title: 3T3-L1,  Vector-1 Input

city: Anshun

first: Longkun

last: Hu

state: Guizhou

address: Machang Town, Yunmanhu Campus of Guizhou Medical University

institute: Guizhou Medical University

description: Library name: Vector-1 input

data_processing:
For ChIP-seq data analysis, the -shift size was set up to 0 for peak calling via MACS2 v2.2.7.1. The command used for read mapping was: bowtie2 -n unal -threads 16 -sensitive -k 3 -q -phred33. To reduce the false positive rate and obtain the high-quality, consistent, and reproducible peaks, the Irreproducible Discovery Rate values between original replicates, the pseudo-replicates which respectively and randomly split from each of the original replicate, and the pseudo-replicates that randomly split after pooling the replicates were calculated by IDR v2.0.4.2 (https://github.com/nboley/idr), respectively. The IDR value of 0.05, 0.02 and 0.01 were used to filter the irreproducible peaks from original replicates, the pseudo-replicates split from original replicates and pooled pseudo- replicates, respectively. We further filtered the peaks of H3K56ac with int(-10*log10qvalue) scores below 25, and rescaled the score column of MACS2's narrowPeak file to the range of 10-1000 to meet the requirement of narrowPeak format.
We produced the visualization files, calculated the library complexity, insert fragment distribution, sample cross correlation, TSS enrichment score, FRiP (fraction of reads in peaks) and the Signal Portion Of Tags (SPOT) to evaluate the quality of ChIP-seq. The signal-to-noise rates were high in all the ChIP-seq libraries. After removing irreproducible peaks, 106,057, 160,476, 116,977 and 79,900 peaks were obtained from H3K56ac ChIP-seq experiments, respectively; 99,743, 108,486, 96,538, 97,990 peaks were obtained from control ChIP-seq experiments, respectively.
MGISEQ-T7 sequencer was used to sequence the various libraries in CHIP sequencing. Trimmomatic v0.32 was used for raw reads filtering; bowtie2 v2.4.4 was used for reads mapping; Picard v2.23.9 and SAMtools v1.9 were used for removing of PCR duplication and low-quality mapping reads; MACS2 v2.2.7.1 was used for peak calling; IDR v2.0.4.2 was used to evaluate the irreproducible discovery rate of peaks; The irreproducible peaks were filtered using custom code (https:// github.com/hcph/wheatATAC).
Assembly: GRCm39
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
A ChIP assay was conducted utilizing a kit from Cell Signaling Technology, USA (catalog number 91820S). 3T3-L1 adipocytes were fixed using 4% formaldehyde and subsequently harvested by scraping for lysis. Cross-linked chromatin samples were extracted using nuclease digestion (37 °C for 20 min) and sonication (20% power for 5 s, followed by 10 s, repeated 30 times in total). Soluble fragmented soluble chromatin was immunoprecipitated for 48 h at 4 °C with H3K56ac antibody and incubated with Protein A/G for 2 h. The beads were then resuspended in ChIP elution buffer, and cross-link reversal was performed at 65 °C for 30 min. The enriched DNA was isolated by incubation with proteinase K and RNase A. After end-repair and A-tailing, the DNA was treated with sequencing adapters and amplified by PCR to obtain the sequencing library.
The library was quantified with the help of Qubit2.0, and the MGISEQ-T7 sequencer was used to sequence the various libraries in accordance with the effective concentration as well as the target data volume. After aligning the reads to the reference mouse genome, the ChIP-seq peaks were identified using MACS version 1.4.2.

tag: cell line

value: Mouse adipocyte


title: 3T3-L1,  Sirt3-OE 1 Input

status: Public on Mar 02 2026

type: SRA

country: China

description: Library name: Sirt3_OE 1 input

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: genotype

value: Sirt3 overexpression

tag: batch


title: Multiome, Bengalese finch HVC, GEX, biol rep 2

city: San Francisco

first: Michael

last: Brainard

state: CA

address: 675 Nelson Rising Ln

country: USA

institute: University of California, San Francisco

description: Library name: hvc_rna_run2

library_source: transcriptomic single cell

data_processing:
FASTQ files were aligned to the Bengalese finch reference genome (lonStrDom2, GCF_005870125.1) using cellranger-arc v2.0.2. Included also in the alignment index were gene models with extended 3' UTRs as described in Colquitt et al., eLife, 2023. Ambient RNA was removed using cellbender v0.3.2 with a false positive rate of 0.05. Using Seurat v5.2.1, nuclei were retained that satisfied the following conditions: 1000 < number of GEX UMIs < 25,000, 1000 < number of ATAC fragments < 30,000, nucleosome signal < 2, and TSS enrichment >1.  Doublets were removed using two methods. First, nuclei were demultiplexed by their genotype using souporcell v1.0, which assigns each nucleus to an individual bird and estimates whether a nucleus is a doublet or singlet. Second, we performed doublet detection using DoubletFinder v2.0.4. Nuclei were retained if they were called a singlet in both approaches. Cluster labels were assigned using Seurat label transfer and labels from the snRNA-seq dataset.
Assembly: lonStrDom2, GCF_005870125.1
Supplementary files format and content: Cellranger-arc output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz

molecule: total RNA

organism: Lonchura striata

source_name: HVC

extract_protocol:
For snRNA/ATAC-seq samples, three to four adult (>120 dph) male Bengalese finches were anesthetized with isoflurane, transcardially perfused with ice-cold carbogenated ACSF, then decapitated. Brains were dissected out into ice-cold carbogenated ACSF then coronally sectioned using a Leica VT1000 vibratome at 300 um. Areas of interest were microdissected out, placed in cryovials, frozen in liquid nitrogen, then transferred to -80C for long-term storage. Nuclei were isolated using a modified version of the Optiprep method. Several stable buffers were prepared before nuclei isolation and stored a 4C: 1.079x Homogenization Buffer Stable Solution ("HBS", 260 mM sucrose, 30 mM KCl, 10 mM MgCl2, 20 mM Tricine-KOH pH 7.8), Diluent Buffer (150 mM KCl, 30 mM MgCl2, 120 mM Tricine-KOH pH 7.8), 50% iodixanol solution (diluted from 60% Optiprep Density Gradient Medium, Sigma, D1556, using Diluent Buffer), and 5X ATAC-RSB (50 mM Tris-HCl pH 7.5, 50 mM NaCl, 15 mM MgCl2). On the day of nuclei isolation, the following buffers were prepared: 1x Homogenization Buffer Unstable Solution ("HBU", HBS to 1x, 1 mM DTT, 0.5 mM spermidine, 0.15 mM spermine, 0.3\% NP-40, 1 U/uL Protector RNase Inhibitor (Sigma 3335402001), 1x Complete Protease Inhibitor (prepared from a 25x solution consisting of one tablet (Sigma, 11697498001) dissolved in 2 mL nuclease-free water)), 30% Iodixanol Solution and 40% Iodixanol Solution (both diluted from 50% iodixonal solution using 1x Homogenization Buffer Unstable Solution), and ATAC-RSB-Tween (1x ATAC-RSB, 0.1\% Tween-20, 1% BSA, and 1 U/uL Protector RNase Inhibitor). Samples from different birds were pooled and 1 mL 1x HBU was added. Samples were incubated on ice for 5 minutes, then transferred to a 2 mL glass dounce (Kimble). Samples were homogenized with 15 strokes of the loose pestle, then 15 strokes of the tight pestle. Samples were transferred to 2 mL tubes then centrifuged for 5 minutes at 350xg at 4C using a swing-out rotor. All but 200 uL of supernatant was removed, the total volume was brought up to 400 uL using 1x HBU, then the pellet was gently resuspended by pipetting. 400 uL 50% iodixanol solution was added and mixed well by pipetting. 600 uL 30% iodixanol solution was layered underneath the 25% iodixonal/tissue layer, followed by 600 uL 40% iodixanol solution underneath the 30% layer. In a pre-chilled swing-out rotor, samples were centrifuged for 20 minutes at 10,000xg at 4C with the brake off. Starting at the top of the solution, enough solution was aspirated off to leave ~200-300 uL above the interface between the 30% and 40% iodixanol layers, which contains nuclei. 200 uL of the nuclei band was aspirated and transferred to a clean 1.5 mL tube containing 1 mL of ATAC-RSB-Tween. Nuclei were centrifuged for 10 minutes at 500xg at 4C using a swing-out rotor. The entire supernatant was carefully removed, followed by addition of 12 uL Nuclei Resuspension Buffer (10X Genomics) and gentle resuspension by pipetting.
Nuclei were counted and their concentrations were adjusted to 800-12,000 nuclei/uL. The nuclei were then loaded onto a Next GEM Chip J (10X Genomics) at numbers targeting 2,500 to 10,000 recovered nuclei. Sequencing libraries for each region were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit. The libraries were then pooled, and sequenced on an Illlumina NovaSeq S4 200 flow cell at the UCSF CAT.

tag: tissue

value: HVC

tag: library type

value: mRNA


title: 3T3-L1, Vector-2

description: Library name: Vector-2

value: WT


title: 3T3-L1, Vector-1

description: Library name: Vector-1


title: Multiome, Bengalese finch HVC, GEX, biol rep 1

description: Library name: hvc_rna_run1


title: 3T3-L1,  Sirt3-OE 2 Input

description: Library name: Sirt3_OE 2 input


title: 3T3-L1, Sirt3-OE 2

description: Library name: Sirt3-OE 2


title: Worm, WT, day10, rep 2

city: La Jolla

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

description:
Library name: Worm_WT_D10_rep2
8148_d10-2

library_source: transcriptomic

data_processing:
Reads were trimmed using Trim Galore!. Alignment was performed using HISAT2 to the worm genome ce10. Quantification was done with featureCounts using exon regions. Differential expression analysis was performed with DESeq2.
Assembly: ce10
Supplementary files format and content: Tab-delimited text files with raw counts per gene per sample from DESeq2.

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Worms were maintained on nematode growth medium (NGM) agar plates seeded with Escherichia coli strain OP50 at 20 °C.

extract_protocol:
Total RNA was isolated from all samples using standard protocols.
Watchmaker mRNA Library Prep Kit (7BK0001) with xGEN Stubby adaptors (IDT, 336338420) and xGEN 10nt UDIs (IDT, 336338436).

treatment_protocol: No treatment was applied prior to RNA extraction.

value: whole organism

value: H2B WT


title: Worm, E73R, day10, rep 1

description:
Library name: Worm_E73R_D10_rep1
8202_d10-2

value: H2B E73R


title: Worm, E73R, day10, rep 2

description:
Library name: Worm_E73R_D10_rep2
8202_d10-3


title: MCEC_Fat4KD_Rep3

city: St. Louis

first: Yoojung

last: Kwon

state: Missouri

address: 660 S Euclid Ave, BJCIH 8th floor, room 8302

department: Pathology and Immunology

institute: Washington University in St. Louis

description:
Library name: BVWDYV_6_FKD_3
Column names in BVWDYV-expression-matrix.tsv: BVWDYV_6_FKD_3

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1.
Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp.
Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0.
Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32.
Assembly: GRCm39_114
Supplementary files format and content: expression matrix for all sample

source_name: MCEC

extract_protocol:
After PBS washing, total RNAs were isolated using Rneasy mini kit (Qiagen).
RNA libraries were prepared under Plasmidsaurus company protocol. Briefly, they convert mRNA into complementary DNA (cDNA) via reverse transcription and second-strand synthesis, followed by tagmentation and library indexing and amplification.

