAseq_mm10_Counts_Merged.tsv
Table_DESeq2_AllNormalizedCounts_PeakNorm.txt
Table_DESeq2_FilteredNormalizedCounts_PeakNorm.txt

value: Suz12 KO


title: PSC-sEV injection treatment, replicate 1, scRNAseq

tag: Sex

value: female


title: RBBP5-dTAG, Suz12 KO, S12N:SD2 expressing ES line (set) treated with DMSO, replicate 3

description: Library name: mrna_set_dmso_Rep3


title: RBBP5-dTAG, Suz12 KO, S12N:SD2 expressing ES line (set) treated with dTAG-13, replicate 1

description: Library name: mrna_set_dtag_Rep1


title: RNA-seq mESCs+Suz12mAID DMSO_Replicate 2

description: Library name: 0hrsIAAR2

value: TCF

value: 48hrs DMSO


title: Pig1_010

tag: subject id

tag: treatorganism

value: P

tag: treatperfusionhr

tag: treat(non)cirrhotic

value: Nc

tag: diagn

value: HL

tag: diagnosis


title: 10x3v31_19D009_Mac_NeuN_T

value: To enrich the retinal ganglion cell nuclei, isolated macular retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle). The nuclei group with strongest 5% FITC signal was collected for RGC enrichment.

value: macula lutea

tag: ethnicity

value: Hispanic or Latin American

tag: age

value: 68 years

tag: donor id

tag: raw matrix_feature_keys

value: gene symbol

value: GENCODE 32

tag: raw matrix_value_units

value: UMI

tag: raw matrix_assays

value: snRNA-seq


title: Pig1_002R

tag: tissue

value: liver

value: male

tag: treatment


title: 19_D009_NeuN

tag: enrichment protocol

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

tag: suspension enrichment_factors

value: NeuN

value: peripheral region of retina

tag: assay

value: FALSE

tag: raw matrix_cellranger_assay_chemistry


title: PSC infection treatment, replicate 3, scRNAseq

tag: Sex

value: female

value: 35-38 weeks old

tag: parasite genotype

value: PSC injection via portal vein

tag: strain


title: RBBP5-dTAG, Suz12 KO, S12N:SD2 expressing ES line (set) treated with DMSO, replicate 2

description: Library name: mrna_set_dmso_Rep2

tag: cell line

tag: cell type

value: mouse embryonic stem cell

tag: genotype

value: RBBP5-FKBP12 knock-in, Suz12 knockout, S12N-SD2 fusion expression

value: DMSO


title: PSC infection treatment, replicate 2, scRNAseq

tag: age


title: 19_D003_Nu

tag: ethnicity

value: European

value: 86 years

tag: donor id

tag: raw matrix_genome_annotation


title: RNAseq_Suz12KO_rep2

value: Mouse embryonic stem cells

value: Suz12 KO


title: PSC infection treatment, replicate 1, scRNAseq


title: RBBP5-dTAG, Suz12 KO, S12N:SD2 expressing ES line (set) treated with DMSO, replicate 1

description: Library name: mrna_set_dmso_Rep1


title: RNAseq_Rbbp5_FKBP_dTAG_rep1


title: 19_D010_NeuN

value: To enrich the retinal ganglion cell nuclei, isolated macular retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle). The nuclei group with strongest 5% FITC signal was collected for RGC enrichment.

value: 88 years

tag: raw matrix_feature_keys

value: gene symbol

value: GENCODE 32

tag: raw matrix_value_units

value: UMI

tag: raw matrix_assays

value: snRNA-seq


title: PBS-HAT injection control, replicate 3, scRNAseq

tag: tissue

value: liver

tag: treatment

value: PBS-HAT injection via tail vein


title: D28_13_NeuN

tag: enrichment protocol

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

tag: suspension enrichment_factors

value: NeuN

value: peripheral region of retina

tag: assay

value: male

value: 67 years

value: FALSE


title: RBBP5-dTAG, Suz12 KO ES line (rs14) treated with dTAG-13, replicate 3

description: Library name: mrna_rs14_dtag_Rep3

value: mouse embryonic stem cell

value: RBBP5-FKBP12 knock-in, Suz12 knockout


title: D013_13_Nu

tag: Sex

value: European

value: 69 years

tag: raw matrix_cellranger_assay_chemistry


title: RNAseq_WT_mESC_rep2

tag: cell line

value: Mouse embryonic stem cells

value: WT


title: RBBP5-dTAG, Suz12 KO ES line (rs14) treated with dTAG-13, replicate 2

description: Library name: mrna_rs14_dtag_Rep2

tag: cell type


title: 19_D008_NeuN

value: female

value: Hispanic or Latin American

value: 64 years

value: gene symbol

value: GENCODE 32


title: RNAseq_WT_mESC_rep1

tag: genotype


title: RNAseq_WT_mESC_rep3


title: RBBP5-dTAG, Suz12 KO ES line (rs14) treated with dTAG-13, replicate 1

description: Library name: mrna_rs14_dtag_Rep1


title: RNAseq_Suz12KO_S12NSD2dead_rep3

value: Suz12 KO + S12N:SD2*


title: D009_13_Nu

value: Asian

tag: age

value: 85 years

value: UMI

value: snRNA-seq


title: RBBP5-dTAG, Suz12 KO ES line (rs14) treated with DMSO, replicate 3

description: Library name: mrna_rs14_dmso_Rep3

value: DMSO


title: PA1 structures, Wnt1-Cre;pMes-Bmp4 mice, E9.5-E9.75 (25 to 27-somite stage) 2

city: Fuzhou

first: Chensheng

last: Lin

state: Fujian

address: 18 Wulongjiangzhong Avenue, Shangjie Town

department: College of Life Sciences

institute: Fujian Normal University

description:
Library name: TG_2
featureCounts on data TG_2: Counts

data_processing:
The adapter and low-quality reads were filtered out through fastp (v0.21.0)
Assembly: mm10
Supplementary files format and content: Tab_delimited txt file includes raw counts for each sample.

source_name: PA1 (first branchial arch)

extract_protocol:
Total RNA was extracted using trizol method. All the RNA samples were assessed for their integrity using Qsep400 instrument. 1 μg of total RNA was used for the construction of sequencing libraries.
RNA-seq were performed by Wuhan IGENEBOOK Biotechnology Co.,Ltd (http://www.igenebook.com) . RNA libraries for RNA-seq were prepared using the VAHTS universal V10 Library Prep Kit for Illumina(NR606,Vazyme). The procedure included polyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription.

value: PA1 (first branchial arch)


title: RBBP5-dTAG, Suz12 KO ES line (rs14) treated with DMSO, replicate 2

description: Library name: mrna_rs14_dmso_Rep2

value: mouse embryonic stem cell

value: RBBP5-FKBP12 knock-in, Suz12 knockout


title: PA1 structures, Wnt1-Cre;pMes-Bmp4 mice, E9.5-E9.75 (25 to 27-somite stage) 1

description:
Library name: TG_1
featureCounts on data TG_1: Counts


title: PA1 structures, wild-type mice, E9.5-E9.75 (25 to 27-somite stage) 2

description:
Library name: WT_2
featureCounts on data WT_2: Counts

value: wild-type


title: RBBP5-dTAG, Suz12 KO ES line (rs14) treated with DMSO, replicate 1

description: Library name: mrna_rs14_dmso_Rep1


title: D013_13_NeuN

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

value: NeuN

value: peripheral region of retina

value: male

tag: ethnicity

value: European

value: 69 years

value: FALSE


title: D19_13_Nu

value: 82 years

tag: donor id

value: gene symbol

value: GENCODE 32


title: RNAseq_Suz12KO_S12NSD2dead_rep2

value: Mouse embryonic stem cells

value: Suz12 KO + S12N:SD2*


title: RNAseq_Suz12KO_WT_rep3

value: Suz12 KO + WT


title: PA1 structures, wild-type mice, E9.5-E9.75 (25 to 27-somite stage) 1

description:
Library name: WT_1
featureCounts on data WT_1: Counts

value: PA1 (first branchial arch)


title: D21_13_Nu

value: 86 years

tag: raw matrix_genome_annotation

value: UMI

value: snRNA-seq


title: RNAseq_Suz12KO_WT_rep2


title: RNAseq_Suz12KO_rep1

value: Suz12 KO


title: 10xATAC_19_D19_Mac_NeuN_1

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

value: NeuN

value: macula lutea

value: 10x scATAC-seq

value: female

tag: raw matrix_feature_keys

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: 19_D003_NeuN

value: peripheral region of retina

value: male

value: European

value: FALSE

value: gene symbol

value: GENCODE 32

tag: raw matrix_value_units


title: RxRM2

city: Portland

first: Brett

last: Davis

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

description: Library name: Sample14

data_processing:
Sequencing quality was checked with FastQC
Raw sequencing reads were trimmed with TrimGalore, using the --rrbs parameter
Trimmed reads were aligned to the mouse reference genome mm10 using Bismark v0.19
Bismark methylation extractor was used to obtain cpg level methylation status in coverage files
Coverage files were used to obtain coverage and methylation rate information for use with Limma for differentially methylated cytosine (DMC) analysis. The DMC results were used as input to comb-p for differentially methylated region (DMR) analysis.
Assembly: mm10
Supplementary files format and content: Methylation rate table containing percent methylation for CpGs passing coverage threshold of minimum 10X coverage in at least 4 replicates per group. Used as input to DMC analysis with Limma.

