title: High-salt-Case2

city: Hefei

first: Lesha

last: Zhang

state: Anhui

address: 81 Meishan road

department: Physiology

institute: Anhui Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
The RNA sequencing (RNA-Seq) Fastq raw data were pruned using Trimmomatic to remove adaptors and lower mass reads. The quality of clean data was assessed using FastQC software. The quality-approved data were mapped to the reference genome of the rat (National Center for Biotechnology Information [NCBI] genome assembly, version Rnor_6.0) using HISAT2 (v2.0.13) and annotated with the annotation file (.gtf) NCBI Rnor_6.0.
The RNA-Seq quantification software Kallisto was used to obtain a count of known messenger RNAs (mRNAs) to compare the differences in transcript expression. Using the edgeR package software (http://bioconductor.org/packages/2.4/bioc/html/edgeR.html), the differences in the number of reads among samples were analyzed.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample

organism: Rattus norvegicus

source_name: Basilar artery smooth muscle cells

growth_protocol: All the animals were fed under free food and water. The high-salt diet comprised rat chow supplied for control group rat and additional 4% (w/w) sodium chloride (NaCl). When the systolic blood pressure levels were determined by tail-cuff method and significantly increased above 30 mmHg in the rats eating the high-salt diet for 4 weeks .

extract_protocol:
All these rats were sacrificed by continuously inhaling carbon dioxide. The rats’ brains were isolated and put in the Kreb’s solution. Brain basilar arteries were isolated, and then unnecessary connective tissues were eliminated by using anatomical microscope. By mechanically removed using wires repeatedly, the endothelial cells were denuded.
All the remain basilar artery smooth muscle cells of each single rat were collected, and then messenger RNAs extractions were performed using Poly A selection of Illumina TruSeq RNA sample preparation protocol to establish the RNA sample libraries.

value: Spraque-Dawley

value: Brain basilar arteries

tag: model

value: high-salt diet induced hypertension


title: High-salt-Case3

status: Public on Apr 02 2020

type: SRA

country: China

library_source: transcriptomic

molecule: polyA RNA

tag: strain

tag: tissue

tag: weight


title: N2_starvation_rep1

type: RNA

city: Baltimore

first: Jiou

last: Wang

state: MD

address: 615 N. Wolfe Street

department: Biochemistry and Molecular Biology

country: USA

institute: The Johns Hopkins University

description: C.elegans were incubated in M9 buffer away from food with gentle rocking for 6 hours prior to freezing at -80℃ and RNA extraction

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing: Affymetrix CEL files were extracted and their data RMA normalized with the Partek GS 6.6 platform.  Partek's Meta-Probeset set was used with RMA normalization to create quantile-normalized gene-level log2 transcript signal values, which were used in subsequent ANOVA analyses.

label: biotin

molecule: total RNA

organism: Caenorhabditis elegans

source_name: entire C. elegans IW314

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual.

growth_protocol: C.elegans were maintained at 20℃ on standard NGM plates with OP50 E.coli prior to experimentaion

extract_protocol: C.elegans were freeze-thawed at -80℃ and total RNA was extracted using RNeasy MiniPrep Kit (Qiagen)

treatment_protocol: C.elegans were incubated in M9 buffer with gentle rocking for 6 hours prior to freezing.  Control animals had food whereas food was withheld from starvation animals.

tag: genotype

value: Wild Type

tag: treatment

value: without food 6 hours

tag: age


title: N2_control_rep2

description: C.elegans were incubated in M9 buffer containing food with gentle rocking for 6 hours prior to freezing at -80℃ and RNA extraction

value: with food


title: PatID:10225001005, Tissue:NL, Visit:BL, Treatment:Placebo

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett ÐPackard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor).

organism: Homo sapiens

label_protocol: GeneChip Affymetrix protocol

extract_protocol: QIAGEN Rneasy Kit

tag: patientid

value: non-lesional skin

tag: visit

value: BL

value: Placebo

tag: pasi

tag: bmi

tag: race

value: WHITE


title: N2_starvation_rep3


title: N2_control_rep1


title: High-salt-Case1


title: Control2


title: 59251 dRybp_Eed-null untreated Rep2

city: Vienna

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

country: Austria

institute: IMBA

description:
dRybp_Eed-null untreated Rep2
59251_Eed-KO_Rybp-AID-C3_0-hrs_Auxin_B.tsv

data_processing:
For ChIP-seq experiment, after standard quality control, the raw reads were mapped to the mm10 genome using bowtie2 (Langmead et al., 2012) and BAM files were obtained as output. For each ChIP-seq sample, we called the peaks using MACS2 (Zhang et al., 2008) with parameter -broad and default q-value cutoff 0.1. In particular, peaks of H2AK119ub1 and H3K27me3 were merged when closer than 5 kilobases; for other ChIP-seq samples,  peaks closer than 2 kilobases were merged. To correct the GC-bias in our samples, we first quantified the bias using the computeGCBias function in deepTools (Ramirez F et al., 2016) excluding called peaks, so that the calculated GC bias reflects the technical biases rather than the CpG islands (CGIs) enriched by PcG proteins and histone modifications during the ChIP reaction. Then, GC-bias file and GC-corrected BAM files were generated from the original BAM files. Finally, biological replicates were merged using SAMtools (Li H et al., 2009).
For RNA-seq experiment, after standard quality control, SlamDunk (Herzog et al., 2017, http://t-neumann.github.io/slamdunk/docs.html) was used to map the raw reads to the mm10 genome and count tables were generated. Two bed files with custom annotations of the 3’ UTR coordinates of AN3-12 mESCs, one for mapping, and one to filter multi-mappers, were kindly provided by Veronika Herzog (Ameres Lab) to improve mapping and counting of the reads. To do differential Expression analysis, the count tables were loaded into R and the DESeq2 package (Love M et al., 2014) was used to calculate pairwise differential expression between different conditions, always using all three replicates per condition.
Genome_build: mm10
Supplementary_files_format_and_content: *.bw files: bigWig Track format of read density coverage in reads per million after extension to 150 base pairs;  *.tsv files: Count file output from SLAMdunk containing the chromosomal coordinates, Gene Name and Strand of the counting windows, T>C conversion rate, Expression (ReadsCPM), T content of the counting window, Coverage on Ts within counting window, T>C Conversion Rate on Ts, Read Count, T>C Read Count and Multimap Counts

organism: Mus musculus

source_name: mouse embryonic stem cells 515D10-C3

growth_protocol: Mouse embryonic stem (mES) cells were cultivated feeder-free in base medium composed of high-glucose-DMEM supplemented with 13.5% fetal bovine serum (Sigma), 10 mM HEPES pH 7.4, 2 mM GlutaMAX (Gibco), 1 mM sodium pyruvate (Sigma), 100 U penicillin/ml (Sigma), 0.1 mg streptomycin/ml (Sigma), 1x non-essential amino acids (Sigma), 50 mM beta-mercaptoethanol (Gibco) and supplemented with 10% FBS (Sigma) and recombinant Leukemia Inhibitory Factor (LIF – produced in-house). Cells were maintained at 37°C with 5% CO2 and passaged every second day.

extract_protocol:
For ChIP-Seq samples: phenol-chloroform extraction
For RNA-Seq samples: RNeasy kit (Qiagen) following the on-column DNase digestion protocol.
For ChIP-Seq samples: Libraries were prepared using the NEXTflex ChIP-Seq kit (Bio Scientific) following the “No size-selection cleanup” protocol.
For RNA-Seq samples: Total RNA was subjected to mRNA 3ʹ end sequencing library preparation (QuantSeq, Lexogen).

treatment_protocol: Mouse embryonic stem cells (mES cells) were cultivated in regular mESC medium (untreated), or treated with 250 μM IAA for the indicated duration of time.

value: untreated


title: Control3


title: PatID:10225001005, Tissue:NL, Visit:W12, Treatment:Placebo


title: 59250 dRybp_Eed-null untreated Rep1

description:
dRybp_Eed-null untreated Rep1
59250_Eed-KO_Rybp-AID-C3_0-hrs_Auxin_A.tsv


title: PatID:10225001004, Tissue:NL, Visit:BL, Treatment:Placebo


title: Control1


title: PatID:10225001004, Tissue:LS, Visit:BL, Treatment:Placebo

value: lesional skin


title: 59249 dRybp_Eed-null untreated Rep3

description:
dRybp_Eed-null untreated Rep3
59249_Eed-KO_Rybp-AID-A12_0-hrs_Auxin_C.tsv

source_name: mouse embryonic stem cells 515D10-A12


title: 59248 dRybp_Eed-null untreated Rep2

description:
dRybp_Eed-null untreated Rep2
59248_Eed-KO_Rybp-AID-A12_0-hrs_Auxin_B.tsv


title: 59247 dRybp_Eed-null untreated Rep1

description:
dRybp_Eed-null untreated Rep1
59247_Eed-KO_Rybp-AID-A12_0-hrs_Auxin_A.tsv


title: 59245 Ring1-null IAA-48h Rep2

description:
Ring1-null IAA-48h Rep2
59245_Ring1A-KO_48-hrs_Auxin_B.tsv

source_name: mouse embryonic stem cells D10B3C10


title: 59244 Ring1-null IAA-48h Rep1

description:
Ring1-null IAA-48h Rep1
59244_Ring1A-KO_48-hrs_Auxin_A.tsv


title: PatID:10225001003, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W

value: Brodalumab 210 mg Q2W


title: PatID:10225001003, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10225001003, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10225001003, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: ARDS304

city: Philadelphia

first: Nadir

last: Yehya

state: PA

address: 6040A Wood Bldg, 3401 Civic Ctr Blvd

institute: Children's Hospital of Philadelphia

description: Genomewide mRNA expression

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C using Human Gene 2.1 ST Array (Affymetrix)

scan_protocol: GeneChips were scanned using the GeneTitan

data_processing: The data were quantile normalized and log2 transformed

source_name: ARDS patient whole blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: n/a; all children had ARDS

value: whole blood

tag: disease state

value: Pediatric acute respiratory distress syndrome (ARDS)


title: ARDS310

description: Genomewide mRNA expression


title: ARDS305

description: Genomewide mRNA expression


title: ARDS301

description: Genomewide mRNA expression


title: ARDS309

description: Genomewide mRNA expression


title: ARDS311

description: Genomewide mRNA expression


title: ARDS312

description: Genomewide mRNA expression


title: PatID:10225001002, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W

value: Brodalumab 140 mg Q2W


title: ARDS298

description: Genomewide mRNA expression


title: 59246 Ring1-null IAA-48h Rep3

description:
Ring1-null IAA-48h Rep3
59246_Ring1A-KO_48-hrs_Auxin_C.tsv


title: ARDS300

description: Genomewide mRNA expression


title: ARDS302

description: Genomewide mRNA expression


title: ARDS299

description: Genomewide mRNA expression


title: PatID:10225001002, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: 59241 Ring1-null untreated Rep1

description:
Ring1-null untreated Rep1
59241_Ring1A-KO_0-hrs_Auxin_A.tsv


title: 59243 Ring1-null untreated Rep3

description:
Ring1-null untreated Rep3
59243_Ring1A-KO_0-hrs_Auxin_C.tsv


title: 59240 Rybp-null IAA-48h Rep3

description:
Rybp-null IAA-48h Rep3
59240_Rybp-KO_48-hrs_Auxin_C.tsv

source_name: mouse embryonic stem cells AN3E9

value: Rybp-null


title: ARDS303

description: Genomewide mRNA expression


title: 59242 Ring1-null untreated Rep2

description:
Ring1-null untreated Rep2
59242_Ring1A-KO_0-hrs_Auxin_B.tsv


title: ARDS297

description: Genomewide mRNA expression


title: ARDS295

description: Genomewide mRNA expression


title: ARDS296

description: Genomewide mRNA expression


title: 59239 Rybp-null IAA-48h Rep2

description:
Rybp-null IAA-48h Rep2
59239_Rybp-KO_48-hrs_Auxin_B.tsv


title: ARDS306

description: Genomewide mRNA expression


title: PatID:10225001001, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: 59238 Rybp-null IAA-48h Rep1

description:
Rybp-null IAA-48h Rep1
59238_Rybp-KO_48-hrs_Auxin_A.tsv


title: ARDS293

description: Genomewide mRNA expression


title: PatID:10225001002, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10225001001, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10225001002, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: ARDS292

description: Genomewide mRNA expression


title: PatID:10225001001, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: ARDS294