value: MCEC

value: Mouse cardiac endothelial cell


title: MCEC_Fat4KD_Rep2

description:
Library name: BVWDYV_5_FKD_2
Column names in BVWDYV-expression-matrix.tsv: BVWDYV_5_FKD_2


title: 3T3-L1,  Vector-2 Input

description: Library name: Vector-2 input


title: Worm, WT, day10, rep 1

description:
Library name: Worm_WT_D10_rep1
8148_d10-1


title: Multiome, Bengalese finch NC, GEX, biol rep 1

description: Library name: nc_rna_run1

source_name: caudal nidopallium

value: caudal nidopallium


title: Worm, E73R, day3, rep 3

description:
Library name: Worm_E73R_D3_rep3
8202_d3-3


title: MCEC_CTRL_Rep2

description:
Library name: BVWDYV_2_WT_2
Column names in BVWDYV-expression-matrix.tsv: BVWDYV_2_WT_2

value: Wildtype


title: Multiome, Bengalese finch HVC, ATAC, biol rep 2

description: Library name: hvc_atac_run2

library_source: genomic single cell

value: ATAC


title: BMDM WT sample, rep 3

city: New Haven

first: Shaoning

last: Jiang

state: CT

address: 310 Cedar Street, BML142

institute: Yale University

description: Library name: BMDM_WT3

data_processing:
Raw sequencing reads were processed using the nf-core/rnaseq pipeline (v3.18.0) [10.5281/zenodo.1400710],
Assembly: GRCm39 mouse reference genome and the Gencode vM36 transcriptome annotation.
Supplementary files format and content: CSV format (Read counts)

source_name: Bone marrow

growth_protocol: BMDMs were collected and cultured following standard growth conditions.

extract_protocol:
Total RNA was extracted from BMDMs using standard RNA isolation procedures.
Paired-end sequencing

treatment_protocol: Samples were prepared accoriding to experimental design comparing WT and KO groups.

value: Bone marrow

value: BMDM


title: Worm, WT, day10, rep 3

description:
Library name: Worm_WT_D10_rep3
8148_d10-3


title: Multiome, Bengalese finch NC, ATAC, biol rep 1

description: Library name: nc_atac_run1


title: Worm, E73R, day3, rep 1

description:
Library name: Worm_E73R_D3_rep1
8202_d3-1


title: Worm, WT, day3, rep 3

description:
Library name: Worm_WT_D3_rep3
8148_d3-3


title: BMDM WT sample, rep 2

description: Library name: BMDM_WT2


title: Multiome, Bengalese finch HVC, ATAC, biol rep 1

description: Library name: hvc_atac_run1


title: MCEC_CTRL_Rep3

description:
Library name: BVWDYV_3_WT_3
Column names in BVWDYV-expression-matrix.tsv: BVWDYV_3_WT_3


title: BMDM WT sample, rep 1

description: Library name: BMDM_WT1


title: Worm, WT, day3, rep 1

description:
Library name: Worm_WT_D3_rep1
8148_d3-1


title: 3T3-L1, Sirt3-OE 1

description: Library name: Sirt3-OE 1


title: BMDM KO sample, rep 1

description: Library name: BMDM_KO1

value: KO


title: MCEC_Fat4KD_Rep1

description:
Library name: BVWDYV_4_FKD_1
Column names in BVWDYV-expression-matrix.tsv: BVWDYV_4_FKD_1


title: BMDM KO sample, rep 3

description: Library name: BMDM_KO3


title: Worm, WT, day1, rep 2

description:
Library name: Worm_WT_D1_rep2
8148_d1-3


title: Worm, WT, day3, rep 2

description:
Library name: Worm_WT_D3_rep2
8148_d3-2


title: Worm, N2, day1, rep 3

description:
Library name: Worm_N2_D1_rep3
N2_d1-3

value: wild-type


title: MCEC_CTRL_Rep1

description:
Library name: BVWDYV_1_WT_1
Column names in BVWDYV-expression-matrix.tsv: BVWDYV_1_WT_1


title: HA KDM6A FL OE rep3

city: Chicago

first: Long

last: Zhao

state: Il

address: 929 E 57th Street

department: Department of Chemistry

institute: University of Chicago

description: Library name: Histone_UTX_WT

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
caRNA MeRIP-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana transcriptome and spike-in sequences using HISAT2. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard. eCLIP-seq: Alignment: After QC, clean reads were aligned to the mouse genome (GRCm39) using STAR. Duplicate reads were filtered based on UMI information using umi_tools. Reads mapped to rRNA were removed. CUT&Tag, CUT&RUN, ATAC-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: TAIR10 or GRCm39
Library strategy: CUT&Run

extract_protocol:
For caRNA MeRIP-seq, caRNA was isolated and non-ribosome RNA was further enriched using RiboMinus transcriptome isolation kit (Invitrogen). 1 μL of 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 0.5-1 μg non-ribosome RNA, followed by fragmentation using RNA Fragmentation Reagents (Invitrogen). 5% of the fragmented RNA was saved as input. m6A immunoprecipitation was performed using the EpiMark N6-Methyladenosine Enrichment Kit (NEB) according to the manufacturer’s instructions. For nascent RNA-seq in mESCs, cells were incubated in media containing 1 mM EU with different time points and lysed with TRIzol (Invitrogen) for total RNA extraction. An equal amount of RNA extracted from EU-labeled Drosophila cells was added to each sample as a spike-in for further normalization. Nascent RNA was captured using the Click-iT™ Nascent RNA Capture Kit (Invitrogen) according to the manufacturer’s instructions. For CLIP-seq in mESCs, cells were UV crosslinked at 400 mJ/cm² (254 nm) once and nuclei were isolated following the cell fractionation protocol. For ATAC-seq, CUT&Tag, CUT&RUN in mESCs, nuclei were isolated by incubation with complete nuclei isolation buffer (Active Motif) according to the manufacturer’s instructions. For ATAC-seq, CUT&Tag, CUT&RUN in Arabidopsis, nuclei were extracted from 10-day-old seedlings after germination.
RNA libraries were constructed using the SMARTer Stranded Total RNA-seq Kit v2 (Takara) according to the manufacturer’s protocol. ATAC-seq was performed by using the ATAC-Seq Kit (Active Motif) according to the manufacturer’s instructions. CUT&Tag was performed by using the CUT&Tag-IT® Core Assay Kit (Active Motif) following the manufacturer’s instructions. CUT&RUN was performed by using the ChIC/CUT&RUN Assay Kit (Active Motif) following the manufacturer’s instructions.

treatment_protocol: All wild-type (WT) and transgenic Arabidopsis lines used in this study were in the Arabidopsis thaliana Columbia (Col-0) background. Seeds were surface sterilized in 10% sodium hypochlorite solution for 10 minutes, washed five times with sterile water, and grown on Murashige and Skoog (MS) medium (PhytoTech Labs) supplemented with 1.5% sucrose and 0.8% agar (pH 5.8). Seedlings were grown under controlled conditions in either a growth chamber or a growth room at 21 °C with a 16-hour light/8-hour dark photoperiod.                                                                                E14TG2a mES cells (ATCC) were cultured in DMEM (Gibco) supplemented with 15% FBS (Gibco), 1% EmbryoMax nucleosides (Sigma), 1% GlutaMAX supplement (Gibco), 1% MEM non-essential amino acids solution (Gibco), 1% Penicillin-Streptomycin (Gibco), 0.1 mM 2-Mercaptoethanol (Gibco), 1000 U/ml LIF (Sigma), 1 µM PD0325901 (Stemcell) and 3 µM CHIR99021 (Stemcell) at 37 °C in a humidified atmosphere with 5% CO2.

value: mESC

value: OE KDM6A FL


title: HA KDM6A del-IDR OE rep3

description: Library name: Histone_UTX_KI

value: OE KDM6A del-IDR


title: P300 Alkbh5 del-cIDR rep3

description: Library name: Histone_P300_KI

value: Alkbh5 del-cIDR


title: HA KDM6B FL OE rep3

description: Library name: Histone_KDM6B_WT

value: OE KDM6B FL


title: Hepatocytes from colorectal cancer liver metastasis (representing healthy liver tissue)

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

country: Japan

institute: IMSUT

description:
Library name: sample4
10x Genomics Flex

data_processing:
The demultiplexing, barcoded processing, and gene counting were performed by conducting CellRanger software v7.0.1.
Assembly: Human hg38
Supplementary files format and content: TSV files for barcodes, features, and count matrix

organism: Homo sapiens

source_name: Liver

extract_protocol:
The use of human liver samples was approved by the Ethics Committee of the Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital (approval number: 3200). Human liver samples were processed within 2 hours of surgical resection by sectioning a 2 cm × 2 cm tissue fragment into 5 mm2 pieces. The tissue fragments were fixed in Fix & Perm Buffer (10X Genomics) containing 4% formaldehyde (Polysciences) at 4°C with moderate agitation for 16–20 hours. Fixation was stopped by adding 1.25 M glycine, and the fragments were washed with tissue resuspension buffer (0.496X PBS (Nacalai Tesque), 50 mM Tris-HCl pH 8.0, 0.02% (w/v) BSA (Sigma), and RNase inhibitors (TOYOBO). The tissues were dissociated into single cells using a gentleMACS Dissociator (Miltenyi) with 0.2 mg/mL of Liberase TL and TH (Roche). Dissociated cells were washed with tissue resuspension buffer, filtered through a 70 μm cell strainer, and stained with MitoBrilliant 646 (Tocris Bioscience, 1:5000 dilution) at 37°C for 30 minutes. Following staining, the cells were washed, and filtered, and nuclei were stained with 2 μg/mL of Hoechst dye (Dojindo). The cell suspension was analyzed using BD FACSAria III flow cytometer (BD Biosciences), and Hoechst+ /MitoBrilliant 646+ hepatocytes were collected in Protein LoBind Tubes (Eppendorf).
Library preparation for single-cell transcriptomes of isolated hepatocytes was performed using the Chromium Fixed RNA Kit (10X Genomics, Human Transcriptome) following the manufacturer’s protocol.

value: Liver

tag: Sex

value: Male


title: Worm, N2, day1, rep 1

description:
Library name: Worm_N2_D1_rep1
N2_d1-1

value: whole organism


title: BMDM KO sample, rep 2

description: Library name: BMDM_KO2


title: Worm, N2, day1, rep 2

description:
Library name: Worm_N2_D1_rep2
N2_d1-2


title: YY1 Alkbh5 del-cIDR rep3

description: Library name: Histone_YY1_KI


title: Worm, WT, day1, rep 1

description:
Library name: Worm_WT_D1_rep1
8148_d1-2

value: H2B WT


title: HA KDM4B del-IDR OE rep3

description: Library name: Histone_KDM4B_KI

value: OE KDM4B del-IDR


title: RO1-016 + exo : healthy

type: RNA

city: Birmingham

first: Jessy

middle: S

last: Deshane

state: AL

address: 1900 University Boulevard

institute: University of Alabama at Birmingham

description: Primary CD4 T cells isolated from the periphery using an enrichment cocktail, co-cultured with or without exosomes with 50IU/ml IL-2 in exosome depeleted human AB serum media.

hyb_protocol: NanoString protocol

scan_protocol: RNA expression was quantified on the nCounter Digital Analyzer

data_processing: Data were normalized utilizing the manufacturer’s positive and negative experimental control probes, as well as 2 housekeeping genes (TUBB and RPL19)

label: NanoString Probe

source_name: healthy_exosome treated

label_protocol: All sample preparations were performed according to the manufacturer’s instructions (NanoString Technologies).

growth_protocol: CD4 T cells were cultured for 7-days with or without autologous BAL exosome treatment in exosome-depleted human AB serum RPMI media supplemented with L-glutamine and 50IU/ml

extract_protocol: mRNA was isolated using the PureLink RNA Mini Kit following the manufacturer's instructions.

treatment_protocol: CD4 T cells were either untreated or treated with autologous BAL exosomes at a ratio of 10:1 exosomes:T cells.

