title: woodchuck 6361 normal tissue surrounding the liver HCC


title: Uterine plexiform leiomyoma (aka sample 1030t)

status: Public on May 01 2008

type: RNA

city: Boston

first: Bradley

middle: J

last: Quade

state: MA

address: 75 Francis Street

department: Pathology

country: USA

institute: Brigham and Women's Hospital

description: Gene expression data from human uterine leiomyoma, plexiform histological subtype

hyb_protocol: Following fragmentation, cRNA was hybridized to the U133 Plus 2.0 microarrays, washed and stained according to the standard Affymetrix protocol at the Harvard Med School - Partners Healthcare Center for Genetics and Genomics.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol at the Harvard Med School - Partners Healthcare Center for Genetics and Genomics.

data_processing: standardy Affymetrix protocol

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: uterus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol at the Harvard Med School - Partners Healthcare Center for Genetics and Genomics.

extract_protocol: Total RNA was isolated using the RNeasy Fibrous Tissue kit (QIAGEN, Valencia, CA) following the manufacturer's instructions.

treatment_protocol: Discarded tumor and normal myometrial tissues were obtained by myomectomy or hysterectomy in the Division of Women's and Perinatal Pathology at Brigham and Women's Hospital.

tag: Gender

value: female

tag: Age

value: 34 years

tag: Karyotype

tag: Race

value: Black

tag: Menstraual Cycle

value: secretory phase

tag: Tumor Size


title: mkk1/mkk2, 24h after BTH, rep-A

city: Kgs. Lyngby

first: Henrik

middle: Bjørn

last: Nielsen

address: Kemitorvet, Building 208,

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

description: Whole wild type plants (Col-0), no BTH treatment.

hyb_protocol: 15 µg of aRNA for each sample was fragmented, labeled and hybridized to Affymetrix ATH1 GeneChips according to the standard Affymetrix protocol.

scan_protocol: Affymetrix

data_processing: The microarray data was pre-processed by RMA (Irizarry et al., 2003; Nucleic Acids Res. 31: e15; Irizarry et al., 2003; Biostatistics 4: 249-264)

label: Biotin

organism: Arabidopsis thaliana

source_name: mkk1/mkk2, 24h after BTH treatment

label_protocol: Samples were amplified and labeled using the MessageAmp™ II-Biotin Enhanced Kit (Ambion).

growth_protocol: Plants were grown in soil (K-jord, Weibull, Sweden) supplemented with 20% vermiculite (skamol), 20% Perlite (Nordisk Perlit Aps), and 0.3% fertilizer (Osmocote Plus, Scotts Europe B.V) either in the green house or in Percival Scientific growth chambers under or short days (8h light; 16h dark) with day temperature of 21°C day and night temperature of 16°C.

extract_protocol: Total RNA was extracted using Trizol Reagent (Ambion, Austin, TX, USA).

treatment_protocol: Spraying with 100µM BTH

tag: BTH treated whole mkk1/mkk2 double knockout (Col-0 background) plants , harvested 5 weeks old


title: Spleen_ko_4m_rep3

city: Memphis

first: Jian

last: Yan

state: TN

address: 956 Court Ave

department: Orthopedics Surgery

institute: University of Tennessee Health Science Center

description: Gene expression data

hyb_protocol: Standard Affymetrix protocol with Fluidics Station 450

scan_protocol: Standard Affymetrix protocol with GeneChip Scanner 3000

data_processing: The data were analyzed with Expressiojn Console 1.1 using default MAS5 method. The target intensity was 500.

organism: Mus musculus

source_name: Mouse spleen at 4 month

label_protocol: Standard Affymetrix protocol

extract_protocol: Trizol

tag: Male BALB/c deficient in Il1rn


title: mkk1/mkk2, 24h after BTH, rep-C


title: mkk1/mkk2, 24h after BTH, rep-B


title: Spleen_ko_4m_rep1

description: Gene expression data


title: mkk1/mkk2, no-treatment, rep-C

source_name: mkk1/mkk2,  no-treatment

treatment_protocol: control treatment

tag: Whole mkk1/mkk2 double knockout (Col-0 background) plants , harvested 5 weeks old


title: Spleen_ko_1m_rep2

description: Gene expression data

source_name: Mouse spleen at 1 month


title: MLL-AF9 expressing cord blood cell, clone 5, grown with serum

city: Cincinnati

first: James

last: Mulloy

state: OH

address: 3333 Burnet Ave

department: Experimental Hematology

institute: Cincinnati Children's Hospital Research Foundation

description: Gene expression data from in vitro cultures of fusion-gene-transduced cord blood cells

hyb_protocol: All hybridization, staining and washing steps were carried out as specified by the Affymetrix technical manual. (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf)

scan_protocol: Affymetrix GeneChip Scanner 3000 7G with GeneChip Operating Software Version 1.4.0.036 (Affymetrix)

data_processing: Data were pre-processed with Microarray Suite version 5.0 function of Bioconductor package (R) using default settings

source_name: Human CD34+ cord blood cells

label_protocol: For cDNA generation, and cRNA labeling we used the ‘One-cycle target labeling’ protocol as described by the respective Affymetrix technical manual. (http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf)

extract_protocol: total RNA from cells was extracted using the Rneasy Mini Kit (Qiagen)

tag: normal donors


title: MLL-AF9 expressing cord blood cell, clone 3, grown serum-free, replicate 1


title: MLL-AF9 expressing cord blood cell, clone 3, grown with serum


title: MLL-AF9 expressing cord blood cell, clone 1, grown serum-free, replicate 1


title: MLL-AF9 expressing cord blood cell, clone 4, grown with serum


title: mkk1/mkk2, no-treatment, rep-A


title: MLL-AF9 expressing cord blood cell, clone 1, grown serum-free, replicate 2


title: MLL-AF9 expressing cord blood cell, clone 3, grown serum-free, replicate 2


title: AML1-ETO expressing cord blood cell, clone 18, grown with serum, replicate 2


title: CBFbeta-MYH11 expressing cord blood cell, clone 6, grown serum-free


title: mkk2, 24h after BTH, rep-C

source_name: mkk2 (Garlic_511-HO1), 24h after BTH treatment

tag: BTH treated whole mkk2 knockout (Garlic_511-HO1; Col-0 background) plants , harvested 5 weeks old


title: mkk2, 24h after BTH, rep-B


title: MLL-AF9 expressing cord blood cell, clone 1, grown with serum


title: mkk1/mkk2, no-treatment, rep-B


title: mkk2, no-treatment, rep-C

source_name: mkk2 (Garlic_511-HO1), no-treatment

tag: Whole mkk2 knockout (Garlic_511-HO1; Col-0 background) plants , harvested 5 weeks old


title: mkk2, 24h after BTH, rep-A


title: CBFbeta-MYH11 expressing cord blood cell, clone 2.2, grown serum-free, replicate 1


title: AML1-ETO expressing cord blood cell, clone 4, grown serum-free


title: mkk1, 24h after BTH, rep-C

source_name: mkk1 (SALK_027645), 24h after BTH treatment

tag: BTH treated whole mkk1 knockout (SALK_027645; Col-0 background) plants , harvested 5 weeks old


title: mkk2, no-treatment, rep-B


title: CBFbeta-MYH11 expressing cord blood cell, clone 2.2, grown serum-free, replicate 2


title: MLL-AF9 expressing cord blood cell, clone 4, grown serum-free


title: mkk2, no-treatment, rep-A


title: mkk1, 24h after BTH, rep-B


title: AML1-ETO expressing cord blood cell, clone 17, grown serum-free, replicate 2


title: mkk1, 24h after BTH, rep-A


title: mkk1, no-treatment, rep-C

source_name: mkk1 (SALK_027645), no-treatment

tag: Whole mkk1 knockout (SALK_027645; Col-0 background) plants , harvested 5 weeks old


title: AML1-ETO expressing cord blood cell, clone 18, grown serum-free, replicate 1


title: mkk1, no-treatment, rep-B


title: mkk1, no-treatment, rep-A


title: Col-0, 24h after BTH, rep-C

source_name: wild type (Col-0), 24h after BTH treatment

tag: BTH treated whole wild type plants (Col-0), harvested 5 weeks old


title: AML1-ETO expressing cord blood cell, clone 18, grown serum-free, replicate 2


title: AML1-ETO expressing cord blood cell, clone 17, grown serum-free, replicate 1


title: Col-0, 24h after BTH, rep-A


title: Col-0, Time 0, rep-B

source_name: wild type (Col-0), before BTH treatment

tag: Whole wild type plants (Col-0), harvested 5 weeks old


title: Col-0, Time 0, rep-A


title: Col-0, Time 0, rep-C


title: Wildtype, biological rep2

status: Public on Apr 30 2008

city: Philadelphia

first: Eric

middle: F.

last: Rappaport

state: PA

address: 3516 Civinc Center Blvd

department: Abramson Research Center

institute: Children's Hospital of Philadelphia

description: Gene expression data from wildtype M. musculus

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430_2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe-level measurements were normalized, summarized and log2-transformed by dCHIP software using perfect-match-only and invariant-set methods.

source_name: lox67 control mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Revision 5, Affymetrix).

growth_protocol: Mutant and control animals were grown in separate cages in the University of Pennsylvania animal facility until time of sacrifice.  Food was removed from the cages 3 hours prior to sacrifice by cervical dislocation without anesthesia.

extract_protocol: Trizol reagent was used according to the manufacturer's instructions to extract total RNA from flash-frozen liver aliquots

treatment_protocol: No treatments were used.  The only difference in the animals was their genotype, with the mutants being liver-conditional knockouts for Pdss2.

tag: Genotype

value: 213-day-old male

tag: 40 mg liver used for RNA extraction


title: Col-0, 24h after BTH, rep-B


title: Mutant, biological rep2

description: Gene expression data from mutant M. musculus

source_name: Alb69 mutant mouse

tag: Age

value: 178-day-old male


title: Wildtype, biological rep1

source_name: lox62 control mouse

value: 209-day-old male (concurrent control to Alb73)

tag: 90 mg liver used for RNA extraction


title: Mutant, biological rep1

source_name: Alb67 mutant mouse

value: 176-day-old male

tag: 70 mg liver used for RNA extraction


title: Mutant, biological rep3

source_name: Alb73 mutant mouse

value: 224-day-old male


title: Wildtype, biological rep3

source_name: lox95 control mouse

value: 140-day-old male


title: bg-CAT treated HUVECs, biological rep3

city: kunming

first: bai

middle: shu

last: liu

state: yunnan

address: jiaochang east road 32#

country: China

institute: kunming institute of zoology

description: Gene expression data from HUVECs treated with bg-CAT (25 nM) for 2 hour

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on human genome-U133 plus 2.0 chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS 1.4),and using Affymetrix default analysis settings and global scaling as normalization method (Microarray Suite version 5.0, MAS5.0). The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: primary cultured HUVECs treated with bg-CAT (25 nM, 2 h)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary cultured HUVECs used in the experiments were confluent monolayers between passages 2 and 3.

