title: 2282: S2 dH1K27me2 IP

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description: genomic DNA

data_processing:
Encoding is Sanger/Illumina 1.9
Quality control of FastQ sequences was assessed using the FastQC software version 0.10.1.
Reads were aligned against the dm3 UCSC genome 2012 release using Bowtie 0.12.5, allowing 2 mismatches in the read seed and considering all possible alignment sites for each read in both Immunoprecipitated and control Input samples (setting an upper limit of 10.000 to limit output file size), in order to compare enrichment proportion for genomic features with multiple copies across the genome (i.e. transposons).
Aligned reads for 2262_2281 and 2282 replicates were merged using samtools 0.12.9
Identification and removal of potential PCR-amplification artifacts was performed with sambamba v0.5.1 using the markdup option and default settings. Coverage TDF tracks were generated with the IGV software version 2.1.16.
Peak calling between IPs and their respective input control in untreated and dH1-depleted cells was performed with MACS 1.4 using options –g dm and leaving the rest as default (p-value < 1e-05).
Gene-level quantification for IP and Input samples was performed using featureCounts from Rsubread 1.34.2 with default options.
Genome_build: dm3
Supplementary_files_format_and_content: Excel XLSX file contains sample counts at Flybase GeneID level (Ensembl71) done with featureCounts using default options (Rsubread 1.34.2)
Supplementary_files_format_and_content: BED file indicate chromosome, start, end and score in MACS 1.4.2 format

source_name: S2 cells

growth_protocol: S2 cells were grown on Schneider’s insect Medium (Sigma) supplemented with 100 μg/ml streptomycin (Gibco), 100 units/ml penicilin (Gibco) and 10% FBS (Gibco)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with polyclonal αdH1K27me2 antibodies (1-3mL). Finally DNA was purified by standard phenol extraction.
10 ng DNA, quantified by Qubit dsDNA HS Assay Kit (Invitrogen) was used for library preparation. Endrepair, adenylation, ligation of adapters and PCR enrichment for 15 cycles was performed using TruSeqRNA Sample Prep Kit (Illumina) according to manufacturer’s recommendations. Purified libraries were quantified by Qubit dsDNA HS Assay Kit (Invitrogen) and size distribution was evaluated using Bioanalyzer DNA 1000 assay (Agilent).

tag: replicate

tag: chip antibody

value: rabbit dH1K27me2 homemade


title: Day 8 Organoids

status: Public on Aug 02 2022

type: SRA

city: Heverlee

first: Adrian

last: Ranga

state: Flanders

address: Celestijnenlaan 200F - Room 03.349

department: Mechanical Engineering

country: Belgium

institute: KU Leuven

library_source: transcriptomic

data_processing:
Raw sequencing data was demultiplexed using the mkfastq pipeline of CellRanger 3.0.2.
Alignment, barcode assignment and UMI quantification was performed using the count pipeline of CellRanger 3.0.2 and mapped to the hg38 genome
Genome_build: hg38
Supplementary_files_format_and_content: processed raw count text file was generated from the Seurat object on R, and contains the raw count of each gene for every cell that remained after the QC step
Supplementary_files_format_and_content: metadata text file was generated from the Seurat object on R, and contains the metadata of each cell that remained after the QC step

molecule: total RNA

organism: Homo sapiens

source_name: Human iPSC derived brain tissue

growth_protocol: Tissue constructs: at day 0, hPSC spheroids were generated in Aggrewell plates, reached ~200 um by day 2, and were embedded in Matrigel and seeded in microfluidic grids, where they were cultured until day 8. Control organoids: at day 0, hPSC spheroids were generated in U-shaped 96well plates, at day 2 spheroids were embedded in Matrigel and cultured in floating suspension until day 8.

extract_protocol:
Organoid and chip samples (non-perfused and perfused) were collected and dissociated using TrypLE for 6 to 7 minutes at 37 degrees Celsius and with mechanical agitation to produce single cells. The TrypLE was neutralized using DMEM with 20% FBS. The single cells were spun down and washed twice with PBS before filtering and loading into the 10X Genomics Chromium Single Cell 3' Kit.
Library preparations for the scRNA-seq was performed using 10X Genomics Chromium Single Cell 3’ Kit, v3 (10X Genomics, Pleasanton, CA, USA). The cell count and the viability of the samples were accessed using LUNA dual fluorescence cell counter (Logos Biosystems) and a targeted cell recovery of 6000 cells was aimed for all the samples. Post cell count and QC, the samples were immediately loaded onto the Chromium Controller. Single cell RNAseq libraries were prepared using manufacturers recommendations (Single cell 3’ reagent kits v3 user guide; CG00052 Rev B), and at the different check points, the library quality was accessed using Qubit  (ThermoFisher) and Bioanalyzer (Agilent). With a sequencing coverage targeted for 50,000 reads per cell, single cell libraries were sequenced either on Illumina’s NovaSeq 6000 or NovaSeq 500 platforms using paired-end sequencing workflow and with recommended 10X; v3 read parameters (28-8-0-91 cycles).

treatment_protocol: Spheroids were kept in Rock inhibitor (Y-27632) for the first 24 hours to enhance aggregation. After culturing in pluripotency medium for the first 6 days, at day 7 neuronal induction was started and continued for 2 days.

tag: experimental time

value: Day 8

tag: setup

value: Suspension

tag: perfusion


title: EHUVEC_deltaVP30deltamucin_8h_1_6

type: RNA

city: Richland

first: Natalie

last: Heller

address: 902 Battelle Blvd.

country: USA

institute: PNNL

hyb_protocol: Hybridization was performed according to Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60 °C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Scanned images were analyzed using Agilent Feature Extraction Software (v11.0.1.1). The limma package for R (available on Bioconductor) was used to perform background correction, quantile normalization (normalizeBetweenArrays), and summarization (avereps) to derive a single normalized intensity value per probe. Outlier samples were detected using PCA and by visual inspection of heatmaps, and all data was re-processed after removing outlier samples. All data processing for each of the biological replicates was performed independently of the other.

source_name: HUVEC cells, deltaVP30-delta-mucin-inoculated, 8h, bioreplicate 1

label_protocol: Total RNA was labeled according to Agilent’s Quick Amp Labeling protocol as part of the Agilent One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent Technology). Total RNA from each sample was linearly amplified and labeled with Cy3-UTP.

growth_protocol: Cells and virus were grown on 10% FBS DMEM supplemented with L-glut, Pen/Strep, nonessential amino acids and sodium pyruvate.

extract_protocol: RNA was extracted with 1mL of Trizol.

treatment_protocol: Cells were infected with a multiplicity of infection of 10.

tag: time

tag: virus


title: Day 8 Perfused

value: Chip

value: Perfusion


title: 2262_2281: S2 dH1K27me2 IP

description: genomic DNA

library_source: genomic

molecule: genomic DNA

organism: Drosophila melanogaster

tag: cell type


title: Day 8 Non-perfused

value: No perfusion


title: RNAseq H2B WT Replicate4

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: Histone H2B Mutant WT Replicate4

data_processing:
The quality of RNA-seq datasets was assessed using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and the reads were then mapped to the human reference genome (hg38) using the spliced read aligner TopHat (v2.0.13) (Kim et al., 2013).
Transcriptome assembly was performed using cufflinks (v2.2.1) with default parameters (Trapnell et al., 2010).  The transcripts were further merged into distinct, non-overlapping sets using cuffmerge, followed by cuffdiff to call the differentially regulated transcripts.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

molecule: polyA RNA

growth_protocol: MDA-MB-231 cells ectopically expressing FLAG-tagged WT, D51A, or D51N H2B, or WT, D68A, or D68N H4 were maintained in RPMI-1640 (Sigma-Aldrich, R8758) supplemented with 10% fetal bovine serum (Sigma-Aldrich, F8067) and 1% penicillin/streptomycin.

extract_protocol:
MDA-MB-231 cells expressing FLAG-tagged wild-type or mutant histones were seeded in 6-well plates.  The cells were collected and total RNA was isolated using the RNeasy kit (Qiagen, 74136) according to the manufacturer’s instructions.
The total RNA was then enriched for polyA+ RNA using Dynabeads Oligo(dT)25 (Life Technologies, 61002).  The polyA+ RNA was then used to generate strand-specific RNA-seq libraries as described previously (Zhong et al., 2011).  The RNA-seq libraries were subjected to QC analyses (i.e., number of PCR cycles required to amplify each library, the final library yield, and the size distribution of final library DNA fragments) and sequenced using an Illumina NextSeq 500 to an average depth of ~40 million reads total per condition.  Two independent biological replicates were used.

treatment_protocol: MDA-MB-231 cells ectopically expressing FLAG-tagged WT, D51A, or D51N H2B were maintained in RPMI-1640 (Sigma-Aldrich, R8758) supplemented with 10% fetal bovine serum (Sigma-Aldrich, F8067) and 1% penicillin/streptomycin.

tag: genotype

value: Histone H2B Mutant WT


title: EHUVEC_deltaVP30deltamucin_0h_5_5

source_name: HUVEC cells, deltaVP30-delta-mucin-inoculated, 0h, bioreplicate 5


title: EHUVEC_deltaVP30deltamucin_0h_1_1

source_name: HUVEC cells, deltaVP30-delta-mucin-inoculated, 0h, bioreplicate 1


title: IMR32_0_1_DMSO_24hr_2_4

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

institute: Ghent University

data_processing:
Library strategy: TrAEL-seq
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated taking UMIs as well as mapping position into account, using UmiBam (v0.2.0; https://github.com/FelixKrueger/Umi-Grinder).
Samples were imported into Seqmonk v1.47, truncated to a single base and quantified %reverse reads in 1kb windows
Genome_build: GRCh38
TrAEL report: The file is a .txt file containing TrAEL-seq read polarity values for IMR32 cells either untreated, or treated for 24h with 689.5 nM 3AP or DMSO alone. Reads were then summed in 200 kb running windows spaced every 10 kb, and read polarity was quantified by (Reverse-Forward)/(Reverse+Forward) and subtracted by 50 ; data is an average of two biological replicates.

source_name: IMR32 (Neuroblastoma cell line)

growth_protocol: The IMR32 cells were cultured in a T-25 flask in RPMI 1640 media, containing 10% FBS, 100 IU/mL Penicillin/Streptomycin, 2mM L-Glutamine. IMR32 cells were allowed to adhere for 48h, after which the medium was replaced by fresh medium and the either the 0.1% DMSO control or 3AP treatment (689.5 nM) was added. After 24h of treatment, the supernatant of each flask was collected and added to the trypsinised cells. After centrifugation  (5 minutes at 1200 rpm), the pellet was washed with ice-cold PBS. 1 x 106 cells per condition were washed with L Buffer (100 mM EDTA pH8, 10 mM Tris pH7.5, 20 mM NaCl) and finally re-suspended in 60 µl of the buffer. The cell suspension was warmed for at least 2 minutes at 50°C before adding to 40µl melted and warm CleanCut agarose. The mixture was vortexed for 5s and directly pipetted into a plug mould and left to solidify for 30 min at 4°C. Each plug was transferred to a 2-ml tube containing 500 μl digestion buffer (10 mM Tris HCl (pH 7.5), 100 mM EDTA, 20 mM NaCl, 1% sodium N-lauroyl sarcosine, 0.1 mg/ml Proteinase K) and incubated overnight at 50°C. Plugs were then washed and RNase T1 treated.

