title: CpG 3h-C57BL/6 control-repeat 4 - mAdbID:91684

city: Frederick

first: Dennis

middle: M

last: Klinman

state: MD

department: CIP

institute: NCI Frederick

description: mAdb experiment ID: 91684

hyb_protocol: Hybridization Protocol Other: Cy-labeled reference and sample cDNAs (10 microliter each) were combined, de-naturated by heating for 2' at 98 C and mixed with 36 microliter of hybridization solution at 42 C (Ambion, Austin, TX). A low volume active mixing chamber was applied to the microarray via an adhesive gasket (MAUI mixer FL, BioMicro Systems, Salt Lake City, Utah), the hybridization solution containing the sample was added to the array, and was placed for 18 h at 42 C in the base unit of the actively mixing MAUI hybridization system (BioMicro Systems, Salt Lake City, Utah). Post hybridization, the arrays were washed in 1X SSC/0.05X SDS and 0.1X SSC, centrifuged to remove remaining liquid with unbound cDNA, and dried.

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48766;; 3.41868 Temperature: 23.5191

data_processing:
Data Processing Protocol
Calculation Method: Data were background corrected, flagged values were removed, spots with both signals less than 100 were filtered out, ratios were log base 2 transformed and lowess intensity dependent normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes. Only genes present on >70% of the arrays were included in the subsequent analysis.

source_name: Universal Mouse Reference RNA

label_protocol:
Cy3 Labeling Protocol
Other: 20 microgram of total RNA (universal reference mouse RNA, Stratagene, La Jolla, CA) was reverse-transcribed using 3 microliter 10X first strand buffer (Stratagene, La Jolla, CA), 2 microliter (1 microgram) Oligo(dT) (Invitrogen, Carlsbad, CA), 3 microliter (150 U) reverse transcriptase (StrataScript HC RT, Stratagene, La Jolla, CA), 2 microliter 20X aminoallyl-dUTP/dNTP mix, and 3 microliter 0.1 M DTT in a final volume of 30 microliter at 42 C for 90 min. cDNA was purified using a MinElute PCR Purification Kit (Qiagen, Valencia, CA). 10 microliter of cDNA was labeled with Cy3 reactive dye (Amersham Biosciences, UK) diluted in 5 microliter of DMSO plus 1.7 microliter of 1M NaHCO3 for 90 min in the dark.

extract_protocol:
Strategene UHR RNA Extraction
Other: not available

tag: Cell type

value: mixture of B-lymphocyte, embryo, kidney, liver, macrophages, mammary gland, muscle, skin, testis, T-lymphocyte

source_name: Untreated - C57BL/6 control

label_protocol:
Cy5 Labeling Protocol
Other: 20 microgram of total RNA was reverse-transcribed using 3 microliter 10X first strand buffer (Stratagene, La Jolla, CA), 2 microliter (1 microgram) Oligo(dT) (Invitrogen, Carlsbad, CA), 3 microliter (150 U) reverse transcriptase (StrataScript HC RT, Stratagene, La Jolla, CA), 2 microliter 20X aminoallyl-dUTP/dNTP mix, and 3 microliter 0.1 M DTT in a final volume of 30 microliter at 42 C for 90 min. cDNA was purified using a MinElute PCR Purification Kit (Qiagen, Valencia, CA). 10 microliter of cDNA was labeled with Cy5 reactive dye (Amersham Biosciences, UK) diluted in 5 microliter of DMSO plus 1.7 microliter of 1M NaHCO3 for 90 min in the dark.

extract_protocol:
RNA Extraction Protocol
Other: Total RNA was extracted from mice spleens using TRIzol reagent (Invitrogen, Carlsbad, CA) as specified by the manufacturer.

tag: Strain

value: spleen


title: Untreated-C57BL/6 TNF-KO-repeat 4 - mAdbID:91686

status: Public on Apr 01 2009

type: RNA

country: USA

description: mAdb experiment ID: 91686

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.4962;; 3.53557 Temperature: 26.2963

molecule: total RNA

organism: Mus musculus

source_name: Untreated - C57BL/6 KO

tag: Gender

value: female

tag: Tissue

tag: genotype/variation gene knock out

tag: genotype/variation

value: TNF knock out


title: CpG 3h-C57BL/6 control-repeat 1 - mAdbID:90771

description: mAdb experiment ID: 90771

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.17423;; 3.67077 Temperature: 27.0898


title: CpG 3h-C57BL/6 TNF-KO-repeat 1 - mAdbID:91311

description: mAdb experiment ID: 91311

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.49834;; 3.47087 Temperature: 24.16


title: Untreated-C57BL/6 TNF-KO-repeat 1 - mAdbID:90774

description: mAdb experiment ID: 90774

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.14524;; 3.64299 Temperature: 28.0663


title: CpG 3h-C57BL/6 TNF-KO-repeat 4 - mAdbID:91689

description: mAdb experiment ID: 91689

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.49254;; 3.57585 Temperature: 27.5475


title: Untreated-C57BL/6 control-repeat 1 - mAdbID:91287

description: mAdb experiment ID: 91287

scan_protocol: Creator: GenePix Pro 6.0.1.25 Scanner: GenePix 4000B [136824] ScanPower: 100;; 100 LaserPower: 3.48369;; 3.53069 Temperature: 29.0124


title: CpG 3h-C57BL/6 TNF-KO-repeat 3 - mAdbID:90257

description: mAdb experiment ID: 90257

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.1196;; 3.68419 Temperature: 26.5709


title: CpG 3h-C57BL/6 TNF-KO-repeat 2 - mAdbID:90265

description: mAdb experiment ID: 90265

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.21299;; 3.70006 Temperature: 29.7449


title: Untreated-C57BL/6 TNF-KO-repeat 2 - mAdbID:90387

description: mAdb experiment ID: 90387

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.10373;; 3.73363 Temperature: 24.3736


title: Untreated-C57BL/6 control-repeat 3 - mAdbID:90390

description: mAdb experiment ID: 90390

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.17057;; 3.65398 Temperature: 27.6696


title: CpG 3h-C57BL/6 control-repeat 3 - mAdbID:90391

description: mAdb experiment ID: 90391

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.15653;; 3.65032 Temperature: 28.28


title: Untreated-C57BL/6 control-repeat 2 - mAdbID:90770

description: mAdb experiment ID: 90770

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.12601;; 3.7553 Temperature: 24.3736


title: Untreated-C57BL/6 TNF-KO-repeat 3 - mAdbID:90256

description: mAdb experiment ID: 90256

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.16782;; 3.65093 Temperature: 28.4021


title: Control ODN-3h-BALB/c WT-repeat 3 - mAdbID:88313

description: mAdb experiment ID: 88313

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.61;; 4.11 Temperature: 34.78

source_name: Control ODN - 3 hrs BALB/c WT

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture of ODN 1612, 1471
Treatment dose: 400 ug
Treatment time: 3 hours
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of equimolar mixture of ODN 1612, 1471. Spleens were surgical removed under sterile conditions after 3 hours.

value: BALB/c


title: CpG ODN-24h-BALB/c WT-repeat 3 - mAdbID:88232

description: mAdb experiment ID: 88232

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.22;; 3.61 Temperature: 27.55

source_name: CpG ODN - 24 hrs BALB/c WT

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 24 hours
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0.5, 1, 3, 9, 24, and 72 hours.


title: Untreated-C57BL/6 control-repeat 4 - mAdbID:90260

description: mAdb experiment ID: 90260

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.18308;; 3.67046 Temperature: 27.2423


title: CpG ODN-72h-BALB/c WT-repeat 3 - mAdbID:88317

description: mAdb experiment ID: 88317

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.43;; 4.05 Temperature: 28.59

source_name: CpG ODN - 72 hrs BALB/c WT

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 72 hours
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0.5, 1, 3, 9, 24, and 72 hours.


title: CpG ODN-9h-BALB/c WT-repeat 4 - mAdbID:88229

description: mAdb experiment ID: 88229

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.39;; 4.07 Temperature: 27.76

source_name: CpG ODN - 9 hrs BALB/c WT

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 9 hours
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0.5, 1, 3, 9, 24, and 72 hours.


title: CpG ODN-24h-BALB/c WT-repeat 2 - mAdbID:88231

description: mAdb experiment ID: 88231

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.48;; 4.08 Temperature: 27.12


title: Control ODN-3h-BALB/c WT-repeat 4 - mAdbID:88314

description: mAdb experiment ID: 88314

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.6;; 4.11 Temperature: 34.69


title: CpG ODN-24h-BALB/c WT-repeat 4 - mAdbID:88233

description: mAdb experiment ID: 88233

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.28;; 3.59 Temperature: 28.52


title: CpG ODN-72h-BALB/c WT-repeat 4 - mAdbID:88318

description: mAdb experiment ID: 88318

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.19;; 3.6 Temperature: 27.43


title: Control ODN-3h-BALB/c WT-repeat 1 - mAdbID:88311

description: mAdb experiment ID: 88311

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.46;; 4.07 Temperature: 29.96


title: CpG ODN-24h-BALB/c WT-repeat 1 - mAdbID:88558

description: mAdb experiment ID: 88558

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.41;; 4.06 Temperature: 29.74


title: CpG ODN-9h-BALB/c WT-repeat 2 - mAdbID:88227

description: mAdb experiment ID: 88227

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.35;; 4.04 Temperature: 27.97


title: Control ODN-3h-BALB/c WT-repeat 2 - mAdbID:88312

description: mAdb experiment ID: 88312

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.52;; 4.07 Temperature: 30.6


title: CpG ODN-1h-BALB/c WT-repeat 3 - mAdbID:88202

description: mAdb experiment ID: 88202

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.6;; 4.11 Temperature: 34.63

source_name: CpG ODN - 1 hrs BALB/c WT

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 1 hours
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0.5, 1, 3, 9, 24, and 72 hours.


title: CpG ODN-9h-BALB/c WT-repeat 3 - mAdbID:88228

description: mAdb experiment ID: 88228

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.34;; 4.05 Temperature: 26.72


title: WuYun3-RSV infected, biological rep1

status: Public on Apr 02 2009

city: Fuzhou

first: Xiaoting

last: Zhang

state: Fujian

address: Jinshan

department: Plant Protection Department

country: China

institute: Fujian Agriculture and Forestry University

description: Gene expression data from RSV-innoculated WuYun3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 degree celsius on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

label: biotin

organism: Oryza sativa

source_name: Tissue: aerial parts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol 5 ug total RNA.

growth_protocol: RSV-innoculated or non-innoculated WuYun3 or KT95-418 rice plants were grown in greenhouse at 25±3C with a daily photoperiodic cycle of 16 hours light and 8 hours.

