title: BAN_10nM DHT_0h_repC


title: BAB_1nM DHT_6h_repB

status: Public on Apr 20 2016

type: RNA

city: Cologne

first: Axel

last: HILLMER

address: Kerpener Str. 62

department: Institute of Pathology

country: Germany

institute: University of Cologne

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was log2 transformation and quantile normalized using the LUMI in R

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: BAB

label_protocol: Biotinylated cRNA were prepared with Epicentre TargetAmp Nano-g Biotin-aRNA labelling kit

extract_protocol: Total RNA was isolated with Qiagen RNeasy kit and on-column DNase treatment according to manufacturer’s recommendation. Quality control was performed with Agilent Bioanalyzer.

tag: cell line

value: BAB

tag: agent

value: DHT

tag: dose

tag: time (treatment duration)


title: BAN_10nM DHT_20h_repB

source_name: BAN

value: BAN


title: BAN_10nM DHT_16h_repA


title: BAN_10nM DHT_20h_repA


title: BAN_10nM DHT_12h_repB


title: BAN_10nM DHT_0h_repB


title: BAN_10nM DHT_24h_repB


title: BAB_1nM DHT_48h_repC


title: BAB_1nM DHT_6h_repC


title: BAB_1nM DHT_48h_repA


title: BAN_10nM DHT_0h_repA


title: BAN_10nM DHT_12h_repA


title: BAB_1nM DHT_6h_repA


title: BAB_1nM DHT_3h_repC


title: BAN_10nM DHT_12h_repC


title: F10-5-P

city: Urbana

first: Junmin

last: Lee

state: IL

address: 1304 W. Green St.

department: Materials Science and Engineering

country: USA

institute: University of Illinois at Urbana-Chanpaign

hyb_protocol: not provided

scan_protocol: Gene expression profiling performed using Illumina iScan Sentrix BeachChip technology at the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign using standard Illumina protocols

data_processing:
Illumina gene array data was preprocessed using GenePattern. The background values were subtracted and hresholded.
The data was then normalized using the quantile method. Heatmaps of fold changes over glass in gene expression were visualized using the Gene-E software package.

organism: Mus musculus

source_name: B16F10 cells cultured on patterned gels for 5 days

label_protocol: not provided

growth_protocol: Adherent B16F0 and B16F10 cells were cultured for five days on spiral patterns, non-patterned gels, or glasses.

extract_protocol: Cells were lysed directly in Trizol reagent (Invitrogen) according to the vendor's instructions. Total RNA from each sample (12 duplicates) was extracted and quantified by photospectrometry using a NanoDrop ND-1000 (ThermoFisher). RNA quality was confirmed by an Agilent Bioanalyzer

tag: cell type

value: skin melanoma


title: F0-5-G

source_name: B16F0 cells cultured on glasses for 5 days


title: F0-5-NP

source_name: B16F0 cells cultured on non-patterned gels for 5 days


title: F10-5-NP

source_name: B16F10 cells cultured on non-patterned gels for 5 days


title: F0-5-P

source_name: B16F0 cells cultured on patterned gels for 5 days


title: BAB_1nM DHT_3h_repA


title: BAB_1nM DHT_3h_repB


title: BAB_1nM DHT_24h_repB


title: BAB_1nM DHT_36h_repC


title: BAB_1nM DHT_30min_repC


title: BAB_1nM DHT_20h_repB


title: BAB_1nM DHT_24h_repC


title: BAB_1nM DHT_36h_repB


title: BAB_1nM DHT_30min_repB


title: BAB_1nM DHT_1h_repA


title: BAB_1nM DHT_15min_repC


title: BAB_1nM DHT_1h_repB


title: BAB_1nM DHT_16h_repA


title: BAB_1nM DHT_12h_repC


title: BAB_1nM DHT_12h_repB


title: BAB_1nM DHT_15min_repB


title: BAB_1nM DHT_24h_repA


title: BAB_1nM DHT_36h_repA


title: BAB_1nM DHT_20h_repC


title: BAB_1nM DHT_15min_repA


title: BAB_1nM DHT_30min_repA


title: BAB_1nM DHT_16h_repC


title: BAB_1nM DHT_20h_repA


title: BAB_1nM DHT_1h_repC


title: BAB_1nM DHT_16h_repB


title: Myc_2

city: Eiheiji

first: Chisato

last: Honjoh

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki

country: Japan

institute: University of Fukui

hyb_protocol: Labeled cDNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GCS3000-7G Scanner.

data_processing:
The data were analyzed with Affymetrix GCS3000 system.
affymetrix-algorithm-name = rma-gene-default
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.19935

organism: Rattus norvegicus

label_protocol: Sense-strand cDNA were generated from total RNA using Ambion WT expression kit (Thermo Fisher) according to the manufacture's instruction. After fragmentaiton, cDNA were subjected to terminal labeling using GeneChip WT terminal labeling kit (Affymetrix) according to the manufacture's instruction.

growth_protocol: RBL-2H3 cells stably expressing Myc-tagged Mincle were cultured in DMEM containig 10% FCS.

extract_protocol: Total RNA was extracted by High pure RNA isolation kit (Roche) according to the manufacture's instruction.

treatment_protocol: Cells were pretreated without or with 2 μM of R406 for 5min, and subsequently stimulated without or with 10 μg/ml of anti-Myc antibody for 2 hr.

value: basophilic leukemia cell line

tag: genotype/variation

value: stably expressing Myc-tagged Mincle

tag: stimulated with

value: anti-Myc antibody


title: control_1

value: none (unstimulated)


title: R406_2

value: anti-Myc antibody in the presence of R406


title: BAB_10nM DHT_6h_repA


title: Myc_1


title: BAB_10nM DHT_6h_repC


title: control_2


title: BAB_10nM DHT_48h_repA


title: R406_1


title: BAB_10nM DHT_30min_repB


title: BAB_10nM DHT_48h_repB


title: BAB_10nM DHT_24h_repC


title: BAB_10nM DHT_48h_repC


title: BAB_10nM DHT_3h_repC


title: BAB_10nM DHT_3h_repA


title: BAB_10nM DHT_24h_repB


title: BAB_10nM DHT_24h_repA


title: BAB_10nM DHT_6h_repB


title: Pla2g2e-KO_P33, skin_Rep1

city: Setagaya

first: Kei

last: Yamamoto

state: Tokyo

address: 2-1-6 kamikitazawa

department: Lipid Metabolism Project

institute: Tokyo Metropolitan Institute of Medical Science

description:
gene expression profile of Pla2g2e-knockout mouse skin
Pla2g2e-KO_P33-1

hyb_protocol: 0.825 µg of Cy3 or Cy5-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit protocol. Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5µm and dye channels of Green and Red with PMT set to 100%, respectively.

data_processing: Agilent Feature Extraction Software (v 11.0.1.1) was used for background subtraction and LOWESS normalization.

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: Pla2g2e-/- mice and littermate controls (C57BL/6 background) were housed in climate-controlled (23 C) pathogen-free facilities with a 12 h light-dark cycle, with free access to standard LFD (CE2; CLEA Japan) and water.

extract_protocol: Total RNA was extracted from skin of 33 days-old mouse and purified using the RNeasy Mini Kit (Qiagen). The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

tag: strain

tag: age

value: 33-days old

tag: tissue

value: skin

value: Pla2g2e +/+

value: Pla2g2e -/-


title: cKO-MPP

city: Tokyo

first: Keiyo

last: Takubo

address: 1-21-1 Toyama Shinjuku-ku

department: Department of Stem Cell Biology

institute: National Center for Global Health and Medicine

description: Transplanted CD34+ Flt3+ LSK cells as multipotent progenitors (MPP) p38 knockout group

hyb_protocol: Gene Expression Wash Pack (5188-5327 : Agilent) was used according to the manufacturer's instruction

scan_protocol: DNA Microarray Scanner (Agilent) was used according to the manufacturer's instruction

data_processing: The scanned images were analyzed with Feature Extraction Ver.9.5.3 (Agilent). Normalization method was 75 percentile shift for each sample, followed by adjusting baseline to median of all sample for each gene. Normalized data were converted to linear scale.

source_name: MPP knockout group

label_protocol: Gene Expression Hybridization Kit (5188-5242 : Agilent) was used according to the manufacturer's instruction

extract_protocol: CFSE-positive cells were sorted into SF-O3 medium and then centrifuged at 340 x g for 10 minutes at 4℃. Cell pellets were lysed in 85uL of RLT buffer plus 1% 2-ME, followed by RNA extraction using Qiagen RNeasy micro kit (74004 : Qiagen) according to the manufacturer's instruction.

treatment_protocol: CD34- Flt3- LSK cells (LT-HSC) or CD34+ Flt3+ LSK cells (MPP) from wild type (WT) or p38 cKO (cKO) mice were sorted using SORP FACS AriaI followed by labbeling with CFSE and transplanted into lethally irradiated mice. Sixteen hours later, CFSE-positive cells were sorted and were subjected to RNA extraction.

tag: Sex

value: Male

value: 10 week old

value: Bone marrow


title: BAB_10nM DHT_36h_repC


title: BAB_1nM DHT_0h_repB


title: Pla2g2e-KO_P33, skin_Rep2

description:
gene expression profile of Pla2g2e-knockout mouse skin
Pla2g2e-KO_P33-2


title: BAB_10nM DHT_30min_repA


title: BAB_1nM DHT_12h_repA


title: BAB_10nM DHT_36h_repA


title: BAB_10nM DHT_3h_repB


title: BAB_10nM DHT_36h_repB


title: BAB_10nM DHT_30min_repC


title: BAB_1nM DHT_0h_repA


title: WT-MPP

description: Transplanted CD34+ Flt3+ LSK cells as multipotent progenitors (MPP)  wild type group

source_name: MPP wild type group


title: BAB_10nM DHT_20h_repC


title: WT-LT-HSC

description: Transplanted CD34- Flt3- LSK cells as long-term hematopoietic stem cells (LT-HSC) wild type group

source_name: HSC wild type group


title: BAB_10nM DHT_20h_repA


title: cKO-LT-HSC

description: Transplanted CD34- Flt3- LSK cells as long-term hematopoietic stem cells (LT-HSC) p38 knockout group

source_name: HSC knockout group


title: BAB_10nM DHT_15min_repB


title: BAB_10nM DHT_16h_repB


title: BAB_10nM DHT_20h_repB


title: BAB_10nM DHT_16h_repC


title: E16 WT2

city: Ames

first: Jeffrey

middle: M

last: Trimarchi

state: IA

address: 3188 Molecular Biology Building

department: GDCB

institute: Iowa State University

description: Gene expression data from the isolated retinas of E16 WT littermates of Plk3-KO mice

hyb_protocol: Amplified RNA was hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays at the Iowa State University GeneChip Facility.

scan_protocol: Amplified RNA was scanned from Affymetrix GeneChip Mouse Genome 430 2.0 arrays at the Iowa State University GeneChip Facility.

