title: Brain, control, 48 hours, VSV-06

city: Shanghai

first: Yihua

last: Zhang

state: Shanghai

address: Fudan University

institute: Fudan University

description:
Library name: Brain, VSV, 06
Column name in Expression.xlsx: VSV_6:read count and VSV_6:fpkm

data_processing:
Sequencing was performed using the Illumina NovaSeq 6000 platform.
RNA-sequencing reads were preprocessed by trimming poly(A) tails and removing low-quality reads with the cutadapt tool
Clean reads were aligned to the Mus musculus GRCm38 genome using Ensembl annotations
Read counts were summarized at the gene level using HTseq
Expression levels were calculated as fragments per kilobase of transcript per million mapped reads (FPKM)
A pseudocount of 1 was added to the FPKM values, followed by log2 transformation. Heatmaps were generated using the pheatmap R package
Paired differential gene expression analysis was conducted using the DESeq R package, considering genes with a fold change > 2 and p-value < 0.05 as significantly differentially expressed
Paired differential gene expression analysis was conducted using the DESeq R package, considering genes with a fold change > 2 and p-value < 0.05 as significantly differentially expressed
Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed using topGO and KAAS, respectively.
Terms or pathways associated with the host antiviral immune response, with a fold change > 2 and p-value < 0.05, were selected for GO term enrichment or KEGG pathway visualization.
Protein-Protein Interaction (PPI) analysis of differentially expressed genes was performed using the STRING database, and the PPI network model was visualized with Cytoscape software
Assembly: Mus musculus GRCm38 genome
Supplementary files format and content: Expression of genes in the brain of mice under the different treatments.

source_name: brain

growth_protocol: WT mice used in the experiments were approved by the Institutional Animal Care and Use Committee of Fudan University

extract_protocol:
The brains were perfused with 4% paraformaldehyde prior to lysis using RNAiso Plus, following the manufacturer's instructions.
The lysates were then sent to Personalbio for cDNA library construction.

treatment_protocol: WT mice were treated with PBS, VSV, or HSV-1 for 48 hours. The brains were obtained from those mice.

value: brain

value: VSV infection


title: Brain, control, 48 hours, VSV-05

status: Public on Feb 01 2025

type: SRA

country: China

description:
Library name: Brain, VSV, 05
Column name in Expression.xlsx: VSV_5:read count and VSV_5:fpkm

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

value: WT

tag: treatment


title: F_APR_BLA

city: Nagoya

first: Junfeng

last: Chen

state: 23 - 愛知県

address: Nagoya University

country: Japan

institute: Nagoya University

data_processing:
Mapping and quantification were performed by bowtie (v1.2.3) and RSEM (v1.3.3).
Assembly: Mmul_10
Supplementary files format and content: Excel files include FPM values for each tissue.

organism: Macaca mulatta

source_name: urinary bladder

growth_protocol: Adult rhesus macaques were kept in an open enclosure  with natural light and temperature at the Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Japan. Two meals were provided per day at the estimated ad libitum levels and water was always available ad libitum.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Universal Mini Kit (Qiagen).
3'RNA-Seq library was prepared by the Lasy-Seq v1.1 protocol (https://sites.google.com/view/lasy-seq/)

treatment_protocol: Macaques were immobilized with  10 mg/kg BW ketamine hydrochloride (intramuscularly), and anaesthesized with 80 mg/kg BW pentobarbital (intravenously), and perfused with ice-cold Ames' medium.

tag: sampling point

value: April, 2020

value: urinary bladder

tag: Sex

value: F


title: PVHN_G_Control_19h_RNA_17

type: RNA

city: ITHACA

first: Hector

last: Aguilar-Carreno

state: New York

address: T8016A Veterinary Research Tower

department: Microbiology and Immunology

country: USA

institute: Cornell University

description:
No_VLP_control_19h_rep2
Gene expression at 19h

hyb_protocol: Hybridization was performed using Agilent Microarray Hybridization Chamber at 65°C for 17 hours.

scan_protocol: Scanning was performed using Agilent Scanner G2505C.

data_processing: Background correction was carried out on microarray samples using the maximum likelihood estimation for the normal-exponential convolution model, with an offset of 50, as implemented in Bioconductor's limma package. Samples were then normalized using quantile normalization and outliers were detected using intensity distribution and a boxplot graph followed by hierarchical clustering and PCA analysis of expression profiles using the MVA package.

organism: Homo sapiens

label_protocol: Cy3 labeling was performed using T7 promoter primer and T7 RNA polymerase.

growth_protocol: HEK293T cells were maintained in complete MDEM media with 10% Fetal Bovine Serum, 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol: Total RNA was extracted using Trizol and quantified using the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. mRNAs were converted to cDNAs using AffinityScript reverse transcriptase and oligo-dT promoter primer. The second strand cDNA synthesiswas performed with AffinityScript reverse transcriptase. Cy3 labeled cRNA was synthesized with T7 RNA polymerase mix. cRNAs were purified using RNeasy mini kit. cRNA quantitiy was determined using NanoDrop ND-1000 UV-VIS spectrophotometer and cRNAs were hybridized onto Agilent 4 x 44K human genome microarray slides.

treatment_protocol: For each time-point ten 6-well plates were used, five of them were incubated with NiV or HeV VLPs generated by related FG genes for 2h and 19h time point. Remaining five 6-well plates were used as uninfected controls.

tag: cell line

value: control

tag: time


title: MUTZ3 - RUNX1 ChIP-seq - CL9 - NoAuxin

city: Rotterdam

first: Ruud

last: Delwel

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus MC

description: Library name: CL9_NO_AUXIN_RUNX1

library_source: genomic

data_processing:
Base calling was conducted with bcl2fastq v1.8.4 for runs sequenced on the Hiseq 2500 and v2.20.422 for runs sequenced on the Novaseq 6000
ChIP-seq reads were aligned to the human reference genome build hg19 with bowtie (v1.1.1)
Peak calling was performed with MACS2 (v 2.1.2), using input sequencing data as controls. For transcription factor ChIP-seq, default settings were employed; for histone marks, the --broad argument was used.
For the histone marks H3K9me3 and H3K27me3, domains were also called with EPIC2
Bigwig files were generated for visualization with deepTools bamCoverage (v3.5.1) and the options  --normalizeUsing RPKM --smoothLength 100 --binSize 20
Assembly: hg19
Supplementary files format and content: bigWig files display signal for genome visualization; peaks.txt contain peaks called by MACS2 with the narrowPeak option; broad_peaks.txt files contain peaks called by MACS2 with the broadPeak option; .tsv files contain peaks called by the EPIC2 algorithm

molecule: genomic DNA

source_name: Bone marrow

growth_protocol: MUTZ3 cells were cultured in Alpha mem medium supplemented with 20% supernatant of urinary bladder carcinoma cell line 5637, and 20% FCS. Medium used was supplemented with 50U/ml penicillin and 50 U/ml streptomycin.

extract_protocol:
Cells were pelleted and resuspended in PBS containing 1% formaldehyde, followed by 3x washing using lysis buffer. Lysates were sonicated on a Biorupter and antibody was added. Nexxt, DNA was eluted, decrosslinked and quantified.
10 ng ChIP DNA was used in library preparation using MicroPlex library preparation kit.

treatment_protocol: MUTZ3 MECOM-V5-AID-T2A-GFP cells were treated with auxin in order to induce degradation of MECOM

value: Bone marrow

tag: cell type

value: acute myelomonocytic leukemia

value: NoAuxin

tag: protocol

value: Double-crosslink DSG


title: PVHN_G_Hendra_2h_RNA_15

description:
HeV_FG_VLP_2h_rep5
Gene expression at 2h

value: incubated with HeV_FG_VLP


title: PVHN_G_Control_19h_RNA_18

description:
No_VLP_control_19h_rep3
Gene expression at 19h


title: MUTZ3 - RUNX1 ChIP-seq - CL9 - Auxin

description: Library name: CL9_AUXIN_RUNX1

value: Auxin


title: PVHN_G_Control_19h_RNA_16

description:
No_VLP_control_19h_rep1
Gene expression at 19h


title: F_APR_AMYL

source_name: amygdala lateral nucleus

value: amygdala lateral nucleus


title: Brain, control, 48 hours, VSV-04

description:
Library name: Brain, VSV, 04
Column name in Expression.xlsx: VSV_4:read count and VSV_4:fpkm


title: MUTZ3 - RUNX1 ChIP-seq - CL8 - NoAuxin

description: Library name: CL8_NO_AUXIN_RUNX1


title: Brain, control, 48 hours, VSV-03

description:
Library name: Brain, VSV, 03
Column name in Expression.xlsx: VSV_3:read count and VSV_3:fpkm


title: Brain, control, 48 hours, VSV-02

description:
Library name: Brain, VSV, 02
Column name in Expression.xlsx: VSV_2:read count and VSV_2:fpkm


title: PVHN_G_Hendra_2h_RNA_14

description:
HeV_FG_VLP_2h_rep4
Gene expression at 2h


title: MUTZ3 - RUNX1 ChIP-seq - CL8 - Auxin

description: Library name: CL8_AUXIN_RUNX1


title: PVHN_G_Hendra_2h_RNA_13

description:
HeV_FG_VLP_2h_rep3
Gene expression at 2h


title: MUTZ3 - RNAseq_SLAM - MECOM_V5_AID_Tir1_Clone1 - Auxin_S4U

description: Library name: MUTZ3_V5_AID_GFP_TIR1_CL1_AUXIN_S4U

data_processing:
Base calling was conducted with bcl2fastq v1.8.4 with the settings --no-eamss --mismatches 1
Reads were processed with the SLAM-DUNK pipeline, adapted to take total RNA as input instead of 3’UTR only. Briefly,  a nucleotide conversion-aware read mapping algorithm was used to align reads with a high number of mismatches, followed by masking of single nucleotide reads. Finally, T>C conversions induced by S4U labeling was quantified on a gene level basis.
Assembly: hg19
Supplementary files format and content: tcount.tsv contains gene-level counts, including total reads, T>C converted reads and multimapping reads

extract_protocol:
After 1.5, hours nascent RNA was labeled for 3 hours using 300 µM/ml 4-Thiouridine. At 3 HRS of 4-Thiouridine labeling RNA was isolated using Qiagen rnease mini kit . Alkylation of thiol groups was performed according to manufacturer’s protocol.
500 ng total RNA was used to generate libraries using the KAPA RNA HyperPrep kit with RiboErase

tag: timepoint


title: MUTZ3 - P300 ChIP-seq - CL9 - NoAuxin

description: Library name: CL9_NO_AUXIN_P300


title: Brain, control, 48 hours, VSV-01

description:
Library name: Brain, VSV, 01
Column name in Expression.xlsx: VSV_1:read count and VSV_1:fpkm


title: SPEC2-CDK12-IN-3-03

city: Beijing

first: xuewu

last: you

address: 11 Xizhimen South Street, Xicheng District

institute: peking university peoples' hospital

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: endometrium

growth_protocol: The SPEC-2  cells were cultured in DMEM/F12 medium with 10% fetal bovine serum(FBS). Cells were cultured in humidified 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/23≥ 2.0, RIN≥ 6.5, 28S:18S ≥ 1.0, > 1 μ g) was used to construct sequencing library.
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA.

