title: SCC14

value: Neuropathology, UKSH Luebeck


title: SCC16

status: Public on Sep 25 2022

type: genomic

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

country: Germany

institute: Ludwig Maximilians University Hospital Munich

description:
Not included in analysis
Low tumor cell content

hyb_protocol: Bisulphite converted (using the EpiTect Bisulfite Kit (Qiagen)) DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing:
Statistical analysis was performed using the minfi package running on RStudio version 1.3.1093 based on the statistical language R version 3.5.1
Average beta-Values after normalization using the Noob method

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell RSC FFPE Plus DNA Purification Kit (Custom, AX4920; Promega), according to the manufacturer’s instructions.

tag: methylation class

tag: conventional class

value: SCC

tag: initial diagnosis

value: Squamous cell carcinoma

tag: gender

value: male

tag: age

tag: localization

value: Nasal cavity

tag: tissue source

tag: excluded

value: Not included in analysis

tag: rationale for exclusion

value: Low tumor cell content


title: SCC13

value: NEC-like SMARCA4 ARID1A

value: Paranasal sinus

value: Pathology, Charite Berlin


title: SCC11


title: SCC12


title: Others

description:
Not included in analysis
Noise point

source_name: Others

value: MANEC

value: Mixed adenoneuroendocrine carcinoma

value: Pathology, USB Basel

value: Noise point


title: GPC1

value: GPC

value: Sinunasal glomangioperizytoma


title: Others4

description:
Not included in analysis
Noise point, entity too rare

value: BP SSARC

value: Biphenotypic sinonasal sarcoma, PAX3-FOXO1 fusion-positive

value: Nassal cavity

value: Noise point, entity too rare


title: SCC10

value: SCC

value: Squamous cell carcinoma

value: male


title: Others3

value: RHB MEN

value: Rhabdoid meningeoma

value: female

value: Nasal cavity

value: Neuropathology, Charite Berlin

value: Not included in analysis


title: NEC19

value: NEC-like IDH2

value: NEC

value: Neuroendocrine carcinoma

value: Paranasal sinus

value: Pathology, Charite Berlin


title: SCC9


title: ONB74

value: ONB

value: Olfactory neuroblastoma

value: Pathology, MSKCC New York

tag: related publication

value: Dogan, Mod Pathol 2019


title: ONB73


title: ONB75

value: Others


title: ONB72

value: male


title: ONB70


title: ACC15

value: ACC

value: Adenoid cystic carcinoma


title: ONB76

value: female

value: Nasal cavity, base of skull


title: ONB69

description:
Not included in analysis
Noise point

value: Noise point


title: ONB71


title: SCC19

description:
Not included in analysis
Noise point

value: SCC

value: Squamous cell carcinoma, HPV-related

value: Nasal cavity

value: Not included in analysis


title: SCC17


title: NUT3

value: NUT

value: NUT midline carcinoma

value: Pathology, USB Basel


title: NUT2

value: Pathology, Charite Berlin


title: SCC8

value: Squamous cell carcinoma

value: Paranasal sinus


title: ACC14


title: SCC35

value: Low tumor cell content


title: NUT4

value: male


title: SNUC13

value: SNUC


title: LECA16

value: LECA

value: Lymphoepithelial carcinoma


title: NEC18

description:
Not included in analysis
Bad overall quality

value: NEC

value: Neuroendocrine carcinoma

value: female

value: Nasal cavity, paranasal sinus

value: Bad overall quality


title: NEC16

value: NEC-like SMARCA4 ARID1A

value: Paranasal sinus, left


title: NEC14

value: Neuropathology, UKE Hamburg

value: Capper, Acta Neuropathol 2018

value: Not included in analysis


title: NEC17

description:
Not included in analysis
Noise point

value: Neuropathology, Charite Berlin

value: Noise point


title: LECA15

value: Nasal cavity

value: Pathology, Charite Berlin


title: NEC15

description:
Not included in analysis
Noise point

value: male

value: Others


title: ACC13

value: ACC

value: Adenoid cystic carcinoma


title: SCC7

value: SCC

value: Squamous cell carcinoma

value: Paranasal sinus


title: NEC12

value: NEC-like IDH2

value: NEC

value: Neuroendocrine carcinoma

value: female

value: Pathology, MSKCC New York

value: Dogan, Mod Pathol 2019


title: ACC11

value: Nasal cavity, paranasal sinus


title: SCNEC2

description:
Not included in analysis
Noise point

value: NEC-like SMARCA4 ARID1A

value: SCNEC

value: Small cell neuroendocrine carcinoma

value: Not included in analysis

value: Noise point


title: ADC15

value: ACC

value: ADC

value: Adenocarcinoma

value: male

value: Nasal cavity

value: Pathology, Charite Berlin


title: NEC13

value: NEC-like IDH2

value: NEC


title: SCNEC4

description:
Not included in analysis
Noise point


title: SCNEC1

value: Bad overall quality


title: NEC11

value: Neuroendocrine carcinoma

value: female

value: Pathology, MSKCC New York


title: SCNEC3

description:
Not included in analysis
Noise point

value: NEC-like SMARCA4 ARID1A

value: Dogan, Mod Pathol 2019


title: ACC12

value: Adenoid cystic carcinoma


title: NEC9

description:
Not included in analysis
Noise point

value: Nasal cavity, paranasal sinus

value: Neuropathology, University Frankfurt am Main

value: Not included in analysis


title: NEC10


title: VAKI iNKT GE (14541)

type: SRA

city: Bronx

first: XUSHENG

last: ZHANG

state: NY

address: 1300 Morris Park Ave

department: GENETICS

country: USA

institute: ALBERT EINSTEIN COLLEGE OF MEDICINE

library_source: transcriptomic single cell

data_processing:
CLC Genomics Workbench v 11.0.1
Cell Ranger Pipeline v3.1.0
Assembly: mm10
Supplementary files format and content: HDF5 Feature Barcode Matrix Format
Supplementary files format and content: vloupe (VDJ)

molecule: total RNA

organism: Mus musculus

source_name: VαKI iNKT

extract_protocol:
Mouse spleens were aseptically removed and mechanically disrupted to generate cell suspensions in sterile PBS.  Red blood cells wereremoved by treatment with RBC lysing solution removed by treatment with RBC lysing solution.  Extracellular staining with monoclonal antibodies, CD1d tetramer reagents and live/dead viability dyes was performed at 4ºC to separate T cells and iNKT cells by cell sorting
Cells were loaded into the chips of the Chromium™ Single Cell 5′ Gel Beads Kit, followed by the generation of single-cell Gel Bead-In Emulsions (GEMs) using the Chromium Controller instrument according to the manufacturer’s instructions (10X Genomics).   GEMs were then subjected to library construction using the Chromium™ Single Cell 5′ Library Kit v1 (10X Genomics).  As a first step, reverse transcription was performed, resulting in cDNA tagged with a cell-specific barcode and a unique molecular index (UMI) for each transcript. Fragments were then size selected using SPRI select magnetic beads (Beckman Coulter), and  Illumina sequencing adapters were ligated to the size-selected fragments and re-purified using SPRI select magnetic beads. Finally, sample indexes were incorporated and amplified, followed by a double-sided size selection using SPRI select magnetic beads. The quality of the final library was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies). The samples were then sequenced using a NextSeq instrument  with 150 cycle paired end chemistry (Illumina). To process the sequenced libraries, generation of FASTQ, gene expression and count matrix files and generation of cloupe files were carried out with Cell Ranger software (10X Genomics). For the V(D)J libraries and generation of vloupe files, Cell Ranger V(D)J was used.

tag: tissue

value: Spleen

tag: cell type

value: iNKT

tag: strain

value: VAKI

tag: treatment

value: Sort of iNKT cells


title: B6 iNKT GE (14539)

source_name: C57BL/6 iNKT


title: B6 T GE (15450)

source_name: C57BL/6 T

value: T

value: Sort of T cells


title: VAKI iNKT VDJ (14537)


title: VAKI T GE (14542)

source_name: VαKI T


title: B6 iNKT VDJ (14535)


title: VAKI T VDJ (14538)


title: B6 T VDJ (14536)


title: SNUC11

value: NEC-like IDH2

value: SNUC

value: Nasal cavity

value: Neuropathology, UKM Muenster


title: SNUC10

value: female

value: Nasal cavity, base of skull

value: Neuropathology, GAU Gottingen


title: NEC8

value: NEC

value: Neuroendocrine carcinoma

value: male

value: Pathology, MSKCC New York

value: Dogan, Mod Pathol 2019


title: SNUC12

value: NEC-like SMARCA4 ARID1A

value: Base of skull

value: Others


title: SNUC8

value: Paranasal sinus

value: Neuropathology, Charite Berlin


title: MELA18

value: MELA

value: Mucosal melanoma

value: Pathology, Charite Berlin

value: Jurmeister, J Pathol 2038


title: MELA19

value: Nasal cavity

value: Jurmeister, J Pathol 2039


title: MELA20

value: female

value: Jurmeister, J Pathol 2040


title: MELA17

value: Jurmeister, J Pathol 2037


title: SNUC9

description:
Not included in analysis
Noise point

value: SNUC

value: male

value: Not included in analysis

value: Noise point


title: MELA21

value: Jurmeister, J Pathol 2041


title: MELA16

value: Jurmeister, J Pathol 2036


title: SUNE-1_CLIP

city: Guangzhou

first: Zi-Qi

last: Zheng

address: Dong Feng East Road No.651

country: China

institute: Sun Yat-sen University Cancer Center

library_source: transcriptomic

data_processing:
library strategy: CLIP-seq
The libraries were loaded on cBot (Illumina) to generate cluster and sequenced on the Illumina HiSeqXten platform. The RNA-seq reads were mapped to the human reference genome sequence (hg38) assembly by Hisat2 (Version 2.1.0).
Stringtie (version 1.3.3) was used to count the number of fragments of each known gene downloaded from Ensembl (Homo sapiens GRCh38)，NONCDED（v5.0）,lncrnadb（v.2.0）,lncipedia（v.5.0）.
After mapping, we removed genes with fewer than 10 fragments in all of the samples.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: SuppTab-delimited text files include RPKM values for each sample

growth_protocol: HONE-1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum.

extract_protocol:
CLIP RNA was collected according to the CLIP protocol in the paper’s methods section. Briefly, RNA was cross-linked with RNA binding protein under ultraviolet irradiation. After the RNA-protein complex was precipitated by anti-ACLY antibody, RNA was eluted and subjected to RNA sequencing. We constructed Illumina sequencing libraries according to the modified strand-specific RNA sequencing protocol. We isolated non-coding RNA and coding RNA from 3 μg of purified total RNA using a ribo-zero kit for rRNA removal. After isolation, we eluted and fragmented the RNA samples at 94°C for 8 min with Elute-Prime-Fragment Mix. Subsequently, we performed first-strand cDNA synthesis using SuperScriptII (Invitrogen, Carlsbad, CA. USA). The product with Second Strand Marking Master Mix were incubated at 16°C for 1 hour to synthesize the second-strand cDNA. After 3’ ends adenylation, we ligated the DNA fragments with TruSeq adapters and the product was amplified using TruSeq PCR primers.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: nasopharyngeal carcinoma

tag: antibody

value: anti-ACLY


title: LP08 Light-1

city: Anseong-si, Gyeonggi-do

first: Heewon

last: Moon

address: 4726,Seodong-daero, Daedeok-myeon

country: South Korea

institute: Chung-ang university

description: replicate 1

data_processing:
Quality of the RNA-seq reads were evaluated using the FastQC software
The raw reads were trimmed and quality-filtered before alignment, and those with more than 90 % threshold (Q>30) were used for mapping. B. rapa reference genome was obtained from Ensembl and were used using the TopHat2 software with default parameters
Aligned reads were converted to digital counts using featureCounts and were analyzed using edgeR.
Differentially expressed genes (DEGs) were identified based on a 0.05 p-value and a cutoff of two-fold difference in expression.
Assembly: B. rapa reference genome was obtained from Ensembl
Supplementary files format and content: tab-delimited text files with raw gene counts for individual samples

organism: Brassica rapa

source_name: whole plant

extract_protocol:
Total RNA was extracted from whole seedling samples using RNeasy Mini Kit (Qiagen, Germany) and treated with DNase I (New England Biolabs, USA) to remove genomic DNA contamination.
RNA-seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., USA) according to the manufacturer’s instructions.

