title: DSS day 15, replicate 1

description: Affymetrix Technical Manual

source_name: Intestine from rats that received 2% Dextran sodium sulphate (DSS)

tag: Rat received 2% Dextran sodium sulphate (DSS)


title: DSS day 17, replicate 1

status: Public on Nov 01 2008

type: RNA

city: Granada

first: Antonio

last: Suarez

state: Granada

address: Pharmacy Faculty, Campus Cartuja s/n

department: Biochemistry and Molecular Biology

country: Spain

institute: University of Granada

description: Affymetrix Technical Manual

hyb_protocol: Affymetrix Technical Manual

scan_protocol: Affymetrix Technical Manual

data_processing: Affymetrix Technical Manual

label: Affymetrix Technical Manual

molecule: total RNA

organism: Rattus norvegicus

source_name: Intestine from rats that received 0% Dextran sodium sulphate (DSS)

label_protocol: Affymetrix Technical Manual

extract_protocol: Affymetrix Technical Manual

tag: Sprague-Dawley female rat

tag: Tissue

value: full-thickness colon

tag: Rat received 0% Dextran sodium sulphate (DSS)


title: B10 TCR:HEL single positive rep 3

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

description: B10  CD4+ transgenic TCR:HEL thymocytes- negative selection thymocytes

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

label: biotin

organism: Mus musculus

source_name: CD4+ positive mouse thymocyte

label_protocol: Affymetrix GeneChip Eukaryotic Small Sample Target Labelling Assay Version II protocol was used on total RNA from 100000-1000000 cells

growth_protocol: Mice were 6-8 weeks old.

extract_protocol: Total RNA was extracted from sorted thymus using trizol and further purified using RNeasy spin columns.

treatment_protocol: The mice and cells were not treated.

tag: B10,TCR:HEL double transgenic 6-8 week old female mouse, CD4+ positive thymocytes


title: DSS day 13, replicate 3

description: Affymetrix Technical Manual


title: B10 TCR:HEL single positive rep 2


title: DSS day 19, replicate 2

description: Affymetrix Technical Manual


title: 4SC_New_Cy3

type: genomic

city: Toronto

first: Paul

middle: C

last: Boutros

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: HybridizationDate: 7-Dec-04, ArrayBatch: New, Antibody: SC, SampleID: 4SC

hyb_protocol: The mixed DNA was resuspended in 5 μL of H2O and mixed with 85 μL hybridization mix (100 μL of DIG Easy Hyb solution (Roche 603 558), 5 μL of 10 mg/mL calf thymus DNA (Sigma D8661), 5 μL of 10 mg/mL yeast tRNA (Invitrogen 15401-029)). The resulting solution was incubated at 65 °C for 2 minutes, then cooled to room temperature and applied to a CpG island array slide (UHN Microarray Centre HCGI12K) and incubated overnight at 42 °C in a hybridization chamber.  After hybridization, the microarray slide was washed once with washing buffer 1 (1x SSC, 0.1% SDS) at 50°C for 5 minutes. This was followed by a wash with washing buffer 1 (room temperature for 5 minutes) and 2 washes with washing buffer 2 (0.2x SSC for 5 minutes) and one final wash with washing buffer 3 (0.1x SSC for 5 minutes at room temperature). The slide was then dried by spinning at 700 rpm for 15 minutes. To preserve the Cy5 dye from ozone-dependent degradation, which was observed during the summertime when the hybridization occurred, the slides were then dipped in DyeSaver 2 (Genisphere Q500600) and allowed to air dry.

scan_protocol: The microarray slides were scanned using a Gene Pix 4000B scanner (Axon Instruments) at multiple PMT voltages. Array images were first manually examined for image artifacts, and then quantitated using GenePix Pro (v6.0.1.27). A scan that maximized the dynamic range without saturating high-intensity signals was selected and carried forward for analysis. This scan was quantified using the “circular” segmentation algorithm.

data_processing: All data were pre-processed using the variance-stabilizing normalization algorithm (VSN). VSN was implemented in the R statistical environment (v2.4.1) in the BioConductor open-source project. Version 1.12.0 of the vsn package was employed, with print-tip groups used as strata, and default parameterization except for using 1000 iterations for fitting (increased from the default of 10).

molecule: genomic DNA

organism: Homo sapiens

source_name: Growing HL60 Cells

label_protocol: A total of 3 μg of amplified DNA from the antibody sample, no antibody, or IgG sample were vacuum desiccated and resuspended in 2.5 μL of H2O (Sigma W4502). 4.5 μL of 0.1 M NaHCO3 at pH 9 was added. The DNA was resuspended by vortexing several times. 2 μL of Cy3 or Cy5 dye (Amersham, PA23001 and PA25001 respectively) were added to the sample. The mix was incubated for 1.5 hours at room temperature in the dark. After incubation, 35 μL of 100 mM Na-Acetate pH5.2 was added and topped with H2O (Sigma W4502) to a total volume of 100 μL for each sample. The fluorescent labeled probes were purified using QIAquick PCR Purification kit (Qiagen 28106). The DNA was eluted with 50 μL of EB buffer from the kit, heated to 65°C. The 100 μL combined ChIP and no antibody samples were vacuum desiccated using a SpeedVac for 60 minutes at maximum heat.

extract_protocol: Exponentially growing HL60 cells were cross-linked with 1% formaldehyde for 10 minutes at 37 °C. The crosslinking reaction was quenched by addition of glycine to a final concentration of 0.125 M for 5 minutes, followed by two washes with phosphatebuffered saline (PBS). Cells were resuspended in cell lysis buffer (5 mM PIPES pH 8, 85 mM KCl, 0.5% [v/v] NP40, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) for 10 minutes on ice and then pelleted (5000 rpm, 5 minutes, 4 °C). The pellet was resuspended in 1 mL of nuclei lysis buffer (50mM Tris-HCl pH 8.1, 10mM EDTA, 1% SDS, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) for 10 minutes on ice and then sonicated using 8 pulses (12-13 Watts, setting 10, 10 seconds per pulse, 45 seconds on ice between pulses) from a Model 60 Sonic Dismembrator (Fisher Scientific 15-338-53) to generate fragments between 600 bp and 1000 bp. Lysates were centrifuged for 10 minutes at 21,000 x g at 4 °C. Supernatants were diluted into an equal volume with IP dilution buffer (0.01% SDS, 1.1% Triton-X100, 1.2mN EDTA, 16.7mM Tris-HCl pH 8.1, 0.2% Sarkosyl, 1 mM PMSF, 10 μg/mL aprotinin, 10 μg/mL leupeptin) and precleared for 30 minutes at 4 °C with protein G-PLUS agarose beads (Santa Cruz Biotechnology  sc-2002). Prior to use, G-PLUS agarose beads were blocked with salmonsperm DNA at a final concentration of 50 μg/mL and rotated overnight at 4 °C. Diluted and cleared extracts corresponding to 10 x 106 HL60 cells were incubated and rotated at 4°C for approximately 12 to 16 hours with each of the following antibodies: no-antibody control, 0.7 μg normal rabbit IgG (Santa Cruz Biotechnology sc-2027), 0.7 μg N262 (Santa Cruz Biotechnology sc-764), for the N262 home-made unpurified and purified antibodies, we determined empirically, by serial dilutions, the amount of antibody to be used. 50 μL of salmon sperm DNA pre-blocked Protein G-PLUS agarose beads were added to each sample, incubated on a rotating platform at 4 °C for 3 hours. Each pellet was washed once with 1.4 mL of sonication buffer and then twice with 1.4 mL of high salt buffer (0.1% [v/v] SDS, 1% [v/v] Triton X-100, 1 mM EDTA, 50 mM HEPES, 500 mM NaCl, 0.1% [w/v] sodium deoxycholate) and then once with 1.4 mL LiCl Buffer (250 mM LiCl, 1% [v/v] NP-40, 1% [w/v] sodium deoxycholate, 1 mM EDTA, 1 mM Tris pH 8) and finally twice with 1.4 mL TE pH 8 (10 mM Tris pH8, 1 mM EDTA). For each wash, the pellets were mixed for 5 minutes at room temperature then pelleted (3000 rpm, 30 seconds, room temperature). After the last wash, the pellets were eluted in 300 μL of Elution buffer (1% [w/v] SDS, 10 mM Tris pH 8, 5 mM EDTA), incubated at 65 °C for 15 minutes, and then pelleted (3000 rpm, 3 minutes, room temperature). Crosslinks were reversed in the presence of 200 mM NaCl at 65 °C over-night and samples were treated with RNase A (Sigma R5500). After ethanol precipitation, the samples were resuspended in 100 μL of TE (10 mM Tris, pH 7.5, 1 mM EDTA), 25 μL of 5x proteinase K buffer (1.25% SDS, 50 mM Tris, pH 7.5, 25 mM EDTA), and 1.5 μL of proteinase K (Roche 1413783) and incubated at 42 °C for 2 hours. DNA was extracted from each sample using phenol:chloroform:isoamyl alcohol (25:24:1), then precipitated with 1/10th volume of 3 M sodium acetate (pH 5.3), 5 μg of glycogen, and 2 volumes of ethanol at -20 °C overnight. Pellets were collected by microcentrifugation and resuspended in 60 μL of H2O.

tag: CellLine

tag: SampleType

value: NoAntibody

source_name: Growing HL60 cells

value: Myc ChIP


title: B10 TCR double positive rep 3

description: B10 pre-selection transgenic TCR thymocytes

source_name: double positive mouse thymocyte

tag: B10,TCR transgenic 6-8 week old female mouse, double positive thymocytes


title: DSS day 15, replicate 2

description: Affymetrix Technical Manual


title: DSS day 15, replicate 3

description: Affymetrix Technical Manual


title: B10 TCR double positive rep 2


title: 4HM_New_Cy3

description: HybridizationDate: 7-Dec-04, ArrayBatch: New, Antibody: HM, SampleID: 4HM


title: 4HM_New_Cy5


title: DSS day 13, replicate 2

description: Affymetrix Technical Manual


title: DSS day 11, replicate 2

description: Affymetrix Technical Manual


title: DSS day 13, replicate 1

description: Affymetrix Technical Manual


title: B10 TCR double positive rep 1


title: DSS day 11, replicate 1

description: Affymetrix Technical Manual


title: 3SC_New_Cy3

description: HybridizationDate: 7-Dec-04, ArrayBatch: New, Antibody: SC, SampleID: 3SC


title: DSS day 11, replicate 3

description: Affymetrix Technical Manual


title: DSS day 9; replicate 3

description: Affymetrix Technical Manual


title: 3SC_New_Cy5


title: DSS day 9, replicate 1

description: Affymetrix Technical Manual


title: B10 TCR single positive rep 3

description: B10  CD4+ transgenic TCR thymocytes- positive selection thymocytes

tag: B10,TCR transgenic 6-8 week old female mouse, CD4+ positive thymocytes


title: 4SC_Old_Cy5

description: HybridizationDate: 3-Dec-04, ArrayBatch: Old, Antibody: SC, SampleID: 4SC


title: DSS day 9, replicate 2

description: Affymetrix Technical Manual


title: B10 TCR single positive rep 1


title: 3HM_New_Cy5

description: HybridizationDate: 7-Dec-04, ArrayBatch: New, Antibody: HM, SampleID: 3HM


title: B10 TCR single positive rep 2


title: 4HM_Old_Cy3

description: HybridizationDate: 3-Dec-04, ArrayBatch: Old, Antibody: HM, SampleID: 4HM


title: 3HM_New_Cy3


title: DSS day 7, replicate 2

description: Affymetrix Technical Manual

data_processing: Bioconductor

source_name: Intestine from rats that received 5% Dextran sodium sulphate (DSS)

tag: Rat received 5% Dextran sodium sulphate (DSS)


