title: R6 3

status: Public on Nov 18 2006

type: RNA

city: ILLKIRCH

first: Gretta

last: ABOU-SLEYMANE

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing: MAS 5.0 algorithms - Global data normalization

label: Biotinylated cRNA

molecule: total RNA

organism: Mus musculus

source_name: Retina

tag: Strain

tag: Gender

value: Male

tag: Age

value: 9 weeks (Moderate stage)

tag: Transgene

value: Mutant huntingtin


title: R6 4


title: HUVEC cells transduced with vMIP-II 2

status: Public on Nov 11 2006

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

country: USA

institute: The Scripps Research Institute

description: HUVEC COntrol Sample 1

hyb_protocol: Standard Affymetrix

data_processing: Affymetrix GCOS signal Intensities

label: SAPE

organism: Homo sapiens

source_name: Human Umbilical Vein Endothelial Cells

label_protocol: Ambion Message Amp II with biotin

extract_protocol: Trizol RNA extraction

tag: HUVEC cells transduced with vMIP-II 2


title: HUVEC Control 1

description: HUVEC COntrol Sample 1

tag: Control cells


title: HUVEC Control 3

description: HUVEC COntrol Sample 1

tag: Huvec cells


title: HUVEC cells transduced with vMIP-II 1

description: HUVEC COntrol Sample 1

tag: HUVEC cells transduced with vMIP-II 1


title: R6 2


title: Liver_Hp-Hx null_rep4

status: Public on Nov 01 2006

city: Trieste

first: Diego

last: Vozzi

address: Via dell'Istria

department: Dipartimento di Scienze della Riproduzione

country: Italy

institute: Ospedale Burlo-Garofalo

description: The mice used in the experiments [wild-type (Hp+/Hx+/), Hp-null (Hp-/-Hx+/), Hx-null (Hp+/Hx-/-), and HpHx-null (Hp-/-Hx-/-)] were littermates derived by breeding F1 double heterozygous Hp+/-Hx+/- mice in the mixed genetic background C57/BLJ6 X 129Sv.

data_processing: Log (base 2) [Arithmetic median from channel 2/Arithmetic median from channel 1]. Locfit Normalization; Filter: Signal/Noise Threshold=2.5 and Standard Deviation Regularization , Low Intensity Filter (all intensity median value above 400 were removed)

source_name: Reference pool wild-type mice

tag: Pool of liver from at least 5 wild-type (Hp+/Hx+/) mice

source_name: Hp-Hx knockout mouse

tag: Pool of liver from at least 5 haptoglobin-hemopexin null mice. The mice were littermates derived by breeding F1 double heterozygous Hp+/-Hx+/- mice in the mixed genetic background C57/BLJ6 X 129Sv.


title: Liver_Hp-Hx null_rep2

tag: Pool of liver from at least 5 wild-type (Hp+/Hx+/) mice.


title: parent_3X3_6days

status: Public on Nov 10 2006

type: MPSS

city: Hayward

first: Christian

middle: D

last: Haudenschild

address: 25861 Industrial Blvd

institute: Solexa, Inc.

description:
whole organism:
Library Oyst.F3M3_ful01
Oysters larvae
Age: 6 days
Sex: undifferentiated
cDNA library:
Library 	DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment)
Sequence length	17 bp
MPSS:
runs
Oyst.F3M3_ful01.3357F.a	8/9/2002	598046	19292	QC Passed
Oyst.F3M3_ful01.3357T.b	8/9/2002	577307	22128	QC Passed
Oyst.F3M3_ful01.3357F.c	8/9/2002	559781	19636	QC Passed
Run group:
Total Beads successfully sequenced - 1735134
Total Distinct Signatures - 27446

data_processing: run group

label: MPSS

organism: Magallana gigas

source_name: oyster parent 3X3 larvae

treatment_protocol: The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634.  Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library.  The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.

tag: whole organism:

tag: Library Oyst.F3M3_ful01

tag: Oysters larvae

value: 6 days

tag: Sex

value: undifferentiated

tag: cDNA library:

tag: Sequence length	17 bp

tag: MPSS:

tag: runs

tag: Run group:

tag: Total Distinct Signatures - 27446


title: HUVEC Control 2

description: HUVEC COntrol Sample 1

tag: Huvec Cells


title: Liver_Hp-Hx null_rep1


title: Liver_Hp null_rep3

source_name: Hp knockout mouse

tag: Pool of liver from at least 5 haptoglobin null mice. The mice were littermates derived by breeding F1 double heterozygous Hp+/-Hx+/- mice in the mixed genetic background C57/BLJ6 X 129Sv.


title: Liver_Hp null_rep1


title: Liver_Hx null_rep4

source_name: Hx knockout mouse

tag: Pool of liver from at least 5 hemopexin null mice. The mice were littermates derived by breeding F1 double heterozygous Hp+/-Hx+/- mice in the mixed genetic background C57/BLJ6 X 129Sv.


title: Liver_Hp null_rep4


title: parent_5X5_6days

description:
whole organism: Library Oyst.F5M5_ful01 Oysters larvae Age: 6 days Sex: undifferentiated cDNA library: Library DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment) Sequence length 17 bp MPSS: runs
 Oyst.F5M5_ful01.3359F.b 8/8/2002 705467 19897 QC Passed Oyst.F5M5_ful01.3359F.a 8/8/2002 681356 21191 QC Passed Oyst.F5M5_ful01.3359T.a 8/8/2002 555701 17618 QC Passed Oyst.F5M5_ful01.3359T.b 8/8/2002 499852 19303 QC Passed
 Run group: Total Beads successfully sequenced - 2442376 Total Distinct Signatures - 25553

source_name: oyster parent 5X5 larvae

treatment_protocol: The mRNA was processed according to the MPSS protocol as outlined in the publications : Brenner, S., et al. (2000) Proc Natl Acad Sci U S A 97(4):1665-1670 and Brenner, S. et al., Nat. Biotechnol 18(6): 630-634. Briefly, the mRNA was reverse transcribed and the cDNA was digested with DpnII. The cDNA fragment starting at the 3' most DpnII site and ending with the polyA was cloned into a Megaclone vector library. The resulting library was amplified and loaded onto microbeads. About 1.6 million microbeads were loaded into each flow cell and the signature sequences were determined by a series of enzymatic reactions as outlined in the above publications. The abundance for each signature was converted to transcripts per million (tpm) for the purpose of comparisons between samples.

tag: whole organism

value: Library Oyst.F5M5_ful01 Oysters larvae Age:6 days Sex:undifferentiated cDNA library:Library DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment) Sequence length 17 bp MPSS:runs

tag: Run group


title: Liver_Hx null_rep3

description:
The mice used in the experiments [wild-type (Hp+/Hx+/), Hp-null (Hp-/-Hx+/), Hx-null (Hp+/Hx-/-), and HpHx-null (Hp-/-Hx-/-)] were littermates derived by breeding F1 double heterozygous Hp+/-Hx+/- mice in the mixed genetic background C57/BLJ6 X 129Sv.
(Hx=Hemopexin; Hp= Haptoglobin )
At least 5 adult mice were perfused via aorta with PBS, sacrificed and their liver pooled.


title: hybrid_3X5_6days

description:
whole organism: Library Oyst.F5M3_ful01 Oysters larvae Age: 6 days Sex: undifferentiated cDNA library: Library DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment) Sequence length 17 bp MPSS: runs
 Oyst.F5M3_ful01.3364T.b 8/9/2002 462881 21213 QC Passed Oyst.F5M3_ful01.3364F.b 8/9/2002 586917 24163 QC Passed Oyst.F5M3_ful01.3364F.a 8/9/2002 556938 21709 QC Passed Oyst.F5M3_ful01.3364T.a 8/9/2002 544843 23102 QC Passed
 Run group: Total Beads successfully sequenced - 2151579 Total Distinct Signatures - 28741

source_name: oyster hybrid 3X5 larvae

value: Library Oyst.F5M3_ful01 Oysters larvae Age:6 days Sex:undifferentiated cDNA library:Library DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment) Sequence length 17 bp MPSS:runs


title: Liver_Hp null_rep2


title: Liver_Hx null_rep2

description: The mice used in the experiments  [wild-type (Hp+/Hx+/), Hp-null (Hp-/-Hx+/), Hx-null (Hp+/Hx-/-), and HpHx-null (Hp-/-Hx-/-)] were littermates derived by breeding F1 double heterozygous Hp+/-Hx+/- mice in the mixed genetic background C57/BLJ6 X 129Sv.

tag: Pool of liver from at least 5 wild-type (Hp+/hx+/) mice.

tag: Pool of liver from at least 5 hemopexin null (Hx-) mice. The mice were littermates derived by breeding F1 double heterozygous Hp+/-Hx+/- mice in the mixed genetic background c57/BLJ6X 129 Sv.


title: Liver_Hp-Hx null_rep3

tag: Pool of liver from at least 5 wild-type (Hp+/Hx+/) mice.

tag: Pool of liver from at least 5 haptoglobin-hemopexin null mice. The mice were littermates derived by breeding F1 double heterozygous Hp+/-Hx+/- mice in the mixed genetic background C57/BLJ6 X 129Sv.


title: Liver_Hx null_rep1

description:
The mice used in the experiments  [wild-type (Hp+/Hx+/), Hp-null (Hp-/-Hx+/), Hx-null (Hp+/Hx-/-), and HpHx-null (Hp-/-Hx-/-)] were littermates derived by breeding F1 double heterozygous Hp+/-Hx+/- mice in the mixed genetic background C57/BLJ6 X 129Sv.
(Hx=Hemopexin; Hp= Haptoglobin )

At least 5 adult mice were perfused via aorta with PBS, sacrificed and their liver pooled.


title: MRC5_4 hours_UV exposure_M01_4H/4C

status: Public on Nov 17 2006

city: Hsinchu

first: ChengWei

last: Chang

address: 101, Section 2 Kuang Fu Road

department: bmes

country: Taiwan

institute: nthu

description: Data processing will be described in detail in our website http://140.114.106.30/publication/kuchang/

hyb_protocol: Two-step hybridizations were performed. During the first hybridization, cDNA products was pipetted onto the array. Then, the array was incubated in the hybridization chamber in a water bath at 65℃ for 16 to 20 hours for the probe/target hybridization. At the second hybridization, the 3DNA dendrimer was pipetted onto the array and the array was submerged in a 65℃ water bath for only 2 to 3 hours for capture primer – 3DNA dendrimer hybridization. After hybridization, array was washed with SSC and SDS mixed buffer suggested by manufacturer’s instruction of 3DNA array 350 kit.

scan_protocol: Barcode=12766240 "PMTGain=700	500" Scanner=GenePix 4100A 01 [100641] "LaserPower=2.91	3.12" Temperature=29.79 "ScanPower=100	100"

data_processing: Spots were first selected by (1) excluding spots defined as flag or absent (2) keeping only channels with signal - background / SD of background greater than 1 (3) keeping spot diameter greater 75μm (4) eliminating spots with intensity CV greater than 100 in ether channel. The log ratio of the last spots were calculated and normalized by pin-wised LOWESS fit normalization.

