title: replicative senescent hVSMC-03

description:
hVSMC-03
17H-20M-04-P11C_S7_L001

source_name: human vascular smooth muscle cell

value: cell


title: proliferative hVSMC-02

status: Public on Jul 27 2021

type: SRA

city: Semenyih

first: Yuh-Fen

last: Pung

address: Jalan Broga

country: Malaysia

institute: University of Nottingham Malaysia

description:
hVSMC-02
16H-22M-03-P6C_S5_L001

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA 1.8
Rawreads were QC and trimmed using Cutadapt
Trimmed reads were aligned to Homo sapiens reference genome (GRCh38) using miRDeep2
Mapped transcripts were aligned with miRBase version 22
Known mature miRNAs were analyzed for differential expression using edgeR
Genome_build: GRCh38
Supplementary_files_format_and_content: One MS Excel files containing normalized reads of mature miRNAs in all samples. Two MS Excel files containing differentially expressed miRNAs (normalized count, fold change, p values and FDR values) in cells and exosomes

molecule: total RNA

organism: Homo sapiens

growth_protocol: HVSMCs were first maintained in Smooth Muscle Basal Medium (SmBM) (Lonza, Switzerland) then underwent gradual SmBM replacement with Dulbecco’s Modified Eagle Medium (DMEM), supplemented with 2% L-glutamine, 1% penicillin-streptomycin and 10% FBS. Media was changed every 48 hr.

extract_protocol:
RNA extraction was carried out using miRNeasy Micro Kit (QIAGEN, Germany).
Libraries for sequencing were prepared according to the manufacturer’s protocol TruSeq Small RNA Library Prep (Illumina, San Diego CA).
RNA sequencing was carried out using NextSeq 500 Mid v2 Kit, 150 cycles (Illumina, San Diego CA).

treatment_protocol: Cells were continuousely passaged until replicative senescence was achieved. No treatment was performed.

tag: source

tag: condition

value: proliferative


title: proliferative hVSMC-Exo-01

description:
hVSMC-Exo-01
18H-14M-06-P5X_S12_L001

source_name: human vascular smooth muscle cell-derived exosomes

value: exosomes


title: proliferative hVSMC-Exo-03

description:
hVSMC-Exo-03
17H-20M-04-P7X_S10_L001


title: proliferative hVSMC-Exo-02

description:
hVSMC-Exo-02
16H-22M-03-P6X_S6_L001


title: replicative senescent hVSMC-02

description:
hVSMC-02
16H-22M-03-P19C_S3_L001

value: replicative senescent


title: replicative senescent hVSMC-Exo-03

description:
hVSMC-Exo-03
17H-20M-04-P11X_S8_L001


title: proliferative hVSMC-01

description:
hVSMC-01
18H-14M-06-P5C_S11_L001


title: replicative senescent hVSMC-Exo-02

description:
hVSMC-Exo-02
16H-22M-03-P19X_S4_L001


title: Huh7.DMSO_2

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

description: DMSO

data_processing:
Base calling was done using Illumina software
Sequenced reads were mapped to hg19 version of mouse genome using RNA-STAR using parameters (outFilterMultimapNmax=10 and outFilterType="BySJout")
Counts are obtained using qcount in quasR and CPM (counts per million) was computed for each sample
Genome_build: hg19
Supplementary_files_format_and_content: txt file and contains counts as CPM values for each sample

source_name: hepatocyte derived cellular carcinoma cell line

growth_protocol: Huh7-Parental, Huh7-IR and Huh7-CR cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich, D5671) supplemented with 10% Fetal Bovine Serum (FBS, 10%; Sigma-Aldrich), 2 mM glutamine (Sigma-Aldrich, G7513), 100 U penicillin (Sigma-Aldrich) and 0.1 mg/ml streptomycin (Sigma-Aldrich). All cell lines were grown at 37°C, 5% CO2, 95% humidity.

extract_protocol:
Total RNA was isolated from the samples above using the miRNeasy Mini Kit (Qiagen, 217004) with on-column DNAse digestion according to the manufacturer’s instructions.
RNA-sequencing libraries were prepared from total RNA using poly(A) enrichment with the TruSeq stranded mRNA Sample prep from Illumina using 200 ng input RNA. QC was performed with a fragment analyzer using DNF-473-33-SS NGS Fragment 1-6000bp kit. The RNA-sequence libraries were sequenced on a NextSeq 500 using 75 cycles kit High Output (Illumina).

treatment_protocol: Huh7-IR,Huh7-CR cell lines were treated with 7μM Sorafenib to maintain the Sorafenib resistance

tag: treatment

value: Untreated


title: Huh7.parental_2

description: Parental


title: Huh7.CR_2

description: Sorafenib (7µm)

value: Sorafenib (7µm)


title: Hep3B.DMSO_2

description: DMSO


title: Huh7.IR_2

description: Sorafenib (7µm)


title: Hep3B.CR_2

description: Sorafenib (7µm)


title: replicative senescent hVSMC-01

description:
hVSMC-01
15H-18M-01-P7C_S1_L001


title: Hep3B.parental_2

description: Parental


title: proliferative hVSMC-03

description:
hVSMC-03
17H-20M-04-P7C_S9_L001


title: Huh7.CR_1

description: Sorafenib (7µm)


title: Huh7.IR_1

description: Sorafenib (7µm)


title: Huh7.DMSO_1

description: DMSO


title: Huh7.parental_1

description: Parental


title: Hep3B.CR_1

description: Sorafenib (7µm)


title: Hep3B.DMSO_1

description: DMSO


title: Hep3B.parental_1

description: Parental


title: FGFR1_ChIP-Seq Rep2 [CAMA1_Erdafitinib_Rep2]

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Center

library_source: genomic

data_processing:
Reads were mapped to hg38 assembly using bowtie2
Low quality reads were filtered using samtools
Removed duplicates using picard
Peaks were called using macs2
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-seq signal in bigwig format

molecule: genomic DNA

source_name: CAMA1 cells

growth_protocol: Cells were cultured in 15-cm dishes. ChIP-protocol applied when confluence of 70-80% was reached.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody conjugated with Gammabind G sepharose beads.
Libraries from ChIPed DNA were prepared using KAPA Hyper Library Preparation Kit. Samples were end repaired, 3' ends adenylated and barcoded with multiplex adapters, followed by size selection with Ampure XP beads and PCR amplification.  Samples were next quantified by Qubit and validated on the Agilent Tapestation 4200, normalized and pooled, and then run on the Illumina NextSeq 500 using 75 cycle SBS v2.5 reagents

treatment_protocol: Cells were cultured for 24 h in serum free media before treatment with FGF2 5 ng/ml ± erdafitinib 250 nM for 3 h.