tag: subject status

value: healthy

tag: treatment

value: autologous BAL exosome

value: primary CD4 T cell


title: HA KDM4A FL OE rep3

description: Library name: Histone_KDM4A_WT

value: OE KDM4A FL


title: P300 WT rep3

description: Library name: Histone_P300_WT

value: WT


title: RO1-005 no exo: healthy

value: untreated


title: Hepatocytes from patients with hepatocellular carcinoma accompanied by cirrhosis (representing cirrhotic liver tissue)

description:
Library name: sample3
10x Genomics Flex


title: JD46 no exo : asthmatic

value: asthmatic


title: YY1 WT rep3

description: Library name: Histone_YY1_WT

value: mESC


title: Worm, E73R, day3, rep 2

description:
Library name: Worm_E73R_D3_rep2
8202_d3-2

value: H2B E73R


title: H3K9me3 KDM4B del-IDR OE rep3

description: Library name: Histone_H3K9me3_KDM4B_KI


title: HA KDM4B FL OE rep3

description: Library name: Histone_KDM4B_WT

value: OE KDM4B FL


title: RO1-016 no exo : healthy


title: RO1-008 + exo: healthy


title: RO1-008 no exo: healthy


title: H3K9me3 KDM4B FL OE rep3

description: Library name: Histone_H3K9me3_KDM4B_WT


title: JD46 + exo : asthmatic

source_name: asthmatic_exosome treated


title: HA KDM6B del-IDR OE rep3

description: Library name: Histone_KDM6B_KI

value: OE KDM6B del-IDR


title: HA KDM4A del-IDR OE rep3

description: Library name: Histone_KDM4A_KI

value: OE KDM4A del-IDR


title: RO1-012+ exo: asthmatic


title: H3K9me3 KDM4A FL OE rep3

description: Library name: Histone_H3K9me3_KDM4A_WT


title: H3K4me3 Alkbh5 del-cIDR rep3

description: Library name: Histone_H3K4me3_KI

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
caRNA MeRIP-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana transcriptome and spike-in sequences using HISAT2. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard. eCLIP-seq: Alignment: After QC, clean reads were aligned to the mouse genome (GRCm39) using STAR. Duplicate reads were filtered based on UMI information using umi_tools. Reads mapped to rRNA were removed. CUT&Tag, CUT&RUN, ATAC-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: TAIR10 or GRCm39
Library strategy: CUT&Tag

value: Alkbh5 del-cIDR


title: H3K9me3 KDM4A del-IDR OE rep3

description: Library name: Histone_H3K9me3_KDM4A_KI


title: H3K27me3 KDM6A FL OE rep3

description: Library name: Histone_H3K27me3_UTX_WT

value: OE KDM6A FL


title: D40 human-chimp intraspecies pools, CHIR0.4-0.8, replicate 3, MULTISEQ

first: Alex

last: Pollen

address: 651 4th Street

institute: UCSF

description: Library name: D40_CH3_MULTISEQ

library_source: other

data_processing:
Demultiplexing of species and cell line identity was done using cellbouncer (https://github.com/nkschaefer/cellbouncer)
snRNA-seq and snATAC-seq library FASTQs were pre-processed using cellranger-arc version 2.0.2 (10x Genomics) and aligned to either an ancestral genome or to individual species genomes hg38 (human), panTro6 (chimpanzee), ponAbe3 (orangutan), and rheMac10 (rhesus macaque)
For snRNA-seq data: cell doublets were deteced and removed based on species and individual demultiplexing. During the processign of the GEX data, cells with more than 15% mitochondrial reads or more then 10% ribosomal reads were removed. Cells were also filtered based on the number of genes (< 1,000 or > 7,500 for D40-100, and <500 or > 7,500 for D16) and reads (< 1,000) and any gene detected in less than 10 cells was removed. Counts in cells were then normalized by read depth (CPM normalization), log transformed and then scaled to unit variance and zero mean, with a max value of 10.
To obtain clusters with merged species identities, we applied Batch Integration of batch-balanced k-nearest neighbors (BBKNN) to the developmental data sets. Because rotenone exposure reduced cell type marker gene expression and made it more difficult to delineate homologous cell types across species, we used a slightly different approach to integrate and cluster the rotenone data set. we performed reciprocal PCA (rPCA)-based integration to integrate data from each sequencing library for each species and rotenone time point using Seurat default rPCA parameters.We classified cells as DA neurons if they belonged to subclusters with marker expression of established DA markers, including TH, NR4A2, EN1 and LMX1A.
For snATAC-seq data: Signac v1.13.9003152 was used to quantify counts for each species for the original peak set called for each species (after merging across cell types), CrossPeak consensus peaks, and CrossPeak species-only peaks in each species’ own genome coordinates. Cells that passed snRNA-seq quality filters and had cell type identities assigned based on snRNA-seq were included, and further filtered (quality metrics calculated based on each species’ original peak set) to retain cells with TSSenrichment (as calculated with Signac function TSSEnrichment()) > 2 and counts > 1000.
Fragment count matrix for scATAC-seq was generated using PycisTopic from the fragments files output by cellranger using consensus peak set defined in each species.
MULTIseq library FASTQs were processed using py-multi-seq (https://github.com/mtvector/py-multi-seq)
Assembly: Individual species' genomes:hg38 (human), panTro6 (chimpanzee), ponAbe3 (orangutan), and rheMac10 (rhesus macaque). Ancestral genome: our reference data were aligned and annotated in a prior study (Mao et al. 2021, PMID: 33953399).The authors aligned many human and nonhuman primate genomes using Progressive Cactus (Armstrong et al. 2020, PMID: 33177663) and annotated them using the Comparative Annotation Toolkit (CAT) (Fiddes et al. 2018, PMID: 29884752) with the human Gencode annotation v33 (Frankish et al. 2021, PMID: 33270111) as the source for homology-based annotations. The genome assembly versions that we used from this alignment were hg38 (human), panTro6 (chimpanzee), ponAbe3 (orangutan), and rheMac10 (rhesus macaque). As part of its alignment strategy, Progressive Cactus imputes the genome of the most recent common ancestor of each group of genomes it aligns, and we chose to use the Homo/Pan most recent common ancestor (MRCA) for snRNA-seq alignment to mitigate reference bias toward either the human or chimpanzee lineage.
Supplementary files format and content: GEX_pre-QC.h5ad files contain GEX data with RNA counts after alignments on each species’ reference genome. It includs all cells before quality control and filtering.
Supplementary files format and content: GEX_processed-clustered.h5ad files contain GEX data with RNA counts after alignments on each species’ reference genome. It includs cells that passed quality control and filtering and that were used for clustering.
Supplementary files format and content: GEX_ancestral_sce.rds files are SingleCellExperiment objects with RNA counts after alignments to the ancestral genome
Supplementary files format and content: D80-rotenone-exp_GEX.h5ad contains GEX data from the rotenone experiment, before subsetting DA lineage cells
Supplementary files format and content: D80-rotenone-exp_GEX_DA_subset.h5ad contains GEX data from the rotenone expeiement, after subsetting the DA lineage cells that were used for the analysis in Figure 7
Supplementary files format and content: D40-100_ATAC_human_specific_sce.rds and D40-100_ATAC_chimp_specific_sce.rds files are SingleCellExperiment objects with human-specific or chimp-specific ATAC peaks counts
Supplementary files format and content: D40-100_ATAC_consensus_sce.rds is a SingleCellExperiment object with consensus ATAC peaks counts for  human, chimp, and rhesus
Supplementary files format and content: D40-100_ATAC_seurat.rds is a Seurat object with consensus ATAC peaks - data integrated across species including the UMAP calculated
Supplementary files format and content: cistopic_obj.pk files are fragment count matrices for scATAC-seq
Supplementary files format and content: multiseq_calls.csv list the MULTIseq call assignment after demultiplexing with py-multi-seq
Supplementary files format and content: MULTIseq_counts.txt are MULTIseq count tables after demultiplexing with py-multi-seq

molecule: other

organism:
Pan troglodytes
Homo sapiens

extract_protocol:
D16 ventral midbrain progenitors were dissociated for 10 min in Accutase, counted and distributed into Eppendorf tubes at 1-2 million cells per tube. The cells were centrifuged at 400 x g for 5 min and all liquid was removed before the tubes were dipped into an isopentane bath on dry ice for flash freezing To isolate the nuclei from D16 progenitors, the 10x Genomics demonstrated protocol 'Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing' (CG000365 - Rev B) was used with a few modifications. The cells were incubated for 4 min on ice in 0.1x lysis buffer and washed in wash buffer containing 2% BSA.  After the final wash, nuclei were passed through a 40 μm Flowmi Cell Strainer. For MULTIseq labeling, the nuclei were incubated with the barcode-Anchor LMO mix at a concentration of 50 nM and subsequently incubated with the Co-Anchor LMO at 50 nM. D40, 80 and 100 organoids were cut into smaller pieces under a dissection microscope using scalpels (halves or quarters depending on time point). For the D40 time point, 20 organoids were placed in each tube and for D80-100, 10-15 organoids were used. The tubes were centrifuged at 100x g for 2 min to remove all the liquid and then dipped into an isopentane bath on dry ice for flash freezing. To isolate nuclei from organoids, the 10x demonstrated protocol Nuclei Isolation from Embryonic Mouse Brain for 'Single Cell Multiome ATAC + Gene Expression Sequencing' (CG000366 - Rev C) was used and the organoid pieces were incubated for 5 + 5 min on ice in 0.1x lysis buffer and then washed in wash buffer containing 2% BSA. For the D80 and D100 organoid samples, two additional x washes were added to the procedure to remove as much debris as possible. After the final wash, nuclei were passed through a 40 μm Flowmi Cell Strainer. For MULTIseq labeling, the nuclei were incubated with the barcode-Anchor LMO mix at a concentration of 50 nM and subsequently incubated with the Co-Anchor LMO at 50 nM.
Library was constructed according to manufacturer's instructions (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, CG000338 Rev C). To prepare the MULTIseq library, 10 μl of the product from ‘Pre-Amplification SPRI Cleanup’ (Step 4.3 in above protocol) portion of the 10x was used and libraries were constructed as described in McGinnis et al. 2019 [PMID: 31209384]

value: PSC-derived midbrain organoids


title: RO1-014 + exo: healthy


title: RO1-005 + exo: healthy


title: RO1-004 no exo: asthmatic


title: H3K27me3 KDM6A del-IDR OE rep3

description: Library name: Histone_H3K27me3_UTX_KI

value: OE KDM6A del-IDR


title: H3K4me3 WT rep3

description: Library name: Histone_H3K4me3_WT


title: RO1-012 no exo: asthmatic


title: RO1-014 no exo: healthy


title: H3K27me3 KDM6B del-IDR OE rep3

description: Library name: Histone_H3K27me3_KDM6B_KI


title: D40 human-chimp intraspecies pools, CHIR0.4-0.8, replicate 3, GEX

description: Library name: D40_CH3_GEX


title: H3K27me3 KDM6B FL OE rep3

description: Library name: Histone_H3K27me3_KDM6B_WT

value: OE KDM6B FL


title: D40 human-chimp intraspecies pools, CHIR0.4-0.8, replicate 3, ATAC

description: Library name: D40_CH3_ATAC


title: H3K27ac WT rep3

description: Library name: Histone_H3K27ac_WT


title: caRNA KDM6A FL OE rep3

description: Library name: Histone_caRNA_UTX_WT

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
caRNA MeRIP-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana transcriptome and spike-in sequences using HISAT2. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard. eCLIP-seq: Alignment: After QC, clean reads were aligned to the mouse genome (GRCm39) using STAR. Duplicate reads were filtered based on UMI information using umi_tools. Reads mapped to rRNA were removed. CUT&Tag, CUT&RUN, ATAC-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: TAIR10 or GRCm39


title: D40 human-chimp intraspecies pools, CHIR0.4-0.8, replicate 2, MULTISEQ

description: Library name: D40_CH2_MULTISEQ


title: D40 human-chimp intraspecies pools, CHIR0.4-0.8, replicate 2, ATAC

description: Library name: D40_CH2_ATAC


title: caRNA KDM6A del-IDR OE rep3

description: Library name: Histone_caRNA_UTX_KI


title: D40 human-chimp intraspecies pools, CHIR0.4-0.8, replicate 2, GEX

description: Library name: D40_CH2_GEX


title: RO1-004 + exo: asthmatic


title: H3K27ac Alkbh5 del-cIDR rep3

description: Library name: Histone_H3K27ac_KI


title: caRNA KDM6B FL OE rep3

description: Library name: Histone_caRNA_KDM6B_WT


title: D40 human-chimp intraspecies pools, CHIR0.4-0.8, replicate 1, GEX

description: Library name: D40_CH1_GEX


title: caRNA KDM4B FL OE rep3

description: Library name: Histone_caRNA_KDM4B_WT


title: caRNA KDM4A FL OE rep3

description: Library name: Histone_caRNA_KDM4A_WT


title: D16 human-chimp intraspecies pools, CHIR0.4-0.8, replicate 2, MULTISEQ

description: Library name: D16_CH2_MULTISEQ

value: PSC-derived midbrain progenitors


title: D40 human-chimp intraspecies pools, CHIR0.4-0.8, replicate 1, MULTISEQ

description: Library name: D40_CH1_MULTISEQ


title: caRNA KDM4B del-IDR OE rep3

description: Library name: Histone_caRNA_KDM4B_KI

value: OE KDM4B del-IDR


title: D16 human-chimp intraspecies pools, CHIR0.4-0.8, replicate 2, ATAC

description: Library name: D16_CH2_ATAC


title: D16 human-chimp intraspecies pools, CHIR0.4-0.8, replicate 2, GEX

description: Library name: D16_CH2_GEX


title: ATAC KDM6A FL OE rep3

description: Library name: Histone_ATAC_UTX_WT


title: caRNA KDM4A del-IDR OE rep3

description: Library name: Histone_caRNA_KDM4A_KI


title: Upstream tandem hiPSC, induced, rep2

city: Cambridge

first: Christopher

middle: Patrick

last: Johnstone

state: Massachusetts

department: Chemical Engineering

institute: Massachusetts Institute of Technology

description:
Library name: upstream_tandem_induced_rep2
Library type is Region Capture Micro-C

