title: hiPS clone M4C2 p4

city: Montpellier

first: John

last: De Vos

address: 80 av. Augustin Fliche

department: Institute for Research in Biotherapy

country: France

institute: University Hospital of Montpellier

description:
Newborn human foreskin fibroblasts were transduced with four lentiviral vectors expressing Oct4, Sox2, Lin28 or Nanog under the control of the human EF1α promoter (Yu et al., 2007, Science vol. 318 pp. 1917-20). Colonies with a full pluripotent morphology were picked up after 35 days, further expanded and characterized.
The transcriptome of this hiPS was compared to the transcriptome of the parental fibroblast cells, partially reprogrammed cells and hESC cells.

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

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

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

source_name: Induced human pluripotent stem cell clone M4C2 passage 4

label_protocol: Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.

growth_protocol: The culture medium used for hiPS derivation and culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).

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

tag: clone

value: induced human pluripotent stem cells


title: hiPS clone M4C10 p4

status: Public on May 01 2010

type: RNA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Induced human pluripotent stem cell clone M4C10 passage 4

tag: cell type


title: hiPS clone M5VC2 p4

source_name: Induced human pluripotent stem cell clone M5VC2 passage 4


title: Bulk sensitive control replicate 1

status: Public on Apr 20 2010

city: NEW DELHI

first: Awadhesh

last: Pandit

state: DELHI

address: LBS BUILDING

country: India

institute: NRC ON PLANT BIOTECHNOLOGY

description: Gene expression profile of salt sensitive bulk in control

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GCOS 1.2

organism: Oryza sativa Indica Group

source_name: salt sensitive bulk in control conditions

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated by using TRIzol Reagent (Sigma) RNA samples were processed as recommended by Affymetrix (Affymetrix geneChip Expression Analysis Technical manual; Affymetrix)

tag: age

value: Seedling 10 days after germination

tag: variety

value: Bulk salt sensitive recombinant

tag: phenotype

value: Bulk salt sensitive


title: HFF1

description:
For the purpose of a reprogramming experiment, newborn human foreskin fibroblasts were transduced with four lentiviral vectors expressing Oct4, Sox2, Lin28 or Nanog under the control of the human EF1α promoter (Yu et al., 2007, Science vol. 318 pp. 1917-20). Partially and fully reprogrammed hIPS clones were obtained. This sample is the parental foreskin fibroblasts HFF1 cell line.
The transcriptome of this HFF cell sample was compared to the transcriptome of fully and partially reprogrammed cells, and hESC cells.

source_name: Human foreskin fibroblasts HFF1

growth_protocol: The culture medium used for human foreskin fibroblasts HFF1 cells comprised DMEM Iscove, 10% fetal bovine serum and Pencillin-Streptomycin.

tag: cell line

value: human foreskin fibroblasts


title: HESC_HD129_p6

description:
This human embryonic stem cell line was derived on an irradiated human fibroblast feeder, in 20% KO-SR medium, from a cystic fibrosis embryo as evidenced by preimplantation genetic diagnostic (PGD). RNA extraction was carried out at p6.
HD129 was compared to a compendium of 84 transcriptome covering a broad range of adult tissues and other human embryonic stem cell lines.

label: Biotin

source_name: Human embryonic stem cell line HD129/FE08-005-L1 obtained from a cystic fibrosis embryo

growth_protocol: The culture medium used for hESCs derivation and culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).

value: human embryonic stem cells

tag: embryo characteristic

value: cystic fibrosis


title: Bulk sensitive stressed replicate 1

description: Gene expression profile of salt sensitive bulk in stress (150mM NaCl treatment for 24 hrs)

source_name: salt sensitive bulk in stress conditions


title: Bulk tolerant stressed replicate 2

description: Gene expression profile of salt tolerant bulk in stress (150mM NaCl treatment for 24 hrs)

source_name: salt tolerant bulk in stress conditions

value: Bulk salt tolerant recombinant

value: Bulk salt tolerant


title: Partially reprogrammed clone INT_M4C1p4

description:
Newborn human foreskin fibroblasts were transduced with four lentiviral vectors expressing Oct4, Sox2, Lin28 or Nanog under the control of the human EF1α promoter (Yu et al., 2007, Science vol. 318 pp. 1917-20). Partially reprogrammed cells that displayed neither a fibroblast morphology nor a bona fide hiPS morphology were picked up and further expanded and characterized.
The transcriptome of partially reprogrammed cells was compared to the transcriptome of the parental fibroblast cells, fully reprogrammed human induced pluripotent stem cells and hESC.

source_name: Partially reprogrammed human induced pluripotent stem cells clone INT_M4C1p4

value: partially reprogrammed human induced pluripotent stem cells


title: Bulk tolerant control replicate 2

description: Gene expression profile of salt tolerant bulk in control

source_name: salt tolerant bulk in control conditions


title: HESC_HD83_p24

description:
This human embryonic stem cell line was derived on irradiated human fibroblasts, in 20% KO-SR medium and 10 ng/ml bFGF, from a normal embryo. RNA extraction was carried out at p24.
HD83 was compared to a compendium of 84 transcriptome covering a broad range of adult tissues and other human embryonic stem cell lines.

source_name: Human embryonic stem cell line HD83/FE07-135-L1

value: normal


title: Bulk sensitive stressed replicate 2


title: Partially reprogrammed clone GRA_M5C1p3

source_name: Partially reprogrammed human induced pluripotent stem cells clone GRA_M5C1p3


title: Bulk tolerant stressed replicate 1


title: Bulk sensitive control replicate 2


title: Partially reprogrammed clone GRA_M5VC1p3

source_name: Partially reprogrammed human induced pluripotent stem cells clone GRA_M5VC1p3


title: Partially reprogrammed clone INT_M4C1-1p5

source_name: Partially reprogrammed human induced pluripotent stem cells clone INT_M4C1-1p5


title: Bulk tolerant control replicate 1


title: 9704

status: Public on Aug 20 2010

city: Stanford

first: Hongjuan

last: Zhao

state: CA

address: 300 Pasteur Drive

department: Urology, Edwards Building R116

country: USA

institute: Stanford University

description:
Simple annotation: Kidney, tumor tissue
Image: http://smd.stanford.edu/MicroArray/gifs/2003-10/45569.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: GenePix 4000A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Stratagene Universal Human Reference RNA

label_protocol: not provided

extract_protocol: not provided

tag: reference

source_name: 9710 Total RNA

value: Kidney, tumor tissue

tag: stage of clear cell renal cell carcinoma

value: ch


title: Untreated control rep1

status: Public on Aug 15 2010

city: New York

first: Qiaoran

last: Xi

state: NY

address: 1275, York ave.

department: Cancer biology and genetics

institute: MSKCC

description: E14Tg2A.4 cells were untreated

hyb_protocol: 10 ug cRNA were hybridized to the affymetrix MOE 430 2.0 chips

scan_protocol: genechips were scanned using the Hewiett-Packard genearray scanner

data_processing: MAS 5.0

organism: Mus musculus

source_name: Mouse Embryonic stem cells(E14Tg2A.4)

label_protocol: biotinylated cRNA were prepared from 10ug of total RNA using the standard labeling techniques for affymetrix chips

extract_protocol: USB total RNA extraction kit


title: BY4741 delta izh2 log phase 2

status: Public on Mar 31 2010

city: Tsukuba

first: Jun

last: Shima

state: Ibaraki

address: 2-1-12 Kannondai

country: Japan

institute: National Food Research Institute

description: BY4741 delta izh2

hyb_protocol: At 45 degree for 16 hr

scan_protocol: GeneChip Scanner

data_processing: GeneChip Operating System (GCOS)

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae BY4741 delta izh2

label_protocol: According to the Affymetrix user's manual

extract_protocol: Hot phenol method

tag: genotype

value: delta izh2

tag: genetic background


title: BY4741 delta izh2 log phase 1

description: BY4741 delta izh2


title: RD-ES

status: Public on Apr 01 2010

type: genomic

city: Tokyo

first: Motohiro

last: Kato

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
RD-ES

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: CNAG/AsCNAR 3.0

molecule: genomic DNA

source_name: Ewing Sarcoma derived cell line, RD-ES

label_protocol: Affymetrix standard protocol

extract_protocol: As per PUREGENE DNA extracting kit

value: RD-ES


title: BY4741 delta eos1 log phase 2

description: BY4741 delta eos1

source_name: S. cerevisiae BY4741 delta eos1

value: delta eos1


title: UTP-ES1

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
UTP-ES1

source_name: Ewing Sarcoma derived cell line, UTP-ES1


title: KP-PN-TTBm2

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
KP-PN-TTBm2

source_name: Ewing Sarcoma derived cell line, KP-PN-TTBm2


title: BY4741 delta eos1 log phase 1

description: BY4741 delta eos1


title: BY4741 log phase 2

source_name: S. cerevisiae BY4741

value: wild-type


title: BY4741 log phase 1


title: SJES-7

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
SJES-7

source_name: Ewing Sarcoma derived cell line, SJES-7


title: SK-N-MC

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
SK-N-MC

source_name: Ewing Sarcoma derived cell line, SK-N-MC

value: SK-N-MC


title: SWR-rep5r

status: Public on Mar 03 2010

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

hyb_protocol: Labeled test and reference cDNAs were mixed with 35 µg of mouse Cot1 DNA, 35 µg of poli-dA in a solution containing 0.1% SDS and 3.5X SSC. Slides were place in closed hybridization chambers and incubated for 16-20 hrs in a water bath at 65°C. Washes in 2X SSC-0.1% SDS, 1X SSC, 0.2X SSC, and 0.05X SSC were performed sequentially, 1-min each.

scan_protocol: Microarrays were quickly dried and scanned at 10-µm resolution in a ScanArray-Lite scanner (Perkin Elmer, MA). PMT was adjusted to obtain maximal signal intensities with minimal saturation

data_processing: Microarray images were saved in TIFF format and extracted as GenePix result (gpr) files using GenePix Pro III software (Molecular Devices, CA).  Data was subjected to print-tip (local) Loess normalization and scale adjustment with the DNMAD tool (http://dnmad.bioinfo.cnio.es) and then filtered/imputed for missing values with the preP tool (http://prep.bioinfo.cnio.es/).

source_name: reference RNA

label_protocol: 12 µg of total RNA were primed with 1 µg of random hexamers plus 1 µg of oligo-dT at 75°C for 10 min, then reversed transcribed at 42°C for 2.5 h with 500 U SuperScript II (Invitrogen), and 0.5 mM each dATP, dCTP, dGTP, 0.2 mM dTTP, and 0.1 mM dUTP-Cy3 (or Cy5, when corresponded).

