title: PF-nSene-3

data_processing:
The sequencing data were aligned to mouse reference genome (mm10) using Rsubread (v2.4.3). Raw counts were obtained from read alignments through refGene for gene counts or RepeatMasker annotation for TEs, and then further transferred into CPM by edgeR (v3.32.1).
After filtering out low-expression genes with CPM lower than 0.1, differential expression was analyzed with the linear model using limma (v3.46.0).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with raw element counts for every repeat elements and every sample

source_name: mouse primary pulmonary fibroblast

growth_protocol: Cultured in DMEM with 10% FBS and 1X antibiotics under 5%O2 hypoxia incubator

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions. Removal of rRNA from total RNA (1 mg) was carried out using NEBNext rRNA Depletion Kit (New England Biolabs).
RNA-seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs). After the conversion of the linear dsDNA libraries to single-stranded circular DNA libraries (Universal Library Conversion Kit, MGI Tech, Guangdong, China), the pooled libraries were sequenced on a DNBSEQ-G400RS (MGI Tech) using paired-end mode (2×100 bp).

treatment_protocol: Cellular senescence was firstly synchronized by 16 hours 9 mM RO3306, and then induced by 5 mM Nutlin 3a for 48 hours. After that, 100 nM BI-2536 was treated to exclude proliferative cells for total 12 days.

value: Nutlin 3a-induced senescent

value: mouse primary pulmonary fibroblast

tag: molecule type

value: rRNA depleted RNA


title: embryo_Cu_0.156uM_96hpf

status: Public on Aug 27 2022

type: SRA

city: WuHan

first: Guan

middle: Peng

last: Peng

state: HuBei

address: shizishan street

department: college of informatics

country: China

institute: Huazhong Agricultural University

description: embryos at 96hpf (hours post  fertilization)

library_source: transcriptomic

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with TopHat2
The FPKM was calculated by Cufflinks v2.1.1
Genome_build: Download the genome from http://ftp.ensembl.org/pub/release-85/fasta/danio_rerio/dna/
Supplementary_files_format_and_content: tab-delimited text files include the FPKM value with echo gene for echo sample

molecule: total RNA

organism: Danio rerio

source_name: embryo, Cu 0.156uM 96hpf

growth_protocol: embryos (F1) cultured in normal water environment

extract_protocol:
RNA extraction using Trizol reagent
Performed in the Beijing Genomics Institute

treatment_protocol: 50-60 embryos (F1) from each group

tag: cell type

tag: treatment

value: embryos whose parents were exposed to 0.156μM Cu (F0 fish)

tag: genotype

value: wild-type zebrafish (AB) at 3 months (F0 fish)


title: embryo_0.078uM_Cu

library_source: genomic

data_processing:
Raw reads were filtered for adapter and low quality reads by Trimmomatic
Clean reads mapped to the reference genome with BatMeth2
The methylation level were calculated by BatMeth2
Genome_build: Download the genome from http://ftp.ensembl.org/pub/release-85/fasta/danio_rerio/dna/
Supplementary_files_format_and_content: Show the echo site methylation level with detected

molecule: genomic DNA

source_name: embryo, 0.078uM Cu

extract_protocol:
Genomic DNA extraction using the ammonium acetate method
Genomic DNA (>100 ng) from each sample were used to construct the DNA library

treatment_protocol: 50-60 embryos (F1) from each group/sperms of 10-12 adult zebrafish  (F0) for each group

value: embryos at 96hpf (hours post  fertilization)

value: embryos whose parents were exposed to 0.078μM Cu (F0 fish)


title: Cas9+ER-HoxB8 cells day 0 replicate 3

city: Berkeley

first: Sarah

middle: Ann

last: Stanley

state: California

address: Li Ka Shing Center 500C, mc3370

department: School of Public Health

country: USA

institute: University of California, Berkeley

data_processing:
Fastq files were generated and demultiplexed using Illumina bcl2fastq2 v2.20 and default settings, on a server running CentOS Linux 7
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: hematopoetic cell

growth_protocol: Opti-MEM (Gibco) supplemented with 10% FBS, 1% SCF supernatant produced by a CHO cell line, 2 mM GlutaMax supplement (Gibco), 30 mM β-mercaptoethanol, and 1 mM β-estradiol

extract_protocol:
RNA was extracted using TRIZOL and cleaned on a Qiagen RNAeasy kit
Kapa Biosystems library preparation kit

treatment_protocol: β-estradiol was removed on day 0

tag: tissue

value: hematopoetic cell

tag: cell line

value: Cas9+ER-HoxB8 neutrophil

value: neutrophil

value: estradiol withdrawal


title: Ginseng, hairy roots, rep2 (mRNA-seq)

city: Zhengzhou

first: yanyong

last: cao

state: henan

address: No. 116, Huayuan Road

institute: Henan Academy of Agricultural Sciences

data_processing:
Firstly, fastp and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was also verified using fastp. including the Q20, Q30 and GC-content of the clean data.
All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0.
Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'.
The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene). All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/), Gene ontology (GO) (http://www.geneontology.org), SwissProt (http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.kegg.jp/kegg/) and eggNOG (http://eggnogdb.embl.de/) databases using DIAMOND[3] with a threshold of Evalue<0.00001.
Salmon was used to perform expression level for Unigenes by calculating TPM.
Assembly: NA
Supplementary files format and content: genes_expression
Supplementary files format and content: Trinity.gene.fasta

organism: Panax ginseng

source_name: hairy roots

growth_protocol:
This study took ginseng hairy roots as the research object, exogenously added ginsenoside Ro to regulate the growth of hairy roots, and measured the changes in its physiological and saponin content.
Place the germination paper with the seeds into a 2-gallon plastic container (a plastic bucket works fine). Fill bucket with tap water so it reaches up to 1/4 of the paper height. Incubate in a growth chamber for 6 days with a light-dark cycle of 16 hr light at 27°C and 8 hr dark at 24°C, and ~50% humidity

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).
RNA-seq:We performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: It was found that ginseng hairy roots grew significantly under Ro-0.5 mg/L stress.

value: hairy roots

value: tissue

tag: stress

value: control

tag: dose


title: PDL1-negative-1

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

country: Japan

institute: IMSUT

data_processing:
The sequencing data were aligned to human genome (hg19) using STAR aligner (v2.5.2a)
HTSeq (v0.11.2) was used to obtain the raw gene counts from the read alignments.
Differential expression analysis was performed using DESeq2 (v1.22.2).
The genes whose FPKM positively correlated with PD-L1 (R^2>0.95) were inputted into iRegulon (v1.3) on Cytoscape platform (v3.8.2).
20kb centered around TSS were considered as promoter region of each gene and normalized enrichment score (NES) was cut-off at 3 as a threshold.
Assembly: hg19
Supplementary files format and content: xlsx files include FPKM values for all samples.
Supplementary files format and content: xlsx files include iRegulon predicted candidates of transcription factor binding site which were enriced in promoter regions of PD-L1 correlated genes.

molecule: polyA RNA

organism: Homo sapiens

source_name: human foreskin fibroblast cellline HCA2

growth_protocol: Cultured in DMEM with 10% FBS and 1X antibiotics

extract_protocol:
Total RNA was extracted using ISOGEN (Nippon Gene) according to the manufacturer's instructions. PolyA-tailed mRNA was selected with beads using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA).
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA) according to the manufacturer's instructions.

treatment_protocol: Cellular senescence was induced by 24 hours 100 nM doxorubicin and further maintained under 100 nM BI-2536 to exclude proliferative cells for total 12 days

tag: cell cycle state

value: Doxorubicin-induced senescent

tag: pd-l1 expression

value: negative

value: human foreskin fibroblast cell line HCA2


title: PF-nSene-1

value: Nutlin 3a-induced senescent


title: PF-nSene-2

value: mouse primary pulmonary fibroblast


title: Cas9+ER-HoxB8 cells day 2 replicate 2


title: Cas9+ER-HoxB8 cells day 2 replicate 3


title: embryo_Cu_0.156uM_24hpf

description: embryos at 24hpf (hours post  fertilization)

source_name: embryo, Cu 0.156uM 24hpf


title: embryo_Cu_0.078uM_24hpf

source_name: embryo, Cu 0.078uM 24hpf

value: embryos at 24hpf (hours post  fertilization)


title: PF-Quie-2

value: Quiescence

value: rRNA depleted RNA


title: Normal-3

value: Proliferative

value: positive


title: PDL1-negative-2


title: Normal-2


title: Cas9+ER-HoxB8 cells day 2 replicate 1

value: hematopoetic cell


title: Cas9+ER-HoxB8 cells day 0 replicate 1

value: Cas9+ER-HoxB8 neutrophil


title: embryo_Control_96hpf

source_name: embryo, Control 96hpf

value: embryos at 96hpf (hours post  fertilization)

value: embryos whose parents were exposed to normal water environment (F0 fish)

value: wild-type zebrafish (AB) at 3 months (F0 fish)


title: HUVECs, Resveratrol3

status: Public on Aug 26 2022

city: Hefei

first: Wenqi

last: Zhao

address: No. 96 Jinzhai Road

institute: University of Science and Technology of China

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen), in which known and novel, coding and noncoding transcripts were included
Expression level of gene was calculated by RSEM(v1.2.12).
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text file includes FPKM, TPM, read_count values for each Sample

source_name: blood vessel

growth_protocol: Cells were cultured in M200 media supplemented with 5% FBS and 1X ECGS

extract_protocol:
Total RNA was harvested using RNAeasy Mini Kit from Qiagen.
RNA libraries were prepared for sequencing using rRNA Removal Library Construction Protocol.  DNBSEQ-MGI2000 sequencing instrument.

treatment_protocol: HUVECs were treated with DMSO or resveratrol (20μM) for 24 hours.

value: endothelium

value: Human Umbilical Vein Endothelial Cells

value: WT

value: resveratrol


title: embryo_Cu_0.078uM_96hpf

source_name: embryo, Cu 0.078uM 96hpf

value: embryos whose parents were exposed to 0.078μM Cu (F0 fish)


title: D032: Male 3 yr Lung rep 2

city: Cincinnati

first: LungMAPP

last: DCC

state: OH

address: 3333 Burnet Ave

institute: LungMAP DCC

data_processing:
For each sequenced snATAC-Seq libraries, we obtained four FASTQ files paired-end DNA reads as well as the combinatorial indexes for i5 (768 different PCR indices) and T7 (96 different tagmentation indices). We selected all reads with <= 2 mistakes per individual index (Hamming distance between each pair of indices is 4) and subsequently integrated the full barcode at the beginning of the read name in the FASTQ files (https://gitlab.com/Grouumf/ATACdemultiplex/). Next, we used trim galore (v.0.4.4) to remove adapter sequences from reads prior to read alignment. We aligned reads to the hg19 reference genome using bwa mem (v.0.7.17) (Li and Durbin, 2009) and subsequently used samtools (Li et al., 2009) to remove unmapped, low map quality (MAPQ<30), secondary, and mitochondrial reads. We then removed duplicate reads on a per-cell basis using MarkDuplicates (BARCODE_TAG) from the picard toolkit. As an initial quality cutoff, we set a minimum of 1,000 reads (unique, non-mitochondrial) and observed 120,090 cells passing this threshold.    We used a previously described pipeline to identify snATAC-seq clusters (Chiou et al., 2019). Briefly, we used scanpy (Wolf et al., 2018) to uniform read depth-normalize and log-transform read counts within 5 kb windows. We then identified highly variable (hv) windows (min_mean=0.01, min_disp=0.25) and regressed out the total read depth across hv windows (usable counts) within each experiment. We then merged cells across experiments and extracted the top 50 PCs, using Harmony (Korsunsky et al., 2019) to correct for potential confounding factors including donor-of-origin and biological sex. We used Harmony-corrected components to build a nearest neighbor graph (n_neighbors=30) using the cosine metric, which was used for UMAP visualization (min_dist=0.3) and Leiden clustering (resolution=1.5) (Traag et al., 2019).    Prior to the final clustering results, we performed iterative clustering to identify and remove cells mapping to clusters with aberrant quality metrics. First, we removed 3,183 cells mapping in clusters with low read depth. Next, we removed 20,718 cells mapping in clusters with low fraction of reads in peaks. Finally, we re-clustered the cells at high resolution and removed 5,209 cells mapping in potential doublet sub-clusters. On average, these sub-clusters had higher usable counts, promoter usage, and accessibility at more than one marker gene promoter. After removing all of these cells, our final clusters consisted of 90,980 cells. To identify marker genes for each cluster, we used linear regression models with gene accessibility as a function of cluster assignment and usable counts across single cells.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file and .mtx
Library strategy: snATAC-seq

