title: 13282

description: 25W DEN + 5W IgG (control) surrounding (non-tumour) tissue

source_name: 25W DEN + 5W IgG surrounding tissue


title: Whole DRG tissue, biological replicate 3

status: Public on Dec 23 2014

type: RNA

city: Boston

first: Isaac

middle: M

last: Chiu

state: MA

address: 3 Blackfan Circle

department: Neurology

country: USA

institute: Boston Children's Hospital

description: RNA from whole homogenized tissue of pooled lumbar DRG samples

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 18 hr on Affymetrix mouse Gene ST version 1.0 chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Affymetrix CEL files were analyzed with the Robust Mutli-array Average (RMA) algorithm as the normalization method with quantile normalization, background correction, and median scalin. using the GenePattern (http://www.broadinstitute.org/cancer/software/genepattern) software platform.

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: DRG from WT C57BL/6 mice

label_protocol: 100 ng total RNA was amplified using the GeneChip WT cDNA syntehsis and amplification kit (Affymetrix).  cDNA synthsis, biotinylation of cRNA, fragmentation, and labeling was according to standard Affymetrix protocols.

growth_protocol: SNS-Cre mice were bred with Rosa26-TdTomato mice to generate SNS-Cre/TdTomato reporter mice.   Parv-Cre mice were bred with Rosa26-TdTomato mice to generate Parv-Cre/TdTomato mice. These strains of mice were used for FACS sorting of distinct DRG sensory neurons.  We also used WT C57BL/6 mice as a source of total DRG tissue RNA.

extract_protocol: RNA was extraced by sequential Qiazol extraction and Qiagen Rneasy micro column purification with genomic DNA digest.

treatment_protocol: Dorsal root ganglia (DRG) were dissected from adult mice (7-20 week old) of different fluorescent strains, treated with Collagenase/Dispase enzyme digestion for cell dissociation.   Total dorsal root ganglia (lumbar to thoracic segments) were dissected from mice and pooled for FACS sorting (3 mice were pooled/sample).  Flow cytometry and fluorescent gating strategies were used to isolate distinct subtypes of DRG somatosensory neurons, utilizing IB4-FITC surface staining, SNS-Cre/TdTomato, and/or Parv-TdTomato staining to set gates (TdTomato high expressing cells were sorted to obtain just cell bodies).  Ssurface IB4-FITC in combination with SNS-Cre/TdTomato labels non-peptidergic neurons (IB4+SNS-Cre/TdT+), with concurrent sorting of IB4- SNS-Cre lineage neurons (IB4-SNS-Cre/TdT+).

tag: genotype/variation

value: naïve C57BL/6

tag: tissue

value: Whole DRG tissue


title: Isolectin B4 positive SNS-Cre/Tdtomato+ DRG neurons, biological replicate 1

description: RNA from Isolectin B4-FITC positive SNS-Cre/TdTomato FACS sorted neurons from pooled DRG samples

source_name: DRG from SNS-Cre/R26TdTomato mice

value: SNS-Cre/TdTomato+

value: FACS purified IB4 positive Dorsal root ganglia sensory neurons


title: SNS-Cre/TdTomato+ DRG neurons, biological replicate 3

description: RNA from SNS-Cre/TdTomato FACS sorted neurons from pooled DRG samples

value: FACS purified Dorsal root ganglia sensory neurons


title: Isolectin B4 positive SNS-Cre/Tdtomato+ DRG neurons, biological replicate 2


title: Parv-Cre/TdTomato+ DRG neurons, biological replicate 4

description: RNA from Parv-Cre/TdTomato FACS sorted neurons from pooled DRG samples

source_name: DRG from Parv-Cre/R26TdTomato reporter mice

value: Parv-Cre/Tdtomato


title: SNS-Cre/TdTomato+ DRG neurons, biological replicate 2


title: Parv-Cre/TdTomato+ DRG neurons, biological replicate 3


title: Isolectin B4 negative SNS-Cre/Tdtomato+ DRG neurons, biological replicate 1

description: RNA from Isolectin B4-FITC negative SNS-Cre/TdTomato FACS sorted neurons from pooled DRG samples

value: FACS purified IB4 negative Dorsal root ganglia sensory neurons


title: 13279

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: 25W saline + 5W αPlGF (treatment) healthy tissue

hyb_protocol: Purified and labeled cRNA (600 ng of Cy3 labeled cRNA) was hybridised on Agilent Sureprint G3 Mouse GE 8x60k Microarrays followed by (manual) washing, according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.7.3.1).

data_processing: The dataset contains the Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v10.7.3.1) after an additional quantile normalization. Intensities were base 2 log-transformed.

source_name: 25W saline + 5W αPlGF

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 100 ng of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted to antisense cRNA, amplified and labeled with Cyanine 3-CTP (Cy3) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

extract_protocol: Qiagen

tag: strain

tag: gender

value: male

tag: age

value: 210 days

value: liver (healthy)

tag: induction

value: 25W saline

tag: treatment

value: 5 weeks αPlGF-treatment


title: SNS-Cre/TdTomato+ DRG neurons, biological replicate 4


title: Parv-Cre/TdTomato+ DRG neurons, biological replicate 1


title: SNS-Cre/TdTomato+ DRG neurons, biological replicate 1


title: Isolectin B4 positive SNS-Cre/Tdtomato+ DRG neurons, biological replicate 3


title: 13274

description: 25W DEN + 5W IgG (control) tumour tissue

source_name: 25W DEN + 5W IgG tumour tissue

value: liver tumor

value: 25W diethylnitrosamine

value: 5 weeks IgG-control


title: Isolectin B4 negative SNS-Cre/Tdtomato+ DRG neurons, biological replicate 2


title: Parv-Cre/TdTomato+ DRG neurons, biological replicate 2


title: OVA-DC (VS)

city: Pittsburgh

first: Lisa

middle: Helene

last: Butterfield

state: PA

address: 5117 Centre Ave.

department: Medicine

institute: University of Pittsburgh

hyb_protocol: Fifteen micrograms of purified, amplified, biotin labeled cRNA was fragmented and hybridized on to Affymetrix Human Genome HGU133A 2.0 arrays (Affymetrix Corp.,Santa Clara, CA) for 18 hours.

scan_protocol: Washing, staining and scanning of arrays was performed on the Affymetrix Fluidics Station 450 and Scanner 3000 immediately after completion of hybridization.

data_processing: Microarray data was processed using the Expression Console software (Affymetrix) with signal intensity calculated by Microarray Suite version 5.0 (MAS 5.0). The intensity data was imported into Partek software (Partek Genomics Suite, St. Louis, MO) for statistical comparison using the unpaired Students T test for each transcript corrected for false detection rate (q value) to control for Type 1 errors arising from multiple tests.

label: biotin

organism: Homo sapiens

source_name: human monocyte derived DC induced by chicken ovalbumin (OVA)

label_protocol: In vitro transcription was performed using the Ambion MessageAmp Premier assay protocol (Ambion Inc, Austin, TX) starting with 100ng of purified total RNA.  Confirmation of cRNA diversity was obtained using the Bioanalyzer 2100 to generate an electrophoretogram for each IVT reaction regarding sample yield, integrity, and size diversity against a Universal Human Reference RNA (Stratagene, La Jolla, CA).

growth_protocol: CD14+ monocytes were isolated from PBMC using magnetic cell sorting (Miltenyi Biotec) and cultured for 5 days in 800 IU/ml rGM-CSF (Sargramostim; Genzyme) and 500 IU/ml rIL-4 (R&D Systems).

extract_protocol: RNeasy Mini Kit (Cat#: 74104) from Qiagen according to kit instructions.

treatment_protocol: Purified ovalbumin (OVA; Fisher Scientific), human cord serum AFP (Cell Sciences; purity >95% by SDS-PAGE), and HCC cell line culture-derived AFP (Bio-Rad; purity >95% by SDS-PAGE) were added to cultures at 10 mg/ml

tag: donor

value: healthy adult

tag: cell type

value: human monocyte derived dendretic cells


title: NAFP-DC (VS)

source_name: human monocyte derived DC induced by cord blood AFP (nAFP)


title: 13275

description: 25W DEN + 5W αPlGF (treatment) tumour tissue

source_name: 25W DEN + 5W αPlGF tumour tissue


title: 13273


title: 13277

description: 25W DEN + 5W αPlGF (treatment) surrounding (non tumour) tissue

source_name: 25W DEN + 5W αPlGF surrounding tissue

value: liver (non-tumor)


title: 13278

description: 25W saline + 5W IgG (control) healthy tissue

source_name: 25W saline + 5W IgG


title: BM-CD138+, diagnosis (MM58)

city: Bologna

first: Carolina

last: Terragna

address: Via Massarenti, 9

department: Department of Experimental, Diagnostic and Specialty Medicine - DIMES

country: Italy

institute: Institute of Hematology "L.A.Seràgnoli"

description: BM-CD138+, diagnosis

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Array Scanner 7G

data_processing: The data were analyzed with Partek Genomics Suite 6.6, using RMA as normalization and summarization

source_name: BM-CD138+ cell fraction obtained from newly diagnosed Multiple Myeloma patient

label_protocol: Samples with at least 30ng/uL RNA were labelled for gene expression profiling, using the Affymetrix One-cycle Gene Chip microarray system, according to the standard Affymetrix procedures.

extract_protocol: Quiagen RNeasy  extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Pre-treatment plasma cells (PC) were purified from mononuclear bone marrow cells obtained by Ficoll-Hypaque density gradient centrifugation using anti-CD138 micro beads on an AutoMacs Magnetic Cell Separator (MACS system, Miltenyi Biotec, Auburn, CA). CD138+ cell fractions were than stored at -80°C in guanidium thiocyanate, until use.

tag: disease state

value: multiple myeloma

tag: neuropathy > 2

value: no


title: 13276


title: TAFP-DC (JM)

source_name: human monocyte derived DC induced by tumor AFP (tAFP)


title: NAFP-DC (JM)


title: TAFP-DC (VS)


title: OVA-DC (KK)


title: OVA-DC (JM)


title: NAFP-DC (KK)


title: 13272


title: 13271


title: BM-CD138+, diagnosis (MM46)

description: BM-CD138+, diagnosis


title: NAFP-DC (ST)


title: TAFP-DC (KK)


title: TAFP-DC (DP)


title: 13270


title: OVA-DC (DP)


title: BM-CD138+, diagnosis (MM45)

description: BM-CD138+, diagnosis


title: TAFP-DC (ST)


title: 13268


title: OVA-DC (ST)


title: NAFP-DC (DP)


title: MCC13_2

city: Bethesda

last: Brownell

state: MD

address: 10 Center Drive

department: Dermatology Branch

institute: National Cancer Institute

hyb_protocol: The samples were hybridized to Affymetrix Human U133A 2.0 GeneChips.

scan_protocol: The chips were scanned on Affymetrix GeneChip Scanner 3000G.

data_processing: All microarray expression analysis was performed using R. The R package “affy” was used to read in probe intensity data, and the Robust Multi-Array Average (RMA) procedure from the “affy” package was used for background correction, quantile normalisation and probeset summarization. Data for platform GPL570 was normalized with a subset of data from GSE36133 (see supplementary file on Series record)and processed with ComBat to remove batch effects.

source_name: MCC13 cell line

label_protocol: RNA (100 ng) was reverse-transcribed and labeled with biotin using the Affymetrix 3' IVT Express Kit following manufacturer's protocol.

growth_protocol: Mkl-1, WaGa, MCC13, MCC26, and UISO cells were grown and passaged in RPMI-1640 medium (Gibco by Life Technologies) supplemented with 10% FBS (Hyclone – Thermo Fisher), 100 U/mL penicillin, 0.1 mg/mL streptomycin, and 0.1 mg/ml Normocin (InvivoGen).

