title: Tumor biopsy [P-229_re-analysis]

description: Reanalysis of GSM1668699


title: Tumor biopsy [P-263_re-analysis]

status: Public on Mar 29 2016

type: RNA

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

description: Reanalysis of GSM1668704

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Cervical tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: 1-4 tumor samples wer collected from each patient at the time of diagnosis

extract_protocol: In cohort 1, RNA was extracted with Trizol reagent, followed by double precipitation with isopropanol and final precipitation with 5M lithium chloride. In cohort 2, RNA was extracted by use of the miRNeasy mini kit. RNA from different biopsies of the same tumor was pooled. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80 C until used for analysis.

tag: figo stage

tag: histology

value: Squamous cell carcinoma

tag: hypoxia classifier

value: More hypoxic

tag: cohort

value: Cohort 2


title: Tumor biopsy [P-280_re-analysis]

description: Reanalysis of GSM1668710

value: Less hypoxic


title: Stable K562 transductants_ control_ rep2

city: Bei Jing

first: Junwu

last: Zhang

address: 5 Dong Dan San Tiao

country: China

institute: National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences,

data_processing: The raw intensity of Illumina RNA expression array was scanned and extracted using BeadArray Reader (illumina, San Diego, CA), with the data corrected by background subtraction and normalized in GenomeStudio V2010.2 Gene Expression module (illumina, San Diego, CA). We normalized the intenstiy data with average normalization algorithom. Individual RNAs were examined using the detection p-value metric provided by Illumina in which the signal generated from each RNA is compared to negative controls. A threshold of p<0.05 was used as a cutoff. RNAs that did not reach this threshold were eliminated from the analysis.

source_name: Leukemic cell line Stable control transductants

label_protocol: The samples were prepared with the Illumina TotalPrepRNA Amplification Kit for Illumina arrays; Standard Illumina beadarray probe synthesis

growth_protocol: The human chronic myelogenous leukemia cell line K562 is maintained in RPMI-1640 medium (Gibco, BRL, UK) containing 2 mM glutamine, 25 mM HEPES, 1.5 g/L sodium bicarbonate, 10 % fetal calf serum (FCS, Gibco, BRL), 50 U/mL penicillin and 50 μg/mL streptomycin (Sigma, Saint Louis, MO, USA) at 37°C in 5% CO2.

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.

tag: cell line

tag: cell type

value: human chronic myelogenous leukemia cells

tag: genotype/variation

value: control


title: 22A

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

country: United Kingdom

institute: The Institute of Cancer Research

description: 22after excision

hyb_protocol: Hybridized to the Illumina HumanHT-12 V4.0 expression BeadChip or Illumina HumanWG-6 v3.0 expression BeadChip using the standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol of iScan.

data_processing:
The data were transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization.
The Sample data table includes values only for those probes that are in-common between Platforms GPL6884 and GPL10558.

source_name: breast tumour, LumA, after excision

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

extract_protocol: mRNA from paired excised tumour biopsies after resection and after X-ray were extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

tag: Sex

value: female

tag: disease

value: primary ER+ breast carcinoma

tag: subtype

value: LumA

tag: tissue

value: breast tumour

tag: sampling time

value: after excision

tag: delay

value: 25 minutes


title: Mutant, biological rep3

city: Toyoake

first: Hideo

last: Hagihara

address: 1-98 Dengakugakubo, Kutsukake-cho

department: Institute for Comprehensive Medical Science

country: Japan

institute: Fujita Health University

description: Gene expression data from the DG of mutant mouse (24-h LA: 18924.18)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 (GCS3000)

data_processing: The data were analyzed with Affymetrix Expression Cosole (version 1.1). The normalization used in RMA is quantile normalization.

organism: Mus musculus

source_name: DG of adult mutant mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

extract_protocol: Trizol extraction of total RNA and cleanup byRNeasy Micro kit (QIAGEN) was performed according to the manufacturer's instructions.

value: Dentate gyrus

tag: genotype

value: Mutant

tag: age

tag: backgrond


title: 11B

description: 11after x-ray

source_name: breast tumour, basal, after x-ray

value: Basal

value: after x-ray

value: 31 minutes


title: Mutant, biological rep9

description: Gene expression data from the DG of mutant mouse (24-h LA: 17325.24)


title: Tumor biopsy [P-264_re-analysis]

description: Reanalysis of GSM1668705

value: Squamous cell carcinoma


title: 22B

description: 22after x-ray

source_name: breast tumour, LumA, after x-ray


title: Stable K562 transductants_ control_ rep1


title: Mutant, biological rep8

description: Gene expression data from the DG of mutant mouse (24-h LA: 66742.98)


title: 21A

description: 21after excision

value: 35 minutes


title: Tumor biopsy [P-226_re-analysis]

description: Reanalysis of GSM1668698

value: Cohort 2


title: 20A

description: 20after excision

source_name: breast tumour, LumB, after excision

value: LumB

value: 30 minutes


title: 21B

description: 21after x-ray


title: 19B

description: 19after x-ray

source_name: breast tumour, normal, after x-ray

value: Normal

value: 20 minutes


title: 19A

description: 19after excision

source_name: breast tumour, normal, after excision

value: female

value: primary ER+ breast carcinoma


title: 16A

description: 16after excision

value: LumA

value: breast tumour


title: 16B

description: 16after x-ray


title: 17B

description: 17after x-ray

source_name: breast tumour, LumB, after x-ray


title: E14Tg2A_10DIV_AgoIP

city: Genova

first: Luca

last: Pandolfini

state: Genova

address: Via Enrico Melen 83, Building B

department: Center for Human Technologies

country: Italy

institute: Istituto Italiano di Tecnologia - I

description:
IP RNA
Profile of RNA resulting from Argonaute immunoprecipitation of cytoplasmic RNA-protein complexes in E14Tg2A ES cells at 10 days of in vitro differentiation (NPC/Neu)

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2564C) using one color scan default setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (GE1_107_Sep09 and Grid: 028005_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities. Data were background-corrected and normalized between arrays by means of Bioconductor package limma (Smyth, 2005).

source_name: E14Tg2A at 10DIV, Argonaute IP

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng of RNA using the LowInput QuickAmp Labeling Kit One-Color (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Murine embryonic stem cell line E14Tg2A was cultured on gelatin-coated tissue culture dishes at a density of 40,000 cells/cm2. ES cell medium, which was changed daily, contained GMEM, 10% Fetal Calf Serum, 2mM Glutamine, 1mM sodium Pyruvate, 1mM non-essential amino acids, 0.05mM β-mercaptoethanol, 100 U/mL Penicillin/Streptomycin and 1000 U/mL recombinant mouse LIF. Chemically defined minimal medium (CDMM) for neural induction consisted of DMEM/F12, 2mM Glutamine, 1mM sodium Pyruvate, 0.1mM non-essential amino acids, 0.05mM β-mercaptoethanol, 100 U/mL Penicillin/Streptomycin supplemented with N2/B27 (no vitamin A). The protocol of ES neuralization consisted of three steps: during Step-I, dissociated ES cells were washed with DMEM/F12, aggregated in agar-coated culture dishes (65,000 cells per cm2) and cultured as floating aggregates in CDMM for 2 days. The second day, 75% of CDMM was renewed. In Step-II, ES cell aggregates were dissociated and cultured in adhesion (65,000 cells per cm2) on Poly-ornithine (20 μg/ml in sterile water, 24 hours coating at 37°C) and natural mouse Laminin (2.5 μg/ml in PBS, 24 hours coating at 37°C) for 4 days, changing CDMM daily. In Step-III, after a second dissociation, ES cells were cultured 4 additional days in CDMM devoid of B27 supplement to drive terminal differentiation, using the same type of seeding density and coated surface described for Step II. Serum employed for Trypsin inactivation was carefully removed by washing with DMEM/F12.

extract_protocol: Total RNA was extracted with NucleoSpin RNA II columns (Macherey–Nagel). RNA from three different independent sets of experiments was pooled. RNA quality was assessed with Agilent Bioanalyzer RNA 6000 Nano kit.

treatment_protocol: Cellular mRNAs that are bound by Argonaute proteins were isolated employing RIP-Assay Kit for microRNA (MBL Japan), according to the manufacturer's instructions. Anti-pan Ago Antibody, clone 2A8 (Millipore; MABE56) was used for IP.  For each single experiment, we started from 10^7 cells collected pooling 3 to 10 different samples.

tag: strain

tag: treatment

value: Ago-IP

tag: days in vitro


title: Stable K562 transductants _ ZNF16 over-expression_rep2

source_name: Leukemic cell line Stable transductants with ZNF16 over-expression

value: human chronic myelogenous leukemia cells

value: overexpressing ZNF16 over-expression


title: Stable K562 transductants _ ZNF16 over-expression_rep1


title: Tumor biopsy [P-081_re-analysis]

description: Reanalysis of GSM1668689

tag: figo stage

tag: histology

tag: hypoxia classifier

value: Less hypoxic


title: 14A

description: 14after excision

value: after excision

value: 25 minutes


title: E14Tg2A_EpiSC_exELA

description: Gene expression of E14Tg2A ES cell-derived Epiblast-Like Aggregates (ELA) after administration of FGF2 and Activin A

source_name: E14Tg2A at 0DIV, total RNA

growth_protocol: Murine embryonic stem cell line E14Tg2A was cultured on gelatin-coated tissue culture dishes at a density of 40,000 cells/cm2. ES cell medium, which was changed daily, contained GMEM, 10% Fetal Calf Serum, 2mM Glutamine, 1mM sodium Pyruvate, 1mM non-essential amino acids, 0.05mM β-mercaptoethanol, 100 U/mL Penicillin/Streptomycin and 1000 U/mL recombinant mouse LIF.

treatment_protocol: Chemically defined minimal medium (CDMM) for EpiSC induction consisted of DMEM/F12, 2mM Glutamine, 1mM sodium Pyruvate, 0.1mM non-essential amino acids, 0.05mM β-mercaptoethanol, 100 U/mL Penicillin/Streptomycin supplemented with N2/B27 (no vitamin A), Activin A (20 ng/mL) and FGF2 (12 ng/mL).