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

treatment_protocol: Primary cultured HUVECs treated with bg-CAT (25 nM) at 37 degree for 2 hour and PBS-treated cells as a normal control.

tag: The primary cultured HUVECs were confirmed by positive staining of indirect immunofluorescence with thrombomodulin (monoclonal antibody).


title: WT-ESTRADIOL-REP1

city: Singapore

first: Hao

last: Yu

address: Lower Kent Ridge Road

department: Biological Sciences

country: Singapore

institute: National University of Singapore

hyb_protocol: According to the manufacturer’s instructions (Affymetrix, Santa Clara, California, USA)

data_processing: The Affymetrix microarray suite software package (MAS 5.0) was used to scan and obtain signals. MAS generated data files (.CEL files) were used as the input for pre-processing using the software package RMA to summarize probe sets and normalize signal intensities. Further analysis and filtering was done using GeneSpring (Agilent). All samples were normalized per chip to the 50th percentile and per gene to median signals.

source_name: Arabidopsis seedling, wild type, estradiol treated, 8h

extract_protocol: Total RNAs were extracted by using RNeasy Plant Mini Kit (Qiagen)

tag: ecotype

value: columbia;

tag: age


title: Arabidopsis seedling gl1

city: Columbus

first: Manli

middle: Yang

last: Davis

address: 318 W.12th Ave

department: Plant Cellular and Molecular Biology

institute: The Ohio State University

description: We are comparing the gene expression between gl1 mutant and wild type Arabidopsis seedlings. Only green tissues were used.

hyb_protocol: For each array, 2.2 µg of cDNA is hybridized onto Arabidopsis ATH1 Genome GeneChips® (Affymetrix Inc., USA), designed in collaboration with TIGR, containing more than 22,500 probe sets representing approximately 24,000 genes.  The array is based on information from the international Arabidopsis sequencing project that was formally completed in December, 2000. In parallel and subsequent to the genome's completion, TIGR reannotated the entire genome in a project funded by the National Science Foundation and the resulting data was used in the design of this array.  Hybridization is allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

scan_protocol: GeneChips are scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA) and CEL files are generated from DAT files using GeneChip® Operating Software (GCOS) software (Affymetrix Inc., USA). The probe set signals are generated using the RMA algorithm in ArrayAssist 3.4 (Stratagene) and are used to determine differential gene expression by pair-wise comparisons. The genes that are altered by two-fold either way are sorted and used for further interpretation of the microarray data.

data_processing: Affy-GUI, normalized by RMA.

source_name: Arabidopsis seedling gl1

label_protocol: Following confirmation of RNA quality, Ovation™ Biotin RNA Amplification and Labeling System (NuGen Technologies, Inc., San Carlos, CA) is used to prepare amplified, biotin-labeled cDNA from total RNA for following manufacturer’s instructions. Briefly, first strand cDNA is synthesized from 25 ng of total RNA using a unique first strand DNA/RNA chimeric primer and reverse transcriptase. Following double strand cDNA generation, amplification of cDNA is achieved by utilizing an isothermal DNA amplification process that involves repeated SPIA™ DNA/RNA primer binding, DNA duplication, strand displacement and RNA cleavage. The amplified SPIA™ cDNA is purified and subjected to a two-step fragmentation and labeling process. The fragmented/biotinylated cDNA content is measured in a ND-1000 spectrophotometer and the quality was analyzed on an RNA 6000 Nano LabChip (Agilent) using Agilent Bioanalyzer 2100.

growth_protocol: 22 degree, long day condition, 16 hours light and 8 hours dark.

extract_protocol: Qiagen RNeasy Plant RNA extraction kit

tag: Arabidopsis seedlings, grown on MS medium for 20 days, green tissues were used.


title: WT-ESTRADIOL-REP2

scan_protocol: According to the manufacturer’s instructions (Affymetrix, Santa Clara, California, USA)


title: HY213-ESTRADIOL-REP2

source_name: Arabidopsis seedling, estradiol treated, 8h

label_protocol: According to the manufacturer’s instructions (Affymetrix, Santa Clara, California, USA)


title: bg-CAT treated HUVECs, biological rep4

tag: Primary cultured HUVECs used in the experiments were confluent monolayers between passages 2 and 3.


title: bg-CAT treated HUVECs, biological rep1


title: HUVECs normal Control, biological rep1

description: Gene expression data from normal control HUVECs

source_name: primary cultured HUVECs treated with PBS as a normal control


title: HUVECs normal Control, biological rep3


title: HUVECs normal Control, biological rep4


title: Arabidopsis seedling ttg1

description: We are comparing the gene expression between ttg1 mutant and wild type L.er Arabidopsis seedlings. Only green tissues were used.

data_processing: Affy-GUI. Normarlized by RMA.

source_name: Arabidopsis seedlings, 20 days old

tag: Arabidopsis seedlings, 20 days old, green tissues only.


title: HUVECs normal Control, biological rep2


title: HY213-MOCK-REP2

source_name: Arabidopsis seedling, mock treated, 8h


title: bg-CAT treated HUVECs, biological rep2


title: Arabidopsis seedling wild type

description: We are comparing the gene expression between wild type and three mutant Arabidopsis seedlings. Only green tissues were used.

hyb_protocol: For each array, 2.2 µg of cDNA is hybridized onto Arabidopsis ATH1 Genome GeneChips® (Affymetrix Inc., USA), designed in collaboration with TIGR, containing more than 22,500 probe sets representing approximately 24,000 genes. The array is based on information from the international Arabidopsis sequencing project that was formally completed in December, 2000. In parallel and subsequent to the genome's completion, TIGR reannotated the entire genome in a project funded by the National Science Foundation and the resulting data was used in the design of this array. Hybridization is allowed to continue for 16 hours at 45ºC followed by washing and staining of microarrays in a Fluidics Station 450 (Affymetrix Inc., USA).

source_name: Wild type Arabidopsis seedling, 20 days old


title: HY213-ESTRADIOL-REP1


title: HY213-MOCK-REP1

tag: ecotype columbia;


title: Arabidopsis seedling gl3egl3

description: This experiment was done to compare the gene expression between L.er wild type seedlings and gl3egl3 double mutants.

source_name: Arabidopsis seedling 20 days old

growth_protocol: Long day condition, 16 hours light and 8 hours dark. 22 degree.

extract_protocol: RNA was extracted with Qiagen RNeasy Plant RNA extraction kit.

tag: Arabidopsis L.er seedling, grown on MS medium for 20 days.


title: Mock Infection A

city: Aurora

first: Christopher

middle: D

last: Coldren

state: CO

address: 12700 East 17th Place

department: Medicine

institute: University of Colorado School of Medicine

description: Mock Infected HMVEC-L

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GCRMA

source_name: Mock Infected HMVEC-L (Mock A)

label_protocol: Approximately 5 micrograms of total RNA was processed to produce biotinylated cRNA targets using the older (ENZO) Affymetrix protocol

extract_protocol: Cells in culture were harvested, homogenized, and total RNA was extracted using the Qiagen MiniElute protocol (Qiagen, Valencia, CA).


title: Infection C

description: HHV8 Infected HMVEC-L

source_name: HHV8 Infected HMVEC-L (Inf C)


title: Infection B

description: HHV8 Infected HMVEC-L

source_name: HHV8 Infected HMVEC-L (Inf B)


title: Infection A

description: HHV8 Infected HMVEC-L

source_name: HHV8 Infected HMVEC-L (Inf A)


title: Mock Infection B

description: Mock Infected HMVEC-L

source_name: Mock Infected HMVEC-L (Mock B)


title: U-EML replicate 3

status: Public on Apr 29 2008

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

institute: Harvard Medical School

description: Gene expression data from embryos U-EML cells

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Expression values, present/absent calls and associated P values were calculated using MAS5 algoriothm

source_name: U-EML cells

growth_protocol: EML cells were plated in 45mls of normal growth medium plus 10U/ml of human erythropoietin (Epo; Ortho) at 75,000 cells/ml in a T75 culture flask and cultured for two days.

extract_protocol: Total RNA extraction was performed using the RNEasy kit from Qiagen per manufacturer's protocol. Total RNA was subsequently treated with DNase to remove contaminating genomic DNA.

treatment_protocol: The cells were plated in T150 flasks (25,000 cells/ml and 90mls total) in SCF-reduced growth medium (this is the same as growth medium except with only 4% BHK-MKL conditioned medium) plus 10U/ml Epo. After three days, an additional 10U/ml of Epo was added, without changing the medium. After 2 days, the number of differentiated (c-Kit-) cells ranged from 50-75% of the culture.

tag: multipotential hematopoietic cells


title: U-EML replicate 1


title: E-EML replicate 3

description: Gene expression data from embryos D-EML cells

source_name: E-EML cells


title: U-EML replicate 2


title: E-EML replicate 1


title: Mock Infection C

description: Mock Infected HMVEC-L

source_name: Mock Infected HMVEC-L (Mock C)


title: E-EML replicate 2


title: uterus_4MJW061208170

city: San Diego

first: John

middle: R

last: Walker

state: CA

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description: uterus

data_processing: gcRMA

source_name: uterus

label_protocol: For samples containing more than two µg total RNA available after pooling, standard Affymetrix single amplification was performed using two µg total RNA. For pooled samples containing less than two µg total RNA, 100 ng total RNA (or 50 ng for thymocyte_SP_CD8+) was used in a standard Affymetrix double amplification protocol.

extract_protocol: RNA extraction from mammalian cells or tissues was performed using RNeasy kits (Qiagen, Valencia, CA) or a standard Trizol protocol. If tissue amounts were more than 50 mg per mouse when dissected, tissues were pulverized while frozen. RNA was prepared separately for every mouse in order to identify samples with potentially degraded RNA. Trizol-extracted RNA was purified with a Qiagen RNeasy column. For bone marrow macrophages, osteoblasts, and osteoclasts, contaminating genomic DNA was removed during the RNeasy cleanup using DNaseI (Qiagen, Valencia, CA). The integrity and concentration of RNA was determined via microfluidic analysis on a bio-analyser (Agilent Technologies, Palo Alto, CA) or by analysis on a BioRad Experion. Pooling occurred at the RNA level.