extract_protocol: Total RNA was extracted from cell lines using the RNeasy Mini Kit (Qiagen Cat. No. 74104). All samples were treated with RNase-free DNase (Qiagen Cat. No. 79254).

tag: cell line

value: MCC13 cell line

value: cell line

value: negative


title: 13267


title: MCC13_3


title: UISO_7

source_name: UISO cell line

value: UISO cell line


title: MCC26_3

source_name: MCC26 cell line

value: MCC26 cell line


title: 13264

value: male

value: 210 days


title: MCC13_1


title: WaGa_7

source_name: WaGa cell line

value: WaGa cell line

value: positive


title: 13266

value: liver (healthy)

value: 25W saline


title: 13263

value: liver tumor

value: 25W diethylnitrosamine

value: 5 weeks αPlGF-treatment


title: 13265

value: liver (non-tumor)


title: miR-544 antagomir_microRNA_expression

city: Jupiter

first: Donald

middle: G.

last: Phinney

state: Florida

address: 130 Scripps Way Bldg A215

department: Molecular Medicine

institute: The Scripps Research Institute

description: miRNA expression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 45C on Affymetrix GeneChip miRNA 3.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Genechip Operating software package using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: MDA-MB-231 cells grown under hypoxic conditions (<1% O2) for a period of 5 days

extract_protocol: Extracted using Zymo Research QuickRNA Miniprep according to manufacturer's instructions

treatment_protocol: MDA-MB-231 cells treated with either miR-544 antagomir or Compound 1 24 hours prior to subjecting to hypoxic conditions

value: breast cancer cell line


title: MCC26_2


title: Compound 1_microRNA_expression

description: miRNA expression data


title: WaGa_6


title: WaGa_3


title: WaGa_5


title: UISO_6


title: WaGa_4


title: SK-MC01

scan_protocol: The chips were scanned on Affymetrix GeneChip Scanner 3000 7G.

source_name: MC01 cell line

growth_protocol: MC01 cells were grown and passaged in RPMI-1640 medium (Gibco by Life Technologies) supplemented with 10% FBS (Hyclone – Thermo Fisher), 100 U/mL penicillin, 0.1 mg/mL streptomycin, and 1xNEAA.

value: MC01 cell line


title: WaGa_2


title: MCC26_1


title: UISO_3


title: UISO_5


title: WaGa_1


title: UISO_4


title: Mkl-1_6

source_name: Mkl-1 cell line

value: Mkl-1 cell line


title: Compound 1_gene_expression

description: Gene level analysis

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized overnight at 45C on the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.


title: Mkl-1_5

value: cell line


title: hMSCs grown on graphene

city: Seoul

first: YooJung

last: Lee

address: Department of Life Science, Dongguk University-Seoul, 3–26 Phil-dong, Chung-gu

department: Life science

country: South Korea

institute: Dongguk University

description: Gene expression data from hBM-MSCs grown on graphene

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the GeneChip® Mouse Gene 1.0 ST arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used.

source_name: hMSCs grown in neuronal differentiation medium for 7 days on graphene

label_protocol: 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA( cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: Human bone marrow mesenchymal stem cells (hBM-MSCs) were cultured in non-hematopoietic (NH) stem cell medium.

extract_protocol: RNA was isolated using RNeasy Mini Kit (Qiagen, USA) as per manufacturer’s protocol.

treatment_protocol: HMSCs replaced to neuronal differentiation medium (NM) composed of DMEM/F12 with 5 mM KCl, 1 µM hydrocortisone, 10 µM forskolin, 2 µM valproic acid and 5 µg/ml insulin, and then exposed to ELF-EMF for 7 days

value: Human bone marrow derived mesenchymal stem cells


title: UISO_2

value: UISO cell line

value: negative


title: 13262

value: male

value: 5 weeks IgG-control


title: miR-544 antagomir_gene_expression

description: Gene level analysis


title: hMSCs grown on graphene and ELF-EMF

description: Gene expression data from hBM-MSCs grown on glass and ELF-EMF

source_name: hMSCs grown in neuronal differentiation medium for 7 days on glass and ELF-EMF


title: Mkl-1_4


title: UISO_1


title: LT08

source_name: SCLC tumor

value: SCLC tumor

value: tissue


title: Mkl-1_3

value: positive


title: Mkl-1_1


title: hMSCs grown on glass

description: Gene expression data from hBM-MSCs grown on glass

source_name: hMSCs grown in neuronal differentiation medium for 7 days on glass


title: LT07


title: LT06


title: LT11


title: LT03


title: Mkl-1_2


title: LT05


title: LT04


title: MT22

source_name: MCC tumor

value: MCC tumor

value: yes

value: early

tag: recurrence

value: N


title: m3ck-28°C-rep3

city: Qingdao

first: Qian

last: Wang

address: 7 Nanhai Road

country: China

institute: Institute of Oceanology, Chinese Academy of Sciences

description: Gene expression at normal temperature in transgenic fish

hyb_protocol: Each slide was hybridized with 1.65 µg Cy3-labeled cRNA using the Gene Expression Hybridization Kit (Agilent technologies Santa Clara, USA) in Hybridization Oven (Agilent technologies Santa Clara, USA). After 17 hours hybridization, slides were washed with Gene Expression Wash Buffer Kit (Agilent technologies Santa Clara, USA).

scan_protocol: Slides were scanned using Agilent Microarray Scanner (Agilent technologies Santa C lara, USA) with default settings, Dye channel: Green, Scan resolution=5 μm, PMT 100%, 10%, 16 bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, USA). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, USA).

organism: Danio rerio

source_name: transgenic zebrafish, normal temperature 28°C, replicate 3

label_protocol: Total RNA was amplified and labeled with Cy3-CTP by Low Input Quick Amp Labeling Kit, One-Color (Agilent technologies, Santa Clara, CA, USA), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (QIAGEN, GmBH, Germany).

growth_protocol: Wild-type and transgenic fish were reared at 28°C ± 0.5°C and under a photoperiod regime of 14/10 h light/dark. Water quality was maintained by circulation with a filtration system.

extract_protocol: RNA samples were extracted from whole zebrafish with Trizol Reagent (Invitrogen, CA, USA). RNA quality as expressed by the RNA integrity number (RIN) was determined on an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) and then purified with an RNeasy mini kit (QIAGEN GmBH, Germany) with the RNase-Free DNase Set (QIAGEN).

treatment_protocol: The F2 generation was raised to the age of 3 months (2.17 ± 0.02 cm, 0.42 ± 0.01 g) before use in the cold acclamation experiment.  13°C was selected to represent cold stress. Cold stress was applied for 2 h according to previous study and our own preliminary experiments. Before cold treatment, the fish were transferred to tanks with small openings in the bottom and allowed to stand for one day. They were gently moved to the cold bath for the experiment. The groups (n = 30 per group) were designated m3ck-13°C, m3ck-28°C, wt-13°C, and wt-28°C. After temperature stress for 2 h, the fish were anesthetized with 100 mg/L MS222 and transferred immediately into liquid nitrogen.

tag: line

value: transgenic zebrafish

tag: temperature


title: MT20

value: late

value: Y


title: m3ck-13°C-rep3

description: Gene expression at low temperature in transgenic fish

source_name: transgenic zebrafish, low temperature 13°C, replicate 3


title: MT23


title: LT02


title: MT21


title: m3ck-28°C-rep2

source_name: transgenic zebrafish, normal temperature 28°C, replicate 2


title: m3ck-13°C-rep1

source_name: transgenic zebrafish, low temperature 13°C, replicate 1


title: MT16

value: no


title: wt-13°C-rep1

description: Gene expression at low temperature in wild type fish

source_name: wild type zebrafish, low temperature 13°C, replicate 1

value: wild type zebrafish


title: m3ck-13°C-rep2

source_name: transgenic zebrafish, low temperature 13°C, replicate 2


title: m3ck-28°C-rep1

source_name: transgenic zebrafish, normal temperature 28°C, replicate 1


title: LT01


title: MT18


title: MT19


title: MT15


title: MT24


title: wt-13°C-rep3

source_name: wild type zebrafish, low temperature 13°C, replicate 3


title: 13269

source_name: 25W DEN + 5W αPlGF tumour tissue

value: 210 days

value: liver tumor

value: 25W diethylnitrosamine

value: 5 weeks αPlGF-treatment


title: wt-13°C-rep2

source_name: wild type zebrafish, low temperature 13°C, replicate 2


title: MT14

value: negative


title: wt-28°C-rep3

description: Gene expression at normal temperature in wild type fish

source_name: wild type zebrafish, normal temperature 28°C, replicate 3


title: MT10


title: MT12


title: MT13


title: MT11


title: MT17


title: MT03


title: MT04


title: wt-28°C-rep2

source_name: wild type zebrafish, normal temperature 28°C, replicate 2


title: MT06


title: MT05


title: MT01


title: MT07


title: wt-28°C-rep1

source_name: wild type zebrafish, normal temperature 28°C, replicate 1


title: healthy living liver donor_LD3

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: healthy living liver donor biopsy: LD3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Bioconductor (v2.5) Lumi package.

source_name: healthy living liver donor

label_protocol: Biotinylated cDNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion)

extract_protocol: For total RNA extraction cryopreserved liver tissue samples were homogenized in TRIzol reagent (Invitrogen, San Diego, CA, USA) using pestle and nuclease-free 1,5ml reaction tubes (Ambion). Total RNA was then extracted following the manufacturers guidelines and quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA).

tag: patient status

value: non-transplanted controls

value: liver biopsy


title: MT09

value: tissue

value: positive


title: tolerant_before immunosuppression_H56P

description: stable HCV-infected liver recipients Tolerant before immunosuppression: H56P

source_name: tolerant_before immunosuppression (IS)

value: stable HCV-infected liver recipients

tag: operational tolerance

value: tolerant

tag: biopsy timepoint

value: before immunosuppression


title: healthy living liver donor_LD2

description: healthy living liver donor biopsy: LD2

tag: tissue


title: tolerant_before immunosuppression_H51P

description: stable HCV-infected liver recipients Tolerant before immunosuppression: H51P


title: healthy living liver donor_LD8

description: healthy living liver donor biopsy: LD8


title: tolerant_after immunosuppression_H56PST

description: stable HCV-infected liver recipients Tolerant after immunosuppression: H56PST

source_name: tolerant_12 months after IS discontinuation

value: after immunosuppression


title: healthy living liver donor_LD4

description: healthy living liver donor biopsy: LD4


title: healthy living liver donor_LD1

description: healthy living liver donor biopsy: LD1


title: non-tolerant_before immunosuppression_W60P

description: stable HCV-infected liver recipients non-tolerant before immunosuppression: W60P

value: non-tolerant


title: MT02

source_name: MCC tumor

value: MCC tumor

value: early

value: Y


title: non-tolerant_before immunosuppression_W103P

description: stable HCV-infected liver recipients non-tolerant before immunosuppression: W103P


title: healthy living liver donor_LD5

description: healthy living liver donor biopsy: LD5


title: non-tolerant_after immunosuppression_H39PST

description: no stable HCV-infected liver recipients non-tolerant after immunosuppression: H39PST

source_name: non-tolerant_at the time of rejection

value: no stable HCV-infected liver recipients


title: non-tolerant_after immunosuppression_W82PST

description: no stable HCV-infected liver recipients non-tolerant after immunosuppression: W82PST


title: healthy living liver donor_LD6

description: healthy living liver donor biopsy: LD6


title: non-tolerant_before immunosuppression_W52P

description: stable HCV-infected liver recipients non-tolerant before immunosuppression: W52P


