title: JAXCoh4

status: Public on Oct 22 2009

first: Dan

last: Littman

address: 540 1st ave

institute: NYU Medical Center

description: Strain C57BL/6

hyb_protocol: According to Affymetrix protocols

scan_protocol: According to Affymetrix protocols

data_processing: GeneSpring GX10, RMA

source_name: Taconic (co-housed)

label_protocol: According to Affymetrix protocols

growth_protocol: C57BL/6 mice were obtained from Taconic Farms or Jackson Laboratory and housed under SPF conditions in isolator cages. Swiss-Webster germ-free (GF) and conventionally raised (SPF) mice were purchased from Taconic Farms and housed at the NYU School of Medicine animal facility.

treatment_protocol: For cohousing experiments mice were transferred into an isolator cage with the corresponding line for the indicated time. Jackson mice were housed in isolator cages in the same room and on the same diet for at least 4 weeks. For inoculation of germ-free mice with SFB, fecal pellets were collected from SFB-monocolonized mice using sterilized test tubes in the vinyl-isolator and were preserved frozen under dry ice until immediately before oral administration.  SFB colonizations were performed by oral gavage with 300-400 l of suspension obtained by homogenizing the fecal pellets from SFB-mono donor mice in water. Control mice were gavaged with water or homogenates prepared from their own feces.

tag: strain

value: Small intestine

tag: flora

value: Taconic (co-housed)


title: Granulosa cell with GFP, biological rep1

status: Public on Oct 23 2009

type: RNA

city: Saint-Hyacinthe

first: Derek

last: Boerboom

state: QC

address: 3200 Sicotte

department: Département de biomédecine Vétérinaire

country: Canada

institute: Université de Montréal, Faculty of veterinary medicine

description: Control group

hyb_protocol: hybridization was done by the Microarray Core Facility of the Baylor College of Medicine (Houston, TX).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 High-Resolution Scanning Patch.

data_processing: Microarray data were analyzed using FlexArray 1.3 software (Génome Québec, Montréal, Québec, Canada). Ad-Wnt4, Ad-Cre and control Ad-GFP data were processed using the robust multiarray average algorithm (RMA) for normalization, background correction and expression value calculation.Robustness of the data was further enhanced by the EB (Wright and Simon) algorithm and P-value calculation. A P-value threshold of 0.05 and 3-fold (Ad-Wnt4) or 2-fold (Ad-Cre) change cut-off values were used for identification of differentially expressed genes. Overlap between genes regulated by Ad-Wnt4 and Ad-Cre was also determined using this software.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Granulosa cells were obtained from 20-26 day-old mice of various genotypes 48h after eCG treatment.

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

growth_protocol: Granulosa cells were obtained from 20-26 day-old mice of various genotypes 48h after eCG treatment, using the needle puncture method. For experiments involving cell culture, cells were suspended in DMEM/F-12 medium (Invitrogen) with 1% fetal bovine serum and allowed to attach overnight at a final density of ~50%.

extract_protocol: RNeasy mini kit (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were infected with adenoviruses to express eGFP or Cre, or overexpress WNT4 for 24h in serum-free medium.

tag: treatment protocol

value: Cells were then infected with adenoviruses to express eGFP.

tag: cell type

value: granulosa cell


title: MCF-7 PARP-1 Replicate 2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

country: USA

institute: UT Southwestern Medical Center

hyb_protocol: Standard hybridization to Affymetrix U133A 2.0 microarray.

scan_protocol: Standard scanning protocol using GeneChip Scanner.

data_processing: The raw data were processed by Affymetrix GCOS software to obtain detection calls and signal values, and then normalized by scaling. Signals were then used in further analysis, namely batch effect adjusted and log2 median-normalized using COMBAT R.

label: Biotin

organism: Homo sapiens

source_name: MCF-7 PARP-1 Replicate 2

label_protocol: Seven μg of total RNA were subjected to One-Cycle Target Labeling Assay (Affymetrix) to generate biotinylated cRNA targets for hybridization to Affymetrix U133A 2.0 microarray.

extract_protocol: Total RNA was prepared using Trizol Reagent according to the manufacturer’s instructions (Invitrogen) and was further purified using RNeasy columns (Qiagen).

tag: MCF-7 PARP-1 Replicate 2


title: GFSFB3

city: New York

state: NY

description: Strain Swiss-Webster

source_name: Segmented Filamentous Bacteria

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

value: Swiss-Webster

tag: tissue

value: Segmented Filamentous Bacteria


title: GF2

description: Strain Swiss-Webster

source_name: Germ free

value: Germ free


title: ES cells in PBS-rep1

first: Christine

last: Richardson

address: St Nicholas Av

department: Institute for Cancer Genetics

institute: Columbia University

description: ESC cultured in PBS alone at 37 degrees and 5% CO2

hyb_protocol: Following fragmentation, 12 ul of cRNA were hybridized for 16 hr at 45C on Mouse MG_U74Av2 Oligonucleotide Array. Arrays were washed and stained in the Affymetrix Fluidics Station using protocol EukGE-WS2v5_450

scan_protocol: Arrays were scanned using scanner M10

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 500. Filtering and Statistical Analysis was done using GeneSpring version 6.

source_name: mouse ES cells control

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: E14tg2a mouse embryonic stem cells having two targeted I-SceI sites (Clone C2, Ref:Richardson and Jasin, Nature 2000) were cultured at 37 C and 5% CO2

treatment_protocol: C2 cells were treated in PBS with or without 100 uM or 5 mM hydrogen peroxide for 15 or 30 min, respectively. Following treatment cells were recovered in maintenance medium for 1 hour before RNA extraction and microarray hybridization.

tag: genotype

value: E14tg2a with two I-Sce sites

tag: agent

value: control


title: 08SE858HGU133Plus2.0

city: Campus de la Universidad Autónoma de Madrid

first: Ismael

last: Santa-Maria

state: Madrid

address: Nicolás Cabrera 1

department: Biologia Molecular

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45ºC on a GeneChip Human U133Plus2.0 Genome Array.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450, and they were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with GeneSpring GX software using RMA and global median normalization method.

source_name: Human entorhinal cortex

label_protocol: IVT labeling kit affymetrix

extract_protocol: Rneasy Mini Kit and QIAshredder (Qiagen)

value: brain


title: GF3

description: Strain Swiss-Webster


title: JAX4

description: Strain C57BL/6

source_name: Jackson

value: Jackson


title: JAXCoh2

description: Strain C57BL/6


title: GFSFB1

description: Strain Swiss-Webster


title: GF1

description: Strain Swiss-Webster


title: JAXCoh1

description: Strain C57BL/6


title: GFSFB2

description: Strain Swiss-Webster


title: JAXCoh3

description: Strain C57BL/6


title: JAX3

description: Strain C57BL/6


title: CCD_ZT0_pool1

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

hyb_protocol: The generated cDNAs (5 µg) were fragmented, biotinylated and hybridized using the NuGen FL-Ovation cDNA Biotin Module V2 following the manufacturer’s instructions. The resulting targets were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays.

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) for each tissues separately.

source_name: microdissected cortical collecting ducts - ZT0

label_protocol: For each sample, 10 ng of total RNA were amplified and labeled using the WT-Ovation Pico RNA Amplification System V1, ( NuGen, catalog # 3300-12,) and labeling with FL-Ovation cDNA Biotin Module V2 (NuGen, catalog #4200-12).

growth_protocol: Male C57BL/6J male mice (Janvier, France) weighing 25-30 g were used in the microarray experiments. The animals were maintained on the standard laboratory chow diet and adapted to 12h-light/12h-dark cycle for two weeks before experiments. During the last three days of the adaptation period, the access to the animal room was forbidden to avoid any interference of the external noise with the animal circadian cycle.

extract_protocol: Microdissection of DCT/CNT or CCD was performed from collagenase-treated kidneys. Microarray RNA from microdissected DCT/CNT or CCD was isolated and purified with RNA clean up purification kits from Qiagen. All RNA quantities were assessed by NanoDrop-ND-1000 spectrophotometer and the quality of RNA was controlled on Aligent 2100 bioanalyzer chips.

treatment_protocol: Animals were sacrificed for microdissection every 4 hours, i.e. at ZT0, ZT4, ZT8, ZT12, ZT16 and ZT20 (ZT – Zeitgeber (circadian) time, indicates time of light-on as ZT0 and time of light-off as ZT12).

value: left kidney

tag: weight

tag: gender

value: male


title: JAX1

description: Strain C57BL/6


title: JAX2

description: Strain C57BL/6


title: DCT/CNT_ZT20_pool1

source_name: microdissected distal convoluted tubules and connecting tubules - ZT20


title: CCD_ZT8_pool2

source_name: microdissected cortical collecting ducts - ZT8


title: CCD_ZT4_pool1

source_name: microdissected cortical collecting ducts - ZT4


title: CCD_ZT0_pool2


title: CCD_ZT20_pool2

source_name: microdissected cortical collecting ducts - ZT20


title: DCT/CNT_ZT0_pool2

source_name: microdissected distal convoluted tubules and connecting tubules - ZT0


title: DCT/CNT_ZT8_pool1

source_name: microdissected distal convoluted tubules and connecting tubules - ZT8


title: CCD_ZT20_pool1


title: CCD_ZT12_pool2

source_name: microdissected cortical collecting ducts - ZT12


title: DCT/CNT_ZT12_pool1

source_name: microdissected distal convoluted tubules and connecting tubules - ZT12


title: DCT/CNT_ZT16_pool2

source_name: microdissected distal convoluted tubules and connecting tubules - ZT16


title: CCD_ZT16_pool2

source_name: microdissected cortical collecting ducts - ZT16


title: DCT/CNT_ZT8_pool2


title: CCD_ZT4_pool2


title: CCD_ZT16_pool1


title: DCT/CNT_ZT20_pool2


title: CCD_ZT12_pool1


title: SKP sample 6

city: Toronto

first: Freda

last: Miller

state: ON

address: 555 University Avenue

institute: Hospital for Sick Children

description: SKP colonies

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) and scanned at the HSC Microarray Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: The data were background corrected and normalized using standard RMA procedure implemented in the Affymetrix Expression Console software. The preprocessed  data were analysed using the LIMMA Bioconductor package to identify genes that show significant evidence of differential expression between SKPs and Sox:EGFP-positive cells.

source_name: skin-derived precursor cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Neonatal back skin (P4) from Sox2:EGFP mice was processed as described in the paper to yield a single cell suspension. Cells were stained with biotin conjugated anti-cd34 antibody and visualized with a PECy7 conjugated streptavidin secondary antibody. Sox2:EGFP-positive, cd34-negative cells were sorted directly into RNAlater (Ambion). For RNA isolation of  SKPs, primary SKPs were generated from neonatal (P4) mouse skin as described in the paper. Spherical SKP colonies were collected.

extract_protocol: RNA was extracted using Trizol (Invitrogen).

tag: passage

value: primary

value: skin-derived precursor cells


title: DCT/CNT_ZT16_pool1


title: DCT/CNT_ZT12_pool2


title: DCT/CNT_ZT4_pool2

source_name: microdissected distal convoluted tubules and connecting tubules - ZT4


title: CCD_ZT8_pool1


title: DCT/CNT_ZT0_pool1


title: DCT/CNT_ZT4_pool1


title: monocytes differentiated in GM-CSF +/- FSK donor 2

city: Seattle

first: Joseph

middle: A

last: Beavo

state: WA

address: 1959 NE Pacific St

department: Pharmacology

institute: University of Washington

hyb_protocol: Samples were hybridized to HEEBO (Invitrogen) slides 1-66 overnight at 42 degrees C in hybridization solution (50% formamide, 5x SSC, 0.1% SDS, 0.1 mg/ml mouse CotI DNA, 10 ug/ml Poly A, 5x Denhardt's Reagent)

scan_protocol: Scanned using an Axon GenePix 4000A scanner and the GenePix Pro 3.0 software

data_processing: Raw data files were uploaded into the Genespring program (Agilent), combined into one experiment and Lowess normalized. Array analyses were performed on plates 1-66 of the HEEBO library.

label_protocol: Amplification and labeling were performed using the Ambion Amino Allyl MessageAmp II amplification kit following the manufacturer’s instructions.  Total RNA (2 µg) was amplified using a single round of amplification.  The aRNA (15 µg) was coupled to a dye and purified

growth_protocol: Human CD14+ monocytes were isolated from buffy coats using magnetic selection with CD14+ beads. Cells were cultured for 6 days in the presence of GM-CSF +/- 25 uM forskolin.

extract_protocol: Total RNA was isolated using the Qiagen Rneasy kit according to the manufacturer's protocol

treatment_protocol: Cells were either untreated or treated with 25 uM forskolin for 6 days.

