title: Donor 3 scATAC-seq

city: Columbus

first: Patrick

last: Collins

state: Ohio

address: 460 West 12th Avenue, Biomedical Research Tower 770

department: Microbial Infection and Immunity

institute: The Ohio State University

description: Library name: Sample 3

library_source: genomic single cell

data_processing:
Fastq files were demultiplexed and aligned to the GRCh38 human reference genome using the 10x cloud system Ranger, the Cell Ranger Count v7.1.0. The snATAC-seq data processing pipeline, including quality control, genome alignment, peak calling, normalization and UMAP clustering was carried out using the Signac and Seurat tools. Reads were filtered to remove any contigs or repeats. Peaks under 3 kb were removed and only cells with more than 200 unique fragments were included. Peak annotation was performed using the reference package from 10x Genomics GRCh38-2020-A.
Assembly: GRCh38-2020-A
Supplementary files format and content: filtered_peak_bc_matrix.h5 is a file where each row of the matrix represents a region of the genome (a peak), that is predicted to represent a region of chromatin accessibility. The fragment file includes unique fragments across all cells.

source_name: Blood

extract_protocol:
Blood samples used were obtained from Versiti Ohio, Red Cross.  Natural killer (NK) cells were isolated from peripheral blood mononuclear cells (PBMCs) using the RosetteSep™ Human NK Cell Enrichment Cocktail (STEMCELL Technologies). Whole blood was first mixed with the RosetteSep™ NK cell enrichment cocktail, which selectively depletes unwanted cell populations by crosslinking them to red blood cells (RBCs). Following the addition of the cocktail, density gradient centrifugation was performed using Ficoll-Paque to separate enriched NK cells from the remaining blood components.
Library preparation and quality control were subsequently performed according to the 10X Genomics scATAC-seq protocol.

value: Blood

value: NK cells


title: Sample_MKL1 DNase rep2

status: Public on May 24 2025

type: SRA

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

country: USA

institute: NCI, NIH

library_source: genomic

data_processing:
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq and DNase-seq peaks were called by MACS2 version 2.1.0.  DNase was run in paired-end mode
The enhancers were identified using ROSE2 pipeline in bamliquidator 1.3
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
HiChIP: Paired end reads were mapped once to the human genome (hg19), and in parallel also mapped to the mouse genome (mm10), using bowtie2 within the HiC-pro pipeline
HiChIP: Mapped read pairs were then filtered first for junction validity (containing two fragments from restriction digestion), then duplicates were removed, using HiC-pro pipeline
HiChIP: AQuA factor incorporation was done by calculating the Contacts Per Million (CPM=Raw contact frequency matrix*1,000,000/total valid contacts), then converting to Reference normalized Contacts Per Million (RCPM=CPM*hg19 valid contacts/mm10 valid contacts).
HiChIP: Contact maps were converted to Juicebox compatible *.hic file format using the hicpro2juicebox.sh tool (https://github.com/nservant/HiC-Pro) provided with HiC-pro, and matrices were extracted using the Juicer33 dump tool (https://github.com/theaidenlab/juicer/wiki/Data-Extraction).
Assembly: Hg19
Supplementary files format and content: peak files are tab delimited text files for each sample.
Supplementary files format and content: HiChIP: processed file is in Juicer and Juicebox compatible .hic format, that is a contact matrix

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MCC cell lines were grown in RPMI with 10% FBS, 100U/ml penicillin and 0.1 mg/mL streptomycin.

extract_protocol:
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.  DNase-seq DNA purification was performed by column (MiniElute PCR purification kit, Qiagen).
Standard Illumina barcodes were introduced during library preparation

treatment_protocol: Samples were then harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies.  Proteinase K activation at 55 ˚C for 1 hour was followed by DNA purification by column (MiniElute PCR purification kit, Qiagen).

tag: cell line

tag: cell type

value: Merkel Cell carcinoma (MCC) cell line

tag: antibody

tag: enrichment target

value: DNase

tag: treatment

value: untreated

tag: molecule subtype

value: DNA (DNase-enriched)


title: Sample_MCC26 DNase rep2


title: Arabidopsis, gcn5-7, 12DAG, A, Rep1

city: Yangling

first: Su

middle: Ying

last: Pei

state: Shaanxi

address: No. 3 Taicheng Road

department: College of Life Sciences and Institute of Future Agriculture

country: China

institute: Northwest A&F University

description:
Library name: gcn5_7_RNASEQ_A_R1
Treatment

library_source: transcriptomic

data_processing:
Paired-end reads were subjected to filtering and trimming using the fastp tool (version 0.23.4).The clean reads were aligned to the TAIR 10 genome (https://www.arabidopsis.org/) using HISAT2 (VERSION 2.2.1).
Assembly: TAIR 10
Supplementary files format and content: Txt files include TPM values for each sample.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: 12DAG seedling

growth_protocol: Plants were grown on soil mixture in a growth chamber under long-day conditions at ~21°C.  seeds were stratified for 4 days at 4°C, and seedlings were harvested 12 days after germination.

extract_protocol:
total RNA was extracted by using RNA extraction  columns (Axygen, UE-MN-MS-RNA-250) following the manufacturer’s instructions.
RNA-Seq libraries  were constructed by BGI company.

tag: tissue

value: 12DAG seedling

tag: genotype


title: Donor 2 scATAC-seq

description: Library name: Sample 2

value: NK cellls


title: SA3336

city: West Haven

first: S

last: Agabiti

address: 840 West Campus Drive

department: Genetics

institute: Yale University

data_processing:
Signal intensities are converted to individual base calls during a run using the system's Real Time Analysis (RTA3) software. Base calls are transferred from the machine's dedicated personal computer to the Yale High Performance Computing cluster via a 1 Gigabit network mount for downstream analysis. Primary analysis - sample de-multiplexing and alignment to the mouse genome - is performed using Illumina's CASAVA 1.8.2 software suite bcl2fastq2/2.20.0-GCCcore-10.2.0.
Reads were trimmed using cutadapt, FASTQC, and Trim Galore. Alignment was done using STAR and downstream analysis was done using DESeq2 on R.
Assembly: UCSC mm10
Supplementary files format and content: normalized expression counts and differential expression analysis of adenomas and adenocarcinomas

molecule: polyA RNA

organism: Mus musculus

source_name: Lung

growth_protocol: Autochthonous lung tumors were generated in genetically-engineered mice and isolated at 30-31 weeks post-intratrachael instillation with lentiviral Cre.

extract_protocol:
Flash frozen tumor samples were biopulverized in liquid nitrogen and RNA was extracted using the Qiagen All Prep Kit per manufacturer's instructions. RNA quality and purity was assessed using an Agilent Bioanalyzer.
mRNA is purified from approximately 200ng of total RNA with oligo-dT beads and sheared by incubation at 94C in the presence of Mg (Roche Kapa mRNA Hyper Prep Cat# KR1352). Following first-strand synthesis with random primers, second strand synthesis and A-tailing are performed with dUTP for generating strand-specific sequencing libraries. Adapter ligation with 3’ dTMP overhangs are ligated to library insert fragments. Library amplification amplifies fragments carrying the appropriate adapter sequences at both ends. Strands marked with dUTP are not amplified. Indexed libraries are quantified by qRT-PCR using a commercially available kit (Roch KAPA Biosystems Cat#KK4854) and insert size distribution determined by either the Agilent Bioanalyzer. Samples with a yield of ≥ 0.5 ng/ul and a size distribution of 150-300bp are used for sequencing.

treatment_protocol: All mice were housed in specific-pathogen free cages and given free access to food and water ad libitum. Lentiviral Cre was administered to all mice via intratracheal instillation.

value: Lung

value: Treated with Lentiviral Cre


title: Clec5a_KO_CLP_3

city: Shenyang

first: Chunfeng

last: Liu

state: Liaoning

address: No.36 SanHao Street

institute: Shengjing Hospital of China Medical University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software（version2.20）. Sample demultiplexing, barcode processing and single-cell 3’gene counting by using the Cell Ranger pipeline(https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger，version 5.0.1) and scRNA-seq data were aligned to Ensembl genome, a total of 64,581 single cell captured from 3 WT littermates and 3 CLEC5A-/- mice were processed using 10X Genomics Chromium Single Cell 3’Solution. The Cell Ranger output was loaded into Seurat(version 3.1.1) be used to Dimensional reduction, clustering, and analysis of scRNA-seq data. Overall, 55,177 cells passed the quality control threshold: all genes expressed in less than three cells （default parameters：1 cell）were removed, number of genes expressed per cell >500 as low cut-off, the percent of mitochondrial-DNA derived gene-expression <25%. To visualize the data, we further reduced the dimensionality of all cells using Seurat and used t-SNE to project the cells into 2D space. The steps includes: Using the LogNormalize method of the Normalization function of the Seurat software to calculated the expression value of genes; PCA (Principal component analysis) analysis was performed using the normalized expression value, and the top 10 PCs were used to do clustering and t-SNE analysis；Selecting weighted Shared Nearest Neighbor (SNN) graph-based clustering method to find clusters. Marker genes for each cluster were identified with default parameters via the FindAllMarkers function in Seurat. This selects markers genes which are expressed in more than 10% of the cells in a cluster and average log(Fold Change) of greater than 0.26.
Assembly: Ensembl genome GRCm39 reference genome
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The lung tissue was placed in a sterile RNase-free culture dish containing an appropriate amount of calcium-free and magnesium-free 1 × PBS on ice and cut it into pieces, and then they were washed with 1 × PBS and remove non-purpose tissues. Tissues were dissociated into single cells in dissociation solution (0.35% collagenase IV5,2 mg/ml papain, 120 Units/ml DNase I) in 37 ℃ water bath with shaking for 20 min at 100 rpm. Digestion was terminated with 1× PBS containing 10% fetal bovine serum（FBS，V/V）, and the resulting cell suspension was filtered and centrifuged at 300g for 5 min at 4 °C. The cell pellet was resuspended in 100ul 1× PBS (0.04% BSA) and added with 1 ml 1× red blood cell lysis buffer to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300g for 5 min at room temperature. The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads and remove dead cells. Then the suspension was resuspended in 1× PBS (0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C（repeat twice）. The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability (above 85%) was confirmed by trypan blue exclusion, and single cell suspensions were counted and concentration adjusted to 700-1200 cells/μl.
Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’kit (V3).The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run, 150bp) by LC-Bio Technology co.ltd. at a minimum depth of 20,000 reads per cell.

value: CLP


title: input1,INPUT

city: Shanghai

first: jia

last: zhang

address: Ruijin 2nd Road 197

institute: Shanghai Jiao Tong University School of Medicine Department of Hypertension

description: Library name: input1,INPUT

data_processing:
ChIP-seq reads were aligned to the hg38 reference genome using Bowtie2 (2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control
Assembly: GRCh38
Supplementary files format and content: bigwig files were generated using Deeptools (3.5.0)

source_name: Primary human umbilical vein endothelial cells

growth_protocol: Human umbilical vein endothelial cells were cultured in Endothelial Cell Medium containing 5% fetal bovine serum, 50 mg/mL Endothelial Cell Growth Supplement, and 100 U/mL penicillin and streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature and quenched with 125 mM glycine. Cells were lysed in lysis buffer and then sonicated using a M220 focused ultrasonicator.


title: Sample_MKL1 DNase rep1


title: Sample_MCC26 DNase rep1


title: Clec5a_KO_CLP_2

description: 10X Genomics


title: GFP_AD_ACA

description: Library name: Tumor

data_processing:
The reads were aligned to the mm10-2020-A reference transcriptome to include introns using Cell Ranger count (v.7.1.0; 10x Genomics).
To remove ambient RNA, raw matrices generated from Cell Ranger were inputted into Cellbender (Snapshot 11) using remove-background and run on the Terra platform with an FPR set to 0.01. Doublets were detected using Scrublet (v0.2.1) via doublet_detection (Snapshot 2) on Terra.
Seurat_5.0.5 was used for downstream analyses. Cell barcodes with (1) 500-5000 genes; (2) 1000-10,000 transcript UMIs; and (3) less than 10% mitochondrial counts were included in the analysis. Data were normalized with a global scaling “LogNormalize” method and a scale factor of 10,000.
We performed feature selection with the “vst” method and 2,000 features, scaled the data with all genes, performed principal component analysis (PCA) for dimensionality reduction, and clustered single nucleus gene expression with the Louvain algorithm.
Assembly: mm10-2020-A
Supplementary files format and content: csv and matrix files

source_name: lung

extract_protocol:
Lung tumors were dissected from mice and flash frozen. Nuclei were isolated using a salt-based buffer and NP-40 with mincing on ice. Nuclei were washed, resuspended and counted prior to loading onto a 10x Chromium chip.
Libraries were constructed using the 10x Chromium single cell 3' library kit according to manufacturer protocol.