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

treatment_protocol: Untreated

tag: Age

value: 32th day after germination


title: CpG ODN-3h-BALB/c WT-repeat 3 - mAdbID:88205

description: mAdb experiment ID: 88205

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.36;; 4.05 Temperature: 25.69

source_name: CpG ODN - 3 hrs BALB/c WT

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 3 hours
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0.5, 1, 3, 9, 24, and 72 hours.


title: Untreated-BALB/c WT-repeat 6 - mAdbID:88176

description: mAdb experiment ID: 88176

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.23;; 3.6 Temperature: 27.79

source_name: Untreated BALB/c WT


title: CpG ODN-72h-BALB/c WT-repeat 2 - mAdbID:88316

description: mAdb experiment ID: 88316

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.36;; 4.08 Temperature: 27.49


title: CpG ODN-72h-BALB/c WT-repeat 1 - mAdbID:88315

description: mAdb experiment ID: 88315

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.35;; 4.04 Temperature: 25.84


title: CpG ODN-3h-BALB/c WT-repeat 4 - mAdbID:88206

description: mAdb experiment ID: 88206

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.3;; 3.59 Temperature: 29.35


title: Untreated-BALB/c WT-repeat 3 - mAdbID:88174

description: mAdb experiment ID: 88174

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.66;; 4.15 Temperature: 35.09


title: CpG ODN-3h-BALB/c WT-repeat 1 - mAdbID:88222

description: mAdb experiment ID: 88222

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.42;; 4.08 Temperature: 30.26


title: CpG ODN-0.5h-BALB/c WT-repeat 3 - mAdbID:88166

description: mAdb experiment ID: 88166

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.35;; 4.05 Temperature: 22.51

source_name: CpG ODN - 0.5 hrs BALB/c WT

treatment_protocol:
Treatment type: oligodeoxynucleotide
Agent: equimolar mixture CpG ODN 1555, 1466
Treatment dose: 400 ug
Treatment time: 0.5 hours
In-vivo treatment: Mice were injected intraperitoneal (i.p.) with 400ug of an equimolar mixture of CpG ODN 155 and 1466. Spleens were surgical removed under sterile conditions after 0.5, 1, 3, 9, 24, and 72 hours.


title: Untreated-BALB/c WT-repeat 5 - mAdbID:88175

description: mAdb experiment ID: 88175

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.16;; 3.64 Temperature: 25.32


title: Untreated-BALB/c WT-repeat 1 - mAdbID:88172

description: mAdb experiment ID: 88172

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.29;; 4.06 Temperature: 26.94


title: Untreated-BALB/c WT-repeat 4 - mAdbID:88163

description: mAdb experiment ID: 88163

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.67;; 4.15 Temperature: 35.15


title: CpG ODN-3h-BALB/c WT-repeat 2 - mAdbID:88224

description: mAdb experiment ID: 88224

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.56;; 4.13 Temperature: 34.44


title: CpG ODN-1h-BALB/c WT-repeat 4 - mAdbID:88203

description: mAdb experiment ID: 88203

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.59;; 4.13 Temperature: 34.6


title: CpG ODN-9h-BALB/c WT-repeat 1 - mAdbID:88226

description: mAdb experiment ID: 88226

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.34;; 4.05 Temperature: 26.17


title: CpG ODN-0.5h-BALB/c WT-repeat 4 - mAdbID:88167

description: mAdb experiment ID: 88167

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.4;; 4.06 Temperature: 26.48


title: CpG ODN-1h-BALB/c WT-repeat 2 - mAdbID:88154

description: mAdb experiment ID: 88154

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.36;; 4.04 Temperature: 28.74


title: CpG ODN-0.5h-BALB/c WT-repeat 1 - mAdbID:88164

description: mAdb experiment ID: 88164

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.24;; 3.58 Temperature: 29.2


title: adenocarcinoma 4174

city: Koto-ku

first: Yuichi

last: Ishikawa

state: Tokyo

address: 3-8-31 Ariake

country: Japan

institute: Cancer Insitute

description: Primary adenocarcinoma

organism: Homo sapiens

source_name: adenocarcinoma 4174

source_name: lung reference mix


title: adenocarcinoma 3896

description: Primary adenocarcinoma

source_name: adenocarcinoma 3896


title: adenocarcinoma 4412

description: Primary adenocarcinoma

source_name: adenocarcinoma 4412


title: adenocarcinoma 3947

description: Primary adenocarcinoma

source_name: adenocarcinoma 3947


title: CpG 3h-C57BL/6 control-repeat 2 - mAdbID:90262

description: mAdb experiment ID: 90262

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.1547;; 3.66344 Temperature: 27.8832

source_name: Universal Mouse Reference RNA


title: adenocarcinoma 3836

description: Primary adenocarcinoma

source_name: adenocarcinoma 3836


title: normal 792

description: Normal lung

source_name: normal 792


title: normal 709

description: Normal lung

source_name: normal 709


title: CpG ODN-1h-BALB/c WT-repeat 1 - mAdbID:88153

description: mAdb experiment ID: 88153

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.36;; 4.04 Temperature: 28.43


title: Untreated-BALB/c WT-repeat 2 - mAdbID:88207

description: mAdb experiment ID: 88207

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.36;; 4.05 Temperature: 27.91


title: normal 798

description: Normal lung

source_name: normal 798


title: normal 865

description: Normal lung

source_name: normal 865


title: CpG ODN-0.5h-BALB/c WT-repeat 2 - mAdbID:88165

description: mAdb experiment ID: 88165

scan_protocol: Creator: GenePix Pro 5.1.0.19 Scanner: GenePix 4000B [94877] ScanPower: 100;; 100 LaserPower: 3.31;; 3.58 Temperature: 29.68


title: adenocarcinoma 3985

description: Primary adenocarcinoma

source_name: adenocarcinoma 3985


title: normal 835

description: Normal lung

source_name: normal 835


title: squamous cell carcinoma 4617

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 4617


title: normal 589

description: Normal lung

source_name: normal 589


title: normal 574

description: Normal lung

source_name: normal 574


title: normal 598

description: Normal lung

source_name: normal 598


title: squamous cell carcinoma 3951

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 3951


title: normal 579

description: Normal lung

source_name: normal 579

source_name: lung reference mix


title: squamous cell carcinoma 4485

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 4485


title: squamous cell carcinoma 3726

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 3726


title: squamous cell carcinoma 4395

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 4395


title: squamous cell carcinoma 3532

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 3532


title: squamous cell carcinoma 3002

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 3002


title: squamous cell carcinoma 3062

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 3062


title: squamous cell carcinoma 3536

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 3536


title: squamous cell carcinoma 3156

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 3156


title: squamous cell carcinoma 3453

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 3453


title: squamous cell carcinoma 2674

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 2674


title: squamous cell carcinoma 3813

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 3813


title: squamous cell carcinoma 3124

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 3124


title: squamous cell carcinoma 2901

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 2901


title: squamous cell carcinoma 4136

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 4136


title: squamous cell carcinoma 3340

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 3340


title: normal 845

description: Normal lung

source_name: normal 845


title: squamous cell carcinoma 3097

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 3097

source_name: lung reference mix


title: squamous cell carcinoma 3320

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 3320


title: squamous cell carcinoma 2459

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 2459


title: adenocarcinoma 4364

description: Primary adenocarcinoma

source_name: adenocarcinoma 4364


title: squamous cell carcinoma 2379

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 2379


title: squamous cell carcinoma 2417

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 2417


title: squamous cell carcinoma 2187

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 2187


title: squamous cell carcinoma 2169

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 2169


title: squamous cell carcinoma 2025

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 2025


title: squamous cell carcinoma 1897

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1897


title: squamous cell carcinoma 1854

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1854


title: squamous cell carcinoma 1824

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1824


title: adenocarcinoma 4372

description: Primary adenocarcinoma

source_name: adenocarcinoma 4372


title: squamous cell carcinoma 1555

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1555


title: squamous cell carcinoma 1606

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1606


title: squamous cell carcinoma 1806

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1806


title: squamous cell carcinoma 1601

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1601


title: squamous cell carcinoma 1509

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1509

source_name: lung reference mix


title: squamous cell carcinoma 1737

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1737


title: squamous cell carcinoma 1649

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1649


title: squamous cell carcinoma 1195

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1195


title: squamous cell carcinoma 1071

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1071


title: squamous cell carcinoma 1051

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1051


title: squamous cell carcinoma 2492

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 2492


title: squamous cell carcinoma 1438

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1438


title: squamous cell carcinoma 694

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 694


title: squamous cell carcinoma 1654

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1654


title: squamous cell carcinoma 1288

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 1288


title: squamous cell carcinoma 674

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 674


title: squamous cell carcinoma 972

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 972


title: squamous cell carcinoma 2204

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 2204


title: normal 699

description: Normal lung

source_name: normal 699


title: Dark Agouti-rep4

status: Public on Mar 31 2009

city: Indianapolis

first: Charles

middle: H

last: Turner

state: IN

address: 723 W. Michigan St. SL 220C

department: Biomedical Engineering

institute: Indiana University Purdue University Indiapanolis

description: Gene expression data from proximal femur

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

organism: Rattus norvegicus

source_name: Bone, Femur

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

extract_protocol: Whole femora were harvested from 4-week-old F344, LEW, COP and DA animals.  RNA was isolated from proximal femora using Trizol (Invtirogen, CA) and Rneasy Mini Kit (Qiagen Inc., CA) according to the manufacturer’s directions.

tag: proximal femur


title: squamous cell carcinoma 564

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 564


title: Dark Agouti-rep1


title: Copenhagen 2331-rep3


title: Copenhagen 2331-rep4


title: Dark Agouti-rep3


title: Dark Agouti-rep2


title: Copenhagen 2331-rep1


title: Lewis-rep2


title: Lewis-rep1


title: Fischer 344-rep3


title: Copenhagen 2331-rep2


title: Embryonic heart age 20 replica 7

status: Public on Mar 30 2009

city: Raleigh

first: Jean

middle: Eduardo

last: de Oliveira

state: NC

address: 2711 Founders Dr

department: Poultry Science

institute: North Carolina State University

description:
Embryonic heart: age E20 replica 7
Sample:  E20_em185_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.

hyb_protocol: mix of 33 pmol of both samples was resuspended with 33 µl Pronto! Long Oligo Hybridization solution and applied to pre-hybrydized microarray slides with spotted area coved with a 25 X 40 mm glass coverslip; slides were hybridized in Corning Hybridization

scan_protocol: scanned on ScanArray Gx Plus (PerkinElmer) set to 65% lazer power Images were quantified using ScanAlyze Software (version 2.50).

data_processing: Log2 transformed data was submitted to ratio analysis and LOWESS normalization using JMP Genomics Software (SAS Institute)

organism: Gallus gallus

source_name: Total RNA from heart embryos day 20 labeled with cyanine-5 (red)

label_protocol: 5µg of total RNA were primed with 3µg of random primers and 2µg of oligo(dt) primer, heated at 70C for 10 min, then reverse transcribed at 42C for 2h with 3.2 µl ChipShot Reverse Transcriptase and 4 µl aminoallyl-sNTPs; cDNA was indirect labeled with CyDy

growth_protocol: broilers eggs incubated under standard conditions

extract_protocol: Total RNA extracted using a single-step, modified acid guanidinium thiocyanate/phenol/chloroform extraction method (Chomczynski and Saachi, 1987).

treatment_protocol: 8 eggs were sampled at each age (7, 15, 19 and 20 days of incubation) to harvest the heart; tissue preserved in RNA Later solution (Ambion, Inc).

value: heart


title: Embryonic heart age 20 replica 8

description:
Embryonic heart: age E20 replica 8
Sample:  E20_em203_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.


title: Embryonic heart age 20 replica 5

description:
Embryonic heart: age E20 replica 5
Sample:  E20_em171_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.


title: Embryonic heart age 19 replica 8

description:
Embryonic heart: age E19 replica 8
Sample:  E19_em127_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.

source_name: Total RNA from heart embryos day 19 labeled with cyanine-5 (red)


title: Embryonic heart age 20 replica 6

description:
Embryonic heart: age E20 replica 6
Sample:  E20_em183_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.


title: Lewis-rep4


title: Embryonic heart age 15 replica 5

description:
Embryonic heart: age E15 replica 5
Sample:  E15_em49_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.

source_name: Total RNA from heart embryos day 15 labeled with cyanine-5 (red)


title: Embryonic heart age 15 replica 8

description:
Embryonic heart: age E15 replica 8
Sample:  E15_em65_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.


title: Embryonic heart age 19 replica 5

description:
Embryonic heart: age E19 replica 5
Sample:  E19_em95_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.


title: Embryonic heart age 19 replica 7

description:
Embryonic heart: age E19 replica 7
Sample:  E19_em119_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.


title: Fischer 344-rep1


title: Embryonic heart age 7 replica 7

description:
Embryonic heart: age E7 replica 7
Sample:  E7_em88_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.

source_name: Total RNA from heart embryos day 7 labeled with cyanine-5 (red)


title: Embryonic heart age 7 replica 8

description:
Embryonic heart: age E7 replica 8
Sample:  E7_em89_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.


title: Embryonic heart age 15 replica 6

description:
Embryonic heart: age E15 replica 6
Sample:  E15_em61_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.


title: Embryonic heart age 15 replica 7

description:
Embryonic heart: age E15 replica 7
Sample:  E15_em63_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.


title: Fischer 344-rep2


title: Embryonic heart age 20 replica 4

description:
Embryonic heart: age E20 replica 4
Sample:  E20_em207_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.

source_name: Total RNA from heart embryos day 20 labeled with cyanine-3 (green)


title: Embryonic heart age 7 replica 5

description:
Embryonic heart: age E7 replica 5
Sample:  E7_em85_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.


title: Embryonic heart age 7 replica 6

description:
Embryonic heart: age E7 replica 6
Sample:  E7_em87_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.


title: Embryonic heart age 19 replica 6

description:
Embryonic heart: age E19 replica 6
Sample:  E19_em101_Cy5
For raw data, see embryo_Cy5_raw_data.txt linked to the Series record.


title: Embryonic heart age 20 replica 3

description:
Embryonic heart: age E20 replica 3
Sample:  E20_em193_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.