title: non-tolerant_before immunosuppression_H39P

description: stable HCV-infected liver recipients non-tolerant before immunosuppression: H39P


title: healthy living liver donor_LD7

description: healthy living liver donor biopsy: LD7


title: non-tolerant_before immunosuppression_H37P

description: stable HCV-infected liver recipients non-tolerant before immunosuppression: H37P


title: non-tolerant_before immunosuppression_H29P

description: stable HCV-infected liver recipients non-tolerant before immunosuppression: H29P


title: non-tolerant_before immunosuppression_H38P

description: stable HCV-infected liver recipients non-tolerant before immunosuppression: H38P


title: non-tolerant_before immunosuppression_W82P

description: stable HCV-infected liver recipients non-tolerant before immunosuppression: W82P


title: non-tolerant_before immunosuppression_H2P

description: stable HCV-infected liver recipients non-tolerant before immunosuppression: H2P


title: non-tolerant_after immunosuppression_H52PST

description: no stable HCV-infected liver recipients non-tolerant after immunosuppression: H52PST


title: non-tolerant_before immunosuppression_W6P

description: stable HCV-infected liver recipients non-tolerant before immunosuppression: W6P


title: non-tolerant_after immunosuppression_H2PST

description: no stable HCV-infected liver recipients non-tolerant after immunosuppression: H2PST


title: non-tolerant_before immunosuppression_H3P

description: stable HCV-infected liver recipients non-tolerant before immunosuppression: H3P


title: non-tolerant_before immunosuppression_H12P

description: stable HCV-infected liver recipients non-tolerant before immunosuppression: H12P


title: non-tolerant_before immunosuppression_W55P

description: stable HCV-infected liver recipients non-tolerant before immunosuppression: W55P


title: tolerant_before immunosuppression_W61P

description: stable HCV-infected liver recipients tolerant  before immunosuppression: W61P


title: tolerant_after immunosuppression_W58PST

description: stable HCV-infected liver recipients tolerant  after immunosuppression: W58PST


title: tolerant_after immunosuppression_W61PST

description: stable HCV-infected liver recipients tolerant  after immunosuppression: W61PST


title: tolerant_after immunosuppression_H58PST

description: stable HCV-infected liver recipients tolerant  after immunosuppression: H58PST


title: tolerant_after immunosuppression_W44PST

description: stable HCV-infected liver recipients tolerant  after immunosuppression: W44PST


title: tolerant_before immunosuppression_W43P

description: stable HCV-infected liver recipients tolerant  before immunosuppression: W43P


title: tolerant_before immunosuppression_W58P

description: stable HCV-infected liver recipients tolerant  before immunosuppression: W58P


title: tolerant_before immunosuppression_H9P

description: stable HCV-infected liver recipients tolerant  before immunosuppression: H9P


title: tolerant_after immunosuppression_H40PST

description: stable HCV-infected liver recipients tolerant  after immunosuppression: H40PST


title: tolerant_before immunosuppression_H33P

description: stable HCV-infected liver recipients tolerant  before immunosuppression: H33P


title: tolerant_after immunosupression_H1PST

description: stable HCV-infected liver recipients tolerant  after immunosupression: H1PST


title: tolerant_after immunosuppression_H33PST

description: stable HCV-infected liver recipients tolerant  after immunosuppression: H33PST


title: tolerant_after immunosuppression_H11PST

description: stable HCV-infected liver recipients tolerant  after immunosuppression: H11PST


title: tolerant_after immunosuppression_H24PST

description: stable HCV-infected liver recipients tolerant  after immunosuppression: H24PST


title: tolerant_before immunosuppression_H17P

description: stable HCV-infected liver recipients tolerant  before immunosuppression: H17P


title: tolerant_after immunosuppression_H17PST

description: stable HCV-infected liver recipients tolerant  after immunosuppression: H17PST


title: tolerant_after immunosuppression_H9PST

description: stable HCV-infected liver recipients tolerant  after immunosuppression: H9PST


title: tolerant_before immunosuppression_W44P

description: stable HCV-infected liver recipients tolerant  before immunosuppression: W44P


title: MZ1774 mock rep 4

city: Bonn

first: Moritz

last: Kebschull

address: Welschnonnenstr. 17

department: Department of Periodontology

country: Germany

institute: University of Bonn

description: replicate 4

scan_protocol: Standard Illumina scan protocol

data_processing: Data were analyzed using R/Bioconductor and limma.

source_name: human ccRCC cell line

label_protocol: Standard Illumina labeling protocol

growth_protocol: The human ccRCC cell line MZ1774 was grown in RPMI 1640 medium supplemented with 10% FCS, 100 I.U./ml penicillin, 100 µg/ml streptomycin as well as 5 µg/ml plasmocin (InvivoGen).

extract_protocol: Total RNA was extracted from MZ1774 cells using the RNAeasy Mini Kit (Qiagen) with on column Dnase digest.

treatment_protocol: Cells were transduced with lentivirus containing either a shRNA-cassette targeting human YAP or the empty pLKO.1 backbone. Cells stably expressing the constructs were selected using puromycin selection (3,0 µg/ml) and were constantly grown in the presence of selection antibiotic.

tag: infection status

value: mock-transduced control

value: human ccRCC cell line


title: MZ1774 mock rep 2

description: replicate 2


title: tolerant_before immunosuppression_H8P

description: stable HCV-infected liver recipients tolerant  before immunosuppression: H8P


title: tolerant_before immunosuppression_H11P

description: stable HCV-infected liver recipients tolerant  before immunosuppression: H11P


title: tolerant_after immunosupression_H1I

description: stable HCV-infected liver recipients tolerant  after immunosupression: H1I


title: MZ1774 mock rep 1

description: replicate 1


title: MZ1774 mock rep 3

description: replicate 3


title: MZ1774 YAPshRNA rep 3

description: replicate 3

value: stably expressing shRNA directed against YAP


title: BM-CD138+, diagnosis (MM03)

description: BM-CD138+, diagnosis

source_name: BM-CD138+ cell fraction obtained from newly diagnosed Multiple Myeloma patient

value: multiple myeloma

value: no


title: MZ1774 YAPshRNA rep 2

description: replicate 2


title: tolerant_before immunosupression_H1P

description: stable HCV-infected liver recipients tolerant  before immunosupression: H1P

value: liver biopsy


title: MCC13_3_GPL570

hyb_protocol: The samples were hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Array.

scan_protocol: The chips were scanned on Affymetrix GeneChip Scanner 3000G. Data were collected using Affymetrix GeneChip Command Console (AGCC) Software.

source_name: MCC13 cell line

value: MCC13 cell line

value: cell line

value: negative


title: MZ1774 YAPshRNA rep 4

description: replicate 4


title: MZ1774 YAPshRNA rep 1

description: replicate 1


title: MCC13_2_GPL570


title: MCC26_3_GPL570

source_name: MCC26 cell line

value: MCC26 cell line


title: MCC13_1_GPL570


title: MCC26_2_GPL570


title: MCC26_1_GPL570


title: UISO_9_GPL570

source_name: UISO cell line

value: UISO cell line


title: WaGa_6_GPL570

source_name: WaGa cell line

value: WaGa cell line

value: positive


title: UISO_8_GPL570


title: Tsetse_fly_midgut-Infection_self_cleared-sample33

city: Montpellier

first: Anne

last: Geiger

address: Laboratoire de Recherches et de Coordination sur les Trypanosomoses TA,A-17 / G Campus international de Baillarguet

country: France

institute: UMR 177 IRD-CIRAD

description: Total RNA Glossina palpalis gambiensis, Trypanosoma brucei gambiense infection self cleared, 10 days after infected blood meal, sample 33

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was added to 250 ml of 2x Agilent hybridization buffer and hybridized to Agilent Sodalis glossinidius custom Oligo Microarrays (earray Design ID = 041518; earray Slide Layout = IS-15744-8-V1) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09GE1_107_Sep09 and Grid: 041518_D_F_20120607) to obtain background subtracted and spatially detrended Processed Signal intensities. All data were normalized by quantile normalization.

organism: Sodalis glossinidius

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 5µg RNA using the Chipshot Direct labeling and Clean-Up System kit (Promega) according to the manufacturer's instructions

extract_protocol: Total RNA was extracted from fly midgut by TRIzol (Invitrogen) according to the manufacturer's instructions

treatment_protocol: Flies were exposed to Trypanosoma brucei gambiense infected mices.

tag: status

value: Infection self-cleared

tag: timepoint

value: 10 days

value: infective blood meal

tag: source gender

value: female fly

tag: source tissue

value: Tsetse fly midgut


title: WaGa_5_GPL570


title: Tsetse_fly_midgut-Infection_self_cleared-sample32

description: Total RNA Glossina palpalis gambiensis, Trypanosoma brucei gambiense infection self cleared, 10 days after infected blood meal, sample 32

tag: treatment


title: Tsetse_fly_midgut-Control-sample3

description: Total RNA Glossina palpalis gambiensis, 10 days after uninfected bloodmeal, sample 3

value: Control

value: non infective blood meal


title: WaGa_4_GPL570


title: Tsetse_fly_midgut-Infection_self_cleared-sample34

description: Total RNA Glossina palpalis gambiensis, Trypanosoma brucei gambiense infection self cleared, 10 days after infected blood meal, sample 34


title: UISO_6_GPL570


title: UISO_5_GPL570


title: Tsetse_fly_midgut-Infection_self_cleared-sample31

description: Total RNA Glossina palpalis gambiensis, Trypanosoma brucei gambiense infection self cleared, 10 days after infected blood meal, sample 31


title: Mkl-1_6_GPL570

source_name: Mkl-1 cell line

value: Mkl-1 cell line


title: Tsetse_fly_midgut-Control-sample4

description: Total RNA Glossina palpalis gambiensis, 10 days after uninfected bloodmeal, sample 4


title: UISO_7_GPL570


title: Mkl-1_4_GPL570


title: whole_blood_S5

city: Harbin

first: Wenliang

last: Zhu

address: 246 Xuefu Road

institute: the Second Affiliated Hospital of Harbin Medical University

description: MiRNA expression of pooled whole blood from patients with postmenopausal osteoporosis, which spine T-scores were in the range from -4.0 to -3.0.

hyb_protocol: Cy3-labelled cRNA of 0.6 μg (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agient blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 25 μl of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-046065 Mouse miRNA Microarray V19.0 8x60K(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0 (Agilent). Probe that at least 100.0 percent of samples in any 1 condition out of 2 conditions have flags in Detected were maintained.

source_name: Pooled whole blood, postmenopausal osteoporosis, -4.0 ≤ Spine T-score < -3.0

label_protocol: Total RNA of 0.1 μg were dephosphorylated, denaturated and then labeled with Cyanine-3-CTP (Cy3) using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions,then followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

extract_protocol: Five mL of whole blood was obtained from each participant. The whole blood sample was then lysed using Red Blood Cells (RBC) Lysis Solution (Beyotime, china), centrifugated for 10 min (450×g). Trizol reagent (Invitrogen, Shanghai, China) was used to extract RNA from precipitates. The above operation was completed within 30 min after blood collection from clinic. The obtained RNA eluate was stored at -80 °C. After the work of blood sample collection was finished, all of the RNA extraction samples were defrosted and separately pooled into six subgroups regarding the spine T-score values (Table 1), and then restored at -80 °C for further experiments.

