title: TRE3G (IGHG1) c22 +Dox Sg1 rep2

city: Freiburg im Breisgau

first: Maximilian

middle: Christian

last: von der Linde

address: Stefan-Meier-Straße 17

department: Institute for Medical Bioinformatics and Systems Medicine (IBSM)

institute: University Medical Center Freiburg

description:
Library name: C22_inf_184+Dox_Sg1
PE300

data_processing:
Reads were trimmed for standard adapters with cutadapt. Poor quality (Q<25) 3’ bases were trimmed with trimmomatic by averaging over a sliding window of 5nt. Read pairs were then filtered for minimum remaining length (200nt for read 1, 100nt for read 2) using cutadapt. Read mates were merged down to make combined single-end reads with FLASH allowing 10% mismatch between the mates.
Obvious erroneous mergers were removed by selecting combined reads with lengths within ±30nt of the amplicon length using cutadapt, The remaining combined reads were aligned with Bowtie2, using the “–very-sensitive-local” alignment mode and only the fixed variable region sequence and its immediate vicinity as reference.
Alignments were split into strata by the number of mismatches reported, using a custom Perl script. For each stratum a pile-up was generated with samtools (Li et al., 2009) taking into account only bases with quality of at least 30.
The pileups were then quantified with a custom Python script and the resulting mutation counts were processed and visualized with custom scripts in R (v3.5.1), with the help of additional R packages (ggplot2 , ggrepel, patchwork).
Background mutation profiles were controlled for by subtracting the corresponding mutation frequencies in control samples from the frequencies in the samples of interest, at each position and for each substitution type. Annotation of hot and cold spots was created by means of regex search for the corresponding patterns in the reference sequence.
Code for the workflow and the custom scripts is available on Github at https://github.com/PavriLab/IgH_VDJ_MutPE .
Assembly: NCBI HG38
Supplementary files format and content: bedGraph format files showing coverage tracks that can be visualized in genome browser
Library strategy: MutPE-seq

source_name: Ramos

growth_protocol: see Methods

extract_protocol:
cells were harvested and gen.DNA prepared by PCI extraction and EtOH precipitation
2 rounds of PCRs were used to add adapter sequences and dual barcoding for paired-end sequencing on Illumina platform

treatment_protocol: see Methods

value: Ramos

value: Burkitt's Lymphoma

value: with Dox

tag: target


title: HDBI58 Cord Blood Day 17 GFP mid LARRY

status: Public on Jun 16 2025

type: SRA

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

description: 10x amplicon

library_source: transcriptomic single cell

data_processing:
Except for SITTA3, SITTA6 and SITTA7, the demultiplexing, cell calling and counting were performed with cellranger v.6.0.1
SITTA3, SITTA6 and SITTA7 were fetched from the lost reads. This is because the i5 primers is in the opposite direction to what appears in the sequencing. Consequently, we manually demultiplexed the corresponding samples.
Assembly: hg19
Supplementary files format and content: adata_meta.h5ad is the adata object containing all the processed data and the metadata for all the 10 samples used in this work

molecule: polyA RNA

organism: Homo sapiens

source_name: cord blood

growth_protocol: MEM conditions (Belluschi et al., Nature Communications). SCF, Flt3, TPO, EPO, IL-6, IL-3, IL-11, GM-CSF, IL-2, IL-7, Lipids

extract_protocol:
Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics) following manufacturer’s protocols
Following post GEM-RT cleanup and cDNA amplification, 10ul of clean cDNA was taken for targeted lineage barcode enrichment. To target the barcode, we used a similar strategy to that described in Weinreb et al 2020, Science. Primers targeting the LARRY vector and Illumina overhangs were used, with specific 10x sample indexes to allow for muliplexing of the samples for sequencing. the following primers were used, i5_AATGATACGGCGACCACCGAGATCTACACNNNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT and i7_CAAGCAGAAGACGGCATACGAGATNNNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACCGTTGCTAGGAGAGACCATATG. AMPure or SPRI bead cleanup was performed (0.7 ratio). Library quality and size was verified using Aglient Tapestation and libraries were spiked into the original GEX 10x library for sequencing.

tag: tissue

value: cord blood

tag: cell type

tag: treatment

value: LARRY


title: TRE3G (IGHG1) c22 -Dox Sg1 rep2

country: Germany

description:
Library name: C22_inf_184-Dox_Sg1
PE300

library_source: genomic

molecule: genomic DNA

tag: cell line

tag: genotype

value: no Dox


title: HDBI58 Cord Blood Day 10 GFP+ LARRY

description: 10x amplicon


title: GBC-4

city: taiyuan

first: ming

last: gao

state: Shanxi

address: NO.56 Xinjian South Road

country: China

institute: Shanxi Medical University

library_source: transcriptomic

data_processing:
Illumina Casava 1.8 software was used for basecalling
Raw data (raw reads) in fastp format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and reads with low quality. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were conducted using the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the read numbers mapped to each gene.
Differential expression analysis of two groups (five biological replicates per group) was performed using the DESeq2 R package (1.20.0).
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include FPKM values and read count numbers for each sample

molecule: total RNA

source_name: adjacent tumor tissue

extract_protocol:
The total RNA samples for RNA-seq were extracted using TRIzol reagent and then treated with DNaseⅠ in order to eliminate the DNA contamination. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used to prepared the RNA-seq libraries according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adjacent tumor tissue


title: TRE3G (IGHG1) c14 -Dox Sg1 rep2

description:
Library name: C14_inf_184-Dox_Sg1
PE300


title: TRE3G (IGHG1) c22 +Dox Sg1 rep1

description:
Library name: C22_TRE3Gg1_e3_+Dox_184inf_g1
PE300


title: HDBI58 Cord Blood Day 17 GFP mid


title: HDBI58 Cord Blood Day 17 GFP high LARRY

description: 10x amplicon


title: TRE3G (IGHG1) c14 +Dox Sg1 rep2

description:
Library name: C14_inf_184+Dox_Sg1
PE300


title: TRE3G (IGHG1) c14 +Dox Sg1 rep1

description:
Library name: C14_TRE3Gg1_e3_+Dox_184inf_g1
PE300


title: HDBI58 Cord Blood Day 3 GFP+ LARRY

description: 10x amplicon


title: TRE3G (IGHG1) c22 -Dox Sg1 rep1

description:
Library name: C22_TRE3Gg1_e3_-Dox_184inf_g1
PE300


title: HDBI58 Cord Blood Day 10 GFP-


title: HDBI58 Cord Blood Day 10 GFP+


title: TRE3G (IGHG1) c14 -Dox Sg1 rep1

description:
Library name: C14_TRE3Gg1_e3_-Dox_184inf_g1
PE300


title: 22F_Pa+NC

city: Hanover

first: Sharanya

last: Sarkar

state: NH

address: Dewey Field Road, HB 7550

department: Microbiology and Immunology

country: USA

institute: Geisel School of Medicine at Dartmouth

description:
Library name: 190276_04
Donor 22F

data_processing:
Prepared libraries were pooled and sequenced on a NextSeq2000 platform, aiming at 10 million single-end 100 bp reads per sample.
Paired-end reads were processed by trimming with Cutadapt v4.056 followed by alignment to the GRCh38 human genome reference using Hisat2 v2.2.1 (RRID:SCR_015530)57.
Gene expression levels were quantified with FeatureCounts v2.0.158, using Human Ensembl v97 as the reference annotation.
Alignment and quantification metrics were assessed with Samtools v1.15.1 (RRID:SCR_001105)59 and Picard v2.27.160.
Assembly: hg38 (GRCh38)
Supplementary files format and content: tsv file containing raw counts alinged to hg38 genome

source_name: lung

growth_protocol: pHBEC were maintained in BronchiaLife basal medium (Lifeline Cell Technology, Frederick, MD, Cat. No. LM-0007) at 37°C with 5% CO₂. The medium was supplemented with the BronchiaLife B/T LifeFactors Kit (Lifeline Cell Technology, Cat. No. LS-1047) and antibiotics (penicillin, 10,000 U/mL; streptomycin, 10,000 μg/mL; Sigma-Aldrich, Cat. No. P4333). Cells were used for experiments between passages 4 and 9, and the data was not dependent on the passage number. Samples were seeded on 24-mm permeable supports (Corning, Catalog #3407) pre-coated with type IV collagen (Sigma-Aldrich, Catalog #C-7521). The cells were cultured in air-liquid interface media (University of North Caroline, Chapel Hill) of  at 37°C for 3 - 4 weeks to establish polarized monolayer.

extract_protocol:
RNA was isolated from HBECs using the miRNeasy Kit (Qiagen, Germantown, MD, Catalog #217004). cDNA synthesis was performed with 1 µg of RNA as input, using SuperScript IV (Invitrogen, Grand Island, NY, Catalog #18090050).
A total of 100 ng of RNA was used as input for library preparation following the QuantSeq FWD workflow (Lexogen) according to the manufacturer’s protocol.

treatment_protocol: P. aeruginosa PA14 (3 × 10⁸/mL) was introduced to the apical side of the monolayers for 1 hour. Subsequently, either PC, NC MSC EVs, or let-7b MSC EVs (2 × 10⁹/mL) were added for an additional 5 hours, completing a 6-hour treatment period. One monolayer of pHBEC served as a second control, receiving neither P. aeruginosa nor EVs, while another monolayer was treated only with P. aeruginosa with no EVs.

value: lung

value: primary bronchial epithelial cells

value: homozygous delta-F508

value: PA and negative control MSC EV


title: TRE3G (IGHG3) D3 uninf -Dox rep1

description:
Library name: D3_e3_-Dox_uninf_g3
PE300

value: D3 (wt IGH)


title: HDBI58 Cord Blood Day 3 GFP-


title: TRE3G (IGHG3) c17 -Dox Sg3 rep3

description:
Library name: C17_TRE3Gg3_e3_-Dox_184inf_g3
PE300


title: TRE3G (IGHG3) c17 +Dox Sg3 rep3

description:
Library name: C17_TRE3Gg3_e3_+Dox_184inf_g3
PE300


title: HDBI58 Cord Blood Day 3 GFP+


title: TRE3G (IGHG3) c9 +Dox Sg3 rep3

description:
Library name: C9_TRE3Gg3_e3_+Dox_184inf_g3
PE300


title: 22F_UT

description:
Library name: 190276_01
Donor 22F

value: Untreated


title: Set2-MRGR-Dex10nm-rep3

city: Research Triangle Park

first: Tatsuya

last: Sueyoshi

state: NC

address: 111 TW Alexander Drive

department: DIR

institute: NIEHS, NIH

data_processing:
Reads were mapped to the hg19 reference genome via STAR v2.6.0c with parameters "--outFilterMultimapNmax 10 --outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --quantMode GeneCounts --limitBAMsortRAM 24900000000 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical", with a STAR index built from a version of the genome assembly excluding haplotype chromosomes and using gene models as defined by UCSC refGene as of March 3 2017.
Read counts per gene were collected from the STAR outputs.
Signal tracks were generated by STAR v2.6.0c with parameters "--runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigStrand Unstranded --outWigNorm RPM", then converted to bigWig format via UCSC utility bedGraphToBigWig.
Assembly: hg19
Supplementary files format and content: Normalized coverage tracks in bigWig format.
Supplementary files format and content: Counts per gene per sample in tab-delimited text format.

extract_protocol:
Total RNA was isolated using the RNeasy mini kit (Qiagen)
All RNA-seq libraries (non-strand-specific, paired end) were prepared with the TruSeq RNA Sample Prep kit (Illumina, San Diego, CA).  Poly(A) enrichment was conducted on the total RNA samples as outlined in the TruSeq protocol.

value: pTet-Off transformed stable cell line

value: constitutive GR + MR expression

tag: expression level

value: expresses high levels of GR and MR

value: dexamethasone, 10nm


title: TRE3G (IGHG3) D3 uninf -Dox rep2

description:
Library name: D3_e3_-Dox_uninf_g3_2
PE300

value: Ramos


title: TRE3G (IGHG3) c9 -Dox Sg3 rep3

description:
Library name: C9_TRE3Gg3_e3_-Dox_184inf_g3
PE300

value: Burkitt's Lymphoma


title: Set2-MRGR-Dex10nm-rep2


title: Set2-MRGR-Dex10nm-rep1


title: HDBI58 Cord Blood Day 17 GFP high


title: TRE3G (IGHG3) c17 -Dox Sg3 rep2

description:
Library name: C17_TRE3Gg3_e2_-Dox_184inf_g3
PE300


title: Set2-MRGR-veh-rep4

value: DMSO


title: TRE3G (IGHG3) c17 +Dox Sg3 rep2

description:
Library name: C17_TRE3Gg3_e2_+Dox_184inf_g3
PE300

value: with Dox


title: TRE3G (IGHG3) c9 +Dox Sg3 rep2

description:
Library name: C9_TRE3Gg3_e2_+Dox_184inf_g3
PE300


title: Set2-MRGR-veh-rep2


title: Set2-MRGR-veh-rep3


title: TRE3G (IGHG3) c9 -Dox Sg3 rep2

description:
Library name: C9_TRE3Gg3_e2_-Dox_184inf_g3
PE300


title: Set2-MR-Dex10nm-rep4

value: constitutive MR expression

value: expresses high levels of MR


title: TRE3G (IGHG3) c9 +Dox Sg3 rep1

description:
Library name: C9_TRE3Gg3_e1_+Dox_184inf_g3
PE300


title: Set2-MR-Dex10nm-rep3


title: TRE3G (IGHG3) c17 -Dox Sg3 rep1

description:
Library name: C17_TRE3Gg3_e1_-Dox_184inf_g3
PE300

value: no Dox


title: Set2-MRGR-veh-rep1


title: Set2-MR-Dex10nm-rep2


title: Set2-MRGR-Dex10nm-rep4


title: Set2-MR-Dex10nm-rep1


title: Set2-MR-veh-rep4


title: MRC5 no Dox Control Rep2

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description: Library name: MRC5 Control Rep 2

data_processing:
A concatenated fasta file was created using cDNA sequences from release 110 of Ensembl for the human genome and Towne-HCMV genome generated from sequencing map in Murphy et al. 2003 (PMID: 14657367) and genbank sequences, which was then used to construct a Salmon index. Expression for each transcript was quantified from raw reads using Salmon v1.9 with libType set as automatic. DESeq261 (v1.30.1) in R (v4.0.3) was used first to perform all pairwise comparisons for WT and macroH2A1 KO across time points, between the two genotypes.
The expression matrix across genotypes and time points was transformed using the “rlog” function in DESeq2
Assembly: Release 110 of Ensembl for the human genome and Towne-HCMV genome generated from sequencing map in Murphy et al. 2003 (PMID: 14657367) and genbank sequences
Supplementary files format and content: A TSV file generated using the "results" command in DESeq2 comparing WT and macroH2A KO for each time point.

