title: Heart, Chronic kidney disease (CKD), Male, 9175, Infarct

description: Library name: JUW03_35

value: CKD


title: Heart, Chronic kidney disease (CKD), Male, 9174, Infarct

status: Public on Apr 20 2026

type: SRA

city: Aachen

first: Julia

last: Wollenhaupt

address: Pauwelsstraße 30

department: Institute for Molecular Cardiovascular Research

country: Germany

institute: Uniklinik RWTH Aachen

description: Library name: JUW03_34

library_source: transcriptomic

data_processing:
Raw sequences from fastq files were aligned to the Ensembl reference mouse cDNA (GRCm39 v109) by kallisto (v0.48.0)
The transcript read counts were assembled to gene level using the R package tximport (v1.22.0) based on the Ensembl gene annotation GTF file (v109).
Only protein-coding genes and transcripts were included for further analysis based on the Ensembl gene annotation GTF file (v109).
Genes with an average count no more than 5 were filtered out.
Assembly: GRCm39 v109
Supplementary files format and content: Expression_read_counts.tsv
Supplementary files format and content: Tab-delimited text file includes read count values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: Heart infarct

growth_protocol: All animals were fed with a western type diet for 4 weeks. Then the Chronic kidney disease (CKD) group was fed with a western type diet containing 0.3% adenine for 10 days followed by a western type diet containing 0,15% adenine for additional 11 days (4 days before MI induction and 7 days post-MI). The control group received a western type diet for the entire period.

extract_protocol:
RNA was extracted by using the Qiagen RNeasy Micro Kit with inclusion of a DNAse-treatment step, all according to manufacturer's instructions.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

treatment_protocol: Cardiac tissue was rinsed with ice-cold PBS and snap-frozen in liquid nitrogen directly after organ explantation, after which it was stored at -80°C until RNA extraction.

tag: tissue

value: Heart infarct

tag: Sex

value: Male

tag: strain

tag: genotype

value: ApoE-/-

tag: treatment


title: Heart, Chronic kidney disease (CKD), Male, 9172, Infarct

description: Library name: JUW03_33


title: KCP_FOSL2_KO_RNA-seq_1

city: New York

first: Wilfred

last: Wong

state: NY

address: 430 E 67th St

country: USA

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
Transcriptome alignment by Salmon
Tximport to obtain transcript level quantification before gene summarization.
Differential expression by DESeq2 1.16.1
Assembly: hg19
Supplementary files format and content: tar of Salmon quantification

molecule: genomic DNA

organism: Homo sapiens

source_name: Pancreatic (hPSC derived)

growth_protocol: Pancreatic progenitor cells grown in PO condition were suspended in 30 ul of Matrigel dome and applied to the bottom of each well of non-tissue culture treated 48 well plate to solidify. The Matrigel dome was overlaid with 0.4 ml of DMEM-F12 base medium supplied with Glutamax, Penicillin/Streptomycin, B27TM supplement, 1mM N-acetyle-L-cystein, 10mM Nicotinamide, 0.5uM A83-01, 100ng/ml hNoggin, 50ng/ml hEGF, 10nM hGastrin I, 100ng/ml hFGF10, 500ng/ml Rsp1.

extract_protocol:
Total RNA was extracted using Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: POs were treated with doxycycline to introduce mutations. RNA was extracted from POs at paired passages across genotypes. In case of ERK inhbitor treatment,  LY3214996 was used at 1uM and POs were incubated for 4 days. DMSO was used as control.  KCP POs transduced with lentivirus coding the sgRNA against AP-1 factors were indicated.

value: Pancreatic (hPSC derived)

tag: cell line

tag: cell type

value: Pancreatic progenitor organoid

value: KCP with AP-1 KO

value: KCP at P8 were transduced with FOSL2 sgRNA and harvested 6 weeks later at P8+6


title: K_RNA-seq_2

value: K

value: K PO P21


title: Astrocyte, Control, rep1

city: Niigata-shi

first: Tokiharu

last: Sato

state: Niigata

address: 1-757 Asahimachidori, Chuo-ku

department: Department of System Pathology for Neurological Disorders

country: Japan

institute: Niigata University, Brain Research Institute

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-01

data_processing:
Raw sequence reads were trimmed and their quality was assessed by Trimmomatic (version 0.39) and FastQC (version 0.11.9) programs, respectively. Trimmed reads were then aligned to the mouse genome (GRCm39/m32) by the STAR aligner (version 2.7.9a) with default parameters. Read counts and transcript per million (TPM) values were calculated using RSEM program (version 1.3.1) at default setting.
Assembly: GRCm39/m32
Supplementary files format and content: tab-delimited text file including raw counts for each sample.

source_name: Cervical cord

extract_protocol:
mRNA extractions were performed by RiboTag-HA based immunoprecipitation and Rneasy Plus Micro kit (Qiagen).
cDNA libraries were prepared by the SMART-seq v4 Ultra Low Input RNA kit (TAKARA) and Nextera XT DNA Library Preparation kit (Illumina) according to manufacture’s instructions.

value: Cervical cord

value: Control


title: KCP_FOSL1_KO_RNA-seq_2

value: KCP at P8 were transduced with FOSL1 sgRNA and harvested 7 weeks later at P8+7


title: KCP_FOSL1_KO_RNA-seq_3

value: KCP at P8 were transduced with FOSL1 sgRNA and harvested 8 weeks later at P8+8


title: K_RNA-seq_1

value: K PO P20


title: Heart, Control, Male, 9171, Infarct

description: Library name: JUW03_32


title: Heart, Control, Male, 9170, Infarct

description: Library name: JUW03_31


title: Astrocyte, Control, rep2

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-02


title: Astrocyte, Control, rep3

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-03


title: KCP_JUNB_KO_RNA-seq_1

value: KCP at P8 were transduced with JUNB sgRNA and harvested 6 weeks later at P8+6


title: K_RNA-seq_3

value: K PO P22


title: V2a, Day 28, rep3

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-15

value: Day 28


title: Astrocyte, Day 3, rep1

description:
2 × 75 bp paired-end
Aldh1l1.txt
Aldh1l1-04

value: Day 3


title: GFP_RNA-seq_3

value: GFP control

value: GFP PO P22


title: KCP_FOS_KO_RNA-seq_3

value: Pancreatic (hPSC derived)

value: KCP at P8 were transduced with FOS sgRNA and harvested 8 weeks later at P8+8


title: GFP_RNA-seq_2

value: Pancreatic progenitor organoid

value: GFP PO P21


title: KCP_FOSL1_KO_RNA-seq_1

value: KCP with AP-1 KO

value: KCP at P8 were transduced with FOSL1 sgRNA and harvested 6 weeks later at P8+6


title: KCP_FOSL2_KO_RNA-seq_2

value: KCP at P8 were transduced with FOSL2 sgRNA and harvested 7 weeks later  at P8+7


title: Heart, Control, Male, 9184, Remote

description: Library name: JUW03_30

source_name: Heart remote

value: Heart remote

value: Male

value: ApoE-/-

value: Control


title: KCP_FOS_KO_RNA-seq_2

value: KCP at P8 were transduced with FOS sgRNA and harvested 7 weeks later at P8+7


title: Heart, Control, Male, 9183, Remote

description: Library name: JUW03_29


title: GFP_RNA-seq_1

value: GFP PO P20


title: V2a, Day 28, rep2

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-14

value: Cervical cord

value: Day 28


title: ATAC_KCPS_2

data_processing:
Align to hg19 reference genome using bowtie2-2.4.1
Peak calling to generate signal tracks on on individual replicates using macs2 2.2.7.1 with options -B -p 1e-2 -f BAMPE
Assembly: hg19
Supplementary files format and content: Coverage track in bigWig format

growth_protocol: POs were suspended in 30 ul of Matrigel dome and applied to the bottom of each well of non-tissue culture treated 48 well plate to solidify. The Matrigel dome was overlaid with 0.4 ml of DMEM-F12 base medium supplied with Glutamax, Penicillin/Streptomycin, B27TM supplement, 1mM N-acetyle-L-cystein, 10mM Nicotinamide, 0.5uM A83-01, 100ng/ml hNoggin, 50ng/ml hEGF, 10nM hGastrin I, 100ng/ml hFGF10, 500ng/ml Rsp1.

extract_protocol:
Organoids were extracted from the matrigel by cell recovery solution, trypsinized into single cell suspension. 50,000 cells were lysed in ATAC lysis buffer and tagmented based on omni-ATAC-seq protocol.
ATAC libraries were prepared for sequencing using standard Illumina Nextera DNA Library Preparation protocols.

treatment_protocol: In case of ERK inhbitor treatment,  LY3214996 was used at 1uM and POs were incubated for 4 days. DMSO was used as control.

value: KCPS


title: ATAC_KCP_2

value: KCP


title: V2a, Day 14, rep1

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-10

value: Day 14


title: V2a, Day 14, rep2

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-11


title: Heart, Chronic kidney disease (CKD), Male, 9177, Remote

description: Library name: JUW03_24

value: CKD


title: KCP_NT_RNA-seq_3

value: Pancreatic (hPSC derived)

value: Pancreatic progenitor organoid

value: KCP with control sgRNA

value: KCP at P8 were transduced with control sgRNA and harvested 8 weeks later  at P8+8


title: Heart, Chronic kidney disease (CKD), Male, 9178, Remote

description: Library name: JUW03_25


title: ATAC_KCPS_1


title: Heart, Chronic kidney disease (CKD), Male, 9176, Remote

description: Library name: JUW03_23


title: HBMECs, OE_CircOGDH 3

city: Guangzhou,

first: Wei

last: Chen

state: Guangdong

address: Huangpu Avenue West

country: China

institute: Jinan University First Affiliated Hospital

data_processing:
The libraries were purified by DNA clean beads (VAHTS DNA Clean Beads, N411) for size selection for 200-300 bp fragments. and analyzed on Agilent 2100 Bioanalyzer (Agilent) for measuring fragment size distribution. The qualified libraries were sequenced on Illumina Nova Seq 6000.
Assembly: hg38
Supplementary files format and content: fpkm and fastq

source_name: Blood vessels

extract_protocol:
RNA was harvested using Trizol method.1.5 ug of total RNA was used for the construction of sequencing libraries.
The resultant RNAs samples were reverse-transcribed for library construction with NEB Next® VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina, NR604.

value: Blood vessels

value: HBMECs

value: Human Brain Microvascular Endothelial Cells

value: CircOGDH overexpression

value: no


title: KCP_FOS_KO_RNA-seq_1

value: KCP with AP-1 KO

value: KCP at P8 were transduced with FOS sgRNA and harvested 6 weeks later at P8+6


title: ATAC_KCP_1


title: Heart, Chronic kidney disease (CKD), Male, 9179, Remote

description: Library name: JUW03_26

value: Heart remote

value: Male

value: ApoE-/-

value: Control


title: V2a, Day 7, rep3

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-09

value: Cervical cord

value: Day 7


title: KCP_NT_RNA-seq_1

value: Pancreatic (hPSC derived)

value: KCP at P8 were transduced with control sgRNA and harvested 6 weeks later  at P8+6


title: V2a, Day 14, rep3

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-12

value: Day 14


title: Heart, Control, Male, 9182, Remote

description: Library name: JUW03_28


title: KCP_NT_RNA-seq_2

value: Pancreatic progenitor organoid

value: KCP with control sgRNA

value: KCP at P8 were transduced with control sgRNA and harvested 7 weeks later  at P8+7


title: Heart, Control, Male, 9180, Remote

description: Library name: JUW03_27


title: HBMECs, OE_CircOGDH 2

value: Blood vessels

value: HBMECs

value: Human Brain Microvascular Endothelial Cells


title: ATAC_KP_2

value: KP


title: ATAC_KP_1


title: V2a, Day 28, rep1

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-13

value: Day 28


title: V2a, Day 7, rep1

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-07


title: Heart, Chronic kidney disease (CKD), Male, 9175, Remote

description: Library name: JUW03_22

value: Heart remote

value: CKD


title: V2a, Day 7, rep2

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-08


title: ATAC_KC_2

value: KC


title: V2a, Day 3, rep3

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-06

value: Day 3


title: ATAC_KC_1


title: Heart, Chronic kidney disease (CKD), Male, 9174, Remote

description: Library name: JUW03_21

value: Male

value: ApoE-/-


title: HBMECs, OE_CircCtrl  3

value: CircCtrl

value: no


title: V2a, Day 3, rep2

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-05

value: Cervical cord


title: Heart, Chronic kidney disease (CKD), Male, 9173, Remote

description: Library name: JUW03_20


title: HBMECs, OE_CircCtrl  2


title: ATAC_K_1

value: Pancreatic (hPSC derived)

value: Pancreatic progenitor organoid

value: K


title: V2a, Control, rep3

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-03

value: Control


title: ATAC_K_2


title: Heart, Control, Male, 9170, Remote

description: Library name: JUW03_17


title: Heart, Control, Male, 9171, Remote

description: Library name: JUW03_18


title: V2a, Control, rep2

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-02


title: HBMECs, OE_CircOGDH 1

value: Blood vessels

value: HBMECs

value: CircOGDH overexpression


title: HBMECs, OE_CircCtrl  1

value: Human Brain Microvascular Endothelial Cells


title: V2a, Control, rep1

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-01


title: ATAC_GFP_2

value: GFP (control)


