title: fy-5 KO 3


title: CD57- CD4+ TEM_rep 3

status: Public on Apr 27 2023

type: SRA

city: Acton

first: Zhi-Ping

last: Feng

state: ACT

address:
131 Garran Road, John Curtin School Of Medical Research Building (Level 3, Stage 1)
, The Australian National University

country: Australia

institute: JCSMR

library_source: transcriptomic

data_processing:
The RNA sequencing data of all 12 samples were assessed by FastQC, and aligned to human genome GRCh38 using HISAT2 (version 2.1.0) and sorted with SAMtools, and mapped reads were assigned and counted based on gene annotations by FeatureCount.
Lowly expressed genes were excluded for the downstream analysis, the genes with at least 0.5 count per million reads in more than 3 samples were selected.
Counts were normalized by trimmed mean of M values (TMM) method and transformed by voom with sample quality adjustment, then the data was fitted in a linear model and moderated t-statistics with empirical Bayes method, and the different expression genes were determined by Benjamini-Hochberg adjusted P value < 0.05, and visualized with glimma.
Supplementary_files_format_and_content: text format of raw exon level count for all samples

molecule: total RNA

organism: Homo sapiens

source_name: PBMCs

growth_protocol: No growth protocol. Fresh FACS-isolated cells from PBMCs of healthy donors

extract_protocol:
Different indicated T cell subsets are FACS-purified from PBMCs of three healthy donors with >95% purity. Cells are immediated submmited to GenElute Total RNA isolation kit (Sigma) for total RNA extraction according to the instruction, and the quality and integrity of RNA samples are validated by Bioanalyzer (Agilent) with RIN values > 8.0.
The mRNA library is prepared by ACRF Biomolecular Resource Facility at ANU using Illumina TruSeq Stranded mRNA Library Prep kit and sequenced in one high-output flow cell with 75 bp single-end reads by NextSeq500 sequencer (Illumina), each sample was covered with at least 25 million reads.

treatment_protocol: No treatment protocol. Fresh FACS-isolated cells from PBMCs of healthy donors

tag: marker

value: Viability Dye eFluo 780- CD4+ CD8- CD57- CD45RA- CCR7-

tag: sample type


title: fy-4 KO 2

city: Dresden

first: Scientific Computing

last: Facility

address: Pfotenhauerstrasse 108

country: Germany

institute: MPI-CBG

data_processing:
Basecalling was performed with bcl2fastq
Reads were mapped using STAR v2.7.3a (--outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 3 1 1 1)
Abundance estimation was performed with STAR v2.7.3a (--quantMode GeneCounts)
Assembly: GRCh38.p10, Ensembl_v88
Supplementary files format and content: Raw counts

source_name: HeLa Kyoto

growth_protocol: Adherent grown HeLa cells were allowed to reach 1-2 million cells

extract_protocol:
RNA was extracted using the RNeasy MinElute Cleanup Kit (Qiagen) according to the manufacterers protocol
mRNA was treated using the NEBNext rRNA depletion Kit (human, mouse, rat) from New England Biolabs (NEB) according to the manufacturer’s instructions to remove ribosomal RNA. Subsequently, the samples were subjected to the workflow for strand specific RNA-Seq library preparation (NEBNext Ultra II Directional RNA Library Prep, NEB).

treatment_protocol: After detachment cells were pelleted by centrifugation (2000 x g, 5 min, 4 °C), washed twice with PBS and lysed by adding Trizol reagent

tag: cell line

value: HeLa Kyoto

tag: genotype

value: fy-4 knock-out


title: MGD1567B

city: Los Angeles

first: Valerie

last: Arboleda

address: 615 Charles E. Young Drive South

country: USA

institute: UCLA

data_processing:
Arboleda Lab Pipeline
Samples were demultiplexed after sequencing.
Raw reads were then aligned against the Gencode human genome version hg38 (GR38) version 31 using STAR 2.7.0e with default parameters.
Gene counts from raw reads were generated using featureCounts 1.6.5 from the Subread package. Only reads that uniquely mapped to exons of a gene were counted per gene. Differential expression analysis was completed using DESeq2 v1.24.0, adjusting for sample gender.
Assembly: GR38
Supplementary files format and content: Text files include raw count values for each sample, csv files include DESeq normalized counts per sample

source_name: Patient-Derived

extract_protocol:
Whole blood samples were collected and purified using MagMAX for Stabilized Blood Tubes RNA Isolation Kit (Qiagen, #3341894) with DNase treatment. 1ug of total RNA was used to construct libraries.
RNA libraries for RNA-seq were prepared using QIAseq FastSelect −rRNA HMR (Qiagen, #334386) and lllumina Truseq® Stranded Total RNA Library Prep Gold (Illumina, 20020599)

value: Patient-Derived

tag: cell type

value: Whole Blood


title: RNAseq E10.5 PA2 wt  3

city: Basel

first: Filippo

middle: M.

last: RIJLI

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

data_processing:
HiSeq 2500: Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
NovaSeq 6000: Illumina RTA 3.4.4 and bcl2fastq2 v2.20 was used for basecalling and demultiplexing.
Reads of single-end and paired-end datasets were aligned to the reference genome using the QuasR Bioconductor package (REF: PMID: 25417205, version 1.34.0) by the qAlign function with parameters aligner="Rhisat2" (REF: PMID: 25751142, version 1.12.0) and splicedAlignment=TRUE.
Alignments overlapping genes from the TxDb.Mmusculus.UCSC.mm10.knownGene Bioconductor package (https://doi.org/doi:10.18129/B9.bioc.TxDb.Mmusculus.UCSC.mm10.knownGene, version 3.4.7) were quantified using the qCount function from the QuasR Bioconductor package (REF: PMID: 25417205, version 1.34.0) with parameter orientation = "opposite".
Assembly: mm10/ GRCm38
Supplementary files format and content: Comma-seperated text files with gene annotation (ENTREZID, number of exonic bases, ENSEMBL gene ID, gene symbol) and raw alignment counts for each gene and sample.

organism: Mus musculus

source_name: Cranial neural crest cells

extract_protocol:
Embryonic tissues were micro-dissected at E10.5, E12.5 or E14.5. Dissected tissue from E10.5 and E12.5 embryos was kept in 1× PBS on ice, then treated with 0.5% trypsin/1× EDTA at 37 °C for 10 minutes and immediately put on ice. Dissected tissue from E14.5 embryos was kept in 1× PBS on ice, then treated with papain digestion mix (10 mg ml−1 papain, 2.5 mM cysteine, 10 mM HEPES (pH 7.4), 0.5 mM EDTA and 0.9× DMEM) for 7 min at 37 °C and immediately put on ice. The tissue was rinsed once in ice-cold 1× DMEM/10% FBS, followed by two washes in ice-cold 1× DMEM. Tissue was dissociated by pipetting. Cranial NCCs from embryos with genotype Wnt1::Cre;ROSARFP were filtered and collected by FACS. After sorting, cranial NCCs were pelleted by centrifugation for 5 minutes, 1000 rpm at 4°C. Total RNA was extracted using the Single Cell RNA Purification Kit (NORGEN, 51800) with genomic DNA digestion using an RNase-Free DNase I Kit (NORGEN, 25710) according to the manufacturers’ protocol. For each sample, three independent biological replicates were prepared.  For sequencing of total RNA, unstranded RNA-Seq libraries were prepared using Illumina TruSeq RNA Library Prep Kit v2 according to manufacturers’ instructions. Sequencing was performed on an Illumina HiSeq 2500 machine (50 bp read length, single-end)  or an Illumina NovaSeq machine (50bp read length, paired-end).
IlluminaTruSeqTotalRNA

value: Cranial neural crest cells

tag: location

tag: developmental stage

value: WT


title: L28BME rep3

city: Lund

first: Mohamed

last: Eldeeb

address: DMH, BMC B12

country: Sweden

institute: Lund University

data_processing:
Analysis was carried out using CLC Genomics Workbench (version 20.0.2) and CLC Genomics Server (version 20.0.2).
Assembly: GRCm38

source_name: Bone marrow

extract_protocol:
GMLPs were sorted from ME or L28BME mice and cultured for 3 days in the presence of DOX. Total RNA was isolated using the Single Cell RNA Purification Kit (Norgen Biotek).
Library preparation was performed using QIAseq miRNA Library Prep kit.

tag: tissue

value: Bone marrow

value: GMLP

value: LIN28B MLL-ENL

tag: treatment

value: In vitro culture with DOX


title: fy-4 KO 3


title: RNAseq E10.5 PA3 wt  1


title: CD57+ CD4+ TEM_rep 1

value: Viability Dye eFluo 780- CD4+ CD8- CD57+ CD45RA- CCR7-

value: Fresh FACS-isolated cells from PBMCs of healthy donors


title: L28BME rep2


title: MGD1613B


title: CD57+ CD4+ TEM_rep 2


title: RNAseq E10.5 PA3 delta-E3  2


title: CD57+ CD4+ TEMRA_rep 3

value: Viability Dye eFluo 780- CD4+ CD8- CD57+ CD45RA+ CCR7-


title: RNAseq E10.5 PA3 wt  3


title: CD57+ CD4+ TEMRA_rep 1


title: RNAseq E10.5 PA3 wt  2


title: ME rep3

value: MLL-ENL


title: fy-2 KO 3

value: fy-2 knock-out


title: RNAseq E14.5-Pinna  3

value: Pinna


title: fy-2 KO 2


title: RNAseq E14.5-Pinna  2


title: fy-2 KO 1


title: RNAseq E10.5 PA2 wt  1


title: RNAseq E12.5-Pinna  3


title: ME rep1


title: fy-1 KO 3

value: fy-1 knock-out


title: RNAseq E12.5-Pinna  1


title: L28BME rep1


title: RNAseq E12.5-Pinna  2


title: RNAseq E10.5-PA2  3


title: fy-1 KO 2

value: HeLa Kyoto


title: RNAseq E14.5-Pinna  1


title: fy-4 KO 1

value: fy-4 knock-out


title: wt 3

value: wildtype


title: ME rep2


title: siSRSF3, n=2

city: Suwon

first: Su Bin

last: Lim

state: Gyeonggi-do

address: Worldcup-Ro 164, Yeongtong-Gu

country: South Korea

institute: Ajou University School of Medicine

description: Sample 4

data_processing:
Altanalyze 2.1.4.4
Assembly: Human genome in Ensembl (version EnsMart72)
Supplementary files format and content: exp.NC_SR3_SR7.txt: Tab-delimited text file includes gene-level expression values (RPKMs) for mRNAs for all samples.
Supplementary files format and content: transcript.NC_SR3_SR7.txt: Tab-delimited text file includes transcript-level expression values (TPMs) for mRNAs for all samples.

source_name: Human diploid fibroblast

extract_protocol:
Total RNA from human diploid fibroblasts was extracted using NucleoSpin RNA Plus kit (MACHEREY-NAGEL).
RNA libraries were prepared using TruSeq Stranded Total RNA Kit with Ribo-Zero Gold.