title: DSS day 5, replicate 2

description: Affymetrix Technical Manual


title: DSS day 3, replicate 2

description: Affymetrix Technical Manual


title: DSS day 7, replicate 1

description: Affymetrix Technical Manual


title: 4HM_Old_Cy5


title: DSS day 7, replicate 3

description: Affymetrix Technical Manual


title: DSS day 5, replicate 3

description: Affymetrix Technical Manual


title: DSS day 3, replicate 3

description: Affymetrix Technical Manual


title: 4SC_Old_Cy3


title: DSS day 5, replicate 1

description: Affymetrix Technical Manual


title: DSS day 1, replicate 3

description: Affymetrix Technical Manual


title: 3SC_Old_Cy3

description: HybridizationDate: 3-Dec-04, ArrayBatch: Old, Antibody: SC, SampleID: 3SC


title: 3HM_Old_Cy3

description: HybridizationDate: 3-Dec-04, ArrayBatch: Old, Antibody: HM, SampleID: 3HM


title: 3HM_Old_Cy5


title: 1SC_Old_Cy5

description: HybridizationDate: 17-Nov-04, ArrayBatch: Old, Antibody: SC, SampleID: 1SC


title: 2SC_New_Cy3

description: HybridizationDate: 4-Nov-04, ArrayBatch: New, Antibody: SC, SampleID: 2SC


title: 1HM_Old_Cy5

description: HybridizationDate: 17-Nov-04, ArrayBatch: Old, Antibody: HM, SampleID: 1HM


title: DSS day 1, replicate 2

description: Affymetrix Technical Manual


title: 2HM_Old_Cy3

description: HybridizationDate: 26-Nov-04, ArrayBatch: Old, Antibody: HM, SampleID: 2HM


title: Healthy control, replicate 5

description: Affymetrix Technical Manual

source_name: Intestine from healthy control rats

tag: Rat received water


title: TNBS day 2, replicate 3

description: Affymetrix Technical Manual

data_processing: Normalized with Bioconductor

label: Biotin

source_name: Intestine from rats that received 10mg TNBS in 50% ethanol at day 0

extract_protocol: Trizol reagent

tag: Rat received an enema of 10mg TNBS in 50% ethanol at day 0


title: 1SC_Old_Cy3

description: HybridizationDate: 26-Nov-04, ArrayBatch: Old, Antibody: SC, SampleID: 1SC


title: Healthy control, replicate 6

description: Affymetrix Technical Manual

tag: rat received water


title: Healthy control, replicate 2

description: Affymetrix Technical Manual

tag: Sprague-Dawley female rats

tag: Tissue:full-thickness colon


title: 2SC_Old_Cy3

description: HybridizationDate: 26-Nov-04, ArrayBatch: Old, Antibody: SC, SampleID: 2SC


title: 2SC_Old_Cy5

description: HybridizationDate: 17-Nov-04, ArrayBatch: Old, Antibody: SC, SampleID: 2SC


title: 2SC_New_Cy5


title: DSS day1, replicate 1

description: Affymetrix Technical Manual


title: Healthy control, replicate 1

description: Affymetrix Technical Manual


title: Helathy control, replicate 3

description: Affymetrix Technical Manual


title: 1SC_New_Cy3

description: HybridizationDate: 4-Nov-04, ArrayBatch: New, Antibody: SC, SampleID: 1SC


title: Growing_HL60_CpG_Rep12

description: HL60 Myc ChIP replicate 12

value: IgG ChIP


title: 2HM_Old_Cy5

description: HybridizationDate: 17-Nov-04, ArrayBatch: Old, Antibody: HM, SampleID: 2HM


title: Growing_HL60_CpG_Rep9

description: HL60 Myc ChIP replicate 9


title: Growing_HL60_CpG_Rep10

description: HL60 Myc ChIP replicate 10


title: Growing_HL60_CpG_Rep7

description: HL60 Myc ChIP replicate 7


title: 2HM_New_Cy3

description: HybridizationDate: 4-Nov-04, ArrayBatch: New, Antibody: HM, SampleID: 2HM


title: 1SC_New_Cy5


title: 1HM_Old_Cy3

description: HybridizationDate: 26-Nov-04, ArrayBatch: Old, Antibody: HM, SampleID: 1HM


title: Growing_HL60_CpG_Rep13

description: HL60 Myc ChIP replicate 13


title: 1HM_New_Cy3

description: HybridizationDate: 4-Nov-04, ArrayBatch: New, Antibody: HM, SampleID: 1HM


title: DSS day 3, replicate 1

description: Affymetrix Technical Manual


title: Growing_HL60_CpG_Rep11

description: HL60 Myc ChIP replicate 11


title: 2HM_New_Cy5


title: 1HM_New_Cy5


title: Growing_HL60_CpG_Rep5

description: HL60 Myc ChIP replicate 5


title: Growing_HL60_CpG_Rep8

description: HL60 Myc ChIP replicate 8


title: CHC599T-U133A

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

description: see [Rebouissou et al., submitted].

hyb_protocol: Hybridization was performed using 20 µg of cRNA per hybridization (GeneChip Fluidics Station 400), following the manufacturer’s protocols (Affymetrix, Santa Clara, CA).

scan_protocol: Array images were digitized by using Microarray Suite 5.0 (MAS5) software, embedded in the Affymetrix GeneChip Operating Software (Affymetrix, Santa Clara, USA).

data_processing: Gene intensity derivation was carried out from the raw numerical data (CEL files) by using the R package affy [Gautier et al., Bioinformatics 2004, 20: 307-15], available as part of the Bioconductor project [Gentleman et al., Genome Biol 2004, 5: R80], and the DNA-Chip analyzer (dChip) program [Li & Wong, PNAS 2001, 98: 31-6]. Probe sets corresponding to control genes or having a “_x_” annotation were masked yielding a total of 19,787 probe sets available for further analyses. Background subtraction, normalization and expression summaries for every probe set were calculated with the log-scale robust multi-array analysis (RMA) algorithm using a background adjusted PM intensities model [Irizarry et al., Nucleic Acids Research 2003, 31: e15], and with the model-based expression indexes (MBEI) calculation following a PM/MM difference model [Li & Wong, PNAS 2001, 98: 31-6].

label_protocol: For each case, 5 µg of total RNA were labeled according to the protocols provided by the manufacturer (Affymetrix, Santa Clara, CA).

extract_protocol: Frozen tissue sample specimens, in pieces from 50 to 150 mg each, were removed from the freezer, immediately placed into 700 µl of lysis Buffer RLT (Qiagen, Germany) together with stainless steel beads and homogenized using a Mixer Mill MM 300 (Qiagen, Germany), at 30 Hz over a period of 3 min. Then, homogenization was carried on as described in the commonly used RNeasy™ procedure.

tag: Sample

tag: Gender

value: female;

tag: Age at onset

value: 47 years;

tag: Disease

value: Focal nodular hyperplasia;

value: tumor liver.


title: Growing_HL60_CpG_Rep1

description: HL60 Myc ChIP replicate 1


title: Growing_HL60_CpG_Rep2

description: HL60 Myc ChIP replicate 2


title: Growing_HL60_CpG_Rep4

description: HL60 Myc ChIP replicate 4


title: Growing_HL60_CpG_Rep3

description: HL60 Myc ChIP replicate 3


title: CHC597T-U133A

description: see [Rebouissou et al., submitted].

tag: Tissue


title: Lean untreated male 4

city: New York

first: Anthony

last: Ferrante

state: NY

address: 1150 St. Nicholas Ave. Rm. 243

department: Medicine

country: USA

institute: Columbia University

description: no additional information

hyb_protocol: cRNA was fragmented and hybridized to microarrays according Affymetrix's protocol.

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

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

source_name: Perigonadal Tissue

label_protocol: cRNA was generated from total RNA using the SuperScript II (Invitrogen, Carlsbad CA) according to the manufacturer's protocol followed by a in vitro transcription protocol using the Affymetrix labeling kit according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted from adipose tissue using the Trizol Reagent (Invitrogen, Carlsbad CA).  RNA samples were further purified using RNAeasy (Qiagen, Inc).  Extraction and purification were carried out according ot the manufacturer's protocols.

tag: Age

value: 22 weeks old

tag: Genotype

value: wt

tag: Treatment


title: Diet Induced Obesity untreated male 2

description: no additional information

value: Diet Induced Obesity (Diet # D12451; Research Diets Inc., New  Brunswick, New Jersey, USA)


title: Growing_HL60_CpG_Rep6

description: HL60 Myc ChIP replicate 6

tag: CellLine

tag: SampleType


title: Diet Induced Obesity Pioglitazone treated male 4

description: no additional information

value: Diet Induced Obesity (Diet # D12451; Research Diets Inc., New  Brunswick, New Jersey, USA); Pioglitazone 10mg/kg/day, 2 weeks


title: Diet Induced Obesity Pioglitazone treated male 1

description: no additional information


title: Diet Induced Obesity Pioglitazone treated male 3

description: no additional information


title: Diet Induced Obesity untreated male 3

description: no additional information


title: CHC565T-U133A

description: see [Rebouissou et al., submitted].

value: 44 years;


title: Diet Induced Obesity Pioglitazone treated male 2

description: no additional information


title: ob/ob untreated male 1

description: no additional information

value: ob/ob


title: Diet Induced Obesity untreated male 1

description: no additional information


title: ob/ob untreated male 3

description: no additional information


title: Lean untreated male 3

description: no additional information


title: Healthy control, replicate 4

description: Affymetrix Technical Manual


title: CHC566T-U133A

description: see [Rebouissou et al., submitted].

value: 53 years;


title: 3SC_Old_Cy5


title: ob/ob untreated male 2

description: no additional information


title: ob/ob untreated male 4

description: no additional information


title: ob/ob β3 Adrenergic Agonist Treated female 1

description: no additional information

value: CL316243 (β3 Adrenergic Agonist) 3mg/kg/day for 2 weeks


title: Lean untreated male 1

description: no additional information


title: Ay/+ untreated female 4

description: no additional information

value: ay/+


title: Ay/+ Pioglitazone treated female 1

description: no additional information

value: Pioglitazone 10mg/kg/day, 2 weeks


title: Ay/+ Pioglitazone treated female 3

description: no additional information

value: Pioglitazone, 2 weeks


title: Lean untreated male 2

description: no additional information


title: ob/ob β3 Adrenergic Agonist Treated female 2

description: no additional information


title: ob/ob Pioglitazone treated female 3

description: no additional information


title: ob/ob untreated female 2

description: no additional information


title: ob/ob Pioglitazone treated female 1

description: no additional information


title: Ay/+ Pioglitazone treated female 2

description: no additional information


title: ob/ob Pioglitazone treated female 2

description: no additional information


title: ob/ob untreated female 3

description: no additional information


title: StreptococcusmutansΔcodY_FMC_rep3

status: Public on Oct 31 2008

city: Gainesville

first: Robert

middle: A

last: Burne

state: FL

address: 1600 SW Archer Rd. BOX 100424

department: Oral Biology

institute: University of Florida

description: S. mutans codY knockout

hyb_protocol: Hybridizations were carried out in a Maui 4-chamber hybridization system (BioMicro Systems, Salt Lake City, Utah) for 17 h at 42ºC. The slides were then washed according to TIGR protocols (SOT# M008, version 2.1, 11/06).

scan_protocol: The slides were scanned using a GenePix Scanner (Axon Instruments Inc., Union City, CA).

data_processing: After the slides were scanned, single-channel images were loaded into TIGR Spotfinder software and overlayed. A spot grid was created according to TIGR specifications and manually adjusted to fit all spots within the grid, then the intensity values of each spot were measured. Data was normalized using Microarray data analysis software (MIDAS), by using LOWESS and Iterative Log Mean Centering with default settings.