data_processing:
Reads trimmed with TrimGalore (v0.6.10) and aligned with Bowtie2 (v2.5.4) with setting --very-sensitive-local
Micro-C junctions were identified, sorted, and deduplicated using pairtools (v1.1.3)
Junctions were summarized into contact matrices, iteratively balanced, and coarsened into a series of zoom levels using cooler (v0.10.4). The smallest zoom level used 500bp bins
Assembly: GRCh38.p14, edited at the CLYBL locus according to genomic modifications
Supplementary files format and content: *rep*.mcool files represent cooler contact-matrices iteratively balanced within the capture region
Supplementary files format and content: *rep*.gwidebalance.mcool represent cooler contact-matrices iteratively balanced over the entire genome. This is more noisy because of the region-capture, but is compared to the capture-region balance in supplemental figures.
Supplementary files format and content: *merged*.mcool files represent cooler contact-matrices iteratively balanced within the capture region. These files merge contacts across both bioreplicates.
Supplementary files format and content: *merged*.gwidebalance.mcool files represent cooler contact-matrices iteratively balanced over the entire genome. These files merge contacts across both bioreplicates.

source_name: LU99 STRAIGHT-IN DUAL

growth_protocol: Maintained in StemFlex™ Medium (Thermo Scientific A3349401) with 100 U/mL Penicillin-Streptomycin (Gibco 15140122) on plates coated with 5 ug/mL Laminin-521 (STEMCELL Technologies 200-0117).

extract_protocol:
Following the protocol of Goel et al. 2023 (https://doi.org/10.1038/s41588-023-01391-1), in brief, cells were crosslinked with both formaldehyde and DSG. The resulting cross-linked chromatin was fragmented using MNase and ligated after end-repair with biotinylated dNTPs as in Micro-C.
Following the protocol above, after selection for the ligated junctions, cross-links were reversed and indexed libraries were prepared following the NEB Ultra II DNA Library Prep kit. Using the Twist Target Enrichment protocol and using an oligo pool targeting the regions listed above, the libraries were region-captured, re-amplified, and sent for sequencing.

treatment_protocol: Induced conditions treated with 1 ug/mL doxycycline for three days.

value: LU99 STRAIGHT-IN DUAL

value: hiPSC

tag: genetic modification

value: doxycycline


title: ATAC KDM6A del-IDR OE rep3

description: Library name: Histone_ATAC_UTX_KI


title: ATAC KDM6B FL OE rep3

description: Library name: Histone_ATAC_KDM6B_WT


title: ATAC KDM6B del-IDR OE rep3

description: Library name: Histone_ATAC_KDM6B_KI


title: D16 human-chimp intraspecies pools, CHIR0.4-0.8, replicate 1, MULTISEQ

description: Library name: D16_CH_MULTISEQ


title: ATAC KDM4B del-IDR OE rep3

description: Library name: Histone_ATAC_KDM4B_KI


title: ATAC KDM4A FL OE rep3

description: Library name: Histone_ATAC_KDM4A_WT

value: OE KDM4A FL


title: D16 human-chimp intraspecies pools, CHIR0.4-0.8, replicate 1, GEX

description: Library name: D16_CH_GEX


title: Upstream tandem hiPSC, induced, rep1

description:
Library name: upstream_tandem_induced_rep1
Library type is Region Capture Micro-C


title: caRNA KDM6B del-IDR OE rep3

description: Library name: Histone_caRNA_KDM6B_KI


title: Convergent hiPSC, induced, rep2

description:
Library name: convergent_induced_rep2
Library type is Region Capture Micro-C


title: D16 human-chimp intraspecies pools, CHIR0.4-0.8, replicate 1, ATAC

description: Library name: D16_CH_ATAC


title: ATAC KDM4B FL OE rep3

description: Library name: Histone_ATAC_KDM4B_WT


title: D40 human-chimp intraspecies pools, CHIR0.4-0.8, replicate 1, ATAC

description: Library name: D40_CH1_ATAC


title: ATAC KDM4A del-IDR OE rep3

description: Library name: Histone_ATAC_KDM4A_KI


title: Upstream tandem hiPSC, uninduced, rep2

description:
Library name: upstream_tandem_uninduced_rep2
Library type is Region Capture Micro-C

value: control


title: Convergent hiPSC, induced, rep1

description:
Library name: convergent_induced_rep1
Library type is Region Capture Micro-C


title: Convergent hiPSC, uninduced, rep2

description:
Library name: convergent_uninduced_rep2
Library type is Region Capture Micro-C


title: ATAC Alkbh5 KO rep3

description: Library name: Histone_ATAC_ALKBH5_KO

value: mESC

value: Alkbh5 KO


title: Upstream tandem hiPSC, uninduced, rep1

description:
Library name: upstream_tandem_uninduced_rep1
Library type is Region Capture Micro-C


title: Nascent RNA WT 60min  rep3

description: Library name: EU_WT_60

value: WT


title: ATAC Alkbh5 del-cIDR rep3

description: Library name: Histone_ATAC_ALKBH5_KI


title: TNF+VL-Rv-1

city: Boston

last: Chiang

state: MA

address: 60 Fenwood Rd. 3016Q

department: Anesthesiology

institute: Brigham and Women's Hospital

description:
Library name: Sample 7
Q6BQGS_7_7-C1-TNF+Rx

data_processing:
RNRNAseq was carried out by Plasmidsaurus (https://plasmidsaurus.com/) using Illumina sequencing and a 3’ end counting approach to capture differential gene expression.
RNA concentrations were determined using a fluorescence based plate reader assay and normalize sample concentrations before proceeding.
For sequencing library preparation, mRNA was converted into complementary DNA (cDNA) via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification.
method is heavily biased towards the 3' end. The read length is ~90bp and all of the reads align within the last ~400nt of the transcript.
FastQ generation and demux with BCL Convert v4.3.6 and fqtk v0.3.1.
Assembly: GRCh38 assembly
Supplementary files format and content: txt files with raw counts and TPM values
Supplementary files format and content: txt files with raw counts and TPM values

source_name: HUVEC

extract_protocol:
mRNA were extracted for RNA-seq
Pre-made library – no library preparation performed

value: HUVEC

value: endothelial cells

value: TNF+VL-Rv


title: Nascent RNA WT 20min  rep3

description: Library name: EU_WT_20


title: TNF+VL-Rv-2

description:
Library name: Sample 8
Q6BQGS_8_8-C2-TNF+Rx


title: Nascent RNA WT 40min  rep3

description: Library name: EU_WT_40


title: ATAC WT rep3

description: Library name: Histone_ATAC_ALKBH5_WT


title: TNF-3

description:
Library name: Sample 6
Q6BQGS_6_6-B3-TNF

value: TNF


title: Nascent RNA WT 10min  rep3

description: Library name: EU_WT_10


title: TNF+VL-Rv-3

description:
Library name: Sample 9
Q6BQGS_9_9-C3-TNF+Rx


title: Nascent RNA Alkbh5 KO 60min rep3

description: Library name: EU_KO_60


title: vehicle control-3

description:
Library name: Sample 3
Q6BQGS_3_3-A3-control

value: vehicle


title: TNF-2

description:
Library name: Sample 5
Q6BQGS_5_5-B2-TNF


title: TNF-1

description:
Library name: Sample 4
Q6BQGS_4_4-B1-TNF


title: Convergent hiPSC, uninduced, rep1

description:
Library name: convergent_uninduced_rep1
Library type is Region Capture Micro-C


title: Nascent RNA Alkbh5 KO 40min rep3

description: Library name: EU_KO_40


title: Nascent RNA Alkbh5 del-cIDR 60min rep3

description: Library name: EU_KI_60

value: Alkbh5 del-cIDR


title: hiPSC differentiated for day 22, s

city: Leiden

first: Susana

last: Chuva de Sousa Lopes

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: Leiden University Medical Center

description: Library name: D22_99_ARB27s

data_processing:
For all samples Cell Ranger Single Cell Software Suite 8.0.0 was used to perform sample demultiplexing, barcode processing,  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38 (refdata-cellranger-GRCh38-2020-A)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: hiPSC

extract_protocol:
Cells were dissociated using Accutase for 15min at 37C, filtered through a 35um strainer, ressuspended in 0.5% BSA/DPBS and FACS-sorted for live cells (7AAD-negative cells).
Sequencing libraries were prepared according to the user guide of the 10x Genomics Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit 16 rxns PN-1000414

tag: day of_culture


title: Nascent RNA Alkbh5 KO 10min rep3

description: Library name: EU_KO_10


title: vehicle control-1

description:
Library name: Sample 1
Q6BQGS_1_1-A1-control


title: Nascent RNA Alkbh5 del-cIDR 20min rep3

description: Library name: EU_KI_20


title: Nascent RNA Alkbh5 del-cIDR 10min rep3

description: Library name: EU_KI_10


title: hiPSC differentiated for day 22, repl 1

description: Library name: D22_99_ARB27sfa_1


title: hiPSC differentiated for day 22, repl 2

description: Library name: D22_99_ARB27sfa_2


title: Nascent RNA Alkbh5 del-cIDR 40min rep3

description: Library name: EU_KI_40


title: hiPSC differentiated for day 22

description: Library name: D22_99_ARB27


title: eCLIP-seq IP ALKBH5 FL rep3

description: Library name: CLIP_ALKBH5_WT_IP1

molecule: nuclear RNA


title: hiPSC differentiated for day 5

description: Library name: D5_99wt


title: hiPSC differentiated for day 0

description: Library name: D0_99wt


title: Upstream tandem hiPSC, uninduced, Pol II (ser2), rep2

description:
Library name: upstream_tandem_uninduced_rep2_polII
polII

data_processing:
Reads trimmed with TrimGalore (v0.6.10) and aligned with Bowtie2 (v2.5.4) with setting --very-sensitive-local
Alignments deduplicated with MarkDuplicatesSpark / GATK4 (v4.6.2.0)
Reads that were duplicates, non-properly paired, or had a mapping quality under 3 were filtered with Sambamba (v1.0.1)
Reads aligned to the spike-in Drosophila genome were quantified to determine a cellular input normalization constant.
Normalized summary bigwigs computed with bamCoverage / deeptools (v3.5.6)
Assembly: GRCh38.p14, edited at the CLYBL locus according to genomic modifications. The spike-in genome used was GCF_000001215.4.
Supplementary files format and content: Bigwig files are provided for each condition, showing read mappings to the edited genomes.
Library strategy: CUT&Tag

extract_protocol:
Cells were bound to ConA beads alongside spike-in Drosophila nuclei, then permeabilized and bound with one of four primary antibodies: Pol II (ser2) (Cell Signaling Technologies 13499S), H3K27ac (Active Motif 39133), H3K27me3 (Active Motif 91167), or H3K4me3 (Active Motif 39915). Cells were prepared following the CUT&Tag-IT Express kit (Active Motif 53177).
Nextera-compatible combinatorial dual-index primers were used to index the libraries (Active Motif 53155).

