title: hES cells in N2B27 - 2h stimulated with BMP4

description: BMP4-treated sample in a short-term BMP4 stimulation experiment

growth_protocol: N2B27 medium contained DMEM/F12 (Hyclone), N2 and B27 supplements (Invitrogen), 0.5% BSA (fraction V, Invitrogen), non-essential amino acids, glutamine, pen/strep (Invitrogen), 0.1 mM ß-mercaptoethanol, and 20 ng/ml FGF2 (Peprotech). BMP4 (R&D) was used at 50 ng/ml.

treatment_protocol: Cells were adapted to N2B27-based chemically defined medium, replated, and, three days after passaging, stimulated with BMP4 for 2h.


title: AFFX100KHINDIIISKOV3_ATCC

status: Public on Mar 11 2008

type: genomic

city: King of Prussia

first: Joel

last: Greshock

state: PA

address: 2301 Renaissance Blvd.

department: Translational Medicine, Oncology

country: USA

institute: GlaxoSmithKline

description: Ovary

hyb_protocol: Hybridizations were performed according to the standard manufacturer's describe in Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix.

scan_protocol: Scanning was done using an Affymetrix 3000 microarray scanner.  Specifications can be found in Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix

data_processing: Image files were analyzed using the dChip software.  A panel of chips (n = 12)  assayed with germline DNA served as a reference in order to calculate a test/reference ratio.  The ratios were then subject global normalization that assumed that the median copy number is  diploid (2n; log2 Ratio = 0).

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: SKOV3 Cell Line

label_protocol: 250 ng Genomic DNA was biotinylated as described by manufacturer (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix)

growth_protocol: Cells were grown in in RPMI 1640 supplemented with 10% heat-inactivated FBS

extract_protocol: Genomic DNA was isolated from cultured cells with Mini DNeasy kit (Qiagen, Inc.)

tag: Ovary cell line SKOV3; training set; lapatinib IC50 = 1.25 uM (intermediate sensitivity)


title: AFFX100KHINDIIISKMEL28

description: Melanoma

source_name: SKMEL28 Cell Line

tag: Melanoma cell line SKMEL28; training set; lapatinib IC50 = 5.9 uM (resistant)


title: H9 hES cells grown in MEF-CM, then for 1 day in UM

status: Public on Mar 12 2008

type: RNA

city: Münster

first: Boris

last: Greber

address: Röntgenstraße 20

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: This sample presents the control for accompanying samples re-stimulated with MEF-conditioned medium or unconditioned medium plus Activin A, TGFß1, and Gremlin.

hyb_protocol: Employing materials and protocols by Illumina Inc.; hybridisation: 17h at 55 degrees Celsius

scan_protocol: Using an Illumina scanner; gain factor: 2

data_processing: In BeadStudio 1.5, biological replicates were grouped, background subtracted and normalised using the "cubic spline" algorithm. Value = "25" denotes expression below ca. 50% of the detection threshold.

molecule: total RNA

source_name: human embryonic stem cells

label_protocol: Linear amplification kit Ambion #IL1791 following the manufacturer's instructions. Input amount: 400ng of total RNA; IVT: 7h

extract_protocol: Qiagen RNeasy kit with on-column DNA digestion following the manufacturer's instructions

treatment_protocol: H9 cells were grown for 3 days in MEF-conditioned medium, then starved for 1 day in unconditioned medium plus 10 ng/ml FGF2.

tag: line H9


title: AFFX100KHINDIIIT47D

description: Breast

source_name: T47D Cell Line

tag: Breast cell line T47D; training set; lapatinib IC50 = 4.83 uM (resistant)


title: AFFX100KHINDIIISKBR3

description: Breast

source_name: SKBR3 Cell Line

tag: Breast cell line SKBR3; training set; lapatinib IC50 = 0.032 uM (sensitive)


title: Drosophila CL8 sample 1

city: Columbus

first: Amanda

last: Simcox

state: OH

address: 484 W. 12th Avenue

department: Molecular Genetics

institute: The Ohio State University

description: Affymetrix standard reagents and protocols were used for labeling, hybridizing and scanning.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: R and bioconductor were used to preprocess and analyze the data

organism: Drosophila melanogaster

source_name: Drosophila Cell Culture

label_protocol: Affymetrix standard protocol

extract_protocol: Qiagen RNeasy

tag: Cell line, Drosophila


title: AFFX100KHINDIIINCIN87

description: Gastric

source_name: NCIN87 Cell Line

tag: Gastric cell line NCI-N87; training set; lapatinib IC50 = 0.028 uM (sensitive)


title: H9 hES cells grown in MEF-CM, then for 1 day in UM, then for 4h in MEF-CM

description: This is one of two treatment samples from a re-stimulation experiment using MEF-conditioned medium or unconditioned medium plus Activin A, TGFß1, and Gremlin.

treatment_protocol: H9 cells were grown for 3 days in MEF-conditioned medium, then starved for 1 day in unconditioned medium plus 10 ng/ml FGF2, then re-stimulated with MEF-CM for 4h.


title: AFFX100KHINDIIIMDA_MB_453

description: Breast

source_name: MDA_MB_453 Cell Line

tag: Breast cell line MDA-MB-453; training set; lapatinib IC50 = 0.079 uM (sensitive)


title: AFFX500KNSPSCC12

source_name: SCC-12 Cell Line

tag: Head/Neck cell line SCC12; validation set; lapatinib IC50 = 0.674 uM (sensitive)


title: AFFX100KHINDIIIMDA_MB_468_A

description: Breast

source_name: MDA_MB_468 Cell Line

tag: Breast cell line MDA-MB-468; training set; lapatinib IC50 = 2.32 uM (intermediate sensitivity)


title: AFFX100KHINDIIIRKO

description: Colon

source_name: RKO Cell Line

tag: Colon cell line RKO; training set; lapatinib IC50 = 5.48 uM (resistant)


title: AFFX500KNSPSCC25

source_name: SCC-25 Cell Line

tag: Head/Neck cell line SCC25; validation set; lapatinib IC50 = 0.222 uM (sensitive)


title: AFFX100KHINDIIIMCF7

description: Breast

source_name: MCF7 Cell Line

tag: Breast cell line MCF-7; training set; lapatinib IC50 = 4.82 uM (resistant)


title: AFFX100KHINDIIIMDA_MB_231

description: Breast

source_name: MDA_MB_231 Cell Line

tag: Breast cell line MDA-MB-231; training set; lapatinib IC50 = 7.01 uM (resistant)


title: AFFX500KNSPCAL27

source_name: CAL27 Cell Line

tag: Head/Neck cell line Cal27; validation set; lapatinib IC50 = 0.308 uM (sensitive)


title: AFFX100KHINDIIIPC3

description: Prostate

source_name: PC3 Cell Line

tag: Prostate cell line PC3; training set; lapatinib IC50 = 7.15 uM (resistant)


title: AFFX100KHINDIIIMX_1

description: Breast

source_name: MX_1 Cell Line

tag: Breast cell line MX-1; training set; lapatinib IC50 = 5.55 uM (resistant)


title: AFFX100KHINDIIINCIH322

description: Lung

source_name: NCIH322 Cell Line

tag: Lung cell line NCI-H322; training set; lapatinib IC50 = 0.92uM (sensitive)


title: AFFX500KNSPSCC4

source_name: SCC-4 Cell Line

tag: Head/Neck cell line SCC4; validation set; lapatinib IC50 = 1.851 uM (intermediate sensitivity)


title: AFFX500KNSPSCC13

source_name: SCC-13 Cell Line

tag: Head/Neck cell line SCC13; validation set; lapatinib IC50 = 1.063 uM (intermediate sensitivity)


title: AFFX500KNSPSW579

source_name: SW579 Cell Line

tag: Head/Neck cell line SW579; validation set; lapatinib IC50 = 3.074 uM (resistant)


title: AFFX500KNSPRPMI2650

source_name: RPMI-2650 Cell Line

tag: Head/Neck cell line RPMI-2650; validation set; lapatinib IC50 = 2.913 uM (resistant)


title: T31 Cell Line 9 Replica 1

status: Public on Mar 13 2008

city: Los Angeles

first: Christopher

last: Park

state: CA

address: 23-151 CHS, 650 Charles E. Young Drive

department: Molecular and Medical Pharmacology

institute: UCLA

description: Biological Replica 1, log10 ratios are cy5/cy3

hyb_protocol: Standard Agilent Hybridization protocols for expression microarrays were followed, 17 hour hybridization time

scan_protocol: Arrays were scanned on an Agilent carousel scanner following maufacturer's instructions.  Agilent Feature Extractor software was used to extract the data.

data_processing: The expression data was normalized using GeneSpring (Agilent Technologies).  Each value was divided by the control channel and each chip normalized to the 50th percentile for the measurements taken from that chip.

organism: Cricetulus griseus

source_name: Total RNA from cell line A23 labeled with cy5

label_protocol: 20 ug of total RNA was labeled using the Agilent Fluorescent Direct Labeling Protocol

growth_protocol: RH and A23 cells were cultured in DMEM + 10% FBS + 1x Pen-strep, plated in T75 flasks until 75% confluent.  Harvested by trypsinization, then pelleting.

extract_protocol: RNA isolation was done with Qiagen RNeasy Mini Kit per protocol recommended by the manufacturer.

tag: hamster fibroblast cell line

organism:
Cricetulus griseus
Mus musculus

source_name: Total RNA from Radiation Hybrid Panel T31, cell line 9

tag: Fragments of mouse strain 129aa fused with hamster cell line A23


title: AFFX500KNSPSCC9

source_name: SCC-9 Cell Line

tag: Head/Neck cell line SCC9; validation set; lapatinib IC50 = 0.331 uM (sensitive)


title: AFFX500KNSPSCC15

source_name: SCC-15 Cell Line

tag: Head/Neck cell line SCC15; validation set; lapatinib IC50 = 0.171 uM (sensitive)


title: AFFX100KHINDIIIHN5

description: Heand/Neck

source_name: HN5 Cell Line

tag: Heand/Neck cell line HN5; training set; lapatinib IC50 =  0.029 uM (sensitive)


title: AFFX100KHINDIIICOLO205

description: Colon

source_name: COLO205 Cell Line

tag: Colon cell line COLO205; training set; lapatinib IC50 =  7.70 uM (resistant)


title: AFFX100KHINDIIIA549

description: Lung

source_name: A549 Cell Line

tag: Lung cell line A549; training set; lapatinib IC50 =  4.98 uM (resistant)


title: AFFX100KHINDIIIHCT116

description: Colon

source_name: HCT116 Cell Line

tag: Colon cell line HCT-116; training set; lapatinib IC50 =  5.87 uM (resistant)


title: AFFX100KHINDIIIBT474

description: Breast

source_name: BT474 Cell Line

tag: Breast cell line BT474; training set; lapatinib IC50 =  0.025 uM (sensitive)


title: AFFX500KNSPFaDu

source_name: FaDu Cell Line

tag: Head/Neck cell line FaDu; validation set; lapatinib IC50 = 0.216 uM (sensitive)


title: AFFX100KHINDIIIDLD1

description: Colon

source_name: DLD1 Cell Line

tag: Colon cell line DLD1; training set; lapatinib IC50 =  3.63 uM (resistant)


title: AFFX100KHINDIIILnCap

description: Prostate

source_name: LnCap Cell Line

tag: Prostate cell line LnCap; training set; lapatinib IC50 = 4.69 uM (resistant)


title: AFFX100KXBASKBR3

description: Breast

source_name: SKBR3 Cell Line

tag: Breast cell line SKBR3; training set; lapatinib IC50 = 0.032 uM (sensitive)


title: AFFX100KXBANCIH322

description: Lung

source_name: NCIH322 Cell Line

tag: Lung cell line NCI-H322; training set; lapatinib IC50 = 0.92uM (sensitive)


title: AFFX100KXBAPC3

description: Prostate

source_name: PC3 Cell Line

tag: Prostate cell line PC3; training set; lapatinib IC50 = 7.15 uM (resistant)


