title: GN5, Rapamycin, Rep3

status: Public on Sep 20 2009

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

description: Derived from WB-F344 cell line using NNN

hyb_protocol: cRNA (750ng) was hybridized at 58°C for 16 hours on a RatRef-12 Expression BeadChips.  BeadChips were washed and stained as outlined in the Illumina protocol.

scan_protocol: BeadChips were scanned using the Illumina Iscan.

data_processing: Scanned files were quantile normalized using BeadStudio software (Illumina).  The data was further analyzed using Partek software, version 6.3 (Partek).  For gene expression comparisons, genes with detection p-values >0.01 from BeadStudio or fold-change less than 1.2 were excluded from further analyses.  A two-sample t-test using p-value cutoff of 0.05 with multiple test correction (Bejamini and Hochberg false discovery rate) was applied for each gene to determine if the gene was differentially expressed in the pairwise comparison.  Triplicate control and rapamycin samples from each cell line were used in these comparisons.

label: Biotin

source_name: GN5 cells, 50nM Rapamycin

label_protocol: Biotinylated cRNA was prepared from 500ng of total RNA using the TotalPrep RNA Amplification kit (Applied Biosystems) according to the manufacturer's directions.

growth_protocol: GN5 cells were cultured in DMEM/F12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution.  H5D cells were cultured in Waymouth MB 752/1 containing 10% fetal bovine serum and 0.1% antibiotic-antimycotic solution.  All cells were grown at 37°C with 5.0% carbon dioxide.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  Total RNA was further purified using the RNeasy kit (Qiagen). RNA quality was evaluated using the Agilent Bioanalyzer.

treatment_protocol: 10^6 cells were plated on 100mm plates and allowed to attach overnight.  Cells were treated with DMSO vehicle or 50nM rapamycin for 24 hours.

tag: rapamycin response

value: Intermediate

tag: doubling time

tag: tumorigenic

value: Yes


title: GN5, Rapamycin, Rep2

type: RNA

country: USA

molecule: total RNA

organism: Rattus norvegicus


title: H5D, Rapamycin, Rep2

description: Derived from azo-dye induced hepatocellular carcinoma in Fischer rat

source_name: H5D cells, 50nM Rapamycin


title: GN5, Rapamycin, Rep1


title: GN5, Control, Rep1

source_name: GN5 cells, Vehicle Control


title: H5D, Rapamycin, Rep1


title: GN5, Control, Rep2


title: GN5, Control, Rep3


title: H5D, Control, Rep3

source_name: H5D cells, Vehicle Control


title: H5D, Rapamycin, Rep3


title: H5D, Control, Rep2


title: Normal Lung_NL5

status: Public on Sep 21 2009

city: Brisbane

first: Santiyagu

middle: Mary

last: Savarimuthu Francis

state: Queensland

address: Level 1, Clinical Sciences Building, The Prince Charles Hospital, Rode Road

department: School of Medicine

country: Australia

institute: The University of Queensland

description: After the purification samples were combined for hybridization, the labeled cDNAs were co-hybridized to 22K oligo microarrays.

hyb_protocol: Amersham hybridization protocol was used

scan_protocol: GMS418 confocal scanner was used according to manufacturer’s instructions

data_processing: Raw images were imported into Imagene V5.1 (BioDiscovery, CA, USA) to extract pixel intensities and to flag spots with poor/absent signal. The raw background subtracted signal median for each probe was imported into GeneSpring GX V7.3 (Agilent Technologies, Inc., CA, USA) for analysis. Data was normalized (Lowess) and probe signals filtered on pixel intensity (for both red and green channels any spots less than 20 units or greater than 65,000 units were excluded) and consistent spot morphology. Only spots flagged present in at least 50% of samples were included. For each probe, the logarithm to the base 2 of the ratio between the intensity in the tumor sample (red) channel and the reference (green) channel was used as the expression value for the probe.

organism: Homo sapiens

source_name: Universal Reference RNA

label_protocol: Synthesis of the labelled first strand cDNA was conducted using Amersham CyScribe Post-Labelling kit with starting material of 20 ug of total RNA. The amino-allyl labeled dNTP mix was added to the reaction to generate amino-allyl labelled second strand cDNA.  Following the hydrolysis reaction, single-stranded cDNA probes were purified using Amersham GFX columns. Dye coupling reactions were performed by mixing the cDNA samples with Amersham Cy3 (reference) or Cy5 (Normal Lung) and incubating in the dark. The reactions were purified with Amersham GFX columns to remove the unincorporated/quenched dyes.

extract_protocol: Total RNA was extracted using TRizol following manufacturer's instructions

tag: sample type

value: Human Universal Reference RNA (Stratagene)

source_name: Normal Lung Sample 5

tag: gender

value: F

tag: % predicted fev1

tag: % predicted kco

tag: age

tag: pack years

tag: age quit smoking


title: H5D, Control, Rep1


title: L1236 IP/T

city: Groningen

first: Lu Ping

last: Tan

address: Hanzeplein 1

department: Department of Pathology

country: Netherlands

institute: University Medical Center Groningen

description: L1236 Ago2 immunoprecipitated fraction compared against total cell lysate fraction

hyb_protocol: Equal amounts of Cy3 or Cy5 labeled cRNA samples derived from the Ago2 immunoprecipitated or flow through fraction and from the total cell lysate fraction were mixed and hybridized in a dye swap design at 65°C overnight on Agilent 44k 60mer Human Whole Genome Oligo Microarray.

scan_protocol: On the following day, slides were washed and signals were scanned with GenePix 4000B (Agilent).

data_processing: Signal intensities from scanned images were processed and converted into Linear and Lowess normalized data using Agilent Feature Extraction software version 9.1. Probes with no expression (ie. signal intensity similar to background) were filtered out in all tested RNA Samples.

source_name: Ago2 coimmunoprecipitated RNA

label_protocol: First strand cDNA was synthesized from 200ng RNA, followed by cRNA amplification and labeling with Cy3 or Cy5 according to manufacturer's protocol (Agilent). Purification of Cy3 or Cy5 labeled cRNA was carried out with Qiagen RNeasy Mini kit.

growth_protocol: Both Hodgkin lymphoma cell lines, L428 and L1236 were cultured in RPMI 1640 supplemented with ultraglutamine, 100 U/mL penicillin/streptomycin, and 5% or 10% fetal bovine serum (Cambrex Biosciences, Walkersville, USA), respectively. Cells were diluted 1:2 on the day prior to Ago2 immnunoprecipitation.

extract_protocol: RNA was isolated using Trizol and glycogen (Invitrogen) as a carrier in the ethanol precipitation step.

tag: cell line

tag: cell type

value: Hodgkin lymphoma cell line

source_name: RNA from total cell lysate fraction


title: WB-F344, Rapamycin, Rep2

description: Normal diploid rat liver epithelial cell line derived from adult male Fischer rat

hyb_protocol: Fragmented cRNA (10 ug) was hybridized for 16 hour at 45°C on a Affymetrix GeneChip Rat Genome 230 2.0 array.  Arrays were washed using the Affymetrix fluidics station and stained with strepavidinphycoerythrin.

scan_protocol: Arrays were scanned on a Affymetrix GeneChip Scanner 3000.

data_processing: The data was analyzed using GeneSpring GX 7.3 (Agilent Technologies).  Microarray fluorescence signals were normalized using Robust Multiarray Average (RMA).  For gene expression comparisons, genes with expression values less than 100 or fold change less than 1.2 were excluded from further statistical analyses.  A two-sample t-test using p-value cut-off of 0.05 with multiple test correction (Benjamini and Hochberg false discovery rate) was applied for each gene to determine if the gene were differentially expressed in the pair wise comparisons.  Triplicate control and rapamycin samples from each cell line were used in these comparisons.

source_name: WB-F344 cells, 50nM Rapamycin

label_protocol: Biotinylated cRNA was prepared from 5 ug of total RNA using the one cycle target kit from Affymetrix according to the manufacturer's instructions.

growth_protocol: Cells were cultured in DMEM/F-12 containing 10% fetal bovine serum, 2mM L-glutamine and 0.1% antibiotic-antimycotic solution.  Cells were cultured at 37°C with 5.0% carbon dioxide.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturers instructions.  RNA was further purified using the Uneasy kit (Qiagen).  RNA quality was evaluated using the Agilent Bioanalyzer.

treatment_protocol: 10^6 cells were plated per 100mm plate and allowed to attach overnight.  Cells were treated with 50nM Rapamycin or DMSO vehicle for 24 hours.

value: Sensitive

value: No


title: WB-F344, Rapamycin, Rep3


title: WB311, Rapamycin, Rep2

description: Spontaneously derived from WB-F344 cell line

source_name: WB311 cells, 50nM Rapamycin

value: Resistant


title: WB311, Control, Rep1

source_name: WB311 cells, Vehicle Control


title: WB311, Control, Rep2


title: MDA-MB-231 cells testosterone treated

status: Public on Sep 19 2009

city: Heraklion

first: George

last: Notas

address: PO BOX 2208

department: Medicine

country: Greece

institute: University of Crete

description: Testosterone treated sample

hyb_protocol: Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual)

data_processing: Genespring GX V10 (Agilent, Foster City, CA)

label: BIOTIN

source_name: MDA-MB-231 cells testosterone treated

growth_protocol: MDA-MB-231 cells were cultured in RPMI-1640 medium, supplemented with 10% charcoal treated fetal bovine serum (FBS), in a humidified atmosphere of 5% CO2 in air, at 37°C. Culture media and serum were from Gibco BRL (Life Technologies, Paisley, UK).

extract_protocol: Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Düren, Germany

treatment_protocol: Cells were serum starved for 6 hours and then treated with 10-7M Testosterone in charcoal-treated serum for 3 hours.

tag: tissue type

value: breast cancer


title: WB311, Control, Rep3


title: WB311, Rapamycin, Rep3


title: WB-F344, Control, Rep2

source_name: WB-F344 cells, Vehicle Control


title: WB-F344, Control, Rep1


title: WB-F344, Control, Rep3


title: Cbfb-deficient Treg_rep2

city: Kyoto

first: Akihiko

last: Kitoh

address: 53 Shogoin Kawahara-cho

department: Institute for Frontier Medical Sciences

country: Japan

institute: Kyoto University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data analyses were done with the use of MeV (v4.2) (Saeed et al., 2003 Biotechniques 34, 374-378).

label: biotin

organism: Mus musculus

source_name: Cbfb-deficient Treg

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted with the RNeasy Micro Kit (QIAGEN) according to the manufacturer's instructions.

value: peripheral CD4+CD25hi cells

tag: mouse genotype

value: Cbfb-flox/flox, Foxp3-ires-Cre

value: male

value: 16 weeks

tag: tissue

value: purified CD4+CD25hi cells from spleen and lymph nodes


title: WB311, Rapamycin, Rep1


title: Control Treg_rep3

source_name: Control Treg

value: Cbfb-flox/wt, Foxp3-ires-Cre


title: T47D inducible EglN2 shRNA Day 0 replicate 2

city: Boston

first: Qing

last: Zhang

state: MA

address: 44 Binney St

department: Medical Oncology

institute: DFCI

description: T47D inducible EglN2 shRNA  Doxycycline treatment Day 0 replicate 2

hyb_protocol: The fragmented cDNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The Human ST 1.0 array  chips are then transferred to a fluidics instrument that performs washes to remove cDNA that has not hybridized to its complementary oligonucleotide probe. The bound cDNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000. These scans were used to generate CEL files for each array.

