title: SCCAP1M4B

city: Memphis

first: Katherine

middle: S

last: Barker

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

description: Gene expression data from CAP1-deficient cells

hyb_protocol: The cRNA pellet was suspended in 10 µl of RNase-free water, and 10 µg was fragmented at 95°C for 35 min in 200 mM Tris-acetate (pH 8.1), 500 mM potassium acetate, and 150 mM magnesium acetate. The fragmented cRNA was hybridized for 16 h at 45°C to an Affymetrix custom expression array (CAN07a520619F; manufactured by Affymetrix) for C. albicans. Arrays were washed at 25°C with 6x SSPE (1x SSPE is 0.18 M NaCl, 10 mM NaH2PO4, and 1 mM EDTA [pH 7.7]) and 0.01% Tween 20 followed by a stringent wash at 50°C with 100 mM MES (morpholineethanesulfonic acid), 0.1 M NaCl, and 0.01% Tween 20. Affymetrix Fluidics Station 450 was used for hybridizations and washes according to standard EukGE-WS2v5 protocol. The arrays were then stained with phycoerythrin-conjugated streptavidin (Molecular Probes).

scan_protocol: The fluorescence intensities were determined using a GCS 3000 high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using software resident in the GeneChip operating system, version 2.0 (Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity of 250. The signal intensity for each gene was calculated as the average intensity difference, represented by (PM –MM)/number of probe pairs, where PM and MM denote perfectly matched and mismatched probes, respectively.

data_processing: Probe sets were deleted from subsequent analysis if they were called absent by the Affymetrix criterion and displayed an absolute value below 20 in all experiments. The expression value of each gene was normalized to the median expression of all genes in each chip as well as to the median expression for that gene across all chips in the study. A pairwise comparison of gene expression was performed for each matched experiment.

organism: Candida albicans

source_name: SCCAP1M4B strain

label_protocol: First- and second-strand cDNA was synthesized from 15 µg total RNA, using a SuperScript double-stranded cDNA synthesis kit (Invitrogen) and an oligo-dT24-T7 primer (Proligo) according to the manufacturers' instructions. cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription, using T7 promoter-coupled double-stranded cDNA as a template and a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics). Double-stranded cDNA synthesized from the previous steps was washed twice with 70% ethanol and suspended in 22 µl of RNase-free water. The cDNA was incubated as recommended with reaction buffer, biotin-labeled ribonucleotides,dithiothreitol, RNase inhibitor mix, and T7 RNA polymerase for 5 h at 37°C. The labeled cRNA was separated from unincorporatedribonucleotides with a Chroma Spin-100 column (Clontech) and was ethanol precipitated at –20°C overnight.

growth_protocol: Cells were grown overnight at 30deg Celsius in YPD (1% yeast extract, 2% peptone, and 1% dextrose) with agitation, and these saturated cultures were used to seed 20ml YPD cultures (OD600= 0.2) which were grown with agitation for 3hrs at 30deg Celsius.

extract_protocol: RNA was isolated from frozen cell pellets using the hot-phenol method (Schmitt, M. E., T. A. Brown, and B. L. Trumpower. 1990. Nucleic Acids Res. 18:3091-3092.). Briefly, cells were resuspended in 12 ml AE buffer (50 mM sodium acetate [pH 5.2] and 10 mM EDTA) at room temperature, after which 800 µl 25% sodium dodecyl sulfate and 12 ml acid phenol (Fisher Scientific, Houston, TX) were added. The cell lysate was then incubated for 10 min at 65°C with vigorous shaking each minute, cooled on ice for 5 min, and subjected to centrifugation for 15 min at 11,952 x g. The supernatants were transferred to new tubes containing 15 ml chloroform, mixed, and subjected to centrifugation at 200 x g for 10 min. RNA was precipitated from the resultingaqueous layer by mixing that portion in new tubes with 1 volume of isopropanol and 0.1 volume of 2 M sodium acetate [pH 5.0] and subjecting the mixture to centrifugation at 17,211 x g for 35 min at 4°C. The supernatants were removed, the pellet was resuspended in 10 ml 70% ethanol, and the RNA was collected by centrifugation at 17,211 x g for 20 min at 4°C. The supernatants were again removed, and the RNA was resuspended in 50 to 200 µl diethyl pyrocarbonate-treated water. The RNA was stored at –80°C until needed.


title: Trichoderma reesei during first physical contact with the plant pathogen Rhizoctonia solani dye switch

status: Public on Jul 01 2011

type: RNA

city: Paris

first: Stéphane

last: LE CROM

address: 46 rue d'Ulm

department: Biology Institute - IBENS

country: France

institute: École normale supérieure

hyb_protocol: 1.5µg of labelled cDNA is mixed with one volume of 2X GE buffer (Agilent) and 10% of blocking agent. The hybridization sample volume is dispense on the selected microarray and incubated overnight at 65°C in a hybridization oven (Agilent). The array slides are washed 1 minute in "wash 1 buffer" at room temperature and one minute in "wash 2 buffer" at 37°C. The array slides are then air dryed and ready for scaning.

scan_protocol: Slides were scanned on an Agilent G2505C DNA microarray scanner and the TIFF images extracted using the Agilent Feature Extraction software (version 10.5.1.1) using the 20 bit coding ability.

data_processing: Data pretreatment was applied on each result file to discard flagged spots by Feature Extraction software. The data were normalised without background subtraction by the global Lowess method performed with the Goulphar software (Lemoine, 2006).

molecule: total RNA

organism: Trichoderma reesei

source_name: Total RNA extracted from T reesei control.

label_protocol: 1.5 µg RNA are retro transcribed using Superscript III retro transcriptase. The cDNA are purified using QiaQuick column (Quiagen) and incubated 1 hour at room temperature in presence of 0,05M NaBicarbonate and NHS-ester Cy5.The coupling is stoped by addition of hydroxylamine to a final concentration of 0,6M. Labeled cDNA are purified using QiaQuick column.

extract_protocol: Peripheral hyphal zones from each confrontation stage were harvested and shock frozen in liquid nitrogen. Mycelia were ground to a fine powder under liquid nitrogen and total RNA was isolated using the guanidinium thiocyanate method (Sambrook, 2001).

treatment_protocol: As control T. reesei was confronted with itself and harvested at contact.

tag: condition

value: Control

source_name: Total RNA extracted from T reesei during contact with Rhizoctonia solani.

treatment_protocol: For mycoparasitism confrontation assays T. reesei was grown on potato dextrose agar plates (BD Dicfo, Franklin Lakes, NJ, USA), covered with cellophane, in constant light at 25°C and harvested when the mycelia were at contact of the mycelia of the host fungus Rhizoctonia solani.

value: during contact with Rhizoctonia solani


title: Glioma_PDGFRa+_tumor_NSC-Cre-3

city: Houston

first: Roel

last: Verhaak

state: TX

address: 1400 Pressler St

department: Bioinformatics and Comp Bio

country: USA

institute: MD Anderson Cancer Center

description: The tumor sample was dissociated and the PDGFRa+ glioma tumor cells were enriched by immunopanning method and the total RNA was extracted for microarray analysis. Total RNA was fluorescently labeled and hybridized directly against a common reference sample generated from the RNA pool of four WT P17 mouse brain neocortex. However, in this study, we only focused on the channel of the tumor sample to get their intensity values, but ignored the reference channel signals.

hyb_protocol: The hybridization was followed by the  “Two-Color Microarray-Based Gene Expression Analysis” protocol provided by the manufacture (Agilent).

scan_protocol: The images were scanned by a GenePix 4000B scanner and the intensity values were extracted by using the Agilent Feature Extraction Software.

data_processing: After scanning the images by using a GenePix 4000B scanner, the intensity values were extracted by using the Agilent Feature Extraction Software. In this study, we only focused on the channel of the tumor sample to get their intensity values, but ignored the reference channel signals. Probe sequences were downloaded from the Agilent website and aligned to a transcript sequence database consisting of 49,040 Mus musculus genes from Ensembl57. After removing probes that did not align, or aligned with more than 5 mismatches (n=19,194), or probes that aligned to multiple genes (n=2,283), 23,006 probes representing 17,585 genes remained. Expression profiles were quantile normalized and log transformed. Expression values for genes represented by multiple probes were collapsed by taking the mean value of the set of probes.

organism: Mus musculus

source_name: Non-purified secondary glioma sample, induced by NSC-Cre

label_protocol: Total RNA from all samples were labeled with either Cy3 or Cy5 following the “Two-Color Microarray-Based Gene Expression Analysis” protocol provided by the manufacture (Agilent).

growth_protocol: All samples were from fresh tumor tissue.

extract_protocol: Tumor tissue or purified cells were homogenized into 50 ul TRIZOL. Immediately add 450 ul TRIzol and incubate the homogenized samples for 5 minutes at 15 to 30°C. Freeze samples at -80°C until used for RNA extraction.  Thaw samples, immediately add 100 ul of chloroform. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 g for 15 minutes at 4°C.  Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIZOL used for homogenization.  Remove aqueous phase (around 280 ul) and transfer to new 1.5 ml tube. Add 5 ug (1 ul) polyacrylamide to sample. Add 250 ul of isopropyl alcohol. Invert a few time to mix. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at no more than 12,000 °— g for 10 minutes at 4°C.  Remove the supernatant with a 1 ml pipet tip, leaving no more than around 10 ul at the bottom of the tube. Add 950 ul 75% ethanol (room temperature) to the RNA pellet. Mix the sample by inverting and centrifuge at 7,500 g for 5 minutes at 4°C.  Remove the supernatant with 1 ml pipet tip. Quick spin to collect all residual liquid at the bottom. Remove ALL the residual liquid with 20 ul pipet tip.  Dry the RNA pellet for 1-2 minutes and then pipet 6.5 ul RNase free water onto the pellet. Let sample stand for 2 minutes, then pipet gently to completely re-suspend pellet.  Measure RNA concentration using 2.0 ul sample on Nanodrop.