value: whole plant


title: LP08 Dark-3

description: replicate 3


title: Chiifu Dark-2

description: replicate 2


title: Chiifu Light-3

description: replicate 3


title: Chiifu Dark-1

description: replicate 1


title: Chiifu Light-1

description: replicate 1


title: LP08 Light-2

description: replicate 2


title: Chiifu Dark-3

description: replicate 3


title: LP08 Dark-2

description: replicate 2


title: LP08 Dark-1

description: replicate 1


title: LP08 Light-3

description: replicate 3


title: MELA14

value: MELA

value: Mucosal melanoma

value: Paranasal sinus

value: Jurmeister, J Pathol 2034


title: Chiifu Light-2

description: replicate 2


title: MELA13

value: Nasal cavity, paranasal sinus

value: Pathology, USB Basel

value: Jurmeister, J Pathol 2033


title: WT_24h.2_control_for Cyal

type: RNA

city: Freiburg

first: Wolfgang

middle: R.

last: Hess

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

description:
Slide Format: 8 x 60 K
Slide LayoutIS-62976-8-V2
Design ID75764

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09 for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and quantile normalized.

organism: Synechocystis sp. PCC 6803

source_name: PCC6803, WT, 24 h HC, replicate 2

label_protocol: DNase-treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol. Further details of the labeling and hybridization protocol were published in:  Voß,B. and Hess,W.R. (2014) The identification of bacterial non-coding RNAs through complementary approaches. In Handbook of RNA Biochemistry. WILEY-VCH, Weinheim, Germany, Vol. 2, pp. 787–800.

growth_protocol: Liquid cultures in buffered BG11 media at 30°C under constant light with an intensity of 130 µmol photons m-2 s-1 and constant bubbling. The media for High Carbon (HC) and Low Carbon (LC) cultures was buffered with TES/KOH until a pH of 8 and 7. HC cultures were bubbled with CO2-enriched air (5%, v/v), while LC cultures with ambient air (0.04% CO2).

extract_protocol: RNA was prepared using a hot phenol-based protocol.

treatment_protocol: Cells were shifted to LC conditions at an OD750 of 0.8-1. Following the shift, the cultures were sampled after 3 h and 24 h for the transcriptome analysis by filtration.

tag: genotype

value: WT

value: 24 h high carbon conditions


title: MELA15

tag: methylation class

value: female

value: Nasal cavity

value: Pathology, Charite Berlin

value: Jurmeister, J Pathol 2035


title: WT_3h.2_control_for Cyal

source_name: PCC6803, WT, 3 h HC, replicate 2

value: 3 h high carbon conditions


title: MELA11

tag: conventional class

value: male

value: Jurmeister, J Pathol 2031


title: MELA12

tag: initial diagnosis

value: Jurmeister, J Pathol 2032


title: WT_0h.1_control_for Cyal

source_name: PCC6803, WT, LC, replicate 1

value: low carbon conditions


title: WT_0h.2_control_for Cyal

source_name: PCC6803, WT, LC, replicate 2


title: HONE-1_CLIP

value: nasopharyngeal carcinoma

value: anti-ACLY


title: WT_3h.1_control_for Cyal

source_name: PCC6803, WT, 3 h HC, replicate 1


title: MELA9

value: MELA

value: Mucosal melanoma

tag: gender

value: Jurmeister, J Pathol 2029


title: MELA8

tag: age

value: Jurmeister, J Pathol 2028


title: MELA10

tag: localization

value: Jurmeister, J Pathol 2030


title: MELA4

tag: tissue source

value: Jurmeister, J Pathol 2024


title: MELA6

value: Jurmeister, J Pathol 2026


title: MELA7

value: female

value: Nasal cavity

value: Jurmeister, J Pathol 2027


title: MELA5

value: Pathology, Charite Berlin

value: Jurmeister, J Pathol 2025


title: MELA3

value: Jurmeister, J Pathol 2023


title: MELA1

value: male

value: Jurmeister, J Pathol 2021


title: CyaI_3h.2

source_name: PCC6803, CyaI, 3 h HC, replicate 2

value: delta-cyaI

value: 3 h high carbon conditions


title: CyaI_0h.2

source_name: PCC6803, CyaI, LC, replicate 2

value: low carbon conditions


title: MCC10

value: MCC

value: Merkel-cell carcinoma

value: Bridge of nose, orbit


title: CyaI_24h.2

source_name: PCC6803, CyaI, 24 h HC, replicate 2

value: 24 h high carbon conditions


title: MCC9

value: Neuropathology, Charite Berlin


title: MCC8

value: Bridge of nose, paranasal sinus


title: Ribo, Young, 2

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

country: Japan

institute: RIKEN

description: Ribosome profiling

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: SacCer3
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribo-seq

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: The diploid wild-type yeast strain BY4743 was grown in synthetic defined (SD) medium at 25°C and harvested at early log phase. Yeast cells were washed twice in 0.6 mL phosphate-buffered saline (PBS) and incubated with EZ-Link Sulfo-NHS-LC-LC-Biotin reagent for 30 min at room temperature. Biotin-labeled cells were resuspended in SD medium and batch-cultured in flasks at 25°C for 13 h. Grown cells were filtered, washed once with PBS, and mixed with magnetic streptavidin beads at room temperature for 30 min. After magnet for 10 min, the supernatant fraction containing daughter cells (Young) and the magnet-bound fraction containing beaded mother cells (Middle) were carefully collected. Beaded mother cells were then loaded to MAD system. Cells were allowed to bind for 10 min before resumption of pumping (50 RPM; flow rate ~25 mL/h) and air flow (25–33% of max output; approximately 1 PSI). The loaded cells were then grown in MAD for 24 h at 25°C. Beaded cells were washed with SD medium twice and collected (Aged).

extract_protocol:
Cells were filtered, scraped, and soaked in liquid nitrogen with 600 µl of lysis buffer. The frozen cells and lysis buffer grains were milled by a Multi-beads Shocker at 2,800 rpm for 15 sec.
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification. For RNA-Seq, TruSeq Stranded mRNA Library Prep Kit (Illumina).
Ribosome profiling and RNA-seq

value: Yeast cells

value: Wild type

value: Young


title: MCC7

value: female

value: Dorsum nasi, bridge of nose, paranasal sinus, orbit

value: Pathology, Charite Berlin


title: Ribo, Young, 1

description: Ribosome profiling


title: MELA2

value: MELA

value: Mucosal melanoma

value: Nasal cavity

value: Jurmeister, J Pathol 2022


title: HONE-1_siT1_1_RNAseq

data_processing:
The libraries were loaded on cBot (Illumina) to generate cluster and sequenced on the Illumina HiSeqXten platform. The RNA-seq reads were mapped to the human reference genome sequence (hg38) assembly by Hisat2 (Version 2.1.0).
Stringtie (version 1.3.3) was used to count the number of fragments of each known gene downloaded from Ensembl (Homo sapiens GRCh38)，NONCDED（v5.0）,lncrnadb（v.2.0）,lncipedia（v.5.0）.
After mapping, we removed genes with fewer than 10 fragments in all of the samples and performed differential expression analysis using R/Bioconductor package edgeR (version 3.0.8).
Genome_build: hg38
Supplementary_files_format_and_content: SuppTab-delimited text files include FPKM values for each sample

extract_protocol:
TRIzol reagent was used to extract total RNA from HONE-1 cell line. We constructed Illumina sequencing libraries according to the modified strand-specific RNA sequencing protocol. Briefly, we isolated non-coding RNA and coding RNA from 3 μg of purified total RNA using a ribo-zero kit for rRNA removal. After isolation, we eluted and fragmented the RNA samples at 94°C for 8 min with Elute-Prime-Fragment Mix. Subsequently, we performed first-strand cDNA synthesis using SuperScriptII (Invitrogen, Carlsbad, CA. USA). The product with Second Strand Marking Master Mix were incubated at 16°C for 1 hour to synthesize the second-strand cDNA. After 3’ ends adenylation, we ligated the DNA fragments with TruSeq adapters and the product was amplified using TruSeq PCR primers.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HONE-1 cells were treated with TINCR siRNA or control siRNA using RNAiMax reagent. The cells were harvested after transfection at 48h for assays.

value: nasopharyngeal carcinoma

tag: transfection

value: si-TINCR 1#


title: HONE-1_siNC_1_3_1_RNAseq

value: si-scrambled


title: HONE-1_siA3_1_RNAseq

value: si-ACLY 2#


title: HONE-1_siT2_1_RNAseq


title: HONE-1_siT3_1_RNAseq

value: si-TINCR 2#


title: HONE-1_siNC_2_3_1_RNAseq


title: HONE-1_siNC_2_2_1_RNAseq


title: HONE-1_siNC_1_1_1_RNAseq


title: HONE-1_siA1_1_RNAseq

value: si-ACLY 1#


title: HONE-1_siNC_1_2_1_RNAseq


title: HONE-1_siA2_1_RNAseq


title: HONE-1_siNC_2_1_1_RNAseq


title: WT_24h.1_control_for Cyal

source_name: PCC6803, WT, 24 h HC, replicate 1

value: WT

value: 24 h high carbon conditions


title: ICO_DM_4d_donor2

city: Utrecht

first: Arif Ibrahim

last: Ardisasmita

address: Heidelberglaan 100

department: Pediatrics

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Raw sequencing reads were processed using Galaxy web-based platform (https://usegalaxy.eu/)
Sample quality was assessed using FastQC tool (Galaxy Version 0.72). Low quality reads and adapter sequences were trimmed using Cutadapt (Galaxy Version 1.66.6).
Alignment and quantificiation of gene expression were performed using RNA STAR tool (Galaxy Version 2.7.2b).
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts of all samples

source_name: Adult Liver

growth_protocol: Organoids from intrahepatic cholangiocytes and fetal hepatocytes were grown as previously described (Huch et al., 2015. https://doi.org/10.1016/j.cell.2014.11.050 ; Hendriks et al., 2021. https://doi.org/10.1038/s41596-020-00411-2).

extract_protocol:
Total RNA was isolated using Trizol LS reagent (Invitrogen).
Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex).

treatment_protocol: Hepatic differentiation of intrahepatic cholangiocyte organoids were performed as previously described (Huch et al., 2015. https://doi.org/10.1016/j.cell.2014.11.050).

value: Adult Liver

tag: donor

value: Intrahepatic cholangiocyte organoids

value: Hepatocyte differentiation


title: ICO_DM_8d_donor2


title: FHO_donor4

source_name: Fetal Liver

value: Fetal Liver

value: Fetal hepatocyte organoids

value: Expansion media


title: FHO_donor3


title: MCC6

value: MCC

value: Merkel-cell carcinoma

value: male

value: Dorsum nasi

value: Pathology, Charite Berlin


title: Liver_donor2

value: Liver tissue


title: CyaI_24h.1

source_name: PCC6803, CyaI, 24 h HC, replicate 1

value: delta-cyaI


title: CyaI_3h.1

source_name: PCC6803, CyaI 3 h HC, replicate 1

value: 3 h high carbon conditions


title: Ribo, Middle, 2

description: Ribosome profiling

value: Yeast cells

value: Wild type

value: Middle


title: CyaI_0h.1

source_name: PCC6803, CyaI, LC, replicate 1

value: low carbon conditions


title: ICO_DM_8d_donor1

value: Adult Liver

value: Intrahepatic cholangiocyte organoids

value: WT


title: ICO_DM_4d_donor1

value: Hepatocyte differentiation


title: MCC5

value: female


title: ICO_EM_donor1

value: Expansion media


title: Ribo, Aged

description: Ribosome profiling

value: Aged


title: Liver_donor1


title: MCC4

value: MCC

value: Merkel-cell carcinoma

value: male


title: MCC3

value: Bridge of nose, paranasal sinus

value: Pathology, Charite Berlin


title: ICO_EM_donor2


title: RNA, Young, 2

description: RNA-Seq

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: SacCer3
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

value: Young


title: MCC2

value: Orbit, paranasal sinus


title: WSB, biol rep: 3

city: Bar Harbor

first: Petko

last: Petkov

state: ME

address: 600 Main St

institute: The Jackson Laboratory

library_source: genomic

data_processing:
RRBS data were processed using a bismark-based pipeline modified from Thompson et al. (2018). The pipeline uses Trim Galore! 0.6.3 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for QC, followed by the trimRRBSdiversityAdaptCustomers.py script from NuGen for trimming the diversity adapters. This script is available at: https://github.com/nugentechnologies/NuMetRRBS
All samples had comparable quality levels and no outstanding flags. Total number of reads was 45-90 million, with an average read length of about 50 bp. Quality scores were mostly above 30 (including error bars), with the average above 38. Duplication level was reduced to <2 for about 95% of the sequences.
High quality reads were aligned to a custom strain pseudogenomes, using bowtie2 as implemented in Bismark 0.22. The pseudogenomes were created by incorporating strain-specific SNPs and indels into the reference genome using g2gtools (https://github.com/churchill-lab/g2gtools), allowing a more precise characterization of methylation patterns.
Bismark methylation extractor tool was then used for creating a bed file of estimated methylation proportions for each animal, which was then translated to the reference mouse genome (GRCm38) coordinates using g2gtools. Unlike other liftover tools, g2gtools does not throw away alignments that land on indel regions. B6 samples were aligned directly to the reference mouse genome (mm10).
Assembly: mm10

source_name: liver

extract_protocol:
DNA was isolated from cells using the DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer’s protocol following the proceedure for cultured cells.   DNA concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the Qubit 3.0 dsDNA BR Assay (Thermo Scientific).
RRBS libraries were using the Ovation RRBS Methyl-Seq System (NuGEN) according to the manufacturer’s protocols.  Briefly, the protocol entails, MspI digestion of genomic DNA, adapter ligation, final repair, bisulfite conversion, and PCR amplification.  The quality and concentration of the libraries were assessed using the Bioanalyzer High Sensitivity DNA Analysis kit (Agilent Technologies) and KAPA Library Quantification Kit (Roche Sequencing and Life Science), respectively, according to the manufacturers’ instructions.