source_name: Biopsy from small airway

extract_protocol:
Lung tissue was homogenized using mortar and pestle on liquid nitrogen. 1 ml nuclei permeabilization buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 0.1% IGEPAL-CA630 (Sigma) and 0.01% Digitonin (Promega) in water (Corces et al., 2017)) was added to 30 mg of ground lung tissue and tissue was resuspended by pipetting for 8-15 times. Nuclei suspension was incubated for 10 min at 4°C and filtered with 30 μm filter (CellTrics).
Combinatorial barcoding single nucleus ATAC-seq was performed as described previously with modifications (Cusanovich et al., 2015; Fang et al., 2019; Preissl et al., 2018) and using new sets of oligos for tagmentation and PCR. Nuclei suspension was pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf) and resuspended in 500 μL high salt tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% DMF) and counted using a hemocytometer. Concentration was adjusted to 2,000 nuclei/9 μl, and 2,000 nuclei were dispensed into each well of one 96-well plate. For tagmentation, 1 μL barcoded Tn5 transposomes (Fang et al., 2019) was added using a BenchSmart™ 96 (Mettler Toledo), mixed five times and incubated for 60 min at 37 °C with shaking (500 rpm). To inhibit the Tn5 reaction, 10 μL of 40 mM EDTA were added to each well with a BenchSmart™ 96 (Mettler Toledo) and the plate was incubated at 37 °C for 15 min with shaking (500 rpm). Next, 20 μL 2 x sort buffer (2 % BSA, 2 mM EDTA in PBS) was added using a BenchSmart™ 96 (Mettler Toledo). All wells were combined into a FACS tube and stained with 3 μM Draq7 (Cell Signaling). Using a SH800 (Sony), 20 2n nuclei were sorted per well into eight 96-well plates (total of 768 wells) containing 10.5 μL EB (25 pmol primer i7, 25 pmol primer i5, 200 ng BSA (Sigma). Preparation of sort plates and all downstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). After addition of 1 μL 0.2% SDS, samples were incubated at 55 °C for 7 min with shaking (500 rpm). 1 μL 12.5% Triton-X was added to each well to quench the SDS. Next, 12.5 μL NEBNext High-Fidelity 2× PCR Master Mix (NEB) were added and samples were PCR-amplified (72 °C 5 min, 98 °C 30 s, (98 °C 10 s, 63 °C 30 s, 72°C 60 s) × 12 cycles, held at 12 °C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRI Beads (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRI Beads (Beckmann Coulter, 1.5x). Libraries were quantified using a Qubit fluorimeter (Life technologies) and the nucleosomal pattern was verified using a Tapestation (High Sensitivity D1000, Agilent).
Single-nucleus ATAC-Seq libraries were sequenced on a HiSeq4000 or NextSeq500 sequencer (Illumina) using custom sequencing primers with following read lengths: 50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2).

tag: age

value: 3 yr

tag: Sex

value: M

tag: race

value: White

tag: clinpathdx

value: Normal growth and development

tag: assessement of tissue quality

value: Very Good

tag: type of death

value: DBD

tag: Cause of death

value: Head Trauma


title: HUVECs, Control3

value: vehicle


title: Normal-1

value: Proliferative

value: positive

value: human foreskin fibroblast cell line HCA2


title: PF-Quie-3

value: Quiescence

value: mouse primary pulmonary fibroblast

tag: molecule type

value: rRNA depleted RNA


title: PF-Quie-1

tag: cell type


title: Cas9+ER-HoxB8 cells day 0 replicate 2

value: hematopoetic cell

value: Cas9+ER-HoxB8 neutrophil

value: neutrophil

tag: treatment

value: estradiol withdrawal


title: HUVECs, Resveratrol2

value: endothelium

value: Human Umbilical Vein Endothelial Cells

tag: genotype

value: WT

value: resveratrol


title: HUVECs, Resveratrol1

tag: tissue


title: Primed CRISPRaLTR7Yctrl  rep1

city: Haining

first: Xinyu

last: Xiang

address: East Haizhou Road

department: Zhejiang University-University of Edinburgh Institute

institute: Zhejiang University

data_processing:
Quality control was performed by FastQC v0.11.8 (Andrews, 2010). For sequence trimming, first 10bp were discarded by cutadapt v1.18 (Martin, 2011).
STAR v2.7.0e (Dobin et al., 2013) was used for alignment by using human reference genome GRCh38.97. Reads with maximal 1000 multiple mapped sites and no more than 3 mismatches were retained, and only the best hit was kept (--outFilterMultimapNmax 1000, --outFilterMismatchNmax 3, --outSAMmultNmax 1). TE annotation file GRCh38 from repeatmasker (http://repeatmasker.org/) and gene annotation file GRCh38.97 from Ensembl (Howe et al., 2021) was applied to all genomics analysis.
Quantification for both gene and TE were calculated by FeatureCounts v2.0.0  (Liao et al., 2014). For gene quantification, only unique mapped reads were included (-p -B -P -C), while for TE quantification, multiple mapped reads were also included (-p -B -P -C -M).
Differentially expressed genes (DEGs) and transposable elements (DE-TEs) were generated by R package DESeq2 v1.26.0 (Love et al., 2014). Only features with mean RPKM greater than 1 in either control or treatment group were retained. Differentially expressed features were obtained from two-fold change and 0.05 FDR filtering criteria.
Genome_build: hg38
Supplementary_files_format_and_content: txt format; count file for each sample

source_name: Primed H1 human embryonic stem cells

growth_protocol: Primed ESCs were grown in mTeSR till reaching 60-70% confluency, and naïve ESCs were grown in FINE culture condition after research 50% confluency

extract_protocol:
RNA was harvested using Trizol reagent and purified.
library was prepared according to illumina RNAseq non-stranded Library Prep Kit

treatment_protocol: Primed ESCs were transfected with CRISPRa-LTR7Y or pLVTH-KLF5 plasmid for three days before collcted for RNA-seq

value: Primed H1 human embryonic stem cells

tag: culture condition

value: mTeSR

value: CRISPRa LTR7Y control

tag: passage number


title: embryo_Control_24hpf

source_name: embryo, Control 24hpf

value: embryos at 24hpf (hours post  fertilization)

value: embryos whose parents were exposed to normal water environment (F0 fish)

value: wild-type zebrafish (AB) at 3 months (F0 fish)


title: HUVECs, Control2

value: vehicle


title: HUVECs, Control1


title: BA9_Suicide_3_380

type: genomic

city: Chicago

first: Dennis

middle: R

last: Grayson

state: IL

department: Psychiatry

institute: University of Illinois Chicago

hyb_protocol: DNA was bisulfite converted (EZ DNA methylation kit, Zymo Research, Irvine, CA) then amplified, fragmented and hybridised to Illumina Infinium® MethylationEPICBeadChip  using standard Illumina protocol

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

data_processing: R (v 3.5.3) and the minfi package (v 1.28.4) were used to read the idat files and compute methylated,  unmethylated, detection p-values, and normalized beta values per probe

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol, taking place after hybridization

extract_protocol: DNA was extracted from FAC sorted nuclei using the Dneasy Blood and Tissue Kit (Qiagen). Amounts of DNA were quantified using Qubit dsDNA BroadRange Assay Kit and Qubit fluorometer.

value: brain, prefrontal cortex BA9

tag: group

value: Suicide

tag: batch

value: White

tag: gender

value: Female

tag: pmi(hours)


title: BA9_Suicide_3_845

tag: age

value: Male


title: BA9_Control_3_363

value: Control

tag: race


title: BA9_Suicide_2_848

value: Black


title: BA9_Control_3_364


title: BA9_Suicide_3_402


title: BA9_Control_3_412


title: BA9_Control_2_868


title: BA9_Control_2_697


title: BA9_Control_3_324


title: BA9_Suicide_3_229


title: BA9_Control_3_375


title: BA9_Suicide_2_777


title: BA9_Control_2_870


title: BA9_Control_2_435


title: BA9_Control_3_384


title: BA9_Control_2_814


title: BA9_Suicide_3_745


title: BA9_Suicide_2_863


title: BA9_Suicide_2_753


title: BA9_Suicide_3_496


title: BA9_Suicide_2_890


title: BA9_Control_3_323


title: BA9_Suicide_2_850


title: BA9_Control_2_607


title: BA9_Suicide_2_885


title: BA9_Control_2_871


title: isolated HSC from Mx1Cre pos Lhx2 f/f  _7 (Lhx2 ko)

type: RNA

city: NEW YORK

first: Robert

middle: F

last: Schwabe

state: NY

address: 1130 ST NICHOLAS AVE - ROOM 916B

department: Medicine

institute: Columbia University

description: Microarray of FACS-sorted HSC from Lhx2 ko mice

hyb_protocol: cDNA was hybridized to Mouse Genome 1.0ST GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the RMA algorithm as implemented in Bioconductor/R.

label: Biotin

source_name: liver

label_protocol: 150 ng RNA was used for cDNA synthesis using Ambion 3' IVT WT expression and terminal labeling kits with Robust Multichip Algorithm normalization.

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

extract_protocol: RNA was isolated by column purification (Qiagen) and quantification by NanoDrop spectrophotometer.

treatment_protocol: Mice were treated 3 times with poly(I:C). HSC were isolated from livers 2 weeks after poly(I:C) treatment using density centrifugation and subsequent retinoid autofluorescence-based FACS sorting as previously described (Mederacke et al, Nat Protocol 2015). Hepatic stellate cells were lysed immediately after FACS sorting.

tag: strain

value: Mx1Cre+; Lhx2 floxed;  C57BL/6J background

value: 2 weeks after poly:IC induce Mx1Cre activation

value: FACS-sorted VitA+ Hepatic Stellate Cells


title: BA9_Control_2_761


title: isolated HSC from Lhx2 f/f  3

description: Microarray of FACS-sorted HSC from Lhx2 floxed (wt) mice

value: Lhx2 floxed;  C57BL/6J background


title: isolated HSC from Mx1Cre pos Lhx2 f/f  _6 (Lhx2 ko)


title: isolated HSC from Lhx2 f/f  2


title: isolated HSC from Mx1Cre pos Lhx2 f/f  _8 (Lhx2 ko)


title: isolated HSC from Mx1Cre pos Lhx2 f/f  _5 (Lhx2 ko)


title: CD43-/B220+ Splenocytic B cells, CD37KO, Biological replicate 2

city: Nijmegen

first: Annemiek

middle: van

last: Spriel

address: Geert Grooteplein Zuid 28

department: Tumor Immunology Lab

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

description: Littermates

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps
Samples were processed with Gene 1.0 ST Arrays in triplicate. CD43-/B220+ splenocytic B cell CEL files were normalized as a single group and RMA signals were obtained.

source_name: CD43-/B220+ Splenocytic B cells, CD37KO

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mice were kept in enriched shelters in a pathogen-free facility with 12h:12h light:dark cycle with temperatures between 18-22°C and a humidity between 40-60%, and had ad libitum access to food (R/M H chow, Sniff, Soest, Germany) and water.