data_processing: Transcript-level expression values of approximately 33297 empirically supported transcripts on the Human Gene ST 1.0 array  were derived using RMA implemented in Affymetrix® Expression Console™ (Affymetrix, Santa Clara, CA). The gene annotations used for each transcript were from the annotation file obtained from Affymetrix (http://www.affymetrix.com).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were grown in 37 degree incubator with 5% CO2

extract_protocol: Total RNA was extracted with Rneasy kit according to the manufacturer's recommendation

treatment_protocol: Treatment with Doxycyline (1 ug/ml)

value: breast carcinoma


title: Cbfb-deficient Treg_rep3


title: T47D cells testosterone-BSA treated

description: Testosterone-BSA treated sample

scan_protocol: Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual)

source_name: T47D cells testosterone-BSA treated

growth_protocol: T47D cells were cultured in RPMI-1640 medium, supplemented with 10% charcoal treated fetal bovine serum (FBS), in a humidified atmosphere of 5% CO2 in air, at 37°C. Culture media and serum were from Gibco BRL (Life Technologies, Paisley, UK).

treatment_protocol: Cells were serum starved for 6 hours and then treated with 10-7M Testosterone-BSA in charcoal-treated serum for 3 hours.


title: MDA-MB-231 cells testosterone-BSA treated

description: Testosterone-BSA treated sample

label_protocol: Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual)


title: Control Treg_rep2


title: MDA-MB-231 cells untreated

description: Control sample

source_name: MDA-MB-231 cells untreated

treatment_protocol: Cells were serum starved for 6 hours and then treated with charcoal-treated serum for 3 hours.


title: WB-F344, Rapamycin, Rep1


title: T47D Scr Day 2 Replicate 1

description: T47D Scr Doxycycline treatment Day 2 Replicate 1


title: T47D Scr Day 0 Replicate 2

description: T47D Scr Doxycycline treatment Day 0 Replicate 2


title: T47D Scr Day 0 Replicate 1

description: T47D Scr Doxycyline treatment Day 0 Replicate 1


title: T47D inducible EglN2 shRNA Day 2 replicate 1

description: T47D inducible EglN2 shRNA Doxycycline treatment Day 2 replicate 1


title: Henle407_infected_4hr

status: Public on Sep 17 2009

city: Ithaca

first: Chia-Hsin

last: Ju

state: NY

address: VMC C5 151 Cornell University

institute: Cornell University

description: Human intestinal epithelial cell line Henle 407

hyb_protocol: The pre-hybridization and hybridization protocol are performed according to the manufacture instructions (SA Biosciences, Frederick, MD). See: http://www.sabiosciences.com/support_manual.php

scan_protocol: Images of the array were developed on X-ray films.   Image data sets were scanned using ScanAlyze software (Eisen Lab), and the data were processed using Microsoft Excel software.

data_processing: Image data sets were scanned and analyzed using ScanAlyze (Eisen Lab), and Microsoft Excel software.  Background adjustment was performed by subtracting the lowest measured value on the membrane from the values of all genes.  The signals from the expression of each gene on the array were normalized against the signal from the internal housekeeping gene GAPDH to obtain the processed data sets.   Fold changes were calculated as the normalized ratio of average experimental processed data sets divided by the average medium control processed data sets.

source_name: Henle 407 cells

label_protocol: Labeling of cRNA was done by using Oligo GEArray TrueLabeling-AMP™ 2.0 Kit (SA Biosciences, Frederick, MD) according to the manufacture instructions.

growth_protocol: Henle 407 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with containing 2 mM L-glutamine, 50 units/ml penicillin, 50 µg/ml streptomycin, 10 mM HEPES, 1 mM sodium pyruvate, and 10% low endotoxin fetal bovine serum.

extract_protocol: Total RNA of Henle 407 cells infected with T. gondii RH was extracted at 4 hr post infection using the RNeasy mini kit (QIAGEN, Valencia, CA) according to the manufacture instructions.

value: Henle 407


title: T47D Scr Day 2 Replicate 2

description: T47D Scr Doxycylcine treatment Day 2 Replicate 2


title: T47D inducible EglN2 shRNA Day 0 replicate 1

description: T47D inducible EglN2 shRNA Doxycycline treatment Day 0 replicate 1


title: iPS strain with low potency 1

first: Shinji

last: Kaichi

address: Kawahara-machi54, Shogoin, Sakyo-ku

department: Pediatrics

institute: Kyoto university

description: Biological replicate 1 of 2., harvested after several passages.

hyb_protocol: According to http://www.3d-gene.com and http://www.ambion.com/jp/techlib/prot/fm_1753.pdf. 3D-Gene Mouse Oligo chip 24k (Toray Industries Inc., Tokyo, Japan) was used(23,522 distinct genes). For efficient hybridization, this microarray has 3-dimensions that is constructed with a well as the space between the probes and cylinder-stems with 70-mer oligonucleotide probes on the top. The Cy3- or Cy5- labeled aRNA pools and hybridization buffer, and hybridized for 16 h. The hybridization was performed using the supplier's protocols (www.3d-gene.com).

scan_protocol: ScanArray® Lite (PerkinElmer, Inc.) was used according to http://www.3d-gene.com and http://www.ambion.com/jp/techlib/prot/fm_1753.pdf.

data_processing: Hybridization signals were scanned using ScanArray Lite Scanner (PerkinElmer),and processed by GenePixPro version5.0(Molecular Devices). Detected signals for each gene were normalized by global normalization method (Cy3/Cy5 ratio median=1). Genes with Cy3/Cy5 normalized ratios greater than 2.0 or less than 0.5 were defined, respectively, as commonly up- or down-regulated genes. We used MicroSoft Office Excel 2003 for the data normalization and filtering.

source_name: mouse induced pluripotentstem cells 1

label_protocol: 1ug of total RNA was used as described at http://www.3d-gene.com and http://www.ambion.com/jp/techlib/prot/fm_1753.pdf. Total RNA was labeled with Cy3- or Cy5- using the Amino Allyl MessageAMP II aRNA Amplification Kit (Applied Biosystems, CA, U.S.A.).

growth_protocol: Cells were cultured on gelatinized-plates with no feeder cells.

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

value: induced pluripotent stem cells

tag: cell strain

tag: phenotype

value: low potency

tag: genome/variation

value: transfected with Oct3/4, Sox2, c-myc, and klf4

value: normal potency


title: Henle407_Uninfected_4hr

extract_protocol: Total RNA of Henle 407 cells that were uninfected was extracted using the RNeasy mini kit (QIAGEN, Valencia, CA) according to the manufacture instructions.


title: T47D cells testosterone treated

description: Testosterone treated sample

source_name: T47D cells testosterone treated


title: Mesenchymal Stem Cells From Umbilical Cord and Umbilical Cord Blood - Donor 3, Replicate 2

status: Public on Sep 18 2009

city: Sao Paulo

first: Yuri

middle: Barros

last: Moreira

state: SP

address: Av. Prof. Lineu Prestes 748 sala 1200

department: Biochemistry

country: Brazil

institute: Universidade de Sao Paulo

description: Biological replicate 3 of 4. UC tissues and UCB paired sample from donor 3, at the second passage.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridizatio Kit Plus)

scan_protocol: Scanned on a Genepix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA). Images were quantified using Agilent Feature Extraction Software (version A.9.0)

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed Red signal/processed Green signal or the inverse

source_name: Total RNA from Umbilical Cord Mesenchimal Stem Cells labeled with Cyanine-3 (green).

label_protocol: Low RNA Input Amplification Kit (Agilent).

extract_protocol: TriZol procedure

value: Umbilical Cord Mesenchymal Stem Cells

tag: passages

source_name: Total RNA from Umbilical Cord Blood Mesenchimal Stem Cells labeled with Cyanine-5 (green).

value: Umbilical Cord Blood Mesenchymal Stem Cells


title: Mesenchymal Stem Cells From Umbilical Cord and Umbilical Cord Blood - Donor 2, Replicate 1

description: Biological replicate 2 of 4. UC tissues and UCB paired sample from donor 2, at the second passage.

source_name: Total RNA from Umbilical Cord Blood Mesenchimal Stem Cells labeled with Cyanine-3 (green).

source_name: Total RNA from Umbilical Cord Mesenchimal Stem Cells labeled with Cyanine-5 (green).


title: Mesenchymal Stem Cells From Umbilical Cord and Umbilical Cord Blood - Donor 1,  Replicate 2

description: Biological replicate 1 of 4. UC tissues and UCB paired sample from donor 1, at the second passage.


title: Mesenchymal Stem Cells From Umbilical Cord and Umbilical Cord Blood - Donor 4, Replicate 2

description: Biological replicate 4 of 4. UC tissues and UCB paired sample from donor 4, at the second passage.


title: Wild-type 061212MJA_ANIGERa_AR31

city: Leiden

first: Benjamin

middle: M.

last: Nitsche

state: The Netherlands

address: Sylviusweg 72

department: Institute of Biology

institute: Leiden University

hyb_protocol: The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, staining and scanning of the chips. The Affymetrixprotocols are strictly followed. The Affymetrix custom Aspergilus niger Genome Arrays are used for hybridization. To the 270 μl hybridization cocktail, 30 μl labeled material is added according the manual of the Affymetrix One Cycle Target Labeling Kit.

scan_protocol: Standard Affymetrix protocol

data_processing: MAS 5

organism: Aspergillus niger

source_name: fungal mycelium

label_protocol: The Affymetrix One-Cycle Target Labeling Kit and Control Reagents (#900493) are used to synthesize Biotin-labeled cRNA. From each RNA sample 2 μg is used for the labeling experiments.

growth_protocol: Freshly harvested conidia (5x10^9) from strain T312 and ramosa-1 were used to inoculate 5 l FM. Cultivations were performed in a BioFlo3000 bioreactor (New Brunswick Scientific), where temperature, pH (set to 3) and agitation speed were controlled on- line using the program NBS Biocommand. The cultivation program followed four consecutive phases: 1) 2װ C, agitation speed 250 rpm, headspace aeration, 13 h; 2) 37C, agitation speed 750 rpm, parger aeration, 4 h; 3) 25C, agitation speed 750 rpm, sparger aeration, 3 h; 4) 37 C, agitation speed 750 rpm, sparger aeration, 1 h.

extract_protocol: Total RNA was isolated from homogenized mycelial samples using TRIzol reagent (Invitrogen).

treatment_protocol: Freshly harvested conidia (5×109) from strain T312 and ramosa-1 were used to inoculate 5 l FM. Cultivations were performed in a BioFlo3000 bioreactor (New Brunswick Scientific), where temperature, pH (set to 3) and agitation speed were controlled on- line using the program NBS Biocommand. The cultivation program followed four consecutive phases: 1) 24°C, agitation speed 250 rpm, headspace aeration, 13 h; 2) 37°C, agitation speed 750 rpm, sparger aeration, 4 h; 3) 25°C, agitation speed 750 rpm, sparger aeration, 3 h; 4) 37°C, agitation speed 750 rpm, sparger aeration, 1 h. Biomass samples for RNA extraction for microarray analyis were taken after step 4.

tag: strain

value: wild-type


title: Mesenchymal Stem Cells From Umbilical Cord and Umbilical Cord Blood - Donor 4, Replicate 1


title: Mesenchymal Stem Cells From Umbilical Cord and Umbilical Cord Blood - Donor 1, Replicate 1


title: Ramosa-1 061212MJA_ANIGERa_AR28


title: Ramosa-1 061212MJA_ANIGERa_AR32


title: Ramosa-1 061212MJA_ANIGERa_AR30


title: Mesenchymal Stem Cells From Umbilical Cord and Umbilical Cord Blood - Donor 2, Replicate 2


title: Mesenchymal Stem Cells From Umbilical Cord and Umbilical Cord Blood - Donor 3, Replicate 1


title: T47D cells untreated

description: Control sample

source_name: T47D cells untreated


title: Wild-type 061212MJA_ANIGERa_AR29


title: Wild-type 061212MJA_ANIGERa_AR27


title: iPS strain with low potency 2

description: Biological replicate 2 of 2., harvested after several passages.


