title: RC17_after_mesDA_2_G7


title: 4C_P0_cortex_GA2_d_del_rep2

status: Public on Mar 01 2020

type: SRA

city: Shanghai

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

country: China

institute: Shanghai JiaoTong University

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: cortex neuron

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

tag: strain

tag: tissue

value: cortex neuron

tag: age

tag: line

value: CBS d deletion

tag: genotype

value: CBS d -/-


title: Ctrl_2_RSs_2

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5690 rosemont boulevard

country: Canada

institute: HMR

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: Retinal sheets derived from iPSCs

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

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

tag: cell type

value: iPSCs-derived Retinal sheet

tag: disease state

value: Ctrl


title: 4C_P0_cortex_GA2_bc_del_rep1

value: CBS bc deletion

value: CBS bc -/-


title: RC17_after_mesDA_2_G6

city: Uppsala

first: Asa

middle: Kristina

last: Bjorklund

address: Box 596

department: Cell and Molecular Biology

country: Sweden

institute: Uppsala University

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

molecule: polyA RNA

source_name: Human graft in rat brain

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)

value: R

tag: sortingmethod

value: GFP

tag: plate


title: Ctrl_ES_RSs_2


title: 4C_P0_cortex_GA2_a_del_rep2

value: CBS a deletion

value: CBS a -/-


title: sarcoma classifier reference case 108

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 108

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

source_name: sarcoma sample

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

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

value: sarcoma

tag: material preparation

value: KRYO


title: Ctrl_2_RSs_1


title: sarcoma classifier reference case 109

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 109

value: FFPE


title: RC17_after_mesDA_2_G4


title: sarcoma classifier reference case 107

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 107


title: sarcoma classifier reference case 110

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 110


title: RC17_after_mesDA_2_G5


title: Ctrl_ES_RSs_1


title: 4C_P0_cortex_GB6_e_del_rep2

value: CBS e deletion

value: CBS e -/-


title: 4C_P0_cortex_GB6_e_del_rep1


title: RC17_after_mesDA_2_G3


title: Ctrl_3_RSs_2


title: RC17_after_mesDA_2_G11


title: sarcoma classifier reference case 106

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 106


title: RC17_after_mesDA_2_G12


title: sarcoma classifier reference case 105

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 105


title: RC17_after_mesDA_2_G2


title: Ctrl_3_RSs_1


title: 4C_P0_cortex_GA2_a_del_rep1


title: RC17_after_mesDA_2_G10


title: 4C_P0_cortex_GB6_bc_del_rep2


title: sarcoma classifier reference case 103

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 103


title: sarcoma classifier reference case 102

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 102


title: 4C_P0_cortex_GB6_be_del_rep2

value: CBS b-e deletion

value: CBS b-e -/-


title: sarcoma classifier reference case 104

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 104


title: sarcoma classifier reference case 101

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 101


title: RC17_after_mesDA_2_G1


title: 4C_P0_cortex_GB6_be_del_rep1

value: cortex neuron


title: RC17_after_mesDA_2_F8


title: RC17_after_mesDA_2_F9


title: sarcoma classifier reference case 99

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 99


title: 4C_P0_cortex_GB2_be_del_rep2


title: 4C_P0_cortex_GB2_be_del_rep1


title: 4C_P0_cortex_GB2_bc_del_rep2


title: SU2C24

city: Boston

first: David

middle: T

last: Ting

state: MA

address: 149 E 13th street

department: Cancer Center

country: USA

institute: Massachusetts General Hospital

data_processing:
Reads aligned to HG38
Deduplicated BAM files used with HTSeq-Count to create count tables
Data was analyzed with DESeq2 for differential expresison analysis
Genome_build: GRCH38
Supplementary_files_format_and_content: Raw and normalized read counts in Text format

source_name: primary purified circulating tumor cells

extract_protocol:
RNA isolation was performed using the AllPrep kit (Qiagen) including the optional on column DNAse treatment (Qiagen) per manufacturer's protocol.
To generate libraries for total RNA sequencing the Illumina Smarter Stranded Total RNA-Seq kit v2 (Cat No#634413) was used according to the manufacturer's instructions. Pooled libraries were sequenced on an Illumina NextSeq 500 sequencer.

treatment_protocol: CTCs were purified from whole blood utilizing the CTC-iChip as described in the publication

