title: Hipk2 ko mTEC CD80low rep2

city: Heidelberg

first: Kristin

last: Rattay

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center

description: biological repilate to sample 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Scanning of the microarray was done by using a Beadstation array scanner; settings were adjusted to a scaling factor of 1 and PMT settings at 430. The data extraction was done for all beads individually and outliers were removed when > 2.5 MAD (median absolute deviation). All remaining data points were used for the calculation of the mean average signal for a given probe and the standard deviation for each probe was calculated.

data_processing: The data were normalised using quantile normalisation in R

source_name: mouse medullary thymic epithelial cells (mTECs)

label_protocol: Biotin-labeled cRNA for hybridization was prepared according to Illumina`s recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine et al. 1992). In brief, 200 ng total RNA was used for cDNA synthesis, followed by an in vitro transcription step for amplification and labeling to synthesize biotin-labelled cRNA using the MessageAmp II RNA amplification kit (Ambion) and biotin-16-UTP (Roche).

extract_protocol: Total RNA of primary sorted mTECs was isolated and purified using the High Pure RNA Isolation Kit (Roche Diagnostics) according to the manufacturers` protocol. Quality control was performed using Agilent Bioanalyser.

value: TEC-specific Hipk2 gene knockout

tag: cell population

value: mTECs CD80low


title: Adrenal male 3

status: Public on Jan 05 2015

type: RNA

city: Macclesfield

first: Russell

last: Huby

state: Cheshire

address: Alderley Park

country: United Kingdom

institute: AstraZeneca

hyb_protocol: Hybridization mixes including control oligos and biotin-labelled cRNA were prepared following the Affymetrix protocol. Hybridisation to Affymetrix RAE230_2 rat genechips® was carried out overnight at 45oC rotating at 60 rpm. Bound biotinylated probes were revealed with strptavidin-phycoerythrin complex according to the Affymetrix protocol.

scan_protocol: Scanning was carried out with an Affymetric 3000 scanner using the RAE_230_V2 protocol

data_processing: R bioconductor was used for primary analysis, analysis was using GC-RMA-s

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: normal adrenal tissue

label_protocol: cDNA, biotin-labelled cRNA and fragmented hybridization probes were prepared using the Affymetrix IVT kit (Affymetrix CA.).

growth_protocol: Rats were housed 2-3 per cage

extract_protocol: RNA was purified from lysates using Qiagen RNeasy mini columns according to the manufacturer’s instructions. Nucleic acid (RNA) purity was determined according to the 260/280nM absorbance ratio using a Nanodrop-1000 (Thermo Scientific). Samples were accepted only if the ratio fell between 1.8 and 2.2. Otherwise, RNA was re-extracted from new samples of frozen tissue. RNA integrity was assessed using the 2100 Bioanalyser (Agilent). Samples with an RNA integrity number (RIN) <7 were rejected, and re-processed.

treatment_protocol: Rats were humanely killed at a designated establishment by halothane inhalation, which is an appropriate method under Schedule 1 of the Act.Organs and tissues were removed and cleaned of extraneous tissue by a 5-person necropsy team within 5 min  of death, then frozen in liquid nitrogen. Pancreas was prioritized for rapid freezing, since its mRNA is known to be particularly vulnerable to degredation. Tissue samples from each animal weighing 100-250 mg were taken from frozen samples and homogenized immediately in RNeasy lysis buffer. Care was taken to ensure samples were taken consistently from the same region of tissue for each individual, and that they were representative of the whole organ (e.g. radial segments of kidney were taken from the equator in each case).

tag: tissue

value: adrenal tissue

tag: Sex

value: male

tag: strain

value: Han Wistar-derived rats (AlpkHsdBrlHan:WIST)


title: Adipose female 4

source_name: normal adipose tissue

value: adipose tissue

value: female


title: Adipose male 1


title: Hipk2 ko mTEC CD80high rep2

description: biological repilate to sample 4

organism: Mus musculus

tag: genotype/variation

value: mTECs CD80high


title: TU_FS_1

city: London

first: Vladimir

last: Zhurov

state: ON

address: 1151 Richmond Street

department: Biology

country: Canada

institute: University of Western Ontario

description: Gene expression of tomato plants in FS scenario

hyb_protocol: 5.5 ug of single stranded cDNA was hybridized for 16 h at 45 °C on GeneChip EUTOM3 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix, Santa Clara, CA).

scan_protocol: Scanning was done following Affymetrix guidelines on a GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA).

data_processing: CEL files were processed in Bioconductor using RMA workflow with standard settings and GPL16358 platform CDF.

organism: Solanum lycopersicum

source_name: Feeding site samples, bio rep 1

label_protocol: Biotin end labeled single strand cDNA was prepared according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual (Affymetrix, Santa Clara, CA).

growth_protocol: Plants were grown under 200-250 µmol m-2 s-1 cool-white fluorescent light at 25 °C with a 16:8 h (light/dark) photoperiod in controlled growth chambers.

extract_protocol: RNA samples were processed in triplicate from pooled samples of two plants per treatment. 3 terminal leaflets of leaf 3 were used. Total RNA was prepared using the RNeasy Plant RNA extraction kit (Qiagen, Venlo, Netherlands).

treatment_protocol: In time course scenario 100 adult female spider mites were applied onto terminal leaflet of leaf 3 per plant and allowed to feed for 1, 3, 6, 12 or 24 h. In feeding site scenario leaflets were covered with hundreds of mites that were allowed to feed for 1 h.

value: 3 terminal leaflets of leaf 3

tag: cultivar

value: Heinz 1706

tag: age

value: 1 month old


title: Adipose male 4


title: ihep_j2_mixture_day1_replicate1

status: Public on Jan 04 2015

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

country: USA

institute: Koch Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: R version 2.15.0 (x86_64-pc-linux-gnu), affyPLM_1.32.0, preprocessCore_1.18.0, gcrma_2.28.0, affy_1.34.0, Biobase_2.16.0

organism: Homo sapiens

source_name: iPS-Hepatocytes cultured alone for 1 day combined with J2 RNA following lysis

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

growth_protocol: Induced pluripotent stem cells were plated on matrigel at confluency (1.25e6 cells/6 well plate well) in Rock inhibitor Y27632 10uM), exposed to Activin A, BMP4, FGF, and HGF as described previously (Si-Tayeb, Hepatology ), cultured for 15 days, and replated in Aggrewells in human hepatocyte media (Chen AA, PNAS 2011)

extract_protocol: RNA was purified using the QIAgen Rneasy kit

treatment_protocol: iPS-Hepatocytes were removed from culture and replated into Aggrewells at a ratio of 1:1 with J2 stromal cells for 1 day. As control, post-culture mixing of isolated RNA was done.

tag: cell type

value: iPS-Hepatocytes

tag: j2 fibroblast status

value: J2 RNA mixed - Day1


title: Hipk2 ko mTEC CD80low rep1

description: biological repilate to sample 7


title: Adipose female 1


title: Hipk2 wt mTEC CD80low  rep2

description: biological repilate to sample 1

value: mating wildtype control


title: Hipk2 wt mTEC CD80high rep2

description: biological repilate to sample 2


title: Hipk2 wt mTEC CD80high rep1

description: biological repilate to sample 6


title: Adipose male 2


title: ihep_j2_coculture_day1_replicate1

source_name: iPS-Hepatocytes cultured with J2 stromal cells for 1 day

value: Coculture - Day1


title: Hipk2 wt mTEC CD80low rep1

description: biological repilate to sample 5


title: Hipk2 ko mTEC CD80high rep1

description: biological repilate to sample 8


title: ihep_j2_day1_replicate1

source_name: iPS-Hepatocytes cultured alone for 1 day

value: No J2 - Day1


title: ihep_j2_coculture_day1_replicate2


title: Lrig1null adjcent normal [1736-RJC-21]

city: Nashville

first: Robert

last: Coffey

state: TN

address: 2213 Garland Ave

department: Medicine/GI

institute: Vanderbilt University Medical Center

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: scanned with Affymetrix using AGCC v. 1.1

data_processing:
analyzed on Affymetrix Expression Console v. 1.1
MoGene-1_0-st-v1.r4.qcc
MoEx-1_0-st-v1.r2.dt1.mm9.comprehensive.mps

source_name: proximal duodenum

label_protocol: Samples were enzymatically fragmented and  the probe was prepared with Ambion Expression Target preparation Kit P/N 4411974.

growth_protocol: Age matched Lrig1null mice bearing duodenal adenomas and wildtype mice

extract_protocol: Total RNA isolated with Rneasy (with Dnase digestion)  and used to probe the Affymetrix Mouse Gene 1.0 ST chip

tag: background

value: 129S7/SvEv and C57/BL6

value: Normal duodenal epithelium

tag: genotype

value: Lrig1-CreERT2/CreERT2 (Lrig1-/-)


title: wildtype control [1736-RJC-26]

value: wildtype


title: wildtype control [1736-RJC-25]


title: Lrig1null adjcent normal [1736-RJC-23]


title: Lrig1null tumor [1736-RJC-22]

source_name: proximal duodenal tumor

value: Duodenal tumor


title: Lrig1null tumor [1736-RJC-24]


title: Normal 3-3 [miRNA)

status: Public on Jan 03 2015

city: Baltimore

first: Florin

last: Selaru

address: 720 Rutland Ave Ross 950

institute: the Johns Hopkins

description:
Normal 3-3
Gene expression

hyb_protocol: The RNA samples were hybridized on the miRCURY™ LNA Array (v.18.0), followed by washing steps.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner.

