title: RNG_Macrophage_Sindividu121

status: Public on Aug 31 2008

city: Paris

first: Francois

last: Cambien

state: France

address: 91 Bd de l'Hôpital

department: Cardiovascular Genomics

institute: INSERM

description: All RNA preparation were checked with Agilent Bioanalyser (RNA 6000 nano-kit) and only RNA with RNA integrity number (RIN) > 8 were accepted for RNA amplification.

hyb_protocol: Hybridizations were performed using the Agilent in situ hybridization kit. For each sample, 750 ng of Cy5-labeled, linearly amplified cRNA was mixed with equal amounts of Cy3-labelled, linearly amplified reference cRNA. The mixture was then fragmented by incubation with the fragmentation buffer at 60°C for 30 minutes. An equal amount of 2x hybridization buffer was added to the fragmented cRNA mixture and hybridized to whole-genome oligo arrays (Human-25K, Réseau National des Génopoles, France) at 60°C for 17 hours

scan_protocol: Fluorescent images of hybridized microarrays were obtained with a GenePix 4000 Axon Instruments scanner and provessed with the GenePix software (Axon Instruments).

data_processing:
The Bioconductor packages marray and Limma were used to perform quality control and preprocessing.
Background correction method: normexp
Within array print-tip loess normalization was performed for each spot followed by between array quantile normalization.
bad spots were not included in the analysis.

source_name: Human macrophage labeled with Cy5

label_protocol: RNA was amplified and labeled with Cy5

growth_protocol: The human monocytes CD14+ obtained after MACS separation were cultured at a concentration of 1x 106 cells/ml in pure RPMI 1640 medium in P6 Petri dishes. After 1h of incubation at 37°C, non adherent cells were removed and the medium was replaced with RPMI 1640 Glu+ medium supplemented with 100U/ml penicillin, 100 µg/ml streptomycin and 10 % FCS, together with 10 ng/ml of macrophage colony stimulating-factor (M-CSF, SIGMA). Cells were incubated for 6 days at 37°C/5% CO2 to induce the phagocytic differentiation.

extract_protocol: RNA was extracted from whole blood using RNeasy mini kit of Qiagen.

treatment_protocol: For the isolation of PMBC from anti-coagulated blood and removal of dead cells, a density gradient centrifugation using Ficoll–Paque (GE Healthcare) gradient was used. PMBC were washed with PBS and the supernatant completely removed. The cell pellet was re-suspended in 80 µl of PBS/BSA buffer per 107 total cells and 10 µl of MACS CD14 (Miltenyi Biotec) were added carefully, mixed and incubated for 15 min at 6°-12°C. The cells were washed by adding 10-20X labelling volume of buffer, centrifuged at 300 g for 10 min. The cells were re-suspended in 500 µl of buffer before magnetic separation as described by the manufacturer.

tag: Age

tag: Gender

value: Female

tag: Tissue

value: Whole blood

tag: Cell type

value: macrophage

tag: Patient with symptoms of acute coronary syndrome who had undergone coronary angiography (who had one stenosis >50 % diagnosed in at least one major coronary artery).

source_name: Pool of 50 different monocyte and macrophage samples

label_protocol: RNA was amplified and labeled with Cy3

extract_protocol: RNA was extracted from whole blood using RNeasy mini kit of Qiagen according to the manufacturer’s instructions.

treatment_protocol: 1µg total RNA from 50 different samples were mixed, then 750ng mixed total RNA was amplified and labelled with Cy3

tag: Patients with symptoms of acute coronary syndrome who had undergone coronary angiography (who had one stenosis >50 % diagnosed in at least one major coronary artery)


title: MS11 vs. pilT 9h (biol. rep 2)

status: Public on Sep 01 2008

type: RNA

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: Features were extracted with an image analysis tool version A.9.5.3 using the GE2-V5_95_Feb07 protocol (Agilent Technologies).

hyb_protocol: Labeled samples was mixed and hybridized to 8x15K custom-made microarray according to the supplier`s protocol (Agilent Technologies). Washing of the hybridized arrays was done with the SSC protocol according supplier`s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies).

data_processing: Data analysis was carried out on the Rosetta Inpharmics platform Resolver Version 7.0. Ratio profiles were combined in an error-weighted fashion with Resolver to create ratio experiments. A 1.75-fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis set highly significant (P-value > 0.05), robust and reproducible.   The LogRatio (base 10) represents Cy5/Cy3 for each sample pair.  Values were generated with FE 9.5.3.1. software (Agilent Technologies) using the GE2-v4_95_Feb07 protocol and default settings. In brief, background, signal biases and errors were calculated applying Signal Correction - Calculate Surface Fiting, Spatial Detrending and the Most Conservative error model. Dye biases were corrected with the Dye Normalization Probe Selection Method using Rank Consistent Probes and the normalization correction methods Linear and Lowess. To determine if a feature is differentially expressed, three measures are important: LogRatio, LogRatioError and the PValueLogRatio. The LogRatio (VALUE) is the log (base 10) of the ratio of the red channel signal to the green channel signal after background adjustment and dye bias correction.  LogRatioError is the error about the mean of the log ratio.  PValueLogRatio is a measure of confidence that a feature was identified as being differentially expressed. The log ratio error was determined by the error model and therefore was used to help assess the significance of the computed log ratio. The p-value was calculated using the logratio and the log ratio error. Genes with lower p-values have higher confidence of being differentially expressed.  In order to combine dye-reversal color-swaps, a negative polarity was added to one of the arrays.

molecule: total RNA

organism: Neisseria gonorrhoeae

label_protocol: Equal amounts (10 µg) of total bacterial RNA were reverse transcribed. cDNA was labeled with Cy3 or Cy5 using the CyScribe Postlabelling Kit (GE Healthcare) and labeled cDNA purified using the CyScribe GFX purification kit (GE Healthcare)

extract_protocol: Qiagen RNeasy including on-column DNase-digest

tag: Neisseria gonorrhoeae strain MS11 (wild type)

source_name: pilT

tag: Neisseria gonorrhoeae strain pilT (pilT mutant)


title: Sample3/Promega Female

type: genomic

city: Santa Clara

first: Peter

last: Tsang

state: CA

address: 5301 Stevens Creek Blvd.

department: Agilent Labs

country: USA

institute: Agilent Technologies

hyb_protocol: See manufacturer website: <http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=52010>

scan_protocol: Scanned on an Agilent G2505B Scanner

data_processing: Agilent Feature Extraction v9.5.3.1, default CGH parameters

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Agilent DNA labeling kit

extract_protocol: Puregene Genomic DNA Purification Kit

source_name: Promega Female

extract_protocol: Performed by Promega

tag: Promega Female Genomic DNA Lot #24472701


title: RNG_Macrophage_Sindividu028

country: France

value: male


title: RNG_Monocyte_Sindividu101

source_name: Human monocyte labeled with Cy5

value: monocyte


title: pilT vs. MS11 9h (biol. rep 3)

description: features were extracted with an image analysis tool version A.9.5.3 using the GE2-V5_95_Feb07 protocol (Agilent Technologies).

scan_protocol: scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies).


title: pilT vs. MS11 9h (biol. rep 2)


title: Sample8/Promega Male

source_name: Promega Male

tag: Promega Male Genomic DNA Lot #24472601


title: Sample5/Promega Male


title: Sample6/Promega Male


title: Sample10/Promega Male


title: pilT vs. MS11 9h (biol. rep 1)

tag: Neisseria gonorrhoeae strain MS11 (wildtype)


title: RNG_Monocyte_Sindividu061


title: Sample8/Sample8

description: Patient8, Self/Self


title: Replicate Sall4 ChIP-chip in W4 ES cells

city: Las Vegas

first: Yupo

last: Ma

state: NV

address: 1 Breakthrough Way

institute: Nevada Cancer Institute

description: MM8 RefSeq Promoter array tiling array (2.5kb)

hyb_protocol: Standard Nimblegen hybridization kits and protocols were used

scan_protocol: Arrays were scanned by NimbleGen

data_processing: Arrays were processed using Nimblegens standard protocols using NimbleScan for data extraction

organism: Mus musculus

label_protocol: Standard Nimblegen ChIP labeling protocol

growth_protocol: Cells were grown with Knockout DMEM supplemented with 15% fetal bovine serum, 1x non-essential amino acids, LIF, Glutamine, and beta-mercaptoethanol.

extract_protocol: ChIP-chip was performed starting with 10^8 cells and following the NimbleGen ChIP-chip protocol to extract IP DNA.

treatment_protocol: No treatment of cells prior to ChIP

tag: Germ-line competent mouse ES cell line W4


title: Sample2/Promega Female


title: Sample7/Promega Male (Replicate 1)

description: Patient7 Replicate 1


title: Sample4/Promega Female


title: Sample1/Promega Female


title: RNG_Macrophage_Sindividu061


title: MS11 vs. pilT 9h (biol. rep 1)


title: MS11 vs. pilT 9h (biol. rep 3)


title: Sample9/Promega Female


title: RNG_Monocyte_Sindividu121


title: RNG_Monocyte_Sindividu020


title: SALL4 ChIP-chip in W4 mouse ES cells

tag: Mouse germ-line competent ES cells from the cell line W4


title: RNG_Monocyte_Sindividu026


title: RNG_Macrophage_Sindividu021


title: RNG_Monocyte_Sindividu021


title: RNG_Monocyte_Sindividu011


title: RNG_Macrophage_Sindividu020


title: RNG_Macrophage_Sindividu026


title: RNG_Macrophage_Sindividu011


title: RNG_Monocyte_Sindividu015


title: RNG_Monocyte_Pool41


title: RNG_Monocyte_Pool40


title: RNG_Macrophage_Sindividu015


title: RNG_Monocyte_Sindividu016


title: RNG_Macrophage_Sindividu016


title: Sample7/Promega Male (Replicate 2)

description: Patient7 Replicate 2


title: RNG_Macrophage_Pool41


title: RNG_Macrophage_Pool40


title: RNG_Monocyte_Pool38


title: RNG_Macrophage_Pool38


title: RNG_Macrophage_Pool37


title: RNG_Monocyte_Pool37


title: RNG_Macrophage_Pool35


title: RNG_Macrophage_Pool36


title: RNG_Monocyte_Pool36


title: RNG_Monocyte_Pool33


title: RNG_Macrophage_Pool33


title: RNG_Monocyte_Pool35


title: RNG_Monocyte_Pool32


title: RNG_Monocyte_Pool34


title: RNG_Monocyte_Pool30


title: RNG_Macrophage_Pool34


title: RNG_Monocyte_Pool28


title: RNG_Monocyte_Pool29


title: RNG_Macrophage_Pool30


title: RNG_Macrophage_Pool31


title: RNG_Macrophage_Pool28


title: RNG_Monocyte_Pool27


title: RNG_Macrophage_Pool29


title: RNG_Monocyte_Pool31


title: RNG_Macrophage_Sindividu101


title: RNG_Monocyte_Pool26


title: RNG_Monocyte_Pool25


title: RNG_Macrophage_Pool27


title: RNG_Monocyte_Pool23


title: RNG_Monocyte_Pool24


title: RNG_Macrophage_Pool23


title: RNG_Macrophage_Pool26


title: RNG_Macrophage_Pool24


title: RNG_Monocyte_Pool21


title: RNG_Macrophage_Pool22


title: RNG_Monocyte_Pool22


title: RNG_Monocyte_Pool19


title: RNG_Monocyte_Pool20


title: RNG_Macrophage_Pool20


title: RNG_Macrophage_Pool25


title: RNG_Macrophage_Pool18


title: RNG_Monocyte_Pool18


title: RNG_Macrophage_Pool21


title: RNG_Macrophage_Pool19


title: RNG_Monocyte_Pool17


title: RNG_Monocyte_Pool16


title: RNG_Monocyte_Sindividu028


title: RNG_Macrophage_Pool17


title: RNG_Macrophage_Pool11


title: RNG_Macrophage_Pool5


title: RNG_Monocyte_Pool14


title: RNG_Macrophage_Pool13


title: RNG_Monocyte_Pool11


title: RNG_Macrophage_Pool8


title: RNG_Monocyte_Pool6


title: RNG_Macrophage_Pool10


title: RNG_Macrophage_Pool15


title: Sample10/Promega Male


title: RNG_Macrophage_Pool16


title: RNG_Monocyte_Pool15


title: RNG_Macrophage_Pool12


title: RNG_Monocyte_Pool5


title: RNG_Monocyte_Pool8


title: RNG_Monocyte_Pool13


title: RNG_Macrophage_Pool14


title: RNG_Macrophage_Pool32


title: RNG_Monocyte_Pool4


title: RNG_Macrophage_Pool7


title: RNG_Monocyte_Pool7


title: RNG_Monocyte_Pool10


title: RNG_Macrophage_Pool9


title: RNG_Monocyte_Pool12


title: RNG_Macrophage_Pool6


title: RNG_Monocyte_Pool9


title: Sample9/Promega Female


title: RNG_Macrophage_Pool2


title: RNG_Monocyte_Pool2


title: RNG_Macrophage_Pool4


title: Sample6/Promega Male


title: Sample5/Promega Male


title: Sample7/Promega Male (Replicate 1)

description: Patient7 Replicate 1


title: Sample8/Sample8

description: Patient8, Self/Self


title: Sample7/Promega Male (Replicate 2)

description: Patient7 Replicate 2


title: deceased, 7960

status: Public on Aug 29 2008

city: Göteborg

first: Elin

last: Karlsson

address: Blå stråket 2

department: Oncology

country: Sweden

institute: Göteborg University

description: lymph-node-negative breast cancer

hyb_protocol: The probes were purified using ChipShot™ labelling cleanup system (Promega). The hybridizations were carried out using Pronto! Micro Array reagent systems (Corning Inc.). For each sample, labelled tumour cDNA and reference cDNA were co-precipitated and hybridised to the oligoarray slide.  After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Genepix 6.0.0.45 (Axon Instruments).

