title: sarcoma classifier reference case 939

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 939


title: sarcoma classifier reference case 937

status: Public on Mar 01 2020

type: genomic

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 937

hyb_protocol: Illumina protocol

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

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

molecule: genomic DNA

organism: Homo sapiens

source_name: sarcoma sample

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

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

tag: tissue

value: sarcoma

tag: material preparation

value: FFPE


title: RC17_before_13_F10

type: SRA

city: Uppsala

first: Asa

middle: Kristina

last: Bjorklund

address: Box 596

department: Cell and Molecular Biology

country: Sweden

institute: Uppsala University

library_source: transcriptomic

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

molecule: polyA RNA

source_name: Cell culture

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

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

tag: cell type

tag: sortingmethod

value: size

tag: plate


title: sarcoma classifier reference case 935

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 935


title: RC17_before_13_F2


title: RC17_before_13_E8


title: sarcoma classifier validation case 93

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 93

value: KRYO


title: sarcoma classifier validation case 98

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 98


title: sarcoma classifier reference case 1049

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1049


title: sarcoma classifier validation case 92

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 92


title: sarcoma classifier reference case 914

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 914


title: sarcoma classifier reference case 911

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 911


title: sarcoma classifier reference case 917

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 917


title: RC17_before_13_E3


title: RC17_before_13_E5


title: RC17_before_13_E6


title: sarcoma classifier validation case 90

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 90


title: RC17_before_13_E2


title: RC17_before_13_D8


title: sarcoma classifier reference case 909

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 909


title: RC17_before_13_D7


title: sarcoma classifier validation case 89

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 89


title: sarcoma classifier validation case 88

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 88


title: sarcoma classifier reference case 905

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 905


title: RC17_before_13_D5


title: RC17_before_13_D6


title: sarcoma classifier validation case 87

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 87


title: RC17_before_13_D3


title: RC17_before_13_E7


title: sarcoma classifier validation case 86

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 86


title: RC17_before_13_C9


title: RC17_before_13_C7


title: sarcoma classifier validation case 91

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 91


title: RC17_before_13_C8


title: RC17_before_13_C6


title: sarcoma classifier validation case 84

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 84


title: RC17_before_13_C2


title: RC17_before_13_C3


title: RC17_before_13_C11


title: sarcoma classifier validation case 85

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 85


title: sarcoma classifier validation case 83

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 83


title: sarcoma classifier reference case 888

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 888


title: sarcoma classifier reference case 904

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 904


title: sarcoma classifier reference case 893

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 893


title: sarcoma classifier validation case 82

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 82


title: sarcoma classifier reference case 899

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 899


title: sarcoma classifier reference case 886

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 886


title: RC17_before_13_D10


title: sarcoma classifier reference case 872

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 872


title: sarcoma classifier reference case 875

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 875


title: sarcoma classifier validation case 81

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 81


title: RC17_before_13_B9


title: RC17_before_13_C10


title: RC17_before_13_B6


title: RC17_before_13_B8


title: RC17_before_13_B7


title: sarcoma classifier validation case 79

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 79


title: sarcoma classifier reference case 867

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 867


title: sarcoma classifier validation case 80

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 80


title: RC17_before_13_B12


title: sarcoma classifier reference case 865

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 865


title: RC17_before_13_B2


title: RC17_before_13_A9


title: RC17_before_13_B3


title: sarcoma classifier reference case 889

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 889


title: RC17_before_13_B4


title: sarcoma classifier validation case 78

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 78


title: sarcoma classifier reference case 860

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 860


title: RC17_before_13_A3


title: RC17_before_13_A6


title: RC17_before_13_A12


title: RC17_before_13_A11


title: RC17_before_13_A7


title: sarcoma classifier validation case 77

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 77


title: sarcoma classifier reference case 842

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 842


title: RC17_before_12_H9


title: sarcoma classifier validation case 75

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 75


title: sarcoma classifier reference case 827

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 827


title: RC17_before_12_H8


title: RC17_before_12_H7


title: sarcoma classifier reference case 828

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 828


title: sarcoma classifier validation case 74

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 74


title: RC17_before_12_H5


title: RC17_before_12_H6


title: sarcoma classifier reference case 826

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 826


title: RC17_before_13_A8


title: sarcoma classifier validation case 73

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 73


title: sarcoma classifier reference case 825

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 825


title: RC17_before_12_H4


title: sarcoma classifier validation case 72

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 72


title: sarcoma classifier reference case 824

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 824


title: sarcoma classifier validation case 76

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 76


title: sarcoma classifier validation case 71

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 71


title: RC17_before_12_H12


title: sarcoma classifier reference case 823

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 823


title: RC17_before_12_H3


title: RC17_before_12_H11


title: RC17_before_12_H10


title: sarcoma classifier validation case 70

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 70


title: sarcoma classifier reference case 822

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 822


title: sarcoma classifier validation case 69

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 69


title: RC17_before_12_G9


title: RC17_before_12_G8


title: sarcoma classifier validation case 68

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 68


title: sarcoma classifier reference case 821

