title: VCAN-knockdown vs Control (72h Proliferation) Replicate 8

description: VCAN Knockdown versus Control, 72h proliferation, cell culture plate 4 (dye swap), replicate 8 of 8.

growth_protocol: Satellite cells were isolated from the pectoralis major muscle of 7-week-old male RBC2 line turkeys and plated in 24-well gelatin-coated cell culture plates in antibiotic free plating media.  Satellite cell cultures were transfected cells with the appropriate siRNA or mock-transfected to a final concentration of 20 pM of each siRNA and 1.5 µL lipofectamine 2000 (Invitrogen) contained in 100 µL Opti-MEM I Reduced Serum medium (Invitrogen) per well.  The transfection mixture was added to the cells and incubated for 5 hours at 37 °C in a 95% air/5% CO2 incubator.  After incubation, the medium was replaced with growth medium containing McCoy’s 5A (Sigma-Aldrich, St. Louis, MO) containing 10% chicken serum (Gemini BioProducts, West Sacramento, CA), and 5% horse serum (Gemini BioProducts) with 0.1% antibiotic/antimycotic (Gemini BioProducts).  Every 24 hours after the transfection for 72 hours, plates were removed, wells were rinsed with PBS, and samples were stored at -70 °C until RNA extraction.

value: 72h Proliferation


title: Arctowski_Deschampsia_12

status: Public on Jun 01 2012

type: genomic

city: Rio de Janeiro

first: Lia

last: Teixeira

state: RJ

address: Av. Carlos Chagas Filho, 373

country: Brazil

institute: Universidade Federal do Rio de Janeiro

hyb_protocol: Slides were pre-hybridized for 1 h at 37°C with a DIG easy hybridization solution (Roche Applied Science, Laval, QC, Canada) containing 5% BSA. Samples were then assigned randomly to a sub-array and hybridization was carried out for approximately 20 h at 37°C on a Slide Booster apparatus (Implen, Calabasas, CA). Slides were washed three times for 5 minutes at 37°C in 0.1X SSC / 0.1% SDS followed by a single wash for 5 minutes at 37°C in 0.1X SSC.

scan_protocol: Slides were scanned in a ScanArray GX PLUS Microarray Scanner (Perkin-Elmer, Boston, MA) at a resolution of 10 µm.

data_processing:
Images were transferred to QuantArray (Perkin-Elmer) where each spot was identified and quantified. Data was then exported to Excel where net spot intensity was calculated by subtracting the background signal from the target spot intensity.
A spot was scored as “present” if its net intensity was at least 3 times higher than the median net intensity of all spots. For a taxon to be scored as present, all of its triplicate spots had to be scored as present. The results from the 16S rRNA gene microarray were only used in the binary form (presence/absence of taxa).

molecule: genomic DNA

organism: Bacteria

source_name: Admiralty Bay, King George Island, Antarctic

label_protocol: For the microarray assays all the triplicate rhizosphere and bulk soil samples from the six sample sites were used (47 samples). A 16S rRNA gene fragment was amplified using the universal primers F1-R13 (Lane 1991). The PCR mixture comprised 1 µl of template DNA (10 - 20 ng), 20 pmol of universal primers, 5 µl of 10 x PCR  buffer (Fermentas, Burlington, Ontario, CA), 1.5 mM MgCl2, 2.5 U of Taq DNA polymerase (Fermentas), 0.2 mM of each dNTP and sterile filtered water to a final volume of 50 µl. The temperature profile included an initial denaturation step at 94°C for 5 min, 35 cycles of a denaturation step at 94°C for 30s, a primer annealing step at 50°C for 30s and an extension step at 72°C for 45s, followed by a final step of 7 min at 72°C. PCR products were purified using the PureLink TM PCR purification Kit (Invitrogen Canada, Burlington, Ontario, CA).

growth_protocol: The study used a non culturable method to access the bacterial communities in soils and rhizospheres

extract_protocol: The DNA extractions were made using the Fast DNA Spin Kit for soil (QBIOgene, Carlsbad, CA) following the manufacturer’s instructions.

treatment_protocol: To assess the bacterial communities associated with the rhizospheres of both vascular plants, 5 g of the roots with aggregated soil was shaken in a saline solution (NaCl 0.85%) for 2 hours. Then 50 mL of the supernatant was centrifuged for 10 minutes at 9,000 rpm, and 0.5 g of the pelleted soil was used for DNA extraction. For the bulk soil, 0.5g of each sample was used for the extractions

tag: source

value: Rhizosphere from Deschampsia antarctica


title: Epithelial Mock 5h rep8

type: RNA

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

description: Replicate 8

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were analysed in Genespring GX7.3 software. Measurements less than 0.01 was set to 0.01. Data was then normalised at the 50th percentile.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: 16HBE14 human bronchial epithelial cells,5h,mock-infected

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with NanoDrop 1000 instrument.

tag: cell type

tag: infection status

value: Mock-infected

tag: time (hours)


title: Epithelial Mock 5h rep7

description: Replicate 7

value: 16HBE14 human bronchial epithelial cells


title: irma_64j_4 with array type Cotton from Affymetrix

city: Evry

first: Delphine

last: Gey

address: 2 rue Gaston Crémieux

department: URGV

country: France

institute: INRA

description: Genes involved in somatic embryogenesis?

hyb_protocol: labelled extract quantity: 10ug

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

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

label: Biotin

organism: Gossypium

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

growth_protocol: see supplementary file on the Series record

extract_protocol: Qiagen RNeasy plant mini kit extraction; irma_64j_4:1ug.

treatment_protocol: no treatment

tag: variety

value: irma from NEmb

tag: age


title: 1a_64j_4 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; 1a_64j_4:1ug.

value: 1a batch of seeds from Coker310


title: VCAN-knockdown vs Control (48h Differentiation) Replicate 1

city: East Lansing

first: Kelly

middle: R

last: Sporer

state: MI

address: 3365 Anthony Hall

department: Food Science and Human Nutrition

country: USA

institute: Michigan State University

description: VCAN Knockdown versus Control, 48h differentiation, cell culture plate 1, replicate 1 of 8.

hyb_protocol: Fragmented, Cy3-coupled aRNA was mixed with its Cy5-coupled partner, and the mixtures were brought to 110 μL with 68°C SlideHyb 1 (Ambion, Inc.) and incubated at 68°C for 5 min.  These dye-coupled mixtures were then hybridized to oligonucleotide microarrays (described previously) for 18 h in a GeneTac Hybridization Station (Genomic Solutions, Ann Arbor, MI) using the following conditions: 54°C for 18 h, followed by a medium-stringency wash at 42°C (2X SSC, 0.1% SDS), a high-stringency wash (0.2X SSC, 0.1% SDS) at 22°C, and a wash with postwash buffer (0.2X SSC) at 22°C.  Arrays were then rinsed in 2X SSC and Nanopure H2O, dried by centrifugation at 500 × g for 5 min.

scan_protocol: Scanned with a GenePix 4000B (Molecular Devices, Sunnyvale, CA) scanner. Image analysis was performed using GenePix Pro 6.0, and spot intensities were exported as GPR files.

data_processing: Fluorescence intensity data was normalized for dye intensity bias using the LOESS procedure of the normalizeWithinArray function of the Bioconductor R software LIMMA (Smyth 2004).

organism: Meleagris gallopavo

source_name: Total RNA from turkey muscle satellite cell

label_protocol: Total RNA for use in microarrays was amplified using two rounds of amplification with the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Inc.) per manufacturer instructions.  Briefly, 1 μg total RNA was incubated with T7 Oligo(dT) primer for 10 min at 70°C then reverse transcribed into cDNA at 42°C for 2 h.  Second strand synthesis was performed at 16°C for 2 h.  Double-stranded cDNA was then purified, and in vitro transcription was performed at 37°C for 6 h.  The resulting aRNA was purified and quantified using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA).  For the dye coupling procedure, 15 μg aRNA was coupled to either Cy3 or Cy5 fluorescent dye (GE Healthcare, Piscataway, NJ) in the dark at room temperature for 1 hour until the reaction was quenched by the addition of 4M hydroxylamine.  Dye-coupled aRNA was purified and quantified, then 5 μg was fragmented to 60-200 nucleotide segments using RNA Fragmentation Reagents (Ambion, Inc.) at 70°C for 15 min in preparation for microarray hybridization.

growth_protocol: Satellite cells were isolated from the pectoralis major muscle of 7-week-old male RBC2 line turkeys and plated in 24-well gelatin-coated cell culture plates in antibiotic free plating media.  Satellite cell cultures were transfected cells with the appropriate siRNA or mock-transfected to a final concentration of 20 pM of each siRNA and 1.5 µL lipofectamine 2000 (Invitrogen) contained in 100 µL Opti-MEM I Reduced Serum medium (Invitrogen) per well.  The transfection mixture was added to the cells and incubated for 5 hours at 37 °C in a 95% air/5% CO2 incubator.  After incubation, the medium was replaced with growth medium containing McCoy’s 5A (Sigma-Aldrich, St. Louis, MO) containing 10% chicken serum (Gemini BioProducts, West Sacramento, CA), and 5% horse serum (Gemini BioProducts) with 0.1% antibiotic/antimycotic (Gemini BioProducts).  The growth medium was changed every 24 hours until the cells reached 60-65% confluency.  Differentiation was induced by changing the medium to Dulbecco’s Modified Eagle Medium (DMEM; Sigma-Aldrich) containing 3% horse serum, 0.1 mg/mL porcine gelatin (Sigma-Aldrich), and 1.0 mg/mL BSA (Sigma-Aldrich) with 10 µg/mL gentamicin (Invitrogen), and 0.1% antibiotic/antimycotic.  The differentiation medium was changed daily.  After 48 h of differentiation, the plates were removed, washed with PBS, and stored at -70 °C until analysis.

extract_protocol: Total RNA was extracted from cell culture plates (n = 4) using TRIReagent (Molecular Research Center, Cincinnati, OH) following manufacturer's instructions.  RNA integrity and concentration was determined using an Agilent 2100 Bioanlyzer (Santa Clara, CA).