value: endometrium

value: epithelial


title: MUTZ3 - P300 ChIP-seq - CL9 - Auxin

description: Library name: CL9_AUXIN_P300


title: PVHN_G_Hendra_2h_RNA_12

description:
HeV_FG_VLP_2h_rep2
Gene expression at 2h


title: Brain, control, 48 hours, HSV-1-06

description:
Library name: Brain, HSV-1, 06
Column name in Expression.xlsx: HSV1_6:read count and HSV1_6:fpkm

value: HSV-1 infection


title: SPEC2-CDK12-IN-3-01


title: Brain, control, 48 hours, HSV-1-05

description:
Library name: Brain, HSV-1, 05
Column name in Expression.xlsx: HSV1_5:read count and HSV1_5:fpkm

value: brain


title: SPEC2-CDK12-IN-3-02


title: MUTZ3 - P300 ChIP-seq - CL8 - NoAuxin

description: Library name: CL8_NO_AUXIN_P300


title: Brain, control, 48 hours, HSV-1-04

description:
Library name: Brain, HSV-1, 04
Column name in Expression.xlsx: HSV1_4:read count and HSV1_4:fpkm


title: MUTZ3 - P300 ChIP-seq - CL8 - Auxin

description: Library name: CL8_AUXIN_P300


title: PVHN_G_Nipah_2h_RNA_10

description:
NiV_FG_VLP_2h_rep5
Gene expression at 2h

value: incubated with NiV_FG_VLP


title: PVHN_G_Hendra_2h_RNA_11

description:
HeV_FG_VLP_2h_rep1
Gene expression at 2h


title: PVHN_G_Nipah_2h_RNA_9

description:
NiV_FG_VLP_2h_rep4
Gene expression at 2h


title: MUTZ3 - input ChIP-seq Double - MUTZ3_3E7 - no_tx

description: Library name: MUTZ37_NEG10_input_H3K27AC

value: Histone


title: SPEC2-control03


title: F_APR_AMYC

source_name: amygdala central nucleus

value: April, 2020

value: amygdala central nucleus


title: Brain, control, 48 hours, HSV-1-03

description:
Library name: Brain, HSV-1, 03
Column name in Expression.xlsx: HSV1_3:read count and HSV1_3:fpkm

value: WT


title: F_APR_ADG

source_name: adrenal gland

value: adrenal gland

value: F


title: MUTZ3 - H3K27ac ChIP-seq - CL9 - NoAuxin

description: Library name: MUTZ3_EVI1V5AIDTIR1_CL9_H3K27AC

value: Bone marrow

value: acute myelomonocytic leukemia


title: SPEC2-control02

value: control


title: Brain, control, 48 hours, HSV-1-02

description:
Library name: Brain, HSV-1, 02
Column name in Expression.xlsx: HSV1_2:read count and HSV1_2:fpkm


title: PVHN_G_Nipah_2h_RNA_8

description:
NiV_FG_VLP_2h_rep3
Gene expression at 2h


title: SPEC2-control01


title: MUTZ3 - H3K27ac ChIP-seq - CL9 - Auxin

description: Library name: MUTZ3_EVI1V5AIDTIR1_CL9_AUXIN_H3K27AC


title: Brain, control, 48 hours, HSV-1-01

description:
Library name: Brain, HSV-1, 01
Column name in Expression.xlsx: HSV1_1:read count and HSV1_1:fpkm


title: Brain, control, 48 hours, PBS-06

description:
Library name: Brain, Control, 06
Column name in Expression.xlsx: PBS_6:read count and PBS_6:fpkm

value: PBS


title: MUTZ3 - H3K27ac ChIP-seq - CL8 - NoAuxin

description: Library name: MUTZ3_EVI1V5AIDTIR1_CL8_H3K27AC

value: NoAuxin


title: young inflorescence of progeny with fw2.3-WT genotype replicate 3

city: Athens

first: Esther

last: van der Knaap

state: GA

address: 111 Riverbend Rd

institute: UNIVERSITY OF GEORGIA

description: Library name: B3_CRRA200011726-1a_H57KFDSXY_L1

data_processing:
The sequencing reads were trimmed by the Cutadapt tool and aligned to SL4.0 reference genome using STAR RNA-seq aligner
the read count was carried out by R package Rsubread. Reads normalization and differential expression analysis was performed using R package edgeR; genes with log2 FC > 1 or < − 1 and p-value < 0.05 were considered as differentially expressed.
Assembly: SL4.0
Supplementary files format and content: individual Comma-separated values file contains raw read count for each sample
Supplementary files format and content: Comma-separated values file contains normalized RPKM of all samples

molecule: polyA RNA

organism: Solanum lycopersicum var. cerasiforme

source_name: young inflorescence

growth_protocol: tomato plants were cultivated in greenhouse condition without pruning. Plants with contrasting genotypes were arranged randomly and received same lighting and watering condition prior to tissue collection.

extract_protocol:
Total RNA was extracted from the ground tissues using Trizol reagent (Life technologies) according to the manufacture’s specifications. The quality and quantity of the RNA were examined by Agilent Bioanalyzer 2100 system (Agilent Technologies) at the Georgia Genomics and Bioinformatics Core at University of Georgia, Athens. Equal quantity of RNA from two plants of the same fw2.3 genotype was pooled to form six pools, three of each genotype.
Non-strand-specific RNA library construction was performed by Novogene  library construction service

treatment_protocol: Young inflorescence tissues with the largest floral buds smaller than 2mm long were removed from plants by a forcep and immediately frozen in liquid nitrogen

value: young inflorescence


title: young inflorescence of progeny with fw2.3-WT genotype replicate 2

description: Library name: B2_CRRA200011725-1a_H57KFDSXY_L1


title: PVHN_G_Nipah_2h_RNA_7

description:
NiV_FG_VLP_2h_rep2
Gene expression at 2h


title: PVHN_G_Nipah_2h_RNA_6

description:
NiV_FG_VLP_2h_rep1
Gene expression at 2h


title: PVHN_G_Control_2h_RNA_4

description:
No_VLP_control_2h_rep4
Gene expression at 2h


title: MUTZ3 - H3K27ac ChIP-seq - CL8 - Auxin

description: Library name: MUTZ3_EVI1V5AIDTIR1_CL8_AUXIN_H3K27AC

value: Auxin


title: MUTZ3 - Input ChIP-seq - CL9 - NoAuxin - EXP1

description: Library name: MUTZ3_EVI1V5AIDGFP_TIR1_CL9_INPUT_CTBP

value: Single-crosslink


title: young inflorescence of progeny with fw2.3-WT genotype replicate 1

description: Library name: B1_CRRA200011724-1a_H57KFDSXY_L1


title: PVHN_G_Control_2h_RNA_5

description:
No_VLP_control_2h_rep5
Gene expression at 2h


title: young inflorescence of progeny with fw2.3-D genotype replicate 3

description: Library name: A3_CRRA200011723-1a_H57KFDSXY_L1


title: Brain, control, 48 hours, PBS-04

description:
Library name: Brain, Control, 04
Column name in Expression.xlsx: PBS_4:read count and PBS_4:fpkm


title: PVHN_G_Control_2h_RNA_2

description:
No_VLP_control_2h_rep2
Gene expression at 2h


title: young inflorescence of progeny with fw2.3-D genotype replicate 2

description: Library name: A2_CRRA200011722-1a_H57KFDSXY_L1


title: PVHN_G_Control_2h_RNA_3

description:
No_VLP_control_2h_rep3
Gene expression at 2h


title: young inflorescence of progeny with fw2.3-D genotype replicate 1

description: Library name: A1_CRRA200011721-1a_H57KFDSXY_L1


title: MUTZ3 - H3K9ME3 ChIP-seq - CL9 - NoAuxin - EXP2

description: Library name: MUTZ3_EVI1V5AIDGFP_TIR1_CL9_H3K9ME3

value: Double-crosslink DSG


title: Brain, control, 48 hours, PBS-01

description:
Library name: Brain, Control, 01
Column name in Expression.xlsx: PBS_1:read count and PBS_1:fpkm

value: brain


title: Brain, control, 48 hours, PBS-02

description:
Library name: Brain, Control, 02
Column name in Expression.xlsx: PBS_2:read count and PBS_2:fpkm


title: MUTZ3 - CTBP2 ChIP-seq - CL9 - NoAuxin - EXP2

description: Library name: MUTZ3_EVI1V5AIDGFP_TIR1_CL9_CTBP_EXP2


title: Brain, control, 48 hours, PBS-05

description:
Library name: Brain, Control, 05
Column name in Expression.xlsx: PBS_5:read count and PBS_5:fpkm


title: MUTZ3 - H3K27ME3 ChIP-seq - CL9 - NoAuxin - EXP2

description: Library name: MUTZ3_EVI1V5AIDGFP_TIR1_CL9_H3K27ME3


title: CHZ_treated_3

city: Lübeck

first: Yamil

middle: Abdala

last: Maluje

state: Schleswig- Holstein

address: Ratzeburger Allee 160

department: Institute of Experimental Dermatology

country: Germany

institute: University of Luebeck

description:
Library name: 001T0015
Norm_lcpm_matrix_Exp1_CHZ_Treated_vs_Untreated.txt

data_processing:
Sequencing reads were mapped to Mus musculus GRCm39 release 107 using  STAR (version 2.7.3a)
Raw counts extraction and normalization was done using edgeR (version 4.0.16) and log2 transformed
Assembly: Mus musculus GRCm39 release 107
Supplementary files format and content: tab-delimited text file includes log2-CPM  values for each Sample

growth_protocol: Ba/F3 cells were maintained in RPMI 1640 medium containing 10% fetal calf serum and 1% Penicillin and streptomycin and maintained in humidified atmosphere with 5% Co2 and 37C.

extract_protocol:
RNA was isolated using the Trizol method, and samples were stored at -80°C.
VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina NR605 was used to construct the mRNA library and strand-specific mRNA library in strict accordance with the protocol provided by Vazyme.

treatment_protocol: Ba/F3 cells expressing JAK2-V617F were treated with either 1μM ruxolitinib or 1 μM CHZ868 or  DMSO for 6 hours, and RNA was isolated from these cells and RNA-seq analysis was performed using BMK GmbH (Münster, Germany). For ruxolitinib washout RNA-seq analysis, Ba/F3 cells expressing JAK2-V617F were treated with 1μM ruxolitinib for 1 hour, after which ruxolitinib was washed out by repeated (3x) PBS washing and incubated without ruxolitinib for 6 hours. Similarly, CHZ868 washout RNA-seq analysis, Ba/F3 cells expressing JAK2-V617F were treated with 1μM CHZ868 for 1 hour, after which rCHZ868 was washed out by repeated (3x) PBS washing and incubated without CHZ868 for 6 hours.

value: murine interleukin-3 dependent pro-B cell line

value: CHZ868 6 hours


title: MUTZ3 - CTBP2 ChIP-seq - CL9 - NoAuxin - EXP1

description: Library name: MUTZ3_EVI1V5AIDGFP_TIR1_CL9_CTBP_EXP1


title: MUTZ3 - Input ChIP-seq TF - MUTZ3_3E7 - no_tx

description: Library name: MUTZ37_NEG10_input_RUNX_MYB


title: Sample GB99

city: San Giuliano Terme

first: Paolo

last: Aretini

state: Pisa

address: Via Ferruccio Giovannini 13

country: Italy

institute: Fondazione Pisana per la Scienza

description:
Library name: GB99
Column name in TPM_Data.txt: GB99

data_processing:
Sequence reads were mapped to GRCh38  using STAR-2.7.9a
TPM (Transcripts Per Kilobase Million) were calculate with RSEM using the command rsem-calculate-expression
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text includes TPM (Transcripts Per Kilobase Million) for each samples

source_name: Glioblastoma Fresh Tissue

extract_protocol:
RNA was extracted using the Maxwell® 16 Tissue LEV Total RNA Purification Kit. 500ng of total RNA was used to construct the sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA, following the manufacturer's recommendations

value: Glioblastoma Fresh Tissue

tag: batch


title: Brain, control, 48 hours, PBS-03

description:
Library name: Brain, Control, 03
Column name in Expression.xlsx: PBS_3:read count and PBS_3:fpkm


title: Sample GB97

description:
Library name: GB97
Column name in TPM_Data.txt: GB97


title: MUTZ3 - H3K9ME3 ChIP-seq - CL9 - Auxin - EXP2

description: Library name: MUTZ3_EVI1V5AIDGFP_TIR1_CL9_AUXIN_H3K9ME3


title: CHZ_treated_2

description:
Library name: 001T0014
Norm_lcpm_matrix_Exp1_CHZ_Treated_vs_Untreated.txt


title: Sample GB96

description:
Library name: GB96
Column name in TPM_Data.txt: GB96


title: CHZ_treated_1

description:
Library name: 001T0013
Norm_lcpm_matrix_Exp1_CHZ_Treated_vs_Untreated.txt


title: PVN_E_E19_FG2_17Hr

description:
FG2_17h_rep4
FG2 gene expression 17h

treatment_protocol: FG and mutants transfections for 17h time point. Remaining five 6-well plates were used as uninfected controls.