source_name: Sample harvested at 4 hours after UV irradiation

label_protocol: 3DNA Array 350 kit was used for fluorescence labeling on cDNA. Each total RNA (5μg) sample was reversely transcribed by Superscript II to single strand cDNA with the capture primer. cDNA was then purified by microcon YM-30 column and was blocked by addictive 0.5μg of Cot1 human DNA.

growth_protocol: The MRC-5 cell, obtained from the American Type Culture Collection (ATCC, MA, USA) was grown in the complete growth medium and was incubated at 37 oC and 5 % CO2 in air atmosphere. The complete growth medium was the α-MEM medium supplemented with antibiotic (100 U/ml penicillin plus 10ug/ml streptomycin), and 10% heat-inactivated fetal bovine serum. The medium was replenished every 48 h after cell passage. Cells were routinely subcultivated in cell culture petri dishes of 100 mm2 every 3-4 days with 1:3 subcultivation ratio. In the beginning of subcultivation, the cell layer was briefly rinsed with 2 ml of 0.25% (w/v) trypsin-0.53 mM EDTA in 15 ~ 20 seconds after removal of whole medium with serum. Then we incubated the culture dish at 37 oC to facilitate dispersal in 1.5~2 min. We add fresh complete growth medium 10 ml per petri dish and aspirate cells by gently pipeting. Finally we add appropriate aliquots of the cell suspension to new petri dishes. The entire experiments were performed at passages 21 to 28.

extract_protocol: Total RNA was extracte by lying directly in the 100mm petri dish with 1.0 ml TRIzol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instruction and then purified by RNeasy kit (Qiagen, Inc., Valencia, CA).

tag: Cell strain, Gender

value: male, Age:14 weeks, Tissue: hung fibroblast,

source_name: Control samples corresponding to 4H

treatment_protocol: No


title: hybrid_5X3_6days

description:
whole organism: Library Oyst.F3M5_ful01 Oysters larvae Age: 6 days Sex: undifferentiated cDNA library: Library DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment) Sequence length 17 bp MPSS: runs
 Oyst.F3M5_ful01.3358F.b 8/8/2002 593744 16306 QC Passed Oyst.F3M5_ful01.3358F.a 8/8/2002 651271 17662 QC Passed Oyst.F3M5_ful01.3358T.a 8/8/2002 531946 18009 QC Passed Oyst.F3M5_ful01.3358T.b 8/8/2002 491956 15885 QC Passed
 Run group: Total Beads successfully sequenced - 1826157 Total Distinct Signatures - 22954

source_name: hybrid 5X3 larvae

value: Library Oyst.F3M5_ful01 Oysters larvae Age:6 days Sex:undifferentiated cDNA library:Library DpnII restriction - (classic MPSS, cloning DpnII to poly A fragment) Sequence length 17 bp MPSS:runs


title: PT_10b+

status: Public on May 30 2006

city: Bet-Dagan

first: Carmiya

last: Bar-Or

address: Hamaccabim

department: Genomics

country: Israel

institute: ARO

description:
RNA Source:
RNA was extracted from nematode-infected and non-infected (control) potato plants. Following is a detailed description of plant growth and inoculation. Eggs of root-knot nematodes (Meloidogyne javanica) were extracted from greenhouse cultures and second-stage juveniles (J2) were hatched in tap, sterile water on 30 µm sieves. Solanum tubersum cv. Desiree explants (stem including an axillary bud) were sectioned, under sterile conditions from in vitro growing seedlings and transferred to Magenta boxes containing Gamborg's media. Seedlings, 4 weeks post transferring to Gamborg's media were planted in pots containing autoclaved quartz sand. Three weeks later the plants were infected with 3000 M. javanica infective juveniles, applied to the soil in tap, sterile water. Control (non-infected) plants were mock-inoculated with tap, sterile water. Roots from 6 infected and 6 non-infected plants were collected following 5 and at 10 days. Roots were observed under the microscope, and nematode feeding sites were selectively dissected, from young lateral roots. To control for the effect of tissue sectioning on gene expression, young lateral roots of the non-infected plants were dissected similarly to the infected roots, and collected. Dissected roots were snapped-freeze in liquid nitrogen and immediately stored in -80 C freezer. The experiment for each time point was duplicated, each duplicate derived from independent biological repeat.

RNA Samples:
Total RNA was extracted with the RNeasy Kit (Qiagen, Valencia, CA) from infected and non-infected roots, and comprised test RNA samples. In addition, equal amounts of 20 ug were pooled from all of test RNA samples to form a reference sample, in which every test sample was equally represented (Churchill, 2002). The test and reference RNA samples were subjected to amplification with the MessageAmp aRNA kit (Ambion, Austin, TX), using as starting material 2.5 to 5 µg of total RNA. These resulted in nine samples, a reference sample and 8 test samples designated: '5a-', '5a+', '10a-', '10a+', '5b-', '5b+', '10b-', '10b+' for non-infected (-) or infected (+), 5 or 10 d and first (a) or second (b) biological repeat.

Microarray Experiment Design:
Each test RNA sample was co-hybridized with the reference RNA sample, according to a microarray experiment reference design

hyb_protocol: Bar-Or C, Kapulnik Y, Koltai H: A broad characterization of the transcriptional profile of the compatible tomato response to the plant parasitic root knot nematode Meloidogyne javanica. Eur J Plant Pathol 2005, 111:181-192.

data_processing: GeneSpring (GeneSpring 5.1; Silicon Genetics, Redwood City, CA) was used for Lowess normalization, where 35% of the data served for smoothing. Channel2 (control channel) values lower than 40 were set to 40. Channel1 was divided by Channel2, and this ratio was Log2 transformed.

organism: Solanum tuberosum

tag: Strain

value: Solanum tubersum cv. Desiree; Tissue:Roots; Age:~7 weeks; Treatment:10 days post nematode-incoluation;

value: Solanum tubersum cv. Desiree; Tissue:Roots; RNA Source:A mix of nematode infected and non-infected roots at 5, 10 and 15 days of infection/non-infection.


title: Characterization of an Arabidopsis thaliana mutant deficient in the GAPC gene-3

status: Public on Oct 31 2006

city: Rosario

first: Paula

last: Casati

state: Santa Fe

address: Suipacha 531

department: Biological Sciences

country: Argentina

institute: Universidad Nacional de Rosario

description: Normalization between the Cy3 and Cy5 fluorescent dye emission channels was achieved by adjusting the levels of both image intensities. The experiments were repeated three times with samples from different experiments, as biological replicates. In dye swapping experiments, the RNA samples from different experiments were labeled reciprocally, both as a biological and technical repetition for comparing the reproducibility of the experiments.The hybridization intensities of each microarray element were measured using ScanAlyze 4.24 (available at http://genome-www4.stanford.edu/MicroArray/SMD /restech.html). The two channels were normalized in log space using the z-score normalization on a 95% trimmed data set. We removed unreliable spots according to the following criteria: spots flagged as having false intensity caused by dust or background on the array were removed; and spots for which intensity was less than three fold above background were also eliminated. Data from multiple experiments were normalized (Bolstad et al., 2003) and signals from spots from different experiments were analyzed using Significance Analysis of Microarrays using the one class response (SAM, Tusher et al., 2001, http://www-stat.stanford.edu/~tibs/SAM/.), with a false discovery rate <10%.

hyb_protocol: Labeled samples were mixed and then hybridized to a microarray for 15 h at 60C. The slides were washed at room temperature in three wash steps: 2x SSC, 0.5% SDS; 0.5x SSC; and 0.05x SSC for 5 min each with gentle shaking.

scan_protocol: The slides were scanned with a GenePix 4000B Scanner

data_processing: Significance Analysis of Microarrays

organism: Arabidopsis thaliana

source_name: WT arabidopsis plants

tag: The experimental RNA sample was directly labeled with Cy3-dUTP fluorescent dye

source_name: GAPC mutant arabidopsis plant

tag: The experimental RNA sample was directly labeled with Cy5-dUTP fluorescent dye


title: Characterization of an Arabidopsis thaliana mutant deficient in the GAPC gene-2

source_name: GAPC mutant plant


title: PT_05b+

scan_protocol: Bar-Or C, Kapulnik Y, Koltai H: A broad characterization of the transcriptional profile of the compatible tomato response to the plant parasitic root knot nematode Meloidogyne javanica. Eur J Plant Pathol 2005, 111:181-192.

value: Solanum tubersum cv. Desiree; Tissue:Roots; Age:~7 weeks; Treatment:5 days post nematode-incoluation;


title: PT_05a+


title: PT_10b-

value: Solanum tubersum cv. Desiree; Tissue:Roots; Age:~7 weeks; Treatment:10 days post mock-incoluation;


title: PT_05b-

value: Solanum tubersum cv. Desiree; Tissue:Roots; Age:~7 weeks; Treatment:5 days post mock-incoluation;

value: Solanum tubersum cv. Desiree; Tissue:Roots; RNA Source:A mix of nematode infected and non-infected roots at 5, 10 and 15 days of infection/non-infection


title: PP_10b+

hyb_protocol: Rensink WA, Iobst S, Hart A, Stegalkina S, Liu J and Buell CR: Gene expression profiling of potato response to cold, heat,, and salt stress; Funct Integr Genomics (2005) 5:210-207.


title: PT_10a+


title: Characterization of an Arabidopsis mutant deficient in the GAPC gene-1

tag: The experimental RNA sample wasdirectly labeled with Cy3-dUTP fluorescent dye

source_name: WT arabidopsis plant


title: PP_10b-

scan_protocol: Rensink WA, Iobst S, Hart A, Stegalkina S, Liu J and Buell CR: Gene expression profiling of potato response to cold, heat,, and salt stress; Funct Integr Genomics (2005) 5:210-207.


title: E19_epithelial cells_strain2

status: Public on Apr 29 2006

city: Providence

first: Juan

last: Sanchez-Esteban

state: RI

address: 101 Dudley Street

department: Pediatrics

institute: Women & Infants Hospital/Brown Medical School

description: Total RNA was extracted from E19 type II cells using TRIzol reagent and the Rneasy Mini Kit. RNA was reverse-transcribed into cDNA with a T7-(dT)24 oligomer to prime the first-strand synthesis. DNA polymerase and DNA ligase were included in the synthesis of the second strand. After phase lock gel phenol/chloroform cDNA extraction and ethanol precipitation, double stranded cDNA was converted into cRNA. Following cleanup, fragmentation of the cRNA for target preparation was done according to the Affymetrix GeneChip Expression Analysis Protocol. After hybridization cocktails preparation, the Affymetrix rat E230A GeneChip array was hybridized with the fragmented labelled cRNA for 16 h at 45 °C as described in the Affymetrix Technical Analysis Manual. GeneChips, bound to streptavidin-phycoerythrin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Agilent G2500A GeneArray Scanner

data_processing: data were processed using Microarray Suite software, v. 5.0 (MAS 5.0) to yield expression values. These values were calculated from the difference in signal intensity following hybridization with "perfect match" (PM) and "mismatch" (MM) oligonucleotides in each probe

label: biotin

organism: Rattus norvegicus

source_name: E19 type II epithelial cells, 16 h, strain

label_protocol: conversion of double stranded cDNA into biotin-labeled cRNA was accomplished using the BioArray High Yield RNA Transcript Labeling kit (T7) (Enzo Diagnostics, Farmingdale, NY) according to the manufacturer’s instructions.

