title: LS8817, Cycling, H3K27ac, rep1, techrep 1

description:
Library name: LS8817_Cycling_H3K27ac_rep1_1
RPGC normalized bigwig files, merged across both biological replicates for Cycling samples with CUT&Tag performed on H3K27ac. H3K27ac.Union.all.conditions.bed is the master peak set across all samples as a bed file.
Cycling_K27ac_merged_RPGCnorm.bw


title: TH119

status: Public on Jun 22 2026

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: NoABMRM

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human heart biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: tissue

value: heart biopsy


title: scHH1_CA09

type: SRA

city: Durham

first: Liuyang

last: Wang

state: NC

address: 0049 CARL Building

country: USA

institute: Duke University

description:
Library name: DCK-sc19
10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing results were processed using the 10X Genomics CellRanger v7.0.1 pipeline. Ambient RNA was removed with CellBender v.0.3.0.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: B cell

extract_protocol:
Cell samples were counted and checked for viability on a Guava EasyCyte HT system by 7-AAD staining before they were diluted to 1 million cells/mL with an intended capture of 25,000 cells/sample.
10x Chromium Single Cell 3’ platform version 3.1

tag: cell line

value: B cell

tag: cell type

value: LCL

tag: genotype

value: WT

tag: treatment

value: infected with Influenza CA09 strain


title: scHH2_CA09

description:
Library name: DCK-sc16
10X Genomics


title: TH117

source_name: ABMRM


city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description:
Library name: 3358475_D283_KDM2B_degradation_rescued_by_KDM2B_JmjC_mutation_Rep3
RNA_seq

library_source: transcriptomic

data_processing:
Reads were adapter/quality trimmed, aligned to hg38, and summarized to gene-level expression values. Gene-level matrices were generated for downstream analysis.
Assembly: hg38
Supplementary files format and content: Tab-separated text files with gene-level count, FPKM, and TPM matrices.

extract_protocol:
Total RNA was isolated using a column-based RNA extraction kit following the manufacturer protocol.
RNA-seq libraries were prepared using a standard mRNA library preparation workflow and sequenced on an Illumina NovaSeq platform (paired-end).

value: medulloblastoma cell line


title: TH116


title: TH115


description:
Library name: 3358474_D283_KDM2B_degradation_rescued_by_KDM2B_JmjC_deletion_Rep3
RNA_seq


description:
Library name: 3358473_D283_KDM2B_degradation_rescued_by_KDM2B_CXXC_deletion_Rep3
RNA_seq


description:
Library name: 3358472_D283_KDM2B_degradation_rescued_by_KDM2B_Rep3
RNA_seq


title: TH112


title: TH111


title: TH113


title: 3358471_D283_KDM2B_degradation_Rep3

description:
Library name: 3358471_D283_KDM2B_degradation_Rep3
RNA_seq


title: TH114


title: 3358470_D283_Ctrl_Rep3

description:
Library name: 3358470_D283_Ctrl_Rep3
RNA_seq


title: TH110


title: TH109


description:
Library name: 3358469_D283_KDM2B_degradation_rescued_by_KDM2B_JmjC_mutation_Rep2
RNA_seq


description:
Library name: 3358468_D283_KDM2B_degradation_rescued_by_KDM2B_JmjC_deletion_Rep2
RNA_seq


description:
Library name: 3358467_D283_KDM2B_degradation_rescued_by_KDM2B_CXXC_deletion_Rep2
RNA_seq


title: TH107


description:
Library name: 3358466_D283_KDM2B_degradation_rescued_by_KDM2B_Rep2
RNA_seq


title: TH106


title: TH105


title: TH108


title: 3358465_D283_KDM2B_degradation_Rep2

description:
Library name: 3358465_D283_KDM2B_degradation_Rep2
RNA_seq


title: 3358464_D283_Ctrl_Rep2

description:
Library name: 3358464_D283_Ctrl_Rep2
RNA_seq


title: TH104


description:
Library name: 3358463_D283_KDM2B_degradation_rescued_by_KDM2B_JmjC_mutation_Rep1
RNA_seq


description:
Library name: 3358462_D283_KDM2B_degradation_rescued_by_KDM2B_JmjC_deletion_Rep1
RNA_seq


description:
Library name: 3358461_D283_KDM2B_degradation_rescued_by_KDM2B_CXXC_deletion_Rep1
RNA_seq


title: TH102


title: TH103


title: TH101


title: TH100


title: ILPr01,preoperative ILE,baseline

status: Public on Jun 23 2026

city: Hangzhou

first: Zhongyu

last: Wu

state: Zhejiang Province

address: 3 East Qingchun Road

department: Sir RunRun Shaw Hospital,School of Medicine

country: China

institute: Zhejiang University

description: Library name: ILPr01

library_source: genomic

data_processing:
Relative abundance: Top 20 taxa of each sample at each taxonomic ranks (Phylum, Class, Order, Family, Genus, Species) were selected to plot the distribution histogram of relative abundance in Perl through SVG function. Alpha and Beta Diversity: For analyzing community diversity, richness, and evenness, alpha diversity was calculated using Shannon and Simpson indices in QIIME2. Beta diversity was performed with Principal Coordinates Analysis (PCoA) and Adonis analysis. Community difference analysis: T-test, and linear discriminant analysis effect size (LEfSe) were conducted to characterize community structure differentiation. Function Prediction: PICRUSt2 (V2.3.0) was applied to predict metagenomic functions based on marker genes. Canonical correspondence analysis (CCA) were used to explore interspecies symbiosis and environmental impacts on community structure, reflecting correlations between environmental factors and genus/species abundance.
Continuous variables were expressed as mean with standard deviation and compared using the Student’s T test. Categorical data, on the other hand, were represented as frequencies and percentages, and comparisons were made using the Pearson χ2 test or the Fisher exact test, depending on suitability. A two-sided p value less than 0.05 was considered statistically significant. All data analyses were conducted using the R software package (version 4.0).
Assembly: 16S rRNA gene reference database(Silva 138.1)
Supplementary files format and content: Processed data are ASV feature count matrix (tab-delimited TSV format). Rows represent individual ASVs, columns correspond to sample IDs, and values denote raw sequencing read counts of each ASV across all fecal samples. Taxonomic classification results assigned against SILVA 138.1 database are also provided in the feature table.
Library strategy: 16S rRNA-seq

molecule: genomic DNA

organism: human feces metagenome

source_name: feces

extract_protocol:
16S rRNA genes of distinct regions (16SV3-V4) were amplified used specific primer with the barcode. All PCR reactions were carried out with 15 µL of Phusion® High-Fidelity PCR Master Mix (New England Biolabs); 0.2µM of forward and reverse primers, and about 10 ng template DNA. Thermal cycling consisted of initial denaturation at 98℃ for 1 min, followed by 30 cycles of denaturation at 98℃ for 10s, annealing at 50℃ for 30 s, and elongation at 72℃ for 30s and 72℃ for 5 min. The PCR products were purified using magnetic bead purification. Samples were mixed in equidensity ratios based on the concentration of PCR products.
After thorough mixing, the PCR products were detected and target bands were recovered. Sequencing libraries were generated and indexes were added. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

value: feces


description:
Library name: 3358460_D283_KDM2B_degradation_rescued_by_KDM2B_Rep1
RNA_seq


title: TH99


title: 3358459_D283_KDM2B_degradation_Rep1

description:
Library name: 3358459_D283_KDM2B_degradation_Rep1
RNA_seq


title: 3358458_D283_Ctrl_Rep1

description:
Library name: 3358458_D283_Ctrl_Rep1
RNA_seq


title: freshDMB006_K36me2TH

description:
Library name: 3316390_freshDMB006_K36me2TH
CUT&RUN

data_processing:
Reads were adapter/quality trimmed, aligned to hg38, and duplicate-marked. Normalized coverage tracks (bigWig) were generated for visualization and comparison.
Assembly: hg38
Supplementary files format and content: bigWig (CRall.bw) normalized coverage tracks.
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN was performed on isolated nuclei using target-specific antibodies with spike-in control, followed by DNA purification using a standard CUT&RUN workflow.
Sequencing libraries were prepared using a low-input DNA library preparation workflow and sequenced on an Illumina NovaSeq platform (paired-end).


title: Young_H3K4me3_ChIP_3

city: Barcelona

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

country: Spain

institute: IRB Barcelona

description: Library name: K4me3_Y_3

data_processing:
ChIP-seq reads were trimmed, adapters were removed and low-quality reads were discarded by using Trimmomatic v.0.36, TRAILING:5, SLIDINGWINDOW:4:5 MINLEN:36
ChIP-seq reads were aligned to the mm10 genome with Burrows-Wheeler aligner v.0.7.12, -n 2 -l 20 -k 1 -t 2.
Aligned reads from the individual biological replicates were merged into one single .bam file, and duplicates were removed using SAMtools v.1.5.
Peaks were called using MACS2 v.2.1.1 with the parameters: -q 0.01 –nomodel –extsize 300 -B –SPMR. Peaks were called against the inputs (input_K4me3_Y and input_K4me3_O) for all ChIPs.
H3K4me3 and H3K27ac: Peaks with FDR 0.01 (which is, peak score>20) were considered as significant H3K4me3 and H3K27ac peaks for further analysis. H3K4me1: Peaks were called against the same input in H3K4me3 ChIP-seq. Peaks with FDR 0.01 (which is, peak score>20) were considered as significant H3K4me1 peaks for further analysis.
Assembly: mm10
Supplementary files format and content: bed

organism: Mus musculus

source_name: epidermis

extract_protocol:
20 million cells were fixed with with 1% methanol-free formaldehyde for 10 minutes. After quenching and cell lysis, nuclear extract was sonicated using a Bioruptor Pico (Diagenode). For IP, 20ug of chromatin were used and incubated with 1.6 ul of anti-H3K4me1 (ab8895, Abcam) with rotation overnight at 4ºC. After immunoprecipitated chromatin was eluted, DNA was purified with the QIAquick PCR Purification Kit (28106, Qiagen).
Libraries were carried out using the NEBNext Ultra DNA Library Prep for Illumina kit (E7370) or the NEBNext® Ultra II DNA Library Prep for Illumina® kit (E7645) using the manufacturer’s protocol. In brief, ChIP-enriched DNA and input DNA were subjected to end repair and the addition of “A” bases to 3’ ends, NEB adapter’s ligation and USER excision. For all purification steps, AgenCourt AMPure XP beads (A63882, Beckman Coulter) were used. Library amplification was performed by PCR using NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs, E6440, E6442, E6444, E6446). Analysis of final libraries was carried out using either an Agilent Bioanalyzer or Fragment analyzer High Sensitivity assay (5067‐4626 or DNF‐474) to estimate the quantity and check size distribution. Quantification of these final libraries was done by quantitative PCR using the KAPA Library Quantification Kit (KK4835, KapaBiosystems, 07960204001 Roche).

treatment_protocol: Epidermal cells suspensions were obtained from the skin of adult (18-25 weeks old) and aged (80-90 weeks old) mice that were sacrificed at ZT4.

value: epidermis

tag: age

value: Young

tag: condition

value: IP

tag: replicate


title: freshDMB006_IgG

description:
Library name: 3316387_freshDMB006_IgG
CUT&RUN


title: DMB006_IgG.

description:
Library name: 3316385_DMB006_IgG
CUT&RUN


title: Rcmb37_K36me2CST

description:
Library name: 3316384_Rcmb37_K36me2CST
CUT&RUN


title: TH97


title: Rcmb37_IgG.

description:
Library name: 3316383_Rcmb37_IgG
CUT&RUN


title: TH98


title: TH94


title: Med1512_K36me2TH

description:
Library name: 3316382_Med1512_K36me2TH
CUT&RUN


title: TH93


title: TH96


title: TH95


title: Med1512_IgG.

