title: BT935 MRD Control

description: Cell line engrafted in NSG mice and grown as orthotopic tumors.

data_processing:
FASTQ files were first filtered using a bespoke Perl script to remove reads shorter than 36bp.
Filtered FASTQ files were aligned to Gencode v25 gene annotations and hg38 genome build using the STAR short-read aligner (v2.4.2a)
Read count files generated by STAR were merged with gene annotations in R
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text read counts

source_name: Glioblastoma multiforme cell line

extract_protocol:
Total RNA was isolated from human GBM cells sorted from mouse brains using Norgen total RNA purification kit following the manufacturer's instructions.
Sequencing libraries were prepared using Illumina stranded totalRNA kits following the manufacturer's protocol.

treatment_protocol:
1E6 GBM cells (BT428, BT799, BT935, BT954 and MBT06) were injected in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mouse brains as follows. Mice were anesthetized using gas anesthesia (Isoflurane: 2.5%). Using a 15-blade scalpel a 1.5 cm vertical midline incision was made on top of the skull. A small burr hole was then made (2-3 mm anterior to the coronal suture, 3 mm lateral to midline) using a drill held perpendicular to the skull. A Hamilton syringe was used to inject 10μL of cell suspension of GBM cells into the frontal lobe. The syringe was inserted through the burr hole at a 30 degree angle to a depth of 5mm. The incision was closed using interrupted stitches and sutures were sealed with a tissue adhesive. Mice were identified using ear notches and placed in recovery cages. Mice were monitored weekly for signs of illness and sacrificed at endpoint.
Once tumor engraftment was confirmed using MRI, mice were randomly assigned to control or treatment groups and chemoradiotherapy treatment was started. For mice in the combined chemoradiotherapy arm, 50 mg/kg TMZ was oral gavaged one hour before cranial irradiation was administered to mice. The mouse shield is designed such that only the head of the mice is irradiated.

value: Glioblastoma multiforme cell line

tag: tumor stage

value: Miniminal residual disease


title: 236_F1_EB_9D_3A_SC_Batch1

status: Public on Jan 23 2023

type: SRA

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

country: Italy

institute: University of Turin

library_source: transcriptomic

data_processing:
Following quality controls (performed with FastQC v0.11.2 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc)), sequencing reads were processed with Trim Galore! v0.5.0 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) to perform quality and adapter trimming (parameters: --stringency 3 –q 20). Trimmed reads were next aligned to the mouse reference genome (mm10/GRCm38.p6) using STAR v2.7.1a with options: --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.04. Gene expression levels were quantified with featureCounts v1.6.1 (options: -t exon -g gene_name) using the GENCODE Release M23 annotation. Multi-mapped reads were excluded from quantification.
Genome_build: mm10/GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited text file of raw read counts matrix per gene/cell.

molecule: total RNA

organism: Mus musculus

source_name: Mouse Embryoid Bodies

growth_protocol: E14 mouse WT and mutant (Dnmt3a -/-   and Dnmt3b -/-) ESCs were cultured in high-glucose DMEM (Euroclone) supplemented with 15% FBS (Millipore Corp., Billerica, MA, USA), 0.1 mmol/l nonessential amino acids (Invitrogen), 1 mmol/l sodium pyruvate (Invitrogen), 0.1 mmol/l β-mercaptoethanol, 1500 U/ml Leukemia Inhibitory Factor (LIF; Millipore), 25 U/ml penicillin, and 25 μg/ml streptomycin. To induce formation of EBs, Wild type and mutant ESCs were transferred using trypsin to low-attachment plates (CORNING) in Alpha-MEM (BE02-002F LONZA) supplemented with 10% KOSR (10828-028 GIBCO), 5% FBS (Millipore), 1% nonessential amino acids (Invitrogen), 1% sodium pyruvate (Invitrogen), 0.1 mmol/l β-mercaptoethanol, 25 U/ml penicillin and 25 μg/ml streptomycin. Medium was changed every 3 days.

extract_protocol:
Full length single cell RNA-seq was performed using a modified version of the Smart-seq2 protocol.
Briefly, individual cells are sorted into 96 well plates containing lysis buffer in presence of RNase inhibitor, dNTPs and OligodT. Reverse transcription of the polyadenylated RNA will be performed with SuperScriptII and Template Switching Oligos. The resulting cDNA will be amplified with 25 cycles of PCR and libraries will be prepared for sequencing with standard NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75bp reads), reaching a median of ~ 578,000 generated reads per cell.

tag: strain

tag: cell type

value: Embryoid Bodies (EB)

tag: genotype

value: Dnmt3a -/- (3AKO)

tag: Stage

tag: batch


title: BT799 MRD Control

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Neurospheres derived from minimally-cultured human GBM samples were plated on polyornithine- laminin coated plates for adherent growth. Adherent cells were replated in low-binding plates and cultured as tumorspheres, which were maintained as spheres upon serial passaging in vitro. These cells retained their self-renewal potential and were capable of in vivo tumor formation.

tag: cell line


title: 236_F12_EB_9D_3A_SC_Batch2


title: 236_F11_EB_9D_3A_SC_Batch2


title: MBT06_MRD_CON

description: vehicle-treated, MBT06 line at minimal residual disease (MRD) state

data_processing:
Raw FASTQ files were aligned to the hg19 genome using STAR aligner (STAR v2.5.2b), and the CellRanger (v2.1.1) pipeline was used to obtain the filtered gene x cell raw count matrix.
Raw count matrices were loaded into a Seurat object (Seurat R package, v 4.0.4), and filtered to retain cells with (i) 200 – 9000 recovered genes per cell and (ii) less than 60% mitochondrial content.
sctransform (sctransform R Package, v 0.3.2) was used to normalize and scale count matrix values
Genome_build: hg19
Supplementary_files_format_and_content: raw count matrix with cell-level meta data.

source_name: Primary human glioblastoma cells

extract_protocol:
Single-cell library preparation was carried out as per the 10X Genomics Chromium single-cell protocol using the v2 chemistry reagent kit (10X Genomics, Plesanton, CA, USA). Cell suspensions were loaded onto individual channels of a Chromium Single-Cell Chip along reverse transcription (RT) master mix and single cell 3’ gel beads, aiming for 1000 captured cells per sample. Following generation of gel bead-in-emulsions (GEMs), cDNA was underwent a two-stage purification process with Dynal MyONE Silane beads (Thermo Fisher Scientific), followed by SPRISelect beads (Beckman Coulter). RT and cDNA amplification were performed using a 96-well Veriti Thermocycler (Life Technologies). Amplified cDNA purified using SPRIselect beads and sequencing libraries were generated with unique sample indexes (SI). Dual sided SPRIselect cleanup was used to clean up samples and size select. Libraries were sequenced on an Illumina 2500 in Highoutput mode at the Princess Margaret Genomics Centre (Toronto, ON) using the 10X Genomics recommended sequencing parameters.  Samples were quantified by Kapa Library Quantification kit (Roche) and normalized to achieve the desired median read depth per cell
10x genomics

treatment_protocol:
1x106 GBM cells (BT799 or MBT06) were injected in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mouse brains as previously described. Briefly, mice were anesthetized using gas anesthesia (Isoflurane: 2.5%). Using a 15-blade scalpel a 1.5 cm vertical midline incision was made on top of the skull. A small burr hole was then made (2-3 mm anterior to the coronal suture, 3 mm lateral to midline) using a drill held perpendicular to the skull. A Hamilton syringe was used to inject 10μL of cell suspension of GBM cells into the frontal lobe. The syringe was inserted through the burr hole at a 30o angle to a 5 mm depth. The incision was closed using interrupted stitches and sutures were sealed with a tissue adhesive. Mice were identified using ear notches and placed in recovery cages. Mice were monitored weekly for signs of illness and sacrificed at endpoint.
Once tumor engraftment was confirmed using MRI, mice were randomly assigned to control or treatment groups and chemoradiotherapy treatment was started. For mice in the combined chemoradiotherapy arm, 50 mg/kg TMZ was oral gavaged one hour before cranial irradiation was administered to mice. The mouse shield is designed such that only the head of the mice is irradiated.

tag: stage of disease

value: Recurrent disease

tag: treatment

value: Vehicle Treated (Control)

value: primary Human Glioblastoma cells


title: 236_E8_EB_9D_3A_SC_Batch1


title: SS-7-168-2

description: Minimal residual disease

library_source: genomic

data_processing:
Library strategy: Barcode sequencing
FASTQ files were processed using a bespoke Perl script.  Each read was examined to identify one of the three expected library codes (CCAA, ACGT, or TGGA) followed by eight bases corresponding to the vector sequence (eg: ATCGATAC), allowing up to one mismatched base for each feature.
The 18 base barcode sequence preceding the vector sequence was extracted, and all unique barcode sequences were counted.  All barcode count files, one per sample, were then merged into a single matrix.
Noise was reduced by merging barcodes within a Hamming distance of two into a single barcode record, where the barcode with the highest average abundance was retained as the “parent” barcode and counts summed.
Technical replicates were combined by summing counts across replicates, and barcodes that were observed in only one sample were removed as potential artefacts.
Genome_build: N/A
Supplementary_files_format_and_content: Barcode (col1) and count (col2); tab delimited

molecule: genomic DNA

extract_protocol:
Once tumor engraftment was confirmed using MRI, mice were randomly assigned to control or treatment groups and chemoradiotherapy treatment was started. For mice in the combined chemoradiotherapy arm, 50 mg/kg TMZ was oral gavaged one hour before cranial irradiation was administered to mice. The mouse shield is designed such that only the head of the mice is irradiated.
Gentra Puregene Tissue kit was used to extract all genomic DNA from full mouse brains. Considering that the GBM tumor population in a mouse brain is expected to be significantly smaller, especially at the MRD timepoint, we optimized genomic DNA extraction protocols for snap-frozen mouse brain samples and performed nested-PCR to amplify the 137 bp barcode region for genomic sequencing. Spike-in control barcoded HEK293 cells were added to mouse brain samples for gDNA extraction to estimate clone size. We used NEB UltraQ II polymerase to amplify the 137 bp  barcode regions using nested-PCR, which were then visualized on a 3% agarose gel. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: 1E6 GBM cells (BT428, BT799, BT935, BT954 and MBT06) were injected in NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mouse brains as previously described1. Briefly, mice were anesthetized using gas anesthesia (Isoflurane: 2.5%). Using a 15-blade scalpel a 1.5 cm vertical midline incision was made on top of the skull. A small burr hole was then made (2-3 mm anterior to the coronal suture, 3 mm lateral to midline) using a drill held perpendicular to the skull. A Hamilton syringe was used to inject 10μL of cell suspension of GBM cells into the frontal lobe. The syringe was inserted through the burr hole at a 30o angle to a 5 mm depth. The incision was closed using interrupted stitches and sutures were sealed with a tissue adhesive. Mice were identified using ear notches and placed in recovery cages. Mice were monitored weekly for signs of illness and sacrificed at endpoint.

