title: E9.5 KLF1-/- KLF2-/- erythroid-14

city: Richmond

first: Christopher

last: Pang

address: 401 College Street

institute: Virginia Commonwealth University

description: Comparison between mouse embryonic day 9.5 (E9.5) wild-type, KLF1-/-, KLF1-/- KLF2-/- yolk sac microdissected erythroid precursors

hyb_protocol: Fifteen μg of labeled erythroid RNA was fragmented and 10 μg was hybridized to Affymetrix GeneChip Mouse Genome 430A 2.0 arrays for 18 hours (Affymetrix Inc.). The 8 microarrays were washed and stained with streptavidin–phycoerythrin as described (Redmond et al., Blood Cells Molecules and Diseases 2006, 37:27).

scan_protocol: Image analysis was performed on the E9.5 WT, KLF1-/-, and KLF1-/-KLF2-/- erythroid yolk sac data set using the GeneChip Operating System version 1.4 (GCOS1.1, Affymetrix Inc.). The image of the scanned array was stored as a DAT file using the Affymetrix software.

data_processing: Quality control parameters such as scaling factors used to normalize the chips, average background and noise were also analyzed. The raw intensities for each probe set were stored in electronic formats by the GCOS software. Scaling factors used to normalize the chips to a target value (TGT), and in this study, the TGT was set at 100. Probe set expression summaries were calculated with the Probe set expression summaries were calculated with the Robust Multi-average (RMA) algorithm (Irizarry et al., 2003). RMA expression summaries were obtained for wildtype,  KLF1-/-, and KLF1-/-KLF2-/- erythroid GeneChips using the rma function in the affy package in R/Bioconductor. Thereafter control probe sets were removed leaving 22,626 probe sets for statistical analysis. A moderated t-test was used to compare the 8 WT and 3 KLF1-/- samples using the limma Bioconductor package (Gentleman et al., 2004; Smyth et al., 2004) in the R programming environment (http://www.R-project.org), and to identify the probe sets that were significantly differentially expressed. The Jonckheere-Terpstra test for trend was performed to identify probe sets having significantly decreasing expression across the 8 wild-type, 3 KLF1-/-, and 3 KLF1-/-KLF2-/- samples.

source_name: E9.5 KLF1-/- KLF2-/- erythroid-14

label_protocol: Ten to 20 ng of WT, KLF1-/-, and KLF1-/-KLF2-/- erythroid RNA was used to generate double stranded cDNA with the T7-oligo (dT) primer according to the Affymetrix GeneChip Two cycle target labeling protocol (Affymetrix Inc., Santa Clara, CA, USA). Labeled cRNA yield and purity was determined as described (Redmond et al., 2006).

growth_protocol: Timed-pregnant mice were anesthetized and sacrificed. E9.5 yolk sacs were dissected from the embryo and cryoprotected in PBS with 20% sucrose.

extract_protocol: Total RNA was isolated from WT, KLF1-/-, and KLF1-/-KLF2-/- erythroid cells using reagents from the (ToTALLY RNA isolation kit; Ambion Inc., Austin, TX, USA) and quality assessment by capillary electrophoresis were performed as previously described (Redmond et al., Blood Cells Molecules and Diseases 2006, 37:27).

treatment_protocol: E9.5 yolk sacs tissues were rinsed once in 1:1 20% sucrose PBS:Optimal Cutting Temperature freezing media (OCT, Tissue-Tek), then OCT alone and frozen. A small portion of the embryo tail was used for PCR genotyping. Eight micron E9.5 sections were stained with the LCM frozen section staining kit (Molecular Devices, Mountain View, CA, USA) and used for laser capture dissection experiments. The ArcturusXT™ laser capture microdissection (LCM) instrument (Applied Biosystems, Inc.) was used to isolate erythroid cells from yolk sac cryosections obtained from WT, KLF1-/-, and KLF1-/-KLF2-/- embryos. The manufacturer’s protocol was followed for preparing the instrument, isolating the cells, and visually inspecting the isolated erythroid cells on the LCM cap.

tag: strain

value: FVB/N

tag: genotype/variation

value: embryonic day 9.5

value: erythroid cells


title: RSV_4

status: Public on Mar 12 2012

type: RNA

city: COLUMBUS

first: IOANNIS

last: IOANNIDIS

state: OH

address: 700 CHILDRENS DRIVE

department: VACCINES AND IMMUNITY

country: USA

institute: NATIONWIDE CHILDRENS HOSPITAL

description: gene expression after 2h rsv infection (harvested 48h after treatment)

hyb_protocol: Hybridization was performed following the manufacturer's protocols

scan_protocol: Microarray slides were hybridized overnight, washed and then scanned with Agilent G2505C Microarray Scanner. This high resolution scanner represents the very latest technology from Agilent for Arrays and features an industry-leading extended dynamic range of 106 (20-bits) for high sensitivity scanning without saturation, low-level detection resulting from optimized precision optics, broad dynamic range, minimal spectral cross talk that enables detection of weak features. The information about each probe on the array was extracted from the image data using Agilent Feature Extraction 10.5 (FE). This data is stored in the FE “.txt” files. The raw intensity values from these files is imported into the mathematical software package “R”, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White specifically for this analysis.

data_processing: Preprocessing refers to the procedures used to convert raw probe intensities into useful gene expression measurements. For analysis of Agilent Expression data this process consists of : Reading in the FE extraction files and extraction the median intensity values for each probe on the array. These intensities are not background corrected (this has been shown to only introduce noise), but are corrected for any scanner offset that was added to the original raw values (see Analysis Log file for details). The dataset is filtered to remove positive control elements and any elements that have been flagged as outliers. Present (P), Marginal (M) or Absent (A) calls are made for each element on the array using in-house methodologies that take into account both the results of FE probe detection statistics and the intensities of the negative controls elements on the array. Data normalization is the process of removing unwanted non-biological variation that might exist between arrays in a microarray experiment. Sources of such variation might include scanner-setting differences, the quantities of mRNA hybridized, processing order and many other factors. Regardless of the normalization approach used, the underlying assumption of the normalization algorithm is that the number of genes changing expression between conditions is relatively small or that an equivalent number of genes increase and decrease in expression. Agilent One-Color Analysis: The median green (Cy3) intensities are normalized between the arrays using the Quantile Normalization package in “R” (Bolstad et al., 2003). Quantile normalization is a non-linear probe-level normalization that results in the same empirical distribution of intensities for each array.This is a significantly more robust approach than simply normalizing to the median value of each array. The expression of each condition was normalized to its respective control: Influenza infected hAECs were normalized to the median of the Mock_Flu samples and RSV infected hAECs were normalized to the Mock_RSV samples. For the latter Genespring GX v7.3.1 was used.

molecule: total RNA

organism: Homo sapiens

source_name: 2h RSV infection

label_protocol: The concentration of the samples provided was determined using the NanoDrop® ND-1000 UV-Vis Spectrophotometer. RNA samples were analyzed by the FGC using an Agilent 2100 Bioanalyzer Lab-On-A-Chip Agilent 6000 Series II chip to determine the integrity of the samples. The RNA was of high quality and all samples passed our QC cutoff. Sample labeling and hybridization was performed according to the manufacturer’s protocols.

growth_protocol: Human airway tracheobronchial epithelial cells from non-cystic fibrosis patients were obtained from airway specimens resected at lung transplantation following Nationwide Children’s Hospital Institutional Review Board-approved protocols. Epithelial cells were removed from the mainstream bronchi by protease digestion and plastic adherence, and plated at a density of 300,000 cells per well on permeable Transwell-Col supports. Cultures were maintained under air-liquid interface (ALI) for 4 to 6 weeks to form well differentiated, polarized cultures that resemble the in vivo pseudostratified mucociliary epithelium as previously described (Pickles et al., 1998).

extract_protocol: RNA was isolated from the AEC cultures after direct lysis of cells with TRIzol (Invitrogen) and application of the resulting aqueous phase to Qiagen RNeasy Mini Columns. 2 ug of total RNA was reversed transcribed in a 20 ul volume using Applied Biosystem’s high capacity reverse transcription Kit. mRNA expression was determined for 1ul of cDNA with the PRISM 7500 sequence detection system (Applied Biosystems) using SYBR green dye and gene specific primers designed using Primer express software. Primer sets for the P protein of RSV were (F) 5’ AGTGCAGGACCTACATCTGCTC and (R) 5’ AGCTGTTGGCTATGTCCTTGG , while for the NP protein of Influenza virus  were (F) 5 ’ CCAGGAAATGCTGAGATCGAAG  and (R)  5’ TACACACAGGCAGGCAGACAAG 3’. Data were normalized to glyceraldehyde-3-phosphate dehydrogenase (GAPDH), for which the set of primers we used were (F) 5’ GCAAATTCCATGGCACCGT and (R) 5’ TCGCCCCACTTGATTTTGG. The fold increase in mRNA expression was determined using the ddCt method with mock-treated cultures as calibrator.

treatment_protocol: Influenza A/Udorn/72 (H3N2) viruses were grown in eggs, and virus titers were determined by an immunofluorescence foci assay. A laboratory stock of rgRSV244 (Hallak et al., 2000) was propagated in HEp-2 cells, and RSV infectivity was determined by plaque assay. hAEC cultures were exposed to 2 x 10^5 PFU influenza Udorn (MOI of apical cells of 1), 1 x 10^6 PFU rgRSV244 (MOI of apical cells of 5), or mock treated for 2 h, and harvested after 24 and 48 hours of incubation, respectively.

tag: cell type

value: primary polarized airway epithelial cells


title: RSV_3


title: RSV_1


title: E9.5 FVB/N erythroid cells-12

label: biotin

organism: Mus musculus

source_name: E9.5 FVB/N erythroid cells-12

value: wildtype

tag: age


title: E9.5 KLF1-/- KLF2-/- erythroid-13

source_name: E9.5 KLF1-/- KLF2-/- erythroid-13


title: INFLUENZA_1

description: gene expression after 2h influenza infection (harvested 24h after treatment)

source_name: 2h influenza infection


title: E9.5 FVB/N erythroid cells-11

source_name: E9.5 FVB/N erythroid cells-11


title: INFLUENZA_4


title: E9.5 KLF1-/- KLF2-/- erythroid-15

source_name: E9.5 KLF1-/- KLF2-/- erythroid-15


title: E9.5 KLF1-/- erythroid-5

source_name: E9.5 KLF1-/- erythroid-5


title: E9.5 FVB/N erythroid cells-4

source_name: E9.5 FVB/N erythroid cells-4


title: MOCK_1 (for RSV)

description: gene expression after 2h mock treatment (harvested 48h after treatment)


title: RSV_2


title: INFLUENZA_2


title: E9.5 KLF1-/- erythroid-6

source_name: E9.5 KLF1-/- erythroid-6


title: E9.5 KLF1-/- erythroid-8

source_name: E9.5 KLF1-/- erythroid-8


title: E9.5 FVB/N erythroid cells-10

source_name: E9.5 FVB/N erythroid cells-10


title: MOCK_3 (for RSV)


title: E9.5 FVB/N erythroid cells-3

source_name: E9.5 FVB/N erythroid cells-3


title: INFLUENZA_3


title: MOCK_4 (for RSV)


title: MOCK_4 (for Influenza)

description: gene expression after 2h mock treatment (harvested 24h after treatment)


title: MOCK_3 (for Influenza)


title: MOCK_2 (for Influenza)


title: E9.5 FVB/N erythroid cells-2

source_name: E9.5 FVB/N erythroid cells-2


title: E9.5 FVB/N erythroid cells-9

source_name: E9.5 FVB/N erythroid cells-9


title: MOCK_2 (for RSV)


title: STAT1-/-_mock_3

scan_protocol: Microarray slides were hybridized overnight, washed and then scanned with Agilent G2505C Microarray Scanner. This high resolution scanner represents the very latest technology from Agilent for Arrays and features an industry-leading extended dynamic range of 106 (20-bits) for high sensitivity scanning without saturation, low-level detection resulting from optimized precision optics, broad dynamic range, minimal spectral cross talk that enables detection of weak features. The information about each probe on the array was extracted from the image data using Agilent Feature Extraction 10.5 (FE). This data is stored in the FE '.txt' files. The raw intensity values from these files is imported into the mathematical software package 'R', which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White specifically for this analysis.