value: liver

tag: Sex

value: 12 weeks

value: WSB/EiJ

value: hepatocytes


title: PWK, biol rep: 3

tag: tissue

value: PWK/PhJ


title: LECA13

value: LECA

value: Lymphoepithelial carcinoma

value: Nasal cavity

value: Neuropathology, UKSH Luebeck


title: RNA, Middle, 2

description: RNA-Seq

tag: cell type

value: Yeast cells

value: Wild type

value: Middle


title: WSB, biol rep: 2

value: female

tag: strain


title: RNA, Young, 1

description: RNA-Seq


title: WSB, biol rep: 4


title: RNA, Middle, 1

description: RNA-Seq


title: Ribo, Middle, 1

description: Ribosome profiling


title: LECA14

value: male


title: RNA, Aged, 2

description: RNA-Seq

value: Aged


title: RNA, Aged, 1

description: RNA-Seq


title: PWK, biol rep: 1


title: LECA11


title: ONB68

value: NEC-like SMARCA4 ARID1A

value: ONB

value: Olfactory neuroblastoma

value: Nasal cavity, paranasal sinus, base of skull

value: Neuropathology, LMU Muenchen

tag: related publication

value: Capper, Acta Neuropathol 2018


title: LECA9

value: Pathology, Charite Berlin


title: LECA10

value: LECA


title: NZO, biol rep: 1

value: liver

value: 12 weeks

value: NZO/HlLtJ

value: hepatocytes


title: NZO, biol rep: 3


title: NZO, biol rep: 2


title: LECA7

value: Undifferentiated carcinoma, EBV positive

value: Nasal cavity


title: LECA12

value: Lymphoepithelial carcinoma

value: Neuropathology, UKSH Luebeck


title: PWK, biol rep: 2

value: female

value: PWK/PhJ


title: NOD, biol rep: 1

value: NOD/ShiLtJ


title: CAST, biol rep: 5

value: CAST/EiJ


title: DBA, biol rep: 4


title: LECA8


title: DBA, biol rep: 2


title: NOD, biol rep: 3


title: DBA, biol rep: 3


title: CAST, biol rep: 1


title: B6, biol rep: 4


title: CAST, biol rep: 4


title: B6, biol rep: 1


title: NOD, biol rep: 2


title: B6, biol rep: 2


title: EMB_RMS2

value: EMB RMS

value: Embryonal rhabdomyosarcoma

value: male

value: Others

value: Koelsche, Nature Comm 2021


title: NEC2

value: NEC-like IDH2

value: NEC

value: Neuroendocrine carcinoma

value: Paranasal sinus, orbit

value: Capper, Acta Neuropathol 2018


title: ONB63

value: ONB

value: Olfactory neuroblastoma

value: Nasal cavity, base of skull


title: ONB64


title: EMB_RMS1

value: female


title: LECA5

value: LECA

value: Lymphoepithelial carcinoma

value: Nasal cavity

value: Pathology, Charite Berlin


title: ONB62

value: Base of scull


title: LECA4

value: male


title: LECA3

value: Neuropathology, Charite Berlin


title: LECA6

description:
Not included in analysis
Noise point

tag: excluded

value: Not included in analysis

tag: rationale for exclusion

value: Noise point


title: ONB61

value: NEC-like IDH2

value: Neuropathology, WWU Muenster


title: ONB60

value: Neuropathology, LMU Muenchen


title: ONB58

value: Others

value: Capper, Acta Neuropathol 2018


title: ONB59

value: ONB

value: Olfactory neuroblastoma

value: Paranasal sinus, base of skull


title: LECA1

value: LECA


title: EWS13

value: EWS

value: Ewing's sarcoma

value: Low tumor cell content


title: LECA2

value: Lymphoepithelial carcinoma

value: Nasal cavity


title: 129S1, biol rep: 1

value: liver

value: female

value: 12 weeks

value: hepatocytes


title: AJ, biol rep: 1

value: A/J


title: AJ, biol rep: 2


title: AJ, biol rep: 3


title: 129S1, biol rep: 3


title: 129S1, biol rep: 2


title: 129 biol rep 1

data_processing:
Raw sequencing data were put through the quality control program FastQC (0.11.5), and duplicate sequences were removed before downstream analysis.
Transcript sequences were aligned to strain-specific pseudo-genomes, which integrate SNPs and indels from each strain based on the GRCm38 mouse genome build. The B6 samples were aligned directly to the mm10 reference mouse genome. The pseudogenomes were created using g2gtools (http://churchill-lab.github.io/g2gtools/#overview).
We used EMASE (https://github.com/churchill-lab/emase) to quantify the gene expression counts and DESeq2 vst transformation to normalize the gene expression data.
We filtered out transcripts with less than 1 CPM in two or more replicates.
Assembly: mm10
Supplementary files format and content: Read counts for each sample were combined into a single matrix stored in a tab-delimited file (StrainsEffCts9.txt) with genes in rows and samples in columns. The colum names indicate the strain and individual number of the sample. These are also listed in the description field above. The row names indicate the Ensembl ID for each gene.

extract_protocol:
Total RNA was isolated from cells using the RNeasy Mini kit (Qiagen), according to manufacturers’ protocols, including the optional DNase digest step. RNA concentration and quality were assessed using the Nanodrop 2000 spectrophotometer (Thermo Scientific) and the RNA 6000 Nano Assay (Agilent Technologies).
Libraries were constructed using the TruSeq RNA Sample Prep Kit v2 (Illumina), according to the manufacturer’s protocol.  Briefly, the protocol entails isolation of polyA containing mRNA using oligo-dT magnetic beads, RNA fragmentation, first and second strand cDNA synthesis, ligation of Illumina-specific adapters containing a unique barcode sequence for each library, and PCR amplification.  The quality and concentration of the libraries were assessed using the DNA 1000 Kit (Agilent Technologies) and KAPA Library Quantification Kit (Roche Sequencing and Life Science), respectively, according to the manufacturers’ instructions.


title: 129 biol rep 3


title: WS biol rep 4

value: WSB/EiJ


title: ND biol rep 1

value: NOD/ShiLtJ


title: WS biol rep 3


title: SNUC3

value: NEC-like SMARCA4 ARID1A

value: SNUC

value: male

value: Others

value: Capper, Acta Neuropathol 2018


title: ND biol rep 3


title: SCC4

value: SCC

value: Squamous cell carcinoma

value: Nasal cavity, base of skull

value: Neuropathology, UKE Hamburg


title: ADC14

value: ADC

value: Adenocarcinoma

value: Nasal cavity

value: Pathology, Charite Berlin

value: Not included in analysis

value: Low tumor cell content


title: PK biol rep 2

value: liver

value: hepatocytes

value: female

value: 12 weeks

value: PWK/PhJ


title: PK biol rep 3


title: PK biol rep 1


title: NZ biol rep 3

value: NZO/HlLtJ


title: SCC2

value: male

value: Capper, Acta Neuropathol 2018


title: SCC3

value: SCC

value: Squamous cell carcinoma


title: 129 biol rep 2


title: EMB_RMS3

value: EMB RMS

value: Embryonal rhabdomyosarcoma


title: NZ biol rep 2


title: SCC1

value: k. A.

value: Others


title: NEC7

description:
Not included in analysis
Noise point

value: NEC

value: Neuroendocrine carcinoma

value: Nasal cavity, paranasal sinus

value: Pathology, Charite Berlin

value: Noise point


title: ND biol rep 2

value: liver

value: hepatocytes

value: female

value: NOD/ShiLtJ


title: SCC6

value: male

value: Paranasal sinus


title: WS biol rep 2

value: 12 weeks

value: WSB/EiJ


title: SNUC7

description:
Not included in analysis
Noise point

value: SNUC

value: Nasal cavity

value: Not included in analysis


title: MCC1

value: MCC

value: Merkel-cell carcinoma

value: Bridge of nose


title: CPH21

value: CPH

value: Craniopharyngeoma

value: Sellar region

value: Neuropathology, University Frankfurt am Main


title: DB biol rep 4

value: liver

value: hepatocytes


title: ONB56

value: ONB

value: Olfactory neuroblastoma

value: Neuropathology, UKE Hamburg

value: Capper, Acta Neuropathol 2018

value: Bad overall quality


title: ONB57

value: female

value: Nasal cavity, paranasal sinus

value: Others


title: CA biol rep 4

value: 12 weeks

value: CAST/EiJ


title: NZ biol rep 1

value: NZO/HlLtJ


title: CA biol rep 1


title: B6 biol rep 4


title: ONB55

value: male

value: Nasal cavity, base of skull

value: Not included in analysis


title: DB biol rep 3


title: CA biol rep 5


title: ONB54


title: B6 biol rep 2


title: DB biol rep 2


title: EWS12

value: EWS

value: Ewing's sarcoma

value: Neuropathology, UKGM Giessen/Marburg


title: EWS11

value: Paranasal sinus


title: B6 biol rep 1

value: liver

value: hepatocytes


title: AJ biol rep 3

value: A/J


title: ONB53

value: ONB

value: Olfactory neuroblastoma

value: Base of scull

value: Neuropathology, LMU Muenchen

value: Capper, Acta Neuropathol 2018

value: Bad overall quality


title: NEC6

value: NEC-like IDH2

value: NEC

value: Neuroendocrine carcinoma

value: Paranasal sinus, base of skull

value: Neuropathology, GAU Gottingen


title: AJ biol rep 1

value: female

value: 12 weeks


title: AJ biol rep 2


title: NEC5

value: NEC-like SMARCA4 ARID1A

value: male

value: Crista galli

value: Neuropathology, UKGM Giessen/Marburg


title: H3K4me3, WS, 4

description: BED file: WS_14_dense.bed

data_processing:
The raw sequencing data from both RNA-Seq and ChIP-Seq were put through  the quality control program FastQC (0.11.5), and duplicate sequences were removed before downstream analysis.
We used MACS 1.4.2 to identify peaks in the ChIP-Seq  sequencing data, with a significance threshold of p < 10^-5.  In order to compare peaks across strains, we converted the MACS output  peak coordinates to common B6 coordinates using g2g tools  (https://churchill-lab.github.io/g2gtools/).
We used ChromHMM (1.22) with default parameters to identify 14 chromatin states representing unique combinations of the four chromatin modifications.
Assembly: mm10
Supplementary files format and content: Each processed data file is a bed file detailing the positions of the 14 chromatin states for a single strain. Each file is labeled with the strain name and the number of states in the ChromHMM model, in this case 14. The columns of the processed files are as follows: chromosome, state start position, state end position, state label, score (meaningless in this context), strand (meaningless in this context), thickStart (same as start), thickEnd (same as end), and state color corresponding to the effect of the state on gene expression as shown in the accompanying manuscript (Tyler, Spruce, et al.)

extract_protocol:
Aliquots of 5x10^6 cells were spun down at 200 rpm for 5 min and cross-linked to DNA using 37\% formaldehyde in methanol. All cell samples were stored at -80°C.
ChIP libraries were constructed using 0.4-12.8 ng* of immunoprecipitated or input DNA and the KAPA HyperPrep Kit (Roche Sequencing and Life Science) according to the manufacturer’s protocols.  Briefly, the protocol entails, ligating Illumina specific barcoded adapters, size selection, and PCR amplification.  The quality and concentration of the libraries were assessed using the High Sensitivity D5000 ScreenTape (Agilent Technologies) and KAPA Library Quantification Kit (Roche Sequencing and Life Science), respectively, according to the manufacturers’ instructions.