treatment_protocol: All cell lines and tissues were sourced from 8-10 week old male C57Bl/6 mice, with the exception of female-specific organs, which were sourced from female mice. All procedures were carried out in accordance with local guidelines for animal research. For female tissues, material was pooled from three females, and for each female, on average four embryos resulting in four umbilical cords and placentas were obtained. For other tissues, material was derived from a pool of three males. Biological replicates were defined as independent RNA preparations from independent pools of mice. Technical replicates were defined as independent amplifications from the sample RNA sample.

tag: uterus


title: umbilical_cord_4MJW061208186


title: uterus_4MJW061208169

description: uterus


title: thymocyte_SP_CD4+_4MJW061208174


title: testis_4MJW061208165

description: testis

source_name: testis

tag: testis


title: thymocyte_SP_CD4+_4MJW061208173


title: umbilical_cord_4MJW061208185


title: T-cells_CD4+_4MJW061208114


title: testis_4MJW061208166

description: testis


title: T-cells_CD4+_4MJW061208113


title: T-cells_foxP3+_4MJW06120892


title: thymocyte_SP_CD8+_4MJW061208176


title: thymocyte_DP_CD4+CD8+_4MJW061208172


title: thymocyte_DP_CD4+CD8+_4MJW061208171


title: thymocyte_SP_CD8+_4MJW061208175


title: T-cells_foxP3+_4MJW06120891


title: stomach_4MJW061208163

description: stomach

source_name: stomach

tag: stomach


title: T-cells_CD8+_4MJW061208115


title: spleen_4MJW061208162

description: spleen

source_name: spleen

tag: spleen


title: stomach_4MJW061208164

description: stomach


title: skeletal_muscle_4MJW061208156


title: spinal_cord_4MJW061208159


title: T-cells_CD8+_4MJW061208116


title: spleen_4MJW061208161

description: spleen


title: stem_cells__HSC_4MJW06120878


title: skeletal_muscle_4MJW061208155


title: salivary_gland_4MJW061208182


title: salivary_gland_4MJW061208181


title: spinal_cord_4MJW061208160


title: stem_cells__HSC_4MJW06120877


title: placenta_4MJW061208190

description: placenta

source_name: placenta

tag: placenta


title: placenta_4MJW061208189

description: placenta


title: RAW_264_7_4MJW06120838


title: retinal_pigment_epithelium_4MJW06120894


title: pancreas_4MJW06120814

description: pancreas

source_name: pancreas

tag: pancreas


title: pituitary_4MJW061208151

description: pituitary

source_name: pituitary

tag: pituitary


title: pituitary_4MJW061208152

description: pituitary


title: retinal_pigment_epithelium_4MJW06120893


title: retina_4MJW06120896

description: retina

source_name: retina

tag: retina


title: ovary_4MJW061208149

description: ovary

source_name: ovary

tag: ovary


title: prostate_4MJW061208153

description: prostate

source_name: prostate

tag: prostate


title: pancreas_4MJW06120813

description: pancreas


title: retina_4MJW06120895

description: retina


title: osteoblast_day14_4MJW06120866


title: RAW_264_7_4MJW06120837


title: osteoblast_day5_4MJW06120863


title: osteoblast_day5_4MJW06120864


title: prostate_4MJW061208154

description: prostate


title: ovary_4MJW061208150

description: ovary


title: osteoblast_day21_4MJW06120867


title: osteoclasts_4MJW06120861

description: osteoclasts

source_name: osteoclasts

tag: osteoclasts


title: olfactory_bulb_4MJW061208148


title: osteoblast_day21_4MJW06120868


title: osteoclasts_4MJW06120862

description: osteoclasts


title: osteoblast_day14_4MJW06120865


title: nucleus_accumbens_4MJW061208146


title: nucleus_accumbens_4MJW061208145


title: NK_cells_4MJW06120881


title: NK_cells_4MJW06120882


title: olfactory_bulb_4MJW061208147


title: min6_4MJW06120830


title: neuro2a_4MJW06120833


title: min6_4MJW06120829


title: microglia_4MJW061208184

description: microglia

source_name: microglia

tag: microglia


title: mIMCD-3_4MJW06120832


title: microglia_4MJW061208183

description: microglia


title: nih_3T3_4MJW06120835


title: neuro2a_4MJW06120834


title: mammary_gland_non-lactating_4MJW061208144


title: mast_cells_IgE+antigen_1hr_4MJW06120885


title: mammary_gland_non-lactating_4MJW061208143


title: mast_cells_4MJW06120852


title: mega_erythrocyte_progenitor_4MJW06120880


title: mast_cells_IgE_4MJW06120884


title: mega_erythrocyte_progenitor_4MJW06120879


title: mast_cells_4MJW06120851


title: mast_cells_IgE+antigen_6hr_4MJW06120887


title: macrophage_peri_LPS_thio_7hrs_4MJW06120848


title: nih_3T3_4MJW06120836


title: mast_cells_IgE+antigen_6hr_4MJW06120888


title: mast_cells_IgE+antigen_1hr_4MJW06120886


title: mast_cells_IgE_4MJW06120883


title: mIMCD-3_4MJW06120831


title: mammary_gland__lact_4MJW061208188


title: mammary_gland__lact_4MJW061208187


title: macrophage_peri_LPS_thio_1hrs_4MJW06120846


title: macrophage_peri_LPS_thio_7hrs_4MJW06120847


title: macrophage_peri_LPS_thio_0hrs_4MJW06120843


title: macrophage_peri_LPS_thio_1hrs_4MJW06120845


title: lymph_nodes_4MJW06120839


title: macrophage_bone_marrow_6hr_LPS_4MJW06120858


title: lens_4MJW061208102

description: lens

source_name: lens

tag: lens


title: macrophage_peri_LPS_thio_0hrs_4MJW06120844


title: macrophage_bone_marrow_6hr_LPS_4MJW06120857


title: lacrimal_gland_4MJW061208180


title: lung_4MJW061208142

description: lung

source_name: lung

tag: lung


title: intestine_small_4MJW061208157


title: intestine_large_4MJW061208138


title: lymph_nodes_4MJW06120840


title: lacrimal_gland_4MJW061208179


title: kidney_4MJW061208135

description: kidney

source_name: kidney

tag: kidney


title: liver_4MJW061208139

description: liver

source_name: liver

tag: liver


title: macrophage_bone_marrow_24h_LPS_4MJW06120859


title: iris_4MJW061208106

description: iris

source_name: iris

tag: iris


title: lens_4MJW061208101

description: lens


title: liver_4MJW061208140

description: liver


title: lung_4MJW061208141

description: lung


title: macrophage_bone_marrow_2hr_LPS_4MJW06120856


title: macrophage_bone_marrow_2hr_LPS_4MJW06120855


title: iris_4MJW061208105

description: iris


title: macrophage_bone_marrow_24h_LPS_4MJW06120860


title: macrophage_bone_marrow_0hr_4MJW06120853


title: kidney_4MJW061208136

description: kidney


title: macrophage_bone_marrow_0hr_4MJW06120854


title: intestine_small_4MJW061208158


title: intestine_large_4MJW061208137


title: hypothalamus_4MJW061208134

description: hypothalamus

source_name: hypothalamus

tag: hypothalamus


title: hippocampus_4MJW06120801

description: hippocampus

source_name: hippocampus

tag: hippocampus


title: hypothalamus_4MJW061208133

description: hypothalamus


title: heart_4MJW061208132

description: heart

source_name: heart

tag: heart


title: epidermis_4MJW06120809

description: epidermis

source_name: epidermis

tag: epidermis


title: follicular_B-cells_4MJW06120849


title: follicular_B-cells_4MJW06120850


title: hippocampus_4MJW06120802

description: hippocampus


title: granulo_mono_progenitor_4MJW06120875


title: granulo_mono_progenitor_4MJW06120876


title: granulocytes_mac1+gr1+_4MJW06120870


title: granulocytes_mac1+gr1+_4MJW06120869


title: eyecup_4MJW061208104

description: eyecup

source_name: eyecup

tag: eyecup


title: embryonic_stem_line_V26_2_p16_4MJW06120819


title: embryonic_stem_line_Bruce4_p13_4MJW06120818


title: heart_4MJW061208131

description: heart


title: epidermis_4MJW06120810

description: epidermis


title: eyecup_4MJW061208103

description: eyecup


title: SW480_ezrin RNAi_rep1

city: Taipei

first: Chan-Yen

last: Tsai

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: Yang-Ming University

data_processing: RMA through R based affy module

source_name: SW480, ezrin RNAi

label_protocol: standard Affymetrix procedures

extract_protocol: Suspension growing cells were pelleted by centifugation and RNA extracted by RNeasy Kit (Qiagen).

tag: SW480, stable line of treatment of ezrin RNAi. Incubate in L15 medium, 37.0°C, air 100%


title: Term placenta Grp3HT6

city: Seattle

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymterix.

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

data_processing: GeneTraffic RMA normalization log2

source_name: placenta

label_protocol: Total RNA (2 ug) was labeled and hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays and hybridized according to manufacurer's instructions.

extract_protocol: RNA was extracted from the placental tissue using the RNAesy kit (Quigen) according to the manufacturer's protocol.!Sample_label = biotin

tag: Collection of human placentae was approved by the Institutional Review Board of the University of Washington.  Subjects were excluded if they had any chronic disease, were on chronic medication, were smokers, abused alcohol or drugs.  Term human placenta samples were obtained from scheduled uncomplicated C-sections performed at the University of Washington Medical Center, Seattle, WA.  The 1st (45-59 days) and 2nd (109-115 days) trimester placentae, from uncomplicated elective termination, were provided by Birth Defects Laboratory of the University of Washington.  After collection, the tissues were kept on ice until the placental villus could be dissected and snap-frozen in liquid nitrogen and stored at -80C.


title: SW480_control RNAi_luciferase_rep2

source_name: SW480, control RNAi, luciferase

tag: SW480, stable line of treatment of luciferase RNAi. Incubate in L15 medium, 37.0°C, air 100%


title: Term placenta Grp3HT7

description: Term human placenta samples were obtained from scheduled uncomplicated C-sections performed at the University of Washington Medical Center, Seattle, WA.  The 1st (45-59 days) and 2nd (109-115 days) trimester placentae, from uncomplicated elective termination, were provided by Birth Defects Laboratory of the University of Washington.


title: Term placenta Grp3HT5

treatment_protocol: Term human placenta samples were obtained from scheduled uncomplicated C-sections performed at the University of Washington Medical Center, Seattle, WA.  The 1st (45-59 days) and 2nd (109-115 days) trimester placentae, from uncomplicated elective termination, were provided by Birth Defects Laboratory of the University of Washington.


