title: exochew run3

city: Blacksburg

first: Ramu

last: Anandakrishnan

state: VA

address: 1410 Prices Fork Rd., Lab 101

department: Biomedical Sciences

institute: Edward Via College of Osteopathic Medici

description: Library name: ecoli

data_processing:
DNA sequencing data in FASTQ format were mapped to the mouse reference genome (GRCm39 for Mus musculus strain C57BL/6J) using NVIDIA Parabricks GPU-PBBWA-mem (v4.3.0-1). The samtools utility (v 1.13) was used to calculate coverage and read depth from mapped sequencing data45. The MACS2 (v 2.2.9.1) was used to identify enriched peak regions and the likely binding site within these regions. The MEME (v 5.5.6) was used to identify sequence motifs in the sequencing data.
Assembly: ecoli: GCF_000019425.1, mouse: GCF_000001635.27 (GRCm39)
Supplementary files format and content: NA_peaks.xls Excel file containg peaks identified by MACS2

organism: Escherichia coli

source_name: strain

growth_protocol: Mouse cell line, NMuMG, and human cell lines, A549 and HeLa cells were grown in DMEM with a high glucose medium containing 10% FBS (Gibco).

extract_protocol:
Cells were grown to sub-confluency in 10 cm plates, trypsinized, washed with PBS, and finally, lysed by adding 10 mM Tris (pH 7.4), 1 mM EDTA (pH 8), and 1% SDS. Chromosomal DNA was prepared using a Quick-DNA Midiprep Plus Kit (Zymogen; D4075).
The hnRNP K pull down products were converted to dsDNA using an IDT xGEN ssDNA & LowInput DNA Library Prep Kit (Cat # 10009859) through the extension step according to manufacturer’s instructions. The Oxford Nanopore Ligation Sequencing Kit (Cat # SQK-LSK114) was then used to ligate adapters and prepare the dsDNA, according to the manufacturer’s instructions

treatment_protocol: Fragmented dsDNA pools were treated with either T7 Exonuclease (T7 exo) or E. coli Exonuclease III (Exo III) to generate ssDNA pools according to manufacturer’s instructions (NEB). Briefly, 20 µg of sonication products were treated in a 1 mL reaction volume with 20 units of T7 exo (catalog # M0263; NEB). The reaction was conducted at 25⁰C for 30 min and stopped by 11 mM EDTA. For Exo III reaction, 5 µg dsDNA pool was treated with 50 units of Exo. III (catalog #M0206; NEB) in 50 µL volume. The reaction was conducted at 37⁰C for 30 min and stopped by 11 mM EDTA.

value: strain

value: K12 DH10B

value: exochew


title: RPE, Old control, Replicate 2

status: Public on Sep 19 2025

type: SRA

city: Seoul

first: Hyewon

last: Chung

address: 120 Neungdong-ro, Gwangjin-gu

country: South Korea

institute: Konkuk University

description:
Library name: lib-Cont-2-RPE
Cont-2-RPE_1

library_source: transcriptomic

data_processing:
Raw sequencing reads were trimmed to remove adapters and low-quality bases, then aligned to the Mus musculus reference genome (GRCm38, Ensembl) using Bowtie2 v2.3.4.1. Transcript abundance was estimated with featureCounts v1.6.0, and expression levels were reported as read counts and fragments per kilobase of transcript per million mapped reads (FPKM). Differentially expressed genes (DEGs) were identified using DESeq2 (p-value < 0.05, fold-change cutoff 1.5), z-score normalized, and subjected to hierarchical clustering based on Pearson correlation with Perseus software (v.1.6.1.1). Functional enrichment analysis of DEGs was performed with g:Profiler using Gene Ontology Biological Processes (GO-BPs) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and significant terms were selected using a Benjamini–Hochberg false discovery rate (FDR) threshold of 0.05. Enriched biological processes and pathways were visualized as networks in Cytoscape with the Enrichment Map plugin.
Assembly: GRCm38
Supplementary files format and content: tab-delimited xlsx file includes raw counts (RC) and FPKM

molecule: total RNA

organism: Mus musculus

source_name: Retinal pigment epithelium

extract_protocol:
Total RNA from retinal pigment epithelial was extracted using TRIzol reagent according to manufacturer's instructions. 0.5 ug of total RNA was used to generate sequencing libraries.
0.5 µg of total RNA was used to generate sequencing libraries with the Illumina TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, Inc., 20020599, San Diego, CA, USA).

tag: tissue

value: Retinal pigment epithelium

tag: age

value: aged

tag: genotype

value: Wild type

tag: treatment

value: Control


title: ATACseq_TBKLT2_7weeks

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

country: USA

institute: Northwestern University

library_source: genomic

data_processing:
Reads were aligned to mouse reference genome mm10.
Assembly: mm10
Supplementary files format and content: *.bw: bigWig file, which is a track of the smoothed transposition sites across the genome.

molecule: genomic DNA

source_name: GFP+ Treg

extract_protocol: ATACseq (Assay for transposase accessible chromatin with sequencing).

tag: strain

value: BATF knock-out

tag: cell type

value: Spleenocytes

value: 5-7 weeks


title: RPE, Vuti, Replicate 1

description:
Library name: lib-4112-1-RPE
4112-1-RPE_1

value: Vutiglabridin


title: ATACseq_TBKLT1_7weeks


title: TS603-GFP V2

first: Thomas

middle: Kieran

last: Sears

address: 303 E. Superior St.

department: Neurological Surgery

description: Library name: TS603-GFP V2

data_processing:
Raw reads were assessed for quality using FastQC and trimmed using Trim Galore v0.4.4 and Cutadapt v 1.14.
Aligned BAM files were generated using STAR and normalized TPM gene counts were generated using the Salmon algorithm
Assembly: hg38
Supplementary files format and content: Processed data files are presented as normalized TPMs

organism: Homo sapiens

growth_protocol: Serum-free, non-adherent gliomasphere cultures in Glioma Stem Cell Media (GSCM)

extract_protocol:
RNA was extracted using Qiagen's RNEasy Plus Mini Kit
RNA libraries were constructed using Complete Genomics' DNBSEQ Fast RNA Library Preparation Kit

treatment_protocol: 500 nM belinostat for 24 hours in IDH1/2 mutant glioma cultures with lentivirus-mediated overexpression of YAP 5SA or TAZ 4SA

tag: cell line

value: glioma stem-like cells

value: GFP

value: DMSO vehicle for 24 hours


title: ATACseq_WLT2_7weeks

value: Wild-type


title: non-PDA, Case14

status: Public on Sep 18 2025

city: Tokyo

first: Yuto

last: Baba

address: 35 Shinanomachi Shinjuku-ku

country: Japan

institute: Keio University School of Medicine

description:
Library name: KB7
FFPE Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were aligned to GRCh38 genome to gene expression count using Space Ranger's default settings.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: filtered gene–barcode expression matrix
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissues and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissues
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissues
Supplementary files format and content: tisse_positions.csv: list of spatial barcodes and the corrdinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Non-Prostatic ductal adenocarcinoma (PDA)

extract_protocol:
FFPE tissue blocks were sectioned at 4 μm thickness with a microtome.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacture's construction.


title: RPE, Old control, Replicate 1

description:
Library name: lib-Cont-1-RPE
Cont-1-RPE_1


title: non-PDA, Case12

description:
Library name: KO7
FFPE Spatial transcriptome sequencing

value: Non-Prostatic ductal adenocarcinoma (PDA)


title: PDA, Case3

description:
Library name: KB14
FFPE Spatial transcriptome sequencing

source_name: Prostatic ductal adenocarcinoma (PDA)

value: Prostatic ductal adenocarcinoma (PDA)


title: PDA, Case1

description:
Library name: KB1
FFPE Spatial transcriptome sequencing


title: TS603-GFP V1

description: Library name: TS603-GFP V1


title: C. Elegans, 1st generation Normoxia, replicate 2

city: St. Louis

first: Eric

middle: Lieberman

last: Greer

state: MO

address: 660 S Euclid Ave

institute: Washington University School of Medicine

description: 1st expo N2

data_processing:
Fastq files were checked for quality using FastQC before being filtered out with a Q score of 30 or above and trimmed for adapters using CutAdapt 4.0.
The trimmed reads were then aligned to the C. Elegans genome (WS235) using bowtie2 and samtools was used to convert sam outputs to sorted bam files.
FeatureCounts was used to count raw reads of genes using sorted bam files and count matrix is generated.
Assembly: WS235
Supplementary files format and content: tab-delimited text file include raw counts for each sample

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole worm, L4 stage

growth_protocol: Worms are grown on agar plates with OP50 bacteria and kept at 20 degrees C. To synchronize large plates of worms by lifestage, adult worms after laying eggs will be gently pippeted away with M9 buffer, leaving only the eggs on the bacterial lawn.

extract_protocol:
Frozen whole worm pellets are lysed and homogenized with TRI Reagent and a Kontes pellet pestle motor before total RNA is extracted using Direct-zol RNA Miniprep Kit from Zymo Research. mRNA is enriched from total RNA samples using NEXTFLEX Poly(A) Beads 2.0. In total 24 samples were prepared for RNA-seq libraries with 500 ng mRNA as starting material.
RNA-Seq libraries are prepared using NEXTFLEX Rapid Directional RNA-Seq Kit 2.0.

treatment_protocol: Once at the L4 life stage, worms are either exposed to normoxia (kept in incubator with normal atmospheric oxygen levels) or hypoxia (0.1% oxygen) for 16 hours in an Eppendorf Galaxy 48R incubator. After 16 hours of exposure, hypoxia-treated worms are moved back into incubator with nomal oxygen levels. After normoxia or hypoxia exposure, worms are washed off the plate using M9 buffer and allowed to settle to the bottom and the excess buffer is removed. A small aliquot of the worm pellet is transferred onto a new agar plate to lay eggs and the rest of the pellet is frozen by dipping microcentrifuge tube into liquid nitrogen. This process is repeated for each generation and all worm pellets are stored at -80 degrees C until extraction.

value: whole worm, L4 stage

value: WT

value: Normoxia


title: ATACseq_WLT1_7weeks


title: exochew pulldown 2025-03-13

description: Library name: mouse

source_name: mammary gland

value: mammary gland

value: NMuMG

value: cell line

value: exochew pulldown


title: ONEP subject 3 skin biopsy

city: Beijing

first: Qitian

last: Fu

state: Beijing

address: Liangxiang Campus, Beijing Technology and Business University, Gongchen Sub-district, Fangshan District, Beijing

department: Department of Cosmetics, School of Light Industry Science and Engineering

country: China

institute: Beijing Technology and Business University, Beijing, China

description:
Library name: ONEP_s3
A21:fpkm

data_processing:
Raw sequencing data in FASTQ format were quality-controlled and filtered using Fastp (version 0.22.0) to obtain clean data. The filtered reads were then mapped to the reference genome using HISAT2 (version 2.1.0)
Assembly: GRCh38 (Ensembl release 108)
Supplementary files format and content: The processed data file is a tab-delimited text file containing a gene expression matrix. Rows represent genes (annotated with Ensembl gene IDs, e.g., ENSG00000000003). Columns represent individual samples, with each sample containing two data columns: ‘read count‘ (raw counts of aligned fragments per gene) and ‘fpkm‘ (Fragments Per Kilobase of transcript per Million mapped reads, a normalized expression value).

source_name: skin

extract_protocol:
Total RNA was isolated from facial skin microbiopsy samples using TRIzol Reagent (Invitrogen Life Technologies) according to the manufacturer's instructions. RNA concentration, quality, and integrity were assessed using a NanoDrop spectrophotometer (Thermo Scientific)
Sequencing libraries were constructed from 3 μg of total RNA per sample using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (or a similar proprietary Illumina protocol). Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The purified mRNA was fragmented using divalent cations under elevated temperature in Illumina proprietary fragmentation buffer. First-strand cDNA was synthesized using random oligonucleotides and SuperScript II reverse transcriptase. Second-strand cDNA synthesis was performed using DNA Polymerase I and RNase H. The remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3' ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated. cDNA fragments of 400-500 bp in length were size-selected and purified using the AMPure XP system (Beckman Coulter). DNA fragments with ligated adapters were enriched by 15 cycles of PCR using Illumina PCR Primer Cocktail. The final library quality and quantity were assessed using the Agilent High Sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent Technologies)