treatment_protocol: Induced conditions treated with 1 ug/mL doxycycline for three days

tag: antibody

value: Pol II (ser2)


title: vehicle control-2

description:
Library name: Sample 2
Q6BQGS_2_2-A2-control


title: eCLIP-seq Input ALKBH5 FL rep3

description: Library name: CLIP_ALKBH5_WT_IN


title: Nascent RNA Alkbh5 KO 20min rep3

description: Library name: EU_KO_20


title: Upstream tandem hiPSC, uninduced, H3K27ac, rep2

description:
Library name: upstream_tandem_uninduced_rep2_H3K27ac
H3K27ac


title: Upstream tandem hiPSC, induced, Pol II (ser2), rep2

description:
Library name: upstream_tandem_induced_rep2_polII
polII


title: eCLIP-seq Input ALKBH5 del-cIDR rep3

description: Library name: CLIP_ALKBH5_KI_IN


title: Upstream tandem hiPSC, uninduced, H3K4me3, rep2

description:
Library name: upstream_tandem_uninduced_rep2_H3K4me3
H3K4me3


title: Upstream tandem hiPSC, uninduced, H3K27me3, rep2

description:
Library name: upstream_tandem_uninduced_rep2_H3K27me3
H3K27me3


title: Upstream tandem hiPSC, induced, H3K27me3, rep2

description:
Library name: upstream_tandem_induced_rep2_H3K27me3
H3K27me3


title: Upstream tandem hiPSC, induced, H3K27ac, rep2

description:
Library name: upstream_tandem_induced_rep2_H3K27ac
H3K27ac


title: Upstream tandem hiPSC, induced, H3K4me3, rep2

description:
Library name: upstream_tandem_induced_rep2_H3K4me3
H3K4me3


title: Cardiomyocytes_no_treat_C3

first: Yuehong

address: 160 Pujian Road

institute: Harbin medical university

description: piRNAs expression with no treatment

hyb_protocol: 1.5 ug of cyanine 3-labeled, linearly amplified cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Genome Oligo Microarrays (one-color) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with 2x GEx Hybridization Buffer HI-RPM (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61 x 21.6 mm), Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, piRNAs that 1 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed piRNAs between two groups were identified through Volcano Plot filtering. Finally, Hierarchical Clustering was performed to show the distinguishable piRNAs expression pattern among samples.

source_name: neonatal mouse cardiomyocytes

label_protocol: Cyanine-3-CTP labeled cRNA was prepared from 1 ug total RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA of different-treated cardiomyocytes was isolated by using TRIzol (Takara, Beijing, China), following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: According to the experimental protocol, cardiomyocytes were exposed to high glucose (HG, 40 mM) combined with palmitate (Palm, 300 mM). Then collected the cardiomyocytes for Mouse piRNA microarray

value: cardiomyocytes

value: no treatment


title: caRNA m6A IP Alkbh5 KO rep3

description: Library name: caMeRIP_ALKBH5_KO_IP

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
caRNA MeRIP-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana transcriptome and spike-in sequences using HISAT2. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard. eCLIP-seq: Alignment: After QC, clean reads were aligned to the mouse genome (GRCm39) using STAR. Duplicate reads were filtered based on UMI information using umi_tools. Reads mapped to rRNA were removed. CUT&Tag, CUT&RUN, ATAC-seq: Alignment: Reads were aligned to the mouse or Arabidopsis thaliana genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: TAIR10 or GRCm39
Library strategy: MeRIP-Seq


title: Upstream tandem hiPSC, uninduced, H3K4me3, rep1

description:
Library name: upstream_tandem_uninduced_rep1_H3K4me3
H3K4me3

value: LU99 STRAIGHT-IN DUAL


title: Cardiomyocytes_high_glucose_palmitate_H2

description: piRNAs expression with high glucose and palmitate treatment

value: high glucose and palmitate treatment


title: Upstream tandem hiPSC, uninduced, Pol II (ser2), rep1

description:
Library name: upstream_tandem_uninduced_rep1_polII
polII

value: hiPSC


title: Cardiomyocytes_high_glucose_palmitate_H1


title: Upstream tandem hiPSC, uninduced, H3K27me3, rep1

description:
Library name: upstream_tandem_uninduced_rep1_H3K27me3
H3K27me3


title: caRNA m6A IP Alkbh5 del-cIDR rep3

description: Library name: caMeRIP_ALKBH5_KI_IP


title: Donor 6, dentin-adherent cells, treated with live S. mutans

city: Regensburg

first: Sandra

last: Pohl

address: Franz-Josef-Strauß-Allee 11

department: Department of Conservative Dentistry and Periodontology

country: Germany

institute: University Hospital Regensburg

description:
Library name: D6_DAC_bac
column name in counts_raw.txt: D6_DAC_bac

data_processing:
processed FASTQ files were aligned to the GRCh38 reference genome with STAR (v2.7.4a)
Uniquely mapped reads were extracted using featureCounts from the Subread package (v2.0.0)
Batch effects were removed with the removeBatchEffect function from limma (v3.60.4)
Differentially expressed genes (logFC±1.5, padj ≤ 0.05) were identified using the DeSeq2 package
Assembly: Homo_sapiens reference genome GRCh38 (gencode_release 29)
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text file include donor-effect corrected VST values for each sample

source_name: dental pulp cells

growth_protocol: Dental pulp cells were maintained in αMEM supplemented with 10% FBS and antibiotic-antimycotic at 37°C and 5% CO2.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (#74104, Qiagen)
Illumina® Stranded mRNA Prep, Ligation (#20040532, Illumina). 300ng of total RNA was used for the construction of libraries.

treatment_protocol: DPCs and DACs were seeded in 6-well plates and infection with γ-irradiated and live Streptococccus mutans was carried out 72 hours after cell seeding

value: dental pulp cells

value: dentin-adherent pulp cells

value: 6 hours with live S. mutans


title: eCLIP-seq IP ALKBH5 del-cIDR rep3

description: Library name: CLIP_ALKBH5_KI_IP1

value: mESC


title: Cardiomyocytes_high_glucose_palmitate_H3


title: Donor 6, dentin-adherent cells, treated with gamma-irradiated S. mutans

description:
Library name: D6_DAC_gamma
column name in counts_raw.txt: D6_DAC_gamma

value: 6 hours with gamma-irradiated S. mutans


title: Upstream tandem hiPSC, uninduced, H3K27ac, rep1

description:
Library name: upstream_tandem_uninduced_rep1_H3K27ac
H3K27ac

value: control


title: caRNA m6A Input WT rep3

description: Library name: caMeRIP_ALKBH5_WT_IN

value: WT


title: Cardiomyocytes_no_treat_C1

description: piRNAs expression with no treatment


title: Upstream tandem hiPSC, induced, Pol II (ser2), rep1

description:
Library name: upstream_tandem_induced_rep1_polII
polII

value: doxycycline


title: Upstream tandem hiPSC, induced, H3K4me3, rep1

description:
Library name: upstream_tandem_induced_rep1_H3K4me3
H3K4me3


title: caRNA m6A IP WT rep3

description: Library name: caMeRIP_ALKBH5_WT_IP


title: Cardiomyocytes_no_treat_C2

description: piRNAs expression with no treatment


title: Donor 6, dentin-adherent cells, control

description:
Library name: D6_DAC_ctr
column name in counts_raw.txt: D6_DAC_ctr

value: no


title: Upstream tandem hiPSC, induced, H3K27me3, rep1

description:
Library name: upstream_tandem_induced_rep1_H3K27me3
H3K27me3


title: caRNA m6A Input Alkbh5 del-cIDR rep3

description: Library name: caMeRIP_ALKBH5_KI_IN


title: caRNA m6A Input Alkbh5 KO rep3

description: Library name: caMeRIP_ALKBH5_KO_IN

value: Alkbh5 KO


title: Divergent hiPSC, uninduced, Pol II (ser2), rep2

description:
Library name: divergent_uninduced_rep2_polII
polII


title: Upstream tandem hiPSC, induced, H3K27ac, rep1

description:
Library name: upstream_tandem_induced_rep1_H3K27ac
H3K27ac


title: Donor 6, dental pulp cells, treated with live S. mutans

description:
Library name: D6_DPC_bac
column name in counts_raw.txt: D6_DPC_bac

value: central dental pulp cells


title: Divergent hiPSC, uninduced, H3K4me3, rep2

description:
Library name: divergent_uninduced_rep2_H3K4me3
H3K4me3


title: Donor 6, dental pulp cells, treated with gamma-irradiated S. mutans

description:
Library name: D6_DPC_gamma
column name in counts_raw.txt: D6_DPC_gamma


title: Divergent hiPSC, uninduced, H3K27me3, rep2

description:
Library name: divergent_uninduced_rep2_H3K27me3
H3K27me3


title: H3K27me3 KDM6A FL OE rep2

description:
Library name: SAMPLES48
Peak files; Bigwig files

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
Alignment: Reads were aligned to the mouse genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: GRCm39
Supplementary files format and content: fastq, bam, sam, bigwig
Library strategy: CUT&Tag

source_name: mESC

growth_protocol: E14TG2a mES cells (ATCC) were cultured in DMEM (Gibco) supplemented with 15% FBS (Gibco), 1% EmbryoMax nucleosides (Sigma), 1% GlutaMAX supplement (Gibco), 1% MEM non-essential amino acids solution (Gibco), 1% Penicillin-Streptomycin (Gibco), 0.1 mM 2-Mercaptoethanol (Gibco), 1000 U/ml LIF (Sigma), 1 µM PD0325901 (Stemcell) and 3 µM CHIR99021 (Stemcell) at 37 °C in a humidified atmosphere with 5% CO2. HEK293T cells (ATCC) were maintained in DMEM (Gibco) supplemented with 10% FBS (Gibco) and 1% Penicillin-Streptomycin (Gibco) at 37 °C with 5% CO2.

extract_protocol:
mESCs nuclei were isolated by incubation with Complete Nuclei Isolation Buffer according to the manufacturer's instructions.
ATAC-seq was performed by using the ATAC-Seq Kit (Active Motif) according to the manufacturer's instructions.
CUT&Tag was performed by using the CUT&Tag-IT® Core Assay Kit (Active Motif) following the manufacturer's instructions.
CUT&RUN was performed by using the ChIC/CUT&RUN Assay Kit (Active Motif) following the manufacturer's instructions.

value: OE KDM6A FL


title: H3K27me3 KDM6A FL OE rep1

description:
Library name: SAMPLES47
Peak files; Bigwig files


title: Donor 6, dental pulp cells, control

description:
Library name: D6_DPC_ctr
column name in counts_raw.txt: D6_DPC_ctr


title: Divergent hiPSC, induced, Pol II (ser2), rep2

description:
Library name: divergent_induced_rep2_polII
polII

value: Pol II (ser2)


title: Divergent hiPSC, uninduced, H3K27ac, rep2

description:
Library name: divergent_uninduced_rep2_H3K27ac
H3K27ac


title: Donor 5, dentin-adherent cells, treated with gamma-irradiated S. mutans

description:
Library name: D5_DAC_gamma
column name in counts_raw.txt: D5_DAC_gamma


title: Divergent hiPSC, induced, H3K4me3, rep2

description:
Library name: divergent_induced_rep2_H3K4me3
H3K4me3


title: Donor 5, dentin-adherent cells, treated with live S. mutans

description:
Library name: D5_DAC_bac
column name in counts_raw.txt: D5_DAC_bac


title: Donor 5, dentin-adherent cells, control

description:
Library name: D5_DAC_ctr
column name in counts_raw.txt: D5_DAC_ctr


title: Divergent hiPSC, induced, H3K27me3, rep2

description:
Library name: divergent_induced_rep2_H3K27me3
H3K27me3


title: Divergent hiPSC, uninduced, H3K27me3, rep1

description:
Library name: divergent_uninduced_rep1_H3K27me3
H3K27me3


title: Divergent hiPSC, induced, Pol II (ser2), rep1

description:
Library name: divergent_induced_rep1_polII
polII


title: Divergent hiPSC, uninduced, H3K27ac, rep1

description:
Library name: divergent_uninduced_rep1_H3K27ac
H3K27ac


title: Divergent hiPSC, induced, H3K4me3, rep1

description:
Library name: divergent_induced_rep1_H3K4me3
H3K4me3


title: H3K27me3 KDM6A del-IDR OE rep1

description:
Library name: SAMPLES45
Peak files; Bigwig files

value: OE KDM6A del-IDR


title: Donor 5, dental pulp cells, treated with gamma-irradiated S. mutans

description:
Library name: D5_DPC_gamma
column name in counts_raw.txt: D5_DPC_gamma


