title: A4gnt null 10W

status: Public on Sep 30 2011

type: RNA

city: Matsumoto

first: Jun

last: Nakayama

address: Asahi 3-1-1

department: Graduate School of Medicine

country: Japan

institute: Shinshu University

hyb_protocol: 1.65 µg of Cy3-labeled cRNA were heat fragmented and applied to Agilent Whole Murine Genome Oligo ver. 2 (4 x 44K) arrays using a Gene Expression Hybridization kit (Agilent Technologies). Hybridization was carried out at 65ºC for 17 hours, and washing was performed using the Gene Expression Wash Pack (Agilent Technologies).

scan_protocol: Slides were scanned with an Agilent Technologies Microarray Scanner, and the images were processed by Feature Extraction software (Agilent Technologies) with background correction to prepare the raw date output files.

data_processing: Normalization was carried out using a percentile shift algorithm with parameter 75, and then data filtering was performed, using GeneSpring GX 11.0 software (Agilent Technologies).

molecule: total RNA

organism: Mus musculus

source_name: gastric mucosa, A4gnt null, 10 weeks

label_protocol: Cy3-labeled cRNA was synthesized using the Quick Amp Labeling kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from the gastric mucosa stripped from the muscular layer of the glandular stomach using the RNeasy kit (Qiagen, Hilden, Germany).

tag: strain

tag: genotype

value: A4gnt null

tag: age

value: 10 weeks

tag: tissue

value: gastric mucosa


title: A4gnt null 50W

source_name: gastric mucosa, A4gnt null, 50 weeks

value: 50 weeks


title: 2008 veraison grapes, EL35, biological replicate 2

city: Lisboa

first: Ana

middle: Margarida

last: Fortes

address: Campus da FCUL

department: Plant Biology

country: Portugal

description: Gene expression data from skin and pulp of veraison grapes

hyb_protocol: Each sample was added to a hybridization solution containing 100mM 2-(N-morpholino) ethanesulfonic acid, 1 M NaCl, and 20mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC .

scan_protocol: Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix) and scanned at 1.56 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix).

data_processing: Robust Muti-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization. Next, differential expression analysis was performed with the Bayes t-statistics from the linear models for Microarray data (limma), included in the affylmGUI package. P-values were corrected for multiple-testing using the Benjamini-Hochberg’s method

label: biotin

organism: Vitis vinifera

source_name: veraison grapes

label_protocol: cDNA was synthesized from 4 µg of total RNA using One-cycle target labeling and control reagents (Affymetrix, Santa Clara, CA) to produce biotin labeled cRNA which was then fragmented at 94ºC for 35 min into 35-200 bases in length

growth_protocol: Grapevine plants were growing at Plansel´s vines located in Montemor-o-Novo (Southern Portugal).

extract_protocol: Total RNA was isolated essentially as described by Rerie et al. (1991, Mol Gen Genet) using phenol/ chloroform with modifications

treatment_protocol: Grapes corresponding to the developmental stages of EL 32, 34, 35, 36, and 38 (E-L refers to the modified Eichhorn and Lorenz developmental scale) were immediately frozen in liquid nitrogen and transported to the lab in dry ice. Grapes were grinded in liquid nitrogen and seeds removed with a pincet

tag: developmental stage

tag: variety

value: Trincadeira

value: pulp and skin


title: 2008 ripe grapes, EL36, biological replicate 3

description: Gene expression data from skin and pulp of ripe grapes

source_name: ripe grapes


title: Wild type 50W

source_name: gastric mucosa, wild type, 50 weeks

value: wild type


title: 2008 green grapes, EL32, biological replicate 2

description: Gene expression data from skin and pulp of green grapes

source_name: green grapes


title: 2008 ripe grapes, EL36, biological replicate 1


title: 2008 ripe grapes, EL36, biological replicate 2


title: 2008 green grapes, EL32, biological replicate 3


title: A4gnt null 5W

source_name: gastric mucosa, A4gnt null, 5 weeks

value: 5 weeks


title: 2007 ripe grapes, EL36, biological replicate 2


title: 2007 veraison grapes, EL35, biological replicate 2


title: Wild type 10W

source_name: gastric mucosa, wild type, 10 weeks


title: 2007 veraison grapes, EL35, biological replicate 3


title: 2008 veraison grapes, EL35, biological replicate 3


title: 2007 medium green grapes, EL34, biological replicate 3

description: Gene expression data from skin and pulp of medium green grapes

source_name: pre-veraison grapes


title: 2007 veraison grapes, EL35, biological replicate 1


title: 2007 ripe grapes, EL36, biological replicate 1


title: 2007 medium green grapes, EL34, biological replicate 1


title: 2008 green grapes, EL32, biological replicate 1


title: 2007 green grapes, EL32, biological replicate 1


title: 2008 veraison grapes, EL35, biological replicate 1


title: 2007 ripe grapes, EL36, biological replicate 3


title: Wild type 5W

source_name: gastric mucosa, wild type, 5 weeks


title: 2007 green grapes, EL32, biological replicate 2


title: 2007 green grapes, EL32, biological replicate 3


title: 2007 medium green grapes, EL34, biological replicate 2


title: Sec01 vs. Sec27 hybridization

city: Cambridge

first: Timothy

last: Sackton

state: MA

address: 16 Divinity Ave

department: Organismic and Evolutionary Biology

country: USA

institute: Harvard University

hyb_protocol: Genisphere 3DNA system

scan_protocol: Axon Scanner and GenePix software

data_processing:
All arrays were background corrected using the 'normexp' method and normalized using 'loess' and 'quantile'. Bioconductor/limma software used. Data is presented as the log2 normalized ratio 635/532; probes not used in analysis have blank values.
FLAG field is 1 for usable, high quality spots, and 0 for spots that were disregarded in the manuscript

organism: Drosophila simulans

label_protocol: Genisphere 3DNA system

extract_protocol: Standard total RNA preps with Trizol

tag: line

tag: Sex

value: male

value: 3 – 5 day old adult


title: Ya23 vs. Ya24 hybridization


title: Sec27 vs. Sec01 hybridization


title: Ya24 vs. Ya26 hybridization


title: Sec03 vs. Ya23 hybridization


title: Sec01 vs. Ya19 hybridization


title: Sec03 vs. Ya19 hybridization


title: Ya26 vs. Ya19 hybridization


title: Ya19 vs. Ya23 hybridization


title: Ya24 vs. Ya23 hybridization


title: Ya26 vs. Ya24 hybridization


title: Sec03 vs. Sec01 hybridization


title: Sec08 vs. Sec03 hybridization


title: Ya23 vs. Sec03 hybridization


title: Ya24 vs. Sec08 hybridization


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_48hour timepoint_replicate1

first: Julien

last: Bauer

state: Cambridgeshire

address: Tennis court road

country: United Kingdom

institute: Cambridge University

description:
ME180-T48-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_48hour timepoint_replicate1
Replicate 1

hyb_protocol: Standard Illumina scanning protocol

scan_protocol: biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays

data_processing: Raw data were filtered to remove any non detected probe (detection pvalue above 0.01 for all samples) and then normalised using quantile normalisation. The software used is the lumi package from bioconductor (R).

organism: Homo sapiens

source_name: metastatic site: omentum

label_protocol: Standard Illumina hybridisation protocol

growth_protocol: Cell lines cultured under standard tissue culture conditions - incubated at 37C and in 5% CO2,  described in Ng et al 2007, PMID: 17516585

extract_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep kit for Illumina arrays

treatment_protocol: Cells treated with recombinant OSM (R&D systems) @10 ng/ml added directly to the tissue culture media where appropriate for duration indicated by the time point

tag: cell line

tag: cell line source

value: American Type Culture Collection (ATCC) number HTB_33

tag: anatomical site

value: Cervix

tag: gender

value: Female

tag: osmr expression status

value: Under

tag: time


title: Sec27 vs. Sec08 hybridization


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_48hour timepoint_replicate2

description:
ME180-T48-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_48hour timepoint_replicate2
Replicate 2


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_24hour timepoint_replicate1

description:
ME180-T24-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_24hour timepoint_replicate1
Replicate 1


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_24hour timepoint_replicate3

description:
ME180-T24-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_24hour timepoint_replicate3
Replicate 3


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_24hour timepoint_replicate2

description:
ME180-T24-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_24hour timepoint_replicate2
Replicate 2


title: Sec01 vs. Sec03 hybridization


title: Sec27 vs. Ya24 hybridization


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_12hour timepoint_replicate3

description:
ME180-T12-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_12hour timepoint_replicate3
Replicate 3


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_12hour timepoint_replicate2

description:
ME180-T12-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_12hour timepoint_replicate2
Replicate 2


title: Sec08 vs. Ya23 hybridization


title: Sec27 vs. Ya26 hybridization


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_12hour timepoint_replicate1

description:
ME180-T12-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_12hour timepoint_replicate1
Replicate 1


title: Sec03 vs. Sec08 hybridization


title: Sec01 vs. Ya26 hybridization


title: Ya23 vs. Sec08 hybridization


title: Ya19 vs. Sec03 hybridization


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_4hour timepoint_replicate3

description:
ME180-T4-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_4hour timepoint_replicate3
Replicate 3


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_4hour timepoint_replicate2

description:
ME180-T4-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_4hour timepoint_replicate2
Replicate 2


title: Ya19 vs. Ya26 hybridization


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_4hour timepoint_replicate1

description:
ME180-T4-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_4hour timepoint_replicate1
Replicate 1


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_1hour timepoint_replicate1

description:
ME180-T1-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_1hour timepoint_replicate1
Replicate 1


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_1hour timepoint_replicate2

description:
ME180-T1-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_1hour timepoint_replicate2
Replicate 2


title: Ya26 vs. Sec27 hybridization


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_0hour timepoint_replicate3

description:
ME180-T0-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_0hour timepoint_replicate3
Replicate 3