data_processing: Preprocessing refers to the procedures used to convert raw probe intensities into useful gene expression measurements. For analysis of Agilent Expression data this process consists of : Reading in the FE extraction files and extraction the median intensity values for each probe on the array. These intensities are not background corrected (this has been shown to only introduce noise), but are corrected for any scanner offset that was added to the original raw values (see Analysis Log file for details). The dataset is filtered to remove positive control elements and any elements that have been flagged as outliers. Present (P), Marginal (M) or Absent (A) calls are made for each element on the array using in-house methodologies that take into account both the results of FE probe detection statistics and the intensities of the negative controls elements on the array. Data normalization is the process of removing unwanted non-biological variation that might exist between arrays in a microarray experiment. Sources of such variation might include scanner-setting differences, the quantities of mRNA hybridized, processing order and many other factors. Regardless of the normalization approach used, the underlying assumption of the normalization algorithm is that the number of genes changing expression between conditions is relatively small or that an equivalent number of genes increase and decrease in expression. Agilent One-Color Analysis: The median green (Cy3) intensities are normalized between the arrays using the Quantile Normalization package in 'R' (Bolstad et al., 2003). Quantile normalization is a non-linear probe-level normalization that results in the same empirical distribution of intensities for each array.This is a significantly more robust approach than simply normalizing to the median value of each array.The expression of each condition then was normalized to its respective control: wild type mAECs infected with WSN were normalized to wild type mock treated mAECs, IFNaR-/- mAECs infected with WSN were normalized to IFNaR-/- mock treated mAECs etc.

source_name: STAT1-/-_mock treatment

growth_protocol: Wild type balb/c mice were purchased from Harlan Laboratories, while balb/c IFNAR-/- mice and STAT1-/- mice were breed in house. All animals were maintained in BL2 containment under pathogen-free conditions. The Institutional Animal Care and Use Committee approved all the animal studies described in this work. Tracheal epithelial cell isolation and culture was performed as previously described (Rowe et al., 2004; You et al., 2002). Non-adherent cells were seeded onto 12mm 0.4 µM clear polyester membranes (Corning-Costar) previously coated with a collagen solution. After reaching confluence cells were incubated under ALI and when the transepithelial resistance was >1,000 W cm2 the basolateral media was replaced with fresh media every other day. Cultures were routinely used for experimentation 10-14 days post ALI.

extract_protocol: RNA was isolated from the AEC cultures after direct lysis of cells with TRIzol (Invitrogen) and application of the resulting aqueous phase to Qiagen RNeasy Mini Columns. 2 ug of total RNA was reversed transcribed in a 20 ul volume using Applied Biosystem’s high capacity reverse transcription Kit.

treatment_protocol: mAEC cultures derived from balb/c WT, IFNAR-/- and STAT1-/- mice were exposed to 2 x 105 PFU influenza WSN for 2 h or mock inoculated and harvested 24 h post infection.

tag: strain background

value: BALB/c

value: primary polarized airway epithelial cell cultures


title: STAT1-/-_wsn_3

description: gene expression after 2h infection with WSN (harvested 24h after infection)

source_name: STAT1-/-_2h infection with WSN


title: blood_control9353_rep4

city: marseille

first: adil

last: ef

address: 27 bd jean Moulin

country: France

institute: URMITE

hyb_protocol: Performed according to Agilent's protocol

scan_protocol: Scan performed by DNA microarray scanner (Agilent Technologies)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1 (Agilent) using default parameters.

source_name: peripheral blood

label_protocol: RNA was amplified and labeled with Cy3 using Agilent Low RNA Input Fluorescent Linear Amplification Kit

growth_protocol: Peripheral blood was drawn at the admission of patients in PAXgene tubes (Qiagen).

extract_protocol: RNA was extracted using according to the manufacturer’s recommendations, which included a DNase step. The quality and quantity of isolated RNAs were assessed using the Nanodrop (Thermo Scientific) and 2100 Bioanalyzer (Agilent Technologies), and the RNAs were eluted in 80 µL of water and stored at -20°C

tag: disease state


title: blood_control9353_rep2


title: STAT1-/-_mock_1


title: STAT1-/-_wsn_2


title: IFNaR-/-_wsn_3

source_name: IFNaR-/-_2h infection with WSN

value: IFNaR-/-


title: MOCK_1 (for Influenza)


title: IFNaR-/-_wsn_2


title: IFNaR-/-_wsn_1


title: STAT1-/-_wsn_1


title: blood_control9352_rep3


title: blood_IE_noEmb4889_rep1

value: excluded after admission for infective endocarditis


title: blood_control9353_rep5


title: blood_control1069_rep1


title: MUT24 Control MUT24

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

description: 24 hours

hyb_protocol: standard Agilent protocol

scan_protocol: Scanned on an G2565BA DNA microarray scanner (Agilent) Images were quantified using Agilent Feature Extraction Software (ver. 9.5.3).

data_processing: Agilent Feature Extraction Software (v 9.5.3) was used for background subtraction and LOWESS normalization.

label_protocol: Amount of nucleic acid labeled: 1µg. Amplification: by RNA polymerases. Commercial "Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelinlg)" kit by following manufacturer instructions. Agilent manual G4140-90050 Ver. 5.7 March 2008. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of either Cy3-CTP or Cy5-CTP fluorophores. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).

growth_protocol: Cells were seed and  growth in RPMI 10% FBS media.

extract_protocol: Total RNA fraction. RNA Integrity Numbers were in the range 9 to 10 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.

treatment_protocol: Cells were seed and  growth in RPMI 10% FBS media and then  treated with or without 2ng/ul of Doxiciclyne for different times 6 hour, 12 hours, and 24 hours

tag: cell line

tag: transgene

tag: time

value: 24 hours

tag: treatment

value: doxycycline


title: MUT6 Control MUT6

description: 6 hours

value: 6 hours


title: blood_IE_noEmb4888_rep4


title: IFNaR-/-_mock_3

source_name: IFNaR-/-_mock treatment


title: Control MUT12 MUT12 2

description: 12 hours

value: 12 hours


title: blood_IE_Emb4889_rep3

value: infective endocarditis


title: IFNaR-/-_mock_2


title: STAT1-/-_mock_2


title: Control WT12 WT12

description: 12 hours


title: Control MUT6 MUT6 2

description: 6 hours


title: IFNaR-/-_mock_1


title: blood_IE_noEmb4887_rep3


title: WT12 Control WT12

description: 12 hours


title: blood_IE_Emb4888_rep3


title: wildtype_wsn_1

source_name: wildtype_2h infection with WSN

value: wild type


title: Control WT24 WT24

description: 24 hours


title: Control MUT12 MUT12 1

description: 12 hours


title: Control MUT6 MUT6 1

description: 6 hours


title: wildtype_mock_3

source_name: wildtype_mock treatment


title: wildtype_wsn_3


title: blood_IE_Emb4887_rep4


title: blood_IE_noEmb4886_rep3


title: blood_IE_Emb4887_rep1


title: Control MUT24 MUT24 2

description: 24 hours


title: blood_IE_noEmb4886_rep1


title: wildtype_wsn_2


title: Control WT24 WT24 1

description: 24 hours


title: wildtype_mock_1


title: wildtype_mock_2


title: Control WT6 WT6

description: 6 hours


title: blood_IE_Emb4886_rep4


title: LTL313B

status: Public on Mar 11 2012

city: Vancouver

first: Yuzhuo

last: Wang

state: BC

address: 675 West 10th Avenue

department: Experimetnal Therapeutics

country: Canada

institute: BC Cancer Research Centre

description: Gene expression in non-metastatic prostate cancer xenograft tissue.

hyb_protocol: Samples were hybridized on Agilent Whole Human Genome Oligo Microarrays (Design ID 014850).

scan_protocol: Standard Agilent protocol.

data_processing: Data was processed with Agilent Feature Extraction 10.5.1 and analyzed in Agilent GeneSpring 7.3.1.

label_protocol: Samples were prepared following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0. An input of 100ng of total RNA was used to generate Cyanine-3-labeled cRNA.

growth_protocol: Transplantable xenograft tissue was maintained in the sub-renal site of NOD/SCID mice.

extract_protocol: RNA was prepared using Trizol (Invitrogen, Burlington, ON) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: non-metastatic prostate cancer


title: LTL313H

description: Gene expression in metastatic prostate cancer xenograft tissue.

source_name: metastatic prostate cancer xenograft

value: metastatic prostate cancer


title: Eosinophils_replicate 2

status: Public on Mar 10 2012

city: Ann Arbor

first: Bryan

middle: C

last: Petersen

state: MI

address: 109 Zina Pitcher, 4620 BSRB

department: Pathology

institute: University of Michigan

description: Lung, IL-25 treated

hyb_protocol: Following Labeling, 4 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: Eosinophils

label_protocol: Biotinylated cDNA were prepared according to the Nugen Ovation V2 kit protocol from 50 ng total RNA (ovation pico WTA system V2. PN3302)

growth_protocol: 6–8 week old female 4get mice received daily intra-tracheal injections (0.5 μg recombinant IL-25 (R&D) in 50 μL PBS) for 4 days to induce antigen-independent type 2 inflammation.

extract_protocol: 400,000 cells were collected by FACS for each sample and lysed directly upon sorting in RLT lysis buffer. Total RNA was isolated with Qiagen kits according to manufacturer's instructions.

treatment_protocol:
Lung tissue was processed via enzymatic digestion with 1 mg/ml collagenase A (Roche) in RPMI 1640 (Invitrogen) with 5% FCS (Atlas Biologicals) and 2 U DNase (Sigma-Aldrich) at 37°C for 1 hour, and cells dispersed by passing digest through an 18-gauge cannula.  Following RBC lysis,
MACS columns (Miltenyl) were used to enrich for CD11b+ myleoid populations.  Cells were pooled from 4 donor mice and stained for flow cytometry using standard techniques.  Cells surface markers used to discriminate between inflammatory subsets are listed in the sample description column.

tag: cell surface markers

value: IL-4/GFP- IL-5rα+ F4/80- MHCIIlo CD11b+ Gr-1hi

tag: background strain

tag: tissue type

value: lung

value: Eosinophils


title: Neutrophils_replicate 1

description: Lung, IL-25 treated

source_name: Neutrophils

value: IL-4/GFP- IL-5rα- F4/80- MHCIIlo CD11b+ Gr-1+

value: Neutrophils


title: Macrophages_replicate 2

description: Lung, IL-25 treated

source_name: Macrophages

value: IL-4/GFP- IL-5rα- F4/80+ MHCII+ CD11b+ Gr-1-

value: BALB/c

value: Macrophages


title: T2M cells_replicate 2

description: Lung, IL-25 treated

value: IL-4/GFP+ IL-5rα- F4/80+ MHCIIlo CD11b+ Gr-1mid


title: T2M cells_replicate 3

description: Lung, IL-25 treated


title: Eosinophils_replicate 1

description: Lung, IL-25 treated


title: Neutrophils_replicate 2

description: Lung, IL-25 treated


title: Salivary gland of C57BL/6J male mouse at 16 wks, biological replicate 5

city: Gainesville

first: Ammon

middle: B

last: Peck

state: FL

address: 1945 SW 16th Avenue

department: Department of Infectious Diseases & Pathology

institute: University of Florida

description: Gene expression profiles within the salivary glands of C57BL/6J male mice at 16 weeks of age

hyb_protocol: Fragmented cRNA was hybridized for 16 h at 45°C to the array chips (Affymetrix). Genechips were washed ans stained in the Affymetrix Fluidics Station 400.