value: Primary tumour

value: Chemo+radiotherapy

tag: molecule subtype

value: DNA amplicon

tag: technical replicate

tag: biological replicate


title: SS-7-169-3

description: Minimal residual disease


title: SS-7-117

description: Recurrent tumor


title: SS-7-115

description: Minimal residual disease


title: SS-7-169-1

description: Minimal residual disease


title: BT428 MRD Control


title: 236_F10_EB_9D_3A_SC_Batch2


title: 236_E1_EB_9D_3A_SC_Batch1


title: SS-7-58

description: Recurrent tumor

value: Recurrent tumor


title: 236_E7_EB_9D_3A_SC_Batch1


title: SS-7-169-2

description: Minimal residual disease


title: 236_E6_EB_9D_3A_SC_Batch1


title: SS-7-53

description: Engraftment Control


title: SS-7-168-1

description: Minimal residual disease


title: SS-7-168-3

description: Minimal residual disease


title: 236_D8_EB_9D_3A_SC_Batch1


title: 236_D9_EB_9D_3A_SC_Batch2


title: 236_E3_EB_9D_3A_SC_Batch1


title: 236_E4_EB_9D_3A_SC_Batch1


title: SS-7-113

description: Engraftment Control


title: 236_E9_EB_9D_3A_SC_Batch2


title: SS-7-97

description: Engraftment Control


title: 236_E5_EB_9D_3A_SC_Batch1


title: SS-7-82

description: Recurrent tumor


title: SS-7-105

description: Recurrent tumor


title: SS-6-158

description: Minimal residual disease


title: 236_D2_EB_9D_3A_SC_Batch1


title: SS-6-157

description: Minimal residual disease


title: 236_D6_EB_9D_3A_SC_Batch1


title: SS-6-163

description: Minimal residual disease


title: 236_D7_EB_9D_3A_SC_Batch1


title: 236_E12_EB_9D_3A_SC_Batch2


title: SS-6-160

description: Minimal residual disease


title: SS-6-164

description: Minimal residual disease


title: SS-6-162

description: Minimal residual disease


title: SS-6-159

description: Minimal residual disease


title: 236_E11_EB_9D_3A_SC_Batch2


title: SS-6-145

description: Minimal residual disease


title: SS-6-143

description: Minimal residual disease


title: SS-6-161

description: Minimal residual disease


title: SS-6-142

description: Minimal residual disease


title: 236_C8_EB_9D_3A_SC_Batch1


title: 236_D3_EB_9D_3A_SC_Batch1


title: 236_E2_EB_9D_3A_SC_Batch1


title: 236_E10_EB_9D_3A_SC_Batch2


title: SS-6-154

description: Minimal residual disease


title: 236_D12_EB_9D_3A_SC_Batch2


title: 236_D1_EB_9D_3A_SC_Batch1


title: 236_D4_EB_9D_3A_SC_Batch1


title: 236_D11_EB_9D_3A_SC_Batch2


title: 236_D5_EB_9D_3A_SC_Batch1


title: 236_C5_EB_9D_3A_SC_Batch1


title: 236_C6_EB_9D_3A_SC_Batch1


title: SS-6-141

description: Minimal residual disease


title: SS-6-117

description: Recurrent tumor


title: SS-6-119

description: Recurrent tumor


title: SS-6-118

description: Recurrent tumor


title: SS-6-151

description: Minimal residual disease


title: SS-6-120

description: Recurrent tumor


title: 236_C9_EB_9D_3A_SC_Batch2


title: SS-6-123

description: Minimal residual disease


title: SS-6-116

description: Recurrent tumor


title: SS-6-111

description: Recurrent tumor


title: SS-6-101

description: Recurrent tumor


title: 236_C2_EB_9D_3A_SC_Batch1


title: 236_B9_EB_9D_3A_SC_Batch2


title: 236_C4_EB_9D_3A_SC_Batch1


title: 236_B8_EB_9D_3A_SC_Batch1


title: 236_D10_EB_9D_3A_SC_Batch2


title: 236_C7_EB_9D_3A_SC_Batch1


title: 236_C1_EB_9D_3A_SC_Batch1


title: 236_C12_EB_9D_3A_SC_Batch2


title: 236_B6_EB_9D_3A_SC_Batch1


title: SS-6-114

description: Engraftment Control


title: SS-6-122

description: Minimal residual disease


title: SS-6-103

description: Recurrent tumor


title: SS-6-97

description: Engraftment Control


title: 236_B1_EB_9D_3A_SC_Batch1


title: SS-6-99

description: Minimal residual disease


title: SS-6-98

description: Minimal residual disease


title: 236_C11_EB_9D_3A_SC_Batch2


title: 236_C3_EB_9D_3A_SC_Batch1


title: SS-6-95

description: Engraftment Control


title: 236_C10_EB_9D_3A_SC_Batch2


title: SS-6-104

description: Recurrent tumor


title: 236_B5_EB_9D_3A_SC_Batch1


title: 236_B7_EB_9D_3A_SC_Batch1


title: SS-6-90

description: Recurrent tumor


title: SS-6-100

description: Recurrent tumor


title: 236_B2_EB_9D_3A_SC_Batch1


title: 236_B4_EB_9D_3A_SC_Batch1


title: SS-6-89

description: Engraftment Control


title: SS-6-85

description: Engraftment Control


title: 236_B11_EB_9D_3A_SC_Batch2


title: 236_A8_EB_9D_3A_SC_Batch1


title: 236_A9_EB_9D_3A_SC_Batch2


title: SS-6-96

description: Engraftment Control


title: SS-6-88

description: Recurrent tumor


title: 236_A4_EB_9D_3A_SC_Batch1


title: 236_A7_EB_9D_3A_SC_Batch1


title: 236_B10_EB_9D_3A_SC_Batch2


title: 236_A6_EB_9D_3A_SC_Batch1


title: SS-6-94

description: Minimal residual disease


title: SS-6-81

description: Recurrent tumor


title: 236_A2_EB_9D_3A_SC_Batch1


title: 236_B12_EB_9D_3A_SC_Batch2


title: 236_A12_EB_9D_3A_SC_Batch2


title: SS-6-79

description: Minimal residual disease


title: SS-6-87

description: Recurrent tumor


title: 236_A5_EB_9D_3A_SC_Batch1


title: 236_B3_EB_9D_3A_SC_Batch1


title: SS-6-80

description: Minimal residual disease


title: SS-6-75

description: Retransplant from CON


title: SS-6-74

description: Retransplant from CON


title: 236_A1_EB_9D_3A_SC_Batch1


title: SS-6-86

description: Minimal residual disease


title: 236_A3_EB_9D_3A_SC_Batch1


title: SS-6-83

description: Recurrent tumor


title: 236_A11_EB_9D_3A_SC_Batch2


title: 234_H9_EB_9D_WT_SC_Batch2

value: WT


title: SS-6-73

description: Retransplant from CON


title: SS-6-84

description: Engraftment Control


title: SS-6-71

description: Minimal residual disease


title: 234_H8_EB_9D_WT_SC_Batch1


title: SS-6-72

description: Retransplant from CON


title: 234_H4_EB_9D_WT_SC_Batch1


title: 236_A10_EB_9D_3A_SC_Batch2


title: 234_H7_EB_9D_WT_SC_Batch1


title: SS-6-70

description: Recurrent tumor


title: SS-6-68

description: Engraftment Control


title: 234_H5_EB_9D_WT_SC_Batch1


title: SS-6-62

description: Recurrent tumor


title: SS-6-63

description: Engraftment Control


title: 234_G9_EB_9D_WT_SC_Batch2


title: SS-6-39

description: T0 Control


title: 234_H6_EB_9D_WT_SC_Batch1


title: SS-6-66

description: Recurrent tumor


title: SS-6-59

description: Recurrent tumor


title: 234_H3_EB_9D_WT_SC_Batch1


title: 234_H1_EB_9D_WT_SC_Batch1


title: 234_G8_EB_9D_WT_SC_Batch1


title: SS-6-38

description: T0 Control


title: SS-6-37

description: Retransplant from TR


title: 234_G6_EB_9D_WT_SC_Batch1


title: SS-6-61

description: Minimal residual disease


title: SS-6-67

description: Minimal residual disease


title: 234_G5_EB_9D_WT_SC_Batch1


title: SS-6-60

description: Recurrent tumor


title: 234_G7_EB_9D_WT_SC_Batch1


title: SS-6-54

description: Minimal residual disease


title: SS-6-36

description: Retransplant from TR


title: SS-6-35

description: Retransplant from TR


title: 234_H2_EB_9D_WT_SC_Batch1


title: 234_G3_EB_9D_WT_SC_Batch1


title: SS-6-33

description: Engraftment Control


title: SS-6-30

description: Recurrent tumor


title: 234_G2_EB_9D_WT_SC_Batch1


title: SS-6-34

description: Retransplant from TR


title: 234_G11_EB_9D_WT_SC_Batch2


title: SS-6-29

description: Minimal residual disease


title: 234_G12_EB_9D_WT_SC_Batch2


title: SS-6-28

description: Recurrent tumor


title: SS-6-27

description: Recurrent tumor


title: SS-6-24

description: Engraftment Control


title: 234_G4_EB_9D_WT_SC_Batch1


title: SS-6-23

description: Recurrent tumor


title: SS-6-26

description: Recurrent tumor


title: 234_F7_EB_9D_WT_SC_Batch1


title: 234_G1_EB_9D_WT_SC_Batch1


title: SS-6-25

description: Engraftment Control


title: SS-6-3

description: T0 Control


title: 234_F2_EB_9D_WT_SC_Batch1


title: 234_F9_EB_9D_WT_SC_Batch2


title: SS-6-17

description: Minimal residual disease


title: 234_F6_EB_9D_WT_SC_Batch1


title: 234_G10_EB_9D_WT_SC_Batch2


title: SS-6-20

description: Recurrent tumor


title: SS-6-16

description: Minimal residual disease


title: 234_F11_EB_9D_WT_SC_Batch2


title: 234_F5_EB_9D_WT_SC_Batch1


title: 234_F12_EB_9D_WT_SC_Batch2


title: 234_F4_EB_9D_WT_SC_Batch1


title: SS-5-164

description: Minimal residual disease


title: SS-6-1

description: T0 Control


title: 234_F8_EB_9D_WT_SC_Batch1


title: 234_F3_EB_9D_WT_SC_Batch1


title: 234_F1_EB_9D_WT_SC_Batch1


title: SS-5-162

description: Minimal residual disease


title: SS-5-163

description: Minimal residual disease


title: 234_E4_EB_9D_WT_SC_Batch1


title: 234_F10_EB_9D_WT_SC_Batch2


title: 234_E7_EB_9D_WT_SC_Batch1


title: 234_E6_EB_9D_WT_SC_Batch1


title: 234_E8_EB_9D_WT_SC_Batch1


title: SS-5-159

description: Minimal residual disease


title: 234_E9_EB_9D_WT_SC_Batch2


title: SS-5-158

description: Minimal residual disease


title: 234_E3_EB_9D_WT_SC_Batch1


title: SS-5-157

description: Minimal residual disease


title: 234_E2_EB_9D_WT_SC_Batch1


title: SS-5-151

description: Minimal residual disease


title: 234_E5_EB_9D_WT_SC_Batch1


title: 234_E12_EB_9D_WT_SC_Batch2


title: 234_E1_EB_9D_WT_SC_Batch1


title: SS-6-2

description: T0 Control


title: SS-5-161

description: Minimal residual disease


title: SS-5-145

description: Minimal residual disease


title: SS-5-143

description: Minimal residual disease


title: SS-5-154

description: Minimal residual disease


title: 234_D7_EB_9D_WT_SC_Batch1


title: 234_D8_EB_9D_WT_SC_Batch1


title: SS-5-122

description: Minimal residual disease


title: 234_E11_EB_9D_WT_SC_Batch2


title: SS-5-142

description: Minimal residual disease


title: SS-5-121

description: Engraftment Control


title: SS-5-117

description: Recurrent tumor


title: 234_D5_EB_9D_WT_SC_Batch1


title: 234_D6_EB_9D_WT_SC_Batch1


title: SS-5-119

description: Recurrent tumor


title: 234_E10_EB_9D_WT_SC_Batch2


title: 234_D9_EB_9D_WT_SC_Batch2


title: SS-5-118

description: Recurrent tumor


title: 234_D4_EB_9D_WT_SC_Batch1


title: SS-5-120

description: Recurrent tumor


title: SS-5-160

description: Minimal residual disease


title: SS-5-123

description: Minimal residual disease


title: SS-5-116

description: Recurrent tumor


title: SS-5-115

description: Minimal residual disease


title: 234_D10_EB_9D_WT_SC_Batch2


title: 234_D3_EB_9D_WT_SC_Batch1


title: 234_D1_EB_9D_WT_SC_Batch1


title: 234_D2_EB_9D_WT_SC_Batch1


title: SS-5-114

description: Engraftment Control


title: 234_C9_EB_9D_WT_SC_Batch2


title: 234_D11_EB_9D_WT_SC_Batch2


title: SS-5-113

description: Engraftment Control


title: SS-5-141

description: Minimal residual disease


title: SS-5-111

description: Recurrent tumor


title: 234_C8_EB_9D_WT_SC_Batch1


title: SS-5-105

description: Recurrent tumor


title: 234_C6_EB_9D_WT_SC_Batch1


title: SS-5-106

description: T0 Control


title: 234_C5_EB_9D_WT_SC_Batch1


title: SS-5-103

description: Recurrent tumor


title: SS-5-107

description: T0 Control


title: 234_D12_EB_9D_WT_SC_Batch2


title: 234_C3_EB_9D_WT_SC_Batch1


title: SS-5-108

description: T0 Control


title: SS-5-102

description: Recurrent tumor


title: 234_C7_EB_9D_WT_SC_Batch1


title: 234_C4_EB_9D_WT_SC_Batch1


title: 234_C11_EB_9D_WT_SC_Batch2


title: 234_C1_EB_9D_WT_SC_Batch1


title: SS-5-101

description: Recurrent tumor


title: 234_C2_EB_9D_WT_SC_Batch1


title: SS-5-98

description: Minimal residual disease


title: SS-5-96

description: Engraftment Control


title: 234_B7_EB_9D_WT_SC_Batch1


title: 234_B8_EB_9D_WT_SC_Batch1


title: SS-5-97

description: Engraftment Control


title: SS-5-95

description: Engraftment Control


title: SS-5-100

description: Recurrent tumor


title: 234_C10_EB_9D_WT_SC_Batch2


title: SS-5-94

description: Minimal residual disease


title: SS-5-104

description: Recurrent tumor


title: SS-5-99

description: Minimal residual disease


title: 234_B4_EB_9D_WT_SC_Batch1


title: 234_B5_EB_9D_WT_SC_Batch1


title: SS-5-92

description: T0 Control


title: 234_B12_EB_9D_WT_SC_Batch2


title: SS-5-89

description: Engraftment Control


title: 234_B1_EB_9D_WT_SC_Batch1


title: SS-5-90

description: Recurrent tumor


title: 234_B3_EB_9D_WT_SC_Batch1


title: SS-5-91

description: T0 Control


title: 234_B6_EB_9D_WT_SC_Batch1


title: 234_B11_EB_9D_WT_SC_Batch2


title: SS-5-84

description: Engraftment Control


title: 234_A9_EB_9D_WT_SC_Batch2


title: SS-5-83

description: Recurrent tumor


title: 234_B2_EB_9D_WT_SC_Batch1


title: 234_B9_EB_9D_WT_SC_Batch2


title: SS-5-87

description: Recurrent tumor


title: 234_C12_EB_9D_WT_SC_Batch2


title: SS-5-82

description: Recurrent tumor


title: 234_A7_EB_9D_WT_SC_Batch1


title: SS-5-93

description: T0 Control


title: 234_A8_EB_9D_WT_SC_Batch1


title: SS-5-86

description: Minimal residual disease


title: SS-5-81

description: Recurrent tumor


title: 234_A4_EB_9D_WT_SC_Batch1


title: SS-5-88

description: Recurrent tumor


title: SS-5-77

description: T0 Control


title: SS-5-80

description: Minimal residual disease


title: 234_A12_EB_9D_WT_SC_Batch2


title: 234_A10_EB_9D_WT_SC_Batch2


title: 234_A3_EB_9D_WT_SC_Batch1


title: 234_A6_EB_9D_WT_SC_Batch1


title: 234_A5_EB_9D_WT_SC_Batch1


title: SS-5-78

description: T0 Control


title: SS-5-75

description: Retransplant from CON


title: 211_H9_EB_3D_3B_SC_Batch2

value: Dnmt3b -/- (3BKO)