data_processing: The scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: human normal liver tissue

label_protocol: The RNA samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit following the manufacturer's recommendations.

extract_protocol: RNA was extracted from 3 pairs of HCC and paired normal liver tissues using the TRIzol® Reagent (Invitrogen Life Technologies) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: normal liver

tag: gender

value: male


title: HCC 3-1 [miRNA)

description:
HCC 3-1
Gene expression

source_name: human HCC

value: hepatocellular carcinoma (HCC)


title: Lrig1null adjcent normal [1736-RJC-16]


title: HCC 2-1 [miRNA)

description:
HCC 2-1
Gene expression


title: Normal 1-3 [miRNA)

description:
Normal 1-3
Gene expression


title: Normal 2-3 [miRNA)

description:
Normal 2-3
Gene expression


title: Lrig1null tumor [1736-RJC-12]


title: Lrig1null adjcent normal [1736-RJC-19]


title: Lrig1null adjcent normal [1736-RJC-14]


title: Lrig1null tumor [1736-RJC-20]


title: wildtype control [1736-RJC-10]


title: HCC 1-1 [miRNA)

description:
HCC 1-1
Gene expression


title: K299 IRF4 shRNA +Dox 48h

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

hyb_protocol: hybridization was performed with HumanHT-12 v4 Expression Bead Chip kit (Illumina) according to manufacturer's protocol

scan_protocol: scanning was performed according to manufacturer's protocol

data_processing: The preprocessing pipeline was implemented in Mathworks MATLAB(R) and works similar to preprocessing Affymetrix CEL files: Measured gene expressions were imported on raw bead level (cf. supplementary TXT files). All 24 microarrays were preprocessed and normalized together. Their intensities distributions for all measured beads were equalized by quantile normalization. The background mode was fitted and removed and a spot filter was applied to exclude too dim beads (< mean background intensity). Intensities were log2-transformed and aggregated by measured sequence to form beadsets. Beadsets with more than 50% of their beads excluded by the spot filter were also excluded. Further analysis was performed on gene level using manufacturer’s annotations. For genes having multiple beadsets the one with the highest expression (in average over all arrays) was selected.

source_name: ALCL cell line K299

label_protocol: RNA was transcribed and labeled by Illumina TotalPrep RNA Amplification kit according to manufacturer's protocol

growth_protocol: cell line DEL/FEPD/K299 was maintained in RPMI medium with 10%FBS at 37°C with 5% CO2

extract_protocol: total RNA was extracted with NucleoSpin RNAII kit (Illumina) according to manufacturer's protocol

treatment_protocol: cell line DEL/FEPD/K299 was retrovirally transduced with IRF4 shRNA, transduced cells were selected by puromycin and IRF4 shRNA expression was induced by doxycyline.

tag: irf4 shrna expression

value: induced by doxycycline

tag: duration in hours

tag: cell line

value: ALCL cell line K299


title: FEPD IRF4 shRNA +Dox 96h

source_name: ALCL cell line FEPD

value: ALCL cell line FEPD


title: PLC5 siGALNT1-2

city: Taipei

first: Min-Chuan

last: Huang

address: No. 1, Sec. 1, Ren-Ai RD, Taipei, Taiwan, R.O.C.

department: Graduate Institute of Anatomy and Cell Biology

country: Taiwan

institute: National Taiwan University

description: Gene expression after 48 hours transfection

hyb_protocol: Agilent Gene Expression Hybridization Kits was used for hybridization according to the manufacturer’s instruction. Briefly, 16 ul of dye labeled cDNA in water was fragmented at 98°C for 3 mins in a reaction volume of 40 ul containing 4 ul Agilent 10x blocking agenr and 20 ul of Agilent 2xGExHybridization Buffer HI-RPM and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K v2 Microarray (G4851B) at 65°C and rotated at 10 rpm for 17 hours. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (US9230696) using one color scan setting for 8x60k array slides (Scan Area 61x21.6mm, Scan resolution 2um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label: Alexa/CyDye

source_name: PLC5 siGALNT1-2

label_protocol: cDNA prepared from 10μg of total RNA were labeled with aa-dUTP using Invitrogen SuperScriptTM Plus Indirect cDNA Labeling System according to the manufacturer's protocol, followed by aa-cDNA column purification (QIAGEN, Valencia, CA).  Alexa/CyDye was incorporated to aa-cDNA followed by column purification with Alexa/CyDye-cDNA cRNA purification (Qiagen).

growth_protocol: HA22T and PLC5 were cultured in DMEM supplemented with 10% FBS and 0.1 % penicillin and streptomycin

extract_protocol: RNA was prepared using the GeneJET RNA Purification kit (Thermo Scientific, Catelog number: K0731) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer (Bio-Rad) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

treatment_protocol: HA22T and PLC5 cells were transfected with 10 nM non-targeting and GALNT1 specific siRNA (Thermo Scientific, ON-TARGET plus SMART pool L-011280-01-0005) with Lipofectamine RNAiMAX (Invitrogen) for 48 hours and extracted for total RNA

tag: hepatocellular carcinoma cell line

tag: transfectant

value: GALNT1 siRNA


title: FEPD IRF4 shRNA +Dox 72h


title: PLC5 siGALNT1-3

source_name: PLC5 siGALNT1-3


title: K299 IRF4 shRNA +Dox 24h


title: HA22T siControl-3

source_name: HA22T siControl-3

value: Control siRNA


title: PLC5 siControl-3

source_name: PLC5 siControl-3


title: DEL IRF4 shRNA +Dox 72h

source_name: ALCL cell line DEL

value: ALCL cell line DEL


title: FEPD IRF4 shRNA +Dox 24h


title: FEPD IRF4 shRNA +Dox 48h


title: K299 IRF4 shRNA +Dox 96h


title: K299 IRF4 shRNA +Dox 72h


title: PLC5 siControl-2

source_name: PLC5 siControl-2


title: HA22T siGALNT1-3

source_name: HA22T siGALNT1-3


title: PLC5 siControl-1

source_name: PLC5 siControl-1


title: DEL IRF4 shRNA +Dox 96h


title: HA22T siGALNT1-1

source_name: HA22T siGALNT1-1


title: Lrig1null tumor [1736-RJC-15]


title: DEL IRF4 shRNA +Dox 48h


title: HA22T siGALNT1-2

source_name: HA22T siGALNT1-2


title: K299 IRF4 shRNA -Dox 96h

value: not induced


title: K299 IRF4 shRNA -Dox 48h


title: K299 IRF4 shRNA -Dox 72h


title: HA22T siControl-2

source_name: HA22T siControl-2


title: DEL IRF4 shRNA +Dox 24h


title: PLC5 siGALNT1-1

source_name: PLC5 siGALNT1-1


title: HA22T siControl-1

source_name: HA22T siControl-1


title: DEL IRF4 shRNA -Dox 72h


title: K299 IRF4 shRNA -Dox 24h


title: FEPD IRF4 shRNA -Dox 48h


title: DEL IRF4 shRNA -Dox 24h


title: FEPD IRF4 shRNA -Dox 96h


title: DEL IRF4 shRNA -Dox 96h


title: FEPD IRF4 shRNA -Dox 72h


title: DEL IRF4 shRNA -Dox 48h


title: Normal 2-3 (mRNA, lncRNA)

description:
NORMAL 2-3
Gene expression

hyb_protocol: The labeled cRNAs were hybridized onto the Agilent-033010 Arraystar Human LncRNA Array v2.0 (8 x 60K). Hybridization was performed in Agilent's SureHyb Hybridization Chambers.

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that had at least 1 out of 6 samples with flags in Present or Marginal (All Targets Value) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering. Pathway analysis and GO analysis were applied to determine the roles these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable LncRNAs and mRNAs expression pattern among samples.

source_name: human normal liver tissue

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling. Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method.

extract_protocol: Total RNA was extracted from 3 pairs of HCC and paired normal liver tissues using the TRIzol® Reagent (Invitrogen Life Technologies) following the manufacturer's recommendations. Total RNA from each sample was quantified by the NanoDrop ND-1000, and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. mRNA was purified from 1 ug total RNA after removal of rRNA (mRNA-ONLY Eukaryotic mRNA Isolation Kit, Epicentre).


title: 150 min rep1

city: Beijing

first: Liang

last: Yin

address: N0.1 Beichen Road

country: China

institute: institute of microbiology, chinese acadmy of science

description: Gene expression at 120 min after cells salt shock

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: The scanned images were analyzed with Feature Extraction software (Agilent technologies, Santa Clara, CA, US) with default settings. The values on the Series record represent normalized signal intensity by using Quantile algorithm.