description:
Library name: 3316379_Med1512_IgG
CUT&RUN


title: Med2312_K36me2TH

description:
Library name: 3316378_Med2312_K36me2TH
CUT&RUN


title: Med2312_IgG

description:
Library name: 3316375_Med2312_IgG
CUT&RUN


title: TH91


title: TH89


title: TH92


title: TH90


title: Rcmb28_K36me2TH

description:
Library name: 3316374_Rcmb28_K36me2TH
CUT&RUN


title: Rcmb28_IgG

description:
Library name: 3316371_Rcmb28_IgG
CUT&RUN


title: TH88


title: Med1712_K36me2TH

description:
Library name: 3316366_Med1712_K36me2TH
CUT&RUN


title: TH87


title: Rcmb20_IgG

description:
Library name: 3316367_Rcmb20_IgG
CUT&RUN


title: Med1712_IgG

description:
Library name: 3316363_Med1712_IgG
CUT&RUN


title: Rcmb20_K36me2TH

description:
Library name: 3316370_Rcmb20_K36me2TH
CUT&RUN


title: TH85


title: Med113_K36me2TH

description:
Library name: 3316362_Med113_K36me2TH
CUT&RUN


title: TH84


title: Med113_IgG

description:
Library name: 3316359_Med113_IgG
CUT&RUN


title: TH82


title: H3K27me3_120hr-dTAG-2

description:
Library name: 3371511_H3K27me3_120hr-dTAG-2
CUT&RUN


title: TH83


title: TH80


title: TH86


title: H3K27me3_120hr-dTAG-3

description:
Library name: 3371512_H3K27me3_120hr-dTAG-3
CUT&RUN


title: H3K27me3_120hr-dTAG-1

description:
Library name: 3371510_H3K27me3_120hr-dTAG-1
CUT&RUN


title: TH81


title: TH79


title: TH78


title: H3K4me1_120hr-dTAG-2

description:
Library name: 3371509_H3K4me1_120hr-dTAG-2
CUT&RUN


title: H3K4me1_120hr-dTAG-1

description:
Library name: 3371508_H3K4me1_120hr-dTAG-1
CUT&RUN


title: TH77


title: H3K4me3_120hr-dTAG-2

description:
Library name: 3371507_H3K4me3_120hr-dTAG-2
CUT&RUN


title: TH75


title: H3K4me3_120hr-dTAG-1

description:
Library name: 3371506_H3K4me3_120hr-dTAG-1
CUT&RUN


title: TH74


title: H3K27me3_120hr-DMSO-3

description:
Library name: 3371505_H3K27me3_120hr-DMSO-3
CUT&RUN


title: TH76


title: H3K27me3_120hr-DMSO-2

description:
Library name: 3371504_H3K27me3_120hr-DMSO-2
CUT&RUN


title: H3K27me3_120hr-DMSO-1

description:
Library name: 3371503_H3K27me3_120hr-DMSO-1
CUT&RUN


title: TH73


title: H3K4me1_120hr-DMSO-2

description:
Library name: 3371502_H3K4me1_120hr-DMSO-2
CUT&RUN


title: H3K4me1_120hr-DMSO-1

description:
Library name: 3371501_H3K4me1_120hr-DMSO-1
CUT&RUN


title: TH72


title: TH71


title: H3K4me3_120hr-DMSO-2

description:
Library name: 3371500_H3K4me3_120hr-DMSO-2
CUT&RUN


title: TH69


title: TH68


title: H3K4me3_120hr-DMSO-1

description:
Library name: 3371499_H3K4me3_120hr-DMSO-1
CUT&RUN


title: TH67


title: H2K119ub_48hr-dTAG-2

description:
Library name: 3365847_H2K119ub_48hr-dTAG-2
CUT&RUN


title: H2K119ub_48hr-dTAG-1

description:
Library name: 3365846_H2K119ub_48hr-dTAG-1
CUT&RUN


title: H2K119ub_12hr-dTAG-2

description:
Library name: 3365845_H2K119ub_12hr-dTAG-2
CUT&RUN


title: H2K119ub_12hr-dTAG-1

description:
Library name: 3365844_H2K119ub_12hr-dTAG-1
CUT&RUN


title: TH65


title: TH64


title: TH66


title: H2K119ub_48hr-DMSO-1

description:
Library name: 3365843_H2K119ub_48hr-DMSO-1
CUT&RUN


title: H2K119ub_12hr-DMSO-1

description:
Library name: 3365842_H2K119ub_12hr-DMSO-1
CUT&RUN


title: H2K119ub_0hr-2

description:
Library name: 3365841_H2K119ub_0hr-2
CUT&RUN


title: H2K119ub_0hr-1

description:
Library name: 3365840_H2K119ub_0hr-1
CUT&RUN


title: TH61


title: TH70


title: TH63


title: TH62


title: TH59


title: TH60


title: BCOR_48hr-dTAG-2

description:
Library name: 3365839_BCOR_48hr-dTAG-2
CUT&RUN


title: TH58


title: BCOR_48hr-dTAG-1

description:
Library name: 3365838_BCOR_48hr-dTAG-1
CUT&RUN


title: BCOR_12hr-dTAG-2

description:
Library name: 3365837_BCOR_12hr-dTAG-2
CUT&RUN


title: TH57


title: BCOR_12hr-dTAG-1

description:
Library name: 3365836_BCOR_12hr-dTAG-1
CUT&RUN


title: TH56


title: BCOR_48hr-DMSO-1

description:
Library name: 3365835_BCOR_48hr-DMSO-1
CUT&RUN


title: BCOR_12hr-DMSO-1

description:
Library name: 3365834_BCOR_12hr-DMSO-1
CUT&RUN


title: BCOR_0hr-2

description:
Library name: 3365833_BCOR_0hr-2
CUT&RUN


title: IgG_dtag

description:
Library name: 3340856_IgG_dtag
CUT&RUN


title: TH54


title: TH53


title: BCOR_0hr-1

description:
Library name: 3365832_BCOR_0hr-1
CUT&RUN


title: TH50


title: TH51


title: H3K36me2_Th_120hr-dTAG-2

description:
Library name: 3340854_H3K36me2_Th_120hr-dTAG-2
CUT&RUN


title: H2K119ub_120hr-dTAG-2

description:
Library name: 3340852_H2K119ub_120hr-dTAG-2
CUT&RUN


title: TH48


title: TH49


title: TH47


title: TH55


title: TH46


title: BCOR_120hr-dTAG-2

description:
Library name: 3340850_BCOR_120hr-dTAG-2
CUT&RUN


title: H2K119ub_120hr-dTAG-1

description:
Library name: 3340851_H2K119ub_120hr-dTAG-1
CUT&RUN


title: TH45


title: BCOR_120hr-dTAG-1

description:
Library name: 3340849_BCOR_120hr-dTAG-1
CUT&RUN


title: TH44


title: IgG_DMSO

description:
Library name: 3340848_IgG_DMSO
CUT&RUN


title: H3K36me2_Th_120hr-DMSO-2

description:
Library name: 3340846_H3K36me2_Th_120hr-DMSO-2
CUT&RUN


title: TH42


title: H3K36me2_Th_120hr-DMSO-1

description:
Library name: 3340845_H3K36me2_Th_120hr-DMSO-1
CUT&RUN


title: TH43


title: H2K119ub_120hr-DMSO-2

description:
Library name: 3340844_H2K119ub_120hr-DMSO-2
CUT&RUN


title: H2K119ub_120hr-DMSO-1

description:
Library name: 3340843_H2K119ub_120hr-DMSO-1
CUT&RUN


title: H3K36me2_Th_120hr-dTAG-1

description:
Library name: 3340853_H3K36me2_Th_120hr-dTAG-1
CUT&RUN


title: TH40


title: TH41


title: BCOR_120hr-DMSO-2

description:
Library name: 3340842_BCOR_120hr-DMSO-2
CUT&RUN


title: TH38


title: BCOR_120hr-DMSO-1

description:
Library name: 3340841_BCOR_120hr-DMSO-1
CUT&RUN


title: TH39


title: rabbitIgG120hr-dTAG

description:
Library name: 3327578_rabbitIgG120hr-dTAG
CUT&RUN


title: rabbitIgG_0hr

description:
Library name: 3327577_rabbitIgG_0hr
CUT&RUN


title: Mcm4-Flag ChIP-Exo 30min released, rep3

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Primary analysis RTA 2.11.3 and Secondary analysis bcl2fastq2_2.20.0
Sequencing was conducted on an Illumina MiSeq system with 40 base pair single-end reads
Sequencing reads were mapped to sacCer3 genome using Bowtie2 aligner (v. 2.3.5)
Bigwig files were generated for visualizing with genome browser using deeptools (version 3.2.1)
Normalisation of each sample to sequencing read depth using deeptools  --normalizeUsing CPM option.
Peaks were called using ChExMix software (v 0.45) .
Genome_build: sacCer3
Supplementary_files_format_and_content: Bigwig files of normalised data
Supplementary_files_format_and_content: Bed files with called peaks

organism: Saccharomyces cerevisiae

source_name: crosslinked culture

growth_protocol: Cells were grown in 100ml YPD from overnight cultures to OD600 0.6 at 220 rpm and 30°C followed by 2 hrs α-factor arrest at 25°C, 220 rpm and released in 100 ml warm media.

extract_protocol:
Lysates were prepared using standard procedures, sonicated chromatin clarified and Flag-tagged proteins immunprecipitated.
Immunoprecipitated DNA was treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation. After phosphorylation, the first adapter was ligated using T4 DNA Ligase and T4 Polynucleotidekinase. Gaps were filled with phi29 polymerase and 5’ DNA ends were digested using lambda exonuclease. DNA was eluted from resin, de-crosslinked and purified. The second adapter was ligated and DNA purified. After 18 cycles of amplification, DNA libraries were gel extracted using the NEB Monarch PCR & DNA Cleanup Kit according to the manufacturer’s instructions to allow elution with smaller volumes. Libraries were quantified using Qubit fluorometry (Thermo Fisher, dsDNA HS Assay) and qPCR (KAPA Illumina library quantification) before pooling and Illumina next generation sequencing.

treatment_protocol: media was supplemented with 100 nM rapamycin 0.5hrs before releasing and upon release.

