title: RNA of 5 mg/L NP for 180 min treatment, biological rep3

city: Istanbul

first: Ceyhun

last: Bereketoglu

address: Goztepe

country: Turkey

institute: Marmara University

hyb_protocol: The purification and fragmentation steps were carried out using GeneChip reagents and fragmented aRNA was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies). A total of 5 µg of aRNA was hybridized on arrays for 16-h at 45⁰C.The arrays were then loaded into a fluidics station for washing and staining using Aﬀymetrix Command Consoles Software (AGCC) 3.0.1 Fluidics Control Module with Mini_euk2v3.

scan_protocol: Arrays were scanned on an Aﬀymetrix GeneChip Scanner 3000.

data_processing: CEL files obtained from the analyzed arrays were normalized via quantile normalization using RMA as applied in the affy package of R/Bioconductor suite of tools for the analysis of transcriptomics data. Significantly expressed genes were identified from the normalized log-expression values using the multiple testing option of LIMMA .

organism: Saccharomyces cerevisiae

source_name: RNA of yeast cells exposed to 5 mg/L NP for 180 minutes

label_protocol: 100 ng of total RNA was used to synthesize first-strand cDNA and the first-stranded cDNA was converted into a double-stranded DNA with GeneChip 3’ IVT Express Kit (Affymetrix Inc). In vitro transcription and synthesis of biotin-labelled aRNA were performed using the double-stranded DNA as a template.

growth_protocol: YPD broth was inoculated with 1% of yeast pre-culture and incubated at 30⁰C, 180 RPM in incubator shaker

extract_protocol: Extraction of total RNA was performed with RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cultures at mid-exponential phase were treated with 1 mg/L and 5 mg/L NP prepared in ethanol while controls were treated with the same volume of ethanol for 120 and 180 minutes.

tag: strain


title: ko_contr_3mon_septa_rep3

status: Public on Mar 01 2020

type: RNA

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with GenePix software V5.2 (MDS).

data_processing: Raw data was further processed using R and limma. Mean spot intensities were background corrected with the function nec and quantile normalized.

molecule: total RNA

organism: Mus musculus

source_name: knock-out, control, 3 months, smoke-exposedpta, replicate 3

label_protocol: Purified total RNA was amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Bemmel, Netherlands). Per sample, 2µg amplified cDNA was Cy-labeled using the SureTag DNA labeling kit (Agilent, Waldbronn, Germany).

growth_protocol: Mice  (C57BL/6-Noxo1(tm1881_17.2Arte)) were grown under standard conditions with a.d. food and water supply in standard cages with 5 animals per cage. From week 12 mice were exposed to smoke for 8 months.

extract_protocol: QIAgen RNeasy Micro Kit

treatment_protocol: Mice are exposed to cigarette smoke (Kentucky 3R4FTabacco Research cigarettes; smoke generator RGB01 (Burkhart, Hamburg, Germany)  over 8 months for 5 days per week and 6h per day with a particle concentration of 140 mg/m³.

tag: mouse id


title: sarcoma classifier reference case 295

type: genomic

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

institute: University Hospital Heidelberg, Intitute of Pathology

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 295

hyb_protocol: Illumina protocol

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

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

molecule: genomic DNA

organism: Homo sapiens

source_name: sarcoma sample

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

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

tag: tissue

value: sarcoma

tag: material preparation

value: KRYO


title: fetal_before_5_G12

type: SRA

city: Uppsala

first: Asa

middle: Kristina

last: Bjorklund

address: Box 596

department: Cell and Molecular Biology

country: Sweden

institute: Uppsala University

library_source: transcriptomic

data_processing:
All reads were aligned to the human (hg19) genome using STAR v2.3.0e (Dobin et al. 2013)
Non-uniquely mapped reads were removed using Samtools
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in Ensembl ( June 2015)
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values are provided as rpkms and counts (comma separated text files)

molecule: polyA RNA

source_name: Cell culture

growth_protocol: Ventral midbrain human embryonic stem cells have been generated following the Nature protocols: Nolbrant et al 2017.

extract_protocol:
Single cells have been extracted from tissue using Papain Dissociation System (Worthington). cDNA was generated from FACS sorted single cells (ventral midbrain human embryonic stem cells before grafting, fetal cells before and after grafting were sorted for size, ventral midbrain human embryonic stem cells after grafting were sorted for GFP expression) using Smart-seq2 protocol (Picelli et al. Nature Methods 2013).  ERCC spike-in RNA was added to the lysis buffer.
Nextera XT DNA sample preparation index kit, 96 indices (Illumina)

tag: cell type

value: Fetal

tag: sortingmethod

value: size

tag: plate


title: sarcoma classifier reference case 447

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 447

value: FFPE


title: sarcoma classifier reference case 294

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 294


title: sarcoma classifier reference case 446

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 446


title: fetal_before_5_G11


title: sarcoma classifier reference case 293

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 293


title: ko_contr_3mon_septa_rep2

source_name: knock-out, control, 3 months, smoke-exposedpta, replicate 2


title: sarcoma classifier reference case 445

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 445


title: fetal_before_5_G2


title: fetal_before_5_G10


title: sarcoma classifier reference case 292

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 292


title: sarcoma classifier reference case 291

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 291


title: sarcoma classifier reference case 443

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 443


title: fetal_before_5_F9


title: fetal_before_5_F6


title: RNA of 5 mg/L NP for 180 min treatment, biological rep2

label: biotin


title: fetal_before_5_F8


title: sarcoma classifier reference case 442

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 442


title: RNA of 1 mg/L NP for 180 min treatment, biological rep2

source_name: RNA of yeast cells exposed to 1 mg/L NP for 180 minutes


title: sarcoma classifier reference case 290

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 290


title: sarcoma classifier reference case 289

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 289


title: RNA of 1 mg/L NP for 180 min treatment, biological rep1


title: sarcoma classifier reference case 441

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 441


title: fetal_before_5_F5


title: RNA of 1 mg/L NP for 180 min treatment, biological rep3


title: sarcoma classifier reference case 288

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 288


title: sarcoma classifier reference case 440

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 440


title: sarcoma classifier reference case 439

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 439


title: fetal_before_5_F3


title: fetal_before_5_F2


title: sarcoma classifier reference case 287

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 287


title: RNA of 5 mg/L NP for 180 min treatment, biological rep1


title: control RNA for 180 min treatment, biological rep3

source_name: RNA of yeast cells exposed to no NP for 180 minutes


title: sarcoma classifier reference case 444

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 444


title: control RNA for 180 min treatment, biological rep2


title: sarcoma classifier reference case 286

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 286


title: fetal_before_5_F12


title: sarcoma classifier reference case 438

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 438


title: sarcoma classifier reference case 437

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 437


title: fetal_before_5_F11


title: control RNA for 180 min treatment, biological rep1


title: RNA of 5 mg/L NP for 120 min treatment, biological rep3

source_name: RNA of yeast cells exposed to 5 mg/L NP for 120 minutes


title: sarcoma classifier reference case 284

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 284


title: sarcoma classifier reference case 436

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 436


title: fetal_before_5_F10


title: RNA of 5 mg/L NP for 120 min treatment, biological rep2


title: RNA of 5 mg/L NP for 120 min treatment, biological rep1


title: sarcoma classifier reference case 283

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 283


title: fetal_before_5_E9


title: RNA of 1 mg/L NP for 120 min treatment, biological rep3

source_name: RNA of yeast cells exposed to 1 mg/L NP for 120 minutes


title: sarcoma classifier reference case 429

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 429


title: RNA of 1 mg/L NP for 120 min treatment, biological rep2


title: RNA of 1 mg/L NP for 120 min treatment, biological rep1


title: sarcoma classifier reference case 282

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 282


title: fetal_before_5_E7


title: sarcoma classifier reference case 428

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 428


title: sarcoma classifier reference case 285

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 285


title: control RNA for 120 min treatment, biological rep3

source_name: RNA of yeast cells exposed to no NP for 120 minutes


title: sarcoma classifier reference case 280

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 280


title: fetal_before_5_E6


title: sarcoma classifier reference case 427

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 427


title: sarcoma classifier reference case 426

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 426


title: Cardiff_CTL33n1_83_A_2

city: Cambridge

first: Maxwell

last: Gold

state: MA

address: 21 Ames St

country: USA

institute: MIT

library_source: genomic

data_processing:
fastq files were aligned to hg38 genome assembly using Bowtie2
The ENCODE blacklist regions and PCR duplicates were removed (using SAMtools and Picard)
Peak calling was done using MACS2 (--nomodel –shift -100 –extsize 200 settings and q-value<0.05)
The consensus peak file for all samples was generated using Diffbind
Genome_build: hg38
Supplementary_files_format_and_content: bed files for read density at specific loci

source_name: medium spiny neuron-like

growth_protocol: iPSC were grown and matrigel and in mTESR and then differentiated into medium spiny neuron-like cells using a combination of growth factors, growth medium, and chemical inhibitors

extract_protocol:
DNA was purified from iMNs using the DNeasy Blood & Tissue Kit (Qiagen), according to the manufacturer’s instructions (as described in pubmed 27146274)
DNA were prepared for high-throughput sequencing according to Illumina's instructions and sequenced on an Illumina platform following the manufacturer’s standard protocol (as described in pubmed 27146274)