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_1hour timepoint_replicate3

description:
ME180-T1-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_1hour timepoint_replicate3
Replicate 3


title: Sec08 vs. Sec27 hybridization


title: Ya26 vs. Sec01 hybridization


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_0hour timepoint_replicate2

description:
ME180-T0-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_0hour timepoint_replicate2
Replicate 2


title: Ya23 vs. Ya19 hybridization


title: 2010Dkai2nd DD12h

city: Tokyo

first: Hideo

last: Iwasaki

address: TWIns 1F 2-2 Wakamatsu-cho, Shinjuku

department: Electrical Engineering & Bioscience

institute: Waseda University

description: Gene expression data from Synechococcus elongatus PCC 7942

hyb_protocol: Following fragmentation, 1.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Synechococcus Custom Arrays (Syel6301a520114F). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: GeneChip Operating Software (GCOS) ver 1.2.1.001 was used to detect each fluorescent spot (30 match+mismatch primers per each gene) and determine the raw signal using Affymetrix default settings.  These values were divided by corresponding genomic DNA signals (genomic DNA sample) which had been deposited in GSE14225 (Sample GSM356504). GCOS values before dividing by corresponding genomic DNA signal is provided on the as a supplementary file on the Series record.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: DkaiABC at DD 12, rep2 (2010 June)

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix prokaryotic protocol from 10 ug total RNA (Expression Analysis Technical Manual)

growth_protocol: Synechococcus cells were grown in continuous culture systems at 30C in DD after two 12h:12h dark:light cycles

extract_protocol: Total RNAs were extracted with a modified hot-phenol extraction method

treatment_protocol: Cells were collected at indicated times and stored at -80C until use

tag: genotype/variation

value: kaiABC-null strain containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)


title: 2010Dkai2nd DD8h

source_name: DkaiABC at DD 8, rep2 (2010 June)


title: Ya19 vs. Sec01 hybridization


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_48 hour timepoint_replicate1

description:
MS751-T48-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_48 hour timepoint_replicate1
Replicate 1

source_name: metastatic site: lymph node

value: American Type Culture Collection (ATCC) number HTB_34


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_48 hour timepoint_replicate3

description:
MS751-T48-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_48 hour timepoint_replicate3
Replicate 3


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_48 hour timepoint_replicate2

description:
MS751-T48-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_48 hour timepoint_replicate2
Replicate 2


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_0hour timepoint_replicate1

description:
ME180-T0-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_0hour timepoint_replicate1
Replicate 1


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_24hour timepoint_replicate2

description:
MS751-T24-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_24hour timepoint_replicate2
Replicate 2


title: Ya24 vs. Sec27 hybridization


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_24hour timepoint_replicate3

description:
MS751-T24-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_24hour timepoint_replicate3
Replicate 3


title: 2010Dkai2nd DD4h

source_name: DkaiABC at DD 4, rep2 (2010 June)


title: Sec08 vs. Ya24 hybridization


title: cervical squamous cell carcinoma cell line_ATCC number HTB_33_48hour timepoint_replicate3

description:
ME180-T48-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_33_48hour timepoint_replicate3
Replicate 3


title: 2010Dkai2nd DD2h

source_name: DkaiABC at DD 2, rep2 (2010 June)


title: 2010Dkai2nd DD30min

source_name: DkaiABC at DD 0.5, rep2 (2010 June)


title: 2010Dkai2nd DD1h

source_name: DkaiABC at DD 1, rep2 (2010 June)


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_24hour timepoint_replicate1

description:
MS751-T24-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_24hour timepoint_replicate1
Replicate 1


title: 2010Dkai2nd DD0h

source_name: DkaiABC at DD 0, rep2 (2010 June)


title: 2010Dkai1st DD12h

source_name: DkaiABC at DD 12, rep1 (2010 June)


title: 2010Dkai1st DD8h

source_name: DkaiABC at DD 8, rep1 (2010 June)


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_12hour timepoint_replicate2

description:
MS751-T12-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_12hour timepoint_replicate2
Replicate 2


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_12hour timepoint_replicate3

description:
MS751-T12-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_12hour timepoint_replicate3
Replicate 3


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_1hour timepoint_replicate3

description:
MS751-T1-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_1hour timepoint_replicate3
Replicate 3


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_4hour timepoint_replicate3

description:
MS751-T4-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_4hour timepoint_replicate3
Replicate 3


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_1hour timepoint_replicate2

description:
MS751-T1-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_1hour timepoint_replicate2
Replicate 2


title: 2010Dkai1st DD4h

source_name: DkaiABC at DD 4, rep1 (2010 June)


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_4hour timepoint_replicate2

description:
MS751-T4-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_4hour timepoint_replicate2
Replicate 2


title: 2010Dkai1st DD30min

source_name: DkaiABC at DD 0.5, rep1 (2010 June)


title: 2010Dkai1st DD2h

source_name: DkaiABC at DD 2, rep1 (2010 June)


title: 2010Dkai1st DD0h

source_name: DkaiABC at DD 0, rep1 (2010 June)


title: 2010Dkai1st DD1h

source_name: DkaiABC at DD 1, rep1 (2010 June)


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_12hour timepoint_replicate1

description:
MS751-T12-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_12hour timepoint_replicate1
Replicate 1


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_1hour timepoint_replicate1

description:
MS751-T1-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_1hour timepoint_replicate1
Replicate 1


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_48hour timepoint_replicate3

description:
SW756-T48-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_48hour timepoint_replicate3
Replicate 3

source_name: primary site

value: American Type Culture Collection (ATCC) number CRL_10302

value: Over


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_0hour timepoint_replicate3

description:
MS751-T0-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_0hour timepoint_replicate3
Replicate 3


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_0hour timepoint_replicate2

description:
MS751-T0-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_0hour timepoint_replicate2
Replicate 2


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_4hour timepoint_replicate1

description:
MS751-T4-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_4hour timepoint_replicate1
Replicate 1


title: 2010WT2nd DD4h

description: Gene expression data from Synechococcus elongatus PCC 7942

source_name: WT at DD 4, rep2 (2010 June)

value: wild type containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)


title: 2010WT2nd DD8h

source_name: WT at DD 8, rep2 (2010 June)


title: 2010WT2nd DD12h

source_name: WT at DD 12, rep2 (2010 June)


title: 2010WT2nd DD2h

source_name: WT at DD 2, rep2 (2010 June)


title: 2010WT2nd DD1h

source_name: WT at DD 1, rep2 (2010 June)


title: 2010WT1st DD12h

source_name: WT at DD 12, rep1 (2010 June)


title: 2010WT2nd DD30min

source_name: WT at DD 0.5, rep2 (2010 June)


title: 2010WT1st DD8h

source_name: WT at DD 8, rep1 (2010 June)


title: 2010WT1st DD4h

source_name: WT at DD 4, rep1 (2010 June)


title: 2010WT2nd DD0h

source_name: WT at DD 0, rep2 (2010 June)


title: 2010WT1st DD30min

source_name: WT at DD 0.5, rep1 (2010 June)


title: 2010WT1st DD1h

source_name: WT at DD 1, rep1 (2010 June)


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_48hour timepoint_replicate1

description:
SW756-T48-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_48hour timepoint_replicate1
Replicate 1


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_24hour timepoint_replicate1

description:
SW756-T24-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_24hour timepoint_replicate1
Replicate 1


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_12hour timepoint_replicate3

description:
SW756-T12-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_12hour timepoint_replicate3
Replicate 3


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_24hour timepoint_replicate2

description:
SW756-T24-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_24hour timepoint_replicate2
Replicate 2


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_4hour timepoint_replicate3

description:
SW756-T4-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_4hour timepoint_replicate3
Replicate 3


title: 2010WT1st DD0h

source_name: WT at DD 0, rep1 (2010 June)


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_12hour timepoint_replicate2

description:
SW756-T12-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_12hour timepoint_replicate2
Replicate 2


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_12hour timepoint_replicate1

description:
SW756-T12-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_12hour timepoint_replicate1
Replicate 1


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_1hour timepoint_replicate2

description:
SW756-T1-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_1hour timepoint_replicate2
Replicate 2


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_4hour timepoint_replicate1

description:
SW756-T4-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_4hour timepoint_replicate1
Replicate 1


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_1hour timepoint_replicate3

description:
SW756-T1-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_1hour timepoint_replicate3
Replicate 3


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_4hour timepoint_replicate2

description:
SW756-T4-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_4hour timepoint_replicate2
Replicate 2


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_48hour timepoint_replicate2

description:
SW756-T48-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_48hour timepoint_replicate2
Replicate 2


title: Mock-inocualted SAMPLE replicate 4

city: Beijing

first: Zaifeng

last: Fan

address: Yuanmingyuan west road No.2

country: China

institute: China Agricultural University

description: Gene Expression after inoculation

hyb_protocol: Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized tfor 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: After hybridization the microarray slides were washed according to the standard Agilent protocol and scanned on a microarry scanned at 550nm using an Agilent microarry scanner (G2505B).

data_processing: The information produced by scanner was loaded into the image analysis program Feature Extraction version 9.5 to establish standard data for statistical analysis

organism: Zea mays

source_name: Mock-inoculated maize

label_protocol: A 2µg aliquot of total RNA from sample inoculated and mock-inoculated respectively was used to synthesis fluorophore-labelled cRNA using cyanine 3-CTP (Cy3C). Samples were purified using the Qiagen RNeasy kit. The quality of cyanine-labelled cRNA samples, including yield, concentration, amplification efficiency and abundance of cyanine- fluorophore, was determined by a ND-1000 spectrophotometer

extract_protocol: The aerial parts of whole plants were harvested.Total RNA was extracted from RBSDV infected and mock-inoculated plants. To reduce the experimental variation, 4 sets of seedlings, each set including 10 virus-infected seedlings and 10 mock-inoculated ones, were harvested. Each set of 10 seedlings were homogenized with mortar and pestle in liquid nitrogen as one sample, and RNA is extracted by using Trizol agent

treatment_protocol: The seedlings of 15-day-old (3 leaves) were exposed to plant hopper which carried RBSDV (5 insects each seedling) for 3 days in specific inoculation chamber. The inoculated plants were taken out after removing insect completely, and grew in greenhouse at 25oC under natural sunlight until white streak emerged.

