title: LPMCs Group 3 Hashtags

first: Ahmed

middle: Nabil

last: Hegazy

address: Hindenburgdamm 30

department: Department of Gastroenterology, Infectious Diseases and Rheumatology

institute: Charité - University Medicine Berlin

description: 10X Genomics

library_source: other

data_processing:
After sequencing, fastq files were processed using Cell Ranger 5.0.0 and the genome reference (refdata-gex-mm10-2020-A) annotation. The obtained count matrix was taken as an input for the data analysis with use of Seurat v4.0.1 and v5.0.161. Hashtag sequences used to label individual mice were imported and combined. For the normalization of the data LogNormalize function was used. Seurat’s default method was used for scaling. Hashtag demultiplexing (representing the three biological replicates per genotype) was performed based on Seurat’s HTODemux with the parameter ‘positive-quantile’ at 0.99. Doublets, untagged and low quality (low UMI counts, high % of mitochondrial genes) cells were filtered out. After ranking by residual variance, 2000 variable genes were determined. 30 principal components were computed and stored. Integration of the single cell data was done using the Seurat pipeline. Next, the Harmony package (https://github.com/immunogenomics/harmony) was also applied to integrate gene-cell matrix of epithelial in order to increase the quality of the integration. UMAP and t-distributed stochastic neighbor embedding were run using the first 20 principal components. Transcriptionally similar clusters were identified using shared nearest neighbor modularity optimization, with a resolution of 0.3. Signature genes were identified using the FindAllMarkers function in default parameter settings (only.pos = TRUE, min.pct = 0.25, logfc.threshold = 0.25). Epithelial and immune contaminants from stromal dataset were excluded from downstream analysis. The cluster with unclear gene expression profile and poor quality from LPMC dataset was also excluded from downstream analysis.  Heatmaps and dotplots for the single-cell data were plotted with Seurat’s DoHeatmap and DotPlot function, respectively, using default settings. Differential gene expression analysis was performed with the use of FindMarkers function (min.pct = 0.25, logfc.threshold = 0.25).
Assembly: mm10-2020-A
Supplementary files format and content: .csv files and matrix files in .h5 format

molecule: protein

source_name: colon

growth_protocol: Colitis was induced by gavage of Helicobacter hepaticus and anti-IL-10R administration.

extract_protocol:
The lamina propria mononuclear cells (LPMC), stromal, and epithelial cells were sorted by FACS and were individually hash-tagged per mouse group and cell type. Then, the single cell suspensions were obtained and applied to the 10x Genomics workflow for cell capturing and scRNA gene expression (GEX) and CITE-Seq library preparation using the Chromium Single Cell 5’ Library & Gel Bead Kit version 2 (dual index) and the Single Cell 5’ Feature Barcode Library Kit (10x Genomics).
After cDNA amplification, the CITE-Seq libraries were prepared separately using the Dual Index Kit TN Set A while, the final GEX libraries were obtained after fragmentation, adapter ligation, and final Index PCR using the Dual Index Kit TT Set A. Qubit HS DNA assay kit (Life Technologies) was used for library quantification and fragment average sizes were determined using the Fragment Analyzer with the HS NGS Fragment Kit (1-6000bp) (Agilent).

value: colon

value: Primary cells

value: Immune cells

value: wild type

value: untreated


title: Mycelium, MU636 - Replicate 2

status: Public on Mar 28 2025

type: SRA

city: Murcia

first: Carlos

last: Lax

address: Facultad de Biología

department: Genetics and Microbiology

country: Spain

institute: University of Murcia

description:
Library name: MU636_B
Dataset S4.xlsx

library_source: transcriptomic

data_processing:
Raw paired-end (PE)  and single-end reads from M. lusitanicus RNA-seq datasets were quality-checked using FastQC v0.11.9
Adapters were removed with Trim Galore! V.0.4.3.1
Reads with a Phred quality score (q) ≤32 and/or a total length < 20 nt were removed from the analysis
Assembly: Mucor lusitanicus (CBS 277.49) v2 (https://mycocosm.jgi.doe.gov/pages/search-for-genes.jsf?organism=Mucci2)
Supplementary files format and content: Spreadsheet including counts, log2FC, differential expression statistics and functional annotation for every gene

molecule: total RNA

organism: Mucor lusitanicus

source_name: Mycelium

growth_protocol: MU636 and MU412 strains were grown on solid YPG media  at 26 ºC for 24 hours

extract_protocol:
Total RNA was extracted using the mirVana kit (AM1561) and treated with DNase (Sigma, On-Column DNaseI treatment set)
NEBNext® Ultra™ Directional RNA Library Prep Kit

tag: tissue

value: Mycelium


title: LPMCs Group 2 Hashtags

status: Public on Mar 27 2025

city: Berlin

country: Germany

description: 10X Genomics

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: H.h.+anti-IL10R, day 18 after colitis induction


title: Stroma Group 3 Hashtags

description: 10X Genomics

value: stromal cells


title: Stroma Group 3 Transcripts

description: 10X Genomics

library_source: transcriptomic single cell


title: Stroma Group 2 Hashtags

description: 10X Genomics


title: Epcam Group 3 Hashtags

description: 10X Genomics

value: epithelial cells


title: Epcam Group 2 Hashtags

description: 10X Genomics


title: Stroma Group 2 Transcripts

description: 10X Genomics


title: Epcam Group 3 Transcripts

description: 10X Genomics


title: LPMCs Group 2 Transcripts

description: 10X Genomics


title: healthy_donor_plasma_exosomes_rep2

type: RNA

city: Hefei

first: Qianqian

last: Tao

state: Anhui

address: Meishan Road, Shushan District, Hefei City, Anhui Province

country: China

institute: The First Affiliated Hospital of Anhui University of Chinese Medicine

description: micro RNA level  in human blood

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 55°C for 20 hoursin a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

source_name: peripheral blood-derived exosomes; replicate 2

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

extract_protocol: RNA was prepared using the mirVana™ PARIS™ Kit (Ambion Inc., Austin, TX) following the manufacturer's recommendations.

value: plasma

tag: disease state

value: healthy donor


title: Epcam Group 2 Transcripts

description: 10X Genomics


title: M101,S4L

city: Heraklion

first: Matthieu

middle: David

last: Lavigne

address: Nikolaou Plastira 100

country: Greece

institute: IMBB-FORTH

description: Library name: NGS1660

data_processing:
The quality of the raw sequences in output FASTQ files was assessed with the FastQC software. Reads were aligned to the human (hg38) genome with the Hisat2 aligner (hisat2 -p32 -x $REFERENCE_GENOME -q fastq/$FILE_ID.fastq -S $FILE_ID.sam -- score-min L,0,-0.5 -k 2). Htseq-counts was utilized to summarize reads at the gene level (htseq-count -f bam -s yes-I gene_id bam/$FILE_ID.bam data/refs/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf>$COUNTS_DIR/NGS$FI LE_ID). DEA was conducted by running EdgeR  via SARTools 1.5.0  using weighted trimmed mean of the log expression ratios (trimmed mean of M values (TMM)) as a normalization method, no batch correction and a cpmCutoff of 1 for genes to be tested. For each pairwise comparison (stage IV, S4 vs. stage III, S3) and early progressors (Short RFS/PFS, S) vs. long responders (Long RFS/PFS, L), DEGs in either group of the comparison were defined by applying the following thresholds |Log2FC or LFC| >1 and p-value <0.05, which was considered statistically significant in order to limit the stringency of FDR testing and help us to account for anticipated interpatient variability.
Assembly: hg38
Supplementary files format and content: edger output with normalised read counts and pairwise test results.

molecule: polyA RNA

source_name: PBMC

growth_protocol: Peripheral blood (5-7 mL) from patients was collected in EDTA Vacutainer blood collection tubes (Becton Dickinson) from melanoma subjects. Peripheral blood mononuclear cells (PBMC) were isolated on Histopaque-1077 density gradient (cat. #10771, Sigma), according to the manufacturer's instructions. Blood was initially diluted 1:1 with PBS and carefully layered over Histopaque medium. Ficoll gradients were centrifuged at 1800 rpm for 30 minutes with no brake at room temperature. After the centrifugation, the PBMC layer was collected from each sample and cells were washed with PBS.After PBMCs isolation, an amount of approximately 10x106 cells per sample was resuspended in 1ml of freezing medium and was stored in cryovials at -80oC. In order to sort CD3+CD4+cell subpopulation from frozen PBMCs, thawing procedure was followed for the selected 28 samples. Briefly, cryopreserved PBMCs were resuspended in a nutrient medium consisting of FBS and plain RPMI (Thermo Fisher Scientific, USA) and placed into 37oC on water bath for a few seconds. Centrifugation was followed at 400g for 7 minutes at room temperature and the pellet was resuspended in 5% FBS/PBS. PBMCs were stained with the conjugated antibodies CD3 (PE, Cat. #300308, Clone: HIT3a, Biolegend) and CD4 (PerCP/Cy5.5, Cat. #317428, Clone: OKT4, Biolegend) to identify and sort CD3+CD4+T-lymphocytes. After sorting, the CD3+CD4+T-cell population was resuspended in β-mercaptoethanol and cell lysis solution, to continue with RNA extraction.

extract_protocol:
Total RNA was extracted using NucleoSpin RNA XS (Macherey-Nagel; cat. #740955.50) as per the manufacturer’s protocol. The quantity and quality of RNA samples were analyzed using Agilent RNA 6000 Nano kit with the bioanalyzer from Agilent.
The RNA samples with RNA integrity number (RIN)>7 were used for library construction using the 3′ mRNA-Seq Library Prep Kit FWD for Illumina (QuantSeq-LEXOGEN) as per the manufacturer’s instructions. Amplification was controlled for obtaining optimal unbiased libraries across samples by assessing the number of cycles (ranging from 20-24) required by qPCR. DNA High Sensitivity Kit for bioanalyzer was used to assess the quantity and quality of libraries, according to the manufacturer’s instructions (Agilent). Libraries were multiplexed and sequenced on an Illumina Nextseq 500 at the genomics facility of IMBB FORTH according to the manufacturer’s instructions.

value: PBMC

tag: batch


title: M102,S4L

description: Library name: NGS1661


title: M87,S4S

description: Library name: NGS1655


title: M97,S3S

description: Library name: NGS1659


title: M95,S4S

description: Library name: NGS1657


title: M86,S4S

description: Library name: NGS1654


title: LPMCs Group 3 Transcripts

description: 10X Genomics


title: M79,S3S

description: Library name: NGS1652


title: M82,S3S

description: Library name: NGS1653


title: M73,S4S

description: Library name: NGS1651


title: M68,S3S

description: Library name: NGS1649


title: M91,S3S

description: Library name: NGS1656


title: M64,S4S

description: Library name: NGS1648


title: M63,S3L

description: Library name: NGS1647


title: M55,S3S

description: Library name: NGS1645


title: M53,S3L

description: Library name: NGS1644


title: M59,S3L

description: Library name: NGS1646


title: M52,S4L

description: Library name: NGS1643


title: M51,S4L

description: Library name: NGS1642


title: M9,S4L

description: Library name: NGS1638


title: M8,S4L

description: Library name: NGS1637


title: M6,S4L

description: Library name: NGS1636


title: A375, Anti-H3K9Ac, CUT&RUN, biol rep 1

city: Iowa City

first: Jeremy

last: Chang

state: IA

address: 285 Newton Rd

department: Surgery

country: USA

institute: University of Iowa

description: Library name: A375WT_9Ac_Bio_rep_1

library_source: genomic

data_processing:
Reads were trimmed using Trim Galore Version 0.6.3 (Developed by Felix Krueger at the Babraham Institute) and Bowtie2 version 2.1.0 (Langmead and Salzberg, 2012) was used to map the reads against the hg19 genome assembly.
Assembly: hg19
Supplementary files format and content: narrow peak bed file and bigwig file
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: cell line

growth_protocol: cells are grown in appropriate media (SKMEL28 = RPMI, A375 = DMEM) supplemented with 10% FBS and 1% Penicillin/streptomycin at 37 degrees celcius with 5% Co2. Cells were plated into separate flasks for biologic replicates and media was changed 24 hours before harvest.

