title: nonNE_AT2deplete_247 [H9_C48_012015_IL6205_N707_N502_S42]

first: Mark

middle: A

last: Krasnow

address: 279 Campus Dr

department: Biochemistry

institute: Stanford University School of Medicine

data_processing:
CASAVA 1.8.2 (Illumina) was used for base-calling, demultiplexing, and generation of fastq files.
Prinseq, FASTQC, cutadapt, and Trim Galore were used as previously described (Ooi, Mantalas, et al. PLoS ONE 2017) to trim exogenous sequences and remove short, low complexity, and overrepresented reads.
Kallisto v0.43.0 was used in paired-end mode with default settings to align groomed reads to the NCBI RefSeq mouse transcriptome (mouse.rna.fna.gz downloaded from ftp://ftp.ncbi.nlm.nih.gov/refseq/M_musculus/mRNA_Prot on April 7, 2014), modified to exclude model (XR_/XM_) ascensions and to include ERCC (Thermo Fisher) and ZsGreen (Clontech) sequences.
ERCC alignments were separated from endogenous fragments (paired-end reads), and cells with fewer than 300,000 endogenous fragments were removed. Fragment counts were converted to transcripts per million (TPM) by normalizing first for the effective transcript length in that cell (retrieved from the eff_length kallisto output), then second for the parental cell’s total aligned endogenous fragments, and finally multiplying by one million. One additional cell that exhibited low/erratic housekeeping gene expression was also removed, yielding a final dataset of 225 cells including 100 that were identified from C1 cell capture photomicrographs as ZsGreen+ and hence NE in origin.
Transcript measurements were summed over splice isoforms to collapse the gene expression table from 32,887 transcripts to 24,173 genes.
Cell types were assigned using a combination of canonical pulmonary marker genes and RaceID2 cell clustering analysis. For RaceID2, gene expression was represented as TPM+1 (non-log transformed or otherwise normalized) and included all 13,023 genes expressed (TPM>10) in at least any 5 of the 225 cells. All default parameters were used except: clustnr=10, boonr=100 (clustexp function); max_iter=1e3 (comptsne function); outminc=2^5, outlg=3, probthr=1e-4 (findoutliers function).
NE transitional cells were identified by principal component analysis (PCA) of NE cells using highly variable genes (n=244 with TPM>10 in at least 3 cells), with gene expression represented as centered and scaled log2 TPM+1 values. Eight transitional cells that separated along the first two principal components were selected visually and assigned to target identities using canonical pulmonary marker genes.
Genome_build: NCBI RefSeq mouse transcriptome (mouse.rna.fna.gz downloaded from ftp://ftp.ncbi.nlm.nih.gov/refseq/M_musculus/mRNA_Prot on April 7, 2014)
Supplementary_files_format_and_content: YO_MAK_countsTranscripts_withERCCs_082619.txt – tab-delimited text, fragment (paired read) counts aligned per cell generated by kallisto including ERCCs
Supplementary_files_format_and_content: YO_MAK_tpmTranscripts_withoutERCCs_082619.txt – tab-delimited text, counts aligned per cell normalized to transcripts per million (TPM) excluding ERCCs

molecule: polyA RNA

growth_protocol: Mice were maintained in 12hr light/dark cycle with food and water provided ad libitum.

extract_protocol:
Mice were euthanized by CO2 asphyxiation, perfused with ~2ml PBS into the right cardiac ventricle, and lungs (excluding the trachea) dissected. Lung tissue was dissociated by cutting into small pieces with surgical scissors then enzymatically digesting the pieces in HBSS containing collagenase type 4 (Worthington), dispase (Corning), and trypsin-EDTA (Thermo Fisher) for one hour at 37°C with rotation, with intermittent pipette trituration. Following digestion, enzymes were quenched and digested suspensions were pressed through a 40μm cell strainer (Corning) and red blood cells lysed by osmotic shock. Genotype (but not gender) matched lungs were then pooled and depleted for endothelial cells and leukocytes using anti-CD31 and anti-CD45 decorated magnetic microbeads and MACS separation columns (Miltenyi Biotec). Finally, cells were labeled with fluorophore-coupled primary antibodies (EpCAM-PE-Cy7, CD31-APC, CD45-APC, and F4/80-APC) for 30 minutes at 4°C, and were resuspended in PBS containing 2% FBS, 2mM EDTA, and 1μg/ml DAPI as a live/dead cell indicator before proceeding to FACS. NE cells were purified by sorting for ZsGreen and EpCAM expression and against CD31, CD45, and F4/80 expression and DAPI incorporation (indicating dead cells) from Ascl1CreERT2 or CGRPCreERT2 samples. Non-NE cells were captured from CreERT2 allele-negative littermates or in separate purification rounds from Lyz2Cre samples, sorting in the same way as before except against ZsGreen expression to de-enrich for AT2 cells. Single purified cells were captured on Fluidigm C1 medium-sized IFCs, imaged, lysed, and mRNAs plus spiked-in ERCCs (Thermo Fisher) amplified using parallelized Smart-Seq reactions on-chip (21 PCR cycles, Fluidigm).
Amplified cDNAs were collected from IFCs, quantified by Bioanalyzer (Agilent), and samples containing >0.05ng/μl total cDNA in the 300-5,000 bp range were selected for analysis. Libraries were concentration-normalized by dilution, then prepared for sequencing by tagmentation using Nextera XT DNA Library Preparation (12 PCR cycles, Illumina) and clean-up purification using Agencourt AMPure XP beads (Beckman Coulter). Sequencing libraries were re-quantified prior to sequencing in paired-end format (75 cycles each) on a Illumina NextSeq 500.

treatment_protocol: Adult Ascl1CreERT2; Rosa26LSL-ZsGreen or CGRPCreERT2; Rosa26LSL-ZsGreen mice (roughly equal numbers of 2-3 month old male and female littermates, 6-10 mice per collection round) were administered a single 4mg intraperitoneal injection of tamoxifen (Sigma) 4-7 days prior to analysis to fluorescently label NE cells. In separation purification rounds, single adult Lyz2Cre; Rosa26LSL-ZsGreen mice (in which alveolar type 2 (AT2) and pulmonary macrophages and neutrophils are fluorescently labeled) were analyzed without prior tamoxifen administration.

tag: strain

value: Mixed

value: Lyz2-Cre; Rosa26-lslZsGreen

tag: age

value: 2-3 months

value: Lung

tag: facs strategy

value: ZsGreen- EpCAM+ CD31- CD45- F4/80- DAPI-

tag: assigned cell type

value: ciliated


title: nonNE_AT2deplete_246 [H1_C43_012015_IL6205_N707_N501_S40]

status: Public on Oct 03 2019

type: SRA

city: Stanford

state: CA

country: USA

library_source: transcriptomic

organism: Mus musculus

tag: genotype/variation

tag: tissue

value: club


title: nonNE_AT2deplete_244 [G10_C90_012015_IL6205_N706_N508_S50]


title: nonNE_AT2deplete_243 [F9_C36_012015_IL6205_N706_N505_S45]


title: nonNE_AT2deplete_241 [F7_C34_012015_IL6205_N706_N503_S43]


title: nonNE_AT2deplete_233 [D3_C19_012015_IL6204_N705_N504_S32]


title: nonNE_AT2deplete_245 [G9_C42_012015_IL6205_N706_N507_S48]


title: nonNE_AT2deplete_231 [C3_C13_012015_IL6204_N705_N501_S26]


title: nonNE_AT2deplete_240 [F4_C81_012015_IL6205_N706_N502_S41]


title: nonNE_AT2deplete_237 [F11_C83_012015_IL6205_N706_N506_S46]


title: nonNE_AT2deplete_234 [D6_C69_012015_IL6204_N705_N505_S34]


title: nonNE_AT2deplete_230 [C10_C64_012015_IL6204_N705_N503_S30]


title: nonNE_AT2deplete_239 [F3_C33_012015_IL6205_N706_N501_S39]


title: nonNE_AT2deplete_235 [D7_C24_012015_IL6204_N705_N506_S36]


title: nonNE_AT2deplete_228 [B5_C56_012015_IL6204_N704_N507_S37]


title: nonNE_AT2deplete_232 [C9_C16_012015_IL6204_N705_N502_S28]


title: nonNE_AT2deplete_227 [B2_C08_012015_IL6204_N704_N506_S35]


title: donor3_on gel (RNA-Seq)

status: Public on Oct 04 2019

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

description:
SAMPLE 6
processed_data.txt

data_processing:
Preprocessing of raw data was performed with SortMeRNA (https://www.ncbi.nlm.nih.gov/pubmed/23071270) to exclude rRNA sequences and TrimGalore for adapter trimming. Reads were aligned with the STAR aligner (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/) and count tables were created with HTSeq (https://academic.oup.com/bioinformatics/article/31/2/166/2366196). Differential gene expression analysis was performed using the R package DESeq2 (http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: hg19
Supplementary_files_format_and_content: processed_data.txt

molecule: total RNA

organism: Homo sapiens

source_name: iPSCs differentiated toward MSCs

growth_protocol: MSCs were isolated from bone marrow after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Aachen (permit number: EK128/09). MSCs from three different donors (passage 2) were infected with pCXLE-based episomal plasmids (Addgene, Cambridge, MA, USA) carrying the OCT3/4, SOX2, KLF4, LIN28 and L-MYC genes. Established iPSCs were cultured on TCP coated with vitronectin (0.5 µg/cm²) in StemMACS iPS-Brew XF (all Miltenyi Biotec GmbH, Bergisch Gladbach, Germany).

extract_protocol:
RNA was isolated using the Macherey-Nagel RNA Plus Kit.
QuantSeq 3´-mRNA Library Prep/Lexogen, Standard 3' Seq (SR, 50 cycles)

treatment_protocol: Three different iPSC lines (donors 1-3) were differentiated toward MSCs with the following conditions: iPSCs were either seeded onTCP, on fibrin gel or within fibrin gel. Differentiation toward MSCs was initiated by medium change to Dulbecco ́s modified Eagle ́s medium-Low Glucose (DMEM-LG, Gibco/Thermo Fisher Scientific, Darmstadt, Germany) supplemented with 10% human platelet lysate (hPL-medium), 5 U/ml heparin (Rotexmedica, Trittau, Germany), 10 µM of the Rho-associated protein kinase (ROCK) inhibitor Y-27632 (Abcam, Cambridge, UK), and 250 U/ml aprotinin (Nordic Pharma, Reading, UK). Differentiation was stopped after 21 days.

tag: individual

value: donor 3

tag: cell type

value: iPSCs differentiated toward MSCs

tag: growth protocol

value: on gel


title: MA9+EV_ChIPseq_input_1

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

library_source: genomic

data_processing:
Quality control performed on fastq files using FastQC version 0.11.7
RNA-seq fastq files were trimmed for quality using Cutadapt version 1.18, parameters = -q20,20 --minimum-length 30; ATAC-seq and ChIP-seq fastq files were trimmed for quality, adapter removal, and polyG removal using AfterQC version 0.9.6, parameters = -q20 -u 19 -p19 -s 25
RNA-seq fastq files were aligned to the mouse genome using STAR version 2.6.0c, parameters = genomeGenerate: --sjdbOverhang 49, Alignment: --outSamtype BAM SortedByCoordinate; ATAC-seq and ChIP-seq files were aligned to the mouse genome using Bowtie2 version 2.3.4.3, parameters = --very-sensitive -X 2000
RNA-seq aligned BAM files were assigned to genes and features were counted using HTSeq 0.11.0, parameters= -s reverse -r pos
RNA-seq count files were analyzed for differential expression using DESeq2 version 3.8, parameters = alpha = 0.05 lfcThreshold = log2(1.5)
ChIP-seq and ATAC-seq aligned BAM files were sorted and filterd for quality using SAMtools version 1.9, parameters = view -b -q 25 -f 0x2
ChIP-seq and ATAC-seq filtered BAM files had duplicates removed using Picard version 2.18.19
ChIP-seq and ATAC-seq filtered and deduplicated BAM files were used for peak calling using MACS version 2.1.2; 10% input was used as control for ChIP-seq experiments; parameters varied for different conditions: for H3K9ac ChIP-seq =  -f BAMPE -g mm --keep-dup all; for H3K9me3 and H3K79me2 ChIP-seq = -f BAMPE -g mm --scale-to-large --braod --keep-dup all; for ATAC-seq = -f BAM -g mm --nomodel --shift -100 --extsize 200 --keep-dup all
ChIP-seq BAM files were converted to bigwig files using the bamCoverage tool from deepTools version 3.1.3, parameters = --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000
ATAC-seq pileup files from MACS peak calling were converted to bigwig files using the bamCoverage tool from deepTools version 3.1.3, parameters = --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2150570000 --extendReads
Genome_build: GRCm38 (M20 build from GENCODE)
Supplementary_files_format_and_content: RNAseq counts files contain the HTSeq assigned genes and count from the aligned BAM files; ChIP-seq and ATAC-seq BAM files contain the filtered and deduplicated aligned reads to the mouse genome.