value: Human diploid fibroblast

value: SRSF3 KD

tag: replicate

value: biol rep 2


title: siSRSF7, n=1

description: Sample 5

value: SRSF7 KD

value: biol rep 1


title: siSRSF3, n=1

description: Sample 3


title: siSRSF7, n=2

description: Sample 6


title: wt 2


title: RNAseq E10.5-PA2  2

value: Cranial neural crest cells

value: WT


title: siNC, n=2

description: Sample 2

value: negative control


title: RNAseq E10.5-PA2  1


title: RNAseq E10.5 PA2 wt  2


title: wt 1


title: CTCF, E10.5, PA2

library_source: genomic

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Reads were mapped to the reference genome using bowtie2 with default settings (version 2.4.2) and converted to bam files using samtools (version 1.2)
BigWig files containing the number of alignments per 100bp window in the genome and per million alignments in each sample were calculated using the qExportWig function from the QuasR Bioconductor package (version 1.34.0)
Assembly: mm10/ GRCm38
Supplementary files format and content: bigWig

molecule: genomic DNA

extract_protocol:
Embryonic tissues were micro-dissected at E10.5, E12.5 or E14.5. Dissected tissue from E10.5 and E12.5 embryos was kept in 1× PBS on ice, then treated with 0.5% trypsin/1× EDTA at 37 °C for 10 minutes and immediately put on ice. Dissected tissue from E14.5 embryos was kept in 1× PBS on ice, then treated with papain digestion mix (10 mg ml−1 papain, 2.5 mM cysteine, 10 mM HEPES (pH 7.4), 0.5 mM EDTA and 0.9× DMEM) for 7 min at 37 °C and immediately put on ice. The tissue was rinsed once in ice-cold 1× DMEM/10% FBS, followed by two washes in ice-cold 1× DMEM. Tissue was dissociated by pipetting. Then the dissociated cells were cross-linked with 1% formaldehyde for 10 min at room temperature (RT) and quenched with 125 mM glycine for 5 min at RT. Cells were spun down (1600 rpm, 10 minutes, 4 °C). Cranial NCCs with genotype Wnt1::Cre;ROSARFP were filtered and collected by FACS.
NEBNextUltra for Illumina

tag: chip antibody

value: CTCF (Cell Signaling, CST 2899)


title: fy-1 KO 1


title: siNC, n=1

description: Sample 1


title: H3K4me2, rep2, wt, E14.5, Pinna

value: H3K4me2 (Millipore, Cat. #07-030)


title: CTCF, E10.5, Md

value: Md


title: H3K27ac, rep2, wt, E14.5, Pinna

value: H3K27ac (abcam, ab4729)


title: H3K4me2, wt, E14.5, Pinna

value: Pinna


title: Primary tumor from case 11

city: Sendai

first: Tomohiko

last: Ishikawa

state: Miyagi

address: 1-1 Seiryo-machi, Aoba-ku

department: Otolaryngology - Head and Neck Surgery

country: Japan

institute: Tohoku University Graduate School of Medicine

data_processing:
HISAT2
StringTie
Assembly: hg19
Supplementary files format and content: A spreadsheet file (xlsx) include FPKM and TPM values and Read count for each Sample

source_name: Tumor

growth_protocol: Surgically resected primary tumor tissues are collected into media immediately after resection. Collected tumors are brought to our LAB on ice, some of them were frozen into OCT compound and other were cultured. After confirming the tissue is composed of tumor cells through histological examination, we isolated RNA from the frozen tissue. For cell culture, the tumor tissues were washed and digested with enzymes, and then pelleted. The pelleted tissues were devided into 2 tubes and one was applied for orgnoid culture and the other was applied for monolayer culture. The culture cells were passaged every 7-21 days. When  the culture cells successfully expanded, they were collected and isolated RNA.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).0.5-1.0µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA LT Sample Prep Kit Gold (Illumina) following manufacturer's protocols.

treatment_protocol: No treatment

value: Tumor


title: H3K27ac, wt, E14.5, Pinna


title: Organoid culture cells from case 11

source_name: Organoid culture cells

value: Organoid culture cells


title: H3K27me3, rep2, wt, E12.5, Pinna

value: H3K27me3 (Millipore, Cat. # 07-449)


title: MS_MGD1549

data_processing:
Quality of reads were assessed using FastQC.
Raw reads were then aligned to GENCODE Human genome version hg38 (GR38) version 31 using BWA-MEM.
BAM files were then sorted, indexed, filtered against chrX, chrY, and MT reads using SAMtools. Picard tools were then used to generate insert size histograms and remove duplicates from BAM files.
Narrow peaks from each sample were called using MACS2 callpeak; any peak that overlapped by at least one base was then merged using BEDtools merge. Reads overlapping merged peaks were counted using featureCounts.
Reads overlapping merged peaks were counted using featureCounts. Peaks were annotated using annotatePeaks.pl from HOMER to the nearest gene or regulatory element, including exon, intron, promoter, 5’ untranslated region (UTR), 3’ UTR, and other genomic features.
DESeq2 was used to identify differentially open peaks between disease and control samples, adjusting for sample gender. Peaks with p-adjusted value (Benjamini-Hochberg) less than 0.05 were classified as significantly differentially open (Wald’s test), and fold changes were shrunk using approximate posterior estimation for GLM coefficients.
Assembly: GR38
Supplementary files format and content: Text files include raw peak count values for each sample, csv files include DESeq normalized peak counts per sample

growth_protocol: Patient- derived fibroblast cell lines were grown in DMEM (Gibco™, #11-995-073), 10% FBS, 1% Non-essential Amino Acid (100X, Gibco™, 11140-050) and 1% PenStrep at 37℃ in 5% CO2 incubators.

extract_protocol:
50,000 freshly isolated cells per line were treated with Tn5 transposase.
ATAC-seq libraries were prepared according to established protocol (Corces, 2017). 50,000 freshly isoated cells per fibroblast line was used as input. After purification and PCR amplification for library generation, the libraries were double-sided bead purified using AMPure XP beads (Beckman, A63881) to remove contaminating primer dimers. All libraries were quantified on the Qubit 4.0 and library quality was assessed using Agilent High Sensitivity DNA Tapestation (Agilent, 5067-5584) before multiplexing and sequencing on a Nextseq 550 for Libraries  to a minimum of 40 million paired-end reads per sample with 75bp length.

value: Patient-Derived

value: Fibroblast

value: Control


title: Monolayer culture cells from case 11

source_name: Monolayer culture cells

value: Monolayer culture cells


title: Primary tumor from case 6


title: H3K27me3, wt, E12.5, Pinna


title: H3K4me2, rep2, wt, E12.5, Pinna


title: Organoid culture cells from case 6


title: H3K4me2, wt, E12.5, Pinna


title: Caki-1_siINSR-1

type: RNA

city: Tokushima city

first: Kei

last: Daizumoto

address: 3-18-15, Kuramoto-cho

institute: Tokushima University Graduate School of Biomedical Sciences.

description: Caki-1 cell line was co-cultured with human renal glomerular endothelial cells (HGECs) treated with si-RNA of INSR (HGEC-siINSR). Gene expression alteration was analyzed using microarray.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >20.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE v3 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent, 5190-2305) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seventy-two hours after transfection, HGECs were seeded into 6-well ThinCert™ cell culture inserts, and 2.5 ml of Caki-1 cell suspension containing 8x104 cells/ml in CS-C Complete Medium was placed into a 6-well plate. The inserts were placed in each well of the 6-well plate, and co-cultures were maintained for 24 h.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (G2938C, Agilent Technologies, Santa Clara, CA).

treatment_protocol: 786-O cell line and Caki-1 cell line were co-cultured with HGECs with down-regulated INSR. Small interfering RNA oligonucleotides were used to knock down INSR in HGEC. Non-silencing RNA duplex was used as a negative control. Transfection with 10 nM of small interfering RNA of INSR to HGECs was performed using Lipofectamine RNAiMAX (Thermo Fisher Scientific) with the forward transfection method.

value: Human RCC cell

value: HGECs with down-regulated INSR


title: Monolayer culture cells from case 6


title: H3K27me3, rep2, wt, E14.5, Pinna

value: Cranial neural crest cells


title: H3K27ac, rep2, wt, E12.5_Pinna

value: WT


title: H3K27me3, wt, E14.5, Pinna


title: Caki-1_siCont-1

description: Caki-1 cell line was co-cultured with human renal glomerular endothelial cells (HGECs) treated with Non-silencing RNA duplex. Gene expression alteration was analyzed using microarray.

value: Non-silencing RNA duplex was used as a negative control in HGEC

value: Control HGECs


title: Caki-1_siCont-2


title: Caki-1_siINSR-2

value: Small interfering RNA oligonucleotides were used to knock down INSR in HGEC


title: H3K27ac, wt, E12.5, Pinna


title: 786-O_siINSR-2

description: 786-O cell line was co-cultured with human renal glomerular endothelial cells (HGECs) treated with si-RNA of INSR (HGEC-siINSR). Gene expression alteration was analyzed using microarray.


title: AML single-cell_multiplexed_feature_1

city: Houston

first: Pavel

last: Sumazin

state: TX

address: 1102 Bates St

department: Pediatric

institute: Baylor College of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The barcoded processing, antibody hashing, dehashing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) and CITE-seq-Count program by Immunai Company.
Assembly: hg19
Supplementary files format and content: A Seurat object as a .RDS file format provided which includes cell count data plus sample-timepoint annotation and cluster IDs.

source_name: marrow

extract_protocol:
Single-cell samples were submitted to the Immunai Company immediately after preparation for 10x chromium Single Cell RNA sequensing.
Single-cell gene expression libraries were prepared according to the Chromium NextGEM Single Cell Gene Expression 3v3.1 kit (10x Genomics). Briefly, single cells, reverse transcription reagents, gel beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMs (Gel Bead-In-Emulsion). Full-length cDNA was synthesized and barcoded within each GEM. Subsequently, GEMs were broken, and cDNA was pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA was amplified by PCR. The amplified product was fragmented prior to end-repair, A-tailing, and adaptor ligation.
Final libraries were generated by amplification. Sequencing of single-cell libraries was performed by the Immuni company. To reach an estimated 20K reads per cell, samples were sequenced at a depth of 200M reads on the NovaSeq 6000 platform (Illumina).

value: marrow

tag: Sex

value: pooled male and female

tag: diagnosis

value: pediatric AML

tag: timepoint

value: multiplexed sample:Diagnosis or relapse


title: Epithelial_BulkATAC_K4_3

city: New York City

first: Cassandra

last: Burdziak

state: New York

address: 417 E 68th St

institute: Memorial Sloan Kettering Cancer Center

description: 10x Genomics (3' kit, v2.0)

data_processing:
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences using trimgalore
Reads were aligned to mouse assembly mm9 using bowtie2 (v2.2.2) with default parameters.
Read count tables were created using featureCounts v1.6.0.
To create density files, the signal was normalised using the scalefactors from DESeq2 converted to BigWig using BEDTools.
Assembly: mm9

source_name: pancreas

growth_protocol: When indicated, 5 weeks-old KC;RIK (p48-Cre;RIK;LSLKrasG12D) littermate male mice were treated with 8 hourly intraperitoneal injections of 80 μg/kg caerulein (Bachem) for 2 consecutive days.

extract_protocol:
Lysis Buffer 10mM Tris·Cl, pH 7.4; 10mM NaCl; 3mM MgCl2; 0.1% (v/v) Igepal CA-630 (Buenrostro et al., 2015 protocol)
Buenrostro et al., 2015 protocol

treatment_protocol: Pancretata were harvested from the indicated mouse models and processed for FACS sorting using Collagenase (1 mg/mL) & Dispase (2 U/mL) mix digestion solution and Gentle-MACS dissociator (mTDK_1 protocol), followed by a 0.05% Trypsin-EDTA step. Cell suspensions were incubated with Fc block and CD45-APC or CD45-APC-Cy7 antibody to mark immune cells. Live pancreatic epithelial cells (marked as mKate2-positive, CD45-negative and DAPI-negative) were sorted using Aria3 sorter, and collected in 2% 1x PBS buffer containing 2% fetal bovine serum (FBS).

value: sorted primary pancreatic epithelial cells (mKate2+)

value: pancreas

tag: condition

tag: model

value: KC;RIK-shBrd4.552(Off Dox)

tag: alleles

value: KC-GEMM-ESC derived from p48-9C ESCs (Saborowski et al., PNAS, 2013) targeted with the TRE-GFP-shRNA against Brd4 (sh552) - OFF DOX

tag: sorting strategy

tag: time point_(analyses)

value: 41 weeks old

value: Male


title: AML single-cell_multiplexed_feature_2

description: 10x Genomics


title: AML single-cell_multiplexed_GEX_2

description: 10x Genomics


title: LT.046.P.FFPE

city: St. Louis

first: Emilee

middle: N

last: Kotnik

state: MO

address: 660 S. Euclid Ave

department: Center for Reproductive Health Sciences

institute: Washington University in St. Louis

data_processing:
Transcript read counts were obtained using Kallisto version: v0.43.1 and gene-level read counts were calculated using GRCh37 in Ensembl
Quality control and normalization of the raw count data were performed using the R/Bioconductor package edgeR version 3.28
Normalization factors were calculated using the Trimmed Mean of M-values (TMM) normalization method in edgeR to account for compositional biases in libraries between each pair of samples.
Assembly: GRCh37
Supplementary files format and content: Gene Abundance files generated using KALLISTO

source_name: tumor omentum

extract_protocol:
RNA was extracted FFPE or FF tumors with Qiagen RNeasy Kit
Illumnia TruSeq Stranded Total RNA library kit according to manufactuers protocol

value: tumor omentum

value: female

value: Priamry ovarian tumor cells

tag: age at_diagnosis

tag: figo stage

value: IIIC

tag: tumor histology

value: High Grade Serous


title: LT.046.M.FFPE

source_name: ovary tumor

value: ovary tumor

tag: cell type

value: Metastatic ovarian tumor cells


title: 786-O_siINSR-1

tag: cell line

value: Human RCC cell

value: Small interfering RNA oligonucleotides were used to knock down INSR in HGEC

tag: genotype

value: HGECs with down-regulated INSR


title: Epithelial_BulkATAC_K4_2

description: 10x Genomics (3' kit, v2.0)

tag: tissue

tag: treatment


title: Epithelial_BulkATAC_K4_1

description: 10x Genomics (3' kit, v2.0)

value: KC;RIK


title: LT.045.M.FFPE


title: 786-O_siCont-2

description: 786-O cell line was co-cultured with human renal glomerular endothelial cells (HGECs) treated with Non-silencing RNA duplex. Gene expression alteration was analyzed using microarray.