treatment_protocol: The si RNA sequences were designed using Invitrogen’s BLOCK-iT RNAi designer.  The primer sequences targeting versican corresponding to the coding region 7278 to 7296 were 5’-GCUCAUCAGUGAUCCAUUA-3’ (sense) and 5’-UAAUGGAUCACUGAUGAGC-3’ (antisense).  The siRNAs were purchased from Invitrogen in the desalted, pre-annealed duplex form.  The transfection of the siRNAs into the satellite cells were done using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s recommended conditions.

tag: transfection

value: VCAN-siRNA

tag: cell growth stage

value: 48h Differentiation

value: muscle satellite cell

value: Control


title: Epithelial Mock 6h rep4

description: Replicate 4

source_name: 16HBE14 human bronchial epithelial cells,6h,mock-infected


title: VCAN-knockdown vs Control (48h Differentiation) Replicate 2

description: VCAN Knockdown versus Control, 48h differentiation, cell culture plate 1 (dye swap), replicate 2 of 8.


title: VCAN-knockdown vs Control (72h Proliferation) Replicate 7

description: VCAN Knockdown versus Control, 72h proliferation, cell culture plate 4, replicate 7 of 8.


title: 1a_64j_3 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; 1a_64j_3:1ug.


title: Epithelial Mock 5h rep6

description: Replicate 6


title: Epithelial Mock 6h rep2

description: Replicate 2


title: irma_64j_3 with array type Cotton from Affymetrix

extract_protocol: Qiagen RNeasy plant mini kit extraction; irma_64j_3:1ug.


title: Epithelial Mock 5h rep5

description: Replicate 5


title: FHMbrain_21d_propanolol_rep4

city: Costa Mesa

first: Alvine

middle: C

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

institute: Southern California Coastal Water Research Project

description:
P51
Gene expression profiling after 21-day exposure to 10 µg/L propanolol

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.9 pmol Cy3/ug cRNA) was fragmented using the Agilent Gene Expression Hybridization kit and hybridized onto  custom-designed fathead minnow (15K oligonulceotide) arrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 min with GE Wash Buffer 1 (Agilent), GE Wash buffer 2 (Agilent) kept at 37°C , then 30 sec in Stabilization and Drying solution (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_10and Grid: 019597_D_F_20080305) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Pimephales promelas

source_name: whole brain, 21d, 10µg/L propanolol, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low Input Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen).  Cy3 dye incorporation and cRNA yield were measured with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using STAT-60 (Tel-Test) following the manufacturer's instructions and RNA was resuspended in RNA secure (Ambion) to remove RNAse contamination. RNA was treated with TURBO DNA-free (Ambion) to remove DNA contamination and purified using RNeasy wcolumns (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: Stage

value: reproductive adults


title: Arctowski_soil_C

value: Bulk soil


title: VCAN-knockdown vs Control (72h Proliferation) Replicate 5

description: VCAN Knockdown versus Control, 72h proliferation, cell culture plate 3, replicate 5 of 8.


title: Arctowski_Deschampsia_11


title: Epithelial Mock 5h rep4

description: Replicate 4


title: Arctowski_colobanthus_C

value: Rhizosphere from Colobanthus quitensis


title: VCAN-knockdown vs Control (72h Proliferation) Replicate 6

description: VCAN Knockdown versus Control, 72h proliferation, cell culture plate 3 (dye swap), replicate 6 of 8.


title: VCAN-knockdown vs Control (72h Proliferation) Replicate 4

description: VCAN Knockdown versus Control, 72h proliferation, cell culture plate 2 (dye swap), replicate 4 of 8.


title: Arctowski_colobanthus_B


title: Epithelial Mock 6h rep5

description: Replicate 5


title: Ipanema_soil_C


title: VCAN-knockdown vs Control (72h Proliferation) Replicate 2

description: VCAN Knockdown versus Control, 72h proliferation, cell culture plate 1 (dye swap), replicate 2 of 8.


title: FHMbrain_21d_propanolol_rep1

description:
P32
Gene expression profiling after 21-day exposure to 10 µg/L propanolol

source_name: whole brain, 21d, 10µg/L propanolol, replicate 1


title: VCAN-knockdown vs Control (72h Proliferation) Replicate 3

description: VCAN Knockdown versus Control, 72h proliferation, cell culture plate 2, replicate 3 of 8.


title: FHMbrain_21d_propanolol_rep3

description:
P41
Gene expression profiling after 21-day exposure to 10 µg/L propanolol

source_name: whole brain, 21d, 10µg/L propanolol, replicate 3


title: VCAN-knockdown vs Control (72h Proliferation) Replicate 1

description: VCAN Knockdown versus Control, 72h proliferation, cell culture plate 1, replicate 1 of 8.


title: Arctowski_colobanthus_A


title: FHMbrain_21d_propanolol_rep2

description:
P35
Gene expression profiling after 21-day exposure to 10 µg/L propanolol

source_name: whole brain, 21d, 10µg/L propanolol, replicate 2


title: Arctowski_Deschampsia_10


title: Epithelial Mock 5h rep1

description: Replicate 1


title: Epithelial Mock 5h rep2

description: Replicate 2


title: FHMbrain_21d_control_rep4

description:
C44
Gene expression profiling after 21-day exposure to 10 µg/L propanolol

source_name: whole brain, 21d, solvent control, replicate 4


title: Epithelial Mock 4h rep8

description: Replicate 8

source_name: 16HBE14 human bronchial epithelial cells,4h,mock-infected


title: Ipanema_deschampsia_2


title: Ipanema_soil_B


title: FHMbrain_21d_control_rep2

description:
C29
Gene expression profiling after 21-day exposure to 10 µg/L propanolol

source_name: whole brain, 21d, solvent control, replicate 2


title: MGP-knockdown vs Control (48h Differentiation) Replicate 8

description: MGP Knockdown versus Control, 48h differentiation, cell culture plate 4 (dye swap), replicate 8 of 8.

treatment_protocol: The si RNA sequences were designed using Invitrogen’s BLOCK-iT RNAi designer.  The primer sequences targeting MGP corresponding to the coding region 348 to 366 were 5’-GGACUUCCACCUGUGUGAA-3’ (sense) and UUCACACAGGUGGAAGUCC-3’ (antisense).   The siRNAs were purchased from Invitrogen in the desalted, pre-annealed duplex form.  The transfection of the siRNAs into the satellite cells were done using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s recommended conditions.

value: MGP-siRNA


title: Epithelial Mock 5h rep3

description: Replicate 3


title: Ipanema_deschampsia_3


title: Ipanema_soil_A


title: Epithelial Mock 4h rep6

description: Replicate 6


title: FHMbrain_21d_control_rep3

description:
C38
Gene expression profiling after 21-day exposure to 10 µg/L propanolol

source_name: whole brain, 21d, solvent control, replicate 3


title: Ipanema_deschampsia_1


title: MGP-knockdown vs Control (48h Differentiation) Replicate 7

description: MGP Knockdown versus Control, 48h differentiation, cell culture plate 4, replicate 7 of 8.


title: Ipanema_colobanthus_3


title: MGP-knockdown vs Control (48h Differentiation) Replicate 5

description: MGP Knockdown versus Control, 48h differentiation, cell culture plate 3, replicate 5 of 8.


title: Ipanema_colobanthus_2


title: Epithelial Mock 4h rep4

description: Replicate 4


title: MGP-knockdown vs Control (48h Differentiation) Replicate 6

description: MGP Knockdown versus Control, 48h differentiation, cell culture plate 3 (dye swap), replicate 6 of 8.


title: Epithelial Mock 4h rep3

description: Replicate 3


title: Epithelial Mock 4h rep7

description: Replicate 7


title: FHMbrain_21d_control_rep1

description:
C26
Gene expression profiling after 21-day exposure to 10 µg/L propanolol

source_name: whole brain, 21d, solvent control, replicate 1


title: MGP-knockdown vs Control (48h Differentiation) Replicate 4

description: MGP Knockdown versus Control, 48h differentiation, cell culture plate 2 (dye swap), replicate 4 of 8.


title: Epithelial Mock 4h rep5

description: Replicate 5


title: MGP-knockdown vs Control (48h Differentiation) Replicate 3

description: MGP Knockdown versus Control, 48h differentiation, cell culture plate 2, replicate 3 of 8.


title: Epithelial Mock 4h rep2

description: Replicate 2


title: MGP-knockdown vs Control (48h Differentiation) Replicate 2

description: MGP Knockdown versus Control, 48h differentiation, cell culture plate 1 (dye swap), replicate 2 of 8.


title: Epithelial Mock 4h rep1

description: Replicate 1


title: Ipanema_colobanthus_1


title: Epithelial Mock 3h rep8

description: Replicate 8

source_name: 16HBE14 human bronchial epithelial cells,3h,mock-infected


title: walR mutantVsParent_replicate_3

city: Heidelberg

first: Benjamin

middle: Peter

last: Howden

state: Victoria

address: Studley Rd

department: Infectious Diseases

country: Australia

institute: Austin Health

description:
TPS3190vsJKD6004r3
Biological replicate 3 of 3

hyb_protocol: 50 ul of cDNA hybridisation mixture was applied to array slide and covered with LifterSlip coverslips (Erie Scienctific), then incubated overnight at 42°C.

scan_protocol: GenePix 4000B

data_processing: Images were  quantified and then imported into BASE and analysed using Bioconductor and Limma. After global lowess normalization the log-ratios for each array sclaed so that the median absolute deviation was the same between arrays. The fold ratio for gene expression for the walKR mutant strains (TPS3103 and TPS3190) compared to the parent (JKD6009 and JKD6004) were calculated.

organism: Staphylococcus aureus

label_protocol: 5 µg of total RNA was reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 0.5 mM each dATP, dCTP, dGTP, with 0.2 mM dTTP, 0.3 mM aa-dUTP. After cDNA collection, aminoallyl-labelled cDNA was resuspended in 0.1 M sodium bicarbonate buffer (pH 9.3), then incubated with cy3 or cy5 for 2 hours at room temperature.

growth_protocol: Isolates grown in BHI broth to exponential phase (OD600 = 0.5)

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

treatment_protocol: 1 ml of culture was added to 0.5 ml of RNA stabilization reagent (RNAlater, Qiagen) and allowed to stand for 10 min after mixing

tag: isolate characteristics

value: walR mutant (SNP)

value: Normal phenotype


title: walR mutantVsParent_replicate_2

description:
TPS3190vsJKD6004r2
Biological replicate 2 of 3


title: walR mutantVsParent_replicate_1

description:
TPS3190vsJKD6004r1
Biological replicate 1 of 3


title: walK mutantVsParent_replicate_2

description:
TPS3130vsJKD6009r2
Biological replicate 2 of 3

value: walK mutant (SNP)


title: qseC / wild type

city: Dallas

first: Cristiano

middle: Gallina

last: Moreira

state: TX

address: 6000 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: qseC Cy3/ wild type Cy5

hyb_protocol: Description of cDNA hybridization (Richardson AR, Payne EC, Younger N, Karlinsey JE, Thomas VC, Becker LA, Navarre WW, Castor ME, Libby SJ, Fang FC. Multiple targets of nitric oxide in the tricarboxylic acid cycle of Salmonella enterica serovar Typhimurium. Cell Host Microbe 2011 Jul 21;10(1):33-43).

data_processing:
(Richardson AR, Payne EC, Younger N, Karlinsey JE, Thomas VC, Becker LA, Navarre WW, Castor ME, Libby SJ, Fang FC. Multiple targets of nitric oxide in the tricarboxylic acid cycle of Salmonella enterica serovar Typhimurium. Cell Host Microbe 2011 Jul 21;10(1):33-43).
The fold change data are calculated in the lowess normalized mutant/WT.