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 821


title: sarcoma classifier reference case 820

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 820


title: sarcoma classifier reference case 819

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 819


title: RC17_before_12_G6


title: RC17_before_12_G5


title: sarcoma classifier validation case 66

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 66


title: RC17_before_12_G4


title: RC17_before_12_G3


title: RC17_before_12_H2


title: RC17_before_12_G12


title: sarcoma classifier validation case 65

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 65


title: RC17_before_12_G11


title: sarcoma classifier reference case 817

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 817


title: RC17_before_12_G10


title: sarcoma classifier reference case 818

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 818


title: RC17_before_12_H1


title: sarcoma classifier validation case 64

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 64


title: sarcoma classifier reference case 816

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 816


title: RC17_before_12_G1


title: RC17_before_12_F9


title: sarcoma classifier reference case 815

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 815


title: RC17_before_12_G2


title: RC17_before_12_F8


title: sarcoma classifier validation case 62

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 62


title: RC17_before_12_F7


title: RC17_before_12_G7


title: sarcoma classifier validation case 67

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 67


title: RC17_before_12_F6


title: sarcoma classifier reference case 814

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 814


title: sarcoma classifier validation case 61

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 61


title: RC17_before_12_F4


title: sarcoma classifier validation case 60

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 60


title: RC17_before_12_F2


title: sarcoma classifier reference case 813

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 813


title: sarcoma classifier reference case 812

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 812


title: RC17_before_12_F12


title: RC17_before_12_F11


title: sarcoma classifier validation case 59

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 59


title: RC17_before_12_F10


title: sarcoma classifier reference case 810

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 810


title: sarcoma classifier reference case 811

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 811


title: RC17_before_12_E9


title: sarcoma classifier validation case 57

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 57


title: sarcoma classifier validation case 63

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 63


title: RC17_before_12_F1


title: sarcoma classifier validation case 56

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 56


title: RC17_before_12_E8


title: RC17_before_12_E7


title: sarcoma classifier reference case 809

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 809


title: sarcoma classifier reference case 808

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 808


title: RC17_before_12_E4


title: sarcoma classifier validation case 55

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 55


title: RC17_before_12_E6


title: RC17_before_12_E5


title: RC17_before_12_E2


title: RC17_before_12_E3


title: RC17_before_12_F3


title: sarcoma classifier validation case 54

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 54


title: sarcoma classifier reference case 807

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 807


title: sarcoma classifier reference case 806

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 806


title: RC17_before_12_E11


title: sarcoma classifier validation case 53

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 53


title: sarcoma classifier reference case 805

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 805


title: RC17_before_12_E10


title: RC17_before_12_E12


title: sarcoma classifier validation case 58

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 58


title: RC17_before_12_E1


title: RC17_before_12_D9


title: sarcoma classifier validation case 51

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 51


title: sarcoma classifier validation case 52

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 52


title: RC17_before_12_D8


title: RC17_before_12_D7


title: sarcoma classifier reference case 803

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 803


title: sarcoma classifier reference case 804

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 804


title: sarcoma classifier validation case 50

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 50


title: sarcoma classifier reference case 802

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 802


title: RC17_before_12_D6


title: sarcoma classifier validation case 48

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 48


title: sarcoma classifier reference case 801

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 801


title: RC17_before_12_D2


title: RC17_before_12_D3


title: RC17_before_12_D5


title: sarcoma classifier reference case 800

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 800


title: sarcoma classifier validation case 47

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 47


title: RC17_before_12_D12


title: RC17_before_12_D11


title: sarcoma classifier reference case 799

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 799


title: sarcoma classifier reference case 798

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 798


title: RC17_before_12_D10


title: RC17_before_12_C9


title: RC17_before_12_D1


title: sarcoma classifier validation case 45

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 45


title: RC17_before_12_C8


title: sarcoma classifier reference case 797

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 797


title: sarcoma classifier validation case 44

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 44


title: sarcoma classifier reference case 796

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 796


title: sarcoma classifier validation case 43

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 43


title: RC17_before_12_D4


title: sarcoma classifier reference case 795

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 795


title: HEC-1-B_scRNA_43

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

country: China

institute: Shanghai JiaoTong University

description: single-cell RNA-seq

data_processing:
Single-cell RNA-seq reads were aligned to the hg38_tran genome assembly using hisat2 version 2.1.0 with parameters:-p 8 --mp 7,6 --sp 3,2 --rdg 6,5 --dta-cufflinks -x
File format is transformed to BAM using samtools version 1.9.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks version 2.2.1.
Genome_build: hg38_tran
Supplementary_files_format_and_content: fpkm_tracking files include FPKM values for each Sample.

source_name: HEC-1-B cell

extract_protocol:
Trypsin was added to the culture dish and the single cells were suspended in the culture medium. Single cells were then picked under the microscope by using a micro capillary pipette into the thin-walled PCR tube containing 2 µl of cell lysis buffer, 1 µl of oligo-dT primer and 1 µl of dNTP mix.
First, reverse transcription is performed, the cDNA was pre-amplification by PCR. The cDNA library was then purified, tagmented, and ligated with adapters using the Nextera XT DNA Library Preparation kit (Illumina FC-131-1096). Finally, the adapter-ligated fragments were further amplified by PCR and purified with AMPure XP beads (Beckman).

tag: cell line

tag: genotype

value: wild type


title: RC17_before_12_C7


title: sarcoma classifier validation case 49

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 49


title: CHIP_HEC-1-B_2FWD_CTCF_rep1

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 wig files include RPM values for each Sample