value: Non-silencing RNA duplex was used as a negative control in HGEC

value: Control HGECs


title: Epithelial_BulkATAC_K3_3

description: 10x Genomics (3' kit, v2.0)

value: sorted primary pancreatic epithelial cells (mKate2+)

value: pancreas

value: Caerulein / Week 3

value: 8-9 weeks old


title: LT.044.P.FFPE

value: tumor omentum


title: 786-O_siCont-1


title: LT.044.M.FFPE

value: female


title: Epithelial_BulkATAC_K3_1

description: 10x Genomics (3' kit, v2.0)

value: Male


title: LT.043.P.FFPE

value: Priamry ovarian tumor cells

value: IIIC


title: LT.043.M.FFPE

value: ovary tumor

value: High Grade Serous


title: LT.042.P.FFPE


title: AML single-cell_multiplexed_GEX_1

description: 10x Genomics

value: marrow

value: pooled male and female

value: pediatric AML

value: multiplexed sample:Diagnosis or relapse


title: LT.045.P.FFPE


title: mouse E12 neocortex

first: Liang

last: Chen

state: CA

address: 1050 Childs Way

institute: University of Southern California

data_processing:
The libraries were mapped to mouse reference genome (GRCm38/mm10) with the Gencode annotation (Release M12)  using the STAR aligner (Dobin et al., 2013). The parameters for STAR were specified as “--outFilterType BySJout --outFilterMultimapNmax 1 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 ”.
Genome_build: GRCm38/mm10

source_name: mouse E12 neocortex

extract_protocol:
Total RNA were extracted using TRIzol reagent (Thermo Fisher Scientific) according to the manufacturer's instructions. DNase I (Thermo Fisher Scientific) was used to remove DNA contamination from RNA samples.
RINs were determined by Bioanalyzer (Agilent). RNA-seq libraries were constructed using Illumina TruSeq Stranded Total RNA LT Sample Prep kits.

tag: strain

tag: developmental stage

value: neocortex


title: PCHi-C_WT_E14.5_Pinna_1

data_processing:
Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
Capture HiC libraries are first analyzed with HiCUP (version 0.6.1) (Wingett, 2015), then significant interactions are identified using CHiCAGO (version 1.24.0) (Cairns, 2016). CHiCAGO pipeline is used with the recommended parameters for six cutter restriction enzymes (Freire-Pritchett, 2021):   minFragLen=150 and maxFragLen=40000, maxLBrownEst=1500000 and binsize=20000.
Interactions with a CHiCAGO score of 5 are considered as high-confidence interactions. Significant interactions are plotted as arcs linking baits to OE using the python api pygenometrack.
Assembly: GRCm38/mm10
Supplementary files format and content: tab separated text file containing locations of baits, other ends and Chicago interaction scores

extract_protocol:
Dissected tissue from E10.5 and E12.5 embryos was kept in 1× PBS on ice, then treated with 0.5% trypsin/1× EDTA at 37 °C for 10 minutes and immediately put on ice. Dissected tissue from E14.5 embryos was kept in 1× PBS on ice, then treated with papain digestion mix (10 mg ml−1 papain, 2.5 mM cysteine, 10 mM HEPES (pH 7.4), 0.5 mM EDTA and 0.9× DMEM) for 7 min at 37 °C and immediately put on ice. The tissue was rinsed once in ice-cold 1× DMEM/10% FBS, followed by two washes in ice-cold 1× DMEM. Tissue was dissociated by pipetting. Dissociated cells were cross-linked with 2% paraformaldehyde for 10 min at room temperature (RT) and quenched with 125 mM glycine for 5 min at RT. Cells were spun down (1600 rpm, 10 minutes, 4 °C) and resuspended in cold 1× PBS. Cranial NCCs with genotype Wnt1::Cre;ROSARFP or Hoxa2EGFP were filtered and collected by FACS. Cells were spun down (1600 rpm, 10 minutes, 4°C), supernatant removed, and cell pellets were flesh-frozen and stored at -80°C.
Promoter capture Hi-C was performed as described previously {Schoenfelder, 2018}  with adaptations to our system. The input material per PCHi-C experiment was 2.5 – 5 × 10^6 cells. Cells were incubated in 1mL ice-cold lysis buffer (10 mM Tris-HCl pH 8, 0.2% (vol/vol) NP-40, 10 mM NaCl,1× protease inhibitor cocktail (Roche)) for 30 min with periodical mixing, followed by centrifugation to pellet nuclei (760xg, 5 min., 4°C). Cell nuclei were resuspended in 358 µL  ice-cold 1.25× NEBuffer 2, 11 µL  of 10% SDS was added, and nuclei were incubated at 37°C, shaking at 950 rpm, for 1 hour. Then 75 µL of 10% Triton X-100 was added and cell nuclei incubated at 37°C, shaking at 950 rpm, for 1 hour. A 5 μL aliquot was taken as a control for undigested chromatin (stored at − 20 °C). For HindIII digestion 10 µL of HindIII enzyme (NEB, cat. no. R0104T) was added, incubated 6 hours at 37°C shaking at 950 rpm, followed by addition of another 10 µL of HindIII and overnight incubation at 37°C shaking at 950 rpm. A 5 μL aliquot was taken to test digestion efficiency (stored at − 20 °C). To fill in and biotinylate the restriction fragment overhangs 60 µL of biotinylation master mix (6 µL 10× NEBuffer 2, 2 µL H2O, 1.5 µL 10 mM dATP, 1.5 µL 10 mM dGTP, 1.5 µL 10 mM dTTP, 37.5 µL 0.4 mM biotin-14-dATP, and 10 µL 5U/μl Klenow (DNA polymerase I large fragment, NEB M0210L)) was added, incubated for 75 min at 37°C mixing regularly by pipetting, and then placed on ice. Next, 454 µL ligation master mix (100 µL 10× ligation buffer (NEB B0202), 10 µL 10 mg/mL BSA, 344 µL nuclease-free H2O) and 25 µL 1U/µL T4 DNA ligase (Invitrogen 15224-024) was added for overnight blunt end ligation in a water bath at 16°C. The next day ligated samples were incubated for a further 30 min at room temperature. The re-ligated chromatin products and test aliquots were de-cross-linked for at least 6 hours by adding 100 μL and 2.5 μL proteinase K (10 mg/mL), incubated at 65 °C. Afterwards, 12 μL or 0.5 μL of 10 mg/ml RNase A was added to the samples and test aliquots, respectively, and incubated for 60 min at 37 °C. Next, chromatin was precipitated by adding 1 volume of phenol:chloroform:isoamyl alcohol (25:24:1) (PC) to the samples and test aliquots, vigorously shaking them, followed by centrifugation at maximum speed of a table top centrifuge (~ 13,000 rpm) at room temperature for 5 min. The upper phase containing the chromatin was transferred to a new 15 mL tube. To reduce loss of DNA 1 mL of TLE buffer (10 mM Tris HCl (pH 8.0), 0.1 mM EDTA) was added to tube containing PC and residual chromatin, tube was vigorously mixed, followed by centrifugation at maximum speed of a table top centrifuge (~ 13,000 rpm) at room temperature for 5 min. The upper phase containing the chromatin was transferred to the 15 mL tube. One tenth volume of 3 M sodium acetate was added to the chromatin sample mixed by vortexing, followed by the addition of 3 volumes 100% ethanol and vortexing to mix. The samples were frozen at − 80 °C for at least 2h. The precipitated chromatin was isolated by centrifugation at maximum speed for 45 min at 4 °C. The chromatin pellet was washed twice with 2mL freshly prepared 70% ethanol and centrifuged at maximum speed for 15 min at 4 °C in between washes. Finally, the chromatin pellet was dried at room temperature and resuspended in 100 μL TLE buffer. To check the Hi-C library DNA, 1:50 dilution of the sample, and the undigested and digested controls were loaded on a 1.5% agarose gel. The DNA concentration of the Hi-C library was determined using Qubit™ dsDNA HS assay kit.For PCHi-C 10 µg DNA (split into two 5 µg aliquots) were used for library preparation. The next steps were performed per 5 µg aliquot. The DNA was sonicated using Covaris S220 (peak incidence power: 175W; duty factor: 10%; cycles per burst: 200; time: 120s) in a volume of 130 µL in a Covaris microTUBE to obtain 100 – 1000 bp long DNA fragments. End repair, dATP-tailing and Adapter ligation was performed on beads. For this, 100 µL of Dynabeads™ MyOne™ Streptavidin T1 (Invitrogen) were washed twice with 400 µL Tween Buffer (TWB; 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween 20) and resuspended in 400 µL 2× binding buffer (2×BB; 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2 M NaCl). The volume of the sonicated DNA was increased to 400 µL with TLE. DNA was mixed with washed beads (800 µL total volume) and incubated at RT for 45 min rotating at 5 rpm. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by a wash with 400 µL 1×BB, then with 100 µL 1×ligation buffer, and resuspended in 50 µL 1× ligation buffer. For end repair each aliquot was mixed on ice with 50 µL 2.5 mM dNTP mix (12.5 μL of 10 mM of each dNTP), 18 μL of  T4 DNA Polymerase (NEB M0203), 18 μL of T4 PNK (NEB M0201), 3.7 μL of DNA polymerase I large fragment (Klenow; NEB M0210), and 360.1 μL of H2O, and then incubated at 20°C for 60 min. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by two washes with 500 µL 1×TWB, one wash with 500 µL 1×BB, one wash with 500 µL TLE and resuspended in 415 µL TLE. For dATP-tailing each aliquot was mixed with 50 µL 10× NEBuffer 2, 5 µL 10 mM dATG and 20 µL 5 U/µL Klenow exo-minus, and then incubated at 37°C for 30 min. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by two washes with 500 µL 1×TWB, one wash with 500 µL 1×BB, one wash with 200 µL 1× ligation buffer and resuspended in 100 µL 1× ligation buffer. For PCHi-C adaptor ligation 4 µL 15 µM pre-annealed PE adapters (described in Schoenfelder et al., 2018) and 4 µL NEB T4 Ligase 400 U/mL (NEB, M0202) were added to each aliquot and incubated 2 h at room temperature. For Hi-C 10 µL 15 µM TruSeq DNA Sgl index adapters (Illumina, Cat. No. 20016329) and 4 µL NEB T4 Ligase 400 U/mL (NEB, M0202) were added to each aliquot and incubated 2 h at room temperature. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by two washes with 500 µL 1×TWB, one wash with 500 µL 1× BB, one wash with 200 µL 1×BB, one wash with 100 µL 1× NEBuffer 2, one wash with 50 µL 1× NEBuffer 2 and resuspended in 50 µL 1× NEBuffer 2. At this point all aliquots per PCHi-C sample were pooled. For on-bead PCHi-C library amplification a reaction master mix was prepared, reaction volume per PCR tube was 25 µL (PCHi-C: 5 µL 5× Herculase II reaction buffer (Agilent), 0.25 µL 100 mM dNTPs, 2 µL PE PCR primer 1.0 {Schoenfelder, 2018}, 2 µL PE PCR primer 2.0 {Schoenfelder, 2018}, 0.5 µL Polymerase (Herculase, Agilent), 2.5 µL Hi-C DNA on beads, 12.75 µL nuclease-free H2O; Hi-C: 12.5 µL KAPA HiFi HotStart ReadyMix (Roche), 2.5 µL Illumina primer mix (contained in KAPA HiFi HotStart Library Amplification Kit), 2.5 µL Hi-C DNA on beads, 7.5 µL nuclease-free H2O) and PCR was run under the following conditions: 30s at 98 °C; 6-7 cycles of: 10 s at 98 °C, 30 s at 65 °C, 30 s at 72 °C; 7 min at 72 °C. Post-amplification PCR reactions per sample were pooled and DNA was cleaned up using AMPure XP beads and eluted in nuclease-free H2O. Obtained DNA was used directly for Hi-C sequencing or for promoter-capture as described in Schoenfelder et al., 2018. Sequencing was performed on an Illumina NextSeq 500 (75bp read length, paired-end).
PCHi-C

value: Cranial neural crest cells

tag: location

value: Pinna

value: WT


title: PCHi-C_WT_E14.5_Pinna_2


title: LT.042.M.FFPE

tag: Sex

value: Metastatic ovarian tumor cells


title: LT.041.P.FFPE


title: PCHi-C_WT_E12.5_Pinna_2


title: Epithelial_BulkATAC_K3_2

description: 10x Genomics (3' kit, v2.0)

value: sorted primary pancreatic epithelial cells (mKate2+)

value: pancreas

tag: condition

value: KC;RIK

value: Caerulein / Week 3

value: 8-9 weeks old


title: LT.041.M.FFPE

value: female

value: IIIC


title: PCHi-C_KO_E10.5_PA2_2


title: PCHi-C_WT_E12.5_Pinna_1


title: LT.040.M.FFPE

value: ovary tumor

value: High Grade Serous


title: PCHi-C_KO_E10.5_PA2_1


title: LT.039.P.FFPE

value: tumor omentum

value: Priamry ovarian tumor cells


title: PCHi-C_WT_E10.5_PA2_1


title: Mixture6

description: 10x Genomics

data_processing:
The barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mixture of Cell lines

growth_protocol: MCF7 cells were cultured in DMEM with 10% FBS; T47D cells were cultured in RPMI with 10% FBS; BT474 cells were cultured in DMEM with 10% FBS and 15µg/ml insulin; Thp1 and Jurkat cells were cultured in RPMI with 10% FBS and 1% L-glutamine; hMSCs were cultured using the MSCGM BulletKit from Lonza. All cell lines were cultured with 1% penicillin-streptomycin (ThermoFisher Scientific) and maintained at 37ºC in a humidified incubator with 5% CO2. All cell lines were confirmed to be free of mycoplasma contamination by DNA staining with Hoechst (ThermoFisher Scientific) or Syto 82 (ThermoFisher Scientific). DMEM, RPMI, and L-glutamine were purchased from ThermoFisher Scientific, and FBS and bovine insulin were purchased from Sigma.

