title: ATAC-seq_D11_IROrganoids_TGFB1_rep2

first: Lei

address: No.2 Sipailou

institute: Southeast University

data_processing:
For RNA-seq, raw sequencing reads (fastq) were first quality checked using fastQC (v0.11.3) and were further aligned to mouse (mm9) genomes using Tophat2 (v2.1.0) to generate bam files. Cuffquant (v2.2.1) was used to generate cxb files from bam files. Cuffnorm (v2.2.1) was performed to calculate FPKM values using quartile normalization. Cuffdiff (v2.2.1) was applied to identify differentially expressed genes between groups using quartile normalization and per-condition dispersion.
For scRNA-seq of organoid samples, prior to processing, a mouse STAR reference was generated using a mouse genome FASTA build from the Ensembl 102 release and GTF annotations from GENCODE (GRCm39 vM29 2022.04) using STAR’s genomeGenerate function. BCLs derived from Illumina sequencing of PIPseq samples were demultiplexed and output in FASTQ format using BCL-convert v4.0.3. Barcode whitelisting and error correction were performed using PIPseeker v0.55. Reads passing this stage were then aligned to the mouse reference genome using STARsolo (STAR v2.7.10a). An aligned, sorted BAM file was generated by STAR, which included required information for RNA velocity analysis. Cell calling was performed using PIPseeker’s transcript-count thresholding approach and sensitivity 3 was chosen for all samples, which most closely targeted the first inflection point after the knee point on the barcode-rank plot. For sorted Ki67-RFP+ DAPI- cells, samples were processed in the same way, but using salmon v1.4 instead of STAR. A reference genome was first built from the same sources as above using the salmon index command with a 19-bp k-mer size.
For ATAC-seq, paired-end ATAC-seq fastq file was quality checked using fastQC. ATAC-seq adapter sequences were removed from each read file using CutAdapt (v1.9.1). Each read file was then aligned to the mouse mm9 genome using bowtie2. Picard (v2.18.27) was used to determine the median alignment size of each alignment bam file. Peak region bed files were called from each alignment bam file using MACS2 (v2.1.0). MACS2 was run with a “shift” distance of -0.5 times the median alignment size and an “extsize” distance equal to the median alignment size for each alignment bed file. The peak files were filtered against ENCODE blacklist, which is known to yield false ChIP-seq signals due to the inaccuracies of a particular genome assembly. BEDtools was used to subtract the sites on the ENCODE blacklist.
Assembly: RNA-seq and ATAC-seq: mm9; scRNA-seq: mm39
Supplementary files format and content: RNA-seq: fpkm_table.txt files.
Supplementary files format and content: scRNA-seq: barcodes.tsv, genes.tsv, and matrix.mtx files.
Supplementary files format and content: ATAC-seq: bigwig, Peaks BED files.

source_name: Primary intestinal organoids

extract_protocol:
Primary cultured organoids were collected by removing Matrigel using cold PBS. Matrigel droplets containing organoids were disrupted. Organoids were pelleted by centrifugation at 300 g for 3 minutes at 4 °C and washed with cold PBS. After removing the PBS and Matrigel, organoids were resuspended in 1 mL pre-warmed (37 °C) TrypLE, and rotated at 37 °C for 15 to 30 minutes until organoids were dissociated into single cells (confirmed via microscope). Cells were pelleted at 300 g for 3 minutes at 4 °C, and washed with cold PBS. Cells were passed through SP Bel-Art Flowmi 40 μm cell strainer and collected into a new protein LoBind tube.
30,000 cells were prepared as mentioned above and used for ATAC-seq as described previously (Buenrostro et al., 2013; Buenrostro et al., 2015) with slight modifications. Briefly, cells were centrifuged at 500 g for 5 minutes at 4°C and resuspended in ice-cold lysis buffer (10 mM Tris, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40). Cells were then centrifuged at 500 g for 10 minutes at 4°C. The isolated nuclear pellets were incubated with a 50 μl reaction of Tn5 Transposase (Illumina Tagment DNA Enzyme and Buffer Large Kit 20034198) for 30 minutes at 37°C. The transposed chromatin was purified with MinElute PCR purification kit (QIAGEN REF 28004), and PCR was amplified with high-fidelity 2X PCR Master Mix (New England Biolabs M0541). One-third of the maximum fluorescent intensity during a qPCR trial run was used to determine the additional cycles for library prep.
NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs).

value: Primary intestinal organoids

value: WT

value: 4 Gy IR on Day 4, 2 ng/mL TGFB1 on Day 6 for 24h


title: 202905570063_R05C01

status: Public on Feb 08 2023

type: genomic

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

description:
Methylation data from tumor sample
Sample 189

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
processed data file includes: Average Beta

molecule: genomic DNA

organism: Homo sapiens

source_name: PIS DICER1

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: tissue

value: tumor

tag: tissue preparation

value: FFPE


title: ATAC-seq_D11_IROrganoids_TGFB1_rep3

type: SRA

city: Nanjing

last: Chen

country: China

library_source: genomic

organism: Mus musculus

tag: strain

tag: genotype

tag: treatment


title: 202905570063_R02C01

description:
Methylation data from tumor sample
Sample 186


title: ATAC-seq_D11_IROrganoids_TGFB1_rep1


title: ATAC-seq_D11_IROrganoids_Vehicle_rep2

value: 4 Gy IR on Day 4, Vehicle on Day 6 for 24h


title: FL-1 dioestrus rep5

city: Bonn

first: Ulrich

last: Schweizer

state: NRW

address: Nussallee 11

department: Institut für Biochemie und Molekularbiologie

institute: Universitätsklinikum Bonn

library_source: transcriptomic

data_processing:
Sequence reads were trimmed with bbduk.sh following manufacturer's protocol. ref=/data/resources/polyA.fa.gz,/data/resources/truseq.fa.gz k=13 ktrim=r useshortkmers=t mink=5 qtrim=t trimq=10 minlength=20
Reads were aligned with STAR aligner following the manufacturer's protocol. STAR  --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1   --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20   --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD  --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
Numbers of sequences aligned to transcripts were counted with STAR aligner
Assembly: GRCm38.101
Supplementary files format and content: raw counts for each Sample; table with 2 columns in .tab format, column1: Ensemble Gene Accession Number, column2: corresponding counts

molecule: total RNA

source_name: granulosa cells

extract_protocol:
RNA: total RNA was extracted using TRIzol Reagent (Invitrogen) recommended by manufacturer.
Libraries were prepared with the QuantSeq 3’ mRNA-Seq Fw. Library Prep Kit (Lexogen) and sequenced to 10M raw reads on an Illumina HiSeq 2500 machine, following the manufacturer’s protocols.

value: granulosa cells

tag: developmental stage

value: diestrus


title: 202905570063_R01C01

description:
Methylation data from tumor sample
Sample 185


title: ATAC-seq_D11_IROrganoids_Vehicle_rep1


title: 205605880173_R07C01

description:
Methylation data from tumor sample
Sample 193

source_name: SLCT


title: duxa_2_input

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides and keeping only filtered reads longer than 15 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 104) with STAR 2.7.10a (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Aligned reads were filtered to remove: duplicates with Picard 2.27.1 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), spliced, multi-mapping, ribosomal, or mitochondrial reads.
Peak calling was performed with Macs version 3.0.0a6 with FDR < 0.1 (Zhang et al., Model-based Analysis of ChIP-Seq). Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
Peaks were unified to represent a common set of regions for all samples and counts were produced with bigWigAverageOverBed (UCSC Toolkit).
The raw count matrix was normalized with DESeq2 version 1.30.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
Peaks were annotated with the gene + promoter (TSS +- 5000 nt) with the largest overlap based on Ensembl release 104.
Assembly: hg38

extract_protocol:
DNA was purified using the NucleoSpin Gel and PCR Clean-up kit (Macherey-Nagel, 740609)
2-3ng of DNA was used as input for TruSeq ChIP Library Preparation Kit (Illumina) with following modifications. Instead of gel-based size selection before final PCR step, libraries were size selected by SPRI-bead based approach after final PCR with 18 cycles. In detail, samples were 1st cleaned up by 1x bead:DNA ratio to eliminate residuals from PCR reaction, followed by 2-sided-bead cleanup step with initially 0.6x bead:DNA ratio to exclude larger fragments. Supernatant was transferred to new tube and incubated with additional beads in 0.2x bead:DNA ratio for eliminating smaller fragments, like adapter and primer dimers. Bound DNA samples were washed with 80% ethanol, dried and resupended in TE buffer. Library integrity was verified with LabChip Gx Touch 24 (Perkin Elmer). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry with 1x75bp single end setup.

tag: cell line

tag: transfected with

value: plasmid encoding for a V5-epitope tagged DUXA

tag: chip antibody

value: none (input)


title: 205624630011_R02C01

description:
Methylation data from tumor sample
Sample 194


title: WT rep5

first: Dominik

last: Schaack

address: Im Neuenheimer Feld 420

institute: Heidelberg University Hospital

data_processing:
Sequenced reads were depleted from ribosomal reads using SortMeRNA v2.1b and trimmed for adaptor sequences and low-quality reads by Trimmomatic v0.36. Remaining reads were then mapped to Gencode Release M17 primary assembly reference genome utilizing STAR v2.6.0c considering read strand specificity.
After conversion to sorted binary alignment format (BAM) by SAMtools v1.8.3, sample-wise count tables were generated by htseq-count v0.9.1 with the “-s yes” option set. In case technical replicates were present, count tables were summarized per sample.
Assembly: Gencode Release M17 (GRCm38.p6)
Supplementary files format and content: Tab-delimited text files include raw count values for each gene

source_name: Whole lung tissue

extract_protocol:
RNA was extracted from whole lung tissue by RNeasy mini kit (Qiagen, Venlo, Netherlands)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole lung tissue

value: wild type


title: 202905570034_R06C01

description:
Methylation data from tumor sample
Sample 184


title: ATAC-seq_D7_IROrganoids_TGFB1_rep3


title: 202232290190_R02C01

description:
Methylation data from tumor sample
Sample 183


title: ATAC-seq_D7_IROrganoids_TGFB1_rep2


title: 202232290177_R05C01

description:
Methylation data from tumor sample
Sample 181


title: FL-1 dioestrus rep2


title: ATAC-seq_D7_IROrganoids_Vehicle_rep3


title: 202232290177_R04C01

description:
Methylation data from tumor sample
Sample 180


title: 202905570063_R03C01

description:
Methylation data from tumor sample
Sample 187


title: 202232290177_R03C01

description:
Methylation data from tumor sample
Sample 179


title: ATAC-seq_D7_IROrganoids_Vehicle_rep2


title: ATAC-seq_D11_IROrganoids_Vehicle_rep3


title: FL-1 oestrus rep4

value: estrus


title: RNA-seq of LHCN-M2 cells with inducible sDUX treated with doxycycline for 12 hrs replicate 2

city: Minneapolis

first: Micah

last: Gearhart

state: MN

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

department: Genetics, Cell Biology and Development

country: USA

institute: University of Minnesota

description: sDUX dox12hr rep2

data_processing:
Paired-end Illumina sequencing reads were trimmed with TrimGalore (0.6.0).
Transcript abundance was quantified using the human Gencode annotations (v38) using Salmon (v 1.9) with the GC-bias correction option.
Counts were imported into R (4.2.1) using tximport (v 1.24.0). Differentially expressed genes were identified with DESeq2 (v1.36.0).
Assembly: GRCh38
Supplementary files format and content: Excel table of normalized FPKMs and Raw Counts and rdata object containing annotated DESeq2 dataset.
Supplementary files format and content: NarrowPeak format for called peaks and bigWig files of merged coverage.

molecule: polyA RNA

source_name: cell line

growth_protocol: LHCN-M2 immortalized human myoblasts were cultured in F10 medium (HyClone) with 20% FBS (Peak Serum), 2-mercaptoethanol 1x (Gibco), 10-9 M dexamethasone (Sigma), 10 ng/mL bFGF (Peprotech), Glutamax (Gibco), and Penicillin/Streptomycin (P/S, Gibco) at 37°C and 5% CO2

extract_protocol:
NEB Next library kit
RNA-seq samples were extracted with Zymo RNA extraction kit.

treatment_protocol: Cells were mock treated or treated with doxycycline as indicated.