value: skin


title: ONEP subject 1 skin biopsy

description:
Library name: ONEP_s1
A19:fpkm


title: ONEP subject 4 skin biopsy

description:
Library name: ONEP_s4
A22:fpkm


title: ONEP subject 2 skin biopsy

description:
Library name: ONEP_s2
A20:fpkm


title: C. Elegans, 1st generation Normoxia, replicate 1

description: 1st expo N1


title: ONEP subject 5 skin biopsy

description:
Library name: ONEP_s5
A23:fpkm


title: OEPC subject 5 skin biopsy

description:
Library name: OEPC_s5
A17:fpkm


title: OEPC subject 3 skin biopsy

description:
Library name: OEPC_s3
A15:fpkm


title: OEPC subject 2 skin biopsy

description:
Library name: OEPC_s2
A14:fpkm


title: OEP subject 6 skin biopsy

description:
Library name: OEP_s6
A12:fpkm


title: PDA, Case2

description:
Library name: KB12
FFPE Spatial transcriptome sequencing


title: OEPC subject 6 skin biopsy

description:
Library name: OEPC_s6
A18:fpkm


title: OEP subject 4 skin biopsy

description:
Library name: OEP_s4
A10:fpkm


title: OEPC subject 4 skin biopsy

description:
Library name: OEPC_s4
A16:fpkm


title: OEPC subject 1 skin biopsy

description:
Library name: OEPC_s1
A13:fpkm


title: OEP subject 1 skin biopsy

description:
Library name: OEP_s1
A7:fpkm


title: OEP subject 2 skin biopsy

description:
Library name: OEP_s2
A8:fpkm


title: OEP subject 5 skin biopsy

description:
Library name: OEP_s5
A11:fpkm


title: DNEP subject 4 skin biopsy

description:
Library name: DNEP_s4
A4:fpkm


title: non-PDA, Case13

description:
Library name: KB4
FFPE Spatial transcriptome sequencing


title: OEP subject 3 skin biopsy

description:
Library name: OEP_s3
A9:fpkm


title: DNEP subject 1 skin biopsy

description:
Library name: DNEP_s1
A1:fpkm


title: Jurkat cell stimulated ATAC-seq rep2

city: Guangzhou

first: Mulin Jun

last: Li

state: Guangdong

address: No. 9 Jinsui Road, Guangzhou

institute: Guangzhou Women and Children's Medical Center

description: Library name: Jurkat_stimulated_ATAC-seq_rep2

data_processing:
The ATAC-seq analysis sequences, including adapters and low-quality reads, were trimmed for all 150-bp paired-end ATAC-seq reads.
The clean reads were aligned to the human reference genome (GRCh37/hg19) using Bowtie2 (v2.2.1) with the default parameters.
All the samples were processed separately, and duplicate reads were removed.
The ATAC-seq peak regions of each sample were called using MACS2 (v2.1.1) with default parameters.
Assembly: GRCh37/hg19
Supplementary files format and content: bigWig

source_name: Jurkat cell

growth_protocol: Jurkat (Clone E6-1) cell line (ATCC, CRL-9855) was cultured in Iscove’s Modified Eagle’s Medium (IMDM; Thermo Fisher Scientific, 31980030) containing 10% FBS and Penicillin and Streptomycin. All cell lines were authenticated by Short Tandem Repeat (STR) and tested no mycoplasma contamination utilizing the Quantiative PCR mycoplasma detection kit (Sigma-Aldrich, MP0040A).

extract_protocol:
Jurkat cells were pretreated with DNase I (Thermo Fisher Scientific, EN0521) to digest DNA from dead cells and to eliminate free-floating DNA. The cells were counted using Crystal Violet (Sigma-Aldrich, C0775), and approximately 50,000 cells from each sample were resuspended in 1 ml of cold ATAC-Resuspension Buffer (RSB), which contained 3 mM MgCl2 (Sigma-Aldrich, M2670), 10 mM Tris-HCl (pH 7.5) (Thermo Fisher Scientific, 15567027), and 10 mM NaCl (Sigma-Aldrich, S7653) in sterile H2O. After centrifugation, the supernatant was discarded, and the cell pellets were resuspended in 50 μl of cold RSB containing 0.1% Tween-20 (Sigma-Aldrich, P1379), 0.1% NP-40 (Thermo Fisher Scientific, FNN0021), and 0.01% Digitonin (Sigma-Aldrich, D141). Following lysis, 1 ml of RSB containing 0.1% Tween-20 was added, and the tube was inverted several times to ensure thorough mixing. After centrifugation, the supernatant was removed, and the nuclei were resuspended in 50 μl of Transposition Mix (Vazyme, TD501). The transposition reaction was then incubated at 37°C for 25 minutes with shaking at 1,500 x g. The reaction products were purified using the QIAquick PCR Purification Kit (QIAGEN, 28106).
The ATAC-seq library was prepared with the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501) and the TruePrep Index Kit V2 for Illumina (Vazyme, TD202), following the kit’s instructions.

treatment_protocol: Anti-CD28 and anti-CD3 antibodies were utilized to activate T cells as previously described (Simeonov et al. Nature, 2017). Briefly, the culture plate was coated with 10 µg/ml of anti-CD28 (TONBO Biosciences, 40-0289) for 12 hours at 4°C prior to cell inoculation. Jurkat or CD4+ T cells were then seeded with 10 µg/ml of anti-CD3 (40-0038). The cells were harvested 24 hours later for subsequent experimental analysis.

value: Jurkat cell

value: Cells derived from human T cells

value: anti-CD3/CD28 stimulated


title: DNEP subject 2 skin biopsy

description:
Library name: DNEP_s2
A2:fpkm


title: DNEP subject 6 skin biopsy

description:
Library name: DNEP_s6
A6:fpkm


title: AML346

city: Munich

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

department: Research Unit Apoptosis in Hematopoietic Stem Cells

country: Germany

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany

description: Library name: AML346

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
Reads were mapped to a concatenated genome of human and mouse (hg38, mm10).
Quantification was done with ENSEMBL gene models (Homo_sapiens:GRCh38.84, Mus_musculus:GRCm38.85)
Mouse reads were excluded for further analysis
Supplementary files format and content: cell (columns) and gene (rows) -wise read counts

source_name: AML PDX line

growth_protocol: PDX cells were amplified in NSG mice and reisolated from bone marrow

extract_protocol:
prime-seq (Janjic et al., 2022)
Library was constructed using the prime-seq protocol

treatment_protocol: mice were not treated

tag: mutations panel

tag: karyotype

value: interstitielle 5q Del / interstitielle 13q Del

tag: disease status

value: R

tag: age group

value: pediatric

value: patient derived xenograft cells

tag: disease

value: acute myeloid leukemia


title: DNEP subject 3 skin biopsy

description:
Library name: DNEP_s3
A3:fpkm


title: COLO320DM_CUT&Tag-ecSEcombo-perturbation-rep1

city: Seattle

first: Chia-Lin

last: Wei

state: WA

address: 3720 15th Ave NE

department: The Northwest Genomics Center (NWGC)

institute: University of Washington

data_processing:
Raw reads in fastq format were trimmed with Trim Galore version: 0.6.6 (command: trim_galore  --stringency 3 -q 20 -e .20 --length 15)
Alignment to human genome was done with bowtie2_2.3.5 (options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 15 -X 700)
Aligned reads were quality filtered with samtools view (-F 4 -F 2048 -q 30)
Bigwig for visualization was generated with 'bedtools genomecov' and bedGraphToBigWig
Peaks were generaged with MACS2 2.2.7.1 with option: -g hs -f BAMPE -q 0.01 --keep-dup all --SPMR -B
Assembly: hg38
Supplementary files format and content: Bigwig format for fold-change visualization
Supplementary files format and content: Narrow peak file from MACS2 output
Library strategy: CUT&Tag

source_name: COLO320 DM

growth_protocol: Cells were cultivated in a humidified incubator set to 37°C and 5% CO2. PC3 DM cells were cultivated in F-12K (Kaighn's modification of Ham's F-12 medium) (30-2004, ATCC) supplemented with 10% FBS. COLO320 DM cells were grown in RPMI-1640 medium (30-2001, ATCC) supplemented with 10% FBS.

extract_protocol:
CUT&Tag was performed on 50,000 nuclei by using rabbit anti-H3K9me (39765, Active Motif) and CUTANA CUT&Tag Kit (14-1101, Epicypher) as instructed in manufacturer’s manual except that digitonin was omitted from buffers as it is not required with use of nuclei (PMID: 32913232).
Libraries are prepared based on CUTANA CUT&Tag Kit (14-1101, Epicypher) as instructed in manufacturer’s manual.

treatment_protocol: Adherent cells were seeded in 24-well plates then transfected with 700 ng sgRNA plasmid DNA using lipofectamine LTX for PC3 DM-derived lines or lipofectamine 3000 for COLO320 DM-based cell lines following manufacturer’s instructions (Thermofisher Scientific). Cells were collected 3 days after transfection

value: COLO320 DM

value: Colorectal adenocarcinoma

value: ecSEcombo-perturbation


title: DNEP subject 5 skin biopsy

description:
Library name: DNEP_s5
A5:fpkm


title: ONEP subject 6 skin biopsy

description:
Library name: ONEP_s6
A24:fpkm


title: COLO320DM_CUT&Tag-ecSE3-perturbation-rep3


title: AML573

description: Library name: AML573

value: DNMT3A, IDH2, FLT3-ITD, WT1, MLL-PTD

value: older adults


title: COLO320DM_CUT&Tag-ecSE3-perturbation-rep2


title: Jurkat cell resting ATAC-seq rep2

description: Library name: Jurkat_resting_ATAC-seq_rep2

value: resting


title: COLO320DM_CUT&Tag-ecSEcombo-perturbation-rep3


title: AML959

description: Library name: AML959

value: NPM1, FLT3-ITD, DNMT3A, TET2

value: ND


title: AML538

description: Library name: AML538

value: DNMT3A, IDH1

value: CN w/o FLT3-ITD

value: adults (unspecified)


title: COLO320DM_CUT&Tag-ecSEcombo-perturbation-rep2


title: AML602

description: Library name: AML602

value: DNMT3A, TET2, NPM1, FLT3-ITD, CEBPA, JAK3

value: complex

value: adults


title: COLO320DM_CUT&Tag-ecSE4-perturbation-rep3


title: AML663

description: Library name: AML663

value: FLT3-ITD, WT1

value: R

value: pediatric


title: AML810

description: Library name: AML810

value: FLT3-ITD, DCLK1, NPM1, DNMT3A

value: Trisomie 8

value: ID

value: young adults

value: patient derived xenograft cells

value: acute myeloid leukemia


title: AML491

description: Library name: AML491

value: DNMT3A, BCOR, NRAS, KRAS, ETV6, PTPN11, RUNX1


title: AML980

description: Library name: AML980

value: DNMT3A, TET2, NPM1, FLT3-TKD, ASXL1, FLT3-ITD

value: CN with NPM1 and FLT3-ITD

value: older adults


title: COLO320DM_CUT&Tag-ecSE4-perturbation-rep1

value: COLO320 DM

value: Colorectal adenocarcinoma


title: COLO320DM_CUT&Tag-vector-rep2

value: vector


title: COLO320DM_CUT&Tag-vector-rep1


title: COLO320DM_CUT&Tag-ecSE3-perturbation-rep1


title: COLO320DM_RNA-seq-ecSEcombo-perturbation-rep3

data_processing:
1. RNA-seq reads in fastq format were trimmed with trim_galore with the following options: --stringency 3 -q 20 -e .20 --length 15 --paired (Trim Galore version: 0.6.6; Cutadapt version: 3.2)
2. The trimmed reads then were aligned to hg38 with Hisat2.2.1 (option: librarytype='--rna-strandness RF')
3. Gene counting was performed with htseq-count 2.0.2 using the aligned reads (with option  -s reverse -m union -secondary-alignments ignore --supplementary-alignments ignore  -a 30)
4. The aligned reads in bam format was converted to bigwig format for visualization of RNA-seq coverage using "bedtools bamtobed" -> "bedtools genomecov" -> "bedGraphToBigWig"
Assembly: hg38
Supplementary files format and content: htseq-count output for gene count

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (74106, Qiagen).
300 ng of total RNA was used for construction of sequencing libraries using KAPA Stranded mRNA Sequencing Kit (KK8502, KAPA Biosystems) following the manufacturer’s instruction.

value: ecSEcombo-perturbation


title: AML415

description: Library name: AML415

value: FLT3-ITD, NPM1, DNMT3A, IDH1


title: AML640

description: Library name: AML640

value: IDH1, NPM1, FLT3-ITD

value: R


title: AML579

description: Library name: AML579

value: DNMT3A, IDH1, NPM1, FLT3-ITD

value: adults


title: COLO320DM_CUT&Tag-ecSE1-perturbation-rep1


title: AML388

description: Library name: AML388

value: KRAS

value: ID


title: COLO320DM_CUT&Tag-ecSE2-perturbation-rep3


title: COLO320DM_CUT&Tag-ecSE2-perturbation-rep2


title: AML896

description: Library name: AML896

value: DNMT3A, IDH2, FLT3-ITD, NPM1, ASXL2

value: CN

value: patient derived xenograft cells


title: AML372

description: Library name: AML372

value: TP53, KRAS

value: complex including Monosomie 17, Monosmie 7, ETV-Deletion, ATM-Deletion

value: acute myeloid leukemia


title: COLO320DM_CUT&Tag-ecSE2-perturbation-rep1

value: COLO320 DM


title: COLO320DM_CUT&Tag-ecSE1-perturbation-rep3

value: Colorectal adenocarcinoma


title: COLO320DM_CUT&Tag-ecSE4-perturbation-rep2


title: COLO320DM_RNA-seq-ecSEcombo-perturbation-rep1


title: AML842

description: Library name: AML842

value: NPM1, FLT3-ITD, DCLK1, DNMT3A

value: Trisomie 8, komplex aberranter Karyotyp

value: young adults


title: COLO320DM_RNA-seq-ecSE4-perturbation-rep1


title: COLO320DM_CUT&Tag-ecSE1-perturbation-rep2


title: COLO320DM_CUT&Tag-vector-rep3

value: vector


title: COLO320DM_RNA-seq-ecSE3-perturbation-rep2


title: RNAseq data for  MPXV infection in HMC3, replicate #3

city: Kunming

first: Zhengcun

last: Wu

address: No. 935, Jiaoling Road, Wuhua District, Kunming, Yunnan Province

institute: Institute of Medical Biology, Chinese Academy of Medical Sciences

description:
Library name: HMC3-MPXV3
MPXV infection in HMC3, replicate #3

data_processing:
The genome of human genome version of hg38 was used as reference. The sequencing quality were assessed with FastQC (v0.11.5)and then low quality data were filtered using NGSQC (v2.3.3).The clean reads were then aligned to the reference genome using HISAT2 with default parameters. The processed reads from each sample were aligned using HISAT2 against the reference genome. The gene expression analyses were performed with StringTie(v1.3.3b).
Assembly: hg38
Supplementary files format and content: Raw count files of the alignment genomes of all 18 samples

