title: hTERT immortalized cells, empty vector control, passage 70

status: Public on Dec 01 2010

type: RNA

city: Raanana

first: Yuval

last: Tabach

address: Hativat Givaty 30

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: samples were taken at 33 points along the cultivation process and hybridized with the GeneChip Human Genome U133A 2.0 Array. The microarrays were processed using RMA (Irizarry et al. 2003) and normalized.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Prostate

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

extract_protocol: cells were trypsinized and pelleted after 3 days at logarithmic growth stage

treatment_protocol: EP156T immortalized prostate cell cultures were grown in MCDB-153+ media under standard tissue culture conditions

tag: cell type


title: hTERT immortalized cells, mutant p53 vector , passage 70


title: hTERT immortalized cells, dominant negative peptide for p53 vector , passage 80


title: hTERT immortalized cells, mutant p53 vector , passage 30


title: hTERT immortalized cells + mutant p53, passage 80, reps a and b


title: hTERT immortalized cells, empty vector control, passage 50


title: hTERT immortalized cells, dominant negative peptide for p53 vector , passage 60


title: hTERT immortalized cells passage 20

value: hTERT immortalized cells passage 20


title: hTERT immortalized cells + dominant negative peptide for p53, passage 80, reps a and b


title: hTERT immortalized cells, empty vector control, passage 80


title: hTERT immortalized cells, mutant p53 vector , passage 80


title: hTERT immortalized cells, mutant p53 vector , passage 60


title: hTERT immortalized cells, dominant negative peptide for p53 vector , passage 70


title: hTERT immortalized cells, dominant negative peptide for p53 vector , passage 50


title: hTERT immortalized cells passage 10

value: hTERT immortalized cells passage 10


title: hTERT immortalized cells, mutant p53 vector , passage 40


title: hTERT immortalized cells, empty vector control + hRAS, passage 80, reps a and b


title: CD4 3006-6 Day 21

city: Boston

first: Judy

last: Yen

state: MA

address: 620 Albany St., Rm 401H

department: NEIDL/Microbiology

country: USA

institute: Boston University School of Medicine

hyb_protocol: 15 µg of Cy5-labeled sample was mixed with 10 µg of Cy3-labeled reference sample and hybridized using protocols found on http://cmgm.stanford.edu/pbrown/protocols/index.html.  Arrays were hybridized in SciGene Hybex incubators.

scan_protocol: Scanned on Axon 4000B and 4200AL scanners. Images were quantified using GenePix and SpotReader.

data_processing: normalized using regression correlation, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Data were then filtered for signal intensities greater than or equal to 2 (log2 ratio) in either channel via the Stanford Microarray Database.  Data were further processed by subtracting the day 0 log2 ratio from corresponding samples later in the time course from the same subject (supplemental).

source_name: Blood sample taken 21 days post-vaccination with LC16m8

label_protocol: 500 ng of total RNA were reverse-transcribed, linearly amplified through in vitro transcription, and fluorescently labeled using the Ambion Amino Allyl MessageAmp II kit (Applied Biosystems).  Test samples were labeled with Cy5 and reference samples were labeled with Cy3

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

tag: vaccine

tag: day collected

value: CD4+ T cells

source_name: Universal Human Reference from Stratagene

tag: rna source

value: 10 different human cell lines

tag: vendor

value: Stratagene


title: hTERT immortalized cells, mutant p53 vector , passage 50


title: hTERT immortalized cells, passage 80, reps a and b

value: hTERT immortalized cells, passage 80


title: hTERT immortalized cells, empty vector control, passage 60


title: hTERT immortalized cells, dominant negative peptide for p53 vector , passage 40


title: hTERT immortalized cells, empty vector control, passage 30


title: hTERT immortalized cells, empty vector control, passage 40


title: hTERT immortalized cells, mutant p53 vector + hRAS, passage 80, reps a and b


title: hTERT immortalized cells, dominant negative peptide for p53 vector , passage 30


title: hTERT immortalized cells passage 0

value: hTERT immortalized cells passage 0


title: CD4 3013-1 Day 21


title: CD4 3004-0 Day 13

source_name: Blood sample taken 13 days post-vaccination with LC16m8


title: CD4 3011-5 Day 21


title: CD4 3011-5 Day 13


title: CD4 3006-6 Day 13


title: CD4 3013-1 Day 13


title: CD4 3011-5 Day 7

source_name: Blood sample taken 7 days post-vaccination with LC16m8


title: CD4 3013-1 Day 7


title: CD4 3004-0 Day 10

source_name: Blood sample taken 10 days post-vaccination with LC16m8


title: CD4 3013-1 Day 10


title: CD4 3004-0 Day 21


title: CD4 3011-5 Day 10


title: CD4 3006-6 Day 7


title: CD4 3006-6 Day 10


title: Comfrey_2

city: Jefferson

first: Zhiguang Li

state: AR

address: HFT130, 3900 NCTR Road

department: Division of Genetic an Reproductive Toxicology

institute: National Center for Toxicological Research

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Raw intensities experienced the adjustments of data-filtering, log 2 transformation, gene centering and normalization with a cyclic LOWESS (locally weighted regression). MiRNAs with at least one of the 12 intensities larger than the intensity threshold of 32 were considered detectable.

organism: Rattus norvegicus

source_name: Liver

label_protocol: To perform the miRNA array experiment, total RNA (2 to 5 µg) was first size fractionated using a YM-100 Microcon centrifugal filter (Millipore). The small RNAs (< 300 nt) were then 3’-extended with a poly(A) tail using poly(A) polymerase.  Thereafter, an oligonucleotide tags was ligated to the poly(A) tail for later staining with fluorescent dye Cy3.

growth_protocol: All animal procedures followed the recommendations of the NCTR Institutional Animal Care and Use Committee for the handling, maintenance, treatment, and sacrifice of the rats.

extract_protocol: RNAs were isolated from about 60 mg rat liver tissue suspended in RNA-Later ICE (Ambion Inc., Austin, TX) using mirVanaTM miRNA isolation kit (Ambion). This kit combines the advantages of acid-phenol:chloroform extraction and glass solid-phase extraction and can yield high quality of microRNA-retaining total RNAs. RNA concentrations were determined on NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, Delaware) and the qualities were checked on on an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA) using an RNA6000 Nano LabChip (Agilent).

treatment_protocol: Male, 6-week-old Big Blue rats were fed with the basal NIH-31 diet or with the 8% comfrey dosed diet for 12 weeks. The animals were sacrificed at the end of the treatment. The livers were isolated, flash frozen in liquid nitrogen, and stored at - 80°C.

tag: gender

value: Male

tag: age

value: 6 weeks

tag: strain

value: Fisher 344

tag: genotype/variation

value: Big Blue Transgenic

tag: tissue

value: liver

tag: agent

value: comfrey


title: Control_5

value: control


title: Comfrey_1


title: Comfrey_4


title: Control_6


title: Comfrey_6


title: Control_4


title: Comfrey_5


title: Comfrey_3


title: CD4 3013-1 Day 3

source_name: Blood sample taken 3 days post-vaccination with LC16m8


title: CD4 3004-0 Day 7


title: Control_3


title: CD4 3011-5 Day 3


title: Control_1


title: Control_2


title: CD4 3006-6 Day 3


title: CD4 3004-0 Day 3


title: CD4 3013-1 Day 0

source_name: Blood sample taken pre-vaccination with LC16m8


title: CD4 3006-6 Day 0


title: CD4 3024-8 Day 21

source_name: Blood sample taken 21 days post-vaccination with DryVax

value: DryVax


title: CD4 3011-5 Day 0


title: CD4 3004-0 Day 0


title: CD4 3024-8 Day 10

source_name: Blood sample taken 10 days post-vaccination with DryVax


title: CD4 3003-7 Day 13

source_name: Blood sample taken 13 days post-vaccination with DryVax


title: CD4 3019-9 Day 21


title: CD4 3019-9 Day 10


title: CD4 3024-8 Day 7

source_name: Blood sample taken 7 days post-vaccination with DryVax


title: hTERT immortalized cells, dominant negative peptide for p53 vector + hRAS, passage 80, reps a and b


title: CD4 3003-7 Day 21


title: CD4 3019-9 Day 7


title: CD4 3003-7 Day 10


title: CD4 3019-9 Day 13


title: CD4 3024-8 Day 13


title: CD4 3024-8 Day 3

source_name: Blood sample taken 3 days post-vaccination with DryVax


title: CD4 3003-7 Day 3


title: CD4 3019-9 Day 3


title: CD4 3003-7 Day 7


title: CD4 3019-9 Day 0

source_name: Blood sample taken pre-vaccination with DryVax


title: CD4 3024-8 Day 0


title: CD4 3003-7 Day 0

source_name: Blood sample taken pre-vaccination with Dryvax


title: Spt6-HA_vs_noTag_#2

type: genomic

city: Montréal

first: François

last: Robert

state: Québec

address: 110, avenue des Pins Ouest

department: Chromatin and Genomic Expression

country: Canada

institute: Institut de recherches cliniques de Montréal (IRCM)

description: Biological replicate 2 of 2. Spt6 occupancy measured by the IP/Input ratio in WT cells.

hyb_protocol: Resuspend colored pellet in 110uL hybridization buffer (100uL DIGEasy Buffer, 5uL 5mg/mL Salmon Sperm DNA, 20uL 8mg/mL yeast tRNA). Put at 95C for 3 minutes. Put at 65C while waiting for hybridization. Follow standard Agilent chamber hybridization protocols. Incubate 16-20h at 40C in hybridization oven at 20RPM rotation speed. Post-Hybridization Washes: Separate coverslip and slide in Wash buffer #1. Wash slides in Wash buffer #1 for 5 minutes at room temperature on an orbital shaker (cover the dish to avoid light on the slides). Wash in 31C Wash buffer #2 for 5 minutes on an orbital shaker. Take slides out of the buffer slowly to dry them, and allow them to air dry for 1 minute. Wash Buffer #1: 6x SSPE, 0.005% N-lauroylsarcosine. Wash Buffer #2: 0.06x SSPE.    Stripping is done in 500 ml of 5 mM Potassium phosphate buffer pH 6.6. 1. Use a 2L beaker, which can fit a slide rack. Pour the stripping buffer, submerge the rack with slides (from 1 to 10) and heat it up slowly while stirring with a stir bar until the liquid boils with big bubbles. It usually takes 15 to 20 minutes. Do not overboil it. 2. Remove the rack and briefly rinse in a container with water. Slowly remove the rack from the liquid. Cy5 channel will be stripped much better than Cy3, but this does not affect the performance of subsequent hybridizations. Stock solution of 1M Potassium phosphate buffer, pH 6.6: Mix 3.81 ml of 1M K2HPO4 + 6.19 ml of 1M KH2PO4. Dilute 2.5 ml of this 1M solution in 500 ml Milli-Q water to obtain 5mM Potassium phosphate buffer, pH 6.6.

scan_protocol: Axon GenePix 4000B scanner and the GenePix Pro extraction software were used. Scan at 100% laser power for both channels. Set the Pixel Size to 5um / pixel. Set the Lines to average to 1. Set the Focus Position to 0um. Adjust PMTs so that approximately 1-2% spots are saturated. This is done to ensure full dynamic range utilization. Adjust PMTs so that the intensity ratio is 0.9 - 1.1 when looking at intensity values greater than or equal to 3000 on the Intensity / Frequence histogram. Images were quantified using Axon GenePix (version 6.1.0.4).

data_processing: The raw data were corrected (foreground-background) then normalized using the limma's loess function (Yang et al.,2002) in BioConductor (from the ArrayPipe Analysis Pipeline (Hokamp et al., 2004)) and replicates were combined using a weighted average method as described previously (Pokholok et al., 2005).