extract_protocol:
Single-cell samples were submitted to the Baylor College of Medicine Single Cell Genomics Core immediately after preparation. Per sample, 16K cells were loaded, with an expected return of 10K cells.
Single-cell gene expression libraries were prepared according to the Chromium NextGEM Single Cell Gene Expression 3v3.1 kit (10x Genomics). Briefly, single cells, reverse transcription reagents, gel beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMs (Gel Bead-In-Emulsion). Full-length cDNA was synthesized and barcoded within each GEM. Subsequently, GEMs were broken, and cDNA was pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA was amplified by PCR. The amplified product was fragmented prior to end-repair, A-tailing, and adaptor ligation.
Final libraries were generated by amplification. Sequencing of single-cell libraries was performed by the Genomics and RNA Profiling Core at Baylor College of Medicine. To reach an estimated 20K reads per cell, samples were sequenced at a depth of 200M reads on the NovaSeq 6000 platform (Illumina).

value: mixture of Cell lines


title: LT.040.P.FFPE


title: Mixture5

description: 10x Genomics


title: LT.038.P.FFPE


title: LT.038.M.FFPE


title: Mixture4

description: 10x Genomics


title: LT.039.M.FFPE


title: Mixture3

description: 10x Genomics


title: PCHi-C_WT_E10.5_Md_2

value: Md


title: PCHi-C_WT_E10.5_Md_1

value: Cranial neural crest cells


title: LT.037.P.FFPE


title: PCHi-C_WT_E10.5_Mx_2

value: Mx


title: Mixture2

description: 10x Genomics


title: LT.037.M.FFPE


title: Mixture1

description: 10x Genomics


title: PCHi-C_WT_E10.5_Mx_1

value: WT


title: Mix6_c

data_processing:
RNA-Seq reads were aligned and quantified using RSEM (version 1.30) (PMID: 21816040) and Bowtie2 (version 2.10) (PMID: 22388286) to human reference GRCh38 {(GENCODE v32/Ensembl 98)(refdata-gex-GRCh38-2020-A dated 2020-07-07 downloaded from 10X Genomics with GENCODE gtf dated 2019-09-05)}.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: cell lines

extract_protocol:
Cell pellets of approximately 500K cells were prepared in triplicate and flash frozen at the time of the experiment. RNA was extracted using the Qiagen RNeasy Plus mini kit with a genomic DNA elimination column (74104).
Extracted RNA samples were submitted to Novogene for library preparation and sequencing.
Briefly, RNA quality was confirmed, 150bp paired-end mRNA libraries were prepared, and libraries were sequenced at a depth of 20M reads per sample on the NovaSeq 6000 platform (Illumina).

value: cell lines

value: Cell Mixture6


title: PCHi-C_WT_E10.5_FNP_2

value: FNP


title: LT.036.P.FFPE

value: Metastatic ovarian tumor cells


title: LT.036.M.FFPE


title: Mix6_b


title: PCHi-C_WT_E10.5_FNP_1


title: PCHi-C_WT_E10.5_PA2_2


title: Mix6_a


title: Hi-C WT E14.5 Pinna 2

data_processing:
Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
The Hi-C data was mapped and quality controlled with HiCUP  (version 0.6.1) {Wingett, 2015}, the interaction matrix was created with Juicer (version 1.6) {Durand, 2016}, and was transformed into a cool matrix {Abdennur, 2020} with hic2cool (https://github.com/4dn-dcic/hic2cool, version 0.8.3) and HiCExplorer’s hicConvertFormat (version 3.7.2) {Wolff, 2020}.
The TAD calling was applied by HiCExplorer’s hicFindTADs (version 3.7.2) {Ramirez, 2018 }{Wolff, 2018 }. The Hi-C and TAD data was plotted with pyGenomeTracks (version 3.7) {Lopez-Delisle, 2021}.
Assembly: mm10/ GRCm38
Supplementary files format and content: hic

extract_protocol:
Dissected tissue from E10.5 and E12.5 embryos was kept in 1× PBS on ice, then treated with 0.5% trypsin/1× EDTA at 37 °C for 10 minutes and immediately put on ice. Dissected tissue from E14.5 embryos was kept in 1× PBS on ice, then treated with papain digestion mix (10 mg ml−1 papain, 2.5 mM cysteine, 10 mM HEPES (pH 7.4), 0.5 mM EDTA and 0.9× DMEM) for 7 min at 37 °C and immediately put on ice. The tissue was rinsed once in ice-cold 1× DMEM/10% FBS, followed by two washes in ice-cold 1× DMEM. Tissue was dissociated by pipetting. Dissociated cells were cross-linked with 2% paraformaldehyde for 10 min at room temperature (RT) and quenched with 125 mM glycine for 5 min at RT. Cells were spun down (1600 rpm, 10 minutes, 4 °C) and resuspended in cold 1× PBS. Cranial NCCs with genotype Wnt1::Cre;ROSARFP or Hoxa2EGFP were filtered and collected by FACS. Cells were spun down (1600 rpm, 10 minutes, 4°C), supernatant removed, and cell pellets were flesh-frozen and stored at -80°C.
The input material per Hi-C experiment was 1-2 × 106 cells. Cells were incubated in 500 µL ice-cold lysis buffer (10 mM Tris-HCl pH 8, 0.2% (vol/vol) NP-40, 10 mM NaCl,1× protease inhibitor cocktail (Roche)) for 30 min with periodical mixing, followed by centrifugation to pellet nuclei (760xg, 5 min., 4°C). Cell nuclei were resuspended in 179 µL ice-cold 1.25× NEBuffer 2, 5.5 µL of 10% SDS was added, and nuclei were incubated at 37°C, shaking at 950 rpm, for 1 hour. Then 37.5 µL of 10% Triton X-100 was added and cell nuclei incubated at 37°C, shaking at 950 rpm, for 1 hour. A 5 μL aliquot was taken as a control for undigested chromatin (stored at − 20 °C). For HindIII digestion 5 µL of HindIII enzyme (NEB, cat. no. R0104T) was added, incubated 6 hours at 37°C shaking at 950 rpm, followed by addition of another 5 µL of HindIII and overnight incubation at 37°C shaking at 950 rpm. A 5 μL aliquot was taken to test digestion efficiency (stored at − 20 °C). To fill in and biotinylate the restriction fragment overhangs 30 µL of biotinylation master mix (6 µL 10× NEBuffer 2, 2 µL H2O, 1.5 µL 10 mM dATP, 1.5 µL 10 mM dGTP, 1.5 µL 10 mM dTTP, 37.5 µL 0.4 mM biotin-14-dATP, and 10 µL 5U/μl Klenow (DNA polymerase I large fragment, NEB M0210L)) was added, incubated for 75 min at 37°C mixing regularly by pipetting, and then placed on ice. Next, 227 µL ligation master mix (100 µL 10× ligation buffer (NEB B0202), 10 µL 10 mg/mL BSA, 344 µL nuclease-free H2O) and 12.5 µL 1U/µL T4 DNA ligase (Invitrogen 15224-024) was added for overnight blunt end ligation in a water bath at 16°C. The next day ligated samples were incubated for a further 30 min at room temperature. The re-ligated chromatin products and test aliquots were de-cross-linked for at least 6 hours by adding 50 µL and 2.5 μL proteinase K (10 mg/mL), incubated at 65 °C. Afterwards, 6 µL or 0.5 μL of 10 mg/ml RNase A was added to the samples and test aliquots, respectively, and incubated for 60 min at 37 °C. Next, chromatin was precipitated by adding 1 volume of phenol:chloroform:isoamyl alcohol (25:24:1) (PC) to the samples and test aliquots, vigorously shaking them, followed by centrifugation at maximum speed of a table top centrifuge (~ 13,000 rpm) at room temperature for 5 min. The upper phase containing the chromatin was transferred to a new 15 mL tube. To reduce loss of DNA 1 mL of TLE buffer (10 mM Tris HCl (pH 8.0), 0.1 mM EDTA) was added to tube containing PC and residual chromatin, tube was vigorously mixed, followed by centrifugation at maximum speed of a table top centrifuge (~ 13,000 rpm) at room temperature for 5 min. The upper phase containing the chromatin was transferred to the 15 mL tube. One tenth volume of 3 M sodium acetate was added to the chromatin sample mixed by vortexing, followed by the addition of 3 volumes 100% ethanol and vortexing to mix. The samples were frozen at − 80 °C for at least 2h. The precipitated chromatin was isolated by centrifugation at maximum speed for 45 min at 4 °C. The chromatin pellet was washed twice with 2mL freshly prepared 70% ethanol and centrifuged at maximum speed for 15 min at 4 °C in between washes. Finally, the chromatin pellet was dried at room temperature and resuspended in 100 μL TLE buffer. To check the Hi-C library DNA, 1:50 dilution of the sample, and the undigested and digested controls were loaded on a 1.5% agarose gel. The DNA concentration of the Hi-C library was determined using Qubit™ dsDNA HS assay kit.  5 µg DNA (split into two 5 µg aliquots) were used for library preparation. The next steps were performed per 5 µg aliquot. The DNA was sonicated using Covaris S220 (peak incidence power: 175W; duty factor: 10%; cycles per burst: 200; time: 120s) in a volume of 130 µL in a Covaris microTUBE to obtain 100 – 1000 bp long DNA fragments. End repair, dATP-tailing and Adapter ligation was performed on beads. For this, 100 µL of Dynabeads™ MyOne™ Streptavidin T1 (Invitrogen) were washed twice with 400 µL Tween Buffer (TWB; 5 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween 20) and resuspended in 400 µL 2× binding buffer (2×BB; 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 2 M NaCl). The volume of the sonicated DNA was increased to 400 µL with TLE. DNA was mixed with washed beads (800 µL total volume) and incubated at RT for 45 min rotating at 5 rpm. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by a wash with 400 µL 1×BB, then with 100 µL 1×ligation buffer, and resuspended in 50 µL 1× ligation buffer. For end repair each aliquot was mixed on ice with 50 µL 2.5 mM dNTP mix (12.5 μL of 10 mM of each dNTP), 18 μL of  T4 DNA Polymerase (NEB M0203), 18 μL of T4 PNK (NEB M0201), 3.7 μL of DNA polymerase I large fragment (Klenow; NEB M0210), and 360.1 μL of H2O, and then incubated at 20°C for 60 min. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by two washes with 500 µL 1×TWB, one wash with 500 µL 1×BB, one wash with 500 µL TLE and resuspended in 415 µL TLE. For dATP-tailing each aliquot was mixed with 50 µL 10× NEBuffer 2, 5 µL 10 mM dATG and 20 µL 5 U/µL Klenow exo-minus, and then incubated at 37°C for 30 min. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by two washes with 500 µL 1×TWB, one wash with 500 µL 1×BB, one wash with 200 µL 1× ligation buffer and resuspended in 100 µL 1× ligation buffer. For Hi-C 10 µL 15 µM TruSeq DNA Sgl index adapters (Illumina, Cat. No. 20016329) and 4 µL NEB T4 Ligase 400 U/mL (NEB, M0202) were added to each aliquot and incubated 2 h at room temperature. Beads were reclaimed on a magnetic separation stand, supernatant was removed, followed by two washes with 500 µL 1×TWB, one wash with 500 µL 1× BB, one wash with 200 µL 1×BB, one wash with 100 µL 1× NEBuffer 2, one wash with 50 µL 1× NEBuffer 2 and resuspended in 50 µL 1× NEBuffer 2.   For Hi-C library amplification a reaction master mix was prepared, reaction volume per PCR tube was 25 µL (PCHi-C: 5 µL 5× Herculase II reaction buffer (Agilent), 0.25 µL 100 mM dNTPs, 2 µL PE PCR primer 1.0 {Schoenfelder, 2018}, 2 µL PE PCR primer 2.0 {Schoenfelder, 2018}, 0.5 µL Polymerase (Herculase, Agilent), 2.5 µL Hi-C DNA on beads, 12.75 µL nuclease-free H2O; Hi-C: 12.5 µL KAPA HiFi HotStart ReadyMix (Roche), 2.5 µL Illumina primer mix (contained in KAPA HiFi HotStart Library Amplification Kit), 2.5 µL Hi-C DNA on beads, 7.5 µL nuclease-free H2O) and PCR was run under the following conditions: 30s at 98 °C; 6-7 cycles of: 10 s at 98 °C, 30 s at 65 °C, 30 s at 72 °C; 7 min at 72 °C. Post-amplification PCR reactions per sample were pooled and DNA was cleaned up using AMPure XP beads and eluted in nuclease-free H2O. Obtained DNA was used directly for Hi-C sequencing.