tag: strain

tag: chip-antibody

value: anti-Flag F-1804, Sigma

tag: cell cycle status

value: 30 minute release


title: TH37


title: TH36


title: Mcm4-Flag ChIP-Exo 30min released, rep2


title: mouseIgG_120hr-dTAG

description:
Library name: 3327576_mouseIgG_120hr-dTAG
CUT&RUN


title: TH35


title: TH34


title: mouseIgG_0hr

description:
Library name: 3327575_mouseIgG_0hr
CUT&RUN


title: Mcm4-Flag ChIP-Exo 30min released, rep1


title: HA_24hr-dTAG-2

description:
Library name: 3327574_HA_24hr-dTAG-2
CUT&RUN


title: Mcm4-Flag ChIP-Exo G1 arrested, rep3


title: HA_24hr-dTAG-1

description:
Library name: 3327573_HA_24hr-dTAG-1
CUT&RUN


title: HA_24hr-DMSO-2

description:
Library name: 3327572_HA_24hr-DMSO-2
CUT&RUN


title: Mcm4-Flag ChIP-Exo G1 arrested, rep2


title: TH52


title: HA_24hr-DMSO-1

description:
Library name: 3327571_HA_24hr-DMSO-1
CUT&RUN


title: HA_12hr-dTAG-2

description:
Library name: 3327570_HA_12hr-dTAG-2
CUT&RUN


title: HA_12hr-dTAG-1

description:
Library name: 3327569_HA_12hr-dTAG-1
CUT&RUN


title: Mcm4-Flag ChIP-Exo G1 arrested, rep1


title: HA_12hr-DMSO-2

description:
Library name: 3327568_HA_12hr-DMSO-2
CUT&RUN


title: HA_12hr-DMSO-1

description:
Library name: 3327567_HA_12hr-DMSO-1
CUT&RUN


title: TH32


title: TH31


title: TH33


title: TH30


title: HA_0hr-2

description:
Library name: 3327566_HA_0hr-2
CUT&RUN


title: TH29


title: HA_0hr-1

description:
Library name: 3327565_HA_0hr-1
CUT&RUN


title: EZH2_120hr-dTAG-1

description:
Library name: 3327563_EZH2_120hr-dTAG-1
CUT&RUN


title: EZH2_120hr-dTAG-2

description:
Library name: 3327564_EZH2_120hr-dTAG-2
CUT&RUN


title: EZH2_120hr-DMSO-2

description:
Library name: 3327562_EZH2_120hr-DMSO-2
CUT&RUN


title: EZH2_120hr-DMSO-1

description:
Library name: 3327561_EZH2_120hr-DMSO-1
CUT&RUN


title: TH27


title: EZH2_72hr-dTAG-2

description:
Library name: 3327560_EZH2_72hr-dTAG-2
CUT&RUN


title: TH26


title: TH25


title: EZH2_72hr-dTAG-1

description:
Library name: 3327559_EZH2_72hr-dTAG-1
CUT&RUN


title: EZH2_72hr-DMSO-2

description:
Library name: 3327558_EZH2_72hr-DMSO-2
CUT&RUN


title: TH24


title: TH23


title: EZH2_72hr-DMSO-1

description:
Library name: 3327557_EZH2_72hr-DMSO-1
CUT&RUN


title: TH22


title: TH21


title: EZH2_48hr-dTAG-2

description:
Library name: 3327556_EZH2_48hr-dTAG-2
CUT&RUN


title: TH20


title: TH19


title: EZH2_48hr-dTAG-1

description:
Library name: 3327555_EZH2_48hr-dTAG-1
CUT&RUN


title: TH28


title: EZH2_48hr-DMSO-1

description:
Library name: 3327553_EZH2_48hr-DMSO-1
CUT&RUN


title: TH18


title: EZH2_24hr-dTAG-2

description:
Library name: 3327552_EZH2_24hr-dTAG-2
CUT&RUN


title: EZH2_24hr-DMSO-2

description:
Library name: 3327550_EZH2_24hr-DMSO-2
CUT&RUN


title: TH17


title: EZH2_24hr-dTAG-1

description:
Library name: 3327551_EZH2_24hr-dTAG-1
CUT&RUN


title: TH16


title: TH13


title: TH15


title: TH14


title: EZH2_12hr-dTAG-2

description:
Library name: 3327548_EZH2_12hr-dTAG-2
CUT&RUN


title: EZH2_12hr-dTAG-1

description:
Library name: 3327547_EZH2_12hr-dTAG-1
CUT&RUN


title: EZH2_12hr-DMSO-2

description:
Library name: 3327546_EZH2_12hr-DMSO-2
CUT&RUN


title: TH10


title: TH12


title: TH11


title: TH9


title: EZH2_0hr-1

description:
Library name: 3327543_EZH2_0hr-1
CUT&RUN


title: EZH2_0hr-2

description:
Library name: 3327544_EZH2_0hr-2
CUT&RUN


title: Patient 069, WD component

city: Los Angeles

first: Heather

middle: R

last: Christofk

state: CA

address: 615 Charles E Young Dr South

institute: University of California, Los Angeles

description:
Library name: LPS069-WD
10X Genomics

data_processing:
Raw sequencing data were processed with Cell Ranger (10x Genomics) for sample demultiplexing, barcode assignment, gene quantification, and aggregation. Technical background signals were subsequently removed using CellBender (Broad Institute).
Assembly: Homo sapiens (human) genome assembly GRCh38 (hg38)
Supplementary files format and content: Heirarchical data format (.h5)

source_name: liposarcoma

extract_protocol:
Fresh tissue was harvested at the time of surgery from both WD and DD components and stored immediately in liquid nitrogen. Additional tissue from both components was placed in formalin for permanent fixation and then embedded in paraffin. Tumor diagnosis and subtype was validated by expert histological review and DNA FISH (Empire Genomics, SKU MDM2-CHR12-20-GROR) was used to confirm the presence of MDM2 amplification (authors SD, MN). Tumors without MDM2 amplification were excluded. After tumor diagnosis and subtype were confirmed, samples were thawed in RNALaterTM-ICE (ThermoFisher) overnight at -20C. Nuclei were then isolated using the Chromium Nuclei Isolation with RNase Inhibitor Kit (10X Genomics). For DD components, 50mg of tissue was used and for WD components, 250mg of tissue was used from each sample. Nuclei concentration and cell viability was determined using a Countess II FL Automated Cell Counter (ThermoFisher). Cell viability <5% was used as a threshold to ensure high quality nuclei isolation. Samples were also assessed by brightfield microscopy for the presence of significant debris. Single nuclei suspensions generated from each sample were then used to construct 3’GEX cDNA libraries (10x Genomics).
Single nuclei suspensions generated from each sample were used to construct 3’GEX cDNA libraries (10x Genomics) followed by next-generation sequencing via NovaSeq 6000 (Illumina). Demultiplexed sequencing results were aligned to the reference genome and ambient RNA was removed using CellBender. After filtering, 27,333 nuclei were included in the computational analysis pipeline. The R package Seurat was applied to integrate samples, cluster cells, and identify differentially expressed genes. LPS clusters were analyzed by pseudo-time analysis (Monocle3) to establish trajectory inferences between WD and DD subtypes.

value: liposarcoma

tag: tumor component

value: dedifferentiated


title: Patient 069, DD component

description:
Library name: LPS069-DD
10X Genomics

value: well-differentiated


title: TH5


title: EZH2_48hr-DMSO-2

description:
Library name: 3327554_EZH2_48hr-DMSO-2
CUT&RUN


title: TH7


title: EZH2_24hr-DMSO-1

description:
Library name: 3327549_EZH2_24hr-DMSO-1
CUT&RUN


title: Patient 064, WD component

description:
Library name: LPS064-WD
10X Genomics


title: TH4


title: TH3


title: Patient 062, WD component

description:
Library name: LPS062-WD
10X Genomics


title: Patient 064, DD component

description:
Library name: LPS064-DD
10X Genomics


title: TH2


title: Patient 062, DD component

description:
Library name: LPS062-DD
10X Genomics


title: Cartridge4

city: Berlin

first: Schayan

last: Yousefian

address: Hannoversche Str. 28

country: Germany

institute: Charité Universitätsmedizin Berlin

description: Library name: Sample4

data_processing:
BD Rhapsody pipeline 2.0
Assembly: GRCh38
Supplementary files format and content: Count matrix of RNA (WTA) and Antibodies (Abseq) and table containing sample hashing information. Processed data (features, barcodes, matrix) can be directly used for downstream analyses. Sample Tag files can be used for sample demultiplexing.
Library strategy: CITE-seq

source_name: peripheral blood mononuclear cells

extract_protocol:
Patient-derived PBMC samples were thawn and processed according to the BD Rhapsody protocol for single-cell multi-omics.
BD Rhapsody multi-omics (WTA+Abseq+SMK)

value: peripheral blood mononuclear cells


title: Cartridge5

description: Library name: Sample5


title: Cartridge3

description: Library name: Sample3


title: BMDM, Trim14 KO Untreated rep 1

city: Nashville

first: Kristin

middle: L

last: Patrick

state: Tennessee

department: Pathology, Microbiology, and Immunology (PMI)

institute: Vanderbilt University Medical Center

description: Library name: Trim14KOUN rep1

data_processing:
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA).
Trimmed paired-end reads were aligned to the mouse reference genome (GRCm39) using Illuma standard alignment software. Output files were generated as coordinate-sorted BAM files suitable for downstream differential expression and splicing analyses.
Gene-level read counts were quantified and raw count matrices were imported in DESeq2 (v1.46.0), where normalization was performed using the media-of-ratios method to account for library size differences. Differential expression analysis was carried out using DESeq2's negative binomial model with Benjamini-Hochberg correction.
Assembly: GRCm39
Supplementary files format and content: Tab delimited text files with raw counts for each sample
Supplementary files format and content: .xlsx file format, differential gene expression between genotypes and infection time points.

source_name: bone marrow derived macrophages (BMDM)

growth_protocol: DMEM supplemented with 20% FBS and 2% Hepes. Cells cultured at 37C and 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent. Zymo Research Direct-zol kits were used to isolate RNA with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina preparation.

treatment_protocol: BMDMs were infected with low passage Erdman strain Mycobacterium tuberculosis at an MOI = 5 via spinfect. 0 or 4 hours post-infection, RNA was collected.

value: bone marrow derived macrophages (BMDM)

value: macrophage

value: Trim14 KO

value: Untreated


title: BMDM, WT Untreated rep 3

description: Library name: WTUN rep3

value: WT


title: BMDM, WT Untreated rep 1

description: Library name: WTUN rep1


title: TH6

value: heart biopsy


title: Cartridge2

description: Library name: Sample2


title: BMDM, Trim14 KO +Mtb rep 3

description: Library name: Trim14KO4HMTB rep3

value: 4h Mtb


title: Cartridge1

description: Library name: Sample1


title: BMDM, Trim14 KO +Mtb rep 2

description: Library name: Trim14KO4HMTB rep2


title: BMDM, Trim14 KO +Mtb rep 1

description: Library name: Trim14KO4HMTB rep1


title: BMDM, WT +Mtb rep 3

description: Library name: WT4HMTB rep3


title: Rcl331_72hZEN_2 (eRRBS)

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

description: Library name: Sample 35

data_processing:
We use FastQC (FastQC) (v0.11.8) to assess the overall quality of each sequenced sample.
We use TrimGalore (Trim Galore) (v0.4.5) with the following parameters: –adapter AGATCGGAAGAGC -e 0.1 –stringency 6 –length 20 –nextseq 20 –rrbs.
Reads are aligned to hg38 with Bismark (Krueger and Andrews, 2011) (v0.22.1) using Bowtie2 (Langmead and Salzberg, 2012) (v2.3.4) with default settings (multi-seed length of 20bp with 0 mismatches). Alignments below a MAPQ threshold are removed with samtools (Li et al., 2009) (v1.2) and the parameters: -q 10. MethylDackel (MethylDackel) (v0.4.0) then calls methylation rates with parameters -d 5 -D 2000 –mergeContext.
Assembly: hg38
Supplementary files format and content: Methylation calls in pseudo-bedGraph format containing the following columns in the following order: chromosome, start, end, methylation rate, number of alignments/pairs reporting methylated bases, number of alignments/pairs reporting unmethylated bases.

source_name: Prostate

growth_protocol: NCI-H660 cells (CRL-5813) were purchased from ATCC and cultured according to their recommendation. LTL331R cell line was derived from LTL331R PDX and were grown in RPMI1640 (Gibco 11875-093) with 1x insulin, transferrin, selenium, ethanolamine solution (ITS-X; Gibco 51500-056) + 5% FBS (Corning MT35010CV).

extract_protocol:
Total DNA was extracted using a Qiagen AllPrep RNA/DNA mini kit (Qiagen 80204) according to the manufacturer's protocol. 25-75 ng of genomic DNA was digested for 16-18 hours with the MspI restriction enzyme. The digested DNA was purified by phenol-chloroform extraction, then ethanol precipitated in the presence of glycogen and sodium acetate. The precipitated DNA was resuspended in 10mM Tris-Cl pH8.5 (Buffer EB) and processed for end-repair, A-tailing, and ligation of hairpin adapters with methylated cytosines. The ligated DNA was next ran on a 1.8% Low-Range Ultra Agarose Gel in TBE buffer, and fragments of 100-200bp and 200-300bp were excised and separately purified using Qiagen Gel Extraction kit. A 2ul aliquot of each fragment was used to verify proper adapter ligation and size selection by PCR. Samples passing this QC were then subjected to bisulfite conversion with the EZ DNA Methylation Kit, but with the following changes: the samples were incubated in a thermal cycler using the following conditions: 55 cycles: 95C for 30 sec, 50C for 15 min. Hold at 4C. The bisulfite converted samples were cleaned up according to the manufacturer’s protocol and eluted in 40ul of nuclease free water. The samples were next amplified using Roche High Fidelity FastStart system with the following protocol: 94C for 5 minutes; 18 cycles of: denaturing at 94C for 20 seconds, annealing at 60C for 30 seconds, extension at 72C for 1 min. A final extension was done at 72C for 3 minutes and the reactions were kept at 4C until they were cleaned. This final library cleanup was done with Agencourt’s AMPure XP SPRI beads according to the following protocol: The beads were brought to room temperature with gentle agitation for a minimum of 30 minutes. A 1.2X volume (for short fragments) and 1.1X volume (for long fragments) of SPRI beads was added to each sample fragment, and the PCR products were purified per manufacturer’s recommendation using 500ul of 80% ethanol for washes. Each library was eluted into 33ul of elution buffer (10mM Tris-Cl pH 8.5). The libraries were quantified using Qubit’s High Sensitivity ds DNA kit, and the quality was assessed with Agilent’s High Sensitivity D1000 ScreenTape assay.
Libraries for Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) were prepared according to (Garrett-Bakelman et al., 2015)

treatment_protocol: NCI-H660 and LTL331R cell lines were treated with BET inhibitor (500nM ZEN), DNA methyltransferase inhibitor (100nMdAZA), or the combination (500nM ZEN + 100nM dAZA) daily for 72 hrs with corresponding vehicle (DMSO) controls. LTL331R PDXs were grown in the flanks of mice treated with 50mg/kg ZEN daily, 0.8mg/kg dAZA for 5 days followed by a 9-day holiday, or the combination with corresponding vehicle controls.