source_name: left ventricle

growth_protocol: All mouse studies were done using wild-type FVB/N mice. Mice were kept under a 12-hour light/dark cycle in temperatures between 18-23 degrees Celsius with 40-60% humidity, in stress-free/bacteria-free conditions. Mice were caged in groups of three to five whenever possible. Food and water were given ad libitum, and body weight was determined weekly.

extract_protocol:
The mice were euthanized by isoflurane, and the hearts were removed and weighed. DNA was isolated for RRBS-seq.
Genomic DNA from left ventricle samples were digested overnight with MspI (New England Biolabs) to produce sticky ends starting with a CpG. Libraries were then prepared using the NEXTflex Bisulfite-Seq Kit (BioScientific) and bisulfite conversion was performed with the EZ DNA Methylation-Gold Kit (Zymo Research). After quality control, libraries were multiplexed and sequenced on a NovaSeq 6000 at the OHSU Massively Parallel Sequencing Shared Resource to obtain roughly 40 million reads/library

treatment_protocol: To induce maternal obesity, a high-fat diet (Teklad Cat#TD.06415) or its control, a regular diet (RD, PicoLab® Laboratory Rodent Diet Cat # 5L0D), was given to virgin female FVB/NJ mice from six weeks of age and throughout the entire study. After eight weeks of dietary intervention, RD- and HFD-fed female mice were bred to an age-matched RD-fed male. At weaning, male and female offspring from each mother were randomly selected for the study. Offspring were fed the RD only starting from weaning and throughout their life.

value: left ventricle

value: 3 weeks

value: Regular Diet

value: M


title: RBBP5-dTAG ES line (rWT) treated with dTAG-13, replicate 3

description: Library name: mrna_rWT_dtag_Rep3

value: mouse embryonic stem cell

value: RBBP5-FKBP12 knock-in


title: PBS-HAT injection control, replicate 2, scRNAseq

value: 35-38 weeks old

tag: parasite genotype

value: liver

value: PBS-HAT injection via tail vein

tag: strain


title: RBBP5-dTAG ES line (rWT) treated with dTAG-13, replicate 2

description: Library name: mrna_rWT_dtag_Rep2

tag: treatment


title: PBS-HAT injection control, replicate 1, scRNAseq

value: female

tag: tissue


title: RxRM1

description: Library name: Sample13


title: RBBP5-dTAG ES line (rWT) treated with dTAG-13, replicate 1

description: Library name: mrna_rWT_dtag_Rep1


title: 10x3V31_19_D007_Macular_NeuN_T

tag: enrichment protocol

value: To enrich the retinal ganglion cell nuclei, isolated macular retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle). The nuclei group with strongest 5% FITC signal was collected for RGC enrichment.

tag: suspension enrichment_factors

value: NeuN

value: macula lutea

value: 66 years

value: UMI

tag: raw matrix_assays

value: snRNA-seq


title: RNAseq_Suz12KO_S12NSD2_rep3

value: Mouse embryonic stem cells

value: Suz12 KO + S12N:SD2


title: RNAseq_Suz12KO_S12NSD2dead_rep1

value: Suz12 KO + S12N:SD2*


title: RBBP5-dTAG ES line (rWT) treated with DMSO, replicate 3

description: Library name: mrna_rWT_dmso_Rep3

value: DMSO


title: RNAseq_Suz12KO_S12NSD2_rep2


title: RNAseq_Suz12KO_S12NSD2_rep1


title: RBBP5-dTAG ES line (rWT) treated with DMSO, replicate 2

description: Library name: mrna_rWT_dmso_Rep2


title: RxRF2

description: Library name: Sample10

value: left ventricle

value: 3 weeks

value: Regular Diet

tag: Sex

value: F


title: 19_D007_Nu

value: peripheral region of retina

tag: assay

value: male

value: European

value: FALSE

value: gene symbol

tag: raw matrix_cellranger_assay_chemistry

value: GENCODE 32


title: 10xATAC_19_D010_Mac_NeuN_1

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

value: NeuN

value: macula lutea

value: 10x scATAC-seq

value: female

value: 88 years

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: RxRF3

description: Library name: Sample11

value: left ventricle

value: 3 weeks

value: Regular Diet


title: RBBP5-dTAG ES line (rWT) treated with DMSO, replicate 1

description: Library name: mrna_rWT_dmso_Rep1

tag: cell line

tag: cell type

value: mouse embryonic stem cell

tag: genotype

value: RBBP5-FKBP12 knock-in

value: DMSO


title: RNAseq_Suz12KO_S12N_rep3

value: Mouse embryonic stem cells

value: Suz12 KO + S12N


title: RNAseq_Suz12KO_S12N_rep2


title: 10xATAC_19_D6_Mac_NeuN_3

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

value: male

tag: ethnicity

value: European

tag: age

value: >89 years

value: FALSE

tag: donor id


title: RBBP5 ChIP in WT cells, replicate 2

description: Library name: RBBP5 ChIP in WT cells, replicate 2

data_processing:
Raw reads were trimmed using Trim Galore! (Galaxy Version 0.6.10+galaxy0). Quality trimming: Bases with phred score <20 were removed from the 3' end. After trimming, reads shorter than 20 bases were discarded.
Trimmed reads were aligned to mm10 builld of mouse genome using Bowtie2 (Galaxy Version 2.5.3+galaxy1) using default analysis mode, using paired-end settings and options "-I 0 -X 500 --fr", followed by sorting (samtools sort).
Alignments are deduplicated using Samtools fixmate (Galaxy Version 1.21+galaxy0) with -m option, followed by Samtoools markdup (Galaxy Version 1.21+galaxy0) with option -r.
Bigwig files are generated using bamCoverage program (Galaxy Version 3.5.4+galaxy0) using RPKM as normalization method, 50 bp bin size. deepTools' computeMatrix and plotProfile (Galaxy Version 3.5.4+galaxy0) are used to generate composite profile plots.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Embryonic stem cell

extract_protocol:
~25 million cells per genotype were double-crosslinked in 2 mM disuccinimidyl glutarate (DSG) for 30 minutes then  1% formaldehyde for 10 minutes. Crosslinked cells were collected off the plates and snap-frozen as pellets. Cells were lysated in standard buffers and sonicated using Covaris E220 acquistic sonicator following manufacturer's recommendations.
ChIP-seq libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #7645) and adaptor and multiplex oligos from NEBNext® Multiplex Oligos for Illumina® (E6442L).

value: Embryonic stem cell

value: WT

tag: antibody

value: A300-109A, Bethyl Laboratories, Inc


title: HxRM4

description: Library name: Sample8

value: High Fat Diet

value: M


title: RBBP5 ChIP in WT cells, replicate 1

description: Library name: RBBP5 ChIP in WT cells, replicate 1


title: RNAseq_Suz12KO_S12N_rep1


title: HxRM3

description: Library name: Sample7

value: left ventricle

value: 3 weeks


title: 19_D005_Nu

value: peripheral region of retina

value: Hispanic or Latin American

value: 53 years

tag: raw matrix_feature_keys

value: gene symbol

tag: raw matrix_genome_annotation

value: GENCODE 32

tag: raw matrix_value_units

value: UMI

value: snRNA-seq


description: Library name: RBBP5 ChIP in S12N:SD2 cells, replicate 2

tag: tissue

value: mouse embryonic stem cell

value: Suz12(Nterminus)-SETD2(SETdomain) fusion expressing, Suz12 KO


title: 19_D019_NeuN

tag: enrichment protocol

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

value: NeuN

value: female

value: European

value: 82 years

value: FALSE


title: D026_13_Nu

value: male

value: 81 years


title: HxRM2

description: Library name: Sample6

value: left ventricle

value: 3 weeks

tag: treatment

value: High Fat Diet

value: M


description: Library name: RBBP5 ChIP in S12N:SD2 cells, replicate 1

value: Embryonic stem cell

value: A300-109A, Bethyl Laboratories, Inc


title: RNAseq_Suz12KO_WT_rep1

value: Mouse embryonic stem cells

value: Suz12 KO + WT


title: 19_D011_Nu-0605

value: peripheral region of retina

value: >89 years

value: gene symbol

value: GENCODE 32

value: UMI

tag: raw matrix_assays

value: snRNA-seq


title: RNAseq_S12NSUV2_rep2

value: Suz12 KO + S12N:SUV2


title: RxRF4

description: Library name: Sample12

value: Regular Diet

tag: Sex

value: F


title: HxRF4

description: Library name: Sample4

value: left ventricle


description: Library name: RBBP5 ChIP in Suz12 KO cells, replicate 2

value: mouse embryonic stem cell

value: Suz12 KO


title: 10x3v31_19_D005_Macular_NeuN_T

value: To enrich the retinal ganglion cell nuclei, isolated macular retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle). The nuclei group with strongest 5% FITC signal was collected for RGC enrichment.