growth_protocol: Cells were maintained in serum-free DMEM medium.

extract_protocol: Total RNA was extracted from E19 type II cells using TRIzol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA) and purified further using the Rneasy Mini Kit (Invitrogen).

treatment_protocol: After isolation, E19 type II cells were cultured on silastic membranes coated with collagen 1. Next day monolayers were exposed to cyclic strain 5%, 60 cycles/min for 15 min + 2.5% continuous distention for the remaining 45 min of each hour, for 16 h, using the Flexercell FX-4000 Strain Unit

value: CD

tag: Gender

value: male and female

tag: Age

value: Embryonic day 19

tag: Tissue

value: Fetal lung from time-pregnant rats

tag: Cells

value: Type II epithelial


title: E19_epithelial cells_strain1

hyb_protocol: After hybridization cocktails preparation, the Affymetrix rat E230A GeneChip array was hybridized with the fragmented labelled cRNA for 16 h at 45 °C as described in the Affymetrix Technical Analysis Manual.

scan_protocol: GeneChips, bound to streptavidin-phycoerythrin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Agilent G2500A GeneArray Scanner

data_processing: data were processed using Microarray Suite software, v. 5.0 (MAS 5.0) to yield expression values. These values were calculated from the difference in signal intensity following hybridization with with "perfect match" (PM) and "mismatch" (MM) oligonucleotides in each probe


title: PT_10a-


title: PP_10a-


title: puroB replicate 1

status: Public on May 03 2006

city: Stockholm

first: Kyle

middle: Matthew

last: Sousa

address: Scheeles väg 1 A1 Plan 2

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Molecular Neurobiology

description: puroB is a clonal control(puromycin resistant) stable c17.2 neural stem cell line with similar proliferation rate as clone 42 and therefore both were matched for subsequent analysis.

hyb_protocol: standard Affymetrix procedures, no PolyA controls used

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: c17.2 mouse neural stem cell line

label_protocol: Approximately 10 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA). First strand synthesis was carried out by a T7-(dT)24 primer and SuperScript II Reverse Transcriptase (Gibco BRL Life Technologies) using 10?g of total RNA sample (Qiagen) from c17.2 neural stem cells stably transfected with the orphan nuclear receptor Nurr1 (clone42 and clone 48) or stably transfected with empty puromycin control vector (puro B and puroD)

tag: pB  is a clonal control (puromycin resitant) stably-expressing stem cell line


title: E19_epithelial cells_control3

source_name: E19 type II epithelial cells, 16 h, control

treatment_protocol: After isolation, E19 type II cells were cultured on silastic membranes coated with collagen 1. Next day monolayers were maintained on non-strained conditions for 16 h (control)


title: PP_10a+


title: K562_Imatinib_resistant_dup2

status: Public on Mar 31 2006

city: Tokyo

first: Junko

middle: H

last: Ohyashiki

address: 6-7-1, Nishishinjuku, Shinjuku-ku

department: Intractable Immune System Diseases Research Center

country: Japan

institute: Tokyo Medical University

description: A novel structural entity, imatinib (STI571; Novartis, Basel, Switzerland), a potent and selective inhibitor of the tyrosine kinase activity of BCR-ABL, has shown promise against Ph-positive leukemia in human clinical trials. However, the emergence of imatinib resistance in patients with acute forms of Ph-positive leukemia has highlighted the need for overriding chemotherapy to eradicate this disease.

hyb_protocol: Hybridization was carried out automatically using GeneTAC Hybstation (Genomic Solutions, US) according to the supplier’s instruction. The conditions of hybridization were 55oC for 2 hours, 50oC for 2 hours, and 46oC for 2 hours, then 42oC for 12 hours.

scan_protocol: The　hybridized signals were scanned by GenePix 4000B Microarray Scanner (Axon Instruments, Union City, CA, USA).

data_processing: The scanned data was normalized, verified, and analyzed using the Genomic Profiler software (Mitsui Industrial Knowledge, Inc, Tokyo, Japan:http://bio.mki.co.jp/en/product/index.html).

label_protocol: 20 microgram of RNA were labeled using a LabelStar Array kit (Qiagen) , according to the supplier’s instruction.

extract_protocol: Total RNA was extracted using a RNeasy Mini Kit (Qiagen, Germantown, MD, USA).The amount of RNA was measured by NanoDrop (NanoDrop Technologies, Wilmington, DE, USA), then the quality of extracted RNA was checked using a 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

treatment_protocol: K562 cells were cultured with 0.1 microM of imatinib for 2 weeks, and then the concentration of imatinib was gradually increased.  Finally imatinib-resistant K562-IMR cells can grow in the presence of 10 microM of imatinib.

tag: Imatinib-resistant K562-IMR cells

tag: reference


title: K562_Imatinib_resistant_dup1


title: puroD replicate 1

description: puroD is a clonal control(puromycin resistant) stable c17.2 neural stem cell line with similar proliferation rate as clone 48 and therefore both were matched for subsequent analysis.

tag: pD  is a clonal control (puromycin resitant) stably-expressing stem cell line


title: clone 48 replicate 1

description: clone 48 is a clonal Nurr1 stable c17.2 neural stem cell line with similar proliferation rate as puroD and therefore both were matched for subsequent analysis.

tag: c48 is a clonal Nurr1 stably-expressing stem cell line


title: K562_Imatinib_dup1

description: Imatinib (STI571; Novartis, Basel, Switzerland), a potent and selective inhibitor of the tyrosine kinase activity of BCR-ABL

source_name: Imatinib treated K562 cells

treatment_protocol: 5 microMol of imatinib for 12 hrs

tag: A Ph-positive chronic myelogenous leukemia cell line treated with imatinib.


title: K562_BMS_dup2

description: BMS-354825 is a clinically active “next-generation” BCR-ABL inhibitors.

source_name: BMS-354825  treated K562 cells

treatment_protocol: 10 nM of BMS-354825 for 12 hrs.

tag: A Ph-positive chronic myelogenous leukemia cell line treated with BMS-354825.


title: K562_Imatinib_BMS_dup2

description: Imatinib (STI571; Novartis, Basel, Switzerland), a potent and selective inhibitor of the tyrosine kinase activity of BCR-ABL. BMS-354825 is a clinically active “next-generation” BCR-ABL inhibitor.

source_name: K562 cells treated with Imatinib and BMS-354825

tag: BCR-ABL-positive K562 cells were treated with 5 microMol of imatinib and  10 nM of BMS-354825 for 12 hrs.


title: E19_epithelial cells_strain3


title: K562_BMS_dup1

description: BMS-354825 is a  clinically active “next-generation” BCR-ABL inhibitors.

scan_protocol: The hybridized signals were scanned by GenePix 4000B Microarray Scanner (Axon Instruments, Union City, CA, USA).

source_name: BMS treated K562 cells

label_protocol: 20 microgram of RNA were labeled using  a LabelStar Array kit (Qiagen) , according to the supplier’s instruction.

tag: A Ph-positive chronic myelogenous leukemia cell line treated with BMS.


title: C-025-JJN3+CKS1B

city: Little Rock

first: Shaughnessy

middle: Jr.

last: John

state: AR

address: 4301 West Markham St., Slot 776

institute: Myeloma Institute for Research and Therapy

description: JJN3 with CKS1B shRNA

hyb_protocol: standard Affymetrix procedures

source_name: Human myeloma cell line

tag: Human myeloma cell line JJN3


title: B-021-JJN3+CKS1B

description: JJN3 with CKS1B shRNA


title: C-024-JJN3+SCRAMB

description: JJN3 with non-specific scrambled shRNA


title: PT_05a-

tag: Strain

value: Solanum tubersum cv. Desiree; Tissue:Roots; Treatment:5 days post mock-incoluation; Age:~7 weeks


title: A-010-JJN3+SCRAMBLE

description: JJN3 with non-specific scrambled shRNA


title: PP_05a+


title: PP_05b-


title: E19_epithelial cells_control2


title: clone 42 replicate 1

description: clone 42 is a Nurr1 stable c17.2 neural stem cell line with similar proliferation rate as puroB and therefore both were matched for subsequent analysis.

extract_protocol: RNA probes were labeled according to the supplier’s instructions (Affymetrix, Santa Clara, CA, USA). First strand synthesis was carried out by a               T7-(dT)24 primer and SuperScript II Reverse Transcriptase (Gibco BRL Life Technologies) using 10?g of total RNA sample (Qiagen) from c17.2 neural stem cells stably transfected with the orphan nuclear receptor Nurr1 (clone42 and clone 48) or stably transfected with empty puromycin control vector (puro B and puroD)

tag: c42 is aclonal Nurr1 stably-expressing stem cell line


title: ASO T00278950

status: Public on Mar 01 2006

city: Carlsbad

first: Michael

last: Pear

address: 1896 Rutherford Rd

department: Research Informatics

institute: Isis Pharmaceuticals, Inc.

description: mir-122 antisense used is a 2'-O-methoxyethyl phosphorothioate modified antisense RNA oligonucleotide with sequence 5'-ACAAACACCAUUGUCACACUCCA-3'

hyb_protocol: CodeLink Expression Assay protocol

scan_protocol: CodeLink Expression Assay protocol

data_processing: CodeLink Expression Analysis 4.1.0.29054

source_name: liver

label_protocol: CodeLink Expression Assay protocol

extract_protocol: For RNA isolation, liver was homogenized in RNeasy RLT buffer using Polytron homogenizer, layered onto 5.7M CsCl2 and pelleted after overnight centrifugation at 35000 rpm, room temp.  The pellet was resuspended in RLT buffer and RNA was isolated on RNeasy midi columns following the manufacturer's instructions, and including an on-column DNase digestion step.

treatment_protocol: Male C57Bl/6 mice injected i.p. 2x/week for 4 weeks with 50mg/kg miR-122 ASO, sacrificed 2 days after last dose.

tag: Male C57Bl/6  Mice were 10.5 weeks old at time of sacrifice.


title: PP_05b+


title: Saline T00278944

description: Control group

treatment_protocol: Mice injected i.p. 2x/week for 4 weeks with saline, sacrificed 2 days after last dose.


