title: RAW 264.7 – infected with Brucella melitensis for 4hrs – replicate date 08122003

description: See other fields

hyb_protocol: Labeled cRNA was hybridized to GeneChip® Test3 arrays and Murine Genome U74Av2 microarrays (Affymetrix). GeneChip® hybridization, washing and scanning was performed by the University of WI –Biotechnology Center, Gene Expression Center (University of WI, Madison) utilizing all Affymetrix protocols and procedures.  Washing and streptavidin-phycoerythrin staining was completed on a GeneChip Fluidics station 400 (Affymetrix).

scan_protocol: GeneChips were scanned with HP 2500 GeneArray Scanner and signal output analysis completed with MAS5.0 (Affymetrix).

data_processing: Signal output analysis completed with MAS5.0 (Affymetrix).  For statistical analysis arrays were compiled and processed with EBarrays, a statistical analysis package in the comprehensive R archive network.

label_protocol: Target RNA was prepared according to protocols in the Affymetrix GeneChip® Expression Analysis technical manual (Affymetrix, Santa Clara, CA).  In vitro synthesis of biotin-labeled cRNA was completed with Enzo BioArray HighYield RNA Transcript Labeling Kit (Affymetrix).  In vitro transcription clean up was completed over an Rneasy spin column (Qiagen).  Labeled cRNA mixed with fragmentation buffer was incubated at 94°C for 35 minutes.  Final RNA concentration in fragmentation buffer ranged from 0.5-1.1 μg/μL.  Visual confirmation of isolation and fragmentation was completed with agarose gel electrophoresis.

growth_protocol:
RAW 264.7 (TIB-71, ATCC) mouse macrophage (Mφ) cell lines were maintained at 37°C with 5% CO2 in RPMI 1640 (Invitrogen) supplemented with 10% Fetal Bovine Serum, 0.2mM L-glutamine, antibiotic-antimycotic (100 U/mL penicillin G, 100 μg/mL streptomycin, 0.25 μg/mL amphotericin B, Gibco), 1mM sodium pyruvate (SAFC Biosciences), and MEM amino acids (Hyclone).  Macrophages were subcultured as necessary by removing old media, washing with PBS, adding fresh media, scraping cells and diluting cells 1:3 to 1:20.
B. melitensis, B. neotomae, B. ovis were grown in 12- by 75-mm tubes on a shaker platform in BBL Brucella broth (BD Bioscience).  Cultures for infection were grown at 37°C for 2 days prior to infection.

value: Brucella melitensis Gram negative, facultative intracellular pathogen


title: RAW 264.7 - uninfected control – replicate date 10122003

status: Public on Jan 01 2010

type: RNA

city: Madison

first: Gary

last: Splitter

state: WI

address: 1656 Linden Dr

department: Pathobiological Sciences

country: USA

institute: University of Wisconsin - Madison

description: See other fields

hyb_protocol: Labeled cRNA was hybridized to GeneChip® Test3 arrays and Murine Genome U74Av2 microarrays (Affymetrix). GeneChip® hybridization, washing and scanning was performed by the University of WI –Biotechnology Center, Gene Expression Center (University of WI, Madison) utilizing all Affymetrix protocols and procedures.  Washing and streptavidin-phycoerythrin staining was completed on a GeneChip Fluidics station 450 (Affymetrix).

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner 3000 and signal output analysis completed with MAS5.0 as a part of GCOS v1.1.1 (Affymetrix).

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: RAW 264.7, uninfected, 4 hours

label_protocol: Target RNA was prepared according to protocols in the Affymetrix GeneChip® Expression Analysis technical manual (Affymetrix, Santa Clara, CA).  In vitro synthesis of biotin-labeled cRNA was completed with Enzo BioArray HighYield RNA Transcript Labeling Kit (Affymetrix).  In vitro transcription clean up was completed over an RNeasy spin column (Qiagen).  Labeled cRNA mixed with fragmentation buffer was incubated at 94°C for 35 minutes.  Final RNA concentration in fragmentation buffer ranged from 0.5-1.1 μg/μL.  Visual confirmation of isolation and fragmentation was completed with agarose gel electrophoresis.

growth_protocol: RAW 264.7 (TIB-71, ATCC) mouse macrophage (Mφ) cell line was maintained at 37°C with 5% CO2 in RPMI 1640 (Invitrogen) supplemented with 10% Fetal Bovine Serum, 0.2mM L-glutamine, antibiotic-antimycotic (100 U/mL penicillin G, 100 μg/mL streptomycin, 0.25 μg/mL amphotericin B, Gibco), 1mM sodium pyruvate (SAFC Biosciences), and MEM amino acids (Hyclone).  Macrophages were subcultured as necessary by removing old media, washing with PBS, adding fresh media, scraping cells and diluting cells 1:3 to 1:20.

extract_protocol: Total RNA was isolated from macrophage cultures utilizing RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol with the following modifications.  Cells were lysed in RLT and DNA digestion was performed.  RNA from two independent cultures was pooled for each target preparation.  RNA was converted to double stranded cDNA using a synthesis kit (Gibco) except that T-7-(dT)24 oligomer (Genset Corp.) was used.  The double stranded cDNA was isolated with the GeneChip® Sample cleanup module.

treatment_protocol: RAW 264.7 cells for microarray were plated in 75cm2 flasks 12-24hr prior to infection, in supplemented RPMI 1640 without antibiotics at an approximate concentration of 5x 10^6 cells per flask.  Macrophage cells were washed once with PBS and 5 mL fresh media added.  Cells were incubated for 4 hours at 37°C with 5% CO2.  Cells were washed once with PBS and then lysed for RNA collection (RNeasy Mini Kit (Qiagen, Valencia, CA)).

tag: designation

value: RAW 264.7 macrophages

tag: atcc

tag: growth properties

value: adherent

tag: tissue

value: Abelson murine leukemia virus-induced tumor

tag: antigen expression

tag: strain

value: BALB/c mice


title: RAW 264.7 - Uninfected control - replicate date 02262002

description: See other fields

scan_protocol: GeneChips were scanned with HP2500 GeneArray Scanner and signal output analysis completed with MAS5.0 (Affymetrix).

source_name: RAW 264.7, uninfected 4hrs

extract_protocol: Total RNA was isolated from macrophage cultures utilizing RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol with the following modifications.  DNase treated RNA was converted to double stranded cDNA using a synthesis kit (Gibco) except that T-7-(dT)24 oligomer (Genset Corp.) was used.  The double stranded cDNA was isolated with the GeneChip® Sample cleanup module.


title: HBMut3-8-1 biological rep 2

city: Davis

first: Andrew

last: Groover

state: CA

address: 1100 West Chiles Rd

department: Institute of Forest Genetics

institute: USDA Forest Service

description: RNA isolated from single plant

hyb_protocol: Hybridization was performed per manufacturer’s hybridization protocol for IVT Labeling Kit (GeneChip 49 format) using 10ug of cRNA.

scan_protocol: GeneChips were scanned using Affymetrix GCS3000 (7th generation) Scanner.

data_processing: Expression values reflect across-array quantile normalization and gene calls generated using the Robust Multichip Average (RMA) expressed as log2. For information on RMA see Biostatistics 2003 Apr; 4(2): 249-264

label: biotin

organism: Populus tremula x Populus alba

source_name: stem tissue from transgenic HBMut3

label_protocol: Biotinylated cRNA were prepared following stand protocols used with Affymetrix One-Cycle cDNA Synthesis and GeneChip IVT Labeling Kits.  Input RNA amount was 1.5ug.

growth_protocol: Plants (hybrid aspen clone INRA 717-IB4 (P.alba x P. tremula) as WT and transformants in the WT genetic background) were grown under tissue-culture conditions in Magenta boxes under constant white light at room temperature (22C) for 8 weeks.   See K. H. Han et al., 2000 (Plant Cell Reports 19:315-320) for more information.

extract_protocol: 100mg or less freshweight defoliated stem tissues were ground to fine poweder in liquid nitrogen, then RNA extracted by RNeasy mini kit (Qiagen) using buffer RLT.  Final RNA was eluted in H2O. RNA was quantitated using Nanodrop (Thermo Scientific) and its quality checked by Bioanalyzer (Agilent).

treatment_protocol: The WT and transformants were grown under identical conditions in growth chambers.

tag: genome/variation

value: transgenic HBMut3 (Populus REVOLUTA ortholog) mutant

value: stem


title: HBMut3-8-1 biological rep 1

description: RNA isolated from single plant


title: HBMut2-4-1 biological rep 3

description: RNA isolated from single plant

source_name: stem tissue from transgenic HBMut2

value: transgenic HBMut2 (Populus ATHB15/CAN ortholog) mutant


title: HBMut2-4-1 biological rep 2

description: RNA isolated from single plant


title: Wildtype biological rep 3

description: RNA isolated from single plant

source_name: stem tissue from wild type control

value: wildtype control


title: Wildtype biological rep 4

description: RNA isolated from single plant


title: HBMut3-8-1 biological rep 4

description: RNA isolated from single plant


title: Wildtype biological rep 2

description: RNA isolated from single plant


title: Wildtype biological rep 1

description: RNA isolated from single plant


title: HBMut3-8-1 biological rep 3

description: RNA isolated from single plant


title: Rat treated with Saline (vehicle) for 6hr, 6

city: Nutley

first: Charu

last: Kanwal

state: NJ

address: 340 Kingsland Street

department: RIGG

institute: Hoffman-La Roche

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Rat 230 2.0 whole genome array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Chips were pre-processed using robust multichip analysis. Normalized data were fit to  a linear model with dose and time contrasts using the GLM procedure of SAS 9.1 (SAS Institute, Carey NC).

organism: Rattus norvegicus

source_name: Heart, saline, 6hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Affymetrix 3' IVT express kit).

extract_protocol: Total RNA was extracted using Qiagen's RNAeasy kit according to the manufacturer's instructions.

treatment_protocol: Vinblastine (0.5 and 3 mg/kg;  Sigma-Aldrich, Saint-Louis, MO), vincristine (0.1 and 1 mg/kg;  Mayne Pharma, Inc., Lake Forest, IL) and colchicine (0.2 and 2 mg/kg;  Sigma Aldrich) in 0.9% saline or 0.9% saline (n=6 rats/group/time-point) were administered intra-venously.