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: bacteria, qseC mutant

label_protocol: The amino allyl dUTP provides a group onto which Cy3 or Cy5 can be coupled.   Description of cDNA labeling (Richardson AR, Payne EC, Younger N, Karlinsey JE, Thomas VC, Becker LA, Navarre WW, Castor ME, Libby SJ, Fang FC. Multiple targets of nitric oxide in the tricarboxylic acid cycle of Salmonella enterica serovar Typhimurium. Cell Host Microbe 2011 Jul 21;10(1):33-43).

growth_protocol: Two culture tubes of wild type and the qseC mutant, then diluted them 1:100 (my standard method) and grown to OD1.0 in LB broth  (Richardson AR, Payne EC, Younger N, Karlinsey JE, Thomas VC, Becker LA, Navarre WW, Castor ME, Libby SJ, Fang FC. Multiple targets of nitric oxide in the tricarboxylic acid cycle of Salmonella enterica serovar Typhimurium. Cell Host Microbe 2011 Jul 21;10(1):33-43).

extract_protocol: RNA extracted using Qiagen RNA purification kits.   cDNA was synthesized as previously described.   (Richardson AR, Payne EC, Younger N, Karlinsey JE, Thomas VC, Becker LA, Navarre WW, Castor ME, Libby SJ, Fang FC. Multiple targets of nitric oxide in the tricarboxylic acid cycle of Salmonella enterica serovar Typhimurium. Cell Host Microbe 2011 Jul 21;10(1):33-43).

treatment_protocol: Cells where added to RNAprotect (Qiagen) (Richardson AR, Payne EC, Younger N, Karlinsey JE, Thomas VC, Becker LA, Navarre WW, Castor ME, Libby SJ, Fang FC. Multiple targets of nitric oxide in the tricarboxylic acid cycle of Salmonella enterica serovar Typhimurium. Cell Host Microbe 2011 Jul 21;10(1):33-43).

tag: genotype/variation

value: qseC mutant

source_name: bacteria, wild type

value: wild type


title: walK mutantVsParent_replicate_3

description:
TPS3130vsJKD6009r3
Biological replicate 3 of 3


title: MGP-knockdown vs Control (72h Proliferation) Replicate 8

description: MGP Knockdown versus Control, 72h proliferation, cell culture plate 4 (dye swap), replicate 8 of 8.

value: 72h Proliferation


title: MGP-knockdown vs Control (48h Differentiation) Replicate 1

description: MGP Knockdown versus Control, 48h differentiation, cell culture plate 1, replicate 1 of 8.


title: Epithelial Mock 3h rep7

description: Replicate 7

value: 16HBE14 human bronchial epithelial cells

value: Mock-infected


title: MGP-knockdown vs Control (72h Proliferation) Replicate 7

description: MGP Knockdown versus Control, 72h proliferation, cell culture plate 4, replicate 7 of 8.


title: Epithelial Mock 3h rep6

description: Replicate 6


title: MGP-knockdown vs Control (72h Proliferation) Replicate 6

description: MGP Knockdown versus Control, 72h proliferation, cell culture plate 3 (dye swap), replicate 6 of 8.


title: walK mutantVsParent_replicate_1

description:
TPS3130vsJKD6009r1
Biological replicate 1 of 3


title: Epithelial Mock 3h rep5

description: Replicate 5


title: S. mutans ∆fabT mutant pH5 replicate 3

city: Rochester

first: Roberta

last: Faustoferri

state: NY

address: 601 Elmwood Ave. Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

hyb_protocol: The slides were hybridized in a mixture containing equal amounts of labeled test and reference cDNA as described by the protocol from the Pathogen Functional Genomics Research Center (PFGRC) for 16 h at 42°C in a MAUI hybridization chamber (BioMicro Systems, Salt Lake City, UT).  Hybridized slides were washed and scanned using a GenePix 4000b scanner (Molecular Devices, Inc., Sunnyvale, CA).

scan_protocol: Hybridized slides were washed using the method described by the Pathogen Functional Genomics Research Center (PFGRC) and scanned using a GenePix 4000b scanner (Molecular Devices, Inc., Sunnyvale, CA).

data_processing: Data were analyzed using software available at the J. Craig Venter Institute PFGRC website.  Single-channel images of the slides were loaded into Spotfinder and overlaid.  MIDAS software was used to normalize the spot intensity data using LOWESS and iterative log mean centering with default setting, followed by in-slide replicate analysis.  Statistical analysis was carried out with BRB array tools (http://linus.nci.nih.gov/BRB-ArrayTools.html) with a cutoff P-value of 0.01 and a ≥2-fold change of expression.

organism: Streptococcus mutans UA159

source_name: RNA from ∆fabT mutant strain, steady-state pH5

label_protocol: Once RNA was purified as described above, cDNA was generated from 2µg RNA per sample as described by the protocol available from the Pathogen Functional Genomics Research Center (PFGRC) using Invitrogen Superscript III Reverse Transcriptase (Life Technologies, Carlsbad, CA) to increase cDNA yields.Purified cDNAs were coupled to Cy3 (experimental samples) or Cy5 (reference cDNA).

growth_protocol: S. mutans UA159 (parent strain) and MU1591 (∆fabT) were grown in continuous culture to steady-state pH values of 7 and 5 in a BioFlo2000 fermentor at a dilution rate of 0.24h-1 in non-limiting glucose concentrations.

extract_protocol: RNA was isolated from homogenized S. mutans cells grown in continuous culture in TY + 1% glucose medium to steady-state pH values of 7 and 5 by repeated hot acid-phenol: chloroform extractions, and the nucleic acid was precipitated with 1 volume ice-cold isopropanol and one-tenth volume 3M sodium acetate (pH 5) at –20°C overnight.  RNA pellets were resuspended in 80 mL nuclease-free H2O, and treated with DNase I (Ambion) at 37°C for 30 minutes.  RNA concentrations were determined using a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher Scientific, Waltham, MA), and 1 µL samples were run on an agarose gel to verify RNA integrity.  The RNA was purified again using the RNeasy mini kit (Qiagen), including a second on-column DNase treatment that was performed as recommended by the supplier.  Final RNA concentrations were determined spectrophotometrically.

value: ∆fabT mutant

tag: ph

source_name: RNA from parent strain, mid-log

tag: growth phase

value: mid-log


title: S. mutans ∆fabT mutant pH5 replicate 4


title: S. mutans ∆fabT mutant pH5 replicate 2


title: S. mutans ∆fabT mutant pH5 replicate 1


title: Epithelial Mock 3h rep4

description: Replicate 4


title: MGP-knockdown vs Control (72h Proliferation) Replicate 3

description: MGP Knockdown versus Control, 72h proliferation, cell culture plate 2, replicate 3 of 8.


title: Blood, 6hr, 8 Gy, replicate 6

city: Logan

first: Daniel

last: Hyduke

state: UT

address: 4105 Old Main Hill ENGR 402S

department: Biological Engineering

institute: Utah State University

description: Ribopure RNA extraction

hyb_protocol: Cy3-labeled cRNA (1.65 μg) was hybridized to Agilent’s Mouse Whole Genome arrays (G4122F) with Agilent’s GEx Hybridization HI-RPM Buffer.  The samples were hybridized for 16 hours in a rotisserie hybridization oven (G2545A, Agilent),

scan_protocol: The arrays were washed with Agilent’s gene expression wash buffers and scanned with an Agilent DNA Microarray Scanner 2505A in an ozone hood.

data_processing: Image analysis and intra-chip normalization were performed with Feature Extraction 9.5.3.1 (Agilent).  Unless otherwise noted, subsequent analyses were performed with the R statistical analysis framework (Team, 2010) and associated packages (Reimers and Carey, 2006).  Probes that had intensity readings of at least 50 counts (as assessed by Feature Extraction) in over 20% of the test samples (for at least one dose) and 20% of the control samples were retained for analysis.  To account for inter-chip variation, quantile normalization was performed on the retained probes using the R bioconductor limma package (Reimers and Carey, 2006).

organism: Mus musculus

source_name: Blood, 6hr, 8 Gy, replicate 6

label_protocol: Cy3-labeled cRNA was generated from 400 ng total RNA using Agilent’s QuickAMP kit.

growth_protocol: Male C57BL/6N mice, ages 8-12 wks old, were obtained from Charles River Laboratories, Inc. (Wilmington, MA). Mice were housed at Georgetown University under standard 12 hr light and 12 hr dark cycle conditions and given water and regular rodent chow ad libitum. All experimental procedures and animal handling were in accordance with animal protocols approved by the Georgetown University Animal Care and Use Committee.

extract_protocol: RNA was purified using PreAnalytiX’s PAXgene blood RNA system (Qiagen, Valencia, CA) or Ambion’s Mouse RiboPure-Blood RNA isolation kit (Applied Biosystems, Carslbad, CA).  Total RNA quality was assessed with Agilent’s (Carlsbad, CA) RNA 6000 Nano Kit and Bioanalyzer 2100.  Globin RNA was removed with Ambion’s Globinclear Mouse/Rat kit (Applied Biosystems).