title: Embryonic heart age 20 replica 1

description:
Embryonic heart: age E20 replica 1
Sample:  E20_em187_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.


title: Embryonic heart age 20 replica 2

description:
Embryonic heart: age E20 replica 2
Sample:  E20_em191_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.


title: Embryonic heart age 19 replica 1

description:
Embryonic heart: age E19 replica 1
Sample:  E19_em91_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.

source_name: Total RNA from heart embryos day 19 labeled with cyanine-3 (green)


title: Embryonic heart age 19 replica 2

description:
Embryonic heart: age E19 replica 2
Sample:  E19_em97_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.


title: Embryonic heart age 19 replica 3

description:
Embryonic heart: age E19 replica 3
Sample:  E19_em99_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.


title: Embryonic heart age 19 replica 4

description:
Embryonic heart: age E19 replica 4
Sample:  E19_em123_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.


title: Embryonic heart age 7 replica 4

description:
Embryonic heart: age E7 replica 4
Sample:  E7_em90_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.

source_name: Total RNA from heart embryos day 7 labeled with cyanine-3 (green)


title: Embryonic heart age 15 replica 4

description:
Embryonic heart: age E15 replica 4
Sample:  E15_em83_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.

source_name: Total RNA from heart embryos day 15 labeled with cyanine-3 (green)


title: Embryonic heart age 15 replica 1

description:
Embryonic heart: age E15 replica 1
Sample:  E15_em45_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.


title: Embryonic heart age 15 replica 3

description:
Embryonic heart: age E15 replica 3
Sample:  E15_em73_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.


title: Embryonic heart age 15 replica 2

description:
Embryonic heart: age E15 replica 2
Sample:  E15_em53_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.


title: Embryonic heart age 7 replica 2

description:
Embryonic heart: age E7 replica 2
Sample:  E7_em82_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.


title: Embryonic heart age 7 replica 3

description:
Embryonic heart: age E7 replica 3
Sample:  E7_em84_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.


title: Embryonic heart age 7 replica 1

description:
Embryonic heart: age E7 replica 1
Sample:  E7_em81_Cy3
For raw data, see embryo_Cy3_raw_data.txt linked to the Series record.


title: ML-DmD16-c3_Kc167_rep2

status: Public on Mar 20 2009

city: Bloomington

first: Lucy

last: Cherbas

department: CGB

institute: Indiana University

description: The experiment compares transcripts from Kc167 and ML-DmD16-c3 cells, using a dendrimer hybridization procedure.

hyb_protocol: PRE-HYBRIDIZATION. 1. Prepare 50 ml pre-hybridization buffer (5x SSC/0.1% SDS/1% I-block) in a 50 ml screw cap centrifuge tube, and bring to 55 °C. 2. Incubate microarray slide in pre-hybridization buffer at 55 °C for 1.5 hours. 3. Transfer microarray slide to 50 ml tube filled with water and invert gently for 1 minute. Then transfer to new tube with fresh water to wash two times. 4. Centrifuge at 500 rcf for 4 minutes to dry (label end down). cDNA HYBRIDIZATION. 1. Prepare the following cDNA hybridization mix: 12.7 ul of each cDNA synthesis reaction mix, 2.1 ul nuclease-free water, 2.7 ul 2x Formamide-Based hybridization buffer (kit) (total volume 55 ul). 2. Mix (by gentle vortexing) and briefly spin the hybridization mix. 3. Incubate at 80 °C for 10 minutes. 4. Incubate at 55 °C until it is loaded on the microarray slide. 5. Pre-warm the microarray on a slide warmer. 6. Assemble the hybridization solution (55 ul) to the center of the slide. Carefully lower a LifterSlip onto the microarray avoiding bubbles. Place the slide face-up in a hybridization chamber. Pipette 20 μl of water into the wells at either end of the hybridization chamber. Seal the chamber. 7. Submerge the hybridization chamber in a 43 °C water bath and incubate for 14-17 hours. POST-cDNA HYBRIDIZATION WASHES. 1. Disassemble the hybridization chamber. 2. Remove cover slip by immersing the slide in a pre-warmed beaker filled with 400 ml 2x SSC/0.2% SDS at 42-43 °C. 3. Incubate slide in a 50 ml tube of pre-warmed 2x SSC/0.2% SDS at 42 °C for 10-15 minutes. 4. Wash in 2x SSC at room temperature for 10-15 minutes. 5. Wash in 0.2x SSC room temperature for 10-15 minutes. 6. Centrifuge at 500 rcf for 4 minutes to dry. DENDRIMER HYBRIDIZATION. 1. Thaw the 3DNA Capture Reagents (dendrimer solutions) that correspond to the primers used for cDNA synthesis in the dark for 20 minutes. Vortex, spin briefly, and incubate at 55 °C in the dark for 10 minutes. 2. At the same time, thaw 2X Formamide-based hybridization buffer by incubating it at 43 °C. 3. Prepare dendrimer hybridization solution by mixing the following kit components in a microcentrifuge tube: 2.5 ul Alexa Fluor 647 3DNA Array Capture Reagent, 2.5 ul Alexa Fluor 546 3DNA Array Capture Reagent, 27.5 ul 2x formamide-based hybridization buffer, 22.5 ul nuclease-free water (total volume 55 ul). 4. Vortex gently and centrifuge briefly. 5. Incubate at 80 °C for 10 minutes. 6. Assemble the hybridization as for the first hybridization. 7. Submerge the hybridization chamber in a 43 °C water bath and incubate for 5 hours. POST-DENDRIMER HYBRIDIZATION WASHES. 1. Disassemble the hybridization chamber. 2. Remove cover slip by immersing the slide in a pre-warmed beaker filled with 400 ml 2x SSC/0.2% SDS at 65 °C. 3. Incubate slide in a 50 ml tube of pre-warmed 2x SSC/0.2% SDS at 65 °C for 10-15 minutes. 4. Wash in 2x SSC at room temperature for 10-15 minutes. 5. Wash in 0.2x SSC room temperature for 10-15 minutes. 6. Centrifuge at 500 rcf for 4 minutes to dry. 7. Scan as soon as possible.

scan_protocol: The hybridized slides were scanned immediately after hybridization with Genepix Scanner 4000. The scan was done with PMT 650 for both channels.

data_processing: Raw data was extracted from the scanned image using GenePix 6.0 software, and then normalized using OLIN with 'subtract' background correction (http://itb.biologie.hu-berlin.de/~futschik/software/R/OLIN/). Features flagged as "bad" manually or by GenePix were assigned a value of "null" in the VALUE, CH1_NORM, and CH2_NORM columns.

label: Alexa Fluor 546

organism: Drosophila melanogaster

label_protocol:
REVERSE TRANSCRIPTION
1. Use 20 ug of total RNA per reaction with Array50 dendrimer kit.
2. Mix the following reagents in an RNase-free microcentrifuge tube: 20 ug RNA, 1 ul RT primer (for Alexa Fluor 546 dendrimer), nuclease-free water to 6 ul total volume.
3. Mix briefly, and centrifuge briefly.
4. Incubate for 5 minutes at 80 °C.
5. Incubate on ice for 3-5 minutes immediately.
6. Centrifuge briefly, and return to ice.
7. Prepare a reaction mix in a microcentrifuge tube on ice: 2 ul 5X RT buffer, 1 ul 0.1 M DTT, 0.5 ul Superase-in RNase inhibitor (kit), 0.5 ul dNTP mix (kit), 0.5 ul Invitrogen SuperScriptTM III RNase H- Reverse Transcriptase (100 units) (total volume 4.5 ul).
8. Mix gently (do not vortex), and centrifuge briefly.
9. Add 4.5 ul reaction mix to 6 ul RNA-primer annealing reaction (from steps 1-6 above). Mix gently.
10. Incubate for 3 hours at 46 °C.
RNA HYDROLYSIS
1. Add 1 ul 1 M NaOH/100 mM EDTA.
2. Incubate at 65 °C for 10 minutes to stop the reaction and degrade the RNA.
3. Add 1.2 ul 2 M Tris, pH 7.5 to neutralize the reaction.
NOTE: Label is introduced during the hybridization; see hybridization protocol below.

growth_protocol: Cells were grown at 25 °C in Shields and Sang M3 medium (Sigma) supplemented with tissue culture-grade yeast extract (1 g/l), bactopeptone (2.5 g/l), human insulin (10 µg/ml final concentration), and fetal calf serum (heat-inactivated 1 hr at 56º, 10% final concentration).

extract_protocol: Pellet cells by centrifugation in 50 ml Corning tube. Resuspend/wash in 5 ml PBS (put into 15 ml Corning tube). Pellet cells again by centrifugation. Remove supernatant. Lyse cells in TRIzol reagent (.75ml per 5-10 E7 cells) by repetitive pipetting. Incubate at room temp. for 5 minutes. Add .2 ml of chloroform per .75 ml of TRIzol used initially. Shake tubes vigorously for 15 seconds Incubate at room temp. for 2 minutes. Divide into 2 eppendorf tubes per sample(~about 1.267 ml per tube). Centrifuge for 15 minutes at 4 °C at 10,000 x g. Transfer the top aqueous phases to clean tubes. Precipitate the RNA from the aqueous phase by adding .5 ml of isopropenal per .75 ml of TRIzol used initially. Invert tubes once. Incubate samples at room temp. for 10 minutes. Centrifuge for 10 minutes at 4 °C at 10,000 x g. Remove supernatant. Wash RNA pellet once with 75% ethanol, 1 ml per .75 ml of TRIzol used initially. Vortex. Centrifuge at 7,500 x g for 5 minutes at 4 °C. Let pellet air dry for 10 minutes. Dissolve in RNase-free water (DEP treated). Incubate at 30 °C overnight .

treatment_protocol: None treatment

tag: Cell line ML-DmD16-c3

label: Alexa Fluor 647

label_protocol:
REVERSE TRANSCRIPTION
1. Use 20 ug of total RNA per reaction with Array50 dendrimer kit.
2. Mix the following reagents in an RNase-free microcentrifuge tube: 20 ug RNA, 1 ul RT primer (for Alexa Fluor 647 dendrimer), nuclease-free water to 6 ul total volume.
3. Mix briefly, and centrifuge briefly.
4. Incubate for 5 minutes at 80 °C.
5. Incubate on ice for 3-5 minutes immediately.
6. Centrifuge briefly, and return to ice.
7. Prepare a reaction mix in a microcentrifuge tube on ice: 2 ul 5X RT buffer, 1 ul 0.1 M DTT, 0.5 ul Superase-in RNase inhibitor (kit), 0.5 ul dNTP mix (kit), 0.5 ul Invitrogen SuperScriptTM III RNase H- Reverse Transcriptase (100 units) (total volume 4.5 ul).
8. Mix gently (do not vortex), and centrifuge briefly.
9. Add 4.5 ul reaction mix to 6 ul RNA-primer annealing reaction (from steps 1-6 above). Mix gently.
10. Incubate for 3 hours at 46 °C.
RNA HYDROLYSIS
1. Add 1 ul 1 M NaOH/100 mM EDTA.
2. Incubate at 65 °C for 10 minutes to stop the reaction and degrade the RNA.
3. Add 1.2 ul 2 M Tris, pH 7.5 to neutralize the reaction.
NOTE: Label is introduced during the hybridization; see hybridization protocol below.

growth_protocol: Cells were grown at 25 °C in CCM3 medium (HyClone)

tag: Cell line Kc167


title: S2_Kc167_rep3

description: The experiment compares transcripts from Kc167 and S2 cells, using a dendrimer hybridization procedure.

scan_protocol: The hybridized slides were scanned immediately after hybridization with Genepix Scanner 4200. The scan was done with PMT 450 for both channels.

growth_protocol: Cells were grown at 25 °C in Shields and Sang M3 medium (Sigma) supplemented with tissue culture-grade yeast extract (1 g/l), bactopeptone (2.5 g/l), and fetal calf serum (heat-inactivated 1 hr at 56º, 10% final concentration).

tag: Cell line S2


title: S2_Kc167_rep2


title: ML-DmD16-c3_Kc167_rep3


title: S2_Kc167_rep1


title: ML-DmD11_Kc167_rep2

description: The experiment compares transcripts from Kc167 and ML-DmD11 cells, using a dendrimer hybridization procedure.