title: Divergent hiPSC, induced, H3K27ac, rep2

description:
Library name: divergent_induced_rep2_H3K27ac
H3K27ac

value: LU99 STRAIGHT-IN DUAL


title: H3K27me3 KDM6B FL OE rep2

description:
Library name: SAMPLES44
Peak files; Bigwig files

value: OE KDM6B FL


title: Donor 5, dental pulp cells, treated with live S. mutans

description:
Library name: D5_DPC_bac
column name in counts_raw.txt: D5_DPC_bac


title: Downstream tandem hiPSC, uninduced, Pol II (ser2), rep2

description:
Library name: downstream_tandem_uninduced_rep2_polII
polII

value: hiPSC


title: Divergent hiPSC, induced, H3K27me3, rep1

description:
Library name: divergent_induced_rep1_H3K27me3
H3K27me3


title: Divergent hiPSC, induced, H3K27ac, rep1

description:
Library name: divergent_induced_rep1_H3K27ac
H3K27ac


title: Donor 5, dental pulp cells, control

description:
Library name: D5_DPC_ctr
column name in counts_raw.txt: D5_DPC_ctr

value: dental pulp cells


title: H3K27me3 KDM6B FL OE rep1

description:
Library name: SAMPLES43
Peak files; Bigwig files


title: H3K27me3 KDM6B del-IDR OE rep2

description:
Library name: SAMPLES42
Peak files; Bigwig files

value: OE KDM6B del-IDR


title: H3K27me3 KDM6B del-IDR OE rep1

description:
Library name: SAMPLES41
Peak files; Bigwig files


title: Divergent hiPSC, uninduced, Pol II (ser2), rep1

description:
Library name: divergent_uninduced_rep1_polII
polII


title: Donor 4, dentin-adherent cells, treated with live S. mutans

description:
Library name: D4_DAC_bac
column name in counts_raw.txt: D4_DAC_bac

value: dentin-adherent pulp cells

value: 6 hours with live S. mutans


title: Downstream tandem hiPSC, uninduced, H3K4me3, rep2

description:
Library name: downstream_tandem_uninduced_rep2_H3K4me3
H3K4me3


title: H3K27me3 KDM6A del-IDR OE rep2

description:
Library name: SAMPLES46
Peak files; Bigwig files

value: mESC


title: Divergent hiPSC, uninduced, H3K4me3, rep1

description:
Library name: divergent_uninduced_rep1_H3K4me3
H3K4me3

value: control


title: Downstream tandem hiPSC, induced, Pol II (ser2), rep2

description:
Library name: downstream_tandem_induced_rep2_polII
polII


title: Downstream tandem hiPSC, uninduced, H3K27me3, rep2

description:
Library name: downstream_tandem_uninduced_rep2_H3K27me3
H3K27me3


title: Downstream tandem hiPSC, uninduced, H3K27ac, rep2

description:
Library name: downstream_tandem_uninduced_rep2_H3K27ac
H3K27ac


title: Downstream tandem hiPSC, induced, H3K4me3, rep2

description:
Library name: downstream_tandem_induced_rep2_H3K4me3
H3K4me3


title: Downstream tandem hiPSC, induced, H3K27me3, rep2

description:
Library name: downstream_tandem_induced_rep2_H3K27me3
H3K27me3


title: H3K9me3 KDM4B FL OE rep1

description:
Library name: SAMPLES39
Peak files; Bigwig files

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
Alignment: Reads were aligned to the mouse genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: GRCm39
Supplementary files format and content: fastq, bam, sam, bigwig
Library strategy: CUT&Run

value: OE KDM4B FL


title: Donor 4, dentin-adherent cells, control

description:
Library name: D4_DAC_ctr
column name in counts_raw.txt: D4_DAC_ctr


title: H3K9me3 KDM4B del-IDR OE rep2

description:
Library name: SAMPLES38
Peak files; Bigwig files

value: OE KDM4B del-IDR


title: H3K9me3 KDM4B del-IDR OE rep1

description:
Library name: SAMPLES37
Peak files; Bigwig files


title: Downstream tandem hiPSC, uninduced, Pol II (ser2), rep1

description:
Library name: downstream_tandem_uninduced_rep1_polII
polII


title: Downstream tandem hiPSC, induced, H3K27ac, rep2

description:
Library name: downstream_tandem_induced_rep2_H3K27ac
H3K27ac

value: doxycycline


title: Downstream tandem hiPSC, uninduced, H3K4me3, rep1

description:
Library name: downstream_tandem_uninduced_rep1_H3K4me3
H3K4me3


title: Donor 4, dental pulp cells, treated with live S. mutans

description:
Library name: D4_DPC_bac
column name in counts_raw.txt: D4_DPC_bac


title: H3K9me3 KDM4A FL OE rep2

description:
Library name: SAMPLES36
Peak files; Bigwig files

value: OE KDM4A FL


title: Donor 4, dental pulp cells, treated with gamma-irradiated S. mutans

description:
Library name: D4_DPC_gamma
column name in counts_raw.txt: D4_DPC_gamma

value: central dental pulp cells

value: 6 hours with gamma-irradiated S. mutans


title: Donor 4, dentin-adherent cells, treated with gamma-irradiated S. mutans

description:
Library name: D4_DAC_gamma
column name in counts_raw.txt: D4_DAC_gamma


title: H3K9me3 KDM4A FL OE rep1

description:
Library name: SAMPLES35
Peak files; Bigwig files


title: Downstream tandem hiPSC, uninduced, H3K27me3, rep1

description:
Library name: downstream_tandem_uninduced_rep1_H3K27me3
H3K27me3


title: Downstream tandem hiPSC, induced, H3K4me3, rep1

description:
Library name: downstream_tandem_induced_rep1_H3K4me3
H3K4me3


title: H3K9me3 KDM4B FL OE rep2

description:
Library name: SAMPLES40
Peak files; Bigwig files


title: Downstream tandem hiPSC, induced, H3K27ac, rep1

description:
Library name: downstream_tandem_induced_rep1_H3K27ac
H3K27ac


title: Downstream tandem hiPSC, induced, H3K27me3, rep1

description:
Library name: downstream_tandem_induced_rep1_H3K27me3
H3K27me3


title: Donor 3, dentin-adherent cells, treated with live S. mutans

description:
Library name: D3_DAC_bac
column name in counts_raw.txt: D3_DAC_bac


title: Donor 3, dentin-adherent cells, treated with gamma-irradiated S. mutans

description:
Library name: D3_DAC_gamma
column name in counts_raw.txt: D3_DAC_gamma


title: H3K9me3 KDM4A del-IDR OE rep1

description:
Library name: SAMPLES33
Peak files; Bigwig files

value: OE KDM4A del-IDR


title: H3K9me3 KDM4A del-IDR OE rep2

description:
Library name: SAMPLES34
Peak files; Bigwig files


title: Donor 4, dental pulp cells, control

description:
Library name: D4_DPC_ctr
column name in counts_raw.txt: D4_DPC_ctr

value: no


title: Downstream tandem hiPSC, uninduced, H3K27ac, rep1

description:
Library name: downstream_tandem_uninduced_rep1_H3K27ac
H3K27ac

value: LU99 STRAIGHT-IN DUAL


title: Convergent hiPSC, uninduced, Pol II (ser2), rep2

description:
Library name: convergent_uninduced_rep2_polII
polII

value: Pol II (ser2)


title: Downstream tandem hiPSC, induced, Pol II (ser2), rep1

description:
Library name: downstream_tandem_induced_rep1_polII
polII

value: hiPSC


title: Convergent hiPSC, uninduced, H3K4me3, rep2

description:
Library name: convergent_uninduced_rep2_H3K4me3
H3K4me3


title: Convergent hiPSC, uninduced, H3K27me3, rep2

description:
Library name: convergent_uninduced_rep2_H3K27me3
H3K27me3


title: Donor 3, dentin-adherent cells, control

description:
Library name: D3_DAC_ctr
column name in counts_raw.txt: D3_DAC_ctr

value: dental pulp cells


title: HA KDM6A FL OE rep2

description:
Library name: SAMPLES32
Peak files; Bigwig files

value: OE KDM6A FL


title: Convergent hiPSC, induced, Pol II (ser2), rep2

description:
Library name: convergent_induced_rep2_polII
polII


title: Convergent hiPSC, uninduced, H3K27ac, rep2

description:
Library name: convergent_uninduced_rep2_H3K27ac
H3K27ac


title: Donor 3, dental pulp cells, treated with live S. mutans

description:
Library name: D3_DPC_bac
column name in counts_raw.txt: D3_DPC_bac


title: HA KDM6A FL OE rep1

description:
Library name: SAMPLES31
Peak files; Bigwig files


title: Convergent hiPSC, induced, H3K27me3, rep2

description:
Library name: convergent_induced_rep2_H3K27me3
H3K27me3


title: Convergent hiPSC, induced, H3K27ac, rep2

description:
Library name: convergent_induced_rep2_H3K27ac
H3K27ac


title: HA KDM6A del-IDR OE rep1

description:
Library name: SAMPLES29
Peak files; Bigwig files

value: OE KDM6A del-IDR


title: Donor 3, dental pulp cells, control

description:
Library name: D3_DPC_ctr
column name in counts_raw.txt: D3_DPC_ctr


title: Donor 2, dentin-adherent cells, treated with live S. mutans

description:
Library name: D2_DAC_bac
column name in counts_raw.txt: D2_DAC_bac

value: dentin-adherent pulp cells

value: 6 hours with live S. mutans


title: Convergent hiPSC, uninduced, H3K4me3, rep1

description:
Library name: convergent_uninduced_rep1_H3K4me3
H3K4me3

value: control


title: Convergent hiPSC, uninduced, Pol II (ser2), rep1

description:
Library name: convergent_uninduced_rep1_polII
polII


title: Convergent hiPSC, uninduced, H3K27ac, rep1

description:
Library name: convergent_uninduced_rep1_H3K27ac
H3K27ac


title: Convergent hiPSC, induced, Pol II (ser2), rep1

description:
Library name: convergent_induced_rep1_polII
polII


title: Convergent hiPSC, induced, H3K4me3, rep1

description:
Library name: convergent_induced_rep1_H3K4me3
H3K4me3


title: HA KDM6B FL OE rep1

description:
Library name: SAMPLES27
Peak files; Bigwig files

value: mESC

value: OE KDM6B FL


title: Convergent hiPSC, uninduced, H3K27me3, rep1

description:
Library name: convergent_uninduced_rep1_H3K27me3
H3K27me3


title: Upstream tandem hiPSC, uninduced, no virus control, rep2

description: Library name: upstream_tandem_uninduced_novirus_rep2

data_processing:
Reads trimmed with TrimGalore (v0.6.10) and aligned with Bowtie2 (v2.5.4) with setting --very-sensitive-local
Alignments deduplicated with MarkDuplicatesSpark / GATK4 (v4.6.2.0)
Reads that were duplicates, non-properly paired, or had a mapping quality under 3 were filtered with Sambamba (v1.0.1)
Reads aligned to the spike-in Drosophila genome were quantified to determine a cellular input normalization constant.
Normalized summary bigwigs computed with bamCoverage / deeptools (v3.5.6)
Assembly: GRCh38.p14, edited at the CLYBL locus according to genomic modifications. The spike-in genome used was GCF_000001215.4.
Supplementary files format and content: Bigwig files are provided for each condition, showing read mappings to the edited genomes.
Library strategy: CUT&Run

extract_protocol:
Cells were bound to ConA beads alongside spike-in Drosophila nuclei, permeabilized, and bound with an anti-EGFP nanobody fused to MNase. The MNase was activated after washing.
Processed as in CUT&RUN, indexed libraries were prepared following the NEB Ultra II DNA Library Prep kit.

treatment_protocol: Induced conditions treated with 1 ug/mL doxycycline for three days. All conditions except the "no-virus-control" conditions were transduced with lentivirus expressing EGFP-GapR for two days.