title: Seed_Rep3

status: Public on Sep 16 2009

city: Cedar Falls

first: Tilahun

last: Abebe

state: IA

address: 191 McCollum Hall

department: Biology

institute: University of Northern Iowa

description: This is biological replication 3 for seed collected at the grain-filling stage.

hyb_protocol: The labeled cRNA was purified and fragmented. Then, hybridization controls were added to the resulting cRNA and hybridized to the Barley1 GeneChips for 16 h at 45°C. Arrays were washed using the GeneChip® Fluidics Station 450.

scan_protocol: GenChips were scanned using the GeneChip® 3000 Scanner.

data_processing: Cell intensity (CEL) files were imported into Expression Console v 1.1 (Affymetrix) for background correction and normalization using the Microarray Analysis Suite v 5.0 (MAS5) algorithm. Background intensity was corrected as the difference between the perfect match (PM) and mismatch (MM) pair of each probe set. Summarised values were normalized using global scaling. The mean signal of each array was scaled to 500.

organism: Hordeum vulgare

source_name: Seed

label_protocol: Biotinylated cRNA was prepared from total RNA according to the the Affymetrix One-Cycle Target Labeling protocol.

growth_protocol: Barley plants (Hordeum vulgare L.) cv. Morex were grown in a controlled environment chamber at 22°C/18°C day/night temperatures, 60% RH and a 16 h photoperiod. Plants were grown in 20 cm x 25 cm pots and fertilized using Osmocote® slow release fertilizer.

extract_protocol: RNA from the lemma, the palea and the awn was extracted with guanidinium thiocyanate (Chirgwin et al. 1979). Total RNA from the seed was extracted using Tri Reagent (Molecular Research Center Inc., Cincinnati, OH), followed by precipitation of starch with 0.8 M sodium citrate and 1.2 M NaCl according to the manufacturer’s recommendation.

value: Seed


title: Seed_Rep1

description: This is biological replication 1 for seed collected at the grain-filling stage.


title: siRNA-Control-Cy3/siRNA-LATS1/2-A-Cy5

city: Kingston

first: Xiaolong

last: Yang

state: Ontario

address: 88 Stuart Street

department: Pathology and Molecular Medicine

country: Canada

institute: Queen's University

hyb_protocol: Samples were hybridized at 65C for 17hrs

scan_protocol: The slide was scanned with Agilent Microarray Scanner G2565BA

data_processing: Data were normalized using the linear lowess method.  Genes that were differentially expressed at least 1.5-fold on 3 of 4 arrays were scored as significant.  Furthermore, a student's t-test was fun and genes must possess a p-value ≤ 0.05 to be considered signficant.

source_name: HeLa cells treated with control siRNA

label_protocol: For each sample, 200ng total RNA was reversed transcribed, linear amplified, and labeled with either Cy3 or Cy5 using Agilent's Low RNA Input Linear Amplification Kit PLUS, according to instructions

growth_protocol: HeLa cells were maintained in Dulbecco's modified Eagle Medium supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin

extract_protocol: Total RNA was extracted using TRIzol according to manufacturer's instructions.  RNA was further purified using Rneasy Mini Kit (Qiagen)

treatment_protocol: HeLa cells were treated with 10nM control siRNA or a combination of 10nM siRNA targeting LATS1 and 10nM siRNA targeting LATS2

value: Female cervical carcinoma

value: HeLa

source_name: HeLa cells treated with siRNA targeting LATS1 and siRNA targeting LATS2


title: Seed_Rep2

description: This is biological replication 2 for seed collected at the grain-filling stage.


title: Awn_Rep3

description: This is biological replication 3 for awn collected at the grain-filling stage.

source_name: Awn

value: Awn


title: Awn_Rep1

description: This is biological replication 1 for awn collected at the grain-filling stage.


title: siRNA-Control-Cy3/siRNA-LATS1/2-B-Cy5


title: Palea_Rep3

description: This is biological replication 3 for palea collected at the grain-filling stage.

source_name: Palea

value: Palea


title: siRNA-LATS1/2-B-Cy3/siRNA-Control-Cy5


title: Palea_Rep2

description: This is biological replication 2 for palea collected at the grain-filling stage.


title: Patient 27, colonocytes; Control

city: Copenhagen

first: Morten

last: Hansen

address: Blegdamsvej 3B

department: Department of Cellular and Melocular Medicine

country: Denmark

institute: Faculty of Health Sciences

description: Gene expression data from human colonic mucosa

hyb_protocol: The cRNA was fragmented and a hybridization mix was prepared, which included the fragmented target, probe array controls, bovine serum albumin (BSA) and herring sperm DNA. In this experiment, the Affymetrix GeneChip Human Genome U133 Plus 2.0 was applied. The hybridized probe array was subsequently stained with fluorescent protein streptavidin-phycoerythirn (SAPE).

scan_protocol: Scanned with a GeneArray scanner at the excitation wavelength of 488 nm.

data_processing: Scaled and normalized using robust multi-array analysis (RMA) in the statistical software R.

source_name: Colonocytes from human colonic mucosa

label_protocol: In accordance with the Affymetrix protocol and the two-cycle eukaryotic target labelling assay, double-stranded cDNA was synthesized from total RNA and an IVT reaction was subsequently performed to produce biotin-labelled cRNA from the cDNA.

extract_protocol: RNA was extracted with the NucleoSpin® RNA/Protein mini kit (Macherey-Nagel, Düren, Germany) in accordance with the manufactures protocol

tag: Control


title: Awn_Rep2

description: This is biological replication 2 for awn collected at the grain-filling stage.


title: Patient 28, colonocytes; UC non-inflamed

tag: UC non-inflamed


title: siRNA-LATS1/2-A-Cy3/siRNA-Control-Cy5


title: Palea_Rep1

description: This is biological replication 1 for palea collected at the grain-filling stage.


title: Lemma_Rep2

description: This is biological replication 2 for lemma collected at the grain-filling stage.

source_name: Lemma

value: Lemma


title: Patient 26, colonocytes; UC inflamed

tag: UC inflamed


title: Lemma_Rep3

description: This is biological replication 3 for lemma collected at the grain-filling stage.


title: Patient 25, colonocytes; UC non-inflamed


title: Patient 24, colonocytes; UC inflamed


title: Patient 22, colonocytes; Control


title: T47D inducible EglN2 shRNA Day 2 replicate 2

description: T47D inducible EglN2 shRNA Doxycycline treatment Day 2 replicate 2


title: Patient 19, colonocytes; UC non-inflamed


title: Patient 18, colonocytes; UC non-inflamed


title: Patient 15, colonocytes; Control


title: Patient 13, colonocytes; Control


title: Patient 16, colonocytes; Control


title: Patient 11, colonocytes; UC inflamed


title: Patient 20, colonocytes; Control


title: Patient 14, colonocytes; UC inflamed


title: Patient 17, colonocytes; UC non-inflamed


title: Patient 21, colonocytes; UC non-inflamed


title: Patient 10, colonocytes; UC non-inflamed


title: Patient 8, colonocytes; UC non-inflamed


title: Patient 7, colonocytes; UC inflamed


title: Patient 4, colonocytes; Collagen colitis (excluded)

tag: Collagen colitis (excluded)


title: Lemma_Rep1

description: This is biological replication 1 for lemma collected at the grain-filling stage.


title: Patient 9, colonocytes; Control


title: Patient 1, colonocytes; UC inflamed


title: Patient 26, biopsy; UC inflamed

source_name: Biopsy from human colonic mucosa


title: Patient 24, biopsy; UC inflamed


title: Patient 12, colonocytes; Control


title: Patient 3, colonocytes; Control


title: Patient 25, biopsy; UC non-inflamed


title: Patient 20, biopsy; Control


title: Patient 23, biopsy; Control


title: Patient 21, biopsy; UC non-inflamed


title: Sakai vs TW14359, gene expression following epithelial exposure

city: East Lansing

first: galeb

last: abu-ali

state: MI

address: NFSTC

department: NFSTC

institute: michigan state university

description: There are 6088 probes, spotted in duplicate, on the array that target three different E. coli genomes: serotype O157:H7 strains Sakai and EDL-933, serotype K12 MG 1655.

hyb_protocol: Arrays were cross-linked by exposure to 600 mJ UV before blocking in 1% SDS, 5× SSC, and 1 mg/mL BSA at 42°C for 1 hour. After blocking, arrays were washed 2× 5 min in 0.1× SSC and 2× 30 s in H2O. Dried arrays were placed into hybridization cassettes (TeleChem International, Sunnyvale, Calif.) and the cDNA samples were suspended in 10 mM EDTA, denatured at 95°C for 5 min and then mixed with 40 uL of SlideHyb buffer 1 (Ambion) and loaded under a coverslip onto the array. Hybridizations were carried out at 47°C for 16–18 h. After hybridization, arrays were washed in 2× SSC, 0.5% SDS 37C for 5 min, followed by 2× 5 min in 0.1× SSC, 0.1% SDS 37°C, and then 2 × 2.5 min in room temperature 0.1× SSC. Arrays were scanned using an Axon 4000b scanner (Molecular Devices, Sunnyvale, Calif) and images were analyzed using GenePix 6.0 (Molecular Devices).

data_processing:
The microarray data were analyzed using R (v. 2.2.1) and the MAANOVA (v. 0.98.8) package. Raw intensity values from replicate probes were averaged and log2 transformed after normalization with the pin-tip LOWESS method. The normalized intensity values were fitted to a mixed model ANOVA considering array and biological replicates as random factors and dye, strain as fixed factors. The linear model tested was Y (intensity) = array + dye + strain (Sakai or TW14359)+ sample (biological replicate) + error. Significant differences in expression due to strain were determined using the Fs test in MAANOVA which uses a shrinkage estimator for gene-specific variance components that makes no assumption about the variances across genes with 1000 random permutations to estimate the p-values. P values were adjusted for multiple comparisons with the B-H step-up correction implemented in R/MAANOVA.