organism: Bacillus sp. N16-5

source_name: cells, salt shock, 120 min

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Cultures were grown under aerobic conditions at 37°C in round-bottom flasks on different salinities to mid-logarithmic phase. For salt shock experiments, cultures were grown with 0% NaCl to mid-logarithmic phase, then a 32% NaCl stock solution was added to alter salinity from 0% to 8% NaCl.Samples were taken before (0 min) and 10, 30, 60, and 120 min after the onset of stress.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

tag: treatment

value: salt shock, 120 min


title: FEPD IRF4 shRNA -Dox 24h


title: 150 min rep3


title: Normal 3-3 (mRNA, lncRNA)

description:
NORMAL 3-3
Gene expression

tag: tissue


title: 60 min rep3

description: Gene expression at 60 min after cells salt shock

source_name: cells, salt shock, 60 min

value: salt shock, 60 min


title: 150 min rep2


title: HCC 3-1 (mRNA, lncRNA)

description:
HCC 3-1
Gene expression

source_name: human HCC


title: 60 min rep2


title: Normal 1-3 (mRNA, lncRNA)

description:
NORMAL 1-3
Gene expression


title: HCC 2-1 (mRNA, lncRNA)

description:
HCC 2-1
Gene expression


title: 60 min rep1


title: 30 min rep3

description: Gene expression at 30 min after cells salt shock

source_name: cells, salt shock, 30 min

value: salt shock, 30 min


title: Lrig1null tumor [1736-RJC-17]

source_name: proximal duodenal tumor

value: 129S7/SvEv and C57/BL6


title: ColonicMac_Irgm1_mouse2

city: Saint Louis

first: Lulu

last: Sun

state: MO

address: 4940 Parkview Place, 1020 CSRB-NTA

department: Pathology and Immunology

institute: Washington University in St. Louis

hyb_protocol: 750ng of each labeled aRNA were hybridized to 4x44k Agilent Mouse Whole Genome Microarrays for 18 hours at 65C in Sure-Hyb Hybridization Chambers (Agilent Technologies).

scan_protocol: Chambers were disassembled in 0.6x SSC 0.005%Triton X-102 wash for 5 minutes at 40C, then dried with HEPA filtered compressed nitrogen and scanned on on the Agilent Technologies DNA Microarray.

data_processing: Signal normalization was performed using a smoothed windowed piecewise linear regression, trained on log intensities that differed by < 10% rank order between two samples. Local background subtraction was performed for each spot prior to normalization. For each sample, a technical replicate pool was created from the averaged normalized signals of the individual replicate arrays. Within the replicate arrays, a median array was selected as the least distant from the other replicate arrays. All replicate arrays were normalized against the median array prior to calculating the averaged normalized signals of the pool. Probes with technical replicate CV's >= 0.7 were flagged as bad and assigned an intensity value of zero. A final normalization was performed on the averaged Irgm1-/- signals vs. averaged WT signals.

source_name: Isolated colonic macrophages

label_protocol: 5ug of RNA was labeled using Kreatech ULS aRNA Fluorescent Cy3/Cy5 labeling kit (Kreatech Diagnostics).

growth_protocol: Mice were housed in an enhanced barrier specific pathogen-free facility, under a strict 12 hour light cycle and fed autoclaved chow diet (PicoLab Rodent Chow 20, Purina Mills). All mice were maintained on a C57BL/6 background

extract_protocol: Total RNA was extracted from whole tissue or isolated colonic macrophages using the Qiagen RNeasy kit (Qiagen).

value: M

tag: age (weeks)

tag: background strain


title: ColonicMac_WT_mouse3

value: WT

value: F


title: ColonicMac_WT_mouse2


title: ColonicMac_WT_mouse1


title: ColonicMac_Irgm1_mouse3


title: 30 min rep2


title: ColonicMac_Irgm1_mouse1


title: 10 min rep3

description: Gene expression at 10 min after cells salt shock

source_name: cells, salt shock, 10 min

value: salt shock, 10 min


title: SmallIntestine_Irgm1_mouse3

source_name: Duodenum whole tissue


title: HCC 1-1 (mRNA, lncRNA)

description:
HCC 1-1
Gene expression

value: male


title: SmallIntestine_WT_mouse3


title: SmallIntestine_WT_mouse2


title: 10 min rep2


title: SmallIntestine_WT_mouse1


title: SmallIntestine_Irgm1_mouse2


title: 10 min rep1


title: SalivaryGland_WT_mouse3

source_name: Salivary gland whole tissue


title: SalivaryGland_WT_mouse2


title: SalivaryGland_WT_mouse4


title: 30 min rep1


title: Blood 20

type: genomic

first: Dapeng

last: Wang

address: No.7 Beitucheng West Road, Chaoyang District, Beijing 100029, PR China

institute: Beijing Institute of Genomics

description:
Sample name: B20
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: The data was processed by Illumina GenomeStudio software and SNP cluster algorithm.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: Blood

label_protocol: standard Illumina protocol

extract_protocol: Genomic DNA from tumor tissues and blood was isolated using QIAamp DNA Mini Kit (QIAGEN Inc.).

value: Male

value: Blood


title: SmallIntestine_Irgm1_mouse1


title: SalivaryGland_Irgm1_mouse4


title: SalivaryGland_Irgm1_mouse3


title: Blood 17

description:
Sample name: B17
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: 0 min rep3

description: Gene expression at 0 min after cells salt shock

source_name: cells, salt shock, 0 min

value: salt shock, 0 min


title: 0 min rep2


title: Blood 16

description:
Sample name: B16
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).

value: Female


title: SalivaryGland_WT_mouse1


title: Glioma tissue 15

description:
Sample name: T15
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).

source_name: Glioma

value: Glioma

tag: disease state


title: SalivaryGland_Irgm1_mouse2


title: Glioma tissue 14

description:
Sample name: T14
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Glioma tissue 19

description:
Sample name: T19
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: 0 min rep1


title: Glioma tissue 16

description:
Sample name: T16
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Glioma tissue 20

description:
Sample name: T20
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Blood 19

description:
Sample name: B19
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Blood 15

description:
Sample name: B15
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: 15% NaCl rep3

description: Gene expression when cells grown on 15% NaCl to mid-logarithmic phase

source_name: cells grown on 15% NaCl

value: 15% NaCl


title: 15% NaCl rep1


title: 15% NaCl rep2


title: Glioma tissue 18

description:
Sample name: T18
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: SalivaryGland_Irgm1_mouse1


title: 8% NaCl rep3

description: Gene expression when cells grown on 8% NaCl to mid-logarithmic phase

source_name: cells grown on 8% NaCl

value: 8% NaCl


title: Glioma tissue 13

description:
Sample name: T13
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: 8% NaCl rep2


title: Blood 13

description:
Sample name: B13
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: 8% NaCl rep1


title: Glioma tissue 17

description:
Sample name: T17
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Blood 11

description:
Sample name: B11
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: 2% NaCl rep3

description: Gene expression when cells grown on 2% NaCl to mid-logarithmic phase

source_name: cells grown on 2% NaCl

value: 2% NaCl


title: 0% NaCl rep3

description: Gene expression when cells grown on 0% NaCl to mid-logarithmic phase

source_name: cells grown on 0% NaCl

value: 0% NaCl


title: 2% NaCl rep2


title: Glioma tissue 9

description:
Sample name: T9
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: 0% NaCl rep1


title: 0% NaCl rep2


title: Blood 14

description:
Sample name: B14
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: 2% NaCl rep1


title: Glioma tissue 8

description:
Sample name: T8
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Blood 8

description:
Sample name: B8
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Blood 7

description:
Sample name: B7
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Glioma tissue 6

description:
Sample name: T6
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Glioma tissue 5

description:
Sample name: T5
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Blood 5

description:
Sample name: B5
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Blood 6

description:
Sample name: B6
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Blood 4

description:
Sample name: B4
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Blood 3

description:
Sample name: B3
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Blood 2

description:
Sample name: B2
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Glioma tissue 2

description:
Sample name: T2
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Glioma tissue 3

description:
Sample name: T3
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Glioma tissue 4

description:
Sample name: T4
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Blood 1

description:
Sample name: B1
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Blood 18

description:
Sample name: B18
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Glioma tissue 7

description:
Sample name: T7
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Liver_Normal_64

status: Public on Jan 02 2015

city: Shanghai

first: Zhiqiang

last: Li

address: Huashan Road No.1954

department: Bio-X Institutes

institute: Shanghai Jiao Tong University

description: Hybridized to SNP 6.0

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

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

data_processing:
The array image was acquired using GeneChip® Command Console® Software (AGCC). Genotype data were generated using the birdseed algorithm using Affymetrix Power Tools (apt-1.15.0).
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: Biotin

source_name: liver tissues, normal 64

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA of the samples were extracted by using the RNA/DNA Mini Kit (Qiagen, Hilden, Germany). The integrity of the tissue DNA was checked by running in 1% Agarose gel, and concentration was measured by ultraviolet spectroscopy. DNA was diluted to working concentrations of 50 ng/μl for SNP chip genotyping.

tag: population

value: Han Chinese

value: liver


title: Liver_Normal_55

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 55


title: Liver_Normal_62

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 62


title: Liver_Normal_58

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 58


title: Liver_Normal_54

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 54


title: Glioma tissue 1

description:
Sample name: T1
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Liver_Normal_57

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 57


title: Liver_Normal_59

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 59


title: Liver_Normal_61

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 61


title: Liver_Normal_56

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 56


title: Liver_Normal_60

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 60


title: Liver_Normal_53

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 53


title: Glioma tissue 11

description:
Sample name: T11
Genomic DNA extracted from glioma tumors was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).


title: Blood 9

description:
Sample name: B9
Genomic DNA extracted from blood was genotyped using Sentrix HumanCNV370-Quadv3-0 BeadChip (Illumina).

source_name: Blood


title: Liver_Normal_52

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 52


title: IAA 15min rep3

city: Yokohama

first: Yukihisa

last: Shimada

state: Kanagawa

address: Maiokacho, Totsuka

department: Kihara Institute for Biological Science

country: Japan

institute: Yokohama City University

description: IAA 15min

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix GeneAtlas with standard protocol

data_processing: Arrays were normalized with R/Bioconductor's 'oligo' package and calculated by RMA and signals of IDs that are in the platform GPL17133 were extracted.