title: embryonic_stem_line_V26_2_p16_4MJW06120820


title: SW480_control RNAi_luciferase_rep1

description: SW480, stable line of treatment of luciferase RNAi.


title: Term placenta Grp3HT8


title: Second trimester placenta Grp2H17795


title: embryonic_stem_line_Bruce4_p13_4MJW06120817


title: Second trimester placenta Grp2H17812


title: dorsal_root_ganglia_4MJW061208127


title: dorsal_root_ganglia_4MJW061208128


title: Second trimester placenta Grp2H17607


title: dendritic_cells_myeloid_CD8a-_4MJW061208112


title: Second trimester placenta Grp2H17464


title: dendritic_cells_myeloid_CD8a-_4MJW061208111


title: First trimester placenta Grp1H18035


title: First trimester placenta Grp1H18075


title: dendritic_plasmacytoid_B220+_4MJW061208110


title: SW480_ezrin RNAi_rep2

description: SW480, stable line of treatment of ezrin RNAi.


title: dorsal_striatum_4MJW061208129


title: dorsal_striatum_4MJW061208130


title: cornea_4MJW06120899

description: cornea

source_name: cornea

tag: cornea


title: dendritic_cells_lymphoid_CD8a+_4MJW061208108


title: Glioblastoma cell line GBM_U373

first: Yonghong

last: Xiao

address: 450 Brookline Ave., HIM218A

institute: Dana-Farber Cancer Institute

description: Gene expression data from human glioblastoma cell line.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133Plus2.0. The chips are then transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

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: human glioblastoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

tag: Human glioblastoma cell line


title: Glioblastoma cell line GBM_SF763


title: First trimester placenta Grp1H17790


title: common_myeloid_progenitor_4MJW06120873


title: Glioblastoma cell line GBM_U343


title: Glioblastoma cell line GBM_LN464


title: Glioblastoma cell line GBM_U87


title: Glioblastoma cell line GBM_SF767


title: First trimester placenta Grp1H17634


title: dendritic_plasmacytoid_B220+_4MJW061208109


title: common_myeloid_progenitor_4MJW06120874


title: Glioblastoma cell line GBM_LNZ308


title: Glioblastoma cell line GBM_LN444


title: cornea_4MJW061208100

description: cornea


title: Glioblastoma cell line GBM_LN443


title: ciliary_bodies_4MJW06120898


title: ciliary_bodies_4MJW06120897


title: Glioblastoma cell line GBM_LN235


title: Glioblastoma cell line GBM_LN382


title: Glioblastoma cell line GBM_LN340


title: cerebral_cortex_4MJW061208125


title: cerebral_cortex_prefrontal_4MJW061208177


title: cerebral_cortex_prefrontal_4MJW061208178


title: Glioblastoma cell line GBM_LN319


title: cerebral_cortex_4MJW061208126


title: Glioblastoma cell line GBM_LN229

hyb_protocol: Following fragmentation, 10 microg 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.

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

molecule: polyA RNA

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


title: cerebellum_4MJW061208124

description: cerebellum

source_name: cerebellum

tag: cerebellum


title: Glioblastoma cell line GBM_LN18


title: bone_marrow_4MJW06120842


title: C2C12_4MJW06120825


title: C3H_10T1_2_4MJW06120828


title: C3H_10T1_2_4MJW06120827


title: Glioblastoma cell line GBM_Hs683


title: Glioblastoma tumor GBM_311

description: Gene expression data from human glioblastoma tumor.

source_name: human glioblastoma tumor

tag: Human glioblastoma tumor


title: Glioblastoma tumor GBM_355


title: cerebellum_4MJW061208123

description: cerebellum


title: Glioblastoma cell line GBM_LN215


title: bone_marrow_4MJW06120841


title: Glioblastoma tumor GBM_349


title: C2C12_4MJW06120826


title: Glioblastoma tumor GBM_328


title: bone_4MJW06120812

description: bone

source_name: bone

tag: bone


title: bone_4MJW06120811

description: bone


title: bladder_4MJW061208122

description: bladder

source_name: bladder

tag: bladder


title: Glioblastoma tumor GBM_210


title: Glioblastoma tumor GBM_218


title: Glioblastoma tumor GBM_206


title: Glioblastoma tumor GBM_271


title: Glioblastoma tumor GBM_199


title: Glioblastoma tumor GBM_186


title: B-cells_marginal_zone_4MJW06120890


title: Baf3_4MJW06120823


title: Baf3_4MJW06120824


title: Glioblastoma tumor GBM_257


title: Glioblastoma tumor GBM_193


title: bladder_4MJW061208121

description: bladder


title: amygdala_4MJW061208120

description: amygdala

source_name: amygdala

tag: amygdala


title: B-cells_marginal_zone_4MJW06120889


title: Glioblastoma tumor GBM_157


title: adrenal_gland_4MJW061208117


title: adipose_white_4MJW06120804


title: adrenal_gland_4MJW061208118


title: Argyrin A treated 48h

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: MCF7 Argyrin A treated 48h

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

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 150.

source_name: MCF7 Argyrin A treated 48h

growth_protocol: DMEM, FCS Pen/Strep, 37° , 5% CO2

extract_protocol: RNAeasy

treatment_protocol: Velcade, Proteasom inhibitor

tag: genetic modification:

tag: tissue

value: breast adenocarcinoma


title: dendritic_cells_lymphoid_CD8a+_4MJW061208107


title: untreated_1

description: MCF7 untreated

source_name: MCF7 untreated


title: siRNA 24h_1

description: MCF7 siRNA 24h

source_name: MCF7 siRNA 24h


title: adipose_white_4MJW06120803


title: adipose_brown_4MJW06120816


title: Argyrin A treated 24h

description: MCF7 Argyrin A treated 24h

source_name: MCF7 Argyrin A treated 24h


title: Argyrin A treated 14h

description: MCF7 Argyrin A treated 14h

source_name: MCF7 Argyrin A treated 14h


title: siRNA 12h_1

description: MCF7 siRNA 12h

source_name: MCF7 siRNA 12h


title: 3T3-L1_4MJW06120821


title: bortezomib treated 48h

description: MCF7 bortezomib treated 48h

source_name: MCF7 bortezomib treated 48h


title: 3T3-L1_4MJW06120822


title: untreated

description: MCF7 untreated

treatment_protocol: no


title: bortezomib treated 14h

description: MCF7 bortezomib treated 14h

source_name: MCF7 bortezomib treated 14h


title: Wild-type Female Spermathecae

status: Public on Apr 26 2008

city: Baltimore

first: Allan

middle: C

last: Spradling

state: MD

address: 3520 San Martin Dr

department: Embryology

institute: Carnegie Institution/HHMI

description: 4 day old mated adult female spermathecae

hyb_protocol: see Allen and Spradling, Dev 135, 311-321 (2008)

organism: Drosophila melanogaster

source_name: spermathecae dissected from wild-type


title: bortezomib treated 24h

description: MCF7 bortezomib treated 24h

source_name: MCF7 bortezomib treated 24h


title: Hr39(04443) Female Spermathecae

scan_protocol: see Allen and Spradling, Dev 135, 311-321 (2008)

source_name: spermathecae dissected from Hr39(04443)

tag: 4 day old mated adult female spermathecae


title: Hr39(04443) Female Lower Reproductive Tract

description: 4 day old mated adult female lower reproductive tract (without spermathecae)

label: see Allen and Spradling, Dev 135, 311-321 (2008)

source_name: lower reproductive tract (without spermathecae) dissected from Hr39(04443) females


title: amygdala_4MJW061208119

description: amygdala


title: Wild-type Female Lower Reproductive Tract (duplicate)

description: 4 day old mated female lower reproductive tract (without spermathecae); duplicate array

source_name: lower reproductive tract (without spermathecae) dissected from wild-type females

label_protocol: see Allen and Spradling, Dev 135, 311-321 (2008)


title: Wild-type Female Lower Reproductive Tract

description: 4 day old mated adult female lower reproductive tracts (without spermathecae)

extract_protocol: see Allen and Spradling, Dev 135, 311-321 (2008)


title: Hr39(04443) Female Spermathecae (duplicate)

description: 4 day old mated female spermathecae; duplicate array


title: Wild-type Female Spermathecae (duplicate)

hyb_protocol: See Allen and Spradling, Dev 135, 311-321 (2008)

source_name: spermathecae dissected from wild-type (duplicate)

tag: 4 day old mated female spermathecae; duplicate array


title: adipose_brown_4MJW06120815


title: Hr39(04443) Female Lower Reproductive Tract (duplicate)

tag: 4 day old mated female lower reproductive tract (without spermathecae); duplicate array


title: sample 46 _ GEP _ CALL-preB without t(9;22) and TEL deleted

status: Public on Apr 25 2008

city: Padova

first: Andrea

last: Zangrando

address: Via Giustiniani, 3

department: Woman and Child's Health

country: Italy

institute: University of Padova

description:
PAD_00105
Gene expression data from pediatric acute leukemia samples at diagnosis

hyb_protocol: Following fragmentation, 11 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 450DX.

scan_protocol: GeneChips were scanned using the Scan GCS3000Dx.

data_processing: The data were analyzed using R software [www.r-project.org] with BioConductor package [www.bioconductor.org]

source_name: White blood human cells

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

extract_protocol: Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns

treatment_protocol: White blood cells were isolated through Ficoll-Hypaque density gradient centrifugation

tag: Leukemia samples

tag: Bone Marrow sample


title: sample 54 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00121
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 49 _ GEP _ CALL with t(12;21)

description:
PAD_00111
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 73 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00163
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 61 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00134
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 39 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00080
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 32 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00069
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 62 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00135
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 44 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00095
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 67 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00142
Gene expression data from pediatric acute leukemia samples at diagnosis

tag: Peripheral blood sample


title: sample 43 _ GEP _ CALL-preB without t(9;22) and TEL deleted

description:
PAD_00094
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 55 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00122
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 34 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00071
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 30 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00066
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 35 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00075
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 29 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00065
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 33 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00070
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 40 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00081
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 28 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00064
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 23 _ GEP _ CALL-preB without t(9;22) and TEL deleted

description:
PAD_00052
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 68 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00150
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 25 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00057
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 13 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00037
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 16 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00043
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 17 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00045
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 21 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00050
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 51 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00114
Gene expression data from pediatric acute leukemia samples at diagnosis


title: Arabidopsis GGSc1

city: Davis

last: Harada

address: One Shields Avenue

department: Plant Biology

institute: University of California, Davis

description:
Laser capture microdissected (LCM) general seed coat at the globular stage, biological replicate 1
General seed coat collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.