value: Prostate

value: Prostate Cancer Cell Line

value: 500nM ZEN 72hr


title: Rcl331_72hZEN_1 (eRRBS)

description: Library name: Sample 34


title: Rcl331_72hZEN_3 (eRRBS)

description: Library name: Sample 36


title: BMDM, WT +Mtb rep 2

description: Library name: WT4HMTB rep2


title: BMDM, WT +Mtb rep 1

description: Library name: WT4HMTB rep1


title: Rcl331_72hDMSO_2 (eRRBS)

description: Library name: Sample 32

value: DMSO 72hr


title: Rcl331_72hDMSO_1 (eRRBS)

description: Library name: Sample 31


title: Rcl331_72hdAZA_3 (eRRBS)

description: Library name: Sample 30

value: 100nM dAZA 72hr


title: Mouse cerebral vessels Visium spatial gene expression (C_vessels, manual alignment)

city: Aurora

first: Eric

last: Prince

state: CO

address: 12800 E 19th AAve

department: Neurosurgery

institute: University of Colorado Anschutz Medical Campus

description:
Library name: TgNotch3WT_Vasculature
Visium CytAssist (standard), Space Ranger 2.0.1, manual alignment

data_processing:
2023 batch: bcl2fastq used for demultiplexing; Space Ranger 2.0.1 count against mm10-2020-A with Visium Mouse Transcriptome Probe Set v1.0; cerebral vessel samples aligned manually via Loupe alignment JSON (v2).
2024 batch: demultiplexed to FASTQ; Space Ranger 3.1.1 count (Visium HD) vs mm10-2020-A; outputs binned at 2 um, 8 um and 16 um (8 um bin submitted).
Assembly: mm10 (refdata-gex-mm10-2020-A)
Supplementary files format and content: 2023 processed files (per sample): filtered/raw_feature_bc_matrix.h5, metrics_summary.csv, cloupe.cloupe, spatial/ (tissue_positions.csv, scalefactors_json.json, tissue_hires/lowres_image.png, aligned_fiducials.jpg, detected_tissue_image.jpg, cytassist_image.tiff).
Supplementary files format and content: 2024 HD processed files (per sample): metrics_summary.csv, top-level spatial images, and the 8 um bin (square_008um) filtered/raw_feature_bc_matrix.h5, cloupe.cloupe, scalefactors_json.json, tissue_positions.parquet. (2 um and 16 um bins and feature_slice.h5 available on request.)
Library strategy: Spatial Transcriptomics

source_name: Mouse cerebral (brain) vessels, FFPE section

extract_protocol:
FFPE tissue sections placed on 10x Visium CytAssist slides; RNA captured via probe hybridization (Mouse Transcriptome Probe Set v1.0, mm10-2020-A) following the standard 10x Genomics Visium CytAssist for FFPE protocol.
2023 batch: 10x Genomics Visium CytAssist Spatial Gene Expression for FFPE. 2024 batch: 10x Genomics Visium HD Spatial Gene Expression for FFPE (CytAssist). Libraries prepared per the manufacturers standard protocol.

value: cerebral vessels

value: transgenic, TgNotch3^WT

tag: batch

value: 2023 Visium

tag: capture area


title: Mouse cerebral vessels Visium spatial gene expression (D_vessels, manual alignment)

description:
Library name: TgNotch3R169C_Vasculature
Visium CytAssist (standard), Space Ranger 2.0.1, manual alignment

value: transgenic, TgNotch3^R169C


title: Rcl331_72hdAZA_2 (eRRBS)

description: Library name: Sample 29


title: Mouse brain Visium spatial gene expression (A_brain)

description:
Library name: TgNotch3WT_Brain
Visium CytAssist (standard), Space Ranger 2.0.1

source_name: Mouse brain tissue, FFPE section

value: brain


title: Rcl331_72hCombo_3 (eRRBS)

description: Library name: Sample 27

value: 500nM ZEN + 100nM dAZA 72hr


title: p27 KO-exp4

city: Toulouse

first: Arnaud

last: Besson

address: 118 route de Narbonne

department: MCD UMR5077

country: France

institute: Centre de Biologie Integrative - CNRS

description: Library name: p27 KO-exp4

data_processing:
The quality of each raw sequencing file (fastq) was verified with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Fastq were aligned the reference mouse genome (GRCm39) and counted on the GENCODE annotation from database (gtf GRCm39) using STAR aligner (STAR_2.5.4a).
Assembly: reference mouse genome (GRCm39)
Supplementary files format and content: Processed data file in xlsx format. File includes Rwa data nuber, Log Count Per Million and Count Per Million;

source_name: HPV E6 immortalized mouse embryonic fibroblasts

growth_protocol: p27KO and p27WT MEFs were grown for 24 h in DMEM 10% fetal bovine serum at 37C, 5% CO2

extract_protocol:
Cells were lysed in TriReagent (T9424, Sigma Aldrich) and RNA was extracted using Direct-zol RNA Miniprep Plus Kits (Zymo Research) according to the manufacturer’s protocol. RNA integrity was verified on 0.8% agarose gel and quantified using a Nanodrop spectrophotometer.
cDNA was synthetized using SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific) according to the manufacturer’s protocol. RNA-Seq samples were sequenced using Illumina Novaseq (paired-end, 2 x 150 bp long reads, 10M reads/sample).

value: growth in DMEM 24 h


title: p27 KO-exp3

description: Library name: p27 KO-exp3

value: HPV E6 immortalized mouse embryonic fibroblasts


title: EZH2_12hr-DMSO-1

description:
Library name: 3327545_EZH2_12hr-DMSO-1
CUT&RUN


title: p27 KO-exp2

description: Library name: p27 KO-exp2


title: Rcl331_72hCombo_2 (eRRBS)

description: Library name: Sample 26


title: LTL331RPDXcombo_ZENdAZA_3 (eRRBS)

description: Library name: Sample 24

value: LTL331R PDX

value: Prostate Cancer Patient Derived Xenograft

value: 50mg/kg ZEN + 0.8mg/kg dAZA


title: Rcl331_72hCombo_1 (eRRBS)

description: Library name: Sample 25


title: TH8

value: heart biopsy


title: p27 WT clone2-exp4

description: Library name: p27 WT clone2-exp4

value: wild-type


title: LTL331RPDXcombo_ZENdAZA_2 (eRRBS)

description: Library name: Sample 23

value: Prostate


title: p27 WT clone2-exp3

description: Library name: p27 WT clone2-exp3


title: LTL331RPDXcombo_ZENdAZA_1 (eRRBS)

description: Library name: Sample 22


title: LTL331RPDXcombo_ZEN_3 (eRRBS)

description: Library name: Sample 21

value: 50mg/kg ZEN


title: BMDM, Trim14 KO Untreated rep 2

description: Library name: Trim14KOUN rep2

value: bone marrow derived macrophages (BMDM)

value: macrophage

value: Trim14 KO

value: Untreated


title: p27 WT clone2-exp2

description: Library name: p27 WT clone2-exp2


title: Cartridge6

description: Library name: Sample6

value: peripheral blood mononuclear cells


title: p27 WT clone2-exp1

description: Library name: p27 WT clone2-exp1


title: p27 WT clone1-exp4

description: Library name: p27 WT clone1-exp4


title: BMDM, Trim14 KO Untreated rep 3

description: Library name: Trim14KOUN rep3


title: LTL331RPDXcombo_ZEN_2 (eRRBS)

description: Library name: Sample 20


title: TH1


title: LTL331RPDXcombo_ZEN_1 (eRRBS)

description: Library name: Sample 19


title: BMDM, WT Untreated rep 2

description: Library name: WTUN rep2

value: WT


title: p27 WT clone1-exp3

description: Library name: p27 WT clone1-exp3


title: LTL331RPDXcombo_Vehicle_3 (eRRBS)

description: Library name: Sample 18

value: Vehicle


title: p27 WT clone1-exp2

description: Library name: p27 WT clone1-exp2


title: p27 WT clone1-exp1

description: Library name: p27 WT clone1-exp1


title: LTL331RPDXcombo_dAZA_3 (eRRBS)

description: Library name: Sample 15

value: 0.8mg/kg dAZA


title: LTL331RPDXcombo_Vehicle_2 (eRRBS)

description: Library name: Sample 17


title: LTL331RPDXcombo_Vehicle_1 (eRRBS)

description: Library name: Sample 16


title: LTL331RPDXcombo_dAZA_2 (eRRBS)

description: Library name: Sample 14


title: Vein-rPadron07212023, contralateral

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

description:
Library name: Vein-rPadron07212023
10x Genomics

data_processing:
For single cell RNAseq, FASTQ files were generated with Cell Ranger's mkfastq pipeline (version 6.0.2).
The Cell Ranger's count pipeline (version 6.0.2) was used to generate raw gene-barcode matrices from alignment to the 10X Genomics pre-built Cell Ranger mouse reference package (version mm10-2020-A), from GRCm38 Ensembl build 98/GENCODE M23 gene annotations.
Bulk RNAseq was processed through standard pipeline of alignment to the GRCm38 genome with the STAR aligner.
Bulk RNA gene counts were created using the GeneCounts features within STAR against the ENSEMBL M23 gene build
Assembly: GRCm38
Supplementary files format and content: barcodes.tsv.gz is a gzipped text file listing individual cell barcodes included in the sample analysis
Supplementary files format and content: features.tsv.gz is a gzipped tab-delimited file of the gene features included in the gene quantification for each sample
Supplementary files format and content: matrix.mtx.gz is a gzipped tab-delimited file of the counts per feature per cell barcode for each sample
Supplementary files format and content: Final_counts-AVF_timepoints.csv is a comma seperated text file of raw counts per gene

source_name: Vein

extract_protocol:
Contralateral veins and AVFs were harvested at different timepoints. For bulk RNA-seq, tissues were ground to a fine powder in a Spex/Mill 6770 cryogenic grinder, followed by total RNA extraction using Trizol and treatment with DNase I. For single cell RNA-seq, samples were enzymatically digested for 90 minutes at 37°C with shaking using a combination of collagenase type II, soybean trypsin inhibitor, elastase, Dispase, DNAse I, collagenase type XI, hyaluronidase type I, and HEPES in HBSS with Ca2+ and Mg2+. After 90 minutes, an equal volume of Accumax was added to the dissociation mix and incubated for an additional 5 minutes. Single cells were filtered through a 40 μM strainer, washed with HBSS twice, and incubated with red blood cell lysis buffer for 5-10 min. Cells were washed once again with HBSS and resuspended in 0.1% BSA in PBS for counting and RNA sequencing.
Poly(A)-selected bulk mRNA libraries were prepared by Azenta using an ultra-low input RNA sequencing protocol. Libraries were sequenced on the Illumina HiSeq X using a paired-end 150-bp configuration and an output of ~350 million reads per lane. Single cell samples were run using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10X Genomics) with a target capture of 10,000 cells. Each sample was processed on an independent Chromium Single Cell A Chip (10X Genomics) and subsequently run on a thermocycler (Eppendorf). Sequencing libraries were evaluated for quality on the Agilent Tape Station (Agilent Technologies, Palo Alto, CA) and quantified using a Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and qPCR before sequencing on the Illumina NovaSeq 6000.