value: whole blood

tag: gender

value: female

tag: disease

value: postmenopausal osteoporosis

tag: t-score

value: -4.0 ≤ Spine T-score < -3.0

tag: number of patients


title: Tsetse_fly_midgut-Control-sample1

description: Total RNA Glossina palpalis gambiensis, 10 days after uninfected bloodmeal, sample 1


title: whole_blood_S4

description: MiRNA expression of pooled whole blood from patients with postmenopausal osteoporosis, which spine T-scores were in the range from -3.0 to -2.5.

source_name: Pooled whole blood, postmenopausal osteoporosis, -3.0 ≤ Spine T-score ≤ -2.5

value: -3.0 ≤ Spine T-score ≤ -2.5


title: whole_blood_S6

description: MiRNA expression of pooled whole blood from patients with postmenopausal osteoporosis, which spine T-scores were < -4.0.

source_name: Pooled whole blood, postmenopausal osteoporosis, Spine T-score < -4.0

value: Spine T-score < -4.0


title: Tsetse_fly_midgut-Control-sample2

description: Total RNA Glossina palpalis gambiensis, 10 days after uninfected bloodmeal, sample 2


title: whole_blood_S3

description: MiRNA expression of pooled whole blood from patients with postmenopausal osteopenia, which spine T-scores were in the range from -2.5 to -2.0.

source_name: Pooled whole blood, postmenopausal osteopenia, -2.5 < Spine T-score < -2.0

value: postmenopausal osteopenia

value: -2.5 < Spine T-score < -2.0


title: whole_blood_S2

description: MiRNA expression of pooled whole blood from patients with postmenopausal osteopenia, which spine T-scores were in the range from -2.0 to -1.5.

source_name: Pooled whole blood, postmenopausal osteopenia, -2.0 ≤ Spine T-score < -1.5

value: -2.0 ≤ Spine T-score < -1.5


title: Mkl-1_5_GPL570

tag: cell line

value: cell line

value: positive


title: UISO_4_GPL570

value: UISO cell line

value: negative


title: aur2-1 mutant (AAa)

status: Public on Dec 22 2014

type: genomic

city: Taipei

first: Wan-Sheng

last: Lo

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

hyb_protocol: The hybridization procedure was followed the instruction by manufactory (Affymetrix) and performed 16.5 hours.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Probe sequences from the BPMAP specification of the array (At35b-MR_v04-2_TIGRv5) were mapped to the TAIR10 genome by use of BLAT. Intensity normalization involved the AffyTiling package of BioConductor. Probe locations and normalized signals were joined and sorted by use of an in-house perl script
results file descriptions: The results of each chromosome (chromosome 1 to 5; chloroplast and mitochondrial choromosome) were submitted. Each file included the normalized data and the ratios of signal intensity in trisomy (AAA or Aaa) to diploid (Col-0).
results file descriptions: trisomy vs. diploid gDNA were compared

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Trisomy genomic DNA

label_protocol: The gDNA were labeled by using BioPrime DNA labeling system (Invitrogen).

growth_protocol: The plants were cultivated in growth chambers under long-day conditions (16 h-light/8 h-dark) at 22°C.

extract_protocol: The gDNA were extracted by using the DNeasy Plant Mini Kit (Qiagen).

treatment_protocol: No additional treatment before the collection of samples.

tag: ecotype/cultivar

value: rosette leaves

tag: genotype/variation

value: aur2-1 mutant (AAa)


title: Wild type

source_name: diploid genomic DNA

value: Wild type


title: whole_blood_S1

description: MiRNA expression of pooled whole blood from patients with postmenopausal osteopenia, which spine T-scores were in the range from -1.5 to -1.0.

source_name: Pooled whole blood, postmenopausal osteopenia, -1.5 ≤ Spine T-score ≤ -1.0

value: -1.5 ≤ Spine T-score ≤ -1.0


title: 6285609104 _Benign_prostate_cancer_HM450K

city: Melbourne

first: Haroon

last: Naeem

state: Clayton, VIC

address: 15 Innovation Walk (Room G98), Wellington Road

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

description: benign samples from other prostate glands containing Gleason 6 cance

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 (HM450K bead array) Beadchip using standard Illumina protocol

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

data_processing: Raw intensity data was generated using an iScan microarray reader (Illumina).

label: Cy5 and Cy3

source_name: Prostate 6

label_protocol: Standard Illumina Protocol

growth_protocol: Patients undergoing radical prostatectomy for prostate cancer had fresh frozen samples of cancer as well as adjacent benign prostate tissue prospectively stored in a cancer biorepository program (http://www.ncbi.nlm.nih.gov/pubmed/22406482)

extract_protocol: Genomic DNA was extracted from the homogenized samples using the Allprep Micro Kit (Qiagen, CA, USA) following manufacturer’s instructions and bisulfite converted using the Zymo EZ DNA Methylation kit (Zymo Research Corporation, CA, USA). The resulting libraries were hybridized onto the Illumina HumanMethylation450 BeadChip.

value: male

tag: disease state

value: Gleason 6 prostate cancer

value: benign prostate tissues


title: 6264509108_Benign_prostate_cancer_HM450K

source_name: Prostate  1


title: 6264509130_1_Tumor_prostate_cancer_Gleason6_HM450K

description: Gleason 6 cancer

source_name: Prostate 2

value: prostate cancer tumor


title: mouse_liver_WT_4C-2_U74Av2

city: New York

first: Nikolaus

last: Schultz

state: NY

address: 1275 York Ave, Box 460

department: Computational Biology Center

institute: Memorial Sloan-Kettering Cancer Center

description: See Comerford et al., 2003, Oncogene 22: 2515-2530 for a detailed description of the transgene and its regulation.

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: MAS 5.0, target value = 250, Tau = 0.015

label: standard Affymetrix protocol

source_name: Total liver RNA from non-transgenic, wild-type mice fed a 10% protein/70% carbohydrate diet (C) (Purina Mills # 22471) ad libitum for 4 weeks after weaning

label_protocol: standard Affymetrix protocol

extract_protocol: RNA STAT-60 (Tel-Test)

tag: Strain

value: Hybrid B6SJL, Gender:Male, Age:58-60 days old, Tissue:Liver


title: 6285650040 _Benign_prostate_cancer_HM450K

source_name: Prostate 7


title: 6285650050_Benign_prostate_cancer_HM450K

source_name: Prostate 8


title: Col-0 (sfr6-3 control)_5°C_6h

description: Seven-day old Col-0 wt seedlings (control for sfr6-3 mutant) treated at 5°C for 6h before harvest

hyb_protocol: A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix Arabidopsis ATH1 arrays followed by staining and washing in a GeneChip® fluidics station 400 (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were normalized using MAS 5.0 as implemented in the Affy package (version 1.36.1) of Bioconductor. Expression values are represented on a log2-scale.

source_name: Arabidopsis seedlings,  5°C, 6h

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 5 µg of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was converted to double stranded cDNA in a reverse transcription reaction. Subsequently the sample was converted and amplified to antisense cRNA and labeled with biotin in an in vitro transcription reaction. All steps were carried out according to the manufacturers protocol (Affymetrix).

growth_protocol: Plants were grown on 1x Murashige and Skoog medium with 0.8% agar in petri dishes in a SANYO MLR-351 plant growth chamber at 20°C under a 16h light/8h dark cycle. Light levels were 150 mmol/m2/sec.

extract_protocol: Total RNA was extracted from approximately 50 mg of seedling tissue using the Qiagen RNeasy Plant Mini Kit according to the manufacturer's instructions

treatment_protocol: Plants growing on petri dishes were moved to a cold room at 5°C for 6h during the light phase of growth. Plants were harvested rapidly under cold conditons after 6h and frozen immediately in liquid nitrogen.

tag: plant line

tag: age

value: 7 days


title: WT trisomy 2 (AAA)

tag: tissue

value: WT trisomy 2 (AAA)


title: Col-0 (sfr6-2 control)_5°C_6h

description: Seven-day old Col-0 wt seedlings (control for sfr6-2 mutant) treated at 5°C for 6h before harvest


title: sfr6-2_5°C_6h

description: Seven-day old sfr6-2 seedlings treated at 5°C for 6h before harvest


title: mouse_liver_PEPCK-TAg_4C-1_U74Av2

source_name: Total liver RNA from PEPCK-TAg transgenic mice fed a 10% protein/70% carbohydrate diet (C) (Purina Mills # 22471) ad libitum for 4 weeks after weaning


title: mouse_liver_WT_4P-1_U74Av2

source_name: Total liver RNA from non-transgenic, wild-type mice fed a 65% protein/10% carbohydrate diet (P) (Purina Mills # 8091) ad libitum for 4 weeks after weaning

value: Hybrid B6SJL, Gender:Male, Age:50-66 days old, Tissue:Liver


title: 6264509130_2_Tumor_prostate_cancer_Gleason6_HM450K

description: Gleason 6 cancer

source_name: Prostate 3


title: mouse_liver_PEPCK-TAg_4P-1_U74Av2

source_name: Total liver RNA from PEPCK-TAg transgenic mice fed a 65% protein/10% carbohydrate diet (P) (Purina Mills # 8091) ad libitum for 4 weeks after weaning


title: mouse_liver_WT_4P-2_U74Av2


title: 54.7-54.7

hyb_protocol: A mixture of fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix GeneChip Rat Gene 1.0 ST Arrays, followed by staining and washing in a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer's procedures.

data_processing: Data were normalized using RMA as implemented in the Affy package of Bioconductor. Expression values are represented on a log2-scale.

organism: Rattus norvegicus

source_name: Brain, left hemisphere excluding cerebellum, 19min asphyxia during birth, P4

label_protocol: RNA concentration and purity were determined spectrophotometrically using the NanoDrop ND-1000 (NanoDrop Technologies), and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Using the Ambion WT Expression Kit, per sample, an amount of 100 ng of total RNA spiked with bacterial poly-A RNA positive controls (Affymetrix) was converted to double-stranded cDNA in a reverse transcription reaction. Next, the sample was converted and amplified to antisense cRNA in an in vitro transcription reaction which was subsequently converted to single-stranded sense cDNA. Finally, samples were fragmented and labeled with biotin in a terminal labeling reaction according to the Affymetrix WT Terminal Labeling Kit.

growth_protocol: Dams were given standard rodent food ad libitum. Pups were cared for by foster dams.

extract_protocol: Qiagen RNeasy mini kit, protocol available from www.qiagen.com

treatment_protocol: RNAlater was added directly after excision of the material, and then the material was snap frozen and stored at -80degrees Celsius.

tag: strain

value: Sprague Dawley

value: brain (left hemisphere excluding cerebellum)

tag: developmental stage

tag: experimental group

value: PA


title: sfr6-3_5°C_6h

description: Seven-day old sfr6-3 mutant seedlings treated at 5°C for 6h before harvest

value: sfr6-3 (WiscDsLox504A08)


title: 53.1-53.1

source_name: Brain, left hemisphere excluding cerebellum, 30min asphyxia on E17 + 19min asphyxia during birth, P0

value: FAPA


title: IEC119

city: Amsterdam

first: Philip

middle: C

last: Schouten

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

hyb_protocol: According to manufacterer's protocol (Nimblegen Roche)

scan_protocol: 2 um double pass

data_processing: Nimblescan, grid tiff files, generate pair reports followed by using the NimbleScan DNAcopy procedure at default settings

source_name: human breast cancer

label_protocol: With the ENZO 42760 labeling kit for array CGH: 20 uL primers (vial 1) with 500 ng of genomic tumor DNA or Promega Female reference DNA (GG1521) in 19 ul of nuclease free water for 10 minutes at 99 C in pcr machine, followed by 10 minutes of cooling to 4 degrees. Snap freeze and spin. While on ice add 11 ul Cy3 mix (10ul Cy3+1ul Klenow DNA pol (vial 4)) to tumor DNA, and 11 ul Cy5 mix (10ul Cy3+1ul Klenow DNA pol (vial 4)) to reference DNA and incubate in PCR machine for 4 hours at 37 C. Then add 5ul stop buffer (vial 5).  To remove excess nucleotides with Qiagen MinElute PCR purification kit add 275 uL binding buffer (PB) to sample and reference. Put on minElute column and spin 60 sec on 16000 rcf. Add 700 ul Wash Buffer (PE) and centrifuge 60 secs at 16000 rcf. Dry columns by spinning another 60 secs at 16000 rcf. Elute the DNA in 2 steps by adding 2x 10.5 ul of elution buffer (EB). Pool equal amounts of tumor and reference DNA and speedvac into a pellet.