treatment_protocol: Tumor tissue isolation. All dissection tools were sterilized by soaking in Cidex (Allegromedical, Cat 189980) for 10 minutes and then rinsed with autoclaved distilled water prior to dissection. The tools were kept in 70% ethanol between usages. Tumor-carrying mice were euthanized by cervical dislocation, sprayed down with 70% ethanol and then wiped with Betadine to remove loosed fur. The head was cut off with a pair of large dissection scissors and then soaked in 70% ethanol for 45 seconds to 1 minute. The skin down the midline of the head was sliced through with a razor blade. The skull was cut open using a pair of small dissection scissors. Brain tissue was then lift from the skull and washed once with sterilized cold PBS before being embedded into chilled but still liquid 4% low-melting temperature agarose (prepared in 1X PBS) on ice. After the agarose became solid, the brain was sliced into 1mm thick coronal sections and kept in cold SMEM (Invitrogen, #11380) in a Petri Dish on ice. Under a fluorescence dissection scope, tumors were easily identified because of their strong fluorescence. The tumor region was dissected out with a 22.5o straight microsurgical knife (Sharpoint, #72-2201) and then either immediately lyzed in TRYZOL for RNA extraction or further used for purification of OPC-like tumor cells (see below). Adjacent brain slices containing some tumor tissue were preserved in 4% PFA immediately after dissection. These slices were sent for immunohistochemistry and H&E staining for tumor pathology.    OPC-like glioma cells were purified as following:  Purification of OPC-like tumor cells from fresh glioma samples T1, T2 and T3 was performed according to the PDGFRa immunopanning methods previously described for normal OPC cell purification (B. A. Barres et al., Cell 70, 31 (1992); J. D. Cahoy et al., J Neurosci 28, 264 (2008)) with minor modification.     Panning plates preparation        BSL-1 plates: Two Petri dishes (100 x 10 mm, BD Biosciences-Falcon 351058) were incubated with BSL-1 solution (Vector Laboratories, Burlingame, CA, L-1100, 25?g BSL-1 in 10ml DPBS for each plate). The solution was swirled carefully to ensure that each whole Petri dish was completely coated with solution prior to incubation overnight at 4 oC. The next morning, the BSL-1 solution was removed from the plates and 20ml 0.2% BSA (in DPBS) was added to block the plates at room temperature until panning (usually more than 4 hours).         PDGFR? immunopanning plates: Two Petri dishes (100 x 10 mm) were incubated with 10 ml each of a secondary antibody solution containing Tris buffer solution (50 mM pH8.5 Tris-Cl) and 75 µg (30?l) goat anti-rat IgG H+L chain (112-005-167) overnight at 4 oC. The next morning, the secondary antibody solution was removed and the plates were washed three times with 1X DPBS. Subsequently, a primary antibody solution containing 10?l Rat-anti-PDGFR? antibody (CD140a clone APA5, BD Biosciences-Pharmingen, 558774) in 10ml DPBS with 0.1% BSA was added to each plate. The plates were then incubated at room temperature until used. The plates were washed directly before immunopanning.          The whole procedure can be divided into two major parts: cell dissociation and immunopanning, with details described as follows.  Cell dissociation         The dissected tumor tissue was transferred to a 60 mm Petri dish containing 5ml Papain solution and diced into ~1 mm3 pieces. The papain solution includes 1X EBSS (Sigma E7510), 0.5mM EDTA (Sigma E7510), 10mM HEPES (Gibco 15630-080), 26mM NaHCO3 (Sigma S5761-500g, cell culture grade), 0.16mg/ml L-Cysteine (Sigma C-7477, 25g), 20Unit/ml Papain, 1mg/ml DNase (Sigma, DN-25) and was carefully balanced in 5% CO2 at 37oC for at least 30 minutes before use.        The tumor tissue was incubated in Papain solution at 37oC 5% CO2 for 90 minutes (gently agitated every 15 minutes). Afterwards it was transferred into a sterile 15ml Conical polystyrene tube (BD BioScience #352095) and allowed to settle to the bottom of the tube (We used 10ml serological pipette to transfer the tissue to avoid losing the cells at this step). The Papain solution was then pipetted off and 2ml Diluted trypsin inhibitor buffer was added. Diluted trypsin inhibitor includes 1X EBSS, 10mM HEPES, 26mM NaHCO3, 1mg/ml ovomucoid (Sigma T9253-1G), 1mg/ml BSA (Sigma A-9418) and was carefully balanced in 5% CO2 at 37oC for at least 30 minutes before use. After the tissue settled down (~2 minutes), the Diluted trypsin inhibitor buffer was replaced by 2ml fresh Diluted trypsin inhibitor buffer. The tissue was then triturated 8 times with a 5ml Pasteur pipette. After the tissue settled, 1ml of supernatant (containing dissociated cells) was carefully transferred to a new 15ml Conical polystyrene tube and set aside. 1ml fresh Diluted trypsin inhibitor buffer was added to the original tissue, and the trituration procedure was repeated. After the tissue settled, 1ml of supernatant was removed and combined with the other set aside supernatant.  The trituration was repeated until all the Diluted trypsin inhibitor buffer was used (10ml total). The last two rounds of trituration were performed with a 1ml pipette tip to ensure all the visible tissue chunks were fully dissociated into single cells.         Once the tissue was dissociated, 4ml Standard Trypsin inhibitor solution (10mg/ml BSA in Diluted Tripsin inhibitor buffer) was placed in a new 15ml Conical polystyrene tube. Dissociated cell suspension was carefully layered on top of Standard Trypsin inhibitor solution. The layered solution was centrifuged at 220g for 15 minutes followed by immediate removal of the supernatant. Cells were re-suspended in 6ml Panning solution (0.02% BSA, 1mg/ml DNase in 1X DPBS, Invitrogen 14040-182) using a 5ml pipette and centrifuged at 220g for 10 minutes. Cells were re-suspended in 12 ml Panning buffer and passed through a 70?m cell strainer (Fisher 08-771-23) before performing immunopanning.  Immunopanning          The first BSL-1 coated plate was washed 2X with PBS and 1X with DPBS. 100?l of single cell suspension was set aside for cell number counting and cell culture. The remaining cell suspension was poured onto the first BSL-1 plate and incubated at room temperature for 15 minutes. During that incubation time, we counted the living cell number using the Trypan Blue Method and a hemacytometer. The second BSL-1 coated plate was washed 2X with PBS and 1X with DPBS before the supernatant from the first plate was transferred to it.             During the second BSL-1 panning plate, one primary antibody coated plate was washed 3X with 20ml DPBS. The supernatant from the second BSL-1 plate was transferred to the washed primary antibody plate and incubated for 45min. The plate was swirled very gently every 15 min. During the first primary antibody panning plate, the second primary antibody coated plate was washed 3X with 20ml DPBS to deplete the remaining OPC-like tumor cells (Used to collect tumor cells not presenting PDGFR? antigen). During the second primary antibody panning plate, the first primary antibody panning plate was washed 6-8 times with DPBS to remove the non-binding cells. At the end of the last wash the plate was checked under the microscope to visualize floating cells. Additional washes were performed until there were almost zero and certainly less than 5% floating cells.         Cells were collected by incubating the first primary antibody panning plate with 2ml pre-balanced TrypLE (Invitrogen 12605-010) in 5% CO2 at 37oC for 7 minutes. The reaction was then stopped by adding 2ml trypsin inhibitor solution (2mg/ml Ovomucoid, 0.4% BSA in 1X DPBS). Tumor cells were dislodged from the plate surface by squirting with a 1 ml pipette tip. We collected the cells and also the supernatant from the second primary antibody plate and transferred them separately to new 15ml conical polystyrene tubes which were pre-coated with 0.4% BSA at 37C for 1 hour to prevent adherence of cells to the tubes. After centrifuged at 220g for 10min, the cells were washed one time with NSC medium (see cell culture section for recipes) before re-suspension in the same medium for further use (RNA extraction or allografting).

tag: age

value: 3.5 months

tag: genotype

value: MADM, p53-/-, NF1-/-, hGFAP-Cre

tag: tissue

value: Non-purified secondary glioma, induced by NSC-Cre

tag: purification

value: Immunopanned

tag: tumor type

value: Primary

tag: genetic background

value: mixed, significant portion CD1 outbred

source_name: Common reference sample from the RNA pool of four WT P17 mouse brain neocortex

tag: sample type

tag: sample age

value: brain neocortex

value: wild type


title: HEK293T_miR-381_FSK4hr_rep1

city: Philadelphia

first: Anthony

middle: O

last: Olarerin-George

state: PA

address: 835 BRB II/III, 421 Curie Blvd

department: Pharmacology

institute: University of Pennsylvania

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99 degrees C for 5 min and hybridized for 16 h at 45 degrees C. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: RMA normalized expression values calculated with Affymetrix Expression console

label: Biotin

organism: Homo sapiens

source_name: HEK 293T Human embryonic kidney cells

label_protocol: Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10% FBS and 1X PSG.

extract_protocol: Total RNA (including small RNAs) was extracted using Trizol (Invitrogen) and the aqueous phase was purified with RNeasy Mini kit (Qiagen) according to the manufacturers’ protocols.

treatment_protocol: Cells were reverse transfected with RNA using Lipofectamine2000 at a final concentration of 50 nM.  Approximately 72hrs post-transfection, cells were treated with 15uM forskolin for 0, 1 or 4 hrs.

tag: cell line

tag: transfected rna

tag: agent

value: FSK

tag: time


title: Glioma_Crude_2nd_tumor_OPC-Cre

description: This sample was derived from a secondary tumor that was generated by orthotopically grafting 150,000 primary glioma cells into a NOD-SCID mouse brain and waiting for ~ 6 weeks. The geneotype of the primary tumor is: MADM, p53-/-, NF1-/-, NG2-Cre. Total RNA was fluorescently labeled and hybridized directly against a common reference sample generated from the RNA pool of four WT P17 mouse brain neocortex. However, in this study, we only focused on the channel of the tumor sample to get their intensity values, but ignored the reference channel signals.

source_name: Non-purified secondary glioma sample, induced by OPC-Cre

value: Non-purified secondary glioma, induced by OPC-Cre

value: Crude

value: Grafted

value: Common reference sample from the RNA pool of four WT P17 mouse brain neocortex


title: Trichoderma reesei during overgrowth with the plant pathogen Rhizoctonia solani

source_name: Total RNA extracted from T reesei after contact with Rhizoctonia solani.

treatment_protocol: For mycoparasitism confrontation assays T. reesei was grown on potato dextrose agar plates (BD Dicfo, Franklin Lakes, NJ, USA), covered with cellophane, in constant light at 25°C and harvested after T. virens had overgrown the host fungus Rhizoctonia solani by ca. 5 mm.

value: after contact with Rhizoctonia solani


title: Detacap1MRR1R34A

state: TN

description: Gene expression data from CAP1-deficient cells harboring hyperactive MRR1 allele

label: biotin

source_name: deltacap1MRR1R34A strain

value: MRR1P683S/MRR1P683S cap1delta/cap1delta


title: Deltacap1MRR1R34B

source_name: deltacap1MRR1R34B strain


title: Trichoderma reesei during overgrowth with the plant pathogen Rhizoctonia solani dye switch

value: Control


title: HEK293T_miR-381_FSK0hr_rep2

value: untreated


title: PBMCs_Control_8

city: Lisbon

first: Sofia

middle: A

last: Oliveira

state: Portugal

address: Av. Prof Egas Moniz

department: Edificio Egas Moniz

country: Portugal

institute: Instituto de Medicina Molecular

description: scan date 1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 – 7G.

data_processing: Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.

source_name: peripheral blood mononuclear cells

label_protocol: Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.

treatment_protocol: Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.

tag: affected status

value: control

tag: gender

value: male

tag: age at examination

tag: geographical origin

value: Aveiro

tag: immunosuppressors

value: no


title: HEK293T_miR-neg_FSK0hr_rep2

value: negative control


title: Glioma_Crude_2nd_tumor_NSC-Cre

description: This sample was derived from a secondary tumor that was generated by orthotopically grafting 100,000 primary glioma cells into a NOD-SCID mouse brain and waiting for ~ 6 weeks. The geneotype of the primary tumor is: MADM, p53-/-, NF1-/-, Nestin-Cre. Total RNAwas fluorescently labeled and hybridized directly against a common reference sample generated from the RNA pool of four WT P17 mouse brain neocortex. However, in this study, we only focused on the channel of the tumor sample to get their intensity values, but ignored the reference channel signals.

value: MADM, p53-/-, NF1-/-, Nestin-Cre

value: Non-purified secondary glioma, induced by NSC-Cre

value: mixed, significant portion CD1 outbred


title: PBMCs_Control_7

description: scan date 4

value: female

value: Lisbon


title: cord blood isolated CD34+ cells 6

type: genomic

city: Cleveland

first: Kwok Peng

last: Ng

state: OH

address: 9500 Euclid Avenue

department: Ophthalmic Research

institute: Cleveland Clinic

description:
genomic DNA from isolated CD34+ cells
NCD34_6

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Cancer Panel 1 Methylation Microarray using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

source_name: cord blood isolated CD34+ cells

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from bone marrow aspirates samples using Qiagen DNeasy Kit according to standard instructions

tag: cells

value: cord blood isolated CD34+ cells

tag: who diagnosis

value: NORMAL


title: Trichoderma reesei before confrontation with the plant pathogen Rhizoctonia solani

source_name: Total RNA extracted from T reesei before contact with Rhizoctonia solani.