treatment_protocol: γ-irradiation of mice (2 and 8 Gy) and sham-treatment of controls (0 Gy) were conducted with a Cesium-137 source  in a pie cage and in accordance with Georgetown University policy. Mice were euthanized 6 hours post exposure and blood samples were collected by cardiac puncture.

tag: strain

tag: gender

value: male


title: S. mutans UA159 parent strain pH5 replicate 3

source_name: RNA from parent strain, steady-state pH5


title: Epithelial Mock 3h rep3

description: Replicate 3


title: S. mutans UA159 parent strain pH5 replicate 4


title: Epithelial Mock 3h rep2

description: Replicate 2


title: MGP-knockdown vs Control (72h Proliferation) Replicate 5

description: MGP Knockdown versus Control, 72h proliferation, cell culture plate 3, replicate 5 of 8.

source_name: Total RNA from turkey muscle satellite cell

value: muscle satellite cell


title: MGP-knockdown vs Control (72h Proliferation) Replicate 2

description: MGP Knockdown versus Control, 72h proliferation, cell culture plate 1 (dye swap), replicate 2 of 8.

value: Control


title: MGP-knockdown vs Control (72h Proliferation) Replicate 4

description: MGP Knockdown versus Control, 72h proliferation, cell culture plate 2 (dye swap), replicate 4 of 8.


title: S. mutans UA159 parent strain pH5 replicate 2


title: Epithelial Mock 3h rep1

description: Replicate 1


title: S. mutans UA159 parent strain pH5 replicate 1


title: Blood, 6hr, 8 Gy, replicate 5

description: Ribopure RNA extraction

source_name: Blood, 6hr, 8 Gy, replicate 5


title: Epithelial Mock 0h rep7

description: Replicate 7

source_name: 16HBE14 human bronchial epithelial cells,0h,mock-infected


title: DAP-knockdown vs Control (48h Differentiation) Replicate 8

description: DAP Knockdown versus Control, 48h differentiation, cell culture plate 4 (dye swap), replicate 8 of 8.

label_protocol: Total RNA for use in microarrays was amplified using two rounds of amplification with the Amino Allyl MessageAmp™ II aRNA Amplification Kit (Ambion, Inc.) per manufacturer instructions.  Briefly, 150 ng total RNA was incubated with T7 Oligo(dT) primer for 10 min at 70°C then reverse transcribed into cDNA at 42°C for 2 h.  Second strand synthesis was performed at 16°C for 2 h.  Double-stranded cDNA was then purified, and in vitro transcription was performed at 37°C for 6 h.  A total of 900 ng amplified RNA (aRNA) was subjected to another round of amplification using the same protocol.  The resulting aRNA was purified and quantified using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA).  For the dye coupling procedure, 15 μg aRNA was coupled to either Cy3 or Cy5 fluorescent dye (GE Healthcare, Piscataway, NJ) in the dark at room temperature for 1 hour until the reaction was quenched by the addition of 4M hydroxylamine.  Dye-coupled aRNA was purified and quantified, then 5 μg was fragmented to 60-200 nucleotide segments using RNA Fragmentation Reagents (Ambion, Inc.) at 70°C for 15 min in preparation for microarray hybridization.

treatment_protocol: The si RNA sequences were designed using Invitrogen’s BLOCK-iT RNAi designer.  The primer sequences targeting DAP corresponding to the coding region 167 to 85 were 5’-GGAUGAUCAAGACUGGGAATT-3’ (sense) and 5’-UUCCCAGUCUUGAUCAUCC-3’ (antisense).  The siRNAs were purchased from Invitrogen in the desalted, pre-annealed duplex form.  The transfection of the siRNAs into the satellite cells were done using Lipofectamine 2000 (Invitrogen) according to the manufacturer’s recommended conditions.

value: 48h Differentiation

value: DAP-siRNA


title: Blood, 6hr, 8 Gy, replicate 4

description: Ribopure RNA extraction

source_name: Blood, 6hr, 8 Gy, replicate 4


title: Blood, 6hr, 8 Gy, replicate 3

description: Ribopure RNA extraction

source_name: Blood, 6hr, 8 Gy, replicate 3


title: S. mutans ∆fabT mutant pH7 replicate 4

source_name: RNA from ∆fabT mutant strain, steady-state pH7


title: Epithelial Mock 0h rep6

description: Replicate 6


title: Epithelial Mock 0h rep5

description: Replicate 5


title: MGP-knockdown vs Control (72h Proliferation) Replicate 1

description: MGP Knockdown versus Control, 72h proliferation, cell culture plate 1, replicate 1 of 8.


title: Blood, 6hr, 8 Gy, replicate 2

description: Ribopure RNA extraction

source_name: Blood, 6hr, 8 Gy, replicate 2


title: DAP-knockdown vs Control (48h Differentiation) Replicate 6

description: DAP Knockdown versus Control, 48h differentiation, cell culture plate 3 (dye swap), replicate 6 of 8.


title: S. mutans ∆fabT mutant pH7 replicate 3


title: Blood, 6hr, 2 Gy, replicate 5

description: Paxgene RNA Extraction

source_name: Blood, 6hr, 2 Gy, replicate 5


title: DAP-knockdown vs Control (48h Differentiation) Replicate 7

description: DAP Knockdown versus Control, 48h differentiation, cell culture plate 4, replicate 7 of 8.


title: Epithelial Mock 0h rep4

description: Replicate 4


title: DAP-knockdown vs Control (48h Differentiation) Replicate 4

description: DAP Knockdown versus Control, 48h differentiation, cell culture plate 2 (dye swap), replicate 4 of 8.


title: Epithelial Mock 0h rep3

description: Replicate 3


title: S. mutans ∆fabT mutant pH7 replicate 2


title: Blood, 6hr, 8 Gy, replicate 1

description: Ribopure RNA extraction

source_name: Blood, 6hr, 8 Gy, replicate 1


title: Epithelial Mock 0h rep2

description: Replicate 2


title: Blood, 6hr, 2 Gy, replicate 4

description: Ribopure RNA extraction

source_name: Blood, 6hr, 2 Gy, replicate 4


title: Blood, 6hr, 2 Gy, replicate 3

description: Ribopure RNA extraction

source_name: Blood, 6hr, 2 Gy, replicate 3


title: S. mutans ∆fabT mutant pH7 replicate 1


title: DAP-knockdown vs Control (48h Differentiation) Replicate 5

description: DAP Knockdown versus Control, 48h differentiation, cell culture plate 3, replicate 5 of 8.


title: DAP-knockdown vs Control (48h Differentiation) Replicate 3

description: DAP Knockdown versus Control, 48h differentiation, cell culture plate 2, replicate 3 of 8.


title: S. mutans UA159 parent strain pH7 replicate 4

source_name: RNA from parent strain, steady-state pH7


title: Epithelial Mock 0h rep1

description: Replicate 1


title: DAP-knockdown vs Control (48h Differentiation) Replicate 2

description: DAP Knockdown versus Control, 48h differentiation, cell culture plate 1 (dye swap), replicate 2 of 8.


title: DAP-knockdown vs Control (48h Differentiation) Replicate 1

description: DAP Knockdown versus Control, 48h differentiation, cell culture plate 1, replicate 1 of 8.


title: Blood, 6hr, 2 Gy, replicate 1

description: Ribopure RNA extraction

source_name: Blood, 6hr, 2 Gy, replicate 1


title: Blood, 6hr, 0 Gy, replicate 7

description: Paxgene RNA Extraction

source_name: Blood, 6hr, 0 Gy, replicate 7


title: Blood, 6hr, 2 Gy, replicate 2

description: Ribopure RNA extraction

source_name: Blood, 6hr, 2 Gy, replicate 2


title: DAP-knockdown vs Control (72h Proliferation) Replicate 8

description: DAP Knockdown versus Control, 72h proliferation, cell culture plate 4 (dye swap), replicate 8 of 8.


title: DAP-knockdown vs Control (72h Proliferation) Replicate 6

description: DAP Knockdown versus Control, 72h proliferation, cell culture plate 3 (dye swap), replicate 6 of 8.


title: Left ventricle-DOX-Rep3

city: La Coruña

first: Mario

last: Torrado

state: La Coruña

address: Campus de Oza, Edificio El Fortin

department: Institute of Health Sciences

country: Spain

institute: University of La Coruña

hyb_protocol: As described in the Affymetrix GeneChip Expression analysis technical manual (starting from page 2.2.3, Eukaryotic Target Hybridization)

scan_protocol: Scanner GCS3000-7G (Affymetrix); Software GCOS v1.4

data_processing: Software GCOS 1.4; MAS5 algorithm with default settings. Scaling: All probe sets (TGT value: 100)

organism: Sus scrofa

source_name: Sus Scrofa left ventricle-DOX

label_protocol: Ambion MessageAmp Premier kit starting with 150 ng Total RNA

growth_protocol: Neonatal piglets were maintained in a conventional Nurtinger nursery system

extract_protocol: Total RNA was isolated using RNeasy Mini kit (Qiagen) including the on-column digestion of DNA with RNase-free DNase.

treatment_protocol: Deep-frozen cardiac-tissue samples were directly disrupted in RLT buffer (Qiagen) using a high-speed rotor-stator homogenizer (Ultra-Turrax T8) followed by a Proteinase K digestion, as described in the Qiagen Manual

tag: breed

value: Large White

tag: tissue

value: Left ventricle free wall

tag: developmental stage

value: 28-day old


title: Blood, 6hr, 0 Gy, replicate 5

description: Ribopure RNA extraction

source_name: Blood, 6hr, 0 Gy, replicate 5


title: Left ventricle-PBS-Rep2

source_name: Sus Scrofa left ventricle-PBS


title: Left ventricle-DOX-Rep1


title: DAP-knockdown vs Control (72h Proliferation) Replicate 5

description: DAP Knockdown versus Control, 72h proliferation, cell culture plate 3, replicate 5 of 8.

source_name: Total RNA from turkey muscle satellite cell

tag: cell type


title: DAP-knockdown vs Control (72h Proliferation) Replicate 7

description: DAP Knockdown versus Control, 72h proliferation, cell culture plate 4, replicate 7 of 8.