title: AFFX100KXBASKOV3_ATCC

description: Ovary

source_name: SKOV3 Cell Line

tag: Ovary cell line SKOV3; training set; lapatinib IC50 = 1.25 uM (intermediate sensitivity)


title: AFFX100KXBAT47D

description: Breast

source_name: T47D Cell Line

tag: Breast cell line T47D; training set; lapatinib IC50 = 4.83 uM (resistant)


title: AFFX100KHINDIII786O

description: Renal

source_name: 786O Cell Line

tag: Renal cell line 786O; training set; lapatinib IC50 =  1.82 uM (intermediate sensitivity)


title: AFFX100KXBASKMEL28

description: Melanoma

source_name: SKMEL28 Cell Line

tag: Melanoma cell line SKMEL28; training set; lapatinib IC50 = 5.9 uM (resistant)


title: AFFX100KHINDIIIA431

description: Skin, epidermoid

source_name: A431 Cell Line

tag: Skin, epidermoid cell line A431; training set; lapatinib IC50 =  0.23 uM (sensitive)


title: AFFX100KXBARKO

description: Colon

source_name: RKO Cell Line

tag: Colon cell line RKO; training set; lapatinib IC50 =  5.48 uM (resistant)


title: AFFX100KHINDIIIHT29

description: Colon

source_name: HT29 Cell Line

tag: Colon cell line HT29; training set; lapatinib IC50 = 5.24 uM (resistant)


title: Drosophila L2

source_name: Drosophila cell culture

tag: Cell line, Drosophila


title: nucleosome occupancy at anaphase

city: Charlottesville

first: Jie

last: Liu

state: VA

address: 1300 Jefferson Park Avenue

department: Physiology

institute: University of Virginia

description: Nucleosome occupancy data from yeast cells at anaphase

hyb_protocol: 15ug of DNA were hybridized for 16hr at 42ºC on Yeast SC3456a520015F tiling array in an Affymetrix hybridization oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Affymetrix protocol FlexMidi-euk2v3-450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed with GCOS using Affymetrix default analysis settings.

organism: Saccharomyces cerevisiae

source_name: Yeast cells released from G1/S arrest for 95 min

label_protocol: DNA was labeled with biotin-ddUTP by terminal transferase.

growth_protocol: Yeast cells were grown in YPD at 25ºC, arrested at G1/S boundary with 10ug/ml alpha-factor for three hours and then released by adding 50 ug/ml pronase for 95 min.

extract_protocol: Protein was digested by proteinase K and the formaldehyde crosslinking was reversed by incubation at 65ºC overnight. After phenol extraction and ethanol precipitation, RNA was removed by RNase cocktail. Then mononucleosomal DNA was purified from agarose gel and amplified with random priming.

treatment_protocol: Cells were fixed with 2% formaldehyde, followed by removal of cell wall with lyticase. After cell permeabilization, micrococcal nuclease was added to digest chromatin.

tag: Mononucleosomal DNA


title: nucleosome occupancy at anaphase (total)

description: Nucleosome occupancy data from yeast cells at anaphase (total)

extract_protocol: Protein was digested by proteinase K and the formaldehyde crosslinking was reversed by incubation at 65ºC overnight. After phenol extraction and ethanol precipitation, RNA was removed by RNase cocktail. Then the total DNA was purified and amplified with random priming.

tag: Total DNA after micrococcal nuclease digestion without gel purification


title: Total genomic DNA

description: Total genomic DNA hybridization data as normalization signal

source_name: Yeast cells

growth_protocol: Yeast cells were grown in YPD at 25ºC.

extract_protocol: Protein was digested by proteinase K and the formaldehyde crosslinking was reversed by incubation at 65ºC overnight. After phenol extraction and ethanol precipitation, RNA was removed by RNase cocktail. Then the total DNA was sonicated and amplified with random priming.

treatment_protocol: Cells were disrupted with glass beads and nuclei were purified.

tag: Total genomic DNA


title: AFFX100KXBAMX_1

description: Breast

source_name: MX_1 Cell Line

tag: Breast cell line MX-1; training set; lapatinib IC50 = 5.55 uM (resistant)


title: AFFX100KXBAMDA_MB_468_A

description: Breast

source_name: MDA_MB_468 Cell Line

tag: Breast cell line MDA-MB-468; training set; lapatinib IC50 = 2.32 uM (intermediate sensitivity)


title: AFFX100KXBAMDA_MB_453

description: Breast

source_name: MDA_MB_453 Cell Line

tag: Breast cell line MDA-MB-453; training set; lapatinib IC50 = 0.079 uM (sensitive)


title: nucleosome occupancy at G1

description: Nucleosome occupancy data from yeast cells arrested at G1/S by alpha factor

source_name: Yeast cells arrested at G1/S

growth_protocol: Yeast cells were grown in YPD at 25ºC and arrested at G1/S boundary with 10ug/ml alpha-factor for three hours.


title: nucleosome occupancy at late S phase

description: Nucleosome occupancy data from yeast cells at late S phase

source_name: Yeast cells released from G1/S arrest for 40 min

growth_protocol: Yeast cells were grown in YPD at 25ºC, arrested at G1/S boundary with 10ug/ml alpha-factor for three hours and then released by adding 50 ug/ml pronase for 40 min.


title: AFFX100KXBANCIN87

description: Gastric

source_name: NCIN87 Cell Line

tag: Gastric cell line NCI-N87; training set; lapatinib IC50 = 0.028 uM (sensitive)


title: nucleosome occupancy at G2/M

description: Nucleosome occupancy data from yeast cells at G2/M

source_name: Yeast cells released from G1/S arrest for 65 min

growth_protocol: Yeast cells were grown in YPD at 25ºC, arrested at G1/S boundary with 10ug/ml alpha-factor for three hours and then released by adding 50 ug/ml pronase for 65 min.


title: nucleosome occupancy at early S phase

description: Nucleosome occupancy data from yeast cells at early S phase

source_name: Yeast cells released from G1/S arrest for 15 min

growth_protocol: Yeast cells were grown in YPD at 25ºC, arrested at G1/S boundary with 10ug/ml alpha-factor for three hours and then released by adding 50 ug/ml pronase for 15 min.


title: AFFX100KXBAMDA_MB_231

description: Breast

source_name: MDA_MB_231 Cell Line

tag: Breast cell line MDA-MB-231; training set; lapatinib IC50 = 7.01 uM (resistant)


title: AFFX100KXBAMCF7

description: Breast

source_name: MCF7 Cell Line

tag: Breast cell line MCF-7; training set; lapatinib IC50 = 4.82 uM (resistant)


title: AFFX100KXBADLD1

description: Colon

source_name: DLD1 Cell Line

tag: Colon cell line DLD1; training set; lapatinib IC50 =  3.63 uM (resistant)


title: AFFX100KXBACOLO205

description: Colon

source_name: COLO205 Cell Line

tag: Colon cell line COLO205; training set; lapatinib IC50 =  7.70 uM (resistant)


title: AFFX500KSTYSCC9

source_name: SCC-9 Cell Line

tag: Head/Neck cell line SCC9; validation set; lapatinib IC50 = 0.331 uM (sensitive)


title: AFFX100KXBAHCT116

description: Colon

source_name: HCT116 Cell Line

tag: Colon cell line HCT-116; training set; lapatinib IC50 =  5.87 uM (resistant)


title: AFFX100KXBAHN5

description: Heand/Neck

source_name: HN5 Cell Line

tag: Heand/Neck cell line HN5; training set; lapatinib IC50 =  0.029 uM (sensitive)


title: AFFX100KXBAHT29

description: Colon

source_name: HT29 Cell Line


title: AFFX100KXBALnCap

description: Prostate

source_name: LnCap Cell Line

tag: Prostate cell line LnCap; training set; lapatinib IC50 = 4.69 uM (resistant)


title: AFFX500KSTYSCC25

source_name: SCC-25 Cell Line

tag: Head/Neck cell line SCC25; validation set; lapatinib IC50 = 0.222 uM (sensitive)


title: AFFX100KHINDIIIBXPC3

description: Pancreas

source_name: BXPC3 Cell Line

tag: Pancreas cell line BXPC3; training set; lapatinib IC50 =  1.41 uM (intermediate sensitivity)


title: AFFX100KXBABXPC3

description: Pancreas


title: AFFX100KXBABT474

description: Breast

source_name: BT474 Cell Line

tag: Breast cell line BT474; training set; lapatinib IC50 =  0.025 uM (sensitive)


title: AFFX100KXBAA549

description: Lung

source_name: A549 Cell Line

tag: Lung cell line A549; training set; lapatinib IC50 =  4.98 uM (resistant)


title: AFFX500KSTYSCC4

source_name: SCC-4 Cell Line

tag: Head/Neck cell line SCC4; validation set; lapatinib IC50 = 1.851 uM (intermediate sensitivity)


title: AFFX500KSTYSW579

source_name: SW579 Cell Line

tag: Head/Neck cell line SW579; validation set; lapatinib IC50 = 3.074 uM (resistant)


title: AFFX500KSTYSCC15

source_name: SCC-15 Cell Line

tag: Head/Neck cell line SCC15; validation set; lapatinib IC50 = 0.171 uM (sensitive)


title: AFFX500KSTYSCC12

source_name: SCC-12 Cell Line

tag: Head/Neck cell line SCC12; validation set; lapatinib IC50 = 0.674 uM (sensitive)


title: AFFX500KSTYSCC13

source_name: SCC-13 Cell Line

tag: Head/Neck cell line SCC13; validation set; lapatinib IC50 = 1.063 uM (intermediate sensitivity)


title: AFFX500KSTYFaDu

source_name: FaDu Cell Line

tag: Head/Neck cell line FaDu; validation set; lapatinib IC50 = 0.216 uM (sensitive)


title: AFFX100KXBA786O

description: Renal

source_name: 786O Cell Line

tag: Renal cell line 786O; training set; lapatinib IC50 =  1.82 uM (intermediate sensitivity)


title: maize_root_region1_ws-ww_rep2-slideA

status: Public on Mar 01 2008

city: Columbia

first: William

middle: G.

last: Spollen

state: MO

address: 113 Bond Life Sciences Center

department: Informatics Research Core Facility

institute: University of Missouri-Columbia

description: This is the 2nd of 4 biological replications, and one half of a dye-swap pair.

hyb_protocol: The purified Cy3 and Cy5-labeled cDNAs were concentrated to 60 μl and hybridized to the maize oligonucleotide array (GPL1990) for 16-18 h at 42 ºC. Following hybridization, the arrays were washed three times, twice with medium stringency buffer (1X SSC, 0.2% SDS) and once with high stringency buffer (0.1X SSC, 0.2% SDS).

scan_protocol: Washed slides were dried and scanned immediately using a GenePix scanner (GenePix® 4000B, Axon Instruments, Inc.) at 532 nm (17 mW) and 635 nm (10 mW). GenePix Pro 4.1 software was then used to extract spot intensity data.

data_processing: Mean signal intensities were used without background correction and data from all 8 chips (4 reps with dye-swap) were normalized using the Loess transformation.

organism: Zea mays

source_name: maize root region1 water stress 48h rep 2

label_protocol: First strand cDNAs were synthesized from 50 μg of total RNA using anchored oligo(dT)24 primers with SuperScript III RT (Invitrogen, Carlsbad, CA), and aminoallyl-dUTP was incorporated into the cDNAs. The RNA template was removed by treatment with RnaseH (Invitrogen, Carlsbad, CA), and cDNAs were purified to remove unincorporated aminoallyl-dUTP using Microcon 30 spin concentrators (Millipore Corp., Bedford, MA). Following purification, monoreactive-Cye5 or Cye3 dyes (Amersham Biosciences Corp., Piscataway, NJ) were conjugated to aminoallyl-dUTP on the cDNAs and the unconjugated dye was removed using Qiagen PCR purification columns.