value: liver

value: hepatocyte

tag: individual id

value: WSB/EiJ

tag: antibody

value: Millipore #07-473


title: Input, WS, input

description: BED file: WS_14_dense.bed

value: input


title: H3K4me1, WS, 4

description: BED file: WS_14_dense.bed

value: Millipore #07-436


title: H3K4me1, WS, 3

description: BED file: WS_14_dense.bed


title: ONB51

tag: methylation class

tag: conventional class

value: ONB

value: Olfactory neuroblastoma

value: Neuropathology, WWU Muenster

value: Capper, Acta Neuropathol 2018


title: ONB50

tag: initial diagnosis

tag: gender

value: Paranasal sinus, base of skull

value: Neuropathology, LMU Muenchen


title: ATRT7

value: ATRT

value: Atypical teratoid/rhabdoid tumor of the sella region

tag: age

tag: localization

value: Sellar region

value: Others

value: Johann, The American Journal of Surgical Pathology 2018

value: Not included in analysis

value: Bad overall quality


title: ATRT8

value: male

tag: tissue source

value: Neuropathology, University Heidelberg


title: H3K4me3, WS, 3

description: BED file: WS_14_dense.bed

value: liver

value: hepatocyte

value: female

value: WSB/EiJ

value: Millipore #07-473


title: ONB49

description:
Not included in analysis
Noise point

value: ONB

value: Olfactory neuroblastoma

value: Nasal cavity, base of skull

value: Capper, Acta Neuropathol 2018

value: Noise point


title: H3K4me3, WS, 2

description: BED file: WS_14_dense.bed


title: H3K4me1, PK, 3

description: BED file: PK_14_dense.bed

value: PWK/PhJ

value: Millipore #07-436


title: Input, PK, input

description: BED file: PK_14_dense.bed

value: input


title: H3K4me1, WS, 2

description: BED file: WS_14_dense.bed


title: ATRT6

value: ATRT

value: Atypical teratoid/rhabdoid tumor of the sella region

value: Sellar region

value: Others

value: Johann, The American Journal of Surgical Pathology 2018


title: ATRT9

value: Neuropathology, Charite Berlin


title: ONB46

value: NEC-like SMARCA4 ARID1A

value: female

value: Base of scull

value: Pathology, USB Basel


title: ONB52

description:
Not included in analysis
Noise point

value: ONB

value: Olfactory neuroblastoma

value: male

value: Neuropathology, LMU Muenchen

value: Not included in analysis


title: ATRT5


title: H3K4me3, PK, 2

description: BED file: PK_14_dense.bed

value: liver

value: hepatocyte

value: PWK/PhJ

value: Millipore #07-473


title: H3K4me1, PK, 1

description: BED file: PK_14_dense.bed

value: Millipore #07-436


title: ATRT4

value: ATRT

value: Atypical teratoid/rhabdoid tumor of the sella region

value: Sellar region

value: Others


title: H3K4me1, PK, 2

description: BED file: PK_14_dense.bed

value: female


title: ONB44

description:
Not included in analysis
Noise point

value: Paranasal sinus, base of skull

value: Capper, Acta Neuropathol 2018

value: Noise point


title: H3K4me1, NZ, 3

description: BED file: NZ_14_dense.bed

value: NZO/HlLtJ


title: H3K4me1, NZ, 2

description: BED file: NZ_14_dense.bed


title: ONB48

value: ONB

value: Olfactory neuroblastoma

value: male

value: Nasal cavity


title: H3K4me3, PK, 1

description: BED file: PK_14_dense.bed

value: liver

value: hepatocyte


title: ATRT3

value: Johann, The American Journal of Surgical Pathology 2018


title: ONB45

value: NEC-like SMARCA4 ARID1A

value: Base of scull

value: Neuropathology, Tuebingen


title: H3K4me3, NZ, 2

description: BED file: NZ_14_dense.bed

value: Millipore #07-473


title: ONB47

value: Nasal cavity, base of scull

value: Others


title: H3K4me3, PK, 3

description: BED file: PK_14_dense.bed

value: female

value: PWK/PhJ


title: H3K4me3, NZ, 3

description: BED file: NZ_14_dense.bed


title: ONB43

description:
Not included in analysis
Noise point

value: Nasal cavity, paranasal sinus

value: Neuropathology, LMU Muenchen

value: Capper, Acta Neuropathol 2018

value: Not included in analysis

value: Noise point


title: H3K4me1, NZ, 1

description: BED file: NZ_14_dense.bed

value: NZO/HlLtJ

value: Millipore #07-436


title: ONB41

value: ONB

value: Olfactory neuroblastoma

value: male


title: ALV_RMS8

value: ALV RMS

value: Alveolar rhabdomyosarcoma

value: fronto basal

value: Neuropathology, University Frankfurt am Main


title: ALV_RMS7

value: Others

value: Pathology, Charite Berlin


title: Input, NZ, input

description: BED file: NZ_14_dense.bed

value: liver

value: hepatocyte

value: female

value: input


title: H3K4me1, ND, 3

description: BED file: ND_14_dense.bed

value: NOD/ShiLtJ


title: H3K4me3, NZ, 1

description: BED file: NZ_14_dense.bed

value: Millipore #07-473


title: ONB40

value: Nasal cavity

value: Capper, Acta Neuropathol 2018


title: H3K4me1, ND, 2

description: BED file: ND_14_dense.bed

value: Millipore #07-436


title: ALV_RMS6


title: H3K4me3, ND, 2

description: BED file: ND_14_dense.bed


title: H3K4me1, ND, 1

description: BED file: ND_14_dense.bed


title: ATRT2

value: ATRT

value: Atypical teratoid/rhabdoid tumor of the sella region

value: Sellar region

value: Johann, The American Journal of Surgical Pathology 2018


title: ONB39

value: ONB

value: Olfactory neuroblastoma

value: male

value: Base of scull


title: H3K4me3, ND, 3

description: BED file: ND_14_dense.bed

value: liver


title: ONB42

value: NEC-like SMARCA4 ARID1A

value: Others


title: Input, ND, input

description: BED file: ND_14_dense.bed

value: hepatocyte

value: female

value: input


title: ALV_RMS5

value: ALV RMS

value: Alveolar rhabdomyosarcoma

value: Pathology, Charite Berlin


title: ATRT1

description:
Not included in analysis
Noise point

value: ATRT

value: Not included in analysis

value: Noise point


title: H3K27me3, NZ, 2

description: BED file: NZ_14_dense.bed

value: NZO/HlLtJ

value: Millipore #07-449


title: H3K27me3, NZ, 1

description: BED file: NZ_14_dense.bed


title: ALV_RMS4

value: Dorsal base of nose


title: H3K27me3, NZ, 3

description: BED file: NZ_14_dense.bed


title: H3K4me3, ND, 1

description: BED file: ND_14_dense.bed

value: NOD/ShiLtJ

value: Millipore #07-473


title: ONB37

value: ONB

value: Olfactory neuroblastoma

value: Base of scull

value: Capper, Acta Neuropathol 2018


title: ADC13

value: NEC-like SMARCA4 ARID1A

value: ADC

value: Adenocarcinoma

value: male

value: Nasal cavity

value: Pathology, MSKCC New York

value: Dogan, Mod Pathol 2019


title: H3K27me3, 129, 3

description: BED file: 129_14_dense.bed

value: liver

value: hepatocyte

value: female


title: H3K27me3, 129, 1

description: BED file: 129_14_dense.bed

value: Millipore #07-449


title: ONB36

value: Others


title: ONB35


title: H3K27me3, ND, 3

description: BED file: ND_14_dense.bed

value: NOD/ShiLtJ


title: ADC11

value: Adenocarcinoma, intenstinal type

value: Pathology, Charite Berlin


title: ONB33

value: ONB

value: Olfactory neuroblastoma

value: Base of scull


title: H3K27me3, ND, 2

description: BED file: ND_14_dense.bed


title: H3K27me3, 129, 2

description: BED file: 129_14_dense.bed


title: ONB38

value: Lymph node cervical

value: Neuropathology, LMU Muenchen

value: Capper, Acta Neuropathol 2018


title: H3K27me3, AJ, 3

description: BED file: AJ_14_dense.bed

value: A/J


title: ADC10

value: ADC

value: Adenocarcinoma, mucinous

value: Nasal cavity

value: Neuropathology, UKGM Giessen/Marburg


title: ADC9

value: male

value: Pathology, USB Basel


title: H3K27me3, AJ, 2

description: BED file: AJ_14_dense.bed

value: liver

value: hepatocyte

value: female

value: Millipore #07-449


title: H3K27me3, ND, 1

description: BED file: ND_14_dense.bed

value: NOD/ShiLtJ


title: ONB32

value: ONB

value: Olfactory neuroblastoma

value: Others


title: H3K27me3, AJ, 1

description: BED file: AJ_14_dense.bed


title: SCC5

value: SCC

value: Squamous cell carcinoma

value: Paranasal sinus


title: H3K27me3, WS, 4

description: BED file: WS_14_dense.bed

value: WSB/EiJ


title: ONB31

value: Base of scull

value: Capper, Acta Neuropathol 2018


title: H3K27me3, WS, 2

description: BED file: WS_14_dense.bed


title: ADC8

value: ADC

value: Adenocarcinoma

value: Pathology, Charite Berlin


title: ONB34


title: ADC7

value: male


title: H3K27me3, WS, 3

description: BED file: WS_14_dense.bed

value: liver

value: hepatocyte


title: ONB30


title: ONB29

value: female


title: H3K27me3, CA, 4

description: BED file: CA_14_dense.bed

value: CAST/EiJ

value: Millipore #07-449


title: H3K27me3, CA, 5

description: BED file: CA_14_dense.bed


title: Rapamycin ceg1-AA/xrn1D rep2

city: Birmingham

first: Onofrio

last: Zanin

address: School of Biosciences, University of Birmingham, Edgbaston

country: United Kingdom

institute: University of Birmingham

data_processing:
The quality of the data was checked using FastQC v0.11.5 (Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were aligned to the yeast genome R64 (sacCer3) using HISAT2 v2.1.1 and sorted and indexed using SAMtools v1.15.1 (Wysoker et al. 2009). The read count per gene were calculated with LiBiNorm v.2.5 (Dyer et al.) with the following parameters count -u name-root -f  --order=pos --minaqual=10 --mode=intersection-strict --idattr=gene_id --type=exon. Differential expression analysis was performed using DESeq2 package.
Supplementary files format and content: Reads count per gene

growth_protocol: Cells were growth on YPD media at 30° C

extract_protocol:
Total RNA was extracted via acid phenol/chloroform method
Libraries were prepared with Ultra II RNA Library Prep Kit for Illumina (NEB, E7770) and Multiplex Oligos for Illumina (NEB, E7335)

treatment_protocol: Cells were trated with DMSO or rapamycin (fc 1=ug/mL) for 45 min