description: Genomewide mRNA expression


title: 59237 Rybp-null untreated Rep3

description:
Rybp-null untreated Rep3
59237_Rybp-KO_0-hrs_Auxin_C.tsv


title: ARDS291

description: Genomewide mRNA expression


title: 59236 Rybp-null untreated Rep2

description:
Rybp-null untreated Rep2
59236_Rybp-KO_0-hrs_Auxin_B.tsv


title: ARDS288

description: Genomewide mRNA expression


title: ARDS290

description: Genomewide mRNA expression


title: PatID:10216003010, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: ARDS289

description: Genomewide mRNA expression


title: PatID:10216003010, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: 59234 Eed-null IAA-48h Rep3

description:
Eed-null IAA-48h Rep3
59234_Eed-KO_48-hrs_Auxin_C.tsv

source_name: mouse embryonic stem cells 515D10

value: Eed-null


title: ARDS285

description: Genomewide mRNA expression


title: PatID:10266009002, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: ARDS284

description: Genomewide mRNA expression


title: ARDS287

description: Genomewide mRNA expression


title: ARDS286

description: Genomewide mRNA expression


title: PatID:10216003010, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10225001001, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10216003010, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: ARDS283

description: Genomewide mRNA expression


title: 59235 Rybp-null untreated Rep1

description:
Rybp-null untreated Rep1
59235_Rybp-KO_0-hrs_Auxin_A.tsv


title: 59232 Eed-null IAA-48h Rep1

description:
Eed-null IAA-48h Rep1
59232_Eed-KO_48-hrs_Auxin_A.tsv


title: PatID:10216003009, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: ARDS282

description: Genomewide mRNA expression


title: ARDS280

description: Genomewide mRNA expression


title: ARDS281

description: Genomewide mRNA expression


title: 59231 Eed-null untreated Rep3

description:
Eed-null untreated Rep3
59231_Eed-KO_0-hrs_Auxin_C.tsv


title: ARDS278

description: Genomewide mRNA expression


title: PatID:10216003009, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: 59230 Eed-null untreated Rep2

description:
Eed-null untreated Rep2
59230_Eed-KO_0-hrs_Auxin_B.tsv


title: ARDS277

description: Genomewide mRNA expression


title: 59229 Eed-null untreated Rep1

description:
Eed-null untreated Rep1
59229_Eed-KO_0-hrs_Auxin_A.tsv


title: 59228 wild-type IAA-48h Rep3

description:
wild-type IAA-48h Rep3
59228_WT_48-hrs_Auxin_C.tsv

source_name: mouse embryonic stem cells AN312

value: wild-type


title: PatID:10216003009, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: ARDS274

description: Genomewide mRNA expression


title: PatID:10216003009, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: ARDS279

description: Genomewide mRNA expression


title: ARDS269

description: Genomewide mRNA expression


title: ARDS272

description: Genomewide mRNA expression


title: ARDS275

description: Genomewide mRNA expression


title: ARDS276

description: Genomewide mRNA expression


title: ARDS270

description: Genomewide mRNA expression


title: PatID:10216003008, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10216003008, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: 59226 wild-type IAA-48h Rep1

description:
wild-type IAA-48h Rep1
59226_WT_48-hrs_Auxin_A.tsv


title: PatID:10216003008, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: ARDS264

description: Genomewide mRNA expression


title: 59224 wild-type untreated Rep2

description:
wild-type untreated Rep2
59224_WT_0-hrs_Auxin_B.tsv


title: 59225 wild-type untreated Rep3

description:
wild-type untreated Rep3
59225_WT_0-hrs_Auxin_C.tsv


title: 59227 wild-type IAA-48h Rep2

description:
wild-type IAA-48h Rep2
59227_WT_48-hrs_Auxin_B.tsv


title: 59223 wild-type untreated Rep1

description:
wild-type untreated Rep1
59223_WT_0-hrs_Auxin_A.tsv


title: ARDS266

description: Genomewide mRNA expression


title: 65702 dSuz12_Rybp-null H2AK119Ub1-ChIP IAA-48h Rep2

description:
dSuz12_Rybp-null H2AK119Ub1-ChIP IAA-48h Rep2
H2AUb_Rybp.KO.Suz12.AID.B11.Aux_65695.65702.merged.bw

library_source: genomic

molecule: genomic DNA

source_name: mouse embryonic stem cells AN3E9-B11

tag: antibody

value: Cell Signaling (D27C4) #8240


title: ARDS267

description: Genomewide mRNA expression


title: PatID:10216003008, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: ARDS263

description: Genomewide mRNA expression


title: ARDS259

description: Genomewide mRNA expression


title: PatID:10216003007, Tissue:LS, Visit:W12, Treatment:Placebo


title: ARDS256

description: Genomewide mRNA expression


title: ARDS260

description: Genomewide mRNA expression


title: ARDS255

description: Genomewide mRNA expression


title: 65695 dSuz12_Rybp-null H2AK119Ub1-ChIP IAA-48h Rep1

description:
dSuz12_Rybp-null H2AK119Ub1-ChIP IAA-48h Rep1
H2AUb_Rybp.KO.Suz12.AID.B11.Aux_65695.65702.merged.bw


title: ARDS254

description: Genomewide mRNA expression


title: PatID:10216003007, Tissue:NL, Visit:W12, Treatment:Placebo


title: 65701 dSuz12_Rybp-null H2AK119Ub1-ChIP untreated Rep2

description:
dSuz12_Rybp-null H2AK119Ub1-ChIP untreated Rep2
H2AUb_Rybp.KO.Suz12.AID.B11.No.Aux_65694.65701.merged.bw


title: ARDS273

description: Genomewide mRNA expression


title: ARDS252

description: Genomewide mRNA expression


title: ARDS253

description: Genomewide mRNA expression


title: ARDS251

description: Genomewide mRNA expression


title: ARDS246

description: Genomewide mRNA expression


title: PatID:10216003006, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10216003006, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: ARDS247

description: Genomewide mRNA expression


title: ARDS250

description: Genomewide mRNA expression


title: ARDS248

description: Genomewide mRNA expression


title: ARDS249

description: Genomewide mRNA expression


title: ARDS245

description: Genomewide mRNA expression


title: PatID:10216003007, Tissue:NL, Visit:BL, Treatment:Placebo


title: ARDS244

description: Genomewide mRNA expression


title: PatID:10216003006, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: ARDS268

description: Genomewide mRNA expression


title: 65694 dSuz12_Rybp-null H2AK119Ub1-ChIP untreated Rep1

description:
dSuz12_Rybp-null H2AK119Ub1-ChIP untreated Rep1
H2AUb_Rybp.KO.Suz12.AID.B11.No.Aux_65694.65701.merged.bw


title: 61282 dSuz12_Rybp-null H2AK119Ub1-ChIP IAA-24h Rep2

description:
dSuz12_Rybp-null H2AK119Ub1-ChIP IAA-24h Rep2
61276.61282_H2AUb.RybpKO.Suz12AID..Aux_merged.bw


title: 61276 dSuz12_Rybp-null H2AK119Ub1-ChIP IAA-24h Rep1

description:
dSuz12_Rybp-null H2AK119Ub1-ChIP IAA-24h Rep1
61276.61282_H2AUb.RybpKO.Suz12AID..Aux_merged.bw


title: 61281 dSuz12_Rybp-null H2AK119Ub1-ChIP untreated Rep2

description:
dSuz12_Rybp-null H2AK119Ub1-ChIP untreated Rep2
61275.61281_H2AUb.RybpKO.Suz12AID.NoAux_merged.bw


title: ARDS242

description: Genomewide mRNA expression


title: 61275 dSuz12_Rybp-null H2AK119Ub1-ChIP untreated Rep1

description:
dSuz12_Rybp-null H2AK119Ub1-ChIP untreated Rep1
61275.61281_H2AUb.RybpKO.Suz12AID.NoAux_merged.bw


title: 65652 dSuz12_Rybp-null Rnf2-ChIP IAA-48h Rep2

description:
dSuz12_Rybp-null Rnf2-ChIP IAA-48h Rep2
Ring1B_Rybp.KO.Suz12.AID.B11.Aux_65645.65652.merged.bw

value: Cell Signaling (D22F2) #5694


title: ARDS240

description: Genomewide mRNA expression


title: PatID:10216003005, Tissue:LS, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: PatID:10216003005, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: ARDS241

description: Genomewide mRNA expression


title: 65645 dSuz12_Rybp-null Rnf2-ChIP IAA-48h Rep1

description:
dSuz12_Rybp-null Rnf2-ChIP IAA-48h Rep1
Ring1B_Rybp.KO.Suz12.AID.B11.Aux_65645.65652.merged.bw


title: ARDS238

description: Genomewide mRNA expression


title: PatID:10216003005, Tissue:NL, Visit:W12, Treatment:Brodalumab 140 mg Q2W


title: 65651 dSuz12_Rybp-null Rnf2-ChIP untreated Rep2

description:
dSuz12_Rybp-null Rnf2-ChIP untreated Rep2
Ring1B_Rybp.KO.Suz12.AID.B11.No.Aux_65644.65651.merged.bw


title: PatID:10216003005, Tissue:LS, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: ARDS235

description: Genomewide mRNA expression


title: ARDS239

description: Genomewide mRNA expression


title: ARDS234

description: Genomewide mRNA expression


title: ARDS236

description: Genomewide mRNA expression


title: ARDS237

description: Genomewide mRNA expression


title: PatID:10216003006, Tissue:NL, Visit:BL, Treatment:Brodalumab 140 mg Q2W


title: PatID:10216003004, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10216003004, Tissue:LS, Visit:BL, Treatment:Placebo


title: PatID:10216003004, Tissue:NL, Visit:W12, Treatment:Placebo


title: 65644 dSuz12_Rybp-null Rnf2-ChIP untreated Rep1

description:
dSuz12_Rybp-null Rnf2-ChIP untreated Rep1
Ring1B_Rybp.KO.Suz12.AID.B11.No.Aux_65644.65651.merged.bw


title: ARDS232

description: Genomewide mRNA expression


title: 59233 Eed-null IAA-48h Rep2

description:
Eed-null IAA-48h Rep2
59233_Eed-KO_48-hrs_Auxin_B.tsv


title: 61255 dSuz12_Rybp-null Rnf2-ChIP IAA-24h Rep2

description:
dSuz12_Rybp-null Rnf2-ChIP IAA-24h Rep2
61228.61255_Ring1B.RybpKO.Suz12AID..Aux_merged.bw


title: 61228 dSuz12_Rybp-null Rnf2-ChIP IAA-24h Rep1

description:
dSuz12_Rybp-null Rnf2-ChIP IAA-24h Rep1
61228.61255_Ring1B.RybpKO.Suz12AID..Aux_merged.bw


title: ARDS228

description: Genomewide mRNA expression


title: ARDS233

description: Genomewide mRNA expression


title: ARDS227

description: Genomewide mRNA expression


title: 61256 dSuz12_Rybp-null Rnf2-ChIP untreated Rep2

description:
dSuz12_Rybp-null Rnf2-ChIP untreated Rep2
61227.61256_Ring1B.RybpKO.Suz12AID.NoAux_merged.bw


title: ARDS229

description: Genomewide mRNA expression


title: ARDS226

description: Genomewide mRNA expression


title: ARDS225

description: Genomewide mRNA expression


title: 61227 dSuz12_Rybp-null Rnf2-ChIP untreated Rep1

description:
dSuz12_Rybp-null Rnf2-ChIP untreated Rep1
61227.61256_Ring1B.RybpKO.Suz12AID.NoAux_merged.bw


title: PatID:10216003003, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10216003004, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10216003003, Tissue:NL, Visit:W12, Treatment:Placebo


title: ARDS224

description: Genomewide mRNA expression


title: 65700 dRybp_Eed-null H2AK119Ub1-ChIP IAA-48h Rep2

description:
dRybp_Eed-null H2AK119Ub1-ChIP IAA-48h Rep2
H2AUb_Eed.KO.Rybp.AID.A12.Aux.48h_65693.65700.merged.bw


title: PatID:10216003003, Tissue:LS, Visit:BL, Treatment:Placebo


title: ARDS222

description: Genomewide mRNA expression


title: ARDS219

description: Genomewide mRNA expression


title: ARDS220

description: Genomewide mRNA expression


title: ARDS223

description: Genomewide mRNA expression


title: ARDS218

description: Genomewide mRNA expression


title: ARDS221

description: Genomewide mRNA expression


title: PatID:10216003003, Tissue:NL, Visit:BL, Treatment:Placebo


title: 65693 dRybp_Eed-null H2AK119Ub1-ChIP IAA-48h Rep1

description:
dRybp_Eed-null H2AK119Ub1-ChIP IAA-48h Rep1
H2AUb_Eed.KO.Rybp.AID.A12.Aux.48h_65693.65700.merged.bw