molecule: genomic DNA

growth_protocol:
AML cell line generated from mouse bone marrow and grown in culture for 8-12 weeks
MLL-AF9+SETDB1 or MLL-AF9+MSCVpuroEmpty Vector (EV) control cells were generated by harvesting lin- mouse BM and spininfecting with MLL-AF9 and either SETDB1 or EV. Cells were selected for ~3-6 weeks using puromycin in IMDM supplemented with IL-3, SCF, and pen/strep.

extract_protocol:
Cells were fixed with 1%paraformaldehyde, the fixation was quenched with glycine, and the fixed cells were snap-frozen and stored at -80C. Cells were slow thawed on ice for 15 minutes, then lysed in 1% SDS lysis buffer. Chromatin was sheared on a water bath sonicator, and IPs were performed using the indicated antibodies and protein G magnetic beads. DNA was decrosslinked and purified using Qiagen PCR purification kit.
Libraries were prepped using 5ng DNA and the iDeal library prep kit. Amplification cycles of the library preps were optimized using qPCR.

tag: tissue source

value: bone marrow

tag: cell line background

value: MLL-AF9 (MA9) acute myeloid leukemia cell line

tag: retroviral transduction

value: MLL-AF9 + EV control


title: nonNE_AT2deplete_223 [A10_C52_012015_IL6204_N704_N504_S31]


title: nonNE_AT2deplete_236 [E2_C26_012015_IL6205_N705_N507_S47]


title: nonNE_AT2deplete_225 [A2_C02_012015_IL6204_N704_N502_S27]


title: nonNE_AT2deplete_221 [H8_C47_020315_IL6137_N708_N506_S60]

value: stromal


title: nonNE_AT2deplete_220 [H7_C46_020315_IL6137_N708_N505_S58]


title: nonNE_AT2deplete_219 [H3_C45_020315_IL6137_N708_N504_S56]


title: nonNE_AT2deplete_218 [H1_C43_020315_IL6137_N708_N503_S54]


title: nonNE_AT2deplete_242 [F8_C35_012015_IL6205_N706_N504_S44]


title: nonNE_AT2deplete_229 [B8_C11_012015_IL6204_N704_N508_S38]


title: nonNE_AT2deplete_216 [G9_C42_020315_IL6137_N707_N508_S63]


title: nonNE_AT2deplete_226 [A6_C51_012015_IL6204_N704_N503_S29]


title: nonNE_AT2deplete_215 [G7_C40_020315_IL6137_N707_N507_S61]


title: nonNE_AT2deplete_224 [A11_C53_012015_IL6204_N704_N505_S33]


title: nonNE_AT2deplete_214 [G4_C87_020315_IL6137_N707_N506_S59]


title: nonNE_AT2deplete_210 [G12_C88_020315_IL6137_N708_N502_S52]


title: nonNE_AT2deplete_212 [G2_C38_020315_IL6137_N707_N504_S55]


title: nonNE_AT2deplete_208 [F9_C36_020315_IL6136_N706_N508_S48]


title: nonNE_AT2deplete_211 [G1_C37_020315_IL6137_N707_N503_S53]


title: nonNE_AT2deplete_200 [F11_C83_020315_IL6137_N707_N501_S49]


title: nonNE_AT2deplete_204 [F4_C81_020315_IL6136_N706_N504_S40]


title: nonNE_AT2deplete_207 [F7_C34_020315_IL6136_N706_N507_S46]


title: nonNE_AT2deplete_198 [E7_C28_020315_IL6136_N705_N507_S45]


title: nonNE_AT2deplete_199 [E9_C30_020315_IL6136_N705_N508_S47]


title: nonNE_AT2deplete_201 [F12_C82_020315_IL6137_N707_N502_S51]


title: nonNE_AT2deplete_197 [E5_C74_020315_IL6136_N705_N506_S43]


title: nonNE_AT2deplete_196 [E3_C27_020315_IL6136_N705_N505_S41]


title: nonNE_AT2deplete_195 [E2_C26_020315_IL6136_N705_N504_S39]


title: nonNE_AT2deplete_217 [H11_C95_020315_IL6137_N708_N508_S64]


title: nonNE_AT2deplete_194 [E1_C25_020315_IL6136_N705_N503_S37]


title: nonNE_AT2deplete_193 [E12_C76_020315_IL6136_N706_N501_S34]


title: nonNE_AT2deplete_191 [D8_C23_020315_IL6136_N705_N501_S33]


title: nonNE_AT2deplete_192 [D9_C22_020315_IL6136_N705_N502_S35]


title: nonNE_AT2deplete_190 [D6_C69_020315_IL6135_N704_N508_S32]


title: nonNE_AT2deplete_189 [D5_C68_020315_IL6135_N704_N507_S30]


title: nonNE_AT2deplete_203 [F3_C33_020315_IL6136_N706_N503_S38]


title: nonNE_AT2deplete_188 [D4_C67_020315_IL6135_N704_N506_S28]


title: nonNE_AT2deplete_209 [G11_C89_020315_IL6137_N708_N501_S50]


title: nonNE_AT2deplete_213 [G3_C39_020315_IL6137_N707_N505_S57]


title: nonNE_AT2deplete_187 [D3_C19_020315_IL6135_N704_N505_S26]


title: nonNE_AT2deplete_202 [F1_C31_020315_IL6136_N706_N502_S36]


title: nonNE_AT2deplete_206 [F6_C79_020315_IL6136_N706_N506_S44]


title: nonNE_AT2deplete_186 [D2_C20_020315_IL6135_N704_N504_S24]


title: nonNE_AT2deplete_185 [C8_C17_020315_IL6135_N703_N508_S31]


title: nonNE_AT2deplete_184 [C5_C62_020315_IL6135_N703_N507_S29]


title: nonNE_AT2deplete_205 [F5_C80_020315_IL6136_N706_N505_S42]


title: nonNE_AT2deplete_183 [C3_C13_020315_IL6135_N703_N506_S27]


title: nonNE_AT2deplete_182 [C2_C14_020315_IL6135_N703_N505_S25]


title: nonNE_AT2deplete_181 [C1_C15_020315_IL6135_N703_N504_S23]


title: nonNE_AT2deplete_180 [C12_C66_020315_IL6135_N704_N503_S22]


title: nonNE_AT2deplete_179 [C11_C65_020315_IL6135_N704_N502_S20]


title: nonNE_AT2deplete_178 [C10_C64_020315_IL6135_N704_N501_S18]


title: nonNE_AT2deplete_173 [B4_C55_020315_IL6134_N702_N504_S8]


title: nonNE_AT2deplete_174 [B5_C56_020315_IL6134_N702_N505_S10]


title: nonNE_AT2deplete_177 [B9_C10_020315_IL6134_N702_N508_S16]


title: nonNE_AT2deplete_175 [B7_C12_020315_IL6134_N702_N506_S12]


title: nonNE_AT2deplete_172 [B3_C07_020315_IL6134_N702_N503_S6]


title: nonNE_AT2deplete_171 [B2_C08_020315_IL6134_N702_N502_S4]


title: nonNE_AT2deplete_169 [B11_C59_020315_IL6135_N703_N502_S19]


title: nonNE_AT2deplete_168 [B10_C58_020315_IL6135_N703_N501_S17]


title: nonNE_AT2deplete_167 [A7_C06_020315_IL6134_N701_N506_S11]


title: nonNE_AT2deplete_166 [A6_C51_020315_IL6134_N701_N505_S9]


title: nonNE_AT2deplete_162 [A1_C03_020315_IL6134_N701_N501_S1]


title: nonNE_AT2deplete_160 [A11_C53_020315_IL6134_N701_N508_S15]


title: nonNE_AT2deplete_161 [A12_C54_020315_IL6134_N702_N501_S2]


title: nonNE_157 [H3_C45_021715_IL6203_N703_N507_S23]

source_name: nonNE

value: Ascl1-CreERT2; Rosa26-lslZsGreen


title: nonNE_156 [G9_C42_021715_IL6203_N703_N506_S21]


title: nonNE_152 [E3_C27_021715_IL6203_N702_N506_S20]


title: nonNE_153 [F12_C82_021715_IL6203_N703_N505_S18]


title: nonNE_AT2deplete_176 [B8_C11_020315_IL6134_N702_N507_S14]


title: nonNE_149 [C4_C61_021715_IL6203_N701_N508_S24]


title: nonNE_147 [B7_C12_021715_IL6203_N701_N506_S19]


title: nonNE_146 [A2_C02_021715_IL6203_N701_N501_S10]


title: nonNE_155 [F2_C32_021715_IL6203_N703_N502_S13]


title: nonNE_145 [A12_C54_021715_IL6203_N701_N505_S16]


title: nonNE_151 [E2_C26_021715_IL6203_N702_N505_S17]


title: nonNE_144 [A11_C53_021715_IL6203_N701_N504_S15]


title: nonNE_143 [H5_C92_022114_S15]


title: nonNE_AT2deplete_170 [B12_C60_020315_IL6135_N703_N503_S21]


title: nonNE_148 [B9_C10_021715_IL6203_N701_N507_S22]


title: nonNE_141 [G4_C87_022114_S19]


title: nonNE_139 [G1_C37_022114_S12]


title: nonNE_140 [G3_C39_022114_S17]


title: nonNE_138 [G11_C89_022114_S35]


title: nonNE_AT2deplete_165 [A5_C50_020315_IL6134_N701_N504_S7]


title: nonNE_137 [F9_C36_022114_S22]


title: nonNE_AT2deplete_159 [A10_C52_020315_IL6134_N701_N507_S13]


title: nonNE_135 [F3_C33_022114_S16]


title: nonNE_AT2deplete_163 [A4_C49_020315_IL6134_N701_N503_S5]


title: nonNE_136 [F5_C80_022114_S21]


title: nonNE_134 [F2_C32_022114_S9]


title: nonNE_154 [F1_C31_021715_IL6203_N703_N501_S11]


title: nonNE_131 [E4_C75_022114_S18]


title: nonNE_132 [F12_C82_022114_S31]


title: nonNE_133 [F1_C31_022114_S10]


title: nonNE_128 [D1_C21_022114_S11]


title: nonNE_127 [D11_C71_022114_S34]


title: nonNE_130 [E12_C76_022114_S30]


title: nonNE_126 [D10_C70_022114_S24]


title: nonNE_124 [C5_C62_022114_S20]


title: nonNE_123 [C11_C65_022114_S33]


title: nonNE_120 [B12_C60_022114_S29]


title: nonNE_121 [B1_C09_022114_S8]


title: nonNE_142 [G8_C41_022114_S26]


title: nonNE_129 [D9_C22_022114_S28]


title: nonNE_119 [A9_C04_022114_S27]


title: nonNE_117 [A11_C53_022114_S32]


title: NE_CGRP_115 [C_091015_H12_C94_IM816_710_508_S75]

value: CGRP-CreERT2; Rosa26-lslZsGreen

value: ZsGreen+ EpCAM+ CD31- CD45- F4/80- DAPI-

value: NE


title: nonNE_116 [A10_C52_022114_S23]

value: Mixed


title: NE_CGRP_110 [C_091015_G6_C85_IM816_710_517_S86]

value: 2-3 months


title: NE_CGRP_114 [C_091015_H11_C95_IM816_710_507_S66]

value: Lung


title: NE_CGRP_113 [C_091015_H10_C96_IM816_710_506_S56]


title: NE_CGRP_112 [C_091015_G8_C41_IM816_710_503_S22]


title: NE_CGRP_111 [C_091015_G7_C40_IM816_710_502_S10]


title: NE_CGRP_109 [C_091015_G5_C86_IM816_709_508_S74]


title: NE_CGRP_108 [C_091015_G4_C87_IM816_709_507_S65]


title: NE_CGRP_106 [C_091015_G2_C38_IM816_709_505_S45]


title: NE_CGRP_105 [C_091015_G12_C88_IM816_710_505_S46]