extract_protocol: 10 x 10 u slices containing at least 70% tumour cells were cleared of paraffin (2 x 5 min xylene, 2 x 30 s 100% ethanol, 30s 90% ethanol, 30 s 70% ethanol, and rinsed with H2O), treated with 1 M NaSCN at 37 C overnight, and sections of interest (>70% tumour cells) were scraped in 200 ul buffer ATL (Qiagen, cat. no. 51304).  27 ul of proteinase K (15 ug/ull, Roche, cat. no.3115879001) was immediately added, as well as at the end of the day, and at the beginning and end of the next day; samples were constantly shaken at 37 C during the time of digestion. The following day, 40 ul RNase A (20 ug/ul, Sigma, cat. no. R5500) was added to the sample, vortexed, and incubated for 2 min at room temperature. 400 ul of buffer AL (Qiagen, cat.no.51304) was added and incubated for 10 min at 70 C. 420 ul of 100% ethanol was added and vortexed. The sample mixture was spun on a spincolumn (Qiagen, cat. no. 51304) for 1 min at 8,000 rpm. The column was sequentially washed with 500 ul of the following reagents and spun for 1 min at 8,000 rpm: AW1, AW2, and  twice with 80% ethanol. The column was spun dry for 3 min at 14,000 rpm. The sample was eluted with 50 ul of AE buffer by spinning for 1 min at 8,000 rpm.  (Joosse, SA et al, Breast Cancer Res Treat, 2009)

tag: pathologic tumor stage

tag: pathologic nodal stage

tag: grade

tag: er status

tag: pr status

tag: her2 status

source_name: Promega Female Reference genomic DNA G1521

tag: sample type

value: reference


title: 47.1-47.1

source_name: Brain, left hemisphere excluding cerebellum, 30min asphyxia on E17, P4

tag: gender

value: FA


title: 54.1-54.1

source_name: Brain, left hemisphere excluding cerebellum, 19min asphyxia during birth, P0


title: 50.4-50.4

source_name: Brain, left hemisphere excluding cerebellum, control, P4

value: C


title: 45.4-45.4

source_name: Brain, left hemisphere excluding cerebellum, 30min asphyxia on E17 + 19min asphyxia during birth, P4


title: mouse_liver_WT_4C-1_U74Av2


title: mouse_liver_PEPCK-TAg_4P-2_U74Av2


title: 36.2-36.2

source_name: Brain, left hemisphere excluding cerebellum, control, P0


title: 22.1-22.1

source_name: Brain, left hemisphere excluding cerebellum, 30min asphyxia on E17, E21


title: 30.5-30.5


title: mouse_liver_PEPCK-TAg_4C-2_U74Av2


title: 57.1-57.1

source_name: Brain, left hemisphere excluding cerebellum, control, E21


title: IEC118


title: IEC116


title: IEC115


title: 44.2-44.2


title: 49.1-49.1


title: IEC117


title: 34.1-34.1


title: 30.1-30.1

source_name: Brain, left hemisphere excluding cerebellum, 30min asphyxia on E17, P0


title: 44.1-44.1


title: 29.1-29.1


title: 1.9-1.9


title: 51.4-51.4


title: 6264509130_4_Tumor_prostate_cancer_Gleason6_HM450K

description: Gleason 6 cancer

source_name: Prostate 5


title: 35.1-35.1


title: 6264509130_3_Tumor_prostate_cancer_Gleason6_HM450K

description: Gleason 6 cancer

source_name: Prostate 4


title: IEC111


title: IEC110


title: 21.1-21.1


title: IEC112


title: IEC114


title: IEC109


title: IEC107


title: 38.1-38.1


title: IEC108


title: IEC106


title: IEC113


title: IEC105


title: 17.1-17.1


title: 27.4-27.4


title: 4.9-4.9


title: 20.1-20.1


title: 27.1-27.1


title: 36.5-36.5


title: 33.5-33.5


title: 26.1-26.1


title: IEC099


title: 11.1-11.1


title: IEC101


title: IEC096


title: 16.4-16.4


title: 15.1-15.1


title: IEC100


title: 6.4-6.4


title: IEC095


title: IEC094


title: IEC102


title: IEC098


title: 10.3-10.3


title: 16.1-16.1


title: 41.2-41.2


title: IEC103


title: IEC093


title: IEC092


title: IEC097


title: IEC091


title: 6.1-6.1


title: 12.4-12.4


title: IEC090


title: IEC088


title: 4.1-4.1


title: IEC089


title: 1.11-1.11


title: IEC087


title: 14.1-14.1


title: IEC085


title: 12.1-12.1


title: 2.13-2.13


title: IEC084


title: IEC104


title: IEC081


title: 33.1-33.1


title: IEC083


title: 1.7-1.7


title: IEC082


title: 2.8-2.8


title: IEC079


title: 2.1-2.1


title: 1.1-1.1


title: IEC078


title: IEC077


title: IEC080


title: IEC076


title: IEC073


title: IEC074


title: IEC069


title: IEC075


title: IEC067


title: IEC070


title: IEC066


title: IEC065


title: IEC057


title: IEC063


title: IEC072


title: IEC071


title: IEC059


title: IEC060


title: IEC062


title: IEC056


title: 4.6-4.6


title: IEC058


title: IEC064


title: IEC061


title: IEC055


title: IEC050


title: IEC068


title: 8.4-8.4


title: IEC053


title: IEC052


title: IEC054


title: IEC086


title: IEC047


title: IEC048


title: IEC049


title: IEC051


title: IEC045


title: IEC046


title: IEC044


title: IEC043


title: 13044

description: Paenibacillus larvae BRL-230010

hyb_protocol: A mixture of purified and labeled cDNA (Cy3 label: 300 ng; Cy5 label: 300 ng) was hybridised on the Agilent followed by (manual) washing, according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.7.3.1).

data_processing: The dataset contains the Agilent processed signal values (i.e., feature rProcessedSignal/gProcessedSignal from Agilent Feature Extraction v 10.7.3.1). Base 2 log-transformed log-ratios (Cy5/Cy3) were averaged over the replicate probes.

organism: Paenibacillus larvae

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 5 µg of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to single stranded cDNA. Subsequently the sample was labeled Cyanine 5 (Cy5) mono-reactive dye (GE Healthcare) according to the manufacturer’s protocol (two-color microarray-based prokaryote analysis (Fairplay III labeling) - Agilent).

extract_protocol: Prior to RNA extraction thawed aliquots were centrifuged for 2 min at 6708 x g and 4 °C. Bacterial pellets were resuspended in 200 µl TE buffer (30 mM Tris-HCl, 1 mM EDTA, pH 8.0) , containing lysozyme (15 mg/ml) and proteinase K (Qiagen; 1/10 dilution). After 10 sec of vortexing, the samples were incubated for 10 min at room temperature with constant shaking. RNA was isolated with the RNeasy Plus Mini Kit, using the protocol “Purification of Total RNA for Animal Cells” and performing the optional on-column DNase I treatment, according to the manufacturer’s instructions. RNA was eluted twice - first with 30 µl RNase-free water, then with this 30 µl elution - and stored at -80 °C until use.

value: Paenibacillus larvae BRL-230010

tag: condition (time)

value: four hours

tag: condition (treatment)

value: spiking in vitro P. larvae cultures of OD590 of 0.3 with bodily fluids of honeybee larvae (test)

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 5 µg of total RNA spiked with 10 viral polyA transcript controls (Agilent) was converted to single stranded cDNA. Subsequently the sample was labeled Cyanine 3 (Cy3) mono-reactive dye (GE Healthcare) according to the manufacturer’s protocol (two-color microarray-based prokaryote analysis (Fairplay III labeling) - Agilent).

value: one hour


title: 13045

description: Paenibacillus larvae BRL-230010

value: spiking in vitro P. larvae cultures of OD590 of 0.3 with BHIT-broth (control)


title: IEC040


title: IEC042


title: 13043

description: Paenibacillus larvae BRL-230010


title: IEC039


title: IEC038


title: IEC037


title: 13042

description: Paenibacillus larvae BRL-230010


title: IEC036


title: IEC035


title: IEC031


title: 13039

description: Paenibacillus larvae BRL-230010


title: 13041

description: Paenibacillus larvae BRL-230010


title: IEC030


title: IEC029


title: IEC041


title: IEC027


title: IEC034


title: IEC033


title: 13040

description: Paenibacillus larvae BRL-230010


title: IEC025


title: IEC028


title: IEC024


title: 13038

description: Paenibacillus larvae BRL-230010


title: IEC026


title: 13037

description: Paenibacillus larvae BRL-230010


title: IEC021


title: 13034

description: Paenibacillus larvae BRL-230010


title: IEC022


title: IEC032


title: 13032

description: Paenibacillus larvae BRL-230010

source_name: 6-Staal 6B - T4_6

source_name: 5-Staal 5B - C4_5


title: 13035

description: Paenibacillus larvae BRL-230010


title: 13033

description: Paenibacillus larvae BRL-230010

source_name: 1-Staal 1B - C1_1


title: IEC020


title: IEC012


title: IEC019


title: IEC017


title: IEC015


title: IEC011


title: IEC018


title: IEC023


title: IEC016


title: IEC013


title: 13036

description: Paenibacillus larvae BRL-230010


title: IEC009


title: IEC010


title: 13030

description: Paenibacillus larvae BRL-230010


title: qve006

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: GeneChips were hybridized, washed and stained with the standard protocol.

scan_protocol: GeneChips were scanned using the Affymetrix scanner

data_processing: The data were MAS5.0 summarized with GCOS2.3

source_name: HSC cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix  protocol.

extract_protocol: Total RNA was extracted from developing NK cells at various time points using TRIzol Reagent according to the manufacturer's instructions (Life Technologies, Carlsbad, CA).

tag: donor

tag: day

tag: Stage

tag: cell type

value: natural killer (NK) cells


title: IEC006


title: IEC008


title: IEC003


title: 13031

description: Paenibacillus larvae BRL-230010

tag: strain


title: qve007


title: qve004


title: qve008


title: qvc006


title: qve002


title: qvd005


title: qvd006


title: qve003


title: qvd003


title: qvd004


title: qve005


title: qvd007


title: IEC005


title: qvd002


title: IEC001


title: qvc003


title: qvc004


title: qvc002


title: qvc005


title: qvc001


title: patient 35_laser capture microdissection_HCC_non-tumor area E non-malignant heptocytes_115636

first: Patrizia

last: Farci

address: 50 South Drive

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description:
LCM-35-NMH-115636
specimen obtained from the liver of patient 35

hyb_protocol: Following fragmentation, 10 to 18 µg (mean 12.8) of cRNA was hybridized for 16 hr at 45°C on Affymetrics Human U133 Plus 2 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using GeneArray Scanner 3000_7Gplus

data_processing: Affymetrics probeset summaries were computed using RMA algorithm.  Data were then imported to BRB-ArrayTools and subsequent data filtering, median normalization and statistical analyses were performed using this software.