extract_protocol: Total RNA was extracted with Trizol ® following manufacturer´s protocol

tag: strain

value: FVB

tag: gender

value: male

tag: tissue

value: whole organism

value: newborn

source_name: ovary, mouse, SWR

value: SWR

value: female

value: ovary

value: 8 weeks old


title: SWR-rep4r


title: SJES-5

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
SJES-5

source_name: Ewing Sarcoma derived cell line, SJES-5


title: case 30

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
case 30

source_name: Ewing Sarcoma primary sample, case 30

tag: sample id

value: case 30


title: SWR-rep6r


title: SWR-rep3d


title: SK-N-PI

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
SK-N-PI

source_name: Ewing Sarcoma derived cell line, SK-N-PI

value: SK-N-PI


title: case 28

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
case 28

source_name: Ewing Sarcoma primary sample, case 28

value: case 28


title: SWR-rep1d


title: SK-ES

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
SK-ES

source_name: Ewing Sarcoma derived cell line, SK-ES

value: SK-ES


title: SK-N-LO

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
SK-N-LO

source_name: Ewing Sarcoma derived cell line, SK-N-LO

value: SK-N-LO


title: SJES-2

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
SJES-2

source_name: Ewing Sarcoma derived cell line, SJES-2


title: SCMS-ES-1

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
SCMS-ES-1

source_name: Ewing Sarcoma derived cell line, SCMS-ES-1


title: case 31

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
case 31

source_name: Ewing Sarcoma primary sample, case 31

value: case 31


title: SK-N-FI

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
SK-N-FI

source_name: Ewing Sarcoma derived cell line, SK-N-FI

value: SK-N-FI


title: case 27

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
case 27

source_name: Ewing Sarcoma primary sample, case 27

value: case 27


title: SJES-6

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
SJES-6

source_name: Ewing Sarcoma derived cell line, SJES-6


title: FVB-rep4r

source_name: ovary, mouse, FVB


title: FVB-rep5r


title: SJES-1

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
SJES-1

source_name: Ewing Sarcoma derived cell line, SJES-1


title: case 34

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
case 34

source_name: Ewing Sarcoma primary sample, case 34

value: case 34


title: FVB-rep3r

source_name: reference RNA

value: FVB


title: case 33

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
case 33

source_name: Ewing Sarcoma primary sample, case 33

value: case 33


title: case 24

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
case 24

source_name: Ewing Sarcoma primary sample, case 24

value: case 24


title: case 29

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
case 29

source_name: Ewing Sarcoma primary sample, case 29

value: case 29


title: FVB-rep1d

value: male

value: whole organism

value: newborn


title: FVB-rep2d

value: female

value: ovary

value: 8 weeks old


title: case 38

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
case 38

source_name: Ewing Sarcoma primary sample, case 38

value: case 38


title: SJES-3

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
SJES-3

source_name: Ewing Sarcoma derived cell line, SJES-3


title: C57BL6-rep6r

source_name: ovary, mouse, C57BL6


title: C57BL6-rep5r


title: ES-1-OT

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
ES-1-OT

source_name: Ewing Sarcoma derived cell line, ES-1-OT


title: SJES-8

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
SJES-8

source_name: Ewing Sarcoma derived cell line, SJES-8


title: SWR-rep2d

source_name: ovary, mouse, SWR

value: SWR


title: C57BL6-rep4d


title: BalbC-rep5r

source_name: ovary, mouse, BalbC

value: BalbC


title: BalbC-rep3d


title: C57BL6-rep3d


title: BalbC-rep6r


title: C57BL6-rep2d


title: BalbC-rep4r


title: case 25

description:
We have used anonymous normal references (own-lab-generated) for SNP array analysis.
case 25

source_name: Ewing Sarcoma primary sample, case 25

value: case 25


title: BalbC-rep2d


title: BalbC-rep1d


title: 199_A25siEGFP

status: Public on Mar 01 2010

city: Berlin

first: Oleg

last: Tchernitsa

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite

description: Thirteen PCR fragments for houskeeping genes were spotted in another subgrid and were not taken into processing

hyb_protocol: The two samples of cDNA were synthesized from each RNA probe (20 µg) by reverse transcription with oligo-(dT)primers. The oligo-(dT) primers contained capture sequences that are complimentary to Cy3- or Cy5-fluorescent dyes carrying capture reagents. The cDNA samples carrying the appropriate capture sequences were mixed. The concentration of cDNA, hybridization and washing were carried out according to the kit manual. The second round of hybridization was performed in a reaction mix containing equal amounts of 3DNA capture Reagent Cy3 and 3DNA Capture Reagent Cy5. The composition of the reaction mix, hybridization and washing conditions were as described in the Genisphere instruction manual.

scan_protocol: Microarray images were obtained on an Agilent G2565AA scanner at 10 µm resolution.

data_processing: Imagene software (BioDiscovery, Inc) was used for feature extraction. Standard deviation of all spotted replica was evaluated by SAM analysis and mean of all spotted replica was proccessed further. Global normalization was used to median the center the log-ratios on each array in order to adjust for differences in labeling intensitites of the Cy3 and Cy5 dyes. Lowess intensity dependent normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes. The adjusting factor varied over intensity levels.

organism: Rattus norvegicus

source_name: ROSE199 untreated

label_protocol:
We applied dendrimer technology for cDNA labeling and array hybridization using the 3DNA Expression Array Detection Kit for Microarray (Genisphere). The two samples of cDNA
were synthesized from each RNA probe (20 µg) by reverse transcription with oligo-(dT)primers. The oligo-(dT) primers contained capture sequences that are complimentary to Cy3- or Cy5-fluorescent dyes carrying capture reagents.

growth_protocol:
Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)
supplemented with 10% fetal calf serum, 2 mM L-glutamine and antibiotic (standard medium). ROSE 199 cells are derived from rat ovarian surface epithelium (Adams and Auersperg, 1985).

extract_protocol: Total RNA from cells was prepared from sub-confluent cells with the TRIZOL reagent (Invitrogen) according to the manufacturer’s instructions.

tag: rat ovary surface epithelium cell line

source_name: ROSEA25 transfected with siEGFP

treatment_protocol:
At 24 h prior to transfection,4x104 ROSE-RAS cells were seeded into six-well plates. Transfection of siRNA was carried out using Oligofectamine (Life Technologies) and 0.2 µM siRNA duplex as described previously (Elbashir et al., 2001). Cells were transfected with siRNA twice in
24 h-intervals and analyzed 48 h after the first treatment. We also treated cells with transfection reagents only toprovide an additional control besides transfecting scrambled siRNA duplexes.


title: 199_199empty_vector

source_name: ROSE199 transfected with empty vector

treatment_protocol:
Cell were transfected with expression vector pEF6 (Invitrogen). Stable transfectants were selected in standard medium supplemented
with 10 µg/ml blasticidin. Cells transfected with empty vector served as negative controls.


title: 199_A25siHMGA2

source_name: ROSEA25 transfected with siHMGA2 duplex


title: 199_199HMGA2

source_name: ROSE199 transfected with plasmid expressing HMGA2

treatment_protocol:
Cell were transfected with expression vector pEF6 (Invitrogen) conaining HMGA2 construct. Stable transfectants were selected in standard medium supplemented
with 10 µg/ml blasticidin. Cells transfected with empty vector served as negative controls.


title: 199HMGA2_199

source_name: ROSE199 transfected with HMGA2 expression vector


title: A25siHMGA2_199


title: Col_leaf_100mM NaCl_rep1

city: Wuhan

first: Zhulong

last: Chan

state: Hubei

address: Wuchang District, Moshan

country: China

institute: Wuhan Botanic Garden, Chinese Academy of Sciences

description:
Gene expression data in Col in the presence of salt
CEL data is identical to that assigned GEO accession GSM420238

data_processing: All the Affymetrix data files produced with Affymetrix GCOS software (*.CEL files) were analyzed using Bioconductor, a public source software for the analyses of genomic data rooted in the statistical computing environment R. The data were normalized by robust multioiarray normalization of probe-level data with RMA and analyzed using affylmGUI running on R software.

organism: Arabidopsis thaliana

source_name: Col plant, 100mM NaCl, 6 d

label_protocol: Ten µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Seeds of both transgenic and wild type plants were sown as described above with two replicate pots for each genotype and salt combination. Plants were grown at 23/18 °C in the growth chamber under a short-day cycle (10h light/14 h dark) at 350 μmol m-2s-1 and 70% relative humidity in order to increase seedling leaf area and growth while not promoting bolting. Sampling time was performed at 20 DAS by collecting developed but not senescent leaves (about 0.5cm width × 1.5cm length) from at least 15 seedlings.

extract_protocol: Total RNA was extracted and purified using QIAGEN-RNeasy Mini Kit according to guidelines specified by the manufacturer.

treatment_protocol: Plants subjected to salt stress were watered with NaCl solution which was dissolved in ½ Strength Hoagland Solution. Salt treatment started at 14 DAS . Plants were watered from below to field capacity and then sprayed with the same concentration of NaCl solution from the top, ensuring adequate leaching and preventing excess salinity. The concentrations of NaCl supplementation were increased stepwise by 50 mM every 2 days for each line, to the indicated maximum (0, 100 mM). Plants were then watered every 2 days with or without NaCl at the indicated concentrations. The flats were rotated in the growth chamber everyday to minimize the effect of growth condition.

value: leaf

tag: ecotype

value: Col

value: 20 days after sowing


title: M6PR transgenic_leaf_100mM NaCl_rep2

description: Gene expression data in Ws in the presence of salt

source_name: M6PR plant, 100mM NaCl, 6 d


title: Col_leaf_0mM NaCl_rep1

description:
Gene expression data in Col in the absence of salt
CEL data is identical to that assigned GEO accession GSM420236

source_name: Col plant, 0mM NaCl, 6 d


title: C57BL6-rep1d

source_name: reference RNA

value: FVB


title: Col_leaf_100mM NaCl_rep2

description:
Gene expression data in Col in the presence of salt
CEL data is identical to that assigned GEO accession GSM420239


title: M6PR transgenic_leaf_0mM NaCl_rep2

description: Gene expression data in Ws in the absence of salt

source_name: M6PR plant, 0mM NaCl, 6 d


title: M6PR transgenic_leaf_0mM NaCl_rep1


title: M6PR transgenic_leaf_100mM NaCl_rep1


title: Col_leaf_0mM NaCl_rep2

description:
Gene expression data in Col in the absence of salt
CEL data is identical to that assigned GEO accession GSM420237


title: SK-MEL_AMBX_Rep4

status: Public on Feb 28 2010

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

hyb_protocol: Labeled cRNA targets were fragmented at 94ºC for 20 minutes prior hybridization with arrays at 37ºC during 18 hours. After the hybridization, the bioarrays were washed and bound targets were detected following incubation with Cy5-Streptavidin (GE Healthcare, UK). The bioarrays were washed, dried and protected from light. All samples processed in parallel and the arrays were incubated simultaneously using the same working solution to limit technical variation across the experiments.

scan_protocol: Following the hybridization, bioarrays were scanned immediately in a an arrayWoRx scanner (Applied Precision Inc., WA, USA).

data_processing:
CodeLink Expression Analysis software (GE Healthcare) was used to extract background-subtracted spot intensities from microarray images.
To make experiments comparable, intensity data from different hybridizations were normalized by the quantile method.

label: biotin-NTP

label_protocol: Target labeling and hybridization was performed strictly as recommended by the array manufacturer (GE Healthcare, UK). In brief, the purified and high-quality total RNA was used in reverse transcription reactions to convert messenger RNA (mRNA) in double-stranded cDNA prior to biotin labeling. cRNA was synthesized by in vitro transcription of cDNA and simultaneously labeled with biotin-NTP mix. The samples were filtered to recover biotinilated cRNA.

growth_protocol: Cells were cultivated in RPMI 1640 medium (75cm2 flasks) containing 10% (v/v) FBS, and incubated at 37°C and 5% CO2 in humid atmosphere, under standard procedures.

extract_protocol: Total RNA was isolated from Amblyomin-X-treated and untreated control cells using the TRIzol reagent (Invitrogen, Carlsbad, CA) as recommended by the manufacturer. The integrity of RNA samples was assessed by analysis of 28S/18S rRNA ratios following capillary electrophoresis (2100 Bioanalyser, Agilent Technologies Inc), which should be equal or greater than 1.5.

treatment_protocol: Amblyomin-X was added to a final concentration of 1 uM and cells were incubated for 4 hours prior to RNA isolation.

