title: Old_1, Cell 89 of 192 [AS-441390-LR-48372]


title: REM15, dilution 1:8, set 4, replicate 4

status: Public on Apr 27 2022

type: SRA

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

library_source: transcriptomic

data_processing:
Using Qiagen's GeneGlobe Data Analysis Center according to manufacturer´s instructions: trimming.
Using Qiagen's GeneGlobe Data Analysis Center according to manufacturer´s instructions: alignment to GRCh38 reference genome using STAR.
Using Qiagen's GeneGlobe Data Analysis Center according to manufacturer´s instructions: counting of unique molecular identifiers (UMIs) for 386 genes including 6 genomic DNA controls and 10 reference genes.
Raw UMI counts were combined with gene and sample annotations in R (version 3.6.1) (R Core Team, 2017) using SummarizedExperiment (version 1.16.1).
For uses other than differential gene expression (DEG) analysis, read counts were normalized using R function DESeq2::varianceStabilizingTransformation (vst) in “blind” mode (version 1.26.1).
To identify technical bias, quality control and exploration were performed (multidimensional scaling, principal component analysis, and unsupervised hierarchical clustering) in R/Bioconductor.
Statistically differentially expressed genes (DEGs) were identified using R package DESeq2 (version 1.26.1), using Wald as test type, FDR for p-value adjustment and the R function DESeq2::lfcShrink (type=”normal”) for shrinking fold changes of low expressed RNAs.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each gene for a given Sample
Supplementary_files_format_and_content: Matrix of vst-normalized counts for every gene (gene_id, gene_name and control_type given) and every sample

molecule: total RNA

organism: Homo sapiens

source_name: normal human bronchial epithelial cells

growth_protocol: Human airway constructs were differentiated from normal human bronchial epithelial (NHBE) cells (cat. CC-2540, Lonza) in four different sets. The NHBE cells were seeded > 3500 cells/cm2 into cell culture flasks containing LifeFactors® BronchiaLife™ tracheal epithelial cell culture medium (cat. LS-1047) and necessary supplements, and incubated +37 ºC, 5% CO2 for four days. Cells were detached with 0.05% trypsin/EDTA solution and neutralized using trypsin neutralizing solution. Cells were seeded ~140 000 cells/cm2 to Transparent ThinCert™ cell culture inserts pre-treated with 30 µg/mL rat tail collagen type I, and cultured for three days. Culture medium was changed daily. Cell cultures were transferred to air-liquid interface (ALI) in HBTEC Air-Liquid Interface Differentiation Medium including antimicrobial supplement Gentamicin 30 mg/mL and Amphotericin B 15 µg/mL, and cultured for 22 days before the exposure. Culture medium was changed every other day.

extract_protocol:
RNA was extracted using Qiagen RNeasy Plus Mini Kit (Qiagen) including DNase treatment. RNA samples were sent to Sequencing Unit of Finnish Institute for Molecular Medicine (FIMM, Helsinki, Finland) for further RNA quality control and sequencing. RNA quality assessment, library preparation for sequencing, sequencing of RNA amplicons, and data analysis were done according to manufacturer´s instructions (Nordberg et al. 2020).
QIAseq Targeted RNA panel Human Molecular Toxicology Transcriptome (Qiagen) of 386 genes was used for first strand synthesis, molecular barcoding, gene-specific amplification, sample indexing, and library preparation for targeted RNA sequencing according to manufacturer´s instructions.

treatment_protocol: PM sampled with the NIOSH BC251 bio aerosol cyclone sampler were combined with 2 mL of synthetic lung lining fluid (LLF) (Nordberg et al. 2020), mixed, sonicated, and diluted in LLF to three dose levels: 1:16, 1:8, and 1:4. The airway constructs were exposed to the three doses in air liquid interface (+37 °C, 5% CO2, exposure time 24 h). The exposure experiments were conducted in four sets during four months. Paired index and reference houses were always included in the same exposure set.

tag: cell line

value: NHBE

tag: set

tag: subset

tag: replicate

value: FALSE

value: likely

value: likely or highly likely


title: Old_1, Cell 86 of 192 [AS-441384-LR-48372]

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

country: Germany

institute: University of Ulm

data_processing:
Single-end raw reads were aligned to the reference genome using HISAT2
Gene counts were obtained using HTSeq using Mus_musculus.GRCm38.99.gtf
Data matrix count table from individual count files was generated using R and Bioconductor
Assembly: Mus_musculus build GRCm38.99
Supplementary files format and content: tab-delimited text of raw gene expression count matrix

organism: Mus musculus

source_name: Lgr5 high-ISCs

growth_protocol: Lgr5 high-ISCs were sorted in 384 well low bind plates (Eppendorf) containing 1.2 µl lysis buffer (0.1% triton (Sigma-Aldrich), 1U/μl RNase Inhibitor (Takara Bio), 2.5 µM polyT primer (Thermo Fisher Scientific), 2.5 mM dNTPs (Thermo Fisher Scientific)). After sorting the plates spun down and immediately frozen at -80 °C for further processes.

extract_protocol: SMARTER mRNA-Seq: RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell type

value: Lgr5 high-ISCs

tag: sample group

tag: genotype


title: Old_1, Cell 83 of 192 [AS-441378-LR-48372]


title: Old_1, Cell 87 of 192 [AS-441386-LR-48372]


title: ST3-1

city: Madrid

first: Pilar

last: López Nieva

address: Nicolas Cabrera 1

country: Spain

institute: Centro de Biología Molecular Severo Ochoa

description:
SCP21ID00103
Strand specific total RNA-seq (RF)

data_processing:
Aligment using STAR 2.7.1a with separate files for non-chimeric aligment bam and chimeric bam. It is done to both the R1 and R2 file and for each one of them separately (mate1 R1, mate2 R2).
Detection and quantification of the circulars RNA using Detect Module from Circtools, standard parameters
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Excel file with the information about the raw data of the samples
Supplementary_files_format_and_content: a table containing read counts for circRNAs detected. First three columns are chr, circRNA start, circRNA end. From fourth column on are the circRNA read counts, one sample per column, shown in the order given in your samplesheet.
Supplementary_files_format_and_content: circular RNA annotations in BED format
Supplementary_files_format_and_content: host gene expression count table, same setup with CircRNACount file
Supplementary_files_format_and_content: circSkip junctions. The first three columns are the same as in LinearCount/CircRNACount, the following columns represent the circSkip junctions found for each sample

source_name: Thymocytes

growth_protocol: Human postnatal thymocytes were isolated from thymuses removed during cardiac surgery of 7 pediatric patients aged between 1 month and 4 years old

extract_protocol:
Total RNA was obtained using TriPure Reagent (Roche Applied Science, Indianapolis, IN, USA), following manufacturer’s instructions, and treated to removal Ribosomal RNA
High-quality RNA samples (RNA integrity Numbers (RIN) in the range of 7.2–9.8) were used for high-depth Illumina total RNA sequencing (RNA-seq) after ribosomal depletion, with 3 replicates for each thymocyte population (NIMGenetics and Helix BioS, Scientific Park of Madrid, Spain). Image analysis, per-cycle basecalling and quality score assignment were made using Illumina Real Time Analysis software (Illumina, San Diego, CA). BCL files were converted to FASTQ format using Illumina’s Off-Line Basecaller package. RNA-seq libraries resulting from these analyses were sequenced in paired-end format in two different rounds (Illumina HiSeq2000, Illumina Inc., San Diego, CA, USA), leading to 50 bp and 76 bp reads (the latter were trimmed to 50 bp). RNA-seq reads were analysed with the nextpresso pipeline. The quality of sequenced reads was checked with FastQC. Quantification and annotation of circular RNAs and their linear counterparts, was performed using circTools, since it is one of the few bioinformatics tools that allows the alignment of the sequences mates separately, allowing the detection of exonic, exonic-intronic, and intergenic circRNAs and helping to perform internal controls on the sample itself for better identification of chimeric junctions.

treatment_protocol: Human thymic populations were sorted and three differential thymocyte populations were included in the study, as follows: double negative early immature CD34+ (ST1, Stage 1); double positive (CD1A+CD4+CD8+) (ST2, Stage 2); and single positive thymocytes (CD1A-CD4+ and CD1A-CD8+) (ST3, Stage 3). Thymocytes were sorted using magnetic activated cell sorting with autoMACS Pro (Miltenyi Biotec). To isolate early immature thymocytes (ST1), thymocyte suspensions were firstly enriched in CD34+ thymocytes by using the sheep red blood cell technique5. Then, early immature thymocytes were isolated as CD34+ cells with appropriate Ig-coated magnetic MicroBeads. Double Positive thymocytes were directly isolated as CD1A+ cells with CD1A+ MicroBeads. Single positive thymocytes were isolated by removing CD1A- cells then selected with either CD4+ MicroBeads or CD8+ MicroBeads. The purity of the three isolated thymocyte populations was determined by flow cytometry using a FACSCalibur cytometer (Becton Dickinson, San Diego, CA) and the following antibodies: CD34-PE, CD8-APC and CD4-PE (all from MACS Miltenyi Biotec), and CD3-FITC (Beckman Coulter). Purity varied from 95 to 80 per cent. Institutional review board approval was obtained for these studies (CEI 98-1825). The participants provided written informed consent in accordance with the Declaration of Helsinki.

value: Thymocytes

tag: differentiation stage

value: Late Cortical (SP-mix)

tag: immmunophenotype

value: CD4+ or CD8+


title: Old_1, Cell 93 of 192 [AS-441398-LR-48372]


title: Old_1, Cell 94 of 192 [AS-441400-LR-48372]


title: REM15, dilution 1:8, set 4, replicate 1


title: Old_1, Cell 85 of 192 [AS-441382-LR-48372]


title: Old_1, Cell 82 of 192 [AS-441376-LR-48372]


title: Old_1, Cell 84 of 192 [AS-441380-LR-48372]


title: REM15, dilution 1:8, set 4, replicate 3


title: REM15, dilution 1:8, set 4, replicate 2


title: Old_1, Cell 80 of 192 [AS-441372-LR-48372]


title: Old_1, Cell 78 of 192 [AS-441368-LR-48372]


title: Old_1, Cell 79 of 192 [AS-441370-LR-48372]


title: REM15, dilution 1:4, set 4, replicate 2


title: REM15, dilution 1:4, set 4, replicate 3


title: REM15, dilution 1:4, set 4, replicate 4


title: Old_1, Cell 88 of 192 [AS-441388-LR-48372]


title: REM15, dilution 1:4, set 4, replicate 1


title: REM30, dilution 1:16, set 4, replicate 4

value: TRUE

value: possible


title: REM30, dilution 1:16, set 4, replicate 2


title: REM15, dilution 1:16, set 4, replicate 1


title: REM30, dilution 1:16, set 4, replicate 3


title: Old_1, Cell 77 of 192 [AS-441366-LR-48372]


title: REM15, dilution 1:16, set 4, replicate 2


title: Old_1, Cell 76 of 192 [AS-441364-LR-48372]


title: Old_1, Cell 75 of 192 [AS-441362-LR-48372]


title: REM30, dilution 1:16, set 4, replicate 1


title: Old_1, Cell 81 of 192 [AS-441374-LR-48372]


title: Old_1, Cell 74 of 192 [AS-441360-LR-48372]


title: REM30, dilution 1:8, set 4, replicate 4


title: Old_1, Cell 73 of 192 [AS-441358-LR-48372]


title: Old_1, Cell 71 of 192 [AS-441354-LR-48372]


title: REM30, dilution 1:8, set 4, replicate 2


title: REM30, dilution 1:8, set 4, replicate 1


title: Old_1, Cell 72 of 192 [AS-441356-LR-48372]


title: Old_1, Cell 70 of 192 [AS-441352-LR-48372]


title: REM30, dilution 1:4, set 4, replicate 3


title: REM30, dilution 1:4, set 4, replicate 4


title: REM30, dilution 1:4, set 4, replicate 2


title: REM29, dilution 1:16, set 4, replicate 3


title: REM30, dilution 1:4, set 4, replicate 1


title: REM29, dilution 1:16, set 4, replicate 4


title: Old_1, Cell 64 of 192 [AS-441340-LR-48372]


title: Old_1, Cell 65 of 192 [AS-441342-LR-48372]


title: REM30, dilution 1:8, set 4, replicate 3


title: Old_1, Cell 69 of 192 [AS-441350-LR-48372]


title: Old_1, Cell 68 of 192 [AS-441348-LR-48372]


title: Old_1, Cell 66 of 192 [AS-441344-LR-48372]


title: REM29, dilution 1:16, set 4, replicate 1


title: Old_1, Cell 137 of 192 [AS-441486-LR-48372]


title: Old_1, Cell 67 of 192 [AS-441346-LR-48372]


title: Old_1, Cell 63 of 192 [AS-441338-LR-48372]


title: REM29, dilution 1:8, set 4, replicate 2


title: Old_1, Cell 60 of 192 [AS-441332-LR-48372]


title: Old_1, Cell 62 of 192 [AS-441336-LR-48372]