value: CD14+ monocytes from whole blood buffy coat

source_name: Control, monocytes differentiated for 6 days in the presence of GM-CSF + FSK


title: monocytes differentiated in GM-CSF +/- FSK donor 1

source_name: Control, monocytes differentiated for 6 days in the presence of GM-CSF


title: Wild type fibroblasts, biological rep1

city: Columbus

first: Julie

last: Wallace

state: OH

address: 460 W. 12th Ave 840 BRT

institute: OSUCCC

description: Gene expression data from fibroblasts with wild type Pten

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45ºC on Mouse Genome 430 2.0 GeneChips.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Gene expression levels were estimated from GeneChip® probe intensities using WEDGE++ algorithm (WPP), an enhanced integrated version of the published RMA, quantile-normalization and background-correction algorithms.

source_name: Fibroblasts isolated from wild type mouse mammary glands

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Fibroblasts were isolated from mammary gland tissue using a modified protocol for gravity separation.

treatment_protocol: Fibroblasts were grown in 10% FBS DMEM in a 37º incubator with 7% CO2.

value: FVB/N

tag: age

value: 8 Weeks

value: Mammary Gland

value: Fibroblasts

value: PtenloxP/loxP


title: monocytes differentiated in GM-CSF +/- FSK donor 3


title: Pten null fibroblasts, biological rep3

description: Gene expression data from fibroblasts with Pten deletion

source_name: Fibroblasts isolated from mouse mammary glands with Pten deletion in fibroblasts

value: Fsp-cre; PtenloxP/loxP


title: Wild type fibroblasts, biological rep3


title: Wild type fibroblasts, biological rep2


title: Pten null fibroblasts, biological rep2


title: Pten null fibroblasts, biological rep1


title: 55 C Experiment 5 Repeat 1 Chip 13366226 Scanned at PMT Cy5 850 and Cy3 800

type: other

city: Ames

first: Hui-Hsien

last: Chou

state: IA

address: 503 Science II

department: Genetics, Development and Cell Biology

institute: Iowa State University

description: Refer to the series summarizing this data for more sample composition information.

hyb_protocol: The labeled oligos were pooled together and dried in a vacuum dryer at 55 C. Microarray hybridizations were conducted based on the protocol for the rice array (http://www.ricearray.org/rice_protocols.shtml). 200 ul hybridization buffer (made from 60 ul formamide, 50 ul of 20X SSC buffer, 10 ul of 2% SDS, 10 ul of 1 ug/ul hCOT I DNA, 10 ul of 1 ug/ul poly A and 1 ul of 20 ug/ul yeast tRNA filled with water to 200 ul) was used to dissolve the labeled oligos, then heated at 95 C for 30 seconds, and applied to the microarrays. Microarray slides have been pre-hybridized for 30 min with the pre-hybridization buffer (500 ul of 10 mg/ml Bovine serum albumin, 12.5 ml of 20X SSC buffer and 250 ul of 20% SDS filled with water to 50 ml). Hybridization was done using the automatic Lucidea SlidePro Hybridizer (Amersham Biosciences) and allowed to proceed for 16 hours at the hybridization temperature setting.

scan_protocol: Microarray slides were scanned by the GenePix 4100A scanner and analyzed by the GenePix Pro 6 analysis software (Molecular Devices).

data_processing: Data presented here are background subtracted intensity values for each channel from the GenePix report file supplied. Further normalization and scaling are based on multiple hygromycin controls on each chip and are explained in the corresponding publication.

molecule: other

organism: synthetic construct

source_name: Experiment 5 Cy5 sample mixture

label_protocol: 10 ul of the 10 variably diluted oligos for Set 1 were pooled into the same tube. Similarly, 10 ul of the 10 variably diluted oligos for Set 2 were pooled into another tube. 10 ul from each tube and 1 ul of the hygromycin control at 10-7M were then taken out to be coupled with Cy5 fluorescent dye. IDT synthesized oligos included a 5' amino modifier C6 for dye incorporation. The labeled oligos were cleaned using QIAquick PCR Purification Kit (Qiagen) to discard uncoupled dyes.

extract_protocol: not applicable; synthesized oligonucleotide samples

tag: e5 cy5 sample composition:

tag: Conc.   <Set 1>  <Set 2>

source_name: Experiment 5 Cy3 sample mixture

label_protocol: 10 ul of the 10 variably diluted oligos for Set 1 were pooled into the same tube. Similarly, 10 ul of the 10 variably diluted oligos for Set 2 were pooled into another tube. 10 ul from each tube and 1 ul of the hygromycin control at 10-7M were then taken out to be coupled with Cy3 fluorescent dye. IDT synthesized oligos included a 5' amino modifier C6 for dye incorporation. The labeled oligos were cleaned using QIAquick PCR Purification Kit (Qiagen) to discard uncoupled dyes.

tag: e5 cy3 sample composition:


title: 55 C Experiment 4 Repeat 1 Chip 13366225 Scanned at PMT Cy5 850 and Cy3 800

source_name: Experiment 4 Cy5 sample mixture

tag: e4 cy5 sample composition:

source_name: Experiment 4 Cy3 sample mixture

tag: e4 cy3 sample composition:


title: 55 C Experiment 3 Repeat 2 Chip 13366230 Scanned at PMT Cy5 800 and Cy3 750

source_name: Experiment 3 Cy5 sample mixture

tag: e3 cy5 sample composition:

source_name: Experiment 3 Cy3 sample mixture

tag: e3 cy3 sample composition:


title: 55 C Experiment 5 Repeat 2 Chip 13366237 Scanned at PMT Cy5 750 and Cy3 700


title: 55 C Experiment 5 Repeat 1 Chip 13366226 Scanned at PMT Cy5 750 and Cy3 700


title: 55 C Experiment 4 Repeat 2 Chip 13366234 Scanned at PMT Cy5 750 and Cy3 700


title: 55 C Experiment 4 Repeat 2 Chip 13366234 Scanned at PMT Cy5 800 and Cy3 750


title: 55 C Experiment 3 Repeat 2 Chip 13366230 Scanned at PMT Cy5 850 and Cy3 800


title: 55 C Experiment 4 Repeat 1 Chip 13366225 Scanned at PMT Cy5 800 and Cy3 750


title: 55 C Experiment 5 Repeat 2 Chip 13366237 Scanned at PMT Cy5 850 and Cy3 800


title: 55 C Experiment 5 Repeat 1 Chip 13366226 Scanned at PMT Cy5 800 and Cy3 750


title: 55 C Experiment 3 Repeat 2 Chip 13366230 Scanned at PMT Cy5 750 and Cy3 700


title: 55 C Experiment 3 Repeat 1 Chip 13366224 Scanned at PMT Cy5 850 and Cy3 800


title: 55 C Experiment 4 Repeat 2 Chip 13366234 Scanned at PMT Cy5 850 and Cy3 800


title: 55 C Experiment 3 Repeat 1 Chip 13366224 Scanned at PMT Cy5 750 and Cy3 700


title: 55 C Experiment 2 Repeat 2 Chip 13366229 Scanned at PMT Cy5 800 and Cy3 750

source_name: Experiment 2 Cy5 sample mixture

tag: e2 cy5 sample composition:

source_name: Experiment 2 Cy3 sample mixture

tag: e2 cy3 sample compositin:


title: 55 C Experiment 2 Repeat 2 Chip 13366229 Scanned at PMT Cy5 850 and Cy3 800


title: 55 C Experiment 5 Repeat 2 Chip 13366237 Scanned at PMT Cy5 800 and Cy3 750


title: 55 C Experiment 2 Repeat 1 Chip 13366223 Scanned at PMT Cy5 750 and Cy3 700


title: 55 C Experiment 2 Repeat 2 Chip 13366229 Scanned at PMT Cy5 750 and Cy3 700


title: 55 C Experiment 3 Repeat 1 Chip 13366224 Scanned at PMT Cy5 800 and Cy3 750


title: 55 C Experiment 1 Repeat 2 Chip 13366228 Scanned at PMT Cy5 800 and Cy3 750

source_name: Experiment 1 Cy5 sample mixture

tag: e1 cy5 sample composition:

source_name: Experiment 1 Cy3 sample mixture

tag: e1 cy3 sample composition:


title: 55 C Experiment 2 Repeat 1 Chip 13366223 Scanned at PMT Cy5 800 and Cy3 750


title: 55 C Experiment 4 Repeat 1 Chip 13366225 Scanned at PMT Cy5 750 and Cy3 700


title: 55 C Experiment 1 Repeat 2 Chip 13366228 Scanned at PMT Cy5 750 and Cy3 700


title: 55 C Experiment 1 Repeat 1 Chip 13366222 Scanned at PMT Cy5 850 and Cy3 800


title: 55 C Experiment 1 Repeat 2 Chip 13366228 Scanned at PMT Cy5 850 and Cy3 800


title: 55 C Experiment 1 Repeat 1 Chip 13366222 Scanned at PMT Cy5 800 and Cy3 750


title: 60 C Experiment 5 Repeat 1 Chip 13366236 Scanned at PMT Cy5 850 and Cy3 800


title: 55 C Experiment 1 Repeat 1 Chip 13366222 Scanned at PMT Cy5 750 and Cy3 700


title: 60 C Experiment 5 Repeat 2 Chip 13360955 Scanned at PMT Cy5 850 and Cy3 800


title: 60 C Experiment 4 Repeat 2 Chip 13360953 Scanned at PMT Cy5 850 and Cy3 750


title: 60 C Experiment 5 Repeat 1 Chip 13366236 Scanned at PMT Cy5 800 and Cy3 750


title: 60 C Experiment 5 Repeat 1 Chip 13366236 Scanned at PMT Cy5 800 and Cy3 700


title: 60 C Experiment 4 Repeat 2 Chip 13360953 Scanned at PMT Cy5 750 and Cy3 700


title: 60 C Experiment 3 Repeat 1 Chip 13366233 Scanned at PMT Cy5 800 and Cy3 750


title: 60 C Experiment 3 Repeat 1 Chip 13366233 Scanned at PMT Cy5 850 and Cy3 800


title: 60 C Experiment 4 Repeat 1 Chip 13366235 Scanned at PMT Cy5 800 and Cy3 750


title: 60 C Experiment 3 Repeat 2 Chip 13366242 Scanned at PMT Cy5 800 and Cy3 750


title: 60 C Experiment 4 Repeat 2 Chip 13360953 Scanned at PMT Cy5 800 and Cy3 750


title: 147G 16S rRNA gene clone

status: Public on Jan 01 2010

city: Auburn

first: Mark

middle: R

last: Liles

state: AL

address: Rm 316, Rouse Life Sciences Building

department: Biological Sciences

institute: Auburn University

description: This sample is of the 16S rRNA gene PCR amplified using primer sets 31F (division Acidobacteria-specific) and 1492R (universal)

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: mean signal intensity of triplicate probes

organism: uncultured Acidobacteriota bacterium

source_name: 147G 16S rRNA gene clone

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: For E. coli cultures containing the cloned 16S rRNA gene, 2 ml cultures were grown overnight at 37oC.  Plasmid DNA was extracted using a Promega SV96 kit and the cloned Acidobacteria rDNA template was PCR amplified in the presence of Cy3-labeled dCTPs and unincorporated label was removed by Centricon spin columns

extract_protocol: For soil samples, total soil DNA was extracted by MoBio soil kit extraction.  The soil Acidobacteria rDNA template was PCR amplified in the presence of Cy3-labeled dCTPs and unincorporated label was removed by Centricon spin columns

tag: genotype

value: 16S rRNA gene amplicon

tag: source

value: accession AY214899


title: 60 C Experiment 4 Repeat 1 Chip 13366235 Scanned at PMT Cy5 850 and Cy3 800


title: 60 C Experiment 4 Repeat 1 Chip 13366235 Scanned at PMT Cy5 750 and Cy3 700


title: 60 C Experiment 3 Repeat 2 Chip 13366242 Scanned at PMT Cy5 850 and Cy3 800


title: 60 C Experiment 5 Repeat 2 Chip 13360955 Scanned at PMT Cy5 800 and Cy3 750


title: 60 C Experiment 2 Repeat 1 Chip 13366232 Scanned at PMT Cy5 800 and Cy3 750


title: 60 C Experiment 2 Repeat 2 Chip 13366241 Scanned at PMT Cy5 850 and Cy3 800


title: 60 C Experiment 2 Repeat 2 Chip 13366241 Scanned at PMT Cy5 750 and Cy3 700


title: 60 C Experiment 2 Repeat 1 Chip 13366232 Scanned at PMT Cy5 750 and Cy3 700


title: 60 C Experiment 3 Repeat 1 Chip 13366233 Scanned at PMT Cy5 750 and Cy3 700


title: 60 C Experiment 1 Repeat 2 Chip 13366238 Scanned at PMT Cy5 850 and Cy3 800


title: 60 C Experiment 2 Repeat 1 Chip 13366232 Scanned at PMT Cy5 850 and Cy3 800


title: 60 C Experiment 1 Repeat 2 Chip 13366238 Scanned at PMT Cy5 750 and Cy3 700


