title: HG228_vs_MG1655_rep1

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

description: Ethanol tolerant and control cells are grown in minimal media plus 0.04% (w/v) glucose plus 1.5% (v/v) ethanol

hyb_protocol: Samples were hybridized using gene-expression hybridization kit from Agilent. Hybridization was performed overnight for 18 hr in 65C.

scan_protocol: Agilent Technologies Scanner G2505B US22502626 was used to scan the slide.

data_processing: LOWESS normalized, condensed, background subtracted data obtained from processed Green signal/processed Red signal. Agilent Feature Extractionv 9.5 software was used.

organism: Escherichia coli

source_name: Cells in exponential phase

label_protocol: RNA samples were poly adenylated for 30 min (NEB, cat# M0276L) and labeled using Agilent's quick-amp lebeling kit according to the manufacturer's protocol.

growth_protocol: The cells are grown upto mid-log phase in minimal media plus 0.04% (w/v) glucose and 1.5% (v/v) ethanol.

extract_protocol: Total RNA was extracted from each sample using Norgen's Total RNA purification kit (cat# 17200) per manufacturer's instructions.

value: test (Ethanol-tolerant)

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Control cells in exponential phase

value: reference


title: Alkaline induction- 0hr

status: Public on Jun 15 2010

type: RNA

city: Philadelphia

first: Paul

middle: H

last: Davis

state: PA

address: 433 S. University Ave.

department: Biology

country: USA

institute: University of Pennsylvania

hyb_protocol: Hybridization, washing, and scanning of arrays was performed using standard Affymetrix instrumentation and protocols for 11 micron, 169 format arrays.

data_processing: Expression values computed using the RMA implementation (default parameters) from Bioconductor (Gentleman, Carey et al. 2004).

label: biotin

molecule: total RNA

organism: Toxoplasma gondii

source_name: Tissue cultured parasites

label_protocol: Labeled cRNA was created using the One-Cycle Labeling protocol in the Affymetrix GeneChip® IVT Labeling Kit (Santa Clara, CA).

growth_protocol: Parasites were cultured in human foreskin fibroblast (HFF) cells as described in Roos, Donald et al. 1994.

extract_protocol: Prior to host cell rupture, human fibroblast cells were scraped from the flask, collected, and spun at 300g for 9 min.  The resultant pellet was lysed with Buffer RLT from the Qiagen RNeasy Mini Kit (Valencia, CA) and RNA was extracted according to the manufacturer’s instructions.

treatment_protocol: HFF cells in flasks were grown to confluency in D10 media and infected with T. gondii freshly lysed parasites.  4 hours following infection, media was changed ("0hr") to D10 media with the pH adjusted to 8.2.

tag: strain

value: Prugniaud

tag: treatment

value: Alkaline induction- 0hr


title: HG228_vs_MG1655_rep2

state: CA

tag: sample type


title: Alkaline induction- 72hr

scan_protocol: Hybridization, washing, and scanning of arrays was performed using standard Affymetrix instrumentation and protocols for 11 micron, 169 format arrays

treatment_protocol: HFF cells in flasks were grown to confluency in D10 media and infected with T. gondii freshly lysed parasites.  4 hours following infection, media was changed ("0hr") to D10 media with the pH adjusted to 8.2.  Sample was collected after 72hr induction conditions.

value: Alkaline induction- 72hr


title: HCC-1428/LTED, rep 2

city: Nashville

first: Todd

middle: W

last: Miller

state: TN

address: 2220 Pierce Ave, 777 PRB

department: Medicine

institute: Vanderbilt Univ

description: Gene expression data from cells treated with 10% DCC-FBS x 24 hrs (after long-term culture in same medium).

hyb_protocol: 15 ug biotinylated cRNA was fragmented and hybridized to an Affymetrix Genechip Human Genome U133 Plus 2.0 array. Hybridized cRNA was detected using streptavidin coupled to phycoerythrin.

scan_protocol: Genechips were scanned using Genechip Scanner 3000 7G Plus 2 and Genechip Operating System (Affymetrix).

data_processing: Default values were used to grid images (.DAT) and generate .CEL and .CHP files.

organism: Homo sapiens

source_name: HCC-1428/LTED cells

label_protocol: GeneChip One-Cycle Target Labeling and Control reagents kit (Affymetrix).

growth_protocol: Parental cells are maintained in IMEM + 10% FBS + phenol red. LTED cells are maintained in IMEM + 10% DCC-FBS (no phenol red).

extract_protocol: Trizol extraction followed by Qiagen RNeasy column clean-up with on-column DNase digestion.

treatment_protocol: Cells were seeded in 100 mm dishes in triplicate. The following day, cells were washed with PBS, and treated with IMEM + 10% DCC-FBS (no phenol red). Twenty-four hrs later, RNA was harvested.

tag: cell line

tag: cell type

value: breast cancer

tag: lted

value: yes


title: HCC-1428, rep 2

description: Gene expression data from cells treated with 10% DCC-FBS x 24 hrs.

source_name: HCC-1428 cells

value: no


title: HCC-1428/LTED, rep 3


title: HCC-1428/LTED, rep 1


title: HCC-1428, rep 3


title: MDA-361/LTED, rep 2

source_name: MDA-361/LTED cells


title: MDA-361/LTED, rep 3


title: HCC-1428, rep 1


title: MDA-361/LTED, rep 1


title: MDA-361, rep 3

source_name: MDA-361 cells


title: MDA-361, rep 2


title: wt 12 month old (A19)

city: Rockville

first: Radu

last: Cojocaru

state: MD

address: 5635 Fishers Lane, Suite 510

institute: Elsevier

description: Gene Expression Data

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing:
RMA signal intensity data.
The RMA (Robust Multichip Averaging) algorithm is one of the probe summarization options that have been implemented in GeneSpring GX. Within GeneSpring GX, RMA with PM probes is validated against R with bgversion=2.
This PM based method involves three steps:
1. Background Correction: This step is based on the distribution of PM values amongst probes on an Affymetrix array.
2. Normalization: It uses Quantile normalization.
3. Probe summarization: It involves summarizing the log(PM) after background correction of probes which is followed by estimation of expression values using robust procedure called Median Polish.
Moreover, the Data processing in GeneSpring GX works in a sequence of events which involves Summarization -> Log Transformation -> Baseline transformation.
Also, the data is centered around zero because the data is already in log scale and uses baseline transformation. The baseline transformation is performed for each probe based on the median of the log summarized values from all samples which is then subtracted from each of the samples.

label: Biotin

organism: Mus musculus

source_name: flow-sorted rod photoreceptors

label_protocol: Ovation RNA Amplification System V2 (Nugen)

extract_protocol: Rneasy Mini (Qiagen)

treatment_protocol: Flowsorted Rod photorteceptors

tag: genotype (transgenic line)

value: Nrlp-EGFP

value: rod photoreceptors

tag: age

value: 12 months


title: wt 12 month old (D18)

description: Gene Expression Data


title: wt 12 month old (B16)

description: Gene Expression Data


title: Malignant mesothelioma, Y-MESO-30

type: genomic

city: Nagoya

first: Hideki

last: Murakami

state: Aichi

address: 1-1 Kanokoden Chukusa-ku

department: Division of Molecular Oncology

country: Japan

institute: Aichi Cancer Center Institute

description: Malignant mesotehlioma cell line

hyb_protocol: The samples were hybridized for 40 hours using Agilent Oligo aCGH Hybridization Kit according to the manufacture's instructions.

scan_protocol: Arrays were scanned on an Agilent carousel scanner following manufacture's instructions. Agilent Feature Extraction software was used to extract the data.

data_processing: Agilent Feature Extraction software

molecule: genomic DNA

source_name: Pooled normal genomic DNA, Male

label_protocol: The samples were labeled using the Agilent Genomic DNA Labeling Kit PLUS according to manufacture's instructions. DNA was fragmented using restriction enzymes. Random hexamers were used to prim an Exo-Klenow fragment DNA polymerase reaction incorporating CyDye labeled dUTP.

extract_protocol: DNA was prepared by standard techniques.

value: Normal human genomic DNA purchased from Promega

source_name: Y-MESO-30 genomic DNA

value: Human malignant pleural mesothelioma cell line, Y-MESO-30


title: MDA-361, rep 1


title: patient 9, tumor liver

city: Tokyo

first: satow

last: reiko

address: 5-1-1 Tsukiji, Chuo-ku

institute: National Cancer Center Research Institute

hyb_protocol: cRNA probes were hybridized to Human Exon 1.0 ST arrays (Affymetrix), as instructed by the supplier

scan_protocol: scanned by GeneChip Scanner 3000

data_processing: Data analysis was carried out using the ArrayAssist software (Version 5.5.1, Stratagene, La Jolla, CA) and HuEx-1_0-st-v2.r2.dt1.hg18.core.mps for primary analysis.

source_name: tumor liver from patient 9

label_protocol: One µg of total RNA was converted to end-labeled cRNA using the Whole Transcript Sense Target Labeling kit (Affymetrix, Santa Clara, CA)

