title: 2d dark-grown WT(Col-0)/1 hr red light /replicate 2

description: 2d dark grown WT(Col-0) seedlings/1hr Red light(7.5 μmol/m2/S)replicate 2

growth_protocol: Wild-type and pifq mutant seeds were plated in GM medium without sucrose at room temperature as described. During this procedure the seeds were routinely exposed to WL for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness. After stratification, seeds were induced to germinate with a 5-min Rp (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before providing a terminal 5-min FRp (58 μmol/m2/s).

treatment_protocol: Dark 2d 21°C followed by 1 hr Red light (7.5 μmol/m2/s)


title: 2d dark-grown WT seedling/replicate 5

status: Public on Nov 01 2009

type: RNA

city: Albany

first: james

middle: m

last: tepperman

state: CA

address: 800 Buchanan St.

department: Plant and Microbial Biology

country: USA

institute: Plant Gene Expression Center/UC Berkeley

description: 2d dark grown WT(Col-0) seedlings/replicate 5

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: BioConductor software (RMA) to normalize and correct background on all the data

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: whole seedling (root, hypocotyl,cotyledon)

label_protocol: standard Affymetrix procedures

extract_protocol: Total RNA was extracted from ~400 mg (fw) tissue using the method of Chang et al. (Chang, S., Puryear, J. & Cairney, J. (1993) Plant Mol. Biol. Rep. 11, 113-116) followed by further purification using Qiagen RNeasy columns.

treatment_protocol: Dark 2d 21°C

tag: genotype

value: WT (Col-0)


title: 5d stratified seed WT (col-0)/replicate 1

description: stratified seed / WT/replicate 1

source_name: stratified seed

growth_protocol: Wild-type and pifq mutant seeds were plated in GM medium without sucrose at room temperature as described. During this procedure the seeds were routinely exposed to WL for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness.

treatment_protocol: dark 5d 4ºC


title: 5d stratified seed WT (col-0)/replicate 3

description: stratified seed / WT/replicate 3

source_name: 5d stratified seed

growth_protocol: Wild-type and pifq mutant seeds were plated in GM medium without sucrose at room temperature as described. During this procedure the seeds were routinely exposed to WL for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at  in darkness.


title: 2d dark-grown WT seedling/replicate 3

description: 2d dark grown WT(Col-0) seedlings/replicate 2


title: 2d dark-grown WT seedling/replicate 2


title: 2d dark-grown WT seedling/replicate 1

description: 2d dark grown WT(Col-0) seedlings/replicate 1


title: 2d red light grown WT(Col-0) seedlings/replicate 1

description: 2d Red light (6.7 μmol/m2/s)/replicate 1

growth_protocol: Wild-type and pifq mutant seeds were plated in GM medium without sucrose at room temperature as described. During this procedure the seeds were routinely exposed to WL for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness. After stratification, seeds were induced to germinate with a 5-min Rp (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before providing a terminal 5-min FRp (58 μmol/m2/s).Seeds were then placed in constant red light (Rc) (6.7 μmol/m2/s) at 21°C for 45h .

treatment_protocol: 2d Red light (6.7 μmol/m2/s)


title: 2d dark-grown WT(Col-0)/1 hr red light /replicate 3

description: 2d dark grown WT(Col-0) seedlings/1hr Red light/replicate 3


title: 2d dark-grown WT seedling/replicate 4

description: 2d dark grown WT(Col-0) seedlings/replicate 4


title: 2d red light grown WT(Col-0) seedlings/replicate 3

description: 2d Red light (6.7 μmol/m2/s)/replicate 3

growth_protocol: Wild-type and pifq mutant seeds were plated in GM medium without sucrose at room temperature as described. During this procedure the seeds were routinely exposed to WL for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness. After stratification, seeds were induced to germinate with a 5-min Rp (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before providing a terminal 5-min FRp (58 μmol/m2/s).Seeds were then placed in constant red light (Rc) (6.7 μmol/m2/s) at 21°C for 45h


title: 2d dark-grown WT seedling/replicate 6

description: 2d dark grown WT(Col-0) seedlings/replicate 6


title: 5d stratified seed WT (col-0)/replicate 2

description: stratified seed / WT/replicate 2


title: CO5

status: Public on Nov 03 2009

city: Leuven

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

country: Belgium

institute: KULeuven

description: Colonic mucosal gene expression data from control individual

hyb_protocol: Fragmented cRNA (15 µg) was hybridized overnight to the Human Genome U133 Plus 2.0 Array (Affymetrix).

scan_protocol: The arrays were washed and stained with streptavidin-phycoerytrin on an automated Fluidics Station (Affymetrix) and scanned on the Affymetrix 3000 GeneScanner.

data_processing: The resulting image files (.dat files) were analyzed using Affymetrix GCOS software, and intensity values for each probe cell (.cel file) were calculated. Intensity values were scaled to an average of 150 per array according to the method of global scaling provided in the GCOS.

organism: Homo sapiens

source_name: Colonic mucosal biopsy from control individual

label_protocol: Total RNA (2 µg) was reverse-transcribed into cDNA using the SuperScript Choice System (Invitrogen, Carlsbad, CA, USA) with oligo-dT primers containing a T7 RNA polymerase promoter site. cDNA was in vitro transcribed to cRNA and biotin labeled using the IVT labeling kit (Affymetrix, Santa Clara, CA, USA), according to Affymetrix expression analysis technical manual 701021Rev.5. Biotinylated cRNA was purified and fragmented. The quality of labeled and fragmented cRNA, respectively, was assessed with the Agilent 2100 Bioanalyzer.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Benelux B.V.), according to the manufacturer’s instructions. The total RNA integrity and quantity were assessed with the Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and Nanodrop ND-1000 spectrophotometer (Nanodrop technologies), respectively.

tag: tissue

value: Colon

tag: disease

value: Control

tag: response to infliximab

value: Not applicable

tag: before or after first infliximab treatment


title: 2d red light grown pif1pif3pif4pif5 (pifq) mutant/replicate 3

description: 2d red light grown (6.7 μmol/m2/s) pifq mutant/replicate 3

growth_protocol: Wild-type and pifq mutant seeds were plated in GM medium without sucrose at room temperature as described. During this procedure the seeds were routinely exposed to WL for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness. After stratification, seeds were induced to germinate with a 5-min Rp (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before providing a terminal 5-min FRp (58 μmol/m2/s). Seeds were then placed in  constant red light (Rc) (6.7 μmol/ m2/s) at 21°C for 45h.

treatment_protocol: 2d red light grown (6.7 μmol/m-2/s-1)

value: pif1pif3pif4pif5 (pifq) mutant


title: 5d stratified seed/pif1pif3pif4pif5 mutant (pifq)/ replicate 2

treatment_protocol: Seeds were stratified for 5 days at 4ºC in darkness


title: 3T3-L1 adipocyte tissue culture, CLA+metformin fed, biological rep1

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, refer to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G; Pixel size: 1.56 um; Filter: 570 nm

data_processing: The data was analysed using R  2.7.2 with Bioconductor 2.2. Arrays were normalised via gcRMA, and all treatments were compared to the control LA via the limma package. Bonferroni-Hochberg adjusted p-values were used as significance measurement.

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (reaction at 37C for 16h) from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: cell line


title: 5d stratified seed/pif1pif3pif4pif5 mutant (pifq)/ replicate 3


title: 3T3-L1 adipocyte tissue culture, CLA+metformin fed, biological rep2


title: 3T3-L1 adipocyte tissue culture, CLA fed, biological rep2

source_name: 3T3-L1 adipocyte tissue culture, CLA


title: 3T3-L1 adipocyte tissue culture, CLA+metformin fed, biological rep3


title: 3T3-L1 adipocyte tissue culture, CLA fed, biological rep3


title: 2d red light grown pif1pif3pif4pif5 (pifq) mutant/replicate 1

description: 2d red light grown (6.7 μmol/m2/s) pifq mutant/replicate 1

growth_protocol: Wild-type and pifq mutant seeds were plated in GM medium without sucrose at room temperature as described. During this procedure the seeds were routinely exposed to WL for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness. After stratification, seeds were induced to germinate with a 5-min Rp (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before providing a terminal 5-min FRp (58 μmol/m2/s). Seeds were then placed in  constant red light (Rc) (6.7 μmol/m2/s) at 21°C for 45h.

treatment_protocol: 2d red light grown (6.7 μmol/m2/s)


title: 3T3-L1 adipocyte tissue culture, LA fed, biological rep2

source_name: 3T3-L1 adipocyte tissue culture, LA


title: 5d stratified seed/pif1pif3pif4pif5 mutant (pifq)/ replicate 1


title: 2d red light grown pif1pif3pif4pif5 (pifq) mutant/replicate 2

description: 2d red light grown (6.7 μmol/m2/s) pifq mutant/replicate 2


title: 3T3-L1 adipocyte tissue culture, metformin fed, biological rep2


title: 3T3-L1 adipocyte tissue culture, LA fed, biological rep3


title: 3T3-L1 adipocyte tissue culture, metformin fed, biological rep3


title: 3T3-L1 adipocyte tissue culture, metformin fed, biological rep1


title: 2d dark-grown pif1pif3pif4pif5 (pifq) mutant/1 hr red light /replicate 2

description: 2d dark grown pifq mutant seedlings,followed by 1 hr red light (7.5 μmol/m2/s)/replicate 2

treatment_protocol: Dark 2d 21°C followed by 1 hr red light (7.5 μmol/m2/s)


title: 3T3-L1 adipocyte tissue culture, CLA fed, biological rep1


title: 2d dark-grown pif1pif3pif4pif5 (pifq) mutant/replicate 3

description: 2d dark grown pifq mutant seedlings/replicate 3


title: 2d dark-grown pif1pif3pif4pif5 (pifq) mutant/replicate 5

description: 2d dark grown pifq mutant seedlings/replicate 5

growth_protocol: Wild-type and pifq mutant seeds were plated in GM medium without sucrose at room temperature as described. During this procedure the seeds were routinely exposed to WL for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness. After stratification, seeds were induced to germinate with a 5-min Rp (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before providing a terminal 5-min FRp (μmol/m2/s). Seeds were then placed in dark (D) at 21°C for 45h (2d-old seedlings).