title: NE_CGRP_107 [C_091015_G3_C39_IM816_709_506_S55]


title: NE_CGRP_104 [C_091015_G11_C89_IM816_710_504_S34]


title: NE_CGRP_101 [C_091015_F5_C80_IM816_708_508_S73]


title: nonNE_125 [C8_C17_022114_S25]

value: ZsGreen- EpCAM+ CD31- CD45- F4/80- DAPI-


title: NE_CGRP_100 [C_091015_F4_C81_IM816_708_507_S64]


title: NE_CGRP_99 [C_091015_F3_C33_IM816_708_506_S54]


title: NE_CGRP_103 [C_091015_F9_C36_IM816_708_502_S8]


title: NE_CGRP_98 [C_091015_F1_C31_IM816_708_505_S44]


title: NE_CGRP_97 [C_091015_F11_C83_IM816_709_503_S21]


title: NE_CGRP_94 [C_091015_E6_C73_IM816_707_508_S72]


title: NE_CGRP_90 [C_091015_E2_C26_IM816_707_504_S31]


title: NE_CGRP_93 [C_091015_E5_C74_IM816_707_507_S63]


title: NE_CGRP_91 [C_091015_E3_C27_IM816_707_505_S43]


title: NE_CGRP_92 [C_091015_E4_C75_IM816_707_506_S53]


title: NE_CGRP_89 [C_091015_E10_C78_IM816_708_503_S20]


title: NE_CGRP_88 [C_091015_D9_C22_IM816_707_517_S83]


title: NE_CGRP_87 [C_091015_D3_C19_IM816_706_508_S71]


title: NE_CGRP_86 [C_091015_D1_C21_IM816_706_507_S62]


title: NE_CGRP_85 [C_091015_D10_C70_IM816_707_502_S7]


title: NE_CGRP_84 [C_091015_C6_C63_IM816_706_504_S30]


title: NE_CGRP_83 [C_091015_C3_C13_IM816_706_503_S18]


title: NE_CGRP_81 [C_091015_C11_C65_IM816_706_506_S52]


title: NE_CGRP_77 [C_091015_B4_C55_IM816_705_506_S51]


title: NE_CGRP_75 [C_091015_B2_C08_IM816_705_504_S29]


title: NE_CGRP_80 [C_091015_C10_C64_IM816_706_505_S42]


title: NE_CGRP_78 [C_091015_B5_C56_IM816_705_507_S61]


title: NE_CGRP_79 [C_091015_B9_C10_IM816_705_508_S70]


title: NE_CGRP_72 [C_091015_A7_C06_IM816_704_506_S50]


title: NE_CGRP_74 [C_091015_B10_C58_IM816_706_517_S82]


title: NE_CGRP_96 [C_091015_E9_C30_IM816_709_502_S9]


title: NE_CGRP_70 [C_091015_A5_C50_IM816_704_504_S28]


title: NE_CGRP_68 [C_091015_A2_C02_IM816_704_502_S4]


title: NE_CGRP_69 [C_091015_A4_C49_IM816_704_503_S16]


title: NE_CGRP_71 [C_091015_A6_C51_IM816_704_505_S40]


title: NE_CGRP_67 [C_091015_A1_C03_IM816_704_517_S80]


title: NE_CGRP_66 [C_091015_A12_C54_IM816_705_502_S5]


title: NE_CGRP_64 [C_091015_A10_C52_IM816_704_508_S69]


title: NE_CGRP_62 [X08_20_G9_C42_IL5350_N706_N505_S41]


title: NE_CGRP_59 [X08_20_E6_C73_IL5350_N705_N508_S46]


title: NE_CGRP_63 [X08_20_H6_C91_IL5350_N706_N506_S43]


title: NE_CGRP_58 [X08_20_E4_C75_IL5350_N705_N507_S44]


title: NE_CGRP_56 [X08_20_E12_C76_IL5349_N706_N501_S33]


title: NE_CGRP_82 [C_091015_C2_C14_IM816_706_502_S6]


title: NE_CGRP_57 [X08_20_E3_C27_IL5350_N705_N506_S42]


title: NE_CGRP_55 [X08_20_D3_C19_IL5350_N705_N504_S38]


title: NE_CGRP_53 [X08_20_C8_C17_IL5350_N705_N503_S36]


title: NE_CGRP_52 [X08_20_C2_C14_IL5350_N705_N502_S34]


title: NE_CGRP_49 [X08_08_H5_C92_IL5349_N704_N506_S27]


title: NE_CGRP_47 [X08_08_G6_C85_IL5349_N704_N503_S22]


title: NE_CGRP_46 [X08_08_G3_C39_IL5349_N704_N502_S20]


title: NE_CGRP_51 [X08_20_A6_C51_IL5349_N704_N508_S31]


title: NE_CGRP_44 [X08_08_F7_C34_IL5349_N704_N501_S18]


title: NE_CGRP_41 [X08_08_E11_C77_IL5349_N703_N508_S30]


title: NE_CGRP_60 [X08_20_F7_C34_IL5350_N706_N502_S35]


title: NE_CGRP_35 [X08_08_B12_C60_IL5348_N702_N508_S16]


title: NE_CGRP_39 [X08_08_D8_C23_IL5350_N706_N508_S47]


title: NE_CGRP_45 [X08_08_G12_C88_IL5349_N704_N505_S25]


title: NE_CGRP_38 [X08_08_D4_C67_IL5349_N703_N503_S21]


title: NE_CGRP_37 [X08_08_C7_C18_IL5349_N703_N501_S17]


title: NE_CGRP_34 [X08_08_A9_C04_IL5348_N702_N505_S10]


title: NE_CGRP_36 [X08_08_B4_C55_IL5348_N702_N507_S14]


title: NE_CGRP_33 [X08_08_A6_C51_IL5348_N702_N504_S8]


title: NE_CGRP_42 [X08_08_E3_C27_IL5349_N703_N505_S24]


title: NE_CGRP_40 [X08_08_E10_C78_IL5349_N703_N507_S28]


title: NE_CGRP_32 [X08_08_A2_C02_IL5348_N702_N503_S6]


title: NE_CGRP_43 [X08_08_E4_C75_IL5349_N703_N506_S26]


title: NE_CGRP_54 [X08_20_D10_C71_IL5350_N705_N505_S40]


title: NE_CGRP_30 [X06_19_H2_C44_IL5348_N701_N508_S15]


title: NE_CGRP_22 [C_H4_G5_C86_061314_S30]


title: NE_CGRP_28 [X06_19_F5_C80_IL5348_N701_N505_S9]


title: NE_CGRP_29 [X06_19_G3_C39_IL5348_N701_N507_S13]


title: NE_CGRP_21 [C_G1_C8_C17_061314_S9]


title: NE_CGRP_20 [C_D4_F5_C80_061314_S26]


title: NE_CGRP_19 [C_D2_E3_C27_061314_S15]


title: NE_CGRP_24 [X06_19_A2_C02_IL5348_N701_N502_S3]


title: NE_CGRP_18 [C_D1_B1_C09_061314_S6]


title: NE_CGRP_17 [C_C2_E2_C26_061314_S13]


title: NE_CGRP_15 [C_B2_D9_C22_061314_S4]


title: NE_CGRP_16 [C_C1_B2_C08_061314_S5]


title: NE_CGRP_14 [C_A5_G4_C87_061314_S22]


title: NE_CGRP_13 [C_A1_A7_C06_061314_S1]


title: NE_Ascl1_11 [F8_C35_021715_IL6202_N703_N504_S7]


title: NE_Ascl1_8 [E1_C25_021715_IL6202_N702_N504_S6]


title: NE_Ascl1_9 [E4_C75_021715_IL6202_N702_N507_S8]


title: NE_Ascl1_6 [C9_C16_021715_IL6202_N702_N501_S1]


title: NE_Ascl1_5 [A9_C04_021715_IL6202_N701_N503_S4]


title: NE_Ascl1_3 [E9_C30_022114_S1]


title: TRC_bulk_sc_RNAseq

city: New York

first: Jin

last: Zhang

state: NY

address: 3227 Broadway

institute: Columbia University

description: bulk samples: Pkd2l1-expressing sour taste receptor cell pool- #8(plate1-H1) and #200(plate3-H1); control pool- #16(plate1-H2), #24(plate1-H3), #104(plate2-H1), #112(plate2-H2), #120(plate2-H3), #208(plate3-H2), #216(plate3-H3), #296(plate4-H1), #304(plate4-H2), #312(plate4-H3).  Other samples in Pkd2l1_plate1-4 are single sour taste receptor cells.

data_processing:
Paired-end reads were trimmed and aligned to GRCm38 (mm10) using STAR
Reads per million (RPM) counts for each gene were computed using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Reads per million (RPM) counts for each gene

source_name: sour taste receptor cells and control cells

extract_protocol:
Geniculate ganglia from P2rx3-tdTomato animals were isolated and placed in a micro-dish containing 200µl of collagenase/dispase (Roche) solution (4mg/ml in HBSS) at 37oC for 15min. The collagenase/dispase solution was carefully removed without disturbing the tissue, and 200µl papain (Worthington) solution was added to the dish and incubated at 37oC for 15min.  Dissociated ganglion cells were spun down, re-suspended in 500 µl HBSS and placed in a collagen-coated micro-dish. To pick single tdTomato+ ganglion neuron, the cell suspension was monitored with an Olympus IX70 inverted fluorescence microscope through the entire picking process.
Cells were extracted from tongues of Pkd2l1-tdTomato mice. After isolation, cells were fractionated using a fluorescence activated cell sorter (MoFlo Astrios, Beckman Coulter). The tdTomato+ (sour TRCs) and tdTomato- (non-sour TRCs and supporting cells) were sorted (50-100 for cell pools, or single cells) into 96-well plates containing cDNA synthesis buffer.
The single-cell sequencing libraries were prepared using the CEL-Seq method as previously described (Hashimshony et al., 2016; Hashimshony et al., 2012).
The cDNA libraries from TRCs for bulk and single cell sequencing were prepared using the SMART-Seq Ultra Low Input RNA kit (TaKaRa) and the Nextera XT DNA Sample Kit (Illumina) using custom indexed adapters.

tag: genotype

value: Pkd2l1-tdTomato animals

tag: strain background

value: tongue epithelia


title: NE_Ascl1_1 [A4_C49_022114_S5]


title: NE_Ascl1_2 [A6_C51_022114_S3]


title: Tumor 5_PoEMs

city: Leuven

first: Massimiliano

last: Mazzone

address: Herestraat 49

country: Belgium

institute: VIB

data_processing:
Reads were trimmed so as to remove low quality ends (<Q20) using FastX (0.0.14) and adapters using cutadapt (1.15). Reads shorter than 35bp after trimming were removed.
Using FastX (0.0.14) and ShortRead (1.36.1) polyA-reads (>90% A), ambiguous reads (containing N), low quality (more than 50% of the bases < Q25) and artifact reads (all but 3 bases in the read equal one base type) were removed.
Using bowtie (2.3.3.1), contaminants (reads aligning to phix_illumina) were removed
The reads are aligned to the reference genome with STAR 2.5.2b
Per gene read counts were determined using featureCounts (1.5.3)
Genome_build: GRCm3882 (Mus musculus 82)
Supplementary_files_format_and_content: Per gene raw read counts per sample

source_name: 4T1 tumor

extract_protocol:
Mice were sacrificed by cervical disslocation, tumors were collected in PBS and digested with a buffer containing collagenase 1 and dispase. Samples were incubated with red blood cell lysis buffer. Fc receptors on cell surface were blocked with CD16/CD32 antibody. Cells were sorted as viable, CD11B+, F4/80+, PDPN+ or PDPN-.
SMART-Seq pre-amplification

value: tumor-associate macrophages

tag: tumor number

tag: surface markers


title: Tumor 4_non-PoEMs


title: Tumor 6_PoEMs


title: Tumor 4_PoEMs


title: Tumor 6_ non-PoEMs


title: Tumor 2_PoEMs


title: PARE_KO_rep1

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

description: Mitochondria were isolated from homogenized hearts and isolated by differential centrifugation as described previously (Lagouge et al., 2015; Mourier et al., 2014), with some modifications. Hearts were cut and washed three times with ice cold PBS, and once with mitochondrial isolation buffer (MIB) containing 310 mM sucrose, 10 mM Tris-HCl and 0.05 % BSA (w/v) by centrifugation at 4,500 g for 1 min at 4°C. Heart pieces were homogenized in 5 ml of fresh MIB using a Potter S pestle (Sartorius). The homogenate was centrifuged at 1,000 g for 10 min at 4°C and the supernatant was centrifuged at 4,500 g for 15 min at 4°C to isolate mitochondria. Crude mitochondrial pellets were suspended in MIB supplemented with 1x Complete EDTA-free protease inhibitor cocktail (Roche).