tag: cell line

tag: genotype

value: MATalpha tor1-1 fpr1::NAT RPL13AxFKB12::TRP CEG1-FRB::HIS KAN::XRN3

tag: treatment

value: Rapamycin


title: ONB28

value: ONB

value: Olfactory neuroblastoma

value: Nasal cavity, base of skull

value: Others


title: H3K27me3, CA, 1

description: BED file: CA_14_dense.bed

tag: tissue

tag: cell type

tag: Sex


title: ADC6

value: NEC-like IDH2

value: Paranasal sinus

value: Pathology, MSKCC New York

tag: related publication

value: Dogan, Mod Pathol 2019


title: H3K27me3, PK, 2

description: BED file: PK_14_dense.bed

tag: strain

value: PWK/PhJ


title: H3K27me3, PK, 3

description: BED file: PK_14_dense.bed

tag: individual id


title: ONB27

value: Capper, Acta Neuropathol 2018


title: ONB26

value: male


title: Rapamycin ceg1-AA rep1

value: MATalpha tor1-1 fpr1::NAT RPL13AxFKB12::TRP CEG1-FRB::HIS


title: Rapamycin ceg1-AA rep2


title: ONB25

value: female


title: DMSO ceg1-AA/xrn1D rep2

value: DMSO


title: ADC12

value: ADC

value: Adenocarcinoma

value: Pathology, Charite Berlin


title: ONB67

value: ONB

value: Neuropathology, UKGM Giessen/Marburg


title: ADC3


title: H3K27me3, DB, 4

description: BED file: DB_14_dense.bed

value: liver

value: hepatocyte

tag: antibody

value: Millipore #07-449


title: ADC4

tag: methylation class

value: Poorly differentiated adenocarcinoma, intestinal type

value: Nasal cavity

value: Pathology, USB Basel


title: DMSO ceg1-AA/xrn1D rep1

value: MATalpha tor1-1 fpr1::NAT RPL13AxFKB12::TRP CEG1-FRB::HIS KAN::XRN1


title: ONB24

tag: conventional class

value: Olfactory neuroblastoma

value: Nasal cavity, base of skull

value: Others

value: Capper, Acta Neuropathol 2018


title: H3K27me3, DB, 3

description: BED file: DB_14_dense.bed

value: female


title: Rapamycin ceg1-AA/xrn1D rep1

value: Rapamycin


title: ADC5

value: ADC

tag: initial diagnosis

value: Intermediate-grade adenocarcinoma

value: male

value: Neuropathology, UKM Muenster


title: ONB23

value: ONB

tag: gender


title: ADC2

value: Adenocarcinoma

tag: age

value: Pathology, MSKCC New York

value: Dogan, Mod Pathol 2019

tag: excluded

value: Not included in analysis

tag: rationale for exclusion

value: Bad overall quality


title: H3K27me3, DB, 2

description: BED file: DB_14_dense.bed

value: liver

value: hepatocyte

value: Millipore #07-449


title: H3K27me3, PK, 1

description: BED file: PK_14_dense.bed

value: PWK/PhJ


title: DMSO ceg1-AA rep2

tag: cell line

value: MATalpha tor1-1 fpr1::NAT RPL13AxFKB12::TRP CEG1-FRB::HIS

value: DMSO


title: DMSO ceg1-AA rep1

tag: genotype


title: ONB21

value: Olfactory neuroblastoma

value: female

tag: localization

value: Paranasal sinus, base of skull

tag: tissue source

value: Others

value: Capper, Acta Neuropathol 2018


title: ONB22

value: ONB

value: Nasal cavity, paranasal sinus, base of skull

value: Neuropathology, LMU Muenchen


title: H3K27me3, B6, 1

description: BED file: B6_14_dense.bed

tag: tissue

tag: cell type


title: H3K27me3, B6, 4

description: BED file: B6_14_dense.bed

tag: Sex


title: H3K27me3, B6, 2

description: BED file: B6_14_dense.bed

tag: strain


title: ONB20

value: male

value: Nasal cavity, base of skull

tag: related publication


title: NEC4

description:
Not included in analysis
Noise point

value: NEC

value: Neuroendocrine carcinoma

value: Nasopharynx

value: Neuropathology, UKGM Giessen/Marburg

value: Not included in analysis

value: Noise point


title: ACC8

description:
Not included in analysis
Noise point

value: ACC

value: Adenoid cystic carcinoma

value: Nasal cavity

value: Pathology, Charite Berlin


title: ONB19

value: Olfactory neuroblastoma

value: female

value: Paranasal sinus, base of skull, orbit


title: ACC10

value: Paranasal sinus

value: Neuropathology, Charite Berlin

value: Low tumor cell content


title: ACC7

description:
Not included in analysis
Noise point

value: male


title: ACC9


title: Input, DB, input

description: BED file: DB_14_dense.bed

value: liver

value: hepatocyte

tag: individual id

value: input

tag: antibody


title: ONB17

tag: methylation class

value: ONB

tag: conventional class

value: Base of skull

value: Neuropathology, LMU Muenchen

value: Capper, Acta Neuropathol 2018


title: SNUC5

value: NEC-like IDH2

value: SNUC

tag: initial diagnosis

tag: gender

value: Neuropathology, UMG Gotingen


title: ONB18

value: Olfactory neuroblastoma

tag: age

value: Nasal cavity


title: H3K4me1, DB, 3

description: BED file: DB_14_dense.bed

value: female

value: Millipore #07-436


title: ACC6

value: ACC

value: Adenoid cystic carcinoma

value: Paranasal sinus

value: Pathology, Charite Berlin


title: ONB66

value: Base of scull

value: Neuropathology, UKGM Giessen/Marburg


title: H3K4me1, DB, 4

description: BED file: DB_14_dense.bed

value: liver

value: hepatocyte


title: H3K4me3, DB, 4

description: BED file: DB_14_dense.bed

value: Millipore #07-473


title: ONB16

value: ONB

value: Others

value: Capper, Acta Neuropathol 2018


title: SNUC6

value: NEC-like SMARCA4 ARID1A

value: SNUC

value: male

value: Nasal cavity, orbit

value: Neuropathology, GAU Gottingen


title: H3K4me3, DB, 3

description: BED file: DB_14_dense.bed

value: female


title: ONB14

value: Olfactory neuroblastoma

value: Nasal cavity

value: Neuropathology, LMU Muenchen


title: ONB12

value: Neuropathology, WWU Muenster


title: H3K4me1, DB, 2

description: BED file: DB_14_dense.bed

value: Millipore #07-436


title: ONB13


title: ACC5

value: ACC

value: Adenoid cystic carcinoma

value: Neuropathology, Charite Berlin


title: ACC4

value: Pathology, Charite Berlin


title: H3K4me3, DB, 2

description: BED file: DB_14_dense.bed

value: liver

value: hepatocyte

value: Millipore #07-473


title: ONB15

value: ONB

value: Nasal cavity, paranasal sinus, base of skull

value: Capper, Acta Neuropathol 2018


title: ONB11


title: Input, CA, input

description: BED file: CA_14_dense.bed

value: input

value: CAST/EiJ


title: NEC3

value: NEC-like SMARCA4 ARID1A

value: NEC

value: Neuroendocrine carcinoma

value: female

value: Paranasal sinus

value: Pathology, UKM Muenster


title: ACC3

description:
Not included in analysis
Noise point

value: ACC

value: Adenoid cystic carcinoma

value: male

value: Nasal cavity

tag: excluded

value: Not included in analysis

tag: rationale for exclusion

value: Noise point


title: H3K4me1, CA, 5

description: BED file: CA_14_dense.bed

value: liver

value: hepatocyte

value: Millipore #07-436


title: ONB65

value: ONB

value: Olfactory neuroblastoma

value: Base of scull

value: Neuropathology, UKGM Giessen/Marburg


title: H3K4me3, CA, 5

description: BED file: CA_14_dense.bed

value: CAST/EiJ

value: Millipore #07-473


title: ONB9

value: female

value: Neuropathology, LMU Muenchen

value: Capper, Acta Neuropathol 2018


title: ONB10


title: ACC2

value: ACC

value: Adenoid cystic carcinoma

value: Pathology, Charite Berlin


title: 27_Nonlesional_V12

city: Dublin

first: Walter

last: Kolch

address: School of Medicine, University College Dublin, Belfield, Dublin 4.

country: Ireland

institute: Systems Biology Ireland

data_processing:
The reads were aligned and quantified  to the Genome Reference Consortium Human Build 38 using the R package Rsubread with default settings.
Assembly: hg38
Supplementary files format and content: Txt file with raw gene counts for each sample
Supplementary files format and content: csv file with raw gene counts for all samples combined.

source_name: skin

extract_protocol:
RNA isolation was then performed using a Fibrous RNA isolation kit (Qiagen) following the manufacturer’s instruction.
RNA concentration and RIN score were assessed by Nanodrop and Bioanalyzer.

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

value: NL

tag: visit

tag: treatment

value: adalimumab

value: F

tag: smoking status

value: Current

tag: hurley stage

value: II

tag: bmi

tag: abcess count

tag: node count

tag: fistula count

tag: responder

value: YES


title: 28_Nonlesional_V1

tag: tissue

value: Non

value: NO


title: 28_Nonlesional_V12

tag: gender


title: 31_Lesional_V12

value: LS

tag: age


title: 27_Lesional_V1


title: 31_Nonlesional_V1


title: 31_Lesional_V1


title: 27_Lesional_V12


title: 31_Nonlesional_V12


title: 27_Nonlesional_V1


title: 28_Lesional_V1


title: 26_Nonlesional_V1

value: III


title: H3K4me1, CA, 4

description: BED file: CA_14_dense.bed

value: liver

tag: cell type

value: hepatocyte

tag: Sex

value: female

tag: individual id

tag: strain

value: CAST/EiJ

tag: antibody

value: Millipore #07-436


title: H3K4me3, CA, 4

description: BED file: CA_14_dense.bed

value: Millipore #07-473


title: 28_Lesional_V12

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

tag: visit


title: SNUC4

tag: methylation class

value: NEC-like SMARCA4 ARID1A

tag: conventional class

value: SNUC

tag: initial diagnosis

tag: localization

tag: tissue source

value: Neuropathology, Heidelberg


title: ONB7

value: ONB

value: Olfactory neuroblastoma

value: male

value: Nasal cavity, base of skull

value: Neuropathology, LMU Muenchen

tag: related publication

value: Capper, Acta Neuropathol 2018


title: 26_Lesional_V1

tag: tissue

value: LS

tag: treatment

value: adalimumab

tag: gender

value: F

tag: smoking status

value: Current

tag: hurley stage

value: III

tag: bmi

tag: abcess count

tag: node count

tag: fistula count

tag: responder

value: YES


title: ONB8

value: female

tag: age

value: Nasal cavity


title: H3K4me1, CA, 1

description: BED file: CA_14_dense.bed

value: liver

tag: cell type

value: hepatocyte

tag: Sex

tag: individual id

tag: strain

value: CAST/EiJ

tag: antibody

value: Millipore #07-436


title: NUT1

tag: methylation class

value: NUT

tag: conventional class

tag: initial diagnosis

value: NUT midline carcinoma

tag: localization

tag: tissue source

value: Neuropathology, Heidelberg


title: ONB6

value: ONB

value: Olfactory neuroblastoma

tag: gender

value: Paranasal sinus, base of skull

value: Neuropathology, LMU Muenchen

tag: related publication


title: H3K4me3, CA, 1

description: BED file: CA_14_dense.bed

tag: tissue

value: Millipore #07-473


title: 26_Lesional_V12

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

value: LS

tag: visit

tag: treatment

value: adalimumab

value: F

tag: smoking status

value: Current

tag: hurley stage

tag: bmi

tag: abcess count

tag: node count


title: ALV_RMS3

tag: methylation class

value: ALV RMS

tag: conventional class

value: Alveolar rhabdomyosarcoma

value: male

tag: age


title: 25_Nonlesional_V1

value: NL

value: III

tag: fistula count

tag: responder

value: YES


title: Input, B6, input

description: BED file: B6_14_dense.bed

value: liver

tag: cell type

value: hepatocyte

tag: Sex

value: female

tag: individual id

value: input

tag: strain

tag: antibody


title: 26_Nonlesional_V12

tag: tissue

tag: disease

tag: subject

tag: site

tag: visit

tag: gender


title: ALV_RMS2

tag: initial diagnosis

tag: tissue source

value: Neuropathology, Heidelberg


title: 25_Nonlesional_V12

value: skin

tag: treatment

tag: smoking status

tag: hurley stage

tag: bmi

tag: abcess count

tag: node count


title: 24_Lesional_V1

value: hidradenitis suppurativa

tag: age

value: Former

value: II

tag: fistula count

tag: responder

value: NO


title: H3K4me1, B6, 2

description: BED file: B6_14_dense.bed

tag: tissue

tag: cell type

tag: Sex

tag: individual id

tag: strain

tag: antibody

value: Millipore #07-436


title: SNUC2

tag: methylation class

value: NEC-like SMARCA4 ARID1A

tag: conventional class

value: SNUC

tag: initial diagnosis

tag: gender

tag: localization

value: Nasal cavity

value: Pathology, USB Basel


title: H3K4me1, B6, 4

description: BED file: B6_14_dense.bed


title: ONB5

value: ONB

value: Olfactory neuroblastoma

tag: tissue source

value: Neuropathology, LMU Muenchen

tag: related publication

value: Capper, Acta Neuropathol 2018


title: EPX_aptamers_SELEX2

city: Hamilton

first: Monsur

last: Ali

state: ON

address: ETB 303, Biointerface Institute, 1280 Main St West

department: Biointerfaces Institute

country: Canada

institute: McMaster University

data_processing:
library strategy: Random DNA sequences
The raw sequencing data was obatined as fastq file which was processed using Oracle software to sort out the sequences based on the abundance or frequency
The top 50 sequences of each SELEX strategy were selected and transferred in excel spreadsheet for chemical synthesis to test their binding affinity
Assembly: NA
Supplementary files format and content: tab-delimited text files