value: cell line

tag: cell type

value: immortalized human myoblast

tag: lentiviral _transduction

value: FUGW-rtTA and pSAM2-sDUX

value: 200 ng/mL doxycycline for 12 hrs


title: 202232290177_R02C01

description:
Methylation data from tumor sample
Sample 178


title: ATAC-seq_D7_IROrganoids_Vehicle_rep1

value: Primary intestinal organoids


title: RNA-seq of LHCN-M2 cells with inducible sDUX treated with doxycycline for 12 hrs replicate 1

description: sDUX dox12hr rep1


title: FL-1 dioestrus rep4


title: ATAC-seq_D7_Non-IROrganoids_TGFB1_rep3

value: WT

value: 2 ng/mL TGFB1 on Day 6 for 24h


title: 202093110053_R08C01

description:
Methylation data from tumor sample
Sample 177

value: tumor


title: FL-1 oestrus rep2


title: FL-1 dioestrus rep3


title: RNA-seq of LHCN-M2 cells with inducible sDUX mock treated for 12 hrs replicate 2

description: sDUX control rep2

value: Mock treatment 12 hrs


title: ATAC-seq_D7_Non-IROrganoids_TGFB1_rep2


title: FL-1 oestrus rep1


title: 202232290177_R07C01

description:
Methylation data from tumor sample
Sample 182

value: FFPE


title: ATAC-seq_D7_IROrganoids_TGFB1_rep1

value: 4 Gy IR on Day 4, 2 ng/mL TGFB1 on Day 6 for 24h


title: FL-1 dioestrus rep1

value: granulosa cells

value: diestrus


title: 202915470040_R04C01

description:
Methylation data from tumor sample
Sample 175


title: 203020900004_R05C01

description:
Methylation data from tumor sample
Sample 176


title: FL-1 oestrus rep5


title: ATAC-seq_D7_Non-IROrganoids_Vehicle_rep3

value: Vehicle on Day 6 for 24h


title: RNA-seq of LHCN-M2 cells with inducible sDUX mock treated for 12 hrs replicate 1

description: sDUX control rep1


title: 202915470040_R01C01

description:
Methylation data from tumor sample
Sample 173


title: Control dioestrus rep5

value: ctrl


title: RNA-seq of LHCN-M2 cells with inducible DUXB treated with doxycycline for 12 hrs replicate 2

description: DUXB dox12hr rep2

value: FUGW-rtTA and pSAM2-DUXB


title: Control dioestrus rep2


title: ATAC-seq_D7_Non-IROrganoids_Vehicle_rep2


title: 202905570034_R08C01

description:
Methylation data from tumor sample
Sample 172


title: 202915470040_R03C01

description:
Methylation data from tumor sample
Sample 174


title: FL-1 oestrus rep3

value: estrus


title: Control dioestrus rep3


title: RNA-seq of LHCN-M2 cells with inducible DUXB mock treated for 12 hrs replicate 2

description: DUXB control rep2

value: cell line


title: ATAC-seq_D7_Non-IROrganoids_TGFB1_rep1


title: ATAC-seq_D7_Non-IROrganoids_Vehicle_rep1


title: Control dioestrus rep4


title: RNA-seq of LHCN-M2 cells with inducible DUXB treated with doxycycline for 12 hrs replicate 1

description: DUXB dox12hr rep1

value: immortalized human myoblast


title: RNA-seq of LHCN-M2 cells with inducible DUXB mock treated for 12 hrs replicate 1

description: DUXB control rep1


title: Control dioestrus rep1


title: 202905570034_R07C01

description:
Methylation data from tumor sample
Sample 171


title: RNA-seq of LHCN-M2 cells with inducible DUXA-VP64 treated with doxycycline for 12 hrs replicate 2

description: DUXA-VP64 dox12hr rep2

value: FUGW-rtTA and pSAM2-DUXA-VP64


title: 202232290190_R07C01

description:
Methylation data from tumor sample
Sample 170


title: sciATACv2 nanowell-based preparation on mouse whole brain tissue

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

description: accessible chromatin DNA

library_source: genomic single cell

data_processing:
Barcode demultiplexing was performed using a 2-hamming distance match for each of the individual indexes followed by concatenation into a single error-corrected cell index read.
Reads were aligned to the mouse reference genome mm10 followed by rmeoval of duplicate reads, production of a frgaments bed file and loaded into ArchR
Assembly: mm10
Supplementary files format and content: ArchR Rds file containing fragments
Supplementary files format and content: Peaks called using macs2

source_name: whole brain

extract_protocol:
Nuclei were extracted by mincing tissue with a razor blade in ice cold using Nuclei Isolation Buffer (NIB) followed by dounce homogenization in NIB, then spinning down at 500xg, removing the supernatant and resuspending in NIB.
Single-cell combinatorial indexed ATAC-seq was performed by tagmenting nuclei in 96-well plates using uniquely barcoded tagmentaiton complexes followed by pooling tagmented nuclei from all wells, washing in NIB, then distributing nuclei to a 5,184 nanowell chip using the iCell8 instrument for indexed PCR amplificaiton, pooling, and sequencing.

value: whole brain


title: Control oestrus rep5


title: sciATACv1 nanowell-based preparation on mouse whole brain tissue

description: accessible chromatin DNA


title: RNA-seq of LHCN-M2 cells with inducible DUXA-VP64 mock treated for 12 hrs replicate 2

description: DUXA-VP64 control rep2


title: 202232290190_R01C01

description:
Methylation data from tumor sample
Sample 169


title: sciATACv3 nanowell-based preparation on mouse whole brain tissue

description: accessible chromatin DNA


title: Control oestrus rep3


title: Control oestrus rep4


title: Control oestrus rep2


title: 202232290177_R01C01

description:
Methylation data from tumor sample
Sample 166


title: Control oestrus rep1


title: RNA-seq of LHCN-M2 cells with inducible DUXA-VP64 mock treated for 12 hrs replicate 1

description: DUXA-VP64 control rep1


title: 202232290177_R06C01

description:
Methylation data from tumor sample
Sample 167


title: 202232290177_R08C01

description:
Methylation data from tumor sample
Sample 168


title: sh_B7-H3 (1), replicate 1, mRNA-derived cDNA & ADT-derived cDNA

city: Haining

first: Heng-Jia

last: Liu

state: Zhejiang

address: 718 East Haizhou Road

department: International Campus

institute: Zhejiang University - University of Edinburgh

description:
polyA RNA & protein
10x Genomics

library_source: transcriptomic single cell

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and ADT barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT  sequences were concatenated and treated as Custom library with default settings (v6.0.1) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v4.0.0 (cell and gene filtering, ADT identification, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: subcutaneous tumors

extract_protocol:
Gene and protein expression libraries were prepared using Chromium Next GEM Single-Cell 3’ Gel Bead and Library Kit (10x Genomics, V.3.1) according to the manufacturer's instructions
GEM-RT was performed in a 96-Deep Well Reaction Module: 53 oC for 45 min, 85 oC for 5 min; end at 4 oC. After RT, GEMs were broken down, then the cDNA and DNA barcodes were cleaned up with DynaBeads MyOne Silane Beads. cDNA was amplified with 96-Deep Well Reaction Module: 98 oC for 15 s, 67 oC for 20 s, and 72 oC for 1 min; 72 oC for 1 min; end at 4 oC. Followed by size selection to separate the amplified cDNA molecules for 3’ Gene Expression and Cell Surface Protein library construction SPRIselect Reagent.

value: subcutaneous tumors

value: Wild-type C57BL/6J

value: Tsc2-deficient 105K

tag: library type

value: mRNA

tag: antibodies/tags

value: TotalSeqA-0209 anti-mouse TCR Vγ1.1/Cr4,TotalSeqA-0204 anti-mouse CD28,TotalSeqA-0557 anti-mouse CD38,TotalSeqA-0109 anti-mouse CD16/32,TotalSeqA-0157 anti-mouse CD45.2,TotalSeqA-0904 anti-mouse CD31,TotalSeqA-0210 anti-mouse TCR Vγ3,TotalSeqA-0119 anti-mouse Siglec H,TotalSeqA-0811 anti-mouse CD317 (BST2, PDCA-1),TotalSeqA-0841 anti-mouse Ly49D,TotalSeqA-0852 anti-mouse CD226 (DNAM-1),TotalSeqA-0201 anti-mouse CD103,TotalSeqA-0877 anti-mouse JAML,TotalSeqA-0552 anti-mouse CD304 (Neuropilin-1),TotalSeqA-0564 anti-mouse Folate Receptor β (FR-β),TotalSeqA-0571 anti-mouse IgD,TotalSeqA-0849 anti-mouse CD80,TotalSeqA-0927 anti-mouse CD159a (NKG2AB6),TotalSeqA-0182 anti-mouse CD3,TotalSeqA-0194 anti-mouse CD137,TotalSeqA-1009 anti-mouse CD94,TotalSeqA-0015 anti-mouse Ly-6G,TotalSeqA-0851 anti-mouse CD1d (CD1.1, Ly-38),TotalSeqA-0905 anti-mouse CD107a (LAMP-1),TotalSeqA-0824 anti-mouse P2X7R,TotalSeqA-0448 anti-mouse CD204 (Scavenger R1),TotalSeqA-0596 anti-mouse ESAM,TotalSeqA-0848 anti-mouse TIGIT (Vstm3),TotalSeqA-0231 anti-mouse H-2Kb bound to SIINFEKL,TotalSeqA-0810 anti-mouse CD138 (Syndecan-1),TotalSeqA-0225 anti-mouse CD196 (CCR6),TotalSeqA-0184 anti-mouse CD335 (NKp46),TotalSeqA-0565 anti-mouse MERTK (Mer),TotalSeqA-0012 anti-mouse CD117 (c-kit),TotalSeqA-0910 anti-mouse/rat CD61,TotalSeqA-0250 anti-mouse/human KLRG1 (MAFA),TotalSeqA-0833 anti-mouse CD194 (CCR4),TotalSeqA-0903 anti-mouse CD40,TotalSeqA-0096 anti-mouse CD45,TotalSeqA-0075 anti-mouse CD90.2,TotalSeqA-0930 anti-mouse Ly108,TotalSeqA-1013 anti-mouse CD365 (Tim-1),TotalSeqA-0104 anti-mouse CD102,TotalSeqA-0839 anti-mouse Ly49H,TotalSeqA-0440 anti-mouse CD169/Siglec-1,TotalSeqA-0226 anti-mouse CD106,TotalSeqA-0879 anti-mouse IL-21 Receptor,TotalSeqA-0377 anti-mouse CD197 (CCR7),TotalSeqA-0836 anti-mouse DR3 (TNFRSF25),TotalSeqA-0437 anti-mouse/human CD207,TotalSeqA-0002 anti-mouse CD8a,TotalSeqA-0111 anti-mouse CD5,TotalSeqA-0825 anti-mouse CD371 (CLEC12A),TotalSeqA-0880 anti-mouse GITR-L,TotalSeqA-0227 anti-mouse CD122 (IL-2Rβ),TotalSeqA-0881 anti-mouse CD272 (BTLA),TotalSeqA-1019 anti-mouse CD215 (IL-15Rα),TotalSeqA-0882 anti-mouse PIR-A/B,TotalSeqA-0093 anti-mouse CD19,TotalSeqA-0847 anti-mouse CD278 (ICOS),TotalSeqA-0107 anti-mouse CD21/CD35 (CR2/CR1),TotalSeqA-1006 anti-mouse CD160,TotalSeqA-0556 anti-mouse CD370 (CLEC9A, DNGR1),TotalSeqA-0554 anti-mouse CD309 (VEGFR2, Flk-1),TotalSeqA-0178 anti-mouse CD45.1,TotalSeqA-0098 anti-mouse CD135,TotalSeqA-0198 anti-mouse CD127 (IL-7Rα),TotalSeqA-0113 anti-mouse CD93 (AA4.1, early B lineage),TotalSeqA-0105 anti-mouse CD115 (CSF-1R),TotalSeqA-0573 anti-mouse CD140a,TotalSeqA-0840 anti-mouse Ly49G,TotalSeqA-0108 anti-mouse CD23,TotalSeqA-0809 anti-mouse CD200R3,TotalSeqA-0114 anti-mouse F4/80,TotalSeqA-1016 anti-mouse CD157 (BST-1),TotalSeqA-0854 anti-mouse CD199 (CCR9),TotalSeqA-0835 anti-mouse CD314 (NKG2D),TotalSeqA-0228 anti-mouse CD183 (CXCR3),TotalSeqA-0130 anti-mouse Ly-6A/E (Sca-1),TotalSeqA-0837 anti-mouse IL-33Rα (IL1RL1, ST2),TotalSeqA-0193 anti-mouse CD357 (GITR),TotalSeqA-0834 anti-mouse CD39,TotalSeqA-0560 anti-mouse CD68,TotalSeqA-0214 anti-human/mouse integrin β7,TotalSeqA-0237 Rat IgG1, λ Isotype Ctrl,TotalSeqA-0449 anti-mouse CD326 (Ep-CAM),TotalSeqA-0200 anti-mouse CD86,TotalSeqA-0121 anti-mouse TCR γ/δ,TotalSeqA-0070 anti-human/mouse CD49f,TotalSeqA-1007 anti-mouse CD85k (gp49 Receptor),TotalSeqA-0197 anti-mouse CD69,TotalSeqA-0883 anti-mouse CD26 (DPP-4),TotalSeqA-0120 anti-mouse TCR β chain,TotalSeqA-0013 anti-mouse Ly-6C,TotalSeqA-0857 anti-mouse CD34,TotalSeqA-0555 anti-mouse CD36,TotalSeqA-0429 anti-mouse CD48,TotalSeqA-0561 anti-mouse CD79b (Igβ),TotalSeqA-0376 anti-mouse CD195 (CCR5),TotalSeqA-0884 anti-mouse DLL1,TotalSeqA-0885 anti-mouse CD270 (HVEM),TotalSeqA-0887 anti-mouse CD339 (Jagged 1),TotalSeqA-0442 anti-mouse Notch 1,TotalSeqA-0888 anti-mouse Notch 4,TotalSeqA-0850 anti-mouse CD49a,TotalSeqA-0421 anti-mouse CD49b,TotalSeqA-0570 anti-mouse/rat CD29,TotalSeqA-0241 Armenian Hamster IgG Isotype Ctrl,TotalSeqA-0916 anti-mouse CD124 (IL-4Rα),TotalSeqA-0073 anti-mouse/human CD44,TotalSeqA-0808 anti-mouse CCR3 (CD193),TotalSeqA-0235 anti-mouse TCR Vβ8.1, 8.2,TotalSeqA-0846 anti-mouse CD185 (CXCR5),TotalSeqA-0444 anti-mouse CXCR4,TotalSeqA-0191 anti-mouse/rat/human CD27,TotalSeqA-0212 anti-mouse CD24,TotalSeqA-0014 anti-mouse/human CD11b,TotalSeqA-0595 anti-mouse CD11a,TotalSeqA-0895 anti-mouse/human Mac-2 (Galectin-3),TotalSeqA-0117 anti-mouse I-A/I-E,TotalSeqA-0115 anti-mouse FcεRIα,TotalSeqA-0076 anti-mouse/human CD15 (SSEA-1),TotalSeqA-0381 anti-mouse Panendothelial Cell Antigen,TotalSeqA-0232 anti-mouse MAdCAM-1,TotalSeqA-0112 anti-mouse CD62L,TotalSeqA-1012 anti-mouse CD178 (FasL),TotalSeqA-0562 anti-mouse CD83,TotalSeqA-0190 anti-mouse CD274 (B7-H1, PD-L1),TotalSeqA-0812 anti-mouse CD105,TotalSeqA-0091 Mouse IgG2a, κ isotype Ctrl,TotalSeqA-0090 Mouse IgG1, κ isotype Ctrl,TotalSeqA-0092 Mouse IgG2b, κ isotype Ctrl,TotalSeqA-0354 anti-mouse  TCR Vβ5.1, 5.2,TotalSeqA-0875 anti-mouse TLR4 (CD284)/MD2 Complex,TotalSeqA-0443 anti-mouse CD41,TotalSeqA-0813 anti-mouse CD9,TotalSeqA-0925 anti-mouse CD253 (TRAIL),TotalSeqA-0106 anti-mouse CD11c,TotalSeqA-1010 anti-mouse CD205 (DEC-205),TotalSeqA-0559 anti-mouse CD63,TotalSeqA-0807 anti-mouse CD200R (OX2R),TotalSeqA-0380 anti-rat CD90/mouse CD90.1,TotalSeqA-0195 anti-mouse CD134 (OX-40),TotalSeqA-0079 anti-mouse CD200 (OX2),TotalSeqA-0827 anti-mouse CD22,TotalSeqA-0422 anti-mouse CD172a (SIRPα),TotalSeqA-0097 anti-mouse CD25,TotalSeqA-0118 anti-mouse NK-1.1,TotalSeqA-0078 anti-mouse CD49d,TotalSeqA-0103 anti-mouse/human CD45R/B220,TotalSeqA-0116 anti-mouse Ly-6G/Ly-6C (Gr-1),TotalSeqA-0439 anti-mouse CD201 (EPCR),TotalSeqA-0441 anti-mouse CD71,TotalSeqA-0558 anti-mouse CD55 (DAF),TotalSeqA-0924 anti-mouse CD252 (OX40 Ligand),TotalSeqA-0892 anti-mouse CD2,TotalSeqA-0001 anti-mouse CD4,TotalSeqA-0450 anti-mouse IgM,TotalSeqA-0229 anti-mouse/rat CD62P (P-selectin),TotalSeqA-0004 anti-mouse CD279 (PD-1),TotalSeqA-0003 anti-mouse CD366 (Tim-3),TotalSeqA-0567 anti-mouse Tim-4,TotalSeqA-1008 anti-mouse CD51,TotalSeqA-0236 Rat IgG1, κ isotype Ctrl,TotalSeqA-0238 Rat IgG2a, κ Isotype Ctrl,TotalSeqA-0240 Rat IgG2c, κ Isotype Ctrl,TotalSeqA-0095 Rat IgG2b, κ Isotype Ctrl,TotalSeqA-0110 anti-mouse CD43,TotalSeqA-0417 anti-mouse CD163,TotalSeqA-0415 anti-P2RY12,TotalSeqA-0431 anti-mouse CD170 (Siglec-F),TotalSeqA-0563 anti-mouse CX3CR1,TotalSeqA-0909 anti-mouse CD182 (CXCR2),TotalSeqA-0926 anti-mouse CD186 (CXCR6),TotalSeqA-0424 anti-mouse CD14,TotalSeqA-0889 anti-mouse CAT-1 (SLC7A1),TotalSeqA-0426 anti-mouse CD192 (CCR2),TotalSeqA-0907 anti-mouse CD198 (CCR8),TotalSeqA-0192 anti-mouse CD20,TotalSeqA-0917 anti-mouse CD95 (Fas),TotalSeqA-0203 anti-mouse CD150 (SLAM),TotalSeqA-0937 anti-mouse CD202b (Tie-2),TotalSeqA-0122 anti-mouse TER-119/Erythroid Cells,TotalSeqA-0890 anti-mouse 4-1BB Ligand (CD137L),TotalSeqA-0893 anti-mouse CD120b (TNF R Type II/p75),TotalSeqA-0876 anti-mouse CD300c/CD300d/MAIR-II,TotalSeqA-1011 anti-mouse CD155 (PVR),TotalSeqA-0077 anti-mouse CD73,TotalSeqA-0914 anti-mouse CD273 (B7-DC, PD-L2),TotalSeqA-0388 anti-mouse CD152,TotalSeqA-0211 anti-mouse TCR Vγ2,TotalSeqA-0566 anti-mouse CD301b,TotalSeqA-0891 anti-mouse ENPP1 (PC1),TotalSeqA-0842 anti-mouse Ly-49A,TotalSeqA-0074 anti-mouse CD54,TotalSeqA-0230 anti-mouse CD8b (Ly-3),TotalSeqA-0416 anti-mouse CD300LG (Nepmucin),TotalSeqA-0568 anti-mouse/rat XCR1,