value: FG2 transfection


title: PVN_E_E17_FG2_17Hr

description:
FG2_17h_rep2
FG2 gene expression 17h


title: PVN_E_E20_FG2_17Hr

description:
FG2_17h_rep5
FG2 gene expression 17h


title: Ruxo_treated_3

description:
Library name: 001T0012
Norm_lcpm_matrix_Exp1_Ruxo_Treated.txt

value: Ruxo 6 hours


title: PVN_E_E16_FG2_17Hr

description:
FG2_17h_rep1
FG2 gene expression 17h


title: MUTZ3 - H3K27ME3 ChIP-seq - CL9 - Auxin - EXP2

description: Library name: MUTZ3_EVI1V5AIDGFP_TIR1_CL9_AUXIN_H3K27ME3


title: PVHN_G_Control_2h_RNA_1

description:
No_VLP_control_2h_rep1
Gene expression at 2h


title: Sample GB98

description:
Library name: GB98
Column name in TPM_Data.txt: GB98


title: Sample GB79

description:
Library name: GB79
Column name in TPM_Data.txt: GB79


title: PVN_E_E15_F3F5G_17Hr

description:
F3F5G_17h_rep5
F3F5G gene expression 17h

value: F3F5G transfection


title: MUTZ3 - CTBP2 ChIP-seq - CL9 - Auxin - EXP1

description: Library name: MUTZ3_EVI1V5AIDGFP_TIR1_CL9_AUXIN_CTBP_EXP1


title: Ruxo_treated_2

description:
Library name: 001T0011
Norm_lcpm_matrix_Exp1_Ruxo_Treated.txt


title: Sample Gb92_ctrl

description:
Library name: Gb92_ctrl
Column name in TPM_Data.txt: Gb92_ctrl


title: Ruxo_treated_1

description:
Library name: 001T0010
Norm_lcpm_matrix_Exp1_Ruxo_Treated.txt


title: MUTZ3 - H3K27ME3 ChIP-seq - CL8 - NoAuxin - EXP1

description: Library name: MUTZ3_EVI1V5AIDGFP_TIR1_CL8_H3K27ME3


title: PVN_E_E14_F3F5G_17Hr

description:
F3F5G_17h_rep4
F3F5G gene expression 17h


title: Sample GB75-3

description:
Library name: GB75-3
Column name in TPM_Data.txt: GB75-3


title: PVN_E_E18_FG2_17Hr

description:
FG2_17h_rep3
FG2 gene expression 17h


title: PVN_E_E13_F3F5G_17Hr

description:
F3F5G_17h_rep3
F3F5G gene expression 17h


title: DMSO_wash_3_exp3

description:
Library name: 001T0009
Norm_lcpm_matrix_Exp3_DMSO_wash_CHZ_wash.txt

value: DMSO 1 hour


title: MUTZ3 - H3K9ME3 ChIP-seq - CL8 - Auxin - EXP1

description: Library name: MUTZ3_EVI1V5AIDGFP_TIR1_CL8_AUXIN_H3K9ME3

value: Bone marrow


title: DMSO_wash_2_exp3

description:
Library name: 001T0008
Norm_lcpm_matrix_Exp3_DMSO_wash_CHZ_wash.txt


title: Sample GB78

description:
Library name: GB78
Column name in TPM_Data.txt: GB78


title: Sample GB75-2

description:
Library name: GB75-2
Column name in TPM_Data.txt: GB75-2


title: MUTZ3 - H3K27ME3 ChIP-seq - CL8 - Auxin - EXP1

description: Library name: MUTZ3_EVI1V5AIDGFP_TIR1_CL8_AUXIN_H3K27ME3

value: acute myelomonocytic leukemia


title: DMSO_wash_1_exp3

description:
Library name: 001T0007
Norm_lcpm_matrix_Exp3_DMSO_wash_CHZ_wash.txt


title: PVN_E_E12_F3F5G_17Hr

description:
F3F5G_17h_rep2
F3F5G gene expression 17h


title: Sample GB75-1

description:
Library name: GB75-1
Column name in TPM_Data.txt: GB75-1


title: PVN_E_E10_WT_FG_17Hr

description:
WT_FG_17h_rep5
WT FG gene expression 17h

value: WT FG transfection


title: CHZ_wash_3

description:
Library name: 001T0006
Norm_lcpm_matrix_Exp3_DMSO_wash_CHZ_wash.txt

value: CHZ868 1 hour


title: MUTZ3 -  ATAC-seq - CL9 - Auxin - 4HRS

description: Library name: MUTZ3_V5AID_EVI1GFP_CL9_AUXIN_4HRS

data_processing:
Base calling was conducted with bcl2fastq v1.8.4 for runs sequenced on the Hiseq 2500 and v2.20.422 for runs sequenced on the Novaseq 6000
ATAC-seq reads were aligned to the human reference genome build hg19 with bowtie2 (v2.3.4.1)
Bigwig files were generated for visualization with deepTools bamCoverage (v3.5.1) and the options  --normalizeUsing RPKM --smoothLength 100 --binSize 20
Peak calling was performed with MACS2 (v 2.1.2), using input sequencing data as controls. For transcription factor ChIP-seq, default settings were employed; for histone marks, the --broad argument was used.
Bigwig files were generated for visualization with deepTools bamCoverage (v3.5.1) and the options  --normalizeUsing RPKM --smoothLength 100 --binSize 20
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Cells were pelleted and washed using PBS. Next, nuclei were isolated by lysing cells in 1mL lysis buffer. Lysates were incubated on ice 5 minutes and nuclei were pelleted and resuspended in 50 µl transpose mix containing 2.5 µl TD1 transposase. Samples were incubated 30 minutes at 37° and DNA was purified using Qiagen’s PCR min elute kit
DNA was amplified using indexed primers.


title: Sample GB58

description:
Library name: GB58
Column name in TPM_Data.txt: GB58


title: MUTZ3 -  ATAC-seq - CL9 - Auxin - 24HRS

description: Library name: MUTZ3_V5AID_EVI1GFP_CL9_AUXIN_24HRS


title: MUTZ3 -  ATAC-seq - CL9 - no_tx - 4HRS

description: Library name: MUTZ3_V5AID_EVI1GFP_CL9_4HRS


title: Sample GB146_

description:
Library name: GB146_
Column name in TPM_Data.txt: GB146_


title: CHZ_wash_1

description:
Library name: 001T0004
Norm_lcpm_matrix_Exp3_DMSO_wash_CHZ_wash.txt


title: Sample GB143-2

description:
Library name: GB143-2
Column name in TPM_Data.txt: GB143-2


title: MUTZ3 - H3K9ME3 ChIP-seq - CL8 - NoAuxin - EXP1

description: Library name: MUTZ3_EVI1V5AIDGFP_TIR1_CL8_H3K9ME3

value: NoAuxin


title: DMSO_treated_3

description:
Library name: 001T0003
Norm_lcpm_matrix_Exp1_CHZ_Treated_vs_Untreated.txt

value: DMSO 6 hours


title: MUTZ3 -  ATAC-seq - CL8 - Auxin - 4HRS

description: Library name: MUTZ3_V5AID_EVI1GFP_CL8_AUXIN_4HRS

value: Auxin


title: DMSO_treated_2

description:
Library name: 001T0002
Norm_lcpm_matrix_Exp1_CHZ_Treated_vs_Untreated.txt


title: PVN_E_E9_WT_FG_17Hr

description:
WT_FG_17h_rep4
WT FG gene expression 17h


title: Sample GB143-1

description:
Library name: GB143-1
Column name in TPM_Data.txt: GB143-1


title: PVN_E_E8_WT_FG_17Hr

description:
WT_FG_17h_rep3
WT FG gene expression 17h


title: PVN_E_E7_WT_FG_17Hr

description:
WT_FG_17h_rep2
WT FG gene expression 17h


title: PVN_E_E11_F3F5G_17Hr

description:
F3F5G_17h_rep1
F3F5G gene expression 17h


title: Sample GB140-2

description:
Library name: GB140-2
Column name in TPM_Data.txt: GB140-2


title: PVN_E_E6_WT_FG_17Hr

description:
WT_FG_17h_rep1
WT FG gene expression 17h


title: MUTZ3 -  ATAC-seq - CL8 - no_tx - 4HRS

description: Library name: MUTZ3_V5AID_EVI1GFP_CL8_4HRS


title: CHZ_wash_2

description:
Library name: 001T0005
Norm_lcpm_matrix_Exp3_DMSO_wash_CHZ_wash.txt


title: PVN_E_E5_Control_17Hr

description:
No_transfection_control_rep5
Control gene expression 17h

value: Control


title: PVN_E_E3_Control_17Hr

description:
No_transfection_control_rep3
Control gene expression 17h


title: DMSO_wash_3

description:
Library name: DMSO_wash_3
Norm_lcpm_matrix_jak.txt


title: MUTZ3 -  ATAC-seq - CL8 - no_tx - 24HRS

description: Library name: MUTZ3_V5AID_EVI1GFP_CL8_24HRS


title: Sample GB140-1

description:
Library name: GB140-1
Column name in TPM_Data.txt: GB140-1


title: PVN_E_E4_Control_17Hr

description:
No_transfection_control_rep4
Control gene expression 17h


title: DMSO_wash_2

description:
Library name: DMSO_wash_2
Norm_lcpm_matrix_jak.txt


title: MUTZ3 -  ATAC-seq - CL9 - no_tx - 24HRS

description: Library name: MUTZ3_V5AID_EVI1GFP_CL9_24HRS


title: Sample GB136

description:
Library name: GB136
Column name in TPM_Data.txt: GB136


title: MUTZ3 - 4C - VP_CEBPA42kbEnhancer - CL9 - Auxin

description: Library name: plus42kb_cebpa_enh_VP_MUTZ3_V5AIDTIR1_cl9_with_auxin

data_processing:
Base calling was conducted with bcl2fastq v1.8.4 for runs sequenced on the Hiseq 2500 and v2.20.422 for runs sequenced on the Novaseq 6000
Demultiplexing and clipping of the primer sequences was performed by an in-house algorithm.
4C-seq reads were aligned to the human reference genome build hg19 with bowtie (v1.1.1)
Using in-house algorithms, a fragmented virtual genome was generated based on the restriction site positions of the chosen restriction enzymes and reads not mapping to these fragments were excluded from the BAM files. The number of reads mapping to each non-blind fragment (i.e. delimited by both a primary and a secondary restriction enzyme cutting sites) was quantified and then normalized by library size. Tracks containing this information were converted to bigWIg format using the UCSC wigToBigwig tool
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: 4C-Seq

extract_protocol:
Sample preparation was performed as previously described (van de Werken et al., 2012). In short, genomic regions that are spatially proximal in the cell nucleus were fixated by formaldehyde-induced crosslinks. The DNA was fragmented with DpnII as a primary restriction enzyme, Csp6I as a secondary 4 bp-cutter. To identify and quantify fragments that were ligated to the genomic region of interest, a two-step PCR was performed as previously described
In a second PCR step, universal primers were used that contain the Illumina adapters. The amplicons were analyzed using next generation sequencing on the IIlumina NovaSeq platform.


title: DMSO_wash_1

description:
Library name: DMSO_wash_1
Norm_lcpm_matrix_jak.txt


title: Sample GB132

description:
Library name: GB132
Column name in TPM_Data.txt: GB132


title: MUTZ3 - 4C - VP_CEBPA42kbEnhancer - CL9 - NoAuxin

description: Library name: plus42kb_cebpa_enh_VP_MUTZ3_V5AIDTIR1_cl9_no_auxin


title: MUTZ3 -  ATAC-seq - CL8 - Auxin - 24HRS

description: Library name: MUTZ3_V5AID_EVI1GFP_CL8_AUXIN_24HRS


title: Sample GB141

description:
Library name: GB141
Column name in TPM_Data.txt: GB141


title: Sample GB130

description:
Library name: GB130
Column name in TPM_Data.txt: GB130


title: DMSO_treated_1

description:
Library name: 001T0001
Norm_lcpm_matrix_Exp1_CHZ_Treated_vs_Untreated.txt


title: PVN_E_E2_Control_17Hr

description:
No_transfection_control_rep2
Control gene expression 17h


title: Ruxo_wash_3

description:
Library name: Ruxo_wash_3
Norm_lcpm_matrix_jak.txt

value: Ruxo 1hour


title: PVN_E_E1_Control_17Hr

description:
No_transfection_control_rep1
Control gene expression 17h


title: Ruxo_wash_2

description:
Library name: Ruxo_wash_2
Norm_lcpm_matrix_jak.txt


title: MUTZ3 - 4C - VP_CEBPA42kbEnhancer - CL8 - Auxin

description: Library name: plus42kb_cebpa_enh_VP_MUTZ3_V5AIDTIR1_cl8_with_auxin


title: MUTZ3 - 4C - VP_CEBPA42kbEnhancer - CL8 - NoAuxin

description: Library name: plus42kb_cebpa_enh_VP_MUTZ3_V5AIDTIR1_cl8_no_auxin


title: PVN_D_D35_WT_FG_notag_21Hr

description:
WT_FG_notag_21h_rep5
WT FG no-tag gene expression 21h

treatment_protocol: FG and mutants transfections for 21h time point. Remaining five 6-well plates were used as uninfected controls.

value: WT FG no-tag transfection


title: Sample GB129

description:
Library name: GB129
Column name in TPM_Data.txt: GB129


title: Ruxo_wash_1

description:
Library name: Ruxo_wash_1
Norm_lcpm_matrix_jak.txt

value: murine interleukin-3 dependent pro-B cell line


title: PVN_D_D34_WT_FG_notag_21Hr

description:
WT_FG_notag_21h_rep4
WT FG no-tag gene expression 21h


title: CD8 T cells NK depleted

city: Columbus

first: Zihai

last: Li

state: Ohio

address: 2255 Kenny Rd

institute: The Ohio State University

description:
Library name: CD8NK
10x Genomics

library_source: transcriptomic single cell

data_processing:
CD8+ T cells were isolated from tumor samples using the FACS Melody system (BD Bioscience) and processed using the 10X platform. BCL files were converted into FASTQ files using the Cell Ranger software (10x Genomics Cell Ranger 6.1.2). The Cell Ranger software performed tasks such as trimming adapters and primer sequences, mapping reads to the mm10 reference genome, and quantifying expression levels. Cells with read counts between 1400 and 7500 were selected to eliminate empty droplets or doublets/multiplets, and those with < 15% mitochondrial counts were retained to remove low-quality and dying cells. Subsequently, Seurat software (version 4.0.6) was employed for downstream analysis, utilizing the count data generated by Cell Ranger. Initially, integration of both the α-NK1.1 and control datasets were performed, followed by count normalization using the LogNormalize approach. Low-dimensional visualization was generated using the UMAP algorithm, and cell clustering was executed using the Louvain algorithm. Marker genes conserved between α-NK1.1 and controls were identified for each cell cluster, and differentially expressed (DE) genes between α-NK1.1 and controls were determined through a Wilcoxon rank sum test with multiple testing adjustments using the Bonferroni approach. Subsequently, regulon analysis and pseudo-time analysis were conducted using the IRIS3 and the Slingshot software, respectively (51,61). scRNA-seq analysis of the melanoma tumor model was performed as described in the companion paper (Pozniak, Landeloos, Roda et al.). The CD8+ T cell data matrix was isolated from the dataset, and a similar approach to the one mentioned above was applied. Frequency and marker expression patterns were evaluated, and the NKRT signature generated from MC38 was applied.
Assembly: mm10
Supplementary files format and content: CSV format, gene-cell raw count matrix and metadata for each cell

source_name: Tumor

extract_protocol:
Nine days after tumor implantation, MC38 tumor samples were collected from both control and NK cell-depleted mice. The harvested tumor samples were mechanically minced and enzymatically digested using collagenase types I and IV. The digested samples were neutralized with BSA and filtered through a 70 μm cell strainer. The resulting single-cell suspension was stained with a viability dye, followed by surface marker staining. Live CD8+ T cells were then sorted using the BD FACS Melody system.
Library construction was performed according to the manufacturer’s instructions (single cell 5’ V2 protocol, 10X genomics).