source_name: LCM_HCC_non-tumor area E_non-malignant heptocytes

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 ng total RNA (GeneChip Expression Analysis Technical Manual, 2005-2006, Affymetrix).

extract_protocol: Extraction of total RNA was performed using Trizol according to the manufacturer's instructions.

tag: subject condition

value: HBV-associated HCC patient

tag: patient id

value: patient 35

tag: distance from the tumor center

value: non-tumor area E

tag: tissue type

value: non-malignant heptocytes

value: laser capture-microdissected (LCM) hepatocytes


title: hu-beta-celline_siRFX6_rep4

city: Paris

first: Raphael

last: Scharfmann

state: Paris

address: 123,boulevard de Port-Royal

institute: INSERM-Institut Cochin , Bâtiment Cassini

description: si RFX6 treated EndoC-βH2 cells

hyb_protocol: One-Color Microarray-Based Gene Expression Analysis- Low Input Quick Amp Labeling (version 6.5, May 2010). Complementary RNA (cRNA) samples were linearly amplified and labeled with cyanine3 starting from 50ng of total RNA. Following fragmentation, labeled cRNA were hybridized on Agilent “SurePrint G3 Human Gene Expression 8x60K Microarray” (Design ID 028004), for 17hrs at 65°C under 10rpm.

scan_protocol: AgilentG3_GX_1Color (scan resolution : 3 µm, Tiff : 20 bit). After washes, the slides were scanned using an Agilent G2565CA microarray Scanner System, at a 3μM resolution in a 20-bit scan mode, according to the “AgilentG3_GX_1Color” protocol.Raw.tif images were then extracted using Agilent “Feature Extraction, version 10.10.1.1” following “GE1_1010_Sep10” protocol.

data_processing: The scanned images were analyzed with Feature Extraction sofware (Agilent) version 10.10.1.1 to obtain gprocessed signal data

growth_protocol: EndoC-βH2 cells (Scharfmann et al, 2014, JCI)) were cultured in low-glucose (5.6 mM) Dulbecco’s modified Eagle’s medium (DMEM; Sigma-Aldrich) containing L-glutamine and sodium pyruvate, supplemented with 2% BSA fraction V (Roche Diagnostics), 50 µM 2-mercaptoethanol, 10mM nicotinamide (Calbiochem), 5.5 µg/ml transferrin (Sigma-Aldrich), 6.7 ng/ml selenite (Sigma-Aldrich), 100 U/ml penicillin and 100 µg/ml streptomycin. Cells were seeded at a density of 5x104 cells/cm2 on Matrigel (1%) / fibronectin (2µg/ml) (Sigma-Aldrich) coated plates and cultured at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted from EndoC-βH2 cells using RNeasy Micro kit (Qiagen).

treatment_protocol: For siRNA-based gene knockdown studies, EndoC-βH2 cells were transfected using Lipofectamin RNAiMAX (life technologies) following manufacturer’s instructions with minor modifications. Briefly, freshly trypsinized EndoC-βH2 cell suspension (5x104 cells/cm2) were incubated with lipofectamin-siRNA complex in Opti-MEM containing 2-mercaptoethanol, nicotinamide, transferrin and selenite for 3-4 minutes and next plated. 3-5h later, the medium was replaced. ON-TARGETplus siRNA SMARTpool for human RFX6 gene (~30 nM) and ON-TARGETplus Non-targeting pool (siNT) (Dharmacon, Thermo Scientific) were used.  Cells were harvested 72 h post transfection for further analysis.

value: EndoC-βH2 cells


title: IEC004

source_name: human breast cancer

tag: pathologic tumor stage

tag: pathologic nodal stage

tag: grade


title: IEC002

tag: er status

tag: pr status

tag: her2 status

source_name: Promega Female Reference genomic DNA G1521


title: patient 98_laser capture microdissection_HCC_non-tumor area E non-malignant heptocytes_115642

description:
LCM-98-NMH-115642
specimen obtained from the liver of patient 98

value: patient 98

tag: sample type


title: hu-beta-celline_siRFX6_rep3

description: si RFX6 treated EndoC-βH2 cells

label_protocol: One-Color Microarray-Based Gene Expression Analysis- Low Input Quick Amp Labeling (version 6.5, May 2010)


title: patient 53_laser capture microdissection_HCC_tumor area A malignant hepatocytes_115637

description:
LCM-53-MH-115637
specimen obtained from the liver of patient 53

source_name: LCM_HCC_tumor area A_malignant hepatocytes

value: patient 53

value: tumor area A

value: malignant hepatocytes


title: patient 111_laser capture microdissection_HCC_non-tumor area E non-malignant heptocytes_115648

description:
LCM-111-NMH-115648
specimen obtained from the liver of patient 111

value: patient 111


title: hu-beta-celline_siRFX6_rep1

description: si RFX6 treated EndoC-βH2 cells


title: patient 28_laser capture microdissection_HCC_non-tumor area E non-malignant heptocytes_115634

description:
LCM-28-NMH-115634
specimen obtained from the liver of patient 28

value: patient 28


title: patient 35_laser capture microdissection_HCC_tumor area A malignant hepatocytes_115635

description:
LCM-35-MH-115635
specimen obtained from the liver of patient 35


title: patient 53_laser capture microdissection_HCC_non-tumor area E non-malignant heptocytes_115638

description:
LCM-53-NMH-115638
specimen obtained from the liver of patient 53


title: patient 105_laser capture microdissection_HCC_non-tumor area E non-malignant heptocytes_115644

description:
LCM-105-NMH-115644
specimen obtained from the liver of patient 105

value: patient 105


title: hu-beta-celline_siNT_rep4

description: si Control treated EndoC-βH2 cells


title: patient 125_laser capture microdissection_HCC_non-tumor area E non-malignant heptocytes_115650

description:
LCM-125-NMH-115650
specimen obtained from the liver of patient 125

value: patient 125


title: patient 125_laser capture microdissection_HCC_tumor area A malignant hepatocytes_115649

description:
LCM-125-MH-115649
specimen obtained from the liver of patient 125


title: hu-beta-celline_siNT_rep3

description: si Control treated EndoC-βH2 cells


title: patient 92_laser capture microdissection_HCC_tumor area A malignant hepatocytes_115639

description:
LCM-92-MH-115639
specimen obtained from the liver of patient 92

value: patient 92


title: patient 28_laser capture microdissection_HCC_tumor area A malignant hepatocytes_115633

description:
LCM-28-MH-115633
specimen obtained from the liver of patient 28


title: patient 98_laser capture microdissection_HCC_tumor area A malignant hepatocytes_115641

description:
LCM-98-MH-115641
specimen obtained from the liver of patient 98


title: patient 92_laser capture microdissection_HCC_non-tumor area E non-malignant heptocytes_115640

description:
LCM-92-NMH-115640
specimen obtained from the liver of patient 92


title: hu-beta-celline_siRFX6_rep2

description: si RFX6 treated EndoC-βH2 cells


title: patient 4_laser capture microdissection_HCC_non-tumor area E non-malignant heptocytes_115632

description:
LCM-4-NMH-115632
specimen obtained from the liver of patient 4N

value: patient 4N


title: patient 111_laser capture microdissection_HCC_tumor area A malignant hepatocytes_115647

description:
LCM-111-MH-115647
specimen obtained from the liver of patient 111


title: hu-beta-celline_siNT_rep2

description: si Control treated EndoC-βH2 cells


title: patient 4_laser capture microdissection_HCC_tumor area A malignant hepatocytes_115631

description:
LCM-4-MH-115631
specimen obtained from the liver of patient 4M

value: patient 4M


title: patient 110_laser capture microdissection_HCC_non-tumor area E non-malignant heptocytes_115646

description:
LCM-110-NMH-115646
specimen obtained from the liver of patient 110

value: HBV-associated HCC patient

value: patient 110


title: patient 110_laser capture microdissection_HCC_tumor area A malignant hepatocytes_115645

description:
LCM-110-MH-115645
specimen obtained from the liver of patient 110


title: hu-beta-celline_siNT_rep1

description: si Control treated EndoC-βH2 cells


title: patient 98_whole liver tissue_HCC_non-tumor area E_104658

description:
WLT-98-E-104658
specimen obtained from the liver of patient 98

source_name: whole liver tissue_HCC_non-tumor area E

value: non-tumor area E

value: whole liver tissue (WLT)


title: patient 98_whole liver tissue_HCC_non-tumor area E_104656

description:
WLT-98-E-104656
specimen obtained from the liver of patient 98


title: patient 105_laser capture microdissection_HCC_tumor area A malignant hepatocytes_115643

description:
LCM-105-MH-115643
specimen obtained from the liver of patient 105

value: laser capture-microdissected (LCM) hepatocytes


title: Gene expression in malO mutant biol rpt 4

city: Clayton

first: Julian

middle: I

last: Rood

state: Victoria

address: Wellington Road

department: Microbiology

hyb_protocol: Microarrays were pre-hybridised in a solution of 25 % formamide, 5X SSC, 0.1 % SDS and 10 mg/ml of herring sperm DNA at 42˚C for 45 mins.  Labelled cDNA was hybridised to the prehybridised microarrays according to the instructions provided with the Geneisphere 3DNA 900MPX kit

scan_protocol: The dried microarrays were scanned using a GMS418 microarray scanner (Affymetrix), scans were aquired using GMS scanner software (V.1.51.0.42) (Affymetrix) and quantified using Imagene version 5.1 (BioDiscovery).

data_processing: Quantified ImaGene files from four independant microarray experiments were analysed using the LIMMA software package for R.  Each microarray experiment was performed using an independant biological replicate, thus providing four independant biological replicates with two dye-swaps.  Spot intensities were firstly normalised per print tip group before being normalised between arrays using a Lowess algorithm.  Spot intensities were then log2 transformed and expression values calculated as the ratio of log2 intensity of malO mutant/wild-type.

organism: Clostridium perfringens str. 13

source_name: malO mutant during stationary phase

label_protocol: cDNA synthesis and labelling with Cy3 or Cy5 using 4 μg of total RNA was performed according to the Genisphere 3DNA 900MPX kit (Genisphere) according to the manufacturer's instructions.

growth_protocol: Bacterial strains were cultured for 10 hrs at 37˚C in sterile TPYG broth (5 % [w/v] tryptone, 0.5 % [w/v] proteose peptone, 0.3 % [w/v] yeast extract and 0.1 % [w/v] sodium thioglycolate, supplimented with sterile glucose to a final concentration of 0.38 % [v/v] after autoclaving) under anaerobic conditions.

extract_protocol: Cells were harvested from 15 ml aliquots of bacterial culture by centrifugation at 5800 x g for 10 mins.  Cell pellets were treated with lysozyme (10 mg/ml) for 15 mins prior to RNA extraction using TriZol (Invitrogen) according to the manufacturer's instructions.  Repeated rounds to DNase I digestion and Trizol extraction were performed until  DNA contaminiation was removed.

