title: sarcoma classifier reference case 877

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 877


title: monocyte-derived macrophages untreated donor permissive 668

status: Public on Mar 01 2020

type: SRA

city: Frederick

first: Marieli

last: Gonzalez-Cotto

state: Maryland

department: Cancer & Inflammation Program

country: USA

institute: National Cancer Institute

library_source: transcriptomic

data_processing:
BAM files were converted to fastq, followed by Fast QC
Align fastq files to Genecode mouse reference using STAR (with soft trimming)
Post-alignment quality control with RNASeqQC
Subreads counting on aligned BAM files (using RefSeq gtf file)
Genome_build: hg19
Supplementary_files_format_and_content: CPM

molecule: total RNA

organism: Homo sapiens

growth_protocol: Blood was drawn into PAXgenes for RNA extraction or PBMC's were isolated from blood by percoll gradient  and differentiated with hMCSF for 6 days.

extract_protocol:
Total RNA was isolated using the High-Pure Rna isolation kit (Roche, 11828665001), as per manufacturer's instructions (with the addition that 2-mercaptoethanol (1%v/v) was added to the lysis buffer. RNA quality was checked on Agilent Bioanalyzer.  All samples used have high quality score.
TruSeq Stranded RNA-Seq with poly (A) selection
Illumina HiSeq2500, stranded, paired-end, barcoded, Sequence read length: 126 bp

treatment_protocol: differentiated macrophages were treated with 100ng/ml LPS or PBS for 8 or 12 hours

tag: donor

tag: genotype

value: permissive for TREML4 (CT)

tag: tissue

value: blood

tag: cell type

value: monocyte-derived macrophages

tag: stimulation

value: unstimulated


title: EBF1KO_780_p3_6

city: Freiburg im Breisgau

first: Josip

middle: Stefan

last: Herman

address: Stuebeweg 51

department: Quantitative Single Cell Biology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
KO_2
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 1
Illumina barcode: RPI6
Barcode sequence: GCCAAT

data_processing:
For image acquisition, intensity extraction and basecalling HiSeq Control Software 2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2 was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14.
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus.
The right read (R2) of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction (Baker et al., 2005). Reads mapping to multiple loci were discarded.
The left read (R1) contains the barcode information: the first six bases corresponded to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch. The left read was not used for quantification.
For each cell barcode, the number of UMIs per transcript were counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs were converted into transcript counts (Grün et al., 2014).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-delimited text files, columns represent each cell barcode (total barcodes used = 192), rows represent the geneid and the values in the file are the quantified number of transcripts.

organism: Mus musculus

source_name: Bone marrow stromal cells

growth_protocol: Hematopoietic stroma cells and hematopoietic progenitors were isolated from Ebf1+/+ Prx1-Cre and Ebf1 fl/fl Prx1-Cre.

extract_protocol:
Intact bones (femora and tibia) were chopped into small fragments and crushed in FACS buffer (PBS-2% FCS) using pestle and mortar. Bone marrow cells were collected and RBC lysis was performed. Next, the cells were washed with FACS buffer and stained for analysis. For sorting of HSPCs the cells were enriched by magnetic depletion. Briefly, the BM cells were labeled with a cocktail of biotinylated antibodies (CD3, CD19, B220, CD11b, Gr1 and Ter119) and then with streptavidin-conjugated magnetic nanobeads (BioLegend). The Lineage- cells obtained were stained with following antibodies: anti-lineage (CD3, CD19, B220, CD11b, Gr1 and Ter119), anti-Sca1, anti-c-kit, anti-CD135, anti-CD48, anti-150, and then further purified by FACS sorting. The immunophenotypes of assayed hematopoietic cells were as follow: LSKs (Lin-Sca1+c-kit+), HSCs (CD135-CD48-CD150+LSK), MMP3 (CD135-CD48+CD150-LSK), MPP4 (CD135+ CD150-LSK), CLPs (Lin-Sca1loc-kitloIL-7Rα+CD135+), pro-B cells (B220+CD43+), pre-B cells (B220loCD43-), rec-B cells (B220hiCD43-), B cells (B220+CD19+), T cells (CD3+), myeloid cells (Mac1+Gr1+) and erythroid cells (Ter119+). For non-hematopoietic BM cell isolation, the bone chips were digested with 0.3% collagenase type II and 0.02% DNase I at 37°C for 45 min with gentle shaking. After enzymatic digestion, the cells were filtered, washed with FACS buffer, and stained accordingly. CAR cells were identified as CD45-CD31-Lin-PDGFRα+Sca1-, PαS cells were identified as CD45-CD31-Lin-PDGFRα+ Sca1+.
The aRNA was reversely transcribed in order to generate libraries for sequencing, as previously described. 1 µl of custom random hexamer RT primers (GCCTTGGCACCCGAGAATTCCANNNNNN) and 0.5 µl of 10mM dNTP were added to the aRNA. The samples were incubated at 65˚C for 5 min and cooled to 4˚C afterwards. Thereafter 4 µl of First Strand Reaction Mix containing SuperScript™ II Reverse Transcriptase and Buffer (Invitrogen, 18064014) and RnaseOUT™ (Invitrogen, 10777019) was added and samples were first incubated at 25˚C for 10 min followed by incubation at 42˚C for 1 hour. To every sample 2 µl of one uniquely indexed RPI index primer and 2 µl of RP1 primer (TruSeq Library Prep, sequences available from Illumina), 25 µl of Phusion® High-Fidelity PCR Master Mix with HF Buffer (NEB, M0531) and 11 µl of nuclease-free water were added. PCR was performed using 98˚C for 30 s as initial step, followed by 11 cycles of amplification (98˚C for 10 s, 60˚C for 30 s, 72˚C for 30 s) and a final extension at 72˚C for 10 min. To each sample 1 volume (50 µl) of Agencourt® AMPure XP beads (Beckman Coulter, A63881) was added and the samples were incubated at 25˚C for 15 min. The samples were incubated for 5 min on a magnetic stand (96 well format), the supernatant was removed and the beads were washed twice by adding 180 µl of 80 % ethanol and by incubating for 40 s. Ethanol was removed and beads were dried for 10 min at room temperature. DNA was eluted with 25 µl nuclease-free water and the purification was repeated with an adjusted volume of magnetic beads (25 µl). After the final step the samples were eluted in 10 µl nuclease-free water. DNA concentration and fragment size were determined using the Qubit® dsDNA HS Assay Kit (Invitrogen, Q32854) and the Agilent High Sensitivity DNA Kit for Bioanalyzer (Agilent Technologies, 5067-4627), respectively. Libraries were sequenced on an Illumina HiSeq 2500 System in high output run mode at a depth of 150000 to 200000 reads per cell.

treatment_protocol: No treatment.

tag: strain/background

value: bone marrow

tag: genotype/variation

value: Ebf1 fl/fl Prx1-Cre

value: bone marrow stromal cells


title: EBF1KO_780_p3_7

description:
KO_2
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 1
Illumina barcode: RPI7
Barcode sequence: CAGATC


title: sarcoma classifier reference case 611

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 611

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

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.

value: sarcoma

tag: material preparation

value: FFPE


title: monocyte-derived macrophages untreated donor permissive 568


title: sarcoma classifier reference case 882

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 882


title: KO_887_3

description:
KO_3
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 1
Illumina barcode: RPI7
Barcode sequence: CAGATC


title: sarcoma classifier reference case 876

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 876


title: sarcoma classifier reference case 874

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 874


title: sarcoma classifier reference case 610

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 610


title: monocyte-derived macrophages untreated donor permissive 157


title: sarcoma classifier reference case 873

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 873


title: EBF1KO_780_p2_4

description:
KO_2
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 1
Illumina barcode: RPI4
Barcode sequence: TGACCA


title: sarcoma classifier reference case 608

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 608


title: sarcoma classifier reference case 871

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 871


title: monocyte-derived macrophages untreated donor permissive 851


title: EBF1KO_780_p3_5

description:
KO_2
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 1
Illumina barcode: RPI5
Barcode sequence: ACAGTG


title: EBF1KO_780_p2_3

description:
KO_2
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 1
Illumina barcode: RPI3
Barcode sequence: TTAGGC


title: EBF1KO_780_p2_2

description:
KO_2
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 1
Illumina barcode: RPI2
Barcode sequence: CGATGT


title: sarcoma classifier reference case 607

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 607


title: isolated PBMC's untreated donor permissive 851

source_name: unstimulated PBMCs

value: PBMCs


title: isolated PBMC's untreated donor permissive 668


title: sarcoma classifier reference case 606

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 606


title: sarcoma classifier reference case 870

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 870


title: sarcoma classifier reference case 609

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 609


title: EBF1KO_780_p2_1

description:
KO_2
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 1
Illumina barcode: RPI1
Barcode sequence: ATCACG


title: sarcoma classifier reference case 605

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 605


title: sarcoma classifier reference case 869

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 869

value: KRYO


title: isolated PBMC's untreated donor permissive 157


title: CARwt_2

description:
WT_1
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 2
Illumina barcode: RPI2
Barcode sequence: CGATGT

value: Ebf1+/+ Prx1-Cre


title: sarcoma classifier reference case 866

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 866


title: sarcoma classifier reference case 603

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 603


title: sarcoma classifier reference case 604

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 604


title: CARwt_4

description:
WT_1
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 2
Illumina barcode: RPI4
Barcode sequence: TGACCA


title: CARwt_3

description:
WT_1
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 2
Illumina barcode: RPI3
Barcode sequence: TTAGGC


title: sarcoma classifier reference case 864

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 864


title: sarcoma classifier reference case 868

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 868


title: Cardiff_HD109n1_09_A

city: Irvine

first: Ryan

middle: Gar-Lok

last: Lim

state: California

address: 845 Health Sciences Rd.