value: Wistar (Crl:Wi(Han))

tag: gender

value: male

value: heart

tag: treatment

value: saline

tag: treatment time


type: mixed

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

description: JR32 strain grown to post-exponential phase, replicate 2.

hyb_protocol: Hybridization was performed as previously described (Hovel-Miner, G 2009. JB, 191:2461).

scan_protocol: Scanning and image acquisition was performed on a Scan Array Express (Perkin Elmer) using ScanArray 3.0 software as previously described (Hovel-Miner, G 2009. JB, 191:2461).

data_processing: Local background was removed from spot signal intensity and the noise signal was estimated by recording the average signal intensity of 10 negative controls printed on the chip. Normalisation of signal intensity was carried out by calculating the fold increase over the noise signal value.

label: AlexaFluor 546.

organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

source_name: Total RNA isolated from strain JR32 grown to post-exponential phase.

label_protocol: 15 ug of Total RNA was labeled with amino-allyl dUTP during reverse transcriptase and subsequently coupled with the succinimidyl ester fluorescent dye AlexaFluor 546 as previously described (Hovel-Miner, G 2009. JB, 191:2461).

extract_protocol: TRIzol reagent (Invitrogen).

label: AlexaFluor 647.

molecule: genomic DNA

source_name: Genomic DNA used as reference channel.

label_protocol: 5 ugh of genomic DNA was labeled with amino-allyl dUTP with klenow fragment and random hexamer as previously described (Porwollik, S. 2001. Mutat Res 483:1).

extract_protocol: Wizard Genomic Purification Kit (Promega).


title: HBMut2-4-1 biological rep 1

description: RNA isolated from single plant


title: IL-17-non-producing hybridoma DE3-2

city: Fukuoka

first: Kensuke

last: Shibata

address: 3-1-1, Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using robust spline normalization in R

source_name: IL-17-non-producing hybridoma

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

growth_protocol: hybridomas were maintained in RPMI supplimented with 10% fetal calf serum.

extract_protocol: RNA was extracted with Rneasy Mini Kit(QIAGEN). Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: hybridoma


title: ES Cells+ESC medium+DAPT 4 hrs N2B27 medium+1% O2+DAPT 6 hrs 3

status: Public on Dec 31 2009

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

description: Biological replicate 3

hyb_protocol: 750ng of each labelled cRNA sample was hybridized to MouseRef-8 v1.1 Expression BeadChip microarrays (Illumina) according to manufacturer specifications.

scan_protocol: Microarrays were scanned on the BeadArray Reader (Illumina, USA) at scan factor 1 as per manufacturer specifications.

data_processing:
The microarray data was subjected to background subtraction on the BeadStudio Data Analysis software (Illumina) and normalized using the Cross-correlation method (Chua et al., 2006).
Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.

source_name: ES cells, ESC medium+DAPT, 4hrs, N2B27 medium+1% O2+DAPT, 6 hrs

label_protocol: 500ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion).

growth_protocol: ES cells were maintained on gelatin (Sigma) coated dishes (Corning) in ESC medium consisting of DMEM (Gibco) supplemented with 5% ESC tested FCS (Sigma), 5% KSR (Gibco), pyruvate (Gibco), non-essential amino acids, beta-mercaptoethanol and LIF at 6% CO2 at 37˚C.

extract_protocol: Following the respective treatments, cells were washed with PBS, trypsinised, resuspended in RNAlater and stored at -20°C. Total RNA extraction was performed using the RNeasy Mini kit (Qiagen) according to the manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent) using the RNA 6000 Nano Chip kit (Agilent) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >9) for all samples.

treatment_protocol: 2,000,000 cells were plated into gelatin-coated 10cm dishes in ESC medium or N2B27 medium consisting of a 1:1 ratio of DMEM/F12 and Neurobasal media supplemented with 0.5% N2 (Gibco) 0.5% B27 (GIBCO, San Diego, California, United States), and 2-mercaptoethanol and glutamine. For the relevant treatments doxycycline was used at a concentration of 2ug/ml (SIGMA) and DAPT at 2.5ng/ml (Calbiochem). In experiments where Notch signaling was pharmacologically blocked, DAPT in ESC medium was applied 4 hours before initiation of array conditions. Hypoxic culture was achieved with an Invivo2 Hypoxia Workstation 400 at 1% oxygen pressure, 6% CO2 37˚C.

value: 1% O2+DAPT

value: Male

value: ES cells

tag: developmental stage

value: Blastocyst


title: LNCaP sphere biol repl 3

city: Frederick

first: Maria

middle: Ana

last: Duhagon

state: MD

address: 1050 Boyles St.

department: Laboratory of Cancer Prevention

institute: NCI-Frederick

description: putative stem cells

hyb_protocol: Purified labelled samples and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers and incubated in an Agilent hybridization ove, and then washed following vendor instructions (G2534-90001).

scan_protocol: Slides were scanned on a GenePix 4000B scanner (Molecular Devices, Sunnyvale,CA, USA) at 5uM resolution

data_processing: Images were quantified using GenePix Pro 6.1 with Agilent's 014850_D_20070207.gal file generating GPR files. GPR files were then imported in Partek Genomic Suite and normalized using LOESS.

organism: Homo sapiens

source_name: LNCaP cell line spheres 7 days in SCM-1% KO

label_protocol: 10 µg of total RNA were was labeled by reverse transcription with Superscript II (Invitrogen) and oligo-dT in the presence of Cy3-dUTP for Universal RNA reference control (Universal Human Reference RNA Stratagene p/n 740000) or Cy5-dUTP for the samples

growth_protocol: Spheres were grown in SCM medium (DMEM:F12 plus 10 ng/mL bFGF, 20 ng/mL EGF, 5 mg/mL insulin, and 0.4% BSA) supplemented with 1% KO serum replacement (Invitrogen/Gibco, p/n 10828-028) at a density of 2500 cells/mL. Parental cell line was grown in RPMI-1640-10% FBS. Regular tissue culture flask treated to improve cell attachment were used in both cases.

extract_protocol: Total RNA extracted using miRNeasy kit from Qiagen

treatment_protocol: Spheres were grown from a single cell suspension of bulk LNCaP washed three times in PBS and plated at low density in SCM-1%KO. The cultures were grown for 7 days and floating spheres were then isolated.

tag: culture type

value: sphere

tag: reference


title: LNCaP sphere biol repl 1

description: putative stem cells

source_name: Universal Human Reference RNA Stratagene


title: LNCaP sphere biol repl 2

description: putative stem cells

value: Universal Human Reference RNA Stratagene


title: ES Cells+ESC medium+DAPT 4 hrs N2B27 medium+1% O2+DAPT 6 hrs 4

description: Biological replicate 4


title: LNCaP parental biol repl 3

description: putative differentiated cells

source_name: LNCaP cell line parental cultures in RPMI-1640-10% FBS

value: adherent


title: LNCaP parental biol repl 2

description: putative differentiated cells


title: ES Cells+ESC medium+DAPT 4 hrs N2B27 medium+1% O2+DAPT 6 hrs 2

description: Biological replicate 2


title: ES Cells+ESC medium+DAPT 4 hrs N2B27 medium+1% O2+DAPT 6 hrs 1

description: Biological replicate 1


title: LNCaP parental biol repl 1

description: putative differentiated cells


title: 24h Ssa family 8_control_replicate 1

city: Moncton

first: Francis

last: LeBlanc

state: NB

address: 343 University Ave.

department: Aquatic Animal Health

institute: Fisheries & Oceans Canada

description: no additional information

hyb_protocol: Hybridization, including washes and drying steps, were carried out on a HS400 automated hybridization station (Tecan, Switzerland) using a reference design. Slides where washed 3 times in 0.1x SSC, 0.2 % SDS at 23°C for 30s, 2 times in 0.2X SSC at 23°C for 30s, followed by a 1h pre-hybridization at 49°C in 5x SSC, 0.01% SDS, 1% BSA and washed with post hybridization buffer (2X SSC, 0.014% SDS) at 49°C for 1 min. Slides were then hybridized for 16 hours using a temperature shift that varied between 49°C and 53°C every hour with a hybridization mix composed of 20 µl of Alexa555 labeled cDNA (experimental samples), 20 µl of Alexa647 labeled cDNA (Reference RNA), 120µl of SlideHybTM Glass Array Hybridization Buffer # 3 (Ambion, CA, USA) and 1.5µl of a custom oligo LNA dT blocker consisting of a 20mer thymine (T) sequence where every second base is an LNA-thymine. The hybridization mix was pre-heated at 90°C for 5 min and then cooled to 49°C prior to being injected on the slides. Following hybridization, slides where washed 4 times with post hybridization buffer at 49°C, 39°C, 30°C, 30°C respectively, followed by 2 washes at room temperature in 1X SSC and 0.2X SSC and then dried with nitrogen.

scan_protocol: Microarray slides were scanned at a resolution of 10µm using a ScanArray Gx microarray scanner (Perkin Elmer, MA, USA). PMT were adjusted to obtain an equal amount of signal from each dye

data_processing: Numerical intensities and descriptive statitistics as well as flag value for each spot were extracted using the SpotReader feature extraction software (Niles Scientific, CA, USA). Flag values computed were then used to filter out genes that had missing values (-50,-75,-100 flag values) on more than 40 percent of the total number of slides used in each statistical analysis performed. Background corrected median value for each spot remaining after filtering were log2 transformed and normalized using a global Loess method. Resulting values were expressed as normalized log2 ratios (log2 value of the experimental sample minus the log2 value of the reference sample) for each spot. A Significance Analysis of Microarray (SAM) test was used to identify gene differentially expressed by comparing the log2 ratios of infected fish (n=~8) to those of control fish (n=~8)  for each time-point.

label: Alexa 555

organism: Salmo salar

source_name: Head-kidney_control_8 (24h)

label_protocol: Experimentals RNA's from infected and control Atlantic salmon were labeled with Alexa 555 using the Superscript Plus Direct Labeling System (Invitrogen, CA, USA) following the manufacturer's protocol. The reference RNA was labeled in Alexa 647 using the same protocol.