treatment_protocol: Gene expression was compared between a malO mutant of C. perfringens strain 13 and wild-type during stationary phase growth

tag: genotype

value: malO mutant

source_name: wild-type strain 13 during stationary phase

value: wild-type


title: Gene expression in malO mutant biol rpt 3


title: patient 98_whole liver tissue_HCC_non-tumor area E_104643

description:
WLT-98-E-104643
specimen obtained from the liver of patient 98

value: patient 98


title: Gene expression in malO mutant biol rpt 2


title: patient 98_whole liver tissue_HCC_non-tumor area E_99408

description:
WLT-98-E-99408
specimen obtained from the liver of patient 98


title: patient 92_whole liver tissue_HCC_non-tumor area E_103096

description:
WLT-92-E-103096
specimen obtained from the liver of patient 92


title: patient 92_whole liver tissue_HCC_non-tumor area E_103095

description:
WLT-92-E-103095
specimen obtained from the liver of patient 92


title: patient 92_whole liver tissue_HCC_non-tumor area E_103098

description:
WLT-92-E-103098
specimen obtained from the liver of patient 92


title: patient 98_whole liver tissue_HCC_non-tumor area E_104657

description:
WLT-98-E-104657
specimen obtained from the liver of patient 98


title: Gene expression in malO mutant biol rpt 1


title: patient 92_whole liver tissue_HCC_non-tumor area E_103093

description:
WLT-92-E-103093
specimen obtained from the liver of patient 92


title: patient 98_whole liver tissue_HCC_non-tumor area E_99409

description:
WLT-98-E-99409
specimen obtained from the liver of patient 98


title: patient 92_whole liver tissue_HCC_non-tumor area E_99407

description:
WLT-92-E-99407
specimen obtained from the liver of patient 92


title: patient 125_whole liver tissue_HCC_non-tumor area E_106719

description:
WLT-125-E-106719
specimen obtained from the liver of patient 125


title: patient 125_whole liver tissue_HCC_non-tumor area E_106715

description:
WLT-125-E-106715
specimen obtained from the liver of patient 125


title: ldl1 ldl2 seedlings Replicate 3

city: Strasbourg

first: Wen-Hui

last: Shen

address: 12 rue du General Zimmer

institute: IBMP-CNRS

description: Biological replicate 3 of ldl1 ldl2 seedlings

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software was used for background subtraction. Signal intensity were normalized using Quantile method. Signal : raw Cy3 signal intensity ; Log2NormSignal : Log2 transformed Normalized Signal

source_name: ldl1 ldl2_3 seedlings

label_protocol: 2 µg of total RNA were labeled according Aligent's instructions. Please see manufacture’s web site at http://www.aligent.com/

growth_protocol: Plants were grown in the greenhouse under 12h light and 12h dark at 22°C.

extract_protocol: Total RNA was extracted using the Trizol reagent (Invitrogen) followed by Rneasy mini kit (Qiagen) clean-up according to manufacturer's instructions.

tag: ecotype

value: Columbia

tag: organ

value: seedlings

tag: age

value: 16 day old

tag: genotype/variation

value: ldl1 ldl2


title: clf sdg26 seedlings Replicate 3

description: Biological replicate 3 of clf sdg26 seedlings

hyb_protocol: Please see manufacture’s web site at http://www.aligent.com/

source_name: clf sdg26_3 seedlings

value: clf sdg26


title: patient 125_whole liver tissue_HCC_non-tumor area E_106714

description:
WLT-125-E-106714
specimen obtained from the liver of patient 125

value: patient 125


title: patient 92_whole liver tissue_HCC_non-tumor area E_99406

description:
WLT-92-E-99406
specimen obtained from the liver of patient 92

value: patient 92


title: patient 111_whole liver tissue_HCC_non-tumor area E_112265

description:
WLT-111-E-112265
specimen obtained from the liver of patient 111

value: patient 111


title: clf seedlings Replicate 3

description: Biological replicate 3 of clf seedlings

source_name: clf_3 seedlings

value: clf


title: ldl1 ldl2 sdg26 seedlings Replicate 3

description: Biological replicate 3 of ldl1 ldl2 sdg26 seedlings

source_name: ldl1 ldl2 sdg26_3 seedlings

value: ldl1 ldl2 sdg26


title: ldl1 ldl2 sdg25 seedlings Replicate 3

description: Biological replicate 3 of ldl1 ldl2 sdg25 seedlings

source_name: ldl1 ldl2 sdg25_3 seedlings

value: ldl1 ldl2 sdg25


title: patient 110_whole liver tissue_HCC_non-tumor area E_106733

description:
WLT-110-E-106733
specimen obtained from the liver of patient 110

value: HBV-associated HCC patient

value: patient 110

value: non-tumor area E


title: patient 110_whole liver tissue_HCC_non-tumor area E_106734

description:
WLT-110-E-106734
specimen obtained from the liver of patient 110

value: whole liver tissue (WLT)


title: patient 125_whole liver tissue_HCC_non-tumor area E_106739

description:
WLT-125-E-106739
specimen obtained from the liver of patient 125


title: atx1 sdg26 seedlings Replicate 3

description: Biological replicate 3 of atx1 sdg26 seedlings

source_name: atx1 sdg26_3 seedlings

value: atx1 sdg26


title: patient 105_whole liver tissue_HCC_non-tumor area E_112257

description:
WLT-105-E-112257
specimen obtained from the liver of patient 105

value: patient 105


title: patient 110_whole liver tissue_HCC_non-tumor area E_106732

description:
WLT-110-E-106732
specimen obtained from the liver of patient 110


title: patient 53_whole liver tissue_HCC_non-tumor area E_99470

description:
WLT-53-E-99470
specimen obtained from the liver of patient 53

value: patient 53


title: patient 110_whole liver tissue_HCC_non-tumor area E_99411

description:
WLT-110-E-99411
specimen obtained from the liver of patient 110


title: atx1 seedlings Replicate 3

description: Biological replicate 3 of atx1 seedlings

source_name: atx1_3 seedlings

value: Columbia

value: seedlings


title: patient 53_whole liver tissue_HCC_non-tumor area E_99471

description:
WLT-53-E-99471
specimen obtained from the liver of patient 53


title: sdg25 sdg26 seedlings Replicate 3

description: Biological replicate 3 of sdg25 sdg26 seedlings

source_name: sdg25 sdg26_3 seedlings

value: 16 day old

value: sdg25 sdg26


title: sdg25 seedlings Replicate 3

description: Biological replicate 3 of sdg25 seedlings

source_name: sdg25_3 seedlings


title: patient 35_whole liver tissue_HCC_non-tumor area E_103068

description:
WLT-35-E-103068
specimen obtained from the liver of patient 35

value: patient 35


title: patient 110_whole liver tissue_HCC_non-tumor area E_99410

description:
WLT-110-E-99410
specimen obtained from the liver of patient 110


title: patient 35_whole liver tissue_HCC_non-tumor area E_103079

description:
WLT-35-E-103079
specimen obtained from the liver of patient 35


title: patient 35_whole liver tissue_HCC_non-tumor area E_103069

description:
WLT-35-E-103069
specimen obtained from the liver of patient 35


title: Wild-type seedlings Replicate 3

description: Biological replicate 3 of Wild-type seedlings

source_name: WT_3 seedlings

value: wild type


title: patient 35_whole liver tissue_HCC_non-tumor area E_99467

description:
WLT-35-E-99467
specimen obtained from the liver of patient 35


title: patient 35_whole liver tissue_HCC_non-tumor area E_99459

description:
WLT-35-E-99459
specimen obtained from the liver of patient 35


title: patient 35_whole liver tissue_HCC_non-tumor area E_99466

description:
WLT-35-E-99466
specimen obtained from the liver of patient 35


title: ldl1 ldl2 sdg25 seedlings Replicate 2

description: Biological replicate 2 of ldl1 ldl2 sdg25 seedlings

source_name: ldl1 ldl2 sdg25_2 seedlings


title: sdg26 seedlings Replicate 3

description: Biological replicate 3 of sdg26 seedlings

source_name: sdg26_3 seedlings


title: ldl1 ldl2 sdg26 seedlings Replicate 2

description: Biological replicate 2 of ldl1 ldl2 sdg26 seedlings

source_name: ldl1 ldl2 sdg26_2 seedlings


title: ldl1 ldl2 seedlings Replicate 2

description: Biological replicate 2 of ldl1 ldl2 seedlings

source_name: ldl1 ldl2_2 seedlings

value: ldl1 ldl2


title: patient 28_whole liver tissue_HCC_non-tumor area E_99444

description:
WLT-28-E-99444
specimen obtained from the liver of patient 28

source_name: whole liver tissue_HCC_non-tumor area E

value: patient 28


title: patient 35_whole liver tissue_HCC_non-tumor area E_99455

description:
WLT-35-E-99455
specimen obtained from the liver of patient 35


title: atx1 sdg26 seedlings Replicate 2

description: Biological replicate 2 of atx1 sdg26 seedlings

source_name: atx1 sdg26_2 seedlings


title: patient 28_whole liver tissue_HCC_non-tumor area E_99445

description:
WLT-28-E-99445
specimen obtained from the liver of patient 28


title: patient 35_whole liver tissue_HCC_non-tumor area E_99458

description:
WLT-35-E-99458
specimen obtained from the liver of patient 35


title: patient 98_whole liver tissue_HCC_non-tumor area D_104655

description:
WLT-98-D-104655
specimen obtained from the liver of patient 98

source_name: whole liver tissue_HCC_non-tumor area D

value: patient 98

value: non-tumor area D


title: patient 98_whole liver tissue_HCC_non-tumor area D_104654

description:
WLT-98-D-104654
specimen obtained from the liver of patient 98

value: HBV-associated HCC patient


title: clf seedlings Replicate 2

description: Biological replicate 2 of clf seedlings

source_name: clf_2 seedlings

value: clf


title: clf sdg26 seedlings Replicate 2

description: Biological replicate 2 of clf sdg26 seedlings

source_name: clf sdg26_2 seedlings

value: clf sdg26


title: patient 35_whole liver tissue_HCC_non-tumor area E_99465

description:
WLT-35-E-99465
specimen obtained from the liver of patient 35

value: non-tumor area E

value: whole liver tissue (WLT)