title: SS-5-76

description: T0 Control


title: SS-5-74

description: Retransplant from CON


title: SS-5-72

description: Retransplant from CON


title: 234_B10_EB_9D_WT_SC_Batch2


title: SS-5-79

description: Minimal residual disease


title: 211_H8_EB_3D_3A_SC_Batch1


title: SS-5-73

description: Retransplant from CON


title: SS-5-71

description: Minimal residual disease


title: 211_H6_EB_3D_3A_SC_Batch1


title: SS-5-67

description: Minimal residual disease


title: 211_H5_EB_3D_3A_SC_Batch1


title: SS-5-70

description: Recurrent tumor


title: 211_H7_EB_3D_3A_SC_Batch1


title: 234_A11_EB_9D_WT_SC_Batch2


title: 211_H2_EB_3D_3A_SC_Batch1


title: 211_H4_EB_3D_3A_SC_Batch1


title: 211_H1_EB_3D_3A_SC_Batch1


title: SS-5-63

description: Engraftment Control


title: 211_G8_EB_3D_3A_SC_Batch1


title: SS-5-62

description: Recurrent tumor


title: SS-5-61

description: Minimal residual disease


title: SS-5-60

description: Recurrent tumor


title: 211_H3_EB_3D_3A_SC_Batch1


title: SS-5-58

description: Recurrent tumor


title: SS-5-59

description: Recurrent tumor


title: 211_G9_EB_3D_3B_SC_Batch2


title: SS-5-66

description: Recurrent tumor


title: 211_G7_EB_3D_3A_SC_Batch1


title: SS-5-53

description: Engraftment Control


title: 211_G2_EB_3D_3A_SC_Batch1


title: 211_G11_EB_3D_3B_SC_Batch2


title: SS-5-49

description: Retransplant T0 Control


title: 211_G5_EB_3D_3A_SC_Batch1


title: 211_G3_EB_3D_3A_SC_Batch1


title: 211_F9_EB_3D_3B_SC_Batch2


title: SS-5-38

description: T0 Control


title: SS-5-37

description: Retransplant from TR


title: SS-5-54

description: Minimal residual disease


title: SS-5-30

description: Recurrent tumor


title: 211_G4_EB_3D_3A_SC_Batch1


title: 211_G6_EB_3D_3A_SC_Batch1


title: 211_F6_EB_3D_3A_SC_Batch1


title: SS-5-39

description: T0 Control


title: 211_F3_EB_3D_3A_SC_Batch1


title: 211_F4_EB_3D_3A_SC_Batch1


title: 211_G10_EB_3D_3B_SC_Batch2


title: SS-5-28

description: Recurrent tumor


title: SS-5-36

description: Retransplant from TR


title: SS-5-35

description: Retransplant from TR


title: SS-5-26

description: Recurrent tumor


title: SS-5-34

description: Retransplant from TR


title: SS-5-25

description: Engraftment Control


title: SS-5-33

description: Engraftment Control


title: 211_F1_EB_3D_3A_SC_Batch1


title: 211_F8_EB_3D_3A_SC_Batch1


title: 211_F7_EB_3D_3A_SC_Batch1


title: SS-5-24

description: Engraftment Control


title: SS-5-29

description: Minimal residual disease


title: 211_F2_EB_3D_3A_SC_Batch1


title: SS-5-20

description: Recurrent tumor


title: 211_G12_EB_3D_3B_SC_Batch2


title: 211_G1_EB_3D_3A_SC_Batch1


title: SS-5-48

description: Retransplant T0 Control


title: SS-5-17

description: Minimal residual disease


title: 211_E9_EB_3D_3B_SC_Batch2


title: SS-5-27

description: Recurrent tumor


title: SS-5-16

description: Minimal residual disease


title: 211_F11_EB_3D_3B_SC_Batch2


title: 211_E3_EB_3D_3A_SC_Batch1


title: 211_F10_EB_3D_3B_SC_Batch2


title: SS-5-23

description: Recurrent tumor


title: 211_E4_EB_3D_3A_SC_Batch1


title: 211_F5_EB_3D_3A_SC_Batch1


title: 211_F12_EB_3D_3B_SC_Batch2


title: 211_E7_EB_3D_3A_SC_Batch1


title: SS-4-161

description: Minimal residual disease


title: SS-5-6

description: Retransplant T0 Control


title: SS-4-159

description: Minimal residual disease


title: SS-5-5

description: Retransplant T0 Control


title: 211_E10_EB_3D_3B_SC_Batch2


title: SS-4-158

description: Minimal residual disease


title: SS-4-164

description: Minimal residual disease


title: 211_D8_EB_3D_3A_SC_Batch1


title: 211_E5_EB_3D_3A_SC_Batch1


title: SS-4-160

description: Minimal residual disease


title: 211_E6_EB_3D_3A_SC_Batch1


title: SS-4-157

description: Minimal residual disease


title: SS-5-3

description: T0 Control


title: 211_E1_EB_3D_3A_SC_Batch1


title: 211_E2_EB_3D_3A_SC_Batch1


title: SS-5-2

description: T0 Control


title: SS-4-163

description: Minimal residual disease


title: 211_E8_EB_3D_3A_SC_Batch1


title: 211_D9_EB_3D_3B_SC_Batch2


title: SS-4-154

description: Minimal residual disease


title: SS-4-162

description: Minimal residual disease


title: 211_E11_EB_3D_3B_SC_Batch2


title: SS-5-1

description: T0 Control


title: 211_E12_EB_3D_3B_SC_Batch2


title: Tie2+ Fibroblast like cells_LV-shTEK-D3 [A9_shTEK-D3]

city: Helsinki

first: Andrey

last: Anisimov

address: Haartmaninkatu 8

department: Faculty of medicine

country: Finland

institute: University of Helsinki

data_processing:
The following software packages embedded in the Chipster analysis platform (v4; https://chipster.csc.fi) were used for analysis
The quality of the reads in the Fastq files were anaysed using fastqc.
Trimmomatic tool was used to trim the reads
HISAT2 package for paired end reads was employed to align the reads to mouse genome GRCm38.95
HTSeq count tool to quantify the aligned reads per gene
Genome_build: GRCm38.95
Supplementary_files_format_and_content: tab-delimited text files include count aligned reads per genes performed with HTSeq tool for each sample

source_name: Tie2+ Fibroblast like cells_LV-shTEK-D3

extract_protocol:
FACS sorted mice aortic Tie2+ Fibroblast like cells (TF) were cultured, transfected with LV-SCR, LV-shTEK-A or LV-shTEK-D, after puromycin selection. The RNA from these cells were purified using Macherey-Nagel Nucleospin RNA mini Kit (#740955.50, Macherey-Nagel) according to the manufacturer’s instruction
cDNA library was synthesized using BGI DNBSeq Stranded mRNA KIT (BGI, Hongkong), The library quality was determined using bioanalyzer and sequenced using MGISEQ-2000 System with the following specifications: 1 X 100bp, 20M paired end reads.

tag: Sex

value: Male

tag: genotype background

value: Wild type mice

tag: tissue

value: Aorta

value: with lenti viral vectors encoding mouse TEK-D construct


title: SS-4-142

description: Minimal residual disease

value: Glioblastoma multiforme cell line


title: SS-4-141

description: Minimal residual disease


title: SS-4-123

description: Minimal residual disease


title: SS-4-145

description: Minimal residual disease


title: Tie2+ Fibroblast like cells_LV-shTEK-A2 [A5_shTEK-A2]

source_name: Tie2+ Fibroblast like cells_LV-shTEK-A2

value: with lenti viral vectors encoding mouse TEK-A construct


title: Tie2+ Fibroblast like cells_LV-shTEK-A3 [A8_shTEK-A3]

source_name: Tie2+ Fibroblast like cells_LV-shTEK-A3


title: Tie2+ Fibroblast like cells_LV-shTEK-A1 [A2_shTEK-A1]

source_name: Tie2+ Fibroblast like cells_LV-shTEK-A1


title: Tie2+ Fibroblast like cells_LV-shTEK-D1 [A3_shTEK-D1]

source_name: Tie2+ Fibroblast like cells_LV-shTEK-D1


title: SS-4-151

description: Minimal residual disease


title: 211_D7_EB_3D_3A_SC_Batch1

value: Embryoid Bodies (EB)


title: 211_D1_EB_3D_3A_SC_Batch1

value: Dnmt3a -/- (3AKO)


title: Tie2+ Fibroblast like cells_LV-SCR1 [A1_SCR1]

source_name: Tie2+ Fibroblast like cells_LV-SCR1

value: with lenti viral vectors encoding scrambled construct


title: 211_D3_EB_3D_3A_SC_Batch1


title: 211_C9_EB_3D_3B_SC_Batch2


title: SS-4-122

description: Minimal residual disease

value: Vehicle Treated (Control)


title: 211_D6_EB_3D_3A_SC_Batch1


title: 211_D4_EB_3D_3A_SC_Batch1


title: Tie2+ Fibroblast like cells_LV-shTEK-D2 [A6_shTEK-D2]

source_name: Tie2+ Fibroblast like cells_LV-shTEK-D2


title: 211_D2_EB_3D_3A_SC_Batch1


title: SS-4-121

description: Engraftment Control


title: 211_C8_EB_3D_3A_SC_Batch1


title: SS-4-143

description: Minimal residual disease


title: 211_D11_EB_3D_3B_SC_Batch2


title: 211_D5_EB_3D_3A_SC_Batch1


title: Tie2+ Fibroblast like cells_LV-SCR3 [A7_SCR3]

source_name: Tie2+ Fibroblast like cells_LV-SCR3


title: 211_D10_EB_3D_3B_SC_Batch2


title: SS-4-119

description: Recurrent tumor


title: SS-4-118

description: Recurrent tumor


title: SS-4-115

description: Minimal residual disease


title: 211_C5_EB_3D_3A_SC_Batch1


title: SS-4-114

description: Engraftment Control


title: Tie2+ Fibroblast like cells_LV-SCR2 [A4_SCR2]

source_name: Tie2+ Fibroblast like cells_LV-SCR2


title: SS-4-116

description: Recurrent tumor


title: 211_C7_EB_3D_3A_SC_Batch1


title: SS-4-120

description: Recurrent tumor


title: Day0, Aco

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

country: USA

institute: Cincinnati Children's Hospital Research Foundation

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was processed through 10X Genomics CellRanger v2.2.0 using default parameters to obtain the gene expression matrices
Assembly: mm10 or Aco_one
Supplementary files format and content: Tab-separated values files and matrix files

organism: Acomys cahirinus

source_name: skin

extract_protocol:
Single-cell suspensions were processed through Chromium 10X to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: ear skin

value: skin

tag: age

value: Adult


title: 211_C3_EB_3D_3A_SC_Batch1


title: 211_C4_EB_3D_3A_SC_Batch1


title: 211_C11_EB_3D_3B_SC_Batch2


title: SS-4-113

description: Engraftment Control

value: Primary tumour

value: DNA amplicon


title: Treg (Repeat), mRNA-derived cDNA

city: Pittsburgh

first: Jian

last: Cui

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

data_processing:
Sequenced samples were demultiplexed, aligned and gene/barcode matrices were generated following the pre-processing pipeline with Cell Ranger software (10X Genomics version 6.0.0). The procedure included converting Illumina BCL files to FASTQs, which were aligned with mouse genome refdata-gex-mm10-2020-A as a reference for getting the gene/barcode matrices.
Further processing was done with Seurat (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis, etc..).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: spleen

extract_protocol:
Briefly, single-cell splenic suspensions were incubated with a cocktail of the following biotinylated antibodies at 4oC for 15 min: CD11b (M1/70), CD11c (N418), CD19 (6D5), CD45R/B220 (RA3-6B2), TCRgd (GL3), PanNK (DX5), CD105 (MJ7/18), CD16/32 (93) and Ter119 (TER-119). Non-T cells were removed by incubating the suspension with streptavidin-coated magnetic beads at 4oC for 15 min, followed by magnetic separation. The unbound pure T cells were incubated with pooled MHC class I tetramer (APC) (GP33, GP276, NP396) and then stained for viability using Live/Dead Fixable eFluor 780. T cells from individual mice were identified via labeling with uniquely barcoded TotalSeq-C antibodies towards pan-CD45 and MHC at 1:100 according to the manufacturer’s protocol during surface staining (Biolegend). Tregs and Tetramer+ CD8+ T cells were purified via fluorescently activated cell sorting using a BD Aria. Live cells were spun down, resuspended in 0.04% PBS-BSA (Fisher #MT20031CV and Sigma #A9418-100G), and counted to determine a cell stock concentration. A cell suspension volume was calculated to capture approximately 7,000 cells per sub-population.
Cells were added to a Master Mix containing Reagent mix, RT Primers, Additive A, and RT Enzyme Mix to create a reaction for Tregs and one for Tetramer+ CD8+ T cells. These reactions were then loaded into separate lanes on Chromium Chip A and run through the 10X Genomics Chromium Controller. All libraries were sequenced on a NovaSeq™ 6000 S2 kit for 150 cycles at the UPMC Genome Core. Each Gene Expression library was sequenced at a depth of at least 20,000 reads/cell. Each Feature Barcode and TCR library was sequenced at a minimum depth of 5,000 reads/cell.