tag: sample type

value: primary human sample

value: purified circulating tumor cells

tag: patient diagnosis

value: localized PDAC


title: SU2C25


title: SU2C23


title: sarcoma classifier reference case 100

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 100


title: RC17_after_mesDA_2_F7


title: sarcoma classifier reference case 98

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 98


title: 4C_P0_cortex_GB6_bc_del_rep1

value: CBS bc deletion


title: 4C_P0_cortex_GB2_bc_del_rep1

value: CBS bc -/-


title: sarcoma classifier reference case 96

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 96


title: SU2C19


title: SU2C20


title: 4C_P0_cortex_GA4_e_del_rep1


title: RC17_after_mesDA_2_F5

value: R


title: RC17_after_mesDA_2_F6

value: GFP


title: 4C_P0_cortex_GA4_e_del_rep2


title: RC17_after_mesDA_2_F3


title: sarcoma classifier reference case 95

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 95


title: 4C_P0_cortex_GA4_de_del_rep2

value: CBS de deletion

value: CBS de -/-


title: SU2C22


title: RC17_after_mesDA_2_F2


title: SU2C18


title: SU2C17


title: RC17_after_mesDA_2_F12


title: 4C_P0_cortex_GA4_de_del_rep1


title: SU2C16


title: 4C_P0_cortex_GA4_d_del_rep2

value: CBS d deletion

value: CBS d -/-


title: SU2C15


title: RC17_after_mesDA_2_F11


title: sarcoma classifier reference case 93

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 93

value: sarcoma

value: FFPE


title: sarcoma classifier reference case 92

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 92


title: RC17_after_mesDA_2_F10


title: 4C_P0_cortex_GA4_d_del_rep1


title: SU2C21


title: sarcoma classifier reference case 97

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 97


title: SU2C14


title: 4C_P0_cortex_GA4_be_del_rep2


title: sarcoma classifier reference case 91

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 91


title: sarcoma classifier reference case 90

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 90


title: RC17_after_mesDA_2_F1


title: RC17_after_mesDA_2_E9


title: SU2C13


title: 4C_P0_cortex_GA4_be_del_rep1


title: 4C_P0_cortex_GA4_bcd_del_rep2

value: CBS bcd deletion

value: CBS bcd -/-


title: sarcoma classifier reference case 89

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 89


title: RC17_after_mesDA_2_E8


title: sarcoma classifier reference case 94

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 94


title: 4C_P0_cortex_GA4_bcd_del_rep1


title: sarcoma classifier reference case 87

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 87


title: 4C_P0_cortex_GA4_bc_del_rep2


title: SU2C12


title: SU2C11


title: SU2C10


title: sarcoma classifier reference case 88

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 88


title: RC17_after_mesDA_2_E7


title: SU2C09


title: 4C_P0_cortex_GA4_bc_del_rep1


title: RC17_after_mesDA_2_E6


title: RC17_after_mesDA_2_E5


title: sarcoma classifier reference case 86

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 86


title: sarcoma classifier reference case 85

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 85


title: 4C_P0_cortex_GA4_a_del_rep2

value: CBS a deletion

value: CBS a -/-


title: SU2C08

value: primary human sample


title: 4C_P0_cortex_GA4_a_del_rep1

value: cortex neuron


title: RC17_after_mesDA_2_E4


title: sarcoma classifier reference case 84

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 84


title: SU2C07

value: purified circulating tumor cells

value: localized PDAC


title: RC17_after_mesDA_2_E3


title: SU2C06


title: 4C_P0_cortex_B13_e_del_rep1

value: CBS e deletion

value: CBS e -/-


title: RC17_after_mesDA_2_E2

value: R

value: GFP


title: 4C_P0_cortex_B13_e_del_rep2


title: sarcoma classifier reference case 82

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 82


title: RC17_after_mesDA_2_E12


title: sarcoma classifier reference case 83

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 83


title: 4C_P0_cortex_B13_de_del_rep2

value: CBS de deletion

value: CBS de -/-


title: SU2C04


title: sarcoma classifier reference case 81

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 81


title: RC17_after_mesDA_2_E11


title: 4C_P0_cortex_B13_de_del_rep1


title: SU2C03


title: 4C_P0_cortex_B13_d_del_rep2

value: CBS d deletion

value: CBS d -/-


title: SU2C02


title: RC17_after_mesDA_2_E1


title: sarcoma classifier reference case 78

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 78

value: sarcoma

value: FFPE


title: 4C_P0_cortex_B13_d_del_rep1


title: 4C_P0_cortex_B13_be_del_rep2

value: CBS b-e deletion

value: CBS b-e -/-


title: SU2C01


title: sarcoma classifier reference case 79

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 79


title: RC17_after_mesDA_2_D8


title: 4C_P0_cortex_B13_be_del_rep1


title: RC17_after_mesDA_2_D7


title: sarcoma classifier reference case 76

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 76


title: SU2C05


title: RC17_after_mesDA_2_D6


title: sarcoma classifier reference case 77

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 77


title: metPDAC17

value: metastatic PDAC


title: metPDAC18

value: primary human sample


title: sarcoma classifier reference case 75

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 75


title: sarcoma classifier reference case 74

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 74


title: RC17_after_mesDA_2_E10


title: 4C_P0_cortex_B13_bcd_del_rep1

value: cortex neuron

value: CBS bcd deletion

value: CBS bcd -/-


title: metPDAC15

value: purified circulating tumor cells


title: 4C_P0_cortex_B13_bcd_del_rep2


title: 4C_P0_cortex_B13_bc_del_rep2

value: CBS bc deletion

value: CBS bc -/-


title: metPDAC16


title: metPDAC14


title: RC17_after_mesDA_2_D4

value: R

value: GFP


title: sarcoma classifier reference case 80

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 80


title: sarcoma classifier reference case 73

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 73


title: metPDAC13


title: RC17_after_mesDA_2_D2


title: sarcoma classifier reference case 72

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 72


title: sarcoma classifier reference case 71

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 71


title: metPDAC12


title: 4C_P0_cortex_B13_a_del_rep2

value: CBS a deletion

value: CBS a -/-


title: RC17_after_mesDA_2_D12


title: 4C_P0_cortex_B13_a_del_rep1


title: RC17_after_mesDA_2_D11


title: metPDAC11


title: sarcoma classifier reference case 69

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 69


title: RC17_after_mesDA_2_D5


title: metPDAC10


title: sarcoma classifier reference case 68

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 68


title: metPDAC09


title: 4C_P0_cortex_B9_e_del_rep1

value: CBS e deletion

value: CBS e -/-


title: sarcoma classifier reference case 67

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 67

value: sarcoma

value: FFPE


title: RC17_after_mesDA_2_D1


title: RC17_after_mesDA_2_C9


title: RC17_after_mesDA_2_D3


title: 4C_P0_cortex_B9_de_del_rep1

value: CBS de deletion

value: CBS de -/-


title: RC17_after_mesDA_2_D10


title: 4C_P0_cortex_B13_bc_del_rep1


title: metPDAC07

value: primary human sample

value: metastatic PDAC


title: 4C_P0_cortex_B9_de_del_rep2

value: cortex neuron


title: RC17_after_mesDA_2_C8


title: sarcoma classifier reference case 66

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 66


title: 4C_P0_cortex_B9_d_del_rep2

value: CBS d deletion

value: CBS d -/-


title: sarcoma classifier reference case 65

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 65


title: sarcoma classifier reference case 70

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 70


title: metPDAC06

value: purified circulating tumor cells


title: metPDAC05


title: sarcoma classifier reference case 64

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 64


title: RC17_after_mesDA_2_C5


title: metPDAC04


title: 4C_P0_cortex_B9_be_del_rep1

value: CBS b-e deletion

value: CBS b-e -/-


title: 4C_P0_cortex_B9_be_del_rep2


title: sarcoma classifier reference case 63

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 63


title: RC17_after_mesDA_2_C7

value: R

value: GFP


title: RC17_after_mesDA_2_C4


title: metPDAC03


title: 4C_P0_cortex_B9_e_del_rep2


title: RC17_after_mesDA_2_C3


title: sarcoma classifier reference case 61

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 61


title: sarcoma classifier reference case 62

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 62


title: RC17_after_mesDA_2_C2


title: 4C_P0_cortex_B9_bcd_del_rep1

value: CBS bcd deletion

value: CBS bcd -/-


title: sarcoma classifier reference case 60

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 60


title: metPDAC01


title: 4C_P0_cortex_B9_d_del_rep1


title: locPDAC17

value: localized PDAC


title: RC17_after_mesDA_2_C12


title: RC17_after_mesDA_2_C11


title: 4C_P0_cortex_B9_bc_del_rep2

value: CBS bc deletion

value: CBS bc -/-


title: sarcoma classifier reference case 59

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 59

value: sarcoma

value: FFPE


title: 4C_P0_cortex_B9_bc_del_rep1


title: 4C_P0_cortex_B9_a_del_rep2

value: CBS a deletion

value: CBS a -/-


title: locPDAC15

value: primary human sample


title: sarcoma classifier reference case 57

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 57


title: locPDAC16


title: sarcoma classifier reference case 56

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 56


title: RC17_after_mesDA_2_C1


title: 4C_P0_cortex_B9_bcd_del_rep2

value: cortex neuron


title: metPDAC02

value: metastatic PDAC


title: RC17_after_mesDA_2_B9


title: locPDAC14

value: purified circulating tumor cells


title: 4C_P0_cortex_B6_e_del_rep2

value: CBS e deletion

value: CBS e -/-


title: locPDAC13


title: RC17_after_mesDA_2_B8

value: R


title: 4C_P0_cortex_B9_a_del_rep1


title: 4C_P0_cortex_B6_e_del_rep1


title: RC17_after_mesDA_2_B6

value: GFP


title: locPDAC12


title: sarcoma classifier reference case 58

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 58


title: 4C_P0_cortex_B6_de_del_rep2

value: CBS de deletion

value: CBS de -/-


title: RC17_after_mesDA_2_C10


title: locPDAC11

value: localized PDAC


title: locPDAC10


title: sarcoma classifier reference case 53

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 53


title: sarcoma classifier reference case 52

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 52


title: RC17_after_mesDA_2_B4


title: sarcoma classifier reference case 54

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 54


title: sarcoma classifier reference case 51

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 51


title: locPDAC09


title: 4C_P0_cortex_B6_de_del_rep1


title: RC17_after_mesDA_2_B3


title: sarcoma classifier reference case 50

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 50

value: KRYO


title: sarcoma classifier reference case 55

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 55


title: locPDAC08


title: 4C_P0_cortex_B6_d_del_rep1

value: CBS d deletion

value: CBS d -/-


title: RC17_after_mesDA_2_B2


title: locPDAC07


title: sarcoma classifier reference case 49

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 49

value: sarcoma

value: FFPE


title: locPDAC06


title: RC17_after_mesDA_2_B12


title: 4C_P0_cortex_B6_be_del_rep2

value: CBS b-e deletion

value: CBS b-e -/-


title: 4C_P0_cortex_B6_be_del_rep1

value: cortex neuron


title: RC17_after_mesDA_2_B10


title: 4C_P0_cortex_B6_bcd_del_rep2

value: CBS bcd deletion

value: CBS bcd -/-


title: RC17_after_mesDA_2_B5


title: 4C_P0_cortex_B6_d_del_rep2


title: metPDAC08

value: primary human sample

value: purified circulating tumor cells

value: metastatic PDAC


title: 4C_P0_cortex_B6_bcd_del_rep1


title: locPDAC05


title: sarcoma classifier reference case 47

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 47


title: 4C_P0_cortex_B6_bc_del_rep2

value: CBS bc deletion

value: CBS bc -/-


title: sarcoma classifier reference case 46

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 46


title: RC17_after_mesDA_2_A9

value: R

value: GFP


title: sarcoma classifier reference case 45

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 45

value: KRYO


title: RC17_after_mesDA_2_B1


title: locPDAC04

value: localized PDAC


title: locPDAC02


title: sarcoma classifier reference case 44

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 44


title: RC17_after_mesDA_2_A8


title: RC17_after_mesDA_2_A7


title: 4C_P0_cortex_B6_a_del_rep2

value: CBS a deletion

value: CBS a -/-


title: sarcoma classifier reference case 48

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 48

value: sarcoma


title: sarcoma classifier reference case 43

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 43

value: FFPE


title: 4C_P0_cortex_B6_a_del_rep1


title: sarcoma classifier reference case 42

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 42


title: HD21

value: healthy donor


title: RC17_after_mesDA_2_A5


title: sarcoma classifier reference case 41

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 41


title: locPDAC03


title: RC17_after_mesDA_2_A4


title: HD20


title: HD19


title: 4C_P0_cortex_GA2_be_del_rep2

value: cortex neuron

value: CBS b-e deletion

value: CBS b-e -/-


title: 4C_P0_cortex_GA2_be_del_rep1


title: RC17_after_mesDA_2_A3


title: sarcoma classifier reference case 40

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 40


title: RC17_after_mesDA_2_A2


title: sarcoma classifier reference case 39

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 39


title: HD17

value: primary human sample


title: sarcoma classifier reference case 38

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 38


title: 4C_P0_cortex_GC3_be_del_rep2


title: locPDAC01

value: purified circulating tumor cells


title: RC17_after_mesDA_2_A12


title: HD16


title: sarcoma classifier reference case 37

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 37


title: RC17_after_mesDA_2_A6


title: RC17_after_mesDA_2_A10


title: 4C_P0_cortex_GC3_wt_rep2

value: Wild Type

value: wild type


title: 4C_P0_cortex_GC3_wt_rep1


title: HD15


title: sarcoma classifier reference case 36

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 36


title: RC17_after_mesDA_2_A1


title: 4C_P0_cortex_GC3_d_del_rep2

value: CBS d deletion

value: CBS d -/-


title: sarcoma classifier reference case 35

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 35


title: HD14


title: HD18


title: RC17_after_mesDA_28_H9

value: B

value: GFP


title: sarcoma classifier reference case 34

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 34


title: HD12


title: HD13


title: RC17_after_mesDA_28_H7


title: 4C_P0_cortex_GC3_be_del_rep1


title: 4C_P0_cortex_GB8_wt_rep2


title: 4C_P0_cortex_GB8_wt_rep1


title: 4C_P0_cortex_B6_bc_del_rep1

value: CBS bc deletion

value: CBS bc -/-


title: 4C_P0_cortex_GC3_d_del_rep1


title: RC17_after_mesDA_28_H5


title: HD10


title: sarcoma classifier reference case 33

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 33


title: HD11


title: sarcoma classifier reference case 32

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 32


title: sarcoma classifier reference case 31

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 31


title: HD09

description: HD.SS


title: RC17_after_mesDA_28_H4


title: sarcoma classifier reference case 30

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 30


title: 4C_P0_cortex_GB7_wt_rep1


title: 4C_P0_cortex_GB1_wt_rep2


title: sarcoma classifier reference case 29

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 29


title: RC17_after_mesDA_28_H3


title: HD08


title: 4C_P0_cortex_GB1_wt_rep1


title: RC17_after_mesDA_28_H8


title: RC17_after_mesDA_28_H2


title: HD07


title: sarcoma classifier reference case 28

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 28


title: RC17_after_mesDA_28_H1


title: sarcoma classifier reference case 27

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 27


title: HD06


title: RC17_after_mesDA_28_G9


title: 4C_P0_cortex_GA8_wt_rep2


title: sarcoma classifier reference case 26

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 26


title: 4C_P0_cortex_GA6_wt_rep2


title: RC17_after_mesDA_28_G7


title: 4C_P0_cortex_GA8_wt_rep1


title: sarcoma classifier reference case 25

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 25


title: 4C_P0_cortex_GA6_wt_rep1


title: RC17_after_mesDA_28_G5


title: 4C_P0_cortex_GB7_wt_rep2


title: HD05

description: HD.LL


title: HD04


title: 4C_P0_cortex_GA4_wt_rep2


title: sarcoma classifier reference case 23

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 23


title: HD03


title: HD01

description: HD.DL


title: sarcoma classifier reference case 22

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 22


title: RC17_after_mesDA_28_G4


title: HD02

description: HD.DM


title: 4C_P0_cortex_GA4_wt_rep1


title: RC17_after_mesDA_28_G3


title: RC17_after_mesDA_28_G2


title: 4C_P0_cortex_GA3_wt_rep2


title: 4C_P0_cortex_GA3_wt_rep1


title: sarcoma classifier reference case 21

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 21


title: RC17_after_mesDA_28_G8


title: HC2 CD38high

first: Eri

last: Katsuyama

state: Massachusetts

address: 330 Brookline Avenue, CLS 937

department: Rheumatology

institute: Harvard Medical School, Division of Rheumatology Beth Israel Deaconess Medical Center

data_processing:
atropos Adapter trimming
bowtie2 Alignment
Peak-calling macs2
QC with FastQC
Grey-listing, blacklisting, and chrM removal
Genome_build: hg19
Supplementary_files_format_and_content: bed file, holds macs2 peak calls from the Nucleosome Free Regions for proper ATAC-seq analysis for Differentially Enriched Region detection in R (DiffBind).