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

data_processing: Microarray data were processed and normalized using RMA.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using the RNeasy Mini-Kit (Qiagen, Valencia, CA), as per the manufacturer’s protocol.

value: Salivary gland (minus lymph nodes)

value: 16 week

tag: gender

value: Male


title: Salivary gland of C57BL/6J male mouse at 12 wks, biological replicate 2

description: Gene expression profiles within the salivary glands of C57BL/6J male mice at 12 weeks of age

value: 12 week


title: T2M cells_replicate 1

description: Lung, IL-25 treated


title: Salivary gland of C57BL/6J male mouse at 16 wks, biological replicate 4


title: Salivary gland of C57BL/6J male mouse at 12 wks, biological replicate 3


title: E9.5 FVB/N erythroid cells-1

source_name: E9.5 FVB/N erythroid cells-1

value: FVB/N

value: wildtype

value: embryonic day 9.5

value: erythroid cells


title: Salivary gland of C57BL/6J male mouse at 8 wks, biological replicate 4

description: Gene expression profiles within the salivary glands of C57BL/6J male mice at 8 weeks of age

value: 08 week


title: Salivary gland of C57BL/6J male mouse at 4 wks, biological replicate 4

description: Gene expression profiles within the salivary glands of C57BL/6J male mice at 4 weeks of age

value: 04 week


title: Salivary gland of C57BL/6J male mouse at 12 wks, biological replicate 1


title: Salivary gland of C57BL/6J male mouse at 16 wks, biological replicate 3


title: Salivary gland of C57BL/6J male mouse at 8 wks, biological replicate 5


title: Salivary gland of C57BL/6J male mouse at 16 wks, biological replicate 2


title: Salivary gland of C57BL/6J male mouse at 12 wks, biological replicate 4


title: Macrophages_replicate 1

description: Lung, IL-25 treated

value: lung


title: Salivary gland of C57BL/6J male mouse at 16 wks, biological replicate 1


title: Salivary gland of C57BL/6J male mouse at 4 wks, biological replicate 1


title: Salivary gland of C57BL/6J male mouse at 12 wks, biological replicate 5


title: Salivary gland of C57BL/6J male mouse at 8 wks, biological replicate 1


title: RNA from FFPE tumor tissue TP15A

city: Mexico City

first: Alfredo

last: Hidalgo-Miranda

address: Periferico Sur 4124, Torre Zafiro II, piso 6

country: Mexico

institute: National Institute of Genomic Medicine

description: Tumor

data_processing: To determine the expression level of each miRNA, the comparative Ct (2-ΔΔCt) method was used. RNU44 and RNU48 showed the most stable expression between samples and were selected for normalization across all experiments. All analyses were done using R (HTqPCR, gplots-bioconductor). The data in the normalized Matrix represents the delta CT based on the comparison against endogenous controls in the plattform (nucleolar RNAs RNU44 and RNU48), which showed the highest estability in their expression among our samples.

label: fam

source_name: Breast Tumor

label_protocol: MicroRNA expression analysis. The Megaplex TLDA, v2.0 (TaqMan® Low Density Array) platform was used to measure miRNA expression. There are two plates in this system: plate A, containing well-characterized and widely expressed microRNAs, while plate B presents less characterized microRNAs. The combined plates evaluate the expression of 667 unique human specific microRNAs (present in V14 of the Sanger miRBase) in parallel.

extract_protocol: Frozen tissues were disrupted with a Tissue Ruptor and total RNA was obtained using the Trizol protocol. For the FFPE tissues, total RNA was isolated with the Recoverall kit.

value: Breast Tumor


title: RNA from FFPE tumor tissue TP80A

description: Tumor


title: RNA from FFPE tumor tissue TP59A

description: Tumor


title: RNA from fresh frozen tumor tissue T59A

description: Tumor


title: RNA from FFPE tumor tissue TP122A

description: Tumor


title: Salivary gland of C57BL/6J male mouse at 4 wks, biological replicate 2


title: Salivary gland of C57BL/6J male mouse at 8 wks, biological replicate 3


title: Salivary gland of C57BL/6J male mouse at 8 wks, biological replicate 2


title: RNA from tumor tissue T149A

description: Tumor

data_processing: To determine the expression level of each miRNA, the comparative Ct (2-ΔΔCt) method was used. RNU44 and RNU48 showed the most stable expression between samples and were selected for normalization across all experiments. All analyses were done using R (HTqPCR, gplots-bioconductor).

tag: activation agent

value: Tumor


title: Salivary gland of C57BL/6J male mouse at 4 wks, biological replicate 5


title: Salivary gland of C57BL/6J male mouse at 4 wks, biological replicate 3


title: RNA from tumor tissue T110A

description: Tumor


title: RNA from tumor tissue T128A

description: Tumor


title: RNA from tumor tissue T123A

description: Tumor


title: RNA from tumor tissue T106A

description: Tumor


title: RNA from tumor tissue T107A

description: Tumor


title: RNA from tumor tissue T129A

description: Tumor


title: RNA from tumor tissue T142A

description: Tumor


title: RNA from tumor tissue T146A

description: Tumor


title: RNA from tumor tissue T82A

description: Tumor


title: RNA from tumor tissue T122A

description: Tumor


title: RNA from tumor tissue T81A

description: Tumor


title: RNA from tumor tissue T79A

description: Tumor


title: RNA from tumor tissue T80A

description: Tumor


title: RNA from tumor tissue T74A

description: Tumor


title: RNA from tumor tissue T73A

description: Tumor


title: RNA from tumor tissue T150A

description: Tumor


title: RNA from tumor tissue T50A

description: Tumor


title: RNA from tumor tissue T58A

description: Tumor


title: RNA from tumor tissue T75A

description: Tumor


title: RNA from tumor tissue T71A

description: Tumor


title: RNA from tumor tissue T41A

description: Tumor


title: RNA from tumor tissue T97A

description: Tumor


title: RNA from tumor tissue T30A

description: Tumor


title: RNA from tumor tissue T105A

description: Tumor


title: RNA from tumor tissue T15A

description: Tumor


title: RNA from normal tissue C83A

description: Control

source_name: Normal adjacent

value: Normal adjacent breast

value: control


title: RNA from normal tissue C152A

description: Control


title: RNA from normal tissue C151A

description: Control


title: RNA from tumor tissue T13A

description: Tumor


title: RNA from tumor tissue T150B

description: Tumor

data_processing: To determine the expression level of each miRNA, the comparative Ct (2-ΔΔCt) method was used. RNU44 and RNU48 showed the most stable expression between samples and were selected for normalization across all experiments. All analyses were done using R (HTqPCR, gplots-bioconductor). The data in the normalized Matrix represents the delta CT based on the comparison against endogenous controls in the plattform (nucleolar RNAs RNU44 and RNU48), which showed the highest estability in their expression among our samples. The fold change data represents the log2 of the fold change, and represents the 2-delta delta CT of the comparison between the tumors and the normal tissues (normal tissues were used as calibrators). In the fold change matrix, you will see that the number of targets is less than in the normalized matrix, this is because we only reported the fold changes of those targets which were detected in at least 80% of the samples.


title: RNA from tumor tissue T146B

description: Tumor


title: RNA pool from 12 normal tissues C2A

description: Control

source_name: Normal adjacent (pool of 12)


title: RNA from tumor tissue T129B

description: Tumor


title: RNA from tumor tissue T142B

description: Tumor


title: RNA from tumor tissue T128B

description: Tumor


title: RNA from tumor tissue T149B

description: Tumor


title: RNA from tumor tissue T122B

description: Tumor


title: RNA from tumor tissue T110B

description: Tumor


title: RNA from tumor tissue T5A

description: Tumor


title: RNA from tumor tissue T106B

description: Tumor


title: RNA from tumor tissue T123B

description: Tumor


title: RNA from tumor tissue T105B

description: Tumor


title: RNA from tumor tissue T107B

description: Tumor


title: RNA from normal tissue C150A

description: Control


title: RNA from tumor tissue T97B

description: Tumor


title: RNA from tumor tissue T82B

description: Tumor


title: RNA from tumor tissue T81B

description: Tumor


title: RNA from tumor tissue T80B

description: Tumor


title: RNA pool from 5 normal tissues C1A

description: Control

source_name: Normal adjacent (pool of 5)


title: RNA from tumor tissue T79B

description: Tumor


title: RNA from tumor tissue T75B

description: Tumor


title: RNA from tumor tissue T74B

description: Tumor


title: RNA from tumor tissue T58B

description: Tumor


title: RNA from tumor tissue T71B

description: Tumor


title: endometrium24

city: Sosnowiec

first: Urszula

last: Mazurek

address: Jedności 8

department: Department of Molecular Biology

country: Poland

institute: Medical University of Silesia

hyb_protocol: 15ug of fragmented cRNA were hybridized on HGU133A microarray (Affymetrix). Hybrydization was performed for 16h at 45C. Gene chip was washed and stained with use  GeneChip® Fluidics Station 450 - protocol EukGE-WS2v4 .

scan_protocol: Scan was made with use of GeneArray Scanner G2500A (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0). Data were normalizated using RMA Express

source_name: endometrium control

label_protocol: Biotinylated cRNA were prepared according to Affymetrix protocol  from 5-8ug of total RNA (Gene Expression Analysis Technical Manual, Affymertix).

extract_protocol: Total RNA was extracted with Trizol Reagend according to the manufacturer's instructions.

value: endometrium control


title: RNA from tumor tissue T73B

description: Tumor


title: endometrium19

source_name: endometrium cancer G2

value: endometrium cancer G2


title: endometrium22


title: endometrium18


title: endometrium20


title: endometrium15

source_name: endometrium cancer G3

value: endometrium cancer G3


title: RNA from tumor tissue T55B

description: Tumor


title: endometrium14


title: endometrium13


title: endometrium12

source_name: endometrium cancer G1

value: endometrium cancer G1


title: endometrium17


title: Cumulus cells-MII-P2-rep2

city: Montpellier

first: Said

last: Assou

address: 80, Av. Augustin Flich

institute: INSERM

description: Human cumulus cells was mechanically separated from oocytes and lysed for RNA extraction

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.

label: Biotin

source_name: Cumulus cells-MII

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol “3’ IVT express protocol”, starting from 100 ng total RNA

extract_protocol: Total RNA was isolated using RNeasy micro kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer

value: ovary

value: cumulus cells


title: endometrium16


title: Cumulus cells-MII-TH10


title: endometrium21


title: Cumulus cells-MII-2


title: endometrium9


title: RNA from tumor tissue T41B

description: Tumor


title: Cumulus cells-MII-1


title: RNA from tumor tissue T30B

description: Tumor


title: RNA from tumor tissue T55A

description: Tumor


title: Cumulus cells-MII-OZ2


title: CRD vs 690T

type: genomic

city: Daejeon

first: Myung Soon

last: Kim

address: Yeusung-gu

department: R&D

country: South Korea

institute: Genomictree

description: methylation profiling in 690T sample

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential Oligo aCGH/ChIP-on-chip Wash buffer1, 2, ACN, and Stabilization and Drying Solution as following manufacturer's instructions.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.3.2.1).