title: ARDS217

description: Genomewide mRNA expression


title: 65699 dRybp_Eed-null H2AK119Ub1-ChIP untreated Rep2

description:
dRybp_Eed-null H2AK119Ub1-ChIP untreated Rep2
H2AUb_Eed.KO.Rybp.AID.A12.No.Aux.48h_65692.65699.merged.bw


title: PatID:10216003002, Tissue:NL, Visit:W12, Treatment:Placebo


title: ARDS216

description: Genomewide mRNA expression


title: PatID:10216003002, Tissue:LS, Visit:W12, Treatment:Placebo


title: ARDS215

description: Genomewide mRNA expression


title: 65692 dRybp_Eed-null H2AK119Ub1-ChIP untreated Rep1

description:
dRybp_Eed-null H2AK119Ub1-ChIP untreated Rep1
H2AUb_Eed.KO.Rybp.AID.A12.No.Aux.48h_65692.65699.merged.bw


title: 61279 dRybp_Eed-null H2AK119Ub1-ChIP IAA-24h Rep2

description:
dRybp_Eed-null H2AK119Ub1-ChIP IAA-24h Rep2
61274.61279_H2AUb.EedKO.RybpAID..Aux_merged.bw


title: ARDS213

description: Genomewide mRNA expression


title: FVB Her2 11279 Primary tumor gDNA

city: Bethesda

first: Maxwell

last: Lee

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description: gDNA isolated from flash frozen tissue

data_processing:
Library strategy: DNA-seq
Samples were trimmed of adapters using Trimmomatic software (0.39)
The trimmed reads were aligned to 316 the mm10 reference mouse genome using BWA (0.7.17) or Bowtie (2-2.3.5.1) mapping software
SAMtools (1.9) mpileup, 317 GATK (3.8-1) Mutect2, and Strelka (2.7.1) were used to identify potential variants and the variants were filtered for known 318 polymorphisms from mgp.v5 (ftp://ftp-mouse.sanger.ac.uk/current_snps /mgp.v5.merged.snps_ all.dbSNP142 .vcf.gz) and 319 variants with Phred-scaled quality score of < 30 were removed
Annotation was performed by Annovar (2018-04-16).
High probability SNVs were identified after reads were visualized in IGV and false positives were removed from the data. Select SNVs validated by Sanger sequencing performed by the CCR Genomics Core.
Genome_build: mouse mm19
Supplementary_files_format_and_content: vcf files include variants for each sample

source_name: Primary tumor

extract_protocol:
Mice were bred and allowed to age until a humane endpoint was reached. Primary tumors and lung metastases were isolated and snap frozen in cryo vials using liquid nitrogen. Tissue was stored at -80 and gDNA was later isolated using the gDNA purification using ZR-Duet DNA/RNA MiniPrep kit from Zymo Research.  (cat.no. D7001)
Exome libraries were prepared using an Agilent SureSelectXT Mouse All Exon Kit for target enrichment. Libraries were barcoded and pooled before sequencing on an Illumina HiSeq3000 or HiSeq4000 to an average depth of 40x.

treatment_protocol: genetically engineered mice were allowed to age until a humane endpoint was reached, no treatment was applied

value: Primary tumor

tag: oncogenic driver

value: Genetically engineered / Autochthonous

value: FVBn/J x FVBn/J

tag: mouse id


title: ARDS214

description: Genomewide mRNA expression


title: FVB Her2 11276 Lung met gDNA

description: gDNA isolated from flash frozen tissue

source_name: Lung met

value: Lung metastatic tumor


title: ARDS212

description: Genomewide mRNA expression


title: PatID:10216003002, Tissue:LS, Visit:BL, Treatment:Placebo

value: BL

value: Placebo


title: ARDS211

description: Genomewide mRNA expression


title: PatID:10216003002, Tissue:NL, Visit:BL, Treatment:Placebo

value: non-lesional skin

value: WHITE


title: FVB Her2 11279 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: FVB Her2 11276 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: 61274 dRybp_Eed-null H2AK119Ub1-ChIP IAA-24h Rep1

description:
dRybp_Eed-null H2AK119Ub1-ChIP IAA-24h Rep1
61274.61279_H2AUb.EedKO.RybpAID..Aux_merged.bw


title: FVB Her2 11175 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: 61280 dRybp_Eed-null H2AK119Ub1-ChIP untreated Rep2

description:
dRybp_Eed-null H2AK119Ub1-ChIP untreated Rep2
61273.61280_H2AUb.EedKO.RybpAID.NoAux_merged.bw

value: untreated


title: FVB Her2 11175 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: ARDS210

description: Genomewide mRNA expression

value: whole blood


title: 61273 dRybp_Eed-null H2AK119Ub1-ChIP untreated Rep1

description:
dRybp_Eed-null H2AK119Ub1-ChIP untreated Rep1
61273.61280_H2AUb.EedKO.RybpAID.NoAux_merged.bw


title: ARDS208

description: Genomewide mRNA expression

value: Pediatric acute respiratory distress syndrome (ARDS)


title: FVB Her2 10684 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: 65650 dRybp_Eed-null Rnf2-ChIP IAA-48h Rep2

description:
dRybp_Eed-null Rnf2-ChIP IAA-48h Rep2
Ring1B_Eed.KO.Rybp.AID.A12.Aux.48h_65643.65650.merged.bw


title: PatID:10216003001, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W

value: Brodalumab 210 mg Q2W


title: ARDS230

description: Genomewide mRNA expression


title: ARDS209

description: Genomewide mRNA expression


title: PatID:10216003001, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W

value: lesional skin


title: FVB Her2 10681 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: 65649 dRybp_Eed-null Rnf2-ChIP untreated Rep2

description:
dRybp_Eed-null Rnf2-ChIP untreated Rep2
Ring1B_Eed.KO.Rybp.AID.A12.No.Aux.48h_65642.65649.merged.bw


title: 65643 dRybp_Eed-null Rnf2-ChIP IAA-48h Rep1

description:
dRybp_Eed-null Rnf2-ChIP IAA-48h Rep1
Ring1B_Eed.KO.Rybp.AID.A12.Aux.48h_65643.65650.merged.bw


title: FVB Her2 10403 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: FVB Her2 10684 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: FVB Her2 10362 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: FVB Her2 10402 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: FVB Her2 10402 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: FVB Her2 10361 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: PatID:10216003001, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: FVB Her2 10681 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: 61226 dRybp_Eed-null Rnf2-ChIP IAA-24h Rep1

description:
dRybp_Eed-null Rnf2-ChIP IAA-24h Rep1
61226.61253_Ring1B.EedKO.RybpAID..Aux_merged.bw


title: 61253 dRybp_Eed-null Rnf2-ChIP IAA-24h Rep2

description:
dRybp_Eed-null Rnf2-ChIP IAA-24h Rep2
61226.61253_Ring1B.EedKO.RybpAID..Aux_merged.bw


title: 65642 dRybp_Eed-null Rnf2-ChIP untreated Rep1

description:
dRybp_Eed-null Rnf2-ChIP untreated Rep1
Ring1B_Eed.KO.Rybp.AID.A12.No.Aux.48h_65642.65649.merged.bw


title: FVB Her2 10359 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: PatID:10216003001, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10216001009, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10216001006, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: ARDS207

description: Genomewide mRNA expression


title: PatID:10216001005, Tissue:LS, Visit:W12, Treatment:Placebo


title: PatID:10216001006, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10216001009, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: PatID:10216001005, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10216001005, Tissue:NL, Visit:W12, Treatment:Placebo


title: 61254 dRybp_Eed-null Rnf2-ChIP untreated Rep2

description:
dRybp_Eed-null Rnf2-ChIP untreated Rep2
61225.61254_Ring1B.EedKO.RybpAID.NoAux_merged.bw


title: PatID:10216001005, Tissue:LS, Visit:BL, Treatment:Placebo


title: FVB Her2 10359 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: FVB Her2 10362 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: FVB Her2 10357 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: FVB Her2 10361 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: 61225 dRybp_Eed-null Rnf2-ChIP untreated Rep1

description:
dRybp_Eed-null Rnf2-ChIP untreated Rep1
61225.61254_Ring1B.EedKO.RybpAID.NoAux_merged.bw


title: FVB Her2 10306 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: FVB PyMT 10548 Lung met E gDNA

description: gDNA isolated from flash frozen tissue

value: PyMT


title: FVB PyMT 10548 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: FVB Her2 10306 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: FVB PyMT 10548 Lung met C gDNA

description: gDNA isolated from flash frozen tissue


title: PatID:10216001004, Tissue:NL, Visit:W12, Treatment:Placebo


title: PatID:10216001004, Tissue:LS, Visit:W12, Treatment:Placebo


title: 61283 dRnf2_Ring1-null H2AK119Ub1-ChIP untreated Rep2

description:
dRnf2_Ring1-null H2AK119Ub1-ChIP untreated Rep2
61278.61283_H2AUb.Ring1AKO.AID.Ring1B.NoAux_merged.bw

source_name: mouse embryonic stem cells D10B3C10-B10


title: FVB Her2 10403 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: PatID:10216001004, Tissue:NL, Visit:BL, Treatment:Placebo


title: PatID:10216001004, Tissue:LS, Visit:BL, Treatment:Placebo


title: FVB Her2 10357 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: FVB PyMT 10548 Lung met A gDNA

description: gDNA isolated from flash frozen tissue


title: 61278 dRnf2_Ring1-null H2AK119Ub1-ChIP untreated Rep1

description:
dRnf2_Ring1-null H2AK119Ub1-ChIP untreated Rep1
61278.61283_H2AUb.Ring1AKO.AID.Ring1B.NoAux_merged.bw


title: 61237 dRnf2_Ring1-null Rnf2-ChIP IAA-24h Rep1

description:
dRnf2_Ring1-null Rnf2-ChIP IAA-24h Rep1
61237.61258_Ring1B.Ring1AKO.AID.Ring1B..Aux_merged.bw


title: 61258 dRnf2_Ring1-null Rnf2-ChIP IAA-24h Rep2

description:
dRnf2_Ring1-null Rnf2-ChIP IAA-24h Rep2
61237.61258_Ring1B.Ring1AKO.AID.Ring1B..Aux_merged.bw


title: FVB PyMT 10507 Lung met C gDNA

description: gDNA isolated from flash frozen tissue


title: 61284 dRnf2_Ring1-null H2AK119Ub1-ChIP IAA-24h Rep2

description:
dRnf2_Ring1-null H2AK119Ub1-ChIP IAA-24h Rep2
61277.61284_H2AUb.Ring1AKO.AIDRing1B..Aux_merged.bw


title: FVB PyMT 10507 Lung met B gDNA

description: gDNA isolated from flash frozen tissue


title: FVB PyMT 10507 Lung met E gDNA

description: gDNA isolated from flash frozen tissue


title: FVB PyMT 10507 Lung met D gDNA

description: gDNA isolated from flash frozen tissue


title: FVB PyMT 10548 Lung met D gDNA

description: gDNA isolated from flash frozen tissue


title: PatID:10216001003, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: FVB PyMT 10418 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: FVB PyMT 10507 Lung met A gDNA

description: gDNA isolated from flash frozen tissue


title: PatID:10216001003, Tissue:LS, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: 61259 dRnf2_Ring1-null Rnf2-ChIP untreated Rep2

description:
dRnf2_Ring1-null Rnf2-ChIP untreated Rep2
61238.61259_Ring1B.Ring1AKO.AIDRing1B.NoAux_merged.bw


title: FVB PyMT 10548 Lung met B gDNA

description: gDNA isolated from flash frozen tissue


title: 61277 dRnf2_Ring1-null H2AK119Ub1-ChIP IAA-24h Rep1

description:
dRnf2_Ring1-null H2AK119Ub1-ChIP IAA-24h Rep1
61277.61284_H2AUb.Ring1AKO.AIDRing1B..Aux_merged.bw


title: 61238 dRnf2_Ring1-null Rnf2-ChIP untreated Rep1

description:
dRnf2_Ring1-null Rnf2-ChIP untreated Rep1
61238.61259_Ring1B.Ring1AKO.AIDRing1B.NoAux_merged.bw


title: FVB PyMT 10418 Lung met C gDNA

description: gDNA isolated from flash frozen tissue


title: PatID:10216001003, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: 65712 Rybp-null Pcgf1-ChIP untreated Rep2

description:
Rybp-null Pcgf1-ChIP untreated Rep2
Pcgf1_AN3E9.No.Aux.48h_65705.65712.merged.bw

value: Rybp-null

value: Abcam ab202395


title: FVB PyMT 10507 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: 65705 Rybp-null Pcgf1-ChIP untreated Rep1