extract_protocol:
½ an agarose plug of cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µl TrAEL-seq adaptor 1 ([App]NNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTUGCGCAGGCCATTGGCC[BtndT]GCGCUACACTCTTTCCCTACACGACGCT) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs were equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2µl 10 mM dNTPs and 1µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined. An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA chip (Agilent 5067-4626). Ideal cycle number should bring final library to final concentration of 1-3 nM, noting that the final library will be 3 cycles more concentrated than the test anyway. 21 µl of library was then amplified with 2 µl each of NEBNext Universal and chosen Index primer and 25 µl NEBNext Ultra II Q5 PCR master mix using same conditions as above for calculated cycle number. Amplified library was cleaned with 40 µl AMPure XP beads (Beckman A63881) and eluted with 26 µl 0.1x TE, then 25 µl of this was again purified with 20µl AMPure XP beads and eluted with 11µl 0.1x TE.

value: IMR32 (Neuroblastoma cell line)

tag: treatment

value: DMSO


title: EHUVEC_deltaVP30deltamucin_0h_3_3

source_name: HUVEC cells, deltaVP30-delta-mucin-inoculated, 0h, bioreplicate 3


title: RNAseq H2B WT Replicate3

description: Histone H2B Mutant WT Replicate3


title: RNAseq H2B WT Replicate2

description: Histone H2B Mutant WT Replicate2


title: EHUVEC_deltaVP30deltamucin_0h_2_2

source_name: HUVEC cells, deltaVP30-delta-mucin-inoculated, 0h, bioreplicate 2


title: ErbB4 KO cortex rep 3

city: Ann Arbor

first: Gabriel

last: Corfas

state: MI

address: 1150 West Medical Center Dr.

department: Otolaryngology

institute: University of Michgian

data_processing:
Fastq reads were converted into sanger reads with FASTQ Groomer. Reads were mapped to the mouse genome (mm9) using HISAT. Read counts were obtained with Htseq-count.
Differential gene expression between genotypes was obtained with DeSeq2
Assembly: mm9
Supplementary files format and content: raw gene counts for every gene per sample
Supplementary files format and content: differential gene expression

organism: Mus musculus

source_name: Cortex

extract_protocol:
Cortices were dissected and stored in RNAlater until lysis. RNA was extracted with Qiagen Rneasy kit with on-column DNase digestion, following the manufacturer's protocol.
cDNA library preparation was performed by the University of Michigan DNA sequencing core using standard Illumina protocols.

tag: strain

tag: tissue

value: cortex

tag: age

value: ErbB4 -/-


title: ErbB4 KO cortex rep 2


title: ErbB4 KO cortex rep 4


title: JF40

city: Rochester

first: Sundeep

last: Khosla

state: MN

address: 200 1st St SW

department: Endocrinology Research

institute: Mayo Clinic

data_processing:
Sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing software (version 3) and SCS data collection software (version 1.4.8)
Base calling was performed using Illumina RTA (version 1.12.4.2)
Paired-end reads from the raw RNAseq data were aligned using TopHat (version 2.0.6)
Quality control assessments were made using RSeQC software
Gene counts were generated using HTSeq software and gene annotation files were obtained from Illumina
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include count values for each Sample.

source_name: INK-ATTAC mouse, bred onto a C57BL/6 background

growth_protocol: INK-ATTAC transgenic mice were  bred onto a C57BL/6 background

extract_protocol: We obtained tibia diaphyses. The centrifuged bones were isolated using an Rneasy Micro Kit (Quiagen, Valenciy, CA) and treated with the Turbo DNA-freeTM Kit (Life Technologies, Grand Island, NY) to remove potential contaminationg DNA that may lead to false-positive amplification.

treatment_protocol: INK-ATTAC mice (6-12 months=young) were compared to INK-ATTAC mice (20 months=old), treated with either Vehicle or 10 mg of AP20187 per kg body mass [drug/body mass]) twice weekly beginning at 20 months of age for a total of 4 months.

value: bone

tag: treatment age

value: young

tag: treatment gropu

value: veh


title: JF39

value: INK-ATTAC mouse, bred onto a C57BL/6 background


title: RNAseq H2B WT Replicate1

description: Histone H2B Mutant WT Replicate1


title: JF41


title: ErbB4 KO cortex rep 1


title: 2232: S2 input

description: genomic DNA

value: none (input)


title: RPMI7951-A

city: New Taipei City

first: Shaochen

last: Lee

address: 510 Zhongzheng Rd., Xinzhuang Dist.

department: School of Medicine

country: Taiwan

institute: FuJen Catholic University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

source_name: culture cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: The cells were maintained in DMEM or MEM medium supplemented with 10% (v/v) FBS, 100 units/ml penicillin, and 100 ug/ml streptomycin under 5% CO2 with 100% humidity at 37 degree

extract_protocol: RNA was extracted with Trizol reagent

treatment_protocol: The suspended cells were derived from adherent cells by plating  onto sterile plastic dishes at the density of 4x10^5 cells per 10 ml under the same culture medium as adherent culture did.

value: adherent melanoma

tag: cell line


title: A2058-S

value: suspended melanoma


title: RNAseq H2B D51N Replicate4

description: Histone H2B Mutant D51N Replicate4

value: Histone H2B Mutant D51N


title: JF37


title: WT cortex rep 4

value: WT


title: HS695t-S


title: A2058-A


title: WT cortex rep 3


title: HS695t-A


title: RNAseq H2B D51N Replicate3

description: Histone H2B Mutant D51N Replicate3


title: JF36


title: JF35


title: RNAseq H2B D51N Replicate1

description: Histone H2B Mutant D51N Replicate1


title: JF34


title: RNAseq H2B D51N Replicate2

description: Histone H2B Mutant D51N Replicate2


title: JF27

value: old

value: ap


title: JF28


title: JF31


title: JF29


title: WT cortex rep 1


title: JF38


title: WT cortex rep 2


title: JF30


title: NKC_siEZH2_rep2

city: Goettingen

first: Lennart

middle: Viktor

last: Versemann

address: Robert-Koch-Strasse 40

department: Department of Gastroenterology, gastrointestinal Oncology and Endocrinology

country: Germany

institute: University Medical Center Goettingen

data_processing:
Single-end 50bp reads were aligned to mouse genome MGSCv37/mm9 by TopHat (Version 2.1.1)
Transcripts were counted by htseq-count (Version 0.9.1)
Transcripts normalization and differential expression analysis were performed by Cuffnorm (Version 2.2.1.2) and Cuffdiff (version 2.2.1.5) with FDR cutoff 0.05
Genome_build: mm9
Supplementary_files_format_and_content: Cufflinks showing changes in transcript expression from Cuffdiff
Supplementary_files_format_and_content: Normalized abundance measurement from Cuffnorm containing FPKM values for genes in all the treatment conditions
Supplementary_files_format_and_content: Matrix table with raw gene counts.txt corresponding with gene names

source_name: Primary PDAC cell line

growth_protocol: Primary PDAC mouse cell lines (KC, KPC, NKC, KNPC) were established as previously described (Hingorani et al., 2003, Hingorani et al., 2005, Baumgart et al., 2014, Singh et al., 2015). Cells were cultured in Dulbecco’s modified Eagle’s Medium containing 4.5 g/L D-Glucose, L- Glutamine supplemented with 10% fetal calf serum (FCS) and 1% non-essential amino acids (NEAA) at a humified 37 °C incubator with 5 % carbon dioxide supply.

extract_protocol:
Total RNA was harvested by TRIzol method from triplicate samples and quality was assessed by running 500 ng RNA on an agarose gel.
Libraries were prepared from 500 ng RNA using Truseq RNA Library Prep Kit v2 according to manufacturer’s instructions. mRNA was captured by RNA purification beads and eluted. The first strand and second strand cDNA were synthesized and the overhangs of the fragments were repaired into blunt ends. The 3’ end was added with a single adenine to prevent mutual ligation during the following adapter conjugation. Finally, the DNA fragments with both flow-cell-hybridization adapters were amplified and the library was quantified by Agilent Bioanalyzer 2100.

treatment_protocol: To transiently knockdown EZH2 (Ambion, AM16708, ID: 61436), cells were transfected with 60 nM small interfering RNA (siRNA) using siLentFect lipid reagent (Bio-Rad, 170-3362) in 200 µl OptiMEM (Gibco, 31985-062). Silencer Negative Control No. 1 siRNA (Ambion, 4611) was used as the negative control.

value: Primary PDAC cell line

value: siRNA EZH2


title: RNAseq H2B D51A Replicate2

description: Histone H2B Mutant D51A Replicate2

value: Histone H2B Mutant D51A


title: JF24


title: NKC_siEZH2_rep3


title: RNAseq H2B D51A Replicate3

description: Histone H2B Mutant D51A Replicate3


title: NKC_siCtrl_rep3

value: siRNA Control


title: NKC_siEZH2_rep1


title: RNAseq H2B D51A Replicate1

description: Histone H2B Mutant D51A Replicate1


title: JF33


title: ChIPseq WT plus A485 Input rep1

description: ChIPseq WT plus A485 Input replicate1

data_processing:
 The quality of the ChIP-seq datasets was assessed using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). ChIP-seq raw reads were aligned separately to the human reference genome (hg38) and the spike-in Drosophila reference genome (dm3) using Bowtie2 (v2.3.2) (Langmead and Salzberg, 2012).
  Only one alignment is reported for each read and duplicate reads were filtered using the Picard MarkDuplicates tool.  Uniquely mapped Drosophila reads were counted in the sample containing the least number of drosophila mapped reads and used to generate a normalization factor for random downsampling.  Reads were converted into bigwig files using BEDTools (v2.29.0) genomecov function (Quinlan and Hall, 2010) for visualization in the UCSC Genome Browser.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

growth_protocol: MDA-MB-231 cells ectopically expressing FLAG-tagged WT, D51A, or D51N H2B were maintained in RPMI-1640 (Sigma-Aldrich, R8758) supplemented with 10% fetal bovine serum (Sigma-Aldrich, F8067) and 1% penicillin/streptomycin.