value: lung

value: tumor


title: WT_lung

description: Library name: WT

value: Vehicle control


title: Donor 1 scATAC-seq

description: Library name: Sample 1


title: ATF3 KO persister rep3

status: Public on May 23 2025

city: La Jolla

first: August

last: Williams

state: CA

address: 9500 Gilman Dr.

department: Dermatology

institute: UC San Diego

description:
Library name: ATF3_KO_persister_3
ATF3-pers-3_S143

data_processing:
Partek 12.1.0.
trimmed 3' Phred > 35.
hg38 ref mapping with STAR 2.7.8
Ensembl 112 release
Assembly: hg38
Supplementary files format and content: tab-delim text file includes raw counts for each sample

source_name: Cell line

extract_protocol:
Rneasy Mini Kit (Qiagen, 74104)
Illumina Stranded mRNA Prep

value: Cell line

value: Cancer cell

value: 250 nM dabrafenib + 25 nM trametinib- 14 days


title: ATF3 KO persister rep2

description:
Library name: ATF3_KO_persister_2
ATF3-pers-2_S142


title: MKN45 cells

city: Xuzhou

first: Peidong

last: Ni

address: 199 Jiefang South Road

department: General Surgery

institute: xuzhou central hospital

description: Library name: sample 1

data_processing:
we used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression. Then difference expression of genes was analyzed by DESeq (1.30.0) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05. At the same time, We used R language Pheatmap(1.0.8) software package to perform bi-directional clustering analysis of all different genes of samples. We geted heatmap according to the expression level of the same gene in different samples and the expression patterns of different genes in the same sample with Euclidean method to alculate the distance and Complete Linkage method to cluster.
Assembly: GRCh38
Supplementary files format and content: MKN45 v MKN45-R.DESeq.xlsx
Supplementary files format and content: diff_gene_of_all_groups.xlsx
Supplementary files format and content: all_cluster.xlsx

growth_protocol: The cells were cultured in RPMI-1640 medium, and the former medium was supplemented with 10% fetal bovine serum and 1% antibiotics (a mixture of 100mg/ml streptomycin and 100 U/ml penicillin). All cells were incubated in a humidified environment at 37°C with 5% CO₂.

extract_protocol:
RNA as extracted using the Trizol kit of Beyotime Company. 3 micrograms of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina) by Shanghai Personal Biotechnology Cp. Ltd.

value: gastric cancer cells

value: parental

value: WT


title: MDA-MB-231, B-input

city: Guangzhou

first: Hongyan

last: Huang

state: --- Select One ---

address: 253 Industrial Avenue middle, Haizhu District, Guangzhou

institute: Southern Medical University, Zhujiang hospital

data_processing:
Not Provided
Assembly: hg18

source_name: human breast cancer cell line

extract_protocol: RNA of catenin IP was extracted from the MDA-NB-231 using phenol-alcohol, sheared to approximately 300-500 bp using a Covaris S220 instrument.

value: human breast cancer cell line


title: Arabidopsis, gcn5-7, 12DAG, A, Rep2

description:
Library name: gcn5_7_RNASEQ_A_R2
Treatment


title: Arabidopsis, gcn5-7 arp6-1, 12DAG, A, Rep3

description:
Library name: gcn5_7arp6_1_RNASEQ_A_R3
Treatment

value: gcn5-7 arp6-1


title: ATF3 KO untreated rep3

description:
Library name: ATF3_KO_parental_3
ATF3-par-3_S134

value: untreated


title: ATF3 KO untreated rep1

description:
Library name: ATF3_KO_parental_1
ATF3-par-1_S132


title: WT_CLP_1

description: 10X Genomics


title: Pooled mouse EBs at day 21 with CRISPR perturbations from a pilot experiment

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

description: Library name: pilot_screen

data_processing:
Single-cell transcriptome data (10X) were processed using Cell Ranger 7.2.0 with default settings, followed by filtering of low-quality cells based on UMI counts, detected genes, and doublet detection. Additional quality control included filtering cells based on mitochondrial and ribosomal read percentages.
Assembly: GRCm38
Supplementary files format and content: The gene-by-cell matrix (sparse matrix), cell and gene metadata (CSV)

source_name: Embryoid bodies (EBs)

extract_protocol:
To obtain a single-cell suspension for downstream single-cell experiments, EBs at a given time point, typically at day 21 for the mosaic perturbation screens or at day 7, 14, or 21 for the wildtype time series experiment, were collected into 50 mL conical tubes at a density of three plates per tube and allowed to settle by gravity. The old CA medium was carefully removed and replaced with PBS (-/-) for two sequential washes, allowing EBs to settle by gravity after each wash. After removing the final wash, 3 mL of 0.25% trypsin was added to the tube, and the EBs were incubated at 37C for 5 min with gentle agitation. To achieve a uniform single-cell suspension, the trypsinized EBs were carefully pipetted up and down using a P1000 pipette followed by quenching with CA medium. The cell suspension was passed through a 40 um cell strainer, centrifuged at 300g for 5 min, and the cell pellet resuspended to a final concentration of 2 million cells / mL. FAC sorting was performed to enrich for a clean single-cell population, after which the cells were centrifuged at 400g for 5 min and resuspended in cold PBS containing 0.04% BSA at a concentration of approximately 1200 cells/uL. The resulting single-cell suspension was then processed following the 10x Genomics protocol as per the manufacturer’s instructions, loading 16K cells per lane for an estimated recovery of 10K cells.  For dissociating monoclonal EBs into a single-cell suspension, CA media was removed from each 2 mL tube, and 750 µL of 0.25% trypsin was added. Tubes were incubated at 37°C on a thermomixer set to 1100 rpm, with dissociation monitored under an epifluorescence microscope at 5-minute intervals. At the 10-minute mark, gentle trituration with a P1000 pipette was performed to aid dissociation, with additional trypsin added if necessary. Complete dissociation was typically achieved within 20 minutes. Trypsin was inactivated by adding CA media, and the cell suspension was further diluted before being passed through a 45 µm strainer into a 50 mL conical tube containing 10 mL of CA media. Cells were counted using a hemocytometer, transferred to a 15 mL conical tube for ease of handling, and centrifuged at 400g for 5 minutes. The supernatant was removed, and the cell pellet was resuspended in PBS + 0.04% BSA. The initial cell concentration was adjusted to 2400 cells/µL. A second cell count was performed, and the suspension was further diluted to a final concentration of 1200 cells/µL. Single-cell suspensions from each condition were then processed using the 10X Genomics High Throughput (HT) kit, with cells loaded across 16 lanes.
Wild-Type Time Series: Libraries were prepared using the 10x Genomics Single Cell 3' v2 kit. Three time points (days 7, 14, and 21) were sequenced, with one lane per time point, for a total of three lanes. Final libraries were sequenced on a NextSeq 500 using a 75-cycle high-output kit (R1: 26 bp, I1: 8 bp, I2: 0 bp, R2: 57 bp).  Pilot Screen: Libraries were prepared using the 10x Genomics Single Cell 3' v3 kit. Replicate 1: Six lanes were sequenced: two lanes for CRISPRcut sorted, two lanes for CRISPRi sorted, one lane for CRISPRcut unsorted, and one lane for CRISPRi unsorted. Final libraries were sequenced on a NextSeq 500 using two 75-cycle high-output kits (R1: 26 bp, I1: 8 bp, I2: 0 bp, R2: 57 bp). Replicate 2: Six lanes were sequenced: three lanes for CRISPRcut and three lanes for CRISPRi. Final libraries were sequenced on a NextSeq 500 using two 75-cycle high-output kits (R1: 28 bp, I1: 8 bp, I2: 0 bp, R2: 55 bp).  All TF Screen: Libraries were prepared using the 10x Genomics Single Cell 3' v3 kit. A total of 32 lanes were sequenced for CRISPRcut. Final libraries were sequenced by the Northwest Genomics Center on a NovaSeq 6000 using one S2 flow cell and one S4 flow cell (R1: 28 bp, R2: 80 bp, I1: 10 bp).  125TF Screen: Libraries were prepared using the 10x Genomics Single Cell 3' v3 kit. A total of 32 lanes were sequenced for CRISPRcut. Final libraries were sequenced by the Northwest Genomics Center using both a NovaSeq 6000 with one S4 flow cell (R1: 28 bp, I1: 10 bp, I2: 0 bp, R2: 91 bp) and a NextSeq 2000 with a P3 100-cycle kit (R1: 28 bp, I1: 8 bp, I2: 0 bp, R2: 91 bp).  piggyFlex and monoclonal EB validation: Sequencing was performed using four lanes of the 10X Genomics Single Cell 3' v3 kit, with two lanes allocated for replicate 1 and two lanes for replicate 2. Final libraries, capturing both gene expression and directly captured gRNAs, were sequenced on a NextSeq 2000 P2 100-cycle kit (R1: 28 bp, I1: 8 bp, I2: 0 bp, R2: 91 bp). Organoid barcode (BC) transcripts were separately sequenced using a NextSeq High 75-cycle kit (R1: 28 bp, I1: 10 bp, I2: 0 bp, R2: 53 bp).  TF screen in monoclonal EBs: Sequencing for the TF screen in monoclonal EBs was performed using 16 lanes of the 10X Genomics Single Cell 3’ HT Kit v3.1, with 12 lanes dedicated to conditions 1–10 and 4 lanes for condition 11. Final libraries, capturing gene expression, directly captured gRNAs, and organoid BCs, were sequenced on a NextSeq 2000 P3 100-cycle kit (R1: 28 bp, I1: 10 bp, I2: 10 bp, R2: 90 bp).

value: Embryoid bodies (EBs)


title: Arabidopsis, Columbia-0, 12DAG, A, Rep1

description:
Library name: Columbia-0_RNASEQ_A_R1
Control

value: 12DAG seedling


title: 150 pooled wildtype mouse EBs, with profiles captured at day 7, 14, and 21

description: Library name: wildtype_EB


title: DFFB KO persister+AP1i rep2

description:
Library name: DFFB_KO_persister_AP1i_2
DFFB-pers-ap1-2_S148

value: 250 nM dabrafenib + 25 nM trametinib + 20 uM T5224- 14 days


title: DFFB KO persister rep2

description:
Library name: DFFB_KO_persister_2
DFFB-pers-2_S139


title: Arabidopsis, Columbia-0, 12DAG, A, Rep2

description:
Library name: Columbia-0_RNASEQ_A_R2
Control


title: DFFB KO untreated rep3

description:
Library name: DFFB_KO_parental_3
DFFB-par-3_S131


title: MDA-MB-231, B-catenin


title: ATF3 KO persister+AP1i rep2

description:
Library name: ATF3_KO_persister_AP1i_2
ATF3-pers-ap1-2_S151


title: ATF3 KO persister+AP1i rep3

description:
Library name: ATF3_KO_persister_AP1i_3
ATF3-pers-ap1-3_S152


title: ATF3 KO persister+AP1i rep1

description:
Library name: ATF3_KO_persister_AP1i_1
ATF3-pers-ap1-1_S150


title: ATF3 KO persister rep1

description:
Library name: ATF3_KO_persister_1
ATF3-pers-1_S141

value: 250 nM dabrafenib + 25 nM trametinib - 14 days


title: DFFB KO persister+AP1i rep1

description:
Library name: DFFB_KO_persister_AP1i_1
DFFB-pers-ap1-1_S147


title: ATF3 KO untreated rep2

description:
Library name: ATF3_KO_parental_2
ATF3-par-2_S133


title: A375 WT persister rep2

description:
Library name: A375_persister_2
WT-pers-2_S11


title: DFFB KO untreated rep2

description:
Library name: DFFB_KO_parental_2
DFFB-par-2_S130


title: A375 WT persister+AP1i rep3

description:
Library name: A375_persister_AP1i_3
WT-pers-ap1-3_S146


title: DFFB KO persister rep1

description:
Library name: DFFB_KO_persister_1
DFFB-pers-1_S138


title: DFFB KO persister rep3

description:
Library name: DFFB_KO_persister_3
DFFB-pers-3_S140


title: DFFB KO untreated rep1

description:
Library name: DFFB_KO_parental_1
DFFB-par-1_S129


title: Jurkat target genes PacBio

city: PHILADELPHIA

first: YUNTIAN

last: FU

state: PA

address: 265 S. 37th Street

institute: University of Pennsylvania

description:
Library name: sample6
10X genomics

data_processing:
The demultiplexing, barcode processing, isoform quantification for Nanopore sequencing is done by LongcellPre (https://github.com/yuntianf/LongcellPre)
The demultiplexing, barcode processing, isoform quantification for PavBio sequencing is done by IsoSeq (https://isoseq.how/)
Assembly: Human hg38
Supplementary files format and content: Tab-seperated value files
Supplementary files format and content: Sparse matrix files

source_name: T-Cell

growth_protocol: Jurkat (ATCC TIB-152) and Cas9-stable Jurkat (SL555, GeneCopoeia, Inc., Rockville, MD, USA) cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% FBS.