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

tag: Age

tag: Sex

value: male

tag: Diagnosis

value: hepatitis C


title: ZR75-1/LTED, rep 3

source_name: ZR75-1/LTED cells


title: Malignant mesothelioma, Y-MESO-26B

description: Malignant mesotehlioma cell line

source_name: Y-MESO-26B genomic DNA

value: Human malignant pleural mesothelioma cell line, Y-MESO-26B


title: Malignant mesothelioma, Y-MESO-25

description: Malignant mesotehlioma cell line

source_name: Y-MESO-25 genomic DNA

value: Human malignant pleural mesothelioma cell line, Y-MESO-25


title: Malignant mesothelioma, Y-MESO-29

description: Malignant mesotehlioma cell line

source_name: Y-MESO-29 genomic DNA

value: Human malignant pleural mesothelioma cell line, Y-MESO-29


title: wt 5 month old (B29)

description: Gene Expression Data

value: 5 months


title: ZR75-1/LTED, rep 1


title: ZR75-1/LTED, rep 2


title: Malignant mesothelioma, Y-MESO-12

description: Malignant mesotehlioma cell line

source_name: Pooled normal genomic DNA, Female

source_name: Y-MESO-12 genomic DNA

value: Human malignant pleural mesothelioma cell line, Y-MESO-12


title: wt 5 month old (A30)

description: Gene Expression Data


title: wt 12 month old (AR16)

description: Gene Expression Data


title: wt 5 month old (C29)

description: Gene Expression Data


title: ZR75-1, rep 3

source_name: ZR75-1 cells


title: wt 5 month old (A29)

description: Gene Expression Data


title: Malignant mesothelioma, Y-MESO-22

description: Malignant mesotehlioma cell line

source_name: Y-MESO-22 genomic DNA

value: Human malignant pleural mesothelioma cell line, Y-MESO-22


title: wt 1.5 month old (D21)

description: Gene Expression Data

value: 1.5 months


title: Malignant mesothelioma, Y-MESO-21

description: Malignant mesotehlioma cell line

source_name: Y-MESO-21 genomic DNA

value: Human malignant pleural mesothelioma cell line, Y-MESO-21


title: Malignant mesothelioma, Y-MESO-28

description: Malignant mesotehlioma cell line

source_name: Y-MESO-28 genomic DNA

value: Human malignant pleural mesothelioma cell line, Y-MESO-28


title: ZR75-1, rep 2

value: breast cancer

value: no


title: wt 1.5 month old (E21)

description: Gene Expression Data

value: Nrlp-EGFP

value: rod photoreceptors


title: wt 1.5 month old (B21)

description: Gene Expression Data


title: liver cells_bmp6-rgmc_rep1

city: Portland

first: Mahta

last: Nili

state: OR

address: 3181 SW Sam Jackson Park Road

department: Biochemistry and Molecular Biology

institute: Oregon Health & Science University

description: Gene expression data from Hep3B cells treated with BMP6 and RGMc for 4 hours.

hyb_protocol: Affymetrix Human Gene 1.0 ST arrays were hybridized to 4 ug of labeled, amplified single-stranded cDNA, washed, stained and scanned according to the protocol described in WT Sense Target Labeling Assay Manual v 4

scan_protocol: Scanning was performed on an Affymetrix GeneChip Scanner 3000 7G

data_processing: Image processing of sample DAT files to generate sample CEL files was completed in Affymetrix GeneChip Command Console software.  Each array was analyzed using Affymetrix Expression Console software to summarize probe set data to the gene level and to calculate quality assessment metrics.  The raw microarray data was normalized by the robust multichip average algorithm using the web-based data analysis software GeneSifter®.

label_protocol: 100ng of total RNA was amplified and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol v4.

growth_protocol: Confluent Hep3B cells were serum-starved for 16 hours.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by sodium acetate/ethanol precipitation.

treatment_protocol: BMP(2 or 6) and Noggin or RGMc were pre-incubated for 3 hour at 20C prior to treatment of Hep3B cells.  Treatment of cells was 4 hours prior to RNA extraction.

value: hepatoma

tag: agent

value: BMP6 and RGMc


title: MCF-7/LTED, rep 3

source_name: MCF-7/LTED cells

value: yes


title: ZR75-1, rep 1


title: liver cells_bmp6-rgmc_rep2

source_name: Hep3B cells treated with BMP6 and RGMc for 4 hours


title: Malignant mesothelioma, Y-MESO-9

description: Malignant mesotehlioma cell line

value: Normal human genomic DNA purchased from Promega

source_name: Malignant mesothelioma, Y-MESO-9

value: Human malignant pleural mesothelioma cell line, Y-MESO-9


title: Malignant mesothelioma, Y-MESO-8D

description: Malignant mesotehlioma cell line

source_name: Malignant mesothelioma cell line

value: Human malignant pleural mesothelioma cell line, Y-MESO-8D


title: liver cells_bmp6-noggin_rep2

description: Gene expression data from Hep3B cells treated with BMP6 and Noggin for 4 hours.

value: BMP6 and Noggin


title: MCF-7/LTED, rep 2


title: Malignant mesothelioma, Y-MESO-27

description: Malignant mesotehlioma cell line

source_name: Pooled normal genomic DNA, Male

source_name: Y-MESO-27 genomic DNA

value: Human malignant pleural mesothelioma cell line, Y-MESO-27


title: MCF-7/LTED, rep 1


title: Malignant mesothelioma, ACC-MESO-4

description: Malignant mesotehlioma cell line

label_protocol: The samples were labeled using the Agilent Genomic DNA Labeling Kit PLUS according to manufacture's instructions. DNA was fragmented using restriction enzymes. Random hexamers were used to prim an Exo-Klenow fragment DNA polymerase reaction incorporating CyDye labeled dUTP

source_name: ACC-MESO-4 genomic DNA

value: Human malignant pleural mesothelioma cell line, ACC-MESO-4


title: liver cells_bmp6-noggin_rep1

source_name: Hep3B cells treated with BMP6 and Noggin for 4 hours


title: MCF-7, rep 3

source_name: MCF-7 cells


title: Malignant mesothelioma, ACC-MESO-1

description: Malignant mesotehlioma cell line

source_name: ACC-MESO-1 genomic DNA

value: Human malignant pleural mesothelioma cell line, ACC-MESO-1


title: liver cells_bmp2-rgmc_rep1

description: Gene expression data from Hep3B cells treated with BMP2 and RGMc for 4 hours.

value: BMP2 and RGMc


title: liver cells_bmp6_rep1

description: Gene expression data from Hep3B cells treated with BMP6 for 4 hours.


title: Hybridization of H630-cTFT vs H630 (dye swap)

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description: Expression analysis of parental H630 cell line vs TFT-resistant cell line.

hyb_protocol: cDNA was incubated at room temperature for 1 hour with fluorolink monofunctional Cy5 or Cy3 dye (Amersham, Roosendaal, The Netherlands) followed by 15 minutes of 4 mol/L hydroxylamine treatment. Uncoupled dyes were removed using Qiaquick PCR purification columns (Qiagen, Leusden, The Netherlands) and mixed with 12 µg poly(dA) (Amersham), 60 µg yeast tRNA (Sigma-Aldrich Chemie, Zwijndrecht, The Netherlands), and 24 µg Cot-1 DNA (Invitrogen). The labeled target was dissolved in 127-µL hybridization mixture containing 46% formamide (Invitrogen), 9.5% dextran sulfate (U.S. Biochemical Corp., Cleveland, USA), 2x SSC, and 0.2% SDS. The labeled target was heated to 70°C for 10 minutes and annealed at 37°C for 1 hour. Slides were hybridized at 37°C overnight (14h). After hybridization, the slides were washed in the HybArray 12, with 50% formamide (Fluka, Sigma-Aldrich Chemie), 2x SSC (pH 7) at 35°C for 15 minutes followed by PI buffer (0.1 mol/L sodium phosphate, 0.1% Igepal Ca630 (pH 8)) at room temperature and three washes of 0.2x SSC, 0.1x SSC, and 0.01x SSC at room temperature followed by centrifugation.

scan_protocol: Arrays were scanned using a laser scanner (ScanArray Express, PerkinElmer, Zaventem, Belgium).

data_processing:
Spot analysis and quality control were fully automated using BlueFuse version 2.0 (BlueGnome, Cambridge, UK).
The intensity values were corrected for the mean intensity of the array, by dividing the intensity by the mean intensity. Ratios were calculated by dividing the intensity of the resistant cell line by that of the parental cell line. For expression array pathway analysis, log2 values of the ratios were used.

label_protocol: Single stranded cDNA was synthesized from 30 µg of total RNA by reverse transcription using aminoallyl-labeled dUTP (Ambion Ltd., Huntingdon, UK). Labeling with fluorolink monofunctional Cy5 or Cy3 dye (Amersham, Roosendaal, The Netherlands) was described in detail previously . Qiaquick PCR purification columns (Qiagen, Westburg B.V., Leusden, The Netherlands) were used to remove the uncoupled dyes.

growth_protocol: H630-cTFT was acquired by exposing H630 cells continuously to stepwise increasing concentrations of TFT, starting at 0.5 µM over a period of 12 months. This resulted in the cell line H630-cTFT that is cultured in 20 µM TFT and has an IC50 concentration of 168 µM TFT.

extract_protocol: Total RNA isolations from separate harvests of cells were performed using the TriZol method according to the manufacturer's protocol (Invitrogen, Leek, The Netherlands).

tag: cell line description

value: acquired by exposing H630 cells continuously to TFT

value: derived from a human colorectal carcinoma


title: liver cells_bmp2-rgmc_rep2

source_name: Hep3B cells treated with BMP2 and RGMc for 4 hours


title: Wild-type_liver rep3

city: Ibaraki

first: Katsutaka

last: Oishi

address: Tsukuba

institute: AIST

description: Gene expression data from Wild_type_mouse_liver

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Preprocessing for the probe level data was performed using robust multi-array analysis (RMA) algorithm to obtain expression level data.