growth_protocol: Cultured in Gibco DMEM with 10% FBS, 1mM sodium pyruvate, and 1% penicillin-streptomycin  and at 37°C with 5% CO2 and tested for mycoplasma contamination approximately once every 2 months

extract_protocol:
RNA was harvested using New England BioLabs Monarch® Total RNA Miniprep Kit (T2010S) as per kit instructions.
RNA was quantified by Nanodrop and integrity was analyzed with the 4200 Tapestation Bioanalyzer system (Agilent). 500 ng of total RNA with an RNA Integrity Number (RIN) >9.5 were used to prepare sequencing libraries with the TruSeq Stranded mRNA Library Prep Kit (20020594; Illumina). Library concentrations were measured with Qubit dsDNA HS Assay Kit (Q32854; Thermo Fisher Scientific) and then analyzed with Agilent High Sensitivity D5000 ScreenTape System and pooled. Libraries were sequenced with 100-bp paired-end reads on an  NovaSeq X+ 10B flow cell  at the Fred Hutch Genomics Core Facility.

treatment_protocol: MRC5 with dox-inducible trans-genes (PMID: 21533215) were grown to 100 %confluence. Media was changed and then cells were left for 7 days. After 7 days 2 μg/mL was added to cells. After 24 hours cells were harvested using 0.5% trypsin.


title: MRC5 no Dox Control Rep1

description: Library name: MRC5 Control Rep 1


title: Luciferase Rep3

description: Library name: Luciferase Rep3


title: Set2-MR-veh-rep2


title: Set2-MR-veh-rep1


title: Luciferase Rep2

description: Library name: Luciferase Rep2


title: Set2-GR-Dex10nm-rep4

value: constitutive GR expression

value: expresses high levels of GR


title: Set2-GR-Dex10nm-rep3


title: IE2 Rep3

description: Library name: IE2 Rep3


title: Set2-GR-Dex10nm-rep2


title: TRE3G (IGHG3) c17 +Dox Sg3 rep1

description:
Library name: C17_TRE3Gg3_e1_+Dox_184inf_g3
PE300


title: IE2 Rep2

description: Library name: IE2 Rep2


title: Set2-GR-Dex10nm-rep1


title: IE2 Rep1

description: Library name: IE2 Rep1


title: IE1 Rep3

description: Library name: IE1 Rep3


title: Set2-GR-veh-rep4


title: Set2-GR-veh-rep3


title: TRE3G (IGHG3) c9 -Dox Sg3 rep1

description:
Library name: C9_TRE3Gg3_e1_-Dox_184inf_g3
PE300


title: IE1 Rep1

description: Library name: IE1 Rep1


title: Set2-GR-veh-rep1


title: Set2-GR-veh-rep2


title: MRC5 no Dox Control Rep3

description: Library name: MRC5 Control Rep 3


title: Set2-off-Dex10nm-rep4

value: wild type

value: undetectable/low levels of GR and MR


title: IE1_deltaCTD Rep3

description: Library name: IE1_CTD Rep3


title: Set2-MR-veh-rep3


title: IE1_deltaCTD Rep2

description: Library name: IE1_CTD Rep2


title: Set2-off-Dex10nm-rep3


title: IE1_deltaCTD Rep1

description: Library name: IE1_CTD Rep1


title: Luciferase Rep1

description: Library name: Luciferase Rep1


title: Set2-off-Dex10nm-rep1


title: Set2-off-veh-rep4


title: HepG2_P2WC8_cDNA_G1, G1 phase

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description: Library name: HepG2_P2WC8_cDNA_G1

data_processing:
gDNA bedgraphs were generated using the single cell Repliseq pipeline (Muira et al. 2020). cDNA samples were processed using Seurat pipeline.
Assembly: GRCh38
Supplementary files format and content: gDNA bedgraphs were generated using the single cell Repliseq pipeline (Muira et al. 2020).
Supplementary files format and content: cDNA samples were processed using Seurat pipeline and the counts table of genes (Ensembl Release 107) persent per cell was generated.

source_name: nucleus

growth_protocol: ATCC-formulated Eagle's Minimum Essential Medium, Catalog No. 30-2003. + 10% FBS.

extract_protocol:
gDNA and mRNA were extracted from single HepG2 nuclei using an in house protocol. mRNA was pulled down on magnetic beads with poly T tailed primers using the SMART-Seq2 strategy. gDNA in the supernatant was separated into wells before the in house amplification.
Nextera XT DNA Library Prep Kit was used for for each sample. Nextera XT 96-index kit was used to barcode each sample. All samples were pooled together before sequencing on the same chip.

value: nucleus

value: Human liver cancer cell line

tag: time point

value: G1 phase


title: HepG2_P2WC6_cDNA_S5, S phase

description: Library name: HepG2_P2WC6_cDNA_S5

value: S phase


title: HepG2_P2WC7_cDNA_G2, G2 phase

description: Library name: HepG2_P2WC7_cDNA_G2

value: G2 phase


title: Set2-off-veh-rep3

value: pTet-Off transformed stable cell line


title: Set2-off-veh-rep2


title: Set1-MRGR-Aldo1nm-rep4

value: constitutive GR + MR expression

value: expresses high levels of GR and MR

value: aldosterone, 1nm


title: HepG2_P2WC4_cDNA_S3, S phase

description: Library name: HepG2_P2WC4_cDNA_S3


title: HepG2_P2WB5_cDNA_S4, S phase

description: Library name: HepG2_P2WB5_cDNA_S4


title: Set1-MRGR-Aldo1nm-rep3


title: HepG2_P2WC3_cDNA_S2, S phase

description: Library name: HepG2_P2WC3_cDNA_S2


title: Set2-off-veh-rep1

value: DMSO


title: HepG2_P2WB4_cDNA_S3, S phase

description: Library name: HepG2_P2WB4_cDNA_S3


title: HepG2_P2WC5_cDNA_S4, S phase

description: Library name: HepG2_P2WC5_cDNA_S4


title: Set1-MRGR-Aldo1nm-rep2


title: HepG2_P2WA2_cDNA_S1, S phase

description: Library name: HepG2_P2WA2_cDNA_S1


title: HepG2_P2WA4_cDNA_S3, S phase

description: Library name: HepG2_P2WA4_cDNA_S3


title: HepG2_P2WB3_cDNA_S2, S phase

description: Library name: HepG2_P2WB3_cDNA_S2


title: Set1-MRGR-Dex1nm-rep4

value: dexamethasone, 1nm


title: Set1-MRGR-Aldo1nm-rep1


title: IE1 Rep2

description: Library name: IE1 Rep2


title: Set1-MRGR-Dex1nm-rep3


title: HepG2_P2WA8_cDNA_G1, G1 phase

description: Library name: HepG2_P2WA8_cDNA_G1


title: fresh hippocampal from PNE female 2

type: genomic

city: SANTIAGO

first: RODRIGO

last: VIDAL

state: METROPOLITANA

address: Avenida Libertador Bernardo O'Higgins nº 3363.  Estación Central

department: BIOLOGY

country: Chile

institute: UNIVERSIDAD DE SANTIAGO

description: hippocampal DNA from PNE treatment

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to mouse Infinium Methylation BeadChip using standard Illuminca protocol

scan_protocol: Arrays were imaged using Tecan LIHA 1, iScan and standard recommended Illumina scanner setting

data_processing:
Champ and GenomeStudio Methylation Module packages  in R environment (4.1.1)
Average Beta

label: Cy3 and Cy5

organism: Mus musculus

source_name: fresh hippocampal

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from bilateral hippocampal samples using the DNeasy Blood and Tissue Kit following the manufacturer’s instructions.

value: fresh hippocampal

tag: Sex

value: female

value: PNE


title: HepG2_P4WC8_cDNA_G1, G1 phase

description: Library name: HepG2_P4WC8_cDNA_G1


title: HepG2_P4WC7_cDNA_G2, G2 phase

description: Library name: HepG2_P4WC7_cDNA_G2


title: Set2-off-Dex10nm-rep2

value: dexamethasone, 10nm


title: HepG2_P4WC6_cDNA_S5, S phase

description: Library name: HepG2_P4WC6_cDNA_S5


title: Set1-MRGR-Dex1nm-rep2


title: HepG2_P4WC5_cDNA_S4, S phase

description: Library name: HepG2_P4WC5_cDNA_S4


title: HepG2_P4WC4_cDNA_S3, S phase

description: Library name: HepG2_P4WC4_cDNA_S3


title: fresh hippocampal from PNE male 3

description: hippocampal DNA from PNE treatment

value: male


title: Set1-MRGR-Dex1nm-rep1


title: HepG2_P4WC2_cDNA_S1, S phase

description: Library name: HepG2_P4WC2_cDNA_S1


title: fresh hippocampal from PNE male 2

description: hippocampal DNA from PNE treatment


title: HepG2_P4WB2_cDNA_S1, S phase

description: Library name: HepG2_P4WB2_cDNA_S1


title: fresh hippocampal from PNE male 1

description: hippocampal DNA from PNE treatment


title: HepG2_P4WA8_cDNA_G1, G1 phase

description: Library name: HepG2_P4WA8_cDNA_G1


title: Set1-MRGR-veh-rep3


title: HepG2_P4WA7_cDNA_G2, G2 phase

description: Library name: HepG2_P4WA7_cDNA_G2


title: HepG2_P4WB6_cDNA_S5, S phase

description: Library name: HepG2_P4WB6_cDNA_S5


title: fresh hippocampal from PNE female 3

description: hippocampal DNA from PNE treatment


title: Set1-MRGR-veh-rep2


title: HepG2_P4WA2_cDNA_S1, S phase

description: Library name: HepG2_P4WA2_cDNA_S1


title: HepG2_P4WA4_cDNA_S3, S phase

description: Library name: HepG2_P4WA4_cDNA_S3


title: fresh hippocampal from control female 2

description: hippocampal DNA from healthy control

value: Control


title: HepG2_P4C3_cDNA_S2, S phase

description: Library name: HepG2_P4C3_cDNA_S2

value: nucleus


title: fresh hippocampal from control female 4

description: hippocampal DNA from healthy control


title: Set1-MR-Aldo1nm-rep4

value: constitutive MR expression

value: expresses high levels of MR


title: Set1-MRGR-veh-rep1


title: HepG2_P4C1_cDNA_G1, G1 phase

description: Library name: HepG2_P4C1_cDNA_G1

value: Human liver cancer cell line

value: G1 phase


title: HepG2_P4WA3_cDNA_S2, S phase

description: Library name: HepG2_P4WA3_cDNA_S2

value: S phase


title: fresh hippocampal from PNE female 1

description: hippocampal DNA from PNE treatment


title: Set1-MR-Aldo1nm-rep3

value: pTet-Off transformed stable cell line


title: fresh hippocampal from control female 1

description: hippocampal DNA from healthy control


title: fresh hippocampal from control male 3

description: hippocampal DNA from healthy control


title: HepG2_P4B7_cDNA_G2, G2 phase

description: Library name: HepG2_P4B7_cDNA_G2

value: G2 phase


title: HepG2_P4B8_cDNA_G1, G1 phase

description: Library name: HepG2_P4B8_cDNA_G1


title: HepG2_P4B5_cDNA_S4, S phase

description: Library name: HepG2_P4B5_cDNA_S4


title: Set1-MR-Aldo1nm-rep2

value: aldosterone, 1nm


title: HepG2_P4B3_cDNA_S2, S phase

description: Library name: HepG2_P4B3_cDNA_S2


title: fresh hippocampal from control male 2

description: hippocampal DNA from healthy control


title: Set1-MRGR-veh-rep4

value: constitutive GR + MR expression

value: expresses high levels of GR and MR

value: DMSO


title: HepG2_P4B1_cDNA_G1, G1 phase

description: Library name: HepG2_P4B1_cDNA_G1


title: Set1-MR-Aldo1nm-rep1


title: HepG2_P4A9_cDNA_G1, G1 phase

description: Library name: HepG2_P4A9_cDNA_G1


title: HepG2_P4A6_cDNA_S5, S phase

description: Library name: HepG2_P4A6_cDNA_S5


title: Set1-MR-Dex1nm-rep4

value: dexamethasone, 1nm


title: HepG2_P4A5_cDNA_S4, S phase

description: Library name: HepG2_P4A5_cDNA_S4


title: HepG2_P4A1_cDNA_G1, G1 phase

description: Library name: HepG2_P4A1_cDNA_G1


title: Mouse cell, cellSp_713_EE_3, rep 3

city: Shenzhen

first: Jian-Kang

last: Zhu

state: Guangdong

address: 1088 Xueyuan Blvd, Nanshan

institute: Southern University of Science and Technology

description: Library name: hepa1-6 713split-3

data_processing:
Adapter/quality trimming: fastp v0.23.4 (-q20 -u30).
Alignment: STAR v2.7.11a to GRCm38/mm10 (mismatch <= 2).
Gene counts: featureCounts v2.0.1; normalization/DE: DESeq2 v1.38.0.
Assembly: mm10
Supplementary files format and content: Tab-delimited HTSeq output listing Ensembl gene IDs and raw read counts

extract_protocol:
Total RNA (1 µg) was isolated from mouse hepatocytes/cell lines using TRIzol.
Libraries were built with NEBNext Ultra RNA Library Prep Kit (Illumina) with poly-A selection, 250–300 bp size selection, 12-cycle PCR, and QC on an Agilent 2100.