value: Pinna


title: Mix5_c

value: Cell Mixture5


title: LT.034.M.FFPE

value: female


title: Mix5_b


title: Hi-C WT E12.5 Pinna 2


title: Mix5_a


title: LT.033.M.FFPE

value: IIIC


title: LT.034.P.FFPE

value: ovary tumor


title: Hi-C WT E14.5 Pinna 1


title: Mix4_b

value: Cell Mixture4


title: LT.033.P.FFPE

value: High Grade Serous


title: Mix4_c


title: Hi-C WT E10.5 Md 1


title: Hi-C WT E10.5 PA2 1


title: ATAC_WT_E14.5_Pinna_5

data_processing:
Illumina RTA 2.4.11 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing.
The adapter sequence CTGTCTCTTATACACA was trimmed from the 3’ end of all samples using cutadapt (version 3.7)(Martin, 2011) with overlap=1. The trimmed reads were aligned with bowtie2 (version 2.4.2) with the options --fr, --minins 0, --maxins 1000, --nodiscordant and --dovetail, and converted to bam files using samtools  (version 1.2)(Danecek et al., 2021; Li et al., 2009).
BigWig files containing the number of alignments per 100bp window in the genome and per million alignments in each sample were calculated using the qExportWig function from the QuasR Bioconductor package (REF: PMID: 25417205, version 1.34.0).
Assembly: mm10/ GRCm38
Supplementary files format and content: bigWig

extract_protocol:
Embryonic tissues were micro-dissected at E10.5, E12.5 or E14.5. Dissected tissue from E12.5 embryos was kept in 1× PBS on ice, then treated with 0.5% trypsin/1× EDTA at 37 °C for 10 minutes and immediately put on ice. Dissected tissue from E14.5 embryos was kept in 1× PBS on ice, then treated with papain digestion mix (10 mg ml−1 papain, 2.5 mM cysteine, 10 mM HEPES (pH 7.4), 0.5 mM EDTA and 0.9× DMEM) for 7 min at 37 °C and immediately put on ice. The tissue was rinsed once in ice-cold 1× DMEM/10% FBS, followed by two washes in ice-cold 1× DMEM. Tissue was dissociated by pipetting. Cranial NCCs with genotype Wnt1::Cre;ROSARFP were filtered and collected by FACS.
To identify open chromatin regions, we used the Assay for Transposase Accessible Chromatin (ATAC-seq) protocol, performed according to Buenrostro et al., 2015 with minor modifications as described previously in Minoux et al., 2017 (PMID: 28360266).


title: LT.032.P.FFPE


title: Mix4_a


title: ST.030.P.FF


title: ATAC_WT_E14.5_Pinna_4


title: LT.032.M.FFPE

value: tumor omentum

value: Priamry ovarian tumor cells


title: ST.030.M.FF


title: ATAC_WT_E14.5_Pinna_3


title: ST.029.P.FF


title: ATAC_WT_E14.5_Pinna_2


title: Mix3_c

value: Cell Mixture3


title: LIN28BMLLENL_3

data_processing:
Demultiplexing was performed using the bcl2fastq2 software. Read Mapping was performed using the HISAT2 software. Quantification of the expression levels of each gene was carried out using StringTie. Differentially expressed genes (DEG) analysis was performed using DESeq2.
Assembly: GRCm38

extract_protocol:
GMLPs were sorted from ME or L28BME mice and cultured for 3 days in the presence of DOX. Total RNA was isolated using the Single Cell RNA Purification Kit (Norgen Biotek).
Library preparation was performed using TruSeq Stranded mRNA Library Prep (20020594, Illumina).

value: Bone marrow

value: GMLP

value: In vitro culture with DOX


title: Hi-C WT E12.5 Pinna 1

value: Cranial neural crest cells

value: WT


title: LIN28BMLLENL_2


title: Mix3_a

value: cell lines


title: ATAC_WT_E14.5_Pinna_1


title: ST.029.M.FFPE


title: LIN28BMLLENL_1


title: ATAC_WT_E12.5_Pinna_3


title: ST.028.M.FFPE

value: IIIA


title: Mix2_c

value: Cell Mixture2


title: Mix2_a


title: MLLENL_2

value: MLL-ENL


title: Mix2_b


title: ST.027.P.FF

value: female

value: Metastatic ovarian tumor cells


title: ATAC_WT_E12.5_Pinna_2

value: Pinna


title: MLLENL_1


title: Mix3_b


title: Mix1_c

value: Cell Mixture1


title: RNA-seq Dppa3 KO female E13.5 rep3

city: Fukuoka

first: Wan Kin

last: Au Yeung

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

department: Medical Institute of Bioregulation

institute: Kyushu University

data_processing:
WGBS data was mapped to mouse genome mm10 using Bismark v0.20.0. RNA-seq data was analyzed using HISAT2 v2.0.5 and StringTie v2.1.4.
Genome_build: mm10/GRCm38
Supplementary_files_format_and_content: The CG coverage files are tab-delimited, 1-based genomic coordinates for every covered CG site in the experiment and are in the following format: <chromosome> <start position> <end position> <methylation level> <methylated cytosine> <unmethylated cytosine>.
Supplementary_files_format_and_content: FPKM values are tab-delimited text files for each sample and are in the following format: <chromosome> <geneName> <start position> <end position> <control rep1 FPKM> <control rep2 FPKM> <control rep3 FPKM> <StellaKO rep1 FPKM> <StellaKO rep2 FPKM> <StellaKO rep3 FPKM>

source_name: primordial germ cell (PGC)

growth_protocol: All animal experiments were performed under the ethical guidelines of Kyushu University, the Institutional Animal Care and Use Committee at Harvard Medical School. All mice used in this manuscript were euthanized by CO2 asphyxiation.

extract_protocol:
Total RNA was extracted from PGCs using Trizol reagent (Thermo Fisher Scientific).
WGBS (PBAT) libraries were constructed as previously described (Miura et al., 2012; Au Yeung et al., 2019). RNA-seq libraries were constructed using NEBNext rRNA Depletion Kit, NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, and NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) (NEB).

treatment_protocol: GFP-positive PGCs were isolated using a FACSMelody system (BD Bioscience).

tag: Stage

value: primordial germ cell (PGC)

value: Dppa3-/-; Oct3/4-Egfp


title: Mix1_b


title: ATAC_WT_E10.5_PA2_2


title: ATAC_WT_E10.5_PA2_1


title: ST.026.P.FF

value: ovary tumor

value: Priamry ovarian tumor cells

value: IV

value: mixed- serous, endometrioid


title: Mix1_a


title: RNA-seq Dppa3 KO female E13.5 rep2


title: ST.026.M.FFPE

value: tumor omentum


title: ST.028.P.FF

value: High Grade Serous


title: hMSC_3

source_name: cell line

value: cell line

value: hMSC

value: Mesenchymal stem cells


title: ME_rep4

data_processing:
Analysis was carried out using CLC Genomics Workbench (version 20.0.2) and CLC Genomics Server (version 20.0.2).
Assembly: GRCm38

extract_protocol:
GMLPs were sorted from WT or iME mice and cultured for 3 days in the presence of DOX. Total RNA was isolated using the Single Cell RNA Purification Kit (Norgen Biotek).
Library preparation was performed using QIAseq miRNA Library Prep kit.

value: Bone marrow

value: GMLP

value: iMLL-ENL

value: In vitro culture with DOX


title: ME_rep3


title: RNA-seq Dppa3 KO female E13.5 rep1

value: female


title: hMSC_2


title: ST.025.P.FF

value: IIIC


title: MLLENL_3

value: MLL-ENL


title: ATAC_WT_E12.5_Pinna_1

value: Cranial neural crest cells

value: Pinna

value: WT


title: hMSC_1


title: RNA-seq control female E13.5 rep2

value: primordial germ cell (PGC)

value: Stella+/-; Oct3/4-Egfp


title: ST.027.M.FFPE

value: tumor omentum

value: Metastatic ovarian tumor cells


title: ME_rep1


title: ST.025.M.FFPE

value: High Grade Serous


title: Jurkat_3

value: cell line

value: Jarkat

value: Lymphocytes


title: ST.023.M.FFPE

value: ovary tumor

value: IV


title: Jurkat_2


title: WT_rep3

value: Bone marrow

value: GMLP

value: In vitro culture with DOX


title: ST.022.P.FF

value: female

value: Priamry ovarian tumor cells


title: WT_rep4


title: Jurkat_1


title: ST.022.M.FFPE


title: RNA-seq control female E13.5 rep1


title: WGBS Dppa3 KO female E16.5

value: Dppa3-/-; Oct3/4-Egfp


title: WT_rep2

value: WT


title: WGBS control female E16.5

value: primordial germ cell (PGC)


title: WGBS Dppa3 KO female E13.5 rep2


title: RNA-seq control female E13.5 rep3

value: Stella+/-; Oct3/4-Egfp


title: WT_rep1


title: Thp1_3

value: Monocytes


title: ME_rep2

value: iMLL-ENL


title: ST.021.P.FF

value: tumor omentum

value: High Grade Serous


title: ST.021.M.FFPE

value: Metastatic ovarian tumor cells


title: Thp1_1

value: cell line


title: 20126: Zprox1ab_4dpf scRNA-seq

city: Melbourne

first: Tyrone

state: VIC

address: 305 Grattan St

department: Bioinformatics Core (RRID: SCR_025901); Organogenesis and Cancer Program

institute: Peter MacCallum Cancer Centre

data_processing:
Where necessary fastq files were made using Cell Ranger [14] (version 3.1.0 or 3.0.2) mkfastq.  Sequencing QC was assessed using FastQC 0.11.6 and MultiQC viewer for aggregated reports.
Cell Ranger count and aggr were used to generate aggregated count files mapped to GRCz11 (Ensembl 101), without depth normalisation.
Doublets were identified from the filtered aggregated count files using Scrublet [15] in Python version 3.6 and filtered from subsequent analyses.  For the MZprox1-/- mutant and Zprox1-/- mutant datasets filtered aggregated count files were processed, sc-transform normalised, filtered and clustered (louvain) using Seurat version 2.0 [16] and 3.0 [17] respectively for R statistical software version 4.0.2. QC was evaluated before and after normalisation using plot functions in Seurat and scater 1.20.1 [18], and all thresholds and settings are described in scripting.  Cluster solutions were evaluated using ClusTree [19].
Datasets used in the atlas of lymphangiogenesis were processed, filtered, merged and log-normalised using Seurat version 3.0 [17], with QC and settings as above.  Merged data was clustered and normalised using CSS simspec [20] and clustering and cluster evaluation performed on this object only, as described above.  For all scRNA-seq datasets cluster phenotype was determined using the expression of key markers (Supplementary Table), with the aid of CellXGene visualisation software [21].  All downstream analysis and plotting were performed using Seurat version 3.0 [17] using default settings.
For velocity analysis, loom files containing RNA velocity information were first generated from the 10X data associated with each sample using velocyto.R 0.6. Relevant sample subsets were then combined with loompy 3.0.6. From pre-computed Seurat UMAPs in scRNA-seq processing and analysis, cell barcode and associated metadata were obtained and combined with the loom files. With the combined velocity scores and cell metadata, velocity maps were plotted with velocyto.R 0.6 and overlaid on the UMAPs.
Genome_build: GRCz11
Supplementary_files_format_and_content: features, barcodes and matrices output by cellranger for each sample

organism: Danio rerio

source_name: embryo

growth_protocol: Zebrafish work was conducted in compliance with animal ethics committees at University of Queensland and Peter MacCallum Cancer Centre. The uq52bh (dut) mutant was isolated in a previously described genetic screen [7]. The genetic mapping approach was performed as previously described [8, 9].

