title: sp9rna_P5_primary_ovary_post-NACT

city: Beijing

first: Yumei

last: Wu

address: Dongcheng District, Qi-he-lou Street No.17

institute: Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University

description:
Library name: sp9rna
HGSOC tumor sample processed for 10x Genomics single-cell RNA-seq (gene expression matrix).

data_processing:
Raw base call files were demultiplexed and converted to FASTQ files.
Reads were aligned to the human reference genome and gene expression matrices were generated using Cell Ranger (10x Genomics).
Gene-barcode matrices (matrix.mtx, barcodes.tsv, features.tsv) were generated for each sample.
Downstream analyses (quality control, normalization, clustering and cell type annotation) were performed using standard single-cell RNA-seq analysis workflows.
Assembly: GRCh38 (hg38).
Supplementary files format and content: Processed data are provided as 10x Genomics gene expression matrices, including matrix.mtx (sparse count matrix), barcodes.tsv (cell barcodes), and features.tsv (gene/features annotations) for each sample.

source_name: ovary

growth_protocol: human tumor tissues

extract_protocol:
Tumor tissues were transported at 4°C in tissue preservation solution and processed on ice. Tissues were washed with PBS, minced into 1–2 mm³ pieces, and enzymatically digested at 37°C for 15–30 min with gentle trituration every 5 min. Digestion was quenched with DMEM containing FBS. Cell suspensions were filtered through 70 μm and 40 μm strainers, centrifuged at 500 g for 5 min at 4°C, and resuspended in PBS to obtain single-cell suspensions. Cell viability was assessed using a Luna fluorescence cell counter (viability >80%), and the final concentration was adjusted to 700–1200 cells/μL for downstream library preparation.
Single-cell gene expression libraries were prepared using the 10x Genomics Chromium Single Cell 5’ kit v2. Single-cell suspensions, gel beads, and partitioning oil were loaded onto a Chromium Chip K to generate GEMs. Within GEMs, cells were lysed and reverse transcription was performed to generate barcoded and UMI-tagged cDNA. After emulsion breakage, cDNA was purified with magnetic beads and amplified by PCR. Libraries were constructed following the manufacturer’s instructions and sequenced on an Illumina platform.

treatment_protocol: Samples were collected at different clinical stages (pre-NACT, post-NACT, and platinum-sensitive recurrence

value: ovary

tag: subject status

value: advanced-stage HGSOC patient

tag: subject id

tag: tissue type

value: post-NACT


title: BEAS2B,Control,2

status: Public on Mar 03 2026

type: SRA

city: BeiJing

first: Chun

last: Chang

address: 49 North Huayuan Road

country: China

institute: Peking University Third Hospital

description:
Library name: Sample2
C2_1

library_source: transcriptomic

data_processing:
Quality control: Raw reads were filtered using fastp (v0.19.7) to remove adapter contamination, low-quality bases (Qphred ≤ 5 exceeding 50% of read length), and reads containing ambiguous 'N' bases.
Alignment: Clean reads were aligned to the GRCh38 reference genome using HISAT2 (v2.0.5) with default parameters.
Quantification: Gene expression counts were obtained with featureCounts (v1.5.0-p3). FPKM values were calculated for expression normalization.
Differential expression: For samples with biological replicates, DESeq2 (v1.20.0) was used to identify differentially expressed genes (threshold: |log2FC| ≥ 1 & padj ≤ 0.05).
Functional enrichment: GO and KEGG enrichment analyses were performed using clusterProfiler (v3.8.1).
Assembly: The reference genome used was GRCh38 (Genome Reference Consortium Human Build 38), corresponding to the file ebi_39_homo_sapiens_grch38_primary_assembly.
Supplementary files format and content: gene_fpkm.txt: Table with FPKM-normalized expression values for each gene in all samples.

molecule: total RNA

organism: Homo sapiens

source_name: Lung

extract_protocol:
Total RNA was extracted from cultured cells using the Trizol reagent (Ambion/Invitrogen, USA) according to the manufacturer's instructions. RNA integrity was assessed using an Agilent 2100 Bioanalyzer.
Strand-specific RNA-seq libraries were constructed. mRNA was enriched from total RNA using Oligo(dT) beads and fragmented. First-strand cDNA was synthesized with random hexamers, followed by second-strand synthesis using dUTP instead of dTTP. After end repair, A-tailing, and adapter ligation, the second strand was digested with USER enzyme. The library was then amplified and purified.

tag: tissue

value: Lung

tag: cell line

tag: cell type

value: bronchial epithelial cells

tag: genotype

value: WT

tag: treatment


title: sp6rna_P3_primary_ovary_pre-NACT

description:
Library name: sp6rna
HGSOC tumor sample processed for 10x Genomics single-cell RNA-seq (gene expression matrix).

library_source: transcriptomic single cell

molecule: polyA RNA

value: pre-NACT

tag: batch


title: sp10rna_P6_recurrent_pelvic_tumor_platinum-sensitive_recurrence

description:
Library name: sp10rna
HGSOC tumor sample processed for 10x Genomics single-cell RNA-seq (gene expression matrix).

source_name: pelvic recurrent tumor

value: pelvic recurrent tumor

value: platinum-sensitive recurrence


title: sp5rna_P2_metastatic_omentum_post-NACT

description:
Library name: sp5rna
HGSOC tumor sample processed for 10x Genomics single-cell RNA-seq (gene expression matrix).

source_name: omentum

value: omentum


title: sp8rna_P4_primary_ovary_post-NACT

description:
Library name: sp8rna
HGSOC tumor sample processed for 10x Genomics single-cell RNA-seq (gene expression matrix).


title: sp7rna_P3_metastatic_peritoneum_pre-NACT

description:
Library name: sp7rna
HGSOC tumor sample processed for 10x Genomics single-cell RNA-seq (gene expression matrix).

source_name: peritoneum

value: peritoneum


title: sp3rna_P2_metastatic_omentum_pre-NACT

description:
Library name: sp3rna
HGSOC tumor sample processed for 10x Genomics single-cell RNA-seq (gene expression matrix).


title: BEAS2B,HDM,24h,1

description:
Library name: Sample7
H1_1

value: HDM


title: sp4rna_P2_primary_ovary_post-NACT

description:
Library name: sp4rna
HGSOC tumor sample processed for 10x Genomics single-cell RNA-seq (gene expression matrix).


title: sp2rna_P1_primary_ovary_pre-NACT

description:
Library name: sp2rna
HGSOC tumor sample processed for 10x Genomics single-cell RNA-seq (gene expression matrix).


title: sp1rna_P1_primary_ovary_pre-NACT

description:
Library name: sp1rna
HGSOC tumor sample processed for 10x Genomics single-cell RNA-seq (gene expression matrix).


title: AdV-C5 wt- and AdV-C5-CMV-E1A- coinfected 12-h sample replicate 3

city: Zurich

first: Maarit

last: Suomalainen

address: Winterthurerstrasse 190

department: DMLS

country: Switzerland

institute: University of Zurich

description: Library name: 12hwtCMV3

data_processing:
Reads were trimmed with fastp v0.23.4. Non-default trimming options were --trim_poly_x
Expression values were computed using STAR and featureCounts. As reference GRCh38.p13 builds was used. Gene annotation were from GENCODE Release R27. AC_000008.1 was used as a reference for AdV-C5.
SNP information was stripped of the reads using Bamboozle
Assembly: GRCh38.p13
Supplementary files format and content: TXT files with read counts

growth_protocol: Precursor macrophages from EB-factories were differentiated into macrophages for seven days in X-VIVO5 medium supplemented with 1% Glutamax, 100 units/100ug penicillin/streptomycin, 100ng/ml M-CSF, 25ng/ml IL3, 50 uM 2-mercaptoethanol, with change of medium after three days

extract_protocol:
Cells were washed with PBS, resuspended in Trizol, incubated at RT for 15min and centrifuged at 16000xg for 30 sec. Supernatant was mixed with equal volume of EtOH and RNA was isolated with Zymo Research Quick-RNA miniprep plus kit according to manufacturer's protocol
RNA was prepared for sequencing using the Illumina TruSeq Stranded Total RNA kit according to the manufacturer's protocol. Ribosomal RNA depletion was done with Ribo-Zero rRNA removal kit

treatment_protocol: Cells were incubated with the viruses for 12 h, followed by 0-h or 15-h further incubation in virus-free medium

value: human iPSC-derived macrophage


title: AdV-C5 wt-infected 12-h sample replicate 1

description: Library name: 12hwt1


title: AdV-C5 wt-infected 12-h sample replicate 3

description: Library name: 12hwt3


title: noninfected control 12-h sample replicate 1

description: Library name: 12hNI1


title: ChIP_ubH2B_9J24h_rep4

city: Leiden

first: Martijn

middle: S.

last: Luijsterburg

state: zuid-holland

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

description: Library name: ChIP_ubH2B_9J24h_rep4

library_source: other

data_processing:
Sequences were trimmed using TrimGalore (Version 0.6.5). Reads were aligned to the GRCh38.p14 primary assembly using bwa-mem tools (BWA (Version 0.7.17). Only uniquely mapping and high-quality reads (> q30) were included in the analyses. Duplicate reads were removed using Samtools (Version 1.11) with fixmate -m and markdup -r settings. Bam files were converted into TagDirectories (with fixed fragment length 150) and UCSC genome tracks using HOMER tools (Version 4.8.2). Example genome tracks were generated in IGV (Version 2.4.3).
A list of 49,948 gene-coordinates of GRCh38 was obtained from the UCSC genome database selecting the “knownCanonical” table containing the canonical transcription start sites per gene. To prevent contamination of binding profiles, genes from this list were selected to be non-overlapping with at least 2 kb between genes and a minimal size of 3 kb (n=9,944). The selected gene coordinates were updated to GRCh38.p14. From this, a set of 3,000 actively transcribed genes was selected by calculating read-densities of BrU-seq data in the first 3kb of the gene in WT cells, using the AnnotatePeaks.pl tool of HOMER with default settings. From these 3,000 actively transcribed genes, subselections of genes were defined based on gene size, as indicated per analysis. Read-density profiles around TSS coordinates were defined using the AnnotatePeaks.pl tool of HOMER, followed by normalizing the averaged metaprofiles to their internal maximum intensity (around the TSS). Individual datasets were subsequently processed into heatmaps or binding profiles using R (Version 4.3.1) and Rstudio (Version 1.1.423).
Assembly: Hg38
Supplementary files format and content: Averages_ubH2BChIP_-5to100kb200bin_Above50-100-150kb.xlsx: excel file containing average readcounts around the TSS (from -5kb to +50/100kb with 200bp bins); averaged are signals of genes with indicated genelength
Supplementary files format and content: GeneList_Details_TSSfiles.txt: TSS coordinates for 9,588 canonical genes selected for downstream analyses; table includes genelength and readcount of BrUseq signal in first 3kb of the genes
Supplementary files format and content: *_TagDir_norm.bw: all files ending on .bw are bigwig files of the indicated condition, ready to be visualized against Hg38

molecule: other

growth_protocol: Cell lines were cultured at 37°C in an atmosphere of 5% CO2 in DMEM GlutaMAX (Thermo Fisher Scientific) supplemented with penicillin/streptomycin (Sigma), and 8% fetal bovine serum (FBS; Bodinco BV or Thermo Fischer Scientific (Gibco)).

extract_protocol:
Chromatin was sonicated to approximately one nucleosome using the Bioruptor Pico (Diagenode), 10 cycles of 30s ON/30 s OFF in a 4°C water bath. ubH2B ChIP was performed using ~28 µg of chromatin with 3 µl of ubH2B antibody (Cell Signaling; #5546S) by overnight incubation at 4 °C. Protein-chromatin-pull down followed with a 1:1 mix of protein A and protein G Dynabeads (Thermo Fisher; 10001D, 10003D). ChIP samples were extensively washed and purified using Qiagen MinElute kit.
Sample libraries were prepared using Hifi Kapa sample prep kit and A-T mediated ligation of Nextflex adapters or xGen UDI-UMI adapters. Samples were sequenced using an Illumina NovaSeq X, using paired-end sequencing with 150 bp from each end.

treatment_protocol: Cells were grown to 80-90% confluency and crosslinked with 0.5 mg/mL disuccinimidyl glutarate (DSG; Thermo Fisher) in PBS for 45 min at room temperature. Cells were washed once with PBS followed by incubation with 1% FA for 20 min at RT. Fixation was stopped by the addition of glycine in PBS to a final concentration of 0.1 M for 3 min at RT. This was followed by washing with cold PBS and collection of the cells in 0.25% Triton X-100, 10 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0), and 20 mM Hepes (pH 7.6) in miliQ. Chromatin was pelleted by centrifugation for 5 min at 400 × g and incubated in 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 50 mM Hepes (pH 7.6) in miliQ for 10 min at 4 °C. Chromatin was again pelleted by centrifugation and resuspended in ChIP-buffer (0.15 % SDS, 1 % Triton X-100, 150 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 20 mM Hepes (pH 7.6) in miliQ) to a final concentration of 15 × 106 cells/mL.

value: hTERT-immortalized retinal pigment epithelial cells

value: RPE1 iCas9 p53/puro-dKO

value: UV-C 9J/m2, 24hours recovery


title: noninfected control 12-h sample replicate 2

description: Library name: 12hNI2


title: noninfected control 12-h sample replicate 3

description: Library name: 12hNI3


title: AdV-C5 wt- and AdV-C5-CMV-E1A- coinfected 12-h sample replicate 2

description: Library name: 12hwtCMV2


title: AdV-C5 wt-infected 27-h sample replicate 3

description: Library name: 24hwt3


title: AdV-C5 wt- and AdV-C5-CMV-E1A- coinfected 27-h sample replicate 1

description: Library name: 24hwtCMV1


title: AdV-C5 wt- and AdV-C5-CMV-E1A- coinfected 12-h sample replicate 1

description: Library name: 12hwtCMV1


title: AdV-C5 wt- and AdV-C5-CMV-E1A- coinfected 27-h sample replicate 3

description: Library name: 24hwtCMV3


title: noninfected control 27-h sample replicate 1

description: Library name: 24hNI1


title: AdV-C5 wt- and AdV-C5-CMV-E1A- coinfected 27-h sample replicate 2

description: Library name: 24hwtCMV2


title: PD MI Sensitive mtNPM1 AML2 500 nM SNDX-50469 replicate 2

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

country: USA

institute: MD Anderson Cancer Center

description:
Library name: KBr_AML_274_500_nM_VTP_3
KBr_AML_274_500_nM_VTP_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to hg38 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

source_name: cell line

growth_protocol: All patient-derived post-MPN sAML cells were cultured in 20% FBS containing RPMI media. HS5 cells were cultured in high glucose formulated DMEM media supplemented with 10% FBS and 1% Glutamine.