extract_protocol:
Jurkat (ATCC TIB-152) and Cas9-stable Jurkat (SL555, GeneCopoeia, Inc., Rockville, MD, USA) cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium (A3160702, Gibco) supplemented with 10% FBS (A3160702, Gibco).
Single-cell cDNA and gene expression libraries of cell lines are generated by Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v2 (10X Genomics, Pleasanton, CA, USA) as per the manufacturer’s protocol.  The cDNA and gene expression libraries are amplified with 16 and 14 cycles of PCR respectively. The quality of gene expression libraries is confirmed using 2% E-Gel (Thermo Fisher Scientific, Waltham, MA, USA). The libraries are then quantified using Qubit (Invitrogen) and sequenced on Illumina sequencers (Illumina, San Diego, CA, USA).

treatment_protocol: The oligonucleotide pool for gRNA library targeting splicing factors were cloned to lentiGuide-Puro plasmid (Addgene plasmid #52963) and produced lentiviruses were transduced to Cas9 stable Jurkat cells using spinoculation at 800g for 30 min at 32 °Celsius.

value: T-Cell

value: Jurkat

value: wild


title: A375 WT persister+AP1i rep2

description:
Library name: A375_persister_AP1i_2
WT-pers-ap1-2_S145


title: A375 WT untreated rep2

description:
Library name: A375_parental_2
WT-par-2_S127


title: A375 WT persister rep3

description:
Library name: A375_persister_3
WT-pers-3_S12


title: DFFB KO persister+AP1i rep3

description:
Library name: DFFB_KO_persister_AP1i_3
DFFB-pers-ap1-3_S149


title: U2OS-Flp-In-TREx - siNC ChIP anti MePCE

city: Austin

first: Blerta

last: Xhemalçe

state: Texas

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

description: Library name: ChIPBX142

data_processing:
The adapter sequences in each raw fastq file (fastq) were trimmed using Trim Galore. The quality of each processed fastq file was then assessed with FastQC. Subsequently, the reads were aligned to the reference human genome hg19 using the bwa mem alignment method. SAMtools was employed to remove low-quality mapped reads by filtering out reads with a mapping quality score of less than 10, as well as PCR duplicates. Each read was extended by 200 bp to account for the full fragment length during further analysis using deepTools bamCoverage.
Assembly: hg19
Supplementary files format and content: bw files

growth_protocol: Cells were grown in DMEM containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 μg/mL streptomycin and 2 mM L-glutamine (PSQ) and supplemented with 100 µg/mL of Zeocin and 15 µg/mL of Blasticidin.

extract_protocol:
After siRNA depletion, cells were fixed with 1% formaldehyde for 10 minutes at room temperature and quenched with 20 mM Glycine for 5 min. Post quenching, the cells were lysed and chromatin was sonicated using a Bioruptor (Diagenode) instrument.
Libraries were constructed using the NEBNext Ultra II kit following manufacturer’s instructions.

treatment_protocol: Cells were reverse-transfected with siNC (Control) and siMePCE in two rounds at 0h and 48h, and cells were processed for ChIP at 96h.

value: siNC


title: U2OS-Flp-In-TREx - siMePCE ChIP anti GFP (Control)

description: Library name: ChIPBX141

value: siMePCE


title: A375 WT untreated rep3

description:
Library name: A375_parental_3
WT-par-3_S128

value: Cell line

value: Cancer cell


title: U2OS-Flp-In-TREx - siMePCE ChIP anti MePCE

description: Library name: ChIPBX143


title: A375 WT untreated rep1

description:
Library name: A375_parental_1
WT-par-1_S126


title: A375 WT persister rep1

description:
Library name: A375_persister_1
WT-pers-1_S10


title: siIFITM1-3

city: Chicago

first: Han

last: Peng

state: IL

address: 303 E Chicago Ave, Ward 9-120

institute: Feinberg School of Medicine, Northwestern University

data_processing:
follow the protocol from manufacturer
Assembly: hg38
Supplementary files format and content: excel

source_name: cornea/limbus

extract_protocol:
HLECs were transfected with a 5 nM siRNA pool against IFITM1 (Invitrogen, Carlsbad, CA, USA) or nontarget control (Invitrogen, Carlsbad, CA, USA) as previously described for 3 days. Then, cells were processed for total RNA isolation using miRNeasy kit (Qiagen, Hilden, Germany). Expression profiling was conducted using a Next-Generation Sequencing platform at Northwestern University Center for Genetic Medicine core. Gene differential expression profiles obtained from RNA-seq analysis were subjected to gene ontology analysis using DAVID.
follow the instructions from manufacturer

value: cornea/limbus

value: HLECs


title: siIFITM1-2


title: U2OS-Flp-In-TREx - siNC input

description: Library name: ChIPBX138


title: U2OS-Flp-In-TREx - siNC ChIP anti GFP (Control)

description: Library name: ChIPBX140


title: U2OS-Flp-In-TREx - siMePCE input

description: Library name: ChIPBX139


title: sicontrol3

value: siControl


title: siIFITM1-1


title: A375 WT persister+AP1i rep1

description:
Library name: A375_persister_AP1i_1
WT-pers-ap1-1_S144


title: sicontrol2


title: RL_PM_EP300_Mosun_24h_S2

city: Houston

first: Haopeng

last: Yang

state: TX

address: 7455 Fannin ST

department: Lymphoma and Myeloma

institute: The University of Texas MD Anderson Cancer Center

data_processing:
CUT&RUN: Sequencing quality control was evaluated by FastQC. Paired-end CUT&RUN raw reads were trimmed to remove adapter sequences using Trimmomatic and then aligned to version 19 of the human reference genome (hg19) using Bowtie2 with options: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Aligned reads were sorted by coordinates and tested for mapped fragment size distribution by Samtools. The final aligned and sorted Bam files were used for further processing. Visualization was assessed by converting the final Bam files to Bigwig files using the ‘bamCoverage’ command in deepTools with option: --normalizeUsing RPKM -e -bs 50 and evaluated in IGV browser. CUT&RUN peaks were called by MACS2 callpeak with option: -g hs -B -f BAM -q 0.01. IgG controls were used for comparison. Each technical repeat and biological repeat were separately processed.
ATAC-seq: Technical duplicates of each ATAC-seq samples were combined and sequencing quality control was evaluated by FastQC. Fastq files of paired-end ATAC-seq data were trimmed to remove adapter sequences using Trimmomatic and then aligned to version 19 of the human reference genome (hg19) using BWA (Burrows-Wheeler Aligner). Aligned reads were sorted by coordinates and filtered out mitochondrial DNA and black-listed regions by Samtools. Duplicate read pairs were marked and removed using the ‘MarkDuplicates’ command in picard tools. The final aligned, sorted and filtered Bam files were used for further analysis. ATAC-seq visualization was assessed by converting the final Bam files to Bigwig files using the ‘bamCoverage’ command in deepTools and corrected for Tn5 insertion. ATAC-seq peaks were called from Tn-5 corrected insertions using MACS2 callpeak with option ‘-g hs -q 0.05 -f BAMPE and -B’.
ChIP-seq:The sequencing files were first demultiplexed and trimmed based on the eight-nucleotide barcode using previously described pipeline, allowing one mismatch on the first eight-nucleotide from read 121. The demultiplexed reads were then evaluated by FastQC then aligned to the hg19 genome using BWA (Burrows-Wheeler Aligner). Duplicate read pairs were marked and removed using the ‘MarkDuplicates’ command in picard tools. The H3K27ac peaks were called using MACS2 callpeak with option ‘-g hs -B -f BAM -q 0.01’. Input controls were used for comparison during peak calling.
RNA-seq: Data was trimmed with Trimmomatic, and both pre- and post-trimming quality controls were evaluated by FastQC. The trimmed data were aligned to version 19 of the human reference genome (hg19) using STAR (2-pass). Samples with at least 20 million uniquely mapping reads were retained for further analysis. Reads count was performed with the ‘Htseq-count’ command in HTSeq with option: -m union -f bam -i gene_id -s reverse -t exon --additional-attr=gene_name. Reads count filtering was applied to the DESeqDataSet matrix to keep only rows that have at least 10 reads total.
Assembly: hg19
Supplementary files format and content: bigwig, bed (for CUT&RUN ATAC-seq and ChIP-seq)
Supplementary files format and content: csv files with normalized counts (For RNA-seq)
Library strategy: CUT&RUN

source_name: RL

growth_protocol: Cell were cultured in RPMI medium with 10% FBS and 1X penicillin/streptomycin.

extract_protocol:
Cells were collected and washed by PBS. After final wash, nuclei were isolated using nuclei extraction buffer and then washed twice with wash buffer. Five-hundred thousand nuclei were counted and incubated with activated Concanavalin A coated beads and subsequently mixed with antibody in antibody buffer for overnight incubation on nutator in a cold room. IgG controls were set in parrel for antibody enrichment and specificity validation. Nuclei were then washed three times with digitonin buffer and incubated with PAG-MNase for 10 minutes at room temperature. After 10 minutes of incubation, nuclei were washed three times again with digitonin buffer and resuspended with prechilled low salt high Ca2+ buffer  to initiate 1-hour digestion at 0 °C. The reaction was terminated by switching into stop buffer and incubating at 37 °C for 10 minutes to release digested DNA from the nuclei. DNA was then purified with Ampure beads size selection (0.5X to remove large fragment and 2X to recover desired nucleosomal DNA fragments).
NGS libraries were generated with KAPA Hyper Prep Kits (Roche KK8502) using 14 cycles of PCR amplification. Libraires were validated on a Tapestation 4200 (Agilent G2991BA), quantified by Qubit High Sensitivity dsDNA Kit (Life Technologies Q32854), multiplexed and sequenced on a NovaSeq6000 using 100-10-10-100bp reads format.

treatment_protocol: For CD40 stimulation, stimulation medium were prepared by incubation of 40 uL of CD40 ligand and 40 uL of cross-linking antibody mixture at room temperature for 30 minutes and subsequently adding into 10 mL of RPMI+10%FBS and 2 uL of IL4. Cells were seeded at 0.5 million per mL of CD40 stimulation medium at 37 °C. Negative control group was set in the absence of CD40 ligand multimer and IL4. For bi-specific antibody experiment, B tumor cell lines were stained with CellTrace™ Far Red and CD4+ T cells were stained with CellTrace™ Violet. After mixing as desired ratio (1:1), cells were cultured in RPMI supplemented with 10% FBS in the presence of 100 ng/mL mosunetuzumab for 12-hour and 24-hour respectively, prior to sorting. Co-culture right after mixing without mosunetuzumab treatment was set as 0-hour treatment group.