title: E14Tg2A_6DIV_totRNA

description:
total RNA
Gene expression of E14Tg2A ES cells at 6 days of in vitro differentiation (NPC)

source_name: E14Tg2A at 6DIV, total RNA

value: total RNA


title: 17A

description: 17after excision


title: 15A

description: 15after excision

value: 40 minutes


title: E14Tg2A_0DIV_Ctrl

description: Gene expression of control E14Tg2A ES cells at 0 days of in vitro differentiation (ES)

source_name: E14Tg2A at 0DIV, Ctrl

growth_protocol: Murine embryonic stem cell line E14Tg2A was cultured on gelatin-coated tissue culture dishes at a density of 40,000 cells/cm2. ES cell medium, which was changed daily, contained GMEM, 10% Fetal Calf Serum, 2mM Glutamine, 1mM sodium Pyruvate, 1mM non-essential amino acids, 0.05mM β-mercaptoethanol, 100 U/mL Penicillin/Streptomycin and 1000 U/mL recombinant mouse LIF. Chemically defined minimal medium (CDMM) consisted of DMEM/F12, 2mM Glutamine, 1mM sodium Pyruvate, 0.1mM non-essential amino acids, 0.05mM β-mercaptoethanol, 100 U/mL Penicillin/Streptomycin supplemented with N2/B27 (no vitamin A). For epiblast-like aggregate (ELA) formation, dissociated ES cells were washed with DMEM/F12, aggregated in agar-coated culture dishes (65,000 cells per cm2) and cultured as floating aggregates in CDMM for 2 days.

extract_protocol: Total RNA was extracted with NucleoSpin RNA II columns (Macherey–Nagel). RNA from three different sets of independent experiments was pooled. RNA quality was assessed with Agilent Bioanalyzer RNA 6000 Nano kit.

treatment_protocol: 5-Azacytidine (AZA; 50 nM) and 5-Carboxy-8-hydroxyquinoline (CHQ; 100 μM) were tested by addition during ELA formation. For shRNA-mediated knock-down of SmarcA4, ES cells underwent two rounds of spinoculation with a self-inactivating lentiviral vector carrying a DsRed-IRES-Puromycin resistance cassette with the shRNA against SmarcA4, driven by the strong ubiquitous promoter EF1α (shBrg1); transduced cells were selected in puromycin (0.75μg/mL) for 48h before ELA formation.

value: Ctrl


title: Tumor biopsy [P-009_re-analysis]

description: Reanalysis of GSM1668686

value: Squamous cell carcinoma

value: More hypoxic

tag: cohort

value: Cohort 2


title: E14Tg2A_2DIV_CHQ

description: Gene expression of E14Tg2A ES cells at 2 days of in vitro differentiation (ELA) in the presence of lysine demethylase inhibitor 5-Carboxy-8-hydroxyquinoline (CHQ; 100 μM)

source_name: E14Tg2A at 2DIV, CHQ

value: CHQ


title: E14Tg2A_10DIV_totRNA

description:
total RNA
Gene expression of E14Tg2A ES cells at 10 days of in vitro differentiation (NPC/Neu)

source_name: E14Tg2A at 10DIV, total RNA


title: E14Tg2A_6DIV_AgoIP

description:
IP RNA
Profile of RNA resulting from Argonaute immunoprecipitation of cytoplasmic RNA-protein complexes in E14Tg2A ES cells at 6 days of in vitro differentiation (NPC)

source_name: E14Tg2A at 6DIV, Argonaute IP


title: 14B

description: 14after x-ray

value: female

value: Normal

value: after x-ray


title: E14Tg2A_2DIV_shSA4

description: Gene expression of E14Tg2A ES cells at 2 days of in vitro differentiation (ELA) after knock-down of SmarcA4 by by lentiviral transduction of a targeting shRNA

source_name: E14Tg2A at 2DIV, shBrg1

value: SmarcA4 RNAi


title: E14Tg2A_EpiSC

description: Gene expression of E14Tg2A ES cells after administration of FGF2 and Activin A

source_name: E14Tg2A at 0DIV, Argonaute IP


title: E14Tg2A_2DIV_AZA

description: Gene expression of E14Tg2A ES cells at 2 days of in vitro differentiation (ELA) in the presence of de novo methyltransferase inhibitor 5-Azacytidine (AZA; 50nM)

source_name: E14Tg2A at 2DIV, AZA

value: AZA


title: 15B

description: 15after x-ray

value: primary ER+ breast carcinoma

value: LumA

value: breast tumour


title: 13B

description: 13after x-ray

value: LumB

value: 30 minutes


title: E14Tg2A_2DIV_Ctrl

description: Gene expression of control E14Tg2A ES cells at 2 days of in vitro differentiation (ELA)

source_name: E14Tg2A at 2DIV, Ctrl


title: 10B

description: 10after x-ray


title: Tumor biopsy [P-218]

source_name: Cervical tumor

value: Less hypoxic


title: 9B

description: 9after x-ray


title: 9A

description: 9after excision

source_name: breast tumour, LumB, after excision

value: after excision


title: E14Tg2A_0DIV_AgoIP

description:
IP RNA
Profile of RNA resulting from Argonaute immunoprecipitation of cytoplasmic RNA-protein complexes in E14Tg2A ES cells at 0 days of in vitro differentiation (ES)

value: Ago-IP


title: E14Tg2A_2DIV_AgoIP

description:
IP RNA
Profile of RNA resulting from Argonaute immunoprecipitation of cytoplasmic RNA-protein complexes in E14Tg2A ES cells at 2 days of in vitro differentiation (ELA)

source_name: E14Tg2A at 2DIV, Argonaute IP


title: 7A

description: 7after excision

source_name: breast tumour, LumA, after excision

value: 25 minutes


title: 8A

description: 8after excision

value: 20 minutes


title: Cell line [CaSki O2]

description: CaSki O2.AVG_Signal

source_name: Uterine cervical cancer

growth_protocol: The cells were incubated in Dulbecco's Modified Eagle medium with GlutaMAX supplemented with 10% fetal calf serum (FCS) and 100 U/ml penicillin/streptomycin (Gibco) under a 5% CO2 atmosphere at 37°C, and subcultured twice a week.

extract_protocol: RNA was extracted using RNeasy MiniKit (Quiagen), according to the manufacturers’ instructions.  Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were plated out in plastic dishes (3x10^5 cells for 6 cm dishes, 9x10^5 for 10 cm dishes) 24 h prior to exposure to hypoxic (0.2% O2, 5% CO2) or normoxic (95% air, 5% Co2) conditions for 24 h at 37°C. The hypoxia treatment was performed in an Invivo2200 chamber (Ruskinn Technology Ltd, Bridgend, UK) with accurate O2 and CO2 controls.

tag: cell line

value: CaSki

value: Squamous cell carcinoma

tag: exposed to

value: normoxic (95% air, 5% Co2) conditions for 24 h at 37°C (untreated)


title: Tumor biopsy [P-143]

value: More hypoxic

value: Cohort 2


title: E14Tg2A_0DIV_totRNA

description:
total RNA
Gene expression of E14Tg2A ES cells at 0 days of in vitro differentiation (ES)

value: total RNA


title: E14Tg2A_2DIV_totRNA

description:
total RNA
Gene expression of E14Tg2A ES cells at 2 days of in vitro differentiation (ELA)

source_name: E14Tg2A at 2DIV, total RNA


title: Tumor biopsy [P-127]

value: Adenocarcinom

value: Adeno


title: Cell line [CaSki Hyp]

description: CaSki Hyp.AVG_Signal

value: hypoxic (0.2% O2, 5% CO2) conditions for 24 h at 37°C


title: 13A

description: 13after excision

tag: Sex

value: female

tag: disease

value: primary ER+ breast carcinoma

value: breast tumour


title: 2B

description: 2after x-ray

source_name: breast tumour, LumA, after x-ray

tag: subtype

value: LumA

tag: tissue

value: after x-ray


title: Cell line [SiHa Hyp]

description: SiHa Hyp.AVG_Signal

value: SiHa


title: 2A

description: 2after excision

tag: sampling time

value: after excision

tag: delay


title: 8B

description: 8after x-ray

value: 20 minutes


title: Ileal Mucosa from a Chron's disease sample (6)

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

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

source_name: Ileal mucosa

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

extract_protocol: Total RNA was isolated from mucosal samples using RNeasy mini kit (Qiagen) following the manufacturer's instructions. RNA quantity and integrity were evaluated using RNA 6000 Nano Chip in a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA) and was judged to be acceptable if the 28S/18S ribosomal fragments ratio was over 1.5 and the RNA integrity number (RIN) was over 6. RNA samples were stored at -80°C until measurement.

value: ileal mucosa

tag: disease status

value: CHRON


title: Ileal Mucosa from a Chron's disease sample (5)


title: Cell line [SiHa O2]

description: SiHa O2.AVG_Signal

value: Squamous cell carcinoma

value: normoxic (95% air, 5% Co2) conditions for 24 h at 37°C (untreated)


title: Ileal Mucosa from a Healthy sample (4)

description: Ileal Mucosa from a Healthy sample (4)

value: HEALTHY


title: 7B

description: 7after x-ray

value: 25 minutes


title: Ileal Mucosa from a Healthy sample (3)

description: Ileal Mucosa from a Healthy sample (3)


title: Ileal Mucosa from a Healthy sample (5)

description: Ileal Mucosa from a Healthy sample (5)


title: Ileal Mucosa from a Chron's disease sample (4)


title: Ileal Mucosa from a Healthy sample (2)

description: Ileal Mucosa from a Healthy sample (2)


title: Ileal Mucosa from a Chron's disease sample (2)


title: Ileal Mucosa from a Chron's disease sample (3)


title: Ileal Mucosa from a Healthy sample (1)

description: Ileal Mucosa from a Healthy sample (1)


title: I100

city: Toronto

first: James

last: Ellis

state: Ontario

address: 686 Bay Street

department: Developmental and Stem Cell Biology

country: Canada

institute: Hospital for Sick Children

hyb_protocol: Standard protocol at the Centre for Applied Genomics at the Hospital for Sick Children, Canada

data_processing: Raw intensity values were exported and analyzed using the R limma package.  To compare gene expression between our WT sample and the three WBS samples, the probe IDs were converted to nuIDs to improve annotation consistency. The neqc function (16) was used for background correction and quantile normalization. The data were log2 transformed and probes with detection p-values >0.01 in all samples were removed for downstream analyses (22134 probes remaining out of 47320). To perform gene set enrichment analysis, all probes were ranked by the t-statistic produced by a empirical Bayes statistics (eBayes) of the resulting linear model (lmfit) of the microarray. We used gene sets form the Gene Ontology: Biological Process database and filtered out datasets that were overly large (>900 genes) or overly small (<15 genes). Gene sets enriched at an FDR of <0.1 were used to construct an Enrichment Map (17) in Cytoscape (18) to visualize gene set interconnectedness and identify perturbed cellular functions.