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3' IVT Express Kit (Affymetrix) from 250ng total RNA.

extract_protocol: Total RNA (250 ng) was extracted using RNAiso (Takara Bio Inc., Otsu, Japan).

tag: genotype/variation

value: wild type (with Jcl:ICR background)

value: 6-12 weeks

tag: gender

value: male

value: control


title: liver cells_bmp2_rep2

description: Gene expression data from Hep3B cells treated with BMP2 for 4 hours.

value: hepatoma


title: liver cells_untreated_rep1

description: Gene expression data from untreated Hep3B cells.

source_name: untreated Hep3B cells


title: liver cells_bmp2-noggin_rep2

description: Gene expression data from Hep3B cells treated with BMP2 and Noggin for 4 hours.

value: BMP2 and Noggin


title: Wild-type_liver rep1


title: liver cells_bmp2-noggin_rep1

source_name: Hep3B cells treated with BMP2 and Noggin for 4 hours


title: MCF-7, rep 2

value: breast cancer

value: no


title: liver cells_untreated_rep2


title: liver cells_bmp6_rep2

source_name: Hep3B cells treated with BMP6 for 4 hours


title: Wild-type_liver_bezafibrate-treated_5days rep3

description: Gene expression data from Wild_type_mouse_liver_treated_with_bezafibrate

value: bezafibrate


title: liver cells_bmp2_rep1

source_name: Hep3B cells treated with BMP2 for 4 hours


title: Hybridization of H630-cTFT vs H630


title: MCF-7, rep 1


title: Wild-type_liver_bezafibrate-treated_5days rep2


title: Wild-type_liver rep2


title: cone at T165, biological rep1

city: Basel

first: Erik

last: Cabuy

address: Maulbeerstrasse 66

department: Single Cell Genomics

country: Switzerland

institute: Friedrich Miescher Institute

description: Gene expression data of 300 FACSed RD cones at 165 days

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 7000 7G (Affymetrix).

data_processing: The CEL files were aquired using the GeneChip Command Console (Affymetrix). Quality control and gene expression value estimates were obtained after RMA and quantile normalization in R (Bioconductor 'Affy' package).

source_name: Mouse retinal cones, dissected after 165 days

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from 8 ug total RNA (Expression Analysis Technical Manual, 2005, Rev2 and GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual, Rev4, Affymetrix).

growth_protocol: All animal experiments and procedures were approved by the Swiss Veterinary Office. The animals were maintained under a 12-hour light-dark cycle.

extract_protocol: Extraction of total RNA was performed according to the PicoPure RNA Isolation kit manufacturer's instructions.

treatment_protocol: AAVs were subretinally administrated in P21-28 old mice. Mice were kept until indicated ages and used for gene array experiments.

tag: mouse model

value: f-RD

tag: tissue

value: retina

value: RD cone photoreceptors

value: C3H/HeNCrl (Pde6brd1)

value: 165 days

tag: treatment protocol

value: mCAR-eNpHR-EYFP


title: Malignant mesothelioma, Y-MESO-14

description: Malignant mesotehlioma cell line

value: Normal human genomic DNA purchased from Promega

source_name: Y-MESO-14 genomic DNA

value: Human malignant pleural mesothelioma cell line, Y-MESO-14


title: cone at T165, biological rep2

tag: strain


title: PPARalpha-null_liver_bezafibrate-treated_5days rep3

description: Gene expression data from PPARalpha-null_mouse_liver

value: PPARalpha-null (crossed 129S4SvJae-PPARalphatm1Gonz/J with Jcl:ICR)


title: Wild-type_liver_bezafibrate-treated_5days rep1

value: wild type (with Jcl:ICR background)

value: 6-12 weeks


title: Hybridization of H630-4TFT vs H630

growth_protocol: H630-4TFT was acquired by exposing H630 cells intermittently (4 hr exposure every 7 days) to TFT, starting at 5 µM TFT in a period of 12 months. This resulted in the cell line H630-4TFT that is cultured in 250 µM TFT 4hr/weekly and has an IC50 concentration of 660 µM TFT.

value: acquired by exposing H630 cells intermittently to TFT

value: derived from a human colorectal carcinoma


title: Hybridization of H630-4TFT vs H630 (dye swap)


title: cone at T165, biological rep3


title: cone at T220, biological rep4

description: Gene expression data of 500 FACSed RD cones at 220 days

source_name: Mouse retinal cones, dissected after 220 days

value: 220 days

value: mCAR-EGFP


title: cone at T165, biological rep4


title: wt 1.5 month old (C21)

description: Gene Expression Data

source_name: flow-sorted rod photoreceptors

value: Nrlp-EGFP

value: rod photoreceptors

value: 1.5 months


title: PPARalpha-null_liver_bezafibrate-treated_5days rep2

value: male

value: bezafibrate


title: PPARalpha-null_liver_bezafibrate-treated_5days rep1


title: cone at T220, biological rep2

value: f-RD

value: retina

value: RD cone photoreceptors

value: C3H/HeNCrl (Pde6brd1)


title: cone at T110, biological rep4

description: Gene expression data of 500 FACSed RD cones at 110 days

source_name: Mouse retinal cones, dissected after 110 days

value: 110 days


title: Clock_mutant_liver_bezafibrate-treated_5days rep2

description: Gene expression data from Clock_mutant_mouse_liver

value: Clk/Clk mutant (with Jcl:ICR background)


title: cone at T220, biological rep3


title: cone at T110, biological rep2


title: cone at T220, biological rep1


title: non-specific targeted control siRNA transfected MDA-MB-231 cells

city: Aarhus

first: Zhangle

last: Zhou

address: Wilhelm Meyers Allé 4

department: Human Genetics

country: Denmark

institute: Aarhus University

description: control siRNA treated sample

hyb_protocol: Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining.

scan_protocol: HumanWG-6 Expression BeadChips are scanned on the Illumina BeadArray Reader.

data_processing:
BeadStudio software Gene Expression module version 3.2.7 in quantile normalization was used.
Fluorescence emission by Cy3 is quantitatively detected for downstream analysis. The BeadStudio software extracted gene expression data from images collected from the Illumina BeadArray Reader. The BeadStudio application executes data analysis of Differential Analysis-Determining if gene expression levels have changed between two experimental groups. Resulting files can be exported to most standard databases and gene expression analysis programs.
Differential Expression Algorithms were used to compare the condition group to the reference group by the model of Illumina Custom. Compute the p value and differential score 'Diff Score', DiffScore =(10sgn(I cond – I ref)log10(p)). The diff score of 13 corresponds to a p-value of 0.05, the diff score of 20 corresponds to a p-value of 0.01, and the diff score of 30 corresponds to a p-value of 0.001. A positive diff score represents up regulation, while negative represents down regulation.

source_name: Human breast cancer cell line MDA-MB-231

label_protocol: Illumina Gene Expression protocols applied a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides.

growth_protocol: the cell lines were grown in Dulbecco’s modified Eagle medium (Invitrogen) supplemented with 10% fetal calf serum (FCS) and penicillin and streptomycin.

extract_protocol: RNA extraction was performed with TRI-reagent (Sigma) according to the manufacturer’s instructions.

treatment_protocol: MDA-MB-231 cells were transfected with TransIT-siQUEST® Transfection Reagent (MIR2110) according to the protocol provided by the manufacturer. Cells were seeded into a 6-well plate to obtain 25% confluence on the following day.  4 μl of the TransIT-siQUEST Transfection Reagent was diluted into 250 μl serum-free media, mixed thoroughly by pipetting. Then 20 nM NSD3L directed siRNA 5’-AUUAGUUACACUGUUCUCGUG (dTdT)-3’ was added to the diluted TransIT-siQUEST Reagent, using nonspecifically targeted siRNA 5’-AGGUAGUGUAAUCGCCUUG (dTdT)-3’ as negative control. The complex was mixed by gentle pipetting and incubated at room temperature for 20 min. The TransIT-siQUEST Reagent/siRNA complex mixture was then added to cultured cells containing 1250 μl complete medium. After 48 h incubation, the siRNA was transfected again and incubated for another 48 h. Cells were collected and RNA was purified.