tag: suspension enrichment_factors

value: NeuN

value: macula lutea

tag: assay

value: male

value: Hispanic or Latin American

value: 53 years

value: FALSE


title: RNAseq_S12NSUV2_rep1

tag: cell line

value: Mouse embryonic stem cells


description: Library name: RBBP5 ChIP in Suz12 KO cells, replicate 1

value: Embryonic stem cell

tag: cell type

value: A300-109A, Bethyl Laboratories, Inc


title: 10xATAC_D028_13_Mac_NeuN_2

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

value: 10x scATAC-seq

value: European

value: 67 years

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: HxRF3

description: Library name: Sample3

value: left ventricle

value: 3 weeks

value: High Fat Diet

value: F


title: RxRF1

description: Library name: Sample9

value: Regular Diet


title: HxRF2

description: Library name: Sample2


description: Library name: RBBP5 ChIP in S12N:SD2(deadSET) cells, replicate 2

value: mouse embryonic stem cell

tag: genotype

value: Suz12(Nterminus)-SETD2(deadSETdomain) fusion expressing, Suz12 KO


title: D018_26_13_Nu

value: peripheral region of retina

value: female,male

tag: ethnicity

value: 81 years,>89 years

value: FALSE

value: gene symbol

tag: raw matrix_cellranger_assay_chemistry

value: GENCODE 32

value: UMI

value: snRNA-seq


title: RNAseq_S12NSUV2_KDM4i_100nM_rep3

value: Mouse embryonic stem cells

value: Suz12 KO + S12N:SUV2

value: KDM4-specific inhibitor QC6352


description: Library name: RBBP5 ChIP in S12N:SD2(deadSET) cells, replicate 1

value: Embryonic stem cell

value: A300-109A, Bethyl Laboratories, Inc


title: 10xATAC_19_D6_Mac_NeuN_1

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

value: NeuN

value: macula lutea

value: 10x scATAC-seq

value: male

value: European

tag: age

value: >89 years

tag: donor id

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: RNAseq_S12NSUV2_rep3


title: KDM5B ChIP in WTcells, replicate 2

description: Library name: KDM5B ChIP in WTcells, replicate 2

value: mouse embryonic stem cell

value: WT

tag: antibody

value: A301-813A, Bethyl Laboratories, Inc


title: RNAseq_S12NSUV2_KDM4i_50nM_rep3

value: Mouse embryonic stem cells

value: Suz12 KO + S12N:SUV2


title: RNAseq_S12NSUV2_KDM4i_100nM_rep1

value: KDM4-specific inhibitor QC6352


title: trimodulin + ampicillin (S.pn.) #3

city: Berlin

first: Peter

last: Pennitz

address: Charitéplatz 1

department: Department of Infectious Diseases, Respiratory Medicine and Critical Care

country: Germany

institute: Charité – Universitätsmedizin Berlin

description: Library name: nomv_spn_igm_amp_3

data_processing:
The quality of sequencing reads was assessed with FASTQC (v0.11.9).  Subsequently, reads were input into SeA-SnaP: (Se)q (A)nalysis (Sna)kemake (P)ipeline (https://github.com/bihealth/seasnap-pipeline). Briefly, reads were mapped with the STAR aligner (v2.7.3a) to the mm10/GRCm38 mouse genome  using GENCODE annotation version M12.  Next, featureCounts (v2.0.0) was used to count reads in exons and generate a read count table.
Assembly: mm10/GRCm38 mouse genome
Supplementary files format and content: tab-separated text output from featureCounts(v2.0.0), for each gene id (column 1),  raw read count is provided (column 7).

source_name: whole blood

extract_protocol:
Whole blood (500 µl) was lysed in TRIzol™ LS Reagent (Thermo Fisher Scientific, Waltham, USA). RNA was extracted using the Direct-zol RNA Miniprep protocol (Zymoresearch) according to the manufacturer’s instructions.
Library preparation was performed using the Illumina TruSeq stranded mRNA Kit

value: whole blood


title: trimodulin + ampicillin (S.pn.) #2

description: Library name: nomv_spn_igm_amp_2


title: 10xATAC_19_D19_Mac_NeuN_3

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

value: female

value: 82 years

value: FALSE

tag: raw matrix_feature_keys


title: D005_13_Nu

value: peripheral region of retina

value: male

value: 80 years

value: gene symbol

tag: raw matrix_genome_annotation

value: GENCODE 32

tag: raw matrix_value_units

value: UMI

value: snRNA-seq


title: RNAseq_S12NSUV2_KDM4i_50nM_rep2


title: trimodulin (S.pn.) #4

description: Library name: nomv_spn_igm_noamp_4

tag: tissue


title: KDM5B ChIP in WT cells, replicate 1

description: Library name: KDM5B ChIP in WT cells, replicate 1

value: Embryonic stem cell

value: mouse embryonic stem cell

value: WT


description: Library name: KDM5B ChIP in S12N:SD2 cells, replicate 2

value: Suz12(Nterminus)-SETD2(SETdomain) fusion expressing, Suz12 KO

value: A301-813A, Bethyl Laboratories, Inc


title: D19_13_NeuN

tag: enrichment protocol

value: NeuN

value: European


title: RNAseq_S12NSUV2_KDM4i_50nM_rep1

value: Mouse embryonic stem cells

value: Suz12 KO + S12N:SUV2

tag: treatment

value: KDM4-specific inhibitor QC6352


title: 19_D011_NeuN-0605

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

value: peripheral region of retina

tag: Sex

value: female

value: >89 years

value: FALSE

tag: raw matrix_assays


title: trimodulin (S.pn.) #1

description: Library name: nomv_spn_igm_noamp_1

value: whole blood


title: trimodulin (S.pn.) #2

description: Library name: nomv_spn_igm_noamp_2


title: RNAseq_S12NSUV2dead_rep3

value: Suz12 KO + S12N:SUV2*


title: RNAseq_S12NSUV2_KDM4i_100nM_rep2


title: trimodulin + ampicillin (S.pn.) #4

description: Library name: nomv_spn_igm_amp_4


title: D017_18_13_NeuN

tag: suspension enrichment_factors

tag: assay

value: female,male

value: >89 years,65 years

value: gene symbol

value: GENCODE 32

value: UMI

value: snRNA-seq


title: RNAseq_S12NSUV2dead_rep2

tag: cell line

tag: cell type


title: ampicillin (S.pn.) #4

description: Library name: nomv_spn_noigm_amp_4


description: Library name: KDM5B ChIP in Suz12 KO cells, replicate 1

value: Embryonic stem cell

value: mouse embryonic stem cell

tag: genotype

value: Suz12 KO

value: A301-813A, Bethyl Laboratories, Inc


title: 19_D006_NeuN

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

value: NeuN

value: male

tag: ethnicity

value: European

tag: raw matrix_cellranger_assay_chemistry


title: ampicillin (S.pn.) #3

description: Library name: nomv_spn_noigm_amp_3


title: RNAseq_S12NSUV2dead_KDM4i_100nM_rep3

description:
RNAseq_mm10_Counts_Merged.tsv
Table_DESeq2_AllNormalizedCounts_PeakNorm.txt
Table_DESeq2_FilteredNormalizedCounts_PeakNorm.txt

value: Mouse embryonic stem cells

value: KDM4-specific inhibitor QC6352


title: 10xATAC_19_D3_Mac_NeuN_3

value: macula lutea

value: 10x scATAC-seq

tag: age

value: 86 years

value: FALSE

tag: donor id

value: genomic coordinates

value: fragment ends

value: snATAC-seq


description: Library name: KDM5B ChIP in S12N:SD2(deadSET) cells, replicate 1

value: Embryonic stem cell

value: Suz12(Nterminus)-SETD2(deadSETdomain) fusion expressing, Suz12 KO

tag: antibody


title: RNAseq_S12NSUV2dead_KDM4i_100nM_rep2

value: Suz12 KO + S12N:SUV2*


title: RBBP5-dTAG, Suz12 KO, S12N:SD2 expressing ES line (set) treated with dTAG-13, replicate 3