growth_protocol: Seeds were imbibed for 24 h in 1 mM CaSO4, then germinated for 28 h in vermiculite well-moistened with 1 mM CaSO4 at 29°C in the dark. Seedlings with primary roots 12-20 mm in length were transplanted into vermiculite mixed with pre-determined amounts of 1 mM CaSO4 to create either high (-0.03 MPa) or low (-1.6 MPa) water potential and grown under near-saturating humidity conditions to prevent further drying of the media. Root tips were collected at 48h after transplant to vermiculite of either high or low water potential.

extract_protocol: The apical 12 mm of each root was sectioned into three regions based on previously-characterized longitudinal expansion rate profiles: region 1, 0-3 mm plus the root cap; region 2, 3-7 mm; region 3, 7-12 mm. Samples were immediately frozen in liquid nitrogen. Total RNA was isolated using Trizol reagent following the manufacturer’s instructions (Invitrogen Corp., Carlsbad, CA). Residual DNA was removed by Dnase I (Invitrogen, Carlsbad, CA) treatment for 15 min at room temperature, followed by use of RNeasy columns (Qiagen, Valencia, CA).

treatment_protocol: See the growth protocol.

tag: Region 1 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of low water potential.

source_name: maize root region1 control 48h rep 2

tag: Region 1 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of high water potential.


title: maize_root_region1_ws-ww_rep1-slideA

description: This is the 1st of 4 biological replications, and one half of a dye-swap pair.

source_name: maize root region1 water stress 48h rep 1

source_name: maize root region1 control 48h rep 1


title: maize_root_region2_ws-region3_ww_rep4-slideA

description: This is the 4th of 4 biological replications, and one half of a dye-swap pair.  Stressed region 2 was compared with control region 3 as a developmental control to the comparison of stressed region 2 with control region 2.

hyb_protocol: The purified Cy3 and Cy5-labeled cDNAs were concentrated to 60 μl and hybridized to the maize oligonucleotide array (GPL1992) for 16-18 h at 42 ºC. Following hybridization, the arrays were washed three times, twice with medium stringency buffer (1X SSC, 0.2% SDS) and once with high stringency buffer (0.1X SSC, 0.2% SDS).

source_name: maize root region2 water stress 48h rep 4

tag: Region 2 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of low water potential.

source_name: maize root region3 control 48h rep 4

tag: Region 3 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of high water potential.


title: AFFX500KSTYRPMI2650

source_name: RPMI-2650 Cell Line

tag: Head/Neck cell line RPMI-2650; validation set; lapatinib IC50 = 2.913 uM (resistant)


title: maize_root_region1_ww-ws_rep2-slideA


title: maize_root_region1_ww-ws_rep1-slideA


title: maize_root_region1_ws-ww_rep3-slideA

description: This is the 3rd of 4 biological replications, and one half of a dye-swap pair.

source_name: maize root region1 water stress 48h rep 3

source_name: maize root region1 control 48h rep 3


title: maize_root_region3_ww-region2_ws_rep4-slideA


title: maize_root_region2_ws-region3_ww_rep2-slideA

description: This is the 2nd of 4 biological replications, and one half of a dye-swap pair.  Stressed region 2 was compared with control region 3 as a developmental control to the comparison of stressed region 2 with control region 2.

source_name: maize root region2 water stress 48h rep 2

source_name: maize root region3 control 48h rep 2


title: maize_root_region3_ww-region2_ws_rep2-slideA


title: maize_root_region3_ww-region2_ws_rep1-slideA

description: This is the 1st of 4 biological replications, and one half of a dye-swap pair.  Stressed region 2 was compared with control region 3 as a developmental control to the comparison of stressed region 2 with control region 2.

source_name: maize root region3 control 48h rep 1

source_name: maize root region2 water stress 48h rep 1


title: maize_root_region2_ws-region3_ww_rep1-slideA


title: maize_root_region3_ww-region2_ws_rep3-slideA

description: This is the 3rd of 4 biological replications, and one half of a dye-swap pair.  Stressed region 2 was compared with control region 3 as a developmental control to the comparison of stressed region 2 with control region 2.

source_name: maize root region3 control 48h rep 3

source_name: maize root region2 water stress 48h rep 3


title: maize_root_region2_ws-ww_rep3-slideA

source_name: maize root region2 control 48h rep 3

tag: Region 2 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of high water potential.


title: maize_root_region2_ww-ws_rep4-slideA

description: This is the 4th of 4 biological replications, and one half of a dye-swap pair.

source_name: maize root region2 control 48h rep 4


title: maize_root_region2_ws-region3_ww_rep3-slideA


title: maize_root_region2_ws-ww_rep4-slideA


title: maize_root_region2_ww-ws_rep3-slideA


title: maize_root_region2_ww-ws_rep2-slideA

source_name: maize root region2 control 48h rep 2


title: maize_root_region1_ww-ws_rep4-slideA

source_name: maize root region1 control 48h rep 4

source_name: maize root region1 water stress 48h rep 4


title: maize_root_region2_ws-ww_rep1-slideA

source_name: maize root region2 control 48h rep 1


title: AFFX500KSTYCAL27

source_name: CAL27 Cell Line

tag: Head/Neck cell line Cal27; validation set; lapatinib IC50 = 0.308 uM (sensitive)


title: maize_root_region1_ws-ww_rep4-slideA


title: Hoxc6 KO prostate-1

city: Atlanta

first: Colleen

middle: D

last: McCabe

state: GA

address: 615 Michael St

institute: Emory University

description: Comparison of HOXC6 knockout and HOXC6 WT mouse prostates

hyb_protocol: Employing materials and protocols by Illumina Inc; hybridization overnight at 55 degC

scan_protocol: Using an Illumina scanner; Standard scan factor

data_processing: Raw data was normalized using Beadstudio

organism: Mus musculus

source_name: Hoxc6 KO mouse prostate

label_protocol: 50ng of total RNA was labeled using TotalPrep from Ambion following the manufacturer's instructions

extract_protocol: Rneasy kit was used per manufacturer's instructions to isolate total RNA from flash frozen mouse prostates.


title: Human hypoxia 3 (miRNA array)

type: other

city: Birmingham

first: Grier

last: Page

state: AL

institute: University of Alabama at Birmingham

hyb_protocol: Standard Assuragen protocol was used

scan_protocol: The Cy3 fluorescence on the arrays was scanned at an excitation wavelength of 532nm using a GenePix 4200AL scanner (Molecular Devices, Union City, CA).

data_processing: Data presented here for each sample was generated by computing the global Variance Stabilization Normalization (VSN; Huber et al., 2002) of all the arrays within the project.

label: Cy3 succinimide esters

molecule: other

source_name: HT29 Cell lines

label_protocol: mirVana™ miRNA Labeling Kit

growth_protocol: Cells were cultured in media (HT29: McCoy’s 5a medium supplemented with 7% Fetal Bovine Serum (FBS)) for 5-7 days (media bathing both the apical and basolateral compartments) at 37°C (5% CO2 - 95% air gas mixture).

extract_protocol: microRNA enriched fraction obtained by passing total RNA through a flashPAGE™ Fractionator apparatus (Ambion, Inc., Austin, TX) and cleaned.

treatment_protocol: In some monolayers, media was removed from the apical side to expose cells to air (A/L or air-liquid interface).

tag: Cells were cultured in media (HT29

tag: Media was not removed from the apical side to expose cells to air (A/L or air-liquid interface)


title: Human hypoxia 2 (miRNA array)

value: McCoy’s 5a medium supplemented with 7% Fetal Bovine Serum (FBS)) for 5-7 days (media bathing both the apical and basolateral compartments) at 37°C (5% CO2 - 95% air gas mixture)


title: Hoxc6 WT prostate-2

source_name: Hoxc6 WT mouse prostate


title: maize_root_region2_ws-ww_rep2-slideA


title: Hoxc6 KO prostate-2


title: Human normoxia 1 (miRNA array)

tag: Media was removed from the apical side to expose cells to air (A/L or air-liquid interface)


title: 3-Month Epiphycan/Biglycan-deficient-2

city: Houston

first: Jason

last: Schultz

state: TX

address: 2121 W. Holcombe Bvld

institute: Texas A&M HSC-IBT

hyb_protocol: All hybridizations done as descibed in Affymetrix expression manual.

scan_protocol: The GeneArray™ Scanner uses an argon-ion laser to excite fluorescent molecules incorporated into the nucleic acid target to generate a quantitative hybridization signal. With precise optics, the GeneArray™ scanner focuses the laser on 3-micron spots within each of the thousands of probe features contained on the GeneChip® probe array. A high-resolution image of the probe array is displayed in real time during scanning, and fluorescence intensity data is automatically stored in a raw file.

data_processing: MAS 5.0

source_name: tibio-femoral joint

label_protocol: Standard in-vitro transcription using biotin-labeled nucleotides (ENZO BioArray High Yield kit)

extract_protocol: Trizol-mediated organic extraction followed by Qiagen RNeasy column purification as per manufacturer's instruuctions.

tag: Strain

value: C57/Bl6:129 hybrid Gender:male Source:tibio-femoral joint Age:3 Months Genotype:Epiphycan and Biglycan double-null animals


title: Hoxc6 KO prostate-3


title: 3-Month Epiphycan/Biglycan-deficient-1

source_name: Tibio-femoral joint tissue


title: Human normoxia 3 (miRNA array)


title: maize_root_region1_ww-ws_rep3-slideA

source_name: maize root region1 control 48h rep 3

source_name: maize root region1 water stress 48h rep 3


title: Hoxc6 WT prostate-3


title: maize_root_region2_ww-ws_rep1-slideA

source_name: maize root region2 water stress 48h rep 1


title: 3-Month WT-1

value: C57/Bl6:129 hybrid Gender:male Source:tibio-femoral joint Age:3 Months


title: Human hypoxia 1 (miRNA array)


title: HIGK cells infected with Aggregatibacter actinomycetemcomitans, biological rep4

city: Gainesville

first: Martin

last: Handfield

state: FL

address: 1600 SW Archer Road, BOX 100424

department: Oral Biology

institute: University of Florida

description:
Gene expression data from Aggregatibacter actinomycetemcomitans-infected HIGK cells.
Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)

hyb_protocol: Following fragmentation,  human HG U133-A oligonucleotide microarrays (Affymetrix) were hybridized for 16 h at 45C, stained with phycoerythrin-conjugated streptavidin and washed according to the Affymetrix protocol (EukGE-WS2v4).

scan_protocol: GeneChips were scanned with an Affymetrix fluidics station, and scanned with an Affymetrix GeneChip 3000 scanner.

data_processing: The data were analyzed with Affymetrix GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label_protocol: cRNA synthesis was performed with 10 ug of total cellular RNA, based on the Affymetrix protocol. Double-stranded cDNA was synthesized according to a standardized protocol (SuperScript doublestranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). cRNA was transcribed in vitro, incorporating biotinylated nucleotides by using a BioArray high-yield RNA transcript labeling kit (T7) (Enzo Life Sciences, Farmingdale, NY).

growth_protocol: HIGK cells were cultured under 5% CO2 in keratinocyte serum-free medium (K-SFM, Gibco/Invitrogen, Carlsbad, CA) supplemented with: 0.05 mM calcium chloride, 200 mM L-glutamine (Gibco/Invitrogen, Carlsbad, CA).

extract_protocol: Total RNA was extracted, DNAse-treated, purified and quantified according to standard  methods (Qiagen and Affymetrix).

treatment_protocol: Bacteria at mid-log phase were harvested and washed by centrifugation, and resuspended in antibiotic-free K-SFM media. HIGK cells (10e7) were co-cultured with bacteria to give a total association (adhered plus invaded) of approximately 2500 organisms per epithelial cell. Numbers of adhered and invaded organisms were confirmed in parallel experiments by plate counting. After 2 hours at 37C in 5% CO2, the HIGK cells were lysed with Trizol (Invitrogen) prior to RNA extraction.

tag: HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).

tag: HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.