data_processing: Intensities were calculated by median spot - median background. Flagged spots and spots for which background adjusted intensities were <0 or >65 000 were excluded as well as spots with intensities below 20 in both channels. Intensities below 20 in one channel were set to 20 to compensate for extreme quotients. pin-based Lowess normalization were performed with 12 blocks in each group

source_name: breast cancer tumor, deceased patient

label_protocol: Probes labelled with Cy3 were synthesized from 5 µg of the total tumour RNA and reference labelled with Cy5 were synthesized from 5 µg of commercial reference RNA by reverse transcription.

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

tag: fresh frozen tumour

tag: estrogen receptor negative

tag: progesterone receptor negative

tag: aneuploid

tag: duct

tag: breast preserving surgery

tag: age at diagnosis

tag: tumour size

value: 17 mm

tag: post surgical chemo therapy

source_name: Universal Human Reference RNA purchased from Stratagene

tag: control


title: Sample8/Promega Male


title: deceased, 8138

description: lymph-node-negative breast cancer

tag: mastectomy

value: 40 mm


title: deceased, 9253

description: lymph-node-negative breast cancer

tag: estrogen receptor positive

tag: progesterone receptor positive

tag: diploid

tag: lob

value: 18 mm


title: Sample1/Promega Female

tag: Promega Female Genomic DNA Lot #24472701


title: deceased, 6915

description: lymph-node-negative breast cancer

tag: tubular

value: 20 mm


title: deceased, 7807

description: lymph-node-negative breast cancer

tag: fresh frozen tumour

tag: multiploid


title: deceased, 7313

description: lymph-node-negative breast cancer

tag: estrogen receptor negative

tag: progesterone receptor negative

value: 16 mm


title: deceased, 6640

description: lymph-node-negative breast cancer

tag: aneuploid

tag: duct

tag: post surgical hormonal therapy


title: deceased, 8903

description: lymph-node-negative breast cancer

tag: comedo

tag: breast preserving surgery

tag: age at diagnosis

tag: tumour size

tag: post surgical radio therapy


title: Sample3/Promega Female


title: deceased, 9138

description: lymph-node-negative breast cancer

tag: mastectomy

tag: control


title: deceased, 8018

description: lymph-node-negative breast cancer

tag: medullary

tag: post surgical chemo therapy


title: deceased, 8402

description: lymph-node-negative breast cancer

value: 15 mm


title: deceased, 6865

description: lymph-node-negative breast cancer

tag: estrogen receptor positive

tag: diploid

value: 19 mm


title: deceased, 6839

description: lymph-node-negative breast cancer

tag: fresh frozen tumour


title: deceased, 7453

description: lymph-node-negative breast cancer

value: 21 mm


title: deceased, 6316

description: lymph-node-negative breast cancer

tag: progesterone receptor positive


title: Sample2/Promega Female

tag: Promega Female Genomic DNA Lot #24472701


title: deceased, 6381

description: lymph-node-negative breast cancer


title: deceased, 7670

description: lymph-node-negative breast cancer

tag: aneuploid


title: Sample4/Promega Female


title: deceased, 4302

description: lymph-node-negative breast cancer

tag: duct

value: 65 mm


title: deceased, 6195

description: lymph-node-negative breast cancer

tag: estrogen receptor negative

tag: progesterone receptor negative

value: 12 mm


title: deceased, 11045

description: lymph-node-negative breast cancer

tag: adenocarcinoma

tag: breast preserving surgery


title: deceased, 4296

description: lymph-node-negative breast cancer

tag: age at diagnosis

tag: tumour size

tag: post surgical hormonal therapy


title: deceased, 6039

description: lymph-node-negative breast cancer

tag: control


title: 10 year survivor, 7647

description: lymph-node-negative breast cancer

source_name: breast cancer tumor, 10 year survivor

tag: mastectomy

value: 42 mm


title: 10 year survivor, 7547

description: lymph-node-negative breast cancer

value: 26 mm

tag: post surgical radio therapy

tag: post surgical chemo therapy


title: 10 year survivor, 7700

description: lymph-node-negative breast cancer

tag: diploid


title: 10 year survivor, 8009

description: lymph-node-negative breast cancer

tag: fresh frozen tumour

tag: estrogen receptor positive


title: 10 year survivor, 8576

description: lymph-node-negative breast cancer

tag: progesterone receptor positive


title: 10 year survivor, 7631

description: lymph-node-negative breast cancer

tag: multiploid


title: 10 year survivor, 8467

description: lymph-node-negative breast cancer

tag: lob

value: 30 mm


title: 10 year survivor, 7418

description: lymph-node-negative breast cancer

tag: estrogen receptor negative

tag: aneuploid

tag: duct


title: 10 year survivor, 7613

description: lymph-node-negative breast cancer

tag: progesterone receptor negative

tag: breast preserving surgery


title: deceased, 10068

description: lymph-node-negative breast cancer

tag: age at diagnosis

tag: tumour size


title: 10 year survivor, 7173

description: lymph-node-negative breast cancer

tag: mucinous

tag: post surgical hormonal therapy

tag: control


title: 10 year survivor, 8007

description: lymph-node-negative breast cancer

tag: post surgical radio therapy


title: 10 year survivor, 7641

description: lymph-node-negative breast cancer

tag: mastectomy

value: 22 mm


title: 10 year survivor, 6866

description: lymph-node-negative breast cancer

tag: fresh frozen tumour

value: 55 mm

tag: post surgical chemo therapy


title: 10 year survivor, 7512

description: lymph-node-negative breast cancer

tag: estrogen receptor positive

tag: progesterone receptor positive


title: 10 year survivor, 7680

description: lymph-node-negative breast cancer

value: 32 mm


title: 10 year survivor, 8388

description: lymph-node-negative breast cancer


title: 10 year survivor, 7011

description: lymph-node-negative breast cancer

tag: diploid

value: 29 mm


title: 10 year survivor, 7198

description: lymph-node-negative breast cancer


title: 10 year survivor, 6880

description: lymph-node-negative breast cancer

value: 17 mm


title: 10 year survivor, 5550

description: lymph-node-negative breast cancer

tag: estrogen receptor negative

value: 35 mm


title: 10 year survivor, 6130

description: lymph-node-negative breast cancer

tag: aneuploid

value: 56 mm


title: 10 year survivor, 6061

description: lymph-node-negative breast cancer

tag: duct

value: 40 mm


title: L2L3 E2 2

status: Public on Aug 25 2008

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

label: Biotin

source_name: PGC1 L2L3, E2

label_protocol: One step IVT from 10 ug totaql RNA, followed by biotin labeling of fragmented cRNA.

growth_protocol: For microarray experiments, MCF-7 cells were cultured in estrogen-free media for two days before adenoviral infection

extract_protocol: Total RNA was extracted using Quagen RNEasy kit following manufacturer's protocol.

treatment_protocol: Adenoviral infection was performed at an MOI of 50. Twelve hours after infection cells were treated with estradiol (10nM) or vehicle and harvested 12 h thereafter.

tag: Cell line

tag: Infection

value: PGC1 L2L3

tag: Treatment

value: E2 10 nM


title: 10 year survivor, 4194

description: lymph-node-negative breast cancer

tag: progesterone receptor negative

tag: age at diagnosis

tag: tumour size


title: WT E2 2

source_name: PGC1 WT,E2

value: PGC1 WT


title: 2x9 E2 2

source_name: PGC1 2x9, E2

value: PGC1 2x9


title: 2x9 ETOH 2

source_name: PGC1 2x9, EtOH

value: Vehicle


title: S. aureus Fusidic Acid Induction_A2

city: Las Cruces

first: John

middle: E

last: Gustafson

email: jgustafs@nmsu.edu, amuthai@gmail.com

state: NM

address: PO Box 30001 Dept. 3AF

department: Department of Biology and Molecular Biology Program

institute: New Mexico State University

description: Genes analyzed using these programs were further sorted and grouped based on their function using our in-house software Staphylococcus aureus Gene Sorter (SAGS).

hyb_protocol: Purified labelled cDNA was hybridised with S. aureus genome microarray version 4 as previously described by Mongodin et al. (2003) and Riordon et al. (2007). Briefly, the slides were prehybridized in a buffer containing 5X SSC, 0.1% SDS and 0.1% BSA, and then washed and blown to dry. The two differentially labelled cDNA samples were dried and the resuspended in hybridization solution [40% deionized formamide, 5X SSC, 0.1% SDS, 0.6 µg/µl sheared Salmon sperm DNA (Ambion)]. The labelled cDNA samples were hybridized with the slides at 42 °C for 18-20 h. After hybridization, the slides were washed in low stringency buffer (2X SSC, 0.1% SDS) for 2 min, then in medium stringency (0.1x SSC, 0.1% SDS) buffer for 5 min and finally high stringency buffer (0.1x SSC) for 10 min.

scan_protocol: Hybridization signals were scanned using an Axon4000B scanner (Molecular Devices, Sunnyvale, CA ) with Acuity 4.0 software and scans were saved as TIFF image.

data_processing: Scans were analyzed using TIGR-Spotfinder (www.tigr.org/software/) software and the local background was subsequently subtracted. The data set was normalized by applying the LOWESS algorithm using TIGR-MIDAS (www.tigr.org/software/) software. The normalized log2 ratio of test/reference signal for each spot was recorded. Genes with less than three data points were considered unreliable, and their data points were discarded. The averaged log2 ratio for each remaining gene on the six replicate slides was ultimately calculated. Significant changes of gene expression were identified with SAM (significance analysis of microarrays; www.tat.stanford.edu/~tibs/SAM/index.html software using one class mode.

organism: Staphylococcus aureus

source_name: S. aureus, Fusidic Acid Treated

label_protocol: cDNA was generated by using random hexamers (Invitrogen) as primers for reverse transcription. The primers were annealed (70°C for 10 min, followed by snap-freezing in ice for 1 min) to total RNA (2 μg) and were extended with SuperScript II reverse transcriptase (Invitrogen) with 0.1 M dithiothreitol 12.5 mM dNTP/ aa-UTP (Ambion, Austin, TX) mix at 42°C overnight. Residual RNA was removed by alkaline treatment followed by neutralization, and cDNA was purified with a QIAquick PCR purification kit (Qiagen). Purified aminoallyl-modified cDNA was then labeled with Cy3 or Cy5 mono-functional NHS ester cyanogen dyes (Amersham Pharmacia Biotech, Piscataway, NJ) according to the manufacturer’s instruction.