department: MIND

institute: UC Irvine

description:
Cardiff_HD109n1_09_R_2
HD sample Total RNAseq

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence or low-quality sequence, and then mapped to hg19 whole genome using tophat2
gene counts were quantified using htseq and raw counts were used for normalization and differential stats using deseq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

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:
Qiagen RNeasy Kit and QIAshredders for cell lysis. 1 µg of RNA with RIN values >9 were used for library preparation and ribozero gold was used for rRNA depletion
RNA libraries were prepared for sequencing using standard Illumina protocols for stranded total RNAseq

value: iPSC-derived MSN-like

tag: condition

value: HD


title: CARwt_1

description:
WT_1
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 2
Illumina barcode: RPI1
Barcode sequence: ATCACG


title: sarcoma classifier reference case 601

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 601


title: Cardiff_HD71n3_81_A

description:
Cardiff_HD71n3_81_R_2
HD sample Total RNAseq


title: CARko_8

description:
KO_1
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 2
Illumina barcode: RPI8
Barcode sequence: ACTTGA


title: CARko_7

description:
KO_1
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 2
Illumina barcode: RPI7
Barcode sequence: CAGATC


title: sarcoma classifier reference case 862

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 862


title: sarcoma classifier reference case 861

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 861


title: Cardiff_HD66n4_02_A

description:
Cardiff_HD66n4_02_R_2
HD sample Total RNAseq


title: sarcoma classifier reference case 600

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 600


title: sarcoma classifier reference case 598

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 598


title: CARko_6

description:
KO_1
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 2
Illumina barcode: RPI6
Barcode sequence: GCCAAT


title: isolated PBMC's untreated donor permissive 878


title: Cardiff_CTL33n1_83_A

description:
Cardiff_CTL33n1_83_R_2
CTL sample Total RNAseq

value: control


title: sarcoma classifier reference case 859

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 859


title: CARko_5

description:
KO_1
mRNA
Library of 96 cells
CEL-Seq2 (Hashimshony et al. 2016, Genome Biology, DOI: 10.1186/s13059-016-0938-8)
Sequencing runs: 2
Illumina barcode: RPI5
Barcode sequence: ACAGTG


title: Cardiff_HD53n3_03_A

description:
Cardiff_HD53n3_03_R_2
HD sample Total RNAseq


title: RNA-seq_Treg_WT_rep3

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Reads were trimmed using Trim Galore v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the Nextera adapter sequence.
Mapping of RNA-Seq data was performed using HISAT2 v2.1.0 against the mouse NCBIM37 genome. Hits were again filtered to remove mappings with MAPQ scores of <20.
Genome_build: NCBIM37
Supplementary_files_format_and_content: The RNA-Seq report is tab-delimited and shows annotated gene coordinates and their log2(RPM) values as follows: <gene name>, <Chromosome>, <Start>, <End>, <Probe strand>,<Ensembl ID>, <Description> and then values for samples <columns 8-19>.

source_name: Spleen

growth_protocol: CD4+ Foxp3GFP+ Treg and CD4+ Foxp3GFP¬– Tconv cells were sorted by FACS from WT and Enh-KO Foxp3GFP reporter animals. Briefly, total CD4+ T cells were pre-enriched from single cell spleen suspensions using magnetic negative selection (eBioscience) prior to FACS sorting of GFP+ and GFP– CD4+ T cells using a BD Influx instrument (Becton Dickinson Biosciences). Cells were sorted into solutions of RPMI 1640 medium supplemented with 20% FBS and pellets were stored in RNAlater (Ambion) at -80 °C.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer instructions.
Barcoded libraries were prepared using the SmartSeq2 protocol as previously described {Picelli, 2014 #31} using a Hamilton NGS-STAR library preparation automation system at the BI Sequencing Facility and sequenced using a HiSeq 2500 (Illumina).
PCR products were barcoded (indexed) and sequenced on Illumina HiSeq 2500

value: Spleen

value: WT


title: sarcoma classifier reference case 597

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 597


title: sarcoma classifier reference case 596

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 596


title: sarcoma classifier reference case 863

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 863


title: sarcoma classifier reference case 858

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 858


title: Cardiff_CTL18n2_25_A

description:
Cardiff_CTL18n2_25_R_2
CTL sample Total RNAseq


title: sarcoma classifier reference case 599

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 599


title: sarcoma classifier reference case 595

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 595


title: RNA-seq_Treg_WT_rep1


title: sarcoma classifier reference case 594

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 594


title: RNA-seq_Treg_WT_rep2


title: Cardiff_CTL18n6_25_A

description:
Cardiff_CTL18n6_25_R_2
CTL sample Total RNAseq


title: RNA-seq_Treg_KO_rep3

value: Lrrc32 +70Kb Enh KO


title: sarcoma classifier reference case 855

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 855


title: Cardiff_HD46n10_04_A

description:
Cardiff_HD46n10_04_R_2
HD sample Total RNAseq


title: sarcoma classifier reference case 854

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 854


title: Cardiff_HD71n3_81_B

description:
Cardiff_HD71n3_81_R_3
HD sample Total RNAseq


title: isolated PBMC's untreated donor permissive 568

value: permissive for TREML4 (CT)

value: blood


title: RNA-seq_Treg_KO_rep2


title: RNA-seq_Treg_KO_rep1


title: RNA-seq_Tconv_WT_rep3


title: Cardiff_HD109n1_09_B

description:
Cardiff_HD109n1_09_R_3
HD sample Total RNAseq


title: sarcoma classifier reference case 852

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 852


title: sarcoma classifier reference case 857

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 857


title: Cardiff_HD53n3_03_B

description:
Cardiff_HD53n3_03_R_3
HD sample Total RNAseq


title: sarcoma classifier reference case 851

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 851


title: sarcoma classifier reference case 591

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 591


title: sarcoma classifier reference case 590

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 590


title: sarcoma classifier reference case 592

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 592


title: sarcoma classifier reference case 593

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 593


title: sarcoma classifier reference case 850

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 850


title: Cardiff_HD46n10_04_B

description:
Cardiff_HD46n10_04_R_3
HD sample Total RNAseq


title: sarcoma classifier reference case 589

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 589


title: Cardiff_CTL33n1_83_B

description:
Cardiff_CTL33n1_83_R_3
CTL sample Total RNAseq


title: sarcoma classifier reference case 856

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 856


title: sarcoma classifier reference case 588

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 588


title: RNA-seq_Tconv_WT_rep1


title: Cardiff_CTL28n6_14_A

description:
Cardiff_CTL28n6_14_R_2
CTL sample Total RNAseq


title: RNA-seq_Tconv_KO_rep3


title: sarcoma classifier reference case 587

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 587


title: Cardiff_CTL28n6_14_B

description:
Cardiff_CTL28n6_14_R_3
CTL sample Total RNAseq


title: sarcoma classifier reference case 853

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 853


title: Cardiff_HD66n4_02_B

description:
Cardiff_HD66n4_02_R_3
HD sample Total RNAseq


title: sarcoma classifier reference case 848

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 848


title: RNA-seq_Tconv_KO_rep2


title: sarcoma classifier reference case 586

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 586


title: sarcoma classifier reference case 847

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 847


title: Cardiff_CTL18n6_25_B

description:
Cardiff_CTL18n6_25_R_3
CTL sample Total RNAseq


title: RNA-seq_Tconv_WT_rep2


title: RNA-seq_Tconv_KO_rep1


title: Cardiff_CTL18n2_25_B

description:
Cardiff_CTL18n2_25_R_3
CTL sample Total RNAseq


title: sarcoma classifier reference case 585

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 585


title: loi_2

city: Bethesda

first: Apratim

last: Mitra

state: MD

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

data_processing:
Raw data from the Illumina HiSeq2500 was aligned to mouse genome version mm10 using STAR v2.5.3a.
Reads within exons of genes (n=24421, from Illumina iGenomes archive which downloaded the annotation from UCSC genome browser on March 6, 2013) were calculated using featureCounts v1.4.6-p3.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table of raw sequencing reads for each gene per sample (24421 genes x 4 samples).