value: High-invasive human breast cancer cell line

tag: sirna

value: non-specific targeted control siRNA


title: cone at T110, biological rep1


title: Clock_mutant_liver_bezafibrate-treated_5days rep3

value: 6-12 weeks


title: Prostate testosterone 3 day rep6

status: Public on Jun 14 2010

first: Simon

last: Hayward

department: Urologic Surgery

institute: Vanderbilt University Medical Center

hyb_protocol: After hybridization, the arrays were washed in 2X SSC/0.1% SDS at 55° C with agitation for 5 minutes then washed with two successive 5 minute washes with 1x SSC and 0.1xSSC at RT.

scan_protocol: The washed arrays were dried by centrifugation at 50xg for 5 minutes and immediately scanned using a GenePix 4000B microarray scanner [Axon Instruments, Union City, CA].

data_processing: Due to the considerable variation inherent in individual patients, the time 0 for each tissue sample was used as the control or reference sample rather than a standard reference sample across the entire experiment. Data were normalized by Lowess. Day 0 vs. day 0 pool of 6 reference have normalized ratios set to 1

source_name: human prostate in testosterone-treated mouse, 3 day

label_protocol: Dried-down targets were then resuspended in 50ul of MWG Hyb Buffer (Ocimum Biosolutions, cat#1180-200000) and 1 ug of Poly A RNA (Sigma, P9403) was added to each target. The targets were heat denatured and then hybridized 16 hours at 42C on a Maui Hyb Station.

extract_protocol: RNA was extracted using TRIzol (Life Technologies, Inc., Gaithersburg, MD), followed by a second RNA isolation using RNeasy (Qiagen Inc., Valencia, CA) with DNAse treatment. Microarray services were performed by the Vanderbilt Microarray Shared Resource.

treatment_protocol: 6mm diameter cores obtained intraoperatively from fresh RP specimens were procured from the right and left TZ and PZ from mid to base and from mid to apex and histologic analysis was performed on frozen sections of full thickness cross sections.

tag: treatment

value: intact, +testosterone

tag: time (days)

value: prostate xenograft

source_name: pool of 6 samples of human prostate in castrated mouse, 0 day

value: castrated

tag: time


title: Prostate testosterone 14 day rep6

source_name: human prostate in testosterone-treated mouse, 14 day


title: Prostate testosterone 14 day rep5


title: Prostate testosterone 1 day rep6

source_name: human prostate in testosterone-treated mouse, 1 day


title: Prostate testosterone 7 day rep5

source_name: human prostate in testosterone-treated mouse, 7 day


title: Prostate testosterone 7 day rep3


title: NSD3L-directed siRNA transfected MDA-MB-231 cells

description: target siRNA treated sample

tag: cell type

tag: cell line

value: NSD3L-directed siRNA


title: Prostate testosterone 7 day rep6


title: Prostate testosterone 0 day rep5

source_name: human prostate in testosterone-treated mouse, 0 day


title: Prostate testosterone 7 day rep4


title: Prostate testosterone 3 day rep5


title: Prostate testosterone 1 day rep4


title: Prostate testosterone 1 day rep5


title: Prostate testosterone 0 day rep4


title: Clock_mutant_liver_bezafibrate-treated_5days rep1

tag: age


title: Prostate testosterone 3 day rep3


title: Prostate testosterone 14 day rep4


title: Prostate testosterone 3 day rep4


title: Prostate testosterone 14 day rep3


title: Prostate testosterone 0 day rep3


title: Prostate testosterone 1 day rep2


title: Prostate testosterone 1 day rep3


title: Prostate testosterone 3 day rep2


title: Prostate testosterone 7 day rep2


title: Prostate testosterone 0 day rep2


title: Prostate castrated 14 day rep6

source_name: human prostate in castrated mouse, 14 day


title: Prostate testosterone 1 day rep1


title: Prostate testosterone 3 day rep1


title: Prostate castrated 1 day rep6

source_name: human prostate in castrated mouse, 1 day


title: Prostate castrated 14 day rep4


title: Prostate testosterone 0 day rep1


title: Prostate testosterone 14 day rep1


title: Prostate castrated 0 day rep5

source_name: human prostate in castrated mouse, 0 day


title: Prostate testosterone 7 day rep1

source_name: human prostate in testosterone-treated mouse, 7day


title: Prostate castrated 1 day rep4


title: Prostate castrated 14 day rep5


title: Prostate castrated 7 day rep6

source_name: human prostate in castrated mouse, 7 day


title: Prostate castrated 0 day rep6


title: Prostate castrated 1 day rep5


title: Prostate castrated 0 day rep4


title: Prostate castrated 7 day rep5


title: Prostate castrated 7 day rep4


title: Prostate testosterone 14 day rep2


title: Prostate castrated 14 day rep2


title: Prostate castrated 1 day rep3


title: Prostate castrated 7 day rep3


title: Prostate castrated 3 day rep4

source_name: human prostate in castrated mouse, 3 day


title: Prostate castrated 0 day rep3


title: Prostate castrated 3 day rep2


title: Prostate castrated 1 day rep2


title: Prostate castrated 14 day rep3


title: Prostate castrated 7 day rep2


title: NSC_FBS_V3

city: Boston

first: Haoqiang

last: Ying

state: MA

address: 44 Binney St.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 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.

data_processing: Arrays were normalized using MAS5.

source_name: p53-null NSC, vector

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

extract_protocol: Trizol extraction of total RNA followed by Rneasy column cleanup was performed according to the manufacturer's instructions.

treatment_protocol: p53-null NSCs were infected with retrovirus expressing either control vector or PlagL2, and cultured in 1% FBS for 24 hr.

value: primary p53-null neural stem cells

tag: retroviral expression

value: vector


title: NSC_FBS_L3

source_name: p53-null NSC, PlagL2


title: Prostate testosterone 0 day rep6


title: NSC_FBS_L2


title: Prostate castrated 14 day rep1


title: Subject 200

first: Benjamin

middle: A

last: Raby

address: 181 Longwood Avenue

institute: Channing Laboratory

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Arrays were read using the BeadArray scanner (Illumina) and analyzed using BeadStudio (version 3.1.7) without background correction. Raw expression intensities were processed using the lumi package  with background adjustment with RMA convolution of each array followed by VSN normalization.

source_name: primary peripheral blood CD4+ lymphocytes

label_protocol: Standard Illumina label protcol

extract_protocol: Total RNA was extracted using the RNeasy Mini Protocol

tag: subject

value: Subject 200

tag: disease state

value: asthma

value: peripheral blood

value: CD4+ lymphocyte

tag: sex

value: M


title: Prostate castrated 0 day rep2


title: Subject 195

value: Subject 195


title: Prostate castrated 3 day rep1


title: Prostate castrated 7 day rep1


title: Subject 197

value: Subject 197


title: Subject 199

value: Subject 199

value: F


title: Subject 194

value: Subject 194


title: Subject 193

value: Subject 193


title: Subject 192

value: Subject 192


title: NSC_FBS_L1


title: Subject 196

value: Subject 196


title: Prostate castrated 0 day rep1

value: castrated

value: prostate xenograft


title: Subject 198

value: Subject 198


title: Subject 189

value: Subject 189


title: Subject 191

value: Subject 191


title: Prostate castrated 3 day rep3


title: Subject 188

value: Subject 188

value: asthma


title: Prostate castrated 1 day rep1


title: Subject 187

value: Subject 187

value: peripheral blood

value: CD4+ lymphocyte


title: Subject 182

value: Subject 182


title: NSC_FBS_V1

value: primary p53-null neural stem cells

value: vector


title: cone at T110, biological rep3

source_name: Mouse retinal cones, dissected after 110 days

value: f-RD

value: retina

value: RD cone photoreceptors

tag: genotype/variation

value: C3H/HeNCrl (Pde6brd1)