organism: Arabidopsis thaliana

source_name: 7 day old seedlings treated 15min

label_protocol: GeneChip WT Terminal Labeling and Control Kit

growth_protocol: Seedlings were grown for 7 days at 22 degrees.

extract_protocol: Rneasy Plant Miini Kit (Quagen)

treatment_protocol: Seedlings were treated with plant hormones for 30 min, 1 h, or 3 h.

tag: genotype/variation

value: wildtype

tag: ecotype

tag: age

value: 7 day old

tag: developmental stage

value: seedling

value: IAA

tag: time


title: Liver_Normal_45

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 45

tag: gender


title: Liver_Normal_49

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 49


title: Liver_Normal_46

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 46


title: Liver_Normal_50

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 50


title: Liver_Normal_51

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 51


title: IAA 3h rep3

description: IAA 3h

source_name: 7 day old seedlings treated 3h


title: mock 15min rep3

description: mock 15min

source_name: 7 day old seedlings untreated 15min

value: mock


title: Liver_Normal_47

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 47

value: male


title: Liver_Normal_41

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 41


title: mock 3h rep3

description: mock 3h

source_name: 7 day old seedlings untreated 3h


title: Liver_Normal_44

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 44


title: IAA 15min rep2

description: IAA 15min


title: mock 15min rep2

description: mock 15min


title: IAA 3h rep2

description: IAA 3h


title: Liver_Normal_42

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 42


title: mock 3h rep2

description: mock 3h


title: Liver_Normal_28

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 28


title: Liver_Normal_63

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 63


title: Liver_Normal_33

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 33


title: Liver_Normal_39

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 39


title: Liver_Normal_32

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 32


title: Liver_Normal_40

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 40


title: Liver_Normal_34

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 34


title: IAA 15min rep1

description: IAA 15min

source_name: 7 day old seedlings treated 15min


title: mock 15min rep1

description: mock 15min


title: Liver_Normal_43

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 43


title: IAA 3h rep1

description: IAA 3h


title: Liver_Normal_26

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 26


title: Liver_Normal_29

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 29


title: Liver_Normal_31

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 31


title: Liver_Normal_30

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 30


title: Liver_Normal_25

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 25


title: Liver_Normal_23

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 23


title: Liver_Normal_37

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 37


title: mock 3h rep1

description: mock 3h

source_name: 7 day old seedlings untreated 3h


title: Liver_Normal_38

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 38


title: Liver_Normal_27

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 27


title: Liver_Normal_36

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 36


title: Liver_Normal_24

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 24


title: Liver_Normal_21

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 21


title: Liver_Normal_35

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 35


title: proximal colon-Low High vitamin D-mom 15

city: Toronto

first: Elena

last: Comelli

address: 150 College Street

department: Nutritional Sciences

institute: University of Toronto

description: low vitamin D during pregnancy and lactation and high vitamin D after weaning

hyb_protocol: BeadChips were incubated at 58oC with rotation speed 5 for 18 hours

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalisation with GeneSpring

source_name: mouse proximal colon

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep-96 RNA amplification kit for Illumina arrays

extract_protocol: RNA was extracted with mirVana™ miRNA Isolation Kit (Ambion, Carlsbad, CA), following the manufacturer’s protocol and stored at -80°C. The concentration and purity of RNA samples were assessed using a Nanodrop 1000 Spectrophotometer (Nanodrop Technologies, Wilmington, DE). RNA quality was further confirmed by an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

tag: strain

value: 129/SvEvIL-10 KO

value: 3 months

value: proximal colon


title: proximal colon- High Low vitamin D-mom 10B

description: high vitamin D during pregnancy and lactation and low vitamin D after weaning


title: proximal colon- High Low vitamin D-mom 10

value: high vitamin D during pregnancy and lactation and low vitamin D after weaning


title: proximal colon-Low High vitamin D-mom 12B

value: low vitamin D during pregnancy and lactation and high vitamin D after weaning


title: proximal colon- High High vitamin D-mom 10B

description: high vitamin D during pregnancy and lactation and high vitamin D after weaning


title: proximal colon-Low Low vitamin D-mom 13A

description: low vitamin D during pregnancy and lactation and low vitamin D after weaning


title: Liver_Normal_48

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 48


title: proximal colon- High High vitamin D-mom 5A

value: high vitamin D during pregnancy and lactation and high vitamin D after weaning


title: Liver_Normal_19

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 19


title: MDDC_uninfected_donor-979

city: Notre Dame

first: Mary

middle: Ann

last: McDowell

state: Indiana

address: 210 Galvin Life Science Center

department: Biological Sciences

institute: University of Notre Dame

description:
979-UI-04h
RNA_human-monocyte-derived-dendritic-cell_uninfected_donor-979
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells which are uninfected and is the fifth of five biological replicates

hyb_protocol: Labeled cDNAs were hybridized to 12-plex NimbleGen Homo sapiens Expression Arrays (platform accession number GPL16025), featuring 45,033 probes representing 23,752 gene transcripts, using Hybridization Kit, LS (Roche NimbleGen) and Wash Buffer Kit (Roche NimbleGen) per manufacturer's recommendations.

scan_protocol: Image acquisition of arrays was performed using a NimbleGen MS 200 Microarray Scanner, at a 2 micron resolution.

data_processing:
NimbleGen array image data were processed using NimbleScan (version 2.5) to extract intensity values for each gene. NimbleScan software automates the pre-processing of NimbleGen microarray image data, including identifying the location of each probe, extraction of intensity data from the image, background correction, and obtaining expression summary values for each gene using a probe-level summarization method RMA (Robust Multi-Array Average).
Averages of RMA normalized gene probeset (consisting of three probes per gene) with intensity values two times greater than that of each array background values were retained for downstream analysis. Any values that did not pass this filter are listed as NULL.

label_protocol: 25ng of high quality RNA was converted to double stranded cDNA using Sigma TransPlex Complete Whole Transcriptome Amplification Kit (Sigma). RNA degradation, double stranded cDNA purification, and cDNA precipitation was conducted following NimbleGen Gene Expression Array user’s guide protocols (Roche NimbleGen). A Nanodrop ND-2000 (ThermoScientific) was used to determine total RNA and double stranded cDNA concentrations. Sample cDNAs were Cy3-labeled using NimbleGen Single Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations.

growth_protocol: CD14+ monocytes of four anonymous healthy adult female human donors (Central Indiana Regional Blood Center, Indianapolis, IN) were isolated from peripheral blood mononuclear cells by positive selection using an AutoMACS separator (Miltenyi Biotec) after isolation using lymphocyte separating media (Cellgro) following manufacturer protocols. The purity of separated monocytes was determined by flow cytometry analysis on a MCL500 flow cytometer (Beckman Coulter) using fluorescent antibody staining for CD14, CD19, CD45, and CD3 (Biolegend). Enriched monocytes were differentiated into dendritic cells (MDDC) by treatment with granulocyte-macrophage colony-stimulating factor (GM-CSF; 2,000 U/mL) and interleukin-4 (IL-4; 800 U/mL) recombinant cytokines (Peprotech) on days 0, 3, and 6 after plating in six-well plates at 2.5 × 10^6 cells/mL in complete RPMI medium (10% fetal bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine). Immature MDDC were harvested on day 7 and plated in 6-well plates at 2 × 10^6 cells in 2 mL complete RPMI medium per well in the absence of exogenous cytokine. The phenotype puritiess of DCs was determined by flow cytometry analysis of CD1a, CD14, HLA-DR, CD40, CD80, and CD86 expression. All infections were performed with Leishmania major Friedlin V1 strain (NIH) and Leishmania donovani 1S strain (ATCC #30142) parasites. All parasites were cultured at 26°C without CO2 in complete medium 199 (20% heat-inactivated fetal bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine, 40 mM HEPES, 0.1 mM adenine in 50 mM HEPES, 5 mg/mL hemin in 50% triethanolamine, and 1 mg/mL biotin). Parasites tested negative for mycoplasma using a Mycoplasma PCR detection set (Takara) and tested below the detection limits for endotoxin using a Limulus Amoebocyte Lysate kit (Charles River Laboratories). Infective-stage metacyclic promastigotes were isolated by use of a Ficoll gradient as previously described (PMID: 11748963) and opsonized with 5% normal human serum prior to infection at a concentration of ten parasites to one host cell. Infection rates were determined at the end of each experiment by DiffQuick staining of cytospin whole cell preparations and visualization by light microscopy.

extract_protocol: Total RNA from uninfected or Leishmania-infected human MDDCs was isolated using an RNEasy kit (Qiagen). Bioanalyzer 2100 (Agilent Technologies) and RNA 6000 Nano kits (Agilent Technologies) were used to determine total RNA integrity.

treatment_protocol: After 4, 8, or 24 hours post-infection, MDDCs were harvested washing in medium and application of 0.5 mM EDTA (Gibco) in 1X PBS (Cellgro). Cell harvests were spun down, washed, and pellets resuspended in RNAlater RNA Stabilization Solution (Applied Biosystems).

tag: host cell type

value: Monocyte derived dendritic cell

tag: donor id number

tag: infecting parasite species

value: Uninfected

tag: parasite strain

tag: time post-infection


title: Pooled rpfF_DP+DSF2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: The labeled cRNA samples were hybridized on to a Genotypic Custom Gene Expression Xanthomonas oryzicola  8x15k (AMADID: 41087).  600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanned on an Agilent Technologies G2505C scanner and Images were quantified using Agilent Feature Extraction Software 10.7

data_processing: The 75th percentile Shift normalization was done using GeneSpring GX 11.5 Software.