tag: cell type

value: ER+/FGFR1-amplified breast cancer cells

tag: passage

value: less than 10

tag: antibody

value: Anti-FGFR1 (Abcam - ab10646)

value: FGF2 5 ng/ml + erdafitinib 250 nM 3 h


title: Hep3B.IR_2

description: Sorafenib (7µm)


title: CAMA1_Veh_Rep2

description:
total RNA extracted CAMA1 cells
Ctrl_Rep2

data_processing:
Reads were mapped to hg38 assembly using STAR
Expression counts were estimated using Featurecounts tool from SubRead package
Genome_build: hg38
Supplementary_files_format_and_content: Raw expression count

growth_protocol: Cells were cultured in 10-cm dishes

extract_protocol:
Cells were harvested and RNA was purified using a RNA purification kit (Maxwell, Promega).
Samples were run on the Agilent Tapestation 4200 to ensure use of only high quality RNA (RIN Score ≥8). The Qubit fluorometer was used to determine sample concentration prior to preparation of libraries. One μg of total DNAse treated RNA was then prepared with the TruSeq Stranded mRNA Library Prep Kit from Illumina. Poly-A RNA was purified and fragmented before strand specific cDNA synthesis. cDNAs were then a-tailed and indexed adapters were ligated. After adapter ligation, samples were PCR amplified and purified with AmpureXP beads, then validated again on the Agilent Tapestation 4200.  Before being normalized and pooled, samples were quantified by Qubit then run on the Illumina NextSeq 500 using V2.5 reagents

treatment_protocol: Cells were cultured for 24 h in serum free media before treatment with Vehicle (PBS) or FGF2 5 ng/ml for 6h, prior to RNA-extraction protocol

value: ER+/FGFR1-amp breast cancer cells


title: CAMA1_FGF2_Rep1

description:
total RNA extracted CAMA1 cells
FGF2-stim_Rep1


title: Input

data_processing:
Reads were mapped to hg38 assembly using bowtie2
Low quality reads were filtered using samtools
Removed duplicates using picard
Peaks were called using macs2
Genome_build: hg38
Supplementary_files_format_and_content: ChIP-seq peaks files in bed format

source_name: MCF7(FGFR1)(SP-)(NLS) cells

treatment_protocol: Cells were cultured for 48 h in estradiol-deprived media before collection for ChIP-Seq


title: CAMA1_FGF2_Rep2

description:
total RNA extracted CAMA1 cells
FGF2-stim_Rep2


title: INPUT_3_4

value: FGF2 5 ng/ml 3 h


title: MCF7(FGFR1)(SP-)(NLS)_RNA-Seq_Rep2

data_processing:
Reads were mapped to hg38 assembly using tophat
Expression counts were estimated using Featurecounts tool from SubRead package
Genome_build: hg38
Supplementary_files_format_and_content: Raw expression count

treatment_protocol: Cells were cultured for 48 h in estradiol-deprived media before RNA-extraction protocol

value: ER+ breast cancer cells

tag: strain/genotype

value: MCF7(FGFR1)(SP-)(NSL) cells


title: FGFR1_ChIP-Seq Rep1 [CAMA1_Erdafitinib_Rep1]


title: FGFR1_ChIP-Seq Rep1


title: FGFR1_ChIP-Seq Rep3


title: CAMA1_Veh_Rep3

description:
total RNA extracted CAMA1 cells
Ctrl_Rep3


title: CAMA1_FGF2_Rep3

description:
total RNA extracted CAMA1 cells
FGF2-stim_Rep3


title: FGFR1_ChIP-Seq Rep2 [CAMA1_FGF2_Rep2]


title: FGFR1_ChIP-Seq Rep1 [CAMA1_FGF2_Rep1]


title: MCF7EV_RNA-Seq_Rep1

source_name: MCF7EV cells

value: MCF7EV cells


title: Hep3B.IR_1

description: Sorafenib (7µm)


title: MCF7EV_RNA-Seq_Rep2


title: MCF7EV_RNA-Seq_Rep3


title: MCF7(FGFR1)(SP-)(NLS)_RNA-Seq_Rep1


title: CAMA1_Cntrl_RNA-Seq_Rep3

description: total RNA extracted from CAMA1 cells

tag: cell line


title: INPUT_5_6


title: CAMA1_Cntrl_RNA-Seq_Rep2

description: total RNA extracted from CAMA1 cells


title: CAMA1_siFOXA1 input

growth_protocol: Cells were cultured in 15-cm dishes. ChIP-protocol applied when confluence of 70-80% was reached. For siNT vs siFOXA1 FGFR1:ChIP-Seq, cells were collected for CHiP 72 h post-transfection


title: CAMA1_siFOXA1_FGFR1_ChIP-Seq Rep2


title: CAMA1_siNT input


title: CAMA1_siFOXA1_FGFR1_ChIP-Seq Rep1


title: CAMA1_Veh_Rep1

description:
total RNA extracted CAMA1 cells
Ctrl_Rep1


title: MCF7(FGFR1)(SP-)(NLS)_RNA-Seq_Rep3


title: CAMA1_siNT_FGFR1_ChIP-Seq Rep2


title: CAMA1_siNT_FGFR1_ChIP-Seq Rep1


title: CAMA1_FOXA1_ChIP-Seq_Rep1


title: CAMA1_Pol II S5P_ChIP-Seq_Rep1

value: Anti-Rpb1 CTD (4H8) (CST - #2629)


title: CAMA1_H3K4Me3 Input


title: CAMA1_FOXA1 input


title: CAMA1_Cntrl_RNA-Seq_Rep1

description: total RNA extracted from CAMA1 cells


title: CAMA1_Pol II input


title: CAMA1_H3K27ac Input


title: CAMA1_H3K27ac_ChIP-Seq Rep1

value: Anti-Histone H3K27ac (Abcam ab4729)


title: CAMA1_FGFR1_ChIP-Seq Rep2


title: CAMA1_FGFR1 Input


title: CAMA1_FGFR1_ChIP-Seq Rep1


title: FGFR1_ChIP-Seq Rep2


title: CAMA1_H3K4me3_ChIP-Seq Rep1

value: Anti-Histone H3K4me3 (Abcam ab8580)


title: CAMA1_H3K4me3_ChIP-Seq Rep2


title: CAMA1_Pol II S5P_ChIP-Seq_Rep2


title: CAMA1_H3K27ac_ChIP-Seq Rep2


title: colorectal cancer sample AUS2_575

type: RNA

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

description: Gene-level expression values derived using Transcriptome Analysis Console (TAC 4.0) software.