value: RL

value: B cell Lymphoma

value: CREBBP Y1503C

value: Mosunetuzumab+CD4 T cells

tag: time

value: 24 hours

value: Rabbit polyclonal anti-EP300 RRID:AB_185565


title: RL_PM_EP300_Mosun_24h_S1


title: RL_PM_EP300_Mosun_12h_S2

value: 12 hours


title: sicontrol1


title: RL_PM_EP300_Mosun_12h_S1


title: RL_PM_EP300_Mosun_0h_S1

value: 0 hour


title: RL_PM_EP300_Mosun_0h_S2


title: RL_WT_EP300_Mosun_12h_S2

value: CREBBP WT


title: RL_WT_EP300_Mosun_24h_S1


title: RL_WT_EP300_Mosun_12h_S1


title: RL_WT_EP300_Mosun_0h_S2


title: RL_WT_EP300_Mosun_0h_S1


title: RL_PM_CREBBP_Mosun_24h_S1

value: Rabbit polyclonal anti-CREBBP RRID:AB_2083940


title: RL_PM_CREBBP_Mosun_0h_S1


title: RL_PM_CREBBP_Mosun_12h_S2


title: RL_PM_CREBBP_Mosun_0h_S2


title: RL_PM_CREBBP_Mosun_12h_S1


title: RL_WT_CREBBP_Mosun_24h_S2


title: RL_WT_CREBBP_Mosun_12h_S1


title: RL_WT_CREBBP_Mosun_0h_S2


title: RL_PM_H3K27Ac_Mosun_24h_S2

value: Mouse monoclonal anti-H3K27Ac RRID:AB_2608307


title: RL_PM_H3K27Ac_Mosun_12h_S2


title: RL_PM_H3K27Ac_Mosun_12h_S1


title: RL_WT_CREBBP_Mosun_12h_S2


title: RL_PM_H3K27Ac_Mosun_24h_S1


title: RL_WT_CREBBP_Mosun_0h_S1


title: RL_WT_CREBBP_Mosun_24h_S1


title: RL_PM_H3K27Ac_Mosun_0h_S2


title: RL_WT_EP300_Mosun_24h_S2


title: RL_PM_H3K27Ac_Mosun_0h_S1


title: RL_WT_H3K27Ac_Mosun_12h_S1


title: RL_WT_H3K27Ac_Mosun_24h_S1


title: RL_WT_H3K27Ac_Mosun_12h_S2


title: RL_WT_H3K27Ac_Mosun_24h_S2


title: RL_WT_H3K27Ac_Mosun_0h_S2


title: RL_WT_H3K27Ac_Mosun_0h_S1


title: HT_PM_EP300_with_CD40_S1

source_name: HT

value: HT


title: RL_PM_CREBBP_Mosun_24h_S2


title: HT_WT_EP300_with_CD40_S2


title: HT_WT_EP300_without_CD40_S2

value: No treatment


title: HT_PM_EP300_without_CD40_S2


title: RL_WT_EP300_with_CD40_S2


title: RL_PM_EP300_with_CD40_S2


title: HT_WT_EP300_with_CD40_S1


title: HT_PM_EP300_without_CD40_S1


title: RL_PM_EP300_with_CD40_S1


title: HT_WT_EP300_without_CD40_S1


title: RL_PM_EP300_without_CD40_S2


title: RL_WT_EP300_with_CD40_S1


title: RL_WT_EP300_without_CD40_S2


title: RL_WT_EP300_without_CD40_S1


title: HT_PM_CREBBP_with_CD40_S2


title: HT_WT_CREBBP_with_CD40_S1


title: HT_PM_CREBBP_without_CD40_S2


title: HT_WT_CREBBP_without_CD40_S2


title: HT_WT_CREBBP_without_CD40_S1


title: HT_PM_CREBBP_without_CD40_S1


title: HT_WT_CREBBP_with_CD40_S2


title: RL_PM_CREBBP_with_CD40_S1


title: RL_WT_CREBBP_with_CD40_S2


title: RL_PM_CREBBP_with_CD40_S2


title: RL_WT_CREBBP_without_CD40_S2


title: RL_PM_CREBBP_without_CD40_S2


title: RL_PM_CREBBP_without_CD40_S1


title: RL_WT_CREBBP_without_CD40_S1


title: RL_PM_EP300_without_CD40_S1


title: HT_PM_CREBBP_with_CD40_S1


title: HT_PM_H3K27Ac_with_CD40_S2


title: HT_PM_EP300_with_CD40_S2


title: HT_WT_H3K27Ac_with_CD40_S2


title: HT_PM_H3K27Ac_without_CD40_S2


title: HT_WT_H3K27Ac_without_CD40_S2


title: RL_WT_H3K27Ac_with_CD40_S2


title: HT_PM_H3K27Ac_without_CD40_S1


title: RL_PM_H3K27Ac_with_CD40_S2


title: RL_PM_H3K27Ac_with_CD40_S1


title: RL_WT_CREBBP_with_CD40_S1


title: RL_WT_H3K27Ac_with_CD40_S1


title: RL_PM_H3K27Ac_without_CD40_S1


title: HT_WT_H3K27Ac_without_CD40_S1


title: RL_WT_H3K27Ac_without_CD40_S2


title: HT_WT_H3K27Ac_with_CD40_S1


title: HT_Y1503C_A7_IgG_S2

value: Rabbit polyclonal IgG RRID:AB_2923178


title: RL_PM_H3K27Ac_without_CD40_S2


title: HT_R1446C_C12_IgG_S2

value: CREBBP R1446C


title: RL_WT_H3K27Ac_without_CD40_S1


title: HT_Y1482N_G25_IgG_S2

value: CREBBP Y1482N


title: HT_KO_D31_IgG_S2

value: CREBBP KO


title: HT_KO_B36_IgG_S2


title: HT_WT_B13_IgG_S2


title: HT_Y1482N_G3_IgG_S2


title: HT_R1446C_A1_IgG_S2


title: HT_Y1503C_A7_IgG_S1


title: HT_Y1482N_G25_IgG_S1


title: HT_WT_A13_IgG_S2


title: HT_PM_H3K27Ac_with_CD40_S1


title: HT_Y1482N_G3_IgG_S1


title: HT_KO_B36_IgG_S1


title: HT_R1446C_A1_IgG_S1


title: HT_KO_D31_IgG_S1


title: RL_Y1503C_A18_IgG_S2

value: RL


title: RL_Y1482N_F30_IgG_S2

value: B cell Lymphoma


title: HT_WT_B13_IgG_S1


title: HT_WT_A13_IgG_S1


title: RL_KO_3B3_IgG_S2


title: RL_R1446C_G2C20_IgG_S2


title: RL_WT_G2C24_IgG_S2


title: RL_Y1503C_A20_IgG_S1

value: CREBBP Y1503C


title: RL_Y1503C_A18_IgG_S1


title: RL_Y1482N_C5_IgG_S1


title: RL_R1446C_G2C20_IgG_S1


title: RL_Y1482N_F30_IgG_S1


title: RL_R1446C_2B3_IgG_S1


title: RL_WT_2B5_IgG_S1


title: RL_KO_3B3_IgG_S1


title: RL_WT_G2C24_IgG_S1


title: HT_Y1503C_A7_EP300_S2


title: HT_Y1482N_G3_EP300_S2


title: RL_Y1482N_C5_IgG_S2


title: RL_Y1503C_A20_IgG_S2


title: HT_Y1482N_G25_EP300_S2


title: RL_WT_2B5_IgG_S2


title: RL_R1446C_2B3_IgG_S2


title: HT_KO_B36_EP300_S2


title: RL_KO_2A1_IgG_S2


title: HT_R1446C_A1_EP300_S2


title: HT_KO_D31_EP300_S2


title: HT_WT_A13_EP300_S2


title: HT_Y1482N_G25_EP300_S1


title: HT_Y1503C_A7_EP300_S1


title: HT_R1446C_C12_EP300_S1


title: HT_KO_D31_EP300_S1


title: HT_R1446C_A1_EP300_S1


title: HT_KO_B36_EP300_S1


title: RL_KO_2A1_IgG_S1


title: HT_WT_B13_EP300_S1


title: HT_WT_A13_EP300_S1


title: RL_Y1482N_F30_EP300_S2


title: RL_Y1503C_A18_EP300_S2


title: RL_R1446C_2B3_EP300_S2


title: HT_R1446C_C12_EP300_S2


title: RL_WT_G2C24_EP300_S2


title: RL_KO_3B3_EP300_S2


title: RL_Y1503C_A20_EP300_S2


title: RL_KO_2A1_EP300_S2


title: RL_Y1503C_A18_EP300_S1


title: RL_Y1482N_C5_EP300_S1


title: HT_Y1482N_G3_EP300_S1


title: HT_WT_B13_EP300_S2


title: RL_R1446C_2B3_EP300_S1


title: RL_KO_3B3_EP300_S1


title: RL_WT_G2C24_EP300_S1


title: RL_KO_2A1_EP300_S1


title: RL_WT_2B5_EP300_S1


title: RL_R1446C_G2C20_EP300_S2


title: HT_R1446C_C12_CREBBP_S2


title: HT_Y1503C_A7_CREBBP_S2


title: HT_Y1482N_G25_CREBBP_S2


title: HT_R1446C_A1_CREBBP_S2


title: RL_Y1482N_C5_EP300_S2


title: HT_Y1482N_G3_CREBBP_S2


title: HT_KO_D31_CREBBP_S2


title: HT_Y1482N_G25_CREBBP_S1


title: HT_Y1503C_A7_CREBBP_S1


title: HT_Y1482N_G3_CREBBP_S1


title: RL_WT_2B5_EP300_S2


title: HT_WT_B13_CREBBP_S2


title: RL_Y1503C_A20_EP300_S1


title: HT_R1446C_C12_CREBBP_S1


title: HT_R1446C_A1_CREBBP_S1


title: RL_R1446C_G2C20_EP300_S1


title: HT_WT_B13_CREBBP_S1


title: HT_KO_B36_CREBBP_S1


title: HT_KO_D31_CREBBP_S1


title: HT_WT_A13_CREBBP_S1


title: RL_Y1503C_A20_CREBBP_S2


title: RL_Y1482N_F30_EP300_S1


title: RL_Y1503C_A18_CREBBP_S2


title: RL_Y1482N_C5_CREBBP_S2


title: RL_R1446C_G2C20_CREBBP_S2


title: RL_Y1482N_F30_CREBBP_S2


title: HT_KO_B36_CREBBP_S2


title: HT_WT_A13_CREBBP_S2


title: RL_R1446C_2B3_CREBBP_S2


title: RL_KO_3B3_CREBBP_S2


title: RL_WT_G2C24_CREBBP_S2


title: RL_KO_2A1_CREBBP_S2


title: RL_Y1482N_F30_CREBBP_S1


title: RL_WT_2B5_CREBBP_S2


title: RL_Y1503C_A18_CREBBP_S1


title: RL_Y1503C_A20_CREBBP_S1


title: RL_Y1482N_C5_CREBBP_S1


title: RL_R1446C_2B3_CREBBP_S1


title: RL_R1446C_G2C20_CREBBP_S1


title: RL_KO_3B3_CREBBP_S1


title: HT_Y1503C_A7_BRD4_S2

value: Rabbit polyclonal anti-BRD4 EpiCypher Cat#13-2003


title: RL_WT_G2C24_CREBBP_S1


title: RL_WT_2B5_CREBBP_S1


title: RL_KO_2A1_CREBBP_S1


title: HT_Y1482N_G25_BRD4_S2


title: HT_Y1482N_G3_BRD4_S2


title: HT_R1446C_A1_BRD4_S2


title: HT_KO_D31_BRD4_S2


title: HT_WT_B13_BRD4_S2


title: HT_KO_B36_BRD4_S2


title: HT_Y1503C_A7_BRD4_S1


title: HT_Y1482N_G25_BRD4_S1


title: HT_R1446C_C12_BRD4_S1


title: HT_R1446C_A1_BRD4_S1


title: HT_KO_B36_BRD4_S1


title: HT_WT_A13_BRD4_S1


title: HT_WT_B13_BRD4_S1


title: HT_KO_D31_BRD4_S1


title: RL_Y1503C_A18_BRD4_S2


title: RL_Y1503C_A20_BRD4_S2


title: RL_R1446C_2B3_BRD4_S2


title: RL_KO_3B3_BRD4_S2


title: RL_Y1482N_C5_BRD4_S2


title: RL_Y1482N_F30_BRD4_S2


title: RL_WT_G2C24_BRD4_S2


title: RL_KO_2A1_BRD4_S2


title: RL_R1446C_G2C20_BRD4_S2


title: RL_WT_2B5_BRD4_S2


title: RL_Y1482N_F30_BRD4_S1


title: HT_WT_A13_BRD4_S2


title: RL_Y1503C_A18_BRD4_S1


title: RL_Y1482N_C5_BRD4_S1


title: HT_R1446C_C12_BRD4_S2


title: RL_KO_3B3_BRD4_S1


title: RL_R1446C_2B3_BRD4_S1


title: RL_Y1503C_A20_BRD4_S1


title: RL_KO_2A1_BRD4_S1


title: HT_Y1482N_G3_BRD4_S1


title: RL_WT_G2C24_BRD4_S1


title: RL_WT_2B5_BRD4_S1


title: HT_Y1503C_A7_H3K4me1_S2

value: Rabbit mixed monoclonal anti-H3K4me1 RRID:AB_2923143


title: HT_Y1482N_G25_H3K4me1_S2


title: HT_R1446C_C12_H3K4me1_S2


title: HT_Y1482N_G3_H3K4me1_S2


title: HT_R1446C_A1_H3K4me1_S2


title: HT_KO_D31_H3K4me1_S2


title: HT_KO_B36_H3K4me1_S2


title: HT_R1446C_A1_H3K4me1_S1


title: HT_R1446C_C12_H3K4me1_S1


title: HT_Y1503C_A7_H3K4me1_S1


title: HT_WT_A13_H3K4me1_S2


title: HT_Y1482N_G25_H3K4me1_S1


title: RL_R1446C_G2C20_BRD4_S1


title: HT_KO_D31_H3K4me1_S1


title: HT_WT_B13_H3K4me1_S1


title: HT_KO_B36_H3K4me1_S1


title: RL_Y1503C_A18_H3K4me1_S2


title: RL_Y1503C_A20_H3K4me1_S2


title: RL_Y1482N_F30_H3K4me1_S2


title: RL_R1446C_G2C20_H3K4me1_S2


title: RL_Y1482N_C5_H3K4me1_S2


title: HT_WT_A13_H3K4me1_S1


title: RL_R1446C_2B3_H3K4me1_S2


title: RL_KO_2A1_H3K4me1_S2


title: RL_KO_3B3_H3K4me1_S2


title: RL_WT_2B5_H3K4me1_S2


title: HT_WT_B13_H3K4me1_S2


title: RL_Y1503C_A20_H3K4me1_S1


title: RL_Y1503C_A18_H3K4me1_S1


title: RL_R1446C_2B3_H3K4me1_S1


title: RL_Y1482N_C5_H3K4me1_S1


title: HT_Y1482N_G3_H3K4me1_S1


