title: wild type GFP positive rep 1A

tag: These are wild-type embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-positive cells were collected using FACS.


title: wild type GFP negative rep 1B

status: Public on Jan 01 2006

type: RNA

city: Brookline

first: Sung

middle: Eun

last: Choe

state: MA

address: 258 Harvard St #164

country: USA

institute: Wyeth Research

description: These are wild-type embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-negative cells were collected using FACS.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Bioconductors' affy package in conjunction with Choe et al.'s goldenspike package (Choe et al. Genome Biol. 2005).

label: biotin

molecule: total RNA

organism: Drosophila melanogaster

source_name: nonmesodermal cells

label_protocol: Approximately 2.5-3 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: The embryos were dounce homogenized into a single cell suspension. These cells were then FACS sorted. The GFP-negative cells from this sort comprise this sample.


title: Pnt gain of function rep 2A

description: These are embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells, as well as a UAS-Pnt^{P2VP16} insertion that yields constitutively activated Pnt within these Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-positive cells were collected using FACS.

source_name: mesodermal cells

extract_protocol: The embryos were dounce homogenized into a single cell suspension. These cells were then FACS sorted. The GFP-positive cells from this sort comprise this sample.


title: wild type GFP positive rep 1C

description: These are wild-type embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-positive cells were collected using FACS.


title: wild type GFP positive rep 1B


title: wild type GFP negative rep 1A

tag: These are wild-type embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-negative cells were collected using FACS.


title: spi loss of function rep 1C

description: These are spi-mutant embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-positive cells were collected using FACS.


title: spi loss of function rep 1A

tag: These are spi-mutant embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-positive cells were collected using FACS.


title: FGFR gain of function rep 1C

description: These are embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells, as well as UAS-lambda-Htl and UAS-Dof insertions that yield constitutively activated FGFR within these Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-positive cells were collected using FACS.


title: spi loss of function rep 1B


title: FGFR gain of function rep 1B

tag: These are embryos with Twi-GAL4 and UAS-GFP insertions that target GFP fluorescence to Twist expressing cells, as well as UAS-lambda-Htl and UAS-Dof insertions that yield constitutively activated FGFR within these Twist expressing cells.  Embryos were collected and aged at 25°C to 5.5-7.5 hours after egg deposition (Stage 11).  GFP-positive cells were collected using FACS.


title: RA_F

status: Public on Dec 10 2004

city: Berlin

first: Ute

last: Ungethuem

department: Core Center for Functional Genome Research

country: Germany

institute: Charité University Hospital

description: pooled synovial tissues from rheumatoid arthritis patients

hyb_protocol: The radioactive cDNA was purified using Sephadex columns, denatured and added to denatured salmon sperm and human placenta DNA as blocking reagents. To aid grid positioning during image analysis radioactively labelled 1 ng kanamycin cDNA was added to the complex probe. This mixture was added to 10 ml hybridisation buffer (1M NaCl, 1% SDS, 0.1xSSC) and hybridised overnight at 65°C and then washed three times for 20 min at 65°C (0.1% SDS, 0.1X SSC).

scan_protocol: The filters were exposed for approx. 6 hours on Fuji BAS screens and signal intensities were read out using a Fuji Bas-1800 reader (Fuji Photo Film).

data_processing: Signal intensities for every cDNA clone and background spots were determined using the Visual Grid software (GPC-Biotech, Munich). Raw intensities were background corrected by subtracting the local background (estimated block-wise) and normalised.

label: alpha 33P-dCTP

organism: Homo sapiens

source_name: rheumatoid arthritis

label_protocol: 20 microgram of tota RNA was primed with oligodT(12-18) and reverse transcribed with AMV (Roche) in the presence of alpha 33P-dCTP (Amersham Pharmacia Biotech).

growth_protocol: synovectomy

extract_protocol: Total RNA was isolated using TRIzol Reagent (Invitrogen) followed by column based clean up (RNeasy, Qiagen).

treatment_protocol:
sample 1:
non-steroidal anti-inflammatory drugs (NSAID), disease modifying antirheumatic drugs (DMARD), steroids
sample 2:
steroids
sample 3:
no treatment

tag: sample 1:

tag: age

tag: gender

value: female

tag: sample 2

tag: sample 3:

value: male


title: RA_E

description: synovial tissues from rheumatoid arthritis patient

treatment_protocol: non-steroidal anti-inflammatory drugs (NSAID)


title: ND_8

description: pooled synovial tissues from normal donors

source_name: normal donor

label_protocol: 20 microgram of tota RNA was primed with oligodT(12-18) and reverse transcribed with AMV (Roche) in the presence of alpha 33P-dCTP (Amersham Pharmacia Biotech)

treatment_protocol: no treatment


title: ND_7

tag: sample 1


title: ND_6

tag: sample 3

tag: sample 4

value: unknown


title: RA_D

treatment_protocol:
sample 1:
non-steroidal anti-inflammatory drugs (NSAID), disease modifying antirheumatic drugs (DMARD)
sample 2:
disease modifying antirheumatic drugs (DMARD), steroids


title: RA_C

treatment_protocol: disease modifying antirheumatic drugs (DMARD), non-steroidal anti-inflammatory drugs (NSAID)


title: ND_9


title: E3.5 blastocyst 100

status: Public on Feb 03 2006

city: Bunkyo-ku

first: Shin

last: Kobayashi

state: Tokyo

address: 1-5-45 yushima

department: Medical Research Institute

country: Japan

institute: Tokyo Mdical & Dental University

description: Total RNAs were extracted from over 200 male or female sex-separated blastocysts using an ISOGEN in the presence of 1µg of yeast tRNA as a carrier.

