title: CD3+GPR15- RNA-seq

first: Jörg

last: Hackermüller

address: Permoserstr. 15

institute: Helmholtz Centre for Environmental Research - UFZ

description: total RNA, ribosomal RNA depleted

data_processing:
Adapters were clipped from the sequencing reads using cutadapt (v 1.5).
Reads were mapped to the human genome version hg19 using TopHat2 (v2.0.13).
Read counts for Gencode v24-annotated transcripts were determined using htseqcount (v 0.6.1p1) with mode intersection-strict.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file listing read counts for each gencode annotated gene and sample.

source_name: CD3+GPR15- T cells

extract_protocol:
Peripheral Blood Mononuclear Cells (PBMCs) were obtained by density-gradient centrifugation using Ficoll-Paque (GE Healthcare, Solingen, Germany). GPR15+CD3+ and GPR15-CD3+ T cells were separated by flow cytometric cell sorting after antibody staining of PBMCs for CD3 and GPR15 surface proteins. Flow-cytometric cell sorting was performed at the laboratory of cytometry of the Core Facility at the University of Leipzig. Total RNA was extracted using miRNeasy Mini Kit® in combination with QIAcube® (QIAGEN GmbH, Hilden, Germany) and TURBO DNA-freeTM Kit (Thermo Fisher Scientific Inc., Waltham, MA, USA).
Ribosomal RNAs were removed from total RNA using the Ribo-Zero H/M/R Magnetic Kit (Epicentre, Madison, WI, USA) according to the manufacturer’s instructions. A strand-specific library for transcriptome sequencing was prepared using the ScripSeqv2 Kit (Epicentre) following the manufacturer’s instructions. The library concentration was determined using an Agilent 2100 Bioanalyzer system with a High Sensitivity DNA Kit (Agilent, Santa Clara, CA, USA) according to the manufacturer’s instructions and relying on the concentration of fragments between 200 and 600 nt in size. 19 pmol of library were clustered on one lane of an Illumina paired-end flow cell and 2x100nt were sequenced according to the manufacturer’s instructions using the v3 Cluster Generation and SBS Sequencing Kits (Illumina, San Diego, CA, USA) on a HiSeq2000 system.

tag: cd3 surface expression

value: positive

tag: gpr15 surface expression

value: negative

value: T cells


title: NC567_CK

status: Public on Jan 04 2019

type: SRA

city: Changsha

first: Xianwen

last: Zhang

state: Hunan

address: 1 Nongda Road Furong district

country: China

institute: Hunan Agricultural University

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
Filtering of adaptors and low-quality sequence with fastx_toolkit-0.0.13.2
Alignment with miRBase, ncRNA, piRNA and Rfam databases using CLC genomics_workbench 6.1
Prediction of novel miRNAs with sRNA Toolkit
Expression analysis with DEGseq R combined with perl
Supplementary_files_format_and_content: annonated and normalized abundance file

molecule: total RNA

organism: Nicotiana tabacum

source_name: Leaf

growth_protocol: Both NC567 and Taiyan8 were cultured in plastic pots in a ventilated greenhouse. The seedlings with 6-8 leaves were moved into a growth chamber (Binder, Tuttlingen, Germany) and cultured at about 6  ℃ with humidity of 80% (16/8 h, light/dark).

extract_protocol:
The third leaf from the top from three plants were collected at 0 h (as control) and 24 h after cold treatment, washed carefully, and separately frozen in liquid nitrogen and stored at  80  ℃ prior to RNA extraction.
Approximately 5 µg of small RNA of each group was used for library preparation and sequencing. Small RNA sized at 18–30 nt was gel-purified. 59 and 39 Illumina RNA adapters were ligated to the small RNA molecules. The adapter-ligated small RNAs were then reversely transcribed and amplified for 15 cycles with PCR. Then 4 small RNA libraries were constructed and sequenced according to the Illumina HiSeq 2500 platform sequencing protocols.

tag: developmental stage

value: 5-6-leaf stage

tag: tissue

value: the third leaf from the top

tag: time point

value: 0 h

tag: stress

value: control


title: Pulmonary enteric adenocarcinoma resection 4

type: genomic

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

country: Germany

institute: Ludwig Maximilians University Hospital Munich

description:
201869690097_R04C01
PEAD_4

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing: Statistical analysis was performed using the minfi package running on RStudio version 1.1.444 based on the statistical language R version 3.4.2.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Lung resection

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction from FFPE samples was performed according the manufacturer’s instructions (Maxwell RSC FFPE Plus DNA Purification Kit, Custom, AX4920, Promega, Madison, USA).

tag: gender

value: female

tag: age

tag: primary site

value: Right lower lobe

tag: metastatic site

value: Bone


title: MCF-7_RM+DOX_60h_rep1

type: RNA

city: Quezon City

first: Jortan

middle: Oste

last: Tun

state: National Capital Region

address: Velasquez Street

department: Marine Science Institute

country: Philippines

institute: University of the Philippines

description: RM+DOX 1

hyb_protocol: The aRNA was then fragmented and hybridized to Affymetrix PrimeView Human Expression Arrays for 16 hours at 45°C with rotation at 60 rpm. All the samples were processed using the same reagent kit.

scan_protocol: Arrays were then washed and stained using the FS450_0001 fluidics protocol and scanned using an Affymetrix 3000 7G scanner (S/N: 54716600).

data_processing:
The scanned images were inspected for hybridization efficiency. CEL files generated from AGCC (GeneChip Command Console Software) were also imported into Transcriptome Analysis Console (TAC 4.0) software for Data QC. RMA normalization were performed on the samples to generate the quality control (QC) metrics.
Q_probeset_summarize-Version = V916
affymetrix-algorithm-name =
rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0
affymetrix-array-type = PrimeView
program_name = q_probeset_summarize.exe

label: biotin

label_protocol: The RNA samples were processed according to the Affymetrix 3’ IVT PLUS protocol and Origen Lab’s SOP for 3’ IVT PLUS analysis. Briefly, 100 ng of total RNA was reverse transcribed to produce cDNA, which was subsequently used as a template to create biotin-labeled aRNA (amplified RNA).

growth_protocol: MCF-7 cells were maintained at 37°C, 5% CO2 in 10% MEM supplemented with 2 mM L-glutamine, 1X non-essential amino acids, 1 mM sodium pyruvate, 1.5 g/L sodium bicarbonate (Sigma-Aldrich®), 100 units of penicillin, and 100 μg/mL streptomycin, and 0.01 mg/mL recombinant human insulin (Sigma-Aldrich®). Culture media were renewed every 2-3 days, and cells were subcultured when 80-90% confluent. Only cells that have > 90% viability, passage number < 8, and in the log phase of growth were used for assays.

extract_protocol: MCF-7 cells were lysed using QIAshredder, followed by RNA extraction using QIAgen RNeasy mini kit and sent to Origen Labs Inc. (Singapore) within 24 h for microarray hybridization using Affymetrix PrimeView Human Expression Arrays.

treatment_protocol: MCF-7 cells were treated with near IC50 concentrations of RM (6.25 nM), DOX (313 nM) and its combination for 60 h. Individual drug treatments and vehicle control were prepared in duplicates, while the combination treatment was prepared in triplicates.

tag: cell line

tag: cell type

tag: treatment

value: IC50 concentrations of RM+DOX combination for 60h


title: CD3+GPR15+ RNA-seq

description: total RNA, ribosomal RNA depleted

source_name: CD3+GPR15+ T cells


title: MCF-7_DOX_60h_rep2

description: DOX 2

value: IC50 concentrations of DOX (313 nM) for 60h


title: NC567_24 h

treatment_protocol: 6  ℃ with humidity of 80% (16/8 h, light/dark).

value: cold


title: Al stress vs. control Replicate 3

city: Gifu

first: Kazutaka

last: Kusunoki

state: Gifu

address: 1-1 Yanagido

department: Faculty of Applied Biological Sciences

country: Japan

institute: Gifu University

description: Biological replicate 3 of 3. 10 day-old seedlings of Col-4 were treated with hydroponic culture with or without Al at pH4.5 for 24 h, and the roots were harvested.

hyb_protocol: 0.825 micro g of Cy3- and Cy5-labelled cRNA (specific activity >10.0 pmol Cy3 or Cy5 per micro g cRNA) were fragmented with Gene Expression Hybridization Kit (5188-5242, Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 micro litter of 2x GE hybridization buffer HI-PRM was added to the fragmentation mixture and hybridized to Agilent Arabidopsis 3 Oligo Microarray (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Scanned on the Agilent G2508B scanner

data_processing: Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Arabidopsis thaliana

source_name: Col-4, Al 24 h

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA were prepared from 1 micro g of total RNA using the Two-Color Quick Amp Labeling kit (5190-0444, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).

growth_protocol: Col-4 of Arabidopsis were grown hydroponically in the 2% modified MGRL solution  (0 µM AlCl3, pH 5.5, 2% MGRL containing 200 µM CaCl2)  for 10 days. All seedlings were kept under 12 h illuminations per day (30 µmol m–2 s–1) at 25°C .

extract_protocol: Total RNA was isolated by the method of Suzuki et al. (2004).

treatment_protocol: Root of the seedlings were exposed to toxic solutions containing 6 µM Al (pH5.0), 3 µM Cd, 1.3 µM Cu or 10 mM NaCl at pH 5.0 for 24 hrs at growth conditions.

tag: background

value: root

source_name: Col-4, control 24 h


title: MCF-7_RM_60h_rep2

description: RM 3

value: IC50 concentrations of RM (6.25 nM) for 60h


title: Al stress vs. control Replicate 2

description: Biological replicate 2 of 3. 10 day-old seedlings of Col-4 were treated with hydroponic culture with or without Al at pH4.5 for 24 h, and the roots were harvested.


title: Cd stress vs. control Replicate 3

description: Biological replicate 3 of 3. 10 day-old seedlings of Col-4 were treated with hydroponic culture with or without Cd at pH4.5 for 24 h, and the roots were harvested.

source_name: Col-4, Cd 24 h


title: Metastatic colorectal cancer resection 2

description:
201465940044_R07C01
MCC_2

source_name: Lung metastasis resection

value: male

value: Sigmoid

value: Left upper lobe


title: MCF-7_RM+DOX_60h_rep3

description: RM+DOX 3


title: MCF-7_RM_60h_rep1

description: RM 1b


title: MCF-7_0.1%DMSO_60h_rep2

description: Neg 2

value: 0.1% DMSO for 60h


title: MCF-7_0.1%DMSO_60h_rep1

description: Neg 1


title: Cu stress vs. control Replicate 3

description: Biological replicate 3 of 3. 10 day-old seedlings of Col-4 were treated with hydroponic culture with or without Cu at pH4.5 for 24 h, and the roots were harvested.

source_name: Col-4, Cu 24 h


title: Pulmonary enteric adenocarcinoma resection 2

description:
201465930047_R02C01
PEAD_2

value: Right upper lobe


title: LC183T

status: Public on Jan 03 2019

city: Bunkyo-ku

first: Kaoru

last: Mogushi

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

institute: Tokyo Medical and Dental University

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) were performed following the manufacturer's instruction by using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner 3000.

data_processing: The microarray data of 152 tumorous and 91 adjacent liver tissues from HCC patients as well as 14 normal liver were normalized by robust multichip analysis (RMA) using affy package in R/Bioconductor.

