title: Non-Recurrent-NSCLC-6


title: Non-Recurrent-NSCLC-1

status: Public on Dec 01 2009

type: RNA

city: Minneapolis

first: David

middle: A.

last: Potter

state: MN

address: 420 Delaware St. SE

department: Division of Hematology, Oncology and Transplantation

country: USA

institute: University of Minnesota

description: Gene expression data from patient with non-recurrent cancer (frozen NSCLC tumor tissue)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on HGU133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: non-recurrent NSCLC tumor

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

extract_protocol: Resected tumor tissue was placed in liquid nitrogen immediately following resection. Specimens were homogenized using a Polytron homogenizer (Brinkmann Instruments, Westbury, NY) in ice-cold Trizol reagent (Gibco BRL, Gaithersburg, MD). Trizol extraction was followed by clean-up using the Qiagen RNeasy Mini-kit.

tag: from patient with non-recurrent cancer


title: Recurrent-NSCLC-6

description: Gene expression data from patient with recurrent cancer (frozen NSCLC tumor tissue)

source_name: recurrent NSCLC tumor

tag: from patient with recurrent cancer


title: Recurrent-NSCLC-8


title: Recurrent-NSCLC-4


title: Recurrent-NSCLC-7


title: Recurrent-NSCLC-5


title: SAMA0198_CAU_Discovery

status: Public on Oct 31 2009

city: Chapel Hill

first: Jonathan

middle: C

last: Schisler

state: NC

address: MBRB, Rm 2340C

department: McAllister Heart Institute

institute: The University of North Carolina at Chapel Hill

hyb_protocol: Labeled subject cRNA was co-hybridized to Agilent G4112A Whole Human Genome 44K oligonucleotide arrays with equimolar amounts of Cyanine-3 labeled UHRR. Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.  After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Axon Instruments GenePix 4000b scanner.

data_processing: The data were processed using GenePix Pro 6 software and uploaded to UNC microarray database (http:\\genome.unc.edu).  Microarray data were normalized via the loess local intensity normalization method of Smyth and Speed, and probes were filtered for features having a normalized intensity of < 30 aFU in both channels. Probes were removed if <70% of the data were present across all samples.  Missing data points were imputed using the k nearest-neighbors algorithm (k = 17). 1

source_name: Stratagene UHRR reference

label_protocol: 500 ng of total RNA were amplified and labeled with Cy3-CTP using the Agilent Low Input RNA amplification kit exactly as described by the manufacturer.

extract_protocol: RNA wasrecovered from leukocytes using a modified one-step acid guanidinium thiocyanate-phenol-chloroform extraction (RNA-STAT60, Tel-Test, TX).  RNA was subsequently post-purified using the RNeasy Mini-kit from Qiagen in accordance with the manufacturer’s instructions.  RNA quantity, purity and integrity were assessed by spectrophotometry and microcapillary electrophoresis on an Agilent BioAnalyzer 2100.  RNA isolation from samples was completed within two hours, exceeding the standards of the Consortium for Expression Profiles in Sepsis.

tag: pool of human cell line RNA

source_name: Whole blood, mononuclear cell extract

growth_protocol: Blood (30 ml) was drawn early in the day from subjects fasted for at least eight hours to minimize the signals associated with nutritional and diurnal cycles from the microarray data. Blood was processed within fifteen minutes of the time of blood draw.  Eight milliliters were collected into a tube containing EDTA and a proprietary mixture of proteinase inhibitors (Becton, Dickinson and Co., Cockeysville, MD) to provide a sample of plasma for fructosamine assays.  The balance (22 ml) of blood was collected into 3 x 7 -ml Na-EDTA Vacutainer tubes (Becton, Dickinson and Co., Cockeysville, MD).  Whole blood was treated with ten volumes of carbonate-buffered 150 mM NH4Cl to lyse red blood cells; the remaining leukocytes were washed and concentrated by centrifugation.

tag: Caucasian

tag: Discovery


title: rAAV-HGFK1_MEC_36hr_sample

status: Public on Nov 30 2009

city: Hong Kong

first: Wing-Sze

last: Leung

address: 8S03, Kadoorie Biological Sciences Building, The University of Hong Kong

department: Computer Science

country: Hong Kong

institute: The University of Hong Kong

description: Mice microvessel endothelial cells were treated with rAAV-HGFK1 for 36 hours

hyb_protocol: Five micrograms of RNA with a 28S:18S ribosomal RNA ratio of 2.0 (±0.3) was used for microarray hybridization. The fragmented complementary RNA was hybridized with the GeneChip® Mouse Genome 430 2.0 Array chips using the Hybridization Oven 640 (Affymetrix)

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

data_processing: Affymetrix Microarray Suite (MAS) 5.0 software

label: Biotin

organism: Mus musculus

source_name: 36-hr treatment of mice microvessel endothelial cells with rAAV-HGFK1

label_protocol: Standard labelling protocol of Fluidics Station 400 (Affymetrix)

extract_protocol: Total RNA was extracted from cultured cells using RNeasy® Mini Kit (Qiagen, Valencia, CA).

tag: Cells used

value: Mice microvessel endothelial cells (MEC) were purchased from the American Type Culture Collection (Manassas, VA).  Dulbecco’s modified Eagle’s medium (DMEM), fetal bovine serum (FBS) and trypsin-EDTA were products of Invitrogen (Carlsbad, CA).  The mice MEC were maintained as monolayer culture in DMEM medium supplemented with 5% and 10% FBS respectively (complete DMEM) at 37C, 5% CO2.


title: Recurrent-NSCLC-3


title: SAMA0200_CAU_Validation

tag: Validation


title: rAAV-EGFP_MEC_36hr_control

description: Mice microvessel endothelial cells were treated with rAAV-EGFP for 36 hours

source_name: 36-hr treatment of mice microvessel endothelial cells with rAAV-EGFP

value: Mice microvessel endothelial cells (MEC) were purchased from the American Type Culture Collection (Manassas, VA).  Dulbecco’s modified Eagle’s medium (DMEM), fetal bovine serum (FBS) and trypsin-EDTA were products of Invitrogen (Carlsbad, CA).  The mice MEC were maintained as monolayer culture in DMEM medium supplemented with 5% and 10% FBS respectively (complete DMEM) at 37C, 5% CO2.


title: Recurrent-NSCLC-1


title: SAMA0197_AA_Validation

tag: African American


title: Recurrent-NSCLC-2


title: SAMA0195_CAU_Validation


title: SAMA0194_CAU_Validation


title: SAMA0191_CAU_Discovery


title: SAMA0199_CAU_Validation


title: SAMA0193_CAU_Validation


title: SAMA0192_AA_Validation


title: SAMA0196_AA_Discovery


title: rAAV-HGFK1_McA-RH7777_36hr_sample

description: McA-RH7777 cells were treated with rAAV-HGFK1 for 36 hours

hyb_protocol: Five micrograms of RNA with a 28S:18S ribosomal RNA ratio of 2.0 (±0.3) was used for microarray hybridization. The fragmented complementary RNA was hybridized with the GeneChip® Rat genome 230 2.0 Array chips (Affymetrix, Santa Clara, CA) with 30,000 genes/EST transcripts, using the Hybridization Oven 640 (Affymetrix).

scan_protocol: Standard scanning protocol of GeneChip Scanner 3000 (Affymetrix)

organism: Rattus norvegicus

source_name: 36-hr treatment of McA-RH7777 with rAAV-HGFK1

tag: Cell line

value: rat hepatocellular carcinoma cell line McA-RH7777


title: SAMA0190_CAU_Validation


title: SAMA0189_CAU_Validation


title: rAAV-EGFP_McA-RH7777_36hr_control

description: McA-RH7777 cells were treated with rAAV-EGFP for 36 hours

source_name: 36-hr treatment of McA-RH7777 with rAAV-EGFP


title: SAMA0186_AA_Validation


title: SAMA0187_AA_Discovery


title: SAMA0188_CAU_Discovery


title: SAMA0179_CAU_Validation


title: SAMA0182_AA_Validation


title: SAMA0180_CAU_Validation


title: SAMA0183_AA_Validation


title: SAMA0170_CAU_Validation


title: SAMA0169_CAU_Validation


title: SAMA0177_CAU_Validation


title: SAMA0162_CAU_Validation


title: SAMA0164_CAU_Validation


title: SAMA0173_CAU_Validation


title: SAMA0174_CAU_Discovery


title: SAMA0178_AA_Validation


title: SAMA0155_AA_Validation


title: SAMA0185_CAU_Validation


title: SAMA0154_CAU_Validation


title: SAMA0176_CAU_Discovery


title: MS-Q1

status: Public on Nov 26 2009

city: Villamayor

first: M Belen

last: Suárez

state: Salamanca

address: Rio Duero

department: CIALE

country: Spain

institute: Universidad de Salamanca

description: Biological replicate 1 of 2

hyb_protocol: Nimblegen protocol

scan_protocol: Nimblegen protocol

data_processing:
Background: RMA convolution model (Irizarry et al. 2003)
Normalization: quantile-based (Irizarry et al. 2003)
Normalization 2: chipset probe scale