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Bulk RNA Libraries were constructed following standard Illumina protocols for RNA sequencing in a sequencing and microarray core facility. Indexed cDNA libraries were minimally PCR amplified, pooled and sequenced.

treatment_protocol: Patient derived post MPN sAML cells were treated with tasquinimod (20 uM) for 16 hours at 37°C and harvested into RNA lysis buffer. HS5 cells were transfected with si-NT and si-TLR4 alone or treated with 20 uM of tasquinimod. Lysed cells were frozen at -80°C until they were processed for total RNA.

value: cell line

value: Primary AML Blast

value: Leukemia

value: Acute myeloid leukemia


title: AdV-C5 wt-infected 27-h sample replicate 1

description: Library name: 24hwt1


title: noninfected control 27-h sample replicate 3

description: Library name: 24hNI3


title: PD MI Sensitive mtNPM1 AML2 500 nM SNDX-50469 replicate 1

description:
Library name: KBr_AML_274_500_nM_VTP_2
KBr_AML_274_500_nM_VTP_2


title: AdV-C5 wt-infected 12-h sample replicate 2

description: Library name: 12hwt2


title: AdV-C5 wt-infected 27-h sample replicate 2

description: Library name: 24hwt2


title: PD MI Sensitive mtNPM1 AML2 Control replicate 2

description:
Library name: KBr_AML_274_0_2
KBr_AML_274_0_2

value: DMSO Control


title: PD MI Sensitive mtNPM1 AML1 Control replicate 1

description:
Library name: KBr_DF16835_0_1
KBr_DF16835_0_1


title: Pla6T_r1 short-read RNAseq

city: Boston

first: Evan

middle: Michael

last: Appleton

state: MA

address: 75 Kneeland St.

institute: Colossal Biosciences

description:
Library name: PC-emC6-SV40_r1
Column name in countTable_hyrax.txt: SF_1

data_processing:
We performed analysis using an Expression Analysis RNASeq workflow. Reads were trimmed using TrimGalore (V0.6.7), to remove low quality (qual < 25) ends of reads and remove reads < 35bp. Trimmed reads are aligned to a reference genome using STAR (default) or HiSAT2. BAMs from the same sample generated by multiple runs were merged using Samtools. The abundance of transcripts and genes were assessed using FeatureCount to generate raw gene counts, StringTie to generate FPKM and Salmon to generate raw transcript counts. Sample comparisons and differential gene/transcript expression analysis were performed using EdgeR, DESeq2 and IsoformSwitchAnalyzeR. Variant calling was called with DeepVariant and Freebayes. MA plots were generated with DESeq2 (v3.18) and ggpubr (v0.6.0).
Assembly: GCF_024166365.1_mEleMax1_primary_haplotype_genomic.fna
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Procavia capensis

source_name: Induced pluripotent stem cells

growth_protocol: emiPSCs were grown in highly customized growth conditions as defined in the manuscript. Elephant primary endothelial cells were grown in 30% FBS/1% antibiotic/antimycotic /1% Non-essential AA/ EGM-2 media.

extract_protocol:
RNeasy Plus Universal Mini Kit (Qiagen 73404)
Proprietary to Novogene, Inc.

value: Induced pluripotent stem cells

value: TF-overexpression of elephant OSKMNL and SV40 T-antigen


title: PD MI Sensitive mtNPM1 AML1 500 nM SNDX-50469 replicate 2

description:
Library name: KBr_DF16835_VTP_3
KBr_DF16835_VTP_3


title: PD MI Sensitive mtNPM1 AML1 500 nM SNDX-50469 replicate 1

description:
Library name: KBr_DF16835_VTP_2
KBr_DF16835_VTP_2


title: PD MI resistant mtNPM1 AML3 500 nM SNDX-50469 replicate 2

description:
Library name: KBr_AML_401_VTP_2
KBr_AML_401_VTP_2


title: PD MI resistant mtNPM1 AML3 500 nM SNDX-50469 replicate 1

description:
Library name: KBr_AML_401_VTP_1
KBr_AML_401_VTP_1


title: PD MI resistant mtNPM1 AML3 Control replicate 1

description:
Library name: KBr_AML_401_0_1
KBr_AML_401_0_1


title: noninfected control 27-h sample replicate 2

description: Library name: 24hNI2


title: PD MI resistant mtNPM1 AML2 500 nM SNDX-50469 replicate 1

description:
Library name: KBr_AML340_500nMVTP_1
KBr_AML340_500nMVTP_1


title: PD MI Sensitive mtNPM1 AML1 Control replicate 2

description:
Library name: KBr_DF16835_0_2
KBr_DF16835_0_2


title: CD11c+KLRG1+CD127- CD8 T cells, rep2

city: San Antonio

first: Yidong

last: Chen

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: Library name: AT_2_2

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat2 algorithm (v2.0.8b)
gene count measurements were obtained using HTSeq algorithm and using refseq annotation
Assembly: mm9
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA from sorted cells was isolated using RNeasy Micro Kit (QIAGEN) and quantified using nanodrop and Agilent bioanalyzer.
RNA-seq libraries were prepared according to SMART-seq2 protocol, with the following modifications: PCR preamplification to 10-12 cycles, two rounds beads cleanup with 1:1 ratio after cDNA synthesis, and 0.6-0.8 dual beads cleanup for Nextera XT DNA-seq library purification. Each library was bar-coded and then pooled for sequencing run with 50bp single-read sequencing protocol.

treatment_protocol: Male C57BL/6J mice, 6 weeks old, were treated with αCD137 antibody on day 0, 3 and 6 and single cell suspensions were isolated from the livers on day 8. Intrahepatic CD11c+KLRG1+CD127- and CD11c-KLRG1+CD127- CD8 T cells were sorted using BD FACSAria cell sorter (n=4/group).  CD8 T cells were defined as live CD45+MHCII-NK1.1-TCRβ+CD8α+CD4-.

value: Liver

tag: strain

value: CD11c+KLRG1+CD127- CD8 T cells


title: PD MI resistant mtNPM1 AML1 Control replicate 2

description:
Library name: KBr_AML233_0_2
KBr_AML233_0_2


title: PD MI resistant mtNPM1 AML1 Control replicate 1

description:
Library name: KBr_AML233_0_1
KBr_AML233_0_1


title: PD MI resistant mtNPM1 AML2 500 nM SNDX-50469 replicate 2

description:
Library name: KBr_AML340_500nMVTP_2
KBr_AML340_500nMVTP_2


title: PD MI resistant mtNPM1 AML2 Control replicate 1

description:
Library name: KBr_AML340_0_1
KBr_AML340_0_1


title: PD MI resistant MLL1r AML5 500 nM SNDX-50469 replicate 2

description:
Library name: KBr_AML550_500nM_VTP_2
KBr_AML550_500nM_VTP_2


title: PD MI resistant mtNPM1 AML1 500 nM SNDX-50469 replicate 1

description:
Library name: KBr_AML233_500nMVTP_1
KBr_AML233_500nMVTP_1


title: PD MI resistant MLL1r AML5 Control replicate 1

description:
Library name: KBr_AML550_0_1
KBr_AML550_0_1


title: PD MI resistant MLL1r AML5 Control replicate 2

description:
Library name: KBr_AML550_0_2
KBr_AML550_0_2


title: PD MI resistant MLL1r AML5 500 nM SNDX-50469 replicate 1

description:
Library name: KBr_AML550_500nM_VTP_1
KBr_AML550_500nM_VTP_1


title: PD MI resistant MLL-AF9 AML4 500 nM SNDX-50469 replicate 1

description:
Library name: KBr_AML_346_500_nM_VTP_1
KBr_AML_346_500_nM_VTP_1


title: PD MI resistant MLL-AF9 AML4 500 nM SNDX-50469 replicate 2

description:
Library name: KBr_AML_346_500_nM_VTP_2
KBr_AML_346_500_nM_VTP_2


title: PD MI resistant MLL-AF9 AML4 Control replicate 2

description:
Library name: KBr_AML_346_0_2
KBr_AML_346_0_2


title: PD MI resistant mtNPM1 AML1 500 nM SNDX-50469 replicate 2

description:
Library name: KBr_AML233_500nMVTP_2
KBr_AML233_500nMVTP_2


title: PD MI Sensitive mtNPM1 AML2 Control replicate 1

description:
Library name: KBr_AML_274_0_1
KBr_AML_274_0_1


title: PD MI Sensitive MLL-AF9 AML 500 nM SNDX-50469 replicate 2

description:
Library name: KBr_DF68555_VTP_3
KBr_DF68555_VTP_3


title: PD MI resistant mtNPM1 AML2 Control replicate 2

description:
Library name: KBr_AML340_0_2
KBr_AML340_0_2


title: PD MI Sensitive MLL-AF9 AML 500 nM SNDX-50469 replicate 1

description:
Library name: KBr_DF68555_VTP_2
KBr_DF68555_VTP_2


title: PD MI resistant mtNPM1 AML3 Control replicate 2

description:
Library name: KBr_AML_401_0_2
KBr_AML_401_0_2


title: PD MI Sensitive MLL-AF9 AML Control replicate 2

description:
Library name: KBr_DF68555_0_3
KBr_DF68555_0_3


title: PD MI resistant MLL-AF9 AML3 500 nM SNDX-50469 replicate 2

description:
Library name: KBr_AML371_500nM_VTP_2
KBr_AML371_500nM_VTP_2


title: PD MI resistant MLL-AF9 AML3 Control replicate 2

description:
Library name: KBr_AML371_0nM_3
KBr_AML371_0nM_3


title: PD MI Sensitive MLL-AF9 AML Control replicate 1

description:
Library name: KBr_DF68555_0_2
KBr_DF68555_0_2


title: PD MI resistant MLL-AF9 AML4 Control replicate 1

description:
Library name: KBr_AML_346_0_1
KBr_AML_346_0_1


title: PD MI resistant MLL-AF9 AML3 500 nM SNDX-50469 replicate 1

description:
Library name: KBr_AML371_500nM_VTP_1
KBr_AML371_500nM_VTP_1


title: PD MI resistant MLL-AF9 AML2 500 nM SNDX-50469 replicate 1

description:
Library name: KBr_AML323_500VTP_1
KBr_AML323_500VTP_1


title: MV4-11-MITR 500 nM SNDX-50469 replicate 1

description:
Library name: KBr_MV411_VTPR_VTP_1000_2
KBr_MV411_VTPR_VTP_1000_2

value: AML cell line


title: PD MI resistant MLL-AF9 AML2 Control replicate 2

description:
Library name: KBr_AML323_0_2
KBr_AML323_0_2


title: MV4-11-MITR 500 nM SNDX-50469 replicate 2

description:
Library name: KBr_MV411_VTPR_VTP_1000_3
KBr_MV411_VTPR_VTP_1000_3


title: PD MI resistant MLL-AF9 AML3 Control replicate 1

description:
Library name: KBr_AML371_0nM_2
KBr_AML371_0nM_2


title: PD MI resistant MLL-AF9 AML1 Control replicate 2

description:
Library name: KBr_AML297_0_2
KBr_AML297_0_2


title: PD MI resistant MLL-AF9 AML2 500 nM SNDX-50469 replicate 2

description:
Library name: KBr_AML323_500VTP_2
KBr_AML323_500VTP_2


title: PD MI resistant MLL-AF9 AML2 Control replicate 1

description:
Library name: KBr_AML323_0_1
KBr_AML323_0_1


title: MV4-11 Parental 500 nM SNDX-50469 replicate 1

description:
Library name: KBr_MV411_VTP_1000_2
KBr_MV411_VTP_1000_2


title: MV4-11 MITR Control replicate 1

description:
Library name: KBr_MV411_VTPR_Ctrl_2
KBr_MV411_VTPR_Ctrl_2


title: MV4-11 parental Control replicate 2

description:
Library name: KBr_MV411_Ctrl_3
KBr_MV411_Ctrl_3


title: MV4-11 Parental 500 nM SNDX-50469 replicate 2

description:
Library name: KBr_MV411_VTP_1000_3
KBr_MV411_VTP_1000_3


title: PD MI resistant MLL-AF9 AML1 500 nM SNDX-50469 replicate 2

description:
Library name: KBr_AML297_500VTP_3
KBr_AML297_500VTP_3


title: MV4-11 MITR Control replicate 2

description:
Library name: KBr_MV411_VTPR_Ctrl_3
KBr_MV411_VTPR_Ctrl_3


title: OCI-AML3 MITR Control replicate 1

description:
Library name: KBr_OCI3_VTPR_Ctrl_1
KBr_OCI3_VTPR_Ctrl_1


title: MV4-11 parental Control replicate 1

description:
Library name: KBr_MV411_Ctrl_2
KBr_MV411_Ctrl_2


title: OCI-AML3-MITR 500 nM SNDX-50469 replicate 2

description:
Library name: KBr_OCI3_VTPR_VTP_1000_3
KBr_OCI3_VTPR_VTP_1000_3


title: OCI-AML3 MITR Control replicate 2

description:
Library name: KBr_OCI3_VTPR_Ctrl_3
KBr_OCI3_VTPR_Ctrl_3


title: PD MI resistant MLL-AF9 AML1 500 nM SNDX-50469 replicate 1

description:
Library name: KBr_AML297_500VTP_2
KBr_AML297_500VTP_2


title: OCI-AML3-MITR Control ChIP input

description:
Library name: KBc_OCI3_MITR_Ctrl_input
KBc_OCI3_MITR_Ctrl_input

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.05
bigWig files were generated using the bamCoverage. broadPeak files were generated using MACS v2 with default settings.
Assembly: GRCh38
Supplementary files format and content: broadPeak

molecule: genomic DNA

source_name: lymphocyte

growth_protocol: UCSD-AML1 and AML191 cells were cultured in 20% FBS containing RPMI media supplemented with 10 ng/mL of GM-CSF.

