title: 5655508058_F

description: replicate 1


title: 5655508058_C

status: Public on Oct 02 2012

type: RNA

city: Herston

first: Amy

middle: McCart

last: Reed

state: Queensland

address: Royal Brisbane & Women's Hospital Campus

department: UQ Centre for Clinical Research

country: Australia

institute: University of Queensland

description: replicate 1

hyb_protocol: Refer to the Illumina beadarray Assay System Manual.

data_processing: Processed data were log2-transformed then quantile normalized using the lumi Bioconductor package.

molecule: total RNA

organism: Homo sapiens

source_name: negative control

extract_protocol: Using formalin-fixed, paraffin-embedded HCC tissues, total RNA was extracted using Roche High Pure FFPE Kit.

value: Negative

value: Dec Trial

value: FFPE tissue sample

value: no


title: 5141777059_B

description: replicate 2

scan_protocol: Refer to the Illumina beadarray Assay System Manual.

source_name: lung

value: 8 G (lung)

value: Autopsy

value: AUG-10 B


title: 5141777059_A

description: replicate 2

source_name: liver

label_protocol: Refer to the Illumina beadarray Assay System Manual.

value: liver


title: 5655508058_A

description: replicate 1

source_name: pooled breast positive control

value: positive (10A)


title: 5141777045_F

description: replicate 1


title: 5141777045_H

description: replicate 1

source_name: positive control

value: positive (15A)


title: 5141777045_E

description: replicate 1

source_name: healthy breast tissue

value: breast


title: 5141777045_G

description: replicate 1

value: 6 F (lung)


title: 5141777043_F

description: replicate 2

value: lung


title: Sinorhizobium meliloti AB9, stationary phase growth, biological rep3

city: Stanford

first: Melanie

middle: J

last: Barnett

state: CA

address: 371 Jane Stanford Way

department: Biology

country: USA

institute: Stanford University

hyb_protocol: For the heat shock experiment, four micrograms of biotinylated cDNA was hybridized to each chip at 48 degrees celsius for 16 hours as described by Barnett et al. 2004. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. The stationary phase experiment was performed similarly, except twelve micrograms of biotinylated cDNA was hybridized to each chip.

scan_protocol: Chips were scanned at the Stanford PAN facility using an Affymetrix scanner 3000 7G

data_processing: The data were analyzed using Affymetrix software GCOS v1.4 with Affymetrix default analysis setting and global scaling as the normalization method. The mean target intensity of each array was arbitrarily set to 500. Affymetrix Data Mining Tool v3.1 was used for data mining as previously described by Barnett et al. 2004.

label: biotin

organism: Sinorhizobium meliloti

source_name: rpoH1 rpoH2 double mutant

label_protocol: cDNA was fragmented and biotinylated as described by Barnett et al. 2004.

growth_protocol:
For the heat shock experiment: cultures were diluted to OD595=0.05 in 65 ml LB/MC and allowed to grow to mid exponential phase (OD595=0.5-0.7).  Each wild-type culture was split such that 30 ml remained at 30°C for 15 minutes as a control, and 30 ml was heat-shocked for 15 minutes at 42°C.
For the stationary phase experiment: overnight cultures were grown in LB/MC medium, diluted to OD595 = 0.05 the next day, and allowed to grow overnight.  Cells (8 ml) were washed twice and diluted to OD595=0.05 in 300 ml M9 sucrose minimal medium. Cultures were incubated with shaking for 48 hours, until late stationary phase.

extract_protocol: Total RNA was extracted using a Qiagen RNeasy kit with modifications as described by Barnett et al. 2004 Proc Natl Acad Sci USA volume 101 pages 16636 to 16641.

treatment_protocol: Stop solution (5% buffer equilibrated phenol in ethanol) was added to bacterial cultures, at one tenth the culture volume, before centrifugation at 4 degrees celsius. Bacterial cell pellets were frozen in liquid nitrogen and stored at -80 degrees celsius until RNA extraction.

tag: strain

value: AB9 (Valerie Oke)

tag: genotype/variation

value: rpoH1 rpoH2 double mutant

tag: treatment

value: Grown to late stationary phase in M9 sucrose minimal medium


title: 5141777045_C

description: replicate 2

source_name: chest wall

value: 2 AB (chest wall)


title: 5141777059_C

description: replicate 3


title: Sinorhizobium meliloti AB3, stationary phase growth, biological rep1

source_name: rpoH2 insertion mutant

value: AB3 (Valerie Oke)

value: rpoH2 insertion mutant


title: 5141777045_B

description: replicate 1

source_name: spleen

value: spleen

value: FFPE tissue sample


title: Sinorhizobium meliloti VO3128, stationary phase growth, biological rep2

source_name: rpoH1 insertion mutant

value: VO3128 (Valerie Oke)

value: rpoH1 insertion mutant


title: Sinorhizobium meliloti VO3128, stationary phase growth, biological rep3


title: Sinorhizobium meliloti AB9, stationary phase growth, biological rep2


title: Sinorhizobium meliloti AB9, stationary phase growth, biological rep1


title: 5141777043_E

description: replicate 2

value: Autopsy

value: AUG-10 B

value: no


title: Anethol_Replicate 1

city: Beltsville

first: Duk Kyung

last: Kim

state: MD

address: Bldg. 1043, BARC-East

institute: USDA, ARS

description: Biological replicate 1 of 2

hyb_protocol: With the use of Agilent’s Gene Expression Hybridization Kit (Cat# 5188-5242), 825ng of cyanine 3-labeled and cyanine 5-labeled linearly amplified cRNA was added to individual hybridization cocktails and then fragmented. At hybridization each well contained one cy3 and one cy5 labeled sample and control per pair.  The hybridization cocktail is then dispensed into the wells of gasket slides (4 samples/slide: Cat# G2534-60012) on top of which a Chicken 4x44K Gene Expression Microarray, (Cat# G2519F, AMADID 015068) was placed.  This microarray “sandwich” was then sealed in a hybridization chamber.  The microarrays were hybridized at 65°C rotating at 10 RPMs for 17 hours.  Slides were washed in Agilent’s Gene Expression Wash Buffers according to manufacturer recommendations.

scan_protocol: The microarrays were scanned on the Agilent Microarray Scanner.  Scanner data extraction and analysis was performed using Feature Extraction software version 10.7.3.1.

data_processing: Data quality was evaluated by reviewing ten standard QC metrics generated by the Agilent Technologies Feature Extraction Software version 10.7.3.1. Microarrays were determined to be free of any large artifacts (≥ 10% of total surface area) that could have affected the quality of the data.

organism: Gallus gallus

label_protocol: Using Agilent’s 2-Color Quick Amp Labeling Kit, (Cat# 5190-0444), 0.5 to 1 ug of RNA (Agilent suggested: total RNA input range 50 ng - 2 μg) and Spike-In (2-Color RNA Spike-In Kit Cat# 5188-5279) were denatured in the presence of a T7 promoter primer.  Reverse Transcriptase was used to reverse-transcribe the mRNA.  cDNA was used as a template for in vitro transcription where a T7 RNA polymerase simultaneously amplified target material and incorporated cyanine 3- or cyanine 5-labeled CTP.  Labeled cRNA was purified using spin columns from the Qiagen RNeasy Mini Kit and the quantity and quality of the cRNA was determined by Nanodrop ND-1000 UV-VIS spectrophotometer.

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

tag: age

value: day 14

tag: tissue

value: Intestinal IEL

value: Broiler


title: 5141777043_H

description: replicate 2


title: 5141777043_C

description: replicate 1

source_name: healthy lymph node

value: LN


title: Anethol_Replicate 2

description: Biological replicate 2 of 2 (Dye-exchange of Replicate 1)


title: 5141777045_A

description: replicate 1

value: 10 D 1 (liver)


title: 5141777045_D

description: replicate 1

value: lung


title: 5141777043_D

description: replicate 2

value: positive (15A)


title: 5141777043_G

description: replicate 2

value: 6 F (lung)


title: Sinorhizobium meliloti AB9, heat shock, biological rep3

value: AB9 (Valerie Oke)

value: rpoH1 rpoH2 double mutant

value: 42°C for 15 minutes in LB/MC medium


title: 5505171007_C

description: replicate 1

source_name: lymph node metastasis

value: LobLN

value: AUG-10 A

value: FFPE tissue sample


title: Sinorhizobium meliloti AB9, heat shock, biological rep2


title: Sinorhizobium meliloti AB9, heat shock, biological rep1


title: Sinorhizobium meliloti Rm1021, stationary phase growth, biological rep1

source_name: wild type

value: Rm1021 (Valerie Oke)

value: wild type

value: Grown to late stationary phase in M9 sucrose minimal medium


title: Sinorhizobium meliloti Rm1021, stationary phase growth, biological rep2


title: Sinorhizobium meliloti VO3128, stationary phase growth, biological rep1

value: VO3128 (Valerie Oke)

value: rpoH1 insertion mutant


title: 5141777043_A

description: replicate 1

value: 2 AB (chest wall)

value: Autopsy

value: AUG-10 B

value: no


title: Sinorhizobium meliloti AB3, stationary phase growth, biological rep2

value: AB3 (Valerie Oke)

value: rpoH2 insertion mutant


title: 5141777043_B

description: replicate 1

value: liver


title: Sinorhizobium meliloti AB3, stationary phase growth, biological rep3


title: Sinorhizobium meliloti Rm1021, stationary phase growth, biological rep3


title: Sinorhizobium meliloti VO3128, heat shock, biological rep3


title: Sinorhizobium meliloti AB3, heat shock, biological rep3


title: Sinorhizobium meliloti AB3, heat shock, biological rep2


title: Sinorhizobium meliloti Rm1021, heat shock, biological rep3


title: Sinorhizobium meliloti AB3, heat shock, biological rep1


title: ccpA_TY1-cy3

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description: Biological replicate 1 of 4.