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

source_name: CRD

label_protocol: 4 µg of amplified enriched DNA were labeled using Bioprime kit as following manufacturer's instructions

extract_protocol:
genomic DNA extracted using Qiaquick DNA mini kit following manufacturer's instructions
enrichment protocol: 0.5ug sonicated gDNA was incubated with MBD2bt protein, and then purification using Magnetic bead.

tag: sample type

value: pooled DNA of 12 adjacent normal samples

value: enriched methylated DNA of colorectal tumor tissue


title: RNA from tumor tissue T15B

description: Tumor


title: Cumulus cells-MII-P3-rep2


title: endometrium7


title: RNA from tumor tissue T13B

description: Tumor


title: Cumulus cells-MI-P2-2

source_name: Cumulus cells-MI


title: CRD vs 688T

description: methylation profiling in 688T sample


title: RNA from tumor tissue T5B

description: Tumor


title: RNA from tumor tissue T50B

description: Tumor


title: Cumulus cells-MII-FS8


title: CRD vs 396T

description: methylation profiling in 396T sample


title: Cumulus cells-MII-BP5


title: endometrium6


title: RNA from normal tissue C152B

description: Control


title: endometrium8


title: endometrium5


title: CRD vs 684T

description: methylation profiling in 684T sample


title: Cumulus cells-MI-FE11


title: Cumulus cells-MI-MS3


title: endometrium4


title: CRD vs 244T

description: methylation profiling in 244T sample


title: CRD vs 713T

description: methylation profiling in 713T sample


title: CRD vs 211T

description: methylation profiling in 211T sample


title: Cumulus cells-MI-FA9


title: RNA from normal tissue C151B

description: Control


title: Cumulus cells-MI-GL2


title: RNA from normal tissue C83B

description: Control


title: RNA pool from 12 normal tissues C2B

description: Control


title: CRD vs 332T

description: methylation profiling in 332T sample


title: CRD vs 387T

description: methylation profiling in 387T sample


title: endometrium2


title: RNA from normal tissue C150B

description: Control


title: Cumulus cells-MI-CM11


title: Cumulus cells-MI-FA2


title: CRD vs 330T

description: methylation profiling in 330T sample


title: RNA pool from 5 normal tissues C1B

description: Control


title: Cumulus cells-MI-CD2


title: endometrium3


title: Cumulus cells-GV-TH1

source_name: Cumulus cells-GV


title: Control_7

city: Chicoutimi

first: Catherine

last: Laprise

state: Qc

address: 555 Boul. Université

institute: Université du Québec à Chicoutimi

description: Gene expression data from non EBS subject, without any stimulation.

hyb_protocol: Hybridation was done at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and EBS-MP samples.

scan_protocol: Scanning was done using a GeneArray Scanner at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and EBS-MP samples.

data_processing: The scanned images were analyzed using the Microarray Analysis Suite 5.0 (MAS5, Affymetrix) and the raw image fils obtained (.CEL) were used for statistical analyses. Affy and Limma packages in Bioconductor (www.bioconductor.org) using R2.12.0 were used to perform quality tests, RMA normalization and Smyth's moderated t-test.

source_name: Keratinocytes

label_protocol: Probe labelling was done at the McGill University and Genome Quebec Innovation Centre (www.genomequebec.mcgill.ca) and was performed in parallele for control and EBS-MP samples.

growth_protocol: The Biopsies were mechanically homogenized (Rotor/Stator homogeniser, PowerGen).

extract_protocol: RNA was extracted using the RNEasy Fibrous Tissue Midi Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: No treatment before extraction.

tag: cells

value: Keratinocytes from skin biopsies with no stimulation.

value: healthy


title: Cumulus cells-GV-P1_rep2


title: Control_6


title: Control_5


title: CRD vs 685NT

description: methylation profiling in 685NT sample

value: enriched methylated DNA of adjacent normal tissue


title: CRD vs 714NT

description: methylation profiling in 714NT sample


title: Cumulus cells-GV-PB8


title: CRD vs 689NT

description: methylation profiling in 689NT sample


title: Control_4


title: CRD vs 212NT

description: methylation profiling in 212NT sample


title: Cumulus cells-GV-MS2


title: CRD vs 356T

description: methylation profiling in 356T sample


title: CRD vs 340T

description: methylation profiling in 340T sample


title: CRD vs 245NT

description: methylation profiling in 245NT sample


title: Mouse intestinal crypt cells_LGR4  null mice_day 1_ replica 2

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description: Sample were hybridized to MEEBO arrays containing 38784 mouse 70mer oligonucleotide probes (Stanford Functional Genomics Facility, California, USA).

hyb_protocol: Slides were incubated at 42°C for 60 min in the following preheated (42°C) solution: 5xSSC, SDS 0.1%, HEPES 24mM, BSA 0.1mg/ml. Slides were rinsed for 30s in deionized water followed by a centrifugation at 800 rpm for 10 min. Cyanine-labeled cRNA samples were mixed with 30 µg of mouse cot-1, incubated for 2 min at 100°C, centrifuged for 10 min at 13,000 rpm, and then kept at 65°C. After hybridization of the samples on the microarray slides overnight at 65°C, slides were washed twice for 2 min at 60°C with 2xSSC, 0.03% SDS, once 2 min at 60°C with 2xSSC, and finally briefly washed in 0.2xSSC at room temperature. They were dried by centrifugation at 800 rpm for 13 min and stored in the dark at room temperature.

scan_protocol: Slides were scanned using a Molecular Devices 4000B laser scanner and expression levels were quantified using GenePix Pro 6.1 image analysis software (Axon Instruments, CA, USA). Image acquisitions were performed with automatic photomultiplier gains (PMT) adjustement. Artifact-associated spots were eliminated by both visual and software guided flags.

data_processing: A non-linear Lowess (locally weighted scatter plot) normalization method was carried out. VALUE is the normalized Log (base 2) ratio of the median of Channel 1 to Channel 2.

label_protocol: Double-stranded cDNA was synthesized from 1 µg of total RNA, followed by production of antisense RNA containing the modified nucleotide 5-(3-aminoallyl)-UTP using the Amino Allyl MessageAmpTM II aRNA Amplification kit (Ambion, Texas, USA). Labelling with Cy5 or Cy3 (GE Healthcare Bio-Sciences, New Jersey, USA) was performed for 30min in 50% DMSO at room temperature in a dark environment

growth_protocol: Crypt medium was supplemented with 2 mM L-Glutamine, penicillin-streptomycin cocktail and 2% fetal bovine serum. After 6-10 days in culture, organoids were harvested, dissociated with 2.5 mg ml-1 dispase II (Roche), and replated in fresh Matrigel. In experiments with P0 progenitors, 1 μM JAG-1 (Anaspec) was added to the Matrigel and culture medium was supplemented with 10 μM Y-27632 (Sigma). Wnt3a (Milteny, Germany) was added to Matrigel and medium (100 ng/ml), and its bioactivity was checked using the C2C12 myoblast differentiation and TOPflash reporter assays.

extract_protocol: total RNA from ex vivo crypt cultures was extracted using the Mirvana kit (Ambion, Texas, USA)

treatment_protocol: Animal procedures were conducted in accordance with the guidelines of the European Communities Directive 86/609/EEC regulating animal research and were approved by the Local Ethical Committee. Animals were housed in a temperature (21±1°C) and humidity (55±10%)-controlled room with a 12 h light: 12 h dark cycle. Food and water were available ad libitum.

tag: genotype

value: Lgr4/Gpr48^Gt mice back-crossed on a CD1(Leighton et al., 2001)

value: intestinal crypt cells

tag: culture

value: day 1

source_name: Mouse intestinal crypt cells_normal mice

value: wild type


title: Mouse intestinal crypt cells_LiCl treatment_LGR4  null mice_day 1_ replica 2

source_name: Mouse intestinal crypt cells with LiCl treatment_LGR4  null mice

value: day 1 with LiCl treatment

source_name: Mouse intestinal crypt cells with LiCl treatment_normal mice


title: Cumulus cells-GV-GL3

tag: cell type


title: Control_3


title: Mouse intestinal crypt cells_LGR4  null mice_day 1_ replica 1

tag: strain background


title: Liver: congenital hypothyroidism vs intact_Replicate 4

city: Las Palmas de Gran Canaria

first: Leandro

last: Fernandez-Perez

state: Las Palmas

address: Dr. Pasteur s/n-Campus of San Cristobal

department: Clinical Sciences

institute: University of Las Palmas de Gran Canaria

description: Biological replicate 4 of 4. Liver with congenital hypothyroidism vs untreated control

hyb_protocol: Oligoarrays were hybridized according to the manufacturer’s protocol (ProntoTM Plus System, Promega).

scan_protocol: Scnanned with GenePix Microarray Scanner (Axon Instruments, CA).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. GenePix software was used.

organism: Rattus norvegicus

source_name: rats with congenital hypothyroidism (CH)

label_protocol: Five micrograms of high-quality total RNA from liver was reversed-transcribed, labelled, and hybridized according to the manufacturer’s protocol (ProntoTM Plus System, Promega). After 16 h of hybridization, the slides were scanned using the GenePix Microarray Scanner

growth_protocol: Animals were kept under a constant dark/light cycle, and in a controlled temperature (21-23 ºC) environment, and had free access to standard diet (A04 SAFE Panlab, Barcelona, Spain) and tap water throughout the experiment. For mating purposes, four females were housed overnight with two males starting at 21:00 h. The indirect MMI exposure method (i.e., through maternal milk) utilized in this experiment has been extensively employed to induce a transitory congenital-neonatal hypothyroidism (CH) for the determination of short- and long-term physiological effects. Briefly, 0.02 % MMI was administered in the drinking water to pregnant rats from GD12 until weaning at post-natal day (PND) 30. The MMI-containing water was changed twice per week. Untreated rats served as concurrent euthyroid and age-matched controls (INTACT).