molecule: polyA RNA

organism: Trichoderma harzianum

source_name: Trichoderma harzianum CECT 2413 grown in liquid basal medium in the presence of chitin

label_protocol: Dye labeled 9mer random priming

extract_protocol: Trizol method

tag: Organism

value: Trichoderma harzianum

tag: Strain

value: CECT 2413

tag: Medium

value: Murashige & Skoog Media with chitin (1% w/v)

tag: Time


title: SAMA0171_CAU_Validation


title: SAMA0152_CAU_Validation


title: MS-G1

description: Biological replicate 1 of 2

source_name: Trichoderma harzianum CECT 2413 grown in liquid basal medium in the presence of glucose

value: Murashige & Skoog Media with glucose (2% w/v)


title: MS-P1

description: Biological replicate 1 of 2

source_name: Trichoderma harzianum CECT 2413 grown in liquid basal medium interacting with tomato plants

value: Murashige & Skoog Media with alive tomato plants


title: MS-2

description: Biological replicate 2 of 2

source_name: Trichoderma harzianum CECT 2413 grown in liquid basal medium

value: Murashige & Skoog Media


title: MS-G2

description: Biological replicate 2 of 2


title: SAMA0146_AA_Validation


title: MS-P2

description: Biological replicate 2 of 2


title: SAMA0149_CAU_Discovery


title: MS-1

description: Biological replicate 1 of 2


title: SAMA0143_CAU_Validation


title: MS-Q2

description: Biological replicate 2 of 2


title: SAMA0141_CAU_Validation


title: SAMA0142_CAU_Validation


title: SAMA0144_CAU_Validation


title: SAMA0134_AA_Validation


title: SAMA0131_CAU_Validation


title: SAMA0120_AA_Validation


title: SAMA0123_CAU_Discovery


title: SAMA0110_CAU_Validation


title: SAMA0135_AA_Validation


title: SAMA0147_CAU_Discovery


title: SAMA0125_AA_Validation


title: SAMA0112_CAU_Discovery


title: SAMA0133_AA_Validation


title: SAMA0121_CAU_Validation


title: SAMA0132_CAU_Validation


title: SAMA0138_CAU_Validation


title: SAMA0128_CAU_Validation


title: SAMA0137_CAU_Validation


title: SAMA0127_AA_Discovery


title: SAMA0114_CAU_Validation


title: SAMA0129_CAU_Validation


title: SAMA0119_CAU_Validation


title: SAMA0116_CAU_Validation


title: SAMA0140_AA_Discovery


title: SAMA0122_AA_Validation


title: SAMA0126_AA_Discovery


title: SAMA0145_AA_Discovery


title: SAMA0136_CAU_Validation


title: SAMA0113_AA_Discovery


title: SAMA0106_CAU_Discovery


title: SAMA0101_CAU_Validation


title: SAMA0105_AA_Validation


title: SAMA0102_CAU_Validation


title: SAMA0095_CAU_Validation


title: SAMA0099_CAU_Validation


title: SAMA0100_AA_Validation


title: SAMA0107_AA_Validation


title: SAMA0097_CAU_Validation


title: SAMA0098_AA_Discovery


title: SAMA0090_CAU_Validation


title: SAMA0092_CAU_Validation


title: SAMA0109_AA_Discovery


title: SAMA0139_CAU_Discovery


title: SAMA0085_AA_Validation


title: SAMA0089_CAU_Validation


title: SAMA0083_CAU_Validation


title: SAMA0091_CAU_Validation


title: SAMA0088_CAU_Validation


title: SAMA0104_CAU_Validation


title: SAMA0087_CAU_Validation


title: SAMA0093_CAU_Discovery


title: SAMA0084_AA_Validation


title: SAMA0094_CAU_Discovery


title: SAMA0086_CAU_Discovery


title: SAMA0080_CAU_Validation


title: SAMA0079_AA_Validation


title: SAMA0081_CAU_Validation


title: SAMA0078_AA_Discovery


title: SAMA0076_CAU_Validation


title: SAMA0082_CAU_Validation


title: SAMA0065_CAU_Discovery


title: SAMA0074_AA_Validation


title: SAMA0064_CAU_Validation


title: SAMA0061_CAU_Validation


title: SAMA0075_CAU_Validation


title: SAMA0062_AA_Discovery


title: SAMA0066_AA_Discovery


title: SAMA0072_CAU_Discovery


title: SAMA0055_AA_Validation


title: SAMA0059_AA_Validation


title: SAMA0054_AA_Validation


title: SAMA0057_CAU_Validation


title: SAMA0070_CAU_Discovery


title: SAMA0069_AA_Validation


title: SAMA0056_CAU_Discovery


title: SAMA0053_CAU_Validation


title: SAMA0052_CAU_Discovery


title: SAMA0048_CAU_Discovery


title: SAMA0049_AA_Validation


title: SAMA0050_AA_Validation


title: SAMA0051_CAU_Validation


title: SAMA0063_CAU_Discovery


title: SAMA0047_CAU_Validation


title: SAMA0046_CAU_Validation


title: SAMA0041_CAU_Validation


title: SAMA0045_AA_Validation


title: SAMA0044_CAU_Validation


title: SAMA0039_AA_Discovery


title: SAMA0043_CAU_Validation


title: SAMA0038_CAU_Validation


title: SAMA0030_AA_Validation


title: SAMA0035_CAU_Validation


title: SAMA0034_CAU_Validation


title: SAMA0033_CAU_Validation


title: SAMA0028_CAU_Validation


title: SAMA0019_CAU_Discovery


title: SAMA0031_CAU_Validation


title: SAMA0032_CAU_Discovery


title: SAMA0037_CAU_Validation


title: SAMA0025_AA_Validation


title: SAMA0029_CAU_Validation


title: SAMA0023_AA_Discovery


title: SAMA0014_CAU_Validation


title: SAMA0026_CAU_Discovery


title: SAMA0015_CAU_Validation


title: SAMA0036_CAU_Discovery


title: SAMA0018_AA_Validation


title: SAMA0022_CAU_Discovery


title: SAMA0027_CAU_Validation


title: SAMA0021_CAU_Validation


title: SAMA0017_CAU_Validation


title: SAMA0016_CAU_Validation


title: SAMA0020_CAU_Discovery


title: SAMA0013_CAU_Validation


title: SAMA0010_CAU_Discovery


title: SAMA0012_CAU_Validation


title: SAMA0009_AA_Discovery


title: SAMA0006_CAU_Validation


title: SAMA0001_CAU_Validation


title: SAMA0008_CAU_Validation


title: SAMA0007_CAU_Validation


title: PSI_vs_PSII_Wlight

status: Public on Jul 30 2009

city: Chicago

first: christos

last: Noutsos

country: Germany

institute: University of Chicago

description: we wanted to check for the expression levels of genes under the specific light of either PSI or PSII in relation with a reference.

hyb_protocol: GST arrays were pre-hybridised for at least 30 min at 65 °C in 30 ml of Church buffer (0.5 M Na2HPO4, pH 7.2; 7% SDS; 1 mM EDTA) including 300 µl of denatured salmon sperm DNA (10 mg/ml). Hybridisation was carried out at 65 °C overnight after adding the labelled cDNA probe. Filters were washed at 65 °C successively for 15 min and 30 min in 2times SSPE (1times SSPE: 150 mM NaCl, 10 mM NaH2PO4, 1 mM EDTA, pH 7.4), 0.1% SDS, followed by a final washing step at room temperature in 50 mM NaH2PO4 (pH 7.0), 1.2 mM EDTA, 0.2% SDS for 30 min. Filters were finally wrapped in plastic foil and exposed to phosphoimager plates (Molecular Dynamics). At least three experiments with different filters and independent cDNA probes derived from plant material corresponding to pools of at least 50 individuals were performed for each condition or genotype, thus minimising variation between individual plants, filters or probes.