title: 50 C Experiment 5 Repeat 2 Chip 13366221 Scanned at PMT Cy5 800 and Cy3 750


title: 60 C Experiment 1 Repeat 2 Chip 13366238 Scanned at PMT Cy5 800 and Cy3 750


title: 60 C Experiment 2 Repeat 2 Chip 13366241 Scanned at PMT Cy5 800 and Cy3 750


title: 60 C Experiment 1 Repeat 1 Chip 13366231 Scanned at PMT Cy5 850 and Cy3 800


title: 60 C Experiment 1 Repeat 1 Chip 13366231 Scanned at PMT Cy5 800 and Cy3 750


title: 50 C Experiment 5 Repeat 1 Chip 13366214 Scanned at PMT Cy5 850 and Cy3 800


title: 50 C Experiment 5 Repeat 2 Chip 13366221 Scanned at PMT Cy5 750 and Cy3 700


title: 50 C Experiment 5 Repeat 1 Chip 13366214 Scanned at PMT Cy5 800 and Cy3 750


title: 60 C Experiment 1 Repeat 1 Chip 13366231 Scanned at PMT Cy5 750 and Cy3 700


title: 50 C Experiment 4 Repeat 1 Chip 13366213 Scanned at PMT Cy5 750 and Cy3 700


title: 50 C Experiment 5 Repeat 1 Chip 13366214 Scanned at PMT Cy5 750 and Cy3 700


title: 50 C Experiment 4 Repeat 2 Chip 13366220 Scanned at PMT Cy5 800 and Cy3 750


title: 50 C Experiment 4 Repeat 1 Chip 13366213 Scanned at PMT Cy5 800 and Cy3 750


title: 50 C Experiment 4 Repeat 2 Chip 13366220 Scanned at PMT Cy5 750 and Cy3 700


title: 50 C Experiment 3 Repeat 2 Chip 13366219 Scanned at PMT Cy5 800 and Cy3 750


title: 50 C Experiment 3 Repeat 1 Chip 13360952 Scanned at PMT Cy5 800 and Cy3 750


title: 50 C Experiment 3 Repeat 2 Chip 13366219 Scanned at PMT Cy5 750 and Cy3 700


title: 50 C Experiment 3 Repeat 1 Chip 13360952 Scanned at PMT Cy5 850 and Cy3 800


title: 50 C Experiment 3 Repeat 2 Chip 13366219 Scanned at PMT Cy5 850 and Cy3 800


title: 50 C Experiment 2 Repeat 2 Chip 13366218 Scanned at PMT Cy5 800 and Cy3 550


title: 50 C Experiment 2 Repeat 1 Chip 13360950 Scanned at PMT Cy5 800 and Cy3 650


title: 50 C Experiment 2 Repeat 2 Chip 13366218 Scanned at PMT Cy5 750 and Cy3 500


title: 50 C Experiment 3 Repeat 1 Chip 13360952 Scanned at PMT Cy5 750 and Cy3 700


title: 50 C Experiment 2 Repeat 1 Chip 13360950 Scanned at PMT Cy5 850 and Cy3 800


title: 50 C Experiment 4 Repeat 2 Chip 13366220 Scanned at PMT Cy5 850 and Cy3 800


title: 50 C Experiment 2 Repeat 1 Chip 13360950 Scanned at PMT Cy5 750 and Cy3 550


title: 50 C Experiment 2 Repeat 1 Chip 13360950 Scanned at PMT Cy5 750 and Cy3 500


title: 50 C Experiment 1 Repeat 2 Chip 13366215 Scanned at PMT Cy5 800 and Cy3 750


title: 50 C Experiment 1 Repeat 1 Chip 13360948 Scanned at PMT Cy5 850 and Cy3 800


title: 50 C Experiment 1 Repeat 2 Chip 13366215 Scanned at PMT Cy5 750 and Cy3 700


title: 50 C Experiment 1 Repeat 1 Chip 13360948 Scanned at PMT Cy5 750 and Cy3 700


title: 48 C Experiment 5 Repeat 2 Chip 13366136 Scanned at PMT Cy5 800 and Cy3 750


title: 50 C Experiment 1 Repeat 1 Chip 13360948 Scanned at PMT Cy5 800 and Cy3 750


title: 48 C Experiment 5 Repeat 2 Chip 13366136 Scanned at PMT Cy5 850 and Cy3 800


title: 50 C Experiment 1 Repeat 2 Chip 13366215 Scanned at PMT Cy5 850 and Cy3 800


title: 48 C Experiment 5 Repeat 1 Chip 13366130 Scanned at PMT Cy5 800 and Cy3 750


title: 48 C Experiment 5 Repeat 1 Chip 13366130 Scanned at PMT Cy5 850 and Cy3 800


title: 48 C Experiment 4 Repeat 1 Chip 13366128 Scanned at PMT Cy5 850 and Cy3 800


title: 48 C Experiment 4 Repeat 2 Chip 13366134 Scanned at PMT Cy5 850 and Cy3 800


title: 48 C Experiment 4 Repeat 2 Chip 13366134 Scanned at PMT Cy5 750 and Cy3 700


title: 48 C Experiment 4 Repeat 1 Chip 13366128 Scanned at PMT Cy5 750 and Cy3 700


title: 48 C Experiment 2 Repeat 2 Chip 13366132 Scanned at PMT Cy5 750 and Cy3 700


title: 48 C Experiment 5 Repeat 1 Chip 13366130 Scanned at PMT Cy5 750 and Cy3 700


title: 48 C Experiment 3 Repeat 1 Chip 13366127 Scanned at PMT Cy5 800 and Cy3 750


title: 48 C Experiment 2 Repeat 1 Chip 13360923 Scanned at PMT Cy5 850 and Cy3 800


title: 48 C Experiment 3 Repeat 1 Chip 13366127 Scanned at PMT Cy5 850 and Cy3 800


title: 48 C Experiment 4 Repeat 2 Chip 13366134 Scanned at PMT Cy5 800 and Cy3 750


title: 48 C Experiment 1 Repeat 2 Chip 13366131 Scanned at PMT Cy5 800 and Cy3 750


title: 48 C Experiment 2 Repeat 2 Chip 13366132 Scanned at PMT Cy5 800 and Cy3 750


title: 48 C Experiment 4 Repeat 1 Chip 13366128 Scanned at PMT Cy5 800 and Cy3 750


title: 48 C Experiment 1 Repeat 2 Chip 13366131 Scanned at PMT Cy5 850 and Cy3 800


title: 48 C Experiment 1 Repeat 1 Chip 13360922 Scanned at PMT Cy5 800 and Cy3 750


title: 48 C Experiment 2 Repeat 1 Chip 13360923 Scanned at PMT Cy5 750 and Cy3 700


title: 48 C Experiment 2 Repeat 2 Chip 13366132 Scanned at PMT Cy5 850 and Cy3 800


title: 48 C Experiment 1 Repeat 2 Chip 13366131 Scanned at PMT Cy5 750 and Cy3 700


title: 48 C Experiment 2 Repeat 1 Chip 13360923 Scanned at PMT Cy5 800 and Cy3 750


title: 45 C Experiment 5 Repeat 2 Chip 13360934 Scanned at PMT Cy5 800 and Cy3 750


title: 48 C Experiment 1 Repeat 1 Chip 13360922 Scanned at PMT Cy5 850 and Cy3 800


title: 45 C Experiment 5 Repeat 1 Chip 13360928 Scanned at PMT Cy5 750 and Cy3 700


title: 48 C Experiment 1 Repeat 1 Chip 13360922 Scanned at PMT Cy5 750 and Cy3 700


title: 45 C Experiment 5 Repeat 2 Chip 13360934 Scanned at PMT Cy5 750 and Cy3 700


title: 45 C Experiment 5 Repeat 1 Chip 13360928 Scanned at PMT Cy5 800 and Cy3 750


title: 45 C Experiment 5 Repeat 1 Chip 13360928 Scanned at PMT Cy5 850 and Cy3 750


title: 45 C Experiment 4 Repeat 2 Chip 13360933 Scanned at PMT Cy5 800 and Cy3 750


title: 45 C Experiment 3 Repeat 2 Chip 13360932 Scanned at PMT Cy5 850 and Cy3 800


title: 45 C Experiment 4 Repeat 1 Chip 13360927 Scanned at PMT Cy5 850 and Cy3 800


title: 45 C Experiment 3 Repeat 1 Chip 13360926 Scanned at PMT Cy5 850 and Cy3 800


title: 45 C Experiment 4 Repeat 1 Chip 13360927 Scanned at PMT Cy5 750 and Cy3 700


title: 45 C Experiment 4 Repeat 1 Chip 13360927 Scanned at PMT Cy5 800 and Cy3 750


title: 45 C Experiment 2 Repeat 2 Chip 13360931 Scanned at PMT Cy5 850 and Cy3 800


title: 45 C Experiment 4 Repeat 2 Chip 13360933 Scanned at PMT Cy5 850 and Cy3 800


title: 45 C Experiment 2 Repeat 2 Chip 13360931 Scanned at PMT Cy5 750 and Cy3 700


title: 45 C Experiment 2 Repeat 1 Chip 13360925 Scanned at PMT Cy5 850 and Cy3 800


title: 45 C Experiment 4 Repeat 2 Chip 13360933 Scanned at PMT Cy5 750 and Cy3 700


title: 45 C Experiment 2 Repeat 2 Chip 13360931 Scanned at PMT Cy5 800 and Cy3 750


title: 45 C Experiment 1 Repeat 2 Chip 13360929 Scanned at PMT Cy5 800 and Cy3 700


title: 45 C Experiment 3 Repeat 2 Chip 13360932 Scanned at PMT Cy5 800 and Cy3 750


title: 45 C Experiment 3 Repeat 1 Chip 13360926 Scanned at PMT Cy5 750 and Cy3 700


title: 45 C Experiment 3 Repeat 1 Chip 13360926 Scanned at PMT Cy5 800 and Cy3 750


title: 45 C Experiment 2 Repeat 1 Chip 13360925 Scanned at PMT Cy5 750 and Cy3 700


title: 45 C Experiment 3 Repeat 2 Chip 13360932 Scanned at PMT Cy5 750 and Cy3 700


title: 45 C Experiment 2 Repeat 1 Chip 13360925 Scanned at PMT Cy5 800 and Cy3 750


title: 45 C Experiment 1 Repeat 2 Chip 13360929 Scanned at PMT Cy5 850 and Cy3 800


title: 45 C Experiment 1 Repeat 1 Chip 13360924 Scanned at PMT Cy5 850 and Cy3 800


title: 45 C Experiment 1 Repeat 2 Chip 13360929 Scanned at PMT Cy5 700 and Cy3 600


title: 53 C Experiment 5 Repeat 2 Chip 13360946 Scanned at PMT Cy5 800 and Cy3 750


title: 45 C Experiment 1 Repeat 1 Chip 13360924 Scanned at PMT Cy5 750 and Cy3 700


title: 53 C Experiment 5 Repeat 1 Chip 13360940 Scanned at PMT Cy5 850 and Cy3 800


title: 53 C Experiment 5 Repeat 2 Chip 13360946 Scanned at PMT Cy5 750 and Cy3 700


title: 53 C Experiment 5 Repeat 2 Chip 13360946 Scanned at PMT Cy5 850 and Cy3 800


title: 45 C Experiment 1 Repeat 1 Chip 13360924 Scanned at PMT Cy5 800 and Cy3 750


title: 53 C Experiment 4 Repeat 1 Chip 13360938 Scanned at PMT Cy5 800 and Cy3 750


title: 53 C Experiment 5 Repeat 1 Chip 13360940 Scanned at PMT Cy5 800 and Cy3 750


title: 53 C Experiment 4 Repeat 2 Chip 13360945 Scanned at PMT Cy5 800 and Cy3 750


title: 53 C Experiment 5 Repeat 1 Chip 13360940 Scanned at PMT Cy5 750 and Cy3 700


title: 53 C Experiment 3 Repeat 2 Chip 13360944 Scanned at PMT Cy5 850 and Cy3 800


title: 53 C Experiment 3 Repeat 2 Chip 13360944 Scanned at PMT Cy5 800 and Cy3 750


title: 53 C Experiment 3 Repeat 1 Chip 13360937 Scanned at PMT Cy5 750 and Cy3 700


title: 53 C Experiment 3 Repeat 2 Chip 13360944 Scanned at PMT Cy5 750 and Cy3 700


title: 53 C Experiment 2 Repeat 2 Chip 13360943 Scanned at PMT Cy5 850 and Cy3 800


title: 53 C Experiment 4 Repeat 1 Chip 13360938 Scanned at PMT Cy5 850 and Cy3 800


title: 53 C Experiment 4 Repeat 2 Chip 13360945 Scanned at PMT Cy5 750 and Cy3 700


title: 53 C Experiment 2 Repeat 2 Chip 13360943 Scanned at PMT Cy5 750 and Cy3 700


title: adipose_stemcell_rep3

city: Nijmegen

first: Bastiaan

last: Jansen

address: PO Box 9101

department: Tumor Immunology

country: Netherlands

institute: Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Center Nijmegen

description: AdAS

hyb_protocol: 17 hours at 45 degrees in Affymetrix hybridization oven at 60 rpm,washing and staining in  Fluidics station 450 using stain cocktails: SAPE and antibody solution, (protocol FS450_0001)

scan_protocol: GeneChip scanner 3000 7G

data_processing: RMA + GC correction

source_name: Adipose tissue

label_protocol: GeneChip WT Terminal Labeling Kit

growth_protocol: Cells from 3 different donors per stem cell type were cultured under proliferative, non-differentiating conditions.