hyb_protocol: PRE-HYBRIDIZATION. 1. Prepare 50 ml pre-hybridization buffer (5x SSC/0.1% SDS/1% I-block) in a 50 ml screw cap centrifuge tube, and bring to 55 °C. 2. Incubate microarray slide in pre-hybridization buffer at 55 °C for 1.5 hours. 3. Transfer microarray slide to 50 ml tube filled with water and invert gently for 1 minute. Then transfer to new tube with fresh water to wash two times. 4. Centrifuge at 500 rcf for 4 minutes to dry (label end down). cDNA HYBRIDIZATION. 1. Prepare the following cDNA hybridization mix: 12.7 ul of each cDNA synthesis reaction mix, 2.1 ul nuclease-free water, 2.7 ul 2x Formamide-Based hybridization buffer (kit) (total volume 55 ul). 2. Mix (by gentle vortexing) and briefly spin the hybridization mix. 3. Incubate at 80 °C for 10 minutes. 4. Incubate at 55 °C until it is loaded on the microarray slide. 5. Pre-warm the microarray on a slide warmer. 6. Assemble the hybridization solution (55 ul) to the center of the slide. Carefully lower a LifterSlip onto the microarray avoiding bubbles. Place the slide face-up in a hybridization chamber. Pipette 20 μl of water into the wells at either end of the hybridization chamber. Seal the chamber. 7. Submerge the hybridization chamber in a 43 °C water bath and incubate for 14-17 hours. POST-cDNA HYBRIDIZATION WASHES. 1. Disassemble the hybridization chamber. 2. Remove cover slip by immersing the slide in a pre-warmed beaker filled with 400 ml 2x SSC/0.2% SDS at 42-43 °C. 3. Incubate slide in a 50 ml tube of pre-warmed 2x SSC/0.2% SDS at 42 °C for 10-15 minutes. 4. Wash in 2x SSC at room temperature for 10-15 minutes. 5. Wash in 0.2x SSC room temperature for 10-15 minutes. 6. Centrifuge at 500 rcf for 4 minutes to dry. DENDRIMER HYBRIDIZATION. 1. Thaw the 3DNA Capture Reagents (dendrimer solutions) that correspond to the primers used for cDNA synthesis in the dark for 20 minutes. Vortex, spin briefly, and incubate at 55 °C in the dark for 10 minutes. 2. At the same time, thaw 2X Formamide-based hybridization buffer by incubating it at 43 °C. 3. Prepare dendrimer hybridization solution by mixing the following kit components in a microcentrifuge tube: 2.5 ul Cy5 3DNA Array Capture Reagent, 2.5 ul Cy3 3DNA Array Capture Reagent, 27.5 ul 2x formamide-based hybridization buffer, 22.5 ul nuclease-free water (total volume 55 ul). 4. Vortex gently and centrifuge briefly. 5. Incubate at 80 °C for 10 minutes. 6. Assemble the hybridization as for the first hybridization. 7. Submerge the hybridization chamber in a 43 °C water bath and incubate for 5 hours. POST-DENDRIMER HYBRIDIZATION WASHES. 1. Disassemble the hybridization chamber. 2. Remove cover slip by immersing the slide in a pre-warmed beaker filled with 400 ml 2x SSC/0.2% SDS at 65 °C. 3. Incubate slide in a 50 ml tube of pre-warmed 2x SSC/0.2% SDS at 65 °C for 10-15 minutes. 4. Wash in 2x SSC at room temperature for 10-15 minutes. 5. Wash in 0.2x SSC room temperature for 10-15 minutes. 6. Centrifuge at 500 rcf for 4 minutes to dry. 7. Scan as soon as possible.

scan_protocol: The hybridized slides were scanned immediately after hybridization with Genepix Scanner 4200. The scan was done with PMT 400 for both channels.

label_protocol:
REVERSE TRANSCRIPTION
1. Use 20 ug of total RNA per reaction with Array50 dendrimer kit.
2. Mix the following reagents in an RNase-free microcentrifuge tube: 20 ug RNA, 1 ul RT primer (for Cy3 dendrimer), nuclease-free water to 6 ul total volume.
3. Mix briefly, and centrifuge briefly.
4. Incubate for 5 minutes at 80 °C.
5. Incubate on ice for 3-5 minutes immediately.
6. Centrifuge briefly, and return to ice.
7. Prepare a reaction mix in a microcentrifuge tube on ice: 2 ul 5X RT buffer, 1 ul 0.1 M DTT, 0.5 ul Superase-in RNase inhibitor (kit), 0.5 ul dNTP mix (kit), 0.5 ul Invitrogen SuperScriptTM III RNase H- Reverse Transcriptase (100 units) (total volume 4.5 ul).
8. Mix gently (do not vortex), and centrifuge briefly.
9. Add 4.5 ul reaction mix to 6 ul RNA-primer annealing reaction (from steps 1-6 above). Mix gently.
10. Incubate for 3 hours at 46 °C.
RNA HYDROLYSIS
1. Add 1 ul 1 M NaOH/100 mM EDTA.
2. Incubate at 65 °C for 10 minutes to stop the reaction and degrade the RNA.
3. Add 1.2 ul 2 M Tris, pH 7.5 to neutralize the reaction.
NOTE: Label is introduced during the hybridization; see hybridization protocol below.

tag: Cell line ML-DmD11

label_protocol:
REVERSE TRANSCRIPTION
1. Use 20 ug of total RNA per reaction with Array50 dendrimer kit.
2. Mix the following reagents in an RNase-free microcentrifuge tube: 20 ug RNA, 1 ul RT primer (for Cy5 dendrimer), nuclease-free water to 6 ul total volume.
3. Mix briefly, and centrifuge briefly.
4. Incubate for 5 minutes at 80 °C.
5. Incubate on ice for 3-5 minutes immediately.
6. Centrifuge briefly, and return to ice.
7. Prepare a reaction mix in a microcentrifuge tube on ice: 2 ul 5X RT buffer, 1 ul 0.1 M DTT, 0.5 ul Superase-in RNase inhibitor (kit), 0.5 ul dNTP mix (kit), 0.5 ul Invitrogen SuperScriptTM III RNase H- Reverse Transcriptase (100 units) (total volume 4.5 ul).
8. Mix gently (do not vortex), and centrifuge briefly.
9. Add 4.5 ul reaction mix to 6 ul RNA-primer annealing reaction (from steps 1-6 above). Mix gently.
10. Incubate for 3 hours at 46 °C.
RNA HYDROLYSIS
1. Add 1 ul 1 M NaOH/100 mM EDTA.
2. Incubate at 65 °C for 10 minutes to stop the reaction and degrade the RNA.
3. Add 1.2 ul 2 M Tris, pH 7.5 to neutralize the reaction.
NOTE: Label is introduced during the hybridization; see hybridization protocol below.


title: ML-DmD16-c3_Kc167_rep1


title: CME L1_Kc167_rep1

description: The experiment compares transcripts from Kc167 and CME L1 cells, using a dendrimer hybridization procedure.

source_name: CME L1

growth_protocol: Cells were grown at 25 °C in Shields and Sang M3 medium (Sigma) supplemented with tissue culture-grade yeast extract (1 g/l), bactopeptone (2.5 g/l), human insulin (5 µg/ml final concentration), and fly extract (DA Currie, MJ Milner, and CW Evans, The growth and differentiation in vitro of leg and wing imaginal disc cells from Drosophila melanogaster. Development 1988 102: 805-814) (2.5% final concentration), and fetal calf serum (heat-inactivated 1 hr at 56º, 10% final concentration).

tag: Cell line CME L1


title: squamous cell carcinoma 778

description: Primary squamous cell carcinoma

source_name: squamous cell carcinoma 778

source_name: lung reference mix


title: ML-DmD11_Kc167_rep3


title: ML-DmD11_Kc167_rep4


title: CME L1_Kc167_rep2

tag: cell line CME L1


title: ML-DmD4-c1_Kc167_rep2

description: The experiment compares transcripts from Kc167 and ML-DmD4-c1 cells, using a dendrimer hybridization procedure.

tag: Cell line ML-DmD4-c1


title: CME L1_Kc167_rep3


title: ML-DmD11_Kc167_rep1


title: ML-DmD4-c1_Kc167_rep3


title: CME Cl.8+_Kc167_rep3

description: The experiment compares transcripts from Kc167 and CME Cl.8+ cells, using a dendrimer hybridization procedure.

source_name: CME Cl.8+

tag: Cell line CME Cl.8+


title: ML-DmBG2-c2_Kc167_rep2

description: The experiment compares transcripts from Kc167 and ML-DmBG2-c2 cells, using a dendrimer hybridization procedure.

tag: Cell line ML-DmBG2-c2


title: ML-DmBG3-c2_Kc167_rep1

description: The experiment compares transcripts from Kc167 and ML-DmBG3-c2 cells, using a dendrimer hybridization procedure.

tag: Cell line ML-DmBG3-c2


title: ML-DmD4-c1_Kc167_rep1


title: ML-DmBG2-c2_Kc167_rep3


title: CME Cl.8+_Kc167_rep1


title: CME Cl.8+_Kc167_rep2


title: ML-DmBG2-c2_Kc167_rep1

hyb_protocol: PRE-HYBRIDIZATION. 1. Prepare 50 ml pre-hybridization buffer (5x SSC/0.1% SDS/1% I-block) in a 50 ml screw cap centrifuge tube, and bring to 55 °C. 2. Incubate microarray slide in pre-hybridization buffer at 55 °C for 1.5 hours. 3. Transfer microarray slide to 50 ml tube filled with water and invert gently for 1 minute. Then transfer to new tube with fresh water to wash two times. 4. Centrifuge at 500 rcf for 4 minutes to dry (label end down). cDNA HYBRIDIZATION. 1. Prepare the following cDNA hybridization mix: 12.7 ul of each cDNA synthesis reaction mix, 2.1 ul nuclease-free water, 2.7 ul 2x Formamide-Based hybridization buffer (kit) (total volume 55 ul). 2. Mix (by gentle vortexing) and briefly spin the hybridization mix. 3. Incubate at 80 °C for 10 minutes. 4. Incubate at 55 °C until it is loaded on the microarray slide. 5. Pre-warm the microarray on a slide warmer. 6. Assemble the hybridization solution (55 ul) to the center of the slide. Carefully lower a LifterSlip onto the microarray avoiding bubbles. Place the slide face-up in a hybridization chamber. Pipette 20 μl of water into the wells at either end of the hybridization chamber. Seal the chamber. 7. Submerge the hybridization chamber in a 43 °C water bath and incubate for 14-17 hours. POST-cDNA HYBRIDIZATION WASHES. 1. Disassemble the hybridization chamber. 2. Remove cover slip by immersing the slide in a pre-warmed beaker filled with 400 ml 2x SSC/0.2% SDS at 42-43 °C. 3. Incubate slide in a 50 ml tube of pre-warmed 2x SSC/0.2% SDS at 42 °C for 10-15 minutes. 4. Wash in 2x SSC at room temperature for 10-15 minutes. 5. Wash in 0.2x SSC room temperature for 10-15 minutes. 6. Centrifuge at 500 rcf for 4 minutes to dry. DENDRIMER HYBRIDIZATION. 1. Thaw the 3DNA Capture Reagents (dendrimer solutions) that correspond to the primers used for cDNA synthesis in the dark for 20 minutes. Vortex, spin briefly, and incubate at 55 °C in the dark for 10 minutes. 2. At the same time, thaw 2X Formamide-based hybridization buffer by incubating it at 43 °C. 3. Prepare dendrimer hybridization solution by mixing the following kit components in a microcentrifuge tube: 2.5 ul Alexa Fluor 546 3DNA Array Capture Reagent, 2.5 ul Alexa Fluor 647 3DNA Array Capture Reagent, 27.5 ul 2x formamide-based hybridization buffer, 22.5 ul nuclease-free water (total volume 55 ul). 4. Vortex gently and centrifuge briefly. 5. Incubate at 80 °C for 10 minutes. 6. Assemble the hybridization as for the first hybridization. 7. Submerge the hybridization chamber in a 43 °C water bath and incubate for 5 hours. POST-DENDRIMER HYBRIDIZATION WASHES. 1. Disassemble the hybridization chamber. 2. Remove cover slip by immersing the slide in a pre-warmed beaker filled with 400 ml 2x SSC/0.2% SDS at 65 °C. 3. Incubate slide in a 50 ml tube of pre-warmed 2x SSC/0.2% SDS at 65 °C for 10-15 minutes. 4. Wash in 2x SSC at room temperature for 10-15 minutes. 5. Wash in 0.2x SSC room temperature for 10-15 minutes. 6. Centrifuge at 500 rcf for 4 minutes to dry. 7. Scan as soon as possible.