source_name: isolated CD8CD38 T cells

extract_protocol: omniATAC

treatment_protocol: sorted by Facs Aria and frozen in banbanker

value: human T cells


title: sarcoma classifier reference case 24

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 24

value: sarcoma


title: sarcoma classifier reference case 20

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 20

value: FFPE


title: HC2 CD38low


title: sarcoma classifier reference case 19

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 19


title: RC17_after_mesDA_28_G11


title: RC17_after_mesDA_28_G12


title: sarcoma classifier reference case 18

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 18


title: HC1 CD38high


title: 4C_P0_cortex_GA1_wt_rep2


title: 4C_P0_cortex_GA1_wt_rep1


title: 4C_P0_cortex_GA12_wt_rep2


title: CD38low SLE2


title: sarcoma classifier reference case 17

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 17


title: sarcoma classifier reference case 16

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 16


title: RC17_after_mesDA_28_G1


title: RC17_after_mesDA_28_F9


title: CD38low SLE1


title: 4C_P0_cortex_GA12_wt_rep1


title: CD38high SLE2


title: sarcoma classifier reference case 15

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 15


title: 4C_P0_cortex_GA10_wt_rep2


title: 4C_P0_cortex_GA10_wt_rep1


title: sarcoma classifier reference case 14

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 14


title: RC17_after_mesDA_28_F7


title: sarcoma classifier reference case 13

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 13


title: organ donor distal ASC [DISTAL_ASC_6]

city: New Haven

first: Michael

last: Simons

state: CT

address: 3oo George St, Suite 773

department: Department: Internal Medicine Cardiology

institute: Yale University

description: fresh frozen tissue

data_processing:
RNA-Seq reads were aligned to the human reference genome (human genome build 38 GRCh38) using short reads aligner STAR
Quantification of gene expression was performed using RSEM with GENCODE annotation (human release 27)
Genes with 1 count per million in less than 10% of samples were removed
Read counts were normalized using the trimmed mean of M-values method (TMM) and differentially expressed genes were identified (edgeR R package)
Differentially expressed genes with a false discovery corrected p-value <= 0.01 were used for further analysis (heatmaps and functional enrichment).
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene counts from RSEM

source_name: normal

extract_protocol:
High-quality total RNA was extracted from fresh frozen tissues
RNA libraries were prepared for sequencing using standard protocols

tag: experimental condition

value: media from normal aorta


title: RC17_after_mesDA_28_F8


title: CD38high SLE1


title: 4C_P0_cortex_CBSf_bcd_del_rep2

value: cortex neuron

value: CBS bcd deletion

value: CBS bcd -/-


title: 4C_P0_cortex_CBSf_bcd_del_rep1


title: RC17_after_mesDA_28_F6


title: RC17_after_mesDA_28_G10


title: RC17_after_mesDA_28_F5


title: HC1 CD38low


title: sarcoma classifier reference case 12

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 12


title: organ donor distal ASC [DISTAL_ASC_5]

description: fresh frozen tissue


title: sarcoma classifier reference case 11

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 11


title: 4C_P0_cortex_B9_wt_rep2


title: organ donor mid ASC [MID_ASC_6]

description: fresh frozen tissue


title: organ donor mid ASC [MID_ASC_5]

description: fresh frozen tissue


title: 4C_P0_cortex_B9_wt_rep1


title: RC17_after_mesDA_28_F4


title: 4C_P0_cortex_B8_wt_rep2


title: organ donor distal ASC [DISTAL_ASC_4]

description: fresh frozen tissue


title: RC17_after_mesDA_28_F2


title: RC17_after_mesDA_28_F3


title: 4C_P0_cortex_B8_wt_rep1


title: organ donor distal ASC [DISTAL_ASC_3]

description: fresh frozen tissue


title: organ donor mid ASC [MID_ASC_4]

description: fresh frozen tissue


title: 4C_P0_cortex_B7_wt_rep2


title: sarcoma classifier reference case 8

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 8


title: RC17_after_mesDA_28_F12


title: RC17_after_mesDA_28_F11


title: sarcoma classifier reference case 7

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 7


title: sarcoma classifier reference case 5

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 5


title: organ donor mid ASC [MID_ASC_3]

description: fresh frozen tissue


title: 4C_P0_cortex_B6_wt_rep2


title: 4C_P0_cortex_B7_wt_rep1


title: sarcoma classifier reference case 10

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 10


title: RC17_after_mesDA_28_F10


title: sarcoma classifier reference case 6

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 6


title: RC17_after_mesDA_28_F1


title: organ donor distal ASC [DISTAL_ASC_2]

description: fresh frozen tissue


title: organ donor mid ASC [MID_ASC_2]

description: fresh frozen tissue


title: sarcoma classifier reference case 9

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 9

value: KRYO


title: 4C_P0_cortex_B6_wt_rep1


title: sarcoma classifier reference case 4

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 4


title: 4C_P0_cortex_B5_wt_rep2


title: organ donor distal ASC [DISTAL_ASC_1]

description: fresh frozen tissue


title: RC17_after_mesDA_28_E8


title: sarcoma classifier reference case 2

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 2


title: RC17_after_mesDA_28_E7


title: 4C_P0_cortex_B5_wt_rep1


title: RC17_after_mesDA_28_E5


title: sarcoma classifier reference case 3

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 3


title: aneurysm neck [AN_NECK_6]

description: fresh frozen tissue

source_name: aneurysm

value: media from aortic aneurysm


title: sarcoma classifier reference case 1

description:
Methylation data from sarcoma sample
REFERENCE_SAMPLE 1


title: RC17_after_mesDA_28_E4


title: 4C_P0_cortex_GA2_wt_rep2

value: Wild Type


title: aneurysm belly [AN_BELLY_6]

description: fresh frozen tissue


title: 4C_P0_cortex_GA2_wt_rep1

value: wild type


title: RC17_after_mesDA_28_E3


title: aneurysm neck [AN_NECK_5]

description: fresh frozen tissue


title: RC17_after_mesDA_28_E12


title: 4C_P0_cortex_B22_wt_rep1


title: 4C_P0_cortex_B21_be_del_rep2

value: CBS b-e deletion

value: CBS b-e -/-


title: RC17_after_mesDA_28_E2

value: B


title: RC17_after_mesDA_28_E11

value: GFP


title: aneurysm neck [AN_NECK_4]

description: fresh frozen tissue


title: organ donor mid ASC [MID_ASC_1]

description: fresh frozen tissue


title: aneurysm belly [AN_BELLY_4]

description: fresh frozen tissue


title: 4C_P0_cortex_B21_be_del_rep1


title: RC17_after_mesDA_28_E10


title: aneurysm neck [AN_NECK_3]

description: fresh frozen tissue


title: RC17_after_mesDA_28_E1


title: 4C_P0_cortex_B20_wt_rep2


title: 4C_P0_cortex_B20_wt_rep1


title: 4C_P0_cortex_B18_wt_rep2


title: aneurysm neck [AN_NECK_2]

description: fresh frozen tissue


title: RC17_after_mesDA_28_D9


title: aneurysm belly [AN_BELLY_5]

description: fresh frozen tissue


title: 4C_P0_cortex_B22_wt_rep2


title: 4C_P0_cortex_B18_wt_rep1


title: aneurysm belly [AN_BELLY_2]

description: fresh frozen tissue


title: RC17_after_mesDA_28_D8


title: aneurysm neck [AN_NECK_1]

description: fresh frozen tissue


title: RC17_after_mesDA_28_D7


title: 4C_P0_cortex_B17_wt_rep1


title: RC17_after_mesDA_28_D5


title: aneurysm belly [AN_BELLY_1]

description: fresh frozen tissue


title: RC17_after_mesDA_28_D6


title: 4C_P0_cortex_B16_wt_rep2


title: aneurysm belly [AN_BELLY_3]

description: fresh frozen tissue


title: _700_4_ZK

city: Moscow

first: Daniil

last: Nikitin

address: Miklucho-Maklaya

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

data_processing:
RNA sequencing FASTQ files were processed with STAR aligner28 in “GeneCounts” mode19 with the Ensembl human transcriptome annotation (Build version GRCh38 and transcript annotation GRCh38.89). Ensembl gene IDs were converted to HGNC gene symbols using Complete HGNC dataset (https://www.genenames.org/, database version from 2017 July 13)
Genome_build: GRCh38
Supplementary_files_format_and_content: the file "mergede_protein_coding_counts.tab" contains raw counts for protein coding genes in a tab-delimited format

source_name: Glioblatoma, recurrent stem cells

growth_protocol: Glioma stem cells were isolated from freshly resected tumor tissue using the Brain Tissue Dissociation Kit (P) (Miltenyi Biotec GmbH, Germany). Single cell suspensions were maintained in NeuroBasal medium supplemented with the B27 component (Invitrogen Life technologies), human fibroblast growth factor (FGF, 10 ng/m) and epidermal growth factor (EGF, 20 ng/mL) (Biochrom GmbH, Merck KGaA, Germany). Self-renewal capacity was evaluated by using the extreme limited dilution assay. In brief, after dissociation, vital cells were seeded in 24-well plates at a defined density, typically from 100 to 1000 cells/ml, and incubated for 4-6 weeks to allow for clonal spheres formation.