hyb_protocol: Samples were hybridized onto Affymetrix Human Transcriptome 2.0 Arrays according to the manufacturer's protocol (Affymetrix).

scan_protocol: Array scanning was performed according to the manufacturer's protocol (Affymetrix).

data_processing: Gene-level expression signals were obtained from raw data CEL files by the RMA procedure implemented in the Transcriptome Analysis Console (TAC 4.0) software using defult settings.

label: biotin

source_name: Colorectal cancer patient

label_protocol: RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

extract_protocol: Total RNA was isolated from colorectal cancer tissue samples using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

tag: tissue

value: colorectal cancer tissue sample


title: CAMA1_FOXA1_ChIP-Seq_Rep2


title: colorectal cancer sample S720_prim_T1


title: colorectal cancer sample AUS2_538


title: colorectal cancer sample AUS2_578


title: colorectal cancer sample AUS2_569


title: CRLM 89_T9

description: Gene-level expression values using RMA by Transcriptome Analysis Console (TAC 4.0) software using defult settings.

data_processing: Gene-level expression signals were obtained from raw CEL files by the gene-level RMA procedure implemented in the Transcriptome Analysis Console (TAC 4.0) software using defult settings.

label_protocol: 100 ng total RNA was amplified, fragmented and labelled according to the Affymetrix GeneChip HT WT User Guide.

extract_protocol: Total RNA was isolated from CRLM tissue samples using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

value: colorectal cancer liver metastasis tissue sample

tag: patient number

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender

value: Male

tag: synchronous liver metastases

value: Yes

tag: r status liver

tag: extra heaptic disease

value: No

tag: kras mutation

value: Mut

tag: nras mutation

value: WT

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

value: NeoAdjuvant

tag: patient number in figure 1 in paper


title: colorectal cancer sample AUS2_761

tag: tissue


title: colorectal cancer sample AUS2_850


title: CRLM 89_T1-2

tag: patient number

tag: tumor number

tag: sample number

tag: repeated hepatic resection


title: CRLM 89_T3-1

tag: gender

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease


title: CRLM 89_T11

tag: kras mutation

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery


title: CRLM 89_T8

tag: lms from random forest prediction model

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: colorectal cancer sample AUS2_370

tag: tissue


title: colorectal cancer sample AUS2_808


title: CRLM 89_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 87_T1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 89_T2

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: colorectal cancer sample AUS2_573


title: colorectal cancer sample AUS2_570


title: colorectal cancer sample AUS2_745


title: CRLM 84_T1

value: Female

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 89_T3-2

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: colorectal cancer sample AUS2_568


title: CRLM 532_T2-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 87_2_T1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 89_T5

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 63_T1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 532_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 503_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 503_T6

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 63_T2

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 53_T2

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 503_T2-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 486_T3-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 503_T3-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 467_2_T3-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 523_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 486_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 467_2_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 42_T2

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 467_2_T2-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 467_2_T2-2

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 486_T2-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 467_2_T1-2

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 36_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 36_T1-2

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 35_T2-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 42_T3

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 42_2_T1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 42_T4

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 42_T5

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 441_T2-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 42_T1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 38_T4

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 35_T4-2

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 35_T4-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 35_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 333_T1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time

value: Naive


title: CRLM 338_T1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 27_T2

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 327_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 27_T1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 254_T1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 251_T2-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 235_T1-2

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 234_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 224_3_T2-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 250_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 218_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 224_3_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 217_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 231_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 222_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 190_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 246_T2-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 192_T3-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 229_T2

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 220_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 214_T3-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 200_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 204_T1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 191_T1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 202_T2-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 201_T1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 197_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 211_T3-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 189_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 180_T2-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 183_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 188_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 238_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 182_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 179_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 195_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 177_T-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 170_T3-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 171_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 176_T3-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 143_T3

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 152_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 153_T3

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 163_T2

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 150_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 172_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 156_T3-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 161_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 144_T3-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 166_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 151_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 164_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 149_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 154_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 146_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 142_T3

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 145_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 142_T1-2

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 142_T5

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 157_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 155_T2

tag: patient number

value: NotIncluded

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 142_T4

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 142_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 141_T5-2

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 141_T3-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 141_T4-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 135_T2-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 141_T2-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 141_3_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 141_T1-2

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 141_3_T3-2

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 141_T4-2

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 142_T2

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 141_3_T3-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 124_T1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 128_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 141_T3-2

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 141_3_T4-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 141_T2-2

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 141_3_T4-2

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 127_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 133_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 134_T2-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 141_T5-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 138_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 141_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 139_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 136_T2-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 129_T1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 130_T1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 125_T2

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 168_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 123_T2

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 123_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 119_T2

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 121_T1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 118_2_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 114_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 119_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 121_T2

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 112_T3-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 113_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 112_2_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 114_T1-2

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 110_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 114_T1-3

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 115_2_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 117_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 114_T1-4

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 109_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 116_T2

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 104_T3

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 105_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 107_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 103_T3

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 106_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 101_2_T2-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 100_T1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 109_T2-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 099_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 095_T5-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 103_T4

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 097_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 095_T3-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 090_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 095_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 079_T2

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 091_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 079_T1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 095_T2-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 093_T4

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 081_T1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 078_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 083_T2-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 077_T4-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 093_T2-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 088_T2-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 080_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 088_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 087_3_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 082_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 077_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 093_T3-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 083_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 076_T5

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 077_T3-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 076_T2-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 076_T3-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 073_2_T4

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 071_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 070_T2

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 076_T4

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 067_T2

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 065_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 069_T1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 065_T5

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 066_T1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 069_2_T3

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 064_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 059_T3

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 067_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 059_T1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 061_T1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 061_T4

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 062_T1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 058_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 060_T1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 059_T5

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 061_T6

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 061_T3

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 058_T3

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 056_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 073_2_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 052_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 076_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 059_T4-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 070_T1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 075_T1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 051_T1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 050_T6

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 049_T1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 050_T9

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 050_T4

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 050_T2

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 050_T3

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 047_2_T5

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 048_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 047_T1-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 050_T5

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 045_T5

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 049_T2

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 047_T3

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 048_T2-1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 047_T2-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 045_T4-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 047_T4

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 045_T3-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 045_T6

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 045_T2-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 043_T4

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 045_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 043_T3

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 041_T1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 043_2_T1-1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 032_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 039_T1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 040_T1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 030_T1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 028_T1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 029_T1-1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 044_T1-1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 020_T1-1

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 017_T2

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 025_T5

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 025_T3

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 021_T1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 016_T4

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 015_T1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 012_T1

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 016_T3

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 013_T1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 016_T5

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 057_T1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 009_T3