hyb_protocol: Following fragmentation, five micrograms of cDNA was hybridized for 18 hr at 45°C with the GeneChip ATH1 Arabidopsis Genome Array. GeneChips were washed and stained using the EukGE-WS2V4_450 protocol in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymetrix GeneChip Operating system 1.4 (GCOS) using default analysis settings and global scaling as a normalization method. The mean target intensity of each array was set to 500.

source_name: Arabidopsis globular stage general seed coat captured by LCM

label_protocol: 2 to 4 ng of total RNA was amplified using the WT-Ovation Pico RNA Amplification System (NuGEN, San Carlos, CA). cDNAs were fragmented and labeled with NuGEN FL-Ovation™ cDNA Biotin Module V2.

growth_protocol: Plants were grown in a Conviron chamber under continuous light with fluorescent lamps at 20°C and 50% - 70% relative humidity.

extract_protocol: Total RNA was extracted using the RNaqueous Micro-Kit (Ambion, Austin, TX) using a modified protocol incorporating an on-column DNase treatment (Qiagen RNase-Free DNase Set) during column washes.

treatment_protocol: Siliques with length between 1.1 and 1.4 cm containing globular stage seeds were collected from 38-46 day old plants. Seeds were either dissected out of siliques or left in sub-divided siliques and fixed in 3:1 (v/v) ethanol to acetic acid and embedded in paraffin.  Microdissection of compartments was carried out on 5 or 7 um sections using a Leica LMD6000 system. Compartments were only captured from seeds with globular embryos 24-32 um in diameter, as determined by a medial section through the embryo proper.

tag: Genotype


title: Arabidopsis GPSc2

description:
Laser capture microdissected (LCM) chalazal seed coat at the globular stage, biological replicate 2
Chalazal seed coat collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis globular stage chalazal seed coat captured by LCM


title: Arabidopsis GGSc2

description:
Laser capture microdissected (LCM) general seed coat at the globular stage, biological replicate 2
General seed coat collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.


title: Arabidopsis GPSc1

description:
Laser capture microdissected (LCM) chalazal seed coat at the globular stage, biological replicate 1
Chalazal seed coat collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.


title: Arabidopsis GCE3

description:
Laser capture microdissected (LCM) chalazal endosperm at the globular stage, biological replicate 3
Chalazal endosperm collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis globular stage chalazal endosperm captured by LCM


title: sample 10 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00031
Gene expression data from pediatric acute leukemia samples at diagnosis


title: sample 9 _ GEP _ CALL-preB without t(9;22)

description:
PAD_00030
Gene expression data from pediatric acute leukemia samples at diagnosis


title: Arabidopsis GCE1

description:
Laser capture microdissected (LCM) chalazal endosperm at the globular stage, biological replicate 1
Chalazal endosperm collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.


title: Arabidopsis GSUS3

description:
Laser capture microdissected (LCM) suspensor at the globular stage, biological replicate 1
Suspensors collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis globular stage suspensor captured by LCM


title: Arabidopsis GSUS4b

description:
Laser capture microdissected (LCM) suspensor at the globular stage, biological replicate 2
Suspensors collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.


title: Arabidopsis GEP6

description:
Laser capture microdissected (LCM) embryo proper at the globular stage, biological replicate 2
Embryo proper collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis globular stage embryo proper captured by LCM


title: Arabidopsis GMPE1

description:
Laser capture microdissected (LCM) micropylar endosperm at the globular stage, biological replicate 1
Micropylar endosperm collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis globular stage micropylar endosperm captured by LCM


title: Arabidopsis GEP5

description:
Laser capture microdissected (LCM) embryo proper at the globular stage, biological replicate 1
Embryo proper collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.


title: Arabidopsis GMPE2

description:
Laser capture microdissected (LCM) micropylar endosperm at the globular stage, biological replicate 2
Micropylar endosperm collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.


title: Arabidopsis GPE2

description:
Laser capture microdissected (LCM) peripheral endosperm at the globular stage, biological replicate 1
Peripheral endosperm collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis globular stage peripheral endosperm captured by LCM


title: Rb family deficient 3

city: palo alto

first: Patrick

last: Viatour

address: 350 pasteur drive

institute: Stanford University

description: Gene expression from FACS sorted KLS cells

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

scan_protocol: Genechips were scanned according to the manufacturer protocol.

data_processing: Data were analyzed using R (cran.r-project.org) and Bioconductor (www.bioconductor.org) software.  Background correction, normalization and calculation of gene expression values by model-fitting was performed using the Robust Multiarray Average procedure.

source_name: Rb family deficient HSCs (KLS cells)

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

growth_protocol: Recombination was activated in 6 weeks old mice (Mx1Cre inducible system). KLS cells were FACS sorted 2 months after the recombination.

extract_protocol: Trizol extractions on Total RNA was performed according to the manufacturer instructions.

treatment_protocol: untreated

tag: genotype


title: Arabidopsis GCE2

description:
Laser capture microdissected (LCM) chalazal endosperm at the globular stage, biological replicate 2
Chalazal endosperm collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.


title: Rb family deficient 2


title: Arabidopsis GPE3

description:
Laser capture microdissected (LCM) peripheral endosperm at the globular stage, biological replicate 2
Peripheral endosperm collected from seeds containing globular embryos 24 to 32 um in diameter as determined by median section using the LEICA LMD6000 system for microdissection.

source_name: Arabidopsis globular stage peripherial endosperm captured by LCM


title: Wild Type 2

source_name: Wild Type HSCs (KLS cells)


title: Wild Type 1


title: Rb family deficient 1


title: Arabidopsis, root cells, stele, -Fe, replicate 3

status: Public on Apr 24 2008

city: Durham

first: Terri

middle: Anita

last: Long

state: NC

department: Biology

institute: Duke University

description: Gene expression data from isolated stele cells after roots were treated treated to -Fe media for 24 hours

hyb_protocol: Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

source_name: Protoplasted and FACS sorted root cells

label_protocol: Fragmented cRNA probes were prepared using the two-cycle amplification protocol by Affymetrix.

growth_protocol: Seeds were surface sterilized for 2 minutes in 70% ethanol, the ethanol was removed, then replaced with 30% Bleach and 0.02% Triton X-100 for 15 minutes. Seeds were rinsed 3 times with sterile water, stratified for 4˚C for 2 days, then placed on standard media. Standard media is 1X Murashige and Skoog salt mixture in which ferrous sulfate is replaced with 100mM Fe(III)-EDTA, 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH.  –Fe media is 1X Murashige and Skoog salt mixture in which ferrous sulfate is replaced with 0.3mM Ferrozine. Nylon mesh was placed on top of the solidified media and seeds were planted at ~20 seeds/cm in two rows.

extract_protocol: RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH).

treatment_protocol: Samples were prepared as in Birnbaum et al. (2005) Nat. Methods for roots grown under standard conditions.  For -Fe treated samples, roots were transferred to -Fe media for 24 hours before protoplasting.

tag: Ecotype

value: Columbia

tag: Age

value: Seedling roots, 6 days after germination

tag: GFP-reporter

tag: Growth Media

value: Standard media for 6 days, transferred to -Fe media for 24 hours before protoplasting


title: Arabidopsis, root cells, endodermis and quiescent center, -Fe, replicate 2

description: Gene expression data from isolated endodermal and quiecent center cells after roots were treated to -Fe media for 24 hours

scan_protocol: Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.


title: Arabidopsis, root cells, endodermis and quiescent center, -Fe, replicate 3


title: Arabidopsis, root cells, cortex, -Fe, replicate 3

description: Gene expression data from isolated cortex cells after roots were treated to -Fe media for 24 hours

value: CORTEX


title: Arabidopsis, root cells, endodermis and quiescent center, -Fe, replicate 1


title: Arabidopsis, root cells, cortex, -Fe, replicate 2


title: Arabidopsis, root cells, columella root cap, -Fe, replicate 3

description: Gene expression data from isolated columella root cap cells after roots were treated to -Fe media for 24 hours


title: Arabidopsis, root cells, stele, -Fe, replicate 2


title: Arabidopsis, root cells, columella root cap, -Fe, replicate 1


title: Arabidopsis, root cells, cortex, -Fe, replicate 1


title: Arabidopsis, root cells, stele, -Fe, replicate 1


title: Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 4

description: Gene expression data from isolated epidermal and lateral root cap cells after roots were treated to -Fe media for 24 hours


title: Arabidopsis, root cells, columella root cap, -Fe, replicate 2


title: Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 2


title: Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 1


title: Arabidopsis, whole roots, -Fe, 3 hour, rep 1

description: Gene expression data from whole roots grown under standard conditions for 5 days and transferred to -Fe media for 3 hours

source_name: whole roots

label_protocol: Fragmented cRNA probes were prepared using the one-cycle amplification protocol by Affymetrix.

extract_protocol: Approximately 320 roots were collected per replicate.  Samples were briefly sonicated to disrupt the tissue.  RNA was extracted using the RNAeasy Plant Mini Kit (Qiagen).

treatment_protocol: Seedlings were grown for 5 days before transfer to -Fe media.  Transfers were staggered such that all roots were harvested within 3 hours of each other on the sixth day of growth.  Roots were cut with a razor blade 0.5 mm below the root/hypocotyl junction and collected into RNA extraction buffer.  Approximately 320 roots were collected per replicate, with two biological replicates being performed per time point.  Samples were briefly sonicated to disrupt the tissue.