scan_protocol: Images were read using the Storm phosphoimager (Molecular Dynamics) and imported into the ArrayVision program (version 4; Imaging Research Inc.) and quantified

data_processing: Perl scripts were used to remove values of poorly hybridised spots using a cut-off level of 20% above local backgrounds and to eliminate data for duplicate spots that differed by more than 50%. Signals differing more than 2.5-fold in consecutive hybridisations were considered as significantly up- or down-regulated. Normalisation of signals was performed with reference to all spots on the array using the reference setting of ArrayVision. For the light- versus dark-grown experiments, signals were also normalised to four HISTONE 2A-like genes (GIs: 3269284, 4585900, 3776566, 1922944).

organism: Arabidopsis thaliana

source_name: thylakoid membranes exposed to a light shift from PSI specific light to PSII using a control plant exposed to white light

label_protocol: After transfer of the mixture to 43 °C, 1 µl of Superscript Reverse Transcriptase (200 U/µl, GibcoBRL) was added and reverse transcription was performed for 1 h. RNA was hydrolysed by adding 1 µl of 1% SDS, 1 µl of 0.5 M EDTA, and 3 µl of 3 M NaOH, and incubating at 65 °C for 30 min, followed by 15 min at room temperature. The mixture was neutralised by adding 1 µl of 1 M Tris-HCl (pH 5 3) and 3 µl of 2 M HCl. cDNAs were precipitated after addition of 5 µl of 3 M sodium acetate (pH 5.3), 5 µl of tRNA (10 mg/µl) and 60 µl of iso-propanol at -20 °C for 30 min. The labelled cDNA was recovered by centrifugation, dried and resuspended in 100 µl of sterile water.

extract_protocol: Total RNA for array or hybridisations was isolated from 1 to 5 g of leaf material from 3-week-old plants (light/dark-grown plants: 7-day-old seedlings) using the method adapted from Chomczynski and Sacchi (1987) and TRIzol reagent (Life Technologies). A mixture of oligonucleotides (2.5 pmol each) matching the 1,827 genes in antisense orientation ('antisense primer mix') and 25-30 µg total RNA were denatured for 10 min at 70 °C and then annealed by cooling to room temperature. 6 µl of 5times Superscript buffer (GibcoBRL), 3 µl of 0.1 M DTT, 3 µl of 10 mM dNTP-mix (except for 50 µM dCTP), and 3 µl of 33PagrdCTP (3.7times105 Bq/µl) were added.

tag: one month old leaves from arabidopsis plants


title: SAMA0005_CAU_Discovery


title: PSI_vs_PSII_8h

source_name: thylakoid membranes exposed to a light shift from PSI specific light to PSII for 8 hours


title: PSI_vs_PSII_48h

source_name: thylakoid membranes exposed to a light shift from PSI specific light to PSII for 48 hours


title: Transient transfection

status: Public on Aug 15 2009

city: Los Angeles

first: Nyam-Osor

last: Chimge

state: CA

address: 2250 Alcazar street

department: IGM

institute: USC

description: MEFs were transfected for 24h

hyb_protocol: hybridized overnight at 65C, hybridization have been performed at Keck facility, Yale University.

scan_protocol: Genepix 5, Axon Instruments, image analyses have been performed at Keck facility, Yale University.

data_processing: linear normalization method, VALUE is Median of Ratios (635/532; exp/ref)

source_name: Control MEFs

label_protocol: aminoallyl labeling

extract_protocol: RNeasy, Qiagen

tag: Control MEFs

source_name: Dlx3 expressing cells

tag: Dlx3 expressing cells


title: PSI_vs_PSII_2h

source_name: thylakoid membranes exposed to a light shift from PSI specific light to PSII for 2 hours


title: SAMA0004_CAU_Discovery


title: Transient transfection biorepeat

description: MEFs were transfected for 24h


title: Biorepeat of Stable transfection

description: Stable expressing MEF cells

source_name: empty plasmid transfection

tag: empty plasmid transfection

source_name: Dlx3 expressing plasmid transfection in MEFs


title: PSII_vs_PSI_30min

source_name: thylakoid membranes exposed to a light shift from PSII specific light to PSI for 30 min


title: PSII_vs_PSI_WL

source_name: thylakoid membranes exposed to a light shift from PSII specific light to PSI using as a control plant exposed to white light.


title: PSII_vs_PSI_48h

source_name: thylakoid membranes exposed to a light shift from PSII specific light to PSI for 48 hours


title: PSI_vs_PSII_30min

source_name: thylakoid membranes exposed to a light shift from PSI specific light to PSII for 30 min


title: Stable transfection

description: Stable expressing MEF cells

tag: Dlx3 expressing plasmid transfection in MEFs


title: PSII_vs_PSI_8h

source_name: thylakoid membranes exposed to a light shift from PSII specific light to PSI for 8 hours


title: PSII_vs_PSI_2h

source_name: thylakoid membranes exposed to a light shift from PSII specific light to PSI for 2 hours


title: SAMA0003_CAU_Discovery

source_name: Stratagene UHRR reference

source_name: Whole blood, mononuclear cell extract


title: Human Somatic Reference RNA Sample 18

status: Public on Jul 01 2009

city: Detroit

first: Stephen

middle: A

last: Krawetz

state: MI

address: 275 E. Hancock, CS Mott Center

department: Obstetrics and Gynecology

institute: Wayne State University

description: Ambion universal reference RNA

hyb_protocol: Hybridization to Illumina Sentrix Expression BeadChip, staining and washing were carried out as described (Illumina, Wallingford).

scan_protocol: Scanning procedures were carried out as described by Illumina, Wallingford.

data_processing: The data were analyzed with Illumina Bead Studio.  Raw data was used without further normalization due to the high inherent variability in sperm RNA contributions.

source_name: Human Somatic Reference Total RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA (Whole-Genome Gene Expression with IntelliHyb Seal System Manual, 2006, Illumina).

extract_protocol: Semen was collected then treated with Somatic Cell Lysis Buffer (0.1% sodium dodecyl sulfate [SDS], 0.5% Triton X-100) on ice for 30 minutes. Lack of somatic cell contamination and sperm count were established by microscopic examination. RNA was isolated from sample using Trizol. Samples were then treated with RNase-free DNase I

tag: Somatic Reference RNA


title: SAMA0002_AA_Discovery

tag: pool of human cell line RNA


title: Human Somatic Reference RNA Sample 13

description: Ambion universal reference RNA


title: Human Somatic Reference RNA Sample 17

description: Ambion universal reference RNA


title: Human Somatic Reference RNA Sample 15

description: Ambion universal reference RNA


title: Human Somatic Reference RNA Sample 16

description: Ambion universal reference RNA


title: Human Somatic Reference RNA Sample 14

description: Ambion universal reference RNA


title: Human Somatic Reference RNA Sample 12

description: Ambion universal reference RNA


title: Human Somatic Reference RNA Sample 6

description: Ambion universal reference RNA


title: Human Somatic Reference RNA Sample 9

description: Ambion universal reference RNA


title: Human Somatic Reference RNA Sample 3

description: Ambion universal reference RNA


title: Human Somatic Reference RNA Sample 10

description: Ambion universal reference RNA


title: Human Somatic Reference RNA Sample 8

description: Ambion universal reference RNA


title: Human Somatic Reference RNA Sample 4

description: Ambion universal reference RNA


title: Human Somatic Reference RNA Sample 2

description: Ambion universal reference RNA


title: Human Somatic Reference RNA Sample 11

description: Ambion universal reference RNA


title: Human Somatic Reference RNA Sample 5

description: Ambion universal reference RNA


title: Human Somatic Reference RNA Sample 7

description: Ambion universal reference RNA


title: Spermatozoal RNA profile from a normally fertile individual: Sample 226

source_name: Normal Human Spermatozoa

tag: Semen from a normally fertile donor, fertility demonstrated by fathering a child.


title: Total Testis RNA Sample 1

description: Total commercial reference Testis RNA

source_name: Total Testis RNA

tag: Total Human Testis reference RNA.


title: Total Testis RNA Sample 3

description: Total commercial reference Testis RNA


title: Human Somatic Reference RNA

description: Ambion universal reference RNA


title: Total Testis RNA Sample 4

description: Total commercial reference Testis RNA


title: Spermatozoal RNA profile from a normally fertile individual: Sample 229


title: Spermatozoal RNA profile from a normally fertile individual: Sample 239


title: Spermatozoal RNA profile from a normally fertile individual: Sample 90


title: Spermatozoal RNA profile from a normally fertile individual: Sample 168


title: Spermatozoal RNA profile from a normally fertile individual: Sample 255


title: Spermatozoal RNA profile from a normally fertile individual: Sample 190


title: Spermatozoal RNA profile from a normally fertile individual: Sample 263


title: Spermatozoal RNA profile from a normally fertile individual: Sample 234


title: Spermatozoal RNA profile from a normally fertile individual: Sample 215


title: Spermatozoal RNA profile from a normally fertile individual: Sample 133


title: Spermatozoal RNA profile from a normally fertile individual: Sample 262


title: Spermatozoal RNA profile from a normally fertile individual: Sample 156


title: Total Testis RNA Sample 2

description: Total commercial reference Testis RNA


title: Spermatozoal RNA profile from a normally fertile individual: Sample 102


title: SH1000_mepR_postexp_rep2

city: Pearl River

first: Ellen

last: Murphy

state: NY

address: 401 N. Middletown Road

department: Vaccines

institute: Wyeth Research

description: Staphylococcus aureus strains SH1000 wildtype and mepR were grown in duplicate to exponential and post-exponential phase.