extract_protocol:
Cells were harvested via scraping and washed with 1x PBS and subsequently 2x Ca-free wash buffer as described in protocol. 200k cells were counted out for each sample (i.e. antibody) and samples were prepared via CUT&RUN protocol
fragemented genomic DNA libraries were generated with KAPA HyperPrep Kit (Roche)

value: cell line

value: melanoma


title: M69,S3L

description: Library name: NGS1650


title: A375, Anti-H3K9Ac, CUT&RUN, biol rep 2

description: Library name: A375WT_9Ac_Bio_rep_2


title: SKMEL28, Anti-MITF, CUT&RUN, biol rep 4

description: Library name: SKMEL28WT_MITF_Bio_rep_4


title: D6, Anti-MITF, CUT&RUN, biol rep 2

description: Library name: D6_MITF_bio_rep_2

value: MITF-KO D6


title: D6, Anti-H3K27Ac, CUT&RUN, biol rep 2

description: Library name: D6_27Ac_bio_rep_2


title: M43,S3S

description: Library name: NGS1641


title: D6, Anti-H3K4Me3, CUT&RUN, biol rep 2

description: Library name: D6_4me3_bio_rep_2


title: D6, Anti-IgG, CUT&RUN, biol rep 1

description: Library name: D6_IgG_bio_rep_1


title: D6, Anti-H3K4Me3, CUT&RUN, biol rep 1

description: Library name: D6_4me3_bio_rep_1


title: D6, Anti-MITF, CUT&RUN, biol rep 1

description: Library name: D6_MITF_bio_rep_1


title: M12,S4S

description: Library name: NGS1640


title: SKMEL28, Anti-H3K27Me3, CUT&RUN, biol rep 2

description: Library name: SKMEL28WT_27me3_bio_rep_2


title: SKMEL28, Anti-H3K27Me3, CUT&RUN, biol rep 1

description: Library name: SKMEL28WT_27me3_bio_rep_1


title: SKMEL28, Anti-IgG, CUT&RUN, biol rep 3

description: Library name: SKMEL28WT_IgG_Bio_rep_3


title: D6, Anti-IgG, CUT&RUN, biol rep 2

description: Library name: D6_IgG_bio_rep_2


title: A375 TFE3KO, Anti-IgG, CUT&RUN, biol rep 1

description: Library name: A375TFE3KO_IgG_Bio_rep_1


title: SKMEL28, Anti-H3K4me3, CUT&RUN, biol rep 1

description: Library name: SKMEL28WT_4Me3_bio_rep_1


title: A375 TFE3KO, Anti-TFE3, CUT&RUN, biol rep 2

description: Library name: A375TFE3KO_TFE3_Bio_rep_2


title: SKMEL28, Anti-H3K27AC, CUT&RUN, biol rep 1

description: Library name: SKMEL28WT_27AC_bio_rep_1


title: U2OS, TDP43-mNLS-Clover not_aggregated (sorted), rep3

city: Leuven

first: Kristofer

middle: James

last: Davie

address: Herestraat 49

department: Center for Brain and Disease Research

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

description:
Library name: NoAggregates_Rep3
Stranded RNA-seq

data_processing:
bases2fastq version 2.0 was used to generate fastq files from raw AVITI basecalls
Raw, paired FASTQ files were first filtered using fastp v0.23.2.
Filtered FASTQ files were mapped to, and quantified against the hg38 genome using STAR v.2.7.11a.
All junctions were identified per sample using regtools v1.0.0 with the junctions command the following arguments: -a 6 -m 30 -M 500000 -s RF.
Following junction identification, junctions were quantified using the leafcutter_cluster_regtools.py script from leafcutter
Assembly: hg38
Supplementary files format and content: All_Samples_Counts.csv: Comma separated file with raw strand specific counts per sample.
Supplementary files format and content: Leafcutter_Junction_Counts.txt.gz: Gzip compressed space delimitted file containing counts per junction for each sample

source_name: U2OS TDP-43-mNLS-Clover (DOX-induced)

growth_protocol: standard cell culture conditions were used (DMEM + 10% FBS)

extract_protocol:
The Innuprep 2.0 Total RNA extraction kit was used following the manufacturers guidelines.
Illumina stranded mRNA Library prep kit, following manufacturers guidelines

treatment_protocol: Cell transfection with recombinant TDP-43 LCD fibril seeds was performed with lipofectamine-3000 (Invitrogen) according to the manufacturer's instructions.

value: U2OS TDP-43-mNLS-Clover (DOX-induced)

value: no fibril seeds


title: A375 TFE3KO, Anti-TFE3, CUT&RUN, biol rep 1

description: Library name: A375TFE3KO_TFE3_Bio_rep_1


title: D6, Anti-H3K27Me3, CUT&RUN, biol rep 2

description: Library name: D6_27me3_bio_rep_2


title: D6, Anti-H3K27Ac, CUT&RUN, biol rep 1

description: Library name: D6_27Ac_bio_rep_1


title: WT muscle, AAV, 7 dpi, sample 1

city: Madrid

first: Roberto

last: Silva-Rojas

address: Calle de Melchor Fernández Almagro 3

institute: Spanish Nacional Center for Cardiovascular Research

data_processing:
Sequencing reads were pre-processed by a pipeline that used FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to asses read quality, and Cutadapt80 to remove adaptor remains from Illumina and to discard reads that were shorter than 30 bp.
The resulting reads were mapped against reference transcriptome GRCm38.99 and quantified with RSEM81, using Bowtie as aligner. The expected expression counts calculated with RSEM were processed with a pipeline that used Limma package82, from Bioconductor, for normalization and differential expression testing, taking only into account those genes expressed with at least 1 count per million (CPM) in at least three samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

source_name: Tibialis anterior

growth_protocol: Mice were euthanized by euthanized CO2 inhalation, tibialis anterior dissected and frozen in liquid nitrogen.

extract_protocol:
Muscles were mechanically lysed using CK28 beads (Bertin Technologies) and RNA extracted using TRI reagent (Sigma) following manufacturer´s instructions.
NEBNext Ultra II Directional RNA Library preparation kit (New England Biolabs) according to manufacturer’s instructions.

treatment_protocol: Muscles were injected with saline buffer or AAV virus encoding GFP-TEV protease fusion protein 3, 7 or 21 days prior to dissection.

value: Tibialis anterior

value: WT

value: AAV

tag: timepoint

value: 7 dpi


title: D6, Anti-H3K27Me3, CUT&RUN, biol rep 1

description: Library name: D6_27me3_bio_rep_1


title: healthy_donor_plasma_exosomes_rep4

description: micro RNA level  in human blood

source_name: peripheral blood-derived exosomes; replicate 4


title: A375, Anti-IgG, CUT&RUN, biol rep 2

description: Library name: A375WT_IgG_Bio_rep_2

value: wild type


title: A375 TFE3KO, Anti-MITF, CUT&RUN, biol rep 2

description: Library name: A375TFE3KO_MITF_Bio_rep_2


title: SKMEL28, Anti-H3K4me3, CUT&RUN, biol rep 2

description: Library name: SKMEL28WT_4Me3_bio_rep_2


title: A375, Anti-TFE3, CUT&RUN, biol rep 2

description: Library name: A375WT_TFE3_Bio_rep_2


title: A375, Anti-TFE3, CUT&RUN, biol rep 1

description: Library name: A375WT_TFE3_Bio_rep_1


title: WT muscle, AAV, 7 dpi, sample 3


title: A375, Anti-MITF, CUT&RUN, biol rep 1

description: Library name: A375WT_MITF_Bio_rep_1


title: A375 TFE3KO, Anti-IgG, CUT&RUN, biol rep 2

description: Library name: A375TFE3KO_IgG_Bio_rep_2


title: sg, Anti-IgG, CUT&RUN, biol rep 2

description: Library name: sg_IgG_Bio_rep_2

value: MITF-KO D2, TFE3-KO


title: sg, Anti-IgG, CUT&RUN, biol rep 1

description: Library name: sg_IgG_Bio_rep_1


title: sg, Anti-MITF, CUT&RUN, biol rep 2

description: Library name: sg_MITF_Bio_rep_2


title: sg, Anti-TFE3, CUT&RUN, biol rep 2

description: Library name: sg_TFE3_Bio_rep_2


title: D2, Anti-IgG, CUT&RUN, biol rep 1

description: Library name: D2_IgG_Bio_rep_1

value: MITF-KO D2


title: sg, Anti-MITF, CUT&RUN, biol rep 1

description: Library name: sg_MITF_Bio_rep_1


title: D2, Anti-TFE3, CUT&RUN, biol rep 2

description: Library name: D2_TFE3_Bio_rep_2


title: A375 TFE3KO, Anti-MITF, CUT&RUN, biol rep 1

description: Library name: A375TFE3KO_MITF_Bio_rep_1


title: D2, Anti-TFE3, CUT&RUN, biol rep 1

description: Library name: D2_TFE3_Bio_rep_1


title: A375, Anti-IgG, CUT&RUN, biol rep 1

description: Library name: A375WT_IgG_Bio_rep_1


title: SKMEL28, Anti-TFE3, CUT&RUN, biol rep 2

description: Library name: SKMEL28WT_TFE3_Bio_rep_2


title: SKMEL28, Anti-TFE3, CUT&RUN, biol rep 1

description: Library name: SKMEL28WT_TFE3_Bio_rep_1


title: D2, Anti-MITF, CUT&RUN, biol rep 1

description: Library name: D2_MITF_Bio_rep_1


title: A375, Anti-MITF, CUT&RUN, biol rep 2

description: Library name: A375WT_MITF_Bio_rep_2


title: SKMEL28, Anti-MITF, CUT&RUN, biol rep 1

description: Library name: SKMEL28WT_MITF_Bio_rep_1


title: GVO_H3K36me3_KO.Kdm2a_KO.Kdm2b_KO_rep1

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
The quality of the data was assessed using the qQCReport function of the QuasR bioconductor package (v1.40.0)
Alignments wre generated against the mouse mm10 genome (Mmusculus.UCSC.mm10) using the qAlign function of the quasR bioconductor package (v1.40.0)  with parameters: paired="fr"
Assembly: mm10
Supplementary files format and content: BigWig (.bw) processed files were generated using the qExportWig function  of the quasR bioconductor package (v1.40.0)  with parameters: binsize=100, scaling=1e6
Library strategy: Cut&Run

source_name: fully grown germinal vesicle oocytes

extract_protocol:
Ovaries were dissected out in M2 medium (Merck; M7167) supplemented with Milrinone (25 μM) and cumulus cells were removed from oocytes by mouth-pipetting using thin glass needles. 300 to 500, 200 and 200 fully grown oocytes were used for making libraries detecting the genome-wide distribution of H2AK119ub, H3K36me2 and H3K36me3 marks, respectively. After treating with antibodies and Protein A/G MNase, digested DNA fragments were purified by Phenol/CIAA and Ethanol precipitation.
Libraries were prepared according to the instructions using the NEBNext Ultra II DNA Library Prep Kit. KAPA HiFi HotStart Ready Mix was used for PCR enrichment of adapter-ligated DNA.