extract_protocol:
Chromatin immunoprecipitation followed by Tn5 mediated tagmentation of de-crosslinked fragments.
Libraries were constructed following standard Illumina protocols for paired end indexing for ChIP-Seq. DNA fragments were PCR amplified for 12-15 cycles. SPRI beads were used to double-size select fragments in the range of 250 bp.

treatment_protocol: AML cells were treated with 100 nM of FHD-286 for 16 hours at 37°C and cryopreserved in freezing buffer composed of 90% FBS+ 10% DMSO until the time of nuclei isolation and Tn5 tagmentation.

value: lymphocyte

value: Untreated


title: OCI-AML3-MITR 500 nM SNDX-50469 replicate 1

description:
Library name: KBr_OCI3_VTPR_VTP_1000_1
KBr_OCI3_VTPR_VTP_1000_1


title: OCI-AML3 parental Control  replicate 2

description:
Library name: KBr_OCI3_Par_Ctrl_3
KBr_OCI3_Par_Ctrl_3


title: OCI-AML3-MITR Control H3K27Ac ChIP

description:
Library name: KBc_OCI3_MITR_Ctrl_H3K27Ac
KBc_OCI3_MITR_Ctrl_H3K27Ac


title: OCI-AML3 parental Control  replicate 1

description:
Library name: KBr_OCI3_Par_Ctrl_2
KBr_OCI3_Par_Ctrl_2


title: OCI-AML3 Control ChIP input

description:
Library name: KBc_OCIAML3_Ctrl_input
KBc_OCIAML3_Ctrl_input


title: OCI-AML3 Parental 500 nM SNDX-50469 replicate 2

description:
Library name: KBr_OCI3_Par_VTP_1000_2
KBr_OCI3_Par_VTP_1000_2


title: MV4-11-MITR Control H3K27Ac ChIP

description:
Library name: KBc_MV_VTPR_Control_H3K27Ac
KBc_MV_VTPR_Control_H3K27Ac


title: MV4-11 Control ChIP input

description:
Library name: KBc_MV411_Control_input
KBc_MV411_Control_input


title: OCI-AML3 Control H3K27Ac ChIP

description:
Library name: KBc_OCIAML3_Ctrl_H3K27Ac
KBc_OCIAML3_Ctrl_H3K27Ac


title: MV4-11-MITR Control ChIP input

description:
Library name: KBc_MV411_VTPR_Control_input
KBc_MV411_VTPR_Control_input


title: OCI-AML3 Parental 500 nM SNDX-50469 replicate 1

description:
Library name: KBr_OCI3_Par_VTP_1000_1
KBr_OCI3_Par_VTP_1000_1


title: HeLa cell line, deletion of ZC3H4 SRG, replicate 2

city: Milano

first: Gaurav

last: Mandana

address: Via Adamello 16

country: Italy

institute: European Institute of Oncology

description: Library name: HeLa_4Su_RGG_Rep2

data_processing:
Strand-specific paired-end reads (51 bp) were trimmed and clipped for quality control with Trimmomatic v0.38 (PMID: 24695404). Read quality was subsequently assessed with FastQC v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Reads were aligned to the hg38 reference genomes (GENCODE, https://www.gencodegenes.org/human/release_33.html) using TopHat v2.1.1 (PMID:23618408), allowing up to two mismatches and using the option ‐‐b2-very-sensitive ‐‐library-type fr-firststrand. Indels due to sequencing errors were identified using Bowtie2 v2.2.5 (PMID: 19261174). Only uniquely mapping reads were retained (–g 1). All experiments were conducted in triplicate.
Tracks (*.bigWig files) were generated using bamCoverage from deepTools v3.5.0 (PMID:27079975) (-bs 1 --normalizeUsing RPKM --outFileFormat bigwig -filterRNAstrand forward or --filterRNAstrand reverse)
Assembly: hg38 (GENCODE) https://www.gencodegenes.org/human/release_33.html
Supplementary files format and content: Strand specific tracks (bigWig)

source_name: HeLa

growth_protocol: HeLa cells were cultured in DMEM with 10% Fetal Bovine serum (Euroclone ECS0180L), 1% penicillin/streptomycin

extract_protocol:
Total RNA was extracted using Trizol (Thermofisher cat. 15596026)
cDNA libraries were generated using 100 ng of 4sU-labeled RNA with the TruSeq Stranded Total RNA Sample Prep Kit (Illumina RS-122-2301), including the ribosomal RNA depletion step.

treatment_protocol: Two guide RNAs (gRNAs) were designed and cloned into the pX330A-Puro-1x2 vector (Addgene plasmid #58766, incorporating a puromycin resistance cassette downstream of the Cas9 coding sequence). One set of gRNAs targeted the intronic regions flanking exons 8-9 and 11-12 of the ZC3H4 locus to remove the three zinc finger motif. The second set of gRNAs targeted the intronic regions flanking exons 3-4 and 8-9 of the ZC3H4 locus to remove the SR/RG-rich region. The plasmids were transfected in HeLa cells using Fugene HD transfection reagent (Promega E2311)

value: HeLa

value: uterus adenocarcinoma


title: PD MI resistant MLL-AF9 AML1 Control replicate 1

description:
Library name: KBr_AML297_0_1
KBr_AML297_0_1


title: HeLa cell line, deletion of ZC3H4 SRG, replicate 3

description: Library name: HeLa_4Su_RGG_Rep3


title: MV4-11 Control H3K27Ac ChIP

description:
Library name: KBc_MV4_11_Control_H3K27Ac
KBc_MV4_11_Control_H3K27Ac


title: sgROSA HiChIP

city: New York

first: Yohana

middle: E

last: Ghebrechristos

state: NY

address: 550 1st Ave.

department: Pathology

institute: NYU Grossman School of Medicine

description: Library name: Sample 1

data_processing:
Align to reference genome GRCh37/hg19 human reference genome using bwa
The reads used for downstream analyses were classified as accepted intra-chromosomal read-pairs by the GenomicTools tools-hic filter command on the hic-bench platform
Interaction matrices for each chromosome separately were created by the hic-bench platform at 40kb resolution.
To account for variances in read counts of more distant loci, distance normalization for each chromosome matrix was performed.
Looping analysis was performed using the “loops” and “loops-diff” steps within the hic-bench platform.
Assembly: hg19
Supplementary files format and content: HiChIP loop interactions, BEDPE format
Library strategy: Hi-ChIP

source_name: human cell line

growth_protocol: REH cells were grown at 37 degrees in RPMI. Cells were transduced with sgRNAs targeting ERG or a non-targeting control (ROSA) and were collected for downstream studies four days after transduction.

extract_protocol:
After in-situ proximity ligation, samples were sonicated on Covaris LE 220 at 4C, 300W, 15% duty factor, 200 cycles per burst, for 300 seconds. Samples are then precleared with protein G beads for an hour and subsequently incubated with 5μg of H3K27AC antibody (ab4729, Lot:GR3231988) at 4C overnight. After IP, libraries were amplified and quantified using KAPA Library Amplification kit
HiChIP libraries were generated using the Arima-HiC+ kit (A410232) with Swift Biosciences® Accel-NGS® 2S Plus DNA Library Kit (Cat # 21024) and Indexing kit (Cat # 26148) according to manufacturer’s protocol with minor modifications

value: b-acute lymphoblastic cell line

value: REH

tag: chip antibody

value: H3K27ac Abcam #ab4729

value: sgROSA


title: sgERG HiChIP

description: Library name: Sample 2

value: sgERG


title: human immortalized skeletal muscle cell, siNFIX, rep3

city: Shanghai

first: Shuang

last: Liu

address: No.274 Zhijiang Middle Road

department: orthopedics

institute: Shanghai Municipal Hospital of Traditional Chinese Medicine

description: Library name: Sample6

data_processing:
Raw sequence reads were generated by base calling using CASAVA and stored in FASTQ format.
Low-quality reads and adaptor sequences were removed, and clean reads were evaluated for Q20, Q30, and GC content.
Clean paired-end reads were aligned to the reference genome (Homo sapiens GRCh38) using HISAT2 v2.2.1 with default parameters.
Gene-level counts were obtained using HTSeq v2.0.2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Cat# DP424, TIANGEN, Beijing, China). The concentration, purity, and integrity of RNA were assessed using a NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA, USA). Three micrograms of RNA were used as input material for the RNA sample preparations.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and fragmented using divalent cations under elevated temperature in Illumina fragmentation buffer. First-strand cDNA was synthesized using random oligonucleotides and SuperScript II, followed by second-strand synthesis with DNA Polymerase I and RNase H. After end repair and adenylation of 3′ ends, Illumina PE adapters were ligated. cDNA fragments of 400–500 bp were selected using the AMPure XP system and amplified by 15 cycles of PCR with Illumina PCR Primer Cocktail. PCR products were purified using the AMPure XP system and quantified with an Agilent Bioanalyzer 2100 prior to sequencing.

value: skeletal muscle

value: human immortalized skeletal muscle cells

value: myoblast


title: human immortalized skeletal muscle cell, siCtrl, rep3

description: Library name: Sample3


title: human immortalized skeletal muscle cell, siNFIX, rep2

description: Library name: Sample5


title: human immortalized skeletal muscle cell, siCtrl, rep1

description: Library name: Sample1


title: HeLa cell line, Control, replicate 3

description: Library name: HeLa_4Su_Ctrl_Rep3

value: Wild Type


title: human immortalized skeletal muscle cell, siCtrl, rep2

description: Library name: Sample2


title: HCT116 cells, ZC3H4, FLAG-IP

description:
Library name: ZC3H4_noFLAG_FLAG_IP
FLAG M2: Sigma-Aldrich, Cat# F3165

data_processing:
From strand specific paired-end reads (51bp), unique molecular identifiers (UMIs) were extracted using umi_tools (v1.1.6) (PMID: 28100584) with parameters --random-seed 1 --extract-method=regex
Reads were trimmed using cutadapt (v5.1) with parameters --quality-cutoff 6 -m 18
Reads were trimmed, mapped to the human repeat database, and the unmapped reads from this step mapped to the human genome, as described in PMID: 35322209
Read alignments were deduplicated using umi_tools (v1.1.6) (PMID: 28100584) with parameters --paired --extract-umi-method=read_id --method=unique
Read alignments with mapping quality > 10 were extracted from the output alignments using samtools (v1.3.1)
Reads were filtered against blacklist regions  (https://github.com/Boyle-Lab/Blacklist)
Read 2 from each alignment was extracted for further analysis using samtools (v1.3.1)
bigWig files of read 2 were generated using deeptools (v 3.5.0) bamCoverage with parameters –binSize 1 and --sizeFactor with manually calculated scaling factor (10^9/num.reads).
the read 2 alignments were used to call peaks using CLIPper (https://github.com/YeoLab/clipper/)
Assembly: hg38 (GENCODE) https://www.gencodegenes.org/human/release_33.html
Supplementary files format and content: Strand specific tracks (bigWig)

growth_protocol: HCT-116 cells and their ZC3H4-mAID derivative were cultured in McCoy’s 5A medium supplemented with 10% South American serum, 1% penicillin/streptomycin and 1% L-Glutamax.

extract_protocol:
Crosslinked cells were lysed with iCLIP lysis buffer (50mM Tris-HCl pH 7.4, 100mM NaCl, 1% NP-40, 0.1% SDS, 0.5% Sodium deoxycholate, 1:200 Proteinase Inhibitor and sonicated, followed by 5 min treatment with RNase I  at 37°C to fragment RNA.
RNA from IPs was dephosphorylated with FastAP for 15 min at 37°C. T4 PNK was added for 20 min at 37°C at low pH, and a color-balanced pair of 3′ RNA adaptors (RNA_X1A/X1B or RNA_X2A/X2B) was ligated with T4 RNA ligase for 75 min at 25°C. Input samples were dephosphorylated with FastAP and phosphorylated with T4 PNK for 20 min at 37°C at low pH, and the 3′ RNA adaptor, RiL19, was ligated with T4 RNA ligase for 75 min at 25°C. Reverse transcription was then performed with AffinityScript using the AR17 primer for 55 min at 45°C, followed by ExoSAP-IT treatment to remove unincorporated primers. RNA was then degraded by alkaline hydrolysis (1M NaOH, 70°C, 12 min), and the 3′ DNA adaptor, rand103Tr3, was ligated with T4 RNA ligase overnight at 25°C. The D5x/D7x pair of primers was used in a qPCR reaction to determine the required amplification cycles, followed by PCR with Q5 polymerase (NEB M0492) using Combinatorial dual (CD) index adapters and the libraries were purified using 1,8x solid-phase reversible immobilization (SPRI) beads (Agencourt AMPure XP, Beckman Coulter).