title: Angiopoietin-like proteins stimulate ex vivo expansion of hematopoietic stem cells 121003C

city: Cambridge

first: Cheng Cheng

last: Zhang

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute

description: Successful ex vivo expansion of hematopoietic stem cells (HSCs) would greatly benefit the treatment of disease and the understanding of critical questions of stem cell biology. Microarray studies showed that the HSC supportive mouse fetal liver CD3+ cells specifically expressed angiopoietin-like 2 (Angptl2) and angiopoietin-like 3 (Angptl3). When highly enriched HSCs were cultured in the presence of Angptl2 or Angptl3 together with saturating levels of other growth factors for 10 days, a 24 or 30 fold net expansion of long-term HSCs was observed by reconstitution analysis. The coiled-coil domain of Angptl2 mediated the effects of Angptl2 on HSC expansion. Furthermore, angiopoietin-like 5, angiopoietin-like 7, and microfibril-associated glycoprotein 4 also supported expansion of HSCs in culture.

hyb_protocol: Standard protocol for Affymetrix gene chips was used. Briefly, biotinylated cRNA was hybridized onto chips in 1X MES hybridization buffer for 16 hr. The fluidics station was then used to wash/stain with streptavidin-phycoerythrin.

scan_protocol: ScanArray Express HT as scanner, and Microarray Suite as software. Standard protocol.

data_processing: Microarray data was analyzed by Microarray Suite

label: phycoerythrin

source_name: mouse fetal liver

label_protocol: Total RNA was extracted from cells using Trizol according to the manufacturer’s recommendations (Life Technologies Inc, Rockville, MD).  After quantification by spectrophotometry and 1.2% agarose gel electrophoresis, 15 micro gram of total RNA was used for first strand and second strand cDNA synthesis, followed by in vitro transcription using Ambion T7 MegaScript Kit to produce biotinylated cRNAs.

growth_protocol: FACS sorted cells were cultured for 3 days at a density of 106 cells / ml in IMDM with 10% FBS, and 20 ng/ml SCF, 30 ng/ml Flt - 3 ligand, and 10 ng/ml IL - 6 in a well of a U - bottom 96 - well plate before RNAs were isolated.

tag: Mouse day 15 fetal liver Gr-1+ cells


title: Saline T00278945

description: Control group


title: Saline T00278946

description: Control group


title: PP_05a-


title: Saline T00278943

description: Control group


title: Angiopoietin-like proteins stimulate ex vivo expansion of hematopoietic stem cells 102203C

extract_protocol: Total RNA was extracted from cells using Trizol according to the manufacturer’s recommendations (Life Technologies Inc, Rockville, MD).  After quantification by spectrophotometry and 1.2% agarose gel electrophoresis, 15 micro gram of total RNA was used for first strand and second strand cDNA synthesis, followed by in vitro transcription using Ambion T7 MegaScript Kit to produce biotinylated cRNAs.

treatment_protocol: FACS sorted cells were cultured for 3 days at a density of 106 cells / ml in IMDM with 10% FBS, and 20 ng/ml SCF, 30 ng/ml Flt - 3 ligand, and 10 ng/ml IL - 6 in a well of a U - bottom 96 - well plate before RNAs were isolated.

tag: Mouse day 15 fetal liver CD3+ cells


title: E19_epithelial cells_control1

scan_protocol: GeneChips, bound to streptavidin-phycoerythrin, were processed using the Affymetrix GeneChip Fluidics Station 400 and scanned with an Agilent G2500A GeneArray Scanner (Agilent Technologies).

data_processing: Data were processed using Microarray Suite software, v. 5.0 (MAS 5.0) to yield expression values. These values were calculated from the difference in signal intensity following hybridization with "perfect match" (PM) and "mismatch" (MM) oligonucleotides in each probe

source_name: E19 type II epithelial cells, 16h, control

tag: Gender:male and female

tag: Age

tag: Tissue

value: Type II epithelial cells


title: Angiopoietin-like proteins stimulate ex vivo expansion of hematopoietic stem cells

treatment_protocol:
Cultured 3 different cell types
-> Total RNA isolation -> dscDNA -> Biotinylated cRNA -> hybridization to Affymetrix U74Bv2 and U74Cv2 mouse chips


title: K563_BMS_resistant_dup2

description: BMS-354825 is a clinically active “next-generation” BCR-ABL inhibitor.

treatment_protocol: K562 cells were cultured with 0.5 nM of BMS-354825 for 2 weeks, and then the concentration of BMS-354825 was gradually increased. Finally BMS-354825-resistant K562-BMSR cells can grow in the presence of 10 nM of BMS-354825.

tag: BMS-354825 resistant K562 cells

value: K562 (MOCK)


title: A-011-JJN3+CKS1B

description: JJN3 with CKS1B shRNA


title: K563_BMS_resistant_dup1

treatment_protocol: K562 cells were cultured with 0.5 nM of BMS-354825 for 2 weeks, and then the concentration of BMS-354825 was gradually increased.  Finally BMS-354825-resistant K562-BMSR cells can grow in the presence of 10 nM of BMS-354825.

tag: reference


title: naive vs. S.pneumoniae 12h

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: Microarray experiments were done as two-color hybridizations. RNA labeling was performed with a Fluorescent Linear Amplification Kit (Agilent Technologies). In brief, cDNA was reverse transcribed from 4 µg of total RNA (derived from five lungs in each group and time point, respectively) with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with either cyanine 3-CTP (Cy3-CTP) or cyanine 5-CTP (Cy5-CTP) and T7 polymerase. The fluorescent-labeled antisense cRNA was precipitated overnight with LiCl, ethanol washed and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP and A650nm for Cy5-CTP. Before hybridization, 1.25 µg labeled cRNA of each product were fragmented and mixed with control targets and hybridization buffer according to the supplier's protocol (Agilent Technologies). Hybridizations were done overnight for approximately 17 h at 60°C. The slides were washed according to the manufacturer's manual and scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies). In order to compensate dye specific effects, and to ensure statistically relevant data, a color swap was performed. The RNA samples were labeled vice verse with the two fluorescent dyes (fluorescence reversal).

data_processing: Agilent FE 6.1.1.1 / Rosetta Resolver Built 3.2.2

source_name: naive

tag: C57Bl/6 naive control mice received 20 µl of sterile PBS by transnasal application.

source_name: S.pneumoniae infected 12h

tag: C57Bl/6 mice were infected with 5 x 10e6 colony forming units (cfu) of S. pneumoniae in 20µl phosphate-buffered saline by transnasal application. Preparation of mouse lungs was performed at 12 h after infection.


title: B-020-JJN3+SCRAMBLE+poly

description: JJN3 with non-specific scrambled shRNA


title: 10_15_04 37˚C J774.1 EGDe vs ∆mogR

status: Public on Feb 11 2006

city: Boston

first: Aimee

last: Shen

address: Armenise Building, rm 313, 200 Longwood Avenue

department: Microbiology and Molecular Genetics

institute: Harvard University

description: RNA was harvested from intracellular bacteria grown at 37˚C in J774 cells

data_processing: Gene Pix Pro 3.0 software

organism: Listeria monocytogenes

source_name: ∆mogR

tag: ∆mogR strain grown overnight at 30˚C, 10_10_04 RNA sample, 9hr intracellular growth inside J774 macrophage-like cells (MOI = 1:1)

source_name: EGDe wild-type

label_protocol: 9 hr intracellular growth in J774 macrophage-like cells

tag: EGDe strain grown overnight at 30˚C, 10_10_04 RNA sample, 9hr intracellular growth inside J774 macrophage-like cells (MOI = 1:1)


title: 10_19_04 37˚C J774.1 EGDe vs ∆mogR

description: RNA was harvested from intracellular EGDe and ∆mogR bacteria grown at 37˚C in J774 cells then competitively hybridized

tag: ∆mogR strain grown overnight at 30˚C, 10_05_04 RNA sample, 9hr intracellular growth inside J774 macrophage-like cells (MOI = 1:1)

tag: EGDe strain grown overnight at 30˚C, 10_05_04 RNA sample, 9hr intracellular growth inside J774 macrophage-like cells (MOI = 1:1)


title: K562_BMS_imatinib_dup1

source_name: K562 cells treated with imatinib and BMS-354825

tag: BCR-ABL-positive K562 cells were treated with 5 microMol of imatinib and 10 nM of BMS-354825 for 12 hrs.


title: K562_Imatinib_dup2

tag: A Ph-positive chronic myelogenous leukemia cell line treated with Imatinib.


title: Angiopoietin-like proteins stimulate ex vivo expansion of hematopoietic stem cells 090604C

source_name: mouse adult spleen

tag: Mouse adult spleen CD3+ cells


title: 10_17_04 BHI RT1 EGDe vs ∆mogR

description: RNA was harvested from 24hr cultures grown at RT lying flat in 10mL BHI.

growth_protocol: 24 hr RT lying flat in 10 mL BHI

tag: 7_14_05 RNA sample


title: ASO T00278947

tag: Male C57Bl/6  Mice were 10.5 weeks old at time of sacrifice.


title: Angiopoietin-like proteins stimulate ex vivo expansion of hematopoietic stem cells 102204C

tag: Mouse day 15 fetal liver CD3+ cells


title: 10_15_04 BHI RT1 EGDe vs ∆mogR

tag: 10_10_04 RNA sample


title: ASO T00278948


title: ASO T00278949


title: Angiopoietin-like proteins stimulate ex vivo expansion of hematopoietic stem cells 090603B


title: Saline T00278942

description: Control group

data_processing: CodeLink Expression Analysis	4.1.0.29054


title: HeLa_TP090705_29_HG-U133A_2_IMFGN0023

status: Public on Feb 05 2006

city: RTP

first: Todd

last: Page

state: NC

address: 6 Davis Dr

institute: CIIT

description: TP090705_29_HG-U133A_2_IMFGN0023: This is a repeat of one sample, that was masked in the orginial array (completed 8/31/05). These samples are from the 6_22_05 experiment, they are the siLUC samples

data_processing: affylmGUI, The Walter and Eliza Hall Institute of Medical Research

source_name: Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: Cervical carcinoma, Separation Type: trypsin, Harvest Time Point: 4, Units of Harvest Time Point: hr

growth_protocol:
Growth Media: DMEM_10%FBS_P/S
Amount of Media: 5
Units of Media: ml
Growth Conditions: 37 C_5% CO2

extract_protocol: Extraction Method: Qiagen_RNeasy_Kit

treatment_protocol:
in vitro Treatment: siLuc (Sense 5\'-rCrGUrArCrGrCrGrGrArAUrArCUUrCrGrCTT-3’ Antisense 5’-UrCrGrArArGUrAUUrCrCrGrCrGUrArCrGTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 52, Units of Duration: hrs, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 1.5, Units of Duration: hrs, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: convection, Dose or Concentration: 43, Units of Dose or Concentration: degree Celcius

tag: Array Type

tag: Units of Amount

value: ug

tag: Ratio

tag: RNA Integrity Number

tag: Bioanalyzer Results

value: excellent

tag: Sample Preservation


title: ASO T00278951


title: HeLa_TP082505_22_HG-U133A_2_IMFGN0023

description: TP082505_22_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

source_name: Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL2, Number of Cells Seeded: 2.20E+05, Cell Type: Cervical Carcinoma, Separation Type: Trypsin, Harvest Time Point: 0.5, Units of Harvest Time Point: hr