value: medium spiny neuron-like

tag: diagnosis

value: Control patient


title: control RNA for 120 min treatment, biological rep1


title: Cardiff_CTL33n1_83_A_3


title: sarcoma classifier reference case 425

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 425


title: fetal_before_5_E3


title: sarcoma classifier reference case 424

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 424


title: Cardiff_CTL18n6_25_A_3


title: sarcoma classifier reference case 279

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 279


title: sarcoma classifier reference case 278

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 278


title: fetal_before_5_E11


title: sarcoma classifier reference case 277

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 277


title: Cardiff_CTL18n2_25_A_3


title: Cardiff_CTL18n6_25_A_2


title: fetal_before_5_E1


title: sarcoma classifier reference case 281

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 281


title: sarcoma classifier reference case 276

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 276


title: Cardiff_CTL18n2_25_A_2


title: sarcoma classifier reference case 423

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 423


title: fetal_before_5_D8


title: control RNA for 120 min treatment, biological rep2


title: sarcoma classifier reference case 422

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 422


title: Cardiff_CTL28n6_14_A_3


title: fetal_before_5_E4


title: fetal_before_5_D7


title: sarcoma classifier reference case 275

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 275


title: sarcoma classifier reference case 274

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 274


title: sarcoma classifier reference case 421

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 421


title: sarcoma classifier reference case 420

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 420


title: fetal_before_5_D6


title: Cardiff_CTL28n6_14_A_2


title: sarcoma classifier reference case 273

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 273


title: Cardiff_HD46n10_04_A_3

value: Huntington's Disease


title: sarcoma classifier reference case 419

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 419


title: sarcoma classifier reference case 272

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 272


title: Cardiff_HD46n10_04_A_2


title: fetal_before_5_D5


title: sarcoma classifier reference case 271

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 271


title: sarcoma classifier reference case 416

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 416


title: fetal_before_5_D2


title: Cardiff_HD53n3_03_A_2


title: fetal_before_5_D12


title: Cardiff_HD53n3_03_A_3


title: sarcoma classifier reference case 415

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 415


title: sarcoma classifier reference case 270

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 270


title: fetal_before_5_C9


title: sarcoma classifier reference case 399

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 399


title: sarcoma classifier reference case 269

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 269


title: fetal_before_5_C8


title: Cardiff_HD46n10_04_C_3

description:
HD_46n10_rep2
MarkDuplicates_on_data_127

data_processing:
fastq files were aligned to the hg38 genome assembly using Bowtie2
The ENCODE blacklist regions and PCR duplicates were removed (using SAMtools and Picard)
Peak calling was done using MACS2 (--broad flag, q-value<0.1)
Genome_build: hg38
Supplementary_files_format_and_content: bed files for read density at specific loci

source_name: HD Sample H3K4me3 ChIP-Seq

extract_protocol:
Chromatin was digested with 150 units of MNase (NEB, M0247S) for 10min at 37°C. The digestion reaction was stopped with 10mM EDTA. The chromatin was incubated with 1ul of k4me3 (Millipore, 07-473) overnight and 20ul of Protein G beads (ThermoFisher, 10004D) were added for 2hr incubation at 4°C on the following day
Immunoprecipitated DNA and nonspecific IgG-bound DNA were prepared for high-throughput sequencing according to Illumina's instructions and sequenced on an Illumina platform following the manufacturer’s standard protocol.

tag: subject status

value: huntington's disease (HD)

value: iPSC-derived medium spiny neuron-like cells

tag: chip antibody

value: H3K4me3 (Millipore, 07-473)


title: sarcoma classifier reference case 268

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 268


title: Cardiff_HD53n3_03_C_5

description:
HD_53n3_rep5
MarkDuplicates_on_data_126


title: fetal_before_5_C7


title: sarcoma classifier reference case 387

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 387


title: sarcoma classifier reference case 267

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 267


title: Cardiff_HD53n3_03_C_4

description:
HD_53n3_rep4
MarkDuplicates_on_data_125


title: fetal_before_5_C6


title: Cardiff_HD46n10_04_C_2

description:
HD_46n10_rep1
MarkDuplicates_on_data_124


title: sarcoma classifier reference case 266

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 266


title: sarcoma classifier reference case 417

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 417


title: sarcoma classifier reference case 320

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 320


title: Cardiff_HD53n3_03_C_3

description:
HD_53n3_rep3
MarkDuplicates_on_data_123


title: fetal_before_5_C4


title: fetal_before_5_C3


title: sarcoma classifier reference case 319

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 319


title: sarcoma classifier reference case 264

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 264


title: sarcoma classifier reference case 263

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 263


title: Cardiff_HD53n3_03_C_1

description:
HD_53n3_rep1
MarkDuplicates_on_data_121


title: fetal_before_5_C2


title: fetal_before_5_C12


title: sarcoma classifier reference case 317

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 317


title: sarcoma classifier reference case 318

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 318


title: sarcoma classifier reference case 454

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 454


title: fetal_before_5_C11


title: sarcoma classifier reference case 262

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 262


title: sarcoma classifier reference case 316

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 316


title: sarcoma classifier reference case 261

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 261


title: Cardiff_CTL33n1_83_C_3

description:
CTR_33n1_rep3
MarkDuplicates_on_data_116

source_name: Control Sample H3K4me3 ChIP-Seq

value: control


title: Cardiff_CTL18n2_25_C_3

description:
CTR_18n2_rep2
MarkDuplicates_on_data_117


title: sarcoma classifier reference case 315

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 315


title: Cardiff_CTL18n2_25_C_2

description:
CTR_18n2_rep1
MarkDuplicates_on_data_115


title: Cardiff_HD53n3_03_C_2

description:
HD_53n3_rep2
MarkDuplicates_on_data_122


title: sarcoma classifier reference case 259

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 259


title: Cardiff_CTL18n6_25_C_3

description:
CTR_18n6_rep2
MarkDuplicates_on_data_114


title: sarcoma classifier reference case 386

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 386


title: sarcoma classifier reference case 258

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 258


title: fetal_before_5_B8


title: fetal_before_5_C1


title: sarcoma classifier reference case 260

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 260


title: sarcoma classifier reference case 265

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 265


title: sarcoma classifier reference case 314

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 314


title: Cardiff_CTL33n1_83_C_2

description:
CTR_33n1_rep2
MarkDuplicates_on_data_112


title: sarcoma classifier reference case 313

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 313


title: sarcoma classifier reference case 312

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 312


title: sarcoma classifier reference case 257

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 257


title: fetal_before_5_B5


title: sarcoma classifier reference case 311

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 311


title: sarcoma classifier reference case 256

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 256


title: fetal_before_5_C10


title: fetal_before_5_B4


title: sarcoma classifier reference case 310

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 310


title: Cardiff_CTL18n6_25_C_2

description:
CTR_18n6_rep1
MarkDuplicates_on_data_111


title: fetal_before_5_B2


title: sarcoma classifier reference case 255

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 255


title: sarcoma classifier reference case 309

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 309


title: sarcoma classifier reference case 254

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 254


title: sarcoma classifier reference case 308

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 308


title: Cardiff_CTL28n6_14_C_3

description:
CTR_28n6_rep3
MarkDuplicates_on_data_113


title: sarcoma classifier reference case 252

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 252


title: sarcoma classifier reference case 253

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 253


title: fetal_before_5_B7


title: sarcoma classifier reference case 306

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 306


title: sarcoma classifier reference case 307

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 307


title: fetal_before_5_B11


title: Cardiff_CTL33n1_83_C_1

description:
CTR_33n1_rep1
MarkDuplicates_on_data_108


title: fetal_before_5_B10


title: sarcoma classifier reference case 251

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 251


title: sarcoma classifier reference case 305

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 305


title: S_1_preN

city: Hannover

last: Sedding

address: Carl-Neubergstr. 1

department: Cardiology

institute: Hannover Medical School

description: readcount.txt

data_processing:
Libraries were fed into Illumina HiSeq machines
Original data were transformed to Sequence Readss by base calling.
Error rates were transformed by the Phred scores.
GC content distribution was evaluated and reads were filtered.
Mapping to a reference genome was performed using TopHat2.
Visualization of Mapping status was generated by the Integrative Genomic Viewer (IGV)
HTSeq software was used to analyze gene expression using the union mode.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data file was generated by Novogene.

source_name: Human coronary artery mooth muscle cells, lonza, Basel, Switzerland

growth_protocol: SMC were cultured in smooth muscle cell growth medium with supplements (2000601, 2010601, Provitro, Berlin, Germany).  Cells were maintained at 37°C and 5% CO2. Primary cells between passage 3 and 5 were used for all experiments. Cells were routinely split at a 1:3 ratio and cultured to subconfluence.

extract_protocol:
RNA was isolated by Novogene and quality control was performed using a nanodrop device, agarose gel electrophoresis and a bioanalyzer integrity control (Agilent 2100).
mRNA was enriched using oligo(dT) beads and fragmented randomly in fragmentation buffer. cDNA was synthesized using random hexamers and reverse transcriptase. A second-strand synthesis buffer (Illumina) was added to generate the second strand by nick-translation. The final cDNA library was generated after purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment (all performed by Novogene)

treatment_protocol: Transient transfection of synthetic precursor miRNAs (pre-miRs; Ambion ®) was performed according to the manufacturer’s instructions. Briefly, cells were split 1-3 days before transfection to reach 70% confluence. Constructs were mixed with Lipofectamine® 2000 (Thermo Fisher Scientific, MA, USA) and incubated in Opti-MEM® I media (31985-047, Gibco, Thermo Fisher Scientific, MA, USA). Cells were suspended in antibiotic-free media before addition of liposomal complexes . Cells were incubated for 8 hours before the media was changed to fresh media containing 10 % FCS. Cells were scraped in RLT buffer (Qiagen, Hilden, Germany) and RNA was isolated by Novogene.

value: smooth muscle cells

tag: passage

value: between passages 3 and 5

tag: transfection

value: pre-negative 50 nM (AM17110, Negative Control #1, Ambion, Thermo Fisher, MA, USA)

tag: transfection agent

value: Lipofectamine 2000

tag: genotype


title: fetal_before_5_B1


title: sarcoma classifier reference case 250

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 250


title: Cardiff_CTL28n6_14_C_1

description:
CTR_28n2_rep1
MarkDuplicates_on_data_109


title: S_2_p146

description: readcount.txt

value: pre-miR-146a 50nM (AM17110/PM10722, Ambion, Thermo Fisher, MA, USA)

value: miRNA-146a overexpression


title: sarcoma classifier reference case 249

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 249

value: sarcoma

value: KRYO


title: fetal_before_5_B12

value: Fetal

value: size


title: sarcoma classifier reference case 304

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 304


title: fetal_before_5_A9


title: H_5_pNeg

data_processing:
Libraries were fed into Illumina HiSeq machines
Original data were transformed to Sequence Reads by base calling.
Error rates were transformed by the Phred scores.
GC content distribution was evaluated and reads were filtered.
Mapping to a reference genome was performed using TopHat2.
Visualization of Mapping status was generated by the Integrative Genomic Viewer (IGV)
HTSeq software was used to analyze gene expression using the union mode.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files were generated by Novogene.