title: S. mutans UA159 parent strain pH7 replicate 3

source_name: RNA from parent strain, mid-log


title: S. mutans UA159 parent strain pH7 replicate 1


title: Left ventricle-PBS-Rep1


title: S. mutans UA159 parent strain pH7 replicate 2


title: Left ventricle-PBS-Rep3


title: Blood, 6hr, 0 Gy, replicate 6

description: Paxgene RNA Extraction

source_name: Blood, 6hr, 0 Gy, replicate 6


title: Blood, 6hr, 0 Gy, replicate 3

description: Ribopure RNA extraction

source_name: Blood, 6hr, 0 Gy, replicate 3


title: Left ventricle-DOX-Rep2


title: DAP-knockdown vs Control (72h Proliferation) Replicate 4

description: DAP Knockdown versus Control, 72h proliferation, cell culture plate 2 (dye swap), replicate 4 of 8.


title: Blood, 6hr, 0 Gy, replicate 4

description: Ribopure RNA extraction

source_name: Blood, 6hr, 0 Gy, replicate 4


title: Blood, 6hr, 0 Gy, replicate 2

description: Ribopure RNA extraction

source_name: Blood, 6hr, 0 Gy, replicate 2


title: Blood, 6hr, 0 Gy, replicate 1

description: Ribopure RNA extraction

source_name: Blood, 6hr, 0 Gy, replicate 1


title: 13602906 - 2_I_F2 vs 2_NI_F2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

description: What are the genes implicated in the efficiency of nitrogenous nutrition when A.thaliana is inoculated with a PGPR (Plant Growth Promoting Rhizobacteria)?

hyb_protocol: 2_NI_F2 Cy5 / 2_I_F2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,600V,laser power 100%, Cy5:635nm,pmt voltage 770V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: aerial - Media Temperature 21°c Light  day /night 16/8

extract_protocol: 2_NI_F2:20ug. (Promega.pdf)

tag: ecotype

value: columbia

tag: dev.stage (boyes et al. plant cell 2001)

tag: treatment

growth_protocol: aerial - Media MM + 2 mM nitrate hygrometry in vitro Temperature 21°c Light  day /night 16/8

extract_protocol: 2_I_F2:20ug. (Promega.pdf)

treatment_protocol: Name:PGPR - environmental treatment - pgpr,phyllobacterium stm196:time 7day . Plantlets grew 7 days on medium with various nitrogen concentrations (0,5, 2 or 20 mM) and with 10^8 cfu/ml of Phyllobacterium STM196, a PGPR (Plant Growth Promoting Rhizobacteria)

value: phyllobacterium stm196:time 7day .


title: DAP-knockdown vs Control (72h Proliferation) Replicate 3

description: DAP Knockdown versus Control, 72h proliferation, cell culture plate 2, replicate 3 of 8.


title: ABI3 ChIP-chip_bio1_array 2

city: Gatersleben

first: Gudrun

last: Moenke

address: Corrensstr. 3

country: Germany

institute: IPK

description:
ABI3_bio1_array 2
biological replicate 1
Agilent Feature Extraction file:
US81403230_251479910021_S01_ChIP_105_Dec08.txt

hyb_protocol: 5 µg of both labeled samples were combined and mixed with Agilent-Blocking and -Hybridization buffer and 50 µg Cot-1DNA, f.v. 520 µl. After incubation for 3 min at 95°C and 30 min at 37°C, followed by centrifugation (1 min, 17,900g), 460 µl of the supernatant were used for hybridisation with each of the two 244K arrays in an Agilent-Hybrdization oven at 65°C (20rpm, 40 h), followed by sequential washing steps (performed by ATLAS GmbH Berlin).

scan_protocol: Scanning was performed using an Agilent DNA Microarray Scanner (Model G2505C) and Scan Control Software (version A.8.3.1) of Agilent

data_processing: For primary data processing Agilent Feature Extraction Software (Version 10.5.1.1) was used.

source_name: Control (input) non-immunoprecipitated chromatin fragments, seeds

label_protocol: DNA fragments were labeled  with Cy3-dUTP(ChIP sample) and Cy5-dUTP (control) using the Agilent Genomic DNA labelling Kit (Agilent Technologies) according to the manufacturer's instructions.

growth_protocol: Arabidopsis plants were grown on soil, with a 16 h light/ 8 h dark cycle

extract_protocol: Chromatin was isolated from unripe seeds of Arabidopsis thaliana Col-0, harvested 11-13 days after pollination. Cross-linking was done with 1% formaldehyde  for 20 min under vacuum, terminated by addition of glycine with a final concentration of 125 mM. Seeds were Potter-homogenized, filtered and the nuclei collected by centrifugation. Nuclear membranes were dissolved with detergents and  the chromatin was collected by high speed centrifugation. Chromatin was fragmented to an average size of 500 bp by ultra sonic treatment.   10 µg chromatin were combined with 2 µg anti-ABI3 antibody. The antibody-chromatin complex was captured by protein A coated magnetic beads (Invitrogen). After different washings the TF-DNA complex was eluted from the beads at 65°C for 15 min using 1% SDS. Eluates were incubated overnight at 65°C to reverse the cross-links. DNA  fragments were purified using a QIAquick PCR Purification Kit (Qiagen) and their concentration was determined with a NanoDrop 3300 (Thermo Fisher Scientific) fluorescence spectrophotometer. An aliquot (0.5 µg) of non-immunoprecipitated chromatin served as input control.   DNA fragments were blunted and ligated  with the  adapters oJW102  and oJW103 (Young lab:jura.wi.mit.edu/young_public/hESregulation/ChIP.html).  Adapter-ligated fragments were amplified using oJW102 as sole primer.

value: seed

tag: days after pollination

source_name: Chromatin fragments precipitated with anti-ABI3 antibody, seeds

tag: chip antibody

value: anti-ABI3 (raised against amino acid 2-237 of ABI3 in rabbits; selfmade)


title: 13602900 - 0.5_I_F2 vs 0.5_NI_F2

hyb_protocol: 0.5_NI_F2 Cy5 / 0.5_I_F2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 0.5_NI_F2:20ug. (Promega.pdf)

growth_protocol: aerial - Media MM + 0.5 mM nitrate hygrometry in vitro Temperature 21°c Light  day /night 16/8

extract_protocol: 0.5_I_F2:20ug. (Promega.pdf)


title: ABI3 ChIP-chip_bio2_array 2

description:
ABI3_bio2_array 2
biological replicate 2
Agilent Feature Extraction file:
US81403230_251479910020_S01_ChIP_105_Dec08.txt


title: 13602905 - 0.5_NI_F2 vs 0.5_I_F2

hyb_protocol: 0.5_I_F2 Cy5 / 0.5_NI_F2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: DAP-knockdown vs Control (72h Proliferation) Replicate 1

description: DAP Knockdown versus Control, 72h proliferation, cell culture plate 1, replicate 1 of 8.

tag: transfection

tag: cell growth stage

value: 72h Proliferation


title: 13501855 - 20_I_F2 vs 20_NI_F2

hyb_protocol: 20_NI_F2 Cy5 / 20_I_F2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 20_NI_F2:20ug. (Promega.pdf)

growth_protocol: aerial - Media MM + 20 mM nitrate hygrometry in vitro Temperature 21°c Light  day /night 16/8

extract_protocol: 20_I_F2:20ug. (Promega.pdf)


title: C-PNW-MM

city: Beaverton

first: Maria

last: Smit

state: OR

address: 20000 NW Walker Rd

department: Environmental and Biomolecular Systems

institute: Oregon Health and Science University

description: a sector of an ElectraSense 4X2K microarray with 2240 features representing 2200 unique probes was hybridized with an aliquot of biotin--labeled Pseudo-nitzschia ITS1 amplicon preparation

hyb_protocol: Hybridization of ElectraSense™ microarrays was performed as recommended by the manufacturer. The microarrays were hybridized at 51˚C for 1-2 hours, using biotin-labeled cDNA targets, 1.5-2 mg per sector for the 4X2K format.

scan_protocol: Hybridized microarrays were used for electrochemical signal detection using the ElectraSense Reader (CombiMatrix) with the corresponding kit as described by the manufacturer.

data_processing: Signal quantification was done by the ElectraSense Reader software during scanning. Data were analyzed using the Probe Weaver software from CombiMatrix, and HybAnalysis software from CustomArray Inc. Data QC was done with scatter plot analysis of duplicate hybridizations, and calculation of pair-wise correlation coefficients among samples using NCI-supported software BRB-ArrayTools (http://linus.nci.nih.gov/pilot/index.html). Then the duplicate samples were used to calculate average normalized signal intensities for each probe in each sample. Detection of ribotype presence was done by using HybAnalysis software to combine multiple probe hybridization signals into ‘sumscores’ for each ITS1 sequence represented on microarrays. The first step was normalization of microarray hybridization signals at the level of individual probes by conversion into Z-values (standard values). Z-value for a probe in a particular hybridization was calculated as the difference between the probe signal intensity and the mean intensity of all signals in this hybridization divided by the standard deviation of all signals. Thus, hybridization signals are transformed into deviations from the population mean, with a standard deviation of 1.0. To include a measurement of probe specificity into the sumscore calculations, the probes were assigned with statistical weights, probe weight values (PWV) that were inversely correlated with the number of calculated non-cognate target hits. A probe produced a calcultaed hit to a target ribotype if the Tm of the probe:target hybridization was at least 55°C. In this case, the corresponding PWV for the probe hybridization to the target ribotype was expressed as 1.0 (number of hits to self) divided by the number of calculated hits to all other targets sequences. Finally, for each target ribotype, the sum of all PWV was normalized to 1.0 (the weighed average approach). PWV were used as multipliers for analysis of each microarray hybridization to transform the probe-level Z-values into sumscores at the ribotype level. A sumscore value was generated for a target ribotype in a given microarray hybridization as the sum of Z-values of each probe multiplied by the corresponding PWV.

organism: Pseudo-nitzschia

source_name: filtered laboratory cell culture

label_protocol: The DNA targets corresponding to the internal transcribed spacer 1 sequences (ITS1) of the diatom genus Pseudo-nitzschia, were amplified from total genomic DNA samples using PCR with the following specific primers: PnAIIF, 5'-TCTTCATTGTGAATCTGA-3', and PnAIIR, 5'-CTTTAGGTCATTTGGTT-3' (Hubbard, Rocap et al. 2008). PCR was done with 10 ng of total genomic DNA, 0.2 uM of each primer, and AmpliTaq Gold 360 Master Mix (Applied Biosystems, Foster City, CA, USA). The reaction consisted of an initial denaturation at 94˚C for 2 min, followed by 30 cycles of 94˚C for 30 s, 50˚C for 30 s, and 72˚C for 2 min. PCR products were analyzed by gel electrophoresis using the FlashGel® System (Lonza), and then purified with the QIAquick PCR purification kit (Qiagen, Valencia, CA). Biotin labeling was done using LabelIT uArray Biotin Kit (Mirus Bio, Madison, WI) as described by the manufacturer. Finally, the biotin-labeled DNA targets were purified using Illustra ProbeQuant G-50 Micro Columns (GE Healthcare, Piscataway, NJ), and applied for microarray hybridization.