title: 2d dark-grown pif1pif3pif4pif5 (pifq) mutant/replicate 4

description: 2d dark grown pifq mutant seedlings/replicate 4

growth_protocol: Wild-type and pifq mutant seeds were plated in GM medium without sucrose at room temperature as described. During this procedure the seeds were routinely exposed to WL for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness. After stratification, seeds were induced to germinate with a 5-min Rp (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before providing a terminal 5-min FRp (58 μmol/m2/s). Seeds were then placed in dark (D) at 21°C for 45h (2d-old seedlings).


title: 2d dark-grown pif1pif3pif4pif5 (pifq) mutant/replicate 2

description: 2d dark grown pifq mutant seedlings/replicate 2


title: 2d dark-grown pif1pif3pif4pif5 (pifq) mutant/1 hr red light /replicate 1

description: 2d dark grown pifq mutant seedlings,followed by 1 hr red light (7.5 μmol/m2/s)/replicate 1


title: Tim-Gal4-Pdf-Gad80 cells from larva, biological replicate 3

status: Public on Oct 31 2009

city: Ashburn

first: Ken

last: Sugino

state: VA

address: 19700 Helix Dr

institute: Janelia Research Campus

description: Sorted GFP positive cells from Tim-Gal4;Pdf-Gal80;UAS-YFP line.

hyb_protocol: Following fragmentation, 15 or 20 ug of cRNA were hybridized for 18 hr at 45C on GeneChip Drosophila v2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with the Affymetrix GeneArray Scanner G3000.

data_processing: The data were processed with GCRMA algorithm in the Bioconductor with default settings.

organism: Drosophila melanogaster

source_name: brain, TimGal4-PdfGal80-GFP positive cells

label_protocol: Biotinylated cRNA were prepared using two rounds of T7 in vitro transcription based aRNA amplification (Affymetrix Small Sample Target Labeling Assay Version II) from about 0.1 to 0.4 ng of total RNA.

growth_protocol: Flies were growth under standard conditions in 12hs light and 12hs dark cycles

extract_protocol: PicoPure RNA Isolation Kit (Arcturus) was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: About 50 larval or adult heads were dissected at around ZT12, digested with protease, dissociated and GFP positive cells were collected.

tag: source

value: brain

tag: developmental stage

value: larva

tag: cell type

value: Tim-Gal4 and Pdf-Gal80


title: Eyes from adult, biological replicate 2

description: Eye dissected from fly head

source_name: eye

value: eye

value: adult


title: Eyes from adult, biological replicate 1

description: Eye dissected from fly head


title: 2d dark-grown pif1pif3pif4pif5 (pifq) mutant/1 hr red light /replicate 3

description: 2d dark grown pifq mutant seedlings,followed by 1 hr red light (7.5 μmol/m2/s)/replicate 3


title: Eyes from adult, biological replicate 3

description: Eye dissected from fly head


title: 3T3-L1 adipocyte tissue culture, LA fed, biological rep1


title: Tim-Gal4-Pdf-Gad80 cells from larva, biological replicate 2


title: Pdf cells from larva, biological replicate 1

description: Sorted GFP positive cells from Pdf-Gal4;UAS-GFP line.

source_name: brain, Pdf-GFP postive cells


title: Pdf cells from larva, biological replicate 2


title: Tim-Gal4-Pdf-Gad80 cells from larva, biological replicate 1


title: Tim cells from larva, biological replicate 3

description: Sorted GFP positive cells from Tim-Gal4;UAS-YFP line.

source_name: brain, Tim-GFP positive cells


title: Elav cells from larva, biological replicate 1

description: Sorted GFP positive cells from Elav-Gal4;UAS-GFP line.

source_name: brain, Elav-GFP positive cells


title: Pdf cells from larva, biological replicate 3


title: Tim cells from larva, biological replicate 1


title: Elav cells from larva, biological replicate 3


title: Tim cells from larva, biological replicate 2


title: Elav cells from larva, biological replicate 2


title: Col-0 wt Hypoxic Replicate No. 2

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

country: Italy

institute: Sant'Anna School of Advanced Studies

description: no additional description required

hyb_protocol: Affymetrix standard hybridization protocol

scan_protocol: Affymetrix standard scan protocol

data_processing: GC-RMA algorithm

source_name: Arabidopsis seedlings

label_protocol: Affymetrix standard labeling protocol

growth_protocol: Arabidopsis thaliana, Columbia-0 ecotype, was used in all experiments. Seeds were sterilized with ethanol 70% (1 min), 0.85% sodium hypochlorite (10 min) and rinsed with sterile water (6 times). Seedlings were grown on Murashige and Skoog half-strength medium (agar 0.8%) containing 30 mM sucrose. The plates were incubated in the dark at 4°C for two days (vernalization, to promote homogeneous germination) and then transferred to 23°C for seven days under light/dark 12/12 photoperiod before the treatments. Seedlings were grown under aerobic conditions.

extract_protocol: Total RNA was extracted from whole 7-day old plants using the RNeasy kit (Qiagen). RNA quality was assessed by agarose gel electrophoresis and spectrophotometry. RNA was processed for use on Affymetrix Arabidopsis Genome GeneChip arrays.

treatment_protocol: This sample represents hypoxic wt Col-0. Arabidopsis seedlings, 7d-old.

tag: growth stage

value: seedling

tag: ecotype

value: Columbia 0, wt

tag: age

value: 7 days

tag: germination

value: aerobic

tag: growth conditions

value: Murashige-Skoog growth conditions, half-strength, sucrose 30 mM, 23°C, light/dark 12/12 photoperiod

tag: treatment

value: hypoxic treatment


title: 35S::HRE2 Hypoxic Replicate No. 2

description: no additional description required

treatment_protocol: This sample represents hypoxic transgenic 35S::HRE2. Arabidopsis seedlings, 7d-old.

value: Columbia 0, 35S::HRE2


title: 35S::HRE2 Hypoxic Replicate No. 1

description: no additional description required


title: Col-0 wt Hypoxic Replicate No. 1

description: no additional description required


title: 35S::HRE1 Hypoxic Replicate No. 2

description: no additional description required

treatment_protocol: This sample represents hypoxic 35S::HRE1 Col-0. Arabidopsis seedlings, 7d-old.

value: Columbia 0, 35S::HRE1


title: Col-0 wt Aerobic Replicate No. 1

description: no additional description required

treatment_protocol: This sample represents aerobic wt Col-0. Arabidopsis seedlings, 7d-old.

value: untreated control


title: Col-0 wt Aerobic Replicate No. 2

description: no additional description required


title: 35S::HRE1 Hypoxic Replicate No. 1

description: no additional description required


title: Heart_swim_rep1

city: Pittsburgh

first: Cristi

middle: Lara

last: Galindo

state: Pennsylvania

address: 200 Lothrop Avenue

institute: University of Pittsburgh

description: Study was performed to compare pathological versus physiological cardiac hypertrophy

hyb_protocol: per manufacturer, in UTSW Microarray Core

data_processing: Data were analyzed using GeneSifter (VizX Labs, Seattle, WA) and Spotfire DecisionSite 9.0 (Spotfire, Inc., Somerville, MA). Data were normalized using robust-multi average (RMA) method, and signals for each group were averaged before performing Student’s t test with Benjamini and Hochberg correction and pairwise comparisons for sedentary mice versus mice that received ISO treatment or were exercised. Genes were considered as altered if the folds-change was at least 1.5 and adjusted p value ≤ 0.05.

source_name: Heart

growth_protocol: All mice were housed in the Animal facility at University of Texas Southwestern Medical Center (UTSW), Dallas, TX, in accordance with the standards set forth in the Guide for the Care and Use of Laboratory Animals (NIH Publication No. 85-23, revised 1996).  All experimental procedures for this study were approved by the Institutional Animal Care and Use Committee at UTSW.

extract_protocol: Total RNA from left ventricles of experimental animals was isolated using TRIzol Reagent (Invitrogen Corporation, Carlsbad, CA) per manufacturer’s instructions and purified by phenol-chloroform extraction and ethanol precipitation.

treatment_protocol: Pathological cardiac hypertrophy was investigated using the isoproterenol-induced subacute myocardial injury model as previously described [28]. Briefly, animals were anesthetized with 1.5% isoflurane (Smiths Medical PM, Waukesha, WI) in 98.5% oxygen and a 1 cm incision made on the back of each animal between the shoulder blades. An Alzet 1007D micro-osmotic pump (DURECT Corporation, Cupertino, CA) containing isoproterenol (ISO, Sigma-Aldrich, St. Louis, MO), at 40 mg.kg-1.d-1, dissolved in 0.9% NaCl was inserted into the infrascapular subcutaneous tissue and the incision sutured. After 10 days of ISO administration, mice were sacrificed, and left ventricles were collected and processed for subsequent assays. Experimental physiological cardiac hypertrophy was induced via exercise, as previously described [29]. Briefly, mice were placed in buckets of pre-warmed water maintained at ~30 oC with low-watt heat lamps and allowed to swim for 90 minutes twice daily. At the beginning of the experiment, mice were acclimated to the exercise routine gradually, beginning with 10 minutes twice daily and increasing in increments of 10 minutes per day, until 90 minutes was obtained. After 8 weeks of swimming, mice were sacrificed and heart samples (left ventricles) collected and processed for each assay. Sedentary mice confined to cages served as negative controls.