treatment_protocol: DRB was added to cells at a final concentration of 100µM for 3 hours. Following DRB removal, cells were washed twice with pre-warmed 1x PBS, and then incubated with pre-warmed growth medium for 5-15 minutes. For complementation assays, ZC3H4-mAID cells were first infected with lentiviruses carrying wild type or mutant forms of ZC3H4 and grown in Tetracycline-free media. Endogenous ZC3H4 was then depleted by treating infected cells with 200µM Auxin for 8 hours, followed by doxycycline treatment for 16 hours, with concentrations adjusted for each mutant to mimic endogenous ZC3H4 expression levels.

value: colorectal carcinoma

value: Wild type

value: UNTREATED


title: HCT116 cells, ZC3H4-3xFLAG, FLAG-IP

description:
Library name: ZC3H4_FLAG_IP_A
FLAG M2: Sigma-Aldrich, Cat# F3165


title: ZC3H4_AID HCT-116 cell line, pCW57.1- HA_ZC3H4_deltaSRG, IP, replicate 2

description:
Library name: eCLIP_ZC3H4_delRGG_R2
HA tag: ThermoFisher 2-2.2.14

value: 24h Doxycycline 2ng/mL, 16h Auxin


title: ZC3H4_AID HCT-116 cell line, pCW57.1- HA_ZC3H4_deltaSRG, IP, replicate 1

description:
Library name: eCLIP_ZC3H4_delRGG_R1
HA tag: ThermoFisher 2-2.2.14


title: ZC3H4_AID HCT-116 cell line, pCW57.1- HA_ZC3H4_deltaSRG, INPUT, replicate 1

description:
Library name: eCLIP_INPUT_ZC3H4_delRGG_R1
HA tag: ThermoFisher 2-2.2.14


title: ZC3H4_AID HCT-116 cell line, pCW57.1- HA_ZC3H4_delta3xCCCH3, IP, replicate 2

description:
Library name: eCLIP_ZC3H4_cdlCCCH3_R2
HA tag: ThermoFisher 2-2.2.14

value: 24h Doxycycline 5ng/mL, 16h Auxin


title: ZC3H4_AID HCT-116 cell line, pCW57.1- HA_ZC3H4_delta3xCCCH3, IP, replicate 1

description:
Library name: eCLIP_ZC3H4_delCCCH3_R1
HA tag: ThermoFisher 2-2.2.14


title: ZC3H4_AID HCT-116 cell line, pCW57.1- HA_ZC3H4_WT, IP, replicate 2

description:
Library name: eCLIP_ZC3H4_WT_R2
HA tag: ThermoFisher 2-2.2.14

value: ZC3H4-3xFLAG_mAID, pCW57.1-HA_ZC3H4_WT


title: ZC3H4_AID HCT-116 cell line, pCW57.1- HA_ZC3H4_WT, IP, replicate 1

description:
Library name: eCLIP_ZC3H4_WT_R1
HA tag: ThermoFisher 2-2.2.14


title: ZC3H4_AID HCT-116 cell line, 5 min after DRB treated release, INPUT, replicate 1

description:
Library name: eCLIP_INPUT_ZC3H4_DRB5min_IP_R1
FLAG M2: Sigma-Aldrich, Cat# F3165

value: 5 min release after 3h DRB 100 µM


title: ZC3H4_AID HCT-116 cell line, pCW57.1- HA_ZC3H4_delta3xCCCH3, INPUT, replicate 1

description:
Library name: eCLIP_INPUT_ZC3H4_delCCCH3_R1
HA tag: ThermoFisher 2-2.2.14


title: ZC3H4_AID HCT-116 cell line, pCW57.1- HA_ZC3H4_WT, INPUT, replicate 1

description:
Library name: eCLIP_INPUT_ZC3H4_WT_R1
HA tag: ThermoFisher 2-2.2.14


title: ZC3H4_AID HCT-116 cell line, 5 min after DRB treated release, IP, replicate 2

description:
Library name: eCLIP_ZC3H4_DRB5min_IP_R2
FLAG M2: Sigma-Aldrich, Cat# F3165


title: ZC3H4_AID HCT-116 cell line, IP, replicate 2

description:
Library name: eCLIP_ZC3H4_IP_R2
FLAG M2: Sigma-Aldrich, Cat# F3165


title: human immortalized skeletal muscle cell, siNFIX, rep1

description: Library name: Sample4


title: HeLa cell line, deletion of ZC3H4 SRG replicate 1

description: Library name: HeLa_4Su_RGG_Rep1

value: HeLa

value: uterus adenocarcinoma


title: ZC3H4_AID HCT-116 cell line, 5 min after DRB treated release, IP, replicate 1

description:
Library name: eCLIP_ZC3H4_DRB5min_IP_R1
FLAG M2: Sigma-Aldrich, Cat# F3165


title: ZC3H4_AID HCT-116 cell line, DMSO treated, IP, replicate 1

description:
Library name: eCLIP_ZC3H4_DMSO_IP_R1
FLAG M2: Sigma-Aldrich, Cat# F3165

value: 3h DMSO


title: ZC3H4_AID HCT-116 cell line, DMSO treated, IP, replicate 2

description:
Library name: eCLIP_ZC3H4_DMSO_IP_R2
FLAG M2: Sigma-Aldrich, Cat# F3165


title: ZC3H4_AID HCT-116 cell line, INPUT, replicate 2

description:
Library name: eCLIP_INPUT_ZC3H4_IP_R2
FLAG M2: Sigma-Aldrich, Cat# F3165


title: ZC3H4_AID HCT-116 cell line, IP, replicate 1

description:
Library name: eCLIP_ZC3H4_IP_R1
FLAG M2: Sigma-Aldrich, Cat# F3165


title: ZC3H4_AID HCT-116 cell line, transfected delRGG, 24h Auxin, 16h Doxycycline 2 ng/mL, replicate 2

description: Library name: TTseq_HCT-116_mutants_RGG_DOX_replicate_2

data_processing:
Strand specific paired-end reads (61bp) were trimmed using Trimmomatic in paired end mode (v0.38) (PMID: 24695404)
Reads were aligned to the human genome (hg38) using STAR (v2.7.7a) (PMID: 23104886) with parameters --outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.3.
Read alignments with mapping quality > 10 were extracted from the output alignments using samtools (v1.3.1) (PMID: 19505943).
Reads were filtered against blacklist regions  (https://github.com/Boyle-Lab/Blacklist)
bigWig files were generated using deeptools (v 3.5.0) (PMID: 27079975) bamCoverage with parameters –binSize 1 --normalizeusing RPKM -filterRNAstrand forward or --filterRNAstrand reverse.
Assembly: hg38 (GENCODE) https://www.gencodegenes.org/human/release_33.html
Supplementary files format and content: Strand specific, RPKM normalized tracks (bigWig)

growth_protocol: HCT-116 cells were cultured in McCoy’s 5A medium supplemented with 10% South American serum, 1% penicillin/streptomycin (Sigma P4333), and 1% L-Glutamax (Gibco 35050061).

treatment_protocol: Cells were treated with 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) to precisely control RNA polymerase II transcription initiation in the presence or absence of auxin-induced ZC3H4 depletion. ZC3H4 transgenes were expressed using doxycycline in ZC3H4-deficient cells to assess the functional complementation capacity of ZC3H4 mutants. For specific details, refer to individual sample metadata.

value: ZC3H4-3xFLAG_mAID, pCW57-ZC3H4_deltaSRG

value: 24h Auxin, 16h Doxycycline 2 ng/mL


title: ZC3H4_AID HCT-116 cell line, DMSO treated, INPUT, replicate 1

description:
Library name: eCLIP_INPUT_ZC3H4_DMSO_IP_R1
FLAG M2: Sigma-Aldrich, Cat# F3165


title: ZC3H4_AID HCT-116 cell line, transfected WildType, UNTREATED, replicate 1

description: Library name: TTseq_HCT-116_mutants_WT_NT_replicate_1

value: ZC3H4-3xFLAG_mAID, pCW57-ZC3H4_WT


title: ZC3H4_AID HCT-116 cell line, transfected WildType, 24h Auxin, replicate 1

description: Library name: TTseq_HCT-116_mutants_WT_AUX_replicate_1

value: 24h Auxin


title: ZC3H4_AID HCT-116 cell line, transfected WildType, UNTREATED, replicate 2

description: Library name: TTseq_HCT-116_mutants_WT_NT_replicate_2


title: ZC3H4_AID HCT-116 cell line, transfected delRGG, UNTREATED, replicate 2

description: Library name: TTseq_HCT-116_mutants_RGG_NT_replicate_2


title: ZC3H4_AID HCT-116 cell line, transfected delRGG, UNTREATED, replicate 1

description: Library name: TTseq_HCT-116_mutants_RGG_NT_replicate_1


title: ZC3H4_AID HCT-116 cell line, transfected delRGG, 24h Auxin, 16h Doxycycline 2 ng/mL, replicate 1

description: Library name: TTseq_HCT-116_mutants_RGG_DOX_replicate_1


title: ZC3H4_AID HCT-116 cell line, transfected delRGG, 24h Auxin, replicate 2

description: Library name: TTseq_HCT-116_mutants_RGG_AUX_replicate_2


title: ZC3H4_AID HCT-116 cell line, transfected WildType, 24h Auxin, 16h Doxycycline 5 ng/mL, replicate 1

description: Library name: TTseq_HCT-116_mutants_WT_DOX_replicate_1

value: 24h Auxin, 16h Doxycycline 5 ng/mL


title: ZC3H4_AID HCT-116 cell line, transfected delCCCH3, 24h Auxin, 16h Doxycycline 5 ng/mL, replicate 1

description: Library name: TTseq_HCT-116_mutants_CCCH3_DOX_replicate_1


title: ZC3H4_AID HCT-116 cell line, transfected WildType, 24h Auxin, 16h Doxycycline 5 ng/mL, replicate 2

description: Library name: TTseq_HCT-116_mutants_WT_DOX_replicate_2


title: ZC3H4_AID HCT-116 cell line, transfected delRGG, 24h Auxin, replicate 1

description: Library name: TTseq_HCT-116_mutants_RGG_AUX_replicate_1


title: ZC3H4_AID HCT-116 cell line, transfected WildType, 24h Auxin, replicate 2

description: Library name: TTseq_HCT-116_mutants_WT_AUX_replicate_2


title: ZC3H4_AID HCT-116 cell line, transfected delCCCH3, 24h Auxin, 16h Doxycycline 5 ng/mL, replicate 2

description: Library name: TTseq_HCT-116_mutants_CCCH3_DOX_replicate_2


title: ZC3H4_AID HCT-116 cell line, transfected delCCCH3, UNTREATED, replicate 1

description: Library name: TTseq_HCT-116_mutants_CCCH3_NT_replicate_1


title: ZC3H4_AID HCT-116 cell line, transfected DPA, 24h Auxin, replicate 2

description: Library name: TTseq_HCT-116_mutants_DPA_AUX_replicate_2

value: ZC3H4-3xFLAG_mAID, pCW57-ZC3H4_DPR/DPA


title: ZC3H4_AID HCT-116 cell line, transfected DPA, UNTREATED, replicate 1

description: Library name: TTseq_HCT-116_mutants_DPA_NT_replicate_1


title: ZC3H4_AID HCT-116 cell line, INPUT, replicate 1

description:
Library name: eCLIP_INPUT_ZC3H4_IP_R1
FLAG M2: Sigma-Aldrich, Cat# F3165


title: ZC3H4_AID HCT-116 cell line, 24h Auxin washout, replicate 2

description: Library name: TTseq_HCT-116_Auxin_washout_24h_replicate_2


title: ZC3H4_AID HCT-116 cell line, transfected DPA, 24h Auxin, 16h Doxycycline 10 ng/mL, replicate 2

description: Library name: TTseq_HCT-116_mutants_DPA_DOX_replicate_2

value: 24h Auxin, 16h Doxycycline 10 ng/mL


title: ZC3H4_AID HCT-116 cell line, transfected DPA, 24h Auxin, replicate 1

description: Library name: TTseq_HCT-116_mutants_DPA_AUX_replicate_1

value: colorectal carcinoma


title: ZC3H4_AID HCT-116 cell line, transfected DPA, 24h Auxin, 16h Doxycycline 10 ng/mL, replicate 1

description: Library name: TTseq_HCT-116_mutants_DPA_DOX_replicate_1


title: ZC3H4_AID HCT-116 cell line, transfected delCCCH3, 24h Auxin, replicate 1

description: Library name: TTseq_HCT-116_mutants_CCCH3_AUX_replicate_1


title: ZC3H4_AID HCT-116 cell line, 24h Auxin washout, replicate 1

description: Library name: TTseq_HCT-116_Auxin_washout_24h_replicate_1


title: ZC3H4_AID HCT-116 cell line, transfected DPA, UNTREATED, replicate 2

description: Library name: TTseq_HCT-116_mutants_DPA_NT_replicate_2


title: ZC3H4_AID HCT-116 cell line, UNTREATED, replicate 1

description: Library name: TTseq_HCT-116_NonTreated_replicate_1


title: ZC3H4_AID HCT-116 cell line, UNTREATED, replicate 2

description: Library name: TTseq_HCT-116_NonTreated_replicate_2


title: ZC3H4_AID HCT-116 cell line, transfected delCCCH3, 24h Auxin, replicate 2

description: Library name: TTseq_HCT-116_mutants_CCCH3_AUX_replicate_2


title: ZC3H4_AID HCT-116 cell line, 24h Auxin, replicate 2

description: Library name: TTseq_HCT-116_Auxin_24h_replicate_2


title: ZC3H4_AID HCT-116 cell line, 24h Auxin, replicate 1

description: Library name: TTseq_HCT-116_Auxin_24h_replicate_1


title: ZC3H4_AID HCT-116 cell line, 4h Auxin, 3h DRB, 15 mins washout, replicate 3