molecule: genomic DNA

organism: Saccharomyces cerevisiae

label_protocol: Blunting: Do everything on ice! Add 70uL of the blunting solution (11uL NEB Buffer #2, 0.5uL BSA 10mg/mL, 0.5uL 20mM dNTPs, 0.2uL T4 DNA Polymerase 3U/uL, 57.8uL ddH2O) to 40uL of the resuspended DNA obtained at the end of the cleanup step. For WCEs, use 2uL + 38uL ddH2O instead of 40uL. Incubate 20 minutes at 12C. Add 11.5uL 3M NaOAc, pH 5.2, and 0.5uL Glycogen 20mg/mL and vortex briefly. Extract with 120uL Phenol/Chloroform/Isoamyl alcohol (25:24:1). Transfer 110uL to a new tube, and add 230uL -20C 100% EtOH. Put at -80C for 30min, then spin 20 minutes at 4C. Wash the pellet with 500uL -20C 70% EtOH and spin 15 minutes at 4C. Resuspend the pellet in 25uL ddH2O and place on ice.    Ligation: Thaw everything on ice, and do all manipulations on ice. Add 25uL of ligase mix (10uL 5x T4 Ligase Buffer, 6.7uL 15uM unidirectional linkers, 0.5uL T4 DNA Ligase, High Concentration, 8uL ddH2O) to the resuspended pellet from the blunting step. Incubate overnight at 16C. Add 6uL 3M NaOAc, pH 5.2, and vortex. Add 130uL -20C 100% EtOH and centrifuge 20 minutes at 4C. Wash the pellet (should be a smear on the side of the tube) with 500uL -20C 70% EtOH. Spin 15 minutes at 4C. Dry the pellet and resuspend in 25uL ddH2O.     Labeling: Add 15uL of PCR Labeling mix (4uL 10x ThermoPol Buffer, 2uL 5mM aa-dUTP mix, 1.25uL Oligo FR1, 7.75uL ddH2O) to the pellet from the ligation step. Start the PCR program, and during the first step (4 minutes at 55C), add 10uL of the polymerase mix (1uL 10x ThermoPol buffer, 1uL Taq Polymerase 5U/uL, 0.01uL Pfu Polymerase Turbo 2.5U/uL, 8uL ddH2O). PCR cycling conditions: 1) 5:00 at 55C 2) 5:00 at 72C 3) 2:00 at 95C 4) 0:30 at 95C 5) 0:30 at 55C 6) 1:00 at 72C 7) Repeat steps 4-6 31 more times. 8) 4:00 at 72C 9) Forever at 4C Purify PCR reactions with Qiagen PCR Cleanup kits, following their protocol BUT use a phosphate wash buffer and a phosphate elution buffer instead of their buffers PE and EB, respectively. Also, wash the columns only once, and elute twice with 30uL elution buffer. Speed-vac the eluate to dryness. Resuspend the pellets with fresh 4.5uL 0.1M Sodium Carbonate Buffer, pH 9.0. Add 4.5uL of the appropriate NHS-ester Cy-dye. Fresh tubes of NHS-ester Cy-dye should be resuspended in 73uL DMSO. Mix well, and incubate at room temperature in the dark for one hour. Add 35uL 0.1M NaOAc, pH 5.2. Purify using the Qiagen PCR Cleanup protocol using all their buffers, but wash only once and elute twice in 30uL. It is a good idea to elute both samples of a pair (Cy5 and Cy3) in the same tube to avoid DNA loss upon later resuspension. Speed-vac until 10-20uL are left, or to drynes+B33s. Phosphate Wash Buffer (100mL): 0.5mL 1M KPO4, pH 8.5 15.25mL ddH2O 84.25mL 95% EtOH Solution will be cloudy upon mixing. Phosphate Elution Buffer (10mL): 0.04mL 1M KPO4, pH 8.5 9.96mL ddH2O 1M KPO4, pH 8.5 (10mL): 9.5mL 1M K2HPO4 0.5mL 1M KH2PO4 1M Sodium Carbonate Buffer, pH 9.0 (100mL): 10.8g Na2CO3 80mL ddH2O pH to 9.0 with concentrated HCl Adjust volume to 100mL with ddH2O DILUTE 1:10 WHEN USING! Solution will change composition over time. Use only if less than a month old. Reference: Drouin S., Robert F. Methods (in press).

growth_protocol: 50 mL of YPD were inoculated with 1 ml of overnight culture and incubated at 30C to OD600 0.5. The cells were crosslinked for 30 minutes at RT with formaldehyde at a final concentration of 1 %. Crosslinking was quenched for 10 minutes by the addition of glycine to a final concentration of 125mM.

extract_protocol: Crosslinked cells were washed twice with 50mL ice cold TBS, resuspended in 500uL lysis buffer (50mM HEPES-KOH, pH 7.5 140mM NaCl 1mM EDTA 1% Triton X-100 0.1% Na-deoxycholate 1mM PMSF 1mM Benzamidine 10ug/mL Aprotinin 1ug/mL Leupeptin 1ug/mL Pepstatin) and acid-washed glass beads were added to the meniscus. Cells were lysed using bead-beater (3x1 min, with 5min breaks on ice). The whole cell extract was mixed with 500ul of lysis buffer and centrifuged at 14000rpm for 1 minute. The pellet was resuspended in 1 ml of lysis buffer and washed twice more. The resulting extract was sonicated 6x9 minutes (30 sec on/1 min off) using a Diagenode sonicator and subsequently centrifuged at 14000rpm for 5 minutes. The supernatant containing the sonicated chromatin was transferred to a new tube.    For the immunoprecipitation, antibodies were pre-incubated at the below indicated concentration overnight at 4C with 50ul of pan mouse IgG Dynabeads (Invitrogen), which were previously washed 2x with cold TBS + 0.5% BSA. The antibody-bound beads were washed 2x in 1 mL of ice-cold lysis buffer containing protease inhibitors and resuspended in 30ul lysis buffer per IP. 860ul of chromatin were added to the antibody-bound beads and incubated overnight at 4C. The beads were then washed twice with 1mL ice cold lysis buffer, twice with 1mL ice cold lysis buffer (500mM NaCl), twice with ice cold ChIP wash buffer (10mM Tris-HCl, pH 8.0 250mM LiCl 0.5% NP40 0.5% Na-deoxycholate 1mM EDTA) and once with ice cold TE. The bound proteins were eluted and crosslinks were reversed by incubating the beads with 50ul of TE-SDS1% overnight in a 65C oven to minimize evaporation. The 8WG16 anti-CTD of Rpb1 antibody (Covance) was used at 15ul per immunoprecipitation. The anti-HA 12CA5 antibody (provided by Brad Cairns, University of Utah) was used at 7ul per immunoprecipitation.    To clean up the DNA, the chromatin-containing supernatant was mixed with 350ul of TE containing 3ul of RNAseA (10mg/mL) and 2ul of glycogen (20mg/mL) and incubated for 2 hours at 37C.  To digest the proteins, 15ul of 10% SDS and 7.5ul Proteinase K (20mg/ml) were added and the mixture was incubated for an additional 2 hours at 37C. The samples were extracted 2x with 400uL phenol/chloroform/isoamyl alcohol (25:24:1). The DNA was precipitated with 1 mL of 100% ethanol and 14uL of 5M NaCl, the samples were centrifuged at 14,000rpm for 20 minutes at 4C. The DNA pellet was washed in 1 mL of 70% ethanol, dried and resuspended in 60ul of TE.

tag: antibody

value: HA 12CA5 (provided by Brad Cairns, University of Utah)

value: wt with HA tag

value: wt


title: RNAPII_vs_noAb_#1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/Input ratio in WT cells.

value: 8WG16 anti-CTD of Rpb1

tag: antibody manufacturer

value: Covance

tag: antibody catalog #

tag: lot #


title: RNAPII_vs_noAb_#2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/Input ratio in WT cells.


title: Spt6-HA_vs_noTag_#1

description: Biological replicate 1 of 2. Spt6 occupancy measured by the IP/Input ratio in WT cells.


title: CD19 3006-6 Day 10

value: CD19+ B cells

value: 10 different human cell lines


title: CD19 3011-5 Day 10

value: Stratagene


title: CD19 3011-5 Day 21


title: CD19 3004-0 Day 10


title: CD19 3013-1 Day 13


title: Spt6-HA_vs_noTag--37C_#1

description: Biological replicate 1 of 2. Spt6 occupancy measured by the IP/Input ratio in WT cells at 37C.

data_processing: The raw data were corrected (foreground-background) then normalized using the limma's loess function (Yang et al.,2002) in BioConductor (from the ArrayPipe Analysis Pipeline (Hokamp et al., 2004)) (using Bioconductor packages: Biobase version 1.12.1 and limma version 2.9.1; R version 2.4.0) and replicates were combined using a weighted average method as described previously (Pokholok et al., 2005).

growth_protocol: 50 mL of YPD were inoculated with 1 ml of overnight culture and incubated at 37C to OD600 0.5. The cells were crosslinked for 30 minutes at RT with formaldehyde at a final concentration of 1 %. Crosslinking was quenched for 10 minutes by the addition of glycine to a final concentration of 125mM.


title: CD19 3006-6 Day 21


title: CD19 3013-1 Day 10


title: CD19 3004-0 Day 13


title: CD19 3013-1 Day 21


title: CD19 3006-6 Day 13


title: Spt6-HA_vs_noTag--37C_#2

description: Biological replicate 2 of 2. Spt6 occupancy measured by the IP/Input ratio in WT cells at 37C.


title: CD19 3011-5 Day 13


title: RNAPII_vs_noAb--37C_#2

description: Biological replicate 2 of 2. RNAPII occupancy measured by the IP/Input ratio in WT cells at 37C.


title: CD19 3013-1 Day 7


title: RNAPII_vs_noAb--37C_#1

description: Biological replicate 1 of 2. RNAPII occupancy measured by the IP/Input ratio in WT cells at 37C.


title: CD19 3013-1 Day 0


title: CD19 3011-5 Day 7


title: CD19 3011-5 Day 0


title: CD19 3004-0 Day 3


title: CD19 3006-6 Day 3


title: CD19 3011-5 Day 3


title: CD19 3006-6 Day 0


title: CD19 3006-6 Day 7


title: CD19 3019-9 Day 21


title: CD19 3004-0 Day 0


title: CD19 3003-7 Day 21


title: CD19 3024-8 Day 21


title: CD19 3004-0 Day 21


title: CD19 3024-8 Day 13


title: CD19 3003-7 Day 13


title: CD19 3019-9 Day 10


title: CD19 3019-9 Day 13


title: CD19 3003-7 Day 0


title: CD19 3019-9 Day 7


title: CD19 3019-9 Day 0


title: CD19 3003-7 Day 3


title: CD19 3019-9 Day 3


title: CD19 3024-8 Day 7


title: CD19 3003-7 Day 7


title: PBMC 3011-5 Day 21

value: PBMC


title: CD19 3024-8 Day 3


title: CD19 3003-7 Day 10


title: CD19 3024-8 Day 0


title: PBMC 3004-0 Day 13


title: PBMC 3006-6 Day 21


title: PBMC 3004-0 Day 21


title: PBMC 3013-1 Day 21


title: PBMC 3013-1 Day 10


title: CD19 3004-0 Day 7


title: PBMC 3013-1 Day 13


title: PBMC 3011-5 Day 13


title: PBMC 3006-6 Day 13


title: PBMC 3011-5 Day 10


title: PBMC 3006-6 Day 7


title: PBMC 3006-6 Day 10


title: PBMC 3013-1 Day 7


title: PBMC 3004-0 Day 10


title: PBMC 3013-1 Day 3


title: PBMC 3011-5 Day 3


title: PBMC 3011-5 Day 7


title: PBMC 3004-0 Day 3


title: PBMC 3006-6 Day 3


title: PBMC 3008-2 Day 13


title: PBMC 3019-9 Day 13


title: PBMC 3013-1 Day 0


title: PBMC 3011-5 Day 0


title: PBMC 3003-7 Day 13


title: PBMC 3006-6 Day 0


title: PBMC 3004-0 Day 0


title: PBMC 3019-9 Day 21


title: PBMC 3024-8 Day 13


title: PBMC 3024-8 Day 21


title: PBMC 3003-7 Day 21


title: PBMC 3024-8 Day 10


title: PBMC 3019-9 Day 10


title: PBMC 3008-2 Day 10


title: PBMC 3003-7 Day 7


title: PBMC 3024-8 Day 3


title: PBMC 3008-2 Day 3


title: PBMC 3008-2 Day 7


title: PBMC 3024-8 Day 7


title: PBMC 3003-7 Day 10


title: PBMC 3003-7 Day 3


title: PBMC 3024-8 Day 0


title: PBMC 3003-7 Day 0


title: PBMC 3008-2 Day 0


title: PBMC 3004-0 Day 7


title: PBMC 3019-9 Day 7


title: PBMC 3019-9 Day 3


title: PBMC 3019-9 Day 0


title: w1118 replicate 3

city: Salt Lake City

first: Carl

last: Thummel

state: UT

department: Human Genetics

institute: University of Utah

description: biological replicate 3 of 3

hyb_protocol: Fluorescently labeled cRNA samples (825 ng each) were fragmented and combined with Agilent Hi-RPM Hybridization Buffer.  Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers.  Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization oven and were incubated at 65ºC for 17 hours with a rotational speed of 10 rpm.  Following incubation, the microarray slide was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; room temperature) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; 31ºC) for 1 minute each.  Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner.  The scanner performs simultaneous detection of Cyanine-3 and Cyanine-5 signal on the hybridized slide.  Data captured from the scanned microarray image is saved as a TIF file.