tag: sample source

value: Eight-week old male C57BL/6 mice, purchased from the Jackson Laboratory

value: heart left ventricle

tag: protocol

value: exercise-induced cardiac hypertrophy


title: 35S::HRE2 Aerobic Replicate No. 1

description: no additional description required

treatment_protocol: This sample represents aerobic transgenic 35S::HRE2. Arabidopsis seedlings, 7d-old.


title: Heart_control_rep1

scan_protocol: per manufacturer, in UTSW Microarray Core

source_name: Heart, left ventricle

value: control


title: Vehicle treated mesenchyme, biological rep 3

city: Ann Arbor

first: William

last: Zacharias

state: MI

address: 109 Zina Pitcher Place

department: Department of Cell and Developmental Biology

institute: University of Michigan Medical School

description: Gene expression data from isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Vehicle for 24 hours

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized  to MOE 430.2 microarrays (9 total chips, three replicate chips for each treatment; Affymetrix, Santa Clara, CA) by the University of Michigan Cancer Center Microarray Core Facility. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The .DAT files were obtained by Affymetrix GCOS software. Then the .CEL files were analyzed using Robust Muti-array Average (RMA) for background adjustment, normalization and summrization to obtain gene expression data matrix.

source_name: Isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Vehicle for 24 hours

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

growth_protocol: Embryos from C57Bl/6J mice were collected from timed pregnant females, with the day of vaginal plug detection considered day 0.5. Intestine was removed, seperated from epithelium using Cell Recovery Solution (BD Biosciences) and cultured on collagen matrix in DMEM with 10% FBS and 1% Hepes

extract_protocol: Total RNA was isolated with TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy kit (Qiagen, Valencia, CA), per the manufacturers’ instructions.

treatment_protocol: For the microarray experiment, a total of 6 wells of each treatment were collected and randomly pooled into one of three samples for replicate analysis.

value: small intestinal mesenchyme

tag: genotype

value: C57Bl/6J mice

value: E18.5 mouse embryo

tag: agent


title: 35S::HRE1 Aerobic Replicate No. 2

description: no additional description required

label: Biotin

growth_protocol: Arabidopsis thaliana, Columbia-0 ecotype, was used in all experiments. Seeds were sterilized with ethanol 70% (1 min),  0.85% sodium hypochlorite (10 min) and rinsed with sterile water (6 times). Seedlings were grown on  Murashige and Skoog half-strength medium (agar 0.8%) containing 30 mM sucrose. The plates were incubated in the dark at 4°C for two days (vernalization, to promote homogeneous germination) and then transferred to 23°C for seven days under light/dark 12/12 photoperiod before the treatments. Seedlings were grown under aerobic conditions.

extract_protocol: Total RNA was extracted from whole 7-day old plants using the RNeasy kit (Qiagen). RNA quality was assessed by agarose gel electrophoresis and spectrophotometry. RNA was processed for use on Affymetrix  Arabidopsis Genome GeneChip arrays.

treatment_protocol: This sample represents aerobic transgenic 35S::HRE1. Arabidopsis seedlings, 7d-old.


title: Heart_control_rep2

label: per manufacturer, in UTSW Microarray Core

tag: tissue


title: 35S::HRE1 Aerobic Replicate No. 1

description: no additional description required


title: Heart_ISO_rep1

label_protocol: per manufacturer, in UTSW Microarray Core

value: isoproterenol-induced cardiomyopathy


title: 35S::HRE2 Aerobic Replicate No. 2

description: no additional description required

value: seedling


title: Heart_ISO_rep3


title: Heart_swim_rep2


title: Ihh treated mesenchyme, biological rep 3

description: Gene expression data from isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Ihh for 24 hours

source_name: Isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Ihh for 24 hours

value: Ihh ligand


title: Heart_ISO_rep2


title: Heart_swim_rep3


title: Ihh treated mesenchyme, biological rep 2


title: Vehicle treated mesenchyme, biological rep 1


title: Vehicle treated mesenchyme, biological rep 2


title: Shh treated mesenchyme, biological rep 1

description: Gene expression data from isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Shh for 24 hours

source_name: Isolated E18.5 intestinal mesenchyme cultured for 48 hours and treated with Shh for 24 hours

value: Shh ligand


title: Heart_control_rep3


title: Ihh treated mesenchyme, biological rep 1


title: Shh treated mesenchyme, biological rep 2


title: Shh treated mesenchyme, biological rep 3


title: WT mouse on Day 14, No.3

status: Public on Oct 30 2009

city: Kyoto

first: Sakata

last: Daiji

state: Kyoto

address: Yoshida-konoe, Sakyo

department: pharmacology

country: Japan

institute: Kyoto University

description: Gene expression data in development of fibrosis

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 17 hr at 45C on Affymetrix mouse 430 2.0 Array.

scan_protocol: GeneChips were scanned using GCS3000.

data_processing: GeneChip Operating Software 1.4 was used for normalization. The mean target for each array was arbitrarily set to 500.

source_name: Lung of WT mice on Day 14 after bleomycin

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 6 ug total RNA .

extract_protocol: Sepasol extraction of total RNA from lung was performed.

treatment_protocol: Mice were instilled intratracheally with bleomycin (1 mg/kg) in 40 ul saline on Day 0.

tag: gender

value: female

value: lung


title: WT mouse on Day 14, No.2


title: WT mouse on Day 7, No.4

source_name: Lung of WT mice on Day 7 after bleomycin


title: WT mouse on Day 14, No.5


title: WT mouse on Day 14, No.1


title: WT mouse on Day 7, No.3


title: WT mouse on Day 14, No.4


title: FP-KO mouse on Day 7, No.4

source_name: Lung of FP-KO mice on Day 7 after bleomycin


title: WT mouse on Day 7, No.1


title: WT mouse on Day 7, No.2


title: FP-KO mouse on Day 14, No.4

source_name: Lung of FP-KO mice on Day 14 after bleomycin


title: FP-KO mouse on Day 7, No.3


title: WT mouse on Day 0, No.2

description: Gene expression data at baseline

source_name: Lung of WT mice on Day 0 after bleomycin


title: WT mouse on Day 0, No.3

description: Gene expression data at baseline


title: FP-KO mouse on Day 14, No.2


title: FP-KO mouse on Day 7, No.1


title: WT mouse on Day 0, No.4

description: Gene expression data at baseline


title: WT mouse on Day 0, No.1

description: Gene expression data at baseline


title: FP-KO mouse on Day 14, No.1


title: FP-KO mouse on Day 14, No.3


title: FP-KO mouse on Day 7, No.2


title: FP-KO mouse on Day 0, No.4

description: Gene expression data at baseline

source_name: Lung of FP-KO mice on Day 0 after bleomycin


title: FP-KO mouse on Day 0, No.2

description: Gene expression data at baseline


title: FP-KO mouse on Day 0, No.1

description: Gene expression data at baseline


title: FP-KO mouse on Day 0, No.3

description: Gene expression data at baseline


title: mouse erythroleukemia_G9a knockdown_replicate 2, GCRMA

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description: G9a knockdown

hyb_protocol: Affymetrix standard.

scan_protocol: Affymetrix standard.

data_processing: GCRMA normalization using R.

source_name: MEL, G9a knockdown

label_protocol: Affymetrix standard.

growth_protocol: RPMI medium containing 10% fetal bovine serum; 1% glutamine; penicillin and streptomycin 2% DMSO were added for 4 days to induce erythroid differentiation.

extract_protocol: The RNA was extracted and purified using the RNeasy Mini Kit (Qiagen) including the on-column DNAse I digestion step.

treatment_protocol: Knock down was induced by adding 5 micrograms/ml final of Dox in the culture medium.

value: mouse erythroleukemia


title: mouse erythroleukemia_G9a knockdown_replicate 1, MAS5

description: G9a knockdown


title: mouse erythroleukemia_wild type_replicate 3, MAS5

description: wild type

source_name: MEL, wild type


title: 15P-1.16 Rhox5-negative

status: Public on Oct 29 2009

city: San Diego

first: miles

last: wilkinson

address: 4168 Front Street

department: reproduction

institute: ucsd

description: stably transfected with a murine Rhox5 full-legth cDNA; expression levels lowest

hyb_protocol: Following fragmentation, cRNA were hybridized to mouse4302 Array according to standard Affymetrix hybridization protocols (EukGE-WS2v5_450).

scan_protocol: GeneChips were scanned using the GCS3000 high resolution scanner

data_processing: Expression data was processed within GeneSpring 5.1 using the MAS 5 algorithm.

source_name: 15P-1 Sertoli cell line

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

growth_protocol: The 15P-1 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 50 mg/ml of both penicillin and streptomycin.  The cells were grown at 37oC in 5% CO2 atmosphere and split when ~80% confluent.