treatment_protocol: To collect fully grown germinal vesicle oocytes (GVOs) from 4 to 7 week-old female mice, 100 μl of Hyper Ova (CARD) were injected 46-52 h before the collection.

value: fully grown germinal vesicle oocytes

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre

tag: antibody

tag: strain


title: SKMEL28, Anti-IgG, CUT&RUN, biol rep 2

description: Library name: SKMEL28WT_IgG_Bio_rep_2


title: sg, Anti-TFE3, CUT&RUN, biol rep 1

description: Library name: sg_TFE3_Bio_rep_1


title: GVO_H3K36me3_Ctrl.Kdm2a_KO.Kdm2b_KO_rep1

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ


title: SKMEL28, Anti-MITF, CUT&RUN, biol rep 2

description: Library name: SKMEL28WT_MITF_Bio_rep_2


title: GVO_H3K36me2_KO.Kdm2a_KO.Kdm2b_dCxxC_rep2

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC; Zp3-cre

value: mouse anti-H3K36me2 antibody (1:100; Cosmo bio; MABI0332)


title: GVO_H3K36me2_KO.Kdm2a_KO.Kdm2b_dCxxC_rep1


title: GVO_H3K36me3_Ctrl.Kdm2a_KO.Kdm2b_KO_rep2


title: GVO_H3K36me2_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_rep1

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC


title: GVO_H2AK119ub_KO.Kdm2a_KO.Kdm2b_KO_rep1

value: rabbit anti-H2AK119ub1 (1:100; Cell Signaling Technology; 8240)


title: GVO_H2AK119ub_KO.Kdm2a_KO.Kdm2b_KO_rep2


title: GVO_H3K36me2_Ctrl.Kdm2a_KO.Kdm2b_KO_rep1


title: GVO_H2AK119ub_KO.Kdm2a_KO.Kdm2b_dCxxC_rep2


title: GVO_H2AK119ub_KO.Kdm2a_KO.Kdm2b_dCxxC_rep1


title: GVO_H2AK119ub_Ctrl.Kdm2a_KO.Kdm2b_KO_rep2


title: GVO_H2AK119ub_Ctrl.Kdm2a_KO.Kdm2b_KO_rep1


title: GVO_H2AK119ub_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_rep1


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep14

data_processing:
The quality of the data was assessed using FastQC (v0.11.8) and adapters were trimmed using TrimGalore (v0.6.2) with parameters “--illumina --stringency 5 --clip_r1 6 --three_prime_clip_r1 6”. Alignment to mm10 genome and deduplication was done using Bismark (v0.22.3) with parameters “--local --non_directional”.
Assembly: mm10
Supplementary files format and content: BigWig (.bw) processed files were generated using export.bw function from rtracklayer Bioconductor package after merging biological replicates for each genotype.

extract_protocol:
Fully grown germinal vesicle stage oocytes were freshly collected from ovaries in M2 medium supplemented with Milrinone (25μM). After removing the zona-pellucida by treating with acidic Tyrode’s solution, oocytes were washed in PBS supplemented with 0.05% Polyvinyl alcohol, lysed in RLT Plus buffer (Qiagen) and frozen in the deep-freezer. One library was prepared from a pool of 10 oocytes and approximately 13 libraries were prepared for each genotype.
DNA in cell lysate was subjected to bisulfite conversion reaction using EZ Methylation Direct kit followed by DNA purification using PureLink micro kit. Bisulfite converted DNA strand was amplified by Klenow Fragment (3’-5’ exo-) followed by Exonuclease I treatment and SPRI purification. Adapter oligo was tagged to the DNA fragments by Klenow Fragment (3’-5’ exo-) and tagged fragments were purified using Ampure XP beads. KAPA HiFi HotStart PCR Kit was used for library amplification with NEBNext Multiplex Oligos for illumina. Indexed libraries were purified by using AMPure XP beads.


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep13


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep11


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep8


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep7


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep6


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep4


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep2


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_KO_rep1


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_dCxxC_rep14


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_dCxxC_rep13


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_dCxxC_rep12


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_dCxxC_rep11


title: D2, Anti-IgG, CUT&RUN, biol rep 2

description: Library name: D2_IgG_Bio_rep_2

value: cell line

value: melanoma


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_dCxxC_rep10


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_dCxxC_rep9


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_dCxxC_rep8


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_dCxxC_rep7


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_dCxxC_rep5


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_dCxxC_rep4


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_dCxxC_rep1


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_dCxxC_rep2


title: GVO_WGBS_KO.Kdm2b_dCxxC_rep14

value: Kdm2b flox-CxxC/flox-CxxC; Zp3-cre


title: GVO_WGBS_KO.Kdm2b_dCxxC_rep13


title: HET mKo muscle, AAV, 7 dpi, sample 1

value: Tibialis anterior

value: HET mKO


title: GVO_WGBS_KO.Kdm2b_dCxxC_rep12


title: GVO_WGBS_KO.Kdm2b_dCxxC_rep9


title: SP late pre-hib 4

city: Tromsoe

first: Shona

last: Wood

address: Hansine Hansens veg 18

country: Norway

institute: UiT

description: Short photoperiod 8-12 weeks late pre-hibernation

data_processing:
Mapping was performed using STARaligner and the standard settings (Dobin et al. 2013). Reads were mapped to the golden hamster genome (BCM_Maur_2.0, ref.seq: GCF_017639785.1) and the annotation was provided by NCBI (GCF_017639785.1_BCM_Maur_2.0_genomic.gtf). The mapping rate was 88%. Feature counts was used to count the mapped reads to genes, using these parameters: featureCounts -p -t exon -g gene_id, on average 70% of alignments were assigned to an annotated feature.
Assembly: BCM_Maur_2.0, ref.seq: GCF_017639785.1
Supplementary files format and content: Txt files containing the raw counts for each sample

organism: Mesocricetus auratus

source_name: Laser captured ependymal region (tancyte enriched)

extract_protocol:
The RNA was extracted from the microdissected tissue using the Qiagen all prep DNA/RNA micro kit (80284) following the supplied instructions. The RNA integrity numbers were determined by TapeStation high sensitivity RNA analysis (5067-5579, 5067-5581, 5067-5580, Agilent) and all used samples had a RNA integrity numbers (RIN) between 7 to 9.
RNA-seq library construction was performed by BGI using their standard RNAseq protocol and Illumina high seq 4000. Quality control checks and barcode removal according to BGI protocol.

treatment_protocol: Three months old male golden hamsters (Mesocricetus auratus) were housed under long photoperiod (LP, 14 hr of light/24 hrs) and an ambient temperature of 22°C. Animals had ad libitum access to food and water throughout the experiment and received nesting material and a wooden stick in their home cage. Three weeks prior to the experiment, isoflurane anesthesia was given, and an iButton (Maxim) was implanted in the abdominal cavity to record body temperature. At the start of the experiment, one group were kept on LP at 22°C and were sampled immediately prior to the photoperiodic switch and at the end of the experiment (LP). The remaining animals were transferred to short photoperiod (SP, 10 hr of light/24 hrs) and an ambient temperature of 8°C to initiate hibernation. Animals were sampled 4 weeks after transfer to SP (pre-hibernation), after 8-12 weeks of SP prior to intiating T-A cycling (late pre-hibernation), or after three T-A cycles either when interbout euthermic (IBE) or torpid. The average IBE duration in this experiment was approximately 24 hours, animals were sampled late in their interbout euthermia phase (23 hours). Torpid animals were sampled at their mid-point of torpor, which in this experiment was 13 hours. After approximately 20 weeks of SP exposure, animals spontaneously stopped hibernating and were sampled at least 2 weeks after the last torpor bout (refractory).   Animals were anesthetised with 4% isoflurane and cervical dislocation was performed. The brains (6 per group) were covered with pre-cooled OCT, snap frozen in chilled isopentane over dry ice and 95% ethanol and sectioned on the cryostat (-20 ⁰C; (CM3050 S, Leica Biosystems)) at 20 µm. The brains were cut in series to cover the whole medio-basal hypothalamic region on two slides.  For LASER capture microdissection (LCMD) each animal had 6-8 membrane slides (415190-9081-000, Carl Zeiss) of 8 sections. Slides were stored at -80 ⁰C until further use. Immediately before LCMD the membrane slides were stained using cresyl violet as described previously (Melum et al. 2024). When ready, the slides were transferred to the laser micro dissector (PALM MicroBeam system, Zeiss) with the PALMRobo software (V4.8, Zeiss) and microdissection was completed within 45 minutes to minimize RNA degradation. LCMD was carried out at 10x, with the following settings: Cut energy = 42-49; Cut focus = 84; LPC Energy = 58; LPC focus =84, to capture the tanycytes on the transfer film of the microdissection caps (415190-9211-000, Carl Zeiss). The dorsal ventral extent of the area was determined by two times the PT width for each animal to correct for size differences. The width of the LCMD-sample was strived to be two to three cell bodies. When done, the tube was closed and snap frozen on dry ice and stored at -80 ⁰C.

tag: age

value: 6 months

tag: Sex

value: male

value: short photoperiod 8 degrees


title: GVO_WGBS_KO.Kdm2b_dCxxC_rep10


title: GVO_WGBS_KO.Kdm2b_dCxxC_rep8


title: GVO_WGBS_KO.Kdm2b_dCxxC_rep6


title: HOMO mKO muscle, NaCl, 3 dpi, sample 3

value: HOMO mKO

value: Saline

value: 3 dpi


title: GVO_WGBS_KO.Kdm2b_dCxxC_rep7

value: fully grown germinal vesicle oocytes


title: GVO_WGBS_KO.Kdm2b_dCxxC_rep5


title: GVO_WGBS_KO.Kdm2b_dCxxC_rep3


title: GVO_WGBS_KO.Kdm2b_dCxxC_rep4


title: GVO_WGBS_KO.Kdm2b_dCxxC_rep11


title: GVO_WGBS_KO.Kdm2b_dCxxC_rep1


title: SP refractory 6

description: Short photoperiod refractory animal reproductive

value: Laser captured ependymal region (tancyte enriched)

value: 8 months


title: GVO_WGBS_KO.Kdm2a_KO.Kdm2b_dCxxC_rep3

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC; Zp3-cre


title: GVO_WGBS_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_rep14

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC


title: GVO_WGBS_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_rep13


title: GVO_WGBS_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_rep12


title: GVO_WGBS_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_rep10


title: GVO_WGBS_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_rep9


title: GVO_WGBS_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_rep11


title: GVO_WGBS_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_rep7


title: GVO_WGBS_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_rep6


title: GVO_WGBS_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_rep3


title: GVO_WGBS_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_rep5


title: GVO_WGBS_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_rep4


title: GVO_WGBS_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_rep2


title: w.o. CA monocytes9

city: Moscow

first: Yegor

middle: S

last: Chegodaev

address: 8, Baltiyskaya st.