data_processing: TIF files generated from the scanned microarray image are loaded into Agilent Feature Extraction Software version 9.5.1.1.  The software automatically positions a grid and finds the centroid positions of each feature on the microarray.  This information is used to perform calculations that include feature intensities, background measurements and statistical analyses.  Data generated by the software is recorded as a tab-delimited text file. The data were quantile-normalized using R and are presented in log base 2.

organism: Drosophila melanogaster

source_name: w1118 L3 larvae

label_protocol: The Agilent Two-Color Quick Amp Labeling Kit is used to generate fluorescently labeled cRNA for two-color microarray hybridizations.  Agilent RNA spike-in controls are combined with input total RNA samples (50 to 1000 ng).  The polyadenylated fraction of the total RNA sample is primed with oligo dT/T7 RNA polymerase promoter oligonucleotide sequences and cDNA synthesis is accomplished through the addition of MMLV-RT.   Following cDNA synthesis, T7 RNA polymerase and dye-labeled nucleotides are combined with the reaction mixture to simultaneously amplify the target material through the generation of cRNA and incorporate either cyanine 3-CTP or cyanine 5-CTP.  Fluorescently labeled, cRNA molecules are purified from the reaction mixture using the Qiagen RNeasy mini kit.  The concentration of the purified samples is determined using a NanoDrop ND-1000 spectrophotometer.

growth_protocol: Larvae were grown on molasses agar plates supplemented with yeast paste and allowed to develop at 25ºC. Late second instar larvae were collected based on size and spiracle morphology and allowed to develop for 18 more hours.

extract_protocol: Total RNA extracted using Tripure (Roche) following manufacturer's instructions and DNase treated using Qiagen Rneasy + DNase

treatment_protocol: No treatment

tag: food source

value: yeast paste

tag: developmental stage

value: L3 larvae


title: w1118 replicate 2

description: biological replicate 2 of 3


title: DHR38 replicate 2

description: biological replicate 2 of 3

source_name: DHR38 L3 larvae


title: DHR38 replicate 3

description: biological replicate 3 of 3


title: w1118 replicate 1

description: biological replicate 1 of 3


title: 17472002

city: London

first: Gareth

last: Wilson

address: 23 Huntley Street

country: United Kingdom

institute: UCL Cancer Institute

description: MeDIP vs. INPUT Whole Blood Genomic DNA.

hyb_protocol: Nimblegen protocol.

scan_protocol: Nimblegen protocol.

data_processing: Raw data was loess, then quantile normalised.

source_name: MeDIP on whole blood DNA, control

label_protocol: Nimblegen protocol.

extract_protocol: Peripheral whole blood used for DNA extraction.

tag: phenotype

value: whole blood

tag: medip antibody

value: Eurogentec 5'-methylcytosine Ab

tag: sample type

value: MeDIP

source_name: whole blood DNA input, control

value: Control

value: input


title: DHR38 replicate 1

description: biological replicate 1 of 3


title: 17477302

value: control


title: 15667002


title: 15671202


title: 15661302


title: 15675402


title: 15675102

source_name: MeDIP on whole blood DNA, type 2 diabetes

value: type 2 diabetes

source_name: whole blood DNA input, type 2 diabetes


title: 15702002


title: 15678402


title: 15790002


title: 15830102


title: 15660302


title: 15675302


title: 15660402


title: 15660602


title: 15672102


title: 15693002


title: 15656902


title: 15660202


title: 15666002


title: 15655902


title: 14273002


title: 15660502


title: 15651402


title: 15660002


title: 15657202


title: 15651802


title: 11286302


title: 11430002


title: 14282702


title: 11284602


title: 11285102


title: 11285802


title: 14284702


title: 11218002


title: 11218202


title: 11284302


title: CD4 3008-2 Day 13

tag: vaccine

value: DryVax

tag: day collected

tag: cell type

value: CD4+ T cells

source_name: Universal Human Reference from Stratagene

tag: rna source


title: 10763302


title: 10730502


title: CD4 3008-2 Day 21

tag: vendor


title: 10730702


title: CD4 3008-2 Day 10


title: 10731802


title: CD4 3008-2 Day 0


title: CD4 3008-2 Day 7


title: 10711102


title: CD19 3008-2 Day 21


title: CD4 3008-2 Day 3


title: 10587402


title: 10731502


title: CD19 3008-2 Day 13


title: 10586302


title: CD19 3008-2 Day 10


title: CD19 3008-2 Day 0


title: CD19 3008-2 Day 7


title: PBMC 3008-2 Day 21


title: 10722202


title: CD19 3008-2 Day 3


title: 10710602


title: 10586502


title: 10710502


title: 10711002


title: 10588402


title: H vs L hatchability Experiment 1 dye swap

status: Public on Nov 16 2010

city: Taichung

first: Mu-Chiou

last: Huang

address: 250 Kuo-Kuang Rd

country: Taiwan

institute: National Chung-Hsing University

description: The low hatchability group RNA as control samples for comparison to the high hatchability group

hyb_protocol: Hybridization was performed in HybChamber™ (GeneMachines, Bethesda, MD, USA) at 65℃ overnight. Arrays were then washed by 0.5xSSC/0.01% SDS, 0.06xSSC/0.01% SDS and 0.06xSSC for 15min each at room temperature prior to drying and scanning.

scan_protocol: Arrays were scanned using a GenePix 4000B microarray scanner (Axon Instruments, Union City, CA, USA). GenePix Pro 4.1 software was then used to acquire the array image, and export the GPR files containing the spot intensity of raw data.

data_processing: Spot intensities were calculated using the median value of all spots for analysis. Poor-quality spots (flag≠0) were filtered, followed by background substraction, and rescalling by Quantile normalization using Avadis software (Strand Life Science, Redwood City, CA, USA). Net intensities of less than 500 in the normalized data were removed and the remaining signals were transformed to log2 and analyzed for the detection of significantly differentially-expressed transcripts using t-test unpaired.

organism: Anas platyrhynchos

source_name: magnum from the high hatchability group

label_protocol: Pooled total RNA prepared from the magnums of animals in both the high-hatchability and low-hatchability groups were reverse-transcribed in the presence of Cy5-dUTP and Cy3-dUTP (MicroMax, PerkinElmer, MA, USA), respectively, and vice versa, to create labeled cDNA targets for dye-swap hybridization.

extract_protocol: Total RNA was isolated by the RareRNA reagent (GenePure, Kaysville, UT, USA) in accordance with the manufacturer's instructions.

value: magnum

tag: hatchability

value: high hatchability group

source_name: magnum from the low hatchability group

value: low hatchability group


title: 10710202

tag: tissue


title: H vs L hatchability Experiment 1


title: ENU_Day 120_2

status: Public on Nov 04 2010

type: other

description:
This mouse was sacrificed 120 days after ENU treatment
small RNA with length less than 200 nucleotides
PCR Array analysis of miRNA expression: Two hundred nanograms of enriched small RNA were converted into 1st strand cDNA using RT2 miRNA First Strand Kit (SABiosciences Corporation, Frederick, MD).  The cDNAs were mixed with 2 × RT2 SYBR Green PCR Master Mix (SABiosciences) and dispersed into 384-well Mouse Genome miRNA PCR Array (MAM-3100A, SABiosciences) with 10 μl/well of the mixture.  The PCR Array contained a panel of primer sets for 376 mouse miRNAs, four small RNAs as the internal controls and four qualification controls.  The real-time qRT-PCR was performed on 7900 real-time PCR systems (Applied Biosystems Inc., Foster, CA) with the following cycling parameters: 95 0C for 10 mins, then 40 cycles of 950C for 15 s, 60 0C for 15 s and 72 0C for 30 s.  SYBR Green fluorescence was recorded from every well during the annealing step of each cycle.  The threshold cycle (Ct) value of each sample was calculated with software SDS 2.3 (Applied Biosystems).  To calculate Cts, we set threshold line as 0.15 and kept it the same across all of the analyses.  The baseline was automatically defined by the software.

data_processing: Normalization and statistical analysis were done in SABiosciences online PCR array data analysis web portal. Four genes, snoRNA251, snoRNA202, snoRNA142, and U6, were used as endogenous controls to calculate ∆Ct.  Ttest’s were done between the ∆Ct’s of control group and the treatment group at each time point.  The fold change (FC) for each miRNA was calculated using ∆∆Ct method.  The formula: FC = 2^ [-(mean of ∆Ct values of treated samples - mean of ∆Ct values of control samples)] was used for up-regulated gene while FC= - 2^ (mean of ∆Ct values of treated samples - mean of ∆Ct values of control samples) was used for the down-regulations. miRNAs with p value < 0.01 and the absolute of FC > 2.0 were considered as differentially expressed miRNAs.

label: SYBR Green

molecule: other

organism: Mus musculus

source_name: Liver

label_protocol: Two hundred nanograms of enriched small RNA were converted into 1st strand cDNA using RT2 miRNA First Strand Kit (SABiosciences Corporation, Frederick, MD). The cDNAs were mixed with 2 × RT2 SYBR Green PCR Master Mix (SABiosciences).

extract_protocol: About 60 mg tissue was cut from each frozen liver sample and suspended in RNAlater-ICE (Ambion Inc., Austin, TX).  The tissue pieces were transferred to 600 μl RNA lysis/binding buffer and minced using Tissue Tearor™ (Biospec products Inc., Bartlesville, OK).  MiRNAs were isolated using mirVana™ miRNA isolation kit (Ambion) that was able to specifically enrich small RNAs with length of less than 200 nucleotides.  The isolated RNAs were resolved in 100 μl nuclease-free water (Ambion).  RNA concentrations were determined using Nanodrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, Delaware).  The quality of RNA samples were characterized on an Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA) using an RNA6000 Nano LabChip (Agilent).

treatment_protocol: The animal treatment protocol was described previously (Wang et al. 2004).  Simply, six-month-old female mice were injected intraperitoneally with a single dose of 120 mg / kg body weight ENU (CAS# 759–73–9, Sigma, St. Louis, MO) or the vehicle dimethylsulfoxide (DMSO, Sigma).  Groups of 4 or 5 animals were sacrificed on post-treatment days 1, 3, 7, 15, 30, and 120 for the ENU treatment and post-treatment days 1 and 30 for the control treatment (Figure 1).  The tissues were isolated and frozen in -80C.  The liver samples were used for this study.  All animal experiments were conducted by following the recommendations set forth by our Institutional Animal Care and Use Committee.