source_name: HUVEC

growth_protocol: HUVEC were cultured in EGM2 media with supplements (CC-3156, CC-4147, Lonza, Basel, Switzerland).  Cells were maintained at 37°C and 5% CO2. Primary cells between passage 3 and 5 were used for all experiments. Cells were routinely split at a 1:3 ratio and cultured to subconfluence.

value: HUVEC


title: fetal_before_5_A8


title: sarcoma classifier reference case 303

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 303

value: FFPE


title: H_4_p146


title: fetal_before_5_A7


title: H_6_p146


title: Cardiff_CTL28n6_14_C_2

description:
CTR_28n6_rep2
MarkDuplicates_on_data_110


title: H_3_preN


title: fetal_before_5_A6


title: Global mapping of binding sites of Nrf2 in SAS sphere cells

city: Taipei

first: Jeng-Fan

last: Lo

address: No. 155, Section 2, Li-Nong Street, Taipei, 11221, Taiwan

country: Taiwan

institute: National Yang-Ming University

description: Sample SS Nrf2 (csv)

data_processing:
Basecalls performed using RTA1.17.21.3_CAS1.8.2
ChIP-seq reads were aligned to the GRCh38 genome assembly using CLC Genomics Workbench v7.5 with the following configurations:
Adaptor quality checked using CLC Genomics Workbench v7.5
Reads were aligned to GRCh38 using CLC Genomics Workbench v7.5
Aligned reads were sorted with CLC Genomics Workbench v7.5
Number of reads was counted using  CLC Genomics Workbench v7.5
Genome_build: GRCh38
Supplementary_files_format_and_content: Window size used for peak calling. Tab-delimited text files (CSV) include Region site,  Length and P-value.

source_name: HNSCC

growth_protocol: Cells were seeded at a density of 7.5×10e4 live cells/10-mm dish in defined selection medium (DMEM/F12 medium (GIBCO) containing with N2 supplement (GIBCO), 10 ng/mL human recombinant basic fibroblast growth factor-basic (FGF) and 10 ng/mL Epidermal Growth Factor (EGF) (R&D Systems, Minneapolis, MN). The medium was changed every other day until the sphere formation was achieved by approximately 4 weeks

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: HNSCC sphere cells

value: Nrf2 (Abcam, catalog number:sc-722X, lot/batch number:H2013)


title: sarcoma classifier reference case 246

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 246


title: sarcoma classifier reference case 245

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 245


title: sarcoma classifier reference case 247

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 247


title: Global mapping of binding sites of Nrf2 in SAS sphere cells_Input

description: Sample SS Nrf2 (csv)


title: Global mapping of binding sites of Nrf2 in SAS cells

description: Sample S Nrf2 (csv)

value: HNSCC parental cells


title: fetal_before_5_A3


title: sarcoma classifier reference case 244

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 244


title: fetal_before_5_A2


title: Global mapping of binding sites of Nrf2 in SAS cells_Input

description: Sample S Nrf2 (csv)


title: B6_liver_009

city: Nuthetal

first: Pascal

last: Gottmann

address: Arthur-Scheunert-Allee 114-116

institute: Deutsches Institut für Ernährungsforschung

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-014868 Whole Mouse Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities. Data was filtered using 0.1 quantile cutoff to eliminate low level signals.

source_name: high fat diet

label_protocol: Cy3-labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit from Agilent according to the manufacturer's instructions, followed by RNeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from murine tissue using TRIzol™ reagent (Invitrogen, Germany). From parental NZO and B6 mice (6 weeks of age), samples of liver were aliquoted for RNA extraction. The procedure was carried out according to manufacturer’s instructions. RNA quality was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Germany) and the manufacturer’s instructions were followed to measure RNA integrity (RIN). Samples with RIN values >8 were subsequently selected for microarray analysis.

treatment_protocol: Mice were fed a high fat diet (45%, fat, Research Diets)

value: liver

tag: gender

value: male

tag: age

value: 6 weeks-old


title: sarcoma classifier reference case 248

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 248


title: sarcoma classifier reference case 243

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 243


title: fetal_before_5_A10


title: fetal_before_5_A12


title: B6_liver_015


title: sarcoma classifier reference case 241

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 241


title: sarcoma classifier reference case 242

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 242


title: fetal_before_5_A1


title: B6_liver_010


title: sarcoma classifier reference case 239

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 239


title: fetal_before_4_H8


title: B6_liver_011


title: sarcoma classifier reference case 238

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 238


title: fetal_before_4_H3


title: sarcoma classifier reference case 236

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 236


title: sarcoma classifier reference case 237

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 237


title: NZO_liver_003

value: NZO/HiBomDife


title: NZO_liver_007


title: RC17_after_mesDA_4_B8

source_name: Human graft in rat brain

value: R

value: GFP


title: sarcoma classifier reference case 240

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 240


title: sarcoma classifier reference case 235

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 235


title: RC17_after_mesDA_4_B7


title: fetal_before_4_H9


title: NZO_liver_009


title: RC17_after_mesDA_4_B9


title: RC17_after_mesDA_4_B6


title: NZO_liver_011


title: fetal_before_4_H6


title: sarcoma classifier reference case 233

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 233


title: RC17_after_mesDA_4_B5


title: RC17_after_mesDA_4_B4


title: sarcoma classifier reference case 232

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 232


title: RC17_after_mesDA_4_B3


title: sarcoma classifier reference case 231

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 231


title: sarcoma classifier reference case 230

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 230


title: RC17_after_mesDA_4_B12


title: sarcoma classifier reference case 229

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 229


title: sarcoma classifier reference case 228

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 228


title: sarcoma classifier reference case 234

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 234


title: RC17_after_mesDA_4_B2


title: sarcoma classifier reference case 227

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 227


title: RC17_after_mesDA_4_B11


title: AGM V+61+E+ bulk engineered culture

city: Seattle

first: Brandon

last: Hadland

state: WA

address: 1100 Fairview Avenue N., D2-115, P.O. Box 19024

institute: Fred Hutchinson Cancer Research Center

description:
Sample12
scRNA-seq (10X V2)
sample11-12.RDS
sample11-12_P.RDS

data_processing:
The Cell Ranger 2.1.1 pipeline (10X Genomics) was used to align reads to the mm10 reference genome and generate feature barcode matrix, filtering low-quality cells using default parameters.
The Monocle (v.2.99.3) platform was used for downstream analysis, combining read-depth normalized data across samples where applicable
Genome_build: mm10
Supplementary_files_format_and_content: 10X Cell Ranger output files in filtered feature-barcode matrix: "genes.tsv" contains gene information, "barcodes.tsv" contains cellular barcodes, and "matrix.mtx" contains a sparse matrix of UMIs
Supplementary_files_format_and_content: Monocle cell data set files: "SampleX.RDS" contains monocle cell data sets for sample(s) X imported from 10Xoutput files; "SampleX_P.RDS" contains cell data set for sample(s) X following pre-processing, dimensionality reduction, and clustering steps

source_name: Hematopoietic cells

growth_protocol: Cultured cells were grown in the presence of serum-free media (X-vivo 20, with recombinant stem cell factor (SCF) at 100 ng/ml, and interleukin-3 (IL-3) and thrombopoietin (TPO) each at 20 ng/ml, for co-culture)

extract_protocol:
FACS-isolated primary cells or cultured cells harvested by trypsinization (for AGM-EC) or pipetting (for co-cultured hematopoietic cells) were washed with PBS/0.04% ultrapure BSA, and resuspended in PBS/BSA for loading into the 10X Genomics Chromium Single Cell B Chip, and processed in the Chromium single cell controller
The 10X Genomics Version 2 single cell 3’ kit was used to prepare single cell mRNA libraries with the Chromium i7 Multiplex Kit, according to manufacturer protocols.  Sequencing was performed for pooled libraries from each sample on an Illumina NextSeq 500 using the 75 cycle, high output kit

tag: cell type(s)

value: Hematopoietic cells-cultured


title: AGM V+61+E+ bulk EC co-culture

description:
Sample11
scRNA-seq (10X V2)
sample11-12.RDS
sample11-12_P.RDS

tag: strain


title: RC17_after_mesDA_4_B10


title: sarcoma classifier reference case 226

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 226

source_name: sarcoma sample


title: sarcoma classifier reference case 225

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 225


title: RC17_after_mesDA_4_A8


title: AGM V+61+E+ EC co-culture 1

description:
Sample9
scRNA-seq (10X V2)
sample9.RDS
sample9_P.RDS


title: RC17_after_mesDA_4_B1


title: EB227 D492M 3D Well 5

city: Baltimore

first: Winston

last: Timp

state: MD

address: 3400 N. Charles St. Clark 102A

department: Biomedical Engineering

institute: Johns Hopkins University

description: D492M is derived from D492 after endothelial induced EMT

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: iScan system according to standard Illumina Protocol

data_processing: minfi (Bioconductor) processing of idat files

label: Cy5 and Cy3

source_name: genomic DNA from D492M cell line cultured in reconstituted basement membrane matrix (3D rBM)

label_protocol: Standard Illumina Protocol

growth_protocol: D492 (10000 cells) and D492M (25000 cells) were grown in 3D-rBM in triplicate in a 24-well plate for 14 days

extract_protocol: Colonies were extracted from 3D-rBM with gentle shaking on ice in PBS - EDTA (5 mM) solution. DNA was extracted using the PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific, #K182002) according to standard instructions.