value: Vein

tag: Sex

value: pooled male and female


title: AVF24_21, late

description:
Library name: 24
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane

source_name: AVF

value: AVF

value: Male


title: AVF7-rPadron1207, early

description:
Library name: AVF7-rPadron1207
10x Genomics


title: LTL331RPDXcombo_dAZA_1 (eRRBS)

description: Library name: Sample 13

value: LTL331R PDX

value: Prostate Cancer Patient Derived Xenograft


title: AVF23_21, late

description:
Library name: 23
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: Rcl331_72hDMSO_3 (eRRBS)

description: Library name: Sample 33

value: Prostate Cancer Cell Line

value: DMSO 72hr


title: H660_72hZEN_3 (eRRBS)

description: Library name: Sample 12

value: Prostate

value: 500nM ZEN 72hr


title: AVF19_21, late

description:
Library name: 19
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane

value: Female


title: H660_72hZEN_2 (eRRBS)

description: Library name: Sample 11


title: AVF17_21, late

description:
Library name: 17
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: H660_72hZEN_1 (eRRBS)

description: Library name: Sample 10


title: AVF15_10, mid

description:
Library name: 15
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: AVF16_21, late

description:
Library name: 16
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: AVF14_10, mid

description:
Library name: 14
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: H660_72hdAZA_3 (eRRBS)

description: Library name: Sample 6

value: 100nM dAZA 72hr


title: H660_72hDMSO_3 (eRRBS)

description: Library name: Sample 9


title: AVF13_10, mid

description:
Library name: 13
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: H660_72hDMSO_1 (eRRBS)

description: Library name: Sample 7


title: AVF12_10, mid

description:
Library name: 12
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: Rcl331_72hdAZA_1 (eRRBS)

description: Library name: Sample 28


title: H660_72hdAZA_2 (eRRBS)

description: Library name: Sample 5


title: Mouse brain Visium spatial gene expression (B_brain)

description:
Library name: TgNotch3R169C_Brain
Visium CytAssist (standard), Space Ranger 2.0.1

value: brain

value: transgenic, TgNotch3^R169C

value: 2023 Visium


title: H660_72hdAZA_1 (eRRBS)

description: Library name: Sample 4


title: AVF9_10, mid

description:
Library name: 9
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: AVF10_3, early

description:
Library name: 10
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: AVF7_3, early

description:
Library name: 7
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: AVF6_3, early

description:
Library name: 6
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: H660_72hCombo_3 (eRRBS)

description: Library name: Sample 3

value: 500nM ZEN + 100nM dAZA 72hr


title: H660_72hCombo_2 (eRRBS)

description: Library name: Sample 2


title: H660_72hCombo_1 (eRRBS)

description: Library name: Sample 1


title: N3_Ctrl

city: Zurich

first: Gerhard

last: Schratt

address: Winterthurerstrasse 190

department: HEST

country: Switzerland

institute: ETH Zürich

description: Library name: C_1

data_processing:
Reads were mapped to GRCh38.p13 and counted with Salmon. Sample A_2 had to be sequenced in two runs to acquire a sufficent amount of reads. Both runs were then mapped together.
Differential expression analysis was performed using edgeR. An SVA-correction was applied to account for technical variation.
For further infos please see the methods section of the publication.
Assembly: Ensembl107
Supplementary files format and content: comma-seperated text files including counts and SVA-corrected logcpm values for each sample
Supplementary files format and content: comma-seperated text files including differential expression analyses of both individual miRNA overexpression concentration against the control as well as a combined DEA.

source_name: Transfection of negative control

growth_protocol: SH-Sy5y neuroblastoma cells (ECACC) were cultured in DMEM/F12 with Glutamax (Invitrogen – 31331028), 10% heat inactivaed FBS (Fisher Scientific – 10500064) and Pen/Strep (100 U/ml).

extract_protocol:
RNA was extracted using the miRVana kit (Thermo).
RNA libraries were prepared using the NEB Next Ultra RNA Library Prep Kit for Illumina

treatment_protocol: Cells were transfected with miRNA mimics for 48h.

value: Neuroblastoma cell line

value: NegCtrl


title: AVF4_3, early

description:
Library name: 4
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: AVF3_3, early

description:
Library name: 3
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: N3_MiR_10nM

description: Library name: C_2

source_name: Transfection of miR-1229 mimic (20pmol) and negative control (20pmol)


title: p27 KO-exp1

description: Library name: p27 KO-exp1

value: HPV E6 immortalized mouse embryonic fibroblasts

value: growth in DMEM 24 h


title: N2_MiR_20nM

description: Library name: B_3

source_name: Transfection of miR-1229 mimic (40pmol)


title: AVF2_3, early

description:
Library name: 2
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane

value: AVF

value: Male


title: N3_MiR_20nM

description: Library name: C_3


title: AVF5_3, early

description:
Library name: 5
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: AVF1_3, early

description:
Library name: 1
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: N2_MiR_10nM

description: Library name: B_2


title: Vein633, contralateral

description:
Library name: 633
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane

value: Vein


title: N2_Ctrl

description: Library name: B_1


title: Vein35, contralateral

description:
Library name: 35
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: N1_MiR_20nM

description: Library name: A_3


title: Vein632, contralateral

description:
Library name: 632
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: Vein34, contralateral

description:
Library name: 34
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: Rcl331_72hZEN_3

description: Library name: Sample 44

data_processing:
Sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Reads were trimmed using cutadapt v2.3 (Martin, 2011). FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010). Fastq Screen v0.13.0 was used to screen for various types of contamination (Wingett and Andrews, 2018).FastQC was used in an additional post-alignment step to ensure that only high-quality data were used for expression quantitation and differential expression. Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016).
Reads were mapped to the reference genome GRCh38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Assembly: hg38
Supplementary files format and content: The columns of the counts.txt files are: (1) ensemble gene name; (2) gene symbol; (3) sample read count

extract_protocol:
Total RNA was extracted using a Qiagen AllPrep RNA/DNA mini kit (Qiagen 80204) according to the manufacturer's protocol.
The libraries were barcoded, pooled, and sequenced using paired-end, 151 bp sequencing at the University of Michigan Advanced Genomics Core.

value: LTL331R Cell Line

value: Prostate Cancer Cell Line


title: N1_MiR_10nM

description: Library name: A_2


title: Vein28, contralateral

description:
Library name: 28
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: Vein31, contralateral

description:
Library name: 31
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane


title: TKO_Input_1, ChIP-seq

description: Library name: Sample 9

data_processing:
We use FastQC (FastQC) (v0.11.8) to assess the overall quality of each sequenced sample. We use TrimGalore (TrimGalore) (v0.4.5) and cutadapt (Martin) (v1.15) with the following parameters: –illumina -e 0.1 –stringency 6 –length 20 –nextseq 20. We align trimmed reads to mm10 with Bowtie2 (Langmead and Salzberg, 2012) (v2.3.4.1) using default parameters with the exception of the following flags: -X 2000. Alignments are filtered with samtools (Li et al., 2009) (v1.2) using the flags: -F4 -F8 -f3 -q10 -F1024. Alignments completely overlapping blacklisted regions (ENCODE Blacklist Regions) are removed with bedtools (Quinlan and Hall, 2010) (v2.28.0). Sample-wise peaks are called with macs2 (Zhang et al., 2008) (v2.1.2) with flags: –format BAMPE –gsize mm.
Peaks over all samples are merged with bedops (Neph et al., 2012) (v2.4.36) for the purpose of principal component analysis and unsupervised clustering to assess the similarity of samples. Read cross-correlations within samples are plotted using phantompeakqualtools (Landt et al., 2012). MultiQC (Ewels et al., 2016) (v1.7) generates a report combining FastQC, trimming, alignment, and duplicate calling over all the samples. The software DeepTools is used to calculate coverage and IP efficiency plots (Ramírez et al., 2016) (v3.3.0).
Assembly: mm10
Supplementary files format and content: bigwig file for each sample

growth_protocol: SKO, DKO, DKOcr105, and TKO cells were cultured in DMEM/high glucose (Gibco 11995-065) with L-glutamine (Gibco 35050-061), sodium pyruvate (Gibco 11360-070), and 10% FBS (Corning MT35010CV). DKOcr298 was cultured in phenol-red free DMEM/high glucose (Gibco 31053-028) with L-glutamine (Gibco 35050-061), sodium pyruvate (Gibco 11360-070), and 10% charcoal-stripped FBS (Millipore Sigma F6765).

extract_protocol:
ChIP experiments were performed as previously described (doi:10.1038/nprot.2006.27) using anti-H3K27Ac (Active Motif 39133) or rabbit IgG (Millipore 12-370).
DNA quantitation was performed using the Qubit HS dsDNA. Assessment of fragment size was done with the TapeStation HS D1000 assay. Sequencing libraries were prepared using the Swift Accel-NGS 2S Plus DNA kit and 2S Combinatorial Dual Indexing kit, according to the manufacturer’s instructions. Each library was prepared with 10 ng of DNA. The final library amplification was performed with 6 cycles of PCR amplification. Quality control of the libraries was done with the Qubit HS dsDNA and TapeStation HS D1000 kit. Libraries were quantitated using the KAPA Library Quantitation Kit for Illumina platforms. The concentrations obtained were used to pool the libraries, and this pool was submitted to the UM Advanced Genomics Core for sequencing on the NovaSeq6000, using an S1 flow cell and paired-end 50 nucleotides chemistry.

treatment_protocol: ChIP-seq was performed on untreated cells

value: Prostate

value: TKO

tag: chip antibody

value: None/Input

value: DMSO 24hr


title: Rcl331_72hZEN_2

description: Library name: Sample 43

value: 500nM ZEN 72hr


title: Rcl331_72hZEN_1

description: Library name: Sample 42


title: Rcl331_72hDMSO_3

description: Library name: Sample 41

value: DMSO 72hr


title: TKO_H3K27ac_2, ChIP-seq

description: Library name: Sample 8


title: Vein27, contralateral

description:
Library name: 27
Illumina, 2x150bp, ~350M PE reads (~105GB), single index, per lane

value: Female


title: N1_Ctrl

description: Library name: A_1


title: Rcl331_72hDMSO_2

description: Library name: Sample 40


title: Rcl331_72hdAZA_3

description: Library name: Sample 38

value: 100nM dAZA 72hr


title: DKOCr298_Input_1, ChIP-seq

description: Library name: Sample 3


title: TKO_H3K27ac_1, ChIP-seq

description: Library name: Sample 7


title: SKO_Input_1, ChIP-seq

description: Library name: Sample 6

value: SKO


title: Rcl331_72hDMSO_1

description: Library name: Sample 39


title: SKO_H3K27ac_1, ChIP-seq

description: Library name: Sample 4


title: DKOCr298_H3K27ac_2, ChIP-seq

description: Library name: Sample 2


title: LTL331RPDXcombo_ZENdAZA_3

description: Library name: Sample 32

value: LTL331R PDX

value: Prostate Cancer PDX

value: 50mg/kg ZEN + 0.8mg/kg dAZA


title: Rcl331_72hCombo_2

description: Library name: Sample 34

value: 500nM ZEN + 100nM dAZA 72hr


title: TKO_72hZEN_3, ERRBS

description: Library name: Sample 39

data_processing:
We use FastQC (FastQC) (v0.11.8) to assess the overall quality of each sequenced sample.
We use TrimGalore (Trim Galore) (v0.4.5) with the following parameters: –adapter AGATCGGAAGAGC -e 0.1 –stringency 6 –length 20 –nextseq 20 –rrbs.
Reads are aligned to mm10 with Bismark (Krueger and Andrews, 2011) (v0.22.1) using Bowtie2 (Langmead and Salzberg, 2012) (v2.3.4) with default settings (multi-seed length of 20bp with 0 mismatches). Alignments below a MAPQ threshold are removed with samtools (Li et al., 2009) (v1.2) and the parameters: -q 10. MethylDackel (MethylDackel) (v0.4.0) then calls methylation rates with parameters -d 5 -D 2000 –mergeContext.
Assembly: mm10
Supplementary files format and content: Methylation calls in pseudo-bedGraph format containing the following columns in the following order: chromosome, start, end, methylation rate, number of alignments/pairs reporting methylated bases, number of alignments/pairs reporting unmethylated bases.

treatment_protocol: TKO and DKOcr298 cells were treated with DMSO for 24hrs; TKO and DKOcr298 were treated with BET inhibitor (500nM ZEN), DNA methyltransferase inhibitor (100nMdAZA), or the combination (500nM ZEN + 100nM dAZA) daily for 72 hrs with corresponding vehicle (DMSO) controls.