description: Library name: merged_set_dtag_rep3

data_processing:
RRBS sequencing reads were processed using Trim Galore! (Galaxy Version 0.6.7+galaxy0) with --rrbs setting enabled. Low quality ends (phred score threshold 20) were trimmed and reads that became shorther than 20 base were discarded.
Bismark mapper (Galaxy Version 0.22.1+galaxy4) was used to align trimmed reads on mm10 in-silico bisulfite transformed genome with default settings. The reads were also aligned to lambda phage genome (NC_001416.1) to assess the bisulfite conversion efficiency.
The alignments were then used to call cytosine methylation through Bismark methyl extractor (Galaxy Version 0.22.1).
bismark2bedgraph module(https://felixkrueger.github.io/Bismark/bismark/methylation_extraction/) was used to convert methyl extractor output (only for CpG context) to bedgraph and coverage files. bismark.cov files were then processed to generate input files for differential methylation analysis. For differentially methylated CpGs at PRC2 sites, methylKit package (1.32.1) was used in R (4.4.2) environment. Bases with coverage below 10X and bases that have >99.9th percentile of coverage in each sample were filtered out and coverages were normalized between the samples by median. Initial PCA analysis demonstrated clustering of the replicates. Cytosines were filtered for their overlaps with H3K27me3 Cut&Run peakset using GenomicRanges (1.58.0) and their contexts (islands, shores, shelves, inter) were assigned using R-package Annotatr version 1.32.0. CpGs with methylation percentage difference >10% at q value < 0.01 were considered differentially methylated cytosine (DMCs). Mean percent methylation was calculated at H3K27me3 and CpG-island associated DMCs.
Assembly: mm10
Supplementary files format and content: bismark.cov files with position-specific methylation percentage and count columns.

extract_protocol:
Genomic DNA extracts were procesed as per manufacturer's recommendation. Genomic DNA was digested with MspI enzyme overnight.
MspI-digested gDNA was end-repaired using NEBNExt Ultra II End Prep enzyme (NEB, E7645S) and NEBNext EM-seq adapter (NEB, E7140S)  was ligated using NEBNExt Ultra II Ligation mix (NEB, E7645S).Size-selected DNA was bisulfite-converted and purified using EZ DNA Methylation Lightning Kit (Zymo, D5030). Bisulfite-converted libraries were barcoded and amplified using NEBNext Multiplex Oligos for EM-seq (NEB, E7140S) and EpiMark HotStart Taq polymerase (M0490S).Libraries were then cleaned up with Zymo Cleanup kit.

treatment_protocol: Forty thousands cells were plated per well of a 6-well plate one day before the treatment with 500 nM dTAG-13 or 0.1% DMSO for 24 hours. At the end of the treatment period, culture medium was removed and genomic DNA was extracted using Qiagen DNeasy Blood & Tissue Kit as manufacturer's protocol.

value: mouse embryonic stem cell

value: RBBP5-FKBP12 knock-in, Suz12 knockout, S12N-SD2 fusion expression


title: D27_13_Nu

value: peripheral region of retina

value: 77 years

tag: raw matrix_feature_keys

value: gene symbol

tag: raw matrix_genome_annotation

value: GENCODE 32

value: UMI

value: snRNA-seq


title: ampicillin (S.pn.) #1

description: Library name: nomv_spn_noigm_amp_1

tag: tissue

value: whole blood


title: RNAseq_S12NSUV2dead_KDM4i_100nM_rep1

value: Mouse embryonic stem cells

value: KDM4-specific inhibitor QC6352


title: placebo (S.pn.) #4

description: Library name: nomv_spn_noigm_noamp_4


description: Library name: KDM5B ChIP in S12N:SD2 cells, replicate 1

value: Suz12(Nterminus)-SETD2(SETdomain) fusion expressing, Suz12 KO

value: A301-813A, Bethyl Laboratories, Inc


title: ampicillin (S.pn.) #2

description: Library name: nomv_spn_noigm_amp_2


title: RBBP5-dTAG, Suz12 KO, S12N:SD2 expressing ES line (set) treated with dTAG-13, replicate 2

description: Library name: merged_set_dtag_rep2


title: D009_13_NeuN

tag: enrichment protocol

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

value: NeuN

value: male

value: Asian

value: 85 years

value: FALSE

tag: raw matrix_value_units


title: 10xATAC_19_D3_Mac_NeuN_2

value: macula lutea

value: 10x scATAC-seq

tag: Sex

value: European

value: 86 years

value: genomic coordinates

value: fragment ends

value: snATAC-seq


description: Library name: KDM5B ChIP in Suz12 KO cells, replicate 2

value: Embryonic stem cell

value: mouse embryonic stem cell

value: Suz12 KO


title: RBBP5-dTAG, Suz12 KO, S12N:SD2 expressing ES line (set) treated with dTAG-13, replicate 1

description: Library name: merged_set_dtag_rep1

value: RBBP5-FKBP12 knock-in, Suz12 knockout

tag: treatment


title: RNAseq_S12NSUV2dead_KDM4i_50nM_rep3

value: Mouse embryonic stem cells

value: Suz12 KO + S12N:SUV2*

value: KDM4-specific inhibitor QC6352


title: 19_D011_Nu

value: peripheral region of retina

value: female

value: >89 years

value: gene symbol

value: GENCODE 32

value: UMI

tag: raw matrix_assays

value: snRNA-seq


title: placebo (S.pn.) #3

description: Library name: nomv_spn_noigm_noamp_3

value: whole blood


title: RNAseq_S12NSUV2dead_KDM4i_50nM_rep2


title: placebo (S.pn.) #2

description: Library name: nomv_spn_noigm_noamp_2


title: RNAseq_S12NSUV2dead_rep1


title: RNAseq_S12NSUV2dead_KDM4i_50nM_rep1


title: RBBP5-dTAG, Suz12 KO, S12N:SD2 expressing ES line (set) treated with DMSO, replicate 3

description: Library name: merged_set_dmso_rep3

value: DMSO


title: 19_D009_Nu

tag: assay

value: male

value: Hispanic or Latin American

value: 68 years

value: FALSE


title: placebo (S.pn.) #1

description: Library name: nomv_spn_noigm_noamp_1


description: Library name: KDM5B ChIP in S12N:SD2(deadSET) cells, replicate 2

value: Embryonic stem cell

tag: cell line

value: mouse embryonic stem cell

value: Suz12(Nterminus)-SETD2(deadSETdomain) fusion expressing, Suz12 KO

value: A301-813A, Bethyl Laboratories, Inc


title: 19_D011_NeuN

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

tag: suspension enrichment_factors

value: NeuN

value: peripheral region of retina

value: European


title: RBBP5-dTAG, Suz12 KO, S12N:SD2 expressing ES line (set) treated with DMSO, replicate 2

description: Library name: merged_set_dmso_rep2

tag: cell type

tag: genotype

value: RBBP5-FKBP12 knock-in


title: RBBP5-dTAG, Suz12 KO, S12N:SD2 expressing ES line (set) treated with DMSO, replicate 1

description: Library name: merged_set_dmso_rep1


title: trimodulin (PBS) #4

description: Library name: nomv_pbs_igm_noamp_4


title: 10xATAC_D028_13_Mac_NeuN_1

value: macula lutea

value: 10x scATAC-seq

tag: ethnicity

value: 67 years

value: genomic coordinates

value: fragment ends

value: snATAC-seq


title: trimodulin (PBS) #3

description: Library name: nomv_pbs_igm_noamp_3

value: whole blood


title: RBBP5-dTAG, Suz12 KO ES line (rs14) treated with dTAG-13, replicate 3

description: Library name: merged_rs14_dtag_rep3

value: RBBP5-FKBP12 knock-in, Suz12 knockout, S12N-SD2 fusion expression


title: 10xATAC_19_D19_Mac_NeuN_2

value: female

tag: age

value: 82 years

value: FALSE


title: RBBP5-dTAG, Suz12 KO ES line (rs14) treated with dTAG-13, replicate 2

description: Library name: merged_rs14_dtag_rep2

value: mouse embryonic stem cell


title: trimodulin (PBS) #2

description: Library name: nomv_pbs_igm_noamp_2


title: CnR_H2AK119ub1_Suz12KO_S12NSD2dead_rep2

data_processing:
ChIP and CUT&RUN sequencing reads were trimmed and filtered for quality and adapter content using v0.4.5 of TrimGalore with a quality setting of 15 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore), and running version 1.15 of Cutadapt and version 0.11.5 of FastQC.
Trimmed reads were aligned to mouse assembly mm10 with v2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
Mapped reads were deduplicated using MarkDuplicates in v2.16.0 of Picard Tools.
Except for H3K9me3 CUT&RUN samples, data were normalized to sequencing depth (to ten million uniquely mapped reads) and normalized bigwig files were created using DeepTools v3.3.0 by running BamCoverage.
For H3K9me3, 10,000bp windows were generated from the mm10 genome using BedTools v2.27.1 by running Makewindows, and bins containing H3K27me3 peaks were removed by running Intersect with the setting -v. BedTools Multicov was used to count aligned reads from H3K9me3 bam files over the 10,000bp windows, and size factors were estimated with the estimateSizeFactorsForMatrix function in DESeq2 v1.34.0. Size factors were used when running deepTools BamCoverage to create normalized bigwig files. For a list of scaling factors and validation of normalizations, refer to Supplementary Fig. 1.
Assembly: mm10
Supplementary files format and content: BigWig
Library strategy: CUT&RUN