organism: Streptococcus mutans

source_name: S. mutans ΔcodY

label_protocol: All RNAs were purified as described above and used to generate cDNA according to the protocol provided by TIGR with the following minor modifications. The amount of RNA in each reaction was increased to 10 ug and the molar ratio of dTTP:aa-dUTP was increased to 1:2. SuperscriptIII Reverse transcriptase (Invitrogen, Gaithersburg, MD) was used to increase cDNA yields. Purified cDNAs were coupled with indocarbocyanine (Cy3)-dUTP

growth_protocol: Cells were grown in the chemically-defined medium FMC to an OD600 of 0.3 in 5% CO2 at 37°C

extract_protocol: RNA from S. mutans was isolated from 50 ml cultures that were grown under the desired conditions and harvested by centrifugation at 4ºC. Pelleted cells were resuspended in 400 ml of DEPC-treated water, 800 ml of RNA protect reagent (QIAGEN, Inc., Chatsworth, CA) was added, and the samples were incubated at room temperature for 5 min with vortexing for 10 s at one minute intervals. Cells were then pelleted, resuspended in 500 ml Tris-EDTA (50:10) buffer and transferred to 1.5 ml screw cap tubes containing sterile glass beads (0.1 mm avg. diam.; Biospec, Bartlesville, OK), 100 ml of 1% SDS and 650 ml of acid phenol:chloroform (5:1). The mixture was homogenized in a Bead Beater twice for 40 s and chilled on ice for 2 min between cycles. Samples were centrifuged for 30 min at maximum speed at 4ºC. Two additional hot acid phenol:chloroform extractions were performed followed by one extraction with chloroform:isoamyl-alcohol (24:1). RNA was precipitated in the presence of isopropanol and sodium acetate, pH 5, at -20ºC for 1 h, followed by multiple washes with 70% ethanol, one wash with 99% ethanol, and drying in vacuo. RNA was resuspended in DEPC-treated water and digested with DNAseI (Ambion, Austin, TX). The RNA was re-purified and treated on-column with DNaseI using the RNeasy mini kit (QIAGEN, Inc., Chatsworth, CA), as recommended by the supplier.

tag: Strain

value: Δcody

tag: codY deletion mutant

source_name: S. mutans UA159 grown in BHI

label_protocol: All RNAs were purified as described above and used to generate cDNA according to the protocol provided by TIGR with the following minor modifications. The amount of RNA in each reaction was increased to 10 ug and the molar ratio of dTTP:aa-dUTP was increased to 1:2. SuperscriptIII Reverse transcriptase (Invitrogen, Gaithersburg, MD) was used to increase cDNA yields. Purified cDNAs were coupled with indocarbocyanine (Cy5)-dUTP

growth_protocol:
Growth Media: Brain Heart Infusion
OD600: 0.5
5% CO2, 37°C

tag: Wild-type


title: ob/ob untreated female 4

description: no additional information


title: Ay/+ untreated female 3

description: no additional information


title: Ay/+ untreated female 2

description: no additional information


title: StreptococcusmutansUA159_FMC_rep3

description: S. mutans wildtype control

source_name: S. mutans UA159

tag: wildtype


title: Lean untreated female 3

description: no additional information


title: StreptococcusmutansUA159_FMC_rep1

description: S. mutans wildtype control


title: Lean untreated female 4

description: no additional information


title: ob/ob untreated female 1

description: no additional information


title: Lean untreated female 1

description: no additional information


title: Lean untreated female 2

description: no additional information


title: Ay/+ untreated female 1

description: no additional information


title: CTCF K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 3

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: Ludwig Institute for Cancer Research

description: Chromatin immunoprecipitation was performed using antibodies against CTCF and formaldehyde crosslinked chromatin from K562 Chromatin cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions.

hyb_protocol: NimbleGen hybridization protocol

scan_protocol: NimbleGen scan protocol

data_processing: The value is log2R normalized using the limma R package method=loess

source_name: Chromatin immunoprecipitated DNA from K562 Chromatin cells using CTCF antibody

extract_protocol: immunoprecipitated chromatin

tag: cells

value: K562 Chromatin immunoprecipitated chromatin

source_name: Input Chromatin K562 Chromatin cells.

extract_protocol: input chromatin

value: K562 Chromatin input chromatin


title: CTCF K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 1


title: CTCF K562 Chromatin ENCODE NimbleGen hg17 tiling array replicate 2


title: StreptococcusmutansΔcodY_FMC_rep4

description: S. mutans codY knockout


title: Plasma_GVHD-_77

type: protein

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

description: bottom array on slide, data not used, batch 2

hyb_protocol: Arrays were incubated with 500 ul of protein array blocking buffer for 30 minutes on an orbital shaker prior to hybridizations. The eluents containing the labeled plasma proteins from one individual sample and one aliquot of the reference pool were hybridized to each of the arrays overnight.  After repeated washes, the chips were probed with the fluorescent reporter molecules (streptavidin-DY647 and anti-fluorescein-DY547) for 1 hour at room temperature, washed, and dried.

scan_protocol: The slides were scanned within 24-48 hours with an Axon 4000A scanner, using settings recommended for Cy3 and Cy5 detection, to obtain images representing the individual sample (the 532 channel, channel 1) and the reference pool (the 635 channel, channel 2).

data_processing: Dot intensity measures were performed with Genepix 3.0, and the “median of ratios” (the median of the intensity ratios at each pixel in a dot) used as the initial measure of the ratio of individual sample to reference pool.  A total of only 81 dots were flagged as unusable in all of the arrays.  Each antibody is dotted in triplicate on the arrays, and we computed the geometric mean of the 3 ratios from these replicate dots as our unadjusted values for each antibody (with now just one piece of missing data).  A major difficulty of the analysis was the large non-specific signal in the 532 channel, with intense signals even in the two control arrays made in batch 2, one of which used unlabeled sera only, and the other which used a biotin-ULS labeled reference pool sample versus an unlabeled sample. Let Di be the average of the 532 channel intensities for these two test arrays for the i-th antibody, and let Mi be the minimum of the 532 channel intensities for the i-th antibody for the 42 arrays of major interest (which was sometimes less than Di).  We used a conservative estimate of non-specific 532 channel intensity of Ci = min(Di, Mi-200) to adjust the ratios as follows. Let Rij be the unadjusted average ratio and Sij the average 635-channel intensity for the i-th antibody on the j-th array.  We adjusted the ratios by using Rij – (Ci/Sij), and then took base-2 logarithms to obtain the adjusted log-ratios.  The adjusted log-ratios were normalized to an artificial standard computed by median centering these values for each array, and then averaging across arrays for each antibody.  Using the median centered array data we selected the 60 antibodies with smallest standard deviation across arrays, and forced the mean for these 60 antibodies on each array to agree with the same mean for the standard. We excluded data from 2 hybridizations that had very bright dots and appeared as outliers in preliminary principal components analysis (samples 47 and 77).   We then fit a two-way ANOVA model with terms for batch, sample type (+GVHD or –GVHD), and their interactions (no interactions gave p<.01).  In the matrix we have removed batch effects by forcing the the mean log-ratio in each batchs to be equal so that the data can be more easily compared.  We also provide a supplemental data file holding the data where batch effects were not removed.

label: Fluorescein-ULS

molecule: protein

source_name: Plasma

label_protocol: 4 ul aliquots of each of 21 GVHD+ and 21 GVHD-  plasma samples were combined to form a reference pool, which was labeled with biotin-ULS for 2 hours at 42 degrees C, and a second aliquot of each individual sample labeled with Fluorescein-ULS.  Then 5 ul of 10X KREAstop was added for 5 minutes to each of the reaction tubes and free-ULS- reagent was removed using spin columns.

extract_protocol: Twenty milliliters of blood was collected from each patient. Blood was collected in EDTA-containing Vacutainers (Becton Dickinson, Franklin Lakes, NJ) to prevent clotting. Plasma was obtained by Ficoll (Amersham, Piscataway, NJ) gradient centrifugation of whole blood at 1,600 rpm  for 30 min within 3 h of collection. The plasma was carefully removed from mononuclear cells, aliquoted without the addition of protease inhibitors into cryovials and stored at -80 degrees C until use.