treatment_protocol: For mycoparasitism confrontation assays T. reesei was grown on potato dextrose agar plates (BD Dicfo, Franklin Lakes, NJ, USA), covered with cellophane, in constant light at 25°C and harvested when the mycelia were ca. 5 mm apart the host fungus Rhizoctonia solani.

tag: condition

value: before contact with Rhizoctonia solani


title: SCCAP1M4A

source_name: SCCAP1M4A strain

tag: genotype


title: Glioma_Crude_OPC-Cre_3

description: Total RNA was fluorescently labeled and hybridized directly against a common reference sample generated from the RNA pool of four WT P17 mouse brain neocortex. However, in this study, we only focused on the channel of the tumor sample (Cy3 channel in this data) to get their intensity values, but ignored the reference channel signals.

source_name: Non-purified glioma sample, induced by NSC-Cre

tag: age

value: 8 months

tag: tissue

value: Non-purified glioma, induced by NSC-Cre

tag: purification

value: Crude

tag: tumor type

value: Primary

value: Common reference sample from the RNA pool of four WT P17 mouse brain neocortex

value: brain neocortex

value: wild type


title: Trichoderma reesei before confrontation with the plant pathogen Rhizoctonia solani) dye switch

value: Control


title: PBMCs_Control_5

description: scan date 4

value: control

value: no


title: SC5314

description: Gene expression data from wildtype cells

source_name: SC5314 strain

value: MRR1/MRR1 CAP1/CAP1 (wildtype)


title: SCMRR1R34A

description: Gene expression data from cells harboring hyperactive MRR1 allele

source_name: SCMRR1R34A strain


title: HEK293T_miR-132_FSK1hr_rep1

tag: cell line

value: FSK


title: Glioma_Crude_OPC-Cre_2

tag: genetic background

value: mixed, significant portion CD1 outbred

tag: sample type

tag: sample age


title: Glioma_Crude_NSC-Cre_1

value: 6 months

value: MADM, p53-/-, NF1-/-, hGFAP-Cre


title: HEK293T_miR-neg_FSK4hr_rep1

tag: transfected rna

value: negative control

tag: agent

tag: time


title: Glioma_Crude_NSC-Cre_2

value: 4 months

value: MADM, p53-/-, NF1-/-, Nestin-Cre


title: SCMRR1R34B

source_name: SCMRR1R34B strain


title: HEK293T_miR-neg_FSK1hr_rep1


title: PBMCs_Control_2

description: scan date 2

tag: affected status

tag: gender

value: female

tag: age at examination

tag: geographical origin

value: Guarda


title: Glioma_Crude_NSC-Cre_3

value: Non-purified glioma, induced by NSC-Cre

value: Crude

value: Primary


title: PBMCs_Control_4

description: scan date 2

value: Lisbon

tag: immunosuppressors


title: HEK293T_miR-132_FSK4hr_rep1


title: HEK293T_miR-132_FSK0hr_rep1

value: untreated


title: Glioma_Crude_OPC-Cre_1

tag: genotype

value: Common reference sample from the RNA pool of four WT P17 mouse brain neocortex

value: brain neocortex

value: wild type


title: prion infected vs normal endpoint, rep6 (printrun 4.1)

city: Winnipeg

first: Rhiannon

middle: LCH

last: Huzarewich

state: MB

address: 1015 Arlington St.

department: Molecular PathoBiology

country: Canada

institute: Public Health Agency of Canada

hyb_protocol: Pre-hybridization of the slides was performed to reduce background signal by incubating them in a slide rack containing pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) at 42ºC for 45 min. Once the pre-hybridization was complete, the slides were washed in nuclease-free water for 5 min. in a slide rack shaking at 100 rpm and then dipped once into isopropanol and spin dried in a slide spinner. The 22x60I mm Lifterslips (Erie Scientific Company) were also dipped once into isopropanol and wiped dry with a kimwipe. The Lifterslip (Erie Scientific Company) was placed on top of the slide silica gel side down, and the whole assembly was placed at 55°C until it was ready for hybridization. Slides were used within 5 min. of prehybridization. 5 μg of each labeled aRNA sample was either dried down to 9 μl using the DNA speed vac (Savant) or was brought up to 9 μl with nuclease-free water to prepare them for fragmentation. The labeled aRNA was then fragmented using Ambion’s RNA Fragmentation Reagents (Ambion, Cat. 8740) and procedure for fragmentation was performed according to the manufacturer’s protocol. Once fragmentation was complete, 27 μl of Formamide Hybridization buffer (22.5 µl Deionized formamide,18.75 µl 20X SSC, 0.75 µl 10% SDS,1.0 µl COT1-DNA,1.0 µl Poly(A)-DNA,10 µl nuclease-free H2O) was added to 11 ul of each fragmented labeled aRNA sample and each control and infected sample were mixed together for a competitive hybridization. The samples from above were added to each prehybridized slide by pipetting the 75 µl of the labeled probe mixture underneath the Lifterslip (Erie Scientific Company) slowly until the mixture spread uniformly across the array via capillary action. About 4 ml of DIG Easy Hyb buffer (Roche, Cat. 1034946) was added to the bottom reservoir in the hybridization chamber (Genetix, New Milton, Hampshire, UK) to provide a humid environment during hybridization. The hybridization chambers were sealed and incubated overnight (14-16 hrs.) at 55°C. Once hybridization was complete, the Lifterslips were removed by gently dipping the slide into pre-warmed (42ºC) Low Stringency wash buffer (2X SSC and 0.5% SDS) repeatedly until it dislodged. They were then washed two times for 5 min. at 110 rpm in a slide rack on a shaker each in Low Stringency wash buffer (pre-warmed to 42°C) and High Stringency wash buffer (0.5X SSC and 0.2% SDS). For the third and final wash, the slides were washed once in 0.05x SSC (Ambion, 20x SSC buffer, Cat. 9763) for 5 mins. at 110 rpm in a slide rack on a shaker. Slides were dried immediately in a slide spinner and placed in a light tight slide container until they could be scanned.

scan_protocol: Slides were scanned using the Agilent Microarray Scanner system with surescan technology (v.6.3).

data_processing: Microarray .TIFF images were uploaded into Array-Pro (MediaCybernetics, version 4.5) and spots were identified and grids constructed. To construct grids, the different grid options that were specifically selected for were whole cell area to measure the raw signal intensity of the spot, local corners for the background calculations, trimmed background subtracted from raw intensity for the net intensity measurement, and finally, normalization was not enabled in this program as this was done in subsequent programs. The data obtained was stored in and normalized using the GeneTraffic Microarray Database and Analysis System (version 2.6, Iobion Informatics). Normalization of raw intensities was performed using a linear regression smoothing algorithm (Loess best-fit) over the individual array subgrids and the subsequent normalized gene list containing log2 ratios were obtained.

label: AlexaFluor 555

source_name: Prion Infected Splenic cells, endpoint

label_protocol: Production of aRNA from total RNA was accomplished using the MessageAmpII kit (Ambion) following manufacturer's instructions. Each aRNA was split into two samples (for dye-swapping) and labeled each with AlexaFluor 555 carboxylic acid, succinimidyl ester dye (Invitrogen) or AlexaFluor 647 (Invitrogen)

extract_protocol: Total RNA extracted using RNeasy Mini Kit (Qiagen) following manufacturer's instructions

tag: strain of mouse

value: VM

tag: inoculum

value: 22A (scrapie)

tag: inoculation type

value: IP

tag: date of inoculation

label: AlexaFluor 647

source_name: Normal Splenic cells, endpoint

value: PBS


title: PBMCs_Control_6

description: scan date 4

value: control

value: no


title: HEK293T_miR-381_FSK1hr_rep1

tag: cell line

value: FSK


title: prion infected vs normal endpoint, rep5 (printrun 4.1)


title: PBMCs_Control_3

description: scan date 3

value: female


title: prion infected vs normal endpoint, rep4 (printrun 4.1)


title: prion infected vs normal endpoint, rep3 (printrun 4.1)


title: PBMCs_Control_1

description: scan date 1

value: Aveiro


title: PBMCs_BD_14

description: scan date 3

value: BD patient

value: male


title: HEK293T_miR-381_FSK0hr_rep1


title: HEK293T_miR-neg_FSK0hr_rep1

value: negative control


title: prion infected vs normal endpoint, rep2 (printrun 4.1)


title: PBMCs_BD_15

description: scan date 3

value: Lisbon

value: yes


title: 12295-anti-miR-NC (negative control)-2

city: Rehovot

first: Einat

last: Sitbon

address: 10 Plaut St

country: Israel

institute: Rosetta Genomics

hyb_protocol: Hybridization was done using GeneChip® Hybridization, Wash, and Stain Kit, according to manufacturer instructions. In short hybridization was done in hybridization buffer at 45C over night. The GeneChip® Fluidics Station 450/250 is used to wash and stain the GeneChip® ST Arrays. It is operated using GCOS.

scan_protocol: The GeneChip® Scanner 3000 7G was used to scan the chips. It is controlled by GeneChip® Operating Software (GCOS).

data_processing: Data was analyzed by RMA on the arrays using the expression console software by Affymetrix.

source_name: HepG2 hepatocellular carcinoma cell line

label_protocol: DNA is labeled by terminal deoxynucleotidyl transferase (TdT) with the Affymetrix® proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Cells were grown in MEM–Eagle (+Earl's BBS), w/NEAA and 10% FBS with additions of sodium bicarbonate and sodium pyruvate.

extract_protocol: EZ-RNA II kit from Biological Industries, Israel, was used for total RNA extraction from cell lines.

treatment_protocol: Cells were transfected with Oligofectamine (Invitrogen, Cat# 12252011) according to manufacturer instructions.

tag: treatment

value: anti-miR-NC (negative control)


title: prion infected vs normal endpoint, rep1 (printrun 4.1)


title: PBMCs_BD_13

description: scan date 2


title: 37C_exp_vs_7C_exp_rep4

city: Ithaca

first: Teresa

middle: M

last: Bergholz

state: NY

address: 405 Stocking Hall

department: Food Science

institute: Cornell University

description: 7C exp/37C exp_rep4

hyb_protocol: Dye-coupled cDNA samples were hybridized to JCVI L. monocytogenes v4 microarrays following the TIGR #M008 protocol.  Hybridizations were conducted at 42°C for 18 h.

scan_protocol: Arrays were scanned using an Axon 4000b scanner, and images analyzed with GenePix 6.0.

data_processing: Raw intensity values for each array were normalized using pin-tip LOWESS in R with the MAANOVA package.  Signals from the two replicate probes on each array were averaged and log2 transformation applied.  Differences in transcript levels were determined using a mixed model ANOVA that tested for significant differences due to growth temperature (7C and 37C), time after salt stress (0%, 2.5%, 5%, 10%, 20% of lag phase and during exponential growth), and the interaction of these two factors using the following linear model:  array + dye + sample (biological replicate) + temperature + time + temperature*time.  The random effects were biological replicate and array, whereas the fixed effects were dye, temperature, and time.  Significant changes in expression were determined by calculating the p values for the Fs statistic for each gene using 1,000 random permutations, and the p values were adjusted for multiple comparisons using the Benjamini-Hochberg correction.

organism: Listeria monocytogenes

label_protocol: 4ug RNA was reverse transcribed using SuperscriptIII (Invitrogen) and random hexamers.  cDNA was purified with PCR cleanup columns (Qiagen), and amino-allyl-labeled cDNA was coupled with either Cy3 or Cy5 (GE Biosciences).

growth_protocol: Cells were grown in Brain Heart Infusion (BHI) broth without shaking, to mid-exponential phase at 7C and 37C.  Mid-exponential phase cells were transferred to BHI + 6% NaCl at the same incubation temperature, and were grown without shaking.