title: ML-DmD21_Kc167_rep3

description: The experiment compares transcripts from Kc167 and ML-DmD21 cells, using a dendrimer hybridization procedure.

hyb_protocol: PRE-HYBRIDIZATION. 1. Prepare 50 ml pre-hybridization buffer (5x SSC/0.1% SDS/1% I-block) in a 50 ml screw cap centrifuge tube, and bring to 55 °C. 2. Incubate microarray slide in pre-hybridization buffer at 55 °C for 1.5 hours. 3. Transfer microarray slide to 50 ml tube filled with water and invert gently for 1 minute. Then transfer to new tube with fresh water to wash two times. 4. Centrifuge at 500 rcf for 4 minutes to dry (label end down). cDNA HYBRIDIZATION. 1. Prepare the following cDNA hybridization mix: 12.7 ul of each cDNA synthesis reaction mix, 2.1 ul nuclease-free water, 2.7 ul 2x Formamide-Based hybridization buffer (kit) (total volume 55 ul). 2. Mix (by gentle vortexing) and briefly spin the hybridization mix. 3. Incubate at 80 °C for 10 minutes. 4. Incubate at 55 °C until it is loaded on the microarray slide. 5. Pre-warm the microarray on a slide warmer. 6. Assemble the hybridization solution (55 ul) to the center of the slide. Carefully lower a LifterSlip onto the microarray avoiding bubbles. Place the slide face-up in a hybridization chamber. Pipette 20 μl of water into the wells at either end of the hybridization chamber. Seal the chamber. 7. Submerge the hybridization chamber in a 43 °C water bath and incubate for 14-17 hours. POST-cDNA HYBRIDIZATION WASHES. 1. Disassemble the hybridization chamber. 2. Remove cover slip by immersing the slide in a pre-warmed beaker filled with 400 ml 2x SSC/0.2% SDS at 42-43 °C. 3. Incubate slide in a 50 ml tube of pre-warmed 2x SSC/0.2% SDS at 42 °C for 10-15 minutes. 4. Wash in 2x SSC at room temperature for 10-15 minutes. 5. Wash in 0.2x SSC room temperature for 10-15 minutes. 6. Centrifuge at 500 rcf for 4 minutes to dry. DENDRIMER HYBRIDIZATION. 1. Thaw the 3DNA Capture Reagents (dendrimer solutions) that correspond to the primers used for cDNA synthesis in the dark for 20 minutes. Vortex, spin briefly, and incubate at 55 °C in the dark for 10 minutes. 2. At the same time, thaw 2X Formamide-based hybridization buffer by incubating it at 43 °C. 3. Prepare dendrimer hybridization solution by mixing the following kit components in a microcentrifuge tube: 2.5 ul Cy3 3DNA Array Capture Reagent, 2.5 ul Cy5 3DNA Array Capture Reagent, 27.5 ul 2x formamide-based hybridization buffer, 22.5 ul nuclease-free water (total volume 55 ul). 4. Vortex gently and centrifuge briefly. 5. Incubate at 80 °C for 10 minutes. 6. Assemble the hybridization as for the first hybridization. 7. Submerge the hybridization chamber in a 43 °C water bath and incubate for 5 hours. POST-DENDRIMER HYBRIDIZATION WASHES. 1. Disassemble the hybridization chamber. 2. Remove cover slip by immersing the slide in a pre-warmed beaker filled with 400 ml 2x SSC/0.2% SDS at 65 °C. 3. Incubate slide in a 50 ml tube of pre-warmed 2x SSC/0.2% SDS at 65 °C for 10-15 minutes. 4. Wash in 2x SSC at room temperature for 10-15 minutes. 5. Wash in 0.2x SSC room temperature for 10-15 minutes. 6. Centrifuge at 500 rcf for 4 minutes to dry. 7. Scan as soon as possible.

tag: Cell line ML-DmD21


title: ML-DmBG3-c2_Kc167_rep2


title: ML-DmBG3-c2_Kc167_rep3


title: ML-DmD21_Kc167_rep2


title: Fischer 344-rep4

description: Gene expression data from proximal femur


title: ML-DmD21_Kc167_rep1


title: ML-DmD20-c5_Kc167_rep4

description: The experiment compares transcripts from Kc167 and ML-DmD20-c5 cells, using a dendrimer hybridization procedure.

tag: Cell line ML-DmD20-c5

tag: Cell line kc167


title: ML-DmD20-c2_Kc167_rep2

description: The experiment compares transcripts from Kc167 and ML-DmD20-c2 cells, using a dendrimer hybridization procedure.

tag: Cell line ML-DmD20-c2


title: ML-DmD20-c5_Kc167_rep1


title: S2_5 hours ecdysone_rep2

description: The experiment compares transcripts from control and ecdysone-treated cells, using a dendrimer hybridization procedure.

source_name: S2, 5 hours ecdysone treated, rep2

treatment_protocol: 5 hours 1E-6 M 20-hydroxyecdysone + 0.01% ethanol

tag: Cell line S2, ecdysone treated

source_name: S2, 5 hours ethanol treated, control,  rep2

treatment_protocol: 5 hours 0.01% ethanol

tag: Cell line S2, ethanol treated, control


title: S2_5 hours ecdysone_rep1

source_name: S2, 5 hours ecdysone treated, rep1

source_name: S2, 5 hours ethanol treated, control,  rep1


title: ML-DmD20-c5_Kc167_rep2


title: S2_5 hours ecdysone_rep4

source_name: S2, 5 hours ecdysone treated, rep4

source_name: S2, 5 hours ethanol treated, control,  rep4


title: S2_5 hours ecdysone_rep3

source_name: S2, 5 hours ecdysone treated, rep3

source_name: S2, 5 hours ethanol treated, control,  rep3


title: ML-DmD20-c2_Kc167_rep4


title: ML-DmD20-c2_Kc167_rep3


title: CME-L1_5 hours ecdysone_rep3

source_name: CME-L1, 5 hours ecdysone treated, rep3

tag: Cell line CME-L1, ecdysone treated

source_name: CME-L1, 5 hours ethanol treated, control,  rep3

tag: Cell line CME-L1, ethanol treated, control


title: ML-DmD20-c5_Kc167_rep3

tag: Cell line Kc167


title: CME-L1_5 hours ecdysone_rep2

source_name: CME-L1, 5 hours ecdysone treated, rep2

source_name: CME-L1, 5 hours ethanol treated, control,  rep2


title: Lewis-rep3

source_name: Bone, Femur

tag: proximal femur


title: ML-DmD20-c2_Kc167_rep1


title: ML-DmD21_5 hours ecdysone_rep3

source_name: ML-DmD21, 5 hours ecdysone treated, rep3

tag: Cell line ML-DmD21, ecdysone treated

source_name: ML-DmD21, 5 hours ethanol treated, control,  rep3

tag: Cell line ML-DmD21, ethanol treated, control


title: ML-DmD21_5 hours ecdysone_rep2

source_name: ML-DmD21, 5 hours ecdysone treated, rep2

source_name: ML-DmD21, 5 hours ethanol treated, control,  rep2


title: ML-DmD20-c5_5 hours ecdysone_rep2

source_name: ML-DmD20-c5, 5 hours ecdysone treated, rep2

tag: Cell line ML-DmD20-c5, ecdysone treated

source_name: ML-DmD20-c5, 5 hours ethanol treated, control,  rep2

tag: Cell line ML-DmD20-c5, ethanol treated, control


title: CME-L1_5 hours ecdysone_rep4

source_name: CME-L1, 5 hours ecdysone treated, rep4

source_name: CME-L1, 5 hours ethanol treated, control,  rep4


title: CME-L1_5 hours ecdysone_rep1

source_name: CME-L1, 5 hours ecdysone treated, rep1

source_name: CME-L1, 5 hours ethanol treated, control,  rep1


title: ML-DmD21_5 hours ecdysone_rep1

source_name: ML-DmD21, 5 hours ecdysone treated, rep1

source_name: ML-DmD21, 5 hours ethanol treated, control,  rep1


title: ML-DmD20-c5_5 hours ecdysone_rep3

source_name: ML-DmD20-c5, 5 hours ecdysone treated, rep3

source_name: ML-DmD20-c5, 5 hours ethanol treated, control,  rep3


title: ML-DmD20-c5_5 hours ecdysone_rep1

source_name: ML-DmD20-c5, 5 hours ecdysone treated, rep1

source_name: ML-DmD20-c5, 5 hours ethanol treated, control,  rep1


title: CME L1_Kc167_rep4

source_name: CME L1

tag: Cell line CME L1


title: ML-DmD16-c3_5 hours ecdysone_rep3

source_name: ML-DmD16-c3, 5 hours ecdysone treated, rep3

tag: Cell line ML-DmD16-c3, ecdysone treated

source_name: ML-DmD16-c3, 5 hours ethanol treated, control,  rep3

tag: Cell line ML-DmD16-c3, ethanol treated, control


title: ML-DmD20-c2_5 hours ecdysone_rep4

source_name: ML-DmD20-c2, 5 hours ecdysone treated, rep4

tag: Cell line ML-DmD20-c2, ecdysone treated

source_name: ML-DmD20-c2, 5 hours ethanol treated, control,  rep4

tag: Cell line ML-DmD20-c2, ethanol treated, control


title: ML-DmD20-c2_5 hours ecdysone_rep3

source_name: ML-DmD20-c2, 5 hours ecdysone treated, rep3

source_name: ML-DmD20-c2, 5 hours ethanol treated, control,  rep3


title: ML-DmD20-c2_5 hours ecdysone_rep1

source_name: ML-DmD20-c2, 5 hours ecdysone treated, rep1

source_name: ML-DmD20-c2, 5 hours ethanol treated, control,  rep1


title: ML-DmD11_5 hours ecdysone_rep3

source_name: ML-DmD11, 5 hours ecdysone treated, rep3

tag: Cell line ML-DmD11, ecdysone treated

source_name: ML-DmD11, 5 hours ethanol treated, control,  rep3

tag: Cell line ML-DmD11, ethanol treated, control


title: ML-DmD20-c2_5 hours ecdysone_rep2

source_name: ML-DmD20-c2, 5 hours ecdysone treated, rep2

source_name: ML-DmD20-c2, 5 hours ethanol treated, control,  rep2


title: ML-DmD16-c3_5 hours ecdysone_rep2

source_name: ML-DmD16-c3, 5 hours ecdysone treated, rep2

source_name: ML-DmD16-c3, 5 hours ethanol treated, control,  rep2


title: ML-DmBG2-c2_5 hours ecdysone_rep2

source_name: ML-DmBG2-c2, 5 hours ecdysone treated, rep2

tag: Cell line ML-DmBG2-c2, ecdysone treated

source_name: ML-DmBG2-c2, 5 hours ethanol treated, control,  rep2

tag: Cell line ML-DmBG2-c2, ethanol treated, control


title: ML-DmD11_5 hours ecdysone_rep1

source_name: ML-DmD11, 5 hours ecdysone treated, rep1

source_name: ML-DmD11, 5 hours ethanol treated, control,  rep1


title: ML-DmBG2-c2_5 hours ecdysone_rep3

source_name: ML-DmBG2-c2, 5 hours ecdysone treated, rep3

source_name: ML-DmBG2-c2, 5 hours ethanol treated, control,  rep3


title: ML-DmD16-c3_5 hours ecdysone_rep1

source_name: ML-DmD16-c3, 5 hours ecdysone treated, rep1

source_name: ML-DmD16-c3, 5 hours ethanol treated, control,  rep1


title: ML-DmD11_5 hours ecdysone_rep2

source_name: ML-DmD11, 5 hours ecdysone treated, rep2

source_name: ML-DmD11, 5 hours ethanol treated, control,  rep2


title: ML-DmBG3-c2_5 hours ecdysone_rep2

source_name: ML-DmBG3-c2, 5 hours ecdysone treated, rep2

tag: Cell line ML-DmBG3-c2, ecdysone treated

source_name: ML-DmBG3-c2, 5 hours ethanol treated, control, rep2

tag: Cell line ML-DmBG3-c2, ethanol treated, control


title: ML-DmBG3-c2_5 hours ecdysone_rep3

source_name: ML-DmBG3-c2, 5 hours ecdysone treated, rep3

source_name: ML-DmBG3-c2, 5 hours ethanol treated, control, rep3


title: CME W1 Cl.8+_5 hours ecdysone_rep1

source_name: CME W1 Cl.8+, 5 hours ecdysone treated, rep1

tag: Cell line CME W1 Cl.8+, ecdysone treated

source_name: CME W1 Cl.8+, 5 hours ethanol treated, control, rep1

tag: Cell line CME W1 Cl.8+, ethanol treated, control


title: CME W1 Cl.8+_5 hours ecdysone_rep2

source_name: CME W1 Cl.8+, 5 hours ecdysone treated, rep2

source_name: CME W1 Cl.8+, 5 hours ethanol treated, control, rep2


title: ML-DmBG3-c2_5 hours ecdysone_rep1

source_name: ML-DmBG3-c2, 5 hours ecdysone treated, rep1

source_name: ML-DmBG3-c2, 5 hours ethanol treated, control, rep1


title: ML-DmD4-c1_5 hours ecdysone_rep4

source_name: ML-DmD4-c1, 5 hours ecdysone treated, rep4

growth_protocol:
Cells were grown at 25 °C in Shields and Sang M3 medium (Sigma) supplemented with tissue culture-grade yeast extract (1 g/l), bactopeptone (2.5 g/l), human insulin (10 µg/ml final concentration), and fetal calf serum (heat-inactivated 1 hr at 56º, 10% final concentration).
Cells were used in mid-exponential growth.