hyb_protocol: As described by Dunman et al., (2001). J Bacteriol. 183: 7341-7353

scan_protocol: Hardware:  Affymetrix GeneChip scanner.

data_processing: Software:  MAS5.0.

organism: Staphylococcus aureus

source_name: S. aureus strain SH1000 mepR, labelled cDNA, post-exponential phase

label_protocol: Total RNA was converted to cDNA, fragmented by treatment with DNase (0.6 U/ mg DNA) and end-labeled with biotin using the Enzo Bioarray Terminal Labeling kit (Affymetrix).

growth_protocol: 100 ml LB broth in a 250 ml erlenmeyer flask was inoculated with a single colony from a freshly streaked plate.  Bacterial cells were grown at 37 degrees with shaking at 200 rpm to an A550 nm of 0.4 or 2.0 (corresponding to exponential and post-exponential phase respectively)

extract_protocol: S. aureus cells were lysed using Bio101/Savant #FP120 FastPrep cell disruptor and total RNA was isolated using an Rneasy Mini kit (Qiagen Inc., Valencia, CA) inaccordance with the manufacturers instructions.

value: S. aureus SH1000


title: Spermatozoal RNA profile from a normally fertile individual: Sample 91


title: Spermatozoal RNA profile from a normally fertile individual: Sample 223


title: SH1000_wt_postexp_rep2

source_name: S. aureus strain SH1000 wildtype, labelled cDNA, post-exponential phase


title: SH1000_mepR_postexp_rep1


title: SH1000_wt_exp_rep1

source_name: S. aureus strain SH1000 wt, labelled cDNA, exponential phase


title: Spermatozoal RNA profile from a normally fertile individual: Sample 246


title: SH1000_wt_exp_rep2


title: Spermatozoal RNA profile from a normally fertile individual: Sample 195


title: Spermatozoal RNA profile from a normally fertile individual: Sample 182


title: Spermatozoal RNA profile from a normally fertile individual: Sample 111


title: Spermatozoal RNA profile from a normally fertile individual: Sample 254


title: Spermatozoal RNA profile from a normally fertile individual: Sample 248


title: SH1000_mepR_exp_rep1

source_name: S. aureus strain SH1000 mepR, labelled cDNA, exponential phase


title: SH1000_mepR_exp_rep2


title: SH1000_wt_postexp_rep1


title: Spermatozoal RNA profile from a normally fertile individual: Sample 218


title: Tomato_leaf_In vitro_Sucrose_rep3_dye swap

city: Québec

first: Jean-François

last: Dubuc

address: 2440 boul. Hochelaga

country: Canada

institute: Université Laval

description: Hybridization and study was conducted to measure the impact of short-term sugar deprivation, on an acclimatization time-scale, imposed to plantlet transferred from in vitro to ex vitro culture conditions. We thus submitted in vitro tomato plantlets to sugar deprivation for 24-h in order to better understands the impact of sucrose retrieval upon ex vitro acclimatization.

hyb_protocol: A total of six microarrays were used for this experiment. More precisely, three biological replicates represented by individually grown in vitro plantlet from both treatments were hybridized. Dye swap was conducted as technical replicate in order to minimize dye bias. TOM2 arrays were UV treated at 125 Mj (UVC500, Hoefer, San Francisco, CA) just prior hybridization. SlideHyb buffer #1 (Applied Biosystems) was preheated to 68ºC for 30 minutes. Labelled cDNA was resuspended in 4 μl 10 mM EDTA and heat denatured at 95ºC for 10 min. SlideHyb buffer #1 was added to the labelled cDNA. A lifterSlip (Erie Scientific Company, Partsmouth, NH) was laid down on the array and the hybridization solution injected. The hybridization was carried in a SlideBooster (Advalytix AG, Brunnthal, Germany)) instrument for 17-h at 42°C. Arrays were washed twice in both low and high stringency buffers as suggested by the SlideHyb buffer #1 protocol (Applied Biosystems).

scan_protocol: Slides were scanned using a VersArray ChipReader (BioRad, Mississauga, ON, Canada) at 5 μm. Digital image were acquired with the ChipReader 3.1 software (Bio-Rad).

data_processing: The microarray digital images were transferred to the Array-Pro Analyzer v.4.5 software (Media Cybernetics, Silver Spring, MD, USA) for spot detection and net intensity calculation. The background was estimated using the local ring method. The resulting spot intensities were log2 transformed, normalized using the global Loess method and statistically analysed using the Microarray Analysis of Variance (MAANOVA) software (Wu et al., 2003), which operate under the R programming environment. P-values obtained were submitted to the false discovery rate (FDR) procedure. Genes harbouring an adjusted p-value lower than 0.01 and a fold change higher than 1.5 and lower than -1.5 were identified has been differentially regulated. Transcripts differentially regulated by sucrose treatment were assigned to their respective metabolic function using the MapMan and PageMan profiling tools (Thimm et al., 2004; Usadel et al., 2006).

label: AlexaFluor 555

organism: Solanum lycopersicum

source_name: Tomato plantlet_leaf_in vitro_Suc-24h

label_protocol: Reverse transcription was realized using 20 µg total RNA and Superscript III (Invitrogen). Aminoallyl-dUTP (Applied Biosystems, Streetsville, ON, Canada) was added to the reaction to enable later indirect labelling. The RNA of the hybrid cDNA-RNA was hydrolysed by addition of NaOH 1M and 15 min heating at 65ºC. Reaction was neutralized by adding HCL 1M. A purification step was realized using the Qiaquick PCR purification kit (Qiagen, Mississauga, ON, Canada). Probe labelling was performed using AlexaFluor 555 reactive dye packs (Invitrogen) according to the manufacturer. Briefly, 1 μg of cDNA from each sample were evaporated with Savant speedvac concentrator (Thermo Fisher Scientific, Waltham, MA), resuspended in 5 μl double-distilled water and 3 μl labelling buffer. DMSO (2 μl) was added to each single-use fluorophore vial and vortexed. Sample cDNA was added to AlexaFluor 555 reactive dye vial. Labelling was performed for a three hour period. An equal amount of each probe, ranging between 600 and 800 ng, was pooled and the SlideHyb buffer #1 (Applied Biosystems) added to the solution. TOM2 arrays were UV treated at 125 Mj (UVC500, Hoefer, San Francisco, CA) just prior hybridization. The hybridization was carried in a SlideBooster (Advalytix AG, Brunnthal, Germany)) instrument for 17-h at 42°C. Arrays were washed twice in both low and high stringency buffers as suggested by the SlideHyb buffer #1 protocol (Applied Biosystems).

extract_protocol: The second leaves from tomato plantlets grown 20 days under in vitro culture conditions were harvested after 24-h under 3% sucrose in vitro. Tissue were immediately frozen in liquid nitrogen and stored at -80˚C for further grinding. Total RNA was isolated using Plant RNA Reagent following manufacturer’s protocol (Invitrogen, Burlington, ON, Canada). RNA concentration was measured using a ND-1000 spectrophotometer (Nanodrop, Wilmington, DE). Possible contamination was access with the 260/280nm ratio. RNA quality was confirmed by Agilent 2100 Bioanalyzer (Agilent Biotechnologies, Missisauga, ON, Canada) microfluidics-based platform as described in the “Agilent RNA 6000 Nano Kit Guide”.

treatment_protocol: For the experiment, tomato axillary apices were implanted in Sorbarod cellulose plug (BaumGartner Paper, Lausanne, Switzerland) and each placed solely in double stack magenta vessels (Sigma, Oakville, ON, Canada) containing 50 mL MS liquid medium with 3% sucrose. Apex were grown in a growth chamber (Conviron, Winnipeg, MB, Canada) under 180 µmol photons m-2 s-1, 16-h photoperiod and 23/20°C day/night temperature. After a 20 day period, plantlets were transferred to fresh liquid medium containing 3% sucrose (sugar-feed) for 24-h. The second leaf from each plantlet was harvest, frozen in liquid nitrogen and stored at -80°C.