title: RL_KO_3B3_H3K4me1_S1


title: HT_Y1503C_A7_H3K4me3_S2

value: Rabbit mixed monoclonal anti-H3K4me3 RRID:AB_3076423


title: RL_WT_2B5_H3K4me1_S1


title: HT_Y1482N_G25_H3K4me3_S2


title: RL_KO_2A1_H3K4me1_S1


title: HT_Y1482N_G3_H3K4me3_S2


title: RL_WT_G2C24_H3K4me1_S1


title: HT_KO_D31_H3K4me3_S2


title: HT_R1446C_A1_H3K4me3_S2


title: HT_WT_A13_H3K4me3_S2


title: RL_WT_G2C24_H3K4me1_S2


title: HT_R1446C_C12_H3K4me3_S2


title: HT_R1446C_C12_IgG_S1


title: HT_KO_B36_H3K4me3_S2


title: HT_Y1503C_A7_H3K4me3_S1


title: HT_R1446C_A1_H3K4me3_S1


title: HT_WT_B13_H3K4me3_S2


title: HT_KO_D31_H3K4me3_S1


title: HT_Y1482N_G25_H3K4me3_S1


title: RL_R1446C_G2C20_H3K4me1_S1


title: HT_WT_A13_H3K4me3_S1


title: HT_WT_B13_H3K4me3_S1


title: HT_Y1482N_G3_H3K4me3_S1


title: RL_Y1482N_F30_H3K4me1_S1


title: RL_Y1503C_A18_H3K4me3_S2


title: RL_Y1482N_C5_H3K4me3_S2


title: RL_Y1503C_A20_H3K4me3_S2


title: RL_Y1482N_F30_H3K4me3_S2


title: RL_R1446C_G2C20_H3K4me3_S2


title: RL_R1446C_2B3_H3K4me3_S2


title: RL_KO_3B3_H3K4me3_S2


title: HT_R1446C_C12_H3K4me3_S1


title: RL_KO_2A1_H3K4me3_S2


title: RL_R1446C_G2C20_H3K4me3_S1


title: RL_Y1503C_A18_H3K4me3_S1


title: RL_Y1503C_A20_H3K4me3_S1


title: RL_Y1482N_F30_H3K4me3_S1


title: RL_KO_2A1_H3K4me3_S1


title: RL_WT_G2C24_H3K4me3_S2


title: HT_KO_B36_H3K4me3_S1


title: RL_WT_2B5_H3K4me3_S2


title: RL_Y1482N_C5_H3K4me3_S1


title: RL_WT_G2C24_H3K4me3_S1


title: RL_WT_2B5_H3K4me3_S1


title: RL_KO_3B3_H3K4me3_S1


title: HT_Y1482N_G3_H3K27me3_S2

value: Rabbit monoclonal anti-H3K27me3 EpiCypher Cat#13-0055


title: HT_Y1482N_G25_H3K27me3_S2


title: HT_R1446C_C12_H3K27me3_S2


title: HT_Y1503C_A7_H3K27me3_S2


title: HT_R1446C_A1_H3K27me3_S2


title: HT_WT_A13_H3K27me3_S2


title: HT_KO_B36_H3K27me3_S2


title: HT_Y1482N_G25_H3K27me3_S1


title: HT_WT_B13_H3K27me3_S2


title: HT_Y1503C_A7_H3K27me3_S1


title: HT_KO_D31_H3K27me3_S2


title: HT_Y1482N_G3_H3K27me3_S1


title: HT_R1446C_A1_H3K27me3_S1


title: RL_R1446C_2B3_H3K4me3_S1


title: HT_KO_D31_H3K27me3_S1


title: HT_KO_B36_H3K27me3_S1


title: HT_WT_B13_H3K27me3_S1


title: RL_Y1503C_A18_H3K27me3_S2


title: RL_Y1482N_C5_H3K27me3_S2


title: RL_R1446C_G2C20_H3K27me3_S2


title: RL_Y1482N_F30_H3K27me3_S2


title: RL_R1446C_2B3_H3K27me3_S2


title: HT_WT_A13_H3K27me3_S1


title: RL_WT_G2C24_H3K27me3_S2


title: RL_Y1503C_A20_H3K27me3_S2


title: RL_KO_3B3_H3K27me3_S2


title: RL_Y1482N_F30_H3K27me3_S1


title: RL_WT_2B5_H3K27me3_S2


title: RL_R1446C_2B3_H3K27me3_S1


title: HT_R1446C_C12_H3K27me3_S1


title: RL_Y1503C_A18_H3K27me3_S1


title: RL_Y1503C_A20_H3K27me3_S1


title: RL_KO_3B3_H3K27me3_S1


title: HT_Y1503C_A7_H3K27Ac_S2


title: RL_WT_2B5_H3K27me3_S1


title: HT_Y1482N_G25_H3K27Ac_S2


title: RL_WT_G2C24_H3K27me3_S1


title: RL_KO_2A1_H3K27me3_S1


title: RL_KO_2A1_H3K27me3_S2


title: RL_Y1482N_C5_H3K27me3_S1


title: HT_Y1482N_G3_H3K27Ac_S2


title: HT_R1446C_C12_H3K27Ac_S2


title: HT_R1446C_A1_H3K27Ac_S2


title: HT_KO_D31_H3K27Ac_S2


title: control day 2, C

city: Corvallis

first: Robyn

middle: Leigh

last: Tanguay

state: Oregon

address: 28645 east hwy 34

department: Environmental and Molecular Toxicology

institute: Oregon State University

description: Library name: C2C

data_processing:
Demultiplexing and alignment was performed using the manufacture provided processing platform TempO-SeqR (BioSpyder Technologies, Inc., Carlsbad, CA, United States).
Counts of genes with multiple probes were summed as instructed by the manufacturer resulting in 3112 unique genes
Read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor.
Principal component analysis (PCA) of normalized read counts was used to determine that a batch effect was present based on exposure and RNA extraction day (nested by experimental design).
At this time one control sample ( control day1, B) was identified as an outlier and removed from all future analysis.
The batch effect was removed from unnormalized data using the ComBat_seq function from the SVA R package
Normalzied read counts were normalized by upper quartile normalization using the calcNormFactors function from the Bioconductor package in EdgeR using the 75th percentile of reads per samples as the scaling factor.
Assembly: GRCz11
Supplementary files format and content: .csv file containing raw count data
Supplementary files format and content: .csv file containing batch corrected and normalized data

organism: Danio rerio

source_name: whole animal

extract_protocol:
1mL of 1µm beads and 500µL of lysis buffer were loaded into a round bottom 2mL 96 well plate. 100µL of lysis buffer was added to tube containing pooled embryo samples and 200µL of RNA shield, the full contents of the tube were then transferred to the homogenization plate. The plate was homogenized for 1.5 minutes and centrifuged for 5 minutes at 3000 rcf. 275 µL of the supernatant was then transferred to two plates containing 275µL of ethanol. RNA extraction was performed using the KingFisher Apex system. Briefly this process uses Mag beads to collect RNA from the sample, after series of washes the RNA is eluted in 50µLof ultra-pure water. RNA quality was assessed using the Agilent 4150 TapeStation System. All samples used had RIN scores >9.8. RNA concentration was determined using ThermoFisher Quant-iT RNA Reagent and assay kit and ThermoFisher Varioskan ALF multimode plate reader in triplicate, samples with high variability between reads were repeated in triplicate. The average of the three quantification reads was used for RNA concentration normalization. Each treatment had 4-5 viable RNA extraction replicates, for treatments with 5 viable samples the 4 with the highest concentration and RIN score were used 3 control samples were used from each day group. All 94 samples were normalized to the lowest concentration sample 14.9ng/µL.
1 µL per sample of normalized RNA was used as input for library preparation following manufactures protocol for the 96-sample TempO-Seq S1500 + Zebrafish Surrogate Assay panel (BioSpyder Technologies, Inc., Carlsbad, CA, United States). Briefly, samples were added to the assay plate with an equal volume of 2x enhanced lysis buffer and processed through annealing with detector oligos, digestion, and ligation. Proper amplification was verified using real-time PCR green fluorescence. Library purification was performed using the Macherey-Nagel NucleoSpin Gel and PCR Cleanup Kit following adjustments detailed in the manufacturer’s instructions. PCR amplification products were pooled into a single sequencing library 5 µL each into a 1.5mL Eppendorf tube the pooled purified libraries were sequenced using one lane of the NovaseqX 10 B flow cell (BioSpyder Technologies, Inc., Carlsbad, CA, United States).

treatment_protocol: When the embryos were 6hpf they were bleached in groups of 1000 or less. Embryos were placed in a strainer for transfer between solutions in 500 mL containers. First embryos were placed in system fish water for 1 minute, then transferred to a 0.5% sodium chloride solution for 5 minutes, then transferred to a ___% sodium hypochlorite solution for 1 minute and rinsed in EM for 5 minutes and transferred to a clean glass petri dish. Embryos were then loaded into 2mL glass exposure vials in groups of 8 using a glass pasture pipette. Excess EM was removed and 2mL of fresh EM was immediately added. Chemical stocks were diluted to 200 times the desired exposure concentration of 20 µM using DMSO. 10 µL of diluted chemical stock was added to each vial, vials were immediately capped and inverted 3 times to ensure mixing, no precipitate was observed for any chemicals at the concentrations tested. Vials were loaded into a custom 3D printed vial holder for slow end over end rotation in a dark 28°C incubator overnight. At 24 hours embryos were removed from exposure vials and plated into 96-well plates loaded with 100 µL clean EM. At 48 hpf embryos were collected for RNA extraction, embryos from two exposure vials were kept as holdback for morphological assessment. From the remaining wells, 6 phenotypically normal embryos were collected and pooled in their vial groups into 1.5 mL Eppendorf tubes, placed on ice (~30 sec), excess media removed, placed back on ice (~30 sec), and 200 µL RNA shield added. Five pooled samples were collected from each treatment.

value: whole animal

value: 5D WT

value: control day 2

tag: batch


title: control day 1, C

description: Library name: C1C

value: control day 1


title: HT_KO_B36_H3K27Ac_S2

value: HT

value: Mouse monoclonal anti-H3K27Ac RRID:AB_2608307


title: HT_WT_B13_H3K27Ac_S2

value: CREBBP WT

value: No treatment


title: control day 2, A

description: Library name: C2A


title: control day 1, A

description: Library name: C1A


title: 1,6,7-trimethylnaphthalene, D

description: Library name: 9_D


title: 1,6,7-trimethylnaphthalene, E

description: Library name: 9_E


title: RL_R1446C_G2C20_H3K27me3_S1

value: CREBBP R1446C


title: control day 1, B

description:
Library name: C1B
At this time one control sample ( control day1, B) was identified as an outlier and removed from all future analysis.