title: REM29, dilution 1:8, set 4, replicate 4


title: REM29, dilution 1:8, set 4, replicate 3


title: REM29, dilution 1:16, set 4, replicate 2


title: REM29, dilution 1:8, set 4, replicate 1


title: Old_1, Cell 59 of 192 [AS-441330-LR-48372]


title: REM29, dilution 1:4, set 4, replicate 1


title: Old_1, Cell 58 of 192 [AS-441328-LR-48372]


title: REM29, dilution 1:4, set 4, replicate 2


title: REM28, dilution 1:16, set 4, replicate 4

value: unlikely


title: Old_1, Cell 57 of 192 [AS-441326-LR-48372]


title: REM29, dilution 1:4, set 4, replicate 4


title: Old_1, Cell 55 of 192 [AS-441322-LR-48372]


title: REM29, dilution 1:4, set 4, replicate 3


title: Old_1, Cell 56 of 192 [AS-441324-LR-48372]


title: Old_1, Cell 53 of 192 [AS-441318-LR-48372]


title: Old_1, Cell 54 of 192 [AS-441320-LR-48372]


title: REM28, dilution 1:16, set 4, replicate 3


title: Old_1, Cell 51 of 192 [AS-441314-LR-48372]


title: Old_1, Cell 52 of 192 [AS-441316-LR-48372]


title: Old_1, Cell 50 of 192 [AS-441312-LR-48372]


title: REM28, dilution 1:8, set 4, replicate 4


title: Old_1, Cell 49 of 192 [AS-441310-LR-48372]


title: REM28, dilution 1:16, set 4, replicate 2


title: REM28, dilution 1:8, set 4, replicate 2


title: REM28, dilution 1:8, set 4, replicate 3


title: Old_1, Cell 47 of 192 [AS-441306-LR-48372]


title: REM28, dilution 1:8, set 4, replicate 1


title: Old_1, Cell 48 of 192 [AS-441308-LR-48372]


title: Old_1, Cell 61 of 192 [AS-441334-LR-48372]


title: REM28, dilution 1:4, set 4, replicate 4


title: Old_1, Cell 46 of 192 [AS-441304-LR-48372]


title: Old_1, Cell 45 of 192 [AS-441302-LR-48372]


title: REM28, dilution 1:4, set 4, replicate 3


title: REM28, dilution 1:4, set 4, replicate 2


title: REM28, dilution 1:16, set 4, replicate 1


title: Old_1, Cell 44 of 192 [AS-441300-LR-48372]


title: REM27, dilution 1:16, set 4, replicate 3


title: REM28, dilution 1:4, set 4, replicate 1


title: REM27, dilution 1:16, set 4, replicate 2


title: Old_1, Cell 42 of 192 [AS-441296-LR-48372]


title: REM27, dilution 1:16, set 4, replicate 1


title: REM27, dilution 1:8, set 4, replicate 3


title: Old_1, Cell 39 of 192 [AS-441290-LR-48372]


title: Old_1, Cell 43 of 192 [AS-441298-LR-48372]


title: REM27, dilution 1:8, set 4, replicate 2


title: Old_1, Cell 40 of 192 [AS-441292-LR-48372]


title: Old_1, Cell 37 of 192 [AS-441286-LR-48372]


title: Old_1, Cell 38 of 192 [AS-441288-LR-48372]


title: Old_1, Cell 34 of 192 [AS-441280-LR-48372]


title: REM27, dilution 1:4, set 4, replicate 3


title: Old_1, Cell 35 of 192 [AS-441282-LR-48372]


title: Old_1, Cell 41 of 192 [AS-441294-LR-48372]


title: Old_1, Cell 33 of 192 [AS-441278-LR-48372]


title: Old_1, Cell 32 of 192 [AS-441276-LR-48372]


title: REM27, dilution 1:4, set 4, replicate 2


title: REM27, dilution 1:4, set 4, replicate 1


title: Old_1, Cell 36 of 192 [AS-441284-LR-48372]


title: REM24, dilution 1:16, set 3, replicate 4


title: REM27, dilution 1:8, set 4, replicate 1


title: REM24, dilution 1:16, set 3, replicate 3


title: REM24, dilution 1:16, set 3, replicate 2


title: Old_1, Cell 30 of 192 [AS-441272-LR-48372]


title: Old_1, Cell 28 of 192 [AS-441268-LR-48372]


title: Old_1, Cell 29 of 192 [AS-441270-LR-48372]


title: REM24, dilution 1:8, set 3, replicate 3


title: REM24, dilution 1:8, set 3, replicate 4


title: Old_1, Cell 26 of 192 [AS-441264-LR-48372]


title: REM27, dilution 1:4, set 4, replicate 4


title: REM24, dilution 1:8, set 3, replicate 1


title: REM24, dilution 1:4, set 3, replicate 4


title: Old_1, Cell 24 of 192 [AS-441260-LR-48372]


title: Old_1, Cell 25 of 192 [AS-441262-LR-48372]


title: Old_1, Cell 31 of 192 [AS-441274-LR-48372]


title: Old_1, Cell 22 of 192 [AS-441256-LR-48372]


title: REM24, dilution 1:4, set 3, replicate 2


title: REM24, dilution 1:4, set 3, replicate 3


title: Old_1, Cell 20 of 192 [AS-441252-LR-48372]


title: REM24, dilution 1:4, set 3, replicate 1


title: Old_1, Cell 27 of 192 [AS-441266-LR-48372]


title: Old_1, Cell 18 of 192 [AS-441248-LR-48372]


title: Old_1, Cell 19 of 192 [AS-441250-LR-48372]


title: Old_1, Cell 16 of 192 [AS-441244-LR-48372]


title: REM05, dilution 1:16, set 2, replicate 4


title: REM05, dilution 1:16, set 2, replicate 3


title: Old_1, Cell 17 of 192 [AS-441246-LR-48372]


title: REM05, dilution 1:16, set 2, replicate 2


title: REM24, dilution 1:16, set 3, replicate 1


title: REM05, dilution 1:8, set 2, replicate 4


title: REM05, dilution 1:16, set 2, replicate 1


title: REM24, dilution 1:8, set 3, replicate 2


title: Old_1, Cell 11 of 192 [AS-441234-LR-48372]


title: REM05, dilution 1:8, set 2, replicate 1


title: Old_1, Cell 14 of 192 [AS-441240-LR-48372]


title: Old_1, Cell 23 of 192 [AS-441258-LR-48372]


title: Old_1, Cell 13 of 192 [AS-441238-LR-48372]


title: Old_1, Cell 12 of 192 [AS-441236-LR-48372]


title: REM05, dilution 1:4, set 2, replicate 4


title: Old_1, Cell 10 of 192 [AS-441232-LR-48372]


title: REM05, dilution 1:4, set 2, replicate 2


title: REM05, dilution 1:4, set 2, replicate 3


title: Old_1, Cell 8 of 192 [AS-441228-LR-48372]


title: REM05, dilution 1:4, set 2, replicate 1


title: Old_1, Cell 9 of 192 [AS-441230-LR-48372]


title: Old_1, Cell 7 of 192 [AS-441226-LR-48372]


title: REM27, dilution 1:8, set 4, replicate 4


title: REM05, dilution 1:8, set 2, replicate 3


title: Old_1, Cell 5 of 192 [AS-441222-LR-48372]


title: REM22, dilution 1:16, set 2, replicate 3


title: REM22, dilution 1:16, set 2, replicate 4


title: Old_1, Cell 21 of 192 [AS-441254-LR-48372]


title: Old_1, Cell 4 of 192 [AS-441220-LR-48372]


title: Old_1, Cell 3 of 192 [AS-441218-LR-48372]


title: REM22, dilution 1:8, set 2, replicate 4


title: REM22, dilution 1:8, set 2, replicate 3


title: REM22, dilution 1:16, set 2, replicate 1


title: Old_1, Cell 1 of 192 [AS-441214-LR-48372]


title: REM05, dilution 1:8, set 2, replicate 2


title: Old_1, Cell 2 of 192 [AS-441216-LR-48372]


title: REM22, dilution 1:8, set 2, replicate 1


title: Old_1, Cell 6 of 192 [AS-441224-LR-48372]


title: REM22, dilution 1:4, set 2, replicate 4


title: REM22, dilution 1:16, set 2, replicate 2


title: REM22, dilution 1:4, set 2, replicate 2


title: REM22, dilution 1:4, set 2, replicate 3


title: liver_RNAseq_4F_SC_Dox_minus

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

country: USA

institute: Salk Institute for Biological Studies

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
RNA-Seq: Alignment to the hg19 genome (from illumina iGenome) was performed using the STAR aligner version 2.5.3a using the --outFilterIntronMotifs RemoveNoncanonical parameter. Gene expression was quantified using the HOMER analysis suite version 4.9.1, makeTagDirectory, analyzeRepeats.pl across exons of RefSeq genes.
ATAC-Seq: Adapter sequences were trimmed using TrimGalore v0.4.5 then aligned using bwa mem v0.7.12. Bam files were sorted, fixmated, marked duplicates, indexed, filtered low quality reads by samtools v1.9. For each sample, peaks were called by macs2 v2.1.2 by using command "callpeak --slocal 1000 --qvalue 0.05 -g mm -f BAMPE". The the called narrow peaks from each sample were merged to get a union peak file. Homer v4.9.1 was used to quantify the read counts in each of the union peak by commands makeTagDirectory and analyzeRepeats.
Single-Cell RNA-Seq: Reads were processed using 10X Genomics Cell Ranger pipeline v3.1.0 aligned to Cell Ranger mm10 v1.2.0 reference with default settings
Genome_build: mm10 (illumina iGenome) for RNA-Seq and ATAC-Seq, Cell Ranger mm10 v1.2.0 for Single-Cell RNA-Seq.
Supplementary_files_format_and_content: liver4F_RNA_exons.raw.xlsx contains the raw read count quantified for each gene for the RNA-Seq data. liver4F_ATAC_peakunion.raw.txt contains the raw read count quantified for each peak for the ATAC-Seq data. liver4F_SC_minusDox_filtered_feature_bc_matrix.h5 and liver4F_SC_plusDox_filtered_feature_bc_matrix.h5 are the two compressed filtered cell X gene count table generated for Single-Cell RNA-Seq.

molecule: polyA RNA

source_name: Hep-4F mouse liver tissue

extract_protocol:
RNA-Seq: Isolated livers were homogenized with a polytrone in Trizol immediately after collecting tissues. The extracted RNA was purified with RNeasy Mini Kit (QIAGEN) from the homogenates with DNaseI tretment (RNase-Free DNase Set, QIAGEN) to get rid of genomic DNA.
ATAC-Seq: Frozen liver samples were processed for ATAC-seq using the Omni-ATAC seq protocol [PMID: 28846090]. Briefly, around 20 mg of frozen tissue was used to isolate nuclei via Dounce homogenization followed by density gradient centrifugation. After isolation of nuclei, transposition mixture was added for transposition reaction.
SIngle-cell RNA-Seq: Liver cells were isolated after collagenase perfusion as described before [PMID: 29553556] to get single cell suspension. Briefly, hepatocytes and other cells were isolated separately with different gravity of centrifuge and both fractions were mixed at the same number of cells. Then, the mixture was subjected to scRNA-Seq using Next GEM Single Cell 3’ kit v3.1 (10x Genomics).
RNA-Seq: RNA quality was assessed and all samples had a minimum RNA integrity number (RIN) of 8.6. RNA library preps were prepared using the Illumina TruSeq Stranded Total RNA Sample Prep kit with Ribo-zero Gold (cat. no. RS-122-2301). ATAC-Seq: All ATAC-seq analysis was performed on two biological replicates. Frozen liver samples were processed for ATAC-seq using the omni-ATAC seq protocol (Corces et al, 2017, Nature Methods). Libraries were constructed using published Nextera PCR primers (Buenrostro et al 2013, Nature methods) and checked for quantity on a TapeStation 2200 (Agilent). Single-Cell RNA-Seq: Liver cells were isolated after collagenase perfusion as described before. Briefly, hepatocytes and other cells were isolated separately with different gravity of centrifuge and both fractions were mixed at the same number of cells. Then, these fractions were subjected to scRNA-Seq using Next GEM Single Cell 3’ kit v3.1.
ATAC-Seq: Libraries were constructed using published Nextera PCR primers [PMID: 24097267] followed by checking the quality on a TapeStation2200 (Agilent).
Single-Cell RNA-Seq: Libraries were prepared using Next GEM Single Cell 3’ kit v3.1 (10x Genomics).
stranded paired-end mRNA-seq; paired-end ATAC-Seq; 10X Genomics Chromium v3 3' Single-Cell RNA-Seq

treatment_protocol: Hep4F mice were treated with Dox in drinking water (0.1 mg/ml) and liver samples were collected at the indicated time-points. For carbon tetrachloride (CCl4) treatment, the mice were intraperitoneally injected with CCl4 (Sigma) (5 ul/g mouse of 10% CCl4 in corn oil) once and the livers were collected 3 days after the injection. For Single-Cell-RNA-Seq, Hep4F mice were treated with or without Dox (0.1 mg/ml) in drinking water for 1 day and then Dox water was replaced by normal water. Liver samples were collected 1 day after Dox withdrawal (1d-on_1d-off) and subjected to liver cell isolation.