extract_protocol:
Resected excess tumor tissue samples were coded and used for RNA sequencing and glioma stem cells isolation in accordance with the Approval by the Institutional Review Board of UMM. Tumor tissue samples were processed within 40 min after resection and divided into three portions under sterile hood. One portion was snap-frozen in liquid nitrogen and kept at -80°C for RNA sequencing after evaluation by neuropathologist. Second portion was used for histopathological assessments. Third portion was used for isolating glioma stem cells. Frozen tumor samples were routinely homogenized using the Minilys personal homogenizer and the Precellys Evolution homogenizer (Bertin Instruments). Grinding was performed using a combination from 1.4 mm and 2.8 mm ceramic beads and 20 mg of tumor tissue at 6500 rpm for 30s x 3 and 30s x 2 pause (4°C). RNA extraction was carried out using the Precellys Tissue RNA Kit Safety-Line (Peqlab) following the manufacturer’s protocol.
For library preparations, we used the TruSeq® Stranded Total RNA Library Prep (Illumina®) and the NEBNext® Ultra II Directional RNA Library Prep Kit (New England BioLabs®) according to the manufacturer’s recommendations. Different dual index adaptors were used for multiplexing samples in one sequencing run. Library concentrations and quality were measured using Qubit dsDNA high-sensitivity (HS) kit and QIAxcel capillary electrophoresis system with QIAxcel ScreenGel software (QIAGEN).

tag: patient id

value: Cells

tag: Stage

value: Recurrent

tag: library prep. kit

value: Illumina Library


title: RC17_after_mesDA_28_D4


title: 4C_P0_cortex_B16_wt_rep1


title: _700_3_ZK


title: RC17_after_mesDA_28_D3


title: 4C_P0_cortex_B17_wt_rep2


title: _700_2_ZK


title: 4C_P0_cortex_B13_wt_rep1


title: _700_1_ZK


title: RC17_after_mesDA_28_D12


title: 4C_P0_cortex_B13_wt_rep2


title: _696_1_ZK


title: 4C_P0_cortex_B12_wt_rep2


title: 4C_P0_cortex_B12_wt_rep1


title: 4C_P0_cortex_B10_wt_rep2


title: RC17_after_mesDA_28_D11


title: RC17_after_mesDA_28_D1


title: RC17_after_mesDA_28_D10


title: _677_3_ZK

source_name: Glioblatoma, primary stem cells

value: Primary


title: 4C_P0_cortex_B10_wt_rep1


title: _677_4_ZK


title: RC17_after_mesDA_28_C8


title: _677_2_ZK


title: RC17_after_mesDA_28_D2


title: Primary_MB_35

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

description:
MB_35
202410160065_R01C01

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

scan_protocol: Arrays were imaged using iScan Platform using standard recommended Illumina setting

data_processing: GenomeStudio software v2.0.  Beta values are not normalized.

label: Cy5 and Cy3

source_name: MB ex vivo

label_protocol: Standard Illumina Protocol

growth_protocol: Cerebellar organoids were cultured in vitro and were electroporated at 35 days of differentiation protocol, were dissociated into Neurobasal Medium and injected intracranially into nude mice.  The mice were sacrificed at the experimental endpoint and intraventricularly perfused with 4% PFA, and brains were collected, cryoprotected in 30% sucrose and embedded in Frozen Section Compound.

extract_protocol: Genomic DNA was extracted with phenol- chloroform and precipitated with isopropanol.