value: 2 years

tag: Diagnosis

value: severe congenital neutropenia

tag: Donor type

value: unrelated donor

tag: HLA match

tag: Conditioning

value: full intensity

tag: Blood drawn post BMT

value: 34 days

tag: GVHD stage Skin-Liver-Gut

tag: Followup

value: 390 days

tag: Outcome

value: alive

label: Biotin-ULS

source_name: Plasma, pool of all 42 sample

tag: Plasma, pool of all 42 sample


title: Plasma_reference_pool_unlabeled_rep1

description: top array on slide, control array, batch 2


title: Plasma_GVHD-_86

description: top array on slide, batch 3

tag: Age

value: 50 years

value: acute lymphoblastic leukemia

value: 31 days

value: 776 days

value: dead


title: StreptococcusmutansΔcodY_FMC_rep1

description: S. mutans codY knockout


title: Plasma_GVHD+_55

description: top array on slide, batch 3

value: 45 years

value: chronic myeloid leukemia

value: matched related donor

value: 10 days

value: 95 days


title: Plasma_GVHD-_58

description: top array on slide, batch 3

value: 20 years

value: Hodgkin disease

value: reduced intensity

value: 28 days

value: 180 days


title: Plasma_GVHD+_48

description: top array on slide, batch 3

value: 43 years

value: multiple myeloma

value: 70 days

value: 179 days


title: StreptococcusmutansUA159_FMC_rep4

description: S. mutans wildtype control


title: StreptococcusmutansΔcodY_FMC_rep2

description: S. mutans codY knockout

value: Δcody


title: StreptococcusmutansUA159_FMC_rep2

description: S. mutans wildtype control


title: Plasma_GVHD+_51

description: top array on slide, batch 3

value: 33 years

value: acute myeloid leukemia

value: unrelated donor

value: full intensity

value: 21 days

value: 278 days


title: Plasma_GVHD+_46

description: bottom array on slide, batch 3

value: 38 years

value: acute lymphoblastic leukemia

value: matched related donor

value: 34 days

value: 144 days

value: alive


title: Plasma_GVHD+_47

description: top array on slide, data not used, batch 2

value: 23 years

value: reduced intensity

value: 73 days

value: 188 days

value: dead


title: Plasma_GVHD+_53

description: bottom array on slide, batch 3

value: 26 years

value: 40 days

value: 173 days


title: Plasma_GVHD-_84

description: top array on slide, batch 3

value: 56 years

value: acute myeloid leukemia

value: full intensity

value: 33 days

value: 116 days


title: Plasma_GVHD-_59

description: bottom array on slide, batch 3

value: Non-Hodgkin lymphoma

value: unrelated donor

value: 55 days

value: 763 days


title: Plasma_GVHD+_49

description: bottom array on slide, batch 3

value: 58 years

value: 88 days

value: 245 days


title: Plasma_GVHD-_85

description: bottom array on slide, batch 3

value: 54 years

value: 64 days

value: 920 days

value: alive


title: Plasma_GVHD-_57

description: bottom array on slide, batch 3

value: 37 years

value: acute lymphoblastic leukemia

value: 31 days

value: 305 days


title: Plasma_reference_pool_unlabeled_rep2

description: bottom array on slide, control array, batch 2


title: Plasma_GVHD+_73

description: bottom array on slide, batch 2

value: 29 years

value: Hodgkin disease

value: reduced intensity

value: 24 days

value: 98 days

value: dead


title: Plasma_GVHD-_56

description: top array on slide, batch 3

value: 11 years

value: matched related donor

value: full intensity

value: 59 days

value: 385 days


title: Plasma_GVHD+_61

description: top array on slide, batch 1

value: 31 years

value: acute myeloid leukemia

value: unrelated donor

value: 243 days


title: Plasma_GVHD-_80

description: top array on slide, batch 2

value: 56 years

value: 63 days

value: 971 days

value: alive


title: Plasma_GVHD+_45

description: bottom array on slide, batch 2

value: 57 years

value: myelodysplastic syndrome

value: 14 days


title: Plasma_GVHD+_70

description: bottom array on slide, batch 2

value: 14 years

value: acute lymphoblastic leukemia

value: 76 days

value: dead


title: Plasma_GVHD-_43

description: bottom array on slide, batch 2

value: 58 years

value: matched related donor

value: full intensity

value: 57 days

value: 173 days


title: Plasma_GVHD+_72

description: top array on slide, batch 2

value: 1 years

value: umbilical cord

value: 28 days

value: 120 days


title: Plasma_GVHD-_41

description: top array on slide, batch 2

value: 59 years

value: acute myeloid leukemia

value: unrelated donor

value: 434 days

value: alive


title: Plasma_GVHD-_79

description: bottom array on slide, batch 2

value: 5 years

value: juvenile myelomonocytic leukemia

value: 30 days

value: 309 days


title: Plasma_GVHD+_68

description: top array on slide, batch 2

value: 41 years

value: myelodysplastic syndrome

value: matched related donor

value: 26 days

value: 53 days

value: dead


title: Plasma_GVHD-_44

description: top array on slide, batch 2

value: 67 years

value: reduced intensity

value: 64 days

value: 573 days


title: Plasma_GVHD+_50

description: bottom array on slide, batch 2

value: 25 years

value: chronic myeloid leukemia

value: full intensity

value: 69 days

value: 129 days


title: Plasma_GVHD-_78

description: top array on slide, batch 2

value: 33 years

value: acute myeloid leukemia

value: 28 days

value: 630 days


title: Plasma_GVHD-_52

description: top array on slide, batch 1

value: 65 years

value: acute lymphoblastic leukemia

value: unrelated donor

value: 30 days

value: 1403 days

value: alive


title: Plasma_GVHD-_71

description: bottom array on slide, batch 1

value: 28 years

value: 67 days


title: Plasma_GVHD+_62

description: bottom array on slide, batch 1

value: 54 years

value: 26 days

value: 115 days

value: dead


title: Plasma_GVHD-_74

description: top array on slide, batch 1

value: 52 years

value: matched related donor

value: full intensity

value: 528 days


title: Plasma_GVHD-_69

description: top array on slide, batch 1

value: 49 years

value: acute myeloid leukemia

value: 62 days

value: 1340 days


title: Plasma_GVHD+_63

description: top array on slide, batch 1

value: 55 years

value: 14 days

value: 48 days


title: Plasma_GVHD+_65

description: top array on slide, batch 1

value: 60 years

value: Non-Hodgkin lymphoma

value: 83 days

value: 90 days


title: Plasma_GVHD-_75

description: bottom array on slide, batch 1

value: 11 years

value: acute lymphoblastic leukemia

value: 59 days

value: 385 days

value: alive


title: Plasma_GVHD+_64

description: bottom array on slide, batch 1

value: 36 years

value: unrelated donor

value: full intensity

value: 33 days

value: 432 days

value: dead


title: Plasma_GVHD-_76

description: top array on slide, batch 1

value: 67 years

value: myelodysplastic syndrome

value: reduced intensity

value: 30 days

value: 970 days


title: Plasma_GVHD-_66

description: bottom array on slide, batch 1

value: 39 years

value: Non-Hodgkin lymphoma

value: 29 days

value: 1282 days


title: Plasma_GVHD+_67

description: bottom array on slide, batch 1

value: 20 years

value: 14 days

value: 47 days


title: Plasma_GVHD+_88

description: bottom array on slide, batch 3

value: 58 years

value: unrelated donor

value: 88 days

value: 245 days


title: Plasma_GVHD+_60

description: bottom array on slide, batch 1

value: 63 years

value: matched related donor

value: 65 days

value: 100 days

value: dead


title: Mersacidin16_samples13793G_chip117

status: Public on Oct 23 2008

city: Bonn

first: Peter

last: Sass

state: NRW

address: Sigmund-Freud-Straße 25

department: Institute for Microbiology (IMMIP)

country: Germany

institute: University of Bonn

description: no additional information provided

hyb_protocol: Microarray transcriptional profiling by competitive hybridization of fluorescence-labeled cDNA was performed using the custom PCR product full-genome chip sciTracer (Scienion, Berlin, Germany) containing 2338 unique open reading frames representing 90% of the S. aureus N315 genome (NC_002745). Additional information on the microarray platform is described elsewhere. To increase reproducibility, each experiment was performed 4 times including a dye swap resulting in four chips per competitive comparison with the incorporated dye reversed on two separate arrays. All hybridizations were done with equal amounts of fluorescence-labeled cDNA probes or picomols of dye. Fluorescence-labeled cDNA probes were mixed in hybridization buffer (Scienion) in a total volume of 55 µl and denatured at 95°C for 2 min and subsequently applied to the microarray slide following incubation at 42°C for 72 hours under humidified conditions according to the manufacturer’s instructions. Hybridized microarrays were washed at room temperature in SSC buffer with decreasing salt concentrations (1 x SSC/0.3% SDS for 5 min, 0.2 x SSC for 5 min, 0.06 x SSC for 30s).

scan_protocol: The intensity of fluorescence of the microarray was scanned with a GenePix 4000B scanner (Axon Instruments/Distribution by Biozyme Scientific GmbH, Hessisch Oldendorf, Germany). TIFF images were captured and analysed with GenePixPro4.1 software (Axon Instruments). The actual signal intensity was calculated by substracting the mean value of the local background intensity from the mean value of the signal intensity of the individual spot.

data_processing: The data sets were then normalized by using Acuity 3.1 software (Axon Instruments) and by applying the LOWESS algorithm. Significant changes of gene expression were determined by implementing SAM (significance analysis of microarrays; http://www-stat.stanford.edu/~tibs/SAM/; (Tusher, V. G., R. Tibshirani, and G. Chu. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc.Natl.Acad.Sci.U.S.A 98:5116-5121.)) using the one class response and a false discovery rate of < 1% with a medium number of falsely called significant genes of <1.

organism: Staphylococcus aureus

source_name: Staphylococcus aureus 137/93G

label_protocol: Fluorescence-labeled single-stranded cDNA was obtained by reverse transcription of total RNA. To this end, three different aliquots of total RNA preparations from separate cultures of the respective experiment were pooled to a total amount of 9 µg (3 µg each) and transcribed into cDNA using 100 Units (U) of BioScript reverse transcriptase (Bioline, Luckenwalde, Germany) following the manufacturer’s instructions. For direct cDNA labeling, the total reaction volume of 40 µl contained 75 µg/ml pd(N)6 random hexamers (GE Healthcare - Amersham, NJ, USA), 0.1 mM CyDye3- or CyDye5-dCTPs (GE Healthcare - Amersham) aside from 0.2 mM dCTP, 0.5 mM dATP, 0.5 mM dTTP, 0.5 mM dGTP and 25 U/ml RNase-OUT (Invitrogen, Karlsruhe, Germany). RNA was degraded by alkaline hydrolysis at 65°C and fluorescence-labeled cDNA was purified using the MinElute PCR purification kit (Qiagen). cDNA synthesis and Cy3/Cy5 incorporation was verified using the Nanodrop spectrophotometer (Nanodrop Technologies).

extract_protocol: Exponential-phase cultures of 10 ml for total RNA preparations were grown as aforementioned and fixed by incubation with two volumes of prewarmed RNAprotect Bacteria Reagent (Qiagen, Hilden, Germany) for 5 min at 37°C. The cells were subsequently harvested by 20 min of centrifugation at 4000 rpm and 37°C, and the pellets were shock-frozen in fluid nitrogen and kept at -70°C. The cells were lysed in the presence of 400 µg/ml lysostaphin (Genmedics, Reutlingen, Germany) and total RNA was extracted using the PrestoSpin R bug kit including DNase I treatment (Molzym, Bremen, Germany) following the manufacturer’s instructions. Quality and quantity of total RNA were confirmed by agarose gel electrophoresis and measured using the Nanodrop spectrophotometer (Nanodrop Technologies, Wilmington, USA).

treatment_protocol: S. aureus cultures for RNA preparations were diluted 200-fold from fresh BHI broth overnight cultures and further incubated until they reached an OD600 ~ 1.0. CaCl2 was supplemented to all cultures to a final concentration of 1 mM since Ca2+-ions enhance the bactericidal effect of mersacidin.

tag: Methicillin-resistant S. aureus (MRSA) SA137/93A, isolated from a tracheal secretion and displays heterogeneous intermediate vancomycin resistance (hVISA strain, MIC

value: 8 mg/L in BHI). Subculturing in presence of 6 mg/L vancomycin generated a mutant with homogeneous intermediate vancomycin resistance, that showed an MIC value of 16 mg/L in BHI and was designated SA137/93G. Source:Reipert, A., K. Ehlert, T. Kast, and G.

tag: Bierbaum. 2003. Morphological and genetic differences in two isogenic Staphylococcus aureus strains with decreased susceptibilities to vancomycin. Antimicrob.Agents Chemother.47:568-576.

treatment_protocol: S. aureus cultures for RNA preparations were diluted 200-fold from fresh BHI broth overnight cultures and further incubated until they reached an OD600 ~ 0.5. Next, mersacidin was added in subinhibitory concentrations and the cultures were further grown to an OD600 of ~ 1.0. CaCl2 was supplemented to all cultures to a final concentration of 1 mM since Ca2+-ions enhance the bactericidal effect of mersacidin.


title: Arabidopsis_thrips_2h

status: Public on Oct 25 2008

city: Kaga-gun, Okayama

first: Yoshihiro

last: Narusaka

address: 7549-1, Kibityuo-town Yoshikawa

country: Japan

institute: Research Institute for Biological Sciences

description: Leaves were harvested and then snap-frozen in liquid nitrogen. Samples were stored at -80 ℃ until RNA extraction. To ensure biological reproducibility of the microarray results, the experiment was replicated three to four times with between thirty and seventy plants per sample. To obtain sufficient material for the experiments, samples from replicate experiments were pooled prior to RNA extraction. In addition, we conducted two to three independent microarray analyses with the same RNA for reproducibility of handling. The results demonstrated a high degree of correlation in fold change values between the different data sets. Total RNA was prepared using a TRIZOL Reagent (Invitrogen. Corp., Carlsbad, CA, USA), and subsequent mRNA was prepared using an oligotex mRNA isolation kit (Takara, Shiga, Japan). Labeling of the mRNA sample was carried out as reported previously (Seki et al.(2002) Plant J. 31:279-292). Labeled cDNA was dissolved in 15 ul hybridization buffer (3.4 x SSC, 0.3% SDS), denatured at 100 ℃ heat block for 2 min, left at room temperature for 5 min, and applied directly to the slides. Microarrays were covered with a 22 x 24 mm cover slip and hybridized in a 65 ℃ water bath for 16 to 20 h. Post-hybridization washing was performed 2 x SSC, 0.03% SDS for 2 min, then in 1 x SSC for 2 min, and finally in 0.06 x SSC for 2 min. Then, the slides were immediately dried by centrifugation (1 min at 2500 g). Slides were scanned with a ScanArray Lite (PerkinElmer, Wellesley, MA, USA) and signal calculation for each spot was processed with ScanArray Express Ver.3(PerkinElmer, Wellesley, MA, USA) .

hyb_protocol: The probe samples were denatured by placing them in a 100 ℃ heat block for 2 min, left at room temperature for 5 min, and then used for hybridization. The slides were placed in a sealed hybridization cassette (Telechem International Inc., Sunnyvale, CA) and submerged in a 65 ℃ water bath for 16 to 20 h.

scan_protocol: Slides were scanned with a ScanArray Lite (PerkinElmer, Wellesley, MA, USA) and signal calculation for each spot processed with ScanArray Express Ver.3(PerkinElmer, Wellesley, MA, USA) .

data_processing: A lambda control template DNA fragment (TAKARA) was used as an external control to equalize the hybridization signals generated from different samples (Narusaka et al. 2006). The median of 82 signal values obtained from the lambda control template DNA fragment on the 1.2 K microarray was used as an external control.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Untreated plant (control)

label_protocol: Labeling of the mRNA sample was carried out as reported previously (Seki et al. (2002) Plant J. 31:279-292). Each mRNA sample was reverse-transcribed in the presence of Cy3-dUTP (Amersham Pharmacia, Piscataway, NJ).

growth_protocol: Arabidopsis wild-type plants (ecotype Columbia; Col-0) were grown in soil for 21 days in a growth chamber at 22°C under a 16-h light/ 8-h dark cycle.  The samples were frozen in liquid nitrogen.

extract_protocol: Total RNA was prepared using a TRIZOL Reagent (Invitrogen. Corp., Carlsbad, CA, USA), and then mRNA was prepared using an oligotex mRNA isolation kit (Takara, Shiga, Japan).