source_name: Human liver cancer #LC183, tumorous tissue

label_protocol: Amplified RNA was prepared by using 3' IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted from tissue specimens by using RNeasy Protect Mini Kit (QIAGEN). Contaminating DNA was removed by digestion with RNase-Free DNase Set (QIAGEN). The RNA Integrity Number (RIN) of all the samples was confirmed to be greated than 7.0 by using 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Tissue samples were stored in RNAlater (Thermo Fisher Scientific) at -80°C immediately after dissected.

value: liver cancer tumorous tissue


title: Pulmonary enteric adenocarcinoma resection 3

description:
201465930047_R03C01
PEAD_3

value: Right middle lobe

value: Right chest wall


title: LC180T

source_name: Human liver cancer #LC180, tumorous tissue


title: Al stress vs. control Replicate 1

description: Biological replicate 1 of 3. 10 day-old seedlings of Col-4 were treated with hydroponic culture with or without Al at pH4.5 for 24 h, and the roots were harvested.


title: LC178T

source_name: Human liver cancer #LC178, tumorous tissue


title: LC181T

source_name: Human liver cancer #LC181, tumorous tissue


title: LC175T

source_name: Human liver cancer #LC175, tumorous tissue


title: LC179T

source_name: Human liver cancer #LC179, tumorous tissue


title: Pulmonary enteric adenocarcinoma biopsy 5

description:
201869690097_R05C01
PEAD_5

source_name: Lung biopsy


title: LC176T

source_name: Human liver cancer #LC176, tumorous tissue


title: LC177T

source_name: Human liver cancer #LC177, tumorous tissue


title: LC172T

source_name: Human liver cancer #LC172, tumorous tissue


title: LC182T

source_name: Human liver cancer #LC182, tumorous tissue


title: LC169T

source_name: Human liver cancer #LC169, tumorous tissue


title: Pulmonary enteric adenocarcinoma resection 1

description:
201465940044_R08C01
PEAD_1

source_name: Lung resection

value: Bilateral pulmonary


title: LC173T

source_name: Human liver cancer #LC173, tumorous tissue


title: LC165T

source_name: Human liver cancer #LC165, tumorous tissue


title: LC174T

source_name: Human liver cancer #LC174, tumorous tissue


title: LC171T

source_name: Human liver cancer #LC171, tumorous tissue


title: LC157T

source_name: Human liver cancer #LC157, tumorous tissue


title: LC162T

source_name: Human liver cancer #LC162, tumorous tissue


title: LC159T

source_name: Human liver cancer #LC159, tumorous tissue


title: LC163T

source_name: Human liver cancer #LC163, tumorous tissue


title: LC166T

source_name: Human liver cancer #LC166, tumorous tissue


title: LC164T

source_name: Human liver cancer #LC164, tumorous tissue


title: LC158T

source_name: Human liver cancer #LC158, tumorous tissue


title: LC168T

source_name: Human liver cancer #LC168, tumorous tissue


title: LC170T

source_name: Human liver cancer #LC170, tumorous tissue


title: LC155T

source_name: Human liver cancer #LC155, tumorous tissue


title: LC160T

source_name: Human liver cancer #LC160, tumorous tissue


title: LC151T

source_name: Human liver cancer #LC151, tumorous tissue


title: LC161T

source_name: Human liver cancer #LC161, tumorous tissue


title: LC156T

source_name: Human liver cancer #LC156, tumorous tissue


title: LC154T

source_name: Human liver cancer #LC154, tumorous tissue


title: LC146T

source_name: Human liver cancer #LC146, tumorous tissue


title: LC153T

source_name: Human liver cancer #LC153, tumorous tissue


title: LC149T

source_name: Human liver cancer #LC149, tumorous tissue


title: LC144T

source_name: Human liver cancer #LC144, tumorous tissue


title: LC147T

source_name: Human liver cancer #LC147, tumorous tissue


title: LC148T

source_name: Human liver cancer #LC148, tumorous tissue


title: LC145T

source_name: Human liver cancer #LC145, tumorous tissue


title: LC152T

source_name: Human liver cancer #LC152, tumorous tissue


title: LC167T

source_name: Human liver cancer #LC167, tumorous tissue


title: LC132T

source_name: Human liver cancer #LC132, tumorous tissue


title: LC135T

source_name: Human liver cancer #LC135, tumorous tissue


title: LC141T

source_name: Human liver cancer #LC141, tumorous tissue


title: LC133T

source_name: Human liver cancer #LC133, tumorous tissue


title: LC139T

source_name: Human liver cancer #LC139, tumorous tissue


title: LC140T

source_name: Human liver cancer #LC140, tumorous tissue


title: LC134T

source_name: Human liver cancer #LC134, tumorous tissue


title: LC143T

source_name: Human liver cancer #LC143, tumorous tissue


title: LC150T

source_name: Human liver cancer #LC150, tumorous tissue


title: LC130T

source_name: Human liver cancer #LC130, tumorous tissue


title: LC142T

source_name: Human liver cancer #LC142, tumorous tissue


title: LC136T

source_name: Human liver cancer #LC136, tumorous tissue


title: LC129T

source_name: Human liver cancer #LC129, tumorous tissue


title: LC122T

source_name: Human liver cancer #LC122, tumorous tissue


title: LC123T

source_name: Human liver cancer #LC123, tumorous tissue


title: LC126T

source_name: Human liver cancer #LC126, tumorous tissue


title: LC128T

source_name: Human liver cancer #LC128, tumorous tissue


title: LC125T

source_name: Human liver cancer #LC125, tumorous tissue


title: LC131T

source_name: Human liver cancer #LC131, tumorous tissue


title: LC137T

source_name: Human liver cancer #LC137, tumorous tissue


title: LC121T

source_name: Human liver cancer #LC121, tumorous tissue


title: LC138T

source_name: Human liver cancer #LC138, tumorous tissue


title: LC100T

source_name: Human liver cancer #LC100, tumorous tissue


title: LC111T

source_name: Human liver cancer #LC111, tumorous tissue


title: LC102T

source_name: Human liver cancer #LC102, tumorous tissue


title: LC118T

source_name: Human liver cancer #LC118, tumorous tissue


title: LC106T

source_name: Human liver cancer #LC106, tumorous tissue


title: LC101T

source_name: Human liver cancer #LC101, tumorous tissue


title: LC114T

source_name: Human liver cancer #LC114, tumorous tissue


title: LC107T

source_name: Human liver cancer #LC107, tumorous tissue


title: LC110T

source_name: Human liver cancer #LC110, tumorous tissue


title: LC127T

source_name: Human liver cancer #LC127, tumorous tissue


title: LC103T

source_name: Human liver cancer #LC103, tumorous tissue


title: LC112T

source_name: Human liver cancer #LC112, tumorous tissue


title: LC117T

source_name: Human liver cancer #LC117, tumorous tissue


title: LC096T

source_name: Human liver cancer #LC096, tumorous tissue


title: LC115T

source_name: Human liver cancer #LC115, tumorous tissue


title: LC113T

source_name: Human liver cancer #LC113, tumorous tissue


title: LC120T

source_name: Human liver cancer #LC120, tumorous tissue


title: LC116T

source_name: Human liver cancer #LC116, tumorous tissue


title: LC119T

source_name: Human liver cancer #LC119, tumorous tissue


title: LC109T

source_name: Human liver cancer #LC109, tumorous tissue


title: LC098T

source_name: Human liver cancer #LC098, tumorous tissue


title: LC094T

source_name: Human liver cancer #LC094, tumorous tissue


title: LC099T

source_name: Human liver cancer #LC099, tumorous tissue


title: LC104T

source_name: Human liver cancer #LC104, tumorous tissue


title: LC095T

source_name: Human liver cancer #LC095, tumorous tissue


title: LC097T

source_name: Human liver cancer #LC097, tumorous tissue


title: LC108T

source_name: Human liver cancer #LC108, tumorous tissue


title: LC105T

source_name: Human liver cancer #LC105, tumorous tissue


title: LC092T

source_name: Human liver cancer #LC092, tumorous tissue


title: LC087T

source_name: Human liver cancer #LC087, tumorous tissue


title: LC091T

source_name: Human liver cancer #LC091, tumorous tissue


title: IM4b

city: Gothenburg

first: Jana

last: Biermann

address: Medicinaregatan 1F

country: Sweden

institute: University of Gothenburg

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC_v-1-0 using standard Illumina protocol

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

data_processing:
Results were analyzed with GenomeStudio 2011.1 from Illumina Inc.
Probes were normalized with BMIQ (beta mixture quantile dilation) in the R package “RnBeads”

source_name: Human breast tumour

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated from fresh-frozen tissue specimens using the Wizard Genomic DNA extraction kit, including proteinase K treatment followed by phenol chloroform purification

value: Female

value: Human breast tumour


title: LC085T

source_name: Human liver cancer #LC085, tumorous tissue


title: LC090T

source_name: Human liver cancer #LC090, tumorous tissue


title: LC089T

source_name: Human liver cancer #LC089, tumorous tissue


title: LC082T

source_name: Human liver cancer #LC082, tumorous tissue


title: LC081T

source_name: Human liver cancer #LC081, tumorous tissue


title: LC079T

source_name: Human liver cancer #LC079, tumorous tissue


title: LC093T

source_name: Human liver cancer #LC093, tumorous tissue


title: LC088T

source_name: Human liver cancer #LC088, tumorous tissue


title: BM7a


title: LC077T

source_name: Human liver cancer #LC077, tumorous tissue


title: IS4b


title: LC080T

source_name: Human liver cancer #LC080, tumorous tissue


title: LC075T

source_name: Human liver cancer #LC075, tumorous tissue


title: LC083T

source_name: Human liver cancer #LC083, tumorous tissue


title: LC076T

source_name: Human liver cancer #LC076, tumorous tissue


title: IS4a


title: LC072T

source_name: Human liver cancer #LC072, tumorous tissue


title: BM1b


title: LC084T

source_name: Human liver cancer #LC084, tumorous tissue


title: LC073T

source_name: Human liver cancer #LC073, tumorous tissue


title: LC078T

source_name: Human liver cancer #LC078, tumorous tissue


title: LC069T

source_name: Human liver cancer #LC069, tumorous tissue


title: LC071T

source_name: Human liver cancer #LC071, tumorous tissue


title: LC070T

source_name: Human liver cancer #LC070, tumorous tissue


title: BM7b

source_name: Human breast tumour


title: LC074T

source_name: Human liver cancer #LC074, tumorous tissue


title: LC086T

source_name: Human liver cancer #LC086, tumorous tissue


title: IM4a


title: BM1a


title: IS1a


title: IM9b


title: BS8b


title: LC124T

source_name: Human liver cancer #LC124, tumorous tissue


title: BS8a


title: LC068T

source_name: Human liver cancer #LC068, tumorous tissue


title: IS1b


title: BS7a


title: BS7b


title: RNA sequencing in mmi1 deleted cells (REP 2)

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

country: USA

institute: NCI

data_processing:
Alignment was done using Tophat.
FPKM values were calculated using cufflinks
Genome_build: asm294v2.28
Supplementary_files_format_and_content: Tab delimited text files, from cufflinks

organism: Schizosaccharomyces pombe

source_name: log. growing cells

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures were grown at 32˚C.

extract_protocol:
RNA was extracted using hot phenol method.
NEB Ultra Directional RNA Library Prep kit (NEB, E7420S) was used according to manufacturer's recommendation.
Libraries were analyzed using an Agilent 2100 BioAnalyzer (Agilent) and sequenced on the Illumina NextSeq 500 platform.

treatment_protocol: Genomic deletion of erh1 and mmi1. Genomic mutation of mmi1-W112A.