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

tag: line


title: HEC-1-B_scRNA_42

description: single-cell RNA-seq


title: RC17_before_12_C5


title: sarcoma classifier validation case 41

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 41


title: RC17_before_12_C4


title: HEC-1-B_scRNA_41

description: single-cell RNA-seq


title: sarcoma classifier reference case 794

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 794


title: HEC-1-B_scRNA_40

description: single-cell RNA-seq


title: sarcoma classifier validation case 46

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 46


title: CHIP_HEC-1-B_2FWD_RAD21_rep1


title: sarcoma classifier validation case 40

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 40


title: RC17_before_12_C3


title: sarcoma classifier validation case 39

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 39


title: RC17_before_12_C2


title: HEC-1-B_scRNA_39

description: single-cell RNA-seq


title: HEC-1-B_scRNA_38

description: single-cell RNA-seq


title: HEC-1-B_scRNA_37

description: single-cell RNA-seq


title: sarcoma classifier reference case 791

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 791


title: sarcoma classifier validation case 37

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 37


title: sarcoma classifier reference case 789

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 789


title: RC17_before_12_C11


title: HEC-1-B_scRNA_36

description: single-cell RNA-seq


title: sarcoma classifier validation case 36

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 36


title: sarcoma classifier validation case 42

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 42


title: sarcoma classifier reference case 793

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 793


title: sarcoma classifier reference case 788

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 788


title: sarcoma classifier validation case 35

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 35


title: sarcoma classifier reference case 787

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 787


title: HEC-1-B_scRNA_35

description: single-cell RNA-seq


title: RC17_before_12_C10


title: sarcoma classifier validation case 34

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 34


title: RC17_before_12_C1


title: sarcoma classifier reference case 790

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 790


title: HEC-1-B_scRNA_34

description: single-cell RNA-seq


title: RC17_before_12_B9


title: sarcoma classifier reference case 786

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 786


title: sarcoma classifier reference case 792

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 792


title: HEC-1-B_scRNA_33

description: single-cell RNA-seq


title: RC17_before_12_C6


title: HEC-1-B_scRNA_31

description: single-cell RNA-seq


title: sarcoma classifier validation case 33

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 33


title: HEC-1-B_scRNA_30

description: single-cell RNA-seq


title: sarcoma classifier reference case 785

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 785


title: sarcoma classifier validation case 38

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 38


title: sarcoma classifier reference case 782

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 782


title: HEC-1-B_scRNA_32

description: single-cell RNA-seq


title: RC17_before_12_C12


title: RC17_before_12_B8


title: sarcoma classifier validation case 28

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 28


title: RC17_before_12_B4


title: RC17_before_12_B3


title: RC17_before_12_B7


title: RC17_before_12_B12


title: sarcoma classifier reference case 784

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 784


title: HEC-1-B_scRNA_29

description: single-cell RNA-seq


title: sarcoma classifier reference case 783

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 783


title: sarcoma classifier validation case 30

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 30


title: sarcoma classifier validation case 29

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 29


title: sarcoma classifier validation case 31

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 31


title: sarcoma classifier reference case 779

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 779


title: HEC-1-B_scRNA_27

description: single-cell RNA-seq


title: sarcoma classifier reference case 781

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 781


title: sarcoma classifier validation case 27

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 27


title: HEC-1-B_scRNA_26

description: single-cell RNA-seq


title: RC17_before_12_B11


title: sarcoma classifier validation case 26

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 26


title: HEC-1-B_scRNA_25

description: single-cell RNA-seq


title: sarcoma classifier validation case 25

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 25


title: HEC-1-B_scRNA_28

description: single-cell RNA-seq


title: sarcoma classifier reference case 778

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 778


title: sarcoma classifier reference case 780

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 780


title: sarcoma classifier reference case 777

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 777


title: sarcoma classifier validation case 32

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 32


title: HEC-1-B_scRNA_24

description: single-cell RNA-seq


title: RC17_before_12_B1


title: RC17_before_12_B2


title: RC17_before_12_A9


title: HEC-1-B_scRNA_23

description: single-cell RNA-seq


title: sarcoma classifier validation case 23

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 23


title: sarcoma classifier reference case 776

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 776


title: sarcoma classifier reference case 775

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 775


title: RC17_before_12_A8


title: HEC-1-B_scRNA_22

description: single-cell RNA-seq


title: sarcoma classifier validation case 22

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 22


title: RC17_before_12_A7


title: RC17_before_12_A6


title: sarcoma classifier validation case 21

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 21


title: HEC-1-B_scRNA_21

description: single-cell RNA-seq


title: sarcoma classifier reference case 773

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 773


title: sarcoma classifier validation case 20

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 20


title: HEC-1-B_scRNA_20

description: single-cell RNA-seq


title: RC17_before_12_A5


title: sarcoma classifier reference case 772

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 772


title: sarcoma classifier validation case 24

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 24


title: HEC-1-B_scRNA_19

description: single-cell RNA-seq


title: sarcoma classifier validation case 19

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 19


title: RC17_before_12_A4


title: sarcoma classifier reference case 771

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 771


title: sarcoma classifier validation case 18

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 18


title: HEC-1-B_scRNA_18

description: single-cell RNA-seq


title: sarcoma classifier validation case 17

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 17


title: RC17_before_12_A3


title: sarcoma classifier reference case 769

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 769


title: RC17_before_12_A2


title: sarcoma classifier reference case 770

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 770


title: sarcoma classifier validation case 16

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 16


title: RC17_before_12_A12


title: HEC-1-B_scRNA_17

description: single-cell RNA-seq


title: sarcoma classifier reference case 774

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 774


title: sarcoma classifier reference case 768

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 768


title: HEC-1-B_scRNA_16

description: single-cell RNA-seq


title: sarcoma classifier validation case 15

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 15


title: sarcoma classifier validation case 14

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 14


title: RC17_before_12_A11


title: HEC-1-B_scRNA_15

description: single-cell RNA-seq


title: sarcoma classifier reference case 767

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 767


title: sarcoma classifier reference case 766

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 766


title: RC17_before_12_A1


title: sarcoma classifier validation case 13

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 13


title: HEC-1-B_scRNA_13

description: single-cell RNA-seq


title: RC17_before_11_H8


title: RC17_before_11_H7


title: RC17_before_12_B5


title: sarcoma classifier reference case 765

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 765


title: RC17_before_11_H5


title: sarcoma classifier validation case 12

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 12


title: HEC-1-B_scRNA_10

description: single-cell RNA-seq


title: HEC-1-B_scRNA_12

description: single-cell RNA-seq


title: RC17_before_11_H3


title: sarcoma classifier reference case 764

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 764


title: sarcoma classifier reference case 761

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 761


title: sarcoma classifier reference case 762

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 762


title: HEC-1-B_scRNA_8

description: single-cell RNA-seq


title: sarcoma classifier validation case 11

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 11


title: RC17_before_11_H12


title: sarcoma classifier reference case 760

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 760


title: RC17_before_11_H6


title: sarcoma classifier reference case 763

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 763


title: sarcoma classifier validation case 7

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 7


title: sarcoma classifier validation case 10

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 10


title: RC17_before_11_H10


title: sarcoma classifier validation case 6

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 6


title: HEC-1-B_scRNA_14

description: single-cell RNA-seq


title: HEC-1-B_scRNA_9

description: single-cell RNA-seq


title: RC17_before_11_G9


title: sarcoma classifier validation case 9

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 9


title: HEC-1-B_scRNA_11

description: single-cell RNA-seq


title: HEC-1-B_scRNA_5

description: single-cell RNA-seq


title: RC17_before_11_G8


title: sarcoma classifier validation case 8

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 8


title: sarcoma classifier reference case 756

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 756


title: sarcoma classifier validation case 3

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 3


title: RC17_before_11_G7


title: sarcoma classifier reference case 758

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 758


title: sarcoma classifier validation case 2

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 2


title: HEC-1-B_scRNA_7

description: single-cell RNA-seq


title: RC17_before_11_G6


title: HEC-1-B_scRNA_2

description: single-cell RNA-seq


title: HEC-1-B_scRNA_6

description: single-cell RNA-seq


title: sarcoma classifier validation case 5

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 5


title: RC17_before_11_G5


title: sarcoma classifier reference case 757

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 757


title: sarcoma classifier reference case 1077

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1077


title: RC17_before_11_G3


title: sarcoma classifier reference case 752

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 752


title: sarcoma classifier reference case 1076

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1076


title: sarcoma classifier validation case 4

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 4


title: HEC-1-B_scRNA_4

description: single-cell RNA-seq


title: sarcoma classifier reference case 759

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 759


title: HEC-1-B_scRNA_3

description: single-cell RNA-seq


title: sarcoma classifier reference case 755

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 755


title: RC17_before_11_G2


title: 4NG1

first: Chengzhong

last: Lin

address: Zhizaoju road 639

department: Second Dental Clinic, Ninth People’s Hospital, Shanghai Jiao Tong University, School of Medicine, China

institute: Chengzhong Lin

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: hg19_GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

molecule: total RNA

source_name: Head and neck squamous cell carcinoma cell line HN4, treated with NGF (40 ng/ml)

growth_protocol: HN4 cells were maintained in Dulbecco’s minimum essential medium (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin and 100 μg/ml streptomycin and incubated in a humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were incubated with the vehicle control or NGF (40 ng/ml) for 48 hours