extract_protocol: Total bacterial RNA was extracted from 3 ml of culture which was mixed with 6 ml of bacterial RNA protect solution (Qiagen, Valencia, CA) and the mixture was centrifuged at 3000 rpm for 20 min in swinging-bucket rotor centrifuge to collect the cells. Pellets were resuspended in 1 ml of Trizol (Invitrogen, Grand Island, NY) and the cells were broken using the FastPrep system (Qbiogene, Irvine, CA) at a speed of 6.0 for 40 seconds. From the broken cell lysate RNA was extracted as per the manufacturer’s instructions. Extracted RNA was purified using the RNeasy mini kit (Qiagen). DNase treated and purified mRNA was used for microarray analysis.

treatment_protocol: S. aureus strain SH1000 grown in Muellar-Hinton broth to an OD580nm of 1.0 (37°C, 200 rpm) and then induced with 2 mg/L-1 fusidic acid for 15 min.

tag: S. aureus SH1000

source_name: S. aureus Control


title: S. aureus Fusidic Acid Induction_B2


title: BGAL E2 2

value: BGAL


title: L2L3 E2 3


title: 2x9 ETOH 3


title: WT WTOH 2

source_name: PGC1 WT, EtOH


title: WT E2 1

source_name: PGC1 WT, E2


title: BGAL E2 1

source_name: BGAL, E2


title: 2x9 E2 1


title: BGAL ETOH 1

source_name: BGAL, EtOH


title: BGAL ETOH 2


title: 2x9 ETOH 1


title: BGAL E2 3


title: 2x9 E2 3


title: WT ETOH 1


title: L2L3 E2 1


title: L2L3 ETOH 2

source_name: PGC1 L2L3, EtOH


title: BGAL ETOH 3


title: S. aureus Fusidic Acid Induction_B1


title: L2L3 ETOH 3


title: WT ETOH 3


title: L2L3 ETOH 1


title: S. aureus Fusidic Acid Induction_A1


title: Peripheral Leukocytes vs pool

status: Public on Aug 15 2008

city: Seattle

first: Amit

middle: V

last: Kulkarni

state: WA

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description: Peripheral Leukocytes vs pool

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

molecule: polyA RNA

source_name: Peripheral Leukocytes

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Total RNA isolated using Qiagen RNeasy spin columns with DNAse treatment; polyA+ RNA isolated from total RNA via magnetic bead-based mRNA extraction (Ambion, Poly(A) Purist)

tag: 48 diverse human tissues and cell lines were hybridized to a 17-array set.  Samples were purchased as pools from multiple donors, typically over 10 (Clontech, Mountainview, CA).

source_name: pool

tag: Pooled RNA from 20 diverse disease-free adult tissue pools comprised the reference pool.


title: Melanoma (G361) vs pool

description: Melanoma (G361) vs pool

source_name: Melanoma (G361)


title: Lung Carcinoma (A549) vs pool

description: Lung Carcinoma (A549) vs pool

source_name: Lung Carcinoma (A549)


title: HCT116 vs pool

description: HCT116 vs pool


title: Brain, Medulla Oblongata vs pool

description: Brain, Medulla Oblongata vs pool

source_name: Brain, Medulla Oblongata


title: HeLa(S3) vs pool

description: HeLa(S3) vs pool


title: Brain, Putamen vs pool

description: Brain, Putamen vs pool

source_name: Brain, Putamen


title: Osteosarcoma (MG-63) vs pool

description: Osteosarcoma (MG-63) vs pool

source_name: Osteosarcoma (MG-63)


title: Lung tumor vs pool

description: Lung tumor vs pool

source_name: Lung tumor


title: Breast tumor vs pool

description: Breast tumor vs pool

source_name: Breast tumor


title: Brain, Pons vs pool

description: Brain, Pons vs pool

source_name: Brain, Pons


title: Pancreas vs pool

description: Pancreas vs pool

source_name: Pancreas


title: Fetal Vertebra vs pool

description: Fetal Vertebra vs pool

source_name: Fetal Vertebra


title: Lymphoma Burkitt's (Raji) vs pool

description: Lymphoma Burkitt's (Raji) vs pool

source_name: Lymphoma Burkitt's (Raji)


title: HeLa vs pool

description: HeLa vs pool

source_name: HeLa


title: Brain hypothalamus vs pool

description: Brain hypothalamus vs pool

source_name: Brain hypothalamus


title: Colorectal Adenocarcinoma (SW480) vs pool

source_name: Colorectal Adenocarcinoma (SW480)


title: Colon tumor vs pool

description: Colon tumor vs pool

source_name: Colon tumor


title: Melanoma (G361) vs pool

description: Melanoma (G361) vs pool


title: Peripheral Leukocytes vs pool

description: Peripheral Leukocytes vs pool

source_name: Peripheral Leukocytes


title: HCT116 vs pool

description: HCT116 vs pool

source_name: pool


description: Colorectal Adenocarcinoma (SW480) vs pool


title: HeLa(S3) vs pool

description: HeLa(S3) vs pool


title: Brain, Medulla Oblongata vs pool

description: Brain, Medulla Oblongata vs pool


title: Lung Carcinoma (A549) vs pool

description: Lung Carcinoma (A549) vs pool


title: Brain, Putamen vs pool

description: Brain, Putamen vs pool


title: Breast tumor vs pool

description: Breast tumor vs pool


title: Brain, Pons vs pool

description: Brain, Pons vs pool


title: Pancreas vs pool

description: Pancreas vs pool


title: Lung tumor vs pool

description: Lung tumor vs pool


title: Osteosarcoma (MG-63) vs pool

description: Osteosarcoma (MG-63) vs pool


title: Lymphoma Burkitt's (Raji) vs pool

description: Lymphoma Burkitt's (Raji) vs pool


title: HeLa vs pool

description: HeLa vs pool


title: Fetal Vertebra vs pool

description: Fetal Vertebra vs pool


title: Colon tumor vs pool

description: Colon tumor vs pool


title: Brain hypothalamus vs pool

description: Brain hypothalamus vs pool


title: Peripheral Leukocytes vs pool

description: Peripheral Leukocytes vs pool


title: HCT116 vs pool

description: HCT116 vs pool


title: Melanoma (G361) vs pool

description: Melanoma (G361) vs pool

source_name: Melanoma (G361)


title: HeLa(S3) vs pool

description: HeLa(S3) vs pool


title: Brain, Medulla Oblongata vs pool

description: Brain, Medulla Oblongata vs pool


title: Lung Carcinoma (A549) vs pool

description: Lung Carcinoma (A549) vs pool

source_name: Lung Carcinoma (A549)


title: Brain, Putamen vs pool

description: Brain, Putamen vs pool


title: Breast tumor vs pool

description: Breast tumor vs pool


title: Brain, Pons vs pool

description: Brain, Pons vs pool


title: transgenic RNAiOleosin, biol rep 1, tech rep 1

first: monica

last: schmidt

state: MO

address: 975 n. warson

institute: danforth center

description: rep 2 of 2 for control sample

hyb_protocol: Genechip expression analysis technical manual

data_processing: data was processed by  arrayassist

label: biotin

organism: Glycine max

source_name: transgenic RNAiOle1

extract_protocol:
acid-based phenol extraction to extract total RNA from seeds
Qiagen spin column to clean sample

tag: transgenic RNAiOle 150mg cotyledon


title: Wild type 2

description: rep 2 of 2 for control sample

scan_protocol: Genechip expression analysis technical manual

source_name: 150mg nontransgenic soybean seed, rep2

tag: nontransgenic cotyledon samples 150mg


title: transgenic RNAiOleosin, biol rep 2, tech rep 1

description: biological rep 2, technical rep1 of transgenic RNAiOleosin

source_name: 150mg cotyledon RNAiOle rep 3

label_protocol: Genechip expression analysis technical manual

tag: 150 mg cotyledon RNAioleosin transgenic


title: transgenic RNAiOleosin, biol rep 1, tech rep 2

description: rep 2 of 2 for control sample

source_name: transgenic 150mg cotyledon RNAi0le-2

tag: 150 mg cotyledon RNAioleosin rep2


title: transgenic RNAiOleosin, biol rep 2, tech rep 2

description: done at iowa state

data_processing: done by array assist

source_name: transgenic RNAioleosin cotyledon bio rep 2 tech rep2

tag: 150 mg cotyledon tissue from RNAioleosin suppressed soybean seed


title: Wild type 1

description: rep 1 of 2 for control sample

source_name: cotyledon soybean

extract_protocol:
Acid-based phenol extraction to extract total RNA from seeds
Qiagen spin column to clean sample

tag: 150mg nontransgenic soybean cotyledon


title: L.major MTX60.4 vs WT_replicate 1

status: Public on Aug 01 2008

city: Québec

first: Marc

last: Ouellette

state: Québec

address: 2705 bd Laurier

department: Département médecine

country: Canada

institute: Université Laval

description: Biological replicate 1 of 4

hyb_protocol: Prehybridization and hybridization were performed at 42°C. Slides were prehybridized in 5X Denhardt, 30% formamide, 6X SSPE, 0,5% SDS, 100µg/ml salmon sperm DNA. Then, slides were washed . For hybridization, labelled cDNA probes were dried and resuspended in 2,5X Denhardt, 30% formamide, 6X SSPE, 0,5% SDS, 100µg/ml salmon sperm DNA, 750µg/ml Yeast tRNA. then mixed. Mixed probes were applied on the array under a lifterslip. Hybridization was performed for 16h.

scan_protocol: The Perkin Elmer ScanArray 4000XL Scanner was used for image acquisition. GenePix Pro 6.0 image analysis software (Axon Instruments) was used to quantify the fluorescence signal intensities of the array features

data_processing:
Raw data from GenePix were imported in R 2.2.1 for normalization and statistical analyses were performed using the LIMMA (version 2.7.3) package.
Intra-array normalization was carried out using the ‘print-tip loess’ statistical method and inter-array normalization was done by using the ‘quantiles of A’ method for each array (Yang, 2003).
Multiple testing corrections were done using the FDR method with a threshold p-value of 0.05. Only genes statistically significant with an absolute log ratio greater than 0.58 (log2 1.5) were considered as differentially expressed

organism: Leishmania major

label_protocol: 10 µg of RNA were converted to aminoallyl-dUTP incorporated cDNA using random hexamers (Roche) and the SuperScript III RNase H- Reverse Transcriptase (Invitrogen). Probes were thereafter coupled to the fluorescent dye Alexa Fluor555 or Alexa Fluor647 (Invitrogen) following manufacturer recommendations. Fluorescent probes were then purified with MinElute Spin Columns (QIAGEN) and quantified spectrophotometrically.

growth_protocol: All cells were grown in M199 medium supplemented with 10% heat-inactivated fetal bovine serum and 5 µg/ml hemin at 25 °C. When needed, the apropriate concentration of methotrexate where added.

extract_protocol: Total RNA was isolated from 108 Leishmania cells during the mid-log phase using RNeasy Plus Mini Kit (QIAGEN) as described by the manufacturer. The RNA preparation was treated with TURBO DNase (Ambion) to avoid any genomic contamination

tag: wild-type strain, replicate 1

tag: methotrexate resistant strain, grown in presence of 60 micromolar of drug, replicate 1


title: L.major MTX60.4 vs WT_replicate 2

description: Biological replicate 2 of 4; dyeswap

tag: wild-type strain, replicate 2

tag: methotrexate resistant strain, grown in presence of 60 micromolar of drug, replicate 2


title: L. infantum MTX20.5 vs WT_replicate 1

description: Biological replicate 1 of 4

organism: Leishmania infantum

tag: methotrexate resistant strain, grown in presence of 20 micromolar of drug, replicate 1


title: TF-iodide -48 hours

city: Shinjuku-ku

first: Kanji

last: Sato

state: Tokyo

address: Kawada-cho 8-1

department: Institute of Clinical Endocrinology

country: Japan

institute: Tokyo Women's Medical University

description: Thyroid follicles were cultured with 10-8M & 2x10-5M iodide  for 48 hours

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.7.5).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Iodide 10-8M

label_protocol: 0.5 µg of total RNA were primed with 2 µl of 100 µM T16P7 DNA primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of Low RNA input linear amplification (Agilent), and 10mM dNDP.