tag: genotype/variation

value: mmi1 deletion


title: RNA sequencing in erh1 deleted cells (REP 2)

value: erh1 deletion


title: RNA sequencing in erh1 deleted cells (REP 1)


title: LC062T

source_name: Human liver cancer #LC062, tumorous tissue


title: LC064T

source_name: Human liver cancer #LC064, tumorous tissue


title: RNA sequencing in mmi1 deleted cells (REP 1)


title: RNA sequencing in mmi1(W112A) mutant cells (REP 2)

value: mmi1(W112A) mutant


title: LC065T

source_name: Human liver cancer #LC065, tumorous tissue


title: IM9a


title: LC060T

source_name: Human liver cancer #LC060, tumorous tissue


title: RNA sequencing in mmi1(W112A) mutant cells (REP 1)


title: LC061T

source_name: Human liver cancer #LC061, tumorous tissue


title: DNA sequencing of input whole-cell extract ChIP H3K9me2

library_source: genomic

data_processing:
Alignment was done using BWA-MEM.
Reads per Genomic Content (RPGC) values were obtained using Deeptools suite
Genome_build: asm294v2.29
Supplementary_files_format_and_content: bigWig from Deeptools suite

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 20 minutes. Cells were lysed using bead-beater method. Lysates were sonicated and immunoprecipitations were performed using H3K9me2 antibodies (ab115159). Reverse crosslinking was performed overnight at 65˚C, followed by treatment with RNase A and proteinase K. DNA was purified using QIAquick PCR purification kit (cat. no. 28014).
NEBNext Ultra II DNA Library Prep kit (NEB, E7645S) was used according to manufacturer's recommendation.
Libraries were analyzed using an Agilent 2100 BioAnalyzer (Agilent) and sequenced on the Illumina NextSeq 500 platform.

treatment_protocol: Genomic deletion of erh1. Genomic mutation of mmi1(W112A).

value: wild type cells

tag: antibody

value: input


title: LC059T

source_name: Human liver cancer #LC059, tumorous tissue


title: RNA sequencing in wild-type cells (REP 1)


title: LC063T

source_name: Human liver cancer #LC063, tumorous tissue


title: LC058T

source_name: Human liver cancer #LC058, tumorous tissue


title: LC055T

source_name: Human liver cancer #LC055, tumorous tissue


title: LC054T

source_name: Human liver cancer #LC054, tumorous tissue


title: LC057T

source_name: Human liver cancer #LC057, tumorous tissue


title: LC049T

source_name: Human liver cancer #LC049, tumorous tissue


title: DNA sequencing in erh1 deletion cells (REP 1) ChIP H3K9me2


title: LC050T

source_name: Human liver cancer #LC050, tumorous tissue


title: LC051T

source_name: Human liver cancer #LC051, tumorous tissue


title: LC053T

source_name: Human liver cancer #LC053, tumorous tissue


title: LC048T

source_name: Human liver cancer #LC048, tumorous tissue


title: DNA sequencing in mmi1(W112A) cells (REP 1) ChIP H3K9me2

source_name: log. growing cells

value: mmi1-W112A mutant


title: LC052T

source_name: Human liver cancer #LC052, tumorous tissue


title: DNA sequencing in mmi1(W112A) cells (REP 2) ChIP H3K9me2


title: DNA sequencing in wild-type cells (REP 1) ChIP H3K9me2


title: DNA sequencing in wild-type cells (REP 2) ChIP H3K9me2


title: LC066T

source_name: Human liver cancer #LC066, tumorous tissue


title: LC041T

source_name: Human liver cancer #LC041, tumorous tissue


title: LC036T

source_name: Human liver cancer #LC036, tumorous tissue


title: LC031T

source_name: Human liver cancer #LC031, tumorous tissue


title: LC056T

source_name: Human liver cancer #LC056, tumorous tissue


title: LC046T

source_name: Human liver cancer #LC046, tumorous tissue


title: RNA sequencing in wild-type cells (REP 2)


title: LC024T

source_name: Human liver cancer #LC024, tumorous tissue


title: LC023T

source_name: Human liver cancer #LC023, tumorous tissue


title: LC029T

source_name: Human liver cancer #LC029, tumorous tissue


title: LC032T

source_name: Human liver cancer #LC032, tumorous tissue


title: LC067T

source_name: Human liver cancer #LC067, tumorous tissue


title: LC037T

source_name: Human liver cancer #LC037, tumorous tissue


title: LC044T

source_name: Human liver cancer #LC044, tumorous tissue


title: LC034T

source_name: Human liver cancer #LC034, tumorous tissue


title: LC045T

source_name: Human liver cancer #LC045, tumorous tissue


title: LC042T

source_name: Human liver cancer #LC042, tumorous tissue


title: LC047T

source_name: Human liver cancer #LC047, tumorous tissue


title: LC033T

source_name: Human liver cancer #LC033, tumorous tissue


title: LC043T

source_name: Human liver cancer #LC043, tumorous tissue


title: LC038T

source_name: Human liver cancer #LC038, tumorous tissue


title: LC018T

source_name: Human liver cancer #LC018, tumorous tissue


title: LC019T

source_name: Human liver cancer #LC019, tumorous tissue


title: LC020T

source_name: Human liver cancer #LC020, tumorous tissue


title: LC026T

source_name: Human liver cancer #LC026, tumorous tissue


title: LC027T

source_name: Human liver cancer #LC027, tumorous tissue


title: LC039T

source_name: Human liver cancer #LC039, tumorous tissue


title: LC035T

source_name: Human liver cancer #LC035, tumorous tissue


title: LC025T

source_name: Human liver cancer #LC025, tumorous tissue


title: LC028T

source_name: Human liver cancer #LC028, tumorous tissue


title: LC030T

source_name: Human liver cancer #LC030, tumorous tissue


title: LC040T

source_name: Human liver cancer #LC040, tumorous tissue


title: LC021T

source_name: Human liver cancer #LC021, tumorous tissue


title: LC017T

source_name: Human liver cancer #LC017, tumorous tissue


title: LC022T

source_name: Human liver cancer #LC022, tumorous tissue


title: LC015T

source_name: Human liver cancer #LC015, tumorous tissue


title: LC001T

source_name: Human liver cancer #LC001, tumorous tissue


title: LC006T

source_name: Human liver cancer #LC006, tumorous tissue


title: LC008T

source_name: Human liver cancer #LC008, tumorous tissue


title: LC016T

source_name: Human liver cancer #LC016, tumorous tissue


title: LC002T

source_name: Human liver cancer #LC002, tumorous tissue


title: LC009T

source_name: Human liver cancer #LC009, tumorous tissue


title: LC014T

source_name: Human liver cancer #LC014, tumorous tissue


title: NL014

source_name: Human normal liver #NL014

value: Normal liver


title: LC004T

source_name: Human liver cancer #LC004, tumorous tissue


title: NL013

source_name: Human normal liver #NL013


title: LC010T

source_name: Human liver cancer #LC010, tumorous tissue


title: NL015

source_name: Human normal liver #NL015


title: LC013T

source_name: Human liver cancer #LC013, tumorous tissue


title: LC007T

source_name: Human liver cancer #LC007, tumorous tissue


title: LC011T

source_name: Human liver cancer #LC011, tumorous tissue


title: LC012T

source_name: Human liver cancer #LC012, tumorous tissue


title: LC005T

source_name: Human liver cancer #LC005, tumorous tissue


title: L048T2

description: DNA methylation profile of human liver cancer #L048, recurrent tumorous tissue

hyb_protocol: Standard Illumina protocol

scan_protocol: iScan with standard recommended Illumina scanner setting

data_processing: GenomeStudio software

label: Unmethylated: Cy5, Methylated: Cy3

source_name: Human liver cancer #L048, recurrent tumorous tissue

extract_protocol: Genomic DNA was extracted from tissue specimens by using QIAamp DNA Mini Kit (QIAGEN). The integrity of the obtained DNA was confirmed by using 2100 Bioanalyzer (Agilent Technologies).

value: Liver cancer, recurrent tumorous tissue


title: L048T1

description: DNA methylation profile of human liver cancer #L048, primary tumorous tissue

source_name: Human liver cancer #L048, primary tumorous tissue

value: Liver cancer, primary tumorous tissue


title: L048N1

description: DNA methylation profile of human liver cancer #L048, non-tumorous tissue

source_name: Human liver cancer #L048, non-tumorous tissue

value: Liver cancer, non-tumorous tissue


title: LC003T

source_name: Human liver cancer #LC003, tumorous tissue


title: L045T1

description: DNA methylation profile of human liver cancer #L045, primary tumorous tissue

source_name: Human liver cancer #L045, primary tumorous tissue


title: NL010

source_name: Human normal liver #NL010


title: NL011

source_name: Human normal liver #NL011


title: NL009

source_name: Human normal liver #NL009


title: NL003

source_name: Human normal liver #NL003


title: NL005

source_name: Human normal liver #NL005


title: L047T2

description: DNA methylation profile of human liver cancer #L047, recurrent tumorous tissue

source_name: Human liver cancer #L047, recurrent tumorous tissue


title: NL007

source_name: Human normal liver #NL007


title: NL001

source_name: Human normal liver #NL001


title: NL012

source_name: Human normal liver #NL012


title: dark 13 h

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

description: Diurnally grown culture sampled 13 h after the dark to light transition and 1 h into the dark phase.

data_processing:
Basecalling performed using Illumina RTA software.
Conversion of qseq to fastq format and demultiplexing by in-house scripts
Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR.
Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000
SAM alignments sorted and converted to BAM format by samtools (v1.3).
Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand"
Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4
Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs

organism: Chlamydomonas reinhardtii

source_name: liquid culture

growth_protocol: Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling.

extract_protocol:
Total RNA was purified by extraction with Trizol reagent.
~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries.

treatment_protocol: Samples collected over multiple time points over the course 1 day.

tag: strain

tag: light

value: dark

tag: temperature

tag: carbon dioxide

value: air bubbling


title: NL008

source_name: Human normal liver #NL008

tag: tissue


title: NL006

source_name: Human normal liver #NL006


title: L045T2

description: DNA methylation profile of human liver cancer #L045, recurrent tumorous tissue

source_name: Human liver cancer #L045, recurrent tumorous tissue


title: NL004

source_name: Human normal liver #NL004


title: L046T2

description: DNA methylation profile of human liver cancer #L046, recurrent tumorous tissue

source_name: Human liver cancer #L046, recurrent tumorous tissue


title: NL002

source_name: Human normal liver #NL002


title: L047N1

description: DNA methylation profile of human liver cancer #L047, non-tumorous tissue

source_name: Human liver cancer #L047, non-tumorous tissue


title: L047T1

description: DNA methylation profile of human liver cancer #L047, primary tumorous tissue

source_name: Human liver cancer #L047, primary tumorous tissue


title: L046T1

description: DNA methylation profile of human liver cancer #L046, primary tumorous tissue

source_name: Human liver cancer #L046, primary tumorous tissue


title: light 11 h

description: Diurnally grown culture sampled 11 h into the light phase.

tag: time point

value: light (200 PFD)


title: L046N1

description: DNA methylation profile of human liver cancer #L046, non-tumorous tissue

source_name: Human liver cancer #L046, non-tumorous tissue


title: JHH4_mock

data_processing: The data were normalized by robust multichip analysis (RMA) using affy package in R/Bioconductor.