department: Ministry of Health of the Russian Federation

country: Russia

institute: Institute Of General Pathology And Pathophysiology, Russian Federation

data_processing:
Read quality was assessed using FastQC (v0.11.9). The reads were then aligned to the human genome assembly GRCh38 (hg38) using STAR (v2.7.10b), and alignment quality was evaluated. Gene counts were generated directly during alignment by enabling the --quantMode GeneCount option in STAR.
Assembly: hg38
Supplementary files format and content: csv. the file contains counts data for each sample

source_name: monocytes from PBMC

growth_protocol: Whole blood from patients with and without coronary atherosclerosis was centrifuged for 20 minutes at 1000 rcf. The cellular precipitate was then centrifuged on a Ficoll density gradient (1.077 g/cm³, Paneco, Russia) for 30 minutes at 500 rcf. After centrifugation, the interphase layer was collected, and the cells were incubated in MACS buffer (0.5% BSA, 2 mM EDTA, PBS) with CD14+ MicroBeads (Miltenyi Biotec) for 40 minutes at +4°C. Following incubation, CD14+ monocytes were isolated by immunomagnetic sorting. The isolated monocytes were then lysed using ExtractRNA (Paneco, Russia).

extract_protocol:
Total RNA was extracted from CD14+ monocytes using the Direct-zol RNA MiniPrep Kit (Zymo Research, USA) according to the manufacturer's instructions.
RNA libraries were prepared from 1 µg of total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, USA)

value: monocytes from PBMC

value: monocyte

value: WT


title: w.o. CA monocytes8


title: w.o. CA monocytes10


title: w.o. CA monocytes11


title: w.o. CA monocytes7


title: w.o. CA monocytes5


title: w.o. CA monocytes6


title: w.o. CA monocytes4


title: w.o. CA monocytes3


title: w. CA monocytes9


title: w.o. CA monocytes2


title: w. CA monocytes5


title: w. CA monocytes8


title: w.o. CA monocytes1


title: w. CA monocytes3


title: w. CA monocytes7


title: w. CA monocytes4


title: w. CA monocytes6


title: w. CA monocytes2


title: w. CA monocytes1


title: Lung-Male-C57/Bl6-Old-ZT12-2

city: Lille

first: Joel

last: Haas

address: 1 Rue du Professeur Calmette

country: France

institute: Institut Pasteur de Lille

description: Gene expression data from 18-month-old mouse whole lung at ZT12

hyb_protocol: Following fragmentation, 5.5 µg of ssDNA were hybridised for 16 hr at 45°C on GeneChIP Mouse Gene 2.0 ST array. GeneChips were washed and stained in the affymetrix fluidics station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: The microarray data were analyzed using GIANT tools suite47 on a local instance of Galaxy82. Data were normalized by the Robust Multi-Average method. Transcripts associated with annotated genes were selected for analysis.

label: Biotin

source_name: 18-month-old Mouse whole lungs harvested at ZT12

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (GeneChip WT PLUS Reagent kit, Affymetrix)

growth_protocol: Male specific pathogen-free C57BL/6J young adult mice (2-month-old, 20-25g) and elderly mice (18-month-old, 35-45 g) were fed a standard rodent chow (SAFE A04, SAFE, Augy, France) with water ad libitum and housed in a 12-h light/dark cycle.

extract_protocol: A frozen piece of lung was resuspended in 500 µL of TRIzol and RNA were extracted following the manufacturer protocol. RNA extracts were clean up with Macherey-Nagel micro RNA extraction kit

treatment_protocol: Lungs were perfused with 10 mL ice-cold PBS through using the right cardiac ventricule route. Lungs were snapped-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

tag: gender

value: Male

value: 18 months

value: Whole lung

tag: time


title: Lung-Male-C57/Bl6-Old-ZT12-4


title: SKMEL28, Anti-MITF, CUT&RUN, biol rep 3

description: Library name: SKMEL28WT_MITF_Bio_rep_3

value: cell line

value: melanoma

value: wild type


title: Lung-Male-C57/Bl6-Old-ZT0-2

description: Gene expression data from 18-month-old mouse whole lung at ZT0

source_name: 18-month-old Mouse whole lungs harvested at ZT0


title: Lung-Male-C57/Bl6-Young-ZT12-1

description: Gene expression data from 2-month-old mouse whole lung at ZT12

source_name: 2-month-old Mouse whole lungs harvested at ZT12

value: 2 months


title: Cdca7_11_Input

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

description: Library name: Cdca7_11_Input

data_processing:
Sequenced DNA reads were mapped to the mouse genome mm39 using bowtie (version 1.1.2) with parameters -v 2 -m 1 --best –strata, and only the reads that were mapped to unique position were retained.
To avoid PCR bias, for multiple reads that were mapped to the same genomic position, only one copy was retained.
To generate the signal landscape files (i.e. wiggle/bigwig files), each read was extended to 150 bp long toward its 3' end.
The number of reads covering each genomic position was rescaled to normalize the total number of fragments to 10M and averaged over every 10 bp window.
Assembly: mm39
Supplementary files format and content: wiggle files in bigwig format

growth_protocol: mESCs were cultured in LIF-containing mESC medium in gelatin-coated dishes in the absence of feeder cells.

extract_protocol:
Cells were fixed with 1% formaldehyde. After quenching and cell lysis, chromatin was sonicated.
ChIP-seq libraries were constructed using a KAPA HyperPrep kit (Roche)

treatment_protocol: HA-mCDCA7 expression plasmid was transfected into Cdca7-KO mESCs with lipofectamine 2000, the cells were selected with blasticidin, and individual clones were picked.

value: mouse embryonic stem cell (mESC)

value: Cdca7 KO

value: Reconstituted with HA-mCDCA7

tag: chip antibody


title: Lung-Male-C57/Bl6-Old-ZT0-3


title: Cdca7_11_ChIP

description: Library name: Cdca7_11_ChIP


title: Lung-Male-C57/Bl6-Young-ZT12-4


title: Lung-Male-C57/Bl6-Young-ZT12-2


title: Lung-Male-C57/Bl6-Old-ZT0-4


title: Lung-Male-C57/Bl6-Young-ZT0-4

description: Gene expression data from 2-month-old mouse whole lung at ZT0

source_name: 2-month-old Mouse whole lungs harvested at ZT0


title: Cdca7_10_ChIP

description: Library name: Cdca7_10_ChIP


title: Lung-Male-C57/Bl6-Young-ZT12-3


title: Lung-Male-C57/Bl6-Old-ZT0-1


title: late_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_12

data_processing:
RNA-Seq datasets were aligned to the Mus musculus genome assembly (GRCm38/mm10 Dec. 2011) as single-end (Smart-Seq2 polyA datasets) or paired-end (total random primed datasets) using STAR (Dobin et al. 2013) with parameters “-outFilterMultimapNmax 300 -outMultimapperOrder Random -outSAMmultNmax 1 -alignIntronMin 20 -alignIntronMax 1000000”
RNA-Seq samples for hybrid Bl6 x JF1 F1 2-cell embryos were separately aligned to Bl6 and JF1 genomes obtained by injecting JF1 single-nucleotide polymorphisms (SNPs) into reference mm10 genome using previously published SNP table (Takada et al. 2013). RNA-seq reads were categorized as maternal (Bl6), paternal (JF1) or undefined based on minimal number of mismatches in alignments to both genomes.
Assembly: mm10
Supplementary files format and content: BigWig (.bw) processed files were generated from BAM files using the function qExportWig from QuasR package selecting uniquely mapped reads. BigWig processed files for hybrid Bl6 x JF1 2-cell embryos were generated separately for maternal (files ending with MAT.bw), paternal (files ending with PAT.bw) and total alignments normalized by total number of mapped allelic reads (MAT and PAT) or total number of mapped reads.

source_name: late 2-cell embryo

extract_protocol:
After removing the zona-pellucida by treating with acid tyrode’s solution, oocytes and F1 hybrid 2-cell embryos were washed in PBS supplemented with 0.05% Polyvinyl alcohol and lysed in Smartseq2 lysis buffer.
Libraries were prepared by Smartseq2 protocol. cDNAs were prepared by oligo dT based reverse transcription and template switching using Superscript II reverse transcriptase followed by the pre-amplification PCR using KAPA HiFi HotStart ReadyMix PCR Kit and the purification using AMPure Xp beads. 1ng of pre-amplified cDNA was tagmented by Tn5 transposase and adapter-ligated fragments were amplified with adding Nextera XT indexes followed by the purification using AMPure XP beads. Libraries with different indexes were pooled and submitted to sequencing. For total RNA sequencing GOs were isolated from the d14.0 mice. 60-80 oocytes were pooled and frozen in 100μl of Buffer RL. 4 and 3 biological replicates were prepared for ctrl and Kdm2aKOKdm2bKO, respectively. RNA was purified by using Single Cell RNA Purification Kit (NORGEN; 51800). Libraries were prepared according to Illumina Stranded total RNA-seq protocol with Illumina IDT DNA/RNA UDI indexes.

value: late 2-cell embryo

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC x JF1 WT

value: C57BL/6J x JF1/MsJ


title: Lung-Male-C57/Bl6-Young-ZT0-3


title: Lung-Male-C57/Bl6-Old-ZT12-1


title: late_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_11


title: Lung-Male-C57/Bl6-Young-ZT0-1


title: late_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_10


title: late_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_9


title: late_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_7


title: late_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_8


title: late_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_3


title: late_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_5


title: late_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_6


title: late_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_4


title: early_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_9

source_name: early 2-cell embryo

value: early 2-cell embryo

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ x JF1 WT


title: early_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_8


title: late_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_1


title: late_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_2


title: GVO_H3K36me2_KO.Kdm2a_KO.Kdm2b_KO_rep2

value: fully grown germinal vesicle oocytes

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre

value: mouse anti-H3K36me2 antibody (1:100; Cosmo bio; MABI0332)


title: early_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_7


title: early_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_6


title: early_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_11


title: SKMEL28, Anti-IgG, CUT&RUN, biol rep 1

description: Library name: SKMEL28WT_IgG_Bio_rep_1


title: early_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_5


title: early_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_4


title: WT muscle, NaCl, 3 dpi, sample 3

value: Tibialis anterior

value: WT

value: Saline

value: 3 dpi


title: early_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_2


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_24

source_name: 2-cell embryo

value: 2-cell embryo

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre; JF1 WT


title: early_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_1


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_23


title: GVO_H3K36me2_KO.Kdm2a_KO.Kdm2b_KO_rep1


title: GVO_H3K36me3_KO.Kdm2a_KO.Kdm2b_KO_rep2


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_22


title: early_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_12


title: Lung-Male-C57/Bl6-Old-ZT12-3

value: Male

value: 18 months

value: Whole lung


title: Cdca7_10_Input

description: Library name: Cdca7_10_Input

value: mouse embryonic stem cell (mESC)

