title: ATAC_ANT_Training_m4

description: Library name: ATAC_ANT_Training_m4

data_processing:
Raw sequencing reads were trimmed and filtered for quality (Q>15) and adapter content using version 0.4.5 of TrimGalore and running version 1.15 of cutadapt and version 0.11.5 of FastQC.
Version 2.3.4.1 of bowtie2 was employed to align reads to mouse assembly mm10 and alignments were deduplicated using MarkDuplicates in Picard Tools v2.16.0.
Enriched regions were discovered using MACS2 with a p-value setting of 0.001 using the input control as background and then filtered for blacklisted regions.
The BEDTools suite was used to create ATAC bigwig files normalized using the DESeq2 sizeFactors
Assembly: mm10
Supplementary files format and content: normalized bigwigs

extract_protocol:
Nuclear extraction. Mice were sacrificed within 40-60 minutes from behavioral testing. The anterior thalamus and anterior cingulate of C57Bl6/J mice were dissected, and nuclei were extracted using the percoll gradient method. The dissected tissue was homogenized with 54% percoll (Cytiva) in 1× buffer (50 mM Tris-HCl, pH 7.4; 25 mM KCl; 5 mM MgCl2; 250 mM sucrose) on ice, using a 23 G syringe and a 27 G syringe, 10 strokes each. After homogenization, 10% NP-40 substitute (Roche, cat. no. 11332473001) and 10% Tween-20 were added and incubated for 15 minutes on ice (0.1% final concentration for both NP-40 and Tween-20). Following the incubation, an equal volume of 1× buffer was added and mixed by pipetting. A percoll gradient was prepared by layering 31% and 35% percoll at the bottom of the tube. Nuclei were pelleted in the bottom layer by centrifugation in a swinging bucket (14,000 g, 10 minutes at 4°C). The nuclear pellet was carefully resuspended in blocking buffer (5% BSA/PBS) and incubated for 10 minutes on ice. After blocking, nuclei were labeled by incubation with Alexa Fluor 488-conjugated anti-NeuN antibody (1/2000) for 20 minutes on ice. Nuclei were then washed once in PBS and labeled with 7-AAD (Sigma, cat. no. SML1633). The 7-AAD singlet and NeuN-positive population was sorted by FACS, and the sorted nuclei were used for ATAC-seq.
Libraries were prepared for sequencing using standard Illumina protocols


title: bulkRNA PHC03

status: Public on Sep 28 2025

type: SRA

city: chongqing

first: Ye

last: qian

address: No. 1 Youyi Road, Yuzhong District, Chongqing

country: China

institute: The First Affiliated Hospital of Chongqing Medical University

library_source: transcriptomic

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: GRCh_38
Supplementary files format and content: TXT file contain counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood

extract_protocol:
PBMCs RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Peripheral blood

tag: cell line

value: PBMCs

tag: cell type

value: Immune cells

tag: gender

value: Male

tag: age

tag: sample collection_site

value: Children's Hospital of Chongqing Medical University, Chongqing, China

tag: group

value: Pediatric Healthy Control

tag: sepsis infection_source

tag: ethnicity

value: East Asian


title: bulkRNA PHC02


title: ATAC_ANT_Training_m3

city: New York

first: Richard

last: Koche

state: New York

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: Library name: ATAC_ANT_Training_m3

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Brain, ANT

value: Brain, ANT

value: Neurons (sorted)

tag: genotype


title: bulkRNA PHC01

value: Female


title: ATAC_ANT_Training_m1

description: Library name: ATAC_ANT_Training_m1


title: ATAC_ANT_Test_8_HR_m5

description: Library name: ATAC_ANT_Test_8_HR_m5


title: bulkRNA IC28

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China

value: Adult ICU Control


title: ATAC_ANT_Test_8_HR_m18

description: Library name: ATAC_ANT_Test_8_HR_m18


title: ATAC_ANT_Test_8_HR_m14

description: Library name: ATAC_ANT_Test_8_HR_m14


title: bulkRNA PIC06

value: Pediatric ICU Control


title: bulkRNA IC27


title: bulkRNA IC26


title: ATAC_ANT_Test_8_HR_m12

description: Library name: ATAC_ANT_Test_8_HR_m12


title: bulkRNA IC23


title: ATAC_ANT_Test_20_HR_m22

description: Library name: ATAC_ANT_Test_20_HR_m22


title: bulkRNA IC22


title: ATAC_ANT_Test_20_HR_m20

description: Library name: ATAC_ANT_Test_20_HR_m20


title: bulkRNA IC21


title: bulkRNA PIC01


title: bulkRNA IC20


title: ATAC_ANT_Homecage_m4

description: Library name: ATAC_ANT_Homecage_m4


title: ATAC_ANT_Test_20_HR_m17

description: Library name: ATAC_ANT_Test_20_HR_m17


title: bulkRNA IC19


title: bulkRNA IC18


title: ATAC_ANT_Training_m2

description: Library name: ATAC_ANT_Training_m2


title: ATAC_ANT_Homecage_m3

description: Library name: ATAC_ANT_Homecage_m3


title: bulkRNA IC30


title: bulkRNA IC16


title: ATAC_ANT_Homecage_m2

description: Library name: ATAC_ANT_Homecage_m2


title: ATAC_ANT_Homecage_m1

description: Library name: ATAC_ANT_Homecage_m1


title: ATAC_ACC_Test_d20_rep5

description: Library name: ATAC_ACC_Test_d20_rep5

source_name: Brain, ACC

value: Brain, ACC


title: bulkRNA IC17


title: bulkRNA IC31


title: bulkRNA IC15


title: bulkRNA IC13


title: ATAC_ACC_Test_d20_rep4

description: Library name: ATAC_ACC_Test_d20_rep4


title: bulkRNA IC12


title: ATAC_ACC_Test_d20_rep3

description: Library name: ATAC_ACC_Test_d20_rep3


title: ATAC_ACC_Test_d20_rep2

description: Library name: ATAC_ACC_Test_d20_rep2


title: ATAC_ACC_Test_d20_rep1

description: Library name: ATAC_ACC_Test_d20_rep1


title: bulkRNA IC10


title: ATAC_ANT_Test_20_HR_m23

description: Library name: ATAC_ANT_Test_20_HR_m23


title: bulkRNA IC07


title: ATAC_ACC_Test_d08_rep3

description: Library name: ATAC_ACC_Test_d08_rep3


title: bulkRNA IC05


title: ATAC_ACC_Test_d08_rep2

description: Library name: ATAC_ACC_Test_d08_rep2


title: bulkRNA IC06


title: ATAC_ACC_Test_d08_rep1

description: Library name: ATAC_ACC_Test_d08_rep1


title: ATAC_ACC_Test_d08_rep4

description: Library name: ATAC_ACC_Test_d08_rep4


title: bulkRNA HC44

value: Adult Healthy Control


title: bulkRNA IC02


title: ATAC_ACC_Test_d02_rep1

description: Library name: ATAC_ACC_Test_d02_rep1


title: bulkRNA HC43


title: ATAC_ACC_Test_d02_rep2

description: Library name: ATAC_ACC_Test_d02_rep2


title: bulkRNA IC03


title: bulkRNA HC41


title: bulkRNA HC42


title: bulkRNA HC40


title: bulkRNA HC39


title: ATAC_ACC_Test_d02_rep3

description: Library name: ATAC_ACC_Test_d02_rep3


title: ATAC_ACC_Homecage_rep4

description: Library name: ATAC_ACC_Homecage_rep4


title: bulkRNA IC11


title: bulkRNA HC38


title: ATAC_ACC_Homecage_rep2

description: Library name: ATAC_ACC_Homecage_rep2


title: bulkRNA HC37


title: freshly isolate, male, keap1 KO247

city: Hong Kong

first: Lifang

last: HAN

address: 6202D, Clear Water Bay

department: LIFS

institute: HKUST

data_processing:
fastq files were generated on basespace
Low quality reads and adaptor sequences were trimmed from the raw reads file using BBDuk
Trimmed sequencing reads were mapped to the mouse mm10 genome assembly using the STAR RNA-seq aligner
Gene count table was generated using FeatureCounts from Subread package with following parameters: -p -t exon -g gene_id
Differential analysis was done using DEseq2 package in R
Assembly: mm10 (Mus musculus)
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
Supplementary files format and content: tab-delimited text file containing fpkm values for each sample

source_name: hindlimb muscle

extract_protocol:
Total RNA was extracted with the NucleoSpin RNA XS kit (MACHEREY-NAGEL) following manufacture's instruction
cDNA was synthesized and amplified according to the Smart-Seq2 protocol. Purified cDNA was then fragmented using Tn5 followed by library construction using TruePrep® DNA Library Prep Kit V2 for Illumina.

treatment_protocol: Muscle satellite cells were isolated from hindlimb muscle and immediately frozen with liquid nitrogen

value: hindlimb muscle

tag: Sex

value: male

value: satellite cells

value: Keap1 knockout

tag: strain


title: ATAC_ACC_Homecage_rep1

description: Library name: ATAC_ACC_Homecage_rep1


title: freshly isolate, male, keap1 KO255


title: bulkRNA HC36

value: Peripheral blood

value: PBMCs

value: Immune cells


title: freshly isolate, male, keap1 Hetz249

value: Keap1 heterogeneous


title: bulkRNA HC35

value: Male

value: East Asian


title: bulkRNA HC34


title: bulkRNA HC33


title: freshly isolate, male, keap1 Hetz204


title: freshly isolate, male, keap1 Hetz245


title: bulkRNA HC32


title: freshly isolate, female, keap1 KO188

value: female


title: bulkRNA HC31


title: freshly isolate, female, keap1 KO178


title: ATAC_ACC_Homecage_rep3

description: Library name: ATAC_ACC_Homecage_rep3

value: Neurons (sorted)


title: bulkRNA HC29

value: Female

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China


title: bulkRNA HC30


title: bulkRNA HC28


title: freshly isolate, female, keap1 Hetz164


title: freshly isolate, female, keap1 Hetz165


title: freshly isolate, female, keap1 Hetz181


title: bulkRNA HC27


title: bulkRNA HC26


title: Nrf2-null, Nrf2, ChIP, bench 2

data_processing:
Fastq files were generated on basespace from Novogene
ChIP-seq reads were trimmed by Trim-Galore (0.6.10)
ChIP-seq reads were aligned to the mouse genome (mm10) with bwa (0.7.17). Duplicated reads were removed by samtools (1.6)
Peaks were called using MACS2 (2.2.7.1) with the significance cut-off p<0.001
Highly reproducible peaks were identified by Irreproducible Discovery Rate (IDR) method
Assembly: mm10
Supplementary files format and content: narrowPeak (except for Input sample)

extract_protocol:
Freshly isolated MuSCs were fixed with 1% formaldehyde for 10 minutes. After quenching, cells were subjected to sonication with Covaris S220.
Cell lysates were pre-cleaned by Protein G beads. 1/20 of the lysate was saved as input while the left was incubated with 1.5 μg of Nrf2 antibody.  Libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit.