tag: transduced virus


title: Donor 2, dentin-adherent cells, treated with gamma-irradiated S. mutans

description:
Library name: D2_DAC_gamma
column name in counts_raw.txt: D2_DAC_gamma


title: Donor 2, dentin-adherent cells, control

description:
Library name: D2_DAC_ctr
column name in counts_raw.txt: D2_DAC_ctr


title: HA KDM6B del-IDR OE rep1

description:
Library name: SAMPLES25
Peak files; Bigwig files

value: OE KDM6B del-IDR


title: Donor 2, dental pulp cells, treated with live S. mutans

description:
Library name: D2_DPC_bac
column name in counts_raw.txt: D2_DPC_bac


title: Upstream tandem hiPSC, uninduced, rep2

description: Library name: upstream_tandem_uninduced_rep2


title: HA KDM6A del-IDR OE rep2

description:
Library name: SAMPLES30
Peak files; Bigwig files


title: Donor 3, dental pulp cells, treated with gamma-irradiated S. mutans

description:
Library name: D3_DPC_gamma
column name in counts_raw.txt: D3_DPC_gamma


title: Convergent hiPSC, induced, H3K27ac, rep1

description:
Library name: convergent_induced_rep1_H3K27ac
H3K27ac

value: doxycycline


title: HA KDM6B FL OE rep2

description:
Library name: SAMPLES28
Peak files; Bigwig files


title: HA KDM6B del-IDR OE rep2

description:
Library name: SAMPLES26
Peak files; Bigwig files


title: Convergent hiPSC, induced, H3K27me3, rep1

description:
Library name: convergent_induced_rep1_H3K27me3
H3K27me3


title: Upstream tandem hiPSC, induced, rep2

description: Library name: upstream_tandem_induced_rep2


title: Convergent hiPSC, induced, H3K4me3, rep2

description:
Library name: convergent_induced_rep2_H3K4me3
H3K4me3


title: HA KDM4B FL OE rep1

description:
Library name: SAMPLES23
Peak files; Bigwig files

value: OE KDM4B FL


title: HA KDM4B FL OE rep2

description:
Library name: SAMPLES24
Peak files; Bigwig files


title: Upstream tandem hiPSC, induced, rep1

description: Library name: upstream_tandem_induced_rep1


title: Upstream tandem hiPSC, uninduced, no virus control, rep1

description: Library name: upstream_tandem_uninduced_novirus_rep1


title: Divergent hiPSC, uninduced, rep2

description: Library name: divergent_uninduced_rep2


title: Divergent hiPSC, induced, rep2

description: Library name: divergent_induced_rep2


title: HA KDM4B del-IDR OE rep2

description:
Library name: SAMPLES22
Peak files; Bigwig files

value: OE KDM4B del-IDR


title: HA KDM4B del-IDR OE rep1

description:
Library name: SAMPLES21
Peak files; Bigwig files


title: Donor 2, dental pulp cells, treated with gamma-irradiated S. mutans

description:
Library name: D2_DPC_gamma
column name in counts_raw.txt: D2_DPC_gamma

value: central dental pulp cells

value: 6 hours with gamma-irradiated S. mutans


title: Upstream tandem hiPSC, uninduced, rep1

description: Library name: upstream_tandem_uninduced_rep1

value: LU99 STRAIGHT-IN DUAL


title: Donor 2, dental pulp cells, control

description:
Library name: D2_DPC_ctr
column name in counts_raw.txt: D2_DPC_ctr

value: no


title: Divergent hiPSC, uninduced, no virus control, rep2

description: Library name: divergent_uninduced_novirus_rep2

value: hiPSC


title: Donor 1, dentin-adherent cells, treated with live S. mutans

description:
Library name: D1_DAC_bac
column name in counts_raw.txt:  D1_DAC_bac

value: dental pulp cells


title: Divergent hiPSC, induced, rep1

description: Library name: divergent_induced_rep1


title: Divergent hiPSC, uninduced, rep1

description: Library name: divergent_uninduced_rep1


title: Donor 1, dental pulp cells, treated with live S. mutans

description:
Library name: D1_DPC_bac
column name in counts_raw.txt: D1_DPC_bac


title: Downstream tandem hiPSC, induced, rep2

description: Library name: downstream_tandem_induced_rep2


title: Divergent hiPSC, uninduced, no virus control, rep1

description: Library name: divergent_uninduced_novirus_rep1


title: HA KDM4A FL OE rep2

description:
Library name: SAMPLES20
Peak files; Bigwig files

value: OE KDM4A FL


title: Downstream tandem hiPSC, uninduced, no virus control, rep1

description: Library name: downstream_tandem_uninduced_novirus_rep1


title: Donor 1, dental pulp cells, treated with gamma-irradiated S. mutans

description:
Library name: D1_DPC_gamma
column name in counts_raw.txt: D1_DPC_gamma


title: HA KDM4A FL OE rep1

description:
Library name: SAMPLES19
Peak files; Bigwig files


title: Donor 1, dentin-adherent cells, control

description:
Library name: D1_DAC_ctr
column name in counts_raw.txt: D1_DAC_ctr


title: Downstream tandem hiPSC, uninduced, rep2

description: Library name: downstream_tandem_uninduced_rep2


title: Downstream tandem hiPSC, uninduced, rep1

description: Library name: downstream_tandem_uninduced_rep1


title: Downstream tandem hiPSC, uninduced, no virus control, rep2

description: Library name: downstream_tandem_uninduced_novirus_rep2


title: Donor 1, dentin-adherent cells, treated with gamma-irradiated S. mutans

description:
Library name: D1_DAC_gamma
column name in counts_raw.txt: D1_DAC_gamma


title: HA KDM4A del-IDR OE rep2

description:
Library name: SAMPLES18
Peak files; Bigwig files

value: OE KDM4A del-IDR


title: OPCs multiplexed MU

first: Kenneth Lap Kei

last: Wu

state: Cambridgeshire

address: Cambridge Biomedical Campus, Francis Crick Avenue

country: United Kingdom

institute: MRC LMB

description: Library name: OPC_MU

data_processing:
Demultiplexing, barcode processing and gene counting were performed using Cell Ranger multi software with default settings.
Downstream single-cell sequence analysis was accomplished using Scanpy (version 1.8.1). Gene expression values were normalized to counts per million and log-transformed for comparison across samples.
Assembly: GRCh38
Supplementary files format and content: Matrix file as an Anndata object in .h5ad format

source_name: oligodendrocyte precursors

growth_protocol: Human BMSCs were derived into OPCs according to the protocol detailed in the Methods secion of the study.

extract_protocol:
1 × 10^6 cells at the desired stage were detached with TrypLE or Accutase and resuspended in ice-cold PBS for multiplexing. Cell viability was above 90% for all samples as determined by Trypan Blue exclusion. Cells from each donor at each stage along the induction process were labelled with a unique set of Cell Multiplexing Oligos using Single Cell Gene Expression v3.1 (Dual Index) kit (10X Genomics, CD000391).
After labelling and washing, an equal number of cells from each patient at the same stage in the induction process were mixed for encapsulation, Gel Bead-in Emulsion (GEM) generation and library preparation according to manufacturer’s protocol (Chromium controller, 10X Genomics).

value: oligodendrocyte precursors

value: MU


title: HA KDM4A del-IDR OE rep1

description:
Library name: SAMPLES17
Peak files; Bigwig files


title: Donor 1, dental pulp cells, control

description:
Library name: D1_DPC_ctr
column name in counts_raw.txt:  D1_DPC_ctr


title: Convergent hiPSC, uninduced, no virus control, rep2

description: Library name: convergent_uninduced_novirus_rep2

value: control


title: Downstream tandem hiPSC, induced, rep1

description: Library name: downstream_tandem_induced_rep1


title: ATAC KDM6A FL OE rep2

description:
Library name: SAMPLES16
Peak files; Bigwig files

data_processing:
Quality Control: Sequencing reads were quality-controlled using fastp.
Alignment: Reads were aligned to the mouse genome and spike-in sequences using BWA. Low-quality mapped reads were filtered with samtools, and PCR duplicates were removed using Picard.
Peak Calling: Peaks were identified with MACS2.
Quantification: Reads under peaks (RUP) were calculated using featureCounts.
Normalization: Normalized signals were computed as RUP divided by reads mapped to the spike-in sequences.
Assembly: GRCm39
Supplementary files format and content: fastq, bam, sam, bigwig

value: mESC

value: OE KDM6A FL


title: Convergent hiPSC, uninduced, rep2

description: Library name: convergent_uninduced_rep2


title: ATAC KDM6A FL OE rep1

description:
Library name: SAMPLES15
Peak files; Bigwig files


title: Convergent hiPSC, uninduced, no virus control, rep1

description: Library name: convergent_uninduced_novirus_rep1


title: ATAC KDM6A del-IDR OE rep2

description:
Library name: SAMPLES14
Peak files; Bigwig files

value: OE KDM6A del-IDR


title: Convergent hiPSC, uninduced, rep1

description: Library name: convergent_uninduced_rep1


title: Post-GIM cellsmultiplexed MU

description: Library name: DS_MU

source_name: Neuroprogenitor cells

value: Neuroprogenitor cells


title: Convergent hiPSC, induced, rep1

description: Library name: convergent_induced_rep1

value: doxycycline


title: ATAC KDM6A del-IDR OE rep1

description:
Library name: SAMPLES13
Peak files; Bigwig files


title: Divergent hiPSC, induced, rep2

description:
Library name: divergent_induced_rep2
Library type is Region Capture Micro-C


title: OPCs multiplexed GEX

description: Library name: OPC_GEX

value: GEX


title: Convergent hiPSC, induced, rep2

description: Library name: convergent_induced_rep2


title: Divergent hiPSC, uninduced, rep1

description:
Library name: divergent_uninduced_rep1
Library type is Region Capture Micro-C


title: Downstream tandem hiPSC, induced, rep2

description:
Library name: downstream_tandem_induced_rep2
Library type is Region Capture Micro-C


title: Post-GIM cells multiplexed GEX

description: Library name: DS_GEX


title: Divergent hiPSC, induced, rep1

description:
Library name: divergent_induced_rep1
Library type is Region Capture Micro-C


title: sample1 RNF43 scRNAseq

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: TX

address: 1515 Holcombe Blvd

institute: The University of Texas MD Anderson Cancer Center

description:
Library name: sample1 RNF43
single cell RNAseq of RNF43 specific T cells.

data_processing:
Sequencing data were preprocessed separately using Cell Ranger 2.1.1, which included generating fastq files, aligning reads, and calculating gene-cell expression matrices.
Assembly: GRCh38
Supplementary files format and content: Barcode, feature and expression matrix file output from cell ranger.

source_name: T cells

extract_protocol:
Samples were processed according to an in-house developed protocol and the 10x Genomics Demonstrated Protocol Cell Preparation Guide (Document CG00053). Briefly, after removal of the supernatant, T-cells were gently washed twice in 1.5–3 ml of 0.04% BSA in PBS. Additionally, cells were passed through a 35μm strainer (BD Falcon® 5 ml Round-Bottom Tubes with Cell Strainer Cap, Corning, NY, USA) to eliminate cell clumps. Next, cells were stained with 0.4% Trypan blue and quantified and assessed for viability using the automated cell counting machine Countess 3 (Invitrogen, FL, US).
Single-cell RNA-seq (scRNA)) analyses were performed using the 10x Genomics Single Cell Immune Profiling Solution V1.0 according to the manufacturer’s protocols (10x Genomics V(D)J + 5′ Gene Expression).