data_processing:
Library strategy: PARE
Basecalling was performed by NextSeq Control Software
The 5 bp adapter sequence was trimmed and paired-end reads were merged with CLC Genomics Workbench (Qiagen) if the read overlap exceeded 95% identity.
Merged reads were aligned to the mouse genome (mm10) with Bowtie2, using the --very-sensitive preset parameters with a shortened seed length of 10 nt.
Strand-specific read coverage at the 5ʹ terminal position of aligned reads was calculated with BEDtools genomecov (-d -scale [1e+06/total mapped reads]), normalized to the total number of fragments mapped to the mouse whole genome (reads per million; RPM), and converted to wig format for visualization.
genome build: GRCm38/mm13
processed data files format and content: Strand-specific 5’ end coverage for each sample in wiggle format, normalised by total library size.

source_name: Heart mitochondria

growth_protocol: Mice were housed in standard cages (45 cm × 29 cm × 12 cm) under a 12-h light/dark schedule (lights on 7 am to 7 pm) in controlled environmental conditions of 22 ± 2 °C and 50 + 10% relative humidity and fed a normal chow diet and water were provided ad libitum.

extract_protocol:
RNA was isolated from total hearts or heart mitochondria using the miRNeasy Mini kit (Qiagen) incorporating an on-column RNase-free DNase digestion to remove all DNA.
Total RNA libraries were prepared according to the Illumina TruSeq protocol, using random hexamer primers for cDNA generation and the Ribo-Zero rRNA removal kit for cytoplasmic RNA deptetion. Mitochondrial RNA was prepared according to the PARE protocol as described by German et al. (Nature Protocols, Vol.4 No.3, 2009).

value: Heart

value: 52 weeks

value: Rexo2loxP/loxPloxP/loxP, +/Ckmm


title: PARE_KO_rep3

data_processing:
Library strategy: PARE
Basecalling was performed by NextSeq Control Software
The 5 bp adapter sequence was trimmed and paired-end reads were merged with CLC Genomics Workbench (Qiagen) if the read overlap exceeded 95% identity.
Merged reads were aligned to the mouse genome (mm10) with Bowtie2, using the --very-sensitive preset parameters with a shortened seed length of 10 nt.
Strand-specific read coverage at the 5ʹ terminal position of aligned reads was calculated with BEDtools genomecov (-d -scale [1e+06/total mapped reads]), normalized to the total number of fragments mapped to the mouse whole genome (reads per million; RPM), and converted to wig format for visualization.
genome build: GRCm38/mm15
processed data files format and content: Strand-specific 5’ end coverage for each sample in wiggle format, normalised by total library size.


title: PARE_WT_rep1

data_processing:
Library strategy: PARE
Basecalling was performed by NextSeq Control Software
The 5 bp adapter sequence was trimmed and paired-end reads were merged with CLC Genomics Workbench (Qiagen) if the read overlap exceeded 95% identity.
Merged reads were aligned to the mouse genome (mm10) with Bowtie2, using the --very-sensitive preset parameters with a shortened seed length of 10 nt.
Strand-specific read coverage at the 5ʹ terminal position of aligned reads was calculated with BEDtools genomecov (-d -scale [1e+06/total mapped reads]), normalized to the total number of fragments mapped to the mouse whole genome (reads per million; RPM), and converted to wig format for visualization.
genome build: GRCm38/mm10
processed data files format and content: Strand-specific 5’ end coverage for each sample in wiggle format, normalised by total library size.


title: PARE_WT_rep3

data_processing:
Library strategy: PARE
Basecalling was performed by NextSeq Control Software
The 5 bp adapter sequence was trimmed and paired-end reads were merged with CLC Genomics Workbench (Qiagen) if the read overlap exceeded 95% identity.
Merged reads were aligned to the mouse genome (mm10) with Bowtie2, using the --very-sensitive preset parameters with a shortened seed length of 10 nt.
Strand-specific read coverage at the 5ʹ terminal position of aligned reads was calculated with BEDtools genomecov (-d -scale [1e+06/total mapped reads]), normalized to the total number of fragments mapped to the mouse whole genome (reads per million; RPM), and converted to wig format for visualization.
genome build: GRCm38/mm12
processed data files format and content: Strand-specific 5’ end coverage for each sample in wiggle format, normalised by total library size.


title: PARE_WT_rep2

data_processing:
Library strategy: PARE
Basecalling was performed by NextSeq Control Software
The 5 bp adapter sequence was trimmed and paired-end reads were merged with CLC Genomics Workbench (Qiagen) if the read overlap exceeded 95% identity.
Merged reads were aligned to the mouse genome (mm10) with Bowtie2, using the --very-sensitive preset parameters with a shortened seed length of 10 nt.
Strand-specific read coverage at the 5ʹ terminal position of aligned reads was calculated with BEDtools genomecov (-d -scale [1e+06/total mapped reads]), normalized to the total number of fragments mapped to the mouse whole genome (reads per million; RPM), and converted to wig format for visualization.
genome build: GRCm38/mm11
processed data files format and content: Strand-specific 5’ end coverage for each sample in wiggle format, normalised by total library size.


title: PARE_KO_rep2

data_processing:
Library strategy: PARE
Basecalling was performed by NextSeq Control Software
The 5 bp adapter sequence was trimmed and paired-end reads were merged with CLC Genomics Workbench (Qiagen) if the read overlap exceeded 95% identity.
Merged reads were aligned to the mouse genome (mm10) with Bowtie2, using the --very-sensitive preset parameters with a shortened seed length of 10 nt.
Strand-specific read coverage at the 5ʹ terminal position of aligned reads was calculated with BEDtools genomecov (-d -scale [1e+06/total mapped reads]), normalized to the total number of fragments mapped to the mouse whole genome (reads per million; RPM), and converted to wig format for visualization.
genome build: GRCm38/mm14
processed data files format and content: Strand-specific 5’ end coverage for each sample in wiggle format, normalised by total library size.


title: Tumor 2_non-PoEMs


title: NE_Ascl1_10 [F7_C34_021715_IL6202_N703_N503_S5]


title: Tumor 1_PoEMs


title: Tumor 1_non-PoEMs


title: 3k3-ctrl-d14-smart: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone A

first: Michelle

last: Monje

address: 265 Campus Drive, SIM1 G3035

institute: Stanford University

description:
iPSC differentiation no doxycycline RNA-seq
TRE-H3.3K27M Clone A Control
3k3-ctrl

data_processing:
RNA-seq reads were trimmed of adaptors with cutadapt
Aligned to hg19 with tophat2 v2.1.1
Reads counted in hg19 RefSeq genes using featureCounts
Transcript per million (TPM) for each gene was determined as 1,000,000 * (reads per kilobase of transcript)/(total sum of reads per kilobase of all transcripts)
genome build: hg19
processed data files format and content: TPM spreadsheet

growth_protocol: mTESR1 Complete media with Anti-anti, differentiated under Douvaras 2015 protocol

extract_protocol:
Total RNA purification with RNEasy Kit
Modified Smart-seq2 protocol with oligodT30 VN, ISPCR cDNA amplification, and Nextera XT library preparation

value: healthy control iPSC cell line 2242-1

tag: treatment

value: Day 14 NPCs (d14)


title: 1k9-ctrl-d55-rna: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone A

description:
iPSC differentiation no doxycycline RNA-seq
TRE-H3.1K27M Clone A Control
1k9-ctrl

value: Day 55 eOPCs (d55)


title: 3k16-dox-d14-smart: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone B

description:
iPSC differentiation + doxycycline RNA-seq
TRE-H3.3K27M Clone B Dox
3k16-dox


title: 1k12-dox-d55-rna: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone B

description:
iPSC differentiation + doxycycline RNA-seq
TRE-H3.1K27M Clone B Dox
1k12-dox


title: 3k16-ctrl-d14-smart: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone B

description:
iPSC differentiation no doxycycline RNA-seq
TRE-H3.3K27M Clone B Control
3k16-ctrl


title: 3k3-dox-d14-smart: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone A

description:
iPSC differentiation + doxycycline RNA-seq
TRE-H3.3K27M Clone A Dox
3k3-dox


title: 3k16-ctrl-d55-rna: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone B


title: 1k9-dox-d55-rna: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone A

description:
iPSC differentiation + doxycycline RNA-seq
TRE-H3.1K27M Clone A Dox
1k9-dox


title: Tumor 5_non-PoEMs


title: 3k3-ctrl-d55-rna: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone A


title: 1k12-dox-d14-k27ac: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone B

description:
iPSC differentiation + doxycycline ChIP-seq
TRE-H3.1K27M Clone B Dox
1k12-dox

data_processing:
ChIP-seq reads were trimmed of adaptors with cutadapt
Aligned with bowtie2 v 2.2.4 --very-sensitive to hg19 reference
Reads with quality less than 10 removed with samtools and PCR duplicates removed with Picard MarkDuplicates
Normalization to 1M reads with bedtools version 2.19.1 genomecov -bg -split and then converting to bigwig format with bedGraphToBigWig
Peaks were called using macs2 version 2.1.1.20160309 callpeak on full depth bam files over input controls. Broad peak calling was used for H3K27me3 and EED
genome build: hg19
processed data files format and content: RPM bigwig

extract_protocol:
Cells are fixed with 1% FA. Following ChIP and washes, DNA is purified using Ampure XP
NEBNext Ultra II and NEBNext Multiplex Oligos

tag: antibody

value: H3K27Ac (Active Motif #39133)


title: 1k12-dox-d14-inp: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone B

value: none (input)


title: 1k9-dox-d14-k27ac: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone A

description:
iPSC differentiation + doxycycline ChIP-seq
TRE-H3.1K27M Clone A Dox
1k9-dox


title: 1k12-dox-d55-inp: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone B


title: 1k12-dox-d55-k27ac: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone B


title: 1k9-dox-d14-inp: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone A


title: 1k9-ctrl-d55-k27ac: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone A

description:
iPSC differentiation no doxycycline ChIP-seq
TRE-H3.1K27M Clone A Control
1k9-ctrl


title: 1k9-dox-d55-k27ac: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone A


title: 3k16-dox-d55-inp: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone B

description:
iPSC differentiation + doxycycline ChIP-seq
TRE-H3.3K27M Clone B Dox
3k16-dox


title: 3k16-ctrl-d55-k27ac: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone B

description:
iPSC differentiation no doxycycline ChIP-seq
TRE-H3.3K27M Clone B Control
3k16-ctrl


title: 1k9-ctrl-d55-inp: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone A


title: 1k9-dox-d55-inp: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone A


title: 3k16-ctrl-d55-inp: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone B


title: 3k3-dox-d55-k27ac: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone A

description:
iPSC differentiation + doxycycline ChIP-seq
TRE-H3.3K27M Clone A Dox
3k3-dox


title: 3k16-dox-d55-rna: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone B


title: 3k3-ctrl-d55-k27ac: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone A

description:
iPSC differentiation no doxycycline ChIP-seq
TRE-H3.3K27M Clone A Control
3k3-ctrl


title: 3k3-dox-d55-inp: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone A


title: dipg38.3-k27m: SU-DIPG38 patient-derived DIPG culture

description:
cell culture ChIP-seq
SU-DIPG38 patient-derived DIPG culture
dipg38.3,dipg38.4

source_name: SU-DIPG38 patient-derived DIPG culture

growth_protocol: TSM base + EGF/FGF/PDGF-AA/PDGF-BB, see Grasso 2015

extract_protocol:
Cells are fixed with 1% FA. Following ChIP and washes, DNA is purified using PCI purification
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos

value: Diffuse intrinsic pontine glioma (DIPG)

value: H3K27M (Millipore ABE419)


title: dipg38.3-h3.3: SU-DIPG38 patient-derived DIPG culture


title: dipg38.4-inp: SU-DIPG38 patient-derived DIPG culture


title: 3k3-ctrl-d55-inp: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone A


title: dipg38.4-h3.3: SU-DIPG38 patient-derived DIPG culture


title: dipg36.4-k27m: SU-DIPG36 patient-derived DIPG culture

description:
cell culture ChIP-seq
SU-DIPG36 patient-derived DIPG culture
dipg36.3,dipg36.4