title: mESC_SE_OHT_Suv39h1/2;Setdb1-TKO_Input_spike-in_lot7

status: Public on Apr 19 2026

city: Suita-shi, Osaka

first: Ryo

last: Maeda

address: Yamadaoka 1-3

institute: The University of Osaka

description: Library name: SE-OHT-lot7_Inp

data_processing:
Sequence reads were trimmed to remove possible adapter sequences using fastp (0.23.4) and were mapped to mm10+Dux using Bowtie2 with the following parameters: --no-mixed --no-discordant --no-unal. The bigwig files were generated using bamCompare in deepTools (3.5.2) with the following parameters: -bs $bin --smoothLength $sm --operation ratio --ignoreDuplicates, where $bin is binsize, $sm is 3x$bin. For spike-in ChIP-seq analysis, the sequence reads were also mapped to Drosophila (dm6) using Bowtie2. PCR-duplicated reads were removed using the rmdup command in samtools. Spike-in scaling factors were calculated using a reference-adjusted method (53). Briefly, the ratio of mm10 to dm6 mapped reads was calculated for each sample, and the scaling factor (SF) was determined as follows:  SF = (Reads_mm10_ChIP / Reads_dm6_ChIP) / (Reads_mm10_Input / Reads_dm6_Input)  Spike-normalized bigWig files were generated in two steps. First, ChIP/Input ratio bigWig files were generated using bamCompare in deepTools with the following parameters: -bs $bin --smoothLength $sm --operation ratio. Second, spike-in normalization was applied using bigwigCompare with the same file as both inputs and the following parameters: -b1 sample.bw -b2 sample.bw --operation first --scaleFactors SF:1.0. Replicate samples were integrated by averaging each normalized count using bigwigAverage in deepTools and used for subsequent analyses.
Samples are paired by lot number, where Input and ChIP samples from the same biological replicate share the same lot designation (e.g., mESC_33-6_NT_control_Input_lot1 corresponds to mESC_33-6_NT_control_H3K9me2_lot1).
Assembly: mm10 (+Dux)
Supplementary files format and content: bigWig normalized with Input

source_name: mESCs

growth_protocol: mESCs were maintained in Dulbecco’s Modified Eagle’s Medium (Nacalai Tesque, Japan) containing 10% knockout SR (Invitrogen, USA), 1% fetal calf serum, 1% sodium pyruvate (Gibco, USA), 1% Minimum Essential Medium Non-Essential Amino Acids (Gibco), and 103 U/mL of ESGRO leukemia-inhibiting factor (Millipore, USA) 2x104 U Penicillin-Streptomycin (Thermo Fisher Scientific, USA) and 50 μg Amphotericin B (Sigma-Aldrich, USA). We established a series of H3K9 MTs-deficient mESC lines: the previously established 4OHT-inducible Setdb1-KO (33#6) (Matsui et al 2010), Suv39h1/2-DKO (SE), and Suv39h1/2/G9a-triple KO (TKO) (3S1G) lines (Maeda and Tachibana 2022), and a newly generated G9a-KO (SG) line.

extract_protocol:
mESCs and S2 cells were cross-linked with 25 mM DSG (Thermo Fisher Scientific) for 40 min, followed by 1% formaldehyde for 15 min, and then quenched with 100 mM glycine. Cells were lysed in ChIP Lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.5% NP-40, and protease inhibitor cocktail (Roche, USA)). The precipitate was suspended in SDS buffer (50 mM Tris-HCl pH8.0, 1% SDS, 10 mM EDTA) and 3x volume of 1% Triton buffer (15 mM Tris-HCl pH8.0, 150 mM NaCl, 1 mM EDTA, 1% TritonX-100 and protease inhibitor cocktail) and sonicated using Picoruptor (Diagenode). For spike-in quantification, an aliquot was reverse cross-linked in Salting Method Buffer (20 mM Tris-HCl pH8.0, 400 mM NaCl, 10 mM EDTA, 0.5% SDS) and incubated at 2 h for 60℃. DNA was purified using ChIP DNA Clean and Concentration Kit (Zymo Research, USA), and quantified using Qubit dsDNA High sensitivity Quantification Assay Kit (Thermo Fisher Scientific). mESC and S2 extracts were mixed 9:1 (DNA content) and incubated with 1 μg antibody-bound Sera-Mag SpeedBeads Protein A/G (Cytiva, USA) for 2 h at 4℃. For Lamin B1 spike-in ChIP-seq, 1 μg of anti-Lamin B1 antibody was used together with 0.5 μg of anti-H2Av antibody. Beads were washed sequentially with Low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), High salt buffer (same, 500 mM NaCl), LiCl buffer (10 mM Tris-HCl pH 8.0, 25 mM LiCl, 1 mM EDTA, 1% deoxycholate), and TE buffer (20 mM Tris-HCl pH 8.0, 1 mM EDTA). Chromatin complexes were eluted by Proteinase K (1 mg/mL in Salting Method Buffer, 60°C, 2 h), and DNA was purified using ChIP DNA Clean and Concentration Kit.
ChIP and input DNA were end-repaired, ligated to sequencing adapters, and amplified using ThruPLEX DNA-Seq Kit (TaKaRa). After size-selection and purification with AMPure XP beads (Beckman Coulter, USA), DNA libraries were sequenced with 150-nt paired-end reads on the Illumina Novaseq X Plus (illumina).

treatment_protocol: For conditional KO of Setdb1, mESC lines were cultured in the presence of 800 nM 4OHT (Sigma-Aldrich) for 96 hours.

value: mESCs

tag: chip antibody

value: Input


title: Crtc2+/+, NASH diet

city: tianjin

first: zhanjie

last: xiu

address: HUANHU XI ROAD, TIYUAN BEI, HEXI DISTRICT

institute: TIANJIN MEDICAL UNIVERSITY CANCER INSTITUTE & HOSPITAL

description:
Library name: Sample1
10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat 10, 11. In brief, for each gene and each cell barcode, unique molecule identifiers were counted to construct digital expression matrices. A gene with expression in more than 3 cells was considered convinced, and each cell was required at least 200 expressed genes.
Assembly: mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
Tumors from liver were collected for single-cell RNA sequencing.
The tumors cell suspension was loaded into Chromium microfluidic chips with 3’ chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2 reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (HiSeq 2000) according to the manufacturer’s instructions (Illumina).

treatment_protocol: The Crtc2+/+ and Crtc2-/- mice were intraperitoneally injected with DEN (25 mg/ kg) at age of 2-weeks old. Mice maintain NASH diet from 8 to 26 week and sacrificed after 26 weeks.

value: liver

value: Tumors from liver


title: mESC_SE_OHT_Suv39h1/2;Setdb1-TKO_Input_spike-in_lot4

description: Library name: SE-OHT-lot4_Inp


title: Heart, Chronic kidney disease (CKD), Male, 9172, Remote

description: Library name: JUW03_19

value: Heart remote

value: Male

value: ApoE-/-

value: CKD


title: mESC_SE_OHT_Suv39h1/2;Setdb1-TKO_Input_spike-in_lot1

description: Library name: SE-OHT-lot1_Inp


title: V2a, Day 3, rep1

description:
2 × 75 bp paired-end
Chx10.txt
Chx10-04

value: Cervical cord

value: Day 3


title: Crtc2-/-, NASH diet

description:
Library name: Sample2
10X Genomics


title: ATAC_GFP_1

value: Pancreatic (hPSC derived)

value: Pancreatic progenitor organoid


title: mESC_SE_NT_Suv39h1/2-DKO_Input_spike-in_lot1

description: Library name: SE-NT-lot1_Inp


title: mESC_3S1G_OHT_G9a;Suv39h1/2;Setdb1-QKO_Input_spike-in_lot7

description: Library name: 3S1G-OHT-lot7_Inp


title: mESC_SE_NT_Suv39h1/2-DKO_Input_spike-in_lot4

description: Library name: SE-NT-lot4_Inp


title: mESC_3S1G_OHT_G9a;Suv39h1/2;Setdb1-QKO_Input_spike-in_lot1

description: Library name: 3S1G-OHT-lot1_Inp


title: mESC_3S1G_NT_G9a;Suv39h1/2-TKO_Input_spike-in_lot7

description: Library name: 3S1G-NT-lot7_Inp


title: mESC_3S1G_NT_G9a;Suv39h1/2-TKO_Input_spike-in_lot4

description: Library name: 3S1G-NT-lot4_Inp


title: mESC_3S1G_OHT_G9a;Suv39h1/2;Setdb1-QKO_Input_spike-in_lot4

description: Library name: 3S1G-OHT-lot4_Inp


title: mESC_TT2_LaminB1_lot4

description: Library name: TT2_lot4_P12987

data_processing:
Sequence reads were trimmed to remove possible adapter sequences using FastP (0.23.4) and were mapped to the mm10 genomic sequence containing Dux cluster sequence (mm10+Dux) using Bowtie2 with the following parameters: --no-mixed --no-discordant --no-unal. The bigwig files were generated using bamCompare in deepTools (3.5.2) with the following parameters: -bs $bin --smoothLength $sm --operation ratio --ignoreDuplicates, where $bin is binsize, $sm is 3x$bin.
Samples are paired by lot number, where Input and ChIP samples from the same biological replicate share the same lot designation (e.g., mESC_Inp_lot1 corresponds to mESC_H3K9me3_lot1).
Assembly: mm10 (+Dux)
Supplementary files format and content: bigWig normalized with Input

growth_protocol: mESCs were maintained in Dulbecco’s Modified Eagle’s Medium (Nacalai Tesque, Japan) containing 10% knockout SR (Invitrogen, USA), 1% fetal calf serum, 1% sodium pyruvate (Gibco, USA), 1% Minimum Essential Medium Non-Essential Amino Acids (Gibco), and 103 U/mL of ESGRO leukemia-inhibiting factor (Millipore, USA) 2x104 U Penicillin-Streptomycin (Thermo Fisher Scientific, USA) and 50 μg Amphotericin B (Sigma-Aldrich, USA).

extract_protocol:
mESCs were cross-linked with 25 mM DSG (Thermo Fisher Scientific) for 40 min at RT, followed by 1% formaldehyde for 15 min at RT, and then quenched with 100 mM glycine. Cells were lysed with ChIP Lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.5% NP-40, and protease inhibitor cocktail (Roche, USA)). The precipitate was suspended in SDS buffer (50 mM Tris-HCl pH8.0, 1% SDS, 10 mM EDTA) and 3x volume of 1% Triton buffer (15 mM Tris-HCl pH8.0, 150 mM NaCl, 1 mM EDTA, 1% TritonX-100 and protease inhibitor cocktail), then sonicated using Picoruptor (Diagenode, USA). To quantify the amount of DNA for spike-in ChIP, a portion of the sonicated cell extract was mixed with 2x volume of Salting Method Buffer (20 mM Tris-HCl pH8.0, 400 mM NaCl, 10 mM EDTA, 0.5% SDS) and incubated at 2 h for 60℃. DNA was purified using ChIP DNA Clean and Concentration Kit (Zymo Research, USA), and DNA concentration was determined using Qubit dsDNA High sensitivity Quantification Assay Kit (Thermo Fisher Scientific). Extracts from mESCs and S2 cells were mixed at a ratio of 9:1 (DNA content) and incubated for 2 h at 4℃ with antibodies that were pre-incubated with Sera-Mag SpeedBeads Protein A/G Magnetic Particles (Cytiva, USA). The samples were washed consecutively with Low buffer (20 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton-X100), High buffer (20 mM Tris-HCl pH8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton-X100), LiCl buffer (10 mM Tris-HCl pH8.0, 25 mM LiCl, 1mM EDTA, 1% Deoxycolate), TE buffer (20 mM Tris-HCl pH8.0, 1 mM EDTA). The chromatin-immune complex was treated with 1mg/mL Proteinase K in Salting Method Buffer for 2 h at 60℃. DNA was purified using ChIP DNA Clean and Concentration Kit.
ChIP and input DNA were end-repaired, ligated to sequencing adapters, and amplified using ThruPLEX DNA-Seq Kit (TaKaRa). After size-selection and purification with AMPure XP beads (Beckman Coulter, USA), DNA libraries were sequenced with 150-nt paired-end reads on the Illumina Novaseq X Plus (illumina).