source_name: iPSC-derived neurons, 6 wk

label_protocol: 1 μg of RNA from each iPSC derived neuronal sample; WT, WBS A, WBS B, and WBS I; was submitted to The Centre for Applied Genomics at the Hospital for Sick Children, where manufacturer's protocols were followed

growth_protocol: WBS (A, B and I hiPSC lines) and WT iPSC line (Δ3-4-hiPS #37) (12) were dissociated to form cellular aggregates and cultured in suspension on low cluster plates with media changes everyday in Knockout DMEM containing knockout serum replacement, GlutaMAX-1, non-essential amino acids, 2-marcaptoethanol and supplemented with bFGF (10 ng/ml), SB431542 (10 μM) and Dorsomorphin (2 μM). The media was switched to neural induction media on day 4 containing DMEM-F12, N2, non-essential amino acids, Heparin (2 μg/ml), bFGF (10 ng/ml), SB431542 (10 μM) and Dorsomorphin (2 μM). On day 6, the cellular aggregates were seeded onto polyornithin/laminin coated dishes in neural induction media without SB431542. The cells were fed with fresh media every second day till day 17. On the 17th day of differentiation, the neural rosettes were manually dissected and plated onto polyornithin and laminin coated plates to obtain secondary rosettes. The media was changed every second day with neural induction media without SB431542 and Dorsomorphin. On day 25 of differentiation, the secondary rosettes were manually harvested from the plates and spun down for 2 mins at 600 rpm (69 g) in a swing bucket tabletop centrifuge. The cell pellet was resuspended in 1 ml acutase and incubated for 10 min at room temperature. 1 ml of neural precursor media (DMEM F12, N2, B27+RA, laminin, non-essential amino acids, heparin, bFGF) was added and cells were triturated gently to break apart the rosettes and obtain single cells. Cells were pelleted at 600 rpm (69 g) for 2 mins, resuspend in 2 ml of neuralprecursor media, and plated onto polyornithin/laminin coated plates. For neuronal differentiations, glass cover slips were coated with polyornithin and laminin and placed into 24 well plates. The neural precursor cells were plated at a density of 5 x 104 cells per well in complete neural differentiation media (Neurobasal, N2, non-essential amino acids, BDNF (10 ng/ml), GDNF (10 ng/ml), IGF-1 (10 ng/ml), B27 (without RA), cAMP (1 μM), Ascorbic acid (200 ng/ml), Laminin (1 μg/ml). The media was changed every second day for 6-8 weeks. The protocol was repeated at least three independent times starting from hES/iPS cells.

extract_protocol: Three wells of each WT, WBS A, WBS B, and WBS I differentiated neurons were pooled to extract RNA. BioAnalyzer was used to assess the integrity of the RNA.

tag: cell type

value: iPSC-derived neurons

tag: gender

value: Male

tag: reprogramming method

value: Retrovirus

tag: donor

value: WBS patient

tag: x-inactivation status

tag: mecp2 expression

value: Expressed

value: male

tag: diffwk


title: Ileal Mucosa from a Chron's disease sample (1)


title: F11_12_D

city: Jena

first: Amelia

middle: E

last: Barber

state: Thuringia

address: Adolf-Reichwein-Straße 23

department: Fungal Informatics

country: Germany

institute: Leibniz-HKI

hyb_protocol: Fluroescently labeled cRNA (825 ng) was then fragemented, combined with Hi-RPM Hybridization Buffer (Agilent), and hybridized using a SureHyb Hybridization chamber (Agilent)

scan_protocol: Slides were scanned in a G2505C Microarray Scanner (Agilent)

data_processing:
TIFF files of scanned microarrays were processed using Feature Extraction Software version 10.6 (Agilent). Array data was then log2 transformed, Lowess-normalized, and median centered.
Fold changes were calculated by comparing samples to mock-infected (PBS-injected) controls from the same clutch of embryos.

organism: Danio rerio

source_name: 2 dpf zebrafish embryos injected with sterile PBS

label_protocol: Fluorescently labeled cRNA was synthesized using the Two-Color Low RNA Input Linear Amplifliciation Kit (Agilent)

growth_protocol: Wildtype AB zebrafish were maintained as breeding colonies on a 14h/10h light/dark cycle. Embryos were collected as mixed egg clutes and raised at 28.5C in E3 medium. Bacterial strains were grown statically in modified M9 minimal medium  at 37C for 24 hrs. 1000 ul culture was spun down, washed in sterile PBS, and then resuspended ~800-1200 ul sterile PBS.

extract_protocol: Pools of 18-20 2 dpf zebrafish embryo were manually homogonized and RNA extracted using the Rneasy Plus Universal Kit (Qiagen)

treatment_protocol: 48 hpf zebrafish embryos were inoculated with ~1000 CFU of E. coli strain CFT073, F11, or an equivalent volume of sterile PBS as a control.

tag: agent

value: Sterile PBS

tag: hours post inoculum

source_name: 2 dpf zebrafish embryos infected with E. coli F11

tag: inoculated with

value: E. coli F11


title: B100

scan_protocol: Standard protocol at the Centre for Applied Genomics at the Hospital for Sick Children, Canada


title: WT

description: Sample derived from RTT patient with WT X-chromosome active, ensuring WT MeCP2 expression

value: Rett Syndrome patient with deletion of MeCP2 exon 3 and 4 deletion

value: XaXi

value: female


title: A100


title: F11_12_C


title: Liver_7weeks_mouse-2

city: Pittsburgh

first: Andrew

middle: W.

last: Duncan

state: PA

address: 450 Technology Drive, Suite 300

department: Pathology

country: USA

institute: University of Pittsburgh

hyb_protocol: Hybridization was performed according to manufacturer's instructions (NanoString) with 100 ng of total RNA per reaction. Hybridization was carried out at 65oC for a minimum of 18 hours.

scan_protocol: Hybridized probes were purified according to manufacturer's instructions (NanoString) using the nCounter prep station, and cartridges were scanned on the nCounter Digial Analyzer. High density scan settings were used (600 fileds of view per sample).

data_processing: The raw data were normalized using nSolver Analysis Software 2 (NanoString) based on the counts of four miRNAs that were observed to be relatively consistent at all ages: miR-16, miR-34c, miR-155 and miR-741. Using Partek Genomics Suite 6.6, background values (i.e., the mean of negative control values + 3 standard deviations) were subtracted from each sample, allowing the identification of 99.86% of background noise. miRNAs with background values for all samples analyzed were deleted; in contrast, all other miRNA counts with negative values were “floored” to a minimum value of 0.001. Data were log2 transformed.

label_protocol: As per manufacturers instructions

extract_protocol: Total RNA was isolated from each mouse liver uisng Trizol.

tag: strain

tag: age

value: 7 weeks

value: liver


title: F11_12_A


title: F11_12_B


title: Liver_3weeks_mouse-3

value: 3 weeks


title: F11_6_D


title: Liver_3weeks_mouse-2


title: Liver_7weeks_mouse-1


title: F11_6_C


title: Liver_7weeks_mouse-3


title: F11_6_A


title: Liver_2weeks_mouse-3

value: 2 weeks


title: Liver_3weeks_mouse-1


title: F11_6_B


title: AT1-EP3

type: genomic

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

description: Episomal protein induced iPS cells derived from A-T Disease patient1 fibroblast

hyb_protocol: Affymetrix Hybridization Oven 640 for 16 hrs at 50 deg C with rotation at 60 rpm. Washing and staining was done on an Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done using an Affymetrix Scanner 3000 7G with autoloader.

data_processing: For detecting CNV calls, the Affymetrix Genotyping Console 4.1.1 algorithm was used. CNV locations are based on the human genome assembly of March 2006 (hg18). Samples were normalized to Affymetrix HapMap reference dataset hybridized on the same platform. For CNV calls, regional GC correction, 10-kilobase (KB) cut-off value, and a minimum of ten markers were used as analysis configurations. All samples passed quality control requirements.

molecule: genomic DNA

label_protocol: The DNA was prepared for hybridization to Affymetrix SNP 6.0 arrays according to the manufacturer's recommendations.

extract_protocol: Genomic DNA was purified with Qiagen Blood and Tissue DNA kit.

treatment_protocol: Not applicable


title: AT1-EP5

source_name: Episomal protein induced iPS cells derived from A-T Disease patient1 fibroblast


title: Liver_2weeks_mouse-2


title: AT1-EP4

value: Episomal protein induced iPS cells derived from A-T Disease patient1 fibroblast


title: ATF2

description: A-T Disease patient2 fibroblast

source_name: A-T Disease patient2 fibroblast

value: A-T Disease patient2 fibroblast


title: CFT073_12_D

source_name: 2 dpf zebrafish embryos infected with E. coli CFT073

value: E. coli CFT073


title: A2-4 p20

description: Virus induced iPS cells passage20 derived from A-T Disease patient2 fibroblast

value: Virus induced iPS cells derived from A-T Disease patient2 fibroblast


title: AT1-EP1


title: CFT073_12_C


title: CFT073_12_B


title: A1-7 p20

description: Virus induced iPS cells passage20 derived from A-T Disease patient1 fibroblast

value: Virus induced iPS cells derived from A-T Disease patient1 fibroblast


title: A2-1 p4

description: Virus induced iPS cells passage4 derived from A-T Disease patient2 fibroblast


title: A2-4 p5

description: Virus induced iPS cells passage5 derived from A-T Disease patient2 fibroblast


title: A1-7 p8

description: Virus induced iPS cells passage8 derived from A-T Disease patient1 fibroblast


title: Liver_2weeks_mouse-1


title: HCS_11 (BCC control) [lncRNA]

city: Bochum

first: Michael

last: Sand

state: NRW

address: Gudrunstr. 56

department: Depatment of Dermatology, Venereology and Allergology

institute: Ruhr-University Bochum

description: A total of 1851 LncRNAs were shown to be significantly up- and 2165 LncRNAs to be significantly down-regulated with the criteria of FC ≥2 and p<0.05) in BCC compared to mon-lesional skin (control).

hyb_protocol: For hybridization 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarrays which were incubated in an Agilent hybridization oven (Agilent Technology, Santa Clara, USA) for 17 hours at 65°C.

scan_protocol: Finally, arrays were washed, fixed and scanned with Agilent DNA Microarray Scanner G2505C (Agilent Technologies, Santa Clara, USA).

data_processing: Quantile normalization which was applied to raw data and further data processing was performed with GeneSpring GX v12.0 software package (Agilent Technologies, Santa Clara, USA). Only lncRNAs and mRNAs that at least in 3 out of 6 samples have flags in Marginal or Present (“All Targets Value”) were chosen for further data analysis. Hierarchical clustering was performed with R software (version 2.15, http://www.r-project.org/) in order to arrange samples into groups based on their expression levels.

source_name: skin

label_protocol: The samples were amplified with a mixture of oligo (dT) and random priming method (Arraystar Flash RNA Labeling Kit, Arraystar) and transcribed in fluorescent cRNA which was purified by RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturers protocol. Concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) was measured with NanoDrop ND-1000. Next, to 1 μg of each labeled cRNA, 5 μl 10 × Blocking Agent (Agilent Technology, Santa Clara, USA) and 1 μl of 25 × Fragmentation Buffer was added (Agilent Technology, Santa Clara, USA). The mixture was heated at 60 °C for 30 min and 25 μl 2 × GE Hybridization buffer (Agilent Technology, Santa Clara, USA) was added to dilute the labeled cRNA.