extract_protocol: Total RNA from RNAlater preserved salmon head-kidney samples was extracted using TRI reagent (Molecular Research Center, OH, USA) followed by column purification using the Absolutely RNA Miniprep kits (Stratagene, CA, USA) and following the manufacturer’s protocol. A DNase digestion step was performed on each sample to eliminate possible traces of residual genomic DNA. RNA quantification was performed using a NanoDrop 8000 (Thermo Scientific, DE, USA) and RNA quality and integrity was assessed with the Experion automated electrophoresis system (Bio-Rad, TX, USA). Only RNA samples with RNA quality indicator (RQI) values above 8 were hybridized on microarray slides. RNA’s were stored at -70ºC in DEPC treated water containing an RNase inhibitor (Qiagen, ON, Canada) until needed.

value: Head-kidney

tag: time

tag: infection

value: control

label: Alexa 647

source_name: Salmo salar reference RNA

tag: reference source

value: pooled total RNA from 18 healthy Atlantic salmon

value: Reference RNA


title: Global expression profile of HeLa S3 cells, replicate #1

city: Detroit

first: Stephen

middle: A

last: Krawetz

state: MI

address: 275 East Hancock, CS Mott Center

institute: Wayne State University

description: Expression profile from HELA S3 cells.

hyb_protocol: Hybridization to Illumina Sentrix Expression BeadChip, staining and washing was carried out according to the manufacturer’s protocol (Illumina, Wallingford).

scan_protocol: Scanning procedures were carried out as described by Illumina, Wallingford.

data_processing: Data was analyzed using the Illumina Bead Studio software suite.  The average signal for each reporter was cubic-spline normalized between chips to derive a standardized expression value.  Expressed genes were identified by signal values higher than internal spike-in controls for expression (Smax>3000).

source_name: HeLa S3 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA (Whole-Genome Gene Expression with IntelliHyb Seal System Manual, 2006, Illumina).

extract_protocol: Total RNA was isolated using RNeasy (Qiagen Inc., Valencia, CA) according to the manufacturer’s protocol.  The RNA was then amplified using the Illumina RNA amplification system (Ambion, Austin, TX) and 750 ng was used for hybridization.

value: female

value: cultured HeLa S3 cells


title: Aortic Adventitial Fibroblast (AoAF) Global Expression Profile

address: 275 East Hancock Avenue

description: Expression profile from an Aortic Fibroblast cell line.

source_name: Aortic Adventitial Fibroblasts

value: Aortic adventitial fibroblast cell line


title: ES Cells+N2B27 medium+1% O2+Dox 6 hrs 3

description: Biological replicate 3

source_name: ES cells, N2B27 medium+1% O2+Dox, 6 hrs

value: 1% O2+Dox


title: Global expression profile of HeLa S3 cells, replicate #2

description: Expression profile from HELA S3 cells.

source_name: HELA S3 Cells


title: ES Cells+N2B27 medium+1% O2+Dox 6 hrs 1

description: Biological replicate 1


title: ES Cells+N2B27 medium+1% O2 6 hrs 4

description: Biological replicate 4

source_name: ES cells, N2B27 medium+1% O2, 6 hrs


title: ES Cells+N2B27 medium+1% O2+Dox 6 hrs 4

description: Biological replicate 4


title: ES Cells+N2B27 medium+1% O2+Dox 6 hrs 2

description: Biological replicate 2


title: ES Cells+N2B27 medium+1% O2 6 hrs 2

description: Biological replicate 2


title: ES Cells+ESC medium+DAPT 4 hrs N2B27 medium+DAPT 6 hrs 4

description: Biological replicate 4

source_name: ES cells, ESC medium+DAPT, 4hrs, N2B27 medium+DAPT, 6 hrs

value: DAPT


title: ES Cells+N2B27 medium+1% O2 6 hrs 1

description: Biological replicate 1


title: HBMut2-4-1 biological rep 4

description: RNA isolated from single plant

source_name: stem tissue from transgenic HBMut2

value: transgenic HBMut2 (Populus ATHB15/CAN ortholog) mutant

value: stem


title: ES Cells+N2B27 medium+Dox 6 hrs 4b

description: Technical replicate of Biological replicate 4

source_name: ES cells, N2B27 medium+Dox, 6 hrs

value: Dox

value: Male


title: ES Cells+ESC medium+DAPT 4 hrs N2B27 medium+DAPT 6 hrs 1

description: Biological replicate 1

value: ES cells

value: Blastocyst


title: ES Cells+N2B27 medium+Dox 6 hrs 3b

description: Technical replicate of Biological replicate 3


title: ES Cells+N2B27 medium+Dox 6 hrs 3

description: Biological replicate 3


title: ES Cells+N2B27 medium+Dox 6 hrs 2

description: Biological replicate 2


title: ES Cells+ESC medium 6 hrs 4

description: Biological replicate 4

source_name: ES cells, ESC medium, 6 hrs

value: ESC


title: ES Cells+N2B27 medium 6 hrs 1

description: Biological replicate 1

source_name: ES cells, N2B27 medium, 6 hrs


title: ES Cells+N2B27 medium+Dox 6 hrs 4

description: Biological replicate 4


title: ES Cells+N2B27 medium 6 hrs 3

description: Biological replicate 3


title: ES Cells+N2B27 medium+Dox 6 hrs 1

description: Biological replicate 1


title: ES Cells+ESC medium 6 hrs 3

description: Biological replicate 3


title: ES Cells+ESC medium 6 hrs 1

description: Biological replicate 1


title: NM6_lateday_well-watered_rep2

city: Toronto

first: Malcolm

middle: M.

last: Campbell

state: ON

address: 25 Willcocks Street

department: Cell & Systems Biology

institute: University of Toronto

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour before lights were turned off (Late day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0372

hyb_protocol: Affymetrix protocol: Eukaryotic target preparation: Eukaryotic target hybridization.

scan_protocol: Affymetrix protocol: GeneChip Scanner 3000 7G Affymetrix 00-0073.

data_processing: GC-RMA in BioConductor.

organism: Populus maximowiczii x Populus nigra

source_name: DN6, mature leaf, lateday, well-watered

label_protocol: Affymetrix protocol: Eukaryotic target preparation: One-cycle target labeling assay.

growth_protocol: All trees were grown in a climate-controlled growth chamber in 1m tall pots with a 0.1m diameter. Saplings were grown in Sunshine Mix (Sun Gro Horticulture, Vancouver, BC, Canada) with a 16h photoperiod, a maximum daytime temperature of 22°C and a minimum nighttime temperature of 17°C.

extract_protocol: Chang S, Puryear J, Cariney J. 1993. A simple and efficient method for isolating RNA from pine trees. Plant Molecular Biology Reporter. 11:113-11.

treatment_protocol: After 8 weeks of growth without water limitation, no further input of water was given to 50% of plants. The other 50% were watered as before.

tag: clone

value: mature leaf, including petiole

tag: age

value: 8 weeks

value: well-watered

tag: time of day

value: late day


title: NM6_lateday_water-limited_rep2

description:
Clonally propagated.
6 weeks without water limitation followed by 14 days without further input of water.

Leaves collected in the hour before lights were turned off (Late day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0378

source_name: DN6, mature leaf, lateday, water-limited

tag: tissue

value: water-limited


title: NM6_lateday_water-limited_rep3

description:
Clonally propagated.
6 weeks without water limitation followed by 14 days without further input of water.

Leaves collected in the hour before lights were turned off (Late day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0351


title: NM6_lateday_well-watered_rep3

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour before lights were turned off (Late day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0349


title: ES Cells+N2B27 medium 6 hrs 2

description: Biological replicate 2


title: ES Cells+ESC medium 6 hrs 2

description: Biological replicate 2


title: NM6_midday_water-limited_rep2

description:
Clonally propagated.
6 weeks without water limitation followed by 14 days without further input of water.

Leaves collected in the hour in the middle of the photoperiod (Mid-day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0296

source_name: DN6, mature leaf, midday, water-limited

value: mid-day


title: NM6_midday_water-limited_rep1

description:
Clonally propagated.
6 weeks without water limitation followed by 14 days without further input of water.

Leaves collected in the hour in the middle of the photoperiod (Mid-day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0295


title: NM6_midday_water-limited_rep3

description:
Clonally propagated.
6 weeks without water limitation followed by 14 days without further input of water.

Leaves collected in the hour in the middle of the photoperiod (Mid-day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0333


title: NM6_midnight_well-watered_rep3

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour in the middle of the dark period (Midnight).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0346

source_name: DN6, mature leaf, midnight, well-watered

value: midnight


title: ES Cells+N2B27 medium 6 hrs 4

description: Biological replicate 4


title: NM6_lateday_water-limited_rep1

description:
Clonally propagated.
6 weeks without water limitation followed by 14 days without further input of water.

Leaves collected in the hour before lights were turned off (Late day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0350


title: NM6_lateday_well-watered_rep1

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour before lights were turned off (Late day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0347


title: ES Cells+ESC medium+DAPT 4 hrs N2B27 medium+DAPT 6 hrs 3

description: Biological replicate 3


title: NM6_predawn_water-limited_rep3

description:
Clonally propagated.
6 weeks without water limitation followed by 14 days without further input of water.

Leaves collected in the hour before lights were turned on (Pre-dawn).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0384

source_name: DN6, mature leaf, predawn, water-limited

value: pre-dawn


title: NM6_midday_well-watered_rep3

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour in the middle of the photoperiod (Mid-day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0334

source_name: DN6, mature leaf, midday, well-watered


title: NM6_midday_well-watered_rep2

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour in the middle of the photoperiod (Mid-day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0298


title: NM6_predawn_water-limited_rep1

description:
Clonally propagated.
6 weeks without water limitation followed by 14 days without further input of water.

Leaves collected in the hour before lights were turned on (Pre-dawn).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0382


title: NM6_predawn_well-watered_rep3

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour before lights were turned on (Pre-dawn).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0381

source_name: DN6, mature leaf, predawn, well-watered


title: NM6_predawn_water-limited_rep2

description:
Clonally propagated.
6 weeks without water limitation followed by 14 days without further input of water.

Leaves collected in the hour before lights were turned on (Pre-dawn).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0803


title: NM6_midday_well-watered_rep1

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour in the middle of the photoperiod (Mid-day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0297


title: ES Cells+N2B27 medium+1% O2 6 hrs 3

description: Biological replicate 3


title: NM6_midnight_water-limited_rep2

description:
Clonally propagated.
6 weeks without water limitation followed by 14 days without further input of water.