organism: Xanthomonas oryzae pv. oryzicola

source_name: Delta rpfF DP DSF 2

label_protocol: Random hexamer method of labeling was done followed by T7 promoter based-linear amplification to generate labeled complementary RNA (One-Color Microarray-Based Gene Expression Analysis). The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse transcription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity using Nanodrop.

growth_protocol:
Total cellular RNA, directly from plate
Cells were grown in Peptone sucrose media  supplemented with 50µM 2,2- dipyridyl, 200 rpm, 28°C and inoculated in the secondry culture at a cell density of 105 cells/ml (inoculum density) and grown for 24 hours under similar conditions

extract_protocol: Total RNA isolated using Trizol following manufacturer's instructions

treatment_protocol: Xanthomonas oryzae pv. oryzicola wild type, DSF deficient rpfF mutant, rpfF mutant complemented in trans by rpfF gene in plasmid pSC9 grown in peptone sucrose media with 2,2-dipyridyl and rpfF mutant with DSF supplementation on peptone sucrose plate with 2,2-dipyridyl.

tag: genotype

value: three independent cultures of ∆rpfF+DSF

tag: growth

value: after growth in peptone sucrose media supplemented with 2-2, dipyridyl plate


title: MDDC_Leishmania-major-strain-FV1-infected_24HR-post-infection_donor-979

description:
979-FV1-24h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_24HR-post-infection_donor-979
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 24 hours and is the fifth of five biological replicates

value: Leishmania major

value: 24 hours


title: Liver_Normal_18

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 18

value: Han Chinese

tag: tissue

value: liver


title: proximal colon- High Low vitamin D-mom 2A

tag: treatment


title: proximal colon-Low High vitamin D-mom 2


title: Pooled rpfF(pSC9)_DP1

source_name: comp DP 1

growth_protocol:
Total cellular RNA, 24 hrs. growth
Cells were grown in Peptone sucrose media  supplemented with 50µM 2,2- dipyridyl, 200 rpm, 28°C and inoculated in the secondry culture at a cell density of 105 cells/ml (inoculum density) and grown for 24 hours under similar conditions

value: three independent cultures of ∆rpfF(pSC9)

value: after 24 hrs. of growth in peptone sucrose media supplemented with 2-2, dipyridyl


title: Liver_Normal_15

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 15

tag: population

value: male


title: Liver_Normal_17

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 17


title: Pooled rpfF_DP +DSF1

source_name: Delta rpfF DP  DSF1 (2)

value: three independent cultures of ∆rpfF + DSF


title: Liver_Normal_22

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 22


title: Pooled rpfF(pSC9)_DP2

source_name: comp DP2 (2)


title: Pooled YT6_DP2

value: three independent cultures of wild type BXOR1


title: proximal colon-Low High vitamin D-mom 13

value: 129/SvEvIL-10 KO

value: 3 months

value: proximal colon


title: Pooled rpfF_DP1

source_name: Delta rpfF DP1 (2)

value: three independent cultures of ∆rpfF


title: Pooled rpfF_DP2

source_name: Delta rpfF DP2


title: MDDC_Leishmania-major-strain-FV1-infected_8HR-post-infection_donor-979

description:
979-FV1-08h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_8HR-post-infection_donor-979
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 8 hours and is the fifth of five biological replicates

value: Monocyte derived dendritic cell

value: 8 hours


title: MDDC_Leishmania-major-strain-FV1-infected_4HR-post-infection_donor-979

description:
979-FV1-04h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_4HR-post-infection_donor-979
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 4 hours and is the fifth of five biological replicates

value: 4 hours


title: Pooled YT6_DP1


title: Liver_Normal_20

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 20


title: Liver_Normal_16

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 16


title: MDDC_Leishmania-donovani-strain-1S-infected_24HR-post-infection_donor-979

description:
979-1S-24h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-donovani-strain-1S-infected_24HR-post-infection_donor-979
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania donovani (1S strain) parasites for 24 hours and is the fifth of five biological replicates

value: Leishmania donovani


title: Liver_Normal_63

description: RNA sample were labeled and hybridized to the One-Color Agilent 60-mer Whole Human Genome Microarray

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slide.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: liver tissues, normal 63

label_protocol: According to the manufacturer's instructions.

extract_protocol: Total RNA of the human liver tissue samples were extracted by using the RNA/DNA Mini Kit (Qiagen, Hilden, Germany).


title: proximal colon- High High vitamin D-mom 11A

value: high vitamin D during pregnancy and lactation and high vitamin D after weaning


title: proximal colon-Low High vitamin D-mom 3B

value: low vitamin D during pregnancy and lactation and high vitamin D after weaning


title: Liver_Normal_62

source_name: liver tissues, normal 62

value: Han Chinese


title: proximal colon- High High vitamin D-mom 5

source_name: mouse proximal colon


title: Liver_Normal_64

source_name: liver tissues, normal 64

value: liver


title: Liver_Normal_59

source_name: liver tissues, normal 59


title: Liver_Normal_60

source_name: liver tissues, normal 60


title: Liver_Normal_61

source_name: liver tissues, normal 61


title: proximal colon-Low Low vitamin D-mom 13

value: low vitamin D during pregnancy and lactation and low vitamin D after weaning


title: MDDC_Leishmania-donovani-strain-1S-infected_4HR-post-infection_donor-979

description:
979-1S-04h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-donovani-strain-1S-infected_4HR-post-infection_donor-979
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania donovani (1S strain) parasites for 4 hours and is the fifth of five biological replicates


title: Liver_Normal_58

source_name: liver tissues, normal 58


title: proximal colon-Low Low vitamin D-mom 12


title: MDDC_uninfected_donor-977

description:
977-UI-04h
RNA_human-monocyte-derived-dendritic-cell_uninfected_donor-977
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells which are uninfected and is the fourth of five biological replicates

value: Uninfected


title: proximal colon- High High vitamin D-mom 10

value: male


title: proximal colon-Low Low vitamin D-mom 2C


title: MDDC_Leishmania-major-strain-FV1-infected_24HR-post-infection_donor-977

description:
977-FV1-24h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_24HR-post-infection_donor-977
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 24 hours and is the fourth of five biological replicates

value: Leishmania major

value: 24 hours


title: Liver_Normal_05

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 05


title: Liver_Normal_55

source_name: liver tissues, normal 55


title: Liver_Normal_13

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 13


title: Liver_Normal_08

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 08


title: Liver_Normal_51

source_name: liver tissues, normal 51


title: MDDC_Leishmania-donovani-strain-1S-infected_8HR-post-infection_donor-979

description:
979-1S-08h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-donovani-strain-1S-infected_8HR-post-infection_donor-979
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania donovani (1S strain) parasites for 8 hours and is the fifth of five biological replicates


title: Liver_Normal_01

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 01


title: Liver_Normal_02

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 02


title: Liver_Normal_14

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 14


title: Liver_Normal_06

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 06


title: Liver_Normal_07

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 07


title: Liver_Normal_09

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 09


title: Liver_Normal_03

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 03


title: Liver_Normal_50

source_name: liver tissues, normal 50


title: Liver_Normal_49

source_name: liver tissues, normal 49


title: Liver_Normal_53

source_name: liver tissues, normal 53


title: Liver_Normal_57

source_name: liver tissues, normal 57


title: MDDC_Leishmania-major-strain-FV1-infected_8HR-post-infection_donor-977

description:
977-FV1-08h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_8HR-post-infection_donor-977
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 8 hours and is the fourth of five biological replicates


title: Liver_Normal_56

source_name: liver tissues, normal 56


title: proximal colon- High Low vitamin D-mom 8C

source_name: mouse proximal colon

value: 129/SvEvIL-10 KO

value: high vitamin D during pregnancy and lactation and low vitamin D after weaning


title: MDDC_Leishmania-donovani-strain-1S-infected_24HR-post-infection_donor-977

description:
977-1S-24h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-donovani-strain-1S-infected_24HR-post-infection_donor-977
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania donovani (1S strain) parasites for 24 hours and is the fourth of five biological replicates


title: proximal colon- High Low vitamin D-mom 8

value: 3 months

value: proximal colon


title: MDDC_Leishmania-donovani-strain-1S-infected_8HR-post-infection_donor-977

description:
977-1S-08h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-donovani-strain-1S-infected_8HR-post-infection_donor-977
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania donovani (1S strain) parasites for 8 hours and is the fourth of five biological replicates

value: Monocyte derived dendritic cell


title: Liver_Normal_04

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 04


title: Liver_Normal_11

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 11


title: Liver_Normal_47

source_name: liver tissues, normal 47


title: MDDC_Leishmania-donovani-strain-1S-infected_4HR-post-infection_donor-977

description:
977-1S-04h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-donovani-strain-1S-infected_4HR-post-infection_donor-977
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania donovani (1S strain) parasites for 4 hours and is the fourth of five biological replicates


title: Liver_Normal_46

source_name: liver tissues, normal 46


title: Liver_Normal_44

source_name: liver tissues, normal 44


title: Liver_Normal_54

source_name: liver tissues, normal 54


title: Liver_Normal_48

source_name: liver tissues, normal 48


title: proximal colon- High High vitamin D-mom 9


title: Liver_Normal_42

source_name: liver tissues, normal 42


title: Liver_Normal_12

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 12


title: MDDC_Leishmania-major-strain-FV1-infected_8HR-post-infection_donor-902

description:
902-FV1-08h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_8HR-post-infection_donor-902
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 8 hours and is the third of five biological replicates