tag: Cell line ML-DmD4-c1, ecdysone treated

source_name: ML-DmD4-c1, 5 hours ethanol treated, control, rep4

tag: Cell line ML-DmD4-c1, ethanol treated, control


title: ML-DmD4-c1_5 hours ecdysone_rep2

source_name: ML-DmD4-c1, 5 hours ecdysone treated, rep2

source_name: ML-DmD4-c1, 5 hours ethanol treated, control, rep2


title: CME W1 Cl.8+_5 hours ecdysone_rep4

source_name: CME W1 Cl.8+, 5 hours ecdysone treated, rep4

source_name: CME W1 Cl.8+, 5 hours ethanol treated, control, rep4


title: CME W1 Cl.8+_5 hours ecdysone_rep3

source_name: CME W1 Cl.8+, 5 hours ecdysone treated, rep3

source_name: CME W1 Cl.8+, 5 hours ethanol treated, control, rep3


title: ML-DmBG3-c2_5 hours ecdysone_rep4

source_name: ML-DmBG3-c2, 5 hours ecdysone treated, rep4

source_name: ML-DmBG3-c2, 5 hours ethanol treated, control, rep4


title: ML-DmD4-c1_5 hours ecdysone_rep3

source_name: ML-DmD4-c1, 5 hours ecdysone treated, rep3

source_name: ML-DmD4-c1, 5 hours ethanol treated, control, rep3


title: ML-DmBG3-c2_48 hours ecdysone_rep3

source_name: ML-DmBG3-c2, 48 hours ecdysone treated, rep3

treatment_protocol: 48 hours 1E-6 M 20-hydroxyecdysone + 0.01% ethanol

source_name: ML-DmBG3-c2, 48 hours, ethanol treated, control, rep3

treatment_protocol: 48 hours 0.01% ethanol


title: ML-DmD4-c1_5 hours ecdysone_rep1

source_name: ML-DmD4-c1, 5 hours ecdysone treated, rep1

source_name: ML-DmD4-c1, 5 hours ethanol treated, control, rep1


title: ML-DmBG3-c2_48 hours ecdysone_rep1

source_name: ML-DmBG3-c2, 48 hours ecdysone treated, rep1

source_name: ML-DmBG3-c2, 48 hours, ethanol treated, control, rep1


title: ML-DmBG3-c2_48 hours ecdysone_rep2

source_name: ML-DmBG3-c2, 48 hours ecdysone treated, rep2

source_name: ML-DmBG3-c2, 48 hours, ethanol treated, control, rep2


title: ML-DmBG3-c2_24 hours ecdysone_rep3

source_name: ML-DmBG3-c2, 24 hours ecdysone treated, rep3

treatment_protocol: 24 hours 1E-6 M 20-hydroxyecdysone + 0.01% ethanol

source_name: ML-DmBG3-c2, 24 hours, ethanol treated, control, rep3

treatment_protocol: 24 hours 0.01% ethanol


title: ML-DmBG3-c2_48 hours ecdysone_rep4

source_name: ML-DmBG3-c2, 48 hours ecdysone treated, rep4

source_name: ML-DmBG3-c2, 48 hours, ethanol treated, control, rep4


title: ML-DmBG3-c2_24 hours ecdysone_rep4

source_name: ML-DmBG3-c2, 24 hours ecdysone treated, rep4

source_name: ML-DmBG3-c2, 24 hours, ethanol treated, control, rep4


title: ML-DmBG3-c2_12 hours ecdysone_rep3

source_name: ML-DmBG3-c2, 12 hours ecdysone treated, rep3

treatment_protocol: 12 hours 1E-6 M 20-hydroxyecdysone + 0.01% ethanol

source_name: ML-DmBG3-c2, 12 hours, ethanol treated, control, rep3

treatment_protocol: 12 hours 0.01% ethanol


title: ML-DmBG3-c2_24 hours ecdysone_rep2

source_name: ML-DmBG3-c2, 24 hours ecdysone treated, rep2

source_name: ML-DmBG3-c2, 24 hours, ethanol treated, control, rep2


title: ML-DmBG3-c2_12 hours ecdysone_rep2

source_name: ML-DmBG3-c2, 12 hours ecdysone treated, rep2

source_name: ML-DmBG3-c2, 12 hours, ethanol treated, control, rep2


title: ML-DmBG3-c2_12 hours ecdysone_rep4

source_name: ML-DmBG3-c2, 12 hours ecdysone treated, rep4

source_name: ML-DmBG3-c2, 12 hours, ethanol treated, control, rep4


title: CME W1 Cl.8+_48 hours ecdysone_rep3

source_name: CME W1 Cl.8+, 48 hours ecdysone treated, rep3

source_name: CME W1 Cl.8+, 48 hours ethanol treated, control, rep3


title: CME W1 Cl.8+_24 hours ecdysone_rep3

source_name: CME W1 Cl.8+, 24 hours ecdysone treated, rep3

source_name: CME W1 Cl.8+, 24 hours ethanol treated, control, rep3


title: CME W1 Cl.8+_48 hours ecdysone_rep1

source_name: CME W1 Cl.8+, 48 hours ecdysone treated, rep1

source_name: CME W1 Cl.8+, 48 hours ethanol treated, control, rep1


title: ML-DmBG3-c2_12 hours ecdysone_rep1

source_name: ML-DmBG3-c2, 12 hours ecdysone treated, rep1

source_name: ML-DmBG3-c2, 12 hours, ethanol treated, control, rep1


title: CME W1 Cl.8+_48 hours ecdysone_rep2

source_name: CME W1 Cl.8+, 48 hours ecdysone treated, rep2

source_name: CME W1 Cl.8+, 48 hours ethanol treated, control, rep2


title: CME W1 Cl.8+_48 hours ecdysone_rep4

source_name: CME W1 Cl.8+, 48 hours ecdysone treated, rep4

source_name: CME W1 Cl.8+, 48 hours ethanol treated, control, rep4


title: CME W1 Cl.8+_24 hours ecdysone_rep4

source_name: CME W1 Cl.8+, 24 hours ecdysone treated, rep4

source_name: CME W1 Cl.8+, 24 hours ethanol treated, control, rep4


title: CME W1 Cl.8+_12 hours ecdysone_rep2

source_name: CME W1 Cl.8+, 12 hours ecdysone treated, rep2

source_name: CME W1 Cl.8+, 12 hours ethanol treated, control, rep2


title: CME W1 Cl.8+_24 hours ecdysone_rep2

source_name: CME W1 Cl.8+, 24 hours ecdysone treated, rep2

source_name: CME W1 Cl.8+, 24 hours ethanol treated, control, rep2


title: CME W1 Cl.8+_12 hours ecdysone_rep4

source_name: CME W1 Cl.8+, 12 hours ecdysone treated, rep4

source_name: CME W1 Cl.8+, 12 hours ethanol treated, control, rep4


title: CME W1 Cl.8+_12 hours ecdysone_rep3

source_name: CME W1 Cl.8+, 12 hours ecdysone treated, rep3

source_name: CME W1 Cl.8+, 12 hours ethanol treated, control, rep3


title: CME W1 Cl.8+_24 hours ecdysone_rep1

source_name: CME W1 Cl.8+, 24 hours ecdysone treated, rep1

source_name: CME W1 Cl.8+, 24 hours ethanol treated, control, rep1


title: ML-DmD4-c1_48 hours ecdysone_rep1

source_name: ML-DmD4-c1, 48 hours ecdysone treated, rep1

source_name: ML-DmD4-c1, 48 hours, ethanol treated, control, rep1


title: ML-DmD4-c1_48 hours ecdysone_rep3

source_name: ML-DmD4-c1, 48 hours ecdysone treated, rep3

source_name: ML-DmD4-c1, 48 hours, ethanol treated, control, rep3


title: ML-DmD4-c1_24 hours ecdysone_rep4

source_name: ML-DmD4-c1, 24 hours ecdysone treated, rep4

source_name: ML-DmD4-c1, 24 hours, ethanol treated, control, rep4


title: ML-DmD4-c1_24 hours ecdysone_rep3

source_name: ML-DmD4-c1, 24 hours ecdysone treated, rep3

source_name: ML-DmD4-c1, 24 hours, ethanol treated, control, rep3


title: ML-DmD4-c1_48 hours ecdysone_rep4

source_name: ML-DmD4-c1, 48 hours ecdysone treated, rep4

source_name: ML-DmD4-c1, 48 hours, ethanol treated, control, rep4


title: Kc_12 hours ecdysone_rep3

source_name: Kc167 cells, 12 hours ecdysone treated, rep3

growth_protocol: Cells were grown at 25 °C in CCM3 medium (HyClone). Cells were used in mid-exponential growth.

tag: Cell line Kc167, ecdysone treated

source_name: Kc167 cells, ethanol treated, control

tag: Cell line Kc167, ethanol treated, control


title: CME W1 Cl.8+_12 hours ecdysone_rep1

source_name: CME W1 Cl.8+, 12 hours ecdysone treated, rep1

source_name: CME W1 Cl.8+, 12 hours ethanol treated, control, rep1


title: ML-DmD4-c1_12 hours ecdysone_rep2

source_name: ML-DmD4-c1, 12 hours ecdysone treated, rep2

source_name: ML-DmD4-c1, 12 hours, ethanol treated, control, rep2


title: ML-DmD4-c1_12 hours ecdysone_rep1

source_name: ML-DmD4-c1, 12 hours ecdysone treated, rep1

source_name: ML-DmD4-c1, 12 hours, ethanol treated, control, rep1


title: ML-DmD4-c1_24 hours ecdysone_rep1

source_name: ML-DmD4-c1, 24 hours ecdysone treated, rep1

source_name: ML-DmD4-c1, 24 hours, ethanol treated, control, rep1


title: Kc_48 hours ecdysone_rep3

source_name: Kc167 cells, 48 hours ecdysone treated, rep3


title: Kc_48 hours ecdysone_rep1

source_name: Kc167 cells, 48 hours ecdysone treated, rep1


title: Kc_5 hours ecdysone_rep12

source_name: Kc167 cells, 5 hours ecdysone treated, rep12


title: Kc_48 hours ecdysone_rep2

source_name: Kc167 cells, 48 hours ecdysone treated, rep2


title: ML-DmD4-c1_12 hours ecdysone_rep3

source_name: ML-DmD4-c1, 12 hours ecdysone treated, rep3

source_name: ML-DmD4-c1, 12 hours, ethanol treated, control, rep3


title: ML-DmD4-c1_24 hours ecdysone_rep2

source_name: ML-DmD4-c1, 24 hours ecdysone treated, rep2

source_name: ML-DmD4-c1, 24 hours, ethanol treated, control, rep2


title: ML-DmBG2-c2_5 hours ecdysone_rep1

source_name: ML-DmBG2-c2, 5 hours ecdysone treated, rep1

source_name: ML-DmBG2-c2, 5 hours ethanol treated, control,  rep1


title: Kc_24 hours ecdysone_rep2

source_name: Kc167 cells, 24 hours ecdysone treated, rep2

source_name: Kc167 cells, ethanol treated, control


title: Kc_12 hours ecdysone_rep2

source_name: Kc167 cells, 12 hours ecdysone treated, rep2


title: Kc_24 hours ecdysone_rep1

source_name: Kc167 cells, 24 hours ecdysone treated, rep1


title: Kc_24 hours ecdysone_rep3

source_name: Kc167 cells, 24 hours ecdysone treated, rep3


title: Kc_5 hours ecdysone_rep8

source_name: Kc167 cells, 5 hours ecdysone treated, rep8


title: Kc_12 hours ecdysone_rep1

source_name: Kc167 cells, 12 hours ecdysone treated, rep1


title: Kc_5 hours ecdysone_rep10

source_name: Kc167 cells, 5 hours ecdysone treated, rep10


title: Kc_5 hours ecdysone_rep4

source_name: Kc167 cells, 5 hours ecdysone treated, rep4


title: Kc_5 hours ecdysone_rep13

source_name: Kc167 cells, 5 hours ecdysone treated, rep13


title: Illumina expression array-Hela cells treated with IFNgamma for 6hrs rep1

status: Public on Jan 15 2009

city: Toronto

first: Zhaodong

last: Xu

state: Ontario

address: Mc6-424, 399 Bathurst Street

department: Genetics & Development Division

country: Canada

institute: TWRI, UHN

description: Hela cells treated with IFNgamma for 6hrs, RNA was extracted, and hybridized to Illumina BeadChips, replicate 1.