tag: tissue type

value: malignant melanoma


title: SK-MEL_AMBX_Rep2


title: SK-MEL_AMBX_Rep1


title: SK-MEL_AMBX_Rep3


title: SK-MEL_Control_Rep5

treatment_protocol: Untreated.


title: SK-MEL_AMBX_Rep5


title: MIA_AMBX_Rep6

value: pancreatic carcinoma


title: MIA_AMBX_Rep3


title: SK-MEL_Control_Rep1


title: SK-MEL_Control_Rep4


title: MIA_AMBX_Rep5


title: SK-MEL_Control_Rep2


title: MIA_AMBX_Rep2


title: Control MA148 replicate 2

type: mixed

city: Minneapolis

first: Xiaoxiao

last: Zhang

address: 312 Church St. SE

institute: University of Minnesota

hyb_protocol: A mixture of labeled RNA and DNA was hybridized to a miRNA microarray (Thomson et al), inside a MAUI mixer in a MAUI hybridization system (BioMicro® System, Inc, Salt Lake City, UT, USA).     Thomson, J.M., Parker, J., Perou, C.M., and S.M. Hammond. 2004. A custom microarray platform for analysis of microRNA gene expression. Nat. Methods 1: 47-53. Epub 2004 Sep 29.

scan_protocol: Slides were scanned with a ScanArray 5000 machine (Perkin Elmer®, Waltham, MA, USA).

data_processing: BlueFuse (BlueGenome, Cambridge, UK) was used to quantify pixel intensities.  GeneSpring GX 7.3.1 (Agilent Technologies) was used for data normalization.

source_name: Total RNA  MA148 cells, untreated control

label_protocol: Total RNA was ligated to a synthetic linker, 5’-pCU-DY547-3’.  Reference DNA oligonucleotides (Invitrogen) complementary to a subset of mammalian miRNAs were combined and labeled with a ULYSIS® Alexa Fluor® 647 kit.

growth_protocol: MA148  was maintained in RPMI 1640 with 10% fetal bovine serum. HUVEC  was maintained in endothelial growth medium.

extract_protocol: Trizol® reagent (Invitrogen) was used to extract total RNA from  cells

treatment_protocol: MA148 and HUVEC cells were grown in hypoxia chamber, supplied with 3% O2, for 48 hrs.

label: Alexa Fluor 647

molecule: other

source_name: Reference DNA

tag: sample type

value: synthetic DNA oligos corrresponding to human miRNAs


title: MIA_AMBX_Rep4


title: Control MA148 replicate 1


title: Hypoxia treated MA148 replicate 2

source_name: Total RNA  MA148 cells, hypoxia treated


title: MIA_AMBX_Rep1


title: Hypoxia treated MA148 replicate 1


title: SK-MEL_Control_Rep3


title: Hypoxia treated HUVEC replicate 3

source_name: Total RNA  from HUVEC cells, hypoxia treated

value: HUVEC


title: Hypoxia treated HUVEC replicate 2


title: MIA_Control_Rep6


title: MIA_Control_Rep2


title: Hypoxia treated HUVEC replicate 1


title: Control HUVEC replicate 4

source_name: Total RNA  from HUVEC cells, untreated control


title: MIA_Control_Rep1


title: Control HUVEC replicate 3


title: MIA_Control_Rep3


title: Control HUVEC replicate 2


title: MIA_Control_Rep4


title: Control HUVEC replicate 1


title: MIA_Control_Rep5


title: Cu 2+ growth Replicate1A

city: Valencia

first: Miguel

last: Perez-Amador

state: Valencia

address: Avda. de los Naranjos s/n

country: Spain

institute: Inst. Biologia Molecular y Celular de Plantas (IBMCP-CSIC)

description: Seedlings grown in high Cu2+ (MS media plus 10 µM CuSO4) labelled with Cy5, compared with seedlings grown in low Cu2+ (MS media) labelled with Cy3. Biological replica 1, technical replica 1

hyb_protocol: DNA onto slides was rehydrated by placing the slide upside-down over a water bath at 60°C for 10 s, and snap dry onto a heat block at 65°C. Rehydratation was repeated 3 times. DNA was immobilized by UV light by exposing the slides DNA-side-up to 65 mJ in a UV cross-linker (Stratagene). Slides were then washed twice in 0.1% SDS and 4 times in water, 2 min each wash at RT, and finally dipped in 96% ethanol for 1 min and dried by centrifugation at 2000 rpm 1 min at RT. Slides were prehybridized for 30 min at 42°C with 100 µL of prehybridization solution (6x SSC (Sigma), 1% BSA (Sigma) and 0.5% SDS (Sigma)), under a 60x22 mm coverslip LifterSlip (Erie Scientific) in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were rinsed 5 times in H2O in a slide rack at RT and dried by centrifugation at 2000 rpm 1 min at RT. Slides were hybridized immediately.  Both coupled aa-aRNA (Cy3 and Cy5) were mixed and fragmented in the presence of 20 µg of tRNA (Ambion) and 20 µg of poly(A) (Roche) using the RNA fragmentation Reagent (Ambion) as described by the manufacturer, in a final volume of 10 µL. Fragmented aa-aRNA was used directly in the hybridization mix, which contains of 50 µL deionized formamide (Sigma), 30 µL 20x SSC, 5 µL 100x Denhardt´s solution (Sigma), and 5 µL 10% SDS in a final volume of 100 µL. Hybridization mixture was denatured at 95 °C for 5 min, spun briefly, and applied by capillary between a pre-treated slide (see above) and a 60x42 mm coverslip LifterSlip. Slides were incubated o/n at 37°C in a microarray hybridization chamber (ArrayIt Hybridization Cassette, Telechem). Slides were washed sequentially once in 1x SSC 0.1% SDS 5 min at 30°C; once in 0.2x SSC 0.1% SDS 5 min at 30°C; twice in 0.1x SSC 2 min each at 30°C; and finally 0.01x SSC 10 sec at RT. Slides were dried by centrifugation at 2000 rpm 1 min at RT.

scan_protocol: Hybridized microarray slides were scanned at 532-nm for the Cy3 and 635-nm for the Cy5 dyes, with a GenePix 4000B scanner (Axon Molecular Devices, Sunnyvale CA), at 10-nm resolution and 100% laser power.

data_processing: Spot intensities were quantified using GenePix Pro 6.0 microarray-analysis software (Axon Molecular Devices, Sunnyvale CA). Spots with a net intensity in both channels lower than the median signal background plus twice standard deviations were removed as low signal spots.  Data were normalized by median global intensity using the GenePix Pro 6.0 software.

source_name: Seedlings grown in high Cu2+, Biological replica 1, technical replica 1

label_protocol: RNA was amplified using the MessageAmp II aRNA Amplification kit (Ambion), basically as described by the manufacturer. 5-(3-aminoallyl)-UTP (aa-UTP) (Ambion) was incorporated into the amplified RNA (aRNA) at ratio 1:1 with UTP. After purification 7.5 µg of aminoallyl-aRNA (aa-aRNA) were used in a coupling reaction with either fluorescent Cy3 or Cy5 as reactive N-hydroxyl succinimidal dyes (NHS-dyes) (Amersham Pharmacia Biotech, Piscataway, NJ). For this, each aliquot of Cy3 or Cy5 were dissolved in 20 µL of DMSO and used in four coupling reactions. aa-aRNA was dissolved in 15 µL of freshly-made 0.1 M NaCO3 pH 9.0, and mixed with 5 µl of either Cy-3 or Cy-5 dye. Coupling was allowed for 1 h at RT in the dark. Reaction was stopped with 35 µL of 100 mM sodium acetate pH 5.2 and incubated 5 min in the dark. Fluorescent aa-aRNA was purified using a MegaClear purification column (Ambion) as described by the manufacturer. Coupled aa-aRNA (250-300 pmol Cy dye in 5-7 µg aa-aRNA) was dried in a speedvac and dissolved in 2.5 µL of filtered water.

growth_protocol: Seeds were surface sterilized, induced to synchronize germination and incubated in either standard MS medium plates (Murashige and Skoog, 1962) (low Cu2+) or MS supplemented with 10 µM CuSO4 (high Cu2+), at 23°C in a 16h light/8h dark photoperiod.

extract_protocol: Total RNA was extracted from frozen seedlings, using the Total quick RNA kit (Talent srl, Trieste, Italy).

treatment_protocol: Seeds were allow to germinate and seedlings were harvested 8 days later

tag: 8-day-old seedlings

source_name: Seedlings grown in low Cu2+, Biological replica 1, technical replica 1


title: Cu 2+ growth Replicate2A

description: Seedlings grown in high Cu2+ (MS media plus 10 µM CuSO4) labelled with Cy5, compared with seedlings grown in low Cu2+ (MS media) labelled with Cy3. Biological replica 2, technical replica 1

source_name: Seedlings grown in high Cu2+, Biological replica 2, technical replica 1

source_name: Seedlings grown in low Cu2+, Biological replica 2, technical replica 1


title: Cu 2+ growth Replicate2B

description: Seedlings grown in high Cu2+ (MS media plus 10 µM CuSO4) labelled with Cy5, compared with seedlings grown in low Cu2+ (MS media) labelled with Cy3. Biological replica 2, technical replica 2

source_name: Seedlings grown in high Cu2+, Biological replica 2, technical replica 2

source_name: Seedlings grown in low Cu2+, Biological replica 2, technical replica 2


title: Cu 2+ growth Replicate1B

description: Seedlings grown in high Cu2+ (MS media plus 10 µM CuSO4) labelled with Cy5, compared with seedlings grown in low Cu2+ (MS media) labelled with Cy3. Biological replica 1, technical replica 2

source_name: Seedlings grown in high Cu2+, Biological replica 1, technical replica 2

source_name: Seedlings grown in low Cu2+, Biological replica 1, technical replica 2


title: Cu 2+ growth Replicate3A

description: Seedlings grown in high Cu2+ (MS media plus 10 µM CuSO4) labelled with Cy5, compared with seedlings grown in low Cu2+ (MS media) labelled with Cy3. Biological replica 3, technical replica 1

source_name: Seedlings grown in high Cu2+, Biological replica 3, technical replica 1

source_name: Seedlings grown in low Cu2+, Biological replica 3, technical replica 1


title: Cu 2+ growth Replicate3B

description: Seedlings grown in high Cu2+ (MS media plus 10 µM CuSO4) labelled with Cy5, compared with seedlings grown in low Cu2+ (MS media) labelled with Cy3. Biological replica 3, technical replica 2

source_name: Seedlings grown in high Cu2+, Biological replica 3, technical replica 2

source_name: Seedlings grown in low Cu2+, Biological replica 3, technical replica 2


title: Hypoxia treated HUVEC replicate 4


title: Raft_pLXSN_TNF Swap #2

status: Public on Jan 15 2010

city: Sao Paulo

first: Enrique

last: Boccardo

state: Sao Paulo

address: R. João Julião, 245 1º andar

institute: Ludwig Institute for Cancer Research Ltd

description:
PHK = Primary human Keratinocytes
PHK were transduced with pLXSN empty vector and used to seed organotypic cultures.
Cultures were treated with 2 nM human recombinant TNF for 72 hours before harvesting.
Total RNA from monolayer cultures of normal, untreated, PHK was used as reference.