source_name: heart

growth_protocol: Hearts were isolated from six-month old mice for RNA extraction. Only male mice were used for analyses. All mice were bred and housed in accordance with National Institutes of Health and United States Public Health Service policy. Animal research was performed only after protocols were approved by the Eunice Kennedy Shriver National Institute of Child Health and Human Development Animal Care and Use Committee.

extract_protocol:
RNA was isolated from heart tissue using RNeasy Plus Mini kit (Qiagen). Samples with RNA Integrity numbers >9 were used for sequencing. Ribosomal RNA was depleted from 1-5 μg total RNA using the RiboZero Gold kit (Illumina).
Library preparation for the Illumina HiSeq2500 was performed using the TruSeq RNA Sample Prep V2 kit (Illumina). Pooled barcoded libraries were sequenced to generate paired-end 101 bp reads.

value: dICR/dICR

tag: tossie

value: heart


title: Cardiff_HD109n1_09_C

description:
Cardiff_HD109n1_09_R_1
HD sample Total RNAseq


title: sarcoma classifier reference case 845

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 845


title: sarcoma classifier reference case 846

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 846


title: sarcoma classifier reference case 584

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 584


title: sarcoma classifier reference case 583

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 583


title: Cardiff_HD66n4_02_C

description:
Cardiff_HD66n4_02_R_1
HD sample Total RNAseq


title: sarcoma classifier reference case 849

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 849


title: sarcoma classifier reference case 844

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 844


title: wt_1

value: wild type


title: wt_2


title: sarcoma classifier reference case 582

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 582


title: sarcoma classifier reference case 843

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 843


title: Cardiff_HD53n3_03_C

description:
Cardiff_HD53n3_03_R_1
HD sample Total RNAseq


title: sarcoma classifier reference case 581

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 581


title: sarcoma classifier reference case 580

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 580


title: sarcoma classifier reference case 841

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 841


title: Cardiff_CTL33n1_83_C

description:
Cardiff_CTL33n1_83_R_1
CTL sample Total RNAseq


title: Cardiff_CTL28n6_14_C

description:
Cardiff_CTL28n6_14_R_1
CTL sample Total RNAseq


title: sarcoma classifier reference case 839

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 839


title: loi_1


title: Cardiff_HD71n3_81_C

description:
Cardiff_HD71n3_81_R_1
HD sample Total RNAseq


title: sarcoma classifier reference case 840

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 840


title: sarcoma classifier reference case 576

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 576


title: sarcoma classifier reference case 837

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 837


title: sarcoma classifier reference case 579

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 579


title: sarcoma classifier reference case 838

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 838


title: TK1

city: Beijing

first: J

last: Z

address: 1 Beichen West Road, Chaoyang District

department: State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to h19 genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments per Kilobase per Millon Mapped Fragments (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: h19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment


title: sarcoma classifier reference case 575

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 575


title: sarcoma classifier reference case 836

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 836


title: K562_WT_CTCF

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

library_source: genomic

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 bedgraph files include RPM values for each Sample

source_name: K562 cells

growth_protocol: Human endometrial HEC-1-B cells (ATCC) were cultured in MEM medium (Hyclone), supplemented with 10% (v/v) FBS (Gibco), 2 mM glutamine (Gibco), 1 mM sodium pyruvate (Sigma), and 1× penicillin-streptomycin (Gibco). Human K562 cells (ATCC) were cultured in DMEM medium (Hyclone) supplemented with 10% (v/v) FBS and 1× penicillin-streptomycin. Cells were maintained at 37 °C in a humidified incubator containing 5% (v/v) of CO2, and were passaged every three days.

extract_protocol:
4 × 10^6 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.
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: chronic myelogenous leukemia

tag: antibody

value: CTCF

value: wildtype


title: Exosome RNA from  MDA-MB-231 (MM231) cells  treated with 17β-estradiol replicate 2

type: RNA

city: Houston

first: George

last: Calin

state: TX

address: 1881 East Road

department: Experimental Therapeutics

institute: MD Anderson Cancer Center

hyb_protocol: Following fragmentation, 5 micrograms of biotin-labeled sense-strand cDNA fragments in 200 µL of hybridization mix was loaded onto a human Clariom D array and hybridized to probes on the array in a GeneChip Hybridization Oven 645 (Affymetrix) for 16 h at 45°C with 60 rpm rotation.

scan_protocol: GeneChips were scanned using GeneArray G7 scanner (Affymetrix) and quantified into .CEL files with image and signal intensities.

data_processing: Transcriptome Analysis Console software v4.0 (Affymetrix) was used for probe set summarization and robust multiarray average (RMA+DABG) normalization procedures.

label: biotin

source_name: MDA-MB-231 (MM231) Exosome

label_protocol: The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase using the Affymetrix proprietary DNA labeling reagent, which is covalently linked to biotin.

growth_protocol: Cell lines were cultured in Dulbecco's Modified Eagle's Medium (DMEM)/F12 medium (Corning, NY, USA) supplemented with 10% Fetal Bovine Serum (FBS, Sigma-Aldrich, St. Louis, MO, USA) and maintained at 37°C in a humidified atmosphere of 5%CO2.

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

treatment_protocol: MCF7 and MDA231 cells with 60%-70% confluence  were washed with PBS three times and cultured in 10% serum charcoal-free, exosome-free, and phenol-red free DMEM/F12 medium for 72hrs, and starved for 24hrs, and then treated with or without 10nM 17β-estradiol in 10% serum charcoal-free, exosome-free, and phenol-red free DMEM for 48hrs.

value: mammary gland, breast; derived from metastatic site - pleural effusion

value: ER-, PR-, HER-


title: CK1


title: sarcoma classifier reference case 835

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 835

value: sarcoma

value: FFPE


title: sarcoma classifier reference case 573

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 573


title: sarcoma classifier reference case 834

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 834


title: Exosome RNA from  MDA-MB-231 (MM231) cells  treated with 17β-estradiol replicate 1


title: K562_REV-FWD2_mut_CTCF

value: RF2 mutation


title: Exosome RNA from  MDA-MB-231 (MM231) cells  not treated with 17β-estradiol replicate 2


title: Exosome RNA from MCF7 cells not treated with 17β-estradiol replicate 2

source_name: MCF7 Exosome

value: ER+, PR+, HER-


title: sarcoma classifier reference case 577

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 577


title: sarcoma classifier reference case 571

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 571


title: sarcoma classifier reference case 832

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 832


title: Cardiff_CTL18n6_25_C

description:
Cardiff_CTL18n6_25_R_1
CTL sample Total RNAseq

value: iPSC-derived MSN-like

value: control


title: sarcoma classifier reference case 833

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 833


title: sarcoma classifier reference case 572

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 572


title: sarcoma classifier reference case 570

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 570


title: HEC-1-B_WT_CTCF

source_name: HEC-1-B cells

value: human endometrial adenocarcinoma


title: HEC-1-B_WT5_CTCF


title: K562_REV-FWD2_CTCF

value: RF2 insertion


title: sarcoma classifier reference case 569

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 569


title: sarcoma classifier reference case 574

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 574


title: Exosome RNA from  MDA-MB-231 (MM231) cells  not treated with 17β-estradiol replicate 1


title: sarcoma classifier reference case 830

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 830

value: KRYO


title: HEC-1-B_WT4_CTCF


title: sarcoma classifier reference case 568

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 568


title: K562_REV-FWD2_Rad21


title: sarcoma classifier reference case 829

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 829


title: Exosome RNA from MCF7 cells not treated with 17β-estradiol replicate 1


title: sarcoma classifier reference case 567

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 567


title: HEC-1-B_WT3_CTCF


title: Exosome RNA from MCF7 cells  treated with 17β-estradiol replicate 1


title: sarcoma classifier reference case 831

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 831


title: Exosome RNA from MCF7 cells  treated with 17β-estradiol replicate 2


title: sarcoma classifier reference case 602

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 602


title: HEC-1-B_REV2_Rad21

value: R2 insertion


title: HEC-1-B_WT2_CTCF


title: RNA from MDA-MB-231 (MM231) cells  treated with 17β-estradiol replicate 2

source_name: MDA-MB-231 (MM231) cells

value: mammary gland/breast; derived from metastatic site - pleural effusion


title: sarcoma classifier reference case 566

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 566


title: sarcoma classifier reference case 578

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 578


title: sarcoma classifier reference case 565

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 565


title: RNA from MDA-MB-231 (MM231) cells not treated with 17β-estradiol replicate 2


title: RNA from MDA-MB-231 (MM231) cells  treated with 17β-estradiol replicate 1


title: RNA from MDA-MB-231 (MM231) cells not treated with 17β-estradiol replicate 1


title: RNA from MCF7 cells not treated with 17β-estradiol replicate 2

source_name: MCF7 cells


title: RNA from MCF7 cells not treated with 17β-estradiol replicate 1


title: HEC-1-B_REV2_CTCF


title: sarcoma classifier reference case 564

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 564


title: sarcoma classifier reference case 563

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 563


title: sarcoma classifier reference case 485

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 485


title: sarcoma classifier reference case 486

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 486


title: HEC-1-B_REV1_Rad21

value: R1 insertion


title: sarcoma classifier reference case 488

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 488


title: sarcoma classifier reference case 562

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 562


title: sarcoma classifier reference case 487

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 487


title: HEC-1-B_REV1_mut_CTCF

value: R1 mutation


title: E14.1T136A

city: hang zhou

first: qiang

last: zhu

state: zhe jiang

address: yuhangtang road 866

institute: Zhe Jiang university

data_processing:
Illumina paired-end data (for CASAVA 1.8+).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, the clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS
RPKM of each gene was caculated based on the length of gene and reads count mapped to the gene
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: E14.1 cells