tag: cell line

tag: phenotype

value: mesenchymal


title: sarcoma classifier reference case 224

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 224

tag: tissue

value: sarcoma

tag: material preparation


title: E11 AGM V+61+E+ primary s2

description:
Sample8
scRNA-seq (10X V2)
sample5-8.RDS
sample5-8_P.RDS

source_name: Hemogenic/endothelial cells

value: Hemogenic/endothelial cells-primary

tag: developmental stage


title: RC17_after_mesDA_4_A7

tag: cell type

tag: sortingmethod

tag: plate


title: AGM V+61+E+ EC co-culture 2

description:
Sample10
scRNA-seq (10X V2)
sample10.RDS
sample10_P.RDS


title: EB227 D492 3D Well 2

description: D492 is a breast epithelial cell line with stem cell properties

source_name: genomic DNA from D492 cell line cultured in reconstituted basement membrane matrix (3D rBM)

value: epithelial


title: EB227 D492 3D Well 3


title: EB227 D492 3D Well 1


title: RC17_after_mesDA_4_A6


title: sarcoma classifier reference case 223

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 223


title: EB227 D492M 3D Well 6


title: EB227 D492M 3D Well 4


title: E10 AGM V+61+E+ primary s2

description:
Sample6
scRNA-seq (10X V2)
sample5-8.RDS
sample5-8_P.RDS


title: sarcoma classifier reference case 222

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 222


title: E10 AGM V+61+E+ primary s1

description:
Sample5
scRNA-seq (10X V2)
sample5-8.RDS
sample5-8_P.RDS


title: sarcoma classifier reference case 221

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 221


title: RC17_after_mesDA_4_A5


title: AGM-EC4

description:
Sample4
scRNA-seq (10X V2)
sample1-4.RDS
sample1-4_P.RDS

source_name: Endothelial cells

value: Endothelial cells-cultured


title: RC17_after_mesDA_4_A4


title: AGM-EC3

description:
Sample3
scRNA-seq (10X V2)
sample1-4.RDS
sample1-4_P.RDS


title: RC17_after_mesDA_4_A2


title: RC17_after_mesDA_4_A12


title: sarcoma classifier reference case 220

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 220


title: sarcoma classifier reference case 218

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 218


title: AGM-EC2

description:
Sample2
scRNA-seq (10X V2)
sample1-4.RDS
sample1-4_P.RDS


title: RC17_after_mesDA_4_A10


title: E11 AGM V+61+E+ primary s1

description:
Sample7
scRNA-seq (10X V2)
sample5-8.RDS
sample5-8_P.RDS


title: AGM-EC1

description:
Sample1
scRNA-seq (10X V2)
sample1-4.RDS
sample1-4_P.RDS


title: sarcoma classifier reference case 217

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 217


title: RC17_after_mesDA_4_A1


title: Liver, GenX, 5mg/kg, 455

city: Austin

first: Grace

last: Chappell

state: TX

address: 9390 Research Blvd, Bldg 2, Ste. #100

department: Health Sciences

institute: ToxStrategies, Inc.

description: RNA extracted from FFPE tissue

data_processing:
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing
fastqs were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated text file includes raw count values for each gene_probe

source_name: FFPE liver

growth_protocol: Mice were housed and administered test compounds at Charles River Laboratories

extract_protocol:
Formalin-fixed, paraffin-embedded liver tissue was scraped from sections mounted to glass slides directly into lysis buffer.
The TempO-Seq (BioSpyder Industries) targeted expression assay protocol was followed for whole transcriptome library construction using targeted oligomers

treatment_protocol: Male and female Crl:CD1(ICR) mice were exposed to 0, 0.1, 0.5, or 5 mg GenX/kg bw/day by oral gavage for 90 days. The study was conducted at E.I. du Pont de Nemours and Company, DuPont Haskell Global Centers for Health & Environmental Sciences (Delaware, USA) in compliance with all applicable sections of the Final Rules of the Animal Welfare Act regulations (9CFR) and the Guide for the Care of Use of Laboratory Animals (NRC 1996). The study design complied with OECD Section 4 Part 408: Repeated Dose Oral Toxicity Study in Rodents, Guidelines for Testing of Chemicals (1998). Animals were housed individually and were provided tap water and PMI® Nutritional International, LLC Certified Rodent LabDiet® 5002 ad libitum. Doses were formulated in deionized water and prepared weekly and verified analytically.

tag: treatment

value: GenX

tag: concentration

tag: Sex

value: female

value: wildtype


title: sarcoma classifier reference case 219

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 219

value: FFPE


title: IC450S_SNP6

city: East Melbourne

first: Kylie

middle: L

last: Gorringe

state: Victoria

address: St Andrew's Pl

department: Research Division

country: Australia

institute: Peter MacCallum Cancer Centre

description: Sample name: IC450S

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CHP files were generated using the Affymetrix Genotyping Console algorithm Birdseed v2. Total and allele-specific copy number analysis was performed using Partek Genomics Suite 6.5, using both paired copy number generation.
OncoScan MIP arrays were analyzed using Nexus
CEL and CHP files are provided for each sample in the study (Affymetrix SNP 6); normalized data is provided for OncoScan MIP arrays (Each sample has 5 columns: Copy A, Copy B, Copy number, Allele ratio and Allelic difference).

label: Biotin

source_name: Ovarian serous adenomafibroma

label_protocol: As per manufacturer's recommendations (Affymetrix)

extract_protocol: Genomic DNA was extracted from tissues (epithelium and stroma) microdissected mucinous ovarian tumors stained with haematoxylin and eosin, and from lymphcoytes obtained from peripheral blood (for matched normal DNA)  using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and Qubit.

value: tumor stroma

tag: tumor histology

value: Serous adenofibroma

tag: diagnosis

value: Benign serous adenofibroma


title: sarcoma classifier reference case 216

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 216


title: IC591G_SNP6

description: Sample name: IC591G

source_name: Lymphocyte DNA

value: Peripheral Blood Lymphocytes

value: Serous cystadenoma

value: Benign serous cystadenoma


title: IC458S_SNP6

description: Sample name: IC458S

source_name: Ovarian fibroma

value: Fibroma

value: Benign fibroma


title: sarcoma classifier reference case 215

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 215


title: RC17_after_mesDA_3_H8

value: R

value: GFP


title: IC196S_SNP6

description: Sample name: IC196S

source_name: Ovarian serous cystadenoma

value: Ovarian serous cystadenoma


title: IC164G_SNP6

description: Sample name: IC164G

value: Serous cystadenofibroma

value: Benign serous cystadenofibroma


title: IC494S_SNP6

description: Sample name: IC494S


title: Liver, GenX, 5mg/kg, 454

description: RNA extracted from FFPE tissue

value: liver

value: GenX

tag: genotype


title: IC164S_SNP6

description: Sample name: IC164S

source_name: Ovarian serous cystadenofibroma


title: IC591S_SNP6

description: Sample name: IC591S


title: IC450G_SNP6

description: Sample name: IC450G


title: IC181S_SNP6

description: Sample name: IC181S


title: RC17_after_mesDA_3_H6


title: IC425S_SNP6

description: Sample name: IC425S


title: RC17_after_mesDA_3_H4


title: RC17_after_mesDA_3_H7


title: sarcoma classifier reference case 212

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 212

value: sarcoma


title: IC149S_SNP6

description: Sample name: IC149S


title: IC269S_SNP6

description: Sample name: IC269S


title: Liver, GenX, 5mg/kg, 405

description: RNA extracted from FFPE tissue

value: male

value: wildtype


title: IC369S_SNP6

description: Sample name: IC369S

source_name: Normal ovary

value: Ovarian stroma

value: Normal ovary


title: Dof3.2-GR DEX replicate2

city: Yokohama

first: Yukihisa

last: Shimada

state: Kanagawa

address: Maiokacho, Totsuka

department: Kihara Institute for Biological Science

country: Japan

institute: Yokohama City University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix Gene Array Scanner 2500A with the original setting (This means that scanning steps are conducted at a high level of sensitivity to focus on those genes that function in hormone signaling, because their transcripts are relatively less abundant. Under these conditions, signals of highly abundant transcripts may reach saturation)

organism: Arabidopsis thaliana

source_name: Arabidopsis seedling

label_protocol: One-cycle target labeling reagents (Affymetrix)

growth_protocol: Seedlings were grown at 22 degrees.

extract_protocol: guanidine-hydrochloride method

treatment_protocol: Seedlings were treated with DEX for 3 h.

tag: genotype/variation

value: seedling

value: 10µM DEX


title: RC17_after_mesDA_3_H5


title: sarcoma classifier reference case 214

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 214

value: FFPE


title: RC17_after_mesDA_3_H3


title: Liver, GenX, 5mg/kg, 404

description: RNA extracted from FFPE tissue


title: IC148S_SNP6

description: Sample name: IC148S

value: tumor stroma

value: Serous cystadenoma


title: Liver, GenX, 5mg/kg, 451

description: RNA extracted from FFPE tissue

value: female


title: Liver, GenX, 5mg/kg, 453

description: RNA extracted from FFPE tissue


title: RC17_after_mesDA_3_H2

value: R

value: GFP


title: sarcoma classifier reference case 210

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 210


title: Liver, GenX, 5mg/kg, 403

description: RNA extracted from FFPE tissue


title: sarcoma classifier reference case 209

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 209


title: IC236S_SNP6

description: Sample name: IC236S


title: Liver, GenX, 5mg/kg, 402

description: RNA extracted from FFPE tissue


title: Liver, GenX, 5mg/kg, 452

description: RNA extracted from FFPE tissue


title: RC17_after_mesDA_3_H12


title: Dof3.2-GR DEX replicate1


title: RC17_after_mesDA_3_H11


title: IC137S_SNP6

description: Sample name: IC137S

value: Fibroma

value: Benign fibroma


title: IC103S_SNP6

description: Sample name: IC103S

value: Serous cystadenofibroma

value: Benign serous cystadenofibroma


title: Liver, GenX, 5mg/kg, 401

description: RNA extracted from FFPE tissue

value: liver

value: GenX


title: sarcoma classifier reference case 208

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 208

value: sarcoma


title: sarcoma classifier reference case 207

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 207


title: Dof3.2-GR mock replicate2

value: mock


title: IC120S_SNP6

description: Sample name: IC120S


title: sarcoma classifier reference case 206

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 206


title: IC158S_SNP6

description: Sample name: IC158S


title: PPBo+IAA replicate5

growth_protocol: Seedlings were grown for 7 or 8 days at 22 degrees.

treatment_protocol: Seedlings were treated with auxin inhibitors for 3 h.