title: bulkRNA HC25


title: Nrf2-null, Input, bench 2


title: freshly isolate, male, keap1 KO240


title: bulkRNA HC23


title: bulkRNA HC24


title: bulkRNA HC22


title: bulkRNA HC21


title: Nrf2-null, Input, bench 1


title: Keap1-null, Nrf2, ChIP, bench 1


title: bulkRNA HC20


title: bulkRNA HC19


title: Keap1-null, Input, bench 1


title: H3K27ac_HiChIP_mESC_JMJD2BC_EV_R2

city: Guangzhou

first: Xinyi

last: Liu

state: Guangdong

address: No. 74, 2nd Zhongshan Road

institute: Sun Yat-Sen University

data_processing:
Trimming the adaptor sequence: Trim Galore (version 0.6.7, https://github.com/FelixKrueger/TrimGalore), removed the bases with quality below 20 and the adaptor sequences from the 3' end, and filtered the reads with length less than 50nt.
Alignment and pairing: HiC-Pro (PMID: 26619908) was used (version 2.11.1, parameters: 'LIGATION_SITE = GATCGATC' which digested mm9 by MboI).
Supplementary files format and content: *_allValidPairs.tar.gz: valid pairs from Hi-C-Pro. All text files were compressed by tar (version 1.30, https://ftp.gnu.org/gnu/tar/, parameters: '-czvf')
Library strategy: HiChIP

source_name: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing empty vector (negative control of JMJD2BC CMuts)

growth_protocol: Jmjd2/Kdm4afl/fl/bfl/fl/cfl/fl:Rosa26::CreERT2 (Jmjd2/Kdm4fl/fl) ESCs (Pedersen et al., 2016) were cultured as previous study. These cell lines were cultured in ESCs medium containing Dulbecco's modified Eagle medium (DMEM) high-glucose media containing 15% fetal bovine serum (FBS; Gibco), 1mM sodium pyruvate (Gibco, 11360070), 1mM non-essential amino acids (Gibco, 11140076), 1× GlutaMAX (Gibco, 35050061), 0.1mM β-mercaptoethanol (Gibco, 21985023), 1000 U/ml leukemia inhibitory factor, and the 2i inhibitors (1.5 μM CHIR99021, and 0.5 μM PD0325901).

extract_protocol: In-situ Hi-C was performed as described earlier (Rao et al., 2014). Briefly, 15 million ESCs were crosslinked and digested with MboI (NEB, R0148). After digestion, biotin was incorporated into the sticky ends of fragments before ligation. H3K27ac ChIP was performed to enrich for proximity ligations bound to H3K27ac (Mumbach et al., 2016), using H3K27ac antibody (Abcam, ab4729). The quality of libraries was checked by Agilent High Sensitivity DNA kit (Agilent Technologies) before sequencing.

treatment_protocol: 4-hydroxytamoxifen (4-OHT) treatment: to acutely depleted JMJD2/KDM4, Jmjd2/Kdm4fl/fl ESCs were grown in the presence of 500 nM 4-OHT (Sigma-Aldrich, H7904-5MG) for up to 72 hours (for phase separation mutants) or 36 hours (for catalytic mutants) until JMJD2/KDM4 proteins were depleted.

value: mESC

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed empty vector (negative control of JMJD2BC CMuts)

tag: treatment

value: 500 nM 4-OHT (Sigma-Aldrich, H7904-5MG), 36h


title: bulkRNA HC18

value: Adult Healthy Control


title: freshly isolate, female, keap1 KO166

value: hindlimb muscle


title: bulkRNA HC17


title: H3K27ac_HiChIP_mESC_JMJD2BC_EV_R1

source_name: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing catalytic mutants of JMJD2B and JMJD2C

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed catalytic mutants of JMJD2B and JMJD2C


title: H3K27ac_HiChIP_mESC_JMJD2BC_CMuts_R2

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing catalytic mutants of JMJD2B and JMJD2C


title: H3K27ac_HiChIP_mESC_JMJD2BC_CMuts_R1


title: bulkRNA HC16

value: Peripheral blood


title: bulkRNA HC15

value: PBMCs


title: H3K27ac_HiChIP_mESC_hIDR2_R1

source_name: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing hIDR2

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed hIDR2

value: 500 nM 4-OHT (Sigma-Aldrich, H7904-5MG), 72h


title: bulkRNA HC12

value: Immune cells

value: Male


title: bulkRNA HC14

value: East Asian


title: bulkRNA HC13


title: Keap1-null, Nrf2, ChIP, bench 2

value: satellite cells


title: Keap1-null, Input, bench 2


title: H3K27ac_HiChIP_mESC_hIDR2_R2

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing hIDR2


title: bulkRNA HC11

value: Female

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China


title: H3K27ac_HiChIP_mESC_JMJD2C_Mut_hIDR2_R2

source_name: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing IDR-truncated JMJD2C fused with hIDR2

value: mESC

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed IDR-truncated JMJD2C fused with hIDR2


title: bulkRNA HC10

value: Adult Healthy Control


title: H3K27ac_HiChIP_mESC_hIDR1_R1

source_name: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing hIDR1

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed hIDR1


title: Nrf2-null, Nrf2, ChIP, bench 1

value: hindlimb muscle


title: bulkRNA HC09


title: H3K27ac_HiChIP_mESC_hIDR1_R2

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing hIDR1


title: bulkRNA HC08

value: Peripheral blood


title: bulkRNA HC07

value: PBMCs


title: H3K27ac_HiChIP_mESC_JMJD2C_Mut_R2

source_name: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing IDR-truncated JMJD2C

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed IDR-truncated JMJD2C


title: H3K27ac_HiChIP_mESC_JMJD2C_Mut_hIDR1_R1

source_name: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing IDR-truncated JMJD2C fused with hIDR1

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed IDR-truncated JMJD2C fused with hIDR1

value: 500 nM 4-OHT (Sigma-Aldrich, H7904-5MG), 72h


title: bulkRNA HC06

value: Immune cells


title: bulkRNA HC05

value: Male

value: East Asian


title: H3K27ac_HiChIP_mESC_JMJD2C_Mut_R1

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing IDR-truncated JMJD2C


title: bulkRNA HC04


title: bulkRNA HC03


title: bulkRNA HC01


title: H3K27ac_HiChIP_mESC_JMJD2_TKO_R2

source_name: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/-


title: H3K27ac_HiChIP_mESC_Ctrl_R2

value: Non


title: H3K27ac_HiChIP_mESC_Ctrl_R1

value: mESC


title: H3K27ac_HiChIP_mESC_JMJD2C_Mut_hIDR2_R1

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing IDR-truncated JMJD2C fused with hIDR2

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed IDR-truncated JMJD2C fused with hIDR2


title: bulkRNA Abd-S98

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China

value: Adult Sepsis

value: Abdominal


title: 4Cseq_preiPSC_JMJD2C_Mut_hIDR1_R2

data_processing:
Experimental designs of 4C-seq: firstCutter: DpnII (GATC), secondCutter: BfaI (CTAG), view point (bait): chr9:78216149-78216299 (promoter of Dppa5a), the point of interested region: chr9:78350776-78353352 (enhancer of Dppa5a).
Trimming the adaptor sequence: Trim Galore (version 0.6.7, https://github.com/FelixKrueger/TrimGalore), removed the bases with quality below 20 and the adaptor sequences from the 3' end, and filtered the reads with length less than 50nt.
Alignment:  Bowtie2 was used with default parameters and reads with a mapq score less than 30.
Filtering and normalization: Basic4Cseq was used to map reads to build up fragment library, map reads to fragment, filter and normalize reads by default parameter according to above experimental designs. Reads per million mapped reads (RPM) were also calculated by Basic4Cseq and converted to bigwig files by bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/).
Assembly: mm9
Supplementary files format and content: *.bw: bigWig files normalized by RPM from 4C-seq data for viewing in a genome browser.
Library strategy: 4C-seq

source_name: pre-iPSC

growth_protocol: The clonal lines of reprogramming intermediates NS pre-iPSCs, with various variants of JMJD2/KDM4 PiggyBac transgenes, plated on gelatin coated 12 well plate in embryonic stem cell medium (serum/LIF).

extract_protocol: Approximately 5 million NS pre-iPSCs were harvested and crosslinked by formaldehyde. Resuspend cell pellet with 1ml low SDS Hi-C lysis buffer (0.1%SDS; 50mM HEPESKOH, pH7.5; 150mM NaCl; 1mM EDTA; 1% Triton X-100; 0.1% Sodium Deoxycholate) containing protease inhibitors, and incubate on ice for 30 min. Centrifuge at 2500g for 5 min at 4°C to discard supernatant. Then gently resuspend the cell pellet in 50 μl of 0.5% SDS and shake at 900 r.p.m. for exactly 10 minutes at 62°C on the thermomixer. 25 mL of the appropriate 10X New England Biolabs restriction enzyme buffer and 200 units of DpnII (NEB R0543) were added and the chromatin was incubated at 37°C degrees in a thermomixer at 500 RPM for four hours, 200 more units of DpnII (NEB R0543) was added and the reaction was incubated overnight at 37°C degrees in a thermomixer at 500 RPM. Inactivate DpnII incubating the sample for 20 min at 62°C while shaking at 500 rpm and then cool to room temperature. Proximity ligation was performed in a total of 1200 mL with 2000 units of T4 DNA ligase (NEB M020) for six hours at room temperature. After ligation samples were spun down for 5 minutes at 2500 rcf. and resuspended in 300 mL 10 mM Tris-HCl, 1% SDS and 0.5 mM NaCl with 1000 units of Proteinase K. Crosslinks were reversed by incubation overnight at 65°C. Samples were then phenol-chloroform extracted and ethanol precipitated and the second digestion was performed overnight in 450 mL with 50 units of restriction enzyme. BfaI (NEB R0568S) was used for Dppa5a. Samples were phenol-chloroform extracted and ethanol precipitated and the second ligation was performed in 14 mL total with 6700 units of T4 DNA ligase (NEB M020) at 16°C overnight. The sample was amplified unknown interacting sequences by inverse PCR with biotin-tagged oligos. Then, the library of sequency was prepared using the same strategy as the HiChIP

treatment_protocol: The SadCas9-ABI and SpdCas9-PYL , both fused with IDR-truncated mutant of JMJD2C (Mut), Mut-hIDR1 or hIDR1, were targeted to enhancer and promoter of Dppa5a. We induced fusion of JMJD2 phase at enhancer and promoter of Dppa5a by adding ABA for 96h and washed-out. The E-P loop of Dppa5a was evaluated at 168h by 4C-seq with bait in the promoter region of Dppa5a.

value: pre-iPSC

value: 1mM ABA (YuanYe, S18008) 96h and washed-out until 168h


title: 4Cseq_preiPSC_hIDR1_R2


title: 4Cseq_preiPSC_hIDR1_R1


title: bulkRNA Abd-S96

value: Peripheral blood

value: PBMCs


title: bulkRNA Abd-S92

value: Chongqing Emergency Medical Center, Chongqing, China.


title: bulkRNA Abd-S8

value: Immune cells


title: bulkRNA Abd-S97

value: Female


title: 4Cseq_preiPSC_JMJD2C_Mut_hIDR1_R1


title: bulkRNA Abd-S79

value: Male

value: East Asian


title: H3K27ac_HiChIP_mESC_JMJD2C_Mut_hIDR1_R2

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing IDR-truncated JMJD2C fused with hIDR1

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed IDR-truncated JMJD2C fused with hIDR1

value: 500 nM 4-OHT (Sigma-Aldrich, H7904-5MG), 72h


title: 4Cseq_preiPSC_JMJD2C_Mut_R2


title: bulkRNA Abd-S66


title: 4Cseq_preiPSC_JMJD2C_Mut_R1


title: ChIPseq_mESC_hIDR2_YY1_Input_R2

data_processing:
Trimming the adaptor sequence: Trim Galore (version 0.6.7, https://github.com/FelixKrueger/TrimGalore), removed the bases with quality below 20 and the adaptor sequences from the 3' end, and filtered the reads with length less than 50nt.
Alignment: Bowtie2 was used with default parameters and reads with a mapq score less than 30 and PCR duplications were filtered out by using Samtools (PMID: 19505943) (version 1.9, http://samtools.sourceforge.net). After that, reads aligned to the regions in ENCODE blacklist (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/) were discarded through bedtools (PMID: 20110278) (version 2.29.1, https://bedtools.readthedocs.io/en/latest/).
Peak calling: Peaks of ChIP-seq data were called with macs2 (PMID: 18798982) (version 2.1.2, parameters: '-g mm -q 0.05 -m 5 50' for H3K27ac, '-g mm -q 0.05 -m 5 50 --broad' for H3K9me3 using Input as control.
Normalization: Bam files of ChIP-seq data were converted to bigwig by deepTools (version 3.1.1, computeMatrix, https://deeptools.readthedocs.io/en/develop/, 'bamCoverage -bs 10 --normalizeUsing RPKM --ignoreForNormalization chrM -e 200 --centerReads')
Assembly: mm9
Supplementary files format and content: *.bw: bigWig files with bin size of 10bp normalized by RPKM from ChIP-seq data for viewing in a genome browser.
Supplementary files format and content: *_peaks.*Peak: peaks from ChIP-seq data for viewing in a genome browser.