hyb_protocol: samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers

scan_protocol: Scanned on an GenePix 4200L dual-channel laser scanner

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicat : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

organism: Clostridioides difficile

source_name: Mutant ccpA CD630E JIR8094 10H in TY

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 1600 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP,  dCTP. cDNA were then incubated with cy5 or cy3 dyes 1h at room temperature in the dark.

growth_protocol: C.difficile strains CD630E JIR8094, a WT and a mutant ccpA strains, were grown for 10 hours in TY

extract_protocol: Total RNA extracted using RNAPro (FastPrep) and following MP manufacturer's instructions

tag: genotype

value: 10H in TY

source_name: CD630E JIR8094 in TY 8H of growth (reference)

value: 8H in TY


title: Sinorhizobium meliloti Rm1021, no heat shock, biological rep3

value: 30°C for 15 minutes in LB/MC medium


title: Sinorhizobium meliloti Rm1021, heat shock, biological rep1

value: 42°C for 15 minutes in LB/MC medium


title: ccpA_TY4-cy5

description: Biological replicate 4 of 4.


title: Sinorhizobium meliloti VO3128, heat shock, biological rep2


title: ccpA_TY3-cy3

description: Biological replicate 3 of 4.


title: WT_TY4-cy5

description: Biological replicate 4 of 4.

source_name: CD630E JIR8094 10H in TY


title: Sinorhizobium meliloti VO3128, heat shock, biological rep1


title: ccpA_TY2-cy5

description: Biological replicate 2 of 4.


title: Sinorhizobium meliloti Rm1021, no heat shock, biological rep2


title: ccpA_TYG3-cy3

description: Biological replicate 3 of 4.

source_name: Mutant ccpA CD630E JIR8094 10H in TY with 0.5% glucose

growth_protocol: C.difficile strains CD630E JIR8094, a WT and a mutant ccpA strains, were grown for 10 hours in TY with 0.5% glucose

value: 10H in TY with 0.5% glucose


title: ccpA_TYG4-cy5

description: Biological replicate 4 of 4.


title: Sinorhizobium meliloti Rm1021, heat shock, biological rep2

value: Rm1021 (Valerie Oke)


title: WT_TY1-cy3

description: Biological replicate 1 of 4.

value: wild type


title: ccpA_TYG2-cy5

description: Biological replicate 2 of 4.


title: indole treated replicate 2

city: Seoul

first: Jisun

address: Anam-Dong, Sungbuk-Gu

department: Environmental Science and Ecological Engineering

country: South Korea

institute: Korea university

description: Sample 2

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

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

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

organism: Pseudomonas putida KT2440

label_protocol: 10 μg of total RNA were primed with 2 μl of 100 μM T16N2 DNA primer at 70℃ for 10 min, then reversed transcribed at 42℃ for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 μM each dATP, dTTP, dGTP, with 25 μM dCTP, 25 μM label.

growth_protocol: After growth at the early exponential (OD600 of approximately 0.4) phase at 30C with aeration, the cells were then treated with 1 mM indole for 10 min.

extract_protocol: Total RNA extracted using Qiagen RNA miniprep kit following manufacturer's instructions

treatment_protocol: Cells are treated with indole 1 mM for 10 min at 30C.

tag: treated with

value: none (control)

source_name: KT2440_indole treated

value: indole 1 mM for 10 min


title: indole treated replicate 1

description: Sample 1


title: WT_TY2-cy5

description: Biological replicate 2 of 4.


title: WT_TYG3-cy3

description: Biological replicate 3 of 4.

source_name: CD630E JIR8094 10H in TY with 0.5% glucose


title: Sinorhizobium meliloti Rm1021, no heat shock, biological rep1


title: ccpA_TYG1-cy3

description: Biological replicate 1 of 4.


title: WT_TYG4-cy5

description: Biological replicate 4 of 4.


title: WT_TYG2-cy5

description: Biological replicate 2 of 4.


title: BRCA2 Ovarian cancer sample64

type: genomic

city: Madird

first: Maria

middle: Jose

last: García

state: Madrid

address: C/ Melchor Fernández Almagro 3

department: Human Cancer Genetics

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas

description: standard dual color hybridization

hyb_protocol: Hybridization protocol available via www.agilent.com NOTE: Nine samples (highlighted in description) were hybridized using Across Array CGH  method with which reference sample is hybridized to an external array while two test samples can be hybridized to the same array (with different channels/fluorochromes) (Buffart et al., Genes Chromosomes and Cancer, 2008 and Voorham et al., Clinical Cancer Research, 2012).

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: Wave smoothing and median normalization in R/Bioconductor.Calling performed with DNAcopy algorithm.

molecule: genomic DNA

source_name: ovarian tumour

label_protocol: Labeling of test and reference DNA was performed using the Enzo Genomic DNA labeling kit (Enzo Life Sciences ) according to Enzo Life Sciences protocol  as described previously (Buffart et al, Genes Chrom and Cancer, 2008).

extract_protocol: Genomic DNA was extracted from three 10-μm-thick FFPE tissue sections per tumour. After deparaffination and rehydration, sections were haematoxylin and eosin (H&E) stained and tumoral areas were delimited by a pathologist and macrodissected with a surgical blade to ensure at least 80% of tumor content. DNA extraction was performed by standard protocols of proteinase-K overnight digestion and using a column-based commercially available kit following manufacturer´s instructions (QIAamp DNA mini kit; Qiagen, Westburg, Leusden, The Netherlands) DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Buffart et al, J Pathol. 2007 Jan;211(1):45-51.

tag: disease subtype

tag: disease state

value: ovarian carcinoma

value: ovarian tumor

source_name: pooled  blood healthy women

value: blood

tag: sample type

value: pooled  blood healthy women


title: BRCAX Ovarian cancer sample63

description: across array hybridization (see NOTE in the hybridization protocol)

value: BRCAX


title: BRCA1 Ovarian cancer sample62


title: BRCA1 Ovarian cancer sample61


title: BRCA1 Ovarian cancer sample65


title: WT_TYG1-cy3

description: Biological replicate 1 of 4.


title: BRCA1 Ovarian cancer sample66

description: standard dual color hybridization


title: BRCAX Ovarian cancer sample67

description: standard dual color hybridization


title: BRCA1 Ovarian cancer sample68


title: BRCA1 Ovarian cancer sample59


title: WT_TY3-cy3

description: Biological replicate 3 of 4.


title: Mock 46 hours

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

country: United Kingdom

institute: The Genome Analysis Centre

description: Randomised loop design providing dye-swaps between treatments, time points and bioreps

hyb_protocol: The order in which the 288 slides were hybridized and scanned was randomised to minimise the impact on differences between samples of any potential variation in the processing conditions. According to this randomised experimental design combinations of labelled samples were hybridized to slides overnight at 42oC.

scan_protocol: Following hybridization, slides were washed and scanned using an Affymetrix 428 array scanner at 532nm (Cy3) and 635nm (Cy5).

data_processing:
Scanned data were quantified using Imagene 7.5.0 software (BioDiscovery, Inc.).
Quantified microarray data were Lowess normalied within pintip groups and within arrays, then variation due to arrays and dyes was removed by a random effects model, and averaged, in log space, using R/MAANOVA (MicroArray ANalysis Of VAriance) (Wu et al. 2003). Oligo sequences of CATMA array probes were mapped to individual mRNA sequences of transcripts from the TAIR9 genome assembly using BLASTn with e-value cutoff of 0.01.  Additionally, alignments were filtered to exclude alignments shorter than 30bp or with less than 80% sequence identity.

label: Cy3, Cy5

organism: Arabidopsis thaliana

source_name: Mock 46 hours

label_protocol: Cy3 and Cy5 labelled cDNA probes were prepared by reverse transcribing 5µg of aRNA with Cy3- or Cy5- dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50µl hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 0.5µg/µl yeast tRNA [Invitrogen]).

growth_protocol: Arabidopsis plants Col-0 were grown under a 16:8 hr light:dark cycle (lights on 04:00 to 20:00) at 20°C, 60% humidity and light intensity of 100 μmol photons.m-2.s-1. Arabidopsis seed was stratified for three days in 0.1% agar at 4°C before sowing onto Arabidopsis soil mix (Scotts Levingtons F2s compost:sand:fine grade vermiculite in a ratio of 6:1:1).

extract_protocol: Total RNA was isolated from four individual leaves from each sampled time point (arbitrarily labelled as biological replicates A, B, C and D) using TRIzol reagent (Invitrogen), purified with RNeasy columns (Qiagen) and amplified using the MessageAmp II aRNA Amplification kit (Ambion) in accordance with the kit protocol with a single round of amplification.

treatment_protocol: Botrytis cinerea strain pepper1 was sub-cultured on sterile tinned apricot halves in Petri dishes two weeks prior to use of the spores. Sub-cultures were incubated in the dark at 25°C. Spore inoculums were prepared by harvesting spores in water, filtration through glass wool to remove hyphae and suspension in half strength sterile grape juice (Tesco’s Own) to a concentration of 1 x 105 spores/ml. Leaf 7 was tagged on 192, 25-day-old plants. Three days later, leaf 7 from each of these plants was detached and placed on a bed of 0.8\% agar in four propagator trays. Half of the leaves were inoculated with 5-7 (depending on the size of the leaf) 10 μl droplets of B. cinerea inoculum so that droplets were evenly spaced over the leaf. The remaining 96 leaves were mock-inoculated with 5-7 10 μl droplets of sterile half strength grape juice. Each tray contained 24 infected and 24 uninfected leaves randomly arranged. Trays were covered with lids and kept under the same conditions as for plant growth, except the relative humidity was raised to 90%. Leaves were inoculated at 10:30 (time 0). Single infected and control leaves were sampled in a randomised manner from each of the four trays every 2 hours over 48 hours. This gave 4 biological repeats (i.e. 4 individual leaves) for both infected and control treatments at each of the 24 time points. Whole leaf samples were snap frozen in liquid nitrogen at the time of harvesting and stored at -80°C.