value: wild-type

value: LAMIN B1 (12987-1-AP, Proteintech)


title: mESC_3S1G_NT_G9a;Suv39h1/2-TKO_Input_spike-in_lot1

description: Library name: 3S1G-NT-lot1_Inp


title: mESC_TT2_H3K9me2_lot5

description: Library name: TT2_lot5_ab1220

value: H3K9me2 (ab1220, Abcam)


title: mESC_SE_NT_Suv39h1/2-DKO_Input_spike-in_lot7

description: Library name: SE-NT-lot7_Inp


title: mESC_TT2_Input_lot3

description: Library name: TT2_lot3_Inp


title: mESC_TT2_Input_lot2

description: Library name: TT2_lot2_Inp


title: mESC_TT2_Input_lot5

description: Library name: TT2_lot5_Inp


title: mESC_TT2_H3K9me3_lot3

description: Library name: TT2_lot3_39162

value: H3K9me3 (39162, ActiveMotif)


title: mESC_TT2_Input_lot1

description: Library name: TT2_lot1_Inp


title: mESC_TT2_LaminB1_lot2

description: Library name: TT2_lot2_P12987


title: mESC_TT2_H3K9me2_lot1

description: Library name: TT2_lot1_ab1220


title: mESC_TT2_Input_lot4

description: Library name: TT2_lot4_Inp


title: mESC_SE_OHT_Suv39h1/2;Setdb1-TKO_H3K9me2_spike-in_lot7

description: Library name: SE-OHT-lot7_ab1220


title: mESC_TT2_H3K9me3_lot1

description: Library name: TT2_lot1_39162


title: mESC_3S1G_OHT_G9a;Suv39h1/2;Setdb1-QKO_H3K9me2_spike-in_lot7

description: Library name: 3S1G-OHT-lot7_ab1220


title: mESC_3S1G_NT_G9a;Suv39h1/2-TKO_H3K9me2_spike-in_lot7

description: Library name: 3S1G-NT-lot7_ab1220


title: mESC_SE_OHT_Suv39h1/2;Setdb1-TKO_H3K9me2_spike-in_lot4

description: Library name: SE-OHT-lot4_ab1220


title: mESC_SE_OHT_Suv39h1/2;Setdb1-TKO_LaminB1_spike-in_lot4

description: Library name: SE-OHT-lot4_P12987

value: LAMIN B1 (12987-1-AP, Proteintech) & H2Av (61751, Active Motif)


title: mESC_SE_OHT_Suv39h1/2;Setdb1-TKO_H3K9me2_spike-in_lot1

description: Library name: SE-OHT-lot1_ab1220

value: mESCs


title: mESC_SE_OHT_Suv39h1/2;Setdb1-TKO_LaminB1_spike-in_lot1

description: Library name: SE-OHT-lot1_P12987


title: mESC_SE_NT_Suv39h1/2-DKO_LaminB1_spike-in_lot1

description: Library name: SE-NT-lot1_P12987


title: mESC_SE_NT_Suv39h1/2-DKO_H3K9me2_spike-in_lot1

description: Library name: SE-NT-lot1_ab1220


title: mESC_3S1G_OHT_G9a;Suv39h1/2;Setdb1-QKO_LaminB1_spike-in_lot4

description: Library name: 3S1G-OHT-lot4_P12987


title: mESC_SE_NT_Suv39h1/2-DKO_H3K9me2_spike-in_lot4

description: Library name: SE-NT-lot4_ab1220


title: mESC_3S1G_OHT_G9a;Suv39h1/2;Setdb1-QKO_LaminB1_spike-in_lot1

description: Library name: 3S1G-OHT-lot1_P12987


title: mESC_3S1G_OHT_G9a;Suv39h1/2;Setdb1-QKO_H3K9me2_spike-in_lot4

description: Library name: 3S1G-OHT-lot4_ab1220


title: mESC_SE_NT_Suv39h1/2-DKO_H3K9me2_spike-in_lot7

description: Library name: SE-NT-lot7_ab1220


title: mESC_3S1G_NT_G9a;Suv39h1/2-TKO_H3K9me2_spike-in_lot4

description: Library name: 3S1G-NT-lot4_ab1220


title: mESC_3S1G_OHT_G9a;Suv39h1/2;Setdb1-QKO_H3K9me2_spike-in_lot1

description: Library name: 3S1G-OHT-lot1_ab1220


title: mESC_3S1G_NT_G9a;Suv39h1/2-TKO_LaminB1_spike-in_lot1

description: Library name: 3S1G-NT-lot1_P12987


title: RNA_E2C_Kdm3ab-mDKO_mCherry-injection_rep2

description: Library name: E2C_Kdm3ab-mDKO_mCherry-injection_rep2

data_processing:
Sequence reads were first mapped to the mm10 genomic sequence containing Dux cluster sequence (mm10+Dux) using STAR (2.7.10b) with the following parameters: --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100 --outSAMmultNmax 1 --runRNGseed 7 --outMultimapperOrder Random --outReadsUnmapped Fastx --outSAMattributes All --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif (for unstranded RNA-seq data). Because a few reads were mapped to Dux cluster locus in mm10+Dux, the unmapped reads were then mapped to mm10+Dux using Bowtie2 (2.3.4.1) with the following parameters: --no-mixed --no-discordant --no-unal. Using bam file aligned to mm10 transcriptome by STAR, read counts of each gene were calculated using RSEM (1.3.1) with the following parameters: --alignments --estimate-rspd –strandedness [none or reverse] --paired-end (for paired-end). After combining bam files generated with STAR and Bowtie2, read counts of Obox4, Obox8, and Dux were calculated using the count command in samtools (1.9). For Dux, the sum of mapped reads in each Dux locus was used as Dux read count. For Obox4, the sum of mapped reads in Obox4 locus having full-length open reading frame was used as Obox4 read count. Transcripts per million (TPM) were calculated for individual genes.
Assembly: mm10 (+Dux)
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

molecule: polyA RNA

source_name: preimplantation embryo

growth_protocol: We generated oocyte-specific Kdm3a/b conditional double knockout females (Zp3-Cre; Kdm3af/f; Kdm3bf/f). Oocytes from these females were subjected to in vitro fertilization with wild-type sperm to obtain embryos lacking maternal KDM3A/B (Kdm3a/b-mDKO).

extract_protocol:
For RNA-seq of early embryos, 12-20 embryos were pooled per sample. The zona pellucida was removed using acidic Tyrode's solution. Samples were washed three times in 0.2% BSA/PBS, then transferred to 0.1-ml tubes with 0.5 μl residual fluid.
cDNA libraries were prepared using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) for MII oocytes, SMART-Seq v4 Ultra-Low-Input RNA Kit for Sequencing (Takara) or its successor, SMART-Seq mRNA LP (Takara) for E2C and 4C embryos. Libraries were sequenced with paired-end reads on the NextSeq 500, HiSeq 2000, or NovaSeq X Plus (Illumina).

tag: developmenta stage

value: early 2-cell

value: preimplantation embryo

value: maternel Kdm3a/b-DKO


title: RNA_E2C_Kdm3ab-mDKO_Kdm3aWT-injection_rep2

description: Library name: E2C_Kdm3ab-mDKO_Kdm3aWT-injection_rep2


title: mESC_SE_NT_Suv39h1/2-DKO_LaminB1_spike-in_lot4

description: Library name: SE-NT-lot4_P12987


title: RNA_E2C_Kdm3ab-mDKO_Kdm3aHA-injection_rep2

description: Library name: E2C_Kdm3ab-mDKO_Kdm3aHA-injection_rep2


title: RNA_E2C_control_mCherry-injection_rep1

description: Library name: E2C_control_mCherry-injection_rep1

value: control


title: RNA_E2C_Kdm3ab-mDKO_mCherry-injection_rep1

description: Library name: E2C_Kdm3ab-mDKO_mCherry-injection_rep1


title: RNA_E2C_Kdm3ab-mDKO_Kdm3aWT-injection_rep1

description: Library name: E2C_Kdm3ab-mDKO_Kdm3aWT-injection_rep1


title: RNA_E2C_Kdm3ab-mDKO_Kdm3aHA-injection_rep1

description: Library name: E2C_Kdm3ab-mDKO_Kdm3aHA-injection_rep1


title: mESC_3S1G_NT_G9a;Suv39h1/2-TKO_LaminB1_spike-in_lot4

description: Library name: 3S1G-NT-lot4_P12987


title: RNA_4C_WT_mCherry-injection_rep1

description: Library name: 4C_WT_mCherry-injection_rep1


title: RNA_4C_WT_mCherry-injection_rep2

description: Library name: 4C_WT_mCherry-injection_rep2


title: RNA_4C_WT_Kdm3aWT-injection_rep2

description: Library name: 4C_WT_Kdm3aWT-injection_rep2


title: mESC_3S1G_NT_G9a;Suv39h1/2-TKO_H3K9me2_spike-in_lot1

description: Library name: 3S1G-NT-lot1_ab1220


title: RNA_4C_WT_Kdm3aHA-injection_rep2

description: Library name: 4C_WT_Kdm3aHA-injection_rep2


title: RNA_E2C_control_mCherry-injection_rep2

description: Library name: E2C_control_mCherry-injection_rep2


title: RNA_4C_WT_Kdm3aHA-injection_rep1

description: Library name: 4C_WT_Kdm3aHA-injection_rep1


title: D49 Ctrl 2

city: He Fei

first: Yu

last: Hang

address: 宿松路

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 21
D49-Con-2

data_processing:
The fragments were mapped to the ensemble mouse reference genome GRCm39 (version 2020) using the STAR aligner.
Differential expression analysis (DESeq2) identified significant genes (fold change > 2 or < -2, p < 0.05).
Assembly: genome GRCm39 (version 2020)
Supplementary files format and content: Ctrl AMs-LPS AMs-RNAseq.xlsx
Supplementary files format and content: Exel file including raw counts for each Sample

source_name: Alveolar macrophages

extract_protocol:
The cells were lysed in 100 μL of TRIzol and total RNA was extracted with a miRNeasy Micro Kit (Qiagen).
Bulk RNA sequencing was conducted on 4.5–7.5 × 10⁴ alveolar macrophages (AMs) that were pooled from 3–5 individual replicates for each condition. For samples yielding ≥ 100 ng of total RNA, libraries were conducted using the VAHTS Universal V8 RNA-seq Library Prep Kit (Illumina). Poly(A) mRNA was isolated using Oligo(dT) magnetic beads, fragmented via divalent cations and high temperature, and primed with random primers to synthesize first-strand and second-strand cDNA. The purified double-stranded cDNA underwent end repair and dA-tailing in a single reaction, followed by T-A ligation for adaptor attachment to both ends. Size selection of adaptor-ligated DNA was conducted using DNA purification beads, and each sample was PCR-amplified with P5 and P7 primers. Finally, the PCR products were subjected to quality validation.

treatment_protocol: AMs were stimulated for 4 hours with IMDM medium containing 400 ng/mL lipopolysaccharide (LPS) from E. coli 055:B5 (InvivoGen, tlrl-b5lps) or in LPS-free medium (as control) for 4 hours.

value: Alveolar macrophages

value: without LPS


title: D49 LPS 2

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 24
D49-LPS-2

value: with LPS


title: D49 Ctrl 1

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 20
D49-Con-1


title: D49 LPS 1

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 23
D49-LPS-1


title: D21 Ctrl 3

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 17
D21-Con-3


title: D21 Ctrl 2

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 16
D21-Con-2


title: D21 LPS 2

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 19
D21-LPS-2


title: RNA_4C_WT_Kdm3aWT-injection_rep1

description: Library name: 4C_WT_Kdm3aWT-injection_rep1


title: D21 LPS 1

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 18
D21-LPS-1


title: D3 LPS 2

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 10
D3-LPS-2


title: D7 LPS 1

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 13
D7-LPS-1


title: D21 Ctrl 1

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 15
D21-Con-1


title: D7 LPS 2

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 14
D7-LPS-2


title: D3 LPS 1

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 9
D3-LPS-1


title: D49 Ctrl 3

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 22
D49-Con-3


title: D3 Ctrl 2

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 7
D3-Con-2


title: D7 Ctrl 2

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 12
D7-Con-2


title: D1 LPS 1

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 3
D1-LPS-1


title: D3 Ctrl 3

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 8
D3-Con-3


title: D7 Ctrl 1

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 11
D7-Con-1


title: D1 Ctrl 1

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 1
D1-Con-1


title: D1 LPS 3

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 5
D1-LPS-3


title: D1 Ctrl 2

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 2
D1-Con-2


title: D1 LPS 2

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 4
D1-LPS-2


title: mESC_SG_NT_G9a-KO_H3K9me2_spike-in_lot7

description: Library name: SG-NT-lot7_ab1220

data_processing:
Sequence reads were trimmed to remove possible adapter sequences using FastP (0.23.4) and were mapped to the mm10 genomic sequence containing Dux cluster sequence (mm10+Dux) using Bowtie2 with the following parameters: --no-mixed --no-discordant --no-unal. The bigwig files were generated using bamCompare in deepTools (3.5.2) with the following parameters: -bs $bin --smoothLength $sm --operation ratio --ignoreDuplicates, where $bin is binsize, $sm is 3x$bin. For spike-in ChIP-seq analysis, the sequence reads were also mapped to dm6 using Bowtie2. After PCR-duplicated reads were removed using the rmdup command in samtools, normalization factors were calculated as described previously (Orlando et al 2014). Briefly, the normalization factor was calculated as follows: Normalization factor = 1/Nd where Nd is the total number of reads mapped to dm6. Spike-normalized bigwig files were generated using bamCompare in deepTools with the following parameters: -bs $bin --smoothLength $sm --scaleFactorsMethod None --operation ratio --scaleFactors $sf, where $sf is the normalization factor. Replicate samples were integrated by averaging each normalized count using bigwigAverage in deepTools and used for subsequent analyses.
Assembly: mm10 (+Dux)
Supplementary files format and content: bigWig normalized with Input

growth_protocol: mESCs were maintained in Dulbecco’s Modified Eagle’s Medium (Nacalai Tesque, Japan) containing 10% knockout SR (Invitrogen, USA), 1% fetal calf serum, 1% sodium pyruvate (Gibco, USA), 1% Minimum Essential Medium Non-Essential Amino Acids (Gibco), and 103 U/mL of ESGRO leukemia-inhibiting factor (Millipore, USA) 2x104 U Penicillin-Streptomycin (Thermo Fisher Scientific, USA) and 50 μg Amphotericin B (Sigma-Aldrich, USA). We established a series of H3K9 MTs-deficient mESC lines: the previously established 4OHT-inducible Setdb1-KO (#33-6) (Matsui et al 2010), Suv39h1/2-DKO (SE), and Suv39h1/2/G9a-triple KO (TKO) (3S1G) lines (Maeda and Tachibana 2022), and a newly generated G9a-KO (SG) line.