The Sample data table VALUEs represent the end output of all 10 Samples analyzed together.

organism: Escherichia coli

source_name: Sakai

label_protocol: Reverse transcription reactions contained 6ug RNA, 2ug random primers (Invitrogen, Carlsbad, Calif.), 1x first strand buffer (Invitrogen), 10mM DTT, 400U Superscript II (Invitrogen), 0.5mM each dATP, dCTP, and dGTP, 0.3mM dTTP, and 0.2mM reactions wereamino-allyl dUTP. 30uL C. cDNA was purified using PCR incubated overnight at 42 cleanup columns (Qiagen) with Phosphate wash buffer (5mM K2HPO4, pH 8.0, 80%EtOH) and phosphate elution buffer (4mM K2HPO4, pH 8.5). Amino-allyl labeled cDNA was dried and resuspended in 0.1M sodium carbonate pH 9.3 and coupled with either Cy3 or Cy5 (Amersham Biosciences, Piscataway, N.J.). Uncoupled dye was removed by another purfication using the PCR cleanup kit. Concentration of cDNA and amount of incoporated dye was measured for each sample using a Nanodrop spectrophotometer (Ambion).

extract_protocol: 8 ml of the culture was mixed with 1/10V 10% phenol:ethanol buffer to stabilize the RNA, and centrifuged at 4 oC, 4300 × g for 30 min to pellet cells. The supernatant was decanted and cell pellets were suspended in 5 ml of buffer (2 mM EDTA, 20 mM NaOAc, pH 5.2) before mixing with equal volume of hot acid-phenol:chloroform (pH 4.5 with Iso Amyl Alcohol (IAA), 125:25:1) (Ambion, Austin, TX) and incubating at 65 oC with periodic shaking for 10 min. The samples were centrifuged at 3220 × g for 20 min and the supernatant was subjected to further extractions with phenol:chloroform and chloroform:IAA (3). RNA was precipitated overnight at -70 oC in 2.5 volume 100% ethanol and 1/10 volume 3 M sodium acetate pH 5.2. RNA purification and DNase treatment of RNA samples were done with the Rneasy kit (Qiagen, Valencia, CA) and RNA quality was assessed on a formaldehyde-agarose gel.

value: Sakai


title: Patient 22, biopsy; Control


title: Patient 2, colonocytes; UC non-inflamed


title: Patient 5, colonocytes; UC inflamed


title: Patient 16, biopsy; Control


title: Patient 17, biopsy; UC non-inflamed


title: Patient 6, colonocytes; UC inflamed


title: Flutamide treated male at GD 17, biological rep2

status: Public on Jan 15 2010

city: Quebec

first: Eva

last: Bresson

state: Quebec

address: 2705, boul. Laurier, bloc T-1-49

department: Reproduction, santé périnatale et santé de l'enfant

institute: CHUL-CHUQ-Laval University

description: Gene expression data from flutamide treated male fetal lung at GD 17

hyb_protocol: 15ug of fragmented cRNA was hybridized for 16 h at 45°C with constant rotation, using a mouse oligonucleotide array MOE430 2.0 (Genechip, Affymetrix, Santa Clara, CA)

scan_protocol: Chips were scanned using a GeneChip Scanner 3000 G7 (Affymetrix) enabled for High-Resolution Scanning

data_processing: The analysis was performed using the affylmGUI Graphical User Interface for the limma microarray package

source_name: fetal lung of flutamide treated male at GD17

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20ug total RNA consisting of a pool of total RNA from 3  fetuses of 3 different litters for each monoplicate. Each replicate was composed of RNA samples from different individuals (biological triplicate).

extract_protocol: Tri-reagent extraction of total RNA was performed according to the manufacturer's instructions. Each sample was then purified on a CsCl gradient.

treatment_protocol: Pregnant females received a daily sub-cutaneous injection of 200 µl of flutamide (1 mg) or vehicule solution from GD10 to the day prior to harvesting day. Pregnant females were sacrificed by exposure to CO2 at GD17 or GD18.

value: BALB/c

tag: sample type

value: RNA samples from three fetuses of the same sex but from distinct litters were  pooled

value: fetal lung

tag: age

value: fetal gestional day 17


title: Patient 15, biopsy; Control


title: Patient 19, biopsy; UC non-inflamed


title: Patient 13, biopsy; Control


title: Patient 18, biopsy; UC non-inflamed


title: Patient 14, biopsy; UC inflamed


title: Patient 12, biopsy; Control


title: B10.BR-H2k H2-T18a/SgSnJ (drifted) Lin- Bone Marrow

city: Hackensack

first: Michael

last: Appel

state: NJ

address: 30 Prospect AVE-room 350

department: Oncology Research

institute: Hackensack University Medical Center

description: All steps subsequent to Lineage negative cell purification (ie starting with RNA extraction) were performed at SAbiosciences

hyb_protocol: See Oligo GEArray® protocol book starting pg. 16 (HybPlate Basic Protocol) at manufacturers website http://www.sabiosciences.com/support_manual.php

scan_protocol: See Oligo GEArray® protocol book starting pg .27 Image and Data Acquisition and Expression Analysis at manufacturers website http://www.sabiosciences.com/support_manual.php

data_processing: The lowest density reading for a spot on the array was subtracted from the intensity reading for each spot. This yielded a background corrected intensity value for each spot. A normalized value for each spot was obtained through dividing its background corrected intensity by the mean intensity of all spots in the interquartile range (median 50%) of brightness.

source_name: Bone marrow from B10.BR-H2k H2-T18a/SgSnJ (drifted) mice

label_protocol:
See Oligo GEArray TrueLabeling-AMP™ 2.0 Kit protocol at manufacturers website
http://www.sabiosciences.com/support_manual.php

extract_protocol:
See ArrayGrade Total RNA Isolation Kit  protocol at manufacturers website
http://www.sabiosciences.com/support_manual.php

treatment_protocol: Cell suspensions were stained with a Biotin Mouse Lineage Panel {CD3e, CD11b, CD45R, Gr-1, TER-119} (BD Pharmingen) followed by anti-biotin microbeads (Miltenyi Biotec).The labeled cell suspensions were passed through the AutoMacs machine (Miltenyi Biotec) twice and the negative fraction after the second pass through was collected as the lineage negative population. The streptavidin-PE-stained negative fraction was determined to be <4% lineage positive by flow cytometry.

value: B10.BR-H2k H2-T18a/SgSnJ (drifted) from the Jackson Laboratory (Bar Harbor, ME) Gender:Male Tissue:Bone marrow from femurs and tibiae


title: Patient 7, biopsy; UC inflamed


title: Patient 8, biopsy; UC non-inflamed


title: Patient 4, biopsy; Collagen colitis (excluded)


title: Patient 10, biopsy; UC non-inflamed


title: Patient 9, biopsy; Control


title: B10.BR-H2k H2-T18a/SgSnJJrep Lin- Bone Marrow

source_name: Bone marrow from B10.BR-H2k H2-T18a/SgSnJJrep mice

value: B10.BR-H2k H2-T18a/SgSnJJrep from the Jackson Laboratory (Bar Harbor, ME)

tag: gender

value: Male

value: Bone marrow from femurs and tibiae


title: Patient 11, biopsy; UC inflamed


title: Patient 28, biopsy; UC non-inflamed


title: Patient 1, biopsy; UC inflamed


title: Patient 6, biopsy; UC inflamed


title: Continuous flow rep1

city: London

first: Eijiro

last: Maeda

address: Mile End Road

department: Engineering

country: United Kingdom

institute: Queen Mary, University of London

hyb_protocol: According to protocol provided by Illumina

scan_protocol: Scanning procedures were carried out as described by Illumina

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Mesenchymal stem cells

growth_protocol: hMSCs were cultured for eight days within perfused three-dimensional matrices under conditions of oscillatory, continuous or static fluid flow of osteogenic media.

extract_protocol: RNA was extracted and DNase I treated with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: hMSC samples were seeded within porous glass scaffolds following eight days exposure to either a high flow rate oscillatory (10L/24hrs), low flow rate oscillatory (1L/24hrs), continuous (1mL/24hrs) or a static (0mL/24hrs) flow rate condition.  3 RNA samples from each flow rate condition were analysed.

value: hMSCs


title: Patient 5, biopsy; UC inflamed


title: 10L oscillatory rep3

label_protocol: According to protocol provided by Illumina


title: 1L oscillatory rep3


title: Patient 3, biopsy; Control


title: 1L oscillatory rep1


title: Continuous flow rep3


title: 10L oscillatory rep2


title: Continuous flow rep2


title: 10L oscillatory rep1


title: 1L oscillatory rep2


title: Static flow rep2


title: Static flow rep3


title: Patient 2, biopsy; UC non-inflamed


title: Static flow rep1


title: Patient 23, colonocytes; Control


title: breast cancer sample from patient BC160

type: genomic

city: Rockville

first: Robert

middle: J

last: Clifford

state: MD

address: 2115 E Jefferson

department: CCR

institute: NCI

description:
Hybridized to SNP5.0
primary data: Affymetrix *.CHP files for the 250K_Nsp and 250K_Sty microarrays; Affymetrix *.CHP files for the SNP5.0 microarray.

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: Arrays were washed and stained in the Genechip Fluidics Station 450 (Affymetrix) following the manufacturer’s instructions.  Chips were scanned with the Affymetrix GeneChip Scanner 3000.

data_processing: *.CHP files for the 250K_Nsp and 250K_Sty experiments were generated using the Affymetrix Power Tools version 1.8.5 gtype-probeset-genotype program.  *.CHP files for the SNP5.0 experiments were generated using the Affymetrix Power Tools version 1.10.0 apt-probeset-genotype program.

molecule: genomic DNA

source_name: patient BC160

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from tumor samples using the QIAamp DNA mini kit (Qiagen, Inc., Valencia, CA, USA).

tag: histological grade

tag: tnm

tag: er

value: positive

tag: pr

value: negative

tag: invasion

value: yes

tag: node

tag: histopathology type

value: Invasive lobular


title: breast cancer sample from patient BC156

source_name: patient BC156

value: invasive ductal carcinoma


title: breast cancer sample from patient BC155

source_name: patient BC155


title: breast cancer sample from patient BC157

source_name: patient BC157

value: invasive ductal carcinoma with intraductal component


title: breast cancer sample from patient BC161

source_name: patient BC161


title: breast cancer sample from patient BC158

source_name: patient BC158

value: Invasive ductal carcinoma


title: breast cancer sample from patient BC148

source_name: patient BC148

value: infiltrating lobular carcinoma


title: breast cancer sample from patient BC147

source_name: patient BC147

value: Invasive ductal adenocarcinoma; Invasive lobular carcinoma


title: breast cancer sample from patient BC152

source_name: patient BC152


title: breast cancer sample from patient BC144

source_name: patient BC144

value: High-grade DCIS; invasive ductal carcinoma


title: breast cancer sample from patient BC143

source_name: patient BC143

value: Invasive carcinoma


title: breast cancer sample from patient BC141

source_name: patient BC141


title: breast cancer sample from patient BC151

source_name: patient BC151


title: breast cancer sample from patient BC145

source_name: patient BC145

value: Invasive ductal


title: breast cancer sample from patient BC153

source_name: patient BC153

value: infiltrating ductal carcinoma


title: breast cancer sample from patient BC142

source_name: patient BC142

value: no

value: ductal carcinoma in situ


title: breast cancer sample from patient BC159

source_name: patient BC159

value: Invasive ductal carcinoma with extensive intraductal component


title: breast cancer sample from patient BC140

source_name: patient BC140


title: breast cancer sample from patient BC150

source_name: patient BC150


title: breast cancer sample from patient BC154

source_name: patient BC154

value: Mixed ductal-lobular carcinoma


title: breast cancer sample from patient BC146

source_name: patient BC146

value: positive


title: breast cancer sample from patient BC138

source_name: patient BC138


title: breast cancer sample from patient BC149

source_name: patient BC149


title: breast cancer sample from patient BC139

source_name: patient BC139

value: negative


title: breast cancer sample from patient BC137

source_name: patient BC137

value: yes

value: Mixed ductal and lobular invasive carcinoma


title: breast cancer sample from patient BC134

source_name: patient BC134

value: Infiltrating ductal carcinoma


title: breast cancer sample from patient BC133

source_name: patient BC133


title: breast cancer sample from patient BC135

source_name: patient BC135

value: invasive breast carcinoma


title: breast cancer sample from patient BC130

source_name: patient BC130


title: breast cancer sample from patient BC131

source_name: patient BC131


title: breast cancer sample from patient BC132

source_name: patient BC132


title: breast cancer sample from patient BC129

source_name: patient BC129


title: breast cancer sample from patient BC136

source_name: patient BC136


title: breast cancer sample from patient BC127

source_name: patient BC127


title: L_LS_Wk4

status: Public on Oct 30 2009

city: New York

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description: Psoriasis patient

hyb_protocol: 15mg of the biotinylated cRNA was hybridized to Affymetrix Human Genome U133A 2.0 Array (22200 probe sets) (Affymetrix Inc.). The chips were washed and stained with streptavidin-phycoerythin.