tag: gender

value: Female

tag: age

value: 6 months

tag: animal provider

tag: animal name

value: Big Blue Transgenic mice

value: Liver

tag: agent

value: ENU

tag: time (days post-treatment)

value: 120 days


title: ENU_Day 120_3

value: Stratagene


title: ENU_Day 30_4

description:
This mouse was sacrificed 30 days after ENU treatment
small RNA with length less than 200 nucleotides
PCR Array analysis of miRNA expression: Two hundred nanograms of enriched small RNA were converted into 1st strand cDNA using RT2 miRNA First Strand Kit (SABiosciences Corporation, Frederick, MD).  The cDNAs were mixed with 2 × RT2 SYBR Green PCR Master Mix (SABiosciences) and dispersed into 384-well Mouse Genome miRNA PCR Array (MAM-3100A, SABiosciences) with 10 μl/well of the mixture.  The PCR Array contained a panel of primer sets for 376 mouse miRNAs, four small RNAs as the internal controls and four qualification controls.  The real-time qRT-PCR was performed on 7900 real-time PCR systems (Applied Biosystems Inc., Foster, CA) with the following cycling parameters: 95 0C for 10 mins, then 40 cycles of 950C for 15 s, 60 0C for 15 s and 72 0C for 30 s.  SYBR Green fluorescence was recorded from every well during the annealing step of each cycle.  The threshold cycle (Ct) value of each sample was calculated with software SDS 2.3 (Applied Biosystems).  To calculate Cts, we set threshold line as 0.15 and kept it the same across all of the analyses.  The baseline was automatically defined by the software.

value: 30 days


title: 10586802

value: whole blood

value: Eurogentec 5'-methylcytosine Ab

value: MeDIP


title: 10581002

value: control

value: Control

value: input


title: 10585602


title: ENU_Day 120_1


title: ENU_Day 30_2


title: ENU_Day 30_1


title: ENU_Day 30_3


title: 10588202


title: ENU_Day 15_5

description:
This mouse was sacrificed 15 days after ENU treatment
small RNA with length less than 200 nucleotides
PCR Array analysis of miRNA expression: Two hundred nanograms of enriched small RNA were converted into 1st strand cDNA using RT2 miRNA First Strand Kit (SABiosciences Corporation, Frederick, MD).  The cDNAs were mixed with 2 × RT2 SYBR Green PCR Master Mix (SABiosciences) and dispersed into 384-well Mouse Genome miRNA PCR Array (MAM-3100A, SABiosciences) with 10 μl/well of the mixture.  The PCR Array contained a panel of primer sets for 376 mouse miRNAs, four small RNAs as the internal controls and four qualification controls.  The real-time qRT-PCR was performed on 7900 real-time PCR systems (Applied Biosystems Inc., Foster, CA) with the following cycling parameters: 95 0C for 10 mins, then 40 cycles of 950C for 15 s, 60 0C for 15 s and 72 0C for 30 s.  SYBR Green fluorescence was recorded from every well during the annealing step of each cycle.  The threshold cycle (Ct) value of each sample was calculated with software SDS 2.3 (Applied Biosystems).  To calculate Cts, we set threshold line as 0.15 and kept it the same across all of the analyses.  The baseline was automatically defined by the software.

value: 15 days


title: 10588302


title: 10589402


title: ENU_Day 3_5

description:
This mouse was sacrificed 3 days after ENU treatment
small RNA with length less than 200 nucleotides
PCR Array analysis of miRNA expression: Two hundred nanograms of enriched small RNA were converted into 1st strand cDNA using RT2 miRNA First Strand Kit (SABiosciences Corporation, Frederick, MD).  The cDNAs were mixed with 2 × RT2 SYBR Green PCR Master Mix (SABiosciences) and dispersed into 384-well Mouse Genome miRNA PCR Array (MAM-3100A, SABiosciences) with 10 μl/well of the mixture.  The PCR Array contained a panel of primer sets for 376 mouse miRNAs, four small RNAs as the internal controls and four qualification controls.  The real-time qRT-PCR was performed on 7900 real-time PCR systems (Applied Biosystems Inc., Foster, CA) with the following cycling parameters: 95 0C for 10 mins, then 40 cycles of 950C for 15 s, 60 0C for 15 s and 72 0C for 30 s.  SYBR Green fluorescence was recorded from every well during the annealing step of each cycle.  The threshold cycle (Ct) value of each sample was calculated with software SDS 2.3 (Applied Biosystems).  To calculate Cts, we set threshold line as 0.15 and kept it the same across all of the analyses.  The baseline was automatically defined by the software.

value: 3 days


title: ENU_Day 7_5

description:
This mouse was sacrificed 7 days after ENU treatment
small RNA with length less than 200 nucleotides
PCR Array analysis of miRNA expression: Two hundred nanograms of enriched small RNA were converted into 1st strand cDNA using RT2 miRNA First Strand Kit (SABiosciences Corporation, Frederick, MD).  The cDNAs were mixed with 2 × RT2 SYBR Green PCR Master Mix (SABiosciences) and dispersed into 384-well Mouse Genome miRNA PCR Array (MAM-3100A, SABiosciences) with 10 μl/well of the mixture.  The PCR Array contained a panel of primer sets for 376 mouse miRNAs, four small RNAs as the internal controls and four qualification controls.  The real-time qRT-PCR was performed on 7900 real-time PCR systems (Applied Biosystems Inc., Foster, CA) with the following cycling parameters: 95 0C for 10 mins, then 40 cycles of 950C for 15 s, 60 0C for 15 s and 72 0C for 30 s.  SYBR Green fluorescence was recorded from every well during the annealing step of each cycle.  The threshold cycle (Ct) value of each sample was calculated with software SDS 2.3 (Applied Biosystems).  To calculate Cts, we set threshold line as 0.15 and kept it the same across all of the analyses.  The baseline was automatically defined by the software.

value: 7 days


title: ENU_Day 7_1

value: Female


title: ENU_Day 7_2

value: 6 months


title: ENU_Day 15_2

value: Big Blue Transgenic mice


title: ENU_Day 7_3

value: Liver


title: ENU_Day 3_3

value: ENU


title: ENU_Day 3_4


title: ENU_Day 3_1


title: H vs L hatchability Experiment 2

value: magnum

value: low hatchability group

value: high hatchability group


title: ENU_Day 1_4

description:
This mouse was sacrificed one day after ENU treatment
small RNA with length less than 200 nucleotides
PCR Array analysis of miRNA expression: Two hundred nanograms of enriched small RNA were converted into 1st strand cDNA using RT2 miRNA First Strand Kit (SABiosciences Corporation, Frederick, MD).  The cDNAs were mixed with 2 × RT2 SYBR Green PCR Master Mix (SABiosciences) and dispersed into 384-well Mouse Genome miRNA PCR Array (MAM-3100A, SABiosciences) with 10 μl/well of the mixture.  The PCR Array contained a panel of primer sets for 376 mouse miRNAs, four small RNAs as the internal controls and four qualification controls.  The real-time qRT-PCR was performed on 7900 real-time PCR systems (Applied Biosystems Inc., Foster, CA) with the following cycling parameters: 95 0C for 10 mins, then 40 cycles of 950C for 15 s, 60 0C for 15 s and 72 0C for 30 s.  SYBR Green fluorescence was recorded from every well during the annealing step of each cycle.  The threshold cycle (Ct) value of each sample was calculated with software SDS 2.3 (Applied Biosystems).  To calculate Cts, we set threshold line as 0.15 and kept it the same across all of the analyses.  The baseline was automatically defined by the software.

value: Stratagene

value: 1 day


title: ENU_Day 1_5


title: ENU_Day 3_2


title: ENU_Day 1_2


title: ENU_Day 15_4


title: ENU_Day 1_1


title: H vs L hatchability Experiment 2 dye swap


title: DMSO_Day 30_3

description:
This mouse was sacrificed 30 days after DMSO treatment
small RNA with length less than 200 nucleotides
PCR Array analysis of miRNA expression: Two hundred nanograms of enriched small RNA were converted into 1st strand cDNA using RT2 miRNA First Strand Kit (SABiosciences Corporation, Frederick, MD).  The cDNAs were mixed with 2 × RT2 SYBR Green PCR Master Mix (SABiosciences) and dispersed into 384-well Mouse Genome miRNA PCR Array (MAM-3100A, SABiosciences) with 10 μl/well of the mixture.  The PCR Array contained a panel of primer sets for 376 mouse miRNAs, four small RNAs as the internal controls and four qualification controls.  The real-time qRT-PCR was performed on 7900 real-time PCR systems (Applied Biosystems Inc., Foster, CA) with the following cycling parameters: 95 0C for 10 mins, then 40 cycles of 950C for 15 s, 60 0C for 15 s and 72 0C for 30 s.  SYBR Green fluorescence was recorded from every well during the annealing step of each cycle.  The threshold cycle (Ct) value of each sample was calculated with software SDS 2.3 (Applied Biosystems).  To calculate Cts, we set threshold line as 0.15 and kept it the same across all of the analyses.  The baseline was automatically defined by the software.

value: DMSO

value: 30 days


title: DMSO_Day 30_4


title: DMSO_Day 30_2


title: DMSO_Day 30_1


title: ENU_Day 1_3


title: 10582602

value: control

value: whole blood

value: Eurogentec 5'-methylcytosine Ab

value: MeDIP

value: Control


title: DMSO_Day 1_3

description:
This mouse was sacrificed one day after DMSO treatment
small RNA with length less than 200 nucleotides
PCR Array analysis of miRNA expression: Two hundred nanograms of enriched small RNA were converted into 1st strand cDNA using RT2 miRNA First Strand Kit (SABiosciences Corporation, Frederick, MD).  The cDNAs were mixed with 2 × RT2 SYBR Green PCR Master Mix (SABiosciences) and dispersed into 384-well Mouse Genome miRNA PCR Array (MAM-3100A, SABiosciences) with 10 μl/well of the mixture.  The PCR Array contained a panel of primer sets for 376 mouse miRNAs, four small RNAs as the internal controls and four qualification controls.  The real-time qRT-PCR was performed on 7900 real-time PCR systems (Applied Biosystems Inc., Foster, CA) with the following cycling parameters: 95 0C for 10 mins, then 40 cycles of 950C for 15 s, 60 0C for 15 s and 72 0C for 30 s.  SYBR Green fluorescence was recorded from every well during the annealing step of each cycle.  The threshold cycle (Ct) value of each sample was calculated with software SDS 2.3 (Applied Biosystems).  To calculate Cts, we set threshold line as 0.15 and kept it the same across all of the analyses.  The baseline was automatically defined by the software.

value: Female


title: ENU_Day 15_1

value: 6 months

value: 15 days


title: DMSO_Day 1_2

value: Big Blue Transgenic mice

value: Liver


title: DMSO_Day 1_1


title: E2F4 overexpression rep4

status: Public on Nov 01 2010

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description: ch1: TF transfected, ch2: mock transfected

hyb_protocol: Dye-coupled cDNA was combined and hybridized onto the oligo arrays for 14 hr.

scan_protocol: Images were quantified using Genpix 5.1 software.

data_processing: After LOWESS normalization, data sets were further applied to an error model (Hu, et al. 2007. Nat Genet 39: 683-687) through which significant value (X) and p-values were calculated

source_name: epithelial cervix

label_protocol: Total RNA was converted into cDNA and labeled with Cy dyes (Cy3 for control and Cy5 for TF overexpression).

growth_protocol: Hela cells were cultured in DMEM medium containing 10% fetal bovine serum (FBS) and 1% antibiotics (penicillin/streptomycin).

extract_protocol: Total RNA was extracted using Trizol(Invirogen) and 15ug of total RNA from a control and a overexpression sample was coverted into cDNA.

treatment_protocol: Either full length expression constructs or empty vectors as a control were transfected into HeLa cells using Lipofectamine 2000 from Invitrogen.

tag: cell line

tag: overexpression

value: empty vector


title: E2F4, DP-1 and RBL2 overexpression rep1

value: E2F4, DP-1, and RBL2


title: E2F4 and RBL2 overexpression rep1

value: E2F4 and RBL2


title: E2F4 overexpression rep2


title: 10585402

tag: phenotype

tag: medip antibody

value: input


title: E2F4 overexpression rep3


title: E2F4 and DP-1 overexpression rep1

value: E2F4 and DP-1


title: ENU_Day 120_4

value: Stratagene

value: ENU

value: 120 days


title: E2F4, DP-1 and RBL2 overexpression rep2


title: E2F4 overexpression rep1


title: LSD2 knockdown, replicate 1

first: Yujiang

last: Shi

address: 221 Longwood Ave

department: Medicine

institute: Brigham & Women's Hospital

description: Gene expression data from HeLa cells infected with shLSD2 retrovirus

hyb_protocol: Hybridization was performed per the manufacturer's instruction at the DFCI microarray core facility ( (http://chip.dfci.harvard.edu).