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.

source_name: retina

label_protocol: Total RNA was amplified, biotinylated, and fragmented using the Ambrion MessageAmp III RNA amplification kit according to manufacturer's instructions.

growth_protocol: Plk3-KO mice, described in Myer, et al, 2011, were obtained and crossed to C57Bl/6 mice. They were allowed to develop normally in utero alongside WT littermates until the time of interest.

extract_protocol: Total RNA was extracted from isolated retinas using Trireagent according to the manufacturer's instructions.

treatment_protocol: E16 embryos were allowed to develop normally until E16, at which point they were isolated from pregnant dams. Tailclips were taken from each pup for genotyping, while retinas were isolated and washed in 1X PBS before RNA preparation using Trireagent.

value: WT

value: retina


title: E16 KO3

description: Gene expression data from the isolated retinas of E16 Plk3-KO mice


title: BAB_10nM DHT_1h_repC

value: BAB

value: DHT


title: BAB_10nM DHT_16h_repA


title: BAB_10nM DHT_15min_repC


title: BAB_10nM DHT_12h_repC


title: BAB_10nM DHT_12h_repA


title: E16 KO1


title: E16 WT3


title: E16 WT1


title: BAB_10nM DHT_1h_repB


title: E16 KO2


title: BAB_10nM DHT_1h_repA


title: BAB_10nM DHT_15min_repA


title: BAB_10nM DHT_12h_repB


title: BAB_10nM DHT_0h_repA


title: P0 WT1

description: Gene expression data from the isolated retinas of P0 WT littermates of Plk3-KO mice

growth_protocol: Plk3-KO mice, described in Myer, et al, 2011, were obtained and crossed to C57Bl/6 mice. They were allowed to develop alongside WT littermates until the time of interest.

treatment_protocol: Retinas were isolated and washed in 1X PBS.


title: P0 WT3

source_name: retinas of P0 WT littermates of Plk3-KO mice


title: BAB_10nM DHT_0h_repB


title: P0 WT2


title: BAB_10nM DHT_0h_repC


title: P0 KO2

description: Gene expression data from the isolated retinas of P0 Plk3-KO mice

source_name: retinas of P0 Plk3-KO mice


title: P7 WT1

description: Gene expression data from the isolated retinas of P7 WT littermates of Plk3-KO mice


title: P7 WT2

source_name: retinas of P7 WT littermates of Plk3-KO mice


title: P0 KO3


title: BAN_repC

value: BAN


title: BAN_repB


title: Cord blood CD34+_Cultured for  Day 0

city: Ansan

first: Tae Gi

last: Uhm

country: South Korea

institute: hanyang university

description:
Gene expression in CB CD34+ cells
CB day 0 (CD34+ cells)

hyb_protocol: After labeled aRNAs were placed on Agilent Human whole genome 4x44K array (Agilent technologies, CA) and covered by a NimbleGen A4 mixer (Biomicro systems, Inc. UT). The slides were hybridized for 12 hr at 42 ℃ MAUI system (Biomicro systems, Inc. UT). The hybridized slides were washed in 2 X SSC, 0.1 % SDS for 2 min, 1 X SSC for 3 min, and then 0.2 X SSC for 2 min at room temperature. The slides were centrifuged at 3000 rpm for 20 sec to dry.

scan_protocol: The arrays were analyzed using an Agilent scanner with associated software.

data_processing: Gene expression levels were calculated with Feature Extraction v10.7.3.1 (Agilent technologies, CA) Relative signal intensities for each gene were generated using the Robust Multi-Array Average algorithm. The data were processed based on median polish normalization method using the GeneSpring GX 11.0 (Agilent technologies, CA). This normalization method aims to make the distribution of intensities for each array in a set of arrays the same. The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 11.0 (Agilent technologies, CA). Fold change filters included the requirement that the genes be present in at least 200% of controls for up-regulated genes and lower than 50% of controls for down-regulated genes. Hierarchical clustering data were clustered groups that behave similarly across experiments using GeneSpring GX 7.3.1 (Agilent technologies, CA). Clustering algorithm was Euclidean distance, average linkage.

source_name: Cord blood CD34+, Cultured for  Day 0

label_protocol: Each total RNA sample (2ug) was labeled and amplified using ULS aRNA labeling kit(Kreatech diagnostics, Netherlands). The Cy5-labeled aRNAs were resuspended in 10 ㎕ of hybridization solution (GenoCheck, Korea).

growth_protocol: CD34+ cells were seeded in 24-well plates at 1x105 cells/well. The cells were cultured in IMDM  containing 10% FBS, 100 U/ml penicillin, 100 ug/ml streptomycin, and supplemented with a cytokine cocktail of SCF (50 ng/ml), FLT-3L (50 ng/ml), GM-CSF (10 ng/ml), IL-3 (10 ng/ml), and IL-5 (10 ng/ml) for the first 6 days. Cells were then collected, split into 12-well plates at 1x106 cells/well in medium supplemented with IL-3 and IL-5, and cultured with a half medium change for an additional 6 days.

extract_protocol: CD34+ cells were immunomagnetically purified from human CB mononuclear cells using a MACS CD34+ microbead kit. Total RNA was extracted using the TRI REAGENT according to the manufacturer’s instructions.

value: CB CD34+ cells

tag: culture time

value: Day 0


title: BAN_repA


title: BAB_repB


title: P7 KO2

description: Gene expression data from the isolated retinas of P7 Plk3-KO mice

source_name: retinas of P7 Plk3-KO mice


title: P7 WT3


title: AD WT2

description: Gene expression data from the isolated retinas of adult WT littermates of Plk3-KO mice

value: adult


title: Endothelial_cells_24h_PBS (A912_06)

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

institute: University Medical Center Freiburg

hyb_protocol: Biotinylated cRNA was hybridized on GeneChip® Mouse Gene 2.0 ST Arrays , that were stained, washed and scanned following standard procedures.

data_processing: Background correction and normalization was performed using the RMA-Sketch implementation in Affymetrix Expression Console

source_name: endothelial cells, 24h, PBS

label_protocol: Total RNA was amplified using the Ovation PicoSL WTA System V2 and further processed using the Encore Biotin Module according to the instructions supplied by the manufacturer (NuGen).

growth_protocol: Adult mice were sacrificed with a lethal dose of anesthetic, and the cerebrum was isolated and dissected free of the meninges. The brain was homogenized in a Dounce homogenizer, and the resulting homogenate was centrifuged at 4,000 g for 5 min. The pellet was resuspended in 18% dextran solution (molecular weight: 64,000-76,000, Sigma-Aldrich) in DMEM (Gibco) and centrifuged at 6,000 g for 10 min. After removing the supernatant and myelin debris, the pellet was resuspended in DMEM containing 1 mg/mL collagenase/dispase (Roche), 40 µg/mL DNase 1 (Roche), and 0.147 µg/mL tosyllysine chloromethyl ketone (Sigma-Aldrich), and incubated at 37°C for 75 min with occasional agitation to free endothelial cells from pericytes, perivascular macrophages, and remains of the basement membrane. The cell suspension was centrifuged at 4,000 g for 5 min, the supernatant was discarded, and cells were washed and seeded in 6-well plates coated with mouse collagen IV (BD). Cells were subsequently grown in DMEM-F12 (Gibco) supplemented with 10 % fetal bovine serum (PAA Laboratories), 2 mM L-glutamine, 100 IU/mL penicillin, 100 µg/mL streptomycin, 15 U/mL heparin (Biochrom), and 30 µg/mL of endothelial cell growth supplement (Sigma-Aldrich). 4 µg/mL puromycin (Sigma-Aldrich) was added for the first 48 h after preparation to deplete cells of non-endothelial origin.

extract_protocol: Cells were flushed with ice‐cold HBSS. RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer′s instructions.

treatment_protocol: Cells were incubated with IFNbeta (500 U/mL) for 24h.

tag: developmental stage

value: endothelial cells

tag: treatment

value: PBS

tag: time


title: Cord blood CD34+_Cultured for  Day 4

description:
Gene expression in developing CB eosinophils at day 4
CB day 4

source_name: Cord blood CD34+, Cultured for  Day 4

value: Day 4


title: AD WT3

source_name: retinas of adult WT littermates of Plk3-KO mice


title: BAB_repA

source_name: BAB


title: BAB_repC


title: P0 KO1


title: P7 KO1


title: Cord blood CD34+_Cultured for  Day 6

description:
Gene expression in developing CB eosinophils at day 6
CB day 6

source_name: Cord blood CD34+, Cultured for  Day 6

value: Day 6


title: P7 KO3


title: AD KO3

description: Gene expression data from the isolated retinas of adult Plk3-KO mice

source_name: retinas of adult Plk3-KO mice


title: Cord blood CD34+_Cultured for  Day 12

description:
Gene expression in developing CB eosinophils at day 12
CB day 12

source_name: Cord blood CD34+, Cultured for  Day 12

value: Day 12


title: AD KO2


title: Endothelial_cells_24h_IFNb (A912_04)

scan_protocol: Biotinylated cRNA was hybridized on GeneChip® Mouse Gene 2.0 ST Arrays , that were stained, washed and scanned following standard procedures.

source_name: endothelial cells, 24h, Interferon beta

value: Interferon beta


title: Endothelial_cells_24h_IFNb (A912_03)


title: MPP_C

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

hyb_protocol: Affymetrix HG-U133 Plus 2.0 GeneChip arrays hybridization was performed using Affymetrix standard protocols (Affymetrix, Santa Clara, CA).

scan_protocol: Affymetrix HG-U133 Plus 2.0 GeneChip arrays scanning was performed using Affymetrix standard protocols (Affymetrix, Santa Clara, CA). Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis performed with the GeneChip Operating Software (GCOS) software.

data_processing: Preprocessing of the data and normalization was carried out in R ('Affy' package). Specifically, probe level signals have been converted to expression values using the robust multi?array average procedure (RMA); intensity levels have been background adjusted, normalized using quantile normalization, and log2 expression values calculated using median polish summarization. The arrays were annotated using a custom chip definition file, the Gene Annot CDF for Human Gene U133 Plus 2.0 arrays, and the corresponding Bioconductor libraries (GeneAnnot version 2.1.0).

source_name: Myeloid progenitors/precursors (MPP)

label_protocol: Affymetrix HG-U133 Plus 2.0 GeneChip arrays staining was performed using Affymetrix standard protocols (Affymetrix, Santa Clara, CA).

growth_protocol: Committed erythroid and myeloid progenitors/precursors (EPP and MPP) were isolated as pools of CD34lowCD36high and CD34-CD13+ populations, after induction for five days in culture in the presence of SCF, IL3 and either Epo or G-CSF, respectively

extract_protocol: RNA was isolated using RNeasy Plus Mini kit (QIAGEN) and reverse transcribed by GeneChip 3IVT Express kit.

value: Myeloid progenitors/precursors (MPP)


title: Endothelial_cells_24h_PBS (A912_05)


title: Endothelial_cells_24h_IFNb (A912_02)


title: AD WT1


title: Endothelial_cells_24h_PBS (A912_07)


title: EPP_A

source_name: Erythroid progenitors/precursors (EPP)

value: Erythroid progenitors/precursors (EPP)


title: Endothelial_cells_24h_PBS (A912_08)


title: EPEC_WT_rep5

city: Aachen

first: Mathias

last: Hornef

address: Pauwelstr. 30

department: Institute for Medical Microbiology

institute: University Hospital RWTH Aachen

description:
IECs isolated 8 days post-infection from neonate mouse orally infected at birth with WT EPEC. Replicate 5
M4426

hyb_protocol: cRNA fragmentation, hybridization and washing steps were also carried-out exactly as recommended: ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ using the extraction protocol file ‘GE1_107_Sep09.xml’. Extracted microarray raw data were imported into Omics Explorer software v3.0 (Qlucore) under default import settings for Agilent One Color mRNA Microarrays. Accordingly, data processing steps were: 1) removal of control measurements, 2) log base 2 transformation, 3) normalization by shifting to 75 Percentile, 4) averaging of values from on-chip replicates, 5) baseline transformation to the median. Note, that six additional samples have been initially imported into one Qlucore Omics Explorer project. These 6 additional samples have not been utilized in the context of this study. However, baseline transformation in Qlucore Omics Explorer software (see step 5) is based on all samples (including the 6 samples that were finally removed and are not contained in this very GEO series).

source_name: IECs; 8 days post-infection; EPEC WT; replicate 5

label_protocol: Synthesis of Cy3-labeled cRNA was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: Mouse intestinal tissue was incubated for 10 min at 37°C in 0.3 M EDTA. shaken vigorously and epithelial cells were separated from the underlying tissue and immune cells by repeated sedimentation at 1 x g at 4°C (Lotz et al., J. Exp Med. 2006). Flow cytometric analysis revealed less than 1% of CD45+ cells in IEC preparations.

extract_protocol: RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s protocol.

tag: infection

value: EPEC WT

value: intestinal epithelial cells (IECs)

value: 9 days old


title: MPP_A


title: MPP_B


title: AD KO1

value: retina


title: EPEC_WT_rep6

description:
IECs isolated 8 days post-infection from neonate mouse orally infected at birth with WT EPEC. Replicate 6
M4427

source_name: IECs; 8 days post-infection; EPEC WT; replicate 6


title: EPP_C


title: Splenocytes_18h_post_VSVinPBS (A912b_01)

description:
Splenocytes from VSV injected mice
A912b_01_1-1_B6_VSV-M2_18h_2

source_name: Splenocytes, 18h after VSV infection

growth_protocol: Male mice only were used for the experiments. Mice were group housed up to five per cage with 12 h light/dark cycle with lights on at 6 a.m. Food and water were available ad libitum.

extract_protocol: Tissues were dissected and flushed with ice‐cold HBSS. RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer′s instructions.