title: control day 2, B

description: Library name: C2B


title: HT_WT_A13_H3K27Ac_S2


title: 1,6,7-trimethylnaphthalene, A

description: Library name: 9_A


title: HT_Y1482N_G25_H3K27Ac_S1

value: CREBBP Y1482N


title: HT_Y1482N_G3_H3K27Ac_S1


title: 1-ethylnaphthalene, E

description: Library name: 8_E


title: HT_Y1503C_A7_H3K27Ac_S1


title: 1-ethylnaphthalene, C

description: Library name: 8_C


title: HT_R1446C_C12_H3K27Ac_S1


title: HT_R1446C_A1_H3K27Ac_S1


title: 1-ethylnaphthalene, B

description: Library name: 8_B


title: 1-ethylnaphthalene, A

description: Library name: 8_A


title: HT_KO_D31_H3K27Ac_S1

value: CREBBP KO


title: 2,4,5-trimethylnaphthalene, E

description: Library name: 7_E


title: HT_KO_B36_H3K27Ac_S1

value: B cell Lymphoma


title: 2,4,5-trimethylnaphthalene, D

description: Library name: 7_D


title: HT_WT_B13_H3K27Ac_S1


title: 1,6,7-trimethylnaphthalene, B

description: Library name: 9_B


title: 2,4,5-trimethylnaphthalene, B

description: Library name: 7_B


title: 1,4,5-trimethylnaphthalene, D

description: Library name: 6_D


title: RL_Y1503C_A18_H3K27Ac_S2

value: RL

value: CREBBP Y1503C


title: RL_Y1482N_C5_H3K27Ac_S2


title: 1,4,5-trimethylnaphthalene, E

description: Library name: 6_E


title: RL_R1446C_G2C20_H3K27Ac_S2


title: RL_Y1503C_A20_H3K27Ac_S2


title: HT_WT_A13_H3K27Ac_S1


title: RL_Y1482N_F30_H3K27Ac_S2


title: 2,7-dimethylnaphthalene, D

description: Library name: 5_D


title: RL_WT_G2C24_H3K27Ac_S2


title: 1,4,5-trimethylnaphthalene, A

description: Library name: 6_A


title: RL_WT_2B5_H3K27Ac_S2


title: 1,4,5-trimethylnaphthalene, C

description: Library name: 6_C


title: 2,7-dimethylnaphthalene, C

description: Library name: 5_C


title: RL_Y1503C_A20_H3K27Ac_S1


title: 2,3-dimethylnaphthalene, C

description: Library name: 4_C


title: RL_KO_2A1_H3K27Ac_S2


title: RL_R1446C_2B3_H3K27Ac_S2


title: 2,7-dimethylnaphthalene, B

description: Library name: 5_B


title: RL_KO_3B3_H3K27Ac_S2


title: RL_Y1503C_A18_H3K27Ac_S1


title: RL_Y1482N_F30_H3K27Ac_S1


title: 2,3-dimethylnaphthalene, D

description: Library name: 4_D


title: 1,2-dimethylnaphthalene, E

description: Library name: 3_E


title: 2,3-dimethylnaphthalene, E

description: Library name: 4_E


title: 2,3-dimethylnaphthalene, B

description: Library name: 4_B


title: 2,4,5-trimethylnaphthalene, C

description: Library name: 7_C


title: 2,7-dimethylnaphthalene, E

description: Library name: 5_E


title: 1,2-dimethylnaphthalene, D

description: Library name: 3_D


title: RL_Y1482N_C5_H3K27Ac_S1


title: 1,2-dimethylnaphthalene, B

description: Library name: 3_B


title: 1,8-dimethylnaphthalene, E

description: Library name: 2_E


title: 1,2-dimethylnaphthalene, C

description: Library name: 3_C


title: RL_R1446C_2B3_H3K27Ac_S1


title: RL_KO_2A1_H3K27Ac_S1


title: RL_R1446C_G2C20_H3K27Ac_S1


title: 1,8-dimethylnaphthalene, D

description: Library name: 2_D


title: RL_KO_3B3_H3K27Ac_S1


title: 2-ethylnaphthalene, D

description: Library name: 22D


title: RL_WT_2B5_H3K27Ac_S1


title: 2-ethylnaphthalene, C

description: Library name: 22C


title: RL_WT_G2C24_H3K27Ac_S1


title: 2-ethylnaphthalene, B

description: Library name: 22B


title: LPMI462_IgG_S2

source_name: PDX sample LPMI462

value: PDX sample LPMI462

value: isolate human cells

value: Rabbit polyclonal IgG RRID:AB_2923178


title: 1,8-dimethylnaphthalene, B

description: Library name: 2_B

value: whole animal


title: LPMI331_IgG_S1

source_name: PDX sample LPMI331

value: PDX sample LPMI331


title: LPMI331_IgG_S2


title: LPMI147_IgG_S2

source_name: PDX sample LPMI147

value: PDX sample LPMI147


title: 2-ethylnaphthalene, A

description: Library name: 22A

value: 5D WT


title: LPMI462_IgG_S1


title: 1,5-dimethylnaphthalene, B

description: Library name: 21B


title: LPMI147_IgG_S1


title: 1,5-dimethylnaphthalene, D

description: Library name: 21D


title: BM63014_IgG_S2

source_name: PDX sample BM63014

value: PDX sample BM63014

value: CREBBP point mutant


title: 1,5-dimethylnaphthalene, E

description: Library name: 21E


title: BM63014_IgG_S1


title: 1,5-dimethylnaphthalene, A

description: Library name: 21A


title: LPMI386_IgG_S2

source_name: PDX sample LPMI386

value: PDX sample LPMI386


title: naphthalene, D

description: Library name: 20D

value: naphthalene


title: naphthalene, B

description: Library name: 20B


title: DFBL13727_IgG_S1

source_name: PDX sample DFBL13727

value: PDX sample DFBL13727


title: 1,8-dimethylnaphthalene, A

description: Library name: 2_A


title: naphthalene, C

description: Library name: 20C


title: LPMI386_IgG_S1


title: LPMI331_CREBBP_S2

value: CREBBP WT

value: Rabbit polyclonal anti-CREBBP RRID:AB_2083940


title: LPMI462_CREBBP_S2


title: 2,6-diethylnaphthalene, B

description: Library name: 1_B


title: 2,6-diethylnaphthalene, 1D

description: Library name: 1_D


title: 2-butylnaphthalene, E

description: Library name: 19E


title: LPMI147_CREBBP_S1


title: 2,6-diethylnaphthalene, C

description: Library name: 1_C


title: BM63014_CREBBP_S2


title: LPMI462_CREBBP_S1


title: LPMI331_CREBBP_S1


title: 2-butylnaphthalene, C

description: Library name: 19C


title: BM63014_CREBBP_S1


title: LPMI386_CREBBP_S1


title: 2-butylnaphthalene, B

description: Library name: 19B


title: 1,6-dimethylnaphthalene, D

description: Library name: 18D


title: 1,6-dimethylnaphthalene, E

description: Library name: 18E


title: LPMI386_CREBBP_S2


title: 2-butylnaphthalene, A

description: Library name: 19A


title: DFBL13727_IgG_S2


title: DFBL13727_CREBBP_S2


title: 1,6-dimethylnaphthalene, C

description: Library name: 18C


title: 2,6-diethylnaphthalene, E

description: Library name: 1_E


title: DFBL13727_CREBBP_S1


title: 1-methylnaphthalene, E

description: Library name: 17E


title: 1,6-dimethylnaphthalene, B

description: Library name: 18B


title: naphthalene, A

description: Library name: 20A


title: LPMI147_CREBBP_S2


title: 1-methylnaphthalene, C

description: Library name: 17C


title: 1-methylnaphthalene, B

description: Library name: 17B


title: 1-methylnaphthalene, A

description: Library name: 17A


title: 1,4-dimethylnaphthalene, C

description: Library name: 16C


title: TonsilE_CC_EP300_S2

source_name: Human tonsil E

value: Human tonsil E

value: sort centrocytes

value: Rabbit polyclonal anti-EP300 RRID:AB_185565


title: 1,4-dimethylnaphthalene, B

description: Library name: 16B


title: TonsilE_CC_EP300_S1


title: 1,4-dimethylnaphthalene, A

description: Library name: 16A


title: TonsilE_CB_EP300_S2

value: sort centroblasts


title: 1,3-dimethylnaphthalene, E

description: Library name: 15E


title: 1,3-dimethylnaphthalene, D

description: Library name: 15D


title: TonsilB_CC_EP300_S2

source_name: Human tonsil B

value: Human tonsil B


title: TonsilE_CB_EP300_S1


title: 1,3-dimethylnaphthalene, C

description: Library name: 15C


title: FLC30_CREBBP

source_name: Primary FL sample 30

value: Primary FL sample 30

value: sort B cells


title: FLC34_CREBBP

source_name: Primary FL sample 34

value: Primary FL sample 34


title: TonsilB_CC_EP300_S1


title: 1,3-dimethylnaphthalene, A

description: Library name: 15A

value: whole animal


title: FLC33_CREBBP

source_name: Primary FL sample 33

value: Primary FL sample 33


title: TonsilB_CB_EP300_S2


title: 2,7-di-tert-butylnaphthalene, E

description: Library name: 14E

value: 5D WT


title: 2,7-di-tert-butylnaphthalene, B

description: Library name: 14B


title: TonsilA_CC_EP300_S2

source_name: Human tonsil A

value: Human tonsil A


title: 2,7-di-tert-butylnaphthalene, C

description: Library name: 14C


title: TonsilB_CB_EP300_S1


title: 2,7-di-tert-butylnaphthalene, A

description: Library name: 14A


title: FLC24_CREBBP

source_name: Primary FL sample 24

value: Primary FL sample 24

value: CREBBP point mutant


title: 1,4-dimethylnaphthalene, E

description: Library name: 16E


title: TonsilA_CC_EP300_S1


title: FLC27_CREBBP

source_name: Primary FL sample 27

value: Primary FL sample 27


title: FLC23_CREBBP

source_name: Primary FL sample 23

value: Primary FL sample 23


title: TonsilA_CB_EP300_S2


title: 2,6-diisopropylnaphthalene, E

description: Library name: 13E


title: 2,6-diisopropylnaphthalene, D

description: Library name: 13D


title: TonsilE_CC_CREBBP_S2

value: Rabbit polyclonal anti-CREBBP RRID:AB_2083940


title: TonsilA_CB_EP300_S1


title: 2,6-diisopropylnaphthalene, B

description: Library name: 13B


title: TonsilE_CB_CREBBP_S2

value: Human tonsil E


title: 1,7-dimethylnaphthalene, E

description: Library name: 12E


title: 2,6-diisopropylnaphthalene, C

description: Library name: 13C


title: TonsilB_CC_CREBBP_S2

value: sort centrocytes


title: 1,7-dimethylnaphthalene, D

description: Library name: 12D


title: TonsilE_CC_CREBBP_S1


title: TonsilE_CB_CREBBP_S1


title: 1,7-dimethylnaphthalene, C

description: Library name: 12C


title: TonsilB_CC_CREBBP_S1


title: 1,7-dimethylnaphthalene, B

description: Library name: 12B


title: 1,4,6,7-tetramethylnaphthalene, C

description: Library name: 11D


title: 1,4,6,7-tetramethylnaphthalene, E

description: Library name: 11E


title: TonsilB_CB_CREBBP_S2


title: 1,4,6,7-tetramethylnaphthalene, B

description: Library name: 11B


title: TonsilB_CB_CREBBP_S1


title: TonsilA_CC_CREBBP_S2


title: 2-isopropylnaphthalene, E

description: Library name: 10E


title: 1,4,6,7-tetramethylnaphthalene, A

description: Library name: 11A


title: TonsilA_CB_CREBBP_S2


title: 2-isopropylnaphthalene, D

description: Library name: 10D


title: TonsilA_CC_CREBBP_S1


title: HT_Y1503C_A7_ATAC

data_processing:
CUT&RUN: Sequencing quality control was evaluated by FastQC. Paired-end CUT&RUN raw reads were trimmed to remove adapter sequences using Trimmomatic and then aligned to version 19 of the human reference genome (hg19) using Bowtie2 with options: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Aligned reads were sorted by coordinates and tested for mapped fragment size distribution by Samtools. The final aligned and sorted Bam files were used for further processing. Visualization was assessed by converting the final Bam files to Bigwig files using the ‘bamCoverage’ command in deepTools with option: --normalizeUsing RPKM -e -bs 50 and evaluated in IGV browser. CUT&RUN peaks were called by MACS2 callpeak with option: -g hs -B -f BAM -q 0.01. IgG controls were used for comparison. Each technical repeat and biological repeat were separately processed.
ATAC-seq: Technical duplicates of each ATAC-seq samples were combined and sequencing quality control was evaluated by FastQC. Fastq files of paired-end ATAC-seq data were trimmed to remove adapter sequences using Trimmomatic and then aligned to version 19 of the human reference genome (hg19) using BWA (Burrows-Wheeler Aligner). Aligned reads were sorted by coordinates and filtered out mitochondrial DNA and black-listed regions by Samtools. Duplicate read pairs were marked and removed using the ‘MarkDuplicates’ command in picard tools. The final aligned, sorted and filtered Bam files were used for further analysis. ATAC-seq visualization was assessed by converting the final Bam files to Bigwig files using the ‘bamCoverage’ command in deepTools and corrected for Tn5 insertion. ATAC-seq peaks were called from Tn-5 corrected insertions using MACS2 callpeak with option ‘-g hs -q 0.05 -f BAMPE and -B’.
ChIP-seq:The sequencing files were first demultiplexed and trimmed based on the eight-nucleotide barcode using previously described pipeline, allowing one mismatch on the first eight-nucleotide from read 121. The demultiplexed reads were then evaluated by FastQC then aligned to the hg19 genome using BWA (Burrows-Wheeler Aligner). Duplicate read pairs were marked and removed using the ‘MarkDuplicates’ command in picard tools. The H3K27ac peaks were called using MACS2 callpeak with option ‘-g hs -B -f BAM -q 0.01’. Input controls were used for comparison during peak calling.
RNA-seq: Data was trimmed with Trimmomatic, and both pre- and post-trimming quality controls were evaluated by FastQC. The trimmed data were aligned to version 19 of the human reference genome (hg19) using STAR (2-pass). Samples with at least 20 million uniquely mapping reads were retained for further analysis. Reads count was performed with the ‘Htseq-count’ command in HTSeq with option: -m union -f bam -i gene_id -s reverse -t exon --additional-attr=gene_name. Reads count filtering was applied to the DESeqDataSet matrix to keep only rows that have at least 10 reads total.
Assembly: hg19
Supplementary files format and content: bigwig, bed (for CUT&RUN ATAC-seq and ChIP-seq)
Supplementary files format and content: csv files with normalized counts (For RNA-seq)

source_name: HT

value: HT

value: B cell Lymphoma

value: CREBBP Y1503C

value: No treatment


title: 2-isopropylnaphthalene, B

description: Library name: 10B

source_name: whole animal


title: TonsilA_CB_CREBBP_S1

value: sort centroblasts


title: 2-isopropylnaphthalene, A

description: Library name: 10A


title: HT_Y1482N_G3_ATAC

value: CREBBP Y1482N


title: HT_R1446C_C12_ATAC

value: CREBBP R1446C


title: B6.129-Fbn1tm2Rmz/J mice3

city: New Haven

first: Fu

last: Gao

state: CT

address: 55 Prospect Street

description:
Library name: mgR/mgR3
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the cellranger-7.1.0.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: mitral valve

extract_protocol:
Single cells were processed using Chromium Controller (10X Genomics) according to the manufacturer’s protocol.
Library was performed according to the manufacturer’s instructions (scRNA seq 3’ v3 protocol, 10x Genomics).