scan_protocol: Scanning was performed at the DFCI microarray core facility (http://chip.dfci.harvard.edu).

data_processing: Gene expression analysis was performed using dCHIP. Differentially expressed genes with at least 1.5 fold changes were obtained by normalization with either Quantile or Invariant Set method using dChip.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol at the DFCI microarray core facility (http://chip.dfci.harvard.edu)

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% FBS

extract_protocol: Total RNA was extracted by the method of Trizol. At the final step of purification, RNA was loaded onto an RNeasy column (Qiagen) and treated with RNAse free DNAse I.

treatment_protocol: HeLa cells were infected with retrovirus, and harvested for RNA 70 hours post-infection.

value: HeLa cervical carcinoma


title: Control - 2

status: Public on Oct 01 2010

city: Vicksburg

first: Natalia

last: Vinas

state: MS

address: 3909 Halls Ferry Rd

institute: Mississippi State University

description: Two zebrafish brains were pooled per test sample.

hyb_protocol: Standard Agilent two-color protocol (Agilent 60-mer oligo microarray processing protocol).

scan_protocol: The microarrays were washed and scanned with a laser-based detection system (Agilent, Palo Alto, CA). Microarray image processing and data pre-processing were performed using Agilent's Feature Extraction software v 9.5.

data_processing: The intensity of each spot was summarized by the median pixel intensity. A log transformed signal ratio between the experimental (Cy5) channel and the reference (Cy3) channel was calculated for each spot, followed by within-array lowess transformation and between array scale normalization on median intensities.

organism: Danio rerio

source_name: Brain from female zebrafish control

label_protocol: cDNA synthesis, cRNA labelling, amplification and hybridization were performed following the manufacturer's kits and protocols (Agilent Low RNA Input Fluorescent Linear Amplification Kit).

extract_protocol: Total RNA was isolated from brain tissue with the RNA Stat-60 reagent (Tel-test, Friendswood, TX).

treatment_protocol: Adult female zebrafish were injected with 0 ug/g or 0.5 ug/g MeHg in 2 µL Na2CO3 (pH 6.98)/g body weight. After 96 hr, fish were anesthetized using ethyl 3-aminobenzoate methanesulfonate (MS-222, Sigma, St. Louis, MO). Whole brains were removed, flash frozen with liquid nitrogen and stored at 80°C.

tag: strain

tag: genotype

value: wild-type

value: female

tag: developmental stage

value: adult

value: brain

tag: treatment

value: sodium carbonate control

tag: treatment time

value: 96 hrs

source_name: Reference

value: methylmercury and sodium carbonate control

tag: sample type

value: reference pool consisting of equal amounts of RNA from control and methylmercury-treated female zebrafish brain


title: MeHg - 1

source_name: Brain from female zebrafish exposed to methylmercury

tag: tissue

value: methylmercury


title: Scarmbled control knockdown, replicate 2

description: Gene expression data from HeLa cells infected with control retrovirus


title: MeHg - 3

tag: gender


title: ENU_Day 7_4

value: Female

tag: age

value: 6 months

value: Big Blue Transgenic mice

value: Liver

value: 7 days


title: Control - 5


title: Patient 2

status: Public on Oct 28 2010

city: Chicago

first: Ben

last: Katz

state: IL

address: 2300 Children's Plaza, Box # 20

department: Division of Infectious Diseases

institute: Children's Memorial Hospital

hyb_protocol: Fragmented RNA was then hybridized onto the Affymetrix Human Genome U 133 Plus 2.0 array, according to the manufacturer’s recommendations (Gene Chip RHT One-Cycle Target Labeling).

scan_protocol: An automatic fluidic station washed, stained and scanned the sample for fluorescence using an Affymetrix GCS3000 scanner.

data_processing:
The data were analyzed using the average difference values followed by the quantile normalization procedure and absolute calls for the presence or absence of the genes present on the chip in Bioconductor package : affy using R software (version 2.8).
We compared those genes differentially expressed at least two-fold by Patient 1 who demonstrated soluble CD8-suppression with those genes from Patient 2 who exhibited no suppression and analyzed those results based on previous reports in the literature as to what might constitute CAF using the proportion test and what might be expected to be seen in exosomes secreted by CD8+ T-cells. We then compared the gene expression profile of Patient 3 (who exhibited suppression of HIV likely via direct contact, and thus unrelated to CAF) with that of Patients 1 and 2 using Pearson correlation coefficients. Results of differentially expressed gene analysis is provided as a supplementary file on the Series record.

source_name: Blood from an HIV-1 infected adolescent boy

label_protocol: Extracted RNA was reverse transcribed to form double stranded DNA (Invitrogen SuperScript Choice), purified over phenol-chloroform and concentrated via ethanol-precipitation. Biotin-labeled cRNA was then in vitro transcribed (BioArray High-Yield in vitro RNA transcription and labeling kit [Affymetrix]), purified (Qiagen RNeasy spin columns) and fragmented.

extract_protocol: Five x 106 – 107 peripheral blood mononuclear cells were viably-frozen using RNAlater ([Ambion]; to maximize RNA extraction) at the same time the suppression assays were performed. RNA extraction (using the Qiagen RNeasy mini kit) was performed 5-10 months after the cell pellets were frozen.

value: adolescent

tag: sex

value: male

tag: cell type

value: peripheral blood mononuclear cells

tag: hiv disease status

value: no soluble CD8-suppression


title: Control - 3

value: wild-type

value: female


title: MeHg - 2

value: adult

value: brain


title: Patient 1

value: soluble CD8-suppression


title: Patient 3

value: HIV suppression likely via direct contact (unrelated to CAF)


title: Scarmbled control knockdown, replicate 1

source_name: HeLa cells infected with control retrovirus

value: HeLa cervical carcinoma


title: Control - 1

value: sodium carbonate control

value: 96 hrs

value: methylmercury and sodium carbonate control

value: reference pool consisting of equal amounts of RNA from control and methylmercury-treated female zebrafish brain


title: ENU_Day 15_3

value: Female

value: 6 months

tag: animal provider

value: Stratagene

tag: animal name

value: Big Blue Transgenic mice

value: Liver

tag: agent

value: ENU

tag: time (days post-treatment)

value: 15 days


title: Control - 4

value: wild-type

value: female


title: OP9 stromal cell

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal. The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Calvaria of newborn B6C3Fe-a/a-Csf1op/Csf1op mouse

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Cells were maintained with aMEM supplemented with 20% FBS.

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Quiagen).

treatment_protocol: None.

tag: cell line

value: OP9 stromal cell line

tag: protocol

value: control


title: OP9 stromal cell expressing GFP and Delta-like 1

value: GFP and Delta-like 1 expression


title: LSD2 knockdown, replicate 2

source_name: HeLa cells infected with shLSD2 retrovirus

value: HeLa cervical carcinoma


title: OP9 stromal cell expressing GFP

value: GFP expression


title: F8320P3_REP1

status: Public on Sep 10 2010

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

country: France

institute: INRA

description: medicago truncatula (f252)  - dev.stage (boyes et al. plant cell 2001): seedlings at 100°cd after germination (degree day)

hyb_protocol: labelled extract quantity: 15ug

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

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

label: Biotin

organism: Medicago truncatula

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

growth_protocol: hypocotyl - - Sand (SIFRACO quality NE34:SiO2 .99.7%, solid density 2.65 g cm23, mean particle size 200 mm) - 58% hygrometry - 20°c - In the Dark

treatment_protocol: optimal_temp_P3 - 20° time 204h. Seed are sown and grown optimal temperature: 20°C in the dark until the harvesting at 100°Cd after germination

tag: genotype

tag: development stage

value: seedlings at 100°Cd after germination (degree day)


title: A1720P2_REP1

description: medicago truncatula (jemalong)  - dev.stage (boyes et al. plant cell 2001): seedlings at 50°cd after germination (degree day)

treatment_protocol: optimal_temp_P2 - 20° time 118h. Seed are sown and grown at optimal temperature: 20°C in the dark until the harvesting at 50°Cd after germination

value: Jemalong A17

value: seedlings at 50°Cd after germination (degree day)


title: F8310P1_REP1

description: medicago truncatula (f252)  - dev.stage (boyes et al. plant cell 2001): seedlings at 35°cd after germination (degree day)

growth_protocol: hypocotyl - - Sand (SIFRACO quality NE34:SiO2 .99.7%, solid density 2.65 g cm23, mean particle size 200 mm) - 97% hygrometry - 10°c - In the Dark

treatment_protocol: LowTemp_P1 - 10° time 275h. Seed are sown and grown at low temperature: 10°C in the dark until the harvesting at 35°Cd after germination

value: seedlings at 35°Cd after germination (degree day)


title: A1720P2_REP2


title: A1720P3_REP2

description: medicago truncatula (jemalong)  - dev.stage (boyes et al. plant cell 2001): seedlings at 100°cd after germination (degree day)


title: A1720P3_REP1


title: A1710P3_REP1

description: medicago truncatula (jemalong)  - dev.stage (boyes et al. plant cell 2001): seedlings at 100°cd after germination (degree day),  4049

growth_protocol: hypocotyl - - Sand (SIFRACO quality NE34:SiO2 .99.7%, solid density 2.65 g cm23, mean particle size 200 mm) - 97% hygrometry - 10°C - In the Dark

treatment_protocol: LowTemp_P3 - 10° time 670h. Seed are sown and grown at low temperature: 10°C in the dark until the harvesting at 100°Cd after germination


title: F8310P1_REP2


title: A1710P1_REP2

description: medicago truncatula (jemalong)  - dev.stage (boyes et al. plant cell 2001): seedlings at 35°cd after germination (degree day)


title: A1710P2_REP2

treatment_protocol: LowTemp_P2 - 10° time 365h. Seed are sown and grown at low temperature: 10°C in the dark until the harvesting at 50°Cd after germination


title: A1720P1_REP2

treatment_protocol: optimal_temp_P1 - 20° time 92h. Seed are sown and grown at optimal temperature: 20°C in the dark until the harvesting at 35°Cd after germination


title: F8320P2_REP2

description: medicago truncatula (f252)  - dev.stage (boyes et al. plant cell 2001): seedlings at 50°cd after germination (degree day)


title: F8310P2_REP1


title: A1710P1_REP1


title: F8310P3_REP1


title: F8310P3_REP2


title: A1720P1_REP1


title: F8310P2_REP2


title: MeHg - 4

tag: strain

tag: developmental stage

value: adult

value: brain

tag: treatment

value: methylmercury

value: 96 hrs

value: methylmercury and sodium carbonate control

value: reference pool consisting of equal amounts of RNA from control and methylmercury-treated female zebrafish brain


title: C2TSC_3

description: arabidopsis thaliana (col-0)  mutant (35s promoter: :geminivirus C2) - age:10day

organism: Arabidopsis thaliana

source_name: 35s promoter::geminivirus C2 - NaCl

growth_protocol: whole plant - MS plates, 22ºC, long day conditions (16 hours light/8 hours dark)

treatment_protocol: Name:control - genetic treatment - o nacl,nacl 200 mm:time 0 . NaCl was added to MS liquid (final concentration 200mM) for 30 min or 1 h. For control, no salt was added. Treatment was stopped by freezing in liquid nitrogen.

tag: ecotype


title: F8320P2_REP1


title: F8320P3_REP2


title: F8320P1_REP2


title: C2TST_1

source_name: 35s promoter::geminivirus C2 - MeJA

treatment_protocol: Name:MeJA - hormone treatment,biotic stress - compound addition,methyl jasmonate:quantity 50uM time 10hour . Addition of 50uM MeJA to the plate and 10 hour incubation.