growth_protocol: A total of 6 patients with BCC and 6 healthy individuals (control; non-lesional skin) were enrolled in the study.

extract_protocol: Total RNA was extracted with TRIzol (Life Technologies, Carlsbad, USA) following the manufacturers protocol.  RNA quantity and quality was determined with NanoDrop ND-1000 and RNA integrity with standard denaturing agarose gel electrophoresis. To purify mRNA from total RNA, rRNA was removed with mRNA-ONLY™ Eukaryotic mRNA Isolation Kit (Epicentre, Omaha, USA).

treatment_protocol: Punch biopsies (4 mm) were obtained under local anaesthesia and immediately put in RNAlater (Qiagen, Hilden, Germany) and stored at - 80 °C until RNA extraction.

value: Female

value: non-lesional skin (control)


title: A1-3 p23

description: Virus induced iPS cells passage23 derived from A-T Disease patient1 fibroblast


title: Liver_e15.5_mouse-2

value: mixed


title: Liver_e15.5_mouse-3


title: AT1-EP2


title: CFT073_12_A

value: Sterile PBS


title: A2-3 p5

source_name: Virus induced iPS cells passage5 derived from A-T Disease patient2 fibroblast


title: ATF1

description: A-T Disease patient1 fibroblast

source_name: A-T Disease patient1 fibroblast

value: A-T Disease patient1 fibroblast


title: BCC_55T [lncRNA]

source_name: basal cell carcinoma

value: basal cell carcinoma


title: CFT073_6_D


title: H2-2 p20

description: Virus induced iPS cells passage20 derived from Normal Human fibroblast

value: Virus induced iPS cells derived from Normal Human fibroblast


title: MG1655 R258C NusA BR, treated

status: Public on Mar 28 2016

city: Hyderabad

first: M Zuhaib

last: Qayyum

state: Telangana

address: Lab of Transcription, CDFD,

country: India

institute: CDFD

description:
pooled whole cell lysate
MG1655 R258C NusA biological replicate, treated

hyb_protocol: 1000ng of  labeled cRNA samples were mixed and hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: scanned using the Agilent Microarray Scanner

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version  software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Escherichia coli

source_name: Bacterial cell pellet

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using Random hexamer primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

growth_protocol: Bacterial culture grown overnight at 37C, given 1% sub-culturing till OD at 600nm was 0.4

extract_protocol: The RNA extraction from the samples was performed by Qiagen RNeasy Mini Kit with DNAse treatment (Cat.No. 74004) as per manufacturer’s protocol.

treatment_protocol: Treated experimental sets transformed with plasmids containing WT/G181D/R258C NusA. Cells subjected to P1 transduction to delete the genomic counterparts of the respective gene.

tag: plasmid

value: R258C NusA


title: CFT073_6_B


title: Patient-5-Primary -C

city: Kansas City

first: Sufi

last: Thomas

state: Kansas

address: 3901 Rainbow Blvd

department: Otolaryngology

institute: KUMC

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
affymetrix-algorithm-name = birdseed-v2
affymetrix-algorithm-version = 2.4

label: Biotin

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: patient id

value: HNSCC Patient 5

tag: tissue

value: Oral cavity primary tumor of site C


title: BCC_59T [lncRNA]


title: HCS_6 (BCC control) [lncRNA]

value: Male


title: BCC_47T [lncRNA]


title: Patient-5-Primary -B

value: Oral cavity primary tumor of site B


title: HCS_8 (BCC control) [lncRNA]


title: CFT073_6_A


title: MG1655 G181D NusA BR, treated

description:
pooled whole cell lysate
MG1655 G181D NusA biological replicate, treated

value: G181D NusA


title: MG1655 R258C NusA, treated

description:
pooled whole cell lysate
MG1655 R258C NusA, treated


title: H2-1 p23

description: Virus induced iPS cells passage 23 derived from Normal Human fibroblast


title: A2-3 p20

source_name: Virus induced iPS cells passage20 derived from A-T Disease patient2 fibroblast


title: MG1655 G181D NusA, treated

description:
pooled whole cell lysate
MG1655 G181D NusA, treated


title: MG1655 WT NusA, control

description:
pooled whole cell lysate
MG1655 WT NusA, control

value: wild type NusA


title: MG1655 WT NusA BR, control

description:
pooled whole cell lysate
MG1655 WT NusA biological replicate, control


description:
raw file: US83000164_252030410006_S01_GE2_105_Dec08_2_1.txt
E. coli MG1655 ∆Rac G324D, treated-Replicate1-mutant

hyb_protocol: 300ng of Cy3 labeled sample and 300ng of Cy5 labeled sample were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: scanned using the Agilent Microarray Scanner  Data extraction from Images was done using Agilent Feature Extraction software v 10.5.1.1

data_processing: Images Analysis using Agilent Feature Extraction Software Version 11.5 to obtain raw data.Probe intensities generated from feature extraction raw data were split based on channel type and  analysis was performed.

label_protocol: Poly (A)-tails were added to the 3’-end of RNA by using A-plus Poly (A) polymerase tailing kit (Epicentre Biotechnologies).Then  the samples  were labeled using Agilent Quick-Amp labeling Kit (p/n:5190-0444).  Five hundred nanograms each of the samples were incubated with reverse transcription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3-CTP(Agilent) and Cy5-CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

treatment_protocol: Treated experimental sets transformed with plasmids containing Rho (WT/N340S/G324D).Cells subjected to P1 transduction to delete the genomic counterparts of the gene.

tag: genotype

value: delta-rac

value: G324D Rho mutant


description:
raw file: US83000164_252030410006_S01_GE2_105_Dec08_2_1.txt
E. coli MG1655 ∆Rac G324D, treated-Replicate2-mutant


description:
raw file: US83000164_252030410002_S01_GE2_105_Dec08_2_3.txt
E. coli MG1655, WT Rho treated-Replicate2

treatment_protocol: Treated experimental sets transformed with plasmids containing BCM/WT rho. Rho treated cells subjected to P1 transduction to delete the genomic counterparts of the gene.

tag: treatment

value: WT Rho plasmid


title: A1-3 p5

description: Virus induced iPS cells passage5 derived from A-T Disease patient1 fibroblast

tag: cell type

value: Virus induced iPS cells derived from A-T Disease patient1 fibroblast


description:
raw file: US83000164_252030410006_S01_GE2_105_Dec08_1_4.txt
E. coli MG1655 ∆Rac N340S, treated-Replicate1-mutant

value: N340S Rho mutant


description:
raw file: US83000164_252030410006_S01_GE2_105_Dec08_1_4.txt
E. coli MG1655 ∆Rac N340S, treated-Replicate2-mutant


description:
raw file: US83000164_252030410006_S01_GE2_105_Dec08_1_3.txt
E. coli MG1655 ∆Rac WT, control-Replicate2-Wildtype

value: WT Rho


title: Liver_e15.5_mouse-1

tag: gender

value: mixed

value: liver


title: A1-1 p20

description: Virus induced iPS cells passage20 derived from A-T Disease patient1 fibroblast


title: E. coli MG1655, BCM treated-Replicate2

description:
raw file: US83000164_252030410002_S01_GE2_105_Dec08_2_1.txt
E. coli MG1655, BCM treated -Replicate2

value: BCM


title: E. coli MG1655, BCM treated-Replicate1

description:
raw file: US83000164_252030410002_S01_GE2_105_Dec08_2_1.txt
E. coli MG1655, BCM treated -Replicate1


description:
raw file: US83000164_252030410002_S01_GE2_105_Dec08_2_3.txt
E. coli MG1655, WT Rho treated-Replicate1


description:
raw file: US83000164_252030410002_S01_GE2_105_Dec08_1_2.txt
E. coli MG1655, Vector control-Replicate2

value: vector control


title: CFT073_6_C

value: E. coli CFT073

value: Sterile PBS


title: Patient-5-Metastatic -A

value: HNSCC Patient 5

value: Oral cavity metastatic tumor of site A


description:
raw file: US83000164_252030410006_S01_GE2_105_Dec08_1_3.txt
E. coli MG1655 ∆Rac WT, control-Replicate1-Wildtype


title: A1-1 p8

description: Virus induced iPS cells passage8 derived from A-T Disease patient1 fibroblast


title: Patient-5-Normal

value: normal


title: E. coli MG1655, Vector control-Replicate1

description:
raw file: US83000164_252030410002_S01_GE2_105_Dec08_1_2.txt
E. coli MG1655, Vector control -Replicate1


title: LOXL2 delta 72

city: Shantou

first: Haiying

last: Zou

state: Guangdong

address: 22 Xinling Road

department: Department of Biochemistry and Molecular Biology

institute: Shantou University Medical College

description: Gene expression data from KYSE150 cells expressing LOXL2 delta72

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

scan_protocol: GeneChips were scanned using the Affymetrix® GeneChip® Command Console® (AGCC) version 3.0

data_processing: The data were analyzed with Partek GS 6.5 using Affymetrix Expression Console and global scaling as normalization method.

source_name: KYSE150 cells expressing LOXL2 delta72

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3'IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: cell lines were maintained in RPMI 1640 medium (Invitrogen) containing 10% fetal calf serum (FCS)at 5% CO2 at 37℃

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

treatment_protocol: KYSE 150 cells were transfected with vector, pcDNA3.1 LOXL2 WT or pcDNA3.1 LOXL2 delta72, respectively. After 48 hours transfection, RNA extractions were carried out, and the expressions of LOXL2 were examined by RT-PCR. The samples were sent to perfor hybridization on Affymetrix microarrays.

tag: cell line

value: human esophageal squamous carcinoma cell line KYSE150

tag: genotype/variation

value: LOXL2 delta72


title: Patient-5-Metastatic -B

value: Oral cavity metastatic tumor of site B


title: LOXL2 WT

description: Gene expression data from KYSE150 cells expressing LOXL2WT

source_name: KYSE150 cells expressing LOXL2 WT

value: LOXL2 WT


title: Control

description: Gene expression data from KYSE150 cells

source_name: KYSE150 cells control

value: control


title: hyb13811

status: Public on Mar 27 2016

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of purified and labeled cRNA (Cy3 label: 825ng; Cy5 label: 825ng) was hybridised on Agilent's Whole Mouse Genome (4x44K v2) arrays 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: Prior to normalization, data from control spots was removed. We used the processed signals obtained with the Agilent Feature extraction software (version 10.7.3.1). The presented values are log2-(Cy5/Cy3)-ratios.