tag: infection

value: mock

tag: time

value: 46 hours

tag: ecotype

value: leaves


title: Mock 48 hours

source_name: Mock 48 hours

value: 48 hours


title: Mock 40 hours

source_name: Mock 40 hours

value: 40 hours


title: Sporadic Ovarian cancer sample58

description: standard dual color hybridization

value: Sporadic

source_name: patient-matched normal ovarian tissue

value: ovary

value: patient-matched normal ovarian tissue


title: BRCA1 Ovarian cancer sample60

description: standard dual color hybridization


title: Sporadic Ovarian cancer sample57

description: standard dual color hybridization


title: Sporadic Ovarian cancer sample56

description: standard dual color hybridization


title: BRCAX Ovarian cancer sample55

description: standard dual color hybridization


title: Mock 36 hours

source_name: Mock 36 hours

value: 36 hours


title: Mock 44 hours

source_name: Mock 44 hours

value: 44 hours


title: Sporadic Ovarian cancer sample54


title: Sporadic Ovarian cancer sample53


title: Sporadic Ovarian cancer sample51

description: standard dual color hybridization


title: Mock 38 hours

source_name: Mock 38 hours

value: 38 hours


title: Mock 42 hours

source_name: Mock 42 hours

value: 42 hours


title: Mock 24 hours

source_name: Mock 24 hours

value: 24 hours


title: Sporadic Ovarian cancer sample49

description: standard dual color hybridization

value: ovarian carcinoma

value: ovarian tumor


title: Sporadic Ovarian cancer sample50

value: blood

value: pooled  blood healthy women


title: Mock 26 hours

source_name: Mock 26 hours

value: mock

value: 26 hours


title: BRCAX Ovarian cancer sample52

description: standard dual color hybridization

value: BRCAX

source_name: patient-matched peripheral  blood

value: patient-matched peripheral  blood


title: Mock 28 hours

source_name: Mock 28 hours

value: 28 hours

value: leaves


title: Sporadic Ovarian cancer sample46

description: standard dual color hybridization

value: Sporadic

value: ovary


title: Mock 32 hours

source_name: Mock 32 hours

value: 32 hours


title: Mock 20 hours

source_name: Mock 20 hours

value: 20 hours


title: Sporadic Ovarian cancer sample48

description: standard dual color hybridization

value: patient-matched normal ovarian tissue


title: Mock 22 hours

source_name: Mock 22 hours

value: 22 hours


title: Mock 34 hours

source_name: Mock 34 hours

value: 34 hours


title: Sporadic Ovarian cancer sample47

description: standard dual color hybridization

source_name: ovarian tumour

value: ovarian carcinoma


title: Sporadic Ovarian cancer sample44

description: standard dual color hybridization

value: ovarian tumor


title: BRCAX Ovarian cancer sample43

description: standard dual color hybridization

value: blood


title: BRCA1 Ovarian cancer sample41

description: standard dual color hybridization

source_name: pooled  blood healthy women

value: pooled  blood healthy women


title: BRCAX Ovarian cancer sample42

description: standard dual color hybridization


title: Mock 16 hours

source_name: Mock 16 hours

value: mock

value: 16 hours


title: Mock 30 hours

source_name: Mock 30 hours

value: 30 hours


title: Mock 10 hours

source_name: Mock 10 hours

value: 10 hours


title: BRCA2 Ovarian cancer sample45

description: standard dual color hybridization


title: Mock 14 hours

source_name: Mock 14 hours

value: 14 hours


title: Mock 6 hours

source_name: Mock 6 hours

value: 6 hours

value: leaves


title: BRCAX Ovarian cancer sample39

description: standard dual color hybridization

value: BRCAX

source_name: patient-matched normal ovarian tissue

value: ovary


title: Mock 18 hours

source_name: Mock 18 hours

value: 18 hours


title: Sporadic Ovarian cancer sample38

description: standard dual color hybridization

value: Sporadic

value: patient-matched normal ovarian tissue


title: BRCAX Ovarian cancer sample28

description: standard dual color hybridization

value: patient-matched peripheral  blood


title: BRCAX Ovarian cancer sample35

description: standard dual color hybridization

value: ovarian carcinoma


title: Sporadic Ovarian cancer sample33

description: standard dual color hybridization

value: ovarian tumor


title: BRCAX Ovarian cancer sample32

description: standard dual color hybridization

value: blood


title: Sporadic Ovarian cancer sample36

description: standard dual color hybridization


title: BRCAX Ovarian cancer sample31

description: standard dual color hybridization


title: Mock 8 hours

source_name: Mock 8 hours

value: 8 hours


title: Mock 12 hours

source_name: Mock 12 hours

value: mock

value: 12 hours


title: BRCA1 Ovarian cancer sample26

description: standard dual color hybridization


title: BRCAX Ovarian cancer sample37

description: standard dual color hybridization

value: pooled  blood healthy women


title: BRCAX Ovarian cancer sample30

description: standard dual color hybridization


title: BRCA2 Ovarian cancer sample27

description: standard dual color hybridization

source_name: patient-matched peripheral  blood


title: BRCA1 Ovarian cancer sample24

description: standard dual color hybridization


title: BRCAX Ovarian cancer sample22

description: standard dual color hybridization


title: BRCAX Ovarian cancer sample20

description: standard dual color hybridization


title: BRCA1 Ovarian cancer sample25

description: standard dual color hybridization


title: BRCAX Ovarian cancer sample29

description: standard dual color hybridization


title: BRCA1 Ovarian cancer sample21

description: standard dual color hybridization


title: BRCA1 Ovarian cancer sample34

description: standard dual color hybridization


title: BRCA1 Ovarian cancer sample19

description: standard dual color hybridization


title: BRCAX Ovarian cancer sample40

description: standard dual color hybridization


title: BRCA2 Ovarian cancer sample23

description: standard dual color hybridization


title: BRCA1 Ovarian cancer sample17

description: standard dual color hybridization


title: BRCAX Ovarian cancer sample13

description: standard dual color hybridization


title: Mock 2 hours

source_name: Mock 2 hours

value: 2 hours


title: BRCAX Ovarian cancer sample18

description: standard dual color hybridization


title: BRCA1 Ovarian cancer sample12

description: standard dual color hybridization


title: Botrytis 46 hours

source_name: Botrytis 46 hours

value: Botrytis cinerea strain pepper1

value: 46 hours


title: Mock 4 hours

source_name: Mock 4 hours

value: 4 hours

value: leaves


title: BRCA1 Ovarian cancer sample11

description: standard dual color hybridization


title: BRCA2 Ovarian cancer sample15

description: standard dual color hybridization

value: ovary


title: BRCAX Ovarian cancer sample7

description: standard dual color hybridization

value: BRCAX


title: BRCAX Ovarian cancer sample16

description: standard dual color hybridization


title: BRCAX Ovarian cancer sample10

description: standard dual color hybridization


title: Botrytis 48 hours

source_name: Botrytis 48 hours

value: 48 hours


title: BRCAX Ovarian cancer sample6

description: standard dual color hybridization

value: patient-matched normal ovarian tissue


title: Botrytis 44 hours

source_name: Botrytis 44 hours

value: 44 hours


title: Botrytis 42 hours

source_name: Botrytis 42 hours

value: 42 hours


title: Botrytis 38 hours

source_name: Botrytis 38 hours

value: 38 hours


title: BRCAX Ovarian cancer sample9

description: standard dual color hybridization

source_name: ovarian tumour

value: ovarian carcinoma

value: ovarian tumor

source_name: pooled  blood healthy women

value: blood


title: Botrytis 40 hours

source_name: Botrytis 40 hours

value: 40 hours


title: BRCA1 Ovarian cancer sample5

description: standard dual color hybridization

value: pooled  blood healthy women


title: BRCA1 Ovarian cancer sample4

description: standard dual color hybridization

value: patient-matched peripheral  blood


title: BRCAX Ovarian cancer sample1

description: standard dual color hybridization


title: BRCA2 Ovarian cancer sample3

description: standard dual color hybridization


title: BRCA1 Ovarian cancer sample2

description: standard dual color hybridization


title: Botrytis 36 hours

source_name: Botrytis 36 hours

value: Botrytis cinerea strain pepper1

value: 36 hours


title: Botrytis 34 hours

source_name: Botrytis 34 hours

value: 34 hours


title: ΔsigF vs WT- rep3

city: Greifswald

first: Christian

last: Kohler

address: F.-L.-Jahnstrasse 15

department: Department of Microbiology

country: Germany

institute: EMAU

description: 251693810022_sigF deletion- rep3

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: Data were extracted and normalized using Agilent Feature Extraction Software 9.0. Agilent output files were then opened using Excell and the log10 values extracted with no additional processing or filtering

organism: Caulobacter vibrioides NA1000

source_name: WT- dichromate

label_protocol: standard Cy3-dCTP and Cy5-dCTP incorporations  standard Cy3-dCTP incorporation  standard Cy3-dCTP incorporation  standard Cy3-dCTP incorporation

growth_protocol: Overnight cultures were diluted in fresh minimal medium supplemented with glucose to OD= 0.1

treatment_protocol: Exponentially growing cells were exposed to 55 μM potassium dichromate for 30 min

value: wild type

tag: exposed to

value: 55 μM potassium dichromate for 30 min

source_name: ΔsigF- dichromate

value: ΔsigF mutant


title: Botrytis 24 hours

source_name: Botrytis 24 hours

value: 24 hours

value: leaves


title: Botrytis 30 hours

source_name: Botrytis 30 hours

value: 30 hours


title: Hepatocyte AH4

city: Bethesda

first: Daekwan

last: Seo

address: 37 Convent Dr. Rm 4140

department: NCI

institute: NIH

description:
Donor Cells
replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed by using Gene Expression Module v 1.1.1 in Genome Studio V2009.1 from illumina, Inc. The background noise was substrated and quantile normalization was applied.