treatment_protocol:
in vitro Treatment: siLuc (Sense 5'-rCrGUrArCrGrCrGrGrArAUrArCUUrCrGrCTT-3’ Antisense 5’-UrCrGrArArGUrAUUrCrCrGrCrGUrArCrGTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 48.5, Units of Duration: hrs, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: Transfection, Units of Amount of Vehicle: microliter, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 0.5, Units of Duration: hrs, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: Convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius

value: Excellent


title: Angiopoietin-like proteins stimulate ex vivo expansion of hematopoietic stem cells 102202B

tag: Cell type comparison


title: HeLa_TP082505-28_HG-U133A_2_IMFGN0023

description: TP082505-28_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

source_name: Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: Cervical Carcinoma, Separation Type: Trypsin, Harvest Time Point: 4, Units of Harvest Time Point: hr

treatment_protocol:
in vitro Treatment: siLuc (Sense 5'-rCrGUrArCrGrCrGrGrArAUrArCUUrCrGrCTT-3’ Antisense 5’-UrCrGrArArGUrAUUrCrCrGrCrGUrArCrGTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 52, Units of Duration: hrs, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine`, Amount of Vehicle: 0.44, Route of Exposure: Transfection, Units of Amount of Vehicle: microliter, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 1.5, Units of Duration: hrs, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: Convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius


title: Angiopoietin-like proteins stimulate ex vivo expansion of hematopoietic stem cells 121002B

tag: Mouse day 15 fetal liver Gr-1+ cells


title: HeLa_TP082505_20_HG-U133A_2_IMFGN0023

description: TP082505_20_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

source_name: Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL2, Number of Cells Seeded: 2.20E+05, Cell Type: Cervical Carcinoma, Separation Type: Trypsin, Harvest Time Point: 0, Units of Harvest Time Point: hr

treatment_protocol:
in vitro Treatment: siLuc (Sense 5'-rCrGUrArCrGrCrGrGrArAUrArCUUrCrGrCTT-3’ Antisense 5’-UrCrGrArArGUrAUUrCrCrGrCrGUrArCrGTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 48, Units of Duration: hrs, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: Transfection, Units of Amount of Vehicle: microliter, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 0, Units of Duration: hrs, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: Convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius


title: 09_20_04 BHI 37˚C.1 EGDe vs ∆mogR

description: RNA was harvested from cultures of EGDe and ∆mogR grown at 37˚C in BHI and competitively hybridized to TIGR microarrays.

data_processing: gene Pix Pro 3.0 software

tag: ∆mogR strain grown for 24hr lying flat in 10mL BHI at 37˚C, 7_14_04 sample


title: 10_17_04 BHI 37˚C.1 EGDe vs ∆mogR

description: Competitive hybridization of EGDe and ∆mogR total RNA

source_name: ∆mogR, 37˚C

tag: ∆mogR strain, 37˚C, 10_10_04 RNA, 24 hr cultures grown lying flat in 10 mL BHI at 37˚C

tag: EGDe strain, 37˚C, 10_10_04 RNA, 24 hr cultures grown lying flat in 10 mL BHI at 37˚C


title: HeLa_TP082505-27_HG-U133A_2_IMFGN0023

description: TP082505-27_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

source_name: Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: Cervical Carcinoma, Separation Type: Trypsin, Harvest Time Point: 2, Units of Harvest Time Point: hr

treatment_protocol:
in vitro Treatment: siLuc (Sense 5'-rCrGUrArCrGrCrGrGrArAUrArCUUrCrGrCTT-3’ Antisense 5’-UrCrGrArArGUrAUUrCrCrGrCrGUrArCrGTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 50, Units of Duration: hrs, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine`, Amount of Vehicle: 0.44, Route of Exposure: Transfection, Units of Amount of Vehicle: microliter, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 1.5, Units of Duration: hrs, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: Convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius


title: HeLa_TP082505-25_HG-U133A_2_IMFGN0023

description: TP082505-25_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: naive vs. S.pneumoniae 48h

tag: C57Bl/6 naive control mice received 20 µl of sterile PBS by transnasal application.

source_name: S.pneumoniae infected 48h

tag: C57Bl/6 mice were infected with 5 x 10e6 colony forming units (cfu) of S. pneumoniae in 20µl phosphate-buffered saline by transnasal application. Preparation of mouse lungs was performed at 48 h after infection.


title: naive vs. S.pneumoniae 24h

source_name: S.pneumoniae infected 24h

tag: C57Bl/6 mice were infected with 5 x 10e6 colony forming units (cfu) of S. pneumoniae in 20µl phosphate-buffered saline by transnasal application. Preparation of mouse lungs was performed at 24 h after infection.


title: 10_19_04 37˚C J774.2 EGDe vs ∆mogR

tag: EGDe strain grown overnight at 30˚C, 10_05_04 RNA sample, 9hr intracellular growth inside J774 macrophage-like cells (MOI = 1:1)

tag: ∆mogR strain grown overnight at 30˚C, 10_05_04 RNA sample, 9hr intracellular growth inside J774 macrophage-like cells (MOI = 1:1)


title: 10_15_04 37˚C J774.2 EGDe vs ∆mogR

tag: EGDe strain grown overnight at 30˚C, 10_10_04 RNA sample, 9hr intracellular growth inside J774 macrophage-like cells (MOI = 1:1)

tag: ∆mogR strain grown overnight at 30˚C, 10_10_04 RNA sample, 9hr intracellular growth inside J774 macrophage-like cells (MOI = 1:1)


title: 9_20_04 BHI 37˚C.2 EGDe vs ∆mogR

tag: EGDe strain, 37˚C, 7_14_04 RNA, 24 hr cultures grown lying flat in 10 mL BHI at 37˚C

tag: ∆mogR strain, 37˚C, 7_14_04 RNA, 24 hr cultures grown lying flat in 10 mL BHI at 37˚C


title: 10_01_04 BHI 37˚C.1 EGDe vs ∆mogR

tag: EGDe strain, 37˚C, 5_19_04 RNA, 24 hr cultures grown lying flat in 10 mL BHI at 37˚C

tag: ∆mogR strain, 37˚C, 5_19_04 RNA, 24 hr cultures grown lying flat in 10 mL BHI at 37˚C


title: HeLa_01-04-05 TP8_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2

description: 01-04-05 TP8_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

source_name: Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: cervical carcinoma, Separation Type: Trypsin, Harvest Time Point: 2, Units of Harvest Time Point: hr

growth_protocol:
Growth Media: DMEM_10%FBS_P/S
Amount of Media: 5
Units of Media: ml
Growth Conditions: 37 C 5% CO2

treatment_protocol:
in vitro Treatment: siHSF1_#2 (Sense 5’-rArCrArGrCUUrCrCrArCrGUrGUUrCrGrGTT-3’ Antisense 5’-UrCrGrArArCrArCrGUrGrGrArArGrCUrGUTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 50, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 1.5, Units of Duration: hours, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius

tag: Array Type

tag: Ratio

tag: RNA Integrity Number

tag: Bioanalyzer Results

tag: Sample Preservation


title: HeLa_TP082505-19_HG-U133A_2_IMFGN0023

description: TP082505-19_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

source_name: Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: Cervical Carcinoma, Separation Type: Trypsin, Harvest Time Point: 0, Units of Harvest Time Point: hr


title: HeLa_01-04-05 TP4_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2

description: 01-04-05 TP4_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

source_name: Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: cervical carcinoma, Separation Type: Trypsin, Harvest Time Point: 0.5, Units of Harvest Time Point: hr

treatment_protocol:
in vitro Treatment: siHSF1_#2 (Sense 5’-rArCrArGrCUUrCrCrArCrGUrGUUrCrGrGTT-3’ Antisense 5’-UrCrGrArArCrArCrGUrGrGrArArGrCUrGUTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 48.5, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 0.5, Units of Duration: hours, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius


title: 01_25_05 BHI RT EGDe vs ∆mogR

tag: 11_02_04 RNA sample


title: 10_17_04 BHI RT2 EGDe vs ∆mogR

tag: 7_14_05 RNA sample


title: HeLa_01-04-05 TP12_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2

description: 01-04-05 TP12_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

source_name: Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: cervical carcinoma, Separation Type: Trypsin, Harvest Time Point: 4, Units of Harvest Time Point: hr

treatment_protocol:
in vitro Treatment: siHSF1_#2 (Sense 5’-rArCrArGrCUUrCrCrArCrGUrGUUrCrGrGTT-3’ Antisense 5’-UrCrGrArArCrArCrGUrGrGrArArGrCUrGUTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 52, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 1.5, Units of Duration: hours, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius


title: HeLa_01-04-05 TP1_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2

description: 01-04-05 TP1_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

source_name: Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: cervical carcinoma, Separation Type: Trypsin, Harvest Time Point: 0, Units of Harvest Time Point: hr

treatment_protocol:
in vitro Treatment: siHSF1_#2 (Sense 5’-rArCrArGrCUUrCrCrArCrGUrGUUrCrGrGTT-3’ Antisense 5’-UrCrGrArArCrArCrGUrGrGrArArGrCUrGUTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 48, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 0, Units of Duration: hours, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius


title: HeLa_01-04-05 TP10_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2

description: 01-04-05 TP10_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: HeLa_06_21_04 TP-9

description: 06_21_04 TP-9: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

extract_protocol: Extraction Method: Qiagen_Rneasy_Kit

treatment_protocol:
in vitro Treatment: siHSF1_#1 (Sense 5’-rGUrCrGUrCrArArCrArArGrCUrCrAUUrATT-3' Antisense 5’rGrArAUrGrArGrCUUrGUUrGrArCrGrArCTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 50, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 1.5, Units of Duration: hours, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius


title: HeLa_01-04-05 TP11_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2

description: 01-04-05 TP11_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: 10_15_04 BHI RT2 EGDe vs ∆mogR

description: RNA was harvested from 24hr cultures grown at RT lying flat in 10mL BHI.