treatment_protocol: Untreated plants were used

tag: Ecotype

value: Columbia, Age:21 days, Sample:whole plant (except for root)

source_name: Feeding with thrips for 2h

label_protocol: Labeling of the mRNA sample was carried out as reported previously (Seki et al. (2002) Plant J. 31:279-292). Each mRNA sample was reverse-transcribed in the presence of Cy5-dUTP (Amersham Pharmacia, Piscataway, NJ).

growth_protocol: The plants were grown in soil for 21 days in a growth chamber at 22°C under a 16-h light/ 8-h dark cycle. Twenty-five adult females of western flower thrips (Frankliniella occidentalis) were starved for 3 h before feeding on test plants, and were grouped and allowed to feed on each whole test plant in an acrylic cylinder chamber with air ventilation windows covered with a fine mesh. The plants were subjected to feeding treatment for 2 h and then frozen in liquid nitrogen.

treatment_protocol: The 21- day-old plants were feeded by western flower thrips in an acryl cylinder chamber with air ventilation windows covered with a fine mesh. Leaves were harvested 2 h after the feeding and then frozen immediately in liquid nitrogen.


title: Arabidopsis_thrips_24h

growth_protocol: Arabidopsis wild-type plants (ecotype Columbia; Col-0) were grown in soil for 21 days in a growth chamber at 22°C under a 16-h light/ 8-h dark cycle. The samples were frozen in liquid nitrogen.

source_name: Feeding with thrips for 24h

label_protocol: Labeling of the mRNA sample was carried out as reported previously (Seki et al. (2002) Plant J. 31:279-292). Each mRNA sample was reverse-transcribed in the presence of Cy5- dUTP (Amersham Pharmacia, Piscataway, NJ).

growth_protocol: The plants were grown in soil for 21 days in a growth chamber at 22°C under a 16-h light/ 8-h dark cycle. Twenty-five adult females of western flower thrips (Frankliniella occidentalis) were starved for 3 h before feeding on test plants, and were grouped and allowed to feed on each whole test plant in an acrylic cylinder chamber with air ventilation windows covered with a fine mesh. The plants were subjected to feeding treatment for 24 h and then frozen in liquid nitrogen.

treatment_protocol: The 21- day-old plants were feeded by western flower thrips in an acryl cylinder chamber with air ventilation windows covered with a fine mesh. Leaves were harvested 24 h after the feeding and then frozen immediately in liquid nitrogen.


title: Arabidopsis_thrips_5h

extract_protocol:
Total RNA was prepared using a TRIZOL Reagent (Invitrogen. Corp., Carlsbad, CA, USA),
and then mRNA was prepared using an oligotex mRNA isolation kit (Takara, Shiga, Japan).

source_name: Feeding with thrips for 5h

growth_protocol: The plants were grown in soil for 21 days in a growth chamber at 22°C under a 16-h light/ 8-h dark cycle. Twenty-five adult females of western flower thrips (Frankliniella occidentalis) were starved for 3 h before feeding on test plants, and were grouped and allowed to feed on each whole test plant in an acrylic cylinder chamber with air ventilation windows covered with a fine mesh. The plants were subjected to feeding treatment for 5 h and then frozen in liquid nitrogen.

treatment_protocol: The 21- day-old plants were feeded by western flower thrips in an acryl cylinder chamber with air ventilation windows covered with a fine mesh. Leaves were harvested 5 h after the feeding and then frozen immediately in liquid nitrogen.


title: Arabidopsis_thrips_10h

source_name: Feeding with thrips for 10h

growth_protocol: The plants were grown in soil for 21 days in a growth chamber at 22°C under a 16-h light/ 8-h dark cycle. Twenty-five adult females of western flower thrips (Frankliniella occidentalis) were starved for 3 h before feeding on test plants, and were grouped and allowed to feed on each whole test plant in an acrylic cylinder chamber with air ventilation windows covered with a fine mesh. The plants were subjected to feeding treatment for 10 h and then frozen in liquid nitrogen.

treatment_protocol: The 21- day-old plants were feeded by western flower thrips in an acryl cylinder chamber with air ventilation windows covered with a fine mesh. Leaves were harvested 10 h after the feeding and then frozen immediately in liquid nitrogen.


title: Pure and mixed 2h30 exponential phase rep 2

city: Toulouse

first: Muriel

last: Cocaign-Bousquet

address: 135 avenue de Rangueil

department: UMR5504 INSA/CNRS - UMR792 INSA/INRA

institute: Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés

description:
L. lactis pure and mixed culture 2h30 exponential phase replicate 2
Comparison of the transcriptome of L.lactis in a mixed culture with S.cerevisiae and the transcriptome of L.lactis in a pure culture. Samples were taken at 2h30 of exponential growth phase in both cases.

hyb_protocol: Experiments were carried out at the Biochips platform of Toulouse with an automatic hybridization chamber (Discovery from Ventana Medical System, Inc). Pre-hybridization occurred in a freshly prepared solution of 1 % BSA, 2x SSC, 0.2 % SDS over 1.5 h at 50 °C. After automatic washing according to the manufacturer’s instructions, the slides were hybridized for 5 h at 50 °C in 200 µl ChipHybeTM buffer (Ventana Medical System, Inc) containing 3 µl of Cy3-labelled cDNA and 3 µl of Cy5-labelled cDNA. Unlabelled genomic DNA (20 µl at 20 µg.µl-1) was added to the solution (see manuscript in preparation Maligoy et al. 2007. Transcriptome analysis of Lactococcus lactis in co-culture with Saccharomyces cerevisiae). After hybridization, the slides were washed twice in RiboWash® (Discovery from Ventana Medical System, Inc), then 2 min in 0.2x SSC, quickly rinsed in isopropanol, and then dried by centrifugation 5 minutes at 3,000 g.

scan_protocol: Fluorescence signals were captured with a laser scanner at 750pmt (GenePix 4000A from Axon Instrument, CA) and analyzed with the GenePix 3.01 software.

data_processing: Local background was removed from the raw signals with the Bioplot software (Biochips Platform, INSA Toulouse, France, http://biopuce.insa-toulouse.fr). Duplicates were aggregated by mean calculation. A detection threshold was defined as the mean intensity plus three standard deviations of empty spots. Spots with intensities below the detection threshold were tagged ‘negative’ in the Bioplot software. Data were normalized by the ‘all non-negative spots mean’ with Bioplot software.

organism: Lactococcus lactis

source_name: L. lactis 2h30 exponential phase in pure culture

label_protocol: Total RNA was reverse-transcribed and labeled with a cyanine dye (Cy3 for the reference and Cy5 for the test condition) in a direct process using Labelstar array kits (Qiagen). RNA (30 µg) was denatured and then combined with RT-buffer, dNTP mix (0.5 mM final for dATP, dTTP, dCTP; 0.08 mM final for dCTP), random hexamer primers 5 µl (invitrogen), Cy3 or Cy5-labelled dCTP (0.02 mM final), RNase inhibitor 20 units (Qiagen) and labelstar reverse transcriptase (Qiagen). The mix was incubated 2 hours at 37 °C. The reaction was stopped by adding LS solution (Qiagen) and cDNA was purified using MinElute columns (Qiagen). 10 µl were collected for each reaction.

growth_protocol: Lactococcus lactis ssp. lactis IL1403 was grown in a semi-synthetic medium containing glucose (20 g.l-1), yeast extract (10 g.l-1), KH2PO4 (9 g.l-1), K2HPO4 (7.5 g.l-1), MgCl2 (0.2 g.l-1), and ergosterol (6 mg.l-1) dissolved in pure ethanol, and sterilized by filtration (Sartorius 0.2 µm), in anaerobic conditions, under nitrogen atmosphere, in a 2-liters fermentor (Setric Génie Industriel, Toulouse, France) at agitation speed of 350 rpm. The temperature in the fermentor was maintained at 34 °C, and the pH was maintained at 6.6 with automatic addition of KOH (10 N). Inoculation was made with cells from pre-cultures grown on the same medium. Pre-culture cells were harvested during the exponential growth phase and concentrated in order to obtain an initial OD580 of 0.01-0.02 in the fermentor.

extract_protocol: Frozen cell pellets corresponding to 6 mg dry weight were dropped into a pre-cooled 5 ml Teflon vessel. For the co-culture, the 6 mg of cell dry weight containing L. lactis and S. cerevisiae was estimated from the plate count. A 7 mm bead made of tungsten carbide was added. The flask was then shaked at 2600 rpm for 2 minutes into a Mikro-Dismembrator (Braun, Melsungen). Powder was re-suspended into 4 ml of RLT buffer (Qiagen) supplied with beta-mercaptoethanol. Following steps of RNA extraction were done according to Qiagen RNeasy protocol including DNase I treatment. RNA quality and quantification were analyzed using a Bioanalyser Agilent 2100 (Agilent technologies).

tag: strain IL1403

tag: pure culture, 2h30 exponential growth phase

source_name: L. lactis 2h30 exponential phase in mixed culture

growth_protocol: Lactococcus lactis ssp. lactis IL1403 and Saccharomyces cerevisiae CENPK905 were grown together in a semi-synthetic medium containing glucose (20 g.l-1), yeast extract (10 g.l-1), KH2PO4 (9 g.l-1), K2HPO4 (7.5 g.l-1), MgCl2 (0.2 g.l-1), and ergosterol (6 mg.l-1) dissolved in pure ethanol, and sterilized by filtration (Sartorius 0.2 µm), in anaerobic conditions, under nitrogen atmosphere, in a 2-liters fermentor (Setric Génie Industriel, Toulouse, France) at agitation speed of 350 rpm. The temperature in the fermentor was maintained at 34 °C, and the pH was maintained at 6.6 with automatic addition of KOH (10 N). Inoculation was made with cells from pure pre-cultures grown on the same medium. Pre-culture cells were harvested during the exponential growth phase and concentrated in order to obtain an initial OD580 of 0.01-0.02 in the fermentor.

tag: mixed culture with S.cerevisiae, 2h30 exponential growth phase


title: Pure 2h00 and 3h00 exponential phase rep 3

description:
L. lactis pure culture 2h00 and 3h00 exponential phase replicate 3
Transcriptome analysis of L.lactis in a pure culture. Samples were taken at 2h00 (channel 1) and 3h00 (channel 2) of exponential growth phase.

source_name: L. lactis 2h00 exponential phase in pure culture

tag: growth status pure culture, 2h00 exponential growth phase

source_name: L. lactis 3h00 exponential phase in pure culture

tag: growth status pure culture, 3h00 exponential growth phase


title: Pure 2h00 and 3h00 exponential phase rep 2

description:
L. lactis pure culture 2h00 and 3h00 exponential phase replicate 2
Transcriptome analysis of L.lactis in a pure culture. Samples were taken at 2h00 (channel 1) and 3h00 (channel 2) of exponential growth phase.


title: Pure and mixed 2h30 exponential phase rep 1

description:
L. lactis pure and mixed culture 2h30 exponential phase replicate 1
Comparison of the transcriptome of L.lactis in a mixed culture with S.cerevisiae and the transcriptome of L.lactis in a pure culture. Samples were taken at 2h30 of exponential growth phase in both cases.


title: Pure 2h00 and 3h00 exponential phase rep 1

description:
L. lactis pure culture 2h00 and 3h00 exponential phase replicate 1
Transcriptome analysis of L.lactis in a pure culture. Samples were taken at 2h00 (channel 1) and 3h00 (channel 2) of exponential growth phase.

tag: strain IL1403/growth status pure culture, 3h00 exponential growth phase


title: Mersacidin1_samplesSASG511_chip116

description: no additional information provided

source_name: Staphylococcus aureus SG511

tag: Staphylococcus aureus SG511 is a sensitive control strain (methicillin susceptible) from the strain collection of the Robert Koch-Institute, Berlin, Germany.


title: Mersacidin1_samplesSASG511_chip114

description: no additional information provided


title: Mersacidin16_samples13793G_chip026

description: no additional information provided


title: Mersacidin16_samples13793A_chip220

description: no additional information provided

source_name: Staphylococcus aureus 137/93A

value: 8 mg/L in BHI). Source:Reipert, A., K. Ehlert, T. Kast, and G. Bierbaum. 2003. Morphological and genetic differences in two isogenic Staphylococcus aureus strains with decreased susceptibilities to vancomycin. Antimicrob.Agents Chemother. 47:568-576.