extract_protocol: At appropriate time points, a 1/10V of 10% acid phenol in ethanol was added to cultures, which were immediately centrifuged at 4C, 10,000rpm for 20min.  Cell pellets were suspended in TriReagent, and RNA extracted according to manufacturer's protocol.  RNA was treated with DNase, and then purified with Qiagen RNA mini columns according to manufacturer's protocol.

tag: strain

tag: growth temperature

value: 6% NaCl

tag: growth phase

value: exponential phase

source_name: 37C culture, exponential phase, with 6% NaCl


title: 37C_20_vs_7C_20_rep4

description: 7C 20%/37C 20%_rep4

source_name: 37C culture, 20% of lag phase after exposure to 6% NaCl

tag: agent

value: 20% lag phase

source_name: 7C culture, 20% lag phase after exposure to 6% NaCl


title: PBMCs_BD_10

description: scan date 2


title: PBMCs_BD_12

description: scan date 4


title: 37C_10_vs_7C_10_rep4

description: 7C 10%/37C 10%_rep4

value: 10% lag phase

source_name: 37C culture, 10% lag phase after exposure to 6% NaCl


title: 14074-anti-miR-NC (negative control)-1

value: HepG2 hepatocellular carcinoma cell line


title: PBMCs_BD_11

description: scan date 4


title: 7C_NS_vs_exp_rep4

description: 7C exp/NS_rep4

source_name: 7C culture, exponential phase, without salt

value: without salt

source_name: 7C culture, exponential phase, with 6% NaCl


title: 12293-anti-miR-191-2


title: 37C_2.5_vs_7C_2.5_rep4

description: 7C 2.5%/37C 2.5%_rep4

value: 2.5% lag phase

source_name: 37C culture, 2.5% lag phase after exposure to 6% NaCl


title: 14072-anti-miR-191-1


title: 37C_5_vs_7C_5_rep4

description: 7C 5%/37C 5%_rep4

source_name: 37C culture, 5% of lag phase after exposure to 6% NaCl

value: 5% lag phase

source_name: 7C culture, 5% lag phase after exposure to 6% NaCl


title: PBMCs_BD_8

description: scan date 4

source_name: peripheral blood mononuclear cells

value: no


title: PBMCs_BD_9

description: scan date 1


title: CSS15F2 hippocampus 101

city: Utrecht

first: Simone

last: de Jong

address: Universiteitsweg 100

department: Medical Genetics

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were backgroundcorrected in Beadstudio and transformed (vst) and normalised (rsn) in Lumi (R package)

source_name: Mouse Hippocampus

label_protocol: RNA samples were prepared with the Illumina TotalPrep kit amplification and labeling protocol. Amplified and biotinylated CRNA was measured with a ribogreen assay

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. Concentrations were determined using Nanodrop ND-1000

tag: age

value: 3-4 months

value: F

value: CSS15F2 (C57BL/6J host, A/J donor)

tag: brain region

value: Hippocampus left


title: PBMCs_BD_7

description: scan date 3

tag: affected status

value: BD patient

tag: gender

value: female


title: CSS15F2 hippocampus 75


title: CSS15F2 hippocampus 152


title: 7C_NS_vs_10_rep4

description: 7C 10%/NS_rep4

source_name: 7C culture, 10% lag phase after exposure to 6% NaCl


title: CSS15F2 hippocampus 100


title: CSS15F2 hippocampus 20


title: 7C_NS_vs_20_rep4

description: 7C 20%/NS_rep4


title: 37C_NS_vs_exp_rep4

description: 37C exp/NS_rep4

source_name: 37C culture, exponential phase, without salt


title: 7C_NS_vs_2.5_rep4

description: 7C 2.5%/NS_rep4

source_name: 7C culture, 2.5% lag phase after exposure to 6% NaCl


title: 7C_NS_vs_5_rep4

description: 7C 5%/NS_rep4


title: CSS15F2 hippocampus 57


title: CSS15F2 hippocampus 61


title: CSS15F2 hippocampus 40


title: PBMCs_BD_6

description: scan date 2

tag: age at examination

tag: geographical origin

value: Guarda

value: yes


title: 37C_NS_vs_10_rep4

description: 37C 10%/NS_rep4

value: 6% NaCl


title: PBMCs_BD_5

description: scan date 3

tag: immunosuppressors


title: PBMCs_BD_4

description: scan date 2

value: Aveiro


title: CSS15F2 hippocampus 145


title: PBMCs_BD_2

description: scan date 1


title: CSS15F2 hippocampus 86


title: PBMCs_BD_3

description: scan date 1


title: PBMCs_BD_1

description: scan date 1


title: 37C_NS_vs_20_rep4

description: 37C 20%/NS_rep4

value: exponential phase

value: 20% lag phase


title: 37C_NS_vs_5_rep4

description: 37C 5%/NS_rep4


title: 37C_NS_vs_2.5_rep4

description: 37C 2.5%/NS_rep4


title: 37C_exp_vs_7C_exp_rep3

description: 7C exp/37C exp_rep3


title: CSS15F2 hippocampus 156


title: CSS15F2 hippocampus 38


title: 37C_5_vs_7C_5_rep3

description: 7C 5%/37C 5%_rep3


title: 37C_10_vs_7C_10_rep3

description: 7C 10%/37C 10%_rep3

value: 10% lag phase


title: CSS15F2 hippocampus 41


title: CSS15F2 hippocampus 151


title: CSS15F2 hippocampus 102


title: CSS15F2 hippocampus 76


title: 7C_NS_vs_exp_rep3

description: 7C exp/NS_rep3

value: without salt


title: CSS15F2 hippocampus 10


title: CSS15F2 hippocampus 59


title: 7C_NS_vs_20_rep3

description: 7C 20%/NS_rep3


title: CSS15F2 hippocampus 126


title: P.agnes 266 vs P.agnes KPA WTA amplification

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 1.25µg labeled samples were mixed and hybridized without fragmentation in Hi-rpmi hybridization buffer and blocking buffer according to the supplier's protocol (Agilent Technologies)

scan_protocol: Scanning of microarrays was performed with 5µm resolution and extended range using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1.1, Agilent Technologies). The extracted MAGE-ML files were further analyzed on reporter and sequence level with the Rosetta Resolver, Build 7.2.2.0 SP1.31 (Rosetta Biosoftware, Seattle, USA). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.

organism: Cutibacterium acnes

source_name: P.agnes 266

label_protocol: Total RNA samples were amplified with the TransPlex Whole Transcriptome Amplification Kit (Sigma-Aldrich, Munich, Germany) and labeled with BioPrime Plus Array CGH Indirect Genomic Labeling System (Invitrogen, Karlsruhe, Germany). In brief, a library was generated by stand displacement reaction using phi-29 polymerase and quasi-random primers followed by 17 PCR cycles. The resultant cDNA library was labeled with Klenow polymerase in an indirect reaction using animoallyl nucleotides and subsequent chemical NHS-ester Cy-dye coupling.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier. Briefly, 10e8 cells were resuspended in 1 ml TRIzol, shock frozen and stored at 80°C. Cells in Trizol were thawed and further processed for total RNA isolation as described by the manufacturer.

value: P.agnes strain 266  (OD600 0.6)

source_name: P.agnes KPA


title: 7C_NS_vs_10_rep3

description: 7C 10%/NS_rep3


title: CSS15F2 hippocampus 87


title: 37C_2.5_vs_7C_2.5_rep3

description: 7C 2.5%/37C 2.5%_rep3

value: 2.5% lag phase


title: 7C_NS_vs_5_rep3

description: 7C 5%/NS_rep3

value: 5% lag phase


title: P.agnes KPA OD 0.3 vs P.agnes 266 OD 0.3 T7 amplification

hyb_protocol: After precipitation, purification and quantification, 1.25µg labeled samples were mixed and hybridized according to the supplier’s protocol (Agilent Technologies)

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1.1, Agilent Technologies). The extracted MAGE-ML files were further analyzed on reporter and sequence level with the Rosetta Resolver, Build 7.2.2.0 SP1.31 (Rosetta Biosoftware, Seattle, USA). Ratio profiles comprising single hybridizations were combined in an error-weighted fashion to create ratio experiments. A 1.5–fold change expression cut-off for ratio experiments was applied together with anti-correlation of ratio profiles rendering the microarray analysis highly significant (P-value > 0.01), robust and reproducible.

source_name: P.agnes KPA OD 0.3

label_protocol: RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies) using FullSpectrum MultiStart Primer for T7 IVT RNA Amplification (BioCat GmbH, Heidelberg, Germany) as random T7 labeling. In brief, mRNA was reverse transcribed and amplified using a FullSpectrum MultiStart-T7-promotor primer and was labeled with Cyanine 3-CTP.

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier. Briefly, 10e8 cells were resuspended in 1 ml TRIzol, shock frozen and stored at –80°C. Cells in Trizol were thawed and further processed for total RNA isolation as described by the manufacturer.

source_name: P.agnes 266 OD 0.3

label_protocol: RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies) using FullSpectrum MultiStart Primer for T7 IVT RNA Amplification (BioCat GmbH, Heidelberg, Germany) as random T7 labeling. In brief, mRNA was reverse transcribed and amplified using a FullSpectrum MultiStart-T7-promotor primer and was labeled with Cyanine 5-CTP.

value: P.agnes strain 266  (OD600 0.3)


title: CSS15F2 hippocampus 155

value: 3-4 months

value: F


title: CSS15F2 hippocampus 80

value: CSS15F2 (C57BL/6J host, A/J donor)

value: Hippocampus left


title: P.agnes KPA vs P.agnes 266 WTA amplification


title: CSS15F2 hippocampus 129


title: 37C_NS_vs_exp_rep3

description: 37C exp/NS_rep3

source_name: 37C culture, exponential phase, with 6% NaCl


title: 37C_NS_vs_10_rep3

description: 37C 10%/NS_rep3


title: 7C_NS_vs_2.5_rep3

description: 7C 2.5%/NS_rep3


title: 37C_NS_vs_20_rep3

description: 37C 20%/NS_rep3

source_name: 37C culture, 20% of lag phase after exposure to 6% NaCl


title: P.agnes KPA statationary vs P.agnes KPA exponential WTA amplification

source_name: P.agnes KPA statationary

value: P.agnes KPA stationary growth (OD600 0.8)

source_name: P.agnes KPA exponential

value: P.agnes KPA exponential growth (OD600 0.3)


title: CSS15F2 hippocampus 31


title: CSS15F2 hippocampus 113


title: P.agnes KPA exponential vs P.agnes KPA statationary WTA amplification


title: 37C_NS_vs_5_rep3

description: 37C 5%/NS_rep3


title: 37C_NS_vs_2.5_rep3

description: 37C 2.5%/NS_rep3


title: CSS15F2 hippocampus 78


title: CSS15F2 hippocampus 24


title: CSS15F2 hippocampus 43


title: Listeria monocytogenes, 7°C stationary phase vs. 37°C stationary phase

first: Reid

last: Ivy

address: 412 Stocking Hall

description:
ch1: Cy5 (Rep1), Cy3 (Rep2), Cy5 (Rep3), Cy3 (Rep4)
ch2: Cy3 (Rep1), Cy5 (Rep2), Cy3 (Rep3), Cy5 (Rep4)

hyb_protocol: Microarray slide blocking was performed prior to hybridization. Slides were immersed in blocking solution (1% BSA, 5X SSC, 0.1% SDS) at 42°C. After 1 h, the slides were washed for 5 min in 0.1x SSC twice, followed by 30 sec in deionized water and then dried by centrifugation. For the strains to be compared, labeled cDNAs were combined and dried, then suspended in 50μl of hybridization buffer (5X SSC, 0.1% SDS, 0.1mM dithiothreitol (DTT), 0.5X formamide, 0.06 μg/μl salmon sperm DNA in DEPC-treated water). Samples were vortexed for 1 min and denatured at 95°C for 5 min (repeated twice), followed by a brief centrifugation, then applied to the slides using mSeries LifterSlips™ (Erie Scientific). Following overnight hybridization at 42°C, the slides were washed in 2X SSC+0.1% SDS (5 min, 42˚C), with subsequent 5-min washes at room temperature in 2X SSC+0.1% SDS, 2X SSC, and 0.2X SSC, followed by final rinse in deionized water. Slides were dried by centrifugation.