hyb_protocol: Hibridization - Solution: 5 X SSC; 0,1% SDS; 4 ug poly A DNA; 4 ug Cot1 DNA; 5X Denhardts ; 10 ug Salmon sperm, Deyonized formamide 40% / Temperature:42 / Time:16-24hs / Touch Down: 70-55-50-42 Washing - Round 1 - Solution: 2X SSC 0,1% SDS / Temperature:42 / Time:4 min / Washing Number: 1 Washing - Round 2 - Solution: 0,1 SSC 0,1% SSC / Temperature:42 / Time:4 min / Washing Number: 1 Washing - Round 3 - Solution: 0,1X SSC / Temperature:42 / Time:enxaguar / Washing Number: 3 Washing - Round 4 - Solution: 0,1X SSC / Temperature:42 / Time:4 min / Washing Number: 4 Washing - Round 5 - Solution: 0,1X SSC / Temperature:42 / Time:enxaguar lâm por lâm / Washing Number: 5

scan_protocol: Hardware: Perkinelmer / Software: ScanArray

data_processing: Lowesss

source_name: PHK _ pLXSN vector_TNF_72hours

label_protocol: A two-round linear amplification procedure based on T7-driven amplification was carried out. Amplified RNA was then used in a transcriptase reverse reaction into cDNA in the presence of Cy3- or Cy5-labeled dCTP.

extract_protocol: Trizol

tag: cell type

value: primary human keratinocyte

source_name: PHK (Reference)

extract_protocol: kit Pico Pure RNA Isolation Kit


title: Raft_pLXSN_TNF Swap #3


title: Raft_pLXSN_TNF #2


title: Raft_pLXSN_TNF Swap #1


title: Raft_pLXSN Swap #3

description:
PHK = Primary human Keratinocytes
PHK were transduced with pLXSN empty vector and used to seed organotypic cultures.
Total RNA from monolayer cultures of normal, untreated, PHK was used as reference.

source_name: PHK _ pLXSN vector


title: Raft_pLXSN Swap #2


title: Raft_pLXSN_TNF #1


title: Raft_pLXSN #3


title: 070419_ETOH-34

status: Public on Jan 29 2010

city: Albuquerque

first: Daniel

last: Savage

state: NM

address: 1University of New Mexico

department: Neurosciences

institute: University of New Mexico

description: Gene expression data from placenta of ethanol consuming dams

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on affymetrix  rat 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: placenta G20 ETOH

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

growth_protocol: Dams were consuming 5%ethanol in 0.066% saccharine solution or saccharine solution alone (controls)  during their pregnancy, averaging 16ml during a 4hr interval every day.

extract_protocol: Extraction of total RNA was performedwith RNeasy (Qiagen, Valencia,CA) according to the manufacturer's instructions.

treatment_protocol: On Gestational day 20, placentae were removed by cesarian section, saline perfused, frozen in liquid nitrogen and stored at -80C

value: placenta

tag: agent

value: 5% ethanol in 0.066% saccharine solution


title: 070314_ETOH-28


title: Raft_pLXSN_TNF #3


title: 070419-control-25

description: Gene expression data from placenta of control dams

source_name: placenta G20 control

value: saccharine solution alone (control)


title: Raft_pLXSN #1


title: 070419-control-37


title: 070419_ETOH-45


title: Raft_HPV16E7_E26G_TNF #3

description:
PHK = Primary human Keratinocytes
PHK were transduced with pLXSN-HPV16_E7_E26G(mutant) vector and used to seed organotypic cultures. Cultures were treated with 2nM human recombinant TNF for 72 hours before harvesting.
Total RNA from monolayer cultures of normal, untreated, PHK was used as reference.

source_name: PHK expressing HPV16E7 mutant E26G_TNF_72hours


title: 070314_ETOH-20


title: Raft_HPV16E7_E26G_TNF #2


title: Raft_HPV16E7_E26G_TNF Swap #1


title: Raft_HPV16E7_E26G_TNF Swap #2


title: Raft_pLXSN Swap #1


title: Raft_pLXSN #2


title: Raft_HPV16E7_E26G_TNF Swap #3


title: Raft_HPV16E7_E26G Swap #3

description:
PHK = Primary human Keratinocytes
PHK were transduced with pLXSN-HPV16_E7_E26G(mutant) vector and used to seed organotypic cultures.
Total RNA from monolayer cultures of normal, untreated, PHK was used as reference.

source_name: PHK expressing HPV16E7 mutant E26G


title: Raft_HPV16E7_E26G_TNF #1


title: Raft_HPV16E7wt #3 Swap

description:
PHK = Primary Human Keratinocytes.
PHK were transduced with pLXSN-HPV16E7wt vector and used to seed organotypic cultures.
Total RNA from monolayer cultures of normal, untreated, PHK was used as reference.

source_name: PHK expressing HPV16E7wt


title: Raft_HPV16E7_E26G #2


title: Raft_HPV16E7wt_TNF #1

description:
PHK = Primary human Keratinocytes
PHK were transduced with pLXSN-HPV16E7wt vector and used to seed organotypic cultures. Cultures were treated with 2 nM human recombinant TNF for 72 hours before harvesting.
Total RNA from monolayer cultures of normal, untreated, PHK was used as reference.

source_name: PHK expressing HPV16E7wt_TNF_72hours


title: Raft_HPV16E7_E26G Swap #2


title: Raft_HPV16E7wt #2 Swap


title: Raft_HPV16E7_E26G #3


title: Raft_HPV16E7wt_TNF Swap #3


title: Raft_HPV16E7_E26G #1


title: Raft_HPV16E7wt #1


title: Raft_HPV16E7wt_TNF Swap #1


title: Raft_HPV16E7wt_TNF #3


title: 070314-control-48


title: Raft_HPV16E7_E26G Swap #1


title: Raft_HPV16E7wt_TNF #2


title: Flutamide treated male at GD 18, biological rep2

city: Quebec

first: Eva

last: Bresson

state: Quebec

address: 2705, boul. Laurier, bloc T-1-49

department: Reproduction, santé périnatale et santé de l'enfant

country: Canada

institute: CHUL-CHUQ-Laval University

description: Gene expression data from flutamide treated male fetal lung at GD 18

hyb_protocol: 15ug of fragmented cRNA was hybridized for 16 h at 45°C with constant rotation, using a mouse oligonucleotide array MOE430 2.0 (Genechip, Affymetrix, Santa Clara, CA)

scan_protocol: Chips were scanned using a GeneChip Scanner 3000 G7 (Affymetrix) enabled for High-Resolution Scanning

data_processing: The analysis was performed using the affylmGUI Graphical User Interface for the limma microarray package

source_name: fetal lung of flutamide treated male at GD18

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20ug total RNA consisting of a pool of total RNA from 3  fetuses of 3 different litters for each monoplicate. Each replicate was composed of RNA samples from different individuals (biological triplicate).

extract_protocol: Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions. Each sample was then purified on a CsCl gradient.

treatment_protocol: Pregnant females received a daily sub-cutaneous injection of 200 µl of flutamide (1 mg) or vehicule solution from GD10 to the day prior to harvesting day. Pregnant females were sacrificed by exposure to CO2 at GD17 or GD18.

value: BALB/c

value: RNA samples from three fetuses of the same sex but from distinct litters were  pooled

value: fetal lung

tag: age

value: fetal gestional day 18


title: Vehicule (control) female at GD 18, biological rep2

description: Gene expression data from female fetal lung at GD 18

source_name: fetal lung of female at GD18


title: Raft_HPV16E7wt_TNF Swap #2


title: Vehicule (control) female at GD 18, biological rep3


title: Vehicule (control) male at GD 18, biological rep3

description: Gene expression data from male fetal lung at GD 18

source_name: fetal lung of male at GD18


title: Raft_HPV16E7wt #3


title: Vehicule (control) male at GD 17, biological rep2

description: Gene expression data from male fetal lung at GD 17

source_name: fetal lung of male at GD17

value: fetal gestional day 17


title: Vehicule (control) female at GD 17, biological rep3

description: Gene expression data from female fetal lung at GD 17

source_name: fetal lung of female at GD17


title: Flutamide treated male at GD 17, biological rep1

description: Gene expression data from flutamide treated male fetal lung at GD 17

source_name: fetal lung of flutamide treated male at GD17


title: Vehicule (control) male at GD 18, biological rep2


title: Vehicule (control) male at GD 17, biological rep1


title: Vehicule (control) male at GD 17, biological rep3


title: Vehicule (control) female at GD 17, biological rep2


title: Flutamide treated male at GD 18, biological rep3


title: Vehicule (control) male at GD 18, biological rep1


title: Flutamide treated male at GD 18, biological rep1


title: Flutamide treated male at GD 17, biological rep3


title: Vehicule (control) female at GD 18, biological rep1


title: Female; 30d, rep2

status: Public on Jan 01 2010

city: Oxford

first: Steven

last: Sinkins

address: South Parks Rd

department: Department of Zoology

country: United Kingdom

institute: University of Oxford

hyb_protocol: Labelled cRNA was then purified and quantified before hybridization to the arrays using Agilent Technologies’ Gene Expression Hybridization Kit, SureHyb chambers, Microarray Hybridization oven and standard protocols. Hybridized arrays were washed with Agilent Gene Expression Wash Buffers (without the addition of Triton X102) and Stabilization and Drying Solution.

scan_protocol: Microarrays were scanned and feature extraction undertaken by technicians at Oxford Gene Technology. Scans were at 5 µm resolution using the extended dynamic range feature of the Agilent Technologies’ DNA microarray scanner (G2505B)

data_processing: Feature Extraction software (version 9.5.3.1; Agilent Technologies) was used to analyze scanned array image files according to Agilent’s One-colour Gene Expression protocol (GE1-v5_95_Feb07).

organism: Anopheles gambiae

source_name: Pool 5 females (head & thorax only); 30d age

label_protocol: All arrays were experiments were conducted acording to Agilent Technologies' One-colour Microarray-based Gene Expression Analysis protocol (version 5.7). 1 µg of total RNA and 5µl of 1:5000 dilution Agilent One-colour Spike-in mix were amplified and labelled using the Quick Amp Kit protocols (Agilent Technologies) following manufacturer's protocols.

growth_protocol: Anopheles gambiae (strain G3) was reared under standard insectary conditions. Adults were given 10% sucrose solution ad libitum, however no blood meals were provided. Adults emerging within a 24h period were considered a single age class and each age class allocated to separate cages. Adult male and female mosquitoes were collected at 0 (≤ 24 h), 5, 10, 15, 20, 25 and 30 days post-eclosion. The abdomen was dissected and discarded. The heads and thoraces were stored pooled from 5 indivduals.