organism: Mus musculus

source_name: Hepatocyte

label_protocol: Biotinylated cRNA were prepared with the Ambion Totalprep RNA Amplification kit for Illumina arrays

growth_protocol: All experiments were conducted according to the National Institutes of Health (NIH) guidelines for animal care and following a study protocol approved by the National Cancer Institute (NCI) Animal Care and Use Committee. Mice had free access to food and water.

extract_protocol: Total RNA was extracted with Quiagen Rneasy Kit. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyser.

treatment_protocol: HB isolated from a pool of fetal (ED16.5) livers were purified using MACS system and hepatoblast-specific E-cadherin antibody. The cells were cultured in 100-mm dish at 75% confluence and transfected with a mixture of DNA containing 4 μg of pLentG-KOSM, 3.5 μg of pCMV-VSVG, and 2 μg of psPAX2 by Fugene HD. Twenty-four hours after transfection, the supernatant of transfected cells was collected and filtered through a 0.45 μm pore-size filter. The filtered lentiviral particles were concentrated by ultracentrifugation. For virus infection, mouse embryonic fibroblast (MEF) and mouse hepatic lineage cells were seeded in a 6-well plate at 1 × 105 cells per well one day before transduction. The medium was replaced with virus-containing supernatant, incubated for 2-3 hr and then cultured up to 7days with fresh media. For iPSC induction, the infected cells were trypsinized at day 7, plated in 1:5 ratio into six well plates containing feeder cells and incubated until appearance of ES-like cells.

tag: cell type

value: Hepatocyte

tag: genetic background


title: Botrytis 32 hours

source_name: Botrytis 32 hours

value: 32 hours


title: Botrytis 18 hours

source_name: Botrytis 18 hours

value: 18 hours


title: ΔsigF vs WT- rep1

description: 251693810013_sigF deletion- rep1


title: Hepatocyte AH3

description:
Donor Cells
replicate 3


title: Embryonic Stem Cell mES3

description:
Mouse Embryonic Stem Cells
replicate 3

source_name: Embryonic Stem Cell

value: Embryonic Stem Cell


title: Botrytis 20 hours

source_name: Botrytis 20 hours

value: 20 hours


title: Embryonic Stem Cell mES1

description:
Mouse Embryonic Stem Cells
replicate 1


title: Hepatocyte AH1

description:
Donor Cells
replicate 1


title: Botrytis 26 hours

source_name: Botrytis 26 hours

value: 26 hours


title: Embryonic Stem Cell mES4

description:
Mouse Embryonic Stem Cells
replicate 4


title: Botrytis 28 hours

source_name: Botrytis 28 hours

value: 28 hours


title: Hepatoblast HB4

description:
Donor Cells
replicate 2

source_name: Hepatoblast

value: Hepatoblast


title: Embryonic Stem Cell mES2

description:
Mouse Embryonic Stem Cells
replicate 2


title: Hepatocyte AH2

description:
Donor Cells
replicate 2


title: ΔsigF vs WT- rep2

description: 251693810014_sigF deletion- rep2


title: Botrytis 22 hours

source_name: Botrytis 22 hours

value: Botrytis cinerea strain pepper1

value: 22 hours


title: Botrytis 16 hours

source_name: Botrytis 16 hours

value: 16 hours


title: 22Rv1 parental sensitive 3

city: New York

first: Josep

last: Domingo-Domenech

state: New York

address: Annenberg Building, Room 24-16

department: Pathology

institute: Mount Sinai School of Medicine

description:
22RV1 3
Gene expression data from 22Rv1 parental Docetaxel-sensitive cells.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix Human U133 Plus 2.0 or Affymetrix Human U133A 2.0 arrays.

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

data_processing: The data were analyzed with Microarray Suite, MicroDB, and Data Mining tool software (Affymetrix). Quantile normalization and RMA summarization were used to obtain probeset level expression.

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

growth_protocol: Parental Docetaxel-sensitive and resistant cells were grown with RPMI supplemented with 10% FBS alone or under exposure to Docetaxel, respectively, before harvesting total RNA.

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

tag: cell line

value: prostate cancer cells

tag: phenotype

value: docetaxel sensitive


title: 22Rv1 Docetaxel resistant 3

description:
22Rv1-DR 3
Gene expression data from 22Rv1 Docetaxel-resistant cells.

source_name: 22Rv1 Docetaxel-resistant cells

value: docetaxel resistant


title: Botrytis 14 hours

source_name: Botrytis 14 hours

value: 14 hours


title: Hepatoblast HB3

description:
Donor Cells
replicate 1


title: Hepatoblast HB2

description:
Donor Cells
replicate 4


title: Hepatoblast HB1

description:
Donor Cells
replicate 3


title: Botrytis 10 hours

source_name: Botrytis 10 hours

value: 10 hours

value: leaves


title: Fibroblast Derived iPSC mEF-iPSC4

description:
iPSC
replicate 4

source_name: Fibroblast Derived iPSC

value: Fibroblast Derived iPSC


title: HSC-3_vector_48hr culture_rep2

city: Helsinki

first: Suvi-Tuuli

last: Vilen

address: Haartmaninkatu 8

department: Dentistry

country: Finland

institute: University of Helsinki

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

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

data_processing: MAS5-analysis was done to the data.  Scaling parameters: scale to all probe sets; TGT 100. Detection parameters: Alpha1 0.05, Alpha2 0.065, Tau 0.015.

source_name: HSC-3 cell line with control vector

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

growth_protocol: Trypsin-2 overexpressing HSC-3 cells and control vector HSC-3 cells were cultured 48 h in a humid atmosphere of 5% CO2 and 95% air at 37°C in 1:1 DMEM (Lonza) and Ham’s Nutritient Mixture F-12 supplemented with 10% heat-inactivated fetal calf serum, 1 mM natrium pyruvate, 250 ng/ml fungizone (Invitrogen), 100 units/ml penicillin, 100 µg/ml streptomycin, 2 mM L-Glutamine and 0.4 ng/ml hydrocortisone (Sigma-Aldrich ).

extract_protocol: RNA was extracted by Qiagen RNeasy mini kit according to the manufacturer's instruction.

treatment_protocol: Cells were trypsinized, washed tree times with PBS and stored in -80 C.

value: human tongue squamous cell carcinoma

tag: genotype/variation

value: control vector (no trypsin-2 expression)


title: Fibroblast mEF3

description:
Donor Cells
replicate 3

source_name: Fibroblast

value: Fibroblast


title: Fibroblast Derived iPSC mEF-iPSC3

description:
iPSC
replicate 3


title: Fibroblast mEF4

description:
Donor Cells
replicate 4


title: HSC-3_vector_48hr culture_rep3


title: Fibroblast mEF1

description:
Donor Cells
replicate 1


title: HSC-3_vector_48hr culture_rep1


title: Fibroblast mEF2

description:
Donor Cells
replicate 2


title: DU145 Docetaxel resistant 3

description:
DU145-DR 3
Gene expression data from DU145 Docetaxel-resistant cells.

source_name: DU145 Docetaxel-resistant cells


title: Fibroblast Derived iPSC mEF-iPSC2

description:
iPSC
replicate 2


title: DU145 parental sensitive 3

description:
DU145 3
Gene expression data from DU145 parental Docetaxel-sensitive cells.


title: HSC-3_TAT-2_48hr culture_ rep3

source_name: trypsin-2 overexpressing HSC-3 cell line

value: overexpressing trypin-2


title: Botrytis 6 hours

source_name: Botrytis 6 hours

value: 6 hours


title: HSC-3_TAT-2_48hr culture_ rep2


title: BRCA1 Ovarian cancer sample14

description: standard dual color hybridization

source_name: ovarian tumour

value: ovarian carcinoma

value: ovarian tumor

source_name: patient-matched normal ovarian tissue

value: ovary

value: patient-matched normal ovarian tissue


title: Botrytis 12 hours

source_name: Botrytis 12 hours

value: Botrytis cinerea strain pepper1

value: 12 hours


title: Botrytis 4 hours

source_name: Botrytis 4 hours

value: 4 hours


title: Botrytis 2 hours

source_name: Botrytis 2 hours

value: 2 hours


title: Botrytis 8 hours

source_name: Botrytis 8 hours

value: 8 hours


title: ExVivoIslet_24hr_vehicle_rep1

city: Yokohama

first: Jun

last: Shirakawa

state: Kanagawa

address: 3-9, Fuku-ura, Kanazawa-ku

country: Japan

institute: Yokohama City university

description: Gene expression after 24hr in vehicle-treated mouse islets

hyb_protocol: Cy3-labelled cRNA was fragmented by using Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Gene Expression Microarrays (G2519F) in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed with GE Wash Buffer 1 (Agilent) and GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters.

source_name: isolated pancreatic islets, 24hr, vehicle, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

extract_protocol: RNA was prepared using the Rneasy total RNA extraction kit (QIAGEN) following the manufacturer's recommendations.