description: Library name: TTseq_HCT-116_DRB_DRB15_AUX_replicate_3

value: 4h Auxin, 3h DRB


title: ZC3H4_AID HCT-116 cell line, 4h Auxin, 3h DRB, replicate 3

description: Library name: TTseq_HCT-116_DRB_DRB0_AUX_replicate_3


title: ZC3H4_AID HCT-116 cell line, 4h Auxin, 3h DRB, 5 mins washout, replicate 3

description: Library name: TTseq_HCT-116_DRB_DRB5_AUX_replicate_3


title: ZC3H4_AID HCT-116 cell line, 3h DRB 10 mins washout, replicate 3

description: Library name: TTseq_HCT-116_DRB_DRB10_replicate_3

value: 3h DRB


title: ZC3H4_AID HCT-116 cell line, 3h DRB 5 mins washout, replicate 3

description: Library name: TTseq_HCT-116_DRB_DRB5_replicate_3


title: ZC3H4_AID HCT-116 cell line, 3h DMSO, replicate 3

description: Library name: TTseq_HCT-116_DRB_DMSO_replicate_3


title: ZC3H4_AID HCT-116 cell line, 4h Auxin, 3h DRB, 10 mins washout, replicate 3

description: Library name: TTseq_HCT-116_DRB_DRB10_AUX_replicate_3


title: ZC3H4_AID HCT-116 cell line, 4h Auxin, 3h DRB, 10 mins washout, replicate 2

description: Library name: TTseq_HCT-116_DRB_DRB10_AUX_replicate_2


title: ZC3H4_AID HCT-116 cell line, 4h Auxin, 3h DMSO, replicate 2

description: Library name: TTseq_HCT-116_DRB_DMSO_AUX_replicate_2

value: 4h Auxin, 3h DMSO


title: ZC3H4_AID HCT-116 cell line, 3h DRB, replicate 2

description: Library name: TTseq_HCT-116_DRB_DRB0_replicate_2


title: ZC3H4_AID HCT-116 cell line, 4h Auxin, 3h DMSO, replicate 3

description: Library name: TTseq_HCT-116_DRB_DMSO_AUX_replicate_3


title: ZC3H4_AID HCT-116 cell line, 3h DRB, replicate 3

description: Library name: TTseq_HCT-116_DRB_DRB0_replicate_3


title: ZC3H4_AID HCT-116 cell line, 3h DRB 5 mins washout, replicate 2

description: Library name: TTseq_HCT-116_DRB_DRB5_replicate_2


title: ZC3H4_AID HCT-116 cell line, 3h DRB 15 mins washout, replicate 3

description: Library name: TTseq_HCT-116_DRB_DRB15_replicate_3


title: ZC3H4_AID HCT-116 cell line, 3h DRB 15 mins washout, replicate 2

description: Library name: TTseq_HCT-116_DRB_DRB15_replicate_2


title: ZC3H4_AID HCT-116 cell line, 4h Auxin, 3h DRB, 15 mins washout, replicate 2

description: Library name: TTseq_HCT-116_DRB_DRB15_AUX_replicate_2


title: ZC3H4_AID HCT-116 cell line, transfected delCCCH3, UNTREATED, replicate 2

description: Library name: TTseq_HCT-116_mutants_CCCH3_NT_replicate_2

value: UNTREATED


title: ZC3H4_AID HCT-116 cell line, 4h Auxin, 3h DRB, replicate 2

description: Library name: TTseq_HCT-116_DRB_DRB0_AUX_replicate_2


title: ZC3H4_AID HCT-116 cell line, 3h DRB 10 mins washout, replicate 2

description: Library name: TTseq_HCT-116_DRB_DRB10_replicate_2


title: ZC3H4_AID HCT-116 cell line, 3h DMSO, replicate 2

description: Library name: TTseq_HCT-116_DRB_DMSO_replicate_2


title: ZC3H4_AID HCT-116 cell line, 4h Auxin, 3h DRB, 15 mins washout, replicate 1

description: Library name: TTseq_HCT-116_DRB_DRB15_AUX_replicate_1


title: ZC3H4_AID HCT-116 cell line, 4h Auxin, 3h DMSO, replicate 1

description: Library name: TTseq_HCT-116_DRB_DMSO_AUX_replicate_1


title: ZC3H4_AID HCT-116 cell line, 4h Auxin, 3h DRB, 5 mins washout, replicate 2

description: Library name: TTseq_HCT-116_DRB_DRB5_AUX_replicate_2


title: ZC3H4_AID HCT-116 cell line, 4h Auxin, 3h DRB, 10 mins washout, replicate 1

description: Library name: TTseq_HCT-116_DRB_DRB10_AUX_replicate_1


title: ZC3H4_AID HCT-116 cell line, 3h DRB 15 mins washout, replicate 1

description: Library name: TTseq_HCT-116_DRB_DRB15_replicate_1


title: HeLa cell line, Control, replicate 2

description: Library name: HeLa_4Su_Ctrl_R1_Rep2

data_processing:
Strand-specific paired-end reads (51 bp) were trimmed and clipped for quality control with Trimmomatic v0.38 (PMID: 24695404). Read quality was subsequently assessed with FastQC v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Reads were aligned to the hg38 reference genomes (GENCODE, https://www.gencodegenes.org/human/release_33.html) using TopHat v2.1.1 (PMID:23618408), allowing up to two mismatches and using the option ‐‐b2-very-sensitive ‐‐library-type fr-firststrand. Indels due to sequencing errors were identified using Bowtie2 v2.2.5 (PMID: 19261174). Only uniquely mapping reads were retained (–g 1). All experiments were conducted in duplicate.
Tracks (*.bigWig files) were generated using bamCoverage from deepTools v3.5.0 (PMID:27079975) (-bs 1 --normalizeUsing RPKM --outFileFormat bigwig -filterRNAstrand forward or --filterRNAstrand reverse)
Assembly: hg38 (GENCODE) https://www.gencodegenes.org/human/release_33.html
Supplementary files format and content: Strand specific tracks (bigWig)

value: Wild Type


title: ZC3H4_AID HCT-116 cell line, 4h Auxin, 3h DRB, 5 mins washout, replicate 1

description: Library name: TTseq_HCT-116_DRB_DRB5_AUX_replicate_1


title: ZC3H4_AID HCT-116 cell line, 4h Auxin, 3h DRB, replicate 1

description: Library name: TTseq_HCT-116_DRB_DRB0_AUX_replicate_1


title: ZC3H4_AID HCT-116 cell line, siRNA control, Auxin treated, replicate 2

description: Library name: HCT-116 siRNA ctrl_AUX repl2

data_processing:
Strand specific paired-end reads (51bp) Reads were trimmed using Trimmomatic in paired end mode (v0.38) (PMID: 24695404)
Reads were aligned to the human genome (hg38) using STAR (v2.7.7a) (PMID: 23104886) with parameters --outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.3.
Read alignments with mapping quality > 10 were extracted from the output alignments using samtools (v1.3.1) (PMID: 19505943).
Reads were filtered against blacklist regions  (https://github.com/Boyle-Lab/Blacklist)
bigWig files were generated using deeptools (v 3.5.0) (PMID: 27079975) bamCoverage with parameters –binSize 1 --normalizeusing RPKM -filterRNAstrand forward or --filterRNAstrand reverse.
Assembly: hg38 (GENCODE) https://www.gencodegenes.org/human/release_33.html
Supplementary files format and content: Strand specific tracks (bigWig)

treatment_protocol: 25 pmol siRNA was mixed with lipid complexes (Lipofectamine RNAiMAX) in Opti-MEM Medium. After 5 min of incubation, the mixture was added directly to cells in culture medium, in the absence of antibiotic. Cells were treated with Auxin 200 µM, 48h after transfection

value: ZC3H4-3xFLAG_mAID, siRNA control

value: 4h Auxin


title: ZC3H4_AID HCT-116 cell line, siRNA control, replicate 2

description: Library name: HCT-116 siRNA ctrl repl2


title: ZC3H4_AID HCT-116 cell line, siRNA control, replicate 3

description: Library name: HCT-116 siRNA ctrl repl3


title: ZC3H4_AID HCT-116 cell line, 3h DMSO, replicate 1

description: Library name: TTseq_HCT-116_DRB_DMSO_replicate_1


title: ChIP-seq against HA-tagged ZC3H4 DPA construct, treated with auxin and doxycyline, replicate 2

description:
Library name: ChIP_DPA_DPR_ZC3H4_rep2
HA tag: ThermoFisher 2-2.2.14

data_processing:
ChIP-seq libraries were sequenced in paired-end mode; however, only Read 1was used for analysis. Reads were trimmed and clipped for quality control using Trimmomatic v0.38 (PMID: 24695404), and quality was assessed for each sample with FastQC v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). High-quality reads were then aligned to the reference genome using Bowtie2 v2.2.5 (PMID: 19261174) with the options --very-sensitive and --no-unal, and using the pre-built Bowtie2 index. Only uniquely mapping reads were retained for downstream analysis.
Tracks (*.bigWig files) were generated using bamCoverage from deepTools .v3.5.0  (PMID:27079975). Signal is normalized as CPM (Counts Per Million) , scaled by 1000 and computed using 1 bin = 1 nucleotide.
Assembly: hg38 (GENCODE) https://www.gencodegenes.org/human/release_33.html
Supplementary files format and content: bigWig format

growth_protocol: HCT-116 cells were cultured in McCoy’s 5A medium supplemented with 10% South American serum, 1% penicillin/streptomycin and 1% L-Glutamax.

extract_protocol:
The cells were lysed to prepare nuclear extracts. Following chromatin shearing by sonication, the lysates were incubated overnight at 4°C with protein Dynabeads™ M-280 Sheep Anti-Mouse IgG or Anti-Rabbit IgG (Invitrogen 11202D, 11203D) coupled with 10μg of the following antibodies: anti-FLAG M2 (Sigma F3165), anti-Pol II Ser5p (Abcam Ab5131) and anti-Pol II Ser2p (Diagenode C15200005) for endogenous ZC3H4 and Pol II purification, respectively. Following immunoprecipitation, the beads were retrieved using a magnet, washed, and the chromatin was eluted and de-crosslinked overnight at 65°C. DNA was subsequently purified using QIAquick PCR Purification Kit (Qiagen  28104) following the manufacturer instructions, and its quantity was determined using QuantiFluor (Promega)
Library preparation for Illumina sequencing was carried out using a described protocol (PMID: 29706544). The quality and quantity of the purified DNA libraries were assessed using Tapestation (Agilent Technologies) and Qubit (Life Technologies) before being subjected to sequencing on the NovaSeq platform

treatment_protocol: Individual Chip-seq were performed on ZC3H4-3xFLAG_mAID HCT-116 cell line from wild-type or ZC3H4-depleted cells for 4 hours. For specific details, refer to individual sample metadata. Cells were sequentially crosslinked with 2 mM disuccinimidyl glutarate (DSG)  45 min at room temperature, followed by 1% formaldehyde for chromatin fixation (10 min, room temperature). The reaction was quenched with 0.125 M Tris-HCl (pH 7.6)

value: 200 µM Auxin 16 h, 10 ng/mL Doxycycline 24 h


title: ZC3H4_AID HCT-116 cell line, 3h DRB 10 mins washout, replicate 1

description: Library name: TTseq_HCT-116_DRB_DRB10_replicate_1


title: ZC3H4_AID HCT-116 cell line, siRNA control, Auxin treated, replicate 1

description: Library name: HCT-116 siRNA ctrl_AUX repl1


title: ZC3H4_AID HCT-116 cell line, 3h DRB 5 mins washout, replicate 1

description: Library name: TTseq_HCT-116_DRB_DRB5_replicate_1


title: subcutaneous white adipose, total RNA, knock out, rep2

city: St. Louis

first: Clair

last: Crewe

address: 660 S Euclid Avenue

institute: Washington Univeristy in St. Louis

description:
Library name: KO2-RNA-seq
KO2

data_processing:
Total RNA-seq: Base calling and demultiplexing were performed using Illumina’s bcl2fastq software and a custom Python demultiplexing script, allowing a maximum of one mismatch in the index read. Adapter trimming was conducted using TrimGalore (v0.6.0), and reads were aligned to the GENCODE Mouse Release M37 (GRCm39) reference genome using STAR (v2.5.1a). Only uniquely mapped reads were retained for subsequent analysis. Smpd3 intron and exon coordinates were obtained from the UCSC Table Browser. Read quantification was performed using a custom script: read pairs were classified as intronic if both reads mapped within the same Smpd3 intron, and exonic if either read overlapped with any Smpd3 exon.
Assembly: Total RNA-seq: GRCm39
Supplementary files format and content: Total RNA-seq: a .CSV file contains the normalized read count of Smpd3 exonic and intronic regions of control (Ctrl) and knock out (KO) samples

source_name: subcutaneous white adipose

extract_protocol:
12 week-old male mice were fed chow diet supplemented with 600 mg/kg doxycycline for 2 weeks and SVF cells were isolated from sWAT as described above. SVF was harvested from sWAT as described above. After centrifugation the cells were resuspended in 2% FBS in PBS containing propidium iodide (PI; 1:400) for 15 min incubation on ice. After washing, the cells were resuspended in 2% FBS in PBS for sorting of viable cells, PI- cells. FACS was conducted with a BD Bioscience FACSAria cytometer at the Flow Cytometry Core Facility at UT Southwestern.
Total RNA-seq: Total RNA was extracted from adipocytes from control and ad-SMPD3KO mice using RNAqueous Micro Total RNA Isolation Kit (ThermoFisher AM1931), followed by ribosomal RNA (rRNA) depletion with the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat; NEB, E7400). rRNA-depleted RNA was used for library preparation with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, E7530) following the manufacturer’s protocols.