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 007_T1

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: CRLM 003_T1

tag: patient number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 009_T4

tag: tumor number

tag: sample number

tag: repeated hepatic resection

tag: gender


title: CRLM 014_T1

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 003_T2

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model


title: CRLM 016_T2

tag: tissue

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: m-B6-beta-Ran-12-eHiC

city: Madison

first: Sunduz

last: Keles

state: WI

address: 1300 University Ave

department: Biostatistics and Medical Informatics, Statistics

institute: University of Wisconsin-Madison

description:
end_loop.B6.cis.gz
end_loop.B6.trans.gz

data_processing:
The R3 fastq files contain the UMI barcodes which are essential for identifying duplications.
The paired-end eHi-C reads were mapped to mouse genome mm10 using BOWTIE. We trimmed the first 5 bases from every read, took the next 36 bases, and added the 6-base sequence AAGCTT to the 5’ of every read before mapping using the whole 42 bases. The two reads were mapped independently and then merged into pairs using HiCorr pipeline. We then identified and removed duplicated read pairs from the same biological library. PCR duplications were defined as identical PE reads also with the same UMI barcode, which can be found in R3. We estimated a background frequency between any two fragments based on the average reads count of all fragment pairs that have similar lengths, similar gap distance, GC content, and visibility. The statistical method and HiCorr pipeline has been described in previous publication (Lu, L. et al. Molecular Cell 79(2), 521-534)
Genome_build: mm10
Supplementary_files_format_and_content: The fragment-to-fragment raw reads are provided in the txt file.

organism: Mus musculus

source_name: pancreatic islet

growth_protocol: Mice were maintained as instructed.

extract_protocol:
Mouse beta cells were isolated from C57BL/6 islets and subjected to easy Hi-C (eHi-C) to profile the chromatin loopings. Briefly, 30-40K sorted mouse beta cells were used to generate one eHi-C library. The cells were first lysed with a cell lysis buffer, containing 10mM Tris-HCl pH 7.5, 10mM NaCl, 0.2% NP-40 and protease inhibitor cocktail. The exraced nuclei were then digested with HindIII (NEB, Cat#R3104M). After digestion, the proxity ligation was done in intact inclei with T4DNA ligase (Invitrogen,Cat#15224-025) fot at least seven hours. The DNA were then extracted after reverselinking with proteinase K for overnight and then sujected to DpnII (NEB, Cat#R0543L) digestion. The resulting DNA was then self-ligated with T4 DNA ligase to form self-circles. The DNA species those were not able to self-circled were removed by exonulcease treatment. The self-circles were then linearized with a secondary HindIII digestion. And the resulting DNA were used to generate Libraries following a Illumina Truseq system with modified adapters. Overall, we generated 220M reads for each sample, including 40M Cis-contacts. And conbined together, we generated 246M cis-contact reads.
The libraries were constructed following standard Illumina Truseq library preparation protocol.

value: pancreatic islet

tag: strain

tag: cell type

value: beta cell extracted from islets


title: m-B6-beta-Ran-3-eHiC

description:
end_loop.B6.cis.gz
end_loop.B6.trans.gz


title: m-B6-beta-Ran-14-eHiC

description:
end_loop.B6.cis.gz
end_loop.B6.trans.gz


title: CRLM 004_T3

tag: patient number

tag: tumor number

tag: sample number

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 005_T1

tag: repeated hepatic resection

tag: gender

tag: synchronous liver metastases

tag: r status liver

tag: extra heaptic disease

tag: kras mutation


title: CRLM 001_T1

tag: tissue

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: lms from random forest prediction model

tag: 60 months overall survival, time


title: m-B6-beta-Ran-2-eHiC

description:
end_loop.B6.cis.gz
end_loop.B6.trans.gz

tag: strain

tag: cell type


title: m-B6-beta-Ran-1-eHiC

description:
end_loop.B6.cis.gz
end_loop.B6.trans.gz


title: CRLM 006_T1

tag: patient number

tag: tumor number

tag: sample number

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time

tag: 60 months cancer-specific survival, status


title: CRLM 004_T4

tag: repeated hepatic resection

tag: gender

tag: synchronous liver metastases

tag: r status liver

tag: chemotherapy prior to tumor sampling

tag: patient number in figure 1 in paper


title: CRLM 004_T1

tag: tissue

tag: extra heaptic disease

tag: kras mutation

tag: nras mutation

tag: tp53 mutation

tag: lms from initial subtype discovery


title: m-B6-beta-Ran-11-eHiC

description:
end_loop.B6.cis.gz
end_loop.B6.trans.gz

tag: strain

tag: cell type


title: RNA-Seq PWK-M

description: PWK-M

data_processing:
We used RSEM with GENCODE vm18 gene annotation and obtained the gene expression count matrix across protein coding genes on Chromosomes 1-19, and X.
Genes with the lowest 10% variance across the samples were removed from the downstream analysis.
Upper quartile normalization and retaining the genes with non-zero counts in at least 85% of the samples resulted in 13,568 protein-coding genes.
Genome_build: mm10
Supplementary_files_format_and_content: text files containing the quantification of transcript abundance results

growth_protocol: 26-week-old mice

extract_protocol:
Whole-islet RNA was isolated and evaluated for quality. RNA samples were submitted to the Jackson Laboratory high-throughput sequencing core facility. Sample, collection, RNA extraction and sequencing was carried out on in four waves of animals. RNAs were sheared using the E220 Focused-ultrasonicator (Covaris).
The Jackson Laboratory core generated whole genome islet mRNA libraries using the KAPA Hyper Prep Kit for Illumina Sequencing (KAPA Biosystems), targeting an insert size of 300 bp using magnetic bead-based size selection. Libraries from waves 1, 2, and 3 were constructed at the Jackson Laboratory and randomized into pools of samples with TruSeq RNA indices (6 bp). Libraries from wave 4 were constructed at the New York Genome Center and were pooled using 8-bp dual index TruSeq RNA indices. Each pooled RNA sample was sequenced across four randomly assigned lanes on a HiSeq2500 (Illumina) at the New York Genome Center.

treatment_protocol: High-fat diet for all samples.