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

treatment_protocol: The indirect methimazole (MMI) exposure method (i.e., through maternal milk) was utilized in this experimente for a transitory congenital-neonatal hypothyroidism (CH): 0.02 % MMI was administered in the drinking water to pregnant rats from GD12 until weaning at post-natal day (PND) 30. Untreated rats served as concurrent euthyroid and age-matched controls (INTACT).

value: male

tag: age

value: adulthood (PND80)

value: liver

source_name: age-matched intact rats (INTACT)


title: Mouse intestinal crypt cells_LiCl treatment_LGR4  null mice_day 1_ replica 1


title: EBS-MP

description: Gene expression data from EBS-MP subject, without any stimulation.

tag: disease state

value: Epidermolysis bullosa simplex-mottled pigmentation


title: Cumulus cells-GV-BP7


title: Liver: congenital hypothyroidism vs intact_Replicate 3

description: Biological replicate 3 of 4. Liver with congenital hypothyroidism vs untreated control


title: Mouse intestinal crypt cells_LGR4  null mice_day 0.5_ replica 1

value: day 0.5


title: Liver: congenital hypothyroidism vs intact_Replicate 2

description: Biological replicate 2 of 4. Liver with congenital hypothyroidism vs untreated control


title: Control_1


title: Cumulus cells-GV-FE7

value: ovary


title: CRD vs 388NT

description: methylation profiling in 388NT sample


title: Mouse intestinal crypt cells_LGR4  null mice_day 0.5_ replica 2


title: CRD vs 341NT

description: methylation profiling in 341NT sample


title: leaf_Ag-0_dry_3

status: Public on Mar 09 2012

city: Austin

first: David

middle: Lee

last: Des Marais

state: TX

address: 1 University Station C0930

department: Integrative Biology

institute: The University of Texas at Austin

description: cRNA hybridizations to explore gene expression

hyb_protocol: standard Affymetrix protocol using Affymetrix Model 640 hybridization oven

scan_protocol: Affymetrix GeneChip Scanner 3000, GCOS v1.3

data_processing:
Microarray Suite 5, data processed with JMP Genomics, R statistics
RMA in R, custom CDF file, filtering of SFP

organism: Arabidopsis thaliana

source_name: rosette leaf

label_protocol: biotin-labeled targets (cRNA) using a MessageAmp™ II-based protocol

growth_protocol: Arabidopsis accessions were grown in 6x6x5-cm plastic pots filled with ~150 ml Profile™ porous ceramic rooting media.  Plants were thinned to one per pot and were grown and treatments applied in a controlled environment chamber with 10-h photoperiod of 330 µmol m-2 s-1 photosynthetic photon flux density.  Daytime/nighttime temperatures were 23/18 C with 60% relative humidity.  During growth all plants were fertilized with a complete, modified Hoagland's nutrient solution every two days and watered daily.

extract_protocol: Qiagen RNAasy Plant Mini prep, samples initially harvested in RNAlater

treatment_protocol: During the drydown treatment each pot was weighed daily at ‘pre-dawn’ (WTpot&soil) and distilled water was added by pipette at the base of the rosette to bring the percent water remaining (WatRem%) in each pot to the target level for that day (e.g. 90% on day one, 80% on day two, etc.) until a final drying treatment level of ~50% was reached by all pots on the fifth day.  A major goal of the slow drydown treatment was to allow the intact, growing plants to acclimate to the imposed soil moisture stress.  WatRem% was calculated as 100*(WTpot&soil-DWpot&soil)/( FCpot&soil- DWpot&soil).  Wet (control) pots were treated identically, except WatRem% was maintained near 90% for the entire drydown period.

tag: accession

value: Dry

value: rosette leaf


title: Mouse intestinal crypt cells_LGR4  null mice_day 0_ replica 2

value: day 0


title: Transcriptional Profile of the Shigella flexneri Response to Berberine repeat 1

city: Beijing

first: Hua

last: Fu

address: 6#, Rongjing East Street

country: China

institute: Institute of pathogen biology

description: Prior to hybridization, the labeled cDNA was purified with QIAquick polymerase chain reaction (PCR) purification kit (Qiagen).

hyb_protocol: Each pair of labeled cDNA was mixed and dried by vacuum centrifugation. The pairs of the labeled cDNA samples were hybridized to the DNA microarrays following the protocol published at http://www.ifr.ac.uk/safety/microarrays/.

scan_protocol: The slides were scanned using a GenePix 4100A scanner. Fluorescent spots and local background intensities were quantified using GenePix Pro 6.0 software (Axon). Signal intensities were corrected by subtracting the local background value.

data_processing: Signal intensities were corrected by subtracting the local background value. The data set was filtered so that spots flagged as "not found," "bad" and "empty" were excluded from further analysis. Moreover, spots either with signal-to-noise ratio below the detection limit of 3 or containing less than 55% of pixels two standard deviations above background in both channels were discarded from the data set. Lowess normalization was performed with the fluorescent signal ratios (Cy5/Cy3) using MIDAS software (http://www.tigr.org/software/tm4), with a 0.33 smooth parameter.

organism: Shigella flexneri

source_name: S.flexneri 2a strain 301(Sf301)

label_protocol: According to the manufacturer’s instructions, the cDNA was labeled with incorporation of fluorescent dyes (Amersham) except that a different deoxyribonucleotide triphosphate mix was used (10×mix: 1.2 mM each dATP, dGTP, and 2′- deoxythymidine 5′-triphosphate; 0.6 mM dCTP; 10 mM Tris, pH 8.0; 1 mM EDTA). Cy3-dCTP monofunctional dye was selected for control cDNA samples.

extract_protocol: Total RNA was extracted using SV RNA Isolation System (Promega). Reverse transcription of 20 ug RNA from each sample was performed with Superscript II system (Invitrogen) to prepare cDNA.

tag: strain

value: S.flexneri 2a strain 301(Sf301)

value: 0.25% DMSO for 30 min

source_name: S.flexneri 2a strain 301(Sf301) plus Berberine Chloride

label_protocol: According to the manufacturer’s instructions, the cDNA was labeled with incorporation of fluorescent dyes (Amersham) except that a different deoxyribonucleotide triphosphate mix was used (10×mix: 1.2 mM each dATP, dGTP, and 2′- deoxythymidine 5′-triphosphate; 0.6 mM dCTP; 10 mM Tris, pH 8.0; 1 mM EDTA). For drug-treated samples, Cy5-dCTP was used.

value: 160ug/ml Berberine Chloride in 0.25% DMSO for 30 min


title: leaf_Ull2-5_wet_3

tag: treatment

value: Wet


title: Transcriptional Profile of the Shigella flexneri Response to Berberine


title: leaf_Ag-0_wet_2

tag: tissue


title: Mouse intestinal crypt cells_LGR4  null mice_day 0_ replica 1

value: Lgr4/Gpr48^Gt mice back-crossed on a CD1(Leighton et al., 2001)

value: intestinal crypt cells


title: CRD vs 333NT

description: methylation profiling in 333NT sample

value: pooled DNA of 12 adjacent normal samples

value: enriched methylated DNA of adjacent normal tissue


title: leaf_Ag-0_dry_2


title: leaf_Ag-0_wet_1


title: Liver: congenital hypothyroidism vs intact_Replicate 1

description: Biological replicate 1 of 4. Liver with congenital hypothyroidism vs untreated control

value: male


title: leaf_Ull2-5_wet_2


title: Transcriptional Profile of the Shigella flexneri Response to Berberine repeat 2


title: leaf_Ag-0_wet_3


title: Cumulus cells-GV-MS9

value: cumulus cells


title: leaf_Ull2-5_dry_2


title: leaf_Ull2-5_wet_1


title: leaf_Tamm-2_dry_3


title: leaf_Tamm-2_dry_2


title: leaf_Tamm-2_wet_3


title: leaf_Ull2-5_dry_1


title: leaf_Tamm-2_dry_1


title: CRD vs 397NT

description: methylation profiling in 357NT sample


title: leaf_Tamm-2_wet_2


title: leaf_Tamm-2_wet_1


title: CRD vs 691NT

description: methylation profiling in 691NT sample


title: leaf_Omo2-3_wet_2


title: leaf_Omo2-3_dry_2


title: leaf_Omo2-3_wet_1


title: leaf_Omo2-3_dry_1


title: leaf_Got-22_dry_2


title: leaf_Got-22_wet_1


title: CRD vs 357NT

description: methylation profiling in 357NT sample


title: leaf_Omo2-3_dry_3


title: leaf_Eden-1_dry_2


title: leaf_Eden-1_wet_1


title: leaf_Got-22_wet_3


title: leaf_Bil-5_wet_2


title: leaf_Got-22_wet_2


title: leaf_Omo2-3_wet_3


title: leaf_Bil-5_wet_3


title: leaf_Got-22_dry_1


title: leaf_Eden-1_wet_3


title: leaf_Bil-5_wet_1


title: leaf_Got-22_dry_3


title: Control_2

value: Keratinocytes from skin biopsies with no stimulation.

value: healthy


title: leaf_Eden-1_wet_2


title: leaf_Bil-5_dry_1


title: leaf_Eden-1_dry_1


title: leaf_Bil-5_dry_3


title: leaf_Bil-5_dry_2


title: leaf_Ler_dry_3

tag: ecotype

value: Ler


title: leaf_Col_dry_3

value: Col


title: leaf_Ler_wet_3


title: leaf_Ull2-5_dry_3

value: Dry


title: leaf_Eden-1_dry_3

value: rosette leaf


title: leaf_HR-5_dry_3


title: leaf_KNOX-18_dry_3


title: leaf_CIBC-17_dry_3


title: leaf_NFA-10_wet_3


title: leaf_NFA-10_dry_3


title: leaf_SQ-8_dry_3


title: leaf_Col_wet_3


title: leaf_Ler_dry_2


title: leaf_CIBC-17_wet_3


title: leaf_Col_dry_2


title: leaf_HR-5_wet_3


title: leaf_Bur-0_dry_3


title: leaf_Bur-0_wet_3


title: leaf_Ws-2_wet_3


title: leaf_Ts-1_dry_3


title: leaf_SQ-8_dry_2


title: leaf_Ws-2_dry_3


title: leaf_SQ-8_wet_3


title: leaf_NFA-10_dry_2


title: leaf_KNOX-18_wet_3


title: leaf_HR-5_dry_2


title: leaf_CIBC-17_dry_2


title: leaf_SQ-8_wet_2


title: leaf_Ws-2_dry_2


title: leaf_Ts-1_wet_3


title: leaf_Ts-1_dry_2


title: leaf_Bur-0_dry_2


title: leaf_CIBC-17_wet_2


title: leaf_HR-5_wet_2


title: leaf_Col_wet_2


title: leaf_KNOX-18_wet_2


title: leaf_SQ-8_dry_1


title: leaf_Ws-2_wet_2


title: leaf_Bur-0_wet_2


title: leaf_Ler_wet_2


title: leaf_Ts-1_wet_2


title: leaf_NFA-10_wet_2


title: leaf_Ler_dry_1


title: leaf_HR-5_dry_1


title: leaf_CIBC-17_dry_1


title: leaf_KNOX-18_dry_1


title: leaf_Col_wet_1


title: leaf_Ws-2_dry_1


title: leaf_Col_dry_1


title: leaf_NFA-10_dry_1


title: leaf_Bur-0_dry_1


title: leaf_NFA-10_wet_1


title: leaf_SQ-8_wet_1


title: leaf_KNOX-18_wet_1


title: leaf_Ler_wet_1


title: leaf_Ts-1_dry_1


title: 9QSA_2027.stationary.Cy5_wt.stationary.Cy3_14211209_MDS.mev.refIsIA.out

city: Rockville

first: John

last: Braisted

state: MD

address: 9704 Medical Center Dr

department: PFGRC

institute: J Craig Venter Institute

hyb_protocol: Microarray hybridization, scanning, image analysis, normalization, and analysis. Epoxy-coated slides were prehybridized in 5´ SSC (1´ SSC, 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 °C for 60 min. The slides were then washed at room temperature with distilled water, dipped in isopropanol, and spun dry. Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5´ SSC, and 0.1% sodium dodecyl sulfate. Resuspended probes were denatured by heating to 95ºC prior to hybridization. The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 °C. Hybridized slides were washed sequentially in solutions of 1´ SSC-0.2% SDS, 0.1´ SSC-0.2% SDS, and 0.1´ SSC at room temperature, dried, and then scanned with an Axon GenePix 4000 scanner.

scan_protocol: Slides were scanned on an Axon B scanner

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at http://www.tigr.org/software/tm4). Microarray data were normalized by LocFit (LOWESS) Normalization in block mode using TIGR MIDAS software (available at http://www.tigr.org/software/tm4). Median spot intensity values were used to calculate the log2 ratio and fold change. Oligos with intensities less than 10,000 units were subtracted from the analysis to rule out background. All hybridizations were performed with a minimum of 1 flip dye experiment. Each hyb has 3 inslide replicates per oligo to rule out bias data.