title: TKO_72hZEN_2, ERRBS

description: Library name: Sample 38


title: Rcl331_72hCombo_1

description: Library name: Sample 33


title: LTL331RPDXcombo_ZENdAZA_2

description: Library name: Sample 31


title: TKO_72hDMSO_3, ERRBS

description: Library name: Sample 36


title: LTL331RPDXcombo_ZEN_3

description: Library name: Sample 29

value: 50mg/kg ZEN


title: H660_72hDMSO_2 (eRRBS)

description: Library name: Sample 8


title: TKO_72hZEN_1, ERRBS

description: Library name: Sample 37


title: TKO_72hDMSO_2, ERRBS

description: Library name: Sample 35


title: SKO_H3K27ac_2, ChIP-seq

description: Library name: Sample 5


title: LTL331RPDXcombo_ZEN_2

description: Library name: Sample 28


title: LTL331RPDXcombo_ZEN_1

description: Library name: Sample 27


title: LTL331RPDXcombo_ZENdAZA_1

description: Library name: Sample 30


title: LTL331RPDXcombo_Vehicle_3

description: Library name: Sample 26

value: Vehicle


title: TKO_72hDMSO_1, ERRBS

description: Library name: Sample 34


title: TKO_72hdAZA_3, ERRBS

description: Library name: Sample 33


title: TKO_72hdAZA_2, ERRBS

description: Library name: Sample 32


title: TKO_72hdAZA_1, ERRBS

description: Library name: Sample 31


title: TKO_72hCombo_3, ERRBS

description: Library name: Sample 30


title: LTL331RPDXcombo_dAZA_3

description: Library name: Sample 23

value: 0.8mg/kg dAZA


title: LTL331RPDXcombo_Vehicle_1

description: Library name: Sample 24


title: LTL331RPDXcombo_Vehicle_2

description: Library name: Sample 25


title: TKO_72hCombo_2, ERRBS

description: Library name: Sample 29

value: Prostate Cancer Cell Line


title: LTL331RPDXcombo_dAZA_2

description: Library name: Sample 22

value: Prostate


title: TKO_72hCombo_1, ERRBS

description: Library name: Sample 28

value: TKO


title: LTL331RPDXcombo_dAZA_1

description: Library name: Sample 21


title: LTL331R_PDX_5

description: Library name: Sample 20

value: No treatment


title: TKO_24hDMSO_2, ERRBS

description: Library name: Sample 26

value: DMSO 24hr


title: TKO_24hDMSO_3, ERRBS

description: Library name: Sample 27


title: LTL331R_PDX_4

description: Library name: Sample 19


title: TKO_24hDMSO_1, ERRBS

description: Library name: Sample 25


title: LTL331R_PDX_3

description: Library name: Sample 18


title: SKO_24hDMSO_3, ERRBS

description: Library name: Sample 24

value: Pten-/-


title: SKO_24hDMSO_2, ERRBS

description: Library name: Sample 23


title: LTL331R_PDX_1

description: Library name: Sample 16


title: SKO_24hDMSO_1, ERRBS

description: Library name: Sample 22


title: LTL331_PDX_3

description: Library name: Sample 15

value: LTL331 PDX


title: LTL331R_PDX_2

description: Library name: Sample 17


title: LTL331_PDX_2

description: Library name: Sample 14


title: LTL331_PDX_1

description: Library name: Sample 13


title: H660_72hZEN_3

description: Library name: Sample 12

value: 500nM ZEN 72hr


title: DKOCr298_72hZEN_1, ERRBS

description: Library name: Sample 19


title: DKOCr298_72hZEN_2, ERRBS

description: Library name: Sample 20


title: DKOCr298_72hZEN_3, ERRBS

description: Library name: Sample 21


title: DKOCr298_72hDMSO_3, ERRBS

description: Library name: Sample 18

value: DMSO 72hr


title: DKOCr298_72hDMSO_2, ERRBS

description: Library name: Sample 17


title: H660_72hZEN_2

description: Library name: Sample 11


title: DKOCr298_72hDMSO_1, ERRBS

description: Library name: Sample 16


title: DKOCr298_72hdAZA_3, ERRBS

description: Library name: Sample 15

value: 100nM dAZA 72hr


title: H660_72hZEN_1

description: Library name: Sample 10


title: H660_72hDMSO_2

description: Library name: Sample 8


title: H660_72hDMSO_3

description: Library name: Sample 9


title: H660_72hDMSO_1

description: Library name: Sample 7


title: DKOCr298_72hdAZA_1, ERRBS

description: Library name: Sample 13


title: H660_72hdAZA_3

description: Library name: Sample 6


title: DKOCr298_72hCombo_3, ERRBS

description: Library name: Sample 12


title: H660_72hdAZA_2

description: Library name: Sample 5


title: DKOCr298_72hdAZA_2, ERRBS

description: Library name: Sample 14


title: Rcl331_72hdAZA_2

description: Library name: Sample 37

value: LTL331R Cell Line


title: DKOCr298_72hCombo_2, ERRBS

description: Library name: Sample 11


title: DKOCr298_72hCombo_1, ERRBS

description: Library name: Sample 10


title: H660_72hCombo_3

description: Library name: Sample 3


title: Rcl331_72hdAZA_1

description: Library name: Sample 36


title: Rcl331_72hCombo_3

description: Library name: Sample 35


title: DKOCr298_24hDMSO_3, ERRBS

description: Library name: Sample 9


title: DKOCr298_H3K27ac_1, ChIP-seq

description: Library name: Sample 1


title: H660_72hCombo_2

description: Library name: Sample 2


title: H660_72hdAZA_1

description: Library name: Sample 4


title: H660_72hCombo_1

description: Library name: Sample 1


title: DKOCr298_24hDMSO_2, ERRBS

description: Library name: Sample 8


title: DKOCr105_24hDMSO_3, ERRBS

description: Library name: Sample 6


title: baseline HNC004 biol rep1

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

description: Library name: Sample_RA34m2_CTRL

data_processing:
sequencing reads were simultaneously mapped to both the human (GRCh38) and mouse (Mus musculus GRCm39) genomes using STAR v2.7.10.
A count matrix of human-specific reads was generated using xenofilter
Assembly: GRCh38 / GRCm39
Supplementary files format and content: CSV with the matrix of reads counts

source_name: human oral cavity

extract_protocol:
RNA extraction with phenol/chloroform and purification on RNeasy mini columns (Qiagen), according to manufacturer's instructions.
Libraries are prepared with NEBNext UltraII Directional RNA Library Prep Kit for Illumina protocol according supplier recommendations. Briefly the key stages of this protocol are successively, the purification of PolyA containing mRNA molecules using poly-T oligo attached magnetic beads from 1μg total RNA (with the Magnetic mRNA Isolation Kit from NEB), a fragmentation using divalent cations under elevated temperature to obtain approximately 300bp pieces, double strand cDNA synthesis and finally Illumina adapters ligation and cDNA library amplification by PCR for sequencing. Sequencing is then carried out on Paired End 100b reads of Illumina NovaSeq.Image analysis and base calling is performed using Illumina Real Time Analysis (3.4.4) with default parameters.

treatment_protocol: We induced acquired resistance to anti-EGFR therapy in a cetuximab-sensitive PDX model of HNSCC (HNC004) by treating it chronically with anti-EGFR monoclonal antibody (cetuximab, 30 mg/kg/week) until resistance ensues.

value: human oral cavity

value: vehicle (NaCl 0.9%)


title: DKOCr298_24hDMSO_1, ERRBS

description: Library name: Sample 7


title: DKOCr105_24hDMSO_2, ERRBS

description: Library name: Sample 5


title: baseline HNC004 biol rep2

description: Library name: Sample_RA105_CTRL3


title: DKOCr105_24hDMSO_1, ERRBS

description: Library name: Sample 4


title: resistant to cetuximab HNC004 biol rep5

description: Library name: Sample_RA105_CTX11

value: cetuximab


title: DKO_24hDMSO_3, ERRBS

description: Library name: Sample 3

value: DKO


title: DKO_24hDMSO_2, ERRBS

description: Library name: Sample 2


title: DKO_24hDMSO_1, ERRBS

description: Library name: Sample 1


title: resistant to cetuximab HNC004 biol rep2

description: Library name: Sample_ON22_2cx1


title: TKO_24hDMSO_3, ATAC-seq

description: Library name: Sample 15

data_processing:
We use FastQC (FastQC) (v0.11.8) to assess the overall quality of each sequenced sample. We use TrimGalore (TrimGalore) (v0.4.5) and cutadapt (Martin) (v1.15) with the following parameters: –nextera -e 0.1 –stringency 6 –length 20 –nextseq 20. We align trimmed reads to mm10 with Bowtie2 (Langmead and Salzberg, 2012) (v2.3.4.1) with the following parameters: -X 2000 –no-mixed –no-discordant, and defaults multi-seed length of 20bp with 0 mismatches. Duplicate reads are marked with Picard (Picard) (v2.20.2). Alignments to autosomes are kept (i.e. sex chromosomes and mitochondrial alignments are removed), duplicates marked by Picard are removed, and alignments below a MAPQ threshold are removed. These filtering steps are performed with samtools (Li et al., 2009) (v1.2) and the parameters: -q 10 -F 1024.
Reads completely overlapping blacklisted regions (ENCODE Blacklist Regions) are removed with bedtools (Quinlan and Hall, 2010) (v2.28.0). Sample-wise peaks are called with macs2 (Zhang et al., 2008) (v2.1.2) with flags: -f BAM –nomodel –shift -100 –extsize 200 –gsize mm. Peaks over all samples are merged with bedops (Neph et al., 2012) (v2.4.36) for the purpose of principal component analysis and unsupervised clustering to assess the similarity of samples. Finally, MultiQC (Ewels et al., 2016) (v1.7) generates a report combining FastQC, trimming, alignment, and duplicate calling over all the samples. For ATAC specific QC metrics we use ataqv (Ataqv) (v1.0.0).
Assembly: mm10
Supplementary files format and content: bigwig for each sample

extract_protocol:
ATAC-seq libraries were prepared from whole cell suspensions from three biological replicates per cell line by the University of Michigan Epigenomics Core as described previously (doi: 10.1038/nmeth.4396)
We used the Omni-ATAC-Seq protocol (Corces et al., 2017). The final libraries were cleaned using Qiagen MinElute columns and AMPure XP beads before quantitation with the Qubit HS dsDNA kit, and quality assessment on a TapeStation HS D1000 kit. The libraries were pooled and quantitated by qPCR using KAPA’s Illumina Library quantitation kit before PE-150 sequencing on a shared flowcell on the NovaSeq6000 at the Advanced Genomics Core.

treatment_protocol: All cell lines were treated with DMSO for 24hrs


title: resistant to cetuximab HNC004 biol rep1

description: Library name: Sample_ON07_CTX4


title: resistant to cetuximab HNC004 biol rep4

description: Library name: Sample_ON26_cx3


title: resistant to cetuximab HNC004 biol rep3

description: Library name: Sample_ON22-3_cx4


title: Vehicle-treated residual UCLHN04 PDX_biol rep3

description: Library name: E022-TRRL-NT

data_processing:
RNA-seq data preprocessing relies on STAR for alignment and XenofilteR for filtering. Raw reads were aligned to both the host (e.g., mouse) and graft (e.g., human) genomes using STAR 2.7.11. Subsequently, XenofilteR (version 1.6) was used to classify and remove contaminating host reads. The featurecount function fo the Rsubreads package was used to produce the count table.
Assembly: Homo_sapiens.GRCh38  / Mus_musculus_GRCm39
Supplementary files format and content: excel with the matrix of reads counts

source_name: human oral cavity (PDX)

extract_protocol:
RNA extraction with phenol/chloroform and purification on RNeasy mini columns (Qiagen), according to manufacturer's instructions.
Libraries are prepared with NEBNext UltraII Directional RNA Library Prep Kit for Illumina protocol according supplier recommendations.

treatment_protocol: Female nude mice bearing cetuximab-sensitive PDX model of HNSCC (UCLHN04 or HNC004) were weekly treated with anti-EGFR monoclonal antibody (cetuximab, 30 mg/kg/week) until maximal response was observed (i.e. tumor size stabilization for at least 4 weeks).

value: human oral cavity (PDX)

value: no treatment


title: TKO_24hDMSO_1, ATAC-seq

description: Library name: Sample 13

value: Prostate Cancer Cell Line


title: Control_GATA6_replicate2

city: New York

first: Norihiro

last: Goto

state: NY

address: 413 East 69th Street

department: Department of Medicine

institute: Weill Cornell Medicine

description:
Library name: Control_GATA6_replicate2
Control_GATA6_replicate2

data_processing:
Paired-end sequencinq reads were mapped to the UCSC mm9 mouse genome build (genome.ucsc.edu) using Bowtie.
To drop duplicate alignments, BAM files were processed with Picard MarkDuplicates.
BAM files were sorted and merged using Samtools.
Peaks were called using MACS2.
Read counts per peak per sample were quantified using BEDTools.
Assembly: mm9
Supplementary files format and content: GATA6_Consensus_Peaks.count.tsv.gz  is a tab delimited text of counts for GATA6 consensus peaks.
Library strategy: CUT&Run

source_name: Colon cancer organoids

extract_protocol:
Organoids were dissociated using TrypLE Express for 10 min at 37 °C, filtered through a 40 μm cell strainer, and 500,000 cells were collected, centrifuged, and washed twice with PBS. H3K27ac CUT&RUN libraries were prepared using the CUTANA CUT&RUN kit (EpiCypher, 14-1048) according to the manufacturer’s instructions.
CUT&RUN libraries were PCR amplified using NEBNext High-Fidelity 2X PCR Master Mix for the appropriate numbers of cycles determined by qRT-PCR as previously described. 2 x 75 paired-end sequencing was performed on an Illumina NextSeq 500.