value: Head and neck squamous cell carcinoma cells

tag: cell source

value: oral cavity


title: sarcoma classifier reference case 754

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 754


title: sarcoma classifier reference case 749

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 749


title: RC17_before_11_G11


title: HEC-1-B_scRNA_1

description: single-cell RNA-seq


title: sarcoma classifier validation case 1

description:
Methylation data from sarcoma sample
VALIDATION_SAMPLE 1


title: RC17_before_11_G4


title: RC17_before_11_G10


title: sarcoma classifier reference case 753

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 753


title: 4NG3


title: sarcoma classifier reference case 747

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 747


title: 4NG2


title: sarcoma classifier reference case 1069

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1069


title: 4con1

source_name: Head and neck squamous cell carcinoma cell line HN4, untreated


title: sarcoma classifier reference case 751

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 751


title: RC17_before_11_F9


title: sarcoma classifier reference case 1075

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1075


title: RC17_before_11_G12


title: sarcoma classifier reference case 750

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 750


title: 4con2


title: RC17_before_11_F8


title: sarcoma classifier reference case 1073

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1073


title: 4con3


title: sarcoma classifier reference case 746

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 746


title: sarcoma classifier reference case 748

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 748


title: RC17_before_11_F7


title: sarcoma classifier reference case 1072

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1072


title: sarcoma classifier reference case 1068

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1068


title: sarcoma classifier reference case 1066

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1066


title: RC17_before_11_G1


title: sarcoma classifier reference case 1074

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1074


title: sarcoma classifier reference case 745

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 745


title: CD36-KO TAMs-3

type: RNA

city: Houston

first: Pan

last: Su

state: TX

address: 6550 FANNIN STREET

country: USA

institute: Houston Methodist Research Institute

hyb_protocol: Fragmented and labeled ss-cDNA was hybridyzed for 16 hr at 45°C on GeneChip Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: All GeneChips were scanned on an Affymetrix GeneChip Scanner 3000.

data_processing: Normalization was performed using the Robust Multiarray Average and differentially expressed genes between two groups were identified by R/Bioconductor using limma package.

label: biotin

organism: Mus musculus

source_name: Murine primary MΦs

label_protocol: Total RNA was labeled using the GeneChip WT PLUS Reagent Kit.

growth_protocol: Mouse MΦs were cultured in RPMI 1640 medium containing 10% fetal bovine serum and 100 U penicillin / 0.1 mg/ml streptomycin.

extract_protocol: Total RNA were extracted using Rneasy mini kit (Qiagen).

treatment_protocol: Normal mouse MΦs cultured with mouse 5TGM1 multiple myeloma cell line for 72 hours to generate TAMs

tag: genotype/variation

value: CD36 KO TAMs


title: sarcoma classifier reference case 743

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 743


title: sarcoma classifier reference case 742

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 742


title: sarcoma classifier reference case 744

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 744


title: CD36-KO TAMs-1


title: RC17_before_11_F6


title: sarcoma classifier reference case 1065

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1065


title: RC17_before_11_F4


title: sarcoma classifier reference case 741

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 741


title: sarcoma classifier reference case 1064

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1064


title: CD36-KO MΦs-3

value: CD36 KO MΦs


title: RC17_before_11_F3


title: CD36-KO MΦs-2


title: RC17_before_11_F12


title: sarcoma classifier reference case 739

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 739


title: sarcoma classifier reference case 1067

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1067


title: CD36-KO TAMs-2


title: CD36-KO MΦs-1


title: sarcoma classifier reference case 1061

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1061


title: sarcoma classifier reference case 1063

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1063


title: sarcoma classifier reference case 738

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 738


title: sarcoma classifier reference case 740

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 740


title: RC17_before_11_F11


title: RC17_before_11_F10


title: sarcoma classifier reference case 1062

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1062


title: CD36-WT TAMs-2

value: WT TAMs


title: RC17_before_11_F5


title: CD36-WT TAMs-3


title: sarcoma classifier reference case 737

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 737


title: sarcoma classifier reference case 736

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 736


title: RC17_before_11_E9


title: sarcoma classifier reference case 1060

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1060


title: RC17_before_11_E8


title: sarcoma classifier reference case 1045

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1045


title: sarcoma classifier reference case 735

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 735


title: sarcoma classifier reference case 1059

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1059


title: sarcoma classifier reference case 734

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 734


title: CD36-WT TAMs-1


title: sarcoma classifier reference case 733

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 733


title: Treml4-/-  biological rep 1 LPS 12 hr

city: Frederick

first: Marieli

last: Gonzalez-Cotto

state: Maryland

department: Cancer & Inflammation Program

institute: National Cancer Institute

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: mm10
Supplementary_files_format_and_content: CPM values

source_name: macrophage LPS treated for 12 hours

growth_protocol: Total cells from the bone marrow were plated at 7.0 x 10^5 / mL for 5-7 days in complete Dulbecco’s modified eagles media (DMEM) (Gibco #11965) supplemented with 2mM Glutamine, 10% FBS, 100U/mL Penicillin/Streptomicin and 20ng/ml mouse M-CSF allowing for proper BMDM differentiation and growth.

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: After growing BMDM for 6 days in culture, cells were placed in complete culture media and treated with vehicle (PBS) or of LPS (100ng/mL) for  8h or 12h  for proinflammatory activation

tag: background strain

value: bone marrow derived macrophages

tag: stimulation

value: LPS treated for 12 hours


title: RC17_before_11_F1


title: sarcoma classifier reference case 1033

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1033


title: CD36-WT MΦs-3

value: WT MΦs


title: Treml4-/-  biological rep 2 LPS 12hr


title: sarcoma classifier reference case 1057

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1057


title: sarcoma classifier reference case 730

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 730


title: sarcoma classifier reference case 1058

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1058


title: CD36-WT MΦs-2


title: Treml4-/-  biological rep 2 LPS 8hr

source_name: macrophage LPS treated for 8 hours

value: LPS treated for 8 hours


title: Treml4-/-  biological rep 2 control

source_name: macrophage unstimulated

value: unstimulated


title: CD36-WT MΦs-1


title: RC17_before_11_E7


title: RC17_before_11_E4


title: sarcoma classifier reference case 1044

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1044


title: RC17_before_11_E6


title: RC17_before_11_E3


title: sarcoma classifier reference case 729

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 729


title: sarcoma classifier reference case 728

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 728


title: sarcoma classifier reference case 732

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 732


title: RC17_before_11_E5


title: wt biological rep 2 LPS 8hr


title: RC17_before_11_E2


title: sarcoma classifier reference case 1030

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1030


title: RC17_before_11_E12


title: sarcoma classifier reference case 731

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 731


title: Treml4-/- biological  rep 1 LPS 8hr


title: sarcoma classifier reference case 1032

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1032


title: Treml4-/- biological  rep 1 control


title: wt biological rep 2 LPS 12hr


title: sarcoma classifier reference case 1027

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1027


title: sarcoma classifier reference case 1028

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1028


title: sarcoma classifier reference case 727

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 727


title: wt biological rep 1 LPS 12 hr


title: wt biological rep 2 control


title: RC17_before_11_E10


title: wt biological rep 1 LPS 8hr


title: sarcoma classifier reference case 726

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 726


title: sarcoma classifier reference case 1031

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1031


title: sarcoma classifier reference case 1024

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1024


title: sarcoma classifier reference case 725

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 725


title: sarcoma classifier reference case 1025

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1025


title: RC17_before_11_D9


title: sarcoma classifier reference case 724

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 724


title: wt biological rep 1 control


title: ATAC-seq_WT3_Tcon

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.
Bowtie2 was used to map the reads to NCBIM37. Peaks were called using MACS2 and differential analysis was conducted using DiffBind and DESeq2 in R.
Genome_build: NCBIM37
A broadPeak (.broadPeak) file is used by the ENCODE project to provide called regions of signal enrichment based on pooled, normalized (interpreted) data. It is a BED 6+3 format