extract_protocol: RNAeasy kit

tag: strain background

value: 3 Months

value: Spleen:CD43-/B220+ population


title: CD43-/B220+ Splenocytic B cells, CD37KO, Biological replicate 3

description: Littermates


title: isolated HSC from Lhx2 f/f  4


title: BA9_Suicide_3_386


title: Cigar tobacco plants under 200 μmol m-2 s-1 light intensity [T200_1]

city: qingdao

first: ying

middle: xiao

last: wu

state: shangdong

address: China and South Korea the street

department: Cultivation and nutrition center

institute: Tobacco Research Institute, Chinese Academy of Agricultural Sciences

data_processing:
Illumnia CASAVA 1.7 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Hisat software was used to carry out genome localization analysis on filtered sequencing sequences. Hisat default parameters were used. Ntab-K326 AWOJ-SS.fa.gz was used as a reference genome.
FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs) (Trapnell et al., 2010) is the number of fragments per million fragments from a gene per kilobase length. It is the most commonly used method for estimating gene expression level. HTseq software was used to analyze the gene expression level.
Assembly: Ntab-K326 AWOJ-SS.fa.gz
Supplementary files format and content: tab-delimited text files include FPKM values of genes for each sample

organism: Nicotiana tabacum

extract_protocol:
The cigar leaves were taken and quickly frozen in liquid nitrogen to collect RNA.The sequencing library was constructed using NEBNext® Ultra™ RNA Library  Prep Kit for Illumina® and 3ug total RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Leaf

tag: developmental stage

value: Seedling stage


title: Cigar tobacco plants under 200 μmol m-2 s-1 light intensity [T200_3]


title: isolated HSC from Lhx2 f/f  1


title: CD43-/B220+ Splenocytic B cells, WT, Biological replicate 3

description: Littermates

source_name: CD43-/B220+ Splenocytic B cells, WT

value: Wild-Type


title: CD43-/B220+ Splenocytic B cells, CD37KO, Biological replicate 1

description: Littermates


title: Cigar tobacco plants under 200 μmol m-2 s-1 light intensity [T200_2]


title: BA9_Suicide_2_739


title: Cigar tobacco plants under 50 μmol m-2 s-1 light intensity [T50_3]


title: CD43-/B220+ Splenocytic B cells, WT, Biological replicate 1

description: Littermates


title: Cigar tobacco plants under 50 μmol m-2 s-1 light intensity [T50_1]


title: Cigar tobacco plants under 100 μmol m-2 s-1 light intensity [T100_3]


title: CD43-/B220+ Splenocytic B cells, WT, Biological replicate 2

description: Littermates


title: Cigar tobacco plants under 100 μmol m-2 s-1 light intensity [T100_1]


title: Cigar tobacco plants under 50 μmol m-2 s-1 light intensity [T50_2]


title: Cigar tobacco plants under 100 μmol m-2 s-1 light intensity [T100_2]


title: PLL_3

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

hyb_protocol: Following fragmentation and labelling, 2.5 ug of cDNA were hybridized for 16 hr at 45°C onto Affymetrix Mouse ClariomS arrays. Then microarrays were  washed and stained using Affymetrix Fluidics FS450 machines.

scan_protocol: Microarrays were scanned using an Affymetrix GCS3000 7G system

data_processing: Data were normalized using Expression Console from Affymetrix (RMA-GENE analysis)

label: biotin

organism: Rattus norvegicus

source_name: PC12 cells

label_protocol: Biotinylated cDNA were prepared according to the Ovation® Pico WTA System V2 protocol and the Nugen Encore Biotin Module from 500pg total RNA

growth_protocol: PC12 cells, a standard model for neuronal differentiation analysis, were obtained from ATCC (CRL 1721). Cells were expended in T25 tissue culture flasks (Falcon) coated with PLL, using medium 1,  i.e. DMEM + glutamax supplemented with FBS (5%, Hyclone), horse serum (HS) (10%, Invitrogen), non-essential amino acids (1%, Invitrogen) and antibiotic (penicillin, streptomycin) (1%,  Invitrogen)  at 37◦ C in a 5 %CO2 atmosphere. Media were changed every 2-3 days. Subculturing was done when 90% of confluence was reached, by trypsin-EDTA treatment (Invitrogen) to detach cells and seed them at 20% of confluence into new flasks.

extract_protocol: Total RNAs were extracted from PC12 cells cultivated for 3 days on the different surfaces (EDA, HTMS or PLL) using a variant of Trizol. PC12 culture on PLL in presence of NGF was used as a positive control for neural differentiation. Briefly, 1 mL of TriReagent (Invitrogen) was added onto cells, then lysates were collected into 1.5 mL microfuge tubes. Phase separation was performed by adding chloro- form (0.2 mL, Sigma-Aldrich), and total RNA was purified using an RNeasy kit (Qiagen), according to the supplier’s recommended procedure. Total RNA quantity and purity were determined using an ul- traviolet spectrophotometer (NanoDrop ND-1000 Spectrophotometer, NanoDrop Technologies). RNA integrity was checked electrophoretically using the RNA 6000 Nano LabChip kit on Agilent Bioanalyser 2100 (Agilent Technologies). Then RNAs were stored at −80◦C prior to utilization.

treatment_protocol: PC12 cells were used between passage 7 and 17 at a density of 5.103 cm−2. for the experiments on glass coverslips functionalized with EDA or HTMS. Medium 1 without HS (medium 2) was used to slow down cell proliferation. Coverslips were placed into plastic Petri dishes (30 mm in diameter) and 5.104 cm−2 cells were then seeded per dish. PC12 cultured on  PLL coated coverslips were used as negative control. The addition of NGF (100 ng mL−1 , NGF-7S, from the submandibular glands of mice) into the medium 1 of PC12 cultivated on PLL was used as positive control to trigger neurite outgrowth. In each condition, cell morphology was daily observed over 3 days using an inverted light microscope (Olympus CKX41).

tag: cell line

tag: surface

value: PLL


title: PLL_4


title: NGF_3


title: NGF_6


title: HTMS_4

value: HTMS


title: EDA_1

value: EDA


title: NGF_2


title: EDA_4


title: PLL_5


title: Patient 487

city: Sydney

first: Susan

last: Ramus

state: NSW

address: L2, Lowy Cancer Research Centre

country: Australia

institute: UNSW Sydney

hyb_protocol: 700ng/uL RNA was mixed with hybridization buffer and hybridized at 65°C overnight.

data_processing: We used batch effects adjustment, quality control, and normalisation techniques that are applied one patient at a time, single-patient processing [Talhouk et al. 2016]. After quality control assessments, the count data were log2 transformed and centered by the arithmetic mean of the selected housekeeping genes, LDHA, MTG1, POLR1B, TBP.

label: barcode

source_name: Tumor tissue FFPE

label_protocol: Proprietary 'barcode' for each target sequence

extract_protocol: RNA was extracted from FFPE tumor samples using the Qiagen miRNeasy FFPE kit.

value: Tumor tissue FFPE

tag: individual

value: Patient 487

tag: study

value: V

tag: finalstatus

tag: diagnosis

value: Metastases (LGI)

value: Mets (unk primary)

value: LGI

value: Expansile

value: Ovary/presumed ovary

tag: analysis

value: All


title: Patient 490

tag: tissue

value: Patient 490

value: C

tag: stagegroup

value: MOC


title: HTMS_1


title: Patient 489

value: Patient 489

value: L

value: MBOT


title: EDA_6


title: HTMS_3

value: HTMS


title: Patient 485

value: Patient 485


title: Patient 484

value: Tumor tissue FFPE

value: Patient 484

value: E


title: Patient 482

value: Patient 482

value: O

value: Infiltrative


title: Patient 481

value: Patient 481

value: V

value: Expansile


title: Patient 480

value: Patient 480

value: W

value: Ovary/presumed ovary

value: All


title: Patient 479

value: Patient 479

value: MOC


title: Patient 478

value: Patient 478

value: G

value: MBOT


title: Patient 477

value: Tumor tissue FFPE

value: Patient 477

value: L


title: Patient 483

value: Patient 483

value: D

value: predictions/survival


title: Patient 476

value: Patient 476

value: V


title: BA9_Suicide_1_361

value: brain, prefrontal cortex BA9

tag: group

value: Suicide

tag: batch

value: White

tag: gender

value: Male


title: Patient 488

value: Patient 488

value: Metastases (unknown)

value: Mets (panc)

value: UGI

value: Infiltrative

value: Ovary/presumed ovary

value: All


title: Patient 486

value: Tumor tissue FFPE

value: Patient 486

value: F

value: Pancreas

value: Primary pancreatic


title: Patient 468

value: Patient 468


title: Patient 466

value: Patient 466

value: C

value: MOC

value: Expansile


title: Patient 467

value: Patient 467

value: G

value: MBOT

value: predictions/survival


title: Patient 465

value: Patient 465

value: B

value: Benign mucinous neoplasm

value: survival


title: Patient 474

value: Tumor tissue FFPE

value: Patient 474

value: V

value: Ovary/presumed ovary

value: All


title: Patient 475

value: Patient 475


title: Patient 472

value: Patient 472

value: W


title: Patient 470

value: Patient 470

value: T

value: Pancreas

value: Primary pancreatic

value: UGI

value: Infiltrative


title: Patient 469

value: Patient 469

value: G

value: Metastases (LGI)

value: Mets (Appendix)

value: LGI

value: Expansile


title: Patient 462

value: Tumor tissue FFPE

value: Patient 462

value: R

value: MOC

value: Ovary/presumed ovary


title: Patient 473

value: Patient 473

value: V

value: All


title: Patient 460

value: Patient 460


title: Patient 459

value: Patient 459

value: MBOT


title: Patient 464

value: Patient 464

value: B


title: Patient 461

value: Patient 461

value: G


title: Patient 458

value: Patient 458

value: M

value: Infiltrative


title: Patient 457

value: Tumor tissue FFPE

value: Patient 457

value: W


title: BA9_Control_1_485

value: brain, prefrontal cortex BA9

value: Control

tag: age

tag: race

value: White

value: Male

tag: pmi(hours)


title: BA9_Control_1_252

value: Black


title: Patient 454

value: Patient 454

value: V

value: MOC

value: Expansile

value: Ovary/presumed ovary

value: All


title: Patient 447

value: Patient 447


title: Patient 455

value: Patient 455


title: BA9_Suicide_1_453

value: Suicide


title: Patient 448

value: Tumor tissue FFPE

value: Patient 448

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: Patient 452

value: Patient 452

value: MBOT


title: Patient 463

value: Patient 463

value: M


title: Patient 450

value: Patient 450

value: V


title: BA9_Control_1_353

value: brain, prefrontal cortex BA9

value: Control

value: Black

value: Male


title: Patient 453

value: Patient 453

value: D

value: MOC

value: Ovary/presumed ovary

value: predictions/survival


title: Patient 451

value: Tumor tissue FFPE

value: Patient 451

value: J

value: Expansile

value: All


title: BA9_Control_1_268

value: White

value: Female


title: BA9_Suicide_1_244

value: Suicide


title: Patient 444

value: Patient 444

value: L

value: MBOT


title: BA9_Suicide_1_351

value: brain, prefrontal cortex BA9

value: Male


title: BA9_Control_1_355

value: Control


title: Patient 446

value: Patient 446

value: W

value: MOC


title: Patient 443

value: Tumor tissue FFPE

value: Patient 443

value: V

value: Ovary/presumed ovary


title: Patient 442

value: Patient 442

value: R

value: predictions/survival


title: Patient 440

value: Patient 440

value: B

value: All


title: Patient 441

value: Patient 441

value: Infiltrative


title: Patient 445

value: Patient 445

value: M

value: Expansile


title: BA9_Suicide_1_462

value: brain, prefrontal cortex BA9

value: Suicide

value: White

value: Female


title: Patient 449

value: Tumor tissue FFPE

value: Patient 449

value: O

value: MOC

value: MBOT


title: Patient 456

value: Patient 456

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: Patient 439

value: Patient 439

value: S

value: Stomach

value: Primary gastric

value: All


title: Patient 438

value: Patient 438


title: Patient 437

value: Patient 437

value: L

value: Ovary/presumed ovary


title: Patient 436

value: Tumor tissue FFPE

value: Patient 436

value: N

value: Expansile


title: Patient 435

value: Patient 435

value: Q

value: MOC

value: MBOT

value: predictions/survival


title: Patient 429

value: Patient 429

value: O


title: Patient 434

value: Patient 434

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: Patient 430

value: Patient 430

value: L

value: Benign mucinous neoplasm

value: Ovary/presumed ovary

value: survival


title: Patient 431

value: Tumor tissue FFPE

value: Patient 431

value: Expansile

value: All


title: BA9_Suicide_1_350

value: brain, prefrontal cortex BA9

value: Suicide

value: White

value: Male


title: Patient 433

value: Patient 433

value: MBOT


title: Patient 425

value: Patient 425

value: V

value: MOC


title: BA9_Control_1_431

value: Control

value: Female


title: Patient 427

value: Patient 427

value: Metastases (unknown)