value: subcutaneous white adipose

value: stromal vascular fraction

value: adiponectin rtTA, TRE Cre, Smpd3 flox


title: ZC3H4_AID HCT-116 cell line, 3h DRB, replicate 1

description: Library name: TTseq_HCT-116_DRB_DRB0_replicate_1


title: subcutaneous white adipose, total RNA, control, rep2

description:
Library name: C2-RNA-seq
C2

value: adiponectin rtTA, Smpd3 flox


title: subcutaneous white adipose, total RNA, knock out, rep1

description:
Library name: KO1-RNA-seq
KO1


title: HeLa cell line, deletion of ZC3H4 3xCCCH, replicate 2

description: Library name: HeLa_4Su_CCCH3_R1_Rep2

value: HeLa

value: uterus adenocarcinoma


title: HeLa cell line, deletion of ZC3H4 3xCCCH, replicate 1

description: Library name: HeLa_4Su_CCCH3_R1_Rep1


title: HeLa cell line, Control, replicate 1

description: Library name: HeLa_4Su_Ctrl_R1_Rep1


title: ZC3H4 ChIP-seq, untreated, replicate 2

description:
Library name: ChIP_ZC3H4_rep2
FLAG M2: Sigma-Aldrich, Cat# F3165


title: ZC3H4_AID HCT-116 cell line, siRNA control, Auxin treated, replicate 3

description: Library name: HCT-116 siRNA ctrl_AUX repl3


title: subcutaneous white adipose, total RNA, knock out, rep3

description:
Library name: KO3-RNA-seq
KO3


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph + ART558; late; rep2

city: Heidelberg

first: Pei-Chi

last: Wei

state: Baden-Württemberg

address: Im Neuenheim Feld 280

department: Structural and functional genomics

country: Germany

institute: German Cancer Research Center

description:
Library name: iPolq-aph-repliseq-late-rep2
poltheta_aph_rep4_log2smooth_50000.bedgraph

data_processing:
*library strategy: Repli-seq
LAM-HTGTS: a sigularity package https://github.com/brainbreaks/HTGTS
Repli-seq: a sigularity pacakge https://github.com/brainbreaks/HighRes_RepliSeq
Assembly: mm10
Supplementary files format and content: GRO-seq: bigwig files for plus and minus strands.
Supplementary files format and content: LAM-HTGTS: tlx files contain LAM-HTGTS bait and prey junction, sequneces, start, end, and direction (Strand).
Supplementary files format and content: Repli-seq: log2 smoothed ratio file for early and late fractions.

growth_protocol: Mouse neural progenitor cells and primary neural stem/progenitor cells were cultured in NBBG medium (NeralBasalA, 2% B27 supplement without RA, 0.5 mM Glutamax, 10ng/ml human EGF, 10ng/ml mouse FGFb). Neural progenitor cells were then collected for nucleofection (LAM-HTGTS), GRO-seq, or Repli-seq experiments. For Aph treated cells, these cells were treated with 0.5 uM Aph for 72 hours and 0.25 uM for 24 hours. For PolQ inhibition, cells were incubated with 5uM ART558 for 72 hours then with 2.5 uM for 24 hours.

extract_protocol:
Genomic DNA for LAM-HTGTS: cells were lyzed in proteinase K digestion buffer, and genomic DNA were extraced with a standard phenol/chlorofomr protocol. RNA were removed by treating samples with RNAseA prior phenol/chlroform extraction. Genomic DNA for Repli-seq: cells were lyzed in proteinase K digestion buffer, fragmented by a Covaris fragmentation device to 200 bp, and nacent DNA were pulldowned by using an BrdU-specific antiboty.
We follow the published protocol, as indicated below, to construct the libraries. Repli-seq: https://www.nature.com/articles/nprot.2017.148 LAM-HTGTS: https://www.nature.com/articles/nprot.2016.043

treatment_protocol: Cells were treated with indicated concentration of aphidicolin or the veichle control DMSO for the indicated period.

value: ES cell derived NPC

value: ATR558 plus aphidicolin


title: subcutaneous white adipose, total RNA, knock out, rep4

description:
Library name: KO4-RNA-seq
KO4


title: ZC3H4_AID HCT-116 cell line, siRNA control, replicate 1

description: Library name: HCT-116 siRNA ctrl repl1

value: colorectal carcinoma


title: ChIP-seq against HA-tagged ZC3H4 deltaRGG construct, treated with auxin and doxycyline, replicate 2

description:
Library name: ChIP_deltaRGG_ZC3H4_rep2
HA tag: ThermoFisher 2-2.2.14

value: 200 µM Auxin 16 h, 2 ng/mL Doxycycline 24 h


title: Ser5p Pol II ChIP-seq, 4h auxin, replicate 3

description:
Library name: ChIP_Pol2_S5p_AUX_Rep3
RNA polymerase II CTD repeat YSPTSPS (phospho S5): Abcam, Cat# Ab5131

value: 4h Auxin 200 µM


title: ChIP-seq against HA-tagged ZC3H4 deltaRGG construct, treated with auxin and doxycyline, replicate 1

description:
Library name: ChIP_deltaRGG_ZC3H4_rep1
HA tag: ThermoFisher 2-2.2.14


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph + ART558; early; rep1

description:
Library name: iPolq-aph-repliseq-early-rep1
poltheta_aph_rep3_log2smooth_50000.bedgraph


title: ChIP-seq against HA-tagged ZC3H4 DPA construct, treated with auxin and doxycyline, replicate 1

description:
Library name: ChIP_DPA_DPR_ZC3H4_rep1
HA tag: ThermoFisher 2-2.2.14


title: ChIP-seq against HA-tagged ZC3H4 deltaCCCH3 construct, treated with auxin and doxycyline, replicate 2

description:
Library name: ChIP_deltaCCCH3_ZC3H4_rep2
HA tag: ThermoFisher 2-2.2.15

value: 200 µM Auxin 16 h, 5 ng/mL Doxycycline 24 h


title: subcutaneous white adipose, total RNA, control, rep4

description:
Library name: C4-RNA-seq
C4


title: Ser5p Pol II ChIP-seq, 4h auxin, replicate 1

description:
Library name: ChIP_Pol2_S5p_AUX_Rep1
RNA polymerase II CTD repeat YSPTSPS (phospho S5): Abcam, Cat# Ab5131


title: ChIP-seq against HA-tagged ZC3H4 deltaCCCH3 construct, treated with auxin and doxycyline, replicate 1

description:
Library name: ChIP_deltaCCCH3_ZC3H4_rep1
HA tag: ThermoFisher 2-2.2.14


title: subcutaneous white adipose, total RNA, control, rep3

description:
Library name: C3-RNA-seq
C3


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph; early; rep2

description:
Library name: aph-repliseq-early-rep2
aph_rep4_log2smooth_50000.bedgraph

value: APH


title: Ser5p Pol II ChIP-seq, untreated, replicate 1

description:
Library name: ChIP_Pol2_S5p_Rep1
RNA polymerase II CTD repeat YSPTSPS (phospho S5): Abcam, Cat# Ab5131

value: UNTREATED


title: ChIP-seq against HA-tagged ZC3H4 WT construct, treated with auxin and doxycyline, replicate 2

description:
Library name: ChIP_WT_ZC3H4_rep2
HA tag: ThermoFisher 2-2.2.14

value: ZC3H4-3xFLAG_mAID, pCW57.1-ZC3H4_WT


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph + ART558; late; rep1

description:
Library name: iPolq-aph-repliseq-late-rep1
poltheta_aph_rep3_log2smooth_50000.bedgraph


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph + ART558; early; rep2

description:
Library name: iPolq-aph-repliseq-early-rep2
poltheta_aph_rep4_log2smooth_50000.bedgraph


title: ZC3H4 ChIP-seq, untreated, replicate 1

description:
Library name: ChIP_ZC3H4_rep1
FLAG M2: Sigma-Aldrich, Cat# F3165


title: ChIP-seq against HA-tagged ZC3H4 WT construct, treated with auxin and doxycyline, replicate 1

description:
Library name: ChIP_WT_ZC3H4_rep1
HA tag: ThermoFisher 2-2.2.14


title: Ser5p Pol II ChIP-seq, untreated, replicate 3

description:
Library name: ChIP_Pol2_S5p_Rep3
RNA polymerase II CTD repeat YSPTSPS (phospho S5): Abcam, Cat# Ab5131


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph; late; rep1

description:
Library name: aph-repliseq-late-rep1
aph_rep1_log2smooth_50000.bedgraph


title: Spheroid C3A_LX2 cells replicate 3

city: Botucatu

first: Guilherme

middle: Ribeiro

last: Romualdo

state: SP

address: Rua Dr José Barbosa de Barros, 1486

country: Brazil

institute: UNESP

description:
Library name: S_C3A_LX23
Column name in S_C3A_LX2_FPKM.csv: S_C3A_LX23

data_processing:
Raw reads of fastq format were first processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N, and low-quality reads from raw data (Bolger et al., 2014). All the downstream analyses were based on clean data with high quality. Reference genome (GRCh38/hg38) and gene model annotation files were downloaded from the genome website directly. The index of the reference genome was built, and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. The abundance of each transcript was quantified using feature Counts v1.5.0-p3.
Assembly: GRCh38/hg38
Supplementary files format and content: csv. files contain fpkm data for each sample

growth_protocol: The human hepatoma C3A/HepG2 (HB-8065, ATCC, USA, https://www.atcc.org/products/crl-3581) and LX2 cell line was cultured in Eagle's Minimum Essential Medium (MEM) (Vitrocell, Brazil) with low glucose, 1 mM sodium pyruvate, 2 mM L-glutamine, 1% non-essential amino acids, supplemented with 10% fetal bovine serum (FBS) (Gibco, USA), 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco, USA) in T75 flasks in a humidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
After exposure, the medium was removed, cells were washed in phosphate buffer, harvested with a cell scraper and total RNA was isolated using QIAzol lysis reagent and RNeasy column-based system (Qiagen, UK) according to the manufacturer's instructions.
SMARTer Prep Kit according to the manufacturer's instructions

treatment_protocol: Transwell model (2D) - The C3A were seeded in conventional 6-well plates. After 24h, the C3A cells were exposed to empty inserts or inserts (0.4 µm pores, VWR International, USA) containing the LX2 cells. Spheroids model (3D) - C3A cells were cultured alone or with LX2 cells in ultra-low attachment U-shaped 96-well plates (174925, Thermo Fisher Scientific, USA) in “liver-like” 10:1 proportion for 48h until spheroid formation. Cell viability was measured after 24 and 48h post spheroid formation using the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT).

value: Liver

value: Hepatoma cells

value: WT


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph; late; rep2

description:
Library name: aph-repliseq-late-rep2
aph_rep4_log2smooth_50000.bedgraph


title: Spheroid C3A_LX2 cells replicate 1

description:
Library name: S_C3A_LX21
Column name in S_C3A_LX2_FPKM.csv: S_C3A_LX21


title: subcutaneous white adipose, total RNA, control, rep1

description:
Library name: C1-RNA-seq
C1

value: subcutaneous white adipose

value: stromal vascular fraction


title: ChIP-seq input

description: Library name: ChIP_INPUT


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C4; DMSO; early; rep1

description:
Library name: Nrg3-pe-del2-repliseq-early-rep1
n48j18_dmso_rep1_log2smooth_50000.bedgraph

value: solution control (DMSO)


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C4; DMSO; late; rep2

description:
Library name: Nrg3-pe-del2-repliseq-late-rep2
n48j18_dmso_rep2_log2smooth_50000.bedgraph


title: Spheroid C3A_LX2 cells replicate 5

description:
Library name: S_C3A_LX25
Column name in S_C3A_LX2_FPKM.csv: S_C3A_LX25


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C3; DMSO; early; rep1

description:
Library name: Nrg3-pe-del1-repliseq-early-rep1
n26j9_dmso_rep1_log2smooth_50000.bedgraph


title: Spheroid C3A cells replicate 2

description:
Library name: S_C3A2
Column name in S_C3A_FPKM.csv: S_C3A2


title: Spheroid C3A_LX2 cells replicate 4

description:
Library name: S_C3A_LX24
Column name in S_C3A_LX2_FPKM.csv: S_C3A_LX24


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C4; DMSO; early; rep2

description:
Library name: Nrg3-pe-del2-repliseq-early-rep2
n48j18_dmso_rep2_log2smooth_50000.bedgraph


title: Xrcc4-/-::p53-/-; ESC-NPC; parental; Aph; early; rep1

description:
Library name: aph-repliseq-early-rep1
aph_rep1_log2smooth_50000.bedgraph


title: Whole lung tissue in WT mice with bleomycin-induced pulmonary fibrosis

city: Kumamoto

first: Mitsuyoshi

last: Nakao

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

description:
Library name: Sample 1
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made by using Cell Ranger software 2.1.1.
Assembly: Mouse mm10
Supplementary files format and content: barcodes.tsv, features.tsv, and matrix.mtx files for Sample1 and Sample2

extract_protocol:
After anesthetizing the mice, lung perfusion was performed by flushing the heart with saline to remove blood from the lung tissue. After perfusion, the lungs were excised, the right lung was dissected, and finely minced using scissors. Tissue fragments from three mice were pooled and enzymatically digested with a mixture of Dispase, Collagenase, Elastase, and DNase I at 37°C for 25 minutes. The digested tissue was then passed through a 70-μm mesh filter to obtain a single-cell suspension, which was subsequently diluted in PBS containing 10% FBS.
The cDNA library was prepared by Chromium Next GEM sngle cell 3' kit v3.1 for Dual index following manufacturer's instructions.