title: Hoxc6 WT prostate-1


title: AFFX100KXBAA431

description: Skin, epidermoid

source_name: A431 Cell Line

tag: Skin, epidermoid cell line A431; training set; lapatinib IC50 =  0.23 uM (sensitive)


title: HIGK cells infected with Aggregatibacter actinomycetemcomitans, biological rep2

source_name: Human Immortalized Gingival Keratinocyte


title: HOXC6-HA, biological rep 1 (array 1)

description: array 1 of 2

hyb_protocol: MAUI Hybridization system from BioMicro Systems

scan_protocol: Nimblescan uses 5-micron scanning platform by Nimblegen

data_processing: z-score normalized ratios

source_name: anti-HA IP from LNCaP cells expressing HOXC6-HA/YFP

label_protocol: According to standard NimbleGen protocols

growth_protocol: LNCaP cells grown in T-medium containing 10% FBS at 37C and 5% CO2.

extract_protocol: chromatin immunoprecipitation (McCabe et al 2008)

treatment_protocol: Cells were stably infected with lentivirus

tag: IP signal data from LNCaP cells with stable HOXC6-HA/YFP expression

source_name: Input from LNCaP cells expressing HOXC6-HA/YFP

tag: Input signal data from LNCaP cells with stable HOXC6-HA/YFP expression


title: YFP control, biological rep 2 (array 1)

description: array 1 of 2

source_name: anti-HA IP from LNCaP cells expressing YFP

tag: IP signal data from LNCaP cells with stable YFP expression

source_name: input from LNCaP cells expressing YFP

tag: Input signal data from LNCaP cells with stable YFP expression


title: HOXC6-HA, biological rep 2 (array 1)

description: array 1 of 2


title: fibroblast_N1_Patient10

city: Bethesda

first: Eric

last: Billings

state: MD

address: 10 Center Drive

institute: NHLBI

description: Gene expression data comparing TSC skin tumor fibroblasts to fibroblasts from same patient normal appearing skin

hyb_protocol: Following fragmentation 12 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix (HP) GeneArray Scanner G2500A.

data_processing: Microarray Suite Normalization 5.1

source_name: fibroblasts from Patient10

label_protocol: Samples prepared with Affymetrix single round protocol from 2 ug of total RNA

growth_protocol: In vitro with DMEM and 10% Fetal Bovine Serum

extract_protocol: Qiagen RNEasy mini column

tag: Adult

tag: Tissue:Fibroblasts from behind ear


title: HOXC6-HA, biological rep 1 (array 2)

description: array 2 of 2


title: Sham infected HIGK cells, biological rep2 (1778)

description:
Gene expression data from uninfected HIGK cells.
Human Immortalized Gingival Keratinocyte (Oda, D., and Watson, E. (1990) Human oral epithelial cell culture. Improved conditions for reproducible culture in serum-free medium. In Vitro Cell Dev Biol Anim 26: 589–595. Oda, D., Bigler, L., Lee, P., and Blanton, R. (1996) HPV immortalization of human oral epithelial cells: a model for carcinogenesis. Exp Cell Res 226: 164–169.)

treatment_protocol: HIGK cells were sham infected with antibiotic-free K-SFM media. HIGK cells (10e7) were cultured for 2 hours at 37C in 5% CO2, and were lysed with Trizol (Invitrogen) prior to RNA extraction.


title: fibroblast_AF_Patient2

source_name: fibroblasts from Patient2

tag: Tissue:Fibroblasts from AF behind left ear


title: HOXC6-HA, biological rep 2 (array 2)

description: array 2 of 2


title: fibroblast_AF_Patient4

source_name: fibroblasts from Patient4

tag: Tissue:Fibroblasts from AF on nose


title: fibroblast_N1_Patient4

tag: Tissue:Fibroblasts from lower back


title: 3-Month Epiphycan/Biglycan-deficient-3


title: fibroblast_AF_Patient10


title: Human normoxia 2 (miRNA array)


title: fibroblast_AF_Patient12

source_name: fibroblasts from Patient12


title: fibroblast_PF_Patient2

tag: Tissue:Fibroblasts from PF on left 3rd toe


title: Sham infected HIGK cells, biological rep3 (1779)


title: Sham infected HIGK cells, biological rep1 (1777)


title: fibroblast_N1_Patient12


title: fibroblast_PF_Patient10

tag: Tissue:Fibroblasts from PF on right 5th toe


title: fibroblast_PF_Patient4

tag: Tissue:Fibroblasts from PF on right 4th toe


title: fibroblast_N1_Patient2


title: 3-Month WT-2


title: YFP control, biological rep 2 (array 2)

description: array 2 of 2


title: YFP control, biological rep 1 (array 1)

description: array 1 of 2

source_name: Input from LNCaP cells expressing YFP


title: Sham infected HIGK cells, biological rep4 (1780)


title: HIGK cells infected with Aggregatibacter actinomycetemcomitans, biological rep1


title: Diffuse large B-cell lymphoma (3403-S)

city: Granada

first: Ana

middle: Isabel

last: Saez

state: Granada

address: Avda. Dr Oloriz, 16

country: Spain

institute: Red de Bancos de Tumores de Andalucía

hyb_protocol: Hybridizations were performed according to protocols from Affymetrix. Labeled RNA was hybridized to Human Genome U133A microarray (Affymetrix), after quality checking on GeneChips Test 3 Arrays.

scan_protocol: Washing and scanning were performed using Fluidics Station 400 and GeneChip Scanner (Affymetrix Inc.).

data_processing: Expression value for each probe set was calculated using RMAExpress program that uses RMA (robust multi-array average) algorithm

label: BIOTIN

source_name: Lymph Node

label_protocol: Labeling were performed according to protocols from Affymetrix. Briefly,100 ng of total RNA was amplified and labeled using the GeneChip two-cycle cDNA synthesis kit and GeneChip IVT labeling kit (Affymetrix Inc., Santa Clara, CA, USA)

extract_protocol: Total RNA was extracted from purified cell populations using the RNeasy Mini Kit (Qiagen, Valencia, CA,USA) according to the manufacturer’s instructions. The RNAintegrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).

tag: Lymph node cells from Diffuse large B-cell lymphoma


title: Air_control_1week_pool3_Cy5

city: Denver

first: Ivana

middle: V

last: Yang

state: CO

address: 1400 Jackson Street

department: Medicine

institute: National Jewish Health

description: 4 RNA pools of 3 animals each exposed to aerosolized LPS and 4 RNA pools of 3 animals each exposed to air only

hyb_protocol: Hybridizations were performed using Agilent hybridization chambers, oven and 2X hybridization buffer according to their protocol for cDNA hybridizations.

scan_protocol: Arrays were washed using Agilent SSC washes and scanned on the DNA Microarray Scanner (Agilent Technologies).

data_processing: Intensities were extracted from tif images using TIGR Spotfinder and lowess normalized in TIGR MIDAS.

source_name: UMRR

label_protocol: Fluorescently labeled cDNA targets were prepared by reverse transcribing 5 μg of total RNA in the presence of aminoallyl-dUTP followed by chemical coupling of NHS-esters of cyanine 3 (Cy3) or cyanine (Cy5) to the aminoallyl linker, according to published protocols.

extract_protocol: Manufacturer

tag: Stratagene Mouse Universal Reference RNA

tag: Catalog #740100

extract_protocol: Trizol

tag: Strain

tag: Gender

value: male

tag: Age

value: 8 weeks

tag: Treatment

value: air for 5 days

tag: Tissue

value: lung

tag: Time post-treatment

value: at the end of day 5


title: Diffuse large B-cell lymphoma (3437-S)


title: YFP control, biological rep 1 (array 2)

description: array 2 of 2

tag: IP signal data from LNCaP cells with stable YFP expression

tag: Input signal data from LNCaP cells with stable YFP expression


title: Diffuse large B-cell lymphoma (3072-S)


title: Air_control_1week_pool4_Cy5


title: Folicular Lymphoma Grade III (3463-S)

tag: Lymph node cells from Folicular Lymphoma Grade III


title: Diffuse large B-cell lymphoma (3180-S)


title: ChronicLPS_1week_pool3_Cy5

value: aerosolized LPS for 5 days


title: Diffuse large B-cell lymphoma (2748-S)

source_name: Lymph node


title: Air_control_1week_pool1_Cy5


title: Air_control_1week_pool2_Cy5


title: Air_control_1week_pool4_Cy3

value: air control for 5 days


title: Diffuse large B-cell lymphoma (2697-S)

tag: Lymph node cells from Diffuse large B-cell Lymphoma


title: ChronicLPS_1week_pool4_Cy5


title: ChronicLPS_1week_pool2_Cy3

value: at the end of the last LPS inhalation (on day 5)


title: Air_control_1week_pool2_Cy3


title: Diffuse large B-cell lymphoma (2806-S)


title: HIGK cells infected with Aggregatibacter actinomycetemcomitans, biological rep3

tag: HIGK cells were originally obtained by transfection of primary gingival epithelial cells with E6/E7 from HPV (Oda et al., 1990).

tag: HIGK cells were reported to be stable for over 350 passages (Oda et al., 1996). They were originally obtained at passage number 82, and used by passage number 90 for the the experiments described herein.


title: ChronicLPS_1week_pool4_Cy3


title: ChronicLPS_1week_pool2_Cy5


title: Air_control_1week_pool1_Cy3


title: Air_control_1week_pool3_Cy3


title: ChronicLPS_1week_pool1_Cy5


title: Saline_2week_pool1_Cy5

data_processing: Lowess-normalized intensities from Agilent Feature Extraction software were used (DyeNormSignal column).  Data were filtered based on the flag WellAboveBG.  If the flag was 0, then the intensities were set to 0; otherwise they were used as calculated in the DyeNormSignal column.

value: saline

value: 2 weeks


title: Bleomycin_2week_pool1_Cy5

value: 2U/kg bleomycin


title: Bleomycin_1week_pool2_Cy5

value: 1 week


title: Diffuse large B-cell lymphoma (2576-S)


title: ChronicLPS_1week_pool3_Cy3


title: Saline_3week_pool1_Cy3

value: 3 weeks


title: Bleomycin_2weeks_pool2_Cy5


title: Saline_1week_pool1_Cy5


title: Bleomycin_3weeks_pool2_Cy5


title: Bleomycin_1week_pool1_Cy5


title: ChronicLPS_1week_pool1_Cy3


title: Diffuse large B-cell lymphoma (2579-S)


title: Saline_2week_pool1_Cy3

value: 2 week


title: Bleomycin_3weeks_pool2_Cy3

description: For each timepoint (1 week, 2 weeks, 3 weeks), 2 RNA pools of 3 animals each treated intratracheally with bleomycin and 1 RNA pool of 3 animals each treated with saline control.


title: Saline_3week_pool1_Cy5


title: Bleomycin_2weeks_pool1_Cy3


title: Bleomycin_1week_pool2_Cy3


title: rat_liver_day10_feedrestricted_replicate4

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: The mRNA expression profile of the liver from a rat ten days after corn oil vehicle was given with feed-restriction.

hyb_protocol: The microarray facility at The Centre for Applied Genomics, Hospital for Sick Children (Toronto, ON) processed the gene chips as per the manufacturer’s instructions.

data_processing: Array data were loaded into the R statistical environment (v2.4.1) using the affy package (v1.12.2) (Gautier et al., 2004) of the BioConductor open-source project (Gentleman et al., 2004). Data were investigated for spatial and distributional homogeneity. These data were pre-processed with a sequence-specific version of the RMA algorithm (Irizarry et al., 2003) termed GCRMA, as implemented in the gcrma package (v2.6.0) of BioConductor.  Pre-processing was done with all ten-day liver samples together as one group.

organism: Rattus norvegicus

source_name: rat liver after 10 days of feed restriction

growth_protocol: Inbred male Long-Evans (Turku/AB) rats were employed in these studies. Our laboratory has a 20-year history of characterizing a wide range of physiological and toxicological responses of this strain (Pohjanvirta and Tuomisto, 1994). The rats were 11-15 weeks old at the start of the experiments and were free of specific pathogens as evidenced by regular health monitoring. The ambient conditions in the artificially-illuminated, air-conditioned animal room were: lighting 12/12 h (lights on at 7 a.m.), temperature 21.5 ± 1ºC, humidity 55 ± 10%. The rats were individually housed in stainless steel wire-mesh cages with free access to powdered R36 feed (Ewos, Sweden) and water.