title: sh_B7-H3 (1), replicate 2, mRNA-derived cDNA & ADT-derived cDNA

description:
polyA RNA & protein
10x Genomics


title: RNA-seq of LHCN-M2 cells with inducible DUXA treated with doxycycline for 12 hrs replicate 1

description: DUXA dox12hr rep1

value: FUGW-rtTA and pSAM2-DUXA

value: 200 ng/mL doxycycline for 12 hrs


title: 205624640018_R01C01

description:
Methylation data from tumor sample
Sample 165

source_name: AS

value: tumor

value: FFPE


title: RNA-seq of LHCN-M2 cells with inducible DUXA mock treated for 12 hrs replicate 2

description: DUXA control rep2

value: Mock treatment 12 hrs


title: sh_NC, replicate 2, mRNA-derived cDNA & ADT-derived cDNA

description:
polyA RNA & protein
10x Genomics


title: wk36_wt_1

first: Theresa

middle: A

last: Lusardi

state: Oregon

address: 2720 SW Moody Avenue

department: Knight Cancer Institute

institute: OHSU

description:
See readme.txt for barcodes
A single library prepararion was sequenced twice and combined using Cell Ranger

data_processing:
Sequencing from scRNAseq libraries was aligned using Cell Ranger
Expression matrices were processed using Seurat

source_name: Lineage negative bone marrow cells

extract_protocol: 10X scRNAseq libraries were prepared using the NextGem 3' V3.0 kit according to the manufacturers instructions

value: Lineage negative bone marrow cells

value: Asxl1 wild type

tag: timepoint

value: 6 months


title: Inflammatory Monocyte Tumor 15

city: Rochester

first: Scott

last: Gerber

state: NY

address: 601 Elmwood Ave

department: Microbiology and Immunology

institute: University of Rochester

data_processing:
Raw fastq files were prepared by trimming and filtering for quality using fastp-0.20.1, followed by the removal of the adapter sequences.
Files were aligned to mm39 mouse reference genome using STAR-2.7.6a aligner and converted to gene counts utilizing featurcounts-2.0.1 and mouse annotation M27.
DESeq2-1.28.1 package in R-4.0.2 was used to perform differential expression and normalization.
For low expression genes, ifcShrink was applied.
The DEGs were identified using a Wald Test statistic with adjusted p value threshold of =<0.05.
Assembly: mm39 (GRCm39)
Supplementary files format and content: deSeq2*.txt: Tab-delineated text files

source_name: Rectal Tumor

growth_protocol: MC38-luc tumor cells were grown in 2% MAT/P media supplemented with 2% Fetal Bovine Serum and 1% penicillin/streptomycin in vitro prior to tumor implantation into C57BL6 female mice.

extract_protocol:
Total RNA was extracted following the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s protocol.
Sequencing libraries were generated using 150pg of cDNA and the NexteraXT library preparation kit (Illumina) prior to being amplified and hybridized to the Illumina flow cell and sequenced using the NovaSeq 6000 sequencer (Illumina) on the S1 flow cell.

treatment_protocol: Tumors were treated with 5 Gy radiation for 5 consecutive days, in vivo.

value: Rectal Tumor

value: inflammatory monocyte

value: SCRT 5 Gy x 5 Fractions


title: wk36_mut_1

value: Asxl1 -/-


title: 203734290043_R03C01

description:
Methylation data from tumor sample
Sample 160

source_name: PINB


title: RNA-seq of LHCN-M2 cells with inducible DUXA mock treated for 12 hrs replicate 1

description: DUXA control rep1

value: cell line

value: immortalized human myoblast


title: RNA-seq of LHCN-M2 cells with inducible DUXA-VP64 treated with doxycycline for 12 hrs replicate 1

description: DUXA-VP64 dox12hr rep1

value: FUGW-rtTA and pSAM2-DUXA-VP64


title: wk04_mut_1

description:
See readme.txt for barcodes
A single library prepararion was sequenced twice and combined using Cell Ranger.  The 4 Week time point ADT/HTO and WT/KO are all in the same fastq files

value: 4 weeks


title: Inflammatory Monocyte Tumor 14


title: RNA-seq of LHCN-M2 cells with inducible DUXA treated with doxycycline for 12 hrs replicate 2

description: DUXA dox12hr rep2


title: 201868500126_R06C01

description:
Methylation data from tumor sample
Sample 159


title: RNA-seq of LHCN-M2 cells with inducible DUX4 treated with doxycycline for 12 hrs replicate 2

description: DUX4 dox12hr rep2

value: FUGW-rtTA and pSAM2-DUX4


title: 200772280002_R07C01

description:
Methylation data from tumor sample
Sample 157


title: Inflammatory Monocyte Tumor 13


title: wk04_wt_1


title: ChIRP-IP-rep3

city: Duarte

first: Zhen

state: CA

address: 1500 E Duarte Rd

department: DMRI

institute: City of Hope

data_processing:
Adaptors were timmed by Trimmomatic-0.39
Trimmed data was aligned to hg38 with Bowtie2(2.3.5.1)
MACS2 was used for Peak calling
Assembly: hg38

source_name: HUVEC

growth_protocol: HUVECs were grown following the manufacturer's protocol

extract_protocol:
Cells were fixed with 1% glutaraldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor (Diagenode).
The libraries were constructed using the KAPA HyperPrep kit following the user manual.
ChIRP-seq

treatment_protocol: HUVECs were cultured in complete medium and treated with adenovirus overexperssing Ad-LEENE. Cells were harvested after 3 days.

value: HUVEC

value: Human umbilical vein endothelial cells

tag: probes

value: LEENE-targeting probes (Biosearch Technologies)


title: Inflammatory Monocyte Tumor 12


title: 201904410016_R06C01

description:
Methylation data from tumor sample
Sample 149

value: tumor

value: Frozen


title: RNA-seq of LHCN-M2 cells with inducible DUX4 mock treated for 12 hrs replicate 2

description: DUX4 control rep2

value: Mock treatment 12 hrs


title: 200970160009_R06C01

description:
Methylation data from tumor sample
Sample 148

value: FFPE


title: Inflammatory Monocyte Tumor 11


title: HT_7d_Input_Rep1

data_processing:
none provided by the submitter
Assembly: hg38

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor (Diagenode).
The libraries were constructed using the KAPA HyperPrep kit following the user manual.

treatment_protocol: HUVECs were cultured in complete medium. For normal glucose, 25 mM mannitol was added. For high glucose, cells were treated with 25 mM glucose and 5 ng/ml TNFa. Cells were harvested after 3 and 7 days.