value: Tumor

value: CD8+ T cells

value: WT

value: a-NK1.1 antibody


title: Sample GB127

description:
Library name: GB127
Column name in TPM_Data.txt: GB127

value: Glioblastoma Fresh Tissue


title: Sample GB128

description:
Library name: GB128
Column name in TPM_Data.txt: GB128


title: MUTZ3 - 4C - VP_CEBPA_promoter - CL9 - Auxin

description: Library name: cebpa_pr_VP_MUTZ3_V5AIDTIR1_cl9_with_auxin


title: CD8 T cells

description:
Library name: CD8Iso
10x Genomics

value: PBS


title: MUTZ3 - 4C - VP_CEBPA_promoter - CL8 - Auxin

description: Library name: cebpa_pr_VP_MUTZ3_V5AIDTIR1_cl8_with_auxin

value: Bone marrow


title: PVN_D_D32_WT_FG_notag_21Hr

description:
WT_FG_notag_21h_rep2
WT FG no-tag gene expression 21h


title: PVN_D_D33_WT_FG_notag_21Hr

description:
WT_FG_notag_21h_rep3
WT FG no-tag gene expression 21h


title: Sample GB120

description:
Library name: GB120
Column name in TPM_Data.txt: GB120


title: AML12, siCasp8, rep4

city: New York

first: Xiaobo

last: Wang

state: NY

address: 630 W 168tth street

department: Medicine

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming. We perform a pseudoalignment to a kallisto index created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0). We test for differentially expressed genes under various conditions using Sleuth or DESeq2, R packages designed to test differential expression between two experimental groups from RNA-seq counts data.
Assembly: Mouse: GRCm38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

growth_protocol: AML12 mouse hepatocytes were obtained from ATCC (CRL-2254) and cultured in DMEM/F12 medium (Life Technologies, #11320) supplemented with 10% (vol/vol) heat-inactivated FBS (Gibco, #16140-071) and 1X penicillin-streptomycin solution (Corning, 30-002-Cl) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
We use poly-A pull-down to enrich mRNAs from total RNA samples,then proceed with library construction using Illumina TruSeq chemistry.

treatment_protocol: Scrambled siRNA control and Casp8 siRNAs were transfected into AML12 cells using Lipofectamine RNAiMAX at a final concentration of 40 nM siRNA in 24-well plates, following the manufacturer’s protocol.

value: hepatocytes

value: Casp8 knockdown

value: siCasp8 for 48 hours


title: MUTZ3 - 4C - VP_CEBPA_promoter - CL8 - NoAuxin

description: Library name: cebpa_pr_VP_MUTZ3_V5AIDTIR1_cl8_no_auxin

value: acute myelomonocytic leukemia

value: NoAuxin


title: Sample GB119

description:
Library name: GB119
Column name in TPM_Data.txt: GB119


title: Sample GB111

description:
Library name: GB111
Column name in TPM_Data.txt: GB111


title: AML12, siCasp8, rep3


title: AML12, siCasp8, rep2


title: C4_FOXA1(M253K)_Flag_siKMT2D_Rep2 (CUT TAG)

city: guangzhou

first: Mayao

last: Luo

state: guangdong

address: No. 106, Zhongshan 2nd Road

department: Urology

institute: Guangdong Provincial People’s Hospital

description: Library name: sample48

data_processing:
The ChIP-Seq reads were mapped to the hg38 human genome using bowtie2 (v2.2.5) with default parameters. Samtools (v1.6) was used to convert sam files to bam files. MACS2 (v2.2.6) was used to call peaks. Homer (v4.11) was used to perform motif analysis. Integrative Genomics Viewer (IGV) (v2.16.2) was used to visualize peaks of all samples. The CUT&Tag reads were mapped to the hg38 human genome using bowtie2 (v2.2.5) with parameters “-X 2000 --very-sensitive-local -no-discordant”. PCR duplicated reads were removed by sambamba (v0.6.6). SAM files were converted to BAM files using samtools (v1.6). MACS2 (v2.2.6) was used to call peaks with -q 0.05. Deeptools (v3.5.2) was used to convert BAM files to Bigwig files and generate the profile plot and heatmap. Homer (v4.11) was used to perform motif analysis. CUT&Tag signal tracks were visualized by IGV (v2.16.2). R package EdgeR (3.22.5) was used to perform differential peaks analysis.
Assembly: hg38
Supplementary files format and content: Library normalized bigWig files were provided for all samples
Library strategy: CUT&Tag

growth_protocol: LNCaP, C4-2 cells, C4-2 cells experssing mutation FOXA1  were cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
ChIP was performed using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling Technology, 9003), according to the manufacturers’ instructions. Briefly, LNCaP and C4-2 cells were cross-linked, lysed and digested to generate DNA fragments. Digested chromatin was incubated overnight with anti-AR (Cell Signaling Technology, 5153) antibody or control IgG. The purified DNA was used for ChIP-seq library preparation. CUT&Tag was performed using the Hieff NGS® In-Situ DNA Binding Profiling Library Prep Kit for Illumina (Yeasen, 12597ES) according to the manufacturer’s instructions. Briefly, 1x105 of cells were used for the CUT&Tag experiment, cells were collected, washed, incubated with concanavalin A-coated magnetic beads, incubated with primary antibodies, secondary antibodies and cutted by pA-Tn5 transposase to generate DNA fragments.
ChIP Library preparation was done using the NEBNext ultra II DNA library prep kit for Illumina, followed by sequencing on a NovaSeq 6000. For CUT&Taglibrary amplification, puried DNA was mixed with 2×HiFi Amplification Mix and uniquely barcoded i5 and i7 primers provided by Hieff NGS® Tagment Index Kit for Illumina® (Yeasen, 12416)following PCR program and purified by DNA Selection Beads.

value: prostate cancer cell line


title: PVN_D_D30_FG2_21Hr

description:
FG2_21h_rep5
FG2 gene expression 21h

value: FG2 transfection


title: C4_FOXA1(M253K)_Flag_siKMT2D_Rep1 (CUT TAG)

description: Library name: sample47


title: PVN_D_D31_WT_FG_notag_21Hr

description:
WT_FG_notag_21h_rep1
WT FG no-tag gene expression 21h


title: Sample GB110

description:
Library name: GB110
Column name in TPM_Data.txt: GB110


title: AML12, siCasp8, rep1


title: Sample GB108

description:
Library name: GB108
Column name in TPM_Data.txt: GB108


title: PVN_D_D29_FG2_21Hr

description:
FG2_21h_rep4
FG2 gene expression 21h


title: C4_FOXA1(M253K)_Flag_siNC_Rep2 (CUT TAG)

description: Library name: sample46

value: siNC


title: AML12, Scr, rep3

value: scr for 48 hours


title: PVN_D_D28_FG2_21Hr

description:
FG2_21h_rep3
FG2 gene expression 21h


title: PVN_D_D27_FG2_21Hr

description:
FG2_21h_rep2
FG2 gene expression 21h


title: Sample GB107

description:
Library name: GB107
Column name in TPM_Data.txt: GB107


title: PVN_D_D26_FG2_21Hr

description:
FG2_21h_rep1
FG2 gene expression 21h


title: AML12, Scr, rep2


title: Sample GB101-2

description:
Library name: GB101-2
Column name in TPM_Data.txt: GB101-2


title: C4_FOXA1(D226G)_Flag_siKMT2D_Rep1 (CUT TAG)

description: Library name: sample43


title: AML12, Scr, rep1


title: C4_FOXA1(D226G)_Flag_siNC_Rep2 (CUT TAG)

description: Library name: sample42


title: MUTZ3 - 4C - VP_CEBPA_promoter - CL9 - NoAuxin

description: Library name: cebpa_pr_VP_MUTZ3_V5AIDTIR1_cl9_no_auxin


title: C4_FOXA1(D226G)_Flag_siNC_Rep1 (CUT TAG)

description: Library name: sample41


title: PVN_D_D23_FR3AG_21Hr

description:
FR3AG_21h_rep3
FG3AG gene expression 21h

value: FG3AG transfection


title: DU145, SMARCA2/4 degrader, TEAD1

city: South San Francisco

first: Tomasz

last: Włodarczyk

state: California

address: 1 DNA Way

institute: Genentech

description: DNA-seq

data_processing:
ChIP-seq sequence data was processed using an ENCODE-DC/chip-seq-pipeline2 -based workflow (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Briefly, fastq files were aligned on the hg38 human genome reference using Bowtie2 (v2.2.6) followed by alignment sorting (samtools v1.7) of resulting bam files with filtering out of unmapped reads and keeping reads with mapping quality higher than 30. Duplicates were removed with Picard’s MarkDuplicates (v1.126) function, followed by indexation of resulting bam files with samtools. For each bam file, genome coverage was computed with bedtools (v2.26.0), followed by the generation of bigwig (wigToBigWig v377) files. Peaks were called with SPP for each treatment sample using a pooled input alignment (.bam file) as control.
Assembly: GRCh38-2020-A
Supplementary files format and content: bigwig and bed files returned by the encode chip-seq pipeline. They contain information about peak positions.

growth_protocol: MDA-PCa-2b and DU145 cells were obtained from ATCC. MDA-PCa-2b cells were cultured with HCP1 medium (Enzo, catalog number AES-0403), 20% FBS, 1x Glutamine and pen/strep. DU145 was cultured with RPMI-1640 media with 10% FBS and 2mM L-Glutamine. The cells were split every 4-5 days to maintain the appropriate density.

extract_protocol:
Cells (10 x 10^6) were crosslinked by 10-minutes of 1% formaldehyde. Formaldehyde was quenched by the addition of glycine. Nuclei were isolated with ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0). Nuclei were sheared with Covaris sonicator (E220) using the following setup: Fill level – 10, Duty Cycle – 15, PIP – 350, Cycles/Burst – 200, Time – 8-minutes). Sheared chromatin was immunoprecipitated overnight with the following antibodies: SMARCA4 (ab110641), FOSL1 (PA5-66880 – Invitrogen) and TEAD1 (BD #610923). Antibody chromatin complexes were pulled down with Protein A or Protein A/G magnetic beads and washed twice in IP wash buffer I. (1% Triton, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), twice in IP wash buffer II (1% Triton, 0.1% SDS, 500 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), twice in IP wash buffer III. (0.25 M LiCl, 0.5% NP-40, 1mM EDTA, 20 mM Tris, pH 8.0, 0.5% NaDOC) and once in TE buffer (10 mM EDTA and 200 mM Tris, pH 8.0). DNA was eluted from the beads by vigorous shaking for 20-minutes in elution buffer (100mM NaHCO3, 1% SDS). DNA was de-crosslinked overnight at 65C and purified with MinElute PCR purification kit (Qiagen).
Sequencing ready libraries were generated using NEBNext ® Ultra™ II DNA Library Prep Kit for Illumina ® (New England Biolabs E7645). Libraries were quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and profiled using the D5000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on an Illumina sequencer to generate 25 million paired end 50-base pair reads per library.

treatment_protocol: DU145 and MDA-PCa-2b were treated with 100 nM SMARCA2_4.1 (SMARCA2/4 degrader) or DMSO for 24 hours before cells were harvested for ChIP-seq

value: prostate adenocarcinoma

tag: chip antibody

value: BD 610923 ChIP


title: Sample GB101-1

description:
Library name: GB101-1
Column name in TPM_Data.txt: GB101-1


title: PVN_D_D24_FR3AG_21Hr

description:
FR3AG_21h_rep4
FG3AG gene expression 21h


title: PVN_D_D25_FR3AG_21Hr

description:
FR3AG_21h_rep5
FG3AG gene expression 21h


title: P10_Casz1 CKO OHC-16

first: Zhiyong

last: Liu

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

data_processing:
Reads were mapped to the mouse reference genome (mm10) with high quality, using Hisat2 (v2.2.1) with default parameters.
Transcript Per Million (TPM) were calculated by StringTie  (v2.2.1) with default parameters.
Raw counts were calculated by featureCounts (v2.0.1) software.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for smartseq.