growth_protocol: Thyroid follicles  prepared from patients with Graves' disease  were cultured in medium containing NaI (10-8M) or (2X10-5M) and 0.5% serum in 10cm-dishes coated with agarose gel.

extract_protocol: Total RNA was extracted from thyroid follicles using the RNeasy Minikit (Quiagen, Tokyo, Japan)

treatment_protocol: Total RNA was prepared from thyroid follicles treated with or without bTSH (30microU/ml) for 48 hours, or from thyroid follicles treated with NaI 10-8M or NaI 2X10-5M for 48 hours.

tag: human thyroid follicles

source_name: Iodide 2x10-5M


title: L.major MTX60.4 vs WT_replicate 4

description: Biological replicate 4 of 4; dyeswap

tag: wild-type strain, replicate 4

tag: methotrexate resistant strain, grown in presence of 60 micromolar of drug, replicate 4


title: L. infantum MTX20.5 vs WT_replicate 2

description: Biological replicate 2 of 4

tag: methotrexate resistant strain, grown in presence of 20 micromolar of drug, replicate 2


title: TF-bTSH 30 micro U/ml -48 hours

description: Thyroid follicles were cultured with or without bTSH  for 48 hours

source_name: bTSH (-)

source_name: bTSH 30 microU/ml


title: MMT + si erm sample 3

city: Lille

first: Anne

last: Chotteau

address: 1 rue du professeur calmette

institute: CNRS UMR 8161

description: Transcriptome profiles were acquired using novel Applied Biosystems AB1700 technology. All experimental data referred to as MGS V1.0 (Mouse Genome Survey Version 1, ProdNo: 4337467) were generated on the Applied Biosystems AB1700 transcriptome platform (ProdNo: 4338036). These arrays contain probes for 28,218 validated mouse genes.

hyb_protocol: Labeled cRNAs were hybridized according to the supplied protocols (applied Biosystems, ProdNo 4346875)

scan_protocol: Applied Biosystems Expression Array System Software v1.1.1. (ProdNo: 4364137) has been used to acquire the chemiluminescence and fluorescence images and primary data analysis.

label: digoxygenin

source_name: MMT

label_protocol: 1µg were subjected to RT-IVT amplification and labeling according to the manufacturer (applied Biosystems, prodNo 4339628)

growth_protocol: MMT were cultured on culture flasks (Becton Dickinson) in DMEM (Gibco, Invitrogen) supplemented with 10% (v/v) fetal calf serum (FCS, Gibco, Invitrogen), gentamycin (100 IU/ml) and non-essential amino acids (Gibco, Invitrogen)

extract_protocol: total RNA was isolated from MMT cells using RNeasy kit (Qiagen) according to the manufacturer.

treatment_protocol: transfection by siRNA

tag: ATCC CCL-51

tag: Organ

value: mammary gland

tag: Disease

value: tumor


title: MMT + si Ctrl sample 3

data_processing: Applied Biosystems Expression Array System Software v1.1.1.


title: MMT cells sample 2


title: MMT  cells sample 1


title: L. infantum MTX20.5 vs WT_replicate 3

description: Biological replicate 3 of 4; dyeswap

tag: wild-type strain, replicate 3

tag: methotrexate resistant strain, grown in presence of 20 micromolar of drug, replicate 3


title: MMT + si pea3 sample 3


title: MMT + si erm sample 2

treatment_protocol: Transfection by siRNA


title: MMT + si erm sample 1

tag: tissue

tag: disease


title: MMT + si pea3 sample 2


title: MMT + si pea3 sample 4


title: MMT + si pea3 sample 1

tag: Tissue


title: L.major MTX60.4 vs WT_replicate 3

description: Biological replicate 3 of 4

tag: methotrexate resistant strain, grown in presence of 60 micromolar of drug, replicate 3


title: placenta IUGR replicate 7

city: Tromsø

first: Ruth

middle: Hracky

last: Paulssen

address: MH-Bygget Breivika

department: Institute of Clinical Medicine

country: Norway

institute: Universitetet i Tromsø

hyb_protocol: The labeled DIG-cRNA (10 micrograms per microarray) was   then injected into each microarray hybridization chamber. Following hybridization at 55oC for 16   hours, the unbound material was washed from the microarrays. Features that retained bound DIG-  labeled cRNA were visualized using the Applied Biosystems Chemiluminescenct detection Kit.   Anti-DIG alkaline phophatase (Roche Applied science) was used to hydrolyze a   chemiluminescence substrate to generate light at 458 nm

scan_protocol: Images were quantified using the integrated ABI1700 software

data_processing: The pre-normalized intensity values were extracted per spot from the data files. Weak spots   with signal to noise ratio <3.0 and control spots were filtered out. All arrays were normalized   by the Lowess method (Cleveland). Missing expression levels were inferred using the   LSimpute method (Bo et al., 2004). Statistical significance was assigned to the genes by using   the Significance Analysis of Microarrays (SAM) methodology (Tusher et al., 2001). Principal   component analysis method (PCA) was used in order to try to discriminate IUGR from   normal placentas.

label: DIG

source_name: placenta

growth_protocol: patient material

extract_protocol: MagNa Pure Compact RNA isolation Kit (Roche Applied Science)

tag: IUGR


title: L. infantum MTX20.5 vs WT_replicate 4

description: Biological replicate 4 of 4

tag: methotrexate resistant strain, grown in presence of 20 micromolar of drug, replicate 4


title: placenta IUGR replicate 6


title: MMT + si Ctrl sample 2


title: placenta IUGR replicate 8


title: placenta IUGR replicate 5


title: MMT + si Ctrl sample 1


title: placenta IUGR replicate 3


title: placenta IUGR replicate 4


title: Involution day 4 B

city: Glasgow

first: Torsten

last: Stein

address: College of MVLS

department: School of Medicine

country: United Kingdom

institute: University of Glasgow

description: Q2 Inv4.CEL

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MG-U74Av2 chip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned by an Agilent scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. For normalisation, signal intensity was normalised against the overall chip intesity with a mean target signal of 500.

source_name: Involution day 4

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Standard animal house conditions.

extract_protocol: Mammary glands were crushed in liquid Nitrogen forllowed by Trizol extraction of total RNA was performed according to the manufacturer's instructions and Qiagen RNeasy column purification.

treatment_protocol: Mice were mated at 12 weeks of age. Plugs were checked in the morning and day of plug was counted as day 0.5. For force weaning, pups were removed after 7 days of lactation.

tag: total inguinal mammary gland without lymph node

tag: Balb/c


title: Involution day 20 A

description: R1 Inv20.CEL

source_name: Involution day 20


title: Involution day 20 B

description: R2 Inv20.CEL


title: Involution day 4 C

description: Q3 Inv4.CEL


title: placenta IUGR replicate 1


title: Involution day 3 C

description: P3 Inv3.CEL

source_name: Involution day 3


title: Involution day 4 A

description: Q1 Inv4.CEL


title: placenta normal replicate 7

tag: normal


title: placenta normal replicate 6


title: placenta normal replicate 5


title: placenta IUGR replicate 2


title: placenta normal replicate 8


title: placenta normal replicate 4


title: Involution day 2 B

description: O2 Inv2.CEL

source_name: Involution day 2


title: Involution day 20 C

description: R3 Inv20.CEL


title: placenta normal replicate 3


title: placenta normal replicate 2


title: Involution day 3 A

description: P1 Inv3.CEL


title: Involution day 2 C

description: O3 Inv2.CEL


title: Involution day 1 C

description: N3 Inv1.CEL

source_name: Involution day 1


title: Involution day 3 B

description: P2 Inv3.CEL


title: Involution day 1 B

description: N2 Inv1.CEL


title: Involution day 2 A

description: O1 Inv2.CEL


title: Lactation day 7 C

description: M3 Lac7.CEL

source_name: Lactation day 7


title: Involution day 1 A

description: N1 Inv1.CEL


title: placenta normal replicate 1


title: Lactation day 7 B

description: M2 Lac7.CEL


title: Lactation day 7 A

description: M1 Lac7.CEL


title: Pregnancy day 17.5 C

description: J3 P17.5.CEL

source_name: Pregnancy day 17.5


title: Pregnancy day 17.5 A

description: J1 P17.5.CEL


title: Pregnancy day 17.5 B

description: J2 P17.5.CEL


title: Pregnancy day 12.5 C

description: H3 P12.5.CEL

source_name: Pregnancy day 12.5


title: Lactation day 1 A

description: K1 Lac1.CEL

source_name: Lactation day 1


title: Pregnancy day 14.5 A

description: I1 P14.5.CEL

source_name: Pregnancy day 14.5


title: Lactation day 3 B

description: L2 Lac3.CEL

source_name: Lactation day 3


title: Pregnancy day 12.5 B

description: H2 P12.5.CEL


title: Lactation day 1 B

description: K2 Lac1.CEL


title: Lactation day 3 A

description: L1 Lac3.CEL


title: Pregnancy day 12.5 A

description: H1 P12.5.CEL


title: Pregnancy day 14.5 B

description: I2 P14.5.CEL


title: Pregnancy day 8.5 C

description: F3 P8.5.CEL

source_name: Pregnancy day 8.5


title: Lactation day 1 C

description: K3 Lac1.CEL


title: Pregnancy day 14.5 C

description: I3 P14.5.CEL


title: Lactation day 3 C

description: L3 Lac3.CEL


title: Pregnancy day 8.5 A

description: F1 P8.5.CEL


title: Pregnancy day 3 C

description: E3 P3.CEL

source_name: Pregnancy day 3


title: Pregnancy day 3 B

description: E2 P3.CEL


title: Pregnancy day 8.5 B

description: F2 P8.5.CEL


title: Pregnancy day 2 B

description: D2 P2.CEL

source_name: Pregnancy day 2


title: Pregnancy day 2 C

description: D3 P2.CEL


title: Pregnancy day 3 A

description: E1 P3.CEL


title: Pregnancy day 2 A

description: D1 P2.CEL


title: Pregnancy day 1 C

description: C3 P1.CEL

source_name: Pregnancy day 1


title: Pregnancy day 1 B

description: C2 P1.CEL


title: Pregnancy day 1 A

description: C1 P1.CEL


title: Virgin 12 weeks A

description: B1 V12.CEL

source_name: Virgin 12 weeks


title: Virgin 12 weeks B

description: B2 V12.CEL


title: Virgin 12 weeks C

description: B3 V12.CEL


title: Virgin 6 weeks C

description: 3 V6.CEL

source_name: Virgin 6 weeks


title: Virgin 10 weeks C

description: A3 V10.CEL

source_name: Virgin 10 weeks


title: Virgin 10 weeks A

description: A1 V10.CEL


title: Virgin 6 weeks B

description: 2 V6.CEL


title: Virgin 10 weeks B

description: A2 V10.CEL


title: SB7B-INTER_04123

city: Bethesda

first: Jodie

middle: M

last: Fleming

state: MD

address: Bldg 37, 37 Convent drive

department: National Cancer Institute

institute: National Institutes of Health

description: Sections of frozen tissue were subjected to hematoxylin-eosin staining and an AutoPixTM automated LCM system from Arcturus was used to isolate stromal tissue (intra- and inter-lobular) from human mammary gland using static image settings.

hyb_protocol: For each sample, 10 µg of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to a Human U133A microarray for 16 hours at 45ºC.  Following hybridization, the arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.

scan_protocol: The arrays were scanned with an Affymetrix GeneChip® Scanner 3000.

data_processing: Quality check and data analysis were carried out using Affymetrix GeneChip Operating Software (GCOS) and Quality Reporter. All 8 arrays have passed Paradigm Array Labs internal QC metrics.

source_name: Interlobular stromal mammary tissue, patient SB7B

label_protocol: Biotinylated cRNA were prepared using GeneChip Labelling Kit according to the standard Affymetrix protocol

extract_protocol: RNA isolation was performed using standard methods for the isolation of RNA from LCM-derived tissue samples. Each CapSure cap was separately isolated, and RNAs from each specimen were pooled. The quantity of the total RNA sample was determined by spectrophotometry and the size distribution was assessed using an Agilent Bioanalyzer.