value: 8 hours


title: Liver_Normal_52

source_name: liver tissues, normal 52


title: Liver_Normal_43

source_name: liver tissues, normal 43


title: MDDC_Leishmania-major-strain-FV1-infected_24HR-post-infection_donor-902

description:
902-FV1-24h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_24HR-post-infection_donor-902
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 24 hours and is the third of five biological replicates


title: Liver_Normal_39

source_name: liver tissues, normal 39


title: proximal colon-Low High vitamin D-mom 6A

description: low vitamin D during pregnancy and lactation and high vitamin D after weaning


title: MDDC_Leishmania-major-strain-FV1-infected_4HR-post-infection_donor-977

description:
977-FV1-04h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_4HR-post-infection_donor-977
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 4 hours and is the fourth of five biological replicates

value: 4 hours


title: Liver_Normal_38

source_name: liver tissues, normal 38


title: Liver_Normal_41

source_name: liver tissues, normal 41


title: proximal colon-Low Low vitamin D-mom 3B

description: low vitamin D during pregnancy and lactation and low vitamin D after weaning


title: Liver_Normal_40

source_name: liver tissues, normal 40


title: MDDC_Leishmania-major-strain-FV1-infected_4HR-post-infection_donor-902

description:
902-FV1-04h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_4HR-post-infection_donor-902
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 4 hours and is the third of five biological replicates


title: Liver_Normal_37

source_name: liver tissues, normal 37


title: proximal colon-Low Low vitamin D-mom 6

source_name: mouse proximal colon


title: MDDC_uninfected_donor-902

description:
902-UI-04h
RNA_human-monocyte-derived-dendritic-cell_uninfected_donor-902
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells which are uninfected and is the third of five biological replicates


title: Liver_Normal_36

source_name: liver tissues, normal 36


title: proximal colon-High Low vitamin D-mom 14A

description: high vitamin D during pregnancy and lactation and low vitamin D after weaning


title: Liver_Normal_35

description: RNA sample were labeled and hybridized to the One-Color Agilent 60-mer Whole Human Genome Microarray

source_name: liver tissues, normal 35


title: Liver_Normal_34

source_name: liver tissues, normal 34


title: Liver_Normal_33

source_name: liver tissues, normal 33


title: Liver_Normal_30

source_name: liver tissues, normal 30


title: Liver_Normal_32

source_name: liver tissues, normal 32


title: MDDC_Leishmania-donovani-strain-1S-infected_24HR-post-infection_donor-902

description:
902-1S-24h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-donovani-strain-1S-infected_24HR-post-infection_donor-902
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania donovani (1S strain) parasites for 24 hours and is the third of five biological replicates

value: Leishmania donovani


title: Liver_Normal_29

source_name: liver tissues, normal 29


title: Liver_Normal_28

source_name: liver tissues, normal 28


title: Liver_Normal_24

source_name: liver tissues, normal 24


title: MDDC_Leishmania-donovani-strain-1S-infected_8HR-post-infection_donor-902

description:
902-1S-08h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-donovani-strain-1S-infected_8HR-post-infection_donor-902
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania donovani (1S strain) parasites for 8 hours and is the third of five biological replicates


title: Liver_Normal_31

source_name: liver tissues, normal 31


title: MDDC_Leishmania-donovani-strain-1S-infected_4HR-post-infection_donor-902

description:
902-1S-04h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-donovani-strain-1S-infected_4HR-post-infection_donor-902
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania donovani (1S strain) parasites for 4 hours and is the third of five biological replicates


title: MDDC_Leishmania-major-strain-FV1-infected_4HR-post-infection_donor-707

description:
707-FV1-04h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_4HR-post-infection_donor-707
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 4 hours and is the second of five biological replicates


title: MDDC_uninfected_donor-707

description:
707-UI-04h
RNA_human-monocyte-derived-dendritic-cell_uninfected_donor-707
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells which are uninfected and is the second of five biological replicates


title: Liver_Normal_20

source_name: liver tissues, normal 20


title: Liver_Normal_10

description: Hybridized to SNP 6.0

source_name: liver tissues, normal 10


title: Liver_Normal_26

source_name: liver tissues, normal 26


title: Liver_Normal_25

source_name: liver tissues, normal 25


title: MDDC_Leishmania-major-strain-FV1-infected_24HR-post-infection_donor-707

description:
707-FV1-24h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_24HR-post-infection_donor-707
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 24 hours and is the second of five biological replicates


title: MDDC_Leishmania-donovani-strain-1S-infected_24HR-post-infection_donor-707

description:
707-1S-24h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-donovani-strain-1S-infected_24HR-post-infection_donor-707
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania donovani (1S strain) parasites for 24 hours and is the second of five biological replicates


title: MDDC_Leishmania-donovani-strain-1S-infected_8HR-post-infection_donor-707

description:
707-1S-08h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-donovani-strain-1S-infected_8HR-post-infection_donor-707
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania donovani (1S strain) parasites for 8 hours and is the second of five biological replicates


title: Liver_Normal_19

source_name: liver tissues, normal 19


title: Liver_Normal_27

source_name: liver tissues, normal 27


title: Liver_Normal_21

source_name: liver tissues, normal 21


title: MDDC_Leishmania-donovani-strain-1S-infected_4HR-post-infection_donor-707

description:
707-1S-04h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-donovani-strain-1S-infected_4HR-post-infection_donor-707
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania donovani (1S strain) parasites for 4 hours and is the second of five biological replicates


title: Liver_Normal_45

source_name: liver tissues, normal 45


title: Liver_Normal_18

source_name: liver tissues, normal 18


title: Liver_Normal_17

source_name: liver tissues, normal 17


title: Liver_Normal_23

source_name: liver tissues, normal 23


title: Liver_Normal_14

source_name: liver tissues, normal 14


title: Liver_Normal_13

source_name: liver tissues, normal 13


title: Liver_Normal_15

source_name: liver tissues, normal 15


title: MDDC_Leishmania-major-strain-FV1-infected_8HR-post-infection_donor-707

description:
707-FV1-08h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_8HR-post-infection_donor-707
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 8 hours and is the second of five biological replicates


title: Liver_Normal_22

source_name: liver tissues, normal 22


title: Liver_Normal_11

source_name: liver tissues, normal 11


title: Liver_Normal_12

source_name: liver tissues, normal 12


title: MDDC_uninfected_donor-706

description:
706-UI-04h
RNA_human-monocyte-derived-dendritic-cell_uninfected_donor-706
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells which are uninfected and is the first of five biological replicates


title: Liver_Normal_16

source_name: liver tissues, normal 16


title: Liver_Normal_10

source_name: liver tissues, normal 10


title: MDDC_Leishmania-major-strain-FV1-infected_24HR-post-infection_donor-706

description:
706-FV1-24h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_24HR-post-infection_donor-706
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 24 hours and is the first of five biological replicates


title: MDDC_Leishmania-donovani-strain-1S-infected_24HR-post-infection_donor-706

description:
706-1S-24h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-donovani-strain-1S-infected_24HR-post-infection_donor-706
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania donovani (1S strain) parasites for 24 hours and is the first of five biological replicates


title: Liver_Normal_09

source_name: liver tissues, normal 09


title: MDDC_Leishmania-major-strain-FV1-infected_8HR-post-infection_donor-706

description:
706-FV1-08h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_8HR-post-infection_donor-706
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 8 hours and is the first of five biological replicates


title: MDDC_Leishmania-major-strain-FV1-infected_4HR-post-infection_donor-706

description:
706-FV1-04h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_4HR-post-infection_donor-706
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania major (FV1 strain) parasites for 4 hours and is the first of five biological replicates


title: 15 mins exposure to isofurane, biological rep 10

city: Aberdeen

first: Damon

last: Lowes

state: Aberdeenshire

address: IMS, Foresterhill

department: Immunology, Infection and inflammation

institute: University of Aberdeen

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hours @ 45oC to rat 230 2.0 genechips

scan_protocol: Following hybridization and staining, gene chips were scanned using at 3mm resolution using a gene array scanner

data_processing:
The data were analysed using Affymetrix microarray software suite 5.0 (MAS 5.0) using default analysis setting and global scaling as normalization method  and Dchip ver 2010 using a baseline array for normalization and model based expression
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.4.0.38

source_name: Brain cortex from rat exposed to isoflurane

label_protocol: Biotinylated cRNA was prepared according to Affymetrix standard protocol using 10ug total RNA

growth_protocol: 20 week old Sprague Dawley rats between 250-300g

extract_protocol: Total RNA was extracted using TRIZOL (Invitrogen, Paisly, UK). Total RNA was further purified using Quiagen column based methodology (Quiagen Ltd, Manchester, UK)

treatment_protocol: Rats were exposed to isoflurane in oxygen at a concentration of 2% (1.4 MAC) or pure oxygen for 15 minutes and allowed to recover for 6 hours. Brain was removed and cortex dissected and placed into RNA later (Invitrogen, Paisly, UK) for RNA preservation.

value: Sprague Dawley

value: 20 weeks

tag: weight

tag: sample group

value: 15 mins exposure to isofurane

value: brain cortex


title: 15 mins exposure to isofurane, biological rep 9

tag: age


title: dSDH_50

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

hyb_protocol: A sample hybridization cocktail, consisting of the biotin-labeled fragmented sample, hybridization controls and hybridization buffer, was prepared according to Encore® Biotin Module instructions for standard array (49 or 64 format). The sample hybridization cocktail was applied to a GeneChip® Human Genome U133 Plus 2.0 array (Affymetrix) and hybridized for 18 hours at 450C with rotation in an Affymetrix GeneChip® Hybridization Oven.  The following day, the array ‘Wash and Stain’ procedure was performed using the automated Affymetrix GeneChip® Fluidics Station 450 and fluidics script FS450-0004.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: Samples were annotated as SDHx-mutant versus SDHx-wt for 2-group comparison of microarray data using Qlucore Omics Explorer software (QOE v.3).