Leaves collected in the hour in the middle of the dark period (Midnight).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0311

source_name: DN6, mature leaf, midnight, water-limited


title: ES Cells+ESC medium+DAPT 4 hrs N2B27 medium+DAPT 6 hrs 2

description: Biological replicate 2


title: NM6_predawn_well-watered_rep1

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour before lights were turned on (Pre-dawn).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0379


title: NM6_midnight_well-watered_rep2

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour in the middle of the dark period (Midnight).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0373


title: NM6_midnight_well-watered_rep1

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour in the middle of the dark period (Midnight).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0802


title: NM6_midnight_water-limited_rep1

description:
Clonally propagated.
6 weeks without water limitation followed by 14 days without further input of water.

Leaves collected in the hour in the middle of the dark period (Midnight).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0309


title: NM6_midnight_water-limited_rep3

description:
Clonally propagated.
6 weeks without water limitation followed by 14 days without further input of water.

Leaves collected in the hour in the middle of the dark period (Midnight).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0335


title: DN34_midday_water-limited_rep1

description:
Clonally propagated.
6 weeks without water limitation followed by 12 days without further input of water.

Leaves collected in the hour in the middle of the photoperiod (Mid-day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0312

organism: Populus x canadensis

source_name: DN34, mature leaf, midday, water-limited


title: DN34_midday_well-watered_rep1

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour in the middle of the photoperiod (Mid-day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0303

source_name: DN34, mature leaf, midday, well-watered


title: DN34_lateday_water-limited_rep3

description:
Clonally propagated.
6 weeks without water limitation followed by 12 days without further input of water.

Leaves collected in the hour before lights were turned off (Late day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0339

source_name: DN34, mature leaf, lateday, water-limited


title: DN34_midday_well-watered_rep2

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour in the middle of the photoperiod (Mid-day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0304


title: DN34_lateday_well-watered_rep3

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour before lights were turned off (Late day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0367

source_name: DN34, mature leaf, lateday, well-watered


title: DN34_lateday_water-limited_rep1

description:
Clonally propagated.
6 weeks without water limitation followed by 12 days without further input of water.

Leaves collected in the hour before lights were turned off (Late day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0338


title: DN34_midday_water-limited_rep2

description:
Clonally propagated.
6 weeks without water limitation followed by 12 days without further input of water.

Leaves collected in the hour in the middle of the photoperiod (Mid-day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0313


title: DN34_midday_water-limited_rep3

description:
Clonally propagated.
6 weeks without water limitation followed by 12 days without further input of water.

Leaves collected in the hour in the middle of the photoperiod (Mid-day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0336


title: DN34_lateday_water-limited_rep2

description:
Clonally propagated.
6 weeks without water limitation followed by 12 days without further input of water.

Leaves collected in the hour before lights were turned off (Late day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0368


title: DN34_predawn_water-limited_rep3

description:
Clonally propagated.
6 weeks without water limitation followed by 12 days without further input of water.

Leaves collected in the hour before lights were turned on (Pre-dawn).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0371

source_name: DN34, mature leaf, predawn, water-limited


title: DN34_predawn_water-limited_rep1

description:
Clonally propagated.
6 weeks without water limitation followed by 12 days without further input of water.

Leaves collected in the hour before lights were turned on (Pre-dawn).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0370


title: DN34_midday_well-watered_rep3

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour in the middle of the photoperiod (Mid-day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0305


title: DN34_lateday_well-watered_rep2

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour before lights were turned off (Late day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0366


title: DN34_predawn_well-watered_rep3

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour before lights were turned on (Pre-dawn).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0353

source_name: DN34, mature leaf, predawn, well-watered


title: DN34_lateday_well-watered_rep1

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour before lights were turned off (Late day).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0337


title: DN34_predawn_well-watered_rep2

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour before lights were turned on (Pre-dawn).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0369


title: DN34_predawn_water-limited_rep2

description:
Clonally propagated.
6 weeks without water limitation followed by 12 days without further input of water.

Leaves collected in the hour before lights were turned on (Pre-dawn).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0385


title: DN34_midnight_water-limited_rep3

description:
Clonally propagated.
6 weeks without water limitation followed by 12 days without further input of water.

Leaves collected in the hour in the middle of the dark period (Midnight).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0345

source_name: DN34, mature leaf, midnight, water-limited


title: DN34_midnight_well-watered_rep2

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour in the middle of the dark period (Midnight).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0341

source_name: DN34, mature leaf, midnight, well-watered


title: DN34_midnight_well-watered_rep3

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour in the middle of the dark period (Midnight).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0342


city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_7 hour treatment of Sa strain LUG862 rep 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 40C on our custom Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Staphylococcus aureus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: RN6390 is a laboratory S. aureus strain and the parental strain of all other strains used herein. Strains LUG855, LUG776, and LUG862 were kindly provided by M. Gabriela Bowden (Texas A&M University System Health Science Center) [9]. LUG855 contains the φSLT phage carrying among other genes the lukSF genes encoding PVL [9]; LUG776 contains φSLT in which the lukSF genes were deleted [9]; LUG862 is LUG776 carrying a plasmid with the lukSF genes (pLUG534) [9] and was grown with addition of 10 μg/ml chloramphenicol. All strains were kept in glycerol stocks after being received and were not passaged. Tryptic soy broth (TSB) was used for all experiments.  The mutation identified in LUG855 was repaired using the allelic replacement method with plasmid pKOR1 and called LUG855R.

extract_protocol: Total RNA was isolated by use of an RNeasy Mini Kit (Qiagen) recommended by a standard protocol.

treatment_protocol: RNA isolation from cultures grown to early stationary growth phase (7 h)

tag: strain LUG862


description: Gene expression data from_7 hour treatment of Sa strain LUG862 rep 1


description: Gene expression data from_7 hour treatment of Sa strain LUG855R rep 1

tag: strain LUG855R


description: Gene expression data from_7 hour treatment of Sa strain LUG776 rep 3

tag: strain LUG776


description: Gene expression data from_7 hour treatment of Sa strain LUG855 rep 3

tag: strain LUG855


description: Gene expression data from_7 hour treatment of Sa strain LUG855R rep 2


description: Gene expression data from_7 hour treatment of Sa strain LUG855 rep 1


title: DN34_midnight_well-watered_rep1

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour in the middle of the dark period (Midnight).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0340

tag: treatment


description: Gene expression data from_7 hour treatment of Sa strain LUG862 rep 3


title: DN34_predawn_well-watered_rep1

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour before lights were turned on (Pre-dawn).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0352


description: Gene expression data from_7 hour treatment of Sa strain LUG855 rep 2


description: Gene expression data from_7 hour treatment of Sa strain LUG776 rep 1


description: Gene expression data from_7 hour treatment of Sa strain LUG855R rep 3


description: Gene expression data from_7 hour treatment of Sa strain LUG776 rep 2


title: siRNA/PepFec6

city: Tartu

first: Jonas

last: Hälldin

address: Riia st 23

department: Biotech Department

country: Estonia

institute: Tartu University

hyb_protocol: Illumina

scan_protocol: Illumina

data_processing: Output data normalized log 2 transformed, filtered according to rows with significant p-values, using R

label: Biotinylated

source_name: siRNA 50nM; PepFec6

label_protocol: Illumina Total Prep

growth_protocol: Cells were grown in 10% FBS DMEM with Glutamax

extract_protocol: RiboPure (Ambion)

treatment_protocol: Cells were treated in serum free medium for 4 hours. After internalization the medium was changed and complete medium added. Incubation was 24h in total.

value: HeLa


title: siRNA/Lipofectamine 2000

source_name: siRNA 50nM; Lipofectamine 2000


title: DN34_midnight_water-limited_rep1

description:
Clonally propagated.
6 weeks without water limitation followed by 12 days without further input of water.

Leaves collected in the hour in the middle of the dark period (Midnight).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0343


description: Gene expression data from_7 hour treatment of Sa strain RN6390 rep 3

tag: strain RN6390


description: Gene expression data from_7 hour treatment of Sa strain RN6390 rep 2


title: Untreated

source_name: Untreated

tag: cell type


title: NM6_predawn_well-watered_rep2

description:
Clonally propagated.
8 weeks without water limitation.

Leaves collected in the hour before lights were turned on (Pre-dawn).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0380


description: Gene expression data from_7 hour treatment of Sa strain RN6390 rep 1


title: DN34_midnight_water-limited_rep2

description:
Clonally propagated.
6 weeks without water limitation followed by 12 days without further input of water.

Leaves collected in the hour in the middle of the dark period (Midnight).

Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

bot0805


title: P19 cells - 4 days, rep1

city: Stratford

first: Eric

middle: G

last: Moss

address: UMDNJ-SOM/GSBS

department: Molecular Biology

institute: UMDNJ

description: Gene Expression data from unmodified mouse P19 embryonal carcinoma cells

hyb_protocol: The cRNA was fragmented to 35-200 bases length using Affymetrix protocols and hybridized to HG U133 Plus 2.0 array set at 45ºC for 16 hours in an Affymetrix GeneChip® Hybridization Oven 640.

scan_protocol: Each GeneChip was then washed and stained with Streptavidin–Phycoerythrin conjugate (SAPE; Invitrogen Corp.) using an Affymetrix Fluidics Station 450 and scanned on a Affymetrix GeneChip scanner.

data_processing: Scanned image files were analyzed using the Gene Chip Operating System Version 1.4 software, and standard thresholding and filtering operations were used.   The data was normalized using house keeping genes. Normalization assumes that for a subset of genes (i.e., housekeeping genes) the ratio of measured expression averaged over the set should be one.

label_protocol: Isolated total RNA was processed as recommended by Affymetrix, Inc. (Santa Clara, CA). In brief, cDNA was synthesized from the total RNA using the Super-Script Double Stranded cDNA Synthesis kit and T7 Oligo (dT) primers. Using the double stranded cDNA as template, biotin labeled cRNA was generated by in vitro transcription (MEGAscript Labeling Kit) reaction.

extract_protocol: Total RNA was isolated using GenElute mammalian total RNA miniprep kit (Sigma-Aldrich, St. Louis, MO, USA)

treatment_protocol: Cells were aggregated in Petri dishes in alpha-MEM, 2.5% fetal bovine serum, 7.5% bovine serum, and 50 units/mL of penicillin/streptomycin, and 5x10-7M all-trans retinoic acid

tag: control cells


title: mutant p19W164A versus empty vector replicate 2 dye swap

status: Public on Dec 30 2009

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description:
p19W164A versus control biological replicate 2 of 3. Technical replicate 2 of 2.
MO__251209747452_pRK5-W-rep2_Cy5_pRK5-p19-W-rep2_Cy3_DS.gpr

hyb_protocol: Three biological replicate experiments were performed and the empty vector negative control was used as the common reference to test the effect of p19 and p19W164A overexpression. For all three three biological replicates each experimental pair of labelled samples was co-hybridized on two separate microarrays with dye swapping to correct for dye bias effects. Thus, up to six microarray hybridizations were processed for each of the two comparisons -p19 vs empty vector and p19W164A versus empty vector-, totalling 12 array datasets.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT 100% laser power settings and quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular feature finding option.