title: HepG2_P2C1_cDNA_G1, G1 phase

description: Library name: HepG2_P2C1_cDNA_G1


title: Set1-MR-Dex1nm-rep3


title: HepG2_P2B9_cDNA_G1, G1 phase

description: Library name: HepG2_P2B9_cDNA_G1


title: Set1-MR-Dex1nm-rep2


title: Mouse cell, cellSp_713_EE_2, rep 2

description: Library name: hepa1-6 713split-2


title: HepG2_P2B8_cDNA_G1, G1 phase

description: Library name: HepG2_P2B8_cDNA_G1


title: Mouse cell, cellSp_713_EE_1, rep 1

description: Library name: hepa1-6 713split-1


title: HepG2_P2B2_cDNA_S1, S phase

description: Library name: HepG2_P2B2_cDNA_S1


title: Mouse cell, cellSp_573_EE_3, rep 3

description: Library name: hepa1-6 573split-3


title: Set1-MR-veh-rep4


title: HepG2_P2B1_cDNA_G1, G1 phase

description: Library name: HepG2_P2B1_cDNA_G1


title: HepG2_P2B6_cDNA_S5, S phase

description: Library name: HepG2_P2B6_cDNA_S5


title: Set1-MR-Dex1nm-rep1


title: Mouse cell, cellSp_573_EE_2, rep 2

description: Library name: hepa1-6 573split-2


title: Set1-MR-veh-rep3


title: HepG2_P2A5_cDNA_S4, S phase

description: Library name: HepG2_P2A5_cDNA_S4


title: Mouse cell, cellSp_573_EE_1, rep 1

description: Library name: hepa1-6 573split-1


title: fresh hippocampal from control male 1

description: hippocampal DNA from healthy control

value: fresh hippocampal


title: HepG2_P2A6_cDNA_S5, S phase

description: Library name: HepG2_P2A6_cDNA_S5


title: Set1-MR-veh-rep2


title: HepG2_P2A3_cDNA_S2, S phase

description: Library name: HepG2_P2A3_cDNA_S2


title: Set1-MR-veh-rep1


title: HepG2_P2C2_cDNA_S1, S phase

description: Library name: HepG2_P2C2_cDNA_S1


title: HepG2_P2A1_cDNA_G1, G1 phase

description: Library name: HepG2_P2A1_cDNA_G1


title: HepG2_P4C8_gDNA_G1, G1 phase

description: Library name: HepG2_P4C8_gDNA_G1


title: HepG2_P4C7_gDNA_G2, G2 phase

description: Library name: HepG2_P4C7_gDNA_G2


title: Set1-GR-Aldo1nm-rep4

value: constitutive GR expression

value: expresses high levels of GR


title: HepG2_P4C4_gDNA_S3, S phase

description: Library name: HepG2_P4C4_gDNA_S3


title: Mouse cell, cellSp_EE_1, rep 1

description: Library name: hepa1-6 PC384-1


title: Mouse cell, cellSF01_EE_6, rep 6

description: Library name: hepa1-6 PC402+cr31214-3


title: HepG2_P4C6_gDNA_S5, S phase

description: Library name: HepG2_P4C6_gDNA_S5


title: HepG2_P4C5_gDNA_S4, S phase

description: Library name: HepG2_P4C5_gDNA_S4


title: Set1-GR-Aldo1nm-rep3


title: HepG2_P2A7_cDNA_G2, G2 phase

description: Library name: HepG2_P2A7_cDNA_G2


title: Mouse cell, cellSF01_EE_5, rep 5

description: Library name: hepa1-6 PC402+cr31214-2


title: HepG2_P4C2_gDNA_S1, S phase

description: Library name: HepG2_P4C2_gDNA_S1


title: HepG2_P4C1_gDNA_G1, G1 phase

description: Library name: HepG2_P4C1_gDNA_G1


title: Set1-GR-Aldo1nm-rep1


title: HepG2_P4B8_gDNA_G1, G1 phase

description: Library name: HepG2_P4B8_gDNA_G1


title: Mouse cell, cellSF01_EE_4, rep 4

description: Library name: hepa1-6 PC402+cr31214-1


title: Set1-GR-Dex1nm-rep4


title: Mouse cell, cellSF01_EE_3, rep 3

description: Library name: hepa1-6 PC402+cr51214-3


title: Mouse cell, cellSp_EE_3, rep 3

description: Library name: hepa1-6 PC384-3


title: Set1-GR-Dex1nm-rep3


title: HepG2_P4B5_gDNA_S4, S phase

description: Library name: HepG2_P4B5_gDNA_S4


title: Mouse cell, cellSp_EE_2, rep 2

description: Library name: hepa1-6 PC384-2


title: HepG2_P4B3_gDNA_S2, S phase

description: Library name: HepG2_P4B3_gDNA_S2


title: Mouse cell, cellSF01_EE_2, rep 2

description: Library name: hepa1-6 PC402+cr51214-2


title: HepG2_P4B1_gDNA_G1, G1 phase

description: Library name: HepG2_P4B1_gDNA_G1


title: Set1-GR-Dex1nm-rep2


title: Mouse cell, cellSF01_EE_1, rep 1

description: Library name: hepa1-6 PC402+cr51214-1


title: HepG2_P4B2_gDNA_S1, S phase

description: Library name: HepG2_P4B2_gDNA_S1


title: HepG2_P4C3_gDNA_S2, S phase

description: Library name: HepG2_P4C3_gDNA_S2


title: HepG2_P4A9_gDNA_G1, G1 phase

description: Library name: HepG2_P4A9_gDNA_G1


title: Set1-GR-veh-rep4


title: HepG2_P4A8_gDNA_G1, G1 phase

description: Library name: HepG2_P4A8_gDNA_G1


title: HepG2_P4A7_gDNA_G2, G2 phase

description: Library name: HepG2_P4A7_gDNA_G2


title: HepG2_P4A5_gDNA_S4, S phase

description: Library name: HepG2_P4A5_gDNA_S4


title: Mouse cell, cellMock_2, rep 2

description: Library name: hepa1-6 con-2


title: Set1-GR-veh-rep3


title: Mouse cell, cellMock_1, rep 1

description: Library name: hepa1-6 con-1


title: HepG2_P4A4_gDNA_S3, S phase

description: Library name: HepG2_P4A4_gDNA_S3


title: HepG2_P4B7_gDNA_G2, G2 phase

description: Library name: HepG2_P4B7_gDNA_G2


title: HepG2_P4A6_gDNA_S5, S phase

description: Library name: HepG2_P4A6_gDNA_S5


title: Set1-GR-veh-rep2


title: HepG2_P4A3_gDNA_S2, S phase

description: Library name: HepG2_P4A3_gDNA_S2


title: HepG2_P4A1_gDNA_G1, G1 phase

description: Library name: HepG2_P4A1_gDNA_G1


title: Mouse liver, Sp_713_EE_6, Day 30, rep 6

description: Library name: X348-6

source_name: Liver

value: Liver


title: Mouse liver, Sp_713_EE_5, Day 30, rep 5

description: Library name: X348-5


title: HepG2_P2C8_gDNA_G1, G1 phase

description: Library name: HepG2_P2C8_gDNA_G1

value: nucleus


title: Set1-GR-veh-rep1


title: HepG2_P2C7_gDNA_G2, G2 phase

description: Library name: HepG2_P2C7_gDNA_G2


title: Set1-off-Aldo1nm-rep4

value: wild type

value: undetectable/low levels of GR and MR


title: Set1-GR-Dex1nm-rep1


title: HepG2_P2C5_gDNA_S4, S phase

description: Library name: HepG2_P2C5_gDNA_S4

value: Human liver cancer cell line


title: HepG2_P2C6_gDNA_S5, S phase

description: Library name: HepG2_P2C6_gDNA_S5


title: Mouse liver, Sp_713_EE_4, Day 30, rep 4

description: Library name: X348-4


title: HepG2_P2C4_gDNA_S3, S phase

description: Library name: HepG2_P2C4_gDNA_S3


title: Mouse liver, Sp_713_EE_3, Day 30, rep 3

description: Library name: X348-3


title: HepG2_P2C2_gDNA_S1, S phase

description: Library name: HepG2_P2C2_gDNA_S1


title: Set1-off-Aldo1nm-rep3


title: HepG2_P2C3_gDNA_S2, S phase

description: Library name: HepG2_P2C3_gDNA_S2


title: HepG2_P2C1_gDNA_G1, G1 phase

description: Library name: HepG2_P2C1_gDNA_G1

value: G1 phase


title: Mouse liver, Sp_713_EE_2, Day 30, rep 2

description: Library name: X348-2


title: Mouse liver, Sp_713_EE_1, Day 30, rep 1

description: Library name: X348-1


title: HepG2_P2B9_gDNA_G1, G1 phase

description: Library name: HepG2_P2B9_gDNA_G1


title: Set1-off-Aldo1nm-rep1


title: HepG2_P2B8_gDNA_G1, G1 phase

description: Library name: HepG2_P2B8_gDNA_G1


title: HepG2_P2B7_gDNA_G2, G2 phase

description: Library name: HepG2_P2B7_gDNA_G2


title: HepG2_P4A2_gDNA_S1, S phase

description: Library name: HepG2_P4A2_gDNA_S1

value: S phase


title: Set1-off-Dex1nm-rep4

value: pTet-Off transformed stable cell line


title: HepG2_P2B6_gDNA_S5, S phase

description: Library name: HepG2_P2B6_gDNA_S5


title: Set1-off-Dex1nm-rep3


title: HepG2_P2B5_gDNA_S4, S phase

description: Library name: HepG2_P2B5_gDNA_S4


title: Set1-off-Dex1nm-rep2


title: HepG2_P2B4_gDNA_S3, S phase

description: Library name: HepG2_P2B4_gDNA_S3


title: Mouse liver, Sp_573_EE_6, Day 30, rep 6

description: Library name: X342-6


title: HepG2_P2B2_gDNA_S1, S phase

description: Library name: HepG2_P2B2_gDNA_S1


title: HepG2_P2B3_gDNA_S2, S phase

description: Library name: HepG2_P2B3_gDNA_S2


title: Mouse liver, Sp_573_EE_4, Day 30, rep 4

description: Library name: X342-4


title: Set1-off-Dex1nm-rep1


title: Set1-off-Aldo1nm-rep2


title: HepG2_P2B1_gDNA_G1, G1 phase

description: Library name: HepG2_P2B1_gDNA_G1


title: HepG2_P2A8_gDNA_G1, G1 phase

description: Library name: HepG2_P2A8_gDNA_G1


title: Set1-off-veh-rep4


title: Mouse liver, Sp_573_EE_2, Day 30, rep 2

description: Library name: X342-2


title: HepG2_P2A7_gDNA_G2, G2 phase

description: Library name: HepG2_P2A7_gDNA_G2

value: G2 phase


title: Set1-off-veh-rep3


title: HepG2_P2A5_gDNA_S4, S phase

description: Library name: HepG2_P2A5_gDNA_S4


title: Mouse liver, Sp_573_EE_1, Day 30, rep 1

description: Library name: X342-1


title: HepG2_P2A6_gDNA_S5, S phase

description: Library name: HepG2_P2A6_gDNA_S5


title: HepG2_P2A4_gDNA_S3, S phase

description: Library name: HepG2_P2A4_gDNA_S3


title: HepG2_P2A3_gDNA_S2, S phase

description: Library name: HepG2_P2A3_gDNA_S2


title: Mouse liver, Sp_573_EE_5, Day 30, rep 5

description: Library name: X342-5


title: Set1-off-veh-rep2


title: HepG2_P2A2_gDNA_S1, S phase

description: Library name: HepG2_P2A2_gDNA_S1


title: Mouse liver, Sp_EE_18, Day 120, rep 6

description: Library name: X330-6


title: Mouse liver, Sp_EE_17, Day 120, rep 5

description: Library name: X330-5


title: Proximal HIOs_2

city: Boston

first: Pushpinder

last: Bawa

state: Massachusetts

address: 670 Albany St

department: Boston University Medical Campus

institute: Center for Regenerative Medicine

description: 10X Genomics

data_processing:
The sample was processed using the standard Cell ranger pipeline
Reads were mapped to GRCh38
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Assembly: GRCh38 supplemented with GFP
Supplementary files format and content: H5 files

source_name: iPSC-derived HIO

growth_protocol: CDX2-eGFP iPSC knock-in reporter line to track the emergence of hindgut progen, sorted on day 15 for CDX2/GFP positivity and seeded in 3D matrigel. Distal HIOs cultured in CKDCI media, Distal-cAMPs HIOs were cultured in CKDCI with cAMP and proximal HIOs were cultured in IMCK media.