tag: Solanum lycopersicum cv. Trust

label: AlexaFluor 647

source_name: Tomato plantlet_leaf_in vitro_Suc+24h

label_protocol: Reverse transcription was realized using 20 µg total RNA and Superscript III (Invitrogen). Aminoallyl-dUTP (Applied Biosystems, Streetsville, ON, Canada) was added to the reaction to enable later indirect labelling. The RNA of the hybrid cDNA-RNA was hydrolysed by addition of NaOH 1M and 15 min heating at 65ºC. Reaction was neutralized by adding HCL 1M. A purification step was realized using the Qiaquick PCR purification kit (Qiagen, Mississauga, ON, Canada). Probe labelling was performed using AlexaFluor 647 reactive dye packs (Invitrogen) according to the manufacturer. Briefly, 1 μg of cDNA from each sample were evaporated with Savant speedvac concentrator (Thermo Fisher Scientific, Waltham, MA), resuspended in 5 μl double-distilled water and 3 μl labelling buffer. DMSO (2 μl) was added to each single-use fluorophore vial and vortexed. Sample cDNA was added to AlexaFluor 647 reactive dye vial. Labelling was performed for a three hour period. An equal amount of each probe, ranging between 600 and 800 ng, was pooled and the SlideHyb buffer #1 (Applied Biosystems) added to the solution.

extract_protocol: The second leaves from tomato plantlets grown 20 days under in vitro culture conditions were harvested after 24-h under 0% sucrose in vitro. Tissue were immediately frozen in liquid nitrogen and stored at -80˚C for further grinding. Total RNA was isolated using Plant RNA Reagent following manufacturer’s protocol (Invitrogen, Burlington, ON, Canada). RNA concentration was measured using a ND-1000 spectrophotometer (Nanodrop, Wilmington, DE). Possible contamination was access with the 260/280nm ratio. RNA quality was confirmed by Agilent 2100 Bioanalyzer (Agilent Biotechnologies, Missisauga, ON, Canada) microfluidics-based platform as described in the “Agilent RNA 6000 Nano Kit Guide”.

treatment_protocol: For the experiment, tomato axillary apices were implanted in Sorbarod cellulose plug (BaumGartner Paper, Lausanne, Switzerland) and each placed solely in double stack magenta vessels (Sigma, Oakville, ON, Canada) containing 50 mL MS liquid medium with 3% sucrose. Apex were grown in a growth chamber (Conviron, Winnipeg, MB, Canada) under 180 µmol photons m-2 s-1, 16-h photoperiod and 23/20°C day/night temperature. After a 20 day period, plantlets were transferred to fresh liquid medium containing no sucrose for 24-h (sugar-deprived). The second leaf from each plantlet was harvest, frozen in liquid nitrogen and stored at -80°C.


title: Tomato_leaf_In vitro_Sucrose_rep3


title: Tomato_leaf_In vitro_Sucrose_rep1_dye swap


title: Ko_Feminus_rep1_1509

status: Public on Jun 30 2009

city: Berkely

first: Sanchita

last: Bhattacharya

address: 1 Cyclotron Rd

institute: MIT

description: Fetal liver cells from Day E14.5

hyb_protocol: Sample cocktails (200 µl) were used for hybridizations containing 10 µg of cRNA. Microarrays were hybridized overnight, washed in a GeneChip fluidic station 450.

scan_protocol: scanned using the GeneChip Scanner 3000 as described by Affymetrix.

data_processing: The .cel files from Affymetrix were normalized by GCRMA method from S-plus Array Analyzer module

source_name: Fetal liver cells from Day E14.5

label_protocol: Total RNA (1 µg) was amplified for the first strand cDNA synthesis using the Affymetrix one-cycle cDNA synthesis protocol. The second strand DNA synthesis, cleanup of double-stranded cDNA, and biotin-labeling of cRNA were carried out according to the Affymetrix manual. The GeneChip Cleanup module was used to purify the double-stranded cDNA and the biotin-labeled cRNA. The cRNA was quantitated using a NanoDrop ND-1000 UV-vis spectrophotometer (NanoDrop Tecnologies, Rockland, DE).

growth_protocol: Knock out mice were maintained in iron-deficient diet for 3 months.

extract_protocol: Total RNA was extracted after mice were sacrificed and fetal livers were taken day E14.5

treatment_protocol: Knock out (HRI-/-) mice were maintained in iron-deficient diet for 3 months

tag: strain

value: Hri-/- mice (KO)on an inbred B6, 129 mixed genetic background were generated in our laboratory.B6.129P2-Hbbtm1Unc/J mice were obtained from Jackson Laboratory.

tag: Gender:

tag: Age


title: Ko_Feplus_rep2_1452

description: Fetal liver cells from Day E14.5

hyb_protocol: Sample cocktails (200 µl) were used for hybridizations containing 10 µg of cRNA. Microarrays were hybridized overnight, washed in a GeneChip fluidic station 450. scanned using the GeneChip Scanner 3000 as described by Affymetrix.

data_processing: The .cel files from affymetrix were normalized using GCRMA from S-plus array analyzer module

growth_protocol: KO mice were maintianed in normal diet for 3 months.

extract_protocol: Total RNA was extracted after mice were scarificed and fetal livers were taken on day E14.5.

treatment_protocol: Knock out mice (HRI-/-) were maintianed on normal diet for 3 months

value: Hri-/- mice on an inbred B6, 129 mixed genetic background were generated in our laboratory.B6.129P2-Hbbtm1Unc/J mice were obtained from Jackson Laboratory.


title: Ko_Feminus_rep2_1513

description: Fetal liver cells from Day E14.5


title: Tomato_leaf_In vitro_Sucrose_rep2_dye swap


title: Ko_Feminus_rep3_1522

description: Fetal liver cells from Day E14.5


title: Wt_Fe minus_rep3_2008

description: Fetal liver cells from Day E14.5

growth_protocol:
Wildtype mice were maintianed in iron-deficient diet for 3 months.
A state of iron deficiency was induced by placing newborn mice (after weaving) on a low diet containing 5 p.p.m Fe

extract_protocol: Total RNA was extracted after mice were scarificed and featl livers were taken on day E14.5.

treatment_protocol: Wildtype mice were maintianed in iron -deficient diet for 3 months

tag: strain:

value: Embryo E14.5


title: Wt_Fe minus_rep1_1430

description: Fetal livers extracted on day  E14.5

source_name: Fetal livers extracted on day  E14.5


title: Ko_Feplus_rep1_1447a

description: Fetal liver cells extracted on Day E14.5

tag: strain :Hri-/- mice on an inbred B6, 129 mixed genetic background were generated in our laboratory.

tag: B6.129P2-Hbbtm1Unc/J mice (27) were obtained from Jackson Laboratory.


title: HUVEC_EGF_150min_ChipA

city: Vienna

first: Bernhard

last: Schweighofer

address: Lazarettgasse 14

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

description: Gene expression data from HUVEC stimultated with EGF for 150 minutes

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 h 30 min at 45C on GeneChip Human Genome U133 A and B Array.

scan_protocol: GeneChips were scanned using an Affymetrix GeneArray Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using scaling to "Selected Probe Sets" comprising the HGU133A(B)norm.MSK mask file and a target signal of 2000.

source_name: HUVEC, EGF, 150min

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7.5 ug total RNA.

growth_protocol: Quiescent HUVEC were achieved by maintaining dense cultures of 5th passage in complete medium in gelatin-coated 80cm2 flasks for four days without change of medium.