hyb_protocol: Illumina HumanRef-6 BeadChips were hybridized, washed, stained and scanned according to Illumina’s protocol using the updated wash procedure

scan_protocol: Processed arrays were read using Illumina BeadReader according to the manufacturer's instructions.

data_processing: Data were extracted and analyed with Illumina BeadStudio software.

source_name: Hela cells

label_protocol: Targets were prepared from 200 ng total RNA using Illumina TotalPrep RNA Amplification Kit (Ambion, catalog #AMIL1791)

extract_protocol: RNA isolation as previously described (Pattenden et al., EMBO (2002) 21: 1978

tag: Hela cells treated with IFNgamma for 6 hours


title: ML-DmBG3-c2_24 hours ecdysone_rep1

source_name: ML-DmBG3-c2, 24 hours ecdysone treated, rep1

source_name: ML-DmBG3-c2, 24 hours, ethanol treated, control, rep1


title: Illumina expression array-Hela cells treated with IFNgamma for 6hrs rep2

description: Hela cells treated with IFNgamma for 6hrs, RNA was extracted, and hybridized to Illumina BeadChips, replicate 2.


title: Illumina expression array-Hela cells without IFNgamma treatment rep3

description: Hela cells without IFNgamma treatment, RNA was extracted, and hybridized to Illumina BeadChips, replicate 3.

tag: Hela cells without IFNgamma treatment


title: Kc_5 hours ecdysone_rep11

source_name: Kc167 cells, 5 hours ecdysone treated, rep11


title: Kc_5 hours ecdysone_rep2

source_name: Kc167 cells, 5 hours ecdysone treated, rep2


title: Illumina expression array-Hela cells without IFNgamma treatment rep1

description: Hela cells without IFNgamma treatment, RNA was extracted, and hybridized to Illumina BeadChips, replicate 1.

tag: Hela cells treated without IFNgamma treatment


title: Illumina expression array-Hela cells treated with IFNgamma for 24hrs  rep2

description: Hela cells treated with IFNgamma for 24 hours, RNA was extracted, and hybridized to Illumina BeadChips, replicate 2.

extract_protocol: RNA isolation as previously described (Pattenden et al., EMBO (2002) 21: 1978)


title: Illumina expression array-Hela cells treated with IFNgamma for 48hrs rep1

description: Hela cells treated with IFNgamma for 48 hours, RNA was extracted, and hybridized to Illumina BeadChips, replicate 1.


title: Kc_5 hours ecdysone_rep7

source_name: Kc167 cells, 5 hours ecdysone treated, rep7


title: Illumina expression array-Hela cells treated with IFNgamma for 48hrs rep2

description: Hela cells treated with IFNgamma for 48 hours, RNA was extracted, and hybridized to Illumina BeadChips, replicate 2


title: Illumina expression array-Hela cells treated with IFNgamma for 6hrs rep3

description: Hela cells treated with IFNgamma for 6hrs, RNA was extracted, and hybridized to Illumina BeadChips, replicate 3.


title: Illumina expression array-Hela cells without IFNgamma treatment rep2

description: Hela cells without IFNgamma treatment, RNA was extracted, and hybridized to Illumina BeadChips, replicate 2.

tag: Hela cells without IFNgamma treatment.


title: Kc_5 hours ecdysone_rep5

source_name: Kc167 cells, 5 hours ecdysone treated, rep5


title: Illumina expression array-Hela cells treated with IFNgamma for 24hrs rep1

description: Hela cells treated with IFNgamma for 24 hours, RNA was extracted, and hybridized to Illumina BeadChips, replicate 1.


title: Vertical Growth Phase Melanoma  # 16

status: Public on Jan 01 2009

type: genomic

city: Madrid

first: Juan

middle: C

last: Cigudosa

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics

country: Spain

institute: Centro Nacional de Investigaciones Oncologicas - CNIO

description: Comparison of 10 healthy females to 20 primary vertigal growth phase melanoma patients

hyb_protocol: Human cot-1 DNA, Agilent 10x blocking agent and Agilent 2x hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version v:8.1).

data_processing: LINEAR normalized, background subtracted data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

molecule: genomic DNA

source_name: Genomic DNA from VGP Melanoma  sample # 16 labeled with Cyanine-5 (red).

label_protocol: 2 µg of genomic DNA were primed with 20 µl of 2.5x Random Primers at 95°C for 5 min and then labeled with 5µl of 10x dUTP mix, 3 µl of Cy3 or Cy5 dUTP (1.0mM) and 1 µl of Exp-Klenow at 37ºC for 3 hours.

extract_protocol: Total DNA extracted using Quiagen's Tissue Kit following manufacturer's instructions

tag: VGP Melanoma

source_name: Genomic DNA from pooled pheripheral blood of ten healthy female donors

tag: Healthy female donor


title: Vertical Growth Phase Melanoma  # 15

source_name: Genomic DNA from VGP Melanoma  sample # 15 labeled with Cyanine-5 (red).


title: Vertical Growth Phase Melanoma  # 18

source_name: Genomic DNA from VGP Melanoma  sample # 18 labeled with Cyanine-5 (red).


title: Kc_5 hours ecdysone_rep3

source_name: Kc167 cells, 5 hours ecdysone treated, rep3

source_name: Kc167 cells, ethanol treated, control


title: Illumina expression array-Hela cells treated with IFNgamma for 24hrs rep3

description: Hela cells treated with IFNgamma for 24 hours, RNA was extracted, and hybridized to Illumina BeadChips, replicate 3.


title: Kc_5 hours ecdysone_rep6

source_name: Kc167 cells, 5 hours ecdysone treated, rep6


title: Vertical Growth Phase Melanoma  # 20

source_name: Genomic DNA from VGP Melanoma  sample # 20 labeled with Cyanine-5 (red).


title: Vertical Growth Phase Melanoma  # 19

source_name: Genomic DNA from VGP Melanoma  sample # 19 labeled with Cyanine-5 (red).


title: Illumina expression array-Hela cells treated with IFNgamma for 48 hrs rep3

description: Hela cells treated with IFNgamma for 48 hours, RNA was extracted, and hybridized to Illumina BeadChips, replicate 3


title: Vertical Growth Phase Melanoma  # 17

source_name: Genomic DNA from VGP Melanoma  sample # 17 labeled with Cyanine-5 (red).


title: Vertical Growth Phase Melanoma  # 13

source_name: Genomic DNA from VGP Melanoma  sample # 13 labeled with Cyanine-5 (red).


title: Vertical Growth Phase Melanoma  # 12

source_name: Genomic DNA from VGP Melanoma  sample # 12 labeled with Cyanine-5 (red).


title: Kc_5 hours ecdysone_rep1

source_name: Kc167 cells, 5 hours ecdysone treated, rep1

extract_protocol: Pellet cells by centrifugation in 50 ml Corning tube. Resuspend/wash in 5 ml PBS (put into 15 ml Corning tube). Pellet cells again by centrifugation. Remove supernatant. Lyse cells in TRIzol reagent (.75ml per 5-10 E7 cells) by repetitive pipetting. Incubate at room temp. for 5 minutes. Add .2 ml of chloroform per .75 ml of TRIzol used initially. Shake tubes vigorously for 15 seconds Incubate at room temp. for 2 minutes. Divide into 2 eppendorf tubes per sample(~about 1.267 ml per tube). Centrifuge for 15 minutes at 4 °C at 10,000 x g. Transfer the top aqueous phases to clean tubes. Precipitate the RNA from the aqueous phase by adding .5 ml of isopropenal per .75 ml of TRIzol used initially. Invert tubes once. Incubate samples at room temp. for 10 minutes. Centrifuge for 10 minutes at 4 °C at 10,000 x g.	Remove supernatant. Wash RNA pellet once with 75% ethanol, 1 ml per .75 ml of TRIzol used initially. Vortex. Centrifuge at 7,500 x g for 5 minutes at 4 °C. Let pellet air dry for 10 minutes. Dissolve in RNase-free water (DEP treated). Incubate at 30 °C overnight .


title: Vertical Growth Phase Melanoma  # 11

source_name: Genomic DNA from VGP Melanoma  sample # 11 labeled with Cyanine-5 (red).


title: Vertical Growth Phase Melanoma  # 14

source_name: Genomic DNA from VGP Melanoma  sample # 14 labeled with Cyanine-5 (red).


title: ML-DmD4-c1_48 hours ecdysone_rep2

source_name: ML-DmD4-c1, 48 hours ecdysone treated, rep2

source_name: ML-DmD4-c1, 48 hours, ethanol treated, control, rep2


title: Vertical Growth Phase Melanoma  # 5

source_name: Genomic DNA from VGP Melanoma  sample # 5 labeled with Cyanine-5 (red).


title: Vertical Growth Phase Melanoma  # 7

source_name: Genomic DNA from VGP Melanoma  sample # 7 labeled with Cyanine-5 (red).

source_name: Genomic DNA from pooled pheripheral blood of ten healthy female donors


title: Vertical Growth Phase Melanoma  # 6

source_name: Genomic DNA from VGP Melanoma  sample # 6 labeled with Cyanine-5 (red).


title: Vertical Growth Phase Melanoma  # 10

source_name: Genomic DNA from VGP Melanoma  sample # 10 labeled with Cyanine-5 (red).


title: Vertical Growth Phase Melanoma  # 4

source_name: Genomic DNA from VGP Melanoma  sample # 4 labeled with Cyanine-5 (red).


title: Ratio of NO3 to control replicate 2 (Zea mays Version B)

status: Public on Dec 31 2008

city: Beijing

first: Guohua

last: Mi

address: Yuan-Ming-Yuan West Rd 2

department: Plant Nutrition

institute: China Agricultural University

description: Total RNA from nitrate-treated roots.

hyb_protocol: Hybridization protocol is based on a 2X SSC, non formamide hybridization buffer and works well with cDNA target prepared using direct or indirect labeling methods.

scan_protocol: LuxScan 10K/A scanner GenePix Pro 4.0 image analysis software

data_processing: LOWESS normalized

organism: Zea mays

source_name: Zea mayes root

label_protocol: RNA was isolated using Trizol and Qiagen RNAeasy Columns. Then labeled with Cy3 or Cy5.

growth_protocol: solution culture, split-root

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

treatment_protocol: half root treated with 1 mM NO3-

tag: Age

value: day 10

tag: treated duration

source_name: Total RNA from control half-roots.

tag: Tissue

value: Zea mayes root


title: Ratio of NO3 to control replicate 2 (Zea mays Version A)

description: Total RNA from nitrate-treated roots.

source_name: maize root


title: Ratio of NO3 to control replicate 1 (Zea mays Version A)

description: Total RNA from nitrate-treated roots.


title: Vertical Growth Phase Melanoma  # 9

source_name: Genomic DNA from VGP Melanoma  sample # 9 labeled with Cyanine-5 (red).


title: Ratio of NO3 to control replicate 1 (Zea mays Version B)

description: Total RNA from nitrate-treated roots.