treatment_protocol: For VSV-M2 infection mice were injected intravenously with 2 x 106 pfu VSV-M2 or mock infected with PBS. 7 μL of in vivo jetPEI was mixed with 50 μg of nucleic acids (MWG-BIOTECH AG) at a N:P ratio of 7:1 in a volume of 200 μL of 5 % glucose solution (vol/vol), and incubated for 15 min. Subsequently, 50 μg of complexed 5'-triphosphate RNA, the synthetic dsRNA analog poly(I:C) (Invivogen) was injected.

value: wt

tag: gender

value: male

value: VSV

value: splenocytes


title: EPP_B


title: HSPC_C

source_name: Hematopoietic stem/progenitor cells (HSPC)


title: Control_rep3

description:
IECs isolated from a healthy non-infected 9 days old neonate mouse. Replicate 3
M4428

source_name: IECs; 9 days old; uninfected; replicate 3


title: Splenocytes_18h_post_VSVinPBS (A912_21)

description:
Splenocytes from VSV injected mice
A912_21_22-10_Exp230_VSV-M4

value: adult


title: meningioma sample Jed43_MN

city: Jeddah

first: Hans-Juergen

last: Schulten

department: Center of Excellence in Genomic Medicine Research

country: Saudi Arabia

institute: King Abdulaziz University

description:
Jed43_MN
Gene expression data from brain tumor tissue.

hyb_protocol: Following fragmentation, 6 ug of cDNA were hybridized for 17 hr at 45C on GeneChip HuGene-1.0-st arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Data were generated using the Affymetrix Expression Console Software using Affymetrix default analysis settings.
Meningioma and control data were RMA normalized and analyzed with Partek Genomics Suite 6.6. The RMA-normalized data for the control samples are available in 'GSE77259_normalized_data_for_normal_brain_controls.txt', which is linked to the GSE77259 record as a supplementary file.

source_name: meningioma, grade I, psammomatous histology

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

extract_protocol: Total RNA from biospecimens was extracted using the Qiagen RNeasy mini kit according to the manufacturer's instructions. Integrity of RNA was checked by using the Agilent Bioanalyzer.

value: meningioma

tag: tumor grade

value: I

tag: tumor location

value: spinal

tag: histology

value: psammomatous

value: female


title: Control_rep4

description:
IECs isolated from a healthy non-infected 9 days old neonate mouse. Replicate 4
M4429

source_name: IECs; 9 days old; uninfected; replicate 4


title: Control_rep2

description:
IECs isolated from a healthy non-infected 9 days old neonate mouse. Replicate 2
M4290

source_name: IECs; 9 days old; uninfected; replicate 2


title: Splenocytes_18h_post_VSVinPBS (A912_22)

description:
Splenocytes from VSV injected mice
A912_22_22-10_Exp230_VSV-M5_2


title: HSPC_A

value: Hematopoietic stem/progenitor cells (HSPC)


title: EPEC_TTSSKO_rep4

description:
IECs isolated 8 days post-infection from neonate mouse orally infected at birth with ΔescV EPEC. Replicate 4
M4292

source_name: IECs; 8 days post-infection; EPEC ΔescV; replicate 4

value: EPEC ΔescV


title: meningioma sample Jed36_MN

description:
Jed36_MN
Gene expression data from brain tumor tissue.

source_name: meningioma, grade I, meningothelial histology

value: right frontoparietal

value: meningothelial


title: meningioma sample Jed34_MN

description:
Jed34_MN
Gene expression data from brain tumor tissue.

value: left sphenoid wing


title: Endothelial_cells_24h_IFNb (A912_01)

value: endothelial cells

value: Interferon beta


title: EPEC_WT_rep4

description:
IECs isolated 8 days post-infection from neonate mouse orally infected at birth with WT EPEC. Replicate 4
M4291

source_name: IECs; 8 days post-infection; EPEC WT; replicate 4

value: EPEC WT

value: intestinal epithelial cells (IECs)

value: 9 days old


title: HSPC_B


title: Splenocytes_18h_post_PBS (A912_20)

description:
Splenocytes from PBS injected mice (control for VSV infection)
A912_20_22-10_Exp230_PBS3_2

source_name: Splenocytes, 18h after PBS injection

value: wt

value: male

value: PBS (control for VSV infection)

value: splenocytes


title: Splenocytes_18h_post_PBS (A912_18)

description:
Splenocytes from PBS injected mice (control for VSV infection)
A912_18_22-10_Exp230_PBS1

value: adult


title: ArthrospiraPCC8005_Nitrogen_3

city: Mol

first: Rob

last: Van Houdt

address: Boeretang 200

department: Interdisciplinary Biosciences

country: Belgium

institute: SCK-CEN

description: Arthrospira sp. PCC8005 N-limiting conditions

hyb_protocol: 2µg Cy3-labeled cDNA was hybridized to the Arthrospira HX12 array for 18 hours at 42 ºC.

scan_protocol: The arrays were washed and scanned in a MS 200 scanner (Roche-Nimblegen).

data_processing: Raw data files were pre-processed using the “Oligo” package (version 1.24) in BioConductor (version 2.12 / R version 3.0.1).  Pre-processing included i) background correction based on the Robust Multichip Average (RMA) convolution model, ii) quantile normalization to make expression values from different arrays more comparable, and iii) summarization of multiple probe intensities for each probe set to one expression value per gene using the median polish approach. To evaluate changes in gene expression between N-replete and N-limiting conditions, the Bayesian adjusted t-statistics were used as implemented in the “LIMMA” package (version 2.18.0). P-values were corrected for multiple testing using the Benjamini and Hochberg’s method to control for false discoveries. Transcripts were considered significantly differentially expressed when the corresponding adjusted p-value was less than 0.05 and their absolute fold change (FC) was equal or larger than 1 for up-regulated genes, and equal or miner than -1 for the down-regulated ones.

organism: Limnospira indica PCC 8005

label_protocol: The RNA extracts (25 ng) were converted into a cDNA library using the Complete Whole Transcriptome Amplification WTA2 kit according to the instructions of the manufacturer (Sigma-Aldrich). The cDNA was labelled with Cy3 nonamer primers and Klenow polymerization

growth_protocol: The Arthrospira strain PCC 8005 (Pasteur collection, France) was maintained axenic in sterile 250 mL Erlenmeyer flasks on a rotary shaker (120 rpm). The bacterial cultures were incubated at 30°C under a continuous irradiance of ± 39 µmol photons m-2 s-1. The culture medium used was Zarrouck’s medium as modified by Cogne.

extract_protocol: RNA extraction was performed as described in Badri et al. (2015) [44]. Prior to RNA extraction, the biomass sample was mixed with 1 mL Trizol to prevent RNA degradation during defrosting (Invitrogen). Cells were lyzed by a temperature shock procedure (5 min. at 95 °C followed by 5 min. in ice bath). The released RNA was separated from the cell debris by centrifugation (10 000 g, 10 min., 4°C). RNA was purified using the Direct-zol RNA miniprep 2050 kit following the manufacturer's instructions (Zymo Research). DNA was removed using the Ambion TURBO DNA-free kit following the manufacturer's instructions (Life Technologies). The RNA was concentrated using Zymosearch RNA Clean & Concentrator-25 (Laborimpex, Brussels, Belgium). The quantity and purity of the RNA was assessed using a NanoDrop ND-1000 Spectrophotometer (Thermo Scientific). The quality and integrity of RNA was checked with the Bioanalyzer 2100 (Agilent Technologies) according to manufacturer's instructions. Absence of DNA was confirmed by PCR with universal 16S rRNA primers.

treatment_protocol: To evaluate the effect of N limitation on productivity, biomass composition and the transcriptome and proteome of Arthrospira strain PCC 8005, two treatments with three replicates were compared: a control treatment with non-limiting N concentration (100 mg L-1 N) and a N-limited treatment (20 mg L-1 N). Preliminary experiments had shown that N was depleted after 5 days in the N-limited treatments while it remains well above limiting levels up to 10 days in the control treatment (> 35 mg N L-1).

tag: nitrogen

value: limiting


title: meningioma sample Jed18_MN

description:
Jed18_MN
Gene expression data from brain tumor tissue.

source_name: meningioma, grade II, meningothelial histology with brain invasion

value: meningioma

value: II

value: left temporal

value: meningothelial with brain invasion

value: female


title: Splenocytes_24h_post_JetPEI (A912_17)

description:
Splenocytes from jetPEI injected mice (vehicle control for poly(I:C) and 3pRNA)
A912_17_wt-Vehicle4-Milz

source_name: Splenocytes, 24h after jetPEI injection

value: jetPEI (vehicle control for poly(I:C) and 3pRNA)

tag: cell type


title: ArthrospiraPCC8005_Nitrogen_1

source_name: Arthrospira sp. PCC8005 N-limiting conditions


title: pDC_Dex+CpG stimulation

city: He Fei

first: Yongfeng

last: Hong

address: Furong Road 678

country: China

institute: The Second Affiliated Hospital to Anhui Medical University

description:
pDC Dex+CpG stimulation
the purity of cell >95%

hyb_protocol: Standard Exiqon protocol (http://www.exiqon.com/SEEEMS/26.asp)

scan_protocol: Following the washing steps the slides were scanned using the Axon GenePix 4000B microarray scanner. Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing:
Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor.
http://www.exiqon.com/SEEEMS/26.asp
Expressed data were normalized using the Median normalization.

source_name: human primary pDC_Dex+CpG sti

label_protocol: After confirming an adequate RNA concentration using the NanoDrop 1000, the samples were labeled using the miRCURY Hy3 Power labeling kit and hybridized on the miRCURY LNA Array (v.16.0).

extract_protocol: Total RNA was harvested using TRIzol (Invitrogen) and an miRNeasy mini kit (QIAGEN) according to the manufacturer's instructions.

value: pool of 10 healthy PBMCs

value: Dex+CpG stimulation


title: Splenocytes_24h_post_JetPEI (A912_16)

description:
Splenocytes from jetPEI injected mice (vehicle control for poly(I:C) and 3pRNA)
A912_16_wt-Vehicle3-Milz

tag: genotype/variation


title: Control_rep1

description:
IECs isolated from a healthy non-infected 9 days old neonate mouse. Replicate 1
M4286

source_name: IECs; 9 days old; uninfected; replicate 1


title: ArthrospiraPCC8005_CTRL_3

description: Arthrospira sp. PCC8005 control condition

value: normal


title: pDC_Dex stimulation

description:
pDC Dex stimulation
the purity of cell >95%

source_name: human primary pDC_Dex sti

value: Dex stimulation


title: pDC_no-stimulation ctrl

description:
pDC no-stimulation
the purity of cell >95%

source_name: human primary pDC_ctrl

value: no-stimulation


title: Splenocytes_24h_post_JetPEI (A912_15)

description:
Splenocytes from jetPEI injected mice (vehicle control for poly(I:C) and 3pRNA)
A912_15_wt-Vehicle1-Milz

value: wt


title: EPEC_TTSSKO_rep2

description:
IECs isolated 8 days post-infection from neonate mouse orally infected at birth with ΔescV EPEC. Replicate 2
M4284

source_name: IECs; 8 days post-infection; EPEC ΔescV; replicate 2

value: EPEC ΔescV

value: intestinal epithelial cells (IECs)

value: 9 days old


title: EPEC_WT_rep3

description:
IECs isolated 8 days post-infection from neonate mouse orally infected at birth with WT EPEC. Replicate 3
M4287

source_name: IECs; 8 days post-infection; EPEC WT; replicate 3

value: EPEC WT


title: ArthrospiraPCC8005_CTRL_2

source_name: Arthrospira sp. PCC8005 control condition


title: EPEC_WT_rep2

description:
IECs isolated 8 days post-infection from neonate mouse orally infected at birth with WT EPEC. Replicate 2
M4283

source_name: IECs; 8 days post-infection; EPEC WT; replicate 2


title: Splenocytes_24h_post_3pRNAinJetPEI (A912_14)

description:
Splenocytes from 3pRNA treated mice
A912_14_wt-3PRNA4-Milz

source_name: Splenocytes, 24h after 3pRNA injection

value: adult

value: male

value: splenocytes


title: EPEC_TTSSKO_rep3

description:
IECs isolated 8 days post-infection from neonate mouse orally infected at birth with ΔescV EPEC. Replicate 3
M4288

source_name: IECs; 8 days post-infection; EPEC ΔescV; replicate 3


title: ArthrospiraPCC8005_Nitrogen_2

value: limiting


title: Splenocytes_24h_post_3pRNAinJetPEI (A912_13)

description:
Splenocytes from 3pRNA treated mice
A912_13_wt-3PRNA2-Milz


title: EPEC_TTSSKO_rep1

description:
IECs isolated 8 days post-infection from neonate mouse orally infected at birth with ΔescV EPEC. Replicate 1
M4280

source_name: IECs; 8 days post-infection; EPEC ΔescV; replicate 1


title: EPEC_WT_rep1

description:
IECs isolated 8 days post-infection from neonate mouse orally infected at birth with WT EPEC. Replicate 1
M4279

source_name: IECs; 8 days post-infection; EPEC WT; replicate 1


title: Splenocytes_24h_post_3pRNAinJetPEI (A912_12)

description:
Splenocytes from 3pRNA treated mice
A912_12_wt-3PRNA1-Milz


title: HeLa, CD95L, caspase-10 shRNA, biological rep 2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: RNA expression data from CD95L treated HeLa cells, inducible expressing caspase-10 shRNA