source_name: CD4+ Foxp3GFP– Tconv

growth_protocol: CD4+ Foxp3GFP+ Treg and CD4+ Foxp3GFP– Tconv cells were sorted by FACS from WT and Enh-KO Foxp3GFP reporter animals.

extract_protocol:
1e5 cell nuclei were processed as previously described (Buenrostro Nat Methods 2013; Sadiyah et al., 2019)
PCR amplification with Nextera primers Buenrostro 2013

treatment_protocol: Briefly, total CD4+ T cells were pre-enriched from single cell spleen suspensions using magnetic negative selection (eBioscience) prior to FACS sorting of 1e5 GFP+ or GFP– CD4+ T cells using a BD Influx instrument (Becton Dickinson Biosciences) directly into Eppendorf tubes. Cells were pelleted and subjected to ATAC-Seq

value: CD4+ Foxp3GFP- Tconv

value: WT


title: ATAC-seq_WT3_Treg

source_name: CD4+ Foxp3GFP+ Treg

value: CD4+ Foxp3GFP+ Treg


title: sarcoma classifier reference case 1023

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1023

value: sarcoma

value: FFPE


title: sarcoma classifier reference case 722

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 722


title: RC17_before_11_D8

value: size


title: RC17_before_11_E11


title: RC17_before_11_D6


title: sarcoma classifier reference case 1022

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1022


title: RC17_before_11_D5


title: sarcoma classifier reference case 1021

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1021


title: sarcoma classifier reference case 721

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 721


title: sarcoma classifier reference case 1026

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1026


title: ATAC-seq_WT2_Treg


title: RC17_before_11_E1


title: sarcoma classifier reference case 1020

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1020


title: sarcoma classifier reference case 720

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 720


title: sarcoma classifier reference case 719

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 719


title: RC17_before_11_D4


title: ATAC-seq_WT2_Tcon


title: sarcoma classifier reference case 718

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 718

value: KRYO


title: ATAC-seq_WT1_Tcon


title: RC17_before_11_D12


title: sarcoma classifier reference case 1018

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1018


title: sarcoma classifier reference case 723

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 723


title: sarcoma classifier reference case 1019

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1019


title: sarcoma classifier reference case 1017

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1017


title: sarcoma classifier reference case 717

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 717


title: sarcoma classifier reference case 1016

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1016


title: ATAC-seq_KO3_Tcon

value: Lrrc32+ 70k enhancer KO


title: ATAC-seq_KO3_Treg


title: sarcoma classifier reference case 716

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 716


title: RC17_before_11_D11


title: RC17_before_11_D10


title: sarcoma classifier reference case 715

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 715


title: ATAC-seq_WT1_Treg


title: sarcoma classifier reference case 714

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 714


title: ATAC-seq_KO2_Treg


title: sarcoma classifier reference case 1015

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1015


title: RC17_before_11_C9


title: RC17_before_11_D1


title: RC17_before_11_D3


title: ATAC-seq_KO1_Treg


title: sarcoma classifier reference case 713

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 713


title: sarcoma classifier reference case 1013

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1013


title: sarcoma classifier reference case 1014

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1014


title: ATAC-seq_KO1_Tcon


title: sarcoma classifier reference case 1011

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1011


title: RC17_before_11_C8


title: sarcoma classifier reference case 711

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 711


title: RC17_before_11_C6


title: ATAC-seq_KO2_Tcon


title: RC17_before_11_C7


title: sarcoma classifier reference case 1012

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1012


title: sarcoma classifier reference case 710

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 710


title: sarcoma classifier reference case 1009

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1009


title: sarcoma classifier reference case 709

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 709


title: sarcoma classifier reference case 708

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 708


title: RC17_before_11_C4


title: sarcoma classifier reference case 1008

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1008


title: p0_cortex_WT_rep6

data_processing:
Reads were aligned using Hisat2 (version 2.0.4) to the mouse genome (mm9), and the FPKM value was calculated using the Cufflinks program (version2.1.1)
Genome_build: mm9
Supplementary_files_format_and_content: fpkm_tracking: frgaments per kilobase of exon per million reads mapped.

source_name: p0 mouse cortex

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:
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: Cortical cells