extract_protocol: ChIP was performed as previously described (Lee et al., 2006). Briefly, 5×107 –1×108 ESCs were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125mM glycine. Rinsed cells twice with ice cold PBS and then resuspended in Lysis Buffer with protease inhibitor. Chromatin was sonicated into 200–500bp range. Dynabeads (Invitrogen 10004D) pre-blocked with 0.5% BSA were incubated with 10μg antibody for more than 8 hours. Chromatin was added to antibody-bead complex and incubated rotating overnight at 4°C.Beads were washed with each of the following buffers: Wash Buffer (RIPA), TE + 50 mM NaCl at 4°C, followed by washing one time with TE at room temperature. Chromatin were eluted by incubating at 65°C for 45min in elution buffer. Reversal of crosslinking was performed at 65°C overnight. After treated with 10 mg/ml RNaseA and 20 mg/ml proteinase K. DNA fragments were then purified using phenol–chloroform extraction and resuspended in 10mM Tris-HCL. The antibodies were:  JMJD2/KDM4A Bethyl A300-861A, anti-H3K27ac Abcam ab4729, anti-H3K9me3 Abcam ab8898 and anti-YY1 Abcam ab109237.

treatment_protocol: 4-hydroxytamoxifen (4-OHT) treatment: to acutely depleted JMJD2/KDM4, Jmjd2/Kdm4fl/fl ESCs were grown in the presence of 500 nM 4-OHT (Sigma-Aldrich, H7904-5MG) for up to 72 hours until JMJD2/KDM4 proteins were depleted.

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing hIDR2

value: mESC

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed hIDR2


title: bulkRNA Abd-S54

value: Adult Sepsis


title: bulkRNA Abd-S57

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China

value: Abdominal


title: ChIPseq_mESC_hIDR2_YY1_Input_R1


title: ChIPseq_mESC_hIDR2_YY1_R2


title: ChIPseq_mESC_hIDR2_YY1_R1


title: bulkRNA Abd-S51


title: H3K27ac_HiChIP_mESC_JMJD2_TKO_R1

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/-


title: bulkRNA Abd-S47

value: Peripheral blood

value: PBMCs


title: ChIPseq_mESC_JMJD2C_Mut_hIDR2_YY1_Input_R2

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing IDR-truncated JMJD2C fused with hIDR2

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed IDR-truncated JMJD2C fused with hIDR2


title: bulkRNA Abd-S42

value: Immune cells

value: Male


title: ChIPseq_mESC_JMJD2C_Mut_hIDR2_YY1_R2


title: bulkRNA Abd-S83

value: East Asian


title: ChIPseq_mESC_JMJD2C_Mut_hIDR2_YY1_R1


title: bulkRNA Abd-S39


title: ChIPseq_mESC_JMJD2C_Mut_hIDR2_YY1_Input_R1


title: bulkRNA Abd-S37


title: bulkRNA Abd-S24


title: bulkRNA Abd-S35

value: Chongqing Emergency Medical Center, Chongqing, China.


title: bulkRNA Abd-S25


title: ChIPseq_mESC_hIDR1_YY1_Input_R2

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing hIDR1

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed hIDR1

value: 500 nM 4-OHT (Sigma-Aldrich, H7904-5MG), 72h


title: bulkRNA Abd-S198

value: Female


title: ChIPseq_mESC_JMJD2C_Mut_hIDR1_YY1_Input_R2

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing IDR-truncated JMJD2C fused with hIDR1

value: mESC

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed IDR-truncated JMJD2C fused with hIDR1


title: ChIPseq_mESC_hIDR1_YY1_R2


title: bulkRNA Abd-S190

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China

value: Adult Sepsis

value: Abdominal


title: ChIPseq_mESC_hIDR1_YY1_R1


title: ChIPseq_mESC_hIDR1_YY1_Input_R1


title: ChIPseq_mESC_JMJD2C_Mut_hIDR1_YY1_Input_R1


title: bulkRNA Abd-S185

value: Peripheral blood

value: PBMCs


title: ChIPseq_mESC_JMJD2C_Mut_hIDR1_YY1_R2


title: bulkRNA Abd-S165


title: bulkRNA Abd-S197


title: ChIPseq_mESC_JMJD2C_Mut_hIDR1_YY1_R1


title: ChIPseq_mESC_JMJD2C_Mut_YY1_Input_R2

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing IDR-truncated JMJD2C

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed IDR-truncated JMJD2C


title: bulkRNA Abd-S148

value: Immune cells

value: Male


title: ChIPseq_mESC_JMJD2C_Mut_YY1_R2


title: ChIPseq_mESC_JMJD2C_Mut_YY1_R1


title: ChIPseq_mESC_JMJD2C_Mut_YY1_Input_R1


title: bulkRNA Abd-S141

value: East Asian


title: bulkRNA Abd-S159

value: Chongqing Emergency Medical Center, Chongqing, China.


title: bulkRNA Abd-S137


title: bulkRNA Abd-S133


title: ChIPseq_mESC_JMJD2C_FL_YY1_Input_R2

source_name: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing full length JMJD2C

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed full length JMJD2C


title: bulkRNA Abd-S132


title: ChIPseq_mESC_JMJD2C_FL_YY1_Input_R1

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing full length JMJD2C

value: 500 nM 4-OHT (Sigma-Aldrich, H7904-5MG), 72h


title: bulkRNA Abd-S128

value: Female


title: ChIPseq_mESC_JMJD2C_FL_YY1_R1

value: mESC


title: bulkRNA Abd-S126


title: ChIPseq_mESC_JMJD2_TKO_YY1_Input_R2

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/-


title: bulkRNA Abd-S123

value: the First Affiliated Hospital of Chongqing Medical University, Chongqing, China

value: Adult Sepsis


title: bulkRNA Abd-S120

value: Peripheral blood

value: Abdominal


title: ChIPseq_mESC_JMJD2_TKO_YY1_R2


title: ChIPseq_mESC_JMJD2_TKO_YY1_Input_R1


title: bulkRNA Abd-S156

value: PBMCs


title: bulkRNA Abd-S115


title: ChIPseq_mESC_Ctrl_YY1_Input_R2

value: Non


title: bulkRNA Abd-S114

value: Immune cells


title: RNA_Proteins_B

city: Los Angeles

first: Brian

middle: George

last: Dias

state: CA

address: 4650 Sunset Blvd

department: Division of Endocrinology

institute: Children's Hospital Los Angeles

data_processing:
library prep with QIAseq UPXome RNA seq library kit (QIAGEN)
Illumina MiSeq Sequencing
Demultiplexing
STAR aligner
the geneCounts output from the STAR aligner
Assembly: MacaM, INSDC Assembly GCA_003339765.3
Supplementary files format and content: comma-separated text file, mapping statistics
Supplementary files format and content: comma-separated text file, read counts

organism: Macaca mulatta

source_name: Plasma EV

extract_protocol:
Norgen Plasma/Serum RNA Purification Kit
QIAseq UPXome RNA seq library kit (QIAGEN)

treatment_protocol: ProteinaseK, RNAse, and DNAse

value: Plasma EV

tag: subject

value: animal B


title: ChIPseq_mESC_Ctrl_YY1_Input_R1


title: EV_B


title: bulkRNA Abd-S103

value: Male

value: Chongqing Emergency Medical Center, Chongqing, China.

value: East Asian


title: EV_A

value: animal A


title: ChIPseq_mESC_Ctrl_YY1_R2


title: bulkRNA Abd-S102


title: RNA_lipoProteins_B


title: ChIPseq_mESC_Ctrl_YY1_R1


title: dCCA3

city: Jinan

first: Shu

middle: Li

last: zhuang

state: China/Shandong

address: Department of General Surgery, Qilu Hospital, Shandong University, 107, Jinan Culture Road, Jinan, 250012, China.

department: Qilu Hospital

institute: Shandong University

description:
Small RNA
T6

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary files format and content: expression profiles

source_name: Tissue miRNA

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: Cholangiocarcinoma

tag: patient diagnosis

value: distal cholangiocarcinoma(dCCA)


title: bulkRNA Abd-PS27

value: Children's Hospital of Chongqing Medical University, Chongqing, China

value: Pediatric Sepsis


title: ChIPseq_mESC_JMJD2C_FL_YY1_R2

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs overexpressing full length JMJD2C

value: mESC

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/- with overexpressed full length JMJD2C

value: 500 nM 4-OHT (Sigma-Aldrich, H7904-5MG), 72h


title: ChIPseq_mESC_JMJD2_TKO_H3K9me3_Input

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/-


title: dCCA2

description:
Small RNA
T5


title: bulkRNA Abd-PS23

value: Peripheral blood

value: PBMCs

value: Immune cells

value: Abdominal


title: pCCA3

description:
Small RNA
T3

value: perihilar cholangiocarcinoma(pCCA)


title: dCCA1

description:
Small RNA
T4


title: ChIPseq_mESC_JMJD2_TKO_H3K9me3


title: bulkRNA Abd-PS20

value: Male

value: East Asian


title: ChIPseq_mESC_JMJD2_TKO_YY1_R1


title: ChIPseq_mESC_Ctrl_H3K9me3_Input

value: Non


title: RNA_lipoProteins_A

value: Plasma EV

value: animal A


title: pCCA1

description:
Small RNA
T1

value: Cholangiocarcinoma


title: pCCA2

description:
Small RNA
T2


title: RNA_Proteins_A


title: dCCA3_para-tumor

description:
Small RNA
N6

value: adjacent tissue

value: distal cholangiocarcinoma(dCCA)


title: bulkRNA Abd-PS19

value: Children's Hospital of Chongqing Medical University, Chongqing, China

value: Pediatric Sepsis


title: dCCA2_para-tumor

description:
Small RNA
N5


title: bulkRNA Abd-PS13

value: Female


title: ChIPseq_mESC_JMJD2_TKO_H3K27ac_Input_R2

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs

value: mESC

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/-

value: 500 nM 4-OHT (Sigma-Aldrich, H7904-5MG), 72h


title: dCCA1_para-tumor

description:
Small RNA
N4


title: pCCA3_para-tumor

description:
Small RNA
N3


title: bulkRNA Abd-PS07

value: Peripheral blood

value: PBMCs

value: Immune cells

value: Abdominal


title: pCCA1_para-tumor

description:
Small RNA
N1

value: perihilar cholangiocarcinoma(pCCA)


title: pCCA_3

description:
Small RNA
C3

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: miRBase 22.0
Supplementary files format and content: expression profiles

source_name: Bile exosome miRNA

value: Bile exosome

tag: diagnosis


title: bulkRNA Abd-PS05

source_name: Peripheral blood

value: Male

value: East Asian


title: pCCA_2

description:
Small RNA
C2


title: CBDS_2

description:
Small RNA
N2

value: common bile duct stones(CBDS)


title: CBDS_3

description:
Small RNA
N3


title: ChIPseq_mESC_JMJD2_TKO_H3K27ac_R1


title: Subject ID 09 day1_VDJ

city: Chiba

first: Takahiro

last: Aoki

state: Chiba

address: 1-8-1 Inohana Chuo-ku

country: Japan

institute: Chiba University

description: Library name: DK23131_01_VDJ

data_processing:
Basecalls and mapping performed using Cell Ranger ver v7.2.0
Assembly: GRCh38
Supplementary files format and content: TCR VDJ, barcodes, features and matrix tsv files

source_name: Blood

extract_protocol:
The PBMC samples were stored in liquid nitrogen. The samples were thawed and the NK cells (CD3-CD56+) and T cells (CD3+) were sorted by a FACS Aria III device (Becton Dickinson).
Libraries were prepared using Chromium Single Cell 5’ Reagent Kits v2 and Single-Cell V(D)J Enrichment Kit for Human T Cells according to manufacturer’s protocol (10X Genomics).