tag: treatment

tag: time

value: 1 day on 1 day off

tag: tissue

value: liver


title: liver_RNAseq_4F_SC_Dox_plus

description: liver4F_SC_plusDox_filtered_feature_bc_matrix.h5


title: REM22, dilution 1:4, set 2, replicate 1


title: REM20, dilution 1:16, set 2, replicate 4

value: highly likely


title: REM20, dilution 1:16, set 2, replicate 2


title: REM20, dilution 1:16, set 2, replicate 3


title: REM20, dilution 1:16, set 2, replicate 1


title: Old_1, Cell 15 of 192 [AS-441242-LR-48372]


title: REM22, dilution 1:8, set 2, replicate 2


title: REM20, dilution 1:8, set 2, replicate 4


title: REM20, dilution 1:8, set 2, replicate 3


title: REM20, dilution 1:8, set 2, replicate 2


title: REM20, dilution 1:4, set 2, replicate 4


title: REM20, dilution 1:8, set 2, replicate 1


title: REM20, dilution 1:4, set 2, replicate 3


title: REM20, dilution 1:4, set 2, replicate 2


title: REM20, dilution 1:4, set 2, replicate 1


title: REM21, dilution 1:16, set 2, replicate 4


title: REM21, dilution 1:16, set 2, replicate 2


title: REM21, dilution 1:16, set 2, replicate 1


title: REM21, dilution 1:16, set 2, replicate 3


title: REM21, dilution 1:8, set 2, replicate 4


title: REM21, dilution 1:8, set 2, replicate 3


title: REM21, dilution 1:8, set 2, replicate 2


title: REM21, dilution 1:4, set 2, replicate 3


title: REM21, dilution 1:4, set 2, replicate 4


title: REM21, dilution 1:4, set 2, replicate 2


title: REM21, dilution 1:8, set 2, replicate 1


title: REM21, dilution 1:4, set 2, replicate 1


title: REM19, dilution 1:16, set 2, replicate 4


title: REM19, dilution 1:16, set 2, replicate 3


title: REM19, dilution 1:16, set 2, replicate 2


title: 202915600079_R03C01

type: genomic

city: Mexico City

first: José Jaime

last: Martínez Magaña

state: Mexico City

address: Av. Insurgentes Sur 3877, La Fama, Tlalpan,

country: Mexico

institute: Instituto Nacional de Medicina Genómica

description:
202915600079_R03C01_Grn.idat
202915600079_R03C01_Red.idat
TCA
SAMPLE 59

hyb_protocol: The bisulfite-converted DNA was amplified, fragmented, and hybridized with the Infinium MethylationEPIC BeadChip, Illumina using the standard Illumina protocol.

scan_protocol: Standard Illumina iScan settings for Methylation EPIC

data_processing: Raw data was read by minfi package (version 3.14) from IDAT files and converted to rgset from this we calculate the methylated and unmethylated intensities for each sample and probe.

label: Cy3, Cy5

molecule: genomic DNA

source_name: peripheral blood leukocytes

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from peripheral blood leukocytes was entered using standard techniques.

value: peripheral blood leukocytes

tag: age

tag: gender

value: Female

tag: suicide

value: NO


title: 202915600079_R07C01

description:
202915600079_R07C01_Grn.idat
202915600079_R07C01_Red.idat
TCA
SAMPLE 63


title: 202915600079_R02C01

description:
202915600079_R02C01_Grn.idat
202915600079_R02C01_Red.idat
TCA
SAMPLE 58

value: Male


title: 202915600034_R07C01

description:
202915600034_R07C01_Grn.idat
202915600034_R07C01_Red.idat
TCA
SAMPLE 55

value: YES


title: 202915600034_R05C01

description:
202915600034_R05C01_Grn.idat
202915600034_R05C01_Red.idat
TCA
SAMPLE 53


title: 202915590134_R08C01

description:
202915590134_R08C01_Grn.idat
202915590134_R08C01_Red.idat
TCA
SAMPLE 48


title: 202915600034_R03C01

description:
202915600034_R03C01_Grn.idat
202915600034_R03C01_Red.idat
TCA
SAMPLE 51


title: 202915600034_R08C01

description:
202915600034_R08C01_Grn.idat
202915600034_R08C01_Red.idat
TCA
SAMPLE 56


title: REM19, dilution 1:16, set 2, replicate 1

value: NHBE

value: likely


title: 202915590134_R01C01

description:
202915590134_R01C01_Grn.idat
202915590134_R01C01_Red.idat
TCA
SAMPLE 41


title: 202915600034_R01C01

description:
202915600034_R01C01_Grn.idat
202915600034_R01C01_Red.idat
TCA
SAMPLE 49


title: 202915470113_R08C01

description:
202915470113_R08C01_Grn.idat
202915470113_R08C01_Red.idat
TCA
SAMPLE 40


title: REM19, dilution 1:8, set 2, replicate 3

value: likely or highly likely


title: 202915600034_R04C01

description:
202915600034_R04C01_Grn.idat
202915600034_R04C01_Red.idat
TCA
SAMPLE 52


title: REM19, dilution 1:8, set 2, replicate 2


title: REM19, dilution 1:8, set 2, replicate 4


title: 202915600079_R05C01

description:
202915600079_R05C01_Grn.idat
202915600079_R05C01_Red.idat
TCA
SAMPLE 61


title: 202915600079_R06C01

description:
202915600079_R06C01_Grn.idat
202915600079_R06C01_Red.idat
TCA
SAMPLE 62


title: 202915590134_R04C01

description:
202915590134_R04C01_Grn.idat
202915590134_R04C01_Red.idat
TCA
SAMPLE 44


title: 202915590134_R03C01

description:
202915590134_R03C01_Grn.idat
202915590134_R03C01_Red.idat
TCA
SAMPLE 43


title: 202915590134_R06C01

description:
202915590134_R06C01_Grn.idat
202915590134_R06C01_Red.idat
TCA
SAMPLE 46


title: 202915600079_R01C01

description:
202915600079_R01C01_Grn.idat
202915600079_R01C01_Red.idat
TCA
SAMPLE 57


title: 202915600034_R06C01

description:
202915600034_R06C01_Grn.idat
202915600034_R06C01_Red.idat
TCA
SAMPLE 54


title: 202915590134_R05C01

description:
202915590134_R05C01_Grn.idat
202915590134_R05C01_Red.idat
TCA
SAMPLE 45


title: REM19, dilution 1:8, set 2, replicate 1


title: REM19, dilution 1:4, set 2, replicate 3


title: 202915590134_R07C01

description:
202915590134_R07C01_Grn.idat
202915590134_R07C01_Red.idat
TCA
SAMPLE 47


title: 202915600079_R04C01

description:
202915600079_R04C01_Grn.idat
202915600079_R04C01_Red.idat
TCA
SAMPLE 60


title: 202915600034_R02C01

description:
202915600034_R02C01_Grn.idat
202915600034_R02C01_Red.idat
TCA
SAMPLE 50


title: 202915590134_R02C01

description:
202915590134_R02C01_Grn.idat
202915590134_R02C01_Red.idat
TCA
SAMPLE 42


title: REM18, dilution 1:16, set 2, replicate 2


title: REM19, dilution 1:4, set 2, replicate 2


title: REM18, dilution 1:16, set 2, replicate 3


title: REM19, dilution 1:4, set 2, replicate 1


title: REM18, dilution 1:16, set 2, replicate 4


title: 202915470113_R06C01

description:
202915470113_R06C01_Grn.idat
202915470113_R06C01_Red.idat
TCA
SAMPLE 38


title: REM18, dilution 1:16, set 2, replicate 1


title: 202915470113_R05C01

description:
202915470113_R05C01_Grn.idat
202915470113_R05C01_Red.idat
TCA
SAMPLE 37


title: 202915600079_R08C01

description:
202915600079_R08C01_Grn.idat
202915600079_R08C01_Red.idat
TCA
SAMPLE 64

value: No


title: REM18, dilution 1:8, set 2, replicate 3


title: REM18, dilution 1:8, set 2, replicate 4


title: REM18, dilution 1:8, set 2, replicate 2


title: REM18, dilution 1:8, set 2, replicate 1


title: REM18, dilution 1:4, set 2, replicate 4


title: REM19, dilution 1:4, set 2, replicate 4


title: REM18, dilution 1:4, set 2, replicate 3


title: REM18, dilution 1:4, set 2, replicate 2


title: REM18, dilution 1:4, set 2, replicate 1


title: REM17, dilution 1:16, set 2, replicate 3


title: 202915470113_R04C01

description:
202915470113_R04C01_Grn.idat
202915470113_R04C01_Red.idat
TCA
SAMPLE 36


title: REM17, dilution 1:16, set 2, replicate 2


title: 202915470113_R07C01

description:
202915470113_R07C01_Grn.idat
202915470113_R07C01_Red.idat
TCA
SAMPLE 39


title: REM17, dilution 1:16, set 2, replicate 4


title: 202915470113_R01C01

description:
202915470113_R01C01_Grn.idat
202915470113_R01C01_Red.idat
TCA
SAMPLE 33


title: 202915460062_R08C01

description:
202915460062_R08C01_Grn.idat
202915460062_R08C01_Red.idat
TCA
SAMPLE 32


title: 202915470113_R02C01

description:
202915470113_R02C01_Grn.idat
202915470113_R02C01_Red.idat
TCA
SAMPLE 34


title: REM17, dilution 1:8, set 2, replicate 4


title: REM17, dilution 1:16, set 2, replicate 1


title: REM17, dilution 1:8, set 2, replicate 3


title: REM17, dilution 1:8, set 2, replicate 2


title: REM17, dilution 1:8, set 2, replicate 1


title: 202915470113_R03C01

description:
202915470113_R03C01_Grn.idat
202915470113_R03C01_Red.idat
TCA
SAMPLE 35


title: 202915460062_R07C01

description:
202915460062_R07C01_Grn.idat
202915460062_R07C01_Red.idat
TCA
SAMPLE 31


title: 202915460062_R05C01

description:
202915460062_R05C01_Grn.idat
202915460062_R05C01_Red.idat
TCA
SAMPLE 29


title: REM17, dilution 1:4, set 2, replicate 4


title: REM17, dilution 1:4, set 2, replicate 3


title: 202915460057_R06C01

description:
202915460057_R06C01_Grn.idat
202915460057_R06C01_Red.idat
TCA
SAMPLE 22


title: REM17, dilution 1:4, set 2, replicate 2


title: REM17, dilution 1:4, set 2, replicate 1


title: 202915460062_R03C01

description:
202915460062_R03C01_Grn.idat
202915460062_R03C01_Red.idat
TCA
SAMPLE 27


title: 202915460062_R01C01

description:
202915460062_R01C01_Grn.idat
202915460062_R01C01_Red.idat
TCA
SAMPLE 25


title: 202915460062_R04C01

description:
202915460062_R04C01_Grn.idat
202915460062_R04C01_Red.idat
TCA
SAMPLE 28


title: 202915460057_R08C01

description:
202915460057_R08C01_Grn.idat
202915460057_R08C01_Red.idat
TCA
SAMPLE 24


title: 202915460057_R07C01

description:
202915460057_R07C01_Grn.idat
202915460057_R07C01_Red.idat
TCA
SAMPLE 23


title: REM07, dilution 1:16, set 1, replicate 3

value: FALSE


title: REM07, dilution 1:16, set 1, replicate 2


title: 202915420037_R07C01

description:
202915420037_R07C01_Grn.idat
202915420037_R07C01_Red.idat
TCA
SAMPLE 15


title: 202915460057_R04C01

description:
202915460057_R04C01_Grn.idat
202915460057_R04C01_Red.idat
TCA
SAMPLE 20


title: 202915460062_R02C01

description:
202915460062_R02C01_Grn.idat
202915460062_R02C01_Red.idat
TCA
SAMPLE 26


title: 202915420037_R04C01

description:
202915420037_R04C01_Grn.idat
202915420037_R04C01_Red.idat
TCA
SAMPLE 12


title: REM07, dilution 1:8, set 1, replicate 4


title: 202915460057_R01C01

description:
202915460057_R01C01_Grn.idat
202915460057_R01C01_Red.idat
TCA
SAMPLE 17


title: 202915460057_R05C01

description:
202915460057_R05C01_Grn.idat
202915460057_R05C01_Red.idat
TCA
SAMPLE 21


title: 202915460057_R03C01

description:
202915460057_R03C01_Grn.idat
202915460057_R03C01_Red.idat
TCA
SAMPLE 19


title: REM07, dilution 1:8, set 1, replicate 2


title: REM07, dilution 1:8, set 1, replicate 3


title: REM07, dilution 1:8, set 1, replicate 1


title: REM07, dilution 1:4, set 1, replicate 3


title: 202915420037_R02C01

description:
202915420037_R02C01_Grn.idat
202915420037_R02C01_Red.idat
TCA
SAMPLE 10


title: REM07, dilution 1:4, set 1, replicate 2


title: 202915420037_R06C01

description:
202915420037_R06C01_Grn.idat
202915420037_R06C01_Red.idat
TCA
SAMPLE 14


title: REM07, dilution 1:4, set 1, replicate 1


title: 202915420037_R03C01

description:
202915420037_R03C01_Grn.idat
202915420037_R03C01_Red.idat
TCA
SAMPLE 11


title: 202915420037_R05C01

description:
202915420037_R05C01_Grn.idat
202915420037_R05C01_Red.idat
TCA
SAMPLE 13


title: genomic DNA from neocortex of CTR-8

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000)  using standard recommended Illumina scanner setting

data_processing:
Data were processed using R studio (R v4.0.2)
Normalized  Average Beta (Noob + Quantile Normalization; average det p < 0.01)

label: Cy5 and Cy3

source_name: Neocortex CTR-8

extract_protocol: genomic DNA was extracted and purified from 25 mg - 3 mm brain tissue fragments obtained from resective surgery using the DNeasy® Blood & Tissue Kit (Qiagen).