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of Hugene-2_0-st-type from Affymetrix. A Custom CDF Version 18 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: HeLa cells expressing caspase-10 shRNA, CD95L treated

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

growth_protocol: HeLa cells were cultured in DMEM high glucose + GlutaMAX (supplemented with 10 % FCS, 1 % Hepes, and 1 % sodium pyruvate) and maintained at 37 °C and 5 % carbon dioxide

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Quiagen) according to manufacturer´s recommendations

treatment_protocol: Respective shRNA expression was induced for 72 h by the addition of 0.5 µg/ml doxycycline. Cells were prestarved for 4 h in media containing 0.5 % FCS, pretreated for 1 h with 10 µM zVAD-fmk and stimulated for 3 h with 0.1 U/ml CD95L-Fc (self-made; 1 U/ml CD95L-Fc was determined to kill 50 % of parental HeLa cells in 16-20 h)

tag: cell line

value: HeLa

tag: shRNA


title: Splenocytes_24h_post_poly(I:C)inJetPEI (A912_11)

description:
Splenocytes from poly(I:C) treated mice
A912_11_wt-PIC4-Milz_2

source_name: Splenocytes, 24h after poly(I:C) injection

tag: strain


title: Splenocytes_24h_post_poly(I:C)inJetPEI (A912_09)

description:
Splenocytes from poly(I:C) treated mice
A912_09_wt-PIC1-Milz


title: HeLa, CD95L, caspase-10 shRNA, biological rep 3


title: Splenocytes_24h_post_poly(I:C)inJetPEI (A912_10)

description:
Splenocytes from poly(I:C) treated mice
A912_10_wt-PIC3-Milz


title: ArthrospiraPCC8005_CTRL_1

description: Arthrospira sp. PCC8005 control condition


title: Splenocytes_18h_post_PBS (A912b_08)

description:
Splenocytes from PBS injected mice (control for VSV infection)
A912b_08_4-1_B6_PBS_2

source_name: Splenocytes, 18h after PBS injection

value: PBS (control for VSV infection)


title: HeLa, CD95L, caspase-10 shRNA, biological rep 1


title: HeLa, untreated, caspase-10 shRNA, biological rep 3

description: RNA expression data from untreated HeLa cells, inducible expressing caspase-10 shRNA

source_name: HeLa cells expressing caspase-10 shRNA, untreated

value: ctrl


title: Splenocytes_18h_post_PBS (A912b_07)

description:
Splenocytes from PBS injected mice (control for VSV infection)
A912b_07_3-3_B6_PBS


title: HeLa, CD95L, control shRNA, biological rep 2

description: RNA expression data from CD95L treated HeLa cells, inducible expressing control shRNA

source_name: HeLa cells expressing control shRNA, CD95L treated

value: shCTRL


title: HeLa, untreated, caspase-10 shRNA, biological rep 2


title: Splenocytes_18h_post_VSVinPBS (A912b_02)

description:
Splenocytes from VSV injected mice
A912b_02_1-2_B6_VSV-M2_18h

source_name: Splenocytes, 18h after VSV infection

value: VSV


title: HeLa, CD95L, control shRNA, biological rep 1


title: HeLa, untreated, caspase-10 shRNA, biological rep 1


title: Splenocytes_18h_post_PBS (A912b_06)

description:
Splenocytes from PBS injected mice (control for VSV infection)
A912b_06_3-2_B6_PBS


title: Splenocytes_18h_post_VSVinPBS (A912b_04)

description:
Splenocytes from VSV injected mice
A912b_04_2-1_B6_VSV-M2_18h_2


title: embryo at E13.5, Tbx1KO, palatal shelves

city: Bunkyo-ku

first: Noriko

last: Funato

address: 1-5-45 Yushima

institute: Tokyo Medical and Dental University

hyb_protocol: Hybridization was done according to manufacturer's instructions, with Affymetrix® GeneChip® Hybridization Oven 640 and Affymetrix® GeneChip® Fluidics Station 450.

scan_protocol: Affymetrix® GeneChip® Scanner 3000 7G System

data_processing:
Affymetrix® GeneChip® Command Console® Software ver. 3.2, Affymetrix® Expression Console Softwere ver.1.3, RMA-Sketch (RMA-Gene-Default)
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187

source_name: Tbx1KO palatal shelves at E13.5

label_protocol: With 100 ng total RNA, RNA was labeled with Affymetrix GeneChip® WT PLUS Reagent Kit (Part# 902280) according to the manufacturer's instructions.

growth_protocol: Wild-type and Tbx1KO heads or palatal shelves were collected at E12.5 or E13.5.

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

treatment_protocol: Embryos of the appropriate stage were manually selected under the dissecting scope. Collected heads or palatal shleves were freezed with liquid nitrogen, and stored at -80 ºC  until use.

tag: strain background

value: mixed C57BL/6J x FVB/N

value: Tbx1 knockout (KO)

tag: tissue

value: palatal shelves


title: embryo at E12.5, Wild-type, head

source_name: wild-type heads at E12.5

value: wild-type

value: head


title: embryo at E13.5, Wild-type, palatal shelves

source_name: wild-type palatal shelves at E13.5


title: HeLa, untreated, control shRNA, biological rep 3

description: RNA expression data from untreated HeLa cells, inducible expressing control shRNA

source_name: HeLa cells expressing control shRNA, untreated


title: HeLa, untreated, control shRNA, biological rep 2


title: HeLa, CD95L, control shRNA, biological rep 3


title: HeLa, untreated, control shRNA, biological rep 1


title: NICD_rep2

status: Public on Apr 19 2016

city: Philadelphia

first: Yi-An

last: Ko

state: Pennsylvania

address: 415 curie blvd

department: Genetics & Gene Regulation

institute: UPeenn

description: inducible Notch intracellular domain in tubule epithelial cells rep2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Arra. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The data were scanned using a GeneChip scanner in accordance with the Affymetrix protocol.

data_processing: Data were normalized in GeneSpring software using the RMA16 summarization algorithm. Baseline is the median of all samples.

label: Biotin

source_name: whole kidney

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Mouse tissue total RNA was prepared from whole kidneys using TRIzol (Invitrogen). Gene expression studies were performed using the Affymetrix One Cycle labeling kit per the manufacturer’s instructions. For analysis of gene expression data after hybridization and scanning, raw data files were imported into Genespring Software. Database and expression levels were normalized using the RMA16 algorithm. This normalization method is a mathematical technique used to reduce discrepancies in hybridization patterns that might result from variables in target amplification, hybridization conditions, staining, or probe array lot. Normalizations standardize the data to facilitate identification of genuine gene expression difference.

value: kidney

tag: genotype

value: Pax8rtTA TREICNotch1


title: NICD_rep3

description: inducible Notch intracellular domain in tubule epithelial cells rep3


title: embryo at E12.5, Tbx1KO, head

source_name: Tbx1KO heads at E12.5

tag: developmental stage


title: Control_rep2

description: Littermate wild-type control2

value: normal


title: Control_rep3

description: Littermate wild-type control3


title: long-term nintedanib treated endothelial cells, biological rep5

city: Basel

first: Gerhard

last: Christofori

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description: Gene expression data from tumor blood vessel endothelial cells

hyb_protocol: The hybridization cocktail (200μl) containing fragmented biotin-labeled target DNA at a final concentration of 25ng/μl was transferred into Affymetrix GeneChip MoGene-1_0-st-v1 and incubated at 45°C on a rotator in a hybridization oven 640 (Affymetrix) for 17 h at 60 rpm. The arrays were washed and stained on a Fluidics Station 450 (Affymetrix) by using the Hybridization Wash and Stain Kit (Affymetrix, Cat# 900720) and the Fluidics Procedure FS450_0001.

scan_protocol: The GeneChips were processed with an Affymetrix GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: Arrays were normalized by RMA (oligo package from Bioconductor).

source_name: FAC-sorted blood vessel endothelial cells, long-term nintedanib treated

label_protocol: Target synthesis was performed using the following suite of kits provided by Nugen (San Carlos, USA): WT-Ovation Pico (Cat# 3300), WT-Ovation Exon (Cat# 2000) and FL-Ovation Biotin V2 (Cat# 4200).

growth_protocol: Py2T tumor cells were grown in the mammary fat pad of FVB/N female mice and were isolated by FAC-sorting together with endothelial cells

extract_protocol: Total RNA was isolated using TRIzol® LS reagent (Ambion®), RNA Easy Mini Kit (Qiagen) and Absolutely RNA Nanoprep Kit  (Stratagene)

treatment_protocol: Mice were either kept untreated or treated with nintedanib (50mg/kg body weight)

value: tumor blood vessel endothelial cells

tag: treatment

value: long-term (21 days) nintedanib treated


title: long-term nintedanib treated endothelial cells, biological rep3


title: long-term nintedanib treated endothelial cells, biological rep1


title: long-term nintedanib treated endothelial cells, biological rep2


title: long-term nintedanib treated endothelial cells, biological rep4


title: NICD_rep1

description: inducible Notch intracellular domain in tubule epithelial cells rep1


title: short-term nintedanib treated endothelial cells, biological rep3

source_name: FAC-sorted blood vessel endothelial cells, short-term nintedanib treated

value: short-term (7 days) nintedanib treated


title: Control_rep1

description: Littermate wild-type control1


title: untread control endothelial cells, biological rep1

source_name: FAC-sorted blood vessel endothelial cells, untreated

value: Untreated


title: untread control endothelial cells, biological rep3


title: long-term nintedanib treated tumor cells, biological rep4

description: Gene expression data from Py2T cells

source_name: FAC-sorted tumor cells, long-term nintedanib treated

value: Py2T cells (murine breast cancer cell line)


title: short-term nintedanib treated endothelial cells, biological rep1


title: long-term nintedanib treated tumor cells, biological rep1

description: Gene expression data from Py2T cells


title: short-term nintedanib treated tumor cells, biological rep2

description: Gene expression data from Py2T cells

source_name: FAC-sorted tumor cells, short-term nintedanib treated


title: short-term nintedanib treated tumor cells, biological rep4

description: Gene expression data from Py2T cells


title: short-term nintedanib treated endothelial cells, biological rep2


title: MxCre Jak2VF/+ EZH2-/- LT-HSC, biological rep2

city: Syracuse

first: Golam

last: Mohi

state: New York

address: 766 Irving Avenue

department: Pharmacology

institute: SUNY Upstate Medical University

hyb_protocol: 5 μg of cDNA was used for hybridization to the Affymetrix Mouse 2.0 ST Array. Hybridizations were performed in Affymetrix hybridization oven at 45°C for 18 hours.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip Scanner 7G Plus

data_processing: CEL files were analyzed with Partek Genomics Suite software, Version 6.6.

source_name: LT-HSC from MxCre Jak2VF/+ EZH2-/- mice, 12weeks after pI-pC

label_protocol: 10ng mRNA was used to synthesize cDNA utilizing the Ovation Pico WTA System V2 (NuGEN Technologies) and cDNA was Biotin-labeled with Encore Biotin Module (NuGEN Technologies)

growth_protocol: Control, MxCre Jak2VF/+ and MxCre Jak2VF/+ EZH2-/- mice were injected with five doses of pI-pC (300μg/dose) at 4 weeks after birth. BM cells were harvested at 12 weeks after pI-pC injections.