extract_protocol: Total genomic DNA was isolated using FastDNA® SPIN Kit for Soil (MP Biomedicals, Solon, OH) as described by the manufacturer. The resultant genomic DNA was analyzed using rapid gel electrophoresis with FlashGel® System (Lonza, Allendale, NJ).

treatment_protocol: After filtration, samples were preserved in RNAlater and stored at -80oC

tag: sample collection

value: 30 mL of laboratory cell culture was filtered through a 0.2 micron Sterivex filter to collect all cells

tag: location*

tag: longitude

tag: latitude

tag: sampling date and time

tag: salinity (psu)

tag: surface (s) or middle (m)

tag: sampling depth (m)

tag: t(oc)


title: stomach_e11.5_rep1

city: Tsukuba

first: Takaaki

last: Noguchi-Suda

state: Ibaraki

address: Tennoudai 1-1-1

department: Graduate school of life and enviromental sciences

country: Japan

institute: University of Tsukuba

description: Gene expression of stomach at E11.5

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 18 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), and 30 second at room temperature with acetonitrile,  then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides..

data_processing: The scanned images were analyzed with Feature Extraction Software 10. 5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non positive and significant, and Feature Non above background outliers were excluded.

source_name: mouse primordium stomach embryonic day 11.5

label_protocol: RNA was labeled using the ‘Agilent Low Input Quick Amp Kit’ (Agilent Technologies) following the manufacturer’s protocol. Cy3-labeled cRNA was purified with the RNeasy kit (Qiagen). Dye incorporation was assessed with the NanoDrop-1000 Spectrophotometer.

growth_protocol: ICR mouse were harbored following the guidelines of the National Institute of Advanced Industrial Science and Technology Animal Experiment Committee.

extract_protocol: The primordium stomach was dissected from mouse embryo at E11.5. Total RNA was isolated from stomach using the ‘RNeasy micro kit’ (Quiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Male and female mice were mated and the day of identification of a vaginal plug was E0.5. After 11days, mouse embryos were collected as E11.5.

tag: strain

value: ICR

tag: tissue

value: stomach

tag: age

value: embryonic day 11.5


title: 13602901 - 2_NI_F2 vs 2_I_F2

hyb_protocol: 2_I_F2 Cy5 / 2_NI_F2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: ecotype

tag: dev.stage (boyes et al. plant cell 2001)

tag: treatment


title: C-QRLPa-PN2


title: 13501854 - 20_NI_F2 vs 20_I_F2

hyb_protocol: 20_I_F2 Cy5 / 20_NI_F2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: C-MB-B3


title: DAP-knockdown vs Control (72h Proliferation) Replicate 2

description: DAP Knockdown versus Control, 72h proliferation, cell culture plate 1 (dye swap), replicate 2 of 8.

extract_protocol: Total RNA was extracted from cell culture plates (n = 4) using TRIReagent (Molecular Research Center, Cincinnati, OH) following manufacturer's instructions.  RNA integrity and concentration was determined using an Agilent 2100 Bioanlyzer (Santa Clara, CA).

tag: transfection

tag: cell type


title: 13501853 - 0.5_I_F vs 0.5_NI_F

hyb_protocol: 0.5_NI_F Cy5 / 0.5_I_F Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: 0.5_I_F:5ug. (Promega.pdf)


title: C-MB-B3-plus-D5

tag: sample collection


title: C-MB-Bla

tag: location*


title: esophagus_e11.5_rep1

description: Gene expression of esophagus at e11.5

source_name: mouse primordium esophagus embryonic day 11.5

value: esophagus


title: C-MB-D5

tag: longitude


title: 13501852 - 0.5_NI_F vs 0.5_I_F

hyb_protocol: 0.5_I_F Cy5 / 0.5_NI_F Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: C-LP17-PN2

tag: latitude


title: 13501851 - 20_NI_F vs 20_I_F

hyb_protocol: 20_I_F Cy5 / 20_NI_F Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: intestine_e11.5_rep1

description: Gene expression of intestine at E11.5

source_name: mouse primordium intestine embryonic day 11.5

value: intestine


title: 13501847 - 2_I_F vs 2_NI_F

hyb_protocol: 2_NI_F Cy5 / 2_I_F Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: primary astrocytes from the hippocampus, biological rep1

city: Majadahonda

first: Helena

last: Mira

state: Madrid

address: Ctra. Majadahonda-Pozuelo, km 2.2

department: Área de Biología Celular y Desarrollo

institute: Instituto de Salud carlos III

description: gene expression data from astroglial cultures derived from the postnatal mouse hippocampus

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on GeneChip Mouse Genome 430A 2.0 Array. GeneChips were washed and stained according to Affymetrix.

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

data_processing: The data were analyzed with Affymetrix GCOS 1.4 Software. The trimmed mean target intensity of each array was arbitrarily set to 400.

source_name: cultured primary astrocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: P3 brains were dissected in cold PBS; tissue was mechanically dissociated and plated in DMEM with 10% FBS. Adherent cells were shaked at 200 rpm, RT, >2hours to enrich for astroglia and were trypsinized and replated in the same medium and were allowed to form monolayers.

extract_protocol: Total RNA was extracted using RNeasy MINI from Qiagen according to the manufacturer's instructions.

treatment_protocol: Monolayers were kept in DMEM with 10%FBS until RNA extraction.

value: primary astrocytes

tag: brain region

value: hippocampus

value: postnatal day 3


title: primary astrocytes from the olfactory bulb, biological rep1

description: gene expression data from astroglial cultures derived from the postnatal mouse olfactory bulb

value: olfactory bulb


title: primary astrocytes from the ventral mesencephalon, biological rep1

description: gene expression data from astroglial cultures derived from the postnatal mouse ventral mesencephalon

value: ventral mesencephalon


title: 13501849 - 2_NI_F vs 2_I_F

hyb_protocol: 2_I_F Cy5 / 2_NI_F Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13501850 - 20_I_F vs 20_NI_F

hyb_protocol: 20_NI_F Cy5 / 20_I_F Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: C-PN004 Ala

tag: sampling date and time

tag: salinity (psu)


title: primary astrocytes from the subventricular zone , biological rep1

description: gene expression data from astroglial cultures derived from the postnatal mouse subventricular zone

value: subventricular zone


title: Epithelial Mock 0h rep8

description: Replicate 8

hyb_protocol: Standard Illumina hybridization protocol

source_name: 16HBE14 human bronchial epithelial cells,0h,mock-infected

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with NanoDrop 1000 instrument.

tag: infection status

value: Mock-infected

tag: time (hours)


title: SEP09-CM10-S

description:
a sector of an ElectraSense 4X2K microarray with 2240 features representing 2200 unique probes was hybridized with an aliquot of biotin--labeled Pseudo-nitzschia ITS1 amplicon preparation
*Location codes: number shows distance from the coast in km; CR, Columbia River transect in the plume and coastal ocean; NH, Newport Hydroline transect in the coastal ocean at Newport, Oregon; LP, La Push transect in the coastal ocean at La Push, Washington; GH21 and GHQR, locations near Grays Harbor, Washington; CM10, Cape Meares transect in the coastal ocean at Oceanside, Oregon; SAT03, SAT03 station in the Columbia River estuary near Astoria, Oregon (river mile 5).
total microbial assemblage from environmental water

organism: environmental samples

source_name: filtered environmental water sample

value: 1-5 L of environmental water was filtered through a 0.2 micron Sterivex filter to collect all microorganisms

tag: surface (s) or middle (m)

value: S

tag: sampling depth (m)

tag: t(oc)


title: C-Gom-B3


title: locus_coeruleus_PD patient LRRK2 G2019S mutation carrier 2

city: Barcelona

first: Teresa

last: Botta

address: Casanova 143

department: Serveis Científicotècnics

institute: IDIBAPS-Universitat de Barcelona-Hospital Clínic

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing:
Background adjustment by the Robust Multi-Array (RMA) algorithm was applied to probes intensities. Raw probes gene level expression were summarized from the corrected intensities and then quantile normalized.

Genome build: hg18
Exons used in the 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: locus coeruleus, PD with LRRK2 mutation

label_protocol: Samples were enzymatically fragmented and biotinylated using the Affymetrix GeneChip WT sense target labelling and control reagents kit (Affymetrix).

extract_protocol: Brain samples were obtained by donation to the Neurological Tissue Bank (Universitat de Barcelona-Hospital Clínic-IDIBAPS) with a postmortem delay of less than 24h. After histopathological confirmation for Parkinson's disease and genetic study for LRRK2 mutation, locus coeruleus tissue samples were dissected from corresponding brain sections stored at -80ºC. Pieces of tissue were homogenised with a high-speed homogeniser Polytron, and the RNA was extracted using the Rneasy lipid Tissue MiniKit (Qiagen) according to the manufacturer’s instructions and including a DNase digestion with RNase-Free DNase Set (Qiagen). The RNA concentration was measured with a Nanodrop 1000 Spectrophotometer (Thermo Fisher Scientific), and determination of the absorbance at 260 nm and RNA quality were evaluated by 2100 Bioanalyzer (Agilent) assessing the presence of ribosomal RNA 18S and 28S. Isolated RNAs were stored at -80ºC. For real-time qRT-PCR array validation, 2 µgr of total RNA were retrotranscribed by using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems). The real-time TaqMan-PCR assays for each gene were carried out with duplicates of cDNA in 96-well optical plates on a StepOnePlus Real-time PCR System (Applied Biosystems). Pre-designed TaqMan® Gene Expression Assays (AppliedBiosystems) were used for gene amplification.

treatment_protocol: Locus coeruleus samples from brain sections frozen at -80ºC.