source_name: Human hepatocellular carcinoma cell line JHH4 unexposed to 5-aza

extract_protocol: Total RNA was extracted from cells by using RNeasy Protect Mini Kit (QIAGEN). Contaminating DNA was removed by digestion with RNase-Free DNase Set (QIAGEN). The RNA Integrity Number (RIN) of all the samples was confirmed to be greated than 7.0 by using 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Eight human HCC cell lines (Hep3B, HepG2, HLE, HLF, Huh1, Huh7, JHH2 and JHH4) were exposed and unexposed to 5 μM 5-azacitidine, a demethylating agent, for three days.

value: Human hepatocellular carcinoma cell

tag: agent

value: mock


title: JHH2_AZA

source_name: Human hepatocellular carcinoma cell line JHH2 exposed to 5-aza


title: JHH2_mock

source_name: Human hepatocellular carcinoma cell line JHH2 unexposed to 5-aza


title: light 9 h

description: Diurnally grown culture sampled 9 h into the light phase.

value: 9 h


title: JHH4_AZA

source_name: Human hepatocellular carcinoma cell line JHH4 exposed to 5-aza


title: light 5 h

description: Diurnally grown culture sampled 5 h into the light phase.

value: 5 h


title: Huh7_mock

source_name: Human hepatocellular carcinoma cell line Huh7 unexposed to 5-aza


title: Huh7_AZA

source_name: Human hepatocellular carcinoma cell line Huh7 exposed to 5-aza


title: L045N1

description: DNA methylation profile of human liver cancer #L045, non-tumorous tissue

source_name: Human liver cancer #L045, non-tumorous tissue


title: light 3 h

description: Diurnally grown culture sampled 3 h into the light phase.

source_name: liquid culture

value: 3 h


title: L044N1

description: DNA methylation profile of human liver cancer #L044, non-tumorous tissue

source_name: Human liver cancer #L044, non-tumorous tissue


title: L043T2

description: DNA methylation profile of human liver cancer #L043, recurrent tumorous tissue

source_name: Human liver cancer #L043, recurrent tumorous tissue


title: L043N1

description: DNA methylation profile of human liver cancer #L043, non-tumorous tissue

source_name: Human liver cancer #L043, non-tumorous tissue


title: L044T2

description: DNA methylation profile of human liver cancer #L044, recurrent tumorous tissue

source_name: Human liver cancer #L044, recurrent tumorous tissue


title: L043T1

description: DNA methylation profile of human liver cancer #L043, primary tumorous tissue

source_name: Human liver cancer #L043, primary tumorous tissue


title: Huh1_mock

source_name: Human hepatocellular carcinoma cell line Huh1 unexposed to 5-aza


title: light 7 h

description: Diurnally grown culture sampled 7 h into the light phase.

value: 7 h


title: light 1 h

description: Diurnally grown culture sampled 1 h into the light phase.

value: 1 h


title: Huh1_AZA

source_name: Human hepatocellular carcinoma cell line Huh1 exposed to 5-aza


title: HLF_AZA

source_name: Human hepatocellular carcinoma cell line HLF exposed to 5-aza

value: HLF


title: HLE_AZA

source_name: Human hepatocellular carcinoma cell line HLE exposed to 5-aza

value: HLE


title: Q3 mRNA expression

city: Shanghai

first: RUI

last: LIAO

state: Shanghai

address: Yixueyuan Road

department: Zhongshan hospital

institute: Fudan University

description: Gene expression at 24hr after isolation

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: Primary cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the One-Color Quick Amp Labeling Kit (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HSCs were isolated from surgical peritumoral tissues and CAMFs from matched cancer tissues, respectively. Quiescent HSCs were isolated from normal liver tissues from hepatic hemangiomas and prolong culture cells were used as in vitro activated HSCs. Peritumoral HSCs and intratumoral CAMFs were studied at 24 hours after isolation. HSCs from normal livers were studied at 24 hours after isolation (quiescent HSCs) or after 10 days culture (in vitro activated HSCs) without passage, respectively.

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000 and the RNA integrity was assessed by Agilent 2100 Bioanalyzer. For microarray analysis, Agilent Array platform was employed. The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols. Briefly, 1 μg of total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Genome Oligo Array (4x44K, Agilent Technologies). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505B.

value: liver

value: quiescent hepatic stellate cells

tag: passages


title: L044T1

description: DNA methylation profile of human liver cancer #L044, primary tumorous tissue

source_name: Human liver cancer #L044, primary tumorous tissue


title: HepG2_AZA

source_name: Human hepatocellular carcinoma cell line HepG2 exposed to 5-aza


title: HepG2_mock

source_name: Human hepatocellular carcinoma cell line HepG2 unexposed to 5-aza


title: HLF_mock

source_name: Human hepatocellular carcinoma cell line HLF unexposed to 5-aza


title: light 0.5 h

description: Diurnally grown culture sampled 0.5 h into the light phase.


title: L042T2

description: DNA methylation profile of human liver cancer #L042, recurrent tumorous tissue

source_name: Human liver cancer #L042, recurrent tumorous tissue

value: Liver cancer, recurrent tumorous tissue


title: dark 0 h

description: Diurnally grown culture sampled right before the dark to light transition.

value: 0 h


title: A3 mRNA expression

description: Gene expression at 10 days after isolation without passage

value: culture-activated hepatic stellate cells


title: Hep3B_mock

source_name: Human hepatocellular carcinoma cell line Hep3B unexposed to 5-aza


title: Q2 mRNA expression

description: Gene expression at 24hr after isolation


title: A2 mRNA expression


title: HLE_mock

source_name: Human hepatocellular carcinoma cell line HLE unexposed to 5-aza


title: Hep3B_AZA

source_name: Human hepatocellular carcinoma cell line Hep3B exposed to 5-aza


title: A1 mRNA expression


title: dark -0.5 h

description: Diurnally grown culture sampled 0.5 h before the light phase.

source_name: liquid culture

value: dark


title: L042T1

description: DNA methylation profile of human liver cancer #L042, primary tumorous tissue

source_name: Human liver cancer #L042, primary tumorous tissue

value: Liver cancer, primary tumorous tissue


title: T3 mRNA expression

description: Gene expression at 24hr after isolation

value: cancer associated myofibroblasts


title: T1 mRNA expression

description: Gene expression at 24hr after isolation


title: dark -1 h

description: Diurnally grown culture sampled 1 h before the light phase.

value: air bubbling


title: P2 mRNA expression

description: Gene expression at 24hr after isolation

value: peritumoral activated hepatic stellate cells


title: P3 mRNA expression

description: Gene expression at 24hr after isolation


title: T2 mRNA expression

description: Gene expression at 24hr after isolation


title: dark -3 h

description: Diurnally grown culture sampled 3 h before the light phase.


title: dark -5 h

description: Diurnally grown culture sampled 5 h before the light phase.


title: dark -7 h

description: Diurnally grown culture sampled 7 h before the light phase.


title: P1 mRNA expression

description: Gene expression at 24hr after isolation


title: Q1 mRNA expression

description: Gene expression at 24hr after isolation


title: L042N1

description: DNA methylation profile of human liver cancer #L042, non-tumorous tissue

source_name: Human liver cancer #L042, non-tumorous tissue

value: Liver cancer, non-tumorous tissue


title: dark -9 h

description: Diurnally grown culture sampled 9 h before the light phase.


title: L041T2

description: DNA methylation profile of human liver cancer #L041, recurrent tumorous tissue

source_name: Human liver cancer #L041, recurrent tumorous tissue


title: L041T1

description: DNA methylation profile of human liver cancer #L041, primary tumorous tissue

source_name: Human liver cancer #L041, primary tumorous tissue


title: dark -11 h

description: Diurnally grown culture sampled 11 h before the light phase.


title: L040T1

description: DNA methylation profile of human liver cancer #L040, primary tumorous tissue

source_name: Human liver cancer #L040, primary tumorous tissue


title: L041N1

description: DNA methylation profile of human liver cancer #L041, non-tumorous tissue

source_name: Human liver cancer #L041, non-tumorous tissue


title: L040N1

description: DNA methylation profile of human liver cancer #L040, non-tumorous tissue

source_name: Human liver cancer #L040, non-tumorous tissue


title: L040T2

description: DNA methylation profile of human liver cancer #L040, recurrent tumorous tissue

source_name: Human liver cancer #L040, recurrent tumorous tissue


title: replicate sCJD_2

city: Bologna

first: Piero

last: Parchi

state: BO

address: Ospedale Bellaria, Via Altura 1/8

department: DIMES

country: Italy

institute: University of Bologna

description:
technical replicate sample
SAMPLE 21

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: The BeadChips were scanned using the Illumina BeadArray Reader according to standard Illumina scan protocol.

data_processing: The data were extracted and processed by applying a quantile normalization using the Illumina Beadstudio 3.2 software (Illumina).

label: Biotin

source_name: Frontal Cortex

label_protocol: RNA samples were prepared for array analysis using the Illumina TotalPrep™-96 RNA Amplification Kit. Label: Biotin.

extract_protocol: Total RNA was extracted from dissected snap-frozen tissue  according to a BNE optimised common protocol using the RNeasy® tissue lipid mini kit. Quality was assessed using Bioanalyzer.

tag: condition

value: sCJD affected


title: sCJD_10

description: SAMPLE 20


title: sCJD_3

description: SAMPLE 13


title: sCJD_6

description: SAMPLE 16


title: sCJD_8

description: SAMPLE 18


title: sCJD_9

description: SAMPLE 19


title: sCJD_4

description: SAMPLE 14


title: sCJD_5

description: SAMPLE 15


title: sCJD_7

description: SAMPLE 17


title: sCJD_1

description: SAMPLE 11


title: L039T1

description: DNA methylation profile of human liver cancer #L039, primary tumorous tissue

source_name: Human liver cancer #L039, primary tumorous tissue


title: sCJD_2

description: SAMPLE 12


title: Worker vs Queen prepupal hindlegs development_biol-2_dyeswap3

city: Piracicaba

first: Ana

middle: Durvalina

last: Bomtorin

state: São Paulo

address: R Ajudante Albano 847

country: Brazil

institute: Universidade de Sao Paulo

hyb_protocol: The RNA was dye-coupled and combined with hybridization buffer (49% Formamide, 49% SSC 20x and 0.2% SDS), pre-heated at 55° C for 3 min, applied to arrays, and hybridized for 17 h at 42 °C in single slide hybridization chambers placed in a water bath. A series of 30s shaking washes in 2× SSC plus 0.1% SDS; 2× SSC; 0.1× SSC and Milli-Q water at room temperature removed excess probe.

scan_protocol: The hybridized slides were scanned using an Axon Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA) with GENEPIX software (Agilent Technologies, Santa Clara, CA), 10-micron resolution, Cy3 with Green Laser (532 nm), and Cy5 with Red Laser (635 nm). GenePix Pro 6.0 software was used for quantification of the spots and image analysis with default parameters.  The hybridized slides were scanned using an Axon Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA) with GENEPIX software (Agilent Technologies, Santa Clara, CA), 10-micron resolution, Cy3 with Green Laser (532 nm), and Cy5 with Red Laser (635 nm). GenePix Pro 6.0 software was used for quantification of the spots and image analysis with default parameters.

data_processing:
The scan results of the slides read in an Axon Genepix 4000B scanner (Molecular Devices) with GenePix® Pro 6.0 software (Agilent Technologies, Santa Clara, CA) were analyzed using the Limma package of Bioconductor software implemented in R The background was corrected by adding to the background intensities a positive constant (offset correction = 50), which restrains spurious variation in log-ratios, particularly at low intensity spots. The “print-tip loess” normalization was used to correct for within-array dye, and spatial effects and single channel normalization was used to facilitate comparison between arrays. (Queen’s sample intensity/Worker’s sample intensity) was determined for each probe in each array. After applying Bayesian statistics to shrink estimated standard errors, we used the moderated t-statistic test for each gene.
The log2 ratio for worker prepupae samples intensity/ queen prepupae sample intensity was determined for each probe in each array. We obtained single FC values for each probe combining intensities from the two dye-swaps experiments for two technical replicates and the two biological samples (containing 10 microgram aRNA) in the Matrix Table.