tag: Sex


title: RNA-Seq WSB-M

description: WSB-M


title: RNA-Seq WSB-F

description: WSB-F


title: RNA-Seq NZO-F

description: NZO-F


title: RNA-Seq NOD-F

description: NOD-F


title: RNA-Seq NOD-M

description: NOD-M


title: RNA-Seq CAST-M

description: CAST-M


title: CRLM 002_T1

tag: patient number

tag: tumor number

tag: sample number

tag: lms from random forest prediction model

tag: 60 months overall survival, time

tag: 60 months overall survival, status

tag: 60 months cancer-specific survival, time


title: RNA-Seq PWK-F

description: PWK-F


title: RNA-Seq B6-F


title: RNA-Seq B6-M


title: RNA-Seq CAST-F

description: CAST-F


title: RNA-Seq AJ-F

description: AJ-F


title: RNA-Seq NZO-M

description: NZO-M


title: RNA-Seq AJ-M

description: AJ-M


title: PWK-M

description:
PWK-M_ref_default-fdr.05.narrowPeak
PWK_default-fdr.05-idr.05.narrowPeak

data_processing:
Illumina Nextera adapters were trimmed with cutadapt (version 2.0) using the option "-q 30 --minimum-length 36".
Paired-end ATAC-seq reads were aligned to the mouse genome assembly (mm10) with bowtie2 (version 2.3.4.1) with option "-X 800 --no-mixed --no-discordant".
For each sample, unmapped reads were filtered out by  SAMtools view (version 1.8) with option "-F 4" and mitochondrial reads were removed. Duplicated reads were removed with Picard tools (version 2.9.2).
Peaks from individual and pooled samples across sexes of each strain were identified using MOSAiCS at FDR of 0.05. Blacklisted regions and Chr Y regions were filtered.
We employed IDR analysis to obtain reproducible sets of peaks between male and female samples at IDR of 0.05 and leveraged "SignalValue" and "p-value" outputs from IDR analysis as measures of peak-level signal to noise.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

growth_protocol: The ATAC-seq samples were prepared using a selection of 50 average sized mouse islets. The islets were washed with 500 uL of PBS at 4C and pelleted by centrifugation at 100 x g for 1 minute. 300 uL of ATAC Lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) was used to resuspend the islets. The islets were incubated for 20 minutes on ice.

extract_protocol:
After incubating, the islets were lysed by trituration with a 25 gauge needle until intact islets were no longer visible, usually 6 triturations. The lysate was centrifuged at 500 x g for 10 minutes at 4C. This generated a crude nuclei pellet and a supernatant. The supernatant was discarded and the nuclei pellet was washed with 100 uL of ATAC Lysis buffer in order to reduce cytoplasmic and mitochondrial contamination. This mixture was centrifuged at 500 x g for 10 minutes at 4C and the supernatant was removed. Per ATAC-seq sample, a mixture of 25 uL 2x TDE buffer, 22.5 uL nuclease-free water, and 2.5 uL TDE1 transposase enzyme (Nextera DNA Library Prep kit, Illumina) was applied and incubated for 30 minutes in a 37C water bath. The samples were then purified using a MinElute Reaction cleanup kit (Qiagen) and eluted using two sequential aliquots of 10 uL EB buffer.
After purification all ATAC samples were kept at -80C. All ATAC-seq samples were transposed and frozen prior to preparing all libraries. Libraries were amplified using 20 uL of ATAC sample, 2.5 uL Primer-1 (Ad1_noMX, 25 uM working stock), 2.5 uL Primer-2 (Ad2.X, 25 uM working stock), and 25 uL of NEBNext High Fidelity 2x PCR Master Mix. Each ATAC sample was amplified by 12 cycles which was determined by qPCR to be saturating for the libraries. The PCR thermocycler was set to 72C for 5 minutes, 98C for 30 seconds, and then 12 total cycles of 98C for 10 seconds, 63C for 30 seconds, 72C for 1 minute. After amplification the libraries were purified using MinElute PCR purification cleanup kit (Qiagen).


title: WSB-F

description:
WSB-F_ref_default-fdr.05.narrowPeak
WSB_default-fdr.05-idr.05.narrowPeak


title: PWK-F

description:
PWK-F_ref_default-fdr.05.narrowPeak
PWK_default-fdr.05-idr.05.narrowPeak


title: WSB-M

description:
WSB-M_ref_default-fdr.05.narrowPeak
WSB_default-fdr.05-idr.05.narrowPeak


title: RNA-Seq 129-F


title: NZO-F

description:
NZO-F_ref_default-fdr.05.narrowPeak
NZO_default-fdr.05-idr.05.narrowPeak


title: NZO-M

description:
NZO-M_ref_default-fdr.05.narrowPeak
NZO_default-fdr.05-idr.05.narrowPeak


title: NOD-M

description:
NOD-M_ref_default-fdr.05.narrowPeak
NOD_default-fdr.05-idr.05.narrowPeak


title: CAST-F

description:
CAST-F_ref_default-fdr.05.narrowPeak
CAST_default-fdr.05-idr.05.narrowPeak


title: B6-F

description:
B6-F_ref_default-fdr.05.narrowPeak
B6_default-fdr.05-idr.05.narrowPeak


title: B6-M

description:
B6-M_ref_default-fdr.05.narrowPeak
B6_default-fdr.05-idr.05.narrowPeak


title: CAST-M

description:
CAST-M_ref_default-fdr.05.narrowPeak
CAST_default-fdr.05-idr.05.narrowPeak


title: AJ-M

description:
AJ-M_ref_default-fdr.05.narrowPeak
AJ_default-fdr.05-idr.05.narrowPeak


title: RNA-Seq 129-M


title: AJ-F

description:
AJ-F_ref_default-fdr.05.narrowPeak
AJ_default-fdr.05-idr.05.narrowPeak


title: NOD-F

description:
NOD-F_ref_default-fdr.05.narrowPeak
NOD_default-fdr.05-idr.05.narrowPeak


title: WT-2_HiC

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
sequnced using Illumina Hiseq2500 platform
Paired-end .fastq files from in situ Hi-C experiments were processed using the HiC-Pro (version 2.11.4)
Default settings were used to align reads to the mm10 mouse genome, remove duplicate reads, assign reads to DpnII restriction fragments, filter for valid interactions, and generate binned interaction matrices
The validated contact pairs were transformed to Juicer hic files with hicpro2juicebox
Genome_build: mm10
Supplementary_files_format_and_content: .hic formated files

source_name: Mouse liver

growth_protocol: 8-week-old male mice fed with a standard chow diet and after an overnight fast

extract_protocol:
Fixed chromatin was digested using MboⅠ enzyme, followed by biotin incorporation with Biotin-14-dATP. After DNA ligation, the DNA was sonicated and captured with Streptavidin C-1 beads.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Purified DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina NovaSeq6000 platform.
in situ Hi-C

value: Liver

tag: age

value: 8 weeks old

tag: genotype

value: CTCF fl/fl Albcre-

value: male


title: KO-2_HiC

value: CTCF fl/fl Albcre+


title: WT-1_HiC


title: KO-1_HiC


title: WT165_CTCF

data_processing:
sequnced using Illumina Hiseq2500 platform
Raw ChIP-seq reads were trimmed for adaptor sequence, and aligned to the mm10 genome assembly using bwa mem v0.7.12 with default parameters
aligned files were filtered for MAPQ > 5 and sorting, deduplication were processed using PICARD  v1.77
peaks were called using macs2 v2.1.2 with the following setting: -g mm --extsize ($predicted d) --shift {($predicted d)/2} -q 0.001 (--broad-cutoff 0.1 --broad for H3K27ac,H3K27me3 ChIP-seq peak calling)
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.1.3
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak, CPM normalized bigwig