value: 110 days

value: mCAR-EGFP


title: Subject 183

value: Subject 183

value: M


title: Subject 184

value: Subject 184


title: Subject 181

value: Subject 181

value: F


title: Subject 176

value: Subject 176

value: asthma


title: Subject 171

value: Subject 171

value: peripheral blood

value: CD4+ lymphocyte


title: Subject 175

value: Subject 175


title: Subject 179

value: Subject 179


title: Subject 177

value: Subject 177


title: Subject 166

value: Subject 166


title: Subject 167

value: Subject 167


title: Subject 169

value: Subject 169


title: Subject 178

value: Subject 178


title: Subject 174

value: Subject 174


title: Subject 165

value: Subject 165


title: Subject 190

value: Subject 190


title: NSC_FBS_V2

value: primary p53-null neural stem cells

value: vector


title: Subject 180

value: Subject 180

value: M


title: Subject 168

value: Subject 168

value: asthma


title: Subject 186

value: Subject 186

value: peripheral blood

value: CD4+ lymphocyte


title: Subject 185

value: Subject 185


title: Subject 163

value: Subject 163


title: Subject 173

value: Subject 173

value: F


title: Subject 170

value: Subject 170


title: Subject 172

value: Subject 172


title: Subject 161

value: Subject 161


title: Subject 162

value: Subject 162


title: Subject 154

value: Subject 154


title: Subject 164

value: Subject 164


title: Subject 158

value: Subject 158


title: Subject 155

value: Subject 155


title: Subject 151

value: Subject 151

value: M


title: Subject 150

value: Subject 150

value: asthma


title: Subject 145

value: Subject 145

value: peripheral blood

value: CD4+ lymphocyte


title: Subject 147

value: Subject 147


title: Subject 143

value: Subject 143


title: Subject 144

value: Subject 144


title: Subject 141

value: Subject 141


title: Subject 153

value: Subject 153


title: Subject 148

value: Subject 148


title: Subject 157

value: Subject 157

value: F


title: Subject 152

value: Subject 152


title: Subject 142

value: Subject 142


title: Subject 146

value: Subject 146


title: Subject 160

value: Subject 160

value: M


title: Subject 156

value: Subject 156

value: asthma


title: Subject 149

value: Subject 149

value: peripheral blood


title: Subject 140

value: Subject 140

value: CD4+ lymphocyte


title: Subject 139

value: Subject 139


title: Subject 138

value: Subject 138


title: Subject 136

value: Subject 136


title: Subject 134

value: Subject 134


title: Subject 137

value: Subject 137


title: Subject 135

value: Subject 135


title: Subject 129

value: Subject 129


title: Subject 123

value: Subject 123


title: Subject 124

value: Subject 124


title: Subject 131

value: Subject 131

value: F


title: Subject 125

value: Subject 125


title: Subject 133

value: Subject 133

value: asthma


title: Subject 126

value: Subject 126

value: peripheral blood

value: M


title: Subject 128

value: Subject 128

value: CD4+ lymphocyte


title: Subject 132

value: Subject 132


title: Subject 117

value: Subject 117


title: Subject 119

value: Subject 119


title: Subject 118

value: Subject 118


title: Subject 121

value: Subject 121


title: Subject 114

value: Subject 114


title: Subject 127

value: Subject 127


title: Subject 113

value: Subject 113


title: Subject 130

value: Subject 130


title: Subject 120

value: Subject 120


title: Subject 116

value: Subject 116


title: Subject 122

value: Subject 122

value: asthma


title: Subject 111

value: Subject 111

value: peripheral blood


title: Subject 112

value: Subject 112

value: M


title: Subject 159

value: Subject 159

value: CD4+ lymphocyte


title: Subject 115

value: Subject 115


title: Subject 110

value: Subject 110


title: Subject 106

value: Subject 106


title: Subject 109

value: Subject 109


title: Subject 107

value: Subject 107


title: Subject 105

value: Subject 105


title: Subject 100

value: Subject 100


title: Subject 95

value: Subject 95

value: F


title: Subject 102

value: Subject 102


title: Subject 92

value: Subject 92

value: asthma


title: Subject 108

value: Subject 108

value: peripheral blood


title: Subject 101

value: Subject 101

value: M


title: Subject 97

value: Subject 97

value: CD4+ lymphocyte


title: Subject 96

value: Subject 96


title: Subject 103

value: Subject 103


title: Subject 90

value: Subject 90


title: Subject 91

value: Subject 91


title: Subject 87

value: Subject 87


title: Subject 84

value: Subject 84


title: Subject 85

value: Subject 85


title: Subject 99

value: Subject 99


title: Subject 104

value: Subject 104


title: Subject 98

value: Subject 98


title: Subject 93

value: Subject 93

value: asthma

value: F


title: Subject 88

value: Subject 88

value: peripheral blood


title: Subject 81

value: Subject 81

value: M


title: Subject 82

value: Subject 82

value: CD4+ lymphocyte


title: Subject 89

value: Subject 89


title: Subject 94

value: Subject 94


title: Subject 83

value: Subject 83


title: Subject 80

value: Subject 80


title: Subject 72

value: Subject 72


title: Subject 74

value: Subject 74


title: Subject 79

value: Subject 79


title: Subject 64

value: Subject 64


title: Subject 68

value: Subject 68


title: Subject 65

value: Subject 65

value: asthma


title: Subject 66

value: Subject 66


title: Subject 77

value: Subject 77

value: peripheral blood


title: Subject 78

value: Subject 78

value: M


title: Subject 86

value: Subject 86

value: CD4+ lymphocyte


title: Subject 76

value: Subject 76


title: Subject 73

value: Subject 73


title: Subject 67

value: Subject 67


title: Subject 63

value: Subject 63

value: F


title: Subject 70

value: Subject 70


title: Subject 69

value: Subject 69


title: Subject 75

value: Subject 75


title: Subject 60

value: Subject 60


title: Subject 57

value: Subject 57

value: asthma


title: Subject 62

value: Subject 62


title: Subject 55

value: Subject 55

value: peripheral blood


title: Subject 61

value: Subject 61

value: M


title: Subject 56

value: Subject 56

value: CD4+ lymphocyte


title: Subject 71

value: Subject 71


title: Subject 54

value: Subject 54


title: Subject 58

value: Subject 58


title: Subject 59

value: Subject 59


title: Subject 53

value: Subject 53


title: Subject 47

value: Subject 47

value: F


title: Subject 44

value: Subject 44


title: Subject 43

value: Subject 43


title: Subject 46

value: Subject 46

value: asthma


title: Subject 35

value: Subject 35


title: Subject 49

value: Subject 49

value: peripheral blood


title: Subject 41

value: Subject 41

value: M


title: Subject 48

value: Subject 48

value: CD4+ lymphocyte


title: Subject 50

value: Subject 50


title: Subject 52

value: Subject 52


title: Subject 40

value: Subject 40


title: Subject 51

value: Subject 51


title: Subject 39

value: Subject 39


title: Subject 36

value: Subject 36

value: F


title: Subject 38

value: Subject 38


title: Subject 45

value: Subject 45


title: Subject 34

value: Subject 34

value: asthma


title: Subject 31

value: Subject 31


title: Subject 37

value: Subject 37

value: peripheral blood


title: Subject 30

value: Subject 30

value: M


title: Subject 33

value: Subject 33

value: CD4+ lymphocyte


title: Subject 32

value: Subject 32


title: Subject 42

value: Subject 42


title: Subject 29

value: Subject 29


title: Subject 28

value: Subject 28


title: Subject 24

value: Subject 24


title: Subject 25

value: Subject 25


title: Subject 27

value: Subject 27

value: F


title: Subject 23

value: Subject 23


title: Subject 26

value: Subject 26

value: asthma


title: Subject 21

value: Subject 21


title: Subject 18

value: Subject 18

value: peripheral blood


title: Subject 22

value: Subject 22


title: Subject 19

value: Subject 19

value: M


title: Subject 20

value: Subject 20

value: CD4+ lymphocyte


title: SW480, treated with Wortmannin

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

country: Germany

institute: BIH at Charité

description: Gene expression data from SW480 cells treated with Wortmanin for 48 hours

hyb_protocol: Hybridization and post-hybridization procedures were performed according to protocols provided by Affymetrix.

scan_protocol: Arrays were scanned twice at 3µm resolution using a confocal argon laser scanner (Hewlett-Packard, Santa Clara, CA), controlled by Microarray Suite 5.0 software (Affymetrix). Photoemission was detected by a photomultiplier tube through a 570-nm long-pass filter.

data_processing: Computer-generated array images were overlayed with a virtual grid, controlled by Microarray Suite 5.0 software. About 40 pixels within each feature were averaged after discarding outliers and pixels close to feature boundaries.

source_name: SW480 cell line

label_protocol: Labelling of RNA targets were performed according to protocols provided by Affymetrix.

growth_protocol: SW480, HT29 and HCT116 cells were cultured in complete L-15 medium at 37 °C and 5% CO2 in a humified incubator.

treatment_protocol: After 24 hours, the cells were treated once with the indicated inhibitors for 48 hours.