extract_protocol:
The cells were dissociated to a single cell suspension using 0.05% and subsequently sorted for live cells using Calcein blue and CDX2 GFP positivity.
Single Cell RNA sequencing was then preformed using the Chromium Single Cell 3’system according to manufacturers’ instructions (10x Genomics) at the Single Cell Sequencing Core at Boston University Medical Center. All independent differentiations were expanded in parallel and sequenced at day 66 using the 10x Chromium platform on the same day to avoid technical batch effects Day 66 library generated Distal HIO (1) 2,705 cells l and Distal HIO (2) 3,342 cells. We analyzed Distal HIOs in the absence of cAMP (1) 2,619 cells and Distal HIOs in the absence of cAMP (2) 3,038 cells. We analyzed Proximal HIOs  (1) 420  cells and Proximal HIOs (2) 1,711 cells.

value: iPSC-derived HIO

value: BU1 CDX2 GFP

value: iPSC-dervied proximal HIOs in 3D

value: IMCK


title: Proximal HIOs_1

description: 10X Genomics

treatment_protocol: Distal HIOs cultured in CKDCI media, Distal-cAMPs HIOs were cultured in CKDCI with cAMP and proximal HIOs were cultured in IMCK media.


title: BT16 cells treated with Tenovin sample3

city: AURORA

first: Etienne

last: Danis

department: Cancer Center

institute: University of Colorado, Denver - Anschutz Medical Campus

description:
12_S14
Tenovin_vs_DMSO.txt

data_processing:
Alignment to GrCh38 (gSNAP)
FPKD expression derived (Cufflinks)
Differential expression (ANOVA in R)
Assembly: GrCh38
Supplementary files format and content: Tab-delimited text

source_name: cerebellum

growth_protocol: BT16 ATRT cells were cultured in RPMI medium (Life Technologies, Gibco #11875-093) supplemented with 10% fetal bovine serum (FBS; Atlanta Biologicals, Inc. #S11550) and 1% penicillin/streptomycin (Life Technologies, Gibco #15140-122).  Cells were cultured at 37 °C with 95% air and 5% CO2.

extract_protocol:
RNA was extracted from 1e6 cells using the RNEasy Mini Kit (Qiagen)
Sequencing libraries of polyA RNA were prepared using the TruSeq Library Preparation Kit v2 (Agilent)

treatment_protocol: BT16 ATRT cells were treated with DMSO or  1uM Tenovin for 72 hours. For SIRT2 knockdown experiment BT16   cells were transfected with plasmids purchased from the Functional Genomics Shared Resource, University of Colorado (shSIRT2, pLKO1.  #TRCN0000040221 and shNull, MISSION pLKO.1-puro non-Mammalian shRNA Control, Catalog #SHC002).   A total of 2.5 µg plasmid DNA and 7.5 µl Lipofectamine 3000 (Thermo Fisher Scientific, Inc., Cat #L3000-008) was used for transfection at 37 °C. The cells were selected with puromycin (1 µg/ml) following transfection.For each condition three replicates.

value: cerebellum

value: Atypical teratoid rhabdoid tumor

value: Tenovin


title: Distal -cAMP HIOs _2

description: 10X Genomics

value: iPSC-dervied distal HIOs-cAMP in 3D

value: CKDI


title: Mouse liver, Sp_573_EE_3, Day 30, rep 3

description: Library name: X342-3

value: Liver


title: Distal -cAMP HIOs _1

description: 10X Genomics


title: Mouse liver, Sp_EE_16, Day 120, rep 4

description: Library name: X330-4


title: BT16 cells treated with Tenovin sample2

description:
11_S13
Tenovin_vs_DMSO.txt


title: Mouse liver, Sp_EE_15, Day 120, rep 3

description: Library name: X330-3


title: Distal HIOs_1

description: 10X Genomics

value: iPSC-dervied distal HIOs in 3D

value: s

value: CKDCI


title: WT, uninfected, Rep3

source_name: skin

growth_protocol: Cultured in Gibco DMEM with 10% FBS and 1% penicillin-streptomycin at 37°C with 5% CO2 and tested for mycoplasma contamination approximately once every 2 months

extract_protocol:
RNA was harvested using New England BioLabs Monarch® Total RNA Miniprep Kit (T2010S) as per kit instructions.
RNA was quantified by Nanodrop and integrity was analyzed with the 4200 Tapestation Bioanalyzer system (Agilent). 500 ng of total RNA with an RNA Integrity Number (RIN) >9.5 were used to prepare sequencing libraries with the TruSeq Stranded mRNA Library Prep Kit (20020594; Illumina). Library concentrations were measured with Qubit dsDNA HS Assay Kit (Q32854; Thermo Fisher Scientific) and then analyzed with Agilent High Sensitivity D5000 ScreenTape System and pooled. Libraries were sequenced with 100-bp paired-end reads on an Illumina NextSeq2000 sequencer at the Fred Hutch Genomics Core Facility.

treatment_protocol: Lab-adapted strain of HCMV Towne (PMID: 8627734) was used. Monolayers of cells were infected for 1 h at 37°C as previously described (Lilley et al., 2005) An MOI of 1 was used for all conditions.

value: skin

value: HFF-t

value: Tert-immortalized human foreskin fibroblast

value: WT

value: mock viral infection cells incubated for 1 hr in SFM then washed with PBS

tag: time

value: Harvested 4 hp mock infection


title: Mouse liver, Sp_EE_14, Day 120, rep 2

description: Library name: X330-2


title: WT, uninfected, Rep2


title: BT16 cells transduced with SIRT2 targeting shRNA TRCN0000040221 sample3

description:
9_S11
shSIRT2_vs_shNULL.txt


title: WT, uninfected, Rep1


title: Mouse liver, Sp_EE_13, Day 120, rep 1

description: Library name: X330-1


title: BT16 cells transduced with SIRT2 targeting shRNA TRCN0000040221 sample2

description:
8_S10
shSIRT2_vs_shNULL.txt


title: WT, Towne CMV, 72 hpi, Rep3

value: Towne CMV infection incubated for 1 hr then virus removed and cells washed with PBS

value: Harvested 72 hpi


title: WT, Towne CMV, 72 hpi, Rep2


title: Mouse liver, Sp_EE_12, Day 90, rep 6

description: Library name: X309-6


title: Set1-off-veh-rep1

value: pTet-Off transformed stable cell line

value: wild type

value: undetectable/low levels of GR and MR

value: DMSO


title: WT, Towne CMV, 72 hpi, Rep1


title: Mouse liver, Sp_EE_11, Day 90, rep 5

description: Library name: X309-5


title: WT, Towne CMV, 4 hpi, Rep3

value: Harvested 4 hpi


title: BT16 cells transduced with SIRT2 targeting shRNA TRCN0000040221 sample1

description:
7_S9
shSIRT2_vs_shNULL.txt

value: cerebellum

value: Atypical teratoid rhabdoid tumor


title: Distal HIOs_2

description: 10X Genomics

value: iPSC-derived HIO

value: BU1 CDX2 GFP

value: iPSC-dervied distal HIOs in 3D


title: BT16 cells transduced with control shRNA SHC202 sample3

description:
6_S8
shSIRT2_vs_shNULL.txt

value: ShNull


title: WT, Towne CMV, 4 hpi, Rep1

value: skin

value: HFF-t

value: Tert-immortalized human foreskin fibroblast


title: WT, Towne CMV, 4 hpi, Rep2

value: WT


title: BT16 cells treated with Tenovin sample1

description:
10_S12
Tenovin_vs_DMSO.txt

value: Tenovin


title: WT, Towne CMV, 48 hpi, Rep3

value: Towne CMV infection incubated for 1 hr then virus removed and cells washed with PBS

value: Harvested 48 hpi


title: Mouse liver, Sp_EE_10, Day 90, rep 4

description: Library name: X309-4

value: Liver


title: BT16 cells transduced with control shRNA SHC202 sample2

description:
5_S7
shSIRT2_vs_shNULL.txt


title: WT, Towne CMV, 48 hpi, Rep2


title: Mouse liver, Sp_EE_9, Day 90, rep 3

description: Library name: X309-3


title: WT, Towne CMV, 24 hpi, Rep3

value: Harvested 24 hpi


title: WT, Towne CMV, 48 hpi, Rep1


title: Mouse liver, Sp_EE_8, Day 90, rep 2

description: Library name: X309-2


title: WT, Towne CMV, 24 hpi, Rep2


title: BT16 cells treated with DMSO sample 3

description:
3_S5
Tenovin_vs_DMSO.txt

value: DMSO


title: WT, Towne CMV, 24 hpi, Rep1


title: Mouse liver, Sp_EE_7, Day 90, rep 1

description: Library name: X309-1


title: WT, Towne CMV, 16 hpi, Rep3

value: Harvested 16 hpi


title: Mouse cell, cellMock_3, rep 3

description: Library name: hepa1-6 con-3


title: BT16 cells treated with DMSO sample 2

description:
2_S4
Tenovin_vs_DMSO.txt

value: cerebellum


title: Mouse liver, Sp_EE_6, Day 30, rep 6

description: Library name: X308-6


title: Mouse liver, Sp_EE_5, Day 30, rep 5

description: Library name: X308-5


title: WT, Towne CMV, 16 hpi, Rep1


title: mH2A1 KO, uninfected, Rep2

value: mH2A1 KO HFF-t

value: macroH2A1 knockout tert-immortalized human foreskin fibroblast

value: mH2A1 KO

value: mock viral infection cells incubated for 1 hr in SFM then washed with PBS

value: Harvested 4 hp mock infection


title: BT16 cells transduced with control shRNA SHC202 sample1

description:
4_S6
shSIRT2_vs_shNULL.txt

value: Atypical teratoid rhabdoid tumor

value: ShNull


title: mH2A1 KO, uninfected, Rep3

value: skin


title: Mouse liver, Sp_EE_4, Day 30, rep 4

description: Library name: X308-4


title: MR/GR cell, glucocorticoid receptor ChIP, DEX treated

city: Durham

first: John

last: Cidlowski

address: 111 T.W. Alexander Drive

institute: NIEHS

data_processing:
For each sample, raw reads obtained from different sequencing runs were pooled together. These pooled raw reads underwent filtering based on a mean base quality score exceeding 20, and adapters were trimmed using “Trim Galore” (version 0.4, https://github.com/FelixKrueger/TrimGalore). The resulting trimmed reads were mapped to hg19 using Bowtie(56) with the parameters “-m1, -v2 --best --strata -X 1500”. Afterward, aligned read files from replicate samples under each condition or treatment were merged using the 'merge' function in Samtools (Version 1.3.1)(57). Subsequently, duplicates in all merged files were eliminated using Picard (Version 1.115, http://broadinstitute.github.io/picard/). The analysis tool findPeaks from Homer (Version 4.8.3)(58) was utilized to detect ChIP-seq peaks. Its principle involves pinpointing genomic regions with a higher density of sequencing reads than anticipated randomly. The pooled input sample served as a control to account for background noise during peak identification. The findPeaks was executed with parameter “-F 2 -L 0 -C 1.5 -fdr 0.001”.
Assembly: Hg19
Supplementary files format and content: Covergage files are in BigWig format, and peak files are in .bed format

source_name: Cell line

growth_protocol: DMEM/F12 (1:1) (Gibco11330032) 10% fetal bovine serum, 1 x penicillin/streptomycin.  Cells were cultured at 37 °C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min.  After quenching and cell lysis, chromatin was sonicated using
250bp sonicated ChIPSeq samples were obtained using bead size exclusion.  NGS libraries were prepped using Swift’s 2S Sonic DNA library kit (Cat. No 42024) with Swift unique dual 8bp indices.  3-5ng total DNA was used as starting material for both the input and ip samples.  The libraries were subjected to PCR amplification for 3 cycles followed size selection using Agencourt AMPure XP beads from Beckman Coulter.  The average library size ranged from 437bp to 593bp.  The libraries were validated using Agilent’s HS DNA kit on a 2100 bioanlyzer prior to being submitted for sequencing.

treatment_protocol: Dexamethasone, 100 nM or vehicle (DMSO) for 2 hr at 37 °C.