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using trizol (Invitrogen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kitfollowing manufacturer's protocols.

treatment_protocol: cells  were  infected by MPXV at MOI of 0.05,susequently ,the cellwere havested at 24hpi

tag: infection

value: infected by MPXV in 0.05 MOI


title: AML358

description: Library name: AML358

value: ND

value: R

value: pediatric


title: AML788

description: Library name: AML788

value: DNMT3A, NPM1, FLT3-ITD

value: CN with NPM1 and FLT3-ITD

value: ID

value: adults


title: COLO320DM_RNA-seq-ecSE3-perturbation-rep1


title: AML356

description: Library name: AML356

value: KRAS

value: patient derived xenograft cells


title: COLO320DM_RNA-seq-ecSE2-perturbation-rep3


title: RNAseq data for  MPXV infection in HMC3, replicate #1

description:
Library name: HMC3-MPXV1
MPXV infection in HMC3, replicate #1


title: AML981

description: Library name: AML981

value: DNMT3A, TET2, NPM1, FLT3-ITD, FLT3-TKD, WT1, ASXL1

value: older adults

value: acute myeloid leukemia


title: AML979

description: Library name: AML979

value: DNMT3A, NPM1, FLT3-ITD, IDH2, WT1

value: CN w/o FLT3-ITD


title: COLO320DM_RNA-seq-ecSE2-perturbation-rep2

value: COLO320 DM

value: Colorectal adenocarcinoma


title: COLO320DM_RNA-seq-ecSE2-perturbation-rep1


title: RNAseq data for control of HMC3, replicate #2

description:
Library name: HMC3-C2
control of HMC3, replicate #2

value: control


title: AML661

description: Library name: AML661

value: DNMT3A, BCOR, NRAS, ETV6, PTPN11, RUNX1, JAK1, EZH2


title: COLO320DM_RNA-seq-ecSE1-perturbation-rep3


title: AML393

description: Library name: AML393

value: BCOR, KRAS

value: R


title: COLO320DM_RNA-seq-ecSEcombo-perturbation-rep2

value: ecSEcombo-perturbation


title: COLO320DM_RNA-seq-ecSE1-perturbation-rep2


title: COLO320DM_RNA-seq-ecSE4-perturbation-rep3


title: AML664

description: Library name: AML664

value: ND

value: pediatric


title: AML955

description: Library name: AML955

value: DNMT3A, NPM1, WT1

value: adults (unspecified)


title: RNAseq data for  MPXV infection in U87MG, replicate #2

description:
Library name: U87MG-MPXV2
MPXV infection in U87MG, replicate #2

value: infected by MPXV in 0.05 MOI


title: RNAseq data for  MPXV infection in U87MG, replicate #1

description:
Library name: U87MG-MPXV1
MPXV infection in U87MG, replicate #1


title: COLO320DM_RNA-seq-vector-rep3

value: vector


title: RNAseq data for  MPXV infection in HMC3, replicate #2

description:
Library name: HMC3-MPXV2
MPXV infection in HMC3, replicate #2


title: RNAseq data for control of HMC3, replicate #3

description:
Library name: HMC3-C3
control of HMC3, replicate #3


title: COLO320DM_RNA-seq-ecSE1-perturbation-rep1


title: RNAseq data for  MPXV infection in U87MG, replicate #3

description:
Library name: U87MG-MPXV3
MPXV infection in U87MG, replicate #3


title: RNAseq data for control of HMC3, replicate #1

description:
Library name: HMC3-C1
control of HMC3, replicate #1


title: RNAseq data for control of U87MG, replicate #3

description:
Library name: U87MG-C3
control of U87MG, replicate #3


title: RNAseq data for  MPXV infection in SH-SY5Y, replicate #1

description:
Library name: SH-SY5Y-MPXV1
MPXV infection in SH-SY5Y, replicate #1


title: COLO320DM_RNA-seq-ecSE4-perturbation-rep2


title: HiCAR HL-1 cardiomyocytes, CRISPRa enhancer activation, rep 2

city: Durham

first: Taylor

last: Anglen

state: NC

address: 101 Science Drive, CIEMAS Rm. 2323

department: Biomedical Engineering

institute: Duke University

description:
Library name: Sample 5
HiCAR_HL-1_CRISPRa_enhanceractivation_rep2

data_processing:
Read quality was assessed with  nf-core HiCAR pipeline v1.0.0.
Reads was processed using the nf-core HiCAR pipeline v1.0.0, with mm39 as the reference genome.
A contact matrix was created from cooler files generated by the HiCAR pipeline for all reads mapping between mm39 chr14:55110000-55260000.
Differential contact frequency within the region was determined using DESeq2.
Assembly: mm39
Supplementary files format and content: Genome wide cooler files for contact matrix for each samples.
Supplementary files format and content: Tab-delimited text file (single table) including raw counts for binned contacts for all samples mapping to mm39 chr14:55110000-55260000.
Library strategy: HiCAR

growth_protocol: HL-1 cells were culture per manufactures instructions in complete Claycomb medium (Claycomb basal medium + 10% FBS + Norepinephrine (0.1mM final concentration) + 1x Glutamax + 100 U ml−1 penicillin and 100 μg ml−1 streptomycin). dx.doi.org/10.17504/protocols.io.36wgqn2yygk5/v1

extract_protocol:
300,000 HL-1 cells were fixed based on the HiCAR sequencing protocol. dx.doi.org/10.17504/protocols.io.36wgqn2yygk5/v1
HiCAR libraries were prepared based on the original HiCAR protocol. dx.doi.org/10.17504/protocols.io.36wgqn2yygk5/v1
HiCAR libraries underwent targeted enrichment for regions surrounding the Myh6 genetic locus and other cardiac genes.

treatment_protocol:
HL-1 cells were grown with or without myosin enhancer activation for 15 days. dx.doi.org/10.17504/protocols.io.36wgqn2yygk5/v1
HL-1 cells were grown with or without norepinephrine and FBS for the final 72 hours of culture. dx.doi.org/10.17504/protocols.io.36wgqn2yygk5/v1

value: atrial cardiomyocytes

tag: genetic modification

value: Enhancer activation

tag: time

value: Day 15


title: RNAseq data for  MPXV infection in SH-SY5Y, replicate #2

description:
Library name: SH-SY5Y-MPXV2
MPXV infection in SH-SY5Y, replicate #2


title: kr1 (123/p/19)-Rep2

city: Nutley

first: Neeraj

last: Chauhan

state: New Jersey

address: 111 ideation way

institute: Center for Discovery and Innovation, Hackensack Meridian Health

data_processing:
Quality control of raw sequencing reads was done using fastQC v0.11.8
Sequence reads were trimmed to remove the adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the reference genome available on ENSEMBL (https://fungi.ensembl.org/Pichia_kudriavzevii_gca_002166775/Info/Index) using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. The gene hit counts table was used for downstream differential expression analysis.
Using DESeq2, a comparison of gene expression between the two samples was performed. The Wald test was used to generate P values and Log2 fold changes. Genes with p-values < 0.05 and absolute log2 fold changes ≥ 0.585 (1.5fold change) were called differentially expressed genes for each comparison.
Assembly: https://fungi.ensembl.org/Pichia_kudriavzevii_gca_002166775/Info/Index
Supplementary files format and content: Tab-delimited txt file includes raw counts for each sample

organism: Pichia kudriavzevii

source_name: Whole yeast cell

growth_protocol: Both strains grown in YPD liquid medium at 30°C with 200 rpm shaking overnight. Next day, re-inoculated in fresh media and grown for log phase (4hours)

extract_protocol:
Total RNA was purified using the TRI reagent (Sigma). Quality of RNA was assessed on a Bioanalyzer using the RNA6000 Nanochip (Agilent).
mRNA was enriched using oligo(dT) beads (NEB) and subsequently, double-stranded cDNA libraries were generated by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

value: Whole yeast cell

tag: phenotype

value: Fluconazole-susceptible


title: COLO320DM_RNA-seq-ecSE3-perturbation-rep3

value: COLO320 DM

value: Colorectal adenocarcinoma


title: COLO320DM_RNA-seq-vector-rep1


title: RNAseq data for control of U87MG, replicate #2

description:
Library name: U87MG-C2
control of U87MG, replicate #2

value: control


title: RNAseq data for  MPXV infection in SH-SY5Y, replicate #3

description:
Library name: SH-SY5Y-MPXV3
MPXV infection in SH-SY5Y, replicate #3


title: kr1 (123/p/19)-Rep1


title: kr2 (1390/p/18)-Rep2

value: Fluconazole-resistant


title: RNA-Seq of Human sorted BM terminal erythroblasts-M3

city: Zhengzhou

first: Shihui

last: Wang

state: Henan

address: No. 7 Weiwu Road, Zhengzhou, Henan, China

department: Institute of Hematology

institute: Henan Provincial People’s Hospital

description:
Library name: NDMM-3-P7-terminal
NDMM_ery_3rd

data_processing:
Low-quality reads were removed and filtered by fastp[13]. Filtered reads were quantified by Kallisto[14] using the hg38 transcriptome index. Pairwise comparison of two groups was performed by DESeq2 [15].
Assembly: hg38
Supplementary files format and content: Excel files includes raw counts for each Sample

source_name: Bone marrow

extract_protocol:
RNA was extracted from sorted BM primary erythroid progenitor cells or terminal erythroblasts. RNA isolation, cDNA library construction, and sequencing were performed at the Annoroad Gene Technology Institute using the Illumina platform with a PE150 strategy.
RNA was extracted from sorted bone marrow-derived erythroid progenitor cells and terminal erythroblasts, followed by library preparation and Illumina PE150 sequencing. After quality control with fastp, reads were aligned to the hg38 reference genome using kallisto for expression quantification. Differential expression analysis was performed with DESeq2 (|FC|≥1, p<0.05, adjusted p<0.25). Principal component analysis (PCA) was conducted on normalized counts, and Gene Ontology (GO) enrichment analysis was performed using Metascape (p<0.001) to functionally characterize differentially expressed genes.

value: Bone marrow

value: Erythroid-terminal erythroblasts


title: RNA-Seq of Human sorted BM terminal erythroblasts-M2

description:
Library name: NDMM-2-P7-terminal
NDMM_ery_2nd


title: RNAseq data for control of U87MG, replicate #1

description:
Library name: U87MG-C1
control of U87MG, replicate #1


title: HiCAR HL-1 cardiomyocytes, CRISPRa control, rep 1

description:
Library name: Sample 1
HiCAR_HL-1_CRISPRa_control_rep1

value: Control


title: RNAseq data for control of SH-SY5Y, replicate #3

description:
Library name: SH-SY5Y-C3
control of SH-SY5Y, replicate #3


title: HiCAR HL-1 cardiomyocytes, CRISPRa enhancer activation, rep 3

description:
Library name: Sample 6
HiCAR_HL-1_CRISPRa_enhanceractivation_rep3


title: RNAseq data for control of SH-SY5Y, replicate #2

description:
Library name: SH-SY5Y-C2
control of SH-SY5Y, replicate #2


title: HiCAR HL-1 cardiomyocytes, CRISPRa enhancer activation, rep 1

description:
Library name: Sample 4
HiCAR_HL-1_CRISPRa_enhanceractivation_rep1


title: HiCAR HL-1 cardiomyocytes, CRISPRa control, rep 3

description:
Library name: Sample 3
HiCAR_HL-1_CRISPRa_control_rep3


title: COLO320DM_RNA-seq-vector-rep2


title: RNA-Seq of Human sorted BM terminal erythroblasts-H3

description:
Library name: Healthy-3-P7-terminal
healthy_ery_3rd


title: RNA-Seq of Human sorted BM terminal erythroblasts-M1

description:
Library name: NDMM-1-P7-terminal
NDMM_ery_1st


title: RNA-Seq of Human sorted BM terminal erythroblasts-H2

description:
Library name: Healthy-2-P7-terminal
healthy_ery_2nd


title: HiCAR WTC11 derived cardiomyocytes, CRISPRi control, rep 2

description:
Library name: Sample 2
HiCAR_WTC11_cardiomyocyte_CRISPRi_control_rep2

data_processing:
Read quality was assessed with  nf-core HiCAR pipeline v1.0.0.
Reads was processed using the nf-core HiCAR pipeline v1.0.0, with Hg38 as the reference genome.
A contact matrix was created from cooler files generated by the HiCAR pipeline for all reads mapping to hg38 chr14:23,300,000–23,460,000.
Differential contact frequency within the region was determined using DESeq2.
Assembly: hg38
Supplementary files format and content: Genome wide cooler files for contact matrix for each samples.
Supplementary files format and content: Tab-delimited text file (single table) including raw counts for binned contacts for all samples mapping to hg38 chr14:23,300,000–23,460,000.
Library strategy: HiCAR

growth_protocol:
WTC11 cells were maintained in mTeSR+ basal medium with 5x supplement.
WTC11 derived cardiomyocyte cells were maintained in RPM1640 medium supplemented with B27 supplement (ThermoFisher) and 100 units/mL of penicillin, 100 units/mL of streptomycin.