source_name: SU-DIPG36 patient-derived DIPG culture


title: dipg38.3-inp: SU-DIPG38 patient-derived DIPG culture


title: NE_CGRP_76 [C_091015_B3_C07_IM816_705_505_S41]

tag: strain

value: Mixed

value: CGRP-CreERT2; Rosa26-lslZsGreen

tag: age

value: ZsGreen+ EpCAM+ CD31- CD45- F4/80- DAPI-

value: NE


title: dipg36.4-inp: SU-DIPG36 patient-derived DIPG culture


title: dipg36.4-h3.3: SU-DIPG36 patient-derived DIPG culture


title: dipg36.3-h3.3: SU-DIPG36 patient-derived DIPG culture


title: dipg36.3-k27m: SU-DIPG36 patient-derived DIPG culture


title: 1k9-ctrl-d44-k27ac: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone A


title: 3k16-dox-d55-k27ac: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone B


title: dipg36.3-inp: SU-DIPG36 patient-derived DIPG culture


title: dipg13.6-k27m: SU-DIPG13 Pons patient-derived DIPG culture

description:
cell culture ChIP-seq
SU-DIPG13 Pons patient-derived DIPG culture
dipg13.5,dipg13.6


title: 3k3-dox-d55-rna: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone A


title: dipg13.5-k27m: SU-DIPG13 Pons patient-derived DIPG culture


title: dipg13.6-h3.3: SU-DIPG13 Pons patient-derived DIPG culture


title: dipg13.5-inp: SU-DIPG13 Pons patient-derived DIPG culture


title: dipg13.5-h3.3: SU-DIPG13 Pons patient-derived DIPG culture


description:
cnmc856n
PolyA purification, cDNA synthesis, end-reapir, and A-tailing as described in Nagaraja 2017. Indexing with NEBNext Multiplex Oligos
CNMC116 primary normal pons
primary tissue RNA-seq
polyA+ mRNA
primary_dipg-rna.tpm.xlsx

data_processing:
ChIP-seq reads were trimmed of adaptors with cutadapt
Aligned with bowtie2 v 2.2.4 --very-sensitive to hg19 reference
Reads with quality less than 10 removed with samtools and PCR duplicates removed with Picard MarkDuplicates
Normalization to 1M reads with bedtools version 2.19.1 genomecov -bg -split and then converting to bigwig format with bedGraphToBigWig
Peaks were called using macs2 version 2.1.1.20160309 callpeak on full depth bam files over input controls. Broad peak calling was used for H3K27me3 and EED
Genome_build: hg19
Supplementary_files_format_and_content: RPM bigwig
ChIP-Rx reads were trimmed of adaptors with cutadapt
Aligned with bowtie2 v 2.2.4 --very-sensitive to hg19 reference and then unmapped reads (--un-conc) were aligned to dm6 reference
Reads with quality less than 10 removed with samtools and PCR duplicates removed with Picard MarkDuplicates from both hg19 and dm6 alignments
Normalization to 1M dm6 reads with bedtools version 2.19.1 genomecov -bg -split and then converting to bigwig format with bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: RRPM bigwig
RNA-seq reads were trimmed of adaptors with cutadapt
Aligned to hg19 with tophat2 v2.1.1
Reads counted in hg19 RefSeq genes using featureCounts
Transcript per million (TPM) for each gene was determined as 1,000,000 * (reads per kilobase of transcript)/(total sum of reads per kilobase of all transcripts)
Genome_build: hg19
Supplementary_files_format_and_content: TPM spreadsheet
ATAC-seq reads were trimmed of adaptors with cutadapt
Aligned with bowtie2 v 2.2.4 --very-sensitive to hg19 reference
Reads with quality less than 10 removed with samtools and PCR duplicates removed with Picard MarkDuplicates
Normalization to 1M reads with bedtools version 2.19.1 genomecov -bg -split and then converting to bigwig format with bedGraphToBigWig
Full depth technical replicate bam files were then merged with samtools merge and peak calls we performed once more on the merged replicate file using macs2 version 2.1.1.20160309
Genome_build: hg19
Supplementary_files_format_and_content: RPM bigwig
WES/WGS reads were trimmed of adaptors with cutadapt
Reads were aligned to the hg19 reference sequence using bwa mem v0.7.15. PCR duplicates were removed using picardtools MarkDuplicates.
Reads were then processed using GATK best practices, including indel realignment and base recalibration
Variants were called with GATK UnifiedGenotyper
Genome_build: hg19
Supplementary_files_format_and_content: VCF variant calls

source_name: primary pontine tissue

extract_protocol: Tissue is homogenized and total RNA purified with RNEasy kit

value: primary human patient pontine tissue


title: dipg38.4-k27m: SU-DIPG38 patient-derived DIPG culture


description:
dipg38p
PolyA purification, cDNA synthesis, end-reapir, and A-tailing as described in Nagaraja 2017. Indexing with NEBNext Multiplex Oligos
SU-DIPG38 primary tumor
primary tissue RNA-seq
polyA+ mRNA
primary_dipg-rna.tpm.xlsx

source_name: primary tumor tissue

value: primary human patient tumor tissue


description:
dipg36p
PolyA purification, cDNA synthesis, end-reapir, and A-tailing as described in Nagaraja 2017. Indexing with NEBNext Multiplex Oligos
SU-DIPG36 primary tumor
primary tissue RNA-seq
polyA+ mRNA
primary_dipg-rna.tpm.xlsx


description:
dipg33p
PolyA purification, cDNA synthesis, end-reapir, and A-tailing as described in Nagaraja 2017. Indexing with NEBNext Multiplex Oligos
SU-DIPG33 primary tumor
primary tissue RNA-seq
polyA+ mRNA
primary_dipg-rna.tpm.xlsx


description:
dipg14t
PolyA purification, cDNA synthesis, end-reapir, and A-tailing as described in Nagaraja 2017. Indexing with NEBNext Multiplex Oligos
SU-DIPG14 primary tumor
primary tissue RNA-seq
polyA+ mRNA
primary_dipg-rna.tpm.xlsx


description:
cnmc537t
PolyA purification, cDNA synthesis, end-reapir, and A-tailing as described in Nagaraja 2017. Indexing with NEBNext Multiplex Oligos
CNMC13 primary tumor
primary tissue RNA-seq
polyA+ mRNA
primary_dipg-rna.tpm.xlsx


description:
dipg17p
PolyA purification, cDNA synthesis, end-reapir, and A-tailing as described in Nagaraja 2017. Indexing with NEBNext Multiplex Oligos
SU-DIPG17 primary tumor
primary tissue RNA-seq
polyA+ mRNA
primary_dipg-rna.tpm.xlsx


description:
cnmc347t
PolyA purification, cDNA synthesis, end-reapir, and A-tailing as described in Nagaraja 2017. Indexing with NEBNext Multiplex Oligos
CNMC10 primary tumor
primary tissue RNA-seq
polyA+ mRNA
primary_dipg-rna.tpm.xlsx


description:
dipg29t
PolyA purification, cDNA synthesis, end-reapir, and A-tailing as described in Nagaraja 2017. Indexing with NEBNext Multiplex Oligos
SU-DIPG29 primary tumor
primary tissue RNA-seq
polyA+ mRNA
primary_dipg-rna.tpm.xlsx


title: sf5609n Exome capture

description:
sf5609n
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SF509 primary matched normal
primary tissue WES/WGS

source_name: primary matched normal

extract_protocol: Tissues are homogenized and gDNA is extracted with Qiagen Dneasy or Gentra Puregene.

value: primary matched normal tissue


title: dipg39n Exome capture

description:
dipg39n
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG39 primary matched normal
primary tissue WES/WGS


description:
pons01
PolyA purification, cDNA synthesis, end-reapir, and A-tailing as described in Nagaraja 2017. Indexing with NEBNext Multiplex Oligos
SU-Pons01 primary normal pons
primary tissue RNA-seq
polyA+ mRNA
primary_dipg-rna.tpm.xlsx


title: dipg38p Exome capture

description:
dipg38p
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG38 primary tumor
primary tissue WES/WGS


title: dipg36p Exome capture

description:
dipg36p
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG36 primary tumor
primary tissue WES/WGS


title: dipg33n Exome capture

description:
dipg33n
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG33 primary matched normal
primary tissue WES/WGS


title: dipg33p Exome capture

description:
dipg33p
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG33 primary tumor
primary tissue WES/WGS


title: dipg32n Exome capture

description:
dipg32n
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG32 primary matched normal
primary tissue WES/WGS


title: diipg31n Exome capture

description:
diipg31n
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG31 primary matched normal
primary tissue WES/WGS


title: dipg31p Exome capture

description:
dipg31p
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG31 primary tumor
primary tissue WES/WGS


title: dipg23n Exome capture

description:
dipg23n
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG23 primary matched normal
primary tissue WES/WGS


title: dipg27p Exome capture

description:
dipg27p
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG27 primary tumor
primary tissue WES/WGS


title: dipg29p Exome capture

description:
dipg29p
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG29 primary tumor
primary tissue WES/WGS


title: sf5609t Exome capture

description:
sf5609t
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SF509 primary tumor
primary tissue WES/WGS


title: dipg29n Exome capture

description:
dipg29n
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG29 primary matched normal
primary tissue WES/WGS


title: dipg25p Exome capture

description:
dipg25p
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG25 primary tumor
primary tissue WES/WGS


title: dipg38n Exome capture

description:
dipg38n
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG38 primary matched normal
primary tissue WES/WGS


title: dipg14p Exome capture

description:
dipg14p
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG14 primary tumor
primary tissue WES/WGS


title: dipg36n Exome capture

description:
dipg36n
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG36 primary matched normal
primary tissue WES/WGS


title: dipg21p Exome capture

description:
dipg21p
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG21 primary tumor
primary tissue WES/WGS


title: dipg23p Exome capture

description:
dipg23p
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG23 primary tumor
primary tissue WES/WGS


title: dipg17p Exome capture

description:
dipg17p
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG17 primary tumor
primary tissue WES/WGS


title: dipg17n Exome capture

description:
dipg17n
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG17 primary matched normal
primary tissue WES/WGS


title: dipg16t Exome capture

description:
dipg16t
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG16 primary tumor
primary tissue WES/WGS


title: dipg15t Exome capture

description:
dipg15t
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG15 primary tumor
primary tissue WES/WGS


description:
cnmc739t
Libraries amplified with custom primers as described in Corces 2017 and NEBNext HiFi MM.
CNMC56 primary tumor
primary tissue Omni-ATAC

extract_protocol: Tissues are homogenized and nuclei are purified. Following Omni-ATAC, DNA is purified with Ampure XP


description:
cnmc761t
Libraries amplified with custom primers as described in Corces 2017 and NEBNext HiFi MM.
CNMC60 primary tumor
primary tissue Omni-ATAC


title: dipg32p Exome capture

description:
dipg32p
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG32 primary tumor
primary tissue WES/WGS


description:
cnmc854n
Libraries amplified with custom primers as described in Corces 2017 and NEBNext HiFi MM.
CNMC115 primary normal pons
primary tissue Omni-ATAC


description:
dipg32p
Libraries amplified with custom primers as described in Corces 2017 and NEBNext HiFi MM.
SU-DIPG32 primary tumor
primary tissue Omni-ATAC


title: dipg12p Exome capture

description:
dipg12p
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG12 primary tumor
primary tissue WES/WGS


description:
cnmc710t
Libraries amplified with custom primers as described in Corces 2017 and NEBNext HiFi MM.
CNMC51 primary tumor
primary tissue Omni-ATAC


description:
dipg36p
Libraries amplified with custom primers as described in Corces 2017 and NEBNext HiFi MM.
SU-DIPG36 primary tumor
primary tissue Omni-ATAC


title: dipg26p Exome capture

description:
dipg26p
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG26 primary tumor
primary tissue WES/WGS


description:
cnmc347t
Libraries amplified with custom primers as described in Corces 2017 and NEBNext HiFi MM.
CNMC10 primary tumor
primary tissue Omni-ATAC


description:
cnmc537t
Libraries amplified with custom primers as described in Corces 2017 and NEBNext HiFi MM.
CNMC13 primary tumor
primary tissue Omni-ATAC


description:
1k12-dox
NEBNext Ultra II and NEBNext Multiplex Oligos
TRE-H3.1K27M Clone B Dox
iPSC differentiation + doxycycline ChIP-seq