organism: Staphylococcus aureus subsp. aureus str. Newman

source_name: IA Cy3 labeled S. aureus Newman WT stationary

label_protocol: cDNA probes for microarray experiments were generated as follows. Briefly, 2 μg of total RNA in a mixture containing 6 μg of random hexamers (Invitrogen); 0.01 M dithiothreitol; an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma); reaction buffer (Clontech); and 400 units of Powerscript reverse transcriptase (Clontech) were incubated at 42 °C overnight. The resulting RNA template was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 65 °C for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The cDNA probes were eluted with phosphate buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature and incubated for 2 h. Uncoupled label was removed using a Minelute column (Qiagen).

extract_protocol: Ambion miRNA extraction kit

value: Newman WT

source_name: IB Cy5 labeled mutant2027 S. aureus stationary

extract_protocol: ambion miRNA extraction kit

value: Newman delta2027


title: 9QSA_2027.stationary.Cy5_wt.stationary.Cy3_14211206_MDS.mev.refIsIA.out


title: 9QSA_2027.mid.log.Cy5_wt.mid.log.Cy3_14211205_MDS.mev.refIsIA.out

source_name: IA Cy3 labeled S. aureus Newman WT log

source_name: IB Cy5 labeled mutant2027 S. aureus


title: leaf_Bur-0_wet_1


title: leaf_CIBC-17_wet_1


title: leaf_HR-5_wet_1


title: leaf_Ts-1_wet_1


title: 9QSA_2027.mid.log.Cy5_wt.mid.log.Cy3_14211208_MDS.mev.refIsIA.out


title: beta-TC3 cells, 24-hr treatment, DMSO-control, Batch_08, HTA3_B08

city: Cambridge

first: Paul

middle: A

last: Clemons

state: MA

address: 7 Cambridge Center

department: Chemical Biology Program

institute: Broad Institute of Harvard and MIT

description: beta-TC3 cells

hyb_protocol: The biotinylated cRNA targets were normalized, fragmented and hybridized to Affymetrix HT Mouse 430 A peg arrays (Affymetrix 901045). The hybridization and subsequent washing and staining were performed on the Affymetrix GeneChip® Array Station (GCAS) automation platform.

scan_protocol: The arrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332).

data_processing: Expression data (in the form of CEL files) from eight 96-well Affymetrix HT_MG-430A arrays was background corrected, normalized and summarized with RMA using GenePattern.

source_name: beta-TC3 cells

label_protocol: 1 µg of total RNA was used to prepare complementary RNA (cRNA) target with the Genechip® HT One-Cycle cDNA synthesis Kit (Affymetrix 900687) and the GeneChip® HT IVT Labeling Kit (Affymetrix 900688). Total RNA was first reverse transcribed using a T7-Oligo(dT) promoter primer in the first strand cDNA synthesis reaction. Following RNAse H-mediated second strand cDNA synthesis, the double-stranded cDNA was purified and served as a template for an in vitro transcription (IVT) reaction. The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for cRNA amplification and biotin labeling.

growth_protocol: Cell lines αTC1 and βTC3 were cultured in low-glucose DMEM supplemented by 10% FBS, 10 U/ml penicillin and 50 µg/ml streptomycin. 24 h prior to compound treatment, 3 mio. cells were plated per well in a 6-well plate in 1 ml medium.

extract_protocol: RNA was prepared using Qiagen RNeasy kits according to the manufacturer’s protocol.

treatment_protocol: Compounds dissolved at 1000-fold the profiling concentration in DMSO were diluted 1:10 with media and 10 µl were added per well. At the indicated time point (1, 6, 24 h, respectively), cells were lysed in 900 µl buffer RLT (Qiagen) by shaking for 30s, and lysates were immediately frozen in liquid nitrogen.

tag: cell line

value: 24 hrs with DMSO-control


title: beta-TC3 cells, 24-hr treatment, DMSO-control, Batch_10, HTA2_H09

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, DMSO-control, Batch_05, HTA3_A01

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, DMSO-control, Batch_07, HTA9_B03

description: beta-TC3 cells


title: leaf_Ws-2_wet_1


title: beta-TC3 cells, 24-hr treatment, DMSO-control, Batch_07, HTA1_D06

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, DMSO-control, Batch_06, HTA4_F08

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, DMSO-control, Batch_06, HTA5_F07

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 2.4uM, PXD101, Replicate3, Batch_10, HTA2_A02

description: beta-TC3 cells

value: 24 hrs with 2.4uM, PXD101


title: beta-TC3 cells, 24-hr treatment, DMSO-control, Batch_05, HTA7_F07

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 2.4uM, PXD101, Replicate2, Batch_09, HTA2_B03

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, BRD9773, Replicate1, Batch_09, HTA9_C08

description: beta-TC3 cells

value: 24 hrs with 10uM, BRD9773


title: beta-TC3 cells, 24-hr treatment, 2.4uM, PXD101, Replicate1, Batch_07, HTA8_E03

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, BRD5298, Replicate3, Batch_07, HTA4_H06

description: beta-TC3 cells

value: 24 hrs with 10uM, BRD5298


title: beta-TC3 cells, 24-hr treatment, 10uM, BRD9773, Replicate2, Batch_07, HTA8_H11

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, DMSO-control, Batch_09, HTA2_H05

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, DMSO-control, Batch_10, HTA2_D11

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, DMSO-control, Batch_04, HTA6_F10

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, BRD5298, Replicate2, Batch_09, HTA9_D01

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, BRD8451, Replicate3, Batch_07, HTA9_A02

description: beta-TC3 cells

value: 24 hrs with 10uM, BRD8451


title: beta-TC3 cells, 24-hr treatment, DMSO-control, Batch_04, HTA8_E09

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, BRD5298, Replicate1, Batch_08, HTA3_F01

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, BRD9773, Replicate3, Batch_08, HTA4_F12

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, BRD8451, Replicate2, Batch_09, HTA9_C05

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 3uM, BRD-A94377914, Replicate2, Batch_09, HTA2_H10

description: beta-TC3 cells

value: 24 hrs with 3uM, BRD-A94377914


title: beta-TC3 cells, 24-hr treatment, 10uM, BRD8451, Replicate1, Batch_08, HTA4_E05

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 3uM, BRD-A94377914, Replicate1, Batch_08, HTA9_H05

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 3uM, BRD-A94377914, Replicate3, Batch_07, HTA9_B10

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 0.91uM, BRD6929, Replicate2, Batch_09, HTA3_E07

description: beta-TC3 cells

value: 24 hrs with 0.91uM, BRD6929


title: beta-TC3 cells, 24-hr treatment, 10uM, AMI-1, Replicate3, Batch_08, HTA1_B10

description: beta-TC3 cells

value: 24 hrs with 10uM, AMI-1


title: beta-TC3 cells, 24-hr treatment, 10uM, AMI-1, Replicate2, Batch_09, HTA3_F11

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 0.91uM, BRD6929, Replicate3, Batch_07, HTA4_H08

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, AMI-1, Replicate1, Batch_07, HTA8_F06

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, pyroxamide, Replicate3, Batch_08, HTA2_A08

description: beta-TC3 cells

value: 24 hrs with 10uM, pyroxamide


title: beta-TC3 cells, 24-hr treatment, 0.91uM, BRD6929, Replicate1, Batch_08, HTA8_D10

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, ITF-2357, Replicate3, Batch_10, HTA2_G06

description: beta-TC3 cells

value: 24 hrs with 10uM, ITF-2357


title: beta-TC3 cells, 24-hr treatment, 10uM, ITF-2357, Replicate1, Batch_10, HTA2_C07

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, ITF-2357, Replicate2, Batch_10, HTA2_D02

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, 5-azadeoxycytidine, Replicate3, Batch_08, HTA8_B11

description: beta-TC3 cells

value: 24 hrs with 10uM, 5-azadeoxycytidine


title: beta-TC3 cells, 24-hr treatment, 1.5uM, CRA-024781, Replicate3, Batch_08, HTA9_C07

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 1.5uM, CRA-024781, Replicate1, Batch_10, HTA2_E04

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 1.5uM, CRA-024781, Replicate2, Batch_07, HTA1_D07

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, pyroxamide, Replicate2, Batch_10, HTA2_G10

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, pyroxamide, Replicate1, Batch_07, HTA4_G02

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, 5-azadeoxycytidine, Replicate2, Batch_09, HTA3_B04

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, 5-azadeoxycytidine, Replicate1, Batch_07, HTA8_G08

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, RG-0108, Replicate3, Batch_10, HTA2_G11

description: beta-TC3 cells

value: 24 hrs with 10uM, RG-0108


title: beta-TC3 cells, 24-hr treatment, 10uM, zebuarine, Replicate2, Batch_07, HTA8_F10

description: beta-TC3 cells

value: 24 hrs with 10uM, zebuarine


title: beta-TC3 cells, 24-hr treatment, 10uM, zebuarine, Replicate3, Batch_09, HTA3_E08

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, RG-0108, Replicate1, Batch_09, HTA9_H04

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, BIX-01294, Replicate2, Batch_05, HTA4_G12

description: beta-TC3 cells

value: 24 hrs with 10uM, BIX-01294


title: beta-TC3 cells, 24-hr treatment, 10uM, BIX-01294, Replicate3, Batch_07, HTA3_E01

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 0.12uM, HC-toxin, Replicate3, Batch_10, HTA2_D08

description: beta-TC3 cells

value: 24 hrs with 0.12uM, HC-toxin


title: beta-TC3 cells, 24-hr treatment, 0.12uM, HC-toxin, Replicate1, Batch_05, HTA4_D03

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 0.015uM, LBH-589, Replicate2, Batch_06, HTA5_F08

description: beta-TC3 cells

value: 24 hrs with 0.015uM, LBH-589


title: beta-TC3 cells, 24-hr treatment, 0.22uM, trichostatin A, Replicate1, Batch_05, HTA8_E01

description: beta-TC3 cells

value: 24 hrs with 0.22uM, trichostatin A


title: beta-TC3 cells, 24-hr treatment, 0.015uM, LBH-589, Replicate1, Batch_04, HTA8_B06

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 0.22uM, trichostatin A, Replicate2, Batch_07, HTA4_B05

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 0.12uM, HC-toxin, Replicate2, Batch_06, HTA5_F03

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 2uM, scriptaid, Replicate3, Batch_04, HTA6_H03

description: beta-TC3 cells

value: 24 hrs with 2uM, scriptaid


title: beta-TC3 cells, 24-hr treatment, 0.015uM, LBH-589, Replicate3, Batch_05, HTA7_F03

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 2uM, scriptaid, Replicate2, Batch_06, HTA5_F06

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, CI-994, Replicate2, Batch_04, HTA6_D05

description: beta-TC3 cells

value: 24 hrs with 10uM, CI-994


title: beta-TC3 cells, 24-hr treatment, 10uM, CI-994, Replicate3, Batch_06, HTA5_G04

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 0.22uM, trichostatin A, Replicate3, Batch_06, HTA5_F10

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 1.3uM, SAHA, Replicate1, Batch_05, HTA7_F10

description: beta-TC3 cells

value: 24 hrs with 1.3uM, SAHA


title: beta-TC3 cells, 24-hr treatment, 1.3uM, SAHA, Replicate3, Batch_04, HTA6_F09

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, CI-994, Replicate1, Batch_05, HTA7_F05

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 1.1uM, MGCD-0103, Replicate3, Batch_04, HTA6_F01

description: beta-TC3 cells

value: 24 hrs with 1.1uM, MGCD-0103


title: beta-TC3 cells, 24-hr treatment, 1.1uM, MGCD-0103, Replicate2, Batch_06, HTA5_F04

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 1.1uM, MGCD-0103, Replicate1, Batch_05, HTA7_F09

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 2.9uM, MS-275, Replicate2, Batch_10, HTA2_H11

description: beta-TC3 cells

value: 24 hrs with 2.9uM, MS-275


title: beta-TC3 cells, 24-hr treatment, 2.9uM, MS-275, Replicate3, Batch_06, HTA5_F12