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: T136A AHCY


title: HEC-1-B_REV1_CTCF

value: CTCF


title: E14.1WT

value: WT AHCY


title: RNA from MCF7 cells  treated with 17β-estradiol replicate 1

value: mammary gland, breast; derived from metastatic site - pleural effusion


title: sarcoma classifier reference case 561

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 561

value: sarcoma


title: RNA from MCF7 cells  treated with 17β-estradiol replicate 2


title: sarcoma classifier reference case 560

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 560

value: FFPE


title: sarcoma classifier reference case 484

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 484


title: sarcoma classifier reference case 480

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 480


title: sarcoma classifier reference case 559

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 559


title: HEC-1-B_REV-FWD_Rad21

value: RF insertion


title: HEC-1-B_REV-FWD_mut_CTCF

value: RF mutation


title: HEC-1-B_REV-FWD_CTCF


title: sarcoma classifier reference case 434

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 434


title: sarcoma classifier reference case 435

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 435


title: HEC-1-B_FWD_Rad21

value: F insertion


title: sarcoma classifier reference case 557

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 557


title: sarcoma classifier reference case 433

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 433


title: HEC-1-B_FWD_mut_CTCF

value: F mutation


title: sarcoma classifier reference case 556

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 556


title: sarcoma classifier reference case 432

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 432


title: sarcoma classifier reference case 555

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 555


title: sarcoma classifier reference case 431

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 431


title: thoracic_aorta_valsartan_rep4

city: Cheng Du

first: Ke

last: Xu

state: SiChuan

address: No.36, Shuxi Road

institute: Chengdu Kanghong Pharmaceutical Co. Ltd.

description: Gene expression after 28 days in orally administrated with valsartan rat thoracic aorta

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

organism: Rattus norvegicus

source_name: thoracic aorta,valsartan group,replicate 4

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP using the Quick Amp Labeling Kit, One-Color (Agilent, Santa Clara, CA, USA). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The animals are kept in an animal breeding room where the environmental conditions are strictly controlled. The temperature in the rearing room is maintained at 20 to 24 ° C, and the humidity is maintained at 30 to 70%. The temperature and humidity of the rearing room were monitored in real time by a thermometer and hygrometer and recorded twice a day (one in the morning and one in the afternoon). The daylighting of the animal husbandry is controlled by an electronic timed lighting system that turns off the lights for 12 hours every day and on for 12 hours (7:00 AM to19:00 PM). During the experiment, the animals were kept in single cages. They were fed with standard laboratory diet and guaranteed free drinking water.

extract_protocol: The thoracic aorta of all animals was collected for DNA microarray analyses from each group.Total RNA was extracted and purified from thoracic aorta tissue separately by TRIzol® Reagent (Invitrogen life technologies, Carlsbad, CA, USA) and Cleaned-up by RNasey Mini Kit (Qiagen, Valencia, CA, USA). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: SHRs were randomly divided into three groups : model group (n = 8), rats were orally administered with saline (7.5mL.kg-1) for 4 weeks; SXC low-dose group(n = 6), rats were orally administered with SXC (236.25 mg.kg-1) for 4 weeks; SXC high-dose group (n = 6), rats were orally administered with SXC (708.75 mg.kg-1) for 4 weeks; the positive group (n=8), rats were orally administered with valsartan (21.6mg.kg-1) for 4 weeks. The SXC was orally administered at 9:00-10:00 and 12:00-13:00 every day and the valsartan was administered at 14:00-15:00 every day. At 28 days, all rats were killed with intraperitoneal injection of 3% sodium pentobarbital solution (60mg.kg-1).The thoracic aorta dissected from each rat was shredded and immediately stored in liquid nitrogen.

value: thoracic aorta

tag: gender

value: male

value: valsartan


title: HEC-1-B_FWD_CTCF

value: human endometrial adenocarcinoma


title: thoracic_aorta_valsartan_rep5

source_name: thoracic aorta,valsartan group,replicate 5


title: thoracic_aorta_valsartan_rep6

source_name: thoracic aorta,valsartan group,replicate 6


title: sarcoma classifier reference case 558

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 558


title: BM_MNC_Ninjin_11day

city: Fukuoka

first: Daisuke

last: Sugiyama

state: Fukioka

address: 3-1-1, Maidashi, Higasi-ku

department: Incubation Center for Advanced Medical Science (ICAMS)

country: Japan

institute: Kyushu university

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Mouse Gene Expression Microarray 4x44K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: BM_MNC cell, ninjin'yoeito (NYT)

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from cultures of BM MNCs cells using a RiboPureTM Kit (Life Technologies, Carlsbad, CA) following the manufacturer's recommendations. RNA concentration was measured by NANODROP 2000c (Thermo Fisher Scientific).

treatment_protocol: Mouse bone marrow MNCs cultured with and without Ninjin’yeito or negative controls were collected at day 11. MNCs were harvested by flushing femurs of 2–4 months C57BL/6 mice with IMDM (SIGMA-ALDRICH, St. Louis, MO) supplemented with 2% fetal bovine serum (FBS).

tag: strain

value: bone marrow mononuclear cells (BM MNCs)

value: herbal drug ninjin'yoeito (NYT)


title: sarcoma classifier reference case 430

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 430


title: HEC-1-B_a12CBSdel_CTCF

value: a12 CBS deletion


title: sarcoma classifier reference case 554

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 554


title: sarcoma classifier reference case 553

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 553


title: BM_MNC_Negative_11day

source_name: BM_MNC cell, control

value: none (negative control)


title: sarcoma classifier reference case 418

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 418


title: sarcoma classifier reference case 552

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 552


title: HEC-1-B_2REV_2FWD_Rad21

value: RRFF insertion


title: thoracic_aorta_valsartan_rep3

source_name: thoracic aorta,valsartan group,replicate 3


title: sarcoma classifier reference case 414

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 414

source_name: sarcoma sample


title: sarcoma classifier reference case 551

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 551


title: HEC-1-B_2REV_2FWD_mut_CTCF

value: CTCF

value: RRFF mutation


title: thoracic_aorta_valsartan_rep1

source_name: thoracic aorta,valsartan group,replicate 1


title: sarcoma classifier reference case 550

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 550

value: sarcoma


title: HEC-1-B_ac1CBSdel_CTCF

value: ac1 CBS deletion


title: thoracic_aorta_SXC_high_rep6

description: Gene expression after 28 days in orally administrated with high dose SXC rat thoracic aorta

source_name: thoracic aorta,SXC high dose group,replicate 6

value: high dose SXC


title: thoracic_aorta_SXC_high_rep5

source_name: thoracic aorta,SXC high dose group,replicate 5


title: HEC-1-B_2REV_2FWD_CTCF


title: thoracic_aorta_valsartan_rep2

source_name: thoracic aorta,valsartan group,replicate 2


title: sarcoma classifier reference case 413

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 413

value: FFPE


title: thoracic_aorta_SXC_high_rep4

source_name: thoracic aorta,SXC high dose group,replicate 4


title: sarcoma classifier reference case 410

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 410


title: HEC-1-B_2FWD_mut_CTCF

value: FF mutation


title: thoracic_aorta_SXC_high_rep3

source_name: thoracic aorta,SXC high dose group,replicate 3


title: sarcoma classifier reference case 549

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 549


title: sarcoma classifier reference case 548

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 548


title: HEC-1-B_2FWD-2REV_Rad21

source_name: HEC-1-B cells

value: FFRR insertion


title: sarcoma classifier reference case 547

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 547


title: sarcoma classifier reference case 409

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 409


title: sarcoma classifier reference case 408

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 408


title: thoracic_aorta_SXC_high_rep2

source_name: thoracic aorta,SXC high dose group,replicate 2

value: thoracic aorta


title: thoracic_aorta_SXC_high_rep1

source_name: thoracic aorta,SXC high dose group,replicate 1

value: male


title: sarcoma classifier reference case 412

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 412


title: sarcoma classifier reference case 407

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 407


title: HEC-1-B_2FWD_Rad21_2

value: FF insertion


title: sarcoma classifier reference case 411

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 411


title: thoracic_aorta_SXC_low_rep4

description: Gene expression after 28 days in orally administrated with low dose SXC rat thoracic aorta

source_name: thoracic aorta,SXC low dose group,replicate 4

value: low dose SXC


title: thoracic_aorta_SXC_low_rep5

source_name: thoracic aorta,SXC low dose group,replicate 5


title: sarcoma classifier reference case 543

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 543


title: sarcoma classifier reference case 544

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 544


title: sarcoma classifier reference case 406

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 406


title: sarcoma classifier reference case 405

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 405


title: HEC-1-B_WT_rep9

data_processing:
Reads were aligned using Hisat2 (version 2.0.4) to the human genome (GRCh38/hg38), and the FPKM value was calculated using the Cufflinks program (version2.1.1)
Genome_build: hg38
Supplementary_files_format_and_content: fpkm_tracking: frgaments per kilobase of exon per million reads mapped.