extract_protocol: Total RNA was extracted from LT-HSC with RNeasy Plus Mini Kit (Qiagen)

treatment_protocol: Harvested bone marrow cells were stained with antibodies against cell surface markers and LT-HSC (Lin-Sca-1+c-kit+CD34-CD135-) cells were sorted with FACS AriaII (BD)

value: MxCre Jak2VF/+ EZH2-/-

value: bone marrow

value: LT-HSC


title: short-term nintedanib treated tumor cells, biological rep3

description: Gene expression data from Py2T cells


title: long-term nintedanib treated tumor cells, biological rep3

description: Gene expression data from Py2T cells


title: short-term nintedanib treated tumor cells, biological rep1

description: Gene expression data from Py2T cells


title: long-term nintedanib treated tumor cells, biological rep5

description: Gene expression data from Py2T cells


title: long-term nintedanib treated tumor cells, biological rep2

description: Gene expression data from Py2T cells


title: MxCre Jak2VF/+ EZH2-/- LT-HSC, biological rep3


title: MxCre Jak2VF/+ EZH2-/- LT-HSC, biological rep1


title: MxCre Jak2VF/+ LT-HSC, biological rep2

source_name: LT-HSC from MxCre Jak2VF/+ mice, 12weeks after pI-pC

value: MxCre Jak2VF/+


title: MxCre Jak2VF/+ LT-HSC, biological rep3


title: untread control tumor cells, biological rep3

description: Gene expression data from Py2T cells

source_name: FAC-sorted tumor cells, untreated


title: untread control tumor cells, biological rep1

description: Gene expression data from Py2T cells


title: untread control tumor cells, biological rep2

description: Gene expression data from Py2T cells


title: S4 blood_clinical_L type

city: Trieste

first: Giuseppe

last: Legname

address: Via Bonomea, 265

department: Neuroscience

institute: Sissa

description: Gene expression data from blood of cattle intracranially inoculated with L-type BSE. The blood was collected during the clinical phase of the infection.

hyb_protocol: Labelled cRNA was hybridized on GeneChip® Bovine Genome Array containing over 23000 bovine transcripts. cRNA hybridization, washing and staining (Affymetrix fluidic station 450 DX) was performed according to GeneChip®Expression Wash, Stain and Scan protocol developed by Affimetrix®.

scan_protocol: Microarrays were scanned according to GeneChip®Expression Wash, Stain and Scan protocol developed by Affimetrix® and using the GeneChip® Scanner 3000 7G.

data_processing: Cell intensity values from the raw array data were computed using the Affymetrix GeneChip® Operating Software (GCOS). Microarray quality control and statistical analysis were performed in the software system R using the Bioconductor package OneChannelGUI. The LIMMA algorithm was used to compute a linear model fit. Data filtering and normalization was carried out using GC-Robust multi-array analysis (GCRMA) from imported Affymetrix image (.CEL) files. Differentially expressed genes were identified using the “limma package”, applying linear models and moderated t-statistics that implement empirical Bayes regularization of standard errors. The fold change in gene expression was calculated by 2^(M), where M is the log2-fold change (VALUE) after background correction and normalization. A minimum difference threshold of FC +/- 2 with a p value ≤ 0.05 was selected as gene differentially expressed

organism: Bos taurus

source_name: Aberdeen angus, blood, clinical, L type BSE-infection

label_protocol: 120 ng of each total RNA were used as template for the synthesis of biotin-labeled cRNA according to the standard one-cycle amplification and labeling protocol developed by Affymetrix (Santa Clara, CA). Before the hybridization the cRNA was fragmented by incubating the samples in Fragmentation Buffer for 35 minutes at 94°C.

growth_protocol: Cattle were housed in medium security accommodation with no contact to each other, with separate pen entrances and separate equipment. All housed cattle were given hay ad libitum and a daily concentrate ration free from meat and bone meal. Pens were cleaned out daily by husbandry staff.

extract_protocol: 500 µL of fresh blood were stabilized in 1.3 mL RNAlater® Solution and immediately frozen at -20 °C. RNA was isolated from blood according to the RiboPure™-Blood Kit manufacturer’s instructions (Ambion®). DNase I treatment (Ambion®) was included in the RNA extraction protocol to reduce DNA contamination. Purified RNA was eluted in 50 µL elution solution. The quality of total RNA was assessed using a bioanalyzer (Agilent 2100; Agilent Technologies) and RNA was quantified using a ND-1000 Nanodrop spectrophotometer.

treatment_protocol: Cattle were intracerebrally inoculated at 10-11 months of age with 1 ml of 10% brain homogenate of either L-type or H-type BSE . Control animals were not inoculated.

tag: breed

value: Aberdeen angus

tag: inoculation

value: L type BSE-infection

value: female

tag: age at inoculum

value: 10-11 months

value: whole blood


title: c.P6 blood_not inoculated_control

description: Gene expression data from blood of  not inoculated control cattle

source_name: Aberdeen angus, blood, not inoculated control

tag: gender

value: age-matched


title: MxCre Jak2VF/+ LT-HSC, biological rep1


title: c.9 blood_not inoculated_control


title: WT (control) LT-HSC, biological rep1

source_name: LT-HSC from WT mice, 12weeks after pI-pC

value: WT (control)


title: WT (control) LT-HSC, biological rep2


title: c.3 blood_not inoculated_control


title: WT (control) LT-HSC, biological rep3


title: c.2 blood_not inoculated_control


title: c.5 blood_not inoculated_control


title: Airway stem cell, P2 replicate 2

city: Boston

first: Hongmei

last: Mou

state: MA

address: 55 Fruit Street, Jackson 1402

department: The Mucosal Immunology & Biology Research Center

institute: Massachusetts General Hospital

description: replicate 2

hyb_protocol: RNA is hybridized on Illumina Human HT-12 (Translational Genomics Core, MGH), standard protocol

scan_protocol: Data is scaned in Translational Genomics Core, MGH using Standard Illumina scanning protocol

data_processing: quantile normalization

source_name: bronchus

label_protocol: Standard protocol

growth_protocol: the cells are cultured in SAGM + 5-10 micro-molar ROCKi, 1 micro-molar A-83-01, 1 micro-molar DMH-1, 1 micro-molar CHIR99021 and expanded to P2, P8 and P14 (1:10 splitting ratio)

extract_protocol: Total RNA is isolated from human airway stem cells from early to late passages using TRIzol (Invitrogen) and the miRNeasy mini kit (Qiagen) according to manufacturer’s instructions.

value: airway stem cells

tag: passage


title: Airway stem cell, P14 replicate 2

description: replicate 2

source_name: Bronchus


title: c.S6 blood_not inoculated_control


title: c.P3 blood_not inoculated_control


title: Airway stem cell, P8 replicate 3

description: replicate 3


title: Airway stem cell, P14 replicate 1

description: replicate 1


title: EP9 blood_preclinical_L type

description: Gene expression data from blood of cattle intracranially inoculated with L-type BSE. The blood was collected during the preclinical phase of the infection.

source_name: Aberdeen angus, blood, preclinical, L type BSE-infection


title: untread control endothelial cells, biological rep2

value: tumor blood vessel endothelial cells


title: Airway stem cell, P8 replicate 2

description: replicate 2


title: S10 blood_clinical_L type


title: Airway stem cell, P2 replicate 3

description: replicate 3


title: Airway stem cell, P8 replicate 1

description: replicate 1


title: Airway stem cell, P14 replicate 3

description: replicate 3


title: P10 blood_preclinical_L type


title: Airway stem cell, P2 replicate 1

description: replicate 1


title: S3 blood_clinical_L type


title: P5 blood_preclinical_L type


title: P4 blood_preclinical_L type


title: S2 blood_clinical_H type

description: Gene expression data from blood of cattle intracranially inoculated with H-type BSE. The blood was collected during the clinical phase of the infection.

source_name: Aberdeen angus, blood, clinical, H type BSE-infection

value: H type BSE-infection


title: S1 blood_clinical_H type


title: S7 blood_clinical_H type


title: S8 blood_clinical_H type


title: P1 blood_preclinical_H type

description: Gene expression data from blood of cattle intracranially inoculated with H-type BSE. The blood was collected during the preclinical phase of the infection.

source_name: Aberdeen angus, blood, preclinical, H type BSE-infection


title: P2 blood_preclinical_H type


title: siERG T1h Rep4

city: Liège

first: Franck

last: Dequiedt

address: 1 Avenue de l'hôpital

department: GIGA-Research

institute: University of Liège

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised quantile normalisation in R

source_name: HeLa cells

label_protocol: Not provided

growth_protocol: HeLa cells were purchased from ATCC and maintained in 10% FBS-complemented DMEM medium in standard cell culture conditions (37°C, humidified 5% CO2 atmopshere)

extract_protocol: Total RNA was extracted from cell pellets using a NucleoSpin RNA kit (Macherey-Nagel) using DNAse I treatment and according the manufacturer's recommendations

treatment_protocol: cells were treated with Actinomycin D (5 µM) for 0, 0.5, 1, 2 or 4 hours before RNA was extracted

value: HeLa


title: siERG T2h Rep4

description: replicate 4


title: P8 blood_preclinical_H type


title: siERG T4h Rep4

description: replicate 4


title: siCTL T2h Rep4

description: replicate 4


title: siERG T2h Rep3

description: replicate 3


title: siERG T0.5h Rep4

description: replicate 4


title: siERG T0.5h Rep3

description: replicate 3


title: siERG T4h Rep3

description: replicate 3


title: Me10538 (4831258058_J)

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

data_processing: The data were processed and normalized using quantile normalization with BeadStudio software

source_name: Human Melanoma

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

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.

tag: agent

value: untreated


title: siERG T0h Rep4

description: replicate 4


title: siCTL T0.5h Rep4

description: replicate 4


title: P7 blood_preclinical_H type


title: Me10538 (4831258058_K)


title: siCTL T0h Rep4

description: replicate 4


title: siCTL T1h Rep4

description: replicate 4


title: Me10538 (4831258058_L)


title: Me2/59 (4831258058_I)

tag: clone


title: siERG T1h Rep3

description: replicate 3


title: siCTL T4h Rep4

description: replicate 4


title: siERG T0h Rep3

description: replicate 3


title: Me2/59 (4831258058_H)


title: Zfp36l3 heterozygous placenta replicate 3 (paternal)

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
gene expression from heterozygous placenta paternal transmission
L3PHet11

hyb_protocol: Hybridization was done according to the manufacturer's instructions.

scan_protocol: Gene expression was quantified on the nCounter Digital AnalyzerTM.

data_processing: Raw data was normalized using the Nanostring nCounter software.

label_protocol: Label was done according to the manufacturer's instructions.

extract_protocol: RNA was isolated from cells or tissues using the GE Healthcare RNAmini spin kit (guanidine thiocyanate extraction procedure).

value: Zfp36l3 heterozygous

tag: cell type

value: embryonic day 15.5 placenta


title: Zfp36l3 heterozygous placenta replicate 2 (paternal)

description:
gene expression from heterozygous placenta paternal transmission
L3PHet9


title: Zfp36l3 heterozygous placenta replicate 2 (maternal)

description:
gene expression from heterozygous placenta maternal transmission
L3PHet2


title: Zfp36l3 heterozygous placenta replicate 1 (paternal)

description:
gene expression from heterozygous placenta paternal transmission
L3PHet8


title: siCTL T2h Rep3

description: replicate 3


title: Me2/14 (4831258058_F)


title: Zfp36l3 heterozygous placenta replicate 3 (maternal)

description:
gene expression from heterozygous placenta maternal transmission
L3PHet4


title: Me2/14 (4831258058_D)


title: Me2/59 (4831258058_G)


title: siCTL T0.5h Rep3

description: replicate 3


title: Me2/14 (4831258058_E)


title: siERG T4h Rep2

description: replicate 2


title: Me/2/17 (4831258058_C)


title: Me/2/17 (4831258058_A)


title: siCTL T1h Rep3

description: replicate 3


title: siERG T2h Rep2

description: replicate 2


title: siERG T0h Rep2

description: replicate 2


title: Me2/4 (4831258010_J)


title: siCTL T4h Rep2

description: replicate 2


title: siERG T1h Rep2

description: replicate 2


title: Me2/4 (4831258010_L)


title: siERG T0.5h Rep2

description: replicate 2


title: siCTL T4h Rep3

description: replicate 3


title: siCTL T0h Rep3

description: replicate 3


title: Me/2/17 (4831258058_B)


title: ΔIP5_OD1.0profile

city: Bunkyo-Ku

first: tomomi

last: hishinuma

institute: juntendo university

hyb_protocol: Labeled samples were hybridized onto the microarray at 50°C for 16-20 hr. After hybridization, the arrays were washed in the following buffers, and dry by spin slide. 2X SSC/0.05% SDS, for 15 min 0.2X SSC/0.05% SDS, for 15 min 0.5X SSC, for 3 min 0.2X SSC, for 3 min

scan_protocol: Nimblegen MS200

data_processing:
Software: NimbleScan
Algorithm: Robust Multi-Array Analysis (Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Biostatistics. 2003 Apr;4(2):249-64 (PMID 12925520)).
Normalize: global normalization

organism: Staphylococcus aureus

label_protocol: SuperScript Indirect cDNA Labeling System (Invitrogen Life Technologies, Carlsbad, California).