extract_protocol:
Native ChIP was performed as previously described using with 5×106 cells. The cells were trypsinized to release them from the culture dishes, washed, and lysed using Hypotonic Lysis Buffer [50 mM Tris-HCl pH 7.4, 1 mM CaCl2, 0.2% Triton X-100, 250 nM ADP-HPD (Sigma-Aldrich, A0627, a PARG inhibitor), 10 μM PJ34 (Enzo Life Sciences, ALX-270-289, a PARP inhibitor), and protease inhibitor cocktail (Roche)] with micrococcal nuclease for 5 min at 37 °C to recover mono- to tri-nucleosomes.  Nuclei were lysed by brief sonication and dialyzed into RIPA Buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100) for 2 hr at 4 °C.  Soluble material (30 µg) was incubated with 2.5 μg of H2BK12ac antibody bound to 25 μL protein A Dynabeads (Invitrogen) and incubated overnight at 4 °C, with 5% reserved as input.  Magnetic beads were washed as follows: 3x RIPA buffer, 2x RIPA buffer + 300 mM NaCl, 2x LiCl Buffer (250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate), 1x TE + 50 mM NaCl.  Chromatin was eluted and treated with Proteinase K.  The ChIP’d DNA was purified and eluted in water.
ChIP-seq libraries were prepared from 5 ng of ChIP’d DNA following the Illumina TruSeq protocol.  The quality of the libraries was assessed using a D1000 ScreenTape on a 2200 TapeStation (Agilent) and quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher).  Libraries with unique adaptor barcodes were multiplexed and sequenced on an Illumina NextSeq 500 (paired-end, 33 base pair reads).  The ChIP-seq libraries were sequenced to an average depth of ~35 million unique aligned reads per condition.  Two independent biological replicates were used.

treatment_protocol: Cells were grown until 70% confluence and treated with 5 M A485 (Tocris Bioscience, 1104546-89-5) or DMSO vehicle for 2 hours.

tag: agent

tag: antibody

value: none, Input


title: JF32


title: JF23


title: ChIPseq WT plus A485 H2BK12ac rep2

description:
ChIPseq WT plus A485 H2BK12ac replicate2
ChIPseq_WT_Plus_A485_H2BK12ac.bw


title: JF20


title: NKC_siCtrl_rep1


title: JF19


title: JF17


title: KPC_siEZH2_rep3

value: KrasG12D;Trp53R173H/+ ;Cre


title: NKC_siCtrl_rep2


title: JF18

value: bone


title: KPC_siEZH2_rep2


title: JF26


title: ChIPseq WT H2BK12ac rep2

description:
ChIPseq WT H2BK12ac replicate2
ChIPseq_WT_H2BK12ac.bw


title: ChIPseq WT plus A485 H2BK12ac rep1

description:
ChIPseq WT plus A485 H2BK12ac replicate1
ChIPseq_WT_Plus_A485_H2BK12ac.bw


title: JF16


title: RNAseq H2B D51A Replicate4

description: Histone H2B Mutant D51A Replicate4


title: KPC_siEZH2_rep1


title: JF25


title: JF21


title: JF22


title: JF12


title: JF14


title: ChIPseq WT Input rep1

description: ChIPseq WT Input replicate1


title: JF15


title: JF13


title: JF11


title: KPC_siCtrl_rep3


title: JF10


title: KPC_siCtrl_rep2


title: JF8


title: JF9


title: JF7


title: JF6


title: ChIPseq D51N plus A485 H2BK12ac rep2

description:
ChIPseq D51N plus A485 H2BK12ac replicate2
ChIPseq_D51N_Plus_A485_H2BK12ac.bw


title: ChIPseq D51N plus A485 Input rep1

description: ChIPseq D51N plus A485 Input replicate1


title: KPC_siCtrl_rep1


title: ChIPseq WT H2BK12ac rep1

description:
ChIPseq WT H2BK12ac replicate1
ChIPseq_WT_H2BK12ac.bw


title: ChIPseq D51N plus A485 H2BK12ac rep1

description:
ChIPseq D51N plus A485 H2BK12ac replicate1
ChIPseq_D51N_Plus_A485_H2BK12ac.bw


title: JF5


title: ChIPseq D51N Input rep1

description: ChIPseq D51N Input replicate1


title: JF4


title: JF3


title: KNPC_siEZH2_rep2


title: KNPC_siEZH2_rep3


title: ChIPseq D51N H2BK12ac rep2

description:
ChIPseq D51N H2BK12ac replicate2
ChIPseq_D51N_H2BK12ac.bw


title: JF1


title: KNPC_siEZH2_rep1


title: JF2


title: ChIPseq D51N H2BK12ac rep1

description:
ChIPseq D51N H2BK12ac replicate1
ChIPseq_D51N_H2BK12ac.bw


title: ChIPseq D51A plus A485 Input rep1

description: ChIPseq D51A plus A485 Input replicate1


title: KNPC_siCtrl_rep3


title: Parp1KO_12hr_RNAseq_Rep2

data_processing:
mRNA-seq reads were subjected to quality-control using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed to remove adapter sequences (CutAdapt),
aligned to the mouse reference genome (GRCm38/mm10) using Tophat {Trapnell, 2009}
reads were sorted and indexed using Samtools (Li, 2009).
Data were then converted to miso format using MISO (Katz, 2010) followed by visualization with Sashimi (Katz, 2009).
MISO was used to identify significantly altered splicing events upon both PARP-1 depletion and over the course of differentiation with a cutoff of a 0.2 delta psi and bayes factor of 5.
Additionally reads were processed into rmats files using python RMATS with variable read length and clipping allowance.
RMats was used to quantify splicing events within JCEC files by event class with cutoff of a false discovery rate of 5%
Genome_build: mm10

source_name: embryonic stem cells

growth_protocol: mESCs were maintained on a feeder layer of CF6Neo Mouse Embryonic Fibroblasts (ThermoFisher, A34963) in mESC growth medium: Dulbecco’s modified Eagle medium (Gibco, 11965) containing 2 mM L-glutamine (Sigma Aldrich), supplemented with 15% (v/v) fetal bovine serum (Atlanta Biologicals; S11595), 0.1 mM nonessential amino acids (Sigma Aldrich; M7145), 1mM sodium pyruvate (Invitrogen; 11360070), 0.15% LIF (made with LIF expressing COS cells), 1% penicillin/streptomycin (), and 1x B-mercaptoethanol (Gibco, 21985023)

extract_protocol:
total RNA was extracted from mESCs using RNeasy kit (Qiagen, 74136), The integrity of the RNA was assessed and verified using an Experion Automated Electrophoresis System (Bio-Rad) before mRNA-seq libraries were prepared using methods described previously.
polyA+ RNA was enriched using Dynabeads oligo(dT)25 (Invitrogen), heat fragmented, and reverse transcribed using random hexamers in the presence of dNTPs. Second strand cDNA synthesis was performed with dNTPs, but replacing dTTP with dUTP. After end-repair, dA-tailing, ligation to adaptors containing barcode sequences, and size selection using AMPure beads (Agencourt) for an insert length size of 150bp. The synthesized second-strand was digested using uracil DNA glycosylase (Enzymatics). A final PCR reaction was performed using Phusion high-fidelity DNA polymerase (NEB)

treatment_protocol: Feeder cells were depleted for experimental assays by two passages on 0.2% gelatin coated plates. Wild type or Parp1-/- embryonic stem cells were differentiated in ultra-low attachment plates (ThermoFisher, 05-539-101) paired with LIF removal.

tag: differentiation stage


title: Parp1KO_6hr_RNAseq_Rep2


title: KNPC_siCtrl_rep2


title: EHUVEC_deltaVP30deltamucin_72h_5_25

source_name: HUVEC cells, deltaVP30-delta-mucin-inoculated, 72h, bioreplicate 5


title: ChIPseq D51A plus A485 H2BK12ac rep2

description:
ChIPseq D51A plus A485 H2BK12ac replicate2
ChIPseq_D51A_Plus_A485_H2BK12ac.bw


title: KNPC_siCtrl_rep1


title: WildType_72hr_RNAseq_Rep2

value: Wild Type


title: ChIPseq D51A plus A485 H2BK12ac rep1

description:
ChIPseq D51A plus A485 H2BK12ac replicate1
ChIPseq_D51A_Plus_A485_H2BK12ac.bw


title: WildType_12hr_RNAseq_Rep2


title: KC_siEZH2_rep3

value: KrasG12D ;Cre


title: ChIPseq D51A Input rep1

description: ChIPseq D51A Input replicate1


title: ChIPseq D51A H2BK12ac rep2

description:
ChIPseq D51A H2BK12ac replicate2
ChIPseq_D51A_H2BK12ac.bw


title: Parp1KO_72hr_RNAseq_Rep2


title: Parp1KO_72hr_RNAseq_Rep1


title: WildType_6hr_RNAseq_Rep2


title: WildTtype_0hr_RNAseq_Rep2


title: Parp1KO_24hr_RNAseq_Rep1


title: Parp1KO_24hr_RNAseq_Rep2


title: KC_siEZH2_rep1


title: ChIPseq D51A H2BK12ac rep1

description:
ChIPseq D51A H2BK12ac replicate1
ChIPseq_D51A_H2BK12ac.bw


title: KC_siCtrl_rep3


title: Parp1KO_6hr_RNAseq_Rep1


title: Parp1KO_12hr_RNAseq_Rep1


title: Parp1KO_0hr_RNAseq_Rep1


title: Parp1KO_0hr_RNAseq_Rep2


title: ATACseq_H4_WT_rep4

description:
Histone H4WT mutant replicate 4
ATACseq_H4_WT.bw

data_processing:
The quality of the ATAC-seq datasets was assessed using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
The ATAC-seq reads were then aligned to the human genome (hg38) using BWAKit (v0.7.15) (Li and Durbin, 2009).  For unique alignments, duplicate reads with quality score over 10 were filtered out using picard tools (v2.10.3) (http://broadinstitute.github.io/picard/).  The resulting uniquely mapped reads were normalized to the same read depth across all samples and converted into bigWig files using the writeWiggle function from the groHMM package in R (Chae et al., 2015) for visualization in the UCSC Genome Browser
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

extract_protocol:
MDA-MB-231 cells expressing FLAG-tagged wild-type or mutant histones were seeded in 6-well plates.  For individual samples, 5 x 104 cells were collected, washed, and lysed in 50 μL of cold ATAC Resuspension Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin) on ice.  Nuclei were then collected and resuspended in 50 μL of Transposition Mixture (10 mM Tris-HCl pH 7.6, 3 mM MgCl2, 10% dimethylformamide, 100 nM transposase, 0.1% Tween-20, and 0.01% digitonin), and incubated at 37 °C for 30 minutes in a thermomixer at 1,000 RPM.
DNA was collected using a Qiaquick PCR purification kit (Qiagen, 28104) according to the manufacturer’s instructions.  Eluted DNA was amplified using a KAPA non-hot-start PCR kit and purified using AMPure XP beads. The ATAC-seq libraries were subjected to QC analyses (i.e., the final library yield and the size distribution of the final library DNA fragments) and sequenced using an Illumina NextSeq 500 to an average depth of 57 million unique aligned reads per condition.  Two independent biological replicates were used.

value: Histone H4WT mutant


title: WildType_72hr_RNAseq_Rep1


title: WildType_24hr_RNAseq_Rep2


title: KC_siCtrl_rep2


title: ATACseq_H4_WT_rep3

description:
Histone H4WT mutant replicate 3
ATACseq_H4_WT.bw


title: WildType_12hr_RNAseq_Rep1


title: WildType_6hr_RNAseq_Rep1


title: RPMI7951-S


title: KC_siEZH2_rep2


title: WildTtype_0hr_RNAseq_Rep1


title: ABAT cKO_3

city: columbus

first: Ruoning

last: Wang

state: OH

address: 700 Children's Drive

institute: Nationwide children's hospital

description: murine TH0 cell

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to human genome assembly (hg19) (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (v19) .
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: T cell

growth_protocol: Naïve CD4+ T cells isolated from mice were activated with IL-2 as well as plate-bound anti-mCD3/CD28 antibodies for 36hrs.