value: H3K27ac (Active motif #39133)


title: Inflammatory Monocyte Tumor 9

value: Rectal Tumor


title: RNA-seq of LHCN-M2 cells with inducible DUX4 treated with doxycycline for 12 hrs replicate 1

description: DUX4 dox12hr rep1

value: 200 ng/mL doxycycline for 12 hrs


title: HT_7d_Input_Rep2


title: Inflammatory Monocyte Tumor 8

value: inflammatory monocyte

value: SCRT 5 Gy x 5 Fractions


title: Sample 16_4C day5 WT rep3 - view point eSOX17

city: Berlin

first: Helene

last: Kretzmer

address: Ihnestraße 63

department: Genome Regulation

institute: Max Planck Institute for Molecular Genetics

data_processing:
library strategy: 4C library
cHi-C (Sample 1 - Sample 4):
Raw sequence reads of capture Hi-C (cHi-C) were mapped to the hg19 version of the human genome using BWA (v0.7.17-r1188) with parameters (mem -A 1 -B 4 -E 50 -L 0).
Mapped reads were further processed by HiCExplorer (v3.6) to remove duplicated reads and reads from dangling ends, self-circle, self-ligation and same fragments
4Cseq (Sample 5 - Sample 16):
The raw sequencing reads were trimmed by using cutadapt (--discard-untrimmed -e 0.05 -m 25) to remove primer sequences and restriction enzyme sequences. The reads without matching those sequences were removed from further analysis. The remaining reads were then mapped to the reference sequences GRCh37/hg19 by bowtie2 (default parameters). An iterative mapping procedure was performed. Specifically, the full-length reads were first mapped to genome. The unmapped reads were then cut by 5-nt from 3-prime each time until they were successfully mapped to genome. The final mapped reads were assigned to valid fragments. The fragment counts were then normalized by RPM (Reads Per Million) and smoothed by averaging the counts of the closest 5 fragments.
RNAseq (Sample 17 - Sample 40):
All RNAseq samples were pre-processed using cutadapt to remove adapter and trim low quality bases.
Reads were subsequently aligned against the human reference genome hg19 using STAR (parameter: outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --outSAMstrandField intronMotif --outSAMunmapped Within --quantMode GeneCounts).
Stringtie was used for calculation of strand-specific TPMs.
ChIPseq SOX17 (Sample 41 - Sample 52):
The ChIP-seq sequencing data as well as the control input sequencing were aligned to the human reference genome (hg19) using BWA mem using the default parameter.
GATK was used to obtain alignment metrics and remove duplicates.
Peaks were called using the MACS2 (2.1.2_dev) peakcall function using default parameters.
Oxford Nanopore cDNA seq (Sample 53):
Oxford Nanopore Technologies derived runs were processed using the Nanopype pipeline (v1.1.0) .
The basecaller Guppy (v4.0.11) was used with the r9.4.1 high-accuracy configuration. Quality filtering was disabled for any basecalling.
Base-called reads were aligned against the human reference genome hg19 using minimap2 (v2.10) with the Oxford Nanopore Technologies parameter preset for spliced alignments (-ax splice -uf -k14). Only unique alignments (-F 2304) are reported.
Genome_build: hg19
Supplementary_files_format_and_content: h5 of contact counts
Supplementary_files_format_and_content: bedGraph of contact RPM
Supplementary_files_format_and_content: tsv of TPM values
Supplementary_files_format_and_content: bigWig and BED of signal and peaks
Supplementary_files_format_and_content: BAM of read alignment

source_name: 4C seq of day5 endoderm derived WT cells

growth_protocol:
hiPSCs/ESCs culture:
ZIP13K2 hiPSCs were maintained in mTeSR1 (Stemcell Technologies, 85850) on pre-coated culture ware (1:100 diluted Matrigel (Corning, 354234) in KnockOut DMEM (Thermo Fisher Scientific, 10829-018)). Clump-based cell splitting was performed by incubating the cells in final 5 mM EDTA pH 8,0 (Thermo Fisher Scientific, 15575-038) in DPBS (Thermo Fisher Scientific, 14190250) 5 min at 37°C, 5% CO2. Single cell splitting was performed by incubating the cells with Accutase (Sigma-Aldrich, A6964) supplemented with 10 µM Y-27632 (Tocris, 1254) for 15 min at 37°C, 5% CO2. Cell counting was performed using a 1:1 diluted single-cell suspensions in 0,4% Trypan Blue staining-solution (Thermo Fisher Scientific, 15250061) on the Countess II automated cell-counter (Thermo Fisher Scientific). Wash-steps were performed by spinning cell-suspensions at 300 x g 5 min at room temperature (RT).
Endoderm derivation:
To guarantee high reproducibility, constant media-quality, and mTeSR1 compatibility, definitive endoderm differentiations were exclusively performed utilizing the STEMdiff Trilineage Endoderm Differentiation media (Stemcell Technologies, 05230). Single cell suspensions of mTeSR1 maintained ZIP13K2 hiPSCs were seeded into the respective culture formats according to the required cell-number as recommended by the manufacturer’s instructions. Media change using the STEMdiff Trilineage Endoderm Differentiation media was performed on a daily bases according to the manufacturer’s instructions. Cells were then collected at required timepoints by washing the plate with DPBS before single-cell dissociation was performed with Accutase for 15 min at 37°C, 5% CO2. Single cell suspensions of definitive endoderm (EN) differentiated cells were utilized for further downstream analysis (qPCR, Western Blot, FACS etc.).
Generation of pancreatic progenitors:
Pancreatic progenitor (PP) differentiation was performed as previously described 4 with minor changes. Briefly, single cell suspensions of ZIP13K2 hiPSCs (s. hiPS cell culture) were seeded at a density of 5 x 105 cells /cm2 in mTeSR1 supplemented with 10 µM Y-27632. After 24 h, culture medium was replaced with S1-media (Final 11,6 g/L MCDB131, Sigma Aldrich, M8537-1L; 2 mM D-+-Glucose, Sigma Aldrich, G7528-250G; 2,46 g/L NaHCO3, Sigma Aldrich, S5761-500G; 2% FAF-BSA, Proliant Biologicals, 68700-1; 1:50000 of 100 x ITS-X, Thermo Fisher Scientific, 51500056; 1 x GlutaMAX, Thermo Fisher Scientific, 35050-038; 0,25 mM ViatminC, Sigma-Aldrich, A4544-100G; 1% Pen-Strep, Thermo Fisher Scientific, 15140122) supplemented with final 100 ng/ml Activin-A (R&D Systems, 338-AC-01M) and 1,4 µg/ml CHIR99021 (Stemgent, 04-0004-10). The following 2 days, cells were cultured in S1-media supplemented with final 100 ng/ml Activin-A. Next, cells were cultured in S2-media (Final 11,6 g/L MCDB131; 2 mM D-+-Glucose; 1,23 g/L NaHCO3; 2% FAF-BSA; 1:50000 of 100 x ITS-X; 1 x GlutaMAX; 0,25 mM ViatminC; 1% Pen-Strep) supplemented with final 50 ng/ml KGF (Peprotech, 100-19-1MG) for 48 h. After these 48 h, cells were cultured in S3-media (Final 11,6 g/L MCDB131; 2 mM D-+-Glucose; 1,23 g/L NaHCO3; 2% FAF-BSA; 1:200 of 100 x ITS-X; 1 x GlutaMAX; 0,25 mM ViatminC; 1% Pen-Strep) supplemented with final 50 ng/ml KGF (Peprotech, 100-19-1MG), 200 nM LDN193189 (Sigma Aldrich, SML0559-5MG), 0,25 µM Sant-1 (Sigma Aldrich, S4572-5MG), 2 µM Retinoic Acid (Sigma Aldrich, R2625-50MG), 500 nM PDBU (Merck Millipore, 524390-5MG) and 10 µM Y-27632 for 24 h. Finally, cells were cultured in the previous S3-media composition w/o supplementation of LDN193189 for 24 h. Between daily media changes, cells were washed once with 1 x DPBS. Throughout the entire differentiation process, cells were cultured at 37°C, 5% CO2 in 100 µl media /cm2.

extract_protocol: Triplicates of either undifferentiated ZIP13K2 or ZIP13K2-derived EN cultures were collected as described previously. ZIP13K2-derived EN cultures were further quenched with MACS-buffer (Final DPBS, 2 mM EDTA (ThermoFisher Scientific), 0,5% BSA (Sigma-Aldrich)) to obtain a single cell suspension. CXCR4+ cell populations, were enriched using MicroBead Kit (Miltenyi Biotec) following the manufacturer’s instructions. Pre- and post-MACS enriched cell fractions of differentiated cultures were measured for CXCR4-APC signal on the FACS Aria II (Beckton Dickinson) to confirm the cell population purity. Circularized Chromosome Conformation Capture (4C) library preparation of undifferentiated, or differentiated CXCR4+ enriched cell populations was performed according to the Weintraub A.S. et al. protocol7. Briefly, NlaIII (New England Biolabs, R0125) was used as the primary cutter and DpnII (New England Biolabs, R0543) as a secondary cutter. Touchdown PCR on 4C libraries was performed using specific primer-pairs (s. primer list in Suppl. Table 3) for the respective view-points. Illumina sequencing libraries were then prepared and sequenced using 150 paired-end sequencing (300 cycles kit) on a HiSeq 4000 platform at a minimum of 10M fragments/ sample.