extract_protocol: Rneasy column purification

tag: growth protocol

value: Cultured in Low Glucose DMEM, 10% FBS, 100 U/ml penicillin, 0.1 mg/ml streptomycin


title: unrestricted_somatic_stemcell_rep2

description: USSC

source_name: Human cord blood

value: Cultured in Low Glucose DMEM, 30% FBS, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2 mM ultraglutamine, 10-7 M dexamethasone


title: 53 C Experiment 3 Repeat 1 Chip 13360937 Scanned at PMT Cy5 850 and Cy3 800


title: 53 C Experiment 2 Repeat 2 Chip 13360943 Scanned at PMT Cy5 800 and Cy3 750


title: adipose_stemcell_rep2

description: AdAS


title: 53 C Experiment 3 Repeat 1 Chip 13360937 Scanned at PMT Cy5 800 and Cy3 750


title: 53 C Experiment 4 Repeat 2 Chip 13360945 Scanned at PMT Cy5 850 and Cy3 800


title: unrestricted_somatic_stemcell_rep3

description: USSC


title: bonemarrow_stemcell_rep1

description: BM-MSC

source_name: Bone marrow


title: bonemarrow_stemcell_rep3

description: BM-MSC


title: bonemarrow_stemcell_rep2

description: BM-MSC


title: 53 C Experiment 2 Repeat 1 Chip 13360936 Scanned at PMT Cy5 750 and Cy3 700


title: 53 C Experiment 1 Repeat 2 Chip 13360942 Scanned at PMT Cy5 750 and Cy3 700


title: 53 C Experiment 4 Repeat 1 Chip 13360938 Scanned at PMT Cy5 750 and Cy3 700


title: 53 C Experiment 2 Repeat 1 Chip 13360936 Scanned at PMT Cy5 850 and Cy3 800


title: unrestricted_somatic_stemcell_rep1

description: USSC


title: LB broth without glucose (OD2.0)[rep2d]

first: Palmy

last: Jesudhasan

department: Microbiology

institute: University of Texas Southwestern Medical Center

description: The slide was prehybridized following the TIGR SOP # M007

hyb_protocol: The labeling mixtures were further purified using a QIAquick PCR purification kit (Qiagen). Equal amounts of labeled cDNA from the treatment and control were used to hybridize S. Typhimurium LT2 genome microarrays (version 4), obtained from The Institute for Genomic Research (TIGR, Rockville, MD). These arrays were 70 mer-oligo arrays with 4504 ORF each, with 5 replicate spots per ORF. The labeled cDNA was applied to the above arrays. Hybridization was carried out overnight at 42°C in a water bath using Corning hybridization chamber. The pre-and post-hybridization was carried out using the the TIGR SOP #M008.

scan_protocol: The slides was washed and scanned using a GenePix 4100A scanner (Axon Instruments Inc., Union City, CA) at 532 nm (Cy3 channel) and 635 nm (Cy5 channel), and the image was stored for further analysis.

data_processing: The data was normalized in Acuity 4.0 using Lowess normalization method

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: wild type at OD2.0

label_protocol: Total RNA (10 µg) was used to synthesize cDNA using a random primer for reverse transcription (Invitrogen Life Technologies, Carlsbad, CA). The primer was annealed at 70°C for 10 min, followed by snap-freezing in a dry ice-ethanol bath for 30 s and centrifugation for 1 min. The reaction mixture (Superscript III buffer, 0.1 M dithiothreitol, and aminoallyl-deoxyuridine triphosphate mix) was then incubated overnight with Superscript III reverse transcriptase (Invitrogen) at 42°C. Residual RNA was removed by alkaline treatment followed by neutralization, and the cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified cDNAs from the wild type was labeled with Cy-5 mono-Reactive Dye (GE Health Care).

growth_protocol: Grown at 37º C

extract_protocol: Total RNA was isolated from the cultures using an RNeasy mini kit (QIAGEN, Inc., Valencia, CA) according to the manufacturer's protocol. RNAprotect bacteria reagent (QIAGEN, Inc., Valencia, CA) was added to the cultures to stabilize RNA before isolation. The RNase-free DNase set (QIAGEN, Inc., Valencia, CA) was used for on-column DNase digestion to remove residual genomic DNA. The quantity and quality of RNA was examined using ND-1000 spectrophotometer (NanoDrop® Technologies, Wilmington, DE) and bioanalyser 2100 (Agilent Technologies, Santa Clara, CA) respectively.

treatment_protocol: wild type cells were grown in LB broth without glucose until it reaches optical density of 2.0 at 600nm

tag: S. Typhimurium (Accession # 87-26254) poultry isolate obtained from the National Veterinary Service Laboratory, Ames, Iowa.

source_name: mutant at OD2.0

label_protocol: Total RNA (10 µg) was used to synthesize cDNA using a random primer for reverse transcription (Invitrogen Life Technologies, Carlsbad, CA). The primer was annealed at 70°C for 10 min, followed by snap-freezing in a dry ice-ethanol bath for 30 s and centrifugation for 1 min. The reaction mixture (Superscript III buffer, 0.1 M dithiothreitol, and aminoallyl-deoxyuridine triphosphate mix) was then incubated overnight with Superscript III reverse transcriptase (Invitrogen) at 42°C. Residual RNA was removed by alkaline treatment followed by neutralization, and the cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified cDNAs from the mutant was labeled with Cy-3 mono-Reactive Dye (GE Health Care).

treatment_protocol: mutant cells were grown in LB broth without glucose until it reaches optical density of 2.0 at 600nm

tag: PJ002 luxS mutant grown in LB broth until it reaches OD 2.0


title: LB broth without glucose (OD2.0)[rep3d]

description: The slide was pre-hybridized following the TIGR SOP # M007


title: LB broth without glucose (OD2.0)[rep1c]


title: A. niger Xylose rep2

city: Gothenburg

first: wanwipa

last: vongsangnak

address: Kemivägen 10

department: Department of Chemical and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

hyb_protocol: Hybridization was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Fluidics Station FS-400.

scan_protocol: Scanning was done according to the Affymetrix GeneChip Expression Analysis Technical Manual on a GeneChip Scanner 3000.

data_processing: Affymetrix CEL-data files were preprocessed using the statistical language and environment R Language version 2.5. The probe intensities were normalised for background using the robust multiarray average (RMA) method (Irizarry, 2003) using only perfect match (PM) probes. Normalization was performed subsequently using the qspline algorithm (Workman, 2002). Gene expression values were calculated from the PM probes with the medianpolish summary method (Irizarry, 2003). All statistical preprocessing methods were used by invoking them through the affy package (Gautier, 2004).

organism: Aspergillus niger

source_name: Aspergillus niger grown on xylose medium

label_protocol: Labeled was done according to the Affymetrix GeneChip Expression Analysis Technical Manual.

extract_protocol: Total RNA was isolated from ground frozen mycelium using the Qiagen RNeasy Mini Kit.

tag: Strain

value: A. niger BO 1. Medium:Minimal xylose-based medium. Growth conditions:Controlled fermenter kept at pH 4.5. Sampling time:mid-late exponential phase. Replicate no:2.


title: 53 C Experiment 1 Repeat 2 Chip 13360942 Scanned at PMT Cy5 800 and Cy3 750


title: A. niger Xylose rep1

value: A. niger BO 1. Medium:Minimal xylose-based medium. Growth conditions:Controlled fermenter kept at pH 4.5. Sampling time:mid-late exponential phase. Replicate no:1.


title: LB broth without glucose (OD2.0)[rep1d]


title: LB broth without glucose (OD2.0)[rep2c]


title: LB broth without glucose (OD2.0)[rep3c]


title: A. niger Maltose rep3

source_name: Aspergillus niger grown on maltose medium

value: A. niger BO 1. Medium:Minimal maltose-based medium. Growth conditions:Controlled fermenter kept at pH 4.5. Sampling time:mid-late exponential phase. Replicate no:3.


title: A. niger Xylose rep3

value: A. niger BO 1. Medium:Minimal xylose-based medium. Growth conditions:Controlled fermenter kept at pH 4.5. Sampling time:mid-late exponential phase. Replicate no:3.


title: 53 C Experiment 2 Repeat 1 Chip 13360936 Scanned at PMT Cy5 800 and Cy3 750


title: A. niger Maltose rep2

value: A. niger BO 1. Medium:Minimal maltose-based medium. Growth conditions:Controlled fermenter kept at pH 4.5. Sampling time:mid-late exponential phase. Replicate no:2.


title: LB broth without glucose (OD2.0)[rep3a]

label_protocol: Total RNA (10 µg) was used to synthesize cDNA using a random primer for reverse transcription (Invitrogen Life Technologies, Carlsbad, CA). The primer was annealed at 70°C for 10 min, followed by snap-freezing in a dry ice-ethanol bath for 30 s and centrifugation for 1 min. The reaction mixture (Superscript III buffer, 0.1 M dithiothreitol, and aminoallyl-deoxyuridine triphosphate mix) was then incubated overnight with Superscript III reverse transcriptase (Invitrogen) at 42°C. Residual RNA was removed by alkaline treatment followed by neutralization, and the cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified cDNAs from the mutant was labeled with Cy-5 mono-Reactive Dye (GE Health Care).

label_protocol: Total RNA (10 µg) was used to synthesize cDNA using a random primer for reverse transcription (Invitrogen Life Technologies, Carlsbad, CA). The primer was annealed at 70°C for 10 min, followed by snap-freezing in a dry ice-ethanol bath for 30 s and centrifugation for 1 min. The reaction mixture (Superscript III buffer, 0.1 M dithiothreitol, and aminoallyl-deoxyuridine triphosphate mix) was then incubated overnight with Superscript III reverse transcriptase (Invitrogen) at 42°C. Residual RNA was removed by alkaline treatment followed by neutralization, and the cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified cDNAs from the wild type was labeled with Cy-3 mono-Reactive Dye (GE Health Care).


title: LB broth with 0.5% glucose (OD2.0)[rep3_3_d]

treatment_protocol: mutant cells were grown in LB broth with 0.5% glucose until it reaches OD 2.0

tag: S. Typhimurium (Accession # 87-26254) poultry isolate was grown in LB broth with 0.5% glucose until it reaches OD 2.0

treatment_protocol: wild type cells were grown in LB broth with 0.5% glucose until it reaches OD 2.0


title: LB broth without glucose (OD2.0)[rep3b]


title: LB broth without glucose (OD2.0)[rep2b]

source_name: Mutant at OD 2.0


title: A. niger Maltose rep1

value: A. niger BO 1. Medium:Minimal maltose-based medium. Growth conditions:Controlled fermenter kept at pH 4.5. Sampling time:mid-late exponential phase. Replicate no:1.


title: LB broth with 0.5% glucose (OD1.0)[rep2_3_c]

source_name: wild type at OD1.0

treatment_protocol: mutant cells were grown in LB broth with 0.5% glucose until it reaches OD 1.0

tag: S. Typhimurium (Accession # 87-26254) poultry isolate was grown in LB broth with 0.5% glucose until it reaches OD 1.0

source_name: mutant at OD1.0

treatment_protocol: wild type cells were grown in LB broth with 0.5% glucose until it reaches OD 1.0

tag: PJ002 luxS mutant grown in LB broth until it reaches OD 1.0


title: LB broth without glucose (OD2.0)[rep2a]


title: LB broth with 0.5% glucose (OD2.0)[rep3_3_c]


title: LB broth with 0.5% glucose (OD1.0)[rep2_2_c]


title: adipose_stemcell_rep1

description: AdAS


title: A. niger Glucose rep3

source_name: Aspergillus niger grown on glucose medium

value: A. niger BO 1. Medium:Minimal glucose-based medium. Growth conditions:Controlled fermenter kept at pH 4.5. Sampling time:mid-late exponential phase. Replicate no:3


title: LB broth without glucose (OD1.0)[rep3d]

treatment_protocol: wild type cells were grown in LB broth without glucose until it reaches optical density of 1.0 at 600nm

label_protocol: Total RNA (10 µg) was used to synthesize cDNA using a random primer for reverse transcription (Invitrogen Life Technologies, Carlsbad, CA). The primer was annealed at 70°C for 10 min, followed by snap-freezing in a dry ice-ethanol bath for 30 s and centrifugation for 1 min. The reaction mixture (Superscript III buffer, 0.1 M dithiothreitol, and aminoallyl-deoxyuridine triphosphate mix) was then incubated overnight with Superscript III reverse transcriptase (Invitrogen) at 42°C. Residual RNA was removed by alkaline treatment followed by neutralization, and the cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified cDNAs from the mutantwas labeled with Cy-3 mono-Reactive Dye (GE Health Care).