organism: synthetic construct

source_name: spitum

extract_protocol:
After SELEX, the DNA pool was amplified by PCr and applied in sequencing
DNA library was constructed by chemical synthesis with 50 random nucleobases

tag: genotype

value: random DNA library

tag: sample type

value: DNA pool


title: 25_Lesional_V12

tag: disease

tag: subject

tag: site

value: LS

tag: visit

tag: treatment

value: adalimumab

value: F

tag: age

tag: smoking status

value: Current

tag: hurley stage

value: III

tag: bmi

tag: abcess count

tag: node count

tag: fistula count

value: YES


title: EPX_aptamers_SELEX1


title: H3K4me3, B6, 4

description: BED file: B6_14_dense.bed

tag: tissue

value: liver

tag: cell type

value: hepatocyte

tag: Sex

value: female

tag: individual id

tag: strain

tag: antibody

value: Millipore #07-473


title: ONB1

tag: methylation class

tag: conventional class

tag: initial diagnosis

tag: gender

value: male

tag: localization

value: Nasal cavity

tag: tissue source

value: Neuropathology, UKE Hamburg

tag: related publication


title: H3K4me1, B6, 1

description: BED file: B6_14_dense.bed

tag: age

value: Millipore #07-436


title: ONB4

value: ONB

value: Olfactory neuroblastoma

value: Capper, Acta Neuropathol 2018


title: H3K4me3, B6, 2

description: BED file: B6_14_dense.bed


title: 24_Nonlesional_V12

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

value: NL

tag: visit

tag: treatment

tag: smoking status

value: Former

tag: hurley stage

value: II

tag: bmi

tag: abcess count

tag: responder

value: NO


title: EWS10

tag: methylation class

value: EWS

tag: conventional class

value: Ewing's sarcoma

value: Others

value: Capper, Nature 2018


title: Replicate 3

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

department: Immunology

country: France

institute: Institut Pasteur

data_processing:
Library strategy: gene trap
Paired-end sequencing reads with 250 nucleotides of each end in FASTQ files were decoded and adaptor sequence trimmed using by ea-utils tool (https://expressionanalysis.github.io/ea507 utils/). Paired-end reads were merged into single end read using FLASH with at least 10 nucleotide overlap (Magoč and Salzberg, 2011). Merged reads were mapped to the human hg38 reference genome and genetrap sequence using BWA mem (with default settings. Mapped reads with less than 30 nucleotides of genetrap sequence were filtered out. Among mapped read, the part of reads sequence mapped to human reference were annotated by HOMER. The annotated reads were counted and classified into genetic elements including exon, intron, 5’ UTR and 3’ UTR using in-house Perl script.
The insertion sites with less than 50 reads were first removed, hits falling into the coding sequencing of human genes were selected and the relative abundance of hits (read counts of gene X/total read counts) were calculated. Hits detected in at least 2 out of the 3 repeats were selected, and those exhibiting at least a 2-fold increase in enriched group (relative to unenriched control) were considered as significant for validation using siRNA gene silencing.
Genome_build: hg38
Supplementary_files_format_and_content: Table with raw counts of sequencing reads mapped to genic region

extract_protocol:
After the enrichment of mutagenized eHAP harboring cytosolic S. Typhimurium, the cells were incubated in Qiagen buffer AL supplemented with Proteinase K at 56˚C overnight to de-crosslink the cell pellet. In the following day, the genomic DNA were extracted from the cells using Qiagen DNA mini kit
1 μg of extracted genomic DNA was used as template for single-strand amplification. For each reaction, genomic DNA was combined with 0.01 mM dNTPs, 0.085 pmol double-biotinylated primer LTRI, Taq polyermase (1.25 U/rxn) and the supplied buffer (Qiagen). The reaction was performed for 50 cycles, with annealing at 58˚C for 45 s and elongation at 72˚C for 25s. Additional 2.5 U of Taq polymerase was supplemented to each reaction, and another 50 cycles were performed. To capture the biotinylated single-stranded DNA (ssDNA), each PCR reaction was combined in 1 to 1 ratio with DYNAL™ MyOne™ Dynabeads™ Streptavidin C1 (ThermoFisher) resuspended in 2 x binding buffer (6 M LiCl, 10 mM Tris, 1 mM EDTA, pH=7.5) for 2h at room temperature with horizontal shaking at 300 r.p.m. Prior to combination with PCR products, 20 μL of MyOne beads were washed once with 1 x PBS + 0.1% BSA and once with 1 x binding buffer (3 M LiCl, 5 mM Tris, 0.5 mM EDTA, pH=7.5). After capturing of ssDNA, the DNA-beads complex was resuspended in 100 μL of H2O. For the ligation single-stranded linker, the DNA-beads complex was resuspended in a ligation mixture consisting of 10 pmol LC1, 25% PEG 8000, 1 mM hexamine cobalt (III) chloride, 1 mM ATP, 20 U T4 RNA ligase 1 and the supplied buffer (ThermoFisher), and incubated overnight at room temperature with horizontal shaking at 300 r.p.m. On the following day, the DNA-beads complex was washed with H2O (2X) and resuspended in 100 μL of H2O. For the ligation single-stranded linker, the DNA-beads complex was resuspended in a ligation mixture consisting of 10 pmol LC1, 25% PEG 8000, 1 mM hexamine cobalt (III) chloride, 1 mM ATP, 20 U T4 RNA ligase 1 and the supplied buffer (ThermoFisher), and incubated overnight at room temperature with horizontal shaking at 300 r.p.m. On the following day, the DNA-beads complex was washed with H2O (2X) and resuspended in 10 μL of H2O. Subsequent PCR amplification was performed with 5 μL of DNA-beads complex as template, combined with 0.2 mM dNTPs, 8.35 pmol biotinylated primer LTRII, 8.35 pmol LCI, Taq polyermase (1.25 U/rxn) and the supplied buffer (Qiagen). The reaction was performed for 35 cycles, with denaturation at 95˚C for 45 s, annealing at 58˚C for 45 s and elongation at 72˚C for 25s. PCR products from each PCR reaction were captured using DYNAL MyOne Dynabeads Streptavidin C1. For each reaction, the non-biotinylated ssDNA was separated from the biotinylated ssDNA bound to magnetic beads by denaturation using fresh 0.1 N NaOH at room temperature for 10 minutes with horizontal shaking at 300 r.p.m. The second PCR amplification was performed with 5 μL of denatured non-biotinylated ssDNA as template, combined with 0.2 mM dNTPs, 8.35 pmol biotinylated primer LTRIII, 8.35 pmol LCII, Taq polyermase (1.25 U/rxn) and the supplied buffer (Qiagen). The reaction was performed for 35 cycles, with denaturation at 95˚C for 45 s, annealing at 58˚C for 45 s and elongation at 72˚C for 25s. The PCR products were purified using AMPure XP beads according to manufacturer’s manual, and further ligated with illumina adaptor sequences using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs). The prepared libraries were purified using AMPure XP beads and sequenced as 2 x 250 bp on MiSeq Reagent Kit v2 (illumina) using sequencing primer Rd1 Seq Primer and Rd2 Seq Primer from illumina.

treatment_protocol: 30 million eHAP cells were seeded and transduced with gene-trap retrovirus harvested from three combined harvest in the presence of 8 μg/mL protamine sulfate. The mutagenized cells were seeded and infected with S. Typhimurium harboring pSINA1.7,  infected cells were harvested and subjected to cell sorting.

tag: cell type

value: eHAP engineered human chronic leukemia cells transduced with Gene trap cassette retrovirus

value: mutagenized by transduction of retrovirus harboring Gene trap cassette and infected with S. Typhimurium harboring SINA1.2

tag: sorting parameter

value: sorted cells  harboring >= 2-fold increase of cytosolic S. Typhimurium


title: 24_Lesional_V12

tag: tissue

value: LS

value: adalimumab

tag: gender

value: F

tag: node count

tag: fistula count


title: ONB3

value: ONB

tag: initial diagnosis

value: Olfactory neuroblastoma

value: male

tag: age

tag: localization

value: Nasal cavity

tag: tissue source

value: Neuropathology, UKE Hamburg

tag: related publication

value: Capper, Acta Neuropathol 2018


title: EWS9


title: ONB2

value: Paranasal sinus


title: Replicate 2

source_name: eHAP engineered human chronic leukemia cells

tag: treatment


title: Replicate 1


title: 23_Nonlesional_V1

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

value: NL

tag: visit

tag: smoking status

value: Current

tag: hurley stage

value: II

tag: bmi

value: NO


title: H3K4me3, B6, 1

description: BED file: B6_14_dense.bed

tag: tissue

value: liver

tag: cell type

value: hepatocyte

tag: Sex

value: female

tag: individual id

tag: strain

tag: antibody

value: Millipore #07-473


title: EWS8

tag: methylation class

value: EWS

tag: conventional class

tag: initial diagnosis

value: Ewing's sarcoma

tag: gender

tag: age

tag: localization

value: Neuropathology, Heidelberg

value: Capper, Nature 2018


title: 24_Nonlesional_V1

tag: disease

tag: subject

tag: site

tag: treatment

value: adalimumab

value: F

value: Former

tag: abcess count

tag: node count

tag: fistula count

tag: responder


title: Input, AJ, input

description: BED file: AJ_14_dense.bed

tag: tissue

tag: cell type

tag: Sex

tag: individual id

value: input

value: A/J


title: Control

value: eHAP engineered human chronic leukemia cells transduced with Gene trap cassette retrovirus

value: mutagenized by transduction of retrovirus harboring Gene trap cassette and infected with S. Typhimurium harboring SINA1.2

tag: sorting parameter

value: Un-sorted cells


title: H3K4me1, AJ, 2

description: BED file: AJ_14_dense.bed

tag: strain

tag: antibody

value: Millipore #07-436


title: EWS7

tag: methylation class

tag: conventional class

tag: initial diagnosis

tag: gender

value: male

tag: age

tag: tissue source

value: Others

tag: related publication


title: EWS6

value: female

tag: localization


title: 23_Lesional_V12

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

value: LS

tag: visit

tag: treatment

tag: smoking status

value: Current

tag: hurley stage

value: II

tag: bmi

tag: abcess count

tag: node count

tag: fistula count

value: NO


title: 23_Nonlesional_V12

tag: tissue

value: NL

value: adalimumab

value: F

tag: responder


title: SH_LDB1_2

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: NB4 sample with LDB1 knockdown

extract_protocol:
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

tag: cell line

tag: genotype

value: LDB1 knockdown


title: EWS5

data_processing:
Statistical analysis was performed using the minfi package running on RStudio version 1.3.1093 based on the statistical language R version 3.5.1
Average beta-Values after normalization using the Noob method

tag: methylation class

value: EWS

tag: conventional class

tag: initial diagnosis

value: Ewing's sarcoma

tag: gender

tag: age

tag: tissue source

value: Neuropathology, Tuebingen

tag: related publication

value: Capper, Nature 2018


title: SH_LDB1_1


title: H3K4me1, AJ, 1

description: BED file: AJ_14_dense.bed

value: liver

tag: cell type

value: hepatocyte

tag: Sex

tag: individual id

tag: strain

value: A/J

tag: antibody

value: Millipore #07-436


title: 21_Lesional_V1

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

tag: visit

tag: treatment

tag: smoking status

tag: hurley stage

tag: bmi

tag: abcess count

tag: node count

tag: fistula count

value: YES


title: 21_Nonlesional_V1

tag: tissue

tag: gender

tag: age

value: Current

value: II

tag: responder


title: EWS3

tag: methylation class

tag: conventional class

tag: initial diagnosis

value: male

tag: localization

tag: tissue source

value: Others

tag: related publication


title: H3K4me3, AJ, 3

description: BED file: AJ_14_dense.bed

tag: cell type

tag: Sex

value: female

tag: individual id

tag: strain

tag: antibody

value: Millipore #07-473


title: EWS2

value: EWS


title: 21_Nonlesional_V12

tag: disease

tag: subject

tag: site

value: NL

tag: visit

tag: treatment

value: adalimumab

value: F

tag: smoking status

tag: hurley stage

tag: bmi

tag: abcess count

tag: node count


title: SH_NC_2

source_name: NB4 sample with no treatment

tag: cell line

tag: genotype

value: control


title: BM2_02_iPSC

city: Seoul

first: Youn Keong

last: Cho

address: 50-1 Yonsei-ro

department: Department of Laboratory Medicine

institute: Yonsei University College of Medicine

data_processing:
FastQC v0.11.7 was used for quality check.
Sequence reads were treammed using Trimmomatic 0.38.
Trimmed sequence reads were mapped to GRCh37 or hg19 using HISAT2 version 2.1.0.
StringTie version 2.1.3b was used for assemblying RNA-seq alignments.
Assembly: GRCh37 or hg19
Supplementary files format and content: All excel files attached include fold change values calculated using read count, FPKM and TPM for each sample for DEG analysis and their p-values.
Supplementary files format and content: Excel files for "hiPSCs" include the expression levels of genes in CB- and BM-derived hiPSCs compared to those obtained from PB-derived hiPSCs, which were set as the control.  Excel files for "differentiation" include the expression levels of genes in day 13, 20, and 27 during differentiation compared to those in their precursor hiPSCs.