tag: cell line/type

value: ZIP13K2 - hiPSCs

tag: molecule subtype

value: Enriched fragmented gDNA


title: sh_NC, replicate 1, mRNA-derived cDNA & ADT-derived cDNA

description:
polyA RNA & protein
10x Genomics

tag: tissue

value: subcutaneous tumors

value: Wild-type C57BL/6J

value: Tsc2-deficient 105K

value: mRNA

value: TotalSeqA-0209 anti-mouse TCR Vγ1.1/Cr4,TotalSeqA-0204 anti-mouse CD28,TotalSeqA-0557 anti-mouse CD38,TotalSeqA-0109 anti-mouse CD16/32,TotalSeqA-0157 anti-mouse CD45.2,TotalSeqA-0904 anti-mouse CD31,TotalSeqA-0210 anti-mouse TCR Vγ3,TotalSeqA-0119 anti-mouse Siglec H,TotalSeqA-0811 anti-mouse CD317 (BST2, PDCA-1),TotalSeqA-0841 anti-mouse Ly49D,TotalSeqA-0852 anti-mouse CD226 (DNAM-1),TotalSeqA-0201 anti-mouse CD103,TotalSeqA-0877 anti-mouse JAML,TotalSeqA-0552 anti-mouse CD304 (Neuropilin-1),TotalSeqA-0564 anti-mouse Folate Receptor β (FR-β),TotalSeqA-0571 anti-mouse IgD,TotalSeqA-0849 anti-mouse CD80,TotalSeqA-0927 anti-mouse CD159a (NKG2AB6),TotalSeqA-0182 anti-mouse CD3,TotalSeqA-0194 anti-mouse CD137,TotalSeqA-1009 anti-mouse CD94,TotalSeqA-0015 anti-mouse Ly-6G,TotalSeqA-0851 anti-mouse CD1d (CD1.1, Ly-38),TotalSeqA-0905 anti-mouse CD107a (LAMP-1),TotalSeqA-0824 anti-mouse P2X7R,TotalSeqA-0448 anti-mouse CD204 (Scavenger R1),TotalSeqA-0596 anti-mouse ESAM,TotalSeqA-0848 anti-mouse TIGIT (Vstm3),TotalSeqA-0231 anti-mouse H-2Kb bound to SIINFEKL,TotalSeqA-0810 anti-mouse CD138 (Syndecan-1),TotalSeqA-0225 anti-mouse CD196 (CCR6),TotalSeqA-0184 anti-mouse CD335 (NKp46),TotalSeqA-0565 anti-mouse MERTK (Mer),TotalSeqA-0012 anti-mouse CD117 (c-kit),TotalSeqA-0910 anti-mouse/rat CD61,TotalSeqA-0250 anti-mouse/human KLRG1 (MAFA),TotalSeqA-0833 anti-mouse CD194 (CCR4),TotalSeqA-0903 anti-mouse CD40,TotalSeqA-0096 anti-mouse CD45,TotalSeqA-0075 anti-mouse CD90.2,TotalSeqA-0930 anti-mouse Ly108,TotalSeqA-1013 anti-mouse CD365 (Tim-1),TotalSeqA-0104 anti-mouse CD102,TotalSeqA-0839 anti-mouse Ly49H,TotalSeqA-0440 anti-mouse CD169/Siglec-1,TotalSeqA-0226 anti-mouse CD106,TotalSeqA-0879 anti-mouse IL-21 Receptor,TotalSeqA-0377 anti-mouse CD197 (CCR7),TotalSeqA-0836 anti-mouse DR3 (TNFRSF25),TotalSeqA-0437 anti-mouse/human CD207,TotalSeqA-0002 anti-mouse CD8a,TotalSeqA-0111 anti-mouse CD5,TotalSeqA-0825 anti-mouse CD371 (CLEC12A),TotalSeqA-0880 anti-mouse GITR-L,TotalSeqA-0227 anti-mouse CD122 (IL-2Rβ),TotalSeqA-0881 anti-mouse CD272 (BTLA),TotalSeqA-1019 anti-mouse CD215 (IL-15Rα),TotalSeqA-0882 anti-mouse PIR-A/B,TotalSeqA-0093 anti-mouse CD19,TotalSeqA-0847 anti-mouse CD278 (ICOS),TotalSeqA-0107 anti-mouse CD21/CD35 (CR2/CR1),TotalSeqA-1006 anti-mouse CD160,TotalSeqA-0556 anti-mouse CD370 (CLEC9A, DNGR1),TotalSeqA-0554 anti-mouse CD309 (VEGFR2, Flk-1),TotalSeqA-0178 anti-mouse CD45.1,TotalSeqA-0098 anti-mouse CD135,TotalSeqA-0198 anti-mouse CD127 (IL-7Rα),TotalSeqA-0113 anti-mouse CD93 (AA4.1, early B lineage),TotalSeqA-0105 anti-mouse CD115 (CSF-1R),TotalSeqA-0573 anti-mouse CD140a,TotalSeqA-0840 anti-mouse Ly49G,TotalSeqA-0108 anti-mouse CD23,TotalSeqA-0809 anti-mouse CD200R3,TotalSeqA-0114 anti-mouse F4/80,TotalSeqA-1016 anti-mouse CD157 (BST-1),TotalSeqA-0854 anti-mouse CD199 (CCR9),TotalSeqA-0835 anti-mouse CD314 (NKG2D),TotalSeqA-0228 anti-mouse CD183 (CXCR3),TotalSeqA-0130 anti-mouse Ly-6A/E (Sca-1),TotalSeqA-0837 anti-mouse IL-33Rα (IL1RL1, ST2),TotalSeqA-0193 anti-mouse CD357 (GITR),TotalSeqA-0834 anti-mouse CD39,TotalSeqA-0560 anti-mouse CD68,TotalSeqA-0214 anti-human/mouse integrin β7,TotalSeqA-0237 Rat IgG1, λ Isotype Ctrl,TotalSeqA-0449 anti-mouse CD326 (Ep-CAM),TotalSeqA-0200 anti-mouse CD86,TotalSeqA-0121 anti-mouse TCR γ/δ,TotalSeqA-0070 anti-human/mouse CD49f,TotalSeqA-1007 anti-mouse CD85k (gp49 Receptor),TotalSeqA-0197 anti-mouse CD69,TotalSeqA-0883 anti-mouse CD26 (DPP-4),TotalSeqA-0120 anti-mouse TCR β chain,TotalSeqA-0013 anti-mouse Ly-6C,TotalSeqA-0857 anti-mouse CD34,TotalSeqA-0555 anti-mouse CD36,TotalSeqA-0429 anti-mouse CD48,TotalSeqA-0561 anti-mouse CD79b (Igβ),TotalSeqA-0376 anti-mouse CD195 (CCR5),TotalSeqA-0884 anti-mouse DLL1,TotalSeqA-0885 anti-mouse CD270 (HVEM),TotalSeqA-0887 anti-mouse CD339 (Jagged 1),TotalSeqA-0442 anti-mouse Notch 1,TotalSeqA-0888 anti-mouse Notch 4,TotalSeqA-0850 anti-mouse CD49a,TotalSeqA-0421 anti-mouse CD49b,TotalSeqA-0570 anti-mouse/rat CD29,TotalSeqA-0241 Armenian Hamster IgG Isotype Ctrl,TotalSeqA-0916 anti-mouse CD124 (IL-4Rα),TotalSeqA-0073 anti-mouse/human CD44,TotalSeqA-0808 anti-mouse CCR3 (CD193),TotalSeqA-0235 anti-mouse TCR Vβ8.1, 8.2,TotalSeqA-0846 anti-mouse CD185 (CXCR5),TotalSeqA-0444 anti-mouse CXCR4,TotalSeqA-0191 anti-mouse/rat/human CD27,TotalSeqA-0212 anti-mouse CD24,TotalSeqA-0014 anti-mouse/human CD11b,TotalSeqA-0595 anti-mouse CD11a,TotalSeqA-0895 anti-mouse/human Mac-2 (Galectin-3),TotalSeqA-0117 anti-mouse I-A/I-E,TotalSeqA-0115 anti-mouse FcεRIα,TotalSeqA-0076 anti-mouse/human CD15 (SSEA-1),TotalSeqA-0381 anti-mouse Panendothelial Cell Antigen,TotalSeqA-0232 anti-mouse MAdCAM-1,TotalSeqA-0112 anti-mouse CD62L,TotalSeqA-1012 anti-mouse CD178 (FasL),TotalSeqA-0562 anti-mouse CD83,TotalSeqA-0190 anti-mouse CD274 (B7-H1, PD-L1),TotalSeqA-0812 anti-mouse CD105,TotalSeqA-0091 Mouse IgG2a, κ isotype Ctrl,TotalSeqA-0090 Mouse IgG1, κ isotype Ctrl,TotalSeqA-0092 Mouse IgG2b, κ isotype Ctrl,TotalSeqA-0354 anti-mouse  TCR Vβ5.1, 5.2,TotalSeqA-0875 anti-mouse TLR4 (CD284)/MD2 Complex,TotalSeqA-0443 anti-mouse CD41,TotalSeqA-0813 anti-mouse CD9,TotalSeqA-0925 anti-mouse CD253 (TRAIL),TotalSeqA-0106 anti-mouse CD11c,TotalSeqA-1010 anti-mouse CD205 (DEC-205),TotalSeqA-0559 anti-mouse CD63,TotalSeqA-0807 anti-mouse CD200R (OX2R),TotalSeqA-0380 anti-rat CD90/mouse CD90.1,TotalSeqA-0195 anti-mouse CD134 (OX-40),TotalSeqA-0079 anti-mouse CD200 (OX2),TotalSeqA-0827 anti-mouse CD22,TotalSeqA-0422 anti-mouse CD172a (SIRPα),TotalSeqA-0097 anti-mouse CD25,TotalSeqA-0118 anti-mouse NK-1.1,TotalSeqA-0078 anti-mouse CD49d,TotalSeqA-0103 anti-mouse/human CD45R/B220,TotalSeqA-0116 anti-mouse Ly-6G/Ly-6C (Gr-1),TotalSeqA-0439 anti-mouse CD201 (EPCR),TotalSeqA-0441 anti-mouse CD71,TotalSeqA-0558 anti-mouse CD55 (DAF),TotalSeqA-0924 anti-mouse CD252 (OX40 Ligand),TotalSeqA-0892 anti-mouse CD2,TotalSeqA-0001 anti-mouse CD4,TotalSeqA-0450 anti-mouse IgM,TotalSeqA-0229 anti-mouse/rat CD62P (P-selectin),TotalSeqA-0004 anti-mouse CD279 (PD-1),TotalSeqA-0003 anti-mouse CD366 (Tim-3),TotalSeqA-0567 anti-mouse Tim-4,TotalSeqA-1008 anti-mouse CD51,TotalSeqA-0236 Rat IgG1, κ isotype Ctrl,TotalSeqA-0238 Rat IgG2a, κ Isotype Ctrl,TotalSeqA-0240 Rat IgG2c, κ Isotype Ctrl,TotalSeqA-0095 Rat IgG2b, κ Isotype Ctrl,TotalSeqA-0110 anti-mouse CD43,TotalSeqA-0417 anti-mouse CD163,TotalSeqA-0415 anti-P2RY12,TotalSeqA-0431 anti-mouse CD170 (Siglec-F),TotalSeqA-0563 anti-mouse CX3CR1,TotalSeqA-0909 anti-mouse CD182 (CXCR2),TotalSeqA-0926 anti-mouse CD186 (CXCR6),TotalSeqA-0424 anti-mouse CD14,TotalSeqA-0889 anti-mouse CAT-1 (SLC7A1),TotalSeqA-0426 anti-mouse CD192 (CCR2),TotalSeqA-0907 anti-mouse CD198 (CCR8),TotalSeqA-0192 anti-mouse CD20,TotalSeqA-0917 anti-mouse CD95 (Fas),TotalSeqA-0203 anti-mouse CD150 (SLAM),TotalSeqA-0937 anti-mouse CD202b (Tie-2),TotalSeqA-0122 anti-mouse TER-119/Erythroid Cells,TotalSeqA-0890 anti-mouse 4-1BB Ligand (CD137L),TotalSeqA-0893 anti-mouse CD120b (TNF R Type II/p75),TotalSeqA-0876 anti-mouse CD300c/CD300d/MAIR-II,TotalSeqA-1011 anti-mouse CD155 (PVR),TotalSeqA-0077 anti-mouse CD73,TotalSeqA-0914 anti-mouse CD273 (B7-DC, PD-L2),TotalSeqA-0388 anti-mouse CD152,TotalSeqA-0211 anti-mouse TCR Vγ2,TotalSeqA-0566 anti-mouse CD301b,TotalSeqA-0891 anti-mouse ENPP1 (PC1),TotalSeqA-0842 anti-mouse Ly-49A,TotalSeqA-0074 anti-mouse CD54,TotalSeqA-0230 anti-mouse CD8b (Ly-3),TotalSeqA-0416 anti-mouse CD300LG (Nepmucin),TotalSeqA-0568 anti-mouse/rat XCR1,


title: HT_3d_Input_Rep2

value: HUVEC

value: Human umbilical vein endothelial cells


title: 200874540088_R01C01

description:
Methylation data from tumor sample
Sample 147

value: tumor

tag: tissue preparation


title: Inflammatory Monocyte Tumor 7


title: 200772300041_R04C01

description:
Methylation data from tumor sample
Sample 146


title: HT_3d_Input_Rep1


title: 200925700144_R01C01

description:
Methylation data from tumor sample
Sample 158


title: 200772280006_R07C01

description:
Methylation data from tumor sample
Sample 145


title: NM_Input_Rep2


title: Sample 14_4C day5 WT rep1 - view point eSOX17


title: RNA-seq of LHCN-M2 cells with inducible DUX4 mock treated for 12 hrs replicate 1

description: DUX4 control rep1

value: cell line

value: immortalized human myoblast

value: FUGW-rtTA and pSAM2-DUX4

value: Mock treatment 12 hrs


title: NM_Input_Rep1

value: H3K27ac (Active motif #39133)


title: HT_7d_IP_Rep2


title: Sample 13_4C day0 WT rep3 - view point eSOX17

source_name: 4C seq of day0 hiPSCs WT cells


title: Inflammatory Monocyte Tumor 5

value: Rectal Tumor

value: inflammatory monocyte

value: UT


title: Sample 12_4C day0 WT rep2 - view point eSOX17

value: ZIP13K2 - hiPSCs

value: Enriched fragmented gDNA


title: 200772280002_R04C01

description:
Methylation data from tumor sample
Sample 143

value: FFPE


title: Inflammatory Monocyte Tumor 6

value: SCRT 5 Gy x 5 Fractions


title: 200772280002_R06C01

description:
Methylation data from tumor sample
Sample 144


title: Sample 11_4C day0 WT rep1 - view point eSOX17


title: Inflammatory Monocyte Tumor 4


title: Inflammatory Monocyte Tumor 2


title: Sample 9_4C day5 WT rep2 - view point gene


title: HT_3d_IP_Rep2


title: Inflammatory Monocyte Tumor 3


title: HT_7d_IP_Rep1


title: Inflammatory Monocyte Tumor 1


title: HT_3d_IP_Rep1


title: Sample 10_4C day5 WT rep3 - view point gene


title: Granulocyte Tumor 14

value: granulocyte


title: NM_IP_Rep2


title: Sample 15_4C day5 WT rep2 - view point eSOX17


title: Sample 8_4C day5 WT rep1 - view point gene


title: Sample 7_4C day0 WT rep3 - view point gene


title: NM_IP_Rep1


title: Sample 6_4C day0 WT rep2 - view point gene


title: Granulocyte Tumor 12


title: Sample 5_4C day0 WT rep1 - view point gene


title: 127P_L6_3

city: Tulln an der Donau

first: Isabella

last: Zangl

address: Konrad Lorenz Str. 24

department: Insitute for Microbial Genetics

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna

data_processing:
Demultiplexing with bcl2fastq v2.20.0.422
Reads were mapped against reference with bowtie2
Read count was done with Rsubread (default settings)
normalization, filtering of the counted reads and differential gene expression was performed via DESeq2 (rows with <10 counts were filtered out; rest default settings)
Assembly: Candida glabrata CBS183
Supplementary files format and content: comma-limited file with results of differential gene expression (log2Foldchange), one file per comparison

organism: Nakaseomyces glabratus

growth_protocol: Candida glabrata isolates were grown in MRS medium at 37°C, 180rpm overnight. L. fermentum was grown at 37°C, 80rpm overnight.

extract_protocol:
Phenol Chloroform extraction was performed for RNA extraction
NEB mRNA Libraby preparation with poly-A enrichtment

treatment_protocol: Co-cultur: Candida glabrata (starting OD600 =0.1) and L. fermentum (starting OD600=0.05) were incubated in MRS medium at 37°C. 80 rpm for 10 hours; single culture: C. glabrata ( starting OD600=0.1) was inucabated at 37°C, 80rpm for 10 hours.

tag: strain

value: WT

value: co-culture


title: Granulocyte Tumor 11


title: 127P_L6_2

tag: genotype


title: Granulocyte Tumor 10

tag: treatment


title: 132P_L6_3


title: Granulocyte Tumor 6


title: Granulocyte Tumor 5


title: 127P_L6_1


title: Granulocyte Tumor 4


title: Granulocyte Tumor 7


title: 127P_ctrl_2

value: control


title: Granulocyte Tumor 3


title: Granulocyte Tumor 13


title: 132P_L6_2


title: Granulocyte Tumor 2


title: 132P_ctrl_3


title: 127P_ctrl_1


title: Granulocyte Tumor 1


title: 132P_L6_1


title: 132P_ctrl_2


title: TAM Tumor 15

value: macrophage


title: 205624640113_R04C01

description:
Methylation data from tumor sample
Sample 118

source_name: MG

value: tumor


title: 132P_ctrl_1


title: TAM Tumor 14


title: 122P_L6_2


title: 205624630179_R01C01

description:
Methylation data from tumor sample
Sample 105

source_name: MAS/ERMS


title: 205624630179_R02C01

description:
Methylation data from tumor sample
Sample 104


title: 205624630179_R07C01

description:
Methylation data from tumor sample
Sample 103


title: Bone endothelial cell - positive sample - patient77

type: RNA

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: 600 ng of labeled specimens were hybridized on Agilent Human Gene Expression v3 8x60K microarrays.

scan_protocol: After17 hours, slides were washed and scanned using the Agilent Scanner version C (G2505C, Agilent Technologies).