extract_protocol:
Native cells were harvested and 0.4x10^6 cells/per sample were used using standard CUT&RUN protocol: https://www.protocols.io/view/cut-amp-run-targeted-in-situ-genome-wide-profiling-zcpf2vn
Histone modifications were mapped with the standard CUT&RUN library prep protocol:  https://www.protocols.io/view/library-prep-for-cut-amp-run-with- nebnext-ultra-ii-wvgfe3w (2019)

value: Mouse embryonic stem cells

value: H2AK199ub1, CST-D27C4

value: Suz12 KO + S12N:SD2*


title: RBBP5-dTAG, Suz12 KO ES line (rs14) treated with dTAG-13, replicate 1

description: Library name: merged_rs14_dtag_rep1

value: RBBP5-FKBP12 knock-in, Suz12 knockout


title: D30_13_NeuN

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

value: NeuN

value: peripheral region of retina

value: European

value: 73 years

tag: donor id

value: gene symbol

tag: raw matrix_cellranger_assay_chemistry

value: GENCODE 32

value: UMI

value: snRNA-seq


title: CnR_H2AK119ub1_Suz12KO_S12NSD2_rep2

tag: antibody

value: Suz12 KO + S12N:SD2


title: placebo (PBS) #4

description: Library name: nomv_pbs_noigm_noamp_4

value: whole blood


title: trimodulin (PBS) #1

description: Library name: nomv_pbs_igm_noamp_1


title: D017_18_13_Nu

value: female,male

value: >89 years,65 years

value: FALSE

tag: raw matrix_feature_keys

tag: raw matrix_genome_annotation


title: CnR_H2AK119ub1_Suz12KO_WT_rep2

value: Mouse embryonic stem cells

value: H2AK199ub1, CST-D27C4

value: Suz12 KO + WT


title: RBBP5-dTAG, Suz12 KO ES line (rs14) treated with DMSO, replicate 2

description: Library name: merged_rs14_dmso_rep2

value: mouse embryonic stem cell

value: RBBP5-FKBP12 knock-in, Suz12 knockout

value: DMSO


title: CnR_H2AK119ub1_Suz12KO_rep2

value: Suz12 KO


title: 19_D007_NeuN

tag: enrichment protocol

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

value: NeuN

tag: tissue

value: peripheral region of retina

value: male

value: European

value: 66 years


title: RBBP5-dTAG, Suz12 KO ES line (rs14) treated with DMSO, replicate 1

description: Library name: merged_rs14_dmso_rep1

value: RBBP5-FKBP12 knock-in


title: placebo  (PBS) #3

description: Library name: nomv_pbs_noigm_noamp_3

value: whole blood


title: D30_13_Nu

tag: Sex

value: female

value: 73 years

value: gene symbol

value: GENCODE 32

tag: raw matrix_value_units

value: UMI

value: snRNA-seq


title: CnR_H2AK119ub1_WT_mESC_rep2

value: Mouse embryonic stem cells

value: H2AK199ub1, CST-D27C4

value: WT

tag: treatment


title: placebo (PBS) #2

description: Library name: nomv_pbs_noigm_noamp_2


title: CnR_H2AK119ub1_Suz12KO_S12NSUV2dead_rep2

value: Suz12 KO + S12N:SUV2*


title: 10x3V31_19_D016_Macular_NeuN_T

source_name: macula lutea proper

value: To enrich the retinal ganglion cell nuclei, isolated macular retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle). The nuclei group with strongest 5% FITC signal was collected for RGC enrichment.

value: NeuN

value: macula lutea proper

tag: assay

value: 83 years

value: FALSE

tag: raw matrix_assays


title: RBBP5-dTAG, Suz12 KO ES line (rs14) treated with DMSO, replicate 3

description: Library name: merged_rs14_dmso_Rep3

tag: cell line

value: mouse embryonic stem cell

value: RBBP5-FKBP12 knock-in

value: DMSO


title: placebo (PBS) #1

description: Library name: nomv_pbs_noigm_noamp_1

value: whole blood


title: CnR_H2AK119ub1_Suz12KO_S12NSUV2_rep2

tag: cell type

value: Suz12 KO + S12N:SUV2


title: Helicon4, 100mpk, 48hr,rep3 [SH7083_SA91291_S53]

status: Public on Oct 21 2025

city: Cambridge

first: YaGuang

last: Si

state: MA

address: 30 Acorn Park Dr

institute: Fogpharma

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.39
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.7.7a
Host reads were removed with XenofilteR
Unique gene hit counts were calculated by using featureCounts from the R Subread package v.2.4.2
Read filtering, normalization, and differential expression analysis with respect to biological variation was performed with the edgeR package v.4.0.2 in R
Assembly: GRCh38
Supplementary files format and content: CPM from EdgeR for all samples in EXCEL format

extract_protocol:
RNA extraction was performed using NEBNext Ultra II Directional RNA Library Prep Kit following manufacture's instructions (New England BioLabs, Ipswich, MA)
library preparation and sequencing were performed by Fulgent Gentetics (Houston, TX) with TruSeq stranded mRNA library kit on Novaseq S4 Platform with PolyA enrichment.

value: Colorectal adenocarcinoma

tag: dose

tag: time

tag: replicate


title: RBBP5-dTAG ES line (rWT) treated with dTAG-13, replicate 3

description: Library name: merged_rWT_dtag_rep3

tag: genotype

value: RBBP5-FKBP12 knock-in, Suz12 knockout, S12N-SD2 fusion expression


title: 19_D010_Nu

value: peripheral region of retina

value: female

tag: ethnicity

value: European

tag: age

value: 88 years

tag: donor id

value: gene symbol

tag: raw matrix_cellranger_assay_chemistry

value: GENCODE 32

value: UMI

value: snRNA-seq


title: CnR_H2AK119ub1_Suz12KO_S12NSUV2_rep1

value: Mouse embryonic stem cells

tag: antibody

value: H2AK199ub1, CST-D27C4


title: RBBP5-dTAG ES line (rWT) treated with dTAG-13, replicate 2

description: Library name: merged_rWT_dtag_rep2

value: mouse embryonic stem cell


title: GDF3-KO-8

city: Minneapolis

first: Anna

last: Carey

state: Minnesota

address: 312 Church Street SE

department: Biochemistry, Molecular Biology, and Biophysics

institute: University of Minnesota

data_processing:
Analysis of read count matrices was performed using Seurat version 4.3.1 in R. Cells with mitochondrial RNA <7% and an R² of 0.95 for nCount_RNA vs. nFeature_RNA were included. Each sample was normalized using ‘NormalizeData’, and the top 2000 highly variable genes were selected with ‘FindVariableFeatures’. Dimensional reduction and clustering followed the standard Seurat workflow with ‘ScaleData’ and ‘RunPCA’. The top 50 principal components, identified by ‘ElbowPlot’, were used for UMAP visualization via ‘RunUMAP’ and finding nearest neighbors. Clusters and subclusters were identified using the Louvain algorithm with a resolution of 0.2.
Differentially expressed genes (DEGs) were identified by comparing normalized expressed RNAs for each model to RNAs expressed in control cells via the function ‘FindMarkers’ and then merging the results. When comparing clusters, the function ‘FindAllMarkers’ was employed to find marker genes that characterized a specific cluster compared to all other clusters. A minimum of 100 cells from a sample group in a cluster was required for downstream analysis.
Before gene set enrichment analysis (GSEA) or over-representation analysis (ORA), common gene symbols were converted into Entrez gene ids and ensemble ids using the R package biomart, version 3.18, using the dataset "mmusculus_gene_ensembl"16,17. ORA of Gene Ontology (GO) and Reactome (version 1.34.0) terms was conducted using ClusterProfiler (version 3.18.1) using DEGs with an absolute average Log fold change >0 and adjusted p-values <0.05 where analysis occurred separately for up and down-regulated genes using the ‘enrichGO’ and ‘enrichPathway’ functions18,19’20,21. Using the same DEG lists, Reactome Pathway Analysis was employed for GSEA using the function ‘GSEA’ and the Reactome IL-1 family signaling enrichment gene set.
Assembly: GRCh38
Supplementary files format and content: rds objects processed through Seruat

source_name: CD45+ live cells from visceral white adipose tissue (vWAT)

extract_protocol:
Single-cell libraries were prepared in triplicate with >85% cell viability confirmed by trypan blue staining. Cells were resuspended in MEM with 10% FBS at 1200 cells/uL. Library construction used Chromium Next GEM Single Cell 3ʹ dual index Kits v3.1 with Chip G (10x Genomics). About 10,000 single cells were loaded to generate gel bead-in-emulsions (GEMs), lysed, and RNA was barcoded and reverse-transcribed.
GEMs were broken, and cDNA was prepared following the manufacturer’s protocol. cDNA quality was assessed with the Agilent Bioanalyzer and Pico-green. Libraries underwent QC by shallow-sequencing on an Illumina NextSeq and final sequencing on an Illumina Nova Seq S4 capturing ~20,000 paired-end reads per cell. Sequencing libraries were converted into feature-barcode matrices using Cell Ranger (10x Genomics, version 5.0.0) and mapped to GRCh38.