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were balanced by lowess normalization using 0.3 as the span parameter with reduced weights in control and poor quality spots, followed by scaling across chips. Target genes were considered as differentially expressed when above the 95% rank in the B empirical Bayes statistic and a set fold change. All quantitative and statistical analyses were performed using using Limma package in the R. environment (Smyth 2004).

label_protocol: 500 ng of total RNA were reverse transcribed, amplified, labelled by in vitro transcription using the Low Input Linear Amplification Kit (Agilent 5184-3523), and hybridized following the manufacturer’s instructions (SSC wash Agilent 60-mer oligo microarray processing protocol, Version 4.1, April 2004).

growth_protocol: HeLa cells were cultured in DMEM medium supplemented with 10% FBS and penicillin (10.000U/ml) and streptomycin (10 mg/ml), at 37ºC and 5% CO2 and 100% humidity.

extract_protocol: RNA was extracted using standard total RNA extraction protocol (Nucleospin)

tag: Human HeLa Cells transfected with pRK5 empty vector

tag: Human HeLa Cells transfected with pRK5-p19W164A


title: mutant p19W164A versus empty vector replicate 2

description:
p19W164A versus control biological replicate 2 of 3. Technical replicate 1 of 2.
MO__251209747525_pRK5-W-rep2_Cy3_pRK5-p19-W-rep2_Cy5.gpr


title: wild type p19 versus empty vector replicate 3 dye swap

description:
p19 versus control biological replicate 3 of 3. Technical replicate 2 of 2.
MO__251209747529_pRK5-rep3_Cy5_pRK5-p19-rep3_Cy3_DS.gpr

tag: Human HeLa Cells transfected with pRK5-p19


title: P19 cells - 4 days, rep2

source_name: unmodified mouse P19 embryonal carcinoma cells


title: mutant p19W164A versus empty vector replicate 3

description:
p19W164A versus control biological replicate 3 of 3. Technical replicate 1 of 2.
MO__251209747526_pRK5-W-rep3_Cy3_pRK5-p19-W-rep3_Cy5.gpr


title: P19 cells plus LIN28 - 4 days, rep1

description: Gene Expression data from P19 Cells LIN28

source_name: Mouse P19 cells constitutively expressing LIN28A, induced to differentiate with retinoic acid, 4 days.

tag: experimental cells

value: mouse P19 embryonal carcinoma cells (ATCC) constitutively expressing LIN28A, induced to differentiate with retinoic acid, 4 days.


title: wild type p19 versus empty vector replicate 1 dye swap

description:
p19 versus control biological replicate 1 of 3. Technical replicate 2 of 2.
MO__251209747527_pRK5-rep1_Cy5_pRK5-p19-rep1_Cy3_DS.gpr


title: mutant p19W164A versus empty vector replicate 1 dye swap

description:
p19W164A versus control biological replicate 1 of 3. Technical replicate 2 of 2.
MO__251209747530_pRK5-W-rep1_Cy5_pRK5-p19-W-rep1_Cy3_DS.gpr


title: wild type p19 versus empty vector replicate3

description:
p19 versus control biological replicate 3 of 3. Technical replicate 1 of 2.
MO__251209747523_pRK5-rep3_Cy3_pRK5-p19-rep3_Cy5.gpr


title: wild type p19 versus empty vector replicate 2

description:
p19 versus control biological replicate 2 of 3. Technical replicate 1 of 2.
MO__251209747522_pRK5-rep2_Cy3_pRK5-p19-rep2_Cy5.gpr


title: mutant p19W164A versus empty vector replicate 3 dye swap

description:
p19W164A versus control biological replicate 3 of 3. Technical replicate 2 of 2.
MO__251209747451_pRK5-W-rep3_Cy5_pRK5-p19-W-rep3_Cy3_DS.gpr


title: P19 cells plus LIN28 - 4 days, rep2


title: Pre-Treatment breast tumor 11529

city: St Louis

first: Rekha

last: Meyer

state: MO

address: 4320 Forest Park Av

institute: Washington University School of Medicine

description: Stage II or III breast cancer Patient 19

hyb_protocol: 15 ug of biotinylated cRNAs were hybridized to Affymetrix U133Plus2  GeneChipTM oligonucleotide arrays.

scan_protocol: Gene chips were scanned using GS3000.

data_processing: The data were analyzed with Microarray Suite version 5.0(MAS 5.0) algorithm.The arrays were scaled to a target intensity of 1,500.

source_name: Pre-Treatment breast tumor

label_protocol: Biotinylated cRNA were prepared according tot the standard Affymetrix protocol from 6 ug total RNA(Expression analysis Technical Manual, 2001 ,Affymetrix).

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

treatment_protocol: Patients with clinical stage II or III breast cancer were enrolled into a prospective clinical trial of four cycles of epirubicin (75 mg/m2) and docetaxel (75 mg/m2) every 3 weeks prior to surgery and two cycles after surgery. Half of the patients received zoledronic acid every 3 weeks beginning at the time of chemotherapy. Tumor size was measured from mammograms and ultrasound studies prior to treatment. pCR was defined as no residual invasive disease in the breast or lymph nodes. Residual in situ carcinoma was also considered a pCR [18]. Estrogen receptor (ER) and Her-2 status was determined on a diagnostic core obtained before treatment. The mean follow-up was 2 years with annual restaging. This study protocol was approved by the Institutional Review Board at Washington University. Written informed consent was obtained from each patient. RNA was extracted from snap frozen 14-gauge core samples obtained from pre-treatment tumors. Specimens containing more than 40% of tumor on histological examination were analyzed.

tag: gender

value: Female

tag: percent

tag: er

tag: pr

tag: grade

tag: histology

value: IDC

tag: positive nodes

tag: nodes examined

tag: recur

tag: race

value: Caucasian

tag: t stage


title: Pre-Treatment breast tumor 11532

description: Stage II or III breast cancer Patient 21


title: Pre-Treatment breast tumor 11582

description: Stage II or III breast cancer Patient 23

value: African American


title: Pre-Treatment breast tumor 11571

description: Stage II or III breast cancer Patient 22


title: Pre-Treatment breast tumor 11530

description: Stage II or III breast cancer Patient 20


title: Pre-Treatment breast tumor 11585

description: Stage II or III breast cancer Patient 24


title: mutant p19W164A versus empty vector replicate 1

description:
p19W164A versus control biological replicate 1 of 3. Technical replicate 1 of 2.
MO__251209747524_pRK5-W-rep1_Cy3_pRK5-p19-W-rep1_Cy5.gpr


title: wild type p19 versus empty vector replicate 2 dye swap

description:
p19 versus control biological replicate 2 of 3. Technical replicate 2 of 2.
MO__251209747528_pRK5-rep2_Cy5_pRK5-p19-rep2_Cy3_DS.gpr


title: Pre-Treatment breast tumor 11526

description: Stage II or III breast cancer Patient 18


title: Adult type II cells day 5 treated, lung #5

city: San Francisco

first: Philip

middle: L

last: Ballard

address: 513 Parnassus St

department: Neonatology

institute: UCSF

description: gene expession data from cells cultured in presence of DCI

hyb_protocol: Hybridization was performed as per Affymetrix protocol.

scan_protocol: Arrays were scanned using an Affymetrix scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Adult lung type II cells

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

growth_protocol: Fetal cells were cultured 5 days with or without DCI.  Adult cells were harvested after isolation and also cultured 5 days with or without DCI.

extract_protocol: Total RNA was extracted from control and DCI-treated cells using RNA STAT (Tel-Test, Inc., Friendswood, TX) per the manufacturer’s instructions.

treatment_protocol: Cultured cells were exposed to dexamethasone plus 8-Br-cAMP plus isobutylmethylxanthine (DCI-treated) or  diluent (control).

tag: growth protocol

value: cells cultured 5 days

tag: agent

value: DCI

tag: time

value: Day 5


title: wild type p19 versus empty vector replicate 1

description:
p19 versus control biological replicate 1 of 3. Technical replicate 1 of 2.
MO__251209747521_pRK5-rep1_Cy3_pRK5-p19-rep1_Cy5.gpr

tag: Human HeLa Cells transfected with pRK5 empty vector


title: Pre-Treatment breast tumor 11519

description: Stage II or III breast cancer Patient 16


title: Adult type II cells day 5 treated, lung #4


title: Adult type II cells day 0, lung #5

description: gene expression data from freshly isolated cells

value: freshly isolated cells

value: Day 0


title: Adult type II cells day 0, lung #4


title: Adult type II cells day 5 treated, lung #3


title: Adult type II cells day 0, lung #3


title: Adult type II cells day 5 control, lung #5

description: gene expession data from cells cultured under control conditions

value: control


title: Adult type II cells day 5 control, lung #4


title: Adult type II cells day 5 control, lung #3


title: Pre-Treatment breast tumor 11524

description: Stage II or III breast cancer Patient 17


title: Pre-Treatment breast tumor 8209

description: Stage II or III breast cancer Patient 13


title: Pre-Treatment breast tumor 8413

description: Stage II or III breast cancer Patient 15


title: Pre-Treatment breast tumor 8210

description: Stage II or III breast cancer Patient 14


title: Adult type II cells day 5 control, lung #2


title: Pre-Treatment breast tumor 8199

description: Stage II or III breast cancer Patient 11


title: Adult type II cells day 0, lung #2


title: Adult type II cells day 5 treated, lung #2


title: Pre-Treatment breast tumor 8200

description: Stage II or III breast cancer Patient 12


title: Adult type II cells day 0, lung #1


title: Adult type II cells day 5 treated, lung #1


title: Pre-Treatment breast tumor 8191

description: Stage II or III breast cancer Patient 10


title: Pre-Treatment breast tumor 8190

description: Stage II or III breast cancer Patient 9


title: MG1655 pFnrS#3 + arabinose

city: Bethesda

first: Sylvain

last: Durand

address: 5000 Rockville Pike

institute: NICHD

hyb_protocol: Following fragmentation, 6 µg of cDNA was hybridized for 16 hr at 45˚C on GeneChip E.coli Genome 2.0 Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.