title: Mersacidin16_samples13793G_chip025

description: no additional information provided

value: 8 mg/L in BHI).  Subculturing in presence of 6 mg/L vancomycin generated a mutant with homogeneous intermediate vancomycin resistance, that showed an MIC value of 16 mg/L in BHI and was designated SA137/93G.

tag: Source

value: Reipert, A., K. Ehlert, T. Kast, and G. Bierbaum. 2003. Morphological and genetic differences in two isogenic Staphylococcus aureus strains with decreased susceptibilities to vancomycin. Antimicrob.Agents Chemother. 47:568-576.


title: Mersacidin16_samples13793A_chip120

description: no additional information provided


title: Mersacidin1_samplesSASG511_chip113

description: no additional information provided


title: Control vs Mid H2 sample 4

status: Public on Oct 28 2008

city: Bielefeld

first: Anh Vu

last: Nguyen

address: G2-154, CEBITEC, Universitaetsstr. 27

department: Cell and Molecular Biology

institute: Bielefeld University

description: Microarray images from scanned slides were imported into the GenePix Pro. 6.0 program (Axon Instruments). Spots were automatically identified using the built-in spot alignment algorithm based on the information of spot positions provided in the gal file. All spots were checked and adjusted visually. Spots with signals distorted by dusts or high local background as well as spots that were marked absent by the GenePix program were not included in the analyses.

hyb_protocol: Prehybridization Prehybridization was done immediately before hybridization. 1. Incubate slides in prewarmed Prehybridization Solution  at 42ºC for one hour. 2. Transfer arrays to 0.1X SSC and gently agitate at room temperature for 5 min. 3. Repeat step 3 in a fresh bath of 0.1X SSC. 4. Transfer arrays to ddH20 for 30 sec. 5. Dry arrays by spinning for 10 min. Hybridization 1. Resuspend dried cDNAs in 25 µl of milliQ water preheated to 40ºC. 2. Prepare 2X Hybridisation Buffer, keep at 40ºC all the time, to avoid SDS precipitation. 3. Add 25 µl of  2X Hybridisation Buffer to each sample and resuspend thoroughly by pipetting. 4. Boil the samples for 3 min. 5. Meanwhile place arrays on kimwipe on plane surface. Prepare the Fisherbrand Large Coverslips (withour spacers). 6. Spin down the samples and pipett the probe onto the middle of the array. Carefully place Fisherbrand Large Coverslip onto the array. Be sure probe is evenly distributed all along the array. 7. Add 3 drops of 10 µl 3X SSC to the bottom of the array. Seal the chamber and incubate in 42ºC waterbath for 16 hours. Post-Hybridization Washes 1. Preheat two 350 ml jars containing 2X SSC, 0.1% SDS to 42ºC at leats 30 min (best to put the jars filled with buffer in the hot water bath). 2. Just before use, add 800 µl of freshly prepared 1M DTT to 800 mL of each washing solution. 3. Take out the jars. Unmount the hybridization chamber. 4. Take out each slide individually and immediately hold with light dipping in the first preheated 2X SSC, 0.1% SDS jar, until coverslips freely move away from the slides. 5. Transfer slides to a new preheated jar containg 2X SSC, 0.2% SDS and dip gently for 5 min. 6. Transfer slides to 0.1X SSC, 0.1% SDS at room temperature and wash for 5 min. 7. Transfer arrays to 0.1X SSC and wash for 5 min. 8. Rinse arrays in 0.01X SSC for 10 sec and immediately spin-dry for 5 min. 9. Scan the arrays.

scan_protocol: The slides were scanned at 532 nm and 635 nm in an Axon GenePix 4000B scanner at 10-µm resolution. Photomultiplier tube voltages were adjusted to minimize the background signal and the number of saturated spots. Images of the fluorescence at 532 nm (for Alexa Fluor 555) and 635 nm (for Alexa Fluor 647) were recorded and analysed.

data_processing: Raw feature intensities without background subtraction were imported into and  normalized by GeneSpring GX. VALUE is Log (base 2) of the ratio of SAMPLE to CONTROL.

label: Alexa Flour 647 (Invitrogen)

organism: Chlamydomonas reinhardtii

source_name: CC124 - Mid H2 sample 4

label_protocol: In the indirect labelling method, amine-modified cDNA is produced from total RNA by the incorporation of aminoallyl-dUTP (5-(3-aminoallyl)-2’-deoxyuridine 5’-triphosphate)) using reverse transcription. The amine-modified cDNA can then be coupled with reactive dye of specific emission wavelength to produced desired labelled CDNA. In this experiment, total RNA (~ 20 - 40 µg) was denatured at 70°C for 10 min in the presence of 1 µg of oligo dT 12-18 (100 mM) in a reaction volume of 15.5 µl. The reaction was cooled on ice prior to the addition of 6 µl of 5x Superscript II reverse transcriptase first strand buffer (Invitrogen), 1.5 µl of 0.1 M dithiothreitol, 5 µl of deoxynucleoside triphosphate mix (0.9 mM dTTP, 3 mM dATP, 3 mM dGTP, 3 mM dCTP and 1.8 mM aminoallyl-dUTP), 2 µl of Superscript III reverse transcriptase (200 U/µl). The 30 µl reaction was incubated at 50°C in a thermocycler for 3 h and then stopped by heating the reaction to 95oC for 5 min. RNA was hydrolysed by adding 15 µl of 1 M NaOH and incubating at 70 oC for 15 min. The alkalinized solution was neutralized by the addition of 15 µl of 1 M HCl. Amine-modified DNA was purified from the reaction using the Labelled Star purification kit (Qiagen) and was eluted in 20 µl Milli Q water. The purified amine-modified cDNA was concentrated to a 5 µl volume using a vacumm centrifuge. The concentrated cDNA was then labelled with either the Alexa Fluor 555 or Alexa Fluor 647 dye by incubating 5 µl of the concentrated amine-modified cDNA with 3 µl of 0.3 M NaHCO3 and 2 µl of the Alexa Fluor succinimidyl ester dye in DMSO at room temperature for 1 h in the dark. The labelled cDNA from each time point following the initiation of S deprivation was combined with the labelled control cDNA. The labelled sample/control combined cDNA was purified with a Qiagen Labelled Star purification kit (QIAGEN). Purified cDNA was recovered in 25 µl of Milli Q H2O. The incorporation of the fluorescent dyes into cDNA was quantified with a NanoDrop® ND-1000 spectrophotometer.

extract_protocol: Cells were harvested by centrifugation at 3000 x g for 1.5 minutes at 4oC. The resulting cell pellets were immediately frozen in liquid nitrogen and stored at -80oC for later RNA extraction. Frozen cells were stored at -80oC before RNA extraction. RNA was extracted following the centrifugation protocol for plant tissues using the SV Total RNA Isolation System (Promega) without sample grinding. Purified RNA from was eluted in 100 ul of ddH2O.

tag: Mid H2 sample 4

label: Alexa Flour 555 aha-dUTP

source_name: CC124 - Control

tag: Prior to sulfur deprivation for hydrogen production


title: Pure and mixed 2h30 exponential phase rep 3

description:
L. lactis pure and mixed culture 2h30 exponential phase replicate 3
Comparison of the transcriptome of L.lactis in a mixed culture with S.cerevisiae and the transcriptome of L.lactis in a pure culture. Samples were taken at 2h30 of exponential growth phase in both cases.


title: Mersacidin1_samplesSASG511_chip115

description: no additional information provided


title: Mersacidin16_samples13793G_chip118

description: no additional information provided


title: Control vs Zero O2 sample 3 dye swap

label: Alexa Flour 647 aha-dUTP (Invitrogen)

label_protocol: In the direct labelling method, total RNA served as the template for the labelling of DNA by the direct incorporation of Alexa Flour 555 aha-dUTP (5-aminohexylacrylamido-dUTP) or Alexa Flour 647 aha-dUTP (Invitrogen) using reverse transcription. Total RNA (30 - 40 µg total) was denatured at 70°C for 5 min in the presence of 1 µg of 100 mM oligo dT 12-18 in a reaction volume of 16 µl. The reaction was cooled on ice prior to the addition of 6 µl of 5x Superscript II reverse transcriptase first strand buffer, 3 µl of 0.1 M dithiothreitol, 0.5 µl of deoxynucleoside triphosphates (10 mM dTTP, 25 mM dATP, 25 mM dGTP, and 25 mM dCTP), 2 µl of Superscript II reverse transcriptase (200 U/µl), and 2.5 µl of 2 mM Alexa Fluor 555 aha-dUTP or Alexa Fluor 647 aha-dUTP. The reaction was incubated at 50°C in a thermocycler for 3 h and then stopped by heating the reaction to 95oC for 5 min. RNA was hydrolysed by adding 15 µl of 1 M NaOH and incubating at 70 oC for 15 min. The alkalinized solution was neutralized by the addition of 15 µl of 1 M HCl. The labelled DNA from each time point following the initiation of S deprivation was combined with the labelled control DNA, purified with a Qiagen Labelled Star purification kit (QIAGEN), and recovered in 25 µl of Milli Q H2O. The incorporation of the fluorescent dyes into DNA was quantified with a NanoDrop® ND-1000 spectrophotometer.

tag: prior to sulfur deprivation for hydrogen production

source_name: CC124 - Zero O2 sample 3

tag: Zero O2 sample 3


title: Control vs Mid H2 sample 3

source_name: CC124 - Mid H2 sample 3

tag: Mid H2 sample 3

label: Alexa Flour 555 (Invitrogen)


title: Mersacidin16_samples13793A_chip218

description: no additional information provided

treatment_protocol: S. aureus cultures for RNA preparations were diluted 200-fold from fresh BHI broth overnight cultures and further incubated until they reached an OD600 ~ 1.0. CaCl2 was supplemented to all study cultures to a final concentration of 1 mM since Ca2+-ions enhance the bactericidal effect of mersacidin.

value: 8 mg/L in BHI).

treatment_protocol: S. aureus cultures for RNA preparations were diluted 200-fold from fresh BHI broth overnight cultures and further incubated until they reached an OD600 ~ 0.5. Next, mersacidin was added in subinhibitory concentrations and the cultures were further grown to an OD600 of ~ 1.0. CaCl2 was supplemented to all mersacidin study cultures to a final concentration of 1 mM since Ca2+-ions enhance the bactericidal effect of mersacidin


title: Mersacidin16_samples13793A_chip119

description: no additional information provided


title: Control vs Zero O2 sample 4

data_processing: Raw feature intensities without background subtraction were imported into and  normalized by GeneSpring GX. VALUE is Log (base 2) of the ratio SAMPLE to CONTROL.

source_name: CC124 - Zero O2 sample 4

tag: Zero O2 sample 4


title: Control vs Mid O2 sample 2 dye swap

source_name: CC124 - Mid O2 sample 2

tag: Mid O2 sample 2


title: Control vs Zero O2 sample 2

source_name: CC124 - Zero O2 sample 2

tag: Zero O2 sample 2


title: Control vs Peak O2 sample 4

data_processing: Median feature intensities without background subtraction were imported into and  normalized by GeneSpring GX using the Lowess algorithm. VALUE is Log (base 2) of the ratio of SAMPLE to CONTROL.

source_name: CC124 - Peak O2 sample 4

tag: strain

tag: Peak O2

label: Alexa Flour 555 dUTP

tag: Control; prior to sulfur deprivation for hydrogen production


title: Control vs Peak O2 sample 2 dye swap

data_processing: Raw median feature intensities without background subtraction were imported into and  normalized by GeneSpring GX using the Lowess algorithm. VALUE is Log (base 2) of the ratio of SAMPLE to CONTROL.