value: Zheng 58

tag: disease state

value: mock-inoculated


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_1hour timepoint_replicate1

description:
SW756-T1-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_1hour timepoint_replicate1
Replicate 1


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_0hour timepoint_replicate1

description:
SW756-T0-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_0hour timepoint_replicate1
Replicate 1


title: Mock-inoculated SAMPLE replicate 3

description: Gene Expression after inoculation


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_0hour timepoint_replicate2

description:
SW756-T0-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_0hour timepoint_replicate2
Replicate 2


title: RBSDV-inoculated Sample replicate 4

description: Gene Expression after inoculation

source_name: RBSDV-inoculated maize

value: RBSDV-inoculated


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _48hour timepoint_replicate1

description:
CASKI-T48-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _48hour timepoint_replicate1
Replicate 1

source_name: metastatic site: small bowel mesentary

value: American Type Culture Collection (ATCC) number CRL_1550


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _48hour timepoint_replicate3

description:
CASKI-T48-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _48hour timepoint_replicate3
Replicate 3


title: RBSDV-inoculated Sample replicate 3

description: Gene Expression after inoculation


title: Mock-inoculated SAMPLE replicate 1

description: Gene Expression after inoculation


title: RBSDV-inoculated Sample replicate 2

description: Gene Expression after inoculation


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _48hour timepoint_replicate2

description:
CASKI-T48-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _48hour timepoint_replicate2
Replicate 2


title: cervical squamous cell carcinoma cell line_ATCC number HTB_34_0hour timepoint_replicate1

description:
MS751-T0-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number HTB_34_0hour timepoint_replicate1
Replicate 1

source_name: metastatic site: lymph node


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _12hour timepoint_replicate3

description:
CASKI-T12-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _12hour timepoint_replicate3
Replicate 3


title: RBSDV-inoculated Sample replicate 1

description: Gene Expression after inoculation


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _24hour timepoint_replicate3

description:
CASKI-T24-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _24hour timepoint_replicate3
Replicate 3


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _12hour timepoint_replicate2

description:
CASKI-T12-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _12hour timepoint_replicate2
Replicate 2


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _24hour timepoint_replicate2

description:
CASKI-T24-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _24hour timepoint_replicate2
Replicate 2


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _4hour timepoint_replicate2

description:
CASKI-T4-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _4hour timepoint_replicate2
Replicate 2


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _12hour timepoint_replicate1

description:
CASKI-T12-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _12hour timepoint_replicate1
Replicate 1


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _4hour timepoint_replicate3

description:
CASKI-T4-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _4hour timepoint_replicate3
Replicate 3


title: Dnmt3a-KO HSC-3

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

institute: Texas A&M University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MOE 430 2.0 chips. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450

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

data_processing: The raw image and intensity files were generated using GCOS 1.0 software. Normalization and model-based expression measurements were performed with GC-RMA.

label_protocol: Biotinylated cRNA was prepared with the MessageAMP aRNA kit (Ambion) with 2 ronds of in vitro transcription according to the manufacturers protocols

growth_protocol: Mice were house in a specific-pathogen free facility and experiments performed in accordance with Baylor College of Medicine institutional guidelines

extract_protocol: Total RNA was extracted with the RNAqueous kit (Ambion) according to the manufacturers protocols

treatment_protocol: HSCs were purified on a MoFlo cell sorter by phenotype of CD45.2+ Side Population+ / Lineage- / Sca-1+ / c-Kit+ / CD150+.  Samples were reflowed to assess purity and in all cases it was >98%

value: Hematopoietic stem cel

value: mixed

tag: genetic background


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _4hour timepoint_replicate1

description:
CASKI-T4-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _4hour timepoint_replicate1
Replicate 1


title: Control HSC-3

value: wild type


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _24hour timepoint_replicate1

description:
CASKI-T24-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _24hour timepoint_replicate1
Replicate 1


title: Control HSC-2


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _1hour timepoint_replicate3

description:
CASKI-T1-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _1hour timepoint_replicate3
Replicate 3


title: Dnmt3a-KO HSC-2


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _1hour timepoint_replicate2

description:
CASKI-T1-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _1hour timepoint_replicate2
Replicate 2


title: Dnmt3a-KO HSC-1


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _1hour timepoint_replicate1

description:
CASKI-T1-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _1hour timepoint_replicate1
Replicate 1


title: Control HSC-1


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _0hour timepoint_replicate2

description:
CASKI-T0-B
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _0hour timepoint_replicate2
Replicate 2


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _0hour timepoint_replicate3

description:
CASKI-T0-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _0hour timepoint_replicate3
Replicate 3


title: deep_duroc_fibroblast,20 wk (paired with sample 2)

city: Seattle

first: Surawej

last: Numhom

state: WA

department: Surgery

institute: University of Washington

hyb_protocol: Labeled targets were hybridized to the Affymetrix Porcine GeneChip for 16 to 18 hours at 45 oC and 60 rounds per minute (Hybridization Oven 640, Affymetrix, Santa Clara, CA, USA). Spike controls were added to complementary RNA before hybridization. Washing and staining with streptavidine-phycoerythrine was performed in an automatic fluidics station (GeneChip Fluidics Station 400, Affymetrix, Santa Clara, CA, USA).

scan_protocol: Scanning was performed with GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA, USA). The quality of the hybridization and overall chip performance was evaluated by visual inspection of the raw scanned data and the quality control measures in the Affymetrix *.RPT report file.

data_processing: GCOS 1.0 MAS5 data supplied in CHP files

organism: Sus scrofa

source_name: deep_duroc_fibroblast,20 wk

label_protocol: Transcription and labeling of complementary RNA was performed with biotinylated UTP and CTP (Affymetrix IVT labeling Kit). The target complementary RNA was fragmented, washed, and stained according to the manufacturer instructions. The quality and quantity of labeled complementary RNA was evaluated spectrophotometrically and with the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

growth_protocol: Tissue and cells were cultured in DMEM/F12 (Invitrogen, Carlsbad, CA,) with the addition of 10% fetal bovine serum (FBS) (Invitrogen), L-glutamine (2mM) (Invitrogen), antibiotic (100U/mL penicillin; 100ug/mL streptomycin) antimycotic (0.05 ug/mL amphotericin B) (Invitrogen) at 37 oC in an atmosphere of 5% CO2.

extract_protocol: Total RNA was isolated from confluent cultures of dermal cone fibroblasts using TRIzol reagent (Invitrogen, Carlsbad, CA). followed by DNAse digestion on a  RNeasy mini column (Qiagen, Valencia, CA).  RNA quality was assessed using the Agilent RNA 6000 Pico chip and Eukaryote Total RNA Pico with the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA). All RNA preparations had RNA Integrity numbers greater than 8.0 which indicated high quality RNA

tag: depth

value: deep

tag: breed

value: Duroc

tag: cell type

value: fibroblast


title: cervical squamous cell carcinoma cell line_ATCC number CRL_1550 _0hour timepoint_replicate1

description:
CASKI-T0-A
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_1550 _0hour timepoint_replicate1
Replicate 1

value: Cervix

value: Female


title: shallow_duroc_fibroblast,20 wk (paired with sample 4)

source_name: shallow_duroc_fibroblast,20 wk

value: shallow


title: Retina-radiation-rep2

city: Chengdu

first: Chen

last: Jing

address: West China Hospital

department: Department of Neurosurgery

institute: West China Hospital, Sichuan University

description: Gene expression data from radiation retina

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Macaca mulatta

source_name: Retina ipsilateral optic nerve injury

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US)).

extract_protocol: Total RNA was extracted by using Trizol reagent (Invitrogen) according to the manufacturer's instructions

treatment_protocol: Each sample was immediately labled then flashfrozen in liquid nitrogen and stored at -80°C prior to further analysis

tag: tissue

value: Retina

tag: treatment

value: irradiated injury of intraorbital nerve


title: shallow_duroc_fibroblast,20 wk (paired with sample 3)

hyb_protocol: Labeled targets were hybridized to the Affymetrix Porcine GeneChip for 16 to 18 hours at 45 C and 60 rounds per minute (Hybridization Oven 640, Affymetrix, Santa Clara, CA, USA). Spike controls were added to complementary RNA before hybridization. Washing and staining with streptavidine-phycoerythrine was performed in an automatic fluidics station (GeneChip Fluidics Station 400, Affymetrix, Santa Clara, CA, USA).


title: Retina-control-rep3

description: Gene expression data from control retina

source_name: Retina contralateral optic nerve injury

value: control


title: Retina-radiation-rep1


title: deep_duroc_fibroblast,20 wk (paired with sample 1)


title: Retina-radiation-rep3


title: Retina-control-rep1


title: Retina-control-rep2


title: eGFP+ cells, biological rep2

city: Oeiras

middle: Teresa

last: Tavares

address: Rua da Quinta Grande, 6

institute: IGC

description: gene expression data of Hb-eGFP-positive cells

hyb_protocol: 15 µg of fragmented cRNA was used in a 300-µl hybridization containing added hybridization controls. 200 µl of mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0001) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Scanned arrays were analyzed first with GCOS 1.4 software to obtain Absent/Present calls and for subsequent analysis with dChip 2008. The arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method (Li and Wong, 2001). Normalized CEL intensities of the six arrays were used to obtain model-based gene expression indices based on a PM (Perfect Match)-only model.

organism: Gallus gallus

source_name: Hb-eGFP-positive cells of electroporated chick embryos at stage HH5-6