tag: strain

value: wildtype


title: p0_cortex_WT_rep7


title: p0_cortex_WT_rep5


title: p0_cortex_WT_rep8


title: sarcoma classifier reference case 1007

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1007


title: RC17_before_11_C2


title: p0_cortex_WT_rep9


title: sarcoma classifier reference case 707

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 707


title: sarcoma classifier reference case 706

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 706


title: p0_cortex_WT_rep4


title: RC17_before_11_C12


title: sarcoma classifier reference case 1005

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1005


title: p0_cortex_WT_rep3


title: sarcoma classifier reference case 1004

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1004


title: p0_cortex_WT_rep2


title: sarcoma classifier reference case 1010

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1010


title: sarcoma classifier reference case 704

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 704


title: RC17_before_11_C11


title: RC17_before_11_C10


title: RC17_before_11_C5


title: p0_cortex_WT_rep10


title: sarcoma classifier reference case 1003

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1003


title: sarcoma classifier reference case 702

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 702


title: sarcoma classifier reference case 703

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 703


title: p0_cortex_WT_rep1


title: sarcoma classifier reference case 1002

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1002


title: RC17_before_11_C3


title: RC17_before_11_C1


title: p0_cortex_HS5-1inv_rep2


title: sarcoma classifier reference case 1006

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1006


title: RC17_before_11_B9


title: sarcoma classifier reference case 701

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 701


title: sarcoma classifier reference case 705

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 705


title: RC17_before_11_B8


title: sarcoma classifier reference case 712

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 712


title: sarcoma classifier reference case 699

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 699


title: sarcoma classifier reference case 1000

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1000


title: sarcoma classifier reference case 998

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 998


title: sarcoma classifier reference case 1001

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1001


title: sarcoma classifier reference case 698

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 698


title: RC17_before_11_B5


title: RC17_before_11_B7


title: sarcoma classifier reference case 700

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 700


title: sarcoma classifier reference case 697

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 697


title: p0_cortex_HS5-1del_rep1


title: p0_cortex_HS5-1inv_rep1


title: p0_cortex_HS5-1del_rep2


title: p0_cortex_HS5-1binv_rep2


title: sarcoma classifier reference case 997

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 997


title: RC17_before_11_B4


title: RC17_before_11_B2


title: sarcoma classifier reference case 696

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 696


title: RC17_before_11_B3


title: p0_cortex_HS5-1binv_rep1


title: sarcoma classifier reference case 695

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 695


title: RC17_before_11_B6


title: p0_cortex_HS5-1bdel_rep2


title: sarcoma classifier reference case 995

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 995


title: sarcoma classifier reference case 999

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 999


title: sarcoma classifier reference case 694

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 694


title: RC17_before_11_B11


title: p0_cortex_HS5-1adel_rep2


title: sarcoma classifier reference case 994

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 994


title: sarcoma classifier reference case 993

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 993


title: sarcoma classifier reference case 693

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 693


title: p0_cortex_HS5-1adel_rep1


title: sarcoma classifier reference case 996

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 996


title: sarcoma classifier reference case 691

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 691


title: sarcoma classifier reference case 692

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 692


title: sarcoma classifier reference case 690

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 690


title: sarcoma classifier reference case 991

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 991


title: RC17_before_11_B1


title: RC17_before_11_B10


title: Setd8 control Rep 2

city: Rochester

first: Laurie

middle: A

last: Steiner

state: NY

address: 601 Elmwood Avenue

department: Center for Pediatric Biomedical Research

institute: University of Rochester

description:
setd8-control_peaks.narrowPeak
setd8-control_ratio.bw
log2ratio_readCountNorm_mutant_vs_control.bw

data_processing:
bcl2fastq to convert reads to fastq format
trimmomatic was used to perform quality control (SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP: trimmomatic_adapters.fasta:2:30:10 MINLEN:15
quality reads were aligned using bowtie1 -m 1
mitochonrial reads and blacklist reads were removed using samtools
significantly accessible regions were identified using MACS2 --nomodel --shift -100 --extsize 200 -f BAM -B -g mm
replicate bam files were merged using samtools
deeptools bamCompare was used to compute the log2 ratio between setd8-null and control read density while applying sequencing depth normalization
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak, bigwig

source_name: primitive erythroblasts

growth_protocol: Primary cells not subjected to ex vivo culture

extract_protocol:
Primitive erythroblasts were removed from peripheral blood by dissection in PBS supplemented with glucose and BSA
Briefly, nuclei were collected from Setd8 null and control erythroblats following cell lysis and subjected to tagmentation using transpoase (Ilumina Nextera FC121-1030). Samples were then amplified x 5 PCR cycles [980C/45s + 5 x (980C/15s + 630C/30s + 720C/30s) + 720C/1min] using KAPA HiFi HotStart ReadyMix PCR Kit (KK2601/KK2602) and cleaned with Qiagen MiniElute column. The library was then amplified with PCR [980C/45s + Y x (980C/15s + 630C/30s + 720C/30s) + 720C/1min], with the number of cycles (Y) determined through via a qPCR library amplification test. The resulting PCR producte was cleaned using Agencourt AMPure XP magnetic beads (Beckman Coulter A63880)

treatment_protocol: Primary cells not treated ex vivo. Cells were stained for flow cytometry on ice in PBS supplemented with glucose and BSA

tag: embryonic day

value: Peripheral Blood


title: Setd8 control Rep 3


title: sarcoma classifier reference case 689

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 689


title: sarcoma classifier reference case 992

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 992


title: Setd8-null Rep2

description:
setd8-mutant_peaks.narrowPeak
setd8-mutant_ratio.bw
log2ratio_readCountNorm_mutant_vs_control.bw


title: RC17_before_11_A8


title: sarcoma classifier reference case 989

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 989


title: RC17_before_11_A9


title: p0_cortex_HS5-1bdel_rep1


title: Setd8-null Rep1


title: sarcoma classifier reference case 687

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 687


title: sarcoma classifier reference case 988

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 988


title: sarcoma classifier reference case 688

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 688


title: sarcoma classifier reference case 987

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 987


title: RC17_before_11_A7


title: sarcoma classifier reference case 685

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 685


title: RC17_before_11_A6


title: sarcoma classifier reference case 686

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 686


title: sarcoma classifier reference case 986

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 986


title: KO.8.S961

city: Lausanne

first: Ana

last: Rodriguez Sanchez-Archidona

state: Vaud

address: Genopode building - Quartier Sorge

department: CIG

country: Switzerland

institute: University of Lausanne

data_processing:
Reads were mapped with STAR-2.5.3a software to M.musculus-mm15 reference genome.
Read counts for each gene were generated with HTSeq-0.9.1 software using as reference the annotation index GRCm38.83 from ENSEMBL.
Counts were filtered, excluding those genes with less than one count per million in two libraries, and normalized using trimmed mean normalization method (TMM) with 'edgeR'.
Genome_build: M.musculus-mm15 reference genome.
Supplementary_files_format_and_content: Normalized matrix in log2 were raw counts were filtered, excluding those genes with less than one count per million in two libraries, and normalized using trimmed mean normalization method (TMM) with 'edgeR'.

growth_protocol: Islets from 10-12 week-old male mice were isolated by hand-picking following pancreata digestion by Liberase. After overnight recovery in cell culture medium, RNA was extracted on batches of 120-150 islets per mouse.

extract_protocol:
Total RNA from islets was extracted using the RNeasy Plus micro kit (Qiagen, Hombrechtikon, Switzerland).
Integrity of islet RNA was verified on a Fragment Analyzer (Agilent Technologies, Inc., Santa Clara, CA 95051, USA) and all preparations had a RNA quality number (RQN) between 8.2 and 9.3. RNA-seq libraries were prepared using 250ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA). Cluster generation was performed with the resulting libraries using the Illumina TruSeq SR Cluster Kit v4 reagents
Sequenced on the Illumina HiSeq 2500 using TruSeq SBS Kit v4 reagents. A sequencing depth of 31 to 46 million reads using 125bp single-end reads was used.