tag: Interlobular stromal compartment was derived by LCM from frozen normal human mammary gland tissue.


title: SB29R-INTER_04242

source_name: Interlobular stromal mammary tissue, patient SB929R

label_protocol: Biotinylated cRNA were prepared using GeneChip labelling kit according to the standard Affymetrix protocol.


title: SB13L-INTRA_04129

source_name: Intralobular stromal mammary tissue, patient SB13L

tag: Intralobular stromal compartment was derived by LCM from frozen normal human mammary gland tissue.


title: Gene expression profile of TA cells 2

status: Public on Jul 31 2008

city: Stony Brook

first: Maja

last: Matic

state: NY

address: SUNY at Stony Brook

institute: SUNY at Stony Brook

description: no additional information

hyb_protocol: According to standard Affymetrix protocol

source_name: the basal cells that express MHCI, alpha6+/MHCI+ (transient amplifying cells)

extract_protocol: RNeasy Mini Kit

tag: foreskin


title: Gene expression profile of presumptive keratinocyte stem cells

description: no additional information

scan_protocol: According to standard Affymetrix protocol

source_name: the basal cells that have low/negative MHCI expression, alpha6+/MHCI- cells, (putative stem cells)

extract_protocol: RNAeasy mini kit

tag: B- keratinocytes


title: SB27L-INTER_04245

source_name: Interlobular stromal mammary tissue, patient SB27L


title: SB29R-INTRA_04111

source_name: Intralobular stromal mammary tissue, patient SB29R


title: SB7B-INTRA_04125

source_name: Intralobular stromal mammary tissue, patient SB7B


title: Virgin 6 weeks A

description: 1 V6.CEL


title: Gene expression profile of TA cells

description: no additional information

label_protocol: According to standard Affymetrix protocol


title: Unstable mutant line (1)

city: Lisbon

first: Rita

middle: Maria

last: Batista

address: Av Padre Cruz

department: Food safety and nutrition

country: Portugal

institute: Instituto Nacional de Saude Dr. Ricardo Jorge

description: M1 generation of a 100Gy gamma-irradiated line (cv. Nipponbare)

hyb_protocol: Hybridization to the GeneChip Rice Genome Array (Affymetrix). This array contains probes to query 51,279 transcripts representing two rice subspecies (48,564 japonica transcripts and 1,260 transcripts of indica subspecies).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: Microarrays data analysis was performed with Partek Genomics Suite software. Affymetrix CEL files were imported by using the Robust Multichip Average method, which involves four steps: background correction of the perfect match values, quintile normalization across all of the chips in the experiment, Log2 transformation, and median polish summarization. The logged data were used for hierarchical cluster analysis and statistical analysis.

organism: Oryza sativa

label_protocol: Through synthesis of cRNA with incorporation of biotinylated ribonucleotide analogs.

growth_protocol: Treated seeds were then soaked in Yoshida’s medium for germination in the dark for 2 days at 28°C. Seedlings were further grown at 28°C for 10 days under a 12-h photoperiod regime. Twelve-day-old seedlings were frozen in liquid nitrogen and kept at -80°C until RNA extraction.

extract_protocol: RNA was isolated with the RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions. Total RNA was kept at -80°C and sent to the Affymetrix core facility (Instituto Gulbenkian de Ciência, Oeiras, Portugal).

treatment_protocol: Seeds were manually peeled and immersed for 30 min at 50°C in 0.1% Benlate (fungicide). After washing in distilled sterilized water, seeds were surface-disinfected with 70% (vol/vol) ethanol for 1 min and then with a solution of 2% sodium hypochloride with traces of Tween 20, for 30 min, at room temperature. After thorough washing with distilled sterile water seeds were kept overnight in the final wash.

tag: Tissue:six whole seedlings with 12 days

tag: Plant

value: Oryza sativa L. ssp japonica (cv. Nipponbare)


title: Control for the stable mutant rice line

description: Non-transgenic and non-mutagenised rice line (cv. Estrela A)

value: Oryza sativa L. ssp japonica (cv. Estrela A)


title: Gene expression profile of stem cells

description: no additional information


title: Control for the stable mutant rice line (1)

source_name: Non-transgenic and non-mutagenised rice line (cv. Estrela A)


title: SB27L-INTRA_04132

source_name: Intralobular stromal mammary tissue, patient SB27L


title: MCF7 ESRalpha positive breast cancer cell line, siRNA mediated knock-down XBP1 Replicate 2 dyeswap

city: Heidelberg

first: Mark

last: Fellmann

address: INF 580

department: Molecular Genome Analysis

institute: DKFZ

hyb_protocol: ch1 and ch2 together are solved in 50 µl 1x DIG-Easy hybridization buffer (Roche Diagnostics, Mannheim, Germany), containing 10x Denhardts solution and 2 ng/µl Cot1-DNA (Invitrogen); sample was denaturated at 65°C for 2min, hybridzation of arrays were performed in Corning chambers 14h at 37°C; slides were washed twice in 1xSSC+0.1SDS and once in 0.1xSSC+ 0.1SDS before air pressure drying and scanning.

scan_protocol: arrays were scanned with the GenePix 4000B microarray scanner and analyzed using GenePix Pro 4.1 software (Axon Instruments)

data_processing: raw data processing was performed using ArrayMagic (Buness et al., 2005) including VSN normalization method; after removal of bad quality clones, generalized log ratios from 26618 cDNA clones were given in the data table

source_name: cell line MCF7 siRNA _non-silencing_control_4

label_protocol: direct fluorescent labelling of 2 µg amplified RNA, anneling of 0.5µg Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy3-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy3-labeled probes were purified with Microcon YM-30 column.

growth_protocol: cells were cultivated in Minimum Essential Media (1x) (MEM, Invitrogen, Grand Island, NY, USA), supplemented with 10 % fetal calf serum (FCS), 50 U/ml penicillin, and 50 µg/ml streptomycin sulfate, 1% non-essential amino acids (Invitrogen, Grand Island, NY, USA) and 100 µg/ml insulin bovine

extract_protocol: total RNA was extracted using Rneasy mini-prep kit (Qiagen, Hilden, Germany; 2µg total RNA was amplified one round based on T7 RNA Polymerase (Agilent low RNA Input Amplification Kit)

treatment_protocol: chemically synthesized siRNAs (Qiagen, Hilden, Germany) were transfected with HiPerFect (Qiagen, Hilden, Germany) according to standard transfection procedure

tag: construct non-silencing control siRNA_Replicate4

source_name: cell line MCF7 siRNA XBP1_2-2

label_protocol: direct fluorescent labelling of 2 µg amplified RNA, anneling of 0.5µg Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy5-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy5-labeled probes were purified with Microcon YM-30 column.

tag: construct siRNA STAT5B_Replicate2_2


title: Control for the unstable lines (1)

description: Non-transgenic and non-mutagenised rice line (cv. Nipponbare)


title: Control for the stable transgenic rice line (1)

description: Non-transgenic and non-mutagenised rice line (cv. Bengal)

value: Oryza sativa L. ssp japonica (cv. Bengal)


title: Unstable transgenic line

description: T1 generation of an Agrobacterium tumefaciens transformed line (AtRD29A driven BCBF1 gene, hpt gene), cv. Nipponbare

growth_protocol: Treated seeds were then soaked in Yoshida’s medium, supplemented with 30 mg/liter of hygromicin B, for germination in the dark for 2 days at 28°C. Seedlings were further grown at 28°C for 10 days under a 12-h photoperiod regime. Twelve-day-old seedlings were frozen in liquid nitrogen and kept at -80°C until RNA extraction.


title: Mutant stable line (1)

description: gamma-irradiated rice mutant (semidwarf mutant)- Over 10 generations of self-pollination, cv. Estrela A


title: Control for the stable transgenic rice line

source_name: Non-transgenic and non-mutagenised rice line (cv. Bengal)


title: Stable transgenic rice line (1)

description: T3 generation of a transgenic line expressing a single-chain Fv antibody (ScFvT84.66) against a carcinoembryonic antigen (CEA).


title: SB13L-INTER_04252

source_name: Interlobular stromal mammary tissue, patient SB13L


title: Unstable mutant line

source_name: M1 generation of a 100Gy gamma-irradiated line (cv. Nipponbare)


title: Unstable transgenic line (1)

source_name: T1 generation of an Agrobacterium tumefaciens transformed line (AtRD29A driven BCBF1 gene, hpt gene)


title: Control for the unstable lines

source_name: Non-transgenic and non-mutagenised rice line (cv. Nipponbare)


title: Mutant stable line

source_name: gamma-irradiated rice mutant (semidwarf mutant)- Over 10 generations of self-pollination


title: Stable transgenic rice line

source_name: T3 generation of a transgenic line expressing a single-chain Fv antibody (ScFvT84.66) against a carcinoembryonic antigen (CEA)


title: Sample 3 H37rv - Bif1 mutant

city: Padua

first: Roberta

last: Provvedi

address: Via Gabelli 63

department: Biologia

country: Italy

institute: University of Padua

description: Synthesis od labeled samples was performed as described in protocols of the Center for Applies Genomics (www.cag.icph.org)

scan_protocol: After hybridization slides were immediately scanned using a 428TMArray Scanner (Affymetrix). Fluorescence intensities of Cy3 and Cy5 dies at each spot were quantified using the ImaGene software 5.0 (BioDiscovery, Inc.)

data_processing: Data obtained from qualified spots were normalized using the print-tip LOESS implementation included in GEPAS v3.1 (http://gepas.bioinfo.cnio.es/). Values are expressed as ratio Cy5/Cy3 spot's intensity determined from the normalized fluorescence intensity.

organism: Mycobacterium tuberculosis

source_name: Mycobacterium tuberculosis H37Rv culture

growth_protocol: Culture grown to mid-log phase in Middlebrook 7H9 supplemented with ADC

extract_protocol: Manganelli et al. Mol Microbiol (1999) 31:715-724

treatment_protocol: Culture grown in physiological conditions

tag: Strain H37Rv

source_name: Mycobacterium tuberculosis Bif1 mutant culture

tag: Bif1 mutant strain


title: Sample 2 Bif1 mutant - H37rv

tag: Mutant strain Bif1


title: Sample 1 H37rv - Bif1 mutant

source_name: Mycobacterium tuberculosis Bif1 culture


title: 70088

status: Public on Jul 30 2008

city: Melbourne

first: Prof David

last: Bowtell PhD.