data_processing: The data were analyzed with Affymetrix GeneChip operating software (1.4.0.036) using the following expression analysis settings:  1. Scaling: All probe set with target intensity of each array arbitrarily set to 500   2. Normalization: All probe set

organism: Escherichia coli

source_name: Escherichia coli with pFnrS

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 6 µg total RNA (Section 3 Prokaryotic sample and array processing).

extract_protocol: Total RNA was extracted using hot phenol.

tag: strain


title: Adult type II cells day 5 control, lung #1


title: IP-2.1

city: Boston

first: Hailei

last: Zhang

state: MA

address: 44 Binney Street

institute: Dana-Farber Cancer Institute

description: microRNA expression

hyb_protocol: Labeled miRNA were Hybridize at 56°C for 16 hours on Exiqon V. 11.0 miRCURY LNA microRNA platform. Platforms were washed and stained using Tecan HS480 Pro automated hybridization stations.

scan_protocol: Platforms were scanned using the Agilent G2505B Microarray Scanners.

data_processing: Data were normalized using non-linear regression method (LOESS), and unsupervised hierarchical clustering was performed on log2(Hy3/Hy5); ΔLogMediaRatio > 0.50.

source_name: Ink4a/Arf-/- Pten-/- mouse astrocytes

label_protocol: 5'-phosphtes were removed from terminal of microRNAs by Calf Intestinal Alkaline Phosphatase then Hy3/Hy5 fluorescent labels were attached enzymatically to the 3’-end of the miRNAs in the total RNA sample.

extract_protocol: Total RNA was isolated from the HiPure miRNA Isolation Kit (Roche)

tag: cell type

value: Ink4a/Arf-/- Pten-/- mouse astrocytes

source_name: Common reference Pool

tag: cell line

value: Common reference Pool


title: MG1655 pAZ3#1 + arabinose

source_name: Escherichia coli with empty vector (pAZ3)


title: IP-2.2

description: microRNA expression


title: IP-1.2

description: microRNA expression


title: IP-G.1

description: microRNA expression


title: MG1655 pAZ3#2 + arabinose


title: MG1655 pAZ3#3 + arabinose


title: IP-1.1

description: microRNA expression


title: MG1655 pFnrS#2 + arabinose


title: IP-G.2

description: microRNA expression


title: Pre-Treatment breast tumor 8170

description: Stage II or III breast cancer Patient 7

tag: gender

tag: percent


title: Pre-Treatment breast tumor 8189

description: Stage II or III breast cancer Patient 8

tag: er

tag: pr


title: Pre-Treatment breast tumor 7422

description: Stage II or III breast cancer Patient 5

tag: grade

tag: histology


title: Pre-Treatment breast tumor 8159

description: Stage II or III breast cancer Patient 6

tag: positive nodes

tag: nodes examined


title: Pre-Treatment breast tumor 7421

description: Stage II or III breast cancer Patient 4

tag: recur

tag: race


title: MG1655 pFnrS#1 + arabinose


title: Pre-Treatment breast tumor 7415

description: Stage II or III breast cancer Patient 3

tag: t stage


title: Pre-Treatment breast tumor 7412

description: Stage II or III breast cancer Patient 2


title: U-2.2

description: microRNA expression


title: U-G.1

description: microRNA expression


title: U-G.2

description: microRNA expression


title: U-2.1

description: microRNA expression


title: U-1.2

description: microRNA expression


title: Hs-G.1

description: microRNA expression


title: U-1.1

description: microRNA expression


title: Hs-1.1

description: microRNA expression


title: Hs-1.2

description: microRNA expression


title: Hs-2.2

description: microRNA expression


title: Hs-2.1

description: microRNA expression


title: Hs-G.2

description: microRNA expression


title: U87-20.2

description: U87 cell line

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

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

data_processing: The data were analyzed with R Bioconductor affy package

source_name: QK-knockdown U87 transduced with miR-20a

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted using the Micro-to-Midi Total RNA Purification System (Invitrogen)

tag: tumor tissue source

value: Cell line established

tag: tumor organ site

value: Brain

tag: pathological diagonosis

value: Glioma


title: Hs-20-1

description: Hs683 cell line

source_name: QK-knockdown Hs683 cells transduced with and miR-20a


title: U87-mC2

description: U87 cell line

source_name: QK-knockdown U87 transduced with a scrambled non-targeting microRNA (miR-NT)


title: Pre-Treatment breast tumor 7411

description: Stage II or III breast cancer Patient 1


title: Hs-20-2

description: Hs683 cell line


title: U87-20.1

description: U87 cell line


title: Hs683_Gb

description: Hs683 cell line

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Hs683 cells infected with shGFP as control


title: Hs683_Gc

description: Hs683 cell line


title: Hs683_Ga

description: Hs683 cell line


title: IP-20-2

description: Ink4a/Arf-/- Pten-/- primary mouse astrocytes

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

source_name: QK-knockdown Ink4a/Arf-/- Pten-/- mouse astrocytes transduced with miR-20a

value: Cell line:1st deg. culture

value: Normal


title: U87-mC1

description: U87 cell line


title: Hs-C-2

description: Hs683 cell line

source_name: QK-knockdown Hs683 cells transduced with a scrambled non-targeting microRNA (miR-NT)


title: IP-C-1

source_name: QK-knockdown Ink4a/Arf-/- Pten-/- mouse astrocytes transduced with a scrambled non-targeting microRNA (miR-NT)


title: Hs683_1c

description: Hs683 cell line

source_name: Hs683 cells infected with shQk-5


title: IP-C-2


title: Hs683_1a

description: Hs683 cell line


title: IP-Gb

source_name: shGFP inf. Ink/Arf/PTEN ko astroc.

tag: tumor stage

value: Non-Tumor


title: IP-2c

source_name: shQk2 inf. Ink/Arf/PTEN ko astroc.


title: Hs683_2a

description: Hs683 cell line

source_name: Hs683 cells infected with shQk-2


title: IP-2b


title: IP-Gc


title: IP-Ga


title: Hs683_1b

description: Hs683 cell line


title: Hs-C-1

description: Hs683 cell line


title: IP-20-1


title: Hs683_2b

description: Hs683 cell line


title: IP-2a


title: IP-1b

source_name: shQk1 inf. Ink/Arf/PTEN ko astroc.


title: IP-1c


title: Hs683_2c

description: Hs683 cell line


title: DS-TL_sample1

status: Public on Dec 29 2009

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

country: Germany

institute: Goehte University Frankfurt

description: Gene expression data from sorted leukemic blasts (DS-TL)

hyb_protocol: The fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to MOE 430.2 chips overnight at 45°C. The chips were then transferred to a fluidics instrument that performs washes to remove cRNA that had not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.

data_processing: The raw CEL files were imported into dChip and invariant-set normalized with dChip as described in the user's manual (http://biosun1.harvard.edu/complab/dchip/normalizing%20arrays.htm). After normalization, the model-based expression values were calculated by dChip and exported.

source_name: Down syndrome transient leukemia blasts, sample1

extract_protocol: Trizol extraction of total RNA followed by cleaning up using columns from the Promega SV total RNA isolation kit.

tag: cell type

value: sorted leukemic blast cells

tag: disease status

value: Down syndrome transient leukemia


title: ML-DS_sample3

description: Gene expression data from sorted leukemic blasts (ML-DS)

source_name: Down syndrome acute myeloid leukmia blasts, FAB M7, sample3

value: Down syndrome AML FAB M7


title: AML_FABM5_sample2

description: Gene expression data from sorted leukemic blasts (AML FAB M5)

source_name: Acute myeloid leukemia blasts, FAB M5, sample2

value: AML FAB M5


title: AML_FABM7_sample2

description: Gene expression data from sorted leukemic blasts (AML FAB M7)

source_name: Acute myeloid leukemia blasts, FAB M7, sample2

value: AML FAB M7


title: DS-TL_sample2

source_name: Down syndrome transient leukemia blasts, sample2


title: DS-TL_sample3

source_name: Down syndrome transient leukemia blasts, sample3


title: ML-DS_sample2

source_name: Down syndrome acute myeloid leukmia blasts, FAB M7, sample2


title: AML_FABM5_sample1

source_name: Acute myeloid leukemia blasts, FAB M5, sample1


title: AML_FABM7_sample1

source_name: Acute myeloid leukemia blasts, FAB M7, sample1


title: IP-1a


title: ML-DS_sample1

source_name: Down syndrome acute myeloid leukmia blasts, FAB M7, sample1


title: JMJ_mmP (2)

type: genomic

first: Xiaohua

last: Shen

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

description: JMJ ChIP in J1 ES cells on mouse promoter 1.0R chip

hyb_protocol: About 2-4 ug of labeled DNA were hybridized for 16 hr at 45C on tiling arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing:
The data were analyzed with Model-based Analysis of Tiling-arrays for ChIP-chip (MAT) developed by the Liu lab and processed based on MM8 annotation.
MATScore, p value (in form of -10log10_Pvalue), fold-change, FDR, peak position and length were reported for each peak identified by MAT program.

source_name: JMJ ChIP in J1 ES cells

label_protocol: Fragmented DNA was labeled with biotin-N6-ddATP by terminal deoxynucleiotidyl transferase.

growth_protocol: standard culture conditions were used to culture ES cells.

extract_protocol: pulled down chromatin was reversely crosslinked and DNA was precipitated by isopropanol.

treatment_protocol: mouse ES cells were fixed with 0.8% formaldehyde for 10 min at room temperature. Cell lydates were ChIP'ed by antibodies recognizing EZH2 (Ac22, Upstate), SUZ12 (P15, Santa Cruz), JMJ (Abcam) or by using streptavidin-Dyna beads (Invitrogen). DNA fragments were isolated and amplified by LM-PCR. Amplified DNA was fragmented and biotin labeled before hybridiztion.