extract_protocol:
300,000 WTC11 derived cardiomyocytes were fixed based on the HiCAR sequencing protocol.
HiCAR libraries were prepared based on the original HiCAR protocol.
HiCAR libraries underwent targeted enrichment for regions surrounding the MYH6 genetic locus and other cardiac genes.

treatment_protocol:
WTC11 cells were differentiated into cardiomyocytes.
WTC11 derived cardiomyocytes were grown with or without myosin enhancer repression for 15 days.

value: induced pluripotent stem cell derived cardiomyocytes

value: cardiomyocyte differentiation


title: RNA-Seq of Human sorted BM terminal erythroblasts-H1

description:
Library name: Healthy-1-P7-terminal
healthy_ery_1st


title: HiCAR WTC11 derived cardiomyocytes, CRISPRi enhancer repression, rep 3

description:
Library name: Sample 4
HiCAR_WTC11_cardiomyocyte_CRISPRi_enhancerrepression_rep2

value: Enhancer repression


title: HiCAR HL-1 cardiomyocytes, CRISPRa control, rep 2

description:
Library name: Sample 2
HiCAR_HL-1_CRISPRa_control_rep2


title: kr2 (1390/p/18)-Rep1


title: HiCAR WTC11 derived cardiomyocytes, CRISPRi enhancer repression, rep 2

description:
Library name: Sample 3
HiCAR_WTC11_cardiomyocyte_CRISPRi_enhancerrepression_rep1


title: RNA-Seq of Human sorted BM primary erythroid progenitor cells-M1

description:
Library name: NDMM-1-P8-Progenitor
MM_prog_1st

value: primary erythroid progenitor cells


title: HiCAR WTC11 derived cardiomyocytes, CRISPRa enhancer activation, 1uM, rep 2

description:
Library name: Sample 8
HiCAR_WTC11_cardiomyocyte_CRISPRaenhanceractivation_1umET1_rep2

growth_protocol:
WTC11 cells were maintained in mTeSR+ basal medium with 5x supplement. dx.doi.org/10.17504/protocols.io.3byl49mdrgo5/v1
WTC11 derived cardiomyocyte cells were maintained in RPM1640 medium supplemented with B27 supplement (ThermoFisher) and 100 units/mL of penicillin, 100 units/mL of streptomycin. dx.doi.org/10.17504/protocols.io.3byl49mdrgo5/v1

extract_protocol:
300,000 WTC11 derived cardiomyocytes were fixed based on the HiCAR sequencing protocol. dx.doi.org/10.17504/protocols.io.3byl49mdrgo5/v1
HiCAR libraries were prepared based on the original HiCAR protocol.
HiCAR libraries underwent targeted enrichment for regions surrounding the MYH6 genetic locus and other cardiac genes.

treatment_protocol:
WTC11 cells were differentiated into cardiomyocytes. dx.doi.org/10.17504/protocols.io.3byl49mdrgo5/v1
WTC11 derived cardiomyocytes were grown with or without myosin enhancer activation for 15 days. dx.doi.org/10.17504/protocols.io.3byl49mdrgo5/v1
WTC11 derived cardiomyocytes were grown with or without 1uM Endothelin-1 for the last 72 hours of cultured. dx.doi.org/10.17504/protocols.io.3byl49mdrgo5/v1

tag: stimulus

value: 1µM Endothelin-1


title: HiCAR WTC11 derived cardiomyocytes, CRISPRi control, rep 1

description:
Library name: Sample 1
HiCAR_WTC11_cardiomyocyte_CRISPRi_control_rep1


title: HiCAR WTC11 derived cardiomyocytes, CRISPRa enhancer activation,1uM, rep 3

description:
Library name: Sample 10
HiCAR_WTC11_cardiomyocyte_CRISPRaenhanceractivation_1umET1_rep3


title: RNA-Seq of Human sorted BM primary erythroid progenitor cells-M2

description:
Library name: NDMM-2-P8-Progenitor
MM_prog_2nd

tag: tissue


title: RNA-Seq of Human sorted BM primary erythroid progenitor cells-H3

description:
Library name: Healthy-3-P8-Progenitor
healthy_prog_3rd


title: RNA-Seq of Human sorted BM primary erythroid progenitor cells-M3

description:
Library name: NDMM-3-P8-Progenitor
MM_prog_3rd


title: HiCAR WTC11 derived cardiomyocytes, CRISPRa enhancer activation, 0µM, rep 3

description:
Library name: Sample 9
HiCAR_WTC11_cardiomyocyte_CRISPRaenhanceractivation_0umET1_rep3

value: 0µM Endothelin-1


title: RNA-seq WTC11 derived cardiomyocytes, GSK3 inhibition, rep 3

description:
Library name: Sample 6
RNA_WTC11_cardiomyocyte_chir4um_rep3

data_processing:
Consistent quality validation using FastQC v0.11.2 (Babraham Institute). Raw reads were trimmed to remove adapters and bases with average quality score (Q; Phred33) of 20 using a 4-bp sliding window (SlidingWindow:4:20) with Trimmomatic v0.32 (Bolger et al., 2014).
Trimmed reads using Trimmomatic v0.32 to remove adapters, and then align to GRCh38 using the STAR aligner v2.4.1a.
Obtained gene counts with featureCounts from the subread package (version 1.4.6-p4) using the comprehensive gene annotation in Gencode v22.
Conduct differential expression analysis with DESeq2, where gene counts are fitted to a negative binomial generalized linear model, and a Wald test identifies significantly differentially expressed genes.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file (single table) including TPM values and ENSEMBL IDs for all samples and genes in Gencode v22.

growth_protocol:
WTC11 cells were maintained in mTeSR+ basal medium with 5x supplement. dx.doi.org/10.17504/protocols.io.kqdg32rb1v25/v1
WTC11 derived cardiomyocyte cells were maintained in RPM1640 medium supplemented with B27 supplement (ThermoFisher) and 100 units/mL of penicillin, 100 units/mL of streptomycin. dx.doi.org/10.17504/protocols.io.kqdg32rb1v25/v1

extract_protocol:
RNA was harvested using Norgen's Total RNA Plus Purification Kit.
RNA libraries were prepared by Azenta Life Sciences.

treatment_protocol:
WTC11 cells were differentiated into cardiomyocytes. dx.doi.org/10.17504/protocols.io.kqdg32rb1v25/v1
WTC11 derived cardiomyocytes were grown with or without GSK3 inhibition (CHIR99021, 4µM, Cayman Chemical) for 1 week.dx.doi.org/10.17504/protocols.io.kqdg32rb1v25/v1

value: GSK3 inhibition

value: Day 7


title: RNA-Seq of Human sorted BM primary erythroid progenitor cells-H4

description:
Library name: Healthy-4-P8-Progenitor
healthy_prog_4th


title: RNAseq data for control of SH-SY5Y, replicate #1

description:
Library name: SH-SY5Y-C1
control of SH-SY5Y, replicate #1


title: HiCAR WTC11 derived cardiomyocytes, CRISPRa enhancer activation, 0µM, rep 2

description:
Library name: Sample 7
HiCAR_WTC11_cardiomyocyte_CRISPRaenhanceractivation_0umET1_rep2

value: Enhancer activation

value: Day 15


title: HiCAR WTC11 derived cardiomyocytes, CRISPRa control, 1uM, rep 1

description:
Library name: Sample 2
HiCAR_WTC11_cardiomyocyte_CRISPRaControl_1umET1_rep1


title: HiCAR WTC11 derived cardiomyocytes, CRISPRa enhancer activation, 1uM, rep 1

description:
Library name: Sample 6
HiCAR_WTC11_cardiomyocyte_CRISPRaenhanceractivation_1umET1_rep1


title: HiCAR WTC11 derived cardiomyocytes, CRISPRa enhancer activation, 0µM, rep 1

description:
Library name: Sample 5
HiCAR_WTC11_cardiomyocyte_CRISPRaenhanceractivation_0umET1_rep1


title: Canine iPSCs (SUC0329-5 (OMUiD06-UG)), AR, passage 13

city: Stanford

first: Kyomi

middle: J

last: Igarashi

state: CA

address: 265 Campus Drive

department: Genetics

institute: Stanford University

description: Library name: SUC0329-5_p13_in_A+R

data_processing:
Sequence reads were screened for quality (fastQC), then trimmed for adaptor and low-quality sequences (TrimGalore). Trimmed reads were mapped to the Ensembl ROS Cfam 1.0 dog genome (STAR), then raw gene counts generated (featureCounts).
Assembly: ROS Cfam 1.0
Supplementary files format and content: tab-delimited file with raw counts for each sample

organism: Canis lupus familiaris

growth_protocol: Canine induced pluripotent stem cells were cultured in either StemFit (control) or StemFit+10uM IWR1 and 20ng/ml Activin (AR medium)

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA Plus (Macherey-Nagel).
RNA libraries were prepared using the TrueSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacturer's instructions.

value: canine iPSCs

value: Cultured in AR medium


title: RNA-seq WTC11 derived cardiomyocytes, control, rep 3

description:
Library name: Sample 3
RNA_WTC11_cardiomyocyte_control_rep3


title: RNA-seq WTC11 derived cardiomyocytes, GSK3 inhibition, rep 1

description:
Library name: Sample 4
RNA_WTC11_cardiomyocyte_chir4um_rep1


title: Canine iPSCs (SU831162 (OPUiD06-UE-2)), AR, passage 13

description: Library name: SU831162_p13_in_A+R


title: HiCAR WTC11 derived cardiomyocytes, CRISPRa control, 0µM, rep 2

description:
Library name: Sample 3
HiCAR_WTC11_cardiomyocyte_CRISPRaControl_0umET1_rep2


title: RNA-seq WTC11 derived cardiomyocytes, control, rep 2

description:
Library name: Sample 2
RNA_WTC11_cardiomyocyte_control_rep2


title: HiCAR WTC11 derived cardiomyocytes, CRISPRa control, 0µM, rep 1

description:
Library name: Sample 1
HiCAR_WTC11_cardiomyocyte_CRISPRaControl_0umET1_rep1


title: ATAC-seq WTC11 derived cardiomyocytes, GSK3 inhibition, rep 3

description:
Library name: Sample 6
ATAC_WTC11_cardiomyocyte_chir4um_rep3

data_processing:
Read quality was assessed with FastQC and adapters were trimmed with Trimmomatic. Trimmed reads were aligned to the hg38 reference genome using Bowtie (v1.0.0) using parameters -v 2 --best --strata -m 1.
ENCODE blacklisted regions and duplicated reads were removed using Picard MarkDuplicates and bedtools (v2.19.1)
ATAC peaks were called using the MACS2 (v2.1.1) callpeak function. (8) For visualization, deepTools bamCoverage was used to generate bigwig files with counts per million (CPMs) from deduplicated BAM files.
A union peak set was generated from MACS2 narrowPeak files across all samples. Count files for each sample were produced using featureCounts.
Differential accessibility within the union ATAC peak set was determined using DESeq2 (Padj < 0.05).
Assembly: hg38
Supplementary files format and content: bigWig files normalized by library size.
Supplementary files format and content: NarrowPeak files with peak information and signal.