extract_protocol: Total cellular RNA was prepared from cell lines by guanidinium isothiocynate lysis and centrifugation over a 5.7 M CsCl cushion for at least 12h at 180oC. RNA pellet was resuspend in 1mM Sodium Citrate , chloroform:butan-1-ol (4:1) purification and ethanol precipitation.

treatment_protocol: To generate stable Rhox5 expression plasmid transfected clones, 15P-1 cells cultured to ~60% confluency in 100 mm plates were transfected with 2 mg of Rhox5 expression plasmid using lipofectamine (Invitrogen, Carlsbad, CA) and clones resistant to antibiotic (700 mg/ml G418) were selected.

value: male

tag: phenotype

value: low Rhox5 mRNA


title: mouse erythroleukemia_wild type_replicate 2, GCRMA

description: wild type


title: mouse erythroleukemia_G9a knockdown_replicate 3, MAS5

description: G9a knockdown


title: mouse erythroleukemia_wild type_replicate 1, MAS5

description: wild type


title: 15P-1.6 Rhox5-positive

description: stably transfected with a murine Rhox5 full-legth cDNA; expression levels highest

tag: cell line

value: high Rhox5 mRNA


title: 15P-1.24 Rhox5-positive


title: 15P-1.14 Rhox5-negative


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 1039_Kx1 (ChAG associated) replicate 3

status: Public on Oct 27 2009

city: Saint Louis

first: Jeremiah

middle: J

last: Faith

state: MO

address: Campus Box 8510

institute: Washington University in St. Louis

hyb_protocol: Following fragmentation, 25 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GS300

data_processing: The data were normalized using the justRMA() function [with default parameters] from the Bioconductor R package.

molecule: polyA RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12 ug total RNA.

growth_protocol: Cells were grown to 70% confluence in RPMI 1640 medium supplemented with 10% FBS at 37C

extract_protocol: Qiagen RNeasy mini-prep kit.

treatment_protocol: After 24h of infection, medium and non-attached bacteria were washed off and the mouse cells harvested by trypsinization (5mins at 37C). Following neutralization with ice-cold medium, and a PBS wash, cells were flash frozen in liquid nitrogen

value: Cells grown in T75 cell culture flasks

value: 24 hrs


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 345_Kx1 replicate 2

description: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 345_Kx1 (healthy stomach associated)


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 345_Kx2 (ChAG associated) replicate 2


title: Mouse non-progenitor gastric epithelial cells, infected with H.pylori strain HPAG (ChAG associated) replicate 2


title: mouse lymphoid tissue inducer cell

status: Public on Oct 28 2009

city: Sinjuku-ku Shinanomachi

first: kazuyo

last: moro

state: Tokyo

department: Microbiology and Immunology

institute: Keio University school of medicine

description: mouse lymphoid tissue inducer cell, LTi

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operation Software using Affymetrix default analysis settings and global scaling as normalization method.

source_name: cultured Lti cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, ver. 6, Affymetrix).

growth_protocol: Thy-1+CD4- LTi cells were prepared from fetal liver cells as described previously (J. Immunol. 167, 2511-2521, 2001). c-Kit+α4β7+IL-7Rα+ fetal liver cells from day 13 embryos were cultured on TSt4 cells for 17 days.

extract_protocol: Total RNA was extracted from 5 x 105 FALC c-Kit+Sca-1+ cells, LTi cells and DN2 cells after direct sorting into a vial containing ISOGEN LS (Nippon Gene, Tokyo, Japan). Total RNA of LTi cells was also extracted in ISOGEN LS. Total RNA was further purified using an RNeasy Micro Kit (QIAGEN, Tokyo, Japan) and amplified by Two-Cycle Target Labeling method (Affymetrix, Santa Clara, CA). Microarray processing was done by the Central Research Laboratory, Keio University School of Medicine.

treatment_protocol: Mesenteries separated from intestine and mesenteric lymph nodes were cut into small fragments with scissors and digested in Dulbecco's modified Eagle's Medium containing 2 mg/ml collagenase type I and 4% BSA. The supernatant was aspirated off after centrifugation to remove adipocytes. Finally, cells were suspended in Hank’s Balanced Salt Solution containing 10% FCS after filtration through 32 µm nylon mesh.

tag: strain

value: Embryo, Fetal Liver (E13)


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 1039_Kx2 (ChAG associated) replicate 1


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 1039_Kx1 (ChAG associated) replicate 1


title: Mouse non-progenitor gastric epithelial cells, infected with heat-killed H.pylori strain HPAG replicate 2

description: Mouse non-progenitor gastric epithelial cells, infected with heat-killed H.pylori strain HPAG (ChAG associated)


title: mouse thymus double negative 2 cell

description: mouse thymus double negatibe 2 cell, DN2

source_name: sorted DN2 cells

value: Thymus


title: mouse natural helper cell 2

description: mouse natural helper cell, mLSK2

source_name: unstimulated natural helper cells

value: Mesentery


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 1039_Kx2 (ChAG associated) replicate 2


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 345_Kx1 replicate 1

source_name: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 345_Kx1 (healthy stomach associated)


title: Mouse non-progenitor gastric epithelial cells, infected with H.pylori strain HPAG (ChAG associated) replicate 3


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 1039_Kx1 (ChAG associated) replicate 2


title: Mouse non-progenitor gastric epithelial cells, infected with heat-killed H.pylori strain HPAG replicate 1

source_name: Mouse non-progenitor gastric epithelial cells, infected with heat-killed H.pylori strain HPAG (ChAG associated)


title: mouse natural helper cell 1

description: mouse natural helper cell, mLSK1


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 345_Kx1 replicate 3


title: Mouse non-progenitor gastric epithelial cells, infected with heat-killed H.pylori strain HPAG replicate 3


title: Mouse gastric epithelial progenitor cells, infected with heat-killed H.pylori strain HPAG (ChAG associated) replicate 1


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 345_Kx2 (ChAG associated) replicate 1


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG with a hopZ gene deletion, replicate 1


title: Mouse gastric epithelial progenitor cells, infected with heat-killed H.pylori strain HPAG (ChAG associated) replicate 3


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG (ChAG associated) replicate 5


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG (ChAG associated) replicate 6


title: Mouse non-progenitor gastric epithelial cells, infected with H.pylori strain HPAG (ChAG associated) replicate 1


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG with a hopZ gene deletion, replicate 3


title: Mouse gastric epithelial progenitor cells, infected with heat-killed H.pylori strain HPAG (ChAG associated) replicate 2


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG with a hopZ gene deletion, replicate 2


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG (ChAG associated) replicate 4


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 345_Kx2 (ChAG associated) replicate 3


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain 1039_Kx2 (ChAG associated) replicate 3


title: Mouse non-progenitor gastric epithelial cells, uninfected, replicate 5


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG (ChAG associated) replicate 1


title: Mouse gastric epithelial progenitor cells, uninfected, replicate 11


title: Mouse gastric epithelial progenitor cells, uninfected, replicate 8


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG (ChAG associated) replicate 2


title: Mouse gastric epithelial progenitor cells, uninfected, replicate 6


title: Mouse non-progenitor gastric epithelial cells, uninfected, replicate 4


title: Mouse non-progenitor gastric epithelial cells, uninfected, replicate 6


title: Mouse gastric epithelial progenitor cells, uninfected, replicate 5


title: Mouse gastric epithelial progenitor cells, uninfected, replicate 9


title: Mouse gastric epithelial progenitor cells, uninfected, replicate 12


title: Mouse gastric epithelial progenitor cells, infected with H.pylori strain HPAG (ChAG associated) replicate 3


title: Mouse gastric epithelial progenitor cells, uninfected, replicate 10


title: Mouse gastric epithelial progenitor cells, uninfected, replicate 4


title: [10 days-old seedlings]-[wild-type]-[replicate 1b]

status: Public on Oct 20 2009

city: Rosario

first: Ramiro

last: Rodriguez

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

description: Affymetrix instructions

hyb_protocol: Affymetrix instructions

scan_protocol: Affymetrix instructions

source_name: 10 days-old seedlings

label_protocol: Affymetrix instructions

extract_protocol: QIAGEN - RNeasy Plant Mini Kit

tag: Ecotype

tag: Age and tissue:10 days-old seedlings.

tag: Growth

value: Murashige-SkoodS salts, long days, 23 °C.


title: Mouse gastric epithelial progenitor cells, uninfected, replicate 7

tag: cell type


title: [10 days-old seedlings]-[wild-type]-[replicate 2]

description: Affymetrix instructions


title: DHR96 mutant replicate 3

status: Public on Oct 16 2009

city: Salt Lake City

first: Carl

last: Thummel

state: UT

department: Human Genetics

institute: University of Utah

description: Gene expression data from adults

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Data was then subsequently analyzed using SAM to generate a list of genes misregulated in the the DHR96 mutant. Included is a analyze list of genes mis-regulated in the DHR96 mutant made using a 1.3 fold, fold change cut off.

source_name: Adult animal

growth_protocol: Animals were grown to adult hood

treatment_protocol: Animals were aged 7 days on standard Bloomington fly food

value: Whole animal


title: DHR96 mutant replicate 1

description: Gene expression data from adults


title: 2d dark-grown pif1pif3pif4pif5 (pifq) mutant/replicate 1

description: 2d dark grown pifq mutant seedlings/replicate 1

source_name: whole seedling (root, hypocotyl,cotyledon)

treatment_protocol: Dark 2d 21°C

value: pif1pif3pif4pif5 (pifq) mutant


title: ein3-1eil1-1, dark sample, biological rep

city: Peking

first: Shangwei

last: Zhong

address: YiHeYuan West Street

department: Life Science School

country: China

institute: Peking University, China

description: Gene expression data from whole 4-day old etiolated seedlings

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Arabidopsis 4 days dark grown ein3eil1 whole seedlings

growth_protocol: After 3 days cold treatment, Arabidopsis seeds which plated on MS medium, were given 4 hour light for germination induction then grown at 22ºC for 4 days in the darkness.