treatment_protocol: Splenol Tregs and Tetramer+ CD8+ T cell were harvested from Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP mice that remained naïve or were infected with lymphocytic choriomeningitis virus (LCMV) Clone 13 (Cl 13) for 16d

value: spleen

value: Treg

value: Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP

tag: infection

value: naïve or LCMV

tag: library type

value: mRNA

tag: hashtags


title: Treg, mRNA-derived cDNA

tag: cell type


title: Treg, HTO-derived cDNA

description: In the features.tsv file, disregard the human hashtags, namely the h_totalseq_XXXX.

library_source: other

molecule: protein

tag: genotype

value: HTO

value: m_totalseq_1-ACCCACCAGTAAGAC, uninfected-Foxp3Cre-YFP;  m_totalseq_2-GGTCGAGAGCATTCA, infected-Foxp3Cre;  m_totalseq_3-CTTGCCGCATGTCAT, infected-Foxp3Cre;  m_totalseq_4-AAAGCATTCTTCACG, infected-Foxp3Cre;  m_totalseq_5-CTTTGTCTTTGTGAG, uninfected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_6-TATGCTGCCACGGTA, infected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_7-GAGTCTGCCAGTATC, infected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_8-TATAGAACGCCAGGC, infected-Ifngr1L/L_Foxp3Cre-YFP;


title: Treg (Repeat), HTO-derived cDNA

value: m_totalseq_1-ACCCACCAGTAAGAC, uninfected-Foxp3Cre-YFP;  m_totalseq_2-GGTCGAGAGCATTCA, uninfected-Foxp3Cre-YFP;  m_totalseq_3-CTTGCCGCATGTCAT, infected-Foxp3Cre;  m_totalseq_4-AAAGCATTCTTCACG, infected-Foxp3Cre;  m_totalseq_5-CTTTGTCTTTGTGAG, uninfected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_6-TATGCTGCCACGGTA, uninfected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_7-GAGTCTGCCAGTATC, infected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_8-TATAGAACGCCAGGC, infected-Ifngr1L/L_Foxp3Cre-YFP


title: 211_C2_EB_3D_3A_SC_Batch1

tag: strain

value: Embryoid Bodies (EB)

tag: Stage


title: SS-4-105

description: Recurrent tumor

value: Glioblastoma multiforme cell line

tag: cell line

tag: tumor stage

value: Chemo+radiotherapy


title: 211_C6_EB_3D_3A_SC_Batch1

value: Dnmt3a -/- (3AKO)

tag: batch


title: SS-4-108

description: T0 Control

tag: molecule subtype


title: SS-4-104

description: Recurrent tumor

tag: technical replicate


title: 211_C1_EB_3D_3A_SC_Batch1


title: 211_D12_EB_3D_3B_SC_Batch2

value: Dnmt3b -/- (3BKO)


title: 211_C10_EB_3D_3B_SC_Batch2


title: CD8, TCR-derived cDNA

value: CD8 T cells

value: LCMV

value: TCR


title: CD8, HTO-derived cDNA

value: m_totalseq_2-GGTCGAGAGCATTCA, infected-Foxp3Cre;  m_totalseq_3-CTTGCCGCATGTCAT, infected-Foxp3Cre;  m_totalseq_4-AAAGCATTCTTCACG, infected-Foxp3Cre;   m_totalseq_6-TATGCTGCCACGGTA, infected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_7-GAGTCTGCCAGTATC, infected-Ifngr1L/L_Foxp3Cre-YFP;  m_totalseq_8-TATAGAACGCCAGGC, infected-Ifngr1L/L_Foxp3Cre-YFP


title: CD8, mRNA-derived cDNA

value: spleen


title: SS-4-111

description: Recurrent tumor

value: Primary tumour

value: DNA amplicon

tag: biological replicate


title: SS-4-100

description: Recurrent tumor

value: Vehicle Treated (Control)


title: SS-4-103

description: Recurrent tumor


title: 211_B9_EB_3D_3B_SC_Batch2


title: STD.EtOH.Male.GR.1

city: Montreal

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

institute: CHU Ste-Justine Research Center/Université de Montréal

data_processing:
Unique molecular identifiers (UMIs) were filtered out and inserted into the readID of the two sequencing reads for deduplication afterwards using Trim Galore (version 0.6.6).
Low quality sequences and the adaptor sequences were filtered out of the raw sequencing reads using Trim Galore (version 0.6.6).
The sequencing reads were aligned to the mouse reference genome mm10 using Bismark (version 0.22).
Reads deduplication and CpG calling performed with Bismark.
Transformation of Bismark output to MethylKit input format for easier handling
Assembly: mm10
Supplementary files format and content: Input files including DNA methylation values of CpGs for each sample.

source_name: Fetal forebrain

extract_protocol:
Genomic DNA extracted using the QIAamp DNA Mini Kit protocol (Qiagen) and bisulfite-converted using the EZ DNA methylation Gold kit (Zymo Research).
Librairies were produced following the Implicon protocol from Klobučar et al. (2020)

value: Brain cells

value: Fetal forebrain

tag: treatment

value: Standard diet & Ethanol

tag: gender

value: Male


title: Treg, TCR-derived cDNA

tag: tissue

value: Treg

value: Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP

value: naïve or LCMV


title: SS-4-101

description: Recurrent tumor

value: Glioblastoma multiforme cell line


title: 211_C12_EB_3D_3B_SC_Batch2

value: Embryoid Bodies (EB)

value: Dnmt3b -/- (3BKO)


title: STD.EtOH.Male.Normal.2

tag: age


title: STD.EtOH.Male.Normal.1


title: STD.EtOH.Male.GR.2


title: 211_B6_EB_3D_3A_SC_Batch1

value: Dnmt3a -/- (3AKO)


title: STD.EtOH.Female.Normal.2

value: Female


title: STD.EtOH.Female.Normal.1


title: STD.EtOH.Female.GR.2


title: 211_B7_EB_3D_3A_SC_Batch1


title: STD.EtOH.Female.Normal.3


title: STD.CTL.Male.Normal.3

value: Standard diet & Saline (Control)


title: STD.CTL.Male.Normal.2


title: STD.CTL.Male.Normal.1


title: SS-4-96

description: Engraftment Control


title: SS-4-99

description: Minimal residual disease


title: 211_B4_EB_3D_3A_SC_Batch1


title: STD.EtOH.Male.Normal.3


title: STD.CTL.Female.Normal.1


title: 211_B3_EB_3D_3A_SC_Batch1


title: 211_B8_EB_3D_3A_SC_Batch1


title: ENR.EtOH.Male.Normal.2

value: Enriched diet & Ethanol


title: STD.CTL.Female.Normal.3


title: 211_B1_EB_3D_3A_SC_Batch1


title: ENR.EtOH.Male.Normal.1


title: ENR.EtOH.Male.GR.2


title: STD.CTL.Female.Normal.2


title: 211_B2_EB_3D_3A_SC_Batch1


title: SS-4-91

description: T0 Control

value: Primary tumour


title: 211_B12_EB_3D_3B_SC_Batch2


title: SS-4-95

description: Engraftment Control

value: DNA amplicon


title: 211_B11_EB_3D_3B_SC_Batch2


title: SS-4-94

description: Minimal residual disease

value: Vehicle Treated (Control)


title: STD.EtOH.Female.GR.1

value: Brain cells


title: SS-4-89

description: Engraftment Control


title: SS-4-98

description: Minimal residual disease


title: SS-4-92

description: T0 Control


title: ENR.EtOH.Female.GR.1

value: Fetal forebrain


title: ENR.EtOH.Female.Normal.2


title: ENR.EtOH.Female.GR.2


title: ENR.EtOH.Male.GR.1


title: ENR.CTL.Male.Normal.3

value: Enriched diet & Saline (Control)


title: ENR.EtOH.Female.Normal.1


title: 211_A9_EB_3D_3B_SC_Batch2


title: ENR.CTL.Male.Normal.2

value: Male


title: ENR.EtOH.Male.Normal.3


title: 211_B5_EB_3D_3A_SC_Batch1


title: 211_B10_EB_3D_3B_SC_Batch2


title: SS-4-87

description: Recurrent tumor

value: Chemo+radiotherapy


title: HCC1937-orthotopic tumor, NMN_3

city: Beijing

first: Yi

last: Jiang

address: Hai Dian

department: School of Life Sciences

country: China

institute: Tsinghua University

data_processing:
The raw data was filtered with SOAPnuke (v1.4.0) by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 5%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 20%, afterwards clean reads were obtained and stored in FASTQ format. The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5). The expression level of genes was calculated by RSEM (v1.2.8).
Assembly: The clean data were mapped to the reference genome (GCF_000001405.39_GRCh38.p13) by HISAT (v2.1.0).
Supplementary files format and content: TPM

source_name: HCC1937-orthotopic tumor

growth_protocol: NCG (NOD/ShiLtJGpt-Prkdcem26Cd52Il2rgem26Cd22/Gpt) mice were housed in pathogen-free barrier facilities and maintained in a 12-hour light/dark cycle in isolated ventilated cages (maxima six mice per cage), 22-26 °C with sterile pellet food and water supply ad libitum.

extract_protocol:
TRIzol was used to isolate total mRNAs in tumor tissues. Agilent 2200 TapeStation Nucleic Acid System was used to determine the RNA integrity number (RIN) and concentration of all RNA samples (Agilent, CA). For the construction of the cDNA library, RNA samples having a RIN greater than 8.5 were employed. rRNA was depleted using hybridization capture to facilitate the identification of protein-coding RNAs.
DNase I degrade double-stranded and single-stranded DNA contaminant in RNA samples. mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. mRNA were fragmented into small pieces using fragmentation reagent. First-strand cDNA was generated using random hexamer-primed reverse transcription, then was followed by a second-strand cDNA synthesis. The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. This process is to amplify the cDNA fragments with adaptors from previous step. PCR products are purified, and dissolved. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library.

treatment_protocol: For the orthotopic tumor implantation assays, cells were suspended in 100 μL of serum-free medium and injected into the inguinal mammary fat pads of the animals to develop experimental lung metastasis. NCG mice were injected orthotopically with TNBC cells (1 × 10^6 HCC1937 cells). When tumors measured 100-150 mm3, mice were divided into groups for treatment.

value: HCC1937-orthotopic tumor

value: TNBC

value: NCG mice

value: NMN


title: ENR.CTL.Male.Normal.1


title: ENR.EtOH.Female.Normal.3


title: SS-4-93

description: T0 Control

value: Glioblastoma multiforme cell line


title: HCC1937-orthotopic tumor, NMN_4


title: SS-4-88

description: Recurrent tumor


title: 211_A8_EB_3D_3A_SC_Batch1

value: Embryoid Bodies (EB)

value: Dnmt3a -/- (3AKO)


title: SS-4-90

description: Recurrent tumor


title: SS-4-86

description: Minimal residual disease


title: HCC1937-orthotopic tumor, NMN_1


title: HCC1937-orthotopic tumor, NMN_2


title: 211_A7_EB_3D_3A_SC_Batch1


title: SS-4-85

description: Engraftment Control


title: ENR.CTL.Female.Normal.2

value: Female


title: 211_A6_EB_3D_3A_SC_Batch1


title: 211_A5_EB_3D_3A_SC_Batch1


title: 211_A12_EB_3D_3B_SC_Batch2

value: Dnmt3b -/- (3BKO)


title: HCC1937-orthotopic tumor, Vehicle_4

value: Vehicle


title: 211_A4_EB_3D_3A_SC_Batch1


title: ENR.CTL.Female.Normal.3


title: SS-4-83

description: Recurrent tumor

value: Primary tumour

value: DNA amplicon


title: HCC1937-orthotopic tumor, Vehicle_3


title: SS-4-82

description: Recurrent tumor

value: Vehicle Treated (Control)


title: SS-4-81

description: Recurrent tumor


title: HCC1937-orthotopic tumor, Vehicle_1


title: SS-4-80

description: Minimal residual disease


title: SS-4-79

description: Minimal residual disease


title: HCC1937-orthotopic tumor, Vehicle_2


title: SS-4-84

description: Engraftment Control


title: 211_A11_EB_3D_3B_SC_Batch2


title: Flnc global KO sample 2

city: La Jolla

first: Ju

last: Chen

state: California

address: 9500 Gilman Drive 0613

institute: University of California San Diego

data_processing:
Sequencing reads were mapped to GENCODE mouse  transcripts reference (release M22, GRCm38.p6) and transcription levels were quantified using salmon.
Differential expression analysis was carried out using DEseq2 (version: 1.22.2). Benjamini-Hochberg correction for multiple testing was applied to correct p-value of each gene as false discovery rate (FDR). FDR < 0.05 was used as a threshold for differentially-expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include TPM and reads count for each sample

source_name: whole heart

extract_protocol:
E9.5 embryonic hearts were homogenized in TRIzol (Invitrogen) and total RNA was isolated according to the manufacturer’s instructions.
cDNA libraries were prepared using an Illumina TruSeq stranded mRNA kit according to manufacturer’s instructions.

value: whole heart

tag: developmental stage

value: Flnc global knockout


title: Littermate control sample 3

value: control


title: GS-6/7a_N0_primary_tumor (CGH121_PCA)

type: genomic

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

description:
macrodissected FFPE sample
CGH121_PCA

hyb_protocol: Converted gDNA was hybridized on Infinium®MethylationEPIC BeadChips (Illumina, San Diego, CA, USA) according to the manufacturer's protocol.