tag: tissue

value: brain (locus coeruleus)

tag: disease

value: Parkinson's disease (PD) with LRRK2 mutation

tag: neuropathological diagnosis

value: LBP (4) + ARP (IV-C)

tag: gender

value: female

tag: family history of pd

value: not known

tag: age at onset (years)

tag: age at death (years)

tag: post-mortem delay (hours)

tag: l-dopa treatment

value: yes

tag: dopamine-agonists treatment

value: no

tag: l-dopa response (degree if available)

tag: dyskinesia (degree if available)

tag: dyskinesia (years after treatment start)

tag: motor fluctuations

tag: cognitive impairment

tag: hallucinations


title: locus_coeruleus_idiopathic PD patient5

source_name: locus coeruleus, IPD

value: idiopathic Parkinson's disease (IPD)

value: LBP (3-4) + ARP (III/A)

value: male

value: tremor (father)

value: moderated


title: SEP09-CR7-S-751

tag: sample collection

tag: location*

tag: longitude

tag: latitude

tag: sampling date and time

tag: salinity (psu)

tag: surface (s) or middle (m)

tag: sampling depth (m)

tag: t(oc)


title: liver_highB_rep4

city: Gothenburg

first: Marija

last: Cvijovic

address: Chalmers Tvärgata 3

country: Sweden

institute: Chalmers Univeristy of Technology

hyb_protocol: Prehybridization was performed at room temperature for 15min with a prehybridization buffer (25ml 2× MES hybridization buffer and 1% BSA in 50ml DEPC H2O). Fragmented cRNA (6µg/array) was dissolved in hybridization buffer (final concentration 5× SSPE [Ambion], 20% formamide, 0.5mg BSA/ml, 0.1× TE, 0.1mg human Cot-1 DNA [Invitrogen], 0.01% Tween 20). Samples were denatured for 3min at 95°C and hybridized to the biochips at 45°C for 16h, followed by a first washing step at 25°C with 6× SSPE and a second washing step at 45°C with 0.5× SSPE. Fluorescence staining was achieved by incubating the arrays with 5µg/ml streptavidin R-phycoerythrin conjugate (SAPE; Invitrogen) diluted in 6× SSPE containing 2mg BSA/ml at 25°C for 15min. Signal amplification was performed using biotinylated a-streptavidin antibodies (Vector Laboratories), followed by an additional incubation with SAPE.

scan_protocol: Signals were detected using the internal CCD camera system of the RT analyzer (Febit) instrument and quantified using the Geniom Wizard software. Integration times were between 390 and 620?ms, determined automatically by the instrument software.

data_processing:
All statistical calculations were done in R-2.12.2 (www.r-project.org) (1). Comparison of pre- and post normalized arrays was verified with Box and MA plots.  For data analysis limma package was used (2). Data were normalized using ‘quantile’ method , multiple linear models of arrays are fitted with lmFit. Moderated t-statistics and adjusted p-values of differential expression were calculated using the empirical Bayes model. For further analysis Volcano plots of log-fold changes versus log-odds of differential expression were created.
Duplicates were compared and due to expected similarity were treated as one exposure group. Control and High were compared pairwise.

organism: Oncorhynchus mykiss

source_name: liver

label_protocol:
Biotinylated anti - sense RNA (aRNA) was synthesized using MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion®). The
aRNA samples (20 µg) were vacuum dried in a vacuum centrifuge, dissolved in 10 µl water and fragmented according to the manufacturer's protocol.

extract_protocol: Homogenization of the frozen liver tissue was carried out using Tissuelyser (Qiagen, Hilden, Germany) and hepatic total RNA was extracted and purified using QIAcube and RNeasy® Plus Mini Kit (Qiagen). The RNA quantity and quality were assessed by spectrophotometric measurements with the Nanodrop 1000 (NanoDrop Technologies, Wilmington, DE). To ensure that no degradation had occurred, the isolated RNA was analyzed using Experion automated electrophoresis (Bio-Rad, Hercules, CA).

tag: gender

value: Male

tag: age

value: Juvenile

tag: tissue

value: liver

tag: ketoprofen concentration


title: locus_coeruleus_PD patient LRRK2 G2019S mutation carrier 1

tag: disease

tag: neuropathological diagnosis

value: LBP (4)

tag: family history of pd

tag: age at onset (years)

tag: age at death (years)

tag: post-mortem delay (hours)

tag: l-dopa treatment

tag: dopamine-agonists treatment

tag: l-dopa response (degree if available)

tag: dyskinesia (degree if available)

value: yes (severe)

tag: dyskinesia (years after treatment start)


title: SEP09-NH5-S-846

tag: sample collection

value: 1-5 L of environmental water was filtered through a 0.2 micron Sterivex filter to collect all microorganisms

tag: location*

tag: longitude

tag: latitude

tag: sampling date and time

tag: salinity (psu)

tag: surface (s) or middle (m)

value: S

tag: sampling depth (m)


title: liver_highB_rep2

tag: gender

tag: age

tag: tissue

tag: ketoprofen concentration


title: SEP09-LP32-M-774

value: M

tag: t(oc)


title: SEP09-NH10-S-736


title: SEP09-NH20-S-852


title: locus_coeruleus_idiopathic PD patient4

value: brain (locus coeruleus)

tag: disease

tag: neuropathological diagnosis

value: LBP + ARP (III)

value: female

tag: family history of pd

value: tremor (mother)

tag: age at onset (years)

tag: age at death (years)

tag: post-mortem delay (hours)

tag: l-dopa treatment

tag: dopamine-agonists treatment

value: partial

tag: motor fluctuations

tag: cognitive impairment

tag: hallucinations


title: locus_coeruleus_idiopathic PD patient3

value: idiopathic Parkinson's disease (IPD)

value: not known

value: yes

value: no

tag: l-dopa response (degree if available)

value: good

tag: dyskinesia (degree if available)

tag: dyskinesia (years after treatment start)


title: liver_highA_rep4

tag: gender

value: Male

tag: age

value: Juvenile

tag: tissue


title: liver_highB_rep3

value: Female

value: liver

tag: ketoprofen concentration


title: SEP09-CR40-S-760

tag: sample collection

value: 1-5 L of environmental water was filtered through a 0.2 micron Sterivex filter to collect all microorganisms

tag: location*

tag: longitude

tag: latitude

tag: sampling date and time

tag: salinity (psu)

tag: surface (s) or middle (m)

tag: sampling depth (m)

tag: t(oc)


title: locus_coeruleus_idiopathic PD patient1

tag: disease

tag: neuropathological diagnosis

value: Lewy body pathology (LBP,3-4) + Alzheimer related pathology (ARP, I)

tag: family history of pd

tag: age at onset (years)

tag: age at death (years)

tag: post-mortem delay (hours)

tag: l-dopa treatment

tag: dopamine-agonists treatment

tag: motor fluctuations

tag: cognitive impairment

tag: hallucinations


title: locus_coeruleus_control5

source_name: locus coeruleus, control

tag: tissue

value: control

value: no pathological changes (NPC)

tag: gender


title: locus_coeruleus_control1

value: brain (locus coeruleus)


title: liver_highB_rep1

tag: age

tag: ketoprofen concentration


title: liver_highA_rep2


title: locus_coeruleus_control4

value: male


title: SEP08-GH21-M-522

tag: sample collection

tag: location*

tag: longitude

tag: latitude

tag: sampling date and time

tag: salinity (psu)

tag: surface (s) or middle (m)

value: M

tag: sampling depth (m)


title: locus_coeruleus_control2

tag: disease

tag: neuropathological diagnosis

tag: family history of pd

tag: age at death (years)

tag: post-mortem delay (hours)


title: SEP08-SAT03-S-537

value: S

tag: t(oc)


title: liver_highA_rep3

tag: gender

tag: tissue


title: SEP08-NH20-M-498


title: SEP08-CR15-M-510


title: VEGF ROCK2 shRNA replicate 1

city: El Paso

first: Brad

middle: Allen

last: Bryan

state: Texas

address: 5001 El Paso Drive

department: Biomedical Sciences

institute: Texas Tech University Health Sciences Center

description: cultured MS1 pancreatic endothelial cells derived from islet of Langerhans

hyb_protocol: Fragmented cDNA was hybridized at 42˚C overnight using the HybBag mixing system with 1× OneArray Hybridization Buffer (Phalanx Biotech, Belmont, CA, USA), 0.01 mg/ml sheared salmon sperm DNA (Promega, Madison, WI, USA), at a concentration of 0.025 mg/ml labeled target. After hybridization, the arrays were washed according to the OneArray protocol.

scan_protocol: Raw intensity signals for each microarray were captured using a Molecular Dynamics Axon 4100A scanner, and measured using GenePixPro Software

data_processing: Statistical analysis of the datasets was performed with GeneSpring software using an unpaired t-test (p<0.01).  The false discovery rate (FDR) was calculated using the Benjamini Hochberg FDR multiple testing correction.

source_name: VEGF ROCK2 shRNA

label_protocol: Cy5.5 NHS ester (GE Healthcare)

growth_protocol: Engineered MS1 endothelial cells were grown at 100% confluence in Dubecco's modified Eagle's medium supplemented with 10% fetal bovine serum.

extract_protocol: Trizol Plus RNA purification system

treatment_protocol: MS1 endothelial cells stably expressing non-targeting, ROCK1-specific, or ROCK2-specific shRNA plasmids were grown to confluency and treated with sham or 2.5 ng/ml recombinant human vascular endothelial growth factor for 12 hours.

tag: strain

value: islet of Langerhans, endothelium

tag: genotype/variation

value: SV40 transformed, stably expressing ROCK2 shRNA plasmid

tag: treatment


title: VEGF ROCK2 shRNA replicate 2

value: 2.5 ng/ml recombinant human vascular endothelial growth factor


title: SEP08-CR30-S-514

tag: sample collection

tag: location*

tag: longitude


title: VEGF ROCK2 shRNA replicate 3


title: liver_highA_rep1

tag: age

tag: ketoprofen concentration


title: liver_controlB_rep4

value: 0 ug/L


title: liver_controlB_rep1


title: VEGF ROCK1 shRNA replicate 2

source_name: VEGF ROCK1 shRNA

value: SV40 transformed, stably expressing ROCK1 shRNA plasmid


title: Control 3

city: North Adelaide

first: Jozef

last: Gecz

state: South Australia

address: 72 King William Rd

department: Genetics Medicine

institute: SA Pathology

description: RNA extracted from patient with FRAXE associated ID

hyb_protocol: Performed by Australian Genomic Research Facility (AGRF)

data_processing:
CEL files were imported into Partek Genomic Suite Version 6.5 using robust multi array (RMA) normalisation, log 2 transformed. Gene expression was averaged from intensity values of all probesets comprising the genes. P value was caluclated using ANOVA-1-way assuming equal variances.
probe_group_file: HuEx-1_0-st-v2.na29.hg18.probeset
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core

source_name: Primary fibroblast RNA

growth_protocol: Primary fibroblast cell lines were established from skin punch of patients and controls, and maintained in RPMI (Sigma) supplemented with 10% fetal calf sera (FCS), 2mM L-Glutamine and 0.017 mg/ml benzypenicillin (CLS).