extract_protocol:
Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols at the Nationwide Childrens Hospital.

treatment_protocol: no treatment

value: T cell from LNs and spleen

value: 6-8 weeks

value: ABAT cKO


title: ATACseq_H4_WT_rep1

description:
Histone H4WT mutant replicate 1
ATACseq_H4_WT.bw


title: LPA treated, 6 hours, replicate 3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: LPA treated, 6 hours, replicate 3

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and mm10 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene

source_name: bone marrow-derived dendritic cells (BMDC)

extract_protocol:
Total RNA from LPA-treated murine BMDCs was isolated using the RNeasy MinElute kit (Qiagen)
All samples passed the RNA quality control examined by Agilent Bioanalyzer 2100, and mRNA libraries were generated using True-seq non-stranded RNA-seq library preparation protocoland sequenced at the Weill Cornell Epigenomics Core Facility

tag: lpa

value: 6 hours

tag: replicate


title: LPA treated, 6 hours, replicate 2

description: LPA treated, 6 hours, replicate 2


title: LPA treated, 6 hours, replicate 1

description: LPA treated, 6 hours, replicate 1


title: ABAT cKO_2

description: murine TH0 cell


title: ATACseq_H4_D68N_rep4

description:
Histone H4D68N mutant replicate 4
ATACseq_H4_D68N.bw

value: Histone H4D68N mutant


title: ATACseq_H4_D68N_rep3

description:
Histone H4D68N mutant replicate 3
ATACseq_H4_D68N.bw


title: LPA treated, 2 hours, replicate 1

description: LPA treated, 2 hours, replicate 1

value: 2 hours


title: ABAT cKO_1

description: murine TH0 cell


title: LPA treated, 2 hours, replicate 3

description: LPA treated, 2 hours, replicate 3


title: WT_3

description: murine TH0 cell


title: WildType_24hr_RNAseq_Rep1


title: KC_siCtrl_rep1


title: ATACseq_H4_D68N_rep2

description:
Histone H4D68N mutant replicate 2
ATACseq_H4_D68N.bw


title: LPA treated, 2 hours, replicate 2

description: LPA treated, 2 hours, replicate 2


title: untreated, replicate 3

description: untreated, replicate 3

value: untreated


title: untreated, replicate 1

description: untreated, replicate 1


title: WT_2

description: murine TH0 cell


title: ATACseq_H4_WT_rep2

description:
Histone H4WT mutant replicate 2
ATACseq_H4_WT.bw


title: WT_1

description: murine TH0 cell


title: ATACseq_H4_D68A_rep4

description:
Histone H4D68A mutant replicate 4
ATACseq_H4_D68A.bw

value: Histone H4D68A mutant


title: 7dpw_young_v2_2

city: Irvine

first: Remy

last: Vu

address: D288 Med Sci I Health Sciences Rd

institute: University of California, Irvine

description:
chromium kit version Cell barcode suffix for aggr file:
-7
young_v2_matrix.mtx
young_v2_barcodes.tsv
young_v2_genes.tsv
7dpw_young_v2_2_possorted_genome_bam.bam

data_processing:
FASTQ files were aligned utilizing 10x Genomics Cell Ranger 3.1.0.
Each library was aligned to an indexed mm10 genome using Cell Ranger Count.
Cell Ranger Aggr function was used to normalize the number of mapped reads per cells across the libraries.
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output

source_name: Dorsal wound

growth_protocol: All mice were purchased from Jax

extract_protocol: FACS-sorted cells were washed in PBS containing 0.04% BSA and resuspended at a concentration of approximately 1,000 cell/mL. Library generation was performed following the Chromium Single Cell 3ʹ Reagents Kits v2 or v3 (following the CG00052 Rev B. user guide) where we target 10,000 cells per sample for capture. Additional reagents included: nuclease-free water (Thermo Fisher Scientific; AM9937), low TE buffer (Thermo Fisher Scientific; 12090-015), ethanol (Millipore Sigma; E7023-500ML), SPRIselect Reagent Kit (Beckman Coulter; B23318), 10% Tween 20 (Bio-Rad; 1662404), glycerin (Ricca Chemical Company; 3290-32), QIAGEN Buffer EB (QIAGEN; 19086). Each library was sequenced on the Illumina HiSeq 4000 platform to achieve an average of approximately 50,000 reads per cell

value: dorsal skin

value: Young

tag: wound timepoint

value: Wound at 7dpw

tag: chromium kit version


title: 7dpw_young_v2_1

description:
chromium kit version Cell barcode suffix for aggr file:
-6
young_v2_matrix.mtx
young_v2_barcodes.tsv
young_v2_genes.tsv
7dpw_young_v2_1_possorted_genome_bam.bam


title: KO 7dpf_3

city: Warszawa

first: Cecilia

middle: Lanny

last: Winata

address: Ks. Trojdena 4

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

description: replicate 3

data_processing:
Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10.
Low-quality sequences and adapter content were trimmed with cutadapt v. 2.4.
Reads were aligned to the zebrafish genome assembly GRCz10  using STAR v2.7.7a and samtools v1.11
Expression quantification was performed using HTSeq v0.11.2
Differential expression was performed using DESeq2 (R v3.6.3)
Putative RNA editing sites based on DNA- and RNA-seq input were detected using REDiscover (https://github.com/lpryszcz/REDiscover). Options -q 15 -Q 20, were used, i.e. a minimal mapping quality of 15 and a minimal base call quality of 20 were required. Sites that were not homozygous between female and male samples were excluded from the analysis. Alternative alleles were only called when they were present in at least 20% of RNA reads. For simplicity, sites with more than one alternative allele were excluded from the analysis.
Assembly: GRCz10
Supplementary files format and content: tab delimited file format

organism: Danio rerio

source_name: whole zebrafish embryo

growth_protocol: Zebrafish embryos were maintained according to standard protocol (Westerfield et al., 2000) and staged according to standard morphological criteria (Kimmel et al., 1995).

extract_protocol:
Parental genomic DNA was extracted from adult fin-clippings of an individual male and female zebrafish of wild-type ABTL background. For the rest of the samples, 20 pooled embryos from each time point were isolated for RNA extraction. Total RNA was extracted using TRIzol LS (Thermo Fisher Scientific, USA) and cleaned up on the Qiagen Rneasy Mini column (Qiagen, USA). Quality control of extracted RNA was performed using the 2200 TapeStation system from Agilent Technologies (USA). To avoid the bias caused by cytoplasmic polyadenylation during early embryonic stages (Winata et al., 2018), total RNA was rRNA-depleted using Ribo-Zero Magnetic Gold Kit (Human, Mouse, Rat; Epicenter). For the 7 dpf samples, total RNA was subjected to mRNA enrichment using  NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, NEB).
genomic DNA library was constructed using Nextera XT (Illumina, USA) using standard protocol; cDNA synthesis was performed by SMARTer Stranded RNA-seq kit (Clontech Laboratories, USA) as recommended by the manufacturer. For the 7 dpf samples, library was constructed using TruSeq Stranded Total RNA library preparation kit (Illumina, USA)

treatment_protocol: To assess the effect of Adar KD and OE, uninjected wild-type and embryos injected with 1 ng of adar MO or 50 pg of adar mRNA were kept until desired developmental stage.

value: adar-/-

value: whole embryo

tag: developmental stage

value: 7 dpf


title: ATACseq_H4_D68A_rep1

description:
Histone H4D68A mutant replicate 1
ATACseq_H4_D68A.bw


title: untreated, replicate 2

description: untreated, replicate 2


title: ATACseq_H4_D68A_rep2

description:
Histone H4D68A mutant replicate 2
ATACseq_H4_D68A.bw


title: ATACseq_H4_D68N_rep1

description:
Histone H4D68N mutant replicate 1
ATACseq_H4_D68N.bw


title: ATACseq_H2B_WT_rep6

description:
Histone H2B WT mutant replicate 6
ATACseq_H2B_WT.bw

value: Histone H2B WT mutant


title: KO 7dpf_1

description: replicate 1


title: KO 7dpf_2

description: replicate 2


title: ATACseq_H4_D68A_rep3

description:
Histone H4D68A mutant replicate 3
ATACseq_H4_D68A.bw


title: WT 7dpf_2

description: replicate 2

value: WT (ABTL)


title: ATACseq_H2B_WT_rep5

description:
Histone H2B WT mutant replicate 5
ATACseq_H2B_WT.bw


title: WT 7dpf_3

description: replicate 3


title: ATACseq_H2B_WT_rep4

description:
Histone H2B WT mutant replicate 4
ATACseq_H2B_WT.bw


title: WT 7dpf_1

description: replicate 1


title: ATACseq_H2B_WT_rep1

description:
Histone H2B WT mutant replicate 1
ATACseq_H2B_WT.bw


title: ATACseq_H2B_D51N_rep6

description:
Histone H2B D51N mutant replicate 6
ATACseq_H2B_D51N.bw

value: Histone H2B D51N mutant


title: ATACseq_H2B_WT_rep2

description:
Histone H2B WT mutant replicate 2
ATACseq_H2B_WT.bw


title: ATACseq_H2B_WT_rep3

description:
Histone H2B WT mutant replicate 3
ATACseq_H2B_WT.bw


title: CRL-2884 Day 2  Control rep1

city: Birmingham

first: Zsuzsanna

last: Nagy

address: Medical School

country: United Kingdom

institute: University of Birmingham

description:
GD 2 0 1
Gene expression in Schwann like cells after 48 hours in normal culture conditions followed by 48 hours vehicle treatment (0.9%NaCl in water added to normal culture medium at 1:10,000 ratio)

hyb_protocol: Hybridisation was carried out following the manufacturers instructions using the  Agilent  SurePrint G3 Human Unrestricted GE 8x60K array (G4858A- 028004).

scan_protocol: Slides were scanned immediately after washing.

data_processing: The scanned images were analysed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CRL-2884-48 hour culture + 48 hour vehicle (day 2) rep1

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human Schwann-like cells (CRL-2884, ATCC) were cultured in high-glucose DMEM supplemented with 10% of FCS for 48 hours (day 0 timepoint) before treatment.

extract_protocol: Cells were collected into RNAlater. RNA was extracted using the Agilent RNA Isolation Kit. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: ILB was added to the cultures (final concentration: 0.01, 0.1, 1.0 and 10 µg/ml; n=3 for each concentration). Control cultures received only vehicle (0.9% NaCl in water; n=2). Cells were cultured for another 48 hours (day 2 timepoint).