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

tag: sex

value: Female


title: Female; 20d, rep2

source_name: Pool 5 females (head & thorax only); 20d age


title: Raft_HPV16E7wt #2


title: Vehicule (control) female at GD 17, biological rep1


title: Raft_HPV16E7wt #1 Swap


title: Female; 20d, rep1


title: Female; 30d, rep1


title: Female; 10d, rep2

source_name: Pool 5 females (head & thorax only); 10d age


title: Female; 10d, rep1


title: Female; 0d, rep1

source_name: Pool 5 females (head & thorax only); 0d age


title: Female; 0d, rep2


title: Male; 30d, rep2

source_name: Pool 5 males (head & thorax only); 30d age

value: Male


title: Male; 20d, rep1

source_name: Pool 5 males (head & thorax only); 20d age


title: Male; 10d, rep2

source_name: Pool 5 males (head & thorax only); 10d age


title: Shocked with 8% ethanol for 10 min vs. Shocked with 8% ethanol for 10 min hyb12

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

country: Netherlands

institute: NIZO food research

hyb_protocol: Hybridization buffer (Agilent In Situ Hybridization Kit Plus) was added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers at 65 degrees Celcius for 17 h. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. BASE2 plugin used for Lowess normalization. Data not normalized across slides.  Normalization across slides performed internally with Cyber T.

organism: Lactiplantibacillus plantarum WCFS1

source_name: Bacterial culture shocked with 8% ethanol for 10 min, replicate 2

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: For ethanol adapted and control cultures: growth in MRS broth with 8% ethanol or 8% H2O (control) at 20 degrees Celcius until OD600 is 1.0. For ethanol shocked cultures: control cultures harvested at OD600 is 1.0 were shocked for 10 or 30 min with 8% ethanol.

extract_protocol: Cultures were lysed by beat-beating and total RNA was isolated by subsequent fenol extraction

treatment_protocol: Harvested cultures were quenced in extraction mix containing Phenol/Chloroform, SDS, Na-acetate, glass-beads and TE buffer.

source_name: Bacterial culture shocked with 8% ethanol for 10 min, replicate 1


title: Male; 30d, rep1


title: Male; 20d, rep2


title: Control (no ethanol) vs. 8% ethanol adapted for 24h hyb7

source_name: Bacterial culture 8% ethanol adapted for 24h, replica 1

source_name: Control (no ethanol), replicate 2


title: Shocked with 8% ethanol for 10 min vs. Shocked with 8% ethanol for 30 min hyb10

source_name: Bacterial culture shocked with 8% ethanol for 30 min, replicate 2


title: Shocked with 8% ethanol for 30 min vs. Shocked with 8% ethanol for 30 min hyb9

source_name: Bacterial culture shocked with 8% ethanol for 30 min, replicate 1


title: Shocked with 8% ethanol for 10 min vs. Shocked with 8% ethanol for 30 min hyb3


title: 8% ethanol adapted for 24h vs. Shocked with 8% ethanol for 30 min hyb6

source_name: Bacterial culture 8% ethanol adapted for 24h, replica 2


title: Male; 10d, rep1


title: 8% ethanol adapted for 24h vs. 8% ethanol adapted for 24h hyb5


title: Control (no ethanol) vs. 8% ethanol adapted for 24h hyb4

source_name: Control (no ethanol), replicate 1


title: Male; 0d, rep2

source_name: Pool 5 males (head & thorax only); 0d age


title: Male; 0d, rep1


title: Control (no ethanol) vs. Shocked with 8% ethanol for 10 min hyb1


title: Shocked with 8% ethanol for 30 min vs. Shocked with 8% ethanol for 10 min hyb11


title: Shocked with 8% ethanol for 30 min vs. Control (no ethanol) hyb8


title: Unaffected ileum subject N34 NI

city: St Louis

first: Rekha

last: Meyer

state: MO

address: 4320 Forest Park Av

institute: Washington University School of Medicine

hyb_protocol: The resulting probes were hybridized to Agilent Whole Human genome Arrays, using established protocals.

scan_protocol: Arrays are scanned on Axon scanner 4000B (Moleculer Devices, Sunnyvale, CA) to detect Cy3 and Cy5 fluorescence. GenePix Pro 6.1 acquisition and analysis software is used to visualize and analyze the 16-bit TIFF files generated by the scanner

data_processing: A primary statistical analysis of the array data was performed using the significance analysis of microarrays (SAM) procedure.  These analyses were performed on log-transformed mean signal intensities.  SAM assignes a gene-specific t-test (q-value) based on changes in gene expression relative to the standard deviation of repeated measurements for that gene.  the critearia set for differences between groups in the SAM analysis q<0.05, fold change <0.5 or >2.

source_name: macroscopic disease unaffected ileum, specimen from initial total colectomy

label_protocol: The test ileal RNA and a common reference ileal RNA (NOD2s, non IBD) were labled using the Agilent low RNA input linear amplification kit.

growth_protocol: Surgically resected tissue samples were collected from recruited patients.  Diagnosis of Chron's disease was made according to conventional clinical and pathological criteria.  Information about smoking and medication history was also collected from the patients.  Biopsies of macroscopically disease affected and unaffected areas of ileal mucosa were collected from fresh pathologic specimens using Radial Jaw™ 4 large capacity biopsy forceps.  Biopsies of ileal mucosa were also collected from fresh pathological specimens of patients without inflammatory bowel disease undergoing either a right or hemicoletomy or subtotal colectomy for colonic neoplasm or colonic inertia.  A minimum of 4 biopsies were taken within a 2x2 cm2 area from each region.

extract_protocol: RNA samples were amplified using Agilent Linear Ampilfication Kit (Agilent Technologies, CA). 50-250 ng total RNA was mixed with T7 promoter primer in a total volume of 5.8 ul before heating at 65oC for 10 min. 4.4 ul cDNA master mix containing 2 ul 5X first strand buffer, 1 ul 0.1 M DTT, 0.5 ul 10 mM dNTP mix, 0.6 ul MMLV RT and 0.3 ul RNaseOUT were added. The reaction mix was incubated at 40oC for 2 hr and stopped by heating at 65oC for 15 min before cooling and adding 0.5 ul of either 10 mM Cy3-CTP or Cy5-CTP and 14.5 ul transcription master mix containing 3.83 ul nuclearase-free water, 5 ul 4x transcription buffer, 2 ul NTP mix, 1.6 ul 50 % PEG, 0.12 ul RNaseOUT, 0.15 ul inorganic pyrophosphatase and 0.3 ul T7 RNA polymerase. The mix was incubated at 40 oC for 2 hr. The resulting cRNA was purified using RNeasy kit (Qiagen). 1 ug Cy3- and Cy-5 labeled cRNA was mixed and fragmented according to the Agilent Technologies protocol. After overnight hybridization, the arrays were washed and dried according to the commercial protocol.

treatment_protocol: Tissue biopsies were immediately placed in RNA stabilization solution and archived at 80°C.

tag: nod2 genotype

value: WT/WT

tag: nod2 risk alleles (r = risk allele, nr= not risk allele)

value: NOD2nr  control patient

tag: smoking history

value: no smoking history prior

tag: tnf infusion

value: no anti-TNF medication history prior

tag: disease state

value: control

value: unaffected ileum

source_name: macroscopic disease unaffected ileum, specimen from initial right colectomy

value: NOD2 nr control patient


title: Unaffected ileum subject N15 NI

value: NOD2nr control patient


title: Unaffected ileum subject N33 NI


title: Affected ileum subject CD-312 II

source_name: macroscopic disease affected ileum, specimen from initial ileocolic resection

value: InsC/InsC

value: Crohn's disease

value: affected ileum


title: Unaffected ileum subject N13 NI


title: Shocked with 8% ethanol for 30 min vs. Control (no ethanol) hyb2

tag: strain


title: Unaffected ileum subject CD-312 NI

source_name: macroscopic disease unaffected ileum, specimen from initial ileocolic resection

tag: tissue


title: Affected ileum subject CD-256 II


title: Affected ileum subject CD-235 II

value: NOD2r (1 allele)

value: no anti TNF medication history prior


title: Unaffected ileum subject CD-235 NI


title: Unaffected ileum subject CD-19 NI

source_name: macroscopic disease unaffected ileum, resection specimen from initial ileocolic resection


title: Unaffected ileum subject CD-256 NI

source_name: macroscopic disease unaffected ileum, specimen from initial ileocolic resection.


title: Affected ileum subject CD-19 II

source_name: macroscopic disease affected ileum, resection specimen from initial ileocolic resection


title: Affected ileum subject CD-15 II


title: Affected ileum subject CD-22 II


title: NSC_FOXO_WT-3

city: Boston

first: Haoqiang

last: Ying

state: MA

address: 44 Binney St.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

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

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

data_processing: Arrays were normalized using MAS5

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

extract_protocol: Trizol extraction of total RNA followed by Rneasy column cleanup was performed according to the manufacturer's instructions.

tag: cell line

value: FOXO WT


title: E10-Gfp, biological rep3

city: BoSTON

first: jining

last: lu

address: 715 Albany street R304

institute: Boston University

description: Gene expression data fromE10 cell with control lentivirus

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

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

source_name: E10 cells with control lentivirus

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

growth_protocol: Murine non-transformed lung epithelial cells (E10) were grown in DMEM with 10% FBS and antibiotics in 6 well plates.

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

treatment_protocol: Lentiviral infections were performed when cells reached 80%–90% confluency.


title: E10-miR-129, biological rep1

description: Gene expression data from E10 cell infected with miR-129 over-expressing lentivirus

source_name: E10 cells with high expression of miR-129


title: Unaffected ileum subject CD-22 NI


title: E10-miR-129, biological rep2


title: E10-Gfp, biological rep1


title: NSC_FOXO_NULL-2

value: FOXO null


title: E10-miR-129, biological rep3


title: Unaffected ileum subject CD-15 NI


title: E10-Gfp, biological rep2


title: NSC_FOXO_NULL-3


title: NSC_FOXO_WT-2


title: NSC_FOXO_NULL-1


title: Oga Fed L4, biological replicate 1

city: Bethesda

first: Michael

last: Krause

state: MD

address: 5 Center Drive

department: LMB/NIDDK

institute: NIH

hyb_protocol: C. elegans whole genome expression array chips were washed and stained in the Affymetrix Fluidics Station 400s

scan_protocol: Chips were scanned with an Affymetrix Scanner with standard settings

data_processing: Data was analyzed by Micrarray Suite 5.0 (MAS5) and by RMA using the program Partek

organism: Caenorhabditis elegans

source_name: oga mutant L4 animal

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from the total amplified cDNA reaction

growth_protocol: Fed L4 larval stage animals were isolated from wild type and mutant strains

extract_protocol: Trizol extraction of total RNA from 20 L4 animals was performed and cDNA generated and amplified with T7 polymerase one round as described in Fukushige et al., 2006

treatment_protocol: Fed L4 animals were wild type or one of two mutant strains: loss of the O-GlcNAc transferase ogt-1(ok430) and loss of the O-GlcNAcase oga-1(ok1207)

tag: stage

value: L4 larvae


title: Oga Fed L4, biological replicate 2

source_name: oga mutant L4 animall


title: Oga Fed L4, biological replicate 3


title: NSC_FOXO_WT-1


title: Pancreas of PND3 Glis3 mutant mice Vs. WT

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Sample contains RNA from 2 different Glis3 mutant mice

hyb_protocol: For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer ol

scan_protocol: Slides were washed as indicated in the Agilent 60-mer oligo microarray processing protocol and then scanned with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters.

data_processing: Data was obtained using the Agilent Feature Extraction software (v8.1), using defaults for all parameters and loaded into the Rosetta Resolver® system (v6.0) (Rosetta Biosoftware, Kirkland, WA).

source_name: Glis3 mutant pancreas, PND3 mice

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Qiagen RNA easy mini kit with on-column DNAseI treatment

value: post natal day (PND) 3

value: pancreas

source_name: WT Pancreas, PND3 mice


title: Ogt Fed L4, biological replicate 3

source_name: ogt mutant L4 animal


title: Pancreas of PND3 WT mice VS Glis3 Mutant

description: Sample contains RNA from 2 different WT mice


title: Ogt Fed L4, biological replicate 2


title: WT Fed L4, biological rep3

source_name: Wild Type L4 animal

value: wild type


title: Ogt Fed L4, biological replicate 1


title: WT Fed L4, biological rep1


title: WT Starved L1, biological rep2

source_name: Wild Type L1 animal

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA

growth_protocol: Embryos were isolated from wild type and mutant gravid adults by bleach treatment and shaken gently with good aeration in sterile buffer to hatch and collected 48 hours later.