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: Patient  L, lesion, 4 week

label_protocol: For each Affymetrix genechip, 4mg total RNA was reverse-transcribed, amplified, and labeled using BioArray High Yield RNA Transcription Labeling Kit (Enzo Biochem Inc.).

extract_protocol: Cells were lysed in RLT with Beta-2-mercaptoethanol. RNA was extracted using the RNeasy Mini Kit (Qiagen), and DNA was removed with on-column DNAse digestion using RNAse-free DNAse Set (Qiagen). RNA was used for either RT-PCR or gene array.

tag: Patient

value: L

tag: Time

value: 4 weeks

tag: Group

value: responder

tag: Condition

value: lesional


title: breast cancer sample from patient BC128

source_name: patient BC128


title: Heads 2 round amplification, biological rep1

city: Manhattan

first: Kristin

last: Michel

state: KS

address: 267 Chalmers Hall

institute: Kansas State University

description: gene expression data from heads isolated from Anopheles gambiae female adults 1-2 days after eclosion

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

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

data_processing: GCOS 1.4

organism: Anopheles gambiae

source_name: heads isolated from 40 Anopheles gambiae female adults, G3 strain

label_protocol: Total RNA was biotinylated according to the Eukaryotic Target Labeling protocol (Affymetrix), for specific labeling protocol see Samples section

extract_protocol: Total RNA was cleaned up according to the RNeasy Mini protocol for animal cells (Qiagen), for specific extract protocol see Samples section

treatment_protocol: All tissues were isolated from naïve female mosquitoes 1-2 days after eclosion and stored in their respective solutions at -80ºC. For specific treatment protocol, see Samples section

tag: tissue

value: Head

tag: treatment protocol

value: Heads were harvested from 40 females at 4C with dissection scissors. Heads were collected into 200ul Trizol on ice, flash frozen in liquid nitrogen, and stored at -80ºC

tag: rna extraction method

value: Trizol extraction, clean-up with RNeasy Mini protocol (Qiagen)

tag: labeling protocol

value: Two cycle Eukaryotic labeling protocol (affymetrix)

tag: starting amount of total rna

value: 80 ng

tag: strain


title: breast cancer sample from patient BC122

source_name: patient BC122

tag: histological grade

value: infiltrating ductal carcinoma


title: breast cancer sample from patient BC118

source_name: patient BC118

tag: tnm

value: invasive ductal carcinoma


title: breast cancer sample from patient BC126

source_name: patient BC126

tag: er

value: positive

value: Invasive ductal carcinoma


title: breast cancer sample from patient BC121

source_name: patient BC121

value: negative

tag: pr

value: yes


title: breast cancer sample from patient BC125

source_name: patient BC125

tag: invasion


title: breast cancer sample from patient BC120

source_name: patient BC120

tag: node

value: Infiltrating mammary carcinoma with lobular features


title: breast cancer sample from patient BC124

source_name: patient BC124

tag: histopathology type


title: breast cancer sample from patient BC114

source_name: patient BC114

value: Infiltrating lobular carcinoma


title: breast cancer sample from patient BC123

source_name: patient BC123


title: breast cancer sample from patient BC119

source_name: patient BC119

value: Infiltrating ductal adenocarcinoma


title: breast cancer sample from patient BC111

source_name: patient BC111

value: no

value: lobular carcinoma in situ


title: breast cancer sample from patient BC106

source_name: patient BC106

value: Infiltrating ductal carcinoma


title: breast cancer sample from patient BC112

source_name: patient BC112

value: poorly differentiated infiltrating ductal carcinoma


title: breast cancer sample from patient BC116

source_name: patient BC116

value: invasive duct carcinoma


title: breast cancer sample from patient BC115

source_name: patient BC115


title: breast cancer sample from patient BC117

source_name: patient BC117

value: invasive lobular carcinoma


title: CDC38711

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

description:
Data from triplicate probes was averaged. For each probe, see raw data which is supplied as a supplementary file.
We routinely scanned arrays hybridized with Cy5 labeled DNA using both 635 and 532 wavelengths. The Cy3 channel data in the raw data files for these samples can be deleted as it was not used in any data analysis.

hyb_protocol: Labeled DNA was hybridized to arrays for 14 hrs at 42C.

scan_protocol: The arrays were scanned with a GenePix 4000B

data_processing: The log10 (average 635 nm median signal intensity for triplicate probes/average signal intensity of all empty spots on array) was determined.

organism: Clostridium botulinum

source_name: Clostridium botulinum, strain CDC38711

label_protocol: 1 ug of genomic DNA was labeled with Cy5 random primers using Klenow fragment

extract_protocol: Epicenter MasterPure DNA Purification kit (Madison, WI)

tag: toxin subtype

value: A(B)


title: breast cancer sample from patient BC113

source_name: patient BC113

value: DCIS


title: CDC38652

source_name: Clostridium botulinum, strain CDC38652


title: breast cancer sample from patient BC105

source_name: patient BC105

value: Extesive infiltrating carcinoma with ductal and lobular features


title: breast cancer sample from patient BC104

source_name: patient BC104

value: Pleomorphic carcinoma of the breast with bizarre tumor giant cells


title: breast cancer sample from patient BC108

source_name: patient BC108

value: positive


title: CDC38035

source_name: Clostridium botulinum, strain CDC38035


title: breast cancer sample from patient BC110

source_name: patient BC110

value: infiltrating ductal carcinoma


title: CDC38001

source_name: Clostridium botulinum, strain CDC38001


title: breast cancer sample from patient BC109

source_name: patient BC109

value: negative


title: CDC23996

source_name: Clostridium botulinum, strain CDC23996


title: CDC23397

source_name: Clostridium botulinum, strain CDC23397


title: breast cancer sample from patient BC97

source_name: patient BC97

value: intraductal epithelial hyperplasia


title: breast cancer sample from patient BC103

source_name: patient BC103

value: yes

value: Infiltrating poorly differentiated ductal carcinoma


title: CDC23084

source_name: Clostridium botulinum, strain CDC23084


title: CDC23357

source_name: Clostridium botulinum, strain CDC23357


title: breast cancer sample from patient BC102

source_name: patient BC102

value: Marked interstitial fibrosis with sclerosis and lobular atypia, consistent with prior treatment effect


title: breast cancer sample from patient BC94

source_name: patient BC94

value: infiltrating lobular carcinoma


title: breast cancer sample from patient BC98

source_name: patient BC98


title: breast cancer sample from patient BC100

source_name: patient BC100

value: Moderately differentiated infiltrating ductal carcinoma


title: breast cancer sample from patient BC107

source_name: patient BC107

value: Infiltrating ductal carcinoma, mulitfocal


title: CDC21520

source_name: Clostridium botulinum, strain CDC21520


title: breast cancer sample from patient BC96

source_name: patient BC96

value: poorly differentiated infiltrating ductal carcinoma


title: breast cancer sample from patient BC93

source_name: patient BC93


title: breast cancer sample from patient BC101

source_name: patient BC101

value: Infiltrating ductal carcinoma


title: breast cancer sample from patient BC91

source_name: patient BC91


title: breast cancer sample from patient BC99

source_name: patient BC99

value: Mixed infiltrating ductal and lobular carcinoma associated with DCIS


title: breast cancer sample from patient BC90

source_name: patient BC90

value: no

value: Extensive ductal carcinoma in situ


title: breast cancer sample from patient BC88

source_name: patient BC88


title: breast cancer sample from patient BC92

source_name: patient BC92

value: invasive ductal carcinoma


title: breast cancer sample from patient BC95

source_name: patient BC95

value: Well-differentiated infiltrating ductal carcinoma


title: CDC21519

source_name: Clostridium botulinum, strain CDC21519

value: A(B)


title: breast cancer sample from patient BC89

source_name: patient BC89

value: positive

value: Infiltrating ductal carcinoma; carcinoma in situ


title: breast cancer sample from patient BC42_Nsp

description:
Hybridized to 250K_Nsp
primary data: Affymetrix *.CHP files for the 250K_Nsp and 250K_Sty microarrays; Affymetrix *.CHP files for the SNP5.0 microarray.

source_name: patient BC42

value: negative

value: infiltrating ductal carcinoma


title: breast cancer sample from patient BC41_Nsp

source_name: patient BC41

value: yes


title: breast cancer sample from patient BC87

source_name: patient BC87


title: breast cancer sample from patient BC85

source_name: patient BC85


title: breast cancer sample from patient BC86

source_name: patient BC86


title: breast cancer sample from patient BC39_Nsp

source_name: patient BC39

value: ductal carcinoma in situ


title: breast cancer sample from patient BC84

source_name: patient BC84


title: breast cancer sample from patient BC83

source_name: patient BC83


title: breast cancer sample from patient BC36_Nsp

source_name: patient BC36


title: breast cancer sample from patient BC82

source_name: patient BC82

value: inflammatory carcinoma


title: breast cancer sample from patient BC40_Nsp

source_name: patient BC40


title: breast cancer sample from patient BC79

source_name: patient BC79


title: breast cancer sample from patient BC35_Nsp

source_name: patient BC35


title: breast cancer sample from patient BC37_Nsp

source_name: patient BC37

value: infiltrating lobular carcinoma


title: breast cancer sample from patient BC80

source_name: patient BC80


title: breast cancer sample from patient BC81

source_name: patient BC81

value: Ductal adenocarcinoma of colloid type


title: breast cancer sample from patient BC38_Nsp

source_name: patient BC38


title: breast cancer sample from patient BC78

source_name: patient BC78

value: phyllodes tumor


title: breast cancer sample from patient BC76

source_name: patient BC76

value: Invasive ductal carcinoma


title: breast cancer sample from patient BC77

source_name: patient BC77

value: Significant residual invasive lobular carcinoma, involving previous biopsy site


title: breast cancer sample from patient BC33_Nsp

source_name: patient BC33


title: breast cancer sample from patient BC32_Nsp

source_name: patient BC32


title: breast cancer sample from patient BC34_Nsp

source_name: patient BC34


title: breast cancer sample from patient BC73

source_name: patient BC73


title: breast cancer sample from patient BC74

source_name: patient BC74

value: Invasive carcinoma with predominantly lobular features


title: breast cancer sample from patient BC75

source_name: patient BC75

value: Infiltrating lobular carcinoma


title: breast cancer sample from patient BC42_Sty

description:
Hybridized to 250K_Sty
primary data: Affymetrix *.CHP files for the 250K_Nsp and 250K_Sty microarrays; Affymetrix *.CHP files for the SNP5.0 microarray.