extract_protocol: Trizol Reagent (Invitrogen) and RNeasy Mini Kit (QIAGEN)

tag: phenotype

value: Normal


title: Control 2

scan_protocol: Performed by Australian Genomic Research Facility (AGRF)


title: liver_controlB_rep2

value: Male

value: Juvenile


title: VEGF ROCK1 shRNA replicate 3


title: Control 1

label_protocol: Performed by Australian Genomic Research Facility (AGRF)


title: liver_controlB_rep3

value: female

value: liver


title: NOV07-NH10-M-172

value: 1-5 L of environmental water was filtered through a 0.2 micron Sterivex filter to collect all microorganisms

tag: latitude

tag: sampling date and time

tag: salinity (psu)

tag: surface (s) or middle (m)

tag: sampling depth (m)


title: NOV07-CR40-S-165

tag: t(oc)


title: Patient 8

value: FRAXE


title: VEGF ROCK1 shRNA replicate 1


title: VEGF treatment replicate 2

source_name: VEGF treatment

value: SV40 transformed


title: NOV07-LP17-S-239


title: Control 4


title: VEGF treatment replicate 3


title: VEGF treatment replicate 1


title: liver_controlA_rep3

tag: gender


title: MAY09-GHQR-S

value: GHQR


title: MAY09-GH21-M


title: Patient 7


title: Patient 6


title: liver_controlA_rep4

tag: tissue


title: MAY09-LP32-S-592


title: CTR

city: Vancouver

first: Seyed Mehdi

last: Jafarnejad

state: BC

address: Room 436A, 2660 Oak St.

department: Dermatology and Skin Science

country: Canada

institute: The University of British Columbia

description: Control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions (http://www.abmgood.com/miRNA/pdfs/miRNA%20Array%20Analysis_Excel%20Instruction_v10.pdf)
For the normalization it uses the average of four housekeeping genes: SNORD44, SNORD47, SNORD48 and U6-2
Fold Change worksheet reports test/control (i.e., siSox4/siCTR and siSox4+F-Dicer/CTR) ratios.

label: SYBR Green

source_name: human melanoma cell line MMRU

growth_protocol: cells were cultured in DMEM media supplemented with %10 FBS

extract_protocol: Total RNAs were prepared with Qiazol extraction

treatment_protocol: cells were transfected with siRNAs by using SilenFect transfection reagent (BioRad) and with empty-Flag or Flag-Dicer contsructs by using Effectene transfection reagent (Qiagen)

tag: tumor stage

value: metastatic

value: siCTR+empty Flag-vector

tag: cell type

value: human melanoma cell line MMRU


title: ROCK2 shRNA replicate 3

source_name: ROCK2 shRNA

tag: strain

value: islet of Langerhans, endothelium

tag: genotype/variation

tag: treatment

value: saline sham


title: siSox4

description: Test

value: siSox4, Sox4 knockdown


title: ROCK2 shRNA replicate 2

value: SV40 transformed, stably expressing ROCK2 shRNA plasmid


title: siSox4+F-Dicer

description: Test

value: siSox4+-F-Dicer, rescue of Dicer expression in Sox4-knockdown cells


title: siCTR

description: Control

value: siCTR


title: Patient 5


title: MAY09-NH20-M-549

tag: sample collection

tag: location*

tag: longitude

value: M


title: MAY09-CR30-S-567

value: S


title: Patient 4

tag: phenotype


title: JUN08-LP6-M-356

tag: latitude


title: ROCK1 shRNA replicate 2

source_name: ROCK1 shRNA

value: SV40 transformed, stably expressing ROCK1 shRNA plasmid


title: liver_controlA_rep2

value: Female

tag: age

value: Juvenile

value: liver

tag: ketoprofen concentration

value: 0 ug/L


title: Patient 2

value: FRAXE


title: ROCK1 shRNA replicate 1


title: ROCK2 shRNA replicate 1


title: JUN08-CR40-S-337

value: 1-5 L of environmental water was filtered through a 0.2 micron Sterivex filter to collect all microorganisms

tag: sampling date and time

tag: salinity (psu)

tag: surface (s) or middle (m)


title: Cardiac/EB lineage cells

city: Chapel Hill

first: Scott

middle: M

last: Hammond

state: NC

department: Dept Cell and Developmental Biology

institute: University of North Carolina

hyb_protocol: RNA was hybridized to spotted microRNA array, as described in Thomson et al.

scan_protocol: Arrays were scanned on a genepix scanner.

data_processing: Raw intensity values were background subtracted, floored to 100, log transformed, and median centered by array and gene.  Duplicate microRNA spots were averaged to generate the value column.  Only mouse microRNAs (yes in mouse column of platform file) are presented in the value column.

source_name: Cardiac/EB lineage cells

label_protocol: Total RNA was labeled with Cy3 and RNA Ligase, as published (Thomson JM, et al, Nat Methods 1,47-53,2004).

growth_protocol: ES cells were grown under standard conditions.

extract_protocol: Trizol was used for RNA isolation

treatment_protocol: Cells were differentiated in culture along the hematopoietic lineage.  Cells from distinct differentiation stages were collected and RNA prepared.

value: cultured embryonic stem (ES)

tag: cell lineage

value: Cardiac/EB lineage cells


title: Bry+ sorted cells

source_name: Bry+ sorted cells

value: Bry+ sorted cells


title: Patient 3


title: sham treatment replicate 3

source_name: sham treatment

tag: tissue

value: islet of Langerhans, endothelium

value: SV40 transformed

value: saline sham


title: Bry- negative sorted cells

source_name: Bry- negative sorted cells

value: Bry- negative sorted cells


title: ROCK1 shRNA replicate 3


title: Patient 1


title: liver_controlA_rep1

tag: gender

value: Male


title: Hematopoietic lineage cells

source_name: Hematopoietic lineage cells

tag: cell type

value: Hematopoietic lineage cells


title: JUN08-CR15-S-331

hyb_protocol: Hybridization of ElectraSense™ microarrays was performed as recommended by the manufacturer. The microarrays were hybridized at 51˚C for 1-2 hours, using biotin-labeled cDNA targets, 1.5-2 mg per sector for the 4X2K format.

source_name: filtered environmental water sample

value: S

tag: sampling depth (m)

tag: t(oc)


title: JUN08-NH20-S-305


title: sham treatment replicate 2

tag: strain

tag: genotype/variation

tag: treatment


title: Bry+FoxA2+ double positive sorted cells

source_name: Bry+FoxA2+ double positive sorted cells

value: Bry+FoxA2+ double positive sorted cells


title: PChabaudi_24hpi

city: Singapore

first: Peter

last: Preiser

address: 60 Nanyang Drive, School of Biological Sciences

institute: Nanyang Technological University, School of Biological Sciences

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. DNA was labeled with fluorescent dyes and hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Scanning as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. Scanning was carried out with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. Lowess normalization and subsequent filtering for quality control were carried out using Acuity 4.0 (Axon Instruments). Spots were considered of good quality when they were unflagged and had at least 95% of pixels median intensity greater than the local background plus 2 times the standard deviation of the background for either dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy5) divided by the corresponding measurement in the reference channel (Cy3, P. chabaudi RNA reference pool).

organism: Plasmodium chabaudi chabaudi

source_name: Plasmodium chabaudi chabaudi (AS) parasites

label_protocol: Labeling carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

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

tag: culture type

value: in-vivo culture Balb/c mouse

tag: time point

value: 24hr post-sampling

source_name: Plasmodium chabaudi chabaudi (AS) RNA reference pool

value: Plasmodium chabaudi chabaudi (AS)

tag: sample type

value: mix of several samples collected across the 24-hour intraerythrocytic life cycle


title: AUG07-LP17-M-58

tag: sample collection

tag: location*

tag: longitude

tag: latitude

value: M


title: MAY09-NH20-S-550

value: 1-5 L of environmental water was filtered through a 0.2 micron Sterivex filter to collect all microorganisms

tag: sampling date and time

tag: salinity (psu)

tag: surface (s) or middle (m)


title: PChabaudi_18hpi

value: 18hr post-sampling


title: PChabaudi_22hpi

value: 22hr post-sampling


title: AUG07-LP52-S-53


title: AUG07-CR40-M-49


title: Presorted ES cells

source_name: Presorted ES cells

value: cultured embryonic stem (ES)

tag: cell lineage

value: Presorted ES cells


title: PChabaudi_20hpi

value: 20hr post-sampling


title: AUG07-CR15-S-43


title: PChabaudi_16hpi

value: 16hr post-sampling


title: PChabaudi_14hpi

value: 14hr post-sampling


title: PChabaudi_10hpi

value: 10hr post-sampling


title: APR08-LP17-S-296


title: AUG07-NH20-M-22


title: PChabaudi_12hpi

value: 12hr post-sampling


title: sham treatment replicate 1

tag: tissue

value: islet of Langerhans, endothelium

value: SV40 transformed

value: saline sham


title: PChabaudi_8hpi

value: in-vivo culture Balb/c mouse

value: 8hr post-sampling


title: APR08-CR30-M-287

tag: sampling depth (m)


title: APR08-LP6-M-292

tag: t(oc)


title: PChabaudi_6hpi

value: 6hr post-sampling

tag: strain

value: Plasmodium chabaudi chabaudi (AS)

value: mix of several samples collected across the 24-hour intraerythrocytic life cycle


title: PChabaudi_4hpi

value: 4hr post-sampling


title: PChabaudi_2hpi

value: in-vivo culture in Balb/c mouse

value: 2hr post-sampling