growth_protocol:
WTC11 cells were maintained in mTeSR+ basal medium with 5x supplement. dx.doi.org/10.17504/protocols.io.5qpvokj27l4o/v1
WTC11 derived cardiomyocyte cells were maintained in RPM1640 medium supplemented with B27 supplement (ThermoFisher) and 100 units/mL of penicillin, 100 units/mL of streptomycin. dx.doi.org/10.17504/protocols.io.5qpvokj27l4o/v1

extract_protocol:
Nuclei were extract from 50,000 WTC11 derived cardiomyocytes based on the Omni-ATAC-seq protocol
ATAC-seq libraries were prepared based on the Omni-ATAC-seq protocol

treatment_protocol:
WTC11 cells were differentiated into cardiomyocytes. dx.doi.org/10.17504/protocols.io.5qpvokj27l4o/v1
WTC11 derived cardiomyocytes were grown with or without GSK3 inhibition (CHIR99021, 4µM, Cayman Chemical) for 1 week. dx.doi.org/10.17504/protocols.io.5qpvokj27l4o/v1


title: Canine iPSCs (OPUiDO5A), AR, passage 22

description: Library name: OPUiDO5A_p22_in_A+R


title: ATAC-seq WTC11 derived cardiomyocytes, GSK3 inhibition, rep 2

description:
Library name: Sample 5
ATAC_WTC11_cardiomyocyte_chir4um_rep2


title: Canine iPSCs (OPUiDO5A), AR, passage 21

description: Library name: OPUiDO5A_p21_in_A+R


title: Canine iPSCs (SUC0329-5 (OMUiD06-UG)), StemFit, passage 13

description: Library name: SUC0329-5_p13_in_StemFit

value: Cultured in control medium


title: ATAC-seq WTC11 derived cardiomyocytes, GSK3 inhibition, rep 1

description:
Library name: Sample 4
ATAC_WTC11_cardiomyocyte_chir4um_rep1


title: RNA-Seq of Human sorted BM primary erythroid progenitor cells-H1

description:
Library name: Healthy-1-P8-Progenitor
healthy_prog_1st


title: Canine iPSCs (OPUiDO5A), StemFit, passage 22

description: Library name: OPUiDO5A_p22_in_StemFit


title: Canine iPSCs (SU831162 (OPUiD06-UE-2)), StemFit, passage 13

description: Library name: SU831162_p13_in_StemFit


title: ATAC-seq WTC11 derived cardiomyocytes, control, rep 2

description:
Library name: Sample 2
ATAC_WTC11_cardiomyocyte_control_rep2


title: Canine iPSCs (OPUiDO5A), StemFit, passage 21

description: Library name: OPUiDO5A_p21_in_StemFit


title: ATAC-seq WTC11 derived cardiomyocytes, control, rep 3

description:
Library name: Sample 3
ATAC_WTC11_cardiomyocyte_control_rep3


title: HiCAR WTC11 derived cardiomyocytes, CRISPRa control, 1uM, rep 2

description:
Library name: Sample 4
HiCAR_WTC11_cardiomyocyte_CRISPRaControl_1umET1_rep2


title: RNA-seq WTC11 derived cardiomyocytes, GSK3 inhibition, rep 2

description:
Library name: Sample 5
RNA_WTC11_cardiomyocyte_chir4um_rep2


title: iPSC

city: bunkyo-ku

first: Masato

last: Miyoshi

address: yushima

department: Gastroenterology

institute: Tokyo Medical and Dental University

description: Library name: iPSC

data_processing:
The TruSeq Stranded mRNA protocol was used for the preparation of RNA-seq libraries and sequenced on a Illumina NovaSeq 6000, as paired-end, 101 base paires reads.
The sequencing reads were trimmed using Trimmomatic 0.38.
Trimmed  reads were aligned to the GRCh38 genome assembly using HISAT2 version 2.1.0.
Read count extraction and normalization were performed by StringTie version 2.1.3b.
Assembly: GRCh38
Supplementary files format and content: tab-delimited csv files include read counts

extract_protocol:
Total RNA was extracted by RNeasy Micro (QIAGEN, Venlo, Netherlands).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

value: iPSC

tag: group


title: iPS-HSC-Sph-2

description: Library name: iPS-HSC-Sph-2

value: iPS-HSC-Sph


title: K562_BRG1_Plate_1

city: Saint Louis

first: Michael

middle: P

last: Meers

state: Missouri

address: 660 Euclid Ave

description:
Library name: GBe022s9_K562_BRG1-Abcam_Rep1_S9_L001
K562_BRG1-Abcam_Rep1

data_processing:
Raw fastq files were aligned to the UCSC hg38 genome build using Bowtie2, version 2.4.2, with parameters –end-to-end–very-sensitive–no-mixed–no-discordant -q–phred33 -I 10 -X 700.
Mapped reads were filtered using Samtools view -b -F 12 and converted to paired-end BED files containing coordinates for the termini of each read pair.
Paired-end bed files were converted to bedGraph files using BEDTools genomecov with parameter –bg.
Bedgraphs were converted to BigWig files using the UCSC bedgraphToBigwig function for visualization in the Integrative Genomics Viewer Genome Browser.
Assembly: hg38
Supplementary files format and content: bed, bigwig
Library strategy: CUT&Tag

growth_protocol: K562 and RS4-11 cells were cultured in liquid suspension; the former in IMDM (ATCC) with 10% FBS added (Seradigm), and the latter in RPMI (ATCC) with 10% FBS added.

extract_protocol:
Lightly cross-linked nuclei were prepared from cells as described in steps 2–14 of the Bench Top CUT&Tag protocol on protocols.io (https://doi.org/10.17504/protocols.io.bcuhiwt6). In brief, cells were pelleted for 3 minutes at 600g, resuspended in hypotonic NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM spermidine, 10% Triton X-100 and 20% glycerol) and incubated on ice for 10 minutes. The mixture was pelleted for 4 minutes at 1,300g, resuspended in 1× PBS and fixed with 0.1% formaldehyde for 2 minutes before quenching with 60 mM glycine. Nuclei were counted using the ViCell Automated Cell Counter (Beckman Coulter) and frozen at −80 °C in 10% DMSO at a concentration of 1M nuclei/mL for future use. Blood and bone marrow samples were collected at presentation from adult patients with de novo AML on an Institutional Review Board–approved banking protocol (#201011766). Nuclei were extracted from samples according to the nuclei preparation protocol listed above with the following modifications: NE1 hypotonic lysis buffer incubation time was optimized for each individual patient sample based on percentage of trypan blue-positive nuclei yield from input cells, with all samples incubated for between 45 seconds-2 minutes. All patient samples were preserved as native nuclei without formaldehyde crosslinking at a maximum concentration of 1M nuclei/mL. Specific samples for which fewer than 1M nuclei were recovered were preserved at a concentration lower than 1M nuclei/mL.
CUT&Tag-Direct: CUT&Tag-Direct was carried out as previously described (https://doi.org/10.17504/protocols.io.bcuhiwt6). In brief, nuclei were thawed and bound to washed paramagnetic concanavalin A (ConA) beads (Bangs Laboratories) at a concentration of 5 µL washed beads per 50K nuclei, and then incubated with primary antibody at 4 °C overnight in Wash Buffer (10 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and Roche Complete Protease Inhibitor Cocktail) with 2 mM EDTA. Bound nuclei were washed and incubated with 1:100 secondary antibody for 1 hour at room temperature and then washed 2x and incubated in Wash-300 Buffer (Wash Buffer with 300 mM NaCl) with 1:50 5 µM loaded pA–Tn5 for 1 hour at room temperature. Nuclei were washed 2x and tagmented in Wash-300 Buffer with 10 mM MgCl2 for 1 hour at 37 °C and then resuspended sequentially in 50 µl of 10 mM TAPS and 5 µl of 10 mM TAPS with 0.1% SDS and incubated for 1 hour at 58 °C. The resulting suspension was mixed well with 16 µl of 0.9375% Triton X-100, and then 2 µL each of F and R primers and 25 µL 2× NEBNext Master Mix (New England Biolabs) were added for direct amplification with the following conditions: (1) 58 °C for 5 minutes, (2) 72 °C for 5 minutes, (3) 98 °C for 30 seconds, (4) 98 °C 15 seconds, (5) 60 °C for 15 seconds, (6) repeat steps 4–5 13 times, (7) 72 °C for 1 minute and (8) hold at 8 °C. DNA from amplified product was purified using 1.1× ratio of HighPrep PCR Cleanup System (MagBio) and resuspended in 25 µl of 10 mM Tris-HCl with 1 mM EDTA, and concentration was quantified using the Qubit (Thermo Fisher Scientific) and TapeStation (Agilent) systems. Plate-CUT&Tag: CUT&Tag-Direct experiments were carried out in individual wells of twin.tec lo-bind 96-well PCR microplates (Eppendorf) using multi-channel pipettes and reservoirs, with the following modifications: After tagmentation and washing with 10 mM TAPS, beads were resuspended individually well-by-well in 16 µL 10 mM TAPS with 0.1% SDS using a single-channel pipette with vigorous pipette mixing. The plate was sealed and vortexed briefly for 10 seconds at 1000 RPM on a Thermomixer (Eppendorf). The sealed plate was spun briefly in a swinging bucket rotor, then denatured on a 96 well deep block thermal cycler (BioRad) for 1 hour at 58˚C. After denaturation, samples were neutralized with 5 µL 10% Triton X-100, and the plate was re-sealed and vortexed briefly for 10 seconds at 1000 RPM on the Thermomixer. Primers and NEBNext 2x Master Mix were then added, mixed, and the plate amplified according to the CUT&Tag-Direct thermal cycler program on a 96 well block. Libraries were purified and eluted as described above.

value: CML

tag: patient id

tag: method

value: Plate

tag: replicate


title: iPS-HSC-Sph-1

description: Library name: iPS-HSC-Sph-1

tag: cell type


title: rs411_PolII_Plate_2

description:
Library name: GBe022s8_rs411_PolII-Total_Rep2_S8_L001
rs411_PolII-Total_Rep2

tag: cell line

value: ALL

tag: treatment

value: PolII


title: RNA-seq WTC11 derived cardiomyocytes, control, rep 1

description:
Library name: Sample 1
RNA_WTC11_cardiomyocyte_control_rep1

value: induced pluripotent stem cell derived cardiomyocytes

value: cardiomyocyte differentiation

value: Control


title: iPS-HSC-1

description: Library name: iPS-HSC-1

value: iPS-HSC


title: K562_PolII_Plate_2

description:
Library name: GBe022s6_K562_PolII-Total_Rep2_S6_L001
K562_PolII-Total_Rep2


title: iPS-HSC-2

description: Library name: iPS-HSC-2


title: iPS-Hep-2

description: Library name: iPS-Hep-2

value: iPS-Hep


title: rs411_H3K4me3_Plate_2

description:
Library name: GBe022s4_rs411_H3K4me3_Rep2_S4_L001
rs411_H3K4me3_Rep2


title: iPS-Hep-Sph-2

description: Library name: iPS-Hep-Sph-2

value: iPS-Hep-Sph


title: K562_PolII_Plate_1

description:
Library name: GBe022s5_K562_PolII-Total_Rep1_S5_L001
K562_PolII-Total_Rep1


title: CoSp-SortHSC-5

description: Library name: CoSp-SortHSC-5

value: CoSp-SortHSC


title: rs411_IgG_Plate_1

description:
Library name: GBe022s29_rs411_IgG_Rep1_S29_L001
rs411_IgG_Rep1

value: IgG


title: K562_H3K4me3_Plate_2

description:
Library name: GBe022s2_K562_H3K4me3_Rep2_S2_L001
K562_H3K4me3_Rep2


title: iPS-Hep-Sph-1

description: Library name: iPS-Hep-Sph-1


title: CoSp-SortHSC-4

description: Library name: CoSp-SortHSC-4


title: iPS-Hep-1

description: Library name: iPS-Hep-1


title: rs411_IgG_Plate_2

description:
Library name: GBe022s30_rs411_IgG_Rep2_S30_L001
rs411_IgG_Rep2


title: rs411_H3K4me3_Plate_1

description:
Library name: GBe022s3_rs411_H3K4me3_Rep1_S3_L001
rs411_H3K4me3_Rep1


title: K562_IgG_Plate_2

description:
Library name: GBe022s26_K562_IgG_Rep2_S26_L001
K562_IgG_Rep2


title: CoSp-SortHep-2

description: Library name: CoSp-SortHep-2

value: CoSp-SortHep


title: rs411_KMT2A_Plate_1

description:
Library name: GBe022s27_rs411_KMT2A_Rep1_S27_L001
rs411_KMT2A_Rep1


title: K562_IgG_Plate_1

description:
Library name: GBe022s25_K562_IgG_Rep1_S25_L001
K562_IgG_Rep1


title: CoSp-SortHSC-3

description: Library name: CoSp-SortHSC-3


title: rs411_KMT2A_Plate_2

description:
Library name: GBe022s28_rs411_KMT2A_Rep2_S28_L001
rs411_KMT2A_Rep2


title: ATAC-seq WTC11 derived cardiomyocytes, control, rep 1

description:
Library name: Sample 1
ATAC_WTC11_cardiomyocyte_control_rep1

value: Day 7


title: rs411_Menin_Plate_2

description:
Library name: GBe022s24_rs411_Menin_Rep2_S24_L001
rs411_Menin_Rep2

value: Menin


title: rs411_Menin_Plate_1

description:
Library name: GBe022s23_rs411_Menin_Rep1_S23_L001
rs411_Menin_Rep1


title: CoSp-SortHep-3

description: Library name: CoSp-SortHep-3

value: iPSC


title: A549 cells, Ad-mCherry, Replicate 3

city: Hsinchu

first: Chia-Chan

last: Hsu

address: 101, Section2, Kuan-Fu Road

department: Institute of Biotechnology

country: Taiwan

institute: National Tsing Hua University

data_processing:
Illumina Casava software used for basecalling.
FastQC and MultiQC were used to check fastq files for quality.The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Read pairs from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0).
FeatureCounts (v2.0.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Relative Log Expression” normalization (RLE) was performed DEGseq2 (v1.26.0).
Assembly: GRCh38
Supplementary files format and content: xls file contains raw count, TPM and FPKM of each gene for every samples
Supplementary files format and content: xls file contains normalized counts each gene for every samples

source_name: Lung carcinomatous tissue

growth_protocol: A549 cell line was cultured in RPMI-1640  (10% FBS, 2mM L-glutamine and 100U/ml Penicillin-Streptomycin) and passaged evey 3 days.

extract_protocol:
Total RNAs were extracted using NucleoSpin RNA mini kit (#740955.5, MACHEREY-NAGEL) according to the manufacturer's instruction.
RNA libraries were prepared for sequencing using KAPA mRNA HyperPrep Kit Illumina® Platforms protocol

treatment_protocol: Adenovirus was applied to A549 cells at an MOI of 5 for 24 hours of incubation.