extract_protocol:
To dissociate embryos and obtain single cell suspensions, we followed published protocols [13].  To dissociate embryos and obtain single cell suspension, at the desired developmental stage we deyolked embryos by pipetting up and down and rinsing in Calcium free ringers solution, we centrifuged at 2000rpm for 5’ at 4C and remove supernatant and dissociated the cells by incubating in liberase [2.5mg/mL] (Cat #5401119001 Sigma-Aldrich) diluted at a 1:35 ratio in DPBS at 28.5C for approximately 5’, homogenizing the samples during and after the incubation. To stop the reaction, we added CaCl2 to a final concentration of 1-2mM and FBS to a final concentration of 5-10%. We centrifuged at 2000rpm for 5’ at 4C. discarded the supernatant, in order to be able to asses live vs. dead cells, we re-suspend the cells solution  in Zombie Violet TM Viability Dye (Cat# 423113, BioLegend) and incubated for 20’ at RT softly rocking, we rinsed the cells by centrifuging and resuspending in DPBS/EDTA, for ATAC-Seq experiments samples were resuspended in 2%BSA/PBS. Suspension was filtered through a strainer and taken to the FAC sorting facility. In the Flow Cytometry facility, we used the BD FACSAria Fusion sorter (BD Biosciences), we based the selection for the desired population on FSC and SCC, alive cells were selected based on the Zombie Violet profile and double positive cells for the desired transgenics were targeted according to the expression profiles of single cells. Double positive cells were sorted in 300uL 100% FBS in a cold block and taken immediately to the sequencing facility.
Single cell suspensions were sorted by FACS, spun down to concentrate and a cell count was perfomed to determine post-sort viability and cell concentration. Single cell suspension was partitioned and barcoded using the 10X Genomics Chromium Controller (10X Genomics) and the Single Cell 3' Library and Gel Bead Kit (V2; 10X Genomics; PN-120237).  The cells were loaded onto the Chromium Single Cell Chip A (10X Genomics; PN-120236) or B (10X Genomics; PN-1000073 or PN-1000074) to target 10,000 cells. GEM generation and barcoding, cDNA amplification, and library construction was performed according to the 10X Genomics Chromium User Guide. The resulting single cell transcriptome libraries contained unique sample indices for each sample. The libraries were quantified on the Agilent BioAnalyzer 2100 using the High Sensitivity DNA Kit (Agilent, 5067-4626). Libraries were pooled in equimolar ratios, and the pool was quantified by qPCR using the KAPA Library Quantification Kit - Illumina/Universal (KAPA Biosystems, KK4824) in combination with the Life Technologies Viia 7 real time PCR instrument.  After the initial sequencing run, libraries were re-pooled according to estimated captured cells as determined using the Cell Ranger software (10X Genomics).  Denatured libraries were loaded onto an Illumina NextSeq-500 and sequenced using a 150-cycle High-Output Kit as follows: 26bp (Read1), 8bp (i7 index), 98bp (Read2).  Read1 supplies the cell barcode and UMI, i7 the sample index, and Read2 the 3’ sequence of the transcript.

treatment_protocol: All injections were performed as previously described [10]. CRISPR genome editing for tspan18a/b was performed as previously described [11], and all genotyping confirmed using PCR [12].  slc7a7aBAC:slc7a7a-Citrineuom10 and fabp11aBAC:fabp11a-Citrineuom10 recombineering was performed as previously described.

value: embryo

tag: transgenic

tag: facs

value: nEGFP and dsRed2 double positive

tag: platform

value: 10X Chromium scRNA

tag: version

value: Single cell 3' V3

tag: facility

value: Peter Mac Molecular Genomics


title: WGBS Dppa3 KO female E13.5 rep1

value: female


title: WGBS control female E13.5 rep2


title: WGBS control female E13.5 rep1


title: 20049: WT_40hpf scRNA-seq

description: Two sequencing runs on the same library were pooled [20013, 20017]

value: nEGFP positive

value: Single cell 3' V2

value: IMB Sequence Facility UQ


title: ST.020.P.FF

value: Priamry ovarian tumor cells

tag: age at_diagnosis

tag: figo stage

value: IV

tag: tumor histology


title: 20125: WT_4dpf scRNA-seq

tag: genotype

value: WT


title: MCF7_3

tag: tissue

tag: cell line

tag: cell type

value: Breast cancer cells


title: Thp1_2

value: Monocytes


title: ST.023.P.FFPE

value: tumor omentum

value: High Grade Serous


title: ST.020.M.FFPE

value: ovary tumor

value: Metastatic ovarian tumor cells


title: WGBS Dppa3 KO E11.5 rep2

tag: strain

value: primordial germ cell (PGC)

value: Dppa3-/-; Oct3/4-Egfp

value: not determined


title: ST.019.P.FFPE


title: ST.018.P.FF

value: IIIC


title: T47D_3

value: cell line


title: 20048: WT_40hpf scRNA-seq

description: Two sequencing runs on the same library were pooled [20012, 20016]

value: embryo

value: nEGFP positive

value: 10X Chromium scRNA


title: MCF7_1


title: WGBS Dppa3 KO E11.5 rep1


title: 20047: MZprox1ab_40hpf scRNA-seq

description: Two sequencing runs on the same library were pooled [20011, 20015]

value: Single cell 3' V2

value: IMB Sequence Facility UQ


title: ST.018.M.FFPE

value: female

value: Priamry ovarian tumor cells


title: WGBS control E11.5

value: Stella+/-; Oct3/4-Egfp


title: T47D_2

value: Breast cancer cells


title: 20046: MZprox1ab_40hpf scRNA-seq

description: Two sequencing runs on the same library were pooled [20010, 20014]


title: ST.017.P.FFPE

value: IIIA

value: High Grade Serous


title: T47D_1


title: 20045: WT_5dpf scRNA-seq

description: Two sequencing runs on the same library were pooled [20038, 20042]

value: Venus and mCherry double-positive

value: WT

value: Single cell 3' V3


title: NF-67

city: Madison

first: Vanessa

last: Leone

state: WI

address: 1933 Observatory Dr.

institute: University of Wisconsin-Madison

data_processing:
The raw fastq files generated from the RNA-seq analysis were examined by the fastqc to evaluate the quality
The STAR aligner (version 2.4.2a) was used to map the raw reads to the reference mouse genome
The genetic features from Gencode (version M23) were extracted from the resulting bam file produced by STAR
The raw gene expression count matrix was then generated by featureCounts (version subread-1.4.6-p1)
EdgeR (version 3.22.5) was used to filter low-expressed genes where genes expressed below ten counts-per-million (CPM) in 4 samples were removed
Limma-Voom pipeline (version 3.38.3) was applied to normalize the filtered count matrix and perform differential gene expression analysis for pairwise comparisons
Enrichment analysis on significant DEGs with mouse-specific GO terms and KEGG pathways was conducted through Lynx
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene

source_name: Liver

extract_protocol:
Livers were removed and a small section was placed directly in Trizol for subsequent RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were fed one of four purified diets for 8 or 24 weeks

value: Liver

tag: group

value: GF

tag: 8w or 24w

tag: diet

value: FFVHC


title: ST.016.P.FF

value: ovary tumor

tag: Sex

value: Metastatic ovarian tumor cells

value: IIIC


title: NF-66


title: ST.017.M.FFPE

value: tumor omentum


title: BT474_3

value: cell line


title: 20044: WT_3dpf scRNA-seq

description: Two sequencing runs on the same library were pooled [20037, 20041]

value: embryo

tag: transgenic

tag: Stage

value: 10X Chromium scRNA

value: IMB Sequence Facility UQ


title: 20043: WT_40hpf scRNA-seq

description: Two sequencing runs on the same library were pooled [20036, 20040]

tag: facs

value: nEGFP positive

tag: platform


title: MCF7_2

value: Breast cancer cells


title: NF-64


title: 20158: Zprox1ab_4dpf scATAC-seq

data_processing:
Where necessary fastq files were made using Cell Ranger [14] (version 3.1.0 or 3.0.2) mkfastq.  Sequencing QC was assessed using FastQC 0.11.6 and MultiQC viewer for aggregated reports.
Cell Ranger count and aggr were used to generate aggregated count files mapped to GRCz11 (Ensembl 101), without depth normalisation.
Doublets were identified from the filtered aggregated count files using Scrublet [15] in Python version 3.6 and filtered from subsequent analyses.  For the MZprox1-/- mutant and Zprox1-/- mutant datasets filtered aggregated count files were processed, sc-transform normalised, filtered and clustered (louvain) using Seurat version 2.0 [16] and 3.0 [17] respectively for R statistical software version 4.0.2. QC was evaluated before and after normalisation using plot functions in Seurat and scater 1.20.1 [18], and all thresholds and settings are described in scripting.  Cluster solutions were evaluated using ClusTree [19].
Datasets used in the atlas of lymphangiogenesis were processed, filtered, merged and log-normalised using Seurat version 3.0 [17], with QC and settings as above.  Merged data was clustered and normalised using CSS simspec [20] and clustering and cluster evaluation performed on this object only, as described above.  For all scRNA-seq datasets cluster phenotype was determined using the expression of key markers (Supplementary Table), with the aid of CellXGene visualisation software [21].  All downstream analysis and plotting were performed using Seurat version 3.0 [17] using default settings.
For velocity analysis, loom files containing RNA velocity information were first generated from the 10X data associated with each sample using velocyto.R 0.6. Relevant sample subsets were then combined with loompy 3.0.6. From pre-computed Seurat UMAPs in scRNA-seq processing and analysis, cell barcode and associated metadata were obtained and combined with the loom files. With the combined velocity scores and cell metadata, velocity maps were plotted with velocyto.R 0.6 and overlaid on the UMAPs.
Genome_build: GRCz11
Supplementary_files_format_and_content: peaks, barcodes and matrices output by cellranger for each sample

extract_protocol:
Single cell suspensions were sorted by FACS and prepared for nuclei isolation as previously described by 10x Genomics Demonstrated Protocol for Single Cell ATAC Sequencing (CG000169 - Rev D). Cell suspensions were pelleted (300 x g for 5 minutes) and rinsed with PBS + 0.04% BSA. Cells were resuspended in 95uL of freshly prepared lysis buffer (10mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40 Substitute, 0.01% Digitonin, and 1% BSA) and incubated on ice for 1 minute. 100uL of chilled wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA) was used to neutralise the reaction, before the nuclei were pelleted (500 x g for 5 minutes) and resuspended again in 7uL of 1x Nuclei Buffer (10X Genomics Cat# PN-2000153/2000207). Presence of healthy and intact nuclei was assessed by visual inspection on a brightfield microscope using Trypan Blue staining (Thermo Fisher Cat# T10282) and Countess Cell Counting Chamber Slides (Thermo Fisher Cat# C10228).
Single nuclei suspensions were resuspended at approximately 5000 nuclei per L before undergoing tagmentation for 60min at 37C. After tagmentation nuclei were partitioned and barcoded using the 10X Genomics Chromium Controller (10X Genomics) and the Single Cell ATAC Reagent Kit (V1.1; 10X Genomics; PN-1000176 ). Tagmented nuclei were loaded onto the Chromium Single Cell Chip H (10X Genomics; PN-1000162), GEM generation, barcoding and library construction was performed according to the 10X Genomics Chromium User Guide. The resulting single cell ATAC libraries contained unique sample indices for each sample. The libraries were quantified on the Agilent BioAnalyzer 2100 using the High Sensitivity DNA Kit (Agilent, 5067-4626) and pooled in equimolar ratios.  Sequencing was performed on an Illumina NextSeq 500 using a 150-cycle High-Output Kit as follows: 50bp (Read1), 8bp (i7 index), 16bp (i5 index), 50bp (Read2) achieving a read depth of 25,000 read pairs per nucleus.