extract_protocol: Total RNA was isolated using a TRIZOL Reagent system (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Dark grown seedlings.

value: whole 4-day old etiolated seedlings

tag: genotype/variation

value: ein3-1eil1-1 etiolated seedlings accumulated much more protochlorophyllide than WT


title: Wt, dark sample, biological rep

source_name: Arabidopsis 4 days dark grown Wt whole seedlings

value: wildtype


title: Canton S replicate 1

description: Gene expression data from adults

value: Canton-S


title: Wt, dark sample


title: DHR96 mutant replicate 2

description: Gene expression data from adults


title: [10 days-old seedlings]-[35S:miR396]-[replicate 1]

description: Affymetrix instructions


title: [10 days-old seedlings]-[35S:miR396]-[replicate 2]

description: Affymetrix instructions


title: shoot_hypoxia_pCER5_rep2

status: Public on Oct 12 2009

city: Bayreuth

first: Angelika

last: Mustroph

address: Universitaetsstr. 30, NWI

department: Plant Physiology

country: Germany

institute: University Bayreuth

description: Shoot epidermal RNA under hypoxic conditions

hyb_protocol: Hybridizations against Arabidopsis ATH1 Genome Array (GeneChip System®, Affymetrix) chips were performed at 45 °C for 16 h, in the Affymetrix GeneChip Workstation (hybridization oven 640, Fluidics Station 450), using 12 µg of Biotin-labeled aRNA, according to the manufacturer's protocol.

scan_protocol: GeneChips were scanned by use of the Affymetrix GeneChip Workstation Scanner 3000.

data_processing: CEL files from the Affymetrix Chips were processed by use of the R program (http://cran.at.r-project.org/) and Bioconductor packages (http://www.bioconductor.org/). The Robust Multi-chip Average (RMA) normalization was performed using the default settings of the corresponding R function. Present, Marginal or Absent (P/M/A) calls were computed with the affy package.

source_name: 7 day old Arabidopsis Seedling shoots, 2hr hypoxia, pCER5-enriched polysomal mRNA

label_protocol: Total and polysomal RNA samples derived from two or more independent biological replicate experiments were used for microarray hybridization analysis. RNA samples (15 to 100 ng) were used to synthesize double stranded cDNA, using the Two-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA), which was subsequently labelled by use of the GeneChip IVT Labeling Kit (Affymetrix).

growth_protocol: Seeds from transgenics expressing promoter:FLAG-RPL18B (Col-0) were surface sterilized with 95 % (v/v) ethanol for 5 min, followed by 10 min submergence in bleach solution (20 % (v/v) bleach and 0.1 % (v/v) Tween-20), and finally rinsed three times with sterile water. Seeds were stored at 4°C for 3 days, and then plated on solid MS plates (0.43 % (w/v) Murashigi Skoog (MS) salts (Sigma, St. Louis, MO), 0.4 % (w/v) phytagel (Sigma), 1 % (w/v) sucrose, pH 5.7), and placed at a vertical orientation in a growth chamber (Percival Scientific, Inc., http://www.percival-scientific.com/; model CU36L5C8) under long day conditions (16 h light at ~80 µmol photons m-2 s-1/ 8 h darkness) at 23 °C for 7 days.

extract_protocol: All mRNA extraction procedures were performed at 4 °C or on ice. Frozen pulverized tissue was homogenized in Polysome Extraction Buffer (PEB; 200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM ethylene glycol tetraacetic acid (EGTA), 36 mM MgCl2, 1% (v/v) octylphenyl-polyethylene glycol (Igepal CA-630), 1% (v/v) polyoxyethylene(23) lauryl ether (Brig® 35), 1% (v/v) Triton X-100, 1% (v/v) Tween-20, 1% (v/v) polyoxyethylene 10 tridecyl ether, 1% (v/v) sodium deoxycholate, 1 mM dithiothreitol (DTT), 50 µg mL-1 cycloheximide, 50 µg mL-1 chloramphenicol, 0.5 mg mL-1 heparin) using 2.5 mL PEB per mL tissue. A typical extraction was 2 to 3 ml packed volume of frozen pulverised root tissue or 4 to 6 mL shoot tissue. Homogenates were clarified by centrifugation at 16,000 g for 15 min and filtrated with cheesecloth. Six-hundred µL of the supernatant was reserved for isolation of total RNA. To the remaining supernatant 150 µL of EZ-View anti-FLAG agarose beads (Sigma) were added and incubated at 4°C for 2 h with gentle shaking. The beads were recovered by centrifugation at 3,500 g, and washed four times for 5 min each with 6 mL of wash buffer (200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM EGTA, 36 mM MgCl2, 5 mM DTT, 50 µg mL-1 cycloheximide, 50 µg mL-1 chloramphenicol). Polysomes were eluted by resuspension of the washed beads in 300 µL of wash buffer per 100 µl beads that additionally contained 20 U mL-1 of RNase inhibitor (Promega, Madison, WI) and 200 µg mL-1 of [FLAG]3 peptide (Sigma) at 4°C for 30 min. RNA extraction was performed by addition of two volumes of 8 M guanidine-HCl and three volumes of ethanol to the cleared eluate, incubation overnight at –20 °C and pelleting by centrifugation at 15,000 g for 45 min. RNA samples were further purified using RNeasy columns (Qiagen, Valencia, CA) as described previously (Branco-Price et al., 2008). The yield of RNA obtained by immunoprecipitation of ribosome complexes varied in the different p:HF-RPL18 lines, from 1 ng per mL tissue for pKAT:HF-RPL18 to 1 µg per mL tissue for p35S:HF-RPL18. Total RNA was extracted from the same cell lysate of p35S:HF-RPL18 that was used for polysome immunoprecipitation. For this, an aliquot of the homogenized sample was without further modifications precipitated by adding two volumes of 8 M guanidine-HCl and three volumes of ethanol, incubation overnight at –20 °C, pelleting by centrifugation at 15,000 g for 45 min and purification by use of RNeasy columns (Qiagen, Valencia, CA). Quality of RNA was checked with an Agilent 2100 Bioanalyzer.

treatment_protocol: Seven-day old seedlings were subjected to control growth conditions or short hypoxia stress. The stress was imposed by placing the plates containing seedings into sealed lucite chambers into which argon was pumped for 2 h. Treatments started at the end of the light period and took place at 6.5 µM m-1 s-1 light. Control plants were exposed to the same light and temperature conditions but maintained in air. After 2 h, plants were immediately dissected into roots and shoots and frozen in liquid nitrogen within 3 min of removal from the treatment chamber.

tag: Age

value: 7 day old seedlings

tag: Genotype

value: pCER5:His6FLAG-RPL18B (Col-0)

tag: Tissue

value: shoot

tag: Treatment

value: hypoxia


title: shoot_hypoxia_pKAT1_rep1

description: Shoot stomata RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling shoots, 2hr hypoxia, pKAT1-enriched polysomal mRNA

value: pKAT1:His6FLAG-RPL18B (Col-0)


title: Canton S replicate 3

description: Gene expression data from adults


title: shoot_control_pCER5_rep2

description: Shoot epidermal RNA under control conditions

source_name: 7 day old Arabidopsis Seedling shoots, 2hr Control, pCER5-enriched polysomal mRNA

value: control


title: shoot_control_pSultr2;2_rep1

description: Shoot phloem (Sultr2;2) RNA under control conditions

source_name: 7 day old Arabidopsis Seedling shoots, 2hr Control, pSultr2;2-enriched polysomal mRNA

value: pSultr2;2:His6FLAG-RPL18B (Col-0)


title: shoot_control_pCER5_rep1


title: shoot_control_pKAT1_rep1

description: Shoot stomata RNA under control conditions

source_name: 7 day old Arabidopsis Seedling shoots, 2hr Control, pKAT1-enriched polysomal mRNA


title: shoot_control_pKAT1_rep2


title: shoot_hypoxia_pSUC2_rep2

description: Shoot phloem (SUC2) RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling shoots, 2hr hypoxia, pSUC2-enriched polysomal mRNA

value: pSUC2:His6FLAG-RPL18B (Col-0)


title: ein3-1eil1-1, dark sample


title: shoot_hypoxia_pKAT1_rep2


title: shoot_hypoxia_pSUC2_rep1


title: shoot_hypoxia_pCER5_rep1


title: shoot_control_pSultr2;2_rep2


title: shoot_hypoxia_pRBCS_rep1

description: Shoot mesophyll RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling shoots, 2hr hypoxia, pRBCS-enriched polysomal mRNA

value: pRBCS:His6FLAG-RPL18B (Col-0)


title: shoot_hypoxia_pRBCS_rep2


title: shoot_control_pGL2_rep2

description: Shoot trichome RNA under control conditions

source_name: 7 day old Arabidopsis Seedling shoots, 2hr Control, pGL2-enriched polysomal mRNA

value: pGL2:His6FLAG-RPL18B (Col-0)


title: shoot_control_pRBCS_rep2

description: Shoot mesophyll RNA under control conditions

source_name: 7 day old Arabidopsis Seedling shoots, 2hr Control, pRBCS-enriched polysomal mRNA