value: Neocortex

tag: disease state

value: Non-epileptic control

tag: subject id


title: 202915420004_R08C01

description:
202915420004_R08C01_Grn.idat
202915420004_R08C01_Red.idat
TCA
SAMPLE 8


title: REM12, dilution 1:16, set 1, replicate 4

tag: cell line

value: TRUE


title: genomic DNA from neocortex of CTR-7

source_name: Neocortex CTR-7


title: genomic DNA from neocortex of CTR-6

source_name: Neocortex CTR-6


title: REM12, dilution 1:16, set 1, replicate 3

tag: set

value: unlikely


title: REM12, dilution 1:16, set 1, replicate 2

tag: subset


title: 202915420004_R07C01

description:
202915420004_R07C01_Grn.idat
202915420004_R07C01_Red.idat
TCA
SAMPLE 7


title: REM12, dilution 1:16, set 1, replicate 1

tag: replicate


title: REM12, dilution 1:8, set 1, replicate 4


title: genomic DNA from neocortex of CTR-2

source_name: Neocortex CTR-2


title: 202915420004_R05C01

description:
202915420004_R05C01_Grn.idat
202915420004_R05C01_Red.idat
TCA
SAMPLE 5

tag: cell type


title: REM12, dilution 1:8, set 1, replicate 3


title: 202915420004_R06C01

description:
202915420004_R06C01_Grn.idat
202915420004_R06C01_Red.idat
TCA
SAMPLE 6


title: 202915460062_R06C01

description:
202915460062_R06C01_Grn.idat
202915460062_R06C01_Red.idat
TCA
SAMPLE 30


title: REM12, dilution 1:8, set 1, replicate 2


title: genomic DNA from neocortex of CTR-1

source_name: Neocortex CTR-1


title: REM07, dilution 1:4, set 1, replicate 4


title: 202915420004_R03C01

description:
202915420004_R03C01_Grn.idat
202915420004_R03C01_Red.idat
TCA
SAMPLE 3


title: genomic DNA from neocortex of CTR-5

source_name: Neocortex CTR-5


title: 202915420004_R04C01

description:
202915420004_R04C01_Grn.idat
202915420004_R04C01_Red.idat
TCA
SAMPLE 4


title: genomic DNA from hippocampus of CTR-8

source_name: Hippocampus CTR-8

value: Hippocampus


title: REM12, dilution 1:8, set 1, replicate 1


title: REM12, dilution 1:4, set 1, replicate 3


title: MCF7-RescTrans_Rep1

city: Oslo

first: Roza Berhanu

last: Lemma

address: Gaustadalléen 21

department: Center for Molecular Medicine Norway

country: Norway

institute: University of Oslo

description: Transient rescue of FOXA1 KD

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850K Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing: Data was normalized with the minfi (version 1.36.0) R package using within array Noob function followed by quantile normalization following the recommendation by shinyÉpico.

source_name: MCF-7, siFOXA1, 72 hrs, transient rescue 24 hr

growth_protocol: MCF-7 cells (ATCC® HTB-22™ Homo sapiens, epithelial, mammary gland, breast; derived from metastatic site: pleural effusion, adenocarcinoma) were maintained in RPMI-1640-GlutaMAX supplement medium supplemented with 10% FCS (fetal calf serum) and 1% PS (penicillin/streptomycin), and were grown at 37 oC and 5% CO2.

extract_protocol: Genomic DNA from MCF-7 cells transfected with either siCtrl or siFOXA1 and MCF-7 cells subjected to siFOXA1 mediated endogenous KD and rescue with exogenous FOXA1-V5 in three biological replicates was isolated using NucleoSpin® Tissue genomic DNA isolation kit (Machery-Nagel). From each sample, 45 µl genomic DNA amounting to 500 ng concentration was delivered to Genomics core facility at Oslo University hospital, where EPIC array profiling was performed.

treatment_protocol: Control samples were treated with control siRNA, siCtrl (cat.no 1027281, Qiagen). Endogenous FOXA1 protein was targeted with siFOXA1 siRNA (sense 5′-GAGAGAAAAAAUCAACAGC-3′ and antisense 5′-GCUGUUGAUUUUUUCUCUC-3′). Rescue samples were treated with transient expression FOXA1-V5. The siRNA sequences in 10 µM concentrations were delivered to 1 million cells using the lullaby siRNA transfection reagent (OZ biosciences) and kept for 72 hrs. Transient rescue of endogenous FOXA1 KD was made by delivering 2.5 µg of pEF1neo-FOXA1-V5 plasmid to the cells with the lullaby transfection reagents for 24 hours.

value: Transient rescue of FOXA1 KD


title: genomic DNA from neocortex of CTR-4

source_name: Neocortex CTR-4


title: MCF7-siFOXA1_Rep3

description: endogenous FOXA1 KD

source_name: MCF-7, siFOXA1, 72 hrs

value: endogenous FOXA1 KD


title: REM12, dilution 1:4, set 1, replicate 1


title: 202915420004_R01C01

description:
202915420004_R01C01_Grn.idat
202915420004_R01C01_Red.idat
TCA
SAMPLE 1

value: peripheral blood leukocytes


title: REM12, dilution 1:4, set 1, replicate 2


title: genomic DNA from hippocampus of CTR-4

source_name: Hippocampus CTR-4


title: genomic DNA from hippocampus of CTR-2

source_name: Hippocampus CTR-2


title: MCF7-RescTrans_Rep2

description: Transient rescue of FOXA1 KD


title: REM07, dilution 1:16, set 1, replicate 1

source_name: normal human bronchial epithelial cells


title: genomic DNA from hippocampus of CTR-3

source_name: Hippocampus CTR-3


title: MCF7-RescTrans_Rep3

description: Transient rescue of FOXA1 KD


title: genomic DNA from hippocampus of CTR-7

source_name: Hippocampus CTR-7

value: Female


title: genomic DNA from neocortex of ME-12

source_name: Neocortex ME-12

value: MTLE-HS


title: 202915420004_R02C01

description:
202915420004_R02C01_Grn.idat
202915420004_R02C01_Red.idat
TCA
SAMPLE 2

source_name: peripheral blood leukocytes


title: REM10, dilution 1:16, set 1, replicate 2


title: REM10, dilution 1:16, set 1, replicate 3


title: MCF7-siFOXA1_Rep1

description: endogenous FOXA1 KD


title: REM10, dilution 1:16, set 1, replicate 1


title: genomic DNA from neocortex of ME-8

source_name: Neocortex ME-8


title: MCF7-siCtrl_Rep3

description: control

source_name: MCF-7, siCtrl, 72 hrs

value: control


title: genomic DNA from neocortex of ME-7

source_name: Neocortex ME-7

value: Male


title: REM10, dilution 1:8, set 1, replicate 4

value: NHBE


title: genomic DNA from neocortex of ME-11

source_name: Neocortex ME-11


title: genomic DNA from neocortex of ME-5

source_name: Neocortex ME-5


title: genomic DNA from neocortex of ME-6

source_name: Neocortex ME-6


title: MCF7-siCtrl_Rep1

description: control


title: genomic DNA from neocortex of ME-9

source_name: Neocortex ME-9


title: REM10, dilution 1:8, set 1, replicate 3

value: likely


title: genomic DNA from neocortex of ME-2

source_name: Neocortex ME-2


title: genomic DNA from neocortex of ME-4

source_name: Neocortex ME-4


title: REM10, dilution 1:8, set 1, replicate 1

value: likely or highly likely


title: REM10, dilution 1:4, set 1, replicate 4


title: genomic DNA from neocortex of ME-3

source_name: Neocortex ME-3


title: genomic DNA from neocortex of ME-1

source_name: Neocortex ME-1


title: REM10, dilution 1:16, set 1, replicate 4


title: REM10, dilution 1:4, set 1, replicate 1


title: REM12, dilution 1:4, set 1, replicate 4


title: REM10, dilution 1:4, set 1, replicate 3


title: genomic DNA from hippocampus of ME-11

source_name: Hippocampus ME-11


title: REM10, dilution 1:4, set 1, replicate 2

source_name: normal human bronchial epithelial cells


title: REM14, dilution 1:16, set 1, replicate 4


title: REM14, dilution 1:16, set 1, replicate 3


title: genomic DNA from hippocampus of ME-9

source_name: Hippocampus ME-9


title: genomic DNA from hippocampus of ME-8

source_name: Hippocampus ME-8


title: REM14, dilution 1:16, set 1, replicate 2


title: genomic DNA from hippocampus of ME-10

source_name: Hippocampus ME-10


title: genomic DNA from hippocampus of ME-6

source_name: Hippocampus ME-6


title: REM14, dilution 1:8, set 1, replicate 4


title: REM14, dilution 1:16, set 1, replicate 1


title: REM14, dilution 1:8, set 1, replicate 3


title: genomic DNA from hippocampus of CTR-6

source_name: Hippocampus CTR-6


title: genomic DNA from hippocampus of ME-3

source_name: Hippocampus ME-3


title: REM14, dilution 1:8, set 1, replicate 2


title: genomic DNA from hippocampus of ME-1

source_name: Hippocampus ME-1


title: REM14, dilution 1:8, set 1, replicate 1


title: genomic DNA from hippocampus of ME-5

source_name: Hippocampus ME-5


title: REM14, dilution 1:4, set 1, replicate 4


title: rec8_F204S_3Flag_150min_PMSF_HiC

city: Eugene

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

description: Hi-C

library_source: genomic

data_processing:
The paired reads were separately aligned to the fission yeast genome (version ASM294v2.19) using Bowtie2 (version 2.2.9) with the iterative alignment strategy. The aligned reads were assigned the MboI fragments. Redundant paired reads derived from PCR biases, aligned to repetitive sequences, or with low mapping quality (MapQ < 30) were removed. Paired reads potentially derived from self-ligation and undigested products were also discarded.
The fission yeast genome was divided into non-overlapped 20-kb, 5-kb, or 2-kb bins. Raw contact matrices were constructed by counting paired reads assigned to two bins, and Hi-C biases in contact matrices were corrected using the ICE method (Imakaev, 2012). The ICE normalization was repeated 30 times.
ICE normalized contact matrices in .hic format were calculated using the 'pre' function of Juicer_tools (version 1.22.01)
Genome_build: Schizosaccharomyces pombe (ASM294v2.19)
Supplementary_files_format_and_content: ICE normalized Hi-C matrices (20kb, 5kb, 2kb) are provided as .hic format

organism: Schizosaccharomyces pombe

growth_protocol: The cells were grown in YE liquid medium at a density of 5 ~10×10^6 cells/ml at 25°C

extract_protocol:
Asynchronous or meiotic cell culture of 4x10^8 cells was fixed with 3% paraformaldehyde at 26°C for 10 minutes. The fixed cells were disrupted by glass beads (BioSpec Products, Mini-Beadbeater-16) in lysis buffer [50 mM HEPES/KOH pH7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1x Complete (Roche, 11836170001), 1 mM PMSF]. The lysed cells were collected by centrifugation and permeabilized by resuspension with 1.11× NEBuffer 2 (NEB, B7002) containing 0.1% SDS at 62°C for 7 minutes. After SDS was quenched by adding 1/9 volume of 10% Triton X-100, the permeabilized cells were treated with 25 units of MboI (NEB, R0147) at 37°C overnight. The enzyme was inactivated by incubating at 62°C for 20 minutes. After centrifugation, the pellet containing restricted DNA fragments was used in the following procedure. A half volume of fill-in mix [1× NEBuffer 2, 150 µM biotin-14-dATP (Jena Bioscience, NU-835-BIO14), 150 µM dCTP, 150 µM dGTP, 150 µM dTTP, 0.4 units/µl Klenow fragment (NEB, M0210)] was added to the pellet and incubated at 37°C for 45 minutes. Subsequently, 3 volumes of ligation mix [1.33× T4 DNA ligase buffer (NEB, B0202), 1.11% Triton X-100, 133 µg/ml BSA (NEB, B9001), 5.56 units/µl T4 DNA ligase (NEB, M0202)] was added and incubated at room temperature (~25℃) for 4 hours. After the ligation, the pellet was collected by centrifugation, resuspended in Proteinase K solution [10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5% SDS, 0.5 mg/ml proteinase K (Invitrogen, 25530049)], and incubated at 65°C overnight. DNA was purified by phenol-chloroform treatment followed by ethanol precipitation, and then fragmented by sonication with Bioruptor (Diagenode, UCD-200). After the biotin-labeled DNA was pulled down with Dynabeads Streptavidin T1 (Invitrogen, 65601), the beads were washed twice with TNB (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20) at 55°C for 2 minutes.
To ligate the Illumina sequencing adaptors to the biotinylated DNA fragments, the beads were successively treated with end repair mix [1× T4 DNA ligase buffer, 1 mM dATP, 0.5 mM each dNTP, 0.5 units/µl T4 polynucleotide kinase (NEB, M0201), 0.12 units/µl T4 DNA polymerase (NEB, M0203), 0.05 units/µl Klenow fragment] at 25°C for 30 minutes, dA-tailing mix [1× NEBuffer 2, 0.5 mM dATP, 0.25 units/µl Klenow exo- (NEB, M0212)] at 37°C for 30 minutes, and Illumina adaptor ligation mix [0.075x End repair reaction buffer (NEB, E6050), 0.32× Ligation master mix (NEB, E7595), 0.011× Ligation enhancer, 45 nM NEBNext adaptor for Illumina] at 20°C for 15 minutes followed by 0.032 units/µl USER treatment at 37°C for 15 minutes, with two-time washes with TNB at 55°C for 2 minutes after each reaction. The resultant adaptor-ligated Hi-C library was amplified by PCR with 5-7 cycles with Q5 master mix (NEB, M0544) and index primers (NEB, E7335/E7500/E7710/E7730) before 37-bp paired-end sequencing with NextSeq 500 (Illumina).