value: nEGFP and dsRed2 double-positive

value: 10X Chromium scATAC

tag: version

value: ATAC 1.1

tag: facility

value: Peter Mac Molecular Genomics


title: BT474_2


title: BT474_1


title: ST.015.P.FFPE

value: female

value: Priamry ovarian tumor cells

tag: age at_diagnosis

tag: figo stage

value: mixed- serous, endometrioid


title: NF-63

value: Liver

value: GF

value: FFHC


title: 20157: WT_4dpf scATAC-seq

tag: genotype

value: WT


title: ST.015.M.FF

tag: tissue

value: tumor omentum

value: Metastatic ovarian tumor cells

value: IIIC

tag: tumor histology


title: blood.CD4.CD57-.GEX

city: Canberra

first: Yuwei

last: Hao

address: Level 6, Building 10, The Canberra Hospital, Yamba Drive,

institute: JCSMR of ANU

description: 10x Genomics-gene expresssion

data_processing:
The 10X Cell Ranger package (10X Genomics, v6.0.1) was used to process data and align to human genome (GRCh38-2020-A).
Seurat package (v4.1.0) was utilized for gene expression analyses with a standard processing workflow (Satija et al., 2015). Quality control was performed to filter out the low-quality cells (doublets and dead cells). Cells with the number of detected genes between 200 to 2500 and the percentage of mitochondrion reads less than 5 % were selected for downstream analyses.
Unwanted CD19+ B cells, CD8+ T cells, CD14+ and CD300E+ monocytes (about 1 % in total) were removed from the datasets. Highly variable TRBV and TRAV genes were disregarded for the downstream gene expression and cells cluster analyses. UMI count data were normalized by regularized negative binomial regression (SCTransform).
Samples were then integrated to compare their similarities and differences, anchors were identified with SCTransform.
ScRepertoire package (v1.3.5) was used to analyze TCR clonotypes (Borcherding et al., 2020). VDJ contig outputs from the Cell Ranger pipeline were extracted and combined. Clonal space homeostasis looking at the relative space occupied by clones at specific proportions was performed for tonsillar and blood CD57+ and CD57- CD4+ T cells.
Assembly: GRCh38-2020-A
Supplementary files format and content: Comma-separated values for VDJ sequencing
Supplementary files format and content: Tab-separated values files and matrix files for gene expression

source_name: Blood

extract_protocol:
Children with routine tonsillectomy were recruited for tonsils collection, and their blood may be also obtained. After mechanical disruption by surgical blades, tonsillar lymphocytes were collected by gradient centrifugation using Ficoll-Paque Plus tubes (GE Healthcare), and the PBMCs were also collected by gradient centrifugation. CD57+ CD4+ T cells (7AAD- CD19- CD3+ CD4+ CD8- CD57+) and CD57- CD4+ T cells (7AAD- CD19- CD3+ CD4+ CD8- CD57-) from tonsil and blood samples of a child were FACS-purified into 1.5-ml Eppendorf tubes with FACS buffer.
Single cell gene expression and VDJ libraries were prepared by Biomolecular Resource Facility at ANU using Chromium Next GEM Single Cell 5' Kit v2 Dual Index and Single Cell Human TCR Amplification Kit (10x Genomics) according to the manufacturer’s instructions. The library was sequenced in S1 flow cell with 2 x 50 bp paired-end reads by NovaSeq 6000 sequencer (Illumina).

value: Blood

tag: cell type

value: FACS-purified human blood CD4+ CD57- T cells

value: NA (No known genetic defects)

tag: treatment

value: No treatment


title: NF-62

tag: strain

tag: group


title: MDA-MB-231 cells TGF-beta 24h treatment replicate-3

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

data_processing:
RNA-Seq files were processed using the opensource BIOWDL RNAseq pipeline v4.1.0 (https://github.com/biowdl/RNA-seq)
This pipeline performs FASTQ preprocessing (including quality control, quality trimming, and adapter clipping), RNA-Seq alignment, read quantification, and optionally transcript assembly.
FastQC was used for checking raw read QC. Adapter clipping was performed using Cutadapt (v2.10) with default settings.
RNA-Seq reads’ alignment was performed using HISAT (v2.2.0) on GRCh38 human reference genome.
The gene read quantification was performed using stringtie (v1.3.6) with the option of fr-secondstrand. The gene annotation used for quantification was NONCODE version 6
Assembly: GRCh38
Supplementary files format and content: Gene TPM count in TSV format

source_name: human breast cancer cell line

growth_protocol: MCF01A-M1 and MCF10A-M2 cells were maintained in DMEM/F12 (GlutaMAX™ Supplement; Thermo Fisher Scientific; Cat. Nr.: 31331028) containing 5% horse serum (Thermo Fisher Scientific; Cat. Nr.: 26050088), 0.1 μg/ml Cholera toxin (Sigma-Aldrich; Cat. Nr.: C8052), 0.02 μg/ml Epidermal Growth Factor (EGF; Sigma-Aldrich; Cat. Nr.: 01-107), 0.5 μg/ml Hydrocortisone (Sigma-Aldrich; Cat. Nr.: H0135), 10 μg/ml Insulin (Sigma-Aldrich; Cat. Nr.: I6634) and 100 U/ml Penicillin/Streptomycin. MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle medium (DMEM; Thermo Fisher Scientific; 41965062) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific; 16000044) and 100 U/mL penicillin/streptomycin (Thermo Fisher Scientific; 15140163).All the cells were maintained in a 5% CO2, 37 °C, humidified incubator and tested negative for mycoplasma routinely. All the cell lines were checked for authenticity by short tandem repeats (STR) profiling.

extract_protocol:
Total RNA was isolated from the cells by a TRIzol reagent (Thermo Fisher Scientific; 15596026).
Library preparation and sequencing were performed by Beijing Genomics Institute (BGI, Shenzhen, China) using the Illumina platform.

treatment_protocol: Cells were seeded at 80% confluence and cultured in serum-free media overnight. The next day, SB431542 (10 uM) or TGF-beta (5 ng/mL) was added to media. DMSO or ligand buffer was added as vehicle controls, respectively.

tag: cell line

value: MDA-MB-231 cells (triple negative breast cancer cell line)

value: Stimulated with TGF-beta (5 ng/mL) for 24 h


title: ST.014.P.FF

value: ovary tumor

tag: Sex

value: High Grade Serous


title: blood.CD4.CD57+.GEX

description: 10x Genomics-gene expresssion

value: FACS-purified human blood CD4+ CD57+ T cells


title: NF-61

tag: 8w or 24w

tag: diet


title: MDA-MB-231 cells TGF-beta 24h treatment replicate-2


title: NF-60

value: HF


title: ST.014.M.FF

value: female


title: NF-65

value: Liver

value: GF

value: FFVHC


title: tonsillar.CD4.CD57-.GEX

description: 10x Genomics-gene expresssion

source_name: Tonsil

value: Tonsil

value: FACS-purified human tonsillar CD4+ CD57- T cells


title: MDA-MB-231 cells TGF-beta 24h treatment replicate-1


title: ST.013.P.FFPE

value: Priamry ovarian tumor cells

value: IIIC


title: tonsillar.CD4.CD57+.GEX

description: 10x Genomics-gene expresssion

value: FACS-purified human tonsillar CD4+ CD57+ T cells


title: ST.016.M.FF

value: tumor omentum

value: Metastatic ovarian tumor cells


title: blood.CD4.CD57-.VDJ

description: 10x Genomics-VDJ

data_processing:
The 10X Cell Ranger package (10X Genomics, v6.0.1) was used to process data and align to human genome (GRCh38-2020-A).
Seurat package (v4.1.0) was utilized for gene expression analyses with a standard processing workflow (Satija et al., 2015). Quality control was performed to filter out the low-quality cells (doublets and dead cells). Cells with the number of detected genes between 200 to 2500 and the percentage of mitochondrion reads less than 5 % were selected for downstream analyses.
Unwanted CD19+ B cells, CD8+ T cells, CD14+ and CD300E+ monocytes (about 1 % in total) were removed from the datasets. Highly variable TRBV and TRAV genes were disregarded for the downstream gene expression and cells cluster analyses. UMI count data were normalized by regularized negative binomial regression (SCTransform).
Samples were then integrated to compare their similarities and differences, anchors were identified with SCTransform.
ScRepertoire package (v1.3.5) was used to analyze TCR clonotypes (Borcherding et al., 2020). VDJ contig outputs from the Cell Ranger pipeline were extracted and combined. Clonal space homeostasis looking at the relative space occupied by clones at specific proportions was performed for tonsillar and blood CD57+ and CD57- CD4+ T cells.
Assembly: GRCh38-2020-A
Supplementary files format and content: Comma-separated values for VDJ sequencing
Supplementary files format and content: Tab-separated values files and matrix files for gene expression
Library strategy: VDJ-seq

value: Blood

value: FACS-purified human blood CD4+ CD57- T cells

value: NA (No known genetic defects)

value: No treatment


title: ST.013.M.FF

value: High Grade Serous


title: MDA-MB-231 cells TGF-beta 8h treatment replicate-3

value: MDA-MB-231 cells (triple negative breast cancer cell line)

value: Stimulated with TGF-beta (5 ng/mL) for 8 h


title: NF-59

value: Liver

value: HF


title: blood.CD4.CD57+.VDJ

description: 10x Genomics-VDJ

value: FACS-purified human blood CD4+ CD57+ T cells


title: ST.011.P.FF

value: ovary tumor

value: female


title: NF-57

value: GF

value: LF


title: MDA-MB-231 cells TGF-beta 8h treatment replicate-1


title: ST.011.M.FF

value: IIIC


title: NF-56


title: MDA-MB-231 cells TGF-beta 2h treatment replicate-3

value: Stimulated with TGF-beta (5 ng/mL) for 2 h


title: tonsillar.CD4.CD57-.VDJ

description: 10x Genomics-VDJ

value: Tonsil

value: FACS-purified human tonsillar CD4+ CD57- T cells


title: NF-55


title: tonsillar.CD4.CD57+.VDJ

description: 10x Genomics-VDJ

value: FACS-purified human tonsillar CD4+ CD57+ T cells


title: MDA-MB-231 cells TGF-beta 2h treatment replicate-2


title: ST.009.P.FF

value: Priamry ovarian tumor cells

value: III

value: mixed- serous, endometrioid


title: p20191-s012_12_2019BC47_CD4_TOT

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were aligned using STAR v2.7.3a.(Dobin et al.)
Transcript abundance was estimated in STAR during alignment using the algorithm of htseq-count (Anders et al., 2015)
Assembly: GRCh38 Ensemble release 100: Homo_sapiens.GRCh38.dna.primary_assembly.fa, Homo_sapiens.GRCh38.100.gtf
Supplementary files format and content: comma delimited text file containing ensembl ID, gene symbol, gene description and raw read counts for each sample (in columns) for each annotated transcript (in rows).

source_name: CD4 T cells

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from HIV naïve healthy donors (New York Blood Center) using SepMate (STEMCELL, 85460) density gradient centrifugation. A fraction of PBMC was positively selected for total CD8+ T cells (Miltenyi Biotec, 130-045-201) with AutoMACS Pro Separator (Miltenyi Biotec). The cells were resuspended at the concentration of 0.5 x106/ml in RPMI 1640 medium (Fisher Scientific, SH3002701.01) supplemented with 10% fetal bovine serum (VWR Life Science Seradigm, 97068-085) 1% penicillin-streptomycin (Corning, 45000-650), and 1% HEPES (Gibco, 15630080), referred as cRPMI. CD8+ T cells were stimulated with anti-CD3/CD28 (Dynabeads, Thermofisher, 11141D) at a 1:1 ratio in the presence of 30 U/ml IL-2 (R&D system, 202IL050CF) for 72 hours at 37°C in 5% CO2.  The remaining part of the PBMC isolated from HIV naïve healthy donors was used to enrich the memory CD4+ T cells (STEMCELL, 19157). Memory CD4+ T cells were rested in cRPMI at the concentration of 2 x106/mL. On day 3, the cells were washed and infected with HIV-1 89.6 (NIH AIDS Reagent Program 3552) molecular clone at 100 ng/ml p24/million CD4+ T cells. For plasmid preparation and virus production, please refer to Kulpa  et al. (Kulpa et al., 2019). The mCD4 were spinoculated for 2.5 hours at 1200 RCF, polybrene (Sigma H9268) was added to a 1 μg/ml final concentration. The viral supernatant was then removed, and the cells were then resuspended in rested for two hours in cRPMI plus 30U/mL IL2 with 5 µM saquinavir (NIH T cells Reagent Program 4658) as anti-retroviral drug to avoid multiple rounds of infections. HIV-infected memory CD4+ cells were monocultured and co-cultured with  TCR-activated CD8+.