value: Mets (UGI)

value: UGI

value: Infiltrative

value: Ovary/presumed ovary


title: Patient 423

value: Tumor tissue FFPE

value: Patient 423

value: All


title: Patient 422

value: Patient 422

value: R


title: Patient 432

value: Patient 432

value: K

value: Colon

value: Primary CRC

value: LGI


title: Patient 421

value: Patient 421


title: Patient 416

value: Patient 416

value: G

value: MOC

value: Expansile


title: Patient 426

value: Patient 426

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: Patient 417

value: Tumor tissue FFPE

value: Patient 417

value: D

value: Ovary/presumed ovary

value: All


title: Patient 419

value: Patient 419

value: L

value: MBOT


title: Patient 420

value: Patient 420

value: K

value: Colon

value: Primary CRC

value: LGI


title: Patient 424

value: Patient 424

value: I

value: MOC

value: predictions/survival


title: Patient 418

value: Tumor tissue FFPE

value: Patient 418

value: A


title: Patient 413

value: Patient 413

value: V

value: Ovary/presumed ovary


title: Patient 412

value: Patient 412

value: O

value: Expansile

value: All


title: Patient 414

value: Patient 414

value: C

value: MBOT


title: Patient 411

value: Patient 411

value: L


title: Patient 471

value: Patient 471


title: Patient 408

value: Patient 408


title: Patient 409

value: Tumor tissue FFPE

value: Patient 409

value: MOC

value: predictions/survival


title: Patient 407

value: Patient 407

value: V


title: Patient 404

value: Patient 404

value: Ovary/presumed ovary


title: Patient 406

value: Patient 406

value: R

value: Expansile


title: Patient 400

value: Patient 400

value: B

value: Benign mucinous neoplasm

value: survival


title: Patient 399

value: Patient 399

value: MBOT

value: All


title: Patient 402

value: Tumor tissue FFPE

value: Patient 402

value: L


title: Patient 403

value: Patient 403

value: C

value: MOC


title: Patient 405

value: Patient 405

value: K

value: Colon

value: Primary CRC

value: LGI


title: Patient 415

value: Patient 415

value: O

value: Expansile

value: Ovary/presumed ovary


title: Patient 401

value: Patient 401

value: V

value: MBOT


title: Patient 397

value: Tumor tissue FFPE

value: Patient 397

value: T

value: Pancreas

value: Primary pancreatic

value: UGI

value: Infiltrative

value: All


title: Patient 398

value: Patient 398

value: C


title: Patient 395

value: Patient 395

value: B

value: MOC


title: Patient 394

value: Patient 394

value: K

value: Colon

value: Primary CRC

value: LGI


title: Patient 410

value: Tumor tissue FFPE

value: Patient 410

value: V

value: MBOT

value: Ovary/presumed ovary


title: Patient 393

value: Patient 393


title: Patient 396

value: Patient 396

value: X

value: All


title: Patient 391

value: Patient 391

value: L


title: Patient 392

value: Patient 392

value: O

value: MOC

value: Expansile


title: Patient 390

value: Patient 390


title: Patient 389

value: Patient 389


title: Patient 388

value: Tumor tissue FFPE

value: Patient 388


title: C5

city: MADRID

first: José

last: Palacios

state: MADRID

address: CTRA COLMENAR VIEJO KM. 9.100

department: Pathology

country: Spain

institute: Hospital Universitario Ramón y Cajal

description: SAMPLE 21

hyb_protocol: Hybridized for 18 h at 65C (in accordance with the manufacturer's protocol).

scan_protocol: In the nCounter Prep Station.

data_processing: nSolver analysis software (nanoString technologies Inc.).

label: biotin-labelled

source_name: lung

label_protocol: 100-200ng input was hybridized to the mRNA on a thermal cycler overnight and automatically processed and loaded to the nanoString sample cartridge in the nCounter Prep Station, in accordance with the manufacturer's protocol (Specific Fluorescently color-coded reporter probes and biotin-labelled capture probes were necessary).

extract_protocol: RNA was extracted from 10 tissue sections of 5µm obtained from representative paraffin blocks. The RecoverAll Total Nucleic Acid Isolation Kit was used for formalin-fixed paraffin-embedded tissue (Invitrogen) following the manufacturer’s instructions.

tag: subject status

value: lung control


title: Patient 387

value: Patient 387

value: T

value: Pancreas

value: Primary pancreatic

value: UGI

value: Infiltrative


title: C7

description: SAMPLE 23


title: Patient 386

value: Patient 386

value: S

value: Appendix

value: Mets (Appendix)

value: LGI

value: Omentum

value: All


title: IF3

description: SAMPLE 18

value: lung fibrosis


title: IF4

description: SAMPLE 19


title: C6

description: SAMPLE 22


title: C4

description: SAMPLE 20


title: Patient 383

value: Tumor tissue FFPE

value: Patient 383

value: V

value: Metastases (LGI)

value: Mets (unk primary)

value: Ovary/presumed ovary


title: Patient 384

value: Patient 384

value: O

value: MOC

value: Expansile


title: Pt6

description: SAMPLE 15

value: lung covid


title: IF1

description: SAMPLE 16


title: Patient 385

value: Patient 385

value: T

value: Pancreas

value: Primary pancreatic

value: UGI

value: Infiltrative


title: Pt12

description: SAMPLE 14


title: IF2

description: SAMPLE 17

value: lung fibrosis


title: Pt11

description: SAMPLE 13


title: Patient 381

value: Tumor tissue FFPE

value: Patient 381

value: MBOT

value: All


title: Patient 382

value: Patient 382

value: V

value: Ovary/presumed ovary


title: Pt9

description: SAMPLE 12


title: Patient 378

value: Patient 378

value: M

value: MOC


title: Patient 380

value: Patient 380

value: R

value: Expansile


title: Pt14

description: SAMPLE 7

value: lung covid


title: Pt7

description: SAMPLE 6


title: Pt28

description: SAMPLE 11


title: Patient 377

value: Patient 377


title: Patient 376

value: Patient 376

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: Patient 375

value: Tumor tissue FFPE

value: Patient 375

value: All


title: Pt15

description: SAMPLE 8


title: Pt22

description: SAMPLE 10


title: Pt17

description: SAMPLE 9


title: Pt23

description: SAMPLE 2


title: Patient 372

value: Patient 372

value: O

value: Ovary/presumed ovary


title: Patient 374

value: Patient 374

value: B

value: MBOT


title: Pt26

description: SAMPLE 1


title: Patient 379

value: Patient 379

value: V

value: MOC

value: Expansile


title: Patient 371

value: Patient 371

value: C


title: Patient 366

value: Patient 366

value: L


title: Patient 373

value: Tumor tissue FFPE

value: Patient 373

value: S

value: Infiltrative


title: Patient 363

value: Patient 363

value: F

value: Pancreas

value: Primary pancreatic

value: UGI

value: All


title: C1

description: SAMPLE 3

value: lung control


title: Patient 370

value: Patient 370

value: B

value: MBOT

value: Benign mucinous neoplasm

value: Ovary/presumed ovary

value: survival


title: C3

description: SAMPLE 5


title: C2

description: SAMPLE 4


title: Patient 367

value: Tumor tissue FFPE

value: Patient 367

value: V


title: Patient 358

value: Patient 358

value: L

value: MOC

value: predictions/survival


title: Patient 428

value: Patient 428

value: C


title: Patient 365

value: Patient 365

value: All


title: A673_siGATA2_3_(Clariom_D_Human)

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

description: Ewing sarcoma cell line A-673; siRNA induced GATA2 knockdown sample; replicate 3

hyb_protocol: Affymetrix Clariom D Array one-color based hybridization protocol, cDNA samples were hybridized at 45°C for 16 h on separate Affymetrix Human Clariom D™ Arrays.

scan_protocol: Affymetrix GeneChip 3000 Scanner

data_processing:
Data were processed with Transcriptome Analysis Console (version 4.0) using the SST-RMA analysis algorithm.
Clariom_D_Human.r1.pgf
Clariom_D_Human.r1.mps

source_name: Ewing sarcoma cell line

label_protocol: Affymetrix GeneChip WT PLUS Reagent Kit, according to the manufacturer's protocol

growth_protocol: Cell lines were cultured in RPMI 1640 medium with stable glutamine (Biochrom, Berlin, Germany), supplemented with 10% FCS tested to be dox-free (Sigma-Aldrich, Taufkirchen, Germany) and penicillin and streptomycin (final concentrations 100 units/ml and 100µg/ml, respectively; Merck, Darmstadt, Germany) in tissue culture flasks and plates (TPP, Trasadingen, Switzerland) in a fully humidified 5% CO2 atmosphere at 37°C.

extract_protocol: Cells were washed with PBS, lysed in lysis buffer from the Macherey-Nagel (Düren, Germany) NucleoSpin RNA kit. Total RNA was isolated following manufacturer's protocol. RNA was stored at -80°C.

treatment_protocol: Addition of 30 nM siPools for 96 h, medium renewal and retransfection at 48 h.

value: Ewing sarcoma cell line

tag: condition


title: Patient 362

value: Patient 362

value: Expansile


title: Patient 368

value: Patient 368

value: O


title: Patient 364

value: Patient 364

value: MBOT

value: Ovary/presumed ovary


title: Patient 360

value: Tumor tissue FFPE

value: Patient 360

value: K

value: Colon

value: Primary CRC

value: LGI


title: A673_siControl_2_(Clariom_D_Human)

description: Ewing sarcoma cell line A-673; Control sample; replicate 2

value: Control


title: A673_siE2F2_3_(Clariom_D_Human)

description: Ewing sarcoma cell line A-673; siRNA induced E2F2 knockdown sample; replicate 3


title: Patient 369

value: Patient 369

value: V

value: MOC


title: Patient 356

value: Patient 356

value: A

value: All


title: Patient 353

value: Patient 353


title: A673_siGATA2_2_(Clariom_D_Human)

description: Ewing sarcoma cell line A-673; siRNA induced GATA2 knockdown sample; replicate 2

value: Ewing sarcoma cell line


title: Patient 355

value: Patient 355

value: J

value: Expansile


title: Patient 348

value: Tumor tissue FFPE

value: Patient 348

value: L

value: Infiltrative

value: Ovary/presumed ovary


title: Patient 347

value: Patient 347

value: Metastases (unknown)

value: Mets (CRC)

value: LGI


title: A673_siE2F2_1_(Clariom_D_Human)

description: Ewing sarcoma cell line A-673; siRNA induced E2F2 knockdown sample; replicate 1


title: Patient 345

value: Patient 345

value: MBOT


title: Patient 352

value: Patient 352

value: D

value: MOC

value: predictions/survival


title: Patient 342

value: Patient 342

value: O

value: All


title: Patient 343

value: Tumor tissue FFPE

value: Patient 343

value: V

value: Expansile


title: Patient 354

value: Patient 354

value: Ovary/presumed ovary


title: Patient 351

value: Patient 351


title: A673_siE2F2_2_(Clariom_D_Human)

description: Ewing sarcoma cell line A-673; siRNA induced E2F2 knockdown sample; replicate 2

value: Ewing sarcoma cell line


title: Patient 359

value: Patient 359

value: T

value: Pancreas

value: Primary pancreatic

value: UGI

value: Infiltrative


title: Patient 361

value: Patient 361

value: S

value: Colon

value: Mets (CRC)

value: LGI

value: Omentum


title: A673_siControl_3_(Clariom_D_Human)

description: Ewing sarcoma cell line A-673; Control sample; replicate 3

value: Control


title: A673_siControl_1_(Clariom_D_Human)

description: Ewing sarcoma cell line A-673; Control sample; replicate 1


title: Patient 357

value: Tumor tissue FFPE

value: Patient 357

value: V

value: MOC

value: All


title: A673_siGATA2_1_(Clariom_D_Human)

description: Ewing sarcoma cell line A-673; siRNA induced GATA2 knockdown sample; replicate 1