value: CRL-2884 (ATCC)

tag: treatment/time point

value: Day 2  Control


title: ATACseq_H2B_D51N_rep5

description:
Histone H2B D51N mutant replicate 5
ATACseq_H2B_D51N.bw

tag: genotype


title: CRL-2884 Day 2  ILB 10 µg/ml rep3

description:
GD 2 4 3
Gene expression in Schwann like cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (10 µg/ml)

source_name: CRL-2884-48 hour culture + 48 hour ILB 10 µg/ml (day 2) rep3

value: Day 2  ILB 10 µg/ml


title: CRL-2884 Day 2  Control rep2

description:
GD 2 0 2
Gene expression in Schwann like cells after 48 hours in normal culture conditions followed by 48 hours vehicle treatment (0.9%NaCl in water added to normal culture medium at 1:10,000 ratio)

source_name: CRL-2884-48 hour culture + 48 hour vehicle (day 2) rep2


title: CRL-2884 Day 2  ILB 10 µg/ml rep2

description:
GD 2 4 2
Gene expression in Schwann like cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (10 µg/ml)

source_name: CRL-2884-48 hour culture + 48 hour ILB 10 µg/ml (day 2) rep2


title: ATACseq_H2B_D51N_rep4

description:
Histone H2B D51N mutant replicate 4
ATACseq_H2B_D51N.bw


title: CRL-2884 Day 2  ILB 10 µg/ml rep1

description:
GD 2 4 1
Gene expression in Schwann like cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (10 µg/ml)

source_name: CRL-2884-48 hour culture + 48 hour ILB 10 µg/ml (day 2) rep1


title: ATACseq_H2B_D51N_rep3

description:
Histone H2B D51N mutant replicate 3
ATACseq_H2B_D51N.bw


title: CRL-2884 Day 2  ILB 1 µg/ml rep3

description:
GD 2 3 3
Gene expression in Schwann like cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (1 µg/ml)

source_name: CRL-2884-48 hour culture + 48 hour ILB 1 µg/ml (day 2) rep3

value: Day 2  ILB 1 µg/ml


title: NF1-associated glioma #18

type: genomic

city: Stanford

first: David

middle: A.

last: Solomon

state: CA

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

description:
glioma arising in the setting of NF1
205437190143_R06C01

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan instrument following standard recommended Illumina scanner setting

data_processing: Methylation data were preprocessed using the minfi package (v.1.30.0) in R. The detection p-value for each sample was computed. Functional normalization with NOOB background correction and dye-bias normalization was performed.

label: Cy5 and Cy3

source_name: NF1-associated glioma

label_protocol: Standard Illumina protocol

growth_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients.  No ex vivo culture or xenografting was performed.

extract_protocol: Tumor tissue was selectively punched from formalin-fixed, paraffin-embedded tissue blocks using using 2.0 mm disposable biopsy punches (Integra Miltex Instruments, cat# 33-31-P/25) or selectively scraped from unstained sections cut from formalin-fixed, paraffin-embedded tissue blocks.  Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients at time of initial diagnosis before any radiation or chemotherapy had been administered.  No ex vivo culture or xenografting was performed.

tag: patient sex

value: male

tag: patient age

tag: tumor location

value: thalamus


title: NF1-associated glioma #39

description:
glioma arising in the setting of NF1
205437190143_R05C01

value: left temporal


title: NF1-associated glioma #28

description:
glioma arising in the setting of NF1
205437180153_R08C01

value: cerebellum


title: NF1-associated glioma #25

description:
glioma arising in the setting of NF1
205437190143_R07C01

value: female


title: NF1-associated glioma #14

description:
glioma arising in the setting of NF1
205437190143_R08C01

value: brainstem


title: NF1-associated glioma #19

description:
glioma arising in the setting of NF1
205117390138_R05C01


title: NF1-associated glioma #26

description:
glioma arising in the setting of NF1
205117390138_R06C01


title: NF1-associated glioma #11

description:
glioma arising in the setting of NF1
205117390165_R04C01

value: left parietal


title: NF1-associated glioma #41

description:
glioma arising in the setting of NF1
205437180153_R06C01

value: left frontal


title: NF1-associated glioma #24

description:
glioma arising in the setting of NF1
205117390138_R01C01


title: NF1-associated glioma #46

description:
glioma arising in the setting of NF1
205117390138_R07C01


title: NF1-associated glioma #20

description:
glioma arising in the setting of NF1
205437190143_R02C01


title: ATACseq_H2B_D51N_rep2

description:
Histone H2B D51N mutant replicate 2
ATACseq_H2B_D51N.bw


title: ATACseq_H2B_D51A_rep6

description:
Histone H2B D51A mutant replicate 6
ATACseq_H2B_D51A.bw

value: Histone H2B D51A mutant


title: NF1-associated glioma #10

description:
glioma arising in the setting of NF1
205117390138_R04C01


title: NF1-associated glioma #17

description:
glioma arising in the setting of NF1
205437190143_R03C01


title: NF1-associated glioma #16

description:
glioma arising in the setting of NF1
205437180153_R05C01


title: NF1-associated glioma #37

description:
glioma arising in the setting of NF1
205437190143_R01C01


title: NF1-associated glioma #9

description:
glioma arising in the setting of NF1
205437190143_R04C01


title: NF1-associated glioma #32

description:
glioma arising in the setting of NF1
205117390165_R07C01


title: ATACseq_H2B_D51N_rep1

description:
Histone H2B D51N mutant replicate 1
ATACseq_H2B_D51N.bw


title: NF1-associated glioma #31

description:
glioma arising in the setting of NF1
205117390165_R02C01

value: right parietal


title: NF1-associated glioma #15

description:
glioma arising in the setting of NF1
205117390165_R06C01


title: NF1-associated glioma #44

description:
glioma arising in the setting of NF1
205117390138_R03C01


title: CRL-2884 Day 2  ILB 1 µg/ml rep1

description:
GD 2 3 1
Gene expression in Schwann like cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (1 µg/ml)

source_name: CRL-2884-48 hour culture + 48 hour ILB 1 µg/ml (day 2) rep1


title: CRL-2884 Day 2  ILB 0.1 µg/ml rep3

description:
GD 2 2 3
Gene expression in Schwann like cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (0.1 µg/ml)

source_name: CRL-2884-48 hour culture + 48 hour ILB 0.1 µg/ml (day 2) rep3

value: Day 2  ILB 0.1 µg/ml


title: ATACseq_H2B_D51A_rep4

description:
Histone H2B D51A mutant replicate 4
ATACseq_H2B_D51A.bw


title: ATACseq_H2B_D51A_rep5

description:
Histone H2B D51A mutant replicate 5
ATACseq_H2B_D51A.bw


title: ATACseq_H2B_D51A_rep2

description:
Histone H2B D51A mutant replicate 2
ATACseq_H2B_D51A.bw


title: ATACseq_H2B_D51A_rep1

description:
Histone H2B D51A mutant replicate 1
ATACseq_H2B_D51A.bw


title: NF1-associated glioma #30

description:
glioma arising in the setting of NF1
205117390074_R08C01

value: spinal cord


title: NF2-JQ1 rep 2

city: Sioux Falls

first: Michael

last: Kareta

state: SD

address: 2301 East 60th Street North

department: Genetics & Genomics

institute: Sanford Research

data_processing:
Reads were mapped to the human genome (human-UCSC : H.sapiens-UCSC-GRCh38hg38 : downloaded March 22, 2016) using the bowtie version 1.1.2 aligner.
Peaks were identified using macs version 2.1.0.
Genome_build: hg38

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10’, R.T. Cells were incubated with 125 mmol/L glycine for 5’ then washed (2X) with cold PBS, centrifuged and lysed in 2 ml ChIP buffer (150 mmol/L NaCl, 1% Triton X-100, 5 mmol/L EDTA, 10 mmol/L TrisCL pH7.5, 0.5 mmol/L DTT, 0.5% SDS) by rocking for 10’ at 4°C.  DNA was fragmented by sonication to 0.3-0.5 kb DNA fragments (Misonix S-3000, 4oC water bath, 30 minutes (30 seconds on, 30 seconds off, output 8).  Input DNA (7X10^4 cell equivalent) was removed from fragmented DNA and stored at -80°C.  Anti-BRD4 antibody (3 ug/ per condition) (BL-149-2H5, Bethyl Laboratories) and Dynabeads Protein G (90 ul/ per condition) were added to lysate and incubated overnight at 4°C with rocking.  Beads were washed with buffer 1 (150 mmol/L NaCl, 20 mMol/L TrisCl pH 8.0, 5 mmole/L EDTA, 65% w/v sucrose, 1% Triton-X-100, and 0.2% SDS) and then washed with TE buffer.  ChIP and input DNA were resuspended in TE/1% SDS and incubating at 65°C for 18 hours.  SDS was diluted with TE and treated with RNase A (0.2 mg/ml) at 37°C for 2 hours, treated with proteinase K (0.2 mg/ml) 65°C for 2 hours, then DNA was extracted with phenol chloroform isoamyl alcohol and resuspended in TE.
The ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Ilumina (E7645S, New England Biolabs, Inc. Ipswich, MA, USA).  Library preparation followed these steps; end repair, 5’ phosphorylation, dA-tailing, adapter ligation, U excision, cleanup of adaptor-ligated DNA without size selection, and library amplification.  Twelve to 13 cycles were followed by clean-up with 1X Agencourt AMPure XP.  The quality of the libraries was assessed using  Agilent High Sensitivity DNA Kit (5067-4626) on the Agilent 2100 Bioanalyzer and were quantified using NEBNext Library Quant Kit for Illumina (E7630S, New England Biolabs).  Libraries were sequenced using the NextSeq 500 High Output v2 Kit (75 cycles, FC-404-2005) on the NextSeq 500 Platform (Illumina).

treatment_protocol: Cells at ~75% confluency (1X10^7 cells/condition) were treated with DMSO or JQ1 (1uM) for 12 hours at 37oC.