extract_protocol: Trizol extraction of total RNA was performed according to standard protocols

treatment_protocol: Starved L1 animals were wild type or one of two mutant strains: loss of the O-GlcNAc transferase ogt-1(ok430) and loss of the O-GlcNAcase oga-1(ok1207)

value: L1 larvae


title: Biopsy 1, Colon sample

hyb_protocol: 45 min, 42C Prehybridization in solution (1% bovine serum albumine, 5xSSC, 0.1% sodium dodecyl sulfate), washed and dried. Hybridization overnight at 42C in Easyhyb buffer (Roche). Washed twide in 2xSSC and 0.2% sodium dodecyl sulfate, once in 0.5% SSC and twice in 0.2% SSC. All at 37C.

scan_protocol: Arays were scanned using a SacnArray Express 4000 scanner (Perkin Elmer). Quantification was performed using the Imagene software (v4.2, BioDiscovery)

data_processing: Background corrected, log2 ratio determined (Cy5/Cy3).  No further processing performed.  Data as submitted was analyzed by non-parametric methods.

organism: Lactiplantibacillus plantarum

source_name: Colon Sample patient 1

label_protocol: reverse transcription assay (GIBCO BRL) with incorporation of FluoroLink Cy3/Cy5 dUTP (Amersham Biosciences), filtering over Autoseq G50 columns (Amersham Biosciences)

growth_protocol: DNA: o/n culture in MRS at 37C

extract_protocol: DNA: Fast DNA spin kit for soil (bio101) RNA: from biopsy specimens

treatment_protocol: RNA and DNA: none

tag: source

value: colon

source_name: reference


title: Oga starved L1, biological replicate 2

source_name: oga mutant L1 animall


title: Oga starved L1, biological replicate 3

source_name: oga mutant L1 animal


title: WT Starved L1, biological rep3


title: Colony Biofilm Replicate 3

city: SHEFFIELD

first: Joe

last: Latimer

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

institute: University of Sheffield

description: This sample represents two microarray slides, which were each hybridised with Cy3 only

hyb_protocol: Equal quantities of RNA (at least 6 μg) from control and test cultures were labelled using nucleotide analogues of dCTP containing either Cy3 or Cy5 fluorescent dyes.  cDNA synthesis was carried out using 12 μg of RNA, primed with 9 μg pd(N)6 random hexamers (Amersham Biosciences).  Annealing was accomplished by incubation for 10 min at 65oC followed by 10 min at room temperature and 2 min on ice.  Reaction mixtures (20 μl) containing 0.5 mM dATP, dTTP and dGTP, 0.2 mM dCTP, 0.1 mM DTT (Invitrogen) and 1 mM Cy3-dCTP or Cy5-dCTP were incubated for 2 h at 42 oC with 200 units of Superscript II RNase-H Reverse Transcriptase (Invitrogen).  The reaction was terminated with 1 mM NaOH and heated to 65 oC for 10 min to hydrolyse the RNA.  This was then neutralised with 1 M HCl and 1 M TE (pH 8).  cDNA was then purified using a PCR purification kit (Qiagen) to remove unincorporated dNTPs, dye and primers.  cDNA was eluted in 30 μl elution buffer (Qiagen, supplied in kit).  Equal volumes of cDNA were combined and evaporated for approximately 30 min in a SPD 121P SpeedVac® (Thermo Savant, Waltham, MA, USA)

scan_protocol: Images of microarrays were captured by scanning slides using an Affymetrix 428 scanner using the Affymetrix 428 scanner software package (version 1.0).

data_processing: The average fluorescent signal intensity and local background correction for each spot were obtained using commercially available software from Biodiscovery Inc (Imagene, version 4.0 and Genesight, version 3.5).  Spots with a signal intensity lower than the background signal or those with blemishes were omitted from subsequent analysis.  The mean values from each channel were then log2 transformed and normalised using the LOWESS method to remove intensity-dependent effects in the log2 (ratios) values.  The Cy3/Cy5  (or, for replicates 3 and 4, Cy3/Cy3 ratio) fluorescent ratios were calculated form the normalised values.  Data from independent experiments were combined.  Significance analysis of the data used the Student’s t test to determine the probability that the average of the experimental replicates was significantly different from the average of the control replicates. p-values for the data were calculated by treating each slide as a repeat using Genesight.

organism: Escherichia coli

source_name: Escherichia coli Colony Biofilm Interior

growth_protocol: Biofilms were grown on nylon membranes using agar as the source of nutrients and water.  Aliquots of 10 ml Luria agar were transferred to petri dishes to produce layers of agar approximately 3 mm in depth.  Nylon membrane filters (47 mm diameter) with a 0.2 μm pore size (Whatman) were autoclaved in Milli-Q water, dried and placed on the agar surface.  A 100 μl aliquot of an overnight culture (approximately 108 cells) was applied to the membrane as a single spot and allowed to dry.  All of these steps were performed on a level table so as not to introduce unwanted gradients.  Dishes were then inverted and incubated at 37 oC for 24 h.

extract_protocol: Cells were harvested by centrifugation at 5,000 g for 5 min.  Total RNA was purified using the RNeasy Mini kit (Qiagen) according to the supplier’s protocol (the composition of the RNeasy solutions are unknown).  The supernatant was decanted and 200 μl of TE buffer (10 mM Tris, 1 mM EDTA in DEPC-treated water, pH 8) plus lysosyme (Sigma) was used to resuspend the pellet.  This was mixed vigorously and incubated with intermittent shaking for 5 min at room temperature.  Buffer RLT (700 μl) with β-mercaptoethanol (10 μl of 14.3 M β-mercaptoethanol per 1 ml RTL) was then added to the solution.  The lysate was then mixed with 500 μl of absolute ethanol before applying the solution to an RNeasy Mini column.  This was then centrifuged for 15 s at 8,000 x g.  Buffer RW1 (700 μl) was applied to the column and centrifuged to wash the RNA.  At this point an RNase-free DNase on-column digest (Qiagen) was carried out, before the wash process was repeated twice with 500 μl of RPE buffer.  The RNA was eluted twice in one 30 μl volume of RNase-free water and stored at -70 oC.

treatment_protocol: Biofilms were individually removed from the incubator and, using a small scalpel blade and sterile forceps, the distinctive outer perimeter of biofilm growth was cut away from the rest of the biofilm.  The two resulting sections of membrane were submerged in separate volumes of RNAprotect Bacteria Reagent and vortexed to release the cells.  The sections of membrane were then removed from the resulting suspension before RNA extraction.

source_name: Escherichia coli Colony Biofilm Perimeter


title: Colony Biofilm Replicate 2

description: This sample represents one microarray slide, which was hybridised with Cy3 and Cy5

label_protocol: Equal quantities of RNA (at least 6 μg) from control and test cultures were labelled using nucleotide analogues of dCTP containing either Cy3 or Cy5 fluorescent dyes.    cDNA synthesis was carried out using 12 μg of RNA, primed with 9 μg pd(N)6 random hexamers (Amersham Biosciences).  Annealing was accomplished by incubation for 10 min at 65oC followed by 10 min at room temperature and 2 min on ice.  Reaction mixtures (20 μl) containing 0.5 mM dATP, dTTP and dGTP, 0.2 mM dCTP, 0.1 mM DTT (Invitrogen) and 1 mM Cy3-dCTP or Cy5-dCTP were incubated for 2 h at 42 oC with 200 units of Superscript II RNase-H Reverse Transcriptase (Invitrogen).  The reaction was terminated with 1 mM NaOH and heated to 65 oC for 10 min to hydrolyse the RNA.  This was then neutralised with 1 M HCl and 1 M TE (pH 8).  cDNA was then purified using a PCR purification kit (Qiagen) to remove unincorporated dNTPs, dye and primers.  cDNA was eluted in 30 μl elution buffer (Qiagen, supplied in kit).  Equal volumes of cDNA were combined and evaporated for approximately 30 min in a SPD 121P SpeedVac® (Thermo Savant, Waltham, MA, USA)


title: Ogt starved L1, biological replicate 1

source_name: ogt mutant L1 animal


title: Ogt starved L1, biological replicate 2


title: Colony Biofilm Replicate 1


title: WT Starved L1, biological rep1


title: Biopsy 3, Colon sample

source_name: Colon Sample patient 3


title: Ogt starved L1, biological replicate 3


title: Biopsy 2, Colon sample

source_name: Colon Sample patient 2


title: Cotton Ovule 8

status: Public on Dec 31 2009

first: Misook

last: Ha

address: NIH

institute: National Heart Lung Blood Institute

description: A total of 9 hybridization intensities in three biological replicates per miRNA were obtained, and log values of hybridization intensities were used for normalization and statistical analysis.

hyb_protocol: After prehybridization, the chip was hybridized to small RNAs labeled with Cy5 (Mirus Bio, Madison, WI) overnight at 37°C. Posthybridization washes were done sequentially once each with 6XSSPET and 3XSSPET and twice with 0.5XSSPET.

scan_protocol: Hybridized chip was scanned using a Genepix 4000B (Molecular Devices, Sunnyvale, CA), and data were extracted using software provided by CombiMatrix (Mukilteo, WA).

data_processing: If the hybridization intensities of a miRNA were not significantly higher than the background signals, the miRNA was considered to be not expressed.

organism: Gossypium hirsutum

source_name: Cotton Ovule

label_protocol: Small RNAs labeled with Cy5 (Mirus Bio, Madison, WI) overnight at 37°C.

extract_protocol: Small RNAs were enriched from total RNA using mirRVana isolation kit (Ambion, Austin, TX).

tag: cultivar

value: Texas Marker-1 (TM1)

value: Ovule

value: 7 days post anthesis(DPA)


title: Cotton Ovule 7


title: Cotton Ovule 6

value: 0 days post anthesis(DPA)


title: Cotton Ovule 4


title: Cotton Ovule 5


title: Cotton Ovule 9


title: Biopsy 3, Ileum sample

source_name: Ileum Sample patient 3

value: ileum


title: Colony Biofilm Replicate 4


title: Cotton Ovule 3


title: Cotton Ovule 2


title: Cotton Ovule 1


title: Oga starved L1, biological replicate 1


title: WT Fed L4, biological rep2


title: Cotton Leaf 7

source_name: Cotton Leaf

value: Leaf

value: Young Leaf


title: Cotton Leaf 8


title: Cotton Leaf 4


title: Cotton Leaf 6


title: Cotton Leaf 2


title: Cotton Leaf 5


title: Cotton Leaf 3


title: Cotton Leaf 1


title: Cotton Fiber 8

source_name: Cotton Fiber

value: Fiber


title: Cotton Fiber 9


title: Cotton Fiber 6


title: Cotton Fiber 5


title: N1 ovule 7

source_name: N1N1 cotton mutant ovule

value: 3 days post anthesis(DPA)


title: Cotton Fiber 3


title: Cotton Fiber 2


title: Cotton Fiber 1


title: N1 ovule 8


title: Cotton Leaf 9


title: Cotton Fiber 7


title: N1 ovule 9


title: N1 ovule 6


title: N1 ovule 5


title: N1 ovule 4


title: Cotton Fiber 4


title: N1 ovule 2


title: N1 ovule 3


title: N1 ovule 1


title: 80min-2

city: Emeryville

first: Robert

last: Dahl

address: 5885 Hollis St, JBEI

department: Chemical Engineering

institute: University of California-Berkeley

description: Biological replicate 2 of 3

hyb_protocol: Kizer, L., et al., 2008.  Application of Functional Genomics to Pathway Optimization for Increased Isoprenoid Production. Appl. Environ. Microbiol. 74: 3229-3241.

scan_protocol: Arrays were scanned with an Axon 4200 scanner and GenePix Pro 6.0 was used.