value: colorectal cancer

tag: genotype

value: aneuploid

value: passage not known


title: HT29, treated with SH6

description: Gene expression data from HT29 cells treated with SH6 for 48 hours

source_name: HT29 cell line


title: SW480, treated with Ly294001

description: Gene expression data from SW480 cells treated with LY294001 for 48 hours


title: SW480, treated with SH6

description: Gene expression data from SW480 cells treated with SH6 for 48 hours


title: SW480, treated with DMSO

description: Gene expression data from SW480 cells treated with DMSO for 48 hours (control)


title: Subject 17

value: Subject 17


title: Subject 16

value: Subject 16


title: HCT116, treated with SH6

description: Gene expression data from HCT116 cells treated with SH6 for 48 hours

source_name: HCT116 cell line

value: pseudo diploid


title: SW480, treated with SH5

description: Gene expression data from SW480 cells treated with SH-5 for 48 hours


title: HT29, treated with DMSO

description: Gene expression data from HT29 cells treated with DMSO for 48 hours (control)


title: HT29, treated with Wortmannin

description: Gene expression data from HT29 cells treated with Wortmanin for 48 hours


title: HT29, treated with Ly294001

description: Gene expression data from HT29 cells treated with LY294001 for 48 hours


title: Subject 14

value: Subject 14

value: F


title: Subject 13

value: Subject 13

value: asthma


title: HCT116, treated with DMSO

description: Gene expression data from HCT116 cells treated with DMSO for 48 hours (control)


title: Subject 10

value: Subject 10


title: HCT116, treated with Wortmannin

description: Gene expression data from HCT116 cells treated with Wortmanin for 48 hours


title: Subject 11

value: Subject 11

value: peripheral blood


title: HCT116, treated with SH5

description: Gene expression data from HCT116 cells treated with SH-5 for 48 hours


title: Subject 15

value: Subject 15


title: HCT116, treated with Ly294001

description: Gene expression data from HCT116 cells treated with LY294001 for 48 hours


title: HT29, treated with SH5

description: Gene expression data from HT29 cells treated with SH-5 for 48 hours


title: Subject 9

value: Subject 9


title: Subject 8

value: Subject 8


title: Subject 12

value: Subject 12

value: CD4+ lymphocyte

value: M


title: Subject 7

value: Subject 7


title: Subject 6

value: Subject 6


title: Subject 1

value: Subject 1


title: Subject 4

value: Subject 4


title: MEP rep1

status: Public on Jun 13 2010

city: Toronto

first: Kolja

last: Eppert

state: Ontario

address: 101 College St., rm 8-301

country: Canada

institute: University Health Network

description: replicate 1

scan_protocol: Scanned with Illumina’s BeadArray Reader using standard protocols

data_processing: The data were normalised using quantile normalisation in GeneSpring GX10.0.2

source_name: MEP

label_protocol: cRNA was prepared using Ambion - Illumina TotalPrep-96 RNA Amplification Kit

extract_protocol: RNA was extracted using Trizol reagent

value: umbilical cord blood

value: MEP


title: GMP rep1

description: replicate 1

source_name: GMP

value: GMP


title: Subject 5

value: Subject 5

value: asthma


title: Subject 2

value: Subject 2

value: F


title: MEP rep2

description: replicate 2


title: Subject 3

value: Subject 3

value: peripheral blood


title: MLP rep2

description: replicate 2

source_name: MLP

value: MLP


title: CMP rep2

description: replicate 2

source_name: CMP

value: CMP


title: MPP rep2

description: replicate 2

source_name: MPP

value: MPP


title: MLP rep1

description: replicate 1


title: CMP rep3

description: replicate 3


title: GMP rep2

description: replicate 2


title: MPP rep1

description: replicate 1


title: E2A-/- pre-pro-B cell expression rep2

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

institute: University of California, San Diego (UCSD)

description:
Replicates of B cell expression arrested at different developemental stages (untreated).
raw data file: US22502657_251486819907_S01_GE2-v5_95_Feb07_1_2.txt

hyb_protocol: 4x 44 k Agilent arrays were hybridized with 825 ng of each cDNA using the manufacturer's hybridization kit according to the instructions.

scan_protocol: Scanned on an Agilent Technologies Scanner using the extended dynamic range scan mode with a 5 µm pitch. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. Data was further normalized between arrays using a multi-loess technique described in Corbeil et al (Journal of Molecular Endocrinology (2004) 33:1–9). Each channel of this dual-channel hybridization experiment was analyzed separately and two of the channels were not used, so two raw data files are associated with two of the samples in this study.

source_name: E2A-/- pre-pro-B cells

label_protocol: Total RNA (250 ng) of two replicates was amplified and labeled using the Agilent Quick-Amp labeling kit according to the manufacturer's instructions.

growth_protocol: E2A-/-and EBF-/- pre-pro-B cells were cultured on S17 stromal cells in the presence of IL7, SCF, and FLT3 ligand in Iscove’s Modified Dulbecco’s medium and in the presence of 10% FCS, penicillin, streptomycin and L-glutamine. Pro-B cells were isolated from femoral bone marrow of Rag1 knockout mice by positive enrichment of B220+ cells using magnetic separation (Miltenyi) and expanded for 10 d in Opti-MEM medium containing 10% FCS, 2x penicillin/streptomycin/glutamine, and 50 µM ß-mercaptoethanol supplemented with IL-7 and SCF.

extract_protocol: Total RNA was extracted from 5 Mio cells on RNeasy columns (Qiagen) with on-column DNase digestion following the manufacturer's instructions. RNA quality was assessed on an Agilent 2100 BioAnalyzer .

value: E2A-/- pre-pro-B cells

tag: genetic background


title: MLP rep3

description: replicate 3

tag: tissue


title: CMP rep1

description: replicate 1


title: HSC rep3

description: replicate 3

source_name: HSC

value: HSC


title: HSC rep2

description: replicate 2


title: RAG1-/- pro-B cell expression rep2

description:
Replicates of B cell expression arrested at different developemental stages (untreated).
raw data file: US22502657_251486819907_S01_GE2-v5_95_Feb07_1_4.txt

source_name: RAG1-/- proB cells

value: RAG1-/- pro-B cells


title: EBF-/- pre-pro-B cell expression rep2

description:
Replicates of B cell expression arrested at different developemental stages (untreated).
raw data file: US22502657_251486819907_S01_GE2-v5_95_Feb07_1_3.txt

source_name: EBF-/- pre-pro-B cells

value: EBF-/- pre-pro-B cells

value: EBF-/-


title: MPP rep3

description: replicate 3

value: umbilical cord blood


title: EBF-/- pre-pro-B cell expression rep1

source_name: EBF-/- pre-proB cells


title: E2A-/- pre-pro-B cell expression rep1

description:
Replicates of B cell expression arrested at different developemental stages (untreated).
raw data file: US22502657_251486819907_S01_GE2-v5_95_Feb07_1_1.txt

source_name: E2A-/- pre-proB cells


title: DRGs: sciatic nerve entrapment 6 months and decompression 3 months exp rep 2

status: Public on Jun 12 2010

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: Experimental replicate 2 of DRGs  after sciatic nerve entrapment 6 months and decomrpession 3 months

hyb_protocol: Scanned on an Agilent G2565AA scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.9.5.3).

data_processing: Agilent Feature Extraction Software (v 9.5.3) was used for background subtraction and LOWESS normalization.

organism: Rattus norvegicus

source_name: L4-L6 DRGs

label_protocol: The RNA from the experimental and control soleus muscle and DRGs were labeled with Cy3.

growth_protocol: The harvested DRGs and muscles were frozen in isopentane chilled in liquid nitrogen and stored at -80°C.

extract_protocol: 0.5 μg of total RNA was amplified using a Fluorescent Linear Amplification Kit (Agilent Technologies) and labeled with Cy3-CTP

treatment_protocol: Total RNA was extracted using the mirVana miRNA Isolation kit (Ambion, Austin, TX, USA) following manufacturer's instructions

value: Sprague-Dawley

tag: gender

value: male


title: DRGs: sciatic nerve entrapment 6 months and decompression 3 months exp rep 3

description: Experimental replicate 3 of DRGs  after sciatic nerve entrapment 6 months and decomrpession 3 months

tag: strain


title: DRGs: sham operation control

description: Biological replicate 1 of DRGs  as sham operation control


title: DRGs: sciatic nerve entrapment 6 months exp rep 3

description: Experimental replicate 3 of DRGs  after sciatic nerve entrapment 6 months


title: DRGs: sciatic nerve entrapment 6 months and decompression 3 months exp rep 1

description: Experimental replicate 1 of DRGs  after sciatic nerve entrapment 6 months and decomrpession 3 months


title: DRGs: sciatic nerve denervation 6 months exp rep 3

description: Experimental replicate 3 of DRGs  after sciatic nerve denervation 6 months


title: DRGs: sciatic nerve entrapment 6 months exp rep 1

description: Experimental replicate 1 of DRGs  after sciatic nerve entrapment 6 months


title: RAG1-/- pro-B cell expression rep1

source_name: RAG1-/- pro-B cells


title: DRGs: sciatic nerve denervation 6 months exp rep 2

description: Experimental replicate 2 of DRGs  after sciatic nerve denervation 6 months


title: DRGs: sciatic nerve denervation 6 months exp rep 1

description: Experimental replicate 1 of DRGs  after sciatic nerve denervation 6 months


title: HSC rep1

description: replicate 1


title: Soleus muscle: sciatic nerve entrapment 6 months and decompression 3 months exp rep 3

description: Experimental replicate 3 of Soleus muscle  after sciatic nerve entrapment 6 months and decomrpession 3 months

source_name: Soleus muscle


title: Soleus muscle: sciatic nerve entrapment 6 months and decompression 3 months exp rep 1

description: Experimental replicate 1 of Soleus muscle  after sciatic nerve entrapment 6 months and decomrpession 3 months


title: Soleus muscle: sham operation control

description: Biological replicate 1 of Soleus muscle as sham operation control


title: Soleus muscle: sciatic nerve denervation 6 months exp rep 1

description: Experimental replicate 1 of Soleus muscle  after sciatic nerve denervation 6 months