state: VIC

address: Locked Bag 1 A' Beckett St

department: Research Division

country: Australia

institute: PeterMacCallum Cancer Centre

description: Gene expression data from human ovarian tumours

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on GeneChip Affymetrix HG-U133 2.0plus expression array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GS300-7G scanner

data_processing: The data were analyzed with Gene Chip Operating Software Version 1.4 using Affymetrix default analysis settings. The CEL files generated was later normalized using the RMA method

source_name: Ovarian Carcinoma, Serous

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 and column chromotogrpahy

treatment_protocol: Frozen tissue stored at -80oC taken after surgery

tag: Malignant

tag: wild type (BRAF/KRAS)

tag: Grade 3

tag: Stage IIIC

tag: Micropapillary feature NA

tag: (LMP) implants NA

tag: Co-exhistant histology NA

tag: INV Cluster

tag: PRIMARY

tag: arrayed site Ovary

tag: RNA taken from whole tumour sections


title: 70103


title: 93050

tag: not mutation tested


title: 70135


title: 94044


title: 95002

tag: Grade NA

tag: Stage IIIB

tag: Adjacent LMP

tag: LMP Cluster


title: 70144

source_name: Ovarian Tumour, Serous LMP

tag: LMP

tag: mutant BRAF

tag: Grade High

tag: Stage IA

tag: Micropapillary feature Negative

tag: (LMP) implants Negative


title: 70055

tag: mutant ERBB2

tag: Micropapillary feature Positive

tag: (LMP) implants micro-invasive


title: 60267

tag: mutant KRAS

tag: Grade Low

tag: Stage IIIC

tag: (LMP) implants Non-invasive

tag: Co-exhistant histology NA

tag: PRIMARY


title: 70107

tag: Malignant

tag: not mutation tested

tag: Grade 3

tag: Micropapillary feature NA

tag: (LMP) implants NA

tag: INV Cluster

tag: arrayed site Ovary

tag: RNA taken from whole tumour sections


title: 95014


title: 60170

tag: LMP

tag: mutant ERBB2

tag: Stage IIB

tag: Micropapillary feature Negative

tag: LMP Cluster


title: 60214

tag: mutant KRAS

tag: Grade 2

tag: Stage IIIC


title: 70118

tag: wild type (BRAF/KRAS)

tag: Adjacent intraepithelial carcinoma

tag: PRIMARY


title: 60120

tag: Wild Type (BRAF/KRAS/ERBB2)

tag: Grade Low

tag: Stage IIC

tag: (LMP) implants Non-invasive

tag: Co-exhistant histology NA


title: 70148

tag: Malignant

tag: Grade 3

tag: Stage IIIB

tag: Micropapillary feature NA

tag: (LMP) implants NA

tag: INV Cluster

tag: arrayed site Ovary

tag: RNA taken from whole tumour sections


title: 70056

tag: LMP

tag: mutant KRAS

tag: Grade NA

tag: Stage IV

tag: LMP Cluster


title: 60091

tag: wild type (BRAF/KRAS)

tag: Stage IIIC

tag: METASTISIS

tag: arrayed site Peritoneum


title: 60258

tag: Malignant

tag: Co-exhistant histology NA

tag: PRIMARY


title: 60174

tag: not mutation tested

tag: Grade 2

tag: Micropapillary feature NA


title: 70070

tag: mutant BRAF

tag: Grade Low

tag: Stage IA

tag: Micropapillary feature Negative

tag: (LMP) implants micro-invasive

tag: arrayed site Ovary


title: 70057

tag: LMP

tag: Wild Type (BRAF/KRAS/ERBB2)

tag: Grade High

tag: Stage IIIA

tag: Micropapillary feature Positive

tag: (LMP) implants Non-invasive

tag: LMP Cluster

tag: RNA taken from whole tumour sections


title: 60175

tag: Malignant

tag: wild type (BRAF/KRAS)

tag: Grade 3

tag: Stage IIIC

tag: (LMP) implants NA

tag: Co-exhistant histology NA

tag: INV Cluster

tag: PRIMARY


title: 60016

tag: Grade 2

tag: Stage IIIB

tag: Micropapillary feature NA

tag: METASTISIS

tag: arrayed site Peritoneum


title: 60048


title: 44262

tag: LMP

tag: mutant BRAF

tag: Grade NA

tag: Stage IC

tag: Micropapillary feature Positive

tag: arrayed site Ovary


title: 51068

tag: Grade High

tag: Stage IA

tag: LMP Cluster

tag: RNA taken from whole tumour sections


title: 44366

tag: Malignant

tag: wild type (BRAF/KRAS)

tag: Grade 3

tag: Stage IV

tag: (LMP) implants NA

tag: Co-exhistant histology NA

tag: INV Cluster


title: 41310

tag: Stage IIIC

tag: Micropapillary feature NA

tag: METASTISIS

tag: arrayed site Peritoneum


title: 60067

tag: Grade 2


title: 34801


title: 44110

tag: Stage IC

tag: PRIMARY

tag: arrayed site Ovary


title: 44428

tag: not mutation tested


title: 41300

tag: RNA taken from whole tumour sections


title: 44078

tag: Malignant

tag: Stage IIIB


title: 34165

tag: mutant KRAS


title: 32089

tag: wild type (BRAF/KRAS)

tag: Grade 3


title: 44196

tag: Grade NA

tag: Stage IB

tag: (LMP) implants NA

tag: Adjacent LMP

tag: LMP Cluster


title: 51005

tag: Stage IV

tag: Micropapillary feature NA

tag: Adjacent Brenner Tumor

tag: INV Cluster


title: 44349

tag: Co-exhistant histology NA

tag: METASTISIS

tag: arrayed site Peritoneum


title: 51174

tag: LMP

tag: mutant BRAF

tag: Grade High

tag: Stage IA

tag: Micropapillary feature Positive

tag: (LMP) implants Negative

tag: PRIMARY

tag: arrayed site Ovary

tag: RNA taken from whole tumour sections


title: 34019

tag: Malignant

tag: mutant KRAS

tag: Grade 3

tag: Stage IIIC

tag: (LMP) implants NA


title: 41192

tag: wild type (BRAF/KRAS)

tag: Stage IV

tag: Micropapillary feature NA

tag: Co-exhistant histology NA

tag: INV Cluster


title: 32117

tag: LMP

tag: mutant BRAF

tag: Grade Low

tag: Stage IIA

tag: Micropapillary feature Negative

tag: LMP Cluster


title: 51062

tag: Adjacent LMP/MPSC

tag: PRIMARY

tag: arrayed site Ovary

tag: RNA taken from whole tumour sections


title: 34111

tag: Malignant

tag: mutant KRAS

tag: Grade 3

tag: Stage IIIC


title: 32103

tag: not mutation tested

tag: Stage IIIA

tag: Micropapillary feature NA

tag: (LMP) implants NA


title: 34113

tag: wild type (BRAF/KRAS)

tag: Grade 2

tag: Co-exhistant histology NA

tag: INV Cluster


title: 34186

tag: METASTISIS

tag: arrayed site Peritoneum


title: 23202

tag: no co-exhistant histology noted

tag: PRIMARY


title: 27006

tag: arrayed site Ovary

tag: RNA taken from whole tumour sections


title: 23177

tag: LMP

tag: Wild Type (BRAF/KRAS/ERBB2)

tag: Grade High

tag: Stage IC

tag: Micropapillary feature Positive

tag: (LMP) implants Non-invasive

tag: LMP Cluster


title: 23170

tag: Malignant

tag: not mutation tested

tag: Grade 3

tag: Stage IIIC

tag: Micropapillary feature NA

tag: (LMP) implants NA


title: 23167

tag: no co-exhistant histology noted

tag: INV Cluster


title: 23098

tag: Stage IIC

tag: PRIMARY

tag: arrayed site Ovary


title: 23066

tag: LMP

tag: Wild Type (BRAF/KRAS/ERBB2)

tag: Grade Low

tag: Stage IIIA

tag: Micropapillary feature Negative

tag: Co-exhistant histology NA

tag: RNA taken from whole tumour sections


title: 23162

tag: Malignant

tag: wild type (BRAF/KRAS)


title: CML Patient 4 before therapy

city: Duesseldorf

first: Daniela

last: Bruennert

address: Universitaetsstr. 1

department: Clinic for Hematology, Oncology and clin. Immunology

institute: University Clinic Duesseldorf

description: (CML) chronic myeloid leukaemia / CD34+ stem cells before Glivec therapy

hyb_protocol: According to manufacturers instructions

scan_protocol: According to manufacturers instructions

data_processing: MAS 5.0, Scaling Factor 500

source_name: Peripheral Blood

label_protocol:
GeneChip Expression 3’-Amplification One-Cycle-Target Labeling & Control Reagents
(Affymetrix; 900493)

extract_protocol: Qiagen RNeasy mini kit (Qiagen; 74106)

tag: CD34+ cells of CML patient before therapy


title: 23106

tag: Grade 3

tag: Stage IIIC

tag: Micropapillary feature NA


title: CML Patient 6 before therapy


title: CML Patient 5 before therapy


title: CML Patient 2 7 days therapy

description: (CML) chronic myeloid leukaemia / CD34+ stem cells after 7 days of Glivec therapy

tag: CD34+ cells of CML patient after 7 days of Glivec therapy


title: CML Patient 1 7 days therapy


title: CML Patient 6 7 days therapy


title: CML Patient 4 7 days therapy


title: CML Patient 5 7 days therapy


title: 23128

tag: not mutation tested

tag: (LMP) implants NA

tag: Adjacent Serous cystadenoma

tag: INV Cluster

tag: METASTISIS

tag: arrayed site Peritoneum


title: 23077

tag: PRIMARY

tag: arrayed site Ovary


title: 23172

tag: no co-exhistant histology noted


title: 23055

tag: RNA taken from whole tumour sections


title: CML Patient 3 7 days therapy


title: 8261_6month

city: RTP

first: Hongzu

last: Ren

state: NC

address: 109 TW Alexander Dr

institute: US Environmental Protection Agency

description: gene expression data from rat liver samples- 6,11,18,24 months old

hyb_protocol: Samples were hybridized according to the Affymetrix protocol

scan_protocol: Affymetrix protocol using a GeneChip scanner 3000

data_processing: Affymetrix GeneChip microarray suite software was used for washing and scanning.  Expression summaries were calculated using an analysis algorithm adapted from Choe et al. (2005) [PMID: 15693945], in the sequence of "Background correction (MAS5), Quantile normalization (RMA), Perfect match adjustment (MAS5), Median polish (RMA), LOESS normalization.

organism: Rattus norvegicus

source_name: rat liver from 6month F344

label_protocol: Samples were labeled according to the Affymetrix protocol

growth_protocol: Rats were housed at Charles River until 1 week before necropsy. Animal facilities were controlled for temperature (20-24°C) and relative humidity (40-60%), and kept under a 12-h light-dark cycle.

extract_protocol: Total RNA was isolated using the TriReagent procedure (Molecular Research Center, Cincinnati, OH) and the Qiagen Rneasy mini RNA cleanup protocol (Qiagen, Valencia, CA)

treatment_protocol: no treatment

tag: Male F344 rats were obtained from Charles River.

tag: no additional


title: Rpb3 ChIP in S288C Rpb3-TAP strain- Sample1

city: Munich

first: Anna

middle: J.

last: Jasiak

address: Feodor-Lynen-Str. 25

department: Department of Chemistry and Biochemistry

institute: Gene Center, Ludwig-Maximilians-University of Munich

hyb_protocol: Hybridization was performed by imaGenes GmbH, as part of the NimbleGen ChIP-chip service (http://www.imagenes-bio.de/services/nimblegen/chip) following the NimbleGen protocol. See www.nimblegen.com for details.

scan_protocol: Scanning was performed by imaGenes GmbH, as part of the NimbleGen ChIP-chip service (http://www.imagenes-bio.de/services/nimblegen/chip) using Agilent Microarray Scanner http://www.chem.agilent.com/Scripts/PDS.asp?lPage=398 following the manufacturer's guidelines.

data_processing: The data was obtained from log2 of the fluorescent signal from the ChIP DNA divided by the signal from the genomic background. A standard background correction was performed on all such signals by subtracting their genome-wide average.

organism: Saccharomyces cerevisiae

source_name: Rpb3 ChIP in S288C Rpb3-TAP strain - IP sample

label_protocol: Labeling was performed by imaGenes GmbH, as part of the NimbleGen ChIP-chip service (http://www.imagenes-bio.de/services/nimblegen/chip) following the NimbleGen labeling protocol. See www.nimblegen.com for details.

growth_protocol: All yeast strains were grown  in YPD medium, at 30°C untill OD600 0.6-0.8.

extract_protocol: ChIP was performed essentially as described in: Aparicio, O., Geisberg, J. V., Sekinger, E., Yang, A., Moqtaderi, Z., and Struhl, K. (2005) Curr Protoc Mol Biol Chapter 21, Unit 21 23. Briefly, chromatin was sheared with a BioruptorTM UCD-200 (Diagenode) using 25 x 30 sec cycles with 30 sec breaks at an output of 200 W. Before proceeding with immunoprecipitation experiments 20 μl of chromatin solution was put aside and marked an Input sample. For immunoprecipitation of TAP-tagged Rpb3 and Rpb7, IgG SepharoseTM 6 Fast Flow (GE Healthcare) was used.  Precipitation was performed for 3 h at room temperature. For precipitation of Rpb4 and Rpb7 from W303 wild type cells, a mixture of Protein A and Protein G Sepharose was incubated with rabbit-anti-rat IgG antibodies for 1 h at room temperature and then incubated with rat monoclonal antibodies against Rbp4/7 for an additional 4-5 h at room temperature. These coupled beads were incubated overnight at 4°C with chromatin solution.DNA samples were amplified and re-amplified with GenomePlex® Complete Whole Genome Amplification (WGA) Kit and GenomePlex® WGA Reamplification Kit (Sigma) using the Farnham Lab WGA Protocol for ChIP-chip (http://www.genomecenter.ucdavis.edu/farnham/protocol.html). DNA quantity and quality control was performed with a ND-1000 Spectrophotometer (NanoDrop Technologies).