tag: 10_10_04 RNA sample

source_name: ∆mogR


title: HeLa_TP082505_21_HG-U133A_2_IMFGN0023

description: TP082505_21_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: HeLa_06_21_04 TP-5

description: 06_21_04 TP-5: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

treatment_protocol:
in vitro Treatment: siHSF1_#1 (Sense 5’-rGUrCrGUrCrArArCrArArGrCUrCrAUUrATT-3' Antisense 5’rGrArAUrGrArGrCUUrGUUrGrArCrGrArCTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 48.5, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 0.5, Units of Duration: hours, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius


title: HeLa_TP082505-31_HG-U133A_2_IMFGN0023

description: TP082505-31_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

source_name: Sample Type: Cells, Cell Line: HeLa, ATCC Number: CCL-2, Number of Cells Seeded: 2.20E+05, Cell Type: Cervical Carcinoma, Separation Type: Trypsin, Harvest Time Point: 12, Units of Harvest Time Point: hr

treatment_protocol:
in vitro Treatment: siLuc (Sense 5'-rCrGUrArCrGrCrGrGrArAUrArCUUrCrGrCTT-3’ Antisense 5’-UrCrGrArArGUrAUUrCrCrGrCrGUrArCrGTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 60, Units of Duration: hrs, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine`, Amount of Vehicle: 0.44, Route of Exposure: Transfection, Units of Amount of Vehicle: microliter, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 1.5, Units of Duration: hrs, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: Convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius


title: HeLa_06_21_04 TP-12

description: 06_21_04 TP-12: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

treatment_protocol:
in vitro Treatment: siHSF1_#1 (Sense 5’-rGUrCrGUrCrArArCrArArGrCUrCrAUUrATT-3' Antisense 5’rGrArAUrGrArGrCUUrGUUrGrArCrGrArCTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 52, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 1.5, Units of Duration: hours, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius


title: HeLa_01-04-05 TP7_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2

description: 01-04-05 TP7_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: HeLa_TP082505-30_HG-U133A_2_IMFGN0023

description: TP082505-30_HG-U133A_2_IMFGN0023: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: HeLa_06_21_04 TP-1

description: 06_21_04 TP-1: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.

treatment_protocol:
in vitro Treatment: siHSF1_#1 (Sense 5’-rGUrCrGUrCrArArCrArArGrCUrCrAUUrATT-3' Antisense 5’rGrArAUrGrArGrCUUrGUUrGrArCrGrArCTT-3’), Treatment Repeat: 1, Units of Treatment Repeat: dose, Treatment Duration: 48, Units of Duration: hours, Treatment Time: -48, Units of Treatment Time: hrs, Vehicle for Chemical: Lipofectamine 2000, Amount of Vehicle: 0.44, Route of Exposure: transfection, Units of Amount of Vehicle: ul, Dose or Concentration: 3.3, Units of Dose or Concentration: nM
Treatment_2: in vitro Treatment: Heat, 43ºC, Treatment Repeat: 1, Units of Treatment Repeat: exposure, Treatment Duration: 0, Units of Duration: hours, Treatment Time: 0, Units of Treatment Time: hrs, Route of Exposure: convection, Dose or Concentration: 43, Units of Dose or Concentration: degrees Celcius


title: HeLa_01-04-05 TP9_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2

description: 01-04-05 TP9_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: Enigma RNAi replicate 2

status: Public on Feb 04 2006

city: Charlestown

first: Spyros

last: Artavanis-Tsakonas

address: 7308 Building 149, 13th Street

department: MGH Cancer Research Center

institute: Massachusetts General Hospital

description: Kc-167 cells, 5 day treatment with Enigma specific RNAi.

data_processing: gcRMA through R based affylmGUI module

organism: Drosophila melanogaster

source_name: Kc-167 cells Enigma RNAi

label_protocol: Approximately 8 µg of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Suspension growing cells were pelleted by centifugation and RNA extracted by TRIzol.

tag: Kc-167 cells, 5 day treatment with Enigma-specific RNAi. Specifics:1.6X10^6 cells in 0.5mL of serum-free Sang's M3 media incubated for 1 hour with 20ug of dsRNA, subsequently equal volume of M3 media containing 10% serum was added. Cells harvested after 5 days. RNAi efficiency measured by immunoblot.


title: RNAi control replicate 3

source_name: Kc-167 cells control  RNAi (beta-lactamase)

tag: Kc-167 cells, 5 day treatment with beta-lactamase specific RNAi. Specifics:1.6X10^6 cells in 0.5mL of serum-free Sang's M3 media incubated for 1 hour with 20ug of dsRNA, subsequently equal volume of M3 media containing 10% serum was added. Cells harvested after 5 days. RNAi efficiency measured by immunoblot.


title: HeLa_01-04-05 TP2_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2

description: 01-04-05 TP2_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: HeLa_01-04-05 TP3_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2

description: 01-04-05 TP3_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: HeLa_06_21_04 TP-8

description: 06_21_04 TP-8: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: HeLa_01-04-05 TP5_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2

description: 01-04-05 TP5_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: Enigma RNAi replicate 1


title: HeLa_01-04-05 TP6_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2

description: 01-04-05 TP6_HG-U133A_2_Page_IMFGN0023_05-1_HSF1-2: These samples were previously hybridized on HG-U133A version 1 chips.  This experiment repeats these samples on HG-133A version 2 chips.  HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: HeLa_06_21_04 TP-7

description: 06_21_04 TP-7: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: Control_6months_retina2

status: Public on Feb 01 2006

city: Basel

first: Lydia

last: Michaut

address: Klingelbergstrasse 70

country: Switzerland

institute: Biozentrum, Basel University

description:
Strain: C57BL/6
Age: 6 months
Tissue: retina

data_processing: GCOS Acqusition; RMA normalization

source_name: Retina of 6 month old C57BL/6 mouse

extract_protocol: Trizol

tag: Strain

tag: Age

value: 6 months

tag: Tissue

value: retina


title: HeLa_06_21_04 TP-6

description: 06_21_04 TP-6: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: HeLa_06_21_04 TP-2

description: 06_21_04 TP-2: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: HeLa_06_21_04 TP-3

description: 06_21_04 TP-3: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: HeLa_06_21_04 TP-11

description: 06_21_04 TP-11: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: Enigma RNAi replicate 3


title: Control_6months_retina3


title: RPE65_KO_6months_retina6

description:
Strain: RPE65-/-
Age: 6 months
Tissue: retina

source_name: Retina of 6 month old RPE65 -/- mouse


title: RNAi control replicate 1

description: Kc-167 cells, 5 day treatment with beta-lactamase specific RNAi.


title: RPE65_KO_6months_retina5


title: RPE65_KO_4months_retina33

description:
Strain: RPE65-/-
Age: 4 months
Tissue: retina

source_name: Retina of 4 month old RPE65 -/- mouse

value: 4 months


title: HeLa_06_21_04 TP-4

description: 06_21_04 TP-4: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: RNAi control replicate 2


title: HeLa_06_21_04 TP-10

description: 06_21_04 TP-10: HeLa cells were transfected with siRNA 48 hrs prior to heat shock.  At time=0 HeLa cells were placed in a 43C incubator for 1.5 hrs, at the indicated time points RNA was harvested and Affymetrix microarrays were run.


title: Control_6months_retina1


title: Control_4months_retina17

description:
Strain: C57BL/6
Age: 4 months
Tissue: retina

source_name: Retina of 4 month old C57BL/6 mouse


title: RPE65_KO_6months_retina4


title: RPE65_KO_2months_retina1

description:
Strain: RPE65-/-
Age: 2 months
Tissue: retina

data_processing: CGOS Acquisition, RMA normalization

source_name: Retina of 2 month old RPE65-/- mouse

value: 2 months


title: Control_4months_retina24


title: icr_3000188308

city: Sutton

first: Ian

last: Giddings

state: Surrey

address: 15 Cotswold Road

department: Section of Molecular Carcinogenesis

country: United Kingdom

institute: Institute of Cancer Research

description: Amersham hyb buffer, 50% formamide, 3 O/N 42C

data_processing: A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.

source_name: skin fibroblast

tag: gender

value: female

tag: subset

value: control

source_name: stratagene universal human reference RNA

value: unknown

tag: reference

value: Stratagene Universal Human Reference num 740000


title: icr_3000209303


title: Control_2months_retina9

description:
Strain: C57BL/6
Age: 2 months
Tissue: retina

source_name: Retina of 2 month old C57BL/6 mouse


title: Control_2months_retina11


title: Control_4months_retina14


title: RPE65_KO_4months_retina25


title: Control_2months_retina10


title: RPE65_KO_2months_retina3

description:
Stain: RPE65-/-
Age: 2 months
Tissue: retina

source_name: Retina of 2 month old RPE65 -/- mouse

tag: Stain


title: icr_3000206572


title: RPE65_KO_2months_retina2


title: icr_3000209301

description: Amersham hby buffer, 50% formamide, 3 O/N 42C


title: icr_3000209304

description: 50% formamide, amersham hyb buffer, 42C 3 O/N


title: icr_3000209644

description: Amersham Hyb buffer, 50% formamide, 3 O/N 42C


title: icr_3000209302


title: RPE65_KO_4months_retina31


title: icr_3000188312


title: icr_3000209632


title: icr_3000209305


title: icr_3000188319


title: C57BL/6J-Ghrhr<lit> (lit/lit) mice injected with growth hormone (GH), replicate 5

city: Loma Linda

first: Hongrun

last: Yu

address: 11201 Benton Street (151)

department: Musculoskeletal Disease Center

institute: J.L. Pettis Memorial VA Medical Center

description: Output file name: US14702375_16011472013405_S01_A01.txt

hyb_protocol: Two micrograms of fragmented cyanine 3-labeled cRNA of control sample was mixed with equal amounts of cyanine 5-labeled cRNA of GH treated sample, and the mixtures were incubated for 17 hours at 60°C with constant rotation. The slide was then washed in sodium, saline citrate (SSC) buffer, and dried with pressurized nitrogen

scan_protocol: All slides were scanned using an Agilent DNA Microarray scanner and the images were processed and analyzed using Agilent feature extraction software

data_processing: Data were analyzed using GeneSpring 7.0 (Silicon Genetics).  Local background-subtracted median signal intensities were used as intensity measures and the data were normalized using LOWESS normalization.  The genes which had a raw signal of 100 or greater and passed with flag value present were included in the analysis

source_name: C57BL/6J-Ghrhr<lit> (lit/lit), purchased from the Jackson Laboratories, Bar Harbor, Maine

label_protocol: Total bone RNA  was reverse transcribed and linear amplified using a primer containing oligo (dT) and a T7 RNA polymerase promoter. After synthesis of the first and second strands of cDNA, the product was used in an in vitro transcription reaction to generate cRNA in the presence of cyanine 5-labeled UTP

extract_protocol: Bone tissues were ground with Trizol (Invitrogen, Carlsbad, CA). Total RNA was then extracted with an RNeasy Mini Kit (Qiagen Inc., Valencia, CA), and DNase treated with a DNA-free kit (Ambion, Austin, TX)

treatment_protocol:
GH (4mg/kg body weight) injected subcutaneously
mice euthanized at 24 hours after growth hormone injection

tag: two lit/lit mice, age 28 days, bone (including femur and tibia)

source_name: C57BL/6J-Ghrhr<lit> (lit/lit), provided by the Jackson Laboratories, Bar Harbor, Maine

label_protocol: Total bone RNA  was reverse transcribed and linear amplified using a primer containing oligo (dT) and a T7 RNA polymerase promoter. After synthesis of the first and second strands of cDNA, the product was used in an in vitro transcription reaction to generate cRNA in the presence of cyanine 3-labeled UTP