data_processing: Images were analyzed using the Feature Extraction software v10.7.3.1 (Agilent Technologies). Raw data elaboration was carried out with Bioconductor (www.bioconductor.org), using The LIMMA (LInear Models for Microarray Analysis) R package. Background correction was performed with the normexp method with an offset of 50, and quantile was used for the between-array normalization. The empirical Bayes method was used to compute a moderated t-statistics for two-class paired tests

source_name: Bone endothelial cell - positive sample

label_protocol: mRNA from 100 ng of totRNA was amplified, labeled with Cy3 and purified with columns.

growth_protocol: Primary endothelial cells (ECs) were isolated from leftover material (bone and muscle tissues) deriving from patients subjected to hip replacement surgery. ECs were isolated through enzymatic digestion followed by immunomagnetic selection. After a passage in culture with EGM-2 medium (Lonza), muscle (mECs) and bone (bECs) ECs were partly seeded for immunofluorescence on 96 well microplates (Ibidi), partly frozen for RNA extraction and a last aliquot was conserved for subsequent experiments.

extract_protocol: RNA was extracted following standard procedures (PureLink RNA Mini Kit, Ambion).

tag: subject status

tag: subject id

tag: tissue source

value: Bone

value: putative endothelial cells


title: Bone endothelial cell - positive sample - patient2

value: patients subjected to hip replacement surgery


title: BG2_L6_3


title: Bone endothelial cell - positive sample - patient4


title: 122P_L6_1


title: Muscle endothelial cell - positive sample - patient11

value: Muscle


title: TAM Tumor 12

value: Rectal Tumor


title: TAM Tumor 13


title: TAM Tumor 11


title: 205624630180_R04C01

description:
Methylation data from tumor sample
Sample 102


title: Muscle endothelial cell - positive sample - patient2


title: Muscle endothelial cell - positive sample - patient3


title: TAM Tumor 10


title: Muscle endothelial cell - positive sample - patient8


title: 205624630179_R05C01

description:
Methylation data from tumor sample
Sample 101


title: Bone endothelial cell - negative sample - patient9

source_name: Bone endothelial cell - negative sample


title: Muscle endothelial cell - negative sample - patient9


title: Bone endothelial cell - positive sample - patient33


title: BG2_L6_1


title: Bone endothelial cell - positive sample - patient9


title: Muscle endothelial cell - positive sample - patient9


title: Muscle endothelial cell - negative sample - patient25


title: TAM Tumor 9


title: Muscle endothelial cell - positive sample - patient25


title: 122P_ctrl_3


title: 205624630179_R06C01

description:
Methylation data from tumor sample
Sample 100


title: 205624630136_R02C01

description:
Methylation data from tumor sample
Sample 98

source_name: MAS


title: 205624630136_R03C01

description:
Methylation data from tumor sample
Sample 99


title: TAM Tumor 7


title: 122P_ctrl_1


title: 122P_ctrl_2


title: TAM Tumor 8


title: BG2_ctrl_3


title: TAM Tumor 6


title: 205624630136_R05C01

description:
Methylation data from tumor sample
Sample 97


title: TAM Tumor 5


title: BG2_ctrl_2


title: 202259350187_R05C01

description:
Methylation data from tumor sample
Sample 96


title: Bone endothelial cell - negative sample - patient25


title: 205624630144_R08C01

description:
Methylation data from tumor sample
Sample 95


title: BG2_ctrl_1


title: TAM Tumor 4


title: 205624630144_R07C01

description:
Methylation data from tumor sample
Sample 94


title: TAM Tumor 2


title: 205624630144_R06C01

description:
Methylation data from tumor sample
Sample 93


title: 205624630144_R04C01

description:
Methylation data from tumor sample
Sample 92


title: TAM Tumor 1


title: Muscle endothelial cell - negative sample - patient10


title: Muscle endothelial cell - positive sample - patient10


title: Bone endothelial cell - positive sample - patient25


title: Bone endothelial cell - negative sample - patient10


title: Bone endothelial cell - negative sample - patient7


title: Muscle endothelial cell - negative sample - patient7


title: 205624630144_R03C01

description:
Methylation data from tumor sample
Sample 91


title: primEB cells, WT_CTRL, differentiation medium, rep5

city: Basel

first: Jonathan

last: Seguin

address: Spitalstrasse 33

country: Switzerland

institute: UKBB-DBM

description:
WT_CTRL_peaks.broadPeak.gz
WT_CTRL_logFC1.5_fdr0.05_broadPeak.bed.gz

data_processing:
Paired-end reads were mapped to the mouse genome assembly, version mm10, with bowtie2 (version 2.3.4.2)73 using the option '--wrapper basic-0 --maxins 2000 --no-mixed --no-discordant --local'.
The output was sorted and indexed with samtools (version 1.7). Picard markDuplicates (version 2.9.2) was used to collapse samples run on different sequencing lanes.
Coverage tracks per sample were generated by tiling the genome in 20bp windows, counting overlapping reads per window using the function bamCount from the bioconductor package bamsignals (bioconductor version 3.6) and exporting these window counts in bigWig format using the export function of the bioconductor package rtracklayer.
Regions of accessible chromatin were called with macs275 (version 2.1.2) using the option '-f BAM -g 2652783500 --nomodel --shift -100 --extsize 200 --broad --keep-dup all --qvalue 0.05'.
The resulting peak lists of ATAC-seq were cleaned from peaks called in mitochondria and ENCODE blacklist regions. A log-fold-change > 1.5 and FDR<0.05 filter was applied.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: broadPeak, bed (filtered peaks)

source_name: fetal liver

growth_protocol: WT erythroblasts from fetuses from three different pregnant mice were transduced with NFIA-ETO2. After sorting, cells were cultured in maintenance and differentiation medium for 24h. 75x105 cells were washed two times with cold PBS and spun down at 500g for 5 min at 4°C.

extract_protocol:
Purified transposed DNA was eluted in 12μl of elution buffer (10mM Tris-HCl, pH=8). Transposed fragments were amplified using 2X KAPA HiFi HOTSTART Ready mix (Roche) with modified primers72. PCR purification was performed using Qiagen PCR purification kit (Cat no. 28104) according to the manufacturer’s protocol.
Libraries were quality-checked on the Fragment Analyzer (Advanced Analytical, Ames, IA, USA) using the High Sensitivity NGS Fragment Analysis Kit (Cat# DNF-474, Advanced Analytical). AMPure XP beads (Beckman Coulter) Double Size Selection (1.2-0.8x) was performed to enrich for 150-400bp library fragments before mixing library pools for sequencing. Before sequencing with the NovaSeq, the pool of libraries was treated with Free Adapter Blocking Reagent (Illumina) according to manufacturer's specifications.

treatment_protocol: 75x105 cells were washed two times with cold PBS and spun down at 500g for 5 min at 4°C. Supernatant was removed using two pipetting steps. Transposase mixture was prepared (25μl 2x TD buffer, 2.5μl TDE1, 22μl H2O, 0.5μl Digitonin) (FC-121-1030, Illumina; G9441, Promega) and added directly to the pellet followed by disrupting by pipetting. Samples were incubated at 37°C for 30min.

value: fetal liver

value: primary erythroblasts

tag: age


title: 205624630144_R02C01

description:
Methylation data from tumor sample
Sample 90


title: nlp2-3_nlp7-1_Shoot_rep_3

city: Versailles

first: Mickael

last: Durand

address: Route de St-Cyr (RD10)

department: IJPB

country: France

institute: INRAE

data_processing:
Read mapping: Paired-end reads aligned to tair10 genome assembly using HISAT2
Counting : HTSeq
Assembly: tair10
Supplementary files format and content: Genes read count in .xls format
Supplementary files format and content: Genes FPKM in .xls format

organism: Arabidopsis thaliana

source_name: 42 day-old plants

growth_protocol: Seeds were stratified for 3 days at 4°C in the dark and then grown on sand culture supplemented with nutrient solutions (Loudet et al., 2003) containing 5 mM nitrate (non-limiting nitrate supply) in short day photoperiod with an 8-h light/16-h dark cycle at 21°C/18°C, respectively, 65% relative humidity, and a constant 150 μmol m–2 s–1 irradiation.

extract_protocol:
Total RNA was extracted from root and rosette using the RNeasy plant minikit (QIAGEN) including a DNase treatment according to manufacturer’s instructions.
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Co., LTD (Beijing, China). Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions.

tag: ecotype

value: nlp2-3 nlp7-1

value: Shoot


title: TAM Tumor 3

tag: cell type

value: UT


title: 205624630144_R01C01

description:
Methylation data from tumor sample
Sample 89

value: FFPE


title: primEB cells, WT_NFIA-ETO2, differentiation medium, rep4

description:
WT_NE_peaks.broadPeak.gz
WT_NE_logFC1.5_fdr0.05_broadPeak.bed.gz


title: mouse lung adenocaricnoma, KPY-Setd2KO, rep 8

city: Philadelphia

first: Amy

middle: C

last: Gladstein

state: Pennsylvania

address: 421 Curie Blvd Rm 729

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Sequencing libraries were prepared on the Illumina NeoPrep and subjected to 75-bp single-end sequencing on the Illumina NextSeq 500 platform.
Fastq files for each sample were aligned against the mouse genome, build GRCm38.p5, using Salmon (v0.8.2)
Assembly: GRCm38.p5
Supplementary files format and content: Excel spreadsheet with differentially expressed genes between KPY-Ctrl and KPY-Setd2KO
Supplementary files format and content: comma separated values file including raw counts for each sample

source_name: Lung

extract_protocol:
RNA was isolated from cell lines using the Rneasy Mini Kit (Qiagen) per manufacturer's instructions.
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) per manufacturer's instructions.

value: Lung

value: Lung adenocarcinoma


title: mouse lung adenocaricnoma, KPY-Setd2KO, rep 5


title: mouse lung adenocaricnoma, KPY-Setd2KO, rep 6


title: mouse lung adenocaricnoma, KPY-Setd2KO, rep 7


title: mouse lung adenocaricnoma, KPY-Setd2KO, rep 4


title: mouse lung adenocaricnoma, KPY-Setd2KO, rep 3


title: primEB cells, WT_NFIA-ETO2, differentiation medium, rep5


title: nlp2-3_nlp7-1_Shoot_rep_1


title: Bone endothelial cell - positive sample - patient10


title: 205624630138_R08C01

description:
Methylation data from tumor sample
Sample 88

data_processing:
Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta
processed data file includes: Average Beta

extract_protocol: Illumina protocol


title: mouse lung adenocaricnoma, KPY-Setd2KO, rep 2


title: nlp2-3_nlp7-1_Root_rep_3

value: Root


title: Muscle endothelial cell - positive sample - patient7


title: CNO_3

first: Dijun

state: Jiangsu

address: Xianlin

department: Life Sciences

institute: Nanjing University

data_processing:
Illumina Casava1.7 software used for basecalling.
sequenced reads were trimmed to remove adapter and low quality reads with Tim Galore v 0.6.6 program
clean reads were separately aligned to reference genome with orientation mode using the HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances.
Genome_build: mm10

source_name: Brain

extract_protocol:
Brain were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CNO-induced epileptic  model

value: Treated with CNO


title: 205624630138_R07C01

first: Daniel

address: Im Neuenheimer Feld 224

institute: University Hospital Heidelberg, Intitute of Pathology

description:
Methylation data from tumor sample
Sample 87

value: tumor


title: mouse lung adenocaricnoma, KPY-Setd2KO, rep 1


title: nlp2-3_nlp7-1_Root_rep_2


title: 205624630138_R06C01

description:
Methylation data from tumor sample
Sample 86


title: mouse lung adenocaricnoma, KPY-Ctrl, rep 6

value: KPY-Ctrl


title: CNO_2


title: nlp2-3_nlp7-1_Root_rep_1


title: CNO_1


title: 205624630138_R05C01

description:
Methylation data from tumor sample
Sample 85


title: mouse lung adenocaricnoma, KPY-Ctrl, rep 5


title: primEB cells, WT_CTRL, differentiation medium, rep4


title: Bone endothelial cell - positive sample - patient7

value: Bone

value: putative endothelial cells


title: 205624630138_R03C01

description:
Methylation data from tumor sample
Sample 84


title: mouse lung adenocaricnoma, KPY-Ctrl, rep 4


title: 205624630138_R02C01

description:
Methylation data from tumor sample
Sample 83


title: nlp7-1_Shoot_rep_2


title: CNO_Control_3

value: Untreated


title: mouse lung adenocaricnoma, KPY-Ctrl, rep 3


title: CNO_Control_2


title: nlp7-1_Shoot_rep_1


title: CNO_Control_1

value: CNO-induced epileptic model


title: 205624630138_R01C01

description:
Methylation data from tumor sample
Sample 82


title: mouse lung adenocaricnoma, KPY-Ctrl, rep 2


title: nlp7-1_Root_rep_3


title: mouse lung adenocaricnoma, KPY-Ctrl, rep 1


title: KD_6

value: KA-induced TLE model

value: A2aR knock down and treated with KA


title: 205624630136_R08C01

description:
Methylation data from tumor sample
Sample 81


title: KD_5


title: 205624630136_R07C01

description:
Methylation data from tumor sample
Sample 80


title: mouse lung adenocaricnoma, K-Setd2KO, rep 4

data_processing:
Sequencing libraries were prepared on the Illumina NeoPrep and subjected to 75-bp paired-end sequencing on the Illumina NextSeq 500 platform.
Fastq files for each sample were aligned against the mouse genome, build GRCm38.p4, using the STAR aligner (v2.5.2b).
FeatureCounts (v1.5.0-p1) was used to quantify alignments against the mouse genomic annotations from Gencode (vM11).
Assembly: GRCm38.p4
Supplementary files format and content: Excel spreadsheet with differentially expressed genes between K-Ctrl and K-Setd2
Supplementary files format and content: tab delimited text file including raw counts for each sample