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) or Cyanine 5-CTP (Cy5) in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent).

extract_protocol: Gen Elute Mammalian total RNA kit (Sigma)

value: mixed strain

value: conditional liver NIPP1 KO

value: male

value: 2 months

value: untreated


title: Patient-1-Primary -B

value: HNSCC Patient 1

value: laryngeal primary tumor of site B


title: Patient-1-Normal

value: blood

tag: tissue type


title: hyb13808

value: liver


title: hyb13809

source_name: Liver_male_2month_ E111_LKO


title: WT Ly6C-hi monocytes

city: Ann Arbor

first: Sergey

last: Seregin

state: MI

address: 1150 E Medical Center Drive

institute: University of Michigan

description: gene expression data from WT lamina propria sorted CD11b+Ly6C-hi CD3- Ly6G- inflammatory monocytes

hyb_protocol: Following labeling procedure, 3 ug of cDNA were hybridized at 48C on Mouse Gene ST 2.1 arrays, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267)

data_processing: Data was analyzed using the oligo Bioconductor package implemented in the R-statistical environment version 3.1.1. RMA was used to fit log2 transformed expression values

source_name: lamina propria of WT mice, day 10 of AOM/2%DSS

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico kit protocol (GeneChip® WT Pico Reagent Kit Manual P/N 703262 Rev. 1) from 10 ng total RNA

growth_protocol: mice were first injected with 10 mg/kg AOM(Sigma) i.p., followed by 5days of 2% DSS starting on day 5. LP cells were isolated from WT or Nlrp6-/- mice at day 10 of AOM/2%DSS. Ly6Chi monocytes were sorted on a FACS AriaIII at the flow cytometry core facility (University of Michigan). RNA from sorted cells was extracted using RNeasy Micro Kit (Qiagen), and contaminated DNA was removed using a DNA-free kit (Ambion). cDNA was prepared from 10 ng total RNA using the NuGen WT-Pico V2 kit (Ovation PicoSL WTA System V2 P/N 3312). Biotinylated single-stranded cDNA was then prepared from 3 μg cDNA (Encore Biotin Module; catalog nos. 4200-12, 4200-60, and 4200-A01). Single-stranded cDNA was then fragmented, and 3.7 μg cDNA was hybridized for 20 h at 48 °C on Mouse Gene ST 2.1 strip arrays using the Affymetrix Gene Atlas System (software version 1.0.4.267). Arrays were scanned using the same system. Expression values were calculated using a robust multiarray average (RMA). RMA was calculated using the oligo package of bioconductor in R (Version 2.15.1; www.R-project.org). Ratios were generated using normalized raw expression values and then log2 transformed.

value: WT

value: colon


title: hyb13810


title: DM_HF_RBX_10wk, biological rep3

status: Public on Mar 26 2016

city: Boston

first: George

last: King

state: Massachusetts

address: 1 Joslin Place Room 440

institute: Joslin Diabetes Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. The target scaling for all probesets (TGT) was set to 1500.

source_name: STZ stimulated diabetic APOE-/- mouse fed with high fat diet plus RBX for 10 wks from 8 wks old

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: APOE-/- mice purcahsed from The Jackson Laboratory (JAX) at 5wks old and housed in Joslin animal facilities; started being fed with high fat diet (Research Diets, Inc, Cat#D12079B) with or without RBX at age of 8wks for a duration of 10wks.

treatment_protocol: Diabetes was indused at age of 6wks by STZ.

value: high fat diet plus RBX for 10 wks

value: whole aorta

value: APOE-/- mice

value: 18 weeks old

tag: disease state

value: STZ stimulated diabetic


title: DM_HF_RBX_10wk, biological rep4


title: Patient-1-Primary -A

value: laryngeal primary tumor of site A


title: MG1655 G181D NusA BR2, treated

description:
pooled whole cell lysate
MG1655 G181D NusA biological replicate2, treated

hyb_protocol: 4000 ng of labeled Cyanine 3-CTP cRNAs  were fragmented to an average size of approximately 50 to 100 nucleotides with fragmentation buffer at 60°C for 30 minutes and the reaction was stopped by adding 2X GE HI-RPM hybridization buffer (Agilent Technologies, In situ Hybridization kit, Part Number5190-0404).The samples were pipetted onto the gasket slide and hybridized onto array (AMADID G4816A_072220). The hybridization was carried out at 65°C for 16 hours.After hybridization, the slides were washed using Gene Expression Wash Buffer1 (Agilent Technologies, Part Number 5188-5325) at room temperature for 1 minute and Gene Expression Wash Buffer 2 (Agilent Technologies, Part Number 5188-5326) at 37oC for 1 minute. The slides were then washed with Acetonitrile for 30 seconds.

label_protocol: The sample labeling was performed using Quick-Amp Labeling Kit, One Color (Agilent Technologies, Part Number: 5190-0442). 500ng of each samples were denatured along with WT primer with a T7 polymerase promoter (T7 polymerase is extremely promoter-specific. The WT primer mix provided in the kit contains a mixture of oligo dT and random nucleotide-based T7 promoter primers, thus enabling robust generation of cRNA from templates of both eukaryotic and prokaryotic origin.)The cDNA master mix was added to the denatured RNA sample and incubated at 40°C for 2 hours for double stranded cDNA synthesis.The cDNA synthesis reaction was stopped at 65°C for 15 min. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP incorporated during this step and incubated at 40°C for 2:30 hours. The Cyanine 3-CTP labeled cRNA sample was purified using Qiagen RNeasy column (Qiagen, Cat No: 74106). The concentration of cRNA and dye incorporation were determined using Nanodrop-1000

value: G181D NusA


title: Nlrp6-/- Ly6C-hi monocytes

description: gene expression data fromNlrp6-/-  lamina propria sorted CD11b+Ly6C-hi CD3- Ly6G- inflammatory monocytes

source_name: lamina propria ofNlrp6-/- mice, day 10 of AOM/2%DSS

extract_protocol: RNA from sorted cells was extracted using RNeasy Micro Kit (Qiagen)

value: Nlrp6-/- mice


title: DM_HF_RBX_10wk, biological rep1


title: MG1655 G181D NusA BR1, treated

description:
pooled whole cell lysate
MG1655 G181D NusA biological replicate1, treated


title: DM_HF_10wk, biological rep3

source_name: STZ stimulated diabetic APOE-/- mouse fed with high fat diet for 10 wks from 8 wks old

value: high fat diet for 10 wks


title: DM_HF_10wk, biological rep2


title: DM_HF_10wk, biological rep4


title: DM_HF_10wk, biological rep1


title: NDM_HF_RBX_10wk, biological rep3

source_name: Non diabetic APOE-/- mouse fed with high fat diet plus RBX for 10 wks from 8 wks old

value: non diabetic


title: NDM_HF_RBX_10wk, biological rep4


title: Patient-1-Metastatic -A

value: laryngeal metastatic tumor of site A


title: MG1655 R258C NusA BR2, treated

description:
pooled whole cell lysate
MG1655 R258C NusA biological replicate2, treated

value: R258C NuSA


title: NDM_HF_RBX_10wk, biological rep2


title: DM_HF_RBX_10wk, biological rep2


title: MG1655 WT NusA BR1, control

description:
pooled whole cell lysate
MG1655 WT NusA biological replicate1, control

value: wild type NusA


title: NDM_HF_RBX_10wk, biological rep1


title: NDM_HF_10wk, biological rep2

source_name: Non diabetic APOE-/- mouse fed with high fat diet for 10 wks from 8 wks old


title: MG1655 WT NusA BR2, control

description:
pooled whole cell lysate
MG1655 WT NusA biological replicate2, control


title: 5GFP_GFP- DP

city: Leiden

first: Martijn

last: Cordes

state: Zuid-Holland

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: Leiden University Medical Centre

hyb_protocol: Fragmented cDNA was hybridized onto Affymetrix Gene Atlas human U219 arrays. Microarray analysis was done in accordance with previously described guidelines (Staal, 2006 leukemia) by the I-BFM-SG Task Force on gene expression profiling.

scan_protocol: The GeneChips were scanned in an AffymetrixGeneChip Scanner 3000 7G.

data_processing: RAW probe intensity values was measured in two batches. Raw data is normalized per batch with Robust Multi-array Average (RMA), and batch correction is applied using Combat. Probe intensity values are subsequently mean centered per probe set. Gene symbols are mapped using MM9. As a result of the normalization, intensities higher than 0 are relatively up-regulated, and intensities lower than 0 are relatively down-regulated.

source_name: IRES-GFP DP cells

label_protocol: RNA was amplified using the Nugen Ovation V2 system, according to manufacturer's instructions and the resulting product was biotin labeled using the Nugen Encore Biotin system.

extract_protocol: RNA was isolated using the Qiagen RNeasy mini kit or micro kit according to manufacturer protocol (Qiagen). cDNA was prepared using SuperScript III and random primers (Life Technologies, Bleiswijk, The Netherlands). For qRT-PCR, the Universal Probe Library (Roche Diagnostics, Almere, The Netherlands) was used to design primer/probe combinations (except for ABL). Samples were run on the StepOnePlus machine (Applied Biosystems, Life Technologies, Bleiswijk, The Netherlands) using the TaqMan® Universal Master Mix II with UNG (Applied Biosystems). ABL was used as housekeeping gene. The following primers were used: LMO2 Forward 5’-CGAAAGGAAGAGCCTGGAC-3’ Reverse 5’-AAGTAGCGGTCCCAATGTT-3’, HES1 Forward 5’-GAAGCACCTCCGGAACCT-3’ Reverse 5’-GTCACCTCGTTCATGCACTC-3’, ABL as described before21.

treatment_protocol: Virus of LZRS-IRES-GFP and LZRS-LMO2-IRES-GFP were produced as described21. Isolated CD34+ cells were cultured overnight in StemSpan serum-free expansion medium (StemSpan-SFEM, StemCell Technologies Inc., Vancouver, BC, Canada) in the presence of 10 ng/mL stem cell factor (SCF, a gift from Amgen, Thousand Oakes, CS, USA), 20 ng/mL recombinant human thrombopoietin (rhTPO, R&D Systems, Abingdon, UK), 20 ng/mL recombinant mouse insulin-like growth factor 2 (rmIGF-2, R&D Systems) and 10 ng/mL recombinant human fibroblast growth factor-acidic (rhFGF-1, Peprotech, Rocky Hill, NJ, USA). Retronectin (50 µg/mL,Takara Bio Inc, Otsu, Japan) was coated on non-tissue culture treated 48-wells plates (BD Falcon, Bedford, MA, USA) o/n at 4°C. Virus (500 µL) was centrifuged onto the plate for 2 hours at 32°C 1000xg. Supernatant was removed and 1.5*105 isolated cells were added per well and transduced for 2 days.