treatment_protocol: mutant cells were grown in LB broth without glucose until it reaches optical density of 1.0 at 600nm

tag: PJ002 (luxS::cat), luxS mutant of this strain of S. Typhimurium (Accession # 87-26254) poultry isolate obtained from the National Veterinary Service Laboratory, Ames, Iowa.


title: LB broth with 0.5% glucose (OD2.0)[rep3_2_c]


title: LB broth with 0.5% glucose (OD1.0)[rep1_1_c]


title: LB broth with 0.5% glucose (OD2.0)[rep3_2_d]


title: LB broth with 0.5% glucose (OD1.0)[rep1_3_c]


title: A. oryzae Xylose rep1

organism: Aspergillus oryzae

source_name: Aspergillus oryzae grown on xylose medium

value: A. oryzae A1560. Medium:Minimal xylose-based medium. Growth conditions:Controlled fermenter kept at pH 6.0. Sampling time:mid-late exponential phase. Replicate no:1.


title: A. oryzae Xylose rep2

value: A. oryzae A1560. Medium:Minimal xylose-based medium. Growth conditions:Controlled fermenter kept at pH 6.0. Sampling time:mid-late exponential phase. Replicate no:2.


title: LB broth with 0.5% glucose (OD2.0)[rep3_3_b]


title: Human Neural Stem Cell Line F3 Overexpressing NGN1 (replicate)

city: Tokyo

first: Jun-ichi

last: Satoh

address: 2-522-1 Noshio, Kiyose

department: Bioinformatics

country: Japan

institute: Meiji Pharmaceutical University

description: Neural stem cells (NSC) with self-renewal and multipotent properties serve as an ideal cell source for transplantation to treat spinal cord injury, stroke, and neurodegenerative diseases. To efficiently induce neuronal lineage cells from NSC for neuron replacement therapy, we should clarify the intrinsic genetic programs involved in a time and place-specific regulation of human NSC differentiation. Recently, we established an immortalized human NSC clone HB1.F3 to provide an unlimited NSC source applicable to genetic manipulation for cell-based therapy. To investigate a role of neurogenin 1 (Ngn1), a proneural basic helix-loop-helix (bHLH) transcription factor, in human NSC differentiation, we established a clone derived from F3 stably overexpressing Ngn1. Genome-wide gene expression profiling identified 250 upregulated genes and 338 downregulated genes in Ngn1-overexpressing F3 cells (F3-Ngn1) versus wild-type F3 cells (F3-WT). Notably, leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5), a novel stem cell marker, showed a robust increase in F3-Ngn1.

hyb_protocol: Hybridization was performed at 45℃ for 17 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

scan_protocol: The arrays were scanned by the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data expressed as CEL files were normalized by the robust multiarray average (RMA) method with the Expression Console software version 1.1 (Affymetrix).

label_protocol: One hundred ng of total RNA was processed for cRNA synthesis, fragmentation, and terminal labeling with the GeneChip Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix).

growth_protocol: The cells were incubated in the feeding medium composed of Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin. The medium was renewed every three days.

extract_protocol: Total RNA was isolated from subconfluent cells by using the TRIZOL Plus RNA Purification kit (Invitrogen). The quality of total RNA was evaluated on Agilent 2100 Bioanalyzer (Agilent Technologies). Total RNA of F3-WT and F3-Ngn1 was processed for two times (names as 1st and 2nd) different hybridization experiments.

treatment_protocol: Primary cultures of fetal human telencephalon cells were transformed with a retroviral vector pLSNmyc carrying the v-myc oncogene and the neomycin resistance gene. Following selection with G418, a single continuously dividing clone with a capacity to self-renew and differentiate into neurons and glial cells both in vitro and in vivo was isolated and designated HB1.F3. It carried normal human karyotype of 46 XX. After transducing a retroviral vector pBabePNgn1 carrying the open-reading frame (ORF) of the human Ngn1 gene and the puromycin resistance gene into HB1.F3 cells, a single puromycin-resistant clone was selected, expanded, and designated HB1.F3-Ngn1. In the present study, the wild-type HB1.F3 cells and the HB1.F3-Ngn1 cells are abbreviated as F3-WT and F3-Ngn1.

tag: protocol

value: NGN1 overexpression

tag: cells

value: Neural Neural Stem Cell Line F3


title: A. niger Glucose rep2

value: A. niger BO 1. Medium:Minimal glucose-based medium. Growth conditions:Controlled fermenter kept at pH 4.5. Sampling time:mid-late exponential phase. Replicate no:2.


title: LB broth with 0.5% glucose (OD1.0)[rep2_1_c]


title: A. niger Glucose rep1

value: A. niger BO 1. Medium:Minimal glucose-based medium. Growth conditions:Controlled fermenter kept at pH 4.5. Sampling time:mid-late exponential phase. Replicate no:1.


title: LB broth without glucose (OD2.0)[rep1b]


title: Human Neural Stem Cell Line F3 Wild Type (replicate)

value: control


title: LB broth without glucose (OD2.0)[rep1a]


title: A. oryzae Xylose rep3

value: A. oryzae A1560. Medium:Minimal xylose-based medium. Growth conditions:Controlled fermenter kept at pH 6.0. Sampling time:mid-late exponential phase. Replicate no:3.


title: LB broth with 0.5% glucose (OD2.0)[rep3_2_a]


title: LB broth with 0.5% glucose (OD2.0)[rep3_3_a]


title: LB broth with 0.5% glucose (OD2.0)[rep3_2_b]


title: LB broth without glucose (OD1.0)[rep2d]


title: LB broth without glucose (OD1.0)[rep3c]


title: Human Neural Stem Cell Line F3 Wild Type

value: Human Neural Stem Cell Line F3


title: LB broth without glucose (OD1.0)[rep2c]


title: A. oryzae Maltose rep2

source_name: Aspergillus oryzae grown on maltose medium

value: A. oryzae A1560. Medium:Minimal maltose-based medium. Growth conditions:Controlled fermenter kept at pH 6.0. Sampling time:mid-late exponential phase. Replicate no:2.


title: A. oryzae Maltose rep1

value: A. oryzae A1560. Medium:Minimal maltose-based medium. Growth conditions:Controlled fermenter kept at pH 6.0. Sampling time:mid-late exponential phase. Replicate no:1.


title: AML794_6h_rhTpo

city: Philadelphia

first: Anna

last: Kalota

state: PA

address: 421 Curie Blvd

department: Medicine, Hem/Onc

institute: University of Pennsylvania

description: PPG(2127) 794T U133Av2_GC-RMA

hyb_protocol: Hybridization to U133Av2 microarrays was done at 45ºC for 16 h . The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: Standard Affymetrix protocol was used (Cancer Center Microarray Facility at the University of Pennsylvania).

data_processing: Affymetrix Cel files were processed with Stratagene's ArrayAssist to yield chp files containing unlogged GC-RMA expression values and MAS5 detection flags.

source_name: AML Pheresis 6h rhTpo stimulation

label_protocol: Microarray analysis was performed at the Cancer Center Microarray Facility at the University of Pennsylvania in accordance to their standard protocol. Briefly, samples were amplified with the NuGen WT Pico kit and labeled with the FL-Ovation cDNA Biotin Module V2 from NuGen. NuGen's fragmentation and labeling process combines enzymatic and chemical processes for fragmentation and amplified single-stranded cDNA to generate labeled targets suitable for Affymetrix GeneChip arrays. The first step is a combined chemical and enzymatic fragmentation that yields cDNA products ranging from 50-100 bases. In a second step, this fragmented product is labeled via enzymatic attachment of biotin-labeled nucleotide to the 3-hydroxyl end of the fragmented cDNA.

growth_protocol: Cells were grown in suspension culture (37C, 100% in humidity, 5% CO2) using Endothelial Cell Medium-2 (EGM-2) + 2%FBS (Cambrex, East Rutherford, NJ).

extract_protocol: Total RNA was isolated using Qiagen RNeasy kits according to the manufacturer's recommendation.

treatment_protocol: Cells were treated either with 5uM SB559457 of 2.8uM rhTpo for 6h prior to RNA isolation.

tag: cell type

value: peripheral blood cells

tag: disease status

value: Acute myeloid leukemia (AML)

tag: treatment protocol

value: recombinant human Tpo (rhTpo) for 6 hours


title: LB broth without glucose (OD1.0)[rep3b]


title: Human Neural Stem Cell Line F3 Overexpressing NGN1


title: A. oryzae Glucose rep3

source_name: Aspergillus oryzae grown on glucose medium

value: A. oryzae A1560. Medium:Minimal glucose-based medium. Growth conditions:Controlled fermenter kept at pH 6.0. Sampling time:mid-late exponential phase. Replicate no:3.


title: LB broth with 0.5% glucose (OD2.0)[rep3_1_a]


title: LB broth with 0.5% glucose (OD1.0)[rep2_2_b]


title: LB broth with 0.5% glucose (OD1.0)[rep2_2_a]


title: LB broth without glucose (OD1.0)[rep3a]


title: AML794_6h_SB

description: PPG(2126) 794S U133Av2_GC-RMA

source_name: AML Pheresis 6h SB stimulation

value: MPL receptor agonist (SB559457) stimulation


title: LB broth without glucose (OD1.0)[rep2a]


title: A. oryzae Maltose rep3

value: A. oryzae A1560. Medium:Minimal maltose-based medium. Growth conditions:Controlled fermenter kept at pH 6.0. Sampling time:mid-late exponential phase. Replicate no:3.


title: LB broth with 0.5% glucose (OD1.0)[rep1_3_a]

tag: PJ002 luxS mutant grown in LB broth with 0.5% glucose

tag: Salmonella Typhimurium grown in LB with 0.5% glucose


title: A. oryzae Glucose rep2

value: A. oryzae A1560. Medium:Minimal glucose-based medium. Growth conditions:Controlled fermenter kept at pH 6.0. Sampling time:mid-late exponential phase. Replicate no:2.


title: LB broth without glucose (OD1.0)[rep1d]


title: LB broth with 0.5% glucose (OD1.0)[rep2_1_a]


title: AML774_6h_SB

description: PPG(2124) 774S U133Av2_GC-RMA


title: LB broth with 0.5% glucose (OD1.0)[rep1_1_a]


title: A. oryzae Glucose rep1

value: A. oryzae A1560. Medium:Minimal glucose-based medium. Growth conditions:Controlled fermenter kept at pH 6.0. Sampling time:mid-late exponential phase. Replicate no:1.


title: AML680_6h_SB

description: PPG(2122) 680S U133Av2_GC-RMA


title: LB broth with 0.5% glucose (OD1.0)[rep1_2_b]


title: AML680_6h_rhTpo

description: PPG(2123) 680T U133Av2_GC-RMA


title: LB broth without glucose (OD1.0)[rep1a]

tag: S. Typhimurium (Accession # 87-26254) poultry isolate.


title: UVA

city: Vienna

first: Martin

last: Bilban

country: Austria

institute: Medical University of Vienna

description: No additional information.

hyb_protocol: According to standard Affymetrix protocol.

data_processing: MAS 5.0

source_name: human dermal skin fibroblasts

extract_protocol: Trizol followed by RNeasy Mini kit (Qiagen)

tag: human dermal skin fibroblasts treated with 40J/cm² UVA-1 for 4 hrs.

tag: As a light source for UVA-1 a Mutzhas Supersun 5000-type solar simulator (Mutzhas, Munich, Germany) filtered for the emission of UVA-1 (340-390 nm) was used. The maximal amount of UVA-1 radiation used in this study on cells (40 J/cm2) would reach the surface of the skin during 112 minutes of sunlight exposure at noon at a northern latitude of 35°; 30% would reach the dermis

tag: Human neonatal skin fibroblasts (FB) were obtained from Lifeline Cell Technology; Walkersville, MD and grown in Dulbecco's modified Eagle's medium, Gibco (Gaithersburg, MD) supplemented with 10% fetal calf serum (FCS) and penicillin/ streptomycin (1000U per ml, Gibco) to sub-confluence. Fourth passage FB were used at a confluence of 60-70% in 12-well tissue culture plates.


title: AML774_6h_rhTpo

description: PPG(2125) 774T U133Av2_GC-RMA


title: OXPAPC

description: No additional information.

scan_protocol: According to standard Affymetrix protocol.

tag: human dermal skin fibroblasts treated with air-oxidized PAPC (OxPAPC)100µg/ml for 4 hrs. PAPC (1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphorylcholine ) was oxidized by exposure of the dry lipid to air for 72 h to generate OxPAPC.