value: mitral valve


title: Kidney, CLP 24 hrs

city: Durham

first: Jamie

last: Privratsky

state: NC

address: 303 Research Dr., Sands 101

department: Anesthesiology

institute: Duke University

description:
Library name: C24
10X genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made using Cell Ranger software (10X genomics)
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: kidney

extract_protocol:
Mice were perfused with ice-cold PBS via cardiac puncture after which the kidneys were harvested. Kidney digest was performed with liberase TM (0.3 mg/mL, Roche, Basel, Switzerland, #291963), hyaluronidase (10mg/mL, Sigma, H4272), DNaseI (20mg/mL) at 37 ̊C for 20 min. After centrifugation, cell pellets were incubated with ACK lysing buffer (ThermoFisher #A1049201) and again centrifuged. Pellets were incubated with 0.25%trypsin EDTA at 37 ̊C for 10 min with shaking at 100 rpm in bacterial shaker. Trypsin was inactivated using 10% fetal bovine serum in PBS. Cells were then washed and resuspended in DPBS supplemented with 0.04% bovine serum albumin. After filtration through a 30 m strainer, cells were loaded onto 10X Chromium System (10X Genomics) at 1000 cells/mcl
Library was performed according to manufacturer's instructions (single cell 3' v2 protocol, 10x Genomics)

value: kidney

tag: strain

value: wildtype

tag: Sex

value: male

value: Cecal ligation-and-puncture


title: Kidney,  sham

description:
Library name: C0
10X genomics

value: Sham surgery


title: B6.129-Fbn1tm2Rmz/J mice2

description:
Library name: mgR/mgR2
10x Genomics


title: B6.129-Fbn1tm2Rmz/J mice1

description:
Library name: mgR/mgR1
10x Genomics


title: HT_KO_B36_ATAC

value: CREBBP KO


title: HT_WT_B13_ATAC

value: CREBBP WT


title: CD45 positive cells, LC427, MC38

first: Xiaolu

last: Ge

state: Shanghai

address: 650 Xinsongjiang Road

institute: Shanghai General Hospital

description: Library name: S1

data_processing:
The 10x Genomics Cell Ranger v3.0.1 pipeline was used to de-multiplex raw files into FASTQ files, extract barcodes and unique molecular identifiers (UMI), and align reads to the transcriptome GRCm38 (mouse).
This output was imported into the Seurat (v3) R toolkit for downstream analysis. Low-quality cells (<200 genes/cell, >10% mitochondrial genes, and >10% red cell genes) for each sample were excluded. Moreover, we used Single-Cell Remover of Doublets (Scrublet) to remove empty droplets or multiplets.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Tumor tissues were cut into pieces, followed by enzymatic digestion using 0.5 mg/mL collagenase type IV (Roche) and 100U/mL DNase I (Aladdin, China) solution, and were incubated on a shaker (300 rpm) for 30 minutes at 37℃. The digested tissues were homogenized by passage through a 70 μm filter and centrifuged for 15 minutes at 4℃ and 400g. The dead cells were removed from single-cell pellets using  the dead cell removal microbeads (Miltenyi, Germany) and CD45 positive cells were collected with CD45 MicroBeads (Miltenyi, Germany).
Single-cell pellets of CD45+ cells were suspended at a 1 × 106 cells/mL concentration in FACS buffer and then loaded on a single-cell A Chip for Gel Beads-in-Emulsion (GEMs) generation and barcoding according to the manufacturer’s guidelines. Next, reverse transcription, barcoded cDNAs amplification, and quantification were performed to build a scRNA-seq 5′ gene expression (GEX) libraries using the 10X Genomics Chromium Single Cell 5′ Kit v2 and the 10x Chromium Controller (10x Genomics) according to the 10x Single Cell 5′ v2 protocol guidelines. The 5′ mRNA library was sequenced on Illumina’s NovaSeq6000 system with a NovaSeq6000 S4 reagent kit.

treatment_protocol: MC38 cells (2×105) were implanted in C57BL/6 female mice. Mice were treated with LC427 or not.

value: Tumor

value: CD45 positive cells


title: RL_Y1503C_A18_ATAC

source_name: RL

value: RL


title: CD45 positive cells, Vehicle, MC38

description: Library name: S2-2

value: Vehicle


title: HT_WT_A13_ATAC

value: HT

value: B cell Lymphoma


title: HT_Y1482N_G25_ATAC

value: No treatment


title: RL_Y1482N_F30_ATAC

value: CREBBP Y1482N


title: RL_Y1503C_A21_ATAC

value: CREBBP Y1503C


title: RL_Y1482N_C5_ATAC


title: pm1_455

city: Chengdu

first: Qiang

state: Sichuan

address: No. 17, the Third Part of Renmin South Road

institute: SKLB

description: Library name: Sample3

data_processing:
We used the default parameters of Cell Ranger single-cell software suite (v2.2.0) (10x Genomics). The quality of the sample-specific FASTQ file was evaluated by the counts of Cell Ranger which were aligned to the mouse reference genome (GRCm39) using a STAR aligner to generate the digital gene expression matrix. The expression level for each transcript was determined using the number of unique molecular identifiers (UMI) assigned to the transcript. The filtered gene expression matrices were then used for downstream analyses.
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Bone Marrow

extract_protocol:
Bone marrow cells from 5TGM mice were removed erythrocytes by incubating with RBC lysis buffer. Subsequently 1×PBS (0.04% BSA) was used to resuspend the cell precipitate and then centrifuged at 4°C 300g for 5min (repeated twice). The cell activity was detected by trypan blue staining, and it was required to be >85%. The number of cells was counted using a hemocytometer, and the cell concentration was adjusted to 103 cells/μL.
Single-cell suspension was added to the 10x Chromium chip according to the instructions for the 10×Genomics Chromium Single-Cell 3' kit (V3), with the expectation of capturing 10,000-15,000 cells. cDNA amplification and library construction were performed according to standard protocols.

value: Bone Marrow


title: pm2_459

description: Library name: Sample4


title: RL_R1446C_2B3_ATAC

value: CREBBP R1446C


title: RNA siZC3H4 1

city: Boston

first: Claudia

middle: A

last: Mimoso

state: MA

address: 45 Shattuck St. LHRRB

institute: Harvard Medical School

description:
Library name: Sample 16
RNA_siZC3H4_1

data_processing:
Cutadapt v1.14 was used to trim off adapters and low quality ends, using flags -f fastq --match-read-wildcards -m 20 -q 20,20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
For gDNA-derived samples: Bowtie2 v2.3.4.3 was used to map against an index made of the library of 16,462 insert sequences (GSE178230_sequence_inread_full.fa.gz). For bowtie2 mapping, the following parameters were set: --no-discordant --no-mixed --rdg 20,5 --rfg 20,5 --score-min L,0,-0.11. This basically disallowed gaps and allowed up to 3 mismatches on high-quality bases. For RNA-derived samples: Bowtie2 v2.3.4.3 was used to map against an index made of the library of 16,462 insert sequences PLUS spliced versions of these inserts as called by STAR (GSE178230_sequences_unspliced_spliced_pooleddata.fa.gz, with 5 spike sequences added). For bowtie2 mapping, the following parameters were set: --no-discordant --no-mixed --rdg 20,5 --rfg 20,5 --score-min L,0,-0.11. This basically disallowed gaps and allowed up to 3 mismatches on high-quality bases.
Samtools v1.98 was used to output the number of reads mapped to each sequence in the ‘reference genome’.
Assembly: mm10
Supplementary files format and content: counts_gDNA_WDR82ZC3H4KD_Sept2021.txt contains the number of reads mapped to each insert in the library, once column for each gRNA sample.
Supplementary files format and content: counts_RNA_WDR82ZC3H4KD_Sept2021.txt contains the number of reads mapped to each insert (spliced or unspliced version, or spike) in the library, once column for each total-RNA sample.

source_name: mouse embryonic stem cells

growth_protocol: mESCs (CAST/129 hybrid background, female) were cultured on gelatin. KnockOut DMEM (ThermoFisher, 10829018) was used, supplemented with 15% KO serum replacement (ThermoFisher, 10828028), 1X penicillin-streptomycin (MP, TMS-005-C), 1X non-essential amino acids (MP, TMS-001-C), 1% -ME (MP, ES-007-E), 1X GlutaMAX (ThermoFisher, 35050061), 1000 U/ml LIF (Cell Guidance Systems, GFM200), 1 µM MEK inhibitor (Stemgent, PD0325901), and 3 µM GSK3 inhibitor (Stemgent, CHIR99021). mESCs were fed daily and passaged every two days. mESCs were cultured at 37°C with 5% CO2.

extract_protocol:
For gDNA-derived samples: Genomic DNA was extracted using QuickExtract (Lucigen). For total-RNA-derived samples: Cells was pelleted and resuspended in Trizol (Ambion), spike-in RNA was added. RNA was cleaned up using Direct-zol RNA miniprep columns (Zymo Research), treated with RQ1 DNase (Promega), then cleaned up again using a total RNA purification kit (Norgen Biotek Corp).
For gDNA-derived samples: In a first round of PCR, the Oct4 uaRNA locus was amplified from these samples with NEBNext Ultra II Q5, using primers that would not amplify remaining plasmid or aspecific integrations at other loci. Amplicons were cleaned up using 0.9X AMPure XP beads. The amplicons from the first round of PCR were used as template in a PCR with the NEBNext multiplex oligos to generate the sequencing library. Final amplicons were cleaned up using 1x AMPure XP beads (Beckman Coulter), and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed gDNA samples together. After pooling the sample was gel-extracted from a 1% agarose gel to size select. For RNA-derived samples: First, RNA was reverse transcribed with Superscript IV (Thermo Fisher), using a gene-specific primer in mKate2 annealed 221nt downstream of the variable regions. cDNA was RNase-treated and then concentrated using 2x RNA XP beads (Beckman Coulter) to limit the number of parallel PCR reactions that had to be set up. Sequencing libraries were generated through PCR using NEBNext Ultra II Q5 (New England Biolabs) and NEBNext Multiplex oligos, uniquely indexing each sample. Amplicons were cleaned up using 1.5x AMPure XP beads (Beckman Coulter) and concentrations were quantified using the NEBNext Library Quant Kit for Illumina, before mixing indexed samples and checking the size distribution by TapeStation (Agilent).

treatment_protocol: See individual samples. Cells were transfected with 30nM siRNAs, either non-targeting or targeting WDR82 or ZC3H4.