organism: Apis mellifera

label_protocol: RNA amplification was done with and according to Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion). The amplified RNA samples (10 or 20 µg) were used for dual channel microarray hibridization with Cy3 and Cy5 dyes (with dye swaps). Dye swaps were done for each comparison and two slides were used to evaluate the differential expression.

growth_protocol: Workers and queens larvae, prepupae and pupae were obtained from hives of Africanized hybrid Apis mellifera kept in the Experimental Apiary of the University of São Paulo in Ribeirão Preto, Brazil.

extract_protocol: Total RNA were extracted using Trizol following manufacturer's instructions

treatment_protocol: The samples used were naturally grown in the colonies in the Experimental Apiary of the University of São Paulo in Ribeirão Preto, Brazil.

tag: honeybee type

value: W_PP2_2 (pool)

value: hind legs imaginal discs

value: Q_PP2_2 (pool)


title: Worker vs Queen prepupal hindlegs development_biol-2_dyeswap2


title: CTRL_10

description: SAMPLE 10

value: Control


title: CTRL_3

description: SAMPLE 3


title: L038T1

description: DNA methylation profile of human liver cancer #L038, primary tumorous tissue

source_name: Human liver cancer #L038, primary tumorous tissue


title: CTRL_2

description: SAMPLE 2


title: CTRL_7

description: SAMPLE 7


title: CTRL_4

description: SAMPLE 4


title: Worker vs Queen prepupal hindlegs development_biol-2_dyeswap4


title: CTRL_6

description: SAMPLE 6


title: CTRL_5

description: SAMPLE 5


title: CTRL_1

description: SAMPLE 1


title: L039N1

description: DNA methylation profile of human liver cancer #L039, non-tumorous tissue

source_name: Human liver cancer #L039, non-tumorous tissue


title: L039T2

description: DNA methylation profile of human liver cancer #L039, recurrent tumorous tissue

source_name: Human liver cancer #L039, recurrent tumorous tissue


title: L038T2

description: DNA methylation profile of human liver cancer #L038, recurrent tumorous tissue

source_name: Human liver cancer #L038, recurrent tumorous tissue


title: CTRL_8

description: SAMPLE 8


title: Worker vs Queen prepupal hindlegs development_biol-2_dyeswap1


title: Worker vs Queen prepupal hindlegs development_biol-1_dyeswap4

value: Q_PP2_1 (pool)

value: W_PP2_1 (pool)


title: Worker vs Queen prepupal hindlegs development_biol-1_dyeswap3


title: Worker vs Queen prepupal hindlegs development_biol-1_dyeswap2


title: Worker vs Queen prepupal hindlegs development_biol-1_dyeswap1


title: Worker vs Queen larval hindlegs development_biol-2_dyeswap4

data_processing:
The scan results of the slides read in an Axon Genepix 4000B scanner (Molecular Devices) with GenePix® Pro 6.0 software (Agilent Technologies, Santa Clara, CA) were analyzed using the Limma package of Bioconductor software implemented in R The background was corrected by adding to the background intensities a positive constant (offset correction = 50), which restrains spurious variation in log-ratios, particularly at low intensity spots. The “print-tip loess” normalization was used to correct for within-array dye, and spatial effects and single channel normalization was used to facilitate comparison between arrays. (Queen’s sample intensity/Worker’s sample intensity) was determined for each probe in each array. After applying Bayesian statistics to shrink estimated standard errors, we used the moderated t-statistic test for each gene.
The log2 ratio for worker larvae samples intensity/ queen larvae sample intensity was determined for each probe in each array. We obtained single FC values for each probe combining intensities from the two dye-swaps experiments for two technical replicates and the two biological samples (containing 10 microgram aRNA) in the Matrix Table.

value: Q_F1_2 (pool)

value: W_F1_2 (pool)


title: L037T1

description: DNA methylation profile of human liver cancer #L037, primary tumorous tissue

source_name: Human liver cancer #L037, primary tumorous tissue


title: Worker vs Queen larval hindlegs development_biol-2_dyeswap3


title: Worker vs Queen larval hindlegs development_biol-2_dyeswap2


title: L037N1

description: DNA methylation profile of human liver cancer #L037, non-tumorous tissue

source_name: Human liver cancer #L037, non-tumorous tissue


title: L037T3

description: DNA methylation profile of human liver cancer #L037, re-recurrent tumorous tissue

source_name: Human liver cancer #L037, re-recurrent tumorous tissue

value: Liver cancer, re-recurrent tumorous tissue


title: Worker vs Queen larval hindlegs development_biol-2_dyeswap1


title: Worker vs Queen larval hindlegs development_biol-1_dyeswap3

value: W_F1_1 (pool)

value: Q_F1_1 (pool)


title: Worker vs Queen larval hindlegs development_biol-1_dyeswap2


title: Worker vs Queen pupal hindlegs development_biol-2_dyeswap4

data_processing:
The scan results of the slides read in an Axon Genepix 4000B scanner (Molecular Devices) with GenePix® Pro 6.0 software (Agilent Technologies, Santa Clara, CA) were analyzed using the Limma package of Bioconductor software implemented in R The background was corrected by adding to the background intensities a positive constant (offset correction = 50), which restrains spurious variation in log-ratios, particularly at low intensity spots. The “print-tip loess” normalization was used to correct for within-array dye, and spatial effects and single channel normalization was used to facilitate comparison between arrays. (Queen’s sample intensity/Worker’s sample intensity) was determined for each probe in each array. After applying Bayesian statistics to shrink estimated standard errors, we used the moderated t-statistic test for each gene.
The log2 ratio for worker pupae samples intensity/ queen pupae sample intensity was determined for each probe in each array. We obtained single FC values for each probe combining intensities from the two dye-swaps experiments for two technical replicates and the two biological samples (containing 10 microgram aRNA) in the Matrix Table.

value: Q_Pw_2 (pool)

value: W_Pw_2 (pool)


title: L038N1

description: DNA methylation profile of human liver cancer #L038, non-tumorous tissue

source_name: Human liver cancer #L038, non-tumorous tissue


title: Worker vs Queen pupal hindlegs development_biol-2_dyeswap1


title: Worker vs Queen pupal hindlegs development_biol-2_dyeswap2


title: Worker vs Queen pupal hindlegs development_biol-1_dyeswap4

value: Q_Pw_1 (pool)

value: W_Pw_1 (pool)


title: Worker vs Queen pupal hindlegs development_biol-1_dyeswap3


title: Worker vs Queen larval hindlegs development_biol-1_dyeswap1


title: IM9b

hyb_protocol: Hybridization probes were denatured, preannealed, and cohybridized to arrays pretreated with the Universal Microarray Hybridization Kit. Following hybridization, slides were washed at room temperature and dried by centrifugation.

scan_protocol: Images and raw signal intensities were acquired using an Agilent G2505B DNA microarray scanner and GenePix Pro 6.0.1.22 image analysis software

data_processing: Pin-based LOWESS normalized, spot intensities representing the tumor (cy3) and reference (cy5) channels were background-corrected by subtracting the median background from the median foreground signal intensities. BASE database used.

source_name: Human breast tumor

label_protocol: Tumor and reference genomic DNA were differentially labeled using a random labeling kit with Cy3-dCTP and Cy5-dCTP, respectively

tag: gender

value: female

value: Human breast tumor

source_name: Normal female genomic DNA

value: Normal female genomic DNA


title: Worker vs Queen pupal hindlegs development_biol-2_dyeswap3

value: hind legs imaginal discs


title: L036T1

description: DNA methylation profile of human liver cancer #L036, primary tumorous tissue

source_name: Human liver cancer #L036, primary tumorous tissue

value: Liver cancer, primary tumorous tissue


title: Worker vs Queen pupal hindlegs development_biol-1_dyeswap2


title: L035N1

description: DNA methylation profile of human liver cancer #L035, non-tumorous tissue

source_name: Human liver cancer #L035, non-tumorous tissue

value: Liver cancer, non-tumorous tissue


title: L035T1

description: DNA methylation profile of human liver cancer #L035, primary tumorous tissue

source_name: Human liver cancer #L035, primary tumorous tissue


title: IM9a


title: L036N1

description: DNA methylation profile of human liver cancer #L036, non-tumorous tissue

source_name: Human liver cancer #L036, non-tumorous tissue


title: Worker Pupae hindlegs development_biol-2_dyeswap3

data_processing:
The scan results of the slides read in an Axon Genepix 4000B scanner (Molecular Devices) with GenePix® Pro 6.0 software (Agilent Technologies, Santa Clara, CA) were analyzed using the Limma package of Bioconductor software implemented in R The background was corrected by adding to the background intensities a positive constant (offset correction = 50), which restrains spurious variation in log-ratios, particularly at low intensity spots. The “print-tip loess” normalization was used to correct for within-array dye, and spatial effects and single channel normalization was used to facilitate comparison between arrays. (Queen’s sample intensity/Worker’s sample intensity) was determined for each probe in each array. After applying Bayesian statistics to shrink estimated standard errors, we used the moderated t-statistic test for each gene.
The log2 ratio for worker prepupae and pupae samples intensity/ worker larvae sample intensity was determined for each probe in each array. We obtained single FC values for each probe combining intensities from the two dye-swaps experiments for two technical replicates and the two biological samples (containing 10 microgram aRNA) in the Matrix Table.


title: Worker Pupae hindlegs development_biol-2_dyeswap4


title: L034N1

description: DNA methylation profile of human liver cancer #L034, non-tumorous tissue

source_name: Human liver cancer #L034, non-tumorous tissue


title: L035T2

description: DNA methylation profile of human liver cancer #L035, recurrent tumorous tissue

source_name: Human liver cancer #L035, recurrent tumorous tissue

value: Liver cancer, recurrent tumorous tissue


title: Worker Pupae hindlegs development_biol-2_dyeswap1


title: IM8b


title: IM8a


title: Worker Pupae hindlegs development_biol-1_dyeswap4


title: Worker Pupae hindlegs development_biol-2_dyeswap2


title: Worker Pupae hindlegs development_biol-1_dyeswap3


title: IM7b


title: L034T2

description: DNA methylation profile of human liver cancer #L034, recurrent tumorous tissue

source_name: Human liver cancer #L034, recurrent tumorous tissue


title: L034T1

description: DNA methylation profile of human liver cancer #L034, primary tumorous tissue

source_name: Human liver cancer #L034, primary tumorous tissue


title: L037T2

description: DNA methylation profile of human liver cancer #L037, recurrent tumorous tissue

source_name: Human liver cancer #L037, recurrent tumorous tissue


title: Worker Pupae hindlegs development_biol-1_dyeswap2


title: Worker Pupae hindlegs development_biol-1_dyeswap1


title: IM7a


title: Worker Prepupae hindlegs development_biol-2_dyeswap4

value: W_PP2_2 (pool)


title: Worker Prepupae hindlegs development_biol-2_dyeswap3


title: Worker Prepupae hindlegs development_biol-2_dyeswap2


title: IM6b


title: Worker Prepupae hindlegs development_biol-2_dyeswap1


title: L033T2

description: DNA methylation profile of human liver cancer #L033, recurrent tumorous tissue