title: Metanephric_Kidney_E14.5_P1_rep2

city: New Orleans

first: Oliver

last: Wessely

state: LA

address: 1901 Perdido Street

department: Cell Biology & Anatomy

institute: LSU Health Sciences Center

description: MicroRNA profile comparing two different stages of kidney development (E14.5 and P1)

hyb_protocol: performed by Exiqon following their protocol

data_processing: Median of replicated probes for each miRNA, Global Lowess normalization and Log2 transformation of Hy3/Hy5 Ratios.

label_protocol: Performed by Exiqon using the miRCURY Hy3/Hy5 labelling kit

extract_protocol: Trizol followed by RNeasy (Qiagen)

tag: strain

tag: tissue

value: metanephric kidney

tag: age


title: LB broth without glucose (OD1.0)[rep1b]

tag: Wild type of S. Typhimurium (Accession # 87-26254) poultry isolate obtained from the National Veterinary Service Laboratory, Ames, Iowa.


title: AML342_6h_SB

description: PPG(2120) 342S U133Av2_GC-RMA

source_name: AML PBMNC 6h SB stimulation


title: UV-PAPC

description: No additional information.

label_protocol: According to standard Affymetrix protocol.

tag: human dermal skin fibroblasts treated with 100µg/ml UV-PAPC for 4 hrs. PAPC (1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphorylcholine) dried to a thin film on a glass support was irradiated with UVA-1 with 80 J/cm2 to generate UV-PAPC.


title: AML342_6h_rhTpo

description: PPG(2121) 342T U133Av2_GC-RMA

source_name: AML PBMNC 6h rhTPO stimulation


title: AML332_6h_rhTpo

description: PPG(2119) 332T U133Av2_GC-RMA


title: LB broth without glucose (OD1.0)[rep2b]

tag: PJ002 (luxS::cat), luxS mutant of this strain of S. Typhimurium (Accession # 87-26254) poultry isolate obtained from the National Veterinary Service Laboratory, Ames, Iowa.


title: AML332_6h_SB

description: PPG(2118) 332S U133Av2_GC-RMA


title: Metanephric_Kidney_E14.5_P1_rep3

scan_protocol: performed by Exiqon following their protocol


title: LB broth without glucose (OD1.0)[rep1c]

tag: S. Typhimurium (Accession # 87-26254) poultry isolate obtained from the National Veterinary Service Laboratory, Ames, Iowa.


title: Metanephric_Kidney_E14.5_P1_rep1


title: rpob 9-bp-deletion  strains vs. wildtype strains (Cy5/Cy3)

city: Hangzhou

first: Yuejin

last: Hua

state: Zhejiang

address: 268 KaiXuan Road

department: Institute of Nuclear-Agricultural Sciences

country: China

institute: Zhejiang University

description: Biological replicate 1 of 2.

hyb_protocol: Samples were applied to microarrays enclosed in  hybridization chambers. After hybridization, slides were washed sequential. Dye-swap is carried out.

scan_protocol: Scanned on an Genepix 4000B scanner. Images were quantified using Genepix (version 5.0).

data_processing: Prior to channel normalization, microarray outputs were fitered to remove spots of poor signal quality by excluding those data points with a signal mean intensity less than two standard deviations above background in both channels. LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Limma software was used. Furthemore, the replicate spots on each array were merged to one value using lmFit function within Limma.

organism: Deinococcus radiodurans

source_name: Total RNA from rpob 9-bp-deletion  strains labeled with Cyanine-5 (red).

label_protocol: 16 µg of total RNA were primed with 9 µg of Hexadeoxyribonucleotide mixture at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

growth_protocol: Cells were grown in an normal condition.

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

tag: genotype

value: rpob 9-bp-deletion

tag: phenotype

value: low growth rate

source_name: Total RNA from wildtype strains labeled with Cyanine-3 (green).

value: Wild-type

value: normal growth rate


title: RB-PAPC

description: Addition of the O2 generator Rose Bengal (RB).

tag: human dermal skin fibroblasts treated with 100µg/ml Rose Bengal (RB)-PAPC.


title: P14 KO FoxJ1EGFP+

status: Public on Oct 21 2009

city: Raleigh

first: Troy

last: Ghashghaei

state: NC

address: 4700 Hillsborough Street

department: Molecular Biomedical Sciences

institute: North Carolina State University

description: Gene expression data from laser captured FoxJ1-EGFP tissue in postnatal day 14 mouse brain

hyb_protocol: Following fragmentation, 5.5 ug cDNA was hybridized for 16 hr at 45C on the Mouse Gene 1.0 ST.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: RMA

source_name: P14 FoxJ1-EGFP+ tissue FoxJ1 knockout

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol:
Mouse brains were rapidly collected in 10% RNAlater on ice, frozen, and laser capture microscopy was used to isolate FoxJ1-EGFP domains from wildtype and FoxJ1 null brains.
Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: brain/ependymal layer

value: FoxJ1 null

value: postnatal day 14


title: P7 KO FoxJ1EGFP+

description: Gene expression data from laser captured FoxJ1-EGFP tissue in postnatal day 7 mouse brain

source_name: P7 FoxJ1-EGFP+ tissue FoxJ1 knockout

value: postnatal day 7


title: wildtype strains vs. rpob 9-bp-deletion strains(Cy5/Cy3)

description: Biological replicate 2 of 2 with dye-swap.

source_name: Total RNA from wildtype strains labeled with Cyanine-5 (red).

source_name: Total RNA from rpob 9-bp-deletion strains labeled with Cyanine-3 (green).


title: P14 WT FoxJ1EGFP+

source_name: P14 FoxJ1-EGFP+ tissue FoxJ1 wildtype

value: Wildtype


title: P7 WT FoxJ1EGFP+

source_name: P7 FoxJ1-EGFP+ tissue FoxJ1 wildtype


title: P1 KO FoxJ1EGFP+

description: Gene expression data from laser captured FoxJ1-EGFP tissue in postnatal day 1 mouse brain

source_name: P1 FoxJ1-EGFP+ tissue FoxJ1 knockout

value: postnatal day 1


title: PAPC

description: No additional information.

tag: human dermal skin fibroblasts treated with 100µg/ml PAPC for 4 hrs


title: P1 WT FoxJ1EGFP+

source_name: P1 FoxJ1-EGFP+ tissue FoxJ1 wildtype


title: Colon tumor ZZ_TB115A

type: genomic

first: Barry

middle: Stephen

last: Taylor

address: 1275 York Avenue, Box #460

institute: Memorial Sloan-Kettering Cancer Center

description: DNA copy number

hyb_protocol: Per manufacturer's instructions

scan_protocol: Per manufacturer's instructions

data_processing: Agilent Feature Extraction ver9.5.3.1, protocol name: CGH-v4_95_Feb07. Probe-level data was subsequently normalized for local GC content with a two-stage LOESS fit.

molecule: genomic DNA

source_name: tumor DNA

label_protocol: Bioprime Array CHG labeling kit (Invitrogen) using Cy3/Cy5

extract_protocol: Genome DNA was extracted for the cancer cell lines using the Agencourt Genfind v2 kit and the Biomek NX Span-8 #2. DNA was extracted from microdissected samples with standard proteinase K digestion and phenol/chloroform extraction after overnight incubation, shaking at 55C and precipitated with ethanol.

tag: test

value: Colon tumor ZZ_TB115A

source_name: Promega reference DNA

extract_protocol: not applicable

tag: reference

value: Promega reference DNA


title: Colon tumor ZZ_TB120A

description: DNA copy number

value: Colon tumor ZZ_TB120A


title: Colon tumor ZZ_TB063A

description: DNA copy number

value: Colon tumor ZZ_TB063A


title: Colon tumor ZZ_TB079A

description: DNA copy number

value: Colon tumor ZZ_TB079A


title: Colon tumor ZZ_TB154A

description: DNA copy number

value: Colon tumor ZZ_TB154A


title: Colon tumor ZZ_TB061A

description: DNA copy number

value: Colon tumor ZZ_TB061A


title: Colon tumor ZZ_TB071A

description: DNA copy number

value: Colon tumor ZZ_TB071A


title: Colon tumor ZZ_TB034

description: DNA copy number

value: Colon tumor ZZ_TB034


title: Colon tumor ZZ_TB101A

description: DNA copy number

value: Colon tumor ZZ_TB101A


title: Colon tumor ZZ_TB049A

description: DNA copy number

value: Colon tumor ZZ_TB049A


title: Colon tumor ZZ_TB134A

description: DNA copy number

value: Colon tumor ZZ_TB134A


title: Control

description: No additional information.

tag: sham treated human dermal skin fibroblasts.