source_name: patient BC42


title: breast cancer sample from patient BC30_Nsp

source_name: patient BC30

value: infiltrating metaplastic carcinoma


title: breast cancer sample from patient BC31_Nsp

source_name: patient BC31


title: breast cancer sample from patient BC41_Sty

source_name: patient BC41

value: invasive ductal carcinoma


title: breast cancer sample from patient BC28_Nsp

source_name: patient BC28

value: invasive breast carcinoma


title: breast cancer sample from patient BC40_Sty

source_name: patient BC40


title: breast cancer sample from patient BC39_Sty

source_name: patient BC39

value: no


title: breast cancer sample from patient BC38_Sty

source_name: patient BC38

value: positive


title: breast cancer sample from patient BC72

source_name: patient BC72

value: negative


title: breast cancer sample from patient BC37_Sty

source_name: patient BC37


title: breast cancer sample from patient BC71

source_name: patient BC71


title: breast cancer sample from patient BC70

source_name: patient BC70


title: breast cancer sample from patient BC29_Nsp

source_name: patient BC29

value: infiltrating ductal carcinoma


title: breast cancer sample from patient BC25_Nsp

source_name: patient BC25

value: yes


title: breast cancer sample from patient BC27_Nsp

source_name: patient BC27


title: breast cancer sample from patient BC69

source_name: patient BC69

value: Residual mixed invasive ductal and lobular carcinoma


title: breast cancer sample from patient BC26_Nsp

source_name: patient BC26


title: breast cancer sample from patient BC35_Sty

source_name: patient BC35


title: breast cancer sample from patient BC68

source_name: patient BC68


title: breast cancer sample from patient BC67

source_name: patient BC67


title: breast cancer sample from patient BC36_Sty

source_name: patient BC36


title: breast cancer sample from patient BC34_Sty

source_name: patient BC34


title: breast cancer sample from patient BC24_Nsp

source_name: patient BC24


title: breast cancer sample from patient BC65

source_name: patient BC65

value: Invasive carcinoma


title: breast cancer sample from patient BC22_Nsp

source_name: patient BC22


title: breast cancer sample from patient BC23_Nsp

source_name: patient BC23


title: breast cancer sample from patient BC33_Sty

source_name: patient BC33


title: breast cancer sample from patient BC66

source_name: patient BC66


title: breast cancer sample from patient BC63

source_name: patient BC63


title: breast cancer sample from patient BC21_Nsp

source_name: patient BC21


title: breast cancer sample from patient BC64

source_name: patient BC64


title: breast cancer sample from patient BC62

source_name: patient BC62


title: breast cancer sample from patient BC32_Sty

source_name: patient BC32


title: breast cancer sample from patient BC61

source_name: patient BC61


title: breast cancer sample from patient BC29_Sty

source_name: patient BC29


title: breast cancer sample from patient BC18_Nsp

source_name: patient BC18


title: breast cancer sample from patient BC31_Sty

source_name: patient BC31


title: breast cancer sample from patient BC17_Nsp

source_name: patient BC17

value: ductal carcinoma in situ


title: breast cancer sample from patient BC20_Nsp

source_name: patient BC20


title: breast cancer sample from patient BC19_Nsp

source_name: patient BC19


title: breast cancer sample from patient BC28_Sty

source_name: patient BC28


title: breast cancer sample from patient BC16_Nsp

source_name: patient BC16


title: breast cancer sample from patient BC59

source_name: patient BC59


title: breast cancer sample from patient BC60

source_name: patient BC60

value: invasive lobular carcinoma


title: breast cancer sample from patient BC14_Nsp

source_name: patient BC14


title: breast cancer sample from patient BC57

source_name: patient BC57

value: Invasive lobular carcinoma


title: breast cancer sample from patient BC58

source_name: patient BC58

value: In situ and invasive ductal carcinoma


title: breast cancer sample from patient BC25_Sty

source_name: patient BC25

value: infiltrating lobular carcinoma


title: breast cancer sample from patient BC24_Sty

source_name: patient BC24


title: breast cancer sample from patient BC26_Sty

source_name: patient BC26


title: breast cancer sample from patient BC15_Nsp

source_name: patient BC15


title: breast cancer sample from patient BC56

source_name: patient BC56

value: moderately differentiated ductal carcinoma


title: breast cancer sample from patient BC11_Nsp

source_name: patient BC11

value: invasive carcinoma


title: breast cancer sample from patient BC27_Sty

source_name: patient BC27


title: breast cancer sample from patient BC30_Sty

source_name: patient BC30

value: infiltrating metaplastic carcinoma


title: breast cancer sample from patient BC12_Nsp

source_name: patient BC12

value: invasive ductal carcinoma


title: breast cancer sample from patient BC55

source_name: patient BC55


title: breast cancer sample from patient BC13_Nsp

source_name: patient BC13


title: breast cancer sample from patient BC23_Sty

source_name: patient BC23


title: mNSC control at polysomal rna level, biological rep2

status: Public on Sep 28 2009

city: Heidelberg

first: sachin

last: kumar

state: Baden-Württemberg

address: Molecular Neurobiology; German Cancer Research Center; INF 581;

country: Germany

institute: DKFZ

description: primary neurosphere cultures

hyb_protocol: Affymetrix standard protocol

scan_protocol: The expression profiling analysis for mouse NSC was carried out at DKFZ (Heidelberg, Germany). Hybridization and scanning of samples from mNSC were performed at the Microarray Facility of Medical Research Center (Mannheim, Germany).

data_processing: For the polysomal mRNA of mNSC 7 gene chip arrays, and for the total mRNA of mNSC 8 gene chip arrays were analyzed. Data mining was performed by using the ChipInspector analysis software (Genomatix, Munich, Germany) which identifies significant changes based on single probes. The corresponding transcripts were then assigned after a user-defined number of significant probes. For all analyses, a transcript coverage greater than three probes was chosen. After intensity normalisation of each array, significantly changed genes were determined by significance analysis of microarrays (SAM), (Tusher et al., 2001). ChipInspector carries out significance analysis on the single probe level. Normalized probe set level data not provided.

molecule: polyA RNA

source_name: primary mouse neural stem cells isolated from 6 week old female mice

label_protocol: Affymetrix standard protocol

extract_protocol: Polysomal RNA from mouse NSC was isolated by using the phenol-choloroform method. The quality of isolated RNA was controlled by the Lab-on-Chip-System Bioanalyser 2100 (Agilent Technologies, Inc., Palo Alto, CA, USA).

tag: gender

value: female

tag: treatment

value: control

tag: protocol

value: polysomal RNA


title: breast cancer sample from patient BC10_Nsp

source_name: patient BC10

value: negative

value: positive

value: invasive poorly differentiated carcinoma


title: breast cancer sample from patient BC54

source_name: patient BC54

value: yes

value: Metastatic ductal carcinoma


title: breast cancer sample from patient BC22_Sty

source_name: patient BC22

value: infiltrating ductal carcinoma


title: breast cancer sample from patient BC9_Nsp

source_name: patient BC9


title: breast cancer sample from patient BC53

source_name: patient BC53


title: breast cancer sample from patient BC20_Sty

source_name: patient BC20


title: breast cancer sample from patient BC50

source_name: patient BC50


title: breast cancer sample from patient BC21_Sty

source_name: patient BC21


title: breast cancer sample from patient BC52

source_name: patient BC52


title: breast cancer sample from patient BC51

source_name: patient BC51

value: Invasive, poorly differentiated ductal carcinoma


title: breast cancer sample from patient BC19_Sty

source_name: patient BC19


title: breast cancer sample from patient BC8_Nsp

source_name: patient BC8


title: Unvaccinated N19

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

description: Biological replicate 5 of 5

hyb_protocol: The slides were pretreated with 1% BSA fraction V, 5× SSC, 0.1% SDS (30 min at 50°C) and washed with 2 × SSC (3 min) and 0.2 × SSC (3 min) and hybridized overnight at 60°C in a cocktail containing 1.3 × Denhardt’s, 3 × SSC 0.3% SDS, 0.67 µg/µl polyadenylate and 1.4 µg/µl yeast tRNA. After hybridization slides were washed at room temperature in 0.5 x SSC and 0.1% SDS (15 min), 0.5 x SSC and 0.01% SDS (15 min), and twice in 0.06 x SSC (2 and 1 min, respectively)

scan_protocol: Scanned with GenePix4100A

data_processing: LOWESS normalized, median background subtracted from median signal, log2 of processed Red signal/processed Green signal

organism: Salmo salar

source_name: Unvaccinated salmon, high resistance, liver

label_protocol: 20 µg of total RNA were labled with SuperScript™ Indirect cDNA Labelling System (Invitrogen) according to the manufacturer's instruction

growth_protocol: Salmon was maintained in tanks at standard conditions

extract_protocol: Total RNA extracted using Trizol and purifeid with Pure Link (Invitrogen) following manufacturer's instructions

treatment_protocol: Salmon was challenged with Aeromonas salmonicida by cohabitance with carrier fish, that received bacteria via intraperitoneal injection

tag: phenotype

value: high resistance

tag: tissue

value: liver

source_name: Unvaccinated salmon, low resistance, liver, pooled sample

value: low resistance

tag: sample type

value: pooled liver samples


title: Unvaccinated N17

description: Biological replicate 4 of 5


title: breast cancer sample from patient BC49

source_name: patient BC49

value: Invasive ductal carcinoma


title: breast cancer sample from patient BC16_Sty

source_name: patient BC16


title: Unvaccinated N16

description: Biological replicate 3 of 5


title: breast cancer sample from patient BC7_Nsp

source_name: patient BC7


title: breast cancer sample from patient BC15_Sty

source_name: patient BC15


title: Unvaccinated N14

description: Biological replicate 1 of 5


title: Vaccinated N20

description: Biological replicate 6 of 6

source_name: Vaccinated salmon, high resistance, liver

source_name: Vaccinated salmon, low resistance, liver, pooled sample


title: Unvaccinated N15

description: Biological replicate 2 of 5


title: breast cancer sample from patient BC6_Nsp

source_name: patient BC6

value: invasive lobular carcinoma


title: Vaccinated N19

description: Biological replicate 5 of 6


title: Vaccinated N18

description: Biological replicate 4 of 6


title: breast cancer sample from patient BC5_Nsp

source_name: patient BC5

value: invasive ductal carcinoma


title: Vaccinated N16

description: Biological replicate 2 of 6


title: Vaccinated N17

description: Biological replicate 3 of 6


title: breast cancer sample from patient BC17_Sty

source_name: patient BC17

value: no

value: ductal carcinoma in situ


title: breast cancer sample from patient BC4_Nsp

source_name: patient BC4


title: breast cancer sample from patient BC14_Sty

source_name: patient BC14


title: breast cancer sample from patient BC46

source_name: patient BC46

value: poorly differentiated infiltrating ductal carcinoma


title: breast cancer sample from patient BC47

source_name: patient BC47


title: Vaccinated N15

description: Biological replicate 1 of 6


title: breast cancer sample from patient BC18_Sty

source_name: patient BC18

value: negative


title: breast cancer sample from patient BC45

source_name: patient BC45

value: positive


title: breast cancer sample from patient BC3_Nsp

source_name: patient BC3


title: Fenretinde(4HPR)-treated NB4 at 60h

status: Public on Sep 15 2009

city: Bristol

first: Hai

last: Fang

address: Woodland Road

department: Department of Computer Science

institute: University of Bristol

description: Fenretinide-treated time series, treated NB4 cells at 60h

hyb_protocol: Hybridization under the standard protocol.

scan_protocol: Data acquisition was performed using a laser scanner (Axon Instruments, Union City, CA).

data_processing: Intensity-dependent global LOWESS normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: Fenretinde(4HPR)-treated NB4 at 60h_test

label_protocol: Approximately 30μg RNA was reverse transcribed into cDNA primed with oligo (dT) and labeled with Cy3-dCTP (Green fluorescent dye, G) using Superscript II reverse transcriptase (Life Technologies, Inc., Gaithersburg, MD), while the reference used in all hybridizations was labeled with Cy5-dCTP (Red fluorescent dye, R).

growth_protocol: Leukemia-derived NB4 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (Gibco) and antibiotics in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: Total RNA was prepared using TRIzol (Life Technologies, Inc., Gaithersburg, MD) and further purified with RNeasy columns (Qiagen, Valencia, CA).

treatment_protocol: Cells were left untreated (control) or treated with 1 µM fenretinide.  Control cells were harvested at 0, 8, 12, and 15 hours.  Fenretinide treated cells were harvested at 0.25, 0.5, 1, 2, 4, 6, 8, 10, 12, 15, 18, 21, 24, 30, 36, 42, 48, 54, and 60 hours.