molecule: polyA RNA

extract_protocol:
Total RNA from culture cells was extracted using Trizol reagents (Life Technologies) following the manufacturer’s instructions. Total mRNA was prepared from 1 mg total RNA using poly(A) mRNA magnetic isolation reagents (NEB) and fragmented at 94 °C for 15 min. RNA was then reverse-transcribed into cDNA with random primers. After end repairing and A-tailing, cDNA was ligated with adapters and amplified by PCR with Illumina sequencing primers.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human endometrial adenocarcinoma

tag: cell line

value: wildtype

tag: affected genomic location


title: HEC-1-B_2FWD-2REV_mut_CTCF

value: FFRR mutation


title: sarcoma classifier reference case 542

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 542


title: HEC-1-B_2FWD-2REV_CTCF


title: HEC-1-B_WT_rep7


title: sarcoma classifier reference case 404

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 404


title: HEC-1-B_WT_rep6


title: sarcoma classifier reference case 403

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 403


title: thoracic_aorta_SXC_low_rep6

source_name: thoracic aorta,SXC low dose group,replicate 6


title: sarcoma classifier reference case 545

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 545


title: sarcoma classifier reference case 540

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 540


title: thoracic_aorta_SXC_low_rep3

source_name: thoracic aorta,SXC low dose group,replicate 3


title: HEC-1-B_WT_rep8


title: thoracic_aorta_saline_rep8

description: Gene expression after 28 days in orally administrated with saline in rat thoracic aorta

source_name: thoracic aorta,saline group,replicate 8

value: saline


title: thoracic_aorta_SXC_low_rep1

source_name: thoracic aorta,SXC low dose group,replicate 1


title: thoracic_aorta_SXC_low_rep2

source_name: thoracic aorta,SXC low dose group,replicate 2


title: sarcoma classifier reference case 546

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 546

source_name: sarcoma sample


title: HEC-1-B_WT_rep5


title: sarcoma classifier reference case 539

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 539


title: sarcoma classifier reference case 402

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 402


title: HEC-1-B_WT_rep4


title: sarcoma classifier reference case 538

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 538


title: sarcoma classifier reference case 401

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 401


title: sarcoma classifier reference case 541

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 541


title: HEC-1-B_WT_rep2


title: sarcoma classifier reference case 537

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 537


title: sarcoma classifier reference case 398

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 398


title: sarcoma classifier reference case 400

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 400


title: sarcoma classifier reference case 397

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 397


title: HEC-1-B_WT_rep14


title: sarcoma classifier reference case 535

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 535


title: HEC-1-B_WT_rep13


title: thoracic_aorta_saline_rep4

source_name: thoracic aorta,saline group,replicate 4


title: thoracic_aorta_saline_rep6

source_name: thoracic aorta,saline group,replicate 6


title: sarcoma classifier reference case 536

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 536


title: sarcoma classifier reference case 396

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 396


title: thoracic_aorta_saline_rep5

source_name: thoracic aorta,saline group,replicate 5


title: HEC-1-B_WT_rep12


title: sarcoma classifier reference case 394

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 394


title: HEC-1-B_WT_rep3


title: sarcoma classifier reference case 533

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 533


title: sarcoma classifier reference case 395

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 395


title: thoracic_aorta_saline_rep7

description: Gene expression after 28 days in orally administrated with saline in rat thoracic aorta

source_name: thoracic aorta,saline group,replicate 7


title: thoracic_aorta_saline_rep3

source_name: thoracic aorta,saline group,replicate 3


title: thoracic_aorta_saline_rep2

source_name: thoracic aorta,saline group,replicate 2


title: sarcoma classifier reference case 532

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 532


title: HEC-1-B_WT_rep10

source_name: HEC-1-B cells


title: sarcoma classifier reference case 393

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 393


title: HEC-1-B_WT_rep11


title: sarcoma classifier reference case 531

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 531


title: thoracic_aorta_saline_rep1

source_name: thoracic aorta,saline group,replicate 1


title: HEC-1-B_WT_rep1


title: HEC-1-B_REV2_mut_rep4

value: R2 CBS mutation


title: sarcoma classifier reference case 530

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 530


title: sarcoma classifier reference case 392

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 392


title: sarcoma classifier reference case 391

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 391


title: sarcoma classifier reference case 534

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 534


title: sarcoma classifier reference case 529

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 529


title: HEC-1-B_REV2_mut_rep3


title: sarcoma classifier reference case 390

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 390


title: HEC-1-B_REV1_rep4

value: R1 CBS insertion


title: sarcoma classifier reference case 528

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 528

value: KRYO


title: sarcoma classifier reference case 527

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 527

value: sarcoma


title: sarcoma classifier reference case 389

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 389


title: sarcoma classifier reference case 388

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 388


title: HEC-1-B_REV1_rep3


title: sarcoma classifier reference case 526

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 526


title: sarcoma classifier reference case 525

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 525


title: HEC-1-B_FWD_rep1

value: F CBS insertion


title: wt_se_8mon_vessel_rep1

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

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.