value: Cell line

value: MR/GR cell, stable cell line developed for this study

value: This cell line was developed using U-2OS human osteosarcoma cell line

tag: chip antibody

value: Dexamethasone, 100 nM, 2hr


title: MR/GR cell, glucocorticoid receptor ChIP, vehicle treated

value: Vehicle (DMSO)


title: BT16 cells treated with DMSO sample1

description:
1_S3
Tenovin_vs_DMSO.txt


title: MR/GR cell DNA Input


title: mH2A1 KO, Towne CMV, 4 hpi, Rep3

value: Towne CMV infection incubated for 1 hr then virus removed and cells washed with PBS

value: Harvested 4 hpi


title: mH2A1 KO, Towne CMV, 72 hpi, Rep3

value: Harvested 72 hpi


title: mH2A1 KO, Towne CMV, 4 hpi, Rep2


title: mH2A1 KO, Towne CMV, 72 hpi, Rep2


title: mH2A1 KO, Towne CMV, 72 hpi, Rep1


title: Mouse liver, Sp_EE_2, Day 30, rep 2

description: Library name: X308-2

value: Liver


title: GR cell, glucocorticoid receptor ChIP, DEX treated

value: GR cell, stable cell line developed for this study


title: WT, Towne CMV, 16 hpi, Rep2

value: HFF-t

value: Tert-immortalized human foreskin fibroblast

value: WT

value: Harvested 16 hpi


title: mH2A1 KO, Towne CMV, 4 hpi, Rep1

value: mH2A1 KO HFF-t

value: macroH2A1 knockout tert-immortalized human foreskin fibroblast

value: mH2A1 KO


title: mH2A1 KO, Towne CMV, 48 hpi, Rep1

value: skin

value: Harvested 48 hpi


title: mH2A1 KO, Towne CMV, 48 hpi, Rep2


title: mH2A1 KO, Towne CMV, 48 hpi, Rep3


title: GR cell DNA Input

value: Cell line

value: This cell line was developed using U-2OS human osteosarcoma cell line


title: Set1-GR-Aldo1nm-rep2

value: pTet-Off transformed stable cell line

value: constitutive GR expression

value: expresses high levels of GR

value: aldosterone, 1nm


title: mH2A1 KO, Towne CMV, 24 hpi, Rep3

value: Towne CMV infection incubated for 1 hr then virus removed and cells washed with PBS

value: Harvested 24 hpi


title: mH2A1 KO, Towne CMV, 24 hpi, Rep2


title: mH2A1 KO, uninfected, Rep1

value: mock viral infection cells incubated for 1 hr in SFM then washed with PBS

value: Harvested 4 hp mock infection


title: Mouse liver, SF01_EE_11, Day 90, rep 5

description: Library name: X372-5

value: Liver


title: GR cell, glucocorticoid receptor ChIP, vehicle treated

value: GR cell, stable cell line developed for this study

value: Vehicle (DMSO)


title: mH2A1 KO, Towne CMV, 24 hpi, Rep1

value: mH2A1 KO HFF-t

value: macroH2A1 knockout tert-immortalized human foreskin fibroblast


title: Mouse liver, Sp_EE_3, Day 30, rep 3

description: Library name: X308-3


title: OE-3

city: Shanghai

first: Wangsheng

last: Wang

state: Please Select

address: 845 Lingshan Rd.

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava software used for base calling.
After removing the adaptor sequences and low-quality reads, the clean reads were aligned to human genome (GRCh38, NCBI) using Hisat2 with default options
High-throughput sequencing (HTseq)  was used to get gene counts and reads per kilo base per million mapped reads (RPKM) were used to determine gene expression levels
Differential expression analysis was performed using the DESeq2 algorithm
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: amnion

extract_protocol:
Total RNA was extracted from cultured primary amnion fibroblasts prepared from the TNL amnion  using Trizol reagent (Life Technologies Inc., Grand Island, NY)
RNA-sequence libraries were constructed using a TruSeq RNA sample preparation kit (Illumina Inc.) following the manufacturer’s protocol.

value: amnion

value: 72 hours

value: fibroblasts

value: transfection of nS100A9-overexpression vector


title: Mouse liver, SF01_EE_9, Day 90, rep 3

description: Library name: X372-3


title: D3 -Dox rep5

value: Ramos

value: Burkitt's Lymphoma

value: no Dox


title: mH2A1 KO, Towne CMV, 16 hpi, Rep3

value: skin

value: mH2A1 KO

value: Harvested 16 hpi


title: OE-1


title: Mouse liver, SF01_EE_10, Day 90, rep 4

description: Library name: X372-4


title: OE-2


title: NC-3

value: transfection of control vector


title: mH2A1 KO, Towne CMV, 16 hpi, Rep1

value: Towne CMV infection incubated for 1 hr then virus removed and cells washed with PBS


title: mH2A1 KO, Towne CMV, 16 hpi, Rep2


title: Mouse liver, SF01_EE_8, Day 90, rep 2

description: Library name: X372-2

value: Liver


title: Mouse liver, Sp_EE_1, Day 30, rep 1

description: Library name: X308-1


title: NC-2


title: Mouse liver, SF01_EE_12, Day 90, rep 6

description: Library name: X372-6


title: TRE3G (IGHG1) c14 +Dox rep3

value: with Dox


title: Mouse liver, SF01_EE_7, Day 90, rep 1

description: Library name: X372-1


title: AID−/− rep6

data_processing:
Demulitplexed reads were submitted to the CCseqBasicS5 pipeline with following options: bowtie2 alignment to NCBI mm9 , --tric, --flashbases 10
matrices were generated using the modified TriC_matrix_simple_MO.py script
Reads with alt least three interactions were extracted with TriCgetreads.py
Visualisation with pyplot in TriCplot.py
Find more information and scripts at https://github.com/PavriLab/tric
Assembly: NCBI HG38
Supplementary files format and content: Tab separated matrix showing normalized interaction counts
Library strategy: Tri-C

growth_protocol: Complete RPMI medium with LPS and IL4 for activation

extract_protocol:
TriC was performed as described (Downes et al 2022 with modifications desribed in Costea, Schoeberl et al 2022). In short, 10x10^6 or 15x10^6 (0h) cells were crosslinked with 2% HCHO for 8 min at room temperature. After quenching with 0,133M glycine, cells were lysed and nuclei isolated. Next, nuclei were lysed followed by NlaIII digestion (overnight), T4-DNA-ligation (overnight), Proteinase K digestion (overnight) and genomic DNA extraction. DNA was sonicated on Covaris S2 sonicator.
TriC library was prepared of 3x2µg sonicated DNA using NEBUltraII and barcoding PCRs were performed using Nextflex unique dual index barcode sequences. For capture using reagents of the Roche HyperCap target enrichment kit and mouse Cot-1, 1-2µg of libraries were 2x (72h, 24h) hybridized to 2.9nM of individual biotinylated capture probes, followed by streptavidin pull down and PCR amplification using P5 and P7 (Illumina) primer sequences. Samples were multiplexed for sequencing on NextSeq or NovaSeq (Illumina) platforms

value: AID-KO

value: untreated


title: TRE3G (IGHG3) c17 +Dox rep4


title: AID−/− rep5


title: NC-1


title: TRE3G (IGHG3) c17 -Dox rep4


title: TRE3G (IGHG1) c14 -Dox rep3


title: AID−/− rep4


title: TRE3G (IGHG1) c22 +Dox rep2


title: Mouse liver, SF01_EE_3, Day 30, rep 3

description: Library name: X366-3


title: TRE3G (IGHG3) c9 +Dox rep3


title: Mouse liver, SF01_EE_2, Day 30, rep 2

description: Library name: X366-2


title: Mouse liver, SF01_EE_4, Day 30, rep 4

description: Library name: X366-4


title: TRE3G (IGHG1) c14 -Dox rep2


title: D3 -Dox rep4


title: HepG2_P4B6_gDNA_S5, S phase

description: Library name: HepG2_P4B6_gDNA_S5

value: nucleus

value: Human liver cancer cell line

value: S phase


title: TRE3G (IGHG1) c22 +Dox rep3


title: TRE3G (IGHG1) c22 -Dox rep3


title: Mouse liver, SF01_EE_6, Day 30, rep 6

description: Library name: X366-6


title: AID−/− rep3


title: Mouse liver, SF01_EE_1, Day 30, rep 1

description: Library name: X366-1


title: TRE3G (IGHG1) c22 -Dox rep2


title: Mouse liver, Vehicle_6, Day 90, rep 3

description: Library name: X358-3


title: D3 +Dox rep4


title: AID−/− rep2


title: TRE3G (IGHG1) c22 -Dox rep1


title: Mouse liver, SF01_EE_5, Day 30, rep 5

description: Library name: X366-5


title: AID−/− rep1


title: TRE3G (IGHG1) c14 +Dox rep1


title: TRE3G (IGHG1) c22 +Dox rep1


title: TRE3G (IGHG3) c9 -Dox rep3


title: Mouse liver, Vehicle_5, Day 90, rep 2

description: Library name: X358-2


title: TRE3G (IGHG1) c14 -Dox rep1


title: TRE3G (IGHG3) c9 -Dox rep2


title: TRE3G (IGHG3) c17 +Dox rep3


title: AID−/− Eμ−/− 1C4 rep2


title: TRE3G (IGHG1) c14 +Dox rep2


title: Mouse liver, Vehicle_4, Day 90, rep 1

description: Library name: X358-1


title: TRE3G (IGHG3) c17 -Dox rep3


title: Mouse liver, Vehicle_3, Day 30, rep 3

description: Library name: X302-3


title: MOLM13_CutTag_KMT2A (MLL1)

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

institute: Hannover Medical School

description: Library name: MOLM13_CutTag_KMT2A

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human(Gencode GRCh38/hg38) genome using STAR (v2.7.5a; params --alignIntronMax 1 --alignEndsType EndToEnd --alignM atesGapMax 2000 for ChIPseq analysis), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
coverage data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75)
TSS signals were assessed using the bedtools coverage function. Signal values were normalized based on the ratio of hg38-aligning reads in treated and control samples, after deduplication.
Assembly: GRCh38/hg38
Supplementary files format and content: .bigwig file encoding coverage data for visualization in genome browser for all samples
Supplementary files format and content: .txt files containing normalized gene counts for MV4;11 cells and OCI-AML2 cells seperately
Supplementary files format and content: .xlsx files differentiall expression analysis (DESeq2 output) for MV4;11 cells and OCI-AML2 cells seperately
Library strategy: CUT&Tag

source_name: hematopoietic

growth_protocol: human AML cell lines were grown in RPMI+10%FBS+5%Pen/Strep (Gibco) at 5% CO2 and 37°C

extract_protocol:
Extraction of nuclei and Cut&Tag procedure was performed according to Kaya-Okur et al. Nat Commun. 2019 Apr 29;10(1):1930.
Library preparation from tagmented DNA was performed according to Kaya-Okur et al. Nat Commun. 2019 Apr 29;10(1):1930.

treatment_protocol: Cut&Tag was performed on steady-state cells from exponentially growing cultures without drug treatment

value: hematopoietic

value: Myeloid Leukemia (AML)

tag: antibody

value: KMT2A (MLL1)


title: AID−/− Eμ−/− 1C4 rep1

value: Ramos

value: Burkitt's Lymphoma


title: AID−/− Eμ−/− 2B11 rep5


title: MOLM13_CutTag_KAT6B (MORF)

description: Library name: MOLM13_CutTag_KAT6B

value: KAT6B (MORF)


title: Mouse liver, Vehicle_1, Day 30, rep 1

description: Library name: X302-1


title: 202826_PRO_TRE3G_IGHG1_c22_+Dox

description: SR75 High

data_processing:
The 3' adaptors were removed using cutadapt (v1.4.2 Read1: cutadapt -O 5 -a NNNNTGGAATTCTCGGTGCC ) and 9 nucleotides from their 5′ were removed.
The trimmed reads were reverse complemented using fastx_reverse_complement (http://hannonlab.cshl.edu/fastx_toolkit ).
Trimmed reads >18 were aligned using bowtie (v 1.0.0, -v 2 --best --strata --tryhard -m 1 --chunkmbs 256).
Umi-tools was used to extract UMIs and deduplicate based on the UMIs.
Unique mappers from the resulting BAM file were used to create unstranded, stranded and reverse stranded coverage tracks for visualisation using bedtools (v2.27, bedtools genomecov -split -bg, bedtools genomecov  -split -bg -strand '+', bedtools genomecov -split -bg -strand '-') and bedGraphToBigWig from the kent-tools (bedGraphToBigWig v4, bedGraphToBigWig -blockSize=256 -itemsPerSlot=1024).
Normalised coverage tracks were created by dividing the coverage at each position with the total number of aligned reads per million.
Spike-in normalised coverage tracks of the 3’ position were created using bedtools genomecov (v2.27,  bedtools genomecov -3  -bg -scale,  bedtools genomecov -3  -bg -scale '+', bedtools genomecov -3  -bg -scale '-‘)
Assembly: hybrid human drosophila genome (GRCh38.14 (Genome Reference Consortium Human Build 38) and drosophila FlyBase release 5)
Supplementary files format and content: bigWigs of rpm-normalized and spike-in normalized read densities

extract_protocol:
To isolate nuclei, human and Drosphila S2 cells were resuspended in cold Buffer IA (160 mM Sucrose, 10 mM Tris-Cl pH 8, 3 mM CaCl2, 2 mM MgAc2, 0.5% NP-40, 1 mM DTT added fresh), incubated on ice for 3 min and centrifuged at 700 g for 5 min. The pellet was resuspended in nuclei resuspension buffer NRB (50 mM Tris-Cl pH 8, 40% Glycerol, 5 mM MgCl2, 0.1 mM EDTA). For each run-on, 107 nuclei of the sample and, where indicated, 10% Drosophila S2 nuclei were combined in a total of 100 µL NRB and incubated at 30°C for 3 min with 100 µL 2x NRO buffer including 5µl of each 1mM NTPs. Reactions were terminated with TRIzol and RNA extracted as per the manufacturer's protocol.
3’ ligation was performed at 16°C overnight with adapter 5’5Phos/NNNNNNNGAUCGUCGGACUGUAGAACUCUGAAC/3InvdT-3’. RNA was reverse transcribed by SuperScript III RT with RP1 Illumina primer to generate cDNA libraries. Libraries were amplified with barcoding Illumina RPI-x primers and the universal forward primer RP1 using KAPA HiFi Real-Time PCR Library Amplification Kit. Amplified libraries were subjected to gel electrophoresis on 2.5% low melting agarose gel and amplicons from 150 to 350 bp were extracted from the gel, multiplexed and sequenced on Illumina platform NextSeq 550 SR75.