value: Zea mays root


title: Transcriptional responses of Escherichia coli k12 TPEN Chip file #5 TPEN

city: Oxford

first: Michael

middle: W

last: Crowder

state: OH

address: High Street

department: Chemistry and Biochemistry

institute: Miami University

description: Used affymetrix GeneChip Fluidics Stations to follow staining and washing protocol

hyb_protocol: Affymetrix Technical Manual, Prokaryotic Sample and Array Processing Biotin-labeled fragmented cDNA (2.0 µg) was hybridized to E. coli antisense genome arrays (Affymetrix) at 45 °C for 16 h as recommended in the GeneChip technical manual (Affymetrix).

scan_protocol: The data were collected by using Affymetrix GeneChip Scanner 3300.

data_processing:
Affymetrix GeneChip Operating Software (GCOS) Version 1.4, MAS5.0
Details: Intra-chip normalizations were performed using Affymetrix Gene Chip Operating Software (GCOS). Default statistical parameters were used to normalize each chip to the same target intensity (1500) as described in the Affymetrix GeneChip Expression Analysis manual. All nine possible inter-chip comparisons were performed in GCOS. The data were subsequently exported to a Microsoft Excel spreadsheet for manipulation. Multiple filter criteria (genes that were not present in both conditions, genes that were always expressed below 10% of the average array signal (150 for the chips with target intensity of 1500), and genes with p values > 0.05 were excluded from further analysis) were used to reduce the risk of erroneously assigning a gene as differentially-expressed. Consensus “detection p-value”, “change p-value”, and “signal log ratios” were calculated, and the default E. coli array p-value cutoff parameters were applied to these consensus values to estimate the transcript change between two conditions and the transcript presence under each condition. Background-subtracted data sets were used to calculate up-regulated and down-regulated genes based on fold changes of greater than 2.

organism: Escherichia coli

source_name: E. coli K12 strain BW25113 (obtained National BioResource Project, National Institute of Genomics, Japan)

growth_protocol: E.coli grown with aeration in minimal media at 37º C until mid log phase (0.6) and exposed to 10 uM TPEN (N,N,N',N'-tetrakis(2-pyridylmethyl ethylenediamine) for 30 min, cells were then harvested to extract RNA. Minimal medium contains 10 mM glycerol as the sole carbon source. The glycerol was added to a solution containing 40 mM MES (morpholineethanesulfonic acid), 18.69 mM NH4Cl, 13.41 mM KCl, 4.99 mM K2SO4, 68 µM CaCl2, and trace elements (18.5 µM FeCl3 • 6H2O, 600 nM ZnO, 400 nM CuCl2 • 2H2O, 344 nM CoNO3 • 6H2O, 16 µM H3BO3 in distilled water). After the pH was adjusted to 7.4 and autoclaving, the solution was made 1 mM in MgCl2 and 7.6 mM in beta-glycerophosphate (as a phosphate source).

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini kit according to the manufacturer’s protocol.

treatment_protocol: Treatment protocol- E.coli grown in minimal media at 37º C  until mid log phase (0.6) and exposed to 10 μM TPEN (N,N,N',N'-tetrakis(2-pyridylmethyl ethylenediamine) for 30 min, cells were then harvested to extract RNA

tag: ∆(araD-araB)567, ∆lacZ4787(::rrnB-3), lambda-, rph-1, ∆(rhaD-rhaB)568, hsdR514

tag: Datsenko, K. A., and B. L. Wanner. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97:6640-5.


title: Transcriptional responses of Escherichia coli k12 TPEN Chip file #6 TPEN

label_protocol: Affymetrix Technical Manual, Prokaryotic Sample and Array Processing

tag: A commensal strain


title: Transcriptional responses of Escherichia coli k12 TPEN Chip file #1 Control

treatment_protocol: E.coli grown in minimal media at 37º C  until mid log phase (0.6) and harvested to extract RNA

tag: Genotype

value: ∆(araD-araB)567, ∆lacZ4787(::rrnB-3), lambda-, rph-1, ∆(rhaD-rhaB)568, hsdR514


title: Bmicroplus_larvae_pyrethroid_rep2 block1

city: Kerrville

first: Leonel

middle: (Leo)

last: Saldivar

state: TX

address: 2700 Fredericksburg Rd.

department: Agriculture

institute: USDA

description: Custom high-density single channel oligonucleotide arrays were constructed by NimbleGen Systems Inc. (Madison, WI) using ESTs sequences from BmiGI.  The design of the array is such that 14 50mer probes per target were used for 13,601 of the 13,642 potential coding regions.  No mismatch probes are included on the arrays, allowing twice as many probes per target than if mismatches are included.  Probes with randomly generated sequences were also included.  These probes were generated with sequences designed to match the melting temperature (Tm) of the other probes on the array.  These random probes reflect the distribution of non-specific signal intensities for binding events to probes with approximately the same composition as the perfect match probes but with random sequences.  Each microarray chip includes 2 in-slide replicates (spot replicates), which were treated as technical replicates.

hyb_protocol: Hybridizations done at NimbleGen Inc.  Five R. microplus pooled RNA samples were hybridized to the microarrays.  A control and four different acaricides: organophosphate, pyrethroid, ivermectin, and amitraz.  The hybridization was done twice, resulting in a total of ten array hybridizations, i.e. two technical replicates per treatment including control were used.  The oligonucleotide arrays were used to examine differential gene expression between the control and each acaricide.

scan_protocol: The hybridized arrays were scanned with an Axon scanner (Axon Instruments, Union City, CA)

data_processing: The intensity raw values were normalized using quantile normalization to adjust intensity values which arise from variation in the technology rather than from biological differences between the RNA samples. It is important to remove as much of the non-biological variation in signal intensity as possible.  One robust way is by using a ‘complete data method’ of normalization.  The method is called ‘complete data method’ because it makes use of data from all arrays in an experiment to form the normalizing relation.  Quantile normalization is a complete data method and this is what was implemented for our dataset.  The goal of this type of normalization is to equalize the distribution of probe intensities for each array in a set of arrays.   (Bolstad, 2001)   Gene Calls: The gene calls were generated using the Robust Multichip Average (RMA) algorithm.  (Irizarray,et al., 2003A,  Irizarray, et al., 2003B,  Bolstad, 2003)   The software package tools used for normalization and gene calling are available through Bioconductor project at:  www.bioconductor.org

organism: Rhipicephalus microplus

source_name: Larvae

label_protocol: Dye: CY3 single channel

extract_protocol: Total RNA was isolated from 0.1 g larval material, respectively, using two consecutive 40 sec runs in the FastPrep-24 Tissue and Cell Homogenizer and Lysing Matrix D (Qbiogene, Irvine, CA). A setting of 6.0 with a 3 min ice incubation between runs was used, followed by RNA isolation with the Fast RNA Pro Green Kit (Qbiogene) and subsequent lithium chloride precipitation using the Totally RNA Kit reagents (Ambion Inc., Austin, TX).  Approximately 50 mg total RNA was treated with Turbo DNA-free kit (Ambion Inc.) in two 100 ml aliquots each treated with 2 ml of Turbo DNAse per kit protocols.  RNA integrity was verified by formaldehyde gel electrophoresis and staining in GelStar Nucleic Acid Gel Stain (Cambrex Bio Science, Rockland, ME).  Twenty mg of each DNA-free RNA was sent to NimbleGen for use in microarray analysis.

tag: larvae

value: 12-16 days old


title: Transcriptional responses of Escherichia coli k12 TPEN Chip file #2 Control

treatment_protocol: E.coli grown in minimal media at 37º C  until mid log phase (0.6) and cells were harvested to extract RNA

tag: A wild type commensal strain


title: Bmicroplus_larvae_pyrethroid_rep2 block2


title: Bmicroplus_larvae_control_rep2 block2


title: Bmicroplus_larvae_control_rep2 block1


title: Transcriptional responses of Escherichia coli k12 TPEN Chip file #3 control


title: Transcriptional responses of Escherichia coli k12 TPEN Chip file #4 TPEN

tag: Characteristics

value: A  commensal strain


title: Bmicroplus_larvae_organophosphate_rep2 block2


title: Vertical Growth Phase Melanoma  # 1

source_name: Genomic DNA from VGP Melanoma  sample # 1 labeled with Cyanine-5 (red).


title: Vertical Growth Phase Melanoma  # 2

source_name: Genomic DNA from VGP Melanoma  sample # 2 labeled with Cyanine-5 (red).


title: Bmicroplus_larvae_control_rep1 block2


title: Bmicroplus_larvae_control_rep1 block1


title: Bmicroplus_larvae_organophosphate_rep1 block2


title: Vertical Growth Phase Melanoma  # 3

source_name: Genomic DNA from VGP Melanoma  sample # 3 labeled with Cyanine-5 (red).


title: Bmicroplus_larvae_pyrethroid_rep1 block2


title: Vertical Growth Phase Melanoma  # 8

source_name: Genomic DNA from VGP Melanoma  sample # 8 labeled with Cyanine-5 (red).


title: Bmicroplus_larvae_ivermectin_rep1 block2


title: Bmicroplus_larvae_amitraz_rep1 block1


title: Bmicroplus_larvae_amitraz_rep1 block2


title: Bmicroplus_larvae_organophosphate_rep2 block1


title: Bmicroplus_larvae_organophosphate_rep1 block1


title: Kc_5 hours ecdysone_rep9

source_name: Kc167 cells, 5 hours ecdysone treated, rep9

tag: Cell line Kc167, ecdysone treated

source_name: Kc167 cells, ethanol treated, control

tag: Cell line Kc167, ethanol treated, control


title: Bmicroplus_larvae_ivermectin_rep1 block1


title: Bmicroplus_larvae_ivermectin_rep2 block1


title: Bmicroplus_larvae_pyrethroid_rep1 block1


title: Bmicroplus_larvae_ivermectin_rep2 block2


title: Bmicroplus_larvae_amitraz_rep2 block1


title: Third_instar_larval_midgut_WGA_12h_rep1

status: Public on Oct 03 2008

city: Urbana

first: Hongmei

last: LI

state: IL

address: 505 S. Goodwin Ave

department: Entomology

institute: University of Illinois at Urbana-Champaign

description: Gene expression data from the third instar Drosophila larval midgut

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with GCOS software (Affymetrix, Santa Clara, CA)

source_name: Third instar larval midgut, WGA, 12 hours

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Temp: 24°C Humid:60% Light/Dark cycle: 14:10

extract_protocol: Total RNA was isolated by using the TRIzol® Reagent (Invitrogen, Carlsbad, CA) and RNeasy Mini Kit (Qiagen Inc., Valencia, CA) following the manufacturers’ protocol.

treatment_protocol: Third instar of Drosophila melanogaster fed 1% wheat germ agglutinin (WGA) for 12 hr. Insect larval midguts were dissected out in 214 mM NaCl solution, and then transferred to RNAlater® (Ambion Inc., Austin, TX). After dissecting, fifty midguts were pooled in the RNAlater and immediately frozen in liquid nitrogen, then transferred to -80°C. Fifty midguts represented a single replicate for each microarray experiment. Three biological replicates were performed, with one biological replicate per oligoarray for a total of three oligoarrays.

tag: Strain

value: W1118 Age:Third instar, 108-110 hr, then feed on 1% WGA for 12 hr

value: midgut


title: 59036T

status: Public on Sep 30 2008

city: Providence

first: Michele

last: Avissar

state: RI

address: 70 Ship Street

department: Pathology

institute: Brown University

hyb_protocol: Labelled miRNA were hybridized for 16 hr at 42C on miRVANA Bioarrays. Following hybridization, bioarrays were washed 3x and dried.

scan_protocol: Bioarrays were scanned using the GenePix 4200AL scanner.

data_processing: The fluorescent signal associated with the probes and local background was extracted using GenePix Pro and background adjusted fluorescent values were normalized for each microRNA using a variation stabilization transformation method described by Huber et al

source_name: Normal head and neck epithelium

label_protocol: The 3’ ends of the RNA molecules were tailed and labeled using the mirVana™ miRNA Labeling Kit (Ambion) according to the manufacturer’s instructions. Amine-modified nucleotides were incorporated during the poly (A) polymerase mediated tailing reaction, and Cy5 succinimide esters (Amersham Biosciences (GE Healthcare)) were conjugated to the amine moieties on the microRNAs

extract_protocol: Total RNA extraction using mirVANA RNA Isolation Kit (Ambion, Inc., Austin, TX) according to the manufacturer’s protocol for total RNA isolation. RNA was quantified using the ND-1000 spectrophotometer (Nanodrop, Wilmington, DE), aliquoted, and stored at –80°C until needed.

tag: normal