tag: cell line

value: Leukemia-derived cell line NB4

value: fenretinde(4HPR) treated

tag: time

value: 60 hr

source_name: Fenretinde(4HPR)-treated NB4 at 60h_reference

value: control


title: breast cancer sample from patient BC48

source_name: patient BC48

value: yes

value: infiltrating ductal carcinoma


title: Fenretinde(4HPR)-treated NB4 at 54h

description: Fenretinide-treated time series, treated NB4 cells at 54h

source_name: Fenretinde(4HPR)-treated NB4 at 54h_test

value: 54 hr

source_name: Fenretinde(4HPR)-treated NB4 at 54h_reference


title: Fenretinde(4HPR)-treated NB4 at 42h

description: Fenretinide-treated time series, treated NB4 cells at 42h

source_name: Fenretinde(4HPR)-treated NB4 at 42h_test

value: 42 hr

source_name: Fenretinde(4HPR)-treated NB4 at 42h_reference


title: Fenretinde(4HPR)-treated NB4 at 48h

description: Fenretinide-treated time series, treated NB4 cells at 48h

source_name: Fenretinde(4HPR)-treated NB4 at 48h_test

value: 48 hr

source_name: Fenretinde(4HPR)-treated NB4 at 48h_reference


title: breast cancer sample from patient BC2_Nsp

source_name: patient BC2


title: Fenretinde(4HPR)-treated NB4 at 30h

description: Fenretinide-treated time series, treated NB4 cells at 30h

source_name: Fenretinde(4HPR)-treated NB4 at 30h_test

value: 30 hr

source_name: Fenretinde(4HPR)-treated NB4 at 30h_reference


title: breast cancer sample from patient BC1_Nsp

source_name: patient BC1

value: invasive medullary carcinoma


title: breast cancer sample from patient BC12_Sty

source_name: patient BC12

value: invasive ductal carcinoma


title: breast cancer sample from patient BC9_Sty

source_name: patient BC9


title: Fenretinde(4HPR)-treated NB4 at 36h

description: Fenretinide-treated time series, treated NB4 cells at 36h

source_name: Fenretinde(4HPR)-treated NB4 at 36h_test

value: 36 hr

source_name: Fenretinde(4HPR)-treated NB4 at 36h_reference


title: breast cancer sample from patient BC13_Sty

source_name: patient BC13

value: no

value: ductal carcinoma in situ


title: Fenretinde(4HPR)-treated NB4 at 21h

description: Fenretinide-treated time series, treated NB4 cells at 21h

source_name: Fenretinde(4HPR)-treated NB4 at 21h_test

value: 21 hr

source_name: Fenretinde(4HPR)-treated NB4 at 21h_reference


title: Fenretinde(4HPR)-treated NB4 at 18h

description: Fenretinide-treated time series, treated NB4 cells at 18h

source_name: Fenretinde(4HPR)-treated NB4 at 18h_test

value: 18 hr

source_name: Fenretinde(4HPR)-treated NB4 at 18h_reference


title: Fenretinde(4HPR)-treated NB4 at 15h

description: Fenretinide-treated time series, treated NB4 cells at 15h

source_name: Fenretinde(4HPR)-treated NB4 at 15h_test

value: Leukemia-derived cell line NB4

value: 15 hr

source_name: Fenretinde(4HPR)-treated NB4 at 15h_reference


title: Fenretinde(4HPR)-treated NB4 at 10h

description: Fenretinide-treated time series, treated NB4 cells at 10h

source_name: Fenretinde(4HPR)-treated NB4 at 10h_test

value: fenretinde(4HPR) treated

value: 10 hr

source_name: Fenretinde(4HPR)-treated NB4 at 10h_reference


title: Fenretinde(4HPR)-treated NB4 at 24h

description: Fenretinide-treated time series, treated NB4 cells at 24h

source_name: Fenretinde(4HPR)-treated NB4 at 24h_test

value: 24 hr

source_name: Fenretinde(4HPR)-treated NB4 at 24h_reference

value: control


title: Fenretinde(4HPR)-treated NB4 at 12h

description: Fenretinide-treated time series, treated NB4 cells at 12h

source_name: Fenretinde(4HPR)-treated NB4 at 12h_test

value: 12 hr

source_name: Fenretinde(4HPR)-treated NB4 at 12h_reference


title: Fenretinde(4HPR)-treated NB4 at 8h

description: Fenretinide-treated time series, treated NB4 cells at 8h

source_name: Fenretinde(4HPR)-treated NB4 at 8h_test

value: 8 hr

source_name: Fenretinde(4HPR)-treated NB4 at 8h_reference


title: breast cancer sample from patient BC8_Sty

source_name: patient BC8

value: negative

value: positive

value: yes


title: Fenretinde(4HPR)-treated NB4 at 6h

description: Fenretinide-treated time series, treated NB4 cells at 6h

source_name: Fenretinde(4HPR)-treated NB4 at 6h_test

value: 6 hr

source_name: Fenretinde(4HPR)-treated NB4 at 6h_reference


title: Fenretinde(4HPR)-treated NB4 at 4h

description: Fenretinide-treated time series, treated NB4 cells at 4h

source_name: Fenretinde(4HPR)-treated NB4 at 4h_test

value: 4 hr

source_name: Fenretinde(4HPR)-treated NB4 at 4h_reference


title: Fenretinde(4HPR)-treated NB4 at 2h

description: Fenretinide-treated time series, treated NB4 cells at 2h

source_name: Fenretinde(4HPR)-treated NB4 at 2h_test

value: 2 hr

source_name: Fenretinde(4HPR)-treated NB4 at 2h_reference


title: Fenretinde(4HPR)-treated NB4 at 0.5h

description: Fenretinide-treated time series, treated NB4 cells at 0.5h

source_name: Fenretinde(4HPR)-treated NB4 at 0.5h_test

source_name: Fenretinde(4HPR)-treated NB4 at 0.5h_reference


title: Fenretinde(4HPR)-treated NB4 at 1h

description: Fenretinide-treated time series, treated NB4 cells at 1h

source_name: Fenretinde(4HPR)-treated NB4 at 1h_test

value: 1 hr

source_name: Fenretinde(4HPR)-treated NB4 at 1h_reference


title: breast cancer sample from patient BC7_Sty

description:
Hybridized to 250K_Sty
primary data: Affymetrix *.CHP files for the 250K_Nsp and 250K_Sty microarrays; Affymetrix *.CHP files for the SNP5.0 microarray.

source_name: patient BC7

value: infiltrating ductal carcinoma


title: Fenretinde(4HPR)-treated NB4 at 0.25h

description: Fenretinide-treated time series, treated NB4 cells at 0.25h

source_name: Fenretinde(4HPR)-treated NB4 at 0.25h_test

source_name: Fenretinde(4HPR)-treated NB4 at 0.25h_reference


title: Control NB4 at 15h

description: Control time series, untreated NB4 cells, harvested after 15h in culture

source_name: Control NB4 at 15h_test

source_name: Control NB4 at 15h_reference


title: breast cancer sample from patient BC6_Sty

source_name: patient BC6

value: invasive lobular carcinoma


title: breast cancer sample from patient BC5_Sty

source_name: patient BC5

value: invasive ductal carcinoma


title: breast cancer sample from patient BC44

description:
Hybridized to SNP5.0
primary data: Affymetrix *.CHP files for the 250K_Nsp and 250K_Sty microarrays; Affymetrix *.CHP files for the SNP5.0 microarray.

source_name: patient BC44


title: Control NB4 at 12h

description: Control time series, untreated NB4 cells, harvested after 12h in culture

source_name: Control NB4 at 12h_test

value: Leukemia-derived cell line NB4

source_name: Control NB4 at 12h_reference


title: Large cell carcinoma Daffy5T

city: Cambridge

first: Alexis

last: Ramos

address: 7 Cambridge Center

institute: Broad Institute

description: Hybridized to 250K_Sty

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: Raw probe intensities were processed using the GenePattern software package; copy number was computed by dividing the intensity of each probeset by the mean value of that probeset in the five closest normals by Euclidean distance (see Beroukhim et al. PMID: 18077431).  Normalized data was then segmented with GenePattern modules based on the GLAD algorithm.

source_name: Large cell carcinoma Daffy5T

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from samples using the Qiagen Puregene kit and quantitated with PicoGreen.

tag: tumor type

value: Non-small cell lung cancer

tag: tumor subtype

value: Large cell carcinoma

value: primary


title: breast cancer sample from patient BC43

source_name: patient BC43

tag: histological grade

tag: tnm

value: Invasive ductal carcinoma


title: Large cell carcinoma Daffy61T

description: Hybridized to 250K_Sty

source_name: Large cell carcinoma Daffy61T


title: Non-small cell lung cancer 17160

description: Hybridized to 250K_Sty

source_name: Non-small cell lung cancer 17160

value: unspecified


title: Large cell carcinoma Daffy65T

description: Hybridized to 250K_Sty

source_name: Large cell carcinoma Daffy65T


title: breast cancer sample from patient BC11_Sty

source_name: patient BC11

tag: er

tag: pr

value: invasive carcinoma


title: Non-small cell lung cancer 16843

description: Hybridized to 250K_Sty

source_name: Non-small cell lung cancer 16843


title: breast cancer sample from patient BC3_Sty

source_name: patient BC3

value: negative

tag: invasion

tag: node


title: Non-small cell lung cancer 16893

description: Hybridized to 250K_Sty

source_name: Non-small cell lung cancer 16893


title: Control NB4 at 0h

description: Control time series, untreated NB4 cells, harvested after 0h in culture

source_name: Control NB4 at 0h_test

value: control

value: 0 hr

source_name: Control NB4 at 0h_reference


title: Non-small cell lung cancer 16859

description: Hybridized to 250K_Sty

source_name: Non-small cell lung cancer 16859


title: Control NB4 at 8h

description: Control time series, untreated NB4 cells, harvested after 8h in culture

source_name: Control NB4 at 8h_test

value: 8 hr

source_name: Control NB4 at 8h_reference


title: Large cell carcinoma Daffy1T

description: Hybridized to 250K_Sty

source_name: Large cell carcinoma Daffy1T


title: Non-small cell lung cancer 16762

description: Hybridized to 250K_Sty

source_name: Non-small cell lung cancer 16762


title: breast cancer sample from patient BC4_Sty

source_name: patient BC4

value: positive

value: yes

tag: histopathology type


title: Large cell carcinoma Daffy10T

description: Hybridized to 250K_Sty

source_name: Large cell carcinoma Daffy10T


title: Large cell carcinoma Daffy18T

description: Hybridized to 250K_Sty

source_name: Large cell carcinoma Daffy18T


title: Large cell carcinoma Daffy4T

description: Hybridized to 250K_Sty

source_name: Large cell carcinoma Daffy4T


title: breast cancer sample from patient BC2_Sty

source_name: patient BC2


title: breast cancer sample from patient BC10_Sty

source_name: patient BC10

value: invasive poorly differentiated carcinoma


title: Non-small cell lung cancer 16656

description: Hybridized to 250K_Sty

source_name: Non-small cell lung cancer 16656


title: Non-small cell lung cancer BCR-Test-01-045-CP

description: Hybridized to 250K_Sty


title: Non-small cell lung cancer BCR-Test-01-047-CP

description: Hybridized to 250K_Sty


title: Non-small cell lung cancer BCR-Test-01-065-CP

description: Hybridized to 250K_Sty


title: Escherichia coli 8624 qseC deletion mutant grown in DMEM with AI3

city: Baltimore

first: David

middle: A

last: Rasko

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

description:
All protocols were done according to manufacturers specifications:
http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: Data included in file has not been processed other than those protocols within GCOSv1.4