value: IRES-GFP DP cells


title: 10LMO2_GFP+ DP

source_name: LMO2-IRES-GFP cells

growth_protocol: Virus of LZRS-IRES-GFP and LZRS-LMO2-IRES-GFP were produced as described21. Isolated CD34+ cells

value: LMO2-IRES-GFP cells


title: MG1655 R258C NusA BR1, treated

description:
pooled whole cell lysate
MG1655 R258C NusA biological replicate1, treated


title: NDM_HF_10wk, biological rep1


title: 2LMO2_GFP+ DP


title: Wild type rep1.1

city: Helsinki

first: Vinod

last: Kumar

address: Vinkinkaari 9

department: Developmental Biology

country: Finland

institute: University of Helsinki

description: second replica of 1

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: mouse keratinocyte

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

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: Keratinocytes were isolated from E18.5 embryo skin and cultured in keratinocytes specific media until confluency. They were washed in PBS and then trizolated.

tag: cells

value: Keratinocytes

value: wild type


title: NDM_HF_10wk, biological rep4


title: Krt type I KO rep1.1

description: second replica of 1

value: Type I keratin KO


title: RBFOX2 knockdown shRNA3 Rep3

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

hyb_protocol: Hybridization and washing was performed as described in the GeneChip WT PLUS Reagent Kit (Affymetrix).

scan_protocol: Scanning was performed on a 7G scanner and imaged with the AGCC portal.

data_processing:
Cel files were analyzed using Expression Console (build 1.4.1.46, Affymetrix), with RMA normalization and DABG probe-level detection. Only probesets with detection p-value ≤ 0.05 in more than half of the microarray samples were considered for downstream analysis. All probes corresponding to cassette exons profiled on the microarray (comprising exclusion junction, upstream and downstream inclusion junction, and inclusion exonic probes) were identified and normalized against the average signal on a per-gene basis to remove gene expression changes. Student’s t-test was performed on residuals for inclusion probes and exclusion probes separately to identify robust splicing changes, which were quantified by SepScore ( defined as the normalized change in exclusion minus the normalized change in inclusion).
HTA-2_0.r1.pgf
HTA-2_0.r1.Psrs.mps
RMA probeset-level signal estimates, DABG detection flag (Absent or Present), and DABG detection p-value obtained from 'Alt Splice Analysis' performed in Affymetrix Expression Console build 1.4.1.46.

source_name: RBFOX2 knockdown shRNA3

label_protocol: Microarray sample preparation was performed using Ambion WT Expression Kit (Thermo Fisher Scientific). Labeling was performed using GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

growth_protocol: 293T cells were grown in standard media (DMEM + 10% FBS + 1X Penicillin Streptomycin).

extract_protocol: RNA was extracted by standard Trizol extraction.

treatment_protocol: Knockdowns were performed by transforming shRNA plasmid along with lentivirus packaging plasmids in 293T cells, filtering (.45 micron) supernatant, and infecting a new population of 293T cells. After 48 hours, infected cells were Puromycin selected (1 ug / mL) for 10 days, after which RNA and protein were harvested.

tag: protocol

value: RBFOX2 knockdown


title: Wild type rep1

description: replica 1


title: Wild type rep2

description: replica 2


title: Wild type rep3

description: replica 3


title: Patient-5-Primary -A

value: HNSCC Patient 5

value: Oral cavity primary tumor of site A


title: Patient-1-Metastatic -B

value: HNSCC Patient 1

value: laryngeal metastatic tumor of site B


title: HFT_D27

city: Reus

first: Antonio

last: Caimari

state: Tarragona

address: Avinguda Universitat, 1

institute: Centre Tecnològic de Nuctrició i Salut

hyb_protocol: Microarrays where hybridized and washed according to manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

organism: Rattus norvegicus

source_name: epididymal white adipose tissue, at sacrifice, ad libitum conditions

label_protocol: One Color Low Input Quick Amp Labeling Protocol v 6.5 (Agilent)

growth_protocol: Thirty-two 11-weeks-old female virgin rats (Charles River Laboratories, Barcelona, Spain) were mated with males until impregnation, confirmed by the presence of sperm in vaginal smears, and designed as day 0 of pregnancy. Afterwards, the rats were housed singly and were divided into four groups (n=8) depending on the diet and the treatment received during pregnancy and lactation. Two groups were fed with a STD (2.99 Kcal/g; A04, Panlab, Barcelona, Spain) and were orally supplemented every day with either low-fat condensed milk (vehicle) or 25 mg of GSPE per kg body weight dissolved in low-fat condensed milk. The other two groups were fed with a HFD (5.24 Kcal/g; D12492, Research Diets, Inc, NJ, USA) and supplemented with either the vehicle or the GSPE at 25 mg per kg body weight. The morning on which new born litters were found was designated as day 0 of lactation and the litter size was adjusted to ten pups per dam. On day 21 of lactation, after weaning, the male pups were distributed into four experimental groups (n=8) depending on the diet and the treatment received for their mothers: ST group, corresponding to offspring from dams fed the STD and treated with the vehicle; STT group, corresponding to offspring from dams fed the ST and treated with GSPE; HF group, corresponding to offspring from dams fed the HFD and treated with the vehicle; HFT group, corresponding to offspring from dams fed the HFD and treated with GSPE. All the experimental groups were fed with the same diets of their mothers until their sacrifice, at the age of 30 days.

extract_protocol: EWAT total RNA was extracted using Tripure Reagent (Roche Diagnostic Barcelona, Spain) and purified with Qiagen RNeasy Mini Kit spin columns (Izasa, Barcelona, Spain). RNA yield was quantified on a NanoDrop ND-1000 spectrophotometer (NadroDrop Technologies, Wilmington, DE, USA) and its integrity was measured on an Agilent 2100 Bioanalyzer with RNA 6000 Nano chips (Agilent Technologies, South Queensferry, UK).

treatment_protocol: The animals were sacrificed in ad libitum conditions under anaesthesia (pentobarbital sodium, 50 mg/kg body weight). The blood was collected by cardiac puncture and the plasma was obtained by centrifugation and stored at -20°C until analysis. The liver and the different white adipose tissue depots (retroperitoneal –RWAT-, MWAT, epididymal –EWAT- and inguinal –IWAT-) were rapidly removed after death, weighed, frozen in liquid nitrogen and stored at -70°C until RNA analysis.

value: male

value: epididymal white adipose tissue

value: offspring from dams fed a high fat diet and treated with a grape seed procyanidin extract dissolved in low-fat condensed milk (GSPE, 25 mg/kg body weight) during pregnancy and lactation

value: 30 days


title: 2819-2 Type II keratin KO

description: replica 3

source_name: Mouse back skin

extract_protocol: Total 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.

value: Back skin

value: Type II keratin KO


title: RBFOX2 knockdown shRNA2 Rep1

source_name: RBFOX2 knockdown shRNA2


title: RBFOX2 knockdown shRNA1 Rep3

source_name: RBFOX2 knockdown shRNA1


title: Krt type I KO rep1

description: replica 1


title: Non-target control Rep2

source_name: Non-target control

value: shRNA SHC016

value: control


title: HF_D14

value: offspring from dams fed a high fat diet and treated with a placebo (low-fat condensed milk) during pregnancy and lactation


title: HFT_D36


title: 2818-1 Type II keratin KO

description: replica 2


title: RBFOX2 knockdown shRNA1 Rep1


title: HFT_D28


title: 9LMO2_GFP++ DP

value: LMO2-IRES-GFP cells


title: Non-target control Rep3


title: Krt type I KO rep3

description: replica 3

value: Keratinocytes


title: HF_D35


title: 2794-1 Type II keratin KO

description: replica 1


title: 2819-4 Wild type II

description: replica 3

value: wild type


title: Krt type I KO rep2

description: replica 2

value: Type I keratin KO


title: HF_D13


title: HFT_D26


title: 2794-2 Wild type II

description: replica 1


title: 2818-2 Wild type II

description: replica 2


title: HF_D12


title: NDM_HF_10wk, biological rep3

value: high fat diet for 10 wks

value: whole aorta

value: APOE-/- mice

value: 18 weeks old

value: non diabetic


title: RBFOX2 knockdown shRNA2 Rep3

value: RBFOX2 knockdown


title: RBFOX2 knockdown shRNA3 Rep1


title: P1_B5_tissue_(Hs35b_P02R_v01)

status: Public on Mar 25 2016

first: Arturas

last: Petronis

address: 250 College St Rm606

institute: Centre for Addiction and Mental Health

description:
Sample name: T_9
Enterocytes extracted using Warm Chelating method

hyb_protocol: 7 ug ofDNA was hybridized on GeneChip Human Tiling 2.0R Array (B array; Hs35b_P02R) or Mouse Tiling 2.0R Array (A array; Mm35b_P01R) as indicated in ChIP protocol

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 Targeted Genotyping System (GCS 3000 TF system)

data_processing:
Array Data were quantile normalized and log2 transformed. A probe's center defines a 200bp window. The Tiling array intensities were extracted using R2.15.2 and the bioconductor package "AffyTiling". Probe sequences were re-mapped to Hg19 for human and Mm10 for mouse using mrfast2.6.1.0 with maximum edit distance 0. Probe intensities were then smoothed using a pseudomedian filter with a bandwidth of 401 bp.
*.smooth.txt.gz: tab-delimited text files containing post-processed probe intensities, with columns: chromosome, start, intensity

source_name: jejunum lacking enterocytes

label_protocol: GeneChip Double-stranded DNA Terminal Labeling kit (Affymetrix)

extract_protocol: DNA was extracted with standard phenol chloroform and ethanol preicpitation method

treatment_protocol: Enterocytes were extracted from jejunum surgical samples. For each sample, the remaining tissue also extracted and is referred to as jejunum lacking enterocytes

value: mTAG enrichment protocol

tag: individual

tag: sample source

value: Lithuanian University of Health Sciences

tag: Sex

value: F

value: TT

value: jejunum lacking enterocytes


title: HFT_D25

value: male

value: epididymal white adipose tissue

value: offspring from dams fed a high fat diet and treated with a grape seed procyanidin extract dissolved in low-fat condensed milk (GSPE, 25 mg/kg body weight) during pregnancy and lactation

tag: age

value: 30 days


title: RBFOX2 knockdown shRNA2 Rep2


title: 2602-1 Type I keratin KO

description: replica 3

tag: strain

value: Back skin


title: HFT_D24


title: RBFOX2 knockdown shRNA3 Rep2


title: P1_B1_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_7
Enterocytes extracted using Warm Chelating method

value: CC


title: P1_A11_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_6
Enterocytes extracted using Warm Chelating method


title: P1_B3_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_8
Enterocytes extracted using Warm Chelating method

value: CT


title: HF_D10

value: offspring from dams fed a high fat diet and treated with a placebo (low-fat condensed milk) during pregnancy and lactation


title: P2_E9_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_59
Enterocytes extracted using Warm Chelating method


title: P2_E11_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_60
Enterocytes extracted using Warm Chelating method


title: Non-target control Rep1

value: shRNA SHC016

value: control


title: HF_D11


title: P2_E5_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_57
Enterocytes extracted using Warm Chelating method