scan_protocol: Bead Array Slides were scanned using the Illumina Bead Array Reader according to the manufacturer's protocol.

data_processing:
GenomeStudio (version 2011.1) with Methylation Module (version 1.9.0) was used to process the raw image data generated by the BeadArray Reader followed by import and preprocessing using the RnBeads R package. Beta values were normalized using the dasen method from the R watermelon package
matrix_proc_df_111222.txt:  normalized (dasen) Average Beta
signals_df_111222.txt:  Unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: DNA methylation profiling was performed using Illumina Infinium MethylationEPIC 850 k arrays. Processing of DNA Methylation arrays was performed as follows: Bisulfite conversion of 500ng of DNA was done using the EZ DNA Methylation Kit (Zymo Research, Orange, CA, USA)  according to the manufacturer's protocol.

growth_protocol: Serial sections (10 µm) were generated from available formalin-fixed and paraffin-embedded (FFPE) tumor tissue blocks (n=100), with the first and last sections of each series stained with hematoxylin and eosin (HE). The HE stained tissue sections were histopathologically reviewed by a pathologist and the tumor area was defined. If necessary, the annotated tumor area was macro-dissected.

extract_protocol: Simultaneous DNA and RNA extraction using the AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. Isolated DNA was quantified using the Qubit 2.0 fluorometer.

tag: disease state

value: prostate cancer

tag: gleason group

tag: lymph node status

tag: tumor type


title: Flnc global KO sample 3

tag: genotype

tag: strain


title: GS-6/7a_N0_primary_tumor (CGH122_PCA)

description:
macrodissected FFPE sample
CGH122_PCA


title: 211_A3_EB_3D_3A_SC_Batch1

tag: cell type

tag: Stage


title: GS-6/7a_N0_primary_tumor (CGH120_PCA)

description:
macrodissected FFPE sample
CGH120_PCA


title: SS-4-78

description: T0 Control

tag: cell line

tag: tumor stage


title: 210_H9_EB_3D_3A_SC_Batch2

tag: batch


title: 211_A10_EB_3D_3B_SC_Batch2


title: Littermate control sample 2


title: ENR.CTL.Female.Normal.1

value: Brain cells

value: Fetal forebrain

value: Enriched diet & Saline (Control)


title: GS-6/7a_N0_primary_tumor (CGH119_PCA)

description:
macrodissected FFPE sample
CGH119_PCA


title: 210_H7_EB_3D_3B_SC_Batch1


title: 210_H8_EB_3D_3B_SC_Batch1


title: Flnc global KO sample 1


title: 210_H6_EB_3D_3B_SC_Batch1


title: GS-6/7a_N0_primary_tumor (CGH101_PCA)

description:
macrodissected FFPE sample
CGH101_PCA


title: SS-4-76

description: T0 Control

tag: molecule subtype

tag: technical replicate

tag: biological replicate


title: GS-6/7a_N0_primary_tumor (CGH118_PCA)

description:
macrodissected FFPE sample
CGH118_PCA


title: SS-4-77

description: T0 Control


title: GS-9/10_N1_primary_tumor (CGH084_PCA)

description:
macrodissected FFPE sample
CGH084_PCA


title: 210_H5_EB_3D_3B_SC_Batch1


title: Mammary adenocarcinoma, database ID 21-034-01 [HOM.73]

city: Cardiff

first: Matthew

middle: John

last: Smalley

state: Cardiff

address: Hadyn Ellis Building, Maindy Road

department: School of Biosciences

country: United Kingdom

institute: Cardiff University

description:
PCA group 1/2
Lyn low group

data_processing:
Quality trimmed reads were mapped to GRCm38 using STAR (v2.5.1b) with read multimapping filter set to 1 and gtf Gencode GRCm38 vM17.
Exon and gene counts were calculated with featureCounts (v1.5.1).
Differential gene expression was calculated using SARtools using the DESeq2 package.
Assembly: GRCm38 vM17
Supplementary files format and content: xx_raw_normalised_DEGs' excel spreadsheets include raw and normalised counts for each gene for each sample included in that analysis as well as assessment of differential expression of each gene; 'Summarised_DEGs' excel spreadsheet gives the significantly altered genes for all three comparisons

source_name: Mammary tumour

extract_protocol:
Total RNA was isolated from tumour tissue using the RNeasy Minikit (QIAGEN) according to the manufacturer's protocol. Samples for RNAseq analysis underwent an on-column DNase I digestion step for genomic DNA removal prior to further processing. Total RNA quality and quantity was assessed using Agilent 4200 TapeStation and hsRNA or RNA ScreenTapes (Agilent Technologies).
mRNA was isolated from 50ng of total RNA (RIN value >7) using the NEBNext® Poly(A) mRNA magnetic isolation module, (New England BioLabs, NEB, #E7490) and the sequencing libraries were prepared using the NEB® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB, #E7760). The sequencing libraries were prepared following Chapter 1 of the NEB® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs, NEB) protocol. The steps included mRNA isolation, fragmentation and priming, first strand cDNA synthesis, second strand cDNA synthesis, adenylation of 3’ ends, adapter ligation (1:80 dilution) and PCR amplification (14-cycles). Libraries were validated using the Agilent 4200 TapeStation and hsD1000 ScreenTapes (Agilent Technologies) to ascertain the insert size, and the Qubit® (Thermo Fisher Scientific) was used to perform fluorometric quantitation. The manufacturer’s instructions were followed except for the replacement of SPRIselect Beads or NEBNext Sample Purification Beads by AMPure XP beads (Beckman Coulter®) in purification steps. The validated libraries were normalized to 4nM, pooled together and the pool sequenced on an S1 (200 cycle) flow cell using a 2x100bp PE dual index format on the Illumina® NovaSeq6000 sequencing system according to the manufacturer’s instructions. Samples were sequenced to a read depth of at least 35 Million prior to quality trimming with fastp

tag: tissue

value: Mammary tumour

tag: histotype

value: adenocarcinoma (no special type)

tag: Sex

value: Adult


title: Mammary adenocarcinoma, database ID 21-034-02 [HOM.74]

description:
PCA group 1/2
Lyn low group

tag: developmental stage


title: SS-4-75

description: Retransplant from CON

value: Glioblastoma multiforme cell line

value: Recurrent tumor

value: Chemo+radiotherapy


title: Mammary adenocarcinoma, database ID 21-031-02 [HOM.72]

description: PCA group 1/2

value: Female


title: GS-9/10_N1_primary_tumor (CGH042_PCA)

description:
macrodissected FFPE sample
CGH042_PCA

tag: disease state

tag: gleason group


title: SS-4-72

description: Retransplant from CON


title: 210_H3_EB_3D_3B_SC_Batch1

source_name: Mouse Embryoid Bodies

value: Embryoid Bodies (EB)

value: Dnmt3b -/- (3BKO)


title: 210_H4_EB_3D_3B_SC_Batch1


title: GS-6/7a_N1_primary_tumor (CGH028_PCA)

description:
macrodissected FFPE sample
CGH028_PCA

tag: lymph node status

tag: tumor type


title: SS-4-71

description: Minimal residual disease

value: Vehicle Treated (Control)

value: DNA amplicon


title: SS-4-70

description: Recurrent tumor


title: SS-4-68

description: Engraftment Control


title: Mammary adenocarcinoma, database ID 21-027-02 [HET.63]

description: PCA group 1/2

tag: genotype


title: Littermate control sample 1

value: whole heart

tag: strain


title: SS-4-73

description: Retransplant from CON

tag: cell type


title: GS-9/10_N1_lymph_node_met (CGH084_LK)

description:
macrodissected FFPE sample
CGH084_LK


title: 210_H2_EB_3D_3B_SC_Batch1

tag: Stage


title: Mammary adenocarcinoma, database ID 21-022-02 [HOM.70]

description:
PCA group 1/2
Lyn high group


title: Mammary adenocarcinoma, database ID 21-026-02 [WT.59]

description:
PCA group 1/2
Lyn high group

value: BlgCre;Brca1flox/flox;p53 +/-; Lynwt/wt


title: 210_H1_EB_3D_3B_SC_Batch1


title: SS-4-67

description: Minimal residual disease

tag: cell line

tag: tumor stage


title: SS-4-66

description: Recurrent tumor

tag: molecule subtype


title: Mammary adenocarcinoma, database ID 21-022-01 [HOM.56]

description:
PCA group 1/2
Lyn low group


title: Mammary adenocarcinoma, database ID 21-021-01 [HOM.54]

description: PCA group 3/4


title: GS-9/10_N1_primary_tumor (CGH083_PCA)

description:
macrodissected FFPE sample
CGH083_PCA

value: prostate cancer


title: Mammary adenocarcinoma, database ID 21-027-01 [HET.49]

description: PCA group 3/4


title: 210_G8_EB_3D_3B_SC_Batch1

tag: batch


title: Mammary adenocarcinoma, database ID 21-019-01 [HET.48]

description: PCA group 1/2


title: GS-9/10_N1_lymph_node_met (CGH042_LK)

description:
macrodissected FFPE sample
CGH042_LK


title: SS-4-60

description: Recurrent tumor

tag: technical replicate

tag: biological replicate


title: SS-4-61

description: Minimal residual disease


title: GS-9/10_N1_primary_tumor (CGH038_PCA)

description:
macrodissected FFPE sample
CGH038_PCA


title: 210_G5_EB_3D_3B_SC_Batch1


title: GS-9/10_N1_lymph_node_met (CGH083_LK)

description:
macrodissected FFPE sample
CGH083_LK


title: GS-6/7a_N0_primary_tumor (CGH099_PCA)

description:
macrodissected FFPE sample
CGH099_PCA


title: GS-6/7a_N0_primary_tumor (CGH117_PCA)

description:
macrodissected FFPE sample
CGH117_PCA


title: 210_G7_EB_3D_3B_SC_Batch1


title: 210_G3_EB_3D_3B_SC_Batch1


title: 210_G6_EB_3D_3B_SC_Batch1


title: SS-4-62

description: Recurrent tumor


title: Mammary adenocarcinoma, database ID 21-026-01 [WT.42]

description: PCA group 1/2

tag: tissue

tag: histotype


title: GS-6/7a_N1_lymph_node_met (CGH028_LK)

description:
macrodissected FFPE sample
CGH028_LK


title: 210_G9_EB_3D_3A_SC_Batch2

value: Dnmt3a -/- (3AKO)


title: SS-4-58

description: Recurrent tumor


title: Mammary adenocarcinoma, database ID 21-021-02 [HOM.55]

description:
PCA group 1/2
Lyn low group

tag: Sex

tag: developmental stage


title: SS-4-63

description: Engraftment Control


title: Mammary adenocarcinoma, database ID 21-025-01 [WT.41]

description:
PCA group 1/2
Lyn high group


title: 210_G1_EB_3D_3B_SC_Batch1


title: Mammary adenocarcinoma, database ID 21-024-01 [WT.40]

description:
PCA group 1/2
Lyn low group


title: Mammary adenocarcinoma, database ID 21-028-01 [WT.60]

description:
PCA group 1/2
Lyn low group


title: 210_G12_EB_3D_3A_SC_Batch2


title: GS-6/7a_N1_lymph_node_met (CGH027_LK)

description:
macrodissected FFPE sample
CGH027_LK

tag: disease state

tag: gleason group


title: GS-9/10_N1_lymph_node_met (CGH038_LK)

description:
macrodissected FFPE sample
CGH038_LK

tag: lymph node status

tag: tumor type


title: GS-6/7a_N0_primary_tumor (CGH098_PCA)

description:
macrodissected FFPE sample
CGH098_PCA


title: Mammary adenocarcinoma, database ID 21-015-03 [HOM.38]

description:
PCA group 1/2
Lyn low group

tag: genotype


title: 210_G4_EB_3D_3B_SC_Batch1

tag: strain

tag: cell type


title: GS-6/7a_N1_primary_tumor (CGH027_PCA)

description:
macrodissected FFPE sample
CGH027_PCA


title: 210_G11_EB_3D_3A_SC_Batch2

tag: Stage


title: SS-4-48

description: Retransplant T0 Control

tag: cell line

tag: tumor stage


title: 210_G2_EB_3D_3B_SC_Batch1

tag: batch


title: Mammary adenocarcinoma, database ID 21-005-01 [HET.45]

description: PCA group 1/2


title: SS-4-54

description: Minimal residual disease

tag: molecule subtype

tag: technical replicate


title: Mammary adenocarcinoma, database ID 21-023-01 [WT.39]

description:
PCA group 1/2
Lyn high group

tag: tissue


title: SS-4-53

description: Engraftment Control

tag: biological replicate


title: 210_F9_EB_3D_3A_SC_Batch2


title: SS-4-39

description: T0 Control


title: Mammary adenocarcinoma, database ID 20-092-03 [HOM.35]

description:
PCA group 1/2
Lyn low group

tag: histotype

tag: Sex


title: SS-4-59

description: Recurrent tumor


title: 210_F8_EB_3D_3B_SC_Batch1


title: SS-4-38

description: T0 Control


title: SS-4-37

description: Retransplant from TR

value: Primary tumour


title: Mammary adenocarcinoma, database ID 21-015-01 [HOM.37]

description:
PCA group 1/2
Lyn low group

tag: developmental stage


title: SS-4-47

description: Retransplant T0 Control


title: GS-9/10_N1_primary_tumor (CGH081_PCA)

description:
macrodissected FFPE sample
CGH081_PCA

tag: disease state

tag: gleason group


title: GS-6/7a_N0_primary_tumor (CGH115_PCA)