extract_protocol: Rats were euthanized by decapitation with a guillotine, and liver as well as a piece of inguinal WAT were rapidly excised. The adipose sample and small slices of liver (100-200 mg) were snap-frozen in liquid nitrogen and then stored at -80 ºC until analysis. Total RNA was extracted using RNeasy Mini Kits (Qiagen) according to the manufacturer’s instructions. DNase (Qiagen) was used to eliminate genomic DNA as recommended by the manufacturer. RNA yield was quantified by UV spectrophotometry and RNA integrity was verified with an Agilent 2100 Bioanalyser.

treatment_protocol: All rats were given corn oil (4 mL/kg) at the start of the experiment on day 0. Thereafter, the rats subjected to a 10-day APFR (days 0-9): ad libitum – 16 – 14 – 11 – 8 – 6 – 4 – 4 – 2 – 1 g. The entire amount of feed was given at once every day during the light hours.

value: Long-Evans (Turku/AB), Gender:Male, Age:11-15 weeks, Tissue:liver, FeedRestriction:10 days, CornOil:4 mL/kg


title: Bleomycin_2weeks_pool2_Cy3


title: rat_liver_day10_feedrestricted_replicate1

scan_protocol: The microarray facility at The Centre for Applied Genomics, Hospital for Sick Children (Toronto, ON) processed the gene chips as per the manufacturer’s instructions.


title: rat_liver_day10_feedrestricted_replicate2

label_protocol: The microarray facility at The Centre for Applied Genomics, Hospital for Sick Children (Toronto, ON) processed the gene chips as per the manufacturer’s instructions.


title: rat_liver_day10_feedrestricted_replicate5


title: rat_liver_day10_control_replicate5

description: The mRNA expression profile of the liver from a rat ten days after corn oil vehicle was given.

source_name: rat control liver

value: Long-Evans (Turku/AB), Gender:Male, Age:11-15 weeks, Tissue:liver, FeedRestriction:none, CornOil:4 mL/kg


title: Bleomycin_3weeks_pool1_Cy3


title: rat_liver_day4_control_replicate4

description: The mRNA expression profile of the liver from a rat four days after corn oil vehicle was given.

data_processing: Array data were loaded into the R statistical environment (v2.4.1) using the affy package (v1.12.2) (Gautier et al., 2004) of the BioConductor open-source project (Gentleman et al., 2004). Data were investigated for spatial and distributional homogeneity. These data were pre-processed with a sequence-specific version of the RMA algorithm (Irizarry et al., 2003) termed GCRMA, as implemented in the gcrma package (v2.6.0) of BioConductor. Pre-processing was done with all four-day liver samples together as one group.

growth_protocol: Inbred male Long-Evans (Turku/AB) rats were employed in these studies. Our laboratory has a 20-year history of characterizing a wide range of physiological and toxicological responses of this strain (Pohjanvirta and Tuomisto, 1994). The rats were 11-15 weeks old at the start of the experiments and were free of specific pathogens as evidenced by regular health monitoring. The ambient conditions in the artificially-illuminated, air-conditioned animal room were: lighting 12/12 h (lights on at 7 a.m.), temperature 21.5 ± 1ºC, humidity 55 ± 10%. The rats were individually housed in stainless steel wire-mesh cages with free access to pelleted R36 feed (Ewos, Sweden) and water.

treatment_protocol: All rats were given corn oil (4 mL/kg) at the start of the experiment on day 0. Thereafter, the rats subjected to a 4-day APFR were provided the following amounts of feed daily (days 0-3): 18 – 12 – 9 – 6 g. The entire amount of feed was given at once every day during the light hours.


title: rat_liver_day10_control_replicate1


title: rat_liver_day4_restricted_replicate4

description: The mRNA expression profile of the liver from a rat four days after corn oil vehicle was given with feed-restriction.

source_name: rat liver after 4 days of feed restriction

value: Long-Evans (Turku/AB), Gender:Male, Age:11-15 weeks, Tissue:liver, FeedRestriction:4 days, CornOil:4 mL/kg


title: rat_liver_day10_control_replicate4


title: rat_liver_day4_restricted_replicate3


title: rat_liver_day4_restricted_replicate2


title: rat_liver_day4_control_replicate2


title: rat_liver_day10_control_replicate3


title: rat_liver_day4_control_replicate3


title: rat_liver_day10_control_replicate2


title: rat_liver_day10_feedrestricted_replicate3


title: Bleomycin_1week_pool1_Cy3

value: male

extract_protocol: manufacturer


title: rat_adipose_day4_restricted_replicate1

description: The mRNA expression profile of white adipose tissue from a rat four days after corn oil vehicle was given with feed-restriction.

data_processing: Array data were loaded into the R statistical environment (v2.4.1) using the affy package (v1.12.2) (Gautier et al., 2004) of the BioConductor open-source project (Gentleman et al., 2004). Data were investigated for spatial and distributional homogeneity. These data were pre-processed with a sequence-specific version of the RMA algorithm (Irizarry et al., 2003) termed GCRMA, as implemented in the gcrma package (v2.6.0) of BioConductor.  Pre-processing was done with all four-day adipose samples together as one group.

source_name: rat adiopose after 4 days of feed restriction

extract_protocol: Rats were euthanized by decapitation with a guillotine, and liver as well as a piece of inguinal WAT were rapidly excised. The adipose sample and small slices of liver (100-200 mg) were snap-frozen in liquid nitrogen and then stored at -80 ºC until analysis. Total RNA was extracted using RNeasy Lipid Tissue (Qiagen) according to the manufacturer’s instructions. DNase (Qiagen) was used to eliminate genomic DNA as recommended by the manufacturer. RNA yield was quantified by UV spectrophotometry and RNA integrity was verified with an Agilent 2100 Bioanalyser.

value: Long-Evans (Turku/AB), Gender:Male, Age:11-15 weeks, Tissue:white adipose, FeedRestriction:4 days, CornOil:4 mL/kg


title: rat_adipose_day4_restricted_replicate3


title: rat_adipose_day4_control_replicate4

description: The mRNA expression profile of white adipose tissue from a rat four days after corn oil vehicle was given.

source_name: rat control adipose

value: Long-Evans (Turku/AB), Gender:Male, Age:11-15 weeks, Tissue:white adipose, FeedRestriction:none, CornOil:4 mL/kg


title: rat_adipose_day4_restricted_replicate4


title: rat_liver_day4_restricted_replicate1


title: rat_adipose_day4_control_replicate1


title: rat_adipose_day4_restricted_replicate2


title: rat_adipose_day4_control_replicate2


title: MoDCs_PGE2 2h_2

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description: Sample were hybridized to HEEBO arrays containing 44544 human 70mer oligonucleotide probes (Stanford Functional Genomics Facility, California, USA). The data were obtained for four time points and using RNA from two independent donors.

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

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

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

source_name: Monocytes-derived dentritic cells (MoDCs)_PGE2 2h_2

label_protocol: Double-stranded cDNA was synthesized from 1 µg of total RNA, followed by production of antisense RNA containing the modified nucleotide 5-(3-aminoallyl)-UTP using the Amino Allyl MessageAmpTM II aRNA Amplification kit (Ambion, Texas, USA). Label source :GE Healthcare Bio-Sciences, New Jersey, USA).

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from leukocyte-enriched buffy coats of healthy volunteer donors by standard density gradient centrifugation using Lymphoprep solution from Nycomed (Oslo, Norway). 2.5 x 108 PBMC were allowed to adhere during 1 h 30 at 37°C at 5% CO2 in air in 75 cm2 cell-culture flasks. Non adherent cells were removed and adherent cells were cultured in 15 ml medium supplemented with 800 U/mL of granulocyte-macrophage colony-stimulating factor (GM-CSF) and 500 U/mL of IL-4. GM-CSF and IL-4 were also added a second time two days after the adhesion step. 5 days after the adhesion step, the purity of each cell preparation is evaluated by flow cytometry by analysing the expression of two markers of dendritic cells (DCs), human leukocyte antigen (HLA)-DR and CD1a. Moreover, the absence of monocytes, lymphocytes and mature DCs was always checked by staining cell preparation using respectively, CD14, CD3 and CD83 markers. For our experiments, we have only used cell preparations of HLA-DR+ CD1a+ immature DCs displaying at least 95% of purity. Cells were then plated at 106 cells/mL in 24 multiwells in complete medium. Agents were then added for different periods of time.

extract_protocol: RNA was isolated using TRIzol reagent (Life Technologies, Groningen, The Netherlands) and RNeasy kit column (Qiagen, Hilden, Germany).

treatment_protocol: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and stimulated by PGE2 for 2h.

tag: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and stimulated by protaglandin E2 (PGE2) for 2h. Biological replicate 2

source_name: Reference RNA : Unstimulated monocytes-derived dentritic cells

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated from leukocyte-enriched buffy coats of healthy volunteer donors by standard density gradient centrifugation using Lymphoprep solution from Nycomed (Oslo, Norway). 2.5 x 108 PBMC were allowed to adhere during 1 h 30 at 37°C at 5% CO2 in air in 75 cm2 cell-culture flasks. Non adherent cells were removed and adherent cells were cultured in 15 ml medium supplemented with 800 U/mL of granulocyte-macrophage colony-stimulating factor (GM-CSF) and 500 U/mL of IL-4. GM-CSF and IL-4 were also added a second time two days after the adhesion step. 5 days after the adhesion step, the purity of each cell preparation is evaluated by flow cytometry by analysing the expression of two markers of dendritic cells (DCs), human leukocyte antigen (HLA)-DR and CD1a. Moreover, the absence of monocytes, lymphocytes and mature DCs was always checked by staining cell preparation using respectively, CD14, CD3 and CD83 markers. For our experiments, we have only used cell preparations of HLA-DR+ CD1a+ immature DCs displaying at least 95% of purity. Cells were then plated at 106 cells/mL in 24 multiwells in complete medium for different periods of time.

treatment_protocol: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and incubated for 2h.

tag: Reference RNA


title: rat_liver_day4_control_replicate1


title: MoDCs_PGE2 6h_1

source_name: Monocytes-derived dentritic cells (MoDCs)_PGE2 6h_1

treatment_protocol: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and stimulated by PGE2 for 6h.

tag: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and stimulated by protaglandin E2 (PGE2) for 6h.

tag: Biological Replicate1

treatment_protocol: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and incubated for 6h.

value: Unstimulated monocytes-derived dentritic cells


title: MoDCs_PGE2 24h_2

source_name: Monocytes-derived dentritic cells (MoDCs)_PGE2 24h_2

treatment_protocol: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and stimulated by PGE2 for 24h.

tag: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and stimulated by protaglandin E2 (PGE2) for 24h.

tag: Biological replicate 2

treatment_protocol: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and incubated for 24h.


title: MoDCs_PGE2 12h_1

source_name: Monocytes-derived dentritic cells (MoDCs)_PGE2 12h_1

treatment_protocol: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and stimulated by PGE2 for 12h.

tag: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and stimulated by protaglandin E2 (PGE2) for 12h. Biological replicate 1

treatment_protocol: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and incubated for 12h.


title: MoDCs_PGE2 24h_1

source_name: Monocytes-derived dentritic cells (MoDCs)_PGE2 24h_1

tag: Biological replicate 1


title: MoDCs_ATPγS 12h_2

source_name: Monocytes-derived dentritic cells (MoDCs)_ATPγS 12h_2

treatment_protocol: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and stimulated by ATPγS for 12h.

tag: Monocytes-derived dentritic cells (MoDCs) stimulated by ATPγS for 12h; Biological replica 2


title: MoDCs_PGE2 6h_2

source_name: Monocytes-derived dentritic cells (MoDCs)_PGE2 6h_2

tag: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and stimulated by protaglandin E2 (PGE2) for 6h. Biological replicate 2


title: MoDCs_PGE2 12h_2

source_name: Monocytes-derived dentritic cells (MoDCs)_PGE2 12h_2

tag: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and stimulated by protaglandin E2 (PGE2) for 12h. Biological replicate 2


title: MoDCs_PGE2 2h_1

source_name: Monocytes-derived dentritic cells (MoDCs)_PGE2 2h_1

tag: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and stimulated by protaglandin E2 (PGE2) for 2h.