tag: strain background

value: C57Bl6 and 129sv

tag: age

value: 10-12 weeks

tag: Sex

value: male

tag: treatment

value: pancreatic islets


title: KO.7.S961

tag: tissue


title: RC17_before_11_A5

tag: cell type


title: sarcoma classifier reference case 985

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 985

tag: material preparation


title: sarcoma classifier reference case 990

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 990


title: sarcoma classifier reference case 684

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 684


title: RC17_before_11_A2

tag: sortingmethod

tag: plate


title: KO.6.S961


title: sarcoma classifier reference case 683

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 683


title: sarcoma classifier reference case 983

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 983


title: RC17_before_11_A4


title: sarcoma classifier reference case 984

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 984


title: sarcoma classifier reference case 682

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 682


title: RC17_before_11_A10


title: KO.5.S961


title: sarcoma classifier reference case 962

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 962


title: sarcoma classifier reference case 961

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 961


title: RC17_before_11_A11


title: Setd8 control Rep 1

description:
setd8-control_peaks.narrowPeak
setd8-control_ratio.bw
log2ratio_readCountNorm_mutant_vs_control.bw

tag: genotype


title: sarcoma classifier reference case 681

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 681


title: KO.3.S961


title: KO.4.S961


title: KO.2.S961


title: RC17_before_11_A1


title: sarcoma classifier reference case 958

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 958


title: RC17_before_11_B12


title: KO.1.S961


title: sarcoma classifier reference case 680

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 680


title: sarcoma classifier reference case 960

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 960


title: RC17_before_11_A12


title: RC17_after_mesDA_4_G7

source_name: Human graft in rat brain

value: R

value: GFP


title: sarcoma classifier reference case 957

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 957


title: KO.5

value: Saline


title: sarcoma classifier reference case 959

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 959


title: sarcoma classifier reference case 956

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 956


title: KO.4


title: KO.3


title: sarcoma classifier reference case 677

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 677


title: sarcoma classifier reference case 675

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 675


title: RC17_after_mesDA_4_G6


title: sarcoma classifier reference case 676

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 676


title: RC17_after_mesDA_4_G5


title: KO.2


title: RC17_after_mesDA_4_G2


title: sarcoma classifier reference case 954

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 954


title: sarcoma classifier reference case 674

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 674


title: RC17_after_mesDA_4_G11


title: KO.1


title: sarcoma classifier reference case 678

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 678


title: sarcoma classifier reference case 672

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 672


title: sarcoma classifier reference case 673

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 673


title: sarcoma classifier reference case 952

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 952


title: CTL.8.S961

value: control


title: sarcoma classifier reference case 953

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 953


title: RC17_after_mesDA_4_F8


title: sarcoma classifier reference case 955

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 955


title: RC17_after_mesDA_4_F7


title: sarcoma classifier reference case 671

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 671


title: RC17_after_mesDA_4_H5


title: CTL.6.S961


title: KO.6


title: sarcoma classifier reference case 949

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 949


title: CTL.4.S961


title: CTL.5.S961


title: RC17_after_mesDA_4_F4


title: RC17_after_mesDA_4_E9


title: sarcoma classifier reference case 667

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 667


title: CTL.7.S961


title: sarcoma classifier reference case 951

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 951


title: sarcoma classifier reference case 668

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 668


title: sarcoma classifier reference case 669

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 669


title: sarcoma classifier reference case 947

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 947


title: CTL.3.S961


title: CTL.2.S961


title: RC17_after_mesDA_4_E7


title: sarcoma classifier reference case 950

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 950


title: RC17_after_mesDA_4_E2


title: sarcoma classifier reference case 946

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 946


title: sarcoma classifier reference case 664

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 664


title: sarcoma classifier reference case 945

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 945


title: CTL.1.S961


title: RC17_after_mesDA_4_F10


title: sarcoma classifier reference case 670

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 670


title: RC17_after_mesDA_4_F1


title: sarcoma classifier reference case 663

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 663


title: RC17_after_mesDA_4_E12


title: CTL.5


title: sarcoma classifier reference case 666

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 666


title: sarcoma classifier reference case 943

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 943


title: sarcoma classifier reference case 944

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 944


title: sarcoma classifier reference case 662

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 662


title: RC17_after_mesDA_4_D9


title: CTL.6


title: RC17_after_mesDA_4_D8


title: sarcoma classifier reference case 661

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 661


title: sarcoma classifier reference case 941

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 941


title: CTL.3


title: RC17_after_mesDA_4_D7


title: sarcoma classifier reference case 660

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 660


title: RC17_after_mesDA_4_D6


title: sarcoma classifier reference case 936

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 936


title: RC17_after_mesDA_4_D5


title: RC17_after_mesDA_4_E1


title: sarcoma classifier reference case 658

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 658


title: CTL.1


title: CTL.4


title: CTL.2


title: sarcoma classifier reference case 933

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 933


title: sarcoma classifier reference case 934

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 934


title: sarcoma classifier reference case 659

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 659


title: sarcoma classifier reference case 656

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 656


title: RC17_after_mesDA_4_D4


title: sarcoma classifier reference case 932

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 932


title: sarcoma classifier reference case 657

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 657


title: RC17_after_mesDA_4_D12


title: RC17_after_mesDA_4_D2


title: sarcoma classifier reference case 655

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 655


title: sarcoma classifier reference case 940

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 940


title: sarcoma classifier reference case 929

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 929


title: sarcoma classifier reference case 653

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 653


title: sarcoma classifier reference case 930

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 930


title: sarcoma classifier reference case 654

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 654


title: sarcoma classifier reference case 931

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 931


title: sarcoma classifier reference case 652

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 652


title: sarcoma classifier reference case 928

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 928


title: RC17_after_mesDA_4_D11


title: RC17_after_mesDA_4_C7


title: RC17_after_mesDA_4_C6


title: RC17_after_mesDA_4_C8


title: sarcoma classifier reference case 651

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 651


title: sarcoma classifier reference case 927

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 927


title: sarcoma classifier reference case 926

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 926


title: RC17_after_mesDA_4_C5


title: RC17_after_mesDA_4_C4


title: sarcoma classifier reference case 650

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 650


title: sarcoma classifier reference case 648

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 648


title: sarcoma classifier reference case 649

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 649


title: RC17_after_mesDA_4_C3


title: sarcoma classifier reference case 925

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 925


title: sarcoma classifier reference case 924

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 924


title: sarcoma classifier reference case 646

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 646


title: RC17_after_mesDA_4_C12


title: sarcoma classifier reference case 647

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 647


title: RC17_after_mesDA_4_D10


title: sarcoma classifier reference case 923

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 923


title: RC17_after_mesDA_4_C11


title: sarcoma classifier reference case 645

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 645


title: sarcoma classifier reference case 644

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 644


title: WT_890_4

city: Freiburg im Breisgau

first: Josip

middle: Stefan

last: Herman

address: Stuebeweg 51

department: Quantitative Single Cell Biology

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
WT_4
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

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.

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

value: Ebf1+/+ Prx1-Cre

value: bone marrow stromal cells


title: sarcoma classifier reference case 643

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 643

value: sarcoma

value: FFPE


title: sarcoma classifier reference case 921

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 921

value: KRYO


title: RC17_after_mesDA_4_C10


title: sarcoma classifier reference case 920

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 920


title: monocyte-derived macrophages LPS 12h donor non permissive 677

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

source_name: stimulated monocyte-derived macrophages with LPS for 12h

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.