label_protocol: 100ng of total RNA sample was converted to cDNA and SPIA® amplified using the Ovation® FFPE WTA System (NuGEN) following the manufacturers’ instructions. SPIA amplified cDNA was purified using the Agencourt RNAClean XP Kit (Beckman Coulter Genomics) following the Ovation® FFPE WTA System supplementary protocol. Purified cDNA was quantitated using a NanoDrop spectrophotometer. After quantitation, 4ug to 5ug of purified cDNA sample was subject to fragmentation and biotin labeling using the Encore® Biotin Module (NuGEN) following the manufacturers’ instructions.

extract_protocol: For gene expression analysis of FFPE GIST tumors, total RNA was extracted from 0.6 mm tissue cores using the RNeasy FFPE Kit (Qiagen) according to the manufacturers’ instructions.

tag: tumor type

value: dSDH GIST


title: dSDH_51


title: MDDC_Leishmania-donovani-strain-1S-infected_4HR-post-infection_donor-706

description:
706-1S-04h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-donovani-strain-1S-infected_4HR-post-infection_donor-706
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania donovani (1S strain) parasites for 4 hours and is the first of five biological replicates


title: Liver_Normal_07

description: RNA sample were labeled and hybridized to the One-Color Agilent 60-mer Whole Human Genome Microarray

source_name: liver tissues, normal 07

value: Han Chinese

value: liver


title: MDDC_Leishmania-donovani-strain-1S-infected_8HR-post-infection_donor-706

description:
706-1S-08h
RNA_human-monocyte-derived-dendritic-cell_Leishmania-donovani-strain-1S-infected_8HR-post-infection_donor-706
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with Leishmania donovani (1S strain) parasites for 8 hours and is the first of five biological replicates


title: 15 mins exposure to isofurane, biological rep 8

value: male


title: Liver_Normal_05

source_name: liver tissues, normal 05


title: Liver_Normal_08

source_name: liver tissues, normal 08


title: Liver_Normal_06

source_name: liver tissues, normal 06


title: 15 mins exposure to isofurane, biological rep 7


title: dSDH_24

value: SDHx-mutant


title: 15 mins exposure to isofurane, biological rep 6


title: dSDH_47


title: 15 mins exposure to isofurane, biological rep 5


title: dSDH_46


title: WSSV infected_24h_ gills_ replicate 1

city: Chennai

first: Shekhar

middle: M

last: S

state: Tamil Nadu

address: 75, Santhome High Road, R.A.Puram

department: Genetics and Biotechnology

institute: Central Institute of Brackishwater Aquaculture

description: gene expression at 24h after WSSV infection, replicate 1

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5242).

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software

data_processing: Data extraction from Images was done using Feature Extraction software  and Percentile shift Normalization of the data was done in GeneSpring GX

organism: Penaeus monodon

source_name: WSSV infected 24h, gills, replicate 1

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization

extract_protocol: RNA isolation was performed using QIAzol method as per the manufacturer’s instructions.

value: gills

tag: disease state

value: WSSV infected

tag: time point


title: 15 mins exposure to isofurane, biological rep 4

tag: strain

tag: gender


title: Liver_Normal_03

source_name: liver tissues, normal 03


title: WSSV infected_24h_ gills_ replicate 3

description: gene expression at 24h after WSSV infection, replicate 3

source_name: WSSV infected 24h, gills, replicate 3


title: dSDH_20


title: 15 mins exposure to isofurane, biological rep 3


title: dSDH_49


title: Liver_Normal_04

source_name: liver tissues, normal 04


title: dSDH_55


title: Liver_Normal_01

source_name: liver tissues, normal 01


title: dSDH_43


title: WSSV infected_24h_ gills_ replicate 2

description: gene expression at 24h after WSSV infection, replicate 2

source_name: WSSV infected 24h, gills, replicate 2


title: 15 mins exposure to isofurane, biological rep2


title: Oxygen control, biological rep 10

source_name: Brain cortex from rat exposed to oxygen

value: Oxygen control


title: dSDH_44


title: WSSV infected_ 6h_ gills_ replicate 1

description: gene expression at 6h after WSSV infection, replicate 1

source_name: WSSV infected 6h, gills, replicate 1


title: Oxygen control, biological rep 9


title: WSSV infected_ 6h_ gills_ replicate 2

description: gene expression at 6h after WSSV infection, replicate 2

source_name: WSSV infected 6h, gills, replicate 2


title: Liver_Normal_02

source_name: liver tissues, normal 02


title: dSDH_34


title: 15 mins exposure to isofurane, biological rep 1


title: Oxygen control, biological rep 7


title: Oxygen control, biological rep 6


title: uninfected control_ replicate 3

description: uninfected replicate 3

source_name: uninfected control, replicate 3


title: uninfected control_ replicate 2

description: uninfected replicate 2

source_name: uninfected control, replicate 2


title: dSDH_3


title: WSSV infected_ 48h_ gills_ replicate 2

description: gene expression at 48h after WSSV infection, replicate 2

source_name: WSSV infected 48h, gills, replicate 2


title: Oxygen control, biological rep 8


title: WSSV infected_ 48h_ gills_ replicate 3

description: gene expression at 48h after WSSV infection, replicate 3

source_name: WSSV infected 48h, gills, replicate 3


title: dSDH_39


title: dSDH_28


title: dSDH_21


title: uninfected control_ replicate 4

description: uninfected replicate 4

source_name: uninfected control, replicate 4


title: WSSV infected_ 6h_ gills_ replicate 3

description: gene expression at 6h after WSSV infection, replicate 3

source_name: WSSV infected 6h, gills, replicate 3


title: dSDH_17


title: uninfected control_ replicate 1

description: uninfected replicate 1

source_name: uninfected control, replicate 1


title: Oxygen control, biological rep 4


title: Oxygen control, biological rep 3


title: dSDH_1


title: WSSV infected_ 48h_ gills_ replicate 1

description: gene expression at 48h after WSSV infection, replicate 1

source_name: WSSV infected 48h, gills, replicate 1


title: WSSV infected_ moribund stage_ gills_ replicate 3

description: gene expression at moribund stage after WSSV infection, replicate 3

source_name: WSSV infected moribund stage, gills, replicate 3

value: moribund stage


title: dSDH_8


title: Oxygen control, biological rep 2


title: WSSV infected_ moribund stage_ gills_ replicate 1

description: gene expression at moribund stage after WSSV infection, replicate 1

source_name: WSSV infected moribund stage, gills, replicate 1


title: 16h-post LPS 3

status: Public on Jan 01 2015

city: Stanford

first: Hui

last: Zhao

state: California

address: 300 Pasture Drive

department: Pediatrics

institute: Stanford University

data_processing:
Web-based RT2 profiler PCR array data analysis version 3.5
Based on ΔΔCt method to define Fold change

label: SYBR Green

source_name: E9.5 uteri

label_protocol:
According to Manufacturer instruction. Mouse Cytokine & Chemokine RT2 Profiler PCR array (Qiagen, Cat# PAMM-150Z)
Real-time RT-PCR was performed using RT2 real-time SYBR Green/ROX PCR master Mix on Stratagen Mx 3005p qPCR system

extract_protocol: RNA was extracted using Qiagen Rneasy plus kit

treatment_protocol: Pregnant mice were ip administrated with LPS (2.5 ug per mouse) and uteri were collected 8h or 16 h post LPS.

value: FVBn

value: female


title: 8h-post LPS 3


title: 16h-post LPS 2


title: 16h-post LPS 1


title: 8h-post LPS 1


title: 8h-post LPS 2


title: Saline control 3


title: dSDH_10


title: Saline control 1


title: Oxygen control, biological rep 5


title: WSSV infected_ moribund stage_ gills_ replicate 2

description: gene expression at moribund stage after WSSV infection, replicate 2

source_name: WSSV infected moribund stage, gills, replicate 2


title: Oxygen control, biological rep 1


title: Saline control 2


title: UC_inactive_6 [miRNA]

city: Leuven

first: Jan

last: Van der Goten

address: Herestraat 49 bus 701

department: Clinical and Experimental Medicine

country: Belgium

institute: KU Leuven

description: colonic mucosal microRNA expression data from UC patient with inactive disease

hyb_protocol: Incubation at 99°C for 5 minutes, followed by 45°C for another 5 minutes. Hybridization to GeneChip miRNA 2.0 arrays (Affymetrix) was performed under rotation (60 rpm) at 48°C for 16 hours. The arrays were washed and stained on an automated Fluidics Station (Affymetrix).

scan_protocol: Microarrays were scanned on the Affymetrix 3000 GeneScanner. Intensity values for each probe cell (.cel file) were calculated using Affymetrix GeneChip Command Console (AGCC).

data_processing: Quality control of the array data was performed with the Affymetrix miRNA QC Tool, version 1.1.1.0. Data were analyzed using RMA method in Bioconductor (R version 2.15.0).

source_name: colonic mucosal biopsy from UC patient with inactive disease

label_protocol: Total RNA (250 ng) was used in a tailing reaction followed by ligation of the biotinylated signal molecule, using the FlashTag™ Biotin HSR RNA Labeling Kit (Genesphere) protocol for Affymetrix GeneChip miRNA arrays. As recommended, the labeling efficiency is verified with the ELOSA QC assay (Genesphere).