title: Colon tumor ZZ_TB035A

description: DNA copy number

value: Colon tumor ZZ_TB035A


title: Colon tumor ZZ_TB018

description: DNA copy number

value: Colon tumor ZZ_TB018


title: Colon tumor ZZ_TB276A

description: DNA copy number

value: Colon tumor ZZ_TB276A


title: Colon tumor ZZ_TB074A

description: DNA copy number

value: Colon tumor ZZ_TB074A


title: Colon tumor ZZ_TB050A

description: DNA copy number

value: Colon tumor ZZ_TB050A


title: Colon tumor ZZ_TB031A

description: DNA copy number

value: Colon tumor ZZ_TB031A


title: Colon tumor ZZ_TB012A

description: DNA copy number

value: Colon tumor ZZ_TB012A

value: Promega reference DNA


title: Colon tumor ZZ_TB020A

description: DNA copy number

value: Colon tumor ZZ_TB020A


title: Colon tumor ZZ_C80T

description: DNA copy number

value: Colon tumor ZZ_C80T


title: Colon tumor ZZ_TB030A

description: DNA copy number

value: Colon tumor ZZ_TB030A


title: Colon tumor ZZ_TB019A

description: DNA copy number

value: Colon tumor ZZ_TB019A


title: Colon tumor ZZ_TB004A

description: DNA copy number

value: Colon tumor ZZ_TB004A


title: Colon tumor ZZ_TB017A

description: DNA copy number

value: Colon tumor ZZ_TB017A


title: Colon tumor ZZ_C0104A

description: DNA copy number

value: Colon tumor ZZ_C0104A


title: Colon tumor ZZ_C70t

description: DNA copy number

value: Colon tumor ZZ_C70t


title: Colon tumor ZZ_TB036A

description: DNA copy number

value: Colon tumor ZZ_TB036A


title: Colon tumor ZZ_C0126A

description: DNA copy number

value: Colon tumor ZZ_C0126A


title: Colon tumor ZZ_C0081A

description: DNA copy number

value: Colon tumor ZZ_C0081A


title: Colon tumor ZZ_C0097A

description: DNA copy number

value: Colon tumor ZZ_C0097A


title: Colon tumor ZZ_A6141A

description: DNA copy number

value: Colon tumor ZZ_A6141A


title: Colon tumor ZZ_TB054A

description: DNA copy number

value: Colon tumor ZZ_TB054A


title: Colon tumor ZZ_A4779A

description: DNA copy number

value: Colon tumor ZZ_A4779A


title: Colon tumor ZZ_A4674U

description: DNA copy number

value: Colon tumor ZZ_A4674U


title: Colon tumor ZZ_A3536A

description: DNA copy number

value: Colon tumor ZZ_A3536A

value: Promega reference DNA


title: Colon tumor ZZ_C0085A

description: DNA copy number

value: Colon tumor ZZ_C0085A


title: Colon tumor ZZ_A5960U

description: DNA copy number

value: Colon tumor ZZ_A5960U


title: Colon tumor ZZ_A3622U

description: DNA copy number

value: Colon tumor ZZ_A3622U


title: Colon tumor ZZ_A3203U

description: DNA copy number

value: Colon tumor ZZ_A3203U


title: Colon tumor ZZ_A2715A

description: DNA copy number

value: Colon tumor ZZ_A2715A


title: Colon tumor ZZ_A1423U

description: DNA copy number

value: Colon tumor ZZ_A1423U


title: Colon tumor ZZ_A4396U

description: DNA copy number

value: Colon tumor ZZ_A4396U


title: Colon tumor ZZ_A3684U

description: DNA copy number

value: Colon tumor ZZ_A3684U


title: Colon tumor ZZ_A5790A

description: DNA copy number

value: Colon tumor ZZ_A5790A


title: Colon tumor ZZ_9420t

description: DNA copy number

value: Colon tumor ZZ_9420t


title: Colon tumor ZZ_A2434A

description: DNA copy number

value: Colon tumor ZZ_A2434A


title: Colon tumor ZZ_6220t

description: DNA copy number

value: Colon tumor ZZ_6220t


title: Colon tumor ZZ_3531T

description: DNA copy number

value: Colon tumor ZZ_3531T


title: Colon tumor ZZ_A1516

description: DNA copy number

value: Colon tumor ZZ_A1516


title: Colon tumor ZZ_9394t

description: DNA copy number

value: Colon tumor ZZ_9394t


title: Colon tumor ZZ_3862t

description: DNA copy number

value: Colon tumor ZZ_3862t


title: Colon tumor ZZ_A5320A

description: DNA copy number

value: Colon tumor ZZ_A5320A

value: Promega reference DNA


title: Colon tumor ZZ_7925t

description: DNA copy number

value: Colon tumor ZZ_7925t


title: Colon tumor ZZ_3657t

description: DNA copy number

value: Colon tumor ZZ_3657t


title: Colon tumor ZZ_A2561

description: DNA copy number

value: Colon tumor ZZ_A2561


title: Colon tumor ZZ_10258V

description: DNA copy number

value: Colon tumor ZZ_10258V


title: Colon tumor ZZ_8152t

description: DNA copy number

value: Colon tumor ZZ_8152t


title: Colon tumor ZZ_A1716A

description: DNA copy number

value: Colon tumor ZZ_A1716A


title: Colon tumor ZZ_10512A

description: DNA copy number

value: Colon tumor ZZ_10512A


title: Colon tumor ZZ_A1644A

description: DNA copy number

value: Colon tumor ZZ_A1644A


title: Colon tumor ZZ_14938V

description: DNA copy number

value: Colon tumor ZZ_14938V


title: Colon tumor ZZ_10264A

description: DNA copy number

value: Colon tumor ZZ_10264A


title: Colon tumor ZZ_10194A

description: DNA copy number

value: Colon tumor ZZ_10194A


title: Colon tumor ZZ_11053A

description: DNA copy number

value: Colon tumor ZZ_11053A


title: Colon tumor ZZ_12051V

description: DNA copy number

value: Colon tumor ZZ_12051V


title: Colon tumor ZZ_80649U

description: DNA copy number

value: Colon tumor ZZ_80649U


title: Colon tumor ZZ_08018A

description: DNA copy number

value: Colon tumor ZZ_08018A


title: Colon tumor ZZ_10078t

description: DNA copy number

value: Colon tumor ZZ_10078t


title: Colon tumor ZZ_09509A

description: DNA copy number

value: Colon tumor ZZ_09509A

value: Promega reference DNA


title: Colon tumor ZZ_07145A

description: DNA copy number

value: Colon tumor ZZ_07145A


title: Colon tumor ZZ_09728A

description: DNA copy number

value: Colon tumor ZZ_09728A


title: Colon tumor ZZ_06682V

description: DNA copy number

value: Colon tumor ZZ_06682V


title: Colon tumor ZZ_09297A

description: DNA copy number

value: Colon tumor ZZ_09297A


title: Colon tumor ZZ_07061A

description: DNA copy number

value: Colon tumor ZZ_07061A


title: Colon tumor ZZ_06265A

description: DNA copy number

value: Colon tumor ZZ_06265A


title: Colon tumor ZZ_05708A

description: DNA copy number

value: Colon tumor ZZ_05708A


title: Colon tumor ZZ_05885A

description: DNA copy number

value: Colon tumor ZZ_05885A


title: Colon tumor ZZ_06432V

description: DNA copy number

value: Colon tumor ZZ_06432V


title: Colon tumor ZZ_09185A

description: DNA copy number

value: Colon tumor ZZ_09185A


title: Colon tumor ZZ_04549A

description: DNA copy number

value: Colon tumor ZZ_04549A


title: Colon tumor ZZ_05786A

description: DNA copy number

value: Colon tumor ZZ_05786A


title: Colon tumor ZZ_05629A

description: DNA copy number

value: Colon tumor ZZ_05629A


title: Colon tumor ZZ_05839A

description: DNA copy number

value: Colon tumor ZZ_05839A


title: Colon tumor ZZ_05025A

description: DNA copy number

value: Colon tumor ZZ_05025A


title: Colon tumor ZZ_04222V

description: DNA copy number

value: Colon tumor ZZ_04222V


title: TC38b

city: Pittsburgh

first: Thomas

last: Richards

institute: University of Pittsburgh

hyb_protocol: Fifteen micrograms of the labeled cRNA was hybridized to Affymetrix Rhesus Macaque genome 49 format Arrays (GeneChip Rhesus Macaque Genome Array, Cat. No.900656, Affymetrix, Santa Clara, CA, USA), followed by washing and staining with streptavidin phytoerythrin (SAPE) as recommended by the manufacturer.

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

data_processing: Affymetrix GCOS software was used for the scanning of the probe arrays and the probe intensity analysis and normalization was performed using RMA express (Navara et al., 2007).

organism: Macaca mulatta

label_protocol: One microgram of total RNA was used to start the manual target preparation using the Codelink Expression Bioarray System (Amersham Biosciences/GE Healthcare). Briefly,double-stranded cDNA synthesis was performed with a T7oligo (dT) primer, followed by purification. This cDNA was used as a template for in vitro transcription with biotin- labeled nucleotides.

extract_protocol: Total RNA was extracted using the Trizol protocol (Navara et al., 2007) and purified using the Qiagen RNeasy Micro Kit (Valencia, CA) according to the manufacturer's recommendations. RNA quantity and quality were determined using a Nanodrop spectrophotometer and Agilent Bioanalyzer (Navara et al., 2007).

tag: cell type

value: teratoma fibroblasts


title: Colon tumor ZZ_04449A

city: New York

description: DNA copy number

value: Colon tumor ZZ_04449A

value: Promega reference DNA


title: Colon tumor ZZ_04388A

description: DNA copy number

value: Colon tumor ZZ_04388A


title: Colon tumor ZZ_06314A

description: DNA copy number

value: Colon tumor ZZ_06314A


title: Colon tumor ZZ_03465A

description: DNA copy number

value: Colon tumor ZZ_03465A


title: Colon tumor ZZ_04494A

description: DNA copy number

value: Colon tumor ZZ_04494A


title: C3106c

value: nhpESCs


title: TD31c


title: TB38c


title: Colon tumor ZZ_00702A

description: DNA copy number

value: Colon tumor ZZ_00702A


title: Colon cancer cell line MJ_T202

description: DNA copy number

tag: cell line


title: Colon cancer cell line MJ_T196

description: DNA copy number


title: Colon cancer cell line MJ_LS1034

description: DNA copy number


title: M088c

value: skin fibroblasts


title: M032c


title: C3106b


title: TA38a


title: TA31b


title: TB31c


title: M106p1e


title: TD31a


title: TB38a


title: TA38c


title: TE31a


title: TC31b


title: M106p1f


title: TA31a


title: TB31b


title: TB38b


title: C3806c


title: M106p1b


title: TC31c


title: C3806a


title: M088a


title: TB31a


title: TA31c


title: Colon tumor ZZ_04800A

description: DNA copy number

value: Colon tumor ZZ_04800A


title: TD31b


title: Colon tumor ZZ_03544A

description: DNA copy number

value: Colon tumor ZZ_03544A


title: TA38b


title: M088b


title: C3806b


title: M032a


title: TC31a


title: M032b


title: TC38a


title: EMG2+ING

city: Madrid

first: Sergio

last: Callejas

address: Melchor Fernández Almagro, 3

department: Genomics Unit

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

description: no additional information

hyb_protocol: 100 ng of Cy3 labelled RNA were hybridized for 20 hours at 55ºC in a hybridization oven  (G2545A, Agilent) set to 15 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer, according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for miRNA Microarray v1.0 (miRNA Microarray System Protocol, Agilent Technologies). Images provided by the scanner were analyzed using Agilent´s software Feature Extraction version 9.5.3.1.

data_processing: Data files from Feature Extraction were imported into GeneSpring® GX software version 9.0. (Agilent Technologies). Quantile normalization was performed and log2 transformed expression values were obtained for each probe. Probes were also flagged (Present, Marginal, Absent) using GeneSpring® default settings. Probes were filtered for further analysis according to expression (all miRNAs which raw expression levels are within the range 20%-100% of expression in all replicates of at least one condition were retained) and flags (all miRNAs flagged as Present and Marginal in all replicates of at least one condition were retained). Expression ratios of Ing1-deficient vs wild-type mouse MEFs and Doxycycline-induced EMG cells vs uninduced controls were calculated and transformed into a log2 scale

source_name: EMG cell line +Dox (24h)

label_protocol: miRNA Microarray System Protocol (Agilent Technologies) was used to label RNA. Basically, 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3´ end of each RNA molecule by using T4 RNA ligase. Labelled RNA was purified using Micro Bio Spin 6 Columns (Bio-Rad, 732-6221).

extract_protocol: Total RNA was prepared using TriReagent (Sigma), following the manufacturer's protocol.

value: Cell line with inducible expression of p33ING1

tag: agent

value: doxycycline


title: EMG2

description: no additional information

source_name: EMG cell line -Dox (24 h)

value: uninduced (control)


title: EMG1+ING

description: no additional information


title: RR5

city: Los Angeles

first: Rosane

last: Teles

state: CA

address: 10833 Le Conte Ave, CHS 52-121

institute: UCLA

molecule: polyA RNA

source_name: reversal reaction leprosy

extract_protocol: Standard Affymetrix protocol by UCLA DNA microarray core facility (GTC method)

value: skin lesion


title: RR1

hyb_protocol: Standard Affymetrix protocol by UCLA DNA microarray core facility


title: RR6

scan_protocol: Standard Affymetrix protocol by UCLA DNA microarray core facility


title: RR3

data_processing: Standard Affymetrix protocol by UCLA DNA microarray core facility


title: BT10

source_name: borderline tuberculoid leprosy

label_protocol: Standard Affymetrix protocol by UCLA DNA microarray core facility


title: BT9


title: RR2


title: RR4


title: BT8


title: wtD5

description: no additional information

source_name: Wild-type MEFs

value: Mouse embryo fibroblasts (MEFs)

tag: strain

value: Wild-type


title: BT7

tag: tissue


title: RR7


title: TC38c

value: teratoma fibroblasts


title: BT5


title: BT6


title: wtD1

description: no additional information


title: Colon tumor ZZ_05334A

description: DNA copy number

value: Colon tumor ZZ_05334A

value: Promega reference DNA


title: BT3


title: ggO5

description: no additional information

source_name: Ing1-deficient MEFs


title: C3106d


title: BT1


title: ggD4

description: no additional information


title: BT4


title: LL7

source_name: lepromatous leprosy


title: Cells transduced with vector expressing GAB2, not selected (MCF10A GAB2 B Ph)

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description: MCF10A cells transduced with vector expressing GAB2, not selected

hyb_protocol: 1500 ng of cRNA was hyb on human-6 V2 for 16-20 hours. Array washing was performed using wash buffer; an high strincengy temp wash was performed at 55C for 10 minutes. Arrays were stained with SA-Cy3

scan_protocol: The hybridized BeadChips were scanned by Illumina BeadScan scanner and analyzed by Illumina's BeadStudio version 1.5.1.3

data_processing: Data were summarized and rank-invariant normalized using the Illumina Beadstudio software (ver. 1.5.1.3).

label: biotin-SA Cy3

source_name: MCF10A, gab2 B transduced selected

label_protocol: cRNA synthesis was performed using the Illumina TotalPrep RNA amplification kit.

extract_protocol: RNA extraction was performed using Trizol plus RNA purification kit (Invitrogen). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies).


title: TE31b


title: LL5


title: Cells transduced with a Mouse testis cDNA library and selected for growth in the absence of anchorage (MCF10A INFB Ph)

description: MCF10A cells transduced with a Mouse testis cDNA library and selected for growth in the absence of anchorage

source_name: MCF10A, infected B with mouse testis library


title: LL2


title: LL4


title: LL3


title: LL9


title: Cells transduced with vector expressing GFP and selected for growth in the absence of anchorage (MCF10A GFPB Ph)

description: MCF10A cells transduced with vector expressing GFP and selected for growth in the absence of anchorage

source_name: MCF10A, control B selection


title: BT2


title: Cells transduced with vector expressing GFP, not selected (MCF10A GFPB Uns)

description: MCF10A cells transduced with vector expressing GFP, not selected

source_name: MCF10A, control B no selection


title: Cells transduced with vector expressing GAB2 and selected for growth in the absence of anchorage (MCF10A GAB2 A Ph)

description: MCF10A cells transduced with vector expressing GAB2 and selected for growth in the absence of anchorage

source_name: MCF10A, gab2 A transduced selected


title: AALE-KRAS WT, biological rep1

city: La Jolla

first: Pablo

last: Tamayo

address: 3855 Health Sciences Drive MC 0658

department: Moores Cancer Center

institute: UCSD

description: Gene expression data of WT KRAS

hyb_protocol: Following fragmentation, 13.75 ug of cRNA was hybridized for 16 hr at 45C on U133A HTA Human Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The data were scanned using Affymetrix HT Scanner

data_processing: The data were analyzed with RMA (Gene Pattern's ExpressionFileCreator version 8). Parameters: method   RMA  quantile normalization  yes  background correct  yes  compute present absent calls  no  normalization method  none  value to scale to    clm file    annotate probes  yes

source_name: WT KRAS expression

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix HT protocol from 1 ug total RNA. PolyA controls were not added.

growth_protocol: AALE cells (Lundberg et al., Oncogene 2002;21:4577)  were grown in serum free SABM media with supplements using standard culture conditions.