source_name: Human liver cancer #L033, recurrent tumorous tissue


title: Worker vs Queen larval hindlegs development_biol-1_dyeswap4


title: L033N1

description: DNA methylation profile of human liver cancer #L033, non-tumorous tissue

source_name: Human liver cancer #L033, non-tumorous tissue


title: L032N1

description: DNA methylation profile of human liver cancer #L032, non-tumorous tissue

source_name: Human liver cancer #L032, non-tumorous tissue


title: Worker Prepupae hindlegs development_biol-1_dyeswap4

value: W_PP2_1 (pool)


title: L033T1

description: DNA methylation profile of human liver cancer #L033, primary tumorous tissue

source_name: Human liver cancer #L033, primary tumorous tissue


title: L031T1

description: DNA methylation profile of human liver cancer #L031, primary tumorous tissue

source_name: Human liver cancer #L031, primary tumorous tissue


title: IM5b


title: Worker Prepupae hindlegs development_biol-1_dyeswap2


title: Worker Prepupae hindlegs development_biol-1_dyeswap1


title: L031T2

description: DNA methylation profile of human liver cancer #L031, recurrent tumorous tissue

source_name: Human liver cancer #L031, recurrent tumorous tissue


title: IM5a

source_name: Human breast tumor


title: IM6a

source_name: Normal female genomic DNA


title: Queen Pupae hindlegs development_biol-2_dyeswap4

data_processing:
The scan results of the slides read in an Axon Genepix 4000B scanner (Molecular Devices) with GenePix® Pro 6.0 software (Agilent Technologies, Santa Clara, CA) were analyzed using the Limma package of Bioconductor software implemented in R The background was corrected by adding to the background intensities a positive constant (offset correction = 50), which restrains spurious variation in log-ratios, particularly at low intensity spots. The “print-tip loess” normalization was used to correct for within-array dye, and spatial effects and single channel normalization was used to facilitate comparison between arrays. (Queen’s sample intensity/Worker’s sample intensity) was determined for each probe in each array. After applying Bayesian statistics to shrink estimated standard errors, we used the moderated t-statistic test for each gene.
The log2 ratio for queen prepupae and pupae samples intensity/ queen larvae sample intensity was determined for each probe in each array. We obtained single FC values for each probe combining intensities from the two dye-swaps experiments for two technical replicates and the two biological samples (containing 10 microgram aRNA) in the Matrix Table. The fold-change in expression and its standard error for each gene were calculated by fitting a linear regression to the normalized expression data. A Bayesian smoothing procedure was used to shrink the estimated standard errors, with which we calculated the moderated t-statistic for each gene.

value: Q_F1_2 (pool)


title: L032T1

description: DNA methylation profile of human liver cancer #L032, primary tumorous tissue

source_name: Human liver cancer #L032, primary tumorous tissue


title: Queen Pupae hindlegs development_biol-2_dyeswap3


title: Queen Pupae hindlegs development_biol-2_dyeswap2


title: Worker vs Queen pupal hindlegs development_biol-1_dyeswap1


title: L036T2

description: DNA methylation profile of human liver cancer #L036, recurrent tumorous tissue

source_name: Human liver cancer #L036, recurrent tumorous tissue


title: Queen Pupae hindlegs development_biol-2_dyeswap1


title: IM4a


title: IM4b


title: Queen Pupae hindlegs development_biol-1_dyeswap4


title: BM9b


title: Queen Pupae hindlegs development_biol-1_dyeswap3


title: CTRL_9

description: SAMPLE 9

source_name: Frontal Cortex

value: Control


title: Queen Pupae hindlegs development_biol-1_dyeswap2


title: Queen Pupae hindlegs development_biol-1_dyeswap1


title: L030N

description: DNA methylation profile of human liver cancer #L030, non-tumorous tissue

source_name: Human liver cancer #L030, non-tumorous tissue


title: BM9a


title: IM3b


title: Queen Prepupae hindlegs development_biol-2_dyeswap3

value: Q_PP2_2 (pool)


title: Queen Prepupae hindlegs development_biol-2_dyeswap2


title: L030T

description: DNA methylation profile of human liver cancer #L030, tumorous tissue

source_name: Human liver cancer #L030, tumorous tissue

value: Liver cancer, tumorous tissue


title: Queen Prepupae hindlegs development_biol-2_dyeswap4


title: Queen Prepupae hindlegs development_biol-2_dyeswap1


title: L029T

description: DNA methylation profile of human liver cancer #L029, tumorous tissue

source_name: Human liver cancer #L029, tumorous tissue


title: L029N

description: DNA methylation profile of human liver cancer #L029, non-tumorous tissue

source_name: Human liver cancer #L029, non-tumorous tissue


title: L031N1

description: DNA methylation profile of human liver cancer #L031, non-tumorous tissue

source_name: Human liver cancer #L031, non-tumorous tissue


title: IM3a


title: Queen Prepupae hindlegs development_biol-1_dyeswap4

value: Q_PP2_1 (pool)

value: Q_F1_1 (pool)


title: IM2b


title: Queen Prepupae hindlegs development_biol-1_dyeswap2


title: Queen Prepupae hindlegs development_biol-1_dyeswap3


title: IM2a


title: Worker Prepupae hindlegs development_biol-1_dyeswap3

value: W_F1_1 (pool)


title: L028T

description: DNA methylation profile of human liver cancer #L028, tumorous tissue

source_name: Human liver cancer #L028, tumorous tissue


title: L027T

description: DNA methylation profile of human liver cancer #L027, tumorous tissue

source_name: Human liver cancer #L027, tumorous tissue


title: Queen Prepupae hindlegs development_biol-1_dyeswap1


title: L032T2

description: DNA methylation profile of human liver cancer #L032, recurrent tumorous tissue

source_name: Human liver cancer #L032, recurrent tumorous tissue


title: IM1b


title: IM1a


title: IS11b


title: Human healthy HDL [KCV_1E]

city: Nashville

first: Leslie

middle: Roteta

last: Sedgeman

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University

description:
Human healthy HDL - Sample 5
KCV_1E

data_processing:
Cutadapt was used to remove adapters and reads >16 nts in length were aligned to the human (Hg18) genome with 1 mismatch allowance by Bowtie1(v1.1.2) and DEseq2 (v1.18.1)
Genome_build: Hg18
Supplementary_files_format_and_content: tab-delimited text files include DEseq values for each Sample

source_name: HDL

extract_protocol:
plasma was isolated from healthy humans using EDTA. HDL was isolated by immunoprecipitation for ApoAI. RNA was isolated using the Qiagen miRNeasy isolation kit. 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: plasma

tag: rna source

value: HDL

tag: age

value: adult

tag: diagnosis

value: healthy


title: Human healthy HDL [KCV_1I]

description:
Human healthy HDL - Sample 9
KCV_1I


title: Human healthy HDL [KCV_1F]

description:
Human healthy HDL - Sample 6
KCV_1F


title: Human healthy HDL [KCV_1H]

description:
Human healthy HDL - Sample 8
KCV_1H


title: Human healthy HDL [KCV_1G]

description:
Human healthy HDL - Sample 7
KCV_1G


title: Human healthy HDL [KCV_1J]

description:
Human healthy HDL - Sample 10
KCV_1J


title: Human healthy HDL [KCV_1C]

description:
Human healthy HDL - Sample 3
KCV_1C


title: L028N

description: DNA methylation profile of human liver cancer #L028, non-tumorous tissue

source_name: Human liver cancer #L028, non-tumorous tissue


title: L027N

description: DNA methylation profile of human liver cancer #L027, non-tumorous tissue

source_name: Human liver cancer #L027, non-tumorous tissue


title: IS11a

value: female

value: Human breast tumor

value: Normal female genomic DNA


title: Human healthy HDL [KCV_1A]

description:
Human healthy HDL - Sample 1
KCV_1A


title: IS10b


title: IS10a


title: SMARCA4-infected H1703 SMARCA4 ChIP-seq

city: Montreal

first: William

middle: Abraham

last: Pastor

state: QC

address: 3655 Promenade Sir William Osler

department: Biochemistry

institute: McGill University

data_processing:
ChIP-seq: ChIP-seq reads were mapped to the hg19 genome using bowtie2 with default paramters. Duplicate reads were removed using samtools. Bigwig files were generated using DeepTools
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

source_name: H1703 lung cancer cells

extract_protocol: Cells were fixed cells with PBS containing 0.3% formaldehyde for 30 mins rocking at 4 C and quenched by addition of 1/10 volume of 2M glycine with 5 min incubation at room temperature. Fixed cells were then washed once with 1x PBS and resuspended in 1 mL swelling buffer (25mM HEPES-NaOH pH7.5, 10mM KCl, 0.1% NP-40, 1.5mM MgCl2). After incubating 10 mins on ice, dounce homogenizer B was used to break cytoplasmic membrane, 20 strokes. 9mL of MNase digest buffer (15mM HEPES-NaOH pH7.9, 15mM NaCl, 60mM KCl, 0.32M sucrose) was added before spinning down at 2000 RPM for 7 mins at 4 C. Pellet(nuclei) was resuspended in 1 mL MNase digest buffer with 3.3 uL of 1 M CaCl2 and incubated for 15 mins at 37C. 0.5 uL of 2000 U/uL MNase per 107 cells was added for another 15 mins incubation for at 37C. Reaction was then quenched with 10uM EGTA before adding 1mL lysis buffer (20mM Tris-HCl, pH 8.0, 200mM NaCl, 2mM EDTA, 1mM EGTA, 0.2% Na-Deoxycholate, 1% N-lauroylsarcosine) and 1% Triton X-100. Lysate was passed through 21G needle 5 times and spinned down at 13000 g at 4C for 15 minutes. 30ug of SMARCA4 antibody (abcam, ab110641) was added to supernatant with overnight end-over-end mixing at 4C. 50 uL of Protein-G Dynabeads (Invitrogene) per IP was added to lysate and incubated at 4C with rotation for at least 2 hours. Beads were washed 4 times with RIPA buffer for 5 minutes each and once with TE, 50 mM NaCl solution. Elution buffer with 100 uL of 100 mM NaHCO3/1% SDS (make fresh) was added to beads and incubated for 17 mins at 65C on Thermos mixer shaking at 1500 RPM. Supernatant was recovered into a new eppendorf tube followed by adding 5 uL of 5 M NaCl. Samples were decrosslinked overnight at 65C. After incubations with RNAseA (3ul, 10ug/mL) for 30 mins at 37C and Proteinase K (5uL, 10ug/mL) for 1 hour at 55C, DNA was cleaned with DNA clean and concentrate kit (Zymo Research). ChIP-seq libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).