extract_protocol: Total RNA was extracted using the miRVAna miRNA isolation Kit (Ambion), according to the manufacturer's instructions. The integrity and quantity of total RNA and small RNA were assessed with a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies) and a 2100 Bioanalyzer (Agilent) using the Agilent RNA 6000 Nano kit and the Agilent Small RNA kit, respectively.

value: colon

tag: disease

value: UC

tag: disease activity

value: inactive


title: UC_inactive_4 [miRNA]


title: UC_inactive_5 [miRNA]


title: UC_active_10 [miRNA]

description: colonic mucosal microRNA expression data from UC patient with active disease

source_name: colonic mucosal biopsy from UC patient with active disease

value: active


title: UC_active_6 [miRNA]


title: UC_inactive_7 [miRNA]


title: UC_active_9 [miRNA]


title: UC_active_7 [miRNA]


title: UC_active_8 [miRNA]


title: UC_active_1 [miRNA]


title: UC_inactive_3 [miRNA]


title: UC_active_3 [miRNA]


title: control_6 [miRNA]

description: colonic mucosal microRNA expression data from control individual

source_name: colonic mucosal biopsy from control individual

value: control

value: not applicable


title: control_9 [miRNA]


title: control_10 [miRNA]


title: n7 dnNrf2

city: Manchester

first: Svitlana

last: Kurinna

address: Dover Street

institute: University of Manchester

description: n7 dnNrf2

hyb_protocol: Microarray hybridization was performed at 55°C for 20 hours in Agilent's microarray hybridization chambers, followed by wash procedures according to the manufacturer’s recommended protocols

scan_protocol: Microarray was scanned in an Agilent scanner at 5μm resolution, and the array data was extracted with Agilent feature extraction software using the miRNA_105_Jan09 protocol

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used.

source_name: dnNrf2 2

label_protocol: 100ng of total RNA were labeled with Cy3 according to Agilent's labeling protocol

growth_protocol: Mouse skin was collected at newborn mice at P2.5

extract_protocol: Trizol-based total RNA extraction

treatment_protocol: No treatment

value: skin


title: n8 dnNrf2

description: n8 dnNrf2

source_name: dnNrf2 3


title: control_7 [miRNA]


title: UC_active_4 [miRNA]


title: UC_active_2 [miRNA]


title: control_5 [miRNA]


title: control_3 [miRNA]


title: control_4 [miRNA]


title: control_1 [miRNA]


title: UC_active_5 [miRNA]


title: UC_inactive_2 [miRNA]


title: control_2 [miRNA]


title: dSDH_14

value: dSDH GIST


title: n4 dnNrf2 (wt)

description: n4 dnNrf2 (wt)

source_name: wt 2

value: wt


title: n3 dnNrf2 (wt)

description: n3 dnNrf2 (wt)

source_name: wt 1


title: n2 dnNrf2

description: n2 dnNrf2

source_name: dnNrf2 1


title: CMV-caNrf2 24

description: CMV-caNrf2 24

source_name: CMV-caNrf2 2


title: CMV-caNrf2 26

description: CMV-caNrf2 26

source_name: CMV-caNrf2 3


title: CMV-caNrf2 27 (K5Cre(wt)

description: CMV-caNrf2 27 (K5Cre(wt)

source_name: K5Cre(wt) 2


title: CMV-caNrf2 30 (K5Cre(wt)

description: CMV-caNrf2 30 (K5Cre(wt)

source_name: K5Cre(wt) 3


title: CMV-caNrf2 23

description: CMV-caNrf2 23

source_name: CMV-caNrf2 1


title: n5 dnNrf2 (wt)

description: n5 dnNrf2 (wt)

source_name: wt 3


title: CMV-caNrf2 22 (K5Cre(wt)

description: CMV-caNrf2 22 (K5Cre(wt)

source_name: K5Cre(wt) 1


title: 12h rep-2

city: AUBURN

first: chao

last: li

address: 203 swingle hall

institute: auburn university

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Following hybridization, the slides were scanned using a GenePix personal 4100A Scanner (Axon Instruments) and initial analysis were performed with Feature Extraction software v9.5.3 (Agilent).

data_processing: Agilent Feature Extraction Software v9.5.3 was used for background subtraction and LOWESS normalization.

organism: Ictalurus punctatus

source_name: 12h control-2

label_protocol: cDNA was generated from 500 ng of each isolated RNA sample; cRNA was then made using Cy3-CTP or Cy5-CTP incorporation for labeling purposes. The fluorescently labeled cRNA probes were purified using the Qiagen RNeasy Mini Kit (Qiagen Inc., Valencia, CA, USA), and the concentration, fluorescent intensities, and quality of labeled cRNA probes were determined using a Nano-drop spectrophotometer. At each timepoint, 3 Cy3 labeled cRNA and 3 Cy5 labeled cRNA were generated with randomized dye assignments between treatment and control samples.

growth_protocol: Fish were challenged in 3 control and 3 treatment groups per timepoint in each group. Aquaria were randomly divided into sampling timepoints-2 h treatment, 8 h treatment, 12 h treatment, 2 h control, 8 h control, and 12 h control with thirty fish in each aquarium.Immersion experiments were performed in a 25 L bucket with aeration. Briefly, 50 ml of overnight Aeromonas hydrophila cells 1.5×109 were added to water to give a final volume of 5 L (1.5×107 final exposure concentration). Thirty channel catfish were immersed in each bucket for 2 h. After the 2 h immersion, the catfish were distributed to 30 L glass aquaria.

extract_protocol: Total RNA was extracted from tissues using the RNeasy Plus Universal Mini Kit (Qiagen) following manufacturer’s instructions.

tag: infection

value: none, control

source_name: 12h infection-2

value: Aeromonas hydrophila


title: 30m_rep2

city: Copenhagen

first: Josh

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

description: Gene expression data from ESCs cultured for 24 hours in the presence of 250nM PD173074 and then stimulated for 30 minutes with 4OHT to activate c-Raf

hyb_protocol: Samples were then hybridized to the G4852A SurePrint G3 Mouse GE 8x60K Microarray slides (60000 probes, Agilent Technologies).

scan_protocol: Images were scanned using the high sensitivity protocol (AgilentG3_HiSen_GX_1color) on a SureScan microarray scanner (Agilent Technologies) and probe intensities were obtained by taking the gProcessedSignal from the output of Agilent feature extraction software using default settings.

data_processing: Probe intensities were analysed using the NIA Array Analysis tool (http://lgsun.grc.nia.nih.gov/ANOVA/).

source_name: Cultured embryonic stem cells

label_protocol: RNA was amplified into cRNA and 150ng of total RNA was labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies- 5190-2305).

growth_protocol: E14 ESCs were cultured in GMEM (Sigma) supplemented with 10% FBS (Gibco), 100 μM 2-mercaptoethanol (Sigma), 1xMEM non-essential amino acids, 2 mM L-glutamine, 1 mM sodium pyruvate (all from Gibco), and 1000 units/ml LIF (made in-house) on gelatinised tissue culture flasks (Coring)

extract_protocol: Total RNA was collected using  the RNeasy Mini Kit (Qiagen). Genomic DNA was eliminated by DNAse treatment (Qiagen).

treatment_protocol: Pre-treated with 250nM PD173074 for 24 hours, and then stimulated for the indicated times with 250nM 4OHT

tag: cell type

value: E14tg2a ESCs

tag: agent


title: 4h_rep2

description: Gene expression data from ESCs cultured for 24 hours in the presence of 250nM PD173074 and then stimulated for 4 minutes with 4OHT to activate c-Raf


title: 0h_rep2

description: Gene expression data from ESCs cultured for 24 hours in the presence of 250nM PD173074


title: 2h_rep2

description: Gene expression data from ESCs cultured for 24 hours in the presence of 250nM PD173074 and then stimulated for 2 hours with 4OHT to activate c-Raf


title: 1h_rep1

description: Gene expression data from ESCs cultured for 24 hours in the presence of 250nM PD173074 and then stimulated for 1 hour with 4OHT to activate c-Raf


title: 8h rep-3

source_name: 8h control-3

source_name: 8h infection-3


title: 1h_rep2


title: 8h rep-1

source_name: 8h control-1

source_name: 8h infection-1


title: 8h_rep2

description: Gene expression data from ESCs cultured for 24 hours in the presence of 250nM PD173074 and then stimulated for 8 hours with 4OHT to activate c-Raf


title: 2h rep-2

source_name: 2h control-2

source_name: 2h infection-2


title: 8h_rep1


title: 12h rep-3

source_name: 12h control-3

source_name: 12h infection-3


title: 8h rep-2

source_name: 8h control-2

source_name: 8h infection-2


title: 2h rep-1

source_name: 2h control-1

source_name: 2h infection-1


title: 4h_rep1


title: DMSO_rep2

description: Gene expression data from ESCs cultured withour treatment

value: DMSO


title: 0h_rep1


title: 24h_rep2

description: Gene expression data from ESCs cultured for 24 hours in the presence of 250nM PD173074 and then stimulated for 24 hours with 4OHT to activate c-Raf


title: 12h rep-1

source_name: 12h control-1

source_name: 12h infection-1


title: 2h rep-3

source_name: 2h control-3

source_name: 2h infection-3


title: 30m_rep1

source_name: Cultured embryonic stem cells


title: 24h_rep1


title: UC_inactive_1 [miRNA]

source_name: colonic mucosal biopsy from UC patient with inactive disease