treatment_protocol: The cells were collected by centrifuge and washed 2 times by EMM2 (1% glucose) medium lacking NH4Cl (EMM2-N). Then, cells were resuspended in EMM2-N with 50 mg/ml leucine at a density of 5×10^6 cells/ml and incubated at 25°C for 6.5 h to induce G1 arrest. By adding same volume of EMM2-N with 50 mg/ml leucine and 15 µM of 1-NM-PP1 (Toronto Research Chemicals Inc) (5~8×10^6 cells/ml), cells can enter meiosis, and further incubated for 2.5 h or more. Before harvesting the meiotic cells, 1mM PMSF (phenylmethylsulfonyl fluoride, SIGMA) was added to reduce protein degradation.

tag: strain

tag: restriction enzyme

value: MboI


title: REM14, dilution 1:4, set 1, replicate 3


title: rec8_wt_3Flag_150min_PMSF_HiC

description: Hi-C


title: REM14, dilution 1:4, set 1, replicate 2


title: 202915460057_R02C01

description:
202915460057_R02C01_Grn.idat
202915460057_R02C01_Red.idat
TCA
SAMPLE 18

source_name: peripheral blood leukocytes

value: NO


title: rec10_150min_PMSF_HiC

description: Hi-C


title: REM14, dilution 1:4, set 1, replicate 1


title: REM03, dilution 1:16, set 1, replicate 4

value: highly likely


title: rec8_150min_PMSF_HiC

description: Hi-C


title: wpl1_150min_PMSF_HiC

description: Hi-C


title: REM03, dilution 1:16, set 1, replicate 3


title: REM03, dilution 1:16, set 1, replicate 2


title: wt_150min_PMSF_HiC

description: Hi-C


title: REM03, dilution 1:16, set 1, replicate 1


title: rec8_F204S_3Flag_0min_PMSF_HiC

description: Hi-C


title: rec8_wt_3Flag_0min_PMSF_HiC

description: Hi-C


title: REM03, dilution 1:8, set 1, replicate 4


title: REM03, dilution 1:8, set 1, replicate 3


title: rec10_0min_PMSF_HiC

description: Hi-C


title: REM03, dilution 1:8, set 1, replicate 2


title: rec8_0min_PMSF_HiC

description: Hi-C


title: rec12_150min_PMSF_HiC

description: Hi-C


title: rec12_0min_PMSF_HiC

description: Hi-C


title: wt-dip_AS_HiC

description: Hi-C


title: REM03, dilution 1:4, set 1, replicate 4


title: wpl1_0min_PMSF_HiC

description: Hi-C


title: 202915420037_R08C01

description:
202915420037_R08C01_Grn.idat
202915420037_R08C01_Red.idat
TCA
SAMPLE 16


title: REM03, dilution 1:8, set 1, replicate 1


title: wpl1-dip_AS_HiC

description: Hi-C


title: REM03, dilution 1:4, set 1, replicate 2


title: MCF7-siFOXA1_Rep2

description: endogenous FOXA1 KD

source_name: MCF-7, siFOXA1, 72 hrs


title: REM06, dilution 1:16, set 1, replicate 4


title: REM03, dilution 1:4, set 1, replicate 1


title: wt_0min_PMSF_HiC

description: Hi-C


title: REM10, dilution 1:8, set 1, replicate 2


title: MC29

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC. The raw reads were trimmed and filtered using Trimmomatic. The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools.
To identify DMRs, the reference genome was broken into 1000 bp windows. Genomic windows with a mean of less than 10 mapped reads per sample were removed prior to further analysis. The MEDIPS R package was then used to calculate differential coverage between disease and non-disease sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window.
Windows with an edgeR p-value less than an arbitrarily selected threshold were considered DMRs. The DMR edges were extended until no genomic window with a p-value less than 0.1 remained within 1000 bp of the DMR.
CpG density and other information was then calculated for the DMR based on the reference genome.
Assembly: Rnor_6.0
Supplementary files format and content: Read counts in each genomic window for every sample. Library size adjusted read depths are reported as RPKM values.

organism: Rattus norvegicus

source_name: Sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley SD (Harlan) at 70 to 100 days of age were fed ad lib with a standard rat diet and ad lib tap water. The gestating female rats were designated as the F0 generation. The offspring F1, F2 and F3 generations were all aged to 90 days of age and bred within the generation and within the control lineage. F1- F3 generation control lineages were housed in the same room and racks with lighting, food and water. All the animals were aged to 1 year and euthanized for pathology and sperm collected for epigenetic analyses.

extract_protocol:
The epididymis was dissected free of fat and connective tissue, then, after cutting open the cauda, placed into 6 ml of phosphate buffer saline (PBS) for 20 minutes at room temperature. Further incubation at 4ºC will immobilize the sperm. The tissue was then minced, the released sperm pelleted at 4ºC 3,000 x g for 10 min, then resuspended in NIM buffer and stored at -80ºC for further processing. An appropriate amount of rat sperm suspension was used for DNA extraction. Somatic cells and debris were removed by brief sonication (Fisher Sonic Dismembrator, model 300, power 25), then centrifugation and washing 1-2 times in 1X PBS. The resulting pellet was resuspended in 820 µL DNA extraction buffer and 80 µl 0.1M DTT added, then incubated at 65°C for 15 minutes. 80 µl proteinase K (20 mg/ml) was added and the sample was incubated at 55°C for 2-3 hours under constant rotation. Protein was removed by addition of protein precipitation solution (300 µl, Promega A795A), incubation for 15 min on ice, then centrifugation at 13,500 rpm for 30 minutes at 4°C. One ml of the supernatant was precipitated with 2 µl of glycoblue (Invitrogen, AM9516) and 1 ml of cold 100 % isopropanol. After incubation, the sample was spun at 13,500 x g for 30 min at 4°C, then washed with 70% cold ethanol. The pellet was air-dried for about 5 minutes then resuspended in 100 µl of nuclease free water. Genomic DNA was sonicated and run on 1.5% agarose gel for fragment size verification. The sonicated DNA was then diluted with 1X TE buffer to 400 μl, then heat-denatured for 10min at 95˚C, and immediately cooled on ice for 10 min to create single-stranded DNA fragments. Then 100 μl of 5X IP buffer and 5μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added, and the mixture was incubated overnight on a rotator at 4˚C. The following day magnetic beads (Dynabeads M280 Sheep anti-Mouse IgG; Life Technologies 11201D) were pre-washed per manufacturer’s instructions, and 50μl of beads were added to the 500μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h on a rotator at 4˚C. After this incubation, the samples were washed three times with 1X IP buffer using a magnetic rack. The washed samples were then resuspended in 250μl digestion buffer (5mM Tris PH 8, 10.mM EDTA, 0.5% SDS) with 3.5μl Proteinase K (20mg/ml), and incubated for 2-3 hours on a rotator at 55˚C. DNA clean-up was performed using a Phenol-Chloroform-Isoamyl-Alcohol extraction, and the supernatant precipitated with 2μl of glycoblue (20mg/ml), 20μl of 5M NaCl and 500μl ethanol in -20˚C freezer for one to several hours. The DNA precipitate was pelleted, washed with 70% ethanol, then dried and resuspended in 20μl H2O or 1X TE. DNA concentration was measured in Qubit (Life Technologies) with the ssDNA kit (Molecular Probes Q10212).
MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra RNA Library Prep Kit for Illumina (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA from the single-stranded DNA resulting from MeDIP. After this step, the manufacturer’s protocol was followed indexing each sample individually with NEBNext Multiplex Oligos for Illumina. The samples were sequenced on the Illumina HiSeq 2500 at PE50, with a read size of approximately 50 bp and approximately 20 million reads per pool. Twelve libraries were run in one lane.

treatment_protocol: Timed-pregnant females on days 8 through 14 of gestation [53] were administered daily intraperitoneal injections of dimethyl sulfoxide (DMSO) with an equal volume of sesame oil (Sigma) to prevent irritation at the injection site.

value: sperm

tag: generation

tag: control batch

tag: disease

value: kidney, obesity


title: MC28


title: REM06, dilution 1:16, set 1, replicate 1

value: TRUE

value: unlikely


title: MC27


title: REM06, dilution 1:16, set 1, replicate 2


title: 202915420037_R01C01

description:
202915420037_R01C01_Grn.idat
202915420037_R01C01_Red.idat
TCA
SAMPLE 9

value: YES


title: MC26

value: testis


title: MC25


title: REM06, dilution 1:8, set 1, replicate 2


title: MC30

value: kidney


title: REM06, dilution 1:8, set 1, replicate 1


title: MC24

value: obesity


title: REM06, dilution 1:4, set 1, replicate 4


title: MC22

value: nne


title: REM03, dilution 1:4, set 1, replicate 3


title: MC20


title: MCF7-siCtrl_Rep2

description: control

source_name: MCF-7, siCtrl, 72 hrs

tag: treatment

value: control


title: REM06, dilution 1:16, set 1, replicate 3


title: REM02, dilution 1:16, set 1, replicate 4


title: MC18

tag: tissue

value: testis, obesity


title: REM02, dilution 1:16, set 1, replicate 3

value: NHBE


title: REM02, dilution 1:16, set 1, replicate 2

value: likely


title: MC23


title: REM02, dilution 1:16, set 1, replicate 1

value: likely or highly likely


title: MC16


title: REM06, dilution 1:4, set 1, replicate 2


title: MC15


title: MC17


title: REM06, dilution 1:8, set 1, replicate 3


title: genomic DNA from neocortex of CTR-3

source_name: Neocortex CTR-3

value: Male

value: Neocortex

value: Non-epileptic control


title: MC14

value: sperm

value: testis, kidney


title: REM06, dilution 1:4, set 1, replicate 1

value: TRUE


title: MC19


title: MC13


title: MC8


title: REM02, dilution 1:4, set 1, replicate 3


title: MC7

value: prostate


title: REM02, dilution 1:4, set 1, replicate 4


title: REM02, dilution 1:8, set 1, replicate 4


title: REM06, dilution 1:4, set 1, replicate 3

value: unlikely


title: REM02, dilution 1:4, set 1, replicate 1


title: REM04, dilution 1:16, set 1, replicate 4


title: REM02, dilution 1:8, set 1, replicate 3


title: REM02, dilution 1:8, set 1, replicate 2


title: MC5


title: MC3


title: REM04, dilution 1:16, set 1, replicate 2


title: MC4


title: REM04, dilution 1:16, set 1, replicate 3


title: REM04, dilution 1:8, set 1, replicate 2


title: MC2


title: REM04, dilution 1:8, set 1, replicate 4


title: MC1


title: REM06, dilution 1:8, set 1, replicate 4


title: MC21


title: REM02, dilution 1:8, set 1, replicate 1


title: REM04, dilution 1:16, set 1, replicate 1


title: DC60


title: DC59


title: DC58


title: MC6


title: MC10

value: late puberty


title: DC57


title: REM04, dilution 1:4, set 1, replicate 3


title: DC56


title: MC11


title: REM04, dilution 1:8, set 1, replicate 3


title: REM04, dilution 1:4, set 1, replicate 2


title: DC55


title: DC54


title: REM04, dilution 1:4, set 1, replicate 1


title: DC53


title: MC9

value: testis, prostate


title: DC52

value: testis


title: REM01, dilution 1:16, set 1, replicate 2


title: REM01, dilution 1:16, set 1, replicate 3


title: DC49


title: DC50


title: REM01, dilution 1:8, set 1, replicate 2


title: REM01, dilution 1:8, set 1, replicate 3


title: REM01, dilution 1:4, set 1, replicate 4


title: DC46


title: DC45


title: REM04, dilution 1:4, set 1, replicate 4


title: REM01, dilution 1:8, set 1, replicate 4


title: DC47


title: REM01, dilution 1:4, set 1, replicate 3


title: REM04, dilution 1:8, set 1, replicate 1


title: DC44


title: REM01, dilution 1:4, set 1, replicate 1


title: REM01, dilution 1:16, set 1, replicate 1


title: REM01, dilution 1:8, set 1, replicate 1


title: DC43

value: kidney


title: REM01, dilution 1:4, set 1, replicate 2


title: Positive

city: Guangzhou

first: Yiming

last: Yan

address: Wushan Road

country: China

institute: South China Agricultural University

data_processing:
 After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
the high quality clean reads were aligned to the reference genome (GRCg6a) with hisat2 software (v2.0.4)
Genome_build: GRCg6a

organism: Gallus gallus

source_name: DF-1 cell

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DF-1 cell lysate were incubated with negative probe and ALV-miR-p19-01 probe, respectively

value: cell lysate were incubated with ALV-miR-p19-01 probe

tag: cell line/type

value: DF-1 cell


title: DC42


title: DC51


title: DC48


title: DC40


title: DC41


title: REM02, dilution 1:4, set 1, replicate 2

value: NHBE


title: Xenograft untreated with Crenigacestat 4

type: RNA

city: Castellana Grotte (BA)

first: Grazia

last: Serino

address: Via Turi, 27

country: Italy

institute: National Institute of Gastroenterology “S. de Bellis”, Research Hospital

hyb_protocol: The biotinylated DNA was hybridized to the GeneChip Human Transcriptome Array 2.0 Arrays (Affymetrix), containing  containing more than 286263 full length transcripts covering 44,699 coding genes and 22,829 non coding genes selected from Homo sapiens genome databases RefSeq, ENSEMBL and GenBank.