tag: gender

value: F

value: 15 years

value: MB ex vivo

tag: histology

value: Classic

tag: molecular subgroup


title: RC17_after_mesDA_28_C9


title: Primary_MB_36

description:
MB_36
201530470011_R01C01

tag: age

value: 6 years

tag: tissue

value: LC/A


title: Primary_MB_31

description:
MB_31
200992280039_R04C01

value: M

value: 7 years


title: Primary_MB_34

description:
MB_34
201530470040_R08C01


title: Primary_MB_30

description:
MB_30
200992280039_R06C01

value: 8 years


title: 4C_P0_cortex_GA7_wt_rep2

tag: strain

value: cortex neuron

tag: line

value: Wild Type

tag: genotype

value: wild type


title: RC17_after_mesDA_28_C7

tag: cell type

value: B

tag: sortingmethod

value: GFP


title: _677_1_ZK

value: Cells


title: Primary_MB_33

description:
MB_33
200992280037_R03C01

value: 2 years

value: Desmoplastic

value: SHHB


title: Primary_MB_28

description:
MB_28
201530470011_R08C01

value: 16 years


title: _657_2_ZK

value: Primary

value: Illumina Library


title: 4C_P0_cortex_GA7_wt_rep1


title: Primary_MB_25

description:
MB_25
201530470040_R05C01

value: 5 years

value: MB ex vivo


title: 279_670_2_ZK

value: Recurrent


title: Primary_MB_20

description:
MB_20
201530470029_R07C01

value: F

value: Classic


title: Primary_MB_23

description:
MB_23
201530470040_R03C01

value: M

value: 6 years


title: 4C_P0_cortex_GA7_d_del_rep1

value: cortex neuron

value: CBS d deletion

value: CBS d -/-


title: 295_654_1_ZK

value: Cells


title: 4C_P0_cortex_GA7_d_del_rep2


title: Primary_MB_26

description:
MB_26
201496710180_R03C01


title: Primary_MB_32

description:
MB_32
200992280037_R02C01

value: 2 years


title: Primary_MB_24

description:
MB_24
201530470040_R04C01

value: 13 years

value: SHHA


title: Primary_MB_22

description:
MB_22
201530470040_R02C01

value: 9 years


title: Primary_MB_29

description:
MB_29
200992280039_R08C01


title: Primary_MB_21

description:
MB_21
201530470040_R01C01


title: Primary_MB_27

description:
MB_27
201496710180_R02C01

value: 16 years


title: RC17_after_mesDA_28_C12

value: B

value: GFP

tag: plate


title: RC17_after_mesDA_28_C11


title: Primary_MB_19

description:
MB_19
201530470029_R06C01

value: 10 years

value: MB ex vivo


title: 4C_P0_cortex_GA7_e_del_rep2

value: CBS e deletion

value: CBS e -/-


title: 4C_P0_cortex_GA7_de_del_rep1

value: CBS de deletion

value: CBS de -/-


title: 279_670_1_ZK

tag: sample type

value: Recurrent

value: Illumina Library


title: _649_1_ZK

value: Primary


title: RC17_after_mesDA_28_C5


title: 4C_P0_cortex_GA7_e_del_rep1

value: cortex neuron


title: RC17_after_mesDA_28_C3


title: _657_1_ZK

value: Cells


title: 226_645_3_ZK


title: RC17_after_mesDA_28_C2


title: 4C_P0_cortex_GA7_be_del_rep2

value: CBS b-e deletion

value: CBS b-e -/-


title: RC17_after_mesDA_28_B8


title: 4C_P0_cortex_GA7_de_del_rep2


title: _649_2_ZK


title: RC17_after_mesDA_28_B5


title: _568_2_ZK


title: Primary_MB_18

description:
MB_18
201530470029_R05C01

value: M

value: 5 years

value: Classic


title: RC17_after_mesDA_28_C1

value: B

value: GFP


title: 4C_P0_cortex_GA7_bcd_del_rep2

value: CBS bcd deletion

value: CBS bcd -/-


title: 4C_P0_cortex_GA7_bc_del_rep2

value: CBS bc deletion

value: CBS bc -/-


title: Primary_MB_17

description:
MB_17
201530470029_R04C01

value: F

value: MB ex vivo


title: RC17_after_mesDA_28_C10


title: 4C_P0_cortex_GA7_be_del_rep1


title: 226_645_2_ZK

value: Recurrent

value: Illumina Library


title: 4C_P0_cortex_GA7_a_del_rep2

value: cortex neuron

value: CBS a deletion

value: CBS a -/-


title: Primary_MB_16

description:
MB_16
201530470029_R03C01

value: 9 years


title: 4C_P0_cortex_GA7_a_del_rep1


title: 226_645_1_ZK

value: Cells


title: RC17_after_mesDA_28_B7


title: 4C_P0_cortex_GA7_bc_del_rep1


title: Primary_MB_14

description:
MB_14
201530470029_R01C01

value: M


title: 295_619_1_ZK

value: Primary


title: RC17_after_mesDA_28_B4

value: B


title: 4C_P0_cortex_GA7_bcd_del_rep1


title: _568_1_ZK


title: 309_560_1_ZK


title: _501_1_ZK


title: RC17_after_mesDA_28_B1

value: GFP


title: RC17_after_mesDA_28_B3


title: Primary_MB_13

description:
MB_13
201530470010_R01C01

value: 15 years

value: Classic

value: SHHA


title: RC17_after_mesDA_28_B11


title: RC17_after_mesDA_27_H9


title: _565_1_ZK


title: _501_2_ZK


title: RC17_after_mesDA_28_B10


title: 4C_P0_cortex_GA11_wt_rep2

value: Wild Type

value: wild type


title: 4C_P0_cortex_GA11_wt_rep1


title: _459_2_ZK


title: 4C_P0_cortex_GA11_d_del_rep2

value: CBS d deletion

value: CBS d -/-


title: 4C_P0_cortex_GA11_e_del_rep2

value: CBS e deletion

value: CBS e -/-


title: RC17_after_mesDA_28_B12


title: RC17_after_mesDA_27_H8


title: _704_1

source_name: Glioblastoma, recurrent tumor

value: Tissue

value: Recurrent

value: Illumina Library


title: Primary_MB_15

description:
MB_15
201530470029_R02C01

value: F

value: 6 years

value: MB ex vivo


title: _459_1_ZK

value: Cells

value: Primary


title: 4C_P0_cortex_GA11_de_del_rep1

value: cortex neuron

value: CBS de deletion

value: CBS de -/-


title: 4C_P0_cortex_GA11_de_del_rep2


title: Primary_MB_12

description:
MB_12
201530470010_R04C01

value: M

value: LC/A


title: _700_5


title: Primary_MB_4

description:
MB_4
202995640160_R06C01


title: RC17_after_mesDA_27_H7

value: B

value: GFP


title: Primary_MB_9

description:
MB_9
202172220170_R06C01

value: 7 years

value: Classic


title: _700_2

value: Tissue


title: Primary_MB_11

description:
MB_11
202410160065_R03C01

value: 4 years

value: Desmoplastic


title: Primary_MB_1

description:
MB_1
202995640160_R01C01

value: F

value: 13 years

value: WNT


title: RC17_after_mesDA_27_H5


title: Primary_MB_7

description:
MB_7
202995740085_R04C01

value: 6 years

value: MB ex vivo


title: Primary_MB_10

description:
MB_10
202875000110_R02C01


title: RC17_after_mesDA_27_H6


title: Primary_MB_6

description:
MB_6
202995740085_R01C01

value: 10 years


title: RC17_after_mesDA_27_H4


title: Primary_MB_2

description:
MB_2
202995640160_R02C01

value: 15 years


title: RC17_after_mesDA_27_H2


title: Primary_MB_3

description:
MB_3
202995640160_R05C01

value: 8 years


title: 4C_P0_cortex_GA11_be_del_rep2

value: cortex neuron

value: CBS b-e deletion

value: CBS b-e -/-


title: 4C_P0_cortex_GA11_be_del_rep1


title: _700_1

value: Recurrent

value: Illumina Library


title: Primary_MB_8

description:
MB_8
202875000110_R05C01

value: M

value: 17 years

value: LC/A


title: 4C_P0_cortex_GA11_bc_del_rep2

value: CBS bc deletion

value: CBS bc -/-


title: OM_Organoids_2

description:
ORG_2
203030040005_R05C01

source_name: OM G3 organoids in vivo

value: OM G3 organoids in vivo

value: G3 OM Organoids


title: 4C_P0_cortex_GA11_d_del_rep1

value: CBS d deletion

value: CBS d -/-


title: Primary_MB_5

description:
MB_5
202995640160_R07C01

value: F

value: 3 years

value: MB ex vivo

value: Classic


title: 4C_P0_cortex_GA11_e_del_rep1

value: cortex neuron

value: CBS e deletion

value: CBS e -/-


title: RC17_after_mesDA_27_H1

value: B

value: GFP


title: RC17_after_mesDA_27_H11


title: _677_3

source_name: Glioblastoma, primary tumor

value: Tissue

value: Primary

value: Illumina Library


title: 4C_P0_cortex_GA11_bc_del_rep1

value: CBS bc deletion

value: CBS bc -/-


title: _677_2


title: RC17_after_mesDA_27_H10


title: 245_658_3

value: Recurrent

value: NEB library


title: OM_Organoids_1

description:
ORG_1
203030040005_R04C01

value: M

value: OM G3 organoids in vivo

value: G3 OM Organoids


title: RC17_after_mesDA_27_G9


title: RC17_after_mesDA_27_G7


title: 4C_P0_cortex_GA11_bcd_del_rep1

value: CBS bcd deletion

value: CBS bcd -/-


title: 4C_P0_cortex_GA11_bcd_del_rep2

value: cortex neuron


title: 279_670_3


title: 4C_P0_cortex_GA11_a_del_rep2

value: CBS a deletion

value: CBS a -/-


title: 245_658_2


title: 4C_P0_cortex_GA11_a_del_rep1


title: RC17_after_mesDA_27_G6

value: B


title: _677_1


title: 245_658_1


title: 4C_P0_cortex_CBSh_be_inv_rep2

value: CBS b-e inversion

value: CBS b-e -/-


title: RC17_after_mesDA_27_G5

value: GFP


title: RC17_after_mesDA_27_G8


title: RC17_after_mesDA_27_G4


title: 4C_P0_cortex_CBSf_wt_rep2

value: Wild Type

value: wild type


title: RC17_after_mesDA_27_G3


title: 295_654_3

value: Tissue


title: SLV152

city: London

first: Andrew

middle: E

last: Teschendorff

address: 72 Huntley Street

department: UCL Cancer Institute/Institute for Women's Health

country: United Kingdom

institute: University College London

description: Saliva tissue samples

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

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

data_processing: idat files processed using minfi 1.22.1, provided beta-value was generated using Illumina definition and default settings

source_name: genomic DNA from saliva sample SLV152

label_protocol: samples were bisulphite converted using the MagPrep 96-well format kit. Overnight conversion was performed using alternative incubation conditions recommended for Infinium arrays (16 cycles of: 95 degrees for 30 seconds, 50 degrees for 60 minutes)