source_name: Cochlea

extract_protocol:
Cochlear samples were incubated in choline chloride solution containing 20 U/mL papain (Cat# LK003178, Worthington) and 100 U/mL DNase I (Cat# LK003172, Worthington) for 20 min at 37°C, and this was followed by digestion with a protease (Cat# P5147, Sigma; 1 mg/mL) and dispase (Cat# LS02104, Worthington; 1 mg/mL) for 20 min at 25°C. The components of the choline chloride solution contained 92 mM choline chloride, 2.5 mM KCl, 1.2 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 5 mM sodium ascorbate, 2 mM thiourea, 3 mM sodium pyruvate, 10 mM MgSO4.7H2O, 0.5 mM CaCl2.2H2O, and 12 mM N-acetyl-L-cysteine. Next, the post-digested cochlear samples were gently triturated using fire-polished glass Pasteur pipettes (13-678-20b; Fisher) with 4 different pore sizes (largest size the first, and smallest one the last). The picked endogenous IHCs and iOHCs were immediately subjected to reverse-transcription and cDNA amplification using a Smart-Seq HT kit (Cat# 634437, Takara).
Smart-Seq HT kit (Cat# 634437, Takara) was used to generate full-length cDNA. The cDNAs (1 ng each) were tagmented using a TruePrep DNA Library Prep Kit V2 for Illumina (Cat# TD503-02, Vazyme) and a TruePrep Index Kit V2 for Illumina (Cat# TD202, Vazyme).

value: Cochlea


title: DU145, SMARCA2/4 degrader, FOSL1

description: DNA-seq

value: ThermoFisher PA5-66880


title: P10_Casz1 CKO OHC-17


title: C4_FOXA1(M253K)_Flag_siNC_Rep1 (CUT TAG)

description: Library name: sample45


title: P10_Casz1 CKO OHC-15


title: AML12, Scr, rep4

value: WT


title: C4_FOXA1(D226G)_Flag_siKMT2D_Rep2 (CUT TAG)

description: Library name: sample44


title: DU145, SMARCA2/4 degrader, SMARCA4

description: DNA-seq

value: Abcam ab110641


title: PVN_D_D20_FG4G7_21Hr

description:
FG4G7_21h_rep5
FG4G7 gene expression 21 h

value: FG4G7 transfection


title: P10_Casz1 CKO OHC-14


title: Sample GB104

description:
Library name: GB104
Column name in TPM_Data.txt: GB104

value: Glioblastoma Fresh Tissue


title: LNCaP_H3K27ac_siKMT2D_Rep1 (CUT TAG)

description: Library name: sample39

source_name: LNCaP

value: LNCaP


title: DU145, SMARCA2/4 degrader, input

description: DNA-seq


title: PVN_D_D21_FR3AG_21Hr

description:
FR3AG_21h_rep1
FG3AG gene expression 21h


title: PVN_D_D19_FG4G7_21Hr

description:
FG4G7_21h_rep4
FG4G7 gene expression 21 h


title: LNCaP_H3K27ac_siNC_Rep2 (CUT TAG)

description: Library name: sample38


title: PVN_D_D18_FG4G7_21Hr

description:
FG4G7_21h_rep3
FG4G7 gene expression 21 h


title: P10_Casz1 CKO OHC-13


title: DU145, DMSO, TEAD1

description: DNA-seq


title: LNCaP_H3K27ac_siNC_Rep1 (CUT TAG)

description: Library name: sample37


title: PVN_D_D22_FR3AG_21Hr

description:
FR3AG_21h_rep2
FG3AG gene expression 21h


title: LNCaP_H3K4me1_siKMT2D_Rep2 (CUT TAG)

description: Library name: sample36


title: P10_Casz1 CKO OHC-12


title: DU145, DMSO, FOSL1

description: DNA-seq


title: DU145, DMSO, SMARCA4

description: DNA-seq


title: P10_Casz1 CKO OHC-11


title: P10_Casz1 CKO OHC-10


title: LNCaP_H3K4me1_siKMT2D_Rep1 (CUT TAG)

description: Library name: sample35


title: DU145, DMSO, input

description: DNA-seq


title: P10_Casz1 CKO OHC-9


title: PDAC-p5

first: Anirban

last: Maitra

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

description: FFPE Visium ST sequencing

data_processing:
The demultiplexed reads were processed using Space Ranger (v.1.3.1) from 10x Genomics, aligned to the GRCh38 reference genome with default parameters. The resulting unique molecular identifier (UMI) count matrices were then analysed using Seurat (v.4.3) 47 in the R platform (v.4.2.0). Detailed quality control (QC) metrics were generated and evaluated, and spots were carefully filtered to obtain high-quality SRT data for downstream analyses. Briefly, for basic quality filtering, spots with low complexity libraries (UMI count below 100) were filtered out to eliminate low-quality spots. Additionally, spots located within acellular stromal interfaces were excluded and samples with more than 40% low-quality spots were also excluded from subsequent analyses.
Assembly: GRCh38 reference genome
Supplementary files format and content: spatial.tar.gz : Compressed tar archives include processed output from Space Ranger with spatial information
Supplementary files format and content: filtered_feature_bc_matrix.h5 : Filtered feature-barcode matrices in HDF5 format
Library strategy: Spatial Transcriptomics

source_name: PDAC

extract_protocol:
Samples were flash frozen in liquid nitrogen, cryo-sectioned and H&E stained. After sectioning onto the Visium slides, sample processing was performed as described in the Visium 10x Genomics protocol for fresh-frozen tissue samples (15 minutes were used for permealization time).
Library preparation was performed as described in  the Visium Spatial Gene Expression Reagent Kit (PN-1000189), Library Construction Kit (PN-1000196), and Dual Index Plate TT Set A (PN-3000431) as described in the Visium protocol for fresh frozen tissue samples (CG000239).

value: PDAC

tag: age

value: Female

value: No treatment


title: PVN_D_D17_FG4G7_21Hr

description:
FG4G7_21h_rep2
FG4G7 gene expression 21 h


title: P10_Casz1 CKO OHC-8


title: PVN_D_D16_FG4G7_21Hr

description:
FG4G7_21h_rep1
FG4G7 gene expression 21 h


title: PVN_D_D15_F3F5G_21Hr

description:
F3F5G_21h_rep5
F3F5G gene expression 21 h

value: F3F5G transfection


title: PDAC-p4

description: FFPE Visium ST sequencing

value: Male


title: P10_Casz1 CKO OHC-7


title: LNCaP_FOXA1_siKMT2D_Rep2 (CUT TAG)

description: Library name: sample32

value: prostate cancer cell line


title: PDAC-p3

description: FFPE Visium ST sequencing


title: LNCaP_H3K4me1_siNC_Rep2 (CUT TAG)

description: Library name: sample34

value: siNC


title: P10_Casz1 CKO OHC-6


title: LNCaP_FOXA1_siKMT2D_Rep1 (CUT TAG)

description: Library name: sample31


title: LNCaP_H3K27ac_siKMT2D_Rep2 (CUT TAG)

description: Library name: sample40


title: PDAC-p2

description: FFPE Visium ST sequencing


title: PVN_D_D13_F3F5G_21Hr

description:
F3F5G_21h_rep3
F3F5G gene expression 21 h


title: PVN_D_D14_F3F5G_21Hr

description:
F3F5G_21h_rep4
F3F5G gene expression 21 h


title: LNCaP_FOXA1_siNC_Rep2 (CUT TAG)

description: Library name: sample30


title: PVN_D_D11_F3F5G_21Hr

description:
F3F5G_21h_rep1
F3F5G gene expression 21 h


title: PDAC-p1

description: FFPE Visium ST sequencing


title: P10_Casz1 CKO OHC-4


title: LNCaP_FOXA1_siNC_Rep1 (CUT TAG)

description: Library name: sample29


title: PVN_D_D12_F3F5G_21Hr

description:
F3F5G_21h_rep2
F3F5G gene expression 21 h


title: LNCaP_H3K4me1_siNC_Rep1 (CUT TAG)

description: Library name: sample33


title: C4_H3K27ac_siKMT2D_Rep2 (CUT TAG)

description: Library name: sample28


title: P10_Casz1 CKO OHC-5


title: HEK293T_IgG

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

country: France

institute: I.G.B.M.C. - Institut de génétique et de biologie moléculaire et cellulaire

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Peaks were called using MACS 2.1.1 with the "--broad" parameter for H3K27ac and the “-f BAMPE” parameter for TFE3.
Assembly: hg19
Supplementary files format and content: Peak coordinates called by MACS2 in BED format (chromosome/start/end/name/score).
Library strategy: CUT&Tag

source_name: Embryonic Kidney

growth_protocol: The embryonic kidney HEK293T cell line and the derived lines expressing ectopic TFE3 fusions cells were grown in DMEM medium supplemented with glucose (1g/L).

extract_protocol:
Cut&Tag libraries were prepared using the Illumina Nextera adaptors provided by the Active Motif Cut&Tag kit following the manufacturer guidelines.
Cells were plated in 10 cm petri-dish for 48h and harvested using CellStripper solution and washed 2 times in PBS 1X. Cells were counted using Trypan blue and the Countess® II Automated Cell counter (Invitrogen). 500000 cells were used for each native Cut&Tag performed using the Active motif Cut&Tag kit (ref. 53160) following the manufacturer provided protocol.

treatment_protocol: TFE3, NONO-TFE3 and PRCC-TFE3 cDNAs were synthesized by GenScript and subsequently cloned into the all-in-one doxycycline inducible lentiviral pCW57-GFP-P2A-MCS vector (Addgene plasmid #71783) in place of GFP. Lentiviral particles were produced to express independently each of the 3 genes of interest or GFP control by transfection of HEK293T cells with packaging plasmids. Lentiviral particles were purified by filtration and ultracentrifugation and resuspended in PBS. After titration, HEK293T cells were infected at MOI of 1 using polybrene and selected by puromycin addition to the media (1µg/mL). After establishment of the stable cell lines, expression of the proteins of interest was induced by adding of Doxycycline (Dox) in the medium (10µg/mL).

value: Embryonic Kidney

tag: antibody

value: IgG (Abcam 171870)

tag: chip-seq/c&t condition

value: Native


title: C4_H3K27ac_siKMT2D_Rep1 (CUT TAG)

description: Library name: sample27


title: PVN_D_D9_WT_FG_21Hr

description:
WT_FG_21h_rep4
WT FG gene expression 21 h

value: WT FG transfection


title: P10_Casz1 CKO OHC-3

value: Cochlea


title: HEK293T-GFP_TFE3

value: TFE3 (Abcam ab93808)


title: C4_H3K27ac_siNC_Rep2 (CUT TAG)

description: Library name: sample26


title: PVN_D_D10_WT_FG_21Hr

description:
WT_FG_21h_rep5
WT FG gene expression 21 h


title: P10_Casz1 CKO OHC-1


title: HEK293T-PRCC-TFE3_TFE3


title: PVN_D_D8_WT_FG_21Hr

description:
WT_FG_21h_rep3
WT FG gene expression 21 h


title: P10_WT_OHC-48


title: HEK293T-NONO-TFE3_TFE3


title: HEK293T-TFE3_TFE3


title: P10_WT_OHC-47


title: C4_H3K27ac_siNC_Rep1 (CUT TAG)

description: Library name: sample25


title: C4_H3K4me1_siKMT2D_Rep2 (CUT TAG)

description: Library name: sample24


title: UOK109_TFE3_ab93808

source_name: Adult Kidney

growth_protocol: Cells were grown in DMEM medium supplemented with glucose (4.5g/L), 10% heat-inactivated Foetal Calf Serum (FCS), Non-essential amino acid (AANE) and 1% penicillin/streptomycin.