treatment_protocol: Isolated pancreatic islets of 8-weeks old C57BL/6 mice were cultured in 5.6 mM glucose RPMI1640 medium, in the presence of 30 microM GKA or vehicle (DMSO) for 24 hours.

tag: strain

value: pancreatic islet

tag: treatment

value: vehicle


title: ExVivoIslet_24hr_GKA_rep1

description: Gene expression after 24hr in GKA-treated mouse islets

source_name: isolated pancreatic islets, 24hr, GKA, replicate 1

tag: tissue

value: GKA


title: Fibroblast Derived iPSC mEF-iPSC1

description:
iPSC
replicate 1

value: Fibroblast Derived iPSC


title: ExVivoIslet_24hr_GKA_rep2

source_name: isolated pancreatic islets, 24hr, GKA, replicate 2


title: ExVivoIslet_24hr_vehicle_rep2

source_name: isolated pancreatic islets, 24hr, vehicle, replicate 2


title: BRCAX Ovarian cancer sample8

description: standard dual color hybridization

value: BRCAX


title: HSC-3_TAT-2_48hr culture_ rep1

value: human tongue squamous cell carcinoma


title: untagged MYC

city: San Francisco

first: Jose

middle: Christian

last: Perez

department: Microbiology and Immunology

institute: University of California, San Francisco

description: Comparison of IP/input in tagged strains to untagged cells immuniprecipitated with the same antibody.

hyb_protocol: The labeled DNA was purified with Zymo columns (Zymo Research). Equal amounts of ChIP and input DNAs (~3  g each) were mixed and hybridized in a final volume of 500  l containing Agilent hybridization buffer (Agilent), Agilent blocking agent (Agilent), and 50  g of human COT1 DNA (Invitrogen). Arrays were hybridized in a hybridization oven for 40 h at 65 degrees C, and then washed with Agilent Oligo aCGH/ChIP-on-chip wash buffers (Agilent) as described by the manufacturer's protocols..

scan_protocol: Arrays were scanned on a GenePix 4000B scanner following manufacturer's protocol

data_processing: Data normalized using global lowess

organism: Candida albicans

source_name: ChIP DNA from untagged cells

label_protocol: Aminoallyl-dUTP (Ambion) was incorporated into 1-2  g of ChIP and input DNA using Klenow (New England Biolabs) and random DNA nonamers. Dye coupling was carried out by incubating 4-5  g of aminoallyl-dUTP-labeled ChIP and input DNAs with Cy5 or Cy3, respectively.

growth_protocol: Cells were scrapped off Todd Hewitt agar plates after 24h growth at 37 degrees C.

extract_protocol: Formaldehyde (1% final concentration) was added to 200 ml of Candida albicans cultures at OD600 ~0.5. After crosslinking (15 min), glycine (125 mM final concentration) was added to qench the reaction. Cells were washed twice with 1X TBS and lysed by vortexing for ~2h at 4 degrees C in a suspension containing glass beads. Chromatin was sheared in a Diagenode Bioruptor and immuniprecipitated with the respective antibody.

treatment_protocol: No treatment

tag: chip antibody

value: anti-human c-myc

tag: antibody vendor/catalog

value: Invitrogen, AHO0062

source_name: input DNA from untagged cells

treatment_protocol: no treatment

value: input DNA


title: untagged GFP

growth_protocol: Cells were grown in liquid YPD to logarithmic phase at 30 degrees C,

value: GFP

value: Clontech, 632460


title: Smoker 4

city: Iowa City

first: Thomas

middle: B

last: Bair

state: IA

address: 335 EMRB

institute: University of Iowa

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Affymetrix Human Exon 1.0 ST arrays (Part No. 900650), and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 GeneChip Hybridization Oven. Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), and signal amplified with anti-streptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.

scan_protocol: Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade, and data were collected using the GeneChip Operating Software (GCOS) v1.4.

data_processing:
CEL files were imported into PartekGS version 6.5 and normalized using the standard RMA workflow. The gene values were obtained using mean value summarization.

Genome build: hg18
Exons used in analysis: core
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Alveolar macrophages, smoker

label_protocol: Microarray hybridizations were performed at the University of Iowa DNA Facility.  Briefly, 25 nanograms total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN QIAquick PCR Purification column (QIAGEN Cat #28104) according to modifications from NuGEN.  Four ug of SPIA amplified DNA were used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.  Five micrograms of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

extract_protocol: RNA was isolated from alveolar macrophages using the MirVana (Applied Biosystems (ABI), Austin, TX) reagents according to the manufacturer's instructions.

value: alveolar macrophages

tag: smoker

value: yes

tag: pack years


title: Smoker 3


title: GFP-LYS14

source_name: LYS14 ChiP DNA from GFP-LYS14 cells

tag: tagged gene

source_name: input DNA from GFP-LYS14 cells

tag: sample type


title: Smoker 1


title: Hepatoblast Derived iPSC HB-iPSC1

description:
iPSC
replicate 1

source_name: Hepatoblast Derived iPSC

value: Hepatoblast Derived iPSC


title: GFP-LYS144

source_name: LYS144 ChiP DNA from GFP-LYS144 cells

source_name: input DNA from GFP-LYS144 cells


title: Smoker 2


title: 9216-mutant-OF

city: Kansas City

first: Shuyi

last: Chen

state: MO

institute: Stowers Institute for Medical Research

description: gene expression profile of FGFR mutant optic fissure

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

scan_protocol: GeneChips were scanned using the Affymetrix 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 100.

source_name: E11.5 optic fissue-FGFR mutant

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

growth_protocol: time-mated mice

treatment_protocol: embryos are collected at E11.5

tag: age

value: optic fissure


title: GFP-ZCF21

source_name: ZCF21 ChiP DNA from GFP-ZCF21 cells

growth_protocol: Cells were grown in Todd Hewitt Broth to logarithmic phase at 30 degrees C,

source_name: input DNA from GFP-ZCF21 cells


title: Non-smoker 3

source_name: Alveolar macrophages, non-smoker

value: no


title: Hepatoblast Derived iPSC HB-iPSC3

description:
iPSC
replicate 3


title: Hepatoblast Derived iPSC HB-iPSC4

description:
iPSC
replicate 4


title: Hepatocyte Derived iPSC AH-iPSC4

description:
iPSC
replicate 4

source_name: Hepatocyte Derived iPSC

value: Hepatocyte Derived iPSC


title: 9216-control-OF

description: gene expression profile of normal optic fissure

source_name: E11.5 optic fissue-WT


title: Hepatoblast Derived iPSC HB-iPSC2

description:
iPSC
replicate 2


title: Hepatocyte Derived iPSC AH-iPSC3

description:
iPSC
replicate 3


title: Non-smoker 4


title: RTG1-MYC

source_name: RTG1 ChiP DNA from RTG1-MYC cells

source_name: input DNA from RTG1-MYC cells


title: RTG3-MYC

source_name: RTG3 ChiP DNA from RTG3-MYC cells

source_name: input DNA from RTG3-MYC cells


title: 9266-control-OF


title: HMS1-MYC

source_name: HMS1 ChiP DNA from HMS1-MYC cells

growth_protocol: Cells were scrapped off YPD agar plates after 24h growth at 37 degrees C.

source_name: input DNA from HMS1-MYC cells


title: Hepatocyte Derived iPSC AH-iPSC2

description:
iPSC
replicate 2


title: 8711-mutant-OF


title: Intestinal vs. control SmedArray2-Biorep4

status: Public on Oct 01 2012

city: Urbana

first: Noelle

last: James

state: IL

address: 601 S. Goodwin Ave.

department: Cell and Developmental Biology

institute: U of IL / HHMI

description: This is the fourth of four biological replicates used in this experiment, each prepared separately.

hyb_protocol: Labeled aRNA targets were hydrolyzed using RNA Fragmentation Reagents (Ambion/Applied Biosystems) according to the manufacturerʼs instructions.  Combimatrix arrays were hydrated, prehybridized, hybridized, and washed according to the manufacturerʼs protocols.

scan_protocol: Arrays were covered with Imaging Solution and a LifterSlip, and imaged using a GenePix 4000B Scanner and GenePix Pro 6.0 software (Axon Instruments/Molecular Devices).

data_processing: GenePix “.gpr” files were processed using the limma package in Bioconductor (Gentleman et al., 2004; Smyth, 2004). Within-array loess normalization was conducted with the normexp background correction method (Ritchie et al., 2007) and an offset value of 25; the scale method was utilized for between-array normalization. Normalized values for each spot were fitted to a linear model, and moderated t-statistics and adjusted p-values were calculated for each probe on the array.

label: Alexa Fluor 647

organism: Schmidtea mediterranea

source_name: Intestine

label_protocol: ~12 μg aminoallyl-labeled aRNA were coupled to Alexa Fluor 555 or Alexa Fluor 647 succinimidyl ester dyes (Molecular Probes) and purified according to the MessageAmp II protocol. Labeling efficiency was calculated using a NanoDrop spectrophotometer.

growth_protocol: Asexual Schmidtea mediterranea were maintained in 1X Montjuic salts at 21°C (Cebrià  et al., 2005)

extract_protocol: All intestinal cells (2-5 x 10^5) and ~10% of non-intestinal cells (1-3 x 10^6)  were lysed in Trizol (Invitrogen). RNA was isolated according to the manufacturerʼs instructions, using the high-salt step for RNA precipitation. RNA was DNAse-treated, purified, and concentrated using the DNA-free RNA kit (Zymo Research). 500 ng of total RNA were amplified using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion).