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

treatment_protocol: The cells were stimulated by adding 100ng of VEGF or 50ng of EGF to the medium.

tag: HUVEC, passage 5


title: Tomato_leaf_In vitro_Sucrose_rep2


title: Wt_Fe plus_rep3_1441

description: Fetal liver cells scarificed on Day E14.5

data_processing: The .cel files from the Affymetrix were normalized using GC-RMA normalization in S-plus Array analyzer module.

growth_protocol: wild type were maintained in normal diet for 3 months

extract_protocol: RNA Extraction protocol

tag: Strain :

tag: Gender :

tag: Age :

tag: Tissue

value: Fetal liver at E14.5


title: Tomato_leaf_In vitro_Sucrose_rep1


title: HUVEC_VEGF_30min_ChipA

description: Gene expression data from HUVEC stimultated with VEGF for 30 minutes

source_name: HUVEC, VEGF, 30min


title: HUVEC_VEGF_60min_ChipA

description: Gene expression data from HUVEC stimultated with VEGF for 60 minutes

source_name: HUVEC, VEGF, 60min


title: Wt_Fe plus_rep2_1438

description: Total RNA was extracted from Fetal liver  on day E14.5

treatment_protocol: wild type were maintained in normal diet for 3 months


title: HUVEC_EGF_30min_ChipA

description: Gene expression data from HUVEC stimultated with EGF for 30 minutes

source_name: HUVEC, EGF, 30min


title: Wt_Fe plus_rep1_1424

source_name: Total RNA was extracted from Fetal liver  on day E14.5

tag: Wild type  mice were maintained in normal diet for 3 months.


title: HUVEC_ctrl_ChipA

description: Gene expression data from untreated HUVEC

source_name: HUVEC, untreated


title: Crhr1-ko, control, technical replicate 2

city: Munich

first: Cornelia

last: Graf

address: Kraepelinstr. 2-10

institute: MPI of Psychiatry

description: Control mice were injected with metyrapone as the stresses mice. 1-3h later, animals were sacrificed and pituitaries prepared and frozen.

hyb_protocol: Standard Protocol Illumina Sentrix 6 BeadChip microarrays

scan_protocol: StandardWithBackground; ColorChannel = Green; automatic Illumina outlier removal;

data_processing: The raw data were processed using cubic spline normalization of the Illumina BeadStudio Gene Expression Module Version 2.3.47

source_name: pituitaries of Crhr1-ko mice, 30 min restraint stress, sacrificed 1h after stress begin

label_protocol: One round of linear amplification with standard protocol Amino Allyl MessageAmp RNA Amplification Kit (Ambion); Dye coupling with Cy3

extract_protocol: Total RNA of prepared pituitaries was extracted using the TRIzol reagent (Invitrogen) according to manufacturer´s instruction. RNA quality was analyzed by gel electrophoresis.

treatment_protocol: All animals were injected i.p. with metyrapone, 12h (150 mg/kg b.w.) and directly (100 mg/kg b.w.) before 30 min of restraint stress. Basal blood samples were taken by orbital sinus puncture between the second injection and the stress.

tag: 2-3 months of age, pooled together two pituitaries per group


title: HUVEC_EGF_360min_ChipA

description: Gene expression data from HUVEC stimultated with EGF for 360 minutes

source_name: HUVEC, EGF, 360min


title: Spermatozoal RNA profile from a normally fertile individual: Sample 264

source_name: Normal Human Spermatozoa


title: Crhr1-ko, 3h, + stress, technical replicate 2

description: Mice were injected with metyrapone 12h (150 mg/kg b.w.) and directly (100 mg/kg b.w.) before 30 min of restraint stress. 3h after stress begin animals were sacrificed and pituitaries prepared and frozen.


title: HUVEC_VEGF_150min_ChipA

description: Gene expression data from HUVEC stimultated with VEGF for 150 minutes

source_name: HUVEC, VEGF, 150min


title: Ko_Feplus_rep3_1467

description: Fetal liver cells from Day E14.5


title: Crhr1-wt, 3h, + stress, technical replicate 2

source_name: pituitaries of Crhr1-wt mice, 30 min restraint stress, sacrificed 3h after stress begin


title: GN_2

description: GFP siRNA transfected NT2 cells

data_processing: RMA

label: Biotinylated

source_name: GFP siRNA transfected NT2 cells

tag: NT2 cells


title: Crhr1-wt, control, technical replicate 2

source_name: pituitaries of Crhr1-wt mice, control


title: Crhr1-ko, 1h, + stress, technical replicate 2

description: Mice were injected with metyrapone 12h (150 mg/kg b.w.) and directly (100 mg/kg b.w.) before 30 min of restraint stress. 1h after stress begin animals were sacrificed and pituitaries prepared and frozen.


title: HUVEC_EGF_60min_ChipA

description: Gene expression data from HUVEC stimultated with EGF for 60 minutes

source_name: HUVEC, EGF, 60min


title: GN_3

description: GFP siRNA transfected NT2 cells


title: 46N_3

description: let-7 siRNA transfected NT2 cells

source_name: let-7 siRNA transfected NT2 cells

tag: NT2 cells( Embryonic carcinoma cells)


title: 46N_2

description: let-7 siRNA transfected NT2 cells

tag: NT2 cells ( embryonic carcinoma cells)


title: GN_1

description: GFP siRNA transfected NT2 cells

tag: NT2 cells ( Embryonic carcinoma cells)


title: HUVEC_VEGF_360min_ChipA

description: Gene expression data from HUVEC stimultated with VEGF for 360 minutes

source_name: HUVEC, VEGF, 360min


title: Crhr1-ko, 3h, + stress, technical replicate 1


title: HUVEC_VEGF_360min_ChipB


title: HUVEC_VEGF_60min_ChipB


title: 46N_1

description: let-7 siRNA transfected NT2 cells


title: Crhr1-ko, control, technical replicate 1


title: 18H_1

description: Luciferase 2'-O-Methyl oligo transfected HeLa cells

source_name: Luciferase2'-O-Methyl oligo transfected HeLa cells

tag: Hela S3 cells


title: 18H_3


title: Crhr1-wt, control, technical replicate 1


title: HUVEC_VEGF_150min_ChipB


title: HUVEC_VEGF_30min_ChipB


title: Crhr1-wt, 1h, + stress, technical replicate 2

source_name: pituitaries of Crhr1-wt mice, 30 min restraint stress, sacrificed 1h after stress begin


title: 18H_2


title: Crhr1-wt, 3h, + stress, technical replicate 1


title: 13H_3

description: let-7  2'-O-Methyl oligo transfected HeLa cells


title: Wt_Fe minus_rep2_1445

description: Fetal liver cells extracted on Day E14.5

tag: strain :

tag: Gender:


title: Crhr1-ko, 1h, + stress, technical replicate 1


title: Listeria monocytogenes LMB0472_bile stress_rep2

status: Public on Jun 15 2009

city: Pullman

first: Devendra

middle: H

last: Shah

state: WA

address: 100 Dairy Rd

department: Veterinary Microbiology and Pathology

institute: Washington State University

description:
Slide Bar Code: 00089364
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

hyb_protocol: The labeled cDNA pellets were resuspended in 70uL of hybridization buffer (5x denhardt’s/4x SSC) and boiled for 2 minutes. Samples were centrifuged for 1 minute and applied to the slides under Erie Scientific Lifter slips (24x60mM). Hybridizations were conducted in a 45oC water bath in corning hybridization chambers for 18 hours. Post hybridization washes consisted of three 1 minute TNT (Tris/NaCl/Tween) washes (gently shaking). The slides were dried using a Microarray High-Speed Centrifuge (TeleChem International, Inc).

scan_protocol: Applied Precisions ArrayWorx Scanner employing the following settings: CY3 for 0.1s and A488 for 0.3s with a resolution of 9.6um.

data_processing: TIFF images were processed using SPOTfinder software (TIGR TM4 software suite) using the otsu spot setting and employing background subtraction within the spotfinding software. The resultant median intensities were imported into MATlab software (Mathworks, Inc) for lowess normalization. The normalized intensities and ratios were imported into an access database. Spot quality control filtering was conducted in access (Microsoft) and consisted of the following criterion: 1) Signal:Noise ratio must be greater than 2 (A488) or 10 (A555); 2) The mean spot intensity must be within 25% of the median spot intensity; 3) The coefficient of variance for replicate spots must be less than 0.2; 4)Those spots with only a single channel passing the previous three filters were then low-intensity filtered with a cutoff of 4000.

label: AlexaFluor 488

organism: Listeria monocytogenes

label_protocol:
cDNA was generated as follows: 3μg of total RNA and 150ng of random hexamers (RHs) were combined and heated to 70oC for 10 minutes. This RNA:RHs mixture was snap cooled on ice for 1 minute. The remaining reagents from the SuperScriptTM III First Strand Synthesis Kit® (Invitrogen) were added to the following final concentrations: 1.2x RT Buffer; 6.1mM MgCl2; 12mM DTT; 2.7mM dNTP’s (Promega) which contained aa-dUTP (Ambion) at a ratio of 3.5:1; 40U RNaseOUTTM; and 760U SuperScriptTM III. This mixture was incubated for 18h at 42oC. Following the 42oC incubation, EDTA (pH 8.0) and NaOH were added to a final concentration of 0.1M and 0.2M, respectively. This mixture was incubated at 65oC for 15 minutes in order to hydrolyze the RNA. The solution was neutralized by the addition of 1M Tris-HCl pH 7.0 to a final concentration of 0.3M. The cDNA was cleaned up using a QiaQuick PCR clean-up column (Qiagen) with the following modifications: all spins except the elution step were conducted at 6,000 rpms and the column drying spin (step 6) was extended to 5 minutes; the wash buffer and elution buffers consisted of 5mM KPO4/80% EtOH and 4mM KPO4, respectively, to avoid Tris contamination in the cDNA; finally, the elution buffer was preheated to 37oC and the column was incubated at 37oC for 5 minutes prior to elution from the column. The eluted cDNA was dried down in a centrivap for 45 minutes at 40oC. The resultant pellet was either stored at -20oC until later use or resuspended in 5ul of water and incubated for 2-3 hours at 55oC in preparation for a labeling reaction.
The labeling reactions were performed utilizing AlexaFluor 555 and AlexaFluor 488 as per manufacturer’s instructions with the minor modification of an overnight incubation (instead of 1 hour). Labeling reactions were cleaned up as described above for cDNA clean-up, with the replacement of the KPO4 buffers with manufacturer supplied buffers. The eluted labeled cDNA was quantified on a spectrophotometer. cDNA concentrations were calculated and combined such that the same amount of cDNA was used for each condition (control vs. stress). Each hybridization consisted of between 2.4 – 4.6nM cDNA (per condition) and 60 – 480 pmol dye incorporation (per dye)

growth_protocol: All strains were passaged 3 times in BHI at 37oC with moderate shaking for 18 hours prior to stress protocol.