title: LUC2C_2

description: arabidopsis thaliana (col-0)  mutant (pr1 promoter: : luciferase) - age:10day

source_name: pr1 promoter::luciferase - NaCl


title: LUC2C_3


title: C2TSC_2


title: LUC2T_1

source_name: pr1 promoter::luciferase - MeJA


title: LUC2T_3


title: C2TSC_1


title: C2TST_2


title: LSD2_ChIP-chip

description: Results for Flag-HA-LSD2 bound chromatin fragmenst are displayed in a .BAR file type, for viewing with Integrated Genome Browser.

hyb_protocol: Labeling, hybridization, and scanning was performed per the manufacturer's instructions at the DFCI microarray core facility  (http://chip.dfci.harvard.edu)

data_processing: Regions enriched by TAP N-ChIP were identified using algorithm Model-Based Analysis of Tiling arrays (MAT) (Johnson et al., 2006), and displayed by Integrated Genome Browser (IGB).

source_name: Flag-HA ChIP DNA

extract_protocol: Native chromatin of HeLa-S stably expressing FgHA-LSD2 was prepared by micrococcal nuclease digestion as previously described (Umlauf et al., 2004).

treatment_protocol: HeLa cells were subjected to native ChIP, using tandem affinity purification with anti-Flag and anti-HA antibodies

value: HeLa cervical carcinoma cell line

tag: antibodies

value: anti-Flag and anti-HA for FgHA-LSD2

source_name: HeLa genomic DNA


title: C2TST_3


title: LUC2T_2


title: A1710P2_REP1


title: B16F10_rep1

city: yonago

first: hiroyuki

last: kugoh

state: tottori

department: Biomedical Science

institute: Tottori University

description: no additional description

hyb_protocol: Biotinylated cRNA was hybridized with a probe array, washing and staining with a Single Stain procedure were carried out according to the manufacturer's protocol.

scan_protocol: GeneChips were scanned using an Affymetrix Scanner 3000.

data_processing: The expression value (Signal) of each probe set was analysed by Microarray Suite version 5.0 (MAS 5.0). The mean of expression values in each experiment was set at 100 to adjust for minor differences between experiments. A signal log ratio (SLR) of 2 (fold change ≥ 4) in duplicate experiments was used as an arbitrary cut-off for determination of mRNA level changes.

source_name: Parental mouse melanoma B16F10 cells

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, rev 1, Affymetrix).

extract_protocol: Total cellular RNA was extracted using the RNeasy Mini kit (QIAGEN), and was then treated with RNase-free DNase I (WAKO) to remove residual genomic DNA.

value: Parental mouse melanoma cells

tag: passage

value: parental


title: B16F10_#5 hybrid_telomerase-positive_rep2

description: no additional description

source_name: Revertant B16F10 microcell hybrid with human chromosome5, telomerase-positive

value: Microcell hybrid


title: Pta 717 1B4 fuzzy sample rep3

status: Public on Sep 01 2010

city: Kingston

first: Sharon

last: Regan

state: Ontario

address: Biosciences Complex, Queen's University

department: Department of Biology

institute: Queen's University

description: Each sample comprises pooled material from three individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.

hyb_protocol: Affymetrix protocol: Eukaryotic target preparation: Eukaryotic target hybridization

scan_protocol: Affymetrix protocol: GeneChip Scanner 3000 7G Affymetrix 00-0073

data_processing: GC-RMA in BioConductor

organism: Populus tremula x Populus alba

source_name: fuzzy shoot apical meristem

label_protocol: Affymetrix protocol: Eukaryotic target preparation: One-cycle target labeling assay

growth_protocol: Trees were grown under greenhouse conditions at Queen’s University in Kingston, Ontario Canada.  The fuzzy mutant was generated as describe d in Harrison et al. (2007) in a Populus tremula x Populus alba clone 717 1B4 background and all comparisons of fuzzy were made to this hybrid.

extract_protocol: Trizol (Invitrogen)

tag: genetic background

value: Populus tremula x Populus alba clone 717 1B4 activation tagged line – fuzzy

value: acivation tag over-expression of PtaMYB186

tag: tissue

value: Shoot apical meristem


title: E2F4 and DP-1 overexpression rep2

source_name: epithelial cervix

tag: overexpression

value: E2F4 and DP-1

value: empty vector


title: B16F10_#5 hybrid_telomerase-negative_rep1

description: no additional description

source_name: B16F10 microcell hybrid with human chromosome5, telomerase-negative

tag: cell type


title: B16F10_#5 hybrid_telomerase-negative_rep2

description: no additional description


title: B16F10_rep2

description: no additional description


title: Pta 717 1B4 fuzzy sample rep2


title: B16F10_#5 hybrid_telomerase-positive_rep1

description: no additional description


title: E2F4 and RBL2 overexpression rep2

value: E2F4 and RBL2


title: Pta 717 1B4 wildtype sample rep2

source_name: Wild-type shoot apical meristem

value: Populus tremula x Populus alba clone 717 1B4 wild type

value: wild type


title: Pta 717 1B4 fuzzy sample rep1


title: Pta 717 1B4 wildtype sample rep1

description: Each sample comprises pooled material from two individuals. All collected plant materials were flash frozen in liquid nitrogen upon harvesting and stored at -80°C until RNA was extracted.


title: Pta 717 1B4 wildtype sample rep3


title: 100 µg/ml tetracycline_2

status: Public on Aug 31 2010

city: Cordeiropolis

first: Alessandra

middle: Alves

last: De Souza

state: Sao Paulo

address: Rod Anhanguera KM 158

department: Centro de Citricultura Sylvio Moreira

country: Brazil

institute: Instituto Agronomico de Campinas

description: It is the second of three  biological replicates of Xylella fastidosa submited to 100 µg/ml of tetracycline used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following the standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following the standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Xylella fastidiosa 9a5c

source_name: Xylella fastidiosa 9a5c biofilm, treated with 100 µg/ml tetracycline

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following the standard operating protocol. See www.nimblegen.com.

growth_protocol: Bacterial cells were grown in biofilm in PW medium for 15 days in flasks under shaking (130 rpm, 28oC)

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an nanodrop spectophotometer and Bioanalyser 2100.

treatment_protocol: After 15 days of growth, 3 or 7 mM of CuSO4 or 10 or 80 µg/ml of tetracyclin were added to the experiments and after one day the total RNA were extracted. Controls were made withough any substance.

value: tetracycline

tag: dose

value: 100 µg/ml


title: 100 µg/ml tetracycline_3

description: It is the third of three  biological replicates of Xylella fastidosa submited to 100 µg/ml of tetracycline used in this experiment, each from separate cultures.

tag: agent


title: 800 µg/ml tetracycline_1

description: It is the first of three  biological replicates of Xylella fastidosa submited to 800 µg/ml of tetracycline used in this experiment, each from separate cultures.

source_name: Xylella fastidiosa 9a5c biofilm, treated with 800 µg/ml tetracycline

value: 800 µg/ml


title: 800 µg/ml tetracycline_3

description: It is the third of three  biological replicates of Xylella fastidosa submited to 800 µg/ml of tetracycline used in this experiment, each from separate cultures.


title: 100 µg/ml tetracycline_1

description: It is the first of three  biological replicates of Xylella fastidosa submited to 100 µg/ml of tetracycline used in this experiment, each from separate cultures.


title: 800 µg/ml tetracycline_2

description: It is the second of three  biological replicates of Xylella fastidosa submited to 800 µg/ml of tetracycline used in this experiment, each from separate cultures.


title: 7 mM CuSO4_3

description: It is the third of three  biological replicates of Xylella fastidosa submited to 7 mM of CuSO4 used in this experiment, each from separate cultures.

source_name: Xylella fastidiosa 9a5c biofilm, treated with 7 mM CuSO4

value: 7 mM


title: 7 mM CuSO4_2

description: It is the second of three  biological replicates of Xylella fastidosa submited to 7 mM of CuSO4 used in this experiment, each from separate cultures.


title: 7 mM CuSO4_1

description: It is the first of three  biological replicates of Xylella fastidosa submited to 7 mM of CuSO4 used in this experiment, each from separate cultures.


title: 3 mM CuSO4_2

description: It is the second of three  biological replicates of Xylella fastidosa submited to 3 mM of CuSO4 used in this experiment, each from separate cultures.

source_name: Xylella fastidiosa 9a5c biofilm, treated with 3 mM CuSO4

value: 3 mM


title: 3 mM CuSO4_3

description: It is the third of three  biological replicates of Xylella fastidosa submited to 3 mM of CuSO4 used in this experiment, each from separate cultures.


title: GFP Antisense knockdown

city: Toronto

first: Qun

last: Pan

address: 160 College St.

institute: University of Toronto

description: Alternative splicing (AS) of pre-mRNA is utilized by higher eukaryotes to achieve increased transcriptome and proteomic complexity. The serine/arginine (SR) splicing factors regulate tissue- or cell type-specific AS in a concentration and phosphorylation dependent manner. However, the mechanisms that modulate the cellular levels of active SR proteins remain to be elucidated. In the present study, we provide evidence for a role for the long nuclear-retained regulatory RNA (nrRNA), MALAT1 in AS regulation. MALAT1 interacts with SR proteins and influences the distribution of these and other splicing factors in nuclear speckle domains. Depletion of MALAT1 changes AS of endogenous pre-mRNAs, similar to what was observed upon overexpression of SR proteins. Furthermore, MALAT1 regulates cellular levels of phosphorylated forms of SR proteins. Taken together, our results suggest that MALAT1 regulates AS by modulating the levels of active SR proteins. Our results further highlight a novel role for a nrRNA in the regulation of gene expression.

hyb_protocol: Hybridization of Cy3- and Cy5-labelled cDNA synthesized from polyA+RNA from MALAT1-antisense oligo treated or GFP-antisense oligo treated HeLa cells was performed using a HS4800 Pro Hybridization Station (Tecan) at 42°C for 22 hours.

scan_protocol: Microarray slides were scanned with an Agilent microarray scanner at 5µm resolution and TIFF images were processed using Feature Extraction Software (Agilent).

data_processing: Microarray slides were scanned with an Agilent microarray scanner at 5µm resolution and TIFF images were processed using Agilent Feature Extraction Software (version 9.5). Processed data were then analyzed using the GenASAP algorithm (Shai et al., 2006).

source_name: GFP Antisense knockdown

label_protocol: The mRNA (1–2 μg) was reverse-transcribed with random nonamer primers (1 μg per reaction) and T18VN (0.25 μg per reaction) to synthesize cDNA. The reaction contained a 1:1 mixture of 5-(3-aminoallyl) thymidine 5'-triphosphate (Sigma, St. Louis, USA) and thymidine triphosphate (TTP) in place of TTP alone. The cDNA products were bound to QIAquick PCR Purification columns (Qiagen, Hilden, Germany) following the manufacturer's instructions, washed three times with 80% ethanol, and eluted with water. Purified cDNA was reacted with N-hydroxy succinimide esters of Cy3 or Cy5 (Amersham Pharmacia Biotech, Piscataway, USA) following the manufacturer's instructions.

extract_protocol: RNA was extracted using homogenization and Trizol reagent (Invitrogen, Carlsbad, USA) following the instructions from the manufacturer. Prior to cDNA synthesis, polyA+ RNA was purified from total RNA using the Nucleotrap mRNA Midi kit (Clontech) as recommended by the manufacturer with two rounds of purification.

tag: GFP Antisense knockdown


title: A1710P3_REP2

description: medicago truncatula (jemalong)  - dev.stage (boyes et al. plant cell 2001): seedlings at 100°cd after germination (degree day)

value: Jemalong A17

value: seedlings at 100°Cd after germination (degree day)


title: asexual_nanos(RNAi)_rep2

city: Urbana

first: Phillip

last: Newmark

address: C609 CLSL, 601 S. Goodwin Ave.

department: Cell and Developmental Biology

institute: University of Illinois, Urbana-Champaign

description: This sample is of nanos(RNAi) asexual S. mediterranea. It is the second of two nanos(RNAi) biological replicates used in this experiment, each from separate RNAi feeding experiment

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

organism: Schmidtea mediterranea

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Asexual Schmidtea mediterrane were maintained in 1 X Montjuic salts at 21°C (Cebria F, Newmark PA (2005) Development 132:3691–3703.)