tag: clone


title: MOLM13_CutTag_IgG

description: Library name: MOLM13_CutTag_IgG

value: IgG


title: AID−/− Eμ−/− 2B11 rep4


title: MOLM13_CutTag_KAT7 (HBO1)

description: Library name: MOLM13_CutTag_KAT7

value: KAT7 (HBO1)


title: 202825_PRO_TRE3G_IGHG1_c22_-Dox

description: SR75 High

value: no Dox


title: AID−/− Eμ−/− 2B11 rep1


title: AID−/− Eμ−/− 2B11 rep2


title: 202822_PRO_TRE3G_IGHG3_c17_+Dox

description: SR75 High


title: 202824_PRO_TRE3G_IGHG1_c14_+Dox

description: SR75 High


title: 202823_PRO_TRE3G_IGHG1_c14_-Dox

description: SR75 High


title: AID−/− Eμ−/− 2B11 rep3


title: 202821_PRO_TRE3G_IGHG3_c17_-Dox

description: SR75 High


title: A40_1e mouse skin, 12 mg/kg ARN22089 treated twice a day for 1 week

city: Irvine

first: Anand

last: Ganesan

state: CA

address: 839 Health Science Ct.

department: Dermatology

institute: University of California, Irvine

description:
Library name: Inhibitor 3
indvidual raw featureCount txt file for read 1

data_processing:
HISAT2 V2.2.1
Sequence reads were trimmed to remove adaptor sequence using trimmomatic package 0.39 (TruSeq3-PE) and trimmed sequence reads were mapped to the mouse reference UCSC/mm10 (plus ERCC spike-in) genome; first set of single-reads were processed for feature count to the mouse reference UCSC/mm10 (plus ERCC spike-in) transcript.
HISAT2 v2.2.1 and samtools/1.15.1 were used to do the alignment and feature counts. Count matrix was generated in R programming and RUVSeq package was used to normalize (RUVr, residuals) and detemrine differential expression.
Assembly: mm10 and ERCC
Supplementary files format and content: indvidual text file include raw counts for each forward read samples

extract_protocol:
A small piece (3 x 3 cm setion) of the skin is removed and placed in Qiagen buffer RLT (plus mercaptoethanol). Precellys Homogenizer was used to homogenize the skin sample in Precellys beads. Rnasy kit (Qiagen) was used to extract RNA, with DNase I digestion step.
Truseq mRNA stranded library kit

treatment_protocol: Mice were gavaged twice a day for a week with 0 mg/kg vehicle or 12 mg/kg ARN22089

value: skin

value: wildtype


title: A40_2e mouse skin, 12 mg/kg ARN22089 treated twice a day for 1 week

description:
Library name: Inhibitor 4
indvidual raw featureCount txt file for read 1


title: JK242_4e mouse skin, 12 mg/kg ARN22089 treated twice a day for 1 week

description:
Library name: Inhibitor 2
indvidual raw featureCount txt file for read 1


title: 202820_PRO_TRE3G_IGHG3_c9_+Dox

description: SR75 High

value: with Dox


title: RAD21 c9 rep4 8h

value: WT


title: RAD21 c9 rep3 8h


title: MOLM13_CutTag_KAT6A (MOZ)

description: Library name: MOLM13_CutTag_KAT6A

value: KAT6A (MOZ)


title: 122237_PRO_RIEP_rep2

description: SR75 High

value: wt-RIEP

value: untreated +S2


title: 122236_PRO_RIEP_rep1

description: SR75 High


title: A39_3e mouse skin, vehicle treated twice a day for 1 week

description:
Library name: Vehicle 4
indvidual raw featureCount txt file for read 1

value: 0 mg/kg (vehicle)


title: 122231_PRO_D3_rep2

description: SR75 High

value: AID-KO


title: JK242_5e mouse skin, 12 mg/kg ARN22089 treated twice a day for 1 week

description:
Library name: Inhibitor 1
indvidual raw featureCount txt file for read 1


title: Mouse liver, Vehicle_2, Day 30, rep 2

description: Library name: X302-2

value: Liver


title: 1578_1e mouse skin, vehicle treated twice a day for 1 week

description:
Library name: Vehicle 3
indvidual raw featureCount txt file for read 1


title: 122230_PRO_D3_rep1

description: SR75 High


title: RAD21 c9 rep4 0h

value: untreated


title: NCI-H1975_ABE_sgR273H_72hpi_2

city: Dresden

first: Frank

last: Buchholz

address: Tatzberg 47/49

department: UCC / Medical Faculty and University Hospital Carl Gustav Carus

institute: Technische Universität Dresden

description:
Library name: H1975_273_2
raw_counts__new_ESO_HuCC_H1975.csv
Column name: H1975_273_2

data_processing:
Aligned to the human genome GRCh38/hg38 using STAR v2.7.3a for paired-end reads.
Aligned reads fed through featureCounts v2.0.6 of the subread package to generate the count matrix.
Assembly: GRCh38
Supplementary files format and content: Count matrix with sample IDs for columns and Ensembl gene IDs for rows.

source_name: Lung

growth_protocol: H1975, ESO-51 and HuCC-T1 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads following Novogene NGS RNA Library Prep Set protocol. Briefly, after fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP for non-directional library. The non-directional library was complete following end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: All cell lines were infected first with an ABE-GFP-PuroR lentivirus. Then, following puromycin selection, cells were infected with a mutation-targeting sgRNA-TdTomato lentivirus. RNA was isolated at 72 hours post infection.

value: Lung

value: Adenocarcinoma

value: ABE + R273H-correcting-gRNA lentivirus


title: RAD21 c9 rep3 0h

value: Ramos

value: Burkitt's Lymphoma


title: NCI-H1975_ABE_sgR273H_72hpi_1

description:
Library name: H1975_273_1
raw_counts__new_ESO_HuCC_H1975.csv
Column name: H1975_273_1


title: NCI-H1975_ABE_sgVEGF_72hpi_2

description:
Library name: H1975_VEGF_2
raw_counts__new_ESO_HuCC_H1975.csv
Column name: H1975_VEGF_2

value: ABE + VEGFA3-control gRNA lentivirus


title: Jk241_1e mouse skin, vehicle treated twice a day for 1 week

description:
Library name: Vehicle 2
indvidual raw featureCount txt file for read 1

value: skin


title: NCI-H1975_ABE_sgVEGF_72hpi_1

description:
Library name: H1975_VEGF_1
raw_counts__new_ESO_HuCC_H1975.csv
Column name: H1975_VEGF_1


title: RAD21 c9 rep2 8h


title: RAD21 c9 rep1 8h


title: 202819_PRO_TRE3G_IGHG3_c9_-Dox

description: SR75 High

value: no Dox


title: ESO_ABE_sgR175H_72hpi_2

description:
Library name: ESO_175_2
raw_counts__new_ESO_HuCC_H1975.csv
Column name: ESO_175_2

source_name: esophagus

value: esophagus


title: ESO_ABE_sgR175H_72hpi_1

description:
Library name: ESO_175_1
raw_counts__new_ESO_HuCC_H1975.csv
Column name: ESO_175_1


title: 1531_2e mouse skin, vehicle treated twice a day for 1 week

description:
Library name: Vehicle 1
indvidual raw featureCount txt file for read 1

value: wildtype


title: ESO_ABE_sgVEGF_72hpi_1

description:
Library name: ESO_VEGF_1
raw_counts__new_ESO_HuCC_H1975.csv
Column name: ESO_VEGF_1


title: HuCCT1_ABE_sgR175H_72hpi_2

description:
Library name: HuCC_175_2
raw_counts__new_ESO_HuCC_H1975.csv
Column name: HuCC_175_2

value: Intrahepatic cholangiocarcinoma


title: RAD21 c10 rep2 8h

value: WT


title: RAD21 c10 rep1 8h


title: HuCCT1_ABE_sgVEGF_72hpi_2

description:
Library name: HuCC_VEGF_2
raw_counts__new_ESO_HuCC_H1975.csv
Column name: HuCC_VEGF_2


title: HuCCT1_ABE_sgVEGF_72hpi_1

description:
Library name: HuCC_VEGF_1
raw_counts__new_ESO_HuCC_H1975.csv
Column name: HuCC_VEGF_1


title: RAD21 c9 rep2 0h


title: D1 sorted cells, Cocaine-Saline, Replicate 2

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

description: Library name: D1_CS_rep2

data_processing:
The snRNAseq data were imported as distinct 10X Genomics files for each respective sample. These files were subsequently integrated into a unified dataset while preserving the original sample identity, MSN type, and sample condition as metadata attributes.
Assembly: mm10
Supplementary files format and content: Single-cell expression is provided in 10x format in the tar file "10x_processed_files.tar". The tar file includes the accompanying metadata as a tab-delimited file named "metadata.tsv.gz"

molecule: nuclear RNA

source_name: Nucleus Accumbens

extract_protocol:
Nuclei were purified and nuclei were then immediately sorted using a BD FACS Aria II three-laser system with a 100um nozzle. Debris and doublets were first gated based on forward scatter and side scatter, nuclei were then gated as DAPI-positive events (Violet1-A laser), and GFP positive events were sorted directly into 1.5 ml Eppendorf tubes containing TriZol LS (Ambion) and flash frozen on dry ice. Samples ranged from 18,000-60,000 GFP+ nuclei collected for downstream analysis.
Processed with Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3 according to the manufacturer’s instructions to construct the scRNA-seq library.

treatment_protocol: Cocaine hydrochloride (from the National Institute on Drug Abuse) was dissolved in 0.9% saline and administered intraperitoneally at a dose of 20 mg/kg. Mice received saline or cocaine each day for 10 days prior to withdrawal. After 30 days of homecage withdrawal, mice received challenge injections of saline or cocaine and were euthanized 1 hr later. Mice were euthanized by cervical dislocation, and bilateral NAc tissue was rapidly dissected on ice from 1-mm thick coronal sections using a 14G punch and flash frozen on dry ice.

value: Nucleus Accumbens

value: Cocaine-Saline


title: D1 sorted cells, Cocaine-Saline, Replicate 1

description: Library name: D1_CS_rep1


description:
Library name: OCI-AML2_sensitive_SNDX5613_100nM_48h_rep3
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx

data_processing:
Data processing and analysis was perfomed in a Galaxy environment (version: 24.2.3) hosted at Hannover Medical School, Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation
FASTQ files were trimmed using "fastp" (default mode)
trimmed FASTQ files were aligned to the hg38 human genome using "RNA STAR" (default mode)
genome-coverage (generation of bigwig wiles) was conducted using "bamcoverage" (default mode)
aligned reads were counted at each gene using "feature counts" (default mode)
differential gene expression analysis and count normalizations were performed using "DESeq2" (default mode)
Assembly: hg38
Supplementary files format and content: .bigwig file encoding coverage data for visualization in genome browser for all samples
Supplementary files format and content: .txt files containing normalized gene counts for MV4;11 cells and OCI-AML2 cells seperately
Supplementary files format and content: .xlsx files differentiall expression analysis (DESeq2 output) for MV4;11 cells and OCI-AML2 cells seperately

extract_protocol:
RNA was extracted using the RNeasy Mini kit (Qiagen) accoding to the manufacturer's instructions
Poly-A tail selection and library preparation were performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA).

treatment_protocol: treatments were performed using the Menin inhibitor revumenib (SNDX5613) at a dose of 100nM, the KAT6/7 inhibitor PF-9363 at 2.5µM or DMSO as control for 3 days.