value: Lung carcinomatous tissue

value: Adherent

tag: genotype

value: KRAS G12S

value: adenoviral infection

tag: sample group

value: Ad-mCherry


title: K562_H3K4me3_Plate_1

description:
Library name: GBe022s1_K562_H3K4me3_Rep1_S1_L001
K562_H3K4me3_Rep1

value: CML

value: Plate


title: rs411_PolII_Plate_1

description:
Library name: GBe022s7_rs411_PolII-Total_Rep1_S7_L001
rs411_PolII-Total_Rep1

value: ALL

value: PolII


title: A549 cells, Ad-mCherry NRD 51-121, Replicate 2

value: Ad-mCherry NRD 51-121


title: rs411_CTCF_Plate_2

description:
Library name: GBe022s16_rs411_CTCF-Abcam_Rep2_S16_L001
rs411_CTCF-Abcam_Rep2

value: CTCF


title: CoSp-SortHep-1

description: Library name: CoSp-SortHep-1


title: A549 cells, Ad-mCherry, Replicate 2


title: A549 cells, Ad-mCherry, Replicate 1


title: rs411_Myc_Plate_2

description:
Library name: GBe022s20_rs411_Myc_Rep2_S20_L001
rs411_Myc_Rep2

value: Myc


title: K562_CTCF_Plate_2

description:
Library name: GBe022s14_K562_CTCF-Abcam_Rep2_S14_L001
K562_CTCF-Abcam_Rep2


title: rs411_CTCF_Plate_1

description:
Library name: GBe022s15_rs411_CTCF-Abcam_Rep1_S15_L001
rs411_CTCF-Abcam_Rep1


title: GBM171DM-3%HD-1h-rep2_MED1-ChIP

data_processing:
Raw reads in fastq format were trimmed with Trim Galore version: 0.6.6 (command: trim_galore --trim-n --stringency 3 -q 30 -e .20 --length 15 --hardtrim5 51)
Reads alignment to human genome was done with bwa mem (version  0.7.17-r1188)
Deduplication was performed based on the UMI sequence found in the read ID using UMI-tools version: 1.1. (command: umi_tools dedup --umi-separator=":")
Reads were normalized based on  input read depth for peak calling with macs2 2.2.7.1 (command: macs2 callpeak --keep-dup all -B --SPMR --nomodel --extsize 250)
Fold-change ChIP signal  generated using 'macs2 bdgcmp' command, resulting in bigwig files.
Assembly: hg38
Supplementary files format and content: Bigwig format for fold-change visualization
Supplementary files format and content: Narrow peak file from MACS2 output

source_name: GBM171 DM

growth_protocol: Cells were cultivated in a humidified incubator set to 37°C and 5% CO2. PC3 DM cells were cultivated in F-12K (Kaighn's modification of Ham's F-12 medium) (30-2004, ATCC) supplemented with 10% FBS. COLO320 DM cells were grown in RPMI-1640 medium (30-2001, ATCC) supplemented with 10% FBS. GBM171 DM neurospheres were cultivated in ultra-low attachment dishes (Corning) using DMEM/F-12 with GlutaMAX (10565018, Thermofisher Scientific) supplemented with B27 supplement without vitaminA (12587010, ThermoFisher Scientific), 20 ng/ml FGF-Basic (154 a. a.) recombinant Human protein (100-18B, PeproTech), 20 ng/ml EGF recombinant Human protein (AF-100-15, Pepro Tech), 2.5 µg/ml heparin sodium salt (H3149-50KU, Sigma) and penicillin-streptomycin (15140122, ThermoFisher Scientific).

extract_protocol:
Cells were crosslinked with 1% FA and 2mM EGS according to the ChIA-PET protocol (PMC8351913). The chromatins were sonicated and immunoprecipitated with anti-MED1 (A300-793A, Bethyl Laboratories), anti-H3K27ac (39133, Active Motif) or  anti-RNAPII antibodies (920102, Biolegend).
ChIP DNA and matched input DNA were subjected to end-repair, A-tailing and adaptor ligation (IDT xGen Dual Index UMI Adapters) using KAPA Hyper Prep Kit (KK8505, KAPA Biosystems)

treatment_protocol: A 30% v/v solution of 1,6-HD (Sigma Aldrich, 240117) was prepared in basal medium without serum and then further diluted to 3%. cell density of each group was well controlled, as described in ‘Imaging’.

value: GBM171 DM

value: Glioblastoma

tag: chip antibody

value: MED1 (Bethyl Laboratories, #A300-793A)


title: rs411_BRG1_Plate_2

description:
Library name: GBe022s12_rs411_BRG1-Abcam_Rep2_S12_L001
rs411_BRG1-Abcam_Rep2


title: K562_CTCF_Plate_1

description:
Library name: GBe022s13_K562_CTCF-Abcam_Rep1_S13_L001
K562_CTCF-Abcam_Rep1


title: rs411_Myc_Plate_1

description:
Library name: GBe022s19_rs411_Myc_Rep1_S19_L001
rs411_Myc_Rep1


title: A549 cells, Ad-mCherry NRD 51-121, Replicate 3


title: GBM171DM-mock-rep1_Input

value: mock

value: Input


title: K562_Myc_Plate_2

description:
Library name: GBe022s18_K562_Myc_Rep2_S18_L001
K562_Myc_Rep2


title: rs411_BRG1_Plate_1

description:
Library name: GBe022s11_rs411_BRG1-Abcam_Rep1_S11_L001
rs411_BRG1-Abcam_Rep1


title: A549 cells, Ad-mCherry NRD 51-121, Replicate 1

value: Lung carcinomatous tissue


title: GBM171DM_H3K27ac-ChIP-seq

value: Regular

value: H3K27ac (Active Motif, #39133)


title: GBM171DM_RNAPII-ChIP-seq

value: RNAPII (Biolegend, 920102)


title: GBM171DM_Input


title: K562_Myc_Plate_1

description:
Library name: GBe022s17_K562_Myc_Rep1_S17_L001
K562_Myc_Rep1


title: GBM171DM-3%HD-2h-rep1_MED1-ChIP


title: Neutrophil T0 RNA-seq replicate 3

city: Strasbourg

first: Benoit

last: Marteyn

address: 2 allée Konrad Roentgen

country: France

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

description: Library name: P95_T0_N4_S20

data_processing:
RNA-Seq samples were analysed by the GENOM'IC platform (Institut Cochin, Paris, France). Reads were aligned against human genome GRCh38 using STAR v2.7.1a and differential analysis was done on R v3.6.1 using the DESeq2 v1.24.0 package.
Assembly: GRCh38 release 96
Supplementary files format and content: Excel table of the differential analysis between HG and T0 conditions.

source_name: Blood

growth_protocol: Neutrophils were purified from fresh human blood. Blood samples were rapidly transferred into an anoxic chamber (DG250, Don Whitley) for human neutrophil anoxic purification, using oxygen-free media, as previously described. Briefly, whole blood samples were centrifuged at 600 x g for 20 minutes. Platelet rich plasma (PRP) was collected and centrifuged at 2650 x g for 20 min to form platelet poor plasma (PPP). Blood cells were resuspended in NaCl (0.9%) and dextran sulfate (0.72%). After 30 min sedimentation, the neutrophil-containing upper layer was centrifuged at 300 x g for 10 min. Pelleted cells were resuspended in 1 mL PPP and were subsequently separated on a 42% Percoll-plasma (GE Healthcare) gradient by centrifugation at 800 x g for 20 min. Neutrophils were collected from the pellet with remaining red blood cells, which were removed using CD235a (glycophorin) microbeads (Miltenyi Biotec). Purified neutrophils were centrifuged at 300 x g for 10 minutes. Pelleted cells were resuspended in PPP or RMPI 1640 culture medium supplemented with 10 mM Hepes and 3mM glucose, according to experimental settings.

extract_protocol:
Neutrophil mRNA were purified from 5x107 neutrophils either freshly purified or cultured for 18h in anoxia in RPMI 1640 medium supplemented with 10 mM Hepes and 3 mM glucose. Cells were washed once with PBS and centrifuged for 5 minutes at 300 x g. Pelleted cells were lysed in 350 µL RLT buffer (Qiagen). Lysates were resuspended with a needle to increase the lysis efficiency. TRIzol (3 volumes) was added to samples followed by vortex and short spin. 1/5 of the volume of chloroform was added and samples were vortexed and incubated for 3 minutes at room temperature prior to transferring into PLG heavy tubes. Samples were centrifuged for 15 min at 12.000 x g (4°C) and RNA-containing aqueous solution was transferred into a new tube. RNA was purified using the RNeasy Mini Kit (Qiagen) and quantified with a nanodrop, and the quality was assessed with Tapestation.
RNA samples were analysed and sequenced by the GENOM’IC platform (Institut Cochin, Paris, France)

treatment_protocol: T0 = freshly purified neutrophils and HG=neutrophils incubated for 18h at 37°C under anoxic conditions

value: Blood

value: Neutrophil


title: GBM171DM-3%HD-1h-rep1_MED1-ChIP


title: GBM171DM-mock-rep2_MED1-ChIP


title: Neutrophil HG RNA-seq replicate 4

description: Library name: P12_HG_S4

value: HG


title: GBM171DM-mock-rep1_MED1-ChIP


title: COLO320DM-3%HD-2h-rep1_MED1-ChIP

value: COLO320 DM

value: Colorectal adenocarcinoma


title: TNBC1081T

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

data_processing:
Data analysis done in QIAGEN's RAP portal
Trimming of 3'adapter and low quality bases with cut-adapt
Discard reads with less than 16 bp insert sequences or less than 10 bp sequences (defective reads)
Alignment to the reference transcriptome with up to two mismatches tolerated using Bowtie
Assembly: miRBase V.21
Supplementary files format and content: Tab-delimited files includes raw counts or each sample

source_name: Tumor

extract_protocol:
Total RNA was extracted from FFPE tissue samples using the truXTRAC FFPE total RNA (column) kit (Covaris).
Libraries were generated from 100ng of total RNA using the QIAseq miRNA library kit and QIAseq miRNA 96 Index IL kit (QIAGEN)

value: Tumor

tag: obesity category

value: Lean

tag: race

value: Black

tag: age

tag: Stage


title: COLO320DM-3%HD-1h-rep2_MED1-ChIP


title: K562_BRG1_Plate_2

description:
Library name: GBe022s10_K562_BRG1-Abcam_Rep2_S10_L001
K562_BRG1-Abcam_Rep2

value: CML

value: Plate


title: COLO320DM-3%HD-30min-rep2_MED1-ChIP

value: 3% 1,6-HD for 30min

value: MED1 (Bethyl Laboratories, #A300-793A)


title: GBM171DM_MED1-ChIP-seq

value: GBM171 DM

value: Glioblastoma


title: Neutrophil T0 RNA-seq replicate 4

description: Library name: P116_T0_S17


title: Neutrophil T0 RNA-seq replicate 2

description: Library name: P62_T0_S12


title: TNBC1056N

source_name: Normal

value: Normal

value: Obese III

value: White


title: Neutrophil T0 RNA-seq replicate 1

description: Library name: P12_T0_S15

value: Blood


title: GBM171DM-3%HD-2h-rep2_MED1-ChIP


title: COLO320DM-3%HD-3h-rep2_MED1-ChIP


title: COLO320DM_MED1-ChIP-seq

value: Regular


title: TNBC0981T


title: Neutrophil HG RNA-seq replicate 1

description: Library name: N1_HG_S1

value: Neutrophil

value: HG


title: Neutrophil HG RNA-seq replicate 3

description: Library name: N4_HG_S6


title: COLO320DM-3%HD-3h-rep1_MED1-ChIP

value: COLO320 DM

value: Colorectal adenocarcinoma


title: COLO320DM_H3K27ac-ChIP-seq

value: H3K27ac (Active Motif, #39133)


title: COLO320DM-3%HD-2h-rep2_MED1-ChIP


title: TNBC0800T

value: Tumor

value: Lean


title: TNBC1081N

value: Black


title: Neutrophil HG RNA-seq replicate 2

description: Library name: N2_HG_S3


title: COLO320DM-3%HD-1h-rep1_MED1-ChIP


title: TNBC1056T


title: COLO320DM-mock-rep2_MED1-ChIP

value: mock


title: COLO320DM-3%HD-30min-rep1_MED1-ChIP

value: 3% 1,6-HD for 30min

value: MED1 (Bethyl Laboratories, #A300-793A)


title: COLO320DM-mock-rep1_MED1-ChIP


title: TNBC0981N


title: COLO320DM-mock-rep1_Input

value: Input


title: COLO320DM_RNAPII-ChIP-seq

value: RNAPII (Biolegend, 920102)


title: TNBC0800N

value: Normal


title: PC3DM-3%HD-1h-rep2_MED1-ChIP

source_name: PC3 DM

value: PC3 DM

value: Prostatic adenocarcinoma


title: TNBC0735T

value: Obese III

value: White


title: COLO320DM_Input

value: Regular


title: TNBC0794N


title: PC3DM-3%HD-1h-rep1_MED1-ChIP


title: TNBC0793T


title: TNBC0687T


title: PC3DM-mock-rep1_MED1-ChIP


title: PC3DM-3%HD-30min-rep1_MED1-ChIP


title: PC3DM-3%HD-30min-rep2_MED1-ChIP


title: TNBC0823T


title: PC3DM-mock-rep1_Input


title: TNBC0735N


title: TNBC0794T


title: PC3DM_MED1-ChIP-seq


title: TNBC0793N


title: TNBC0687N


title: TNBC0649N


title: PC3DM_Input


title: PC3DM_H3K27ac-ChIP-seq


title: TNBC0644T


title: PC3DM-mock-rep2_MED1-ChIP


title: PC3DM_RNAPII-ChIP-seq


title: TNBC0823N


title: PC3DM_CUT&Tag-ecSEcombo-perturbation-rep3

extract_protocol:
CUT&Tag was performed on 50,000 nuclei by using rabbit anti-H3K9me (39765, Active Motif) and CUTANA CUT&Tag Kit (14-1101, Epicypher) as instructed in manufacturer’s manual except that digitonin was omitted from buffers as it is not required with use of nuclei (PMID: 32913232).
Libraries are prepared based on CUTANA CUT&Tag Kit (14-1101, Epicypher) as instructed in manufacturer’s manual.