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Chicken Genome Arrays, according to the manufacturer’s Two-Cycle Target Labeling Assay. Briefly, 40 ng of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix) was used in a reverse transcription reaction (Two-Cycle DNA synthesis kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in an in vitro transcription (IVT) reaction to generate cRNA (MEGAscript T7 kit; Ambion, Austin, TX). 600 ng of the cRNA obtained was used for a second round of cDNA and cRNA synthesis, resulting in biotinylated cRNA (GeneChip Expression 3’-Amplification Reagents for IVT-Labeling; Affymetrix). Size distribution of the cRNA and fragmented cRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

growth_protocol: Chick embryos were incubated at 37.5ºC for approximately 12 hours

extract_protocol: Embryos were harvested at stage HH5-6 and dissociated into single cell suspensions. The eGFP-positive and eGFP-negative/RFP-positive cell populations were sorted by FACS using a Moflo high-speed cell sorter (Beckman Coulter). Cell populations were collected simultaneously into two different tubes, containing RNAlater (Ambion), and total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Embryos were microinjected and electroporated at stage HH3 with the vector Hb-eGFP, that contains a -255 to -204 bp fragment from the chick Cerberus regulatory region, and the human beta-globin minimal promoter (p1229-eGFP enhancerless vector).

value: Hb-eGFP-positive cells

tag: age

value: embryo

tag: developmental stage


title: RFP+ cells, biological rep2

description: gene expression data of control RFP-positive cells

source_name: Hb-eGFP-negative/RFP-positive cells of electroporated chick embryos at stage HH5-6

value: RFP-positive cells


title: eGFP+ cells, biological rep3


title: RFP+ cells, biological rep3


title: eGFP+ cells, biological rep1


title: 87-NI_BM

city: Genova

first: PAOLA

last: SCARUFFI

state: GE

address: LARGO R. BENZI, 10

country: Italy

institute: "San Martino" Hospital

description: Gene expression

hyb_protocol: Labelled cRNAs were hybridized to whole-genome oligonucleotide microarrays containing 41,000 human transcripts (Agilent Technologies) following the manufacture's instructions (One-color microarray-based gene expression analysis protocol, v5.5). Briefly, 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome 4x44K Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), with the Stabilization solution (Agilent) for 1 minute at room temperature, then dried immediately by rinsing slides into Drying solution (Agilent) for 30 seconds.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%). Microarray performance was assessed by QC metric tool.

data_processing:
The scanned TIFF images were analyzed with Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (Agilent protocol GE1-v5_95_Feb07) to obtain background subtracted and spatially detrended Processed Signal intensities. The output of Feature Extraction was analyzed with the Agi4x44PreProcess package. After within-array median-summarization of probe intensities within replicates, probe intensities were log base 2 transformed and normalized across arrays with the quantile normalization method implemented in Bioconductor.
Bioconductor normalized data are provided as supplementary files on the Series record.

source_name: bone marrow

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA as detailed in the One-color microarray-based gene expression analysis protocol, v5.5 (www.agilent.com). Dye incorporation and cRNA yield were checked with Nanodrop (Thermo Scientific).

extract_protocol: Total RNA was isolated by using the RNAeasy Mini Kit (Qiagen) according to manufacturer’s protocol. Total RNA was quantified and quality control assessed by Nano LabChip® assay on the 2100 Bioanalyzer (Agilent Technologies). Only samples with a RNA Integrity Number >7 were included in the study.

treatment_protocol: To isolate resident BM cells, the BM samples from patients with localized and metastatic NB were subjected to immunomagnetic separation,after lysis of erythrocytes, cells were incubated for 30 minutes at 4°C with the anti-GD2 mAb in the presence of human Fc blocking reagent. After washing, the cell pellet was incubated for 15 minutes at 4°C with goat anti-mouse IgG2a microbeads (Miltenyi). Cells were then washed twice, suspended in 500 uL of sterile ice-cold PBS and loaded onto a MS column (Miltenyi).The GD2 negative fractions were then subjected to RNA extraction.

value: resident bone marrow cells

tag: patient disease status

value: localized Neuroblastoma


title: 84-NI_BM

description: Gene expression


title: Mock-inoculated SAMPLE replicate 2

description: Gene Expression after inoculation

tag: genotype

value: Zheng 58

value: mock-inoculated


title: 98-NI_BM

description: Gene expression


title: 89-NI_BM

description: Gene expression


title: 91-NI_BM

description: Gene expression


title: 88-NI_BM

description: Gene expression


title: 93-NI_BM

description: Gene expression


title: 83-NI_BM

description: Gene expression


title: RFP+ cells, biological rep1


title: 82-NI_BM

description: Gene expression


title: 45-NI_BM

description: Gene expression


title: 76-NI_BM

description: Gene expression


title: 73-NI_BM

description: Gene expression


title: 43-NI_BM

description: Gene expression


title: 86-NI_BM

description: Gene expression


title: 72-NI_BM

description: Gene expression


title: 71-NI_BM

description: Gene expression


title: 74-NI_BM

description: Gene expression


title: 81-NI_BM

description: Gene expression


title: 2010WT1st DD2h

description: Gene expression data from Synechococcus elongatus PCC 7942

source_name: WT at DD 2, rep1 (2010 June)

value: wild type containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)


title: 27-NI_BM

description: Gene expression


title: 55-NI_BM

description: Gene expression


title: 100-I_BM

description: Gene expression

value: metastatic Neuroblastoma


title: 94-I_BM

description: Gene expression


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_0hour timepoint_replicate3

description:
SW756-T0-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_0hour timepoint_replicate3
Replicate 3

source_name: primary site

tag: cell line

tag: cell line source

value: American Type Culture Collection (ATCC) number CRL_10302

value: Over


title: cervical squamous cell carcinoma cell line_ATCC number CRL_10302_24hour timepoint_replicate3

description:
SW756-T24-C
cervical squamous cell carcinoma cell line obtained from the American Type Culture Conditions (ATCC) ATCC number CRL_10302_24hour timepoint_replicate3
Replicate 3

tag: anatomical site

value: Cervix

tag: gender


title: 36-NI_BM

description: Gene expression


title: 64-I_BM

description: Gene expression


title: 60-I_BM

description: Gene expression


title: 96-I_BM

description: Gene expression


title: 78-I_BM

description: Gene expression


title: 26-NI_BM

description: Gene expression


title: 62-I_BM

description: Gene expression


title: 28-NI_BM

description: Gene expression


title: 58-I_BM

description: Gene expression


title: 53-I_BM

description: Gene expression


title: RKO-SPARCL1 on plastic

city: Hangzhou

first: Hang

last: Zhang

address: 88 Jiefang Road

institute: Zhejiang University Cancer Institute

description:
RKO-SPARCL1 cells cultured on plastic dish
CB2009126-RL.CEL

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C 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: Primary data was recorded with Command Console Software 3.1. The qualified data was normalized by Gene Spring Software 11.0 using the MAS 5.0. algorithm.

source_name: RKO-SPARCL1 on plastic

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

growth_protocol: Colon cancer cell line RKO was obtained from American Type Culture Collection (ATCC).The cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (Gibco), penicillin (100 U/ml) and streptomycin (100 μg/ml) at 37°C in 5% CO2.

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

treatment_protocol: We transfect pLXSN-SPARCL1 plasmid and vector control pLXSN into RKO cells.These two cells were cultured on plastic dish and Matrigel coated plastic dish. After 72 hours cells were trypsinized and collected.

value: colon

value: Colon cancer cell line RKO


title: PFX#9

city: KOBE

first: Naoki

last: Nishishita

institute: Founbation for Biomedical Research and Innovation

description: Gene expression data from cells

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45oC, 60 rpm on Gene Chip Human Genome U133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: iPSCs derived from CD34+ cells

label_protocol: Biotinylated cRNA were prepared using GeneChip 3’ IVT Express Kit according to manufacturer’s instructions from 250 ng total RNA.

extract_protocol: Total RNA was extracted with the RNeasy Mini kit, according to manufacturer’s instructions.

treatment_protocol: PFX# iPS cells with a cell scraper and break up the clonies, add 10mL ReproFF medium. Centrifuge at 110G for 5min and discard the supernatant and then wash the cell clump twice with PBS. After centrifuge, remove PBS completely.

value: induced pluripotent stem cells (iPSCs)


title: PFX#2

description: Gene expression data from cells


title: 80-H_BM

description: Gene expression

treatment_protocol: samples were directly subjected to RNA extraction

value: bone marrow

value: healthy young donor


title: 101-H_BM

description: Gene expression


title: PFX#7

description: Gene expression data from cells


title: 67-H_BM

description: Gene expression


title: 68-H_BM

description: Gene expression


title: 69-H_BM

description: Gene expression


title: RKO-pLXSN on plastic

description:
RKO-pLXSN cells cultured on plastic dish
CB2009126-RP.CEL

source_name: RKO-pLXSN on plastic


title: 51-H_BM

description: Gene expression


title: RKO-pLXSN on Matrigel

description:
RKO-pLXSN cells cultured on Matrigel coated plastic dish
CB2009126-RPM.CEL

source_name: RKO-pLXSN on Matrigel


title: 79-H_BM

description: Gene expression


title: Miltefosine sensitive Leishmania donovani (control 1)

city: New Delhi

first: Poonam

last: Salotra

state: Delhi

address: Safdarjung Hospital Campus

department: National Institute of Pathology

country: India

institute: Indian Council of Medical Research

description: Corresponding Wild type miltefosine sensitive parasite (control sample1)

hyb_protocol: The array was hybridized using Gene expression hybridization kit (Agilent Technologies).Hybridization was carried out at 65°C for 17 hours(3 biological replicates for each hybridization)

scan_protocol: Hybridized arrays were washed and scanned in Axon GenePix 4000B scanner.Tiff images extracted using the Feature Extraction softaware (FE) 9.5.3(Agilent technologies).

data_processing: Data analysis was performed using Gene Spring GX 11.0 microarray data and pathway analysis tool. Quantile normalization was performed on samples. PCA scores were generated.t-test (Unpaired) for two groups. Confidence Level (p-value cut-off) < 0.05, fold change analysis was performed to calculate differentially expressed genes.

organism: Leishmania donovani

source_name: leishmania donovani promastigote

label_protocol: Complementary RNA (cRNA) was generated from 1µg of total RNA using Quick-Amp Labeling kit (Agilent technologies) that directly incorporates Cy-3 labeled CTP into the cRNA.