scan_protocol: Chips were washed, stained and scanned on the Affymetrix Complete GeneChip® Instrument System (Affymetrix, Santa Clara, CA), generating digitized image data and raw intensity data.

data_processing: The raw data were preprocessed with background correction and normalization with the Affymetrix Expression Console. The Affymetrix Transcriptome Analysis Console 4.0 was used to identify significantly differential expressed genes using the Limma eBayes method.

label: biotin

source_name: iCCA xenograft mice model

label_protocol: One hundred ng of total RNA total RNA were subjected to two cycles of cDNA synthesis with the Affymetrix WT PLUS expression Kit. The first cycle – first strand synthesis is performed using an engineered set of random primers that exclude rRNA-matching equences and include the T7 promoter sequences. After second-strand synthesis, the resulting cDNA is in vitro transcribed with the T7 RNA polymerase to generate a cRNA. This cRNA is subjected to a second cycle – first strand synthesis in the presence of dUTP in a fixed ratio relative to dTTP. Single strand cDNA is then purified and fragmented with a mixture of uracil DNA glycosylase and apurinic/apirimidinic endonuclease 1 (Affymetrix) in correspondence of incorporated dUTPs. DNA fragments are then terminally labeled by terminal deoxynucleotidyl transferase (Affymetrix) with biotin.

growth_protocol: 5*106 HUCCT1 cells were injected subcutaneously into the right flank of CD1 immunodeficient nude mouse. 2-3 weeks after injection, when tumor masses reached approximately reach the volume of 60-70 mm3, mice were allocated in two experimental groups: a group treated orally (gavage) with vehicle and the other one treated orally (gavage) with Crenigacestat

extract_protocol: Total RNA isolation from tissue was performed using TRIzol® (Thermo Fisher Scientific,Waltham, MA, USA) in combination with TissueLyser homogenizer (Qiagen, Hilden, Germany) according to manufacturer’s instructions. In addition, a column-based purification step has been done by using the RNeasy Mini Kit (Qiagen, Hilden, Germany) and total RNA was then eluted in ribonuclease-free water.  RNA concentration and quality were determined with the NanoDrop Spectrophotometer (Thermo Fisher Scientific, MA, USA) and the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), respectively.

value: Xenograft tumor

value: 1percent Na-CMC, 0.25percent Tween-80, 0.05percent Antifoam in ddH2O

tag: host strain

value: CD1 immunodeficient nude mouse


title: Xenograft untreated with Crenigacestat 3


title: Xenograft treated with Crenigacestat 6

value: Crenigacestat (8 mg/kg)


title: Xenograft untreated with Crenigacestat 2


title: Xenograft treated with Crenigacestat 3


title: Xenograft treated with Crenigacestat 2


title: Xenograft treated with Crenigacestat 1


title: DC38


title: Xenograft treated with Crenigacestat 5


title: Negative

value: cell lysate were incubated with negative probe


title: DC37

value: sperm


title: DC32


title: DC35


title: DC31


title: DC33


title: DC30


title: DC39


title: Xenograft untreated with Crenigacestat 1


title: p_ctrl_3

city: hangzhou

first: wenzheng

last: qu

address: Kaixuan Road

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.
Fragments Per Kilobase of transcript sequence per  Millions (FPKM) were calculated based on the length of the gene and reads count mapped  to this gene.FPKM considers the effect of sequencing depth and gene length for  the reads count at the same time, and is currently the most commonly used method for  estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample and genes.

source_name: aNSC

extract_protocol:
Total RNA was harvested using Trizol reagent from brain samples.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Briefly, the forebrains of adult mice (C57BL6, age of postnatal 8–10 weeks) were cut into small pieces followed by enzymatic digestion, filtering and centrifugation. aNSPCs were cultured with DMEM/F-12 medium containing 2% B27 (Cat# 12587-010, Thermo Fisher Scientific), 20 ng/mL EGF (Cat# 100-15, Peprotech), 20 ng/mL FGF-2 (Cat# 100-18B, Peprotech), 2 mM glutamine (Cat# 5030-149, Thermo Fisher Scientific) and 1% antibiotic–antimycotic (Cat# 15140-122, Thermo Fisher Scientific) at 37 °C in a humidified incubator containing 5% CO2. The medium was half replaced every other day.

value: aNSC

value: untreated


title: Xenograft treated with Crenigacestat 4


title: p_NAD_3


title: p_ctrl_2


title: DC27

value: early puberty


title: DC36


title: DC34

value: prostate, kidney


title: DC26

value: early puberty, prostate


title: p_NAD_2


title: p_NAD_1


title: p_ctrl_1


title: DC28


title: DC24


title: D_NAD_3


title: D_NAD_2


title: D_NAD_1


title: DC22


title: DC21


title: D_ctrl_3


title: D_ctrl_2


title: DC20

value: late puberty


title: DC23

value: prostate


title: DC18


title: leukocytes-ketogenic diet

city: Lexington

first: Qingding

last: Wang

address: 760 Press Ave

institute: University of Kentucky

data_processing:
Raw sequence reads were processed and aligned to the GRCm38 (2020-A) mouse reference transcriptome using the Cell Ranger v6.0.0 pipeline with default parameters. Downstream analysis, such as data preprocessing, normalization, integration, clustering and differential expression analysis were performed in R using the Seurat package (v3.2.0). Cells with more than 5,500 detected genes or for which more than 18,000 RNA molecules detected per cells were excluded from further analysis.  Cells with the total mitochondrial content greater than 6.5% of the total library were also discarded. Genes expressed in fewer than five cells across the dataset were removed. Samples were normalized separately using the sctransform function. The top 2,000 gene features that were repeatedly variable across the datasets were selected and used for identifying integration anchors between the two datasets. Lastly, the integrated dataset was created based on the pre-computed anchors. Dimensionality reduction was performed by the principal components analysis (PCA), and Uniform Manifold Approximation and Projection (UMAP).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix generated by CellRanger: matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz

source_name: MC38 tumor

extract_protocol:
The tumor tissues were collected 14 days post-implantation and single cell suspensiones were prepared. Dead cells were removed from the single cell suspension using the Dead Cell Removal Kit (Miltenyi Biotec, Cat# 130090101). CD45+leukocytes were magnetically labeled and enriched using magnetic beads (Miltenyi Biotec). The isolation procedure was performed according to the manufacturer's instructions.
Library preparation was conducted according to the manufacturer’s instructions using Chromium Next GEM Single Cell 3’ Gene Expression Kit v3.1.  Single indexed, paired-end libraries were sequenced on an Illumina HiSeq2500.

treatment_protocol: MC38 tumors were established by subcutaneously injecting cells (0.5 × 10^6 cells in 50% matrigel in PBS, 100 μL/mouse) into the right flank of 6-8 week old C57BL/6J female mice. Mice were grouped into normal diet control (NC) and ketogenic diet treatment (KD), ketogenic diet was administered from day 4 until endpoint.

value: CD45+ leukocytes isolated from syngeneic MC38 tumors

value: fed with ketogenic diet


title: leukocytes-normal diet

value: fed with normal diet


title: N_si_T01

city: Trieste

first: Maurizio

last: Romano

address: Via A. Valerio 28

department: Department of Life Sciences

institute: University of Trieste

description: Replicate treated with anti-mouse TDP-43 siRNA

data_processing:
Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality.FASTQ format described by four lines:    @HWI-ST1276:71:C1162ACXX:1:1101:1208:2458 1:N:0:CGATGT     NAAGAACACGTTCGGTCACCTCAGCACACTTGTGAATGTCATGGGATCCAT  +  #55???BBBBB?BA@DEEFFCFFHHFFCFFHHHHHHHFAE0ECFFD/AEHH    Line 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line).Line 2 is the raw sequence letters.Line 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again.Line 4 encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence.    The details of Sequencing identifier of Illumina are as follows:    (1) HWI-ST1276:71 HWI-ST1276,Instrument – unique identifier of the sequencer; 71,run number – Run number on instrument  (2) C1162ACXX:1:1101:1208:2458 means the coordinate of read on C1162ACXX(Flowcell ID)flowcell,line 1, 1101 tile is(x=1208,y=2458)  (3) 1:N:0:CGATGT the first number is 1 or 2, 1 means single reads or the first read of paired ends, 2 means the second of paired ends; the second letter means whether reads is adjusted(Y means yes, N means no); the third number represent the number of Control Bits in sequence; six bases on the fourth place is Illumina index sequence.
Data filtering    The Sequenced Reads/raw reads often contain low quality reads or reads with adaptors. It was necessary to filter the raw reads under conditions to get the clean reads. Raw reads filtering conditions are as follows:    (1) Remove reads containing adaptors;  (2) Remove reads containing N > 10% (N represents base that could not be determined);  (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.    RNA-seq Adapter information:    NEBNext® UltraTM RNA Library Prep Kit  RNA 5' Adapter(5'Adaptor)    5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT    RNA 3' Adapter(3'Adaptor,The underlined 6bp bases is Index)    5' GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
Mapping the clean reads to the reference genome or the transcriptome is the basis for the next following analysis. Novogene use STAR to accomplish the mapping. For the spieces(Human and mice) whose gene annotation information are more completed, if only need the differential expression significant genes, can map reads to the transcriptome directly. If research the study of alternative splicing, variation, the fusion gene, the alignment should be carried out at the genome level. In order to avoid losing a lot of effective junction reads, Novogene use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely.
Reads distribution on genome    Reads were mapped to exon, intron and intergenic.  According to the mapping result, summary the percentage of statistics for reads in the genome exon, intron and intergenic region seperately. In general, the gene annotation of the species is more complete (such as mouse and human), the ratio of reads mapped to exon is supposed to be the highest.  Reads mapped to intron may result from the remaining pre-mRNA or alternative splicing event.  Reads mapped to intergenic may due to some ncRNA or DNA fragment contamination or the incomplete gene annotation.
Distribution of mapped reads on chromosome    After getting the information about distribution of mapped reads on genome area, we  focused the distribution of mapped reads on chromosome. On one hand we can get insight into how many regions on chromosome is covered, on the other hand we can get the information about transcription activity on chromosome.    We calculated mapped reads density on every chromosome , then plot based on the mapped reads density. In general, the longer the chromosome is, the more reads were mapped to the chromosome. The statistics of reads mapped to chromosome indicates the relationship between chromosome length and reads number. The plot method are as follows:    (1) 1 Kbp as an unit when window size is set, counting number of reads that mapped to the every base in window;  (2) Mid-value is chosen to represent the number of reads that mapped to the every base in window; the longer chromosome is, the more reads will be calculated(Marquez et al.);  (3) log2 (mid-value) is used to plot.
Gene expression level analysis    The abundance of transcript reflects gene expression level directly. In RNA-seq experiment, we estimate gene expression level by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to be proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.(Mortazavi et al. 2008)
Genome_build: Mus musculus (GRCm38/mm10)
Supplementary_files_format_and_content: fpkm_genename.xlsx: FPMK + Gene annotations (Excel format)
Supplementary_files_format_and_content: readcount_genenames.xlsx: Readcounts + Gene annotations (Excel format)

source_name: Motor Neuron-Like Hybrid Cell Line

growth_protocol: C2C12 immortalized mouse myoblasts (ECACC) were maintained in DMEM (Thermo Fisher Scientific), supplemented with 10% FBS (Thermo Fisher Scientific) and antibiotics/antimycotics (Sigma-Aldrich) under standard conditions.  NSC34 motoneuron-like mouse hybrid cell line (available in house) was cultured in DMEM (Thermo Fisher Scientific) with 5% FBS (Sigma-Aldrich) and antibiotics/antimycotics (Sigma-Aldrich).