tag: Chlamydomonas reinhardtii

tag: Prior to sulphur deprivation for hydrogen production

label: Alexa Flour 555

source_name: Peak O2 Sample 2

tag: During sulphur deprivation of hydrogen production at Peak O2


title: Control vs Mid O2 sample 3

source_name: CC124 - Mid O2 sample 3

tag: Mid O2 sample 3


title: SMC 100 uM homocysteine rep3

status: Public on Oct 21 2008

city: Townsville

first: Jonathan

last: Golledge

state: Queensland

address: School of Medicine

department: School of Medicine

institute: James Cook University

description:
GE Healthcare Amersham CodeLink™ iExpress Assay Reagent Kit
Product booklet Codes: 67601000
4. Description
4.1 CodeLink system summary:
CodeLink™ Expression Bioarray System comprises a set of bioarray
products and tools for gene expression profi ling experiments that
allows monitoring of the mRNA levels of multiple genes
simultaneously. The system includes:
• sets of carefully designed and validated bioarrays with
integrated hybridization chambers that cover a wide range of
discovery genes for several organisms
• cRNA target preparation and hybridization reagents
• optimized protocols for cRNA target preparation and bioarray
processing
• hybridization and post-hybridization parallel processing tools
and fi xtures
• bioarray quantitation analysis software
4.2. Protocol overview
4.2.1. cRNA target preparation
The biotin-labelled cRNA target is prepared by a linear amplifi cation
method. The poly(A)+ RNA (mRNA) subpopulation within the total RNA
population is primed for reverse transcription by a DNA oligonucleotide
containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence. After second-strand cDNA synthesis, the cDNA serves as the
template for an in vitro transcription (IVT) reaction to produce the
target cRNA. The IVT is performed in the presence of biotinylated
nucleotides to label the target cRNA. This method produces
approximately 1 000- to 5 000-fold linear amplifi cation of the input
mRNA.
A set of bacterial mRNA controls is included in each CodeLink iExpress
Assay Reagent Kit to serve as an overall platform performance
control group, and can also be used to estimate the sensitivity of RNA
detection.
13
An independent total RNA control (HeLa) and an exogenous cDNA
IVT control (pTRI-Xef 1 plasmid) are also included in each CodeLink
iExpress Assay Reagent Kit. The HeLa RNA can be used to monitor
overall kit performance; the pTRI-Xef 1 plasmid can be used to
evaluate IVT performance.
4.2.2. Target hybridization and bioarray processing
Hybridization is performed overnight in a temperature-controlled
shaking incubator. Optimized hybridization buffer components
are included in CodeLink iExpress Assay Reagent Kit for use at this
step. The instructions for performing the hybridization and posthybridization
processing steps and bioarray processing are provided
in the CodeLink Gene Expression System: Single-Assay Bioarray
Hybridization and Detection protocol or the CodeLink Gene
Expression System: 16-Assay Bioarray Hybridization and Detection
protocol, depending on the bioarray format to be used.
Post-hybridization processing includes a stringent wash to remove
unbound and non-specifi cally hybridized target molecules, a
secondary-labeling step using a Cy™5-Streptavidin conjugate, and
several washing steps to remove unbound conjugate. Following a
final rinse, the bioarrays are dried by centrifugation and scanned.
Analysis of the bioarrays was done usingwith the CodeLink Expression Analysis software.

hyb_protocol: 10 µg of purified cRNA was fragmented to uniform size and applied to CodeLink Bioarrays (GE Healthcare) in hybridization buffer. Arrays were hybridized at 37ºC for 18 hrs in a temperature-controlled shaking incubator. Arrays were washed in 0.75x TNT at 46º C for 1 hr and stained with Cy5-Streptavidin dye conjugate for 30 min.

scan_protocol: Arrays were scanned with a GenePix™ 4000B scanner.

data_processing: Array data was processed with CodeLink Expression Analysis software (GE Healthcare) and data was analyzed with GeneSpring software (Silicon Genetics). To compare individual expression values across arrays, raw intensity data (generated from CodeLink Expression 2 software) from each gene was normalized to the median intensity of the array. Only genes which had values greater than the background intensity in at least one condition were used for further analysis.

label: biotinylated UTP

source_name: Aortic smooth muscle cells

label_protocol: Biotin-labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample. Briefly, 0.44 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing T7 RNA polymerase promoter 5' to a d(T)24 sequence. After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of biotinylated UTP.

extract_protocol: RNA was extracted from cells using the RNeasy Mini kit (Qiagen) and analysed on the HP 2100 Bioanalyzer (Agilent Technologies) for integrity

tag: CC-2571 cell line Cambrex-Lonza


title: SMC 10 uM homocysteine rep3


title: SMC 100 uM homocysteine rep1


title: SMC 10 uM homocysteine rep1


title: SB57_Stem_ rep1_at anthesis

status: Public on Oct 16 2008

city: Brisbane

first: Gang-Ping

last: Xue

state: Qld

address: 306 Carmody Rd., St Lucia

department: Plant Industry

institute: CSIRO

description: peduncle and penultimate internodes with leaf sheath attached, at anthesis

hyb_protocol: A total of 20ug of biotinylated cRNA was fragmented to the 50-200bp size range and quality control checked using the Bioanalyser 2100 using the NanoChip protocol.  Samples that pass this checkpoint are then prepared for hybridisation to the Affymetrix Wheat Genome GeneChip by preparing a probe cocktail (cRNA at 0.05ug/ul) that includes 1x Hybridisation Buffer (100mM MES, 1m NaCl, 20mM EDTA, 0.01% Tween-20), 0.1mg/ml Herring Sperm DNA, 0.5mg/ml BSA, and 7% DMSO. A total hybridisation volume of 300ul is prepared for each sample and 200ul loaded into a Wheat Genome GeneChip.  The chip is hybridised at 45oC for 16 hours in an oven with a rotating wheel at 60rpm.  After hybridisation the chip is washed and stained with SAPE using the appropriate fluidics script in the Affymetrix Fluidics Station 450.

scan_protocol: The chips are scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The scanner operating software, GCOS, converts the signal on the chip into a DAT file, which will then be used for generating subsequent CEL files for analysis. The raw data in the Affymetrix CEL files of all 16 arrays representing two biological replicates of each of 8 genotypes were normalized using robust multiarray average (Irizarry et al. 2003, Biostatistics 4:249-264),  using the default settings for the Affymetrix package within Bioconductor, running within the R statistical programming environment (http://www.r-project.org/).

organism: Triticum aestivum

source_name: stems of SB57 field replicate 1 at anthesis

label_protocol: Total RNA was quality ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.  cRNA was prepared from 7ug total RNA  using the Affymetrix One Cycle cDNA synthesis kit (Millenium Sciences cat no. 900431).  GeneChip Eukaryotic poly-A RNA spikes (Millenium Sciences cat no. 900433) were added to the reaction to determine the labelling efficiency.  The subsequent cRNA was cleaned using the Affymetrix GeneChip Sample Cleanup kit (Millenium Sciences cat no. 900371).  Upon cleaning of the cRNA the next step was to incorporate biotin into the resultant cRNA using the Affymetrix IVT labelling kit (Millenium Sciences cat no. 900449).  After the IVT process the labelled cRNA was cleaned using the above GeneChip Sample Cleanup kit. The quantity of product was ascertained using the Agilent Bioanalyser 2100 using the NanoChip protocol.

growth_protocol: 8 SB lines were grown under rain-fed conditions with two field replicates of each line in 2005 at the CSIRO Cooper Laboratory at Gatton (latitude 27o  34΄ S, longitude 152o 17΄ E).  The site was on a deep fertile prairie loam soil developed on alluvium with a plant available water holding capacity of about 250 mm to a depth of 1.5 m.  Plot size in each field trial was 6 m x 1.76 m (8 rows) with an inter-row spacing of 22 cm.   Plots were sprayed with herbicides to control weeds and fungicide to prevent foliar diseases.

extract_protocol: Frozen fresh stems (peduncle and penultimate internode with leaf sheath attached) were ground to fine powder in liquid nitrogen. Total RNA was isolated from 1 g of wheat stems using Plant RNA Reagent (Invitrogen, California, USA), according to the manufacturer’s instruction. RNA was further purified through a Qiagen RNeasy column (Qiagen, Australia) after pre-treatment with RNase-free DNase I (Xue and Loveridge, 2004 Plant J 37: 326-339).

treatment_protocol: The stem tops (peduncle and penultimate internode with leaf sheath attached) were sampled at anthesis between 12:00 and 1:00 pm about 2 days after a heavy rain (the soil in the field was still wet at the time of sampling).   Each sample contained 7 to 8 stems from main tillers that were randomly sampled from each plot, immediately dropped into liquid nitrogen, stored at –80oC and used for RNA isolation.

tag: Genotype

value: SB57 from seri M82 x Babax population, top two internodes at anthesis


title: SMC 0 uM homocysteine rep3

source_name: CC-2571 cell line

tag: Cambrex-Lonza


title: SMC 100 uM homocysteine rep2


title: SB69_Stem_ rep2_at anthesis

source_name: stems of SB69 field replicate 2 at anthesis

value: SB69 from seri M82 x Babax population, top two internodes at anthesis


title: SMC 0 uM homocysteine rep2


title: SB57_Stem_ rep2_at anthesis

source_name: stems of SB57 field replicate 2 at anthesis


title: SMC 10 uM homocysteine rep4


title: H1 hESC_4% O2 rep1

status: Public on Oct 22 2008

city: Columbia

first: Toshihiko

last: Ezashi

state: MO

address: 240a CS Bond Life Sciences Center

department: Animal Sciences

institute: University of Missouri-Columbia

description: Gene expression data from human embronic stem cell cultured under 4% oxygen condition

hyb_protocol: The biotin-labeled aRNA (10 ug) was then hybridized to the Affymetrix Human U133 Plus 2.0 gene chip (Affymetrix). Each sample was hybridized to an individual chip, for a total of 6 chips.

scan_protocol: The image data were acquired on an Affymetrix Genechip Scanner 3000.

data_processing: An absolute analysis of the resulting output was performed with Affymetrix Data Mining Tool, Version 3.0 software.

source_name: H1p37 hESC under 4% O2

label_protocol: RNA (5 ug) was used to prepare the biotin-labeled anti-sense RNA (aRNA) target by using the GeneChip® one-cycle target labeling and control reagents (#900493, Affymetrix, Santa Clara, CA).

growth_protocol: Human ESC H1 (WA01) at passage 23 and H9 (WA09) at passage 19 were purchased from WiCell Research Institute (Madison, WI) and cultured in six-well tissue culture plates on a monolayer of γ-irradiated (8,000 cGy) mouse embryonic fibroblast (MEF) feeder cells until passage number 33 and 30, respectively. Thereafter, cells were cultured on a substratum of 1:30 dilutions of Matrigel™ in medium conditioned by MEF.

extract_protocol: RNA was isolated from hESCs by using RNA STAT-60 reagent (Tel-Test Inc, Friendswood, TX) according to the manufacturer's instructions.

treatment_protocol: hESC were cultured in either a standard humidified tissue culture CO2 incubator, set at 5% CO2 in air, or a tri-gas incubator (Heraeus HERAcell 150) at a 4% O2, 5% CO2 setting. Oxygen levels, measured by using a Bacharach CO2/O2 Analyzer (Bacharach, Model 2830), were ~19% in the standard incubator and 3.5–4.5% in the low O2 incubator. To minimize differences unrelated to O2 tension, experimental groups within replicates were cultured in the same medium and passaged at approximately the same time. The H1 and H9 hESC lines had been maintained in a physiological O2 (3-5% O2) atmosphere since passage 26 and 23, respectively. RNA was isolated from H1 cells after 7 days of culture at two independent passage numbers (p37 and p50) and had been maintained on Matrigel™ for 3 and 16 passages, respectively. RNA from H9 cells was isolated at passage 32 and had been grown on Matrigel™ for 3 passages.