growth_protocol: L.donovani parasite isolated from Bone marrow aspirate of Kala azar patient was allowed to grow as promastigote in vitro in Medium 199 and 10% FCS. This isolate was denoted as WT.

extract_protocol: Total parasite RNA was extracted using Trizol reagent according to manufacturer`s instructions.

treatment_protocol: The WT parasite was adapted step wise to 30 ug/ml miltefosine pressure till it attained growth equivalent to its wild type counterpart

tag: strain


title: Miltefosine sensitive Leishmania donovani (control 3)

description: Corresponding Wild type miltefosine sensitive parasite (control sample3)


title: cells stimulated with LPS treated with LPS 3

city: rio de janeiro

first: renata

middle: torres de

last: paiva

state: rio de janerio

address: cidade universitária, centro de tecno

department: Biomedical Engeneering

country: Brazil

institute: Federal University of Rio de Janeiro

description: Analysis used PBMC RNA as control samples for comparison to the experimental samples.

hyb_protocol: Labeled cDNAs were mixed in hybridization buffer, Hybit 2 with formamide (ref HH52, http://arrayit.com ), 18H , 42C. Washing in SSC1X, SDS 0,05% (twice) and SSC 0,06X (once)

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray GX confocal scanner (Packard/Perkin Elmer) and image intensity data were extracted and analysed with Quant Array software

data_processing: QuantArray software.  Background correction and lowess normalization. Log base 2 expression ratios.

source_name: PBMC stimulated with LPS treated with thalidomide

label_protocol: CyScribe First-srand cDNA labeling Kit (GE Healthcare) and labeled cDNA was purified with GFX columns (GE Healthcare)

extract_protocol: TRIZOL reagent, 1mL/10e6 cells

treatment_protocol: Human PBMC were isolated from Human donors by FICOLL /HYPAQUE gradient. 3X10e7 cells were seeded in 20 mL of RPMI medium supplemented with 10% FCS for 24 H

value: PBMC

source_name: PBMC


title: Miltefosine resistant Leishmania donovani (test 1)

description: Lab generated Miltefosine resistant parasite adapted to 30ug/ml drug pressure (Test sample1)


title: Miltefosine sensitive Leishmania donovani (control 2)

description: Corresponding Wild type miltefosine sensitive parasite (control sample2)


title: cells stimulated with LPS treated with LPS 1


title: cells treated with thalidomide 3

source_name: PBMC treated with Thalidomide

source_name: PBMC treated with thalidomide


title: cells stimulated with LPS 2

source_name: PBMC stimulated with LPS


title: cells treated with thalidomide 1


title: cells stimulated with LPS treated with LPS 2


title: Miltefosine resistant Leishmania donovani (test 3)

description: Lab generated Miltefosine resistant parasite adapted to 30ug/ml drug pressure (Test sample3)


title: cells stimulated with LPS 3


title: cells treated with thalidomide 2


title: Miltefosine resistant Leishmania donovani (test 2)

description: Lab generated Miltefosine resistant parasite adapted to 30ug/ml drug pressure (Test sample2)


title: 32-H_BM

description: Gene expression


title: cells stimulated with LPS 1


title: RKO-SPARCL1 on Matrigel

description:
RKO-SPARCL1 cells cultured on Matrigel coated plastic dish
CB2009126-RLM.CEL

source_name: RKO-SPARCL1 on Matrigel


title: l2_1 with array type poplar from Affymetrix

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description: This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl Alcohol Dehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesis pathway. Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expected phenotype (red xylem, reduced CAD activity).Biological question (15 lines max):This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl AlcoholDehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesispathway.Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expectedphenotype (red xylem, reduced CAD activity).

hyb_protocol: labelled extract quantity: 15ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Populus tremula x Populus alba

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: xylem - pHG8-CAD2 plants were amplified from in vitro stocks on the 16th of December 2009. One month later (01/18/2010), they were first acclimatized in a growth room (growing conditions : photoperiod of 16h, 24°C day temperature/ 22°C night temperature, 56% hygrometry). On the 23rd of February, the plants were then transferred to 3L compost-containing pots in the greenhouse. When they reached approximately 1-meter-height, they were staked with 2 poles. On the 23rd of April, the plant were inclined of 30°. The plants were sampled after 26 reached approximately 1-meter-height, they were staked with 2 poles. On the 23rd of April, the plant were inclined of 30°. The plants were sampled after 26 days (19th of May 2010).

extract_protocol: Pool of extract, odx_cad2_1:3ug, odx_cad2_2:3ug, odx_cad2_3:3ug, odx_cad2_4:3ug.

treatment_protocol: no treatment

value: 5 month

value: xylem

tag: knockdown

value: CAD


title: tb_1 with array type poplar from Affymetrix

growth_protocol: xylem - INRA 717-1B4 plants were amplified from in vitro stocks on the 16th of December 2009. One month later (01/18/2010), they were first acclimatized in a growth room (growing conditions : photoperiod of 16h, 24°C day temperature/ 22°C night temperature, 56% hygrometry). On the 23rd of February, the plants were then transferred to 3L compost-containing pots in the greenhouse. When they reached approximately 1-meter-height, they were staked with 2 poles. On the 23rd of April, the plant were inclined of 30°. The plants were sampled after 26 days (19th of May 2010).

extract_protocol: Pool of extract, odx_wt_6:5ug, odx_wt_5:5ug.

value: control


title: ta_2 with array type poplar from Affymetrix

extract_protocol: Pool of extract, odx_wt_2:4ug, odx_wt_4:4ug, odx_wt_3:4ug, odx_wt_5:4ug.


title: l19_2 with array type poplar from Affymetrix

growth_protocol: xylem - pHG8-CAD19 plants were amplified from in vitro stocks on the 16th of December 2009. One month later (01/18/2010), they were first acclimatized in a growth room (growing conditions : photoperiod of 16h, 24°C day temperature/ 22°C night temperature, 56% hygrometry). On the 23rd of February, the plants were then transferred to 3L compost-containing pots in the greenhouse. When they reached approximately 1-meter-height, they were staked with 2 poles. On the 23rd of April, the plant were inclined of 30°. The plants were sampled after 26 days (19th of May 2010).

extract_protocol: Pool of extract, odx_cad19_1:3ug, odx_cad19_2:3ug, odx_cad19_3:3ug, odx_cad19_4:3ug.


title: Cells incubated 60 min with staurosporine vs Cells at time 0

city: Porto

first: Arnaldo

last: Videira

address: Rua Campo Alegre 823

institute: IBMC-Instituto de Biologia Molecular e Celular

description: N. crassa pregrown in liquid media for 5h at 30 ºC (time 0) were incubated for 15, 30, 60 and 120 min in the presence (S) or absence (C) of staurosporine

hyb_protocol: The Pronto! Hybridization Kit (Corning, catalog no. 40076) was used for microarray hybridization according to the manufacturer’s specifications

scan_protocol: Scanned on a GenePix 4000B scanner (Axon Instruments)

data_processing:
GenePix Pro6 software was used to quantify hybridization signals and collect the raw data;Normalized expression values (see Townsend and Hartl 2002) were analyzed by using BAGEL (Bayesian Analysis of Gene Expression Levels)
Bayesian Analysis of Gene Expression Levels (BAGEL, see Townsend and Hartl 2002); http://www.yale.edu/townsend/jeffreytownsend.html

organism: Neurospora crassa

label_protocol: 10 µg of total RNA were used; ChipShot™ Indirect Labeling/Clean-Up System (Promega, catalog no. Z4000) and CyDye Post-Labeling Reactive Dye Pack (GE, catalog no. RPN5661) were used to synthesize and label cDNA according to the manufacturer’s instruction,

growth_protocol:
MM: 1xVogel's (Vogel, 1956 Microbiol. Genet. Bull. 13:42-43) salts with 2% sucrose as a sole carbon source
N. crassa was pregrown in liquid media for 5h at 30 ºC before incubation in the presence or absence of 12.5 µM staurosporine

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

treatment_protocol: Samples frozen in liquid nitrogen and kept at -70ºC

value: FGSC 2489

value: with staurosporine

tag: time

value: 60 min

source_name: Cells at time 0


title: Cells at time 0 vs Cells incubated 120 min without staurosporine

value: without staurosporine

value: 120 min


title: Cells incubated 120 min with staurosporine vs Cells incubated 120 min without staurosporine


title: Cells incubated 120 min without staurosporine vs Cells incubated 60 min without staurosporine


title: Cells incubated 120 min without staurosporine vs Cells incubated 120 min with staurosporine


title: Cells incubated 15 min without staurosporine vs Cells at time 0

value: 15 min


title: Cells incubated 60 min without staurosporine vs Cells incubated 30 min without staurosporine

value: 30 min


title: Cells incubated 30 min without staurosporine vs Cells incubated 15 min without staurosporine


title: Cells at time 0 vs Cells incubated 60 min with staurosporine


title: Cells incubated 120 min with staurosporine vs Cells incubated 60 min with staurosporine


title: Cells incubated 30 min without staurosporine vs Cells incubated 60 min without staurosporine


title: Cells incubated 60 min with staurosporine vs Cells incubated 120 min with staurosporine


title: Cells incubated 120 min without staurosporine vs Cells at time 0


title: Cells incubated 60 min with staurosporine vs Cells incubated 60 min without staurosporine


title: Cells incubated 60 min without staurosporine vs Cells incubated 120 min without staurosporine


title: Cells incubated 15 min without staurosporine vs Cells incubated 30 min without staurosporine


title: Cells incubated 30 min with staurosporine vs Cells incubated 30 min without staurosporine


title: Cells at time 0 vs Cells incubated 15 min without staurosporine


title: Donor9 CCR7hi

city: Dallas

first: Fatema

middle: Zahra

last: Chowdhury

address: 5323 Harry Hines Blvd

department: Immunology

institute: University of Texas Southwestern Medical Center

description:
4818441070_F
CD8+CCR7hiCXCR3lo sorted, rep4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was processed without normalization using GenomeStudio and exported as probe profile .txt file compatible with GeneSpring GX 11. Raw data was normalized once exported to GeneSpring.