value: Ewing sarcoma cell line


title: Patient 344

value: Patient 344

value: C

value: MBOT

value: Ovary/presumed ovary


title: Patient 341

value: Patient 341

value: Expansile


title: Patient 332

value: Patient 332


title: Patient 346

value: Patient 346

value: N


title: Patient 340

value: Patient 340

value: Q

value: predictions/survival


title: Patient 350

value: Tumor tissue FFPE

value: Patient 350

value: G


title: Patient 349

value: Patient 349

value: J

value: MOC


title: Patient 331

value: Patient 331

value: O

value: All


title: Patient 335

value: Patient 335

value: B

value: MBOT

value: Benign mucinous neoplasm

value: Ovary/presumed ovary

value: survival


title: Patient 336

value: Patient 336

value: K

value: Colon

value: Primary CRC

value: LGI


title: Patient 321

value: Tumor tissue FFPE

value: Patient 321


title: Patient 320

value: Patient 320

value: S

value: Mets (CRC)

value: Infiltrative


title: Patient 338

value: Patient 338

value: V

value: All


title: Patient 327

value: Patient 327

value: O

value: MOC

value: MBOT

value: predictions/survival


title: Patient 333

value: Patient 333

value: Ovary/presumed ovary


title: Patient 337

value: Patient 337

value: R


title: Patient 323

value: Tumor tissue FFPE

value: Patient 323

value: Expansile


title: Patient 339

value: Patient 339

value: M


title: Patient 326

value: Patient 326


title: Patient 319

value: Patient 319

value: V


title: Patient 328

value: Patient 328

value: D


title: Patient 329

value: Patient 329

value: G

value: MOC

value: All


title: Patient 330

value: Patient 330

value: I

value: Ovary/presumed ovary


title: Patient 318

value: Tumor tissue FFPE

value: Patient 318

value: L

value: MBOT


title: Patient 334

value: Patient 334

value: predictions/survival


title: Patient 322

value: Patient 322

value: T

value: Pancreas

value: Primary pancreatic

value: UGI

value: Infiltrative


title: Patient 316

value: Patient 316

value: C

value: MOC


title: Patient 317

value: Patient 317

value: V

value: Expansile

value: All


title: Patient 308

value: Tumor tissue FFPE

value: Patient 308

value: O

value: Ovary/presumed ovary


title: Patient 325

value: Patient 325


title: Patient 310

value: Patient 310

value: L

value: MBOT

value: predictions/survival


title: Patient 311

value: Patient 311


title: Patient 302

value: Patient 302

value: R


title: Patient 324

value: Patient 324

value: S

value: Appendix

value: Mets (Appendix)

value: LGI

value: Omentum


title: Patient 315

value: Tumor tissue FFPE

value: Patient 315

value: V

value: MOC

value: Expansile

value: All


title: Patient 313

value: Patient 313

value: G

value: MBOT

value: Ovary/presumed ovary


title: Patient 296

value: Patient 296

value: L

value: Benign mucinous neoplasm

value: survival


title: Patient 307

value: Patient 307


title: Patient 309

value: Patient 309


title: Patient 299

value: Patient 299


title: Patient 295

value: Tumor tissue FFPE

value: Patient 295

value: A


title: Patient 305

value: Patient 305

value: MOC


title: Patient 298

value: Patient 298

value: V

value: All


title: Patient 292

value: Patient 292

value: C

value: MBOT


title: Patient 290

value: Patient 290

value: Expansile

value: Ovary/presumed ovary


title: Patient 288

value: Patient 288

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: Patient 297

value: Tumor tissue FFPE

value: Patient 297

value: L


title: Patient 301

value: Patient 301

value: E

value: MOC


title: CD45+ CD11b+ cells from subdura of mice cured from late-stage T. b. brucei infection, 9 weeks post treatment

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description:
Cured_Subura_YFP
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw data bcl files were demultiplexed using Cellranger mkfastq.
Demultiplexed data was processed using the Cellranger count pipeline.
Assembly: mm10
Supplementary files format and content: h5 files including raw counts (output CellRanger Count) per sample.
Supplementary files format and content: Text metadata files with information per cell.

source_name: subdural meninges

extract_protocol:
Sample preparation for sort: Tissues were dissociated as described in the manuscript. To limit dissociation-induced gene expression, cured vs. control samples were dissociated in the presence of actinomycin D (ActD), as previously described (Van Hove et al., 2019). After tissue dissociation and antibody staining (anti-CD45, anti-CD11b), cells were sorted into RPMI medium, supplemented with 10% (v/v) FCS, 300 μg/ml L-glutamine, 100 units/ml penicillin, 100 μg/ml streptomycin, 1 mM sodium pyruvate (Gibco), 1% (v/v) MEM non-essential amino acids (Gibco) and 1% (v/v) β-mercaptoethanol (Sigma).
Post-sort sample preparation: Sorted cells were centrifuged for 6 min at 4°C at 450 g and resuspended in PBS with 0.04% bovine serum albumin in an estimated concentration of 1000 cells/µl.
To generate single-cell gel beads in emulsion (GEM), single cell suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics). For most samples, the GEMs and scRNA-seq libraries were prepared with the GemCode Single Cell 3’ Gel Bead and Library kit v2 (10x Genomics) and the Chromium i7 Multiplex kit (10x Genomics), according to the manufacturer’s instructions. For the cured versus control samples, a Chromium Next Gem Single Cell 3’ Gel Bead and Library kit v3.1 (10x Genomics) was used. In essence, GEM reverse-transcription was achieved in a 96-deep-well plate by an incubation reaction module at 53°C for 45 min, 85°C for 5 min, finishing at 4°C, generating barcoded complementary DNA (cDNA). Subsequently, GEMs were broken and cDNA was cleaned up with DynaBeads MyOne Silane Beads (ThermoFisher Scientific) and SPRIselect Reagent Kit (Beckman Coulter). Full-length, barcoded cDNA was amplified by a polymerase chain reaction (PCR) in a 96-deep-well reaction module at 98°C for 3 min, 14 cycles of 98°C for 15 s, 67°C for 20 s and 72°C for 1 min, a final cycle at 72°C for 1 min and ending at 4°C. After clean-up using SPRIselect Reagent Kit and enzymatic fragmentation, Illumina-ready sequencing libraries were generated, by library construction through addition of R1 (read 1 primer), P5, P7, i7 sample index and R2 (10x Genomics), via end-repair, A-tailing, adapter ligation, post-ligation SPRIselect cleanup/size selection and sample index PCR. The cDNA content of pre-fragmentation and post-sample index PCR samples was analysed using a 2100 BioAnalyzer (Agilent). The sequencing libraries were loaded onto an Illumina HiSeq4000 or an Illumina NovaSeq6000 flow cell, using the sequencing settings recommended by 10x Genomics.

value: subdural meninges

tag: cell type

tag: strain

value: cured, 9w


title: Patient 312

tag: individual

value: Patient 312

value: V

value: Metastases (unknown)

value: Mets (panc)

value: Infiltrative

value: All


title: Patient 294

value: Patient 294

tag: study

value: B

value: Expansile

value: Ovary/presumed ovary


title: Patient 291

value: Tumor tissue FFPE

value: Patient 291

value: T

tag: finalstatus

value: Pancreas

value: Primary pancreatic

value: UGI


title: Patient 306

value: Patient 306

value: C

tag: diagnosis

value: MBOT


title: Patient 314

value: Patient 314

value: N

value: MOC

tag: analysis


title: Patient 303

tag: tissue

value: Patient 303

value: V

value: All


title: isolated HSC from  YAP f/f  from injured liver (6xCCl4) LYT017

description:
isolated HSC from  YAP f/f  from injured liver (6xCCl4)
RNAseq on FACS-sorted HSC from YAP floxed (wt) mice
Mice were treated with 6xCCl4 (i.p. 0.5 mg/kg, diluted 1:4 in corn oil,) every 3 days. Hepatic Stellate Cells (HSC) were isolated 2 days after the last injection of CCl4 using density centrifugation and subsequent retinoid autofluorescence-based FACS sorting as previously described (Mederacke et al, Nat Protocol 2015). Hepatic stellate cells were lysed immediately after FACS sorting.

data_processing:
Libraries are then sequenced using Illumina NovaSeq 6000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.
RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
Pseudoalignment to a kallisto index was created from transcriptomes (Human: GRCh38; Mouse: GRCm38) using kallisto (0.44.0)
We test for differentially expressed genes under various conditions using Sleuth, an R package designed to compute transcript and gene-level differential expression from kallisto abundance files. The 'HSC_YAPf_vsd.txt' file corresponds to the the results from the variance-stabilizing transformation of the samples.
Assembly: mm10

extract_protocol:
RNA was isolated by column purification (Qiagen) and quantification by NanoDrop spectrophotometer. Bioanalyzer was used to assess the RNA quality.
For STRDPOLYA: we use poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry. For RIBOZERO: We use ribosomal depletion to remove rRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry.

value: YAP floxed; C57BL/6J background

tag: liver damage

value: CCl4 (6 times)

value: FACS-sorted VitA+ Hepatic Stellate Cells


title: CD45+ CD11b+ cells from choroid plexus of non-infected mice (age-matched to cured mice)

description:
Control_CP_YFP
10x Genomics

source_name: choroid plexus

value: choroid plexus

value: non-infected


title: CD45+ CD11b+ cells from choroid plexus of mice cured from late-stage T. b. brucei infection, 9 weeks post treatment

description:
Cured_CP_YFP
10x Genomics

value: cured, 9w


title: Patient 283

value: Tumor tissue FFPE

value: Patient 283

value: S

tag: stagegroup

value: Stomach

value: Primary gastric


title: Patient 282

value: Patient 282

value: C

value: Expansile

value: Ovary/presumed ovary


title: Patient 287

value: Patient 287

value: N

value: MOC


title: Patient 280

value: Patient 280

value: T

value: Pancreas

value: Primary pancreatic

value: UGI

value: Infiltrative

value: All


title: Patient 289

value: Tumor tissue FFPE

value: Patient 289

value: L

value: MBOT


title: Patient 300

value: Patient 300

value: B

value: predictions/survival


title: Patient 304

value: Patient 304

value: V

value: Ovary/presumed ovary


title: isolated HSC from  YAP f/f  from injured liver (6xCCl4) LYT015

value: YAP floxed; C57BL/6J background

value: CCl4 (6 times)

value: FACS-sorted VitA+ Hepatic Stellate Cells


title: isolated HSC from  YAP f/f  from injured liver (6xCCl4) LYT014


title: Patient 285

value: Patient 285

value: O

value: MOC

value: Expansile


title: isolated HSC from  LratCre pos YAP f/f  (YAP ko) from injured liver (6xCCl4) LYT013

description:
isolated HSC from  LratCre pos YAP f/f  (YAP ko) from injured liver (6xCCl4)
RNAseq on FACS-sorted HSC from YAP del (ko) mice
Mice were treated with 6xCCl4 (i.p. 0.5 mg/kg, diluted 1:4 in corn oil,) every 3 days. Hepatic Stellate Cells (HSC) were isolated 2 days after the last injection of CCl4 using density centrifugation and subsequent retinoid autofluorescence-based FACS sorting as previously described (Mederacke et al, Nat Protocol 2015). Hepatic stellate cells were lysed immediately after FACS sorting.