title: Soleus muscle: sciatic nerve entrapment 6 months exp rep 1

description: Experimental replicate 1 of Soleus muscle  after sciatic nerve entrapment 6 months


title: Soleus muscle: sciatic nerve entrapment 6 months exp rep 3

description: Experimental replicate 3 of Soleus muscle  after sciatic nerve entrapment 6 months


title: Soleus muscle: sciatic nerve denervation 6 months exp rep 2

description: Experimental replicate 2 of Soleus muscle  after sciatic nerve denervation 6 months


title: Soleus muscle: sciatic nerve denervation 6 months exp rep 3

description: Experimental replicate 3 of Soleus muscle  after sciatic nerve denervation 6 months


title: Soleus muscle: sciatic nerve entrapment 6 months exp rep 2

description: Experimental replicate 2 of Soleus muscle  after sciatic nerve entrapment 6 months


title: Neonatal cardiomyocytes-rep3

first: Masaki

last: Ieda

address: 1650 Owens street,

institute: Gladstone Institute

description: mouse cardiomyocytes

hyb_protocol: Performed according to the manufacturer's (Affymetrix) recommendations

data_processing: Raw intensities from the CEL files were analyzed using Affymetrix Power Tool (APT, version 1.8.5) to generate robust multi-array average intensity in log2 scale for each probe set. The perfect match intensities for each probe set were corrected for background and quantile-normalized using a robust fit of linear models.

source_name: mouse cardiomyocytes

label_protocol: Ambion MessageAmp II-biotin enhanced kit (manufacturer's recommendations)

extract_protocol: PicoPure RNA Isolation Kit (Arcturus)

value: Neonatal cardiomyocytes

tag: replicate


title: Neonatal cardiac fibroblasts-rep3

description: mouse cardiac fibroblast

scan_protocol: Performed according to the manufacturer's (Affymetrix) recommendations

source_name: mouse cardiac fibroblasts

value: Neonatal cardiac fibroblasts


title: Neonatal cardiac fibroblasts-rep1

description: mouse cardiac fibroblast


title: 4 week reprogramming failed GFP- cells-rep3

description: mouse reprogramming failed fibroblast

source_name: mouse reprogramming failed fibroblasts

value: 4 week reprogramming failed GFP- cells


title: Neonatal cardiomyocytes-rep1

description: mouse cardiomyocytes


title: 4 week iCMs-rep3

description: mouse reprogramming succeeded fibroblast

source_name: mouse iCMs

value: 4 week iCMs


title: Neonatal cardiac fibroblasts-rep2

description: mouse cardiac fibroblast


title: Neonatal cardiomyocytes-rep2

description: mouse cardiomyocytes


title: 4 week reprogramming failed GFP- cells-rep2

description: mouse reprogramming failed fibroblast


title: 4 week iCMs-rep2


title: 2 week iCMs-rep1

value: 2 week iCMs


title: 2 week iCMs-rep2


title: DRGs: sciatic nerve entrapment 6 months exp rep 2

description: Experimental replicate 2 of DRGs  after sciatic nerve entrapment 6 months


title: 2 week reprogramming failed GFP- cells-rep3

description: mouse reprogramming failed fibroblast

value: 2 week reprogramming failed GFP- cells


title: 2 week reprogramming failed GFP- cells-rep2

description: mouse reprogramming failed fibroblast


title: 2 week iCMs-rep3


title: 2 week reprogramming failed GFP- cells-rep1

description: mouse reprogramming failed fibroblast


title: 4 week reprogramming failed GFP- cells-rep1

description: mouse reprogramming failed fibroblast


title: 4 week iCMs-rep1


title: loaded-bone-32d-sample-rep2

city: Indianapolis

first: Charles

last: Turner

state: IN

address: 723 W. Michigan St. SL 220C

department: Biomedical Engineering

institute: Indiana University Purdue University Indiapanolis

description: exon expression data of loaded bone in rat

hyb_protocol: Labeled DNA were hybridized for 17 hr at 45C on Rat Exon 1.0 St Genechips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanned using Affymetrix GeneChip® Scanner 3000 7G

data_processing:
The data were analyzed with Partek Genomics Suite.  RMA was used to import raw data, and a 2-way ANOVA was used to identify differentially expressed transcripts.
probe_group_file: RaEx-1_0-st-v1.r2.pgf
meta-probeset_file: RaEx-1_0-st-v1.r2.dt1.rn4.core.mps

source_name: right forelimb (loaded) from rat

label_protocol: Biotinylated DNA were prepared according to the Affymetrix standard WT protocol using 1ug pretreated with Ribominus (Invitrogen)

extract_protocol: Trizol followed by Qiagen Rneasy and DNA-free kit (Ambion)

treatment_protocol: Right forelimb of each animal was loaded daily.  At the indicated time point (4h, 12h, 1d, 2d, 4d, 6d, 8d, 12d, 16d, 24d, or 32d) ulnae were dissected and snap frozen until RNA isolation.

value: bone (ulna)

tag: stimulation

value: loaded

tag: time point


title: control-bone-32d-sample-rep4

description: exon expression data of untreated bone in rat

source_name: left forelimb (untreated) from rat

value: control


title: loaded-bone-32d-sample-rep1


title: loaded-bone-32d-sample-rep4


title: control-bone-32d-sample-rep3


title: loaded-bone-32d-sample-rep3


title: 390608A02_2010-03-23

city: Rochester

first: Elena

last: Rustchenko

state: NY

address: 601 Elmwood Ave., Box 712

department: Biochemistry & Biophysics

institute: University of Rochester

description: Mixture of DNA from Sor55-Cy3 and 3153A-Cy5 Hyb. to aCGH

hyb_protocol: A total of 31 µg of each labelled DNA samples were combined and hybridized with each array ar 42° C for 72 hours in the Nimblegen Hybridization System.

scan_protocol: NimbleGen MS 200 Microarray scanner was used at a resolution of 2 µm (49 pixels/13 µm feature) per manufacturers protocol (http://www.nimblegen.com/products/lit/scanner_ms200_manual_v1p0.pdf.)

data_processing: Arrays were processed using Nimblegen's standard protocol from Nimblescan 2.5 CGH data analysis.

organism: Candida albicans

source_name: DNA from Sor55

label_protocol: Labeling was performed, as two separate 2 µg of DNA reactions for each strain using either Cy3 or Cy5 conjugated random nanomers for 2 hours at 37° C. as per manufaturers protocol (http://www.nimblegen.com/products/lit/kits_labeling_dual_color_2009_04_22.pdf)

extract_protocol: Genomic DNA isolation according to Sambrook et al. 1989. Moelcular cloning. A laboratory manual. Cold Spring Harbor Laboratory Press: Cold Spring, NY.

value: monosomic for chromosome 5

source_name: DNA from 3153A

value: wild type (parental)


title: control-bone-32d-sample-rep5


title: loaded-bone-32d-sample-rep5


title: control-bone-32d-sample-rep2


title: Soleus muscle: sciatic nerve entrapment 6 months and decompression 3 months exp rep 2

description: Experimental replicate 2 of Soleus muscle  after sciatic nerve entrapment 6 months and decomrpession 3 months


title: loaded-bone-24d-sample-rep1


title: loaded-bone-24d-sample-rep5


title: loaded-bone-24d-sample-rep4


title: 390608A03_2010-03-23


title: 389134A01_2010-03-23

description: Mixture of DNA from 3153A-Cy3 and Sor55-Cy5 Hyb. to aCGH


title: control-bone-16d-sample-rep4


title: control-bone-24d-sample-rep4


title: control-bone-16d-sample-rep3


title: control-bone-32d-sample-rep1


title: control-bone-16d-sample-rep1


title: loaded-bone-16d-sample-rep1


title: control-bone-24d-sample-rep1


title: loaded-bone-24d-sample-rep3


title: loaded-bone-12d-sample-rep4


title: loaded-bone-16d-sample-rep2


title: control-bone-16d-sample-rep5


title: loaded-bone-12d-sample-rep2


title: loaded-bone-16d-sample-rep4


title: loaded-bone-24d-sample-rep2


title: control-bone-16d-sample-rep2


title: control-bone-24d-sample-rep3


title: loaded-bone-12d-sample-rep1


title: loaded-bone-16d-sample-rep5


title: control-bone-24d-sample-rep5


title: loaded-bone-12d-sample-rep3


title: control-bone-24d-sample-rep2


title: control-bone-12d-sample-rep3


title: control-bone-12d-sample-rep4


title: loaded-bone-8d-sample-rep5


title: control-bone-12d-sample-rep1


title: loaded-bone-8d-sample-rep3


title: control-bone-8d-sample-rep2


title: control-bone-8d-sample-rep4


title: control-bone-12d-sample-rep2


title: control-bone-8d-sample-rep5


title: loaded-bone-8d-sample-rep1


title: control-bone-8d-sample-rep3


title: loaded-bone-6d-sample-rep2


title: loaded-bone-6d-sample-rep3


title: loaded-bone-8d-sample-rep4


title: control-bone-6d-sample-rep5


title: control-bone-8d-sample-rep1


title: loaded-bone-6d-sample-rep4


title: control-bone-6d-sample-rep4


title: loaded-bone-8d-sample-rep2


title: control-bone-6d-sample-rep2


title: sda+ LB+Mn (T3) run 2

city: Stanford

first: Sharon

last: Hoover

address: 337 Campus Drive, Lokey 105

department: Department of Biology

institute: Stanford University

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85586.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: G2505B