title: mESC_SG_OHT_G9a;Setdb1-DKO_H3K9me2_spike-in_lot7

description: Library name: SG-OHT-lot7_ab1220


title: mESC_SG_OHT_G9a;Setdb1-DKO_Input_spike-in_lot7

description: Library name: SG-OHT-lot7_Inp

value: Input


title: mESC_33-6_NT_control_Input_spike-in_lot7

description: Library name: 33-6-NT-lot7_Inp


title: mESC_33-6_OHT_Setdb1-KO_H3K9me2_spike-in_lot7

description: Library name: 33-6-OHT-lot7_ab1220


title: mESC_SG_OHT_G9a;Setdb1-DKO_LaminB1_spike-in_lot4

description: Library name: SG-OHT-lot4_P12987


title: D3 Ctrl 1

institute: 合肥综合性国家科学中心大健康研究院

description:
Library name: Sample 6
D3-Con-1


title: mESC_33-6_OHT_Setdb1-KO_Input_spike-in_lot7

description: Library name: 33-6-OHT-lot7_Inp


title: mESC_SG_OHT_G9a;Setdb1-DKO_H3K9me2_spike-in_lot4

description: Library name: SG-OHT-lot4_ab1220


title: mESC_33-6_NT_control_H3K9me2_spike-in_lot7

description: Library name: 33-6-NT-lot7_ab1220


title: mESC_SG_OHT_G9a;Setdb1-DKO_LaminB1_spike-in_lot1

description: Library name: SG-OHT-lot1_P12987


title: mESC_SG_OHT_G9a;Setdb1-DKO_Input_spike-in_lot1

description: Library name: SG-OHT-lot1_Inp


title: mESC_SG_OHT_G9a;Setdb1-DKO_Input_spike-in_lot4

description: Library name: SG-OHT-lot4_Inp


title: mESC_SG_NT_G9a-KO_Input_spike-in_lot7

description: Library name: SG-NT-lot7_Inp


title: mESC_SG_NT_G9a-KO_H3K9me2_spike-in_lot4

description: Library name: SG-NT-lot4_ab1220


title: mESC_SG_NT_G9a-KO_Input_spike-in_lot1

description: Library name: SG-NT-lot1_Inp


title: mESC_SG_NT_G9a-KO_LaminB1_spike-in_lot4

description: Library name: SG-NT-lot4_P12987


title: mESC_SG_NT_G9a-KO_LaminB1_spike-in_lot1

description: Library name: SG-NT-lot1_P12987


title: mESC_SG_NT_G9a-KO_Input_spike-in_lot4

description: Library name: SG-NT-lot4_Inp


title: mESC_SG_OHT_G9a;Setdb1-DKO_H3K9me2_spike-in_lot1

description: Library name: SG-OHT-lot1_ab1220


title: mESC_33-6_OHT_Setdb1-KO_H3K9me2_spike-in_lot1

description: Library name: 33-6-OHT-lot1_ab1220


title: mESC_33-6_NT_control_Input_spike-in_lot4

description: Library name: 33-6-NT-lot4_Inp


title: mESC_33-6_OHT_Setdb1-KO_Input_spike-in_lot4

description: Library name: 33-6-OHT-lot4_Inp


title: mESC_SG_NT_G9a-KO_H3K9me2_spike-in_lot1

description: Library name: SG-NT-lot1_ab1220


title: mESC_33-6_NT_control_LaminB1_spike-in_lot4

description: Library name: 33-6-NT-lot4_P12987


title: mESC_33-6_OHT_Setdb1-KO_LaminB1_spike-in_lot1

description: Library name: 33-6-OHT-lot1_P12987


title: mESC_33-6_OHT_Setdb1-KO_H3K9me2_spike-in_lot4

description: Library name: 33-6-OHT-lot4_ab1220


title: mESC_33-6_OHT_Setdb1-KO_Input_spike-in_lot1

description: Library name: 33-6-OHT-lot1_Inp


title: mESC_33-6_NT_control_H3K9me2_spike-in_lot4

description: Library name: 33-6-NT-lot4_ab1220


title: mESC_33-6_NT_control_Input_spike-in_lot1

description: Library name: 33-6-NT-lot1_Inp


title: mESC_33-6_OHT_Setdb1-KO_LaminB1_spike-in_lot4

description: Library name: 33-6-OHT-lot4_P12987


title: mESC_33-6_NT_control_LaminB1_spike-in_lot1

description: Library name: 33-6-NT-lot1_P12987


title: RNA_mESC_3S1Gi_OHT_Tet-on-Dux:G9a;Suv39h1/2;Setdb1-QKO_dox1_rep2

description:
Library name: 3S1G-OHT_dox1_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X3S1G_OHT_dox1_rep2

extract_protocol:
Total RNA was extracted from mESCs using AllPrep DNA/RNA Mini Kit (Qiagen, Netherlands).
cDNA libraries were prepared using the TruSeq stranded mRNA Library Preparation kit (Illumina, USA). The libraries were sequenced with 150 nt paired-end reads on the Novaseq 6000 (Illumina).


title: mESC_33-6_NT_control_H3K9me2_spike-in_lot1

description: Library name: 33-6-NT-lot1_ab1220


title: RNA_mESC_3S1Gi_OHT_Tet-on-Dux:G9a;Suv39h1/2;Setdb1-QKO_dox0_rep1

description:
Library name: 3S1G-OHT_dox0_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X3S1G_OHT_dox0_rep1


title: RNA_mESC_3S1Gi_OHT_Tet-on-Dux:G9a;Suv39h1/2;Setdb1-QKO_dox0_rep2

description:
Library name: 3S1G-OHT_dox0_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X3S1G_OHT_dox0_rep2


title: RNA_mESC_3S1Gi_NT_Tet-on-Dux:G9a;Suv39h1/2-TKO_dox1_rep2

description:
Library name: 3S1G-NT_dox1_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X3S1G_NT_dox1_rep2


title: RNA_mESC_3S1Gi_OHT_Tet-on-Dux:G9a;Suv39h1/2;Setdb1-QKO_dox1_rep1

description:
Library name: 3S1G-OHT_dox1_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X3S1G_OHT_dox1_rep1


title: RNA_mESC_SGi_OHT_Tet-on-Dux:G9a;Setdb1-DKO_dox1_rep2

description:
Library name: SG-OHT_dox1_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SG_OHT_dox1_rep2


title: RNA_mESC_3S1Gi_NT_Tet-on-Dux:G9a;Suv39h1/2-TKO_dox0_rep2

description:
Library name: 3S1G-NT_dox0_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X3S1G_NT_dox0_rep2


title: RNA_mESC_SGi_OHT_Tet-on-Dux:G9a;Setdb1-DKO_dox0_rep2

description:
Library name: SG-OHT_dox0_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SG_OHT_dox0_rep2


title: RNA_mESC_3S1Gi_NT_Tet-on-Dux:G9a;Suv39h1/2-TKO_dox0_rep1

description:
Library name: 3S1G-NT_dox0_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X3S1G_NT_dox0_rep1


title: RNA_mESC_SGi_OHT_Tet-on-Dux:G9a;Setdb1-DKO_dox1_rep1

description:
Library name: SG-OHT_dox1_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SG_OHT_dox1_rep1


title: RNA_mESC_SGi_NT_Tet-on-Dux:G9a-KO_dox1_rep2

description:
Library name: SG-NT_dox1_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SG_NT_dox1_rep2


title: RNA_mESC_SEi_NT_Tet-on-Dux:Suv39h1/2-DKO_dox1_rep2

description:
Library name: SEZ17-NT_dox1_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SE_NT_dox1_rep2


title: RNA_mESC_3S1Gi_NT_Tet-on-Dux:G9a;Suv39h1/2-TKO_dox1_rep1

description:
Library name: 3S1G-NT_dox1_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X3S1G_NT_dox1_rep1


title: pebS cells, Day4, sample 3

city: Setagaya-ku

first: Satoru

last: Watanabe

state: Tokyo

address: 1-1-1 Sakuragaoka

institute: Tokyo University of Agriculture

description: Library name: PEBS_4d_3

data_processing:
CLC Genomics Workbench ver. 25.0.2
Raw reads were trimmed and quality-filtered (parameter-Quality limit:0.05)
Trimmed reads were mapped to the all genes in Synechococcus 7942 (accession number: CP000100, CP000101) as well as to plasmids carrying FDBR (pBNS_pebAB, pBNS_pebS, and pBNS_pcyX, Supporting information).
Gene expression levels were normalized and quantified as transcripts per million (TPM).
Assembly: CLC Genomics Workbench ver. 25.0.2
Supplementary files format and content: tab-delimited text file inclueds raw counts for each sample

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: PebS over expression

growth_protocol: The cyanobacterium Synechococcus 7942 WT strain and its derivatives were grown photoautotrophically at 30°C under continuous WL illumination (60 μmol photons m−2·s−1) with continuous bubbling of 2% CO2.

extract_protocol:
Total RNA was extracted from exponentially growing cultures of cyanobacteria using PGTX extraction method as previously descrived.
Ribosomal RNA was removed using NEBNext rRNA Depletion Kit (Bacteria) (New England Biolabs). Sequencing libraries with an average insert size of approximately 200 bp were prepared according to the manufacturer's instructions using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs).

value: PebS over expression


title: tumor-49 CpG Epic450k-probeID

city: Geneva

first: Nahuel

last: Simonet

address: 9 chemin des Mines

country: Switzerland

institute: EPFL

description:
Library name: tumor-49_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request

data_processing:
Basecalls were performed using bases2fastq version 1.8.0. Nextera adapters were trimmed with minimal read length tolerated post-trimming: 35 bp.
CUT&Tag-BS/EM data  data were processed using an adapted WGBS pipeline from snakePipes. In brief, sequence alignment was performed using BWAMETH2, which relies on the BWA-MEM as the underlying aligner.  The resulting alignment BAM files were converted to bigwig files using bamCoverage from deepTools. and subsequently scaled based on the number of reads mapped to the spike-in regions.
CpG dinucleotide methylation profiles in the peaks were extracted from the resulting BAM files using MethylDackel60, with the following parameters: --mergeContext, --maxVariantFrac 0.1, --minDepth 5.
CpG methylation calls (MethylDackel output in Bismark coverage format) were lifted over from hg38 to hg19 and intersected with Illumina EPIC 450k probe coordinates.
Assembly: hg19
Supplementary files format and content: bedMethyl

source_name: Genomic DNA from patient

extract_protocol:
DNA-Methylation CUT&Tag For DNA methylation profiling of purified DNA, 50 ng of starting material was used, and MBD-Tn5 cutting was directly induced after a 2-hour binding period without any additional washes. After 1 hr at 37 °C, the reaction was stopped by adding a final concentration of 20 mM EDTA, 0.5% SDS, and 10 mg Proteinase K. The reaction was then incubated at 55 °C for 30 min and finally inactivated at 70 °C for 20 min. The DNA fragments were purified using the ChIP DNA Clean & Concentrator kit (Zymo Research, #D5205). For elution from the columns, 2 pg of Tn5-digested and purified lambda DNA (New England Biolabs, #N3011S) were added as a spike-in normalizer for later analysis.
CUT&Tag based

value: Genomic DNA from patient

value: Tumor biopsy


title: RNA_mESC_SEi_OHT_Tet-on-Dux:Suv39h1/2;Setdb1-TKO_dox0_rep1

description:
Library name: SEZ17-OHT_dox0_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SE_OHT_dox0_rep1


title: Ovarian stroma, unfertilized

city: Qingdao

first: Xinlin

last: Yang

state: Shandong

address: Yushan

institute: Ocean University of China

description:
Library name: Lib_Unfert
Single-cell transcriptome of unfertilized ovarian stroma

data_processing:
The demultiplexing, barcode processing, and gene counting were performed using the Cell Ranger software v9.1.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: Sebastes schlegelii (ASM1467356v1)
Supplementary files format and content: Tab-separated values files (.tsv.gz) and matrix files (.mtx.gz)

organism: Sebastes schlegelii

source_name: ovarian stroma

extract_protocol:
After MS-222 anesthesia and blood removal via the caudal vein, ovaries were dissected into ice-cold PBS and perfused to minimize residual blood. Oocytes or embryos were carefully microdissected to isolate pure ovarian stroma. Approximately 3 mL of minced stromal tissue was digested in 10 mL Trypsin-EDTA (0.25% trypsin, 0.02% EDTA) with gentle trituration for 4 min at room temperature. Digestion was quenched using Leibovitz’s L-15 supplemented with 10% FBS. The cell suspension was filtered through a 40 μm strainer, centrifuged at 400g for 6 min at 4°C, washed once, and resuspended in ice-cold PBS. Cell concentration and viability were assessed using 0.4% trypan blue staining and a hemocytometer.
Single-cell gene-expression libraries were prepared using the Chromium Next GEM Single Cell 3′ v3.1 workflow (10x Genomics) according to the manufacturer’s instructions. Gel beads carrying unique molecular identifiers (UMIs) and cell barcodes were loaded near saturation. After lysis, polyadenylated RNAs hybridized to bead-bound oligo-dT primers. Emulsions were broken and beads were recovered for reverse transcription. During cDNA synthesis, each molecule was tagged at the 5’ end with its UMI and cell barcode. Bead-bound cDNA underwent second-strand synthesis, adaptor ligation, and universal amplification. Libraries were constructed from randomly fragmented whole-transcriptome amplification products. All remaining steps followed the standard 10x Genomics protocol. Libraries were quantified and sequenced on an Illumina NovaSeq X Plus platform with 2x150 bp paired-end reads.