source_name: wild-type, smoke-exposed, 8 months, vessmoke-exposedl, replicate 1

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 385

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 385


title: sarcoma classifier reference case 524

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 524


title: HEC-1-B_FWD_rep2


title: wt_se_8mon_vessel_rep3

source_name: wild-type, smoke-exposed, 8 months, vessmoke-exposedl, replicate 3


title: HEC-1-B_c1del_rep4

value: ac1 CBS deletion


title: wt_se_8mon_vessel_rep4

source_name: wild-type, smoke-exposed, 8 months, vessmoke-exposedl, replicate 4


title: wt_se_8mon_septa_rep4

source_name: wild-type, smoke-exposed, 8 months, smoke-exposedpta, replicate 4


title: sarcoma classifier reference case 384

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 384

value: FFPE


title: wt_se_8mon_vessel_rep2

source_name: wild-type, smoke-exposed, 8 months, vessmoke-exposedl, replicate 2


title: sarcoma classifier reference case 383

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 383


title: HEC-1-B_c1del_rep3


title: wt_se_8mon_septa_rep5

source_name: wild-type, smoke-exposed, 8 months, smoke-exposedpta, replicate 5


title: sarcoma classifier reference case 382

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 382


title: sarcoma classifier reference case 522

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 522


title: sarcoma classifier reference case 523

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 523


title: wt_se_8mon_septa_rep3

source_name: wild-type, smoke-exposed, 8 months, smoke-exposedpta, replicate 3


title: HEC-1-B_c1del_rep2


title: wt_se_8mon_septa_rep2

source_name: wild-type, smoke-exposed, 8 months, smoke-exposedpta, replicate 2


title: wt_se_8mon_septa_rep1

source_name: wild-type, smoke-exposed, 8 months, smoke-exposedpta, replicate 1


title: wt_se_3mon_vessel_rep5

source_name: wild-type, smoke-exposed, 3 months, vessmoke-exposedl, replicate 5


title: sarcoma classifier reference case 381

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 381

source_name: sarcoma sample


title: sarcoma classifier reference case 521

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 521


title: sarcoma classifier reference case 380

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 380


title: HEC-1-B_c1del_rep1


title: wt_se_3mon_vessel_rep4

source_name: wild-type, smoke-exposed, 3 months, vessmoke-exposedl, replicate 4


title: HEC-1-B_a12del_rep2

value: a12 CBS deletion


title: sarcoma classifier reference case 519

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 519


title: sarcoma classifier reference case 520

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 520


title: sarcoma classifier reference case 378

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 378


title: sarcoma classifier reference case 518

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 518


title: sarcoma classifier reference case 379

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 379


title: sarcoma classifier reference case 377

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 377


title: HEC-1-B_a12del_rep1


title: HEC-1-B_2FWD-2REV_rep4

value: FFRR CBS insertion


title: sarcoma classifier reference case 517

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 517


title: HEC-1-B_2FWD-2REV_rep2


title: sarcoma classifier reference case 376

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 376


title: HEC-1-B_2FWD-2REV_rep1


title: sarcoma classifier reference case 516

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 516


title: wt_se_3mon_vessel_rep1

source_name: wild-type, smoke-exposed, 3 months, vessmoke-exposedl, replicate 1


title: wt_se_3mon_vessel_rep3

source_name: wild-type, smoke-exposed, 3 months, vessmoke-exposedl, replicate 3


title: wt_se_3mon_vessel_rep2

source_name: wild-type, smoke-exposed, 3 months, vessmoke-exposedl, replicate 2


title: wt_se_3mon_septa_rep5

source_name: wild-type, smoke-exposed, 3 months, smoke-exposedpta, replicate 5


title: sarcoma classifier reference case 515

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 515


title: sarcoma classifier reference case 375

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 375


title: sarcoma classifier reference case 374

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 374


title: HEC-1-B_2FWD-2REV_mut_rep3

source_name: HEC-1-B cells

value: FFRR CBS mutation


title: sarcoma classifier reference case 373

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 373


title: sarcoma classifier reference case 514

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 514


title: HEC-1-B_2FWD-2REV_mut_rep2


title: sarcoma classifier reference case 372

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 372


title: sarcoma classifier reference case 512

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 512


title: sarcoma classifier reference case 513

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 513


title: sarcoma classifier reference case 371

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 371


title: sarcoma classifier reference case 511

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 511


title: HEC-1-B_2FWD-2REV_mut_rep4


title: tsRNA-GluCUC replicate 3

city: Vienna

first: Schaefer

last: Matthias

state: AT

address: Schwarzspanierstrasse 17-I

department: Cell and Developmental Biology

country: Austria

institute: Medical University Vienna, Center for Anatomy & Cell Biology

description: processed file contains mapped reads to tRNA annotation

data_processing:
quality control (fastqc)
read Trimming (Trimmomatic) -> to remove adapters, barcodes
alignment, using Bowtie2 and tolerant parameters: -N 1 -L 5 -p 20
sam files were used to intersect with the coordinated of the predicted tRNA annotation in ENSEMBL
bed files were converted into tsv files
Genome_build: hg19

source_name: HEK293 cells with inducible Angiogenin expression system

extract_protocol:
HEK293 cells were harvested into ice-cold PBS, pelleted and extracted with self-made Trizol solution (38% (v/v) phenol, 800 mM guanidine thiocyanate, 400 mM ammonium thiocyanate, 100 mM NaOAc, 5% (v/v) glycerol, 0.5% (w/v) N-lauroylsarcosine). Small RNAs were enriched using anion-exchange chromatography followed by affinity capture using 5' amino-modified DNA oligonucleotides complementary to the target RNA covalently immobilized on a NHS-linked sepharose column. Co-purified full length tRNAs were removed from tsRNAs by size exclusion.
100 ng of purified tsRNAs were treated with 0.5 U/µL T4 polynucleotide kinase (NEB) and 166 µM ATP (NEB) for 40 minutes at 37°C. After clean-up using acidic phenol-chloroform extraction followed by isopropanol precipitation, small RNA library preparation was performed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 2) (NEB). cDNA libraries were sequenced on a HiSeq 2500 machine in a spike-in format in single-end 50 (SE50) mode.

treatment_protocol: at 70% confluency, addition of 1 ug/mL doxycylin and incubation for 48 hours before cell harvesting and RNA extraction

tag: nebnext small rna

tag: fragment

value: tRNA


title: tsRNA-GluCUC replicate 2


title: tsRNA-GluCUC replicate 1


title: HEC-1-B_2FWD-2REV_mut_rep1

tag: genotype


title: sarcoma classifier reference case 509

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 509

tag: tissue


title: wt_se_3mon_septa_rep1

source_name: wild-type, smoke-exposed, 3 months, smoke-exposedpta, replicate 1


title: sarcoma classifier reference case 370

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 370


title: wt_contr_8mon_vessel_rep5

source_name: wild-type, control, 8 months, vessmoke-exposedl, replicate 5


title: wt_se_3mon_septa_rep3

source_name: wild-type, smoke-exposed, 3 months, smoke-exposedpta, replicate 3


title: sarcoma classifier reference case 368

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 368


title: wt_se_3mon_septa_rep4

source_name: wild-type, smoke-exposed, 3 months, smoke-exposedpta, replicate 4


title: wt_contr_8mon_vessel_rep3

source_name: wild-type, control, 8 months, vessmoke-exposedl, replicate 3


title: sarcoma classifier reference case 508

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 508


title: wt_se_3mon_septa_rep2

source_name: wild-type, smoke-exposed, 3 months, smoke-exposedpta, replicate 2


title: tsRNA-GlyGCC replicate 3


title: wt_contr_8mon_vessel_rep4

source_name: wild-type, control, 8 months, vessmoke-exposedl, replicate 4


title: wt_contr_8mon_vessel_rep1

source_name: wild-type, control, 8 months, vessmoke-exposedl, replicate 1


title: wt_contr_8mon_vessel_rep2

source_name: wild-type, control, 8 months, vessmoke-exposedl, replicate 2


title: wt_contr_8mon_septa_rep5

source_name: wild-type, control, 8 months, smoke-exposedpta, replicate 5


title: sarcoma classifier reference case 367

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 367

source_name: sarcoma sample


title: tsRNA-GlyGCC replicate 2


title: sarcoma classifier reference case 369

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 369


title: tsRNA-GlyGCC replicate 1


title: sarcoma classifier reference case 510

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 510


title: sarcoma classifier reference case 506

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 506


title: sarcoma classifier reference case 507

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 507


title: sarcoma classifier reference case 365

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 365


title: wt_contr_8mon_septa_rep4

source_name: wild-type, control, 8 months, smoke-exposedpta, replicate 4


title: CRISPRi__EndoNeg__Rep2__Lib1

city: Boston

first: Martha

middle: L.

last: Bulyk

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics

institute: Brigham and Women's Hospital

description:
plasmid DNA
DNA-seq of sgRNA region of improperly differentiated (as determined by FACS of FOXA2 and SOX17) dCas9-KRAB-GFP cells transduced with our sgRNA library and pushed into endoderm

data_processing:
For all samples, we used cutadapt to remove adapters from the raw reads and trim bases with a Phred score < 20.
For RNA-seq samples, we then used kallisto to pseudoalign reads to GENCODE v25 (lifted to hg19) and performed differential expression analysis with sleuth.
For CRISPRi samples, we counted 20 bp sgRNAs in each sample, requiring a perfect match to either the BlpI restriction enzyme site (Set A primers) or the BstXI restriction enzyme site (Set B primers).
Genome_build: hg19
Supplementary_files_format_and_content: Transcript abundances and sgRNA counts

source_name: Endoderm undifferentiated (FOXA2-/SOX17-) dCas9-KRAB-GFP H1 hESC cells

growth_protocol: We cultured H1 cells in mTeSR1 media (STEMCELL Technologies) on Matrigel-coated plates and changed media daily. We passaged the cells every 5-7 days, using Gentle Cell Dissociation Reagent (GCDR) or ReLeSR (STEMCELL Technologies). We used the STEMdiff Definitive Endoderm kit, STEMdiff Early Mesoderm kitto induce endoderm and mesoderm differentiation, respectively. All kits are from STEMCELL Technologies, and differentiation was induced following the manufacturer’s protocol.

extract_protocol:
We isolated DNA from all cells using QIAamp columns (Qiagen), following the manufacturer’s instructions and adding a de-crosslinking step (resuspended cells in 180 µL Buffer ATL and 20 µL proteinase K, incubated at 56oC for 1 h, then 90oC for 1 h, then proceeded with standard QIAamp protocol). Following DNA isolation, we PCR amplified the sgRNA region using 2 different primer sets (Set A and Set B), when possible (i.e., when enough DNA existed to make sequencing libraries).
RNA-seq and plasmid DNA sequencing of sgRNA region

treatment_protocol: We infected dCas9-KRAB-GFP cells with the lentivirally-packaged sgRNA library at an MOI < 0.3 and selected in 1 µg/mL puromycin.