source_name: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone B

extract_protocol: Cells are fixed with 1% FA. Following ChIP and washes, DNA is purified using Ampure XP

value: Day 44 eOPCs (d44)

value: H3K27Ac (Active Motif #39133), H3K27me3 (Active Motif #39155)


description:
1k12-ctrl
NEBNext Ultra II and NEBNext Multiplex Oligos
TRE-H3.1K27M Clone B Control
iPSC differentiation no doxycycline ChIP-seq

value: Day 14 NPCs (d14), Day 26 preOPCs (d26), Day 36 eOPCs (d36), Day 44 eOPCs (d44)


description:
3k16-dox
NEBNext Ultra II and NEBNext Multiplex Oligos
TRE-H3.3K27M Clone B Dox
iPSC differentiation + doxycycline ChIP-seq

source_name: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone B

value: Day 14 NPCs (d14), Day 44 eOPCs (d44)


description:
1k9-ctrl
NEBNext Ultra II and NEBNext Multiplex Oligos
TRE-H3.1K27M Clone A Control
iPSC differentiation no doxycycline ChIP-seq

source_name: healthy control iPSC cell line 2242-1 with TRE-H3.1K27M pB construct, subclone A

value: H3K27Ac (Active Motif #39133), H3K27me3 (Active Motif #39155), H3.3 (Millipore #09-838)


description:
1k9-dox
NEBNext Ultra II and NEBNext Multiplex Oligos
TRE-H3.1K27M Clone A Dox
iPSC differentiation + doxycycline ChIP-seq


description:
3k16-ctrl
NEBNext Ultra II and NEBNext Multiplex Oligos
TRE-H3.3K27M Clone B Control
iPSC differentiation no doxycycline ChIP-seq


description:
3k3-dox
NEBNext Ultra II and NEBNext Multiplex Oligos
TRE-H3.3K27M Clone A Dox
iPSC differentiation + doxycycline ChIP-seq

source_name: healthy control iPSC cell line 2242-1 with TRE-H3.3K27M pB construct, subclone A


description:
vumc10.1,vumc10.2
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
VUMC-10  patient-derived DIPG culture
cell culture ChIP-seq

source_name: patient-derived cell culture

extract_protocol: Cells are fixed with 1% FA. Following ChIP and washes, DNA is purified using PCI purification


description:
dipg6.7,dipg6.8
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG6  patient-derived DIPG culture
cell culture ChIP-seq

value: H3K27Ac (Active Motif #39133), H3.3 (Millipore #09-838), H3K27M (Millipore ABE419)


description:
3k3-ctrl
NEBNext Ultra II and NEBNext Multiplex Oligos
TRE-H3.3K27M Clone A Control
iPSC differentiation no doxycycline ChIP-seq


title: dipg13.6-inp: SU-DIPG13 Pons patient-derived DIPG culture

description:
cell culture ChIP-seq
SU-DIPG13 Pons patient-derived DIPG culture
dipg13.5,dipg13.6


description:
dipg36.1,dipg36.2
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG36  patient-derived DIPG culture
cell culture ChIP-seq

value: H3K27Ac (Active Motif #39133)


description:
dipg27.1,dipg27.2
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG27  patient-derived DIPG culture
cell culture ChIP-seq


description:
dipg29.1,dipg29.2
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG29  patient-derived DIPG culture
cell culture ChIP-seq


description:
pons01
Libraries amplified with custom primers as described in Corces 2017 and NEBNext HiFi MM.
SU-Pons01 primary normal pons
primary tissue Omni-ATAC


description:
dipg38.1,dipg38.2
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG38  patient-derived DIPG culture
cell culture ChIP-seq


title: RNASeq_KO_rep3

data_processing:
Basecalling was performed by HiSeq Control Software
Quality and adapter trimming was performed with Flexbar v2.5
Sequenced reads were aligned to the mouse genome reference sequence (mm10), masked for NUMTs regions, with bowtie2 v2.3.4.1 [57], with the --very-sensitive preset.
Properly paired mitochondrial alignments were extracted, split by template strand and converted to full length RNA fragment BED files, before coverage was calculated with BEDtools genomecov (-d -scale [1e+06/total mapped reads]), normalized to the total number of fragments mapped to the mouse whole genome (reads per million; RPM), and converted to wig format for visualization.
Gene-level counts for the nuclear genome were calculated with featureCounts (-C –p –B –P -s 2) using the GENCODE vM20 annotation and a GENCODE-based mitochondrial annotation with contiguous mt-Atp8/6 and mt-Nd4l/4 intervals, and an approximate 7S RNA annotation (chrM:16035-16188). Count tables were collated in R v3.5.2 and differential expression between conditions was analyzed with DESeq2 v1.22.2.
genome build: GRCm38/mm10
processed data files format and content: Strand-specific normalised coverage tracks (.wig) and gene-level normalised counts for each sample, and DESeq2 differential gene expression results.

source_name: Heart

value: Heart

value: 52 weeks

value: Rexo2loxP/loxPloxP/loxP, +/Ckmm


title: RNASeq_KO_rep2


description:
dipg24.1,dipg24.2
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG24  patient-derived DIPG culture
cell culture ChIP-seq


description:
dipg21.1,dipg21.2,dipg21.5,dipg21.6
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG21  patient-derived DIPG culture
cell culture ChIP-seq


title: MCF7_shBAP1_EZH2

type: genomic

city: Minato-ku

first: Makoto

last: Yamagishi

state: Tokyo

address: 4-6-1, Shirokanedai

country: Japan

institute: The University of Tokyo

hyb_protocol: Hybridization was performed at 65°C for 40h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed at room temperature with Agilent Oligo aCGH/ChIP-on-chip Wash Buffer 1 for 5min and with Agilent Oligo aCGH/ChIP-on-chip Wash Buffer 2 for 5min at 37°C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner C using the two color scan setting for 2x400K microarray slides (Scan Area: 61x21.6 mm, Scan resolution: 3 um, Dye channel: red and green, Tiff: 16bit, XDR ratio: NoXDR)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 using default parameters (protocol: ChIP_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: EZH2 ChIP DNA from MCF7_shBAP1

label_protocol: Labeled DNA was prepared from 2.6 μg of amplified DNA using SureTag DNA Labeling Kit according to the manufacturer's instructions.

extract_protocol: 1×10E7 cells were cross-linked in fixing solution. After 15 min incubation at room temperature, cross-linking was stopped by adding 1.375 M glycine. The cells were centrifuged for 5 min, 1,400 × g at 4°C. The supernatant was discarded and the pellet was washed two times in PBS. After the washes, cell pellets were resuspended in LB1 (50 mM Hepes-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% IGEPAL CA-630, 0.25% Triton X-100) and incubated for 10 min on ice. After centrifugation for 5 min, 1,400 × g at 4°C, the pellet was resuspended in LB2 (10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 min at room temperature. After centrifugation for 5 min, 1,400 × g at 4°C, the nuclei were resuspended in micrococcal nuclease digestion buffer and incubated in 37°C to digest chromatin to the appropriate size fragments. Digestion was stopped by adding 0.5 M EDTA. After centrifugation, nuclei pellets were resuspended in LB3 (10 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-Lauroylsarcosine) and sonicated for 10 min. After sonication and 10 min high-speed centrifugation, sheared chromatin was recovered in the supernatant.

value: Breast cancer cell line

source_name: Input DNA from MCF7_shBAP1


title: MCF7_shARID1A_EZH2

source_name: EZH2 ChIP DNA from MCF7_shARID1A

source_name: Input DNA from MCF7_shARID1A


title: MCF7_shKDM6A_EZH2

source_name: EZH2 ChIP DNA from MCF7_shKDM6A

source_name: Input DNA from MCF7_shKDM6A


description:
dipg19.2,dipg19.3
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG19  patient-derived DIPG culture
cell culture ChIP-seq


title: MCF7_shCtrl_EZH2

source_name: EZH2 ChIP DNA from MCF7_shCtrl

source_name: Input DNA from MCF7_shCtrl


title: RNASeq_KO_rep1


description:
dipg13fl.3,dipg13fl.4
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG13-FL patient-derived DIPG culture
cell culture ChIP-seq


title: MCF7_shBAP1_EZH1

source_name: EZH1 ChIP DNA from MCF7_shBAP1


title: cnmc954n End-repair and A-tailing

description:
cnmc954n
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
CNMC117 primary normal pons
primary tissue ChIP-seq

source_name: primary pontine tissue

extract_protocol: Tissues are homogenized and fixed with 1% FA. Following ChIP and washes, DNA is purified using PCI purification


title: RNASeq_WT_rep3


description:
dipg33.1,dipg33.2
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG33  patient-derived DIPG culture
cell culture ChIP-seq


title: MCF7_shKDM6A_EZH1

source_name: EZH1 ChIP DNA from MCF7_shKDM6A


title: cnmc856n End-repair and A-tailing

description:
cnmc856n
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
CNMC116 primary normal pons
primary tissue ChIP-seq


description:
dipg25.1,dipg25.2
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG25  patient-derived DIPG culture
cell culture ChIP-seq


title: cnmc854n End-repair and A-tailing

description:
cnmc854n
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
CNMC115 primary normal pons
primary tissue ChIP-seq


title: cnmc852n End-repair and A-tailing

description:
cnmc852n
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
CNMC114 primary normal pons
primary tissue ChIP-seq


title: RNASeq_WT_rep2


title: cnmc842t End-repair and A-tailing

description:
cnmc842t
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
CNMC64 primary tumor
primary tissue ChIP-seq

source_name: primary tumor tissue


title: MCF7_shARID1A_EZH1

source_name: EZH1 ChIP DNA from MCF7_shARID1A


title: MCF7_shCtrl_EZH1

source_name: EZH1 ChIP DNA from MCF7_shCtrl


title: RNASeq_WT_rep1


title: cnmc710t End-repair and A-tailing

description:
cnmc710t
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
CNMC51 primary tumor
primary tissue ChIP-seq


title: cnmc347t End-repair and A-tailing

description:
cnmc347t
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
CNMC10 primary tumor
primary tissue ChIP-seq


title: MT_Total_RNAseq

city: Guangzhou

first: Jiajian

last: Zhou

state: Guangdong

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

country: China

institute: Southern Medical University

description: total RNA depleted of ribosomal RNA

data_processing:
Illumina Casava1.8 software was used for basecalling.
RNA-seq reads were mapped to mm9 genome using TopHat2. If multiple reads aligned to the same genomic position, only one read per position was kept for downstream analyses.
Gene expression level was quantified by Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files are plain text files. Each entry represents expression level (RPKM) of all genes in mm9.

growth_protocol: C2C12 myoblasts were grown in DMEM supplemented with 10% FBS, 100 U/ml penicillin and 100 μg of streptomycin (growth medium, GM) in a 5% CO2 humidified incubator at 37°C.

extract_protocol:
For total RNA-seq, total RNAs were extracted from MB or MT C2C12 cells using TRIzol reagent (Invitogen) and then delivered to BGI HK for rRNA depletion; for poly A+ RNA-seq, RNA-seq was performed following the procedures described before (Chen et al., 2017; Zhou et al., 2015). Total RNAs were extracted from C2C12 cells using TRIzol reagent (Invitogen) following the manufacturer’s instructions and then subjected to poly(A) selection (Ambion, 61006).
For total RNA-seq, RNAs were submitted to Beijing Genomic Center, Hong Kong. The libraries were prepared following strand specific RNA-seq library preparation procedures and sequenced on the HiSeq2000 platform; for polyA+ RNA-seq, we prepared the libraries using NEBNext® Ultra™ II RNA Library Preparation Kit (NEB, E7770S) and barcoded libraries were pooled at equal concentration and sequenced on the HiSeq1500 platform.

treatment_protocol: C2C12 myoblasts were induced to differentiation by switching to  DMEM supplemented with 2% horse serum, 100 U/ml penicillin and 100 μg of streptomycin  (differentiation medium, DM) when cell confluence reached 80%-90%. The cells were then cultured in DM for 48 h or 72 h.