value: Adult Kidney


title: PVN_D_D6_WT_FG_21Hr

description:
WT_FG_21h_rep1
WT FG gene expression 21 h


title: C4_H3K4me1_siKMT2D_Rep1 (CUT TAG)

description: Library name: sample23


title: UOK146_TFE3

value: TFE3 (Sigma HPA-023881)


title: C4_H3K4me1_siNC_Rep2 (CUT TAG)

description: Library name: sample22


title: PVN_D_D5_Control_21Hr

description:
No_transfection_control_rep5
Control gene expression 21h

value: Control


title: P10_WT_OHC-45


title: PVN_D_D3_Control_21Hr

description:
No_transfection_control_rep3
Control gene expression 21h


title: PVN_D_D4_Control_21Hr

description:
No_transfection_control_rep4
Control gene expression 21h


title: UOK120_TFE3


title: P10_Casz1 CKO OHC-2


title: TF1_TFE3


title: C4_H3K4me1_siNC_Rep1 (CUT TAG)

description: Library name: sample21


title: C4_FOXA1_siKMT2D_Rep2 (CUT TAG)

description: Library name: sample20


title: PVN_D_D1_Control_21Hr

description:
No_transfection_control_rep1
Control gene expression 21h


title: P10_WT_OHC-43


title: C4_FOXA1_siKMT2D_Rep1 (CUT TAG)

description: Library name: sample19


title: UOK109_TFE3_HPA-023881


title: PVN_D_D7_WT_FG_21Hr

description:
WT_FG_21h_rep2
WT FG gene expression 21 h


title: PVN_D_D2_Control_21Hr

description:
No_transfection_control_rep2
Control gene expression 21h


title: UOK109_IgG


title: C4_FOXA1_siNC_Rep2 (CUT TAG)

description: Library name: sample18


title: P10_WT_OHC-42


title: P10_WT_OHC-46


title: P10_WT_OHC-41


title: Non-tumor liver tissue, Salsalate + Lenvatinib gavaged, biol rep 6

city: Hamilton

first: Russta

last: Fayyazi

state: ON

address: 1280 Main St W

country: Canada

institute: McMaster University

description: Library name: Mouse Combination 6

data_processing:
Raw sequencing files imported into Galaxy (usegalaxy.org) for quality control and processing steps
FastQC tool used to check read quality
Cutadapt tool used to trim adaptor sequences and low quality reads
Remaining reads were mapped reference genome with HISAT2 tool. Cell data was mapped to the hg38 reference human genome. Mouse data was mapped to the mm10 reference mouse genome.
Counts were quantified with the featureCounts tool and imported into R for gene expression analyses
Counts data were VST-normalized in R using the DESeq2 package
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text file includes VST-normalized counts for each sample (in vitro cell data)
Supplementary files format and content: tab-delimited text file includes VST-normalized counts for each sample (in vivo mouse data)

source_name: non-tumor liver

extract_protocol:
RNA was isolated from cells or liver tissue using TRIzolTM (Life Technologies, Grand Island, USA) and purified using RNeasy kit (QIAGEN, Germantown, USA Cat#74106) according manufacturers instruction.
For both cells and liver tissue, RNA-Sequencing RNA sample quality was first assessed using Agilent 2100 Bioanalyzer G2938C with the Aligent RNA6000 Nano Kit (Agilent; Santa Clara, CA, USA). Next, the NEBNext Poly(A) mRNA Isolation Module (NEB, Ipswich, MA, USA) was used for mRNA enrichment, followed by NEBNext® Ultra™ II Directional RNA library kit (NEB, Ipswich, MA, USA) library preparation. Cell libraries were sequenced on an Illumia HiSeq 1500 machine (HiSeq Rapid v2 flow cell, 50bp reads yielding 400M clusters). Mouse libraries were sequenced on an Illumina NextSeq 2000 machine (P2, 2x50 bp).

value: non-tumor liver

tag: cell/mouse line

value: C57BL/6J, Male

value: all non-tumor liver

tag: condition

value: Combination-treated

tag: treatment dose

value: Salsalate 300mg/kg/day + Lenvatinib Mesylate 2.5mg/kg/day

tag: age at_sacrifice_(mice)

value: 38 weeks

tag: ccl4 model_diet_(mice)

tag: ccl4 model_dosage_(mice)

value: (0.32 μg)/g of body weight  1x/wk


title: Set2_B63_FG_21hr

description:
FG_transfection_21h_D
Gene expression at 21h

data_processing: Background correction was carried out on microarray samples using the maximum likelihood estimation for the normal-exponential convolution model, with an offset of 50, as implemented in Bioconductor's limma package. Samples were then normalized using quantile normalization and outliers were detected using intensity distribution and a boxplot graph followed by hierarchical clustering and PCA analysis of expression profiles using the MVA package.

extract_protocol: Total RNA was extracted using Trizol and quantified using the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. mRNAs were converted to cDNAs using AffinityScript reverse transcriptase and oligo-dT promoter primer. The second strand cDNA synthesiswas performed with AffinityScript reverse transcriptase. Cy3 labeled cRNA was synthesized with T7 RNA polymerase mix. cRNAs were purified using RNeasy mini kit. cRNA quantitiy was determined using NanoDrop ND-1000 UV-VIS spectrophotometer and cRNAs were hybridized onto Agilent 4 x 44K human genome microarray slides.

treatment_protocol: For each time-point ten 6-well plates were used, five of them were transfected with HeV genes F, G, and FG combination for 6h, 12h, and 21h time point. Remaining five 6-well plates were used as uninfected controls.

tag: treatment

value: FG transfection


title: P10_WT_OHC-40

tag: tissue


title: P10_WT_OHC-44


title: Set2_B62_FG_21hr

description:
FG_transfection_21h_C
Gene expression at 21h

tag: cell line

tag: time


title: P10_WT_OHC-39


title: Non-tumor liver tissue, Salsalate + Lenvatinib gavaged, biol rep 4

description: Library name: Mouse Combination 4

tag: cell type


title: P10_WT_OHC-38


title: C4_FOXA1_siNC_Rep1 (CUT TAG)

description: Library name: sample17

value: prostate cancer cell line

value: siNC


title: Set2_B61_FG_21hr

description:
FG_transfection_21h_B
Gene expression at 21h


title: Non-tumor liver tissue, Salsalate + Lenvatinib gavaged, biol rep 3

description: Library name: Mouse Combination 3


title: Set2_B59_G_21hr

description:
G_transfection_21h_E
Gene expression at 21h

value: G transfection


title: Non-tumor liver tissue, Salsalate + Lenvatinib gavaged, biol rep 5

description: Library name: Mouse Combination 5


title: Non-tumor liver tissue, Salsalate + Lenvatinib gavaged, biol rep 2

description: Library name: Mouse Combination 2


title: Set2_B64_FG_21hr

description:
FG_transfection_21h_E
Gene expression at 21h


title: C4_AR_siKMT2D_Rep2 (Input)

description: Library name: sample16

data_processing:
The ChIP-Seq reads were mapped to the hg38 human genome using bowtie2 (v2.2.5) with default parameters. Samtools (v1.6) was used to convert sam files to bam files. MACS2 (v2.2.6) was used to call peaks. Homer (v4.11) was used to perform motif analysis. Integrative Genomics Viewer (IGV) (v2.16.2) was used to visualize peaks of all samples. The CUT&Tag reads were mapped to the hg38 human genome using bowtie2 (v2.2.5) with parameters “-X 2000 --very-sensitive-local -no-discordant”. PCR duplicated reads were removed by sambamba (v0.6.6). SAM files were converted to BAM files using samtools (v1.6). MACS2 (v2.2.6) was used to call peaks with -q 0.05. Deeptools (v3.5.2) was used to convert BAM files to Bigwig files and generate the profile plot and heatmap. Homer (v4.11) was used to perform motif analysis. CUT&Tag signal tracks were visualized by IGV (v2.16.2). R package EdgeR (3.22.5) was used to perform differential peaks analysis.
Assembly: hg38
Supplementary files format and content: Library normalized bigWig files were provided for all samples


title: C4_AR_siKMT2D_Rep2 (ChIP)

description: Library name: sample15


title: C4_AR_siNC_Rep2 (Input)

description: Library name: sample12


title: Set2_B58_G_21hr

description:
G_transfection_21h_D
Gene expression at 21h


title: P10_WT_OHC-35


title: C4_AR_siNC_Rep2 (ChIP)

description: Library name: sample11


title: P10_WT_OHC-36


title: Non-tumor liver tissue, Lenvatinib gavaged, biol rep 6

description: Library name: Mouse Lenvatinib 6

value: Lenvatinib-treated

value: Lenvatinib Mesylate 2.5mg/kg/day


title: Non-tumor liver tissue, Salsalate + Lenvatinib gavaged, biol rep 1

description: Library name: Mouse Combination 1


title: Non-tumor liver tissue, Lenvatinib gavaged, biol rep 5

description: Library name: Mouse Lenvatinib 5


title: C4_AR_siNC_Rep1 (Input)

description: Library name: sample10


title: Set2_B57_G_21hr

description:
G_transfection_21h_C
Gene expression at 21h


title: C4_AR_siKMT2D_Rep1 (Input)

description: Library name: sample14


title: Set2_B56_G_21hr

description:
G_transfection_21h_B
Gene expression at 21h


title: Set2_B54_F_21hr

description:
F_transfection_21h_E
Gene expression at 21h

value: F transfection


title: Set2_B55_G_21hr

description:
G_transfection_21h_A
Gene expression at 21h


title: Set2_B60_FG_21hr

description:
FG_transfection_21h_A
Gene expression at 21h


title: P10_WT_OHC-37

value: Cochlea


title: Non-tumor liver tissue, Lenvatinib gavaged, biol rep 4

description: Library name: Mouse Lenvatinib 4


title: P10_WT_OHC-32


title: LNCaP_AR_siKMT2D_Rep2 (Input)

description: Library name: sample8

value: LNCaP


title: Non-tumor liver tissue, Lenvatinib gavaged, biol rep 3

description: Library name: Mouse Lenvatinib 3


title: P10_WT_OHC-31


title: Non-tumor liver tissue, Lenvatinib gavaged, biol rep 2

description: Library name: Mouse Lenvatinib 2


title: LNCaP_AR_siKMT2D_Rep2 (ChIP)

description: Library name: sample7


title: P10_WT_OHC-30


title: Non-tumor liver tissue, Lenvatinib gavaged, biol rep 1

description: Library name: Mouse Lenvatinib 1


title: P10_WT_OHC-29


title: LNCaP_AR_siKMT2D_Rep1 (Input)

description: Library name: sample6


title: Set2_B53_F_21hr

description:
F_transfection_21h_D
Gene expression at 21h


title: P10_WT_OHC-34


title: Non-tumor liver tissue, Salsalate gavaged, biol rep 6

description: Library name: Mouse Salsalate 6

value: Salsalate-treated

value: Salsalate 300mg/kg/day


title: Set2_B52_F_21hr

description:
F_transfection_21h_C
Gene expression at 21h


title: P10_WT_OHC-33


title: LNCaP_AR_siKMT2D_Rep1 (ChIP)

description: Library name: sample5


title: Set2_B50_F_21hr

description:
F_transfection_21h_A
Gene expression at 21h


title: Set2_B51_F_21hr

description:
F_transfection_21h_B
Gene expression at 21h


title: C4_AR_siNC_Rep1 (ChIP)

description: Library name: sample9


title: LNCaP_AR_siNC_Rep2 (Input)

description: Library name: sample4


title: Non-tumor liver tissue, Salsalate gavaged, biol rep 4

description: Library name: Mouse Salsalate 4

value: non-tumor liver

value: C57BL/6J, Male


title: Non-tumor liver tissue, Salsalate gavaged, biol rep 5

description: Library name: Mouse Salsalate 5

value: all non-tumor liver


title: P10_WT_OHC-27


title: LNCaP_AR_siNC_Rep2 (ChIP)

description: Library name: sample3


title: P10_WT_OHC-26


title: Non-tumor liver tissue, Salsalate gavaged, biol rep 3

description: Library name: Mouse Salsalate 3


title: LNCaP_AR_siNC_Rep1 (Input)

description: Library name: sample2


title: P10_WT_OHC-25


title: Set2_B49_Control_21hr

description:
No_transfection_control_21h_E
Gene expression at 21h

value: control


title: Set2_B48_Control_21hr

description:
No_transfection_control_21h_D
Gene expression at 21h


title: Non-tumor liver tissue, Salsalate gavaged, biol rep 2

description: Library name: Mouse Salsalate 2

value: 38 weeks


title: P10_WT_OHC-24


title: LNCaP_AR_siNC_Rep1 (ChIP)

description: Library name: sample1


title: Set2_B47_Control_21hr

description:
No_transfection_control_21h_C
Gene expression at 21h


title: Set2_B46_Control_21hr

description:
No_transfection_control_21h_B
Gene expression at 21h


title: Non-tumor liver tissue, vehicle gavaged, biol rep 6

description: Library name: Mouse Control 6

value: vehicle control

value: (0.32 μg)/g of body weight  1x/wk


title: Non-tumor liver tissue, Salsalate gavaged, biol rep 1

description: Library name: Mouse Salsalate 1


title: C4_CSS_siKMT2D_Rep1

description:
Library name: sample15
Column name in C4_gene_count.txt:CSS_SI1

data_processing:
RNA-seq reads were mapped to the human reference genome (hg38) human genome assembly using HISAT2 (v2.0.5) with default parameters.
Featurecounts (v1.5.0-p3) was used for counting the read numbers.
Assembly: hg38
Supplementary files format and content: tab-deliminated text files include raw gene counts

growth_protocol: LNCaP, C4-2 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was prepared using TRIzol reagent (Life Technologies) following manufacturer’s protocol
Library preparations were performed using the NEBNext Ultra RNA Library Prep Kit for illumina following manufacturer’s protocol

value: prostate cancer cell line


title: C4_AR_siKMT2D_Rep1 (ChIP)

description: Library name: sample13


title: P10_WT_OHC-28


title: P10_WT_OHC-22


title: Non-tumor liver tissue, vehicle gavaged, biol rep 5

description: Library name: Mouse Control 5


title: C4_CSS_siNC_Rep2

description:
Library name: sample14
Column name in C4_gene_count.txt:CSS_NC2

value: siNC


title: Set2_B45_Control_21hr

description:
No_transfection_control_21h_A
Gene expression at 21h


title: Set2_B43_FG_12hr

description:
FG_transfection_12h_D
Gene expression at 12h

value: FG transfection


title: C4_CSS_siNC_Rep1

description:
Library name: sample13
Column name in C4_gene_count.txt:CSS_NC1


title: P10_WT_OHC-21


title: Non-tumor liver tissue, vehicle gavaged, biol rep 4

description: Library name: Mouse Control 4


title: Set2_B42_FG_12hr

description:
FG_transfection_12h_C
Gene expression at 12h


title: Set2_B44_FG_12hr

description:
FG_transfection_12h_E
Gene expression at 12h


title: P10_WT_OHC-20


title: Non-tumor liver tissue, vehicle gavaged, biol rep 3

description: Library name: Mouse Control 3


title: P10_WT_OHC-19


title: C4_CSS_siKMT2D_Rep2

description:
Library name: sample16
Column name in C4_gene_count.txt:CSS_SI2


title: Set2_B41_FG_12hr

description:
FG_transfection_12h_B
Gene expression at 12h


title: C4_DHT_siKMT2D_Rep1

description:
Library name: sample11
Column name in C4_gene_count.txt:DHT_SI1


title: C4_DHT_siNC_Rep2

description:
Library name: sample10
Column name in C4_gene_count.txt:DHT_NC2


title: P10_WT_OHC-18


title: Set2_B40_FG_12hr

description:
FG_transfection_12h_A
Gene expression at 12h


title: P10_WT_OHC-23


title: Set2_B39_G_12hr

description:
G_transfection_12h_E
Gene expression at 12h

value: G transfection


title: P10_WT_OHC-17


title: Naïve spleen CD4 cells [VDJ_mTCR]