value: Colon cancer organoids

tag: recipient mice

value: AKP


title: TKO_24hDMSO_2, ATAC-seq

description: Library name: Sample 14

tag: tissue

value: Prostate

value: TKO


title: SKO_24hDMSO_3, ATAC-seq

description: Library name: Sample 12

tag: cell line

value: SKO

value: Pten-/-

value: DMSO 24hr


title: Control_GATA6_replicate3

description:
Library name: Control_GATA6_replicate3
Control_GATA6_replicate3

tag: cell type


title: Cetuximab-treated residual UCLHN04 PDX_biol rep3

description: Library name: E022-CTX-G

value: Cetuximab


title: SKO_24hDMSO_2, ATAC-seq

description: Library name: Sample 11

tag: genotype


title: GATA6KO_GATA6_replicate3

description:
Library name: GATA6KO_GATA6_replicate3
GATA6KO_GATA6_replicate3


title: Cetuximab-treated residual UCLHN04 PDX_biol rep2

description: Library name: E018-DG

tag: treatment


title: GATA6KO_GATA6_replicate1

description:
Library name: GATA6KO_GATA6_replicate1
GATA6KO_GATA6_replicate1


title: GATA6KO_GATA6_replicate2

description:
Library name: GATA6KO_GATA6_replicate2
GATA6KO_GATA6_replicate2


title: GATA6KO_replicate3

description: Library name: GATA6KO_replicate3

data_processing:
Paired-end RNA-seq data were used to quantify transcripts from the mm10 mouse assembly with the Ensembl version 101 annotation using Salmon version 1.3.0 and gene level summaries were prepared using tximport version 1.16.1
Assembly: mm10
Supplementary files format and content: ngoto_RNAseq_GATA6KO_Ct.txt.gz is a tab delimited text of count data

source_name: AKP organoid

extract_protocol:
Ambion PureLink RNA Mini Kit
NEBNext Ultra II Directional RNA preparation with poly(A) selection

value: AKP organoid


title: SKO_24hDMSO_1, ATAC-seq

description: Library name: Sample 10


title: Cetuximab-treated residual UCLHN04 PDX_biol rep1

description: Library name: E014-TMT-CTX


title: DKOCr298_24hDMSO_3, ATAC-seq

description: Library name: Sample 9


title: GATA6KO_replicate2

description: Library name: GATA6KO_replicate2


title: Vehicle-treated residual UCLHN04 PDX_biol rep1

description: Library name: E014-TL-TMT-D

value: Vehicle


title: Control_replicate3

description: Library name: Control_replicate3

value: Control


title: Control_replicate2

description: Library name: Control_replicate2


title: GATA6KO_replicate1

description: Library name: GATA6KO_replicate1


title: DKOCr298_24hDMSO_2, ATAC-seq

description: Library name: Sample 8


title: Control_replicate1

description: Library name: Control_replicate1


title: Cetuximab-treated residual HNC004 PDX_biol rep3

description: Library name: E012-CTX


title: Vehicle-treated residual HNC004 PDX_biol rep3

description: Library name: E012-CTRL


title: DKOCr298_24hDMSO_1, ATAC-seq

description: Library name: Sample 7


title: Met3_AKP_replicate2

description: Library name: RNA_1237_Met

data_processing:
Paired-end RNA-seq data were used to quantify transcripts from the mm10 mouse assembly with the Ensembl version 101 annotation using Salmon version 1.3.0 and gene level summaries were prepared using tximport version 1.16.1
Assembly: mm10
Supplementary files format and content: ngoto_RNAseq_met_Ct.txt.gz is a tab delimited text of count data


title: Met3_AKP_replicate1

description: Library name: RNA_1235_Met


title: DKOCr105_24hDMSO_3, ATAC-seq

description: Library name: Sample 6


title: Vehicle-treated residual HNC004 PDX_biol rep2

description: Library name: E009-CTRL-C3


title: DKOCr105_24hDMSO_2, ATAC-seq

description: Library name: Sample 5


title: Primary3_AKP_replicate3

description: Library name: RNA_1248_Primary


title: Primary3_AKP_replicate1

description: Library name: RNA_1242_Primary


title: Primary3_AKP_replicate2

description: Library name: RNA_1244_Primary


title: Cetuximab-treated residual HNC004 PDX_biol rep2

description: Library name: E009-CETUX-C2


title: DKOCr105_24hDMSO_1, ATAC-seq

description: Library name: Sample 4


title: Met2_AKP_replicate3

description: Library name: RNA_1188_Met


title: Vehicle-treated residual HNC004 PDX_biol rep1

description: Library name: E005_CTRL


title: DKO_24hDMSO_3, ATAC-seq

description: Library name: Sample 3


title: Met2_AKP_replicate2

description: Library name: RNA_1186_Met


title: Met3_AKP_replicate3

description: Library name: RNA_1238_Met


title: Met2_AKP_replicate1

description: Library name: RNA_1184_Met


title: Cetuximab-treated residual HNC004 PDX_biol rep1

description: Library name: E005_CETUX


title: Primary2_AKP_replicate3

description: Library name: RNA_1177_Primary


title: DKO_24hDMSO_2, ATAC-seq

description: Library name: Sample 2


title: Primary2_AKP_replicate2

description: Library name: RNA_1172_Primary


title: Primary2_AKP_replicate1

description: Library name: RNA_1171_Primary


title: Bone marrow MNCs, Human, Patient 5, IMA+BI3406

city: Salamanca

first: Rósula

last: Garcia Navas

state: Salamanca

address: Campus Miguel de Unamuno, P. Universidad de Coimbra s/n. Lab.1

institute: Centro de Investigación del Cáncer

description:
Library name: S12077Nr20
BM-MNCs from newly diagnosed CML patient treated ex vivo with 500 nM imatinib + 1 µM BI-3406 for 48h.

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (version 2.20)
Adapter trimming was performed using Skewer (v0.2.2). No quality trimming was applied.
Trimmed reads were aligned to mm10 (mouse) or hg19-cegat (human) using STAR aligner (v2.7.3). In human samples, pseudoautosomal regions on chromosome Y were masked
Differential expression analysis was performed using DESeq2 (v1.24.0) in R (v4.0.4), applying a negative binomial model to raw gene counts
Assembly: Mouse: GRCm38 (mm10) Human: GRCh37 (hg19); pseudoautosomal regions on chrY were masked
Supplementary files format and content: Tab-delimited text files including raw read counts (raw_counts.tsv), normalized counts (normalized_counts.tsv), and differential expression analysis results (*_DEA.tsv, *_significant_DEA.tsv). Rows represent Ensembl gene IDs; columns correspond to sample names (library name).

source_name: Bone marrow

growth_protocol: Mouse samples: Bone marrow was isolated directly after treatment in vivo without prior culture. Human samples: BM-MNCs were cultured for 48h ex vivo in IMDM supplemented with recombinant human Flt3L, SCF, IL-3, IL-6, and TPO prior to RNA extraction.

extract_protocol:
Total RNA was extracted from bone marrow cells using the QIAGEN RNeasy Plus Mini Kit, following the manufacturer’s instructions. RNA integrity was confirmed using Qubit 4
Libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (Roche), following the manufacturer’s protocol. Paired-end sequencing was performed on an Illumina NovaSeq 6000 platform

treatment_protocol: Mouse: Mice were treated orally with imatinib (IMA, 60 mg/kg, once daily) and/or BI-3406 (50 mg/kg, twice daily) for 5 weeks. BI-3406 was administered every 6 hours, following a 5 days on / 2 days off schedule. Control,non-transgenic mice and SOS1 KO received vehicle under the same regimen. Human: BM-MNCs from newly diagnosed CML patients were treated ex vivo for 48 hours in IMDM medium supplemented with recombinant human Flt3L, SCF, IL-3, IL-6, and TPO. Treatments included 500 nM imatinib, 1 µM BI-3406, or their combination. Untreated controls were cultured in parallel in the same medium without inhibitors.

value: Bone marrow


title: DKO_24hDMSO_1, ATAC-seq

description: Library name: Sample 1


title: Bone marrow MNCs, Human, Patient 5, BI3406

description:
Library name: S12077Nr19
BM-MNCs from newly diagnosed CML patient treated ex vivo with 1 µM BI-3406 for 48h.


title: Met1_AKP_replicate3

description: Library name: RNA_1027_Met


title: Met1_AKP_replicate2

description: Library name: RNA_1026_Met


title: Met1_AKP_replicate1

description: Library name: RNA_1010_Met


title: TKO_72hZEN_3

description: Library name: Sample 51

data_processing:
Sequencing was performed on a NovaSeq-6000 (Illumina, San Diego, CA) with 300 total cycles of paired-end sequencing (150 cycles per read) according to the manufacturer's protocol. Bcl2fastq2 Conversion Software (Illumina, San Diego, CA) was used to generate demultiplexed Fastq files.
Reads were trimmed using cutadapt v2.3 (Martin, 2011). FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010). Fastq Screen v0.13.0 was used to screen for various types of contamination (Wingett and Andrews, 2018).FastQC was used in an additional post-alignment step to ensure that only high-quality data were used for expression quantitation and differential expression. Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016).
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq.
Assembly: mm10
Supplementary files format and content: The columns of the counts.txt files are: (1) ensemble gene name; (2) gene symbol; (3) sample read count

treatment_protocol: TKO and DKOcr298 cells were treated with BET inhibitors (500nM ZEN or 1µM JQ1) for 24hrs with corresponding vehicle (DMSO) controls; TKO and DKOcr298 were treated with BET inhibitor (500nM ZEN), DNA methyltransferase inhibitor (100nMdAZA), or the combination (500nM ZEN + 100nM dAZA) daily for 72 hrs with corresponding vehicle (DMSO) controls.

value: 500nM ZEN 72hr


title: Bone marrow MNCs, Human, Patient 5, IMA

description:
Library name: S12077Nr18
BM-MNCs from newly diagnosed CML patient treated ex vivo with 500 nM imatinib for 48h.

value: IMA


title: Met3_AKP_replicate3

description: Library name: ATAC_1238_Met

data_processing:
Paired-end ATAC-seq reads were mapped to the UCSC mm9 mouse genome build (genome.ucsc.edu) using Bowtie.
To drop duplicate alignments, BAM files were processed with Picard MarkDuplicates.
BAM files were merged using Samtools.
Peaks were called on the merged BAM using MACS2.
Read counts per peak per sample were quantified using BEDTools.
Assembly: mm9
Supplementary files format and content: ngoto_ATACseq_met_peak_tiled_reads.txt.gz is a tab delimited text of counts for filtered peaks

extract_protocol:
Organoids were dissociated by TrypLE Express for 10 min at 37ºC, passed through a 40 μm filter, and a total of 50,000 cells were centrifuged and washed twice with PBS. Cells are resuspended in 50 μl of buffer with TDE1 enzyme and incubated at 37°C for 30 min with gentle agitation. DNA was isolated using the Qiagen MinElute PCR Purification Kit.
ATAC-seq libraries were PCR amplified using NEBNext High-Fidelity 2X PCR Master Mix for the appropriate numbers of cycles determined by qRT-PCR as previously described. 2 x 75 paired-end sequencing was performed on an Illumina NextSeq 500.


title: TKO_72hZEN_2

description: Library name: Sample 50


title: resistant to cetuximab HNC004 biol rep6

description: Library name: Sample_RA105_CTX3

value: human oral cavity

value: cetuximab


title: Met3_AKP_replicate1

description: Library name: ATAC_1235_Met


title: Bone marrow MNCs, Human, Patient 5, untreated

description:
Library name: S12077Nr17
BM-MNCs from newly diagnosed CML patient. Untreated control.

value: BM


title: Primary3_AKP_replicate3

description: Library name: ATAC_1248_Primary

value: Colon cancer organoids


title: TKO_72hDMSO_3

description: Library name: Sample 48

value: Prostate Cancer Cell Line

value: DMSO 72hr


title: Primary3_AKP_replicate2

description: Library name: ATAC_1244_Primary

value: AKP


title: Bone marrow MNCs, Human, Patient 4, IMA+BI3406

description:
Library name: S12077Nr16
BM-MNCs from newly diagnosed CML patient treated ex vivo with 500 nM imatinib + 1 µM BI-3406 for 48h.