extract_protocol: RNA was extracted using TRIzol (Invitrogen) as per the manufacturer’s instructions with only minor modifications. Briefly, bacterial pellets were resuspended in 3-mL of TRIzol followed by the addition of 0.1mm Zirconia beads (BIOSPEC Products Inc) for cell disruption. This mixture underwent rapid horizontal vortexing for 1 hour at 4oC. The beads were pelleted out by centrifugation and chloroform was added for organic extraction. Phase separation was achieved through centrifugation at which time the aqueous phase was removed to a separate tube. The organic phase was back-extracted by the addition of ultra-pure RNase-free water (ISC Bioexpress) and the phases were separated again as described. This second aqueous phase was added to the first and precipitated with the addition of isopropanol . The RNA was pelleted, washed once in 75% ethanol, air-dried for 15 minutes and resuspended in ultra-pure RNase-free water. A DNase reaction was performed as per manufacturer’s instructions (Promega). Following the DNase reaction, a second organic extraction was performed using TRIzol LS (Invitrogen) as per the manufacturer’s instructions with the following minor modifications: phase-lock heavy gel tubes (Eppendorf) were employed for the phase separation step and the co-precipitant glycoblue (Ambion) was added in the final precipitation step. The final RNA pellet was resuspended in RNAsecure (Ambion) and quantitated using a spectrophotometer. A measure of RNA quality was assessed through 260/280 and 260/230 ratios.

treatment_protocol: A 50-mL culture was grown overnight (18h) in 1xPBS/BHI broth. The culture was split, pelleted via centrifugation, and half was resuspended in 1x PBS/BHI broth, pH 7.4. This was incubated for 1 hour at 37oC. The culture was again pelleted via centrifugation and resuspended in  1xPBS/BHI broth, pH 7.4. This was incubated for 1 hour at 37oC. Finally, the culture was pelleted via centrifugation, and resuspended in HCl acidified 1xPBS/BHI broth, pH 5.5. This was incubated for 1 hour at 37oC. 5-mL was subsequently pelleted for RNA extraction.

tag: Strain

value: Epidemic, serotype 4b, lineage 1

growth_protocol: All strains were passaged 3 times in BHI at 37oC with moderate shaking for 18 hours.

treatment_protocol: A 50-mL culture was grown overnight (18h) in 1xPBS/BHI broth. The culture was split, pelleted via centrifugation, and half was resuspended in HCl acidified 1x PBS/BHI broth, pH 5.5. This was incubated for 1 hour at 37oC. The culture was again pelleted via centrifugation and resuspended in HCl acidified 1xPBS/BHI broth, pH 3.5. This was incubated for 1 hour at 37oC. Finally, the culture was pelleted via centrifugation, and resuspended in HCl acidified 1xPBS/BHI broth, pH 5.5, that also contained 0.3% BILE. This was incubated for 1 hour at 37oC. 10-mL was subsequently pelleted for RNA extraction.


title: Crhr1-wt, 1h, + stress, technical replicate 1


title: Listeria monocytogenes LMB0472_bile stress_rep3

description:
Slide Bar Code: 00091584
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: 13H_2

source_name: let-7 2'-O-Methyl oligo transfected HeLa cells


title: Listeria monocytogenes LMB0469_bile stress_rep3

description:
Slide Bar Code: 00089359
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0472_bile stress_rep1

description:
Slide Bar Code: 00091576
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: HUVEC_ctrl_ChipB


title: Listeria monocytogenes LMB0469_bile stress_rep1

description:
Slide Bar Code: 126460
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0437_bile stress_rep3

description:
Slide Bar Code: 00089352
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

value: Environmental, serotype 1/2a, lineage 2


title: Listeria monocytogenes LMB0446_bile stress_rep3

description:
Slide Bar Code: 00091581
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

value: Environmental, serotype 4b, lineage 1


title: Listeria monocytogenes LMB0446_bile stress_rep1

description:
Slide Bar Code: 126288
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0431_bile stress_rep3

description:
Slide Bar Code: 00089355
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

value: Environmental, serotype 3a, lineage 1


title: Listeria monocytogenes LMB0622_bile stress_rep3

description:
Slide Bar Code: 00091587
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

value: Environmental, serotype 1/2c, lineage 2


title: Listeria monocytogenes LMB0469_bile stress_rep2

description:
Slide Bar Code: 00091577
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0437_bile stress_rep2

description:
Slide Bar Code: 126731
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0498_bile stress_rep3

description:
Slide Bar Code: 00091589
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0437_bile stress_rep1

description:
Slide Bar Code: 126825
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0504_bile stress_rep2

description:
Slide Bar Code: 126298
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: 13H_1

description: let-7  2'-O-Methyl oligo transfected HeLa cells


title: Listeria monocytogenes LMB0622_bile stress_rep2

description:
Slide Bar Code: 126458
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0431_bile stress_rep1

description:
Slide Bar Code: 126290
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0504_bile stress_rep3

description:
Slide Bar Code: 00089727
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0446_bile stress_rep2

description:
Slide Bar Code: 126282
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

data_processing: TIFF images were processed using SPOTfinder software (TIGR TM4 software suite) using the otsu spot setting and employing background subtraction within the spotfinding software. The resultant median intensities were imported into MATlab software (Mathworks, Inc) for lowess normalization. The normalized intensities and ratios were imported into an access database. Spot quality control filtering was conducted in access (Microsoft) and consisted of the following criterion: 1) Signal:Noise ratio must be greater than 2 (A488) or 10 (A555); 2) The mean spot intensity must be within 25% of the median spot intensity; 3) The coefficient of variance for replicate spots must be less than 0.2; 4)Those spots with only a single channel passing the previous three filters were then low-intensity filtered with a cutoff of 4000. Determination of differential gene expression due to acid adaptation and acid stress (irrespective of isolate) was calculated as follows: average fold change ± 2SEM and observed in greater than half of the data set. Analysis for differential gene expression in epidemic vs. environmental isolates, serotype 4b vs. non-4b serotypes, and lineage 1 vs. lineage 2 was conducted in SAS 9.1 (SAS Institute inc.) utilizing both single factor and 2-factor ANOVAs. Variance due to biological replicates were accounted for in the SAS programs employed. All genes with a p<0.05 and Fold Change >2 (up or down) were considered significant differential expression and included in the subsequent gene lists.

treatment_protocol: A 50-mL culture was grown overnight (18h) in 1xPBS/BHI broth. The culture was split, pelleted via centrifugation, and half was resuspended in HCl acidified 1x PBS/BHI broth, pH 5.5. This was incubated for 1 hour at 37oC. The culture was again pelleted via centrifugation and resuspended in HCl acidified 1xPBS/BHI broth, pH 3.5. This was incubated for 1 hour at 37oC. Finally, the culture was pelleted via centrifugation, and resuspended in HCl acidified 1xPBS/BHI broth, pH 5.5, that also contained 3% BILE. This was incubated for 1 hour at 37oC. 10-mL was subsequently pelleted for RNA extraction.