title: atx1 seedlings Replicate 2

description: Biological replicate 2 of atx1 seedlings

source_name: atx1_2 seedlings


title: patient 98_whole liver tissue_HCC_non-tumor area D_104653

description:
WLT-98-D-104653
specimen obtained from the liver of patient 98


title: patient 53_whole liver tissue_HCC_non-tumor area E_99480

description:
WLT-53-E-99480
specimen obtained from the liver of patient 53


title: patient 98_whole liver tissue_HCC_non-tumor area D_104652

description:
WLT-98-D-104652
specimen obtained from the liver of patient 98


title: patient 92_whole liver tissue_HCC_non-tumor area D_107802

description:
WLT-92-D-107802
specimen obtained from the liver of patient 92

value: patient 92


title: patient 92_whole liver tissue_HCC_non-tumor area D_107778

description:
WLT-92-D-107778
specimen obtained from the liver of patient 92


title: patient 92_whole liver tissue_HCC_non-tumor area D_107801

description:
WLT-92-D-107801
specimen obtained from the liver of patient 92


title: sdg26 seedlings Replicate 2

description: Biological replicate 2 of sdg26 seedlings

source_name: sdg26_2 seedlings


title: sdg25 seedlings Replicate 2

description: Biological replicate 2 of sdg25 seedlings

source_name: sdg25_2 seedlings


title: sdg25 sdg26 seedlings Replicate 2

description: Biological replicate 2 of sdg25 sdg26 seedlings

source_name: sdg25 sdg26_2 seedlings


title: patient 92_whole liver tissue_HCC_non-tumor area D_107803

description:
WLT-92-D-107803
specimen obtained from the liver of patient 92


title: patient 125_whole liver tissue_HCC_non-tumor area D_106879

description:
WLT-125-D-106879
specimen obtained from the liver of patient 125

value: patient 125


title: patient 125_whole liver tissue_HCC_non-tumor area D_106878

description:
WLT-125-D-106878
specimen obtained from the liver of patient 125


title: patient 125_whole liver tissue_HCC_non-tumor area D_106892

description:
WLT-125-D-106892
specimen obtained from the liver of patient 125


title: patient 110_whole liver tissue_HCC_non-tumor area D_106889

description:
WLT-110-D-106889
specimen obtained from the liver of patient 110

value: patient 110


title: patient 110_whole liver tissue_HCC_non-tumor area D_106887

description:
WLT-110-D-106887
specimen obtained from the liver of patient 110


title: ldl1 ldl2 sdg26 seedlings Replicate 1

description: Biological replicate 1 of ldl1 ldl2 sdg26 seedlings

source_name: ldl1 ldl2 sdg26_1 seedlings

value: Columbia

value: seedlings

value: ldl1 ldl2 sdg26


title: ldl1 ldl2 seedlings Replicate 1

description: Biological replicate 1 of ldl1 ldl2 seedlings

source_name: ldl1 ldl2_1 seedlings

value: 16 day old


title: Wild-type seedlings Replicate 2

description: Biological replicate 2 of Wild-type seedlings

source_name: WT_2 seedlings

value: wild type


title: patient 110_whole liver tissue_HCC_non-tumor area D_106888

description:
WLT-110-D-106888
specimen obtained from the liver of patient 110


title: patient 35_whole liver tissue_HCC_non-tumor area D_99454

description:
WLT-35-D-99454
specimen obtained from the liver of patient 35

value: patient 35


title: clf sdg26 seedlings Replicate 1

description: Biological replicate 1 of clf sdg26 seedlings

source_name: clf sdg26_1 seedlings


title: patient 98_whole liver tissue_HCC_non-tumor area C_104650

description:
WLT-98-C-104650
specimen obtained from the liver of patient 98

source_name: whole liver tissue_HCC_non-tumor area C

value: non-tumor area C


title: patient 35_whole liver tissue_HCC_non-tumor area D_99453

description:
WLT-35-D-99453
specimen obtained from the liver of patient 35


title: atx1 sdg26 seedlings Replicate 1

description: Biological replicate 1 of atx1 sdg26 seedlings

source_name: atx1 sdg26_1 seedlings

value: atx1 sdg26


title: patient 35_whole liver tissue_HCC_non-tumor area D_99456

description:
WLT-35-D-99456
specimen obtained from the liver of patient 35

value: non-tumor area D


title: patient 98_whole liver tissue_HCC_non-tumor area C_104649

description:
WLT-98-C-104649
specimen obtained from the liver of patient 98

value: HBV-associated HCC patient

value: patient 98


title: atx1 seedlings Replicate 1

description: Biological replicate 1 of atx1 seedlings

source_name: atx1_1 seedlings


title: sdg25 sdg26 seedlings Replicate 1

description: Biological replicate 1 of sdg25 sdg26 seedlings

source_name: sdg25 sdg26_1 seedlings

value: sdg25 sdg26


title: clf seedlings Replicate 1

description: Biological replicate 1 of clf seedlings

source_name: clf_1 seedlings

value: clf


title: patient 105_whole liver tissue_HCC_non-tumor area D_112256

description:
WLT-105-D-112256
specimen obtained from the liver of patient 105

value: patient 105

value: whole liver tissue (WLT)


title: patient 98_whole liver tissue_HCC_non-tumor area C_104651

description:
WLT-98-C-104651
specimen obtained from the liver of patient 98


title: ldl1 ldl2 sdg25 seedlings Replicate 1

description: Biological replicate 1 of ldl1 ldl2 sdg25 seedlings

source_name: ldl1 ldl2 sdg25_1 seedlings

value: ldl1 ldl2 sdg25


title: patient 92_whole liver tissue_HCC_non-tumor area C_107779

description:
WLT-92-C-107779
specimen obtained from the liver of patient 92

value: patient 92


title: patient 98_whole liver tissue_HCC_non-tumor area C_104648

description:
WLT-98-C-104648
specimen obtained from the liver of patient 98


title: patient 35_whole liver tissue_HCC_non-tumor area D_99457

description:
WLT-35-D-99457
specimen obtained from the liver of patient 35

source_name: whole liver tissue_HCC_non-tumor area D


title: patient 125_whole liver tissue_HCC_non-tumor area C_106891

description:
WLT-125-C-106891
specimen obtained from the liver of patient 125

value: patient 125


title: patient 110_whole liver tissue_HCC_non-tumor area C_106885

description:
WLT-110-C-106885
specimen obtained from the liver of patient 110

value: patient 110


title: patient 92_whole liver tissue_HCC_non-tumor area C_107777

description:
WLT-92-C-107777
specimen obtained from the liver of patient 92


title: patient 110_whole liver tissue_HCC_non-tumor area C_106886

description:
WLT-110-C-106886
specimen obtained from the liver of patient 110


title: sdg26 seedlings Replicate 1

description: Biological replicate 1 of sdg26 seedlings

source_name: sdg26_1 seedlings

value: Columbia

value: seedlings


title: patient 111_whole liver tissue_HCC_non-tumor area C_112249

description:
WLT-111-C-112249
specimen obtained from the liver of patient 111

value: patient 111


title: patient 111_whole liver tissue_HCC_non-tumor area C_112263

description:
WLT-111-C-112263
specimen obtained from the liver of patient 111


title: patient 125_whole liver tissue_HCC_non-tumor area C_106890

description:
WLT-125-C-106890
specimen obtained from the liver of patient 125


title: patient 111_whole liver tissue_HCC_non-tumor area C_112264

description:
WLT-111-C-112264
specimen obtained from the liver of patient 111


title: patient 110_whole liver tissue_HCC_non-tumor area C_106884

description:
WLT-110-C-106884
specimen obtained from the liver of patient 110


title: sdg25 seedlings Replicate 1

description: Biological replicate 1 of sdg25 seedlings

source_name: sdg25_1 seedlings

value: 16 day old


title: patient 110_whole liver tissue_HCC_non-tumor area C_106883

description:
WLT-110-C-106883
specimen obtained from the liver of patient 110

value: non-tumor area C


title: patient 105_whole liver tissue_HCC_non-tumor area C_112254

description:
WLT-105-C-112254
specimen obtained from the liver of patient 105


title: patient 53_whole liver tissue_HCC_non-tumor area C_99479

description:
WLT-53-C-99479
specimen obtained from the liver of patient 53

value: patient 53


title: Wild-type seedlings Replicate 1

description: Biological replicate 1 of Wild-type seedlings

source_name: WT_1 seedlings

value: wild type


title: patient 105_whole liver tissue_HCC_non-tumor area C_112255

description:
WLT-105-C-112255
specimen obtained from the liver of patient 105

value: HBV-associated HCC patient


title: patient 53_whole liver tissue_HCC_non-tumor area C_99472

description:
WLT-53-C-99472
specimen obtained from the liver of patient 53


title: patient 53_whole liver tissue_HCC_non-tumor area C_99469

description:
WLT-53-C-99469
specimen obtained from the liver of patient 53


title: patient 35_whole liver tissue_HCC_non-tumor area C_99450

description:
WLT-35-C-99450
specimen obtained from the liver of patient 35

value: patient 35


title: rat heart pretreated with MPE

city: Kuala Lumpur

first: Shin Yee

last: Fung

address: Lembah Pantai

department: Department of Molecular Medicine

country: Malaysia

institute: University of Malaya

description: rat heart pretreated with MPE

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array set. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with GeneChip® Operating Software which analysed the hybridization intensity from the GeneChip® expression probe arrays where data from each array were scaled to an average intensity of 800.

source_name: rat heart pretreated with MPE

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: hearts ( pooled samples, n=6)  were harvested as soon as death occurred or at the end of monitoring period

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: immediately after harvesting of organ(s), they were snap frozen and kept in -80C

tag: tissue

value: heart

tag: treatment

value: pretreated with Mucuna pruriens extract  MPE

tag: strain

value: Sprague-Dawley


title: patient 35_whole liver tissue_HCC_non-tumor area C_99451

city: Bethesda

description:
WLT-35-C-99451
specimen obtained from the liver of patient 35

tag: subject condition

tag: patient id

tag: distance from the tumor center

value: whole liver tissue (WLT)


title: patient 53_whole liver tissue_HCC_non-tumor area C_99478

description:
WLT-53-C-99478
specimen obtained from the liver of patient 53


title: Tak1_2

city: Los Angeles

first: Ekihiro

last: Seki

state: CA

address: 8700 Beverly Blvd., DAVIS, Suite 2099

institute: Cedars-Sinai Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Livers of TAK1 ko mice  sacrificed at 4 weeks

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: No treatment

tag: gender

value: male

value: Alb-Cre/ TAK1 flox

value: liver

value: 4 wk


title: patient 125_whole liver tissue_HCC_tumor area B_106738

description:
WLT-125-B-106738
specimen obtained from the liver of patient 125

source_name: whole liver tissue_HCC_tumor area B

value: patient 125

value: tumor area B


title: rat heart pretreated with MPE and envenomated with NS

value: pretreated with Mucuna pruriens  extract  MPE and Naja sputatrix envenomated


title: patient 35_whole liver tissue_HCC_non-tumor area C_99464

description:
WLT-35-C-99464
specimen obtained from the liver of patient 35


title: rat heart envenomated with NS

description: rat heart envenomated with NS

source_name: rat heart envenomated with NS

value: Naja sputatrix envenomated


title: WT_2

source_name: Livers of WT mice sacrificed at 4 weeks

value: TAK1 flox


title: rat heart normal

description: rat heart normal

source_name: rat heart normal

value: negative control


title: Tak1_1

source_name: Livers of TAK1 ko mice sacrificed at 4 weeks


title: patient 35_whole liver tissue_HCC_non-tumor area C_99452

description:
WLT-35-C-99452
specimen obtained from the liver of patient 35

source_name: whole liver tissue_HCC_non-tumor area C

value: non-tumor area C


title: patient 98_whole liver tissue_HCC_tumor area B_104645

description:
WLT-98-B-104645
specimen obtained from the liver of patient 98

value: HBV-associated HCC patient

value: patient 98


title: patient 92_whole liver tissue_HCC_tumor area B_106747

description:
WLT-92-B-106747
specimen obtained from the liver of patient 92

value: patient 92


title: patient 111_whole liver tissue_HCC_tumor area B_112260

description:
WLT-111-B-112260
specimen obtained from the liver of patient 111

value: patient 111


title: patient 92_whole liver tissue_HCC_tumor area B_106775

description:
WLT-92-B-106775
specimen obtained from the liver of patient 92


title: patient 111_whole liver tissue_HCC_tumor area B_112262

description:
WLT-111-B-112262
specimen obtained from the liver of patient 111


title: WT_1


title: patient 98_whole liver tissue_HCC_tumor area B_104647

description:
WLT-98-B-104647
specimen obtained from the liver of patient 98


title: patient 111_whole liver tissue_HCC_tumor area B_112261

description:
WLT-111-B-112261
specimen obtained from the liver of patient 111


title: patient 105_whole liver tissue_HCC_tumor area B_112252

description:
WLT-105-B-112252
specimen obtained from the liver of patient 105

value: patient 105


title: patient 105_whole liver tissue_HCC_tumor area B_112253

description:
WLT-105-B-112253
specimen obtained from the liver of patient 105

value: whole liver tissue (WLT)


title: patient 53_whole liver tissue_HCC_tumor area B_99477

description:
WLT-53-B-99477
specimen obtained from the liver of patient 53

value: patient 53


title: patient 111_whole liver tissue_HCC_tumor area B_112259

description:
WLT-111-B-112259
specimen obtained from the liver of patient 111


title: patient 110_whole liver tissue_HCC_tumor area B_106725

description:
WLT-110-B-106725
specimen obtained from the liver of patient 110

value: patient 110


title: patient 110_whole liver tissue_HCC_tumor area B_106731

description:
WLT-110-B-106731
specimen obtained from the liver of patient 110