value: Seedling roots, 5 days after germination

value: Standard media for 5 days then transferred to -Fe media

tag: Iron deficiency Treatment length

value: 3 hours


title: Arabidopsis, whole roots, -Fe, 72 hour, rep 2

description: Gene expression data from whole roots grown under standard conditions for 5 days and transferred to -Fe media for 72 hours

value: 72 hours


title: Arabidopsis, whole roots, -Fe, 12 hour, rep 2

description: Gene expression data from whole roots grown under standard conditions for 5 days and transferred to -Fe media for 12 hours

value: 12 hours


title: Arabidopsis, whole roots, -Fe, 24 hour, rep 1

description: Gene expression data from whole roots grown under standard conditions for 5 days and transferred to -Fe media for 24 hours

value: 24 hours


title: Arabidopsis, whole roots, -Fe, 24 hour, rep 2


title: Arabidopsis, whole roots, -Fe, 6 hour, rep 2

description: Gene expression data from whole roots grown under standard conditions for 5 days and transferred to -Fe media for 6 hours

value: 6 hour


title: Arabidopsis, whole roots, -Fe, 48 hour, rep 1

description: Gene expression data from whole roots grown under standard conditions for 5 days and transferred to -Fe media for 48 hours

value: 48 hours


title: Arabidopsis, whole roots, -Fe, 48 hour, rep 2


title: Arabidopsis, whole roots, -Fe, 12 hour, rep 1


title: Arabidopsis, root cells, epidermis and lateral root cap, -Fe, replicate 3


title: Arabidopsis, whole roots, -Fe, 3 hour, rep 2


title: Arabidopsis, whole roots, standard conditions, rep 2

description: Gene expression data from whole roots grown under standard conditions for 5 days and transferred to fresh standard to media for 3 hours

value: Standard media for 5 days then transferred to fresh standard media for 3 hours


title: Arabidopsis, whole roots, -Fe, 6 hour, rep 1


title: Arabidopsis, whole roots, -Fe, 72 hour, rep 1


title: Arabidopsis, whole roots, standard conditions, rep 1


title: Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 1

description: Gene expression data from longitudinal zone 3 isolated from roots grown under standard conditions for 5 days then transferred to -Fe media for 24 hours

source_name: root tissue

growth_protocol: Seeds were surface sterilized for 2 minutes in 70% ethanol, the ethanol was removed, then replaced with 30% Bleach and 0.02% Triton X-100 for 15 minutes. Seeds were rinsed 3 times with sterile water, stratified for 4˚C for 2 days, then placed on standard media. Standard media is 1X Murashige and Skoog salt mixture in which ferrous sulfate is replaced with 100mM Fe(III)-EDTA, 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH.  –Fe media is 1X Murashige and Skoog salt mixture in which ferrous sulfate is replaced with 0.3mM Ferrozine.   Nylon mesh was placed on top of the solidified media and seeds were evenly placed on the mesh in a single row at a density of ~2/cm for all experiments.

extract_protocol: Approximately 15 roots were dissected for each replicate and pooled.  Samples were collected into RNA extraction buffer and briefly sonicated to disrupt the tissue.  RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH).

treatment_protocol: Seedlings were grown for 5 days before transfer to standard media or standard -Fe media.  24 hours after transferring seedlings to media, roots were cut into 4 regions using a razor blade.

value: Standard media for 5 days, transferred to -Fe media for 24 hours before dissection


title: Arabidopsis, root, longitudinal zone 1, -Fe conditions, rep 2

description: Gene expression data from longitudinal zone 1 isolated from roots grown under standard conditions for 5 days then transferred to -Fe media for 24 hours


title: Arabidopsis, root, longitudinal zone 2, -Fe conditions, rep 1

description: Gene expression data from longitudinal zone 2 isolated from roots grown under standard conditions for 5 days then transferred to -Fe media for 24 hours


title: Arabidopsis, root, longitudinal zone 1, -Fe conditions, rep 1


title: Arabidopsis, root, longitudinal zone 3, -Fe conditions, rep 2


title: Arabidopsis, root, longitudinal zone 4, standard conditions, rep 2

description: Gene expression data from longitudinal zone 4 isolated from roots grown under standard conditions for 5 days then transferred to standard media for 1hr

value: Standard media


title: Arabidopsis, root, longitudinal zone 4, standard conditions, rep 1


title: Arabidopsis, root, longitudinal zone 3, standard conditions, rep 2

description: Gene expression data from longitudinal zone 3 isolated from roots grown under standard conditions for 5 days then transferred to standard media for 1hr


title: Arabidopsis, root, longitudinal zone 4, -Fe conditions, rep 2

description: Gene expression data from longitudinal zone 4 isolated from roots grown under standard conditions for 5 days then transferred to -Fe media for 24 hours


title: Arabidopsis, root, longitudinal zone 2, -Fe conditions, rep 2


title: Arabidopsis, root, longitudinal zone 4, -Fe conditions, rep 1


title: Arabidopsis, root, longitudinal zone 3, standard conditions, rep1


title: Arabidopsis, root, longitudinal zone 2, standard conditions, rep 2

description: Gene expression data from longitudinal zone 2 isolated from roots grown under standard conditions for 5 days then transferred to standard media for 1hr


title: Arabidopsis, root, longitudinal zone 2, standard conditions, rep 1


title: Arabidopsis, whole roots, -Fe, replicate 3

description: Gene expression data from whole roots after 24 hours of treatment with -Fe media

source_name: Whole roots

treatment_protocol: Samples were prepared as in Birnbaum et al. (2005) except that roots were transferred to -Fe media for 24 hours before protoplasting or harvested without protoplasting.  Protoplasted cells were passed through the FACS device with all cells being collected.

value: Standard media, transferred to -Fe media  for 24 hours prior to harvesting tissue


title: Arabidopsis, root cells, -Fe, replicate 3

description: Gene expression data from FACS sorted cells from roots treated for 24 hours with -Fe media


title: csn5 (csn5a-2 csn5b) mutant dark replicate 3

city: Freising

first: Claus

last: Schwechheimer

address: Emil-Ramann-Str. 4

department: Plant Systems Biology

institute: TUM

description: csn5 (csn5a-2 csn5b) mutant 7 day old seedlings dark grown

data_processing: Affymetrix Microarray Suite version 5.0

source_name: 7 day old seedlings, dark grown

label_protocol: Approximately 6 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Approximately 80 mg from 7 day old dark grown  csn5 (csn5a-2 csn5b) mutant seedlings were collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: mutant, 7 day old seedlings, dark grown


title: Arabidopsis, root cells, -Fe, replicate 2


title: csn4-1_mutant_dark replicate 1

description: csn4-1 mutant 7 day old seedlings dark grown

extract_protocol: Approximately 80 mg from 7 day old dark grown  csn4-1 mutant seedlings were collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).


title: csn3-1_mutant_dark replicate 1

description: csn3-1 mutant 7 day old seedlings dark grown

extract_protocol: Approximately 80 mg from 7 day old dark grown  csn3-1 mutant seedlings were collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).


title: Arabidopsis, whole roots, -Fe, replicate 2


title: csn5 (csn5a-2 csn5b) mutant dark replicate 1


title: csn4-1_mutant_dark replicate 2


title: Arabidopsis, root, longitudinal zone 1, standard conditions, rep 2

description: Gene expression data from longitudinal zone 1 isolated from roots grown under standard conditions for 5 days then transferred to standard media for 1hr


title: csn5 (csn5a-2 csn5b) mutant dark replicate 2


title: Arabidopsis, whole roots, -Fe, replicate 1


title: csn3-1 mutant dark replicate 2


title: csn4-1_mutant_dark replicate 3


title: Arabidopsis, root cells, -Fe, replicate 1


title: Arabidopsis, root, longitudinal zone 1, standard conditions, rep 1


title: wild type dark replicate 3

description: wild type 7 day old seedlings, dark grown

extract_protocol: Approximately 80 mg from 7 day old dark grown Col wild type seedlings were collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: wild type, 7 day old seedlings, dark grown


title: csn3-1 mutant dark replicate 1


title: wild type dark replicate 1

tag: wild type, 7day old seedlings, dark grown


title: csn5 (csn5a-2 csn5b) mutant light  replicate 2

description: csn5 (csn5a-2 csn5b) mutant 7 day old seedlings light grown

source_name: 7 day old seedlings, light grown

extract_protocol: Approximately 80 mg from 7 day old light grown  csn5 (csn5a-2 csn5b) mutant seedlings were collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: mutant, 7 day old seedlings, light grown


title: csn3-1 mutant light replicate 2

description: csn3-1 mutant 7 day old seedlings light grown

extract_protocol: Approximately 80 mg from 7 day old light grown  csn3-1 mutant seedlings were collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).


title: csn5 (csn5a-2 csn5b)  mutant light  replicate 1


title: csn5 (csn5a-2 csn5b)  mutant light  replicate 3


title: At_Standard_scm-2

city: Stanford

first: Jose

middle: Ramon

last: Dinneny

state: United States

address: 260 Panama St

institute: Carnegie Institution for Science, Department of Plant Biology

description: Gene expression data from root tips of scm plants grown under standard conditions for 5 days and transferred to standard media for 1 hour

hyb_protocol: Standard Affymetrix protocols. Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

data_processing: MAS 5

source_name: root tips

growth_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water.  Seeds were stratified at 4˚C for 2 days before being planted on standard media.  Standard media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH.  Salt media is standard media with varying amounts of NaCl added.  Nylon mesh was placed on top of the solidified media and seeds were evenly placed on the mesh in a single row at a density of ~2/cm for all experiments.

extract_protocol: Approximately 30 roots were collected per replicate.  Samples were briefly sonicated to disrupt the tissue.  RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH).

treatment_protocol: Seedlings were grown for 5 days before being transferred to standard media or media supplemented with 140mM NaCl.  One hour after transfer, a razor blade was used to cut the root ~5 mm above the root tip.  Approximately 30 roots were pooled per replicate.  Two biological replicates were performed per genotype, per condition.  Samples were briefly sonicated to disrupt the tissue.

value: Standard media for 4 days then transferred to media supplemented with 140 mM NaCl

tag: Treatment length

value: 1 hour


title: wild type dark replicate 2


title: At_NaCl_scm-2

description: Gene expression data from root tips of scm plants grown under standard conditions for 5 days and transferred to standard media supplemented with 140mM NaCl for 1 hour

scan_protocol: Standard Affymetrix protocols. Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.

value: Columbia


title: At_Standard_scm-1


title: At_NaCl_cpctry-2

description: Gene expression data from root tips of cpc try plants grown under standard conditions for 5 days and transferred to standard media supplemented with 140mM NaCl for 1 hour

value: cpc-1 try-82


title: At_NaCl_cpctry-1


title: csn3-1 mutant light replicate 3


title: csn3-1 mutant light replicate 1


title: At_Standard_cpctry-1

description: Gene expression data from root tips of cpc try plants grown under standard conditions for 5 days and transferred to standard media for 1 hour


title: At_NaCl_scm-1


title: At_Standard_wermyb23-1

description: Gene expression data from root tips of wer myb23 plants grown under standard conditions for 5 days and transferred to standard media for 1 hour

value: wer-1 myb23-1

value: Standard media for 5 days then transferred to media supplemented with 140 mM NaCl


title: At_NaCl_wermyb23-1

description: Gene expression data from root tips of wer myb23 plants grown under standard conditions for 5 days and transferred to standard media supplemented with 140mM NaCl for 1 hour

value: Seedling roots, 5 days after germination


title: At_Standard_wermyb23-2


title: At_Standard_Col-2

description: Gene expression data from root tips of wild type plants grown under standard conditions for 5 days and transferred to standard media for 1 hour

value: wild type

value: Standard media for 5 days then transferred to standard media


title: At_NaCl_Col-1

description: Gene expression data from root tips of wild type plants grown under standard conditions for 5 days and transferred to standard media supplemented with 140mM NaCl for 1 hour


title: At_Standard_cpctry-2


title: At_Standard_Col-1


title: At_NaCl_wermyb23-2


title: Arabidopsis, whole roots, 140 mM NaCl, 16 hour, replicate 2

description: Gene expression data from whole roots grown under standard conditions for 5 days and transferred to media supplemented with 140 mM NaCl for 16 hours

extract_protocol: Approximately 15 roots were collected per replicate.  Samples were briefly sonicated to disrupt the tissue.  RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH).