description:
macrodissected FFPE sample
CGH115_PCA

tag: lymph node status

tag: tumor type


title: 210_F5_EB_3D_3B_SC_Batch1

tag: strain

tag: genotype


title: 210_F7_EB_3D_3B_SC_Batch1

tag: cell type

tag: Stage


title: GS-6/7a_N0_primary_tumor (CGH114_PCA)

description:
macrodissected FFPE sample
CGH114_PCA


title: SS-4-34

description: Retransplant from TR

tag: cell line

tag: tumor stage


title: GS-9/10_N1_primary_tumor (CGH031_PCA)

description:
macrodissected FFPE sample
CGH031_PCA


title: Mammary adenocarcinoma, database ID 21-001-01 [HET.30]

description: PCA group 3/4


title: GS-9/10_N1_lymph_node_met (CGH031_LK)

description:
macrodissected FFPE sample
CGH031_LK


title: Mammary adenocarcinoma, database ID 21-001-02 [HET.31]

description:
PCA group 1/2
Lyn low group


title: 210_F6_EB_3D_3B_SC_Batch1

tag: batch


title: Mammary adenocarcinoma, database ID 20-071-01 [WT.21]

description:
PCA group 3/4
Lyn high group


title: SS-4-36

description: Retransplant from TR

tag: molecule subtype

tag: technical replicate


title: GS-6/7a_N1_lymph_node_met (CGH023_LK)

description:
macrodissected FFPE sample
CGH023_LK


title: SS-4-35

description: Retransplant from TR

tag: biological replicate


title: GS-6/7a_N1_primary_tumor (CGH023_PCA)

description:
macrodissected FFPE sample
CGH023_PCA


title: 210_F4_EB_3D_3B_SC_Batch1


title: SS-4-30

description: Recurrent tumor


title: SS-4-29

description: Minimal residual disease


title: Mammary adenocarcinoma, database ID 20-087-03 [HET.25]

description:
PCA group 3/4
Lyn high group

tag: tissue

tag: histotype


title: SS-4-33

description: Engraftment Control


title: Mammary adenocarcinoma, database ID 20-094-02 [HET.27]

description: PCA group 1/2

tag: Sex

tag: developmental stage


title: 210_F1_EB_3D_3B_SC_Batch1


title: SS-4-28

description: Recurrent tumor


title: 210_G10_EB_3D_3A_SC_Batch2


title: 210_F12_EB_3D_3A_SC_Batch2


title: GS-9/10_N1_lymph_node_met (CGH079_LK)

description:
macrodissected FFPE sample
CGH079_LK

tag: disease state

tag: gleason group


title: Mammary adenocarcinoma, database ID 20-058-01 [HOM.15]

description: PCA group 1/2


title: GS-9/10_N1_lymph_node_met (CGH026_LK)

description:
macrodissected FFPE sample
CGH026_LK

tag: lymph node status

tag: tumor type


title: GS-9/10_N1_lymph_node_met (CGH081_LK)

description:
macrodissected FFPE sample
CGH081_LK


title: 210_F2_EB_3D_3B_SC_Batch1

tag: strain

tag: genotype


title: GS-6/7a_N1_primary_tumor (CGH022_PCA)

description:
macrodissected FFPE sample
CGH022_PCA


title: Mammary adenocarcinoma, database ID 20-078-04 [HET.19]

description:
PCA group 3/4
Lyn high group


title: 210_E9_EB_3D_3A_SC_Batch2

tag: cell type

tag: Stage


title: 210_F3_EB_3D_3B_SC_Batch1


title: 210_F10_EB_3D_3A_SC_Batch2


title: GS-9/10_N1_primary_tumor (CGH079_PCA)

description:
macrodissected FFPE sample
CGH079_PCA


title: Mammary adenocarcinoma, database ID 20-078-01 [HET.08]

description:
PCA group 3/4
Lyn high group


title: GS-9/10_N1_primary_tumor (CGH026_PCA)

description:
macrodissected FFPE sample
CGH026_PCA


title: Mammary adenocarcinoma, database ID 20-070-01 [WT.20]

description:
PCA group 3/4
Lyn high group


title: 210_E8_EB_3D_3B_SC_Batch1


title: GS-6/7a_N0_primary_tumor (CGH113_PCA)

description:
macrodissected FFPE sample
CGH113_PCA


title: SS-4-24

description: Engraftment Control

tag: cell line

tag: tumor stage


title: Mammary adenocarcinoma, database ID 20-051-01 [HOM.13]

description:
PCA group 1/2
Lyn high group


title: Mammary adenocarcinoma, database ID 20-098-05 [HET.29]

description:
PCA group 1/2
Lyn low group


title: 210_F11_EB_3D_3A_SC_Batch2

tag: batch


title: Mammary adenocarcinoma, database ID 20-035-01 [HOM.12]

description: PCA group 1/2


title: GS-6/7a_N1_lymph_node_met (CGH022_LK)

description:
macrodissected FFPE sample
CGH022_LK


title: GS-6/7a_N0_primary_tumor (CGH096_PCA)

description:
macrodissected FFPE sample
CGH096_PCA


title: SS-4-23

description: Recurrent tumor

tag: molecule subtype

tag: technical replicate


title: 210_E7_EB_3D_3B_SC_Batch1


title: SS-4-27

description: Recurrent tumor

tag: biological replicate


title: SS-4-25

description: Engraftment Control


title: Mammary adenocarcinoma, database ID 20-078-03 [HET.09]

description: PCA group 3/4

tag: tissue

tag: histotype


title: Mammary adenocarcinoma, database ID 20-059-01 [HET.06]

description:
PCA group 1/2
Lyn high group

tag: Sex

tag: developmental stage


title: 210_E5_EB_3D_3B_SC_Batch1


title: 210_E6_EB_3D_3B_SC_Batch1


title: GS-9/10_N1_lymph_node_met (CGH078_LK)

description:
macrodissected FFPE sample
CGH078_LK

tag: disease state

tag: gleason group


title: GS-6/7a_N1_primary_tumor (CGH071_PCA)

description:
macrodissected FFPE sample
CGH071_PCA

tag: lymph node status

tag: tumor type


title: GS-6/7a_N0_primary_tumor (CGH095_PCA)

description:
macrodissected FFPE sample
CGH095_PCA


title: Mammary adenocarcinoma, database ID 20-069-01 [HET.07]

description:
PCA group 1/2
Lyn high group

tag: genotype


title: SS-4-26

description: Recurrent tumor

tag: cell type


title: Mammary adenocarcinoma, database ID 20-046-04 [WT.04]

description:
PCA group 1/2
Lyn low group


title: 210_E3_EB_3D_3B_SC_Batch1

tag: strain

tag: Stage


title: SS-4-16

description: Minimal residual disease

tag: cell line

tag: tumor stage


title: SS-4-20

description: Recurrent tumor

tag: molecule subtype


title: Mammary adenocarcinoma, database ID 20-046-01 [WT.02]

description:
PCA group 1/2
Lyn low group


title: SS-4-5

description: Retransplant T0 Control

tag: technical replicate


title: SS-4-6

description: Retransplant T0 Control

tag: biological replicate


title: GS-6/7a_N1_lymph_node_met (CGH021_LK)

description:
macrodissected FFPE sample
CGH021_LK


title: GS-6/7a_N1_primary_tumor (CGH021_PCA)

description:
macrodissected FFPE sample
CGH021_PCA


title: Mammary adenocarcinoma, database ID 20-046-02 [WT.03]

description:
PCA group 3/4
Lyn high group

tag: tissue


title: 210_E2_EB_3D_3B_SC_Batch1

tag: batch


title: SS-4-3

description: T0 Control


title: GS-6/7a_N0_primary_tumor (CGH092_PCA)

description:
macrodissected FFPE sample
CGH092_PCA


title: GS-6/7a_N1_lymph_node_met (CGH071_LK)

description:
macrodissected FFPE sample
CGH071_LK


title: SS-4-17

description: Minimal residual disease


title: GS-6/7a_N0_primary_tumor (CGH110_PCA)

description:
macrodissected FFPE sample
CGH110_PCA


title: Formative_ESC_MLL3KO_MLL4KO_MLL4_rep2

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

institute: UCSF

description:
CUT&RUN
MLL4_form_DKO_merged.cpm.bw
MLL4_form_WT_dkosub.cpm.bw

data_processing:
Fastq files for CUT&RUN samples were processed using Nextflow and the nf-core CUT&RUN pipeline v1.0.0 beta. In brief, adapters were trimmed using Trim Galore. Paired-end alignment was performed using Bowtie2 and peaks were called using SEACR with a peak threshold of 0.05. We did not normalize peak calls to IgG. Spike in normalization was performed using the E.coli genome K12. However, spike-in normalization resulted in batch effects between replicates. These batch effects were greatly diminished when normalized by CPM. Therefore, all downstream analysis was performed using CPM normalized samples.
Assembly: mm10
Supplementary files format and content: supermatrix for H3K4m1 contains the intersection of naive and formative WT H3K4m1 peaks. Columns 1-3 H3K4m1 peak coordinates, Columns 12-19 Log2CPM RNAseq, Columns 5-10 Diffbind results for H3K4m1 peaks between Naive and Form, Columns 26-37 Log2 Peak densities for H3K4m1 and H3K27a
Supplementary files format and content: bigwig files are generated with deeptools by averaging bam files of replicate
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN was conducted using the protocol from Skene et al. 2018 with the following modifications: Freshly trypsinized cells were bound to activated Concanavalin A beads (Bang Laboratories, CAT#BP531) at a ratio of 2e5 cells/10ul beads in CR Wash buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine with protease inhibitors at room temp. An input of 2e5 cells were used per target. Bead-bound cells were then incubated rotating overnight at 4C in CR Antibody buffer (CR Wash with 0.05% Digitonin, 2mM EDTA) containing primary antibody. We used the following antibodies for CUT&RUN: 1:100 Rabbit anti-H3K4m1 (Abcam, ab4729), Rabbit anti-MLL4 1:100 (provided by Kai Ge), and 1:100 Rabbit IgG isotype control (Abcam, ab171870). After primary, we washed 3 times 5 minutes each with cold CR Dig-wash buffer (CR Wash with 0.05% Digitonin) and incubated with pA-MNase (1:100 of 143ug/mL provided by Steve Henikoff) for 1 hour rotating at 4C. After MNase binding, we washed 3 times 5 each with cold CR Dig-wash buffer, and chilled cells down to 0C using a metal tube rack partially submerged in an ice water slurry. MNase digestion was induced by adding CaCl2 at a final concentration of 2mM. After 30 minutes of digestion, the reaction was quenched using Stop Buffer containing 340mM NaCl, 20mM EDTA, 4mM EGTA, 0.05% Digitonin, 100ug/mL RNAse A, 50ug/mL Glycogen, and approximately 2pg/mL Yeast spike-in DNA (provided by Steve Henikoff). The digested fragments for each sample were then extracted using a phenol chloroform extraction.
Library preparation on samples was conducted using manufacturer’s protocols for NEBNext Ultra II Dna Library Prep Kit (New England BioLabs, CAT#E7645) and NEB Multiplex Dual Index oligos (New England BioLabs, CAT#E7600, #E7780) with the following modifications. We input approximately 10ng of sample for half reactions, we diluted the NEBNext Illumina adaptor 1:25, we used the following PCR cycling conditions: 1 cycle of Initial Denaturation at 98C for 30 seconds, 12+ cycles of Denaturation at 98C for 10 seconds then Annealing/Extension at 65C for 10 seconds, and 1 final cycle of extension at 65C for 5 minutes. Following library preparation, double size selection was performed using Ampure beads and quality and concentration of libraries were determined by an Agilent 4200 Tapestation with High-Sensitivity D1000 reagents before pooling for sequencing.

tag: treatment

value: LIF2i withdrawal, 63hrs

tag: target antibody

value: anti-MLL4 #3 (from Kai Ge)


title: Day0, Mus

description: 10x Genomics

value: ear skin

value: skin

tag: age


title: 210_E1_EB_3D_3B_SC_Batch1


title: SS-4-1

description: T0 Control

value: Glioblastoma multiforme cell line


title: GS-9/10_N1_primary_tumor (CGH078_PCA)

description:
macrodissected FFPE sample
CGH078_PCA

tag: disease state

tag: gleason group


title: Mammary adenocarcinoma, database ID 20-039-01 [WT.01]

description: PCA group 1/2

value: Mammary tumour

tag: histotype

value: adenocarcinoma (no special type)

tag: Sex

tag: developmental stage

value: Adult


title: 210_E12_EB_3D_3A_SC_Batch2

tag: strain

tag: cell type

value: Embryoid Bodies (EB)

tag: genotype


title: GS-9/10_N1_lymph_node_met (CGH076_LK)

description:
macrodissected FFPE sample
CGH076_LK

tag: lymph node status

tag: tumor type


title: Formative_ESC_MLL3KO_MLL4KO_MLL4_rep1


title: 210_E11_EB_3D_3A_SC_Batch2

tag: Stage


title: GS-9/10_N1_primary_tumor (CGH076_PCA)

description:
macrodissected FFPE sample
CGH076_PCA


title: Cre+ pMBMEC, untreated, rep3

city: Epalinges

first: Caroline

last: Pot

address: Chemin des Boveresses 155

department: Department of Clinical Neurosciences

country: Switzerland

institute: Lausanne University Hospital

description: Column name in tab-delimited matrix: CREpNS3

data_processing:
Data processing was performed by the Lausanne Genomic Technologies Facility (GTF) as follows:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013). Reads were aligned against Mus musculus.GRCm38.98 genome using STAR (v. 2.5.3a, Dobin et al. 2013)
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Mus musculus.GRCm38.92 gene annotation
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012).
Assembly: GRCm38.92
Supplementary files format and content: Tab-delimited matrix COUNTS file containing in the first column Ensembl Gene ID, and read count values for each sample in columns 2 to 13. The last five rows of the tab-delimited file contain the summary of numbers of unaligned or ambiguous reads per sample.