extract_protocol:
See reference:
Neoh HM, et al.: Mutated response regulator graR is responsible for phenotypic conversion of Staphylococcus aureus from heterogeneous vancomycin-intermediate resistance to vancomycin-intermediate resistance. Antimicrob Agents Chemother. 2008 Jan;52(1):45-53.

tag: another strain name

tag: background strain

value: deltaIP

value: vraS, msrR, graR mutation (replacement), rpoB mutant (selection with 1 mg/liter rifampin), fdh2 mutation (replacement)

tag: growth

value: up to OD1.0

source_name: ΔIP

value: wild


title: Me2/4 (4831258010_K)


title: Zfp36l3 heterozygous placenta replicate 1 (maternal)

description:
gene expression from heterozygous placenta maternal transmission
L3PHet1

tag: strain


title: Zfp36l3 knockout placenta replicate 5

description:
gene expression from knockout placenta
L3PKO5

source_name: knockout placenta

value: Zfp36l3 knockout


title: Zfp36l3 knockout placenta replicate 3

description:
gene expression from knockout placenta
L3PKO3


title: Zfp36l3 knockout placenta replicate 4

description:
gene expression from knockout placenta
L3PKO4


title: Zfp36l3 knockout placenta replicate 2

description:
gene expression from knockout placenta
L3PKO2


title: ΔIP4_OD1.0profile

value: vraS, msrR, graR mutation (replacement), rpoB mutant (selection with 1 mg/liter rifampin)


title: ΔIP3_OD1.0profile

value: vraS, msrR, graR mutation (replacement)


title: ΔIP2_OD1.0profile

value: vraS, msrR mutation (replacement)


title: siCTL T2h Rep2

description: replicate 2

tag: cell line


title: Zfp36l3 knockout placenta replicate 1

description:
gene expression from knockout placenta
L3PKO1


title: siCTL T1h Rep2

description: replicate 2


title: ΔIP1_OD1.0profile

value: vraS mutation (replacement)


title: Me2/33 (4831258010_I)


title: siCTL T0.5h Rep2

description: replicate 2


title: Zfp36l3 wildtype placenta replicate 5

description:
gene expression from wildtype placenta
L3PWT5

source_name: wildtype placenta

value: Zfp36l3 wild type


title: Me2/33 (4831258010_G)


title: S9 blood_clinical_L type

description: Gene expression data from blood of cattle intracranially inoculated with L-type BSE. The blood was collected during the clinical phase of the infection.

value: Aberdeen angus

value: L type BSE-infection

value: female

value: 10-11 months

tag: tissue

value: whole blood


title: siCTL T0h Rep2

description: replicate 2

value: HeLa


title: Mu50_VCM 10mg/L_OD2.0

tag: genotype (compare to deltaip）

value: vraS, msrR, graR, rpoB, fdh2 mutation

value: up to OD2.0

value: 10min with vancomycin 10mg/L


title: Zfp36l3 wildtype placenta replicate 4

description:
gene expression from wildtype placenta
L3PWT4

tag: genotype

value: embryonic day 15.5 placenta


title: ΔIP5_VCM 10mg/L_OD2.0

value: deltaIP

value: vraS, msrR, graR mutation (replacement), rpoB mutant (selection with 1 mg/liter rifampin), fdh2 mutation (replacement)

tag: treatment


title: Me2/33 (4831258010_H)

value: untreated


title: ΔIP4_VCM 10mg/L_OD2.0

value: vraS, msrR, graR mutation (replacement), rpoB mutant (selection with 1 mg/liter rifampin)


title: ΔIP3_VCM 10mg/L_OD2.0

value: vraS, msrR, graR mutation (replacement)


title: ME665/2 (4831258010_F)


title: siERG T4h Rep1

description: replicate 1


title: ME665/2 (4831258010_E)


title: siERG T2h Rep1

description: replicate 1


title: ME665/2 (4831258010_D)


title: siERG T0.5h Rep1

description: replicate 1


title: Me2/21 (4831258010_C)


title: Zfp36l3 wildtype placenta replicate 1

description:
gene expression from wildtype placenta
L3PWT1


title: siERG T1h Rep1

description: replicate 1


title: Zfp36l3 wildtype placenta replicate 3

description:
gene expression from wildtype placenta
L3PWT3


title: Zfp36l3 knockout trophoblast stem cell differentiated 4 hour Actinomycin D replicate 4

description:
gene expression from knockout trophoblast stem cell differentiated 4 hour Actinomycin D
L3TSKO32

value: Zfp36l3 knockout

value: differentiated trophoblast stem cells


title: Zfp36l3 knockout trophoblast stem cell differentiated 4 hour Actinomycin D replicate 3

description:
gene expression from knockout trophoblast stem cell differentiated 4 hour Actinomycin D
L3TSKO31


title: ΔIP2_VCM 10mg/L_OD2.0

value: vraS, msrR mutation (replacement)


title: Zfp36l3 wildtype placenta replicate 2

description:
gene expression from wildtype placenta
L3PWT2

value: Zfp36l3 wild type


title: ΔIP1_VCM 10mg/L_OD2.0

value: vraS mutation (replacement)


title: siERG T0h Rep1

description: replicate 1


title: ΔIP_VCM 10mg/L_OD2.0


title: Zfp36l3 knockout trophoblast stem cell differentiated 4 hour Actinomycin D replicate 1

description:
gene expression from knockout trophoblast stem cell differentiated 4 hour Actinomycin D
L3TSKO29


title: Mu50_VCM 10mg/L_OD1.0

value: up to OD1.0


title: siCTL T4h Rep1

description: replicate 1


title: siCTL T1h Rep1

description: replicate 1


title: ΔIP5_VCM 10mg/L_OD1.0


title: siCTL T0.5h Rep1

description: replicate 1


title: ΔIP4_VCM 10mg/L_OD1.0


title: Me2/21 (4831258010_B)


title: Me26635 + fotemustine 300μM 6h (4775495006_J)

value: fotemustine

tag: agent concentration

tag: time exposure


title: Me26635 + fotemustine 300μM 6h (4775495006_L)


title: ΔIP3_VCM 10mg/L_OD1.0


title: Me2/21 (4831258010_A)


title: Me26635 6h (4775495006_I)

value: control


title: Zfp36l3 knockout trophoblast stem cell differentiated 2 hour Actinomycin D replicate 4

description:
gene expression from knockout trophoblast stem cell differentiated 2 hour Actinomycin D
L3TSKO28


title: Me26635 6h (4775495006_G)


title: siCTL T0h Rep1

description: replicate 1

value: HeLa


title: Me26635 6h (4775495006_H)


title: Zfp36l3 knockout trophoblast stem cell differentiated 2 hour Actinomycin D replicate 3

description:
gene expression from knockout trophoblast stem cell differentiated 2 hour Actinomycin D
L3TSKO27


title: Me26635 + fotemustine 300μM 6h (4775495006_K)


title: Zfp36l3 knockout trophoblast stem cell differentiated 4 hour Actinomycin D replicate 2

description:
gene expression from knockout trophoblast stem cell differentiated 4 hour Actinomycin D
L3TSKO30


title: Zfp36l3 knockout trophoblast stem cell differentiated 2 hour Actinomycin D replicate 2

description:
gene expression from knockout trophoblast stem cell differentiated 2 hour Actinomycin D
L3TSKO26


title: ΔIP2_VCM 10mg/L_OD1.0


title: Zfp36l3 knockout trophoblast stem cell differentiated 2 hour Actinomycin D replicate 1

description:
gene expression from knockout trophoblast stem cell differentiated 2 hour Actinomycin D
L3TSKO25


title: 1928z-41BBL CD8 replicate 3

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: gene expression data from virally infected CD4 and CD8 cells purified from the same donor

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX human HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. Quantile normalization and background correction are performed.

source_name: CD8 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

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

value: CD8 T cells expressing 1828z-4-1BBL


title: Zfp36l3 knockout trophoblast stem cell differentiated 0 hour Actinomycin D replicate 4

description:
gene expression from knockout trophoblast stem cell differentiated 0 hour Actinomycin D
L3TSKO24


title: ΔIP1_VCM 10mg/L_OD1.0

value: 10min with vancomycin 10mg/L


title: Zfp36l3 knockout trophoblast stem cell differentiated 0 hour Actinomycin D replicate 3

description:
gene expression from knockout trophoblast stem cell differentiated 0 hour Actinomycin D
L3TSKO23


title: Zfp36l3 knockout trophoblast stem cell differentiated 0 hour Actinomycin D replicate 2

description:
gene expression from knockout trophoblast stem cell differentiated 0 hour Actinomycin D
L3TSKO22


title: Zfp36l3 knockout trophoblast stem cell differentiated 0 hour Actinomycin D replicate 1

description:
gene expression from knockout trophoblast stem cell differentiated 0 hour Actinomycin D
L3TSKO21


title: ΔIP_VCM 10mg/L_OD1.0


title: Zfp36l3 knockout trophoblast stem cell undifferentiated replicate 3

description:
gene expression from knockout trophoblast stem cell undifferentiated
L3TSKO19

value: undifferentiated trophoblast stem cells


title: Zfp36l3 knockout trophoblast stem cell undifferentiated replicate 4

description:
gene expression from knockout trophoblast stem cell undifferentiated
L3TSKO20


title: Me4405 + fotemustine 300μM 6h (4775495006_E)


title: Me4405 + fotemustine 300μM 6h (4775495006_F)


title: Me4405 6h (4775495006_C)


title: 1928z-41BBL CD8 replicate 1


title: siCTL T2h Rep1

description: replicate 1


title: Zfp36l3 knockout trophoblast stem cell undifferentiated replicate 2

description:
gene expression from knockout trophoblast stem cell undifferentiated
L3TSKO18


title: 19z1-41BBL CD8 replicate 2

value: CD8 T cells expressing 19z1-4-1BBL


title: 1928z CD8 replicate 3

value: CD8 T cells expressing 1928z


title: Me4405 + fotemustine 300μM 6h (4775495006_D)


title: 19z1-41BBL CD8 replicate 3


title: Me4405 6h (4775495006_B)


title: 19z1 CD8 replicate 3

value: CD8 T cells expressing 19z1


title: Zfp36l3 knockout trophoblast stem cell undifferentiated replicate 1

description:
gene expression from knockout trophoblast stem cell undifferentiated
L3TSKO17


title: 19z1 CD8 replicate 2


title: Zfp36l3 wild type trophoblast stem cell differentiated 4 hour Actinomycin D replicate 4

description:
gene expression from wild type trophoblast stem cell differentiated 4 hour Actinomycin D
L3TSWT16


title: 19z1-41BBL CD8 replicate 1


title: Me4405 6h (4775495006_A)


title: 1928z CD8 replicate 1


title: 1928z CD8 replicate 2


title: Zfp36l3 wild type trophoblast stem cell differentiated 4 hour Actinomycin D replicate 3

description:
gene expression from wild type trophoblast stem cell differentiated 4 hour Actinomycin D
L3TSWT15


title: 19z1 CD8 replicate 1


title: Zfp36l3 wild type trophoblast stem cell differentiated 4 hour Actinomycin D replicate 2

description:
gene expression from wild type trophoblast stem cell differentiated 4 hour Actinomycin D
L3TSWT14


title: 1928z-41BBL CD8 replicate 2


title: Zfp36l3 wild type trophoblast stem cell differentiated 2 hour Actinomycin D replicate 4