treatment_protocol: Seedlings were grown for 4-5 days before transfer to standard media supplemented with 140 mM NaCl.  Transfers were staggered such that all roots were harvested within 3 hours of each other on the sixth day of growth.  Roots were cut with a razor blade 0.5 mm below the root/hypocotyl junction and collected into RNA extraction buffer.  Approximately 15 roots were collected per replicate, with two biological replicates being performed per time point.  Samples were briefly sonicated to disrupt the tissue.

value: 16 hours


title: Arabidopsis, whole roots, 140 mM NaCl, 32 hour, replicate 2

description: Gene expression data from whole roots grown under standard conditions for 5 days and transferred to media supplemented with 140 mM NaCl for 32 hours

value: 32 hours


title: Arabidopsis, whole roots, 140 mM NaCl, 32 hour, replicate 1


title: Arabidopsis, whole roots, 140 mM NaCl, 30 minutes, replicate 2

description: Gene expression data from whole roots grown under standard conditions for 5 days and transferred to media supplemented with 140 mM NaCl for 30 minutes

value: 30 minutes


title: Arabidopsis, whole roots, 140 mM NaCl, 1 hour, replicate 1

description: Gene expression data from whole roots grown under standard conditions for 5 days and transferred to media supplemented with 140 mM NaCl for 1 hour


title: Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 2

description: Gene expression data from isolated protophloem cells after roots were treated with 140 mM NaCl for 1 hour

growth_protocol: Seeds were surface sterilized with 50% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water.  Seeds were stratified at 4˚C for 2 days before being planted on standard media.  Standard media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH.  Salt media is standard media with varying amounts of NaCl added.  Nylon mesh was placed on top of the solidified media and seeds were evenly placed on the mesh at a density of ~20 seeds/cm in two rows.

treatment_protocol: Samples were prepared as in Birnbaum et al. (2005) for roots grown under standard conditions.  For salt treated samples, roots were transferred to 140 mM NaCl for 1hr before protoplasting.  Three replicates were performed per cell type, per condition.  In order to test for the effects of sorting, Col-0 roots were protoplasted after being treated for 1 hour with or without salt treatment.  Cells were passed through the FACS device with all cells being collected.

value: Seedling roots, 6 days after germination

value: Standard media for 6 days, transferred to media supplemented with 140mM NaCl for 1 hour before protoplasting


title: At_NaCl_Col-2


title: Arabidopsis, whole roots, standard conditions, replicate 1

description: Gene expression data from whole roots grown under standard conditions for 5 days


title: Arabidopsis, whole roots, 140 mM NaCl, 30 minutes, replicate 1


title: Arabidopsis, whole roots, 140 mM NaCl, 4 hour, replicate 1

description: Gene expression data from whole roots grown under standard conditions for 5 days and transferred to media supplemented with 140 mM NaCl for 4 hours

value: 4 hours


title: Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 3


title: Arabidopsis, whole roots, 140 mM NaCl, 4 hour, replicate 2


title: Arabidopsis, whole roots, 140 mM NaCl, 1 hour, replicate 2


title: Arabidopsis, whole roots, standard conditions, replicate 2

value: Standard media


title: Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 3

description: Gene expression data from isolated endodermal and quiecent center cells after roots were treated with 140 mM NaCl for 1 hour


title: Arabidopsis, root cells, protophloem, 140 mM NaCl, replicate 1


title: Arabidopsis, root cells, stele, 140 mM NaCls, replicate 2

description: Gene expression data from isolated stele cells after roots were treated with 140 mM NaCl for 1 hour


title: Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 2

description: Gene expression data from isolated columella root cap cells after roots were treated with 140 mM NaCl for 1 hour


title: Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 1


title: Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 2

description: Gene expression data from isolated cortex cells after roots were treated with 140 mM NaCl for 1 hour

value: CORTEX


title: Arabidopsis, root cells, endodermis and quiescent center, 140 mM NaCl, replicate 2


title: Arabidopsis, root cells, stele, 140 mM NaCls, replicate 3


title: Arabidopsis, whole roots, 140 mM NaCl, 16 hour, replicate 1

value: Standard media for 4 days then transferred to media supplemented with 140 mM NaCl


title: Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 3


title: Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 1


title: Arabidopsis, root cells, cortex, 140 mM NaCl, replicate 3


title: Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 2

description: Gene expression data from isolated epidermal and lateral root cap cells after roots were treated with 140 mM NaCl for 1 hour


title: Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 1


title: Arabidopsis, root cells, protophloem, standard conditions, replicate 2

description: Gene expression data from isolated protophloem cells


title: Arabidopsis, root cells, columella root cap, 140 mM NaCl, replicate 1


title: Arabidopsis, root cells, stele, standard conditions, replicate 3

description: Gene expression data from isolated stele cells


title: Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 1

description: Gene expression data from isolated endodermal and quiecent center cells


title: Arabidopsis, root cells, stele, standard conditions, replicate 1


title: Arabidopsis, root cells, stele, 140 mM NaCls, replicate 1


title: Arabidopsis, root cells, protophloem, standard conditions, replicate 1


title: Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 2


title: Arabidopsis, root cells, protophloem, standard conditions, replicate 3


title: Arabidopsis, root cells, cortex, standard conditions, replicate 3

description: Gene expression data from isolated cortex cells


title: Arabidopsis, root cells, epidermis and lateral root cap, 140 mM NaCl, replicate 3


title: Arabidopsis, root cells, stele, standard conditions, replicate 2


title: Arabidopsis, root cells, endodermis and quiescent center, standard conditions, replicate 3


title: Arabidopsis, root cells, columella root cap, standard conditions, replicate 3

description: Gene expression data from isolated columella root cap cells


title: Arabidopsis, root cells, cortex, standard conditions, replicate 1


title: Arabidopsis, root cells, columella root cap, standard conditions, replicate 2


title: Arabidopsis, root cells, cortex, standard conditions, replicate 2


title: Arabidopsis, root cells, epidermis and lateral root cap, standard conditions, replicate 2

description: Gene expression data from isolated epidermal and lateral root cap cells


title: Arabidopsis, root cells, epidermis and lateral root cap, standard conditions, replicate 3


title: Arabidopsis, root cells, epidermis and lateral root cap, standard conditions, replicate 1


title: Arabidopsis, root, longitudinal zone 2, standard conditions, NaCl, replicate 2

description: Gene expression data from longitudinal zone 2 isolated from roots grown under standard conditions for 5 days then transferred to media supplemented with 140 mM NaCl for 1hr

extract_protocol: Approximately 15 sections were dissected for each replicate and pooled.  Samples were collected into RNA extraction buffer and briefly sonicated to disrupt the tissue.  RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH).

treatment_protocol: Seedlings were grown for 5 days before transfer to standard media or standard media supplemented with 140mM NaCl.  One hour after transferring seedlings to media, roots were cut into 4 regions using a razor blade.

value: Standard media for 5 days, transferred to media supplemented with 140mM NaCl for 1 hour before discection


title: Arabidopsis, root, longitudinal zone 2, standard conditions, NaCl, replicate 1

value: Columbia


title: Arabidopsis, root cells, columella root cap, standard conditions, replicate 1


title: Arabidopsis, whole roots, 140 mM NaCl, replicate 1

description: Gene expression data from whole roots after 1 hour of treatment with media supplemented with 140 mM NaCl

treatment_protocol: Samples were prepared as in Birnbaum et al. (2005) except that roots were transferred to 140 mM NaCl for 1hr before protoplasting or harvested without protoplasting.  Protoplasted cells were passed through the FACS device with all cells being collected.

value: Standard media, transferred to 140 mM NaCl for 1 hour prior to harvesting tissue


title: Arabidopsis, root, longitudinal zone 4, standard conditions, replicate 8

description: Gene expression data from longitudinal zone 4 isolated from roots grown under standard conditions for 5 days then transferred to standard media for 1hr


title: Arabidopsis, root, longitudinal zone 4, standard conditions, NaCl, replicate 2

description: Gene expression data from longitudinal zone 4 isolated from roots grown under standard conditions for 5 days then transferred to media supplemented with 140 mM NaCl for 1hr


title: Arabidopsis, root, longitudinal zone 2, standard conditions, replicate 3

description: Gene expression data from longitudinal zone 2 isolated from roots grown under standard conditions for 5 days then transferred to standard media for 1hr


title: Arabidopsis, root, longitudinal zone 1, standard conditions, NaCl, replicate 2

description: Gene expression data from longitudinal zone 1 isolated from roots grown under standard conditions for 5 days then transferred to media supplemented with 140 mM NaCl for 1hr


title: Arabidopsis, root, longitudinal zone 1, standard conditions, NaCl, replicate 1


title: Arabidopsis, root, longitudinal zone 4, standard conditions, replicate 7


title: Arabidopsis, root, longitudinal zone 3, standard conditions, NaCl, replicate 1

description: Gene expression data from longitudinal zone 3 isolated from roots grown under standard conditions for 5 days then transferred to media supplemented with 140 mM NaCl for 1hr


title: Arabidopsis, root, longitudinal zone 4, standard conditions, NaCl, replicate 1


title: Arabidopsis, root, longitudinal zone 3, standard conditions, replicate 6

description: Gene expression data from longitudinal zone 3 isolated from roots grown under standard conditions for 5 days then transferred to standard media for 1hr


title: Arabidopsis, whole roots, 140 mM NaCl, replicate 2


title: Arabidopsis, root cells, 140 mM NaCl, replicate 2

description: Gene expression data from FACS sorted cells from roots treated for 1 hour with media supplemented with 140 mM NaCl, all cells were collected for RNA extraction

value: Standard media, transferred to 140 mM NaCl for 1 hour prior to protoplasting and cell sorting


title: Arabidopsis, root, longitudinal zone 2, standard conditions, replicate 4


title: Arabidopsis, root, longitudinal zone 1, standard conditions, replicate 2

description: Gene expression data from longitudinal zone 1 isolated from roots grown under standard conditions for 5 days then transferred to standard media for 1hr


title: Arabidopsis, root, longitudinal zone 3, standard conditions, NaCl, replicate 2


title: Arabidopsis, root, longitudinal zone 3, standard conditions, replicate 5


title: Arabidopsis, root cells, 140 mM NaCl, replicate 1


title: Arabidopsis, root, longitudinal zone 1, standard conditions, replicate 1


title: wild type replicate 2 light

description: CSN4-1 wild type 7 day old seedlings

source_name: 7 day old seedlings

extract_protocol: Approximately 80 mg from 7 day old light grown CSN4-1 in Col wild type seedlings were collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).