tag: treatment


title: NF1-associated glioma #21

description:
glioma arising in the setting of NF1
205117390165_R03C01

value: unknown


title: NF2-DMSO rep 2

value: DMSO


title: ATACseq_H2B_D51A_rep3

description:
Histone H2B D51A mutant replicate 3
ATACseq_H2B_D51A.bw


title: CRL-2884 Day 2  ILB 0.1 µg/ml rep2

description:
GD 2 2 2
Gene expression in Schwann like cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (0.1 µg/ml)

source_name: CRL-2884-48 hour culture + 48 hour ILB 0.1 µg/ml (day 2) rep2

value: CRL-2884 (ATCC)


title: CRL-2884 Day 2  ILB 0.01 µg/ml rep3

description:
GD 2 1 3
Gene expression in Schwann like cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (0.01 µg/ml)

source_name: CRL-2884-48 hour culture + 48 hour ILB 0.01 µg/ml (day 2) rep3

value: Day 2  ILB 0.01 µg/ml


title: CRL-2884 Day 2  ILB 0.01 µg/ml rep2

description:
GD 2 1 2
Gene expression in Schwann like cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (0.01 µg/ml)

source_name: CRL-2884-48 hour culture + 48 hour ILB 0.01 µg/ml (day 2) rep2


title: NF1-associated glioma #43

description:
glioma arising in the setting of NF1
205117390074_R07C01


title: CRL-2884 Day 2  ILB 1 µg/ml rep2

description:
GD 2 3 2
Gene expression in Schwann like cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (1 µg/ml)

source_name: CRL-2884-48 hour culture + 48 hour ILB 1 µg/ml (day 2) rep2

value: Day 2  ILB 1 µg/ml


title: NF2-DMSO rep 1


title: NF1-associated glioma #34

description:
glioma arising in the setting of NF1
205117390165_R08C01


title: CRL-2884 Day 0 Control rep2

description:
GD 0 2
Gene expression in Schwann like cells after 48 hours in normal culture conditions

source_name: CRL-2884, 48 hour culture (baseline before treatment, day 0) rep2

value: Day 0 Control


title: CRL-2884 Day 2  ILB 0.1 µg/ml rep1

description:
GD 2 2 1
Gene expression in Schwann like cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (0.1 µg/ml)

source_name: CRL-2884-48 hour culture + 48 hour ILB 0.1 µg/ml (day 2) rep1


title: AN11004103_1

city: Lyon

first: PIERRE

last: SAINTIGNY

address: 28 Rue Laennec

country: France

institute: Centre Léon Bérard

description: targeted RNA-seq

data_processing:
Illumina bcl2fastq is used for generation of FASTQ files
HTG EdgeSeq Parser software (version 5.1) is used for alignment to a priori defined target sequences.  Requirements include %Q30 >= 85%, %PF >= 75%, and 180 < CD < 290
Post-sequencing quality control using three quality control metrics: 1) Percent of reads allocated to the Positive control probe must not exceed 15%, 2) Total aligned reads must exceed 1,500,000, and 3) Relative Standard Deviaion (CV) of counts within a sample must exceed 0.1 (CV is calculated after removal of counts from ANT and POS control probes and log2 transformation after addition of 2 to avoid taking the log of 0). A log2 CPM normalization is then processed.

source_name: targeted RNA of patient number 40

extract_protocol:
sample preparation: 10mm2 of 5 micrometer FFPE tumour macrodissection tissue were lysed using HTG Lysis Buffer, followed by proteinase K digestion, and then transferred to an HTG EdgeSeq platform according to manufacturer protocols (HTG Molecular Diagnostics, Inc., Tucson, AZ).
The Oncology Biomarker Panel was used to  capture RNA expression levels of gene targets  on the HTG EdgeSeq platform according to manufacturer protocols (HTG Molecular Diagnostics, Inc., Tucson, AZ). The resulting DNA probes were quantitatively amplified with polymerase chain reaction adding extended primers ,including sequencing primer and sample barcode sequences.
Library samples were cleaned up to remove excess primers, quantitated, pooled and sequenced using Illumina NextSeq500 sequencer using 50-cycles single end ((Illumina, Inc.).

tag: tissue

value: oral cavity squamous cell carcinoma

tag: site

value: BUCCAL MUCOSA

tag: age

tag: Sex

value: Female

tag: smoking/drinking status

value: NSND

tag: pni

value: NO

tag: lvi

tag: pt

tag: pn

tag: cd8_% stain 1 positive cells

tag: pdl1_28.8_% stain 1 positive cells

tag: ido1_% stain 1 positive cells

value: HIGH

value: LOW

tag: os (month)

tag: os (event)

tag: dfs (month)

tag: dfs (event)

tag: hot score

value: HOT


title: AN14001553_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 39

tag: tissue

value: LOWER ALVEOLAR RIDGE

value: Male


title: AN13016492_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 38

tag: site

value: TONGUE

value: YES


title: CRL-2884 Day 0 Control rep1

description:
GD 0 1
Gene expression in Schwann like cells after 48 hours in normal culture conditions

source_name: CRL-2884, 48 hour culture (baseline before treatment, day 0) rep1

tag: cell line

tag: treatment/time point


title: AN13013825_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 37

tag: age

tag: Sex

tag: smoking/drinking status


title: NF1-associated glioma #47

description:
glioma arising in the setting of NF1
205117390074_R05C01

tag: patient sex

value: female

tag: patient age

tag: tumor location

value: brainstem


title: CRL-2266 Day 2  Control rep2

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions followed by 48 hours vehicle treatment (0.9%NaCl in water added to normal culture medium at 1:10,000 ratio)
SD 2 0 2

data_processing: The scanned images were analysed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CRL-2266-48 hour culture + 48 hour vehicle (day 2) rep2

growth_protocol: Human SHSY5Y neuroblastoma cells (CRL-2266, ATCC) were cultured in DMEM:F12 medium supplemented with 10% FCS and 1% GlutaMAX™-I for 48 hours (day 0 timepoint) before treatment.

value: CRL-2266 (ATCC)

value: Day 2  Control


title: CRL-2266 Day 2  ILB 10 µg/ml rep2

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (10 µg/ml)
SD 2 4 2

source_name: CRL-2266-48 hour culture + 48 hour ILB 10 µg/ml (day 2) rep2

value: Day 2  ILB 10 µg/ml


title: CRL-2266 Day 2  ILB 10 µg/ml rep3

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (10 µg/ml)
SD 2 4 3

source_name: CRL-2266-48 hour culture + 48 hour ILB 10 µg/ml (day 2) rep3


title: NF1-associated glioma #8

description:
glioma arising in the setting of NF1
205117390074_R06C01

source_name: NF1-associated glioma

value: left temporal


title: NF1-associated glioma #36

description:
glioma arising in the setting of NF1
205117390074_R04C01

value: cerebellum


title: AN13005962_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 35

value: oral cavity squamous cell carcinoma

value: Female

tag: pni

tag: lvi

tag: pt

tag: pn

tag: cd8_% stain 1 positive cells

tag: pdl1_28.8_% stain 1 positive cells


title: CRL-2266 Day 2  Control rep1

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions followed by 48 hours vehicle treatment (0.9%NaCl in water added to normal culture medium at 1:10,000 ratio)
SD 2 0 1

source_name: CRL-2266-48 hour culture + 48 hour vehicle (day 2) rep1


title: AN13008263_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 36

value: BUCCAL MUCOSA

value: NSND

value: NO

tag: ido1_% stain 1 positive cells

tag: os (month)

tag: os (event)

tag: dfs (month)

tag: dfs (event)

tag: hot score


title: NF2-JQ1 rep 1

tag: treatment

tag: cell line

tag: antibody


title: CRL-2884 Day 2 ILB 0.01 µg/ml rep1

description:
GD 2 1 1
Gene expression in Schwann like cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (0.01 µg/ml)

source_name: CRL-2884-48 hour culture + 48 hour ILB 0.01 µg/ml (day 2) rep1

value: CRL-2884 (ATCC)

tag: treatment/time point

value: Day 2 ILB 0.01 µg/ml


title: CRL-2266 Day 2  ILB 10 µg/ml rep1

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (10 µg/ml)
SD 2 4 1

source_name: CRL-2266-48 hour culture + 48 hour ILB 10 µg/ml (day 2) rep1


title: AN12000309_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 34

tag: tissue

tag: site

tag: age

tag: Sex

tag: smoking/drinking status

value: HIGH

value: LOW

value: HOT


title: AN11003711_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 33

value: TONGUE

tag: pni

tag: lvi

tag: pt

tag: pn

tag: cd8_% stain 1 positive cells


title: AN09007899_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 32

value: YES

tag: pdl1_28.8_% stain 1 positive cells

tag: ido1_% stain 1 positive cells

tag: os (month)

tag: os (event)

tag: dfs (month)


title: AN09001976_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 31

value: LOWER ALVEOLAR RIDGE

tag: dfs (event)

tag: hot score


title: CRL-2266 Day 2  ILB 1 µg/ml rep2

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (1 µg/ml)
SD 2 3 2

source_name: CRL-2266-48 hour culture + 48 hour ILB 1 µg/ml (day 2) rep2

tag: cell line

value: CRL-2266 (ATCC)

tag: treatment/time point

value: Day 2  ILB 1 µg/ml


title: CRL-2266 Day 2  ILB 1 µg/ml rep3

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (1 µg/ml)
SD 2 3 3

source_name: CRL-2266-48 hour culture + 48 hour ILB 1 µg/ml (day 2) rep3


title: AN15011978_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 29

tag: tissue

tag: site

tag: age

value: Male

value: SD

value: COLD


title: CRL-2266 Day 2  ILB 0.1 µg/ml rep3

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (0.1 µg/ml)
SD 2 2 3

source_name: CRL-2266-48 hour culture + 48 hour ILB 0.1 µg/ml (day 2) rep3

value: Day 2  ILB 0.1 µg/ml


title: AN13014817_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 28

value: oral cavity squamous cell carcinoma

value: UPPER ALVEOLAR RIDGE

tag: Sex

value: Female

tag: smoking/drinking status

tag: pni


title: CRL-2266 Day 2  ILB 0.1 µg/ml rep2

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (0.1 µg/ml)
SD 2 2 2

source_name: CRL-2266-48 hour culture + 48 hour ILB 0.1 µg/ml (day 2) rep2


title: AN06001989_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 30

value: FLOOR OF MOUTH

tag: lvi

value: NO

tag: pt

tag: pn


title: AN12005815_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 27

value: NSND

tag: cd8_% stain 1 positive cells

tag: pdl1_28.8_% stain 1 positive cells

tag: ido1_% stain 1 positive cells

value: HIGH


title: CRL-2266 Day 2  ILB 1 µg/ml rep1

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (1 µg/ml)
SD 2 3 1

source_name: CRL-2266-48 hour culture + 48 hour ILB 1 µg/ml (day 2) rep1


title: DEN_255

city: Minneapolis

first: Shijia

last: Zhu

state: Minnesota

address: 1200 Washington Avenue S Suite #175

department: Department of Laboratory Medicine and Pathology

institute: University of Minnesota Medical School

description: DEN-treated cirrhotic rats

data_processing:
Raw reads were aligned to the reference genome (Rattus norvegicus, Rnor_6.0) using the spliced gap aligner STAR, and count-based quantitation was carried out by the Subread package featureCounts at the gene level based on ENSEMBL annotation build (Rnor_6.0.101). The whole-genome transcriptome read count data were normalized and modeled as over-dispersed Poisson data as TMM using a negative binomial model in the Bioconductor package edgeR. For subsequent data analysis, genes with no expression in more than 50% of the samples and low variance across the samples (coefficient of variance < 0.01) were excluded. The rat genes were mapped onto human orthologues based on NCBI Homologene database (build 68), and expression levels of multiple rat genes mapped to a human gene were summarized with their median value.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: gct format; the normalized read count mapped to rat genes and converted to human genes

organism: Rattus norvegicus

extract_protocol:
RNA was isolated using the RNeasy Mini kit (QIAGEN) in accordance with manufacturer’s instructions.
High-quality total RNA samples (RNA Integrity score > 8 by Agilent Bioanalyzer) were subjected to poly A-selected sequencing library preparation using TruSeq RNA Sample Prep Kit ver.2 (Illumina) following manufacturer’s protocol. The libraries were sequenced by NextSeq 550 genome sequencer (Illumina) to generate 100 bp single-end reads.