description:
gene expression from wild type trophoblast stem cell differentiated 2 hour Actinomycin D
L3TSWT12


title: Zfp36l3 wild type trophoblast stem cell differentiated 4 hour Actinomycin D replicate 1

description:
gene expression from wild type trophoblast stem cell differentiated 4 hour Actinomycin D
L3TSWT13


title: 1928z-41BBL CD4 replicate 1

source_name: CD4 cells

value: CD4 T cells expressing 1928z-4-1BBL


title: 1928z-41BBL CD4 replicate 2


title: 1928z-41BBL CD4 replicate 3


title: 1928z CD4 replicate 3

value: CD4 T cells expressing 1928z-1BBL


title: Zfp36l3 wild type trophoblast stem cell differentiated 2 hour Actinomycin D replicate 2

description:
gene expression from wild type trophoblast stem cell differentiated 2 hour Actinomycin D
L3TSWT10


title: 1928z CD4 replicate 1


title: Zfp36l3 wild type trophoblast stem cell differentiated 2 hour Actinomycin D replicate 1

description:
gene expression from wild type trophoblast stem cell differentiated 2 hour Actinomycin D
L3TSWT9


title: Zfp36l3 wild type trophoblast stem cell differentiated 0 hour Actinomycin D replicate 4

description:
gene expression from wild type trophoblast stem cell differentiated 0 hour Actinomycin D
L3TSWT8


title: Zfp36l3 wild type trophoblast stem cell differentiated 2 hour Actinomycin D replicate 3

description:
gene expression from wild type trophoblast stem cell differentiated 2 hour Actinomycin D
L3TSWT11


title: Zfp36l3 wild type trophoblast stem cell differentiated 0 hour Actinomycin D replicate 3

description:
gene expression from wild type trophoblast stem cell differentiated 0 hour Actinomycin D
L3TSWT7


title: heterozygous KO [14267011836-UH6]

city: Honolulu

first: Charles

middle: J

last: Rosser

state: HI

address: 701 Ilalo Street

department: Clinical and Translational Research Program

institute: University of Hawaii Cancer Center

data_processing: Pre-processing and normalization was done using the Partek microarray data analysis software (http://www.partek.com/). Partek pre-processes raw intensity files from microarray experiment using GCRMA’s background subtraction and uses quantile normalization as the normalization technique.

source_name: heterozygous KO_mammary tumor

growth_protocol: All animals were maintained under controlled conditions of humidity (50±10%), light (12/12 hour light/dark cycle) and temperature (23 ± 2˚C) with free access to feeds and water.

extract_protocol: RNA was extracted using Rneasy Plus kit (QIAGEN) in accordance with prescribed protocol provided with the kit.

treatment_protocol: MMTV-neu Tg mice and SPhK1 KO mice were intercrosserd and MMTV-neu Tg mice with homozygous KO, heterozygous KO and wildtype SphK1 were generated.

tag: strain background

value: FVB

tag: genotype/variation

value: MMTV-neu Tg mice with heterozygous KO

value: female

tag: age

value: 35 weeks

value: Mammary tumor


title: WT, suc, biological rep3

city: East Lansing

first: John

last: Ohlrogge

state: MI

address: 612 Wilson Rd

department: Plant Biology

institute: Michigan State University

description: Gene expression from WT seedling on medium with sucrose

hyb_protocol: Hybridization was performed as described by Affymetrix (http://www.affymetrix.com).

scan_protocol: The Scanning of the ATH1 GeneChip arrays was performed as described by Affymetrix (http://www.affymetrix.com).

data_processing: Gene expression data were imported into Expression Console software and Microarray Suite 5.0, with a TGT value of 100 used to generate normalized signal values. For normalization, data from each expression array were scaled so that the overall fluorescence intensity across each chip was equivalent and comparison between arrays was more meaningful. The normalized expression data obtained by MAS 5.0 was downloaded into GeneSpring GX (Agilent Technologies, Palo Alto, CA, USA) and processed following the guided workflow to identify differentially expressed genes between WT and the treated samples. The remaining filtered probe sets were normalized following the standard workflow. After summarizing intensity values across replicate probes, a logarithm to base 2, thresholding to 5, per chip normalization to the 50th percentile, and baseline transformation for each probe set across the 12 samples were sequentially performed on the data. These unmatched probe sets were eliminated before statistical analysis of the expression data. Within the samples with the same condition, a further normalization was performed to standardize the expression data to the mean expression value for each probe set across all three replicates. The quality of microarray data from 12 samples was tested by principle component analysis (PCA).

organism: Arabidopsis thaliana

source_name: Eghit-day-old seedling

label_protocol: The methods for preparation of cRNA from mRNA were performed as described by Affymetrix (http://www.affymetrix.com).

growth_protocol: The ESTpro:FUS3-strong line 2-8 and WT were germinated on 1/2MS medium with or without 1.5% sucrose. Triplicate eight-day-old seedlings were used for RNA extraction.

extract_protocol: Total RNA was extracted by using RNeasy Mini Kit (Qiagen)  according to the manufacturer's instructions.

treatment_protocol: The medium used to germinate line 2-8 was supplemented with 5 µM estradiol as an inducer for FUS3 expression.

tag: genotye/variation

value: WT

value: sucrose


title: WT, no suc, biological rep3

description: Gene expression from WT seedling on medium without sucrose


title: wild-type [14267011838-UH9]

source_name: wild-type_mammary tumor

value: MMTV-neu Tg mice with wildtype SphK1

tag: gender


title: 19z1-41BBL CD4 replicate 3

description: gene expression data from virally infected CD4 and CD8 cells purified from the same donor

tag: cell type

value: CD4 T cells expressing 19z1-4-1BBL


title: control [14267011835-UH12]

source_name: control_mammary tumor


title: Zfp36l3 wild type trophoblast stem cell differentiated 0 hour Actinomycin D replicate 1

description:
gene expression from wild type trophoblast stem cell differentiated 0 hour Actinomycin D
L3TSWT5

value: Zfp36l3 wild type

value: differentiated trophoblast stem cells


title: homozygous KO [14267011837-UH3]

source_name: homozygous KO_mammary tumor

value: MMTV-neu Tg mice with homozygous KO


title: 1928z CD4 replicate 2


title: Zfp36l3 wild type trophoblast stem cell differentiated 0 hour Actinomycin D replicate 2

description:
gene expression from wild type trophoblast stem cell differentiated 0 hour Actinomycin D
L3TSWT6


title: Zfp36l3 wild type trophoblast stem cell undifferentiated replicate 4

description:
gene expression from wild type trophoblast stem cell undifferentiated
L3TSWT4

value: undifferentiated trophoblast stem cells


title: heterozygous KO [14267011833-UH5]


title: Zfp36l3 wild type trophoblast stem cell undifferentiated replicate 1

description:
gene expression from wild type trophoblast stem cell undifferentiated
L3TSWT1


title: Zfp36l3 wild type trophoblast stem cell undifferentiated replicate 3

description:
gene expression from wild type trophoblast stem cell undifferentiated
L3TSWT3


title: Zfp36l3 wild type trophoblast stem cell undifferentiated replicate 2

description:
gene expression from wild type trophoblast stem cell undifferentiated
L3TSWT2


title: homozygous KO [14267011834-UH2]


title: WT, suc, biological rep2


title: WT, no suc, biological rep1


title: WT, suc, biological rep1


title: 19z1-41BBL CD4 replicate 1


title: WT, no suc, biological rep2


title: 19z1 CD4 replicate 3

value: CD4 T cells expressing 19z1


title: 19z1-41BBL CD4 replicate 2


title: heterozygous KO [14267011832-UH4]


title: FUS3, suc, biological rep3

description: Gene expression from FUS3 seedling on medium with sucrose

value: Ectopically expressing FUS3


title: 19z1 CD4 replicate 1


title: FUS3, suc, biological rep2


title: control [14267011831-UH11]


title: FUS3, suc, biological rep1


title: wild-type [14267011830-UH8]


title: homozygous KO [14267011829-UH1]


title: FUS3, no suc, biological rep2

description: Gene expression from FUS3 seedling on medium without sucrose


title: 19z1 CD4 replicate 2


title: Fly_NoListeria_AmpicillinTreatment_216hours_rep2

status: Public on Apr 18 2016

city: Stanford

first: Alexander

last: Louie

state: CA

address: 299 Campus Dr

department: Microbiology and Immunology

institute: Stanford University

hyb_protocol: Samples were hydrized using the Agilent Gene Expression Hybridization Kit (5188-5242) following the manufacture's protocol.

scan_protocol: Samples were scanned using a Agilent Technologies Scanner G2505C and feature intensities were determined by Agilent's Feature Extraction software(v10.7.3.1) using grid 018972_D_F_20110615.

data_processing: We used Genespring v12.1 (Agilent) for normalization and baseline transformed the data. Microarrays were normalized to the 75th percentile. The median expression level on 0 dpi was set as the baseline.

organism: Drosophila melanogaster

source_name: Whole fly, Uninfected, Ampicillin treatment, 216 hours post infection

label_protocol: Samples were labeled using the Quick Amp Labeling Kit, One-Color Agilent (5190-0442) following the manufacture's protocol.

growth_protocol: Flies were maintained on standard dextrose media at 25°C with 65% humidity and 12 hour light/dark cycles. Shortly after eclosion, adult flies were collected into bottles containing dextrose fly media. At least 24hours post eclosion adult flies were anesthetized with carbon dioxide, males were sorted into groups of 20 and placed into vials containing standard dextrose fly media. Experiments were performed on male flies 5-7 days post eclosion.

extract_protocol: For each sample 20 male flies were anesthetized with carbon dioxide, collected into TRIzol, homogenized and stored at -80°C. RNA preparation was preformed using a standard TRIzol RNA protocol.

treatment_protocol: At 5 to 7 days post eclosion male flies were anesthetized with carbon dioxide and were injected with 50nl of Listeria (OD600 = 0.001, or approximately 100CFUs) or left manipulated. Following injection, flies were placed in vials containing dextrose fly media and incubated at 29°C. Samples were separated into three groups: Moribund, recovering and uninfected control. Moribund flies were infected and samples were collected on the following days post infection (dpi): 0.25, 1, 2, 2.25, 3, 4, 5 and 6. Recovering flies were infected and flipped onto dextrose fly media containing 1 mg/ml ampicillin 2 days post infection. Recovering samples were collected on the following dpi: 2.25, 3, 4, 5, 6, 7, 9, and 16. Uninfected control flies were not infected but were flipped onto dextrose fly media containing 1mg/ml ampicillin 2 dpi. Uninfected control samples were collected on the following dpi: 2.25, 3, and 9.