scan_protocol: Arrays were scanned using an Axon 4000b scanner (Molecular Devices, Sunnyvale, Calif) and images were analyzed using GenePix 6.0 (Molecular Devices).

data_processing: Analyses of microarray data were performed in R (version 2.8.0) with Bioconductor LIMMA software (version 2.16.2) (Smyth, 2005). Background correction was performed using the “normexp” method. For normalization within arrays, the data were normalized using print-tip loess method (Smyth & Speed, 2003). The correlation between duplicate spots was calculated (Smyth et al., 2005) and a linear model was fitted to the normalized log ratios and empirical Bayes statistics were applied for differential expression analysis. Any feature that was flagged as "bad", or did not have an "lmo" designation in the Platform, was not included in the analysis or the data table. The data in the table combine the results from the 4 biological replicates.

source_name: L. monocytogenes, 7°C, stationary phase

label_protocol: cDNA was synthesized from purified total RNA and labeled using the SuperScript Plus Indirect cDNA Labeling System according to the manufacturer's protocol with the following modifications. 6 μg total RNA was combined with 1 μl of random primers included in the kit, incubated at 70°C for 5 min. Following 10 min on ice, 6 μl 5X First-Strand buffer, 1.5 μl 0.1M dithiothreitol (DTT), 1.5 μl dNTP mix containing aminoallyl-dATP and aminohexyl-dTTP, 1 μl RNaseOUT and 2 μl SuperScript III Reverse Transcriptase were added to the reaction tube. The reverse transcription reaction was carried out at 42ºC overnight. Remaining RNA was hydrolyzed by addition of 15 μl 1N NaOH (70ºC for 10 min) and then neutralized with 15 μl 1N HCl. Each cDNA sample was purified with the QIAquick PCR purification kit (Qiagen) using RNase-free water for the final elution step. cDNA samples were dried in a SpeedVac until reduced to ~3 μl. Each cDNA sample was combined with 2X Coupling Buffer and then added to a vial of DMSO-suspended Cy3 or Cy5 dyes (GE Healthcare) and the dye coupling reaction was carried out at room temperature overnight. Labeled cDNA samples were purified with the QIAquick PCR purification kit and a final elution step in RNase-free water. Purified, labeled cDNA was quantified with UV spectrophotometer readings at wavelengths appropriate to determine the frequency of incorporation (FOI), which is defined as the number of labeled nucleotides incorporated per 1,000 nucleotides of cDNA. cDNA samples with FOIs between 20-50 were used for microarray hybridization.

growth_protocol: One colony of L. monocytogenes strains 10403S was inoculated into 5 ml BHI broth and grown at 37°C overnight (12-18 h).  The overnight culture was diluted 1:100 into a fresh of 5 ml BHI and grown at 37°C to O.D.600 = 0.4. A 1:100 dilution of this culture was made into 50 ml of 100mM MOPS buffered BHI (pH 7.2) in a 500 ml, side-arm Nephelo flask (Belco) and this culture was grown at 7 deg C with aeration (i.e., 220 rpm) to stationary phase, defined as 120 hr

extract_protocol: RNA was stabilized by adding of 0.5 ml of a 10% acidified phenol in ethanol solution to each sample for a final concentration of 1% phenol.  The bacterial suspensions were immediately pelleted by centrifugation at 1800g for 10 min.  RNA extraction was immediately performed using TRI Reagent (Applied Biosystems) according to the manufacturer’s protocol with slight modifications.  Briefly, cell pellets were resuspended in 5 ml TRI Reagent, combined with 3 cc of 0.1 mm zirconium beads and homogenized by beating in a Mini-Beadbeater-8 (BioSpec Products Inc., Bartlesville, OK) for 4 min.  Tubes were centrifuged at 3200g for 10 min. 1-Bromo-3-chloropropane (0.5 ml) was added to each supernatant, and samples were allowed to phase-separate at room temperature for 10 min.  Samples were then centrifuged at 10,000g for 10 min.  The aqueous phase was removed and combined with 2.5 ml ice-cold isopropanol, allowed to incubate at room temperature for 10 min, and centrifuged for 20 min at 14,000g.  RNA pellets were washed by centrifuging 5 min at 4000g in 70% and 100% ethanol, resuspended in nuclease-free water and stored at -80°C, pending DNase treatment.  DNase treatment was carried out according to RQ1 (Promega, Madison, WI) DNase protocol.  Following DNase treatment, samples were directly purified using the RNeasy minElute cleanup kit (Qiagen), resuspended in nuclease free water, and stored at -80°C.

value: stationary

source_name: L. monocytogenes, 37°C, stationary phase

growth_protocol: One colony of L. monocytogenes strains 10403S was inoculated into 5 ml BHI broth and grown at 37°C overnight (12-18 h).  The overnight culture was diluted 1:100 into a fresh of 5 ml BHI and grown at 37°C to O.D.600 = 0.4. A 1:100 dilution of this culture was made into 50 ml of 100mM MOPS buffered BHI (pH 7.2) in a 500 ml, side-arm Nephelo flask (Belco) and this culture was grown at 37 deg C with aeration (i.e., 220 rpm) to stationary phase, defined as OD600 = 1.0 plus 3 additional hours of incubation

extract_protocol: RNA was stabilized by adding of 0.5 ml of a 10% acidified phenol in ethanol solution to each sample for a final concentration of 1% phenol.  The bacterial suspensions were immediately pelleted by centrifugation at 1800g for 10 min.  RNA extraction was immediately performed using TRI Reagent (Applied Biosystems) according to the manufacturer’s protocol with slight modifications.  Briefly, cell pellets were resuspended in 5 ml TRI Reagent, combined with 3 cc of 0.1 mm zirconium beads and homogenized by beating in a Mini-Beadbeater-8 (BioSpec Products Inc.) for 4 min.  Tubes were centrifuged at 3200g for 10 min. 1-Bromo-3-chloropropane (0.5 ml) was added to each supernatant, and samples were allowed to phase-separate at room temperature for 10 min.  Samples were then centrifuged at 10,000g for 10 min.  The aqueous phase was removed and combined with 2.5 ml ice-cold isopropanol, allowed to incubate at room temperature for 10 min, and centrifuged for 20 min at 14,000g.  RNA pellets were washed by centrifuging 5 min at 4000g in 70% and 100% ethanol, resuspended in nuclease-free water and stored at -80°C, pending DNase treatment.  DNase treatment was carried out according to RQ1 (Promega) DNase protocol.  Following DNase treatment, samples were directly purified using the RNeasy minElute cleanup kit (Qiagen), resuspended in nuclease free water, and stored at -80°C.


title: P.agnes KPA OD 0.6 vs P.agnes 266 OD 0.6 T7 amplification

source_name: P.agnes KPA OD 0.6

source_name: P.agnes 266 OD 0.6


title: P.agnes 266 OD 0.3 vs P.agnes KPA OD 0.3 T7 amplification


title: 37C_20_vs_7C_20_rep3

description: 7C 20%/37C 20%_rep3

source_name: 7C culture, 20% lag phase after exposure to 6% NaCl

value: 6% NaCl


title: P.agnes KPA exponential vs P.agnes KPA statationary T7 amplification

source_name: P.agnes KPA stationary


title: 37C_20_vs_7C_20_rep2

description: 7C 20%/37C 20%_rep2


title: P.agnes 266 OD 0.6 vs P.agnes KPA OD 0.6 T7 amplification


title: P.agnes KPA statationary vs P.agnes KPA exponential T7 amplification


title: 7C_NS_vs_20_rep2

description: 7C 20%/NS_rep2

source_name: 7C culture, exponential phase, without salt


title: Listeria monocytogenes, 7°C log phase vs. 37°C log phase

source_name: L. monocytogenes, 7°C, log phase

growth_protocol: One colony of L. monocytogenes strains 10403S was inoculated into 5 ml BHI broth and grown at 37°C overnight (12-18 h).  The overnight culture was diluted 1:100 into a fresh of 5 ml BHI and grown at 37°C to O.D.600 = 0.4. A 1:100 dilution of this culture was made into 50 ml of 100mM MOPS buffered BHI (pH 7.2) in a 500 ml, side-arm Nephelo flask (Belco) and this culture was grown at 7 deg C with aeration (i.e., 220 rpm) to log phase, defined as OD600 = 0.4

value: log

source_name: L. monocytogenes, 37°C, log phase

growth_protocol: One colony of L. monocytogenes strains 10403S was inoculated into 5 ml BHI broth and grown at 37°C overnight (12-18 h).  The overnight culture was diluted 1:100 into a fresh of 5 ml BHI and grown at 37°C to O.D.600 = 0.4. A 1:100 dilution of this culture was made into 50 ml of 100mM MOPS buffered BHI (pH 7.2) in a 500 ml, side-arm Nephelo flask (Belco) and this culture was grown at 37 deg C with aeration (i.e., 220 rpm) to stationary phase, defined as OD600 = 0.4


title: 7C_NS_vs_exp_rep2

description: 7C exp/NS_rep2

value: exponential phase

source_name: 7C culture, exponential phase, with 6% NaCl


title: 37C_exp_vs_7C_exp_rep2

description: 7C exp/37C exp_rep2


title: 37C_10_vs_7C_10_rep2

description: 7C 10%/37C 10%_rep2

source_name: 37C culture, 10% lag phase after exposure to 6% NaCl


title: 7C_NS_vs_10_rep2

description: 7C 10%/NS_rep2

source_name: 7C culture, 10% lag phase after exposure to 6% NaCl


title: Listeria monocytogenes, 7°C, log phase, acid treated for 15 min

growth_protocol: One colony of L. monocytogenes strains 10403S was inoculated into 5 ml BHI broth and grown at 37°C overnight (12-18 h).  The overnight culture was diluted 1:100 into a fresh of 5 ml BHI and grown at 37°C to O.D.600 = 0.4. A 1:100 dilution of this culture was made into 50 ml of 100mM MOPS buffered BHI (pH 7.2) in a 500 ml, side-arm Nephelo flask (Belco) and this culture was grown at 7 deg C with aeration (i.e., 220 rpm) to log phase, defined as O.D.600 = 0.4.

source_name: L. monocytogenes, 7°C, log phase, 15 min acid

treatment_protocol: A five ml sample of log-phase culture was adjusted to pH 3.5 with 12 N HCl. The suspensions were incubated at 37°C in a water bath for 15 min.