treatment_protocol: One hundred large planarians were fed a mixture of liver homogenate, food coloring, and Feridex (AMAG Pharmaceuticals). Forty-eight hours later, animals were dissociated into single cell suspensions essentially as described (Reddien et al., 2005), with the exception that dispase (Worthington Biochemical, final 0.6U/mL) was substituted for trypsin. Intestinal phagocytes were purified on Miltenyi magnetic columns.

value: Intestinal phagocytes

value: asexual

label: Alexa Fluor 555

source_name: Control

value: non-intestinal cells (column flow-through)


title: 9266-mutant-OF


title: Hepatocyte Derived iPSC AH-iPSC1

description:
iPSC
replicate 1


title: Intestinal vs. control SmedArray2-Biorep3

description: This is the third of four biological replicates used in this experiment, each prepared separately.


title: 8711-control-OF


title: Non-smoker 2


title: Non-smoker 1


title: Day 1 - AM - Bioreactor Run 4 - HTCB - mAdbID:106971

city: Baltimore

first: Bhargavi

last: Kondragunta

address: 1000 Hilltop circle

department: Chemical and Biochemical Engineering

institute: University of Maryland Baltimore County

description: mAdb experiment ID: 106971

hyb_protocol: Hybridization Protocol Other: Polylysine coated glass slides with 36,055 mouse genome chip from Operon were used. These slides included some repeat spots for internal control and were obtained from NCI/CBER microarray facility (Bethesda, MD). The Maui mixing chamber (Biomicro, Salt Lake City, UT) was used for hybridization, with flow-volume of 42 µL. Ambion hybridization buffer was pre-heated to 42oC and 24µL of the buffer was added to 24µL of the clean coupled probe, and injected into the Maui hybridization chamber (Biomicro). The slide was incubated overnight at 42oC, washed with 1X SSC buffer. After the overnight hybridization period, the MAUI mixers were disassembled and the arrays were washed in series with 1X SSC (0.05% SDS) and 0.1X SSC, each for 4 minutes.

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.09;; 3.66 Temperature: 28.19 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.

data_processing:
Data Processing Protocol
Calculation Method: A total of 14589 genes were found to be expressed in the samples tested. This was based on signal filter of >100, and signal to background above 1 standard deviation, as well as size filter for the spots, along with the spot mapping to GAL (NCI Production Gene Array List Files, NIH) files. Lowess normalization (Yang, 2002) was used on the raw data to correct for intensity based bias in 2-color data. In addition 25 bad or not-found genes were filtered out and omitted from gene analysis to avoid false positives.

source_name: Universal Mouse Reference

label_protocol:
Cy3 Labeling Protocol
Other: After reverse transcription of mRNA to cDNA, the cDNA was purified by removing the remaining t-RNA and r-RNA using the Minelute (Qiagen) kit. The probe was eluted using 12 µL of elution buffer. 5µL of coupling buffer(0.2M NaHCO3, pH 9) was added to each sample, and fluorescently labeled with 15 µL of Cy3 dye for the reference sample, and incubated in the dark for 90 minutes. Residual dye was removed afterwards using the same MinElute PCR Purification Kit. Following incubation, the probe was cleaned up to remove residual dye using the Qiagen MinElute kit.

extract_protocol:
Becton-Dickinson Extraction Protocol
Other: not available

tag: reference

value: All-inclusive universal mouse reference RNA pool (Becton, Dickinson, and Co., Franklin Lakes, NJ).

source_name: Day1-AM -HTCB

label_protocol:
HyPer5 Labeling Protocol
Other: After reverse transcription of mRNA to cDNA, the cDNA was purified by removing the remaining t-RNA and r-RNA using the Minelute (Qiagen) kit. The probe was eluted using 12 µL of elution buffer. 5µL of coupling buffer(0.2M NaHCO3, pH 9) was added to each sample, and fluorescently labeled with 15 µL of HyPer5 dye(Amersham, Piscataway, NJ) for the test samples, and incubated in the dark for 90 minutes. Residual dye was removed afterwards using the same MinElute PCR Purification Kit. Following incubation, the probe was cleaned up to remove residual dye using the Qiagen MinElute kit.

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA from the cells was extracted with Trizol (Gibco Brand, Carlsbad, CA) and chloroform (Mallinckrodt, Phillipsburg, NJ), and purified using the RNeasy Mini-Prep Kit (Qiagen Inc., Valencia, CA).

treatment_protocol:
Treatment time: 18-20 hours
In-vitro treatment: For the experiments reported here, each of the biological replicates had cells thawed and passaged for 6-8 passages prior to 5L experimentation. The 5L bioreactor with 4.5L working volume was inoculated at 2.0±0.5 x 105 cells/mL. The culture was allowed to mix well for up to 30 minutes in the 5L bioreactor, following which it was transferred in a sterile manner to minibioreactors (HTCB). Samples were taken for microarray analysis twice daily, approximately 12 hours apart, at the following time-points for all biological replicates - day 1am (18-20 hours), day 2am (42-44 hours), day 3am (67-69 hours), day 3pm (78-80 hours), day 4am (90-92 hours), and day 4pm (102-104 hours). It is to be noted that the last sample used for microarrays was obtained when the culture viability was >80% viability. The samples were used for measuring (1) cells count and viability using a hemocytometer with trypan blue dye (2) ELISA (3) glucose and lactate concentration and (4) Cell pellet for microarrays.

value: A Sp2/0 myeloma based mouse hybridoma cell line (2055.5) secreting an anti-meningitidis-capsular-polysaccharide (anti-MCPS) IgG3 (Rubinstein LJ 1988) was used as the experimental cell line.


title: Day 1 - AM - Bioreactor Run 1 - HTCB - mAdbID:106968

description: mAdb experiment ID: 106968

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.11;; 3.66 Temperature: 27.79 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.


title: Day 4 - PM - Bioreactor Run 3 - HTCB - mAdbID:106659

description: mAdb experiment ID: 106659

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.12;; 3.7 Temperature: 29.29 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.

source_name: Day4-PM -HTCB

treatment_protocol:
Treatment time: 102-104 hours
In-vitro treatment: For the experiments reported here, each of the biological replicates had cells thawed and passaged for 6-8 passages prior to 5L experimentation. The 5L bioreactor with 4.5L working volume was inoculated at 2.0±0.5 x 105 cells/mL. The culture was allowed to mix well for up to 30 minutes in the 5L bioreactor, following which it was transferred in a sterile manner to minibioreactors (HTCB). Samples were taken for microarray analysis twice daily, approximately 12 hours apart, at the following time-points for all biological replicates - day 1am (18-20 hours), day 2am (42-44 hours), day 3am (67-69 hours), day 3pm (78-80 hours), day 4am (90-92 hours), and day 4pm (102-104 hours). It is to be noted that the last sample used for microarrays was obtained when the culture viability was >80% viability. The samples were used for measuring (1) cells count and viability using a hemocytometer with trypan blue dye (2) ELISA (3) glucose and lactate concentration and (4) Cell pellet for microarrays.


title: Day 4 - AM - Bioreactor Run 3 - HTCB - mAdbID:106658

description: mAdb experiment ID: 106658

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.11;; 3.7 Temperature: 29.07 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.

source_name: Day4-AM -HTCB

treatment_protocol:
Treatment time: 90-92 hours
In-vitro treatment: For the experiments reported here, each of the biological replicates had cells thawed and passaged for 6-8 passages prior to 5L experimentation. The 5L bioreactor with 4.5L working volume was inoculated at 2.0±0.5 x 105 cells/mL. The culture was allowed to mix well for up to 30 minutes in the 5L bioreactor, following which it was transferred in a sterile manner to minibioreactors (HTCB). Samples were taken for microarray analysis twice daily, approximately 12 hours apart, at the following time-points for all biological replicates - day 1am (18-20 hours), day 2am (42-44 hours), day 3am (67-69 hours), day 3pm (78-80 hours), day 4am (90-92 hours), and day 4pm (102-104 hours). It is to be noted that the last sample used for microarrays was obtained when the culture viability was >80% viability. The samples were used for measuring (1) cells count and viability using a hemocytometer with trypan blue dye (2) ELISA (3) glucose and lactate concentration and (4) Cell pellet for microarrays.


title: Day 2 - AM - Bioreactor Run 4 - HTCB - mAdbID:106432

description: mAdb experiment ID: 106432

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.12;; 3.76 Temperature: 29.35 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.

source_name: Day2-AM -HTCB

treatment_protocol:
Treatment time: 42-44 hours
In-vitro treatment: For the experiments reported here, each of the biological replicates had cells thawed and passaged for 6-8 passages prior to 5L experimentation. The 5L bioreactor with 4.5L working volume was inoculated at 2.0±0.5 x 105 cells/mL. The culture was allowed to mix well for up to 30 minutes in the 5L bioreactor, following which it was transferred in a sterile manner to minibioreactors (HTCB). Samples were taken for microarray analysis twice daily, approximately 12 hours apart, at the following time-points for all biological replicates - day 1am (18-20 hours), day 2am (42-44 hours), day 3am (67-69 hours), day 3pm (78-80 hours), day 4am (90-92 hours), and day 4pm (102-104 hours). It is to be noted that the last sample used for microarrays was obtained when the culture viability was >80% viability. The samples were used for measuring (1) cells count and viability using a hemocytometer with trypan blue dye (2) ELISA (3) glucose and lactate concentration and (4) Cell pellet for microarrays.


title: Day 4 - PM - Bioreactor Run 4 - HTCB - mAdbID:106323

description: mAdb experiment ID: 106323

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.1;; 3.69 Temperature: 27.79 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.


title: Day 2 - AM - Bioreactor Run 3 - HTCB - mAdbID:106653

description: mAdb experiment ID: 106653

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.09;; 2.74 Temperature: 27.97 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.