description:
Rybp-null Pcgf1-ChIP untreated Rep1
Pcgf1_AN3E9.No.Aux.48h_65705.65712.merged.bw


title: FVB PyMT 10418 Lung met A gDNA

description: gDNA isolated from flash frozen tissue


title: FVB PyMT 10418 Lung met B gDNA

description: gDNA isolated from flash frozen tissue


title: PatID:10216001001, Tissue:NL, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: PatID:10216001001, Tissue:NL, Visit:W12, Treatment:Brodalumab 210 mg Q2W


title: 65711 Eed-null Pcgf1-ChIP untreated Rep2

description:
Eed-null Pcgf1-ChIP untreated Rep2
Pcgf1_515D10.No.Aux.48h_65704.65711.merged.bw

value: Eed-null


title: FVB PyMT 10245 Lung met E gDNA

description: gDNA isolated from flash frozen tissue

value: MOLF/EiJ x FVBn/J


title: FVB PyMT 10418 Lung met E gDNA

description: gDNA isolated from flash frozen tissue

value: Genetically engineered / Autochthonous


title: FVB PyMT 10245 Lung met C gDNA

description: gDNA isolated from flash frozen tissue


title: PatID:10216001001, Tissue:LS, Visit:BL, Treatment:Brodalumab 210 mg Q2W


title: FVB PyMT 10245 Lung met D gDNA

description: gDNA isolated from flash frozen tissue


title: FVB PyMT 10418 Lung met D gDNA

description: gDNA isolated from flash frozen tissue

value: FVBn/J x FVBn/J


title: FVB PyMT 10245 Lung met B gDNA

description: gDNA isolated from flash frozen tissue

value: Lung metastatic tumor


title: 65710 wild-type Pcgf1-ChIP untreated Rep2

description:
wild-type Pcgf1-ChIP untreated Rep2
Pcgf1_AN312.No.Aux.48h_65703.65710.merged.bw

value: wild-type


title: FVB PyMT 10245 Lung met A gDNA

description: gDNA isolated from flash frozen tissue


title: 65703 wild-type Pcgf1-ChIP untreated Rep1

description:
wild-type Pcgf1-ChIP untreated Rep1
Pcgf1_AN312.No.Aux.48h_65703.65710.merged.bw


title: gastric tumor, Wt2

city: Shanghai

first: Liwei

last: AN

address: Yanchang Road

institute: Shanghai Tenth People's Hospital

data_processing:
Illumina platform used for base-calling, fastx_toolkit_0.0.14, SeqPrep, and Sickle softwares used for quality control of sequence reads.
Clean data was assambled for mapped data with Hisat2 software, then mapped to GRCm38.p5 whole genome using Cufflinks software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with RSEM software. Exons from all isoforms of a gene were merged to create one meta-transcript considering paired-end reads, reads length, and fragment length.
Genes were considered significantly differentially expressed under the following criteria: p-adjust < 0.05 & |log2FC| >= 1.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: xls file includes RPKM values for each Sample.

source_name: gastric tumor

growth_protocol: All mice of both sexes were of a C57BL/6 background and housed under specific pathogen-free conditions in automated watered and ventilated cages on a 12-h light/dark cycle.

extract_protocol:
Total mRNA was extracted using TRIZOL Reagent (Cat#15596-018) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies). Illumina Hiseq 4000 SBS Kit (Cat#FC-410-1003) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Tissues of the gastric tumors were dissected into 2-5mm2 fractions, then were lysed with lysis buffer followed by the centrifuged material and washed in cold HEPES (10 mM) buffer.

value: gastric tumor

value: post natal week 20

value: WT


title: gastric tumor, Wt1


title: gastric tumor, Mst4 KO2

value: Mst4 KO


title: gastric tumor, Mst4 KO1


title: 65698 Rybp-null H2AK119Ub1-ChIP untreated Rep2

description:
Rybp-null H2AK119Ub1-ChIP untreated Rep2
H2AUb_AN3E9.No.Aux.48h_65691.65698.merged.bw

value: untreated

value: Cell Signaling (D27C4) #8240


title: FVB PyMT 10245 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: Primary tumor


title: 65704 Eed-null Pcgf1-ChIP untreated Rep1

description:
Eed-null Pcgf1-ChIP untreated Rep1
Pcgf1_515D10.No.Aux.48h_65704.65711.merged.bw


title: FVB PyMT 10204 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: C57BL/10J  x FVBn/J


title: 65691 Rybp-null H2AK119Ub1-ChIP untreated Rep1

description:
Rybp-null H2AK119Ub1-ChIP untreated Rep1
H2AUb_AN3E9.No.Aux.48h_65691.65698.merged.bw


title: FVB PyMT 10204 Lung met E gDNA

description: gDNA isolated from flash frozen tissue

value: PyMT


title: 65697 Eed-null H2AK119Ub1-ChIP untreated Rep2

description:
Eed-null H2AK119Ub1-ChIP untreated Rep2
H2AUb_515D10.No.Aux.48h_65690.65697.merged.bw


title: FVB PyMT 10204 Lung met D gDNA

description: gDNA isolated from flash frozen tissue


title: Phb-cKO-SC-rep2

first: Lingfei

state: Shanghai

address: 138 Yixueyuan Road

institute: Shanghai Medical College Fudan University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mouse reference genome (GRCm38/mm10) using HISAT2 (version 2.1.0) .
Read counts were calculated, and then DESeq (Log2FC > 1 or < -1, FDR < 0.05) was used for differential analysis of gene expression.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: TXT file contain counts for all samples.

source_name: Phb knock-out spermatocytes

growth_protocol: GC2 cells (known cultured spermatocytes) were obtained from the American Type Culture Collection (ATCC) and grown in Dulbecco's modified Eagle's medium (DMEM, Corning) supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% Penicillin–Streptomycin at 37°C under 5% CO2. For spermatocytes isolation, seminiferous tubules were incubated in Gey’s Balanced Salt Solution (GBSS) supplemented with 200 U/ml collagenase and 5 μg/ml DNase I for 10 min at 35°C. The dispersed tubules were resuspended and incubated in 5 ml GBSS containing 200 U/ml collagenase and 0.25% trypsin for 20 min at 37°C with agitation. Following this FBS (Gibco) was added at a final concentration of 5% to inactivate the trypsin. The cell suspension was filtered through 40 μm diameter strainers to remove small clumps and subsequently stained with Hoechst 33342 (5 μg/ml) for 40 min at 37°C. Germ cell populations were enriched by BD Aria II (BD Biosciences) with a 355nm laser. Each isolated population (spermatogonia, spermatocytes, or round spermatids) was collected in PBS and subjected to immunofluorescence staining to evaluate the enrichment.

extract_protocol:
Cells were collected on ice and RNA was extracted from each sample using TRIzol reagent according to the manufacturer’s instruction.
cDNA libraries were generated using NEB Next Ultra Directional RNA Library Prep Kit (NEB) following the manufacturer’s instructions

tag: cell type

value: mouse spermatocytes

value: Phb knock-out


title: Phb-cKO-SC-rep3


title: FVB PyMT 10204 Lung met C gDNA

description: gDNA isolated from flash frozen tissue

tag: model


title: PBMCs_HepaRG_Ketorolac_rep1

city: Nagoya

first: Shingo

last: Oda

state: Aichi

address: 65 Tsurumai-cho, Showa-ku, Nagoya

country: Japan

institute: Nagoya University Graduate School of Medicine

description: Gene expression of PBMCs cocultured with differentiated HepaRG cells in the presence of ketorolac

hyb_protocol: Gene Expression Hybridization Kit (Agilent Technologies) protocol.

scan_protocol: Microarray slides were scanned using Agilent Technologies Microarray Scanner at a scan resolution of 3μm and TIFF file dynamic range of 20bit. The scanned images were quantified using Agilent Feature Extraction Software 12.0.3.1 (Agilent Technologies).

data_processing: All raw signal intensities were normalized by 75 percentile-shift using GeneSpring.

source_name: PBMCs, with HepaRG, Ketorolac, 24 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from total RNA using Low Input Quick Amp Labeling Kit (Agilent Technologies) labelling protocol.

extract_protocol: Total RNA was prepared fro PBMCs using an RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Freshly isolated peripheral blood mononuclear cells (PBMCs) from a healthy volunteer were cocultured with HepG2 or differentiated HepaRG cells in CTL-Test Medium (Cellular Technology Limited; Cleveland, OH) using Falcon culture inserts (0.4-µm pore size, Corning; Corning, NY) and treated with test drugs. The cultures were incubated for 24 hours at 37ºC in a humidified incubator with 5% CO2.

value: PBMCs

tag: gender

value: Male


title: PBMCs_HepaRG_TienilicAcid_rep1

description: Gene expression of PBMCs cocultured with differentiated HepaRG cells in the presence of tienilic acid

source_name: PBMCs, with HepaRG, TienilicAcid, 24 hours


title: PBMCs_HepaRG_Diclofenac_rep1

description: Gene expression of PBMCs cocultured with differentiated HepaRG cells in the presence of diclofenac

source_name: PBMCs, with HepaRG, Diclofenac, 24 hours


title: PBMCs_HepaRG_Trovafloxacin_rep1

description: Gene expression of PBMCs cocultured with differentiated HepaRG cells in the presence of trovafloxacin

source_name: PBMCs, with HepaRG, Trovafloxacin, 24 hours


title: PBMCs_HepaRG_EthacrinicAcid_rep1

description: Gene expression of PBMCs cocultured with differentiated HepaRG cells in the presence of ethacrinic acid

source_name: PBMCs, with HepaRG, EthacrinicAcid, 24 hours


title: PBMCs_HepaRG_Mebendazole_rep1

description: Gene expression of PBMCs cocultured with differentiated HepaRG cells in the presence of mebendazole

source_name: PBMCs, with HepaRG, Mebendazole, 24 hours


title: 65690 Eed-null H2AK119Ub1-ChIP untreated Rep1

description:
Eed-null H2AK119Ub1-ChIP untreated Rep1
H2AUb_515D10.No.Aux.48h_65690.65697.merged.bw

value: Eed-null


title: Control-SC-rep3

source_name: Control spermatocytes

value: Control


title: FVB PyMT 10204 Lung met B gDNA

description: gDNA isolated from flash frozen tissue

tag: tissue

value: Lung metastatic tumor

value: Genetically engineered / Autochthonous

tag: strain


title: 65696 wild-type H2AK119Ub1-ChIP untreated Rep2

description:
wild-type H2AK119Ub1-ChIP untreated Rep2
H2AUb_AN312.No.Aux.48h_65689.65696.merged.bw

tag: genotype

value: wild-type


title: PBMCs_HepaRG_Levofloxacin_rep1

description: Gene expression of PBMCs cocultured with differentiated HepaRG cells in the presence of levofloxacin

source_name: PBMCs, with HepaRG, Levofloxacin, 24 hours


title: FVB PyMT 10204 Lung met A gDNA

description: gDNA isolated from flash frozen tissue


title: Control-SC-rep1


title: 65689 wild-type H2AK119Ub1-ChIP untreated Rep1

description:
wild-type H2AK119Ub1-ChIP untreated Rep1
H2AUb_AN312.No.Aux.48h_65689.65696.merged.bw

tag: treatment


title: 65648 Rybp-null Rnf2-ChIP untreated Rep2

description:
Rybp-null Rnf2-ChIP untreated Rep2
Ring1B_AN3E9.No.Aux.48h_65641.65648.merged.bw

source_name: mouse embryonic stem cells AN3E9

value: Rybp-null

value: Cell Signaling (D22F2) #5694


title: PBMCs_HepaRG_Ketoconazole_rep1

description: Gene expression of PBMCs cocultured with differentiated HepaRG cells in the presence of ketoconazole

source_name: PBMCs, with HepaRG, Ketoconazole, 24 hours


title: PBMCs_HepaRG_Chloroquine_rep1

description: Gene expression of PBMCs cocultured with differentiated HepaRG cells in the presence of chloroquine

source_name: PBMCs, with HepaRG, Chloroquine, 24 hours


title: GC2-PHB KD-rep3

source_name: PHB Knockdown GC2 cell

value: mouse spermatocytes cell line

value: PHB Knockdown


title: Phb-cKO-SC-rep1


title: 65641 Rybp-null Rnf2-ChIP untreated Rep1

description:
Rybp-null Rnf2-ChIP untreated Rep1
Ring1B_AN3E9.No.Aux.48h_65641.65648.merged.bw

value: untreated


title: FVB PyMT 9674 Lung met gDNA

description: gDNA isolated from flash frozen tissue

source_name: Lung Met

value: FVB/NJ  x FVBn/J


title: Control-SC-rep2


title: GC2-PHB KD-rep2


title: FVB PyMT 9742 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: PBMCs_HepaRG_DMSO_rep1