tag: experiment

value: CRISPRi screen

tag: differentiation protocol

value: STEMdiff Definitive Endoderm kit

tag: facs

value: FOXA2/SOX17 double negative cells


title: sarcoma classifier reference case 505

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 505

tag: material preparation


title: wt_contr_8mon_septa_rep2

source_name: wild-type, control, 8 months, smoke-exposedpta, replicate 2


title: sarcoma classifier reference case 504

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 504


title: CRISPRi__EndoNeg__Rep1__Lib2


title: sarcoma classifier reference case 363

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 363


title: sarcoma classifier reference case 503

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 503


title: sarcoma classifier reference case 366

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 366


title: sarcoma classifier reference case 362

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 362


title: CRISPRi__EndoPos__Rep2__Lib1

description:
plasmid DNA
DNA-seq of sgRNA region of properly endoderm-differentiated (as determined by FACS of FOXA2 and SOX17) dCas9-KRAB-GFP cells transduced with our sgRNA library and pushed into endoderm

source_name: Endoderm differentiated (FOXA2+/SOX17+) dCas9-KRAB-GFP H1 hESC cells

value: FOXA2/SOX17 double positive cells


title: sarcoma classifier reference case 501

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 501


title: CRISPRi__EndoNeg__Rep1__Lib1


title: sarcoma classifier reference case 502

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 502


title: wt_contr_8mon_septa_rep3

source_name: wild-type, control, 8 months, smoke-exposedpta, replicate 3


title: wt_contr_8mon_septa_rep1

source_name: wild-type, control, 8 months, smoke-exposedpta, replicate 1


title: wt_contr_3mon_vessel_rep4

source_name: wild-type, control, 3 months, vessmoke-exposedl, replicate 4


title: sarcoma classifier reference case 364

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 364


title: sarcoma classifier reference case 359

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 359


title: sarcoma classifier reference case 360

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 360


title: sarcoma classifier reference case 499

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 499


title: CRISPRi__EndoPos__Rep1__Lib1


title: wt_contr_3mon_vessel_rep2

source_name: wild-type, control, 3 months, vessmoke-exposedl, replicate 2


title: wt_contr_3mon_vessel_rep5

source_name: wild-type, control, 3 months, vessmoke-exposedl, replicate 5


title: sarcoma classifier reference case 361

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 361


title: CRISPRi__DayZero__Rep2__Lib2

description:
plasmid DNA
DNA-seq of sgRNA region of Day Zero undiffereniated dCas9-KRAB-GFP cells transduced with our sgRNA CRISPRi library

source_name: dCas9-KRAB-GFP H1 hESC cells


title: wt_contr_3mon_vessel_rep1

source_name: wild-type, control, 3 months, vessmoke-exposedl, replicate 1


title: sarcoma classifier reference case 358

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 358


title: CRISPRi__EndoPos__Rep1__Lib2


title: sarcoma classifier reference case 497

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 497


title: wt_contr_3mon_septa_rep4

source_name: wild-type, control, 3 months, smoke-exposedpta, replicate 4


title: wt_contr_3mon_septa_rep3

source_name: wild-type, control, 3 months, smoke-exposedpta, replicate 3


title: CRISPRi__DayZero__Rep2__Lib1


title: sarcoma classifier reference case 356

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 356


title: sarcoma classifier reference case 496

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 496


title: wt_contr_3mon_vessel_rep3

source_name: wild-type, control, 3 months, vessmoke-exposedl, replicate 3


title: CRISPRi__DayZero__Rep1__Lib3


title: CRISPRi__DayZero__Rep1__Lib2


title: CRISPRi__DayZero__Rep2__Lib3


title: sarcoma classifier reference case 495

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 495


title: wt_contr_3mon_septa_rep2

source_name: wild-type, control, 3 months, smoke-exposedpta, replicate 2


title: sarcoma classifier reference case 494

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 494


title: sarcoma classifier reference case 355

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 355


title: CRISPRi__DayZero__Rep1__Lib1


title: sarcoma classifier reference case 357

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 357


title: sarcoma classifier reference case 354

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 354


title: sarcoma classifier reference case 353

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 353


title: sarcoma classifier reference case 493

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 493


title: sarcoma classifier reference case 492

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 492


title: sarcoma classifier reference case 352

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 352


title: RNAseq__Meso__Rep1

description:
genomic RNA
RNA-seq of mesoderm cells (paired end)

source_name: Mesoderm differentiated from H1 hESC cells

extract_protocol:
We isolated RNA from each lineage (two replicates each) using the Direct-zol Miniprep RNA kit (Zymo) with the DNase treatment step.
RNA-seq and plasmid DNA sequencing of sgRNA region

value: RNA-seq

value: STEMdiff Early Mesoderm kit


title: sarcoma classifier reference case 498

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 498

source_name: sarcoma sample


title: sarcoma classifier reference case 351

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 351


title: RNAseq__hESC__Rep2

description:
genomic RNA
RNA-seq of hESC cells (paired end)

source_name: H1 hESC cells


title: sarcoma classifier reference case 350

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 350


title: sarcoma classifier reference case 490

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 490


title: ko_se_8mon_vessel_rep2

source_name: knock-out, smoke-exposed, 8 months, vessmoke-exposedl, replicate 2


title: wt_contr_3mon_septa_rep1

source_name: wild-type, control, 3 months, smoke-exposedpta, replicate 1


title: ko_se_8mon_vessel_rep3

source_name: knock-out, smoke-exposed, 8 months, vessmoke-exposedl, replicate 3


title: RNAseq__hESC__Rep1


title: sarcoma classifier reference case 349

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 349


title: sarcoma classifier reference case 489

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 489


title: RNAseq__Endo__Rep2

description:
genomic RNA
RNA-seq of endoderm cells (paired end)

source_name: Endoderm differentiated from H1 hESC cells


title: sarcoma classifier reference case 348

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 348


title: RNAseq__Endo__Rep1


title: RNAseq__Meso__Rep2


title: sarcoma classifier reference case 483

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 483


title: ko_se_8mon_septa_rep5

source_name: knock-out, smoke-exposed, 8 months, smoke-exposedpta, replicate 5


title: ko_se_8mon_vessel_rep4

source_name: knock-out, smoke-exposed, 8 months, vessmoke-exposedl, replicate 4


title: ko_se_8mon_septa_rep4

source_name: knock-out, smoke-exposed, 8 months, smoke-exposedpta, replicate 4


title: ko_se_8mon_vessel_rep1

source_name: knock-out, smoke-exposed, 8 months, vessmoke-exposedl, replicate 1


title: sarcoma classifier reference case 347

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 347


title: sarcoma classifier reference case 482

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 482


title: sarcoma classifier reference case 491

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 491


title: ko_se_8mon_septa_rep2

source_name: knock-out, smoke-exposed, 8 months, smoke-exposedpta, replicate 2


title: ko_se_8mon_septa_rep3

source_name: knock-out, smoke-exposed, 8 months, smoke-exposedpta, replicate 3


title: sarcoma classifier reference case 481

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 481


title: Patient8_ApoE

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
quality controls of paired-end reads were assessed using FastQC tools
Adapter sequences and low-quality bases were trimmed using Cutadapt Alignment was performed by using HISAT2
Uniquely mapped paired-end reads were used for subsequent FeatureCounts for gene level abundance estimation
Limma-voom was employed for DEA
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix, raw count, tab delimited

source_name: Human bronchial cytologic brushings

growth_protocol: Human bronchial epithelial cells were pelleted and suspended in B-ALI™ Growth Basal Medium (#00193516; Lonza, Alpharetta, GA) supplemented with transferrin (#00556822), B-ALI Inducer (#00556823), bovine pituitary extract (#00556824), epinephrine (#00556825), gentamicin/amphotericin B (#00556826), human epidermal growth factor (hEGF, #00556827), hydrocortisone (#00556828), insulin (#00556829), retinoic acid (#00556830), and triiodothyronine (#00556831; Lonza, Alpharetta, GA). The cells were divided into two equal batches and plated into two wells of a 6-well plate.

extract_protocol:
After 24 h, cell culture growth media was collected, and RNA was isolated and stored in TRI Reagent (#R2050-1-200, Zymo Research, Irvine, CA) for analysis.
Sequencing libraries were constructed from 100 to 500 ng of total RNA using the TruSeq® Stranded Total RNA Library Prep (#20020596; Illumina, San Diego, CA) and Ribo-Zero™ rRNA Removal (#MRZH11124; Illumina, San Diego, CA) kits. Fragment size of RNA-seq libraries was verified using 2100 Bioanalyzer Instrument (#G2939BA; Agilent Technologies, Santa Clara, CA) and concentrations were determined using Qubit 4 Fluorometer (#Q33226; ThermoFisher Scientific, Waltham, MA). Libraries were loaded onto HiSeq® 3000 (#SY-401-3001; Illumina, San Diego, CA) for 2 x75 bp paired-end read sequencing. Fastq files were generated using bcl2fastq Conversion Software v2.20 (Illumina, San Diego, CA).
Rigorous quality controls of paired-end reads were assessed using FastQC (Babraham Bioinformatics, Cambridge, UK). If required, adapter sequences and low-quality bases were trimmed using cutadapt software. Reads were aligned to the reference genome using HISAT2 v2.1.0 (Johns Hopkins University Center for Computational Biology, Baltimore, MD). Only uniquely mapped paired-end reads were used for subsequent analyses. featureCounts (WEHI Bioinformatics, Parkville, Melbourne, Victoria, Australia) was used for gene level abundance estimation using GENCODE Comprehensive gene annotations v25. Principal component analysis (PCA) was used to assess outlier samples. Genes were kept in the analysis if they had Counts Per Million (CPM) >1 in at least half the samples. Differential expression analysis comparing APOE-treated versus controls at the gene levels of summarization were then carried out using open-source Limma R package (Bioconductor).  Limma-voom was employed to implement a gene-wise linear modelling which processes the read counts into log2 counts per million (logCPM) with associated precision weights. The logCPM values were normalized between samples using trimmed mean of M-values (TMM). Adjustment for multiple testing was performed by reporting the false discovery rate (FDR) q-values for each feature. Features with q-value <5% were regarded as genome-wide significant. R statistical software environment with the GAGE Bioconductor packages was used to carry out analyses on pre-defined gene ontology (GO) gene sets by conducting two sample t-tests on the log-based fold changes of target gene set and control sets. The GO categories included were Biological Process (BP), Cellular Component (CC), and Molecular Function (MF). FDR q-values were estimated to correct the p-values for the multiple testing issue.