title: shoot_control_pSUC2_rep2

description: Shoot phloem (SUC2) RNA under control conditions

source_name: 7 day old Arabidopsis Seedling shoots, 2hr Control, pSUC2-enriched polysomal mRNA


title: shoot_control_pSUC2_rep1


title: shoot_hypoxia_pGL2_rep1

description: Shoot trichome RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling shoots, 2hr hypoxia, pGL2-enriched polysomal mRNA


title: shoot_control_pRBCS_rep1


title: Canton S replicate 2

description: Gene expression data from adults


title: shoot_hypoxia_pGL2_rep2


title: shoot_hypoxia_p35S_rep2

description: Shoot polysomal RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling shoots, 2hr hypoxia, p35S-enriched polysomal mRNA

value: p35S:His6FLAG-RPL18B (Col-0)


title: shoot_control_p35S_rep2

description: Shoot polysomal RNA under control conditions

source_name: 7 day old Arabidopsis Seedling shoots, 2hr Control, p35S-enriched polysomal mRNA


title: shoot_hypoxia_total_rep3

description: Shoot total RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling shoots, 2hr hypoxia, total mRNA


title: shoot_control_pGL2_rep1


title: shoot_control_total_rep3

description: Shoot total RNA under control conditions

source_name: 7 day old Arabidopsis Seedling shoots, 2hr Control, total mRNA


title: shoot_hypoxia_p35S_rep1


title: shoot_hypoxia_total_rep2


title: shoot_control_total_rep2


title: shoot_control_total_rep1


title: root_hypoxia_pRPL11C_rep2

description: Root meristematic RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr hypoxia, pRPL11C-enriched polysomal mRNA

value: pRPL11C:His6FLAG-RPL18B (Col-0)

value: root


title: shoot_hypoxia_total_rep1


title: shoot_control_p35S_rep1


title: root_hypoxia_pPEP_rep2

description: Root cortex (PEP) RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr hypoxia, pPEP-enriched polysomal mRNA

value: pPEP:His6FLAG-RPL18B (Col-0)


title: root_hypoxia_pPEP_rep1


title: root_hypoxia_pRPL11C_rep1


title: root_control_pPEP_rep2

description: Root cortex (PEP) RNA under control conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr Control, pPEP-enriched polysomal mRNA


title: root_hypoxia_pCO2_rep2

description: Root cortex (CO2) RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr hypoxia, pCO2-enriched polysomal mRNA

value: pCO2:His6FLAG-RPL18B (Col-0)


title: root_control_pCO2_rep1

description: Root cortex (CO2) RNA under control conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr Control, pCO2-enriched polysomal mRNA


title: root_control_pGL2_rep1

description: Root atrichoblast RNA under control conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr Control, pGL2-enriched polysomal mRNA


title: root_hypoxia_pSUC2_rep1

description: Root phloem (SUC2) RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr hypoxia, pSUC2-enriched polysomal mRNA


title: root_control_pCO2_rep2


title: root_control_pSUC2_rep2

description: Root phloem (SUC2) RNA under control conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr Control, pSUC2-enriched polysomal mRNA


title: root_hypoxia_pSHR_rep2

description: Root vascular (SHR) RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr hypoxia, pSHR-enriched polysomal mRNA

value: pSHR:His6FLAG-RPL18B (Col-0)


title: root_control_pSUC2_rep1


title: root_control_pSultr2;2_rep1

description: Root phloem (Sultr2;2) RNA under control conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr Control, pSultr2;2-enriched polysomal mRNA


title: root_control_pPEP_rep1


title: root_control_pGL2_rep3


title: root_hypoxia_pWOL_rep2

description: Root vascular (WOL) RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr hypoxia, pWOL-enriched polysomal mRNA

value: pWOL:His6FLAG-RPL18B (Col-0)


title: root_hypoxia_pWOL_rep1

value: 7 day old seedlings


title: root_hypoxia_pSHR_rep1


title: root_hypoxia_pCO2_rep1


title: root_hypoxia_pGL2_rep2

description: Root atrichoblast RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr hypoxia, pGL2-enriched polysomal mRNA


title: root_control_pWOL_rep1

description: Root vascular (WOL) RNA under control conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr Control, pWOL-enriched polysomal mRNA


title: root_control_pSultr2;2_rep2


title: root_control_pRPL11C_rep1

description: Root meristematic RNA under control conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr Control, pRPL11C-enriched polysomal mRNA


title: root_control_pGL2_rep2


title: root_control_pWOL_rep2


title: root_hypoxia_pSUC2_rep2


title: root_hypoxia_pGL2_rep1


title: root_control_pSHR_rep1

description: Root vascular (SHR) RNA under control conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr Control, pSHR-enriched polysomal mRNA


title: root_hypoxia_pSCR_rep2

description: Root endodermis RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr hypoxia, pSCR-enriched polysomal mRNA

value: pSCR:His6FLAG-RPL18B (Col-0)


title: root_control_pSHR_rep2


title: root_hypoxia_pSCR_rep1


title: root_control_p35S_rep2

description: Root polysomal RNA under control conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr Control, p35S-enriched polysomal mRNA


title: root_control_pRPL11C_rep2


title: root_hypoxia_p35S_rep1

description: Root polysomal RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr hypoxia, p35S-enriched polysomal mRNA


title: root_hypoxia_p35S_rep3


title: root_control_pSCR_rep1

description: Root endodermis RNA under control conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr Control, pSCR-enriched polysomal mRNA


title: root_control_pSCR_rep2


title: root_hypoxia_total_rep3

description: Root total RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr hypoxia, total mRNA


title: root_hypoxia_total_rep4

description: Root total RNA under hypoxic conditions


title: root_control_total_rep3

description: Root total RNA under control conditions

source_name: 7 day old Arabidopsis Seedling roots, 2hr Control, total mRNA


title: root_control_p35S_rep1


title: root_control_total_rep2

description: Root total RNA under control conditions


title: root_control_p35S_rep3


title: roottip_control_pSHR_rep2

description: Root tip vascular (SHR) RNA under control conditions

hyb_protocol: Hybridizations against Arabidopsis ATH1 Genome Array (GeneChip System®, Affymetrix) chips were performed at 45 °C for 16 h, in the Affymetrix GeneChip Workstation (hybridization oven 640, Fluidics Station 450), using 10 µg of Biotin-labeled aRNA, according to the manufacturer's protocol.

source_name: 7 day old Arabidopsis Seedling roottips, 2hr Control, pSHR-enriched polysomal mRNA

label_protocol: Hybridization probe preparation included two linear rounds of target amplification from 400 pg total or immunopurified RNA using the TargetAmp 2-Round Aminoallyl aRNA Amplification kit 1.0 according to the manufacturer’s instructions (Epicentre Biotechnologies, Madison, WI), except that Biotin-11-CTP and Biotin 16-UTP (both Enzo Biochem, Inc., New York, NY) replaced Aminoallyl-UTP, and the 75 mM Ribonucleotides (ATP, GTP, CTP, UTP) replaced the TargetAmp In Vitro Transcription PreMix B. The biotinylated aRNA was purified by use of an RNeasy spin column (Qiagen).

extract_protocol: All mRNA extraction procedures were performed at 4 °C or on ice. Frozen pulverized tissue was homogenized in Polysome Extraction Buffer (PEB; 200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM ethylene glycol tetraacetic acid (EGTA), 36 mM MgCl2, 1% (v/v) octylphenyl-polyethylene glycol (Igepal CA-630), 1% (v/v) polyoxyethylene(23) lauryl ether (Brig® 35), 1% (v/v) Triton X-100, 1% (v/v) Tween-20, 1% (v/v) polyoxyethylene 10 tridecyl ether, 1% (v/v) sodium deoxycholate, 1 mM dithiothreitol (DTT), 50 µg mL-1 cycloheximide, 50 µg mL-1 chloramphenicol, 0.5 mg mL-1 heparin) using 2.5 mL PEB per mL tissue. A typical extraction was 1 to 2 ml packed volume of frozen pulverised root tip tissue. Homogenates were clarified by centrifugation at 16,000 g for 15 min and filtrated with cheesecloth. Six-hundred µL of the supernatant was reserved for isolation of total RNA. To the remaining supernatant 150 µL of EZ-View anti-FLAG agarose beads (Sigma) were added and incubated at 4°C for 2 h with gentle shaking. The beads were recovered by centrifugation at 3,500 g, and washed four times for 5 min each with 6 mL of wash buffer (200 mM Tris-HCl, pH 9.0, 200 mM KCl, 25 mM EGTA, 36 mM MgCl2, 5 mM DTT, 50 µg mL-1 cycloheximide, 50 µg mL-1 chloramphenicol). Polysomes were eluted by resuspension of the washed beads in 300 µL of wash buffer per 100 µl beads that additionally contained 20 U mL-1 of RNase inhibitor (Promega, Madison, WI) and 200 µg mL-1 of [FLAG]3 peptide (Sigma) at 4°C for 30 min. RNA extraction was performed by addition of two volumes of 8 M guanidine-HCl and three volumes of ethanol to the cleared eluate, incubation overnight at –20 °C and pelleting by centrifugation at 15,000 g for 45 min. RNA samples were further purified using RNeasy columns (Qiagen, Valencia, CA) as described previously (Branco-Price et al., 2008). Total RNA was extracted from the same cell lysate of p35S:HF-RPL18 that was used for polysome immunoprecipitation. For this, an aliquot of the homogenized sample was without further modifications precipitated by adding two volumes of 8 M guanidine-HCl and three volumes of ethanol, incubation overnight at –20 °C, pelleting by centrifugation at 15,000 g for 45 min and purification by use of RNeasy columns (Qiagen, Valencia, CA). Quality of RNA was checked with an Agilent 2100 Bioanalyzer.