value: Blood

tag: subject id

value: Subject ID 09

value: immune cells


title: pCCA_1

description:
Small RNA
C1

tag: tissue


title: CBDS_1

description:
Small RNA
N1


title: ChIPseq_mESC_Ctrl_H3K27ac_Input_R2

tag: cell line

value: Non


title: sample 11  E9.5 mouse yolk sac from Hand1 ^H2/H2 embryo

city: Indianapolis

first: Anthony

last: Firulli

email: tfirulli@iupui.edu, tfirulli@iu.edu

state: IN

address: 1044 W Walnut R4302E

department: pediatrics

institute: IU school of medicine

data_processing:
The sequence data were mapped to the mouse reference genome mm10 with STAR-2.5.2b
FeatureCounts (subread-1.5.1) was used to quantify gene expression (parameters applied: "“-s 2 –p –Q 10")
Differential expression analysis was performed using edgeR
Assembly: mouse reference genome mm10
Supplementary files format and content: excel table includeing raw counts, log2 fold change, p-values and FDR

source_name: E9.5 Yolk sac

extract_protocol:
isolation of tissue in RNA later followed by Roche High Pure RNA tissue kit (Cat # 12033674001)
KAPA mRNA Hyperprep Kit (KK8581) was ued to prepare the RNA-seq libraries.

value: E9.5 Yolk sac


title: ChIPseq_mESC_Ctrl_H3K9me3

tag: cell type

value: mESC


title: sample 9  E9.5 mouse yolk sac from Hand1 ^H2/H2 embryo


title: pCCA2_para-tumor

description:
Small RNA
N2

value: adjacent tissue


title: ChIPseq_mESC_Ctrl_H3K27ac_R2


title: Subject ID 09 day21_VDJ

description: Library name: DK23131_03_VDJ

value: day 21


title: Subject ID 08 day1_VDJ

description: Library name: DK23131_04_VDJ

value: Subject ID 08


title: ChIPseq_mESC_Ctrl_H3K27ac_Input_R1


title: sample 8  E9.5 mouse yolk sac from Hand1 ^H2/H2 embryo


title: sample 5  E9.5 mouse yolk sac from T-CRE; Hand1 ^fx/fx embryo

value: T-Cre^+/-; Hand1^fx/fx


title: ChIPseq_mESC_JMJD2_TKO_H3K27ac_Input_R1

value: Jmjd2/Kdm4a-/- / b-/- / c-/-:Rosa26::CreERT2 (Jmjd2/Kdm4-/-) ESCs

value: Jmjd2a -/-, Jmjd2b -/-, Jmjd2c -/-

value: 500 nM 4-OHT (Sigma-Aldrich, H7904-5MG), 72h


title: sample 10  E9.5 mouse yolk sac from Hand1 ^H2/H2 embryo


title: sample 4 E9.5 mouse yolk sac from Hand1^Fx/+ embryo


title: sample 7  E9.5 mouse yolk sac from T-CRE; Hand1 ^fx/fx embryo


title: Subject ID 09 day8_VDJ

description: Library name: DK23131_02_VDJ


title: bulkRNA Abd-PS04

value: Peripheral blood

value: PBMCs

value: Immune cells

tag: gender

value: Children's Hospital of Chongqing Medical University, Chongqing, China

value: Pediatric Sepsis

value: Abdominal


title: sample 3 E9.5 mouse yolk sac from Hand1^Fx/+ embryo


title: ChIPseq_mESC_JMJD2_TKO_H3K27ac_R2


title: RNAseq_mESC_hIDR2_OE

data_processing:
Trimming the adaptor sequence: Trim Galore (version 0.6.7, https://github.com/FelixKrueger/TrimGalore), removed the bases with quality below 20 and the adaptor sequences from the 3' end, and filtered the reads with length less than 50nt.
Alignment: Reads were aligned to mm9 by STAR (PMID: 23104886) with default parameters.
Quantification of gene expression: uniquely mapped reads of RNA-seq data were counted by HTSeq-count with default parameters (PMID: 25260700). Non-unique reads in repetitive regions were counted by bedtools  (PMID: 20110278) (version 2.29.1, https://bedtools.readthedocs.io/en/latest/, multiBamCov with default parameters). Repetitive regions of mm9 were downloaded from https://genome.ucsc.edu/cgi-bin/hgTables.
Normalization: the read counts were normalized by trimmed mean of M values (TMM), and transformed to reads per kilobases per million reads (RPKM) by edgeR (PMID: 19910308).
Assembly: mm9
Supplementary files format and content: ReadCounts_xx.txt: raw read counts of each genes from RNA-seq data for differential expression analysis.
Supplementary files format and content: ReadCounts_RSKM_xx.txt: raw read counts of each repetitive region from RNA-seq.
Supplementary files format and content: RPKM_xx.txt: RPKM of each genes from RNA-seq.

source_name: mESC

growth_protocol: Jmjd2/Kdm4afl/fl/bfl/fl/cfl/fl:Rosa26::CreERT2 (Jmjd2/Kdm4fl/fl) ESCs (Pedersen et al., 2016) and Zscan4-GFP::MERVL-tdTomoto ESCs (Yang et al., 2020) were cultured as previous study. These cell lines were cultured in ESCs medium containing Dulbecco's modified Eagle medium (DMEM) high-glucose media containing 15% fetal bovine serum (FBS; Gibco), 1mM sodium pyruvate (Gibco, 11360070), 1mM non-essential amino acids (Gibco, 11140076), 1× GlutaMAX (Gibco, 35050061), 0.1mM β-mercaptoethanol (Gibco, 21985023), 1000 U/ml leukemia inhibitory factor, and the 2i inhibitors (1.5 μM CHIR99021, and 0.5 μM PD0325901).

extract_protocol: Total RNA was extracted from cell pellets using RNAzol reagent (MRC) and cDNA was synthesized using Primesoript RT Master Mix (Takara).

value: Zscan4-GFP::MERVL-tdTomoto ESCs overexpressing hIDR2

value: Zscan4-GFP::MERVL-tdTomoto with overexpressed hIDR2


title: Subject ID 08 day8_VDJ

description: Library name: DK23131_05_VDJ

value: Blood

value: immune cells


title: ChIPseq_mESC_Ctrl_H3K27ac_R1

value: mESC

value: Non


title: Subject ID 08 day21_VDJ

description: Library name: DK23131_06_VDJ

value: Subject ID 08

value: day 21


title: sample 2 E9.5 mouse yolk sac from Hand1^Fx/+ embryo

value: E9.5 Yolk sac


title: RNAseq_mESC_JMJD2C_Mut_hIDR2_OE

value: Zscan4-GFP::MERVL-tdTomoto ESCs overexpressing IDR-truncated JMJD2C fused with hIDR2

value: Zscan4-GFP::MERVL-tdTomoto with overexpressed IDR-truncated JMJD2C fused with hIDR2


title: sample 1 E9.5 mouse yolk sac from Hand1^Fx/+ embryo


title: Subject ID 12 day1_VDJ

description: Library name: DK23131_07_VDJ

value: Subject ID 12


title: C3

city: Chengdu

first: Shihang

last: Tang

address: GUOXUE 37

institute: West China hospital

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,
Trimmed sequence reads were then mapped to Rat whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Bray N, Pimentel H, Melsted P, et al., Near-optimal RNA-Seq quantification, 2015. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Rattus norvegicus (assembly mRatBN7.2)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: spleen

extract_protocol:
RNA was isolated from the spleen using TRIzol Reagent). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using  standard Illumina protocols, library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: spleen

value: splenocytes

value: WT

value: The rats received an intraperitoneal injection of TAA at the same dosage as the TAA group and received celecoxib (20 mg/kg/day) for the last 8 weeks.


title: RNAseq_mESC_hIDR1_OE

value: Zscan4-GFP::MERVL-tdTomoto ESCs overexpressing hIDR1

value: Zscan4-GFP::MERVL-tdTomoto with overexpressed hIDR1


title: sample 6  E9.5 mouse yolk sac from T-CRE; Hand1 ^fx/fx embryo

value: T-Cre^+/-; Hand1^fx/fx


title: C1


title: RNAseq_mESC_JMJD2C_Mut_hIDR1_OE

value: Zscan4-GFP::MERVL-tdTomoto ESCs overexpressing IDR-truncated JMJD2C fused with hIDR1

value: Zscan4-GFP::MERVL-tdTomoto with overexpressed IDR-truncated JMJD2C fused with hIDR1


title: Subject ID 12 day8_VDJ

description: Library name: DK23131_08_VDJ

value: Blood

value: immune cells


title: T3

value: The rats received an intraperitoneal injection of TAA at a dosage of 200 mg/kg/3 days in the initial 8 weeks and 100 mg/kg/3 days in the last 8 weeks


title: Subject ID 12 day21_VDJ

description: Library name: DK23131_09_VDJ

value: day 21


title: RNAseq_mESC_JMJD2C_Mut_OE

value: mESC

value: Zscan4-GFP::MERVL-tdTomoto ESCs overexpressing IDR-truncated JMJD2C

value: Zscan4-GFP::MERVL-tdTomoto with overexpressed IDR-truncated JMJD2C

value: Non


title: T2

value: spleen


title: Subject ID 09 day1_GEX

description: Library name: DK23131_01_GE

library_source: transcriptomic single cell

value: Subject ID 09


title: N3

value: splenocytes

value: WT

value: control


title: RNAseq_mESC_JMJD2C_FL_OE

value: Zscan4-GFP::MERVL-tdTomoto ESCs overexpressing full length JMJD2C

value: Zscan4-GFP::MERVL-tdTomoto with overexpressed  full length JMJD2C


title: N2


title: T1


title: RNAseq_mESC_JMJD2_TKO_R2

value: 500 nM 4-OHT (Sigma-Aldrich, H7904-5MG), 72h


title: Subject ID 09 day8_GEX

description: Library name: DK23131_02_GE


title: Subject ID 09 day21_GEX

description: Library name: DK23131_03_GE


title: RNAseq_mESC_JMJD2_TKO_R1


title: C6

data_processing:
The raw sequencing data are called raw tags. We obtained clean tags using the SOAPnuke. The filtering rules were as follows: removed low quality tags; removed tags with 5’ primer contaminants; remove tags without 3’ primer; removed tags without insertion; removed tags with poly A; removed tags shorter than 15nt.
After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2. Particularly, cmsearch was performed for Rfam  mapping. In the annotation information of different RNAs, to ensure that each small RNA was mapped to a unique category, we set the following rules: MiRbase(v22) > pirnabank(v1.0) > snoRNA(v1.2 human/plant ) > Rfam (v12.1)> other sRNA. The miRDeep-P2 [4] or miRDeep2[5] package was used to identify potentially novel miRNAs. The potentially novel miRNAs and were named novel_mirXXX, in which XXX is a unique number specified for each novel miRNA candidate.
RNAhybrid, miRanda and TargetScan were used to predict target genes of miRNAs (Only for animal; TargetFinder and TAPIR were used for plant).
The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers. The expression formula is: C is the number of UMIs of reads that were mapped to the small RNA, T is the UMI number of total clean reads of the sample.
Differential expression analysis was performed using the DEGseq (or DESeq2 or PoissonDis) on Dr. Tom Multi-omics Data Mining System. Q value≤ 0.05 (or FDR value≤0.001) was used to judge the significance of expression difference.
Supplementary files format and content: excel,expression profiles