source_name: Escherichia coli 8624 qseC mutant in DMEM with AI3

extract_protocol: Ambion RiboPure RNA Isolation

treatment_protocol: grown to OD600=1.0 in DMEM with AI3

tag: strain

value: Escherichia coli strain 8624 qseC


title: Escherichia coli 8624 qseC mutant grown in  LB

hyb_protocol: All protocols were done according to manufacturers specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

source_name: Escherichia coli 8624 qseC mutant in LB

treatment_protocol: grown to OD600=1.0 in LB

value: Escherichia coli strain 8624 qseC mutant


title: Escherichia coli 8624 qseC deletion mutant grown in DMEM with Epinephrine

scan_protocol: All protocols were done according to manufacturers specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

source_name: Escherichia coli 8624 qseC mutant in DMEM with epinephrine

treatment_protocol: grown to OD600=1.0 in DMEM with Epinephrine


title: breast cancer sample from patient BC1_Sty

source_name: patient BC1

value: invasive medullary carcinoma


title: Non-small cell lung cancer BCR-Test-01-077-CP

description: Hybridized to 250K_Sty


title: Escherichia coli 8624 grown in LB

source_name: Escherichia coli 8624 in LB

label_protocol:
All protocols were done according to manufacturers specifications:
http://www.affymetrix.com/support/technical/manual/expression_manual.affx

value: Escherichia coli strain 8624


title: Escherichia coli 8624 qseB deletion mutant grown in DMEM

treatment_protocol: grown to OD600=1.0 in DMEM

value: Escherichia coli strain 8624 qseB mutant


title: Escherichia coli 8624 kdpE deletion mutant grown in DMEM

value: Escherichia coli strain 8624 kdpE mutant


title: Escherichia coli 8624 qseC deletion mutant grown in DMEM

source_name: Escherichia coli 8624 qseC mutant in DMEM


title: Non-small cell lung cancer 17758

description: Hybridized to 250K_Sty

source_name: Non-small cell lung cancer 17758

value: Non-small cell lung cancer

value: primary


title: Non-small cell lung cancer BCR-Test-01-040-CP

description: Hybridized to 250K_Sty

value: unspecified


title: Escherichia coli 8624 grown in DMEM with Epinephrine

source_name: Escherichia coli 8624

treatment_protocol: grown to OD600=1.0 in DMEM with 50 uM epinephrine

value: Escherichia coli 8624


title: Non-small cell lung cancer S004289T

description: Hybridized to 250K_Sty

source_name: Non-small cell lung cancer S004289T


title: Escherichia coli 8624 grown in DMEM with AI3

treatment_protocol: grown to OD600=1.0 in DMEM with AI3 signaling molecule


title: Lung squamous cell carcinoma cell line H2286

description: Hybridized to 250K_Sty

value: squamous cell carcinoma

value: cell line


title: Bronchio-alveolar carcinoma S004169T

description: Hybridized to 250K_Sty

source_name: Bronchio-alveolar carcinoma S004169T

value: Bronchio-alveolar carcinoma


title: Lung squamous cell carcinoma cell line H1869

description: Hybridized to 250K_Sty


title: E. coli 8624 qseF deletion mutant

data_processing: Data has not been processed other than those protocols within GCOSv1.4

growth_protocol: Escherichia coli 8624 qseF deletion mutant grown in DMEM media


title: Lung squamous cell carcinoma cell line H2170

description: Hybridized to 250K_Sty


title: Non-small cell lung cancer BCR-Test-01-042-CP

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma cell line H2066

description: Hybridized to 250K_Sty


title: Lung squamous cell carcinoma cell line H1703

description: Hybridized to 250K_Sty


title: control vs. TNF-alpha-treated HMEC-1, 4h

city: Tuebingen

first: Peter

last: Rosenberger

address: Waldhoernlestr. 22

department: Anesthesiology

institute: ZMF Universitaet Tuebingen

description: 3 pooled replicates per each condition and microarray.

hyb_protocol: The hybridization procedure was conducted according to the Two-Color Microarray-Based Gene Expression Analysis Protocol (part number G4140-90050). Briefly, 825ng of the correspondiing Cy3- and Cy5-labeled cRNA were combined and hybridized overnight (17 hours at 65°C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent's hybridization chamber and oven. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent's Microarray Scanner System G2505B with the Scan Control Software version A.8.1.3 (Agilent Technologies). Images were read out and quantified using Agilent Feature Extraction Software version 10.2.1.3.

data_processing: Feature Extraction was performed according to the Agilent Feature Extraction Software Reference Guide v9.5. Linear and Lowess data normalization was performed.

source_name: HMEC-1, TNF-alpha-treated, 4h

label_protocol: 1 µg of total RNA (RNA integrity number 9.9 or higher) per each condition was amplified and labeled in the presence of cyanine 3-CTP and cyanine 5-CTP using the Agilent Low RNA Input Linear Amp Kit following the manufacturer's protocol.  Dye-incorporation rate and cRNA output were quantified with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: HMEC-1 cells were grown until confluence was reached.

extract_protocol: Total RNA was extracted using the NucleoSpin RNA II Kit (Macherey & Nagel) following manufacturer's instructions.

treatment_protocol: Confluent HMEC-1 cells were stimulated with 100ng/ml TNF-α (Promokine) for 4h and harvested.

tag: passage

tag: cell type

value: SV-40 immortalized endothelial cells

tag: treatment

value: 100ng/ml TNF-α

tag: treatment time

source_name: HMEC-1, control, 4h

value: untreated


title: Non-small cell lung cancer S003619T

description: Hybridized to 250K_Sty

source_name: Non-small cell lung cancer S003619T

tag: sample type


title: MF patient 12

city: Barcelona

first: Rocio

last: Salgado

address: Passeig Marítim, 25-29

country: Spain

institute: IMIM-Hospital del Mar

description: MFt 12

hyb_protocol: Human cot-1 DNA, Agilent 10x blocking agent and Agilent 2x hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 8.1).

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

source_name: Skin tumor, tumor-stage mycosis fungoides

label_protocol: 2 µg of total DNA previously digested were primed with 20 µl 2.5X Random primers at 95ºC for 5 min. Then the primed DNA was mixed with 10X Buffer, 3 µl Cy3 or Cy5 depending on sample or control DNA labeling and 1µl Exo-Klenow fragment) and incubating at 37ºC for 2 hours.

extract_protocol: Total DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) following the protocol supplied by the manufacturer.

treatment_protocol: Skin biopsies were snap frozen.

tag: gender

value: Male

tag: age

tag: tissue

value: skin tumor

tag: disease

value: tumor-stage mycosis fungoides

source_name: Commercial pools of healthy DNA (Promega, Madison, WI, USA)

value: Female

value: Peripheral blood


title: Non-small cell lung cancer BCR-Test-01-038-CP

description: Hybridized to 250K_Sty

tag: tumor type

tag: tumor subtype

tag: cell line


title: MF patient 10

description: MFt 10


title: Non-small cell lung cancer S004612T

description: Hybridized to 250K_Sty

source_name: Non-small cell lung cancer S004612T


title: MF patient 9

description: MFt 9


title: MF patient 13

description: MFt 13


title: MF patient 7

description: MFt 7


title: control vs. TNF-alpha-treated HMEC-1, 24h

source_name: HMEC-1, TNF-alpha-treated, 24h

treatment_protocol: Confluent HMEC-1 cells were stimulated with 100ng/ml TNF-α (Promokine) for 24h and harvested.

source_name: HMEC-1, control, 24h


title: MF patient 11

description: MFt 11


title: MF patient 6

description: MFt 6


title: MF patient 8

description: MFt 8


title: MF patient 4

description: MFt 4


title: MF patient 5

description: MFt 5


title: MF patient 2

description: MFt 2


title: MF patient 3

description: MFt 3


title: Foot siTUG1 Replicate 2

status: Public on Sep 14 2009

first: Mitchell

last: Guttman

description: lincRNA knock downs

hyb_protocol: Standard Affymetrix protocols for Human U133 Plus 2.0 Array

data_processing: RMA

source_name: Primary Foot Fibroblasts, siRNA-transfected

growth_protocol: Primary human fibroblasts conditions (Rinn et al. 2007)

extract_protocol: Trizol

value: foot

value: primary fibroblasts

tag: sirna

tag: replicate


title: USF1 replicate 3

city: Seattle

first: Christopher

middle: L

last: Plaisier

state: Washington

address: 401 Terry Avenue North

institute: Institute for Systems Biology

hyb_protocol: The cRNA probes were then hybridized using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).

scan_protocol: The chips were scanned using the GeneArray scanner (Affymetrix) to produce CEL files.

data_processing: A rigorous quality control pipeline was developed to prepare the gene expression microarray data for analysis. First, the CEL files were imported into R 2.8.0 using the justRMA function of the Affymetrix library from Bioconductor, which applies background subtraction and quantile normalization. An alternate CDF file (U133Plus2msk.cdf.gz) was used to exclude mis-targeted and nonspecific probes from the microarrays (Zhang et al. 2005), and probesets with less than 7 remaining probes were also excluded. Probesets with more than 50% absent calls were excluded, as calculated using the panp package from Bioconductor. Finally, the ComBat library in R was used to correct for batch effect (Johnson et al. 2007).

source_name: HEK293T cell line

label_protocol: Samples were then converted to cRNA probes using standard Affymetrix protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix P/N 702232).

extract_protocol: Total RNA was collected using the RNeasy Plus Mini Kit (Cat No. 74134) 48 hours after transient transfection of HEK293T cells.


title: MS11 vs. hfq (III)

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

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

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

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

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

organism: Neisseria gonorrhoeae

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

extract_protocol: Qiagen RNeasy including on-column DNase-digest

tag: genotype

value: wildtype (MS11)

tag: biological replicate

value: III

source_name: hfq

value: hfq KO mutant (MS11hfq)


title: Empty vector replicate 2


title: Foot siTUG1 Replicate 3

description: lincRNA knock downs

scan_protocol: Standard Affymetrix protocols for Human U133 Plus 2.0 Array


title: Foot siScramble Replicate1

description: lincRNA knock downs

label_protocol: Standard Affymetrix protocols for Human U133 Plus 2.0 Array

value: Non-targetting siRNA Control


title: USF1 replicate 2


title: hfq vs. MS11 (II)

tag: hfq mut

value: II


title: Empty vector replicate 3


title: USF1 replicate 1


title: SAT69

source_name: Subcutaneous adipose tissue

extract_protocol: Total RNA was extracted by first disrupting the tissue submerged in QIazol (Qiagen Cat. #79306) with a rotor stator homogenizer, layers were separated with Eppendorf Phase Lock gel 2ml tubes (Eppendorf) and the aqueous layer was then cleaned with the RNeasy Lipid Tissue Mini Kit (Qiagen). The integrity of the RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent).

value: Subcutaneous adipose tissue


title: Lung siScramble Replicate2

description: lincRNA knock downs

source_name: Primary Lung Fibroblasts, siRNA-transfected

value: lung


title: Lung siTUG1 Replicate1

description: lincRNA knock downs


title: SAT70


title: MF patient 1

description: MFt 1


title: Empty vector replicate 1


title: Foot siTUG1 Replicate 1

description: lincRNA knock downs


title: Lung siScramble Replicate1

description: lincRNA knock downs


title: Foot siScramble Replicate3

description: lincRNA knock downs


title: Lung siTUG1 Replicate2

description: lincRNA knock downs


title: SAT68


title: hfq vs. MS11 (III)


title: Lung siTUG1 Replicate3

description: lincRNA knock downs


title: Lung siScramble Replicate3

description: lincRNA knock downs