value: Cdca7 KO

value: Reconstituted with HA-mCDCA7


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_21

value: C57BL/6J x JF1/MsJ


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_19


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_16


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_15


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_20


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_18


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_17


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_14


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_13


title: early_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_3

value: early 2-cell embryo

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ x JF1 WT


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_5


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_10


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_6


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_9


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_8


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_11


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_4


title: Lung-Male-C57/Bl6-Young-ZT0-2

value: 2 months


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_3


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_2


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_20

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC; Zp3-cre x JF1 WT


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_19


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_1


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_16


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_KO_12


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_15


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_14


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_13


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_12


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_10


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_17


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_9


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_8


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_6


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_5


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_4


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_2


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_3


title: 2cell_scRNA_KO.Kdm2b_dCxxC_25

value: Kdm2b flox-CxxC/flox-CxxC; Zp3-cre x JF1 WT


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_1


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_18


title: 2cell_scRNA_KO.Kdm2b_dCxxC_21


title: 2cell_scRNA_KO.Kdm2b_dCxxC_23


title: 2cell_scRNA_KO.Kdm2b_dCxxC_22


title: 2cell_scRNA_KO.Kdm2b_dCxxC_20


title: 2cell_scRNA_KO.Kdm2b_dCxxC_18


title: 2cell_scRNA_KO.Kdm2b_dCxxC_17


title: 2cell_scRNA_KO.Kdm2b_dCxxC_15


title: 2cell_scRNA_KO.Kdm2b_dCxxC_16


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_7


title: 2cell_scRNA_KO.Kdm2b_dCxxC_11


title: 2cell_scRNA_KO.Kdm2b_dCxxC_13


title: 2cell_scRNA_KO.Kdm2b_dCxxC_9


title: 2cell_scRNA_KO.Kdm2b_dCxxC_8


title: 2cell_scRNA_KO.Kdm2b_dCxxC_5


title: 2cell_scRNA_KO.Kdm2b_dCxxC_7


title: 2cell_scRNA_KO.Kdm2b_dCxxC_24


title: 2cell_scRNA_KO.Kdm2b_dCxxC_6


title: 2cell_scRNA_KO.Kdm2b_dCxxC_4


title: 2cell_scRNA_KO.Kdm2b_dCxxC_1


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_23


title: 2cell_scRNA_KO.Kdm2b_dCxxC_3


title: 2cell_scRNA_KO.Kdm2b_dCxxC_2


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_24


title: 2cell_scRNA_KO.Kdm2b_dCxxC_19


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_21


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_18


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_22


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_19


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_20


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_17


title: 2cell_scRNA_KO.Kdm2b_dCxxC_12


title: 2cell_scRNA_KO.Kdm2b_dCxxC_10


title: 2cell_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_11


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_16


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_13


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_14


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_11


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_15


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_7


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_6


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_8


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_9


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_5


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_4


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_1


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_2


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_23

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC x JF1 WT


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_22


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_21


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_19


title: D2, Anti-MITF, CUT&RUN, biol rep 2

description: Library name: D2_MITF_Bio_rep_2

value: cell line

value: melanoma

value: MITF-KO D2


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_18

value: 2-cell embryo


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_15


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_16


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_12


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_14


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_13


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_11


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_12


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_10


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_8


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_6


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_10


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_5


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_3


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_2


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_22

value: Kdm2b flox-CxxC/flox-CxxC x JF1 WT


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_4


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_20


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_17


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_3


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_19


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_18


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_17


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_16


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_15


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_13


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_14


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_7


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_9


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_11


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_7


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_8


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_10


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_3


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_4


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_6


title: 2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_1


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_1


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_2


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_20

value: fully grown germinal vesicle oocytes

value: Ring1 -/-; Rnf2 flox/flox; Zp3-cre


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_21


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_21


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_22


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_19


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_20


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_15


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_18


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_12


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_13


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_12


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_14


title: 2cell_scRNA_Ctrl.Kdm2b_dCxxC_5


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_11


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_9


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_10


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_8


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_7


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_3


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_2


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_4


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_24

value: Ring1 -/-; Rnf2 flox/flox


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_1


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_23


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_20


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_19


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_21


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_17


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_22


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_17


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_16


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_15


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_18


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_16


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_12


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_14


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_11


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_5


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_8


title: GVO_scRNA_KO.Ring1_KO.Rnf2_KO_6


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_9


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_7


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_6


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_10


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_4


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_2


title: early_2cell_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_10


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_20

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_1


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_3


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_19


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_18


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_17


title: F1_IL4_2

city: Bethesda

first: Mingming

last: Zhao

address: 9000 Rockville Pike

institute: national institutes of health

description: Library name: F1_IL4_2

data_processing:
TheReal Time Analysis software (RTA 3.9.25) was used for processing raw data files, the Illumina bcl2fastq v2.17 was used to demultiplex and convert binary base calls and qualities to fastq format.
Samples were trimmed for adapters using Cutadapt (1.18) before the alignment.
The trimmed reads were aligned with mm10 reference using Bowtie2(2.2.6) alignment.
The peaks were called using Genrich (0.6.1) (genrich -t sample_sortedByRead.bam -o sample.narroPeak -j -y -r -v -d 150 -m 5 -e chrM,chrY -E blacklist_regions.bed-f sample.bdg -b sample.bed)
Assembly: mm10
Supplementary files format and content: bigwig files were generated using Genrich (0.6.1)

source_name: macrophages

growth_protocol: Macrophage cells were isolated from the peritoneal cells by using EasySep™ Mouse F4/80 Positive Selection Kit (100-0659, Stemcell Technologies)

extract_protocol:
100,000 macrophage cells were subjected to lysis using 100 µl of Lysis buffer (containing 10 mM Tris-Cl at pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, and 0.1% Tween-20). Following a centrifugation at 500g for 10 minutes at 4°C, the resulting nuclei were reconstituted with 50 µl of a transposition mixture (FC-121-1030, Illumina; comprising 1X Tagment DNA buffer, Tn5 Transposase, and nuclease-free H2O), and this mixture was then incubated for 30 minutes at 37°C in a thermomixer. The transposed DNA was subsequently purified using MinElute columns (28004, QIAGEN) and then amplified using Nextera sequencing primers and the NEB high-fidelity 2X PCR master mix for 11 cycles (M0541, New England Biolabs). PCR-amplified DNA was purified using MinElute columns
ATAC-seq samples were pooled and sequenced on NextSeq 2000 P2 using PI lab prepared library and paired-end sequencing.

treatment_protocol: Two replicates were IL-4 treated for 16 days in BL/6. Two replicates were IL-4 treated for 4 days in CB6F1/J(F1) mice

value: macrophages

value: treated with A fusion protein of mouse IL-4 with the Fc portion of IgG1


title: F1_IL4_1

description: Library name: F1_IL4_1


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_16


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_15


title: GVO_scRNA_Ctrl.Ring1_KO.Rnf2_KO_13


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_14


title: F1_Ctrl_1

description: Library name: F1_Ctrl_1

value: untreated


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_12


title: BL6_IL4_1_16day

description: Library name: BL6_IL4_1_16day


title: BL6_IL4_2_16day

description: Library name: BL6_IL4_2_16day


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_10


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_11


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_7


title: BL6_Ctrl_2_16day

description: Library name: BL6_Ctrl_2_16day


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_9


title: young mice

city: guangzhou

first: Liu

last: Congyuan

address: Engineering, Ministry of Education, National-Local Joint Engineering Research Center for Stem Cells and Regenerative Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.

institute: Sun Yat-sen University

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.11
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: testicular tissue

extract_protocol:
2-month-old and 24-month-old mice were anesthetized with Avertin (250 mg/kg) by i.p. injection. After dissection, the testes were immediately placed in ice-cold saline. After fully washing the testes with PBS, the tunica albuginea was carefully removed. The testes were mechanically minced into pieces using microscopic forceps and digested with accutase (Invitrogen, USA) at 37°C for 5 minutes. The accutase activity was halted by adding DMEM/F12 supplemented with 10% fetal bovine serum (Gibco, USA), and the samples were rinsed twice with PBS. The obtained cell suspension was filtered through a 45 μm strainer and centrifuged. At last, cells were resuspended in phosphate-buffered saline (PBS) containing 0.1% BSA (Thermo Fisher Scientific, USA) at a concentration of ~1,000 cells/μL for single-cell sequencing.
The BD Rhapsody system was used to capture the transcriptomic information. Single-cell capture was achieved by randomly distributing a single-cell suspension across microwells using a limited dilution approach. Beads with oligonucleotide barcodes were added in excess to ensure that a bead paired with a cell in each microwell. Cell-lysis buffer was added to allow poly-adenylated RNA molecules to hybridize to the beads. The beads were collected into a single tube for reverse transcription. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification workflow. Sequencing libraries were quantified using a High Sensitivity DNA chip (Agilent, USA) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific, USA). The library for each sample was sequenced using Illumina sequencer (Illumina, CA).

value: testicular tissue

value: stroma cells


title: BL6_Ctrl_1_16day

description: Library name: BL6_Ctrl_1_16day


title: ageg mice


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_3


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_6


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_4


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_1


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_20

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_19


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_17


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_2


title: F1_Ctrl_2

description: Library name: F1_Ctrl_2


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_18


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_15


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_KO_13


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_14


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_13


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_10


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_12


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_11


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_7


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_9


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_8


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_5


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_6


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_3


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_2


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_4


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_1


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_17

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC; Zp3-cre


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_18


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_16


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_20


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_15


title: HC33_S10

city: Oxford

first: Charlotte

last: Brierley

address: University of Oxford, Headley Way

country: United Kingdom

institute: MRC WIMM

description: Library name: s2907205

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v7.0.0)  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: healthy control

extract_protocol:
To investigate the effect of chr21amp on cell differentiation, we performed droplet-based, high-throughput single-cell RNA-seq on Lin-CD34+ cells and total mononuclear cells.
Library were prepared according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: hematopoietic

value: Mononuclear Cells


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_KO_16


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_14


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_11


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_12


title: S28

description: Library name: s2907203

source_name: blast phase MPN


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_13


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_10


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_9


title: S5_S13

description: Library name: s2807205


title: S21

description: Library name: s2807202


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_8


title: HC86_S19

description: Library name: s2907201


title: HC84_S37

description: Library name: s2807201


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_7


title: HC93_S48

description: Library name: s2107205


title: HC78

description: Library name: s2107204


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_4


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_5


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_19


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_3


title: S42

description: Library name: s2107203


title: S17

description: Library name: s2107201


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_2


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_1


title: H1_NPC_eGFP_rep1

city: Beijing

first: wei

last: Shi

address: Chinese Institute for Brain Research, Beijing(CIBR), Jianzan Building, No.26, Science Park Road, Zhongguancun Life Science Park, Changping District, Beijing, China

institute: Chinese institute for brain research

description: Library name: Sample15

data_processing:
Sequencing reads from RNA-seq of transgenic human iNPCs were aligned to the Human reference genome (GRCh38) using Hisat2 (v2-2.1.0)56 with default parameters. The resulting data were converted and sorted with Samtools (v1.0.1)57. Expression values of each gene were quantified as transcripts per million (TPM) using featureCounts (v2.0.0)58.
Assembly: hg38
Supplementary files format and content: csv file for foldchange of each sample.