data_processing: Feature fluorescence intensities [F532 media-B532 and F635media-B635] were extracted using GenePix Pro 6.0.  Local hybridization and intensity-dependent artifacts were removed with Lowess normalization using Standardization and Normalization of Microarray Data (SNOMAD, http://pevsnerlab.kennedykrieger.org/snomadinput.html).  The three replicate spots for each gene were averaged and variance was calculated.

source_name: 80 min, 0.8% butanol

growth_protocol: Individual clones of E. coli DH1 were grown in M9 MOPS media in 300 mL media in 1 L baffled flasks

extract_protocol: Biomass was snap frozen in liquid nitrogen and stored at -80 C prior to extraction with Qiagen RNeasy Midi kits.  RNA integrity was verified with a 2100 Bioanalyzer (Agilent).

value: E. coli DH1

tag: treatment

value: 0.8% n-butanol was added at time 0

tag: time

value: 80 min

source_name: 80 min, unstressed


title: 195min-3

description: Biological replicate 3 of 3

source_name: 195 min, 0.8% butanol

label_protocol: Kizer, L., et al., 2008.  Application of Functional Genomics to Pathway Optimization for Increased Isoprenoid Production. Appl. Environ. Microbiol. 74: 3229-3241.

value: 195 min

source_name: 195 min, unstressed


title: 195min-2

description: Biological replicate 2 of 3


title: 195min-1

description: Biological replicate 1 of 3


title: 80min-1

description: Biological replicate 1 of 3


title: 80min-3

description: Biological replicate 3 of 3


title: 30min-3

description: Biological replicate 3 of 3

source_name: 30 min, 0.8% butanol

value: 30 min

source_name: 30 min, unstressed


title: 30min-2

description: Biological replicate 2 of 3


title: 0min-2

description: Biological replicate 2 of 3

source_name: 0 min, 0.8% butanol

value: 0 min

source_name: 0 min, unstressed


title: 30min-1

description: Biological replicate 1 of 3


title: 0min-3

description: Biological replicate 3 of 3


title: 0min-1

description: Biological replicate 1 of 3


title: age-1(mg44)_rep1

city: Baltimore

first: Catherine

last: Wolkow

address: 251 Bayview Blvd

institute: NIA IRP, NIH

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: Probes with raw fluorescence signals above 100 in wildtype were selected for further analysis as being reliable signals. Expression ratios for each gene were calculated in all 3 strains with respect to wildtype controls. Expression ratios were calculated as z-scores for a statistical evaluation of relative expression and as fold-changes for standardized displays of relative expression. To determine fold-change, raw fluorescence values were first normalized by dividing the fluorescence intensity for a given sample by the average intensity of all samples for the array. Fold-change ratios were then determined by dividing mean normalized value for all replicates of test versus control conditions.

source_name: young adult hermaphrodite

label_protocol: cDNA was labeled with the Quick Amp 2 Color Labeling Kit (Agilent Technologies, Santa Clara, CA)

growth_protocol: Eggs obtained by bleach prep of gravid hermaphrodites and hatched overnight in S basal to synchronize at L1.  L1's were plated onto NG agar with OP50 food and grown 72 hours to L4/young adult stage at 20˚C.

extract_protocol: Total RNA was isolated with Absolutely RNA miniprep kit (Stratagene, La Jolla, CA)

value: age-1(mg44) mutant

value: wildtype (N2)


title: intestine_age-1_rep3

value: intestine-restricted age-1 expression


title: age-1(mg44)_rep2


title: neuron_age-1_rep1

value: neuron-restricted age-1 expression


title: neuron_age-1_rep2


title: MIIIpB (replicate 3)

city: New York

first: steve

last: shen

address: 545 First Ave

institute: New York University

description: Gene expression data from cell line

data_processing: data in this table were processed with RMA method

source_name: MIIIpB (replicate 3)

extract_protocol: Total RNA was isolated from three biological replicates corresponding to MIIpB, MIIIpB and MIIIpB-Smad7 cells using Trizol (Invitrogen) according to the manufacturer’s protocol, and the RNeasy mini-kit (Qiagen) was used to clean-up the RNA

value: cell line derived from a xenograft of the MII cells in nude mice that progressed to carcinoma


title: intestine_age-1_rep1


title: intestine_age-1_rep2


title: MIIpB (replicate 3)

description: Gene expression data from cell line

source_name: MIIpB (replicate 3)

value: MCF10A H-Ras transformed cell line


title: MIIIpB (replicate 1)

description: Gene expression data from cell line

source_name: MIIIpB (replicate 1)


title: neuron_age-1_rep3


title: MIIIpB (replicate 2)

description: Gene expression data from cell line

source_name: MIIIpB (replicate 2)


title: MIIpB (replicate 2)

description: Gene expression data from cell line

source_name: MIIpB (replicate 2)


title: MIIIpBSmad7 (replicate 2)

description: Gene expression data from cell line

source_name: MIIIpBSmad7 (replicate 2)

value: MIII overexpressing the inhibitory Smad8


title: MIIpB (replicate 1)

description: Gene expression data from cell line

source_name: MIIpB (replicate 1)


title: MIIIpBSmad7 (replicate 1)

description: Gene expression data from cell line

source_name: MIIIpBSmad7 (replicate 1)

value: MIII overexpressing the inhibitory Smad7


title: AVZ 47_MCSF_GMCSF

status: Public on Dec 30 2009

city: Paris

first: Seraya

last: Maouche

state: Paris

address: 91 Bd de l'Hôpital

department: Cardiovascular Genomics

institute: INSERM U937

hyb_protocol: Hybridizations were performed using the Agilent in situ hybridization kit. For each sample, 750 ng of Cy5-labeled, linearly amplified cRNA was mixed with equal amounts of Cy3-labelled, linearly amplified reference cRNA. The mixture was then fragmented by incubation with the fragmentation buffer at 60°C for 30 minutes. An equal amount of 2x hybridization buffer was added to the fragmented cRNA mixture and hybridized to whole-genome oligo arrays (Human-25K, Réseau National des Génopoles, France) at 60°C for 17 hours

scan_protocol: Fluorescent images of hybridized microarrays were obtained with a GenePix 4000 Axon Instruments scanner and provessed with the GenePix software (Axon Instruments).

data_processing: The Bioconductor packages marray and Limma were used to perform quality control and preprocessing. Background correction method: normexp Within array print-tip loess normalization was performed for each spot followed by between array quantile normalization. bad spots were filtered out. Log2 ch1/ch2.

source_name: M-CSF monocyte-derived macrophage

label_protocol: RNA was amplified and labeled with Cy3 or Cy5

growth_protocol: The human monocytes CD14+ obtained after MACS separation were cultured at a concentration of 1x 106 cells/ml in pure RPMI 1640 medium in P6 Petri dishes. After 1h of incubation at 37°C, non adherent cells were removed and the medium was replaced with RPMI 1640 Glu+ medium supplemented with 100U/ml penicillin, 100 µg/ml streptomycin and with 10 % FCS and 10 ng/ml of macrophage colony stimulating-factor (M-CSF, SIGMA) or with 10 % FCS and 10 ng/ml of granulocyte macrophage colony-stimulation factor (GM-CSF, SIGM) or with 10 % human serum only. Cells were incubated for 6 days at 37°C/5% CO2 to induce the phagocytic differentiation.

extract_protocol: RNA was extracted from monocytes derived macrohages using RNeasy mini kit of Qiagen.

treatment_protocol: For the isolation of PMBC from Buffy Coat and removal of dead cells, a density gradient centrifugation using Ficoll–Paque (GE Healthcare) gradient was used. PMBC were washed with PBS and the supernatant completely removed. The cell pellet was re-suspended in 80 µl of PBS/BSA buffer per 107 total cells and 10 µl of MACS CD14 (Miltenyi Biotec) were added carefully, mixed and incubated for 15 min at 6°-12°C. The cells were washed by adding 10-20X labelling volume of buffer, centrifuged at 300 g for 10 min. The cells were re-suspended in 500 µl of buffer before magnetic separation as described by the manufacturer.

tag: cell type

source_name: GM-CSF monocyte-derived macrophage

value: GM-CSF induced human monocyte-derived macrophage


title: AVZ 51_GMCSF_Serum

source_name: peritoneal macrophage

value: peritoneal macrophage


title: AVZ 53_MCSF_GMCSF

value: M-CSF induced human monocyte-derived macrophage


title: AVZ 46_MCSF_GMCSF


title: AVZ 50_MCSF_GMCSF


title: AVZ 33_GMCSF_Serum


title: AVZ 31_GMCSF_Serum


title: AVZ 29_GMCSF_Serum


title: AVZ 34_MCSF_Serum


title: AVZ 49_MCSF_Serum


title: AVZ 32_MCSF_Serum


title: AVZ 36_MCSF_GMCSF


title: AVZ 52_MCSF_Serum


title: AVZ 27_GMCSF_Serum


title: AVZ 30_MCSF_Serum


title: AVZ 28_MCSF_Serum


title: experimental CTA versus Flavor only swap1-biological sample3

city: San Juan

first: Sandra

last: Pena de Ortiz

state: PR

address: Gandara Ave., JGD Bldg. Rooms 108, 204

department: Department of Biology

country: Puerto Rico

institute: University of Puerto Rico

hyb_protocol: Cy3 and Cy5-labeled cRNAs were combined, fragmented, and hybridized to a 22K rat 60-mer oligo microarray (Agilent) for 17 h at 60ºC with continuing rotation at 4 rpm. After hybridization, slide arrays were subjected to two successive washes (wash solution 1: 6x SSPE, 0.005% N-Lauroylsarcosine, and wash solution 2: 0.06x SSPE, 0.005% N-Lauroylsarcosine) and dried with the Stabilization and Drying Solution (Agilent).

scan_protocol: Arrays were immediately scanned in a G2505B Microarray Scanner (Agilent) to obtain fluorescence intensities and Cy5/Cy3 ratios for each gene on the array. Scanning parameters were as recommended by the manufacturer. Briefly, the resolution settings for scanning were 10 μm with a sensitivity level of 100% for the photo multiplier tube, which detects fluorescence.

data_processing: Microarray data was extracted with Agilent’s Feature Extraction software (version 5.1) and analyzed using the limma package of Bioconductor. Two comparisons were established between the cRNA samples: CTA versus Flavor-only and CTA versus Toxin-only. For each comparison, the microarray experiment was repeated four times using new biological samples, each consisting of a sample pool from 3 animals. Two of the four biological replicates were performed as dye-swaps in order to correct for dye bias effects. The analysis of the microarray data consisted of the following steps: 1) within-array and between-array normalizations; 2) fitting the data to a linear model; and 3) computing differential gene expression. For normalization purposes23, MA-plots were generated representing the (R,G) data (R=red for Cy5 and G=green for Cy3), in which the log ratio of R versus G (M value = log2 R/G) was plotted against the overall intensity of each spot (A value = log2√(R x G). Within-array normalization was first applied and M-values were normalized within each array using the Global Loess Normalization method.  Aquantile normalization was then applied to the A-values as a method for between-array normalization, to assure that the intensities and log-ratios had similar distributions across arrays.  To estimate the average M-value for each gene and assess differential gene expression, a simple linear model was fitted to the data, and M-value averages and standard deviations for each gene were obtained. To find genes with significant expression changes between groups, empirical Bayes statistics were applied to the data by moderating the standard errors of the estimated M-values24. This moderated t-statistic (ratio of the M-value to its standard error) was calculated by regulating the standard errors across genes and borrowing information from the ensemble of genes to aid with inference about each individual gene. P-values were obtained from the moderated t-statistic and statistical significance was assumed at P < 0.05.