title: P2_E1_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_55
Enterocytes extracted using Warm Chelating method


title: P2_D11_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_54
Enterocytes extracted using Warm Chelating method

value: M


title: 2705-4 Wild type I

description: replica 2

value: wild type


title: 2705-1 Wild type I

description: replica 1


title: 2602-5 Wild type I

description: replica 3


title: HF_D9


title: P2_E3_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_56
Enterocytes extracted using Warm Chelating method

value: mTAG enrichment protocol


title: 2705-2 Type I keratin KO

description: replica 1

value: Type I keratin KO


title: HF_D8


title: HFT_D23


title: P2_D9_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_53
Enterocytes extracted using Warm Chelating method

value: Lithuanian University of Health Sciences

value: F


title: P2_D7_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_52
Enterocytes extracted using Warm Chelating method

value: jejunum lacking enterocytes


title: P2_D3_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_50
Enterocytes extracted using Warm Chelating method


title: P2_D5_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_51
Enterocytes extracted using Warm Chelating method


title: P2_D1_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_49
Enterocytes extracted using Warm Chelating method


title: P2_C11_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_48
Enterocytes extracted using Warm Chelating method


title: P2_C7_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_46
Enterocytes extracted using Warm Chelating method


title: P2_E7_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_58
Enterocytes extracted using Warm Chelating method

value: TT


title: P2_C3_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_44
Enterocytes extracted using Warm Chelating method


title: P1_A7_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_4
Enterocytes extracted using Warm Chelating method


title: P2_B7_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_40
Enterocytes extracted using Warm Chelating method


title: P2_B3_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_38
Enterocytes extracted using Warm Chelating method


title: P2_B1_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_37
Enterocytes extracted using Warm Chelating method


title: P1_F11_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_36
Enterocytes extracted using Warm Chelating method


title: P1_F9_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_35
Enterocytes extracted using Warm Chelating method


title: P1_F7_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_34
Enterocytes extracted using Warm Chelating method


title: RBFOX2 knockdown shRNA1 Rep2

value: RBFOX2 knockdown


title: P1_F5_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_33
Enterocytes extracted using Warm Chelating method


title: P1_A9_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_5
Enterocytes extracted using Warm Chelating method


title: P1_F3_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_32
Enterocytes extracted using Warm Chelating method


title: P1_E9_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_29
Enterocytes extracted using Warm Chelating method


title: P1_F1_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_31
Enterocytes extracted using Warm Chelating method


title: P1_E7_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_28
Enterocytes extracted using Warm Chelating method


title: P1_E11_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_30
Enterocytes extracted using Warm Chelating method


title: P1_A5_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_3
Enterocytes extracted using Warm Chelating method


title: P1_E1_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_25
Enterocytes extracted using Warm Chelating method


title: P1_D9_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_23
Enterocytes extracted using Warm Chelating method


title: P1_E3_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_26
Enterocytes extracted using Warm Chelating method


title: P1_D11_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_24
Enterocytes extracted using Warm Chelating method


title: P2_B5_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_39
Enterocytes extracted using Warm Chelating method


title: P2_C1_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_43
Enterocytes extracted using Warm Chelating method


title: P1_D5_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_21
Enterocytes extracted using Warm Chelating method


title: P1_D7_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_22
Enterocytes extracted using Warm Chelating method


title: P1_C11_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_18
Enterocytes extracted using Warm Chelating method


title: P1_C9_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_17
Enterocytes extracted using Warm Chelating method


title: P1_D3_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_20
Enterocytes extracted using Warm Chelating method


title: P1_C7_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_16
Enterocytes extracted using Warm Chelating method


title: P1_C3_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_14
Enterocytes extracted using Warm Chelating method


title: P1_B11_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_12
Enterocytes extracted using Warm Chelating method


title: P1_B7_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_10
Enterocytes extracted using Warm Chelating method


title: P1_A1_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_1
Enterocytes extracted using Warm Chelating method


title: P1_B9_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_11
Enterocytes extracted using Warm Chelating method


title: P2_F3_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_T_8
Enterocytes extracted using Warm Chelating method


title: P1_E5_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_27
Enterocytes extracted using Warm Chelating method


title: P2_F10_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_T_60
Enterocytes extracted using Warm Chelating method


title: P2_F1_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_T_5
Enterocytes extracted using Warm Chelating method


title: P2_F2_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_T_6
Enterocytes extracted using Warm Chelating method


title: P2_F9_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_T_59
Enterocytes extracted using Warm Chelating method


title: P2_F7_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_T_42
Enterocytes extracted using Warm Chelating method


title: P1_G11_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_T_48
Enterocytes extracted using Warm Chelating method


title: P1_G5_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_T_33
Enterocytes extracted using Warm Chelating method


title: P1_G7_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_T_34
Enterocytes extracted using Warm Chelating method


title: P2_F6_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_T_29
Enterocytes extracted using Warm Chelating method


title: P1_G12_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_C_48
Enterocytes extracted using Warm Chelating method

source_name: enterocytes

tag: relative lactase mrna expression

value: enterocytes


title: P1_G3_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_T_32
Enterocytes extracted using Warm Chelating method

tag: tissue


title: P1_G10_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_C_35
Enterocytes extracted using Warm Chelating method


title: P1_C5_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_15
Enterocytes extracted using Warm Chelating method


title: P1_D1_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_19
Enterocytes extracted using Warm Chelating method


title: P1_G8_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_C_34
Enterocytes extracted using Warm Chelating method


title: P1_C1_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_13
Enterocytes extracted using Warm Chelating method


title: P1_G4_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_C_32
Enterocytes extracted using Warm Chelating method


title: P2_H9_Total input_(Hs35b_P02R_v01)

description:
Sample name: I_T_48
Enterocytes extracted using Warm Chelating method

value: Total input (unenriched)


title: P2_F12_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_C_27
Enterocytes extracted using Warm Chelating method


title: P2_F11_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_C_18
Enterocytes extracted using Warm Chelating method


title: P2_H5_Total input_(Hs35b_P02R_v01)

description:
Sample name: I_T_34
Enterocytes extracted using Warm Chelating method


title: P2_H7_Total input_(Hs35b_P02R_v01)

description:
Sample name: I_T_35
Enterocytes extracted using Warm Chelating method


title: P2_H3_Total input_(Hs35b_P02R_v01)

description:
Sample name: I_T_33
Enterocytes extracted using Warm Chelating method


title: P2_H10_Total input_(Hs35b_P02R_v01)

description:
Sample name: I_C_48
Enterocytes extracted using Warm Chelating method


title: P2_B11_tissue_(Hs35b_P02R_v01)

description:
Sample name: T_42
Enterocytes extracted using Warm Chelating method


title: P2_H8_Total input_(Hs35b_P02R_v01)

description:
Sample name: I_C_35
Enterocytes extracted using Warm Chelating method


title: P1_G9_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_T_35
Enterocytes extracted using Warm Chelating method


title: P2_H1_Total input_(Hs35b_P02R_v01)

description:
Sample name: I_T_32
Enterocytes extracted using Warm Chelating method


title: P2_H4_Total input_(Hs35b_P02R_v01)

description:
Sample name: I_C_33
Enterocytes extracted using Warm Chelating method


title: P1_B6_cells_(Hs35b_P02R_v01)

description:
Sample name: C_9
Enterocytes extracted using Warm Chelating method


title: P2_F5_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_T_12
Enterocytes extracted using Warm Chelating method


title: P2_H2_Total input_(Hs35b_P02R_v01)

description:
Sample name: I_C_32
Enterocytes extracted using Warm Chelating method


title: P2_H6_Total input_(Hs35b_P02R_v01)

description:
Sample name: I_C_34
Enterocytes extracted using Warm Chelating method


title: P2_F4_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_T_11
Enterocytes extracted using Warm Chelating method


title: P1_B4_cells_(Hs35b_P02R_v01)

description:
Sample name: C_8
Enterocytes extracted using Warm Chelating method


title: P2_E12_cells_(Hs35b_P02R_v01)

description:
Sample name: C_60
Enterocytes extracted using Warm Chelating method


title: P1_G6_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_C_33
Enterocytes extracted using Warm Chelating method


title: P2_E10_cells_(Hs35b_P02R_v01)

description:
Sample name: C_59
Enterocytes extracted using Warm Chelating method


title: P1_B2_cells_(Hs35b_P02R_v01)

description:
Sample name: C_7
Enterocytes extracted using Warm Chelating method


title: P1_A12_cells_(Hs35b_P02R_v01)

description:
Sample name: C_6
Enterocytes extracted using Warm Chelating method


title: P2_E8_cells_(Hs35b_P02R_v01)

description:
Sample name: C_58
Enterocytes extracted using Warm Chelating method


title: P2_E4_cells_(Hs35b_P02R_v01)

description:
Sample name: C_56
Enterocytes extracted using Warm Chelating method


title: P2_E2_cells_(Hs35b_P02R_v01)

description:
Sample name: C_55
Enterocytes extracted using Warm Chelating method


title: P2_D8_cells_(Hs35b_P02R_v01)

description:
Sample name: C_52
Enterocytes extracted using Warm Chelating method


title: P2_D6_cells_(Hs35b_P02R_v01)

description:
Sample name: C_51
Enterocytes extracted using Warm Chelating method


title: P2_D10_cells_(Hs35b_P02R_v01)

description:
Sample name: C_53
Enterocytes extracted using Warm Chelating method


title: P2_E6_cells_(Hs35b_P02R_v01)

description:
Sample name: C_57
Enterocytes extracted using Warm Chelating method


title: P2_F8_replicate_(Hs35b_P02R_v01)

description:
Sample name: R_T_58
Enterocytes extracted using Warm Chelating method


title: P2_C12_cells_(Hs35b_P02R_v01)

description:
Sample name: C_48
Enterocytes extracted using Warm Chelating method


title: P2_C2_cells_(Hs35b_P02R_v01)

description:
Sample name: C_43
Enterocytes extracted using Warm Chelating method


title: P2_C8_cells_(Hs35b_P02R_v01)

description:
Sample name: C_46
Enterocytes extracted using Warm Chelating method


title: P2_D2_cells_(Hs35b_P02R_v01)

description:
Sample name: C_49
Enterocytes extracted using Warm Chelating method


title: P2_C4_cells_(Hs35b_P02R_v01)

description:
Sample name: C_44
Enterocytes extracted using Warm Chelating method


title: P1_A10_cells_(Hs35b_P02R_v01)

description:
Sample name: C_5
Enterocytes extracted using Warm Chelating method


title: P2_B6_cells_(Hs35b_P02R_v01)

description:
Sample name: C_39
Enterocytes extracted using Warm Chelating method


title: P2_B4_cells_(Hs35b_P02R_v01)

description:
Sample name: C_38
Enterocytes extracted using Warm Chelating method


title: P1_F10_cells_(Hs35b_P02R_v01)