description: Gene expression of PBMCs cocultured with differentiated HepaRG cells in the presence of DMSO

source_name: PBMCs, with HepaRG, DMSO, 24 hours


title: 65647 Eed-null Rnf2-ChIP untreated Rep2

description:
Eed-null Rnf2-ChIP untreated Rep2
Ring1B_515D10.No.Aux.48h_65640.65647.merged.bw

source_name: mouse embryonic stem cells 515D10


title: PBMCs_HepG2_Levofloxacin_rep1

description: Gene expression of PBMCs cocultured with HepG2 cells in the presence of levofloxacin

source_name: PBMCs, with HepG2, Levofloxacin, 24 hours


title: PBMCs_HepaRG_Amodiaquine_rep1

description: Gene expression of PBMCs cocultured with differentiated HepaRG cells in the presence of amodiaquine

source_name: PBMCs, with HepaRG, Amodiaquine, 24 hours


title: PBMCs_HepG2_Ketorolac_rep1

description: Gene expression of PBMCs cocultured with HepG2 cells in the presence of ketorolac

source_name: PBMCs, with HepG2, Ketorolac, 24 hours


title: GC2-PHB KD-rep1


title: PBMCs_HepG2_Trovafloxacin_rep1

description: Gene expression of PBMCs cocultured with HepG2 cells in the presence of trovafloxacin

source_name: PBMCs, with HepG2, Trovafloxacin, 24 hours


title: FVB PyMT 974 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: 65640 Eed-null Rnf2-ChIP untreated Rep1

description:
Eed-null Rnf2-ChIP untreated Rep1
Ring1B_515D10.No.Aux.48h_65640.65647.merged.bw


title: GC2-Ctrl-rep3

source_name: Control GC2 cell


title: FVB PyMT 965 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: FVB PyMT 9470 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: FVB PyMT 9760 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: GC2-Ctrl-rep1


title: FVB PyMT 9725 Lung met Gdna

description: gDNA isolated from flash frozen tissue


title: FVB PyMT 956 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: 65728 Rybp-null H3K27me3-ChIP untreated Rep2

description:
Rybp-null H3K27me3-ChIP untreated Rep2
H3K27me3_AN3E9_65727.65728.merged.bw

value: Diagenode C15410069


title: 65639 wild-type Rnf2-ChIP untreated Rep1

description:
wild-type Rnf2-ChIP untreated Rep1
Ring1B_AN312.No.Aux.48h_65639.65646.merged.bw

source_name: mouse embryonic stem cells AN312


title: GC2-Ctrl-rep2


title: 65727 Rybp-null H3K27me3-ChIP untreated Rep1

description:
Rybp-null H3K27me3-ChIP untreated Rep1
H3K27me3_AN3E9_65727.65728.merged.bw


title: 49466 Eed-null H3K27me3-ChIP untreated Rep2

description:
Eed-null H3K27me3-ChIP untreated Rep2
515D10_H3K27me3_49466_uniq_GGc.bw


title: CnR_IgG(H3K4me3_H3K27me3_samples)_MM401_Washout_Rep1

city: San Francisco

first: Tomasz

last: Nowakowski

state: Ca

institute: UCSF

data_processing:
RNAseq reads were psuedoaligned to Genocde GRCm38.p5 mouse transriptome with kallisto v0.43.0 using 100 bootstrap samples.
Differential expression was assessed using Sleuth v0.29.0 with transformation function = function(x) log2(x + 0.5) and gene-level aggregation using Ensembl annotations.  qvalue <0.1 and b-value (log2FC) of >0.5 used as thresholds
CnR reads were quality trimmed by BBDuk, removing reads below Q30 score, and aligned to UCSC MM10 genome with Bowtie2 2.2.6 with the following arguments: : --local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700.
Peaks were called using MACS2 using the argument --broad and using IgG samples as control libraries
Differentially enriched chromatin loci were called using diffReps with arguments: -me nb --mode b. Differentially enriched loci outside of statistically called peaks by MACS2 were removed
Genome_build: RNAseq:mouse mm10, Gencode GRCm38.p5 mouse transriptome. CnR: UCSC mm10
Supplementary_files_format_and_content: peaks; abundance.h5

growth_protocol: Proliferative medium (DMEM/F12 with Glutamax, 5% Fetal Bovine Serum, N2 supplement, 35 µg/mL bovine pituitary extract, 20 ng/mL EGF, 20 ng/mL FGF, antibiotic/antimycotic)

extract_protocol:
not provided; requested
CnR

tag: developmental stage

value: Derived from postnatal day 7

value: Ventral V-SVZ cells

value: 25µM MM-401 (in 1% DMSO) added to proliferation media for 10 days, then replaces with normal proliferation media for 10 days


title: FVB PyMT 9760 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

source_name: Primary tumor

value: Primary tumor

value: PyMT


title: CnR_IgG(H3K4me3_H3K27me3_samples)_DMSO_Washout_Rep2

value: 1% DMSO (10 days) added to proliferation media for 10 days, then replaced with normal proliferation media for 10 days


title: 65646 wild-type Rnf2-ChIP untreated Rep2

description:
wild-type Rnf2-ChIP untreated Rep2
Ring1B_AN312.No.Aux.48h_65639.65646.merged.bw


title: 49464 Eed-null H3K27me3-ChIP untreated Rep1

description:
Eed-null H3K27me3-ChIP untreated Rep1
515D10_H3K27me3_49464_uniq_GGc.bw

value: Eed-null


title: PBMCs_HepG2_Mebendazole_rep1

description: Gene expression of PBMCs cocultured with HepG2 cells in the presence of mebendazole

source_name: PBMCs, with HepG2, Mebendazole, 24 hours

value: PBMCs

value: Male


title: PBMCs_HepG2_Chloroquine_rep1

description: Gene expression of PBMCs cocultured with HepG2 cells in the presence of chloroquine

source_name: PBMCs, with HepG2, Chloroquine, 24 hours


title: FVB PyMT 974 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: Genetically engineered / Autochthonous


title: FVB PyMT 9742 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: CnR_IgG(H3K4me3_H3K27me3_samples)_DMSO_Washout_Rep1


title: PBMCs_HepG2_Amodiaquine_rep1

description: Gene expression of PBMCs cocultured with HepG2 cells in the presence of amodiaquine

source_name: PBMCs, with HepG2, Amodiaquine, 24 hours


title: PBMCs_HepG2_Ketoconazole_rep1

description: Gene expression of PBMCs cocultured with HepG2 cells in the presence of ketoconazole

source_name: PBMCs, with HepG2, Ketoconazole, 24 hours


title: CnR_IgG(H3K4me3_H3K27me3_samples)_MM401_Rep1

value: 25µM MM-401 (in 1% DMSO) added to proliferation media for 10 days


title: CnR_IgG(H3K27ac_H3K4me1_samples)_MM401_Washout_Rep2


title: PBMCs_HepG2_Diclofenac_rep1

description: Gene expression of PBMCs cocultured with HepG2 cells in the presence of diclofenac

source_name: PBMCs, with HepG2, Diclofenac, 24 hours


title: PBMCs_HepG2_EthacrinicAcid_rep1

description: Gene expression of PBMCs cocultured with HepG2 cells in the presence of ethacrinic acid

source_name: PBMCs, with HepG2, EthacrinicAcid, 24 hours


title: FVB PyMT 9725 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: CnR_IgG(H3K27ac_H3K4me1_samples)_DMSO_Washout_Rep2


title: CnR_IgG(H3K4me3_H3K27me3_samples)_DMSO_Rep1

value: 1% DMSO (10 days) added to proliferation media for 10 days


title: CnR_IgG(H3K4me3_H3K27me3_samples)_DMSO_Rep2


title: CnR_IgG(H3K27ac_H3K4me1_samples)_MM401_Washout_Rep1


title: 75661 Rybp-null Rybp-ChIP untreated Rep2

description:
Rybp-null Rybp-ChIP untreated Rep2
Rybp_RybpKO.AN3E9_75661_mq_30.bw

source_name: mouse embryonic stem cells AN3E9

value: Rybp-null

value: SIGMA PRS2227


title: PBMCs_HepG2_TienilicAcid_rep1

description: Gene expression of PBMCs cocultured with HepG2 cells in the presence of tienilic acid

source_name: PBMCs, with HepG2, TienilicAcid, 24 hours


title: FVB PyMT 9674 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: FVB PyMT 965 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: 75660 Eed-null Rybp-ChIP untreated Rep2

description:
Eed-null Rybp-ChIP untreated Rep2
Rybp_EedKO.515D10_75660_mq_30.bw

value: untreated


title: CnR_H3K27me3_DMSO_Washout_Rep2


title: 37160 wild-type H3K27me3-ChIP untreated Rep1

description:
wild-type H3K27me3-ChIP untreated Rep1
AN312_H3K27me3_37160_49468_merged_GGc_peakExcluded.bw

value: wild-type


title: 75658 Rybp-null Rybp-ChIP untreated Rep1

description:
Rybp-null Rybp-ChIP untreated Rep1
Rybp_RybpKO.AN3E9_75658_mq_30.bw


title: CnR_IgG(H3K27ac_H3K4me1_samples)_DMSO_Washout_Rep1


title: FVB PyMT 956 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: FVB/NJ  x FVBn/J


title: CnR_IgG(H3K4me3_H3K27me3_samples)_MM401_Rep2

value: Derived from postnatal day 7


title: 49468 wild-type H3K27me3-ChIP untreated Rep2

description:
wild-type H3K27me3-ChIP untreated Rep2
AN312_H3K27me3_37160_49468_merged_GGc_peakExcluded.bw

value: Diagenode C15410069


title: CnR_IgG(H3K27ac_H3K4me1_samples)_MM401_Rep2

value: Ventral V-SVZ cells


title: PBMCs_HepG2_DMSO_rep1

description: Gene expression of PBMCs cocultured with HepG2 cells in the presence of DMSO

source_name: PBMCs, with HepG2, DMSO, 24 hours


title: CnR_H3K27me3_DMSO_Washout_Rep1


title: 75657 Eed-null Rybp-ChIP untreated Rep1

description:
Eed-null Rybp-ChIP untreated Rep1
Rybp_EedKO.515D10_75657_mq_30.bw

source_name: mouse embryonic stem cells 515D10


title: CnR_H3K27me3_MM401_Washout_Rep2

value: 25µM MM-401 (in 1% DMSO) added to proliferation media for 10 days, then replaces with normal proliferation media for 10 days


title: 75659 wild-type Rybp-ChIP untreated Rep2

description:
wild-type Rybp-ChIP untreated Rep2
Rybp_WT.AN312_75659_mq_30.bw


title: FVB PyMT 10081 Lung met

description: gDNA isolated from flash frozen tissue

source_name: Lung met

value: Lung metastatic tumor

value: PyMT


title: CnR_IgG(H3K27ac_H3K4me1_samples)_DMSO_Rep2


title: CnR_H3K27me3_MM401_Washout_Rep1


title: FVB PyMT 10081 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: Primary tumor


title: 75656 wild-type Rybp-ChIP untreated Rep1

description:
wild-type Rybp-ChIP untreated Rep1
Rybp_WT.AN312_75656_mq_30.bw


title: CnR_IgG(H3K27ac_H3K4me1_samples)_DMSO_Rep1


title: 65724 Rybp-null Cbx7-ChIP untreated Rep2

description:
Rybp-null Cbx7-ChIP untreated Rep2
Cbx7_AN3E9_65723.65724.merged.bw

value: Abcam 21873


title: CnR_H3K27me3_DMSO_Rep2


title: FVB PyMT 9958 Lung met

description: gDNA isolated from flash frozen tissue


title: CnR_H3K27me3_DMSO_Rep1


title: CnR_H3K27me3_MM401_Rep2


title: FVB PyMT 9958 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: CnR_H3K27me3_MM401_Rep1


title: CnR_H3K4me3_DMSO_Washout_Rep2

value: 1% DMSO (10 days) added to proliferation media for 10 days, then replaced with normal proliferation media for 10 days


title: CnR_H3K4me1_MM401_Washout_Rep2


title: 52748 Eed-null Cbx7-ChIP untreated Rep1

description:
Eed-null Cbx7-ChIP untreated Rep1
515D10_Cbx7_52748_uniq_GGc.bw

value: Eed-null


title: FVB PyMT 9470 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: Genetically engineered / Autochthonous