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Tagmentation was performed using Nextera DNA library preparation kit (illumina #15028212) according to manufacturer's instructions. Purified DNA was amplified using Nextera PCR primers. Libraries were paired-end sequenced on Illumina HiSeq 2500 system

tag: passages

tag: chip antibody

value: CTCF(Cell signaling, #2889)


title: KO163_CTCF


title: WT_Y_2_PPARg

value: PPARgamma (Cell signaling, #2443)


title: KO7_PPARg


title: D30_Ctrl_H3K27me3_Mint-ChIPseq_Rep2

city: New York

first: Samantha

middle: B

last: Larsen

state: NY

address: 435 East 30th Street

institute: NYU School of Medicine

description: PCR amplified library from genomic DNA

data_processing:
MINT-ChIP reads were processed as shown in van Galen et al (doi::10.1016/j.molcel.2015.11.003) with appropriate modifications made for the T7 barcode adaptor in read2 instead read 1 (van Galen et al). Reads were first demultiplexed by Illumina’s bcl2fastq2 and further demultiplexed using the additional the T7 barcode in read2 (van Galen et al). These demultiplexed reads were aligned to the mm10 genome from the Bsgenome.Mmusculus.UCSC.mm10 Bioconductor package (version 1.4.0) using Rsubread's align method in paired-end mode with fragments between 1 to 5000 base-pairs considered properly paired (Liao Y et al).  Normalized, fragment signal bigWigs were created using the rtracklayer package. For Homer peak calling,  reads were filtered as shown in van Galen et al., with the appropriate modifications for the T7 barcode in read2.  First reads where both pairs are multi mapping and improperly paired are removed and following this fragment duplicates and read pairs with T7 (read 2) duplicates are filtered (van Galen et al). Homer tag directories were created from the filtered BAM files and peak calls made using the Homer’s findPeaks with parameters (-region , -size 1000, -minDist 2500).
Genome_build: mm10

source_name: skin

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.043
NEBNext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: 2-3 postnatal day 60  murine backskin was treated with vanicream for 6 consecutive days

value: female

value: Epidermal Stem Cells

value: wildtype

tag: facs markers

value: ITGA6+, ITGB1+, Sca1+, CD34-

tag: treatment

value: control vanicream for 6 days


title: D30_IMQ_H3K27me3_Mint-ChIPseq_Rep1

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.046
NEBNext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: 2-3 postnatal day 60  murine backskin was treated with Imiquimod for 6 consecutive days

value: Imiquimod for 6 days


title: D30_Ctrl_H3K27me3_Mint-ChIPseq_Rep1

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.042
NEBNext Ultra II DNA Library Prep Kit for Illumina

treatment_protocol: 2-3 postnatal day 60 mice backskin were treated with vanicream for 6 consecutive days


title: D6_IMQ_H3K27me3_Mint-ChIPseq_Rep1

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.038
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D6_Ctrl_H3K27me3_Mint-ChIPseq_Rep2

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.035
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D6_Ctrl_H3K27me3_Mint-ChIPseq_Rep1

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.034
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D30_IMQ_H3K27me3_Mint-ChIPseq_Rep2

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.047
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D30_IMQ_H3K4me1_Mint-ChIPseq_Rep2

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.031
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D30_IMQ_H3K4me1_Mint-ChIPseq_Rep1

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.030
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: WT164_CTCF


title: D30_Ctrl_H3K4me1_Mint-ChIPseq_Rep1

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.026
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 129-F

description:
129-F_ref_default-fdr.05.narrowPeak
129_default-fdr.05-idr.05.narrowPeak

value: Female


title: D6_IMQ_H3K4me1_Mint-ChIPseq_Rep2

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.023
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D30_Ctrl_H3K4me1_Mint-ChIPseq_Rep2

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.027
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: KO8_PPARg


title: D6_IMQ_H3K4me1_Mint-ChIPseq_Rep1

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.022
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: 129-M

description:
129-M_ref_default-fdr.05.narrowPeak
129_default-fdr.05-idr.05.narrowPeak

value: Male


title: D6_Ctrl_H3K4me1_Mint-ChIPseq_Rep1

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.018
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: KO160_CTCF


title: D6_IMQ_H3K27me3_Mint-ChIPseq_Rep2

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.039
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D30_Ctrl_H3K27ac_Mint-ChIPseq_Rep2

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.011
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D30_Ctrl_H3K27ac_Mint-ChIPseq_Rep1

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.010
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D30_IMQ_H3K27ac_Mint-ChIPseq_Rep1

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.014
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D6_IMQ_H3K27ac_Mint-ChIPseq_Rep1

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.006
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D6_IMQ_H3K27ac_Mint-ChIPseq_Rep2

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.007
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D6_Ctrl_H3K27ac_Mint-ChIPseq_Rep1

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.003
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: D30_IMQ_H3K27ac_Mint-ChIPseq_Rep2

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.015
NEBNext Ultra II DNA Library Prep Kit for Illumina


title: KO150_H3K27me3

data_processing:
sequnced using Illumina Hiseq2500 platform
Raw ChIP-seq reads were trimmed for adaptor sequence, and aligned to the mm10 genome assembly using bwa mem v0.7.12 with default parameters
aligned files were filtered for MAPQ > 5 and sorting, deduplication were processed using PICARD  v1.77
peaks were called using macs2 v2.1.2 with the following setting: -g mm --extsize ($predicted d) --shift {($predicted d)/2} -q 0.001 (--broad-cutoff 0.1 --broad for H3K27ac,H3K27me3 ChIP-seq peak calling)
normalized abundance file, bigwig files were generated applying CPM normalization using deeptools v3.1.3
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak, broadPeak, CPM normalized bigwig

source_name: Liver

growth_protocol: ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: tissue

value: H3K27me3 (abcam ab6002)


title: WT_Y_4_PPARg

tag: strain

value: PPARg(Cell signaling 2443S)


title: WT_Y_2_K4me3

value: Liver

value: H3K4me3 (millipore 04-745)


title: WT156_H3K27me3

value: 8 weeks old

value: CTCF fl/fl Albcre-


title: WT_Y_4_K27Ac

value: H3K27ac(abcam ab4729)


title: KO_Y_3_K27Ac

value: CTCF fl/fl Albcre+


title: KO_Y_4_K4me3


title: D6_Ctrl_H3K27ac_Mint-ChIPseq_Rep2

description: PCR amplified library from genomic DNA

tag: cell type


title: CTCF cKO rep3

data_processing:
sequnced using Illumina Hiseq platform
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using STAR v2.5.1 with parameters --sjdbOverhang 100 --twopassMode Basic --chimSegmentMin 20 --quantMode TranscriptomeSAM
Fragments Per Kilobase Million (FPKM), Transcripts Per Kilobase Million(TPM) and raw counts were calculated using RSEM
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count, FPKM, TPM values for each Sample ...