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

treatment_protocol: Cells were transduced with pBP control vector, pBP-KRAS G12V, or pBP-KRAS WT, selected in puromycin, then RNA was harvested 6 days post-infection.

value: Immortalized lung epithelial cells


title: AALE-KRAS WT, biological rep2

description: Gene expression data of WT KRAS


title: AALE-Vector, biological rep2

description: Gene expression data following control vector expression

source_name: Control vector expression


title: Wild-type cells, not selected (MCF10A WTA Uns)

description: Wild-type MCF10A cells, not selected

source_name: MCF10A, wt A cells no selection


title: Cells transduced with vector expressing GAB2 and selected for growth in the absence of anchorage (MCF10A GAB2 B Uns)

source_name: MCF10A, gab2 B transduced no selection


title: AALE-Vector uninfected, biological rep1

description: Gene expression data from vector expression uninfected

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on U133A Human Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The data were scanned using Affymetrix Gene Chip Scanner 3000

source_name: Vector expression uninfected

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

growth_protocol: AALE cells (Lundberg et al., Oncogene 2002;21:4577) expressing oncogenic KRAS or vector alone were grown in serum free SABM media with supplements using standard culture conditions.

treatment_protocol: Cells were infected with TBK1- or GFP-specific lentivirally delivered shRNAs for 4 hours, puromycin selection was initiated 24 hours post-infection, then RNA was harvested 48 hours post-infection.


title: LL1


title: AALE-Vector uninfected, biological rep2


title: Cells transduced with a Mouse testis cDNA library and selected for growth in the absence of anchorage (MCF10A INFA Ph)

source_name: MCF10A, infected A with mouse testis library


title: Cells transduced with vector expressing GFP and selected for growth in the absence of anchorage (MCF10A GFPA Ph)

source_name: MCF10A, control A selection


title: AALE-KRAS, biological rep2

description: Gene expression data following oncogenic KRAS expression

source_name: Oncogenic KRAS expression


title: AALE-Vector + shGFP, biological rep3

description: Gene expression data from vector expression/control suppression

source_name: Vector expression/control suppression


title: Cells transduced with vector expressing GAB2, not selected (MCF10A GAB2 A Uns)

source_name: MCF10A, gab2 A transduced no selection


title: AALE-Vector uninfected, biological rep3


title: AALE-Vector + shGFP, biological rep1


title: Cells transduced with vector expressing GFP, not selected (MCF10A GFPA Uns)

source_name: MCF10A, control A no selection


title: AALE-Vector + shGFP, biological rep2


title: AALE-Vector, biological rep1


title: AALE-Vector + shTBK1, biological rep2

description: Gene expression data from vector expression/TBK1 suppression

source_name: Vector expression/TBK1 suppression


title: Colon tumor ZZ_03393A

description: DNA copy number

source_name: tumor DNA

value: Colon tumor ZZ_03393A

source_name: Promega reference DNA


title: YS LD, biological rep 4

city: Seoul

first: Cheol-Koo

last: Lee

address: Korea University, Biotechnology #318 West building, Anam-dong, Seongbuk-gu

department: Biotechnology

country: South Korea

institute: Korea University

description: Gene expression profile

hyb_protocol: Ten micrograms of fragmented cRNA.  45 degrees C for 16 hours.

scan_protocol: GeneChip scanner 3000G following the Affymetrix standard protocols

data_processing: GCOS 1.3 following the Affymetrix standard protocols

organism: Sus scrofa

source_name: Yorkshire LD

label_protocol: Affymetrix standard methods using GeneChip reagents

growth_protocol: The pigs were raised under the same conditions. The details of conditions and feeding were fully described in the supplementary material of Moon et al., Anim. Genet. 40(1): 115-8 (2009).

extract_protocol: Trizol reagent following the manufacturer's instruction

treatment_protocol: Back muscle between the seventh and ninth ribs were collected.

value: Longissimus dorsi (LD)

tag: breed

value: Yorkshire (YS)

tag: age

value: 6 month old


title: TE31c


title: AALE-Vector + shTBK1, biological rep1


title: YS LD, biological rep 3

description: Gene expression profile


title: AALE-KRAS, biological rep1


title: AALE-KRAS uninfected, biological rep1

description: Gene expression data from KRAS expression uninfected

source_name: KRAS expression uninfected


title: YS LD, biological rep 2

description: Gene expression profile


title: Aspergillus nidulans, glycerol, biological rep2

city: Göteborg

first: Margarita

last: Salazar Peña

address: Kemigården 4

department: Chemical and Biological Engineering

description: Gene expression data from A. nidulans grown in batch cultivations

hyb_protocol: Approximately 15 mg of fragmented cRNA was hybridized for 16 hr at 45 °C on the 3AspergDTU Affymetrix GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Agilent GeneArrayÒ Scanner 3000. Scanned probe array images (.DAT files) were converted into .CEL files using the Affymetrix GeneChip Operating Software.

data_processing: Affymetrix CEL data files were preprocessed using the statistical language R version 2.7.1 and Bioconductor version 2.2. Normalization was performed using the qspline algorithm and gene expression indexes were calculated from the PM probes with the median polish summary method. All statistical preprocessing methods were implemented in affy package using R scripts and limma package.

organism: Aspergillus nidulans

source_name: Fungal  biomass

label_protocol: Biotin-labeled cRNA was prepared from approximately 5 mg of total RNA according to the protocol described in the Affymetrix GeneChipÒ Expression Analysis Technical Manual (Affymetrix and GeneChip. (2007) P/N 702232, Affymetrix, Santa Clara, CA, Revision 2).

growth_protocol: Aspergillus nidulans, Aspergillus oryzae and Aspergillus niger were grown in batch cultivations.

extract_protocol: A. niger and A. nidulans total RNA was isolated using the Qiagen RNeasy Mini Kit according to the protocol for isolation of total RNA from plant and fungi. A. oryzae total RNA was purified by using the Promega RNAgents Total RNA Isolation system following manufacturer’s recommendations.

treatment_protocol: Fungal biomass from each of the Aspergillus fermentation replicates was harvested in the mid exponential phase of growth, filtered, washed, dryed by squeezing, frozen in liquid nitrogen and stored at -80 °C until further processing.

value: FGSC A4


title: Aspergillus nidulans, glycerol, biological rep3


title: AALE-KRAS uninfected, biological rep3


title: Aspergillus nidulans, glycerol, biological rep1


title: AALE-KRAS + shGFP, biological rep2

description: Gene expression data from KRAS expression/control suppression

source_name: KRAS expression/control suppression


title: YS LD, biological rep 1

description: Gene expression profile


title: AALE-KRAS + shGFP, biological rep3


title: AALE-KRAS + shTBK1, biological rep3

description: Gene expression data from KRAS expression/TBK1 suppression

source_name: KRAS expression/TBK1 suppression


title: AALE-KRAS + shTBK1, biological rep2


title: Aspergillus nidulans, glucose, biological rep3


title: AALE-KRAS + shGFP, biological rep1


title: KNP LD, biological rep 3

description: Gene expression profile

source_name: Korean native pig LD

value: Korean native pig (KNP)

value: 7 month old


title: Aspergillus nidulans, glucose, biological rep2


title: Aspergillus oryzae, glycerol, biological rep3

description: Gene expression data from A. oryzae grown in batch cultivations


title: Aspergillus nidulans, glucose, biological rep1


title: AALE-KRAS uninfected, biological rep2


title: AALE-KRAS + shTBK1, biological rep1


title: KNP LD, biological rep 1

description: Gene expression profile


title: KNP LD, biological rep 2

description: Gene expression profile


title: Aspergillus oryzae, glycerol, biological rep1


title: KNP LD, biological rep 4

description: Gene expression profile


title: cultured cells TSC2+/+ rep3

city: Boston

first: Po-Shun

state: MA

address: 1 Blackfan Circle, Karp 6

department: Medicine

institute: Brigham & Women's Hospital

description: cultured cells TSC2+/+ rep3

hyb_protocol: For hybridization to the CodeLink arrays 10 μg of labeled cRNA was fragmented, denatured at 90°C for 5 min, and then hybridized at 37°C for 20 hours. After washing, the arrays were incubated with streptavidin-phycoerythrin and biotinylated anti-streptavidin antibodies. , and the arrays scanned on a GenePix 4000B scanner (Axon Instrument, Sunnyvale, CA).

scan_protocol: The arrays scanned on a GenePix 4000B scanner (Axon Instrument, Sunnyvale, CA).

data_processing: The gene expression levels on each array were normalized to a median expression level of 1.0 using the CodeLink software.

source_name: cultured cells TSC2+/+

label_protocol: RNA was first reverse transcribed using a T7-Oligo (dT) promoter primer, followed by second strand cDNA synthesis using RNase H. Double-stranded cDNA was purified and used as a template in the IVT using T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for to generate biotin-labeled cRNA.

growth_protocol: Cells are in phenol red-free serum-free alpha-MEM media.

extract_protocol: Total RNA was extracted from cells using the Qiagen RNeasy kit (Qiagen Inc., Valencia, CA). The quality of the total RNA was assessed by analysis on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). The ratio of the 28S/18S bands was required to be ≥ 2.0.

tag: tissue type

value: angiomyolipoma (AML) derived from LAM patient

value: TSC2+/+ (TSC2 addback)


title: Aspergillus oryzae, glucose, biological rep3


title: Aspergillus oryzae, glucose, biological rep1


title: Aspergillus oryzae, glycerol, biological rep2


title: Aspergillus niger, glycerol, biological rep3

description: Gene expression data from A. niger grown in batch cultivations


title: cultured cells TSC2+/+ rep2

description: cultured cells TSC2+/+ rep2


title: EMG1

description: no additional information

source_name: EMG cell line -Dox (24 h)

value: Cell line with inducible expression of p33ING1

value: uninduced (control)


title: cultured cells TSC2-/- rep3

description: cultured cells TSC2-/- rep3

source_name: cultured cells TSC2-/-


title: Aspergillus niger, glycerol, biological rep2


title: cultured cells TSC2+/+ rep1

description: cultured cells TSC2+/+ rep1


title: cultured cells TSC2-/- rep2

description: cultured cells TSC2-/- rep2


title: cultured cells TSC2-/- rep1

description: cultured cells TSC2-/- rep1


title: Aspergillus niger, glucose, biological rep3


title: Cells transduced with vector expressing GFP (MCF10A GFP 2 Selected)

description: Transduced with vector expressing GFP

hyb_protocol: 1500 ng of cRNA was hyb on mouse-6 for 16-20 hours. Array washing was performed using wash buffer; an high strincengy temp wash was performed at 55C for 30 minutes. Arrays were stained with SA-Cy3

data_processing: Data are summarized with beadstudio 1.5.1.3 and intentionally not normalized to preserve the asymmetry due to selection and enrichment of a limited number of transcripts.

source_name: MCF20A GFP 2 Selected

label_protocol: cRNA synthesis was performed using the Illumina TotalPrep RNA amplification kit introducing  the following variations: 20 ug of total RNA using pFB specific primer starting from


title: Cells transduced with vector expressing Mouse testis library (MCF10A LIB 2 Unselected)

description: Transduced with vector expressing Mouse testis library

source_name: MCF20A LIB 2 Unselected


title: cultured cells TSC2-/- treated with rapamycin rep3

treatment_protocol: Rapamycin 20nM in serum-free media for 24hr


title: Sample 12

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Affymetrix standard hyb  protocol

scan_protocol: Affymetrix standard scan  protocol

source_name: STAT5 KO

label_protocol: Affymetrix standard label  protocol

growth_protocol: In NIDDK growth core lab protocol

extract_protocol: TRIzol reagent

value: mammary

value: STAT5 KO


title: Cells transduced with vector expressing GFP (MCF10A GFP 2 Unselected)

description: Transduced with vector expressing GFP

source_name: MCF20A GFP 2 Unselected


title: cultured cells TSC2-/- treated with rapamycin rep2


title: Cells transduced with vector expressing Mouse testis library (MCF10A LIB 1 Selected)

source_name: MCF10A LIB 1 Selected


title: Aspergillus niger, glucose, biological rep1


title: Aspergillus oryzae, glucose, biological rep2


title: Aspergillus niger, glucose, biological rep2


title: Sample 10


title: Cells transduced with vector expressing GFP (MCF10A GFP 1 Unselected)

description: Transduced with vector expressing GFP

source_name: MCF10A GFP 1 Unselected


title: cultured cells TSC2-/- treated with rapamycin rep1


title: Sample 11

source_name: STAT5 WT

value: STAT5 WT


title: Cells transduced with vector expressing GFP (MCF10A GFP 1 Selected)

description: Transduced with vector expressing GFP

source_name: MCF10A GFP 1 Selected