title: nlp7-1_Root_rep_1


title: KD_4


title: nlp7-1_Shoot_rep_3


title: nlp2-3_Shoot_rep_3


title: mouse lung adenocaricnoma, K-Setd2KO, rep 2


title: mouse lung adenocaricnoma, K-Setd2KO, rep 3


title: nlp2-3_Shoot_rep_2


title: 203989100004_R08C01

description:
Methylation data from tumor sample
Sample 76


title: nlp2-3_Shoot_rep_1


title: mouse lung adenocaricnoma, K-Setd2KO, rep 1


title: mouse lung adenocaricnoma, K-Ctrl, rep 4

value: K-Ctrl


title: nlp2-3_Root_rep_3


title: APOE_KA_2

value: APOE knock out and treated with KA


title: APOE_KA_1


title: 203989100006_R02C01

description:
Methylation data from tumor sample
Sample 78


title: nlp2-3_Root_rep_2


title: nlp7-1_Root_rep_2


title: 205624630138_R04C01

description:
Methylation data from tumor sample
Sample 75


title: mouse lung adenocaricnoma, K-Ctrl, rep 2


title: mouse lung adenocaricnoma, K-Ctrl, rep 3


title: 203989100006_R04C01

description:
Methylation data from tumor sample
Sample 74

source_name: ERMS


title: 205624630136_R06C01

description:
Methylation data from tumor sample
Sample 79


title: KA-induced TLE model_2

value: Treated with KA


title: APOE_KA_3


title: nlp2-2_Shoot_rep_3

value: Shoot


title: mouse lung adenocaricnoma, K-Ctrl, rep 1

value: Lung


title: KA-induced TLE model_1


title: 203989100005_R08C01

description:
Methylation data from tumor sample
Sample 77

value: FFPE


title: nlp2-2_Shoot_rep_2


title: KA-induced TLE model_4


title: WT_3


title: WT_2


title: KA-induced TLE model_3


title: nlp2-2_Root_rep_3

value: Root


title: 205624640137_R01C01

description:
Methylation data from tumor sample
Sample 70

source_name: PPB II


title: 205624640137_R04C01

description:
Methylation data from tumor sample
Sample 71


title: BG2_L6_2

value: WT

value: co-culture


title: WT_1


title: sfh197f3

city: Brisbane

first: Jasmin

last: Straube

state: QLD

address: 300 Herston Rd

country: Australia

institute: QIMR Berghofer

data_processing:
Reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to the GRCm38 assembly using the gene, transcript, and exon features of Ensembl (release 67) gene model. Expression was estimated using RSEM (version 1.2.30).
Transcripts with zero read counts across all samples were removed prior analysis. Normalisation of RSEM expected read counts was performed by dividing by million reads mapped to generate counts per million (CPM), followed by the trimmed mean of M-values (TMM) method from the edgeR package.
Assembly: GRCm38
Supplementary files format and content: comma-delimited text files include RSEM expected read count values for each sample

source_name: Spleen

extract_protocol:
RNA from Lin-Kit+ spleen cells of leukemic Scl-CreERT:Flt3ITD/ITD C57BL/6J and aged matched controls was isolated using Picopure kit.
cDNA libraries were prepared using the NEBNext Ultra RNA Library Prep kit with the polyA selection module (New England Biolabs) and purified with AMPure beads (Agilent). Libraries were quantified with the KAPA Library Quantification Kit for Illumina (Kapa Biosystems) and pooled. Sequencing was performed on the Illumina NextSeq 500/550 Sequencer High Output mode (1 × 75 bp).

value: Spleen

value: Lineage- Sca1- Kit+

value: tamoxifen

tag: disease state

value: AML


title: sfh197f5


title: sfh212f4


title: H_KA_3


title: nlp2-2_Root_rep_2


title: 205624640167_R08C01

last: Schrimpf

description:
Methylation data from tumor sample
Sample 68

source_name: PPB I

value: tumor


title: 205624630010_R06C01

description:
Methylation data from tumor sample
Sample 73

source_name: SLCT


title: sfh198m5


title: fh2733

value: Healthy


title: nlp2-3_Root_rep_1


title: H_KA_2

last: Chen

value: KA-induced TLE model


title: 205624640167_R05C01

description:
Methylation data from tumor sample
Sample 67


title: fh212f2


title: nlp2-2_Root_rep_1


title: 205624640167_R07C01

description:
Methylation data from tumor sample
Sample 72

source_name: PPB Ir


title: H_KA_1


title: Col-4_Shoot_rep_3


title: nlp2-2_Shoot_rep_1


title: 205624640167_R01C01

description:
Methylation data from tumor sample
Sample 66


title: fh198m2


title: H_Normal_3

value: Untreated


title: 205624640137_R02C01

description:
Methylation data from tumor sample
Sample 69


title: nlp2-3_nlp7-1_Shoot_rep_2

value: nlp2-3 nlp7-1


title: Col-4_Shoot_rep_1


title: fh175f1


title: 205624640167_R02C01

description:
Methylation data from tumor sample
Sample 65


title: H_Normal_2


title: H_Normal_1


title: Col-4_Root_rep_2


title: Col-4_Root_rep_3


title: SPLV2

data_processing:
Reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to the GRCm38 assembly using the gene, transcript, and exon features of Ensembl (release 67) gene model. Expression was estimated using RSEM (version 1.2.30).
Transcripts with zero read counts across all samples were removed prior analysis. Normalisation of RSEM expected read counts was performed by dividing by million reads mapped to generate counts per million (CPM), followed by the trimmed mean of M-values (TMM) method from the edgeR package.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RSEM expected read count values for each sample

source_name: spleen

extract_protocol:
RNA from Lin-Kit+CD45.2 spleen cells of leukemic Scl-CreERT:Flt3ITD/ITD C57BL/6J 4 hours after JQ1 or vehicle treatment was isolated using Picopure kit.
cDNA libraries were prepared using the NEBNext Ultra RNA Library Prep kit with the polyA selection module (New England Biolabs) and purified with AMPure beads (Agilent). Libraries were quantified with the KAPA Library Quantification Kit for Illumina (Kapa Biosystems) and pooled. Sequencing was performed on the Illumina NextSeq 500/550 Sequencer High Output mode (1 × 75 bp).

value: spleen

value: Lineage - Kit+ spleen

value: vehicle


title: 205624650042_R01C01

description:
Methylation data from tumor sample
Sample 63

source_name: NCMH


title: mix_PA_A_3

source_name: astrocyte

value: APOE KO astrocyte

value: Treated with palmitic acid


title: 205624640173_R08C01

description:
Methylation data from tumor sample
Sample 62

value: FFPE


title: SPLV1


title: mix_APOE_3


title: SPLJ8


title: Col-0_Shoot_rep_3

value: WT

value: Shoot


title: SPLJ7


title: 205624630179_R04C01

description:
Methylation data from tumor sample
Sample 60

source_name: MAS/ERMS


title: Col-0_Shoot_rep_2


title: Col-4_Shoot_rep_2


title: OA_2

value: Wild type astrocyte

value: Treated with oleic acid


title: SPLJ11


title: 205624640018_R05C01

description:
Methylation data from tumor sample
Sample 59


title: 205624640137_R03C01

description:
Methylation data from tumor sample
Sample 64


title: SPLV5


title: Col-0_Shoot_rep_1


title: OA_1


title: Col-0_Root_rep_3

value: Root


title: PA_A_2


title: 205624630174_R07C01

description:
Methylation data from tumor sample
Sample 58


title: SFH_1545

source_name: Bone marrow

extract_protocol:
RNA from BM LSKs of Scl-CreERT:Flt3ITD/ITD C57BL/6J and controls was isolated using Picopure kit.
cDNA libraries were prepared using the NEBNext Ultra RNA Library Prep kit with the polyA selection module (New England Biolabs) and purified with AMPure beads (Agilent). Libraries were quantified with the KAPA Library Quantification Kit for Illumina (Kapa Biosystems) and pooled. Sequencing was performed on the Illumina NextSeq 500/550 Sequencer High Output mode (1 × 75 bp).

value: Bone marrow

value: Lineage- Sca1+ Kit+

value: tamoxifen


title: PA_A_1


title: 205624640113_R01C01

description:
Methylation data from tumor sample
Sample 56

source_name: CN

value: tumor


title: Col-0_Root_rep_2


title: Col-4_Root_rep_1


title: SFH_1372

value: Healthy


title: SFH_1631


title: Col-0_Root_rep_1


title: OA_3


title: SF_1536


title: PA_2


title: 205624640075_R07C01

description:
Methylation data from tumor sample
Sample 54


title: SF_1630


title: 205624640113_R02C01

description:
Methylation data from tumor sample
Sample 57


title: PA_1


title: 205624640075_R06C01

description:
Methylation data from tumor sample
Sample 53


title: 205624640075_R08C01

description:
Methylation data from tumor sample
Sample 55


title: APOE_2

value: Untreated


title: 204788470021_R08C01

description:
Methylation data from tumor sample
Sample 52


title: S_1490

value: Scl-CreERT


title: S_1494


title: 205624640136_R02C01

description:
Methylation data from tumor sample
Sample 61

source_name: MG


title: APOE_1


title: PA_3


title: FH_1450


title: CFH_1451


title: KA_A_3

value: Treated with neuronal conditional medium


title: 202259350187_R06C01

description:
Methylation data from tumor sample
Sample 50

source_name: LGESS


title: laeA deletion, 24 hr rep 3

city: Madison

first: Heungyun

middle: Harrison

last: Moon

state: WI

address: 1550 Linden drive

department: Bacteriology

institute: University of Wisconsin-Madison

data_processing:
Mapping of the clean reads to the genome was carried out using Hisat2 version 2.1.
Gene expression level was processed using FeatureCounts version 1.5.0.
DESeq2 version 1.6.3 was used to determine significantly differentially expressed genes (p-value < 0.05 and more than two-fold changes)
Assembly: GCF_000149205.2
Supplementary files format and content: tab-delimited text files include readcount values for each sample

organism: Aspergillus nidulans

source_name: Vegetatively grown cells

growth_protocol: The fungal strains were inoculated into liquid or solid 1% glucose minimal medium (GMM) with appropriate supplements and incubated at 37 °C. To collect vegetatively growing cells (Vege), 5×105 conidia/ml were inoculated into 100 ml liquid GMM and incubated for 24 h at 37 °C, 220 rpm in the dark.

extract_protocol:
Total RNA was isolated using RNeasy Plant Mini Kit (Qiagen) with manufacturer's instructions.
A strand-specific library was prepared using an Illumina TruSeq strand-specific RNA sample preparation system.

value: Vegetatively grown cells

value: laeA deletion


title: veA deletion, 24 hr rep 3

value: veA deletion


title: laeA deletion, 24 hr rep 2


title: KA_A_2

value: APOE KO astrocyte


title: veA deletion, 24 hr rep 1


title: CF_1448


title: 202176290083_R07C01

city: Heidelberg

description:
Methylation data from tumor sample
Sample 49

value: FFPE


title: 202163110077_R04C01

description:
Methylation data from tumor sample
Sample 48


title: KA_A_1

city: Nanjing


title: CF_1382


title: wild-type, 24 hr rep 3

value: wild-type


title: wild-type, 24 hr rep 2


title: OA_A_3


title: laeA deletion, 24 hr rep 1


title: 205624640074_R03C01

description:
Methylation data from tumor sample
Sample 47


title: S_sample235

data_processing:
Reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to the GRCm38 assembly using the gene, transcript, and exon features of Ensembl (release 67) gene model. Expression was estimated using RSEM (version 1.2.30).
Transcripts with zero read counts across all samples were removed prior analysis. Normalisation of RSEM expected read counts was performed by dividing by million reads mapped to generate counts per million (CPM), followed by the trimmed mean of M-values (TMM) method from the edgeR package.
Assembly: GRCm38
Supplementary files format and content: comma-seperated text files include RSEM expected read count values for each sample

extract_protocol:
For Mx1-Cre:FLT3ITD/ITD and control BM, 1x104 to 2x105 LSK cells were sorted into TRIzol® (Thermo Fisher Scientific, Waltham, MA) and RNA was isolated according to the manufacturer`s instruction.
cDNA libraries were prepared using the NEBNext Ultra RNA Library Prep kit with the polyA selection module (New England Biolabs) and purified with AMPure beads (Agilent). Libraries were quantified with the KAPA Library Quantification Kit for Illumina (Kapa Biosystems) and pooled. Sequencing was performed on the Illumina NextSeq 500/550 Sequencer High Output mode (1 × 75 bp).