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 2.9uM, MS-275, Replicate1, Batch_04, HTA6_D06

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 2uM, scriptaid, Replicate1, Batch_05, HTA7_F04

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 4.1uM, BRD-K90919562, Replicate3, Batch_04, HTA6_G05

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 1.3uM, SAHA, Replicate2, Batch_06, HTA5_F02

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 4.1uM, BRD-K90919562, Replicate2, Batch_08, HTA3_G03

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 4.1uM, BRD-K90919562, Replicate1, Batch_09, HTA9_C04

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 3.2uM, BRD-K92415738, Replicate2, Batch_08, HTA3_C07

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 3.2uM, BRD-K92415738, Replicate3, Batch_09, HTA3_C03

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 3.2uM, BRD-K92415738, Replicate1, Batch_04, HTA6_H07

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 1.7uM, chaetocin, Replicate1, Batch_04, HTA6_C05

description: beta-TC3 cells

value: 24 hrs with 1.7uM, chaetocin


title: beta-TC3 cells, 24-hr treatment, 5uM, BRD-K22912318, Replicate1, Batch_09, HTA9_G07

description: beta-TC3 cells

value: 24 hrs with 5uM, BRD-K22912318


title: beta-TC3 cells, 24-hr treatment, 1.4uM, apicidin, Replicate3, Batch_04, HTA6_F06

description: beta-TC3 cells

value: 24 hrs with 1.4uM, apicidin


title: beta-TC3 cells, 24-hr treatment, 3.7uM, BRD-K62233722, Replicate3, Batch_04, HTA7_H05

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 1.4uM, apicidin, Replicate2, Batch_06, HTA4_E02

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 3.7uM, BRD-K62233722, Replicate2, Batch_06, HTA4_D09

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 5uM, BRD-K22912318, Replicate2, Batch_08, HTA4_B01

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 4.3uM, BRD-K17311666, Replicate1, Batch_09, HTA3_H11

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 4.3uM, BRD-K17311666, Replicate2, Batch_08, HTA3_B01

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 1.7uM, chaetocin, Replicate3, Batch_06, HTA4_B03

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, DMSO-control, Batch_10, HTA2_H12

description: beta-TC3 cells

value: 6 hrs with DMSO-control


title: beta-TC3 cells, 24-hr treatment, 1.7uM, chaetocin, Replicate2, Batch_05, HTA8_F07

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 4.3uM, BRD-K17311666, Replicate3, Batch_04, HTA6_F02

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, DMSO-control, Batch_07, HTA9_B09

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, DMSO-control, Batch_06, HTA5_D01

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, DMSO-control, Batch_05, HTA7_C12

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, DMSO-control, Batch_05, HTA3_H05

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 3.7uM, BRD-K62233722, Replicate1, Batch_05, HTA7_F02

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, DMSO-control, Batch_04, HTA8_G03

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, DMSO-control, Batch_08, HTA3_E10

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 1.4uM, apicidin, Replicate1, Batch_05, HTA7_F06

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, DMSO-control, Batch_10, HTA2_G05

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, DMSO-control, Batch_09, HTA9_E06

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, DMSO-control, Batch_04, HTA6_G10

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 2.4uM, PXD101, Replicate2, Batch_10, HTA2_B05

description: beta-TC3 cells

value: 6 hrs with 2.4uM, PXD101


title: beta-TC3 cells, 24-hr treatment, 5uM, BRD-K22912318, Replicate3, Batch_04, HTA1_A12

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 3uM, BRD-A94377914, Replicate3, Batch_07, HTA1_C09

description: beta-TC3 cells

value: 6 hrs with 3uM, BRD-A94377914


title: beta-TC3 cells, 24-hr treatment, 10uM, RG-0108, Replicate2, Batch_07, HTA1_C11

description: beta-TC3 cells

value: 24 hrs with 10uM, RG-0108


title: beta-TC3 cells, 06-hr treatment, 10uM, BRD5298, Replicate2, Batch_08, HTA4_E11

description: beta-TC3 cells

value: 6 hrs with 10uM, BRD5298


title: beta-TC3 cells, 06-hr treatment, 10uM, BRD9773, Replicate3, Batch_10, HTA2_C11

description: beta-TC3 cells

value: 6 hrs with 10uM, BRD9773


title: beta-TC3 cells, 06-hr treatment, 10uM, BRD5298, Replicate3, Batch_10, HTA2_E10

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, BRD9773, Replicate2, Batch_07, HTA1_F03

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 2.4uM, PXD101, Replicate1, Batch_08, HTA9_H06

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, AMI-1, Replicate3, Batch_10, HTA2_A06

description: beta-TC3 cells

value: 6 hrs with 10uM, AMI-1


title: beta-TC3 cells, 06-hr treatment, 3uM, BRD-A94377914, Replicate1, Batch_09, HTA3_H09

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, BRD8451, Replicate3, Batch_07, HTA3_A03

description: beta-TC3 cells

value: 6 hrs with 10uM, BRD8451


title: beta-TC3 cells, 06-hr treatment, 10uM, BRD5298, Replicate1, Batch_07, HTA8_E05

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 0.91uM, BRD6929, Replicate3, Batch_07, HTA8_E02

description: beta-TC3 cells

value: 6 hrs with 0.91uM, BRD6929


title: beta-TC3 cells, 06-hr treatment, 0.91uM, BRD6929, Replicate1, Batch_10, HTA2_F09

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, AMI-1, Replicate2, Batch_07, HTA8_D05

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 0.91uM, BRD6929, Replicate2, Batch_08, HTA4_E09

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 3uM, BRD-A94377914, Replicate2, Batch_08, HTA1_F11

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, BRD9773, Replicate1, Batch_08, HTA4_F09

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, BRD8451, Replicate2, Batch_08, HTA2_D04

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, AMI-1, Replicate1, Batch_08, HTA9_D06

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, BRD8451, Replicate1, Batch_10, HTA2_G04

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, pyroxamide, Replicate2, Batch_07, HTA8_C10

description: beta-TC3 cells

value: 6 hrs with 10uM, pyroxamide


title: beta-TC3 cells, 06-hr treatment, 10uM, ITF-2357, Replicate3, Batch_10, HTA2_F08

description: beta-TC3 cells

value: 6 hrs with 10uM, ITF-2357


title: beta-TC3 cells, 06-hr treatment, 10uM, pyroxamide, Replicate1, Batch_10, HTA2_H03

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 2.4uM, PXD101, Replicate3, Batch_07, HTA3_A10

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, pyroxamide, Replicate3, Batch_08, HTA3_B09

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, ITF-2357, Replicate2, Batch_08, HTA9_F09

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 1.5uM, CRA-024781, Replicate3, Batch_08, HTA3_D08

description: beta-TC3 cells

value: 6 hrs with 1.5uM, CRA-024781


title: beta-TC3 cells, 06-hr treatment, 1.5uM, CRA-024781, Replicate2, Batch_10, HTA2_H06

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, BIX-01294, Replicate3, Batch_07, HTA1_C05

description: beta-TC3 cells

value: 6 hrs with 10uM, BIX-01294


title: beta-TC3 cells, 06-hr treatment, 10uM, RG-0108, Replicate2, Batch_07, HTA4_B06

description: beta-TC3 cells

value: 6 hrs with 10uM, RG-0108


title: beta-TC3 cells, 06-hr treatment, 10uM, ITF-2357, Replicate1, Batch_07, HTA1_D08

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 0.12uM, HC-toxin, Replicate2, Batch_07, HTA1_C03

description: beta-TC3 cells

value: 6 hrs with 0.12uM, HC-toxin


title: beta-TC3 cells, 06-hr treatment, 10uM, BIX-01294, Replicate2, Batch_06, HTA5_E05

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, zebuarine, Replicate2, Batch_08, HTA9_F11

description: beta-TC3 cells

value: 6 hrs with 10uM, zebuarine


title: beta-TC3 cells, 24-hr treatment, 10uM, BIX-01294, Replicate1, Batch_06, HTA4_G04

description: beta-TC3 cells

value: 24 hrs with 10uM, BIX-01294


title: beta-TC3 cells, 06-hr treatment, 10uM, RG-0108, Replicate3, Batch_08, HTA3_A12

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 0.12uM, HC-toxin, Replicate1, Batch_06, HTA5_H06

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 1.5uM, CRA-024781, Replicate1, Batch_07, HTA9_C11

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, RG-0108, Replicate1, Batch_10, HTA2_E11

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, 5-azadeoxycytidine, Replicate1, Batch_08, HTA4_C09

description: beta-TC3 cells

value: 6 hrs with 10uM, 5-azadeoxycytidine


title: beta-TC3 cells, 06-hr treatment, 0.12uM, HC-toxin, Replicate3, Batch_05, HTA7_C08

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 0.22uM, trichostatin A, Replicate3, Batch_06, HTA5_C08

description: beta-TC3 cells

value: 6 hrs with 0.22uM, trichostatin A


title: beta-TC3 cells, 06-hr treatment, 10uM, zebuarine, Replicate3, Batch_10, HTA2_C05

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, 5-azadeoxycytidine, Replicate3, Batch_10, HTA2_D01

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, 5-azadeoxycytidine, Replicate2, Batch_07, HTA4_C03

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, BIX-01294, Replicate1, Batch_05, HTA7_D01

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 2uM, scriptaid, Replicate3, Batch_05, HTA4_B12

description: beta-TC3 cells

value: 6 hrs with 2uM, scriptaid


title: beta-TC3 cells, 06-hr treatment, 10uM, zebuarine, Replicate1, Batch_07, HTA8_E04

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 2uM, scriptaid, Replicate2, Batch_06, HTA5_D02

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 0.22uM, trichostatin A, Replicate2, Batch_05, HTA7_D04

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 0.22uM, trichostatin A, Replicate1, Batch_10, HTA2_D03

description: beta-TC3 cells


title: beta-TC3 cells, 24-hr treatment, 10uM, zebuarine, Replicate1, Batch_08, HTA9_H03

description: beta-TC3 cells

value: 24 hrs with 10uM, zebuarine


title: beta-TC3 cells, 06-hr treatment, 2uM, scriptaid, Replicate1, Batch_04, HTA6_C08

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 0.015uM, LBH-589, Replicate2, Batch_06, HTA5_E07

description: beta-TC3 cells

value: 6 hrs with 0.015uM, LBH-589


title: beta-TC3 cells, 06-hr treatment, 1.1uM, MGCD-0103, Replicate3, Batch_04, HTA6_B12

description: beta-TC3 cells

value: 6 hrs with 1.1uM, MGCD-0103


title: beta-TC3 cells, 06-hr treatment, 0.015uM, LBH-589, Replicate1, Batch_05, HTA4_D04

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 1.1uM, MGCD-0103, Replicate1, Batch_05, HTA7_D03

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 1.1uM, MGCD-0103, Replicate2, Batch_06, HTA5_H05

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 0.015uM, LBH-589, Replicate3, Batch_04, HTA6_A04

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 1.3uM, SAHA, Replicate3, Batch_05, HTA1_B05

description: beta-TC3 cells

value: 6 hrs with 1.3uM, SAHA


title: beta-TC3 cells, 06-hr treatment, 10uM, CI-994, Replicate1, Batch_05, HTA7_C10

description: beta-TC3 cells

value: 6 hrs with 10uM, CI-994


title: beta-TC3 cells, 06-hr treatment, 4.1uM, BRD-K90919562, Replicate3, Batch_08, HTA3_F07