source_name: bile

extract_protocol:
Add 700 μL QIAzol Lysis Reagent to the exosome’s suspension. Mix by vortexing 10 s. Centrifuge for a short time and leave at room temperature for 5min.  Add 140 μL of chloroform/isoamyl alcohol (24:1), invert vigorously up and down for 15 s, and incubate for 2~3 min at room temperature.Centrifuge in 12,000×g for 8min in 4℃. Transfer the supernatant to a new tube. Add ethanol absolute two times of an equal volume to the supernatant, mix thoroughly. Pipet up to all sample into a spin column in a 2 mL collection tube and discard the flow-through.  Wash the column with 500 µL Buffer RPE.  Wash the column with 500 µL Buffer RPE.  Place the RNeasy MinElute spin column into a new 2 mL collection tube. Centrifuge at 12,000×g for 2 min to dry the membrane. Discard the collection tube with the flow-through. Place the RNeasy MinElute spin column in a new 1.5 mL collection tube. Add 20 µL RNase-free water directly to the center of the spin column membrane. Incubate for 1min at room temperature and centrifuge for 1 min at full speed to elute the RNA.
Select the corresponding testing methods for quality inspection according to the requirements of samples and products. Take a certain amount of RNA sample, purified 18-30nt small RNA with PAGE gel. The purified RNA is combined with 3’ Adapter, and incubated. Then combine 5’ Adapter, and incubate. Prepare the Reverse Transcription Reaction Mixture, into the thermocycler and run the program. Prepare the PCR Reaction Mixture, into the thermocycler and run the program.Then the PCR products are purified with PAGE gel, dissolve the recylced products in EB solution.The corresponding library quality control protocol will be selected depending upon product requirements.Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: bile

value: distal cholangiocarcinoma (dCCA)


title: glutamatergic neuronal ADAM17 knockout mice paraventricular nucleus of hypothalamus (A2)

city: Xi’an

first: Jiaxi

last: Xu

address: 76 West Yanta Road

institute: Xi’an Jiaotong University

data_processing:
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36) according to several steps:
1) Removing adaptor sequence if reads contains;
2) Removing low quality bases from reads 3’ to 5’ (Q < 20);
3) Removing low quality bases from reads 5’ to 3’ (Q < 20);
4) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp);
5) Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data was used for further analysis
Assembly: RSeQC (version 2.6.1) was used to statistics the alignment results. The homogeneity distribution and the genome structure were checked by Qualimap (version 2.2.1). BEDTools (version 2.26.0) was used to statistical analysis the gene coverage ratio.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: paraventricular nucleus of hypothalamus Male mouse

extract_protocol:
Total RNA was isolated using the Total RNA Extractor (Tri-zol) kit (B511311, Sangon, China)
Sequencing libraries were constructed using the VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina®, following the manufacturer's recommendations

value: glutamatergic neuronal ADAM17 knockout


title: glutamatergic neuronal ADAM17 knockout mice paraventricular nucleus of hypothalamus (A1)

value: paraventricular nucleus of hypothalamus Male mouse


title: Subject ID 08 day1_GEX

description: Library name: DK23131_04_GE

value: Blood

value: Subject ID 08

value: immune cells


title: N1


title: C5


title: wildtype mice  paraventricular nucleus of hypothalamus (NF1)

source_name: paraventricular nucleus of hypothalamus Female mouse


title: RNAseq_mESC_Ctrl_R1

value: mESC


title: C4


title: C2

value: The rats received an intraperitoneal injection of TAA at the same dosage as the TAA group and received celecoxib (20 mg/kg/day) for the last 8 weeks.


title: wildtype mice  paraventricular nucleus of hypothalamus (N2)


title: N6

value: common bile duct stones (CBDS)


title: Subject ID 08 day21_GEX

description: Library name: DK23131_06_GE

value: day 21


title: Irradiated conditional knockout mice treated with drug

city: Seoul

first: Yoon-Jin

last: Lee

address: Nowon GU

country: South Korea

institute: Korea Institute of Radiological & Medical Sciences

description: Library name: KO

data_processing:
The Single Cell 3’ Protocol produce s Illumina ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 1 2 bp UMI are encoded in Read 1, while Read 2 is used to sequence the cDNA fragment. Sample index sequences are incorporated as the i7 index read. Read 1 and Read 2 are standard Illumina® sequencing primer sites used in paired end sequencing.
Assembly: Mm10
Supplementary files format and content: Single Cell Gene Expression

source_name: Lung

extract_protocol:
The 10x™ GemCode™ Technology samples a pool of ~3,500,000 barcodes to separately index each cell’s transcriptome. It does so by partitioning thousands of cells into nanoliter scale Gel Bead In EMulsions (GEMs), where all generated cDNA share a common 10x Barcode. Libraries are generated and sequenced from the cDNA and the 10x Barcodes are used to associate individual reads back to the individual partitions. To achieve single cell resolution, the cells are delivered at a limiting dilution, such that the majority (~90 99%) of generated GEMs contains no cell, while the remainder largely contain a single cell. Upon dissolution of the Single Cell 3’ Gel Bead in a GEM, primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 1 2 nt Unique Molecular Identifier (UMI), and (iv) a poly dT primer sequence are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded, full length cDNA from poly adenylated mRNA. Afte r incubation, the GEMs are broken and the pooled fractions are recovered.
Enzymatic Fragmentation and Size Selection are used to optimize the cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, Atailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: Lung


title: wildtype mice  paraventricular nucleus of hypothalamus (N1)

value: WT


title: Irradiated wild-type mice

description: Library name: WT


title: N5


title: glutamatergic neuronal ADAM17 knockout mice paraventricular nucleus of hypothalamus (AF1)

value: paraventricular nucleus of hypothalamus Female mouse


title: Subject ID 12 day8_GEX

description: Library name: DK23131_08_GE

value: Subject ID 12


title: ChIPseq_mESC_JMJD2A_Input

value: Non


title: Non-irradiated wild-type mice (control)

description: Library name: NoIR2


title: Subject ID 12 day1_GEX

description: Library name: DK23131_07_GE


title: Subject ID 12 day21_GEX

description: Library name: DK23131_09_GE


title: ChIPseq_mESC_JMJD2A


title: DRG, rosacea model, rep6

status: Public on Sep 27 2025

city: Boston

first: SangGyu

state: Massachusetts

address: 14 Isabella St, #G

institute: Massachusetts General Hospital

description: Library name: DRG-LL8

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCm38 (mm10) whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text files include Read Count, FPKM, TPM values for each Sample

molecule: polyA RNA

source_name: DRG

extract_protocol:
Total RNA was extracted from the tissue with the use of an RNeasy Mini Kit and QIAzol® Lysis Reagent (Qiagen) .
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: DRG


title: RNAseq_mESC_Ctrl_R2


title: N4

value: bile


title: DRG, rosacea model, rep1

description: Library name: DRG-LL3


title: Subject ID 08 day8_GEX

description: Library name: DK23131_05_GE


title: DRG, rosacea model, rep2

description: Library name: DRG-LL4


title: DRG, rosacea model, rep3

description: Library name: DRG-LL5


title: Skin tissue, rosacea model, rep5

description: Library name: Skin-LL7

source_name: Skin

value: Skin


title: Skin tissue, rosacea model, rep6

description: Library name: Skin-LL8


title: Skin tissue, rosacea model, rep3

description: Library name: Skin-LL5


title: Skin tissue, rosacea model, rep1

description: Library name: Skin-LL3


title: Skin tissue, rosacea model, rep2

description: Library name: Skin-LL4


title: DRG, control, rep6

description: Library name: DRG-con6


title: DRG, control, rep5

description: Library name: DRG-con5


title: DRG, control, rep3

description: Library name: DRG-con3


title: DRG, control, rep2

description: Library name: DRG-con2


title: DRG, control, rep1

description: Library name: DRG-con1


title: Skin tissue, control, rep3

description: Library name: Skin-con3


title: Skin tissue, control, rep4

description: Library name: Skin-con4


title: Skin tissue, control, rep1

description: Library name: Skin-con1


title: DRG, control, rep4

description: Library name: DRG-con4


title: DRG, rosacea model, rep5

description: Library name: DRG-LL7


title: DRG, rosacea model, rep4

description: Library name: DRG-LL6


title: Skin tissue, control, rep5

description: Library name: Skin-con5


title: Skin tissue, control, rep2

description: Library name: Skin-con2


title: Skin tissue, control, rep6

description: Library name: Skin-con6


title: MI3

first: Cheng

last: Congyi

state: Shandong

address: No.44, Wenhua West Road

institute: Qilu Hospital of Shandong University

description: Library name: Sample 7

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome mm10 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized FPKM values

source_name: myocardial tissues

extract_protocol:
Total RNA was extracted with an RNA extraction kit (Fastagen Biotech Co., RNAfast200)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: myocardial tissues

value: ligation of left coronary artery


title: Skin tissue, rosacea model, rep4

description: Library name: Skin-LL6


title: NC3

description: Library name: Sample 3

value: sham-operated


title: NC1

description: Library name: Sample 1


title: NC2

description: Library name: Sample 2


title: WT_mESC_2i_10k_K36me2_r1.fq.gz

city: Shanghai

first: Yu

last: Zhang

address: 138 Yi Xue Yuan Road

institute: Fudan university

description: Library name: Sample 37

data_processing:
Paired-end reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove adaptor sequences and reads of low quality. The filtered reads were then mapped to the mm9 genome using Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) with the default parameters. Duplicates were removed with MarkDuplicates.jar. The unique mapped reads were then used to calculate the RPKM (Reads per kilobase per million of sequenced reads), which was further Z-score normalized to minimize the batch and cell type variation. The Pearson correlation was calculated for each sample with two biological replicates (10-kb bin). Replicates with good reproducibility were pooled together for downstream analyses. The UCSC genome browser was used for visualization.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: 2i mESC

growth_protocol: Serum/Lif (S/L) R1 mESCs were cultured in 0.1% gelatin-coated dishes in Dulbecco’s modified Eagle’s medium (Gibco, 11995065) containing 15% FBS (Gibco, 16000-044), 1000 IU/ml leukemia inhibitory factor (Lif) (Merck Millipore, ESG1107), 100 IU/ml penicillin and 100 μg/ml streptomycin (Merck Millipore, TMS-AB2-C), 2 mM GlutaMAX (Gibco, 35050061), 1% EmbryoMax nucleosides (Merck Millipore, ES-008-D), 0.1 mM nonessential amino acids (Gibco, 25-025-CIR), and 0.1 mM 2-mercaptoethanol (Gibco, 21985023). 2i mESCs were cultured on 0.2% gelatin-coated dishes in 2i/Lif medium (N2B27 medium supplemented with 1 μm PD0325901 (Tocris, 41921), 3 μm CHIR99021 (Tocris, 4423) and 1000 IU/ml Lif). Cells were routinely propagated every 2-3 days. The formative EpiLCs were induced as previously described (Hayashi et al., 2011). Briefly, 1.0×105 2i ESCs were plated in a well of a 12-well plate coated with Matrigel (BD, 356230/356231, diluted at a ratio of 1:100 in N2B27 medium). Cells were cultured in N2B27 medium containing activin A (20 ng/ml), bFGF (12 ng/ml), XAV939 (5 μM), and KSR (1%). EpiLCs were collected for analysis at the indicated time point. Embryos were collected in vivo.

extract_protocol:
Embryos or cells were lysed in lysis buffer and subject to Mnase digestion, antibody immunoprecipitation, and subsequent library preparation.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016) with modifications. Briefly, samples were suspended and lysed followed by chromatin fragmentation by micrococcal nuclease (MNase, Sigma-Aldrich, N3755-200UN) at 37°C for 5 min. After being terminated, the supernatant containing chromatin was incubated with 1 μg of primary antibody (H3K36me2, Active motif, 61019; H3K36me3, Active motif, 61021 or 61902) at 4°C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific, 10001D for Protein A and 10004D for Protein G) was added to each sample and incubated at 4°C for 3 hours with rotation. The beads were next washed five times with 150 μl of RIPA buffer and once with 150 μl of LiCl buffer. For each sample, beads were resuspended with 28 μl of H2O, 1 μl of 10× Ex Taq buffer (Takara, RR006B), and 1 μl of proteinase K (NEB, P8107S) and incubated at 55°C for 90 min, followed by incubation at 72°C for 40 min to inactivate the proteinase K. Samples were then subjected to TruSeq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Libraries were sequenced using the Illumina Hiseq X Ten or Novaseq 6000 system according to the manufacturer’s protocol.