source_name: NPC

growth_protocol: Two human ESC lines were used in this paper. The H1 ESC was a gift from Novobiotec. The CB0003 ESC was purchased from the National Stem Cell Resource Center, Institute of Zoology, Chinese Academy of Sciences. Both hESCs were maintained in StemFlex™ Medium (Gibco A3349401) on Matrigel-coated (Corning 354277) culture plates. Cells were subcultured once every 5-7 days by ReLeSR™ Reagent (STEMCELL Technologies 100-0483). Induced neural progenitor cells (iNPCs) were induced from both hESC lines using serum-free STEMdiffTM Neural Induction Medium (STEMCELL Technologies 05835) according to the manufacturer’s instruction. iNPCs were maintained in STEMdiff™ Neural Progenitor Medium (STEMCELL Technologies 05833) with supplement and passaged every 3 days using Accutase dissociation medium (STEMCELL Technologies 07920).

extract_protocol:
For cultured cells, total RNA was isolated using RNAiso Plus reagent (Takara 9108).
The integrity of the total RNA was determined with a Bioanalyzer 2100 or 2200 (Agilent). cDNA libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme). cDNA libraries were sequenced on an Illumina Novoseq using a 150bp paired-end setting.

treatment_protocol: Transfection of ESC and iNPC were performed using the LipofectamineTM Stem Reagent (Invitrogen 2693947). BEND2 and chimera cDNAs tagged with N-terminal 3×HA were cloned into the PB-TRE3G-2A-mNeonGreen vector, which was subsequently co-transfected with PB-EF1a-TET3G and Hyperbase (Transposase) plasmids (ratio 1:1:1) into CB0003 hESCs using LipofectamineTM Stem Reagent (Invitrogen, 2693947). Successfully integrated cells (mNeoGreen control iNPCs or HA-MN1:BEND2-2A-mNeonGreen knockin iNPCs) were screened with puromycin containing StemFlex™ medium. Transgene expression was induced by doxycycline.

value: NPC

value: neural progenitor cell

value: ctrl overexpression


title: H1_NPC_eGFP_rep2

description: Library name: Sample16


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_19

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_20

value: fully grown germinal vesicle oocytes


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_18


title: NPC_MN1_rep2

description: Library name: Sample13

value: MN1  Knock in


title: NPC_BEND2_rep2

description: Library name: Sample11

value: BEND2 Knock in


title: NPC_ctrl_rep2

description: Library name: Sample12

value: ctrl Knock in


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_16


title: H1_NPC_BD2_rep2

description: Library name: Sample10

value: BD2 overexpression


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_15


title: NPC_MN1-BEND2_rep2

description: Library name: Sample14

value: MN1-BEND2 Knock in


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_14


title: H1_NPC_BD2-VP16_rep2

description: Library name: Sample8

value: BD2-VP16 overexpression


title: GVO_scRNA_KO.Kdm2a_KO.Kdm2b_dCxxC_6


title: H1_NPC_MN1-CXXC5_rep2

description: Library name: Sample9

value: MN1-CXXC5 overexpression


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_13


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_12


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_17


title: NPC_MN1-BEND2_rep1

description: Library name: Sample7


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_10


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_9


title: NPC_BEND2_rep1

description: Library name: Sample4


title: H1_NPC_BD2_rep1

description: Library name: Sample3


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_11


title: NPC_MN1_rep1

description: Library name: Sample6


title: NPC_ctrl_rep1

description: Library name: Sample5


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_8


title: H1_NPC_MN1-CXXC5_rep1

description: Library name: Sample2


title: Bone marrow, MCAO

city: Shanghai

first: Guo

last: Yunlu

address: 160 Pujian Rd

department: Anesthesiology

institute: Renji Hospital, Shanghai Jiao Tong University School of Medicine

description:
Library name: bone-marrow-mcao
BD Rhapsody

data_processing:
We applied fastp with default parameters to filter the adaptor sequence and remove the low-quality reads to obtain clean data. UMI tools was applied for single-cell transcriptome analysis to identify the cell barcode whitelist. The UMI-based clean data was mapped to the mouse genome (mm10 Ensemble version 91) utilizing STAR mapping with customized parameters from the UMI-tools standard pipeline to determine the UMIs counts of each sample.
Seurat R package (4.0.6) (https://satijalab.org/Seurat/) was used for cell normalization, dimension reduction, clustering and further analysis.
Assembly: Mouse mm10
Supplementary files format and content: Matrix file of normalized counts (G.DUIZHAO samples correspond to control mice, G.ZUZHONG samples correspond to MCAO mice,)

source_name: Bone marrow

extract_protocol:
Bone marrow were flushed from tibias and femurs with PBS/1% BSA and filtered through a 40 μm cell strainer and centrifuged at 300g for 5min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec).
BD Rhapsody system was used to capture the transcriptomic information of the bone marrow sample-derived single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across > 200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation, so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to capture oligos on the beads. Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). Sequencing was performed by Illumina Novaseq6000 (Illumina, San Diego, CA) on a 150 bp paired-end run.

treatment_protocol: Middle cerebral artery occlusion (MCAO) model

value: Bone marrow

value: All bone marrow cells

value: 8-10 weeks old

value: male

value: WT

value: MCAO


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_7


title: Bone marrow, control

description:
Library name: bone-marrow-control
BD Rhapsody

value: control


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_6


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_5


title: H1_NPC_BD2-VP16_rep1

description: Library name: Sample1

value: NPC

value: neural progenitor cell


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_4

value: fully grown germinal vesicle oocytes

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-CxxC/flox-CxxC


title: Human_iNPC

description: Library name: Sample2

data_processing:
Sequencing reads from RNA-seq of transgenic human iNPCs were aligned to the Human reference genome (GRCh38) using Hisat2 (v2-2.1.0)56 with default parameters. The resulting data were converted and sorted with Samtools (v1.0.1)57. Expression values of each gene were quantified as transcripts per million (TPM) using featureCounts (v2.0.0)58.
Assembly: hg38
Supplementary files format and content: csv file for counts of each sample.

source_name: neural progenitor cell


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_2

source_name: fully grown germinal vesicle oocytes


title: Differentiated_iNPC

description: Library name: Sample1


title: IL34LacZ/+ brain macrophages and vascular cells

city: Zurich

first: Hannah

middle: Jade

last: Van Hove

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

institute: University of Zurich

description: Library name: HET

data_processing:
The libraries were sequenced on a NovaSeq sequencer in line with 10x Genomics recommendations (paired-end reads) with a depth of 50,000 reads per cell. Cell Ranger software (10x Genomics, v.3.1.0) was used to demultiplex, process raw data, and align the reads to the GENCODE reference build GRCm38.p6 Release M23, followed by summarizing the unique molecular identifier (UMI) counts. A filtered gene-cell count matrix was generated by Cell Ranger’s built-in cell-calling algorithms.
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: Whole brain

extract_protocol:
All methods are listed in the associated manuscript.
The quality of the single-cell suspension was assessed using a hemocytometer under a Leica DM IL LED Fluo microscope, and cell quantity was evaluated with an automated cell counter (LUNA-FX7, Logos). Cells were loaded into the 10x Genomics Chromium platform, and library preparation was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3ʹ Reagent kits v3.1 protocol).

value: Whole brain

value: mural cells (MCs) and fibroblasts (FBs) (CD13+ and/or CD140a+O4- cells), endothelial cells (ECs) (CD31+), astrocytes (AC) (ACSA-2+), BAMs (CD11bhiF4/80+) and microglia (CD11b+F4/80hi)


title: IL34LacZ/LacZ brain macrophages and vascular cells

description: Library name: KO


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_1


title: GVO_scRNA_KO.Kdm2b_dCxxC_20

value: Kdm2b flox-CxxC/flox-CxxC; Zp3-cre


title: Female Spleen Control Biol Rep 5

city: Cologne

first: Sebastian

last: Grönke

address: Joseph-Stelzmann Str. 9b

department: Biological Mechanisms of Ageing

institute: Max-Planck Institute for Biology of Ageing

description: Library name: Sample 111

data_processing:
Libraries read processing was automated using Flaski (v3.11.34) [88], developed by the Bioinformatics Core Facility at the MPI for Biology of Ageing (Cologne, Germany).
Differential gene expression was analysed using DESeq2 (v1.24.0)  in R (v3.6.3).
Assembly: Raw reads were mapped to the mm39 ENSEMBL build 105 using kallisto (v0.46.1). Gene counts were quantified in the same step
Supplementary files format and content: Excel file containing FPKM and differential expression analysis

source_name: Spleen

extract_protocol:
Total RNA was isolated from 4-10mg of spleen, muscle and kidney using TrIzol. Samples were treated with DNAase using the Turbo DNAse kit (ThermoFisher Scientific) to remove genomic DNA.
poly(A)+ mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation kit (New England BioLabs, Prior to first strand synthesis, samples were randomly primed (5’ d(N6) 3’ [N=A,C,G,T]) and fragmented. First strand synthesis was done using the Protoscript II Reverse Transcriptase for approximately 40 minutes at 42⁰C. All remaining steps for library construction were done according to the NEBNext Ultra™ II Non- Directional RNA Library Prep Kit for Illumina, RNA Seq with 50 million 150 bp paired-end reads/sample

value: Spleen

value: 24 months

value: Female

value: C3B6F1 wild type

value: Control


title: GVO_scRNA_KO.Kdm2b_dCxxC_19


title: GVO_scRNA_KO.Kdm2b_dCxxC_18


title: Female Spleen Control Biol Rep 4

description: Library name: Sample 110


title: GVO_scRNA_KO.Kdm2b_dCxxC_17


title: CHLA06_Corin_2

city: Boston

first: Robert

last: Fisher

state: MA

address: 609 Albany St

department: Dermatology

institute: Boston University

description:
Library name: CHLA06_Corin_2
DEG_p05_CHO6.csv

data_processing:
Reads were trimmed and low-quality reads were removed using fastp
Reads were quasi-aligned to the GRCh38 reference genome using Salmon
Salmon quant files were used for differential analysis using DESeq2. The Wald test was used to generate p-values and log2 fold changes.
Assembly: hg38/Gencodev44
Supplementary files format and content: CSV files; DESeq2 outputs of differential gene expression p <0.05; salmon quant files for the processed raw unnormalized counts

growth_protocol: BT37 cell lines were cultured in RPMI (Invitrogen, Thermo Fisher Scientific) supplemented with 10% FBS, 2 mM L-glutamine, and 1% penicillin/streptomycin. CHLA06 cells were cultured in EF Media containing 30% Hams F12 (Invitrogen, Thermo Fisher Scientific), 70% DMEM (Invitrogen, Thermo Fisher Scientific), 1x antibiotic/antimycotic (#A5955, Sigma-Aldrich), 2 mM L-glutamine (#25030-081, Life Technologies), 2% B27 with vitamin A (#12586-010, Gibco), 20 ng/mL EGF (#AF-100-15-1MG, PeproTech), 20 ng/mL FGF-2 (#100-18B-1MG, PeproTech), and 5 ug/mL heparin (#H3149-100KU, Sigma). Media was passed through a 0.22 um filter before use. All cell lines were maintained in a 37°C incubator at 5% CO2.