value: HCl (pH 3.5)

tag: treatment time

value: 15 min


title: CSS15F2 hippocampus 29

source_name: Mouse Hippocampus


title: 7C_NS_vs_5_rep2

description: 7C 5%/NS_rep2

source_name: 7C culture, 5% lag phase after exposure to 6% NaCl

value: without salt


title: Listeria monocytogenes, 7°C, stationary phase, acid treated for 15 min

label_protocol: cDNA was synthesized from purified total RNA and labeled using the SuperScript Plus Indirect cDNA Labeling System according to the manufacturer's protocol with the following modifications. 6 μg total RNA was combined with 1 μl of random primers included in the kit, incubated at 70°C for 5 min. Following 10 min on ice, 6 μl 5X First-Strand buffer, 1.5 μl 0.1M dithiothreitol (DTT), 1.5 μl dNTP mix containing aminoallyl-dATP and aminohexyl-dTTP, 1 μl RNaseOUT and 2 μl SuperScript III Reverse Transcriptase were added to the reaction tube. The reverse transcription reaction was carried out at 42ºC overnight. Remaining RNA was hydrolyzed by addition of 15 μl 1N NaOH (70ºC for 10 min) and then neutralized with 15 μl 1N HCl. Each cDNA sample was purified with the QIAquick PCR purification kit (Qiagen) using RNase-free water for the final elution step. cDNA samples were dried in a SpeedVac until reduced to ~3 μl. Each cDNA sample was combined with 2X Coupling Buffer and then added to a vial of DMSO-suspended Cy3 or Cy5 dyes (GE Healthcare, Piscataway, NJ) and the dye coupling reaction was carried out at room temperature overnight. Labeled cDNA samples were purified with the QIAquick PCR purification kit and a final elution step in RNase-free water. Purified, labeled cDNA was quantified with UV spectrophotometer readings at wavelengths appropriate to determine the frequency of incorporation (FOI), which is defined as the number of labeled nucleotides incorporated per 1,000 nucleotides of cDNA. cDNA samples with FOIs between 20-50 were used for microarray hybridization.

growth_protocol: One colony of L. monocytogenes strains 10403S was inoculated into 5 ml BHI broth and grown at 37°C overnight (12-18 h).  The overnight culture was diluted 1:100 into a fresh of 5 ml BHI and grown at 37°C to O.D.600 = 0.4. A 1:100 dilution of this culture was made into 50 ml of 100mM MOPS buffered BHI (pH 7.2) in a 500 ml, side-arm Nephelo flask (Belco) and this culture was grown at 7 deg C with aeration (i.e., 220 rpm) to stationary phase, defined as 120 hr.

extract_protocol: RNA was stabilized by adding of 0.5 ml of a 10% acidified phenol in ethanol solution to each sample for a final concentration of 1% phenol.  The bacterial suspensions were immediately pelleted by centrifugation at 1800g for 10 min.  RNA extraction was immediately performed using TRI Reagent (Applied Biosystems, Foster City, CA) according to the manufacturer’s protocol with slight modifications.  Briefly, cell pellets were resuspended in 5 ml TRI Reagent, combined with 3 cc of 0.1 mm zirconium beads and homogenized by beating in a Mini-Beadbeater-8 (BioSpec Products Inc., Bartlesville, OK) for 4 min.  Tubes were centrifuged at 3200g for 10 min. 1-Bromo-3-chloropropane (0.5 ml) was added to each supernatant, and samples were allowed to phase-separate at room temperature for 10 min.  Samples were then centrifuged at 10,000g for 10 min.  The aqueous phase was removed and combined with 2.5 ml ice-cold isopropanol, allowed to incubate at room temperature for 10 min, and centrifuged for 20 min at 14,000g.  RNA pellets were washed by centrifuging 5 min at 4000g in 70% and 100% ethanol, resuspended in nuclease-free water and stored at -80°C, pending DNase treatment.  DNase treatment was carried out according to RQ1 (Promega, Madison, WI) DNase protocol.  Following DNase treatment, samples were directly purified using the RNeasy minElute cleanup kit (Qiagen, Germantown, Maryland), resuspended in nuclease free water, and stored at -80°C.

source_name: L. monocytogenes, 7°C, stationary phase, 15 min acid

treatment_protocol: A five ml sample of stationary-phase culture was adjusted to pH 3.5 with 12 N HCl. The suspension was incubated at 37°C in a water bath for 15 min.


title: Listeria monocytogenes, 37°C, stationary phase, acid treated for 5 min

description:
ch1: Cy3 (Rep1), Cy5 (Rep2), Cy3 (Rep3), Cy5 (Rep4)
ch2: Cy5 (Rep1), Cy3 (Rep2), Cy5 (Rep3), Cy3 (Rep4)

growth_protocol: One colony of L. monocytogenes strains 10403S was inoculated into 5 ml BHI broth and grown at 37°C overnight (12-18 h).  The overnight culture was diluted 1:100 into a fresh of 5 ml BHI and grown at 37°C to O.D.600 = 0.4. A 1:100 dilution of this culture was made into 50 ml of 100mM MOPS buffered BHI (pH 7.2) in a 500 ml, side-arm Nephelo flask (Belco) and this culture was grown at 37 deg C with aeration (i.e., 220 rpm) to stationary phase, defined as OD600 = 1.0 plus an additional 3 hr incubation

source_name: L. monocytogenes, 37°C, stationary phase, 5 min acid

treatment_protocol: A five ml sample of stationary-phase culture was adjusted to pH 3.5 with 12 N HCl. The suspension was incubated at 37°C in a water bath for 5 min.

value: 5 min


title: Listeria monocytogenes, 37°C, stationary phase, acid treated for 15 min

source_name: L. monocytogenes, 37°C, stationary phase, 15 min acid


title: Listeria monocytogenes, 37°C, log phase, acid treated for 5 min

growth_protocol: One colony of L. monocytogenes strains 10403S was inoculated into 5 ml BHI broth and grown at 37°C overnight (12-18 h).  The overnight culture was diluted 1:100 into a fresh of 5 ml BHI and grown at 37°C to O.D.600 = 0.4. A 1:100 dilution of this culture was made into 50 ml of 100mM MOPS buffered BHI (pH 7.2) in a 500 ml, side-arm Nephelo flask (Belco, Vineland, NJ) and this culture was grown at 37 deg C with aeration (i.e., 220 rpm) to log phase, defined as O.D.600 = 0.4.

source_name: L. monocytogenes, 37°C, log phase, 5 min acid

treatment_protocol: A five ml sample of log-phase culture was adjusted to pH 3.5 with 12 N HCl. The suspensions were incubated at 37°C in a water bath for 5 min.


title: CSS15F2 hippocampus 26


title: 37C_2.5_vs_7C_2.5_rep2

description: 7C 2.5%/37C 2.5%_rep2

value: 2.5% lag phase

source_name: 37C culture, 2.5% lag phase after exposure to 6% NaCl


title: CSS15F2 hippocampus 99


title: Listeria monocytogenes, 7°C, stationary phase, acid treated for 5 min

source_name: L. monocytogenes, 7°C, stationary phase

source_name: L. monocytogenes, 7°C, stationary phase, 5 min acid


title: CSS15F2 hippocampus 153


title: Listeria monocytogenes, 37°C, log phase, acid treated for 15 min

source_name: L. monocytogenes, 37°C, log phase, 15 min acid


title: 37C_5_vs_7C_5_rep2

description: 7C 5%/37C 5%_rep2

source_name: 37C culture, 5% of lag phase after exposure to 6% NaCl

value: 5% lag phase


title: Rosetting-R29_timepoint5

city: Edinburgh

first: Antoine

last: Claessens

address: West Mains Road

department: Institute of Immunology and Infection Research

country: United Kingdom

institute: Edinburgh university

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA)

scan_protocol: Scanning as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA)

data_processing: All arrays were visually inspected using GenePix and any bad quality spots (signal below background or dust on the chip) were flagged out. After gridding, the data were loaded onto the Acuity 4.0 software. Each array was then normalized with Lowess (locally weighted least squares regression).   A dataset with all time points was created using the following parameters: only unflagged spots and spots with median intensities (green or red) greater than the local background plus 2 times the standard deviation of the background were used.

organism: Plasmodium falciparum

source_name: Rosetting R29 parasites, timepoint 5

label_protocol: Each aminoallyl-cDNA sample was coupled to Cy5 (red dye) while Cy3 (green dye) was added to the pool. Cy5-labelled time point samples were mixed with the same amount of Cy3-labelled pool sample.

growth_protocol: R29 was cultured at 2% haematocrit with group A erythrocytes. The culture medium used was RPMI 1640 medium supplemented with 25 mM Hepes, 2 mM glutamine, 25mM glucose, 25 μg/ml gentamicin, adjusted with 1M NaOH to pH 7.2 to 7.4 with 10% pooled normal human serum.

extract_protocol: The tube with TRIzol solution was thawed on ice. Two volumes chloroform (Sigma) were added per volume packed cells. After mixing, the tube was incubated on ice for 5min then centrifuged at 3600g for 40min at 4°C without brakes. The supernatant (aqueous layer) was carefully transferred into a fresh tube without disturbing the pellet. The same volume of ice-cold isopropanol (Sigma) was added and the tube was incubated at 4°C overnight. The next day, the tube was centrifuged at 3600g for 60 min at 4°C. The supernatant was discarded and the pellet was resuspended and washed with ice-cold 70% ethanol (Sigma). After another centrifugation at 3600g and 4°C for 10min, the supernatant was completely but carefully removed using a fine Pasteur pipette. The tube was left upside down to air dry for 15 to 60min until no liquid was visible. The dried pellet was resuspended with 25μl of warm DEPC-H2O then placed on ice. RNA concentration was measured using a spectrophotometer. For RNA, ten times the culture packed cell volume of room temperature TRIzol reagent (Invitrogen 15596-026) was added, and after thorough mixing, stored at -80°C. 12μg of RNA from the R29 non-rosetting parasites at each of the 6 time points was combined together to form the reference pool. The pool and 12μg of each individual time point sample from both rosetting and non-rosetting parasites were then used for first-strand cDNA synthesis using an amino-allyl dye coupling protocol

treatment_protocol: In the three weeks prior to RNA collection, sorbitol lysis was carried out twice at 12 hour intervals in every asexual cycle. For the time course, schizont stage cultures were examined hourly until the first ring was seen, then sorbitol lysis was carried out 12 hours later, giving ring stage parasites within an 12-hour time window. Samples were collected for RNA immediately after sorbitol lysis (time point 1), and then 8-hourly, resulting in 6 time points covering the entire intra-erythrocytic life cycle.

tag: sample type

value: rosetting

tag: developmental stage

value: Timepoint 5

source_name: R29minus pool

value: Pool of the 6 timepoints


title: CSS15F2 hippocampus 104

value: 3-4 months

value: F

value: CSS15F2 (C57BL/6J host, A/J donor)


title: CSS15F2 hippocampus 127

value: Hippocampus left


title: Rosetting-R29_timepoint4

source_name: Rosetting R29 parasites, timepoint 4

value: Timepoint 4


title: CSS15F2 hippocampus 77


title: CSS15F2 hippocampus 115


title: Rosetting-R29_timepoint3

source_name: Rosetting R29 parasites, timepoint 3

value: Timepoint 3


title: CSS15F2 hippocampus 108


title: 7C_NS_vs_2.5_rep2

description: 7C 2.5%/NS_rep2

source_name: 7C culture, exponential phase, without salt

source_name: 7C culture, 2.5% lag phase after exposure to 6% NaCl

value: 6% NaCl


title: Rosetting-R29_timepoint2

source_name: Rosetting R29 parasites, timepoint 2

value: Timepoint 2


title: 37C_NS_vs_5_rep2

description: 37C 5%/NS_rep2

source_name: 37C culture, exponential phase, without salt

value: exponential phase


title: 37C_NS_vs_exp_rep2

description: 37C exp/NS_rep2

source_name: 37C culture, exponential phase, with 6% NaCl


title: Rosetting-R29_timepoint6

source_name: Rosetting R29 parasites, timepoint 6

value: Timepoint 6


title: Listeria monocytogenes, 7°C, log phase, acid treated for 5 min

source_name: L. monocytogenes, 7°C, log phase

value: log

source_name: L. monocytogenes, 7°C, log phase, 5 min acid

value: HCl (pH 3.5)


title: Non-rosetting-R29_timepoint6

source_name: Non rosetting R29 parasites, timepoint 6

value: non-rosetting


title: Non-rosetting-R29_timepoint2

source_name: Non rosetting R29 parasites, timepoint 2


title: Rosetting-R29_timepoint1

source_name: Rosetting R29 parasites, timepoint 1

value: Timepoint 1


title: Non-rosetting-R29_timepoint4

source_name: Non rosetting R29 parasites, timepoint 4


title: 37C_20_vs_7C_20_rep1

description: 7C 20%/37C 20%_rep1

source_name: 7C culture, 20% lag phase after exposure to 6% NaCl

value: 20% lag phase

source_name: 37C culture, 20% of lag phase after exposure to 6% NaCl


title: 37C_NS_vs_10_rep2

description: 37C 10%/NS_rep2

source_name: 37C culture, 10% lag phase after exposure to 6% NaCl

value: 10% lag phase

value: without salt


title: 37C_exp_vs_7C_exp_rep1

description: 7C exp/37C exp_rep1

source_name: 7C culture, exponential phase, with 6% NaCl


title: 7C_NS_vs_exp_rep1

description: 7C exp/NS_rep1


title: 37C_NS_vs_20_rep2

description: 37C 20%/NS_rep2


title: Non-rosetting-R29_timepoint1

source_name: Non rosetting R29 parasites, timepoint 1

source_name: R29minus pool

value: Pool of the 6 timepoints


title: 37C_2.5_vs_7C_2.5_rep1

description: 7C 2.5%/37C 2.5%_rep1

source_name: 37C culture, 2.5% lag phase after exposure to 6% NaCl

value: 2.5% lag phase


title: female floral bud

city: beijing

first: ye

middle: mei

last: xia

address: qinghua eastern road 35#

department: faculty of biology

country: China

institute: beijing forestru university

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Populus tomentosa

source_name: mixed collection of floral bud at various development stages

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Female (5082) and male (LM50) trees of P. tomentosa growing in the nursery, Beijing Forestry University

extract_protocol: Total RNA was isolated seperately according to a published protocol (Shujun Chang, 1993).