title: wild-type, 24 hr rep 1


title: 205624640074_R02C01

description:
Methylation data from tumor sample
Sample 46


title: 204788470022_R01C01

description:
Methylation data from tumor sample
Sample 51

value: Frozen


title: OA_A_2

value: Treated with oleic acid


title: veA deletion, 24 hr rep 2


title: SF_sample227


title: OA_A_1


title: 205605880167_R04C01

description:
Methylation data from tumor sample
Sample 45


title: 205624640167_R06C01

description:
Methylation data from tumor sample
Sample 44

source_name: PPB III


title: SFH_sample274

value: AML


title: SFH_sample273

value: Bone marrow


title: A_KA_2

value: Wild type astrocyte

value: Treated with APOE KO neuronal conditional medium


title: SFH_sample270

value: Lineage- Sca1+ Kit+


title: 205624640137_R08C01

description:
Methylation data from tumor sample
Sample 43

value: tumor


title: A_KA_1


title: 205624640137_R07C01

description:
Methylation data from tumor sample
Sample 42


title: FH_sample271

value: Healthy


title: 205061430174_R01C01

description:
Methylation data from tumor sample
Sample 41


title: KA_3


title: KA_2


title: SF_sample230


title: 204076520023_R04C01

description:
Methylation data from tumor sample
Sample 40


title: FH_sample236


title: KA_1


title: 202761400077_R07C01

description:
Methylation data from tumor sample
Sample 39


title: SFH_212_F4

data_processing:
Reads were trimmed for adapter sequences using Cutadapt v1.11 and aligned using bwa v0.7.15. Duplicated reads were marked using Picard v2.19
Duplicated reads or reads without mapped mate were removed using samtools v1.9.
Peaks were called using MACS2 v2.1 with default parameters.
Bedgraphs were generated and normalised using bedtools2 v2.27.1 genomecov.
Assembly: mm9
Supplementary files format and content: Bigwigs were generated from normalised bedgraphs using homer v4.9 bedGraphToBigWig.

extract_protocol: BM LSK+ from Scl-CreERT:FLT3ITD/ITD and aged matched FLT3ITD/ITD mice post tamoxifen induction when mice presented with AML.

value: Lineage low  Sca1+ cKit+


title: ADCC.28

city: Brescia

first: Stefano

last: Calza

state: Brescia

address: Viale Europa 11

department: DMMT

institute: University of Brescia

description: gene expression

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Data were processed using R version 4.2.1 and Bioconductor, with package oligo

label: biotin

source_name: FFPE tissue

label_protocol: not provided

extract_protocol: not provided

value: Adenoid cystic carcinoma (ACC)

value: Patient 28


title: A_KA_3


title: Control_3

value: Untreated


title: ADCC.102

description: gene expression

value: Patient 102


title: 205624640137_R05C01

description:
Methylation data from tumor sample
Sample 38


title: SFH_211_F3


title: ADCC.25

description: gene expression

value: Patient 25


title: Control_2


title: 205624640173_R01C01

description:
Methylation data from tumor sample
Sample 37

value: FFPE


title: ADCC.41

description: gene expression

value: Patient 41


title: SFH_201_F6


title: Control_1


title: 205624640167_R04C01

description:
Methylation data from tumor sample
Sample 36


title: ADCC.53

description: gene expression

value: Patient 53


title: ADCC.103

description: gene expression

value: Patient 103


title: ADCC.60

description: gene expression

value: Patient 60


title: ADCC.47

description: gene expression

value: Patient 47


title: SFH_197_F3

value: Bone marrow


title: RNA-seq_Ephb2_liver_rep3

first: Yang

last: Xiao

state: PA

address: 12-193 Smilow Translational Research Center, 3400 Civic Center Boulevard

institute: UNIVERSITY OF PENNSYLVANIA

description:
liver_rawread_counts.csv
liver_Deseq2_output.csv

data_processing:
The raw fastq files of snRNA-seq were mapped to Mus musculus assembly GRCm38 (mm10) using CellRanger (3.0.2). Unique molecular identifiers (UMI) count matrices were imported into Seurat (3.2.0) (Stuart et al., 2019) to generate Seurat object to each experiment.
The raw fastq files of mouse livers and human livers were mapped to Mus musculus genome assembly GRCm38 (mm10) and Homo sapiens genome assembly GRCh38 (hg38) respectively using Cellranger-atac (1.2.0). The fragment count matrix was imported into ArchR
The raw fastq files of RNA-seq were mapped to Mus musculus assembly GRCm38 (mm10) using STAR (2.5.4) with --quantMode GeneCounts to generate gene count matrix. The matrix was imported into R package DEseq2 to quantify gene expression
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: raw counts files and metadata of cell identity with assigned cluster identity for snRNA-seq; fragment counts files and metadata with assigned cluster identity for snATAC-seq; raw counts files and Deseq2 output for RNA-seq

source_name: whole liver

growth_protocol: C57BL/6J mice were housed in the animal facility with 12h dark/light cycle (7:00am to 7:00pm) and ad libitum access to food and water

extract_protocol:
For snRNA-seq and snATAC-seq, liver nuclei were isolated and loaded to 10X Genomics Chromium controller
For liver RNA-seq, RNA were extracted from whole liver using Trizol and Qiagen RNeasey Mini kit.
For Stellate Cell RNA-seq, RNA were extracted from stellate cells isolated from livers injected with AAV-TBG-GFP and AAV-TBG-Ephb2.
snRNAseq libraries were prepared according to manufacturer’s instructions of Chromium Next GEM Single Cell 3′ Kit
snATACseq libraries were prepared according to manufacturer’s instructions of Chromium Next GEM Single Cell ATAC kit
liver RNA-seq were submitted to Novogene for library preparation
Stellate Cell RNA-seq were prepared according to  manufacturer’s instructions of KAPA RNA HyperPrep with RiboErase
snRNA-seq, snATAC-seq, bulk RNA-seq

treatment_protocol:
C57BL/6J  were fed normal chow or modified ALIOS diet for 3 months or 9 months
C57BL/6J  were injected with AAV8-TBG-GFP or AAV-TBG-Ephb2 and fed normal chow for a week

value: whole liver

value: injected with AAV8-TBG-Ephb2

value: force expression of Ephb2


title: 205624640167_R03C01

description:
Methylation data from tumor sample
Sample 35

source_name: PPB II

value: tumor


title: RNA-seq_Ephb2_liver_rep2


title: FH_2733

value: Lineage low  Sca1+ cKit+


title: 205624640137_R06C01

description:
Methylation data from tumor sample
Sample 34


title: RNA-seq_Ephb2_liver_rep1


title: 205624640173_R07C01

description:
Methylation data from tumor sample
Sample 33

source_name: PB


title: ADCC.105

description: gene expression

value: Adenoid cystic carcinoma (ACC)

value: Patient 105


title: FH_212_M3


title: ADCC.6

description: gene expression

value: Patient 6


title: RNA-seq_GFP_liver_rep3

value: injected with AAV8-TBG-GFP

value: control


title: FH_212_F2


title: 205624640173_R05C01

description:
Methylation data from tumor sample
Sample 32

value: FFPE


title: SFH_197_F6


title: RNA-seq_GFP_liver_rep2


title: 205624630179_R03C01

description:
Methylation data from tumor sample
Sample 31


title: 205624630174_R08C01

description:
Methylation data from tumor sample
Sample 30


title: FH_192_F3


title: RNA-seq_GFP_liver_rep1


title: snATAC-seq_ALIOS_9mo

value: modified ALIOS diet for 9 months


title: FH_191_F5


title: 205624630136_R04C01

description:
Methylation data from tumor sample
Sample 29

source_name: MAS


title: primEB cells, WT_NFIA-ETO2, differentiation medium, rep3

description:
WT_NE_peaks.broadPeak.gz
WT_NE_logFC1.5_fdr0.05_broadPeak.bed.gz

source_name: fetal liver

value: fetal liver

value: primary erythroblasts


title: primEB cells, WT_NFIA-ETO2, differentiation medium, rep2


title: 205624630136_R01C01

description:
Methylation data from tumor sample
Sample 28


title: ADCC.20

description: gene expression

value: Patient 20


title: ADCC.44

description: gene expression

value: Patient 44


title: snATAC-seq_ALIOS_3mo

value: modified ALIOS diet for 3 months


title: snATAC-seq_NC_9mo

value: whole liver

value: Normal chow for 9 months


title: ADCC.50

description: gene expression

value: Patient 50


title: 205624630150_R04C01

description:
Methylation data from tumor sample
Sample 26

source_name: ERMS

value: tumor


title: 205624640018_R03C01

description:
Methylation data from tumor sample
Sample 27


title: snATAC-seq_NC_3mo_rep2

value: Normal chow for 3 months


title: primEB cells, WT_NFIA-ETO2,  differentiation medium, rep1


title: snATAC-seq_NC_3mo_rep1


title: 205624630150_R03C01

description:
Methylation data from tumor sample
Sample 25


title: ADCC.26

description: gene expression

value: Adenoid cystic carcinoma (ACC)

value: Patient 26


title: ADCC.33

description: gene expression

value: Patient 33


title: ADCC.7

description: gene expression

value: Patient 7


title: 205624630150_R02C01

description:
Methylation data from tumor sample
Sample 24


title: snRNA-seq_ALIOS_9mo


title: ADCC.56

description: gene expression

value: Patient 56


title: TKO_Day5.scRNAseq

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Removed the low quality reads; Bsmap was used to map the CMS-IP sequences to mm10.
Macs2 was used to call CMS-IP peaks; 10x single cell data was analyzed using Seurat v3.
DESeq2 was used to call differential 5hmC peaks.
Genome_build: mm10
Supplementary_files_format_and_content: csv and bigwig

source_name: mESC day5 TKO

growth_protocol: E14-NKX2-5-EmGFP mESC (18) was purchased from Mutant Mouse Resource & Research Centers (MMRRC). Cells were cultured on mitomycin C treated mouse embryonic fibroblasts (MEF) as feeder cells. The culture medium includes Knock-out Dulbecco's Modified Eagle's Medium (Gibco), 15% fetal bovine serum (Omega), 0.5% penicillin-streptomycin (Gibco), 0.1 mM non-essential amino acids (Gibco), 0.1mM 2-mercaptoetanol (Sigma), and 103 U/mL of leukemia inhibitory factor (Millipore).The handing drop differentiation in mESCs was conducted according to the previous protocol (20). Briefly, mESCs were suspended in differentiation culture medium without leukemia inhibitory factor (LIF). Embryonic bodies (EBs) were formed by culturing cells within drops on the up-turned inner surface of the lid of the dishes for 2 days. EBs then were collected from the lids and cultured in the non-adhesive dishes to expand for additional 3 days. The expanded EBs were then cultured in the cell culture dishes to allow them attach for next 5 days.

extract_protocol:
Genomic DNA was isolated using Qiagen DNeasy Blood and Tissue kit. RNA was isolated using Qiagen RNeasy mini kit.
CMS-IP library construction: DNA was sheared using Covaris Adaptive Focused Acoustic to the center at 200 bp. DNA fragments were size selected and ligated with methylated adaptors and treated with sodium bisulfite (invitrogen). The extra adapters were removed by AmpurXP (Beckman). The DNA was then denatured for 10 minutes at 95 °C (0.4 M NaOH, 10 mM EDTA), neutralized by the addition of cold 2M ammonium acetate (pH 7.0) for 10 min on ice. Then denatured DNA fragments were incubated with 1 μl anti-CMS antiserum in 1x IP buffer (10 mM sodium phosphate pH 7.0, 140 mM NaCl, 0.05% Triton X-100) for 2 h at 4 °C, and then precipitated with protein A/G beads. Precipitated DNA was eluted with proteinase K, purified with phenol chloroform, amplified and enriched by 10-12 cycles PCR using Kapa HiFi uracil polymerase. RNA-seq library construction is followed standard illumina library construction protocols. MethylC-seq: DNA was sheared using Covaris Adaptive Focused Acoustic to the center at 300 bp. DNA fragments were size selected and ligated with methylated adaptors and treated with sodium bisulfite (invitrogen). Libraries were enriched by 4-6 cycles PCR using Kapa HiFi uracil polymerase.

treatment_protocol: No treatment

value: embryonic stem cell (ESC)

tag: genotype/variation

value: Tet-triple knockout (TKO)


title: WT_Day5.scRNAseq

source_name: mESC day5 WT

value: wild type


title: 205624630150_R01C01

department: Neuropathology

description:
Methylation data from tumor sample
Sample 23

value: FFPE


title: ADCC.58

description: gene expression

value: Patient 58


title: ADCC.4

description: gene expression

value: Patient 4


title: snRNA-seq_NC_9mo


title: ADCC.88

description: gene expression

value: Patient 88


title: ADCC.85

description: gene expression

value: Patient 85


title: ADCC.86

description: gene expression

value: Patient 86


title: snRNA-seq_NC_3mo

value: whole liver


title: 205624630146_R07C01

description:
Methylation data from tumor sample
Sample 21

value: tumor


title: WT-Day2.CMSIP2

source_name: mESC day2


title: ADCC.48

description: gene expression

value: Patient 48


title: 205624630146_R06C01

description:
Methylation data from tumor sample
Sample 20


title: ADCC.107

description: gene expression

value: Adenoid cystic carcinoma (ACC)

value: Patient 107


title: WT-Day0.CMSIP2

source_name: mESC day0


title: 205624630146_R02C01

description:
Methylation data from tumor sample
Sample 19


title: Total epidermal cells from WT mice at P21

city: Shanghai

first: Yueqing

last: Xue

state: 上海市

address: 319 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and  paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, 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.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: raw counts and fpkm

source_name: skin

extract_protocol:
Digest the skin samples to get the epidermal cells and RNA was harvested using Trizol reagent.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: skin

value: epidermal cells

tag: Sex

value: Female

value: post natal day 21

value: WT


title: WT-Day0.CMSIP1

value: embryonic stem cell (ESC)

value: wild type