value: C2C12 myoblasts

tag: cell line

tag: culture conditions

value: DM 72 hours


title: MB_Total_RNAseq

description: total RNA depleted of ribosomal RNA

value: DM -24 hours


title: cnmc537t End-repair and A-tailing

description:
cnmc537t
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
CNMC13 primary tumor
primary tissue ChIP-seq

tag: tissue


title: cnmc741t End-repair and A-tailing

description:
cnmc741t
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
CNMC57 primary tumor
primary tissue ChIP-seq


title: sf5609t End-repair and A-tailing

description:
sf5609t
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SF509 primary tumor
primary tissue ChIP-seq


title: MCF7_shKDM6A_H3K27me3

source_name: H3K27me3 ChIP DNA from MCF7_shKDM6A


title: MCF7_shARID1A_H3K27me3

source_name: H3K27me3 ChIP DNA from MCF7_shARID1A


title: dipg36p End-repair and A-tailing

description:
dipg36p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG36 primary tumor
primary tissue ChIP-seq


title: dipg38p End-repair and A-tailing

description:
dipg38p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG38 primary tumor
primary tissue ChIP-seq


title: dipg33p End-repair and A-tailing

description:
dipg33p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG33 primary tumor
primary tissue ChIP-seq


title: MCF7_shBAP1_H3K27me3

source_name: H3K27me3 ChIP DNA from MCF7_shBAP1


title: dipg31p End-repair and A-tailing

description:
dipg31p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG31 primary tumor
primary tissue ChIP-seq


title: dipg32p End-repair and A-tailing

description:
dipg32p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG32 primary tumor
primary tissue ChIP-seq


title: cnmc112t End-repair and A-tailing

description:
cnmc112t
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
CNMC7 primary tumor
primary tissue ChIP-seq


title: MCF7_shCtrl_H3K27me3

source_name: H3K27me3 ChIP DNA from MCF7_shCtrl


title: LCL_shMLL2_H3K27me3

source_name: H3K27me3 ChIP DNA from LCL_shMLL2

value: EBV infected LCL

source_name: Input DNA from LCL_shMLL2


title: LCL_shMLL2_H3K4me3

source_name: H3K4me3 ChIP DNA from LCL_shMLL2


title: dipg27p End-repair and A-tailing

description:
dipg27p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG27 primary tumor
primary tissue ChIP-seq

value: primary human patient tumor tissue


title: pons01 End-repair and A-tailing

description:
pons01
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-Pons01 primary normal pons
primary tissue ChIP-seq

value: primary human patient pontine tissue


title: LCL_shCtrl_H3K27me3

source_name: H3K27me3 ChIP DNA from LCL_shCtrl

source_name: Input DNA from LCL_shCtrl


title: dipg26p End-repair and A-tailing

description:
dipg26p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG26 primary tumor
primary tissue ChIP-seq


title: dipg39p End-repair and A-tailing

description:
dipg39p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG39 primary tumor
primary tissue ChIP-seq


title: dipg25p End-repair and A-tailing

description:
dipg25p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG25 primary tumor
primary tissue ChIP-seq


title: dipg23p End-repair and A-tailing

description:
dipg23p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG23 primary tumor
primary tissue ChIP-seq


title: LCL_shCtrl_H3K4me3

source_name: H3K4me3 ChIP DNA from LCL_shCtrl


title: LCL_shMLL2_EZH2

source_name: EZH2 ChIP DNA from LCL_shMLL2


title: dipg21p End-repair and A-tailing

description:
dipg21p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG21 primary tumor
primary tissue ChIP-seq


title: dipg29p End-repair and A-tailing

description:
dipg29p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG29 primary tumor
primary tissue ChIP-seq


title: dipg17p End-repair and A-tailing

description:
dipg17p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG17 primary tumor
primary tissue ChIP-seq


title: LCL_shCtrl_EZH2

source_name: EZH2 ChIP DNA from LCL_shCtrl


title: 446-456M1

type: RNA

city: Tainan

first: Wen-Chun

last: Liu

address: 138 Sheng-Li Road

country: Taiwan

institute: National Cheng Kung University

description: Gene expression of Huh7 cells with genotype C HBV HBsAg mutation C446G/A456G expression

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint Microarray (Agilent Technologies, USA) at 65°C for 17 h. After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature. Raw signal data was normalized by quantile normalization for differential expressed genes discovering.

source_name: Huh7 cell, with genotype C HBV HBsAg mutation C446G/A456G expression

label_protocol: 0.2 μg of total RNA from transfected Huh7 cells was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: Huh-7 human hepatoma cells were grown at 37°C in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, under an atmosphere of 5% CO2. A total of 3 × 105 Huh7 cells per well were seeded in a six-well plate 24 hours prior to transfection. Wild-type or mutant envelope expression vectors were transfected into Huh7 cells by using lipofectamine 3000 (Thermo Fisher Scientific) according to the manual of the manufacturer.

extract_protocol: After transfection, the cells were washed with cold PBS and then cells were harvested. Total RNA was extracted from Huh7 cells using TRIzol reagent (Life Technologies, Grand Island, NY, USA) and chloroform extraction. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Plasmid pEGFP-N1-HBVS-genoB/C encodes the wild-type envelope protein under the transcriptional control of CMV promoter. The plasmid pEGFP-N1-HBVS-genoB was used as the template for mutagenesis to create mutations T216C, A273G, and double mutant T216C/A273G at small surface (S) region, with the QuikChange site-directed mutagenesis kit (Stratagene, La Jolla, CA). The plasmid pEGFP-N1-HBVS-genoC was used as the template for mutagenesis to create mutations A293G, C446G, A456G, A293G/C446G, C446G/A456G, A293G/A456G, and triple mutant A293G/C446G/A456G at small S region. All mutants were confirmed by DNA sequencing.

value: hepatoma

tag: transfectant


title: dipg15t End-repair and A-tailing

description:
dipg15t
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG15 primary tumor
primary tissue ChIP-seq


title: 293M1

description: Gene expression of Huh7 cells with genotype C HBV HBsAg mutation A293G expression

source_name: Huh7 cell, with genotype C HBV HBsAg mutation A293G expression

tag: cell type


title: TripleM1

description: Gene expression of Huh7 cells with genotype C HBV HBsAg mutation A293G/C446G/A456G expression

source_name: Huh7 cell, with genotype C HBV HBsAg mutation A293G/C446G/A456G expression


title: 293-446M1

description: Gene expression of Huh7 cells with genotype C HBV HBsAg mutation A293G/C446G expression

source_name: Huh7 cell, with genotype C HBV HBsAg mutation A293G/C446G expression


title: 446M1

description: Gene expression of Huh7 cells with genotype C HBV HBsAg mutation C446G expression

source_name: Huh7 cell, with genotype C HBV HBsAg mutation C446G expression


title: 456M1

description: Gene expression of Huh7 cells with genotype C HBV HBsAg mutation A456G expression

source_name: Huh7 cell, with genotype C HBV HBsAg mutation A456G expression


title: 293-456M1

description: Gene expression of Huh7 cells with genotype C HBV HBsAg mutation A293G/A456G expression

source_name: Huh7 cell, with genotype C HBV HBsAg mutation A293G/A456G expression


title: Left ventricle tissue of end-stage DCM patients (20TW01940)

city: Singapore

first: Sonia

last: Chothani

address: 8 College Road

country: Singapore

institute: Duke-NUS school of medicine

description: Ribosome protected fragment

data_processing:
Library strategy: Ribo-seq
Raw sequencing data were demultiplexed with bcl2fastq V2.19.0.316 and the adaptors were trimmed using Trimmomatic19 V0.36, retaining reads longer than 20 nt post-clipping. RNA-seq reads were further clipped with FASTX Toolkit V0.0.14 to 29nt, to allow comparison directly with Ribo-seq reads. Reads were aligned using bowtie20 to known rRNA, tRNA and mt-rRNA sequences (RNACentral21, release 5.0), aligned reads were filtered out to obtain only RPFs (Ribosome protected fragments). Alignment to the human genome (hg38) was done using STAR22. Gene expression was quantified on the CDS (coding sequence region) using uniquely mapped reads (Ensembl database release GRCh38 v86 combined with additional transcripts from RefSeq GRCh38, latest version downloaded January 2018) with feature counts23.
Genome_build: hg38
Supplementary_files_format_and_content: count matrix for protein coding genes across 30 samples

extract_protocol:
Briefly, snap-frozen cell pellets or 50-100 mg of tissue, previously powdered under liquid nitrogen, were lysed in 1ml cold lysis buffer (formulation as in TruSeq Ribosome Profile, Illumina) supplemented with 0.1mg/ml cycloheximide (CHX) to stabilize ribosomal subunits and prevent post-lysis translocation. Homogenized and cleared lysates were then footprinted with Truseq Nuclease (Illumina) according to manufacturer’s instructions. Ribosomes were purified using Illustra Sephacryl S400 columns (GE Healthcare) and the protected RNA fragments were extracted with standard phenol:chloroform:isoamylalcohol technique.
Following ribosomal RNA removal (Mammalian RiboZero Magnetic Gold, Illumina), sequencing libraries were prepared out of the footprinted RNA. Ribo-seq libraries were pooled to perform multiplex sequencing on Illumina Hiseq machines.

value: Left ventricle tissue

tag: sequencing

value: Ribo-seq


title: dipg14p End-repair and A-tailing

description:
dipg14p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG14 primary tumor
primary tissue ChIP-seq

source_name: primary tumor tissue


title: dipg12p End-repair and A-tailing

description:
dipg12p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG12 primary tumor
primary tissue ChIP-seq


title: Left ventricle tissue of end-stage DCM patients (20ST01399)

description: Ribosome protected fragment


title: dipg4p End-repair and A-tailing

description:
dipg4p
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG4 primary tumor
primary tissue ChIP-seq


title: LCL_shMLL2_EZH1

source_name: EZH1 ChIP DNA from LCL_shMLL2


title: 12-11WT1

description: Gene expression of Huh7 cells with genotype C wildtype HBV HBsAg expression

source_name: Huh7 cell, with genotype C wildtype HBV HBsAg expression


title: TL-Om1_OR-S1_BRG1

source_name: BRG1 ChIP DNA from TL-Om1_OR-S1

value: ATL cell line

source_name: Input DNA from TL-Om1_OR-S1


title: Left ventricle tissue of end-stage DCM patients (20TU01919)

description: Ribosome protected fragment


title: TL-Om1_GSK126_BRG1

source_name: BRG1 ChIP DNA from TL-Om1_GSK126

source_name: Input DNA from TL-Om1_GSK126


title: Left ventricle tissue of end-stage DCM patients (20SD01837)

description: Ribosome protected fragment


title: Left ventricle tissue of end-stage DCM patients (20RW01403)

description: Ribosome protected fragment


title: LCL_shCtrl_EZH1

source_name: EZH1 ChIP DNA from LCL_shCtrl

source_name: Input DNA from LCL_shCtrl


title: Left ventricle tissue of end-stage DCM patients (20RP01833)

description: Ribosome protected fragment


title: dipg16t End-repair and A-tailing

description:
dipg16t
End-repair and A-tailing performed as described in Nagaraja 2017. Adaptor ligation and indexing with NEBNext Multiplex Oligos
SU-DIPG16 primary tumor
primary tissue ChIP-seq


title: monocytes.SEP-14

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

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

country: Spain

institute: Josep Carreras Research Institute (IJC)

description:
CD14+CD66bneg cells
SEP-14

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

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

data_processing:
Rstudio
the normalization method: Average Beta

label: Cy3, Cy5

source_name: Peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from sorted monocytes using the ReliaPrep FFPE gDNA Miniprep System (Promega) according to standard instructions

tag: sofa

tag: Sex

value: F

tag: donor

value: SEPSIS

tag: batch


title: TL-Om1_DMSO_BRG1

source_name: BRG1 ChIP DNA from TL-Om1_DMSO

source_name: Input DNA from TL-Om1_DMSO


title: Left ventricle tissue of end-stage DCM patients (20RL01528)

description: Ribosome protected fragment


title: monocytes.SEP-13

description:
CD14+CD66bneg cells
SEP-13

value: M


title: 216M1

description: Gene expression of Huh7 cells with genotype B HBV HBsAg mutations T216C expression

source_name: Huh7 cell, with genotype B HBV HBsAg mutation T216C expression


title: Left ventricle tissue of end-stage DCM patients (20PL01827)

description: Ribosome protected fragment


title: monocytes.SEP-12

description:
CD14+CD66bneg cells
SEP-12


title: Left ventricle tissue of end-stage DCM patients (20PD01198)

description: Ribosome protected fragment


title: Left ventricle tissue of end-stage DCM patients (20NB01855)

description: Ribosome protected fragment


title: 273M1

description: Gene expression of Huh7 cells with genotype B HBV HBsAg mutation A273G expression