tag: ecotype

value: 10 µM PPBo, 1 µM IAA


title: RC17_after_mesDA_3_H10


title: RC17_after_mesDA_3_H1


title: Liver, GenX, 0.5mg/kg, 354

description: RNA extracted from FFPE tissue

tag: strain

value: wildtype


title: PPBo+IAA replicate4

value: seedling


title: sarcoma classifier reference case 204

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 204

value: FFPE


title: RC17_after_mesDA_3_G7


title: IC79S_SNP6

description: Sample name: IC79S

value: Ovarian stroma

value: Normal ovary


title: IC148G_SNP6

description: Sample name: IC148G

value: Peripheral Blood Lymphocytes

value: Serous cystadenoma

value: Ovarian serous cystadenoma


title: Liver, GenX, 0.5mg/kg, 352

description: RNA extracted from FFPE tissue

value: female


title: sarcoma classifier reference case 203

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 203


title: sarcoma classifier reference case 205

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 205


title: sarcoma classifier reference case 202

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 202


title: sarcoma classifier reference case 213

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 213


title: RC17_after_mesDA_3_G6

value: R

value: GFP


title: RC17_after_mesDA_3_G5


title: IAA replicate5

value: 100 nM IAA


title: PPBo replicate4

value: 10 µM PPBo


title: IC24S_SNP6

description: Sample name: IC24S

value: tumor stroma


title: sarcoma classifier reference case 201

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 201

value: sarcoma


title: Dof3.2-GR mock replicate1

value: mock


title: PPBo replicate5


title: Mock replicate5


title: sarcoma classifier reference case 200

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 200


title: Liver, GenX, 0.5mg/kg, 304

description: RNA extracted from FFPE tissue

value: liver

value: GenX

value: male


title: sarcoma classifier reference case 199

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 199

value: FFPE


title: RC17_after_mesDA_3_G4


title: RC17_after_mesDA_3_G2


title: IC7S_SNP6

description: Sample name: IC7S


title: Mock replicate4

value: seedling


title: sarcoma classifier reference case 198

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 198


title: PEO-IAA+IAA replicate3

value: 10 µM PEO-IAA, 1 µM IAA


title: Liver, GenX, 0.5mg/kg, 353

description: RNA extracted from FFPE tissue

value: wildtype


title: IAA replicate4


title: RC17_after_mesDA_3_G12


title: Liver, GenX, 0.5mg/kg, 302

description: RNA extracted from FFPE tissue


title: PEO-IAA+IAA replicate2


title: IC158G_SNP6

description: Sample name: IC158G

value: Peripheral Blood Lymphocytes

value: Serous cystadenofibroma

value: Benign serous cystadenofibroma


title: sarcoma classifier reference case 211

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 211


title: sarcoma classifier reference case 197

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 197


title: Liver, GenX, 0.1mg/kg, 255

description: RNA extracted from FFPE tissue

value: female


title: RC17_after_mesDA_3_G10

value: R

value: GFP


title: RC17_after_mesDA_3_G11


title: Liver, GenX, 0.5mg/kg, 355

description: RNA extracted from FFPE tissue


title: PEO-IAA+IAA replicate1


title: Liver, GenX, 0.5mg/kg, 301

description: RNA extracted from FFPE tissue


title: sarcoma classifier reference case 195

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 195


title: sarcoma classifier reference case 196

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 196


title: RC17_after_mesDA_3_G3


title: sarcoma classifier reference case 194

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 194


title: Liver, GenX, 0.1mg/kg, 254

description: RNA extracted from FFPE tissue


title: IC10S_SNP6

description: Sample name: IC10S


title: RC17_after_mesDA_3_F9


title: RC17_after_mesDA_3_G1


title: IC7G_SNP6

description: Sample name: IC7G

value: Serous cystadenoma

value: Ovarian serous cystadenoma


title: RC17_after_mesDA_3_G9


title: Liver, GenX, 0.5mg/kg, 303

description: RNA extracted from FFPE tissue


title: Liver, GenX, 0.1mg/kg, 252

description: RNA extracted from FFPE tissue


title: PEO-IAA replicate3

value: 10 µM PEO-IAA


title: PEO-IAA replicate1


title: sarcoma classifier reference case 193

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 193

value: sarcoma


title: RC17_after_mesDA_3_F8


title: IC103G_SNP6

description: Sample name: IC103G


title: Liver, GenX, 0.5mg/kg, 351

description: RNA extracted from FFPE tissue

value: liver


title: Liver, GenX, 0.1mg/kg, 253

description: RNA extracted from FFPE tissue

value: GenX


title: Liver, GenX, 0.1mg/kg, 205

description: RNA extracted from FFPE tissue

value: male


title: Liver, GenX, 0.1mg/kg, 251

description: RNA extracted from FFPE tissue


title: sarcoma classifier reference case 191

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 191

value: FFPE


title: RC17_after_mesDA_3_F7


title: RC17_after_mesDA_3_F6


title: IC33S_SNP6

description: Sample name: IC33S

value: tumor stroma

value: Fibroma

value: Benign fibroma


title: Liver, GenX, 0.1mg/kg, 204

description: RNA extracted from FFPE tissue

value: wildtype


title: Kynurenine replicate3

value: seedling

value: 30 µM Kynurenine


title: RC17_after_mesDA_3_F5


title: sarcoma classifier reference case 189

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 189


title: Liver, GenX, 0.1mg/kg, 203

description: RNA extracted from FFPE tissue


title: PEO-IAA replicate2


title: sarcoma classifier reference case 190

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 190


title: RC17_after_mesDA_3_F4


title: Kynurenine replicate1


title: Kynurenine replicate2


title: RC17_after_mesDA_3_F3


title: Liver, GenX, 0.1mg/kg, 202

description: RNA extracted from FFPE tissue


title: sarcoma classifier reference case 188

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 188


title: IC4S_SNP6

description: Sample name: IC4S


title: IAA replicate3

value: 1 µM IAA


title: sarcoma classifier reference case 187

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 187


title: sarcoma classifier reference case 186

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 186


title: RC17_after_mesDA_3_F12

value: R


title: Liver, control, 155

description: RNA extracted from FFPE tissue

value: control

value: 0mg/kg (control)

value: female


title: Liver, control, 154

description: RNA extracted from FFPE tissue


title: RC17_after_mesDA_3_F2

value: GFP


title: IAA replicate1


title: sarcoma classifier reference case 185

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 185

value: sarcoma


title: IAA replicate2


title: sarcoma classifier reference case 184

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 184


title: Liver, control, 153

description: RNA extracted from FFPE tissue

value: liver


title: RC17_after_mesDA_3_F11


title: Mock replicate3

value: mock


title: Blastocyst_C

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

data_processing:
IMultiplexed sequencing reads that passed filters were trimmed to remove low quality reads and adaptors. The quality of reads after filtering was examined using fastQC, followed by alignment to the goat genome (Capra hircus – ARS1) by STAR (2.5.3a) with default parameters. Individual mapped reads were quantified to calculate FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values using RefSeq genes as reference. Genes with FPKM > 0.1 in at least one sample were kept in downstream analysis for Pearson correlation, Principle Component Analysis (PCA) and cluster analysis using R. Differential gene expression analysis was performed using Partek Flow GSA algorithm with default parameters. The genes are deemed differentially expressed if a false discovery rate (FDR) of < 0.05 and fold change > 2. IPA (Ingenuity Pathway Analysis) were used to reveal the Gene Ontology (GO) and pathways, respectively.
Identification of stage-specific genes was performed as previously described 5 and expression pattern clusters were generated by the unsupervised hierarchical clustering analysis using R.
Genome_build: Capra hircus – ARS1
Supplementary_files_format_and_content: FASTQ

organism: Capra hircus

source_name: embryos

extract_protocol: Not provided

value: embryos


title: Blastocyst_B


title: sarcoma classifier reference case 182

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 182

value: FFPE


title: Liver, GenX, 0.1mg/kg, 201

description: RNA extracted from FFPE tissue

value: GenX

value: male


title: sarcoma classifier reference case 183

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 183


title: Mock replicate1


title: RC17_after_mesDA_3_F10


title: Blastocyst_A


title: Mock replicate2


title: RC17_after_mesDA_3_F1


title: sarcoma classifier reference case 181

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 181


title: Liver, control, 105

description: RNA extracted from FFPE tissue


title: Morula_C


title: Liver, control, 151

description: RNA extracted from FFPE tissue


title: Liver, control, 104

description: RNA extracted from FFPE tissue


title: sarcoma classifier reference case 180

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 180

value: KRYO


title: Morula_B


title: RC17_after_mesDA_3_E7


title: Morula_A

description: The reverse read file was corrupt and not included in this submission


title: Liver, control, 103

description: RNA extracted from FFPE tissue

value: wildtype


title: Liver, control, 152

description: RNA extracted from FFPE tissue


title: 16cell_C


title: Liver, control, 102

description: RNA extracted from FFPE tissue


title: sarcoma classifier reference case 179

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 179


title: RC17_after_mesDA_3_E6


title: sarcoma classifier reference case 178

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 178


title: RC17_after_mesDA_3_E5


title: sarcoma classifier reference case 177

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 177


title: 16cell_B


title: RC17_after_mesDA_3_E4


title: sarcoma classifier reference case 176

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 176


title: Liver, GenX, 0.5mg/kg, 305

description: RNA extracted from FFPE tissue


title: WT+CTX5_macrophage

first: Michael

last: Hemann

state: Massachusetts

address: 500 Main St, Building 76 Room 301

department: Koch Institute

institute: Massachusetts Institute of Technology

description:
processed data file:
mouseCells_rawCounts.txt
D17-134022

data_processing:
Read pairs were combined into a single fastq with well/UMI information concatenated with the second read name, reads sharing sequence and UMI information were collapsed into single exemplars and aligned against either a joint human/murine genome (hg19 and mm9) assembly with BWA mem v. 0.7.12-r1039 with flag -t 16 [http://bio-bwa.sourceforge.net/ ].
Subsequently bam files were sorted by read positions and indexed using samtools v 0.1.18 [Li2009].
The UMI is located in read 1, bp 7-16.
Gene expression was estimated based on reads mapping near the 3' end of transcripts using ESAT [Derr2016] with the following parameters -task score3p -alignments $sample_list   -wLen 50 -wExt 5000 -wOlap 0 -sigTest 0.01 -multimap ignore, poiting to a refseq-based gene annotation (hg19 and mm9, as downloaded from the UCSC Genome Browser) and gene-level data were used for downstream analyses
Genome_build: mm9/hg19
Supplementary_files_format_and_content: Tab-delimited txt file with gene-level counts

source_name: bone marrow macrophage cells

growth_protocol: Lymphoma PDX cells are transplanted into NSG mice and harvested along with macrophages from the bone marrow ('B' in sample names) and/or spleen ('S' in sample names) after treatment with single or combination chemotherapy