value: 2i mESC

tag: chip antibody

value: H3K36me2 (active motif, 61019)

tag: developmental stage


title: NC4

description: Library name: Sample 4


title: WT_mESC_SL_10k_K36me2_r1.fq.gz

description: Library name: Sample 38

source_name: S/L mESC

value: S/L mESC


title: WT_D3_EpiLC_10k_K36me2_r1.fq.gz

description: Library name: Sample 36

source_name: Day3 EpiLC

value: Day3 EpiLC


title: Nsd1KO_D3_EpiLC_10k_K36me2_r1.fq.gz

description: Library name: Sample 33

value: Nsd1 KO


title: Nsd1KO_mESC_2i_10k_K36me2_r1.fq.gz

description: Library name: Sample 34


title: Nsd1KO_mESC_SL_10k_K36me2_r1.fq.gz

description: Library name: Sample 35


title: M121

city: Dallas

first: Todd

last: Aguilera

state: TX

address: 2280 Inwood Rd

department: Molecular radiation biology

institute: UTSouthwestern- Medical Center

description: Library name: Sample31

data_processing:
Raw reads were quality-controlled with FastQC (version 0.12.0), trimmed using Trimmomatic (version 0.32), Counts quantified with RSEM (version 1.3.3) and imported to R using tximport (version 1.30.0)
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw count for each Sample

source_name: KPC36 tumor

extract_protocol:
RNA from tumor tissue samples stored in RNAlater at -80C was extracted using Qiagen RNeasy Plus Kits, and RNA quality was assessed with a Nanodrop 2000 and Agilent 2100 Bioanalyzer. Samples with RNA integrity numbers (RIN) >7.0 were used
Libraries were prepared using Illumina Stranded mRNA Prep kit according to manufacturer protocol

value: KPC36 tumor

value: Malignant


title: M124

description: Library name: Sample32


title: M119

description: Library name: Sample30


title: M098

description: Library name: Sample28


title: M117

description: Library name: Sample29


title: M097

description: Library name: Sample27


title: M096

description: Library name: Sample26


title: MI1

description: Library name: Sample 5

value: WT


title: M048

description: Library name: Sample24


title: MI2

description: Library name: Sample 6


title: M043

description: Library name: Sample23


title: M034

description: Library name: Sample20


title: M035

description: Library name: Sample21


title: M025

description: Library name: Sample17


title: M023

description: Library name: Sample16


title: M037

description: Library name: Sample22


title: M027

description: Library name: Sample18


title: M017

description: Library name: Sample13


title: M016

description: Library name: Sample12


title: M019

description: Library name: Sample15


title: M008

description: Library name: Sample10


title: M018

description: Library name: Sample14


title: M029

description: Library name: Sample19


title: D077

description: Library name: Sample7


title: M007

description: Library name: Sample9


title: M015

description: Library name: Sample11


title: D068

description: Library name: Sample6


title: D051

description: Library name: Sample5


title: D046

description: Library name: Sample4


title: Dorsal root ganglia, vehicle ip administration in the E2(+) group, rep1

city: Tokyo

first: Yuki

last: Uchida

state: Shinagawa

address: 1-5-8 Hatanodai

department: Department of Physiology

institute: Showa University School of Medicine

data_processing:
Trimmomatic software (Version 0.38)
Trimmomatic software (Version 0.38) was used to trim low quality bases (< 20) and adapter sequences, applying the following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36.
The trimmed reads were then aligned to the reference genome using the RNA-seq aligner HISAT2 (Version 2.1.0).
Samtools (Version 1.9) was utilized to convert the resulting .sam files from HISAT2 into .bam files.
These .bam files were subsequently used to estimate the abundance of uniquely mapped reads using featureCounts (Version 1.6.3).
Assembly: Rattus_norvegicus.Rnor_6.0.104
Supplementary files format and content: bw file

source_name: dorsal root ganglia

extract_protocol:
Total RNA was extracted from the DRG using the RNeasyⓇ Plus Universal Mini Kit (QIAGEN, Tokyo, Japan), according to the manufacturer’s protocol. 1 μg of total RNA was used for the construction of sequencing library.
cDNA libraries (150-bp × 2 paired-end reads) were prepared using the NEBNextⓇ Poly(A) mRNA Magnetic Isolation Module kit (Cat No. E7490) and NEBNEXTⓇ UltraTMII Directional RNA Library Prep Kit (Cat No. E7760) (New England Biolabs, MA, USA).

treatment_protocol: At 10:00 at the experiment day, a rat was administrated i.p. vehicle (0.002% dimethyl sulfoxide [DMSO; FUJIFILM Wako Pure Chemical Corporation] in phosphate-buffered saline [PBS]; 200 μL) and TREK1 and TREK2 agonists (ostruthin (Toronto Research Chemicals, Toronto, ON, Canada) 4.2 μg/0.002% DMSO in PBS; 200 μL).

value: dorsal root ganglia

value: vehicle and E2(+)


title: Dorsal root ganglia, ostruthin ip administration in the E2(+) group, rep1

value: ostruthin and E2(+)


title: Dorsal root ganglia, vehicle ip administration in the E2(-) group, rep1

value: vehicle


title: D045

description: Library name: Sample3


title: Dorsal root ganglia, ostruthin ip administration in the E2(-) group, rep1

value: ostruthin


title: M095

description: Library name: Sample25


title: D017

description: Library name: Sample2


title: SZ8511 cells, AZ628 2μM, 24h-biol rep3

city: Beijing

first: lairong

last: song

state: 北京

address: South Fourth Ring West Road 119, Fengtai District

institute: Beijing Tiantan hospital

data_processing:
The libraries were multiplexed and loaded on an Illumina HiSeq instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment: Reference genome sequences and gene model annotation files of relative species were downloaded from genome website UCSC.
Hisat2 (v2.2.1) was used to index reference genome sequence. Clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Expression analysis : In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: hg38
Supplementary files format and content: CSV files includes raw counts for each sample.
Supplementary files format and content: CSV files includes raw counts for each sample.

extract_protocol:
Total RNA was extracted with TRIzol reagent, and 1ug of total RNA was used per sample for library construction.
cDNA libraries for sequencing were constructed using the NEB kit (#7530; New England Biolabs) following the instructions.

value: high-grade meningioma cells


title: D001

description: Library name: Sample1


title: SZ8511 cells, AZ628 2μM, 24h-biol rep2


title: KPC63_IO

description: Library name: Sample 3

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 using  Gene Expression
Assembly: mm10
Supplementary files format and content: Hierarchical Data Formats HDF5 and matrix files

source_name: Tumor and TDLN

extract_protocol:
KPC63 tumors were established by injecting 1×10⁶ cells (1:1 PBS) subcutaneously into mouse hind legs. Tumor draining lymph nodes (TDLNs) were collected from three mice per treatment group, gently homogenized, and filtered through 40 μm filters in serum-supplemented medium. Tumor tissue underwent enzymatic digestion (HBSS/RPMI, 3% FetalClone II, DNAse I, Y-27632, Collagenase IV) for 45 min at 37°C. After filtration, RBC lysis, and resuspension in FetalClone II/10% DMSO, cells were stored in liquid nitrogen. For analysis, cells were revived in RPMI/5% FetalClone II, counted, and adjusted to 1000 cells/μL in 0.04% BSA/PBS. Samples were processed using 10x Chromium single cell 3' kit (V3 chemistry) to capture 10,000 cells, following standard protocol. Libraries were sequenced via NovaSeq to 50,000 reads per cell.
Cells were loaded according to standard protocol of the Chromium single cell 5′ kit, capturing 10,000 cells (V3 chemistry). All subsequent procedures, including library construction, were performed according to the standard manufacturer’s protocol. Single-cell libraries were sequenced on NovaSeq (Illumina) to a depth of 50,000 reads per cell

value: Tumor and TDLN

value: TME and TDLNs cells

value: Immunotherapy


title: SZ8511 cells, AZ628 2μM, 24h-biol rep1


title: KPC63_XRT

description: Library name: Sample 2

value: Photon


title: M001

description: Library name: Sample8


title: SZ8511 cells, DMSO, 24h-biol rep2

value: DMSO control


title: KPC63_Ctrl

description: Library name: Sample 1

value: Control


title: SZ8511 cells, DMSO, 24h-biol rep1


title: dKO

city: Kunming

first: lei

last: shi

state: Yunnan

address: No.17 Longxin Road

institute: Kunming Institute of Zoology

description: Library name: Sample2

data_processing:
Single-cell data analysis was performed using the Seurat R package. Feature barcode matrices were processed and analyzed using the Seurat RunUMAP function for nonlinear dimension reduction. Comparative analysis between control and Mcmbp/Trp53 dKO samples was conducted using the FindIntegrationAnchors function, which identifies anchors representing cells with similar biological states based on canonical correlation analysis. Integrated analyses were then performed on all cells following the standard Seurat package workflow.
Assembly: Mouse mm10
Supplementary files format and content: Table separated value files and matrix files

source_name: cortex

extract_protocol:
This study was involved samples pooled together for single cell sequencing. We  pooled 3 samples together as control (wild type or heterozygote), and 4 samples  as dKO (Emx1-Cre Mcmbp/Trp53 double conditional KO).
Single-cell RNA processing was performed using SeekOne® Digital Droplet (SeekOne® DD) system and associated kits from SeekOne Bio, including: SeekOne® DD S3 Microarray Kit (SEEKGENE, K00202-0201), SeekOne® DD Single-Cell Purification Kit (SEEKGENE, K00202-0205), SeekOne® DD Single-Cell Whole-Sequence Microbead Kit (SEEKGENE, K00801-0202), SeekOne® DD Single-Cell Full Sequence Reverse Transcription Kit (SEEKGENE, K00801-0203) and SeekOne® DD Library Construction Kit (SEEKGENE, K00202-0204). The SeekOne® DD platform enables comprehensive processing from single-cell nucleic acid labeling to full-sequence transcriptome library construction. The system employs microfluidic-based water-in-oil droplet technology for single-cell isolation and capture. RNA molecules from individual cells are labeled using nucleic acid-modified Barcoded Beads, and full-length coding and non-coding RNAs are captured using random primers. Intracellular rRNA and mitochondrial contamination are eliminated using proprietary blocker technology. Libraries were constructed following the "SeekOne® DD Single-Cell Whole Sequence Transcriptome Kit Instruction Manual" to ensure compatibility with high-throughput sequencers. Quality control criteria for qualified libraries included: main peak fragment size range: 450-900 bp, absence of small fragments (verified by Agilent 4200 TapeStation), Minimum library concentration: 1 ng/μL (measured by Qubit 4.0). If small fragments were detected, additional 0.6x purification steps were performed until complete removal was achieved.

value: cortex

value: Embryonic 15.5 days

value: Emx1-Cre Mcmbp/Trp53 dKO

tag: batch


title: IOMM-Lee cells, AZ628 1μM, 24h-biol rep3

source_name: IOMM-Lee

value: IOMM-Lee


title: Ctrl

description: Library name: Sample1

value: control


title: IOMM-Lee cells, AZ628 1μM, 24h-biol rep1


title: IOMM-Lee cells, AZ628 1μM, 24h-biol rep2


title: Prkaa1_KO_IP_H3K9ac_exp2

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

description: Library name: Prkaa1 KO, IP, H3K9ac, exp2

data_processing:
The quality of the generated fastq files was examined with the FASTQC software. Fastq files were aligned against mm10 mouse genome with Bowtie2 aligner. The output files were filtered for low quality reads, duplicates, blacklist regions and mitochondrial genome entries with custom made pipeline from Bedtools and Samtools. Peak calling was performed with MACS2 callpeak command with default parameters. For H3K9ac only, we defined the broadpeaks. Bedgraph files were generated with MACS2 bdgcomp using the subtract option to remove the respective Input signal from the IP signal, and then converted to bigwig format. Input file for experiment 1 is common for both H3K9ac and PCAF IP files for every condition.
Assembly: mm10
Supplementary files format and content: Bed files with peaks.
Supplementary files format and content: Bigwig files for every sample depicting IP signal after subtraction of Input signal.