source_name: Peripheral blood

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmo kit ofr Illumina arrays.

extract_protocol: RNA was extracted using the Arcturus PicoPure RNA Isolation kit in accordance with the prescribed protocol with the kit and on-column DNase treatment was performed prior to elution step. Quality control was performed with Agilent Bioanalyzer

tag: culture stimulator

tag: culture condition

value: Ex vivo


title: Cells incubated 60 min without staurosporine vs Cells incubated 60 min with staurosporine


title: Cells incubated 15 min with staurosporine vs Cells incubated 15 min without staurosporine

source_name: Cells incubated 15 min wit staurosporine


title: Donor8 CXCR3hi

description:
4818441070_C
CD8+CCR7loCXCR3hi sorted, rep3


title: Donor7 CCR7hi

description:
4818441070_B
CD8+CCR7hiCXCR3lo sorted, rep2


title: Donor9 CXCR3hi

description:
4818441070_E
CD8+CCR7loCXCR3hi sorted, rep4


title: Donor7 CXCR3hi

description:
4818441070_A
CD8+CCR7loCXCR3hi sorted, rep2


title: Cells incubated 30 min without staurosporine vs Cells incubated 30 min with staurosporine


title: Donor8 CCR7hi

description:
4818441070_D
CD8+CCR7hiCXCR3lo sorted, rep3


title: Donor6 CCR7hi

description:
4818441056_F
CD8+CCR7hiCXCR3lo sorted, rep1


title: Donor6 CXCR3hi

description:
4818441056_E
CD8+CCR7loCXCR3hi sorted, rep1


title: Donor5 IL-12+IFN-a Div

description:
4818441056_D
IL-12+IFN-a, Divided (CFSElo sorted), rep5

tag: sorted cells

value: divided

value: In vitro


title: Cells incubated 15 min without staurosporine vs Cells incubated 15 min with staurosporine


title: Cells incubated 60 min with staurosporine vs Cells incubated 30 min with staurosporine


title: Cells incubated 30 min with staurosporine vs Cells incubated 60 min with staurosporine


title: Cells incubated 15 min with staurosporine vs Cells incubated 30 min with staurosporine


title: Donor5 Neut Div

description:
4818441055_D
Neutralized, Divided (CFSElo sorted), rep5

tag: cell type

value: neutralized


title: Donor4 IFN-a Div

description:
4810781051_F
IFN-a, Divided (CFSElo sorted), rep4

value: IFN-a


title: Cells incubated 30 min with staurosporine vs Cells incubated 15 min with staurosporine


title: Cells at time 0 vs Cells incubated 120 min with staurosporine


title: Donor4 IFN-a Undiv

description:
4810781051_E
IFN-a, Undivided (CFSEhi sorted), rep4

value: undivided


title: Donor4 IL-12 Div

description:
4810781051_D
IL-12, Divided (CFSElo sorted), rep4


title: Donor5 IL-12 Div

description:
4818441055_F
IL-12, Divided (CFSElo sorted), rep5


title: Dono5 IL-12+IFN-a Undiv

description:
4818441056_C
IL-12+IFN-a, Undivided (CFSEhi sorted), rep5


title: Donor5 IFN-a Div

description:
4818441056_B
IFN-a, Divided (CFSElo sorted), rep5


title: Donor3 IL-12+IFN-a Div

description:
4463361139_F
IL-12+IFN-a, Divided (CFSElo sorted), rep3


title: Donor5 Neut Undiv

description:
4818441055_C
Neutralized, Undivided (CFSEhi sorted), rep5


title: Donor5 IL-12 Undiv

description:
4818441055_E
IL-12, Undivided (CFSEhi sorted), rep5


title: Donor4 IL-12+IFN-a Undiv

description:
4818441055_A
IL-12+IFN-a, Undivided (CFSEhi sorted), rep4


title: Cells incubated 15 min with staurosporine vs Cells at time 0

description: N. crassa pregrown in liquid media for 5h at 30 ºC (time 0) were incubated for 15, 30, 60 and 120 min in the presence (S) or absence (C) of staurosporine


title: Donor4 IL-12 Undiv

description:
4810781051_C
IL-12, Undivided (CFSEhi sorted), rep4


title: Cells at time 0 vs Cells incubated 15 min with staurosporine


title: Cells incubated 120 min with staurosporine vs Cells at time 0


title: Donor5 IFN-a Undiv

description:
4818441056_A
IFN-a, Undivided (CFSEhi sorted), rep5


title: Donor4 IL-12+IFN-a Div

description:
4818441055_B
IL-12+IFN-a, Divided (CFSElo sorted), rep4


title: Donor3 IFN-a Div

description:
4463361139_E
IFN-a, Divided (CFSElo sorted), rep3


title: Donor3 IL-12 Div

description:
4463361139_D
IL-12, Divided (CFSElo sorted), rep3


title: Donor4 Neut Div

description:
4810781051_B
Neutralized, Divided (CFSElo sorted), rep4


title: Donor4 Neut Undiv

description:
4810781051_A
Neutralized, Undivided (CFSEhi sorted), rep4


title: Donor3 Neut Div

description:
4463361139_C
Neutralized, Divided (CFSElo sorted), rep3


title: SBSR-AKS cells, growing adherent to the culture dish

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

country: Germany

description: Gene expression data from established Ewing tumor cells after transfection with siRNAs

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on HG_U133A Microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Expression Console 1.1 using the MAS5.0 algorithm and Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Ewing tumor cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Ewing tumor cell lines were grown under standard conditions

value: SBSR-AKS

value: EWS-FLI1 translocation type 1

tag: growth conditions

value: SBSR-AKS cells growing adherent to the culture dish


title: Donor2 IL-12 Div

description:
4457260037_B
IL-12, Divided (CFSElo sorted), rep2


title: SBSR-AKS cells, transfected with siRNA GPR64-4

description:
Gene expression data from established Ewing tumor cells after transfection with siRNAs
SBSR-AKS siRNA-GPR64-4

source_name: Ewing tumor cell line, transfected with siRNA specific for GPR64

growth_protocol: Established Ewing tumor cell lines were grown under standard conditions

treatment_protocol: Cells were transfected with siRNAs with specificity for CHM1, GPR64, or non-specific control siRNA.

value: Ewing tumor cell line SBSR-AKS

tag: protocol

value: siRNA-mediated GPR64 knockdown


title: SBSR-AKS cells, transfected with siRNA GPR64-1

description:
Gene expression data from established Ewing tumor cells after transfection with siRNAs
SBSR-AKS siRNA-GPR64-1


title: Donor3 Neut Undiv

description:
4457260037_E
Neutralized, Undivided (CFSEhi sorted), rep3


title: A673 cells, transfected with siRNA CHM1-4

description:
Gene expression data from established Ewing tumor cells after transfection with siRNAs
A673 siRNA-CHM1-4

source_name: Ewing tumor cell line, transfected with siRNA specific for CHM1

value: Ewing tumor cell line A673

value: siRNA-mediated CHM1 knockdown


title: SBSR-AKS cells, transfected with siRNA-CHM1-1

description:
Gene expression data from established Ewing tumor cells after transfection with siRNAs
SBSR-AKS siRNA-CHM1-1


title: Donor2 IL-12+IFN-a Div

description:
4457260037_D
IL-12+IFN-a, Divided (CFSElo sorted), rep2


title: Donor3 IFN-a Undiv

description:
4463361139_A
IFN-a, Undivided (CFSEhi sorted), rep3


title: A673 cells, transfected with siRNA GPR64-1

description:
Gene expression data from established Ewing tumor cells after transfection with siRNAs
A673 siRNA-GPR64-1


title: SBSR-AKS cells, transfected with control siRNA

description:
Gene expression data from established Ewing tumor cells after transfection with siRNAs
SBSR-AKS control siRNA

source_name: Ewing tumor cell line, transfected with control siRNA

value: control siRNA


title: Donor3 IL-12 Undiv

description:
4457260037_F
IL-12, Undivided (CFSEhi sorted), rep3


title: A673 cells, transfected with control siRNA

description:
Gene expression data from established Ewing tumor cells after transfection with siRNAs
A673 control siRNA


title: Donor3 IL-12+IFN-a Undiv

description:
4463361139_B
IL-12+IFN-a, Undivided (CFSEhi sorted), rep3


title: SBSR-AKS cells, transfected with siRNA-CHM1-4

description:
Gene expression data from established Ewing tumor cells after transfection with siRNAs
SBSR-AKS siRNA-CHM1-4


title: Donor2 Neut Div

description:
4457260037_A
Neutralized, Divided (CFSElo sorted), rep2


title: A673 cells, transfected with siRNA GPR64-4

description:
Gene expression data from established Ewing tumor cells after transfection with siRNAs
A673 siRNA-GPR64-4


title: P18_Parkinson's disease (PD) patient

city: Lisbon

first: Sofia

middle: A

last: Oliveira

state: Portugal

address: Av. Prof Egas Moniz

department: Edificio Egas Moniz

institute: Instituto de Medicina Molecular

description: Image analysis was carried out using the ImaGene 7.0 software (BioDiscovery, Inc., USA) and the resulting ImaGene output files were analyzed using the Limma package  (Smyth GK Stat Appl Genet Mol Biol. 2004; 3:Article3) implemented using R freeware (http://cran.r-project.org/).

hyb_protocol: RNA samples were sent to Exiqon (Vedbaek, Denmark) for miRNA profiling. Briefly, the Hy3-labeled sample and the Hy5-labeled common reference pool were co-hybridized to the miRCURYTM locked nucleic acid (LNA) array (version 10.0) using a Tecan (Austria) HS4800 hybridization station.

scan_protocol: Arrays were scanned with an Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and stored in an ozone-free environment in order to prevent potential bleaching of the fluorescent dyes.