title: DNA from Non neoplastic kidney control 10

type: genomic

city: Caserta

first: Abu

last: Saadat

state: Caserta

address: Via Vivaldi, 43

department: Department of Environmental, Biological and Pharmaceutical Sciences and Technologies

country: Italy

institute: Università degli Studi della Campania Luigi Vanvitelli

description: DNA from Non neoplastic kidney control

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized according to Illumina's standard protocol

scan_protocol: Arrays were imaged using iSCAN BeadArray reader

data_processing:
R library minfi and ChAMP
processed value definition: Normalized Beta value

label: Cy3 and Cy5

source_name: Kidney

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using standard phenol-chloroform-isoamyl alchohol protocol

value: Kidney

value: Female

tag: tissue type

value: Non neoplastic kidney control


title: DNA from Non neoplastic kidney control 7

description: DNA from Non neoplastic kidney control

value: Male


title: ILPr02,preoperative ILE,baseline

description: Library name: ILPr02

data_processing:
Relative abundance: Top 20 taxa of each sample at each taxonomic ranks (Phylum, Class, Order, Family, Genus, Species) were selected to plot the distribution histogram of relative abundance in Perl through SVG function. Alpha and Beta Diversity: For analyzing community diversity, richness, and evenness, alpha diversity was calculated using Shannon and Simpson indices in QIIME2. Beta diversity was performed with Principal Coordinates Analysis (PCoA) and Adonis analysis. Community difference analysis: T-test, and linear discriminant analysis effect size (LEfSe) were conducted to characterize community structure differentiation. Function Prediction: PICRUSt2 (V2.3.0) was applied to predict metagenomic functions based on marker genes. Canonical correspondence analysis (CCA) were used to explore interspecies symbiosis and environmental impacts on community structure, reflecting correlations between environmental factors and genus/species abundance.
Continuous variables were expressed as mean with standard deviation and compared using the Student’s T test. Categorical data, on the other hand, were represented as frequencies and percentages, and comparisons were made using the Pearson χ2 test or the Fisher exact test, depending on suitability. A two-sided p value less than 0.05 was considered statistically significant. All data analyses were conducted using the R software package (version 4.0).
Assembly: 16S rRNA gene reference database(Silva 138.1)
Supplementary files format and content: Processed data are ASV feature count matrix (tab-delimited TSV format). Rows represent individual ASVs, columns correspond to sample IDs, and values denote raw sequencing read counts of each ASV across all fecal samples. Taxonomic classification results assigned against SILVA 138.1 database are also provided in the feature table.
Library strategy: 16S rRNA-seq

source_name: feces

extract_protocol:
16S rRNA genes of distinct regions (16SV3-V4) were amplified used specific primer with the barcode. All PCR reactions were carried out with 15 µL of Phusion® High-Fidelity PCR Master Mix (New England Biolabs); 0.2µM of forward and reverse primers, and about 10 ng template DNA. Thermal cycling consisted of initial denaturation at 98℃ for 1 min, followed by 30 cycles of denaturation at 98℃ for 10s, annealing at 50℃ for 30 s, and elongation at 72℃ for 30s and 72℃ for 5 min. The PCR products were purified using magnetic bead purification. Samples were mixed in equidensity ratios based on the concentration of PCR products.
After thorough mixing, the PCR products were detected and target bands were recovered. Sequencing libraries were generated and indexes were added. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

value: feces


title: DNA from Non neoplastic kidney control 6

description: DNA from Non neoplastic kidney control


title: [RNA-Seq] Donor_1_OSS

city: Newcastle upon Tyne

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

institute: Newcastle University

description:
Library name: SW1_S37
Donor_1_OSS

data_processing:
Sequenced paired-end 76bp on Illumina HiSeq4000
The paired-end RNA-seq reads were quality assessed using FastQC (v 0.11.3), FastQ Screen (v 0.9.2).
The reads were  quality trimmed with Trimmomatic (v 0.36) and mapped against the reference genome (hg38) using STAR (version 2.7.2b).
Counts per gene were calculated by STAR (version 2.7.2b). using annotation from GENCODE (version32)
Assembly: hg38
Supplementary files format and content: mRNA_raw_counts.tsv: tab-delimited text containing unnormalized gene-level counts

source_name: primary Human Coronary Artery Endothelial Cell

growth_protocol: HCAECs in MV2

extract_protocol:
RNA purification performed using Norgen total RNA plus kit
Illumina TruSeq Stranded mRNA

treatment_protocol: 72 hours culture under flow using parallel plate flow apparatus

value: OSS


title: Bone marrow MNCs, Human, Patient 4, BI3406

description:
Library name: S12077Nr15
BM-MNCs from newly diagnosed CML patient treated ex vivo with 1 µM BI-3406 for 48h.


title: TKO_72hDMSO_2

description: Library name: Sample 47

source_name: Prostate

value: Prostate

value: TKO


title: Met2_AKP_replicate2

description: Library name: ATAC_1186_Met


title: Bone marrow MNCs, Human, Patient 4, IMA

description:
Library name: S12077Nr14
BM-MNCs from newly diagnosed CML patient treated ex vivo with 500 nM imatinib for 48h.

value: Bone marrow


title: Met2_AKP_replicate1

description: Library name: ATAC_1184_Met


title: Bone marrow MNCs, Human, Patient 4, untreated

description:
Library name: S12077Nr13
BM-MNCs from newly diagnosed CML patient. Untreated control.


title: Control_GATA6_replicate1

description:
Library name: Control_GATA6_replicate1
Control_GATA6_replicate1


title: Primary2_AKP_replicate3

description: Library name: ATAC_1177_Primary


title: Primary2_AKP_replicate2

description: Library name: ATAC_1172_Primary


title: TKO_72hdAZA_3

description: Library name: Sample 45

value: 100nM dAZA 72hr


title: Primary2_AKP_replicate1

description: Library name: ATAC_1171_Primary


title: Bone marrow MNCs, Human, Patient 3, IMA+BI3406

description:
Library name: S12077Nr12
BM-MNCs from newly diagnosed CML patient treated ex vivo with 500 nM imatinib + 1 µM BI-3406 for 48h.


title: Vehicle-treated residual UCLHN04 PDX_biol rep2

description: Library name: E018-TMT-CTL

value: human oral cavity (PDX)

value: no treatment


title: Met1_AKP_replicate2

description: Library name: ATAC_1026_Met


title: TKO_72hdAZA_2

description: Library name: Sample 44


title: Bone marrow MNCs, Human, Patient 3, BI3406

description:
Library name: S12077Nr11
BM-MNCs from newly diagnosed CML patient treated ex vivo with 1 µM BI-3406 for 48h.


title: Met1_AKP_replicate1

description: Library name: ATAC_1010_Met


title: in vivo microglia pIC 12h-4

city: Bonn

first: Paolo

last: Salomoni

address: Venusberg-Campus 1, Building 99

institute: DZNE

data_processing:
Raw FASTQ files were trimmed by Trimgalore (ver. 0.6.10).
Read alignment to genome (mm10) and read count of transposable elements were done by SQuIRE (ver. 0.9.9.92).
Assembly: mm10
Supplementary files format and content: TE read counts

source_name: brain

extract_protocol:
RNA was extracted using RNeasy mini plus kit (Qiagen). 5 ng of total RNA was used for construction of sequencing libraries.
RNA library for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq kit v2-Pico Input Mammalian following manufacturer's protocols.

value: brain

value: microglia

value: wild type

value: poly I:C

tag: timepoint


title: in vivo microglia pIC 12h-3


title: Bone marrow MNCs, Human, Patient 3, IMA

description:
Library name: S12077Nr10
BM-MNCs from newly diagnosed CML patient treated ex vivo with 500 nM imatinib for 48h.

value: IMA


title: Bone marrow MNCs, Human, Patient 3, untreated

description:
Library name: S12077Nr9
BM-MNCs from newly diagnosed CML patient. Untreated control.

value: BM


title: in vivo microglia pIC 12h-2


title: TKO_72hCombo_2

description: Library name: Sample 41

value: Prostate Cancer Cell Line

value: 500nM ZEN + 100nM dAZA 72hr


title: in vivo microglia pIC 12h-1


title: in vivo microglia PBS 12h-4

value: PBS


title: in vivo microglia PBS 12h-3


title: TKO_72hCombo_1

description: Library name: Sample 40


title: in vivo microglia PBS 12h-2


title: Bone marrow MNCs, Human, Patient 2, BI3406

description:
Library name: S12077Nr7
BM-MNCs from newly diagnosed CML patient treated ex vivo with 1 µM BI-3406 for 48h.


title: in vivo microglia PBS 12h-1


title: TKO_24hZEN_3

description: Library name: Sample 39

value: 500nM ZEN 24hr


title: Bone marrow MNCs, Human, Patient 2, IMA+BI3406

description:
Library name: S12077Nr8
BM-MNCs from newly diagnosed CML patient treated ex vivo with 500 nM imatinib + 1 µM BI-3406 for 48h.


title: Bone marrow MNCs, Human, Patient 2, IMA

description:
Library name: S12077Nr6
BM-MNCs from newly diagnosed CML patient treated ex vivo with 500 nM imatinib for 48h.


title: in vitro Daxx KO NPCs+Cre+Daxx restoration-1 [S514Nr4]

description:
20200214_countTable_daxxKo.txt
S514Nr4

data_processing:
Raw FASTQ files were trimmed by Trimgalore and aligned to genome mm10 by STAR. SAM files were filter by mapq>=10 and transformed to BAM by samtools. Gene count table was created by featureCounts.
Assembly: mm10
Supplementary files format and content: read counts from featureCounts

source_name: E13.5 embryo cortex

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 5 ng of total RNA was used for contruction of sequencing libraries.
RNA library for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq kit v2-Pico Input Mammalian following manufacturer's protocols.

value: E13.5 embryo cortex

value: neuron progenetor cells

value: Daxx flox/flox

value: Transfection with Cre and pMSCV-Daxx


title: Donor_2_ESS

description:
Library name: SW6_S6
Donor_2_ESS

data_processing:
Sequenced paired-end 76bp on Illumina HiSeq4000
The R1 RNA-seq reads were quality assessed using FastQC (v 0.11.3), FastQ Screen (v 0.9.2).
The R1 reads were quality trimmed and filtered for length with Cutadapt v1.18 (min length 18nt, max length 26nt), and mapped against the reference genome (hg38) using Bowtie v1.1.1
Counts per gene were calculated using featureCounts with annotation from miRBasev22
Assembly: hg38
Supplementary files format and content: miR_raw_counts.tsv: tab-delimited text containing unnormalized counts for each miRNA

extract_protocol:
RNA purification performed using Norgen total RNA plus kit
NEBNext® Multiplex Small RNA Library Prep Set for Illumina®

value: primary Human Coronary Artery Endothelial Cell

value: ESS


title: in vitro Daxx KO NPCs+Cre+Daxx restoration-2 [S514Nr9]

description:
20200214_countTable_daxxKo.txt
S514Nr9


title: TKO_24hZEN_2

description: Library name: Sample 38

value: Prostate

value: TKO


title: TKO_24hZEN_1

description: Library name: Sample 37


title: in vitro Daxx WT NPCs+Cre-2 [S514Nr8]

description:
20200214_countTable_daxxKo.txt
S514Nr8

value: Daxx wt/wt

value: Transfection with pCAG-Cre construct


title: Bone marrow MNCs, Human, Patient 1, IMA+BI3406

description:
Library name: S12077Nr4
BM-MNCs from newly diagnosed CML patient treated ex vivo with 500 nM imatinib + 1 µM BI-3406 for 48h.

value: Bone marrow


title: in vitro Daxx WT NPCs+Cre-1 [S514Nr1]

description:
20200214_countTable_daxxKo.txt
S514Nr1


title: in vitro Daxx KO microglia LPS-48h-2 [15403]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15403_merged

value: brain

value: microglia

value: Cx3cr1CreERT,Daxx flox/flox

value: Tamoxifen, LPS


title: Bone marrow MNCs, Human, Patient 1, IMA

description:
Library name: S12077Nr2
BM-MNCs from newly diagnosed CML patient treated ex vivo with 500 nM imatinib for 48h.

value: IMA


title: in vitro Daxx KO microglia LPS-48h-1 [15402]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15402_merged


title: TKO_24hJQ1_1

description: Library name: Sample 34

value: Prostate Cancer Cell Line

value: 1µM JQ1 24hr


title: in vitro Daxx WT microglia LPS-48h-2 [15400]

description:
20210824_count_byFeatureCount_s2_daxxKoLpsTimeCourse_rnaseq.txt
15400_merged

value: Cx3cr1CreERT,Daxx wt/wt


title: Bone marrow MNCs, Human, Patient 1, untreated

description:
Library name: S12077Nr1
BM-MNCs from newly diagnosed CML patient. Untreated control.

value: BM


title: TKO_24hDMSO_2

description: Library name: Sample 32

value: DMSO 24hr