value: ecSEcombo-perturbation


title: TNBC0644N


title: TNBC0408T


title: PC3DM_CUT&Tag-ecSEcombo-perturbation-rep2


title: TNBC0408N


title: PC3DM_CUT&Tag-ecSEcombo-perturbation-rep1


title: PC3DM_CUT&Tag-ecSE6-perturbation-rep3


title: TNBC0497T


title: PC3DM_CUT&Tag-ecSE2-perturbation-rep3


title: TNBC0497N


title: PC3DM_CUT&Tag-ecSE7-perturbation-rep2


title: PC3DM_CUT&Tag-ecSE7-perturbation-rep1


title: PC3DM_CUT&Tag-ecSE6-perturbation-rep1


title: TNBC0343T


title: PC3DM_CUT&Tag-ecSE6-perturbation-rep2


title: TNBC0319T


title: TNBC0319N


title: TNBC0649T


title: TNBC0255T


title: TNBC0255N


title: TNBC0252T


title: TNBC0252N


title: PC3DM_CUT&Tag-ecSE1-perturbation-rep1


title: PC3DM_CUT&Tag-ecSE2-perturbation-rep2


title: PC3DM_CUT&Tag-ecSE2-perturbation-rep1


title: PC3DM_RNA-seq-ecSEcombo-perturbation-rep3

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (74106, Qiagen).
300 ng of total RNA was used for construction of sequencing libraries using KAPA Stranded mRNA Sequencing Kit (KK8502, KAPA Biosystems) following the manufacturer’s instruction.


title: TNBC0182N


title: TNBC0240N


title: PC3DM_CUT&Tag-vector-rep2

value: vector


title: PC3DM_CUT&Tag-ecSE1-perturbation-rep2


title: PC3DM_RNA-seq-ecSEcombo-perturbation-rep2


title: TNBC0240T


title: TNBC0181T


title: TNBC0343N


title: TNBC0181N


title: PC3DM_CUT&Tag-vector-rep1


title: TNBC0171T


title: PC3DM_CUT&Tag-ecSE1-perturbation-rep3


title: TNBC0168T


title: PC3DM_RNA-seq-ecSEcombo-perturbation-rep1


title: PC3DM_RNA-seq-ecSE6-perturbation-rep3


title: TNBC0168N


title: TNBC0653N


title: PC3DM_RNA-seq-ecSE6-perturbation-rep2


title: PC3DM_RNA-seq-ecSE6-perturbation-rep1


title: TNBC0171N


title: TNBC0150N


title: PC3DM_RNA-seq-ecSE7-perturbation-rep2


title: PC3DM_RNA-seq-ecSE7-perturbation-rep3


title: TNBC0182T


title: PC3DM_RNA-seq-ecSE7-perturbation-rep1


title: TNBC0150T


title: PC3DM_RNA-seq-ecSE2-perturbation-rep1


title: PC3DM_RNA-seq-ecSE2-perturbation-rep2


title: TNBC_1115

data_processing:
FASTQ files were uploaded to Partek Flow
Contaminants removed with Bowtie v2.2.5
Aligned to STAR v2.6.1d
Quantification with RefSeq 96 (release 2020-11-02) and normalized using loess normalization method implemented using Bioconductor R-package LIMMA
Assembly: Reference genome hg38
Supplementary files format and content: txt file containing raw counts

source_name: Breast

extract_protocol:
TNBC tissues from African American AA and EA women with or without obesity from Louisiana were used as source of RNA. Covaris kits (truXTRAC FFPE total NA (column)) were used for RNA extraction following the manufacturer's instructions. The RNA was treated with DNaseI, quantified by Qubit (Invitrogen), and qualified high sensitivity RNA Agilent chips
Genomic libraries were constructed using the Illumina TruSeq RNA Exome protocol. Briefly, 300 ng of total RNA (DV200≥30) were fragmented and used as template for the generation of double-stranded cDNA to which adapters were ligated. DNA fragments were enriched by PCR and the size of the fragments checked on Agilent Bioanalyzer 2100 DNA chips. Exome regions are captured, cleaned, pooled and enriched by PCR. Finally, the library quality and concentration are checked and diluted to the suggested final concentration for sequencing in an Illumina NextSeq500 at 2 x 75 bp

tag: tissue id

value: Breast

tag: chemotherapy

tag: bmi

tag: summary stage

value: Unknown

tag: grade


title: PC3DM_RNA-seq-ecSE1-perturbation-rep2


title: PC3DM_RNA-seq-ecSE1-perturbation-rep3


title: TNBC_1089

tag: tissue


title: TNBC_1114


title: PC3DM_RNA-seq-ecSE1-perturbation-rep1


title: TNBC_1112


title: TNBC_1101


title: TNBC_1087


title: PC3DM_RNA-seq-vector-rep3


title: PC3DM_RNA-seq-vector-rep2


title: TNBC_1084


title: TNBC_1083


title: PC3DM_RNA-seq-vector-rep1


title: TNBC_1082


title: PC3DM_RNA-seq-ecSE2-perturbation-rep3


title: GBM171DM_RNA-seq-3%HD-4h-rep2

data_processing:
1. RNA-seq reads in fastq format were trimmed with trim_galore with the following options: --stringency 3 -q 20 -e .20 --length 15 --paired (Trim Galore version: 0.6.6; Cutadapt version: 3.2)
2. The trimmed reads then were aligned to hg38 with Hisat2.2.1 (option: librarytype='--rna-strandness RF')
3. Gene (gencode v36) quantification  was performed with htseq-count 2.0.2 using the aligned reads (with option  -s reverse -m union -secondary-alignments ignore --supplementary-alignments ignore  -a 30)
Assembly: hg38
Supplementary files format and content: Gene count from htseq-count output

value: GBM171 DM

value: Glioblastoma


title: TNBC_1077


title: TNBC_1074


title: TNBC_1072


title: GBM171DM_RNA-seq-3%HD-2h-rep2


title: GBM171DM_RNA-seq-mock-rep2

value: mock


title: TNBC_1079


title: COLO320DM_RNA-seq-3%HD-4h-rep2

value: COLO320 DM

value: Colorectal adenocarcinoma


title: COLO320DM_RNA-seq-3%HD-4h-rep1


title: TNBC_1066

value: Black


title: TNBC_1056


title: TNBC_1051


title: TNBC_1049


title: GBM171DM_RNA-seq-3%HD-4h-rep1


title: GBM171DM_RNA-seq-3%HD-2h-rep1


title: COLO320DM_RNA-seq-3%HD-2h-rep2


title: TNBC_1047


title: COLO320DM_RNA-seq-3%HD-2h-rep1


title: COLO320DM_RNA-seq-3%HD-1h-rep2


title: COLO320DM_RNA-seq-3%HD-1h-rep1


title: TNBC_1038


title: TNBC_1037


title: COLO320DM_RNA-seq-mock-rep2


title: COLO320DM_RNA-seq-mock-rep1


title: TNBC_1028


title: TNBC_1027


title: PC3DM_RNA-seq-3%HD-2h-rep1


title: TNBC_1021


title: PC3DM_RNA-seq-3%HD-1h-rep2


title: GBM171DM_RNA-seq-mock-rep1


title: PC3DM_RNA-seq-3%HD-2h-rep2


title: TNBC_1060


title: TNBC_1020


title: PC3DM_RNA-seq-3%HD-1h-rep1


title: TNBC_1013


title: PC3DM_RNA-seq-mock-rep2


title: TNBC_1008


title: PC3DM_RNA-seq-mock-rep1


title: PC3DM_ChIATAC-ecSEcombo-perturbation-merged

data_processing:
Chia-PET Utilities (CPU, https://github.com/cheehongsg/CPU) tool was used mainly to process raw read in fastq format:
1. Linker detection:  'cpu stag -A ACGTGATATTTCACGACTCT -W -T 18'
2. Mapping to human genome: 'cpu memaln -T 30'
3. Pairing tags: 'cpu pair -s 8000'
4. Deduplication 'cpu dedup -g'
4. Paired-End Tag clustering: 'cpu cluster -s 8000 -M -B 1000 -5 5,-20 -3 5,480'
5. Peak calling was done with MACS 2.2.7.1  using non redundant reads  with option: --keep-dup all --nomodel -g hs --shift -75  --extsize 150  -B --SPMR. Coverage file in bigWig format was generated from MACS output (treat_pileup.bdg file) using  bedGraphToBigWig.
6. The cis interaction with PET count 2 or more (BE2) were used to call significant interactions using ChiaSig (option: -c 3 -p -m 8000); then double-anchor peak supported significant interactions (DA.bedpe file) represents high confident list.
Assembly: hg38
Supplementary files format and content: Bigwig format for fold-change visualization
Supplementary files format and content: Narrow peak file from MACS2 output
Library strategy: ChIATAC

growth_protocol: Cells were cultivated in a humidified incubator set to 37°C and 5% CO2. PC3 DM cells were cultivated in F-12K (Kaighn's modification of Ham's F-12 medium) (30-2004, ATCC) supplemented with 10% FBS.

extract_protocol:
Cells were crosslinked with 2% FA and 2mM EGS. Cells were lyzed and chromatins were fragmentized with Alu I and HpyCH4V enzymes at 37 ˚C.  After overnight digestion, digested nucleus was then subjected to proximity ligation overnight at 16 ˚C.
The nucleus were then tagmented and linker-conjucated fragments were enriched using streptoavidin-beads. Libraries were prepared and sequenced as previously described (PMID: 36639381).

treatment_protocol: Adherent cells were seeded in 24-well plates then transfected with 700 ng sgRNA plasmid DNA using lipofectamine LTX for PC3 DM-derived lines following manufacturer’s instructions (Thermofisher Scientific). Cells were collected 3 days after transfection


title: TNBC_1007


title: PC3DM_ChIATAC-ecSE1-perturbation-merged


title: TNBC_0990


title: TNBC_0984


title: TNBC_1040


title: TNBC_0977


title: GBM171DM_ChIA-PET-mock-rep2

data_processing:
Raw fastq files were fed into Chia-pipe pipeline (https://doi.org/10.1126/sciadv.aay2078). Alignment to hg38 was done.
The pipeline generates PETs (paired-end tags) in the simple juicebox (HiC visualization)  format, as well as  intra (cis) and inter (trans) chromosomal interactions  with PET counts. The cis interaction with PET count 2 or more (BE2) were used to call significant interactions using ChiaSig (option: -c 3 -t 1 -p -m 8000)  [Paulsen et al. 'A statistical  model of ChIA-PET data for accurate detection of chromatin 3Dinteractions', Nucleic acids research. (2014)]
Peak calling was done with MACS 2.2.7.1  using the intermediate file 'for.BROWSER.bam' with option: --keep-dup all --nomodel -g hs
Assembly: hg38
Supplementary files format and content: Paired-end tag interaction text file in Hi-C juice short format for Juicebox visualization
Supplementary files format and content: Significant interaction from Chia-Sig output
Library strategy: ChIA-PET

extract_protocol:
Cells were crosslinked with 1% FA and 2mM EGS according to the ChIA-PET protocol (PMC8351913). Cells were lyzed and chromatins were fragmentized with Alu I enzymes (R0137L, NEB) at 37 ˚C.  After overnight digestion, digested nucleus was then subjected to proximity ligation overnight at 16 ˚C. The ligated chromatins were sonicated and immunoprecipitated by anti-RNAPII antibodies (920102, Biolegend). The immunoprecipitated DNAs were then tagmented and linker-conjucated fragments were enriched using streptoavidin-beads. Libraries were prepared and sequenced as previously described (PMC8119378).
The immunoprecipitated DNAs were then tagmented and linker-conjucated fragments were enriched using streptoavidin-beads. Libraries were prepared and sequenced as previously described (PMC8119378).