treatment_protocol: Mice were euthanized by cervical dislocation under anaesthesia and visceral white adipose tissue (vWAT) was harvested; vWAT was digested using collagenase II digestion buffer and a single cell suspension of the stromovascular fraction was isolated and stained prior to fluorescence associated cell sorting for the CD45+ live cell population.

tag: tissue

value: GDF3 KO

value: No challenge


title: WT-7

value: CD45+ live cells from visceral white adipose tissue (vWAT)

value: WT


title: CnR_H2AK119ub1_Suz12KO_S12NSD2dead_rep1

value: Suz12 KO + S12N:SD2*


title: D018_26_13_NeuN

tag: enrichment protocol

value: To enrich for neurons, isolated retinal nuclei were stained with a mouse anti-NeuN monoclonal antibody for 30 minutes at 4°C. The stained nuclei were sorted with a BD Aria II flow sorter (70μm nozzle).

tag: suspension enrichment_factors

value: NeuN

tag: Sex

value: female,male

value: 81 years,>89 years

value: FALSE

tag: raw matrix_feature_keys

tag: raw matrix_genome_annotation


title: RBBP5-dTAG ES line (rWT) treated with dTAG-13, replicate 1

description: Library name: merged_rWT_dtag_rep1

tag: cell line

value: RBBP5-FKBP12 knock-in, Suz12 knockout

tag: treatment


title: MCF7_TMXplusFasting_Rep6

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

institute: Netherlands Cancer Institute

data_processing:
Sequencing data were aligned to the human reference genome hg38 using HISAT2 (v2.1.0), and the number of reads per gene was measured with HTSeq count (v0.5.3)
Assembly: hg38/GRCh38
Supplementary files format and content: .tsv, gene count values for each sample

source_name: Breast cancer

growth_protocol: MCF7 cells were xenografted in mice and 2 weeks after 4 week cycle of treatment was performed: Control (ad libitum diet); Tamoxifen (30mg/Kg; 5 days a week), fasting (water-only diet 48h/week) and combination of tamoxifen and fasting

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen, Germany) following manufacturer´s instructions.
Illumina

value: Breast cancer

tag: cell type

value: xenograft

value: Tamoxifen+Fasting (TMX+Fasting)


title: GDF3-KO-6


title: RBBP5-dTAG ES line (rWT) treated with DMSO, replicate 3

description: Library name: merged_rWT_dmso_rep3

value: DMSO


title: RBBP5-dTAG ES line (rWT) treated with DMSO, replicate 2

description: Library name: merged_rWT_dmso_rep2

value: RBBP5-FKBP12 knock-in


title: MCF7_TMXplusFasting_Rep5


title: MCF7_TMXplusFasting_Rep4


title: WT-3


title: CnR_H2AK119ub1_Suz12KO_WT_rep1

value: Mouse embryonic stem cells

value: H2AK199ub1, CST-D27C4

value: Suz12 KO + WT


title: GDF3-KO-2

value: CD45+ live cells from visceral white adipose tissue (vWAT)

value: GDF3 KO

value: No challenge


title: CnR_H2AK119ub1_Suz12KO_rep1

value: Suz12 KO


title: CnR_H2AK119ub1_Suz12KO_S12NSUV2dead_rep1

value: Suz12 KO + S12N:SUV2*


title: CnR_H2AK119ub1_WT_mESC_rep1

value: WT


title: MCF7_TMXplusFasting_Rep3


title: WT-1


title: smash_eif4a3_danoprevir_mRNA_bio_rep_3_LRS

city: New Haven

first: Alexandra

last: Bergfort

state: CT

address: 333 Cedar Street

department: Molecular Biophysics & Biochemistry

institute: Yale University

description: Library name: sample18

data_processing:
mRNA-Illumina: Paired-end read mates were generated in .fastq format. Illumina adapters were trimmed using fastp 0.24.0. Reads were mapped to the GRCh38.p14 genome (GENCODE release 44) using STAR 2.7.11b with settings  --runMode alignReads -outSAMtype BAM SortedByCoordinate. Resulting .bam files were indexed with samtools 1.21. Splicing was quantified running whippet on fastp outputs. Gene expression was determined using featureCounts(subread 2.0.8) followed by DESeq2 analysis. All downstream analyses were carried out using custom python scripts that utilize the output files from DESeq2 and whippet.
nRNA-Illumina: Paired-end read mates were generated in .fastq format. Illumina adapters were trimmed using fastp 0.24.0. Reads were mapped to the GRCh38.p14 genome (GENCODE release 44) using STAR 2.7.11b with settings  --runMode alignReads –outSAMattributes All --outSAMtype BAM --SortedByCoordinate. Resulting .bam files were indexed with samtools 1.21. Junction reads were quantified using splice-q 1.0.0 and splicing per intron (SPI) values were calculated using a custom python script using the splice-q output files. Splicing order was calculated using insplico with the STAR outputs as input files.
mRNA-PacBio: Adapters were trimmed and data pre-processed using fastplong 0.2.2. Reads were mapped to the GRCh38.p14 genome (GENCODE release 44) using flair align 2.0.0.
Assembly: GRCh38.p14 genome (GENCODE release 44)
Supplementary files format and content: whippet outputs as comma delimited files, providing Percent Spliced In (PSI) values for the different treatment conditions.
Supplementary files format and content: FeatureCount output as txt files providing read counts for the hg38 genome. Input for DESeq2.
Supplementary files format and content: DESeq2 results as comma delimited files, providing change in gene expression between different treatment conditions.
Supplementary files format and content: splice-q outputs as tab delimited files providing info aboout read numbers over splice junctions
Supplementary files format and content: insplico outputs as comma delimited files providing info about splicing order of introns surrounding the listed exons.
Supplementary files format and content: block_junction_coverage as a comma delimited file, providing info about coordinates of blocks of exons spliced collectively and the read coverage of the respective block skipping junctions

growth_protocol: All cells were cultivated at 37°C in Dulbecco's modified Eagle's medium (DMEM) GLutaMAX (Thermo Fisher Scientific, 10569010) supplemented with 10% fetal bovine serum (Gibco, A5670701) and 1% penicillin/streptomycin (Thermo Fisher Scientific, 15140122). In addition, medium for SMASh-EIF4A3 cells was supplemented with 1 ug/mL Puromycin (Thermo Fisher Scientific, A1113803) and 10 ug/mL Blasticidine (Thermo Fisher Scientific, A1113903). Medium for 293 Flp-In T-REx  – EIF4A3 cells was supplemented with 15 ug/mL Blasticidine and 150 ug/mLHygromycin (Thermo Fisher Scientific, 10687010).

extract_protocol:
mRNA: To harvest, cells were washed off the 6-wells with 500 uL ice cold PBS and then centrifuged for 1 minute at 1000g in a tabletop centrifuge. PBS was removed, cells were resuspended in 1 mL TRIzol (Thermo Fisher Scientific, 15596018) and RNA extracted according to the manufacturer protocol. Subsequently RNA was further purified via the RNeasy Mini Kit (Qiagen, 74104), including DNase digestion (RNase-Free DNase Set, Qiagen, 79254).
Nascent RNA (nRNA): Cells were fractionated and nascent RNA was extracted from chromatin as described in Reimer K, Neugebauer K, Curr Prot 2020 (PMID: 33440169). For Illumina short read sequencing, the protocol was followed until step 40 (including poly(A)+ depletion but excluding ribosomal RNA (rRNA) depletion) and samples were subsequently used for library preparation, that included rRNA depletion (see below). For PacBio long-read sequencing of nascent RNA, rRNA depletion was carried out following the complete protocol.
mRNA-Illumina sequencing: Extracted RNA was used to prepare RNA-seq libraries using the KAPA mRNA HyperPrep Kit (Kapa Biosystems). The RNA-seq library was sequenced on the Illumina Novaseq X Plus platform generating ~25 milliion paired-end reads per sample.
nRNA-Illumina sequencing:  Extracted RNA was used to prepare RNA-seq libraries using the KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems). The RNA-seq library was sequenced on the Illumina Novaseq X Plus platform generating ~100 milliion paired-end reads per sample.
mRNA-PacBio: The Iso-Seq libraries were prepared according to PacBio’s Preparing Iso-Seq® Libraries using SMRTbell® Prep Kit 3.0 manual. 1.05x SMRTbell clean-up was done to size select 500bp and above fragments and one SMRT library was prepared and run on two SMRTcells. Primer annealing and polymerase binding reactions were prepared using the Binding Calculator from PacBio, based on sample volume, concentration, and insert size using default settings. The SMRTbell libraries were annealed to sequencing primers and then bound to polymerase using the Sequel® II Binding Kit 3.1 before being loaded onto the PacBio Sequel II sequencer. Sequencing was performed for 24 hours of movie time.