tag: cell line

value: lung cancer


title: SMARCA2-infected H1703 H3K4me3 ChIP

extract_protocol: Cells were fixed in complete media with 1% formaldehyde for 10 minutes at room temperature or 0.3% formaldehyde for 30 minutes at 4ºC then quenched by addition of 0.125 M glycine for 5 minutes at room temperature and 15 minutes on ice. Fixed cells were then pelleted and washed once with 1x PBS before snap-freezing on dry-ice. Cell pellets were lysed in three successive buffers for 10 minutes each at 4ºC while rotating end-over-end (LB1: 50 mM HEPES-KOH pH 7.5, 120 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, LB2: 10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, LB3: 10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine). Lysates were then sonicated with a Branson450D cup-horn system to produce chromatin fragments between 100 and 600 bps. Triton X-100 was added to cell lysate and then centrifuged at 20,000 g for 15 minutes at 4ºC to pellet debris. Supernatant equivalent to 10 million cells brought to a final volume of 500 µL using LB3 was used for each immunoprecipitation. A quantity of sonicated chromatin was set aside as 10% input. 2 µg of Histone H3 acetyl K27 (abcam, ab4729) or Histone H3 tri-methyl K4 (abcam, ab8580) antibodies were added to the lysate for overnight incubation at 4ºC. Protein G Magnetic Dynabeads® (ThermoFisher Scientific) were used for pulldown. Immunoprecipitated chromatin bound to dynabeads was washed with four successive buffers (LSB: 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA; MSB: 20 mM Tris-HCl pH 8.0, 250 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA; LiCl wash: 10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate, 1 mM EDTA; 1x TE: 10 mM Tris-HCl pH 8.0, 1 mM EDTA). Chromatin was then eluted from dynabeads in 150 µL EB (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) by incubating at 65ºC for 30 minutes. Immunoprecipitated samples and input were incubated overnight at 65ºC to denature formaldehyde crosslinking. Samples were then treated with RNaseA (ThermoFisher Scientific) followed by proteinase K (Sigma Aldrich) before phenol/chloroform extraction. DNA was precipitated using 5M NaCl, glycoblue (Ambion) and 100% absolute ethanol overnight at -80ºC. DNA was pelleted by centrifuging at 20,000 g for 30 minutes at 4ºC followed by a 70% ethanol wash. Final DNA pellet was resuspended in 50 uL of 1x TE buffer and placed in speedvac for 3 minutes. ChIP-seq libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).


title: SMARCA4-infected H1703 H3K4me3 ChIP


title: Control-infected H1703 H3K4me3 ChIP


title: L026N

description: DNA methylation profile of human liver cancer #L026, non-tumorous tissue

source_name: Human liver cancer #L026, non-tumorous tissue

value: Liver cancer, non-tumorous tissue


title: SMARCA2-infected H1703 H3K27Ac ChIP


title: L025N

description: DNA methylation profile of human liver cancer #L025, non-tumorous tissue

source_name: Human liver cancer #L025, non-tumorous tissue


title: IS9b

source_name: Human breast tumor

source_name: Normal female genomic DNA


title: L026T

description: DNA methylation profile of human liver cancer #L026, tumorous tissue

source_name: Human liver cancer #L026, tumorous tissue


title: SMARCA4-infected H1703 H3K27Ac ChIP


title: IS9a


title: Human healthy HDL [KCV_1B]

description:
Human healthy HDL - Sample 2
KCV_1B


title: Control-infected H1703 H3K27Ac ChIP


title: SMARCA4-infected H1703 Input for SMARCA4 ChIP-seq


title: L024T

description: DNA methylation profile of human liver cancer #L024, tumorous tissue

source_name: Human liver cancer #L024, tumorous tissue


title: IS8b


title: SMARCA2-infected H1703 ChIP Input


title: SMARCA4-infected H1703 ChIP Input


title: IS8a


title: Control-infected H1703 ChIP Input


title: Human healthy HDL [KCV_1D]

description:
Human healthy HDL - Sample 4
KCV_1D


title: IS7b


title: SMARCA4-infected H1703 ATAC-seq

data_processing:
ATAC-seq: ATAC-seq reads were mapped to the hg19 genome using bowtie, with the parameters -X 2000 -m 1 -p 4. Duplicate reads were removed using samtools. Bigwig files were generated using DeepTools
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

extract_protocol: ATAC-seq was performed as published (Corces et al. 2017 "An improved ATAC-seq protocol reduced background and enables interrogation of frozen tissues") without any modifications


title: L025T

description: DNA methylation profile of human liver cancer #L025, tumorous tissue

source_name: Human liver cancer #L025, tumorous tissue


title: L024N

description: DNA methylation profile of human liver cancer #L024, non-tumorous tissue

source_name: Human liver cancer #L024, non-tumorous tissue


title: IS7a


title: hiPSC_SeroNeurons_3

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the hg38 genome was performed using the STAR aligner version 2.5.3a using the --outFilterIntronMotifs RemoveNoncanonical parameter
Gene expression was quantified using the HOMER analysis suite and differential gene expression was carried out using the DESeq2 package v1.18.1 using duplicates to copute within-group dispersion. FDR < 0.05 and log2 fold change greater than 0.5
Genome_build: hg38

source_name: skin biopsy

growth_protocol: The growth protocols have been described in our study (Vadodaria et al)

extract_protocol:
in vitro derivation from human iPSC
RNA libraries were prepared for sequencing using standard Illumina protocols

value: induced pluripotent stem cells derived 5HT neurons

tag: genotype

value: neurotypical


title: L023T

description: DNA methylation profile of human liver cancer #L023, tumorous tissue

source_name: Human liver cancer #L023, tumorous tissue


title: hiPSC_SeroNeurons_1


title: IS6b


title: Control-infected H1703 ATAC-seq


title: L022N

description: DNA methylation profile of human liver cancer #L022, non-tumorous tissue

source_name: Human liver cancer #L022, non-tumorous tissue


title: IS6a


title: hiPSC_3

value: induced pluripotent stem cells


title: L021T

description: DNA methylation profile of human liver cancer #L021, tumorous tissue

source_name: Human liver cancer #L021, tumorous tissue


title: SMARCA2-infected H1703 ATAC-seq


title: hiPSC_1


title: Donor 3 Flu+ Whole PBMC

city: Melbourne

first: Hyon Xhi

last: Tan

state: Victoria

address: 792 Elizabeth St

department: Department of Microbiology and Immunology

country: Australia

institute: The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity

description:
Raw counts - Whole PBMC.txt
EdgeR - Whole PBMC.txt
D4

data_processing:
RNAseq analysis was performed using the web-based Galaxy platform maintained by Melbourne Bioinformatics.
Reads were mapped to the Homo sapiens reference genome (hg19) using HISAT2 and reads were quantified using HTSeq.
Differential counts were analyzed using the edgeR Bioconductor package
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files reporting raw counts (Htseq) and normalized abundance measurements (EdgeR output)

source_name: Human PBMC

extract_protocol:
RNA was isolated from sorted cells using a QIAGEN RNeasy Plus Micro Kit, as per manufacturer's protocol.
Illumina Truseq Stranded mRNA kit was use for library construction. RNA libraries were prepared for sequencing using standard Illumina protocols

value: PBMC

tag: cell type

value: Whole PBMC

tag: treatment

value: 12 hour exposure to influenza-infected A549 cells


title: IS5b


title: L022T

description: DNA methylation profile of human liver cancer #L022, tumorous tissue

source_name: Human liver cancer #L022, tumorous tissue

value: Liver cancer, tumorous tissue


title: Donor 3 Flu- Whole PBMC

value: 12 hour exposure to non-infected A549 cells


title: IS5a


title: L020N

description: DNA methylation profile of human liver cancer #L020, non-tumorous tissue

source_name: Human liver cancer #L020, non-tumorous tissue


title: Donor 3 Flu- CD3- CD56+ NK cells

description:
Raw counts - NK.txt
EdgeR - NK.txt
D4

value: CD3-CD56+ NK cells


title: IS4b


title: hiPSC_2


title: Donor 2 Flu- Whole PBMC

description:
Raw counts - Whole PBMC.txt
EdgeR - Whole PBMC.txt
D2


title: L021N

description: DNA methylation profile of human liver cancer #L021, non-tumorous tissue

source_name: Human liver cancer #L021, non-tumorous tissue


title: Donor 2 Flu+ Whole PBMC


title: L020T

description: DNA methylation profile of human liver cancer #L020, tumorous tissue

source_name: Human liver cancer #L020, tumorous tissue


title: Donor 1 Flu+ Whole PBMC

description:
Raw counts - Whole PBMC.txt
EdgeR - Whole PBMC.txt
D1


title: L019T

description: DNA methylation profile of human liver cancer #L019, tumorous tissue

source_name: Human liver cancer #L019, tumorous tissue


title: IS4a


title: Donor 1 Flu- Whole PBMC


title: L019N

description: DNA methylation profile of human liver cancer #L019, non-tumorous tissue

source_name: Human liver cancer #L019, non-tumorous tissue


title: IS3a

source_name: Human breast tumor


title: Donor 2 Flu+ CD3- CD56+ NK cells

description:
Raw counts - NK.txt
EdgeR - NK.txt
D2


title: IS3b

source_name: Normal female genomic DNA


title: Donor 1 Flu- CD3- CD56+ NK cells

description:
Raw counts - NK.txt
EdgeR - NK.txt
D1


title: L018N

description: DNA methylation profile of human liver cancer #L018, non-tumorous tissue

source_name: Human liver cancer #L018, non-tumorous tissue


title: L018T

description: DNA methylation profile of human liver cancer #L018, tumorous tissue

source_name: Human liver cancer #L018, tumorous tissue


title: Donor 1 Flu+ CD3- CD56+ NK cells

description:
Raw counts - NK.txt
EdgeR - NK.txt
D1


title: Donor 2 Flu- CD3- CD56+ NK cells

description:
Raw counts - NK.txt
EdgeR - NK.txt
D2


title: IS2a


title: L017T

description: DNA methylation profile of human liver cancer #L017, tumorous tissue

source_name: Human liver cancer #L017, tumorous tissue


title: BM8b


title: L023N

description: DNA methylation profile of human liver cancer #L023, non-tumorous tissue

source_name: Human liver cancer #L023, non-tumorous tissue


title: BM8a


title: L016T

description: DNA methylation profile of human liver cancer #L016, tumorous tissue

source_name: Human liver cancer #L016, tumorous tissue


title: hiPSC_SeroNeurons_2

source_name: skin biopsy


title: bHLH49 overexpressing, repeat 2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 Fluidics Station using the protocolFS450_0002, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the GeneChip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.30.0).

source_name: 4-day-old seedlings from bHLH49 overexpressor, grown on MS, harvested root tips

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: All seeds were sterilized in 25% bleach/75% ethanol solution for 10 minutes and were afterwards washed twice with 70% ethanol and once with 100% ethanol. Dried seed were plated on half-strength Murashige and Skoog (MS) medium and the appropriate antibiotic (in concentration: 50 mg/l kanamycin or 15 mg/l phosphinothricin) for selection of transgenic seeds. After 24hours incubation at 4°C, the plants were grown under long-day conditions at 22°C in a growth room.

extract_protocol: Total RNA was isolated using Trizol-Chloroform extraction followed by clean-up using the RNeasy Plant Mini kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Seedlings were grown for 4 days on MS medium, whereafter roots were harvested and used for total RNA extraction.

value: root

tag: ecotype

tag: genotype/variation

value: bHLH49 overexpressor


title: L015N

description: DNA methylation profile of human liver cancer #L015, non-tumorous tissue

data_processing: GenomeStudio software

source_name: Human liver cancer #L015, non-tumorous tissue


title: IS1b


title: L016N

description: DNA methylation profile of human liver cancer #L016, non-tumorous tissue

source_name: Human liver cancer #L016, non-tumorous tissue


title: L015T

description: DNA methylation profile of human liver cancer #L015, tumorous tissue

source_name: Human liver cancer #L015, tumorous tissue


title: Wild-type, repeat 3

source_name: 4-day-old seedlings from wild-type, grown on MS, harvested root tips

value: wild-type


title: Orkambi_026_V2

city: Columbus

first: Benjamin

middle: T.