extract_protocol:
Cell lysis and RNA extraction were performed using the QIAGEN RNeasy Plus Mini kit for human lymphoma PDX cells and the QIAGEN RNeasy Plus Mini kit for mouse macrophages
RNA samples were quantified and quality assessed using an Advanced Analytical Fragment Analyzer. 20ng of totalRNA was used for library preparation with ERCC Spike-in control Mix A (Ambion 10-6 final dilution). All steps were performed on a Tecan EVO150. 3’DGE-custom primers 3V6NEXT-bmc#1-24 are added to a final concentration of 1.2uM. (5'-/5Biosg/ACACTCTTTCCCTACACGACGCTCTTCCGATCT[BC6]N10T30VN-3'  where  5Biosg = 5’  biotin, [BC6] = 6bp barcode specific to each sample/well, N10 = Unique Molecular Identifiers, Integrated DNA technologies).
After addition of the oligonucleotides, samples were denatured at 72C for 2 minutes followed by addition of SMARTScribe RT per manufacturer’s recommendations with Template-Switching oligo5V6NEXT (12uM, [5V6NEXT : 5’-iCiGiCACACTCTTTCCCTACACGACGCrGrGrG-3’  where  iC: iso-dC, iG: iso-dG, rG: RNA G ]) and incubation at 42C for 90’ followed by inactivation at 72C for 10’.
Following the template switching reaction, cDNA from 24 wells containing unique well identifiers were pooled together and cleaned using RNA Ampure beads at 1.0X. cDNA was eluted with 90 ul of water followed by digestion with Exonuclease I at 37C for 45 minutes, inactivation at 80C for 20 minutes.  Single stranded cDNA was then cleaned using RNA Ampure beads at 1.0X and eluted in 50ul of water.
Second strand synthesis and PCR amplification was done using the Advantage 2 Polymerase Mix (Clontech) and the SINGV6 primer (10 pmol, Integrated DNA Technologies 5’-/5Biosg/ACACTCTTTCCCTACACGACGC-3’ ). 12 cycles of PCR was performed followed by clean up using regular SPRI beads at 1.0X, and was eluted with 20ul of EB. Successful amplification of cDNA was confirmed using the Fragment Analyzer. Illumina libraries are then produced using standard Nextera tagmentation substituting P5NEXTPT5-bmc primer (25μM, Integrated DNA Technologies, (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCG*A*T*C*T*-3’  where  * = phosphorothioate bonds. ) in place of the normal N500 primer.
Final libraries were cleaned using SPRI beads at 1X and quantified using the Fragment Analyzer and qPCR before being loaded for paired-end sequencing using the Illumina NextSeq500.

treatment_protocol: Vehicle, doxorubicin, alemtuzumab, cyclophosphamide or a combination of alemtuzumab and cyclophosphamide are intraperitoneally administered into tumor-bearing NSG mice. Tumor-free NSG mice are also treated with vehicle or cyclophosphamide for analysis of cyclophosphamide's effects on bone marrow macrophages.

value: macrophage

value: Cyclophosphamide, non-tumor bearing mice

value: Bone marrow


title: RC17_after_mesDA_3_E3

source_name: Human graft in rat brain

value: R


title: 8cell_C


title: Liver, control, 101

description: RNA extracted from FFPE tissue

value: control


title: WT+CTX4_macrophage

description:
processed data file:
mouseCells_rawCounts.txt
D17-134021


title: 16cell_A


title: sarcoma classifier reference case 175

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 175


title: RC17_after_mesDA_3_E9


title: RC17_after_mesDA_3_E8


title: sarcoma classifier reference case 174

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 174


title: RC17_after_mesDA_3_E2


title: RC17_after_mesDA_3_E12


title: 8cell_A


title: sarcoma classifier reference case 173

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 173


title: RC17_after_mesDA_3_E11


title: WT+CTX2_macrophage

description:
processed data file:
mouseCells_rawCounts.txt
D17-134019


title: 4cell_C


title: sarcoma classifier reference case 172

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 172


title: 4cell_B


title: WT+CTX1_macrophage

description:
processed data file:
mouseCells_rawCounts.txt
D17-134018


title: RC17_after_mesDA_3_E10


title: 4cell_A


title: RC17_after_mesDA_3_E1


title: sarcoma classifier reference case 170

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 170


title: sarcoma classifier reference case 171

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 171


title: WT4_macrophage

description:
processed data file:
mouseCells_rawCounts.txt
D17-134016

value: untreated, non-tumor bearing mice


title: WT5_macrophage

description:
processed data file:
mouseCells_rawCounts.txt
D17-134017


title: 2cell_C


title: 8cell_B


title: 2cell_B


title: WT+CTX3_macrophage

description:
processed data file:
mouseCells_rawCounts.txt
D17-134020


title: WT3_macrophage

description:
processed data file:
mouseCells_rawCounts.txt
D17-134015


title: RC17_after_mesDA_3_D9


title: RC17_after_mesDA_3_D7


title: sarcoma classifier reference case 169

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 169


title: 2cell_A


title: WT2_macrophage

description:
processed data file:
mouseCells_rawCounts.txt
D17-134014


title: sarcoma classifier reference case 168

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 168


title: WT1_macrophage

description:
processed data file:
mouseCells_rawCounts.txt
D17-134013


title: Oocyte_C

source_name: oocytes

value: oocytes


title: D3-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165072

value: Doxorubicin


title: sarcoma classifier reference case 166

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 166

source_name: sarcoma sample

value: sarcoma


title: RC17_after_mesDA_3_D5

value: GFP


title: RC17_after_mesDA_3_D6


title: Oocyte_B


title: sarcoma classifier reference case 165

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 165


title: RC17_after_mesDA_3_D4


title: D1-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165070


title: Oocyte_A


title: RC17_after_mesDA_3_D3


title: D2-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165071


title: sarcoma classifier reference case 163

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 163


title: sarcoma classifier reference case 164

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 164


title: sarcoma classifier reference case 162

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 162


title: RC17_after_mesDA_3_D8


title: RC17_after_mesDA_3_D2


title: V2-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165068

value: Vehicle


title: sarcoma classifier reference case 167

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 167


title: V3-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165069


title: sarcoma classifier reference case 161

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 161


title: RC17_after_mesDA_3_D12


title: RC17_after_mesDA_3_D11


title: SMC TGFbR2 ApoE 2M HFD

city: New Haven

last: Simons

state: CT

address: 3oo George St, Suite 773

department: Department: Internal Medicine Cardiology

institute: Yale University

description:
SMC TGFbR2 KO Apoe mice feed with 2M HFD
apoe_dko_2m_combined_count_tmm_relaxed_filter_noApoeTgfbr2.csv

data_processing:
UMI-tools is used for the end to end processing of scRNA-Seq data
Identified cell barcodes and UMI in the read sequence, which are then extracted from Read 1 and added to Read 2 read name. STAR,was used to map extracted reads from Read 2 to the reference mouse genome build 38 (GRCm38), followed by assigning reads to genes using featureCounts tool from the subread package (version 1.6.0). Quantification was performed using UMI-tools count function to find the number of unique UMIs mapping to each gene (GENCODE mouse annotation, release M15).
Count data was filtered by: removing cells for which UMI count was less than 3,000 or total number of detected genes was less than 1,500; removing genes that were not expressed in less than or equal to 5% of the remaining cells in at least one sample
ApoE and TGFβR2 UMI counts were removed from the processed data matrix
Genome_build: GRCm38, version M15 (Ensembl 90)
Supplementary_files_format_and_content: CSV files include raw and TMM values for all samples

source_name: ascending aorta

extract_protocol:
Digest the mice ascending aorta and sort GFP positive cells (smooth muscle cells)
Libraries were prepared for sequencing at Yale using Chromium™ system (10x Genomics)

treatment_protocol: mice were fed with HFD for 1 to 4 months

value: TGFBetaRiSMC-Apoe

tag: diet

value: HFD


title: SMC TGFbR2 ApoE ND

description:
SMC TGFbR2 KO Apoe mice feed with ND
apoe_dko_0m_combined_count_tmm_relaxed_filter_noApoeTgfbr2.csv

value: ND


title: SMC TGFbR2 ApoE 1M HFD

description:
SMC TGFbR2 KO Apoe mice feed with 1M HFD
apoe_dko_1m_combined_count_tmm_relaxed_filter_noApoeTgfbr2.csv


title: SMC TGFbR2 ApoE 4M HFD

description:
SMC TGFbR2 KO Apoe mice feed with 4M HFD
apoe_dko_4m_combined_count_tmm_relaxed_filter_noApoeTgfbr2.csv


title: comb3-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165066

value: Alemtuzumab + cyclophosphamide


title: Apoe 4M HFD

description:
ApoE mice feed with 4M HFD
apoe_dko_4m_combined_count_tmm_relaxed_filter_noApoeTgfbr2.csv

value: Apoe-/-


title: sarcoma classifier reference case 160

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 160

value: FFPE


title: sarcoma classifier reference case 159

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 159


title: comb2-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165065

value: macrophage


title: RC17_after_mesDA_3_D1


title: comb1-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165064


title: sarcoma classifier reference case 158

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 158


title: WT3-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165063


title: RC17_after_mesDA_3_C9


title: sarcoma classifier reference case 157

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 157


title: Apoe ND

description:
ApoE mice feed with ND
apoe_dko_0m_combined_count_tmm_relaxed_filter_noApoeTgfbr2.csv


title: V1-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165067


title: RC17_after_mesDA_3_C8


title: RC17_after_mesDA_3_D10


title: sarcoma classifier reference case 156

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 156


title: Apoe 1M HFD

description:
ApoE mice feed with 1M HFD
apoe_dko_1m_combined_count_tmm_relaxed_filter_noApoeTgfbr2.csv


title: RC17_after_mesDA_3_C7


title: A3-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165060

value: Alemtuzumab


title: CHIP_P0_cortex_WT_RAD21_rep1

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

country: China

institute: Shanghai JiaoTong University

data_processing:
Reads were mapped to the reference genome (GRCh37/hg19、NCBI37/mm9) or the modified genome with insertions using the Bowtie program.
Peaks were called by the MACS program (version 1.4.2) with a cutoff P value of 10−5.
Genome_build: UCSC hg19、NCBI37/mm9
Supplementary_files_format_and_content: zipped wig files include RPM values for each Sample

source_name: Cortex neuron

extract_protocol:
4 × 106 of cells were cross-linked by 1% formaldehyde in 10% FBS/PBS for 10 min at room temperature. Cells were then lysed twice with ice-cold lysis buffer (20 mM Tris-HCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate and 1× protease inhibitors, pH 7.5) for 10 min with slow rotations.
The lysed cells were then sonicated to obtain DNA fragments of about 200-500 bp using the Biorupter system (high energy, with working time of 30 seconds and resting time of 30 seconds, 30 cycles). After removal of the insoluble debris, the lysate was incubated with specific antibodies against CTCF (07-729; Millipore), RAD21 (ab992; Abcam), or H3K27ac (ab4729; Abcam) and purified by protein A-agarose beads (16-157; Millipore). NIPBL ChIP-seq were from recently published data49. ChIP DNA was extracted and prepared for high throughput sequencing using a DNA library preparation kit for Illumina (NEB). ChIP-seq libraries were sequenced on a HiSeq X Ten Platform (Illumina).