source_name: Bone Marrow

extract_protocol:
RNA was extracted using RNeasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

value: Wt

tag: tissue

value: Bone Marrow

tag: cell type

value: hiPSC

tag: time

value: Day 0


title: BM1_03_D27

value: Erythroid differentiation

value: Day 27


title: 23_Lesional_V1

value: skin

value: hidradenitis suppurativa

value: LS

tag: gender

tag: age

value: Current

tag: fistula count

tag: responder

value: NO


title: H3K27ac, WS, 3

description: BED file: WS_14_dense.bed

value: liver

value: hepatocyte

tag: Sex

value: female

tag: individual id

tag: strain

value: WSB/EiJ

tag: antibody

value: abcam ab4729 Lot GR288020-1


title: EWS1

extract_protocol: Semi-automated DNA extraction was performed on the Maxwell RSC Instrument using the Maxwell RSC FFPE Plus DNA Purification Kit (Custom, AX4920; Promega), according to the manufacturer’s instructions.

tag: methylation class

value: EWS

tag: conventional class

tag: initial diagnosis

value: Ewing's sarcoma

value: male

tag: localization

tag: tissue source

value: Others

tag: related publication

value: Capper, Nature 2018


title: EWS4


title: SH_NC_1

tag: cell line

tag: genotype

value: control


title: BM1_03_D20

value: Wt

tag: tissue

value: Bone Marrow

tag: cell type

value: hiPSC

tag: treatment

value: Erythroid differentiation

tag: time

value: Day 20


title: H3K4me1, AJ, 3

description: BED file: AJ_14_dense.bed

tag: age

value: A/J

value: Millipore #07-436


title: CPH20

value: CPH

value: Craniopharyngioma

tag: gender

value: Sellar region

value: Neuropathology, Tuebingen


title: H3K4me3, AJ, 2

description: BED file: AJ_14_dense.bed

value: liver

value: hepatocyte

tag: Sex

value: female

tag: individual id

value: Millipore #07-473


title: H3K27ac, WS, 4

description: BED file: WS_14_dense.bed

tag: strain

value: WSB/EiJ

tag: antibody

value: abcam ab4729 Lot GR288020-1


title: CPH19

tag: methylation class

tag: conventional class

value: Neuropathology, Erlangen

value: Capper, Nature 2018


title: CPH18

tag: initial diagnosis

value: male

tag: localization


title: H3K4me3, AJ, 1

description: BED file: AJ_14_dense.bed


title: BM1_03_D13

value: Wt

value: Bone Marrow

value: hiPSC

value: Erythroid differentiation

value: Day 13


title: BM1_03_iPSC

description:
data2_BM_differentiation.xlsx
data2_hiPSCs.xlsx

value: control

value: Day 0


title: CB2_YJI_iPSC

source_name: Cord Blood

value: Cord Blood


title: 18_Lesional_V1

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

value: LS

tag: visit

value: adalimumab

value: F

tag: smoking status

value: Current

tag: hurley stage

value: II

tag: bmi

tag: abcess count

tag: node count

tag: fistula count

tag: responder

value: NO


title: 18_Nonlesional_V12

tag: tissue

value: NL

tag: treatment

tag: gender

tag: age


title: 18_Nonlesional_V1


title: 16_Lesional_V12


title: H3K27ac, WS, 2

description: BED file: WS_14_dense.bed

value: liver

tag: cell type

value: hepatocyte

tag: Sex

value: female

tag: individual id

tag: strain

value: WSB/EiJ

tag: antibody

value: abcam ab4729 Lot GR288020-1


title: H3K27ac, NZ, 3

description: BED file: NZ_14_dense.bed

value: NZO/HlLtJ


title: H3K27ac, PK, 2

description: BED file: PK_14_dense.bed

value: PWK/PhJ


title: CB1_CES_D13

tag: genotype

value: Wt

value: Cord Blood

value: hiPSC

value: Erythroid differentiation

tag: time

value: Day 13


title: 14_Nonlesional_V1

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

tag: visit

value: adalimumab

value: F

tag: smoking status

tag: hurley stage

value: III

value: YES


title: CPH16

tag: methylation class

value: CPH

tag: conventional class

tag: initial diagnosis

value: Craniopharyngioma

value: male

tag: localization

value: Sellar region

tag: tissue source

value: Neuropathology, Erlangen

tag: related publication

value: Capper, Nature 2018


title: CPH15

tag: gender

tag: age


title: CPH14


title: CPH17


title: H3K27ac, NZ, 2

description: BED file: NZ_14_dense.bed

tag: tissue

value: liver

tag: cell type

value: hepatocyte

tag: Sex

value: female

tag: individual id

tag: strain

value: NZO/HlLtJ

tag: antibody

value: abcam ab4729 Lot GR288020-1


title: CB1_CES_iPSC

description:
data2_CB_differentiation.xlsx
data2_hiPSCs.xlsx

tag: genotype

value: Wt

value: Cord Blood

value: hiPSC

tag: treatment

value: control

tag: time

value: Day 0


title: 14_Lesional_V1

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

value: LS

tag: visit

value: adalimumab

value: F

tag: smoking status

value: Current

tag: hurley stage

value: III

tag: bmi

tag: abcess count

tag: node count

tag: fistula count

tag: responder

value: YES


title: 18_Lesional_V12

tag: tissue

tag: gender

tag: age

value: II

value: NO


title: CB1_CES_D27

tag: genotype

tag: cell type

value: Erythroid differentiation

value: Day 27


title: H3K27ac, NZ, 1

description: BED file: NZ_14_dense.bed

value: liver

value: hepatocyte

tag: Sex

value: female

tag: individual id

tag: strain

value: NZO/HlLtJ

tag: antibody

value: abcam ab4729 Lot GR288020-1


title: 16_Lesional_V1

value: skin

tag: disease

tag: subject

tag: site

tag: visit

tag: treatment


title: 21_Lesional_V12

value: hidradenitis suppurativa

tag: smoking status

tag: hurley stage

tag: bmi

tag: abcess count

tag: node count


title: 14_Nonlesional_V12

tag: tissue

value: NL

tag: gender

tag: age

tag: fistula count

tag: responder


title: CB1_CES_D20

tag: genotype

value: Wt

value: Cord Blood

tag: cell type

value: hiPSC

tag: time

value: Day 20


title: H3K27ac, ND, 3

description: BED file: ND_14_dense.bed

tag: Sex

tag: individual id

tag: strain

value: NOD/ShiLtJ

tag: antibody


title: CPH12

tag: methylation class

value: CPH

tag: conventional class

tag: initial diagnosis

value: Craniopharyngioma

value: male

tag: localization

value: Sellar region

tag: tissue source

value: Neuropathology, Erlangen

tag: related publication

value: Capper, Nature 2018


title: PB2_LEK_iPSC

source_name: Peripheral Blood

tag: tissue

value: Peripheral Blood

tag: treatment

value: control

value: Day 0


title: CPH11

tag: gender

tag: age

value: Neuropathology, Heidelberg


title: H3K27ac, PK, 1

description: BED file: PK_14_dense.bed

value: liver

value: hepatocyte

value: female

value: PWK/PhJ

value: abcam ab4729 Lot GR288020-1


title: 14_Lesional_V12

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

value: LS

tag: visit

value: adalimumab

value: F

tag: smoking status

value: Current

tag: hurley stage

value: III

tag: bmi

tag: abcess count

tag: node count

tag: fistula count

tag: responder

value: YES


title: H3K27ac, PK, 3

description: BED file: PK_14_dense.bed

tag: cell type

tag: Sex

tag: individual id

tag: strain

tag: antibody


title: PB1_CJY_D27

tag: genotype

value: Wt

tag: tissue

value: Peripheral Blood

value: hiPSC

tag: treatment

value: Erythroid differentiation

tag: time

value: Day 27


title: PB1_CJY_D20

value: Day 20


title: 13_Nonlesional_V1

tag: disease

tag: subject

tag: site

value: NL

tag: visit

tag: gender

tag: age

value: II

value: NO


title: PB1_CJY_D13

value: Day 13


title: CPH10

tag: methylation class

value: CPH

tag: conventional class

tag: initial diagnosis

value: Craniopharyngioma

value: female

tag: localization

value: Sellar region

tag: tissue source

value: Neuropathology, Heidelberg

tag: related publication

value: Capper, Nature 2018


title: 13_Lesional_V1

value: skin

value: hidradenitis suppurativa

value: LS

value: adalimumab

value: F

tag: smoking status

value: Current

tag: hurley stage

tag: bmi

tag: abcess count

tag: node count

tag: fistula count

tag: responder


title: CPH13


title: CPH9


title: 12_Nonlesional_V1

tag: tissue

tag: disease

tag: subject

tag: site

tag: treatment

value: Former

value: III


title: PB1_CJY_iPSC

description:
data2_PB_differentiation.xlsx
data2_hiPSCs.xlsx

tag: genotype

value: Wt

value: Peripheral Blood

tag: cell type

value: hiPSC

value: control

tag: time

value: Day 0


title: CPH8

tag: methylation class

value: CPH

tag: conventional class

tag: initial diagnosis

value: Craniopharyngioma

tag: gender

value: female

tag: age

tag: localization

tag: tissue source


title: H3K27ac, ND, 1

description: BED file: ND_14_dense.bed

value: liver

value: hepatocyte

tag: Sex

tag: individual id

tag: strain

value: NOD/ShiLtJ

tag: antibody

value: abcam ab4729 Lot GR288020-1


title: H3K27ac, DB, 4

description: BED file: DB_14_dense.bed

tag: tissue


title: H3K27ac, ND, 2

description: BED file: ND_14_dense.bed


title: 12_Nonlesional_V12

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

value: NL

tag: visit

value: adalimumab

tag: smoking status

tag: hurley stage

tag: bmi

tag: abcess count

tag: node count

tag: fistula count

tag: responder

value: NO


title: CPH7

tag: methylation class

tag: conventional class

tag: initial diagnosis

tag: gender

tag: age

tag: localization

value: Sellar region

tag: tissue source

value: Neuropathology, Erlangen

tag: related publication

value: Capper, Nature 2018


title: JHH-7 cells, sgFGFR1/3/4, biol rep 3

city: Beijing

first: yue

last: cui

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences，Beijing

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence.
Trimmed sequence were mapped to GRCh38/hg38 whole genome using Botwie2.
Read count extraction and normalization were performed using RSEM.
Assembly: hg38
Supplementary files format and content: *.txt: Tab-delimited text files with matrix table including FPKM values for every gene and every sample.

growth_protocol: HuH-7 and JHH-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated from in vitro cultured cells using TRNzol (Tiangen).
RNA-seq library construction and sequencing were performed by Berry Genomics (Berry Genomics, Beijing, China).