tag: antibody

value: JMJ


title: Undifferentiated HepaRG, biological replicate 2

city: Kansas City

first: Steven

last: Hart

state: KS

address: 3901 Rainbow Blvd

department: Pharmacology, Toxicology & Therapeutics

institute: University of Kansas Medical Center

hyb_protocol: 200ul hybridization solution per GeneChip using GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Single Scan

data_processing: R/Bioconductor

source_name: Undifferentiated elongate HepaRG

label_protocol: In-vitro Transcription using the GeneChip 3` IVT Express Kit

extract_protocol: Trizol

tag: cell line

value: HepaRG

tag: differentiation state

value: undifferentiated

tag: gender

value: female


title: Undifferentiated HepaRG, biological replicate 3


title: Undifferentiated HepaRG, biological replicate 1


title: Testis_Bisphenol_treatmentC2_Rep2

status: Public on Jun 01 2010

city: Madrid

first: Luis

middle: A.

last: Lopez-Fernandez

address: Dr. Esquerdo 46

department: Pharmacy

institute: Hospital General Universitario Gregorio Marañon

description:
Dye-Swap replicates were performed: one slide hybridized with experimental and control targets labeled with Cy3 and Cy5, respectively; and the second slide with the same type of targets but inversely labeled. Target refers to labeled aRNA while probe refers to the oligonucleotides spotted on the microarray platform.
Imaging and data generation were carried out using a GenePix 4000B (Axon Instruments) and associated software from Axon Instruments, Inc. The microarray slides were scanned with dual lasers with wavelength frequencies to excite Cy3 and Cy5. Images were captured in TIFF files. Information extraction for a given spot was based on the median value for the signal pixels minus the median value for the background pixels to produce a gene set data file for all the DNA spots. The Cy3 and Cy5 fluorescence signal intensities were normalized.

hyb_protocol: Prehybridization was performed at 42ºC for 30-45 minutes in 6X SSC, 0.5% SDS and 1% BSA. Slides were rinsed five times with destilled water. Cy5 and Cy3 amplified RNA (aRNA) probes were mixed (150 pmol of each label) with 10 µg of PolyA (Sigma) and 1 µg of Cot-DNA (Invitrogen) in a final volume of 40 µl of hybridization buffer (50% formamide, 6X SSC, 0.5% SDS, 5X Denhardt’s). The probe was denatured at 95ºC for 5 minutes and applied to the slide using a coverslip. Slides were then incubated at 42ºC for 16h in hybridization chambers (Array-It). After incubation, slides were washed twice with 0.1X SSC, 0.1% SDS for 5 minutes each, three times with 0.1X SSC for 5 minutes and finally in distilled water for 10 seconds. Slides were dried by centrifugation at 563g for 1 minute.

scan_protocol: Images from Cy3 and Cy5 channels were equilibrated and captured with an Axon 4000B scanner (Axon Instruments) and spots quantified using GenePix 5.1 software (Axon). GPR files were then included in almaZen database software (Bioalma). Signals were background subtracted, and normalized by total intensity and lowess_print_tip_group.

data_processing: GPR files with raw data were introduced in almaZen database software (http://www.Bioalma.com). Signals were background subtracted, and normalized by total intensity and Print_tip_group_Lowess.

label_protocol: Starting with total RNA from pools (Three animals), full length cDNAs were synthesized from oligo(dT) primers bearing a T7 promoter. These cDNAs were used as template for in vitro transcription by T7-RNA-Polymerase to amplify the mRNAs; following the Amino Allyl MessageAmp™ aRNA Kit (Ambion, Inc.) protocol. The amplified mRNAs (aRNA) were labeled either with Cy3 or Cy5 dyes, using Amersham CyDye Post-Labeling Reactive Dyes (Amersham Biosciences). The incorporated dye was spectrophotometrically quantified using NanoDrop (NanoDrop Technologies)

extract_protocol: Total RNA from testes of animals was extracted using TRIzol reagent (Invitrogen), according to the manufacturer’s standard protocol. RNA samples were spectrophotometrically quantified using NanoDrop (NanoDrop Technologies). To minimize the effect of inter-individual expression variability we made pools of RNA from at least 3 individual RNA samples from each experimental condition (same quantity of total RNA per sample). Pools of RNA were checked for quality performing Experion analysis (Bio-Rad Laboratories).

treatment_protocol: No treatment. Testis from four weeks mice were collected and RNA isolated.

tag: strain

value: Male

tag: tissue

value: Testis

tag: age

value: four weeks

tag: agent

value: not exposed to chemical compounds.

label_protocol: Starting with total RNA from pools (three animals), full length cDNAs were synthesized from oligo(dT) primers bearing a T7 promoter. These cDNAs were used as template for in vitro transcription by T7-RNA-Polymerase to amplify the mRNAs; following the Amino Allyl MessageAmp™ aRNA Kit (Ambion, Inc.) protocol. The amplified mRNAs (aRNA) were labeled either with Cy3 or Cy5 dyes, using Amersham CyDye Post-Labeling Reactive Dyes (Amersham Biosciences). The incorporated dye was spectrophotometrically quantified using NanoDrop (NanoDrop Technologies).

treatment_protocol: Mothers were exposed to Bisphenol A (in ethanol) two weeks before mating, maintained during pregnancy,and then the offspring treated with the same dose during four weeks after birth, 50 mg/l. Male offspring were sacrificed to obtain the testis four weeks after birth.


title: HepG2, biological replicate 2


title: Differentiated HepaRG, biological replicate 1

source_name: Differentiated well-confluent HepaRG

value: differentiated


title: Differentiated HepaRG, biological replicate 3


title: Liver, biological replicate 1

source_name: Liver

value: liver


title: Liver, biological replicate 2


title: HepG2, biological replicate 3


title: HepG2, biological replicate 1


title: JMJ_mmP (1)


title: Liver, biological replicate 3


title: JMJ_mmP (3)


title: SUZ12_mmP (1)

description: SUZ12 ChIP in J1 ES cells on mouse promoter 1.0R chip

source_name: SUZ12 ChIP in J1 ES cells


title: Differentiated HepaRG, biological replicate 2


title: bfJMJ_A (3)

description: bfJMJ bioChIP in CJ7 cells on A chip

source_name: bfJMJ bioChIP in CJ7 cells

value: bfJMJ


title: bfEED_mmP

description: bfEED bioChIP in J1 ES cells on mouse promoter 1.0R chip

source_name: bfEED bioChIP in J1 ES cells

value: bfEED


title: Input_mmP (6)

description: genomic DNA input from CJ7 cells on mouse promoter 1.0R chip

source_name: genomic DNA input from CJ7 cells


title: Input_mmP (5)

description: genomic DNA input from J1 cells on mouse promoter 1.0R chip

source_name: genomic DNA input from J1 cells


title: EZH2_mmP

description: EZH2 ChIP in J1 ES cells on mouse promoter 1.0R chip

source_name: EZH2 ChIP in J1 ES cells


title: bfJMJ_A (2)

description: bfJMJ bioChIP in CJ7 cells on A chip


title: SUZ12_mmP (2)


title: Input_mmP (4)


title: Input_A (3)

description: genomic DNA input from Ezh2-/- cells on A chip

source_name: genomic DNA input from Ezh2-/- cells


title: Input_mmP (3)


title: null day-8 (b)

description: Jmj (-/-) mutant ES cells at day 8 of LIF withdrawal, biological rep 2

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

data_processing: The data were analyzed with dChip.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: ES cell differentiation was induced by LIF withdrawal and cells were collected at various time points from day 0 to day 8.

value: Jmj (-/-) mutant embryonic stem (ES) cells


title: null day-6 (d)

description: Jmj (-/-) mutant ES cells at day 6 of LIF withdrawal, biological rep 4


title: bfJMJ_G (2)

description: bfJMJ bioChIP in CJ7 cells on G chip


title: Input_mmP (2)


title: Input_A (1)

description: genomic DNA input from J1 cells expressing bfEZH1on A chip


title: bfJMJ_A (1)

description: bfJMJ bioChIP in CJ7 cells on A chip


title: Input_A (2)

description: genomic DNA input from CJ7 cells on A chip


title: Input_mmP (1)


title: null day-8 (a)

description: Jmj (-/-) mutant ES cells at day 8 of LIF withdrawal, biological rep 1


title: bfJMJ_G (3)

description: bfJMJ bioChIP in CJ7 cells on G chip


title: null day-6 (c)

description: Jmj (-/-) mutant ES cells at day 6 of LIF withdrawal, biological rep 3


title: bfJMJ_G (1)

description: bfJMJ bioChIP in CJ7 cells on G chip


title: Input_G (2)

description: genomic DNA input from CJ7 cells on G chip


title: null day-6 (b)

description: Jmj (-/-) mutant ES cells at day 6 of LIF withdrawal, biological rep 2


title: Input_G (3)

description: genomic DNA input from Ezh2-/- cells on G chip


title: null day-4 (e)

description: Jmj (-/-) mutant ES cells at day 4 of LIF withdrawal, biological rep 5


title: null day-6 (a)

description: Jmj (-/-) mutant ES cells at day 6 of LIF withdrawal, biological rep 1


title: Input_G (1)

description: genomic DNA input from J1 cells expressing bfEZH1on G chip


title: null day-6 (e)

description: Jmj (-/-) mutant ES cells at day 6 of LIF withdrawal, biological rep 5


title: bfJMJ_E (3)

description: bfJMJ bioChIP in CJ7 cells on E chip


title: null day-4 (d)

description: Jmj (-/-) mutant ES cells at day 4 of LIF withdrawal, biological rep 4


title: bfJMJ_E (2)

description: bfJMJ bioChIP in CJ7 cells on E chip


title: null day-4 (c)

description: Jmj (-/-) mutant ES cells at day 4 of LIF withdrawal, biological rep 3


title: liver_PPARd_ko_fasted_repl_2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

description: no additional information

hyb_protocol: Hybridisation of 5.5ug labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Washing and staining of the arrays was done on a Affymetrix 450 fluidics stations using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Arrays where then scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor XPS library (v1.4.8), utilizing the antigenomic probes as background estimates.