title: MoDCs_ATPγS 24h_2

source_name: Monocytes-derived dentritic cells (MoDCs)_ATPγS 24h_2

treatment_protocol: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and stimulated by ATPγS for 24h.

tag: Monocytes-derived dentritic cells (MoDCs) stimulated by ATPγS for 24h; Biological replica 2


title: MoDCs_ATPγS 2h_2

source_name: Monocytes-derived dentritic cells (MoDCs)_ATPγS 2h_2

treatment_protocol: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and stimulated by ATPγS for 2h.

tag: Monocytes-derived dentritic cells (MoDCs) stimulated by ATPγS for 2h; Biological replica 2


title: rat_adipose_day4_control_replicate3

tag: Strain


title: MoDCs_ATPγS 2h_1

source_name: Monocytes-derived dentritic cells (MoDCs)_ATPγS 2h_1

tag: Monocytes-derived dentritic cells (MoDCs) stimulated by ATPγS for 2h; Biological replica 1

tag: Unstimulated monocytes-derived dentritic cells.


title: MoDCs_ATPγS 6h_1

source_name: Monocytes-derived dentritic cells (MoDCs)_ATPγS 6h_1

treatment_protocol: Monocytes-derived dentritic cells were plated at 106 cells/mL in 24 multiwells in complete medium and stimulated by ATPγS for 6h.

tag: Monocytes-derived dentritic cells (MoDCs) stimulated by ATPγS for 6h; Biological replica 1


title: MoDCs_ATPγS 24h_1

source_name: Monocytes-derived dentritic cells (MoDCs)_ATPγS 24h_1

tag: Monocytes-derived dentritic cells (MoDCs) stimulated by ATPγS for 24h; Biological replica 1

tag: Reference RNA


title: MoDCs_ATPγS 6h_2

source_name: Monocytes-derived dentritic cells (MoDCs)_ATPγS 6h_2

tag: Monocytes-derived dentritic cells (MoDCs) stimulated by ATPγS for 6h; Biological replica 2


title: MoDCs_ATPγS 12h_1

source_name: Monocytes-derived dentritic cells (MoDCs)_ATPγS 12h_1

tag: Monocytes-derived dentritic cells (MoDCs) stimulated by ATPγS for 12h; Biological replica 1


title: Saccharomyces cerevisiae ssy1T9  s288c wt

city: Cambridge

first: Christian

last: Landry

state: MA

address: 16 Divinity avenue

department: OEB

institute: Harvard University

description: see Brown et al.

hyb_protocol: Genisphere 3DNA System

scan_protocol: Axon scnanner and Genepix

data_processing: Spots of bad quality were given negative flags

source_name: Saccharomyces cerevisiae ssy1T9

label_protocol: Genisphere 3DNA System

extract_protocol: See Townsend, Cavalieri and Hartl 2003, PMID: 12716989: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=search&term=12716989

tag: Saccharomyces cerevisiae ssy1T9

source_name: Saccharomyces cerevisiae s288c wt

tag: Saccharomyces cerevisiae s288c wt


title: Saccharomyces cerevisiae ssy1T9  ssy1KO

description: see Brown et al.

source_name: Saccharomyces cerevisiae ssy1KO

tag: Saccharomyces cerevisiae ssy1KO


title: Saccharomyces cerevisiae ssy1KO s288c wt

description: see Brown et al.


title: Saccharomyces cerevisiae s288c wt ssy1T9

description: see Brown et al.


title: maize_root_region3_ww-region2_ws_rep4-slideB

description: This is the 4th of 4 biological replications, and one half of a dye-swap pair.  Stressed region 2 was compared with control region 3 as a developmental control to the comparison of stressed region 2 with control region 2.

hyb_protocol: The purified Cy3 and Cy5-labeled cDNAs were concentrated to 60 μl and hybridized to the maize oligonucleotide array (GPL1993) for 16-18 h at 42 ºC. Following hybridization, the arrays were washed three times, twice with medium stringency buffer (1X SSC, 0.2% SDS) and once with high stringency buffer (0.1X SSC, 0.2% SDS).

source_name: maize root region3 control 48h rep 4

treatment_protocol: See the growth protocol.

tag: Region 3 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of high water potential.

source_name: maize root region2 water stress 48h rep 4

tag: Region 2 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of low water potential.


title: maize_root_region3_ww-region2_ws_rep3-slideB

source_name: maize root region3 control 48h rep 3

source_name: maize root region2 water stress 48h rep 3


title: Saccharomyces cerevisiae s288c wt ssy1KO

description: see Brown et al.


title: maize_root_region3_ww-region2_ws_rep1-slideB

description: This is the 1st of 4 biological replications, and one half of a dye-swap pair.  Stressed region 2 was compared with control region 3 as a developmental control to the comparison of stressed region 2 with control region 2.

source_name: maize root region3 control 48h rep 1

source_name: maize root region2 water stress 48h rep 1


title: maize_root_region2_ws-region3_ww_rep1-slideB


title: maize_root_region2_ww-ws_rep3-slideB

description: This is the 3rd of 4 biological replications, and one half of a dye-swap pair.

source_name: maize root region2 control 48h rep 3

tag: Region 2 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of high water potential.


title: maize_root_region2_ws-ww_rep4-slideB

description: This is the 4th of 4 biological replications, and one half of a dye-swap pair.

source_name: maize root region2 control 48h rep 4


title: Effects of nitric oxide on Salmonella adapted to pH 4.4 (3)

city: Aurora

first: Travis

middle: J

last: Bourret

department: Microbiology

institute: University of Colorado Health Sciences Center

hyb_protocol: Microarray slides were blocked with succinic anhydride in 1-methyl-2-pyrrolidinone according to the following protocol.  Array slides were UV cross-linked at 650mJ.  Array slides were then dipped into a solution of 0.18% SDS for 2 min and rinsed 3X in ddH2O.  Arrays were then placed in a solution of succinic anhydride, 1-methyl-2-pyrrolidinone, sodium borate.  Washed slides in heated ddH2O for 2 min, followed by a wash in 100% ethanol.  Arrays were then dried by centrifugation.  Equal amounts of Cy3- or Cy5-labeled cDNAs were prepared in hybridazation solution with a final concentration of 25% formamide, 5X SSC, and 0.1% SDS.  The hybridization solution was placed onto the surface of of the printed microarray slide.  A coverslip was carefully placed on top of the array and the samples were hybridized to the Salmonella array in a Corning Hybridization Chamber at 42 degrees C overnight.  After hybridization, slides were washed once in 2X SSC, 0.1% SDS for  5 min at 42 degrees C, once in 0.1X SSC, 0.1% SDS for 10 min at room temperature and 4 times in 0.1X SSC for 1 min at room temperature.  The slide was rinsed in 96% ethanol for 5 seconds and dried by centrifugation.

scan_protocol: Microarrays scanned on a Genepix 4000A® microarray scanner were analyzed using the Genepix software (Molecular Devices, Sunnyvale, CA).

data_processing: Cy3 and Cy5 median signal intensities were derived by subtracting background intensity from spot-boundary signal intensities.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella adapted at pH 4.4 for 1 hour

label_protocol: Fluorescently labeled cDNAs were generated using Superscript-II reverse transcriptase in a reaction containing 1.2 µg/ml of random hexanucleotides, 4 µl Cy3- or Cy5-labelled dUTP (Amersham, Piscataway, NJ) and biased nucleotides (25mM dCTP, 25mM dATP, 25mM dGTP, and 10mM dTTP) and 50 µg of total RNA.  Contaminating RNA was removed by hot alkali treatment and cDNAs purified using the Qiagen PCR Purification kit (Qiagen, Valencia, CA).

growth_protocol: Salmonella Typhimurium was grown overnight in Luria Bertani growth medium for 20 h.  Bacteria were subcultured 1:50 in minimal E salts + 0.4% glucose, pH 7.0.  Followed growth to mid-log phase and pelleted bacteria by centrifugation.  Bacteria were resuspended in minimal E salts + 0.4% glucose, pH 4.4 for 1 h at 37 degrees C with shaking prior to RNA extraction.

extract_protocol: Salmonella cultures were mixed with a phenol (5%)/ethanol (95%) solution and placed on ice for 20 min.  RNA was extracted from bacteria using the SV Total RNA Isolation kit according to manufacturer's insturctions.

tag: Salmonella enterica serovar Typhimurium ATCC 14028s grown in minimal EG medium, pH 4.4 for 1 hour.

source_name: Salmonella adapted at pH 4.4 for 1 hour + 250µM spermine NONOate

tag: Salmonella enterica serovar Typhimurium ATCC 14028s grown in minimal EG medium, pH 4.4 for 1 hour in the presence of 250µM spermine NONOate.


title: Effects of nitric oxide on Salmonella adapted to pH 4.4 (2)


title: maize_root_region1_ww-ws_rep3-slideB

hyb_protocol: The purified Cy3 and Cy5-labeled cDNAs were concentrated to 60 μl and hybridized to the maize oligonucleotide array (GPL1991) for 16-18 h at 42 ºC. Following hybridization, the arrays were washed three times, twice with medium stringency buffer (1X SSC, 0.2% SDS) and once with high stringency buffer (0.1X SSC, 0.2% SDS).

source_name: maize root region1 control 48h rep 3

tag: Region 1 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of high water potential.

source_name: maize root region1 water stress 48h rep 3

tag: Region 1 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of low water potential.


title: maize_root_region2_ww-ws_rep4-slideB


title: maize_root_region3_ww-region2_ws_rep2-slideB

description: This is the 2nd of 4 biological replications, and one half of a dye-swap pair.  Stressed region 2 was compared with control region 3 as a developmental control to the comparison of stressed region 2 with control region 2.

source_name: maize root region3 control 48h rep 2

source_name: maize root region2 water stress 48h rep 2


title: maize_root_region1_ww-ws_rep4-slideB

source_name: maize root region1 control 48h rep 4

source_name: maize root region1 water stress 48h rep 4


title: maize_root_region2_ww-ws_rep2-slideB

description: This is the 2nd of 4 biological replications, and one half of a dye-swap pair.

source_name: maize root region2 control 48h rep 2


title: maize_root_region2_ws-region3_ww_rep2-slideB


title: maize_root_region1_ww-ws_rep2-slideB

source_name: maize root region1 control 48h rep 2

source_name: maize root region1 water stress 48h rep 2


title: maize_root_region1_ws-ww_rep4-slideB


title: maize_root_region1_ws-ww_rep2-slideB


title: maize_root_region2_ws-ww_rep3-slideB


title: Effects of nitric oxide on Salmonella adapted to pH 4.4

hyb_protocol: Microarray slides were blocked with succinic anhydride in 1-methyl-2-pyrrolidinone according to the following protocol.  Array slides were UV cross-linked at 650mJ.  Array slides were then dipped into a solution of 0.18% SDS for 2 min and rinsed 3X in ddH2O.  Arrays were then placed in a solution of succinic anhydride, 1-methyl-2-pyrrolidinone, sodium borate.  Washed slides in heated ddH2O for 2 min, followed by a wash in 100% ethanol.  Arrays were then dried by centrifugation.  Equal amounts of Cy3- or Cy5-labeled cDNAs were prepared in hybridazation solution with a final concentration of 25% formamide, 5X SSC, and 0.1% SDS.  The hybridization solution was placed onto the surface of of the printed microarray slide.  A coverslip was carefully placed on top of the array and the samples were hybridized to the Salmonella array in a Corning Hybridization Chamber at 42 degrees C overnight.  After hybridization, slides were washed once in 2X SSC, 0.1% SDS for 5 min at 42 degrees C, once in 0.1X SSC, 0.1% SDS for 10 min at room temperature and 4 times in 0.1X SSC for 1 min at room temperature.  The slide was rinsed in 96% ethanol for 5 seconds and dried by centrifugation.