source_name: Huh7 cell, with genotype B HBV HBsAg mutation A273G expression


title: dipg39p Exome capture

description:
dipg39p
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
SU-DIPG39 primary tumor
primary tissue WES/WGS


title: 2-8WT1

description: Gene expression of Huh7 cells with genotype B wildtype HBV HBsAg expression

source_name: Huh7 cell, with genotype B wildtype HBV HBsAg expression


title: monocytes.SEP-11

description:
CD14+CD66bneg cells
SEP-11


title: Left ventricle tissue of end-stage DCM patients (20MS01733)

description: Ribosome protected fragment


title: monocytes.SEP-10

description:
CD14+CD66bneg cells
SEP-10


title: Left ventricle tissue of end-stage DCM patients (20MH01879)

description: Ribosome protected fragment


title: Left ventricle tissue of end-stage DCM patients (20ML01902)

description: Ribosome protected fragment


title: Left ventricle tissue of end-stage DCM patients (20MH01845)

description: Ribosome protected fragment


title: monocytes.SEP-9

description:
CD14+CD66bneg cells
SEP-9


title: Left ventricle tissue of end-stage DCM patients (20MG01931)

description: Ribosome protected fragment


title: TL-Om1_GSK126_ARID1A

source_name: ARID1A ChIP DNA from TL-Om1_GSK126


title: Left ventricle tissue of end-stage DCM patients (20LB01727)

description: Ribosome protected fragment


title: SUDHL8_OR-S1_EZH2

source_name: EZH2 ChIP DNA from SUDHL8_OR-S1

value: DLBCL cell line

source_name: Input DNA from SUDHL8_OR-S1


title: SUDHL8_DMSO_EZH2

source_name: EZH2 ChIP DNA from SUDHL8_DMSO

source_name: Input DNA from SUDHL8_DMSO


title: monocytes.SEP-8

description:
CD14+CD66bneg cells
SEP-8


title: TL-Om1_DMSO_ARID1A

source_name: ARID1A ChIP DNA from TL-Om1_DMSO


title: Left ventricle tissue of end-stage DCM patients (20MC01828)

description: Ribosome protected fragment


title: SUDHL8_OR-S1_EZH1

source_name: EZH1 ChIP DNA from SUDHL8_OR-S1


title: monocytes.SEP-7

description:
CD14+CD66bneg cells
SEP-7


title: TL-Om1_OR-S1_ARID1A

source_name: ARID1A ChIP DNA from TL-Om1_OR-S1

source_name: Input DNA from TL-Om1_OR-S1


title: Left ventricle tissue of end-stage DCM patients (20JW01850)

description: Ribosome protected fragment


title: Left ventricle tissue of end-stage DCM patients (20JH01781)

description: Ribosome protected fragment


title: Left ventricle tissue of end-stage DCM patients (20GR01807)

description: Ribosome protected fragment


title: SUDHL8_DMSO_EZH1

source_name: EZH1 ChIP DNA from SUDHL8_DMSO


title: monocytes.SEP-6

description:
CD14+CD66bneg cells
SEP-6


title: Left ventricle tissue of end-stage DCM patients (20GC01665)

description: Ribosome protected fragment


title: SUDHL8_OR-S1_H3K27me3

source_name: H3K27me3 ChIP DNA from SUDHL8_OR-S1


title: SUDHL8_DMSO_H3K27me3

source_name: H3K27me3 ChIP DNA from SUDHL8_DMSO


title: monocytes.SEP-5

description:
CD14+CD66bneg cells
SEP-5

source_name: Peripheral blood


title: monocytes.SEP-4

description:
CD14+CD66bneg cells
SEP-4


title: Left ventricle tissue of end-stage DCM patients (20DM01835)

description: Ribosome protected fragment


title: Left ventricle tissue of end-stage DCM patients (20DH01701)

description: Ribosome protected fragment


title: Left ventricle tissue of end-stage DCM patients (20CS01710)

description: Ribosome protected fragment


title: MCF7_EZH2EZH1_EZH1

source_name: EZH1 ChIP DNA from MCF7_EZH2EZH1

source_name: Input DNA from MCF7_EZH2EZH1


title: monocytes.SEP-3

description:
CD14+CD66bneg cells
SEP-3


title: Left ventricle tissue of end-stage DCM patients (20DW01830)

description: Ribosome protected fragment


title: monocytes.SEP-2

description:
CD14+CD66bneg cells
SEP-2


title: Left ventricle tissue of end-stage DCM patients (20CM01195)

description: Ribosome protected fragment


title: Left ventricle tissue of end-stage DCM patients (20CP01865)

description: Ribosome protected fragment


title: Left ventricle tissue of end-stage DCM patients (20JB01682)

description: Ribosome protected fragment


title: monocytes.SEP-1

description:
CD14+CD66bneg cells
SEP-1


title: Left ventricle tissue of end-stage DCM patients (20CT01836)

description: Ribosome protected fragment


title: MCF7_EZH2Y641F_EZH1

source_name: EZH1 ChIP DNA from MCF7_EZH2Y641F

source_name: Input DNA from MCF7_EZH2Y641F


title: Left ventricle tissue of end-stage DCM patients (20AP01457)

description: Ribosome protected fragment

tag: disease state

value: end-stage DCM


title: cnmc739t Exome capture

description:
cnmc739t
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
CNMC56 primary tumor
primary tissue WES/WGS

source_name: primary tumor tissue


title: MCF7_EZH2EZH1_FLAG

source_name: FLAG ChIP DNA from MCF7_EZH2EZH1


title: monocytes.SIRS-4

description:
CD14+CD66bneg cells
SIRS-4

value: SIRS


title: 216-273M1

description: Gene expression of Huh7 cells with genotype B HBV HBsAg mutation T216C-A273G expression

source_name: Huh7 cell, with genotype B HBV HBsAg mutation T216C-A273G expression


title: cnmc761t Exome capture

description:
cnmc761t
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
CNMC60 primary tumor
primary tissue WES/WGS


title: cnmc537t Exome capture

description:
cnmc537t
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
CNMC13 primary tumor
primary tissue WES/WGS


title: cnmc347t Exome capture

description:
cnmc347t
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
CNMC10 primary tumor
primary tissue WES/WGS


title: MCF7_EZH2Y641F_FLAG

source_name: FLAG ChIP DNA from MCF7_EZH2Y641F

value: Breast cancer cell line


title: cnmc842t Exome capture

description:
cnmc842t
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
CNMC64 primary tumor
primary tissue WES/WGS


title: monocytes.SIRS-3

description:
CD14+CD66bneg cells
SIRS-3


title: cnmc112t Exome capture

description:
cnmc112t
Exome capture and library prep performed with Agilent SureSelect XT Human All Exon v6 or Nextera Rapid Capture Exome kits
CNMC7 primary tumor
primary tissue WES/WGS


title: MCF7_EZH2WT_FLAG

source_name: FLAG ChIP DNA from MCF7_EZH2WT

source_name: Input DNA from MCF7_EZH2WT


title: TL-Om1_shCtrl_SUZ12

source_name: SUZ12 ChIP DNA from TL-Om1_shCtrl

source_name: Input DNA from TL-Om1_shCtrl


title: MCF7_EZH2WT_EZH1

source_name: EZH1 ChIP DNA from MCF7_EZH2WT


title: Primary human fibroblasts  Fib_41_bsl_RNA

description:
Fib_41_bsl_RNA
poly(A) RNA

data_processing:
Raw sequencing data were demultiplexed with bcl2fastq V2.19.0.316 and the adaptors were trimmed using Trimmomatic45 V0.36, retaining reads longer than 20 nt post-clipping. RNA-seq reads were further clipped with FASTX Toolkit V0.0.14 to 29nt, to allow comparison directly with Ribo-seq reads. Reads were aligned using bowtie46 to known rRNA, tRNA and mt-rRNA sequences (RNACentral47, release 5.0), aligned reads were filtered out to obtain only RPFs. Alignment to the human genome (hg38) was done using STAR48. Gene expression was quantified on the CDS (coding sequence region) using uniquely mapped reads (Ensembl database release GRCh38 v86 combined with additional transcripts from RefSeq GRCh38, latest version downloaded January 2018) with feature counts49. Genes with mean transcripts per million mapped reads, TPM < 1 in either RNA-seq or Ribo-seq across all conditions were removed before downstream analysis. Ribotaper50 was used to obtain the in-frame reads around the start and stop codon. These p-sites were then visualized across samples and genes. Heatmap for the ribosome drop-off was generated using pheatmap 1.0.8 R package51. Data quality check was done using MultiQC52. Principal component analysis was carried out using prcomp function in R. Individual gene batch effect for ITGA7 was removed using limma package53 in R.
Genome_build: hg38
Supplementary_files_format_and_content: Count matrix file consisting of genes as rows and samples as columns

source_name: Patient 4

extract_protocol:
Human atrial fibroblasts were prepared and cultured as described previously12. All the experiments were carried out at low cell passage (<P4). In all experiments, cells were starved in serum-free DMEM for 16 hours prior to TGFβ1 stimulation. Stimulated fibroblasts were compared to unstimulated fibroblasts that have been grown for the same duration under the same conditions (serum-free DMEM), but without the stimuli.
Ribosome profiling was performed as previously described16. Briefly, snap-frozen cell pellets or 50-100 mg of tissue, previously powdered under liquid nitrogen, were lysed in 1ml cold lysis buffer (formulation as in TruSeq Ribosome Profile, Illumina) supplemented with 0.1mg/ml cycloheximide (CHX) to stabilize ribosomal subunits and prevent post-lysis translocation. Homogenized and cleared lysates were then footprinted with Truseq Nuclease (Illumina) according to manufacturer’s instructions. Ribosomes were purified using Illustra Sephacryl S400 columns (GE Healthcare) and the protected RNA fragments were extracted with standard phenol:chloroform:isoamylalcohol technique. Following ribosomal RNA removal (Mammalian RiboZero Magnetic Gold, Illumina), sequencing libraries were prepared out of the footprinted RNA. Ribo-seq libraries were pooled to perform multiplex sequencing on Illumina Hiseq machines. To prepare polyA+ RNA-seq libraries from primary cardiac fibroblasts, total RNA was extracted with Trizol from one 10cm dish per condition. Following cleanup with RNeasy kit (Qiagen), ~500ng of each sample were further processed with the Truseq Stranded mRNA kit (Illumina). Barcoded RNA-seq libraries were pooled and sequenced on the Illumina HiSeq platform.
The RNAseq data for the heart tissue was derived from Henig et al24. To prepare polyA+ RNA-seq libraries from primary cardiac fibroblasts, total RNA was extracted with Trizol from one 10cm dish per condition. Following cleanup with RNeasy kit (Qiagen), ~500ng of each sample were further processed with the Truseq Stranded mRNA kit (Illumina). Barcoded RNA-seq libraries were pooled and sequenced on the Illumina HiSeq platform.

value: Cardiac fibroblasts

value: RNA-seq


title: monocytes.SIRS-2

description:
CD14+CD66bneg cells
SIRS-2


title: monocytes.CON-11

description:
CD14+CD66bneg cells
CON-11

value: HD


title: Primary human fibroblasts at 2hrs after stimulation with TGFB1 Fib_41_2hr_RNA

description:
Fib_41_2hr_RNA
poly(A) RNA


title: monocytes.CON-10

description:
CD14+CD66bneg cells
CON-10


title: TL-Om1_shEZH2_H3K27me3

source_name: H3K27me3 ChIP DNA from TL-Om1_shEZH2

source_name: Input DNA from TL-Om1_shEZH2


title: Primary human fibroblasts  Fib_34_bsl_RNA

description:
Fib_34_bsl_RNA
poly(A) RNA

source_name: Patient 3


title: monocytes.CON-9

description:
CD14+CD66bneg cells
CON-9

source_name: Peripheral blood


title: Primary human fibroblasts at 24hrs after stimulation with TGFB1 Fib_41_24hr_RNA

description:
Fib_41_24hr_RNA
poly(A) RNA


title: monocytes.CON-8

description:
CD14+CD66bneg cells
CON-8


title: TL-Om1_shEZH1_H3K27me3

source_name: H3K27me3 ChIP DNA from TL-Om1_shEZH1

source_name: Input DNA from TL-Om1_shEZH1


title: Primary human fibroblasts at 24hrs after stimulation with TGFB1 Fib_34_24hr_RNA

description:
Fib_34_24hr_RNA
poly(A) RNA