value: LratCre+; YAP floxed; C57BL/6J background


title: isolated HSC from  LratCre pos YAP f/f  (YAP ko) from injured liver (6xCCl4) LYT016


title: Patient 293

value: Tumor tissue FFPE

value: Patient 293

value: All


title: Patient 286

value: Patient 286

value: C

value: MBOT


title: Patient 284

value: Patient 284


title: CD45+ CD11b+ cells from subdura of non-infected mice (age-matched to cured mice)

description:
Control_Subura_YFP
10x Genomics

value: subdural meninges

value: non-infected


title: Patient 276

value: Patient 276

value: V

value: Ovary/presumed ovary


title: Patient 275

value: Patient 275

value: B

value: predictions/survival


title: Patient 281

value: Patient 281

value: T

value: Pancreas

value: Primary pancreatic

value: UGI

value: Infiltrative


title: Patient 279

value: Tumor tissue FFPE

value: Patient 279

value: G

value: MOC


title: isolated HSC from  YAP f/f  from injured liver (6xCCl4) LYT004

value: YAP floxed; C57BL/6J background

value: CCl4 (6 times)

value: FACS-sorted VitA+ Hepatic Stellate Cells


title: Patient 273

value: Patient 273

value: I

value: Ovary/presumed ovary

value: All


title: Patient 274

value: Patient 274

value: V

value: MBOT


title: isolated HSC from  YAP f/f  from injured liver (6xCCl4) LYT005


title: isolated HSC from  LratCre pos YAP f/f  (YAP ko) from injured liver (6xCCl4) LYT006

value: LratCre+; YAP floxed; C57BL/6J background


title: Patient 278

value: Patient 278

value: S

value: Expansile


title: Patient 277

value: Tumor tissue FFPE

value: Patient 277

value: M

value: Infiltrative


title: isolated HSC from  LratCre pos YAP f/f  (YAP ko) from injured liver (6xCCl4) LYT008

value: CCl4 (6 times)


title: Patient 272

value: Patient 272

value: O

value: MOC


title: PMs,wt vsv,0h

city: Tian Jin

first: Yang

last: Cao

address: No. 94 Weijin Road

institute: Nankai University

data_processing:
Illumina Casava1.7 software used for basecalling
Sequence reads were trimmed for adaptor sequence,and masked for low-complexity or low-quality sequence ，then mapped to mm10 whole genome using bowtie v0.12.2 with parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al,Nucleic Acids Research,2009 .In short ,exons from all isforms.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: peritoneal macrophages

extract_protocol:
Retinasn were removed,flash frozen on dry ice ,and RNA was harvested using Trizol reagent Illumina TruSeq RNA Sample Prep Kit(Cat#FC-122-1001) was used with 1ug of total RNA for the construction
RNA libraries for RNA-seq were prepared using standard Illumina protocols.

value: peritoneal macrophages

tag: genotype

value: WT

tag: treatment

value: vsv( Vesicular stomatitis virus) infection

tag: timepoint

value: hour 0


title: Patient 267

value: Patient 267

value: C

value: MBOT

value: Ovary/presumed ovary

value: predictions/survival


title: Patient 271

value: Tumor tissue FFPE

value: Patient 271

value: V

value: All


title: PMs,wt vsv,8h

value: hour 8


title: Patient 266

value: Patient 266

value: K

value: Colon

value: Primary CRC

value: LGI


title: Patient 268

value: Patient 268

value: R

value: Metastases (unknown)

value: Mets (UGI)

value: UGI

value: Infiltrative


title: IgG, replicate 1, RIP-seq

city: Beijing

first: Di

last: Liu

address: No. 45 West Street, Beijing

institute: Xuanwu Hospital, Capital Medical University

data_processing:
Firstly, all RIP-seq data were processed to remove adapter sequences and low-quality bases using Trimmomatic (version 0.36). Then, the reads were mapped to the mouse genome (mm10) of GENCODE (Version M22) using STAR (Version 2.7.3a). Salmon (version 1.1.0) was used to estimate the expression levels (TPM normalization) of each detected gene.
Assembly: mm10
Supplementary files format and content: Processed data files included counts info for each replicate in csv format

source_name: caudal half

extract_protocol:
10 μL Protein A Dynabeads were added to 500 μL RIPA buffer containing proteinase inhibitor cocktail, rotated 1-2 min at RT and placed on the magnet stand to remove supernatant. Then pre-treated beads were resuspended with 50 μL RIPA buffer containing 1 μg indicated RIP antibodies, rotated and incubated at 4 °C for 4-6 hours, and then placed on the magnet stand to remove the supernatant.
The cDNA libraries were generated as previously reported with a litter modification[16]. Instead of a single cell, a certain volume of RNA solution was added into the reverse transcription system for reverse transcription After that, cDNA was sonicated to ~300 bp fragments by Covaris S2 system and purified with QIAGEN PCR purification kit. Then libraries were generated using KAPA Hyper Prep Kit Illumina® platforms following the manufacture’s protocol.

value: caudal half

value: WT

tag: age


title: Runx1, replicate 2, RIP-seq


title: Runx1, replicate 1, RIP-seq


title: Patient 269

value: Tumor tissue FFPE

value: Patient 269

value: L

value: MOC

value: Expansile

value: Ovary/presumed ovary


title: Patient 265

value: Patient 265

value: F

value: Pancreas

value: Primary pancreatic

value: All


title: Patient 264

value: Patient 264

value: MBOT

value: Benign mucinous neoplasm

value: survival


title: IgG, replicate 2, RIP-seq

value: caudal half


title: Patient 262

value: Patient 262

value: V


title: RPE, MertkOV3, P25, Biol rep 1

city: New Haven

first: Yemsratch

middle: Tadesse

last: Akalu

state: CT

address: 300 Cedar Street

department: Immunobiology

institute: Yale University

description:
P25_RPE_normalizedcount_all samples.txt
MertKOV3_1

data_processing:
Raw reads were subjected to trimming by btrim to remove sequencing adaptors and low-quality regions.
Reads were mapped to the mouse genome (GRCm38) using STAR
After counts are collected, Deseq2 package was run to identify differentially expressed genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files which include normalized counts for each sample

source_name: RPE

extract_protocol:
RNA from BMDMs or RPE cells was extracted using Rneasy Mini kit (Qiagen) following manufacturer’s instructions.
Libraries were prepared following the illumina paired-end sequencing protocol as detailed here (https://medicine.yale.edu/keck/ycga/sequencing/illumina/1_21591_284_12501_v1.pdf)

value: RPE

value: epithelial

value: Mertk knockout version 3

value: none, direct ex-vivo use


title: RPE, MertkOV2, P25, Biol rep 2

description:
P25_RPE_normalizedcount_all samples.txt
MertKOV2_2

value: Mertk knockout version 2


title: RPE, MertkOV2, P25, Biol rep 3

description:
P25_RPE_normalizedcount_all samples.txt
MertKOV2_3


title: RPE, MertkOV2, P25, Biol rep 1

description:
P25_RPE_normalizedcount_all samples.txt
MertKOV2_1


title: Patient 260

value: Tumor tissue FFPE

value: Patient 260

value: Ovary/presumed ovary


title: Patient 270

value: Patient 270

value: L

value: MOC


title: RPE, MertkOV3, P25, Biol rep 2

description:
P25_RPE_normalizedcount_all samples.txt
MertKOV3_2


title: Patient 259

value: Patient 259

value: Expansile

value: All


title: RPE, MertkOV3, P25, Biol rep 3

description:
P25_RPE_normalizedcount_all samples.txt
MertKOV3_3


title: RPE, MertkOV1, P25, Biol rep 6

description:
P25_RPE_normalizedcount_all samples.txt
MertKOV1_6

value: Mertk knockout version 1


title: Patient 258

value: Patient 258

value: E

value: Infiltrative


title: Patient 261

value: Patient 261

value: S

value: Colon

value: Primary CRC

value: LGI


title: Patient 263

value: Tumor tissue FFPE

value: Patient 263

value: V

value: MOC (anaplastic)


title: Patient 257

value: Patient 257

value: MBOT

value: Ovary/presumed ovary


title: Patient 256

value: Patient 256

value: L

value: MOC

value: All


title: RPE, MertkOV1, P25, Biol rep 5

description:
P25_RPE_normalizedcount_all samples.txt
MertKOV1_5

value: RPE

value: epithelial

value: Mertk knockout version 1

value: none, direct ex-vivo use


title: RPE, MertkOV1, P25, Biol rep 2

description:
P25_RPE_normalizedcount_all samples.txt
MertKOV1_2


title: RPE, MertkOV1, P25, Biol rep 3

description:
P25_RPE_normalizedcount_all samples.txt
MertKOV1_3


title: RPE, MertkOV1, P25, Biol rep 4

description:
P25_RPE_normalizedcount_all samples.txt
MertKOV1_4


title: RPE, MertkOV1, P25, Biol rep 1

description:
P25_RPE_normalizedcount_all samples.txt
MertKOV1_1


title: Patient 255

value: Patient 255

value: W


title: RPE, C57BL/6, P25, Biol rep 5

description:
P25_RPE_normalizedcount_all samples.txt
C57BL/6_5

value: wildtype


title: Patient 254

value: Tumor tissue FFPE

value: Patient 254

value: R


title: RPE, C57BL/6, P25, Biol rep 6

description:
P25_RPE_normalizedcount_all samples.txt
C57BL/6_6


title: Patient 252

value: Patient 252

value: H

value: Infiltrative


title: RPE, C57BL/6, P25, Biol rep 4

description:
P25_RPE_normalizedcount_all samples.txt
C57BL/6_4


title: Patient 250

value: Patient 250

value: K

value: Colon

value: Primary CRC

value: LGI


title: RPE, C57BL/6, P25, Biol rep 3

description:
P25_RPE_normalizedcount_all samples.txt
C57BL/6_3

value: RPE

value: epithelial


title: Patient 249

value: Patient 249

value: All


title: Patient 247

value: Patient 247

value: V

value: MOC

value: Expansile

value: Ovary/presumed ovary


title: Patient 248

value: Tumor tissue FFPE

value: Patient 248

value: S

value: Appendix

value: Mets (Appendix)


title: RPE, C57BL/6, P25, Biol rep 1

description:
P25_RPE_normalizedcount_all samples.txt
C57BL/6_1

value: wildtype

value: none, direct ex-vivo use


title: BMDM, MertkOV3, Biol rep 3

description:
BMDMs_normalizedcount_all samples.txt
MertKOV3_3

source_name: BMDMs

value: BMDMs

value: immune

value: Mertk knockout version 3

value: macrophage differentiation


title: BMDM, MertkOV3, Biol rep 2

description:
BMDMs_normalizedcount_all samples.txt
MertKOV3_2


title: BMDM, MertkOV3, Biol rep 1

description:
BMDMs_normalizedcount_all samples.txt
MertKOV3_1


title: Patient 246

value: Patient 246

value: MBOT

value: All


title: BMDM, MertkOV2, Biol rep 3

description:
BMDMs_normalizedcount_all samples.txt
MertKOV2_3

value: Mertk knockout version 2


title: Patient 245

value: Patient 245

value: H

value: MOC

value: Infiltrative


title: BMDM, MertkOV2, Biol rep 2

description:
BMDMs_normalizedcount_all samples.txt
MertKOV2_2


title: Patient 253

value: Tumor tissue FFPE

value: Patient 253

value: K

value: Colon

value: Primary CRC

value: LGI


title: BMDM, MertkOV2, Biol rep 1

description:
BMDMs_normalizedcount_all samples.txt
MertKOV2_1

value: BMDMs

value: immune


title: BMDM, MertkOV1, Biol rep 2

description:
BMDMs_normalizedcount_all samples.txt
MertKOV1_2

value: Mertk knockout version 1

value: macrophage differentiation


title: Patient 244

value: Patient 244

value: W

value: Ovary/presumed ovary


title: BMDM, MertkOV1, Biol rep 3

description:
BMDMs_normalizedcount_all samples.txt
MertKOV1_3


title: Patient 241

value: Patient 241

value: M

value: Expansile

value: All


title: BMDM, C57BL/6, Biol rep 3

description:
BMDMs_normalizedcount_all samples.txt
C57BL/6_3

value: wildtype


title: BMDM, MertkOV1, Biol rep 1

description:
BMDMs_normalizedcount_all samples.txt
MertKOV1_1


title: Patient 242

value: Tumor tissue FFPE

value: Patient 242

value: O

value: MOC

value: Infiltrative


title: Patient 251

value: Patient 251

value: V

value: MBOT


title: Patient 243

value: Patient 243

value: S

value: Colon

value: Mets (CRC)

value: LGI

value: Peritoneum, NOS


title: Patient 238

value: Patient 238

value: Primary CRC


title: Patient 240

value: Patient 240

value: Expansile

value: Ovary/presumed ovary

value: All


title: Patient 237

value: Tumor tissue FFPE

value: Patient 237

value: C

value: Metastases (LGI)

value: Mets (LGI)


title: BMDM, C57BL/6, Biol rep 1

description:
BMDMs_normalizedcount_all samples.txt
C57BL/6_1

value: BMDMs

value: immune

value: wildtype

value: macrophage differentiation


title: Patient 239

value: Patient 239

value: J

value: MBOT


title: RPE, C57BL/6, P25, Biol rep 2

description:
P25_RPE_normalizedcount_all samples.txt
C57BL/6_2

value: RPE

value: epithelial

value: none, direct ex-vivo use


title: Patient 235

value: Patient 235

value: O

value: MOC

value: Expansile

value: Ovary/presumed ovary


title: BMDM, C57BL/6, Biol rep 2

description:
BMDMs_normalizedcount_all samples.txt
C57BL/6_2


title: Patient 236

value: Tumor tissue FFPE

value: Patient 236

value: I

value: All


title: Patient 234

value: Patient 234

value: V


title: Patient 233

value: Patient 233

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: Patient 231

value: Patient 231

value: Infiltrative


title: Patient 230

value: Patient 230

value: S

value: Appendix

value: Mets (Appendix)