title: 52749 Eed-null Cbx7-ChIP untreated Rep2

description:
Eed-null Cbx7-ChIP untreated Rep2
515D10_Cbx7_52749_uniq_GGc.bw


title: CnR_H3K4me1_DMSO_Washout_Rep2


title: CnR_H3K4me1_DMSO_Washout_Rep1


title: FVB PyMT 10135 Lung met

description: gDNA isolated from flash frozen tissue


title: 37146 Eed-null Cbx7-ChIP untreated Rep3

description:
Eed-null Cbx7-ChIP untreated Rep3
515D10_Cbx7_37146_uniq_GGc.bw


title: CnR_IgG(H3K27ac_H3K4me1_samples)_MM401_Rep1

value: 25µM MM-401 (in 1% DMSO) added to proliferation media for 10 days


title: FVB PyMT 10135 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: CnR_H3K4me1_DMSO_Rep2

value: 1% DMSO (10 days) added to proliferation media for 10 days


title: CnR_H3K4me3_DMSO_Washout_Rep1


title: FVB PyMT 10136 Lung met

description: gDNA isolated from flash frozen tissue


title: 65723 Rybp-null Cbx7-ChIP untreated Rep1

description:
Rybp-null Cbx7-ChIP untreated Rep1
Cbx7_AN3E9_65723.65724.merged.bw

value: Rybp-null


title: CnR_H3K4me3_MM401_Washout_Rep2


title: FVB PyMT 10136 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: 65722 wild-type Cbx7-ChIP untreated Rep2

description:
wild-type Cbx7-ChIP untreated Rep2
Cbx7_AN312_65721.65722.merged.bw

value: untreated


title: CnR_H3K4me1_MM401_Washout_Rep1


title: CnR_H3K4me1_DMSO_Rep1


title: 65721 wild-type Cbx7-ChIP untreated Rep1

description:
wild-type Cbx7-ChIP untreated Rep1
Cbx7_AN312_65721.65722.merged.bw

value: wild-type


title: FVB PyMT 10009 Lung met

description: gDNA isolated from flash frozen tissue

value: FVB/NJ  x FVBn/J


title: CnR_H3K4me1_MM401_Rep2

value: Derived from postnatal day 7


title: 65720 Rybp-null Eed-ChIP untreated Rep2

description:
Rybp-null Eed-ChIP untreated Rep2
Eed_AN3E9_65719.65720.merged.bw

value: Active Motif 61203


title: CnR_H3K4me3_MM401_Washout_Rep1

value: Ventral V-SVZ cells


title: FVB PyMT 10009 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: CnR_H3K4me3_DMSO_Rep2


title: CnR_H3K4me1_MM401_Rep1


title: 65719 Rybp-null Eed-ChIP untreated Rep1

description:
Rybp-null Eed-ChIP untreated Rep1
Eed_AN3E9_65719.65720.merged.bw


title: FVB PyMT 10157 Lung met

description: gDNA isolated from flash frozen tissue


title: CnR_H3K27ac_DMSO_Washout_Rep2


title: CnR_H3K4me3_MM401_Rep2


title: FVB PyMT 10157 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: 37123 Eed-null Eed-ChIP untreated Rep1

description:
Eed-null Eed-ChIP untreated Rep1
515D10_Eed_37123_49446_merged_GGc_peakExcluded.bw


title: CnR_H3K27ac_DMSO_Washout_Rep1


title: FVB PyMT 10183 Lung met

description: gDNA isolated from flash frozen tissue


title: CnR_H3K27ac_MM401_Washout_Rep2

value: 25µM MM-401 (in 1% DMSO) added to proliferation media for 10 days, then replaces with normal proliferation media for 10 days


title: CnR_H3K27ac_MM401_Washout_Rep1


title: FVB PyMT 10183 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: CnR_H3K4me3_MM401_Rep1


title: 72h_APF_2

city: Martinsried

first: Nikolai

middle: Li-Heng

last: Hoermann

state: Bavaria

address: Am Klopferspitz 18

department: Circuits-Computation-Models

country: Germany

institute: Max Planck Institute of Neurobiology

data_processing: Cellranger v3

organism: Drosophila melanogaster

source_name: T4/T5 neurons

extract_protocol:
following Harzer et al. 2013 (Nature Methods)
10X genomics protocol v3

value: 72 hours after pupa formation

value: SS00324-Gal4 recombined with UAS-mCD8::GFP

value: T4/T5 neurons


title: 65718 wild-type Eed-ChIP untreated Rep2

description:
wild-type Eed-ChIP untreated Rep2
Eed_AN312_65717.65718.merged.bw


title: 65717 wild-type Eed-ChIP untreated Rep1

description:
wild-type Eed-ChIP untreated Rep1
Eed_AN312_65717.65718.merged.bw


title: 49908 wild-type Input untreated Rep3

description:
wild-type Input untreated Rep3
merged_Input_49475_49911_49908_GGc.bw


title: MOLF PyMT NoTag2/8/17 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: Primary tumor

value: PyMT

value: MOLF/EiJ x FVBn/J


title: MOLF PyMT NoTag2/8/17 Lung met

description: gDNA isolated from flash frozen tissue

value: Lung metastatic tumor

value: Genetically engineered / Autochthonous


title: 72h_APF_1


title: 49911 wild-type Input untreated Rep2

description:
wild-type Input untreated Rep2
merged_Input_49475_49911_49908_GGc.bw


title: MOLF PyMT 9879 Lung met

description: gDNA isolated from flash frozen tissue


title: 60h_APF_1

value: 60 hours after pupa formation


title: 49446 Eed-null Eed-ChIP untreated Rep2

description:
Eed-null Eed-ChIP untreated Rep2
515D10_Eed_37123_49446_merged_GGc_peakExcluded.bw

value: Eed-null


title: MOLF PyMT 9879 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: CnR_H3K4me3_DMSO_Rep1

value: 1% DMSO (10 days) added to proliferation media for 10 days


title: 49475 wild-type Input untreated Rep1

description:
wild-type Input untreated Rep1
merged_Input_49475_49911_49908_GGc.bw

value: wild-type

value: untreated


title: FVB PyMT 9756 Lung met

description: gDNA isolated from flash frozen tissue

value: FVB/NJ  x FVBn/J


title: 48h_APF_2

value: 48 hours after pupa formation


title: FVB PyMT 9756 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: 48h_APF_1


title: MOLF PyMT 9998 Lung met

description: gDNA isolated from flash frozen tissue


title: 36h_APF_1

value: 36 hours after pupa formation


title: 60h_APF_2


title: RNAseq_MM401_washed_out_Control_Rep1

description:
DMSO_Rep1_10day_washout_S53
DMSO_Rep1_10day_washout_S17_L005

extract_protocol:
Total RNA was isolated by Trizol (Life Technologies), purified using Direct-zol (Zymo) kit with on-column DNAse treatment.
Strand-specific, poly(A) selected cDNA libraries were generated using TruSeq Stranded mRNA kit (Illumina, #20020594).

value: Derived from postnatal day 7

value: Ventral V-SVZ cells

value: 1% DMSO (10 days) added to proliferation media for 10 days, then replaced with normal proliferation media for 10 days


title: CnR_H3K27ac_DMSO_Rep2


title: CnR_H3K27ac_MM401_Rep1

value: 25µM MM-401 (in 1% DMSO) added to proliferation media for 10 days


title: mdx_qsc_2

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Read quality trimming with Reaper (quality > Q20 in window of 20 nt, minimum length >15)
Mapping of reads versus mouse genome version mm10 using STAR 2.6.1d (--outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMatchNmin 20 -alignEndsProtrude 10 ConcordantPair)
Reads were counted per gene with featureCounts 1.6.3 from the Subread package using default parameters. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
The raw gene counts per sample were joined to a matrix and normalized with DESeq2 1.18.1.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: The tab-delimited text file (matrix.txt) contains DESeq normalized counts for all expressed genes.

source_name: quiescent satellite cells

extract_protocol:
FACS purified MuSCs were immediately proccessed for sample preparation.
Between 10.000 and 20.000 FACS sorted cells were used for library preparation using the Takara SMARTer Stranded Total RNA-Seq Kit v2 Pico Input Mammalian.

value: muscular dystrophy (mdx)

value: quiescent satellite cells


title: wt_qsc_2

value: wild type


title: mdx_qsc_1


title: mdx_qsc_3


title: CnR_H3K27ac_DMSO_Rep1


title: MOLF PyMT 9998 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: Primary tumor

value: PyMT

value: MOLF/EiJ x FVBn/J


title: RNAseq_MM401_washed_out_Control_Rep2

description:
DMSO_Rep2_10day_washout_S54
DMSO_Rep2_10day_washout_S18_L005


title: RNAseq_MM401_washed_out_Rep2

description:
MM401_Rep2_10day_washout_S56
MM401_Rep2_10day_washout_S20_L005

value: 25µM MM-401 (in 1% DMSO) added to proliferation media for 10 days, then replaces with normal proliferation media for 10 days


title: RNAseq_MM401_washed_out_Rep1

description:
MM401_Rep1_10day_washout_S55
MM401_Rep1_10day_washout_S19_L005


title: CnR_H3K27ac_MM401_Rep2


title: 24h_APF_2

value: 24 hours after pupa formation

value: SS00324-Gal4 recombined with UAS-mCD8::GFP

value: T4/T5 neurons


title: MOLF PyMT 9994 Lung met

description: gDNA isolated from flash frozen tissue

value: Lung metastatic tumor

value: Genetically engineered / Autochthonous


title: RNAseq_MM401_Control_Rep2

value: 1% DMSO (10 days) added to proliferation media for 10 days


title: 24h_APF_1


title: RNAseq_MM401_Control_Rep1

value: Derived from postnatal day 7


title: 36h_APF_2

value: 36 hours after pupa formation


title: RNAseq_MM401_treated_Rep2

value: Ventral V-SVZ cells


title: MOLF PyMT 9994 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: MOLF PyMT 9884 Lung met

description: gDNA isolated from flash frozen tissue


title: RNAseq_MM401_treated_Rep1

value: 25µM MM-401 (in 1% DMSO) added to proliferation media for 10 days


title: MOLF PyMT 10125 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: wt_qsc_2

data_processing:
Trimmomatic version 0.36 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Mapping of reads versus mouse genome version mm10 using STAR 2.6.1d (--outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMatchNmin 20 -alignEndsProtrude 10 ConcordantPair)
Reads were counted per gene with featureCounts 1.6.3 from the Subread package using default parameters. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
The raw gene counts per sample were joined to a matrix and normalized with DESeq2 1.18.1.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: The tab-delimited text file (matrix.txt) contains DESeq normalized counts for all expressed genes.


title: rm_qsc_2

value: muscular dystrophy (mdx/Ripk3mKO)


title: mdx_qsc_1

value: muscular dystrophy (mdx)

value: quiescent satellite cells


title: RNAseq_UBC-CreER;Mll1_Control_Rep1

description:
UBC_MLL_Het_Vent_Rep1_S61
UBC_MLL_Het_Vent_Rep1_S21_L005

value: 100nM 4-OHT  (in 1% EtOH) added to proliferation media for 4 days (2 passages)


title: wt_qsc_2

data_processing:
Read quality trimming with Trimmomatic 0.33 (SLIDINGWINDOW:5:15 CROP:500 MINLEN:15)
Mapping of reads versus mouse genome version mm10 using STAR 2.5.3a (--outFilterMismatchNoverLmax 0.2 --outFilterScoreMinOverLread 0.66 --outFilterMatchNminOverLread 0.66 --outFilterMatchNmin 20 --alignIntronMax 1 --alignSJDBoverhangMin 999 --outFilterMultimapNmax 1 --alignEndsProtrude 10 ConcordantPair)
Deduplication of reads using Picard 2.9.0
Peak calling using MACS2 version 2.1.0 (-q 0.0001)
Removal of peaks overlapping ENCODE blacklisted regions
Merging of peaks of all samples to a unified set
Recount of reads per union peaks per sample
Normalization of union peak counts using DESeq2
Annotation of peaks based on GENCODE vM15 (most closely located TSS +-5000 nt of the peak center)
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: The tab-delimited text file contains DESeq normalized unified peaks

extract_protocol:
FACS purified MuSCs were immediately proccessed for ATACseq sample preparation.
Between 10.000 and 20.000 FACS sorted cells were used for ATAC Library preparation using Tn5 Transposase from Nextera DNA Sample Preparation Kit (Illumina). Cell pellet was resuspended in 50µl PBS annd mixed with 25µl TD-Buffer, 2.5µl Tn5, 0.5µl 10% NP-40 and 22µl water. Cell/Tn5 mixture was incubeated at 37°C for 30min with occasional snap mixing. Transposase treatment was followed by 30min incubation at 50°C together with 500mM EDTA pH8.0 for optimal recovery of digested DNA fragments. For neutralisation of EDTA 100µl of 50mM MgCl2 was added followed by purification of the DNA fragments by MinElute PCR Purification Kit (Qiagen). Aplification of Library together with Indexing was performed as described elsewere (Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (2013) Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang & William J Greenleaf. Nature Methods. doi:10.1038/nmeth.2688). Libraries were mixed in equimolar ratios and sequenced on NextSeq500 platform using V2 chemistry.