treatment_protocol: Samples from different stages were frozen rapidly in liquid nitrogen and stored at −80 °C until use.

tag: tissue

value: floral bud

value: female


title: 37C_5_vs_7C_5_rep1

description: 7C 5%/37C 5%_rep1

source_name: 7C culture, 5% lag phase after exposure to 6% NaCl

value: 5% lag phase

source_name: 37C culture, 5% of lag phase after exposure to 6% NaCl


title: 37C_NS_vs_2.5_rep2

description: 37C 2.5%/NS_rep2

source_name: 37C culture, exponential phase, without salt


title: Non-rosetting-R29_timepoint5

source_name: Non rosetting R29 parasites, timepoint 5

value: Timepoint 5


title: male floral bud

value: male


title: 37C_10_vs_7C_10_rep1

description: 7C 10%/37C 10%_rep1

value: 6% NaCl

source_name: 7C culture, 10% lag phase after exposure to 6% NaCl


title: Non-rosetting-R29_timepoint3

source_name: Non rosetting R29 parasites, timepoint 3

value: Timepoint 3


title: 7C_NS_vs_20_rep1

description: 7C 20%/NS_rep1

source_name: 7C culture, exponential phase, without salt

value: exponential phase


title: 7C_NS_vs_10_rep1

description: 7C 10%/NS_rep1


title: 37C_NS_vs_exp_rep1

description: 37C exp/NS_rep1

source_name: 37C culture, exponential phase, with 6% NaCl


title: 37C_NS_vs_10_rep1

description: 37C 10%/NS_rep1


title: 7C_NS_vs_5_rep1

description: 7C 5%/NS_rep1


title: 37C_NS_vs_5_rep1

description: 37C 5%/NS_rep1


title: 37C_NS_vs_20_rep1

description: 37C 20%/NS_rep1


title: 7C_NS_vs_2.5_rep1

description: 7C 2.5%/NS_rep1

source_name: 7C culture, 2.5% lag phase after exposure to 6% NaCl


title: B. breve UCC2003 grown in MRS vs B. breve UCC2003 grown in vivo experiment 3

type: mixed

first: Aldert

last: Zomer

address: Yalelaan 1

department: Department of Infectious Diseases and Immunology,Faculty of Veterinary Medicine

institute: Utrecht University

hyb_protocol: Labelled and amplified cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis (v4.0) manual (publication number G4140-90050).

scan_protocol: Following hybridization, microarrays were washed as described in the manuals and scanned using Agilent's DNA microarray scanner G2565A.

data_processing: The scanning results were converted to data files with Agilent's Feature Extraction software (version 9.5) using standard settings as described in the Agilent's Feature Extraction manual.

organism: Bifidobacterium breve UCC2003

source_name: Bifidobacterium breve UCC2003 grown in MRS

label_protocol:
cDNA from total RNA was synthesized using the cDNA synthesis and labelling kit DSK-001 (Kreatech) according to the manufacturer’s instructions
1 μl of each cDNA solution was labelled with Cy3 using Cy3-ULS from the cDNA synthesis and labelling kit DSK-001 (Kreatech, Amsterdam, The Netherlands) according to the manufacterers instructions.

growth_protocol: Bifidobacterium breve UCC200 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), made from first principles, supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and 1% (w/v) of glucose solution as the sole carbon source. Strain was grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5 .

extract_protocol: RNA isolation, RNA quality control was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

treatment_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

tag: growth stage

value: exponential

tag: carbon source

value: glucose

source_name: ceaca of Balb/C mice colonized with B. breve UCC2003

label_protocol: 1 μl of each cDNA solution (10 ng) was amplified in triplicate using the GenomiPhi™ V2 DNA Amplification Kit (Amersham Biosciences) according to the manufacturer's protocol and labelled with Cy5 using Cy5-ULS from the cDNA synthesis and labelling kit DSK-001 (Kreatech).

growth_protocol: Seven-week-old male, BalbC mice were housed in individually vented cages (Animal care systems, Colorado) under a strict 12 h light cycle. Mice (n = 5 per group) were fed a standard polysaccharide-rich mouse chow diet and water ad libidum. Mice were inoculated by oral gavage (109 cfu of B. breve UCC2003 pPKCM7 in 100 ul of PBS ). Fecal pellets were collected at intervals over 25 days to enumerate bacteria. Twenty five days after inoculation, mice were sacrificed and their intestinal tracts quickly dissected. Aliquots of small intestine, caecum and large intestine were harvested for determination of colony forming units (cfu) (serial dilution plating on RCA agar plates with appropriate antibiotics). Caeca were placed in RNAlater for immediate RNA isolation.

extract_protocol: Bacterial mRNA was extracted from caecal RNA preparations using the MicrobEnrich and MicrobExpress kits (Ambion) according to the manufacturer’s instructions. cDNA from bacterial mRNA was synthesized using the cDNA synthesis and labelling kit DSK-001 (Kreatech) according to the manufacturer’s instructions.

treatment_protocol: Caeca, isolated from mice, were placed in RNAlater (Ambion) and immediately processed. Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77)

tag: source tissue

value: Mus musculus balb/c ceacum

value: 25 days


title: DGcvB-control biological experiment 2

hyb_protocol: Labeled samples were mixed and hybridized to 8x15K custom-commercial microarrays overnight at 65ºC using 1x Hi hybridization buffer together with blocking buffer according to the supplier`s recommendations (Agilent Technologies). Washing of the hybridized arrays was done with the SSC protocol according supplier`s protocol (Agilent Technologies).

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

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent Technologies). To compensate for unequal dye incorporation, data centering to zero was performed for each individual microarray on the slide separately. Microarray data were analysed using GeneSpring 7.3 (Agilent) and genes were considered to be differentially expressed if they displayed ≥2-fold changes in both replicates and were statistically significantly different (Student's t-test; p<0.05)

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: DGcvB-control

label_protocol: Total RNA was labelled by random priming according to the protocols described at the IFR (Institute of Food Research, Norwich) website (www.ifr.ac.uk/safety/microarrays/protocols.html). Briefly, 10 µg RNA were reverse transcribed and labeled with Cy3-conjugated dCTP (Pharmacia) using 200 units of StrataScript and random octamers (Invitrogen).

extract_protocol: Salmonella RNA was isolated using the Promega SV total RNA purification kit

tag: strain

value: S.typhimurium SL1344

tag: plasmid

value: pBAD

source_name: WT

label_protocol: Chromosomal DNA (400 ng) was labeled with Cy5-dCTP using the Klenow fragment.

extract_protocol: Genomic DNA isolated using the Qiagen 'Genomic DNA' Kit (Cat. No.: 19060 for the buffer kit; 10243 for the columns)


title: 37C_NS_vs_2.5_rep1

description: 37C 2.5%/NS_rep1

tag: growth temperature

tag: agent

value: without salt

tag: growth phase


title: B. breve UCC2003 grown in MRS vs B. breve UCC2003 grown in vivo experiment 2

tag: age


title: CFU-E +EPO 0.5U at 24h

status: Public on Jun 30 2011

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

hyb_protocol: 15 µg labelled cRNA were hybridized onto the Mouse Genome 2.0 GeneChip® Arrays (Affymetrix, CA, USA) for 16h at 45°C using Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix).

data_processing: R/Bioconductor

source_name: CFU-E  +EPO 0.5U at 24h

label_protocol: Biotinylated cRNA was generated from 1.5 µg total RNA using the One-Cycle Target Labeling Assay (Affymetrix).

growth_protocol: E13.5 Balb/c mouse embryos were dissected from the uterus of sacrificed females

extract_protocol: RNeasy Mini Plus Kit (Qiagen, Hilden, Germany)

treatment_protocol: Fetal livers were resuspended in PBS/ 0.3% BSA and passed through a 40 µm cell strainer (BD Biosciences). Fetal liver cells (FLC´s) were treated with 10 ml Red Blood Cell Lysis Buffer (Sigma-Aldrich) to remove erythrocytes. For sorting TER119− erythroid progenitors, FLC´s were incubated with rat antibodies against the following surface markers: GR1, CD41, CD11b, CD14, CD45R/B220, CD4, CD8 (BD Pharmingen), Ter119 (gift from Albrecht Müller, Julius-Maximilians-University, Würzburg, Germany) and with YBM/42 (gift from Suzanne M. Watt, University of Oxford, Oxford, UK) for 20 min at 4°C. After washing cells were incubated for 20 min at 4°C with anti-rat antibody-coupled magnetic beads and negatively sorted with MACS columns according to the manufacturer's instructions (Miltenyi Biotech). Sorted CFU-E were cultivated for 12-14 h in IMDM (Invitrogen), 30% fetal calf serum (FCS), and 50 µM µ-mercaptoethanol supplemented with 0.5 U/ml Epo (Cilag-Jansen).

value: BALB/c

value: E13.5 embryos

value: liver


title: Anaplastic neuroepithelial tumour, probably anaplastic oligoastrocytoma

city: Oslo

first: Hanne-Sofie

last: Dahlback

address: Montebello

department: Section for Cancer Cytogenetics

country: Norway

institute: The Norwegian Radium Hospital

hyb_protocol: The protocol used for hybridization and labeling of the samples was the “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic labeling for Blood Cells or Tissues (with a High Throughput option) Version 6.1, August 2009”.

scan_protocol: All slides were scanned with the Agilent DNA Microarray Scanner with Surescan High-Resolution technology and data extracted using the Agilent Feature Extraction Software v. 10.5.1.1 as described in the Agilent Oligo aCGH protocol.