tag: listeria infection status

value: Uninfected

tag: ampicillin treatment

value: Ampicillin treatment

value: whole fly

value: male

value: adult 5-7 day post-eclosion

value: w1118 (Bloomington Stock number 6326)


title: Fly_NoListeria_AmpicillinTreatment_216hours_rep1


title: control [14267011828-UH10]

value: FVB

value: female

value: 35 weeks

value: Mammary tumor


title: FUS3, no suc, biological rep1


title: FUS3, no suc, biological rep3


title: Fly_NoListeria_AmpicillinTreatment_216hours_rep3


title: Fly_NoListeria_AmpicillinTreatment_54hours_rep2

source_name: Whole fly, Uninfected, Ampicillin treatment, 54 hours post infection


title: Fly_NoListeria_AmpicillinTreatment_72hours_rep3

source_name: Whole fly, Uninfected, Ampicillin treatment, 72 hours post infection


title: Fly_NoListeria_AmpicillinTreatment_54hours_rep1


title: Fly_NoListeria_AmpicillinTreatment_72hours_rep2


title: Fly_Listeria_AmpicillinTreatment_384hours_rep3

source_name: Whole fly, Listeria infected, Ampicillin treatment, 384 hours post infection

value: Listeria infected


title: Fly_NoListeria_AmpicillinTreatment_0hours_rep3

source_name: Whole fly, Uninfected, No treatment, 0 hours post infection

value: No treatment


title: wild-type [14267011827-UH7]

value: MMTV-neu Tg mice with wildtype SphK1


title: Fly_NoListeria_AmpicillinTreatment_54hours_rep3


title: Fly_NoListeria_AmpicillinTreatment_72hours_rep1


title: Fly_Listeria_AmpicillinTreatment_216hours_rep3

source_name: Whole fly, Listeria infected, Ampicillin treatment, 216 hours post infection


title: Fly_NoListeria_AmpicillinTreatment_0hours_rep2


title: Fly_Listeria_AmpicillinTreatment_168hours_rep3

source_name: Whole fly, Listeria infected, Ampicillin treatment, 168 hours post infection


title: Fly_Listeria_AmpicillinTreatment_384hours_rep1


title: Fly_Listeria_AmpicillinTreatment_384hours_rep2


title: Fly_Listeria_AmpicillinTreatment_120hours_rep3

source_name: Whole fly, Listeria infected, Ampicillin treatment, 120 hours post infection


title: Fly_Listeria_AmpicillinTreatment_144hours_rep3

source_name: Whole fly, Listeria infected, Ampicillin treatment, 144 hours post infection


title: Fly_Listeria_AmpicillinTreatment_168hours_rep1


title: Fly_Listeria_AmpicillinTreatment_216hours_rep2


title: Fly_Listeria_AmpicillinTreatment_168hours_rep2


title: Fly_Listeria_AmpicillinTreatment_144hours_rep1


title: Fly_Listeria_AmpicillinTreatment_120hours_rep2


title: Fly_NoListeria_AmpicillinTreatment_0hours_rep1


title: Fly_Listeria_AmpicillinTreatment_96hours_rep3

source_name: Whole fly, Listeria infected, Ampicillin treatment, 96 hours post infection


title: Fly_Listeria_AmpicillinTreatment_120hours_rep1


title: Fly_Listeria_AmpicillinTreatment_96hours_rep1


title: Fly_Listeria_AmpicillinTreatment_96hours_rep2


title: Fly_Listeria_AmpicillinTreatment_72hours_rep1

source_name: Whole fly, Listeria infected, Ampicillin treatment, 72 hours post infection


title: Fly_Listeria_AmpicillinTreatment_54hours_rep3

source_name: Whole fly, Listeria infected, Ampicillin treatment, 54 hours post infection


title: Fly_Listeria_NoTreatment_96hours_rep3

source_name: Whole fly, Listeria infected, No treatment, 96 hours post infection


title: Fly_Listeria_AmpicillinTreatment_72hours_rep3


title: Fly_Listeria_NoTreatment_144hours_rep3

source_name: Whole fly, Listeria infected, No treatment, 144 hours post infection


title: Fly_Listeria_AmpicillinTreatment_144hours_rep2


title: Fly_Listeria_NoTreatment_144hours_rep2


title: Fly_Listeria_NoTreatment_96hours_rep1


title: Fly_Listeria_NoTreatment_120hours_rep2

source_name: Whole fly, Listeria infected, No treatment, 120 hours post infection


title: Fly_Listeria_AmpicillinTreatment_54hours_rep2


title: Fly_Listeria_NoTreatment_120hours_rep1


title: Fly_Listeria_NoTreatment_120hours_rep3


title: Fly_Listeria_NoTreatment_72hours_rep2

source_name: Whole fly, Listeria infected, No treatment, 72 hours post infection


title: Fly_Listeria_NoTreatment_96hours_rep2


title: Fly_Listeria_NoTreatment_54hours_rep3

source_name: Whole fly, Listeria infected, No treatment, 54 hours post infection


title: Fly_Listeria_NoTreatment_72hours_rep1


title: Fly_Listeria_AmpicillinTreatment_72hours_rep2


title: Fly_Listeria_AmpicillinTreatment_54hours_rep1


title: Fly_Listeria_NoTreatment_72hours_rep3


title: Fly_Listeria_NoTreatment_54hours_rep2


title: Fly_Listeria_NoTreatment_144hours_rep1


title: Fly_Listeria_NoTreatment_48hours_rep2

source_name: Whole fly, Listeria infected, No treatment, 48 hours post infection


title: Fly_Listeria_NoTreatment_24hours_rep1

source_name: Whole fly, Listeria infected, No treatment, 24 hours post infection


title: Fly_Listeria_NoTreatment_24hours_rep3


title: Fly_Listeria_NoTreatment_54hours_rep1


title: Fly_Listeria_NoTreatment_24hours_rep2


title: Fly_Listeria_NoTreatment_48hours_rep1


title: Fly_Listeria_NoTreatment_48hours_rep3


title: Fly_Listeria_NoTreatment_6hoursi_rep3

source_name: Whole fly, Listeria infected, No treatment, 6 hours post infection


title: Non_Survivor4_Day11

first: David

middle: S

last: Schneider

state: CALIFORNIA

address: 299 Campus Drive

hyb_protocol: Standard Illumina hybridization protocol using streptavidin-Cy3 for detection.

scan_protocol: Standard Illumina scanning protocol. Slides were scanned on an Illumina Beadstation.

data_processing: Data was normalized using percentile normalization with GeneSpring 12.1-GX and a baseline transformation (median of all samples) was applied.

source_name: Whole blood

extract_protocol: RNA was extracted from 10 ul of whole blood using the Mouse RiboPure Blood RNA isolation kit (Ambion-Life Technologies). Quality control was performed using the Agilent 2100 BioAnalyzer. RNA was amplified using Ambion Illumina RNA amplificicatin kit with biotin UTP labeling.

treatment_protocol: Whole blood was stored in 500 ul of RNA later in -80 C until further processed.

tag: mouse

tag: red blood cells

tag: parasite density

tag: temperature

tag: weight

tag: days post infection

tag: outcome


title: Fly_Listeria_NoTreatment_6hours_rep1

tag: tissue

tag: strain


title: Non_Survivor4_Day4


title: Non_Survivor4_Day0


title: Non_Survivor4_Day1


title: Non_Survivor4_Day3


title: Non_Survivor4_Day7


title: Non_Survivor4_Day8


title: Non_Survivor3_Day4


title: Fly_Listeria_NoTreatment_6hours_rep2


title: Non_Survivor4_Day9


title: Non_Survivor3_Day8


title: Non_Survivor3_Day7


title: Non_Survivor3_Day6


title: Non_Survivor3_Day9


title: Non_Survivor3_Day5


title: Non_Survivor4_Day10


title: Non_Survivor4_Day6


title: Non_Survivor4_Day2


title: Non_Survivor4_Day5


title: Non_Survivor3_Day3


title: Non_Survivor2_Day7


title: Non_Survivor2_Day9


title: Non_Survivor2_Day8


title: Non_Survivor3_Day0


title: Non_Survivor3_Day2


title: Non_Survivor3_Day1


title: Non_Survivor2_Day0


title: Non_Survivor2_Day2


title: Non_Survivor1_Day6


title: Fly_Listeria_AmpicillinTreatment_216hours_rep1


title: Non_Survivor1_Day1


title: Control2_Day24

value: Control


title: Non_Survivor2_Day6


title: Non_Survivor1_Day5


title: Non_Survivor2_Day3


title: Non_Survivor1_Day2


title: Non_Survivor2_Day5


title: Non_Survivor1_Day0


title: Non_Survivor1_Day3


title: Control2_Day0


title: Non_Survivor1_Day8


title: Control1_Day24


title: Control2_Day8


title: Control2_Day10


title: Non_Survivor2_Day1


title: Control1_Day14


title: Non_Survivor1_Day4


title: Control2_Day14


title: Control1_Day10


title: Non_Survivor2_Day4


title: Control1_Day8


title: Survivor3_Day24

value: Survivor


title: Control1_Day0


title: Wt-1Control 3

city: Valencia

first: Julia

last: Hillung

state: Valencia

address: Ingeniero Fausto Elio s/n

department: IBMCP

country: Spain

institute: CSIC-UPV

description: negative control

scan_protocol: GenePix

data_processing: Agilent ProcessedSignal (Agilent Feature Extraction Software) was standardized using quantile normalization.

source_name: whole plant, non-infected

label_protocol: See Agilent Technologies's web site at http://www.agilent.com/ Quick Amp Labeling Kit One Color labeled with Cy3

growth_protocol: plants were mantained in a BSL-2 greenhouse at 16:8h light:dark and 24:20 day:night temperature until sample collection on 21 days post infection.

extract_protocol: Invitek, InviTrap® Spin Plant RNA Mini Kit, following manual

treatment_protocol: Plants infected with tobacco etch potyvirus isolate At17b (TEV-At17b), with in each host ecotype evolved isolates derived from TEV-At17b and control non-infected plants.

tag: host ecotype

tag: viral lineage

value: mock

tag: block


title: Survivor3_Day23


title: Survivor3_Day22


title: Survivor3_Day21


title: Survivor3_Day20


title: Wt-1Control 4

description: negative control

hyb_protocol: See Agilent Technologies's web site at http://www.agilent.com/


title: Survivor3_Day25


title: Wt-1Control 2

description: negative control


title: Survivor3_Day16


title: Survivor3_Day19


title: Wt-1Control 1

description: negative control


title: St-0_Control 4

description: negative control


title: Wt-1 infected replicate 1

description: non-evolved

source_name: whole plant, infected

value: ancestral, TEV-At17b


title: Wt-1 infected replicate 3

description: non-evolved


title: Wt-1 infected replicate 5

description: non-evolved


title: St-0_Control 2

description: negative control


title: Wt-1 infected replicate 4

description: non-evolved


title: Survivor3_Day11


title: Survivor3_Day14


title: Survivor3_Day12


title: Survivor3_Day13


title: Survivor3_Day18


title: St-0_Control 3

description: negative control


title: Wt-1 infected replicate 2

description: non-evolved


title: Survivor3_Day17


title: Survivor3_Day15


title: St-0 infected replicate 5

description: non-evolved


title: Survivor3_Day9


title: Survivor3_Day10


title: Survivor3_Day7


title: St-0 infected replicate 4

description: non-evolved


title: Survivor3_Day8


title: Survivor3_Day4


title: St-0 infected replicate 1

description: non-evolved


title: Ler-0_Control 5

description: negative control


title: St-0_Control 1

description: negative control


title: Survivor3_Day5


title: Survivor3_Day6


title: Survivor3_Day2


title: St-0 infected replicate 2

description: non-evolved


title: Ler-0_Control 1

description: negative control


title: Ler-0_Control 2

description: negative control


title: Survivor3_Day0


title: Survivor2_Day23


title: Survivor2_Day25


title: Ler-0 infectede replicate 3

description: non-evolved


title: Ler-0 infectede replicate 4

description: non-evolved


title: Survivor3_Day1


title: Ler-0 infectede replicate 5

description: non-evolved


title: Survivor3_Day3


title: Ler-0_Control 4

description: negative control


title: St-0 infected replicate 3

description: non-evolved


title: Ler-0 infectede replicate 2

description: non-evolved


title: Survivor2_Day24


title: Survivor2_Day22


title: Ler-0_Control 3

description: negative control


title: Survivor2_Day21


title: Ei-2_Control 3

description: negative control


title: Ei-2_Control 4

description: negative control


title: Survivor2_Day20


title: Survivor2_Day18


title: Ei-2_Control 2

description: negative control


title: Ei-2_Control 1

description: negative control


title: Ler-0 infectede replicate 1

description: non-evolved


title: Survivor2_Day19


title: Ei-2 infected replicate 2

description: non-evolved


title: Survivor2_Day17


title: Ei-2 infected replicate 5

description: non-evolved


title: Ei-2 infected replicate 4

description: non-evolved


title: Ei-2 infected replicate 3

description: non-evolved


title: Survivor2_Day15


title: Survivor2_Day14


title: Ei-2 infected replicate 1

description: non-evolved


title: Survivor2_Day16


title: Survivor2_Day12


title: Survivor2_Day13


title: Survivor2_Day9


title: Survivor2_Day11


title: Di-2_Control 4

description: negative control


title: Di-2_Control 1

description: negative control


title: Di-2 infected replicate 5

description: non-evolved


title: Di-2_Control 2

description: negative control


title: Survivor2_Day8


title: Di-2_Control 3

description: negative control


title: Survivor2_Day7


title: Di-2 infected replicate 2

description: non-evolved


title: Survivor2_Day5


title: Di-2 infected replicate 4

description: non-evolved


title: Survivor2_Day10


title: Di-2 infected replicate 1

description: non-evolved


title: Survivor2_Day4


title: Survivor2_Day3


title: control non-infected plant ecotype Ler-0_plant 10

description: negative control


title: control non-infected plant ecotype Wt-1_plant 4

description: negative control


title: Survivor2_Day2