title: Listeria monocytogenes LMB0508_bile stress_rep2

description:
Slide Bar Code: 126296
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

value: Epidemic, serotype 1/2b, lineage 1


title: Listeria monocytogenes LMB0503_bile stress_rep1

description:
Slide Bar Code: 00088024
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

value: Epidemic, serotype 1/2a, lineage 2


title: Listeria monocytogenes LMB0429_bile stress_rep3

description:
Slide Bar Code: 00089357
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0508_bile stress_rep1

description:
Slide Bar Code: 00088021
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0496_bile stress_rep3

description:
Slide Bar Code: 00091590
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0508_bile stress_rep3-2

description:
Slide Bar Code: 00089729
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0508, pH 5.5, technical replicate

source_name: LMB0508, pH 5.5/0.3% BILE, technical replicate


title: Listeria monocytogenes LMB0503_bile stress_rep3

description:
Slide Bar Code: 126069
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0508_bile stress_rep3

description:
Slide Bar Code: 126823
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0498_bile stress_rep 1

description:
Slide Bar Code: 126071
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0496_bile stress_rep2

description:
Slide Bar Code: 126565
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0472_acid stress_rep1

description:
Slide Bar Code: 126742
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0472, neutral pH

treatment_protocol: 50-mL cultures were grown overnight (18h) in 1xPBS/BHI broth. The cultures were split, pelleted via centrifugation (rcf), and half was resuspended in neutral (pH 7.4) 1x PBS/BHI broth. This was incubated for 1 hour at 37oC. The culture was again pelleted (as before) and resuspended again in a neutral (pH 7.4) 1xPBS/BHI.  This was incubated for 1 hour at 37oC.  After the incubation was complete a 5-mL aliquot was collected for RNA extraction.

treatment_protocol: 50-mL cultures were grown overnight (18h) in 1xPBS/BHI broth. The culture was split, pelleted via centrifugation, and resuspended in HCl acidified 1xPBS/BHI broth pH 5.5. This was incubated for 1 hour at 37oC. The culture was again pelleted (as before) and resuspended in HCl acidified 1xPBS/BHI broth pH 3.5.  This was incubated for 1 hour at 37oC.  After the incubation was complete a 10-mL aliquot was collected for RNA extraction.


title: Listeria monocytogenes LMB0504_bile stress_rep 1

description:
Slide Bar Code: 126070
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0469_acid stress_rep2

description:
Slide Bar Code: 00091578
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0469, neutral pH


title: Listeria monocytogenes LMB0503_bile stress_rep 2

description:
Slide Bar Code: 126820
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0498_bile stress_rep 2

description:
Slide Bar Code: 126562
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0429_acid stress_rep3

description:
Slide Bar Code: 00089734
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0429, neutral pH


title: Listeria monocytogenes LMB0446_acid stress_rep3

description:
Slide Bar Code: 00091582
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0446, neutral pH


title: Listeria monocytogenes LMB0437_acid stress_rep1

description:
Slide Bar Code: 126824
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0437, neutral pH


title: Listeria monocytogenes LMB0496_bile stress_rep 1

description:
Slide Bar Code: 125278
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0429_acid stress_rep1

description:
Slide Bar Code: 125282
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0431_acid stress_rep1

description:
Slide Bar Code: 125290
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0431, neutral pH


title: Listeria monocytogenes LMB0469_acid stress_rep3

description:
Slide Bar Code: 00089360
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0472_acid stress_rep3

description:
Slide Bar Code: 00091585
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0622_acid stress_rep2

description:
Slide Bar Code: 126454
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0622, neutral pH


title: Listeria monocytogenes LMB0446_acid stress_rep2

description:
Slide Bar Code: 126455
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0508_acid stress_rep2

description:
Slide Bar Code: 126450
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0508, neutral pH


title: Listeria monocytogenes LMB0446_acid stress_rep1

description:
Slide Bar Code: 125289
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0622_acid stress_rep1

description:
Slide Bar Code: 125727
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0504_acid stress_rep1

description:
Slide Bar Code: 125803
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0504, neutral pH


title: Listeria monocytogenes LMB0437_acid stress_rep2

description:
Slide Bar Code: 126730
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0469_acid stress_rep1

description:
Slide Bar Code: 126733
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0503_acid stress_rep2

description:
Slide Bar Code: 126446
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0503, neutral pH


title: Listeria monocytogenes LMB0437_acid stress_rep3

description:
Slide Bar Code: 00089353
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0622_acid stress_rep3

description:
Slide Bar Code: 00089735
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0508_acid stress_rep1

description:
Slide Bar Code: 125709
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0503_acid stress_rep3

description:
Slide Bar Code: 00089739
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0504_acid stress_rep2

description:
Slide Bar Code: 126449
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0431_acid stress_rep3

description:
Slide Bar Code: 00089733
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0503_acid stress_rep1

description:
Slide Bar Code: 125706
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0508_acid stress_rep3-2

description:
Slide Bar Code: 00089742
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0508, neutral pH, technical replicate


title: Listeria monocytogenes LMB0508_acid stress_rep3-3

description:
Slide Bar Code: 126445
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0508, pH 3.5, technical replicate


title: Listeria monocytogenes LMB0498_acid stress_rep2

description:
Slide Bar Code: 126448
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0498, neutral pH


title: Listeria monocytogenes LMB0498_acid stress_rep3

description:
Slide Bar Code: 00089741
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0508_acid stress_rep3

description:
Slide Bar Code: 125802
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0437_acid adaptation_rep2

description:
Slide Bar Code: 126726
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

treatment_protocol: 50-mL cultures were grown overnight (18h) in 1xPBS/BHI broth. The cultures were split, pelleted via centrifugation (rcf), and resuspended in neutral (pH 7.4) 1x PBS/BHI broth. These were incubated for 1 hour at 37oC. 5-mL pellets were collected for subsequent RNA extraction.

treatment_protocol: 50-mL cultures were grown overnight (18h) in 1xPBS/BHI broth. The cultures were split, pelleted via centrifugation (rcf), and resuspended in HCl acidified 1xPBS/BHI broth pH 5.5. These were incubated for 1 hour at 37oC. 5-mL pellets were collected for subsequent RNA extraction.


title: Listeria monocytogenes LMB0496_acid stress_rep3

description:
Slide Bar Code: 00089740
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

source_name: LMB0496, neutral pH


title: Listeria monocytogenes LMB0472_acid adaptation_rep2

description:
Slide Bar Code: 00089358
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0498_acid stress_rep1

description:
Slide Bar Code: 125801
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0469_acid adaptation_rep3

description:
Slide Bar Code: 00089362
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0437_acid adaptation_rep3

description:
Slide Bar Code: 00089354
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0446_acid adaptation_rep3

description:
Slide Bar Code: 00091583
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0496_acid stress_rep1

description:
Slide Bar Code: 125800
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0496_acid stress_rep2

description:
Slide Bar Code: 126447
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0437_acid adaptation_rep1

description:
Slide Bar Code: 126459
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0472_acid adaptation_rep3

description:
Slide Bar Code: 00091586
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0429_acid adaptation_rep3

description:
Slide Bar Code: 00089351
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0431_acid adaptation_rep1

description:
Slide Bar Code: 126291
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0469_acid adaptation_rep2

description:
Slide Bar Code: 00091580
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0429_acid adaptation_rep1

description:
Slide Bar Code: 126293
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0446_acid adaptation_rep1

description:
Slide Bar Code: 126289
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0469_acid adaptation_rep1

description:
Slide Bar Code: 126732
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0622_acid adaptation_rep2

description:
Slide Bar Code: 126457
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0446_acid adaptation_rep2

description:
Slide Bar Code: 126283
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0431_acid adaptation_rep3

description:
Slide Bar Code: 00089356
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0508_acid adaptation_rep2

description:
Slide Bar Code: 126297
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0508_acid adaptation_rep1

description:
Slide Bar Code: 00088022
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0503_acid adaptation_rep3

description:
Slide Bar Code: 00089730
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0496_acid adaptation_rep2

description:
Slide Bar Code: 126439
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0504_acid adaptation_rep3

description:
Slide Bar Code: 00089728
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0503_acid adaptation_rep2

description:
Slide Bar Code: 126435
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0503_acid adaptation_rep1

description:
Slide Bar Code: 126068
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0504_acid adaptation_rep2

description:
Slide Bar Code: 126300
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0496_acid adaptation_rep1

description:
Slide Bar Code: 126064
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0498_acid adaptation_rep3

description:
Slide Bar Code: 125285
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.

value: Epidemic, serotype4b, lineage 1


title: Listeria monocytogenes LMB0496_acid adaptation_rep3

description:
Slide Bar Code: 00089732
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0498_acid adaptation_rep2

description:
Slide Bar Code: 126438
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0508_acid adaptation_rep3

description:
Slide Bar Code: 126451
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.


title: Listeria monocytogenes LMB0508_bile stress_rep3-3

description:
Slide Bar Code: 00088025
There were three distinct stresses: acid adaptation (pH5.5); acid stress (pH 3.5); bile stress (0.3% Bile/pH 5.5).
All strains underwent 3 biological replicates. Biological replicates that did not correlate with each other (pearson correlation >0.6) were discarded from downstream analysis.