source_name: Liver from PPARbeta/delta ko mouse fasted for 24h, biological replicate 2

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 100ng of total RNA without rRNA reduction.A detailed description can be found in the User Manual, Chapter 3 (P/N 701880, revision 5).

growth_protocol: Livers were dissected from wildtype or PPARbeta/delta knock-out mice that were either fed or fasted for 24h.

extract_protocol: Total RNA was prepared from mouse livers using TRIzol reagent and whereafter purified total RNA was isolated using Qiagen RNEasy columns.

treatment_protocol: Male wildtype or PPARbeta/delta mice were either fed or fasted for 24 hours. At the end of the experiment, mice were anaesthetized with a mixture of isofluorane (1.5%), nitrous oxide (70%) and oxygen (30%), after which the mice were sacrificed by cervical dislocation. Livers were dissected, snap frozen in liquid nitrogen and kept at -80ºC until further analysis. For RNA analyses, tissue from the same part of the liver lobe was used.

tag: genotype/variation

value: PPARβ/δ knockout mutant

tag: protocol

value: fasted


title: bfJMJ_E (1)

description: bfJMJ bioChIP in CJ7 cells on E chip


title: null day-4 (b)

description: Jmj (-/-) mutant ES cells at day 4 of LIF withdrawal, biological rep 2


title: 256746-ES-rehyb-15-080930

city: Baltimore

middle: Stephen

last: Schafer

address: CRB1, Room 252a, 1650 Orleans St.

department: Pediatrics and Oncology

institute: Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins

hyb_protocol: See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details

scan_protocol: Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.

data_processing: Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as “failed.” These “failed” loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, “Methylated” loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either “methylated” or “failed”) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167.

source_name: MspI: CD34+ selected cord blood

label_protocol: Random 9-mers pre-labeled with either Cy3 or Cy5

extract_protocol: Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)

tag: sample source

value: Infant, normal, CD34+ selected cord blood

source_name: HpaII: CD34+ selected cord blood


title: 256743-ES-rehyb-14-080930

source_name: MspI: CD19+ selected cord blood

value: Infant, normal, CD19+ selected cord blood

source_name: HpaII: CD19+ selected cord blood


title: liver_PPARd_ko_fasted_repl_1

description: no additional information

source_name: Liver from PPARbeta/delta ko mouse fasted for 24h, biological replicate 1


title: 2567386-ES-rehyb-16-081006


title: liver_PPARd_ko_fasted_repl_3

description: no additional information

source_name: Liver from PPARbeta/delta ko mouse fasted for 24h, biological replicate 3


title: 256735-ES-rehyb-13-080930


title: liver_PPARd_ko_fed_repl_2

description: no additional information

source_name: Liver from PPARbeta/delta ko fed mouse, biological replicate 2

value: fed


title: null day-4 (a)

description: Jmj (-/-) mutant ES cells at day 4 of LIF withdrawal, biological rep 1


title: liver_PPARd_ko_fed_repl_4

description: no additional information

source_name: Liver from PPARbeta/delta ko fed mouse, biological replicate 4


title: null day-2 (e)

description: Jmj (-/-) mutant ES cells at day 2 of LIF withdrawal, biological rep 5


title: liver_PPARd_ko_fed_repl_3

description: no additional information

source_name: Liver from PPARbeta/delta ko fed mouse, biological replicate 3


title: 256742-ES-rehyb-12R-080923


title: Input_E (3)

description: genomic DNA input from Ezh2-/- cells on E chip


title: Input_E (2)

description: genomic DNA input from CJ7 cells on E chip


title: null day-2 (d)

description: Jmj (-/-) mutant ES cells at day 2 of LIF withdrawal, biological rep 4


title: 251497-ES-rehyb-6-080923

source_name: MspI: Pre-B ALL blasts, MLL-wt, TEL/AML+

value: Child, Pre-B cell ALL, t(12;21):TEL/AML

source_name: HpaII: Pre-B ALL blasts, MLL-wt, TEL/AML+


title: liver_PPARd_ko_fed_repl_1

description: no additional information

source_name: Liver from PPARbeta/delta ko fed mouse, biological replicate 1


title: Input_E (1)

description: genomic DNA input from J1 cells expressing bfEZH1on E chip


title: bfJMJ_D (3)

description: bfJMJ bioChIP in CJ7 cells on D chip

source_name: bfJMJ bioChIP in CJ7 cells


title: null day-2 (c)

description: Jmj (-/-) mutant ES cells at day 2 of LIF withdrawal, biological rep 3


title: bfJMJ_D (2)

description: bfJMJ bioChIP in CJ7 cells on D chip


title: null day-2 (b)

description: Jmj (-/-) mutant ES cells at day 2 of LIF withdrawal, biological rep 2


title: null day-2 (a)

description: Jmj (-/-) mutant ES cells at day 2 of LIF withdrawal, biological rep 1


title: bfJMJ_D (1)

description: bfJMJ bioChIP in CJ7 cells on D chip


title: liver_PPARd_wt_fasted_repl_5

description: no additional information

source_name: Liver from PPARbeta/delta wt mouse fasted for 24h, biological replicate 5

value: wt


title: null day-0 (c)

description: Jmj (-/-) mutant ES cells at day 0 (undifferentiated), biological rep 3


title: 251499-ES-rehyb-7-080923


title: liver_PPARd_wt_fasted_repl_4

description: no additional information

source_name: Liver from PPARbeta/delta wt mouse fasted for 24h, biological replicate 4


title: Input_D (3)

description: genomic DNA input from Ezh2-/- cells on D chip

source_name: genomic DNA input from Ezh2-/- cells


title: null day-0 (b)

description: Jmj (-/-) mutant ES cells at day 0 (undifferentiated), biological rep 2


title: 256598-ES-9R-090108

source_name: MspI: Pre-B ALL balsts, MLL-wt, hyperdiploid

value: Child, Pre-B cell ALL, hyperdiploid

source_name: HpaII: Pre-B ALL blasts, MLL-wt, hyperdiploid


title: Input_D (2)

description: genomic DNA input from CJ7 cells on D chip

source_name: genomic DNA input from CJ7 cells


title: liver_PPARd_wt_fasted_repl_2

description: no additional information

source_name: Liver from PPARbeta/delta wt mouse fasted for 24h, biological replicate 2

value: Male


title: null day-0 (a)

description: Jmj (-/-) mutant ES cells at day 0 (undifferentiated), biological rep 1


title: 251502-ES-rehyb-10-080923


title: Fl/Fl day-8 (b)

description: Jmj (fl/fl) wild-type ES cells at day 8 of LIF withdrawal, biological rep 2

value: Jmj (fl/fl) wild-type embryonic stem (ES) cells


title: liver_PPARd_wt_fasted_repl_1

description: no additional information

source_name: Liver from PPARbeta/delta wt mouse fasted for 24h, biological replicate 1


title: liver_PPARd_wt_fed_repl_4

description: no additional information

source_name: Liver from PPARbeta/delta wt fed mouse, biological replicate 4


title: 256564-ES-2R-090108

source_name: MspI: Pro-B ALL blasts, MLL-r

value: Infant, Pro-B cell ALL, t(4;11)(q23;21):MLL/AF4

source_name: HpaII: Pro-B ALL blasts, MLL-r


title: 251500-ES-rehyb-8-080923


title: 251491-ES-rehyb-3-080923

value: Infant, Pro-B cell ALL, t(11;19)(q23;p13):MLL/ENL


title: Input_D (1)

description: genomic DNA input from J1 cells expressing bfEZH1on D chip


title: Fl/Fl day- 8 (a)

description: Jmj (fl/fl) wild-type ES cells at day 8 of LIF withdrawal, biological rep 1


title: liver_PPARd_wt_fed_repl_3

description: no additional information

source_name: Liver from PPARbeta/delta wt fed mouse, biological replicate 3


title: bfJMJ_B (3)

description: bfJMJ bioChIP in CJ7 cells on B chip


title: bfJMJ_F (3)

description: bfJMJ bioChIP in CJ7 cells on F chip


title: bfJMJ_C (3)

description: bfJMJ bioChIP in CJ7 cells on C chip


title: bfJMJ_B (2)

description: bfJMJ bioChIP in CJ7 cells on B chip


title: liver_PPARd_wt_fasted_repl_3

description: no additional information

source_name: Liver from PPARbeta/delta wt mouse fasted for 24h, biological replicate 3


title: 251494-ES-rehyb-5-080923


title: bfJMJ_C (2)

description: bfJMJ bioChIP in CJ7 cells on C chip


title: bfJMJ_F (2)

description: bfJMJ bioChIP in CJ7 cells on F chip


title: 251278-ES-rehyb-1-080923


title: liver_PPARd_wt_fed_repl_1

description: no additional information

source_name: Liver from PPARbeta/delta wt fed mouse, biological replicate 1


title: Fl/Fl day-6  (a)

description: Jmj (fl/fl) wild-type ES cells at day 6 of LIF withdrawal, biological rep 1


title: liver_PPARd_wt_fed_repl_2

description: no additional information

source_name: Liver from PPARbeta/delta wt fed mouse, biological replicate 2


title: bfJMJ_B (1)

description: bfJMJ bioChIP in CJ7 cells on B chip


title: bfJMJ_F (1)

description: bfJMJ bioChIP in CJ7 cells on F chip


title: Fl/Fl day-6 (b)

description: Jmj (fl/fl) wild-type ES cells at day 6 of LIF withdrawal, biological rep 2


title: 251493-ES-rehyb-4-080923

description: CHOP 206


title: bfJMJ_C (1)

description: bfJMJ bioChIP in CJ7 cells on C chip


title: Input_F (3)

description: genomic DNA input from Ezh2-/- cells on F chip


title: Input_C (3)

description: genomic DNA input from Ezh2-/- cells on C chip


title: Input_B (2)

description: genomic DNA input from CJ7 cells on B chip


title: Fl/Fl day-4 (b)

description: Jmj (fl/fl) wild-type ES cells at day 4 of LIF withdrawal, biological rep 2


title: Fl/Fl day -4 (a)

description: Jmj (fl/fl) wild-type ES cells at day 4 of LIF withdrawal, biological rep 1


title: Input_F (2)

description: genomic DNA input from CJ7 cells on F chip


title: Input_F (1)

description: genomic DNA input from J1 cells expressing bfEZH1on F chip