treatment_protocol: Seven-day old seedlings were subjected to control growth conditions or short hypoxia stress. The stress was imposed by placing the plates containing seedings into sealed lucite chambers into which argon was pumped for 2 h. Treatments started at the end of the light period and took place at 6.5 µM m-1 s-1 light. Control plants were exposed to the same light and temperature conditions but maintained in air. After 2 h, the root tip region was immediately harvested by cutting 1 cm from the apex of the root. Root tips were frozen in liquid nitrogen within 3 min of removal from the treatment chamber.

value: 1 cm root tip


title: roottip_control_pSHR_rep1


title: roottip_hypoxia_pWOL_rep1

description: Root tip vascular (WOL) RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling roottips, 2hr hypoxia, pWOL-enriched polysomal mRNA

value: hypoxia


title: roottip_control_pWOL_rep1

description: Root tip vascular (WOL) RNA under control conditions

source_name: 7 day old Arabidopsis Seedling roottips, 2hr Control, pWOL-enriched polysomal mRNA


title: roottip_hypoxia_pSHR_rep2

description: Root tip vascular (SHR) RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling roottips, 2hr hypoxia, pSHR-enriched polysomal mRNA


title: roottip_hypoxia_pWOL_rep2


title: root_control_total_rep1

description: Root total RNA under control conditions


title: roottip_hypoxia_pSHR_rep1


title: root_hypoxia_total_rep1

description: Root total RNA under hypoxic conditions


title: roottip_control_pWOL_rep2


title: root_control_total_rep4

description: Root total RNA under control conditions


title: roottip_hypoxia_pSCR_rep2

description: Root tip endodermis RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling roottips, 2hr hypoxia, pSCR-enriched polysomal mRNA


title: roottip_control_total_rep2

description: Root tip total RNA under control conditions

source_name: 7 day old Arabidopsis Seedling root tips, 2hr Control, total mRNA


title: roottip_control_pSCR_rep2

description: Root tip endodermis RNA under control conditions

source_name: 7 day old Arabidopsis Seedling roottips, 2hr Control, pSCR-enriched polysomal mRNA


title: roottip_control_p35S_rep2

description: Root tip polysomal RNA under control conditions

source_name: 7 day old Arabidopsis Seedling roottips, 2hr Control, p35S-enriched polysomal mRNA


title: roottip_hypoxia_p35S_rep2

description: Root tip polysomal RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling roottips, 2hr hypoxia, p35S-enriched polysomal mRNA


title: roottip_hypoxia_total_rep2

description: Root tip total RNA under hypoxic conditions

source_name: 7 day old Arabidopsis Seedling root tips, 2hr hypoxia, total mRNA


title: roottip_control_pSCR_rep1


title: roottip_control_total_rep1


title: roottip_hypoxia_p35S_rep1


title: roottip_control_p35S_rep1


title: roottip_hypoxia_pSCR_rep1


title: Whole Larvae Feeding biological rep2

status: Public on Oct 08 2009

city: Glasgow

first: Jing

last: Wang or Venkat Chintapalli

state: Scotland

address: Dumbarton Road

department: Molecular Genetics

country: United Kingdom

institute: University of Glasgow

description:
Complete whole larvae
amplification: 1-round

hyb_protocol: Following fragmentation, 10 ug of cRNA (or according to the affy IVT protocol)  were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GCOS1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Whole Larvae Feeding

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix)

growth_protocol: Wild-type Drosophila melanogaster (Canton S strain) were raised on standard medium on a 12:12 h L:D cycle, at 23C, and at 55% r.h. To facilitate the collection of accurately staged adults, a laying population of around 12 males and 12 females were transferred to fresh vials daily. When adults subsequently emerged, they were transferred to fresh vials on the day of emergence, and used 7 days later. Where larvae were used, these were third instar.

extract_protocol: Total RNA was extracted using RNeasy Micro kit (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Flies were anaesthetised briefly by chilling on ice, then immediately dissected.

value: Canton-S, 30 feeding third instar larvae


title: Whole Larvae Feeding biological rep1


title: Adult Male Ejaculatory Duct biological rep1

description:
The male ejaculatory ducts including bulb after removing testes and acc. Glands.
amplification: 1-round

source_name: Adult Male Ejaculatory Duct

value: Canton-S 60 male flies, 7 days old


title: Adult Heart biological rep4

description:
The Dorsal abdominal heart, necessarily including some adherent tissues (such as fat body)
amplification: IVT-Express

source_name: Adult Heart

value: Canton-S, 15 female and  15 male flies, 7 days old


title: roottip_hypoxia_total_rep1


title: Adult Male Ejaculatory Duct biological rep2


title: Adult Male Ejaculatory Duct biological rep3


title: Adult Male Ejaculatory Duct biological rep4


title: Whole Larvae Feeding biological rep4


title: Adult Heart biological rep3


title: Adult Eye biological rep2

description:
Dissected from the brain and the rest of the head capsule. So includes plenty of cuticle.
amplification: IVT-Express

source_name: Adult Eye

value: Canton-S, 30 female and  30 male flies, 7 days old


title: Adult Heart biological rep2


title: Adult Eye biological rep1


title: Adult Eye biological rep4


title: Adult Eye biological rep3


title: Adult Fatbody biological rep3

description:
Identifiable fat body from the thorax and abdomen.
amplification: 1-round

source_name: Adult Fatbody


title: Whole Larvae Feeding biological rep3


title: Adult Fatbody biological rep1


title: Adult Heart biological rep1


title: 5th Passage Drosophila S2 Cells biological rep3

description:
Drosophila Schneider' s Cells at 5th passage
amplification: 1-round

source_name: 5th Passage Drosophila S2 Cells

value: Drosophila S2 (Schneider) cells (5th passage) 5million


title: 5th Passage Drosophila S2 Cells biological rep4


title: Larval Feeding Trachea biological rep3

description:
The major tracheal trunks, excluding spiracles and obvious adherent tissues.
amplification: IVT-Express

source_name: Larval Feeding Trachea

value: Canton-S, 100 feeding third instar larvae


title: Adult Fatbody biological rep2


title: 5th Passage Drosophila S2 Cells biological rep1


title: Larval Feeding Trachea biological rep2


title: Larval Feeding Central Nevous System biological rep1

description:
The brain and thoracic ganglia.
amplification: 1-round

source_name: Larval Feeding Central Nervous System


title: Larval Feeding Central Nevous System biological rep2


title: Larval Feeding Fatbody biological rep4

description:
Prominent lateral fat bodies.
amplification: 1-round

source_name: Larval Feeding Fatbody


title: 5th Passage Drosophila S2 Cells biological rep2


title: Larval Feeding Fatbody biological rep2


title: Larval Feeding Central Nevous System biological rep3


title: Larval Feeding Trachea biological rep1


title: Larval Feeding Carcass biological rep4

description:
What’s left after the other tissues have been removed.
amplification: 1-round

source_name: Larval Feeding Carcass


title: Larval Feeding Fatbody biological rep3


title: Larval Feeding Carcass biological rep1


title: Larval Feeding Trachea biological rep4


title: Larval Feeding Carcass biological rep2


title: Larval Feeding Carcass biological rep3


title: Larval Feeding Malpighian Tubule biological rep2

description:
Both anterior and posterior tubules with their common ureters, severed at the junction with the gut.
amplification: 1-round

source_name: Larval Feeding Malpighian Tubule

value: Canton-S, 50 feeding third instar larvae


title: Larval Feeding Fatbody biological rep1


title: Larval Feeding Malpighian Tubule biological rep3


title: Larval Feeding Central Nevous System biological rep4


title: Larval Feeding Malpighian Tubule biological rep4


title: Larval Feeding Malpighian Tubule biological rep1


title: GC-990412T

status: Public on Oct 06 2009

city: Basel

first: Chia-Huey

last: Ooi

address: Grenzacherstrasse 124

country: Switzerland

institute: F. Hoffmann-La Roche Ltd.

description: Series of 200 primary gastric tumors

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000 7G.