data_processing: Background correction was performed using the normexp method (with offset=10). Intensities of good quality spots were then subjected to within-array (loess method) normalization. Intensities lower than 1.5 times the median signal intensity of the respective slide and label were discarded. The calling of a miRNA on a particular array fails if two or more of the four replicated capture probes for this miRNA are flagged as bad quality spots by the image analysis software. Differential expression between controls and PD patients was assessed using linear regression analysis and empirical Bayes methods implemented in the Limma package.

source_name: PD patient P18

label_protocol: RNA sample was sent to Exiqon (Vedbaek, Denmark) for miRNA profiling. 1µg of total RNA was labeled with the miRCURY Hy3 power labeling kit.

extract_protocol: Approximately 16 ml of whole blood was collected by venipuncture into two BD Vacutainer CPT glass tubes (Becton-Dickinson, Franklin Lakes, USA). Whithin two hours of blood collection, peripheral blood mononuclear cells (PBMCs) were isolated from the CPT tubes by centrifugation (30 min, 2800 rpm, room temperature) and washed twice with PBS (15 min, 1300 rpm, 4ºC). Total RNA containing small RNAs was extracted from PBMCs using the miRNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions, aliquoted and stored at -80ºC. All samples passed extensive quality controls (e.g. OD260/OD280 between 1.8 and 2.1 in the Nanodrop ND1000 and RIN (RNA Integrity Number) > 7 in the Agilent 2100 Bioanalyser).

tag: disease state

value: parkinson´s disease patient (with tremor and bradykinesia)

tag: updrs score

tag: sex

value: Female

tag: age

value: 69 yrs

tag: tissue

value: PBMCs

source_name: Common reference pool

label_protocol: RNA samples were sent to Exiqon (Vedbaek, Denmark) for miRNA profiling. 1µg of total RNA from each of the 39 samples was pooled and labeled with the miRCURY Hy5 power labeling kit.

extract_protocol: Same protocol as channel 1

tag: sample

value: Pool composed of 39 samples (the 32 samples under study and 7 additional samples which were later excluded from differential expression analysis due to array quality control problems).


title: P17_Parkinson's disease (PD) patient

source_name: PD patient P17

value: parkinson´s disease patient (with rigidity, bradykinesia, and postural disturbance)

value: 68 yrs


title: P19_Parkinson's disease (PD) patient

source_name: PD patient P19

value: 70 yrs


title: P15_Parkinson's disease (PD) patient

source_name: PD patient P15

value: 67 yrs


title: P16_Parkinson's disease (PD) patient

source_name: PD patient P16

value: parkinson´s disease patient (with tremor, rigidity, and bradykinesia)


title: Donor2 IL-12+IFN-a Undiv

description:
4457260034_F
IL-12+IFN-a, Undivided (CFSEhi sorted), rep2

value: undivided

value: In vitro


title: A673 cells, transfected with siRNA CHM1-1

description:
Gene expression data from established Ewing tumor cells after transfection with siRNAs
A673 siRNA-CHM1-1

tag: cell line

tag: genotype

value: EWS-FLI1 translocation type 1


title: SBSR-AKS cells, growing in suspension

description: Gene expression data from established Ewing tumor cells after transfection with siRNAs

value: SBSR-AKS

value: SBSR-AKS cells growing in suspension


title: Donor2 IFN-a Undiv

description:
4457260034_E
IFN-a, Undivided (CFSEhi sorted), rep2

value: IFN-a


title: Donor2 IFN-a Div

description:
4457260037_C
IFN-a, Divided (CFSElo sorted), rep2

value: divided


title: whole bone marrow-irradiated-PTH-rep3

city: Ann Arbor

first: Amy

middle: J

last: Koh

state: MI

address: 1011 N. University Ave.

department: POM

institute: University of Michigan

description: gene expression from bone marrow flush in 16 day old mice irradiated at d10 and treated for 5 days with PTH

hyb_protocol: Following Labeling, 4 ug of cDNA were hybridized for 16 hr at 45C on Mouse gene ST 1.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical environment. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: whole bone marrow, irradiated on d10, PTH treatment d11-d15

label_protocol: Biotinylated cDNA were prepared according to the Nugen Applause protocol from 100 ng total RNA (Nugen Applause WT-AMP ST V1 Manual, version 29 April 2009, NuGEN).

growth_protocol: B6 mice were grown to 10 days of age

extract_protocol: Long bones were harvested and flushed with Trizol.  Extraction of total RNA was performed according to the manufacturer's instructions.  RNA was cleaned up using the the Qiagen RNEasy Kit.

treatment_protocol: Mice were sub-lethally irradiated for 2 fractions of 310cGy at 10 days of age, then PTH administration began 24 hours later for 5 days.

tag: treatment

tag: strain

value: whole bone marrow flush


title: Donor2 IL-12 Undiv

description:
4457260034_D
IL-12, Undivided (CFSEhi sorted), rep2


title: whole bone marrow-irradiated-PTH-rep2

value: irradiated on d10, PTH treatment d11-d15


title: P13_Parkinson's disease (PD) patient

source_name: PD patient P13

value: parkinson´s disease patient (with rigidity and bradykinesia)

value: Female

value: 62 yrs


title: P14_Parkinson's disease (PD) patient

source_name: PD patient P14

value: parkinson´s disease patient (with tremor, bradykinesia, and postural disturbance)

value: 64 yrs

value: PBMCs

value: Pool composed of 39 samples (the 32 samples under study and 7 additional samples which were later excluded from differential expression analysis due to array quality control problems).


title: P12_Parkinson's disease (PD) patient

source_name: PD patient P12

value: parkinson´s disease patient (with tremor and rigidity)

value: 61 yrs


title: P11_Parkinson's disease (PD) patient

source_name: PD patient P11

value: 58 yrs


title: P8_Parkinson's disease (PD) patient

source_name: PD patient P8

value: parkinson´s disease patient (with tremor, rigidity, and postural disturbance)

value: Male

value: 70 yrs


title: P7_Parkinson's disease (PD) patient

source_name: PD patient P7

value: parkinson´s disease patient (with rigidity and postural disturbance)

value: 68 yrs


title: P9_Parkinson's disease (PD) patient

source_name: PD patient P9

value: parkinson´s disease patient (with tremor, rigidity, and bradykinesia)

value: 71 yrs


title: P6_Parkinson's disease (PD) patient

source_name: PD patient P6

value: parkinson´s disease patient (with rigidity, bradykinesia, and postural disturbance)

value: 65 yrs


title: whole bone marrow-irradiated-PTH-rep1

value: irradiated on d10, PTH treatment d11-d15

value: whole bone marrow flush


title: P10_Parkinson's disease (PD) patient

source_name: PD patient P10

value: parkinson´s disease patient (with rigidity and bradykinesia)


title: whole bone marrow-nonirradiated-PTH-rep3

description: gene expression from bone marrow flush in 16 day old mice treated for 5 days with PTH

source_name: whole bone marrow, PTH treatment d11-d15

value: PTH treatment d11-d15


title: Donor1 IL-12 Div

description:
4457260006_F
IL-12, Divided (CFSElo sorted), rep1

source_name: Peripheral blood

value: divided

value: In vitro


title: whole bone marrow-nonirradiated-vehicle-rep2

description: gene expression from bone marrow flush in 16 day old mice treated for 5 days with Vehicle

source_name: whole bone marrow, vehicle treatment d11-d15

value: vehicle treatment d11-d15


title: Donor2 Neut Undiv

description:
4457260034_C
Neutralized, Undivided (CFSEhi sorted), rep2

value: neutralized

value: undivided


title: whole bone marrow-irradiated-vehicle-rep3

description: gene expression from bone marrow flush in 16 day old mice irradiated at d10 and treated for 5 days with Vehicle

source_name: whole bone marrow, irradiated on d10, vehicle treatment d11-d15


title: whole bone marrow-irradiated-vehicle-rep1

value: irradiated on d10, vehicle treatment d11-d15


title: Donor1 IL-12 Undiv

description:
4457260006_B
IL-12, Undivided (CFSEhi sorted), rep1


title: Donor1 IFN-a Div

description:
4457260034_A
IFN-a, Divided (CFSElo sorted), rep1

value: IFN-a


title: whole bone marrow-irradiated-vehicle-rep2


title: Donor1 Neut Div

description:
4457260006_E
Neutralized, Divided (CFSElo sorted), rep1


title: Donor1 IL-12+IFN-a Div

description:
4457260034_B
IL-12+IFN-a, Divided (CFSElo sorted), rep1


title: Donor1 IL-12+IFN-a Undiv

description:
4457260006_D
IL-12+IFN-a, Undivided (CFSEhi sorted), rep1


title: whole bone marrow-nonirradiated-vehicle-rep3


title: whole bone marrow-nonirradiated-PTH-rep1


title: Donor1 IFN-a Undiv

description:
4457260006_C
IFN-a, Undivided (CFSEhi sorted), rep1


title: P5_Parkinson's disease (PD) patient

description: Image analysis was carried out using the ImaGene 7.0 software (BioDiscovery, Inc., USA) and the resulting ImaGene output files were analyzed using the Limma package  (Smyth GK Stat Appl Genet Mol Biol. 2004; 3:Article3) implemented using R freeware (http://cran.r-project.org/).

source_name: PD patient P5

value: parkinson´s disease patient (with tremor, rigidity, bradykinesia, and postural disturbance)

value: Male

value: 64 yrs

value: PBMCs

source_name: Common reference pool

value: Pool composed of 39 samples (the 32 samples under study and 7 additional samples which were later excluded from differential expression analysis due to array quality control problems).


title: whole bone marrow-nonirradiated-PTH-rep2


title: whole bone marrow-nonirradiated-vehicle-rep1


title: Control pool, replication 3

city: NOTRE DAME

first: David

middle: W

last: Severson

state: IN

address: Galvin Life Science

department: Dept. of Biological Sciences

institute: University of Notre Dame

description:
Three independent feeding experiments were done to obtain three biological replicates of samples for both the strains and the post-infection time points. These consisted of four DENV2 infected samples (Moyo-S-3hr, Moyo-R-3hr, Moyo-S-18hr and Moyo-R-18hr, post-infection, respectively) and a control sample that consisted of RNA isolated at the same time points following uninfected blood meals and pooled across strains and time of sampling. Thus, a total of 15 independent samples were used for array hybridizations.