tag: Strain:S288C Rpb3-TAP (ATCC 201388:MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0), Open Biosystems

tag: IP sample

tag: IP with IgG Sepharose beads

source_name: Rpb3 ChIP in S288C Rpb3-TAP strain - Input sample

tag: Input chromatin

tag: background DNA


title: 23053

tag: Malignant

tag: wild type (BRAF/KRAS)

tag: Grade 3

tag: Stage IIIC

tag: Micropapillary feature NA


title: 8245_6month


title: mock ChIP in W303 wt strain

description: Mock-input

source_name: mock ChIP in W303 wt strain - IP sample

tag: Strain

tag: mock IP - IgG Sepharose incubated with W303 wt chromatin

source_name: mock ChIP in W303 wt strain - Input sample


title: Rpb4/7 ChIP in W303 wt strain

source_name: Rpb4/7 ChIP in W303 wt strain - IP sample

tag: IP with monoclonal antibody for Rpb4/7

source_name: Rpb4/7 ChIP in W303 wt strain - Input sample


title: 23030

tag: (LMP) implants NA

tag: Co-exhistant histology NA

tag: INV Cluster

tag: PRIMARY

tag: arrayed site Ovary


title: 23036

tag: LMP

tag: mutant BRAF

tag: Grade High

tag: Micropapillary feature Negative

tag: (LMP) implants micro-invasive

tag: LMP Cluster

tag: RNA taken from whole tumour sections


title: 8230_6month

tag: Male F344 rats were obtained from Charles River.

tag: no additional


title: Rpb3 ChIP in S288C Rpb3-TAP strain- Sample3

tag: Strain:S288C Rpb3-TAP (ATCC 201388:MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0), Open Biosystems

tag: IP sample

tag: IP with IgG Sepharose beads

tag: Input chromatin

tag: background DNA


title: Rpb7 ChIP in S288C Rpb7-TAP strain- Sample1

source_name: Rpb7 ChIP in S288C Rpb7-TAP strain - IP sample

tag: Strain:S288C Rpb7-TAP (ATCC 201388:MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0), Open Biosystems

source_name: Rpb7 ChIP in S288C Rpb7-TAP strain - Input sample


title: 23052

tag: Stage IA

tag: Micropapillary feature NA

tag: (LMP) implants NA

tag: Co-exhistant histology NA

tag: PRIMARY


title: 8005_11month

source_name: rat liver from 11month F344


title: Rpb3 ChIP in S288C Rpb3-TAP strain- Sample2

tag: Dye exchange


title: CML Patient 2 before therapy

tag: CD34+ cells of CML patient before therapy


title: 7525_18month

source_name: rat liver from 18month F344


title: 8095_11month


title: 8200_6month


title: CML Patient 3 before therapy


title: CML Patient 1 before therapy


title: 8035_11month


title: 7975_11month


title: Rpb7 ChIP in S288C Rpb7-TAP strain- Sample2


title: 22048

tag: Malignant

tag: wild type (BRAF/KRAS)

tag: Grade 2

tag: Stage IIC

tag: INV Cluster

tag: arrayed site Ovary


title: 7450_18month

tag: Male F344 rats were obtained from Charles River.

tag: no additional


title: 7434_18month


title: 7060_24month

source_name: rat liver from 24month F344


title: 22029

tag: Grade 3

tag: Stage IV

tag: no co-exhistant histology noted

tag: RNA taken from whole tumour sections


title: 7075_24month


title: 22027

tag: LMP

tag: mutant KRAS

tag: Grade Low

tag: Stage IIA

tag: Micropapillary feature Negative

tag: (LMP) implants Non-invasive

tag: LMP Cluster


title: 22012

tag: Malignant

tag: not mutation tested

tag: Stage IIIC

tag: Micropapillary feature NA

tag: (LMP) implants NA

tag: Co-exhistant histology NA

tag: PRIMARY


title: 22023

tag: Grade 2

tag: INV Cluster

tag: arrayed site Ovary


title: 7030_24month

tag: Male F344 rats were obtained from Charles River.

tag: no additional


title: 6985_24month


title: 7421_18month


title: 22002

tag: LMP

tag: mutant BRAF

tag: Grade High

tag: Stage IIIB

tag: Micropapillary feature Positive

tag: RNA taken from whole tumour sections


title: BN46 12month high dose

description: gene expression data from rat liver samples- 4,12,24 months old

source_name: rat liver from 12month Brown Norway exposed to toluene

growth_protocol: Rats were housed individually. Animal facilities were controlled for temperature (20-24°C) and relative humidity (40-60%), and kept under a 12-h light-dark cycle.

treatment_protocol: 1.0g/kg body weight toluene by gavage in corn oil

tag: Male Brown Norway rats were obtained from Charles River through NIA.


title: 20046

tag: Malignant

tag: mutant KRAS

tag: Stage IIIA


title: BN43 12month high dose


title: BN71 24month high dose

source_name: rat liver from 24month Brown Norway exposed to toluene


title: BN45 12month high dose


title: BN51 24month control

source_name: rat liver from 24month Brown Norway


title: BN25 12month control

source_name: rat liver from 12month Brown Norway


title: BN69 24month high dose


title: BN53 24month control


title: BN52 24month control


title: BN22 4month high dose

source_name: rat liver from 4month Brown Norway exposed to toluene


title: BN27 12month control


title: BN29 12month control


title: BN70 24month high dose


title: 488

source_name: Ovarian Carcinoma, Serous

tag: not mutation tested

tag: Grade 3

tag: Stage III

tag: Micropapillary feature NA

tag: (LMP) implants NA

tag: Co-exhistant histology NA


title: BN21 4month high dose

tag: no additional


title: 479

tag: Grade 2

tag: Stage IV

tag: INV Cluster

tag: METASTISIS

tag: arrayed site Other


title: Rpb3 ChIP in W303 Rpb3-TAP strain

source_name: Rpb3 ChIP in W303 Rpb3-TAP strain - IP sample

tag: Strain

tag: IP sample

tag: IP with IgG Sepharose beads

source_name: Rpb3 ChIP in W303 Rpb3-TAP strain - Input sample

tag: Input chromatin

tag: background DNA


title: 525

tag: Malignant

tag: wild type (BRAF/KRAS)

tag: Stage IIIC

tag: PRIMARY

tag: arrayed site Ovary

tag: RNA taken from whole tumour sections


title: 424

tag: Grade 3

tag: Micropapillary feature NA

tag: (LMP) implants NA

tag: Co-exhistant histology NA

tag: arrayed site Peritoneum


title: hog1Dmsn2/4D vs  hog1D +glucose rep1

status: Public on Jul 29 2008

city: Cambridge

first: Andrew

middle: P

last: Capaldi

state: MA

address: Bauer 307, 7 Divinity Ave

department: MCB

institute: Harvard University

description:
hog1Dmsn2/4D vs  hog1D +glucose rep1
251338410986t.gpr

hyb_protocol: Labelled cDNA was hybridized and the arrays washed following the Agilent protocols with 200ng of cDNA in each channel

scan_protocol: Arrays were scanned on an Axon 4000b and the images quantified in Genepix 5

data_processing: Data in table were normalized using the LOWESS like function in Rosetta Resolver.  Genes were included in the table if one channel (Cy3 or Cy5) was 1.5 fold above that of the negative control spots

source_name: hog1Dmsn2/4D +0.75M Glucose

label_protocol: polyA RNA was converted into cDNA using reverse transcription with amino allyl UTP in the mix.  The sample was then labelled with Cy5 or Cy3 by incubation with the N-terminal ester of the appropriate dye.

growth_protocol: An overnight culture of cells was used to innoculate a culture to OD 0.05 in YEPD media and then grown to OD =0.58-0.60 (at 30 C shaking at 200 rpm) before harvesting (250ml) by filtration and snap freezing or treatment with stress and then filtration and snap freezing.

extract_protocol: Total RNA was isolated using Hot Phenol/Chloroform followed by NaAC, Isoproponal ppt.  Poly A RNA was then isolated using oligodT cellulose.  See manuscript for further details

treatment_protocol: Cells treated with KCl stress had YEPD at 30 C +KCl (or Glucose) added to the medium to a final concentration of 0.375M (0.75M) for 20min.

tag: strain EY0690 (w303)

source_name: hog1D +0.75M glucose (20min)


title: hog1Dmsn2/4D vs  hog1D +glucose rep2

description:
hog1Dmsn2/4D vs  hog1D +glucose rep2
251338411522b.gpr


title: hog1Dmsn2/4D vs  msn2/4D +glucose rep1

description:
hog1Dmsn2/4D vs  msn2/4D +glucose rep1
251338410986b.gpr

source_name: msn2/4D +0.75M glucose (20min)


title: hog1D +glucose rep2

description:
hog1D +glucose rep2
251338410961b.gpr

source_name: hog1D +0.75M Glucose

source_name: wt +0.75M Glucose (20min)


title: msn2/4D +glucose rep3

description:
msn2/4D +glucose rep3
251338410985b.gpr

source_name: msn2/4D +0.75M Glucose


title: BN4 4month control

source_name: rat liver from 4month Brown Norway

tag: Male Brown Norway rats were obtained from Charles River through NIA.

tag: no additional


title: BN3 4month control


title: BN19 4month high dose


title: msn2/4D +glucose rep1

description:
msn2/4D +glucose rep1
251338410719b.gpr


title: 261

tag: not mutation tested

tag: Grade 2

tag: Stage IV

tag: INV Cluster


title: BN5 4month control


title: msn2/4D +glucose rep2

description:
msn2/4D +glucose rep2
251338410961t.gpr


title: hog1Dmsn2/4D vs  hog1D +glucose rep3

description:
hog1Dmsn2/4D vs  hog1D +glucose rep3
251338411522t.gpr


title: hog1Dmsn2/4D vs  msn2/4D +glucose rep3

description:
hog1Dmsn2/4D vs  msn2/4D +glucose rep3
251338411523b.gpr


title: hog1D +glucose rep3

description:
hog1D +glucose rep3
251338410985t.gpr


title: hog1Dmsn2/4D vs  msn2/4D +glucose rep2

description:
hog1Dmsn2/4D vs  msn2/4D +glucose rep2
251338411523t.gpr


title: Confluent hMSC patient 3080 (time course III)

city: Derio

first: Lourdes

last: Osaba

address: Parque Tecnologico de Bizkaia. Ed. 801

country: Spain

institute: Progenika Biopharma

description: gene expression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45ºC on GeneChip Human U133Plus2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix)

data_processing: The data were analyzed with GeneSpring GX software using RMA and global median normalization method

source_name: hMSC, confluence

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

growth_protocol: hMSC obtained from bone marrow  were maintained in alpha MEM, supplemented with 10% FBS, 100 U/mL penicillin, 0.1 mg/mL streptomycin, 100 μmol/L ascorbic acid-2 phosphate and 10-8 M dexamethasone  at 37°C in  5% CO2-humidified atmosphere. To obtain the formation of mineral nodules, 10 mM β-glycerophosphate was added to the hMSC cultures following the second confluence.

extract_protocol: Rneasy Mini kit according to manufacturer's instructions

tag: male


title: wt +glucose rep2

description:
wt +glucose rep2
251338410956t.gpr

source_name: wt +0.75M Glucose

source_name: wt in YEPD


title: HeLa cells transfected with miR-181 duplex versus control transfected HeLa, 24 hours

first: Whitehead

last: Institute

address: 9 Cambridge Center

department: Genome Technology Core

institute: Whitehead Institute

description: Expression profiling comparison of mRNAs in miRNA-181-transfected HeLa cells vs. mock-transfected HeLa cells

hyb_protocol: Agilent Sure Hybe Protocol

scan_protocol: Agilent Scanner

data_processing: Agilent Feature Extraction Software, Protocol: GE2-v5_95_Feb07

source_name: Mock transfected HeLa cells, 24 hours

label_protocol: Agilent 1 Cycle Labelling Standard Protocol

growth_protocol: HeLa cells were grown in SILAC DMEM media.