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Roy J. Carver Biotechnology Center (University of Illinois at Urbana-Champaign, Urbana, IL USA).

value: nanos(RNAi)

tag: phenotype

value: germ cell-less

value: asexual


title: juvenile sexual_control(RNAi)_rep2

description: This sample is of control(RNAi) juvenile sexual S. mediterranea. It is the second of two nanos(RNAi) biological replicates used in this experiment, each from separate RNAi feeding experiment

source_name: juvenile sexual_control(RNAi)

growth_protocol: Sexual Schmidtea mediterrane were maintained in 0.75 X Montjuic salts at 18°C

value: control

value: normal

value: sexual


title: juvenile sexual_nanos(RNAi)_rep2

description: This sample is of nanos(RNAi) juvenile sexual S. mediterranea. It is the second of two nanos(RNAi) biological replicates used in this experiment, each from separate RNAi feeding experiment

source_name: juvenile sexual_nanos(RNAi)


title: asexual_control(RNAi)_rep2

description: This sample is of control(RNAi) asexual S. mediterranea. It is the second of two nanos(RNAi) biological replicates used in this experiment, each from separate RNAi feeding experiment


title: asexual_control(RNAi)_rep1

description: This sample is of control(RNAi) asexual S. mediterranea. It is the first of two control(RNAi) biological replicates used in this experiment, each from separate RNAi feeding experiment


title: 1,25-vitD, donor 6

city: DEBRECEN

first: LAJOS

last: SZELES

address: Egyetem tér

country: Hungary

institute: UNIVERSITY OF DEBRECEN

hyb_protocol: 10 ug of fragmented biotinylated cRNA was hybridized for 16 hr at 45C on GeneChip HG133_plus2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
CHP file were generated by Affymetrix Expression Console, using RMA algorithm.
Details:
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.19935

source_name: differentiating monocyte-derived dendritic cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA using 3` IVT Expression kit (Affymetrix).

growth_protocol: CD14+ monocyte were cultured in the presence of IL4 and GMCSF

extract_protocol: RNeasy mini kit was used to extract total RNA (according to the manufacturer's instructions).

treatment_protocol: Cells were treated with various nuclear receptor agonists

tag: donor

value: monocyte-derived dendritic cells

value: 1,25-dihydroxyvitamin D3

tag: nuclear receptor agonist type

value: VDR agonist


title: juvenile sexual_control(RNAi)_rep1

description: This sample is of control(RNAi) juvenile sexual S. mediterranea. It is the first of two control(RNAi) biological replicates used in this experiment, each from separate RNAi feeding experiment

tag: genotype


title: 1,25-vitD, donor 4


title: asexual_nanos(RNAi)_rep1

description: This sample is of nanos(RNAi) asexual S. mediterranea. It is the first of two nanos(RNAi) biological replicates used in this experiment, each from separate RNAi feeding experiment

tag: strain


title: 1,25-vitD, donor 5


title: juvenile sexual_nanos(RNAi)_rep1

description: This sample is of nanos(RNAi) juvenile sexual S. mediterranea. It is the first of two nanos(RNAi) biological replicates used in this experiment, each from separate RNAi feeding experiment


title: autoreactive replicate 2 (sample B4)

city: Denver

first: Roberta

last: Pelanda

state: CO

address: 1400 Jackson Street

department: Immunology

institute: National Jewish Health

description: cells were sorted via Moflo cell sorter from untreated mice and directly frozen

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies).  Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight at 65ºC to Agilent Whole Mouse Genome Oligo Microarrays 4x44K using Agilent's recommended hybridization chamber and oven.  The microarrays were then washed once with 6x SSPE buffer containing 0.005% N-laurosylsarcosine for 1 min at room temperature followed by a second wash with pre-heated 0.06x SSPE buffer (37ºC) containing 0.005% N-laurosylsarcosine for 1 min.  The last washing was performed with acetonitrile for 30 sec.

scan_protocol: Scanned on an Agilent's DNA microarray scanner (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES 9.1.1.1) was used to read out and process the microarray image files. The dye biasis were corrected by using a linear/lowess normalization method. The data were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware, version 2.2) for determination of differential gene expression. The Resolver software export a gene list with all normalized Cy5/Cy3-log10 ratios, Cy5/Cy3-fold changes, sequence description, p-values, etc., referred to as gene ratio list.

source_name: pooled B220+CD23–CD43–IgD– autoreactive immature B cells replicate 2

label_protocol: 0.5 ug of each RNA sample was amplified and labeled using the Agilent Low RNA Input Linear Amp Kit (Agilent Technologies) following manifacturer's protocol.

growth_protocol: no manipulation of mice or cells was performed.

extract_protocol: Total RNA was extracted using standard protocol (NucleoSpin RNA II kit from Macherey-Nagel) and its quality analyzed via the Agilent 2100 Bioanalyzer platform and expert software (Agilent Technologies).

treatment_protocol: bone marrow cells were treated with ACK buffer to lyse erythrocytes, and then stained with anti-CD43, anti-IgD, anti-CD23, and anti-B220 antibodies.  Stained cells were ran on a Moflo cell sorter to sort B220+ CD43,IgD,CD23-negative cells.  Cells were analyzed for purity,  flash frozen in liquid nitrogen, and stored at -80C until shipment to Miltenyi Biotec in dry ice. Miltenyi Biotec performed all subsequent manipulations.

tag: genotype/variation

value: bone marrow

source_name: pooled B220+CD23–CD43–IgD– non-autoreactive immature B cells

value: BALB/c


title: control, donor 2

value: vehicle


title: autoreactive replicate 1 (sample B3)

source_name: pooled B220+CD23–CD43–IgD– autoreactive immature B cells replicate 1


title: 3 mM CuSO4_1

description: It is the first of three  biological replicates of Xylella fastidosa submited to 3 mM of CuSO4 used in this experiment, each from separate cultures.


title: control_3

description: It is the third of three control biological replicates used in this experiment, each from separate cultures.

source_name: Xylella fastidiosa 9a5c biofilm, untreated control

value: untreated


title: control_2

description: It is the second of three control biological replicates used in this experiment, each from separate cultures.


title: control_1

description: It is the first of three control biological replicates used in this experiment, each from separate cultures.


title: F8320P1_REP1

description: medicago truncatula (f252)  - dev.stage (boyes et al. plant cell 2001): seedlings at 35°cd after germination (degree day)

tag: development stage

value: seedlings at 35°Cd after germination (degree day)


title: KO_stationary phase_rep1

status: Public on Aug 20 2010

city: Lucknow

first: Bhupendra

middle: Narain

last: Singh

state: U P

address: M G Marg

department: Microbiology

country: India

institute: Central Drug Research Institute

description: KO_stationary phase_rep1

hyb_protocol: 600 ng of Cy3 labelled cRNA was fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were performed using Gene Expression Hybridization kit (Agilent Technologies) as per manufacture's protocol. Hybridization was carried out in Agilent’s Surehyb Chambers at 65 °C for 16 h. The hybridized slides were washed using Agilent Gene Expression wash buffers: two washes, first for 1 min at room temparature and second for 1 min at 37 °C.

scan_protocol: slides were washed using Agilent Gene Expression wash buffers and scanned using the Agilent Microarray Scanner G Model G2565BA at 5 micron resolution.

data_processing: Data extraction from scanned images was done using Feature Extraction software v 10.5.1.1 of Agilent Technology. analysed using GeneSpring GX v 7.3.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended one color Per Chip and Per Gene Data Transformation. Set measurements less than 0.01 to 0.01 per chip, normalize to 50th percentile per gene, and normalize to specific samples.

organism: Mycolicibacterium smegmatis MC2 155

source_name: Mycobacterium smegmatis ΔsigF mutant stationary phase cells

label_protocol: cRNA was labelled with Cy3 as per Agilent 1-color labeling protocol (Version 5.5, February 2007). Typically, 2 µg total RNA was used in each labelling reaction.

growth_protocol: M. smegmatis strains were grown in DifcoTM MiddleBrook 7H9 broth base (BD Biosciences, Sparks, MD, USA) with 0.2% glycerol (v/v) and 0.05% Tween-80 (Sigma-Aldrich, St Louis, MO, USA) supplemented with 10% albumen dextrose catalase (BD Biosciences) (v/v) at 37 °C with continuous shaking

extract_protocol: Total RNA was extracted using Trizol Method. Briefly, cells from 10 ml culture were harvested by centrifugation at 2500×g for 5 min and suspended in 1 ml RNAlaterTM (Ambion). From this 250 µl of cell suspension was pelleted to which 500 µl Trizol and acid washed glass beads (Sigma) were added. The samples were vortexed vigorously for 15 mins. After centrifugation, the supernatant was collected. To this 150 µl of chloroform was added followed by centrifugation. The upper aqueous phase was collected and precipitation was done using isopropanol. The pellet was washed with 70% ethanol and air-dried. The RNA was resuspended in 20 µl of RNase-free water. RNA concentration and purity was determined at an optical density ratio of 260/280 using the Nanodrop® ND-1000 spectrophotometer (NanoDrop Technologies) and the integrity of total RNA was verified on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano LabChip (Agilent Technologies). Total RNA with OD260/OD280 >1.8 and OD260/OD230 ≥ 0.7 was used for microarray experiments. RNA was stored at −80 °C until use

value: ΔsigF mutant

tag: growth phase

value: stationary phase


title: Malat1 Antisense knockdown

source_name: Malat1 Antisense knockdown

tag: Malat1 Antisense knockdown


title: KO_stationary phase_rep2

description: KO_stationary phase_rep2


title: KO_log phase_rep2

description: KO_log phase_rep2

source_name: Mycobacterium smegmatis ΔsigF mutant log phase cells

value: log phase


title: WT_stationary phase_rep2

description: WT_stationary phase_rep2

source_name: Mycobacterium smegmatis stationary phase cells

value: wild type


title: WT_log phase_rep2

description: WT_log phase_rep2

source_name: Mycobacterium smegmatis log phase cells


title: KO_log phase_rep1

description: KO_log phase_rep1


title: WT_log phase_rep1

description: WT_log phase_rep1


title: WT_stationary phase_rep1

description: WT_stationary phase_rep1


title: inducible brsR strain

status: Public on Aug 15 2010

city: Oklahoma City

first: Justin

last: Merritt

state: OK

address: 975 NE 10th St BRC364

department: Oral Biology

institute: University of Oklahoma Health Sciences Center

description: Gene transcription data from planktonic culture OD600=0.3

hyb_protocol: Following fragmentation, 3 μl of cDNA were hybridized for 16 hr at 47℃ on GeneChip S. mutans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a laser scanner 7G (Affymetrix)

data_processing: Data were analyzed with Affymetrix Gene Chip Operating Software version 1.4 (GCOS 1.4)

organism: Streptococcus mutans

source_name: Streptococcus mutans UA140

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Cells were grown overnight in chemically-defined medium with 0.5% glucose as carbon source. Overnight culture was diluted 1:30 in CDM with 1% (wt/vol) lactose.

extract_protocol: Cells were lysed using beat-beater. Extraction of total RNA was performed using Ambion RiboPure Bacteria kit according to the manufacturers protocol.

treatment_protocol: Cells were grown to OD600 = 0.3 and harvested by centrifugation.

value: planktonic cells

value: ΔbrsRM /pFW5::PlacA-brsR


title: LUC2C_1

description: arabidopsis thaliana (col-0)  mutant (pr1 promoter: : luciferase) - age:10day

source_name: pr1 promoter::luciferase - NaCl

tag: ecotype


title: CytoplasmicRNA_Control-siRNA_3

city: Kyoto

first: Seiji

last: Masuda

state: Kyoto

address: Kitashirakara oiwaketyo

department: Graduate School of Biostudies

institute: Kyoto university

description: Expression data with cytoplasmic RNA, Human Gene 1.0 ST array (Affymetrix)

hyb_protocol: Labeling and hybridization were performed according to Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Data processing was done with Affymetrix Expression Console (PM background, quantile normalization, iterPLIER)

molecule: cytoplasmic RNA

source_name: Control

growth_protocol: HeLa S3 cells were grown in Dulbecco's modified Eagle medium containing 10% fatal bovine serum.