value: hematopoietic

value: myeloid leukemia (AML)


title: D1 sorted cells, Saline-Cocaine, Replicate 2

description: Library name: D1_SC_rep2

value: Saline-Cocaine


title: RAD21 c9 rep1 0h

city: Freiburg im Breisgau

first: Maximilian

last: von der Linde

institute: University Medical Center Freiburg

value: untreated


title: D1 sorted cells, Cocaine-Cocaine, Replicate 1

description: Library name: D1_CC_rep1

value: Cocaine-Cocaine


title: ESO_ABE_sgVEGF_72hpi_2

description:
Library name: ESO_VEGF_2
raw_counts__new_ESO_HuCC_H1975.csv
Column name: ESO_VEGF_2

value: Adenocarcinoma


title: RAD21 c10 rep2 0h

value: Ramos


description:
Library name: OCI-AML2_sensitive_SNDX5613_100nM_48h_rep2
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


description:
Library name: OCI-AML2_sensitive_SNDX5613_100nM_48h_rep1
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


title: D1 sorted cells, Saline-Cocaine, Replicate 1

description: Library name: D1_SC_rep1


description:
Library name: OCI-AML2_sensitive_PF9363_2.5uM_48h_rep3
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


description:
Library name: OCI-AML2_sensitive_PF9363_2.5uM_48h_rep2
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


title: RAD21 c10 rep1 0h

value: Burkitt's Lymphoma


title: D1 sorted cells, Cocaine-Cocaine, Replicate 2

description: Library name: D1_CC_rep2


description:
Library name: OCI-AML2_sensitive_PF9363_2.5uM_48h_rep1
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


title: OCI-AML2_sensitive_DMSO_rep2

description:
Library name: OCI-AML2_sensitive_DMSO_rep2
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


title: D1 sorted cells, Saline-Saline, Replicate 1

description: Library name: D1_SS_rep1

value: Saline-Saline


title: IGHG3TRE3G c9 rep2 (+ Dox)

value: with Dox


title: OCI-AML2_sensitive_DMSO_rep1

description:
Library name: OCI-AML2_sensitive_DMSO_rep1
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


description:
Library name: OCI-AML2_resistant_SNDX5613_100nM_48h_rep3
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


title: HuCCT1_ABE_sgR175H_72hpi_1

description:
Library name: HuCC_175_1
raw_counts__new_ESO_HuCC_H1975.csv
Column name: HuCC_175_1

value: Liver

value: ABE + R273H-correcting-gRNA lentivirus


title: D2 sorted cells, Cocaine-Cocaine, Replicate 2

description: Library name: D2_CC_rep2


title: IGHG3TRE3G c9 rep2 (- Dox)

value: no Dox


description:
Library name: OCI-AML2_resistant_SNDX5613_100nM_48h_rep2
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


title: IGHG3TRE3G c9 rep1 (+ Dox)


title: D2 sorted cells, Cocaine-Cocaine, Replicate 1

description: Library name: D2_CC_rep1


description:
Library name: OCI-AML2_resistant_SNDX5613_100nM_48h_rep1
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


description:
Library name: OCI-AML2_resistant_PF9363_2.5uM_48h_rep3
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


title: IGHG3TRE3G c9 rep1 (- Dox)


description:
Library name: OCI-AML2_resistant_PF9363_2.5uM_48h_rep1
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


title: D2 sorted cells, Cocaine-Saline, Replicate 2

description: Library name: D2_CS_rep2


description:
Library name: OCI-AML2_resistant_PF9363_2.5uM_48h_rep2
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


title: OCI-AML2_resistant_DMSO_rep3

description:
Library name: OCI-AML2_resistant_DMSO_rep3
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


title: IGHG3TRE3G c17 rep2 (+ Dox)


title: D2 sorted cells, Cocaine-Saline, Replicate 1

description: Library name: D2_CS_rep1


title: D2 sorted cells, Saline-Cocaine, Replicate 2

description: Library name: D2_SC_rep2


title: IGHG3TRE3G c17 rep2 (- Dox)


title: MV411_MEN1-WT_SNDX5613_100nM_48h_rep3

description:
Library name: MV411_MEN1-WT_SNDX5613_100nM_48h_rep3
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx


title: OCI-AML2_resistant_DMSO_rep1

description:
Library name: OCI-AML2_resistant_DMSO_rep1
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


title: IGHG3TRE3G c17 rep1 (+ Dox)


title: MV411_MEN1-WT_SNDX5613_100nM_48h_rep2

description:
Library name: MV411_MEN1-WT_SNDX5613_100nM_48h_rep2
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx


title: D1 sorted cells, Saline-Saline, Replicate 2

description: Library name: D1_SS_rep2


title: D2 sorted cells, Saline-Cocaine, Replicate 1

description: Library name: D2_SC_rep1


title: OCI-AML2_sensitive_DMSO_rep3

description:
Library name: OCI-AML2_sensitive_DMSO_rep3
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx


title: MV411_MEN1-WT_PF9363_2.5uM_48h_rep3

description:
Library name: MV411_MEN1-WT_PF9363_2.5uM_48h_rep3
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx


title: D2 sorted cells, Saline-Saline, Replicate 2

description: Library name: D2_SS_rep2


title: MV411_MEN1-WT_PF9363_2.5uM_48h_rep2

description:
Library name: MV411_MEN1-WT_PF9363_2.5uM_48h_rep2
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx


title: IGHG3TRE3G c17 rep1 (- Dox)


title: MV411_MEN1-WT_DMSO_rep3

description:
Library name: MV411_MEN1-WT_DMSO_rep3
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx


title: D2 sorted cells, Saline-Saline, Replicate 1

description: Library name: D2_SS_rep1


title: IGHG1TRE3G c22 rep2 (- Dox)


title: MV411_MEN1-WT_SNDX5613_100nM_48h_rep1

description:
Library name: MV411_MEN1-WT_SNDX5613_100nM_48h_rep1
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx


title: sample 940, CKD, Oxf

city: New York City

first: Florencia

last: Schlamp

state: New York

address: 435 East 30th Street

institute: NYU Langone Health

description: Library name: 940.H_S107

data_processing:
Quality control of sequencing reads was assessed using FastQC v0.11.7 and MultiQC v1.9
Reads were mapped to the mouse reference genome (mm10) using STAR v2.6.1d
Genomic features were assigned using Subread featureCounts v1.6.3
Assembly: mm10
Supplementary files format and content: space-delimited text file includes raw counts per sample per gene

source_name: ventricular myocardium

growth_protocol: Tissues were collected from mice (In-vivo experiment). At sacrifice, mice were anesthetized with ketamine/xylazine and perfused with PBS. Heart tissue was collected and frozen at -80C.

extract_protocol:
Total RNA was extracted from ventricular myocardium using the RNeasy Mini Kit (Qiagen, Hilden, Germany) as per the manufacturer’s protocol
RNA sequencing was performed by the NYU School of Medicine Genome Technology Center on an Illumina Novaseq 6000 instrument.

treatment_protocol: Heart tissue from mice was collected and frozen at -80C after sacrifice, as per the growth protocol.

value: ventricular myocardium

tag: strain

tag: age

value: adult

value: male

tag: sample id

tag: surgery

value: CKD

tag: bacteria

value: Oxf


title: IGHG1TRE3G c22 rep2 (+ Dox)

source_name: Ramos


title: MV411_MEN1-WT_DMSO_rep2

description:
Library name: MV411_MEN1-WT_DMSO_rep2
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx

tag: tissue

value: hematopoietic

value: myeloid leukemia (AML)


title: MV411_MEN1-WT_DMSO_rep1

description:
Library name: MV411_MEN1-WT_DMSO_rep1
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx

tag: cell type


title: IGHG1TRE3G c22 rep1 (+ Dox)

tag: treatment


description:
Library name: MV411_MEN1-M327I_SNDX5613_100nM_48h_rep3
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx

tag: cell line


title: OCI-AML2_resistant_DMSO_rep2

description:
Library name: OCI-AML2_resistant_DMSO_rep2
OCI-AML2_Revumenib-resistant-vs-sensitive_SNDX5613_PF9363_DESeq2_normcounts.txt
OCI-AML2_DEseq2_results.xlsx

tag: genotype


description:
Library name: MV411_MEN1-M327I_SNDX5613_100nM_48h_rep2
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx


description:
Library name: MV411_MEN1-M327I_SNDX5613_100nM_48h_rep1
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx


title: MV411_MEN1-M327I_PF9363_2.5uM_48h_rep3

description:
Library name: MV411_MEN1-M327I_PF9363_2.5uM_48h_rep3
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx


title: IGHG1TRE3G c14 rep2 (+ Dox)


title: MV411_MEN1-M327I_PF9363_2.5uM_48h_rep2

description:
Library name: MV411_MEN1-M327I_PF9363_2.5uM_48h_rep2
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx


title: IGHG1TRE3G c22 rep1 (- Dox)


title: MV411_MEN1-M327I_PF9363_2.5uM_48h_rep1

description:
Library name: MV411_MEN1-M327I_PF9363_2.5uM_48h_rep1
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx


title: IGHG1TRE3G c14 rep2 (- Dox)


title: sample 933, CKD, Oxf

description: Library name: 933.H_S102


title: MV411_MEN1-WT_PF9363_2.5uM_48h_rep1

description:
Library name: MV411_MEN1-WT_PF9363_2.5uM_48h_rep1
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx


title: sample 934, CKD, Oxf

description: Library name: 934.H_S103


title: MV411_MEN1-M327I_DMSO_rep2

description:
Library name: MV411_MEN1-M327I_DMSO_rep2
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx


title: MV411_MEN1-M327I_DMSO_rep3

description:
Library name: MV411_MEN1-M327I_DMSO_rep3
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx


title: sample 932, CKD, Oxf

description: Library name: 932.H_S101


title: MV411_MEN1-M327I_DMSO_rep1

description:
Library name: MV411_MEN1-M327I_DMSO_rep1
MV411_M327I-vs-WT_SNDX5613_PF9363_DESeq2_normcounts.txt
MV411_DEseq2_results.xlsx


title: RT4_LEADR_KD_02

city: Rome

first: Artem

last: Smirnov

address: Via Montpellier 1

department: Dept. of Exper. Medicine

country: Italy

institute: University of Rome "Tor Vergata"

description:
Library name: RT4_LEADR_KD_02
K_05

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses werebasedon the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then, FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package(1.20.0). The resulting P-value was adjusted using the Benjamini and Hochberg’s methods to control the error discovery rate. The corrected P-value ≤ 0.05 & |log2 (foldchange)| ≥1 was set as the threshold of significant differential expression.
Assembly: hg19
Supplementary files format and content: Gene quantification (gene_count.xls and gene_fpkm.xls) as well as differentially expressed genes are provided (DEGs.xls).

source_name: Cultured cells

growth_protocol: RT4 cells (ATCC; HTB-2) were cultured in McCoy′s medium (Gibco) supplemented with heat-inactivated 10% Fetal Bovine Serum (Invitrogen) and penicillin/streptomycin (100 µg/mL, Gibco). Cells were maintained at 37 °C and 5% CO2 humidified atmosphere. Cells were routinely checked for possible mycoplasma contamination through MycoAlert Mycoplasma Detection Kit (Lonza).

extract_protocol:
Total RNA was isolated from cells by using RNeasy Mini Kit (QIAGEN, Hilden, Germany) with 45 min DNase I digestion (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, sizeselection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection

treatment_protocol: Cells were seeded at density of 150.000 cells per well in a 6 well plate 24h prior transfection. Then the culture medium was removed, and cells were transfected with specific siRNAs for 48 h, using Optimem medium (Thermo Fisher Scientific) and Lipofectamine-RNAiMAX reagent (Thermo Fisher Scientific) according to the manufacturer’s protocol. One hunderd pmol of control siRNA (scr, mission siRNA universal negative control #1 SIC001, Sigma) or LEADR-specific (AACUGGGUGCUUUAUAUAGGA, Sigma) siRNAs were used.

value: Cultured cells

value: Bladder cancer

value: WT

value: LEADR siRNA


title: IGHG1TRE3G c14 rep1 (+ Dox)

address: Stefan-Meier-Straße 17

value: Ramos

value: Burkitt's Lymphoma


title: RT4_LEADR_KD_01

description:
Library name: RT4_LEADR_KD_01
K_04


title: sample 931, CKD, Oxf

description: Library name: 931.H_S100


title: RT4_LEADR_KD_03

description:
Library name: RT4_LEADR_KD_03
K_06


title: IGHG1TRE3G c14 rep1 (- Dox)


title: 182737_PRO_RAD21-AID_c10_8h_IAA

description: SR100 XP

value: 8h_IAA +S2


title: sample 929, sham, Oxf

description: Library name: 929.H_S98

value: sham


title: sample 935, CKD, Oxf

description: Library name: 935.H_S104


title: RT4_SCR_02

description:
Library name: RT4_SCR_02
C_02

value: Scramble siRNA


title: RT4_SCR_01

description:
Library name: RT4_SCR_01
C_01


title: sample 927, sham, Oxf

description: Library name: 927.H_S97


title: sample 936, CKD, Oxf

description: Library name: 936.H_S105


title: 182736_PRO_RAD21-AID_c10_4h_IAA

description: SR100 XP

value: 4h_IAA +S2


title: RT4_SCR_03

description:
Library name: RT4_SCR_03
C_03


title: 182734_PRO_RAD21-AID_c9_8h_IAA

description: SR100 XP


title: LNCaP_sgCtrl, biological replicate 1 (input)

city: Seattle

first: Pete

last: Nelson

state: WA

address: 1100 Eastlake Ave E

department: Human Biology

institute: Fred Hutch Cancer Center

description: Library name: LNCaP_sgCtrl_input_1

data_processing:
Raw FASTQ sequencing data were trimmed using Trimmomatic (v0.39) and aligned to the human genome (hg38) using Burrows-Wheeler Aligner (BWA-mem, v0.7.17).
Alignments with MAPQ scores lower than 30 were filtered out using SAMtools, and ENCODE blacklisted regions were excluded using BEDTools (v2.31.0).
Duplicate reads were identified and removed using Picard MarkDuplicates (v2.25.1).
Peak calling was performed using MACS3 (v3.0.0) with a q-value cutoff of 0.01.
Normalized BigWig files were generated via bamCoverage from deepTools (v3.5.4) using RPGC normalization.
Merged BigWig files were generated by concatenating BAM files from each replicate within the same cell line. Merged BED files were concatenated and merged using bedtools merge. The top 2000 peaks were selected based on the score of each peak, keeping the highest score within the same replicates.
Assembly: hg38
Supplementary files format and content: BigWig
Supplementary files format and content: narrowPeak
Supplementary files format and content: bed

source_name: LNCaP

growth_protocol: RPMI 1640 medium with 10% FBS

extract_protocol:
Fixation was carried out with 1% formaldehyde for 10 minutes at room temperature and subsequently quenched by adding 125 mM glycine. Nuclei were sequentially isolated using ice-cold LB1 buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), followed by ice-cold LB2 buffer (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). Subsequently, nuclear lysis was performed on ice for 10 minutes using ChIP lysis buffer (1% SDS, 5 mM EDTA, 50 mM Tris-HCl, pH 8.1). Chromatin was sheared to approximately 300 bp fragments with a Bioruptor Plus Sonicator (Diagenode). Immunoprecipitation was carried out using an anti-AR antibody (ab108341). Protein-DNA complexes were reverse cross-linked overnight at 65°C. ChIP and input DNA samples were purified the following day with the QIAquick PCR Purification Kit (Qiagen, 28104).
Sequencing libraries were constructed from approximately 0.8 ng ChIP DNA using the ThruPLEX DNA-Seq Prep Kit (Takara Bio, R400675) with 12 cycles of PCR amplification.