treatment_protocol: After anesthetizing the mice, Bleomycin (0.75 mg/kg body weight) dissolved in 50 µl PBS was intratracheally administered to WT and Kdm7a KO mice. Mice were sacrificed on day 21 post-administration, and their lungs were harvested.

value: Lung

value: Whole lung cells

value: Kdm7a WT

value: Intratracheally  administration of Bleomycin


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C3; DMSO; late; rep2

description:
Library name: Nrg3-pe-del1-repliseq-late-rep2
n26j9_dmso_rep2_log2smooth_50000.bedgraph

value: ES cell derived NPC


title: Spheroid C3A cells replicate 5

description:
Library name: S_C3A5
Column name in S_C3A_FPKM.csv: S_C3A5


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C3; DMSO; late; rep1

description:
Library name: Nrg3-pe-del1-repliseq-late-rep1
n26j9_dmso_rep1_log2smooth_50000.bedgraph


title: Spheroid C3A cells replicate 4

description:
Library name: S_C3A4
Column name in S_C3A_FPKM.csv: S_C3A4


title: Sodium Oxamate treatment rep1

first: Huida

last: Ma

address: No. 30 Shuangqing Road, Haidian District

institute: Tsinghua University

description: Library name: shCtrl_SO_B1

data_processing:
1. Sequencing reads were aligned to human genome (hg38) using Hisat2 (v2.1.0). 2. Reads with mapping quality <20 were filtered out using Samtools. 3. Read counts were obtained using htseq-count from HTSeq (v2.0.3) with parameters "-f bam -r pos -t exon --max-reads-in-buffer 1000000000 --stranded no -m union".
Assembly: hg38

extract_protocol:
RNA was harvested using RNAsimple Total RNA Kit (TIANGEN). 1µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using MGIEasy RNA Library Prep Kit/MGI/1000006384

value: Mammary epithelial cell


title: Monolayer C3A_LX2 cells replicate 4

description:
Library name: M_C3A_LX24
Column name in M_C3A_LX2_FPKM.csv: M_C3A_LX24


title: Sodium Oxamate treatment rep2

description: Library name: shCtrl_SO_B2


title: Spheroid C3A cells replicate 3

description:
Library name: S_C3A3
Column name in S_C3A_FPKM.csv: S_C3A3


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C4; DMSO; late; rep1

description:
Library name: Nrg3-pe-del2-repliseq-late-rep1
n48j18_dmso_rep1_log2smooth_50000.bedgraph


title: Xrcc4-/-::p53-/-; ESC-NPC; Nrg3 pe-del C3; DMSO; early; rep2

description:
Library name: Nrg3-pe-del1-repliseq-early-rep2
n26j9_dmso_rep2_log2smooth_50000.bedgraph


title: Spheroid C3A cells replicate 1

description:
Library name: S_C3A1
Column name in S_C3A_FPKM.csv: S_C3A1


title: Monolayer C3A_LX2 cells replicate 3

description:
Library name: M_C3A_LX23
Column name in M_C3A_LX2_FPKM.csv: M_C3A_LX23


title: Monolayer C3A_LX2 cells replicate 2

description:
Library name: M_C3A_LX22
Column name in M_C3A_LX2_FPKM.csv: M_C3A_LX22


title: Whole lung tissue in Kdm7a KO mice with bleomycin-induced pulmonary fibrosis

description:
Library name: Sample 2
10x Genomics

value: Kdm7a KO


title: AF9 knockdown rep2

description: Library name: shAF9_KD_B2


title: Ctrl rep1

description: Library name: shCtrl_B1


title: Monolayer C3A cells replicate 6

description:
Library name: M_C3A6
Column name in M_C3A_FPKM.csv: M_C3A6


title: Monolayer C3A_LX2 cells replicate 5

description:
Library name: M_C3A_LX25
Column name in M_C3A_LX2_FPKM.csv: M_C3A_LX25


title: Monolayer C3A_LX2 cells replicate 1

description:
Library name: M_C3A_LX21
Column name in M_C3A_LX2_FPKM.csv: M_C3A_LX21


title: Monolayer C3A_LX2 cells replicate 6

description:
Library name: M_C3A_LX26
Column name in M_C3A_LX2_FPKM.csv: M_C3A_LX26


title: Ctrl rep2

description: Library name: shCtrl_B2


title: Monolayer C3A cells replicate 5

description:
Library name: M_C3A5
Column name in M_C3A_FPKM.csv: M_C3A5


title: Monolayer C3A cells replicate 3

description:
Library name: M_C3A3
Column name in M_C3A_FPKM.csv: M_C3A3


title: Ela6T_Embryoid_body_d3_r2 short-read RNA-seq

description:
Library name: Ela6T_Embryoid_body_d3_r2
Column name in countTable_chtx_EB.txt: E_6_d3_2
countTable_chtx_EB.txt

organism: Elephas maximus

growth_protocol: Elephant primary cells, rock hyrax primary cells, emiPSCs, and pciPSCs were grown in highly customized growth conditions as detailed in the manuscript. These cell lines were also differentiated with a variety of different protocols as detailed in the manuscript. Please see the methods section of the manuscript for details.

value: 3 Days of embryoid body aggregation in AggreWell low-attachment plate


title: Spheroid C3A_LX2 cells replicate 2

description:
Library name: S_C3A_LX22
Column name in S_C3A_LX2_FPKM.csv: S_C3A_LX22


title: AF9 knockdown rep1

description: Library name: shAF9_KD_B1


title: Monolayer C3A cells replicate 2

description:
Library name: M_C3A2
Column name in M_C3A_FPKM.csv: M_C3A2


title: Monolayer C3A cells replicate 1

description:
Library name: M_C3A1
Column name in M_C3A_FPKM.csv: M_C3A1


title: Ela6T_Embryoid_body_d1_r2 short-read RNA-seq

description:
Library name: Ela6T_Embryoid_body_d1_r2
Column name in countTable_chtx_EB.txt: E_6_d1_2
countTable_chtx_EB.txt

value: 1 Day of embryoid body aggregation in AggreWell low-attachment plate


title: Ela6T_Embryoid_body_d3_r1 short-read RNA-seq

description:
Library name: Ela6T_Embryoid_body_d3_r1
Column name in countTable_chtx_EB.txt: E_6_d3_1
countTable_chtx_EB.txt


title: Ela4T_Embryoid_body_d3_r1 short-read RNA-seq

description:
Library name: Ela4T_Embryoid_body_d3_r1
Column name in countTable_chtx_EB.txt: E_4_d3_1
countTable_chtx_EB.txt


title: Ela6T_Embryoid_body_d1_r1 short-read RNA-seq

description:
Library name: Ela6T_Embryoid_body_d1_r1
Column name in countTable_chtx_EB.txt: E_6_d1_1
countTable_chtx_EB.txt


title: Monolayer C3A cells replicate 4

description:
Library name: M_C3A4
Column name in M_C3A_FPKM.csv: M_C3A4


title: HEK293T cells, recovery after heat shock (37°C for 6 hour), rep1

city: guagnzhou

first: tang

last: guorun

address: xingang

institute: Sun Yat-sen University

description:
Library name: R6-1
column name in readcount.txt: R6-1

data_processing:
Raw reads were quality-controled using FastQC (v0.11.8) and adapters and low-quality bases were removed using Cutadapt (v4.1) with parameters:a AGATCGGAAGAGC -A GATCGTCGGACTG -m 15 -n 2 -j 16. Clean reads were aligned to the human genome (GRCh38) using HISAT2 (v2.2.1). Gene counts were generated with featureCounts (v2.0.2).
Differential expression analysis was performed using DESeq2 (v1.38.3) with adjusted p-value < 0.05 and log2 fold change > 1.
Assembly: GRCh38 (Genome Reference Consortium Human Build 38)
Supplementary files format and content: Gene count matrix (readcount.txt): Tab-delimited file with raw read counts per gene. Gene expression was quantified using featureCounts, and raw counts were normalized using DESeq2's median of ratios normalization method.

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10%fetal bovine serum (FBS) in humidifed atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s protocol.
After rRNA was removed first, RNA sample was fragmented, end repair, adapter ligation, reverse-transcribed and libraries were amplified with 12 PCR cycles.

treatment_protocol: Heat stress treatment is performed at 43°C for 1 hour using water bath. Recovery group were returned to 37°C for 1/6/18 hours after heat stress.

value: embryonic kidney cells

value: 37°C for 6 hour after 43°C for 1 hour


title: Ela6T_Endoderm_r2 short-read RNA-seq

description:
Library name: Ela6T_Endoderm_r2
Column name in countTable_chtx_TL.txt: EN_d5_2
countTable_chtx_TL.txt

data_processing:
We performed analysis using an Expression Analysis RNASeq workflow. Reads were trimmed using TrimGalore (V0.6.7), to remove low quality (qual < 25) ends of reads and remove reads < 35bp. Trimmed reads are aligned to a reference genome using STAR (default) or HiSAT2. BAMs from the same sample generated by multiple runs were merged using Samtools. The abundance of transcripts and genes were assessed using FeatureCount to generate raw gene counts, StringTie to generate FPKM and Salmon to generate raw transcript counts. Sample comparisons and differential gene/transcript expression analysis were performed using EdgeR, DESeq2 and IsoformSwitchAnalyzeR. Variant calling was called with DeepVariant and Freebayes. MA plots were generated with DESeq2 (v3.18) and ggpubr (v0.6.0).
Assembly: GCF_024166365.1_mEleMax1_primary_haplotype_genomic.fna
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

value: Endoderm

value: STEMdiff™ Trilineage Differentiation Kit endoderm media differentiation for 5 days


title: Ela4T_Embryoid_body_d3_r2 short-read RNA-seq

description:
Library name: Ela4T_Embryoid_body_d3_r2
Column name in countTable_chtx_EB.txt: E_4_d3_2
countTable_chtx_EB.txt


title: Ela4T_Embryoid_body_d1_r1 short-read RNA-seq

description:
Library name: Ela4T_Embryoid_body_d1_r1
Column name in countTable_chtx_EB.txt: E_4_d1_1
countTable_chtx_EB.txt


title: Ela6T_Mesoderm_r2 short-read RNA-seq

description:
Library name: Ela6T_Mesoderm_r2
Column name in countTable_chtx_TL.txt: Me_d10_2
countTable_chtx_TL.txt

value: Mesoderm

value: STEMdiff™ Trilineage Differentiation Kit mesoderm media differentiation for 10 days


title: HEK293T cells, recovery after heat shock (37°C for 1 hour), rep2

description:
Library name: R1-2
column name in readcount.txt: R1-2

value: 37°C for 1 hour after 43°C for 1 hour


title: HEK293T cells, heat shock treatment (43°C for 1 hour), rep2

description:
Library name: H1-2
column name in readcount.txt: H1-2

value: 43°C for 1 hour


title: Ela4T_Embryoid_body_d1_r2 short-read RNA-seq

description:
Library name: Ela4T_Embryoid_body_d1_r2
Column name in countTable_chtx_EB.txt: E_4_d1_2
countTable_chtx_EB.txt


title: HEK293T cells, untreated wild-type, rep2

description:
Library name: WT-2
column name in readcount.txt: WT-2

value: untreated wild-type


title: HEK293T cells, recovery after heat shock (37°C for 6 hour), rep2

description:
Library name: R6-2
column name in readcount.txt: R6-2


title: Ela6T_Ectoderm_r1 short-read RNA-seq

description:
Library name: Ela6T_Ectoderm_r1
Column name in countTable_chtx_TL.txt: Ec_d7_1
countTable_chtx_TL.txt

value: Ectoderm

value: STEMdiff™ Trilineage Differentiation Kit ectoderm media differentiation for 7 days


title: HEK293T cells, recovery after heat shock (37°C for 18 hour), rep1

description:
Library name: R18-1
column name in readcount.txt: R18-1

value: 37°C for 18 hour after 43°C for 1 hour


title: Ela6T_Endoderm_r1 short-read RNA-seq

description:
Library name: Ela6T_Endoderm_r1
Column name in countTable_chtx_TL.txt: EN_d5_1
countTable_chtx_TL.txt


title: HEK293T cells, heat shock treatment (43°C for 1 hour), rep1

description:
Library name: H1-1
column name in readcount.txt: H1-1


title: Ela6T_Mesoderm_r1 short-read RNA-seq

description:
Library name: Ela6T_Mesoderm_r1
Column name in countTable_chtx_TL.txt: Me_d10_1
countTable_chtx_TL.txt


title: HEK293T cells, untreated wild-type, rep1

description:
Library name: WT-1
column name in readcount.txt: WT-1


title: Eem6TH_Embryoid_body_d17_r2 short-read RNA-seq

description:
Library name: Eem6TH_Embryoid_body_d17_r2
Column name in countTable_txo_EB_TL.txt: EM_49
countTable_txo_TL_EB.txt

value: 5 Days of embryoid body aggregation, 11 days of outgrowth on Laminin521 coated plate


title: Eem6TH_Embryoid_body_d17_r1 short-read RNA-seq

description:
Library name: Eem6TH_Embryoid_body_d17_r1
Column name in countTable_txo_EB_TL.txt: EM_24
countTable_txo_TL_EB.txt