extract_protocol: Bone tissues were ground with Trizol (Invitron, Carlsbad, CA). Total RNA was then extracted with an RNeasy Mini Kit (Qiagen Inc., Valencia, CA), and DNase treated with a DNA-free kit (Ambion, Austin, TX)

treatment_protocol: PBS injected subcutaneously


title: icr_3000188309


title: icr_3000206573


title: icr_3000209633


title: icr_3000188310


title: icr_3000188311


title: icr_3000188320


title: icr_3000111862


title: C57BL/6J-Ghrhr<lit> (lit/lit) mice injected with growth hormone (GH), replicate 3

description: Output file name: US14702375_16011472013402_S02_A01.txt

treatment_protocol:
GH (4mg/kg body weight) injected subcutaneously
mice euthanized at 6 hours after growth hormone injection


title: icr_3000209643


title: icr_3000188305

description: amersham hyb buffer, 50% formamide, 42C 3O/N


title: icr_3000209642


title: C57BL/6J-Ghrhr<lit> (lit/lit) mice injected with growth hormone (GH), replicate 4

description: Output file name: US12302345_16011472013404_S01_A01.txt


title: icr_3000209328

description: 50% formamide, amersham hyb buffer, 3 O/N 42C


title: icr_3000188314


title: icr_3000188306


title: C57BL/6J-Ghrhr<lit> (lit/lit) mice injected with growth hormone (GH), replicate 6

description: Output file name: US12302345_16011472013406_S01_A01.txt


title: icr_3000209322

description: 50% formamide, amersham hyb buffer, 42C 3O/N


title: icr_3000188521


title: icr_3000115588


title: CGH_2005051122_Embryo1_cell4

type: genomic

city: Leuven

first: Joris

middle: R

last: Vermeesch

address: Herestraat, 49

department: Center for Human Genetics

country: Belgium

institute: Katholic University Leuven

description: Analysis Phi29 amplified single-cell gDNA versus non-amplified gDNA

data_processing: Spot intensities were corrected for local background and only spots with signal intensities at least 1.2-fold above background were included in the analysis and log2 values were calculated. For each array, the normalised ratio was obtained by calculating the median of the log2 signal intensities over all the autosomal fragments with measurements from abnormal chromosomes masked out, and substracting this value from all the signal intensities of the spots on the array

molecule: genomic DNA

source_name: Amplified single-cell (blastomere number 4) gDNA (45,X)

tag: Single-cell gDNA following Phi29 whole genome amplification

source_name: Non-amplified reference gDNA (46,XX)

tag: Reference genomic DNA


title: CGH_2005051129_Embryo1_cell5

source_name: Amplified single-cell (blastomere number 5) gDNA (45,X)


title: icr_3000188313


title: icr_3000209648


title: C57BL/6J-Ghrhr<lit> (lit/lit) mice injected with growth hormone (GH), replicate 1

description: Output file name: US14702375_16011472013356_S01_A01.txt


title: CGH_2005051127_Embryo1_cell3

source_name: Amplified single-cell (blastomere number 3) gDNA (45,X)


title: icr_3000148227


title: C57BL/6J-Ghrhr<lit> (lit/lit) mice injected with growth hormone (GH), replicate 2

description: Output file name: US14702375_16011472013401_S01_A01.txt


title: icr_3000115587


title: icr_3000209330


title: icr_3000148229


title: icr_3000209327


title: icr_3000148226


title: icr_3000188503


title: CGH_2005051170_Embryo1_cell6

source_name: Amplified single-cell (blastomere number 6) gDNA (45,X)


title: icr_3000209601


title: icr_3000209329


title: icr_3000148228


title: CGH_2005051168_Embryo1_cell1

source_name: Amplified single-cell (blastomere number 1) gDNA (45,X)


title: CGH_2005051132_T21_cell2

source_name: Amplified single-cell (number 2) gDNA (47,XY,+21)


title: CGH_2005051169_Embryo1_cell2

source_name: Amplified single-cell (blastomere number 2) gDNA (45,X)


title: icr_3000115557


title: CGH_2005051133_45,X_cell1

source_name: Amplified single-cell (number 1) gDNA (45,X)


title: CGH_2005051150_45,X_cell3

source_name: Amplified single-cell (number 3) gDNA (45,X)


title: CGH_2005051136_T21_cell3

source_name: Amplified single-cell (number 3) gDNA (47,XY,+21)


title: icr_3000188505

source_name: skin fibroblast


title: icr_3000115558

description: amersham hyb buffer, 50% formamide, 42C 3 O/N

source_name: stratagene universal human reference RNA


title: CGH_2005051110_T21_cell1

source_name: Amplified single-cell (number 1) gDNA (47,XY,+21)


title: icr_3000115580


title: icr_3000188318


title: CGH_2005051131_T18_cell2

source_name: Amplified single-cell (number 2) gDNA (47,XY,+18)


title: CGH_2005051142_T13_cell3

source_name: Amplified single-cell (number 3) gDNA (47,XX,+13)

source_name: Non-amplified reference gDNA (46,XY)


title: CGH_2005051134_45,X_cell2

source_name: Amplified single-cell (number 2) gDNA (45,X)


title: CGH_2005051115_T18_cell1

source_name: Amplified single-cell (number 1) gDNA (47,XY,+18)

source_name: Non-amplified reference gDNA (46,XX)


title: CGH_2005051108_T18_cell3

source_name: Amplified single-cell (number 3) gDNA (47,XY,+18)


title: icr_3000115581


title: icr_3000209331


title: icr_3000188506


title: icr_3000188507


title: icr_3000115582


title: icr_3000207631


title: icr_3000115583


title: CGH_2005051140_T13_cell1

source_name: Amplified single-cell (number 1) gDNA (47,XX,+13)


title: icr_3000115585


title: icr_3000209368


title: pH

city: Duesseldorf

first: Birgit

last: Andree

address: Moorenstr. 5

institute: BMFZ

description: Expression profile of erythrocytes

data_processing: MAS 5.0 Normalization to TGT 500

label: biotinylated cRNA

source_name: erythrocytes

label_protocol: cDNA synthesis (Invitrogen), IVT cRNA (Enzo)

tag: healthy donor

tag: male

tag: age 29


title: KL

description: Expression profile of erythrocytes

tag: female

tag: age 28


title: S2

description: Expression profile of erythrocytes

tag: Healthy donor

tag: age 25


title: P

description: Expression profile of erythrocytes

tag: age 26


title: Geb

description: Expression profile of erythrocytes


title: TJ

description: Expression profile of erythrocytes

tag: age 36


title: SNU-475 vs. Universal control 5

status: Public on Jan 31 2006

city: Daejeon

first: Heun-Sik

last: Lee

address: 52 Eoeun-dong, Yuseong-gu

country: South Korea

institute: Korea Reaearch Institute of Bioscience and Biotechnology

description: Pro v4.0 (Axon Instruments, Whipple Road Union City, CA)

hyb_protocol: Genisphere 3DNA Expression Array Detection Kit (Genisphere, Hatfield, PA)

scan_protocol: Scannarray 5000 (Packard, Billerica, MA)

data_processing: braju.com, BRB-ArrayToo

extract_protocol: RNeasy midi-prep (Qiagen, Chatsworth, CA)

tag: Hepatoma cell line

source_name: Universal control

tag: Pooled total RNA from 9 cancer cells (SNU-16, Raji, CaSki, Y-79, MCF7, A431, HCT116, Ovk-4 and Jurkat)


title: icr_3000115586

tag: gender

tag: subset


title: icr_3000209315

description: 50% formamide, amersham hyb buffer, 3 O/N at 42C

tag: reference


title: icr_3000116406


title: icr_3000116405

description: 50% formamide, amersham hyb buffer 42 C 3 O/N


title: SNU-475 vs. Universal control 7

label_protocol: Genisphere 3DNA Expression Array Detection Kit (Genisphere, Hatfield, PA)


title: EU

description: Expression profile of erythrocytes


title: icr_3000188508


title: icr_3000209316


title: SNU-475 vs. Universal control 8


title: icr_3000209313

tag: sample type

value: tissue


title: SNU-475 vs. Universal control 6


title: SNU-449 vs. Universal control 6


title: SNU-449 vs. Universal control 5


title: SNU-449 vs. Universal control 8


title: SNU-387 vs. Universal control 5


title: SNU-368 vs. Universal control 8


title: SNU-449 vs. Universal control 7


title: SNU-387 vs. Universal control 7


title: SNU-387 vs. Universal control 8


title: SNU-387 vs. Universal control 6


title: SNU-182 vs. Universal control 8


title: SNU-354 vs. Universal control 6


title: SNU-368 vs. Universal control 6


title: SNU-354 vs. Universal control 7


title: SNU-368 vs. Universal control 7


title: SNU-368 vs. Universal control 5


title: SNU-182 vs. Universal control 6


title: SNU-182 vs. Universal control 7


title: PLC/PRF/5 vs. Universal control 6


title: Hep3B vs. Universal control 5


title: Hep3B vs. Universal control 8


title: SNU-354 vs. Universal control 5


title: SNU-354 vs. Universal control 8


title: SNU-182 vs. Universal control 5


title: PLC/PRF/5 vs. Universal control 8


title: PLC/PRF/5 vs. Universal control 5


title: Mixed gastric fundic mucosal epithelial cells

status: Public on Jan 26 2006

city: Los Angeles

first: Nils

middle: Werner Georg

last: Lambrecht

address: 11301 Wilshire Blvd, Bldg.113, Rm.325A

department: Physiology

institute: UCLA

description: Agilent Oligonucleotide Expression Microarray (G4130A), hybridized with cRNA derived from a homogenate of freshly scraped gastric fundic mucosal epithelium from rat stomachs.

data_processing: 12 independent microarrays with 3 dye swap experiments. The data are normalized intensities, as retrieved from Agilent's proprietary Feature Extraction Software. VALUE=Mean normalized intensity, SD=Standard deviation.

label: Cy5 or Cy3

source_name: Rat Stomach Fundic Mucosa

tag: Total RNA obtained from homogenate of mixed gastric fundic mucosal cells from freshly isolated rat stomach.


title: Maize juvenile leaf ND101/W23 vs W23 replicate 2

status: Public on Jan 01 2006

city: Stanford

first: Jiong

last: Ma

address: 385 Serra Mall

institute: Stanford University

description: Maize juvenile leaf ND101/W23 vs W23 biological replicate 2

hyb_protocol: 750 ng of each labeled target cRNA were hybed for 17 h at 60¡ãC.

scan_protocol: Data were acquired with an Agilent G2565BA scanner with default settings (100% PMT). Images processed by Agilent Feature Extraction v0.75.

data_processing: After removing saturated spot flagged by Feature Extraction, non-specific hybridizations were estimated by internal negative controls and an iterative approach given the presence of lots of anti-sense probes on the array. Probes with signals (median with background subtracted) above a calculated threshold for at least 2 of the 3 biological replicates were normalized by a combined approach of the rank invariant method (Tseng et al. 2001) and a loess fitness method. Normalized expressions were scaled and outliers flagged. Log base 2 expression ratios were calculated from the normalized expression of the test tissue (A619 or ND101/W23) divided by that of the reference W23 tissue regardless of the dye label of the two samples.