title: GBM171DM_ChIA-PET-mock-rep1


title: TNBC_0974


title: TNBC_0969


title: COLO320DM_ChIA-PET-mock-rep2


title: COLO320DM_ChIA-PET-3%HD-rep1


title: TNBC_0972


title: TNBC_0973


title: COLO320DM_ChIA-PET-mock-rep1


title: COLO320DM_ChIA-PET-3%HD-rep2


title: TNBC_0968


title: TNBC_0956


title: PC3DM_ChIA-PET-3%HD-rep2


title: TNBC_0949


title: PC3DM_ChIA-PET-3%HD-rep1


title: GBM171DM_ChIA-PET-3%HD-rep2


title: TNBC_0979


title: TNBC_0981


title: GBM171DM_ChIA-PET-3%HD-rep1


title: TNBC_0942


title: PC3DM_ChIA-PET-mock-rep2


title: GBM171DM_ChIA-Drop-rep2

data_processing:
Chia-Drop raw files were fed to ChiaDropBox pipeline (https://www.biorxiv.org/content/10.1101/613034v1.full)
The bigwig files provided here were automatically generated by the pipeline.
The ecDNA fragments were collected from ChiaDropBox pipeline output files 'D04_SNBC_READ/R04a_GEMLINE/*FRAGMENT_GEMLINE' which contain read fragments with GEM ID and read supporting the fragments.
Assembly: hg38
Supplementary files format and content: Bigwig format for coverage
Supplementary files format and content: Tab separated text file for annotated chromosomal regions
Library strategy: ChIA-Drop

extract_protocol:
Cells were crosslinked with 1% FA and 2mM EGS according to the ChIA-PET protocol (PMC8351913). Cells were lyzed, and chromatins were fragmentized with Alu I enzymes (R0137L, NEB) at 37 ˚C.  The chromatins were sonicated and immunoprecipitated by anti-RNAPII antibodies (920102, Biolegend). The immunoprecipitated DNAs were then tagmented and linker-conjucated fragments were enriched using streptoavidin-beads. Libraries were prepared and sequenced as previously described (PMC8119378).
The preparation of immunoprecipitated chromatins with RNAPII antibodies (664912, BioLegend) and library construction using Chromium Genome v2 Library Kit & Gel Bead Kit (PN-120258, 10X Genomics) were based on our previous studies (PMC8119378).


title: TNBC_0940


title: PC3DM_ChIATAC-vector-merged

value: WT


title: TNBC_0975


title: PC3DM_ChIA-PET-mock-rep1


title: GBM171DM_ChIA-Drop-rep1


title: COLO320DM_ChIA-Drop-rep2


title: TNBC_0935


title: TNBC_0936


title: COLO320DM_ChIA-Drop-rep1


title: PC3DM_ChIA-Drop-rep2


title: GBM171DM_WGS

data_processing:
Raw reads in fastq format were trimmed with Trim Galore version: 0.6.6 (command: trim_galore --trim-n --stringency 3 -q 30 -e .20 --length 15)
Reads alignment to human genome hg38 was done with bwa mem (version  0.7.17-r1188)
Aligned reads with MAPQ above 30 were filtered from hg38 blacklist for copy number calling with ReadDepth (https://github.com/chrisamiller/readDepth)
Assembly: hg38
Supplementary files format and content: Comma separated text for copy number per chromosomal region
Library strategy: WGS

extract_protocol:
Genomic DNA were extracted using AllPrep DNA/RNA Mini Kit (Qiagen).
Genomic DNA were fragmented to 400 bp and subjected to end-repair, A-tailing and adaptor ligation (IDT for Illumina TruSeq DNA UD Indices) using KAPA Hyper Prep Kit (KK8505, KAPA Biosystems)


title: PC3DM_WGS


title: PC3DM_ChIA-Drop-rep1


title: TNBC_0933


title: TNBC_0930


title: TNBC_0944


title: TNBC_0922


title: HCT116 cells, SDR42E1 overexpression, biol rep3

city: Doha

first: Georges

middle: Michel

last: Nemer

state: Qatar

department: CHLS

country: Qatar

institute: HBKU

data_processing:
CLC Genomics Workbench version 22.0.2 software.
Raw sequence reads were trimmed to eliminate contaminant DNA, PCR duplicates, and adaptor sequences. Reads with a quality lower than Q20 were filtered using CLC Genomics Workbench software.
CLC Genomics Workbench was employed for assembly and mapping of all paired end reads against the latest version of the human genome (Homo sapiens, GRCh38). Outlier samples and genes with average raw counts below 10 were excluded.
Read counts were extracted utilizing CLC Genomics Workbench with default parameters.
Assembly: GRCh38
Supplementary files format and content: Comma-separated values (CSV) file contains raw counts for all samples.

source_name: human colorectal carcinoma line

growth_protocol: All cells were cultured in DMEM with (4.5 g/L) high D-Glucose, (2 mM) Glutamine, and (1 mM) Sodium Pyruvate, supplemented with 10% fetal bovine serum (FBS) and (1X) antibiotic-antimycotic (Gibco). All cell lines were grown under sterile conditions in a monolayer culture at 37°C, with a 5% CO2 atmosphere and 95% air humidity. At 70% to 80% confluency, all cells were harvested through treatment with 0.25% EDTA.

extract_protocol:
Total RNA was isolated from cell lines using 1 mL TRIzol reagent (Invitrogen), according to the manufacturer's guidelines. Subsequently, equivalent amounts of high-quality RNA pools (100–200 ng) were precipitated in a 75% ethanol solution and shipped to Macrogen Inc. (http://macrogen.com, Korea) for total RNA-sequencing library construction and next-generation sequencing.
RNA sequencing libraries were prepared with the TruSeq Stranded Total RNA Library Prep Kit (1000000040499, Illumina), following the instructions.

value: human colorectal carcinoma line

value: spontaneously immortalized, human colorectal carcinoma line

value: Homozygous SDR42E1 overexpression


title: TNBC_0941


title: TNBC_0929


title: TNBC_0909


title: HCT116 cells, SDR42E1 overexpression, biol rep1


title: TNBC_0918


title: HCT116 cells, SDR42E1 knockin, biol rep1

value: Homozygous SDR42E1 knockin


title: TNBC_0917


title: HCT116 cells, SDR42E1 knockin, biol rep3


title: TNBC_0925


title: HCT116 cells, SDR42E1 knockin, biol rep2


title: HCT116 cells, control, biol rep1

value: wild-type control


title: TNBC_0902

value: White


title: TNBC_0899


title: HCT116 cells, control, biol rep3


title: TNBC_0895


title: TNBC_0897


title: WT3_B4_D30

city: Belval

first: Matthieu

last: Gobin

address: 6, avenue du Swing

country: Luxembourg

institute: LCSB

data_processing:
RNA sequencing data were pre-processed on the Galaxy server version 23.2.rc1 following Galaxy training tutorial (REF: see below1-3). Reads were mapped to the human reference genome hg38 using the HISAT2 tool. Mapped reads were counted using the featureCounts function on the BAM output files of HISAT2.
Assembly: hg38
Supplementary files format and content: matrix xls file raw counts

source_name: midbrain oragnoid

extract_protocol: For RNA extraction from each organoid generation batch, 20 organoids were pooled at day 30 and 15 organoids at day 60 of midbrain organoid culture. RNA isolation was done using RNeasy Mini Kit (Qiagen, cat.no. 74106) following 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, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.Library preparations were sequenced on an Illumina platform by Novogene sequencing service.

value: midbrain oragnoid

value: NESC derived midbrain organoids


title: TNBC_0901

value: Breast


title: TNBC_0905

value: Unknown


title: TNBC_0906


title: TNBC_0888


title: WT3_B3_D30


title: TNBC_0876


title: TNBC_0884


title: TNBC_0874


title: TNBC_0869


title: WT3_B2_D60


title: WT3_B1_D60


title: TNBC_0870


title: TNBC_0871

value: Regional


title: WT2_B4_D30


title: WT3_B1_D30


title: TNBC_0868

value: Local


title: WT2_B4_D60


title: TNBC_0867


title: WT2_B3_D30


title: WT2_B3_D60


title: HCT116 cells, control, biol rep2


title: WT3_B4_D60


title: TNBC_0864


title: WT2_B2_D60


title: TNBC_0863


title: TNBC_0858


title: WT2_B2_D30


title: WT3_B2_D30


title: TNBC_0852


title: WT3_B3_D60


title: WT2_B1_D60


title: TNBC_0849


title: TNBC_0850


title: TNBC_0844


title: WT1_B3_D60


title: WT1_B4_D30


title: TNBC_0841


title: TNBC_0823


title: WT2_B1_D30


title: WT1_B2_D60


title: WT1_B2_D30


title: TNBC_0821


title: WT1_B1_D60


title: TNBC_0839


title: TNBC_0794


title: GBA3_B4_D30


title: GBA3_B4_D60


title: WT1_B1_D30


title: TNBC_0810


title: TNBC_0800


title: HCT116 cells, SDR42E1 overexpression, biol rep2


title: TNBC_0793


title: GBA3_B3_D60


title: WT1_B4_D60


title: TNBC_0764


title: GBA3_B2_D60


title: TNBC_0761


title: GBA3_B2_D30


title: TNBC_0760


title: TNBC_0759


title: GBA3_B1_D60


title: TNBC_0755


title: GBA3_B1_D30


title: TNBC_0739


title: GBA2_B4_D60


title: WT1_B3_D30


title: intestine, w1118-GFP

city: Changsha

first: peng

middle: guo

last: fan

state: Hunan

address: Lushan Road

institute: Hunan University

data_processing:
Raw data were preprocessed by using Trimmomatic v0.39.
Filtered reads were aligned to the Drosophila melanogaster genome (dm6) assembly using Bowtie2 v2.5.3.
Conversion of sorted bam files into bigwig files was done using bedtools v2.30.0
Assembly: dm6
Supplementary files format and content: bigwig files were generated using deepTools.
Library strategy: CUT&Tag

organism: Drosophila melanogaster

source_name: midgut

growth_protocol: Flies were raised at 25 ℃ on standard fly food.

extract_protocol:
Female flies were harvested on the fifth-day post eclosion and 30 female midguts were dissected in PBS at RT. Then, single-cell suspension of midgut were prepared by trypsinization and filtration under asepsis condition.
CUT&Tag libraries was performed with CUT&Tag reagent kit (CUT-01, Ruoyu Biotech) according to the manufacturer’s instructions. To amplify the libraries, 16 μl of DNA was mixed with a uniquely barcoded i5 and a uniquely barcoded i7 primer, and amplified using 2×HG Library Mix. The libraries were purified with 1.2 × volume of  Ampure XP beads.

value: midgut

value: intestinal cell

tag: Sex

value: female

tag: antibody

value: GFP


title: TNBC_0732

value: Black


title: GBA2_B4_D30

tag: cell line

tag: cell type


title: TNBC_0735


title: TNBC_0731


title: intestine, w1118-H3K4me3

tag: genotype


title: GBA2_B3_D60

tag: treatment


title: intestine, dorsal-GFP

value: w1118; PBac{dl-GFP.FPTB}VK00033


title: TNBC_0720


title: GBA2_B3_D30


title: intestine, dif-GFP

value: w1118; PBac{Dif-GFP.FPTB}VK00033


title: TNBC_0710


title: TNBC_0712


title: TNBC_0714


title: GBA3_B3_D30


title: GBA2_B2_D60


title: TNBC_0709


title: TNBC_0706


title: tumor, digoxin 1mg/kg, rep3

city: Nanjing

first: chenming

last: xu

address: 163 Xianlin Road, Qixia District

institute: Nanjing university

description: Library name: H_dose3

data_processing:
Raw reads were quality filtered with fastp (v0.22.0) to remove adapters and low quality or ambiguous bases, discarding reads <75 bp after trimming; the remaining high quality clean reads were used for downstream bioinformatic analyses.
Assembly: Clean reads were aligned to the reference genome GRCh38 using HISAT2 (v2.2.1).
Supplementary files format and content: FPKM values for each sample

source_name: tumor

growth_protocol: The 4- to 5-week-old male C57BL/6 mice were housed in filter-topped cages with autoclaved food and water on a 12-hour light/dark cycle.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, 74136).
RNA was quantified on NanoDrop and RNA quality was assessed on an Agilent 2100 Bioanalyzer. First, poly(A)+ mRNA was enriched from total RNA using oligo(dT)-coated magnetic beads and fragmented. Reverse transcriptase was then used to synthesize the first and second strands of cDNA. The cDNA fragments underwent end repair and A-tailing at the 3' ends, followed by ligation of sequencing adapters. After purification to remove incompletely ligated adapters and adapter dimers, libraries were PCR-amplified using primers complementary to the adapter sequences. Finally, the sequencing libraries were purified using magnetic beads. RNA-seq (paired end 150 bp) was performed by illumina NovaSeq 6000.

treatment_protocol: LLC cells (5 × 10^6) were injected subcutaneously into the right flank of mice. Five days later, mice were randomized into three groups and treated intraperitoneally with vehicle (PBS) or digoxin (0.1 or 1 mg/kg).

value: tumor

value: 1mg/kg digoxin


title: TNBC_0705


title: GBA2_B1_D60


title: tumor, digoxin 1mg/kg, rep2

description: Library name: H_dose2


title: TNBC_0700


title: GBA2_B2_D30


title: tumor, digoxin 1mg/kg, rep1

description: Library name: H_dose1


title: GBA2_B1_D30


title: TNBC_0670


title: tumor, digoxin 0.1mg/kg, rep3

description: Library name: D_dose3

value: 0.1mg/kg digoxin


title: TNBC_0667


title: TNBC_0721


title: TNBC_0665

value: White


title: TNBC_0669


title: GBA1_B4_D30

value: midbrain oragnoid

value: UOX


title: tumor, digoxin 0.1mg/kg, rep2

description: Library name: D_dose2


title: GBA1_B4_D60

value: NESC derived midbrain organoids


title: tumor, digoxin 0.1mg/kg, rep1

description: Library name: D_dose1


title: TNBC_0664

value: Breast


title: TNBC_0654


title: TNBC_0653

value: Regional


title: TNBC_0657

value: Local


title: GBA1_B3_D30


title: TNBC_0651


title: TNBC_0649


title: tumor, Vehicle, rep3

description: Library name: NC3

value: Vehicle


title: TNBC_0682


title: GBA1_B2_D60


title: tumor, Vehicle, rep2

description: Library name: NC2


title: TNBC_0646


title: TNBC_0644