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

source_name: primary gastric tumor, GC-990412T

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 to 5 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

extract_protocol: RNeasy mini spin columns (Qiagen) were used according to the manufacturer's instructions.

value: gastric tumor


title: CRL-2072(2)

description: Gene expression of normal skin fibroblasts

source_name: normal skin fibroblasts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

value: skin


title: CRL-2072(3)


title: CRL-2072(1)


title: GC-990424T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990424T


title: GC-990300T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990300T


title: GC-990396T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990396T


title: GC-990475T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990475T


title: GC-990205T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990205T


title: GC-990355T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990355T


title: GC-990515T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990515T


title: GC-990339T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990339T


title: GC-990489T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990489T


title: GC-990111T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990111T


title: GC-990203T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990203T


title: GC-990170T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990170T


title: GC-990474T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990474T


title: GC-990172T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990172T


title: GC-990221T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990221T


title: GC-990136T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990136T


title: GC-990090T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990090T


title: GC-990195T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990195T


title: GC-990119T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990119T


title: GC-990097T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990097T


title: GC-990129T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990129T


title: GC-990413T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990413T


title: GC-990098T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990098T


title: GC-990275T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990275T


title: GC-990089T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990089T


title: GC-990041T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990041T


title: GC-98748381T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-98748381T


title: GC-990071T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990071T


title: GC-990108T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990108T


title: GC-990073T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990073T


title: GC-990046T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990046T


title: GC-990060T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990060T


title: GC-980417T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980417T


title: GC-980386T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980386T


title: GC-990068T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990068T


title: GC-980436T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980436T


title: GC-980418T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980418T


title: GC-980344T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980344T


title: GC-980307T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980307T


title: GC-980305T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980305T


title: GC-980369T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980369T


title: GC-990005T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990005T


title: GC-990044T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990044T


title: GC-980442T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980442T


title: GC-980390T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980390T


title: GC-990024T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990024T


title: GC-980401T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980401T


title: GC-980488T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980488T


title: GC-980319T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980319T


title: GC-980327T [EXCLUDED]

description: Series of 200 primary gastric tumors

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

THIS SAMPLE FOUND NOT TO BE GASTRIC ADENOCARCINOMA AND WAS EXCLUDED FROM THE PUBLISHED ANALYSIS

source_name: primary gastric tumor, GC-980327T


title: GC-980453T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980453T


title: GC-990069T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990069T


title: GC-990010T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-990010T


title: GC-980097T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980097T


title: GC-980269T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980269T


title: Adult Fatbody biological rep4

source_name: Adult Fatbody


title: GC-980211T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980211T


title: GC-980251T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980251T


title: GC-980048T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980048T


title: GC-980028T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980028T


title: GC-980025T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980025T


title: GC-980148T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980148T


title: GC-980056T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980056T


title: GC-980002T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980002T


title: GC-970017T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-970017T


title: GC-82973565T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-82973565T


title: GC-970024T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-970024T


title: GC-980045T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980045T


title: GC-980063T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980063T


title: GC-91228050T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-91228050T


title: GC-980011T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980011T


title: GC-980252T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980252T


title: GC-91515473T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-91515473T


title: GC-980021T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980021T


title: GC-970005T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-970005T


title: GC-970010T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-970010T


title: GC-980001T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980001T


title: GC-87622942T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-87622942T


title: GC-970003T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-970003T


title: GC-78373410T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-78373410T


title: GC-77263387T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-77263387T


title: GC-66811693T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-66811693T


title: GC-76629543T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-76629543T


title: GC-7847924T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-7847924T


title: GC-73291145T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-73291145T


title: GC-61669256T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-61669256T


title: GC-68334421T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-68334421T


title: GC-65256293T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-65256293T


title: GC-57701999T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-57701999T


title: GC-5218170T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-5218170T


title: GC-38877042T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-38877042T


title: GC-58947266T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-58947266T


title: GC-47149013T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-47149013T


title: GC-48982424T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-48982424T


title: GC-6412929T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-6412929T


title: GC-29806547T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-29806547T


title: GC-37262942T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-37262942T


title: GC-43618211T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-43618211T


title: GC-43658255T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-43658255T


title: GC-57689477T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-57689477T


title: GC-49375233T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-49375233T


title: GC-47492137T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-47492137T


title: GC-31231321T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-31231321T


title: GC-46404174T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-46404174T


title: GC-26109694T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-26109694T


title: GC-31661621T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-31661621T


title: GC-32226415T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-32226415T


title: GC-20020455T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-20020455T


title: GC-980095T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-980095T


title: GC-20020846T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-20020846T


title: GC-20263644T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-20263644T


title: GC-20020838T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-20020838T


title: GC-2001190T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2001190T


title: GC-20020999T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-20020999T


title: GC-20020011T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-20020011T


title: GC-2001159T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2001159T


title: GC-20020361T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-20020361T


title: GC-2001206T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2001206T


title: GC-2001135T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2001135T


title: GC-2001229T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2001229T


title: GC-2000986T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000986T


title: GC-2000920T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000920T


title: GC-20020448T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-20020448T


title: GC-2000859T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000859T


title: GC-2000877T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000877T


title: GC-2001120T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2001120T


title: GC-2001241T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2001241T


title: GC-20020195T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-20020195T


title: GC-2001123T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2001123T


title: GC-2001226T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2001226T


title: GC-2001086T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2001086T


title: GC-2000892T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000892T


title: GC-2000963T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000963T


title: GC-20020032T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-20020032T


title: GC-2000752T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000752T


title: GC-2000778T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000778T


title: GC-2000721T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000721T


title: GC-2000696T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000696T


title: GC-83507354T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-83507354T


title: GC-2000676T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000676T


title: GC-2000708T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000708T


title: GC-2000521T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000521T


title: GC-2000639T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000639T


title: GC-2000617T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000617T


title: GC-2000619T [EXCLUDED]

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000619T


title: GC-2000529T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000529T


title: GC-2000518T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000518T


title: GC-2000433T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000433T


title: GC-2000441T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000441T


title: GC-2000479T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000479T


title: GC-2000484T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000484T


title: GC-2000362T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000362T


title: GC-2000472T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000472T


title: GC-2000403T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000403T


title: GC-2000303T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000303T


title: GC-2000286T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000286T


title: GC-2000291T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000291T


title: GC-2000178T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000178T


title: GC-2000175T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000175T


title: GC-2000242T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000242T


title: GC-2000256T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000256T


title: GC-2000201T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000201T


title: GC-2000238T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000238T


title: GC-2000169T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000169T


title: GC-2000159T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000159T


title: GC-2000068T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000068T


title: GC-2000114T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000114T


title: GC-2000346T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000346T


title: GC-2000088T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000088T


title: GC-069-LYK-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-069-LYK-T


title: GC-2000040T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000040T


title: GC-15295992T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-15295992T


title: GC-2000085T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000085T


title: GC-066-OSL-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-066-OSL-T


title: GC-058-CPS-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-058-CPS-T


title: GC-064-SSB-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-064-SSB-T


title: GC-068-QKW-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-068-QKW-T


title: GC-067-LCW-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-067-LCW-T


title: GC-068JW-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-068JW-T


title: GC-043-WKS-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-043-WKS-T


title: GC-047LAK-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-047LAK-T


title: GC-10390127T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-10390127T


title: GC-052-GC-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-052-GC-T


title: GC-051-TGC-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-051-TGC-T


title: GC-039-TSC-T [EXCLUDED]

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-039-TSC-T


title: GC-050-IY-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-050-IY-T


title: GC-042-KS-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-042-KS-T


title: GC-038LYC-T [EXCLUDED]

description: Series of 200 primary gastric tumors

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

THIS SAMPLE FAILED QUALITY CONTROL AND WAS EXCLUDED FROM THE PUBLISHED ANALYSIS

source_name: primary gastric tumor, GC-038LYC-T


title: GC-046CBP-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-046CBP-T


title: GC-032TKK-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-032TKK-T


title: GC-028LGL-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-028LGL-T


title: GC-035PCC-T [EXCLUDED]

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-035PCC-T


title: GC-031KCW-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-031KCW-T


title: GC-017TPC-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-017TPC-T


title: GC-026-GJK-T [EXCLUDED]

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-026-GJK-T


title: GC-011LGE-T [EXCLUDED]

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-011LGE-T


title: GC-024-SWM-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-024-SWM-T


title: GC-025-PHW-T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-025-PHW-T


title: GC-021LAH-T [EXCLUDED]

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-021LAH-T


title: YCC3

description: Series of 25 (unique) gastric cancer cell lines

source_name: gastric cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

value: gastric cancer


title: YCC6


title: TMK1


title: YCC1(1)


title: YCC16


title: SNU5


title: MKN74(2)


title: MKN74(3)


title: YCC10


title: MKN74(1)


title: NCI-N87


title: SNU1


title: YCC1(2)


title: GC-2000732T

description: Series of 200 primary gastric tumors

source_name: primary gastric tumor, GC-2000732T


title: YCC7(1)


title: YCC7(2)


title: MKN7


title: SNU16


title: MKN45(2)


title: MKN28


title: KatoIII

value: KatoIII


title: MKN45(1)


title: Hs746T


title: Ist1


title: MKN45(3)


title: YCC11


title: Fu97


title: MKN1


title: AZ521


title: AGS(2)

value: AGS


title: AGS(1)


title: SCH

value: SCH


title: High Translation Fraction 0.25% YE-1

status: Public on Oct 02 2009

city: La Jolla

first: Brian

middle: Matthew

last: Zid

state: California

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

institute: University of California San Diego

description: Expression profile of the high translation fraction on 0.25%YE

hyb_protocol: 12.5 micrograms of biotin-labeled cRNA was fragmented and hybridized according to the Affymetrix protocol.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip 3000 scanner.

data_processing: Data were processed using Rosetta Resolver (Rosetta Biosoftware); the Affymetrix-Rosetta – Intensity Profile and Experiment Builder pipelines were used. Data processing resulted in average expression values and associated errors as well as a statistic reporting whether the target transcript was detected above background.

source_name: Whole 7-8 old male

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for MessageAmp II-Biotin Enhanced kit (Ambion) starting with 100 ng total RNA.

extract_protocol: Total RNA was separated over a sucrose gradient, then RNA was isolated by Trizol extraction from the high or the low translation fractions.

value: male

tag: diet

value: 6 days on 0.25% YE food


title: Low Translation Fraction 4% YE-2

description: Expression profile of the low translation fraction on 4%YE

value: 6 days on 4% YE food


title: Low Translation Fraction 0.25% YE-1

description: Expression profile of the low translation fraction on 0.25%YE


title: Low Translation Fraction 0.25% YE-2