value: LNCaP

value: prostate tumor cell line

value: sgCtrl


title: LNCaP_sgCtrl, biological replicate 2 (input)

description: Library name: LNCaP_sgCtrl_input_2


title: LNCaP_sgPTGES3, biological replicate 1 (input)

description: Library name: LNCaP_sgPTGES3_input_1


title: 182735_PRO_RAD21-AID_c10_noIAA

description: SR100 XP

value: untreated +S2


title: sample 923, sham, Oxf

description: Library name: 923.H_S93

value: ventricular myocardium

value: adult

value: male

value: Oxf


title: 182733_PRO_RAD21-AID_c9_4h_IAA

description: SR100 XP


title: LNCaP_sgPTGES3, biological replicate 2, technical replicate 1 (ChIP-AR)

description: Library name: LNCaP_sgPTGES3_AR_2.1


title: sample 921, sham, Oxf

description: Library name: 921.H_S91


title: LNCaP_sgPTGES3, biological replicate 1, technical replicate 2 (ChIP-AR)

description: Library name: LNCaP_sgPTGES3_AR_1.2


title: LNCaP_sgPTGES3, biological replicate 2, technical replicate 2 (ChIP-AR)

description: Library name: LNCaP_sgPTGES3_AR_2.2


title: LNCaP_sgPTGES3, biological replicate 1, technical replicate 1 (ChIP-AR)

description: Library name: LNCaP_sgPTGES3_AR_1.1


title: sample 920, CKD, Vehicle

description: Library name: 920.H_S90

value: CKD

value: Vehicle (V)


title: LNCaP_sgCtrl, biological replicate 2, technical replicate 2 (ChIP-AR)

description: Library name: LNCaP_sgCtrl_AR_2.2


title: sample 919, CKD, Vehicle

description: Library name: 919.H_S89


title: LNCaP_sgCtrl, biological replicate 2, technical replicate 1 (ChIP-AR)

description: Library name: LNCaP_sgCtrl_AR_2.1


title: PANC1_WT3

description:
Library name: PANC1_WT3
Column name in raw_counts.csv: PANC1_WT3

source_name: Pancreas; Duct

growth_protocol: A431 and PANC-1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. HT-29 cells were maintained in McCoy's 5a Medium supplemented with 10% fetal bovine serum (FBS) and antibiotics.

treatment_protocol: All cell lines were infected first with an ABE-GFP-PuroR lentivirus. Then, following puromycin selection, cells were infected with a mutation-targeting sgRNA-TdTomato lentivirus. RNA was isolated at 36, 48 and 72 hours post infection

value: Pancreas; Duct

value: Epithelioid Carcinoma

value: PANC1 WT


title: sample 918, CKD, Vehicle

description: Library name: 918.H_S88


title: GP5d p53 reintroduced DNMTi-HDACi Rep3

city: Helsinki

first: Divyesh

last: Patel

address: University of Helsinki

department: Applied Tumor Genomics Program, Research Programs Unit, Faculty of Medicine,

country: Finland

institute: University of Helsinki

description: GP5d_p53_reintroduced_gene_expression_counts.tsv

data_processing:
Trim Galore v.0.6.7 was used to remove adaptor/overepresented sequences, discarding reads left with < 20 bp. FastQC v.0.11.9 was used for quality control.
Reads were also aligned with STAR v.2.5.3a (Dobin et al. 2013).
Gene counts were quantified by using HTSeq-count v.0.11.2 (Anders et al. 2015)
Diffential expression analysis was performed with DESeq2 v.1.32.0 (Love et al. 2014).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene expression counts for each sample.

source_name: Colon

growth_protocol: GP5d cells were grown in DMEM supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptocmycin. OE19 and LNCAP-1F5 cells were cultured in RPMI supplemented with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptomycin. Cells were checked for mycoplasma contamination and were passaged at 80% confluency.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using KAPA stranded mRNA-seq kit for Illumina (Roche) as per manufacturer’s instruction

treatment_protocol:
Cells were treated with distinct chromatin modifier enzyme inhibitors. For DNMT inhibition, cells were treated with 500 nM/L DAC (MedChemExpress, HY-A0004). Media containing DAC were replaced each day for three days. For HDAC inhibition, cells were treated with 500 nmol/L SB939 (MedChemExpress, HY-13322) for 18 hours. For SETDB1 inhibition, cells were treated with 500 nM/L Mitramycin A (MedChemExpress, HY-A0122) for 24 hours. For co-inhibition of DNMT and HDAC, cells were treated with 500 nM/L DAC. DAC containing media were replaced each day for three days followed by 500 nmol/L SB939 for 18 hours and collected for RNA isolation and ChIP-seq. For co-inhibition of DNMT and SETDB1, cells were treated with 500 nM/L DAC. Media containing DAC were replaced each day for three days followed by 500 nM/L Mitramycin A for 24 hours. For co-inhibition of HDAC and SETDB1, GP5d and OE19 cells were treated with 500 nM/L SB939 for 18 hours followed by 500 nM/L Mitramycin A for 24 hours. For DMSO control, cells were treated with DMSO (Fisher, BP231). Media containing DMSO were replaced each day for four days. For p53 reintroduction in GP5d p-53 KO cells, cells were transfected with p53 expressing pIRES2-EGFP-p53 WT plasmid (addgene # 49242). After 24 hours of transfection, cells were treated with combination of DAC (72 hours) and SB939 (18 hours) for co-inhibition of DNMT and HDAC or DMSO control (96 hours).
Generation of GP5d p53-KO and GP5d KAP1 heterozygous cell line is described in Sahu et al., Nat. Gen. (2022)

value: Colon

value: Colon  adenocarcinoma

value: DNMT HDAC co-inhibition


title: GP5d p53 reintroduced DNMTi-HDACi Rep1


title: PANC1_ABE_sgR273H_72hpi3

description:
Library name: PANC1_3dpi3
Column name in raw_counts.csv: PANC1_3dpi3

value: ABE + R273H-correcting-gRNA lentivirus


title: LNCaP_sgPTGES3, biological replicate 2 (input)

description: Library name: LNCaP_sgPTGES3_input_2

value: LNCaP


title: LNCaP_sgCtrl, biological replicate 1, technical replicate 1 (ChIP-AR)

description: Library name: LNCaP_sgCtrl_AR_1.1

value: prostate tumor cell line


title: GP5d p53 reintroduced DNMTi-HDACi Rep2


title: PANC1_ABE_sgR273H_48hpi3

description:
Library name: PANC1_48hpi3
Column name in raw_counts.csv: PANC1_48hpi3


title: sample 916, CKD, Vehicle

description: Library name: 916.H_S86


title: PANC1_ABE_sgR273H_36hpi3

description:
Library name: PANC1_36hpi3
Column name in raw_counts.csv: PANC1_36hpi3


title: GP5d p53 reintroduced DMSO Rep3

value: DMSO Control


title: sample 914, CKD, Vehicle

description: Library name: 914.H_S84


title: sample 925, sham, Oxf

description: Library name: 925.H_S95

value: sham


title: PANC1_ABE_sgR273H_72hpi2

description:
Library name: PANC1_3dpi2
Column name in raw_counts.csv: PANC1_3dpi2


title: PANC1_WT2

description:
Library name: PANC1_WT2
Column name in raw_counts.csv: PANC1_WT2


title: sample 913, CKD, Vehicle

description: Library name: 913.H_S83

value: ventricular myocardium


title: 182732_PRO_RAD21-AID_c9_noIAA

description: SR100 XP

value: Ramos

value: Burkitt's Lymphoma

value: untreated +S2


title: GP5d p53 reintroduced DMSO Rep1


title: sample 910, sham, Vehicle

description: Library name: 910.H_S82

value: adult

value: male


title: PANC1_ABE_sgR273H_48hpi2

description:
Library name: PANC1_48hpi2
Column name in raw_counts.csv: PANC1_48hpi2

value: Pancreas; Duct


title: PANC1_ABE_sgR273H_36hpi2

description:
Library name: PANC1_36hpi2
Column name in raw_counts.csv: PANC1_36hpi2

value: Epithelioid Carcinoma


title: PANC1_WT

description:
Library name: PANC1_WT_2
Column name in raw_counts.csv: PANC1_WT_2

value: PANC1 WT


title: GP5d p53-KO clone2 DNMTi-HDACi Rep3

description: GP5d_p53_KO_clone2_gene_expression_counts.tsv

value: Colon


title: LNCaP_sgCtrl, biological replicate 1, technical replicate 2 (ChIP-AR)

description: Library name: LNCaP_sgCtrl_AR_1.2

value: sgCtrl


title: PANC1_ABE_sgR273H_72hpi

description:
Library name: PANC1_3dpi
Column name in raw_counts.csv: PANC1_3dpi


title: sample 909, sham, Vehicle

description: Library name: 909.H_S81

value: Vehicle (V)


title: PANC1_ABE_sgR273H_48hpi

description:
Library name: PANC1_48hpi
Column name in raw_counts.csv: PANC1_48hpi

value: ABE + R273H-correcting-gRNA lentivirus


title: GP5d p53-KO clone2 DNMTi-HDACi Rep2

value: Colon  adenocarcinoma

value: DNMT HDAC co-inhibition


title: HT29_ABE_sgVEGF_72hpi2

description:
Library name: H_VEGF_72_2
Column name in raw_counts.csv: H_VEGF_72_2

value: Human Adenocarcinoma; Colorectal

value: ABE + VEGFA3-control gRNA lentivirus


title: GP5d p53-KO clone2 DNMTi-HDACi Rep1


title: sample 908, sham, Vehicle

description: Library name: 908.H_S80

value: ventricular myocardium

value: sham


title: HT29_ABE_sgVEGF_72hpi

description:
Library name: H_VEGF_72_1
Column name in raw_counts.csv: H_VEGF_72_1


title: sample 907, sham, Vehicle

description: Library name: 907.H_S79


title: PANC1_ABE_sgR273H_36hpi

description:
Library name: PANC1_36hpi_2
Column name in raw_counts.csv: PANC1_36hpi_2


title: GP5d p53 reintroduced DMSO Rep2

value: DMSO Control


title: HT29_ABE_sgVEGF_48hpi

description:
Library name: H_VEGF_48_1
Column name in raw_counts.csv: H_VEGF_48_1_1


title: HT29_ABE_sgVEGF_36hpi2

description:
Library name: H_VEGF_36_2
Column name in raw_counts.csv: H_VEGF_36_2


title: HT29_ABE_sgVEGF_36hpi

description:
Library name: H_VEGF_36_1
Column name in raw_counts.csv: H_VEGF_36_1_1


title: sample 905, sham, Vehicle

description: Library name: 905.H_S77


title: GP5d p53-KO clone2 DMSO Rep2


title: HT29_ABE_sgQ311*_72hpi2

description:
Library name: H_311_72_2
Column name in raw_counts.csv: H_311_72_2

value: ABE + Q311*-correcting-gRNA lentivirus


title: sample 906, sham, Vehicle

description: Library name: 906.H_S78

value: adult


title: sample 904, sham, Vehicle

description: Library name: 904.H_S76

value: male


title: HT29_ABE_sgQ311*_72hpi

description:
Library name: H_311_72_1
Column name in raw_counts.csv: H_311_72_1


title: OE19, HDACi-SETDB1i  Rep3

description: OE19_Co-inhibition_treatments_gene_expression_counts.tsv

source_name: Esophagus

value: Esophagus

value: Esophageal  adenocarcinoma

value: Wild-type

value: HDAC SETDB1 co-inhibition


title: HT29_ABE_sgQ311*_48hpi

description:
Library name: H_311_48_1
Column name in raw_counts.csv: H_311_48_1_1

value: Colon