title: Day 4 - AM - Bioreactor Run 2 - HTCB - mAdbID:105832

description: mAdb experiment ID: 105832

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.12;; 3.17 Temperature: 29.99 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.


title: Day 3 - AM - Bioreactor Run 4 - 5L - mAdbID:106269

description: mAdb experiment ID: 106269

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.07;; 3.65 Temperature: 26.57 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.

source_name: Day3-AM -5L

treatment_protocol:
Treatment time: 67-69 hours
In-vitro treatment: For the experiments reported here, each of the biological replicates had cells thawed and passaged for 6-8 passages prior to 5L experimentation. The 5L bioreactor with 4.5L working volume was inoculated at 2.0±0.5 x 105 cells/mL. Samples were taken for microarray analysis twice daily, approximately 12 hours apart, at the following time-points for all biological replicates - day 1am (18-20 hours), day 2am (42-44 hours), day 3am (67-69 hours) and day 3pm (78-80 hours). It is to be noted that the last sample used for microarrays was obtained when the culture viability was >80% viability. The samples were used for measuring (1) cells count and viability using a hemocytometer with trypan blue dye (2) ELISA (3) glucose and lactate concentration and (4) Cell pellet for microarrays


title: Day 2 - AM - Bioreactor Run 3 - 5L - mAdbID:106654

description: mAdb experiment ID: 106654

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.11;; 2.49 Temperature: 29.5 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.

source_name: Day2-AM -5L

treatment_protocol:
Treatment time: 42-44 hours
In-vitro treatment: For the experiments reported here, each of the biological replicates had cells thawed and passaged for 6-8 passages prior to 5L experimentation. The 5L bioreactor with 4.5L working volume was inoculated at 2.0±0.5 x 105 cells/mL. Samples were taken for microarray analysis twice daily, approximately 12 hours apart, at the following time-points for all biological replicates - day 1am (18-20 hours), day 2am (42-44 hours), day 3am (67-69 hours) and day 3pm (78-80 hours). It is to be noted that the last sample used for microarrays was obtained when the culture viability was >80% viability. The samples were used for measuring (1) cells count and viability using a hemocytometer with trypan blue dye (2) ELISA (3) glucose and lactate concentration and (4) Cell pellet for microarrays.


title: Intestinal vs. control SmedArray2-Biorep2

description: This is the second of four biological replicates used in this experiment, each prepared separately.


title: Day 3 - AM - Bioreactor Run 3 - HTCB - mAdbID:106655

description: mAdb experiment ID: 106655

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.13;; 3.68 Temperature: 29.5 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.

source_name: Day3-AM -HTCB

treatment_protocol:
Treatment time: 67-69 hours
In-vitro treatment: For the experiments reported here, each of the biological replicates had cells thawed and passaged for 6-8 passages prior to 5L experimentation. The 5L bioreactor with 4.5L working volume was inoculated at 2.0±0.5 x 105 cells/mL. The culture was allowed to mix well for up to 30 minutes in the 5L bioreactor, following which it was transferred in a sterile manner to minibioreactors (HTCB). Samples were taken for microarray analysis twice daily, approximately 12 hours apart, at the following time-points for all biological replicates - day 1am (18-20 hours), day 2am (42-44 hours), day 3am (67-69 hours), day 3pm (78-80 hours), day 4am (90-92 hours), and day 4pm (102-104 hours). It is to be noted that the last sample used for microarrays was obtained when the culture viability was >80% viability. The samples were used for measuring (1) cells count and viability using a hemocytometer with trypan blue dye (2) ELISA (3) glucose and lactate concentration and (4) Cell pellet for microarrays.


title: Day 3 - AM - Bioreactor Run 3 - 5L - mAdbID:106656

description: mAdb experiment ID: 106656

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.07;; 1.86 Temperature: 28.74 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.


title: Day 1 - AM - Bioreactor Run 3 - HTCB - mAdbID:106651

description: mAdb experiment ID: 106651

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.09;; 2.31 Temperature: 29.32 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.


title: Day 1 - AM - Bioreactor Run 4 - 5L - mAdbID:106533

description: mAdb experiment ID: 106533

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.11;; 3.68 Temperature: 27.73 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.

source_name: Day1-AM -5L

treatment_protocol:
Treatment time: 18-20 hours
In-vitro treatment: For the experiments reported here, each of the biological replicates had cells thawed and passaged for 6-8 passages prior to 5L experimentation. The 5L bioreactor with 4.5L working volume was inoculated at 2.0±0.5 x 105 cells/mL. Samples were taken for microarray analysis twice daily, approximately 12 hours apart, at the following time-points for all biological replicates - day 1am (18-20 hours), day 2am (42-44 hours), day 3am (67-69 hours) and day 3pm (78-80 hours). It is to be noted that the last sample used for microarrays was obtained when the culture viability was >80% viability. The samples were used for measuring (1) cells count and viability using a hemocytometer with trypan blue dye (2) ELISA (3) glucose and lactate concentration and (4) Cell pellet for microarrays.


title: Day 3 - PM - Bioreactor Run 4 - 5L - mAdbID:106270

description: mAdb experiment ID: 106270

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.13;; 3.67 Temperature: 29.01 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.

source_name: Day3-PM -5L

treatment_protocol:
Treatment time: 78-80 hours
In-vitro treatment: For the experiments reported here, each of the biological replicates had cells thawed and passaged for 6-8 passages prior to 5L experimentation. The 5L bioreactor with 4.5L working volume was inoculated at 2.0±0.5 x 105 cells/mL. Samples were taken for microarray analysis twice daily, approximately 12 hours apart, at the following time-points for all biological replicates - day 1am (18-20 hours), day 2am (42-44 hours), day 3am (67-69 hours) and day 3pm (78-80 hours). It is to be noted that the last sample used for microarrays was obtained when the culture viability was >80% viability. The samples were used for measuring (1) cells count and viability using a hemocytometer with trypan blue dye (2) ELISA (3) glucose and lactate concentration and (4) Cell pellet for microarrays.


title: Day 2 - AM - Bioreactor Run 2 - HTCB - mAdbID:105830

description: mAdb experiment ID: 105830

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.11;; 2.32 Temperature: 29.68 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.


title: Day 1 - AM - Bioreactor Run 2 - 5L - mAdbID:106602

description: mAdb experiment ID: 106602

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.04;; 3.31 Temperature: 26.33 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.


title: Day 2 - AM - Bioreactor Run 2 - 5L - mAdbID:105833

description: mAdb experiment ID: 105833

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.13;; 3.26 Temperature: 30.08 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.


title: Day 3 - PM - Bioreactor Run 3 - 5L - mAdbID:106657

description: mAdb experiment ID: 106657

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.09;; 1.76 Temperature: 29.1 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.


title: Day 3 - AM - Bioreactor Run 2 - HTCB - mAdbID:105831

description: mAdb experiment ID: 105831

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.12;; 2.36 Temperature: 29.81 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.


title: Intestinal vs. control SmedArray2-Biorep1

description: This is the first of four biological replicates used in this experiment, each prepared separately.

scan_protocol: Arrays were covered with Imaging Solution and a LifterSlip, and imaged using a GenePix 4000B Scanner and GenePix Pro 6.0 software (Axon Instruments/Molecular Devices).


title: Day 3 - AM - Bioreactor Run 4 - HTCB - mAdbID:106272

description: mAdb experiment ID: 106272

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.09;; 3.68 Temperature: 27.27 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.


title: S2R+cells_rnai_msp_rep2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression study after msp RNAi for 6 days

hyb_protocol: 600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner at 5 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software v 10.5.1.1 of Agilent and Normalized using Agilent GeneSpring GX v 10software.

organism: Drosophila melanogaster

source_name: S2R+ cells, msp RNAi perturbation replicate2

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Drosophila S2R+ cells (Drosophila Genomics Resource Center) cultured in Schneider's Insect Medium (Gibco, Invitrogen, CA) supplemented with 10% FBS at ambient temperature and CO2 levels were used for the study.

extract_protocol: RNA was extracted using Qiagen RNeasy Mini Kit as per the manufacturer’s instructions.

treatment_protocol: Genetic perturbation of nuclear morphology was assayed by a 6 day RNAi mediated gene knockdown of Klaroid (koi, CG18584), Lamin (lam, CG6944) and Msp-300 (msp, CG33715) and contrasted to unperturbed cells.

value: S2R+ cells

value: msp RNAi perturbation


title: S2R+cells_rnai_lam_rep2

description: Gene expression study after lam RNAi for 6 days

source_name: S2R+ cells, lam RNAi perturbation replicate2

value: lam RNAi perturbation


title: S2R+cells_rnai_lam_rep1

source_name: S2R+ cells, lam RNAi perturbation replicate1


title: S2R+cells_rnai_msp_rep1

source_name: S2R+ cells, msp RNAi perturbation replicate1


title: S2R+cells_rnai_koi_rep2

description: Gene expression study after koi RNAi for 6 days

source_name: S2R+ cells, koi RNAi perturbation replicate2

value: koi RNAi perturbation


title: Day 3 - AM - Bioreactor Run 2 - 5L - mAdbID:106603

description: mAdb experiment ID: 106603

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.06;; 2.33 Temperature: 27.03 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.


title: S2R+cells_ctrl_rep1

description: Gene expression study after 6 days

source_name: S2R+ cells, unperturbed replicate1


title: S2R+cells_rnai_koi_rep1

source_name: S2R+ cells, koi RNAi perturbation replicate1


title: SD.RA replicate 2

first: Kirstin

last: Replogle

address: 1206 W Gregory Drive

institute: University of Illinois

hyb_protocol: Samples were suspended in SlideHyb#1 (Ambion), applied to slides in Corning Hybridization Chambers, and incubated O/N at 42C. After hybridization, the slides were washed sequentially in 1X SSC, 0.2% SDS; 0.1X SSC, 0.2% SDS; and 0.1X SSC for 5 minutes each, and spun dry.