value: ovarian stroma


title: Ovarian stroma, abnormal-gestation

description:
Library name: Lib_Abnormal
Single-cell transcriptome of abnormal-gestation ovarian stroma


title: RNA_mESC_SGi_OHT_Tet-on-Dux:G9a;Setdb1-DKO_dox0_rep1

description:
Library name: SG-OHT_dox0_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SG_OHT_dox0_rep1


title: pebS cells, Day4, sample 1

description: Library name: PEBS_4d_1


title: RNA_mESC_SGi_NT_Tet-on-Dux:G9a-KO_dox0_rep2

description:
Library name: SG-NT_dox0_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SG_NT_dox0_rep2


title: RNA_mESC_SEi_NT_Tet-on-Dux:Suv39h1/2-DKO_dox1_rep1

description:
Library name: SEZ17-NT_dox1_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SE_NT_dox1_rep1


title: pebS cells, Day4, sample 2

description: Library name: PEBS_4d_2


title: pcyX cells, Day4, sample 1

description: Library name: PCYX_4d_1

source_name: PcyX over expression

value: PcyX over expression


title: RNA_mESC_SEi_OHT_Tet-on-Dux:Suv39h1/2;Setdb1-TKO_dox0_rep2

description:
Library name: SEZ17-OHT_dox0_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SE_OHT_dox0_rep2


title: RNA_mESC_SEi_NT_Tet-on-Dux:Suv39h1/2-DKO_dox0_rep2

description:
Library name: SEZ17-NT_dox0_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SE_NT_dox0_rep2


title: Ovarian stroma, normal-gestation

description:
Library name: Lib_Normal
Single-cell transcriptome of normal-gestation ovarian stroma


title: tumor-48 CpG Epic450k-probeID

description:
Library name: tumor-48_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: pcyX cells, Day4, sample 3

description: Library name: PCYX_4d_3


title: 9:NC+VC

type: RNA

city: Tokyo

first: Akihito

last: Ishigami

address: 35-2 Sakae-cho, Itabashi-ku

institute: Tokyo Metropolitan Institute for Geriatrics and Gerontology

description: Gene expression data from non-treated cells

hyb_protocol: Samples were hybridized to Clariom™ D Assay, rat (Thermo Fisher Scientific).

scan_protocol: The arrays were scanned on a GeneChip Scanner 3000 7G instrument (Thermo Fisher Scientific),.

data_processing: Raw data were normalized by the signal space transformation robust multichip analysis (SST-RMA) algorithm, and quality checks such as labelling and hybridization were performed using Transcriptome Analysis Console (TAC) v4.0.3 (Thermo Fisher Scientific).

label: Biotin

organism: Rattus norvegicus

source_name: Newborn rat epidermal keratinocytes

label_protocol: Labelled cDNA samples were prepared from total RNA using a GeneChip WT PLUS Reagent Kit (Thermo Fisher Scientific).

growth_protocol: Newborn rat epidermal keratinocytes were used in this study. Cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10 % fetal bovine serum , 0.4 µg/mL hydrocortisone, and 1 % penicillin-streptomycin at 37 °C in a humidified atmosphere with 5 % CO₂.

extract_protocol: RNA samples were purified using the RNeasy Mini Kit (QIAGEN, Hilden, Germany).

treatment_protocol: Cells were transfected with or without the combined two siRNAs (1 µM siTet2 + 1 µM siTet3 per well) using Lipofectamine 3000 transfection reagent. After transfection for 24 h, the cells were treated with vitamin C for 12 h before the assays.

value: Newborn rat epidermal keratinocytes

value: vitamin C


title: PEB1 cells, Day4, sample 1

description: Library name: PEBAB1_4d_1

source_name: PebA-PebB over expression

value: PebA-PebB over expression


title: RNA_mESC_SEi_NT_Tet-on-Dux:Suv39h1/2-DKO_dox0_rep1

description:
Library name: SEZ17-NT_dox0_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SE_NT_dox0_rep1

value: mESCs


title: RNA_mESC_SEi_OHT_Tet-on-Dux:Suv39h1/2;Setdb1-TKO_dox1_rep2

description:
Library name: SEZ17-OHT_dox1_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SE_OHT_dox1_rep2


title: 10:siTet2/3+VC

description: Gene expression data from Tet2/3 knockdown-induced cells


title: RNA_mESC_SEi_OHT_Tet-on-Dux:Suv39h1/2;Setdb1-TKO_dox1_rep1

description:
Library name: SEZ17-OHT_dox1_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SE_OHT_dox1_rep1


title: pcyX cells, Day4, sample 2

description: Library name: PCYX_4d_2


title: tumor-47 CpG Epic450k-probeID

description:
Library name: tumor-47_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: WT cells, Day4, sample 1

description: Library name: WT_4d_1

source_name: WT (control)

value: WT (control)


title: tumor-46 CpG Epic450k-probeID

description:
Library name: tumor-46_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: PEB1 cells, Day4, sample 3

description: Library name: PEBAB1_4d_3


title: RNA_mESC_33i_OHT_Tet-on-Dux:Setdb1-KO_dox0.2_rep2

description:
Library name: 33-6-OHT_dox02_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X33.6_OHT_dox02_rep2


title: tumor-45 CpG Epic450k-probeID

description:
Library name: tumor-45_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: mESC-2000cells_H3K9me2

description: Library name: mESC-2000cells_H3K9me2

data_processing:
Sequence reads were trimmed to remove possible adapter sequences using fastp (0.23.4) and were mapped to mm10+Dux using Bowtie2 with the following parameters: --no-mixed --no-discordant --no-unal. The bigwig files were generated using bamCompare in deepTools (3.5.2) with the following parameters: -bs $bin --smoothLength $sm --operation ratio --ignoreDuplicates, where $bin is binsize, $sm is 3x$bin.
Assembly: mm10 (+Dux)
Supplementary files format and content: bigWig normalized with Input.

growth_protocol: mESCs were cultured on irradiated primary mouse embryonic fibroblast feeder layers in DMEM (Wako) supplemented with 20% fetal bovine serum (Biowest), MEM non-essential amino acids (Gibco), GlutaMAX (Gibco), 2-mercaptoethanol (Gibco), penicillin-streptomycin (Gibco), HEPES (Gibco), leukemia inhibitory factor (LIF; Sigma-Aldrich), L-arginine HCl, L-asparagine H2O, SU5402 (2 µM), PD184352 (0.8 µM), and CHIR99021 (3 µM), and maintained at 37°C in 5% CO2.

extract_protocol:
Fully grown oocytes (FGOs) were obtained from 4-week-old hormonally stimulated female mice. Ovaries were transferred to HEPES-buffered KSOM containing 0.2 mM IBMX, follicles were punctured, and cumulus cells were removed mechanically using a narrow-bore glass pipette. For embryo collection, females were superovulated and subjected to in vitro fertilization. Zygotes with two pronuclei were cultured in KSOM to the indicated stages. For CATCH-seq sample collection, polar bodies were removed as described previously (Hayashi and Inoue, 2023). Early two-cell and morula embryos were collected at 20 and 72 h post-insemination, respectively. mESCs were harvested in 9 µl of Nuclei EZ lysis buffer (Sigma) containing protease inhibitor cocktail and 1 mM PMSF. Sample preparation was conducted by adding 1 µl of lysis buffer, followed by 1 µl of detergent mixture (1% Triton X-100 and 1% deoxycholate) and incubating on ice for 5 min. Chromatin fragmentation was performed using 2 U/µl MNase (NEB) in 1× MNase buffer supplemented with 1% PEG6000 and 2 mM dithiothreitol at 21°C for 7.5 min. Digestion was terminated by the addition of 1:10 volume of 100 mM EDTA and 1:12 volume of detergent mixture, followed by 15 min incubation on ice. The chromatin lysates were supplemented with immunoprecipitation buffer (20 mmol/L Tris-HCl (pH 8.0), 2 mmol/L EDTA, 150 mmol/L NaCl, 0.1% Triton X-100, 1× EDTA-free protease inhibitor cocktail, and 0.1 mmol/L PMSF), with 5% volume reserved for input library construction. To the remaining lysate, 30 ng of annealed I-SceI carrier DNA was added. The forward and reverse strands of the carrier DNA were as follows: /5AmMC6/Gtagggataacagggtaattagggataacagggtaattagggataacagggtaattagggataacagggtaattagggataacagggtaattagggataacagggtaatc/3AmMO/ and /5AmMC6/Gattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatccctac/3AmMO/, respectively, where asterisks represent phosphorothioate bonds. For immunoprecipitation reactions, we utilized 0.5 µg of mouse anti-H3K9me2 (MABI0317) conjugated to pre-cleared Dynabeads Protein G mixture. Following overnight immunoprecipitation at 4°C, the chromatin-bead complexes were washed sequentially with low-salt buffer (20 mmol/L Tris-HCl (pH 8.0), 0.1% SDS, 1% Triton X-100, 2 mmol/L EDTA, 150 mmol/L NaCl, 1× EDTA-free proteinase inhibitor cocktail, and 0.1 mmol/L PMSF) and high-salt buffer (20 mmol/L Tris-HCl (pH 8.0), 0.1% SDS, 1% Triton X-100, 2 mmol/L EDTA, 500 mmol/L NaCl, 1× EDTA-free proteinase inhibitor cocktail, and 0.1 mmol/L PMSF), and the chromatin was eluted in ChIP elution buffer (100 mmol/L NaHCO3 and 1% SDS) at 65°C for 1 h. DNA was recovered by phenol-chloroform extraction followed by ethanol precipitation. For comparisons between Kdm3a/b-mDKO embryos and control embryos at the E2C stage, we implemented spike-in normalization by adding a constant number of Drosophila S2 cells during cell lysis and 4 pg of Saccharomyces genomic DNA after chromatin elution.
Adaptor ligation was performed using NEBNext Ultra II DNA Library Prep kit (NEB) at half-scale, and the libraries were purified by 1.8× SPRIselect beads (Beckman Coulter). The DNA was amplified by KAPA Hifi 2X master PCR mix for 13-15 PCR cycles with dual indexing primers. After purification with 0.9× SPRIselect beads, the samples were digested by I-SceI (5 U/µl) at 37°C for 2 h followed by heat inactivation at 65°C for 20 min and purified by 0.9× SPRIselect beads. DNA libraries were sequenced with paired-end reads on the NextSeq2000 (illumina).

tag: developmental stage

value: embryonic stem cell

value: wild-type


title: tumor-44 CpG Epic450k-probeID

description:
Library name: tumor-44_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: PEB1 cells, Day4, sample 2

description: Library name: PEBAB1_4d_2


title: mESC-2000cells_Input

description: Library name: mESC-2000cells_Inp


title: WT cells, Day4, sample 2

description: Library name: WT_4d_2


title: WT cells, Day4, sample 3

description: Library name: WT_4d_3


title: RNA_mESC_33i_OHT_Tet-on-Dux:Setdb1-KO_dox0_rep1

description:
Library name: 33-6-OHT_dox0_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X33.6_OHT_dox0_rep1


title: RNA_mESC_33i_OHT_Tet-on-Dux:Setdb1-KO_dox0.2_rep1

description:
Library name: 33-6-OHT_dox02_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X33.6_OHT_dox02_rep1


title: RNA_mESC_33i_OHT_Tet-on-Dux:Setdb1-KO_dox0_rep2

description:
Library name: 33-6-OHT_dox0_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X33.6_OHT_dox0_rep2


title: mESC-500cells_H3K9me2

description: Library name: mESC-500cells_H3K9me2


title: RNA_mESC_33i_NT_Tet-on-Dux:control_dox0.2_rep2

description:
Library name: 33-6-NT_dox02_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X33.6_NT_dox02_rep2


title: tumor-43 CpG Epic450k-probeID

description:
Library name: tumor-43_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: mESC-500cells_Input

description: Library name: mESC-500cells_Inp


title: WS1-Mock, rpt4

city: Yokohama

first: June-Sik

last: Kim

state: Kanagawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

institute: RIKEN CSRS

description: Library name: WS-Mock-4

data_processing:
The resulting reads were quality-filtered using Trimmomatic-v0.39 with default parameters.
The cleaned reads were aligned to the transcripts of the wheat reference genome RefSeq-v2.1 using the selective alignment method of Salmon-v1.10.0 with default parameters.
Assembly: RefSeq v2.1 (GCF_018294505.1)
Supplementary files format and content: A gzip-compressed file containing Salmon-derived digital transcriptome profiles.