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 2.9uM, MS-275, Replicate2, Batch_04, HTA6_G09

description: beta-TC3 cells

value: 6 hrs with 2.9uM, MS-275


title: beta-TC3 cells, 06-hr treatment, 1.3uM, SAHA, Replicate1, Batch_04, HTA6_C04

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 2.9uM, MS-275, Replicate1, Batch_05, HTA7_D09

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 2.9uM, MS-275, Replicate3, Batch_06, HTA5_C10

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 10uM, CI-994, Replicate2, Batch_06, HTA5_E03

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 1.4uM, apicidin, Replicate2, Batch_05, HTA4_A06

description: beta-TC3 cells

value: 6 hrs with 1.4uM, apicidin


title: beta-TC3 cells, 06-hr treatment, 5uM, BRD-K22912318, Replicate2, Batch_10, HTA2_F02

description: beta-TC3 cells

value: 6 hrs with 5uM, BRD-K22912318


title: beta-TC3 cells, 06-hr treatment, 10uM, CI-994, Replicate3, Batch_04, HTA6_D09

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 1.4uM, apicidin, Replicate1, Batch_06, HTA5_H07

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 4.1uM, BRD-K90919562, Replicate1, Batch_04, HTA4_C01

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 3.2uM, BRD-K92415738, Replicate3, Batch_10, HTA2_H07

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 3.2uM, BRD-K92415738, Replicate2, Batch_08, HTA9_D12

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 4.1uM, BRD-K90919562, Replicate2, Batch_10, HTA2_G12

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 5uM, BRD-K22912318, Replicate1, Batch_08, HTA1_F12

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 3.2uM, BRD-K92415738, Replicate1, Batch_09, HTA2_E08

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 1.3uM, SAHA, Replicate2, Batch_06, HTA5_H08

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 1.4uM, apicidin, Replicate3, Batch_04, HTA6_B07

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 3.7uM, BRD-K62233722, Replicate2, Batch_05, HTA7_C09

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 3.7uM, BRD-K62233722, Replicate3, Batch_04, HTA6_C10

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 3.7uM, BRD-K62233722, Replicate1, Batch_06, HTA5_H09

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 1.7uM, chaetocin, Replicate3, Batch_04, HTA6_G04

description: beta-TC3 cells

value: 6 hrs with 1.7uM, chaetocin


title: beta-TC3 cells, 06-hr treatment, 1.7uM, chaetocin, Replicate2, Batch_06, HTA5_E06

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 4.3uM, BRD-K17311666, Replicate3, Batch_04, HTA9_B11

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 4.3uM, BRD-K17311666, Replicate2, Batch_08, HTA1_G01

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 4.3uM, BRD-K17311666, Replicate1, Batch_09, HTA9_D07

description: beta-TC3 cells


title: beta-TC3 cells, 06-hr treatment, 1.7uM, chaetocin, Replicate1, Batch_05, HTA1_H03

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, DMSO-control, Batch_09, HTA2_D07

description: beta-TC3 cells

value: 1 hr with DMSO-control


title: beta-TC3 cells, 01-hr treatment, DMSO-control, Batch_04, HTA6_A10

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, DMSO-control, Batch_06, HTA5_B08

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, DMSO-control, Batch_06, HTA4_G01

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, BRD9773, Replicate3, Batch_08, HTA1_B12

description: beta-TC3 cells

value: 1 hr with 10uM, BRD9773


title: beta-TC3 cells, 01-hr treatment, DMSO-control, Batch_04, HTA8_D02

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 2.4uM, PXD101, Replicate2, Batch_07, HTA4_F04

description: beta-TC3 cells

value: 1 hr with 2.4uM, PXD101


title: beta-TC3 cells, 01-hr treatment, DMSO-control, Batch_10, HTA2_E06

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, DMSO-control, Batch_08, HTA3_E06

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, DMSO-control, Batch_09, HTA2_G03

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, DMSO-control, Batch_05, HTA7_A09

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, DMSO-control, Batch_07, HTA1_F07

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, BRD9773, Replicate1, Batch_10, HTA2_H04

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, DMSO-control, Batch_07, HTA9_F10

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, DMSO-control, Batch_05, HTA3_A05

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 2.4uM, PXD101, Replicate1, Batch_08, HTA3_G06

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 2.4uM, PXD101, Replicate3, Batch_10, HTA2_B04

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, BRD9773, Replicate2, Batch_07, HTA8_G12

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, BRD5298, Replicate2, Batch_07, HTA8_G05

description: beta-TC3 cells

value: 1 hr with 10uM, BRD5298


title: beta-TC3 cells, 01-hr treatment, 0.91uM, BRD6929, Replicate2, Batch_09, HTA2_E02

description: beta-TC3 cells

value: 1 hr with 0.91uM, BRD6929


title: beta-TC3 cells, 01-hr treatment, 3uM, BRD-A94377914, Replicate2, Batch_08, HTA3_G10

description: beta-TC3 cells

value: 1 hr with 3uM, BRD-A94377914


title: beta-TC3 cells, 01-hr treatment, 10uM, BRD8451, Replicate1, Batch_10, HTA2_F05

description: beta-TC3 cells

value: 1 hr with 10uM, BRD8451


title: beta-TC3 cells, 01-hr treatment, 0.91uM, BRD6929, Replicate3, Batch_07, HTA1_E12

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 3uM, BRD-A94377914, Replicate3, Batch_07, HTA8_E12

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, BRD5298, Replicate1, Batch_08, HTA9_F04

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, BRD8451, Replicate3, Batch_07, HTA8_C03

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 3uM, BRD-A94377914, Replicate1, Batch_10, HTA2_F04

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, BRD8451, Replicate2, Batch_08, HTA9_C06

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, pyroxamide, Replicate2, Batch_07, HTA4_C08

description: beta-TC3 cells

value: 1 hr with 10uM, pyroxamide


title: beta-TC3 cells, 01-hr treatment, 10uM, BRD5298, Replicate3, Batch_09, HTA3_D01

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 1.5uM, CRA-024781, Replicate3, Batch_10, HTA2_B02

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, ITF-2357, Replicate3, Batch_08, HTA3_C09

description: beta-TC3 cells

value: 1 hr with 10uM, ITF-2357


title: beta-TC3 cells, 01-hr treatment, 10uM, AMI-1, Replicate2, Batch_10, HTA2_C09

description: beta-TC3 cells

value: 1 hr with 10uM, AMI-1


title: beta-TC3 cells, 01-hr treatment, 10uM, AMI-1, Replicate3, Batch_08, HTA9_F12

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, ITF-2357, Replicate1, Batch_10, HTA2_C04

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, AMI-1, Replicate1, Batch_07, HTA1_G02

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, ITF-2357, Replicate2, Batch_07, HTA8_C08

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, pyroxamide, Replicate1, Batch_10, HTA2_E05

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 0.91uM, BRD6929, Replicate1, Batch_08, HTA8_F09

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 1.5uM, CRA-024781, Replicate1, Batch_08, HTA1_F01

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 1.5uM, CRA-024781, Replicate2, Batch_07, HTA1_G12

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, 5-azadeoxycytidine, Replicate3, Batch_07, HTA9_F07

description: beta-TC3 cells

value: 1 hr with 10uM, 5-azadeoxycytidine


title: beta-TC3 cells, 01-hr treatment, 10uM, pyroxamide, Replicate3, Batch_08, HTA3_B12

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, RG-0108, Replicate3, Batch_10, HTA2_B11

description: beta-TC3 cells

value: 1 hr with 10uM, RG-0108


title: beta-TC3 cells, 01-hr treatment, 10uM, RG-0108, Replicate2, Batch_07, HTA8_D09

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, 5-azadeoxycytidine, Replicate2, Batch_08, HTA9_E07

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, RG-0108, Replicate1, Batch_08, HTA9_D05

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, BIX-01294, Replicate2, Batch_07, HTA4_B11

description: beta-TC3 cells

value: 1 hr with 10uM, BIX-01294


title: beta-TC3 cells, 01-hr treatment, 10uM, zebuarine, Replicate1, Batch_10, HTA2_G02

description: beta-TC3 cells

value: 1 hr with 10uM, zebuarine


title: beta-TC3 cells, 01-hr treatment, 10uM, zebuarine, Replicate3, Batch_08, HTA3_G01

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, BIX-01294, Replicate3, Batch_06, HTA5_B01

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, 5-azadeoxycytidine, Replicate1, Batch_10, HTA2_G09

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 0.12uM, HC-toxin, Replicate3, Batch_06, HTA1_C12

description: beta-TC3 cells

value: 1 hr with 0.12uM, HC-toxin


title: beta-TC3 cells, 01-hr treatment, 10uM, BIX-01294, Replicate1, Batch_05, HTA7_A10

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, zebuarine, Replicate2, Batch_07, HTA1_H02

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 0.12uM, HC-toxin, Replicate1, Batch_07, HTA8_H06

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 0.12uM, HC-toxin, Replicate2, Batch_05, HTA7_A03

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 0.22uM, trichostatin A, Replicate2, Batch_07, HTA8_F11

description: beta-TC3 cells

value: 1 hr with 0.22uM, trichostatin A


title: beta-TC3 cells, 01-hr treatment, 0.015uM, LBH-589, Replicate3, Batch_06, HTA5_B03

description: beta-TC3 cells

value: 1 hr with 0.015uM, LBH-589


title: beta-TC3 cells, 01-hr treatment, 2uM, scriptaid, Replicate3, Batch_04, HTA6_B03

description: beta-TC3 cells

value: 1 hr with 2uM, scriptaid


title: beta-TC3 cells, 01-hr treatment, 0.015uM, LBH-589, Replicate1, Batch_04, HTA8_F02

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 0.22uM, trichostatin A, Replicate1, Batch_06, HTA5_B06

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 1.1uM, MGCD-0103, Replicate1, Batch_04, HTA6_B04

description: beta-TC3 cells

value: 1 hr with 1.1uM, MGCD-0103


title: beta-TC3 cells, 01-hr treatment, 1.1uM, MGCD-0103, Replicate3, Batch_05, HTA7_A11

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, CI-994, Replicate3, Batch_06, HTA5_A11

description: beta-TC3 cells

value: 1 hr with 10uM, CI-994


title: beta-TC3 cells, 01-hr treatment, 0.015uM, LBH-589, Replicate2, Batch_05, HTA7_A05

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 1.3uM, SAHA, Replicate3, Batch_04, HTA6_A09

description: beta-TC3 cells

value: 1 hr with 1.3uM, SAHA


title: beta-TC3 cells, 01-hr treatment, 10uM, CI-994, Replicate2, Batch_04, HTA6_A07

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 10uM, CI-994, Replicate1, Batch_05, HTA9_H07

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 1.3uM, SAHA, Replicate1, Batch_06, HTA5_C01

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 2uM, scriptaid, Replicate2, Batch_06, HTA5_B10

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 1.3uM, SAHA, Replicate2, Batch_05, HTA7_B01

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 0.22uM, trichostatin A, Replicate3, Batch_05, HTA7_A12

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 2.9uM, MS-275, Replicate2, Batch_05, HTA7_B07

description: beta-TC3 cells

value: 1 hr with 2.9uM, MS-275


title: beta-TC3 cells, 01-hr treatment, 2.9uM, MS-275, Replicate3, Batch_06, HTA5_B07

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 2uM, scriptaid, Replicate1, Batch_05, HTA4_B04

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 1.1uM, MGCD-0103, Replicate2, Batch_06, HTA5_B12

description: beta-TC3 cells


title: beta-TC3 cells, 01-hr treatment, 2.9uM, MS-275, Replicate1, Batch_04, HTA4_F06

description: beta-TC3 cells