extract_protocol:
Liver 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 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 8 weeks-old


title: KO_Y_2_K27Ac


title: CTCF cKO rep1


title: WT_Y_2_K27Ac


title: WT rep4


title: WT rep3


title: D6_Ctrl_H3K4me1_Mint-ChIPseq_Rep2

description: PCR amplified library from genomic DNA

extract_protocol:
Cells were FACS sorted according to characteristics: FACS markers; Cells were lysed and processed per protocol outlines in doi::10.1016/j.molcel.2015.11.019
NEBNext Ultra II DNA Library Prep Kit for Illumina

tag: Sex

value: female


title: CTCF cKO rep4


title: CTCF cKO rep2


title: WT rep2


title: WT rep1


title: A549-ACE2 IFN-beta 6h RNA-Seq

city: HOUSTON

first: Ruoyu

last: Wang

address: 6431 Fannin St

institute: UTHealth McGovern Medical School

data_processing:
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
Genome_build: hg19
Supplementary_files_format_and_content: tsv

growth_protocol: Human lung adenocarcinoma cells A549 expressing human ACE2 (A549-ACE2, #NR53821) was acquired from BEI Resources, Manassas, VA). They were maintained in DMEM/F-12 (1:1, Corning) medium supplemented with 10% FBS (GeneDepot) and blasticidin (100uM).

extract_protocol:
Total RNAs from  A549-ACE2 cells were extracted by TRIzol
total RNAs were used for making strand-specific ribosome-RNA-depleted sequencing library by the NEB Ultra II Directional RNA library kit (E7760L) following manufacturer's instructions.

treatment_protocol: SARS-CoV-2 isolate USA-WA1/2020 (NR-52281; BEI Resources, Manassas, VA) was employed to infect human A549-ACE2 cells (NR53821; Bei Resources, Manassas, VA). For viral infections, serum/antibiotics-free Eagle’s MEM medium supplemented with 1mM HEPES was used. Briefly, cells grown in 10-cm culture dishes at about 70-80% confluency were washed with the serum free medium, viral inoculum was added at 0.1 MOI for 1 hr. After that, non-adsorbed viral particles were gently aspirated out and the monolayers were replenished with 10% FBS containing MEM supplemented with 1mM HEPES. Infected cells were incubated at 37°C with 5% CO2 for 6hr or 24hr post-infection for experiments.

tag: cell line

value: epithelial cell

value: IFN-beta treatment (1000u, 6-hr)


title: A549-ACE2 Mock  rep3 RNA-Seq

value: mock


title: A549-ACE2 SARS-CoV-2 24hpi rep3 RNA-Seq

value: SARS-CoV-2 isolate USA-WA1/2020


title: KO_Y_4_K27Ac


title: CRLM 022_T1

description: Gene-level expression values using RMA by Transcriptome Analysis Console (TAC 4.0) software using defult settings.

extract_protocol: Total RNA was isolated from CRLM tissue samples using the Qiagen Allprep DNA/RNA/miRNA Universal kit, according to the manufacturer's protocol (Qiagen).

value: colorectal cancer liver metastasis tissue sample

tag: patient number

tag: tumor number

tag: repeated hepatic resection

tag: gender

tag: synchronous liver metastases

value: Yes

tag: r status liver

tag: extra heaptic disease

tag: kras mutation

value: Mut

tag: nras mutation

value: WT

tag: tp53 mutation

tag: lms from initial subtype discovery

tag: 60 months cancer-specific survival, status

tag: chemotherapy prior to tumor sampling

value: Naive

tag: patient number in figure 1 in paper


title: A549-ACE2 SARS-CoV-2 24hpi rep2 RNA-Seq

tag: cell type

tag: treatment

tag: chip antibody


title: A549-ACE2 Mock rep2 RNA-Seq

tag: cell line


title: WT_Y_1_K27Ac

tag: tissue

value: Liver

tag: age

tag: strain

tag: genotype


title: A549-ACE2 SARS-CoV-2 6hpi rep2 RNA-Seq


title: A549-ACE2 SARS-CoV-2 6hpi rep1 RNA-Seq


title: A549-ACE2 SARS-CoV-2 24hpi rep1 RNA-Seq


title: A549-ACE2 Mock rep1 RNA-Seq


title: A549-ACE2 RPB1 IFNb ChIP-Seq

data_processing:
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
Immunoprecipitated chromatin DNA was de-crosslinked by 65ºC heating overnight using elution buffer (1% SDS, 0.1M NaHCO3), and then treated by RNase A and proteinase K, which was finally purified by phenol chloroform.
DNA libraries were prepared using NEB Next Ultra II DNA library prep kit for illumina according to manufactorer's instructions

value: RPB1 N terminus, Cell Signaling Technology, #14958S, Lot4


title: A549-ACE2 CTCF SARS-CoV-2 rep2 ChIP-Seq

value: CTCF (Millipore, 07-729)


title: A549-ACE2 RPB1 Veh ChIP-Seq


title: gfp_IHMA87_plate4_rep1

city: Zurich

first: Julian

last: Trouillon

address: Otto-Stern-Weg 3

department: Institute of Molecular Systems Biology

institute: ETH Zurich

description: adaptor-ligated sheared genomic DNA

data_processing:
Library strategy: DAP-seq
Read trimming using Trimmomatic
Alignment using Bowtie2
Peak calling using MACS2
closest features called with BEDtools
Genome_build: PAO1, PA14, IHMA87
Supplementary_files_format_and_content: excel table, list of RRs binding to the promoter region of each gene

organism: Pseudomonas aeruginosa

source_name: purified genomic DNA from liquid cultures

extract_protocol:
After cell-fre protein expression, soluble His-tagged proteins were bound to cobalt magnetic beads and incubated with adaptor-ligated sheared genomic DNA. After washes and isolation of bead-protein-DNA complexes, the bound DNA regions were eluted by heating and then used for library preparation.
DNA libraries were prepared for sequencing using standard Illumina protocols