value: LGI

value: Unknown


title: 16149_LF

city: Kunming

first: Jiandong

last: Shi

state: Yunnan

address: 935# Jiaoling Road

department: Department of Vaccine Research

institute: Institute of Medical Biology

description: total RNA

data_processing:
Cellranger pipeline. The Cell Ranger software was obtained from  10× Genomics website. Alignment, filtering, barcode counting,  and UMI counting were performed with cell ranger count module.  Dimensionality reduction and the first ten principal components  were used to generate clusters by K-means algorithm and graphbased algorithm, respectively.
Seurat pipeline. The other clustering method is Seurat 3.0(R package). Cells whose gene number was less than   200,or gene number ranked in the top 1%, or mitochondrial gene ratio was more than 25% were regarded as   abnormaland filtered out. Dimensionality reduction was performed using PCA, and visualization was realized by   TSNE andUMAP.
Enrichment Analysis. GO enrichment, KEGG enrichment, Reactome enrichment and Disease enrichment (humanonly)  of cluster markers were performed using KOBAS software with Benjamini-Hochberg multiple testingadjustment,  using top 20 markers gene of cluster. The results were visualized using R package.
Single-cell trajectories Analysis. Single-cell trajectories were built with Monocle (R package) that   introducedpseudotime. Genes were filtered by the following criteria: Expressed in more than 10 cells; The average   expressionvalue was greater than 0.1; Qval was less than 0.01 in different analysis.
Assembly: ftp://ftp.ensembl.org/pub/release-100/gtf/macaca_mulatta/Macaca_mulatta.Mmul_10.100.gtf.gz

organism: Macaca mulatta

source_name: lung tissue

extract_protocol:
For cell capture and cDNA  synthesis, single cells were suspended in PBS containing 0.04%  bovine serum albumin. About 8000 cells were added to each  channel, and it is estimated that about 2200 target cells will be  recovered. The captured cells were lysed and the released RNA  was barcoded in a single GEM by reverse transcription. Reverse  transcription was performed on the S1000TM Touch Thermal  Cycler (Bio Rad) at 53 °C for 45 min, then at 85 °C for 5 min and  held at 4 °C. The quality of cDNA was evaluated using Agilent 4200  (CapitalBio Technology, Beijing).
Single-cell suspensions were made using a gentle MACS Octo (Miltenyi Biotec). Single-cell suspensions were loaded onto the Chromium Controller (10× Genomics) for droplet formation. scRNA-seq libraries were constructed by the Single Cell 3’ Library and Gel Bead Kit V3. The libraries were sequenced by an Illumina Novaseq6000 sequencer, the sequencing depth of each cell was at least 100,000 reads, and the pairedend 150 bp (PE150) reading strategy (CapitalBio Technology, Beijing) was adopted.

treatment_protocol: Rhesus monkeys (3-5 kg, 3-5years old) were used for this study. One monkey is infected by intragastric administration with 1x 10^7 PFU of SARS-CoV-2 in 1mL of PBS, and another monkey was intranasally injected with 1x10^6 of SARS-CoV-2 in 200 µl of PBS. One monkey was   Intranasally and intragastrically treated with PBS as a control. We analyzed the tissues collected on the 4 dpi following   Intranasal and intragastrical inoculation.

tag: tissue region

value: left lung

tag: time

value: 4 dpi following intranasally inoculation

tag: animal no.


title: 16001_RF

description: total RNA

value: right lung

value: 4 dpi following intragastric inoculation


title: 16271_RF

description: total RNA

value: uninfected control


title: 16271_LF

description: total RNA


title: 16001_LF

description: total RNA


title: 16149_RF

description: total RNA


title: Patient 227

value: Tumor tissue FFPE

value: Patient 227

value: L

value: MOC

value: Omentum

value: All


title: Patient 228

value: Patient 228

value: V

value: Expansile

value: Ovary/presumed ovary


title: Patient 222

value: Patient 222

value: MBOT


title: Patient 225

value: Patient 225

value: K

value: Colon

value: Primary CRC

value: LGI


title: Patient 224

value: Tumor tissue FFPE

value: Patient 224

value: T

value: Pancreas

value: Primary pancreatic

value: UGI


title: Patient 219

value: Patient 219

value: F

value: All


title: Patient 218

value: Patient 218

value: C

value: Ovary/presumed ovary


title: Patient 220

value: Patient 220

value: I

value: MOC


title: Patient 213

value: Patient 213

value: H

value: Expansile


title: Patient 221

value: Tumor tissue FFPE

value: Patient 221

value: V


title: Patient 232

value: Patient 232

value: Q

value: MBOT

value: predictions/survival


title: Patient 216

value: Patient 216

value: W

value: All


title: Patient 214

value: Patient 214

value: A

value: Ovary/presumed ovary


title: Patient 215

value: Patient 215

value: K

value: Colon

value: Primary CRC

value: LGI


title: Patient 229

value: Tumor tissue FFPE

value: Patient 229


title: Patient 226

value: Patient 226

value: T

value: Pancreas

value: Primary pancreatic

value: UGI

value: Unknown


title: Patient 210

value: Patient 210

value: W

value: MOC

value: All


title: Patient 207

value: Patient 207

value: L

value: Small bowel


title: Patient 209

value: Patient 209

value: C

value: Expansile

value: Ovary/presumed ovary


title: Patient 208

value: Tumor tissue FFPE

value: Patient 208


title: Patient 205

value: Patient 205

value: J


title: Patient 212

value: Patient 212

value: V

value: MBOT


title: Patient 211

value: Patient 211

value: B

value: predictions/survival


title: Patient 199

value: Patient 199

value: All


title: Patient 223

value: Patient 223

value: T

value: Pancreas

value: Primary pancreatic

value: UGI

value: Infiltrative


title: Patient 204

value: Tumor tissue FFPE

value: Patient 204

value: L

value: Ovary/presumed ovary


title: Patient 206

value: Patient 206


title: Patient 217

value: Patient 217

value: V

value: MBOT


title: Patient 202

value: Patient 202

value: B

value: Benign mucinous neoplasm

value: survival


title: Patient 200

value: Patient 200

value: All


title: Patient 192

value: Patient 192

value: C

value: Metastases (CRC)

value: Mets (CRC)

value: LGI


title: Patient 196

value: Tumor tissue FFPE

value: Patient 196

value: G

value: MOC

value: Expansile


title: Patient 197

value: Patient 197

value: W

value: Ovary/presumed ovary


title: Patient 193

value: Patient 193

value: S

value: Colon

value: Mets (Appendix)

value: Omentum


title: Patient 194

value: Patient 194

value: Stomach

value: Mets (gastric)

value: UGI

value: Infiltrative

value: All


title: Patient 190

value: Tumor tissue FFPE

value: Patient 190

value: V


title: Patient 191

value: Patient 191

value: MOC


title: Patient 185

value: Patient 185

value: F

value: Pancreas

value: Primary pancreatic


title: Patient 188

value: Patient 188

value: L

value: Expansile

value: Ovary/presumed ovary


title: Patient 186

value: Patient 186

value: MBOT


title: Patient 201

value: Patient 201

value: R


title: Patient 203

value: Tumor tissue FFPE

value: Patient 203

value: All


title: Patient 183

value: Patient 183

value: V

value: Metastases (LGI)

value: Mets (CRC)

value: LGI


title: Patient 182

value: Patient 182

value: C

value: MOC

value: MOC (anaplastic)

value: Infiltrative


title: Patient 187

value: Patient 187

value: Ovary/presumed ovary


title: Patient 195

value: Patient 195

value: Metastases (unknown)

value: Mets (Appendix)


title: Patient 178

value: Tumor tissue FFPE

value: Patient 178

value: K

value: Colon

value: Primary CRC


title: Patient 189

value: Patient 189

value: V

value: MBOT

value: All


title: Patient 180

value: Patient 180

value: G

value: MOC

value: Expansile


title: Patient 179

value: Patient 179

value: Ovary/presumed ovary


title: Patient 181

value: Patient 181

value: L


title: Patient 175

value: Tumor tissue FFPE

value: Patient 175

value: I


title: Patient 174

value: Patient 174

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: Patient 176

value: Patient 176

value: C

value: MBOT

value: predictions/survival


title: Patient 173

value: Patient 173

value: O

value: MOC

value: Expansile

value: All


title: Patient 184

value: Tumor tissue FFPE

value: Patient 184

value: V

value: Ovary/presumed ovary


title: Patient 170

value: Patient 170

value: L


title: Patient 171

value: Patient 171

value: R


title: human WBC, GB4030477 (iDNase-seq)

city: Bethesda

first: Keji

state: MD

address: 10 Center Dr

department: Systems Biology Center

institute: NHLBI

data_processing:
Basecalls performed
The raw fastq files are read and separated into 480 files corresponding to 96 pairs of cell barcodes over 5 replicates. The 480 pairs are shown in barcode_480.txt. A read is considered as belonging to one of the barcodes if the beginning of read 1 or read 2 contains the same pair of barcodes in the left and right column respectively.  After separting each set of fastq files into 480 files, some base pairs starting from 5' are trimmed and the remaining reads are mapped to the human genome using bowtie2.
The top 30 barcodes are selected from each well based on read count, so 30 nuclei are sorted for each well with doublets removed, where the number removed was calculated based on the collision rate like in (Science. 2015 May 22; 348(6237): 910–914). These are denoted as single cells because of the low likelihood of two cells in the same well having the same barcode. We required that qualifying cells have more than 100 reads and a FRiP greater than 0.1. With these requirements, 4489 cells were obtained, and we were able to identify 218,042 DHSs. For each cell, we calculated the reads that were located within the DHS and stored the results in a matrix.
Genome_build: hg18
barcode_480.txt: two columns, the left column refers to a DNA barcode starting from the 5' end while the right column refers to a DNA barcode starting from the 3' end
peaks_218042_WBC.txt: first column is for chromsome, second column is for DHS start site, and third column is for DHS end site
iDNase_4489_cells_218042_peaks_counts_at_WBC.mtx: This file contains read count data for single cells in MatrixMarket format. Each row corresponds to a non-zero entry with the row, column, and then value specified. Reading the matrix results in a 218042 x 4489 matrix of peaks by cells where each element represents the number of reads located within a DHS site for some single cell.

source_name: WBC

extract_protocol:
DNase-seq human 1.25M 2-step crosslink human healthy T/B/NK/monocyte, final 0.1U/μl DNase digestion 37°C 5 minutes, T cell split #1-15 wells, B cell split #16-30 wells, NK cell split #31-45 wells, monocyte split #46-61 wells, TdT&T4 methods adding P7 barcode adaptor (12.5μl volumn/well 37°C 60 minutes), pool, dilution, counting and redistribute into 96-well plate, total 20 nuclei per well seal completely, 65°C overnight; direct PCR1 (12 cycles), pool all the DNA, EXO I 30 minutes, A-tailing and P5 ligation(rt overnight) , column purification and PCR2(16 cycles), run-e-gel and cut from 200-500bp rc#1 i5-01
The isolated 50M of PBMC suspended by 50ml PBS /MgCl2 are firstly fixed by adding 400μl freshly prepared 0.25M Disuccinimidyl glutarate (DSG, ThermoFisher Scientific, catalog no.20593) and incubate at room temperature for 45 minutes with rotation. After protein-protein fixation by DSG and washing three times by PBS, cells suspended by culture medium DMEM supplemented with 10% FBS are further fixed by the addition of 1:15 volume of 16% (w/v) methanol-free formaldehyde solution (Thermo Fisher Scientific) and incubate at room temperature for 10 minutes. The fixing reaction is terminated by a 1:10 volume of 1.25 M glycine and incubate at room temperature for 5 minutes. The fixed cells are collected by centrifugation at 1320rpm for 7 minutes and washed with PBS. The cells are stored in aliquots (1 × 10e6 cells per tube) at −80°C until use.