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

institute: Tulane University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 or Cell Ranger V(D)J v6.0.1.
Assembly: mm10-3.0.0. for single cell VDJ_GEX. vdj_GRCm38-5.0.0 for single cell VDJ_mTCR.
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-seq

source_name: Spleen

extract_protocol:
The OVA+ cells were enriched by OVA-PE tetramer-pulldown. Splenic CD4+ T cells were enriched by CD4 magnetic beads(MIltenyi). mRNA was extracted from lung single cell suspension using the barcoded Single Cell VDJ 5' Gel Beads onto 10X Chromium Next GEM Chip K.
Library construction was performed according to 10x Genomics Chromium™ Single Cell 5' VDJ v2 enrichment and gene expression.
single cell 5' gene expression and single cell V(D)J dual index libraries

value: Spleen

value: CD4+ T cells

tag: genotype

value: 14 weeks old at the time of euthanasia


title: P10_WT_OHC-16

value: Cochlea


title: day 90 OVA+ cells, replicate 2, scRNAseq [VDJ_mTCR]

description: 10x Genomics

source_name: Lung

value: Lung

value: 10 weeks old at the time of prime immunization


title: Set2_B38_G_12hr

description:
G_transfection_12h_D
Gene expression at 12h


title: P10_WT_OHC-15


title: C4_DHT_siNC_Rep1

description:
Library name: sample9
Column name in C4_gene_count.txt:DHT_NC1


title: LNCaP_CSS_siKMT2D_Rep2

description:
Library name: sample8
Column name in LNCaP_gene_count.txt: LNCaP_CS2

value: LNCaP


title: C4_DHT_siKMT2D_Rep2

description:
Library name: sample12
Column name in C4_gene_count.txt:DHT_SI2


title: LNCaP_CSS_siKMT2D_Rep1

description:
Library name: sample7
Column name in LNCaP_gene_count.txt: LNCaP_CS1


title: P10_WT_OHC-14


title: Set2_B37_G_12hr

description:
G_transfection_12h_C
Gene expression at 12h


title: day 90 OVA+ cells, replicate 1, scRNAseq [VDJ_mTCR]

description: 10x Genomics


title: Non-tumor liver tissue, vehicle gavaged, biol rep 2

description: Library name: Mouse Control 2

value: non-tumor liver

value: C57BL/6J, Male


title: Naïve spleen CD4 cells [VDJ_GEX]

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 or Cell Ranger V(D)J v6.0.1.
Assembly: mm10-3.0.0. for single cell VDJ_GEX. vdj_GRCm38-5.0.0 for single cell VDJ_mTCR.
Supplementary files format and content: Tab-separated values files and matrix files


title: day 184 OVA+ cells, replicate 2, scRNAseq [VDJ_GEX]

description: 10x Genomics


title: LNCaP_CSS_siNC_Rep1

description:
Library name: sample5
Column name in LNCaP_gene_count.txt: LNCaP_CN1


title: LNCaP_CSS_siNC_Rep2

description:
Library name: sample6
Column name in LNCaP_gene_count.txt: LNCaP_CN2


title: Non-tumor liver tissue, vehicle gavaged, biol rep 1

description: Library name: Mouse Control 1

value: all non-tumor liver


title: P10_WT_OHC-12


title: Set2_B35_G_12hr

description:
G_transfection_12h_A
Gene expression at 12h


title: day 184 OVA+ cells, replicate 1, scRNAseq [VDJ_GEX]

description: 10x Genomics


title: day 90 OVA+ cells, replicate 2, scRNAseq [VDJ_GEX]

description: 10x Genomics


title: P10_WT_OHC-10


title: LNCaP_DHT_siNC_Rep2

description:
Library name: sample2
Column name in LNCaP_gene_count.txt: LNCaP_DN2


title: LNCaP_DHT_siKMT2D_Rep1

description:
Library name: sample3
Column name in LNCaP_gene_count.txt: LNCaP_DS1


title: P10_WT_OHC-9


title: day 30 OVA+ cells, replicate 2, scRNAseq [VDJ_GEX]

description: 10x Genomics


title: Set2_B31_F_12hr

description:
F_transfection_12h_B
Gene expression at 12h

value: F transfection


title: Set2_B33_F_12hr

description:
F_transfection_12h_D
Gene expression at 12h


title: day 90 OVA+ cells, replicate 1, scRNAseq [VDJ_GEX]

description: 10x Genomics


title: LNCaP_DHT_siNC_Rep1

description:
Library name: sample1
Column name in LNCaP_gene_count.txt: LNCaP_DN1


title: Set2_B32_F_12hr

description:
F_transfection_12h_C
Gene expression at 12h


title: Set2_B36_G_12hr

description:
G_transfection_12h_B
Gene expression at 12h


title: Set2_B30_F_12hr

description:
F_transfection_12h_A
Gene expression at 12h


title: P10_WT_OHC-7


title: Set2_B34_F_12hr

description:
F_transfection_12h_E
Gene expression at 12h


title: LNCaP_DHT_siKMT2D_Rep2

description:
Library name: sample4
Column name in LNCaP_gene_count.txt: LNCaP_DS2


title: LNCaP_siKMT2D_Rep1_ATAC

description: Library name: sample67

data_processing:
The Fastp tool (v.0.22.0) was used to obtain quality control statistics of the samples.  The ATAC-Seq clean reads were mapped to the hg38 human genome using bowtie2 (v2.2.5) with parameters “-X 2000 --very-sensitive-local -no-discordant”. PCR duplicated reads were removed by sambamba (v0.6.6). SAM files were converted to BAM files using samtools (v1.6). MACS2 (v2.2.6) was used to call peaks with -q 0.05 --extsize 200 –shift 100. Deeptools (v3.5.2) was used to convert BAM files to Bigwig files and generate the profile plot and heatmap. Homer (v4.11) was used to perform motif analysis. ATAC-Seq signal tracks were visualized by IGV (v2.16.2). R package EdgeR (3.22.5) was used to perform differential peaks analysis.
Assembly: hg38
Supplementary files format and content: Library normalized bigWig files were provided for all samples

extract_protocol:
The assay for transposase-accessible chromatin with sequencing (ATAC-seq) samples were prepared in duplicates using Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme Biotech Co. Ltd., TD711) according to the manufacturer’s instructions.
the tagmented DNA was purified by magnetic bead. Libraries were amplified and pair-end reads were sequenced using and Illumina NovaSeq 6000 platform in PE150 mode.

treatment_protocol: knockdown of KMT2D by siRNA


title: Set2_B29_Control_12hr

description:
No_transfection_control_12h_E
Gene expression at 12h

value: control


title: LNCaP_siKMT2D_Rep2_ATAC

description: Library name: sample68


title: COLD_Rep2 RNA-seq

city: Nanjing

first: huang

middle: ran

last: ran

address: weigang 1

institute: Nanjing Agricultural College

data_processing:
Sequenced reads were trimmed for adaptor sequences using fastp
Clean reads were aligned to the B73 reference genome using Hisat2
The number of reads mapped to each gene was counted using FeatureCounts
Assembly: B73 RefGen_v4
Supplementary files format and content: counts

organism: Zea mays

source_name: seedling

growth_protocol: Uniformly pre-germinated seeds of Maize (Zea mays L. “B73”) were transferred to pots with soil and grown in a growth chamber with 16h light and 8h dark cycle at 25-28℃ for 9 days. Then the plants were equally divided into two halves, one for continuing to grow under the normal conditions, another one for cold treatment (COLD) at 4℃ for 24h.

extract_protocol: The whole seedlings of CK or COLD from 10 individual 10-day-old plants were collected using liquid nitrogen and stored at -80℃ for later use.

value: seedling

value: WT

value: COLD


title: Set2_B28_Control_12hr

description:
No_transfection_control_12h_D
Gene expression at 12h


title: COLD_Rep1 RNA-seq


title: P10_WT_OHC-11


title: LNCaP_siNC_Rep2_ATAC

description: Library name: sample66

value: prostate cancer cell line

value: siNC


title: Set2_B27_Control_12hr

description:
No_transfection_control_12h_C
Gene expression at 12h


title: Set2_B26_Control_12hr

description:
No_transfection_control_12h_B
Gene expression at 12h


title: LNCaP_siNC_Rep1_ATAC

description: Library name: sample65


title: day 30 OVA+ cells, replicate 1, scRNAseq [VDJ_GEX]

description: 10x Genomics


title: P10_WT_OHC-8


title: CK_Rep2 RNA-seq


title: CK_Rep1 RNA-seq


title: P10_WT_OHC-13


title: P10_WT_OHC-4


title: C4_siKMT2D_Rep1_ATAC

description: Library name: sample63


title: P10_WT_OHC-6


title: C4_siKMT2D_Rep2_ATAC

description: Library name: sample64


title: P10_WT_OHC-2


title: P10_WT_OHC-3


title: P10_WT_OHC-1


title: C4_siNC_Rep2_ATAC

description: Library name: sample62


title: C4_siNC_Rep1_ATAC

description: Library name: sample61


title: CK light MNase-seq

data_processing:
Sequenced reads were trimmed for adaptor sequences using fastp
MNase-seq clean reads without adaptor sequences were aligned to the maize B73 v4 genome using bowtie2.3.2 with default parameters.
Nucleosome positions and changes were identified using the dpos function of DANPOS2.bigwig files were generated using deeptools bamCoverage with parameters --centerReads -bs 20 --smoothLength 60 --normalizeUsing RPKM and were transformed to wig files using bigWigtoWig software
Assembly: B73 RefGen_v4
Supplementary files format and content: bw

tag: mnase

value: light


title: Set2_B24_FG_6hr

description:
FG_transfection_6h_D
Gene expression at 6h

value: FG transfection


title: Set2_B23_FG_6hr

description:
FG_transfection_6h_C
Gene expression at 6h


title: P10_WT_OHC-5


title: Hematopoietic sample, HTO

first: Matthew

last: Greenblatt

address: 1161 York Ave APT 1a

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICAL COLLEGE

library_source: other

data_processing:
Primary processing of rawATACsequencing data from multiplexed sample libraries was done through the standard Cellranger pipeline (10x Genomics), aligning raw reads to mm10 and generating a fragments.tsv file.
Rawsequencing data for protein and hashtag expression were processed through kallisto bustools (Pachter lab) to create count matrices for antibody derived tags.
Mitochondrial DNA variants were genotyped using the mgatk package v0.6.1
Assembly: mm10
Supplementary files format and content: cellranger-atac output files: filtered_peak_bc_matrix.h5, fragments.tsv.gz, singlecell.csv.gz
Supplementary files format and content: mgatk output files: A.txt.gz, C.txt.gz, G.txt.gz, T.txt.gz, depthTable.txt.gz

molecule: protein

source_name: Femur

extract_protocol:
3-month-old PolGD257A/D257A mouse femurs were extracted and subjected to both mechanical and enzymatic digestion. Cells were co-stained with both FACS antibodies and CITE-seq antibodies and then sorted using a FACS machine for single cell ATAC seq. All skeletal cell population obtained from three mice were kept discrete to run on three individual lanes for sequencing (10X Genomics). Sorted CD45+ hematopoietic cells were polled together to be run on one lane and therefore, hashing was performed to retain the identity of the mouse specimens. Sorted cells were fixed with 1% Paraformaldehyde and cells were gently lyzed (10mM tris-HCl; pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 1% BSA) and resuspended in 1X Nuclei buffer (10X Genomics) prior to be subjected to single cell sequencing optimized for mitochondrial DNA capture.
The library was prepared using the ASAP-seq ptotocol , sequenced with NovaSeq 6000, 2X100 bp.
scATAC-seq targeting mitochondrial DNA