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA sequencing  (150PE, 60M read pair per sample) was performed by Novogene (https://en.novogene.com/).  RNA libraries were prepared for sequencing using standard Illumina protocols.  Library concentration was first quantified using a Qubit 2.0 fluorometer (Life Technologies).  Insert size was checked on an Agilent 2100 and quantified using quantitative PCR (Q-PCR).

treatment_protocol: All experiments were performed with cells of similar passage number (± 2). To silence TDP-43 in C2C12 and NSC34 cells, 40 nM of siTDP (mouse siTDP 5’-CGAUGAACCCAUUGAAAUA-3’, Sigma-Aldrich) or non-targeting siLUC (5’-UAAGGCUAUGAAGAGAUAC-3’, Sigma-Aldrich) were mixed with 54 μl of RNAiMAX (Invitrogen) following the manufacturer’s reverse transfection protocol and applied to cells 700 000 seeded in a 10 cm dish.  48 h later, transfected cells were collected for subsequent analysis.

value: siRNA mouse TDP-43


title: DC15


title: N_si_T03


title: DC16


title: DC14


title: N_si_L02

description: Replicate treated with Control siRNA

value: siRNA Control (Luciferase)


title: C_si_T03

source_name: immortalized mouse myoblasts


title: DC25


title: DC12


title: N_si_L01

description: Replicate treated with Control siRNA


title: DC13

value: testis, kidney


title: DC17

value: kidney


title: DC11

description: raw data files for sample DC11 are included in the submission. Due to low sequencing quality, this sample is not included in the processed data file.11


title: C_si_T02


title: N_si_L03

description: Replicate treated with Control siRNA


title: DC8


title: DC29


title: DC19


title: DC9


title: C_si_T01


title: DC7


title: DC10


title: N_si_T02


title: DC5


title: C_si_L03

description: Replicate treated with Control siRNA


title: DC6


title: C_si_L02

description: Replicate treated with Control siRNA


title: D_ctrl_1


title: DC4


title: DC3


title: Snrpb injected 1-cell embryos

city: London

first: Christopher

middle: Douglas Robert

last: Wyatt

address: Gower street

country: United Kingdom

institute: UCL

description: 1 cell stage embryos after zygotic injection of Snrpb mRNA

data_processing:
vast-tools was used to create raw counts and normalised counts adjusted for multiple mapping (cRPKMs), for mm9.
Supplementary_files_format_and_content: Gene name (column 1); Counts (column 2); Normalised expression: cRPKMs (column 3)

source_name: Whole embryo

extract_protocol:
RNA extraction at either 5h post injection (zygote stage) or 24h post injection (2C stage). RNA was extracted using the Qiagen RNeasy Micro Kit.
For each condition 40 embryos coming from three independent experiments were pooled to extract RNA for sequencing. SMARTer Stranded RNA-Seq Kit was used for library preparation prior to Illumina sequencing. Libraries were sequenced on a  HiSeq2500 machine

treatment_protocol: Microinjection of Snrpb and/or Snrpd2 or mCherry (control) mRNA at one cell stage embryos.

value: B6CBA F1 crosses


title: Snrpb and Snrpd2 injected 1-cell embryos

description: 1 cell stage embryos after zygotic injection of Snrpb and Snrpd2 mRNA


title: Snrpd2 injected 1-cell embryos

description: 1 cell stage embryos after zygotic injection of Snrpd2 mRNA


title: DC1


title: DC2


title: mCherry injected 2-cell embryos

description: 2 cell stage embryos after zygotic injection of mCherry mRNA


title: Snrpb and Snrpd2 injected 2-cell embryos

description: 2 cell stage embryos after zygotic injection of Snrpb and Snrpd2 mRNA


title: Wsm2-_Buffer_rep3 [XY15]

city: Fort Collins

first: Yucong

last: Xie

state: CO

address: 307 Campus delivery

department: Department of Soil and Crop Sciences

institute: Colorado State University

data_processing:
Raw reads of each paired-end library were examined for sequence quality and adaptor sequences were removed using Fastp with default settings
Trimmed paired-end RNA-seq reads were aligned to the reference genome using STAR  2.7.3 with parameters “-outFilterMismatchNmax 6 -alignIntronMax 10000”.
Non-normalized reads were counted with featureCounts (which is a function in subread-2.0.0) with parameters “-t gene -p” and used as input for the R package “DEseq2”
During the STAR 2.7.3 alignment, reads that did not map to IWGSC RefSeq v1.0 were collected with parameter “-outReadsUnmapped” and assembled with Trinity v2.10.0 using the following parameters: “-seqType fq –samples_file<input_file> -max_memory 10G -CPU 20”
Genome_build: Do novo  assembly of unmapped reads
Supplementary_files_format_and_content: Raw counts of mapped reads

organism: Triticum aestivum

source_name: Homogenized whole leaf tissues

growth_protocol: Plants were grown in a Conviron PGR15 growth chamber at CSU, CO, in 12hr light/12hr dark conditions with a 18 °C day/ 15 °C night temperatures.

extract_protocol:
Total RNA was extracted from homogenized whole leaf tissues collected 10 days after inoculation using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO).
The Agilent 2100 bioanalyzer (RNA Nano Chip, Agilent, CA) was used to check RNA integrity. The library construction and sequencing via Illumina HiSeq 2000 were performed by Novogene Co., Ltd (Sacramento, CA, USA), approximately 150 bp paired end (PE) raw reads were generated.

treatment_protocol: The WSMV treatment was prepared with 1:10 (w/v) dilution of the WSMV-infected wheat leaf tissue and 0.01 M potassium phosphate buffer (pH 7.4) and inoculated on two-week-old seedlings. The Buffer treatment were absent for WSMV infected tissues in the inoculum.

tag: genotype

value: Mock or phosphate buffer treated

tag: sample collection time

value: 10 days post inoculation on two week old seedlings

value: Homogenized whole leaf tissues


title: Wsm2-_Buffer_rep1 [XY13]


title: Snrpd2 injected 2-cell embryos

description: 2 cell stage embryos after zygotic injection of Snrpd2 mRNA


title: Wsm2-_Buffer_rep4 [XY16]


title: Wsm2+_Buffer_rep2 [XY6]


title: Wsm2+_Buffer_rep3 [XY7]


title: Wsm2-_WSMV_rep2 [XY10]

value: WSMV treated


title: Wsm2-_Buffer_rep2 [XY14]


title: Wsm2+_Buffer_rep1 [XY5]


title: Wsm2+_Buffer_rep4 [XY8]


title: mCherry injected 1-cell embryos

description: 1 cell stage embryos after zygotic injection of mCherry mRNA


title: Wsm2+_WSMV_rep4 [XY4]


title: Wsm2+_WSMV_rep2 [XY2]


title: Wsm2-_WSMV_rep4 [XY12]


title: C_si_L01

description: Replicate treated with Control siRNA


title: Wsm2-_WSMV_rep3 [XY11]


title: Wsm2-_WSMV_rep1 [XY9]


title: Wsm2+_WSMV_rep3 [XY3]


title: 48hr_22Rv1_Rep3_RNAseq

city: Chicago

first: Debu

last: Chakravarti

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

data_processing:
For single-end reads (ChIP-seq) raw fastq files were aligned with bowtie (v1.2.2, settings: -t --best -m 1) using pre-built genome indexes for both hg38 and mm10, downloaded from source (http://bowtie-bio.sourceforge.net/manual.shtml, NCBI). For paired-end ATAC-seq, reads were aligned with bowtie2 (v2.2.6, settings: --very-sensitive -X 800). For paired-end RNA-seq, reads were aligned to the hg38 reference genome (NCBI, GRCh38.p12) using STAR (43) (v2.7.5, settings: --alignIntronMin 20 --alignIntronMax 500000).
ChIP- and ATAC-seq sequence alignment files were converted to binary format using samtools (version 1.9) and used as input for peaks calling (HOMER, v4.11.1) (settings: -tbp 1, style = factor/histone/dnase).
Using diffBind (v3.12, settings: minMembers = (# of replicates) score=DBA_SCORE_TMM_MINUS_FULL) for differential binding analysis, each timepoint (1-, 4-, 8-, 24- and 48-hr) was compared to DMSO and peaks called by HOMER were used to define a consensus peak list
Visualization for ChIP-seq data including bigwigs, heatmaps and read coverage histograms were generated with deeptools bamCoverage (settings: --binSize 1 --normalizeUsing RPGC –effectiveGenomeSize mouse/human --extendReads    120 –ignoreDuplicates), plotHeatmap and plotProfile function (deepTools v3.3.0)
For paired-end RNA-seq, reads were aligned to the hg38 reference genome (NCBI, GRCh38.p12) using STAR (v2.7.5, settings: --alignIntronMin 20 --alignIntronMax 500000). All fastq files were analyzed for quality control using FastQC (version 0.11.9). Gene count matrices were generated using featureCounts (http://subread.sourceforge.net) with the following NCBI reference genome annotation GTF: “hg38.ncbiRefSeq.gtf” (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/) (subread v1.6.1).
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: ChIP-seq: peak .txt files from HOMER, differential binding table is output from diffBind; RNA-seq: count matrix from featureCounts; ATAC-seq: peak .xls files from macs2

growth_protocol: All cell lines in this study were maintained in RPMI (ThermoFisher, Cat#: 11875093) supplemented with 10% Gibco FBS (REF:26140-079) in a humidified incubator at 37°C with 5% CO2

extract_protocol:
For ChIP-seq, the cell nuclear fraction was clarified from sonicated and histone-DNA complexes were isolated with antibodies. For RNA-seq, total RNA extracts were isolated from MYCi975 and vehicle control treated cells. For ATAC-seq, nuclei were isolated and inspected before Tn5 tagmentation.
As input for library preparation, < 1 ng – 5 ng of immunoprecipitated DNA was used. ChIPseq library preparation was carried out with KAPA Hyper Prep Kit (Cat#: KK8502). For RNAseq, 500 ng of RNA was used as input with a ribosome depletion library kit (KAPA Biosystems, Cat#: KK8560).

treatment_protocol: Cells were isolated 72 hours after plating with a fresh media change 48-hours after plating. Each treatment was given such that isolation 72-hours after plating represents each timepoint.

value: cancer cell line

value: 48hr MYCi - 10 µM


title: DMSO_22Rv1_Rep4_RNAseq


title: 24hr_22Rv1_Rep3_RNAseq

value: 24hr MYCi - 10 µM


title: 24hr_22Rv1_Rep4_RNAseq


title: 48hr_22Rv1_Rep4_RNAseq


title: Wsm2+_WSMV_rep1 [XY1]


title: MYCi_MXD1_Rep2

tag: antibody

value: MXD1 (Proteintech, Cat#:17888-1-AP)


title: DMSO_MXD1_Rep1


title: MYCi_MNT_Rep2

value: MNT (Bethyl Laboratories, A303-627A)


title: DMSO_22Rv1_Rep3_RNAseq


title: DMSO_MXD1_Rep2


title: MYCi_MXD1_Rep1


title: Snrpb injected 2-cell embryos

description: 2 cell stage embryos after zygotic injection of Snrpb mRNA


title: DMSO_MNT_Rep2


title: MYCi_MNT_Rep1


title: DMSO_MNT_Rep1


title: MYCi_MGA_Rep2

value: MGA (Bethyl Laboratories, A302-865A)


title: MYCi_MGA_Rep1


title: DMSO_MGA_Rep2


title: DMSO_MGA_Rep1


title: genomic DNA from meningioma [UT53_RD-20-521]

city: New York

first: Department of Pathology

last: NYU Langone Health

state: NY

address: 240 East 38th Street

department: Department of Pathology

institute: NYU Langone Health Ambulatory Care Center

description:
meningioma sample
UT53_RD-20-521

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Bioconductor R package Minfi (version 1.40.0) in Rstudio.

source_name: membranes

extract_protocol: genomic DNA was extracted and purified from DNA was extracted from formalin-fixed paraffin-embedded (FFPE) meningioma samples using Maxwell Promega FFPE kit (Promega Inc, WI). DNA methylation profiling was performed in accordance to the Illumina methylation microarray protocol guide. The processed microarrays were then scanned using the Illumina iScan to generate the raw methylation probe intensity values.