treatment_protocol: 8-week old male Wistar rats received weekly intraperitoneal injections of 50 mg/kg DEN to induce cirrhosis and HCC, or PBS, once per week over the course of 18 weeks. After 8 weeks, DEN-injured rats were randomly assigned to receive vehicle control (0.5% methylcelluose) or 20 mg/kg captopril by oral gavage daily for 9 weeks. Livers were harvested and analyzed in week 18.

tag: disease status

value: DEN-induced cirrhosis

tag: drug treatment

value: Vehicle treatment


title: AN11005383_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 26

value: BUCCAL MUCOSA

value: LOW

tag: os (month)

tag: os (event)

tag: dfs (month)

tag: dfs (event)

tag: hot score

value: HOT


title: DEN_463

description: DEN-treated cirrhotic rats


title: DEN_457

description: DEN-treated cirrhotic rats


title: PBS_48

description: PBS-treated control rats

value: PBS-treated healthy control

value: No treatment


title: CRL-2266 Day 2  ILB 0.01 µg/ml rep3

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (0.01 µg/ml)
SD 2 1 3

source_name: CRL-2266-48 hour culture + 48 hour ILB 0.01 µg/ml (day 2) rep3

tag: cell line

value: CRL-2266 (ATCC)

tag: treatment/time point

value: Day 2  ILB 0.01 µg/ml


title: PBS_46

description: PBS-treated control rats


title: AN06002534_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 22

tag: tissue

tag: site

value: LOWER ALVEOLAR RIDGE

tag: age

tag: Sex

value: Male

tag: smoking/drinking status

value: SD


title: AN14015205_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 21

value: oral cavity squamous cell carcinoma

value: TONGUE

tag: pni

value: YES

tag: lvi

tag: pt

tag: pn

tag: cd8_% stain 1 positive cells

value: COLD


title: AN07004917_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 23

value: FLOOR OF MOUTH

value: Female

value: NO

tag: pdl1_28.8_% stain 1 positive cells

tag: ido1_% stain 1 positive cells

value: HIGH

tag: os (month)


title: NF1-associated glioma #45

description:
glioma arising in the setting of NF1
205117390074_R02C01

source_name: NF1-associated glioma

tag: patient sex

value: male

tag: patient age

tag: tumor location

value: cerebellum


title: PBS_47

description: PBS-treated control rats

tag: disease status

value: PBS-treated healthy control

tag: drug treatment


title: NF1-associated glioma #35

description:
glioma arising in the setting of NF1
205117390138_R02C01

value: brainstem


title: AN08004973_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 24

tag: tissue

tag: site

value: LOW

tag: os (event)

tag: dfs (month)

tag: dfs (event)

tag: hot score

value: HOT


title: CRL-2266 Day 2  ILB 0.01 µg/ml rep2

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (0.01 µg/ml)
SD 2 1 2

source_name: CRL-2266-48 hour culture + 48 hour ILB 0.01 µg/ml (day 2) rep2

tag: cell line

value: CRL-2266 (ATCC)

tag: treatment/time point

value: Day 2  ILB 0.01 µg/ml


title: Cap_467

description: DEN-treated rats with captopril treatment

value: DEN-induced cirrhosis

value: Captopril


title: NF1-associated glioma #12

description:
glioma arising in the setting of NF1
205117390074_R03C01

value: right temporal


title: CRL-2266 Day 2  ILB 0.1 µg/ml rep1

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (0.1 µg/ml)
SD 2 2 1

source_name: CRL-2266-48 hour culture + 48 hour ILB 0.1 µg/ml (day 2) rep1

value: Day 2  ILB 0.1 µg/ml


title: CRL-2266 Day 0 Control rep1

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions
SD 0 1

source_name: CRL-2266, 48 hour culture (baseline before treatment, day 0) rep1

value: Day 0 Control


title: AN09006271_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 19

value: oral cavity squamous cell carcinoma

value: TONGUE

tag: age

tag: Sex

value: Male

tag: smoking/drinking status

value: SD

tag: pni

tag: lvi

tag: pt

tag: pn

tag: cd8_% stain 1 positive cells


title: AN12004940_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 20

value: Female

value: NSND

value: YES

value: NO

tag: pdl1_28.8_% stain 1 positive cells

tag: ido1_% stain 1 positive cells

tag: os (month)

value: COLD


title: CRL-2266 Day 0 Control rep2

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions
SD 0 2

source_name: CRL-2266, 48 hour culture (baseline before treatment, day 0) rep2


title: Cap_465

tag: disease status

tag: drug treatment


title: AN08002432_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 18

tag: tissue

tag: site

value: BUCCAL MUCOSA

value: HIGH

value: LOW

tag: os (event)

tag: dfs (month)

tag: dfs (event)


title: CRL-2266 Day 2 ILB 0.01 µg/ml rep1

description:
Gene expression in neuroblastoma cells after 48 hours in normal culture conditions followed by 48 hours ILB treatment (0.01 µg/ml)
SD 2 1 1

source_name: CRL-2266-48 hour culture + 48 hour ILB 0.01 µg/ml (day 2) rep1

tag: cell line

value: CRL-2266 (ATCC)

tag: treatment/time point

value: Day 2 ILB 0.01 µg/ml


title: Cap_460

value: DEN-induced cirrhosis

value: Captopril


title: AN15008542_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 17

tag: age

tag: Sex

tag: smoking/drinking status

tag: pni

tag: hot score


title: AN15007448_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 16

tag: lvi

tag: pt

tag: pn

tag: cd8_% stain 1 positive cells

tag: pdl1_28.8_% stain 1 positive cells

value: HOT


title: IOMM-Lee cells, TrichostatinA and G47delta treated [IOMM12]

city: Boston

first: Hiroaki

last: Wakimoto

state: MA

address: 185 Cambridge Street, CPZN-3800

department: Neurosurgery

institute: Massachusetts General Hospital

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N, and low quality reads.
Paied-end clean reads were aligned to the reference genome using Histat2 v2.0.5
The mapped reads were assembled by StringTie (v1.3.3b) to quantitate full-length transcripts representing multiple splice variants for each gene locus.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

source_name: IOMM-Lee

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

extract_protocol:
RNA was extracted using Trizol (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
Second strand cDNA was subjected to end-repair and A tailing, adapter ligation, size selection, USER enzyme digestion and PCR amplification and purification.

treatment_protocol: Cells were treated with mock, HDAC inhibitor, G47Δ or HDAC inhibitor followed by G47Δ. Twenty-four hours after virus infection (29 hours after HDAC inhibitor), cells were collected for total RNA extract

value: IOMM-Lee

tag: cell type

value: Meningioma cells

tag: genotype

value: WT

tag: treatment

value: TrichostatinA and G47delta


title: IOMM-Lee cells, TrichostatinA and G47delta treated [IOMM11]


title: IOMM-Lee cells, Panobinostatin and G47delta treated [IOMM10]

value: Panobinostat and G47delta


title: AN13007426_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 13

tag: tissue

value: oral cavity squamous cell carcinoma

tag: site

value: TONGUE

value: Male

value: SD

tag: ido1_% stain 1 positive cells

tag: os (month)

tag: os (event)

tag: dfs (month)


title: AN14007673_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 14

value: FLOOR OF MOUTH

tag: age

tag: Sex

tag: smoking/drinking status

value: NO

tag: dfs (event)

value: COLD


title: AN1206673_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 12

tag: pni

value: YES

tag: lvi

tag: pt

value: LOW

value: HIGH

tag: hot score


title: NF1-associated glioma #40

description:
glioma arising in the setting of NF1
205117390074_R01C01

tag: patient sex

value: female

tag: patient age

tag: tumor location

value: left temporal


title: AN14015122_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 15

tag: tissue

tag: pn

tag: cd8_% stain 1 positive cells

tag: pdl1_28.8_% stain 1 positive cells


title: AN11004746_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 10

tag: site

tag: ido1_% stain 1 positive cells

tag: os (month)

tag: os (event)


title: AN11000893_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 9

tag: age

tag: Sex

value: Female

tag: smoking/drinking status

value: NSND

tag: dfs (month)

value: HOT


title: AN12003840_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 11

value: HARD PALATE

tag: pni

tag: lvi

tag: pt

tag: dfs (event)


title: IOMM-Lee cells, Panobinostat treated [IOMM6]

tag: cell line

value: IOMM-Lee

tag: cell type

value: Meningioma cells

tag: genotype

value: WT

tag: treatment

value: Panobinostat


title: IOMM-Lee cells, TrichostatinA treated [IOMM8]

value: TrichostatinA


title: IOMM-Lee cells, Panobinostat treated [IOMM5]


title: IOMM-Lee cells, G47delta-treated [IOMM4]


title: IOMM-Lee cells, G47delta-treated [IOMM3]


title: AN10003690_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 6

tag: tissue

value: oral cavity squamous cell carcinoma

value: FLOOR OF MOUTH

value: Male

value: SD

tag: pn

tag: cd8_% stain 1 positive cells

tag: pdl1_28.8_% stain 1 positive cells

tag: hot score


title: AN10003850_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 7

tag: site

value: LOWER ALVEOLAR RIDGE

tag: age

value: NO

value: YES

tag: ido1_% stain 1 positive cells

value: LOW

tag: os (month)

tag: os (event)

value: COLD


title: IOMM-Lee cells, Panobinostatin and G47delta treated [IOMM9]

value: Panobinostat and G47delta


title: IOMM-Lee cells, Untreated Control [IOMM2]


title: AN11000660_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 8

value: BUCCAL MUCOSA

tag: Sex

tag: smoking/drinking status

tag: pni

tag: lvi

tag: dfs (month)


title: IOMM-Lee cells, Untreated Control [IOMM1]

tag: cell line

tag: cell type

tag: genotype


title: AN10001074_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 5

tag: tissue

value: Female

value: NSND

tag: pt

tag: pn

value: HIGH

tag: dfs (event)

value: HOT


title: CH-157 cells, TrichostatinA and G47delta treated [CH12]

value: Meningioma cells

value: WT

tag: treatment

value: TrichostatinA and G47delta


title: AN08007550_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 4

value: oral cavity squamous cell carcinoma

tag: site

value: FLOOR OF MOUTH

tag: age

tag: cd8_% stain 1 positive cells

tag: pdl1_28.8_% stain 1 positive cells

tag: hot score


title: CH-157 cells, TrichostatinA and G47delta treated [CH11]


title: AN08004506_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 3

tag: Sex

tag: smoking/drinking status

value: SD

tag: ido1_% stain 1 positive cells

tag: os (month)

tag: os (event)


title: CH-157 cells, Panobinostatin and G47delta treated [CH10]

tag: cell line

tag: cell type


title: IOMM-Lee cells, TrichostatinA treated [IOMM7]

value: IOMM-Lee

tag: genotype

value: TrichostatinA


title: AN15015635_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 1

tag: tissue

value: Male

tag: pni

value: NO

tag: lvi

tag: pt

tag: dfs (month)


title: CH-157 cells, Panobinostatin and G47delta treated [CH9]