title: gfp_PAO1_plate4_rep2

description: adaptor-ligated sheared genomic DNA


title: gfp_PA14_plate2_rep1

description: adaptor-ligated sheared genomic DNA


title: gfp_PA14_plate4_rep1

description: adaptor-ligated sheared genomic DNA


title: gfp_IHMA87_plate4_rep2

description: adaptor-ligated sheared genomic DNA


title: gfp_IHMA87_plate3_rep2

description: adaptor-ligated sheared genomic DNA


title: gfp_PAO1_plate1_rep1

description: adaptor-ligated sheared genomic DNA


title: gfp_PAO1_plate1_rep2

description: adaptor-ligated sheared genomic DNA


title: gfp_PA14_plate4_rep2

description: adaptor-ligated sheared genomic DNA


title: gfp_IHMA87_plate3_rep1

description: adaptor-ligated sheared genomic DNA


title: gfp_PAO1_plate4_rep1

description: adaptor-ligated sheared genomic DNA


title: CS9_AauR-PA14_46990_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS9_AauR-IHMA87_03895_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS9_AauR-PA14_46990_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS9_AauR-IHMA87_03895_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS8_PhoP-PA14_49180_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS9_AauR-PA1335_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: A549-ACE2 CTCF Mock rep2 ChIP-Seq


title: CS9_AauR-PA1335_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS7_PA1157_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: gfp_PA14_plate2_rep2

description: adaptor-ligated sheared genomic DNA


title: CS8_PhoP-PA1179_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS8_PhoP-IHMA87_04038_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS8_PhoP-PA1179_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS8_PhoP-IHMA87_04038_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS7_PA1157_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS7_PA1157-PA14_49440_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS7_PA1157-IHMA87_04060_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS7_PA1157-PA14_49440_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS5_PirR-PA0929_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS5_PirR-PA0929_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS7_PA1157-IHMA87_04060_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS6_FleR-PA1099_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS6_FleR-IHMA87_04106_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS6_FleR-PA14_50180_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS6_FleR-PA1099_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS5_PirR-IHMA87_04308_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS5_PirR-PA14_52250_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS5_PirR-PA14_52250_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS8_PhoP-PA14_49180_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS6_FleR-IHMA87_04106_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS5_PirR-IHMA87_04308_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS6_FleR-PA14_50180_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS55_IHMA87_06096_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS55_IHMA87_06096-_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS55_IHMA87_06096_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS54_IHMA87_02464-_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS55_IHMA87_06096-_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS54_IHMA87_02464-_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS54_IHMA87_02464-_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS54_IHMA87_02464-_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS53_IHMA87_02165_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS53_IHMA87_02165-_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS53_IHMA87_02165-_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS55_IHMA87_06096-_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS53_IHMA87_02165_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS54_IHMA87_02464_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS53_IHMA87_02165-_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS54_IHMA87_02464_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS52_RcsB-IHMA87_02872_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS52_RcsB-_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS52_RcsB-PA14_59770_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS55_IHMA87_06096-_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS52_RcsB-IHMA87_02872_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS52_RcsB-_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS50_AlgB-PA5483_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS51_MifR-PA5511_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS51_MifR-PA5511_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS50_AlgB-PA5483_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS51_MifR-PA14_72720_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS51_MifR-PA14_72720_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS51_MifR-IHMA87_06056_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS51_MifR-IHMA87_06056_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS50_AlgB-PA14_72380_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS4_TctD-PA14_54510_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS4_TctD-PA0756_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS50_AlgB-IHMA87_06026_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS50_AlgB-IHMA87_06026_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS4_TctD-IHMA87_04501_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS50_AlgB-PA14_72380_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS4_TctD-PA14_54510_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS53_IHMA87_02165-_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS4_TctD-IHMA87_04501_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS49_PA5364_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS52_RcsB-PA14_59770_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS49_PA5364_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS4_TctD-PA0756_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS49_PA5364-PA14_70790_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS49_PA5364-IHMA87_05890_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS48_PhoB-PA5360_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS49_PA5364-IHMA87_05890_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS48_PhoB-PA5360_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS49_PA5364-PA14_70790_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS48_PhoB-PA14_70750_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS48_PhoB-PA14_70750_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS47_AlgR-PA14_69470_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS47_AlgR-IHMA87_05746_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS47_AlgR-PA5261_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS47_AlgR-PA5261_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS47_AlgR-IHMA87_05746_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS48_PhoB-IHMA87_05886_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS47_AlgR-PA14_69470_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS46_AmgR-PA5200_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS46_AmgR-PA5200_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS45_DctD-PA5166_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS46_AmgR-IHMA87_05683_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS45_DctD-PA5166_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS46_AmgR-PA14_68700_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS46_AmgR-IHMA87_05683_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS45_DctD-PA14_68250_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS45_DctD-IHMA87_05647_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS44_NtrC-PA5125_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS44_NtrC-PA5125_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS45_DctD-PA14_68250_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS44_NtrC-PA14_67680_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS44_NtrC-PA14_67680_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS44_NtrC-IHMA87_05600_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS44_NtrC-IHMA87_05600_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS43_AruR-PA4983_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS48_PhoB-IHMA87_05886_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS43_AruR-_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS43_AruR-_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS46_AmgR-PA14_68700_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS43_AruR-PA14_65880_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS42_IrlR-PA4885_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS42_IrlR-PA14_64570_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS42_IrlR-PA14_64570_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS43_AruR-PA4983_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS42_IrlR-PA4885_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS45_DctD-IHMA87_05647_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS42_IrlR-IHMA87_05374_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS41_PmrA-PA4776_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS42_IrlR-IHMA87_05374_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS41_PmrA-PA14_63150_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS41_PmrA-IHMA87_05256_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS41_PmrA-PA4776_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS40_CbrB-PA14_62540_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS40_CbrB-PA4726_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS40_CbrB-PA4726_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS41_PmrA-IHMA87_05256_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA


title: CS40_CbrB-PA14_62540_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS3_AgtR-PA14_07840_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS40_CbrB-IHMA87_05201_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS3_AgtR-PA0601_PAO1_rep2

description: adaptor-ligated sheared genomic DNA


title: CS3_AgtR-PA0601_PAO1_rep1

description: adaptor-ligated sheared genomic DNA


title: CS3_AgtR-IHMA87_00593_IHMA87_rep2

description: adaptor-ligated sheared genomic DNA


title: CS3_AgtR-PA14_07840_PA14_rep1

description: adaptor-ligated sheared genomic DNA


title: CS43_AruR-PA14_65880_PA14_rep2

description: adaptor-ligated sheared genomic DNA


title: CS3_AgtR-IHMA87_00593_IHMA87_rep1

description: adaptor-ligated sheared genomic DNA