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

tag: donor

value: non permissive for TREML4 (TT)

value: blood

value: monocyte-derived macrophages

value: stimulated with LPS for 12h


title: sarcoma classifier reference case 679

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 679


title: sarcoma classifier reference case 642

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 642


title: monocyte-derived macrophages LPS 12h donor non permissive 132


title: WT_890_1

description:
WT_4
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

tag: genotype/variation


title: monocyte-derived macrophages LPS 12h donor non permissive 126


title: monocyte-derived macrophages LPS 12h donor non permissive 068


title: sarcoma classifier reference case 639

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 639


title: WT_867_4

description:
WT_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: RPI4
Barcode sequence: TGACCA


title: sarcoma classifier reference case 918

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 918


title: sarcoma classifier reference case 637

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 637


title: sarcoma classifier reference case 912

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 912


title: sarcoma classifier reference case 922

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 922


title: WT_867_3

description:
WT_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: RPI3
Barcode sequence: TTAGGC


title: WT770_p4_8

description:
WT_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: RPI8
Barcode sequence: ACTTGA


title: sarcoma classifier reference case 916

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 916


title: sarcoma classifier reference case 640

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 640


title: WT_867_2

description:
WT_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: RPI2
Barcode sequence: CGATGT


title: WT_890_3

description:
WT_4
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: monocyte-derived macrophages LPS 8h donor non permissive 126

source_name: stimulated monocyte-derived macrophages with LPS for 8h

value: stimulated with LPS for 8h


title: sarcoma classifier reference case 942

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 942

source_name: sarcoma sample


title: monocyte-derived macrophages LPS 12h donor non permissive 052


title: sarcoma classifier reference case 915

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 915


title: sarcoma classifier reference case 913

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 913


title: monocyte-derived macrophages LPS 8h donor non permissive 677


title: sarcoma classifier reference case 635

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 635


title: sarcoma classifier reference case 638

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 638


title: sarcoma classifier reference case 665

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 665


title: monocyte-derived macrophages LPS 8h  donor non permissive 052


title: sarcoma classifier reference case 634

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 634


title: sarcoma classifier reference case 633

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 633


title: sarcoma classifier reference case 906

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 906


title: monocyte-derived macrophages untreated donor non permissive 677

value: unstimulated


title: sarcoma classifier reference case 641

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 641


title: monocyte-derived macrophages LPS 8h donor non permissive 132


title: WT770_p4_7

description:
WT_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 636

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 636


title: WT770_p1_3

description:
WT_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: WT_890_2

description:
WT_4
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 948

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 948


title: WT770_p4_6

description:
WT_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


title: WT770_p1_2

description:
WT_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 908

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 908


title: WT_867_1

description:
WT_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: RPI1
Barcode sequence: ATCACG


title: sarcoma classifier reference case 907

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 907


title: monocyte-derived macrophages LPS 8h donor non permissive 068


title: WT770_p4_5

description:
WT_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: WT770_p1_4

description:
WT_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: isolated PBMC's untreated donor non permissive 677

source_name: unstimulated PBMCs

value: PBMCs


title: PASwt_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: isolated PBMC's untreated donor non permissive 126


title: sarcoma classifier reference case 626

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 626


title: monocyte-derived macrophages untreated donor non permissive 132


title: sarcoma classifier reference case 632

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 632


title: PASwt_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: PASko_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

value: Ebf1 fl/fl Prx1-Cre


title: sarcoma classifier reference case 631

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 631


title: monocyte-derived macrophages untreated donor non permissive 126


title: WT770_p1_1

description:
WT_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: PASwt_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: sarcoma classifier reference case 629

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 629


title: monocyte-derived macrophages untreated donor non permissive 052


title: sarcoma classifier reference case 898

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 898


title: isolated PBMC's untreated donor non permissive 052


title: sarcoma classifier reference case 624

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 624


title: PASwt_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


title: sarcoma classifier reference case 897

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 897


title: sarcoma classifier reference case 627

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 627


title: sarcoma classifier reference case 896

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 896


title: PASko_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: sarcoma classifier reference case 622

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 622


title: sarcoma classifier reference case 625

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 625


title: monocyte-derived macrophages LPS 12h donor permissive 851

value: permissive for TREML4 (CT)


title: sarcoma classifier reference case 902

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 902


title: sarcoma classifier reference case 623

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 623


title: sarcoma classifier reference case 895

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 895


title: isolated PBMC's untreated donor non permissive 068


title: sarcoma classifier reference case 630

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 630


title: sarcoma classifier reference case 890

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 890


title: isolated PBMC's untreated donor non permissive 132


title: sarcoma classifier reference case 628

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 628


title: sarcoma classifier reference case 620

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 620


title: sarcoma classifier reference case 621

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 621


title: monocyte-derived macrophages LPS 12h donor permissive 878


title: PASko_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 885

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 885


title: sarcoma classifier reference case 619

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 619


title: monocyte-derived macrophages LPS 12h donor permissive 668


title: KO_888_2

description:
KO_4
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


title: KO_888_4

description:
KO_4
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: RPI8
Barcode sequence: ACTTGA


title: sarcoma classifier reference case 892

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 892


title: sarcoma classifier reference case 883

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 883


title: KO_888_3

description:
KO_4
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 618

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 618


title: monocyte-derived macrophages LPS 12h donor permissive 568


title: monocyte-derived macrophages LPS 8h donor permissive 878


title: sarcoma classifier reference case 617

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 617


title: monocyte-derived macrophages LPS 8h donor permissive 668


title: KO_887_4

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: RPI8
Barcode sequence: ACTTGA


title: sarcoma classifier reference case 616

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 616


title: PASko_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: sarcoma classifier reference case 615

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 615


title: sarcoma classifier reference case 614

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 614


title: sarcoma classifier reference case 881

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 881


title: monocyte-derived macrophages LPS 8h donor permissive 851


title: KO_887_2

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: RPI6
Barcode sequence: GCCAAT


title: monocyte-derived macrophages LPS 8h  donor permissive 157


title: sarcoma classifier reference case 879

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 879


title: KO_887_1

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: RPI5
Barcode sequence: ACAGTG


title: KO_888_1

description:
KO_4
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: monocyte-derived macrophages untreated donor non permissive 068


title: monocyte-derived macrophages LPS 12h  donor permissive 157


title: sarcoma classifier reference case 884

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 884


title: monocyte-derived macrophages untreated donor permissive 878


title: sarcoma classifier reference case 613

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 613


title: EBF1KO_780_p3_8

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: RPI8
Barcode sequence: ACTTGA


title: monocyte-derived macrophages LPS 8h donor permissive 568


title: sarcoma classifier reference case 612

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 612