source_name: Endothelium

growth_protocol: pMBMECs were maintained in DMEM with 10% FCS, 50µg/ml of gentamicin, and 1 ng/ml of basic fibroblast growth factor at 37°C and 5% CO2 in a humidified incubator

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen). RNAseq libraries were prepared from 500 ng of total RNA.
Illumina TruSeq Stranded mRNA reagents (Illumina) using a unique dual indexing strategy was used, and following the official protocol automated on a Sciclone liquid handling robot (PerkinElmer).

treatment_protocol: Confluent pMBMECs were treated with IL-1beta at 10ng/ml (IL-1beta) or vehicle (Untreated) for 24h

value: Endothelium

tag: cell line

value: primary mouse brain microvascular endothelial cells

value: Ch25hfl/fl x VE-Cadherin-Cre+

value: Untreated


title: 210_E10_EB_3D_3A_SC_Batch2


title: Formative_ESC_WT_MLL4_rep2

description:
CUT&RUN
MLL4_form_WT_merged.cpm.bw
MLL4_form_WT_dkosub.cpm.bw

value: WT


title: Formative_ESC_MLL3KO_MLL4KO_H3K27a_rep2

description: CUT&TAG

data_processing:
Fastq files for CUT&TAG samples were processed using Nextflow and the nf-core CUT&RUN pipeline v1.0.0 beta. In brief, adapters were trimmed using Trim Galore. Paired-end alignment was performed using Bowtie2 and peaks were called using SEACR with a peak threshold of 0.05. We did not normalize peak calls to IgG. Spike in normalization was performed using the E.coli genome K12. However, spike-in normalization resulted in batch effects between replicates. These batch effects were greatly diminished when normalized by CPM. Therefore, all downstream analysis was performed using CPM normalized samples.
Assembly: mm10
Supplementary files format and content: supermatrix for H3K27a contains the intersection of naive and formative WT H3K27a peaks. Columns 1-3 H3K27a peak coordinates, Columns 5-12 Log2CPM RNAseq, Columns 26-31 Diffbind results for H3K27a peaks between Naive and Form, Columns 32-39 Log2 Peak densities for H3K4m1 and H3K27a
Supplementary files format and content: bigwig files are generated with deeptools by averaging bam files of replicates
Library strategy: CUT&TAG

extract_protocol:
CUT&TAG was conducted using the protocol from (Kaya-Okur et al. 2020) with the following modifications: freshly trypsinized cells were bound to Concanavalin A beads at a ratio of 2e5 cells/7ul beads in CR wash at room temp. We used 2e5 cells as input per sample. Bead-bound cells were then incubated rotating overnight at 4C in CT Antibody buffer (CR Wash with 0.05% Digitonin, 2mM EDTA, 1mg/mL BSA) containing primary antibody. We used the following primary antibodies for CUT&TAG: 1:100 Rabbit anti-H3K27a (Abcam, ab4729), 1:100 Rabbit anti-H3K4m3 (Abcam, ab8580), 1:100 Rabbit IgG isotype control (Abcam, ab171870). After primary, samples were washed 3 times for 5 minutes each using CR Dig-wash buffer and resuspended in 1:100 secondary antibody (Guinea pig anti-rabbit, Antibodies Online #ABIN101961) in CR Dig-wash buffer at 4C for 1 hour rotating at 4C. Samples were then incubated for 1 hour at 4C with 50ul of approximately 25nM homemade pA-Tn5 in CT Dig300 wash buffer (20mM HEPES, 300mM NaCl, 0.01% Digitonin, 0.5mM Spermidine with Roche cOmplete protease inhibitors added). Recombinant Tn5 was purified and loaded with adapters as previously described (Kaya-Okur et al. 2019). After Tn5 incubation, samples were washed 3 times for 5 minutes each with CT Dig300 wash buffer. Tagmentation was then initiated for 1hr at 37C in a thermocycler by adding MgCl2 to 10mM final concentration in 50uL volume. The tagmentation reaction was quenched immediately afterwards by adding 1.6ul of 0.5M EDTA, 1ul of 10mg/mL Proteinase K, and 1ul of 5% SDS. Samples were then incubated at 55C for 2 hours in a thermocycler to denature Tn5 and solubilize tagmented chromatin. After incubation, samples were magnetized and the supernatant was transferred to new wells where SPRI bead purification was performed using homemade beads to select all DNA fragment lengths larger than 100bp. Samples were eluted in 0.1X TE.
Approximately half of each sample was used for library preparation using NEBNext HIFI Polymerase with custom indices synthesized by IDT. An appropriate number of cycles for each target was chosen to prevent overamplification bias. After amplification, libraries were purified with 1.2x homemade SPRI beads to select for fragments >250bp and eluted in 0.1X TE. Quality and concentration of libraries were determined by an Agilent 4200 Tapestation with D1000 reagents before pooling for sequencing.

value: anti-H3K27a (Abcam, #ab4729)


title: GS-6/7a_N1_primary_tumor (CGH069_PCA)

description:
macrodissected FFPE sample
CGH069_PCA

value: prostate cancer


title: Cre+ pMBMEC, untreated, rep2

description: Column name in tab-delimited matrix: CREpNS2

tag: tissue


title: Cre+ pMBMEC, untreated, rep1

description: Column name in tab-delimited matrix: CREpNS1


title: Formative_ESC_WT_MLL4_rep1


title: 210_D7_EB_3D_3B_SC_Batch1

value: Dnmt3b -/- (3BKO)

tag: batch


title: 210_D8_EB_3D_3B_SC_Batch1


title: Cre+ pMBMEC,  IL-1beta, rep2

description: Column name in tab-delimited matrix: CREpIl-1b2

tag: treatment


title: GS-6/7a_N1_lymph_node_met (CGH069_LK)

description:
macrodissected FFPE sample
CGH069_LK


title: GS-6/7a_N1_primary_tumor (CGH020_PCA)

description:
macrodissected FFPE sample
CGH020_PCA


title: SS-4-2

description: T0 Control

tag: tumor stage

value: Primary tumour

tag: molecule subtype

value: DNA amplicon

tag: technical replicate

tag: biological replicate


title: 210_D6_EB_3D_3B_SC_Batch1


title: Formative_ESC_MLL3KO_MLL4KO_H3K27a_rep1

description: CUT&TAG

value: LIF2i withdrawal, 63hrs

tag: target antibody


title: 210_D9_EB_3D_3A_SC_Batch2

value: Dnmt3a -/- (3AKO)


title: 210_D5_EB_3D_3B_SC_Batch1


title: Cre+ pMBMEC,  IL-1beta, rep3

description: Column name in tab-delimited matrix: CREpIl-1b3


title: Formative_ESC_WT_H3K27a_rep1

description: CUT&TAG


title: Formative_ESC_WT_H3K27a_rep2

description: CUT&TAG


title: Cre- pMBMEC, untreated, rep3

description: Column name in tab-delimited matrix: CRE-NS3

value: Ch25hfl/fl x VE-Cadherin-Cre-


title: Cre+ pMBMEC,  IL-1beta, rep1

description: Column name in tab-delimited matrix: CREpIl-1b1


title: GS-6/7a_N0_primary_tumor (CGH091_PCA)

description:
macrodissected FFPE sample
CGH091_PCA

tag: disease state

tag: gleason group


title: GS-9/10_N1_primary_tumor (CGH074_PCA)

description:
macrodissected FFPE sample
CGH074_PCA


title: Naive_ESC_MLL3KO_MLL4KO_H3K27a_rep1

description: CUT&TAG


title: GS-9/10_N1_lymph_node_met (CGH074_LK)

description:
macrodissected FFPE sample
CGH074_LK


title: Cre- pMBMEC, IL-1beta, rep3

description: Column name in tab-delimited matrix: CRE-Il-1b3


title: GS-6/7a_N0_primary_tumor (CGH103_PCA)

description:
macrodissected FFPE sample
CGH103_PCA


title: 210_D1_EB_3D_3B_SC_Batch1

tag: strain


title: 210_E4_EB_3D_3B_SC_Batch1

tag: cell type


title: Formative_ESC_WT_ATAC_rep2

data_processing:
Fastq files for ATAC-seq samples were processed using Nextflow and the nf-core ATAC-seq pipeline v1.2.1. In brief, adapters were trimmed using Trim Galore. Paired-end alignment was performed using BWA and peaks were called using MACS2 in broad peak mode with a cutoff value of 0.1. BAM files were converted to bigWigs. Using read counts from consensus peaks of WT and DKO samples we performed TMM normalization using EdgeR to generate scale factors used during bigWig generation of samples.
Assembly: mm10
Supplementary files format and content: bigwig files are generated with deeptools by averaging bam files of replicates

extract_protocol:
ATAC-seq libraries were generated using the Active Motif commercial kit following the provided protocol with kit components (Active Motif, CAT#53150): Specifically, freshly trypsinized cells were washed with ice cold PBS using 75K cells as input for each sample. Cells were lysed using ice cold ATAC Lysis Buffer and we added 50ul of Tagmentation Master Mix to each sample. We incubated tagmentation reactions at 37C for 30min in a thermomixer set to 800 rpm. We immediately transferred samples to a new tube and performed DNA column purification.
After purification we amplified the libraries using the following PCR conditions: 1 cycle at 72C for 5 minutes, 1 cycle at 98C for 30 seconds, and finally 10 cycles of 98C for 10 seconds, 63C for 30 seconds, 72C for 1 minute. Amplified libraries were purified using 1.2x SPRI bead solution. Quality and concentration of libraries were determined by an Agilent 4200 Tapestation with D1000 reagents before pooling for sequencing.

tag: genotype


title: Cre- pMBMEC, IL-1beta, rep1

description: Column name in tab-delimited matrix: CRE-Il-1b1


title: Naive_ESC_MLL3KO_MLL4KO_H3K27a_rep2

description: CUT&TAG


title: Naive_ESC_WT_H3K27a_rep2

description: CUT&TAG


title: Formative_ESC_WT_ATAC_rep1


title: 210_D10_EB_3D_3A_SC_Batch2


title: Cre- pMBMEC, untreated, rep2

description: Column name in tab-delimited matrix: CRE-NS2


title: Formative_ESC_MLL3CD_MLL4CD_rep2

description: 3'end capture

data_processing:
Adapters for sample FastQ files were trimmed using cutadapt v2.5 followed by alignment to the mm10 genome using STAR align 2.7.2b. Featurecounts from Subread v1.6.4 was used to generate a counts matrix of reads per gene. FastQC v0.11.8 and MultiQC were used to validate quality sequencing and mapping.
The gene count matrix was converted to CPM and filtered for genes greater than 1 cpm in at least two total samples. Samples were normalized using TMM. Next, Log2 CPM averages were calculated for replicates of each sample for scatterplot visualization and nearest neighbor TSS analysis. All transcriptomics analyses were conducted using CPM values from TMM normalization of all samples except for nearest neighbor analysis where WT and DKO were TMM normalized together. To conduct differential gene expression we performed DESeq2 v1.34.0 analysis using the raw gene count matrix as input for each desired comparison.
Assembly: mm10
Supplementary files format and content: csv file containing the average CPMs between replicates for each gene of filtered and TMM-normalized samples

extract_protocol:
Total RNA was extracted and purified from cells using Trizol followed by ethanol precipitation
RNA-seq libraries were generated using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, CAT#A01172) according to their protocol using 200ng of total RNA for input. We utilized the PCR Add-on kit for Illumina (Lexogen, CAT#M02096) to determine an appropriate number of PCR cycles to amplify libraries. Amplified libraries were quantified using Agilent Tapestation 4200. Libraries were pooled and sequenced using a HiSeq 4000 to obtain single end 50bp reads. At least 10 million mapped reads or more per sample were obtained.


title: Naive_ESC_WT_ATAC_rep2


title: 210_D3_EB_3D_3B_SC_Batch1


title: GS-6/7a_N0_primary_tumor (CGH102_PCA)

description:
macrodissected FFPE sample
CGH102_PCA

tag: lymph node status


title: 210_D4_EB_3D_3B_SC_Batch1


title: 210_D2_EB_3D_3B_SC_Batch1


title: GS-6/7a_N1_lymph_node_met (CGH020_LK)

description:
macrodissected FFPE sample
CGH020_LK

tag: tumor type


title: Cre- pMBMEC, untreated, rep1

description: Column name in tab-delimited matrix: CRE-NS1


title: Formative_ESC_MLL3KO_MLL4KO_rep2

description: 3'end capture


title: GS-6/7a_N1_lymph_node_met (CGH015_LK)

description:
macrodissected FFPE sample
CGH015_LK


title: WGBS_ME48h_B77_Rep1

data_processing:
Following quality controls, sequencing reads were processed with Trim Galore! v0.5.0 to perform quality and adapter trimming (parameters: --stringency 3 –q 20 --paired). Trimmed reads were next aligned to the mouse reference genome (UCSC mm10/GRCm38) using Bismark v0.22.3.The bisulfite-converted genome was created using the bismark_genome_preparation utility (parameters: --genomic_composition --bowtie2). Read mapping was performed with the bismark command (parameters: --nucleotide_coverage). Duplicated alignments were removed with the deduplicate_bismark utility and methylation calling was carried out using the bismark_methylation_extractor utility (parameters: --ignore 1 --bedGraph --counts --gzip). Genome-wide cytosine methylation reports with the top and bottom strand methylation evidence pooled into a single CpG dinucleotide entity were obtained using the coverage2cytosine utility (parameters: --zero_based --gzip --merge_CpG).
Assembly: mm10/GRCm38
Supplementary files format and content: BigWig files containing whole-genome CpG methylation scores at single-base resolution.