organism: Triticum aestivum

source_name: whole seedling

growth_protocol: The seeds were imbibed on Petri dishes and incubated for two days in a growth chamber. Five seedlings were then transplanted into 7.5-cm pots containing 85 g of soil and grown under well-watered conditions on trays for three weeks in 22 ˚C / 17 ˚C of 16h day / 8h night.

extract_protocol:
Total RNA was extracted following the manufacturer’s instructions for TRIzol Reagent (Thermo Fisher Scientific).
The mRNA was isolated from total RNA samples using NEXTFLEX Poly(A) Beads 2.0 (PerkinElmer), and sequencing libraries were prepared using the NEXTFLEX Rapid Directional RNA-Seq Kit 2.0 (PerkinElmer).

treatment_protocol: Ten-day-old wheat seedlings were sprayed with 15 mL of either mock solution (0.05% Tween 20 + DMSO) or ABA solution (0.05% Tween 20 + 50 µM ABA). Samples were collected 24 hours after treatment.

value: whole seedling

value: mock


title: tumor-42 CpG Epic450k-probeID

description:
Library name: tumor-42_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: RNA_mESC_SGi_NT_Tet-on-Dux:G9a-KO_dox0_rep1

description:
Library name: SG-NT_dox0_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SG_NT_dox0_rep1


title: tumor-41 CpG Epic450k-probeID

description:
Library name: tumor-41_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: RNA_L2C_Kdm3ab-DKO_rep2

description: Library name: L2C_Kdm3abDKO_rep2

extract_protocol:
For RNA-seq of early embryos, 20 embryos were pooled per sample. The zona pellucida was removed using acidic Tyrode's solution. Samples were washed three times in 0.2% BSA/PBS, then transferred to 0.1-ml tubes with 0.5 μl residual fluid.
cDNA libraries were prepared using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) for MII oocytes, SMART-Seq v4 Ultra-Low-Input RNA Kit for Sequencing (Takara) or its successor, SMART-Seq mRNA LP (Takara) for E2C embryos. Libraries were sequenced with paired-end reads on the NextSeq 500 or Hiseq 2000 (Illumina).

value: late 2-cell

value: preimplantation embryo

value: maternel Kdm3a/b-DKO


title: RNA_mESC_33i_NT_Tet-on-Dux:control_dox0.2_rep1

description:
Library name: 33-6-NT_dox02_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X33.6_NT_dox02_rep1


title: WS1-Mock, rpt3

description: Library name: WS-Mock-3


title: RNA_L2C_Kdm3ab-DKO_rep1

description: Library name: L2C_Kdm3abDKO_rep1


title: RNA_mESC_33i_NT_Tet-on-Dux:control_dox0_rep2

description:
Library name: 33-6-NT_dox0_rep2
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X33.6_NT_dox0_rep2


title: tumor-40 CpG Epic450k-probeID

description:
Library name: tumor-40_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: WS1-Mock, rpt2

description: Library name: WS-Mock-2


title: WS1-Mock, rpt1

description: Library name: WS-Mock-1


title: RNA_mESC_SGi_NT_Tet-on-Dux:G9a-KO_dox1_rep1

description:
Library name: SG-NT_dox1_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: SG_NT_dox1_rep1


title: RNA_L2C_control_rep2

description: Library name: L2C_Ctrl_rep2

value: control


title: RNA_L2C_control_rep1

description: Library name: L2C_Ctrl_rep1


title: tumor-39 CpG Epic450k-probeID

description:
Library name: tumor-39_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request

value: Genomic DNA from patient


title: RNA_mESC_33i_NT_Tet-on-Dux:control_dox0_rep1

description:
Library name: 33-6-NT_dox0_rep1
Column name in raw counts TPM_mESC_33-6s_DuxKO_TetOnDux.txt: X33.6_NT_dox0_rep1


title: tumor-38 CpG Epic450k-probeID

description:
Library name: tumor-38_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request

value: Tumor biopsy


title: WS1-ABA, rpt3

description: Library name: WS-ABA-3

value: ABA


title: WS1-ABA, rpt4

description: Library name: WS-ABA-4


title: RNA_mESC_3S1G_OHT_G9a;Suv39h1/2;Setdb1-QKO_rep2

description:
Library name: 3S1G_OHT_rep2
Column name in raw counts TPM_mESC_33-6s.txt: X3S1G_OHT_rep2


title: RNA_mESC_3S1Gx_OHT_Dux-KO:G9a;Suv39h1/2;Setdb1-QKO_rep1

description:
Library name: 3S1G_OHT-gDux_rep1
Column name in raw counts TPM_mESC_33-6s.txt: X3S1G_DuxKO_OHT_rep1


title: tumor-37 CpG Epic450k-probeID

description:
Library name: tumor-37_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: FGO_H3K9me3_rep2

description: Library name: FGO_K9me3_rep2

data_processing:
Sequence reads were trimmed to remove possible adapter sequences using fastp (0.23.4) and were mapped to mm10+Dux using Bowtie2 with the following parameters: --no-mixed --no-discordant --no-unal. The bigwig files were generated using bamCompare in deepTools (3.5.2) with the following parameters: -bs $bin --smoothLength $sm --operation ratio --ignoreDuplicates, where $bin is binsize, $sm is 3x$bin. For spike-in ChIP-seq analysis, the sequence reads were also mapped to Drosophila (dm6) or Saccharomyces (sacCer3) genomic sequences using Bowtie2. PCR-duplicated reads were removed using the rmdup command in samtools. Spike-in scaling factors were calculated using a reference-adjusted method (Orlando et al Cell Rep 2014). For spike-in CATCH-seq samples (E2C Ctrl and Kdm3a/b-DKO), where Saccharomyces genomic DNA was not added to Input samples, the Input ratio was set to 1. Briefly, the ratio of mm10 to sacCer3 mapped reads was calculated for each sample, and the scaling factor (SF) was determined as follows:  SF = (Reads_mm10_ChIP/ Reads_sacCer3_ChIP) / 1  Spike-normalized bigWig files were generated in two steps. First, ChIP/Input ratio bigWig files were generated using bamCompare in deepTools with the following parameters: -bs $bin --smoothLength $sm --operation ratio. Second, spike-in normalization was applied using bigwigCompare with the same file as both inputs and the following parameters: -b1 sample.bw -b2 sample.bw --operation first --scaleFactors SF:1.0. Replicate samples were integrated by averaging each normalized count using bigwigAverage in deepTools and used for subsequent analyses.
Assembly: mm10 (+Dux)
Supplementary files format and content: bigWig normalized with Input. For control vs. Kdm3a/b-mDKO E2C comparison, spike-in normalized data are shown.

source_name: oocyte

growth_protocol: CATCH-seq was performed as described previously (Zhu et al. 2021; Matsuwaka et al. 2024). For superovulation, 4- to 10-week-old BDF1 females (Jackson Laboratory) were injected with 7.5 IU pregnant mare serum gonadotropin (ASKA Pharmaceutical) followed by 7.5 IU human chorionic gonadotropin (hCG) (ASKA Pharmaceutical) 48 hours later. The cumulus-oocyte complexes were harvested 15–17 h after hCG injection and inseminated with activated spermatozoa from PWK/PhJ males [RBRC00213 (RIKEN BioResource Research Center)] in Human Tubal Fluid medium with 10 mg/ml BSA. Zygotes with two pronuclei were cultured in KSOM at 37.8°C under 5% CO2.

extract_protocol:
The generated BDF1×PWK hybrid embryos were harvested in 9 µl of Nuclei EZ lysis buffer (Sigma) containing protease inhibitor cocktail and 1 mM PMSF. Sample preparation was conducted by adding 1 µl of lysis buffer, followed by 1 µl of detergent mixture (1% Triton X-100 and 1% deoxycholate) and incubating on ice for 5 min. Chromatin fragmentation was performed using 2 U/µl MNase (NEB) in 1× MNase buffer supplemented with 1% PEG6000 and 2 mM dithiothreitol at 21°C for 7.5 min. Digestion was terminated by the addition of 1:10 volume of 100 mM EDTA and 1:12 volume of detergent mixture, followed by 15 min incubation on ice. The chromatin lysates were supplemented with immunoprecipitation buffer (20 mmol/L Tris-HCl (pH 8.0), 2 mmol/L EDTA, 150 mmol/L NaCl, 0.1% Triton X-100, 1× EDTA-free protease inhibitor cocktail, and 0.1 mmol/L PMSF), with 5% volume reserved for input library construction. To the remaining lysate, 30 ng of annealed I-SceI carrier DNA was added. The forward and reverse strands of the carrier DNA were as follows: /5AmMC6/Gtagggataacagggtaattagggataacagggtaattagggataacagggtaattagggataacagggtaattagggataacagggtaattagggataacagggtaatc/3AmMO/ and /5AmMC6/Gattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatccctac/3AmMO/, respectively, where asterisks represent phosphorothioate bonds. For immunoprecipitation reactions, we utilized 0.5 µg of mouse anti-H3K9me2 (MABI0317 (47)) conjugated to pre-cleared Dynabeads Protein G mixture. Following overnight immunoprecipitation at 4°C, the chromatin-bead complexes were washed sequentially with low-salt buffer (20 mmol/L Tris-HCl (pH 8.0), 0.1% SDS, 1% Triton X-100, 2 mmol/L EDTA, 150 mmol/L NaCl, 1× EDTA-free proteinase inhibitor cocktail, and 0.1 mmol/L PMSF) and high-salt buffer (20 mmol/L Tris-HCl (pH 8.0), 0.1% SDS, 1% Triton X-100, 2 mmol/L EDTA, 500 mmol/L NaCl, 1× EDTA-free proteinase inhibitor cocktail, and 0.1 mmol/L PMSF), and the chromatin was eluted in ChIP elution buffer (100 mmol/L NaHCO3 and 1% SDS) at 65°C for 1 h. DNA was recovered by phenol-chloroform extraction followed by ethanol precipitation. For comparisons between Kdm3a/b-mDKO embryos and control embryos at the E2C stage, we implemented spike-in normalization by adding a constant number of Drosophila S2 cells during cell lysis and 4 pg of Saccharomyces genomic DNA after chromatin elution.
Adaptor ligation was performed using NEBNext Ultra II DNA Library Prep kit (NEB) at half-scale, and the libraries were purified by 1.8× SPRIselect beads (Beckman Coulter). The DNA was amplified by KAPA Hifi 2X master PCR mix for 13-15 PCR cycles with dual indexing primers. After purification with 0.9× SPRIselect beads, the samples were digested by I-SceI (5 U/µl) at 37°C for 2 h followed by heat inactivation at 65°C for 20 min and purified by 0.9× SPRIselect beads. DNA libraries were sequenced with paired-end reads on the NextSeq2000 or Novaseq X Plus (illumina).