tag: cell type

value: WBC


title: human WBC, GB4030480 (iDNase-seq)


title: human WBC, GB4030478 (iDNase-seq)


title: human WBC, GB4030479 (iDNase-seq)


title: Patient 169

value: Patient 169


title: human WBC, GB4030476 (iDNase-seq)


title: Patient 168

value: Patient 168

value: MBOT


title: human WBC, GB4030475 (iDNase-seq)


title: human WBC, GB4030474 (iDNase-seq)


title: Patient 177

value: Patient 177


title: Patient 167

value: Patient 167

value: I

value: MOC (anaplastic)


title: human WBC, GB4030473 (iDNase-seq)


title: Patient 166

value: Patient 166

value: Metastases (LGI)

value: Mets (unk primary)

value: LGI

value: All


title: human WBC, GB4030472 (iDNase-seq)


title: Patient 172

value: Tumor tissue FFPE

value: Patient 172

value: V

value: Metastases (unknown)

value: Mets (CRC)

value: Infiltrative

value: Ovary/presumed ovary


title: Patient 164

value: Patient 164

value: MBOT


title: Patient 165

value: Patient 165

value: T

value: Pancreas

value: Primary pancreatic

value: UGI

value: Expansile


title: human WBC, GB4030469 (iDNase-seq)

value: WBC


title: human WBC, GB4030470 (iDNase-seq)


title: Patient 198

value: Patient 198

value: P

value: MOC

value: predictions/survival


title: Patient 163

value: Tumor tissue FFPE

value: Patient 163

value: V

value: All


title: Patient 162

value: Patient 162

value: B

value: Ovary/presumed ovary


title: Patient 161

value: Patient 161

value: C

value: MBOT


title: Patient 160

value: Patient 160

value: Metastases (LGI)

value: Mets (Appendix)

value: LGI


title: human WBC, GB4030467 (iDNase-seq)

value: WBC


title: human WBC, GB4030468 (iDNase-seq)


title: human WBC, GB4030466 (iDNase-seq)


title: human WBC, GB4030465 (iDNase-seq)


title: human WBC, GB4030464 (iDNase-seq)


title: Patient 158

value: Patient 158

value: A

value: MOC

value: Expansile


title: Patient 159

value: Tumor tissue FFPE

value: Patient 159

value: R


title: Patient 156

value: Patient 156

value: All


title: Patient 155

value: Patient 155

value: V

value: Ovary/presumed ovary


title: human WBC, GB4030463 (iDNase-seq)


title: Patient 157

value: Patient 157

value: B

value: MBOT

value: predictions/survival


title: human WBC, GB4030471 (iDNase-seq)

value: WBC


title: Patient 154

value: Patient 154

value: P


title: human WBC, GB4030462 (iDNase-seq)


title: human WBC, GB4030459 (iDNase-seq)


title: Patient 153

value: Patient 153

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: human WBC, GB4030461 (iDNase-seq)


title: human WBC, GB4030460 (iDNase-seq)


title: Patient 151

value: Tumor tissue FFPE

value: Patient 151

value: MOC


title: Patient 152

value: Patient 152

value: H

value: Infiltrative

value: All


title: Patient 150

value: Patient 150

value: G

value: Expansile

value: Ovary/presumed ovary


title: human WBC, GB4030458 (iDNase-seq)

value: WBC


title: human WBC, GB4030455 (iDNase-seq)


title: human WBC, GB4030457 (iDNase-seq)


title: human WBC, GB4030456 (iDNase-seq)


title: Patient 148

value: Patient 148

value: B

value: MBOT

value: predictions/survival


title: Patient 147

value: Patient 147

value: L


title: Patient 145

value: Tumor tissue FFPE

value: Patient 145

value: O


title: Patient 146

value: Patient 146

value: V


title: Patient 149

value: Patient 149

value: H

value: MOC

value: Infiltrative

value: All


title: human WBC, GB4030454 (iDNase-seq)

value: WBC


title: human WBC, GB4030452 (iDNase-seq)


title: human WBC, GB4030453 (iDNase-seq)


title: human WBC, GB4030450 (iDNase-seq)


title: human WBC, GB4030451 (iDNase-seq)


title: Patient 142

value: Patient 142

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: Patient 140

value: Patient 140

value: Expansile

value: Ovary/presumed ovary


title: human WBC, GB4030448 (iDNase-seq)


title: Patient 144

value: Tumor tissue FFPE

value: Patient 144

value: C

value: Appendix

value: Primary appendix

value: LGI


title: Patient 141

value: Patient 141

value: D

value: MOC

value: MBOT

value: predictions/survival


title: human WBC, GB4030449 (iDNase-seq)

value: WBC


title: human WBC, GB4030446 (iDNase-seq)


title: human WBC, GB4030444 (iDNase-seq)


title: human WBC, GB4030443 (iDNase-seq)


title: Patient 138

value: Patient 138

value: S

value: All


title: Patient 135

value: Patient 135

value: V

value: Infiltrative


title: Patient 136

value: Tumor tissue FFPE

value: Patient 136

value: G

value: Expansile

value: Ovary/presumed ovary


title: Patient 143

value: Patient 143


title: human WBC, GB4030440 (iDNase-seq)


title: human WBC, GB4030442 (iDNase-seq)


title: human WBC, GB4030439 (iDNase-seq)


title: Patient 134

value: Patient 134


title: Patient 133

value: Patient 133

value: W

value: MOC


title: Patient 130

value: Patient 130


title: Patient 131

value: Patient 131

value: B

value: MBOT

value: predictions/survival


title: Patient 139

value: Patient 139

value: M


title: human WBC, GB4030438 (iDNase-seq)

value: WBC


title: human WBC, GB4030441 (iDNase-seq)


title: Patient 132

value: Tumor tissue FFPE

value: Patient 132

value: S

value: Stomach

value: Primary gastric

value: UGI

value: All


title: human WBC, GB4030437 (iDNase-seq)


title: Patient 137

value: Patient 137

value: O

value: Ovary/presumed ovary


title: human WBC, GB4030436 (iDNase-seq)


title: human WBC, GB4030435 (iDNase-seq)


title: human WBC, GB4030445 (iDNase-seq)


title: human WBC, GB4030434 (iDNase-seq)


title: human WBC, GB4030447 (iDNase-seq)


title: Patient 128

value: Patient 128

value: V

value: MOC

value: Infiltrative


title: Patient 127

value: Patient 127

value: MBOT


title: Patient 126

value: Patient 126

value: B


title: Patient 129

value: Tumor tissue FFPE

value: Patient 129

value: Expansile


title: Patient 124

value: Patient 124


title: human WBC, GB4030433 (iDNase-seq)

value: WBC


title: Patient 125

value: Patient 125

value: C

value: predictions/survival


title: human WBC, GB4030432 (iDNase-seq)


title: human WBC, GB4030431 (iDNase-seq)


title: human WBC, GB4030430 (iDNase-seq)


title: Patient 122

value: Patient 122

value: E

value: Ovary/presumed ovary

value: All


title: Patient 121

value: Patient 121

value: T

value: Pancreas

value: Primary pancreatic

value: UGI


title: human WBC, GB4030429 (iDNase-seq)


title: human WBC, GB4030428 (iDNase-seq)


title: Patient 123

value: Tumor tissue FFPE

value: Patient 123

value: P

value: MOC

value: MBOT


title: Patient 119

value: Patient 119

value: V


title: human WBC, GB4030425 (iDNase-seq)

value: WBC


title: human WBC, GB4030424 (iDNase-seq)


title: human WBC, GB4030423 (iDNase-seq)


title: Patient 116

value: Patient 116

value: A

value: predictions/survival


title: human WBC, GB4030426 (iDNase-seq)


title: Patient 117

value: Patient 117

value: Infiltrative

value: Ovary/presumed ovary

value: All


title: human WBC, GB4030422 (iDNase-seq)


title: Patient 112

value: Patient 112

value: O

value: Expansile


title: Patient 111

value: Tumor tissue FFPE

value: Patient 111


title: Patient 110

value: Patient 110


title: human WBC, GB4030419 (iDNase-seq)


title: Patient 114

value: Patient 114

value: L

value: MOC

value: MBOT


title: human WBC, GB4030418 (iDNase-seq)

value: WBC


title: Patient 115

value: Patient 115


title: Patient 113

value: Patient 113

value: R

value: predictions/survival


title: Patient 118

value: Patient 118

value: Ovary/presumed ovary


title: human WBC, GB4030413 (iDNase-seq)


title: human WBC, GB4030416 (iDNase-seq)


title: Patient 108

value: Patient 108

value: A

value: All


title: Patient 109

value: Tumor tissue FFPE

value: Patient 109

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: human WBC, GB4030412 (iDNase-seq)


title: Patient 106

value: Patient 106

value: L

value: MOC

value: MBOT


title: human WBC, GB4030411 (iDNase-seq)

value: WBC


title: human WBC, GB4030420 (iDNase-seq)


title: human WBC, GB4030410 (iDNase-seq)


title: human WBC, GB4030427 (iDNase-seq)


title: human WBC, GB4030421 (iDNase-seq)


title: Patient 102

value: Patient 102


title: Patient 101

value: Patient 101

value: Infiltrative


title: Patient 103

value: Patient 103


title: Patient 120

value: Patient 120

value: O

value: Expansile

value: Ovary/presumed ovary


title: Patient 104

value: Tumor tissue FFPE

value: Patient 104

value: V

value: All


title: human WBC, GB4030407 (iDNase-seq)


title: Patient 98

value: Patient 98

value: M


title: human WBC, GB4030405 (iDNase-seq)


title: Patient 105

value: Patient 105

value: MOC


title: Patient 107

value: Patient 107


title: human WBC, GB4030415 (iDNase-seq)

value: WBC


title: human WBC, GB4030414 (iDNase-seq)


title: human WBC, GB4030399 (iDNase-seq)


title: human WBC, GB4030417 (iDNase-seq)


title: human WBC, GB4030400 (iDNase-seq)


title: human WBC, GB4030398 (iDNase-seq)


title: human WBC, GB4030406 (iDNase-seq)


title: Patient 89

value: Patient 89

value: W


title: Patient 96

value: Patient 96


title: human WBC, GB4030404 (iDNase-seq)


title: human WBC, GB4030409 (iDNase-seq)


title: Patient 100

value: Patient 100


title: Patient 93

value: Patient 93

value: Infiltrative


title: human WBC, GB4030401 (iDNase-seq)


title: Patient 83

value: Patient 83

value: MOC (anaplastic)

value: Ovary/presumed ovary


title: human WBC, GB4030408 (iDNase-seq)


title: human WBC, GB4030403 (iDNase-seq)


title: Patient 95

value: Tumor tissue FFPE

value: Patient 95

value: T

value: Pancreas

value: Primary pancreatic

value: UGI

value: Expansile


title: Patient 94

value: Patient 94

value: K

value: Colon

value: Primary CRC

value: LGI

value: All


title: Patient 84

value: Patient 84

value: B

value: MBOT

value: Benign mucinous neoplasm

value: survival


title: Patient 85

value: Tumor tissue FFPE

value: Patient 85

value: C

value: MOC

value: Ovary/presumed ovary


title: Patient 82

value: Patient 82

value: O

value: predictions/survival


title: Patient 97

value: Patient 97

value: Infiltrative


title: Patient 99

value: Patient 99

value: L


title: Patient 90

value: Patient 90

value: V

value: Expansile

value: All


title: human WBC, GB4030402 (iDNase-seq)

value: WBC


title: Patient 91

value: Tumor tissue FFPE

value: Patient 91


title: Patient 88

value: Patient 88

value: E

value: MBOT


title: Patient 92

value: Patient 92

value: P

value: MOC

value: Ovary/presumed ovary


title: Patient 80

value: Patient 80

value: Metastases (LGI)

value: Mets (Appendix)

value: LGI


title: human WBC, GB4030397 (iDNase-seq)


title: human WBC, GB4030393 (iDNase-seq)


title: human WBC, GB4030388 (iDNase-seq)


title: human WBC, GB4030395 (iDNase-seq)


title: human WBC, GB4030394 (iDNase-seq)