value: CAST/129 hybrid background, female

value: mouse embryonic stem cells

value: 30 nM siZC3H4


title: RNA siZC3H4 3

description:
Library name: Sample 18
RNA_siZC3H4_3


title: RL_KO_3B3_ATAC


title: RL_R1446C_G2C20_ATAC


title: HT_R1446C_A1_ATAC


title: con1_456

description: Library name: Sample1


title: RL_KO_2A1_ATAC


title: HT_KO_D31_ATAC


title: con2_457

description: Library name: Sample2


title: RL_WT_G2C24_ATAC


title: RNA siZC3H4 2

description:
Library name: Sample 17
RNA_siZC3H4_2


title: RNA siWDR82 1

description:
Library name: Sample 13
RNA_siWDR82_1

value: 30 nM siWDR82


title: RL_WT_2B5_ATAC


title: RL_PM_Mousn_24h_S1_RNA

description:
RL_PM_Mousn_24h_S1_RNA
RL_mosun_counts_matrix.csv

value: Mosunetuzumab+CD4 T cells

value: 24 hours


title: RL_PM_Mousn_24h_S2_RNA

description:
RL_PM_Mousn_24h_S2_RNA
RL_mosun_counts_matrix.csv


title: RNA siNT 2

description:
Library name: Sample 11
RNA_siNT_2

value: 30 nM siNT


title: RNA siNT 3

description:
Library name: Sample 12
RNA_siNT_3


title: RNA siNT 1

description:
Library name: Sample 10
RNA_siNT_1


title: RL_PM_Mousn_12h_S1_RNA

description:
RL_PM_Mousn_12h_S1_RNA
RL_mosun_counts_matrix.csv

value: 12 hours


title: RL_PM_Mousn_12h_S2_RNA

description:
RL_PM_Mousn_12h_S2_RNA
RL_mosun_counts_matrix.csv

value: RL


title: RL_PM_Mousn_0h_S1_RNA

description:
RL_PM_Mousn_0h_S1_RNA
RL_mosun_counts_matrix.csv

value: 0 hour


title: RL_PM_Mousn_0h_S2_RNA

description:
RL_PM_Mousn_0h_S2_RNA
RL_mosun_counts_matrix.csv


title: gDNA siZC3H4 1

description:
Library name: Sample 7
gDNA_siZC3H4_1


title: gDNA siZC3H4 3

description:
Library name: Sample 9
gDNA_siZC3H4_3


title: RL_WT_Mousn_24h_S1_RNA

description:
RL_WT_Mousn_24h_S1_RNA
RL_mosun_counts_matrix.csv

value: CREBBP WT


title: RL_WT_Mousn_12h_S2_RNA

description:
RL_WT_Mousn_12h_S2_RNA
RL_mosun_counts_matrix.csv

value: B cell Lymphoma


title: RNA siWDR82 3

description:
Library name: Sample 15
RNA_siWDR82_3

value: 32 nM siWDR82


title: gDNA siWDR82 3

description:
Library name: Sample 6
gDNA_siWDR82_3


title: RL_WT_Mousn_12h_S1_RNA

description:
RL_WT_Mousn_12h_S1_RNA
RL_mosun_counts_matrix.csv


title: 207735830003_R12C02

type: genomic

city: New York

first: Abhimanyu

last: Amarnani

state: NY

address: 435 E 30th Street. 4th floor

institute: New York University

hyb_protocol: Illumina

scan_protocol: Illumina

data_processing: Illumina

label: Cy3, Cy5

source_name: Genotyping testing

label_protocol: Illumina

extract_protocol: Genomic DNA extracted was assessed by standard Illumina Infinium ImmunoArray 24v2-0.

tag: gender

value: F

value: B cells

tag: disease state

value: NR


title: RNA siWDR82 2

description:
Library name: Sample 14
RNA_siWDR82_2

value: 31 nM siWDR82


title: gDNA siWDR82 1

description:
Library name: Sample 4
gDNA_siWDR82_1

value: CAST/129 hybrid background, female


title: RL_WT_Mousn_0h_S2_RNA

description:
RL_WT_Mousn_0h_S2_RNA
RL_mosun_counts_matrix.csv


title: gDNA siNT 3

description:
Library name: Sample 3
gDNA_siNT_3

value: mouse embryonic stem cells


title: 207735830003_R11C01

value: ER


title: gDNA siWDR82 2

description:
Library name: Sample 5
gDNA_siWDR82_2


title: 207735830003_R12C01


title: 207735830003_R11C02


title: 207735830003_R10C01


title: gDNA siNT 2

description:
Library name: Sample 2
gDNA_siNT_2


title: 207735830003_R09C02


title: gDNA siZC3H4 2

description:
Library name: Sample 8
gDNA_siZC3H4_2

value: 30 nM siZC3H4


title: 207735830003_R08C02


title: 207735830003_R08C01


title: dTAG Clone D7

description: Library name: Sample 6

data_processing:
All custom scripts described herein are available on the AdelmanLab GitHub (https://github.com/AdelmanLab/NIH_scripts). Dual, 6nt Unique Molecular Identifiers (UMIs) were extracted from read pairs using UMI-tools [10.1101/gr.209601.116]. Read pairs were trimmed using cutadapt 1.14 to remove adapter sequences (-O 1 --match-read-wildcards -m 26). The UMI length was trimmed off the end of both reads to prevent read-through into the mate’s UMI, which will happen for shorter fragments. An additional nucleotide was removed from the end of read 1 (R1), using seqtk trimfq (https://github.com/lh3/seqtk), to preserve a single mate orientation during alignment.
The paired end reads were then mapped to a combined genome index, including both the spike (dm6) and primary (mm10) genomes, using bowtie2 [10.1038/nmeth.1923]. Properly paired reads were retained.
These read pairs were then separated based on the genome (i.e. spike-in vs primary) to which they mapped, and both these spike and primary reads were independently deduplicated, again using UMI-tools. Reads mapping to the reference genome were separated according to whether they were R1 or R2, sorted via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl). We note that this script counts each read once at the exact 3’ end of the nascent RNA.
Because R1 in PRO-seq reveals the position of the RNA 3’ end, the “+” and “-“ strands were swapped to generate bedGraphs representing 3’ end positions at single nucleotide resolution.
samples were spike normalized and combined bedGraphs were generated by summing counts per nucleotide across replicates for each condition.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: PRO-Seq

molecule: nuclear RNA

growth_protocol: mESCs (CAST/129 hybrid background, female) were cultured on gelatin. KnockOut DMEM (ThermoFisher, 10829018) was used, supplemented with 15% KO serum replacement (ThermoFisher, 10828028), 1X penicillin-streptomycin (MP, TMS-005-C), 1X non-essential amino acids (MP, TMS-001-C), 1% B-ME (MP, ES-007-E), 1X GlutaMAX (ThermoFisher, 35050061), 1000 U/ml LIF (Cell Guidance Systems, GFM200), 1 µM MEK inhibitor (Stemgent, PD0325901), and 3 µM GSK3 inhibitor (Stemgent, CHIR99021). mESCs were fed daily and passaged every two days. mESCs were cultured at 37°C with 5% CO2.

extract_protocol:
Cells were permeabilized as in Mimoso and Goldman 2023; run-ons were performed with biotinylated NTPs and then purified.
Purified biotinylated RNAs were ligated to sequencing adapters and amplified by PCR.

treatment_protocol: ZC3H4-dTAG cells were treated with 500nM dTAG13 (Sigma-Aldrich) for 40 minutes.

value: 500nM dTAG13


title: RL_WT_Mousn_24h_S2_RNA

description:
RL_WT_Mousn_24h_S2_RNA
RL_mosun_counts_matrix.csv

value: Mosunetuzumab+CD4 T cells

value: 24 hours


title: 207735830003_R07C02


title: HT_WT_with_CD40_RNA

description:
HT_WT_with_CD40_RNA
RLHT_CD40_counts_matrix.csv

value: HT


title: 207735830003_R07C01

value: M


title: dTAG Clone A9

description: Library name: Sample 5


title: 207735830003_R06C02


title: HT_PM_without_CD40_RNA

description:
HT_PM_without_CD40_RNA
RLHT_CD40_counts_matrix.csv

value: CREBBP Y1503C

value: No treatment


title: dTAG Clone A6

description: Library name: Sample 4


title: HT_WT_without_CD40_RNA

description:
HT_WT_without_CD40_RNA
RLHT_CD40_counts_matrix.csv

value: B cell Lymphoma

value: CREBBP WT


title: DMSO Clone D7

description: Library name: Sample 3

value: DMSO


title: RL_WT_Mousn_0h_S1_RNA

description:
RL_WT_Mousn_0h_S1_RNA
RL_mosun_counts_matrix.csv

value: RL

value: 0 hour


title: 207735830003_R06C01

value: F

value: B cells


title: 207735830003_R04C01

value: NR


title: 207735830003_R03C02

value: ER


title: gDNA siNT 1

description:
Library name: Sample 1
gDNA_siNT_1

value: CAST/129 hybrid background, female

value: mouse embryonic stem cells

value: 30 nM siNT


title: 207735830003_R05C01


title: RL_WT_with_CD40_RNA

description:
RL_WT_with_CD40_RNA
RLHT_CD40_counts_matrix.csv

value: 24 hours


title: 207735830003_R09C01


title: 207735830003_R04C02


title: DMSO Clone A9

description: Library name: Sample 2


title: HT_PM_with_CD40_RNA

description:
HT_PM_with_CD40_RNA
RLHT_CD40_counts_matrix.csv

value: HT


title: 207735830003_R03C01

value: M


title: RL_PM_with_CD40_RNA

description:
RL_PM_with_CD40_RNA
RLHT_CD40_counts_matrix.csv

value: CREBBP Y1503C


title: RL_PM_without_CD40_RNA

description:
RL_PM_without_CD40_RNA
RLHT_CD40_counts_matrix.csv

value: No treatment


title: 207735830003_R02C02


title: 207735830003_R01C02


title: 207735830003_R02C01


title: RL_WT_without_CD40_RNA

description:
RL_WT_without_CD40_RNA
RLHT_CD40_counts_matrix.csv

value: B cell Lymphoma


title: siZC3H4 Repl. 3

description: Library name: Sample 6

data_processing:
Using a custom script (trim_and_filter_PE.pl), FASTQ read pairs were trimmed to 50 bp per mate and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10).
Reads were first mapped to the ERCC spike-in using STAR 2.7.31. Reads not mapping to the spike genome were then used for alignment to mouse (mm10) using parameters --quantMode TranscriptomeSAM GeneCounts --outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --outFilterMismatchNmax 4 --alignSJoverhangMin 8 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0. Duplicates were also removed using STAR.  Stranded coverage bedGraph files were generated from deduplicated BAM files using STAR.
BedGraphs were depth normalized using the normalize_bedGraph custom script.
BedGraph files were converted to the bigWig format, and merged bedGraphs for each experimental condition were generated using bigWigMerge (UCSC tools).
RNAseq reads within exons were summed per gene using featurecounts. RNAseq reads were summed between uaTSS to +3kb for uaRNAs. DESeq2 was used to generate a list of differentially expressed genes after ZC3H4 inhibition. DESeq2 size factors were overwritten to match depth normalization.
Assembly: mm10
Supplementary files format and content: txt

source_name: F121-9 wt mESCs

growth_protocol: Wild-type F121-9 mESCs (CAST/129 hybrid background, female) were grown in serum-free embryonic stem cell (SFES) medium with 1000 U/ml LIF (Cell Guidance Systems, GFM200), 1 µM MEK inhibitor (Stemgent, PD0325901), and 3 µM GSK3 inhibitor (Stemgent, CHIR99021). SFES was composed of 50/50 NeuroBasal medium (Gibco) and DMEM/F12 medium (Gibco), supplemented with 0.5x B-27 (Gibco), 0.5× N-2 (Gibco), 2 mM l-glutamine (Gibco), 0.05% bovine albumin fraction V (Gibco) and 1.5 × 10−4 M monothioglycerol (Sigma).mESCs were fed daily and passaged every two days. mESCs were cultured at 37°C with 5% CO2.

extract_protocol:
Cells were collected in Trizol, ERCC spike-in was added and RNA was extracted using DirectZol columns. Genomic DNA contamination removed using DNAse, and RNA was cleaned up by adding Trizol and extracting RNA using DirectZol columns again. All samples had RIN scores of >9.
800ng purified RNA was used as input to the Illumina TruSeq stranded total RNA kit with Ribo-Zero Gold rRNA depletion. The manufacturer's protocol was followed, but Superscript III was used for first-strand synthesis.

treatment_protocol: See individual samples. Cells were transfected with 30nM siRNAs, either non-targeting or targeting ZC3H4.

value: Mouse embryonic stem cells

value: WT


title: siZC3H4 Repl. 2

description: Library name: Sample 5


title: 207735830003_R01C01


title: HT_Y1503C_PR2_RNA

description:
HT_Y1503C_PR2_RNA
HTPR_all_clones_counts_matrix.csv

value: CREBBP Y1503C EP300 WT


title: 207735830002_R12C02


title: 207735830003_R05C02


title: siZC3H4 Repl. 1

description: Library name: Sample 4


title: 207735830002_R12C01


title: DMSO Clone A6

description: Library name: Sample 1

value: DMSO


title: HT_Y1503C_PR1_RNA

description:
HT_Y1503C_PR1_RNA
HTPR_all_clones_counts_matrix.csv


title: 207735830002_R11C01

value: F


title: 207735830002_R10C02

value: B cells


title: siNT Repl. 3

description: Library name: Sample 3

value: siNT


title: HT_Y1482N_PR1_RNA

description:
HT_Y1482N_PR1_RNA
HTPR_all_clones_counts_matrix.csv

value: CREBBP Y1482N EP300 WT


title: 207735830002_R09C01

value: ER


title: HT_Y1482N_PR2_RNA

description:
HT_Y1482N_PR2_RNA
HTPR_all_clones_counts_matrix.csv


title: 207735830002_R11C02

value: NR


title: 207735830002_R09C02


title: 207735830002_R08C02


title: siNT Repl. 2

description: Library name: Sample 2


title: siNT Repl. 1

description: Library name: Sample 1


title: 207735830002_R07C02


title: 207735830002_R08C01


title: 207735830002_R07C01


title: HT_R1446C_PR1_RNA

description:
HT_R1446C_PR1_RNA
HTPR_all_clones_counts_matrix.csv

value: CREBBP R1446C EP300 WT