description:
Sample name: C_35
Enterocytes extracted using Warm Chelating method


title: P1_F6_cells_(Hs35b_P02R_v01)

description:
Sample name: C_33
Enterocytes extracted using Warm Chelating method


title: P1_F4_cells_(Hs35b_P02R_v01)

description:
Sample name: C_32
Enterocytes extracted using Warm Chelating method


title: P2_B8_cells_(Hs35b_P02R_v01)

description:
Sample name: C_40
Enterocytes extracted using Warm Chelating method


title: P1_A6_cells_(Hs35b_P02R_v01)

description:
Sample name: C_3
Enterocytes extracted using Warm Chelating method


title: P2_D12_cells_(Hs35b_P02R_v01)

description:
Sample name: C_54
Enterocytes extracted using Warm Chelating method


title: P1_F2_cells_(Hs35b_P02R_v01)

description:
Sample name: C_31
Enterocytes extracted using Warm Chelating method


title: P1_E12_cells_(Hs35b_P02R_v01)

description:
Sample name: C_30
Enterocytes extracted using Warm Chelating method


title: P1_E10_cells_(Hs35b_P02R_v01)

description:
Sample name: C_29
Enterocytes extracted using Warm Chelating method


title: P2_D4_cells_(Hs35b_P02R_v01)

description:
Sample name: C_50
Enterocytes extracted using Warm Chelating method


title: P1_A8_cells_(Hs35b_P02R_v01)

description:
Sample name: C_4
Enterocytes extracted using Warm Chelating method


title: P1_E4_cells_(Hs35b_P02R_v01)

description:
Sample name: C_26
Enterocytes extracted using Warm Chelating method


title: P1_E6_cells_(Hs35b_P02R_v01)

description:
Sample name: C_27
Enterocytes extracted using Warm Chelating method


title: P1_D12_cells_(Hs35b_P02R_v01)

description:
Sample name: C_24
Enterocytes extracted using Warm Chelating method


title: P2_B2_cells_(Hs35b_P02R_v01)

description:
Sample name: C_37
Enterocytes extracted using Warm Chelating method


title: P1_E2_cells_(Hs35b_P02R_v01)

description:
Sample name: C_25
Enterocytes extracted using Warm Chelating method


title: P1_E8_cells_(Hs35b_P02R_v01)

description:
Sample name: C_28
Enterocytes extracted using Warm Chelating method


title: P2_B12_cells_(Hs35b_P02R_v01)

description:
Sample name: C_42
Enterocytes extracted using Warm Chelating method


title: P1_D10_cells_(Hs35b_P02R_v01)

description:
Sample name: C_23
Enterocytes extracted using Warm Chelating method


title: P1_D8_cells_(Hs35b_P02R_v01)

description:
Sample name: C_22
Enterocytes extracted using Warm Chelating method


title: P1_D6_cells_(Hs35b_P02R_v01)

description:
Sample name: C_21
Enterocytes extracted using Warm Chelating method


title: 2705-6 Type I keratin KO

description: replica 2

value: Back skin


title: P1_D2_cells_(Hs35b_P02R_v01)

description:
Sample name: C_19
Enterocytes extracted using Warm Chelating method


title: P1_C12_cells_(Hs35b_P02R_v01)

description:
Sample name: C_18
Enterocytes extracted using Warm Chelating method


title: P1_F12_cells_(Hs35b_P02R_v01)

description:
Sample name: C_36
Enterocytes extracted using Warm Chelating method

value: CC


title: P1_D4_cells_(Hs35b_P02R_v01)

description:
Sample name: C_20
Enterocytes extracted using Warm Chelating method

value: CT


title: P1_C6_cells_(Hs35b_P02R_v01)

description:
Sample name: C_15
Enterocytes extracted using Warm Chelating method


title: P1_C2_cells_(Hs35b_P02R_v01)

description:
Sample name: C_13
Enterocytes extracted using Warm Chelating method


title: P1_C4_cells_(Hs35b_P02R_v01)

description:
Sample name: C_14
Enterocytes extracted using Warm Chelating method


title: P1_B12_cells_(Hs35b_P02R_v01)

description:
Sample name: C_12
Enterocytes extracted using Warm Chelating method


title: P1_A2_cells_(Hs35b_P02R_v01)

description:
Sample name: C_1
Enterocytes extracted using Warm Chelating method


title: P1_B8_cells_(Hs35b_P02R_v01)

description:
Sample name: C_10
Enterocytes extracted using Warm Chelating method


title: P1_B10_cells_(Hs35b_P02R_v01)

description:
Sample name: C_11
Enterocytes extracted using Warm Chelating method


title: P1_C10_cells_(Hs35b_P02R_v01)

description:
Sample name: C_17
Enterocytes extracted using Warm Chelating method


title: P1_C8_cells_(Hs35b_P02R_v01)

description:
Sample name: C_16
Enterocytes extracted using Warm Chelating method


title: HepG2_6h_DMSO.S32B1G365

city: MASON

first: Jay

middle: Patrick

last: Tiesman

state: OH

address: PO BOX 8006

department: Global Biotechnology

institute: Procter & Gamble

description: Chemical signature/does response study

hyb_protocol: GeneChip targets were hybridized on Affymetrix U219-96 plates using the GeneTitan single-channel instrument and protocols provided by Affymetrix.

scan_protocol: GeneTitan plates were scanned on a GeneTitan single-channel instrument using protocols provided by Affymetrix.

data_processing: Data was processed using the PLIER algorithm implemented from the Affymetrix Command Console Software.

source_name: HepG2 Human Hepatocyte Carcinoma Cell Line

label_protocol: 500 ng of total RNA was converted to Affymetrix GeneChip targets using the Affymetrix IVT-Express kit and protocols provided by Affymetrix.

growth_protocol: HepG2 human hepatocellular carcinoma cells were purchased from  American Type Culture Collection (Manassas, VA) and grown in Eagle’s Minimum Essential Meidum (EMEM) containing phenol red (ATCC, Manassas, VA) supplemented with 10% fetal bovine serum (FBS) (ATCC), 100 U/ml penicillin and 100 μg/ml streptomycin (ATCC) and maintained at 37°C in an atmosphere of 5% CO2.

extract_protocol: Cells were extracted in QIAgen RLT buffer and total RNA was extracted using the Agencourt RNAdvance Tissue protocol implemented on a Beckman FXp robot using methods provided by Beckman Coulter.

treatment_protocol: Cells (5X10E5 cells/well in 12 well cell culture plates (Corning, Corning ,NY) ) were treated with 3 concentrations of chemical or DMSO vehicle for 6 h.

tag: chemical treatment

value: Vorinostat

tag: dose

tag: replicate

value: Male


title: HepG2_6h_DMSO.S32B1G359

description: Chemical signature/does response study

value: Metformin

tag: gender


title: HFT_D22

value: male

value: epididymal white adipose tissue

tag: treatment

value: offspring from dams fed a high fat diet and treated with a grape seed procyanidin extract dissolved in low-fat condensed milk (GSPE, 25 mg/kg body weight) during pregnancy and lactation

value: 30 days


title: HepG2_6h_DMSO.S32B1G351

description: Chemical signature/does response study

tag: cell line


title: HepG2_6h_DMSO.S32B1G356

description: Chemical signature/does response study

value: Phenformin


title: HepG2_6h_DMSO.S32B1G352

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G355

description: Chemical signature/does response study

value: Amoxicillin


title: HepG2_6h_DMSO.S32B1G363

description: Chemical signature/does response study


title: P1_F8_cells_(Hs35b_P02R_v01)

description:
Sample name: C_34
Enterocytes extracted using Warm Chelating method

value: mTAG enrichment protocol

value: Lithuanian University of Health Sciences

value: F

tag: cell type


title: HepG2_6h_DMSO.S32B1G339

description: Chemical signature/does response study

value: DMSO


title: HepG2_6h_DMSO.S32B1G346

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G345

description: Chemical signature/does response study

value: 6 Aminonicotinamide


title: HepG2_6h_DMSO.S32B1G342

description: Chemical signature/does response study

value: Valproic Acid


title: HepG2_6h_DMSO.S32B1G353

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G344

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G343

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G357

description: Chemical signature/does response study

value: Methanol


title: HepG2_6h_DMSO.S32B1G332

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G335

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G340

description: Chemical signature/does response study

value: Desferrioxamine


title: HepG2_6h_DMSO.S32B1G334

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G329

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G341

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G354

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G364

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G358

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G331

description: Chemical signature/does response study

value: Vorinostat


title: HepG2_6h_DMSO.S32B1G333

description: Chemical signature/does response study

value: Male


title: HepG2_6h_DMSO.S32B1G347

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G330

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G327

description: Chemical signature/does response study

value: Metformin


title: HepG2_6h_DMSO.S32B1G322

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G321

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G316

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G315

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G319

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G309

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G305

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G320

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G306

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G311

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G323

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G312

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G308

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G307

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G300

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G328

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G318

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G293

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G310

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G298

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G299

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G303

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G317

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G295

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G296

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G324

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G294

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G297

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G292

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G304

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G291

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G273

description: Chemical signature/does response study

value: Farnesol


title: HepG2_6h_DMSO.S32B1G285

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G287

description: Chemical signature/does response study

value: DHP


title: HepG2_6h_DMSO.S32B1G284

description: Chemical signature/does response study

value: Trenbolone


title: HepG2_6h_DMSO.S32B1G277

description: Chemical signature/does response study

value: Clobetasol


title: HepG2_6h_DMSO.S32B1G270

description: Chemical signature/does response study

value: Chenodeoxychobe Acid


title: HepG2_6h_DMSO.S32B1G268

description: Chemical signature/does response study

value: Flutamide


title: HepG2_6h_DMSO.S32B1G283

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G271

description: Chemical signature/does response study

value: Tamoxifen


title: HepG2_6h_DMSO.S32B1G290

description: Chemical signature/does response study

value: Dihydroxyvitamin 3


title: HepG2_6h_DMSO.S32B1G282

description: Chemical signature/does response study

value: Bisphenol A


title: HepG2_6h_DMSO.S32B1G276

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G288

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G267

description: Chemical signature/does response study

value: Vinblastine


title: HepG2_6h_DMSO.S32B1G265

description: Chemical signature/does response study

value: Imidacloprid


title: HepG2_6h_DMSO.S32B1G278

description: Chemical signature/does response study

value: NaOH

value: DMSO


title: HepG2_6h_DMSO.S32B1G266

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G269

description: Chemical signature/does response study

value: Tetrachlorodibenzo p dioxin


title: HepG2_6h_DMSO.S32B1G281

description: Chemical signature/does response study


title: HepG2_6h_DMSO.S32B1G275

description: Chemical signature/does response study

value: Methotrexate


title: HepG2_6h_DMSO.S32B1G263

description: Chemical signature/does response study

value: Male