title: HEK293T cells, recovery after heat shock (37°C for 1 hour), rep1

description:
Library name: R1-1
column name in readcount.txt: R1-1


title: Ela6T_Ectoderm_r2 short-read RNA-seq

description:
Library name: Ela6T_Ectoderm_r2
Column name in countTable_chtx_TL.txt: Ec_d7_2
countTable_chtx_TL.txt


title: LAM E209 Human Pulmonary Neoplasm (biol rep 4)

first: Uchenna

last: Unachukwu

state: New York

address: 630 West 168th Street, P&S 7-430

department: Anesthesiology

institute: Columbia University Medical Center

description:
Library name: JUE209-2
10x Genomics

data_processing:
Cell Ranger (v6.1.2; 10x genomics) was used to demultiplex, generate FASTQ files, align reads to the GRCh38 (human), filter both cell- and unique molecular identifier (UMI) barcodes, and count gene expression per cell.
Assembly: GRCh38 (human)
Supplementary files format and content: Tar archive file containing the main outputs from a cellranger count analysis

source_name: Pulmoanry Neoplasm

extract_protocol:
Fresh lung samples were processed within 48 hours of biopsy, rinsed in serum-free DMEM/F12 media under sterile conditions, and non-malignant lung tissue and necrotic areas were removed. Tumors were fragmented with sharp sterile blades, and digested twice consecutively in DMEM containing collagenase I (170mg/L) + 25mg/L DNase I + PennStrepp (1%) in a shaker at 85 rpm and 37°C  for 45 mins each time with vigorous trituration of tissue suspensions between runs. Samples were filtered through a 70 μM nylon cell strainer, sample volumes doubled with DMEM/F12  media, and centrifuged at 300 x g for 5 minutes at room temperature. Cell pellets were resuspended in 1x red blood cell lysis buffer for 10 minutes at room temperature, washed twice in DMEM/F12 media supplemented with 10% FBS and 1% PennStrepp, and resuspended in cell sorting media (PBS supplemented with 0.5% fetal bovine serum). After counting, cells were incubated with sytox green viability dye (1:1000 (v/v)) for 10 minutes in the dark at 4°C prior to cell sorting by flow cytometry using a BD FACS Aria II cell sorter (Becton Dickinson). Sytox Green (-) fractions per sample with cell viability of >85% were adjusted to 1000 cells/µl concentration before sequencing.
Cell suspensions were sequenced using the 10x Genomics 3’ Single Cell Gene Expression (GEX) workflow. Gel bead partitioning and cellular barcoding were done in the 10x Genomics Chromium Single Cell Controller, and library construction was performed using Illumina Single Cell 3’ v3 chemistry according to the Chromium Single Cell 3' GEM library & gel bead kit protocol (version 3; 10x Genomics). Single-cell transcriptome libraries were pooled and sequenced on a NovaSeq6000 System (Illumina).

value: Pulmoanry Neoplasm

value: LAM Lung Tumor

value: Unknown


title: LAM E202 Human Pulmonary Neoplasm (biol rep 1)

description:
Library name: JUE202
10x Genomics


title: Eem4TH_Embryoid_body_d17_r2 short-read RNA-seq

description:
Library name: Eem4TH_Embryoid_body_d17_r2
Column name in countTable_txo_EB_TL.txt: EM_45
countTable_txo_TL_EB.txt


title: LAM E208 Human Pulmonary Neoplasm (biol rep 3)

description:
Library name: JUE209-1
10x Genomics


title: H3K9la rep3

description: Library name: H3K9la_B3

data_processing:
1. We used BWA (v0.7.15) with parameters "mem -k 18" to map the paired-end 150bp reads to hg38. 2. We used Samtools (v1.3.1) for handling SAM and BAM files. Records with mapping quality less than 20 was filtered. 3. We used Picard (v1.107) to remove duplicates. 4. We used bamCoverage from deepTools (v3.3.0) to make a normalized bigwig with RPKM normalization and a bin size of 10bp. ENCODE blacklist regions were excluded. 5. We used MACS2 (v2.1.2) to call peaks with parameters "--nomodel --shift 100 --extsize 200"
Assembly: hg38
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

extract_protocol:
The hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903-1) was used for the test.
CUT&Tag seq libraries were prepared using the hyperactive Universal CUT&Tag Assay Kit (Vazyme, TD903-1). Libraries were amplified 13 cycles and validated by Qubit, AATI and qPCR.

value: Mammary epithelial cell


title: Eem6TH_Embryoid_body_d5_r1 short-read RNA-seq

description:
Library name: Eem6TH_Embryoid_body_d5_r1
Column name in countTable_txo_EB_TL.txt: EM_23
countTable_txo_TL_EB.txt

value: 5 Days of embryoid body aggregation in low-attachment plate


title: Eem4THsh_Embryoid_body_d17_r1 short-read RNA-seq

description:
Library name: Eem4THsh_Embryoid_body_d17_r1
Column name in countTable_txo_EB_TL.txt: EM_22
countTable_txo_TL_EB.txt


title: LAM E204 Human Pulmonary Neoplasm (biol rep 2)

description:
Library name: JUE204
10x Genomics


title: H3K9ac rep2

description: Library name: H3K9ac_B2


title: Eem4TH_Embryoid_body_d5_r2 short-read RNA-seq

description:
Library name: Eem4TH_Embryoid_body_d5_r2
Column name in countTable_txo_EB_TL.txt: EM_43
countTable_txo_TL_EB.txt


title: H3K9la rep1

description: Library name: H3K9la_B1


title: Flag-AF9G77A rep3

description: Library name: G77A_B3


title: Eem4THsh_Embryoid_body_d5_r2 short-read RNA-seq

description:
Library name: Eem4THsh_Embryoid_body_d5_r2
Column name in countTable_txo_EB_TL.txt: EM_46
countTable_txo_TL_EB.txt


title: Eem4THsh_Embryoid_body_d17_r2 short-read RNA-seq

description:
Library name: Eem4THsh_Embryoid_body_d17_r2
Column name in countTable_txo_EB_TL.txt: EM_47
countTable_txo_TL_EB.txt


title: Eem4THsh_Embryoid_body_d5_r1 short-read RNA-seq

description:
Library name: Eem4THsh_Embryoid_body_d5_r1
Column name in countTable_txo_EB_TL.txt: EM_21
countTable_txo_TL_EB.txt


title: Eem6TH_Embryoid_body_d5_r2 short-read RNA-seq

description:
Library name: Eem6TH_Embryoid_body_d5_r2
Column name in countTable_txo_EB_TL.txt: EM_48
countTable_txo_TL_EB.txt


title: Flag-AF9G77A rep1

description: Library name: G77A_B1


title: Eem4TH_Mesoderm_r2 short-read RNA-seq

description:
Library name: Eem4TH_Mesoderm_r2
Column name in countTable_txo_EB_TL.txt: EM_35
countTable_txo_TL_EB.txt

value: STEMdiff™ Trilineage Differentiation Kit mesoderm media differentiation for 5 days


title: H3K9la rep2

description: Library name: H3K9la_B2


title: Flag-KLF2 rep2

description: Library name: Flag-KLF2_B2


title: Flag-AF9WT rep3

description: Library name: Flag-AF9WT_B3


title: H3K9ac rep1

description: Library name: H3K9ac_B1


title: Eem4TH_Ectoderm_r2 short-read RNA-seq

description:
Library name: Eem4TH_Ectoderm_r2
Column name in countTable_txo_EB_TL.txt: EM_34
countTable_txo_TL_EB.txt


title: H3K9ac rep3

description: Library name: H3K9ac_B3


title: Flag-AF9WT rep2

description: Library name: Flag-AF9WT_B2


title: Eem4TH_Ectoderm_r1 short-read RNA-seq

description:
Library name: Eem4TH_Ectoderm_r1
Column name in countTable_txo_EB_TL.txt: EM_9
countTable_txo_TL_EB.txt


title: Eem4TH_Embryoid_body_d17_r1 short-read RNA-seq

description:
Library name: Eem4TH_Embryoid_body_d17_r1
Column name in countTable_txo_EB_TL.txt: EM_20
countTable_txo_TL_EB.txt


title: Flag-vector rep2

description: Library name: Flag_B2


title: Flag-AF9G77A rep2

description: Library name: G77A_B2


title: Eem4TH_Endoderm_r2 short-read RNA-seq

description:
Library name: Eem4TH_Endoderm_r2
Column name in countTable_txo_EB_TL.txt: EM_36
countTable_txo_TL_EB.txt

value: Endoderm


title: Eem4THsh_Mesoderm_r2 short-read RNA-seq

description:
Library name: Eem4THsh_Mesoderm_r2
Column name in countTable_txo_EB_TL.txt: EM_29
countTable_txo_TL_EB.txt


title: Eem4THsh_Endoderm_r1 short-read RNA-seq

description:
Library name: Eem4THsh_Endoderm_r1
Column name in countTable_txo_EB_TL.txt: EM_5
countTable_txo_TL_EB.txt

value: STEMdiff™ Trilineage Differentiation Kit endoderm media differentiation for 5 days


title: Eem4TH_Embryoid_body_d5_r1 short-read RNA-seq

description:
Library name: Eem4TH_Embryoid_body_d5_r1
Column name in countTable_txo_EB_TL.txt: EM_18
countTable_txo_TL_EB.txt


title: Eem4TH_Mesoderm_r1 short-read RNA-seq

description:
Library name: Eem4TH_Mesoderm_r1
Column name in countTable_txo_EB_TL.txt: EM_10
countTable_txo_TL_EB.txt

value: Mesoderm


title: Eem4TH_Endoderm_r1 short-read RNA-seq

description:
Library name: Eem4TH_Endoderm_r1
Column name in countTable_txo_EB_TL.txt: EM_11
countTable_txo_TL_EB.txt


title: AF9 rep2

description: Library name: AF9_B2


title: AF9 rep1

description: Library name: AF9_B1


title: Flag-KLF2 rep1

description: Library name: Flag-KLF2_B1


title: pre-iPSC_r2 short-read RNAseq

description:
Library name: emPRC_r2
Column name in countTable_elemax2.txt: PreiPSC_2

source_name: Partially-reprogrammed induced pluripotent stem cells

value: Chemical reprogramming

value: pre-iPSC


title: Eem4THsh_Endoderm_r2 short-read RNA-seq

description:
Library name: Eem4THsh_Endoderm_r2
Column name in countTable_txo_EB_TL.txt: EM_30
countTable_txo_TL_EB.txt


title: TGFb_INPUT_2

city: Fukuoka

first: Mitsutoki

last: Hatta

state: Fukuoka

address: 2-15-1 Tamura Sawara-ku

institute: Fukuoka Dental College

description: Library name: HaCaT_TGFβ1_INPUT_rep2

data_processing:
Next-generation sequencing was carried out on the Illumina NovaSeq 6000 (Illumina, San Diego, California), utilizing paired-end 150 base-read options.
ChIP-seq reads were trimmed using fastp (version 0.23.2) and subsequently mapped to the human reference genome (GRCh38) using Bowtie2 (version 2.4.5).
Peaks were called using findPeaks from HOMER (version 4.10). Super-enhancers were identified using the ROSE algorithm.
Duplicate sample data underwent irreproducibility discovery rate (IDR) analysis to assess the consistency of the peaks.
Bigwig files were generated using bamCoverage from deepTools (version 3.5.1).
Assembly: GRCh38
Supplementary files format and content: BigWig

source_name: HaCaT

growth_protocol: DMEM, 10% fetal bovine serum, 50 U/mL penicillin, and 50 µg/mL streptomycin. Cells were cultured at 37°C with 5% CO2.

extract_protocol:
Cells were fixed with 0.5% formaldehyde for 5 minutes. After quenching and nuclear extraction, chromatin was digested using microccoccal nuclease.
Library preparation was performed with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA)

treatment_protocol: HaCaT cells were treated with 5 ng/ml of human recombinant TGF-β1 for 48 h to induce the EMT phenotype.

value: HaCaT


title: Flag-AF9F28R rep3

description: Library name: F28R_B3


title: emEC2_r2 short-read RNAseq

description:
Library name: emEC_C2_WT_r2
Column name in countTable_elemax.txt: C2_control_2

source_name: Endothelial cells

extract_protocol:
RNeasy Plus Universal Mini Kit (Qiagen 73404)
Proprietary to Novogene, Inc.

value: Endothelial cells


title: Eem4THsh_Ectoderm_r2 short-read RNA-seq

description:
Library name: Eem4THsh_Ectoderm_r2
Column name in countTable_txo_EB_TL.txt: EM_28
countTable_txo_TL_EB.txt

value: Ectoderm


title: Flag-vector rep1

description: Library name: Flag_B1


title: Flag-AF9F28R rep2

description: Library name: F28R_B2


title: Eem4THsh_Mesoderm_r1 short-read RNA-seq

description:
Library name: Eem4THsh_Mesoderm_r1
Column name in countTable_txo_EB_TL.txt: EM_4
countTable_txo_TL_EB.txt


title: Flag-AF9F28R rep1

description: Library name: F28R_B1


title: Eem4THsh_r1 short-read RNA-seq

description:
Library name: Eem4THsh_r1
Column name in countTable_txo_EB_TL.txt: M18
countTable_txo_TL_EB.txt

value: Induced pluripotent stem cells

value: TF-overexpression of elephant OSKM and SV40 T-antigen and shTP53


title: Eem4THsh_r2 short-read RNA-seq

description:
Library name: Eem4THsh_r2
Column name in countTable_txo_EB_TL.txt: M45
countTable_txo_TL_EB.txt