value: wild type


title: wt_qsc_1


title: MOLF PyMT 9884 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: Primary tumor

value: PyMT

value: MOLF/EiJ x FVBn/J


title: RNAseq_UBC-CreER;Mll1F/F_Rep2

description:
UBC_MLL_Homo_Vent_Rep2_S65
UBC_MLL_Homo_Vent_Rep2_S25_L005


title: RNAseq_UBC-CreER;Mll1_Control_Rep2

description:
UBC_MLL_Het_Vent_Rep2_S62
UBC_MLL_Het_Vent_Rep2_S22_L005


title: rm_qsc_1


title: wt_qsc_1


title: mdx_qsc_2


title: MOLF PyMT 10125 Lung met

description: gDNA isolated from flash frozen tissue


title: wt_qsc_1


title: MOLF PyMT 10237 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: RNAseq_UBC-CreER;Smo_Control_Rep2

description:
SMO_HET_V_2_S10
UBC_Smo_Het_Rep2_167__S59


title: mdx_qsc_2


title: MOLF PyMT 10237 Lung met

description: gDNA isolated from flash frozen tissue


title: H1573_HOXC10_COMBO_3

city: Boston

first: Stephanie

middle: Louise

last: Guerra

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University- Brigham Women's Hospital

description: gene expression data from HOXC10-expressing cells treated with Combined MEKi (PD-0325901) and BRD4i (JQ1)

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: BRB array tools

label_protocol: biotin

growth_protocol: Cells were grown in RPMI supplemented with 10% FBS

extract_protocol: Total RNA was extracted using a trizol extraction followed by Qiagen RNeasy purification

treatment_protocol: Cells stably expressing LACZ or HOXC10 were treated with DMSO (vehicle) or the combination of 500 nM PD-0325901 and 1000uM JQ1 for 24 hours prior to harvest

tag: cell line

value: lung cancer


title: BL6 PyMT 10208 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: C57BL/6J x FVBn/J


title: BL6 PyMT 10208 Lung met

description: gDNA isolated from flash frozen tissue

value: Lung metastatic tumor


title: H1573_HOXC10_DMSO_3

description: gene expression data from HOXC10-expressing cells treated with Vehicle (DMSO)


title: RNAseq_UBC-CreER;Mll1F/F_Rep1

description:
UBC_MLL_Homo_Vent_Rep1_S64
UBC_MLL_Homo_Vent_Rep1_S24_L005


title: mdx_qsc_1


title: RNAseq_UBC-CreER;Smo_Control_Rep1

description:
SMO_HET_V_1_S9
UBC_Smo_Het_Rep1_156__S57


title: H1573_HOXC10_COMBO_2


title: H1573_LACZ_COMBO_1

description: gene expression data from LACZ-expressing cells treated with Combined MEKi (PD-0325901) and BRD4i (JQ1)


title: RNAseq_UBC-CreER;SmoF/F_Rep2

description:
SMO_HOMO_V_2_S12
UBC_Smo_Homo_Rep1_170__S60


title: H1573_LACZ_COMBO_2


title: 3018

city: New Orleans

first: Qinyan

last: Yin

state: Louisiana

address: 1430 Tulane Ave SL8509

department: Department of Medicine

institute: Tulane University

data_processing:
Quality control for fastq files performed using FastQC
Reads were aligned to hg19 reference genome using STAR2.5.3a
Reads were aligned to hg19 reference transcriptome using RSEM
Differential expression testing of cellular genes performed using EBSeq
Virome screening perfomed using custom scripts
Genome_build: Hg19
Supplementary_files_format_and_content: Excel files with virus counts for 740 human viruses plus HERVs

source_name: Lung tissue

extract_protocol:
11 IPF patients and 4 controls, and encompassed patients underwent lung biopsies at the University of Alabama at Birmingham (UAB).
Total RNA was prepared using Qiagen's RNeasy kit. Ribosomal RNA was removed from total RNA for poly(A) selected RNA-sequencing (RNA-seq)
RNA libraries were prepared for sequencing using using TruSeq stranded mRNA (polyA+) from Illumina.

value: Lung tissue

tag: diagnosis

value: Normal

tag: Sex

value: female

tag: age


title: H1573_HOXC10_COMBO_1


title: H1573_LACZ_COMBO_3


title: CAST PyMT 9985 Lung met

description: gDNA isolated from flash frozen tissue

value: Genetically engineered / Autochthonous

value: CAST/EiJ x FVBn/J


title: CAST PyMT 9985 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: H1573_HOXC10_DMSO_2


title: 3017

value: male


title: 3014


title: RNAseq_Ventral_Rep2

value: Derived from postnatal day 7

value: Ventral V-SVZ cells


title: CAST PyMT 9801 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: CAST PyMT 9801 Lung met

description: gDNA isolated from flash frozen tissue


title: H1573_LACZ_DMSO_3

description: gene expression data from LACZ-expressing cells treated with Vehicle (DMSO)


title: RNAseq_RNAseq_Ventral_Rep1


title: 3013


title: RNAseq_Dorsal_Rep2

value: Dorsal V-SVZ cells


title: 2051

value: IPF


title: RNAseq_Dorsal_Rep1


title: BL10 PyMT 9839 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: C57BL/10J x FVBn/J


title: 2049


title: BL10 PyMT 9897 Lung met

description: gDNA isolated from flash frozen tissue


title: 2048


title: H1573_LACZ_DMSO_1


title: MOLF PyMT 9998 PT  [WGS]

description: gDNA isolated from snap frozen tissue

data_processing:
quantile normalized
Samples were trimmed of adapters using Trimmomatic software (0.39)
The trimmed reads were aligned to 316 the mm10 reference mouse genome using BWA (0.7.17) or Bowtie (2-2.3.5.1) mapping software
SAMtools (1.9) mpileup, 317 GATK (3.8-1) Mutect2, and Strelka (2.7.1) were used to identify potential variants and the variants were filtered for known 318 polymorphisms from mgp.v5 (ftp://ftp-mouse.sanger.ac.uk/current_snps /mgp.v5.merged.snps_ all.dbSNP142 .vcf.gz) and 319 variants with Phred-scaled quality score of < 30 were removed
Annotation was performed by Annovar (2018-04-16).
High probability SNVs were identified after reads were visualized in IGV and false positives were removed from the data. Select SNVs validated by Sanger sequencing performed by the CCR Genomics Core.
Genome_build: mouse mm10
Supplementary_files_format_and_content: vcf files include variants for each sample

source_name: primary tumor

extract_protocol:
Mice were bred and allowed to age until a humane endpoint was reached. Primary tumors and lung metastases were isolated and snap frozen in cryo vials using liquid nitrogen. Tissue was stored at -80 and gDNA was later isolated using the gDNA purification using ZR-Duet DNA/RNA MiniPrep kit from Zymo Research.  (cat.no. D7001)
Whole genome sequencing library preparation was performed using the TruSeq DNA Sample Prep kit FC-121-1001.  Samples were barcoded, pooled and sequenced on an Illumina HiSeq4000 to a depth of ~10x per sample. For RNA sequencing, the preparation of mRNA libraries and mRNA sequencing was performed by the Sequencing Facility using the HiSeq2500 instrument with Illumina TruSeq v4 chemistry.

value: primary tumor


title: MOLF PyMT 9998 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue

value: PyMT


title: BL10 PyMT 9897 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: Primary tumor


title: 2044


title: BL10 PyMT 9839 Lung met

description: gDNA isolated from flash frozen tissue


title: MOLF PyMT 9994 PT  [WGS]

description: gDNA isolated from snap frozen tissue

value: MOLF/EiJ x FVBn/J


title: 2042


title: CAST PyMT 10077 Lung met

description: gDNA isolated from flash frozen tissue


title: RNAseq_UBC-CreER;SmoF/F_Rep1

description:
SMO_HOMO_V_1_S11
UBC_Smo_Homo_Rep1_158__S58

value: 100nM 4-OHT  (in 1% EtOH) added to proliferation media for 4 days (2 passages)


title: MOLF PyMT 9994 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue

value: Lung metastatic tumor


title: H1573_LACZ_DMSO_2

value: lung cancer


title: H1573_COMBO_3

description: gene expression data from combo treated cells

treatment_protocol: Cells were treated with DMSO (vehicle), 500 nM PD-0325901, 1000uM JQ1, or the combination for 24 hours prior to harvest


title: MOLF PyMT 9884 PT  [WGS]

description: gDNA isolated from snap frozen tissue


title: CAST PyMT 10055 Lung met

description: gDNA isolated from flash frozen tissue


title: 2032

value: Lung tissue


title: H1573_JQ1_2

description: gene expression data from BRD4i treated cells


title: H1573_HOXC10_DMSO_1


title: H1573_JQ1_3


title: H1573_COMBO_2


title: MOLF PyMT 9884 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue


title: 2025


title: MOLF PyMT 10049 Lung met

description: gDNA isolated from flash frozen tissue


title: CAST PyMT 10055 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: H1573_JQ1_1


title: 2024

value: female


title: MOLF PyMT 10049 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: Genetically engineered / Autochthonous


title: CAST PyMT 10077 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: CAST/EiJ x FVBn/J


title: MOLF PyMT 10047 Lung met

description: gDNA isolated from flash frozen tissue


title: 2041

value: male


title: MOLF PyMT 2817 PT  [WGS]

description: gDNA isolated from snap frozen tissue


title: 2005


title: 2019


title: MOLF PyMT 10047 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: MOLF PyMT 2817 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue


title: H1573_COMBO_1


title: Male Second Thoracic Segment Wing Right 6

city: Bloomington

first: David

middle: M

last: Linz

state: IN

address: Myers Hall 3rd Street

institute: Indiana University

data_processing:
Trimming: Trimmomatic v0.32 parameters: ‘2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:36’
Alignment: Bowtie2 v2.3.2
Counting: RSEM v1.3.0
DE Analysis: DESeq2
Genome_build: O. taurus NCBI Genome Assembly v2.0 (GCF_000648695.1)

organism: Onthophagus taurus

source_name: Male Second Thoracic Segment Wing Right epithelium

extract_protocol:
Qiagen Rneasy Plus Micro Kit
Illumina TruSeq Stranded mRNA Sample Preparation Kit

value: T2 wing

value: Pre-pupae (larval stage)


title: DIP_8oxodG_exp2_G0-arrested MCF10A

city: Naples

first: Stefano

last: Amente

address: via pansini, 5

department: Department of  Molecular Medicine and Medical Biotechnologies

country: Italy

institute: University of Naples "FEDERICO II"

description:
G0-arrested MCF10A cells, exp2
8oxodG_peaks_G0-arrested_MCF10A.bed

data_processing:
Alignments were performed with BWA  to hg18 using default parameters.
The 8-oxodG peaks were identified from uniquely mapped reads without duplicates using MACS and the p-value<1e-5 with fold enrichment >7 were used as cutoff.
Genome_build: hg18
Supplementary_files_format_and_content: SAMtools and BEDtools were used for filtering steps and file formats conversion.

source_name: normal breast cells

growth_protocol: MCF10A cells were cultured in 1:1 mixture DMEM-F12 supplemented with 5% horse serum  for 48hrs and incubated at 37°C in humidified atmosphere with 5% CO2.