extract_protocol:
RNA extraction was done with RNeasy Micro kit (Qiagen, 74004) with on-column DNase digestion. RNA quality was assessed using a Fragment Analyzer (Agilent)
one nanogram of total RNA was used as input for cDNA synthesis using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the Nextera XT DNA Library Preparation kit (Illumina, FC-131-1096). Libraries were validated by capillary electrophoresis on a Fragment Analyzer (Agilent), pooled at equimolar concentrations, and sequenced on an Illumina NovaSeq6000 at 100SR, yielding ~25 million reads per sample

treatment_protocol: Co-culture was in cRPMI plus 30 U/mL IL2 with 5 µM saquinavir, at a 1:1 ratio at a final density of 1x 106 cells/mL. Cells were stained at day 3 (right before the co-culture) either with Cell Trace Dyes Far Red for mCD4 or Violet (Invitrogen, C34571) for CD8+ as follows. The Cell Trace Dyes were resuspended according to the manufacturer protocol, and a 2X mix was prepared before for the staining. 1-10 million cells were collected in 14 ml polypropylene tubes and washed in PBS. The cells were then resuspended in 500 ul of PBS, were gently vortexed (1-2 Speed) and while in motion, 500 μl of 2X mix was added for a final 1X solution. The samples were protected from light and placed in the incubator at 37°C for 15 min to allow the activation of the dyes. To quench the Cell Trace Dyes, the samples were added in 10 ml of cold cRMPI for 10 min and placed on ice in the dark. The cells were extensively washed in culture media and then resuspended at the concentration of 1x106 cells/ml before proceeding to the cell culture. At the end of the 6 days of the cell culture, the cells were harvested and washed in PBS, and then sorted based on the Cell Trace Dye staining done at day 3 with a BD FACSAria II. The samples were kept on ice for during the time of the manipulation and were homogenized in 350 μl of Buffer RLT (Qiagen, 79216) and b-mercaptoethanol right after the sorting and frozen.

tag: subjectid

tag: culture

value: HIV infected memory CD4+ T


title: ST.009.M.FF

data_processing:
Transcript read counts were obtained using Kallisto version: v0.43.1 and gene-level read counts were calculated using GRCh37 in Ensembl
Quality control and normalization of the raw count data were performed using the R/Bioconductor package edgeR version 3.28
Normalization factors were calculated using the Trimmed Mean of M-values (TMM) normalization method in edgeR to account for compositional biases in libraries between each pair of samples.
Assembly: GRCh37
Supplementary files format and content: Gene Abundance files generated using KALLISTO

value: tumor omentum

value: Metastatic ovarian tumor cells


title: MDA-MB-231 cells TGF-beta 2h treatment replicate-1

value: MDA-MB-231 cells (triple negative breast cancer cell line)


title: NF-53

value: Liver


title: NF-54


title: ST.007.P.FF

value: ovary tumor

value: High Grade Serous


title: MDA-MB-231 cells TGF-beta 8h treatment replicate-2

value: Stimulated with TGF-beta (5 ng/mL) for 8 h


title: MDA-MB-231 cells TGF-beta 0h treatment replicate-3

value: Non-stimulated (control)


title: p20191-s011_11_2019BC47_CD4_MONO

value: MONO


title: MDA-MB-231 cells TGF-beta 0h treatment replicate-2


title: p20191-s007_7_2019BC46_CD4_TOT


title: NF-52

value: GF

value: FFVHC


title: NF-58

value: HF


title: NF-51


title: ST.004.P.FFPE

value: female

value: IIIC


title: p20191-s006_6_2019BC46_CD4_MONO


title: ST.004.M.FF


title: NF-50


title: p20191-s002_2_2019BC45_CD4_TOT


title: MDA-MB-231 cells SB 24h treatment replicate-3

value: Stimulated with SB431542 (10 uM) for 24 h


title: MDA-MB-231 cells TGF-beta 0h treatment replicate-1


title: NF-48

value: FFHC


title: MDA-MB-231 cells SB 24h treatment replicate-2


title: p20024-s041_41_2019BC2_CD4_TOT

value: HIV infected memory CD4+ T


title: ST.002.M.FF

value: tumor omentum

value: IV


title: ST.007.M.FF

value: Metastatic ovarian tumor cells


title: NF-47

value: Liver


title: p20024-s032_32_2020BC9_CD4_TOT


title: NF-46


title: ST.001.M.FF


title: MDA-MB-231 cells SB 8h treatment replicate-3

value: MDA-MB-231 cells (triple negative breast cancer cell line)

value: Stimulated with SB431542 (10 uM) for 8 h


title: MDA-MB-231 cells SB 24h treatment replicate-1


title: MDA-MB-231 cells SB 8h treatment replicate-2


title: NF-45


title: MDA-MB-231 cells SB 8h treatment replicate-1


title: NF-44


title: p20024-s027_27_2020BC8_CD4_TOT


title: p20024-s031_31_2020BC9_CD4_MONO


title: F36LV

city: Chicago

first: Igor

last: Efimov

state: Illinois

address: 303 E Superior St

institute: Northwestern University

data_processing:
Adapters and low-quality reads were removed with flexbar.
Mapping with kallisto: Reads were aligned to the GRCh38 human genome assembly with Gencode v37 comprehensive gene annotation with index and quant commands. Estimated isoform-level counts from the kallisto output were summed to genes using tximport R package (v.1.14.2) tximport function.
Assembly: GRCh38, Gencode v37
Supplementary files format and content: Matrix with raw gene counts for every gene and every sample

source_name: Human donor heart

extract_protocol:
Explanted hearts were arrested with the cardioplegic solution and cooled down to +4 °C for transportation. 0.5 cm3 pieces were collected from the left and right atrial free wall, right and left ventricular base, and inferior and superior sinoatrial node. The tissue was flash frozen or stored in RNAlater (Invitrogen) overnight at +4 °C and  stored at -80 °C. Total mRNA was extracted from 40 mg of tissue with RNeasy Fibrous Tissue Mini Kit (Qiagen). RNA purity and yield were quality checked with Agilent Bioanalyzer to satisfy RIN >7 and total RNA amount 3-5 μg.
TruSeq RNA Library Prep Kit (Illumina)

value: Human donor heart

tag: cardiac chamber

value: Left ventricle

value: Female

tag: age

tag: health state

value: healthy


title: F36RA

value: Right atrium


title: F36RV

value: Right ventricle


title: p20191-s001_1_2019BC45_CD4_MONO

value: MONO


title: p20024-s026_26_2020BC8_CD4_MONO


title: ST.002.P.FF

extract_protocol:
RNA was extracted FFPE or FF tumors with Qiagen RNeasy Kit
Illumnia TruSeq Stranded Total RNA library kit according to manufactuers protocol

value: ovary tumor

value: female

value: Priamry ovarian tumor cells

tag: age at_diagnosis

tag: figo stage

value: High Grade Serous


title: NF-49

tag: tissue

value: GF

value: FFHC


title: MDA-MB-231 cells SB 2h treatment replicate-3

value: Stimulated with SB431542 (10 uM) for 2 h


title: NF-43

value: Liver

value: LF


title: MDA-MB-231 cells SB 2h treatment replicate-2

value: MDA-MB-231 cells (triple negative breast cancer cell line)


title: F36LA

value: Human donor heart

value: Left atrium


title: ST.001.P.FF

value: IIIC

tag: tumor histology


title: NF-42


title: p20024-s040_40_2019BC2_CD4_MONO

tag: cell type

value: HIV infected memory CD4+ T


title: p20024-s021_21_2020BC7_CD4_MONO


title: MDA-MB-231 cells SB 2h treatment replicate-1

tag: treatment


title: F35RA

value: Right atrium

value: Female

value: healthy


title: NF-41

tag: strain


title: MDA-MB-231 cells SB 0h treatment replicate-3

value: Stimulated with SB431542 (10 uM) for 0.5 h


title: F39RV

value: Right ventricle


title: F39LA


title: YC6235

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

country: Canada

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

description: Human post-mortem midbrain

data_processing:
Library strategy: Single-nuclei RNA-seq and ATAC-seq
Sequence data was preprocessed by CellRanger-arc (v1.0.1)
RNA data was analyzed by Seurat (v4.0.0)
ATAC data was analyzed by Signac (v1.5.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: RNA count matrix, ATAC peak position, and ATAC fragment files are provided by H5, BED, and TSV format, respectively.

molecule: other

source_name: substantia nigra

growth_protocol: We processed the tissue in a dounce homogenizer and then centrifuged it through 1.5 M sucrose to isolate the nuclei

extract_protocol:
10X Genomics Single Cell Multiome ATAC + Gene Expression kit
Libraries were prepared for sequencing using manufacture protocol

treatment_protocol: We stained the nuclei with 7AAD and sorted to purify nuclei from mitochondria

value: Human post-mortem midbrain

tag: group

value: Young

tag: diagnosis

value: Unaffected Control

value: F

tag: pmi (hours)

tag: rin

tag: repository

value: Maryland

tag: molecule

value: RNA and DNA


title: NF-39

value: Liver

value: SPF

tag: 8w or 24w

tag: diet

value: HF


title: YC914

description: Human post-mortem midbrain

tag: age

tag: Sex

value: M


title: MDA-MB-231 cells SB 0h treatment replicate-2

tag: cell line

value: MDA-MB-231 cells (triple negative breast cancer cell line)


title: NF-40


title: p20024-s022_22_2020BC7_CD4_TOT

tag: subjectid

tag: culture

value: HIV infected memory CD4+ T


title: NF-37

tag: tissue


title: MCF10A-M2 cells TGF-beta 24h treatment replicate-2

source_name: pre-malignant human breast cell line

value: MCF10A cells (normal human breast epithelial cell line) tranformed with HA-Ras

value: Stimulated with TGF-beta (5 ng/mL) for 24 h


title: F26LV

value: Human donor heart

tag: cardiac chamber

value: Left ventricle

value: Female

tag: health state

value: healthy


title: YC5751

description: Human post-mortem midbrain

value: Human post-mortem midbrain

value: Young

value: Unknown


title: YC5928

description: Human post-mortem midbrain

value: Unaffected Control

value: F

value: Maryland


title: YC5813

description: Human post-mortem midbrain

value: RNA and DNA


title: NF-38

tag: strain

value: Liver

value: SPF

value: HF


title: NF-36

tag: group


title: YC5626

description: Human post-mortem midbrain

tag: diagnosis

value: M


title: F26LA

value: Left atrium


title: F26RA

value: Right atrium


title: NF-35


title: MCF10A-M2 cells TGF-beta 24h treatment replicate-1

value: MCF10A cells (normal human breast epithelial cell line) tranformed with HA-Ras

tag: treatment

value: Stimulated with TGF-beta (5 ng/mL) for 24 h


title: NF-34

value: FFVHC


title: MCF10A-M2 cells TGF-beta 8h treatment replicate-3

value: Stimulated with TGF-beta (5 ng/mL) for 8 h


title: YC5442

description: Human post-mortem midbrain

value: Human post-mortem midbrain

tag: pmi (hours)

tag: rin


title: MCF10A-M2 cells TGF-beta 8h treatment replicate-2


title: YC5276

description: Human post-mortem midbrain

value: Young

tag: repository

tag: molecule


title: F26RV

value: Human donor heart

value: Right ventricle

value: Female

value: healthy


title: MCF10A-M2 cells TGF-beta 8h treatment replicate-1


title: MCF10A-M2 cells TGF-beta 2h treatment replicate-3

value: Stimulated with TGF-beta (5 ng/mL) for 2 h


title: YC5346

description: Human post-mortem midbrain

value: Unaffected Control

value: F

value: Maryland

value: RNA and DNA


title: M28LV

value: Left ventricle

value: Male


title: NF-33

value: Liver

value: SPF

tag: 8w or 24w

tag: diet


title: YC4345

description: Human post-mortem midbrain

tag: age

tag: Sex


title: MDA-MB-231 cells SB 0h treatment replicate-1

tag: cell line

value: MDA-MB-231 cells (triple negative breast cancer cell line)

value: Stimulated with SB431542 (10 uM) for 0.5 h


title: M34RV


title: MCF10A-M2 cells TGF-beta 24h treatment replicate-3

value: MCF10A cells (normal human breast epithelial cell line) tranformed with HA-Ras

value: Stimulated with TGF-beta (5 ng/mL) for 24 h


title: P6326

description: Human post-mortem midbrain

value: Human post-mortem midbrain

value: PD

value: Parkinson's disease

value: M


title: M34LV

value: Human donor heart

value: healthy


title: M28RV

value: Right ventricle


title: MCF10A-M2 cells TGF-beta 2h treatment replicate-2

value: Stimulated with TGF-beta (5 ng/mL) for 2 h


title: M34LA

value: Left atrium


title: NF-31

value: FFVHC


title: M34RA

value: Right atrium

value: Male


title: MCF10A-M2 cells TGF-beta 0h treatment replicate-3

value: Non-stimulated (control)


title: NF-29

value: Liver

value: SPF


title: NF-30


title: M26RV


title: MCF10A-M2 cells TGF-beta 0h treatment replicate-2

value: MCF10A cells (normal human breast epithelial cell line) tranformed with HA-Ras


title: NF-32


title: P6323

description: Human post-mortem midbrain

value: Maryland

value: RNA and DNA


title: NF-28

value: FFHC


title: MCF10A-M2 cells TGF-beta 2h treatment replicate-1


title: NF-27


title: P6320

description: Human post-mortem midbrain

value: Human post-mortem midbrain

value: PD

value: Parkinson's disease