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) and Genomic Workbench software (Agilent Technologies Inc., Palo Alto, California, USA). Aberrant DNA copy number intervals identified using the Aberration Detection Method 2 (ADM-2), default threshold setting 6.0, and Fuzzy Zero correction algorithm applied. To ensure the exclusion of very low or very small aberrations, we added a custom-made aberration filter defining a region with a copy number aberration as a region with minimum five probes gained/lost and with minimum absolute average log2 ratio of 0.2 (gain) or -0.2 (loss). A loss defined as homozygous when the log2 ratio was lower than -1, and a gain was regarded as high level amplification when the log2 ratio was higher than 1.

source_name: Human brain

growth_protocol: Fresh-frozen

extract_protocol: Mag-Attract DNA Mini M48 kit (QIAGEN, Hilden, Germany)

tag: gender

value: Female

tag: tumor type

value: Anaplastic neuroepithelial

value: reference


title: B. breve UCC2003 grown in MRS vs B. breve UCC2003 grown in vivo experiment 1


title: CFU-E +EPO 0.5U at 14h

source_name: CFU-E  +EPO 0.5U at 14h


title: CFU-E +EPO 0.5U at 19h

source_name: CFU-E  +EPO 0.5U at 19h


title: CFU-E +EPO 0.5U at 7h

source_name: CFU-E  +EPO 0.5U at 7h


title: Low-grade neuroepithelial tumour (DNET or  low-grade astrocytoma)

label_protocol: The protocol used for hybridization and labeling of the samples was the “Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis Enzymatic labeling for Blood Cells or Tissues (with a High Throughput option) Version 6.1, August 2009”.

value: neuroepithelial tumour


title: CNS-PNET 07-1668

value: Primitive Neuroectodermal Tumors of the Central Nervous System


title: GcvB-R2 biological experiment 2

value: S.typhimurium SL1344 delta gcvB


title: Pilocytic astrocytoma 05-0129

value: Male

value: Pilocytic astrocytoma


title: Glioblastoma 08-1197

value: Glioblastoma


title: CFU-E +EPO 0.5U at 8h

source_name: CFU-E  +EPO 0.5U at 8h


title: CNS-PNET 08-1118


title: CNS-PNET 05-0531


title: Medulloblastoma (classical type)

value: Medulloblastoma


title: CFU-E +EPO 0.5U at 3h

source_name: CFU-E  +EPO 0.5U at 3h


title: CFU-E +EPO 0.5U at 6h

source_name: CFU-E  +EPO 0.5U at 6h


title: CFU-E +EPO 0.5U at 0h

source_name: CFU-E  +EPO 0.5U at 0h


title: Anaplastic oligoastrocytoma

value: Anaplastic oligoastrocytoma


title: Glioblastoma 07-0705


title: CFU-E -EPO at 6h

source_name: CFU-E  -EPO at 6h


title: GcvB-R1 biological experiment 2

value: S.typhimurium SL1344


title: CFU-E +EPO 0.5U at 5h

source_name: CFU-E  +EPO 0.5U at 5h


title: CFU-E -EPO at 5h

source_name: CFU-E  -EPO at 5h


title: CFU-E +EPO 0.5U at 4h

source_name: CFU-E  +EPO 0.5U at 4h


title: Pilocytic astrocytoma 05-0270


title: Cribriform nevroepithelial tumor

value: Cribriform nevroepithelial


title: CNS-PNET (with extensive glial differentiation)


title: GcvB-WT biological experiment 1

source_name: GcvB

value: pBAD-GcvB


title: CFU-E +EPO 0.5U at 2h

source_name: CFU-E  +EPO 0.5U at 2h

value: BALB/c


title: CFU-E -EPO at 1h

source_name: CFU-E  -EPO at 1h

value: E13.5 embryos


title: CFU-E -EPO at 4h

source_name: CFU-E  -EPO at 4h

value: liver


title: DGcvB-control biological experiment 1

source_name: DGcvB-control

value: pBAD

source_name: WT


title: CFU-E -EPO at 3h

source_name: CFU-E  -EPO at 3h


title: GcvB-R2 biological experiment 1


title: CFU-E -EPO at 7h

source_name: CFU-E  -EPO at 7h


title: CFU-E +EPO 0.5U at 1h

source_name: CFU-E  +EPO 0.5U at 1h


title: CFU-E -EPO at 2h

source_name: CFU-E  -EPO at 2h


title: GcvB-WT biological experiment 2


title: GcvB-R1 biological experiment 1


title: femur

city: Shinagawa-ku

first: Tomohiro

last: Taguchi

state: Tokyo

address: 1-5-8 Hatanodai

department: School of Dentistry

country: Japan

institute: Showa University

hyb_protocol: We used Gene Expression Hybridization Kit (Agilent Technologies Inc.) , and cRNA were hybridized for 17 hr.

scan_protocol: Microarrays were washed and scanned using the Agilent Microarray Scanner.

data_processing:
The data were obtained with the Feature Extraction Software (v.9.5.3.1) (Agilent Technologies Inc.).
The resulting data were imported into GeneSpring (Agilent Technologies Inc.) and normalized values were exported.

label: Cyanine 3-CTP

source_name: femur

label_protocol: We used Quick Amp Labeling kit (Agilent Technologies Inc.) ,and followed manufacture's protocol.

extract_protocol: Bones were extirpated from mice. Total RNA was isolated from the bones using an RNeasy Lipid Tissue Midi Kit (Qiagen, Hilden, Germany) .

value: male

value: femur


title: mandible

source_name: mandible

value: mandible


title: maxilla

source_name: maxilla

value: maxilla


title: ilium

source_name: ilium

value: ilium


title: colorectal cancer sample AUS2_183_p1575 [gene-level]

status: Public on May 19 2011

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

institute: Institute for Cancer Research, Oslo University Hospital

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: For analysis at the exon level, raw data were processed (using a custom-made cdf-file; HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf) and analyzed for alternative splicing with the FIRMA algorithm (aroma.affymetrix). For gene-level analysis, raw data were processed with the RMA procedure using Expression Console (Affymetrix; gene-core analysis).

source_name: Colorectal cancer patient

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: For the colorectal cancer samples, total RNA was isolated from <30 mg tissue biopsies using the AllPrep DNA/RNA Mini kit (Qiagen), according to the manufacturer's protocol. For the normal colon mucosa samples, total RNA was isolated from <100 mg tissue biopsies using the Ambion RiboPure kit (Life Technologies), according to the manufacturer's protocol.

value: colorectal cancer biopsy

tag: tumor stage

tag: msi-status


title: colorectal cancer sample AUS2_177_p1569 [gene-level]


title: CFU-E -EPO at 0h

source_name: CFU-E  -EPO at 0h


title: colorectal cancer sample AUS2_165_p1011 [gene-level]

value: MSI-H


title: colorectal cancer sample AUS2_190_p1486 [gene-level]


title: colorectal cancer sample AUS2_197_p1588 [exon-level]


title: colorectal cancer sample AUS2_147_p989 [gene-level]


title: colorectal cancer sample AUS2_184_p1576 [exon-level]


title: colorectal cancer sample AUS2_200_p1591 [exon-level]


title: colorectal cancer sample AUS2_185_p1577 [exon-level]


title: colorectal cancer sample AUS2_144_p966 [gene-level]


title: colorectal cancer sample AUS2_175_p1471 [exon-level]


title: STAT3-KO vs WT

city: Hannover

first: Denise

last: Hilfiker-Kleiner

institute: Medical school Hannover

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit. 850 ng of the corresponding Cy3- and Cy5-labeled cRNA were combined and hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays using Agilent's recommended hybridization chamber and oven. T he microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at room temperature followed by a second wash with preheated to 37°C 0.06x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min and a final wash step with acetonitrile for 30 sec.

scan_protocol: Flurescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent's DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.

source_name: left ventricle tissue pool of STAT3-KO mice

label_protocol: For linear T7-based amplification step 1 µg of total RNA samples were used as starting material. To produce Cy3- and Cy5-labeled cDNAs the RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit following the current manufacturer's.

extract_protocol: Total RNA extracted using the Qiagen Mini-kit following manufacturer's instructions

value: 3 month

tag: genotype

value: mixed (C57Bl6 and SV129)

source_name: left ventricle tissue pool of WT mice

value: WT


title: colorectal cancer sample AUS2_186_p1482 [exon-level]


title: colorectal cancer sample AUS2_183_p1575 [exon-level]


title: colorectal cancer sample AUS2_134_p949 [gene-level]

value: MSS


title: colorectal cancer sample AUS2_187_p1579 [exon-level]


title: colorectal cancer sample AUS2_182_p1478 [exon-level]


title: colorectal cancer sample AUS2_147_p989 [exon-level]


title: colorectal cancer sample AUS2_177_p1569 [exon-level]


title: colorectal cancer sample AUS2_167_p1013 [exon-level]


title: colorectal cancer sample AUS2_165_p1011 [exon-level]


title: colorectal cancer sample AUS2_127_p914 [gene-level]


title: colorectal cancer sample AUS2_169_p1014 [exon-level]


title: colorectal cancer sample AUS2_158_p995 [exon-level]


title: colorectal cancer sample AUS2_171_p1015 [exon-level]


title: colorectal cancer sample AUS2_190_p1486 [exon-level]


title: colorectal cancer sample AUS2_145_p977 [exon-level]


title: colorectal cancer sample AUS2_153_p993 [exon-level]


title: colorectal cancer sample AUS2_134_p949 [exon-level]


title: colorectal cancer sample AUS2_140_p954 [exon-level]


title: colorectal cancer sample AUS2_144_p966 [exon-level]


title: colorectal cancer sample AUS2_117_p906_2 [gene-level]


title: colorectal cancer sample AUS2_127_p914 [exon-level]


title: colorectal cancer sample AUS2_119_p927 [exon-level]


title: colorectal cancer sample AUS2_123_p931 [exon-level]


title: colorectal cancer sample AUS2_129_p934 [exon-level]


title: colorectal cancer sample AUS2_118_p907 [gene-level]


title: colorectal cancer sample AUS2_086_p624 [gene-level]


title: colorectal cancer sample AUS2_093_p649 [gene-level]


title: colorectal cancer sample AUS2_100_p668 [exon-level]


title: colorectal cancer sample AUS2_114_p1356 [exon-level]


title: colorectal cancer sample AUS2_072_p590 [gene-level]


title: colorectal cancer sample AUS2_097_p643 [exon-level]


title: colorectal cancer sample AUS2_117_p906_2 [exon-level]


title: colorectal cancer sample AUS2_098_p665 [exon-level]


title: colorectal cancer sample AUS2_053_p328 [gene-level]

value: MSI-L


title: colorectal cancer sample AUS2_118_p907 [exon-level]


title: colorectal cancer sample AUS2_090_p646 [exon-level]


title: colorectal cancer sample AUS2_093_p649 [exon-level]


title: colorectal cancer sample AUS2_091_p647 [exon-level]


title: colorectal cancer sample AUS2_096_p652 [exon-level]


title: colorectal cancer sample AUS2_084_p622 [exon-level]


title: colorectal cancer sample AUS2_092_p648 [exon-level]


title: colorectal cancer sample AUS2_089_p645 [exon-level]


title: colorectal cancer sample AUS2_130_p935 [exon-level]


title: colorectal cancer sample AUS2_094_p640 [exon-level]


title: colorectal cancer sample AUS2_075_p595 [exon-level]


title: colorectal cancer sample AUS2_055_p536 [exon-level]


title: colorectal cancer sample AUS2_072_p590 [exon-level]


title: colorectal cancer sample AUS2_043_p1327 [gene-level]


title: colorectal cancer sample AUS2_065_p551 [exon-level]


title: colorectal cancer sample AUS2_058_p538 [exon-level]


title: colorectal cancer sample AUS2_037_p304 [gene-level]


title: colorectal cancer sample AUS2_030_p340 [gene-level]


title: colorectal cancer sample AUS2_054_p272 [exon-level]


title: colorectal cancer sample AUS2_031_p478 [gene-level]


title: colorectal cancer sample AUS2_070_p566 [exon-level]


title: colorectal cancer sample AUS2_053_p328 [exon-level]


title: colorectal cancer sample AUS2_044_p268 [exon-level]


title: colorectal cancer sample AUS2_051_p1596 [exon-level]