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

tag: molecule subtype

value: bi-sulphite converted genomic DNA from SLV152


title: 295_654_2

value: Recurrent

value: NEB library


title: _657_1

value: Primary

value: Illumina Library


title: RC17_after_mesDA_27_G2


title: _700_3


title: RC17_after_mesDA_27_G12


title: 4C_P0_cortex_CBSf_e_del_rep2

value: CBS e deletion

value: CBS e -/-


title: 4C_P0_cortex_CBSh_be_inv_rep1

value: cortex neuron


title: SLV151

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV151

value: bi-sulphite converted genomic DNA from SLV151

value: M


title: _700_4


title: RC17_after_mesDA_27_G11

value: B


title: SLV166

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV166

value: bi-sulphite converted genomic DNA from SLV166


title: RC17_after_mesDA_27_G10


title: SLV167

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV167

value: bi-sulphite converted genomic DNA from SLV167


title: 4C_P0_cortex_CBSf_d_del_rep1

source_name: cortex neuron

value: CBS d deletion

value: CBS d -/-


title: RC17_after_mesDA_27_F9

source_name: Human graft in rat brain

value: GFP


title: 4C_P0_cortex_CBSf_d_del_rep2


title: 4C_P0_cortex_CBSf_de_del_rep2

value: CBS de deletion

value: CBS de -/-


title: 383_650_3

value: Tissue


title: 383_650_2

value: NEB library


title: 295_654_1

value: Recurrent


title: 383_650_4

value: Primary


title: 383_650_1


title: RC17_after_mesDA_27_F8


title: 4C_P0_cortex_CBSf_de_del_rep1


title: _649_2

value: Illumina Library


title: RC17_after_mesDA_27_F7


title: SLV168

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV168

value: bi-sulphite converted genomic DNA from SLV168


title: _649_1


title: 4C_P0_cortex_CBSf_be_inv_rep2

value: cortex neuron

value: CBS b-e inversion

value: CBS b-e -/-


title: 4C_P0_cortex_CBSf_wt_rep1

value: Wild Type

value: wild type


title: RC17_after_mesDA_27_F6

value: B


title: 4C_P0_cortex_CBSf_be_inv_rep1


title: 226_645_4


title: SLV165

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV165

value: bi-sulphite converted genomic DNA from SLV165

value: M


title: RC17_after_mesDA_27_F5

value: GFP


title: 4C_P0_cortex_CBSf_e_del_rep1

value: CBS e deletion

value: CBS e -/-


title: 4C_P0_cortex_CBSf_be_del_rep2

value: CBS b-e deletion


title: SLV162

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV162

value: bi-sulphite converted genomic DNA from SLV162


title: 226_645_3

value: Tissue

value: Recurrent

value: NEB library


title: RC17_after_mesDA_27_F4


title: RC17_after_mesDA_27_F3


title: 226_645_1


title: RC17_after_mesDA_27_F12


title: 4C_P0_cortex_CBSf_bc_del_rep1

value: CBS bc deletion

value: CBS bc -/-


title: 357_638_3

value: Illumina Library


title: 226_645_2


title: SLV156

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV156

value: bi-sulphite converted genomic DNA from SLV156


title: SLV160

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV160

value: bi-sulphite converted genomic DNA from SLV160


title: SLV158

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV158

value: bi-sulphite converted genomic DNA from SLV158


title: SLV163

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV163

value: bi-sulphite converted genomic DNA from SLV163


title: 4C_P0_cortex_CBSf_be_del_rep1

value: cortex neuron

value: CBS b-e -/-


title: RC17_after_mesDA_27_F10

value: B

value: GFP


title: SLV161

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV161

value: bi-sulphite converted genomic DNA from SLV161

value: M


title: 357_638_1_1

source_name: Glioblastoma, recurrent tumor


title: RC17_after_mesDA_27_F11


title: 4C_P0_cortex_CBSf_bc_del_rep2


title: RC17_after_mesDA_27_E9


title: 357_638_1


title: 4C_P0_cortex_CBSe_be_inv_rep2

value: CBS b-e inversion


title: 4C_P0_cortex_CBSf_a_del_rep2

value: CBS a deletion

value: CBS a -/-


title: SLV154

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV154

value: bi-sulphite converted genomic DNA from SLV154


title: 357_638_2

value: Tissue

value: Recurrent


title: 4C_P0_cortex_CBSe_be_inv_rep1


title: SLV159

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV159

value: bi-sulphite converted genomic DNA from SLV159

value: F


title: RC17_after_mesDA_27_E8


title: RC17_after_mesDA_27_E7


title: SLV155

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV155

value: bi-sulphite converted genomic DNA from SLV155


title: 402_637_1

source_name: Glioblastoma, primary tumor

value: Primary

value: NEB library


title: 4C_P0_cortex_CBSf_a_del_rep1

value: cortex neuron


title: RC17_after_mesDA_27_E6


title: SLV157

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV157

value: bi-sulphite converted genomic DNA from SLV157


title: SLV164

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV164

value: bi-sulphite converted genomic DNA from SLV164


title: SLV150

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV150

value: bi-sulphite converted genomic DNA from SLV150


title: 402_637_2


title: 139_623_1

value: Illumina Library


title: 123_621_4

source_name: Glioblastoma, second recurrent tumor

value: Secondary Recurrent


title: 4C_P0_cortex_CBSd_be_inv_rep1

source_name: cortex neuron

value: CBS b-e inversion

value: CBS b-e -/-


title: 4C_P0_cortex_CBSbc_be_inv_rep2


title: RC17_after_mesDA_27_E3

source_name: Human graft in rat brain

value: B

value: GFP


title: SLV153

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV153

value: bi-sulphite converted genomic DNA from SLV153

value: M


title: SLV149

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV149

value: bi-sulphite converted genomic DNA from SLV149


title: SLV148

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV148

value: bi-sulphite converted genomic DNA from SLV148


title: RC17_after_mesDA_27_E5


title: 123_621_3

value: Tissue


title: 4C_P0_cortex_CBSbc_be_inv_rep1


title: RC17_after_mesDA_27_E2


title: 4C_P0_cortex_CBSa_be_inv_rep2


title: SLV144

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV144

value: bi-sulphite converted genomic DNA from SLV144


title: SLV147

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV147

value: bi-sulphite converted genomic DNA from SLV147


title: 4C_P0_cortex_B4_be_del_rep2

value: cortex neuron

value: CBS b-e deletion


title: 123_621_2


title: 4C_P0_cortex_CBSa_be_inv_rep1


title: 123_621_1


title: SLV145

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV145

value: bi-sulphite converted genomic DNA from SLV145


title: RC17_after_mesDA_27_E11


title: RC17_after_mesDA_27_E12


title: 4C_P0_cortex_B4_be_del_rep1


title: RC17_after_mesDA_27_E4


title: 295_619_2_2

value: Primary

value: NEB library


title: 295_619_2_1


title: SLV143

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV143

value: bi-sulphite converted genomic DNA from SLV143

value: F


title: SLV146

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV146

value: bi-sulphite converted genomic DNA from SLV146


title: RC17_after_mesDA_27_E10

value: B


title: 295_619_1


title: 4C_P0_cortex_B4_wt_rep2

value: Wild Type

value: wild type


title: SLV142

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV142

value: bi-sulphite converted genomic DNA from SLV142

value: M


title: 4C_P0_cortex_CBSd_be_inv_rep2

value: CBS b-e inversion

value: CBS b-e -/-


title: 4C_P0_cortex_B4_wt_rep1


title: 295_619_1_3

value: Tissue


title: 4C_P0_cortex_B4_e_del_rep2

value: CBS e deletion

value: CBS e -/-


title: 295_619_1_2


title: SLV140

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV140

value: bi-sulphite converted genomic DNA from SLV140


title: 4C_P0_cortex_B4_e_del_rep1

value: cortex neuron


title: 295_619_1_1

source_name: Glioblastoma, primary tumor

value: Primary


title: RC17_after_mesDA_27_D6

value: GFP


title: RC17_after_mesDA_27_D8


title: RC17_after_mesDA_27_D7


title: 279_613_2_2

value: NEB library


title: 4C_P0_cortex_B4_d_del_rep2

value: CBS d deletion

value: CBS d -/-


title: RC17_after_mesDA_27_D5

value: B


title: SLV138

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV138

value: bi-sulphite converted genomic DNA from SLV138


title: 4C_P0_cortex_B4_d_del_rep1


title: 279_613_2_1


title: RC17_after_mesDA_27_D4


title: RC17_after_mesDA_27_D9


title: RC17_after_mesDA_27_D3


title: 279_613_1_1


title: 4C_P0_cortex_B4_de_del_rep2

value: CBS de deletion

value: CBS de -/-


title: 4C_P0_cortex_B4_de_del_rep1


title: 383_591_4


title: SLV139

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV139

value: bi-sulphite converted genomic DNA from SLV139

value: M


title: RC17_after_mesDA_27_D12


title: SLV141

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV141

value: bi-sulphite converted genomic DNA from SLV141

value: F


title: 4C_P0_cortex_B4_bc_del_rep2

value: CBS bc deletion

value: CBS bc -/-


title: 383_591_3

value: Tissue


title: RC17_after_mesDA_27_D10


title: RC17_after_mesDA_27_D11


title: SLV133

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV133

value: bi-sulphite converted genomic DNA from SLV133


title: 4C_P0_cortex_B4_bc_del_rep1

source_name: cortex neuron

value: cortex neuron


title: SLV137

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV137

value: bi-sulphite converted genomic DNA from SLV137


title: 4C_P0_cortex_B4_bcd_del_rep2

value: CBS bcd deletion

value: CBS bcd -/-


title: RC17_after_mesDA_27_D1

source_name: Human graft in rat brain

value: GFP


title: 123_590_4

source_name: Glioblastoma, recurrent tumor

value: Recurrent

value: Illumina Library


title: 4C_P0_cortex_B4_bcd_del_rep1


title: 123_590_2


title: SLV131

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV131

value: bi-sulphite converted genomic DNA from SLV131


title: 4C_P0_cortex_B4_a_del_rep2

value: CBS a deletion

value: CBS a -/-


title: SLV132

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV132

value: bi-sulphite converted genomic DNA from SLV132

value: M


title: 123_590_3


title: SLV136

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV136

value: bi-sulphite converted genomic DNA from SLV136


title: SLV134

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV134

value: bi-sulphite converted genomic DNA from SLV134


title: RC17_after_mesDA_27_C8

value: B


title: 341_571_3

value: Tissue


title: RC17_after_mesDA_27_C7


title: 4C_P0_cortex_B21_wt_rep2

value: Wild Type

value: wild type


title: 4C_P0_cortex_B4_a_del_rep1

value: cortex neuron


title: RC17_after_mesDA_27_C5


title: 123_590_1


title: RC17_after_mesDA_27_C9


title: RC17_after_mesDA_27_C4


title: SLV124

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV124

value: bi-sulphite converted genomic DNA from SLV124


title: 341_571_1


title: 4C_P0_cortex_B21_e_del_rep1

value: CBS e deletion

value: CBS e -/-


title: _568_2A

value: Primary


title: SLV130

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV130

value: bi-sulphite converted genomic DNA from SLV130


title: SLV125

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV125

value: bi-sulphite converted genomic DNA from SLV125

value: F


title: 4C_P0_cortex_B21_e_del_rep2


title: RC17_after_mesDA_27_C3

value: GFP


title: RC17_after_mesDA_27_C2


title: SLV129

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV129

value: bi-sulphite converted genomic DNA from SLV129


title: SLV126

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV126

value: bi-sulphite converted genomic DNA from SLV126

value: M


title: 341_571_2

value: Recurrent

value: Illumina Library


title: 4C_P0_cortex_B21_d_del_rep2

value: CBS d deletion

value: CBS d -/-


title: _568_2

source_name: Glioblastoma, primary tumor

value: Tissue


title: RC17_after_mesDA_27_C12

value: B


title: 4C_P0_cortex_B21_d_del_rep1

value: cortex neuron


title: 4C_P0_cortex_B21_wt_rep1

value: Wild Type

value: wild type


title: SLV128

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV128

value: bi-sulphite converted genomic DNA from SLV128


title: _565_1B

value: Primary


title: _565_1A


title: 4C_P0_cortex_B21_de_del_rep2

value: CBS de deletion

value: CBS de -/-


title: RC17_after_mesDA_27_C1

value: GFP


title: SLV122

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV122

value: bi-sulphite converted genomic DNA from SLV122


title: SLV123

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV123

value: bi-sulphite converted genomic DNA from SLV123


title: 4C_P0_cortex_B21_bc_del_rep2

source_name: cortex neuron

value: CBS bc deletion

value: CBS bc -/-


title: _565_1_2

value: Illumina Library


title: _565_1_3


title: SLV121

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV121

value: bi-sulphite converted genomic DNA from SLV121

value: M


title: _568_2B

value: Tissue


title: SLV127