value: Femur

tag: library type

value: HTO

value: Hematopoietic

tag: strain


title: COLD Medium MNase-seq

value: medium


title: CK Medium MNase-seq


title: Set2_B20_G_6hr

first: Hector

last: Aguilar-Carreno

address: T8016A Veterinary Research Tower

institute: Cornell University

description:
G_transfection_6h_E
Gene expression at 6h

value: G transfection


title: Set2_B21_FG_6hr

description:
FG_transfection_6h_A
Gene expression at 6h


title: Hematopoietic sample, ADT

value: ADT


title: Sigma16HBE_2

city: Boston

first: Peter

last: Castaldi

state: Massachusetts

address: 181 Longwood Avenue

department: Channing Division of Network Medicine

institute: Brigham and Women's Hospital

description: Library name: Sigma16HBE_2

data_processing:
Read quality and trimming was performed with Trim Galore 0.6.7 (cutadapt 4.6) with default parameter values.
For gene and isoform level quantification, isoform counts were estimated with Salmon version 1.10.11 using default parameters and using the GENCODE version 45 GTF.
Assembly: Hg38, gtf=gencode.v45.primary_assembly.annotation.gtf.gz
Supplementary files format and content: salmon.merged.gene_tpm.tsv: count data, one column per sample

growth_protocol: 16HBE cells were cultured in Eagle's minimal essential medium, supplemented with 10% fetal bovine serum, penicillin (50 units/ml), and streptomycin (50 µg/ml). IMR-90 cells, human fetal lung cells immortalized with human telomerase reverse transcriptase (hTERT), were acquired from Dr. William Hahn’s laboratory at the Dana-Farber Cancer Institute. Culturing was conducted with Eagle's minimum essential medium (EMEM), supplemented with 10% fetal bovine serum, penicillin (50 units/ml), and streptomycin (50 µg/ml).

extract_protocol:
RNA samples from various cell lines were extracted by RNAeasy kit (Qiagen) and measured for quality and quantity by Agilent TapeStation systems with RNA ScreenTape assay. Samples with a RIN over 8 were submitted for sequencing for gene expression.
Paired end cDNA libraries were constructed and sequenced on Illumina platforms for an average read depth of ~50 million reads.

value: plain untreated human bronchial epithelial cell line


title: Set2_B22_FG_6hr

description:
FG_transfection_6h_B
Gene expression at 6h


title: Set2_B19_G_6hr

description:
G_transfection_6h_D
Gene expression at 6h


title: CK heavy MNase-seq

value: heavy


title: Hematopoietic sample, ATAC

library_source: genomic single cell

value: ATAC


title: Sigma16HBE_3

description: Library name: Sigma16HBE_3


title: Skeletal sample rep 3, ADT

value: Skeletal


title: COLD  MH-seq

data_processing:
Sequenced reads were trimmed for adaptor sequences using fastp
Chip-seq clean reads without adaptor sequences were aligned to the maize B73 v4 genome using bowtie2.3.2 with default parameters.
Clean reads were used for peak calling using MACS2 with parameters --nomodel -q 0.01 --broad --broad-cutoff 0.1 -g 2.10434e+09 for H3K27me3 and --nomodel -q 0.01 -g 2.10434e+09 for other histone markers.
Assembly: B73 RefGen_v4
Supplementary files format and content: bw

value: seedling


title: Set2_B18_G_6hr

description:
G_transfection_6h_C
Gene expression at 6h


title: Set2_B17_G_6hr

description:
G_transfection_6h_B
Gene expression at 6h


title: Skeletal sample rep 3, ATAC


title: IMR90hTERT_3

description: Library name: IMR90hTERT_3

value: human lung fibroblast cell line that expresses human telomerase reverse transcriptase


title: Skeletal sample rep 2, ADT


title: COLD light MNase-seq

value: WT

value: COLD


title: COLD-H3K9ac

tag: chip antibody


title: IMR90hTERT_2

description: Library name: IMR90hTERT_2


title: CK-H3K9ac

value: control


title: IMR90hTERT_1

description: Library name: IMR90hTERT_1


title: Skeletal sample rep 2, ATAC


title: CAL27, (myc) CHIP

city: Hangzhou

first: Jiong

last: Lyu

state: Zhejiang

address: Rd.Yuhangtang  866

institute: Zhejiang University

description: Library name: CAL27,CHIP

data_processing:
Fastqc,
Trimmomatic
BWA
Chipseeker
MACS
Assembly: Hg38
Supplementary files format and content: Xls files

growth_protocol: CAL27 cell line maintain in DMEM/F12 with 10% FBS

extract_protocol: For Chip-seq, Cells were fixed with 1% formaldehyde,after cell lysis, chormain was sonicated

treatment_protocol: Lentivirus transfect with myc-tag KLF7

value: Tongue cancer

value: myc_KLF7 transfect

value: Lentivirus

tag: antibody


title: COLD-H3K4me3


title: Set2_B15_F_6hr

description:
F_transfection_6h_E
Gene expression at 6h

value: F transfection


title: CAL27, (myc) Input

description: Library name: CAL27,Input


title: Skeletal sample rep 1, ATAC

value: Femur


title: Set2_B13_F_6hr

description:
F_transfection_6h_C
Gene expression at 6h


title: CK MH-seq


title: COLD-H3K27me3


title: K562, niraparib, Replicate 1, 2023 screen

city: Princeton

first: Jia

last: Ling

state: NJ

address: Carl Icahn Laboratory, South Drive

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description:
Library name: 2023 screen, R1_NIRAP
NIRAP.R1

data_processing:
Base-calling was performed using onboard Real Time Analysis (RTA3), v3.4.4. Demultiplexing was performed using deML, a program for maximum likelihood demultiplexing of NGS data, under default parameters. While deML does not indicate a version, commit 036f1c9 from its associated github repository was used for all samples.
To ensure high quality read assignment, we used a two-step aligning and filtering process. Reads consist of 19 nt corresponding to an sgRNA target sequence followed by 21 nt from the associated sgRNA constant region. First, we analyzed the constant region in each read using bowtie2 (v2.3.4.1) to soft trim 19 nt from the 5′ end and map reads to reference constant regions. Reads which mapped constant sequences in the incorrect orientation or which had more than 1 mismatch were discarded using seqtk (v1.3-r117-dirty). We reasoned that these reads represented inactive sgRNAs with defects from cloning. sgRNA target regions from the remaining reads were then analyzed by using bowtie2 to soft trim 21 nt from the 3′ end, isolating only the first 19 nt, and align the remaining read fragments to an sgRNA reference library. Reads with mapping quality ≤ 5 were filtered, and read counts for each position-specific sgRNA pair, or “construct” (denoted by X/Y), were then determined from the remaining aligned reads. For T0 and DMSO-treated samples in the 2022 screen, sequencing was repeated three times due to high percentage of low quality reads caused by incorrect phiX spike-in and reads from three repeats were combined by adding counts from individual runs.
We calculated the median coverage for each sgRNA across replicates in each position and filtered constructs with any sgRNAs demonstrating a median coverage ≤ 35 reads in either position at T0. We then also removed any dual-sgRNA constructs with ＜50 reads in either replicate at T0, and to further avoid effects from low frequency representation, we added a pseudocount of 10 to all surviving construct read counts. Next, we defined an enrichment value for individual constructs as log2 of the fraction of reads (i.e., reference or PARPi) in endpoint samples divided by the fraction of reads for that construct at T0. Enrichments were normalized to non-targeting controls, for γ and τ separately, by subtracting the median enrichment of non-targeting sgRNA pairs (NT/NT) and adjusted by dividing the total number of population doublings that occurred from T0 until endpoint (reference R1 = 8.04, reference R2 = 7.98, PARPi R1 = 5.40, PARPi R2 = 4.98). The resulting values constitute our orientation-dependent γ and τ “construct phenotypes”. To calculate construct ρ phenotypes, we divided the fraction of reads at the PARPi endpoint by the fraction of reads at the reference endpoint, normalized to non-targeting controls, and then adjusted the resulting values by dividing by the difference in the number of population doublings observed in the PARPi-treated and reference arms (R1 = 2.64, R2 = 3.00). To determine individual “sgRNA phenotypes” for each replicate, we averaged the phenotypes of all constructs wherein a given sgRNA was paired with a non-targeting sgRNA, independent of orientation (i.e., including X/NT and NT/X). Similarly, “single-gene phenotypes” were defined as the average of all sgRNA phenotypes for sgRNAs targeting the same gene. Extended discussion of the full analytical process, along with all code for generating genetic interaction scores from counts, is available in an R markdown document in the accompanying Github repository (https://github.com/simpsondl/PARPi_interactions).
Assembly: sgRNA_reference_library.fasta
Supplementary files format and content: For counts files (read_counts2022.txt and read_counts2023.txt), the first two columns contain the guide assigned to each position in the dual-sgRNA construct (FirstPosition and SecondPosition). The remaining six columns give the raw counts (number of reads) assigned to each ordered  combination of guides from each arm/timepoint (T0 [start of screen], DMSO [reference condition], NIRAP [treated with niraparib]) of the relative screen (2022 or 2023) by replicate (R1 or R2).
Supplementary files format and content: For phenotype files (phenotypes2022.txt and phenotypes2023.txt),  the first two columns contain the guide assigned to each position in the dual-sgRNA construct (FirstPosition and SecondPosition). The remaining 9 columns give the 9 calculated phenotypes for each combination of guides. Phenotypes are listed by replicate (R1 or R2) as well as a replicate-averaged value (Avg). Gamma, tau, and rho phenotypes are calculated as described above from raw counts. The file contains only phenotypes for guide combinations passing filters described above.
Supplementary files format and content: sgRNA_reference_library.fasta contains the spacer sequences for all guides in the library.

source_name: cell line

growth_protocol: For the 2023 screen, K562 CRISPRi cells were transduced with the dual-sgRNA CRISPRi lentiviral library with more than 400X representation per construct at a low MOI (~0.25) as described above. Two biological replicates were performed. Cells were maintained at 0.5e6 to 0.6e6 per mL in the multitron incubator and were selected with 3 μg/mL puromycin 2 days post transduction. 9 days post transduction, treatment started (T0). T0 samples were collected from each replicate and the remaining cells of each replicate were divided into two populations, one of which was dosed with 2 μM niraparib and the other with vehicle (DMSO). Cells were split with vehicle or niraparib supplemented media for 3 days (the dosage of niraparib was increased to 3 μM from day 2 onwards, roughly the LC35 determined for cells transduced with the interaction sgRNA library) and maintained at densities between 0.5-0.6e6 cells per mL during the treatment. 4 days after dosing, cells were spun down, resuspended in drug-free media and were allowed to grow for an additional 6 days. A 850X representation was maintained for each arm throughout the entire process. 19 days post transduction, cells were collected from the niraparib-treated arms (PARPi endpoint samples) and DMSO-treated arms (reference endpoint samples), respectively. For the 2022 screen, the screen was performed with the same library as described above with the following differences: 1) library was transduced with a 350X representation; 2) the treated arms were dosed with 2 μM niraparib, split with drug-free media and were spun out of drug 3 days after dosing; 3) cells were harvested 18 days post transduction.

extract_protocol:
For the 2023 screen, cell pellets were processed to generate sequencing libraries as follows. Genomic DNA was extracted using the NucleoSpin® Blood XL, Maxi kit for DNA from blood (Macherey-Nagel) with an RNase A treatment step during cell lysis. For the 2022 screen, the extraction was performed as describe above except that the RNase A treatment step was performed separately after extraction of genomic DNA followed by ethanol precipitation.
The sgRNA loci were amplified with an indexing 5′ primer (5′-AATGATACGGCGACCACCGAGATCTACACNNNNNNNNCAGCACAAAAGGAAACTCACC) and an indexing 3′ primer (5′-CAAGCAGAAGACGGCATACGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNNNNGGCGGTAATACGGTTATCCA). Each reaction (100 μL total volume) contained 10 μg of genomic DNA (measured on NanoDrop) and 1 μM of each primer and was run on the Bio-Rad C1000 thermal cycler with the following program: 1 cycle of 30 seconds at 98 °C; 20 cycles of 10 seconds at 98 °C, followed by 75 seconds at 65 °C; 1 cycle of 5 minute at 65 °C; 4 °C hold. At least 400X coverage was maintained for each sample during PCR amplification. Aliquots of the PCR products were purified for sequencing using SPRIselect Reagent (Beckman Coulter) in two double-sided 0.45X-0.8X reactions and two 0.8X reactions. Indexed samples were pooled in equal molar ratio prior to sequencing.

value: cell line

value: leukemia cell

value: niraparib

tag: batch


title: K562, reference, Replicate 2, 2023 screen

description:
Library name: 2023 screen, R2_DMSO
DMSO.R2

value: DMSO


title: Set2_B11_F_6hr

city: ITHACA

description:
F_transfection_6h_A
Gene expression at 6h


title: CK-H3K27me3