hyb_protocol: Hybridization was carried out for 17 hours using an Agilent’s in situ Hybridization Kit Plus.

scan_protocol: All microarray experiments were carried out following the Agilent’s

data_processing: Hybridized slides were scanned using the Agilen’ts microarray scanner

organism: Mus musculus

label_protocol: Total RNA was labeled using a Low Input Fluorescent Linear Amplification kit (Agilent) following the manufacturer’s instruction.

growth_protocol: B6C3F1 female mice of 8 weeks in age, were superovulated with 5 IU of pregnant mare serum gonadotropin (PMS) followed by 5 IU of human chorionic gonadotropin (hCG) 48 hr later, and were mated with XGFPY male mice.  Four-cell stage embryos were collected from the oviducts 55 hr after the hCG injection and placed in kSOM and incubated in a humidified atmosphere of 5% CO2 in air at 37 ºC for an additional 38 hr.

extract_protocol: RNA was obtained using ISOGEN (NIPPON GENE Inc., Japan) which is based on the acid guanidine thiocyanate-phenol-chloroform extraction method.

treatment_protocol: No treatment

tag: Gender

tag: Age

tag: Tissue

value: whole embryo


title: mut 6 rep1

status: Public on Aug 31 2006

city: Madison

first: Michael

last: Culbertson

state: WI

address: 1525 Linden Drive

department: Genetics

institute: University of Wisconsin

description: Yeast cultures were grown to mid-log phase and harvested at 6 minutes after transcription inhibition by 10ug/ml thiolutin.

data_processing: Robust Multiarray Average

organism: Saccharomyces cerevisiae

source_name: upf1- cell at time point 6

label_protocol: cDNA was synthesized from 15ug total RNA from all samples using oligo(dT) primer. 5ul out of 12ul RnaseH-puriÞed cDNA samples were used to synthesize biotinylated cRNA.

extract_protocol: hot phenol protocol

tag: Yeast strain S288C with UPF1 ORF replaced by KanMX4. Cells harvested at 6 minutes after transcription inhibition.


title: 12778036_Sce15cy5_Sce28cy3Chip1

status: Public on Jul 15 2006

city: Mississauga

first: James

middle: B

last: Anderson

state: Ontario

address: 3359 Mississauga Road N.

department: Biology

country: Canada

institute: University of Toronto

description:
12778036_Sce15cy5_Sce28cy3CRep1
Generation 400 hyb group

data_processing: Log 2 ratio of signal intensity of experimental over the reference strain. Lowess subgrid normalization method.

tag: Sce15. Reference strain

tag: Sce28. Experimental strain. Generation 400


title: Brain_Deprived_4hr_2

status: Public on Feb 27 2006

city: Philadelphia

first: John

middle: E

last: Zimmerman

state: PA

address: 125 South 31st Street

department: Center for Sleep & Respiratory Neurobiology

institute: University of Pennsylvania School of Medicine

description: This is one of seven timepoints (4 Hour deprived) in a study the effects of sleep deprivation on gene expression in the Drosophila brain.

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to 1 microarray. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. Performed by the staff at the Penn Microarray Facility http://www.med.upenn.edu/microarr/index.htm

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature. Performed by the staff at the Penn Microarray Facility http://www.med.upenn.edu/microarr/index.htm

data_processing: Ten time groups were used in this study, each with three biological replicates. Seven time groups were used to determine differential gene expression between normal and sleep-deprived flies while three time groups were used as an experimental control to test for differential gene expression due to the effect of mechanical stimulation. Probe intensity data from all 30 arrays was read into the R software environment (http://www.R-project.org) directly from .CEL files using the R/AFFY package (Gautier et al., 2004). R/AFFY was also used to extract and manipulate probe level data to assess data quality and to create expression summary measures. Normalization was carried out using the robust multi-array average (RMA) method (Irizarry et al., 2003) on all probe intensity data sets together in order to form one expression measure for each gene on each array. Briefly, the RMA method adjusted the background of perfect match (PM) probes, applied a quantile normalization of the corrected PM values, and calculated final expression measures using the median polish algorithm.

label: Biotin

source_name: Whole Brain_Deprived_4hr

label_protocol: All protocols were conducted as described in the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, 5.0 ug of total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP. Performed by the staff at the Penn Microarray Facility http://www.med.upenn.edu/microarr/index.htm

growth_protocol: Females were collected as newly eclosed virgins and kept in populations of 50 flies at 25°C under 12 hour light: 12 hour dark conditions in vials containing standard cornmeal media until time of sacrifice.

extract_protocol: Total RNA was extracted from the pools of 139 (min) to 193 (max) brains using TRIZOL Reagent (U.S.Patent No.5,346,994) following the manufactrurers instructions (Invitrogen)

treatment_protocol: Animals were sacrificed by immersion in >95°C distilled water, removed from water and stored at -70 ° C until tissue dissection performed within 24 hours of sacrifice. Brains were removed from the head and cleared of surrounding tissues using forceps under a dissecting microscope under ice cold insect ringers (130 mM NaCl, 4.7 mM KCl, 1.9 mM CaCl2) and immediately placed in Trizol® Reagent (U.S.Patent No.5,346,994).

tag: Strain

value: Canton-S

value: Female

value: 5 days

value: Whole Brain

tag: Time of Sacrifice

tag: Condition

value: Sleep Deprived