source_name: Spleen

growth_protocol: anti-CD3 (1 ug/ml), anti-CD28 (1 ug/ml), IL-6 (20 ug/ml), IL-1b (20 ug/ml), IL-23 (20 ug/ml) in in RPMI 1640 Medium, GlutaMAX™ supplemented with 10% FBS, 100 U/ml penicillin/streptomycin and 50 uM β-Mercaptoethanol

extract_protocol:
On day 4, 4x10^6 cells from each cell culture were collected, washed and fixed for 10 min in FBS-free RPMI containing 1% formaldehyde at RT and quenched with 0.125M glycine. Fixed cells were washed with ice-cold PBS, nuclei were prepared by cell lysis and chromatin shearing was performed by Covaris sonication. After sonication, an aliquot of sheared chromatin was kept as input. The rest of the sheared chromatin samples were proceeded to immunoprecipitation using antibodies specific for H3K9ac and PCAF. The immunocomplexes were isolated using magnetic beads and washed 6 times with RIPA buffer. DNA was isolated from immunoprecipitated complexes through proteinase K treatment, followed by reverse crosslinking at 65°C. DNA fragments were purified using NGS magnetic beads.
ChIP-seq library construction and sequencing were carried out at the Greek Genome Center (GGC) of BRFAA. Libraries for H3K9ac and PCAF ChIPseq were generated with NEBNext Ultra II DNA Library Prep Kit for Illumina, as indicated by the manufacturer’s guidelines (NEB, E7645L) using 10ng of DNA (chromatin that was not incubated with the antibody was used as input DNA). The quality of the generated libraries was validated with the Agilent bioanalyzer DNA1000 chip. Subsequently, the libraries were quantitated with the qubit HS spectrophotometric method and pooled in equimolar amounts for Sequencing.

treatment_protocol: +/- Activin-A, +/- Dorsomorphin

value: Spleen

value: Activin-A


title: ActA_IP_H3K9ac_exp2

description: Library name: ActA, IP, H3K9ac, exp2

value: Wild type


title: IOMM-Lee cells, DMSO, 24h-biol rep3


title: Prkaa1_KO_Input_exp2

description: Library name: Prkaa1 KO, Input, exp2


title: IOMM-Lee cells, DMSO, 24h-biol rep1


title: PBS_IP_H3K9ac_exp2

description: Library name: PBS, IP, H3K9ac, exp2


title: IOMM-Lee cells, DMSO, 24h-biol rep2


title: ActA_Input_exp2

description: Library name: ActA, Input, exp2


title: ActA_Dorsomorphin_IP_PCAF_exp1

description: Library name: ActA and Dorsomorphin, IP, PCAF, exp1

value: Activin-A + Dorsomorphin


title: SZ8511 cells, KD-SLC7A1, 48h-biol rep3

value: SLC7A1 knockdown


title: SZ8511 cells, KD-SLC7A1, 48h-biol rep1

value: high-grade meningioma cells


title: ActA_IP_PCAF_exp1

description: Library name: ActA, IP, PCAF, exp1


title: SZ8511 cells, KD-Control, 48h-biol rep3

value: wild-type


title: PBS_IP_PCAF_exp1

description: Library name: PBS, IP, PCAF, exp1


title: dko5

data_processing:
Illumina  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm39primary genome using Hisat2
Gene expression counts per sample were calculated. First ly, align RNA seq reads to the mouse genome GRCm39primary  by using  Hista2 to generate sam files; Then, sam files were sorted by samtools to generate sorted sam files; Finally, htseq-count program was used to quantify gene reads counts for every sample.
Assembly: GRCm39primary
Supplementary files format and content: Tab-delimited text files were calculated gene expression read counts  for each Sample

extract_protocol:
Total RNA was extracted from freshly micro-dissected  mouse embryonic cerebral cortex Trizol and RNA Clean & Concentrator Kit
RNA purification, reverse transcription, library construction and sequencing were performed in Sequanta Technologies Co., Ltd at Shanghai according to the manufacturer's instructions. The Globin mRNA was removed using GLOBINclear™ Mouse/Rat Kit (Invitrogen, AM1981). The non-Globin mRNA-focused sequencing libraries from 1µg total RNA were prepared using VAHTS mRNA-seq v3 Library Prep Kit (Vazyme, NR611). PolyA mRNA was purified from total RNA using oligo-dT-attached magnetic beads and then fragmented by fragmentation buffer. Taking these short fragments as templates, first strand cDNA was synthesized using reverse transcriptase and random primers, followed by second strand cDNA synthesis. Then the synthesized cDNA was subjected to end-repair, phosphorylation and 'A' base addition according to Illumina's library construction protocol. Then Illumina sequencing adapters were added to both size of the cDNA fragments. After PCR amplification for DNA enrichment, the AMPure XP Beads (Beckmen, A63880) were used to clean up the target fragments of 200-300 bp. After library construction, Qubit 3.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific) was used to quantify concentration of the resulting sequencing libraries, while the size distribution was analyzed using Agilent BioAnalyzer (Being, CHN). Sequencing was performed using an Illumina Novaseq 6000 following Illumina-provided protocols for 2x150 paired-end sequencing in Sequanta Technologies Co., Ltd.

tag: age

value: dKO


title: SZ8511 cells, DMSO, 24h-biol rep3


title: SZ8511 cells, KD-Control, 48h-biol rep2


title: SZ8511 cells, KD-Control, 48h-biol rep1


title: dko4


title: dko3


title: IOMM-Lee cells, KD-SLC7A1, 48h-biol rep3


title: dko2


title: IOMM-Lee cells, KD-SLC7A1, 48h-biol rep2


title: dko1


title: PBS_Input_exp2

description: Library name: PBS, Input, exp2


title: IOMM-Lee cells, KD-SLC7A1, 48h-biol rep1


title: cko64

value: McmbpcKO


title: IOMM-Lee cells, KD-Control, 48h-biol rep2


title: SZ8511 cells, KD-SLC7A1, 48h-biol rep2


title: IOMM-Lee cells, KD-Control, 48h-biol rep1


title: cko56


title: cko61


title: cko58


title: Untagged ESCs, input for RAD21,CTCF ChIP rep4

city: San Francisco

first: Elphege

middle: P

last: Nora

address: 555 Mission Bay Blvd S

department: CVRI

institute: UCSF

description: Library name: RSC71

data_processing:
Fastq files were aligned to a catenated mm10 and hg38 reference genome using Bowtie2. Reads with a mapq score ≥ 30 were retained and duplicates were removed, using samtools. ChIP bigwigs were generated with the bamCoverage function from deepTools, with scaling factors calculated using the formula (human reads in input) / (mouse reads in input) / (human reads in ChIP) x 15000000. The multiplier of 15000000 was chosen arbitrarily to set the final scaling factors close to 1. Input bigwigs were normalized using RPKM.
To create bigwig files with multiple replicates combined, we took equal numbers of reads from each replicate (samtools view with subsample option), combined them, and created a bigwig normalized by RPKM.
To create lists of ChIP-seq peaks found in multiple replicates, we first used macs2 version 2.2.9.1 to call peaks on each replicate individually. For NIPBL and MAU2 peaks, we used the HA ChIP in untagged cells as the control. For CTCF and H3K27ac peaks, we used the input samples as the control. We used bedtools multiinter to identify the regions that were called as peaks in the majority of replicates. To define the peak widths, we used macs2 again to call peaks using all of the replicates together. We selected the peaks from this list that overlap with the regions called in the majority of replicates (using bedtools intersect -u). Finally, we removed peaks in ENCODE blacklisted regions using bedtools intersect -v.
Assembly: mm10
Supplementary files format and content: bigwig tracks

growth_protocol: mESCs were cultured in 2iSL medium [DMEM + GlutaMAX + sodium pyruvate (ThermoFisher 10569044) supplemented with 15% fetal bovine serum (Gibco SKU A5256701), 550 µM 2-mercaptoethanol (ThermoFisher 21985-023), 1X nonessential amino acids (ThermoFisher 11140-050), 10^4 U of Leukemia Inhibitory Factor (Millipore ESG1107), 1 µM PD0325901 (Apex Bio/Fischer A3013-25), and 3 µM CHIR99021 (Apex Bio/Fischer A3011-100)]. Cells were maintained at a density of 0.2-1.5 x 10^5 cells/cm2 by passaging using TrypLE (ThermoFisher 12605010) every 24-48 hours on 0.1% gelatin-coated dishes (Sigma-Aldrich G1890-100G in 1XPBS) at 37°C and 5% CO2. The medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 6 months and tested negative. To establish neural progenitors (NPCs), 0.2 million FKBP-NIPBL (EA18.1) ESCs were seeded in a T25 gelatinized flask in 2iSL medium. The following day, cells were rinsed twice in 1X PBS and switched to N2B27 medium [50% DMEM/F12 medium (Gibco 31330-038), 50% Neurobasal medium (Gibco 21103-049), 1X GlutaMAX (Gibco 35050061), 0.5X B27 (Gibco 17504-044), 0.5X N2 (Millipore SCM012), and 0.1 mM 2-mercaptoethanol]. After 7 days with daily media changes, cells were detached using TrypLE and seeded on nongelatinized bacterial dishes for suspension culture at 3 million cells per 75 cm2 and cultured in N2B27 containing 10 ng/mL EGF and FGF (Peprotech 315-09 and 100-18B). After 3 days, floating aggregates were seeded on gelatinized dishes. After 2-4 days, poorly attached aggregates were dislodged and discarded, and remaining adherent NPC cells were dissociated using Accutase (Innovative Cell Technologies AT104), passaged twice on gelatinized dishes in N2B27 + EGF/FGF and cryopreserved in 10% DMSO in N2B27 + EGF/FGF. Cells were thawed and cultured on gelatinized dishes in N2B27 + EGF/FGF and passaged by incubating in Accutase for 2-3 minutes at room temperature (RT).