value: full-grown oocyte

value: oocyte

value: B6D2F1 (BDF1)

value: H3K9me3 (39162, ActiveMotif)


title: tumor-36 CpG Epic450k-probeID

description:
Library name: tumor-36_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: RNA_mESC_3S1Gx_OHT_Dux-KO:G9a;Suv39h1/2;Setdb1-QKO_rep2

description:
Library name: 3S1G_OHT-gDux_rep2
Column name in raw counts TPM_mESC_33-6s.txt: X3S1G_DuxKO_OHT_rep2

value: mESCs


title: WS1-ABA, rpt2

description: Library name: WS-ABA-2


title: tumor-35 CpG Epic450k-probeID

description:
Library name: tumor-35_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: FGO_H3K9me3_rep1

description: Library name: FGO_K9me3_rep1


title: RNA_mESC_3S1G_OHT_G9a;Suv39h1/2;Setdb1-QKO_rep1

description:
Library name: 3S1G_OHT_rep1
Column name in raw counts TPM_mESC_33-6s.txt: X3S1G_OHT_rep1


title: FGO_Inp

description: Library name: FGO_Inp

value: Input


title: C-Mock, rpt4

description: Library name: C-Mock-4

value: Cadenza


title: RNA_mESC_3S1G_NT_G9a;Suv39h1/2-TKO_rep2

description:
Library name: 3S1G_NT_rep2
Column name in raw counts TPM_mESC_33-6s.txt: X3S1G_NT_rep2


title: E2C-DKO_H3K9me2_spike-in_rep1

description: Library name: E2C-DKO_K9me2_rep1

value: early 2-cell


title: RNA_mESC_3S1G_NT_G9a;Suv39h1/2-TKO_rep1

description:
Library name: 3S1G_NT_rep1
Column name in raw counts TPM_mESC_33-6s.txt: X3S1G_NT_rep1


title: WS1-ABA, rpt1

description: Library name: WS-ABA-1

value: whole seedling


title: tumor-33 CpG Epic450k-probeID

description:
Library name: tumor-33_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: E2C-DKO_Input_rep2

description: Library name: E2C-DKO_Inp_rep2


title: C-Mock, rpt2

description: Library name: C-Mock-2

value: mock


title: E2C-DKO_Input_rep1

description: Library name: E2C-DKO_Inp_rep1


title: tumor-31 CpG Epic450k-probeID

description:
Library name: tumor-31_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: C-Mock, rpt1

description: Library name: C-Mock-1


title: tumor-34 CpG Epic450k-probeID

description:
Library name: tumor-34_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: C-Mock, rpt3

description: Library name: C-Mock-3


title: E2C-DKO_H3K9me2_spike-in_rep2

description: Library name: E2C-DKO_K9me2_rep2


title: RNA_mESC_SG_OHT_G9a;Setdb1-DKO_rep1

description:
Library name: SG_OHT_rep1
Column name in raw counts TPM_mESC_33-6s.txt: SG_OHT_rep1


title: tumor-32 CpG Epic450k-probeID

description:
Library name: tumor-32_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: E2C-Ctrl_H3K9me2_spike-in_rep2

description: Library name: E2C-Ctrl_K9me2_rep2


title: RNA_mESC_SG_NT_G9a-KO_rep2

description:
Library name: SG_NT_rep2
Column name in raw counts TPM_mESC_33-6s.txt: SG_NT_rep2


title: E2C-Ctrl_H3K9me2_spike-in_rep1

description: Library name: E2C-Ctrl_K9me2_rep1


title: tumor-30 CpG Epic450k-probeID

description:
Library name: tumor-30_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: RNA_mESC_SG_OHT_G9a;Setdb1-DKO_rep2

description:
Library name: SG_OHT_rep2
Column name in raw counts TPM_mESC_33-6s.txt: SG_OHT_rep2


title: tumor-29 CpG Epic450k-probeID

description:
Library name: tumor-29_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: C-ABA, rpt3

description: Library name: C-ABA-3


title: C-ABA, rpt4

description: Library name: C-ABA-4


title: RNA_mESC_SG_NT_G9a-KO_rep1

description:
Library name: SG_NT_rep1
Column name in raw counts TPM_mESC_33-6s.txt: SG_NT_rep1


title: E2C-Ctrl_Input_rep2

description: Library name: E2C-Ctrl_Inp_rep2


title: RNA_mESC_SE_OHT_Suv39h1/2;Setdb1-TKO_rep2

description:
Library name: SE_OHT_rep2
Column name in raw counts TPM_mESC_33-6s.txt: SE_OHT_rep2


title: tumor-28 CpG Epic450k-probeID

description:
Library name: tumor-28_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: C-ABA, rpt2

description: Library name: C-ABA-2


title: E2C-Ctrl_Input_rep1

description: Library name: E2C-Ctrl_Inp_rep1


title: RNA_mESC_SE_OHT_Suv39h1/2;Setdb1-TKO_rep1

description:
Library name: SE_OHT_rep1
Column name in raw counts TPM_mESC_33-6s.txt: SE_OHT_rep1


title: RNA_mESC_SE_NT_Suv39h1/2-DKO_rep2

description:
Library name: SE_NT_rep2
Column name in raw counts TPM_mESC_33-6s.txt: SE_NT_rep2


title: tumor-27 CpG Epic450k-probeID

description:
Library name: tumor-27_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: tumor-26 CpG Epic450k-probeID

description:
Library name: tumor-26_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request


title: Spinal cord, contusion injury + AZ876, 6w, rep3

city: Beijing

first: JianJun

last: Li

address: FengtaiXiluoyuan Road Xiluoyuan 4 Unit No.34 (Xiluoyuan Police Station East), Be

institute: Capital Medical University, School of Rehabilitation

description: Library name: Sample 6

data_processing:
Raw reads were processed using fastp(version 0.23.0)  to remove adapter sequences, reads containing more than 5 ambiguous bases (N), and reads with more than 40% low‑quality bases (Q ≤ 20).
Sliding‑window trimming was applied (window size 4 bp, average quality < 20).
Clean reads were aligned to the reference genome using HISAT2(2.1.0).
Gene‑level read counts were generated for downstream analysis.
Supplementary files format and content: Clean reads are provided in FASTQ format after adapter and quality trimming；Alignment files are provided in SAM/BAM format with coordinate sorting;Gene‑level count matrices are provided in XLSX format.

source_name: Spinal cord

growth_protocol: Mice were housed under SPF conditions at 24–26 °C with 60–70% relative humidity and ambient noise below 60 dB. Animals were maintained on a 12‑h light/dark cycle with free access to food and water

extract_protocol:
Total RNA was extracted from spinal cord tissue using the Magnetic Bead Animal Tissue/Cell RNA Extraction Kit (G3607‑50T, Servicebio, Wuhan, China) according to the manufacturer’s instructions.More than 2 µg of total RNA per sample was used for the construction of sequencing libraries.
Sequencing libraries were prepared using the DNBSEQ‑T7RS High‑Throughput Sequencing Kit (FCL PE100) (Cat. No. 940‑000269‑00, MGI, China) following the manufacturer's protocols.

treatment_protocol: AZ876 stock solution was prepared by dissolving the compound in dimethyl sulfoxide (DMSO) and diluting it 1:9 into 20% SBE‑β‑CD saline solution to obtain the working solution. Following T10 spinal cord contusion injury, mice received intraperitoneal injections of AZ876 at 5 mg/kg once daily for one week, with an injection volume of 100 µL per dose. Control animals received vehicle injections prepared using the same solvent system.

value: Spinal cord

value: WT

value: AZ876 treatment after spinal cord contusion injury

tag: batch


title: Spinal cord, contusion injury + AZ876, 6w, rep2

description: Library name: Sample 5


title: C-ABA, rpt1

description: Library name: C-ABA-1


title: RNA_mESC_SE_NT_Suv39h1/2-DKO_rep1

description:
Library name: SE_NT_rep1
Column name in raw counts TPM_mESC_33-6s.txt: SE_NT_rep1


title: RNA_E2C_Kdm3ab-mDKO_rep1

description: Library name: E2C_Kdm3ab-mDKO_rep1

value: preimplantation embryo

value: maternel Kdm3a/b-DKO


title: RNA_E2C_control_rep2

description: Library name: E2C_control_rep2

value: control


title: brain-organoid-iPSC CpG Epic450k-probeID

description:
Library name: CAU-iPSC_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request

source_name: Human iPSC

value: Human iPSC

value: CAU

value: iPSC


title: brain-organoid-day210 CpG Epic450k-probeID

description:
Library name: CAU-day210_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request

source_name: Human brain organoid d210

value: Human brain organoid d210


title: Spinal cord, contusion injury + AZ876, 6w, rep1

description: Library name: Sample 4


title: Spinal cord, contusion injury, 6w, rep3

description: Library name: Sample 3

value: spinal cord contusion injury


title: RNA_E2C_control_rep1

description: Library name: E2C_control_rep1


title: brain-organoid-day16 CpG Epic450k-probeID

description:
Library name: CAU-day16_CpG
bedMethyl file compatible for crossNN prediction, raw FASTQs avaliable upon request

source_name: Human brain organoid d16

value: Human brain organoid d16


title: RNA_mESC_33-6_OHT_Setdb1-KO_rep1

description:
Library name: 33-6_OHT_rep1
Column name in raw counts TPM_mESC_33-6s.txt: X33-6_OHT_rep1

source_name: mESCs

value: mESCs


title: RNA_E2C_Kdm3ab-mDKO_rep2

description: Library name: E2C_Kdm3ab-mDKO_rep2


title: RNA_mESC_33-6_OHT_Setdb1-KO_rep2

description:
Library name: 33-6_OHT_rep2
Column name in raw counts TPM_mESC_33-6s.txt: X33-6_OHT_rep2


title: Morula_H3K9me2_rep1

description: Library name: Morula_K9me2_BDF1xPWK_rep1

value: Morula

value: B6D2F1 (BDF1) x PWK/PhJ

value: wild-type


title: Morula_H3K9me2_rep2

description: Library name: Morula_K9me2_BDF1xPWK_rep2


title: Spinal cord, contusion injury, 6w, rep1

description: Library name: Sample 1


title: RNA_mESC_33-6_NT_control_rep2

description:
Library name: 33-6_NT_rep2
Column name in raw counts TPM_mESC_33-6s.txt: X33-6_NT_rep2


title: RNA_mESC_33-6_NT_control_rep1

description:
Library name: 33-6_NT_rep1
Column name in raw counts TPM_mESC_33-6s.txt: X33-6_NT_rep1


title: RNA_MII_Kdm3ab-mDKO_rep1

description: Library name: MII_Kdm3ab-mDKO_rep1

value: MII oocyte


title: RNA_MII_Kdm3ab-mDKO_rep2

description: Library name: MII_Kdm3ab-mDKO_rep2


title: TN cerebellum

city: Seoul

first: Jungeun

last: Ji

address: 145 Anam-ro

department: Department of Integrated Biomedical and Life Science

country: South Korea

institute: Korea University

description:
Library name: CR_23_06187_TS_R_JSV_1_S8
10X Visium

data_processing:
Space Ranger (v1.3.1) analysis pipelines were used to align raw FASTQ files to mm10 reference genome and image files.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: filtered count matrix file (h5 format)
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: tissue_hires_image.jpg: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.jpg: low-res image of the tissue
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Library strategy: Spatial Transcriptomics

source_name: Cerebellum

growth_protocol: 6 to 8-week aged male wild-type mice (C57Bl/6N from Orient Bio Inc., Seongnam, Korea), were purchased and acclimated to the facility for at least one week before the experiment. All mice were maintained on a 12 h light/dark cycle with ad libitum access to food and water.

extract_protocol:
60 min after fear conditioning or retrieval test, mice were anesthetized with isoflurane and perfused with normal saline. Extracted brains were flash frozen in isopropyl alcohol at -70 °C. Frozen brains were embedded in optimal cutting temperature (OCT) compound and were stored at -80 °C until sectioning.
Visium libraries were constructed following the manufacturer’s instructions. Sequencing was performed on a Novaseq 6000 platform using S1 sequencing reagents (Illumina, Cat No. 20028318), targeting 120 million reads per library using dual indexing.

treatment_protocol: For fear conditioning, mice were placed in fear conditioning chamber. After 2min exploration period, mice received five CS (30 s, 2800 Hz, 79 dB tone) and US (2 s, 0.5 mA, electrical foot shock) pairings. For tone retrieval test, mice were placed in a novel chamber (cylinder chamber) 24h after conditioning. 2 or 3 CS with a 30-s interval were represented. All behavior tests were performed between 09:00 and 16:00 during the light phase of the light/dark cycle.

value: Cerebellum

value: Wild-type

value: After auditory memory retrieval


title: Morula_Input_rep1

description: Library name: Morula_Inp_BDF1xPWK_rep1

source_name: preimplantation embryo

value: preimplantation embryo

value: Input


title: Knockout 3

city: Guangzhou

first: Tao

last: Gui

address: Huangpu Ave

institute: Jinan University

description:
Library name: Sample 6
ATAC-seq

data_processing:
Bioinformatics workflows encompassed reference genome alignment, chromatin accessibility peak identification, and differential analysis to systematically characterize CD74-dependent regulatory elements mediating LPS-induced chromatin remodeling in macrophage activation
Assembly: GRCm39
Supplementary files format and content: bigWig file

source_name: Bone marrow

extract_protocol:
Prior to analysis, CD74+/+- and CD74-/--derived mBMDMs under LPS stimulation were processed for ATAC-seq profiling using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme #TD711) following manufacturer specifications. Nuclear isolation was achieved through hypotonic lysis coupled with density gradient centrifugation. Isolated nuclei underwent Tn5 transposase-mediated fragmentation and adapter ligation with dual-indexed adapters from the TruePrep Index Kit V3 for Illumina (Vazyme #TD203) to simultaneously tag open chromatin regions and incorporate unique molecular identifiers. Transposed DNA fragments were amplified via limited-cycle PCR using kit-supplied reagents, followed by purification through magnetic bead-based size selection to construct sequencing-optimized libraries
Library quality assurance included fragment distribution analysis (Agilent Bioanalyzer), fluorometric quantification (Qubit 4.0), and diversity assessment via qPCR. Qualified libraries were sequenced on an Illumina HiSeq4000 system, generating raw data for subsequent computational processing.