organism: Zea mays

source_name: Maize ND101/W23 juvenile leaf sample 2

label_protocol: Total RNA (500 ng) was amplified & labeled with Cy5 using Agilent Low RNA Input Fluorescent Linear Amplification Kit.

growth_protocol: Plants grown and dissected at Stanford field; tissue collected and frozen in liquid nitrogen immediately.

extract_protocol: Total RNA were extracted from 30 - 60 mg of frozen tissues with Qiagen RNeasy Mini kit, digested with DNase I, and cleaned up with RNeasy columns.

tag: Maize ND101/W23 juvenile leaf

source_name: Maize W23 juvenile leaf sample 2

label_protocol: Total RNA (500 ng) was amplified & labeled with Cy3 using Agilent Low RNA Input Fluorescent Linear Amplification Kit.

tag: Maize W23 juvenile leaf


title: Hep3B vs. Universal control 6


title: Hep3B vs. Universal control 7


title: HepG2 vs. Universal control 8


title: Maize juvenile leaf ND101/W23 vs W23 replicate 3

description: Maize juvenile leaf ND101/W23 vs W23 biological replicate 3

source_name: Maize W23 juvenile leaf sample 3

source_name: Maize ND101/W23 juvenile leaf sample 3


title: Maize 1 mm anther ND101/W23 vs W23 replicate 1

description: Maize 1 mm anther ND101/W23 vs W23 biological replicate 1

source_name: Maize ND101/W23 1 mm anther sample 1

tag: Maize ND101/W23 1 mm anther

source_name: Maize W23 1 mm anther sample 1

tag: Maize W23 1 mm anther


title: PLC/PRF/5 vs. Universal control 7


title: Maize juvenile leaf ND101/W23 vs W23 replicate 1

description: Maize juvenile leaf ND101/W23 vs W23 biological replicate 1

source_name: Maize ND101/W23 juvenile leaf sample 1

source_name: Maize W23 juvenile leaf sample 1


title: HepG2 vs. Universal control 7


title: Maize mature pollen A619 vs W23 replicate 3

description: Maize mature pollen A619 vs W23 biological replicate 3

source_name: Maize W23 mature pollen sample 3

tag: Maize W23 mature pollen

source_name: Maize A619 mature pollen sample 3

tag: Maize A619 mature pollen


title: HepG2 vs. Universal control 6


title: HepG2 vs. Universal control 5


title: Maize 1 mm anther ND101/W23 vs W23 replicate 2

description: Maize 1 mm anther ND101/W23 vs W23 biological replicate 2

source_name: Maize ND101/W23 1 mm anther sample 2

source_name: Maize W23 1 mm anther sample 2


title: Maize mature pollen A619 vs W23 replicate 2

description: Maize mature pollen A619 vs W23 biological replicate 2

source_name: Maize A619 mature pollen sample 2

source_name: Maize W23 mature pollen sample 2


title: Maize juvenile leaf A619 vs W23 replicate 3

description: Maize juvenile leaf A619 vs W23 biological replicate 3

source_name: Maize A619 juvenile leaf sample 3

tag: Maize A619 juvenile leaf


title: Maize juvenile leaf A619 vs W23 replicate 1

description: Maize juvenile leaf A619 vs W23 biological replicate 1

source_name: Maize A619 juvenile leaf sample 1


title: Maize mature pollen ND101/W23 vs W23 replicate 1

description: Maize mature pollen ND101/W23 vs W23 biological replicate 1

source_name: Maize ND101/W23 mature pollen sample 1

tag: Maize ND101/W23 mature pollen

source_name: Maize W23 mature pollen sample 1


title: Maize mature pollen ND101/W23 vs W23 replicate 3

description: Maize mature pollen ND101/W23 vs W23 biological replicate 3

source_name: Maize ND101/W23 mature pollen sample 3


title: Maize 1 mm anther A619 vs W23 replicate 3

description: Maize 1 mm anther A619 vs W23 biological replicate 3

source_name: Maize W23 1 mm anther sample 3

source_name: Maize A619 1 mm anther sample 3

tag: Maize A619 1 mm anther


title: Maize mature pollen ND101/W23 vs W23 replicate 2

description: Maize mature pollen ND101/W23 vs W23 biological replicate 2

source_name: Maize ND101/W23 mature pollen sample 2


title: MegaViroP7-244

city: San Francisco

first: Joe

last: DeRisi

department: Biochemistry and Biophysics

institute: University of California, San Francisco

data_processing: Median feature intensity minus median background intensity

molecule: polyA RNA

organism: Viruses

source_name: Amplified VP10 poly-A RNA

tag: RNASEL R462Q genotype

value: QQ


title: Maize juvenile leaf A619 vs W23 replicate 2

description: Maize juvenile leaf A619 vs W23 biological replicate 2

source_name: Maize A619 juvenile leaf sample 2

source_name: Maize W23 juvenile leaf sample 2


title: Maize 1.5 mm anther A619 vs W23 replicate 2

description: Maize 1.5 mm anther A619 vs W23 biological replicate 2

source_name: Maize W23 1.5 mm anther sample 2

tag: Maize W23 1.5 mm anther

source_name: Maize A619 1.5 mm anther sample 2

tag: Maize A619 1.5 mm anther


title: 95% ECL cell suspension RNA from Rat Stomach

description: Agilent Oligonucleotide expression microarray (G4130A), hybridized with cRNA derived from a 95% pure ECL cell suspension after digest of rat gastric fundic mucosa.

data_processing: 3 independent microarrays with one dye swap. The data are normalized intensities, as retrieved from Agilent's proprietary Feature Extraction Software. VALUE=Mean normalized intensity, SD=Standard deviation.

source_name: Purified Rat Stomach ECL cells

tag: 95% ECL cell suspension from Rat Stomach


title: Maize 1.5 mm anther ND101/W23 vs W23 replicate 2

description: Maize 1.5 mm anther ND101/W23 vs W23 biological replicate 2

source_name: Maize ND101/W23 1.5 mm anther sample 2

tag: Maize ND101/W23 1.5 mm anther


title: Maize 1 mm anther ND101/W23 vs W23 replicate 3

description: Maize 1 mm anther ND101/W23 vs W23 biological replicate 3

source_name: Maize ND101/W23 1 mm anther sample 3


title: Maize mature pollen A619 vs W23 replicate 1

description: Maize mature pollen A619 vs W23 biological replicate 1

source_name: Maize A619 mature pollen sample 1


title: CGH_2005051141_T13_cell2

description: Analysis Phi29 amplified single-cell gDNA versus non-amplified gDNA

source_name: Amplified single-cell (number 2) gDNA (47,XX,+13)

tag: Single-cell gDNA following Phi29 whole genome amplification

source_name: Non-amplified reference gDNA (46,XY)

tag: Reference genomic DNA


title: Maize 1.5 mm anther ND101/W23 vs W23 replicate 3

description: Maize 1.5 mm anther ND101/W23 vs W23 biological replicate 3

source_name: Maize W23 1.5 mm anther sample 3

source_name: Maize ND101/W23 1.5 mm anther sample 3


title: Maize 1.5 mm anther A619 vs W23 replicate 3

description: Maize 1.5 mm anther A619 vs W23 biological replicate 3

source_name: Maize A619 1.5 mm anther sample 3


title: MegaViroP7-245

source_name: Amplified VP27 poly-A RNA


title: MegaViroP5-196

source_name: Amplified VP46 poly-A RNA

value: RQ


title: MegaViroP8-036

source_name: Amplified VP86 poly-A RNA

value: RR


title: MegaViroP5-197

source_name: Amplified VP49 poly-A RNA


title: MegaViroP5-177

source_name: Amplified VP35 poly-A RNA


title: Maize 1.5 mm anther A619 vs W23 replicate 1

description: Maize 1.5 mm anther A619 vs W23 biological replicate 1

source_name: Maize A619 1.5 mm anther sample 1

source_name: Maize W23 1.5 mm anther sample 1


title: MegaViroP5-178

source_name: Amplified VP42 poly-A RNA


title: MegaViroP5-174

source_name: Amplified VP29 poly-A RNA


title: MegaViroP10-128

source_name: Amplified VP50 poly-A RNA


title: MegaViroP8-032

source_name: Amplified VP90 poly-A RNA


title: Maize 1.5 mm anther ND101/W23 vs W23 replicate 1

description: Maize 1.5 mm anther ND101/W23 vs W23 biological replicate 1

source_name: Maize ND101/W23 1.5 mm anther sample 1


title: MegaViroP7-246

source_name: Amplified VP107 poly-A RNA


title: MegaViroP5-199

source_name: Amplified VP51 poly-A RNA


title: Maize 1 mm anther A619 vs W23 replicate 2

description: Maize 1 mm anther A619 vs W23 biological replicate 2

source_name: Maize A619 1 mm anther sample 2

source_name: Maize W23 1 mm anther sample 2


title: Maize 1 mm anther A619 vs W23 replicate 1

description: Maize 1 mm anther A619 vs W23 biological replicate 1

source_name: Maize A619 1 mm anther sample 1

source_name: Maize W23 1 mm anther sample 1


title: MegaViroP5-195

source_name: Amplified VP45 poly-A RNA


title: MegaViroP5-179

description: HeLa positive control (contains Human papillomavirus type 18)

source_name: Amplified HeLa total RNA


title: MegaViroP8-037

source_name: Amplified VP62 poly-A RNA


title: MegaViroP5-176

source_name: Amplified VP31 poly-A RNA


title: MDA-2D-cy5 and MCF7-2D-cy3

status: Public on Dec 30 2005

city: Duarte

first: Ren-Jing

last: Lin

address: 1500 E. Duarte Rd.

department: Molecular Biology

institute: Beckman Research Institute

description: MDA-2D vs. MCF7-2D

scan_protocol: GenePix pro 4.1

data_processing: After background correction and removal of flagged values, oligonucleotide spots with both F635 and F532 readings lower than the average plus two standard deviations of all ??untargeted?? spots were removed from the raw data.

source_name: A pleural effusion of breast adenocarcinoma

label_protocol: Indirect labeling

growth_protocol: MDA-MB-231 cultured in RPMI-1640 supplemented with 10% FBS and 1% Penicillin/Streptomycin

treatment_protocol: No treatment

tag: MDA-MB-231 cells cultured in flat dish

growth_protocol: MCF7 cultured in DMEM supplemented with 10% FBS, 1% non-essential amino acids and 1% Penicillin/Streptomycin


title: MegaViroP8-030

source_name: Amplified VP79 poly-A RNA


title: MegaViroP5-175

source_name: Amplified VP30 poly-A RNA


title: MegaViroP8-035

source_name: Amplified VP66 poly-A RNA


title: MegaViroP8-031

source_name: Amplified VP88 poly-A RNA