last: Kopp

state: Ohio

address: 700 Children’s Drive

department: Section of Pediatric Pulmonology

institute: Nationwide Children’s Hospital

data_processing:
Each sample was aligned to the GRCh38.p9 assembly of the Homo Sapiens reference from NCBI (http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.35/) using version 2.5.2b of the RNA-Seq aligner STAR
Features were identified from the GFF file that came with the assembly from NCBI.
Feature coverage counts were calculated using version 0.6.1p1 of HTSeq -count
Differentially expressed features were calculated using DESeq2
Genome_build: human NCBI GRCh38.p9
Supplementary_files_format_and_content: Excel spreadsheet containing normalized read counts for each sample (columns U - CB) and differential expression data (columns F - T) for each feature

source_name: whole blood

extract_protocol:
rRNA was removed from 1000ng with TruSeq Stranded Total RNA with Ribo-Zero Globin Complete kit (Illumina, CA)
libraries were constructed from first strand cDNA using TruSeq Stranded Total RNA with Ribo-Zero Globin Complete kit (Illumina, CA)

value: CF

value: whole blood

tag: patient id


title: bHLH49 overexpressing, repeat 1

tag: tissue


title: L017N

description: DNA methylation profile of human liver cancer #L017, non-tumorous tissue

source_name: Human liver cancer #L017, non-tumorous tissue


title: IS1a

extract_protocol: Genomic DNA was isolated from fresh-frozen tissue specimens using the Wizard Genomic DNA extraction kit, including proteinase K treatment followed by phenol chloroform purification

value: female

value: Human breast tumor

value: Normal female genomic DNA


title: Orkambi_026_Base


title: L014T

description: DNA methylation profile of human liver cancer #L014, tumorous tissue

source_name: Human liver cancer #L014, tumorous tissue


title: bHLH49 loss-of-function mutant, repeat 1

source_name: 4-day-old seedlings from bHLH49 mutant, grown on MS, harvested root tips

value: bHLH49 mutant


title: bHLH49 loss-of-function mutant, repeat 2


title: Donor 3 Flu+ CD3- CD56+ NK cells

description:
Raw counts - NK.txt
EdgeR - NK.txt
D4

source_name: Human PBMC


title: Orkambi_025_Base


title: Wild-type, repeat 1


title: BM7b

source_name: Human breast tumor

source_name: Normal female genomic DNA


title: Orkambi_024_V2


title: L014N

description: DNA methylation profile of human liver cancer #L014, non-tumorous tissue

source_name: Human liver cancer #L014, non-tumorous tissue

value: Liver cancer, non-tumorous tissue


title: Wild-type, repeat 2


title: Orkambi_025_V2


title: BM7a


title: L013T

description: DNA methylation profile of human liver cancer #L013, tumorous tissue

source_name: Human liver cancer #L013, tumorous tissue


title: L012T

description: DNA methylation profile of human liver cancer #L012, tumorous tissue

source_name: Human liver cancer #L012, tumorous tissue


title: bHLH49 loss-of-function mutant, repeat 3


title: Orkambi_022_Base


title: Orkambi_021_V2


title: BM6a


title: Orkambi_022_V2


title: Orkambi_024_Base


title: L012N

description: DNA methylation profile of human liver cancer #L012, non-tumorous tissue

source_name: Human liver cancer #L012, non-tumorous tissue


title: BM5b


title: Orkambi_020_V2


title: BM5a


title: IS2b


title: Orkambi_018_V2


title: BM4b


title: Orkambi_017_V2


title: Orkambi_018_Base


title: L011T

description: DNA methylation profile of human liver cancer #L011, tumorous tissue

source_name: Human liver cancer #L011, tumorous tissue


title: L010T

description: DNA methylation profile of human liver cancer #L010, tumorous tissue

source_name: Human liver cancer #L010, tumorous tissue


title: Orkambi_019_V2


title: L011N

description: DNA methylation profile of human liver cancer #L011, non-tumorous tissue

source_name: Human liver cancer #L011, non-tumorous tissue


title: Orkambi_017_Base


title: Orkambi_016_V2


title: BM4a


title: bHLH49 overexpressing, repeat 3

source_name: 4-day-old seedlings from bHLH49 overexpressor, grown on MS, harvested root tips


title: Orkambi_016_Base


title: L009T

description: DNA methylation profile of human liver cancer #L009, tumorous tissue

source_name: Human liver cancer #L009, tumorous tissue


title: Orkambi_015_V2


title: Orkambi_015_Base


title: L010N

description: DNA methylation profile of human liver cancer #L010, non-tumorous tissue

source_name: Human liver cancer #L010, non-tumorous tissue


title: HC_Immune_008

source_name: whole blood

value: healthy control


title: BM3a


title: HC_Immune_006


title: BM2b


title: HC_Auto_095_267


title: HC_Auto_091_263


title: L009N

description: DNA methylation profile of human liver cancer #L009, non-tumorous tissue

source_name: Human liver cancer #L009, non-tumorous tissue


title: BM2a


title: HC_Auto_088_259


title: L008N

description: DNA methylation profile of human liver cancer #L008, non-tumorous tissue

source_name: Human liver cancer #L008, non-tumorous tissue


title: L008T

description: DNA methylation profile of human liver cancer #L008, tumorous tissue

source_name: Human liver cancer #L008, tumorous tissue


title: BS8b


title: HC_Auto_084_255


title: HC_Auto_082_253


title: BS8a


title: 9_Orkambi_006_V2


title: 7_HC_Auto_064_235


title: 8_Orkambi_004_Base


title: L007N

description: DNA methylation profile of human liver cancer #L007, non-tumorous tissue

source_name: Human liver cancer #L007, non-tumorous tissue


title: HC_Auto_093_265


title: 6_Orkambi_002_V2


title: 5_Orkambi_002_Base


title: L007T

description: DNA methylation profile of human liver cancer #L007, tumorous tissue

source_name: Human liver cancer #L007, tumorous tissue


title: BS6b

source_name: Human breast tumor

source_name: Normal female genomic DNA


title: 4_HC_Immune_002


title: BM6b


title: 42_HC_Auto_089_261


title: L006T

description: DNA methylation profile of human liver cancer #L006, tumorous tissue

source_name: Human liver cancer #L006, tumorous tissue


title: 3_HC_Auto_062_233


title: Orkambi_021_Base


title: BS6a


title: Orkambi_020_Base


title: 2_Orkambi_001_V2


title: L005T

description: DNA methylation profile of human liver cancer #L005, tumorous tissue

source_name: Human liver cancer #L005, tumorous tissue


title: L006N

description: DNA methylation profile of human liver cancer #L006, non-tumorous tissue

source_name: Human liver cancer #L006, non-tumorous tissue


title: BS7a


title: BS5b


title: 29_HC_Auto_080_251


title: 27_Orkambi_013_Base


title: 28_Orkambi_014_V2


title: BM3b


title: 25_Orkambi_013_V2


title: 24_Orkambi_012_Base


title: L004T

description: DNA methylation profile of human liver cancer #L004, tumorous tissue

source_name: Human liver cancer #L004, tumorous tissue


title: BS7b


title: 23_HC_Auto_076_247


title: DL4257 phenol-chloroform based method biological repeat 1

city: Edinburgh

first: Benura

last: Azeroglu

address: Alexander Crum Brown Road

country: United Kingdom

institute: University of Edinburgh

data_processing:
Library strategy: Nextera XT
Alignment: reads were mapped to a bespoke reference sequence (DL4201_in_lab_reference_genome) using the default parameters of software BWA (Li H, Durbin R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics. 2010;26(5):589-595).
Data extraction: Depth of coverage was extracted from each de-duplicated alignment file (in .bam) format using SAMtools software (Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16)).
Normalisation: An in-lab R script was used to normalise (based on the total depth) the library size for individual depth of coverage data.
Genome_build: DL4201_in_lab_reference_genome.fasta (GSE107972)
Supplementary_files_format_and_content: Each of the CSV files contains the coordinates of nucleotides of the reference genome (DL4201_in_lab_reference_genome.fasta (GSE107972)) starting from an arbitrary position at the origin of replication of E. coli and covering the circular genome in column 1 under the header "position". Subsequent eight columns contain the depth of coverage data from individual strains under the headers of the corresponding strain names and biological replicates (A for biological replicate 1 or B for biological replicate 2).

organism: Escherichia coli

source_name: Bacterial Cell Lysates

growth_protocol: Cells were grown in LB media supplemented with 0.2% arabinose at 37°C to and OD600nm of 0.2-0.25

extract_protocol:
DNA from samples denoted as phenol-chloroform based method (samples 1-8) was extracted using  phenol-chloroform DNA extraction.
DNA from samples denoted as IN (sample 9-24)  was isolated using the MinElute PCR purification kit (Qiagen).
Samples for phenol-chloroform based method (sample 1-8) were processed following Illumina's protocol from the Nextera XT  library preparation kit, whilst rest of the samples (samples 9-24) were processed following NEB’s protocol from the NEBNext® ChIP-Seq library preparation kit.

treatment_protocol:
Samples denoted as phenol-chloroform based method (samples 1-8) were treated with a series of enzymes.
Samples denoted as IN (sample 9-16) were treated with 1% formaldehyde  to capture protein DNA interactions for 10 min at 22.5C with and quenched using glycine to a final concentration of 0.5M
Samples denoted as IN and sonication based method (sample 9-24) underwent a round of sonication to shear the chromatin using a Diagenode Bioruptor at 30 s intervals for 10 min at high amplitude at 5 °C.

tag: strain

value: BW27784 [delta]ruvAB lacZ:XXX mhpR:XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZX-

value: phenol-chloroform


title: DL4257 phenol-chloroform based method biological repeat 2


title: BS4a


title: L004N

description: DNA methylation profile of human liver cancer #L004, non-tumorous tissue

source_name: Human liver cancer #L004, non-tumorous tissue


title: DL4243 phenol-chloroform based method biological repeat 2

value: BW27784 [delta]ruvAB lacZ:XXX mhpR:XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ::pal246 cynX::GmR  lacIq  lacZX-


title: 26_HC_Auto_078_249


title: BS4b


title: BS5a


title: DL4243 phenol-chloroform based method biological repeat 1


title: BS3b


title: 22_Orkambi_012_V2


title: 21_HC_Immune_004


title: L013N

description: DNA methylation profile of human liver cancer #L013, non-tumorous tissue

source_name: Human liver cancer #L013, non-tumorous tissue


title: DL4201 phenol-chloroform based method biological repeat 2

value: BW27784 lacZ:XXX mhpR:XXX proA::ISceIcs  tsx::ISceIcs  PBAD-sbcDC  lacZ+ cynX::GmR  lacIq  lacZX-


title: 20_Orkambi_010_Base


title: BS3a


title: 1_Orkambi_001_Base


title: L003N

description: DNA methylation profile of human liver cancer #L003, non-tumorous tissue

source_name: Human liver cancer #L003, non-tumorous tissue


title: DL4201 phenol-chloroform based method biological repeat 1


title: L003T

description: DNA methylation profile of human liver cancer #L003, tumorous tissue

source_name: Human liver cancer #L003, tumorous tissue

value: Liver cancer, tumorous tissue


title: 19_HC_Auto_074_245

source_name: whole blood


title: BS2b


title: L002T

description: DNA methylation profile of human liver cancer #L002, tumorous tissue

source_name: Human liver cancer #L002, tumorous tissue


title: 18_Orkambi_010_V2


title: 17_Orkambi_009_Base


title: BS2a


title: 16_HC_Auto_072_243


title: BM1b


title: 14_Orkambi_007_Base


title: L002N

description: DNA methylation profile of human liver cancer #L002, non-tumorous tissue

source_name: Human liver cancer #L002, non-tumorous tissue