tag: cell line

tag: cell type

value: liver cancer cells

tag: genotype

value: FGFR1/3/4 knockout


title: H3K27ac, DB, 2

description: BED file: DB_14_dense.bed

tag: tissue

tag: Sex

tag: individual id

tag: strain

tag: antibody


title: H3K27ac, CA, 1

description: BED file: CA_14_dense.bed

value: CAST/EiJ


title: H3K27ac, CA, 5

description: BED file: CA_14_dense.bed


title: JHH-7 cells, sgFGFR1/3/4, biol rep 2


title: CPH6

value: CPH

value: Craniopharyngioma

value: male


title: JHH-7 cells, sgFGFR3/4, biol rep 1

value: FGFR3/4 knockout


title: JHH-7 cells, sgFGFR3/4, biol rep 2


title: CPH3


title: JHH-7 cells, sgFGFR1/3/4, biol rep 1


title: JHH-7 cells, sgFGFR3/4, biol rep 3


title: CPH5


title: CPH2

value: female


title: H3K27ac, CA, 4

description: BED file: CA_14_dense.bed

value: liver

value: hepatocyte

value: abcam ab4729 Lot GR288020-1


title: 9_Lesional_V1

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

value: LS

tag: visit

tag: treatment

value: F

tag: smoking status

value: Former

tag: hurley stage

value: III

tag: bmi

tag: abcess count

tag: node count

tag: fistula count

tag: responder

value: YES


title: JHH-7 cells, sgFGFR4, biol rep 3

tag: cell line

tag: cell type

value: liver cancer cells

tag: genotype

value: FGFR4 knockout


title: 12_Lesional_V1

tag: tissue

value: adalimumab

tag: gender

tag: age

value: NO


title: 9_Nonlesional_V12

tag: disease

tag: subject

value: NL


title: CPH4

tag: methylation class

value: CPH

tag: conventional class

tag: initial diagnosis

value: Craniopharyngioma

tag: localization

value: Sellar region

tag: tissue source

value: Neuropathology, Heidelberg

tag: related publication

value: Capper, Nature 2018


title: 9_Lesional_V12

value: skin

tag: site

tag: visit

tag: treatment

tag: smoking status

tag: hurley stage

tag: bmi

tag: abcess count

tag: node count


title: 9_Nonlesional_V1

tag: tissue

value: hidradenitis suppurativa

tag: gender

tag: age

tag: fistula count

tag: responder


title: 12_Lesional_V12

tag: disease

tag: subject

value: LS


title: CPH1

tag: methylation class

tag: conventional class

tag: initial diagnosis

value: female

tag: localization

tag: tissue source

value: Neuropathology, Erlangen


title: JHH-7 cells, sgFGFR4, biol rep 2

tag: cell line

tag: cell type

tag: genotype


title: H3K27ac, B6, 1

description: BED file: B6_14_dense.bed

value: liver

value: hepatocyte

tag: Sex

tag: individual id

tag: strain

tag: antibody

value: abcam ab4729 Lot GR288020-1


title: H3K27ac, B6, 2

description: BED file: B6_14_dense.bed

tag: tissue

tag: age


title: H3K27ac, B6, 4

description: BED file: B6_14_dense.bed


title: H3K27ac, DB, 3

description: BED file: DB_14_dense.bed


title: H3K27ac, AJ, 3

description: BED file: AJ_14_dense.bed

value: A/J


title: 7_Nonlesional_V12

tag: site

tag: visit

tag: treatment

value: adalimumab

tag: gender

value: M

tag: smoking status

value: Former

tag: hurley stage

value: II

tag: bmi

tag: abcess count

tag: node count

tag: fistula count

tag: responder

value: YES


title: APA13

tag: methylation class

value: PIT AD

tag: conventional class

tag: initial diagnosis

value: Pituitary adenoma

tag: localization

value: Sellar region

tag: tissue source

tag: related publication


title: H3K27ac, AJ, 1

description: BED file: AJ_14_dense.bed

tag: tissue

tag: cell type

tag: Sex

tag: age

tag: individual id

tag: strain

tag: antibody


title: JHH-7 cells, sgKLB, biol rep 3

tag: cell line

value: liver cancer cells

tag: genotype

value: KLB knockout


title: APA14

tag: gender

value: Capper, Nature 2018


title: APA15

value: female

tag: excluded

value: Not included in analysis

tag: rationale for exclusion

value: Bad overall quality


title: H3K27ac, AJ, 2

description: BED file: AJ_14_dense.bed

value: liver

value: hepatocyte


title: 7_Lesional_V1

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

value: LS

tag: visit

tag: treatment

tag: smoking status

tag: hurley stage

tag: bmi

tag: abcess count

tag: node count

tag: fistula count

tag: responder


title: APA10

tag: methylation class

tag: conventional class

tag: initial diagnosis

tag: age

tag: localization

tag: tissue source

value: Neuropathology, Erlangen

tag: related publication


title: 5_Nonlesional_V1

tag: tissue

tag: disease

tag: subject

tag: site

value: NL

value: adalimumab

tag: gender

value: F

value: Current

value: III

value: NO


title: 7_Lesional_V12

tag: visit

tag: treatment

value: M

tag: smoking status

value: Former

tag: hurley stage

value: II

tag: bmi

value: YES


title: JHH-7 cells, sgKLB, biol rep 2

tag: cell line

tag: cell type

value: liver cancer cells

tag: genotype

value: KLB knockout


title: APA11

tag: methylation class

value: PIT AD

tag: conventional class

tag: initial diagnosis

value: Pituitary adenoma

value: female

tag: age

value: Sellar region

value: Capper, Nature 2018


title: H3K27ac, 129, 1

description: BED file: 129_14_dense.bed

tag: tissue

value: liver

value: hepatocyte

tag: Sex

tag: individual id

tag: strain

tag: antibody

value: abcam ab4729 Lot GR288020-1


title: 5_Lesional_V1

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

value: LS

tag: visit

value: adalimumab

tag: gender

value: F

value: Current

tag: abcess count

tag: node count

tag: fistula count

tag: responder


title: APA9

tag: methylation class

tag: conventional class

tag: localization

tag: tissue source

value: Others


title: APA12

tag: initial diagnosis

value: male

tag: age

value: Neuropathology, Erlangen

tag: related publication


title: JHH-7 cells, sgKLB, biol rep 1

tag: cell line

tag: cell type

value: liver cancer cells

tag: genotype

value: KLB knockout


title: H3K4me1, 129, 3

description: BED file: 129_14_dense.bed

tag: tissue

tag: Sex

value: female

tag: individual id

tag: strain

tag: antibody

value: Millipore #07-436


title: 5_Nonlesional_V12

tag: disease

tag: subject

tag: site

value: NL

tag: visit

tag: treatment

tag: gender

tag: smoking status

tag: hurley stage

value: III

tag: bmi

tag: abcess count

tag: node count

tag: fistula count

value: NO


title: JHH-7 cells, sgNTC, biol rep 3

tag: cell line

tag: cell type

tag: genotype

value: WT


title: H3K27ac, 129, 2

description: BED file: 129_14_dense.bed

tag: tissue

value: liver

value: hepatocyte

tag: Sex

tag: age

tag: individual id

tag: strain

value: abcam ab4729 Lot GR288020-1


title: JHH-7 cells, sgNTC, biol rep 2


title: 5_Lesional_V12

value: skin

tag: disease

value: hidradenitis suppurativa

tag: subject

tag: site

value: LS

tag: visit

value: adalimumab

tag: responder


title: 7_Nonlesional_V1

tag: treatment

tag: gender

value: M

tag: smoking status

value: Former

tag: hurley stage

value: II

tag: bmi

value: YES


title: JHH-7 cells, sgFGFR4, biol rep 1

tag: cell line

tag: cell type

value: liver cancer cells

value: FGFR4 knockout


title: APA8

tag: methylation class

value: PIT AD

tag: conventional class

tag: initial diagnosis

value: Pituitary adenoma

value: female

tag: localization

value: Sellar region

tag: tissue source

value: Others


title: H3K27ac, 129, 3

description: BED file: 129_14_dense.bed

tag: tissue

value: liver

value: hepatocyte

tag: Sex

tag: age

tag: individual id

tag: strain

tag: antibody


title: JHH-7 cells, sgNTC, biol rep 1

tag: genotype

value: WT


title: H3K4me3, 129, 3

description: BED file: 129_14_dense.bed

value: Millipore #07-473


title: input DNA_siACLY

data_processing:
FastQC (v0.11.5) was used for quality control analysis of the sequencing reads, to generate NGS quality control report. Trimmomatic (v0.36) was used to clean the raw reads and filter out the adaptor and low quality reads.
Alignment of the reads to the genome. The reference genome is from hg19. For each sample, we mapped the clean sequence reads to the reference genome using the STAR (v2.5.3a) program. RSeQC (v2.6) was used to evaluate mapped reads distribution, coverage uniformity, strand specificity, etc.
MACS2（v2.1.1）was used to call peak, giving a robust and high resolution ChIP-Seq peak predictions. Peaks were annotated related genes using Homer (v4.10). deepTools (v2.4.1) was used to plot gene coverage of the reads near TSS and TES. ChIPseeker（v1.5.1）was used to depict the reads distribution on chromosomes.
Homer（v4.10）was used to search motif and analyze transcription factors.
Genome_build: hg19
Supplementary_files_format_and_content: called peaks

extract_protocol: ChIP DNA was collected according to the ChIP protocol in the paper’s methods section.

treatment_protocol: HONE-1 cells were treated with ACLY siRNA or control siRNA using RNAiMax reagent. The cells were harvested after transfection at 48h for assays.

value: nasopharyngeal carcinoma

tag: transfection

value: si-ACLY

tag: chip antibody

value: none (input)


title: APA7

tag: gender

value: male

tag: excluded

value: Not included in analysis

tag: rationale for exclusion

value: Bad overall quality


title: HuH-7 cells, sgFGFR3/4, biol rep 3

tag: cell line

tag: cell type

value: liver cancer cells

value: FGFR3/4 knockout


title: APA6

tag: methylation class

tag: conventional class

value: PIT AD

tag: initial diagnosis


title: HuH-7 cells, sgFGFR3/4, biol rep 2


title: input DNA_siScr

value: si-scrambled


title: H3K4me1, 129, 2

description: BED file: 129_14_dense.bed

tag: tissue

value: female

value: Millipore #07-436


title: APA5

value: Pituitary adenoma

tag: localization

value: Sellar region

tag: tissue source

value: Neuropathology, Erlangen

tag: related publication

value: Capper, Nature 2018


title: HuH-7 cells, sgFGFR3/4, biol rep 1


title: APA4

tag: age


title: H3K27ac_ChIPSeq_siACLY

value: ChIP-grade Acetyl-histone H3 (Lys27) antibody (CST, catalog number 8173S)


title: HuH-7 cells, sgFGFR4, biol rep 3

value: FGFR4 knockout


title: H3K27ac_ChIPSeq_siScr

value: nasopharyngeal carcinoma


title: Input, 129, input

description: BED file: 129_14_dense.bed

value: liver

value: hepatocyte

tag: Sex

tag: individual id

value: input

tag: strain

tag: antibody


title: APA3

tag: gender

value: male


title: H3K4me1, 129, 1

description: BED file: 129_14_dense.bed


title: APA2

value: Others


title: H3K4me3, 129, 1

description: BED file: 129_14_dense.bed

value: Millipore #07-473


title: HuH-7 cells, sgFGFR4, biol rep 1

value: liver cancer cells

tag: genotype


title: HuH-7 cells, sgKLB, biol rep 3

value: KLB knockout


title: MC659WT RNA-seq, rep1

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

data_processing:
Alignment was performed using STAR (v2.7.3a) aligner. Reads mapping to ribosomal and mitochondrial genome were removed before performing alignment. The raw read counts were estimated using HTSeq (v0.11.2). Read counts were normalized using DESeq2 to get the normalized counts.
Assembly: mm10 (GRCm38.p6)
Supplementary files format and content: DEseq2 output file including differential analysis results and normalized count table as well as raw count files generated by HTSeq

source_name: Stable cell line from WT  fibrosarcoma

growth_protocol:
[stable cell line protocol] Tumors were dissected from mice approximately 3 months later and digested with collagenase solution [Collagenase, Sigma-Aldrich cat#C0130: 1 mg/mL, Hyaluronidase, Sigma-Aldrich, Cat#H3506: 0.1 mg/mL, and DNase I: 30 U/mL). The tumor cell mixture was then cultured for at least 10 passages to establish stable tumor cell line
The stable cell lines were grown in RPMI 1640 +FBS+ antibiotics

extract_protocol:
Total RNA was purified from tumor cells using the Direct-zol RNA microprep kit according to manufacturer’s instructions (Zymo Research, Irvine CA)
MedGenome Inc Custome library construction
Stranded mRNA-Seq

treatment_protocol: WT and IRF8 KO mice were injected subcutaneously with methylcholanthrene (MCA, Sigma-Aldrich, St Luis, MO) at 100 ug in 100 ul peanut oil per mouse

value: Tumor cell

value: WT

value: soft tissue sarcoma

tag: replicate

value: Replicate 1


title: H3K4me3, 129, 2

description: BED file: 129_14_dense.bed

value: female


title: MC659WT RNA-seq, rep2

tag: cell line

value: Replicate 2


title: APA1

value: PIT AD

value: Pituitary adenoma

value: Sellar region


title: MC654WT RNA-seq, rep2

tag: cell type


title: HuH-7 cells, sgKLB, biol rep 2


title: MC654WT RNA-seq, rep1