tag: human embronic stem cell, NIH code:WA01


title: SMC 100 uM homocysteine rep4


title: SMC 0 uM homocysteine rep4


title: SB3_Stem_ rep1_at anthesis

source_name: stems of SB3 field replicate 1 at anthesis

value: SB3 from seri M82 x Babax population, top two internodes at anthesis


title: SMC 0 uM homocysteine rep1


title: SB109_Stem_ rep2_at anthesis

source_name: stems of SB109 field replicate 2 at anthesis

value: SB109 from seri M82 x Babax population, top two internodes at anthesis


title: SMC 10 uM homocysteine rep2


title: SB10_Stem_ rep2_at anthesis

source_name: stems of SB10 field replicate 2 at anthesis

value: SB10 from seri M82 x Babax population, top two internodes at anthesis


title: SB3_Stem_ rep2_at anthesis

source_name: stems of SB3 field replicate 2 at anthesis


title: SB69_Stem_ rep1_at anthesis

source_name: stems of SB69 field replicate 1 at anthesis


title: SB62_Stem_ rep2_at anthesis

source_name: stems of SB62 field replicate 2 at anthesis

value: SB62 from seri M82 x Babax population, top two internodes at anthesis


title: SB10_Stem_ rep1_at anthesis

source_name: stems of SB10 field replicate 1 at anthesis


title: SB165_Stem_ rep2_at anthesis

source_name: stems of SB165 field replicate 2 at anthesis

value: SB165 from seri M82 x Babax population, top two internodes at anthesis


title: SB62_Stem_ rep1_at anthesis

source_name: stems of SB62 field replicate 1 at anthesis


title: SB169_Stem_ rep2_at anthesis

source_name: stems of SB169 field replicate 2 at anthesis

value: SB169 from seri M82 x Babax population, top two internodes at anthesis


title: SB109_Stem_ rep1_at anthesis

source_name: stems of SB109 field replicate 1 at anthesis


title: SB169_Stem_ rep1_at anthesis

source_name: stems of SB169 field replicate 1 at anthesis


title: SB165_Stem_ rep1_at anthesis

source_name: stems of SB165 field replicate 1 at anthesis


title: luxS mutant with auto-inducer II without glucose biological replicate 3

status: Public on Oct 10 2008

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_auto-inducer II without glucose biological replicate 3

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

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

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

organism: Staphylococcus epidermidis

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

growth_protocol: For microarray experiments, overnight cultures of S. epidermidis (wild-type and luxS mutant) were  1:100 diluted into 50 ml of TSB and incubated at 37°C with shaking at 180 rpm until  grown to mid-logarithmic growth phase.

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

treatment_protocol: After addition of AI-2 to S. epidermidis  1457ΔluxS, incubation was continued for 1 h.


title: luxS mutant with auto-inducer II without glucose biological replicate 2

description: Gene expression data from_auto-inducer II without glucose biological replicate 2


title: YS_Fat_3

status: Public on Oct 15 2008

city: Seoul

first: Cheol-Koo

last: Lee

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

department: Biotechnology

country: South Korea

institute: Korea University

description: GeneChip Porcine Genome Array

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Scaling, log2 transformation and quantile normalization

organism: Sus scrofa

source_name: adipose tissue of YS

label_protocol: Affymetrix protocol

extract_protocol: Affymetrix protocol

tag: Yorkshire pig, 6 month-old


title: luxS mutant with auto-inducer II without glucose biological replicate 1

description: Gene expression data from_auto-inducer II without glucose biological replicate 1


title: KNP_Fat_1

description: GeneChip Porcine Genome Array

source_name: adipose tissue of KNP

tag: Korean native pig, 7 month-old


title: Osteoarthritis

status: Public on Oct 14 2008

city: Fukushima

first: Yoshimi

last: Homma

state: Fukushima

address: 1 Hikarigaoka

department: Department of Biomolecular Science

institute: Fukushima Medical University

description: Cells from passage 2-5 were used for RNA extraction.

hyb_protocol: Hybridization was carried out for 16 hr at 60 rpm at 45 °C using Affymetrix® Hybridization Oven 640 (Affymetrix, Santa Clara, CA, USA)

scan_protocol: The probe array was scanned using Affymetrix GeneChip Scanner 3000.

data_processing: Analysis of the microarray data was carried out using GeneChip® Operating Software (GCOS) version 1.1.

source_name: synovial tissue from patient with osteoarthritis

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

growth_protocol: Cells were maintained in RPMI supplemented with 20% FBS.  The medium was changed every 3 days.

extract_protocol: Total RNA extraction was performed by using Isogen (NIPPON GENE) according to the manufacturer's instructions.

tag: Cell type

value: synovial fibroblast-like cell, Tissue:synovial membrane, Disease:osteoarthritis


title: YS_Fat_4

description: GeneChip Porcine Genome Array


description: Gene expression data from_luxS mutant without glucose biological replicate 2


description: Gene expression data from_luxS mutant without glucose biological replicate 3


title: YS_Fat_1

description: GeneChip Porcine Genome Array

source_name: adipose tissue of Yorkshire


title: Wild type without glucose biological replicate 3

description: Gene expression data from_wild type without glucose biological replicate 3


title: Wild type without glucose biological replicate 2

description: Gene expression data from_wild type without glucose biological replicate 2


title: KNP_Fat_4

description: GeneChip Porcine Genome Array


title: YS_Fat_2

description: GeneChip Porcine Genome Array


title: Rhumatoid arthritis

hyb_protocol: Hybridization was carried out for 16 hr at 60 rpm at 45 °C using Affymetrix® Hybridization

source_name: synovial tissue from patient with rheumatois arthritis

value: synovial fibroblast-like cell, Tissue:synovial membrane, Disease:rheumatoid arthritis


title: KNP_Fat_3

description: GeneChip Porcine Genome Array


description: Gene expression data from_luxS mutant without glucose biological replicate 1


title: Wild type without glucose biological replicate 1

description: Gene expression data from_wild type without glucose biological replicate 1


title: KNP_Fat_2

description: GeneChip Porcine Genome Array


title: KNC_09

status: Public on Oct 06 2008

description: GeneChip Bovine Genome Array

data_processing: global scaling

organism: Bos taurus

source_name: skeletal muscle

extract_protocol:
total RNA: Trizol reagent
poly A RNA: Qiagen oligotex resin

tag: ~2 years Hanwoo (Korean native cattle) longissimus dorci


title: KNC_04

description: GeneChip Bovine Genome Array

tag: ~2 years old Hanwoo (Korean native cattle) longissimus dorsi


title: KNC_05

description: GeneChip Bovine Genome Array


title: KNC_06

description: GeneChip Bovine Genome Array


title: KNC_07

description: GeneChip Bovine Genome Array


title: KNC_03

description: GeneChip Bovine Genome Array


title: KNC_01

description: GeneChip Bovine Genome Array

tag: sample

value: ~2 years old Hanwoo (Korean native cattle) longissimus dorsi


title: KNC_02

description: GeneChip Bovine Genome Array


title: KNC_08

description: GeneChip Bovine Genome Array


title: 0.25% glucose log_0.25_3

status: Public on Oct 02 2008

description: Yeast grown at 0.25% glucose.

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

organism: Saccharomyces cerevisiae

label_protocol: Affymetrix standard protocol

extract_protocol: Trizol reagent LS


title: 0.5% glucose log_0.5_3

description: Yeast grown at 0.5% glucose.


title: 0.5% glucose log_0.5_2

description: Yeast grown at 0.5% glucose.


title: 0.25% glucose log_0.25_2

description: Yeast grown at 0.25% glucose.


title: 0.25% glucose log_0.25_1

description: Yeast grown at 0.25% glucose.


title: 1% glucose log_1_1

description: Yeast grown at 1% glucose.


title: 0.5% glucose log_0.5_1

description: Yeast grown at 0.5% glucose.


title: KNC_10

description: GeneChip Bovine Genome Array


title: 1% glucose log_1_2

description: Yeast grown at 1% glucose.


title: 2% glucose log_2_3

description: Yeast grown at 2% glucose.


title: diabetic mother rep2

status: Public on Oct 01 2008

city: Singapore

first: S Thameem

last: Dheen

address: Medical Drive 10

country: Singapore

institute: National University of Singapore

hyb_protocol: based on Affymetrix genechip hybridization protocol

scan_protocol: based on Affymetrix genechip scaning protocol

data_processing: image captured and processed by Affymetrix GCOS (Gene chip operating system)

source_name: brain of the E11.5 days embryo from diabetic mother

label_protocol: based on Affymetrix genechip labeling protocol

extract_protocol: based on Affymetrix genechip RNA extraction protocol

tag: Strain

value: Swiss Albino mice

tag: Tissue

value: embryonic brain

tag: Stage

value: E11.5 day embryo

tag: Treatment

value: streptozotocin (STZ) induced maternal diabetes


title: 2% glucose log_2_2

description: Yeast grown at 2% glucose.


title: 2% glucose log_2_1

description: Yeast grown at 2% glucose.


title: normal control rep1

source_name: brain of the E11.5 days embryo from normal mice


title: normal control rep2


title: diabetic mother rep1


title: 1% glucose log_1_3

description: Yeast grown at 1% glucose.


title: D. Melanogaster NF Larvae 8

last: Zhou

address: CMG 103, 9500 Gilman Drive, MC0735

department: Pediatrics

institute: University of California, San Diego, School of Medicine

description: Biological replicate 8 of 9 NF 3rd instar larval samles

hyb_protocol: Hybridization buffer were added, and samples were applied to microarrays and hybridized for 18 hours at 64°C in a chamber, after hybridization, slides were washed sequentially with 1.14x SSC/0.0285% SDS, 1.14xSSC, 0.228xSSC, and 0.057x SSC before scanning

scan_protocol: Scanned on an GenePix 4000B scanner Images were quantified using GenePix Pro software

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of ratio of medians

organism: Drosophila melanogaster

source_name: cRNA from 3rd instar larvae labeled with Cyanine-5 (red)

label_protocol: 4 µg of cRNA were primed with 7.5 µg random hexamer at 70°C for 10 min, then reversed transcripted at 42°C for 180 min in the presence of 400 U SuperScript II RTase, 500 µM each dATP, dCTP, dGTP, with 200 µM dUTP, 100 µM Cy5-labeled dUTP, and RNase inhibitor. RNA was then degraded with 35 mM NaOH/  600 µM EDTA, and labeled cDNAs were purified using QIAquick PCR columns

extract_protocol: TriZol procedure

tag: Developmental stage

value: 3rd instar larvae

source_name: Reference cRNA, labeled with Cyanine-3 (green)

label_protocol: 4 µg of cRNA were primed with 7.5 µg random hexamer at 70°C for 10 min, then reversed transcripted at 42°C for 180 min in the presence of 400 U SuperScript II RTase, 500 µM each dATP, dCTP, dGTP, with 200 µM dUTP, 100 µM Cy3-labeled dUTP, and RNase inhibitor. RNA was then degraded with 35 mM NaOH/  600 µM EDTA, and labeled cDNAs were purified using QIAquick PCR columns


title: D. Melanogaster AF Larvae 7

description: Biological replicate 7 of 8 AF 3rd instar larval samles


title: D. Melanogaster AF Larvae 6

description: Biological replicate 6 of 8 AF 3rd instar larval samles


title: D. Melanogaster NF Larvae 9

description: Biological replicate 9 of 9 NF 3rd instar larval samles


title: D. Melanogaster AF Larvae 1

description: Biological replicate 1 of 8 AF 3rd instar larval samles


title: D. Melanogaster NF Larvae 3

description: Biological replicate 3 of 9 NF 3rd instar laval samples


title: D. Melanogaster AF Larvae 3

description: Biological replicate 3 of 8 AF 3rd instar larval samles


title: D. Melanogaster AF Larvae 2

description: Biological replicate 2 of 8 AF 3rd instar larval samles


title: D. Melanogaster NF Larvae 4

description: Biological replicate 4 of 9 NF 3rd instar laval samples


title: D. Melanogaster NF Larvae 5

description: Biological replicate 5 of 9 NF 3rd instar larval samles


title: D. Melanogaster AF Larvae 4

description: Biological replicate 4 of 8 AF 3rd instar larval samles


title: D. Melanogaster NF Larvae 1

description: Biological replicate 1 of 9 NF 3rd instar larval samles


title: D. Melanogaster AF Larvae 8

description: Biological replicate 8 of 8 AF 3rd instar larval samles


title: D. Melanogaster NF Larvae 6

description: Biological replicate 6 of 9 NF 3rd instar larval samles


title: D. Melanogaster NF Larvae 7

description: Biological replicate 7 of 9 NF 3rd instar larval samles


title: D. Melanogaster NF Larvae 2

description: Biological replicate 2 of 9 NF 3rd instar laval samples