extract_protocol:
For all NIPBL and MAU2 ChIP experiments, cells were double crosslinked in DSG followed by formaldehyde. First, cells were dissociated using TrypLE (ESCs) or Accutase (NPCs) and resuspended in culture medium, and 15 million cells were pelleted at 100g for 5 minutes at RT. Supernatant was discarded and cell pellets were washed once in PBS. Cells were resuspended in 10 mL PBS, and DSG (dissolved in DMSO) was added to a final concentration of 2 mM. Cells were fixed at room temperature for 45 minutes with rotation. Cells were then pelleted at 200g for 5 minutes and washed three times with PBS (each time pelleting at 200g for 5 minutes). Cells were then resuspended in 5 mL of 10% FBS prepared in PBS. To this, 5 mL of freshly prepared 2% formaldehyde solution was added to reach a final formaldehyde concentration of 1%. 2% formaldehyde was diluted from 16% methanol-free formaldehyde in 1X PBS with 10% FBS. Resuspended cells were fixed for 10 minutes at RT with rotation. To quench, 0.525 mL of 2.5 M glycine solution in PBS was added (final concentration 0.125 M glycine), and cells were incubated for 5 minutes at RT followed by 15 minutes on ice. Cells were pelleted by centrifuging at 200g for 5 minutes at 4° C. Cell pellets were resuspended in 1 mL of ice-cold 0.125M glycine in PBS, transferred to 1.5 ml tubes, and centrifuged at 300g for 5 minutes at 4° C. Supernatant was discarded and pellets were snap frozen on dry ice and stored at -70°C. For CTCF and RAD21 ChIP experiments, cells were dissociated, pelleted, and fixed in 1% formaldehyde for 10 minutes with the subsequent quenching and washes as above. Fixed cells were thawed on ice, resuspended in 1 mL of ice-cold lysis buffer [10 mM Tris HCl pH 7.5, 10 mM NaCl, 0.2% NP-40 (IGEPAL), 0.2% TritonX-100, 1 mM EDTA, 0.5 mM EGTA, supplemented with fresh protease inhibitor] and incubated on ice for 10 minutes. ~9.75 x 106 mouse nuclei were combined with ~0.25 x 106 double crosslinked HEK nuclei as spike-in. Nuclei were pelleted at 400g for 5 minutes at 4°C, supernatant discarded and nuclear pellets resuspended in 1 mL of shearing buffer (0.5% SDS, 10 mM Tris HCl pH 7.5, supplemented with fresh 1x protease inhibitor). Chromatin was sheared using a Covaris with settings PIP 105, Duty factor 5, Cycles per burst 200, total time 23 minutes for double-crosslinked cells or 15 minutes for formaldehyde-crosslinked cells. After shearing, samples were spun at 13,000 rpm for 5 minutes at 4° C. 2.5% of the sample was removed to use as input, and the remainder of the supernatant was used for ChIP. The ChIP reaction was assembled as follows: 900 ul chromatin, 442 μL 5X ChIP incubation buffer (5% TritonX-100, 0.75 M NaCl, 5 mM EDTA, 2.5 mM EGTA, 50 mM Tris-Cl pH7.5), 40 uL Dynabeads (pre-washed in ChIP incubation buffer), 10 ug HA antibody, 22.5 uL protease inhibitor, and 835.5 uL water. Tubes were incubated overnight at 4°C on a rocker. Following overnight incubation, beads were collected using a magnetic rack and washed sequentially with different wash buffers for 5 minutes each on a rocker at 4°C. Beads were washed twice with 500 μL of cold wash buffer 1 (0.1% SDS, 0.1% Sodium deoxycholate, 1% TritonX-100, 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8), once with 500 μL of cold wash buffer 2 (0.1% SDS, 0.1% Sodium deoxycholate, 1% TritonX-100, 0.5 M NaCl, 1 mM EDTA, 10 mM Tris pH 8), once with 500ul of cold wash buffer 3 [0.25 M LiCl, 0.5% Sodium deoxycholate, 0.5% NP-40 (IGEPAL), 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8], and twice with 500 μL of cold wash buffer 4 (1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8). For elution, beads were resuspended in 200 μL of elution buffer (1% SDS, 0.1M NaHCO3) and incubated on a rocker for 20 minutes at RT. Beads were then separated using a magnetic rack and the eluate (supernatant) was transferred to a fresh tube. Input samples were thawed on ice and elution buffer was added to bring the volume to 200 μL. To each sample, 2 μL of 1 mg/ml RNaseA was added and incubated at 37°C for 30 minutes. To reverse crosslinks, 8 μL of 5 M NaCL and 5 μL of 10 mg/ml Proteinase K was added and samples were incubated overnight at 65°C. DNA was eluted using MinElute kit from Qiagen (28604).
Libraries were prepared using NEBNext Ultra II DNA library prep kit according to the manufacturer’s protocol (E7645S). The entire ChIP sample and 50 ng of the input samples were used for library prep. Libraries were amplified for 16 cycles, followed by 0.9X SPRI bead purification (Bulldog Bio CNGS005). The eluate was run on a 2% E-gel (Invitrogen G401002) and fragments between 200-600bp were excised and eluted using MinElute gel extraction kit (Qiagen 28604). Quality and quantity of libraries were assessed using Qubit and Bioanalyzer High Sensitivity DNA kit. Libraries were sequenced on NextSeq 2000 using 65 bp single-end reads. Some libraries were sequenced in a second lane for additional reads.

treatment_protocol: FKBP12F36V depletion was triggered using 500 nM of PROTAC dTAG-13 (dTAG) (Sigma-Aldrich SML2601) in the culture medium for 24 hours.

value: ESC

value: wild type

value: input


title: Untagged ESCs, RAD21 ChIP, rep4

description: Library name: RSC59


title: Untagged ESCs, CTCF ChIP, rep4

description: Library name: RSC60

value: CTCF_Active Motif_61311


title: Untagged ESCs, input for RAD21,CTCF ChIP rep3

description: Library name: RSC48


title: ctrld3

value: cortex

value: Embryonic 15.5 days

value: McmbpHE


title: ctrld2


title: Untagged ESCs, CTCF ChIP, rep3

description: Library name: RSC37


title: ctrld1


title: Untagged ESCs, RAD21 ChIP, rep3

description: Library name: RSC36


title: ctrl67

value: control


title: Untagged ESCs, input for RAD21,CTCF ChIP rep2

description: Library name: RSC33


title: ctrl65


title: Untagged ESCs, CTCF ChIP, rep2

description: Library name: RSC22


title: ctrl510


title: IOMM-Lee cells, KD-Control, 48h-biol rep3

value: IOMM-Lee


title: Untagged ESCs, RAD21 ChIP, rep2

description: Library name: RSC21


title: Untagged ESCs, CTCF ChIP, rep1

description: Library name: RSC13


title: ctrl54


title: Ctrl_4C_K36me2

description: Library name: Sample 45

value: H3K36me2 (active motif, 61019)

value: WT

value: Control


title: WT_mESC_dTAG48h_RNA_rep1

data_processing:
Paired-end RNA-seq reads were trimmed and mapped to the mm9 genome by TopHat v2.1.1 (Trapnell et al., 2009). FPKM (Fragments per kilobase per million of sequenced reads) for gene expression was calculated using Cufflinks v2.2.1 (Trapnell et al., 2012) based on mm9 refFlat from the UCSC genome annotation database.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: mESC

growth_protocol: Serum/Lif (S/L) R1 mESCs were cultured in 0.1% gelatin-coated dishes in Dulbecco’s modified Eagle’s medium (Gibco, 11995065) containing 15% FBS (Gibco, 16000-044), 1000 IU/ml leukemia inhibitory factor (Lif) (Merck Millipore, ESG1107), 100 IU/ml penicillin and 100 μg/ml streptomycin (Merck Millipore, TMS-AB2-C), 2 mM GlutaMAX (Gibco, 35050061), 1% EmbryoMax nucleosides (Merck Millipore, ES-008-D), 0.1 mM nonessential amino acids (Gibco, 25-025-CIR), and 0.1 mM 2-mercaptoethanol (Gibco, 21985023). 2i mESCs were cultured on 0.2% gelatin-coated dishes in 2i/Lif medium (N2B27 medium supplemented with 1 μm PD0325901 (Tocris, 41921), 3 μm CHIR99021 (Tocris, 4423) and 1000 IU/ml Lif). Cells were routinely propagated every 2-3 days. The formative EpiLCs were induced as previously described (Hayashi et al., 2011). Briefly, 1.0×105 2i ESCs were plated in a well of a 12-well plate coated with Matrigel (BD, 356230/356231, diluted at a ratio of 1:100 in N2B27 medium). Cells were cultured in N2B27 medium containing activin A (20 ng/ml), bFGF (12 ng/ml), XAV939 (5 μM), and KSR (1%). EpiLCs were collected for analysis at the indicated time point.

extract_protocol:
Embryos or cells were lysed and used directly as input materials for subsequent RNA-seq library prepararion.
All RNA libraries were prepared using the Smart-seq2 method as previously reported (Picelli et al., 2014), and were sequenced by the Illumina Hiseq X Ten or Novaseq 6000 system according to the manufacturer’s instructions.

value: mESC

tag: developmental stage/treatment

value: dTAG 48h


title: PR-DUB_OE_4C_K36me2

description: Library name: Sample 46

tag: genotype

value: PR-DUB OE


title: cko51


title: PRC1degNsd1KO_mESC_dTAG48h_RNA_rep2

value: PRC1deg;Nsd1 KO


title: cko66

value: dKO


title: ctrl59


title: EedKO_mESC_K36me2_rep1

description: Library name: Sample 41

value: S/L mESC

value: Eed KO


title: EedKO_mESC_K36me2_rep2

description: Library name: Sample 42


title: PRC1deg_mESC_dTAG48h_RNA_rep1


title: PRC1deg_mESC_dTAG48h_RNA_rep2


title: Nsd1KO_mESC_dTAG48h_RNA_rep1

value: Nsd1 KO


title: Nsd1KO_mESC_dTAG48h_RNA_rep2


title: 4C_Kdm6b_WT_K36me2_rep1

description: Library name: Sample 40

value: KDM6B OE


title: L2C_Ctrl_K36me3_rep2

description: Library name: Sample 32

source_name: late 2-cell

value: late 2-cell

value: H3K36me3 (active motif, 61902)


title: WT_Day3_EpiLC_RNA_rep2

source_name: EpiLC

value: EpiLC


title: WT_Day3_EpiLC_RNA_rep1


title: WT_mESC_K36me2_rep1

description: Library name: Sample 43


title: Untagged ESCs, RAD21 ChIP, rep1

description: Library name: RSC12

value: ESC

value: wild type


title: Untagged ESCs, input for RAD21,CTCF ChIP rep1

description: Library name: RSC18

value: input


title: ctrl57

value: cortex

value: Embryonic 15.5 days

value: control


title: 4C_Kdm6b_Mut_K36me2_rep1

description: Library name: Sample 39

value: H3K36me2 (active motif, 61019)

value: WT

value: Control


title: Nsd1_KO_Day3_EpiLC_RNA_rep2


title: L2C_Ctrl_K36me2_rep2

description: Library name: Sample 30


title: WT_mESC_K36me2_rep2

description: Library name: Sample 44


title: L2C_Ctrl_K36me3_rep1

description: Library name: Sample 31


title: WT_mESC_dTAG48h_RNA_rep2

value: mESC

value: dTAG 48h


title: Nsd1_KO_Day3_EpiLC_RNA_rep1


title: PRC1degNsd1KO_mESC_dTAG48h_RNA_rep1

value: PRC1deg;Nsd1 KO


title: L2C_Ctrl_K36me2_rep1

description: Library name: Sample 29


title: WT_EpiLC_Day0_RNA_rep2

value: 2i mESC


title: L2C_amanitin_K36me3_rep2

description: Library name: Sample 28

value: α-amanitin


title: WT_EpiLC_Day0_RNA_rep1


title: L2C_amanitin_K36me3_rep1

description: Library name: Sample 27

value: late 2-cell


title: Nsd1_KO_EpiLC_Day0_RNA_rep2

value: Nsd1 KO


title: L2C_amanitin_K36me2_rep2

description: Library name: Sample 26


title: Nsd1_KO_EpiLC_Day0_RNA_rep1


title: L2C_amanitin_K36me2_rep1

description: Library name: Sample 25


title: SN_FGO_150_K36me3_rep2

description: Library name: Sample 24

source_name: FGO

value: FGO

value: H3K36me3 (active motif, 61021)

value: SN


title: E85_KO_ExE_RNA_rep1

source_name: Extra-embryonix ectoderm

value: Extra-embryonix ectoderm


title: SN_FGO_150_K36me3_rep1

description: Library name: Sample 23


title: SN_FGO_80_K36me2_rep2

description: Library name: Sample 22


title: E85_KO_Epi_RNA_rep2

source_name: Epiblast

value: Epiblast


title: NSN_FGO_124_K36me3_rep2

description: Library name: Sample 20

value: NSN


title: NSN_FGO_123_K36me3_rep1

description: Library name: Sample 19


title: E85_Ctrl_headfold_RNA_rep2

source_name: Headfold

value: Headfold

value: control


title: SN_FGO_100_K36me2_rep1

description: Library name: Sample 21

value: H3K36me2 (active motif, 61019)

value: WT


title: E85_KO_Epi_RNA_rep1


title: E85_Ctrl_headfold_RNA_rep1


title: NSN_FGO_80_K36me2_rep2

description: Library name: Sample 18


title: E85_Ctrl_ExE_RNA_rep2