extract_protocol: Cytoplasmic RNA was extracted with Sepasol RNA I solution according to manufacture's instruction following to the separation of cytosolic fraction by using lysis buffer (50mM Tris, 100mM NaCl, 5mM MgCl2, 0.5% Triton-X).

treatment_protocol: 20nM of siRNA was transfected with Lipofectamine2000 according to manufacture's instruction.

tag: cell line

value: HeLa S3


title: Control stain, no brsR expression

value: ΔbrsRM /pFW5::PlacA


title: CytoplasmicRNA_UAP56-siRNA_3

label_protocol: Labeling and hybridization were performed according to Affymetrix GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual


title: CytoplasmicRNA_URH49-siRNA_3


title: CytoplasmicRNA_UAP56-siRNA_1


title: CytoplasmicRNA_Control-siRNA_1


title: CytoplasmicRNA_URH49-siRNA_2


title: CytoplasmicRNA_URH49-siRNA_1


title: CytoplasmicRNA_UAP56-siRNA_2


title: CytoplasmicRNA_Control-siRNA_2


title: 3_OCT6_0

status: Public on Aug 02 2010

city: Vienna

first: Elisabeth

last: Hofmann

address: Veterinaerplatz 1

department: Institute of Animal Breeding and Genetics

country: Austria

institute: University of Veterinary Medicine Vienna

description: ABI 1700 mouse whole genome array

data_processing: using GeneSpring software; Data transformation and normalisation: expression values less than 10 were set to 10. Data were normalised to the 50th percentile (intra-array normalisation) and each gene was normalised to the median expression (inter-array normalisation). Data were pre-filtered based on the signal to noise ratio (cut-off level: signal above noise > two-fold in all samples of the respective biological replicate group) and non-changing genes (normalised expression levels from 0,667 to 1,334 in at least 4 of 4 conditions) were substracted.

label: digoxigenin

source_name: fetal-liver macrophages

label_protocol: 20 µg of total RNA was processed according to the manufacturer's instructions to produce digoxigenin-labelled cDNA

growth_protocol: cell suspensions from single fetal livers (d14) were cultured for 5 days in the presence of L929 conditioned medium (as source for M-CSF1), on d6 1x10^6 cells per well were plated in 6-well clusters.

extract_protocol: Total RNA was extracted from 1x10^6 cells lysed in 1 ml TRiZOL reagent.

treatment_protocol: on d7 1x10^6 fetal-liver macrophages were given fresh medium (=untreated) or medium containing poly(I:C) (50 µg/ml) for 8 hours.

tag: treatment

tag: experiment

value: fetal-liver macrophages


title: 2_WT_poly(I:C)

description: ABI 1700 mouse whole genome array

hyb_protocol: according to the manufacturer's instructions

value: poly(I:C) 8 hours

tag: cell type


title: Tumor_initial

status: Public on Aug 30 2010

city: Oslo

first: Hanne-Sofie

middle: S

last: Dahlback

address: Montebello

department: Section for Cancer Cytogenetics

country: Norway

institute: The Norwegian Radium Hospital

hyb_protocol: The protocol used for hybridization and labeling of the samples was the “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic labeling for Blood Cells or Tissues (with a High Throughput option) Version 6.1, August 2009”.

scan_protocol: All slides were scanned with the Agilent DNA Microarray Scanner with Surescan High-Resolution technology and data extracted using the Agilent Feature Extraction Software v. 10.5.1.1 as described in the Agilent Oligo aCGH protocol.

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) and Genomic Workbench software (Agilent Technologies Inc., Palo Alto, California, USA). Aberrant DNA copy number intervals identified using the Aberration Detection Method 2 (ADM-2), default threshold setting 6.0, and Fuzzy Zero correction algorithm applied. To ensure the exclusion of very low or very small aberrations, we added a custom-made aberration filter defining a region with a copy number aberration as a region with minimum five probes gained/lost and with minimum absolute average log2 ratio of 0.2 (gain) or -0.2 (loss). A loss defined as homozygous when the log2 ratio was lower than -1, and a gain was regarded as high level amplification when the log2 ratio was higher than 1.

source_name: Human brain

extract_protocol: Mag-Attract DNA Mini M48 kit (QIAGEN, Hilden, Germany)

tag: disease state

value: giant cell ependymoma

tag: gender

value: Male

extract_protocol: not applicable

tag: reference


title: 3_WT_0

description: ABI 1700 mouse whole genome array

scan_protocol: according to the manufacturer's instructions


title: 2_OCT6_poly(I:C)

description: ABI 1700 mouse whole genome array


title: 2_OCT6_0

description: ABI 1700 mouse whole genome array


title: 1_OCT6_poly(I:C)

description: ABI 1700 mouse whole genome array


title: 3_OCT6_poly(I:C)

description: ABI 1700 mouse whole genome array


title: 3_WT_poly(I:C)

description: ABI 1700 mouse whole genome array


title: 2_WT_0

description: ABI 1700 mouse whole genome array


title: 1_WT_0

description: ABI 1700 mouse whole genome array


title: 1_WT_poly(I:C)

description: ABI 1700 mouse whole genome array


title: Tumor_recurrence

label_protocol: The protocol used for hybridization and labeling of the samples was the “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic labeling for Blood Cells or Tissues (with a High Throughput option) Version 6.1, August 2009”.

value: anaplastic ependymoma


title: 1_OCT6_0

description: ABI 1700 mouse whole genome array


title: Coregonus_bc-moribund_individual9, Sample 60

status: Public on Aug 01 2010

city: Quebec

first: Sébastien

last: Renaut

state: qc

address: 1030 Avenue de la Médecine

department: Biology

institute: Université Laval

description:
Lake whitefish.
One sexually undifferentiated individual - sampling at 280-288 degree days post fertilisation.

hyb_protocol: Microarray were hybridized using Cy3/Cy5 dyes (Genisphere) as detailed  in http://web.uvic.ca/grasp/microarray/protocols/Genisphere_Array_50_Protocol_Revised_v.5.pdf

scan_protocol: Microarrays were scanned using a ScanArray™ Express scanner (Packard Bioscience, Wellesley, MA) and spots were located and quantified using the histogram method in QuantArray 3.0 (Perkin Elmer, Waltham, USA).

data_processing: Data were exported in text format and then analysed in R using MAANOVA package. Data were Lowess normalized. Channels were analyzed independently.

organism: Coregonus clupeaformis

source_name: Frozen individual in toto, bc-moribund

label_protocol: For each sample, 20µg total RNA was retro-transcribed and the cDNA samples labelled using Genisphere 3DNA Array 50 Kit, Invitrogen's Superscript II retro transcriptase and Cyanine-3 and Cyanine-5 fluorescent dyes (Genisphere), following the procedures at http://web.uvic.ca/cbr/grasp/ (Genisphere Array 50 Protocol).

growth_protocol: Whole individuals were stored at -80°C in RNAlater prior to any sampling

extract_protocol: Total RNA was extracted using the Trizol Reagent protocol (Invitrogen, Carlsbad, CA). A pool of five whole embryos preserved in RNA later was homogenized using a bead mill (Qiagen, Germantown, MD) for each sample hybridized on the array. Total RNA was eluted in pure water supplemented with Superase-In™ RNase Inhibitor (Ambion), quantified and quality checked using ExperionTM RNA StdSens Analysis Kit (Bio-Rad, Hercules, CA), then stored at -80°C.

treatment_protocol: Samples were treated with DNAse enzyme prior to labeling.

tag: tissue

value: whole body

tag: develomental stage

value: embryo

tag: type

value: backcross-moribund

tag: sexual differentiation

value: undifferentiated

tag: incubation time

value: 280-288 degree days post fertilisation

tag: individual


title: Coregonus_bc-healthy_individual3, Sample 62

source_name: Frozen individual in toto, bc-healthy

value: backcross-healthy


title: Coregonus_bc-healthy_individual4, Sample 63


title: Coregonus_bc-healthy_individual2, Sample 59


title: Coregonus_bc-healthy_individual1, Sample 58


title: Coregonus_bc-moribund_individual11, Sample 64


title: Coregonus_bc-moribund_individual10, Sample 61


title: Coregonus_bc-healthy_individual7, Sample 54


title: Coregonus_bc-moribund_individual15, Sample 56


title: Coregonus_bc-healthy_individual8, Sample 55


title: Coregonus_bc-moribund_individual16, Sample 57


title: Coregonus_bc-moribund_individual14, Sample 53


title: Coregonus_bc-healthy_individual6, Sample 51


title: Coregonus_bc-healthy_individual2, Sample 46


title: Coregonus_bc-moribund_individual12, Sample 50


title: Coregonus_bc-moribund_individual13, Sample 52


title: Coregonus_dwarf_individual22, Sample 48

source_name: Frozen individual in toto, dwarf

value: dwarf


title: Coregonus_bc-healthy_individual5, Sample 49


title: Coregonus_bc-moribund_individual9, Sample 47


title: Coregonus_normal_individual28, Sample 43

source_name: Frozen individual in toto, normal

value: normal


title: Coregonus_dwarf_individual22, Sample 45


title: Coregonus_bc-healthy_individual2, Sample 41


title: Coregonus_bc-moribund_individual9, Sample 44


title: Root Cortex Cells_Aerated vs Hypoxia_Replicate 2

city: Chikusa-ku

first: Mikio

last: Nakazono

state: Nagoya

address: Furo-cho

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

description: Biological replicate 2 of 3. Root Cortex Cells, Hypoxia, harvested after 12h Waterlogging treatment

hyb_protocol: Gene Expression Hybridization kit part No. 5188-5242

scan_protocol: Agilent scanner model G2505C

data_processing: Data was analyzed by Feature Extraction Software (Version 10.5.1.1, Agilent)

organism: Zea mays

source_name: Root Cortex Cells, Hypoxia, 12 h

label_protocol: Quick Amp Labeling Kit, two-color (Agilent)

growth_protocol: Maize (Zea mays, inbred line B73) kernels were placed on germination paper, rolled-up in the paper, and placed in a flask. Water was added to the flask to keep the paper moist, but not enough to submerge the roots. Seedlings were germinated and grown at 28°C under constant light in a growth chamber for 3 days

extract_protocol: Total RNA was extracted from the LM-isolated cortex cells using the PicoPure™ RNA isolation kit (Molecular Devices) according to the manufacturer’s protocol.

treatment_protocol: For the waterlogging treatments, the primary root (but not the shoots) was waterlogged. Two and half day-old-seedlings were pre-treated with an inhibitor of ethylene perception 1-methylcyclopropene (1-MCP; 1 ppm) for 12 hours before the waterlogging treatment. Three-day-old seedlings were growing under aerated conditions at the same time with other treatments as a control. For all experiments we were using segment from the primary root, 0.5 cm long: from 1.5 to 2 cm from the junction shoot-root. Cortex part of the root was collected using Veritas Laser Microdissection System LCC170 (Molecular Devices)

tag: cultivar

value: inbred line B73

tag: sample

value: Root Cortex Cells from the segment of the primary root, 0.5 cm long:from 1.5 to 2 cm from the junction shoot-root.

value: Waterlogging treatment for 12 h

source_name: Root Cortex Cells, Aerated, 12 h

value: Aerated treatment for 12 h

tag: samples


title: ColorSwap_Root Cortex Cells_Hypoxia vs Hypoxia+MCP_Replicate 3

description: Color Swap replicate 3 of 3. Root Cortex Cells, Hypoxia+MCP, harvested after 12h MCP pretreatment + 12h Waterlogging treatment

source_name: Root Cortex Cells, MCP+Hypoxia, 12 h

value: MCP pretreatment for 12 h + Waterlogging treatment for 12 h