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV127

value: bi-sulphite converted genomic DNA from SLV127


title: RC17_after_mesDA_27_C11

source_name: Human graft in rat brain

value: B


title: _565_1_1


title: RC17_after_mesDA_27_B6


title: 4C_P0_cortex_B21_bcd_del_rep2

value: cortex neuron

value: CBS bcd deletion

value: CBS bcd -/-


title: 309_560_4

value: Primary

value: NEB library


title: SLV120

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV120

value: bi-sulphite converted genomic DNA from SLV120


title: RC17_after_mesDA_27_B9

value: GFP


title: SLV117

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV117

value: bi-sulphite converted genomic DNA from SLV117


title: RC17_after_mesDA_27_B5


title: 309_560_3


title: 4C_P0_cortex_B21_a_del_rep2

value: CBS a deletion

value: CBS a -/-


title: RC17_after_mesDA_27_B4


title: SLV135

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV135

value: bi-sulphite converted genomic DNA from SLV135


title: SLV118

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV118

value: bi-sulphite converted genomic DNA from SLV118


title: RC17_after_mesDA_27_B3


title: SLV119

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV119

value: bi-sulphite converted genomic DNA from SLV119


title: 4C_P0_cortex_B21_bcd_del_rep1


title: 309_560_1


title: RC17_after_mesDA_27_B2


title: 4C_P0_cortex_B17_e_del_rep2

value: CBS e deletion

value: CBS e -/-


title: 151_518_3_3

source_name: Glioblastoma, second recurrent tumor

value: Tissue

value: Secondary Recurrent

value: Illumina Library


title: SLV116

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV116

value: bi-sulphite converted genomic DNA from SLV116

value: M


title: RC17_after_mesDA_27_B12

value: B


title: 4C_P0_cortex_B17_e_del_rep1

value: cortex neuron


title: 151_518_2_3


title: SLV115

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV115

value: bi-sulphite converted genomic DNA from SLV115


title: 309_560_2

value: Primary

value: NEB library


title: SLV112

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV112

value: bi-sulphite converted genomic DNA from SLV112


title: 4C_P0_cortex_B21_de_del_rep1

value: CBS de deletion

value: CBS de -/-


title: RC17_after_mesDA_27_B11

value: GFP


title: SLV110

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV110

value: bi-sulphite converted genomic DNA from SLV110


title: 4C_P0_cortex_B17_d_del_rep1

value: CBS d deletion

value: CBS d -/-


title: 4C_P0_cortex_B17_d_del_rep2


title: 151_518_2_1

value: Tissue


title: SLV111

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV111

value: bi-sulphite converted genomic DNA from SLV111


title: RC17_after_mesDA_27_B1


title: RC17_after_mesDA_27_A9


title: SLV113

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV113

value: bi-sulphite converted genomic DNA from SLV113


title: 4C_P0_cortex_B17_de_del_rep2


title: RC17_after_mesDA_27_A8


title: 4C_P0_cortex_B17_de_del_rep1


title: 4C_P0_cortex_B21_a_del_rep1

value: CBS a deletion

value: CBS a -/-


title: 151_518_1_2

value: Secondary Recurrent

value: Illumina Library


title: RC17_after_mesDA_27_A7

value: B


title: 4C_P0_cortex_B21_bc_del_rep1

value: cortex neuron

value: CBS bc deletion

value: CBS bc -/-


title: 151_518_1_1


title: SLV114

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV114

value: bi-sulphite converted genomic DNA from SLV114

value: M


title: 4C_P0_cortex_B17_be_del_rep2

source_name: cortex neuron

value: CBS b-e deletion

value: CBS b-e -/-


title: RC17_after_mesDA_27_A6

value: GFP


title: 4C_P0_cortex_B17_be_del_rep1


title: 151_518_1_3


title: SLV108

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV108

value: bi-sulphite converted genomic DNA from SLV108


title: RC17_after_mesDA_27_A5


title: RC17_after_mesDA_27_B7


title: _501_2_2

source_name: Glioblastoma, primary tumor

value: Tissue

value: Primary


title: SLV106

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV106

value: bi-sulphite converted genomic DNA from SLV106


title: 4C_P0_cortex_B17_bc_del_rep2


title: RC17_after_mesDA_27_A4

source_name: Human graft in rat brain


title: _501_2_1


title: _501_2


title: SLV109

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV109

value: bi-sulphite converted genomic DNA from SLV109


title: 4C_P0_cortex_B17_bc_del_rep1


title: RC17_after_mesDA_27_A2


title: SLV104

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV104

value: bi-sulphite converted genomic DNA from SLV104


title: _501_1A


title: 4C_P0_cortex_B17_bcd_del_rep1

value: CBS bcd deletion

value: CBS bcd -/-


title: 4C_P0_cortex_B17_bcd_del_rep2


title: _501_1B

value: Illumina Library


title: RC17_after_mesDA_27_A3

value: B


title: RC17_after_mesDA_27_A12


title: 4C_P0_cortex_B17_a_del_rep2

value: cortex neuron

value: CBS a deletion

value: CBS a -/-


title: 151_518_2_2

value: Secondary Recurrent


title: 4C_P0_cortex_B17_a_del_rep1


title: RC17_after_mesDA_27_A11


title: _501_1_2


title: RC17_after_mesDA_27_A1


title: SLV107

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV107

value: bi-sulphite converted genomic DNA from SLV107

value: M


title: _501_1_1


title: SLV101

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV101

value: bi-sulphite converted genomic DNA from SLV101


title: RC17_after_mesDA_27_A10

value: GFP


title: 4C_p0_cortex_CBSe_wt_rep1

value: wild type


title: 4C_p0_cortex_CBSe_wt_rep2


title: 163_488_2

source_name: Glioblastoma, recurrent tumor

value: Tissue

value: Recurrent


title: SLV100

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV100

value: bi-sulphite converted genomic DNA from SLV100


title: SLV102

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV102

value: bi-sulphite converted genomic DNA from SLV102


title: RC17_after_mesDA_25_H9


title: SLV105

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV105

value: bi-sulphite converted genomic DNA from SLV105


title: SLV103

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV103

value: bi-sulphite converted genomic DNA from SLV103


title: 4C_p0_cortex_CBSe_d del_rep2

value: CBS d -/-


title: 4C_p0_cortex_CBSe_d del_rep1


title: 163_488_1

value: Illumina Library


title: 139_478_4

value: Primary


title: 139_478_3


title: RC17_after_mesDA_25_H5

value: B


title: 139_478_2


title: RC17_after_mesDA_25_H4


title: 4C_p0_cortex_CBSe_bcd de_rep2

value: cortex neuron

value: CBS bcd -/-


title: SLV99

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV99

value: bi-sulphite converted genomic DNA from SLV99


title: RC17_after_mesDA_25_H3


title: 139_478_1


title: RC17_after_mesDA_25_H7


title: RC17_after_mesDA_25_H2


title: 4C_p0_cortex_CBSe_bc del_rep1

value: CBS bc -/-


title: 4C_p0_cortex_CBSe_bcd de_rep1


title: 4C_p0_cortex_CBSe_a del_rep2

value: CBS a -/-


title: 181_466_2


title: _501_1_3


title: RC17_after_mesDA_25_H11

value: GFP


title: 4C_p0_cortex_CBSe_bc del_rep2


title: 4C_p0_cortex_CBSe_a del_rep1


title: 181_466_1


title: 181_466_3


title: RC17_after_mesDA_25_H10


title: SLV98

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV98

value: bi-sulphite converted genomic DNA from SLV98

value: M


title: _459_2

value: Tissue


title: 4C_p0_cortex_CBSd_wt_rep2

value: wild type


title: SLV91

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV91

value: bi-sulphite converted genomic DNA from SLV91


title: SLV94

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV94

value: bi-sulphite converted genomic DNA from SLV94


title: SLV95

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV95

value: bi-sulphite converted genomic DNA from SLV95


title: 4C_p0_cortex_CBSd_wt_rep1

source_name: cortex neuron


title: SLV89

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV89

value: bi-sulphite converted genomic DNA from SLV89


title: SLV86

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV86

value: bi-sulphite converted genomic DNA from SLV86

value: F


title: _459_1

source_name: Glioblastoma, primary tumor

value: Primary

value: Illumina Library


title: SLV96

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV96

value: bi-sulphite converted genomic DNA from SLV96


title: RC17_after_mesDA_25_G9

source_name: Human graft in rat brain

value: B


title: RC17_after_mesDA_25_G6


title: RC17_after_mesDA_25_H1


title: 181_429_2


title: SLV82

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV82

value: bi-sulphite converted genomic DNA from SLV82


title: 4C_p0_cortex_CBSd_e del_rep2

value: cortex neuron

value: CBS e -/-


title: SLV97

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV97

value: bi-sulphite converted genomic DNA from SLV97


title: SLV87

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV87

value: bi-sulphite converted genomic DNA from SLV87

value: M


title: 4C_p0_cortex_CBSd_e del_rep1


title: RC17_after_mesDA_25_H12

value: GFP


title: SLV93

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV93

value: bi-sulphite converted genomic DNA from SLV93


title: RC17_after_mesDA_25_G5


title: SLV92

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV92

value: bi-sulphite converted genomic DNA from SLV92


title: 4C_p0_cortex_CBSd_bc del_rep2

value: CBS bc -/-


title: 4C_p0_cortex_CBSd_bc del_rep1


title: RC17_after_mesDA_25_G12


title: 191_349_1

value: Tissue


title: 4C_p0_cortex_CBSd_a del_rep2

value: CBS a -/-


title: 326_330_2


title: SLV83

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV83

value: bi-sulphite converted genomic DNA from SLV83


title: SLV85

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV85

value: bi-sulphite converted genomic DNA from SLV85


title: RC17_after_mesDA_25_G11


title: SLV84

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV84

value: bi-sulphite converted genomic DNA from SLV84


title: RC17_after_mesDA_25_G3


title: 4C_p0_cortex_CBSd_a del_rep1


title: 326_330_1

value: Primary

value: Illumina Library


title: 191_349_2


title: 123_274_2


title: RC17_after_mesDA_25_G10

value: B


title: 4C_p0_cortex_CBSbc_wt_rep2

value: cortex neuron

value: wild type


title: RC17_after_mesDA_25_G1


title: SLV88

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV88

value: bi-sulphite converted genomic DNA from SLV88


title: 341_223_8


title: SLV90

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV90

value: bi-sulphite converted genomic DNA from SLV90

value: F


title: SLV81

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV81

value: bi-sulphite converted genomic DNA from SLV81

value: M


title: 4C_p0_cortex_CBSbc_e del_rep2

source_name: cortex neuron

value: CBS e -/-


title: 4C_p0_cortex_CBSbc_wt_rep1


title: 341_223_7_1

value: NEB library


title: RC17_after_mesDA_25_F8

value: GFP


title: RC17_after_mesDA_25_F9


title: SLV75

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV75

value: bi-sulphite converted genomic DNA from SLV75


title: RC17_after_mesDA_25_F7


title: 4C_p0_cortex_CBSbc_e del_rep1


title: 4C_p0_cortex_CBSbc_de del_rep2

value: CBS de -/-


title: 341_223_6

value: Tissue


title: RC17_after_mesDA_25_F6


title: SLV78

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV78

value: bi-sulphite converted genomic DNA from SLV78


title: 341_223_7

source_name: Glioblastoma, primary tumor

value: Primary


title: 341_223_5

value: Illumina Library


title: RC17_after_mesDA_25_F5

value: B


title: 4C_p0_cortex_CBSbc_d del_rep2

value: cortex neuron

value: CBS d -/-


title: 341_223_4


title: RC17_after_mesDA_25_F4


title: 341_223_3


title: RC17_after_mesDA_25_F3


title: 4C_p0_cortex_CBSbc_d del_rep1


title: SLV76

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV76

value: bi-sulphite converted genomic DNA from SLV76


title: RC17_after_mesDA_25_F2

source_name: Human graft in rat brain


title: RC17_after_mesDA_25_F12


title: 4C_p0_cortex_CBSa_wt_rep2

value: wild type


title: 341_223_1


title: 4C_p0_cortex_CBSbc_a del_rep1

value: CBS a -/-


title: 181_429_1


title: 4C_p0_cortex_CBSbc_a del_rep2


title: RC17_after_mesDA_25_F11


title: 4C_p0_cortex_CBSbc_de del_rep1


title: 341_223_10


title: SLV70

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV70

value: bi-sulphite converted genomic DNA from SLV70


title: 4C_p0_cortex_CBSa_wt_rep1


title: SLV74

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV74

value: bi-sulphite converted genomic DNA from SLV74

value: M


title: 123_274_1


title: RC17_after_mesDA_25_F10


title: SLV72

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV72

value: bi-sulphite converted genomic DNA from SLV72


title: SLV71

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV71

value: bi-sulphite converted genomic DNA from SLV71


title: RC17_after_mesDA_25_F1

value: GFP


title: RC17_after_mesDA_25_E8