scan_protocol: Scanned on an Axon GenePix 4000B scanner Images were quantified using Axon GenePix 6.0.

data_processing: The R/Bioconductor package limma was used with print-tip loess for within array normalization and the Aquantile method for the between array normalization. Data were not background-adjusted.

organism: Zonotrichia leucophrys gambelii

label_protocol: 1 µg of aRNA was primed with 3 µl of 100 µM random hexamer primers at 70C for 10 min, then reversed transcribed at 42C for 16 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM dATP, dCTP, dGTP, 60µM dTTP and 40µM aa-dUTP; RNA was hydrolyzed in the presence of NaOH and EDTA and samples were cleaned up on a spin column. Finally, Cy3 and Cy5 dye esters (GE Healthcare) were coupled to aa-dUTP residues in NaCO3 buffer for 2 hrs at room temp, then neutralized and cleaned on spin columns.

extract_protocol: Experimental samples: Total RNA was extracted using Absolutely RNA Microprep kit (Stratagene). 200ng total RNA was double-amplified using MessageAmp II aRNA kit (Ambion). Universal reference: Total RNA was extracted using Trizol following manufacturer's protocol; samples were Dnase treated and cleaned on a spin column; equal amounts of total RNA from each bird was pooled; total RNA was amplified from this pool using Agilent's Low RNA input linear amplification kit to create sufficient aRNA for 5000 assays.

treatment_protocol: Birds were castrated and synchronized to a Short Day (SD) state to ensure regressed song nuclei, basal levels of Testosterone (T) typical of the non-breeding season, low song rates and unstereotyped song structure, and a low intrinsic spontaneous firing rate in the robust nucleus of the arcopalluim (RA). Then, on Day 0 of the experiment we sacrificed 6 birds. This group of birds, referred to as SD long-term, represents the steady-state of the regressed song control system and served as a baseline for all other groups. We implanted the rest of the birds with a subcutaneous Silastic capsule of T, and shifted them to Long Day (LD) photoperiod. To measure gene expression while the song control system was actively changing from a nonbreeding to a breeding phenotype, 6 birds were sacrificed on each of days 3, 7, and 21 (3LD+T, 7LD+T, and 21LD+T, respectively). By day 21, the song control system has reached its full breeding phenotype, and this time point represents the breeding-state song control system. On Day 21, the subcutaneous T capsules were removed from the remaining birds and they were shifted overnight to SD photoperiod to induce regression of the song control system back to the non-breeding state. On each of days 22 and 23 we sacrificed 6 birds (1SD-T and 2SD-T, respectively) to measure gene expression while the song control system is actively regressing. To control for circadian patterns of gene expression, all birds were sacrificed during the three hour period following their subjective dawn (i.e., lights on).

tag: gender

value: male

value: RA

tag: light

value: Dark cycle:8:16

tag: testosterone at sacrifice

value: No

tag: treatment protocol

value: SD Castrated and photoperiod synchronized control birds, 10 weeks on Short Days (SD), and euthanized.

organism: Taeniopygia guttata

source_name: universal SoNG reference

value: male and female

value: telencephalon

value: Dark cycle:NA

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country


title: 2SD-T.HVC replicate 5

value: HVC

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 2 days.


title: S2R+cells_ctrl_rep2

description: Gene expression study after 6 days

source_name: S2R+ cells, unperturbed replicate2

tag: cell type


title: SD.HVC replicate 6


title: 1SD-T.RA replicate 2

value: 1SD-T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 1 day.


title: 21LD+T.RA replicate 1

value: Dark cycle:20:4

value: Yes

value: 21LD+T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 21 days.


title: 2SD-T.HVC replicate 4

value: 2SD-T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 2 days.


title: 2SD-T.RA replicate 2


title: 7LD+T.RA replicate 1

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 7 days.


title: 2SD-T.RA replicate 4

value: male


title: 1SD-T.HVC replicate 2

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 1 day.


title: 1SD-T.HVC replicate 3

value: Dark cycle:8:16


title: 21LD+T.HVC replicate 5

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 21 days.


title: 3LD+T.HVC replicate 1

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 3 days.


title: 7LD+T.HVC replicate 2

value: male and female


title: 21LD+T.HVC replicate 3

value: telencephalon


title: 3LD+T.RA replicate 6

value: RA

value: Dark cycle:NA


title: 1SD-T.RA replicate 1

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country

value: No


title: 2SD-T.RA replicate 3

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 2 days.


title: SD.RA replicate 6

value: Castrated and photoperiod synchronized control birds, 10 weeks on Short Days (SD), and euthanized.


title: 21LD+T.RA replicate 6

value: Dark cycle:20:4

value: Yes


title: 7LD+T.RA replicate 3


title: 21LD+T.HVC replicate 2

value: HVC

value: 21LD+T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 21 days.


title: 21LD+T.RA replicate 4

value: male


title: 7LD+T.RA replicate6

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 7 days.


title: 7LD+T.HVC replicate 1


title: 7LD+T.HVC replicate 5


title: 3LD+T.RA replicate 2


title: 3LD+T.HVC replicate 2


title: 1SD-T.RA replicate 4

value: Dark cycle:8:16

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 1 day.


title: SD.RA replicate 1

value: SD Castrated and photoperiod synchronized control birds, 10 weeks on Short Days (SD), and euthanized.


title: 21LD+T.HVC replicate 6

value: male and female

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 21 days.


title: 1SD-T.HVC replicate 5

value: telencephalon


title: SD.HVC replicate 4

value: Dark cycle:NA


title: SD.HVC replicate 2

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country


title: 1SD-T.RA replicate 5

value: RA

value: No

value: 1SD-T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 1 day.


title: 1SD-T.HVC replicate 6


title: 2SD-T.RA replicate 1

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 2 days.


title: 2SD-T.HVC replicate 1


title: 2SD-T.HVC replicate 2

value: 2SD-T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 2 days.


title: 7LD+T.RA replicate 2

value: Dark cycle:20:4

value: Yes


title: SD.RA replicate 4

value: male


title: 3LD+T.RA replicate 3

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 3 days.


title: 1SD-T.RA replicate 3

value: Dark cycle:8:16


title: 21LD+T.RA replicate 3


title: 3LD+T.RA replicate 4


title: 7LD+T.HVC replicate 6

value: HVC

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 7 days.


title: 3LD+T.HVC replicate 5

value: male and female


title: 1SD-T.HVC replicate 4


title: SD.HVC replicate 1

value: SD Castrated and photoperiod synchronized control birds, 10 weeks on Short Days (SD), and euthanized.


title: 2SD-T.HVC replicate 6

value: telencephalon


title: 21LD+T.RA replicate 2

value: 21LD+T After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 21 days.

value: Dark cycle:NA


title: 2SD-T.RA replicate 5

value: RA

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country


title: 7LD+T.RA replicate 5


title: Day 3 - PM - Bioreactor Run 2 - 5L - mAdbID:106604

description: mAdb experiment ID: 106604

scan_protocol: Creator: GenePix Pro 5.1.0.16 Scanner: GenePix 4000B [82720] ScanPower: 100;; 100 LaserPower: 3.09;; 1.89 Temperature: 28.16 Scanning Protocol Other: The arrays were then scanned for Cy3 and Hyper5 fluorescent emission intensities using a GenePix 4000B microarray scanner (Axon, Union City, CA) with 5um resolution. Image processing, consisting of automatic and manual spot selection/rejection, and spot identification (gridding) was carried out using GenePix Pro 6.0 software (Axon). Data files were generated containing the gene represented by each spot on the array and the spot's corresponding Cy3 and Hyper5 intensities.

source_name: Universal Mouse Reference

value: All-inclusive universal mouse reference RNA pool (Becton, Dickinson, and Co., Franklin Lakes, NJ).

tag: cell line

value: A Sp2/0 myeloma based mouse hybridoma cell line (2055.5) secreting an anti-meningitidis-capsular-polysaccharide (anti-MCPS) IgG3 (Rubinstein LJ 1988) was used as the experimental cell line.


title: 21LD+T.HVC replicate 1


title: 3LD+T.HVC replicate 4


title: 2SD-T.HVC replicate 3

value: No

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 2 days.


title: 1SD-T.RA replicate 6

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD) for 21 days, then T was removed and the birds were shifted back to Short Days (SD), and euthanized after 1 day.


title: 3LD+T.RA replicate 1

value: male

value: Dark cycle:20:4

value: Yes


title: 7LD+T.RA replicate 4


title: 7LD+T.HVC replicate 4

value: HVC


title: 7LD+T.HVC replicate 3

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 7 days.


title: 1SD-T.HVC replicate 1

value: male and female

value: Dark cycle:8:16


title: SD.HVC replicate 3

value: telencephalon

value: Castrated and photoperiod synchronized control birds, 10 weeks on Short Days (SD), and euthanized.


title: 3LD+T.RA replicate 5

value: Dark cycle:NA

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 3 days.


title: 2SD-T.RA replicate 6

value: Whole telencephalon pool of 30 birds (15 males and 15 females) supplied equally from each of 5 aviaries around the country

value: RA


title: 21LD+T.RA replicate 5

value: After castration and photoperiod synchronization, birds were implanted with subcutaneous Testosterone (T), shifted to Long Days (LD), and euthanized after 21 days.


title: 21LD+T.HVC replicate 4


title: 3LD+T.HVC replicate 3


title: SD.RA replicate 3

value: No