Control-3 was prepared from RNA isolated from individual controls set up along with each of the test samples (MS at 3hr, MS at 18 hr, MR at 3hr and MR at 18hr) for the first biological replication.

hyb_protocol: The array hybridization and washing was performed by NimbleGen as per protocol described at http://www.nimblegen.com/products/lit/exp_userguide_v3p2.pdf

scan_protocol: Scanning was also performed by NimbleGen as described in http://www.nimblegen.com/products/lit/exp_userguide_v3p2.pdf

data_processing: The raw data from array expressions were normalized using quintile normalization method and the Robust Multichip Average (RMA) algorithm by NimbleGen. The Statistical Analysis of Microarray (SAM) program was employed, using the Microsoft Excel addin v1.21, to determine differential expression between test and control samples. The control and infected samples were compared as two-class unpaired response types. The significant gene list was further subjected to filter for the genes that showed either positive (up-regulation) or negative (down-regulation) in both the Moyo-S and Moyo-R strains for both the post-infection time points. This step was performed because each of the test samples were compared to a common uninfected control (prepared by pooling equal amount of the individual control for these samples). This approach was adopted to ensure the identification of genes showing differential expression in response to DENV but not due to genetic differences between the two strains or developmental associated changes between the two observation time points.

organism: Aedes aegypti

source_name: Control pool

label_protocol: The cDNA labeling was performed by NimbelGene. The manufacturer protocol for labeling is as follows. First, the RNA samples are tested for quality control so that they are free of contamination and intact (not degraded). The RNA is then used to prepare first and second strand cDNA. The cDNA is cleaned up and checked for quality control. Then cy3 dye was used to label the cDNA as described in http://www.nimblegen.com/products/lit/exp_userguide_v3p2.pdf.

growth_protocol: Fully engorged females were isolated and maintained at 26 °C with 84% humidity and in a 16-h light/8-h dark cycle. At 3 hr and 18 hr post blood feeding, DENV2 infected and control females were sampled for each strain. Three independent feeding experiments were done to obtain three biological replicates of samples for both the strains and the post-infection time points.

extract_protocol: At the appropriate time point, RNA was extracted from 20 females per sample (the blood meal was removed from each female using a micro syringe needle prior to RNA extractions) using a Qiagen RNAeasy Kit as per manufacturer’s instructions. The RNA quality was assessed by a Bioanalyzer and quantified by a Nanodrop spectrophotometer.

treatment_protocol: The starved females were provided with an artificial infectious blood meal, freshly prepared using defibrinated sheep blood (Colorado Serum Co., CS1122) mixed with (equal volume) a dengue viral suspension. DENV2 strain JAM1409 was cultured using C6/36 mosquito cells until 80-90% confluence in MEM-EBSS media (HyClone SH3002401) supplemented with 25 mM Hepes buffer, 1 mM sodium pyruvate, 0.025 mg/ml Gentamycin, 1x (0.01 mM) non-essential amino acids and 10% fetal bovine serum (heat inactivated). A 0.1 MOI (multiplicity of infection) was used for infecting the mosquito cells. The multiplicity of infection refers to the average number of viral particles that infect a single cell, which for our purpose, is equal to plaque-forming units (pfu) per cell. The flasks were incubated at 28°C for 7 days after which the viral supernatant was obtained by centrifugation at 1500 rpm for 5 min at 4ºC. All DENV infection work was performed in a BSL3 facility.

value: MOYO-S

value: MOYO-R


title: Donor1 Neut Undiv

description:
4457260006_A
Neutralized, Undivided (CFSEhi sorted), rep1


title: P3_Parkinson's disease (PD) patient

source_name: PD patient P3

value: parkinson´s disease patient (with rigidity, bradykinesia, and postural disturbance)

value: 61 yrs


title: P4_Parkinson's disease (PD) patient

source_name: PD patient P4

value: 62 yrs


title: P2_Parkinson's disease (PD) patient

source_name: PD patient P2

value: parkinson´s disease patient (with tremor, rigidity, and bradykinesia)

value: 60 yrs


title: Control pool, replication 2

description:
Three independent feeding experiments were done to obtain three biological replicates of samples for both the strains and the post-infection time points. These consisted of four DENV2 infected samples (Moyo-S-3hr, Moyo-R-3hr, Moyo-S-18hr and Moyo-R-18hr, post-infection, respectively) and a control sample that consisted of RNA isolated at the same time points following uninfected blood meals and pooled across strains and time of sampling. Thus, a total of 15 independent samples were used for array hybridizations.

Control-2 was prepared from RNA isolated from individual controls set up along with each of the test samples (MS at 3hr, MS at 18 hr, MR at 3hr and MR at 18hr) for the first biological replication.


title: Control pool, replication 1

description:
Three independent feeding experiments were done to obtain three biological replicates of samples for both the strains and the post-infection time points. These consisted of four DENV2 infected samples (Moyo-S-3hr, Moyo-R-3hr, Moyo-S-18hr and Moyo-R-18hr, post-infection, respectively) and a control sample that consisted of RNA isolated at the same time points following uninfected blood meals and pooled across strains and time of sampling. Thus, a total of 15 independent samples were used for array hybridizations.

Control-1 was prepared from RNA isolated from individual controls set up along with each of the test samples (MS at 3hr, MS at 18 hr, MR at 3hr and MR at 18hr) for the first biological replication.


title: P1_Parkinson's disease (PD) patient

source_name: PD patient P1

value: parkinson´s disease patient (with rigidity and bradykinesia)

value: 58 yrs


title: C11_control

source_name: Control C11

value: unaffected with parkinson´s disease

value: Female

value: 66 yrs


title: C10_control

source_name: Control C10


title: MOYO-R; 18 hr, replication 3

description:
Three independent feeding experiments were done to obtain three biological replicates of samples for both the strains and the post-infection time points. These consisted of four DENV2 infected samples (Moyo-S-3hr, Moyo-R-3hr, Moyo-S-18hr and Moyo-R-18hr, post-infection, respectively) and a control sample that consisted of RNA isolated at the same time points following uninfected blood meals and pooled across strains and time of sampling. Thus, a total of 15 independent samples were used for array hybridizations.

The Aedes aegypti strain MOYO-R was used. These mosquitoes show 19.56% susceptibility to dengue serotype-2. Early interactions between host and virus is important. So, we profiled the gene expression changes in dengue-2 infected MOYO-R females at 18 hr post infection. The control was prepared in parallel to the test. The control mosquitoes were mock transfected by normal blood meal without dengue.

source_name: MOYO-R; 18 hr


title: C13_control

source_name: Control C13

value: 70 yrs


title: C7_control

source_name: Control C7

value: 57 yrs


title: C8_control

source_name: Control C8


title: C12_control

source_name: Control C12

value: 67 yrs


title: C9_control

source_name: Control C9

value: 63 yrs

value: PBMCs


title: C6_control

source_name: Control C6

value: 51 yrs

value: Pool composed of 39 samples (the 32 samples under study and 7 additional samples which were later excluded from differential expression analysis due to array quality control problems).


title: MOYO-R; 3 hr, replication 3

description:
Three independent feeding experiments were done to obtain three biological replicates of samples for both the strains and the post-infection time points. These consisted of four DENV2 infected samples (Moyo-S-3hr, Moyo-R-3hr, Moyo-S-18hr and Moyo-R-18hr, post-infection, respectively) and a control sample that consisted of RNA isolated at the same time points following uninfected blood meals and pooled across strains and time of sampling. Thus, a total of 15 independent samples were used for array hybridizations.

The Aedes aegypti strain MOYO-R was used. These mosquitoes show 19.56% susceptibility to dengue serotype-2. Early interactions between host and virus is important. So, we profiled the gene expression changes in dengue-2 infected MOYO-R females at 3 hr post infection. The control was prepared in parallel to the test. The control mosquitoes were mock transfected by normal blood meal without dengue.

source_name: MOYO-R; 3 hr

value: MOYO-R


title: MOYO-R; 18 hr, replication 2


title: MOYO-S; 18 hr, replication 1

description:
Three independent feeding experiments were done to obtain three biological replicates of samples for both the strains and the post-infection time points. These consisted of four DENV2 infected samples (Moyo-S-3hr, Moyo-R-3hr, Moyo-S-18hr and Moyo-R-18hr, post-infection, respectively) and a control sample that consisted of RNA isolated at the same time points following uninfected blood meals and pooled across strains and time of sampling. Thus, a total of 15 independent samples were used for array hybridizations.

The Aedes aegypti strain MOYO-S was used. These mosquitoes show 56.60% susceptibility to dengue serotype-2. Early interactions between host and virus is important. So, we profiled the gene expression changes in dengue-2 infected MOYO-S females at 18 hr post infection. The control was prepared in parallel to the test. The control mosquitoes were mock transfected by normal blood meal without dengue.

source_name: MOYO-S; 18 hr

value: MOYO-S


title: MOYO-R; 18 hr, replication 1

description:
Three independent feeding experiments were done to obtain three biological replicates of samples for both the strains and the post-infection time points. These consisted of four DENV2 infected samples (Moyo-S-3hr, Moyo-R-3hr, Moyo-S-18hr and Moyo-R-18hr, post-infection, respectively) and a control sample that consisted of RNA isolated at the same time points following uninfected blood meals and pooled across strains and time of sampling. Thus, a total of 15 independent samples were used for array hybridizations.

The Aedes aegypti strain MOYO-R was used. These mosquitoes show 19.5% susceptibility to dengue serotype-2. Early interactions between host and virus is important. So, we profiled the gene expression changes in dengue-2 infected MOYO-R females at 3 hr post infection. The control was prepared in parallel to the test. The control mosquitoes were mock transfected by normal blood meal without dengue.


title: MOYO-S; 18 hr, replication 2


title: MOYO-R; 3 hr, replication 2