extract_protocol:
Genomic DNA from MCF10A cells was extracted by using Dneasy Blood&Tissue kit. Genomic DNA were sonicated and immunoprecipitated with antibodies anti 8-oxodG O/N. Eluted DNA was processed for library preparation.
Libraries were prepared according to Illumina's instructions

value: normal breast cell line MCF10A

tag: growth phase

tag: chip antibody


title: MOLF PyMT 10048 Lung met

description: gDNA isolated from flash frozen tissue


title: H1573_PD_3

description: gene expression data from MEKi treated cells


title: MOLF PyMT 31717 PT  [WGS]

description: gDNA isolated from snap frozen tissue


title: H1573_Vehicle_3

description: gene expression from vehicle treated cells


title: MOLF PyMT 10390 PT  [WGS]

description: gDNA isolated from snap frozen tissue


title: Male Second Thoracic Segment Wing Left 6

source_name: Male Second Thoracic Segment Wing Left epithelium


title: MOLF PyMT 31717 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue


title: DIP_8oxodG_exp1_repl1_G0-arrested MCF10A

description:
G0-arrested MCF10A cells, exp1, repl1
8oxodG_peaks_G0-arrested_MCF10A.bed


title: H1573_PD_1


title: Male First Thoracic Segment Horn 6

source_name: Male First Thoracic Segment Horn epithelium

value: First Thoracic Segment epithelium


title: DIP_8oxodG_exp1_repl2_G0-arrestedMCF10A

description:
G0-arrested MCF10A cells, exp1, repl2
8oxodG_peaks_G0-arrested_MCF10A.bed


title: Male First Thoracic Segment Dorsal 6

source_name: Male First Thoracic Segment Dorsal epithelium


title: H1573_PD_2


title: hyperreactive platelets

city: Yantai

first: Yeying

last: Sun

state: Shandong

address: Guanhai road No.346

institute: Binzhou medical univerisity

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Tophat v2.0.12 with default parameters
The Fragments per Kilobase of transcript per Million mapped reads (FPKM) were calculated using a protocol from Trapnell et al., nature biotechnology, 2010. FPKM calculation normalizes read count by dividing it by the gene length and the total number of reads mapped to protein-coding genes.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Homo sapiens

extract_protocol:
In order to classify platelets as hyporeactive or hypereactive blood was centrifuged for 15 minutes at 150g to obtain platelet-rich plasma (PRP). Platelet-poor plasma (PPP) were obtained at 400g for 5 minutes. The number of platelets in the PRP was counted using a hemocytometer and adjusted to 200000 and 250000 platelets/  µL using PPP. Platelet aggregation was measured using a Chrono-Log aggregometer(Chrono-Log, Havertown, PA, USA), using ADP (10 µM) as stimulators. Incubation time was 3 minutes at 37°C, stir bar speed was 1200 rpm, and sample run time was 10 minutes after addition of agonist (20 minutes for spontaneous aggregation). Maximal aggregation (%) was collected. The participants were categorized as having hyperreactive or hyporeactive platelets if the maximal aggregation in response to 10  µM ADP was > 60% or < 40%.
Platelets were isolated and purified density centrifugation and immune-depletion of CD45+ cells. RNA in platelets were extracted RNA with TRIzol.
RNA libraries were prepared for sequencing using NEB Next Ultra Directional RNA Library Prep Kit for Illumina

tag: reactivity

value: hyperreacitvity

value: platelets

value: blood


title: hyporeactive platelets

value: hyporeactivity


title: H1573_Vehicle_2


title: H1573_Vehicle_1


title: MOLF PyMT 10062 Lung met

description: gDNA isolated from flash frozen tissue

tag: oncogenic driver

value: PyMT

value: MOLF/EiJ x FVBn/J


title: MOLF PyMT 10062 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

source_name: Primary tumor

value: Primary tumor

tag: mouse id


title: MOLF PyMT 10061 Lung met

description: gDNA isolated from flash frozen tissue

value: Lung metastatic tumor


title: Male First Thoracic Segment Carinated Margin Right 6

source_name: Male First Thoracic Segment Carinated Margin Right epithelium


title: MOLF PyMT 10389 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue


title: MOLF PyMT 10387 PT  [WGS]

description: gDNA isolated from snap frozen tissue

value: primary tumor


title: MOLF PyMT 10387 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue


title: MOLF PyMT 10048 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: Male First Thoracic Segment Posterior Margin 6

source_name: Male First Thoracic Segment Posterior Margin epithelium


title: MOLF PyMT 10245 PT  [WGS]

description: gDNA isolated from snap frozen tissue


title: MOLF PyMT 10000 Lung met

description: gDNA isolated from flash frozen tissue


title: MOLF PyMT 10390 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue


title: Male First Thoracic Segment Anterior Margin 6

source_name: Male First Thoracic Segment Anterior Margin epithelium


title: MOLF PyMT 10389 PT  [WGS]

description: gDNA isolated from snap frozen tissue


title: MOLF PyMT 10245 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue


title: MOLF PyMT 10061 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: Male Abdominal Pupal Support Structures 6

source_name: Male Abdominal Pupal Support Structures epithelium

value: Abdominal epithelium


title: MOLF PyMT 10238 Lung met

description: gDNA isolated from flash frozen tissue

value: Genetically engineered / Autochthonous


title: Male Dorsal Head 6

source_name: Male Dorsal Head epithelium

value: Head epithelium


title: MOLF PyMT 10238 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue

source_name: Lung met


title: MOLF PyMT 10238 PT  [WGS]

description: gDNA isolated from snap frozen tissue


title: Male First Thoracic Segment Carinated Margin Left 6

source_name: Male First Thoracic Segment Carinated Margin Left epithelium


title: MOLF PyMT 10238 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: Male Second Thoracic Segment Wing Right 5


title: BL10 PyMT 9836 Lung met

description: gDNA isolated from flash frozen tissue

value: C57BL/10J x FVBn/J


title: Paternal age effects (12vs16m) on blastocysts transcriptome-rep3

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description: Biological replicates 3 of 4

hyb_protocol: The hybridization of microarray slides 4x44K printed with oligonucleotides by Agilent for all EmbryoGENE related projects using the expression array protocol.

scan_protocol: Scan on a PowerScanner (Tecan) using the autogain function. Images were quantified using ArrayPro version 6.3 (MediaCybernetics)

data_processing: Signal intensity data files were normalized and analyzed using the FlexArray 1.6.1 software (Genome Quebec, URL: http://genomequebec.mcgill.ca/FlexArray). The first step in the data processing was to remove the background of intensity files using a simple background subtraction. Data were then normalized for dye bias using a within-array loess and a between-array « quantile » normalization to minimize array effects. To calculate fold changes of probe intensity, normalized data were assessed using the e Bayes moderated t-test (LIMMA) included in the FlexArray software. A False Discovery Rate algorithm (Benjamini-Hochberg) was also applied.

organism: Bos taurus

source_name: blastocysts

label_protocol: The labelling aRNA was done using  the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: In vitro maturation, fertilization and culture of bovine embryos from slaughter ovaries. For more information, please refer to: Cagnone et al. 2012 Biol Reprod.

extract_protocol:
Total RNA and gDNA were extracted using the AllPrep DNA/RNA Micro Kit (Qiagen)
Amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Thermo Fisher).

tag: sample type

value: IVF with sperm from a 16 months old bull

value: IVF with sperm from a 12 months old bull


title: Male Second Thoracic Segment Wing Left 5

value: T2 wing

value: Pre-pupae (larval stage)


title: MOLF PyMT 10237 PT  [WGS]

description: gDNA isolated from snap frozen tissue

tag: model


title: Male First Thoracic Segment Posterior Margin 5

value: First Thoracic Segment epithelium


title: Paternal age effects (12vs16m) on blastocysts transcriptome-rep4

description: Biological replicates 4 of 4


title: FVB PyMT 10091 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: FVB/NJ x FVBn/J


title: Paternal age effects (12vs16m) on blastocysts transcriptome-rep2

description: Biological replicates 2 of 4


title: FVB PyMT 10091 Lung met

description: gDNA isolated from flash frozen tissue


title: MOLF PyMT 10237 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue


title: Male First Thoracic Segment Horn 5


title: TnBP2

city: Nanjing

first: Yang

last: Yang

state: Jiangsu

address: 163 Xianlin Avenue

institute: Nanjing University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
RSEM  is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model, including the modeling of paired-end (PE) and variable-length reads, fragment length distributions, and quality scores, to determine which transcripts are isoforms of the same gene. FPKM method is used in calculated expression level.
NOISeq method was applied to screen differentially expressed genes between two groups.
Genome_build: No reference genome was found in the NCBI, thus, we deeply sequenced the genome of earthworm and clean reads were de novo assembled into contigs using Trinitysoftware.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Eisenia fetida

source_name: Intestinal tissue

growth_protocol: Earthworms were obtained from a local farming factory (Jurong, China) and acclimatized at 20 ± 1°C for at least one week prior to experiments. After acclimatization, healthy adult earthworms with clear clitellum (weighing approximately 500-600 mg) were chosen for artificial soil test. Artificial soil tests were conducted in 1 L clear glass bottles with 500 g dry artificial soil (final soil moisture 35% (w/w)) following the OECD guidelines. After the prepared soil had stabilized at 20 ± 1°C for one week, 10 earthworms (acclimatized to artificial soil for 24 h) were placed in each container and kept in an incubator at 20 ± 1°C in the dark for 14 days.

extract_protocol:
RNA from each replicate was extracted using the Trizol reagent protocol (TaKaRa Biotechnology, China). The extracted RNA was qualified by 1% agarose gel electrophoresis and quantified by Nanodrop 2000 spectrophotometer (Thermo-Fisher Scientific, USA) with 260/280 ranging from 1.9 to 2.1 and a concentration > 10 ng/L.
RNA libraries were prepared according to the protocol from BGI

treatment_protocol: The intestinal tissues of nine earthworms were pooled into three replicates per treatment (three earthworms per replication) to obtain sufficient amounts of RNA for transcriptomic assessments.

value: Intestinal tissue

value: Exposed to 10 mg/kg TnBP


title: MOLF PyMT 10125 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue

value: PyMT


title: TnBP3


title: MOLF PyMT 10125 PT  [WGS]

description: gDNA isolated from snap frozen tissue

source_name: primary tumor

value: MOLF/EiJ x FVBn/J


title: Male First Thoracic Segment Dorsal 5


title: BL6 PyMT 9777 Lung met

description: gDNA isolated from flash frozen tissue

data_processing:
Library strategy: DNA-seq
Samples were trimmed of adapters using Trimmomatic software (0.39)
The trimmed reads were aligned to 316 the mm10 reference mouse genome using BWA (0.7.17) or Bowtie (2-2.3.5.1) mapping software
SAMtools (1.9) mpileup, 317 GATK (3.8-1) Mutect2, and Strelka (2.7.1) were used to identify potential variants and the variants were filtered for known 318 polymorphisms from mgp.v5 (ftp://ftp-mouse.sanger.ac.uk/current_snps /mgp.v5.merged.snps_ all.dbSNP142 .vcf.gz) and 319 variants with Phred-scaled quality score of < 30 were removed
Annotation was performed by Annovar (2018-04-16).
High probability SNVs were identified after reads were visualized in IGV and false positives were removed from the data. Select SNVs validated by Sanger sequencing performed by the CCR Genomics Core.
Genome_build: mouse mm19
Supplementary_files_format_and_content: vcf files include variants for each sample

extract_protocol:
Mice were bred and allowed to age until a humane endpoint was reached. Primary tumors and lung metastases were isolated and snap frozen in cryo vials using liquid nitrogen. Tissue was stored at -80 and gDNA was later isolated using the gDNA purification using ZR-Duet DNA/RNA MiniPrep kit from Zymo Research.  (cat.no. D7001)
Exome libraries were prepared using an Agilent SureSelectXT Mouse All Exon Kit for target enrichment. Libraries were barcoded and pooled before sequencing on an Illumina HiSeq3000 or HiSeq4000 to an average depth of 40x.

value: C57BL/6J  x FVBn/J


title: Paternal age effects (10vs16m) on blastocysts transcriptome-rep3

description: Biological replicates 3 of 4

value: IVF with sperm from a 10 months old bull


title: Male First Thoracic Segment Carinated Margin Right 5


title: MOLF PyMT 10077 PT  [WGS]

description: gDNA isolated from snap frozen tissue

value: primary tumor


title: TnBP1


title: MOLF PyMT 10077 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue

value: Lung metastatic tumor


title: BL10 PyMT 9836 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue

value: Primary tumor

value: Genetically engineered / Autochthonous


title: BL6 PyMT 9777 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: Male First Thoracic Segment Carinated Margin Left 5


title: Paternal age effects (10vs16m) on blastocysts transcriptome-rep4

description: Biological replicates 4 of 4


title: CK3

value: Control group


title: MOLF PyMT 10062 PT  [WGS]

description: gDNA isolated from snap frozen tissue


title: Paternal age effects (10vs16m) on blastocysts transcriptome-rep1

description: Biological replicates 1 of 4

value: IVF with sperm from a 16 months old bull


title: BL6 PyMT 9780 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: Male First Thoracic Segment Anterior Margin 5


title: CK2


title: BL6 PyMT 9780 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: Male Abdominal Pupal Support Structures 5

value: Abdominal epithelium


title: BL6 PyMT 10172 Primary tumor gDNA

description: gDNA isolated from flash frozen tissue


title: BL6 PyMT 10172 Lung met gDNA

description: gDNA isolated from flash frozen tissue


title: CK1


title: MOLF PyMT 10062 Lung met  [WGS]

description: gDNA isolated from snap frozen tissue