value: ANM

tag: basename

tag: slide

tag: array

tag: gender

value: M

tag: grade

tag: histology

value: ANAPLASTIC MENINGIOMA


title: genomic DNA from meningioma [UT54_RD-20-522]

description:
meningioma sample
UT54_RD-20-522

value: MNG

value: MENINGOTHELIAL MENINGIOMA


title: genomic DNA from meningioma [UT45_RD-20-75]

description:
meningioma sample
UT45_RD-20-75

value: ATM

value: ATYPICAL MENINGIOMA


title: genomic DNA from meningioma [UT59_RD-20-527]

description:
meningioma sample
UT59_RD-20-527

value: TRANSITIONAL MENINGIOMA


title: genomic DNA from meningioma [UT49_RD-20-517]

description:
meningioma sample
UT49_RD-20-517


title: genomic DNA from meningioma [UT47_RD-20-77]

description:
meningioma sample
UT47_RD-20-77


title: genomic DNA from meningioma [UT41_RD-20-71]

description:
meningioma sample
UT41_RD-20-71

value: CHOM

value: CHORDOID MENINGIOMA


title: THP-1 HiC NTC CTL

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

institute: Goethe Universität Frankfurt am Main

description: HiC after 24 h stimulation with vehicle (ethanol) in non-targeting control cells

data_processing:
Hi-C sequencing reads were aligned to the hg19 genome using Bowtie2 (2.4.4) with the –local and –reorder parameters set.
The subsequently generated alignment files were then used to build Hi-C matrices with the HiCExplorer (v3.7.2) tool hicBuildMatrix. The built matrices were then normalized to the smallest of the samples using hicNormalise, and then corrected using iterative correction with hicCorrectMatrix, with the parameter –correctionMethod ICE and thresholds taken from diagnostic plots created using hicCorrectMatrix diagnostic_plot.
Corrected matrices were then used in the construction of relevant viewpoints using chicViewpointBackgroundModel and chicViewpoint. The background model was computed across all identified differential loop anchors in the CTCF HiChIP analysis.
Genome_build: hg19
Supplementary_files_format_and_content: HDF5 files of raw contact matrices produced by HiC-Explorer hicBuildMatrix.

source_name: Cell line

growth_protocol: The cells were grown in RPMI 1640 medium, supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin, and were kept at 37°C in a humidified 95% air/5% CO2 incubator.

extract_protocol:
Briefly, 2.5 x 10^6 THP-1 cells were cross-linked with 2% formaldehyde for 10 min, stopped with glycine, washed twice with PBS and snap-frozen. The thawed cells were lysed in 20 µl lysis buffer (15 min 4°C), then incubated with 24 µl Conditioning solution (19 min 62°C) and 20 µl Stop Solution 2 (15 min 37°C). Digestion with 12 µl Enzymes A1/A2 master mix was performed by sequential incubations of 45 min 37°C, 20 min 65°C and 10 min 25°C. Then, the biotin fill-in was performed with 16 µl Enzyme B master mix (45 min RT), followed by proximity ligation with 82 µl Enzyme C master mix (15 min RT). Proteins were digested with 35.5 µl Enzyme D master mix plus 20 µl Buffer E in the sequential incubations of 30 min 55°C, 90 min 68°C and 10 min 25°C. The DNA was purified using 100 µl AMPureXP beads (Beckman Coulter). After passing the QC1 quality control, 5 µg of each sample was diluted to 100 µl with Elution Buffer supplemented by 1% SDS. Fragmentation to an average fragment size of ≈400 bp was done by 15 cycles sonication in a Bioruptor Plus (Diagenode) with 30 s ON, 30 s OFF at high intensity. Size selection was performed with 60 µl and 40 µl SPRIselect beads (Beckman Coulter). Biotin enrichment was performed with 0.9-2 µg of the size selected DNA using 50 µl Enrichment Beads for < 1 µg DNA and 100 µl for > 1 µg DNA (15 min RT).
Following washes with Wash Buffer and Elution Buffer end repair and adapter ligation were performed: incubation with 20 µl Enzyme W2 master mix (10 min 37°C), washes, incubation with 50 µl Enzyme G3/G4 master mix (20 min 20°C), washes, ligation of a uniquely indexed P7 TruSeq LT Adapter (Swift Biosciences Set A Indexing Kit) in 25 µl Enzyme Y1 master mix (15 min 25°C), washes, ligation of non-indexed P5 TruSeq Universal adapter (Swift Biosciences Indexing Kit) in 50 µl Enzyme B4/B5/B6 master mix, washes, resuspension. The sufficient cycle number was determined with an initial PCR using 2 µl of the resuspended beads. The remainder of the beads was subjected to library amplification. Samples, for which 100 µl Enrichment Beads had been used, were distributed into six 50 µl PCR reactions, while those with 50 µl Enrichment Beads were run in three 50 µl reactions. PCRs were performed using the KAPA 2X HiFi HotStart Ready Mix (KAPA Biosystems), KAPA Library Amplification Primer Mix and EvaGreen (BioRad). The replicate PCR reactions were pooled, separated from the beads and purified with AMPureXP beads (Beckman Coulter). Concentrations were measured using the Qubit dsDNA HS Assay Kit (Thermofisher Scientific) and quality-controled by High Sensitivity DNA Assay on an Agilent Bioanalyzer or by D1000 ScreenTape on a TapeStation (Agilent). Sequencing was performed by Dr. Stefan Günther at Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany, on an Illumina NextSeq 500-PE100.

treatment_protocol: Prior to experiments, cells were grown overnight in phenol red-free medium supplemented with charcoal-stripped FCS and then treated with vehicle (0.1% ethanol (EtOH)) or 100 nM 1,25(OH)2D3 (Sigma-Aldrich) for 24 h.

tag: cell type

value: Monocyte

tag: cell line

value: control


title: THP-1 HiC NTC 1,25D

description: HiC after 24 h stimulation with 100 nM 1,25(OH)2D3 in non-targeting control cells


title: genomic DNA from meningioma [UT28_RD-19-615]

description:
meningioma sample
UT28_RD-19-615

value: ATYPICAL AND INVASIVE MENINGIOMA


title: genomic DNA from meningioma [UT48_RD-20-78]

description:
meningioma sample
UT48_RD-20-78


title: genomic DNA from meningioma [UT58_RD-20-526]

description:
meningioma sample
UT58_RD-20-526


title: 48hr_22Rv1_Rep2_RNA

data_processing:
For single-end reads (ChIP-seq) raw fastq files were aligned with bowtie (v1.2.2, settings: -t --best -m 1) using pre-built genome indexes for both hg38 and mm10, downloaded from source (http://bowtie-bio.sourceforge.net/manual.shtml, NCBI). For paired-end ATAC-seq, reads were aligned with bowtie2 (v2.2.6, settings: --very-sensitive -X 800). For paired-end RNA-seq, reads were aligned to the hg38 reference genome (NCBI, GRCh38.p12) using STAR (43) (v2.7.5, settings: --alignIntronMin 20 --alignIntronMax 500000).
ChIP- and ATAC-seq sequence alignment files were converted to binary format using samtools (version 1.9) and used as input for peaks calling (HOMER, v4.11.1) (settings: -tbp 1, style = factor/histone/dnase).
Using diffBind (v3.12, settings: minMembers = 4 score=DBA_SCORE_TMM_MINUS_FULL) for differential binding analysis, each timepoint (1-, 4-, 8-, 24- and 48-hr) was compared to DMSO and peaks called by HOMER were used to define a consensus peak list
Visualization for ChIP-seq data including bigwigs, heatmaps and read coverage histograms were generated with deeptools bamCoverage (settings: --binSize 1 --normalizeUsing RPGC –effectiveGenomeSize mouse/human --extendReads    120 –ignoreDuplicates), plotHeatmap and plotProfile function (deepTools v3.3.0)
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: ChIP-seq: peak .txt files from HOMER, differential binding table is output from diffBind; RNA-seq: count matrix from featureCounts; ATAC-seq: peak .xls files from macs2

extract_protocol:
For ChIP-seq, the cell nuclear fraction was clarified from sonicated and histone-DNA complexes were isolated with antibodies. For RNA-seq, total RNA extracts were isolated from MYCi and vehicle control treated cells. For ATAC-seq, nuclei were isolated and inspected before Tn5 tagmentation.
As input for library preparation, < 1 ng – 5 ng of immunoprecipitated DNA was used. ChIPseq library preparation was carried out with KAPA Hyper Prep Kit (Cat#: KK8502). For RNAseq, 500 ng of RNA was used as input with a ribosome depletion library kit (KAPA Biosystems, Cat#: KK8560).
multiplex

value: cancer cell line

value: 48hr MYCi - 10 µM


title: genomic DNA from meningioma [UT31_RD-19-618]

description:
meningioma sample
UT31_RD-19-618


title: 48hr_22Rv1_Rep1_RNA


title: 24hr_22Rv1_Rep2_RNA

value: 24hr MYCi - 10 µM


title: genomic DNA from meningioma [UT55_RD-20-523]

description:
meningioma sample
UT55_RD-20-523


title: genomic DNA from meningioma [UT26_RD-19-613]

description:
meningioma sample
UT26_RD-19-613


title: genomic DNA from meningioma [UT52_RD-20-520]

description:
meningioma sample
UT52_RD-20-520


title: genomic DNA from meningioma [UT6_RD-19-593]

description:
meningioma sample
UT6_RD-19-593

value: INVASIVE MENINGIOMA


title: DMSO_22Rv1_Rep2_RNA


title: DMSO_22Rv1_Rep1_RNA


title: MCF7_ATAC_MYCi_Rep3


title: 24hr_22Rv1_Rep1_RNA


title: genomic DNA from meningioma [UT21_RD-19-608]

description:
meningioma sample
UT21_RD-19-608


title: MCF7_ATAC_MYCi_Rep2


title: genomic DNA from meningioma [UT11_RD-19-598]

description:
meningioma sample
UT11_RD-19-598


title: genomic DNA from meningioma [UT51_RD-20-519]

description:
meningioma sample
UT51_RD-20-519


title: genomic DNA from meningioma [UT18_RD-19-605]

description:
meningioma sample
UT18_RD-19-605


title: genomic DNA from meningioma [UT4_RD-19-591]

description:
meningioma sample
UT4_RD-19-591


title: genomic DNA from meningioma [UT8_RD-19-595]

description:
meningioma sample
UT8_RD-19-595


title: MCF7_ATAC_MYCi_Rep1


title: genomic DNA from meningioma [UT13_RD-19-600]

description:
meningioma sample
UT13_RD-19-600


title: genomic DNA from meningioma [UT30_RD-19-617]

description:
meningioma sample
UT30_RD-19-617


title: MCF7_ATAC_DMSO_Rep3


title: MCF7_ATAC_DMSO_Rep2


title: genomic DNA from meningioma [UT7_RD-19-594]

description:
meningioma sample
UT7_RD-19-594


title: MCF7_ATAC_DMSO_Rep1


title: 22Rv1_ATAC_48hr_Rep3


title: 22Rv1_ATAC_48hr_Rep2


title: 22Rv1_ATAC_48hr_Rep1


title: genomic DNA from meningioma [UT35_RD-20-65]

description:
meningioma sample
UT35_RD-20-65

value: CHORDOID AND ATYPICAL


title: 22Rv1_ATAC_DMSO_Rep3


title: 22Rv1_ATAC_DMSO_Rep2


title: 22Rv1_ATAC_DMSO_Rep1


title: MCF7_48hr_Input_R2


title: genomic DNA from meningioma [UT12_RD-19-599]

description:
meningioma sample
UT12_RD-19-599

value: M


title: MCF7_48hr_FOXA1_R2

value: FOXA1 (Bethyl Laboratories, A305-249A)


title: MCF7_48hr_Input_R1


title: genomic DNA from meningioma [UT62_RD-20-530]

description:
meningioma sample
UT62_RD-20-530

value: MNG

value: F


title: genomic DNA from meningioma [UT22_RD-19-609]

description:
meningioma sample
UT22_RD-19-609

value: ATM


title: genomic DNA from meningioma [UT61_RD-20-529]

description:
meningioma sample
UT61_RD-20-529


title: MCF7_48hr_FOXA1_R1


title: genomic DNA from meningioma [UT10_RD-19-597]

description:
meningioma sample
UT10_RD-19-597

value: ATYPICAL MENINGIOMA


title: genomic DNA from meningioma [UT3_RD-19-590]

description:
meningioma sample
UT3_RD-19-590


title: MCF7_DMSO_Input_R2


title: genomic DNA from meningioma [UT29_RD-19-616]

description:
meningioma sample
UT29_RD-19-616


title: genomic DNA from meningioma [UT64_RD-20-532]

description:
meningioma sample
UT64_RD-20-532

value: MENINGOTHELIAL MENINGIOMA


title: MCF7_DMSO_Input_R1


title: genomic DNA from meningioma [UT60_RD-20-528]

description:
meningioma sample
UT60_RD-20-528


title: genomic DNA from meningioma [UT57_RD-20-525]

description:
meningioma sample
UT57_RD-20-525


title: MCF7_DMSO_FOXA1_R2


title: MCF7_DMSO_FOXA1_R1


title: DU145_ab56_MYC_ChIP

value: c-MYC (abcam, ab56-9E11),


title: 9E11_MYC_Rep3


title: genomic DNA from meningioma [UT63_RD-20-531]

description:
meningioma sample
UT63_RD-20-531


title: genomic DNA from meningioma [UT2_RD-19-589]

description:
meningioma sample
UT2_RD-19-589


title: 9E11_MYC_Rep2


title: genomic DNA from meningioma [UT43_RD-20-73]

description:
meningioma sample
UT43_RD-20-73

value: CHOM

value: CHORDOID MENINGIOMA


title: 9E11_Input_Rep3