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

organism: Bacillus subtilis

source_name: Reference pool

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Reference pool

source_name: wild type in LB+Mn at T3 (run 2)

tag: measurement

value: time(change) T3 h

tag: mutated gene

value: sda+

tag: growth condition

value: Mn+

tag: experiment type

value: replicate 2


title: control-bone-6d-sample-rep3


title: sda+ LB (T0) run 3

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85592.gif

source_name: wild type in LB at T0 (run 3)

value: time(change) T0 h

value: Mn-

value: replicate 3


title: loaded-bone-16d-sample-rep3


title: control-bone-6d-sample-rep1


title: sda- LB (T0) run 3

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85593.gif

source_name: sda- in LB at T0 (run 3)

value: delta-sda


title: sda- LB (mid exp) run 2

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85577.gif

source_name: sda- in LB at mid exponential (run 2)

value: time(change) Mid exponential h


title: loaded-bone-6d-sample-rep5


title: sda+ LB+Mn (T3) run 1

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85574.gif

source_name: wild type in LB+Mn at T3 (run 1)

value: replicate 1


title: loaded-bone-4d-sample-rep5


title: loaded-bone-4d-sample-rep3


title: loaded-bone-4d-sample-rep4


title: sda- LB (mid exp) run 3

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85589.gif

source_name: sda- in LB at mid exponential (run 3)


title: sda+ LB (T3) run 1

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85572.gif

source_name: wild type in LB at T3 (run 1)


title: sda+ LB (T0) run 1

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85568.gif

source_name: wild type in LB at T0 (run 1)


title: sda+ LB+Mn (T0) run 1

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85570.gif

source_name: wild type in LB+Mn at T0 (run 1)


title: sda+ LB (T3) run 3

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85596.gif

source_name: wild type in LB at T3 (run 3)


title: sda- LB (T0) run 1

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85569.gif

source_name: sda- in LB at T0 (run 1)


title: control-bone-4d-sample-rep1


title: sda- LB+Mn (T0) run 3

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85595.gif

source_name: sda- in LB+Mn at T0 (run 3)


title: control-bone-4d-sample-rep4


title: sda+ LB (T0) run 2

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85580.gif

source_name: wild type in LB at T0 (run 2)


title: control-bone-4d-sample-rep5

description: exon expression data of untreated bone in rat

source_name: left forelimb (untreated) from rat


title: sda+ LB+Mn (mid exp) run 1

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85566.gif

source_name: wild type in LB+Mn at mid exponential (run 1)


title: sda- LB+Mn (mid exp) run 2

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85579.gif

source_name: sda- in LB+Mn at mid exponential (run 2)


title: sda- LB (T3) run 2

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85585.gif

source_name: Reference pool

source_name: sda- in LB at T3 (run 2)


title: sda+ LB+Mn (T3) run 3

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85598.gif

source_name: wild type in LB+Mn at T3 (run 3)


title: control-bone-4d-sample-rep3


title: loaded-bone-2d-sample-rep4

description: exon expression data of loaded bone in rat

source_name: right forelimb (loaded) from rat


title: loaded-bone-4d-sample-rep1


title: loaded-bone-2d-sample-rep5


title: sda+ LB+Mn (T0) run 3

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85594.gif

source_name: wild type in LB+Mn at T0 (run 3)


title: sda- LB (mid exp) run 1

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85565.gif

source_name: sda- in LB at mid exponential (run 1)


title: loaded-bone-2d-sample-rep2


title: loaded-bone-4d-sample-rep2


title: loaded-bone-2d-sample-rep3


title: sda- LB+Mn (mid exp) run 3

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85591.gif

source_name: sda- in LB+Mn at mid exponential (run 3)


title: sda- LB (T3) run 3

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85597.gif

source_name: sda- in LB at T3 (run 3)


title: control-bone-2d-sample-rep1


title: control-bone-2d-sample-rep5


title: control-bone-4d-sample-rep2


title: control-bone-2d-sample-rep2


title: sda- LB+Mn (T3) run 2

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85587.gif

source_name: sda- in LB+Mn at T3 (run 2)


title: loaded-bone-1d-sample-rep3


title: loaded-bone-1d-sample-rep4


title: sda- LB+Mn (T3) run 1

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85575.gif

source_name: sda- in LB+Mn at T3 (run 1)


title: control-bone-2d-sample-rep4


title: control-bone-2d-sample-rep3


title: sda+ LB (mid exp) run 3

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85588.gif

source_name: wild type in LB at mid exponential (run 3)


title: sda+ LB+Mn (mid exp) run 3

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85590.gif

source_name: wild type in LB+Mn at mid exponential (run 3)


title: sda- LB+Mn (mid exp) run 1

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85567.gif

source_name: sda- in LB+Mn at mid exponential (run 1)


title: control-bone-1d-sample-rep5


title: sda+ LB (mid exp) run 2

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85576.gif

source_name: wild type in LB at mid exponential (run 2)


title: control-bone-1d-sample-rep4

source_name: left forelimb (untreated) from rat


title: loaded-bone-1d-sample-rep5


title: sda- LB (T3) run 1

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85573.gif

source_name: sda- in LB at T3 (run 1)


title: sda+ LB (mid exp) run 1

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85564.gif

source_name: wild type in LB at mid exponential (run 1)


title: loaded-bone-1d-sample-rep2


title: sda- LB+Mn (T3) run 3

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85599.gif

source_name: Reference pool

source_name: sda- in LB+Mn at T3 (run 3)


title: sda- LB+Mn (T0) run 1

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85571.gif

source_name: sda- in LB+Mn at T0 (run 1)


title: sda- LB+Mn (T0) run 2

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85583.gif

source_name: sda- in LB+Mn at T0 (run 2)


title: loaded-bone-1d-sample-rep1

source_name: right forelimb (loaded) from rat


title: loaded-bone-2d-sample-rep1


title: loaded-bone-12h-sample-rep5


title: loaded-bone-12h-sample-rep4


title: control-bone-1d-sample-rep1

description: exon expression data of untreated bone in rat


title: Tomato Heat Tolerant Treated rep-1

city: Varanasi

first: Ashutosh

last: Rai

state: Uttar Pradesh

address: Post Box-1. Jakhini Shahanshapur

department: Crop Improvment

country: India

institute: Indian Institute of Vegetable Research

description:
SAMPLE 22
Gene expression data from Tomato Heat Tolerant treated plants

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: The data were analyzed with Affymetrix Expression Console and RMA version 1.0 as normalization method.

organism: Solanum lycopersicum

source_name: Leave at flowering stage at High temperature (40C) stress condition

growth_protocol: Plants were sown in plastic pots at optimal conditions for tomato plants.

treatment_protocol: Sample 1,2,3,7,8,9,13,14,15,19,20,21 were grown in normal growth conditions without any stress in green house. While sample 4,5,6, and 10,11,12 were subjected to water stress by with holding water for 7 days. Sample 16,17,18 and 22,23,24 were subjected to 40C for 60 min in growth chamber befor sample collection.

value: Heat Tolerant Genotype


title: control-bone-1d-sample-rep2

value: bone (ulna)


title: Tomato Heat Tolerant Treated rep-2

description:
SAMPLE 23
Gene expression data from Tomato Heat Tolerant treated plants


title: sda+ LB+Mn (T0) run 2

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85582.gif

source_name: wild type in LB+Mn at T0 (run 2)


title: Tomato Heat Tolerant Treated rep-3

description:
SAMPLE 24
Gene expression data from Tomato Heat Tolerant treated plants


title: sda+ LB+Mn (mid exp) run 2

description:
Cultures of Bacillus subtilis strains with the genetic background of sda+ or delta-sda were grown in LB and LB+100 micro-M MnCl2 at 37degC until 3 hours after the onset of stationary phase. At 3 timepoints, aliqots were removed and RNA isolated for each culture: 1) Mid exponential, 2) T0 (onset of stationary phase), and 3) T3 (3 hours after onset of stationary phase). cDNA was prepared from each sample using 10 micro-g of RNA. Reference cDNA was prepared from pooled RNA from all samples (common reference for all arrays). Experimental cDNA was labeled with Cy5 dye. Reference cDNA was labeled with Cy3, pooled to homogenize and aliquoted out for each batch. Slides were scanned on an Agilent DNA microarray scanner and images processed with GenePix 3.0.
Image: http://smd.stanford.edu/MicroArray/gifs/2009-10/85578.gif

source_name: wild type in LB+Mn at mid exponential (run 2)


title: control-bone-1d-sample-rep3