tag: wild type, 7 day old seedlings, light grown


title: wild type replicate 3 light

description: CSN4-1 wild type 7 day old seedlings


title: csn4-1_mutant replicate 1

description: csn4-1 mutant 7 day old seedlings light grown

extract_protocol: Approximately 80 mg from 7 day old light grown  csn4-1 mutant seedlings were collected and ground to a fine powder under liquid Nitrogen. Samples were lysed in separate groups in RLT buffer (Qiagen).Total RNA was extracted from the tissue lysate using an RNeasy kit (Qiagen).


title: wild type replicate 1 light

description: CSN4-1 wild type 7 day old seedlings

tag: wild type, 7day old seedlings, light grown


title: csn4-1_mutant replicate 3


title: csn4-1_mutant replicate 2


title: Decidua e17.0, biological rep1

status: Public on Apr 23 2008

first: Kirstin

last: Knox

address: 300 Pasteur Dr.

department: Genetics

institute: Stanford Univeristy

description: Gene expression data from maternal decidua at e17.0

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on the Affymetrix Mouse 430 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: In order to control for differences in overall strength of hybridization, all arrays were normalized to the same median intensity using the dCHIP invariant set method.  Modeling was performed using the dCHIP Perfect Match (PM) modeling algorithm.

source_name: Mouse decidual tissue at embryonic day 17.0, biological replicate 1

label_protocol: For each sample, labeled cRNA was prepared from 10 ug of starting RNA according to Affymetrix  protocols. Briefly, RNA was reverse transcribed and the resulting double stranded cDNA was purified by phenol-chloroform extraction followed by ethanol precipitation.  The cDNA was used as a template for a biotin labeling in vitro transcription.  The resulting cRNA was purified using an Rneasy column, quantified, then fragmented using KOAc RNA fragmentation buffer.

growth_protocol: A minimum of two to three timed pregnant female Swiss Webster mice were sacrificed at each timepoint used in our analysis, generating two to three biological replicates at each stage.  For each pregnancy, the entire litter of fetuses and placentas was dissected.  Fetal tissues were used to confirm staging of the embryos using Theiler’s morphological criteria.

extract_protocol: Each sample was homogenized in Trizol with a rotor homogenizer.  RNA was isolated by chloroform extraction from the Trizol sample, purified using a Qiagen Rneasy column, then ethanol precipitated.  Due to limited tissue availability, two e8.5 placenta samples (Placenta_e8.5-1 and Placenta_e8.5-2) were homogenized in Ambion lysis buffer rather than Trizol.  For these samples, RNA was isolated using the Ambion Rnaqueous Micro kit prior to ethanol precipitation.

treatment_protocol: Placentas were manually dissected into fetal placenta and decidual (maternal) portions, using fine forceps to separate the decidua from the spongiotrophoblast and trophoblast giant cells.  Fetally derived placenta samples and maternally derived placenta samples were pooled separately for each litter, then flash frozen in liquid nitrogen and stored at –80° C until RNA isolation.  Tissues from two to ten placentas from a single litter were combined for each sample except for two of the e8 samples, which were pooled from multiple litters after staging.

tag: Strain

value: Swiss Webster

tag: Tissue

value: decidua (maternal origin)


title: Decidua P0, biological rep2

description: Gene expression data from maternal decidua at P0

source_name: Mouse decidual tissue at postnatal day 0, biological replicate 2


title: Placenta and Decidua e17.0, biological rep 2 (Series 2)

description: Gene expression data from fetal placenta and maternal decidua (undissected) at e17.0

source_name: Mouse placental and decidual tissue (undissected) at embryonic day 17.0, biological replicate 2

growth_protocol: For all dissected samples, a minimum of two to three timed pregnant female Swiss Webster mice were sacrificed at each timepoint used in our analysis, generating two to three biological replicates at each stage. The one exception is e8.5: for this experiment (Series 2) only one of the placenta_e8.5 sample is used (see extract protocol below).  For the two undissected samples, a single C57BL/6 female was sacrificed at e17.0 and two individual, undissected placentas were collected to generate two replicates.  In all cases, fetal tissues were used to confirm staging of the embryos using Theiler’s morphological criteria.

extract_protocol: Each sample was homogenized in Trizol with a rotor homogenizer.  RNA was isolated by chloroform extraction from the Trizol sample, purified using a Qiagen Rneasy column, then ethanol precipitated.  Note: Due to limited tissue availability, two of the full timecourse e8.5 placenta samples (Placenta_e8.5-1 and Placenta_e8.5-2) included in Series 1 were homogenized in Ambion lysis buffer rather than Trizol and were purified with Ambion Rnaqueous rather than Quiagen Rneasy, so are not included in the Series 2 experiment.

treatment_protocol: For dissected samples, placentas were manually dissected into fetal placenta and decidual (maternal) portions, using fine forceps to separate the decidua from the spongiotrophoblast and trophoblast giant cells.  Fetally derived placenta samples and maternally derived placenta samples were pooled separately for each litter, then flash frozen in liquid nitrogen and stored at –80° C until RNA isolation.  Tissues from two to ten placentas from a single litter were combined for each sample except for two of the e8 samples, which were pooled from multiple litters after staging.  For undissected samples, single undissected e17.0 placentas were flash frozen and stored at –80°  C until RNA isolation.

value: placenta and decidua


title: Decidua e17.0, biological rep2

source_name: Mouse decidual tissue at embryonic day 17.0, biological replicate 2


title: Decidua e19.0, biological rep1

description: Gene expression data from maternal decidua at e19.0

source_name: Mouse decidual tissue at embryonic day 19.0, biological replicate 1


title: HeLa Cell Line, unknown: VVdelK3Ldel37N, 6HPI

city: Phoenix

first: Winnie

last: Liang

state: AZ

address: 445 N. Fifth Street

institute: Translational Genomics

description: vaccinia virus infected

source_name: HeLa Cell Line, unknown


title: Decidua e15.0, biological rep1

description: Gene expression data from maternal decidua at e15.0

source_name: Mouse decidual tissue at embryonic day 15.0, biological replicate 1


title: Placenta and Decidua e17.0, biological rep 1 (Series 2)

source_name: Mouse placental and decidual tissue (undissected) at embryonic day 17.0, biological replicate 1


title: Decidua P0, biological rep1

source_name: Mouse decidual tissue at postnatal day 0, biological replicate 1


title: HeLa Cell Line, unknown: VVdelK3Ldel37N, 2HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: mock infected 9HPI

description: vaccinia virus infected


title: Decidua e15.0, biological rep2

source_name: Mouse decidual tissue at embryonic day 15.0, biological replicate 2


title: HeLa Cell Line, unknown: VVdelK3L, 9 HPI

description: vaccinia virus infected


title: Decidua e10.5, biological rep1

description: Gene expression data from maternal decidua at e10.5

source_name: Mouse decidual tissue at embryonic day 10.5, biological replicate 1


title: Decidua e19.0, biological rep2

source_name: Mouse decidual tissue at embryonic day 19.0, biological replicate 2


title: Decidua e12.0, biological rep2

description: Gene expression data from maternal decidua at e12.0

source_name: Mouse decidual tissue at embryonic day 12.0, biological replicate 2


title: HeLa Cell Line, unknown: mock infected 2HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: VVdelK3Ldel37N, 9HPI

description: vaccinia virus infected


title: Decidua e12.0, biological rep1

source_name: Mouse decidual tissue at embryonic day 12.0, biological replicate 1


title: Decidua e10.5, biological rep2

source_name: Mouse decidual tissue at embryonic day 10.5, biological replicate 2


title: HeLa Cell Line, unknown: VVdelK3L, 6 HPI

description: vaccinia virus infected


title: Decidua e9.0, biological rep1

description: Gene expression data from maternal decidua at e9.0

source_name: Mouse decidual tissue at embryonic day 9.0, biological replicate 1


title: HeLa Cell Line, unknown: mock infected 6HPI

description: vaccinia virus infected


title: Decidua e9.0, biological rep2

source_name: Mouse decidual tissue at embryonic day 9.0, biological replicate 2


title: HeLa Cell Line, unknown: VVdel37N, 9 HPI

description: vaccinia virus infected


title: Decidua e8.5, biological rep1, technical rep2

description: Gene expression data from maternal decidua at e8.5

source_name: Mouse decidual tissue at embryonic day 8.5, biological replicate 1, technical replicate 2


title: Placenta P0, biological rep2

description: Gene expression data from fetal placenta at P0

source_name: Mouse placental tissue at postnatal day 0, biological replicate 2

value: placenta (fetal origin)


title: HeLa Cell Line, unknown: VVdelK3L, 2 HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: VV-ADAR/E3L, 9 HPI

description: vaccinia virus infected


title: Placenta P0, biological rep1

source_name: Mouse placental tissue at postnatal day 0, biological replicate 1


title: Decidua e8.5, biological rep2, technical rep2

source_name: Mouse decidual tissue at embryonic day 8.5, biological replicate 2, technical replicate 2


title: Decidua e8.5, biological rep1, technical rep1

source_name: Mouse decidual tissue at embryonic day 8.5, biological replicate 1, technical replicate 1


title: Decidua e8.5, biological rep2, technical rep1

source_name: Mouse decidual tissue at embryonic day 8.5, biological replicate 2, technical replicate 1


title: Placenta e19.0, biological rep2

description: Gene expression data from fetal placenta at e19.0

source_name: Mouse placental tissue at embryonic day 19.0, biological replicate 2


title: HeLa Cell Line, unknown: VV-ADAR/E3L, 2 HPI

description: vaccinia virus infected

source_name: HeLa Cell Line, unknown


title: HeLa Cell Line, unknown: VVE3L Y48F, 6 HPI

description: vaccinia virus infected


title: Placenta e17.0, biological rep2

description: Gene expression data from fetal placenta at e17.0

source_name: Mouse placental tissue at embryonic day 17.0, biological replicate 2


title: HeLa Cell Line, unknown: VVdel37N, 6 HPI

description: vaccinia virus infected


title: HeLa Cell Line, unknown: VV-ATV, 6 HPI

description: vaccinia virus infected


title: Placenta e19.0, biological rep1

source_name: Mouse placental tissue at embryonic day 19.0, biological replicate 1