source_name: Total RNA obtained from amygdala tissue punches from rats exposed to flavor only

label_protocol: Total RNA samples were amplified and labeled using the Low Input Fluorescent Linear Amplification kit (Agilent). Briefly, cDNA was first synthesized by combining 500 ng of RNA with T7 promoter primers, 5X First Strand Buffer, 0.1 M DTT, 10 mM dNTP mix, MMLV reverse transcriptase and RNaseOUT. This reaction mix was incubated at 40ºC for 2 h. From the resulting double stranded cDNA, cRNA synthesis and dye incorporation were performed as follows: cDNA of the first reaction was combined with cyanine-3-CTP (Cy3, 10 mM) or cyanine 5-CTP (Cy5,10 mM) and the Transcription Master Mix (4X transcription buffer, 0.1 M DTT, NTP mix, 50% PEG, RNAseOUT, inorganic pyrophosphatase and T7 RNA polymerase) at 40ºC for 2 h. The fluorescently labeled cRNA products were first purified using RNeasy mini spin columns (QIAGEN), subsequently analyzed for yield and dye incorporation using the NanoDrop, and finally stored at −80ºC until needed. Only samples that presented a concentration of more than 8 pmol/mg (a measurement representing efficient dye incorporation) were used for hybridization as recommended by the manufacturer.

extract_protocol: For this experiment, 4 independent groups of RNA pools each from 3 rats were used as biological replicates, for a total of 12 animals per behavioral group. Rats were decapitated 3 h after behavioral training and their brains were rapidly dissected, chilled in iced cold phosphate buffered saline (PBS), washed with stabilization reagent (RNAlater QIAGEN, Valencia, CA) and then transferred to a rat brain matrix. Amygdalar-enriched tissue punches (3 mm wide) were collected from coronal brain slices using as a reference the Paxino’s Rat Brain Map21, which locates the amygdala between -2.12 mm and -4.52 mm bregma points. Amygdalar tissue from each behavioral group was pooled (n = 3 in each pool), and RNA extraction was done using an RNA isolation Kit (QIAGEN) according to the manufacturer’s instructions and as described by us19,22. The concentration and integrity of RNA were determined using the NanoDrop-1000 Spectrophotometer (NanoDrop Technologies, Rockland, DE) and the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) with an RNA 6000 Nano LabChip® Kit (Agilent).

treatment_protocol: Rats were habituated for 4 days to drink plain water during 10 min each day, using the bottle presentation method. Flavor-Only animals were exposed to the CS and 40 min later injected (i.p) with saline solution

tag: Male Long Evans rats weighing 275-300

source_name: Total RNA obtained from amygdala tissue punches from rats trained in CTA

growth_protocol: Male Long Evans rats were individually caged at 22±ºC in a 12-h light/12-h dark cycle, with food and water ad libitum, except during behavioral tests during which water restriction was utilized at certain points.

treatment_protocol: Rats were habituated for 4 days to drink plain water during 10 min each day, using the bottle presentation method. On day 5, CTA-trained animals were exposed to the novel flavor or CS (0.1% dextrose solution) in the drinking bottle for 10 min. This was followed 40 min later, by an i.p. LiCl injection (100 mg/Kg body weight), used as US in our studies.


title: experimental CTA versus Toxin swap2-biological sample4

growth_protocol: Male Long Evans rats were individually caged at 22±ºC in a 12-h light/12-h dark cycle, with food and water ad libitum, except during behavioral tests during which water restriction was utilized at certain points

source_name: Total RNA obtained from amygdala tissue punches from rats exposed to toxin

label_protocol: Total RNA samples were amplified and labeled using the Low Input Fluorescent Linear Amplification kit (Agilent). Briefly, cDNA was first synthesized by combining 500 ng of RNA with T7 promoter primers, 5X First Strand Buffer, 0.1 M DTT, 10 mM dNTP mix, MMLV reverse transcriptase and RNaseOUT. This reaction mix was incubated at 40ºC for 2 h. From the resulting double stranded cDNA, cRNA synthesis and dye incorporation were performed as follows: cDNA of the first reaction was combined with cyanine-3-CTP (Cy3, 10 mM) or cyanine 5-CTP (Cy5,10 mM) and the Transcription Master Mix (4X transcription buffer, 0.1 M DTT, NTP mix, 50% PEG, RNAseOUT, inorganic pyrophosphatase and T7 RNA polymerase) at 40ºC for 2 h. The fluorescently labeled cRNA products were first purified using RNeasy mini spin columns (QIAGEN), subsequently analyzed for yield and dye incorporation using the NanoDrop, and finally stored at −80ºC until needed. Only samples that presented a concentration of more than 8 pmol/mg (a measurement representing efficient dye incorporation) were used for hybridization as recommended by the manufacturer

treatment_protocol: Rats were habituated for 4 days to drink plain water during 10 min each day, using the bottle presentation method. Toxin-Only animals, exposed to plain water instead of CS and 40 min later injected (i.p) with LiCl


title: experimental CTA versus Flavor only swap2 biological sample4


title: AVZ 35_MCSF_GMCSF


title: experimental CTA versus Toxin swap1-biological sample3

treatment_protocol: Rats were habituated for 4 days to drink plain water during 10 min each day, using the bottle presentation method. Toxin-Only animals were exposed to plain water instead of CS and 40 min later injected (i.p) with LiCl.


title: experimental CTA versus Toxin swap2 biological sample2

treatment_protocol: Rats were habituated for 4 days to drink plain water during 10 min each day, using the bottle presentation method. On day 5, CTA-trained animals were exposed to the novel flavor or CS (0.1% dextrose solution) in the drinking bottle for 10 min. This was followed 40 min later, by an i.p. LiCl injection (100 mg/Kg body weight), used as US in our studies


title: experimental CTA versus Flavor only swap1 biological sample1


title: experimental CTA versus Flavor only swap2 biological sample2

treatment_protocol: Rats were habituated for 4 days to drink plain water during 10 min each day, using the bottle presentation method. Flavor-Only animals were exposed to the CS and 40 min later injected (i.p) with saline solution.


title: experimental CTA versus Toxin swap1 biological sample1


title: Salmonella 48C Treatment Rep2-1

status: Public on Dec 25 2009

city: Fayetteville

first: Arunachalam

last: Muthaiyan

state: AR

address: 2435 N Hatch Ave

department: Food Science

institute: University of Arkansas

description:
Isolated from pools of heart and liver from 4-week-old chickens
Analyses were performed using Acuity 4.0 software.  Slides were normalized using standard settings (ratio based so that the mean of the ratio of means, of all features, were equal to 1.0).

hyb_protocol: Microarray hybridizations were performed by cross hybridization of treatment and control samples.  Along with the hybridizations, technical replications (dye swaps) were also performed.

scan_protocol: Images were captured using a Genepix 4000B (Molecular Devices Corporation, Union City, CA) laser scanner and images processed using GenePix 6.0 software (Molecular Devices Corporation).

data_processing: All spots were manually evaluated, and bad, low signal, absent, or unfound features were not included.  To obtain the final data provided, it was required that elements on each array and on each dye-swap (after mathematical conversion x’ = -x) provided agreement and showed statistically significant similarity, based upon a student t-test, at the p < 0.05 level.  Genes were included in the final dataset that exhibit at least 2.0 fold regulations.

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella Control Cy3

label_protocol: Following the reverse transcriptase reaction, the cDNA was labeled with either CyDye3-dCTP or CyDye5-dCTP (Amersham Biosciences) using the LabelStar kit (Qiagen Inc.) and Random nonamers (Sigma-Aldrich Inc., St. Louis, MO).

extract_protocol: Following incubation, cultures were resuspended immediately in RNAprotect Bacteria Reagent (Qiagen Inc., Valencia, CA).  Total RNA was extracted using RNeasy Protect Bacteria Mini Kit (Qiagen Inc.) and DNA removed using RNase-Free DNase Set (Qiagen Inc.) and used further for microarray analysis.

treatment_protocol: S. Typhimurium ATCC 14028 was grown until mid-log phase at 30°C and maintained at 30°C for 30 min

source_name: Salmonella 48C Treatment Cy5

treatment_protocol: S. Typhimurium ATCC 14028 was grown until mid-log phase at 30°C and heat shocked at 48°C for 30 min.


title: Salmonella 48C Treatment Rep2-2

source_name: Salmonella Control Cy5

source_name: Salmonella  48C Treatment Cy3


title: Salmonella 48C Treatment Rep3-1


title: Salmonella 48C Treatment Rep3-2

source_name: Salmonella 48C Treatment Cy3


title: MIIIpBSmad7 (replicate 3)

description: Gene expression data from cell line

source_name: MIIIpBSmad7 (replicate 3)

value: MIII overexpressing the inhibitory Smad9


title: Salmonella 42C Treatment Rep3-2

source_name: Salmonella 42C Treatment Cy5

treatment_protocol: S. Typhimurium ATCC 14028 was grown until mid-log phase at 30°C and heat shocked at 42°C for 30 min.


title: Salmonella 48C Treatment Rep1-2


title: Salmonella 42C Treatment Rep2-2


title: Salmonella 48C Treatment Rep1-1


title: Salmonella 42C Treatment Rep1-2

source_name: Salmonella 30C Control Cy3


title: Salmonella 42C Treatment Rep2-1

source_name: Salmonella 42C Treatment Cy3


title: Salmonella 42C Treatment Rep1-1

description:
Isolated from heart and liver from 4-week-old chickens.
Analyses were performed using Acuity 4.0 software.  Slides were normalized using standard settings (ratio based so that the mean of the ratio of means, of all features, were equal to 1.0).

source_name: Salmonella 30C Control

source_name: Salmonella 42C Treatment

treatment_protocol: S. Typhimurium ATCC 14028 was grown until mid-log phase at 30°C and heat shocked at 42°C  for 30 min.


title: Sch9Mutant_84hours

city: Los Angeles

first: Huanying

last: Ge

address: 1050 Childs Way, RRI building 408D

department: Biology

institute: Computational biology and bioinformatics

description: Microarray Experiment is done in UCLA DNA array Core Facility

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: we applied the Probe-Treatment-Reference (PTR) method coupled with sub-array normalization to the data. We choose target-reference relations illustrated in the paper to do the pairwise normalization.The normalized data are used to fit the three-factor PTR model according to the target-reference relations for each probe-set and the parameters are estimated by least absolute deviations (LAD).

source_name: Sch9 Mutant

label_protocol: Standard Affymetrix protocol

growth_protocol: Both strains used were obtained from frozen stocks. Each strain was inoculated in 1 mL SDC and grown overnight. Saturated overnight cultures were then diluted. All samples were incubated at 30oC with shaking (220 rpm). Total RNA was isolated at different time points.

extract_protocol: Total RNA was isolated at each time point according to the acid phenol protocol.

treatment_protocol: No other treatment.

tag: Age

value: 84 hours


title: Sch9Mutant_72hours

value: 72 hours


title: Sch9Mutant_108hours

value: 108 hours


title: Sch9Mutant_96hours

value: 96 hours


title: WildType_120hours

source_name: Wild Type

value: 120 hours


title: Sch9Mutant_36hours

value: 36 hours


title: Salmonella 42C Treatment Rep3-1


title: WildType_108hours


title: WildType_96hours


title: WildType_24hours

value: 24 hours


title: Sch9Mutant_24hours


title: Sch9Mutant_48hours

value: 48 hours


title: Sch9Mutant_12hours

value: 12 hours


title: WildType_72hours


title: WildType_84hours


title: WildType_12hours