tag: Salmonella enterica serovar Typhimurium ATCC 14028s grown in minimal EG medium, pH 4.4 for 1 hour

growth_protocol: Salmonella Typhimurium was grown overnight in Luria Bertani growth medium for 20 h.  Bacteria were subcultured 1:50 in minimal E salts + 0.4% glucose, pH 7.0.  Followed growth to mid-log phase and pelleted bacteria by centrifugation.  Bacteria were resuspended in minimal E salts + 0.4% glucose, pH 4.4 in presence of 250µM spermine NONOate for 1 h at 37 degrees C with shaking prior to RNA extraction.


title: Bleomycin_3week_pool1_Cy5

source_name: UMRR

tag: Stratagene Mouse Universal Reference RNA

tag: Catalog #740100

tag: Strain

tag: Gender

tag: Age

value: 8 weeks

tag: Treatment

tag: Tissue

value: lung

tag: Time post-treatment


title: maize_root_region2_ws-ww_rep2-slideB


title: maize_root_region2_ws-region3_ww_rep4-slideB

source_name: maize root region2 water stress 48h rep 4

source_name: maize root region3 control 48h rep 4


title: PAO1 untreated reference PA_ref3

status: Public on Feb 28 2008

city: Kgs. Lyngby

first: Mette

middle: E.

last: Skindersoe

address: Matematiktorvet 1. build. 301

country: Denmark

institute: Technical University of Denmark

description: Gene expression data from exponentially growing P. aeruginosa cultures grown as reference

hyb_protocol: Hybridised for 18 h at 55°C to P. aeruginosa genome microarray GeneChip® (Affymetrix).

scan_protocol: The chips were washed and stained according to the Affymetrix protocol.

data_processing: The microarray hybridization signal intensity was scaled to an overall signal average of 2500 using Affymetrix default analysis settings, and present/marginal/absent (based on evaluation of PerfectMatch (PM) and MisMatch (MM) intensities) was evaluated by the use of the Affymetrix GCOS v1.4 software. Only expression value genes estimated being “Present” were included in the further analyses.

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1 untreated reference PA_ref3

label_protocol: Synthesis of cDNA was performed with 12 microg RNA, 300 ng/microL random primers (Invitrogen™), 1500 U SuperScript III Reverse Transcriptase (Invitrogen™) and 30 U SUPERase۰In™ Rnase Inhibitor (Ambion) according to Affymetrix’s Expression Analysis Protocol. Synthesized cDNA was purified using the QIAquick PCR Purification Kit (QIAGEN) and 3-4 microg cDNA was fragmented using 0.2 U DNase I, FPLC pure™ (Amersham Bioscience) pr. microg cDNA. Fragmented cDNA was terminal labelled with biotin-ddUTP (Enzo Bioarray™ terminal labeling kit).

growth_protocol: ABT medium supplemented with 0.5% cas amino acids were inoculated with exponentially growing P. aeruginosa PAO1 cells to an OD600 of 0.05 and grown at 37°C, 200 rpm in 5 x 500 mL flasks containing 100 mL each.  Samples were retrieved at OD600 2.0

extract_protocol: Samples were retrieved at OD600 2.0, and immediately transferred to two volumes RNAlater (Ambion) and stored at -80°C. RNA was isolated using the “RNeasy Mini Purification Kit” (QIAGEN) according to the provided protocol including the on-column DNase treatment.

treatment_protocol: Exponentially growing cells were added subMIC level antibiotics at OD600 = 0.3

tag: PAO1 untreated reference PA_ref3


title: maize_root_region1_ww-ws_rep1_slideB

description: This is the 1st of 4 biological replications, and one half of a dye-swap pair.

data_processing: Mean signal intensities were used without background correction and data from all 8 chips (4 reps with dye-swap) were normalized using the Loess transformation.

source_name: maize root region1 control 48h rep 1

extract_protocol: The apical 12 mm of each root was sectioned into three regions based on previously-characterized longitudinal expansion rate profiles: region 1, 0-3 mm plus the root cap; region 2, 3-7 mm; region 3, 7-12 mm. Samples were immediately frozen in liquid nitrogen. Total RNA was isolated using Trizol reagent following the manufacturer’s instructions (Invitrogen Corp., Carlsbad, CA). Residual DNA was removed by Dnase I (Invitrogen, Carlsbad, CA) treatment for 15 min at room temperature, followed by use of RNeasy columns (Qiagen, Valencia, CA).

source_name: maize root region1 water stress 48h rep 1


title: maize_root_region1_ws-ww_rep3-slideB


title: maize_root_region1_ws-ww_rep1-slideB


title: PAO1 untreated reference PA_ref2

source_name: PAO1 untreated reference PA_ref2

tag: PAO1 untreated reference PA_ref2


title: PA2663 mutant

status: Public on Feb 22 2008

city: College Station

first: Can

last: Attila

address: 524 Jack E. Brown Bldg.

department: Chemical Eng

institute: Texas A&M University

description: RNA extracted from biofilm cells of P. aeruginosa wild type after 7 hours of growth in LB medium at 30C

hyb_protocol: Following Affymetrix Protocol. After loading hybridization cocktail in Affymetrix P. aeruginosa array, the hybridization was performed at 50C for 16 hours.

scan_protocol: Following Affymetrix Protocol, after washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChip Operating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

label: Biotin

organism: Pseudomonas aeruginosa

source_name: PA2663 mutant

label_protocol: Following Affymetrix Protocol, cDNA was synthesized first using Promega M-MLV Reverse transriptase(Cat#M1705). After removing RNA, DNA fragmentation was performed to obtain and 500-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181)

extract_protocol: After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat#74104)

tag: RNA extracted from biofilm cells of P. aeruginosa PAO1 PA2663 mutant after 7 hours of growth in LB with glass wool at 30C


title: PAO1 untreated reference PA_ref4

source_name: PAO1 untreated reference PA_ref4

tag: PAO1 untreated reference PA_ref4


title: Saline_1week_pool1_Cy3


title: PAO1 wild-type

source_name: PAO1 wild-type

tag: RNA extracted from biofilm cells of P. aeruginosa PAO1 wild type after 7 hours of growth in LB with glass wool


title: PAO1 treated with azithromycin (8 microgram pr. mL)

description: Gene expression data from exponentially growing P. aeruginosa cultures grown in presence of antibiotics


title: maize_root_region2_ws-ww_rep1-slideB

source_name: maize root region2 water stress 48h rep 1

tag: Region 2 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of low water potential.

source_name: maize root region2 control 48h rep 1

tag: Region 2 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of high water potential.


title: PAO1 untreated reference PA_ref1

source_name: PAO1 untreated reference PA_ref1

tag: PAO1 untreated reference PA_ref1


title: PAO1 treated with azithromycin (2 microgram pr. mL)


title: Saccharomyces cerevisiae ssy1KO ssy1T9

description: see Brown et al.

source_name: Saccharomyces cerevisiae ssy1KO

tag: Saccharomyces cerevisiae ssy1KO

source_name: Saccharomyces cerevisiae ssy1T9

tag: Saccharomyces cerevisiae ssy1T9


title: placenta

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

institute: Best Institute

hyb_protocol: Samples were resuspended in 0.5 mL of hybridization buffer (1 M NaCl, 0.5% sodium sarcosine, 50 mM N-morpholino ethane sulfonate, pH 6.5, 33% formamide and 40 g salmon sperm DNA), denatured by heating at 65°C for 5 minutes, and snap-cooled on ice prior to hybridization.  Hybridizations were carried out for 16-24 h at 42°C in a rotating hyb oven.  Slides were then washed (rocking ~30 seconds in 6x SSPE, 0.005% sarcosine, then rocking ~30 seconds in 0.06x SSPE).

scan_protocol: Slides were scanned with a 4000A microarray scanner (Axon Instruments, Union City, CA).

data_processing:
TIFF images were quantified with GenePix 3.0 (Axon Instruments, Union City, CA).  Individual channels were spatially detrended (i.e. overall correlations between spot intensity and position on the slide removed) by high-pass filtering using 5% outliers.  The 16 individual channels were then normalized using Variance Stabilization and transformed to arcsinh values, which are similar to natural log values but are tolerant of negative numbers emerging from high-pass filtering.
The data were submitted as single channel because that is how it was processed, although we actually used Agilent arrays and hybridized two samples to each array.  The data were submitted in this manner because we did not use ratios to interpret the data.

label: direct

source_name: placenta

label_protocol: Integrity of rRNA was confirmed on 1% agarose-formaldehyde gels.  7 g of total RNA was chemically labeled with Ulysis Alexa Fluor 546 or Ulysis Alexa Fluor 647 (Ulysis) according to manufacturer’s instructions.  This protocol labels G residues [203], and there were no predicted RNAs that lacked G residues.

extract_protocol: RNA was purchased from Ambion.

tag: placenta


title: PAO1 treated with ceftazidime (0.25 microgram pr. mL)


title: thymus

source_name: thymus

tag: thymus


title: testis

source_name: testis

tag: testis


title: muscle

source_name: muscle

tag: muscle


title: spleen

source_name: spleen

tag: spleen


title: maize_root_region2_ww-ws_rep1-slideB


title: ovary

source_name: ovary

tag: ovary


title: PAO1 treated with ciprofloxacin (0.04 microgram pr. mL)


title: pachytene

description: Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions and treated with DNAse I (Fermentas). The integrity of the rRNA was confirmed on 1% agarose-formaldehyde gels, and 7 µg of total RNA was chemically labeled with Ulysis Alexa Fluor 546 or Ulysis Alexa Fluor 647 (Molecular Probes) according to the manufacturer’s instructions. This protocol labels G residues (Wiegant et al. 1999), and there are no mouse miRNAs that lack a G residue. Samples were resuspended in 0.5 mL of hybridization buffer (1 M NaCl, 0.5% sodium sarcosine, 50 mM methyl ethane sulfonate at pH 6.5, 33% formamide, and 40 µg salmon sperm DNA), denatured by heating for 5 min at 65°C, and snap-cooled on ice prior to hybridization. Hybridizations were carried out in duplicate (two samples per array labeled with different fluorophores) for 16–24 h at 42°C in a rotating hyb oven. Slides were then washed (rocking for ~30 sec in 6x SSPE, 0.005% sarcosine, then rocking for ~30 sec in 0.06x SSPE) and scanned with a 4000A microarray scanner (Axon Instruments).

data_processing:
TIFF images were quantified with GenePix 3.0 (Axon Instruments). Individual channels were spatially detrended (i.e., overall correlations between spot intensity and position on the slide removed) by high-pass filtering (Shai et al. 2003) using 5% outliers. The 17 individual channels were then normalized using Variance Stabilizing Normalization (Huber et al. 2002) and transformed to arcsinh values, which are similar to natural log values but are tolerant of negative numbers emerging from high-pass filtering. Repeat measurements from separate arrays revealed an average Pearson correlation of 0.82 across 13 repeated tissues for all miRNAs, and 0.94 when restricted to intensities above the 99% negative-control threshold.
The data were submitted as single channel because that is how it was processed, although we actually used Agilent arrays and hybridized two samples to each array.  The data were submitted in this manner because we did not use ratios to interpret the data.

label: direct-labelled fluor

source_name: pachytene

tag: pachytene


title: beta pachytene

hyb_protocol: Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions and treated with DNAse I (Fermentas). The integrity of the rRNA was confirmed on 1% agarose-formaldehyde gels, and 7 µg of total RNA was chemically labeled with Ulysis Alexa Fluor 546 or Ulysis Alexa Fluor 647 (Molecular Probes) according to the manufacturer’s instructions. This protocol labels G residues (Wiegant et al. 1999), and there are no mouse miRNAs that lack a G residue. Samples were resuspended in 0.5 mL of hybridization buffer (1 M NaCl, 0.5% sodium sarcosine, 50 mM methyl ethane sulfonate at pH 6.5, 33% formamide, and 40 µg salmon sperm DNA), denatured by heating for 5 min at 65°C, and snap-cooled on ice prior to hybridization. Hybridizations were carried out in duplicate (two samples per array labeled with different fluorophores) for 16–24 h at 42°C in a rotating hyb oven. Slides were then washed (rocking for ~30 sec in 6x SSPE, 0.005% sarcosine, then rocking for ~30 sec in 0.06x SSPE) and scanned with a 4000A microarray scanner (Axon Instruments).