title: 341_223_2


title: 4C_p0_cortex_CBSa_e del_rep1

value: CBS e -/-


title: 259_667_1

source_name: Glioblastoma, recurrent tumor

value: Tissue

value: Recurrent

value: NEB library


title: SLV68

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV68

value: bi-sulphite converted genomic DNA from SLV68


title: 4C_p0_cortex_CBSa_e del_rep2


title: 4C_p0_cortex_CBSa_de del_rep2

value: CBS de -/-


title: 402_652_1


title: 4C_p0_cortex_CBSa_de del_rep1

value: cortex neuron


title: 245_636_1

value: Primary


title: SLV65

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV65

value: bi-sulphite converted genomic DNA from SLV65

value: F


title: RC17_after_mesDA_25_E6

value: B


title: SLV66

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV66

value: bi-sulphite converted genomic DNA from SLV66


title: SLV80

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV80

value: bi-sulphite converted genomic DNA from SLV80


title: RC17_after_mesDA_25_E7


title: 357_607_2

value: Illumina Library


title: 4C_p0_cortex_CBSa_d del_rep2

value: CBS d -/-


title: RC17_after_mesDA_25_E5


title: RC17_after_mesDA_25_E4


title: 4C_p0_cortex_CBSa_bcd del_rep2

value: CBS bcd -/-


title: RC17_after_mesDA_25_E3

value: GFP


title: 4C_p0_cortex_CBSa_d del_rep1


title: 259_433_1


title: 357_607_1


title: 309_656_1


title: 4C_p0_cortex_CBSa_bcd del_rep1


title: 326_408_1


title: SLV67

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV67

value: bi-sulphite converted genomic DNA from SLV67

value: M


title: RC17_after_mesDA_25_E12


title: SLV62

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV62

value: bi-sulphite converted genomic DNA from SLV62


title: RC17_after_mesDA_25_E11


title: 4C_p0_cortex_CBSa_bc del_rep1

source_name: cortex neuron

value: CBS bc -/-


title: 4C_p0_cortex_CBSa_bc del_rep2


title: 211_20_1

value: Tissue

value: Recurrent


title: SLV59

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV59

value: bi-sulphite converted genomic DNA from SLV59


title: SLV60

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV60

value: bi-sulphite converted genomic DNA from SLV60


title: SLV64

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV64

value: bi-sulphite converted genomic DNA from SLV64


title: RC17_after_mesDA_25_E10


title: SLV77

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV77

value: bi-sulphite converted genomic DNA from SLV77


title: 123_621_5

source_name: Glioblastoma, second recurrent tumor

value: Secondary Recurrent


title: SLV79

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV79

value: bi-sulphite converted genomic DNA from SLV79


title: 4C_p0_cortex_CBSa_b-e del_rep2

value: cortex neuron

value: CBS b-e -/-


title: 151_445_3

value: Illumina Library


title: 367_74_1

source_name: Glioblastoma, primary tumor

value: Primary

value: NEB library


title: 4C_p0_cortex_CBSa_b-e del_rep1


title: RC17_after_mesDA_25_D9

source_name: Human graft in rat brain

value: B

value: GFP


title: 4C_p0_cortex_CBSa_a del_rep2

value: CBS a -/-


title: 151_445_2


title: RC17_after_mesDA_25_E1


title: SLV69

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV69

value: bi-sulphite converted genomic DNA from SLV69

value: M


title: 151_197_2

value: Tissue


title: RC17_after_mesDA_25_D8


title: SLV58

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV58

value: bi-sulphite converted genomic DNA from SLV58


title: SLV61

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV61

value: bi-sulphite converted genomic DNA from SLV61


title: 4C_p0_cortex_CBSa_a del_rep1


title: 151_197_1


title: RC17_after_mesDA_25_D6


title: p0-cortex_bedel_34

description: single-cell RNA-seq

data_processing:
Single-cell RNA-seq reads were aligned to the mm38_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: mm38_tran
Supplementary_files_format_and_content: fpkm_tracking files include FPKM values for each Sample

extract_protocol:
P0 mouse brain was dissected, and the tissue from cerebral cortex was digested with 0.013% of collagenase in Neurobasal Medium (Gibco) at 37℃ for 3 min. The collagenase was neutralized by adding excess amount of Neurobasal Medium. Single-cell suspension was made by gentle pipetting, and then filtered through 100-μm cell strainers.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).

value: CBS b-e-/-


title: RC17_after_mesDA_25_D5


title: DS3_PDX2

city: Cambridge

last: Hemann

address: 500 Main St, Building 76 Room 301

department: Koch Institute

institute: Massachusetts Institute of Technology

description:
processed data file:
PDXCells_rawCounts.txt
D16-165054

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

source_name: Lymphoma PDX cells

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

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

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

value: B cell double-hit lymphoma

tag: treatment

value: Doxorubicin

value: Spleen


title: p0-cortex_bedel_33

description: single-cell RNA-seq

value: cortex neuron


title: DS2_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165053


title: RC17_after_mesDA_25_D4


title: DS1_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165052


title: RC17_after_mesDA_25_D3


title: p0-cortex_bedel_31

description: single-cell RNA-seq


title: p0-cortex_bedel_35

description: single-cell RNA-seq


title: DB3_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165051

value: Bone marrow


title: RC17_after_mesDA_25_D7


title: SLV56

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV56

value: bi-sulphite converted genomic DNA from SLV56


title: SLV54

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV54

value: bi-sulphite converted genomic DNA from SLV54


title: RC17_after_mesDA_25_D2


title: SLV57

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV57

value: bi-sulphite converted genomic DNA from SLV57


title: p0-cortex_bedel_30

description: single-cell RNA-seq


title: DB2_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165050


title: SLV73

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV73

value: bi-sulphite converted genomic DNA from SLV73


title: SLV55

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV55

value: bi-sulphite converted genomic DNA from SLV55

value: F


title: p0-cortex_bedel_32

description: single-cell RNA-seq

source_name: cortex neuron


title: RC17_after_mesDA_25_D12

value: B

value: GFP


title: DB1_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165049


title: RC17_after_mesDA_25_D10


title: p0-cortex_bedel_28

description: single-cell RNA-seq


title: VB3_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165048

value: Vehicle


title: SLV50

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV50

value: bi-sulphite converted genomic DNA from SLV50

value: M


title: RC17_after_mesDA_25_C9


title: p0-cortex_bedel_27

description: single-cell RNA-seq

value: CBS b-e-/-


title: SLV63

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV63

value: bi-sulphite converted genomic DNA from SLV63


title: VB2_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165047

value: B cell double-hit lymphoma


title: RC17_after_mesDA_25_C8


title: p0-cortex_bedel_29

description: single-cell RNA-seq


title: SLV52

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV52

value: bi-sulphite converted genomic DNA from SLV52


title: SLV53

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV53

value: bi-sulphite converted genomic DNA from SLV53


title: VB1_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165046

value: Bone marrow


title: RC17_after_mesDA_25_C7


title: p0-cortex_bedel_25

description: single-cell RNA-seq

value: cortex neuron


title: CB3_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165045

value: Cyclophosphamide


title: CB2_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165044


title: p0-cortex_bedel_23

description: single-cell RNA-seq


title: RC17_after_mesDA_25_C5


title: p0-cortex_bedel_26

description: single-cell RNA-seq


title: SLV48

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV48

value: bi-sulphite converted genomic DNA from SLV48


title: RC17_after_mesDA_25_C6


title: SLV47

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV47

value: bi-sulphite converted genomic DNA from SLV47


title: SLV45

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV45

value: bi-sulphite converted genomic DNA from SLV45


title: p0-cortex_bedel_22

description: single-cell RNA-seq


title: CB1_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165043


title: SLV49

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV49

value: bi-sulphite converted genomic DNA from SLV49

value: F


title: RC17_after_mesDA_25_C4

source_name: Human graft in rat brain

value: B

value: GFP


title: VS3_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165042

value: Vehicle

value: Spleen


title: VS2_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165041


title: p0-cortex_bedel_24

description: single-cell RNA-seq

value: CBS b-e-/-


title: SLV42

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV42

value: bi-sulphite converted genomic DNA from SLV42

value: M


title: p0-cortex_bedel_20

description: single-cell RNA-seq


title: SLV46

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV46

value: bi-sulphite converted genomic DNA from SLV46


title: SLV43

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV43

value: bi-sulphite converted genomic DNA from SLV43


title: RC17_after_mesDA_25_C3


title: SLV44

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV44

value: bi-sulphite converted genomic DNA from SLV44


title: p0-cortex_bedel_19

description: single-cell RNA-seq

value: cortex neuron


title: RC17_after_mesDA_25_C2


title: RC17_after_mesDA_25_C12


title: VS1_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165040

source_name: Lymphoma PDX cells

value: B cell double-hit lymphoma


title: p0-cortex_bedel_18

description: single-cell RNA-seq


title: p0-cortex_bedel_17

description: single-cell RNA-seq


title: SLV38

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV38

value: bi-sulphite converted genomic DNA from SLV38


title: RC17_after_mesDA_25_C11


title: CS1_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165037

value: Cyclophosphamide


title: p0-cortex_bedel_21

description: single-cell RNA-seq


title: SLV40

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV40

value: bi-sulphite converted genomic DNA from SLV40


title: RC17_after_mesDA_25_C1


title: CS2_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165038


title: CS3_PDX2

description:
processed data file:
PDXCells_rawCounts.txt
D16-165039


title: RC17_after_mesDA_25_C10


title: RC17_after_mesDA_25_B8


title: p0-cortex_bedel_16

description: single-cell RNA-seq

source_name: cortex neuron


title: p0-cortex_bedel_15

description: single-cell RNA-seq


title: SLV36

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV36

value: bi-sulphite converted genomic DNA from SLV36


title: SLV39

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV39

value: bi-sulphite converted genomic DNA from SLV39


title: CB2_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165017

value: Bone marrow


title: RC17_after_mesDA_25_B7

value: B

value: GFP


title: CB1_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165016


title: p0-cortex_bedel_13

description: single-cell RNA-seq


title: DB3_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165015

value: Doxorubicin


title: SLV35

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV35

value: bi-sulphite converted genomic DNA from SLV35


title: RC17_after_mesDA_25_B6


title: p0-cortex_bedel_12

description: single-cell RNA-seq

value: CBS b-e-/-


title: RC17_after_mesDA_25_B2


title: SLV37

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV37

value: bi-sulphite converted genomic DNA from SLV37

value: M


title: SLV34

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV34

value: bi-sulphite converted genomic DNA from SLV34

value: F


title: CB3_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165018


title: RC17_after_mesDA_25_B12


title: SLV41

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV41

value: bi-sulphite converted genomic DNA from SLV41


title: p0-cortex_bedel_10

description: single-cell RNA-seq

value: cortex neuron


title: DB2_PDX1

description:
processed data file:
PDXCells_rawCounts.txt
D16-165014

value: B cell double-hit lymphoma


title: SLV31

description: Saliva tissue samples

source_name: genomic DNA from saliva sample SLV31

value: bi-sulphite converted genomic DNA from SLV31


title: p0-cortex_bedel_11

description: single-cell RNA-seq


title: p0-cortex_bedel_9

description: single-cell RNA-seq