value: Bone marrow

value: BMDMs

value: KO

value: LPS


title: Spinal cord, contusion injury, 6w, rep2

description: Library name: Sample 2

value: Spinal cord

value: WT


title: RNA_MII_control_rep1

description: Library name: MII_control_rep1

value: control


title: FC cerebellum

description:
Library name: CR_23_06184_TS_R_JSV_1_S7
10X Visium

value: Fear conditioned


title: HC cerebellum

description:
Library name: CR_23_06182_TS_R_JSV_1_S6
10X Visium

value: Home cage


title: Knockout 1

description:
Library name: Sample 4
ATAC-seq


title: Morula_Input_rep2

description: Library name: Morula_Inp_BDF1xPWK_rep2

value: Morula

value: B6D2F1 (BDF1) x PWK/PhJ


title: RNA_MII_control_rep2

description: Library name: MII_control_rep2

value: MII oocyte


title: Control 3

description:
Library name: Sample 3
ATAC-seq

value: Con


title: FC DCN

description:
Library name: FC-DCN
10X Chromium

data_processing:
Cellranger (v7.1.10) analysis pipelines were used to align raw FASTQ files to mm10 reference genome.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: filtered count matrix file (h5 format)

molecule: nuclear RNA

source_name: Deep cerebellar nuclei

extract_protocol:
30min after fear conditioning or retrieval test, mice were anesthetized and decapitated immediately. Brains were extracted and sectioned using a vibratome (VT1200S, Leica) in pre-chilled ACSF. The DCN were quickly micro-dissected from 300 μm of cerebellar coronal slices and stored at -80 °C.
Chromium 3' libraries were constructed following the manufacturer’s instructions. Sequencing was performed on a Novaseq 6000 platform.

value: Deep cerebellar nuclei

value: Wild-type


title: E2C_H3K9me2_rep1

description: Library name: E2C_K9me2_BDF1xPWK_rep1

value: early 2-cell

value: preimplantation embryo

value: wild-type


title: E2C_Input_rep2

description: Library name: E2C_Inp_BDF1xPWK_rep2

value: Input


title: TN DCN

description:
Library name: Tone-DCN
10X Chromium

value: After auditory memory retrieval


title: Knockout 2

description:
Library name: Sample 5
ATAC-seq

value: Bone marrow

value: BMDMs

value: KO

value: LPS


title: HC DCN

description:
Library name: HC-DCN
10X Chromium


title: peripheral blood leukocytes

city: Birmingham

last: Osuka

state: Alabama

address: 1720 2nd Ave. South, WTI401

institute: The University of Alabama at Birmingham

description:
Library name: PBLs
10x Genomics

data_processing:
Raw sequencing data were processed and read in alignment with the reference human genome (GRCh38/hg38), and gene expression matrices were generated by the 10x Genomics CellRanger v6.1. HTOs were used for multiplexing; detailed HTO-to-sample correspondence is provided in HTO_samples.csv
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood

extract_protocol:
CD45+ cells and EGFP+ cells from tumor tissues were extracted using a cell sorter (ARIA I). CD45+ cells in PB were purified using EasySep Mouse/Human Chimera Isolation Kit (STEMCELL). Cell viability was assessed using trypan blue exclusion; only samples with >90% viability were used. To minimize technical batch variability, samples from humanized and naive mice were harvested on the same day and processed in parallel. Surface staining was performed using TotalSeq™-B anti-human hashtag antibodies described in the BioLegend protocol (TotalSeq™-b or -c with 10x feature barcoding technology.
Following the manufacturer’s protocol, single-cell RNA libraries were prepared using the Chromium Single Cell 3’ Reagent Kits. Briefly, cells were loaded onto the 10x Genomics Chromium to capture approximately 20,000 cells. Reverse transcription and cDNA amplification were performed according to the kit protocol. Libraries were sequenced on Illumina NovaSeq 6000 with paired-end 150 bp reads to a depth of approximately 5000 reads per cell.

value: peripheral blood

value: immune cells


title: E2C_H3K9me2_rep2

description: Library name: E2C_K9me2_BDF1xPWK_rep2


title: Control 2

description:
Library name: Sample 2
ATAC-seq


title: tumor-infiltrating lymphocytes

description:
Library name: TILs
10x Genomics

source_name: brain tumors

value: brain tumors


title: Control 1

description:
Library name: Sample 1
ATAC-seq


title: recurrent GBM tumors

description:
Library name: GBM
10x Genomics

value: tumor cells


title: experiment 2: whole genome resequencing, RpA70-EGFP

status: Public on Apr 18 2026

city: Evanston

first: Shelby

middle: A

last: Blythe

state: IL

address: Northwestern University, Hogan Hall, 2205 Tech Drive

department: Molecular Biosciences

institute: Northwestern University

description: Library name: rpa70_WGS

data_processing:
Barcode-split fastq files were trimmed of adapter sequences using TrimGalore
Adapter-trimmed fastq files were mapped to the dm6 Drosophila reference genome using Bowtie2, with option -X 2000.
Mapped reads were sorted using Samtools
Suspected PCR and optical duplicate mapped reads were marked using Picard MarkDuplicates. Duplicate-filtered mapped reads with mapquality >20 were used in downstream steps. Coverage plots (bigwigs) for experiment 1 were calculated using deeptools for 100 bp bins using Counts-per-million normalized data, and scaled to chromosome M reads as an internal spike in control.
single nucleotide polymorphisms between oreR and RpA70-EGFP were identified using bcftools. Mapped reads from experiment two carrying maternal or paternal SNPs identified from whole-genome resequencing experiments were split into separate files and coverage was computed using deeptools using 25 kbp bins and are presented as counts-per-million normalized data.
Assembly: Drosophila dm6
Supplementary files format and content: bigwig files for samples (merged replicates) are provided showing counts-per-million and internal spike-in normalized average reads over 100 bp bins for experiment 1. For experiment 2, samples were split based on maternal and paternal SNP content and these were merged by biological replicate. Bigwigs are provided showing counts-per-million normalized average reads over 25 kilobase bins.

organism: Drosophila melanogaster

source_name: Whole adult male

growth_protocol: Adult flies were placed in a cage with yeasted apple juice plates and embryos were collected prior to treatment and/or processing for ChIP.

extract_protocol:
Following ChIP fixation (15 minutes Formaldehyde + PBS-triton-X-100 + Heptane) embryos were sorted by stage using RpA70-EGFP fluorescence observed under a stereomicroscope. Interphase embryos with NC10 or earlier nuclear density were collected for the NC1-10 sample, and late NC14 embryos including those with cephalic furrows, but not ventral furrows, were collected for the NC14 sample.
ChIP was performed by initially sonicating chromatin and incubating overnight with a primary antibody. Antibody-DNA complexes were pulled down using protein G dynabeads. Before washing, antibody-DNA complexes were subjected to tagmentation with Illumina Tn5 transposase for 40 minutes at 37°C. Transposed samples were then washed in low and high salt solutions (2x 5' each) followed by one wash in TE buffer. Crosslinks were reversed for 4 hours at 65°C with moderate shaking in the presence of 5 µg/ml ProteinaseK. DNA was cleaned up using a Zymo ChIP Clean and Concentrator kit, and PCR was performed using sets of unique-dual-indexed Nextera PCR primers. Libraries were amplified within the linear range of PCR prior to Ampure clean up. Libraries were pooled as necessary and sent to Admera Health for sequencing on a NovaSeq X platform (paired-end 150 bp reads). Admera returned barcode-split, compressed fastq files for reads 1 and 2.

value: Whole adult male

value: y w; RpA70-EGFP


title: E2C_Input_rep1

description: Library name: E2C_Inp_BDF1xPWK_rep1

value: B6D2F1 (BDF1) x PWK/PhJ


title: experiment 2: RpA70-EGFP x OreR NC1-10 ChIP for H3K27me3, replicate 2

description: Library name: oreR_rpa70_NC10_K27me3_Rep2

source_name: embryo

value: embryo

value: y w/+; RpA70-EGFP/+


title: experiment 2: whole genome resequencing, OreR

description: Library name: oreR_WGS

value: wild-type (OreR)


title: experiment 2: RpA70-EGFP x OreR NC14 ChIP for H3K27me3, replicate 2

description: Library name: oreR_rpa70_NC14_K27me3_Rep2


title: experiment 2: RpA70-EGFP x OreR NC1-10 ChIP for H3K27me2, replicate 2

description: Library name: oreR_rpa70_NC10_K27me2_Rep2


title: experiment 2: RpA70-EGFP x OreR NC14 ChIP for H3K27me3, replicate 1

description: Library name: oreR_rpa70_NC14_K27me3_Rep1


title: experiment 2: RpA70-EGFP x OreR NC1-10 ChIP for total H3, replicate 2

description: Library name: oreR_rpa70_NC10_H3_Rep2


title: experiment 2: RpA70-EGFP x OreR NC14 ChIP for H3K27me2, replicate 2

description: Library name: oreR_rpa70_NC14_K27me2_Rep2


title: experiment 2: RpA70-EGFP x OreR NC14 ChIP for total H3, replicate 2

description: Library name: oreR_rpa70_NC14_H3_Rep2


title: experiment 2: RpA70-EGFP x OreR NC14 ChIP for H3K27me2, replicate 1

description: Library name: oreR_rpa70_NC14_K27me2_Rep1


title: experiment 2: RpA70-EGFP x OreR NC14 ChIP for total H3, replicate 1

description: Library name: oreR_rpa70_NC14_H3_Rep1


title: experiment 2: RpA70-EGFP x OreR NC1-10 ChIP for H3K27me3, replicate 1

description: Library name: oreR_rpa70_NC10_K27me3_Rep1


title: experiment 1: RpA70-EGFP NC14 ChIP for H3K27me2, replicate 2

description: Library name: rpa70_NC14_K27me2_Rep2


title: experiment 2: RpA70-EGFP x OreR NC1-10 ChIP for H3K27me2, replicate 1

description: Library name: oreR_rpa70_NC10_K27me2_Rep1


title: experiment 1: RpA70-EGFP NC14 ChIP for H3K27me3, replicate 2

description: Library name: rpa70_NC14_K27me3_Rep2


title: experiment 1: RpA70-EGFP NC1-10 ChIP for total H3, replicate 2

description: Library name: rpa70_NC10_H3_Rep2


title: experiment 1: RpA70-EGFP NC14 ChIP for H3K27me2, replicate 1

description: Library name: rpa70_NC14_K27me2_Rep1


title: experiment 1: RpA70-EGFP NC1-10 ChIP for H3K27me2, replicate 1

description: Library name: rpa70_NC10_K27me2_Rep1


title: experiment 2: RpA70-EGFP x OreR NC1-10 ChIP for total H3, replicate 1

description: Library name: oreR_rpa70_NC10_H3_Rep1


title: experiment 1: RpA70-EGFP NC1-10 ChIP for IgG (negative control), replicate 1

description: Library name: rpa70_NC10_IgG_Rep1


title: experiment 1: RpA70-EGFP NC14 ChIP for total H3, replicate 1

description: Library name: rpa70_NC14_H3_Rep1


title: experiment 1: RpA70-EGFP NC14 ChIP for IgG (negative control), replicate 1

description: Library name: rpa70_NC14_IgG_Rep1


title: experiment 1: RpA70-EGFP NC14 ChIP for H3K27me3, replicate 1

description: Library name: rpa70_NC14_K27me3_Rep1


title: experiment 1: RpA70-EGFP NC1-10 ChIP for H3K27me2, replicate 2

description: Library name: rpa70_NC10_K27me2_Rep2


title: scRNA-seq of Homo sapiens: 397-06 d121 FNA 2

city: St. Louis

first: Julian

last: Zhou

state: MO

address: 425 S. Euclid Ave.

department: Pathology & Immunology

institute: Washington University in St. Louis

description: Library name: ELAB-WU397-006-d121_FNA_2-GEX

data_processing:
Single cell feature counts for a single library were generated using `cellranger count` from Cell Ranger v6.0.1
Single cell feature counts for multiple libraries were pooled by subsampling to the same effective sequencing depth using `cellranger aggr` from Cell Ranger v6.0.1
Assembly: GRCh38
Supplementary files format and content: matrix.mtx.gz contains a gene expression count matrix stored in the Market Exchange Format for sparse matrices
Supplementary files format and content: features.tsv.gz contains feature information that corresponds to the row indices of matrix.mtx.gz
Supplementary files format and content: barcodes.tsv.gz contains cellular barcodes that correspond to the column indices of matrix.mtx.gz. The trailing dash and number (e.g. -12) indicate the sample from which the cell originated and correspond to the row number for that sample in aggregation.csv.
Supplementary files format and content: aggregation.csv.gz contains sample information. The order of the samples represented as rows in aggregation.csv corresponds to the numbers after the dash (e.g. -12) in barcodes.tsv.gz.

source_name: lymph node

extract_protocol:
Fine-needle aspiration was performed on draining ipsilateral axillary lymph nodes. PBMCs were isolated from blood and further sorted for either plasmablasts or IgDlo B cells.
Libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 5' gene expression workflow.

value: lymph node

value: various

tag: isolate

tag: timepoint

tag: biological replicate


title: experiment 1: RpA70-EGFP NC1-10 ChIP for total H3, replicate 1

description: Library name: rpa70_NC10_H3_Rep1


title: experiment 1: RpA70-EGFP NC1-10 ChIP for H3K27me3, replicate 1

description: Library name: rpa70_NC10_K27me3_Rep1


title: scRNA-seq of Homo sapiens: 397-06 d15 FNA 2

description: Library name: ELAB-WU397-006-d15_FNA_2-GEX


title: experiment 1: RpA70-EGFP NC14 ChIP for total H3, replicate 2

description: Library name: rpa70_NC14_H3_Rep2


title: scRNA-seq of Homo sapiens: 397-06 d57 FNA 2

description: Library name: ELAB-WU397-006-d57_FNA_2-GEX