treatment_protocol: EIF4A3 overexpression (OE) in 293 Flp-In T-REx  – EIF4A3 cells  was induced with 0.1 mg/mL Doxycycline in PBS for 48 hours. EIF4A3 depletion in SMASh-EIF4A3 cells was induced by treatment with 1.5 uM Danoprevir for 24 hours. Control cells were treated with the same volume DMSO.

value: Human embryonic Kidney

value: 1.5 uM Danoprevir, 24 hrs

tag: batch


title: CnR_H3K4me3_RS_S12NSD2_dTAG_rep2

value: H3K4me3, CST-C42D8

value: RS + S12N:SD2


title: MCF7_TMXplusFasting_Rep2

value: Breast cancer

value: xenograft


title: MCF7_TMXplusFasting_Rep1

value: Tamoxifen+Fasting (TMX+Fasting)


title: RBBP5-dTAG ES line (rWT) treated with DMSO, replicate 1

description: Library name: merged_rWT_dmso_rep1

value: mouse embryonic stem cell

value: RBBP5-FKBP12 knock-in

value: DMSO


title: JMJD3_KO_TCM_3A

city: Columbus

first: Stanley

last: Huang

state: Ohio

address: 2255 Kenny Road

department: Department of Microbial Infection and Immunity

institute: The Ohio State University

data_processing:
We used HISAT to align the clean reads to the reference genome and then used StringTie to assemble. We used Bowtie2 to compare clean reads to the reference sequence, and then use RSEM to calculate the expression of genes and transcripts. We used Bowtie2 to align the clean reads to the gene reference sequence, and then count the coverage of the gene.
Assembly: mm10
Supplementary files format and content: includes FPKM for each sample

source_name: Bone marrow

growth_protocol: Bone marrow cells were differentiated in the presence of recombinant mouse M-CSF (20 ng/ml) in complete medium (RPMI 1640 containing 10 mM glucose, 2 mM L-glutamine, 100 U/mL of penicillin/streptomycin and 10% FBS) for 7 days. Fresh complete medium with M-CSF was supplemented on day 6 prior to use.

extract_protocol:
Firstly, the biotin-labeled Ribo-Zero rRNA Removal Kit is used to remove ribosome rRNA of total RNA.Then the un-purified RNA is fragmented under a certain temperature and ion environment. Random primers and reverse transcriptase of TruSeq® Stranded kit are used to synthesize the first-strand cDNA. cDNA library sequencing was performed using Illumina HiSeq
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Day 7 bone marrow-derived macrophages were washed and cultured with or without 70% YUMM1.7 tumor cell-conditioned medium (TCM); or stimulated with IL-4 (20 ng/mL), LPS (10 ng/ml) plus IFN-γ (50 ng/ml) for 24 h at a density of 2 million cells per well in a 6-well plate.

value: Bone marrow

value: JMJD3 cKO


title: smash_eif4a3_danoprevir_mRNA_bio_rep_2_LRS

description: Library name: sample17


title: JMJD3_KO_TCM_2A


title: CnR_H2AK119ub1_Suz12KO_S12NSD2_rep1

value: Mouse embryonic stem cells

value: H2AK199ub1, CST-D27C4

value: Suz12 KO + S12N:SD2


title: JMJD3_KO_TCM_1A


title: CnR_H3K4me3_R-Suz12KO_dTAG_rep2

value: RBBP5-FKBP + Suz12 KO (RS)


title: smash_eif4a3_dmso_mRNA_bio_rep_3_LRS

description: Library name: sample15

value: DMSO, 24 hrs


title: CnR_H3K4me3_Rbbp5-FKBP_dTAG_rep2


title: smash_eif4a3_dmso_mRNA_bio_rep_2_LRS

description: Library name: sample14

value: Human embryonic Kidney


title: JMJD3_WT_TCM_2A

value: JMJD3 WT


title: MCF7_Fasting_Rep1

value: Fasting (48h water-only diet)


title: smash_eif4a3_dmso_mRNA_bio_rep_1_LRS

description: Library name: sample13


title: CnR_H3K4me3_RS_S12NSD2_DMSO_rep2

value: H3K4me3, CST-C42D8

value: RS + S12N:SD2


title: MCF7_TMX_Rep3

value: Breast cancer

value: xenograft

value: Tamoxifen (30mg/Kg) (TMX)


title: JMJD3_WT_TCM_1A


title: CnR_H3K4me3_RS_S12NSUV2_DMSO_rep2

value: RS + S12N:SUV2


title: MCF7_TMX_Rep2


title: MCF7_Fasting_Rep2


title: MCF7_TMX_Rep1


title: YY1325 20°C Input 2

city: Toronto

first: Julie

last: Claycomb

address: 661 University Ave

country: Canada

institute: University of Toronto

description:
Library name: 25-R3-20d-123in
Input2
20d_123_22G_allBiotypes_enriched_2FC_5RPM_triplicate.csv

data_processing:
Adapter sequences were removed using cutadapt (version 1.15, Martin, 2011) using the following command: -a ADAPTER -f fastq -m 16 -M 30 —discard-untrimmed.
The trimmed reads were aligned to the C. elegans PRJNA13758 ce11 genome assembly (WormBase version WS276) with STAR (version 2.6.0c, Dobin et al., 2013) using the following parameters: --runThreadN 12 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 50 --outFilterMultimapScoreRange 0 --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1.
The reads were then counted using a custom R script against publicly available genome annotations. The WormBase version WS276 PRJNA13758 ce11 canonical geneset annotations were used (excluding miRNAs, repeats, and transposons). C. elegans miRNA annotations were obtained from miRBase (release 22.1). For repeats and transposons RepeatMasker+Dfam (ce10, October 2010, RepeatMasker open-4.0.6, Dfam 2.0) annotations were used. The UCSC Lift Genome Annotations tool was used to convert ce10 coordinates to ce11 coordinates. Briefly, the counting script used the findOverlaps function from the GenomicAlignments package (version 1.22.1) to assign reads to features. Multiple aligning reads or reads that align to more than one feature were dealt with by counting reads in a sequential manner to the different gene biotypes in the following order (AS stands for antisense): miRNA, piRNA, rRNA, snoRNA, snRNA, tRNA, ncRNA, lincRNA, repeats AS, protein coding AS, pseudogene AS, lincRNA AS, antisense RNA, rRNA AS, snoRNA AS, snRNA AS, tRNA AS, ncRNA AS, miRNA AS, piRNA AS, protein coding, pseudogene, antisense RNA AS, repeats. For reads that align to more than one feature in the same biotype group, the read count was split between the features based on the fraction of uniquely aligned reads to each of those features (unique weighing).
To determine small RNAs enriched in Argonaute IPs, reads were first normalized to library size (reads per million [RPM]). To determine whether small RNAs against a particular target were enriched in an Argonaute IP, the following calculation was made: enrichment = IP RPM + 0.01/Input RPM + 0.01. The 0.01 represents a pseudocount to eliminate the possibility of dividing by zero. A target was considered enriched if in every replicate it was at least twofold enriched in all replicates and had at least 5 RPM in each of the IP replicates. Where indicated, only reads of length 20-24 nucleotides were considered, representing 22G-RNAs.
Assembly: C. elegans PRJNA13758 ce11 genome assembly (WormBase version WS276)
Supplementary files format and content: For IP experiments, table of enrichment (IP/Input) values.
Supplementary files format and content: For mutant total sRNA data, matrix of count data.