value: cortex

tag: age

tag: line

value: WT


title: CHIP_P0_cortex_WT_RAD21_rep2

tag: tissue


title: A2-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165059

value: Bone marrow


title: sarcoma classifier reference case 155

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 155

tag: material preparation


title: sarcoma classifier reference case 154

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 154


title: RC17_after_mesDA_3_C5

tag: cell type

value: R


title: Apoe 2M HFD

description:
ApoE mice feed with 2M HFD
apoe_dko_2m_combined_count_tmm_relaxed_filter_noApoeTgfbr2.csv


title: RC17_after_mesDA_3_C4

tag: sortingmethod


title: CHIP_P0_cortex_WT_CTCF_rep1


title: sarcoma classifier reference case 152

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 152


title: RC17_after_mesDA_3_C3

tag: plate


title: WT2-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165062

tag: treatment

value: untreated, non-tumor bearing mice


title: RC17_after_mesDA_3_C2


title: 4C_P0_cortex_GB6_de_del_rep2

data_processing:
Library strategy: 4C-seq
Duplicated paired-end reads were removed by FastUniq (version 1.1) program, and only the unique reads were used for analyses using the Bowtie and r3Cseq program.
Reads were aligned to the reference mouse genome (NCBI37/mm9) using the Bowtie program (version 1.2.2)
File format is  transformed to BAM using samtools version 1.9
The reads per million (RPM) value was calculated using the r3Cseq program (version 1.20) in the R package (version 3.3.3)
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: zipped bedGraph files include RPM values for each Sample

source_name: cortex neuron

extract_protocol:
P0 mouse brain was dissected, and the tissue from cerebral cortex was digested with 0.013% of collagenase in Neurobasal Medium (Gibco) at 37℃ for 3 min. The collagenase was neutralized by adding excess amount of Neurobasal Medium. Single-cell suspension was made by gentle pipetting, and then filtered through 100-μm cell strainers (BD Biosciences).  and the suspension were used for QHR-4C experiments. The single-cell suspension were suspended for crosslinking in 900 ml 2% formaldehyde at room temperature for 10 min. The crosslinking reaction was stopped by adding and mixing with 100 ml of 2M glycine for a final concentration of 200 mM. The fixed cells were spin down at 800 g at 4 °C for 5 min and washed twice by suspending briefly in 1 ml ice-cold PBS. Cells were then permeabilized twice with 200 ml ice-cold 4C permeabilization buffer each for 10 min (50 mM Tris–HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, and 1× protease inhibitors).
The cells were then digested overnight at 37 °C with DpnII while shaking at 900 rpm. After inactivation of DpnII at 65 °C for 20 min, proximity ligation was carried out for 24 hr at 16 °C with T4 DNA ligase in 0.1 ml 1 × T4 ligation buffer. The ligated product was then reverse cross-linked and DNA was extracted using phenol-chloroform. Glycogen was added to facilitate DNA precipitation. The precipitated DNA was then dissolved in 50 ml water, and sonicated using the Biorupter system (with low energy setting at a train of 30-second sonication with 30 second intervals for 12 cycles) to obtain DNA fragments ranging from 200 to 600 bp.The captured fragments were linear-amplified using a 5’ biotin-tagged primer complementary to the viewpoint fragment in 100ul of PCR system for a total of 60 cycles. This primer should be neither too close to the DpnII site to facilitate the nested PCR at the final amplification step, nor too far away from the DpnII site to maximize the product amount. The amplification products were denatured by incubating at 95 °C for 5 min, and immediately chilled on ice to obtain ssDNA. The ssDNA was then enriched and purified with Streptavidin Magnetic Beads (Invitrogen) according to the manufacturer’s instructions.  The ssDNA on-beads was then ligated in 15 µl with 0.1 µM of adapters (Supplementary Table 1) at 16 °C for 24 hr. The adapters were generated by annealing two complementary primers matching Illumina P7 sequences. After ligation, free adapters were removed by washing the beads twice with the B/W Buffer (5 mM Tris-HCl, 1 M NaCl, 0.5 mM EDTA, pH 7.5). Finally, the QHR-4C libraries were generated by one-step PCR amplification (94 °C, 2 min; 94 °C, 10 sec, 60 °C, 15 sec, 72 °C, 1 min for 19 cycles; and a final extension at 72 °C, 5 min) with captured ssDNA on beads as the template and a pair of PCR primers. The forward primer matches the Illumina P5 and the viewpoint sequence adjacent to the viewpoint DpnII site with barcodes, and the reverse primer matches Illumina P7 with indexes. The PCR products were purified with a PCR purification kit (Qiagen).

value: cortex neuron

value: CBS de deletion

value: CBS de -/-


title: sarcoma classifier reference case 150

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 150

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

extract_protocol: Illumina protocol

value: sarcoma

value: KRYO


title: RC17_after_mesDA_3_C6

data_processing:
All reads were aligned to the human (hg19) genome using STAR v2.3.0e (Dobin et al. 2013)
Non-uniquely mapped reads were removed using Samtools
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in Ensembl ( June 2015)
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression values are provided as rpkms and counts (comma separated text files)

extract_protocol:
Single cells have been extracted from tissue using Papain Dissociation System (Worthington). cDNA was generated from FACS sorted single cells (ventral midbrain human embryonic stem cells before grafting, fetal cells before and after grafting were sorted for size, ventral midbrain human embryonic stem cells after grafting were sorted for GFP expression) using Smart-seq2 protocol (Picelli et al. Nature Methods 2013).  ERCC spike-in RNA was added to the lysis buffer.
Nextera XT DNA sample preparation index kit, 96 indices (Illumina)