treatment_protocol: Recombinant human APOE (E3 isoform, #350-02; PeproTech, Rocky Hill, NJ) was added to one of the wells at a final concentration of 500 nM.  Research, Irvine, CA) for analysis.

value: apolipoprotein E (500 nM)

tag: age (yrs)


title: Patient7_Control

value: media


title: sarcoma classifier reference case 479

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 479

value: KRYO


title: sarcoma classifier reference case 344

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 344

value: sarcoma


title: sarcoma classifier reference case 345

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 345


title: sarcoma classifier reference case 478

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 478


title: sarcoma classifier reference case 346

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 346


title: Patient8_Control


title: Patient7_ApoE


title: ko_se_3mon_vessel_rep5

source_name: knock-out, smoke-exposed, 3 months, vessmoke-exposedl, replicate 5


title: sarcoma classifier reference case 477

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 477


title: ko_se_8mon_septa_rep1

source_name: knock-out, smoke-exposed, 8 months, smoke-exposedpta, replicate 1


title: sarcoma classifier reference case 343

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 343


title: sarcoma classifier reference case 476

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 476


title: sarcoma classifier reference case 342

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 342


title: ko_se_3mon_vessel_rep4

source_name: knock-out, smoke-exposed, 3 months, vessmoke-exposedl, replicate 4


title: ko_se_3mon_vessel_rep3

source_name: knock-out, smoke-exposed, 3 months, vessmoke-exposedl, replicate 3


title: Patient6_Control


title: Patient5_Control


title: Patient6_ApoE


title: sarcoma classifier reference case 475

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 475

source_name: sarcoma sample


title: sarcoma classifier reference case 340

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 340


title: sarcoma classifier reference case 341

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 341


title: sarcoma classifier reference case 474

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 474


title: ko_se_3mon_vessel_rep2

source_name: knock-out, smoke-exposed, 3 months, vessmoke-exposedl, replicate 2


title: sarcoma classifier reference case 339

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 339


title: Patient5_ApoE


title: sarcoma classifier reference case 473

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 473


title: Patient4_Control


title: ko_se_3mon_vessel_rep1

source_name: knock-out, smoke-exposed, 3 months, vessmoke-exposedl, replicate 1


title: ko_se_3mon_septa_rep5

source_name: knock-out, smoke-exposed, 3 months, smoke-exposedpta, replicate 5


title: sarcoma classifier reference case 338

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 338


title: sarcoma classifier reference case 472

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 472


title: ko_se_3mon_septa_rep4

source_name: knock-out, smoke-exposed, 3 months, smoke-exposedpta, replicate 4


title: Patient4_ApoE


title: ko_se_3mon_septa_rep3

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


title: sarcoma classifier reference case 471

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 471


title: sarcoma classifier reference case 470

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 470


title: Patient3_Control


title: sarcoma classifier reference case 336

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 336


title: Patient3_ApoE


title: ko_se_3mon_septa_rep2

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


title: Patient2_Control


title: sarcoma classifier reference case 469

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 469


title: sarcoma classifier reference case 335

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 335


title: sarcoma classifier reference case 334

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 334


title: sarcoma classifier reference case 500

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 500


title: sarcoma classifier reference case 468

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 468


title: ko_se_3mon_septa_rep1

source_name: knock-out, smoke-exposed, 3 months, smoke-exposedpta, replicate 1


title: Patient1_Control


title: sarcoma classifier reference case 467

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 467


title: Patient2_ApoE


title: sarcoma classifier reference case 332

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 332


title: sarcoma classifier reference case 337

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 337


title: sarcoma classifier reference case 466

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 466


title: sarcoma classifier reference case 331

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 331


title: ko_contr_8mon_vessel_rep4

source_name: knock-out, control, 8 months, vessmoke-exposedl, replicate 4


title: ko_contr_8mon_vessel_rep5

source_name: knock-out, control, 8 months, vessmoke-exposedl, replicate 5


title: ko_contr_8mon_vessel_rep3

source_name: knock-out, control, 8 months, vessmoke-exposedl, replicate 3


title: sarcoma classifier reference case 465

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 465


title: ko_contr_8mon_vessel_rep2

source_name: knock-out, control, 8 months, vessmoke-exposedl, replicate 2


title: fetal_before_5_H9

city: Uppsala

first: Asa

middle: Kristina

last: Bjorklund

address: Box 596

department: Cell and Molecular Biology

country: Sweden

institute: Uppsala University

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)

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 330

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 330

extract_protocol: Illumina protocol

value: FFPE


title: sarcoma classifier reference case 333

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 333


title: sarcoma classifier reference case 464

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 464


title: fetal_before_5_H8


title: sarcoma classifier reference case 463

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 463


title: sarcoma classifier reference case 329

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 329


title: ko_contr_8mon_vessel_rep1

source_name: knock-out, control, 8 months, vessmoke-exposedl, replicate 1


title: ko_contr_8mon_septa_rep5

source_name: knock-out, control, 8 months, smoke-exposedpta, replicate 5


title: fetal_before_5_H6


title: sarcoma classifier reference case 328

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 328


title: fetal_before_5_H5


title: Patient1_ApoE

source_name: Human bronchial cytologic brushings

tag: treatment


title: sarcoma classifier reference case 326

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 326


title: sarcoma classifier reference case 461

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 461


title: sarcoma classifier reference case 327

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 327


title: fetal_before_5_H4


title: fetal_before_5_H12


title: sarcoma classifier reference case 325

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 325


title: sarcoma classifier reference case 460

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 460


title: sarcoma classifier reference case 459

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 459


title: fetal_before_5_H7


title: sarcoma classifier reference case 462

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 462


title: sarcoma classifier reference case 458

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 458


title: sarcoma classifier reference case 324

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 324


title: ko_contr_8mon_septa_rep4

source_name: knock-out, control, 8 months, smoke-exposedpta, replicate 4


title: sarcoma classifier reference case 457

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 457

source_name: sarcoma sample


title: sarcoma classifier reference case 323

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 323


title: ko_contr_8mon_septa_rep2

source_name: knock-out, control, 8 months, smoke-exposedpta, replicate 2


title: ko_contr_8mon_septa_rep1

source_name: knock-out, control, 8 months, smoke-exposedpta, replicate 1


title: fetal_before_5_H10


title: ko_contr_3mon_vessel_rep3

source_name: knock-out, control, 3 months, vessmoke-exposedl, replicate 3


title: ko_contr_3mon_vessel_rep4

source_name: knock-out, control, 3 months, vessmoke-exposedl, replicate 4


title: sarcoma classifier reference case 322

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 322


title: fetal_before_5_H1


title: sarcoma classifier reference case 456

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 456


title: sarcoma classifier reference case 321

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 321


title: fetal_before_5_G9


title: ko_contr_8mon_septa_rep3

source_name: knock-out, control, 8 months, smoke-exposedpta, replicate 3


title: fetal_before_5_H11


title: fetal_before_5_G8


title: sarcoma classifier reference case 301

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 301


title: sarcoma classifier reference case 453

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 453


title: sarcoma classifier reference case 302

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 302


title: sarcoma classifier reference case 300

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 300


title: fetal_before_5_G7


title: sarcoma classifier reference case 452

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 452


title: sarcoma classifier reference case 451

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 451


title: fetal_before_5_G5


title: sarcoma classifier reference case 450

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 450


title: sarcoma classifier reference case 299

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 299


title: fetal_before_5_G3


title: sarcoma classifier reference case 455

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 455


title: fetal_before_5_G4


title: fetal_before_5_G6


title: sarcoma classifier reference case 297

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 297


title: sarcoma classifier reference case 449

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 449


title: sarcoma classifier reference case 298

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 298


title: ko_contr_3mon_septa_rep5

source_name: knock-out, control, 3 months, smoke-exposedpta, replicate 5


title: ko_contr_3mon_vessel_rep1

source_name: knock-out, control, 3 months, vessmoke-exposedl, replicate 1


title: ko_contr_3mon_vessel_rep2

source_name: knock-out, control, 3 months, vessmoke-exposedl, replicate 2


title: sarcoma classifier reference case 296

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 296


title: ko_contr_3mon_septa_rep1

source_name: knock-out, control, 3 months, smoke-exposedpta, replicate 1


title: sarcoma classifier reference case 448

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 448


title: ko_contr_3mon_septa_rep4

source_name: knock-out, control, 3 months, smoke-exposedpta, replicate 4