extract_protocol: Qiagen RNeasy Plus

treatment_protocol: Cells grown in SILAC media containing heavy amino acids (Arg and Lys) were mock-transfected with lipofectamine 2000 (Invitrogen).

tag: Expression profile of mRNAs from mock-transfected HeLa cells for 24 hours

source_name: HeLa cells transfected with miR-181 duplex, 24 hours

treatment_protocol: Cells grown in SILAC media containing light amino acids (Arg and Lys) were transfected with miRNA-181 duplexes.

tag: Expression profile of mRNAs from HeLa cells transfected with miR-181 duplex for 24 hours


title: Confluent hMSC patient 3002 (time course III)

description: gene expression data


title: Confluent hMSC patient 3205 (time course III)

description: gene expression data


title: HeLa cells transfected with miR-124 duplex versus control transfected HeLa, 24 hours

description: Expression profiling comparison of mRNAs in miRNA-124-transfected HeLa cells vs. mock-transfected HeLa cells

source_name: HeLa cells transfected with miR-124 duplex, 24 hours

treatment_protocol: Cells grown in SILAC media containing light amino acids (Arg and Lys) were transfected with miRNA-124 duplexes.

tag: Expression profile of mRNAs from HeLa cells transfected with miR-124 duplex for 24 hours


title: hog1D +glucose rep1

description:
hog1D +glucose rep1
251338410956b.gpr


title: Confluent hMSC patient 3206 (time course III)

description: gene expression data


title: wt +glucose rep1

description:
wt +glucose rep1
251338410720b.gpr


title: HeLa cells transfected with miR-1 duplex versus control transfected HeLa, 24 hours

description: Expression profiling comparison of mRNAs in miRNA-1-transfected HeLa cells vs. mock-transfected HeLa cells

source_name: HeLa cells transfected with miR-1 duplex, 24 hours

treatment_protocol: Cells grown in SILAC media containing light amino acids (Arg and Lys) were transfected with miRNA-1 duplexes.

tag: Expression profile of mRNAs from HeLa cells transfected with miR-1 duplex for 24 hours


description:
hog1Dsko1Dhot1Dmsn2/4D versus sko1Dhot1Dmsn2/4D +KCl rep2
251338411526b.gpr

source_name: hog1Dsko1Dhot1Dmsn2/4D + 0.375M KCl (20min)

source_name: sko1Dhot1Dmsn2/4D +0.375M KCl (20min)


title: hot1Dmsn2/4D versus hot1D +KCl rep3

description:
hot1Dmsn2/4D versus hot1D +KCl rep3
251338411546t.gpr

source_name: hot1Dmsn2/4D + 0.375M KCl (20min)

source_name: hot1D +0.375M KCl (20min)


description:
hog1Dsko1Dhot1Dmsn2/4D versus sko1Dhot1Dmsn2/4D +KCl rep3
251338411526t.gpr


description:
hog1Dsko1Dhot1Dmsn2/4D versus sko1Dhot1Dmsn2/4D +KCl rep1
251338411525b.gpr


title: hot1Dmsn2/4D versus msn2/4D +KCl rep2

description:
hot1Dmsn2/4D versus msn2/4D +KCl rep2
251338411547b.gpr


title: sko1Dmsn2/4D versus sko1D +KCl rep1

description:
sko1Dmsn2/4D versus sko1D +KCl rep1
251338410916t.gpr

source_name: sko1Dmsn2/4D + 0.375M KCl (20min)

source_name: sko1D +0.375M KCl (20min)


title: sko1Dmsn2/4D versus sko1D +KCl rep2

description:
sko1Dmsn2/4D versus sko1D +KCl rep2
251338410919b.gpr


title: hot1Dmsn2/4D versus hot1D +KCl rep1

description:
hot1Dmsn2/4D versus hot1D +KCl rep1
251338410984t.gpr


title: hot1Dmsn2/4D versus hot1D +KCl rep2

description:
hot1Dmsn2/4D versus hot1D +KCl rep2
251338411546b.gpr


title: sko1Dmsn2/4D versus sko1D +KCl rep3

description:
sko1Dmsn2/4D versus sko1D +KCl rep3
251338410919t.gpr


title: hot1Dmsn2/4D versus msn2/4D +KCl rep3

description:
hot1Dmsn2/4D versus msn2/4D +KCl rep3
251338411547t.gpr


title: sko1Dmsn2/4D versus msn2/4D +KCl rep3

description:
sko1Dmsn2/4D versus msn2/4D +KCl rep3
251338410902b.gpr


title: sko1Dmsn2/4D versus msn2/4D +KCl rep2

description:
sko1Dmsn2/4D versus msn2/4D +KCl rep2
251338410916b.gpr


description:
sko1Dhot1Dmsn2/4D versus sko1Dhot1D +KCl rep3
251338410998b.gpr

source_name: sko1Dhot1Dmsn2/4D + 0.375M KCl (20min)

source_name: sko1Dhot1D +0.375M KCl (20min)


title: sko1Dmsn2/4D versus msn2/4D +KCl rep1

description:
sko1Dmsn2/4D versus msn2/4D +KCl rep1
251338410902t.gpr


description:
sko1Dhot1Dmsn2/4D versus msn2/4D +KCl rep2
251338410904b.gpr


title: hot1Dmsn2/4D versus msn2/4D +KCl rep1

description:
hot1Dmsn2/4D versus msn2/4D +KCl rep1
251338410984b.gpr


title: sko1Dhot1D in YEPD rep3

description:
sko1Dhot1D in YEPD rep3
251144714321b.gpr

source_name: sko1Dhot1D in YEPD


description:
sko1Dhot1Dmsn2/4D versus sko1Dhot1D +KCl rep1
251338410940t.gpr


description:
sko1Dhot1Dmsn2/4D versus sko1Dhot1D +KCl rep2
251338410908t.gpr


description:
sko1Dhot1Dmsn2/4D versus msn2/4D +KCl rep1
251338410908b.gpr


description:
sko1Dhot1Dmsn2/4D versus msn2/4D +KCl rep3
251338410959t.gpr


title: sko1Dhog1D versus hog1D YEPD rep1

description:
sko1Dhog1D versus hog1D YEPD rep1
251338410962t.gpr

source_name: sko1Dhog1D versus hog1D in YEPD

source_name: hog1D in YEPD


title: sko1Dhog1D versus hog1D YEPD rep2

description:
sko1Dhog1D versus hog1D YEPD rep2
251338410962b.gpr


title: sko1Dhot1Dhog1D versus hog1D +KCl rep2

description:
sko1Dhot1Dhog1D versus hog1D +KCl rep2
251338410998t.gpr

source_name: sko1Dhot1Dhog1D + 0.375M KCl (20min)

source_name: hog1D +0.375M KCl (20min)


title: sko1Dhot1Dhog1D versus hog1D +KCl rep1

description:
sko1Dhot1Dhog1D versus hog1D +KCl rep1
251338410942t.gpr


title: sko1Dhot1Dhog1D versus hog1D +KCl rep3

description:
sko1Dhot1Dhog1D versus hog1D +KCl rep3
251338410960b.gpr


title: sko1Dhot1D in YEPD rep1

description:
sko1Dhot1D in YEPD rep1
251144713944b.gpr

source_name: wt in YEPD


title: sko1Dhot1D in YEPD rep2

description:
sko1Dhot1D in YEPD rep2
251338410824t.gpr


title: sko1Dhot1D +KCl rep1

description:
sko1Dhot1D +KCl rep1
251144714135t.gpr

source_name: sko1Dhot1D + 0.375M KCl (20min)

source_name: wt in 0.375M KCl (20min)


title: hot1D +KCl rep3

description:
hot1D +KCl rep3
251338410734b.gpr

source_name: hot1D + 0.375M KCl (20min)


title: hot1D +KCl rep2

description:
hot1D +KCl rep2
251338410735t.gpr


title: hot1D in YEPD rep2

description:
hot1D in YEPD rep2
251338410751b.gpr

source_name: hot1D in YEPD


title: sko1Dhot1D +KCl rep2

description:
sko1Dhot1D +KCl rep2
251144714135b.gpr


title: sko1D in YEPD rep3

description:
sko1D in YEPD rep3
251338410751t.gpr

source_name: sko1D in YEPD


title: sko1D in YEPD rep2

description:
sko1D in YEPD rep2
251338410750t.gpr


title: sko1D +KCl rep2

description:
sko1D +KCl rep2
251338410734t.gpr

source_name: sko1D + 0.375M KCl (20min)


title: sko1D +KCl rep1

description:
sko1D +KCl rep1
251144714104t.gpr


title: sko1D in YEPD rep1

description:
sko1D in YEPD rep1
251144714104b.gpr


title: sko1D +KCl rep3

description:
sko1D +KCl rep3
251338410749t.gpr


title: hot1D +KCl rep1

description:
hot1D +KCl rep1
251144714106t.gpr


title: msn2/4D in YEPD rep3

description:
msn2/4D in YEPD rep3
251338410835t.gpr

source_name: msn2/4D in YEPD


title: hot1D in YEPD rep1

description:
hot1D in YEPD rep1
251144714106b.gpr


title: msn2/4D in YEPD rep4

description:
msn2/4D in YEPD rep4
251338410838b.gpr


title: hog1Dmsn2/4D in YEPD rep2

description:
hog1Dmsn2/4D in YEPD rep2
251144713622b.gpr

source_name: hog1Dmsn2/4D in YEPD


title: hog1Dmsn2/4D in YEPD rep1

description:
hog1Dmsn2/4D in YEPD rep1
251144714298t.gpr


title: hog1Dmsn2/4D in YEPD rep3

description:
hog1Dmsn2/4D in YEPD rep3
251338410835b.gpr


title: msn2/4D in YEPD rep1

description:
msn2/4D in YEPD rep1
251144713944t.gpr


title: hog1D in YEPD rep4

description:
hog1D in YEPD rep4
251338410838t.gpr


title: Aging time course - Day 7 - 2

city: Stanford

first: Stuart

last: Kim

department: Department of Developmental Biology

institute: Stanford University Medical Center

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69441.gif
Measurement: time(relative) 7 d

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 940, 18200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.69; Parameter Scan Time = 12:36:59; Parameter PMT Volts = 580; Parameter Scan Date = 2006-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 134295; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.60; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.69; Parameter Scan Time = 12:36:59; Parameter PMT Volts = 660; Parameter Scan Date = 2006-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 133836; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.18; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang

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: Caenorhabditis elegans

source_name: N2 ref.

label_protocol: not provided

extract_protocol: not provided

tag: N2 ref.

source_name: Day 7

tag: Day 7


title: hog1D in YEPD rep3

description:
hog1D in YEPD rep3
251144713943t.gpr


title: msn2/4D in YEPD rep2

description:
msn2/4D in YEPD rep2
251144714297b.gpr


title: Aging time course - Day 7 - 1

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69440.gif
Measurement: time(relative) 7 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 720, 19200; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.61; Parameter Scan Time = 12:43:54; Parameter PMT Volts = 580; Parameter Scan Date = 2006-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 134302; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.62; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.61; Parameter Scan Time = 12:43:54; Parameter PMT Volts = 660; Parameter Scan Date = 2006-01-26; Parameter Pixel Size = 10; Parameter Laser on time = 133843; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.18; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang


title: hog1D in YEPD rep1

description:
hog1D in YEPD rep1
251144713943b.gpr


title: hog1D in YEPD rep2

description:
hog1D in YEPD rep2
251144714297t.gpr


title: Aging time course - Day 4 - 4

description:
Simple annotation: C. elegans, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2006-07/69439.gif
Measurement: time(relative) 4 d

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 940, 18120; Parameter Datafile type = GenePix Results 1.4; Software: type: feature extraction; Performer: Min,,Jiang Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.62; Parameter Scan Time = 11:21:14; Parameter PMT Volts = 610; Parameter Scan Date = 2006-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 134214; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.68; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 37.62; Parameter Scan Time = 11:21:14; Parameter PMT Volts = 590; Parameter Scan Date = 2006-01-20; Parameter Pixel Size = 10; Parameter Laser on time = 133755; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [65491]; Parameter Laser Power = 1.16; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Min,,Jiang

source_name: Day 4

tag: Day 4