source_name: Mouse Meso-Endoderm Cells

growth_protocol: E14 mouse WT and mutant (Dnmt3a -/-   and Dnmt3b -/-) ESCs were cultured in high-glucose DMEM (Euroclone) supplemented with 15% FBS (Millipore Corp., Billerica, MA, USA), 0.1 mmol/l nonessential amino acids (Invitrogen), 1 mmol/l sodium pyruvate (Invitrogen), 0.1 mmol/l β-mercaptoethanol, 1500 U/ml Leukemia Inhibitory Factor (LIF; Millipore), 25 U/ml penicillin, and 25 μg/ml streptomycin. For EpiSC induction, a single-cell suspension was seeded onto Geltrex (A1413202 GIBCO)-coated plates at a density of 10,000 cells cm-2 in N2B27 medium supplemented with 20ng/ml ActivinA (PHC9564 GIBCO) and 12 ng/ml bFGF (PHG0026 GIBCO). The cells were passaged 1:3 as small clumps using Collagenase IV (17104019 GIBCO). EpiSCs were collected for DNA and RNA analyses after 14 days of induction followed by daily medium changes. N2B27 medium is composed by 50% advanced DMEM/F12 (12634028 GIBCO) and 50% Neurobasal medium (21103049 GIBCO), supplemented with 0.5% N2 Supplement (17502048 GIBCO), 1% B27 Supplement (17504044 GIBCO), 0.033% BSA solution (A9647 SIGMA), 50 uM β-mercaptoethanol (M3148 Sigma), 2mM Glutamax (35050038 GIBCO), 100U/ml penicillin and 100 ug/ml streptomycin (DE17-602E LONZA).

extract_protocol:
Genomic DNA was extracted from cells using the DNeasy Blood and Tissue kit (QIAGEN, 69506) following the manufacturer’s instructions.
The whole-genome bisulfite-seq library was prepared starting from 5 μg of sonicated genomic DNA for 2 runs of 10 cycles [30 sec ‘‘ON’’, 30 sec ‘‘OFF’’]. In order to obtain 200 nt fragments. Sonicated DNA was then end-repaired twice, dA-tailed, and ligated to adapters, using the Illumina TruSeq DNA Sample Prep Kit, following manufacturer’s instructions. Adapter-ligated DNA was loaded on an EGel Size select 2% agarose pre-cast gel (Invitrogen), and a fraction corresponding to fragments ranging from 25 0bp to 350bp was recovered. Purified DNA was then subjected to bisulfite conversion using the EpiTect Bisulfite Kit (QIAGEN) following the manufacturer’s instruction except for the double desulfonation after the conversion. Bisulfite-converted DNA was finally enriched by 15 cycles of PCR using Pfu Turbo Cx. HotStart Taq (Agilent). Libraries were sequenced on Illumina Novaseq 6000 System.

value: EpiLC-derived ME

value: Wild type (WT)

tag: clone

tag: Stage


title: 210_C6_EB_3D_3B_SC_Batch1

data_processing:
Following quality controls (performed with FastQC v0.11.2 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc)), sequencing reads were processed with Trim Galore! v0.5.0 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) to perform quality and adapter trimming (parameters: --stringency 3 –q 20). Trimmed reads were next aligned to the mouse reference genome (mm10/GRCm38.p6) using STAR v2.7.1a with options: --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.04. Gene expression levels were quantified with featureCounts v1.6.1 (options: -t exon -g gene_name) using the GENCODE Release M23 annotation. Multi-mapped reads were excluded from quantification.
Genome_build: mm10/GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited text file of raw read counts matrix per gene/cell.

extract_protocol:
Full length single cell RNA-seq was performed using a modified version of the Smart-seq2 protocol.
Briefly, individual cells are sorted into 96 well plates containing lysis buffer in presence of RNase inhibitor, dNTPs and OligodT. Reverse transcription of the polyadenylated RNA will be performed with SuperScriptII and Template Switching Oligos. The resulting cDNA will be amplified with 25 cycles of PCR and libraries will be prepared for sequencing with standard NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 System (single-end 75bp reads), reaching a median of ~ 578,000 generated reads per cell.


title: Cre- pMBMEC, IL-1beta, rep2

description: Column name in tab-delimited matrix: CRE-Il-1b2

tag: tissue

tag: cell line


title: 210_D12_EB_3D_3A_SC_Batch2

tag: batch


title: Naive_ESC_WT_H3K27a_rep1

description: CUT&TAG


title: Formative_ESC_MLL3CD_MLL4CD_rep1

description: 3'end capture

tag: treatment


title: GS-6/7a_N1_primary_tumor (CGH068_PCA)

description:
macrodissected FFPE sample
CGH068_PCA


title: GS-9/10_N1_lymph_node_met (CGH073_LK)

description:
macrodissected FFPE sample
CGH073_LK


title: 210_C9_EB_3D_3A_SC_Batch2


title: 210_C5_EB_3D_3B_SC_Batch1


title: GS-6/7a_N1_lymph_node_met (CGH068_LK)

description:
macrodissected FFPE sample
CGH068_LK


title: Formative_ESC_MLL3CD_MLL4CD_rep3

description: 3'end capture


title: 210_D11_EB_3D_3A_SC_Batch2


title: GS-6/7a_N1_primary_tumor (CGH015_PCA)

description:
macrodissected FFPE sample
CGH015_PCA


title: GS-9/10_N1_primary_tumor (CGH073_PCA)

description:
macrodissected FFPE sample
CGH073_PCA


title: 210_C4_EB_3D_3B_SC_Batch1


title: Naive_ESC_WT_ATAC_rep1


title: 210_C8_EB_3D_3B_SC_Batch1


title: GS-6/7a_N1_primary_tumor (CGH007_PCA)

description:
macrodissected FFPE sample
CGH007_PCA


title: GS-6/7a_N0_primary_tumor (CGH090_PCA)

description:
macrodissected FFPE sample
CGH090_PCA


title: Formative_ESC_MLL3KO_MLL4KO_rep1

description: 3'end capture


title: 210_C3_EB_3D_3B_SC_Batch1


title: WGBS_ME24h_B77_Rep1


title: Formative_ESC_WT_rep2

description: 3'end capture


title: GS-6/7a_N1_lymph_node_met (CGH007_LK)

description:
macrodissected FFPE sample
CGH007_LK


title: Formative_ESC_MLL3KO_MLL4KO_rep3

description: 3'end capture


title: 210_C1_EB_3D_3B_SC_Batch1


title: Formative_ESC_MLL3KO_MLL4fl_rep2

description: 3'end capture


title: GS-9/10_N1_primary_tumor (CGH089_PCA)

description:
macrodissected FFPE sample
CGH089_PCA


title: WGBS_ME48h_B126_Rep1


title: 210_C2_EB_3D_3B_SC_Batch1


title: GS-6/7a_N1_primary_tumor (CGH067_PCA)

description:
macrodissected FFPE sample
CGH067_PCA


title: 210_C7_EB_3D_3B_SC_Batch1


title: WGBS_ME24h_WT_Rep2


title: WGBS_ME48h_WT_Rep1


title: GS-6/7a_N1_lymph_node_met (CGH067_LK)

description:
macrodissected FFPE sample
CGH067_LK


title: Formative_ESC_WT_rep3

description: 3'end capture


title: WGBS_ME48h_WT_Rep2


title: WGBS_ME24h_B126_Rep1


title: GS-9/10_N1_lymph_node_met (CGH089_LK)

description:
macrodissected FFPE sample
CGH089_LK


title: WGBS_ME24h_WT_Rep1


title: Formative_ESC_MLL3KO_MLL4fl_rep1

description: 3'end capture


title: Formative_ESC_MLL3KO_MLL4fl_rep3

description: 3'end capture


title: Sample 6_Lung_HFD_Tie1Tie2Ctrl

data_processing:
The Cell Ranger  mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10
We used the Seurat R package (v3.1) for QC, filtering and analysis of the data (Butler et al. Nature Biotechnology 2018)
Cells were filtered based on the number of genes and the percentage of mitochondrial genes.
For further analysis, Seurat R package was used.
Genome_build: mm10
Supplementary_files_format_and_content: barcode, features, and matrix

growth_protocol: In general, all mice are fed with regular chow diet until the age of 22 weeks (or 26 weeks, as detailed in treatment protocol). At this age of the mice the diet is changed with the high-fat (western) diet for 4 or 20 weeks, as detailed in the treatment protocol.

extract_protocol:
The aortas were harvested in PBS and their surrounding adipose tissues were removed. The aortas were then minced into pieces and digested in DPBS containing 1 mg/ml collagenases Type I (Gibco #17100-017), II (Gibco #17101-015) and IV (Gibco #17104-019) each for 30 minutes at 37oC water bath with mild mixing for a few times during the digestion. After the digestion, the cell suspension was filtered through a 70 μm cell strainer. The red blood cells were lysed with ACK Lysing buffer (Gibco # A10492-01) according to the instructions. Left lobes of the lungs were minced using scissors in a mixture of 0.5 mg/mL Collagenase H (Roche), 0.5 U/mL of Dispase II (Sigma), 1 U/mL DNase I (Thermo Scientific) and 1% (w/v) BSA (Biowest) in 4 mL of phosphate buffered saline (PBS) and incubated at 37ºC with constant agitation for 20 minutes. The slurry was then passed through a 70 µm nylon cell strainer (Corning) and the reaction was stopped with 10 mL of 10% heat-inactivated FBS in FACS-buffer (1% heat-inactivated FBS, 2 mM EDTA in PBS). Red blood cells were lysed by adding 1 mL of Red Blood Cell Lysis buffer (Sigma-Aldrich). The cells were incubated with Fc-blocker, as above, and the alive CD31+DAPI- cells were sorted using a BD Influx flow cytometer in single cell 1 drop setup with a 100 µm nozzle. After the FACS step,  lung ECs were resuspended in PBS containing 0.05% of 0.2 µm filter sterile BSA. Total bone marrow cells were isolated from both (left and right) femur of a mouse by flashing with the FACS buffer (PBS, supllemented with 0.05% BSA).
We used the Chromium Single-Cell 3′RNA-sequencing system (10x Genomics, Pleasanton, CA) with the Reagent Kit v3.1 according to the manufacturer’s instructions.
Sample libraries were sequenced on the Illumina NovaSeq 6000 system using S2 flow cell (Illumina)

treatment_protocol:
For sample 1-4, mice received tamoxifen via gavage at 10 weeks old. Pcsk9-AAV and HFD were started at 26 weeks of age for a total of 4 weeks.
For samples 5-6, mice received tamoxifen via gavage at 10 weeks old. Pcsk9-AAV and HFD were started at 22 weeks of age for a total of 20 weeks.

value: Lung


title: Sample 5_Lung_HFD_Tie1Tie2DCKO


title: 210_C12_EB_3D_3A_SC_Batch2

value: Embryoid Bodies (EB)


title: GS-6/7a_N1_primary_tumor (CGH066_PCA)

description:
macrodissected FFPE sample
CGH066_PCA


title: Naive_ESC_MLL3CD_MLL4CD_rep2

description: 3'end capture


title: 210_C10_EB_3D_3A_SC_Batch2


title: Naive_ESC_MLL3CD_MLL4CD_rep3

description: 3'end capture


title: 210_B9_EB_3D_3A_SC_Batch2


title: Naive_ESC_MLL3KO_MLL4KO_rep3

description: 3'end capture


title: 210_C11_EB_3D_3A_SC_Batch2


title: GS-9/10_N1_lymph_node_met (CGH059_LK)

description:
macrodissected FFPE sample
CGH059_LK


title: 210_B6_EB_3D_3B_SC_Batch1


title: Naive_ESC_MLL3KO_MLL4KO_rep1

description: 3'end capture


title: Naive_ESC_MLL3KO_MLL4KO_rep2

description: 3'end capture


title: GS-6/7a_N1_primary_tumor (CGH005_PCA)

description:
macrodissected FFPE sample
CGH005_PCA


title: Formative_ESC_WT_rep1

description: 3'end capture


title: Sample 4_BM_HFD_Tie2Ctrl

value: Bone Marrow


title: Naive_ESC_MLL3CD_MLL4CD_rep1

description: 3'end capture


title: 210_B8_EB_3D_3B_SC_Batch1


title: GS-9/10_N1_primary_tumor (CGH059_PCA)

description:
macrodissected FFPE sample
CGH059_PCA


title: GS-6/7a_N1_lymph_node_met (CGH005_LK)

description:
macrodissected FFPE sample
CGH005_LK


title: 210_B4_EB_3D_3B_SC_Batch1


title: 210_B7_EB_3D_3B_SC_Batch1


title: Sample 1_Aorta_HFD_Tie2CKO

value: Aorta


title: Sample 3_BM_HFD_Tie2CKO


title: GS-6/7a_N1_lymph_node_met (CGH066_LK)

description:
macrodissected FFPE sample
CGH066_LK


title: GS-9/10_N1_primary_tumor (CGH087_PCA)

description:
macrodissected FFPE sample
CGH087_PCA


title: Naive_ESC_MLL3KO_MLL4fl_rep2

description: 3'end capture


title: Naive_ESC_MLL3KO_MLL4fl_rep3

description: 3'end capture