value: GFP


title: RC17_after_mesDA_3_C12


title: 4C_P0_cortex_GB6_d_del_rep2

value: CBS d deletion

value: CBS d -/-


title: CT2-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165056

value: Cyclophosphamide


title: sarcoma classifier reference case 149

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 149


title: CHIP_P0_cortex_WT_CTCF_rep2


title: CT1-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165055


title: WT1-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165061


title: D3-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165036

value: Doxorubicin


title: sarcoma classifier reference case 148

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 148


title: sarcoma classifier reference case 153

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 153

value: FFPE


title: RC17_after_mesDA_3_C11


title: RC17_after_mesDA_3_C10


title: sarcoma classifier reference case 147

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 147


title: A1-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165058

value: macrophage

value: Alemtuzumab


title: 4C_P0_cortex_GB6_bcd_del_rep2

value: CBS bcd deletion

value: CBS bcd -/-


title: 4C_P0_cortex_GB6_d_del_rep1


title: RC17_after_mesDA_3_C1

value: R


title: sarcoma classifier reference case 192

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 192


title: 4C_P0_cortex_GB6_bcd_del_rep1


title: D1-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165034

value: Bone marrow


title: D2-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165035


title: CT3-mphi_PDX2

description:
processed data file:
mouseCells_rawCounts.txt
D16-165057


title: RC17_after_mesDA_3_B9


title: 4C_P0_cortex_GB6_de_del_rep1

value: cortex neuron


title: sarcoma classifier reference case 146

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 146


title: sarcoma classifier reference case 151

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 151


title: V3-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165033

value: Vehicle


title: sarcoma classifier reference case 145

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 145


title: 4C_P0_cortex_GB6_wt_rep2

value: wt


title: RC17_after_mesDA_3_B8


title: 4C_P0_cortex_GB6_wt_rep1


title: RC17_after_mesDA_3_B7


title: sarcoma classifier reference case 144

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 144

value: sarcoma


title: V2-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165032


title: sarcoma classifier reference case 142

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 142

value: KRYO


title: comb3-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165030

value: Alemtuzumab + cyclophosphamide


title: sarcoma classifier reference case 143

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 143


title: RC17_after_mesDA_3_B6

value: GFP


title: RC17_after_mesDA_3_B5


title: 4C_P0_cortex_GB6_a_del_rep2

value: CBS a deletion

value: CBS a -/-


title: 4C_P0_cortex_GB6_a_del_rep1


title: 4C_P0_cortex_GB2_e_del_rep2

value: CBS e deletion

value: CBS e -/-


title: comb2-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165029

value: macrophage


title: RC17_after_mesDA_3_B4


title: sarcoma classifier reference case 140

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 140


title: RC17_after_mesDA_3_B3


title: 4C_P0_cortex_GB2_de_del_rep2

value: CBS de deletion

value: CBS de -/-


title: sarcoma classifier reference case 139

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 139


title: WT3-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165027

value: untreated, non-tumor bearing mice


title: 4C_P0_cortex_GB2_e_del_rep1


title: 4C_P0_cortex_GB2_de_del_rep1


title: RC17_after_mesDA_3_B2

value: R


title: WT2-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165026

value: Bone marrow


title: sarcoma classifier reference case 137

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 137


title: A3-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165024

value: Alemtuzumab


title: 4C_P0_cortex_GB2_d_del_rep2

value: cortex neuron

value: CBS d deletion

value: CBS d -/-


title: WT1-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165025


title: 4C_P0_cortex_GB2_d_del_rep1


title: RC17_after_mesDA_3_B12


title: V1-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165031

value: Vehicle


title: RC17_after_mesDA_3_B10


title: sarcoma classifier reference case 141

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 141

value: sarcoma

value: KRYO


title: sarcoma classifier reference case 135

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 135


title: sarcoma classifier reference case 136

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 136


title: A2-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165023


title: comb1-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165028

value: Alemtuzumab + cyclophosphamide


title: RC17_after_mesDA_3_B11

value: GFP


title: sarcoma classifier reference case 134

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 134


title: 4C_P0_cortex_GB2_wt_rep2

value: wt


title: sarcoma classifier reference case 138

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 138


title: 4C_P0_cortex_GB2_bcd_del_rep1

value: CBS bcd deletion

value: CBS bcd -/-


title: CT2-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165020

value: macrophage

value: Cyclophosphamide


title: 4C_P0_cortex_GB2_a_del_rep2

value: CBS a deletion

value: CBS a -/-


title: sarcoma classifier reference case 131

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 131


title: RC17_after_mesDA_3_A9

value: R


title: RC17_after_mesDA_3_B1


title: RC17_after_mesDA_3_A7


title: RC17_after_mesDA_3_A6


title: 4C_P0_cortex_GB2_a_del_rep1


title: PaS cells – Ebf1fl/fl;Prx1+/cre – ko Replicate 3

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
The base calling was performed by using BCL2Fastq pipeline (version: 0.3.1) and bcl2fastq (version 2.17.1.14).
RNA-seq: The paired-end RNA-seq datasets were mapped to the mouse reference genome (mm10) using Tophat (v2.0.14).
RNA-seq: The mapped reads were further assembled by using Cufflinks (v2.2.1) and the expression level of the annotated genes (UCSC, mm10) was calculated by Cuffquant. The differential gene expression between the conditions was calculated by using Cuffdiff.
ATAC-seq: The paried-end sequencing reads were trimmed using trim galore (0.4.0), which is a wrapper for the Cutadapt (1.8.1) tools. The trimmed reads were mapped to the mouse genome (mm10) using bowtie2 (2.2.8) with the default settings.
ATAC-seq: The duplicated reads were removed using Picard tools (1.136). The reads mapping to blacklisted regions, mitochondrial genome and the reads with mapping below 30 were removed. The properly mapped reads were used for identifying peaks by MACS2 (2.1.1) with the extsize 125 and q-value cut off 0.01. Peaks were further filtered for a p-value cutoff 10-7.
ATAC-seq: The RPKM normalized tracks for each ATAC-seq replicates were generated using deeptools (version:2.4.1) with the bin size of 50.
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq: The normalized gene expression values (FPKM) calculated by Cuffnorm (v2.2.1) is provided in TXT format. ATAC-seq: The RPKM normalized ATAC-seq profile track is provided in bigWig format.

source_name: Bone marrow CD45-CD31-Lin-PDGFRα+ Sca1+ cells

extract_protocol:
RNA-seq: Total RNA was isolated from the FACS sorted CAR and PaS cells using RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions. The total mRNA was enriched by using Oligo dT magnetic beads. ATAC-seq: minimum of 10.000 cells were resuspended in 50 µL of cold lysis buffer (10 mM Tris·Cl at pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% [v/v] Igepal CA-630) and incubated for 15 min on ice. The supernatant was discarded after centrifugation, and the nuclei were used for transposition reaction using NEB Nextera DNA sample preparation kit.
The RNA-seq libraries were prepared by using SMART-Seq v4 ultra-low input RNA library preparation protocol according to the manufacturer's instructions. The ATAC-seq libraries were prepared using the NEB Nextera DNA sample preparation kit according to the manufacturer's instructions.

value: Bone marrow


title: CT1-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165019


title: 4C_P0_cortex_GB2_bcd_del_rep2

value: cortex neuron


title: 4C_P0_cortex_GB2_wt_rep1


title: sarcoma classifier reference case 133

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 133


title: sarcoma classifier reference case 130

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 130


title: sarcoma classifier reference case 128

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 128


title: RC17_after_mesDA_3_A5


title: RC17_after_mesDA_3_A8


title: A1-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165022

value: Alemtuzumab


title: 4C_P0_cortex_GC3_e_del_rep2

value: CBS e deletion

value: CBS e -/-


title: CT3-mphi_PDX1

description:
processed data file:
mouseCells_rawCounts.txt
D16-165021


title: PaS cells – Ebf1fl/fl;Prx1+/cre – ko Replicate 2


title: sarcoma classifier reference case 132

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 132

value: sarcoma


title: PaS cells – Ebf1fl/fl;Prx1+/cre – ko Replicate 1


title: sarcoma classifier reference case 127

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 127

value: KRYO


title: PaS cells - Ebf1+/+,Prx1+/cre – wt Replicate 3


title: RC17_after_mesDA_3_A3


title: RC17_after_mesDA_3_A2


title: sarcoma classifier reference case 125

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 125


title: sarcoma classifier reference case 129

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 129


title: PaS cells - Ebf1+/+,Prx1+/cre – wt Replicate 1


title: PaS cells - Ebf1+/+,Prx1+/cre – wt Replicate 2


title: 4C_P0_cortex_GC3_e_del_rep1


title: RC17_after_mesDA_3_A4


title: RC17_after_mesDA_3_A12


title: CAR cells – Ebf1fl/fl;Prx1+/cre – ko Replicate 3

source_name: Bone marrow CD45-CD31-Lin-PDGFRα+Sca1- cells


title: sarcoma classifier reference case 124

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 124


title: RC17_after_mesDA_2_H9


title: RC17_after_mesDA_3_A1


title: sarcoma classifier reference case 122

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 122


title: sarcoma classifier reference case 123

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 123


title: 4C_P0_cortex_GC3_de_del_rep2

value: CBS de deletion

value: CBS de -/-


title: RC17_after_mesDA_3_A11

value: GFP


title: CAR cells – Ebf1fl/fl;Prx1+/cre – ko Replicate 2


title: RC17_after_mesDA_2_H8


title: CAR cells – Ebf1fl/fl;Prx1+/cre – ko Replicate 1


title: 4C_P0_cortex_GC3_bc_del_rep2

value: CBS bc deletion

value: CBS bc -/-


title: 4C_P0_cortex_GC3_bcd_del_rep2

value: CBS bcd deletion

value: CBS bcd -/-


title: 4C_P0_cortex_GC3_de_del_rep1


title: 4C_P0_cortex_GC3_bc_del_rep1


title: 4C_P0_cortex_GC3_bcd_del_rep1


title: CAR cells - Ebf1+/+,Prx1+/cre – wt Replicate 3


title: 4C_P0_cortex_GC3_a_del_rep2

value: CBS a deletion


title: RC17_after_mesDA_2_H7


title: sarcoma classifier reference case 126

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 126


title: 4C_P0_cortex_GC3_a_del_rep1

value: CBS a -/-


title: sarcoma classifier reference case 120

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 120


title: RC17_after_mesDA_2_H6

value: R


title: CAR cells - Ebf1+/+,Prx1+/cre – wt Replicate 1

value: Bone marrow


title: sarcoma classifier reference case 119

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 119


title: RC17_after_mesDA_2_H5


title: BBS_1_RSs_2

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5690 rosemont boulevard

country: Canada

institute: HMR

data_processing:
Basecalls was performed using Torrent_suite 5.10
Allignment of the RNAseq was done on the Hg19 genome using Hisat2 v2.1.0 with default parameters and sorted using samtools v1.9.
Gene level counts were determined using featureCounts from subread package
Differential expression analysis was performed using DEseq2 package in R
Genome_build: Hg19
Supplementary_files_format_and_content: tab delimited file with the featurecounts of all our samples.

source_name: Retinal sheets derived from iPSCs

growth_protocol: retinal sheets were differentiated using the protocol published in Zhou et al 2015

extract_protocol:
the retinal sheets were dissociated manually and the RNA was extracted using Rneasy Kit from Quiagen.
Libraries were prepared according to Ion Total RNA-Seq Kit V2 for whole transcriptome libraries.

value: iPSCs-derived Retinal sheet

tag: disease state

value: BBS patients


title: 4C_P0_cortex_GA2_e_del_rep1

value: cortex neuron

value: CBS e deletion


title: RC17_after_mesDA_2_H4


title: 4C_P0_cortex_GA2_de_del_rep2


title: sarcoma classifier reference case 118

last: Schrimpf

address: Im Neuenheimer Feld 224

institute: University Hospital Heidelberg, Intitute of Pathology

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 118

value: sarcoma


title: sarcoma classifier reference case 121

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 121

value: KRYO


title: sarcoma classifier reference case 117

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 117


title: BBS_1_RSs_1


title: sarcoma classifier reference case 114

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 114

value: FFPE


title: RC17_after_mesDA_2_H3

last: Bjorklund

address: Box 596

institute: Uppsala University


title: RC17_after_mesDA_2_H2


title: MKS_2_RSs_2

value: MKS patients


title: sarcoma classifier reference case 116

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 116


title: MKS_2_RSs_1


title: 4C_P0_cortex_GA2_de_del_rep1

value: CBS de deletion

value: CBS de -/-


title: sarcoma classifier reference case 115

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 115


title: CAR cells - Ebf1+/+,Prx1+/cre – wt Replicate 2


title: 4C_P0_cortex_GA2_d_del_rep1

value: CBS d deletion

value: CBS d -/-


title: RC17_after_mesDA_2_H10

value: GFP


title: RC17_after_mesDA_2_H12


title: MKS_1_RSs_2


title: sarcoma classifier reference case 113

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 113


title: 4C_P0_cortex_GA2_bcd_del_rep2

value: CBS bcd deletion

value: CBS bcd -/-


title: 4C_P0_cortex_GA2_e_del_rep2

value: CBS e -/-


title: MKS_1_RSs_1


title: RC17_after_mesDA_2_H1

value: R


title: 4C_P0_cortex_GA2_bcd_del_rep1


title: sarcoma classifier reference case 112

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 112


title: Ctrl_1_RSs_2

value: iPSCs-derived Retinal sheet

value: Ctrl


title: RC17_after_mesDA_2_G9


title: Ctrl_1_RSs_1


title: sarcoma classifier reference case 111

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 111


title: 4C_P0_cortex_GA2_bc_del_rep2

value: cortex neuron

value: CBS bc deletion

value: CBS bc -/-