source_name: mouse beta pachytene

tag: beta pachytene


title: mammary gland

source_name: mammary gland

tag: mammary gland


title: spermatids

scan_protocol: Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions and treated with DNAse I (Fermentas). The integrity of the rRNA was confirmed on 1% agarose-formaldehyde gels, and 7 µg of total RNA was chemically labeled with Ulysis Alexa Fluor 546 or Ulysis Alexa Fluor 647 (Molecular Probes) according to the manufacturer’s instructions. This protocol labels G residues (Wiegant et al. 1999), and there are no mouse miRNAs that lack a G residue. Samples were resuspended in 0.5 mL of hybridization buffer (1 M NaCl, 0.5% sodium sarcosine, 50 mM methyl ethane sulfonate at pH 6.5, 33% formamide, and 40 µg salmon sperm DNA), denatured by heating for 5 min at 65°C, and snap-cooled on ice prior to hybridization. Hybridizations were carried out in duplicate (two samples per array labeled with different fluorophores) for 16–24 h at 42°C in a rotating hyb oven. Slides were then washed (rocking for ~30 sec in 6x SSPE, 0.005% sarcosine, then rocking for ~30 sec in 0.06x SSPE) and scanned with a 4000A microarray scanner (Axon Instruments).

source_name: spermatids

tag: spermatids


title: 2007062803b

status: Public on Feb 20 2008

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

institute: VIB

description: X chromosome-specific Array-CGH of XLMR patient

hyb_protocol: For each hybridisation, 1 µg of the Cy5- and 2 µg of the Cy3- labeled probes, with a specific activity < 40 were mixed together with 50 µg Cot-1 DNA (Invitrogen, Carlsbad, CA). Probe preparation, pre-blocking and washing of the slides was performed as described previously (Van Buggenhout G, et al. 2004. J. Med. Genet. 41: 691-698).

scan_protocol: Arrays were scanned at 532 nm (Cy3) and 635 nm (Cy5) using the Genepix 4000B scanner (Axon Instruments, Aberdeen, UK) and the acquired images were analyzed using the Genepix Pro software (Axon Instruments).

data_processing: Spot intensities were corrected for local background and only those spots with Cy5 as well as Cy3 signal intensities at least 1.7-fold above the local background, were further analyzed. For each clone, a ratio of Cy5 to Cy3 fluorescent intensity was calculated. Normalization of the data was achieved by dividing the fluorescent intensity ratio of each spot by the mean of the ratios of all spots. Finally, the normalized ratio values of the duplicates were averaged and a log2 value was calculated.

label_protocol: Genomic DNA was labeled with the Bioprime DNA Labeling System (Invitrogen, Carlsbad, CA) using Cy3- and Cy5-labelled dCTP's (Amersham Biosciences, Buckinghamshire, UK) as described by the manufacturer. The concentrations and labeling efficiencies were measured with the Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Rockland, DE).

extract_protocol: Genomic DNA from patients as well as from healthy controls was isolated from peripheral blood using the Wizard Genomic DNA purification Kit (Promega, Madison, WI) and using manufacture's protocol.

tag: XLMR patient 46,XY


title: spermatogonia

source_name: spermatogonia

label_protocol: Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions and treated with DNAse I (Fermentas). The integrity of the rRNA was confirmed on 1% agarose-formaldehyde gels, and 7 µg of total RNA was chemically labeled with Ulysis Alexa Fluor 546 or Ulysis Alexa Fluor 647 (Molecular Probes) according to the manufacturer’s instructions. This protocol labels G residues (Wiegant et al. 1999), and there are no mouse miRNAs that lack a G residue. Samples were resuspended in 0.5 mL of hybridization buffer (1 M NaCl, 0.5% sodium sarcosine, 50 mM methyl ethane sulfonate at pH 6.5, 33% formamide, and 40 µg salmon sperm DNA), denatured by heating for 5 min at 65°C, and snap-cooled on ice prior to hybridization. Hybridizations were carried out in duplicate (two samples per array labeled with different fluorophores) for 16–24 h at 42°C in a rotating hyb oven. Slides were then washed (rocking for ~30 sec in 6x SSPE, 0.005% sarcosine, then rocking for ~30 sec in 0.06x SSPE) and scanned with a 4000A microarray scanner (Axon Instruments).

tag: spermatogonia


title: heart

source_name: heart

tag: heart


title: liver

source_name: liver

tag: liver


title: maize_root_region2_ws-region3_ww_rep3-slideB

description: This is the 3rd of 4 biological replications, and one half of a dye-swap pair.  Stressed region 2 was compared with control region 3 as a developmental control to the comparison of stressed region 2 with control region 2.

scan_protocol: Washed slides were dried and scanned immediately using a GenePix scanner (GenePix® 4000B, Axon Instruments, Inc.) at 532 nm (17 mW) and 635 nm (10 mW). GenePix Pro 4.1 software was then used to extract spot intensity data.

source_name: maize root region2 water stress 48h rep 3

label_protocol: First strand cDNAs were synthesized from 50 μg of total RNA using anchored oligo(dT)24 primers with SuperScript III RT (Invitrogen, Carlsbad, CA), and aminoallyl-dUTP was incorporated into the cDNAs. The RNA template was removed by treatment with RnaseH (Invitrogen, Carlsbad, CA), and cDNAs were purified to remove unincorporated aminoallyl-dUTP using Microcon 30 spin concentrators (Millipore Corp., Bedford, MA). Following purification, monoreactive-Cye5 or Cye3 dyes (Amersham Biosciences Corp., Piscataway, NJ) were conjugated to aminoallyl-dUTP on the cDNAs and the unconjugated dye was removed using Qiagen PCR purification columns.

tag: Region 2 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of low water potential.

source_name: maize root region3 control 48h rep 3

tag: Region 3 of maize (Zea mays L. cv FR697) seedlings harvested 48h after transplant to vermiculite of high water potential.


title: BW25113 w/t LB 15h 37C biofilm cells

city: State College

first: Thomas

middle: K.

last: Wood

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from biofilm cells of E. coli K-12 wild type after 15 hours of growth at 37C in LB with glasswool.

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

organism: Escherichia coli

source_name: Channel 1

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit  (Affymetrix, P/N 900181).

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 15 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

tag: RNA extracted from biofilm cells of E. coli K-12 wild type BW25113 after 15 hours of growth at 37ºC in LB with glasswool


title: embryo-ambion

source_name: embryo-ambion

tag: embryo-ambion


title: brain

source_name: brain

tag: brain


title: 7d embryo

source_name: 7d embryo

tag: total RNA - direct labeled


title: H37dosR mutant_hypoxia_1day_rep4

city: Seattle

first: Tige

last: Rustad

state: WA

address: 307 Westlake Avenue N, Suite 500

department: Pathobiology

institute: Seattle Biomedical Research Institute

description: H37dosR mutant_hypoxia_1day_rep4

hyb_protocol: Slides prehybed for >1 hour in prehyb buffer (5X SSC, 0.1% SDS, 1% BSA), washed 2X for 1 minute in water, 15 seconds in isopropanol, dried by centrifugation.  Probes added to slides, sealed in incubation chambers and submerged in 42 degree incubator overnight.  Arrays washed in increasingly stringent washes: 5 minutes at 42 degrees low stringency wash (0.2%SDS, 1XSSC), 10 minutes lower stringency wash (0.2%SDS, 0.1XSSC), 4 times 1 minute in 0.1XSSC, 10 seconds in 0.01XSSC.  Slides dried by centrifugation.

scan_protocol: Arrays scanned in with a GenePix4000B using GenePix 6 scanning software.  Gain adjusted during preview scan to roughly equivalence between channels with a few saturated spots.

data_processing: Data analysis conducted with Acuity 4 software package.  Spots flagged as not found were excised from the dataset.  Remaining features were lowess normalized seperately for each print tip.

organism: Mycobacterium tuberculosis

source_name: Log phase RNA

label_protocol: Standard amino-allyl labelling protocol from TIGR.  cDNA made with Superscript III using aminoallyl dUTP.  cDNA purified using Qiaquick column from Qiagen.  Tags conjugated to reactive Cy dyes in the presence of sodium carbonate.  Excess Cy dye removed with a Qiaquick column from Qiagen.  Probes resuspended in hyb buffer (50% formamide, 5X SSC, and  0.1% SDS) and kept at room temp until added to array slides.

growth_protocol: Grown to mid log phase (OD600 0.3-0.5) in 2L roller bottles with 200-400 mL Middlebrook 7H9 media+ADC and Tween.  Diluted to an OD of 0.1 and transferred to three-armed flask.

extract_protocol: Pellets were bead beat in the presence of trizol.  Aqueus phase isolated using phase lock gel.  RNA precipitated in 50% isopropanol 50% high salt solution ((0.8M Na Citrate, 1.2M NaCl).  RNA purified using Rneasy columns from Qiagen.

treatment_protocol: 0.2% O2 (Balance N2) introduced into flask at a rate of 0.15 cfm and allowed to exit through 0.2 micron filter.  Samples (15-60mL) taken via pipette introduced into the flask while gas continued to flow.  Samples centrifuged for 5 minutes at 3000 RPM to softly pellet, superenatent decanted and pellet flash frozen in dry ice/ethanol bath.

tag: Strain

value: H37dosR mutant Condition:aerobically grown

source_name: dosR_mutant_1d RNA

tag: Strain H37dosR mutant Condition

value: 1 day exposure to 0.2%O2


title: BW25113 yncC deletion mutant LB 15h 37C biofilm cells

description: RNA extracted from biofilm cells of E. coli K-12 yncC deletion mutant after 15 hours of growth at 37C in LB with glasswool

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS)

tag: RNA extracted from biofilm cells of E. coli K-12 yncC deletion mutant after 15 hours of growth at 37ºC in LB with glasswool


title: H37dosR mutant_hypoxia_1day_rep6

description: H37dosR mutant_hypoxia_1day_rep6


title: H37dosR mutant_hypoxia_4day_rep1

description: H37dosR mutant_hypoxia_4day_rep1

source_name: dosR_mutant_4d RNA

value: 4 day exposure to 0.2%O2


title: H37dosR mutant_hypoxia_8hr_rep3

description: H37dosR mutant_hypoxia_8hr_rep3

source_name: dosR_mutant_8h RNA

value: 8 hour exposure to 0.2%O2


title: H37dosR mutant_hypoxia_12hr_rep1

description: H37dosR mutant_hypoxia_12hr_rep1

source_name: dosR_mutant_12h RNA

value: 12 hour exposure to 0.2%O2


title: H37dosR mutant_hypoxia_1day_rep2

description: H37dosR mutant_hypoxia_1day_rep2


title: H37dosR mutant_hypoxia_12hr_rep4

description: H37dosR mutant_hypoxia_12hr_rep4


title: H37dosR mutant_hypoxia_1day_rep3

description: H37dosR mutant_hypoxia_1day_rep3


title: H37dosR mutant_hypoxia_1day_rep1

description: H37dosR mutant_hypoxia_1day_rep1


title: H37dosR mutant_hypoxia_4hr_rep5

description: H37dosR mutant_hypoxia_4hr_rep5

source_name: dosR_mutant_4h RNA

value: 4 hour exposure to 0.2%O2


title: H37dosR mutant_hypoxia_7day_rep1

description: H37dosR mutant_hypoxia_7day_rep1

source_name: dosR_mutant_7d RNA

value: 7 day exposure to 0.2%O2


title: H37dosR mutant_hypoxia_4hr_rep4

description: H37dosR mutant_hypoxia_4hr_rep4


title: H37dosR mutant_hypoxia_4hr_rep2

description: H37dosR mutant_hypoxia_4hr_rep2