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: For the 20°C experiment, worms continuously maintained at 20°C were synchronized by bleaching adults only (excluding laid embryos) and plated on 15 cm NGM plates with 4 ml of OP50 bacteria. They were grown until they reached the young adult stage. For the 26°C experiment, parent worms (maintained at 20°C) were synchronized by chunking embryos onto 9 cm NGM plates seeded with OP50 bacteria. The plates were incubated at 20°C until the worms reached the L4 stage, then transferred to 26°C. After 24 hours, the adults were bleached (excluding laid embryos). Plates were kept at 26°C until the worms reached the young adult stage.

extract_protocol:
The worm pellet was resuspended at a 1:1.5 (v/v) ratio in EDTA buffer, which contained 10% glycerol, 10 mM EDTA, 30 mM HEPES, 100 mM potassium acetate, 2 mM DTT, and 0.1% NP-40, supplemented with protease, RNase, and phosphatase inhibitors: 2x cOmplete EDTA-free protease inhibitor cocktail (Roche), 1:100 SuperaseIN (Thermo Fisher), and 1:100 phosphatase inhibitor cocktails 2 and 3 (Sigma). The resuspended pellet was flash-frozen by adding it drop by drop into liquid nitrogen, and the frozen samples were stored at –80°C until lysate preparation.  The frozen samples were ground in a mortar with liquid nitrogen. Protein lysates were prepared by thawing the frozen powder, sonicating it at a low setting (3 minutes, 15 seconds ON/15 seconds OFF), and centrifuging it at 17,000 x g for 15 minutes, with all steps performed at 4°C. Once thawed, the samples were handled continuously at 4°C or kept on ice. To determine the total protein concentration, either a Lowry assay or a Bradford assay (BioRad) was used. For total sRNA sequencing, an aliquot containing 500 µg of protein was mixed with TRI Reagent (Sigma) and flash-frozen (further description in the RNA isolation step).  To sequence the sRNAs bound to WAGO-4, we performed an immunoprecipitation (IP) protocol. All the assayed strains expressed WAGO-4 tagged with 3xFLAG::GFP tag. For the IPs, 3-6 mg of total protein was used per reaction. To pre-clear the lysate, it was incubated with 20 µL of Binding Control magnetic beads (ChromoTek) at 4°C for an hour with rotation. The lysates were then incubated with GFP-Trap magnetic beads (ChromoTek) at 4°C for an hour with rotation to bind WAGO-4. Both the Binding Control and GFP-Trap magnetic beads were equilibrated with the IP buffer prior to adding the lysate. After binding to the GFP-Trap beads, the beads were washed once with a buffer containing 30 mM HEPES, 400 mM KCl, and 0.4% NP-40 and four washes with IP buffer. All washes were performed by rotating for 10 minutes at 4°C. For each replicate, 2-3 IP reactions were pooled in 200 μL of IP buffer. Next, 720 μL of TRI Reagent (Sigma) was added, and the samples were flash-frozen and stored at –80°C until RNA extraction.  RNA was isolated from the samples containing TRI Reagent (mixed with lysate for the total pool of sRNAs or with the GFP-Trap magnetic beads for the WAGO-4 bound sRNAs, as described above). Samples were vortexed at room temperature for 15 minutes. Then, 10% 1-bromo-3-chloropropane was added and the mixture was centrifuged at 12,000 × g for 15 minutes at 4°C. The aqueous phase was separated and mixed with phenol:chloroform:isoamyl alcohol (pH 4.5) in a 1:1 ratio, followed by centrifugation (12,000 × g for 15 minutes at 4°C). The clear aqueous phase was separated and mixed with 20 µg of glycogen, 0.3 M NaOAc (pH 5.2), and an equal volume of isopropyl alcohol. The RNA was precipitated at -20°C for at least 30 minutes. Samples were centrifuged at 16,000 × g for 30 minutes at 4°C, and the pellet was washed twice with 900 µL of 70% ice-cold ethanol (the centrifugation step between the two washes was at 16,000 × g for 10 minutes at 4°C). The pellet was air-dried at room temperature for 10 minutes and resuspended in 11 µL of nuclease-free water. The RNA concentration was measure using Nanodrop and up to 4 µg was used for the 5′ polyphosphatase reaction (Manufacturer). The reaction was incubated for 30 min at 37 °C and RNA was extracted using phenol:chloroform:isoamyl alcohol as described above. The air-dried pellet was resuspended with 6-7 µL nuclease free water and was used for the library preparation.
Small RNA libraries were created using the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer's instructions. Starting material included 1 μg of total RNA or the entire yield of immunoprecipitated RNA. The resulting DNA libraries were size selected by excising the bands with the size range of ~135–150 bp on 8% PAGE gel (correspond to 16–30 bp RNAs). The DNA was eluted by rotating overnight in 500 μl of DNA Gel Elution buffer at room temperature. Subsequently, the DNA library was precipitated with 20 μg of glycogen 0.3 M sodium acetate (pH 5.2), and an equal volume of isopropyl alcohol; pellets were washed and dried as previously described. They were resuspended in 12 μl of nuclease free water and quantified using a Qubit HS DNA kit (Thermo Fisher). sRNA libraries were pooled in equal amounts and sequenced on Illumina Miniseq and Novaseq 6000.

treatment_protocol: Worms were washed three times with M9 buffer and once with Milli-Q water. The pellet was resuspended in RIPA buffer (Sigma) and flash-frozen by dropping it into liquid nitrogen.

value: whole worm

tag: strain

value: wago-4(gg620[3xflag::gfp::wago-4]) II

tag: temperature

tag: developmental stage

value: young adult

value: A


title: TRAP1_KO_TCM_3A

value: Bone marrow

tag: genotype

value: TRAP1 KO


title: smash_eif4a3_danoprevir_mRNA_bio_rep_1_LRS

description: Library name: sample16

value: 1.5 uM Danoprevir, 24 hrs


title: starvation day5 sample2

city: Boston

first: Yanhui

last: Hu

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description:
Library name: S-7-2_S6
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) using default setting.
The counts matrices were then analyzed in Seurat and batch correction was performed using the Harmony algorithm before creating a UMAP and performing clustering analysis.
Assembly: BDGP6.32
Supplementary files format and content: normalized count matrix, text file
Supplementary files format and content: cell annotation, text file

organism: Drosophila melanogaster

source_name: Whole-body without head

growth_protocol: All flies were kept on standard cornmeal fly food. Crosses were grown at 18°C to inactivate Gal4. Adult offspring flies were collected within 48 hours after emerging, kept at 18°C for another 48 hours and then incubated at 29°C for 7 days to induce transgene expression.

extract_protocol:
Whole-body flies without heads were flash-frozen using liquid nitrogen and were homogenized in 1ml dounce in buffer of 250 mM sucrose, 10 mM Tris pH 8.0, 25 mM KCl, 5mM MgCl, 0.1% Triton-X, 0.5% RNasin plus (Promega, N2615), 1X protease inhibitor (Promega, G652A), 0.1 mM DTT, then filtered through 40 um cell strainer and 40 um Flowmi (BelArt, H13680-0040). Samples were centrifuged, washed, and resuspended in 1 X PBS with 0.5% BSA and 0.5% RNasin plus. The suspension was filtered again with 40 um Flowmi immediately before FACS sorting. Nuclei were stained with DRAQ7TM Dye (Invitrogen, D15106) and sorted using Sony SH800Z Cell Sorter at Systems Biology Flow Cytometry Facility at Harvard Medical School. After sorting, nuclei were collected and re-suspend at 700-800 cells/µl in 1 X PBS buffer with 0.5% BSA and 0.5% RNasin plus. snRNAseq was performed according to the 10X genomics protocol (Chromium Next GEM Single Cell 3’_v3.1_Rev_D)
Libraries were generated according to 10X genomics Next GEM Single Cell 3’ Library and Gel Bead Kit v3.1

treatment_protocol: Female flies were incubated for 7 days at 29°C

value: Whole-body without head

value: PromE-gal4, Tub-gal80ts

value: Female flies were incubated for 5 days at 29°C


title: MCF7_Control_Rep3

value: Control (ad libitum diet)


title: CnR_H3K4me3_Rbbp5-FKBP_DMSO_rep2

value: Mouse embryonic stem cells

value: H3K4me3, CST-C42D8

value: DMSO


title: CnR_H3K4me3_RS_S12NSD2_dTAG_rep1

value: RS + S12N:SD2


title: YY1325 20°C Input 1

description:
Library name: 13-R2-20d-123in
Input1
20d_123_22G_allBiotypes_enriched_2FC_5RPM_triplicate.csv


title: TRAP1_KO_TCM_2A


title: starvation day5 sample1

description:
Library name: S-7-1_S5
10x Genomics


title: TRAP1_KO_TCM_4A


title: MCF7_Control_Rep2

value: Breast cancer

value: xenograft


title: JMJD3_WT_TCM_3A

value: JMJD3 WT


title: CnR_H3K4me3_RS_S12NSUV2_dTAG_rep1

value: RS + S12N:SUV2


title: starvation day2 sample2

description:
Library name: S-5-2_S4
10x Genomics


title: MCF7_Fasting_Rep3

value: Fasting (48h water-only diet)


title: TCM_3A

value: WT TCM


title: CnR_H3K4me3_R-Suz12KO_dTAG_rep1

value: RBBP5-FKBP + Suz12 KO (RS)


title: starvation day2 sample1

description:
Library name: S-5-1_S3
10x Genomics