value: T cells


title: ATAC KDM6B FL OE rep1

description:
Library name: SAMPLES11
Peak files; Bigwig files

value: OE KDM6B FL


title: ATAC KDM6B del-IDR OE rep1

description:
Library name: SAMPLES9
Peak files; Bigwig files

value: OE KDM6B del-IDR


title: RNA-seq from 029 Pre Treatment Rep 2

city: Ann Arbor

first: Patrick

middle: J

last: Grohar

state: MI

address: 1600 Huron Parkway

institute: University of Michigan Medical School

description:
Library name: 029_Pre2
G019_029Pre2

data_processing:
Reads were aligned to hg38 with STAR v 2.7.3a and quantified with RSEM 1.3.3 using gencode 31 annotations. Following quantification, induced and repressed targets were identified and Log2FC was calculated.
Assembly: hg38
Supplementary files format and content: SARC037_expected_counts.txt: Expected count matrix

source_name: Tumor

extract_protocol:
RNA was purified using mechanical disruption and column purification.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Tumor


description:
Library name: downstream_tandem_uninduced_rep2
Library type is Region Capture Micro-C

value: LU99 STRAIGHT-IN DUAL

value: hiPSC


title: BMSCs multiplexed MU

description: Library name: BMSC_MU

source_name: Mesenchymal stem cells

value: Mesenchymal stem cells


title: ATAC KDM6B del-IDR OE rep2

description:
Library name: SAMPLES10
Peak files; Bigwig files


title: TNBC 4T1-Tumor s.q. xenografted in mice, HumCD276-Dxd/IMQ trt group, sample 4

city: COLUMBUS

first: Zhuoxin

last: Zhou

state: OH

address: Gateway Lofts Columbus, 2211 Dublin Rd

institute: Ohio State University

description: Library name: Z24

data_processing:
Perform alignments with HISAT2 to the reference. HISAT2(Mortazavi et al., 2008) uses a graph-based alignment and has succeeded HISAT and TOPHAT2.
Assembly: mm39
Supplementary files format and content: The processed data file was saved in text format, which contains gene ENSEMBL ID, sample names, gene symbol, gene location, gene length, gene biotype and gene description.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit following the manufacturer’s protocol. cDNA library preparation and bulk RNA sequencing were conducted by Novogene America (Sacramento, CA, USA) using the Illumina HiSeq™ X Ten platform.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library.

value: Triple-negative breast cancer


title: ATAC KDM4B FL OE rep2

description:
Library name: SAMPLES8
Peak files; Bigwig files

value: OE KDM4B FL


title: RNA-seq from 029 Post Treatment Rep 3

description:
Library name: 029_Post3
G019_029Po3


title: RNA-seq from 029 Pre Treatment Rep 1

description:
Library name: 029_Pre1
G019_029Pre1


title: BMSCs multiplexed GEX

description: Library name: BMSC_GEX


title: RNA-seq from 029 Pre Treatment Rep 3

description:
Library name: 029_Pre3
G019_029Pre3


title: Upstream tandem hiPSC, uninduced, rep3

description: Library name: upstream_tandem_uninduced_rep3

data_processing:
Reads trimmed with TrimGalore (v0.6.10) and aligned with Bowtie2 (v2.5.4) with setting --very-sensitive-local
Alignments deduplicated with MarkDuplicatesSpark / GATK4 (v4.6.2.0)
Reads that were duplicates, non-properly paired, or had a mapping quality under 3 were filtered with Sambamba (v1.0.1)
Reads aligned to the spike-in ERCC sequences to determine a cellular input normalization constant.
Normalized summary bigwigs computed with bamCoverage / deeptools (v3.5.6)
Assembly: GRCh38.p14, edited at the CLYBL locus according to genomic modifications
Supplementary files format and content: Bigwig files are provided for each condition, showing read mappings to the edited genomes.

extract_protocol:
Extracted with Monarch Total RNA purification kit (NEB T2010) . ERCC spike-in RNA (Mix 1, Thermo Fisher 4456740) was added during lysis.
Processed with NEB Ultra II Directional RNA with Poly(A) selection followed by library prep with unique dual indexes by a core facility.


title: ATAC KDM6B FL OE rep2

description:
Library name: SAMPLES12
Peak files; Bigwig files


title: Divergent hiPSC, uninduced, rep2

description:
Library name: divergent_uninduced_rep2
Library type is Region Capture Micro-C


title: Upstream tandem hiPSC, induced, rep3

description: Library name: upstream_tandem_induced_rep3


title: TNBC 4T1-Tumor s.q. xenografted in mice, HumCD276-Dxd/IMQ trt group, sample 3

description: Library name: Z23


description:
Library name: downstream_tandem_uninduced_rep1
Library type is Region Capture Micro-C


title: TNBC 4T1-Tumor s.q. xenografted in mice, HumCD276-Dxd/IMQ trt group, sample 1

description: Library name: Z21


title: ATAC KDM4B del-IDR OE rep2

description:
Library name: SAMPLES6
Peak files; Bigwig files

value: OE KDM4B del-IDR


title: ATAC KDM4B FL OE rep1

description:
Library name: SAMPLES7
Peak files; Bigwig files


title: Downstream tandem hiPSC, induced, rep1

description:
Library name: downstream_tandem_induced_rep1
Library type is Region Capture Micro-C


title: Upstream tandem hiPSC, uninduced, rep2

description: Library name: upstream_tandem_uninduced_rep2

value: control


title: TNBC 4T1-Tumor s.q. xenografted in mice, HumCD276-Dxd/IMQ trt group, sample 2

description: Library name: Z22


title: RNA-seq from 038 Pre Treatment Rep 2

description:
Library name: 038_Pre2
F001_038Pre2


title: TNBC 4T1-Tumor s.q. xenografted in mice, saline group, sample 3

description: Library name: Z15

value: PBS control


title: RNA-seq from 029 Post Treatment Rep 1

description:
Library name: 029_Post1
G019_029Po1


title: Upstream tandem hiPSC, induced, rep2

description: Library name: upstream_tandem_induced_rep2


title: TNBC 4T1-Tumor s.q. xenografted in mice, saline group, sample 2

description: Library name: Z14


title: Upstream tandem hiPSC, induced, rep1

description: Library name: upstream_tandem_induced_rep1


title: TNBC 4T1-Tumor s.q. xenografted in mice, saline group, sample 4

description: Library name: Z16


title: ATAC KDM4B del-IDR OE rep1

description:
Library name: SAMPLES5
Peak files; Bigwig files

value: mESC


title: ATAC KDM4A FL OE rep1

description:
Library name: SAMPLES3
Peak files; Bigwig files

value: OE KDM4A FL


title: RNA-seq from 038 Pre Treatment Rep 3

description:
Library name: 038_Pre3
F001_038Pre3


title: RNA-seq from 038 Post Treatment Rep 3

description:
Library name: 038_Post3
F001_038Po3


title: TNBC 4T1-Tumor s.q. xenografted in mice, saline group, sample 1

description: Library name: Z13


title: Divergent hiPSC, uninduced, rep3

description: Library name: divergent_uninduced_rep3


title: Upstream tandem hiPSC, uninduced, rep1

description: Library name: upstream_tandem_uninduced_rep1


title: ATAC KDM4A FL OE rep2

description:
Library name: SAMPLES4
Peak files; Bigwig files


title: RNA-seq from 029 Post Treatment Rep 2

description:
Library name: 029_Post2
G019_029Po2


title: RNA-seq from 038 Pre Treatment Rep 1

description:
Library name: 038_Pre1
F001_038Pre1


title: RNA-seq from 038 Post Treatment Rep 1

description:
Library name: 038_Post1
F001_038Po1


title: Bursa, E18, RAG1 knockout, rep3

city: University Park

first: Tae Hyun

last: Kim

state: PA

address: 317 AVBS Building

institute: Penn State University

description: Library name: KO3

data_processing:
STAR 2.7.9a
Htseq
Assembly: GCF_016699485.2_bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: Excel sheet, raw read counts

organism: Gallus gallus

source_name: Bursa

extract_protocol:
Trizol
Illumina TruSeq Stranded Total RNA Library Prep Gold Kit

value: Bursa

value: RAG1 KO


title: ATAC KDM4A del-IDR OE rep1

description:
Library name: SAMPLES1
Peak files; Bigwig files

value: OE KDM4A del-IDR


title: mESC, NSD1KO

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

data_processing:
Raw sequences were processed using Juicer v1.6 with default parameters against hg38 or mm10
Juicer .hic files were converted to cooler .mcool files using hic2cool v0.8.3
Bias vectors were re-computed using the balance module of cooler v0.8.11 with default settings
CNV-aware bias vectors were determined using OneD with default parameters
Boundary scores were calcualted using RobusTAD with default parameters
Compartment scores were computed using cooltools with GC content as the sign-orienting signal
Assembly: hg38
Supplementary files format and content: MCOOL files contain multi-resolution contact maps in the Cooler format
Supplementary files format and content: CSV files contain the first eigenvector of 100-kb balanced matrices (i.e., compartment score)
Supplementary files format and content: TSV files contain RobusTAD boundary scores computed using 50-kb balanced matrices

extract_protocol:
Cells were crosslinked using formaldehyde, after which proximity-ligated DNA was digested using a 4-base cutter restriction enzyme (DpnII) with intact permeabilized nuclei. Following fill in and biotinylation of the resulting 5' overhangs and ligation of the blunt ends, DNA was sheared and then pulled down using streptavidin beads
Libraries were prepared following manufacturer guidelines using the NEB kit, and the amplified libraries were ultimately sequenced in paired-end mode

value: Embryonic stem cell


title: ATAC KDM4A del-IDR OE rep2

description:
Library name: SAMPLES2
Peak files; Bigwig files


title: mESC, WT

value: WT NSD1


title: Divergent hiPSC, induced, rep3

description: Library name: divergent_induced_rep3

value: doxycycline


title: P300 WT rep2

description:
Library name: SAMPLES8
Peak files; Bigwig files

extract_protocol:
mESCs nuclei were isolated by incubation with Complete Nuclei Isolation Buffer according to the manufacturer's instructions.
CUT&RUN was performed by using the ChIC/CUT&RUN Assay Kit (Active Motif) following the manufacturer's instructions.

value: WT


title: RNA-seq from 038 Post Treatment Rep 2

description:
Library name: 038_Post2
F001_038Po2

value: Tumor


title: Divergent hiPSC, uninduced, rep2

description: Library name: divergent_uninduced_rep2

value: LU99 STRAIGHT-IN DUAL

value: hiPSC


title: RNA-seq from 032 Post Treatment Rep 2

description:
Library name: 032_Post2
E5_01032Po2


title: RNA-seq from 032 Post Treatment Rep 3

description:
Library name: 032_Post3
E6_01032Po3


title: P300 WT rep1


title: Bursa, E18, RAG1 knockout, rep1

description: Library name: KO1


title: Bursa, E18, RAG1 knockout, rep2

description: Library name: KO2


title: Divergent hiPSC, induced, rep2

description: Library name: divergent_induced_rep2


title: P300 Alkbh5 del-cIDR rep2

value: Alkbh5 del-cIDR


title: P300 Alkbh5 del-cIDR rep1


title: RNA-seq from 032 Pre Treatment Rep 3

description:
Library name: 032_Pre3
E3_01032Pre3


title: YY1 WT rep2


title: Downstream tandem hiPSC, uninduced, rep3

description: Library name: downstream_tandem_uninduced_rep3


title: Bursa, E18, wild-type, rep3

description: Library name: WT3


title: Downstream tandem hiPSC, induced, rep3

description: Library name: downstream_tandem_induced_rep3


title: Bursa, E18, wild-type, rep2

description: Library name: WT2


title: YY1 WT rep1


title: RNA-seq from 032 Pre Treatment Rep 2

description:
Library name: 032_Pre2
E2_01032Pre2


title: Bursa, E18, wild-type, rep1

description: Library name: WT1


title: RNA-seq from 032 Post Treatment Rep 1

description:
Library name: 032_Post1
E4_01032Po1


title: Divergent hiPSC, induced, rep1

description: Library name: divergent_induced_rep1


description: Library name: downstream_tandem_uninduced_rep2


title: Mouse, Liver, E76R, rep 5

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

description:
Library name: Mouse_Liver_E76R_rep5
Normalized_counts_file_mRNA-seq_liver.tabular
Liver_E76R5

data_processing:
Reads were trimmed using Trim Galore!. Alignment was performed using HISAT2 to the mouse genome mm10. Quantification was done with featureCounts using exon regions. Differential expression analysis was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: No processed data files are included in this submission. Only raw FASTQ files are provided for each sample.

growth_protocol: Mice were housed five per cage and maintained under controlled temperature (22.5 °C) and a 12 h light/dark cycle, with food and water provided ad libitum.

extract_protocol:
Total RNA was isolated from all samples using standard protocols.
Watchmaker mRNA Library Prep Kit with xGEN Stubby adaptors and xGEN 10nt UDIs.

value: Liver

value: Whole tissue

value: H2B E76R


title: YY1 Alkbh5 del-cIDR rep2


title: Mouse, Liver, E76R, rep 4

description:
Library name: Mouse_Liver_E76R_rep4
Normalized_counts_file_mRNA-seq_liver.tabular
Liver_E76R4