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen)
Libraries were constructed by Azenta Inc. Paired end

value: ATRT

value: Corin


title: GVO_scRNA_KO.Kdm2b_dCxxC_15


title: Female Spleen Control Biol Rep 3

description: Library name: Sample 109


title: GVO_scRNA_KO.Kdm2b_dCxxC_16


title: GVO_scRNA_KO.Kdm2b_dCxxC_14


title: CHLA06_Corin_ATAC-seq_2

description: Library name: CHLA06_Corin_2

data_processing:
Reads were quality checked using FastQC (v0.11.8) (Andrews 2010) and were trimmed for the adaptors with Trimmomatic (version 0.39) using default parameters (Bolger et al. 2014).
Reads were aligned to the hg38 genome using bowtie2 (version 2.3.4.3). All the mapped reads to Mitochondria and duplicated reads  were removed using Picard toolkit (http://broadinstitute.github.io/picard/)
ATAC-seq peaks were called by macs2 (version 2.1.2) (Zhang et al. 2008) using default parameters.
Signal-based analyses were done using duplicate filtered read pileup bedGraph files. In order to normalize the ATAC signals in each experiment, area under curve in the bedGraph file were normalized to 1e9. BEDtools
Assembly: hg38/Gencodev44
Supplementary files format and content: Normalized bigwig

growth_protocol: BT37 cell lines were cultured in RPMI (Invitrogen, Thermo Fisher Scientific) supplemented with 10% FBS, 2 mM L-glutamine, and 1% penicillin/streptomycin.CHLA06 cells were cultured in EF Media containing 30% Hams F12 (Invitrogen, Thermo Fisher Scientific), 70% DMEM (Invitrogen, Thermo Fisher Scientific), 1x antibiotic/antimycotic (#A5955, Sigma-Aldrich), 2 mM L-glutamine (#25030-081, Life Technologies), 2% B27 with vitamin A (#12586-010, Gibco), 20 ng/mL EGF (#AF-100-15-1MG, PeproTech), 20 ng/mL FGF-2 (#100-18B-1MG, PeproTech), and 5 ug/mL heparin (#H3149-100KU, Sigma). Media was passed through a 0.22 um filter before use. All cell lines were maintained in a 37°C incubator at 5% CO2.

extract_protocol:
BT37 and CHLA06 cells were seeded 105,000 cells/cm2 and treated with 1 µM Corin and DMSO for 24 h. 100,000 viable cells were aliquoted, and samples were prepared using ATAC-seq kit (Active Motif, 53150). Cells were pelleted at 500 x g for 5 min at 4 °C, washed with PBS and resuspended in ATAC Lysis Buffer followed by centrifugation at 500 x g 10 min at 4 °C. Pelleted nuclei were resuspended in Tagmentation Master Mix (Tagmentation Buffer, PBS, 0.01% Digitonin, 1% Tween 20, H2O and Assembled Transposomes) and incubated at 37 °C for 30 minutes in a thermomixer at 800 rpm. Then, DNA Purification Binding Buffer was added to the samples along with 3 M sodium acetate as required to reach the appropriate pH for binding. Samples were transferred to DNA purification columns and washed with Wash Buffer and eluted with DNA Purification Elution Buffer. Centrifugation of samples were done at 17000 x g for 1 min. Collected samples were amplified using unique combination of index primers with the following cycling conditions: 72 °C for 5 min, 98 °C for 30s, 10 cycles of 98 °C for 10s, 63 °C for 30s and 72 °C for 1min, hold at 4°C. SPRI beads were added to each sample and vortexed and incubated for 5 min for binding and magnetically separated and washed with 80% ethanol solution twice while remaining attached. Following ethanol evaporation, beads were vortexed in DNA Purification Elution Buffer and incubated for 5 min at RT followed by collection of eluted samples.
Library was prepared using ATAC-seq Kit (53150). Sequencing was conducted by Azenta Life Sciences.


title: CHLA06_Corin_1

description:
Library name: CHLA06_Corin_1
DEG_p05_CHO6.csv


title: GVO_scRNA_KO.Kdm2b_dCxxC_13


title: GVO_scRNA_Ctrl.Kdm2a_KO.Kdm2b_dCxxC_3


title: CHLA06_Corin_ATAC-seq_1

description: Library name: CHLA06_Corin_1


title: CHLA06_DMSO_2

description:
Library name: CHLA06_DMSO_2
DEG_p05_CHO6.csv

value: DMSO


title: Female Spleen Control Biol Rep 1

description: Library name: Sample 107


title: CHLA06_DMSO_ATAC-seq_2

description: Library name: CHLA06_DMSO_2


title: GVO_scRNA_KO.Kdm2b_dCxxC_12


title: Male Spleen Control Biol Rep 6

description: Library name: Sample 106

value: Male


title: CHLA06_Corin_3

description:
Library name: CHLA06_Corin_3
DEG_p05_CHO6.csv


title: Male Spleen Control Biol Rep 4

description: Library name: Sample 104


title: Male Spleen Control Biol Rep 5

description: Library name: Sample 105


title: BT37_Corin_3

description:
Library name: BT37_Corin_3
DEG_p05_BT37.csv


title: CHLA06_DMSO_ATAC-seq_1

description: Library name: CHLA06_DMSO_1


title: BT37_Corin_2

description:
Library name: BT37_Corin_2
DEG_p05_BT37.csv


title: Female Spleen Control Biol Rep 2

description: Library name: Sample 108


title: GVO_scRNA_KO.Kdm2b_dCxxC_10


title: BT37_Corin_ATAC-seq_2

description: Library name: BT37_Corin_2


title: Male Spleen Control Biol Rep 3

description: Library name: Sample 103


title: GVO_scRNA_KO.Kdm2b_dCxxC_11


title: Male Spleen Control Biol Rep 2

description: Library name: Sample 102


title: GVO_scRNA_KO.Kdm2b_dCxxC_9


title: BT37_Corin_ATAC-seq_1

description: Library name: BT37_Corin_1


title: GVO_scRNA_KO.Kdm2b_dCxxC_8


title: BT37_DMSO_ATAC-seq_2

description: Library name: BT37_DMSO_2


title: BT37_DMSO_3

description:
Library name: BT37_DMSO_3
DEG_p05_BT37.csv


title: BT37_Corin_1

description:
Library name: BT37_Corin_1
DEG_p05_BT37.csv


title: GVO_scRNA_KO.Kdm2b_dCxxC_7


title: BT37_DMSO_ATAC-seq_1

description: Library name: BT37_DMSO_1


title: Female Spleen Trametinib Biol Rep 5

description: Library name: Sample 100

value: trametinib


title: BT37_DMSO_2

description:
Library name: BT37_DMSO_2
DEG_p05_BT37.csv


title: Male Spleen Control Biol Rep 1

description: Library name: Sample 101


title: BT37_DMSO_1

description:
Library name: BT37_DMSO_1
DEG_p05_BT37.csv


title: Female Spleen Trametinib Biol Rep 4

description: Library name: Sample 99


title: CHLA06_DMSO_1

description:
Library name: CHLA06_DMSO_1
DEG_p05_CHO6.csv


title: TNF-PGE_24h_Rep3

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

description:
EC.US.5803_Male_TNF.PGE_24h_Rep3
rawcounts_PGE.txt

data_processing:
Read quality was assessed and adapters trimmed using FastQC and cutadapt.
Reads were then mapped to the human genome (hg38) and reads in exons were counted against Gencode v27 with STAR Aligner.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: CD14+ monocytes

growth_protocol: Monocytes were cultured overnight before treatment at 37°C, 5% CO2 in RPMI-1640 medium supplemented with 10% heat-inactivated defined FBS, penicillin-streptomycin, L-glutamine and 20 ng/ml human M-CSF.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1Ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNextUltraII RNA Library Prep Kit following manufacturer’s protocols

treatment_protocol: Human CD14+ monocytes were treated with PGE2, TNF or PGE2 + TNF co-stimulation for 3 or 24 hours. For the IFNg priming experiment, CD14+ monocytes were primed with IFNg, and subsequently treated with TNF, PGE2 or TNF+PGE2 for 3h.

value: CD14+ monocytes


title: GVO_scRNA_KO.Kdm2b_dCxxC_4


title: tIMEC cells, ANP32E overexpression and acute RNaseH1 overexpression, rep3, Rloop

city: Trento

first: Sara

last: Lago

address: Via Sommarive 9

department: CIBIO

country: Italy

institute: University od Trento

description: Library name: tIMEC-ANP32E-H1_acute_CUTnRUN_Rloop_R3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic tool with Illumina:HEADCROP
Bam files were aligned on the reference genome, and downsampled randomly to obtain the same reads number for every sample.
Peaks were called using MACS2 tool
Assembly: hg38
Supplementary files format and content: bigWig files of aligned reads
Library strategy: CUT&RUN

source_name: tIMEC

growth_protocol: tIMEC, tIMEC-ANP32E and tIMEC-ANP32E-H1 cells were maintained in DMEM-F12 supplemented with hEGF 10 ng/ml, Insulin 5 μg/ml, Hydrocortisone 0.5 μg/ml, Bovine Pituitary Extract 35 μg/ml and antibiotics Penicillin/Streptomycin 1:100 in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were permeabilized using Digitonin wash buffer and functionalized on Concanavalin coated beads as described in Skene et al. dx.doi.org/10.17504/protocols.io.mgjc3un
Library preparation was performed as described in Skene et al. dx.doi.org/10.17504/protocols.io.mgjc3un by adapting NEBNext Ultra II DNA Library Prep kit and Unique Dual Index.

treatment_protocol: For TOP2A and TOP2B sample preparation: tIMEC, tIMEC-ANP32E and tIMEC-ANP32E-H1 cells were treated for 1h with Etoposide 5 μM (MedChemExpress HY-13629) in order to inhibit the release of Topoisomerases IIA and IIB and improve their immunoprecipitation as reported in Nat Genet. 2019 Jun;51(6):1011-1023.doi: 10.1038/s41588-019-0421-z

value: tIMEC

value: Basal-like breast cancer

value: ANP32E overexpression, RNaseH1 overexpression


title: Female Spleen Trametinib Biol Rep 3

description: Library name: Sample 98


title: TNF-PGE_24h_Rep1

description:
EC.US.5351_Male_TNF.PGE_24h_Rep1
rawcounts_PGE.txt


title: GVO_scRNA_KO.Kdm2b_dCxxC_3

value: fully grown germinal vesicle oocytes


title: Female Spleen Trametinib Biol Rep 2

description: Library name: Sample 97


title: tIMEC cells, ANP32E overexpression and acute RNaseH1 overexpression, rep1, Rloop

description: Library name: tIMEC-ANP32E-H1_acute_CUTnRUN_Rloop_R1


title: TNF-PGE_3h_Rep3

description:
EC.US.5803_Male_TNF.PGE_3h_Rep3
rawcounts_PGE.txt


title: Female Spleen Trametinib Biol Rep 1

description: Library name: Sample 96


title: GVO_scRNA_KO.Kdm2b_dCxxC_1


title: Male Spleen Trametinib Biol Rep 4

description: Library name: Sample 95


title: TNF-PGE_3h_Rep2

description:
EC.US.5803_Female_TNF.PGE_3h_Rep2
rawcounts_PGE.txt


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep3, H2A.Z, Abcam

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_H2AZ_Abcam_R3


title: GVO_scRNA_KO.Kdm2b_dCxxC_6


title: GVO_scRNA_KO.Kdm2b_dCxxC_5


title: TNF-PGE_24h_Rep2

description:
EC.US.5803_Female_TNF.PGE_24h_Rep2
rawcounts_PGE.txt


title: TNF-PGE_3h_Rep1

description:
EC.US.5351_Male_TNF.PGE_3h_Rep1
rawcounts_PGE.txt


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_20

value: Kdm2b flox-CxxC/flox-CxxC


title: Male Spleen Trametinib Biol Rep 3

description: Library name: Sample 94


title: TNF_24h_Rep3

description:
EC.US.5803_Male_TNF_24h_Rep3
rawcounts_PGE.txt


title: Male Spleen Trametinib Biol Rep 2

description: Library name: Sample 93


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_19


title: Male Spleen Trametinib Biol Rep 1

description: Library name: Sample 92


title: tIMEC cells, ANP32E overexpression and acute RNaseH1 overexpression, rep2, Rloop

description: Library name: tIMEC-ANP32E-H1_acute_CUTnRUN_Rloop_R2


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_18


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep3, pS2RNApolII, Abcam

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_pS2RNApolII_Abcam_R3


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep3, pS5RNApolII

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_totRNApolII_R3


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_17


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep3, pRPA32(S33)