tag: treatment


title: BeWo Opti Only 1

city: Gainesville

first: Helen

middle: N

last: Jones

state: Florida

address: 1345 Center Dr

department: Physiology and FUnctional Genomics

institute: University of Florida

description: Sample 7

data_processing:
FastQ-QC: FASTQC,Trimmomatic
RNA seq mapping/count: Bowtie2, FeatureCounts,
Differential Expression analyses: EdgeR
Assembly: hg38
Supplementary files format and content: data matrix of raw count data, not filtered, not normalized

source_name: Bewo

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit, QIAshredder, and on-column DNA digest (Qiagen) following the protocol provided by the manufacturer
poly-A RNA libraries were generated using (NEBNext Ultra Directional RNA Library Prep kit, New England Biolabs, Ipswich, MA and the TruSeq SR Cluster kit v3 Illumina

value: Bewo

value: choriocarcinoma

value: no treatment


title: BeWo Opti Only 2

description: Sample 8


title: CH-157 cells, TrichostatinA treated [CH7]


title: BeWo Opti Only 3

description: Sample 9


title: AN08001336_1

description: targeted RNA-seq

source_name: targeted RNA of patient number 2

tag: site

value: BUCCAL MUCOSA

tag: age

value: YES

tag: pn

tag: cd8_% stain 1 positive cells

value: LOW

tag: dfs (event)

value: COLD


title: BeWo Allstar 3

description: Sample 6

value: siRNA- negative control


title: BeWo Allstar 2

description: Sample 5


title: CH-157 cells, G47delta-treated [CH4]

value: Meningioma cells

value: WT


title: CH-157 cells, G47delta-treated [CH3]


title: CH-157 cells, Panobinostat treated [CH5]

value: Panobinostat


title: CH-157 cells, Panobinostat treated [CH6]


title: CH-157 cells, Untreated Control  [CH1]


title: BeWo Allstar 1

description: Sample 4


title: BeWo Hand 1 KO 3

description: Sample 3

value: siRNA - HAND1/2


title: BeWo Hand 1 KO 2

description: Sample 2


title: BeWo Hand 1 KO 1

description: Sample 1


title: Ishikawa_8hrDMSO_rep2

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

data_processing:
Sequencing reads were aligned to the hg38 build of the human genome using HISAT2.
SAMtools was used to convert SAM files to BAM files.
Genes were defined by the University of California Santa Cruz (UCSC) Known Genes and reads mapped to known genes were assigned with featureCounts.
Within each cell line, read counts were normalized and analyzed for differential expression via the DESeq2 package in R while controlling for the sequencing platform by using the design formula (= ~Sequencer + Treatment), where sequencer reflects the sequencing platform and treatment is 10 nM E2 or DMSO.
Assembly: hg38
Supplementary files format and content: Gene counts (raw, unnormalized) in a tab-delimited text file.

source_name: Ishikawa

growth_protocol: HCI-EC-23 and Ishikawa was cultured in RPMI 1640 (Gibco, 11875119) supplemented with 10% fetal bovine serum (Gibco, 26140079) and 1% penicillin-streptomycin (Gibco, 15140163). Hormone deprived media consisted of phenol red-free RPMI1640 (Gibco, 11835055) supplemented with 10% charcoal-stripped fetal bovine serum (Sigma Aldrich, F6765) and 1% penicillin-streptomycin (Gibco, 15140163). HCI-EC-23 or Ishikawa cell lines were cultured in hormone-deprived media for at least five days prior to experiments using hormones. Cells were incubated at 37°C with 5% CO2.

extract_protocol:
RNA was harvested by washing cells with PBS and lysing cells with buffer RLT plus (Qiagen, 1053393) supplemented with 1% beta-mercaptoethanol (Sigma-Aldrich, M3148). RNA was then purified using the Zymo Quick-RNA Miniprep kit (Zymo Research, R1055).
RNA-seq libraries were generated using the KAPA Stranded mRNA HyperPrep kit (Roche, KK8580/08098115702) using 500 ng of RNA.

treatment_protocol: Media was changed and cells were treated with either 0.1% DMSO (vehicle) or 10 nM E2 in hormone-deprived media for 8 hours.

value: Ishikawa

value: endometrioid adenocarcinoma

value: 0.1% DMSO


title: HCI-EC-23_8hrDMSO_rep2


title: Ishikawa_8hrE2_rep1

value: 10 nM E2


title: Ishikawa_8hrE2_rep2


title: HCI-EC-23_8hrDMSO_rep1


title: Ishikawa_8hrDMSO_rep1


title: HCI-EC-23_8hrE2_rep1


title: HCI-EC-23_8hrE2_rep2


title: CH-157 cells, TrichostatinA treated [CH8]

value: TrichostatinA


title: T16h_LPS_11

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: raw_gene_counts.txt and TPM_genes.txt

data_processing:
RNA-seq reads were assessed for quality and aligned to hg38 (Ensembl Gene annotation build 91 using STAR 2.5.2b)
RNA-seq reads were quantified with RSEM 1.2.31
Genome_build: Ensembl version 91 (hg38)
Supplementary_files_format_and_content: TPM values for all genes (TPM_genes.txt), Gene counts for all genes (raw_gene_counts.txt)

source_name: Bone marrow derived macrophage

growth_protocol: Human MDMs were differentiated from buffy cones using gradient separation (Histopaque 1077, Sigma) and adhesion purification. Following Histopaque separation, peripheral blood mononuclear cells were resuspended in RPMI (Life Technologies), and monocytes were purified by adherence for 1 hour at 37°C, 5% CO2. The monolayer was washed three times with Hank’s Balance Salt Solution (HBSS) to remove non-adherent cells, and monocytes were matured for 5 days in RPMI containing 100 ng/mLmacrophage colony-stimulating factor (M-CSF) (PeproTech, London, UK) and 10% fetal calf serum (Labtech International).

extract_protocol:
Total RNA was extracted from MDMs using Trizol (Invitrogen) and RNeasy mini kit (Qiagen) according to manufacturer's instructions, with an additional purification step by on-column DNase treatment using the RNase-free DNase Kit (Qiagen) to ensure elimination of any genomic DNA. The integrity and quantity of total RNA was determined using a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer (Agilent Technologies).
500 ng of total RNA was used to generate RNA-seq libraries using NEBNext Ultra II Directional RNA Library Prep kit for Illumina, according to the manufacturer's instructions. Briefly, RNA was purified and fragmented using poly-T oligo-attached magnetic beads using two rounds of purification followed by the first and second cDNA strand synthesis. Next, cDNA 3' ends were adenylated and adapters ligated followed by 11 cycles of library amplification. Finally, the libraries were size selected using AMPure XP Beads (Beckman Coulter) purified and their quality was checked using Agilent 2100 Bioanalyzer. Samples were randomized to avoid batch effects and multiplexed libraries were run on a single lane (8 samples/lane) of the HiSeq 2500 platform (Illumina) to generate 100bp paired-end reads.

treatment_protocol: Human MDMs were treated with LPS (100ng/ml) for 30min, 3h, 8h, 16h.

tag: agent

value: LPS

tag: donor

tag: time

value: 16 hr

value: Bone marrow derived macrophage


title: T16h_LPS_2

description: raw_gene_counts.txt and TPM_genes.txt


title: T8h_LPS_11

description: raw_gene_counts.txt and TPM_genes.txt

value: 8 hr


title: T8h_LPS_10

description: raw_gene_counts.txt and TPM_genes.txt


title: T3h_LPS_2

description: raw_gene_counts.txt and TPM_genes.txt

value: 3 hr


title: T3h_LPS_11

description: raw_gene_counts.txt and TPM_genes.txt


title: T8h_LPS_1

description: raw_gene_counts.txt and TPM_genes.txt


title: T3h_LPS_1

description: raw_gene_counts.txt and TPM_genes.txt


title: T16h_LPS_1

description: raw_gene_counts.txt and TPM_genes.txt


title: CH-157 cells, Untreated Control  [CH2]

tag: cell line


title: T30m_LPS_2

description: raw_gene_counts.txt and TPM_genes.txt

tag: cell type


title: T3h_LPS_10

description: raw_gene_counts.txt and TPM_genes.txt


title: T30m_LPS_11

description: raw_gene_counts.txt and TPM_genes.txt


title: T30m_LPS_10

description: raw_gene_counts.txt and TPM_genes.txt


title: T0_11

description: raw_gene_counts.txt and TPM_genes.txt

value: CONTROL

value: 0 hr


title: T0_10

description: raw_gene_counts.txt and TPM_genes.txt


title: T0_1

description: raw_gene_counts.txt and TPM_genes.txt


title: T0_2

description: raw_gene_counts.txt and TPM_genes.txt


title: T8h_LPS_2

description: raw_gene_counts.txt and TPM_genes.txt


title: Ishikawa_8hrDMSO_rep4


title: HepG2 cells, shARHGEF2-1

city: Hefei

first: Yue

address: The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China

country: China

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: hg19
Supplementary files format and content: FPKMs

source_name: liver

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: HepG2 cells were transfected with lentivirus in experimental group to knock down ARHGEF2

value: liver

value: hepatoma carcinoma cell

tag: genotype

value: ARHGEF2 knockdown


title: NCCBC6vs

city: Chuo-ku

first: Jun

last: Nakayama

state: Tokyo

address: Tsukiji 5-1-1

country: Japan

institute: National Cancer Center

data_processing:
Library strategy: Spatial Transcriptomics
Raw sequencing data were processed with the SpaceRanger pipeline (version 1.2.2, 10X Genomics) and mapped to the human genome (GRCh38) to generate matrices of gene counts by spatially barcodes.
Genome_build: GRCh38
Supplementary_files_format_and_content: H5

source_name: Human Breast Cancer

extract_protocol:
A fresh tissue sample was embedded in OCT and stored at -80 °C. Tissue block was cut into 10-μm sections, which were analyzed with a Visium Spatial Gene Expression Kit 3' v1 (10x Genomics) according to the manufacturer’s instructions in the Visium Spatial Gene Expression Reagent Kit User Guide(10X Genomics). The optimal permeabilization time was 24 min. Sliced tissue pieces were stained with H&E, imaged using a BZ-X710 microscope (Keyence, Osaka, Japan) under a 20 x objective, and processed for spatial transcriptomics.
After permeablization, mRNA released from the overlying cells is captured by the primers on the spots. Then spatially barcoded cDNA is synthesied from mRNA. Library preparation was performed included cDNA amplification, fragmentation, hearing and 5′ adaptor and sample index attachment. Sequencing was performed on a DNBSEQ (MGI Tech, Shenzhen, China).

value: DCIS


title: HepG2 cells, shARHGEF2-2

institute: The First Affiliated Hospital of Anhui Medical University

tag: tissue


title: HepG2 cells, shARHGEF2-3


title: Ishikawa_8hrDMSO_rep3


title: Ishikawa_8hrE2_rep4


title: Ishikawa_8hrE2_rep3


title: HepG2 cells, shNC2

value: WT


title: HepG2 cells, shNC3


title: HCI-EC-23_8hrDMSO_rep4


title: HepG2 cells, shNC1


title: HCI-EC-23_8hrDMSO_rep3


title: T30m_LPS_1

description: raw_gene_counts.txt and TPM_genes.txt


title: HCI-EC-23_8hrE2_rep4