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_pRPA32_R3


title: Female Spleen Rapamycin/Trametinib Biol Rep 5

description: Library name: Sample 91

value: rapamycin/trametinib


title: TNF_24h_Rep1

description:
EC.US.5351_Male_TNF_24h_Rep1
rawcounts_PGE.txt


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_16


title: Female Spleen Rapamycin/Trametinib Biol Rep 4

description: Library name: Sample 90

value: Spleen


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep3, Rloop

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_Rloop_R3


title: TNF_3h_Rep2

description:
EC.US.5803_Female_TNF_3h_Rep2
rawcounts_PGE.txt


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep3, TOP2A

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_TOP2A_R3

value: Etoposide 5 μM 1h MedChemExpress HY-13629


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_15


title: TNF_3h_Rep1

description:
EC.US.5351_Male_TNF_3h_Rep1
rawcounts_PGE.txt


title: Female Spleen Rapamycin/Trametinib Biol Rep 3

description: Library name: Sample 89

value: 24 months

value: Female


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep3, p400

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_p400_R3


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_14


title: PGE_24h_Rep3

description:
EC.US.5803_Male_PGE_24h_Rep3
rawcounts_PGE.txt


title: Female Spleen Rapamycin/Trametinib Biol Rep 2

description: Library name: Sample 88

value: C3B6F1 wild type


title: TNF_24h_Rep2

description:
EC.US.5803_Female_TNF_24h_Rep2
rawcounts_PGE.txt


title: Female Spleen Rapamycin/Trametinib Biol Rep 1

description: Library name: Sample 87


title: PGE_24h_Rep2

description:
EC.US.5803_Female_PGE_24h_Rep2
rawcounts_PGE.txt


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_12


title: Male Spleen Rapamycin/Trametinib Biol Rep 4

description: Library name: Sample 86


title: tIMEC cells, ANP32E and RNaseH1 overexpression, rep3, ANP32E, LSBio

description: Library name: tIMEC-ANP32E-H1_CUTnRUN_ANP32E_LSBio_R3


title: PGE_3h_Rep3

description:
EC.US.5803_Male_PGE_3h_Rep3
rawcounts_PGE.txt


title: TNF_3h_Rep3

description:
EC.US.5803_Male_TNF_3h_Rep3
rawcounts_PGE.txt


title: tIMEC cells, ANP32E overexpression, rep3, acH2A.Z

description: Library name: tIMEC-ANP32E_CUTnRUN_acH2AZ_R3

value: ANP32E overexpression


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_11


title: tIMEC cells, ANP32E overexpression, rep3, pS2RNApolII, Abcam

description: Library name: tIMEC-ANP32E_CUTnRUN_pS2RNApolII_Abcam_R3


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_10


title: Male Spleen Rapamycin/Trametinib Biol Rep 1

description: Library name: Sample 83


title: Male Spleen Rapamycin/Trametinib Biol Rep 2

description: Library name: Sample 84


title: Female Spleen Rapamycin Biol Rep 5

description: Library name: Sample 82

value: rapamycin


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_8


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_9


title: PGE_24h_Rep1

description:
EC.US.5351_Male_PGE_24h_Rep1
rawcounts_PGE.txt


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_13


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_7


title: tIMEC cells, ANP32E overexpression, rep3, pRPA32(S33)

description: Library name: tIMEC-ANP32E_CUTnRUN_pRPA32_R3


title: CTRL_24h_Rep2

description:
EC.US.5803_Female_CTRL_24h_Rep2
rawcounts_PGE.txt


title: Female Spleen Rapamycin Biol Rep 3

description: Library name: Sample 80


title: Female Spleen Rapamycin Biol Rep 4

description: Library name: Sample 81


title: tIMEC cells, ANP32E overexpression, rep3, H2A.Z, Abcam

description: Library name: tIMEC-ANP32E_CUTnRUN_H2AZ_Abcam_R3


title: tIMEC cells, ANP32E overexpression, rep3, Rloop

description: Library name: tIMEC-ANP32E_CUTnRUN_Rloop_R3


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_5


title: Male Spleen Rapamycin/Trametinib Biol Rep 3

description: Library name: Sample 85


title: Female Spleen Rapamycin Biol Rep 2

description: Library name: Sample 79


title: tIMEC cells, ANP32E overexpression, rep3, p400

description: Library name: tIMEC-ANP32E_CUTnRUN_p400_R3


title: tIMEC cells, ANP32E overexpression, rep3, TOP2A

description: Library name: tIMEC-ANP32E_CUTnRUN_TOP2A_R3


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_6


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_4


title: Female Spleen Rapamycin Biol Rep 1

description: Library name: Sample 78


title: CTRL_24h_Rep1

description:
EC.US.5351_Male_CTRL_24h_Rep1
rawcounts_PGE.txt


title: CTRL_3h_Rep1

description:
EC.US.5351_Male_CTRL_3h_Rep1
rawcounts_PGE.txt


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_2


title: PGE_3h_Rep2

description:
EC.US.5803_Female_PGE_3h_Rep2
rawcounts_PGE.txt


title: tIMEC cells, ANP32E overexpression, rep3, pS5RNApolII

description: Library name: tIMEC-ANP32E_CUTnRUN_totRNApolII_R3


title: CTRL_3h_Rep3

description:
EC.US.5803_Male_CTRL_3h_Rep3
rawcounts_PGE.txt


title: tIMEC cells, rep3, pS5RNApolII

description: Library name: tIMEC_CUTnRUN_totRNApolII_R3

value: WT


title: tIMEC cells, ANP32E overexpression, rep3, ANP32E, LSBio

description: Library name: tIMEC-ANP32E_CUTnRUN_ANP32E_LSBio_R3


title: CTRL_24h_Rep3

description:
EC.US.5803_Male_CTRL_24h_Rep3
rawcounts_PGE.txt


title: OSM.24h_HCA.7, rep1

city: South San Francisco

first: Juliette

last: Roels

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
RNA sequencing data was preprocessed with the Bioconductor package HTSeqGenie using default parameters. Reads were aligned to the GRCh38 human reference genome.
Differential expression analysis was performed with Limma Voom.
Assembly: GRCh38
Supplementary files format and content: csv file with raw counts

source_name: Colon

growth_protocol: HCA7 cells (obtained from the ECACC) were negativefor mycoplasma and authenticated by RNAseq analysis. Cells were cultured inRPMI-1640 medium with 10% FBS and 2mM L-Glutamineat 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
Total RNA was extracted using the Qiagen RNEasy Mini Kit.
0.1 ug of total RNA was used for library preparation using TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA).
Libraries were multiplexed and sequenced on Illumina HiSeq4000 (Illumina, San Diego, CA) to generate 30 million single-end 50 basepair reads.

treatment_protocol: Cells were stimulated for 24 hours with either PBS or 10 ng/ml human OSM (R&D Systems).

value: Colon

value: Cell Line

value: 10 ng/mL recombinant mouse OSM (in RPMI + 10%FBS + L-glu + pen/strep) for 24h


title: CTRL_3h_Rep2

description:
EC.US.5803_Female_CTRL_3h_Rep2
rawcounts_PGE.txt

value: CD14+ monocytes


title: tIMEC cells, rep3, H2A.Z, Abcam

description: Library name: tIMEC_CUTnRUN_H2AZ_Abcam_R3

value: tIMEC

value: Basal-like breast cancer


title: GVO_scRNA_Ctrl.Kdm2b_dCxxC_3

value: fully grown germinal vesicle oocytes


title: Male Kidney Control Biol Rep 5

description: Library name: Sample 73

source_name: Kidney

value: Kidney

value: Male

value: control


title: Male Spleen Rapamycin Biol Rep 4

description: Library name: Sample 77

value: Spleen


title: tIMEC cells, rep3, acH2A.Z

description: Library name: tIMEC_CUTnRUN_acH2AZ_R3


title: Male Spleen Rapamycin Biol Rep 3

description: Library name: Sample 76

value: 24 months


title: OSM.24h_HCA.7, rep3


title: tIMEC cells, rep3, pS2RNApolII, Abcam

description: Library name: tIMEC_CUTnRUN_pS2RNApolII_Abcam_R3


title: Male Spleen Rapamycin Biol Rep 2

description: Library name: Sample 75


title: OSM.24h_HCA.7, rep2


title: Control.24h_HCA.7, rep2

description: SAM24371791_2368535432_Control.24h_HCA.7

value: No treatment (RPMI + 10%FBS + L-glu + pen/strep only), 24h


title: tIMEC cells, rep3, TOP2A

description: Library name: tIMEC_CUTnRUN_TOP2A_R3

value: Etoposide 5 μM 1h MedChemExpress HY-13629


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_24

source_name: growing oocyte day 14

value: growing oocyte day 14

value: Kdm2a flox-JmJ/flox-JmJ; Kdm2b flox-JmJ/flox-JmJ;Zp3-cre


title: Male Kidney Control Biol Rep 3

description: Library name: Sample 71

value: C3B6F1 wild type


title: Control.24h_HCA.7, rep3

description: SAM24371792_2368535434_Control.24h_HCA.7

value: Colon


title: Male Spleen Rapamycin Biol Rep 1

description: Library name: Sample 74

value: rapamycin


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_23


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_22


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_20


title: Male Kidney Control Biol Rep 4

description: Library name: Sample 72


title: tIMEC cells, rep3, ANP32E, LSBio

description: Library name: tIMEC_CUTnRUN_ANP32E_LSBio_R3

value: WT


title: GO_day14_scRNA_KO.Kdm2a_KO.Kdm2b_KO_21


title: Control.24h_HCA.7, rep1

description: SAM24371790_2368535423_Control.24h_HCA.7

value: Cell Line


title: tIMEC cells, rep3, p400

description: Library name: tIMEC_CUTnRUN_p400_R3

value: tIMEC


title: Male Kidney Control Biol Rep 2

description: Library name: Sample 70